From 3e338b768a5714b8c7bf84c2e587e9b829bb18ae Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 14:13:16 -0400 Subject: [PATCH 001/369] initial copy all pipeline code --- loading_pipeline/CLAUDE.md | 82 + loading_pipeline/README.md | 89 + loading_pipeline/__init__.py | 7 + loading_pipeline/api/__init__.py | 0 loading_pipeline/api/__main__.py | 18 + loading_pipeline/api/app.py | 119 + loading_pipeline/api/app_test.py | 140 + loading_pipeline/api/model.py | 105 + loading_pipeline/api/model_test.py | 87 + loading_pipeline/api/request_handlers.py | 107 + loading_pipeline/bin/__init__.py | 0 loading_pipeline/bin/clickhouse_loader.py | 13 + loading_pipeline/bin/dataproc_vep_init.bash | 63 + .../bin/download_vep_reference_data.bash | 71 + .../bin/migrate_all_projects_to_clickhouse.py | 65 + .../bin/migrate_variants_tables.py | 49 + loading_pipeline/bin/pipeline_worker.py | 110 + loading_pipeline/bin/pipeline_worker_test.py | 182 + .../bin/rsync_reference_data.bash | 52 + 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loading_pipeline/var/test/test_clickhouse_schema.sql create mode 100644 loading_pipeline/var/test/vep/__init__.py create mode 100644 loading_pipeline/var/test/vep/mock_vep_data.py create mode 100644 loading_pipeline/var/vep/GRCh37/vep-GRCh37.json create mode 100644 loading_pipeline/var/vep/GRCh38/vep-GRCh38.json diff --git a/loading_pipeline/CLAUDE.md b/loading_pipeline/CLAUDE.md new file mode 100644 index 0000000000..130889aa15 --- /dev/null +++ b/loading_pipeline/CLAUDE.md @@ -0,0 +1,82 @@ +# CLAUDE.md + +This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository. + +## Quick Commands + +**Python environment setup:** +```bash +pyenv shell 3.11 +uv sync --group dev --locked +``` + +**Run all tests:** +```bash +pyenv shell 3.11 +uv run pytest +``` + +**Run a single test file:** +```bash +pyenv shell 3.11 +uv run pytest loading_pipeline/lib/misc/math_test.py +``` + +**Formatting and linting:** +```bash +pyenv shell 3.11 +uv run ruff format . +uv run ruff check . +``` + +## Project Architecture + +This is a genomic data loading pipeline that ingests variant data from VCF files into ClickHouse via Hail and Luigi. The overall flow: + +``` +VCF Input → Hail Matrix Table → Parquet Files → ClickHouse Staging → Production +``` + +### Core Components + +**`loading_pipeline/lib/tasks/`** — Luigi-based pipeline tasks +- Tasks are defined by their `requires()` method (reverse dependency declaration) +- `RunPipelineTask` is the main entry point that chains together: + - `WriteMetadataForRunTask` (metadata generation) + - `UpdateVariantAnnotationsTableWithNewVariantsTask` (annotation updates) + - `WriteNewEntriesParquetTask` (variant entries → parquet) + - `WriteNewVariantsParquetTask` (variants → parquet) + - `WriteNewVariantDetailsParquetTask` (details → parquet) + - `WriteClickhouseLoadSuccessFileTask` (final atomicity marker) +- Base tasks in `base/` provide shared parameters and utilities + +**`loading_pipeline/lib/annotations/`** — Hail-based variant annotation logic +- Standardizes and reformats VEP, gnomAD, and other annotation fields +- VEP schema defined in `vep*.json` files, parsed in `vep.py` + +**`loading_pipeline/lib/misc/clickhouse/`** — ClickHouse ingestion +- Manages staging table creation and atomic partition movement to production +- Follows the ["Making a Large Data Load Resilient"](https://clickhouse.com/blog/supercharge-your-clickhouse-data-loads-part3) pattern + +**`loading_pipeline/api/`** — REST interface +- `model.py` defines Pydantic schemas for incoming requests +- `app.py` runs an aiohttp server handling load requests + +**`loading_pipeline/bin/pipeline_worker.py`** — Job runner +- Manages asynchronous pipeline jobs requested via the REST API + +### Schema Definitions + +Expected field schemas are defined in `core/dataset_type.py`: +- `col_fields` — variant fields (position, annotation, etc.) +- `entry_fields` — per-sample genotype fields +- `row_fields` — additional row-level metadata + +Test files in `lib/tasks/exports/*_test.py` contain examples of the expected parquet export schemas. + +## Development Notes + +- **Python 3.11 required** — Always activate with `pyenv shell 3.11` before running commands +- **Ruff configuration** — Follows single quotes, 88 char line limit. Test files allow asserts, private access, and high-arity functions +- **ClickHouse tests** — Run locally against a test ClickHouse instance (see README for setup) +- **Tests use pytest** — Not unittest; use `pytest` command directly diff --git a/loading_pipeline/README.md b/loading_pipeline/README.md new file mode 100644 index 0000000000..65910f3f3b --- /dev/null +++ b/loading_pipeline/README.md @@ -0,0 +1,89 @@ +# Seqr Loading Pipeline + +[![Code Build](https://github.com/broadinstitute/seqr-loading-pipelines/actions/workflows/unit-tests.yml/badge.svg?branch=main)](https://github.com/broadinstitute/seqr-loading-pipelines/actions/workflows/unit-tests.yml) +[![Docker Build](https://github.com/broadinstitute/seqr-loading-pipelines/actions/workflows/prod-release.yml/badge.svg?branch=main)](https://github.com/broadinstitute/seqr-loading-pipelines/actions/workflows/prod-release.yml) + +*This repository contains pipelines and infrastructure for loading genomic data from VCF -> ClickHouse to support queries by the _seqr_ application* + +--- + +## 📁 Repository Structure + +### `loading_pipeline/api/` +Contains the interface layer to the _seqr_ application. +- `api/model.py` defines pydantic models for the REST interface. +- `api/app.py` specifies an `aiohttp` webserver that handles load data requests. + +### `loading_pipeline/bin/` +Scripts or command-line utilities used for setup or task execution. +- `bin/pipeline_worker.py` — manages asynchronous jobs requested by _seqr_. + +### `loading_pipeline/deploy/` +Dockerfiles for the loading pipeline itself & any annotation utilities. +Kubernetes manifests are managed separately in [seqr-helm](https://github.com/broadinstitute/seqr-helm/tree/main/charts/pipeline-runner) + +### `loading_pipeline/lib/` +Core logic and shared libraries. +- `annotations` defines hail logic to re-format and standardize fields. +- `methods` wraps hail-defined genomics methods for QC. +- `misc` contains single modules with defined utilities. + - `misc/clickhouse` hosts the logic that manages the parquet ingestion into ClickHouse itself. +- `core` defines key constants/enums/config. +- `reference_datasets` manages parsing of raw reference sources into hail tables. +- `tasks` specifies the Luigi defined pipeline. Note that Luigi pipelines are defined by their requirements, so +the pipeline is defined, effectively, in reverse. + - `WriteClickhouseLoadSuccessFileTask` is the last task, defining a `requires()` method that runs the pipeline either locally or on scalable compute. + - `WriteImportedCallset` is the first task, importing a VCF into a Hail Matrix table, an "imported callset". +- `test` holds a few utilities used by the tests, which are dispersed throughout the rest of the repository. +- `paths.py` defines paths for all intermediate and output files of the pipeline. + +### `loading_pipeline/ops/` +Manual operations scripts. + +### `loading_pipeline/var/` +Static configuration and test files. + +--- + +## ⚙️ Setup for Local Development +The production pipeline runs with python `3.11`. + +### Clone the repo and install python requirements +```bash +git clone https://github.com/broadinstitute/seqr-loading-pipelines.git +cd seqr-loading-pipelines +RUN uv sync --group dev --locked +``` + +### [Install](https://clickhouse.com/docs/getting-started/quick-start/oss) & start ClickHouse with provided test configuration: +> **Note:** We are running ClickHouse `26.3.9-lts` in production. +```bash +curl https://clickhouse.com/ | sh +./clickhouse server --config-file=./seqr-loading-pipelines/loading_pipeline/var/clickhouse_config/test-clickhouse.xml +``` + +### [Run the Tests](https://github.com/broadinstitute/seqr-loading-pipelines/blob/main/.github/workflows/unit-tests.yml#L66-L73) + +### Run an Individual Test +```bash +uv run pytest loading_pipeline/lib/misc/math_test.py +``` + +### Formatting and Linting +```bash +uv run ruff format . +uv run ruff check . +``` + +## 🚪 Schema Entrypoints +- The expected fields and types are defined in `dataset_type.py` as the `col_fields`, `entry_fields`, and `row_fields` properties. Examples +of the SNV_INDEL/MITO/SV/GCNV callset schemas may be found in the tests. +- The VEP schema is defined in JSON within the vep*.json config files, then parsed into hail in `lib/annotations/vep.py`. +- Examples of exported parquets may be found in `lib/tasks/exports/*_parquet_test.py` + + +## 🚶‍♂️ ClickHouse Load Walkthrough +- The Clickhouse Load follows the pattern established in the [Making a Large Data Load Resilient](https://clickhouse.com/blog/supercharge-your-clickhouse-data-loads-part3) blog + - Rows are first loaded into a `staging` database that copies the production `TABLE`s and `MATERIALIZED VIEW`s. + - After all `entries` are inserted, we validate the inserted row count and finalize the per-project allele frequency aggregation. + - Partitions are atomically moved from the `staging` environment to production. diff --git a/loading_pipeline/__init__.py b/loading_pipeline/__init__.py new file mode 100644 index 0000000000..17b3aa3ed3 --- /dev/null +++ b/loading_pipeline/__init__.py @@ -0,0 +1,7 @@ +import datetime + +MAJOR_VERSION = 3 + +__version__ = ( + f'{MAJOR_VERSION}.{datetime.datetime.now(datetime.UTC).strftime("%Y%m%d.%H%M%S")}' +) diff --git a/loading_pipeline/api/__init__.py b/loading_pipeline/api/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/loading_pipeline/api/__main__.py b/loading_pipeline/api/__main__.py new file mode 100644 index 0000000000..38b30d74ef --- /dev/null +++ b/loading_pipeline/api/__main__.py @@ -0,0 +1,18 @@ +from aiohttp import web + +from loading_pipeline.api.app import init_web_app +from loading_pipeline.lib.logger import get_logger + + +def run(): + app = init_web_app() + logger = get_logger(__name__) + web.run_app( + app, + host='0.0.0.0', # noqa: S104 + port=6000, + access_log=logger, + ) + + +run() diff --git a/loading_pipeline/api/app.py b/loading_pipeline/api/app.py new file mode 100644 index 0000000000..90bac06745 --- /dev/null +++ b/loading_pipeline/api/app.py @@ -0,0 +1,119 @@ +import traceback + +import aiofiles +import aiofiles.os +from aiohttp import web, web_exceptions + +from loading_pipeline.api.model import ( + DeleteFamiliesRequest, + LoadingPipelineRequest, + PipelineRunnerRequest, + RebuildGtStatsRequest, + RefreshClickhouseReferenceDataRequest, +) +from loading_pipeline.lib.core.environment import Env +from loading_pipeline.lib.logger import get_logger +from loading_pipeline.lib.misc.runs import is_queue_full, new_run_id +from loading_pipeline.lib.paths import ( + loading_pipeline_queue_dir, + loading_pipeline_queue_path, +) + +logger = get_logger(__name__) + + +@web.middleware +async def error_middleware(request, handler): + try: + return await handler(request) + except web.HTTPError: + logger.exception('HTTPError') + raise + except Exception as e: + logger.exception('Unhandled Exception') + error_reason = f'{e}: {traceback.format_exc()}' + raise web.HTTPInternalServerError(reason=error_reason) from e + + +async def _enqueue_request( + request: web.Request, + model_cls: type[PipelineRunnerRequest], +) -> web.Response: + """Generic helper to enqueue a pipeline request of any type.""" + if not request.body_exists: + raise web.HTTPUnprocessableEntity + + if is_queue_full(): + return web.json_response( + f'Pipeline queue is full. Please try again later. (limit={Env.LOADING_QUEUE_LIMIT})', + status=web_exceptions.HTTPConflict.status_code, + ) + + try: + model_instance = model_cls.model_validate(await request.json()) + except ValueError as e: + raise web.HTTPBadRequest from e + + queue_path = loading_pipeline_queue_path(new_run_id()) + async with aiofiles.open(queue_path, 'w') as f: + await f.write(model_instance.model_dump_json()) + + return web.json_response( + {'Successfully queued': model_instance.model_dump()}, + status=web_exceptions.HTTPAccepted.status_code, + ) + + +async def loading_pipeline_enqueue(request: web.Request) -> web.Response: + return await _enqueue_request( + request, + LoadingPipelineRequest, + ) + + +async def delete_families_enqueue(request: web.Request) -> web.Response: + return await _enqueue_request( + request, + DeleteFamiliesRequest, + ) + + +async def rebuild_gt_stats_enqueue(request: web.Request) -> web.Response: + return await _enqueue_request( + request, + RebuildGtStatsRequest, + ) + + +async def refresh_clickhouse_reference_dataset_enqueue( + request: web.Request, +) -> web.Response: + return await _enqueue_request( + request, + RefreshClickhouseReferenceDataRequest, + ) + + +async def status(_: web.Request) -> web.Response: + return web.json_response({'success': True}) + + +async def init_web_app(): + await aiofiles.os.makedirs( + loading_pipeline_queue_dir(), + exist_ok=True, + ) + app = web.Application(middlewares=[error_middleware]) + app.add_routes( + [ + web.get('/status', status), + web.post('/loading_pipeline_enqueue', loading_pipeline_enqueue), + web.post('/delete_families_enqueue', delete_families_enqueue), + web.post('/rebuild_gt_stats_enqueue', rebuild_gt_stats_enqueue), + web.post( + '/refresh_clickhouse_reference_dataset_enqueue', + refresh_clickhouse_reference_dataset_enqueue, + ), + ], + ) + return app diff --git a/loading_pipeline/api/app_test.py b/loading_pipeline/api/app_test.py new file mode 100644 index 0000000000..f5945c1c41 --- /dev/null +++ b/loading_pipeline/api/app_test.py @@ -0,0 +1,140 @@ +from pathlib import Path + +from aiohttp import web_exceptions +from aiohttp.test_utils import AioHTTPTestCase + +from loading_pipeline.api.app import init_web_app +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + +CALLSET_PATH = str( + Path('loading_pipeline/var/test/callsets/1kg_30variants.vcf').resolve(), +) + + +class AppTest(AioHTTPTestCase, MockedDatarootTestCase): + async def get_application(self): + return await init_web_app() + + async def test_status(self): + async with self.client.request('GET', '/status') as resp: + self.assertEqual(resp.status, 200) + resp_json = await resp.json() + self.assertDictEqual(resp_json, {'success': True}) + + async def test_missing_route(self): + with self.assertLogs(level='ERROR') as _: + async with self.client.request('GET', '/loading_pip') as resp: + self.assertEqual(resp.status, web_exceptions.HTTPNotFound.status_code) + + async def test_loading_pipeline_invalid_requests(self): + with self.assertLogs(level='ERROR') as log: + async with self.client.request('GET', '/loading_pipeline_enqueue') as resp: + self.assertEqual( + resp.status, + web_exceptions.HTTPMethodNotAllowed.status_code, + ) + self.assertTrue( + 'HTTPMethodNotAllowed' in log.output[0], + ) + + with self.assertLogs(level='ERROR') as log: + async with self.client.request('POST', '/loading_pipeline_enqueue') as resp: + self.assertEqual( + resp.status, + web_exceptions.HTTPUnprocessableEntity.status_code, + ) + self.assertTrue( + 'HTTPUnprocessableEntity' in log.output[0], + ) + + body = { + 'callset_path': 'missing.vcf', + 'project_guids': ['project_a'], + 'sample_type': SampleType.WGS.value, + 'reference_genome': ReferenceGenome.GRCh38.value, + 'dataset_type': DatasetType.SNV_INDEL.value, + } + with self.assertLogs(level='ERROR') as log: + async with self.client.request( + 'POST', + '/loading_pipeline_enqueue', + json=body, + ) as resp: + self.assertEqual( + resp.status, + web_exceptions.HTTPBadRequest.status_code, + ) + self.assertTrue( + 'callset_path must point to a file that exists' in log.output[0], + ) + + body = { + 'callset_path': CALLSET_PATH, + 'project_guids': ['project_a'], + 'sample_type': SampleType.WGS.value, + 'reference_genome': ReferenceGenome.GRCh38.value, + 'dataset_type': DatasetType.SNV_INDEL.value, + 'validations_to_skip': ['bad_validation'], + } + with self.assertLogs(level='ERROR') as log: + async with self.client.request( + 'POST', + '/loading_pipeline_enqueue', + json=body, + ) as resp: + self.assertEqual( + resp.status, + web_exceptions.HTTPBadRequest.status_code, + ) + self.assertTrue( + "input_value='bad_validation" in log.output[0], + ) + + async def test_loading_pipeline_enqueue(self): + body = { + 'callset_path': CALLSET_PATH, + 'project_guids': ['project_a'], + 'sample_type': SampleType.WGS.value, + 'reference_genome': ReferenceGenome.GRCh38.value, + 'dataset_type': DatasetType.SNV_INDEL.value, + } + async with self.client.request( + 'POST', + '/loading_pipeline_enqueue', + json=body, + ) as resp: + self.assertEqual( + resp.status, + web_exceptions.HTTPAccepted.status_code, + ) + resp_json = await resp.json() + self.assertDictEqual( + resp_json, + { + 'Successfully queued': { + 'request_type': 'LoadingPipelineRequest', + 'callset_path': CALLSET_PATH, + 'dataset_type': 'SNV_INDEL', + 'project_guids': ['project_a'], + 'reference_genome': 'GRCh38', + 'sample_type': 'WGS', + 'skip_check_sex_and_relatedness': False, + 'skip_expect_tdr_metrics': False, + 'attempt_id': 0, + 'validations_to_skip': [], + }, + }, + ) + + # Second request + body['project_guids'] = ['project_b', 'project_c'] + async with self.client.request( + 'POST', + '/loading_pipeline_enqueue', + json=body, + ) as resp: + self.assertEqual( + resp.status, + web_exceptions.HTTPAccepted.status_code, + ) diff --git a/loading_pipeline/api/model.py b/loading_pipeline/api/model.py new file mode 100644 index 0000000000..4c02078cf6 --- /dev/null +++ b/loading_pipeline/api/model.py @@ -0,0 +1,105 @@ +from typing import Literal + +import hailtop.fs as hfs +from pydantic import ( + AliasChoices, + BaseModel, + Field, + conint, + field_validator, + root_validator, +) + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.misc.clickhouse import ClickhouseReferenceDataset +from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS, SKIPPABLE_VALIDATIONS + +MAX_LOADING_PIPELINE_ATTEMPTS = 5 +STRINGIFIED_SKIPPABLE_VALIDATIONS = [f.__name__ for f in SKIPPABLE_VALIDATIONS] +VALID_FILE_TYPES = ['vcf', 'vcf.gz', 'vcf.bgz', 'mt'] + + +class PipelineRunnerRequest(BaseModel): + request_type: str + + def __init_subclass__(cls, **kwargs): + super().__init_subclass__(**kwargs) + cls.model_fields['request_type'].default = cls.__name__ + + +class LoadingPipelineRequest(PipelineRunnerRequest): + attempt_id: conint(ge=0, le=MAX_LOADING_PIPELINE_ATTEMPTS - 1) = 0 + callset_path: str + project_guids: list[str] = Field( + min_length=1, + frozen=True, + validation_alias=AliasChoices('project_guids', 'projects_to_run'), + ) + sample_type: SampleType + reference_genome: ReferenceGenome + dataset_type: DatasetType + skip_check_sex_and_relatedness: bool = False + skip_expect_tdr_metrics: bool = False + validations_to_skip: list[Literal[*STRINGIFIED_SKIPPABLE_VALIDATIONS]] = [] + + def incr_attempt(self): + if self.attempt_id == (MAX_LOADING_PIPELINE_ATTEMPTS - 1): + return False + self.attempt_id += 1 + return True + + @field_validator('validations_to_skip') + @classmethod + def must_be_known_validation(cls, validations_to_skip): + for v in validations_to_skip: + if v not in set(STRINGIFIED_SKIPPABLE_VALIDATIONS): + msg = f'{v} is not a valid validator' + raise ValueError(msg) + return validations_to_skip + + @root_validator( + pre=True, + ) # the root validator runs before Pydantic parses or coerces field values. + @classmethod + def override_all_validations(cls, values): + if values.get('validations_to_skip') == [ + ALL_VALIDATIONS, + ]: + values['validations_to_skip'] = STRINGIFIED_SKIPPABLE_VALIDATIONS + return values + + @field_validator('callset_path') + @classmethod + def check_valid_callset_path(cls, callset_path: str) -> str: + if not any(callset_path.endswith(file_type) for file_type in VALID_FILE_TYPES): + msg = 'callset_path must be a VCF or a Hail Matrix Table' + raise ValueError(msg) + if '*' in callset_path and not hfs.ls( + callset_path, + ): # note that hfs.ls throws an exception if it cannot find a non-wildcard path + msg = 'callset_path must point to a shard pattern that exists' + raise ValueError(msg) + if '*' not in callset_path and not hfs.exists(callset_path): + msg = 'callset_path must point to a file that exists' + raise ValueError(msg) + return callset_path + + +class DeleteFamiliesRequest(PipelineRunnerRequest): + project_guid: str + family_guids: list[str] = Field( + min_length=1, + frozen=True, + ) + dataset_types: list[DatasetType] = Field(default_factory=lambda: list(DatasetType)) + + +class RebuildGtStatsRequest(PipelineRunnerRequest): + project_guids: list[str] = Field( + min_length=1, + frozen=True, + ) + + +class RefreshClickhouseReferenceDataRequest(PipelineRunnerRequest): + reference_dataset: ClickhouseReferenceDataset diff --git a/loading_pipeline/api/model_test.py b/loading_pipeline/api/model_test.py new file mode 100644 index 0000000000..03bc42ae1a --- /dev/null +++ b/loading_pipeline/api/model_test.py @@ -0,0 +1,87 @@ +import unittest +from pathlib import Path + +from loading_pipeline.api.model import DeleteFamiliesRequest, LoadingPipelineRequest +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType + +CALLSET_PATH = str( + Path('loading_pipeline/var/test/callsets/1kg_30variants.vcf').resolve(), +) + + +class ModelTest(unittest.TestCase): + def test_valid_loading_pipeline_requests(self) -> None: + raw_request = { + 'callset_path': CALLSET_PATH, + 'projects_to_run': ['project_a'], + 'sample_type': SampleType.WGS.value, + 'reference_genome': ReferenceGenome.GRCh38.value, + 'dataset_type': DatasetType.SNV_INDEL.value, + } + lpr = LoadingPipelineRequest.model_validate(raw_request) + self.assertEqual(lpr.reference_genome, ReferenceGenome.GRCh38) + self.assertEqual(lpr.project_guids, ['project_a']) + self.assertEqual(lpr.request_type, 'LoadingPipelineRequest') + self.assertEqual(lpr.attempt_id, 0) + + # Test wildcard VCF + raw_request['callset_path'] = CALLSET_PATH.replace( + '1kg_30variants.vcf', + '1kg_30*.vcf', + ) + lpr = LoadingPipelineRequest.model_validate(raw_request) + + def test_invalid_loading_pipeline_requests(self) -> None: + raw_request = { + 'callset_path': 'a.txt', + 'project_guids': [], + 'sample_type': 'BLENDED', + 'reference_genome': ReferenceGenome.GRCh38.value, + 'dataset_type': DatasetType.SNV_INDEL.value, + 'attempt_id': 5, + } + with self.assertRaises(ValueError) as cm: + LoadingPipelineRequest.model_validate(raw_request) + self.assertTrue( + str(cm.exception).startswith( + '4 validation errors for LoadingPipelineRequest', + ), + ) + + def test_validations_to_skip(self) -> None: + shared_params = { + 'callset_path': CALLSET_PATH, + 'projects_to_run': ['project_a'], + 'sample_type': SampleType.WGS.value, + 'reference_genome': ReferenceGenome.GRCh38.value, + 'dataset_type': DatasetType.SNV_INDEL.value, + } + raw_request = { + **shared_params, + 'validations_to_skip': ['all'], + } + lpr = LoadingPipelineRequest.model_validate(raw_request) + self.assertGreater(len(lpr.validations_to_skip), 2) + + raw_request = { + **shared_params, + 'validations_to_skip': ['validate_sample_type'], + } + lpr = LoadingPipelineRequest.model_validate(raw_request) + self.assertEqual(len(lpr.validations_to_skip), 1) + + raw_request = { + **shared_params, + 'validations_to_skip': ['validate_blended_exome'], + } + with self.assertRaises(ValueError): + LoadingPipelineRequest.model_validate(raw_request) + + def test_delete_families_request(self) -> None: + raw_request = {'project_guid': 'project_a', 'family_guids': []} + with self.assertRaises(ValueError): + DeleteFamiliesRequest.model_validate(raw_request) + raw_request['family_guids'] = ['family_a1'] + dfr = DeleteFamiliesRequest.model_validate(raw_request) + self.assertEqual(dfr.project_guid, 'project_a') + self.assertEqual(dfr.request_type, 'DeleteFamiliesRequest') diff --git a/loading_pipeline/api/request_handlers.py b/loading_pipeline/api/request_handlers.py new file mode 100644 index 0000000000..62e46f0b4d --- /dev/null +++ b/loading_pipeline/api/request_handlers.py @@ -0,0 +1,107 @@ +from collections.abc import Callable +from typing import Any + +import luigi +import luigi.execution_summary + +from loading_pipeline.api.model import ( + DeleteFamiliesRequest, + LoadingPipelineRequest, + PipelineRunnerRequest, + RebuildGtStatsRequest, + RefreshClickhouseReferenceDataRequest, +) +from loading_pipeline.lib.core import DatasetType +from loading_pipeline.lib.logger import get_logger +from loading_pipeline.lib.misc.clickhouse import ( + ClickhouseReferenceDataset, + delete_family_guids, + rebuild_gt_stats, + refresh_clickhouse_reference_data, +) +from loading_pipeline.lib.tasks.write_clickhouse_load_success_file import ( + WriteClickhouseLoadSuccessFileTask, +) + +logger = get_logger(__name__) + + +def run_loading_pipeline( + lpr: LoadingPipelineRequest, + run_id: str, + local_scheduler: bool, + *_: Any, +): + luigi_task_result = luigi.build( + [ + WriteClickhouseLoadSuccessFileTask( + run_id=run_id, + **lpr.model_dump(exclude='request_type'), + ), + ], + detailed_summary=True, + local_scheduler=local_scheduler, + ) + if luigi_task_result.status in { + luigi.execution_summary.LuigiStatusCode.SUCCESS, + luigi.execution_summary.LuigiStatusCode.SUCCESS_WITH_RETRY, + }: + return + raise RuntimeError(luigi_task_result.status.value[1]) + + +def run_delete_families(dpr: DeleteFamiliesRequest, run_id: str, *_: Any): + for dataset_type in dpr.dataset_types: + for reference_genome in dataset_type.reference_genomes: + delete_family_guids( + reference_genome, + dataset_type, + run_id, + **dpr.model_dump(exclude={'request_type', 'dataset_types'}), + ) + + +def run_rebuild_gt_stats(rgsr: RebuildGtStatsRequest, run_id: str, *_: Any): + for dataset_type in DatasetType: + for reference_genome in dataset_type.reference_genomes: + rebuild_gt_stats( + reference_genome, + dataset_type, + run_id, + **rgsr.model_dump(exclude='request_type'), + ) + + +def run_refresh_clickhouse_reference_data( + rcrdr: RefreshClickhouseReferenceDataRequest, + run_id: str, + *_: Any, +): + for dataset_type in DatasetType: + for reference_genome in dataset_type.reference_genomes: + reference_dataset = rcrdr.reference_dataset + if ( + reference_dataset + not in ClickhouseReferenceDataset.for_reference_genome_dataset_type( + reference_genome, + dataset_type, + ) + ): + continue + refresh_clickhouse_reference_data( + reference_genome, + dataset_type, + run_id, + **rcrdr.model_dump(exclude='request_type'), + ) + + +REQUEST_HANDLER_MAP: dict[ + type[PipelineRunnerRequest], + Callable[[PipelineRunnerRequest, str, ...], None], +] = { + LoadingPipelineRequest: run_loading_pipeline, + DeleteFamiliesRequest: run_delete_families, + RebuildGtStatsRequest: run_rebuild_gt_stats, + RefreshClickhouseReferenceDataRequest: run_refresh_clickhouse_reference_data, +} diff --git a/loading_pipeline/bin/__init__.py b/loading_pipeline/bin/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/loading_pipeline/bin/clickhouse_loader.py b/loading_pipeline/bin/clickhouse_loader.py new file mode 100644 index 0000000000..acb9f615c2 --- /dev/null +++ b/loading_pipeline/bin/clickhouse_loader.py @@ -0,0 +1,13 @@ +# This is a shim loader intended to keep previously deployed seqr-platform +# charts that pull a new docker image running. + +import time + + +def main(): + while True: + time.sleep(5) + + +if __name__ == '__main__': + main() diff --git a/loading_pipeline/bin/dataproc_vep_init.bash b/loading_pipeline/bin/dataproc_vep_init.bash new file mode 100755 index 0000000000..ec049e3217 --- /dev/null +++ b/loading_pipeline/bin/dataproc_vep_init.bash @@ -0,0 +1,63 @@ +#!/bin/bash + +# +# VEP init action for dataproc +# +# adapted/copied from +# https://github.com/broadinstitute/gnomad_methods/blob/main/init_scripts/vep105-init.sh +# and gs://hail-common/hailctl/dataproc/0.2.128/vep-GRCh38.sh +# +# NB: This is code used for initializing a dataproc cluster and runs as an intialization +# action when the rest of our code is unavailable. +# + +set -x + +export PROJECT="$(gcloud config get-value project)" +export DEPLOYMENT_TYPE="$(/usr/share/google/get_metadata_value attributes/DEPLOYMENT_TYPE)" +export REFERENCE_GENOME="$(/usr/share/google/get_metadata_value attributes/REFERENCE_GENOME)" +export PIPELINE_RUNNER_APP_VERSION="$(/usr/share/google/get_metadata_value attributes/PIPELINE_RUNNER_APP_VERSION)" +export REFERENCE_DATASETS_DIR="$(/usr/share/google/get_metadata_value attributes/REFERENCE_DATASETS_DIR)" + +# Install docker +apt-get update +apt-get -y install \ + apt-transport-https \ + ca-certificates \ + curl \ + gnupg2 \ + software-properties-common \ + tabix +curl -fsSL https://download.docker.com/linux/debian/gpg | sudo apt-key add - +sudo add-apt-repository "deb [arch=amd64] https://download.docker.com/linux/debian $(lsb_release -cs) stable" +sudo add-apt-repository "deb [arch=amd64] https://download.docker.com/linux/debian $(lsb_release -cs) stable" +apt-get update +apt-get install -y --allow-unauthenticated docker-ce + +# https://github.com/hail-is/hail/issues/12936 +sleep 60 +sudo service docker restart + +cat >/vep.c < +#include + +int +main(int argc, char *const argv[]) { + if (setuid(geteuid())) + perror( "setuid" ); + + execv("/vep.bash", argv); + return 0; +} +EOF +gcc -Wall -Werror -O2 /vep.c -o /vep +chmod u+s /vep + +gcloud storage cp gs://seqr-pipeline-runner-builds/$DEPLOYMENT_TYPE/$PIPELINE_RUNNER_APP_VERSION/bin/download_vep_reference_data.bash /download_vep_reference_data.bash +chmod +x /download_vep_reference_data.bash +./download_vep_reference_data.bash $REFERENCE_GENOME + +gcloud storage cp gs://seqr-pipeline-runner-builds/$DEPLOYMENT_TYPE/$PIPELINE_RUNNER_APP_VERSION/bin/vep /vep.bash +chmod +x /vep.bash + diff --git a/loading_pipeline/bin/download_vep_reference_data.bash b/loading_pipeline/bin/download_vep_reference_data.bash new file mode 100755 index 0000000000..c1784d80ac --- /dev/null +++ b/loading_pipeline/bin/download_vep_reference_data.bash @@ -0,0 +1,71 @@ +#!/usr/bin/env bash + +set -eux + +REFERENCE_GENOME=$1 +VEP_REFERENCE_DATASETS_DIR=${VEP_REFERENCE_DATASETS_DIR:-/var/seqr/vep-reference-data} +DEFAULT_REFERENCE_DATASETS_DIR="gs://seqr-reference-data" +if [[ -n "${REFERENCE_DATASETS_DIR:-}" && "$REFERENCE_DATASETS_DIR" == gs://* ]]; then + echo "Using overridden GCS path: $REFERENCE_DATASETS_DIR" +else + REFERENCE_DATASETS_DIR="$DEFAULT_REFERENCE_DATASETS_DIR" + echo "Using default GCS path: $REFERENCE_DATASETS_DIR" +fi + +case $REFERENCE_GENOME in + GRCh38) + VEP_REFERENCE_DATA_FILES=( + "$REFERENCE_DATASETS_DIR/vep_data/loftee-beta/GRCh38.tar.gz" + + # Raw data files copied from the bucket (https://console.cloud.google.com/storage/browser/dm_alphamissense;tab=objects?prefix=&forceOnObjectsSortingFiltering=false) + # tabix -s 1 -b 2 -e 2 -f -S 1 AlphaMissense_hg38.tsv.gz + "$REFERENCE_DATASETS_DIR/vep/GRCh38/AlphaMissense_hg38.tsv.*" + + # Generated with: + # curl -O ftp://ftp.ensembl.org/pub/release-110/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz > Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz + # gzip -d Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz + # bgzip Homo_sapiens.GRCh38.dna.primary_assembly.fa + # samtools faidx Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz + "$REFERENCE_DATASETS_DIR/vep/GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa.*" + + # Copied from ftp://ftp.ensembl.org/pub/release-110/variation/indexed_vep_cache/homo_sapiens_vep_110_GRCh38.tar.gz + "$REFERENCE_DATASETS_DIR/vep/GRCh38/homo_sapiens_vep_110_GRCh38.tar.gz" + + # Copied from the UTRAnnotator repo (https://github.com/ImperialCardioGenetics/UTRannotator/tree/master) + "$REFERENCE_DATASETS_DIR/vep/GRCh38/uORF_5UTR_GRCh38_PUBLIC.txt" + + "$REFERENCE_DATASETS_DIR/vep/GRCh38/vep-GRCh38.json" + ) + ;; + GRCh37) + VEP_REFERENCE_DATA_FILES=( + "$REFERENCE_DATASETS_DIR/vep_data/loftee-beta/GRCh37.tar.gz" + "$REFERENCE_DATASETS_DIR/vep/GRCh37/homo_sapiens_vep_110_GRCh37.tar.gz" + "$REFERENCE_DATASETS_DIR/vep/GRCh37/Homo_sapiens.GRCh37.dna.primary_assembly.fa.*" + "$REFERENCE_DATASETS_DIR/vep/GRCh37/vep-GRCh37.json" + ) + ;; + *) + echo "Invalid reference genome $REFERENCE_GENOME, should be GRCh37 or GRCh38" + exit 1 +esac + +if [ -f "$VEP_REFERENCE_DATASETS_DIR"/"$REFERENCE_GENOME"/_SUCCESS ]; then + echo "Skipping download because already successful" + exit 0; +fi + +mkdir -p "$VEP_REFERENCE_DATASETS_DIR"/"$REFERENCE_GENOME"; +rm -rf "${VEP_REFERENCE_DATASETS_DIR:?}"/"${REFERENCE_GENOME:?}"/*; + +for vep_reference_data_file in "${VEP_REFERENCE_DATA_FILES[@]}"; do + if [[ $vep_reference_data_file == *.tar.gz ]]; then + echo "Downloading and extracting" "$vep_reference_data_file"; + gsutil cat "$vep_reference_data_file" | tar -xzf - -C "$VEP_REFERENCE_DATASETS_DIR"/"$REFERENCE_GENOME"/ & + else + echo "Downloading" "$vep_reference_data_file"; + gsutil cp "$vep_reference_data_file" "$VEP_REFERENCE_DATASETS_DIR"/"$REFERENCE_GENOME"/ & + fi +done; +wait +touch "$VEP_REFERENCE_DATASETS_DIR"/"$REFERENCE_GENOME"/_SUCCESS diff --git a/loading_pipeline/bin/migrate_all_projects_to_clickhouse.py b/loading_pipeline/bin/migrate_all_projects_to_clickhouse.py new file mode 100755 index 0000000000..bc691738c3 --- /dev/null +++ b/loading_pipeline/bin/migrate_all_projects_to_clickhouse.py @@ -0,0 +1,65 @@ +#!/usr/bin/env python3 +import uuid + +import hailtop.fs as hfs +import luigi + +from loading_pipeline.lib.core import ( + DatasetType, + FeatureFlag, + ReferenceGenome, + SampleType, +) +from loading_pipeline.lib.core.constants import MIGRATION_RUN_ID +from loading_pipeline.lib.paths import project_table_path +from loading_pipeline.lib.tasks import ( + MigrateAllProjectsToClickHouseOnDataprocTask, + MigrateAllProjectsToClickHouseTask, +) +from loading_pipeline.lib.tasks.write_clickhouse_load_success_file import ( + WriteClickhouseLoadSuccessFileTask, +) + +if __name__ == '__main__': + task_cls = ( + MigrateAllProjectsToClickHouseOnDataprocTask + if FeatureFlag.RUN_PIPELINE_ON_DATAPROC + else MigrateAllProjectsToClickHouseTask + ) + run_id_prefix = ( + MIGRATION_RUN_ID + '-' + str(uuid.uuid1().int)[:4] + ) # Note: the randomness is a cache bust for the luigi local scheduler + luigi.build( + [ + task_cls( + reference_genome, + DatasetType.SNV_INDEL, + run_id=run_id_prefix, + attempt_id=0, + ) + for reference_genome in ReferenceGenome + ], + ) + clickhouse_load_tasks = [] + for sample_type in SampleType: + for reference_genome in ReferenceGenome: + for p in hfs.ls( + project_table_path( + reference_genome, + DatasetType.SNV_INDEL, + sample_type, + '*', + ), + ): + project_guid = p.path.split('/')[-1].replace('.ht', '') + clickhouse_load_tasks.append( + WriteClickhouseLoadSuccessFileTask( + reference_genome=reference_genome, + dataset_type=DatasetType.SNV_INDEL, + run_id=f'{run_id_prefix}_{sample_type.value}_{project_guid}', + callset_path='', + sample_type=sample_type, + attempt_id=0, + ), + ) + luigi.build(clickhouse_load_tasks) diff --git a/loading_pipeline/bin/migrate_variants_tables.py b/loading_pipeline/bin/migrate_variants_tables.py new file mode 100755 index 0000000000..a34e9e9026 --- /dev/null +++ b/loading_pipeline/bin/migrate_variants_tables.py @@ -0,0 +1,49 @@ +#!/usr/bin/env python3 +import argparse +import uuid + +import luigi + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome +from loading_pipeline.lib.core.constants import VARIANTS_MIGRATION_RUN_ID +from loading_pipeline.lib.tasks.variants_migration.load_clickhouse_variants_tables import ( + LoadClickhouseVariantsTablesTask, +) + + +def parse_args() -> argparse.Namespace: + parser = argparse.ArgumentParser( + description='Run variants migration Luigi pipeline.', + ) + parser.add_argument( + '--run_all_dataset_types', + action='store_true', + help='If set, runs the pipeline for all dataset types instead of just SNV_INDEL.', + ) + return parser.parse_args() + + +if __name__ == '__main__': + args = parse_args() + for reference_genome, dataset_type in [ + (ReferenceGenome.GRCh37, DatasetType.SNV_INDEL), + (ReferenceGenome.GRCh38, DatasetType.SNV_INDEL), + (ReferenceGenome.GRCh38, DatasetType.MITO), + (ReferenceGenome.GRCh38, DatasetType.SV), + (ReferenceGenome.GRCh38, DatasetType.GCNV), + ]: + if dataset_type != DatasetType.SNV_INDEL and not args.run_all_dataset_types: + continue + run_id_prefix = ( + VARIANTS_MIGRATION_RUN_ID + '-' + str(uuid.uuid1().int)[:4] + ) # Note: the randomness is a cache bust for the luigi local scheduler + luigi.build( + [ + LoadClickhouseVariantsTablesTask( + reference_genome, + dataset_type, + run_id=run_id_prefix, + attempt_id=0, + ), + ], + ) diff --git a/loading_pipeline/bin/pipeline_worker.py b/loading_pipeline/bin/pipeline_worker.py new file mode 100755 index 0000000000..4760cc37b3 --- /dev/null +++ b/loading_pipeline/bin/pipeline_worker.py @@ -0,0 +1,110 @@ +#!/usr/bin/env python3 +import json +import os +import re +import signal +import sys +import time + +from loading_pipeline.api.model import ( + PipelineRunnerRequest, +) +from loading_pipeline.api.request_handlers import REQUEST_HANDLER_MAP +from loading_pipeline.lib.logger import get_logger +from loading_pipeline.lib.misc.clickhouse import ( + drop_staging_db, +) +from loading_pipeline.lib.misc.runs import get_oldest_queue_path +from loading_pipeline.lib.misc.slack import ( + safe_post_to_slack_failure, + safe_post_to_slack_success, +) +from loading_pipeline.lib.paths import ( + loading_pipeline_deadletter_queue_dir, + loading_pipeline_deadletter_queue_path, + loading_pipeline_queue_path, +) + +logger = get_logger(__name__) + + +def signal_handler(*_): + drop_staging_db() + sys.exit(0) + + +signal.signal(signal.SIGINT, signal_handler) +signal.signal(signal.SIGTERM, signal_handler) + + +def parse_run_id(latest_queue_path: str) -> str: + m = re.search( + r'request_(\d{8}-\d{6}-\d{6})\.json', + os.path.basename(latest_queue_path), + ) + if not m: + msg = f'Invalid queue filename: {latest_queue_path}' + raise ValueError(msg) + return m.group(1) + + +def parse_latest_queue_path( + latest_queue_path: str, +) -> PipelineRunnerRequest: + with open(latest_queue_path) as f: + raw_json = json.load(f) + request_type_name = raw_json['request_type'] + request_cls = next( + (cls for cls in REQUEST_HANDLER_MAP if cls.__name__ == request_type_name), + None, + ) + if not request_cls: + msg = f'Unknown request_type: {request_type_name}' + raise ValueError(msg) + return request_cls.model_validate(raw_json) + + +def process_queue(local_scheduler=False): + run_id, prr = None, None + try: + latest_queue_path = get_oldest_queue_path() + if latest_queue_path is None: + return + run_id = parse_run_id(latest_queue_path) + if not run_id: + return + prr = parse_latest_queue_path(latest_queue_path) + REQUEST_HANDLER_MAP[type(prr)](prr, run_id, local_scheduler) + os.remove(latest_queue_path) + safe_post_to_slack_success( + run_id, + prr, + ) + except Exception as e: + logger.exception('Unhandled Exception') + if run_id is None: + return + if hasattr(prr, 'attempt_id') and prr.incr_attempt(): + with open(loading_pipeline_queue_path(run_id), 'w') as f: + f.write(prr.model_dump_json()) + return + safe_post_to_slack_failure( + run_id, + prr, + e, + ) + os.makedirs(loading_pipeline_deadletter_queue_dir(), exist_ok=True) + with open(loading_pipeline_deadletter_queue_path(run_id), 'w') as f: + f.write(prr.model_dump_json()) + os.remove(latest_queue_path) + + +def main(): + while True: + process_queue() + logger.info('Looking for more work') + time.sleep(1) + + +if __name__ == '__main__': + main() diff --git a/loading_pipeline/bin/pipeline_worker_test.py b/loading_pipeline/bin/pipeline_worker_test.py new file mode 100644 index 0000000000..e258d0c573 --- /dev/null +++ b/loading_pipeline/bin/pipeline_worker_test.py @@ -0,0 +1,182 @@ +import json +import os +from unittest.mock import Mock, patch + +import hail as hl +import hailtop.fs as hfs +import luigi +import luigi.worker + +from loading_pipeline.bin.pipeline_worker import process_queue +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.core.environment import Env +from loading_pipeline.lib.misc.clickhouse import ( + ClickhouseReferenceDataset, + get_clickhouse_client, +) +from loading_pipeline.lib.paths import ( + clickhouse_load_success_file_path, + loading_pipeline_deadletter_queue_dir, + loading_pipeline_queue_dir, +) +from loading_pipeline.lib.test.clickhouse_schema_testcase import ( + ClickhouseSchemaTestCase, +) +from loading_pipeline.lib.test.misc import copy_project_pedigree_to_mocked_dir +from loading_pipeline.lib.test.mocked_dataroot_testcase import ( + MockedDatarootTestCase, +) +from loading_pipeline.var.test.vep.mock_vep_data import MOCK_38_VEP_DATA + +TEST_PEDIGREE_3_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_3_remap.tsv' +TEST_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' + + +class MyFailingTask(luigi.Task): + def run(self): + msg = 'This task is designed to fail!' + raise ValueError(msg) + + def output(self): + return luigi.LocalTarget('output.txt') + + +class PipelineWorkerTest(MockedDatarootTestCase, ClickhouseSchemaTestCase): + @patch.object( + ClickhouseReferenceDataset, + 'for_reference_genome_dataset_type', + return_value=[ClickhouseReferenceDataset.CLINVAR], + ) + @patch( + 'loading_pipeline.lib.tasks.write_new_variants_table.load_gencode_ensembl_to_refseq_id', + ) + @patch('loading_pipeline.lib.misc.vep.hl.vep') + @patch('loading_pipeline.lib.misc.slack._safe_post_to_slack') + @patch('loading_pipeline.bin.pipeline_worker.logger') + def test_process_queue_integration_test( + self, + mock_logger, + mock_safe_post_to_slack, + mock_vep: Mock, + mock_load_gencode_ensembl_to_refseq_id: Mock, + mock_for_reference_genome_dataset_type: Mock, + ): + mock_load_gencode_ensembl_to_refseq_id.return_value = hl.dict( + {'ENST00000327044': 'NM_015658.4'}, + ) + mock_vep.side_effect = lambda ht, **_: ht.annotate(vep=MOCK_38_VEP_DATA) + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_3_REMAP, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0113_test_project', + ) + raw_request = { + 'request_type': 'LoadingPipelineRequest', + 'callset_path': TEST_VCF, + 'projects_to_run': ['R0113_test_project'], + 'sample_type': SampleType.WGS.value, + 'reference_genome': ReferenceGenome.GRCh38.value, + 'dataset_type': DatasetType.SNV_INDEL.value, + 'validations_to_skip': ['all'], + } + os.makedirs( + loading_pipeline_queue_dir(), + exist_ok=True, + ) + with open( + os.path.join( + loading_pipeline_queue_dir(), + 'request_20250916-200704-123456.json', + ), + 'w', + ) as f: + json.dump(raw_request, f) + process_queue(local_scheduler=True) + mock_safe_post_to_slack.assert_called_once_with( + ':white_check_mark: Pipeline Runner Request Success! :white_check_mark:\nRun ID: 20250916-200704-123456\n```{\n "attempt_id": 0,\n "callset_path": "loading_pipeline/var/test/callsets/1kg_30variants.vcf",\n "dataset_type": "SNV_INDEL",\n "project_guids": [\n "R0113_test_project"\n ],\n "reference_genome": "GRCh38",\n "request_type": "LoadingPipelineRequest",\n "sample_type": "WGS",\n "skip_check_sex_and_relatedness": false,\n "skip_expect_tdr_metrics": false,\n "validations_to_skip": [\n "validate_allele_depth_length",\n "validate_allele_type",\n "validate_expected_contig_frequency",\n "validate_no_duplicate_variants",\n "validate_sample_type"\n ]\n}```', + ) + with hfs.open( + clickhouse_load_success_file_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + '20250916-200704-123456', + ), + ) as f: + self.assertEqual(f.read(), '') + + client = get_clickhouse_client() + annotations_count = client.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` + """, + )[0][0] + self.assertEqual(annotations_count, 30) + entries_count = client.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` + """, + )[0][0] + self.assertEqual(entries_count, 16) + ac_wgs = client.execute( + f""" + SELECT sum(ac_wgs) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` + """, + )[0][0] + self.assertEqual(ac_wgs, 69) + + @patch('loading_pipeline.lib.misc.slack._safe_post_to_slack') + @patch('loading_pipeline.api.request_handlers.WriteClickhouseLoadSuccessFileTask') + @patch('loading_pipeline.bin.pipeline_worker.logger') + def test_process_failure( + self, + mock_logger, + mock_write_clickhouse_load_success_file_task, + mock_safe_post_to_slack, + ): + raw_request = { + 'request_type': 'LoadingPipelineRequest', + 'callset_path': TEST_VCF, + 'projects_to_run': ['project_a'], + 'sample_type': SampleType.WGS.value, + 'reference_genome': ReferenceGenome.GRCh38.value, + 'dataset_type': DatasetType.SNV_INDEL.value, + } + mock_write_clickhouse_load_success_file_task.return_value = MyFailingTask() + os.makedirs( + loading_pipeline_queue_dir(), + exist_ok=True, + ) + with open( + os.path.join( + loading_pipeline_queue_dir(), + 'request_20250918-200704-123456.json', + ), + 'w', + ) as f: + json.dump(raw_request, f) + process_queue(local_scheduler=True) + process_queue(local_scheduler=True) + process_queue(local_scheduler=True) + process_queue(local_scheduler=True) + process_queue(local_scheduler=True) + mock_safe_post_to_slack.assert_called_once_with( + ':failed: Pipeline Runner Request Failed :failed:\nRun ID: 20250918-200704-123456\n```{\n "attempt_id": 4,\n "callset_path": "loading_pipeline/var/test/callsets/1kg_30variants.vcf",\n "dataset_type": "SNV_INDEL",\n "project_guids": [\n "project_a"\n ],\n "reference_genome": "GRCh38",\n "request_type": "LoadingPipelineRequest",\n "sample_type": "WGS",\n "skip_check_sex_and_relatedness": false,\n "skip_expect_tdr_metrics": false,\n "validations_to_skip": []\n}```\nReason: there were failed tasks', + ) + self.assertEqual(len(os.listdir(loading_pipeline_queue_dir())), 0) + with open( + os.path.join( + loading_pipeline_deadletter_queue_dir(), + 'request_20250918-200704-123456.json', + ), + ) as f: + r = json.load(f) + self.assertEqual(r['request_type'], 'LoadingPipelineRequest') + self.assertEqual(r['attempt_id'], 4) diff --git a/loading_pipeline/bin/rsync_reference_data.bash b/loading_pipeline/bin/rsync_reference_data.bash new file mode 100755 index 0000000000..360a6d6e1a --- /dev/null +++ b/loading_pipeline/bin/rsync_reference_data.bash @@ -0,0 +1,52 @@ +#!/usr/bin/env bash + +set -eux + +REFERENCE_GENOME=$1 +REFERENCE_DATASETS_DIR=${REFERENCE_DATASETS_DIR:-/var/seqr/seqr-reference-data} + + +case $REFERENCE_GENOME in + GRCh38) + ;; + GRCh37) + ;; + *) + echo "Invalid reference genome $REFERENCE_GENOME, should be GRCh37 or GRCh38" + exit 1 +esac + +case $REFERENCE_DATASETS_DIR in + "gs://seqr-reference-data") + echo "Cannot rsync to the authoritative source" + exit 1 + ;; + *) + ;; +esac + +if ! [[ "$REFERENCE_DATASETS_DIR" =~ gs://* ]]; then + mkdir -p $REFERENCE_DATASETS_DIR/$REFERENCE_GENOME; + if [ -f "$REFERENCE_DATASETS_DIR"/"$REFERENCE_GENOME"/_SUCCESS ]; then + echo "Skipping rsync because already successful" + exit 0; + fi +else + result=$(gsutil -q stat "$REFERENCE_DATASETS_DIR"/"$REFERENCE_GENOME"/_SUCCESS || echo 1) + if [[ $result != 1 ]]; then + echo "Skipping rsync because already successful" + exit 0; + fi +fi + +gsutil -m rsync -rd -x '.*\.parquet.*' "gs://seqr-reference-data/v3.2/$REFERENCE_GENOME" $REFERENCE_DATASETS_DIR/$REFERENCE_GENOME +if ! [[ $REFERENCE_DATASETS_DIR =~ gs://* ]]; then + touch "$REFERENCE_DATASETS_DIR"/"$REFERENCE_GENOME"/_SUCCESS +else + # If a different reference datasets dir is provided, sync vep data to the provided bucket. + gsutil cp "gs://seqr-reference-data/vep_data/loftee-beta/$REFERENCE_GENOME.tar.gz" $REFERENCE_DATASETS_DIR/vep_data/loftee-beta/$REFERENCE_GENOME.tar.gz + gsutil -m rsync -rd "gs://seqr-reference-data/vep/$REFERENCE_GENOME" $REFERENCE_DATASETS_DIR/vep/$REFERENCE_GENOME + touch _SUCCESS + gsutil cp _SUCCESS "$REFERENCE_DATASETS_DIR"/"$REFERENCE_GENOME"/_SUCCESS + rm -rf _SUCCESS +fi diff --git a/loading_pipeline/bin/run_task.py b/loading_pipeline/bin/run_task.py new file mode 100755 index 0000000000..37b96c4fb7 --- /dev/null +++ b/loading_pipeline/bin/run_task.py @@ -0,0 +1,10 @@ +#!/usr/bin/env python3 +import sys + +import luigi + +from loading_pipeline.lib.tasks import * # noqa: F403 + +if __name__ == '__main__': + # If run does not succeed, exit with 1 status code. + luigi.run() or sys.exit(1) diff --git a/loading_pipeline/bin/updated_reference_dataset_parquet.py b/loading_pipeline/bin/updated_reference_dataset_parquet.py new file mode 100755 index 0000000000..48547dde77 --- /dev/null +++ b/loading_pipeline/bin/updated_reference_dataset_parquet.py @@ -0,0 +1,37 @@ +#!/usr/bin/env python3 +import argparse + +import luigi + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome +from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset +from loading_pipeline.lib.tasks.reference_data.updated_reference_dataset_parquet import ( + UpdatedReferenceDatasetParquetOnDataprocTask, +) + + +def main(): + parser = argparse.ArgumentParser() + parser.add_argument('--reference-genome', required=True, type=ReferenceGenome) + parser.add_argument('--dataset-type', required=True, type=DatasetType) + parser.add_argument( + '--reference-dataset', + required=True, + type=ReferenceDataset, + ) + args = parser.parse_args() + luigi.build( + [ + UpdatedReferenceDatasetParquetOnDataprocTask( + reference_genome=args.reference_genome, + dataset_type=args.dataset_type, + reference_dataset=args.reference_dataset, + run_id=f'{args.reference_dataset.value.replace("_", "-").lower()}-run', + attempt_id=0, + ), + ], + ) + + +if __name__ == '__main__': + main() diff --git a/loading_pipeline/bin/vep b/loading_pipeline/bin/vep new file mode 100755 index 0000000000..437ffcfe17 --- /dev/null +++ b/loading_pipeline/bin/vep @@ -0,0 +1,21 @@ +#!/bin/bash + +set -eux + +REFERENCE_GENOME=$1 +VEP_REFERENCE_DATASETS_DIR=${VEP_REFERENCE_DATASETS_DIR:-/var/seqr/vep-reference-data} +VEP_DOCKER_IMAGE="gcr.io/seqr-project/vep-docker-image" + +case $REFERENCE_GENOME in + GRCh38) + ;; + GRCh37) + ;; + *) + echo "Invalid reference genome $REFERENCE_GENOME, should be GRCh37 or GRCh38" + exit 1 +esac + +shift # Remove the REFERENCE_GENOME arg. +docker run --platform linux/amd64 -i -v "$VEP_REFERENCE_DATASETS_DIR"/"$REFERENCE_GENOME":/opt/vep/.vep/:ro $VEP_DOCKER_IMAGE:"$REFERENCE_GENOME" \ + /opt/vep/src/ensembl-vep/vep "$@" diff --git a/loading_pipeline/deploy/Dockerfile b/loading_pipeline/deploy/Dockerfile new file mode 100644 index 0000000000..0ae73232ae --- /dev/null +++ b/loading_pipeline/deploy/Dockerfile @@ -0,0 +1,40 @@ +FROM --platform=linux/amd64 docker:dind as BUILD +FROM --platform=linux/amd64 ghcr.io/astral-sh/uv:python3.11-alpine AS UV_BUILD +FROM --platform=linux/amd64 hailgenetics/hail:0.2.138-py3.11 +COPY --from=BUILD /usr/local/bin/docker /usr/local/bin/docker +COPY --from=UV_BUILD /usr/local/bin/uv /usr/local/bin/uv +LABEL maintainer="Broad TGG" + +RUN curl -sSL https://sdk.cloud.google.com | bash +ENV PATH $PATH:/root/google-cloud-sdk/bin + +ARG PIPELINE_RUNNER_APP_VERSION +ENV PIPELINE_RUNNER_APP_VERSION=${PIPELINE_RUNNER_APP_VERSION} + +ENV VIRTUAL_ENV="/.venv" + +# Add build utilities for "annoy" package +# Note that these are getting added into the final runtime image and not the build... +# I (BPB) ran into challenges getting the uv virtual environment synced properly due +# to mismatches between the uv:python3.11-alpine and hail docker python environments. +RUN apt-get update && apt-get install -y build-essential && rm -rf /var/lib/apt/lists/* + +COPY pyproject.toml uv.lock . +RUN uv sync --group prod --no-group dev --locked + +# Application Code +WORKDIR /loading_pipeline +COPY loading_pipeline/api api +COPY loading_pipeline/bin bin +COPY loading_pipeline/lib lib +COPY loading_pipeline/ops ops +COPY loading_pipeline/var/liftover var/liftover + +# Special paths +COPY loading_pipeline/var/spark_config/spark-defaults.conf /usr/local/lib/python3.10/dist-packages/pyspark/conf/spark-defaults.conf +COPY loading_pipeline/bin/vep /vep + + +WORKDIR / +EXPOSE 6000 8082 +CMD ["uv", "run", "python3", "-m", "loading_pipeline.api"] diff --git a/loading_pipeline/deploy/Dockerfile.vep_GRCh37 b/loading_pipeline/deploy/Dockerfile.vep_GRCh37 new file mode 100644 index 0000000000..b585244fb9 --- /dev/null +++ b/loading_pipeline/deploy/Dockerfile.vep_GRCh37 @@ -0,0 +1,12 @@ +FROM ubuntu:18.04 as build + +# NB: This code is a copy of GRCh38 except for the loftee branch. + +RUN apt-get update && apt-get -y install wget libncurses5-dev libncursesw5-dev libbz2-dev liblzma-dev build-essential libz-dev git +RUN wget https://github.com/samtools/samtools/releases/download/1.7/samtools-1.7.tar.bz2 && tar xjvf samtools-1.7.tar.bz2 && cd samtools-1.7 && make && make install +RUN git clone https://github.com/konradjk/loftee.git + +FROM ensemblorg/ensembl-vep:release_110.1 as runtime +RUN cpanm DBD::SQLite +COPY --from=build /usr/local/bin/samtools /usr/local/bin/samtools +COPY --from=build /loftee/ /plugins diff --git a/loading_pipeline/deploy/Dockerfile.vep_GRCh38 b/loading_pipeline/deploy/Dockerfile.vep_GRCh38 new file mode 100644 index 0000000000..f781db8bc8 --- /dev/null +++ b/loading_pipeline/deploy/Dockerfile.vep_GRCh38 @@ -0,0 +1,13 @@ +FROM ubuntu:18.04 as build + +# Adapted from https://hub.docker.com/layers/konradjk/vep95_loftee/latest/images/sha256-d5f1a155293412acb5af4811142ba6907bad1cd708ca4000528f6317b784440e?context=explore +# and https://github.com/broadinstitute/gnomad_methods/blob/main/docker_files/Dockerfile_VEP105 +RUN apt-get update && apt-get -y install wget libncurses5-dev libncursesw5-dev libbz2-dev liblzma-dev build-essential libz-dev git +RUN wget https://github.com/samtools/samtools/releases/download/1.7/samtools-1.7.tar.bz2 && tar xjvf samtools-1.7.tar.bz2 && cd samtools-1.7 && make && make install +RUN git clone -b grch38 https://github.com/konradjk/loftee.git + +FROM ensemblorg/ensembl-vep:release_110.1 as runtime +RUN cpanm DBD::SQLite +COPY --from=build /usr/local/bin/samtools /usr/local/bin/samtools +# semantics of mv vs COPY are different such that we don't need the '*' when moving files. +COPY --from=build /loftee/ /plugins diff --git a/loading_pipeline/docs/Clickhouse_Design_Notes.md b/loading_pipeline/docs/Clickhouse_Design_Notes.md new file mode 100644 index 0000000000..ff050c98dc --- /dev/null +++ b/loading_pipeline/docs/Clickhouse_Design_Notes.md @@ -0,0 +1,202 @@ +# ClickHouse Design Decisions + +## Schema + +### Entries Table +- Grouping by family was most efficient at query-time and was a wash on-disk. +- ORDER BY `project_guid, family_guid, sample_type, is_gnomad_gt_5_percent, is_annotated_in_any_gene, key` + - Support searches on project or family +- PROJECTION on `is_gnomad_gt_5_percent`, `is_annotated_in_any_gene`, `xpos` + - Static view over gnomad constructed at load time. + - Note that an update to gnomad _requires_ rebuilding this!!!! + - I would try to be clever about this, identifying the variants that change when gnomad updates + - From experience, dropping or adding columns NOT in the sorting key is very easy... impossible if it is. + - `is_annotated_in_gene` (lightweight boolean index to support gene search) + - xpos ordering supports sorts on gene/position. +- `geneId_ids` Array(UInt32) + - We _tried_ to make this a bitmap column. However, they are really "partial aggregation state" columns + `AggregateFunction(groupBitmap, UInt64)` and are not cleanly supported in all the right ways downstream. + - We store an array of integers and convert to a bitmap at search time, for a slight performance hit. + - hasAny(`list`, `list`) is trash slow and untenable. + +### Variants Tables +- Searchable fields in `variants_memory`. +- `variants_details` is post-filter and slow (10k per second). Mostly large blobs of strings. +- Live search queries run against `variants_memory` only. At load time, we insert into both tables w/ "on-disk" first. RocksDB inserts are idempotent so can handle retries re-writing the same key multiple times. + +### Reference Data Tables +- One table each per reference data source: `all_variants`, `seqr_variants`, `search`. +- Sourced from raw VCFs/TSVs if possible, `splice_ai` and `dbnsfp` are SLOW and big. +- Dictionaries are mostly [`HASHED_ARRAY`](https://kb.altinity.com/altinity-kb-dictionaries/altinity-kb-sparse_hashed-vs-hashed/) +- Tables with lots of seqr variants ("full rank" in key space) or too small to matter can be "FLAT" arrays. +- `RANGE_HASHED()` for ranges. +- dictGets and JOIN tables are super fast (10M/S) so even N joins is much faster than RocksDB table access. + +### SeqrDB Dicts +- Postgres backed dictionaries. +- Postgres named collection set up in infrastructure. +- These are essential, providing fast access within ClickHouse to Postgres itself. + - Loading references these. + - populating the geneIds field + - Search queries reference them too. +- Performantly refreshable! + +### Incremental vs Refreshable Materialized Views +- Incremental MVs are pointers between two actual tables, when data is inserted into the first it is copied +to the second with a transformation. +- Refreshable MVs are more analagous to other DBs, full data is generated on a schedule or manually. + - All Refreshable MVs in seqr are set to a refresh frequency of every 10 years. +- Incremental MVs cannot be "built". + +### RocksDB +The dependency on RocksDB is the weak point of the ClickHouse backend. The data structure is opaque, hard to reason about and improve, and challenging to query and update. Schema migrations are not supported, backups are manual and failure-prone, and the Engine is not supported in the managed ClickHouse Inc product. It solves a key problem for us, however, supporting fast key-value access over both small and large blobs of strings. + +Only Key/Value access is really supported for the RocksDB tables. Queries such as `SELECT ... WHERE key > 0 and key < 100000` are very slow and should be avoided. + +### Ingestion Architecture & Async Tasks +- Many operations in ClickHouse are asynchrnous and happen in the background. Careful attention must be paid +to ensure things finish reliably and do not leave partial state! +- Load is structured around a `staging` database and [atomic partition movement](https://clickhouse.com/blog/table-cloning). + - All `entries` tables and materialized views are schema-copied into `staging`. + - All data is inserted into `staging`. + - `staging` environment must be 'verified'. + - Dictionaries are rebuilt only in `production` database! +- `entries`/`project_gt_stats`/`gt_stats` cascade was required for reasonable performance +of recomputing allele frequencies. We did try loading without multiple descending views, but re-grouping the whole `entries` table OOMs. + +### History of Nasty Bugs +- Incorrectly named the on-disk tables `/variants/details` instead of `/variants_details` which caused issues because of an existing `/variants` path. +- Missing `affected_status` in materialized view ORDER BY, leading to undefined behavior. +- Mis-typed a gnomad allele frequency, incorrectly rounding down AFs. +- Infinite issues with column ordering, missing fields, and types. + +## Infrastructure + +#### ClickHouse Settings +Essential: +- `max_partition_size_to_drop`/`max_table_size_to_drop` need to be high, we delete the `staging` database +and thus need these to be the size of the largest project. +- `max_bytes_ratio_before_external_group_by`/`max_bytes_ratio_before_external_sort`. These are set to `0.1` and are essential. +During loading and various other operations, large `GROUP BY` can OOM. We have set these to ensure JOINs spill to disk, preferring slowness to crashes! +- `stop_refreshable_materialized_views_on_startup`, prevents all views from starting all at once on server startup. + +Optional: +- `max_query_size`, `max_ast_elements`, `max_expanded_ast_elements`,`max_parser_backtracks`: used internally for large projects with many samples. +- `max_server_memory_usage_to_ram_ratio` instructs ClickHouse to use less of the server's memory. Since we mount `/in-memory-dir` we allocate resources away from ClickHouse without its knowledge. +- `background_pool_size`, `background_merges_mutations_concurrency_ratio`, `number_of_free_entries_in_pool_to_execute_mutation`, `number_of_free_entries_in_pool_to_lower_max_size_of_merge`, `number_of_free_entries_in_pool_to_execute_optimize_entire_partition` allow limiting the number of background threads for background tasks. This has been helpful for protecting search performance at the cost of longer background operations. + +#### Running a Single Host +Clickhouse and the Helm installation support replication and scaling with either a Zookeeper or Clickhouse-Keeper managed cluster. Given our prioritization of Consistency >> Availability, and the complexity of managing a cluster, we've opted for the simplicity of maintaining a single host, accepting the risk of limited downtime both in search and loading. + +#### Backups +We have a cron in the [seqr codebase](https://github.com/broadinstitute/seqr/blob/master/deploy/docker/seqr/clickhouse_backup.py) that manages incremental backups of the the Broad `seqr`'s database. The `rocksdb` tables are backed up with a cloud storage rsync cron. + +#### Project Sub-Partitions +Select `GRCh38/SNV_INDEL` WGS projects are subpartitioned via a static mapping, set up as a one time operation w/ a rough goal of 500m rows per partition. Our largest projects far exceed ClickHouse's recommended maximum partition, and operations on coalesced single partitions are single threaded (slowing down `OPTIMIZE TABLE FINAL` like no other). Supporting sub-partitions lets us parallelize +any `OPTIMIZE TABLE` and in general leads to more manageable chunks of data. + +We did not, however, notice this prior to initial go-live. Thus all non-`GRCh38/SNV_INDEL` tables and early open-source releases do +follow this pattern. We have code and unit-tests to support both partitioning paradigms, and also have an operations script for the manual re-partitioning (`loading_pipeline/ops`). + +## Miscellaneous + +#### Learning About ClickHouse +- PostHog's [Clickhouse explainers](https://posthog.com/blog/clickhouse) +- Andy Pavlo's [DB Course](https://www.youtube.com/watch?v=nhlpwmOBEiE) +- The ClickHouse Documentation. + +#### Debugging Advice +- Logging into the client: +``` +kubectl port-forward services/seqr-clickhouse 9000:9000 + +# In another terminal +./clickhouse client --user seqr_clickhouse_writer --password PASSWORD +``` + +- Reading the query log, for example recent non-insert queries: +``` +select * FROM system.query_log where query_start_time > '2026-05-01' and query not like '%INSERT%'; +``` +Statistics like query time and memory are available here. + +- Manually timing queries. I've generally had a much better experience running a query and inserting into a temp table. For example: +``` +create temporary table t as SELECT transcripts FROM ( + SELECT toUInt32(generate_series) AS key + FROM generate_series(5_000_000, 5_010_000) +) k INNER JOIN `GRCh38/SNV_INDEL/transcripts` t on k.key = t.key; +``` +The alternatives, either returning the full result set to the client or "SELECT COUNT(*)", return biased timings. Either too slow due to networking buffering over the terminal or too fast due to not actually fetching the full result set off of disk. + +- Viewing `Dictionary` usage: +``` +SELECT + name AS dictionary_name, + sum(bytes_allocated) AS bytes_allocated_, + formatReadableSize(sum(bytes_allocated)) AS readable_size +FROM system.dictionaries +GROUP BY dictionary_name +ORDER BY bytes_allocated_ DESC +``` +Broad Seqr's production instance dictionaries consume ~30GB of memory. + +NOTE: I (bpb) believe these numbers are underestimates and don't account for some of the full memory overhead of maintaining these in memory. + +- Viewing `Join` table memory usage: +``` +SELECT + database, + name, + formatReadableSize(total_bytes) +FROM system.tables +WHERE engine IN ('Memory', 'Set', 'Join') +``` +Broad Seqr's production 'Join' tables consume about ~1GB of memory. + +- Viewing disk usage within ClickHouse: +``` +SELECT + disk_name, + database, + `table`, + sum(bytes_on_disk) AS s, + formatReadableSize(sum(bytes_on_disk)) AS size +FROM system.parts +WHERE active = 1 +GROUP BY + disk_name, + database, + `table` +ORDER BY s DESC +``` + +Broad Seqr's production disk usage: +``` + ┌─disk_name─┬─database─┬─table─────────────────────────────────────────────────────────────────────┬─────────────s─┬─size───────┐ +1. │ default │ seqr │ GRCh38/SNV_INDEL/entries │ 2134397010569 │ 1.94 TiB │ +2. │ default │ seqr │ GRCh37/SNV_INDEL/reference_data/splice_ai/all_variants │ 72085843803 │ 67.14 GiB │ +3. │ default │ seqr │ GRCh38/SNV_INDEL/reference_data/splice_ai/all_variants │ 71927088053 │ 66.99 GiB │ +4. │ default │ seqr │ GRCh37/SNV_INDEL/entries │ 39255880565 │ 36.56 GiB │ +5. │ default │ seqr │ GRCh38/SNV_INDEL/project_gt_stats │ 38191863243 │ 35.57 GiB │ +6. │ default │ seqr │ GRCh38/SNV_INDEL/reference_data/gnomad_genomes/all_variants │ 12827564551 │ 11.95 GiB │ + + +SELECT COUNT(*) +FROM `GRCh38/SNV_INDEL/entries` + +Query id: 51d2a78e-de1a-4b75-9131-1e9e1e3a2ecb + + ┌─────COUNT()─┐ +1. │ 68213850227 │ -- 68.21 billion + └─────────────┘ +``` + +- Viewing disk usage outside of ClickHouse: +``` +kubectl exec seqr-clickhouse-shard0-0 -c clickhouse -it -- bash -c 'cd /in-memory-dir; du -h' +``` + +``` +kubectl exec seqr-clickhouse-shard0-0 -c clickhouse -it -- bash -c 'cd /var/seqr/clickhouse-data; du -h' +``` diff --git a/loading_pipeline/docs/Diagrams.md b/loading_pipeline/docs/Diagrams.md new file mode 100644 index 0000000000..14c162759e --- /dev/null +++ b/loading_pipeline/docs/Diagrams.md @@ -0,0 +1,150 @@ +# Pipeline flow, as of 05/06/2026 + +``` + WriteImportedCallsetTask + (VCF → Hail Matrix Table) + | + v + WritePostprocessedCallsetTask + (split multi, deduplicate) + | + v + ValidateCallsetTask + (validation checks) + | + _______________|_______________ + | | + v v + WriteSexCheckTableTask WriteRelatednessCheckTableTask + | | + v v + WriteRelatednessCheckTsvTask + | + v + _____________________|_____________________ + | | + v v + WriteRemappedAndSubsettedCallsetTask WriteRemappedAndSubsettedCallsetTask + (Project 1) (Project N) + | | + |___________________________________________| + | + v + WriteMetadataForRunTask + | + v + WriteNewVariantsTableTask + | + v + UpdateVariantAnnotationsTableWithNewVariantsTask + (Variants with annotations) + | + ______________________+_______________________ + | | | + v v v + WriteNewEntries... WriteNewVariants... WriteNewVariantDetails... + ParquetTask ParquetTask ParquetTask + | | (optional) + | [also requires] | [or just] + | RemappedCallsets | WriteNewVariantsTableTask + | + |_______________________| + | + v + RunPipelineTask + (all parquets ready) + | + v + WriteSuccessFileTask + | + v + WriteClickhouseLoadSuccessFileTask + (load parquets → ClickHouse) +``` + +ClickHouse LSM-Tree + +``` +┌────────────────────────────────────────────────────────────┐ +│ ClickHouse LSM: MemTable → Parts → Merge │ +└────────────────────────────────────────────────────────────┘ + + WRITE PHASE: + ───────────── + + INSERT statements + │ + ▼ + ┌──────────────┐ + │ MemTable │ (In-memory buffer) + │ ~150 MB │ ◄─── Growing as writes arrive + └──────┬───────┘ + │ + (Threshold exceeded) + │ + ▼ + ┌──────────────┐ + │ Flush │ + │ to Disk │ + └──────┬───────┘ + │ + ▼ + ┌──────────────┐ + │ Part (L0) │ ◄─── New immutable part on disk + └──────────────┘ + + + DISK STATE (Multiple Parts): + ────────────────────────────── + + MemTable Disk Parts (sorted by creation) + ┌─────┐ + │ │ ┌──────────┐ + │ │ │ Part(L0) │ ◄─── Recently flushed (small) + │ │ └──────────┘ + │ │ ┌──────────┐ + │ │ │ Part(L0) │ + │ │ └──────────┘ + │ │ ┌──────────┐ + │ │ │ Part(L0) │ + │ │ └──────────┘ + │ │ ┌──────────┐ + │ │ │ Part(L1) │ ◄─── Older (larger) + │ │ └──────────┘ + │ │ ┌──────────┐ + │ │ │ Part(L2) │ + │ │ └──────────┘ + └─────┘ + + + BACKGROUND MERGE (Compaction): + ─────────────────────────────── + + When L0 has ~10 parts: + + ┌──────────┐ + │Part(L0) │ + └────┬─────┘ + │ + ┌────┴─────┬──────────┐ + │ │ │ + ┌───▼──┐ ┌────▼───┐ ┌───▼──┐ + │L0 #1 │ │ L0 #2 │ │ L0#3 │ ──┐ + └──────┘ └────────┘ └──────┘ │ + │ Read + Sort + ┌──────────────────────────────┐ │ + Compress + │ Compaction Process │◄┘ + │ │ + │ 1. Read all rows from L0s │ + │ 2. Merge by primary key │ + │ 3. Sort & compress │ + │ 4. Write to single Part(L1) │ + └───────────────┬──────────────┘ + │ + ▼ + ┌──────────────┐ + │ Part(L1) │ ◄─── One larger part + │ (merged) │ (old L0 parts deleted) + └──────────────┘ + +``` \ No newline at end of file diff --git a/loading_pipeline/docs/Historial_Context.md b/loading_pipeline/docs/Historial_Context.md new file mode 100644 index 0000000000..b21ae3e495 --- /dev/null +++ b/loading_pipeline/docs/Historial_Context.md @@ -0,0 +1,82 @@ +Notes on Loading Pipeline Orchestration + +## Decision to move off of Airflow (late 2024): + - Manual mapping of luigi tasks to Airflow tasks (w/ strings!) + - Cost ($400 a month) + - Small instance (2 cpu/2 gb ram) for schedular and actual compute + - Unbelieveable scaling issues? + - DAG built dynamically, OOMs. + - Parallelism in task execution. + - Maintainability issues + - Lack of shared code with open source repo. + - Airflow system complexity w/ helm. + - Composer "management" + versions. + - Manual environment variables and secrets, lack of cohesion with kubernetes. + - Composer was its own Kubernetes ecosystem! + - GCP integration. + - Hooks for replacing python API calls... (why????) + - Nasty bugs + https://github.com/broadinstitute/seqr/pull/3995/changes + https://github.com/broadinstitute/seqr/pull/4539/changes + https://github.com/broadinstitute/seqr/pull/4646/changes + - Testing difficulties + - Able to test DAG "compile", but not actual execution. + - System complexity (templating, XCom, retries, 'Context') in the way of lean unit and integration tests. + +## Evaluation of other DAG frameworks: + - Prefect/Dagster/Argo Workflows + - Seem to have similar issues as Airflow; complexity does not align with the straightforward needs of the pipeline execution. + +## Current Implementation +- API listens for requests from `seqr` application for asynchronous work. +- Worker with concurrency=1 polls for work. + - One task at a time; coarse-grained lock: + Hail cannot update variants in parallel. + Clickhouse cannot rebuild entire gt_stats in parallel. + - Retries managed within the worker and persisted on disk. + - Failures moved to deadletter queue after 5 retries. +- Loading pipeline runs "Luigi" via --local-scheduler locally or via Dataproc. + - Luigi manages task flow and nothing else. +- Output looks like (as of 05/26): +``` +gs://seqr-hail-search-data/v3.1/GRCh38/SNV_INDEL/runs/20260421-125644-303855/_CLICKHOUSE_LOAD_SUCCESS +gs://seqr-hail-search-data/v3.1/GRCh38/SNV_INDEL/runs/20260421-125644-303855/_SUCCESS +gs://seqr-hail-search-data/v3.1/GRCh38/SNV_INDEL/runs/20260421-125644-303855/metadata.json +gs://seqr-hail-search-data/v3.1/GRCh38/SNV_INDEL/runs/20260421-125644-303855/new_entries.parquet/ +gs://seqr-hail-search-data/v3.1/GRCh38/SNV_INDEL/runs/20260421-125644-303855/new_variant_details.parquet/ +gs://seqr-hail-search-data/v3.1/GRCh38/SNV_INDEL/runs/20260421-125644-303855/new_variants.ht/ +gs://seqr-hail-search-data/v3.1/GRCh38/SNV_INDEL/runs/20260421-125644-303855/new_variants.parquet/ +``` + +### Residues from previous iterations. +- Manual enumeration of consequence terms and SV/Mito types is no longer necessary. + - Was a performance enhancement for Hail backend that can be unrolled. +- `complete()` methods are likely overcomplicated. + - Each task verifies completeness by running this method and if it returns `True`, skips execution. + - Necessary for performance, but as the pipeline has started doing less it is less necessary. + - Historically been the source of many bugs. + - For example, re-running pipeline with a different pedigree... we'd cached the subsetted callset, failed to generate a new one etc. +- Globalizing and Deglobalizing Ids. + - We optimized the hail table structure to move sample ids into globals, this complicates the current logic and is likely unnecessary. + +## Thoughts for future: + - Remove Hail for non SNV_INDEL dataset types and callsets < 500 samples. + - Resolve the "Fatal Flaw", two separate representations of production variants, one in Hail and one in Clickhouse. + - If pipeline fails immediately after "UpdateVariantAnnotationsTableWithNewVariantsTask", next run will have + incorrect "new_variants.parquet". + - Lightweight replacement for Luigi "run()/complete()/output()/requires()" framework. + - Eliminate scheduler in favor or "tasks" table in seqr postgres. + - Running arbitrary docker images: + - Airflow was useful for this, w/ Kubernetes elasticity. + - Need to support external computational biology tools. + - Can we just re-write with agentic coding? + - Remove as much business logic from core pipeline as we can. + - For example, the Terra Data Repository sample fetching. + +## VEP (🗑️) Addendum: + - VEP runs only on new variants via a custom wrapper around Hail's command. + - Internally, HAIL exports a table to VCF and shell execs parallelized docker-VEP processes and then re-imports into a VEP schema. + - On Dataproc, one initialization action syncs VEP reference data to HDFS. + - For open source users, sync to local disk. + - VEP itself is a custom docker build, pushed as a one time operation to seqr's gcr repo. + - GRCh38 and GRCh37 use different schemas, though are both using VEP 110. diff --git a/loading_pipeline/lib/__init__.py b/loading_pipeline/lib/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/loading_pipeline/lib/annotations/__init__.py b/loading_pipeline/lib/annotations/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/loading_pipeline/lib/annotations/enums.py b/loading_pipeline/lib/annotations/enums.py new file mode 100644 index 0000000000..64202a8940 --- /dev/null +++ b/loading_pipeline/lib/annotations/enums.py @@ -0,0 +1,205 @@ +BIOTYPES = [ + 'IG_C_gene', + 'IG_D_gene', + 'IG_J_gene', + 'IG_LV_gene', + 'IG_V_gene', + 'TR_C_gene', + 'TR_J_gene', + 'TR_V_gene', + 'TR_D_gene', + 'IG_pseudogene', + 'IG_C_pseudogene', + 'IG_J_pseudogene', + 'IG_V_pseudogene', + 'TR_V_pseudogene', + 'TR_J_pseudogene', + 'Mt_rRNA', + 'Mt_tRNA', + 'miRNA', + 'misc_RNA', + 'rRNA', + 'scRNA', + 'snRNA', + 'snoRNA', + 'ribozyme', + 'sRNA', + 'scaRNA', + 'lncRNA', + 'Mt_tRNA_pseudogene', + 'tRNA_pseudogene', + 'snoRNA_pseudogene', + 'snRNA_pseudogene', + 'scRNA_pseudogene', + 'rRNA_pseudogene', + 'misc_RNA_pseudogene', + 'miRNA_pseudogene', + 'TEC', + 'nonsense_mediated_decay', + 'non_stop_decay', + 'retained_intron', + 'protein_coding', + 'protein_coding_LoF', + 'protein_coding_CDS_not_defined', + 'processed_transcript', + 'non_coding', + 'ambiguous_orf', + 'sense_intronic', + 'sense_overlapping', + 'antisense', + 'known_ncrna', + 'pseudogene', + 'processed_pseudogene', + 'polymorphic_pseudogene', + 'retrotransposed', + 'transcribed_processed_pseudogene', + 'transcribed_unprocessed_pseudogene', + 'transcribed_unitary_pseudogene', + 'translated_processed_pseudogene', + 'translated_unprocessed_pseudogene', + 'unitary_pseudogene', + 'unprocessed_pseudogene', + 'artifact', + 'lincRNA', + 'macro_lncRNA', + '3prime_overlapping_ncRNA', + 'disrupted_domain', + 'vault_RNA', + 'bidirectional_promoter_lncRNA', + '3prime_overlapping_ncrna', +] + +REGULATORY_BIOTYPES = [ + 'enhancer', + 'promoter', + 'CTCF_binding_site', + 'TF_binding_site', + 'open_chromatin_region', +] + +TRANSCRIPT_CONSEQUENCE_TERMS = [ + 'transcript_ablation', + 'splice_acceptor_variant', + 'splice_donor_variant', + 'stop_gained', + 'frameshift_variant', + 'stop_lost', + 'start_lost', + 'inframe_insertion', + 'inframe_deletion', + 'missense_variant', + 'protein_altering_variant', + 'splice_donor_5th_base_variant', + 'splice_region_variant', + 'splice_donor_region_variant', + 'splice_polypyrimidine_tract_variant', + 'incomplete_terminal_codon_variant', + 'start_retained_variant', + 'stop_retained_variant', + 'synonymous_variant', + 'coding_sequence_variant', + 'mature_miRNA_variant', + '5_prime_UTR_variant', + '3_prime_UTR_variant', + 'non_coding_transcript_exon_variant', + 'intron_variant', + 'NMD_transcript_variant', + 'non_coding_transcript_variant', + 'coding_transcript_variant', + 'upstream_gene_variant', + 'downstream_gene_variant', + 'intergenic_variant', + 'sequence_variant', +] + +MOTIF_CONSEQUENCE_TERMS = [ + 'TFBS_ablation', + 'TFBS_amplification', + 'TF_binding_site_variant', + 'TFBS_fusion', + 'TFBS_translocation', +] + +REGULATORY_CONSEQUENCE_TERMS = [ + 'regulatory_region_ablation', + 'regulatory_region_amplification', + 'regulatory_region_variant', + 'regulatory_region_fusion', +] + +FIVEUTR_CONSEQUENCES = [ + '5_prime_UTR_premature_start_codon_gain_variant', # uAUG_gained + '5_prime_UTR_premature_start_codon_loss_variant', # uAUG_lost + '5_prime_UTR_stop_codon_gain_variant', # uSTOP_gained + '5_prime_UTR_stop_codon_loss_variant', # uSTOP_lost + '5_prime_UTR_uORF_frameshift_variant', # uFrameshift +] + +LOF_FILTERS = [ + 'END_TRUNC', + 'INCOMPLETE_CDS', + 'EXON_INTRON_UNDEF', + 'SMALL_INTRON', + 'ANC_ALLELE', + 'NON_DONOR_DISRUPTING', + 'NON_ACCEPTOR_DISRUPTING', + 'RESCUE_DONOR', + 'RESCUE_ACCEPTOR', + 'GC_TO_GT_DONOR', + '5UTR_SPLICE', + '3UTR_SPLICE', +] + +MITOTIP_PATHOGENICITIES = [ + 'likely_pathogenic', + 'possibly_pathogenic', + 'possibly_benign', + 'likely_benign', +] + +SV_TYPES = [ + 'gCNV_DEL', + 'gCNV_DUP', + 'BND', + 'CPX', + 'CTX', + 'DEL', + 'DUP', + 'INS', + 'INV', + 'CNV', +] + +SV_TYPE_DETAILS = [ + 'INS_iDEL', + 'INVdel', + 'INVdup', + 'ME', + 'ME:ALU', + 'ME:LINE1', + 'ME:SVA', + 'dDUP', + 'dDUP_iDEL', + 'delINV', + 'delINVdel', + 'delINVdup', + 'dupINV', + 'dupINVdel', + 'dupINVdup', +] + +SV_CONSEQUENCE_RANKS = [ + 'LOF', + 'INTRAGENIC_EXON_DUP', + 'PARTIAL_EXON_DUP', + 'COPY_GAIN', + 'DUP_PARTIAL', + 'MSV_EXON_OVERLAP', + 'INV_SPAN', + 'UTR', + 'PROMOTER', + 'TSS_DUP', + 'BREAKEND_EXONIC', + 'INTRONIC', + 'NEAREST_TSS', +] diff --git a/loading_pipeline/lib/annotations/expression_helpers.py b/loading_pipeline/lib/annotations/expression_helpers.py new file mode 100644 index 0000000000..ab0b34c25f --- /dev/null +++ b/loading_pipeline/lib/annotations/expression_helpers.py @@ -0,0 +1,329 @@ +import hail as hl + +from loading_pipeline.lib.annotations.enums import TRANSCRIPT_CONSEQUENCE_TERMS + +TRANSCRIPT_CONSEQUENCE_TERM_RANK_LOOKUP = hl.dict( + hl.enumerate(TRANSCRIPT_CONSEQUENCE_TERMS, index_first=False), +) +HGVSC_CONSEQUENCES = hl.set( + ['splice_donor_variant', 'splice_acceptor_variant', 'splice_region_variant'], +) +OMIT_TRANSCRIPT_CONSEQUENCE_TERMS = [ + 'upstream_gene_variant', + 'downstream_gene_variant', +] +PROTEIN_LETTERS_1TO3 = hl.dict( + { + 'A': 'Ala', + 'C': 'Cys', + 'D': 'Asp', + 'E': 'Glu', + 'F': 'Phe', + 'G': 'Gly', + 'H': 'His', + 'I': 'Ile', + 'K': 'Lys', + 'L': 'Leu', + 'M': 'Met', + 'N': 'Asn', + 'P': 'Pro', + 'Q': 'Gln', + 'R': 'Arg', + 'S': 'Ser', + 'T': 'Thr', + 'V': 'Val', + 'W': 'Trp', + 'Y': 'Tyr', + 'X': 'Ter', + '*': 'Ter', + 'U': 'Sec', + }, +) + + +def _replace_chr_prefix(contig: str): + return contig.replace('^chr', '') + + +def _get_expr_for_contig(locus: hl.expr.LocusExpression) -> hl.expr.StringExpression: + """Normalized contig name""" + return _replace_chr_prefix(locus.contig) + + +def _get_expr_for_contig_number( + locus: hl.expr.LocusExpression, +) -> hl.expr.Int32Expression: + """Convert contig name to contig number""" + return hl.bind( + lambda contig: ( + hl.case() + .when(contig == 'X', 23) + .when(contig == 'Y', 24) + .when(contig[0] == 'M', 25) + .default(hl.int(contig)) + ), + _get_expr_for_contig(locus), + ) + + +def _get_expr_for_formatted_hgvs(csq): + return hl.cond( + hl.is_missing(csq.hgvsp) | HGVSC_CONSEQUENCES.contains(csq.major_consequence), + csq.hgvsc.split(':')[-1], + hl.cond( + csq.hgvsp.contains('=') | csq.hgvsp.contains('%3D'), + hl.bind( + lambda protein_letters: 'p.' + + protein_letters + + hl.str(csq.protein_start) + + protein_letters, + hl.delimit( + csq.amino_acids.split('').map( + lambda pl: PROTEIN_LETTERS_1TO3.get(pl), + ), + '', + ), + ), + csq.hgvsp.split(':')[-1], + ), + ) + + +def get_expr_for_variant_id(table, max_length=None): + """Expression for computing ---. Assumes alleles were split. + + Args: + max_length: (optional) length at which to truncate the --- string + + Return: + string: "---" + """ + contig = _get_expr_for_contig(table.locus) + variant_id = ( + contig + + '-' + + hl.str(table.locus.position) + + '-' + + table.alleles[0] + + '-' + + table.alleles[1] + ) + if max_length is not None: + return variant_id[0:max_length] + return variant_id + + +def get_expr_for_xpos(locus: hl.expr.LocusExpression) -> hl.expr.Int64Expression: + """Genomic position represented as a single number = contig_number * 10**9 + position. + This represents chrom:pos more compactly and allows for easier sorting. + """ + contig_number = _get_expr_for_contig_number(locus) + return hl.int64(contig_number) * 1_000_000_000 + locus.position + + +def get_expr_for_vep_sorted_transcript_consequences_array( + vep_root, + include_coding_annotations=True, + omit_consequences=OMIT_TRANSCRIPT_CONSEQUENCE_TERMS, +): + """Sort transcripts by 3 properties: + + 1. coding > non-coding + 2. transcript consequence severity + 3. canonical > non-canonical + + so that the 1st array entry will be for the coding, most-severe, canonical transcript (assuming + one exists). + + Also, for each transcript in the array, computes these additional fields: + domains: converts Array[Struct] to string of comma-separated domain names + hgvs: set to hgvsp is it exists, or else hgvsc. formats hgvsp for synonymous variants. + major_consequence: set to most severe consequence for that transcript ( + VEP sometimes provides multiple consequences for a single transcript) + major_consequence_rank: major_consequence rank based on VEP SO ontology (most severe = 1) + (see http://www.ensembl.org/info/genome/variation/predicted_data.html) + category: set to one of: "lof", "missense", "synonymous", "other" based on the value of major_consequence. + + Args: + vep_root (StructExpression): root path of the VEP struct in the MT + include_coding_annotations (bool): if True, fields relevant to protein-coding variants will be included + """ + + selected_annotations = [ + 'biotype', + 'canonical', + 'cdna_start', + 'cdna_end', + 'codons', + 'exon', + 'gene_id', + 'gene_symbol', + 'hgvsc', + 'hgvsp', + 'intron', + 'transcript_id', + ] + + if include_coding_annotations: + selected_annotations.extend( + [ + 'amino_acids', + 'lof', + 'lof_filter', + 'lof_flags', + 'lof_info', + 'protein_id', + 'protein_start', + ], + ) + + omit_consequence_terms = ( + hl.set(omit_consequences) if omit_consequences else hl.empty_set(hl.tstr) + ) + + result = hl.sorted( + vep_root.transcript_consequences.map( + lambda c: c.select( + *selected_annotations, + consequence_terms=c.consequence_terms.filter( + lambda t: ~omit_consequence_terms.contains(t), + ), + domains=c.domains.map(lambda domain: domain.db + ':' + domain.name), + major_consequence=hl.cond( + c.consequence_terms.size() > 0, + hl.sorted( + c.consequence_terms, + key=lambda t: TRANSCRIPT_CONSEQUENCE_TERM_RANK_LOOKUP.get(t), + )[0], + hl.null(hl.tstr), + ), + ), + ) + .filter(lambda c: c.consequence_terms.size() > 0) + .map( + lambda c: c.annotate( + category=( + hl.case() + .when( + TRANSCRIPT_CONSEQUENCE_TERM_RANK_LOOKUP.get(c.major_consequence) + <= TRANSCRIPT_CONSEQUENCE_TERM_RANK_LOOKUP.get( + 'frameshift_variant', + ), + 'lof', + ) + .when( + TRANSCRIPT_CONSEQUENCE_TERM_RANK_LOOKUP.get(c.major_consequence) + <= TRANSCRIPT_CONSEQUENCE_TERM_RANK_LOOKUP.get( + 'missense_variant', + ), + 'missense', + ) + .when( + TRANSCRIPT_CONSEQUENCE_TERM_RANK_LOOKUP.get(c.major_consequence) + <= TRANSCRIPT_CONSEQUENCE_TERM_RANK_LOOKUP.get( + 'synonymous_variant', + ), + 'synonymous', + ) + .default('other') + ), + hgvs=_get_expr_for_formatted_hgvs(c), + major_consequence_rank=TRANSCRIPT_CONSEQUENCE_TERM_RANK_LOOKUP.get( + c.major_consequence, + ), + ), + ), + lambda c: ( + hl.bind( + lambda is_coding, is_most_severe, is_canonical: ( + hl.cond( + is_coding, + hl.cond( + is_most_severe, + hl.cond(is_canonical, 1, 2), + hl.cond(is_canonical, 3, 4), + ), + hl.cond( + is_most_severe, + hl.cond(is_canonical, 5, 6), + hl.cond(is_canonical, 7, 8), + ), + ) + ), + hl.or_else(c.biotype, '') == 'protein_coding', + hl.set(c.consequence_terms).contains(vep_root.most_severe_consequence), + hl.or_else(c.canonical, 0) == 1, + ) + ), + ) + + if not include_coding_annotations: + # for non-coding variants, drop fields here that are hard to exclude in the above code + result = result.map(lambda c: c.drop('domains', 'hgvsp')) + + return hl.zip_with_index(result).map( + lambda csq_with_index: csq_with_index[1].annotate( + transcript_rank=csq_with_index[0], + ), + ) + + +def get_expr_for_worst_transcript_consequence_annotations_struct( + vep_sorted_transcript_consequences_root, + include_coding_annotations=True, +): + """Retrieves the top-ranked transcript annotation based on the ranking computed by + get_expr_for_vep_sorted_transcript_consequences_array(..) + + Args: + vep_sorted_transcript_consequences_root (ArrayExpression): + include_coding_annotations (bool): + """ + + transcript_consequences = { + 'biotype': hl.tstr, + 'canonical': hl.tint, + 'category': hl.tstr, + 'cdna_start': hl.tint, + 'cdna_end': hl.tint, + 'codons': hl.tstr, + 'gene_id': hl.tstr, + 'gene_symbol': hl.tstr, + 'hgvs': hl.tstr, + 'hgvsc': hl.tstr, + 'major_consequence': hl.tstr, + 'major_consequence_rank': hl.tint, + 'transcript_id': hl.tstr, + } + + if include_coding_annotations: + transcript_consequences.update( + { + 'amino_acids': hl.tstr, + 'domains': hl.tstr, + 'hgvsp': hl.tstr, + 'lof': hl.tstr, + 'lof_flags': hl.tstr, + 'lof_filter': hl.tstr, + 'lof_info': hl.tstr, + 'protein_id': hl.tstr, + }, + ) + + return hl.cond( + vep_sorted_transcript_consequences_root.size() == 0, + hl.struct( + **{ + field: hl.null(field_type) + for field, field_type in transcript_consequences.items() + }, + ), + hl.bind( + lambda worst_transcript_consequence: ( + worst_transcript_consequence.annotate( + domains=hl.delimit(hl.set(worst_transcript_consequence.domains)), + ).select(*transcript_consequences.keys()) + ), + vep_sorted_transcript_consequences_root[0], + ), + ) diff --git a/loading_pipeline/lib/annotations/fields.py b/loading_pipeline/lib/annotations/fields.py new file mode 100644 index 0000000000..b2eab5796a --- /dev/null +++ b/loading_pipeline/lib/annotations/fields.py @@ -0,0 +1,12 @@ +from collections.abc import Callable +from typing import Any + +import hail as hl + + +def get_fields( + t: hl.Table | hl.MatrixTable, + fns: list[Callable[..., hl.Expression]], + **kwargs: Any, +) -> dict[str, hl.Expression]: + return {fn.__name__: fn(t, **kwargs) for fn in fns} diff --git a/loading_pipeline/lib/annotations/fields_test.py b/loading_pipeline/lib/annotations/fields_test.py new file mode 100644 index 0000000000..fc5f179749 --- /dev/null +++ b/loading_pipeline/lib/annotations/fields_test.py @@ -0,0 +1,118 @@ +from unittest.mock import Mock, patch + +import hail as hl + +from loading_pipeline.lib.annotations.fields import get_fields +from loading_pipeline.lib.core import ( + DatasetType, + ReferenceGenome, +) +from loading_pipeline.lib.misc.vep import run_vep +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase +from loading_pipeline.var.test.vep.mock_vep_data import ( + MOCK_37_VEP_DATA, + MOCK_38_VEP_DATA, +) + + +class FieldsTest(MockedDatarootTestCase): + def setUp(self) -> None: + super().setUp() + + @patch('loading_pipeline.lib.misc.vep.hl.vep') + def test_get_formatting_fields(self, mock_vep: Mock) -> None: + for reference_genome, ht, expected_fields in [ + ( + ReferenceGenome.GRCh38, + hl.Table.parallelize( + [ + { + 'locus': hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + 'alleles': ['A', 'C'], + 'rsid': 'abcd', + }, + ], + hl.tstruct( + locus=hl.tlocus('GRCh38'), + alleles=hl.tarray(hl.tstr), + rsid=hl.tstr, + ), + key=['locus', 'alleles'], + ), + [ + 'check_ref', + 'rg37_locus', + 'rsid', + 'sorted_motif_feature_consequences', + 'sorted_regulatory_feature_consequences', + 'sorted_transcript_consequences', + 'variant_id', + 'xpos', + ], + ), + ( + ReferenceGenome.GRCh37, + hl.Table.parallelize( + [ + { + 'locus': hl.Locus( + contig='1', + position=1, + reference_genome='GRCh37', + ), + 'alleles': ['A', 'C'], + 'rsid': 'abcd', + }, + ], + hl.tstruct( + locus=hl.tlocus('GRCh37'), + alleles=hl.tarray(hl.tstr), + rsid=hl.tstr, + ), + key=['locus', 'alleles'], + ), + [ + 'rg38_locus', + 'rsid', + 'sorted_transcript_consequences', + 'variant_id', + 'xpos', + ], + ), + ]: + mock_vep.return_value = ht.annotate( + vep=MOCK_37_VEP_DATA + if reference_genome == ReferenceGenome.GRCh37 + else MOCK_38_VEP_DATA, + ) + ht = run_vep( # noqa: PLW2901 + ht, + DatasetType.SNV_INDEL, + reference_genome, + ) + self.assertCountEqual( + list( + get_fields( + ht, + DatasetType.SNV_INDEL.formatting_annotation_fns( + reference_genome, + ), + **( + { + 'gencode_ensembl_to_refseq_id_mapping': hl.dict( + {'a': 'b'}, + ), + } + if reference_genome == ReferenceGenome.GRCh38 + else {} + ), + dataset_type=DatasetType.SNV_INDEL, + reference_genome=reference_genome, + ).keys(), + ), + expected_fields, + ) diff --git a/loading_pipeline/lib/annotations/gcnv.py b/loading_pipeline/lib/annotations/gcnv.py new file mode 100644 index 0000000000..e9785419ed --- /dev/null +++ b/loading_pipeline/lib/annotations/gcnv.py @@ -0,0 +1,172 @@ +from typing import Any + +import hail as hl + +from loading_pipeline.lib.annotations import expression_helpers, liftover +from loading_pipeline.lib.annotations.enums import SV_CONSEQUENCE_RANKS, SV_TYPES +from loading_pipeline.lib.core.definitions import ReferenceGenome +from loading_pipeline.lib.misc.gcnv import parse_gcnv_genes + +SV_CONSEQUENCE_RANKS_LOOKUP = hl.dict( + hl.enumerate(SV_CONSEQUENCE_RANKS, index_first=False), +) +SV_TYPES_LOOKUP = hl.dict(hl.enumerate(SV_TYPES, index_first=False)) + + +def _start_and_end_equal(mt: hl.MatrixTable) -> hl.BooleanExpression: + return (mt.sample_start == mt.start) & (mt.sample_end == mt.end) + + +def CN(mt: hl.MatrixTable, **_: Any) -> hl.Expression: # noqa: N802 + return mt.CN + + +def concordance( + mt: hl.MatrixTable, + is_new_gcnv_joint_call: bool, + **_: Any, +) -> hl.Expression: + if is_new_gcnv_joint_call: + return hl.or_missing( + hl.is_defined(mt.GT), + hl.struct( + new_call=mt.no_ovl, + prev_call=hl.len(mt.identical_ovl) > 0, + prev_overlap=hl.len(mt.any_ovl) > 0, + ), + ) + return hl.or_missing( + hl.is_defined(mt.GT), + hl.struct( + new_call=False, + prev_call=~mt.is_latest, + prev_overlap=False, + ), + ) + + +def defragged(mt: hl.MatrixTable, **_: Any) -> hl.Expression: + return mt.defragmented + + +def end_locus( + ht: hl.Table, + reference_genome: ReferenceGenome, + **_: Any, +) -> hl.LocusExpression: + return hl.locus(ht.chr, ht.end, reference_genome.value) + + +def gt_stats(ht: hl.Table, callset_ht: hl.Table, **_: Any) -> hl.Expression: + return hl.struct( + AF=hl.float32(callset_ht[ht.variant_id].sf), + AC=callset_ht[ht.variant_id].sc, + AN=hl.int32(callset_ht[ht.variant_id].sc / callset_ht[ht.variant_id].sf), + Hom=hl.missing(hl.tint32), + Het=hl.missing(hl.tint32), + ) + + +def GT(mt: hl.MatrixTable, **_: Any) -> hl.Expression: # noqa: N802 + return hl.if_else( + (mt.CN == 0) | (mt.CN > 3), # noqa: PLR2004 + hl.Call([1, 1], phased=False), + hl.Call([0, 1], phased=False), + ) + + +def num_exon(ht: hl.Table, **_: Any) -> hl.Expression: + return ht.num_exon + + +def QS(mt: hl.MatrixTable, **_: Any) -> hl.Expression: # noqa: N802 + return mt.QS + + +def rg37_locus( + ht: hl.Table, + **_: Any, +) -> hl.Expression | None: + liftover.add_rg38_liftover() + return hl.liftover( + start_locus(ht, ReferenceGenome.GRCh38), + ReferenceGenome.GRCh37.value, + ) + + +def rg37_locus_end( + ht: hl.Table, + **_: Any, +) -> hl.Expression | None: + liftover.add_rg38_liftover() + return hl.liftover( + end_locus(ht, ReferenceGenome.GRCh38), + ReferenceGenome.GRCh37.value, + ) + + +def sample_end(mt: hl.MatrixTable, **_: Any) -> hl.Expression: + return hl.or_missing( + ~_start_and_end_equal(mt), + mt.sample_end, + ) + + +def sample_gene_ids(mt: hl.MatrixTable, **_: Any) -> hl.Expression: + parsed_genes = parse_gcnv_genes(mt.genes_any_overlap_Ensemble_ID) + return hl.or_missing(parsed_genes != mt.gene_ids, parsed_genes) + + +def sample_start(mt: hl.MatrixTable, **_: Any) -> hl.Expression: + return hl.or_missing( + ~_start_and_end_equal(mt), + mt.sample_start, + ) + + +def sample_num_exon(mt: hl.MatrixTable, **_: Any) -> hl.Expression: + return hl.or_missing( + mt.genes_any_overlap_totalExons != mt.num_exon, + mt.genes_any_overlap_totalExons, + ) + + +def sorted_gene_consequences( + ht: hl.Table, + **_: Any, +) -> hl.Expression: + return hl.array( + ht.gene_ids.map( + lambda gene: hl.Struct( + gene_id=gene, + major_consequence_id=hl.if_else( + ht.cg_genes.contains(gene), + SV_CONSEQUENCE_RANKS_LOOKUP['COPY_GAIN'], + hl.or_missing( + ht.lof_genes.contains(gene), + SV_CONSEQUENCE_RANKS_LOOKUP['LOF'], + ), + ), + ), + ), + ) + + +def start_locus( + ht: hl.Table, + reference_genome: ReferenceGenome, + **_: Any, +) -> hl.LocusExpression: + return hl.locus(ht.chr, ht.start, reference_genome.value) + + +def strvctvre(ht: hl.Table, **_: Any) -> hl.Expression: + return hl.struct(score=hl.parse_float32(ht.strvctvre_score)) + + +def sv_type_id(ht: hl.Table, **_: Any) -> hl.Expression: + return SV_TYPES_LOOKUP[ht.svtype] + + +def xpos(ht: hl.Table, reference_genome: ReferenceGenome, **_: Any) -> hl.Expression: + return expression_helpers.get_expr_for_xpos(start_locus(ht, reference_genome)) diff --git a/loading_pipeline/lib/annotations/liftover.py b/loading_pipeline/lib/annotations/liftover.py new file mode 100644 index 0000000000..41a1085055 --- /dev/null +++ b/loading_pipeline/lib/annotations/liftover.py @@ -0,0 +1,30 @@ +import hail as hl + +from loading_pipeline.lib.core.constants import ( + GRCH37_TO_GRCH38_LIFTOVER_REF_PATH, + GRCH38_TO_GRCH37_LIFTOVER_REF_PATH, +) +from loading_pipeline.lib.core.definitions import ReferenceGenome + + +def add_rg38_liftover() -> None: + rg37 = hl.get_reference(ReferenceGenome.GRCh37.value) + rg38 = hl.get_reference(ReferenceGenome.GRCh38.value) + if not rg38.has_liftover(rg37): + rg38.add_liftover(GRCH38_TO_GRCH37_LIFTOVER_REF_PATH, rg37) + + +def add_rg37_liftover() -> None: + rg37 = hl.get_reference(ReferenceGenome.GRCh37.value) + rg38 = hl.get_reference(ReferenceGenome.GRCh38.value) + if not rg37.has_liftover(rg38): + rg37.add_liftover(GRCH37_TO_GRCH38_LIFTOVER_REF_PATH, rg38) + + +def remove_liftover(): + rg37 = hl.get_reference(ReferenceGenome.GRCh37.value) + rg38 = hl.get_reference(ReferenceGenome.GRCh38.value) + if rg37.has_liftover(rg38): + rg37.remove_liftover(rg38) + if rg38.has_liftover(rg37): + rg38.remove_liftover(rg37) diff --git a/loading_pipeline/lib/annotations/misc.py b/loading_pipeline/lib/annotations/misc.py new file mode 100644 index 0000000000..00f5f68eb4 --- /dev/null +++ b/loading_pipeline/lib/annotations/misc.py @@ -0,0 +1,98 @@ +import hail as hl + +from loading_pipeline.lib.annotations.enums import ( + BIOTYPES, + FIVEUTR_CONSEQUENCES, + LOF_FILTERS, + MITOTIP_PATHOGENICITIES, + MOTIF_CONSEQUENCE_TERMS, + REGULATORY_BIOTYPES, + REGULATORY_CONSEQUENCE_TERMS, + SV_CONSEQUENCE_RANKS, + SV_TYPE_DETAILS, + SV_TYPES, + TRANSCRIPT_CONSEQUENCE_TERMS, +) +from loading_pipeline.lib.core import DatasetType +from loading_pipeline.lib.core.definitions import ReferenceGenome + + +def annotate_formatting_annotation_enum_globals( + ht: hl.Table, + reference_genome: ReferenceGenome, + dataset_type: DatasetType, +) -> hl.Table: + ht = ht.select_globals( + enums=hl.Struct(), + ) + formatting_annotation_names = { + fa.__name__ for fa in dataset_type.formatting_annotation_fns(reference_genome) + } + if 'sorted_motif_feature_consequences' in formatting_annotation_names: + ht = ht.annotate_globals( + enums=ht.enums.annotate( + sorted_motif_feature_consequences=hl.Struct( + consequence_term=MOTIF_CONSEQUENCE_TERMS, + ), + ), + ) + if 'sorted_regulatory_feature_consequences' in formatting_annotation_names: + ht = ht.annotate_globals( + enums=ht.enums.annotate( + sorted_regulatory_feature_consequences=hl.Struct( + biotype=REGULATORY_BIOTYPES, + consequence_term=REGULATORY_CONSEQUENCE_TERMS, + ), + ), + ) + if 'sorted_transcript_consequences' in formatting_annotation_names: + ht = ht.annotate_globals( + enums=ht.enums.annotate( + sorted_transcript_consequences=hl.Struct( + biotype=BIOTYPES, + consequence_term=TRANSCRIPT_CONSEQUENCE_TERMS, + **( + { + 'loftee': hl.Struct( + lof_filter=LOF_FILTERS, + ), + 'utrannotator': hl.Struct( + fiveutr_consequence=FIVEUTR_CONSEQUENCES, + ), + } + if reference_genome == ReferenceGenome.GRCh38 + and dataset_type == DatasetType.SNV_INDEL + else { + 'lof_filter': LOF_FILTERS, + } + ), + ), + ), + ) + if 'mitotip' in formatting_annotation_names: + ht = ht.annotate_globals( + enums=ht.enums.annotate( + mitotip=hl.Struct( + trna_prediction=MITOTIP_PATHOGENICITIES, + ), + ), + ) + if 'sv_type_id' in formatting_annotation_names: + ht = ht.annotate_globals( + enums=ht.enums.annotate( + sv_type=SV_TYPES, + ), + ) + if 'sv_type_detail_id' in formatting_annotation_names: + ht = ht.annotate_globals( + enums=ht.enums.annotate(sv_type_detail=SV_TYPE_DETAILS), + ) + if 'sorted_gene_consequences' in formatting_annotation_names: + ht = ht.annotate_globals( + enums=ht.enums.annotate( + sorted_gene_consequences=hl.Struct( + major_consequence=SV_CONSEQUENCE_RANKS, + ), + ), + ) + return ht diff --git a/loading_pipeline/lib/annotations/mito.py b/loading_pipeline/lib/annotations/mito.py new file mode 100644 index 0000000000..85b65ce75c --- /dev/null +++ b/loading_pipeline/lib/annotations/mito.py @@ -0,0 +1,61 @@ +from typing import Any + +import hail as hl + +from loading_pipeline.lib.annotations.enums import MITOTIP_PATHOGENICITIES + +MITOTIP_PATHOGENICITIES_LOOKUP = hl.dict( + hl.enumerate(MITOTIP_PATHOGENICITIES, index_first=False).extend( + # NB: adding missing values here allows us to + # hard fail if a mapped key is present and has an unexpected value + # but propagate missing values. + [(hl.missing(hl.tstr), hl.missing(hl.tint32))], + ), +) + + +def common_low_heteroplasmy(ht: hl.Table, **_: Any) -> hl.Expression: + return hl.bool(ht.common_low_heteroplasmy) + + +def contamination(mt: hl.MatrixTable, **_: Any) -> hl.Expression: + return ( + hl.parse_float64(mt.contamination) + if mt.contamination.dtype == hl.tstr + else mt.contamination + ) + + +def DP(mt: hl.MatrixTable, **_: Any) -> hl.Expression: # noqa: N802 + is_called = hl.is_defined(mt.GT) + return hl.cond(is_called, hl.int32(hl.min(mt.DP, 32000)), hl.missing(hl.tint32)) + + +def GQ(mt: hl.MatrixTable, **_: Any) -> hl.Expression: # noqa: N802 + is_called = hl.is_defined(mt.GT) + return hl.if_else(is_called, hl.int32(mt.MQ), 0) + + +def haplogroup(ht: hl.Table, **_: Any) -> hl.Expression: + return hl.Struct( + is_defining=ht.hap_defining_variant, + ) + + +def HL(mt: hl.MatrixTable, **_: Any) -> hl.Expression: # noqa: N802 + is_called = hl.is_defined(mt.GT) + return hl.if_else(is_called, mt.HL, 0) + + +def mito_cn(mt: hl.MatrixTable, **_: Any) -> hl.Expression: + return hl.int32(mt.mito_cn) + + +def mitotip(ht: hl.Table, **_: Any) -> hl.Expression: + return hl.Struct( + trna_prediction_id=MITOTIP_PATHOGENICITIES_LOOKUP[ht.mitotip_trna_prediction], + ) + + +def rsid(ht: hl.Table, **_: Any) -> hl.Expression: + return ht.rsid.find(lambda x: hl.is_defined(x)) diff --git a/loading_pipeline/lib/annotations/shared.py b/loading_pipeline/lib/annotations/shared.py new file mode 100644 index 0000000000..abeaaac2e5 --- /dev/null +++ b/loading_pipeline/lib/annotations/shared.py @@ -0,0 +1,51 @@ +from typing import Any + +import hail as hl + +from loading_pipeline.lib.annotations import expression_helpers, liftover +from loading_pipeline.lib.annotations.vep import ( + transcript_consequences_sort, + vep_85_transcript_consequences_select, +) +from loading_pipeline.lib.core.definitions import ReferenceGenome + + +def GT(mt: hl.MatrixTable, **_: Any) -> hl.Expression: # noqa: N802 + return mt.GT + + +def GQ(mt: hl.MatrixTable, **_: Any) -> hl.Expression: # noqa: N802 + is_called = hl.is_defined(mt.GT) + return hl.if_else(is_called, mt.GQ, 0) + + +def rsid(mt: hl.MatrixTable, **_: Any) -> hl.Expression: + return mt.rsid + + +def rg37_locus( + ht: hl.Table, + **_: Any, +) -> hl.Expression | None: + liftover.add_rg38_liftover() + return hl.liftover(ht.locus, ReferenceGenome.GRCh37.value) + + +def xpos(ht: hl.Table, **_: Any) -> hl.Expression: + return expression_helpers.get_expr_for_xpos(ht.locus) + + +def variant_id(ht: hl.Table, **_: Any) -> hl.Expression: + return expression_helpers.get_expr_for_variant_id(ht) + + +def sorted_transcript_consequences( + ht: hl.Table, + **_: Any, +) -> hl.Expression: + return hl.sorted( + ht.vep.transcript_consequences.map( + vep_85_transcript_consequences_select, + ).filter(lambda c: c.consequence_term_ids.size() > 0), + transcript_consequences_sort(ht), + ) diff --git a/loading_pipeline/lib/annotations/snv_indel.py b/loading_pipeline/lib/annotations/snv_indel.py new file mode 100644 index 0000000000..c4fe8cda2a --- /dev/null +++ b/loading_pipeline/lib/annotations/snv_indel.py @@ -0,0 +1,118 @@ +# ruff: noqa: N806 +from typing import Any + +import hail as hl + +from loading_pipeline.lib.annotations import liftover +from loading_pipeline.lib.annotations.enums import ( + MOTIF_CONSEQUENCE_TERMS, + REGULATORY_BIOTYPES, + REGULATORY_CONSEQUENCE_TERMS, +) +from loading_pipeline.lib.annotations.vep import ( + transcript_consequences_sort, + vep_110_transcript_consequences_select, +) +from loading_pipeline.lib.core.definitions import ReferenceGenome + +MOTIF_CONSEQUENCE_TERMS_LOOKUP = hl.dict( + hl.enumerate(MOTIF_CONSEQUENCE_TERMS, index_first=False), +) +REGULATORY_BIOTYPE_LOOKUP = hl.dict( + hl.enumerate(REGULATORY_BIOTYPES, index_first=False), +) +REGULATORY_CONSEQUENCE_TERMS_LOOKUP = hl.dict( + hl.enumerate(REGULATORY_CONSEQUENCE_TERMS, index_first=False), +) + + +def AB(mt: hl.MatrixTable, **_: Any) -> hl.Expression: # noqa: N802 + is_called = hl.is_defined(mt.GT) + return hl.bind( + lambda total: hl.if_else( + (is_called) & (total != 0) & (hl.len(mt.AD) > 1), + hl.float32(mt.AD[1] / total), + hl.missing(hl.tfloat32), + ), + hl.sum(mt.AD), + ) + + +def DP(mt: hl.MatrixTable, **_: Any) -> hl.Expression: # noqa: N802 + is_called = hl.is_defined(mt.GT) + return hl.if_else( + is_called & hl.is_defined(mt.AD), + hl.int32(hl.min(hl.sum(mt.AD), 32000)), + hl.missing(hl.tint32), + ) + + +def rg38_locus( + ht: hl.Table, + **_: Any, +) -> hl.Expression | None: + liftover.add_rg37_liftover() + return hl.liftover(ht.locus, ReferenceGenome.GRCh38.value) + + +def check_ref(ht: hl.Table, **_: Any) -> hl.BooleanExpression: + return hl.is_defined(ht.vep.check_ref) + + +def sorted_motif_feature_consequences( + ht: hl.Table, + **_: Any, +) -> hl.Expression: + # NB: hl.min() doesn't work correctly in the "sorted" key expression, so we have an additional + # is_defined check, even though the expression should work on missing on its own. + # hail bug report incoming. + return hl.or_missing( + hl.is_defined(ht.vep.motif_feature_consequences), + hl.sorted( + ht.vep.motif_feature_consequences.map( + lambda c: c.select( + consequence_term_ids=c.consequence_terms.map( + lambda t: MOTIF_CONSEQUENCE_TERMS_LOOKUP[t], + ), + motif_feature_id=c.motif_feature_id, + ), + ).filter(lambda c: c.consequence_term_ids.size() > 0), + lambda c: hl.min(c.consequence_term_ids), + ), + ) + + +def sorted_regulatory_feature_consequences( + ht: hl.Table, + **_: Any, +) -> hl.Expression: + return hl.or_missing( + hl.is_defined(ht.vep.regulatory_feature_consequences), + hl.sorted( + ht.vep.regulatory_feature_consequences.map( + lambda c: c.select( + biotype_id=REGULATORY_BIOTYPE_LOOKUP[c.biotype], + consequence_term_ids=c.consequence_terms.map( + lambda t: REGULATORY_CONSEQUENCE_TERMS_LOOKUP[t], + ), + regulatory_feature_id=c.regulatory_feature_id, + ), + ).filter(lambda c: c.consequence_term_ids.size() > 0), + lambda c: hl.min(c.consequence_term_ids), + ), + ) + + +def sorted_transcript_consequences( + ht: hl.Table, + gencode_ensembl_to_refseq_id_mapping: hl.tdict(hl.tstr, hl.tstr), + **_: Any, +) -> hl.Expression: + return hl.sorted( + ht.vep.transcript_consequences.map( + vep_110_transcript_consequences_select( + gencode_ensembl_to_refseq_id_mapping, + ), + ).filter(lambda c: c.consequence_term_ids.size() > 0), + transcript_consequences_sort(ht), + ) diff --git a/loading_pipeline/lib/annotations/snv_indel_test.py b/loading_pipeline/lib/annotations/snv_indel_test.py new file mode 100644 index 0000000000..0de91786b0 --- /dev/null +++ b/loading_pipeline/lib/annotations/snv_indel_test.py @@ -0,0 +1,303 @@ +import unittest +from unittest.mock import Mock, patch + +import hail as hl + +from loading_pipeline.lib.annotations import shared, snv_indel +from loading_pipeline.lib.core import DatasetType, ReferenceGenome +from loading_pipeline.lib.misc.vep import run_vep +from loading_pipeline.var.test.vep.mock_vep_data import ( + MOCK_37_VEP_DATA, + MOCK_38_VEP_DATA, +) + + +class SNVTest(unittest.TestCase): + @patch('loading_pipeline.lib.misc.vep.hl.vep') + def test_sorted_transcript_consequences_37( + self, + mock_vep: Mock, + ) -> None: + ht = hl.Table.parallelize( + [ + { + 'locus': hl.Locus( + contig='1', + position=871269, + reference_genome=ReferenceGenome.GRCh37.value, + ), + 'alleles': ['A', 'C'], + }, + ], + hl.tstruct( + locus=hl.tlocus(ReferenceGenome.GRCh37.value), + alleles=hl.tarray(hl.tstr), + ), + key=['locus', 'alleles'], + ) + mock_vep.return_value = ht.annotate(vep=MOCK_37_VEP_DATA) + ht = run_vep( + ht, + DatasetType.SNV_INDEL, + ReferenceGenome.GRCh37, + ) + ht = ht.select( + sorted_transcript_consequences=shared.sorted_transcript_consequences( + ht, + ), + ) + self.assertCountEqual( + ht.sorted_transcript_consequences.collect(), + [ + [ + hl.Struct( + amino_acids='S/L', + canonical=1, + codons='tCg/tTg', + gene_id='ENSG00000188976', + hgvsc='ENST00000327044.6:c.1667C>T', + hgvsp='ENSP00000317992.6:p.Ser556Leu', + transcript_id='ENST00000327044', + biotype_id=39, + consequence_term_ids=[9], + is_lof_nagnag=None, + lof_filter_ids=[0, 1], + ), + hl.Struct( + amino_acids=None, + canonical=None, + codons=None, + gene_id='ENSG00000188976', + hgvsc='ENST00000477976.1:n.3114C>T', + hgvsp=None, + transcript_id='ENST00000477976', + biotype_id=38, + consequence_term_ids=[23, 26], + is_lof_nagnag=None, + lof_filter_ids=None, + ), + hl.Struct( + amino_acids=None, + canonical=None, + codons=None, + gene_id='ENSG00000188976', + hgvsc='ENST00000483767.1:n.523C>T', + hgvsp=None, + transcript_id='ENST00000483767', + biotype_id=38, + consequence_term_ids=[23, 26], + is_lof_nagnag=None, + lof_filter_ids=None, + ), + ], + ], + ) + + @patch('loading_pipeline.lib.misc.vep.hl.vep') + def test_sorted_transcript_consequences_38( + self, + mock_vep: Mock, + ) -> None: + ht = hl.Table.parallelize( + [ + { + 'locus': hl.Locus( + contig='chr1', + position=871269, + reference_genome=ReferenceGenome.GRCh38.value, + ), + 'alleles': ['A', 'C'], + }, + ], + hl.tstruct( + locus=hl.tlocus(ReferenceGenome.GRCh38.value), + alleles=hl.tarray(hl.tstr), + ), + key=['locus', 'alleles'], + ) + mock_vep.return_value = ht.annotate(vep=MOCK_38_VEP_DATA) + ht = run_vep( + ht, + DatasetType.SNV_INDEL, + ReferenceGenome.GRCh38, + ) + ht = ht.select( + sorted_transcript_consequences=snv_indel.sorted_transcript_consequences( + ht, + hl.dict( + {'ENST00000327044': 'NM_015658.4', 'ENST00000477976': 'refseq1'}, + ), + ), + ) + self.assertCountEqual( + ht.sorted_transcript_consequences.collect()[0], + [ + hl.Struct( + amino_acids='S/L', + canonical=1, + codons='tCg/tTg', + gene_id='ENSG00000188976', + hgvsc='ENST00000327044.6:c.1667C>T', + hgvsp='ENSP00000317992.6:p.Ser556Leu', + transcript_id='ENST00000327044', + refseq_transcript_id='NM_015658.4', + mane_select='NM_015658.4', + mane_plus_clinical=None, + biotype_id=39, + consequence_term_ids=[9], + exon=hl.Struct(index=15, total=19), + intron=None, + alphamissense=hl.Struct(pathogenicity=0.10000000149011612), + loftee=hl.Struct( + is_lof_nagnag=None, + lof_filter_ids=[0, 1], + ), + spliceregion=hl.Struct( + extended_intronic_splice_region_variant=False, + ), + utrannotator=hl.Struct( + existing_inframe_oorfs=None, + existing_outofframe_oorfs=None, + existing_uorfs=None, + fiveutr_consequence_id=None, + fiveutr_annotation=None, + ), + ), + hl.Struct( + amino_acids=None, + canonical=None, + codons=None, + gene_id='ENSG00000188976', + hgvsc='ENST00000477976.1:n.3114C>T', + hgvsp=None, + transcript_id='ENST00000477976', + refseq_transcript_id='refseq1', + mane_select=None, + mane_plus_clinical=None, + biotype_id=38, + consequence_term_ids=[23, 26], + exon=hl.Struct(index=13, total=17), + intron=None, + alphamissense=hl.Struct(pathogenicity=0.9700000286102295), + loftee=hl.Struct( + is_lof_nagnag=None, + lof_filter_ids=None, + ), + spliceregion=hl.Struct( + extended_intronic_splice_region_variant=False, + ), + utrannotator=hl.Struct( + existing_inframe_oorfs=None, + existing_outofframe_oorfs=None, + existing_uorfs=None, + fiveutr_consequence_id=None, + fiveutr_annotation=None, + ), + ), + hl.Struct( + amino_acids=None, + canonical=None, + codons=None, + gene_id='ENSG00000188976', + hgvsc='ENST00000483767.1:n.523C>T', + hgvsp=None, + transcript_id='ENST00000483767', + refseq_transcript_id=None, + mane_select=None, + mane_plus_clinical=None, + biotype_id=38, + consequence_term_ids=[23, 13, 26], + exon=hl.Struct(index=1, total=5), + intron=None, + alphamissense=hl.Struct(pathogenicity=None), + loftee=hl.Struct( + is_lof_nagnag=None, + lof_filter_ids=None, + ), + spliceregion=hl.Struct( + extended_intronic_splice_region_variant=True, + ), + utrannotator=hl.Struct( + existing_inframe_oorfs=0, + existing_outofframe_oorfs=1, + existing_uorfs=0, + fiveutr_consequence_id=1, + fiveutr_annotation=hl.Struct( + type='OutOfFrame_oORF', + KozakContext='TTTATGC', + KozakStrength='Weak', + DistanceToCDS=40, + CapDistanceToStart=20, + DistanceToStop=75, + Evidence=False, + AltStop=None, + AltStopDistanceToCDS=None, + FrameWithCDS=None, + StartDistanceToCDS=None, + newSTOPDistanceToCDS=None, + alt_type=None, + alt_type_length=None, + ref_StartDistanceToCDS=None, + ref_type=None, + ref_type_length=None, + ), + ), + ), + ], + ) + + @patch('loading_pipeline.lib.misc.vep.hl.vep') + def test_sorted_other_feature_consequences( + self, + mock_vep: Mock, + ) -> None: + ht = hl.Table.parallelize( + [ + { + 'locus': hl.Locus( + contig='chr1', + position=871269, + reference_genome=ReferenceGenome.GRCh38.value, + ), + 'alleles': ['A', 'C'], + }, + ], + hl.tstruct( + locus=hl.tlocus(ReferenceGenome.GRCh38.value), + alleles=hl.tarray(hl.tstr), + ), + key=['locus', 'alleles'], + ) + mock_vep.return_value = ht.annotate(vep=MOCK_38_VEP_DATA) + ht = run_vep( + ht, + DatasetType.SNV_INDEL, + ReferenceGenome.GRCh38, + ) + ht = ht.select( + sorted_motif_feature_consequences=snv_indel.sorted_motif_feature_consequences( + ht, + ), + sorted_regulatory_feature_consequences=snv_indel.sorted_regulatory_feature_consequences( + ht, + ), + ) + self.assertCountEqual( + ht.sorted_motif_feature_consequences.collect(), + [None], + ) + self.assertCountEqual( + ht.sorted_regulatory_feature_consequences.collect()[0], + [ + hl.Struct( + biotype_id=0, + consequence_term_ids=[0], + regulatory_feature_id='regulatory_2', + ), + hl.Struct( + biotype_id=0, + consequence_term_ids=[2], + regulatory_feature_id='regulatory_1', + ), + ], + ) diff --git a/loading_pipeline/lib/annotations/sv.py b/loading_pipeline/lib/annotations/sv.py new file mode 100644 index 0000000000..e6c3abdd85 --- /dev/null +++ b/loading_pipeline/lib/annotations/sv.py @@ -0,0 +1,254 @@ +# ruff: noqa: N806 +from typing import Any + +import hail as hl + +from loading_pipeline.lib.annotations import liftover +from loading_pipeline.lib.annotations.enums import ( + SV_CONSEQUENCE_RANKS, + SV_TYPE_DETAILS, + SV_TYPES, +) +from loading_pipeline.lib.core.definitions import ReferenceGenome + +CONSEQ_PREDICTED_PREFIX = 'info.PREDICTED_' +CONSEQ_PREDICTED_GENE_COLS = { + 'info.PREDICTED_BREAKEND_EXONIC': hl.tarray(hl.tstr), + 'info.PREDICTED_COPY_GAIN': hl.tarray(hl.tstr), + 'info.PREDICTED_DUP_PARTIAL': hl.tarray(hl.tstr), + 'info.PREDICTED_INTRAGENIC_EXON_DUP': hl.tarray(hl.tstr), + 'info.PREDICTED_INTRONIC': hl.tarray(hl.tstr), + 'info.PREDICTED_INV_SPAN': hl.tarray(hl.tstr), + 'info.PREDICTED_LOF': hl.tarray(hl.tstr), + 'info.PREDICTED_MSV_EXON_OVERLAP': hl.tarray(hl.tstr), + 'info.PREDICTED_NEAREST_TSS': hl.tarray(hl.tstr), + 'info.PREDICTED_PARTIAL_EXON_DUP': hl.tarray(hl.tstr), + 'info.PREDICTED_PROMOTER': hl.tarray(hl.tstr), + 'info.PREDICTED_TSS_DUP': hl.tarray(hl.tstr), + 'info.PREDICTED_UTR': hl.tarray(hl.tstr), +} + +PREVIOUS_GENOTYPE_N_ALT_ALLELES = hl.dict( + { + # Map of concordance string -> previous n_alt_alleles() + # Concordant + frozenset(['TN']): 0, # 0/0 -> 0/0 + frozenset(['TP']): 2, # 1/1 -> 1/1 + frozenset(['TN', 'TP']): 1, # 0/1 -> 0/1 + # Novel + frozenset(['FP']): 0, # 0/0 -> 1/1 + frozenset(['TN', 'FP']): 0, # 0/0 -> 0/1 + # Absent + frozenset(['FN']): 2, # 1/1 -> 0/0 + frozenset(['TN', 'FN']): 1, # 0/1 -> 0/0 + # Discordant + frozenset(['FP', 'TP']): 1, # 0/1 -> 1/1 + frozenset(['FN', 'TP']): 2, # 1/1 -> 0/1 + }, +) + + +SV_TYPES_LOOKUP = hl.dict(hl.enumerate(SV_TYPES, index_first=False)) +SV_TYPE_DETAILS_LOOKUP = hl.dict(hl.enumerate(SV_TYPE_DETAILS, index_first=False)) +SV_CONSEQUENCE_RANKS_LOOKUP = hl.dict( + hl.enumerate(SV_CONSEQUENCE_RANKS, index_first=False), +) + + +def _get_cpx_interval( + x: hl.StringExpression, + reference_genome: ReferenceGenome, +) -> hl.StructExpression: + # an example format of CPX_INTERVALS is "DUP_chr1:1499897-1499974" + type_contig = x.split('_') + contig_pos = type_contig[1].split(':') + pos = contig_pos[1].split('-') + return hl.struct( + type_id=SV_TYPES_LOOKUP[type_contig[0]], + start=hl.locus( + contig_pos[0], + hl.int32(pos[0]), + reference_genome.value, + ), + end=hl.locus( + contig_pos[0], + hl.int32(pos[1]), + reference_genome.value, + ), + ) + + +def _sv_types(ht: hl.Table) -> hl.ArrayExpression: + return ht.alleles[1].replace('[<>]', '').split(':', 2) + + +def alleles(ht: hl.Table, **_: Any) -> hl.ArrayExpression: + return hl.array( + [ + 'N', + hl.if_else( + ( + hl.is_defined(ht.sv_type_detail_id) + & (hl.array(SV_TYPES)[ht.sv_type_id] != 'CPX') + ), + hl.format( + '<%s:%s>', + hl.array(SV_TYPES)[ht.sv_type_id], + hl.array(SV_TYPE_DETAILS)[ht.sv_type_detail_id], + ), + hl.format('<%s>', hl.array(SV_TYPES)[ht.sv_type_id]), + ), + ], + ) + + +def info(ht: hl.Table, **_: Any) -> hl.StructExpression: + return hl.Struct( + ALGORITHMS=ht.algorithms, + END=ht.start_locus.position, + CHR2=ht.end_locus.contig, + END2=ht.end_locus.position, + SVTYPE=hl.array(SV_TYPES)[ht.sv_type_id], + SVLEN=ht.sv_len, + ) + + +def locus(ht: hl.Table, **_: Any) -> hl.LocusExpression: + return ht.start_locus + + +def algorithms(ht: hl.Table, **_: Any) -> hl.Expression: + return hl.str(',').join(ht['info.ALGORITHMS']) + + +def bothsides_support(ht: hl.Table, **_: Any) -> hl.Expression: + return ht['info.BOTHSIDES_SUPPORT'] + + +def CN(mt: hl.MatrixTable, **_: Any) -> hl.Expression: # noqa: N802 + return mt.RD_CN + + +def concordance(mt: hl.MatrixTable, **_: Any) -> hl.Expression: + is_called = hl.is_defined(mt.GT) + was_previously_called = hl.is_defined(mt.CONC_ST) & ~mt.CONC_ST.contains( + 'EMPTY', + ) + num_alt = hl.if_else(is_called, mt.GT.n_alt_alleles(), -1) + prev_num_alt = hl.if_else( + was_previously_called, + PREVIOUS_GENOTYPE_N_ALT_ALLELES[hl.set(mt.CONC_ST)], + -1, + ) + concordant_genotype = num_alt == prev_num_alt + discordant_genotype = (num_alt != prev_num_alt) & (prev_num_alt > 0) + novel_genotype = (num_alt != prev_num_alt) & (prev_num_alt == 0) + return hl.struct( + prev_num_alt=hl.or_missing(discordant_genotype, prev_num_alt), + prev_call=hl.or_missing(is_called, was_previously_called & concordant_genotype), + new_call=hl.or_missing(is_called, ~was_previously_called | novel_genotype), + ) + + +def cpx_intervals( + ht: hl.Table, + reference_genome: ReferenceGenome, + **_: Any, +) -> hl.Expression: + return hl.or_missing( + hl.is_defined(ht['info.CPX_INTERVALS']), + ht['info.CPX_INTERVALS'].map(lambda x: _get_cpx_interval(x, reference_genome)), + ) + + +def end_locus(ht: hl.Table, **_: Any) -> hl.StructExpression: + rg38_lengths = hl.literal(hl.get_reference(ReferenceGenome.GRCh38.value).lengths) + return hl.if_else( + ( + hl.is_defined(ht['info.END2']) + & (rg38_lengths[ht['info.CHR2']] >= ht['info.END2']) + ), + hl.locus(ht['info.CHR2'], ht['info.END2'], ReferenceGenome.GRCh38.value), + hl.or_missing( + (rg38_lengths[ht.locus.contig] >= ht['info.END']), + hl.locus(ht.locus.contig, ht['info.END'], ReferenceGenome.GRCh38.value), + ), + ) + + +def gnomad_svs( + ht: hl.Table, + gnomad_svs_ht: hl.Table, + **_: Any, +) -> hl.Expression: + gnomad_svs_ht = gnomad_svs_ht.drop('locus', 'alleles') + return gnomad_svs_ht.annotate( + ID=gnomad_svs_ht.KEY, + )[ht['info.GNOMAD_V4.1_TRUTH_VID']] + + +def rg37_locus_end( + ht: hl.Table, + **_: Any, +) -> hl.Expression | None: + liftover.add_rg38_liftover() + end = end_locus(ht) + return hl.or_missing( + hl.is_defined(end), + hl.liftover( + hl.locus( + end.contig, + end.position, + reference_genome=ReferenceGenome.GRCh38.value, + ), + ReferenceGenome.GRCh37.value, + ), + ) + + +def start_locus(ht: hl.Table, **_: Any): + return ht.locus + + +def sorted_gene_consequences( + ht: hl.Table, + gencode_gene_symbol_to_gene_id_mapping: hl.tdict(hl.tstr, hl.tstr), + **_: Any, +) -> hl.Expression: + # In lieu of sorted_transcript_consequences seen on SNV/MITO. + mapped_genes = [ + ht[gene_col].map( + lambda gene: hl.struct( + gene_id=gencode_gene_symbol_to_gene_id_mapping.get(gene), + major_consequence_id=SV_CONSEQUENCE_RANKS_LOOKUP[ + gene_col.replace(CONSEQ_PREDICTED_PREFIX, '', 1) # noqa: B023 + ], + ), + ) + for gene_col in CONSEQ_PREDICTED_GENE_COLS + ] + return hl.filter(hl.is_defined, mapped_genes).flatmap(lambda x: x) + + +def strvctvre(ht: hl.Table, **_: Any) -> hl.Expression: + return hl.struct(score=hl.parse_float32(ht['info.StrVCTVRE'])) + + +def sv_len(ht: hl.Table, **_: Any) -> hl.Expression: + return ht['info.SVLEN'] + + +def sv_type_id(ht: hl.Table, **_: Any) -> hl.Expression: + return SV_TYPES_LOOKUP[_sv_types(ht)[0]] + + +def sv_type_detail_id(ht: hl.Table, **_: Any) -> hl.Expression: + sv_types = _sv_types(ht) + return hl.if_else( + sv_types[0] == 'CPX', + SV_TYPE_DETAILS_LOOKUP[ht['info.CPX_TYPE']], + hl.or_missing( + (sv_types[0] == 'INS') & (hl.len(sv_types) > 1), + SV_TYPE_DETAILS_LOOKUP[sv_types[1]], + ), + ) diff --git a/loading_pipeline/lib/annotations/sv_test.py b/loading_pipeline/lib/annotations/sv_test.py new file mode 100644 index 0000000000..25a8413b16 --- /dev/null +++ b/loading_pipeline/lib/annotations/sv_test.py @@ -0,0 +1,171 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.annotations.fields import get_fields +from loading_pipeline.lib.core import DatasetType + + +class SVTest(unittest.TestCase): + def test_sv_export_annotations(self) -> None: + ht = hl.Table.parallelize( + [ + hl.Struct( + id=0, + algorithms='manta', + end_locus=hl.Locus( + contig='chr5', + position=20404, + reference_genome='GRCh38', + ), + start_locus=hl.Locus( + contig='chr1', + position=180928, + reference_genome='GRCh38', + ), + sv_len=123, + sv_type_id=2, + sv_type_detail_id=None, + ), + hl.Struct( + id=1, + algorithms='manta', + end_locus=hl.Locus( + contig='chr1', + position=789481, + reference_genome='GRCh38', + ), + start_locus=hl.Locus( + contig='chr1', + position=789481, + reference_genome='GRCh38', + ), + sv_len=245, + sv_type_id=2, + sv_type_detail_id=None, + ), + hl.Struct( + id=2, + algorithms='manta', + end_locus=hl.Locus( + contig='chr1', + position=6559723, + reference_genome='GRCh38', + ), + start_locus=hl.Locus( + contig='chr1', + position=6558902, + reference_genome='GRCh38', + ), + sv_len=245, + sv_type_id=3, + sv_type_detail_id=2, + ), + hl.Struct( + id=3, + algorithms='manta', + end_locus=hl.Locus( + contig='chr1', + position=6559723, + reference_genome='GRCh38', + ), + start_locus=hl.Locus( + contig='chr1', + position=6558902, + reference_genome='GRCh38', + ), + sv_len=245, + sv_type_id=7, + sv_type_detail_id=6, + ), + ], + hl.tstruct( + id=hl.tint32, + algorithms=hl.tstr, + end_locus=hl.tlocus('GRCh38'), + start_locus=hl.tlocus('GRCh38'), + sv_len=hl.tint32, + sv_type_id=hl.tint32, + sv_type_detail_id=hl.tint32, + ), + key='id', + ) + ht = ht.select( + **get_fields( + ht, + DatasetType.SV.export_vcf_annotation_fns, + ), + ) + self.assertEqual( + ht.collect(), + [ + hl.Struct( + id=0, + locus=hl.Locus( + contig='chr1', + position=180928, + reference_genome='GRCh38', + ), + alleles=['N', ''], + info=hl.Struct( + ALGORITHMS='manta', + END=180928, + CHR2='chr5', + END2=20404, + SVTYPE='BND', + SVLEN=123, + ), + ), + hl.Struct( + id=1, + locus=hl.Locus( + contig='chr1', + position=789481, + reference_genome='GRCh38', + ), + alleles=['N', ''], + info=hl.Struct( + ALGORITHMS='manta', + END=789481, + CHR2='chr1', + END2=789481, + SVTYPE='BND', + SVLEN=245, + ), + ), + hl.Struct( + id=2, + locus=hl.Locus( + contig='chr1', + position=6558902, + reference_genome='GRCh38', + ), + alleles=['N', ''], + info=hl.Struct( + ALGORITHMS='manta', + END=6558902, + CHR2='chr1', + END2=6559723, + SVTYPE='CPX', + SVLEN=245, + ), + ), + hl.Struct( + id=3, + locus=hl.Locus( + contig='chr1', + position=6558902, + reference_genome='GRCh38', + ), + alleles=['N', ''], + info=hl.Struct( + ALGORITHMS='manta', + END=6558902, + CHR2='chr1', + END2=6559723, + SVTYPE='INS', + SVLEN=245, + ), + ), + ], + ) diff --git a/loading_pipeline/lib/annotations/vep.py b/loading_pipeline/lib/annotations/vep.py new file mode 100644 index 0000000000..12af00d8bb --- /dev/null +++ b/loading_pipeline/lib/annotations/vep.py @@ -0,0 +1,182 @@ +from collections.abc import Callable + +import hail as hl + +from loading_pipeline.lib.annotations.enums import ( + BIOTYPES, + FIVEUTR_CONSEQUENCES, + LOF_FILTERS, + TRANSCRIPT_CONSEQUENCE_TERMS, +) + +BIOTYPE_LOOKUP = hl.dict(hl.enumerate(BIOTYPES, index_first=False)) +EXTENDED_INTRONIC_SPLICE_REGION_VARIANT = 'extended_intronic_splice_region_variant' +FIVEUTR_CONSEQUENCES_LOOKUP = hl.dict( + hl.enumerate(FIVEUTR_CONSEQUENCES, index_first=False).extend( + [(hl.missing(hl.tstr), hl.missing(hl.tint32))], + ), +) +LOF_FILTERS_LOOKUP = hl.dict(hl.enumerate(LOF_FILTERS, index_first=False)) +MANE_SELECT_ANNOTATIONS = [ + 'mane_select', + 'mane_plus_clinical', +] +NAGNAG_SITE = 'NAGNAG_SITE' +OMIT_TRANSCRIPT_CONSEQUENCE_TERMS = hl.set( + [ + 'upstream_gene_variant', + 'downstream_gene_variant', + ], +) +PROTEIN_CODING_ID = BIOTYPE_LOOKUP['protein_coding'] +SELECTED_ANNOTATIONS = [ + 'amino_acids', + 'canonical', + 'codons', + 'gene_id', + 'hgvsc', + 'hgvsp', + 'transcript_id', +] +TRANSCRIPT_CONSEQUENCE_TERMS_LOOKUP = hl.dict( + hl.enumerate(TRANSCRIPT_CONSEQUENCE_TERMS, index_first=False), +) + + +def _lof_filter_ids(c: hl.StructExpression) -> hl.ArrayNumericExpression: + return hl.or_missing( + (c.lof == 'LC') & hl.is_defined(c.lof_filter), + c.lof_filter.split('&|,').map(lambda f: LOF_FILTERS_LOOKUP[f]), + ) + + +def _consequence_term_ids(c: hl.StructExpression) -> hl.ArrayNumericExpression: + return c.consequence_terms.filter( + lambda t: ~OMIT_TRANSCRIPT_CONSEQUENCE_TERMS.contains(t), + ).map(lambda t: TRANSCRIPT_CONSEQUENCE_TERMS_LOOKUP[t]) + + +def vep_110_transcript_consequences_select( + gencode_ensembl_to_refseq_id_mapping: hl.tdict(hl.tstr, hl.tstr), +) -> hl.StructExpression: + return lambda c: c.select( + *SELECTED_ANNOTATIONS, + *MANE_SELECT_ANNOTATIONS, + biotype_id=BIOTYPE_LOOKUP[c.biotype], + consequence_term_ids=_consequence_term_ids(c), + exon=hl.bind( + lambda split: hl.or_missing( + hl.is_defined(split), + hl.Struct(index=split[0], total=split[1]), + ), + c.exon.split('/').map(hl.parse_int32), + ), + intron=hl.bind( + lambda split: hl.or_missing( + hl.is_defined(split), + hl.Struct(index=split[0], total=split[1]), + ), + c.intron.split('/').map(hl.parse_int32), + ), + refseq_transcript_id=gencode_ensembl_to_refseq_id_mapping.get(c.transcript_id), + alphamissense=hl.struct( + pathogenicity=c.am_pathogenicity, + ), + loftee=hl.struct( + is_lof_nagnag=c.lof_flags == NAGNAG_SITE, + lof_filter_ids=_lof_filter_ids(c), + ), + spliceregion=hl.struct( + extended_intronic_splice_region_variant=( + hl.is_defined(c.spliceregion) + & c.spliceregion.contains( + EXTENDED_INTRONIC_SPLICE_REGION_VARIANT, + ) + ), + ), + utrannotator=hl.struct( + existing_inframe_oorfs=c.existing_inframe_oorfs, + existing_outofframe_oorfs=c.existing_outofframe_oorfs, + existing_uorfs=c.existing_uorfs, + fiveutr_consequence_id=FIVEUTR_CONSEQUENCES_LOOKUP[c.fiveutr_consequence], + # Annotation documentation here: + # https://github.com/ImperialCardioGenetics/UTRannotator?tab=readme-ov-file#the-detailed-annotation-for-each-consequence + # NB: + fiveutr_annotation=c.fiveutr_annotation['1'].annotate( + AltStopDistanceToCDS=hl.parse_int32( + c.fiveutr_annotation['1'].AltStopDistanceToCDS, + ), + CapDistanceToStart=hl.parse_int32( + c.fiveutr_annotation['1'].CapDistanceToStart, + ), + DistanceToCDS=hl.parse_int32( + c.fiveutr_annotation['1'].DistanceToCDS, + ), + DistanceToStop=hl.parse_int32( + c.fiveutr_annotation['1'].DistanceToStop, + ), + Evidence=hl.or_missing( + # Just in case a weird value ("NA" or anything else) propagates + ( + (c.fiveutr_annotation['1'].Evidence == 'True') + | (c.fiveutr_annotation['1'].Evidence == 'False') + ), + hl.bool(c.fiveutr_annotation['1'].Evidence), + ), + StartDistanceToCDS=hl.parse_int32( + c.fiveutr_annotation['1'].StartDistanceToCDS, + ), + newSTOPDistanceToCDS=hl.parse_int32( + c.fiveutr_annotation['1'].newSTOPDistanceToCDS, + ), + alt_type_length=hl.parse_int32( + c.fiveutr_annotation['1'].alt_type_length, + ), + ref_StartDistanceToCDS=hl.parse_int32( + c.fiveutr_annotation['1'].ref_StartDistanceToCDS, + ), + ref_type_length=hl.parse_int32( + c.fiveutr_annotation['1'].ref_type_length, + ), + ), + ), + ) + + +def vep_85_transcript_consequences_select( + c: hl.StructExpression, +) -> hl.StructExpression: + return c.select( + *SELECTED_ANNOTATIONS, + biotype_id=BIOTYPE_LOOKUP[c.biotype], + consequence_term_ids=_consequence_term_ids(c), + is_lof_nagnag=c.lof_flags == NAGNAG_SITE, + lof_filter_ids=_lof_filter_ids(c), + ) + + +def transcript_consequences_sort( + ht: hl.Table, +) -> Callable[[hl.StructExpression], hl.StructExpression]: + return lambda c: hl.bind( + lambda is_coding, is_most_severe, is_canonical: ( + hl.cond( + is_coding, + hl.cond( + is_most_severe, + hl.cond(is_canonical, 1, 2), + hl.cond(is_canonical, 3, 4), + ), + hl.cond( + is_most_severe, + hl.cond(is_canonical, 5, 6), + hl.cond(is_canonical, 7, 8), + ), + ) + ), + c.biotype_id == PROTEIN_CODING_ID, + hl.set(c.consequence_term_ids).contains( + TRANSCRIPT_CONSEQUENCE_TERMS_LOOKUP[ht.vep.most_severe_consequence], + ), + hl.or_else(c.canonical, 0) == 1, + ) diff --git a/loading_pipeline/lib/core/__init__.py b/loading_pipeline/lib/core/__init__.py new file mode 100644 index 0000000000..44e5aaab40 --- /dev/null +++ b/loading_pipeline/lib/core/__init__.py @@ -0,0 +1,17 @@ +from loading_pipeline.lib.core.dataset_type import DatasetType +from loading_pipeline.lib.core.definitions import ( + ReferenceGenome, + SampleType, + Sex, +) +from loading_pipeline.lib.core.environment import Env +from loading_pipeline.lib.core.feature_flag import FeatureFlag + +__all__ = [ + 'DatasetType', + 'Env', + 'FeatureFlag', + 'ReferenceGenome', + 'SampleType', + 'Sex', +] diff --git a/loading_pipeline/lib/core/constants.py b/loading_pipeline/lib/core/constants.py new file mode 100644 index 0000000000..a1a5affaf2 --- /dev/null +++ b/loading_pipeline/lib/core/constants.py @@ -0,0 +1,14 @@ +import os + +MIGRATION_RUN_ID = 'hail_search_to_clickhouse_migration' +VARIANTS_MIGRATION_RUN_ID = 'annotations_to_variants_tables' +GRCH37_TO_GRCH38_LIFTOVER_REF_PATH = ( + 'gs://hail-common/references/grch37_to_grch38.over.chain.gz' + if os.environ.get('HAIL_DATAPROC') == '1' + else 'loading_pipeline/var/liftover/grch37_to_grch38.over.chain.gz' +) +GRCH38_TO_GRCH37_LIFTOVER_REF_PATH = ( + 'gs://hail-common/references/grch38_to_grch37.over.chain.gz' + if os.environ.get('HAIL_DATAPROC') == '1' + else 'loading_pipeline/var/liftover/grch38_to_grch37.over.chain.gz' +) diff --git a/loading_pipeline/lib/core/dataset_type.py b/loading_pipeline/lib/core/dataset_type.py new file mode 100644 index 0000000000..1e018f7104 --- /dev/null +++ b/loading_pipeline/lib/core/dataset_type.py @@ -0,0 +1,385 @@ +from collections.abc import Callable +from enum import StrEnum + +import hail as hl + +from loading_pipeline.lib.annotations import gcnv, mito, shared, snv_indel, sv +from loading_pipeline.lib.core.definitions import ReferenceGenome +from loading_pipeline.lib.core.environment import Env + +MITO_MIN_HOM_THRESHOLD = 0.95 +ZERO = 0.0 + + +class DatasetType(StrEnum): + GCNV = 'GCNV' + MITO = 'MITO' + SNV_INDEL = 'SNV_INDEL' + SV = 'SV' + + @property + def reference_genomes(self) -> list[ReferenceGenome]: + return { + DatasetType.SNV_INDEL: [ReferenceGenome.GRCh37, ReferenceGenome.GRCh38], + DatasetType.MITO: [ReferenceGenome.GRCh38], + DatasetType.GCNV: [ReferenceGenome.GRCh38], + DatasetType.SV: [ReferenceGenome.GRCh38], + }[self] + + def table_key_type( + self, + reference_genome: ReferenceGenome, + ) -> hl.tstruct: + default_key = hl.tstruct( + locus=hl.tlocus(reference_genome.value), + alleles=hl.tarray(hl.tstr), + ) + return { + DatasetType.GCNV: hl.tstruct(variant_id=hl.tstr), + DatasetType.SV: hl.tstruct(variant_id=hl.tstr), + }.get(self, default_key) + + def table_key_format_fn( + self, + reference_genome: ReferenceGenome, + ) -> Callable[[hl.StructExpression], str]: + if self in {DatasetType.GCNV, DatasetType.SV}: + return lambda s: s.variant_id + return ( + lambda s: f'{s.locus.contig if reference_genome == ReferenceGenome.GRCh37 else s.locus.contig.replace("chr", "")}-{s.locus.position}-{"-".join(s.alleles)}' + ) + + @property + def col_fields( + self, + ) -> list[str]: + return { + DatasetType.SNV_INDEL: {}, + DatasetType.MITO: { + 'contamination': {hl.tstr, hl.tfloat64}, + 'mito_cn': hl.tfloat64, + }, + DatasetType.SV: {}, + DatasetType.GCNV: {}, + }[self] + + @property + def entries_fields( + self, + ) -> list[str]: + return { + DatasetType.SNV_INDEL: { + 'GT': hl.tcall, + 'AD': hl.tarray(hl.tint32), + 'GQ': hl.tint32, + }, + DatasetType.MITO: { + 'GT': hl.tcall, + 'DP': hl.tint32, + 'MQ': {hl.tfloat64, hl.tint32}, + 'HL': hl.tfloat64, + }, + DatasetType.SV: { + 'GT': hl.tcall, + 'CONC_ST': hl.tarray(hl.tstr), + 'GQ': hl.tint32, + 'RD_CN': hl.tint32, + }, + DatasetType.GCNV: { + 'any_ovl': hl.tstr, + 'defragmented': hl.tbool, + 'genes_any_overlap_Ensemble_ID': hl.tstr, + 'genes_any_overlap_totalExons': hl.tint32, + 'identical_ovl': hl.tstr, + 'is_latest': hl.tbool, + 'no_ovl': hl.tbool, + 'sample_start': hl.tint32, + 'sample_end': hl.tint32, + 'CN': hl.tint32, + 'GT': hl.tstr, + 'QS': hl.tint32, + }, + }[self] + + @property + def row_fields( + self, + ) -> list[str]: + return { + DatasetType.SNV_INDEL: { + 'rsid': hl.tstr, + 'filters': hl.tset(hl.tstr), + }, + DatasetType.MITO: { + 'rsid': hl.tset(hl.tstr), + 'filters': hl.tset(hl.tstr), + 'common_low_heteroplasmy': hl.tbool, + 'hap_defining_variant': hl.tbool, + 'mitotip_trna_prediction': hl.tstr, + 'vep': hl.tstruct, + }, + DatasetType.SV: { + 'locus': hl.tlocus(ReferenceGenome.GRCh38.value), + 'alleles': hl.tarray(hl.tstr), + 'filters': hl.tset(hl.tstr), + 'info.AC': hl.tarray(hl.tint32), + 'info.AF': hl.tarray(hl.tfloat64), + 'info.ALGORITHMS': hl.tarray(hl.tstr), + 'info.BOTHSIDES_SUPPORT': hl.tbool, + 'info.AN': hl.tint32, + 'info.CHR2': hl.tstr, + 'info.CPX_INTERVALS': hl.tarray(hl.tstr), + 'info.CPX_TYPE': hl.tstr, + 'info.END': hl.tint32, + 'info.END2': hl.tint32, + 'info.N_HET': hl.tint32, + 'info.N_HOMALT': hl.tint32, + 'info.GNOMAD_V4.1_TRUTH_VID': hl.tstr, + 'info.StrVCTVRE': hl.tstr, + 'info.SVLEN': hl.tint32, + **sv.CONSEQ_PREDICTED_GENE_COLS, + }, + DatasetType.GCNV: { + 'cg_genes': hl.tset(hl.tstr), + 'chr': hl.tstr, + 'end': hl.tint32, + 'filters': hl.tset(hl.tstr), + 'gene_ids': hl.tset(hl.tstr), + 'lof_genes': hl.tset(hl.tstr), + 'num_exon': hl.tint32, + 'sc': hl.tint32, + 'sf': hl.tfloat64, + 'start': hl.tint32, + 'strvctvre_score': hl.tstr, + 'svtype': hl.tstr, + }, + }[self] + + @property + def excluded_filters(self) -> hl.SetExpression: + return { + DatasetType.SNV_INDEL: hl.empty_set(hl.tstr), + DatasetType.MITO: hl.set(['PASS']), + DatasetType.SV: hl.set(['PASS', 'BOTHSIDES_SUPPORT']), + DatasetType.GCNV: hl.empty_set(hl.tstr), + }[self] + + @property + def invalid_allele_types(self) -> hl.SetExpression: + return { + DatasetType.SV: hl.set([hl.genetics.allele_type.AlleleType.UNKNOWN]), + }.get( + self, + hl.set( + [ + hl.genetics.allele_type.AlleleType.UNKNOWN, + hl.genetics.allele_type.AlleleType.SYMBOLIC, + ], + ), + ) + + def has_gencode_ensembl_to_refseq_id_mapping( + self, + reference_genome: ReferenceGenome, + ) -> bool: + return ( + self == DatasetType.SNV_INDEL and reference_genome == ReferenceGenome.GRCh38 + ) + + def expect_tdr_metrics( + self, + reference_genome: ReferenceGenome, + ) -> bool: + return ( + self == DatasetType.SNV_INDEL and reference_genome == ReferenceGenome.GRCh38 + ) + + @property + def has_gencode_gene_symbol_to_gene_id_mapping(self) -> bool: + return self == DatasetType.SV + + @property + def has_multi_allelic_variants(self) -> bool: + return self == DatasetType.SNV_INDEL + + @property + def family_entries_filter_fn(self) -> Callable[[hl.StructExpression], bool]: + return { + DatasetType.GCNV: lambda e: hl.is_defined(e.GT), + }.get(self, lambda e: e.GT.is_non_ref()) + + @property + def can_run_validation(self) -> bool: + return self == DatasetType.SNV_INDEL + + @property + def check_sex_and_relatedness(self) -> bool: + return self == DatasetType.SNV_INDEL + + @property + def veppable(self) -> bool: + return self == DatasetType.SNV_INDEL + + def formatting_annotation_fns( + self, + reference_genome: ReferenceGenome, + ) -> list[Callable[..., hl.Expression]]: + GRCh37_fns = { # noqa: N806 + DatasetType.SNV_INDEL: [ + shared.rsid, + shared.variant_id, + shared.xpos, + shared.sorted_transcript_consequences, + snv_indel.rg38_locus, + ], + DatasetType.MITO: [ + mito.common_low_heteroplasmy, + mito.haplogroup, + mito.mitotip, + mito.rsid, + shared.variant_id, + shared.xpos, + shared.sorted_transcript_consequences, + ], + DatasetType.SV: [ + sv.algorithms, + sv.bothsides_support, + sv.cpx_intervals, + sv.end_locus, + sv.gnomad_svs, + sv.sorted_gene_consequences, + sv.start_locus, + sv.strvctvre, + sv.sv_type_id, + sv.sv_type_detail_id, + sv.sv_len, + shared.xpos, + ], + DatasetType.GCNV: [ + gcnv.end_locus, + gcnv.num_exon, + gcnv.sorted_gene_consequences, + gcnv.start_locus, + gcnv.strvctvre, + gcnv.sv_type_id, + gcnv.xpos, + ], + } + if reference_genome == ReferenceGenome.GRCh37: + return GRCh37_fns[self] + return { + DatasetType.SNV_INDEL: [ + shared.rsid, + shared.variant_id, + shared.xpos, + shared.rg37_locus, + snv_indel.check_ref, + snv_indel.sorted_transcript_consequences, + snv_indel.sorted_regulatory_feature_consequences, + snv_indel.sorted_motif_feature_consequences, + ], + DatasetType.MITO: [ + *GRCh37_fns[DatasetType.MITO], + shared.rg37_locus, + ], + DatasetType.SV: [ + *GRCh37_fns[DatasetType.SV], + shared.rg37_locus, + sv.rg37_locus_end, + ], + DatasetType.GCNV: [ + *GRCh37_fns[DatasetType.GCNV], + gcnv.rg37_locus, + gcnv.rg37_locus_end, + ], + }[self] + + @property + def genotype_entry_annotation_fns(self) -> list[Callable[..., hl.Expression]]: + return { + DatasetType.SNV_INDEL: [ + shared.GQ, + snv_indel.AB, + snv_indel.DP, + shared.GT, + ], + DatasetType.MITO: [ + mito.contamination, + mito.DP, + mito.HL, + mito.mito_cn, + mito.GQ, + shared.GT, + ], + DatasetType.SV: [ + sv.CN, + sv.concordance, + shared.GQ, + shared.GT, + ], + DatasetType.GCNV: [ + gcnv.concordance, + gcnv.defragged, + gcnv.sample_end, + gcnv.sample_gene_ids, + gcnv.sample_num_exon, + gcnv.sample_start, + gcnv.CN, + gcnv.GT, + gcnv.QS, + ], + }[self] + + @property + def variant_frequency_annotation_fns(self) -> list[Callable[..., hl.Expression]]: + return { + DatasetType.GCNV: [ + gcnv.gt_stats, + ], + }.get(self, []) + + @property + def filter_invalid_sites(self): + return self == DatasetType.SNV_INDEL + + @property + def should_export_to_vcf(self): + return self == DatasetType.SV + + @property + def export_all_callset_variants(self): + return self == DatasetType.GCNV + + @property + def export_vcf_annotation_fns(self) -> list[Callable[..., hl.Expression]]: + return { + DatasetType.SV: [ + sv.locus, + sv.alleles, + sv.info, + ], + }[self] + + @property + def should_write_new_variant_details(self): + return self == DatasetType.SNV_INDEL + + @property + def overwrite_male_non_par_calls(self) -> None: + return self == DatasetType.SV + + @property + def re_key_by_seqr_internal_truth_vid(self) -> None: + return self == DatasetType.SV + + @property + def dataproc_primary_workers(self) -> int: + if self == DatasetType.SNV_INDEL: + return Env.GCLOUD_DATAPROC_PRIMARY_WORKERS + return 1 + + @property + def dataproc_preemptibles(self) -> int | None: + if self == DatasetType.SNV_INDEL: + return Env.GCLOUD_DATAPROC_SECONDARY_WORKERS + return 1 diff --git a/loading_pipeline/lib/core/definitions.py b/loading_pipeline/lib/core/definitions.py new file mode 100644 index 0000000000..6ccce95e43 --- /dev/null +++ b/loading_pipeline/lib/core/definitions.py @@ -0,0 +1,86 @@ +from enum import StrEnum + +import hail as hl + + +class Sex(StrEnum): + FEMALE = 'F' + MALE = 'M' + UNKNOWN = 'U' + XXX = 'XXX' + X0 = 'X0' + XXY = 'XXY' + XYY = 'XYY' + + @property + def imputed_sex_values(self) -> list[str]: + return { + Sex.MALE: ['Male'], + Sex.FEMALE: ['Female'], + Sex.UNKNOWN: ['', 'Unknown'], + }.get(self, [self.name]) + + +class ReferenceGenome(StrEnum): + GRCh37 = 'GRCh37' + GRCh38 = 'GRCh38' + + @property + def v02_value(self) -> str: + return self.value[-2:] + + @property + def hl_reference(self) -> hl.ReferenceGenome: + return hl.get_reference(self.value) + + @property + def standard_contigs(self) -> set[str]: + return { + *self.hl_reference.contigs[:25], + } + + @property + def optional_contigs(self) -> set[str]: + return { + ReferenceGenome.GRCh37: { + 'Y', + 'MT', + }, + ReferenceGenome.GRCh38: { + 'chrY', + 'chrM', + }, + }[self] + + @property + def mito_contig(self) -> str: + return { + ReferenceGenome.GRCh37: 'MT', + ReferenceGenome.GRCh38: 'chrM', + }[self] + + @property + def x_contig(self) -> str: + return 'X' if self == ReferenceGenome.GRCh37 else 'chrX' + + def contig_recoding(self, include_mt: bool = False) -> dict[str, str]: + recode = { + ReferenceGenome.GRCh37: { + f'chr{i}': f'{i}' for i in ([*list(range(1, 23)), 'X', 'Y']) + }, + ReferenceGenome.GRCh38: { + f'{i}': f'chr{i}' for i in ([*list(range(1, 23)), 'X', 'Y']) + }, + }[self] + + if include_mt and self == ReferenceGenome.GRCh38: + recode.update({'MT': 'chrM'}) + if include_mt and self == ReferenceGenome.GRCh37: + recode.update({'chrM': 'MT'}) + + return recode + + +class SampleType(StrEnum): + WES = 'WES' + WGS = 'WGS' diff --git a/loading_pipeline/lib/core/definitions_test.py b/loading_pipeline/lib/core/definitions_test.py new file mode 100644 index 0000000000..b53d88cd18 --- /dev/null +++ b/loading_pipeline/lib/core/definitions_test.py @@ -0,0 +1,144 @@ +import unittest + +from loading_pipeline.lib.core.definitions import ReferenceGenome + + +class TestReferenceGenomeProperties(unittest.TestCase): + def test_v02_value(self): + self.assertEqual(ReferenceGenome.GRCh37.v02_value, '37') + self.assertEqual(ReferenceGenome.GRCh38.v02_value, '38') + + def test_hl_reference(self): + hl_37_reference = ReferenceGenome.GRCh37.hl_reference + self.assertEqual(hl_37_reference.name, 'GRCh37') + + hl_38_reference = ReferenceGenome.GRCh38.hl_reference + self.assertEqual(hl_38_reference.name, 'GRCh38') + + def test_standard_contigs(self): + expected_37_contigs = { + '3', + '12', + '21', + '2', + '1', + '7', + '13', + '8', + '11', + '22', + 'MT', + '14', + 'Y', + '18', + '19', + '20', + '17', + 'X', + '10', + '15', + '16', + '4', + '5', + '9', + '6', + } + self.assertEqual(ReferenceGenome.GRCh37.standard_contigs, expected_37_contigs) + + expected_38_contigs = { + 'chr10', + 'chr11', + 'chr17', + 'chr18', + 'chr9', + 'chr22', + 'chr3', + 'chrY', + 'chr7', + 'chr6', + 'chr13', + 'chr19', + 'chr16', + 'chrX', + 'chr12', + 'chr2', + 'chr21', + 'chr20', + 'chr8', + 'chrM', + 'chr5', + 'chr4', + 'chr14', + 'chr1', + 'chr15', + } + self.assertEqual(ReferenceGenome.GRCh38.standard_contigs, expected_38_contigs) + + def test_optional_contigs(self): + self.assertEqual(ReferenceGenome.GRCh37.optional_contigs, {'Y', 'MT'}) + self.assertEqual(ReferenceGenome.GRCh38.optional_contigs, {'chrY', 'chrM'}) + + def test_contig_recoding(self): + expected_37_recode = { + 'chr1': '1', + 'chr2': '2', + 'chr3': '3', + 'chr4': '4', + 'chr5': '5', + 'chr6': '6', + 'chr7': '7', + 'chr8': '8', + 'chr9': '9', + 'chr10': '10', + 'chr11': '11', + 'chr12': '12', + 'chr13': '13', + 'chr14': '14', + 'chr15': '15', + 'chr16': '16', + 'chr17': '17', + 'chr18': '18', + 'chr19': '19', + 'chr20': '20', + 'chr21': '21', + 'chr22': '22', + 'chrX': 'X', + 'chrY': 'Y', + 'chrM': 'MT', + } + self.assertDictEqual( + ReferenceGenome.GRCh37.contig_recoding(include_mt=True), + expected_37_recode, + ) + + expected_38_recode = { + '1': 'chr1', + '2': 'chr2', + '3': 'chr3', + '4': 'chr4', + '5': 'chr5', + '6': 'chr6', + '7': 'chr7', + '8': 'chr8', + '9': 'chr9', + '10': 'chr10', + '11': 'chr11', + '12': 'chr12', + '13': 'chr13', + '14': 'chr14', + '15': 'chr15', + '16': 'chr16', + '17': 'chr17', + '18': 'chr18', + '19': 'chr19', + '20': 'chr20', + '21': 'chr21', + '22': 'chr22', + 'X': 'chrX', + 'Y': 'chrY', + 'MT': 'chrM', + } + self.assertDictEqual( + ReferenceGenome.GRCh38.contig_recoding(include_mt=True), + expected_38_recode, + ) diff --git a/loading_pipeline/lib/core/environment.py b/loading_pipeline/lib/core/environment.py new file mode 100644 index 0000000000..87d81e46d4 --- /dev/null +++ b/loading_pipeline/lib/core/environment.py @@ -0,0 +1,83 @@ +import os +from dataclasses import dataclass +from typing import Literal + +# NB: using os.environ.get inside the dataclass defaults gives a lint error. +LOCAL_DISK_MOUNT_DIR = os.environ.get('LOCAL_DISK_MOUNT_DIR', '/var/seqr') +HAIL_TMP_DIR = os.environ.get('HAIL_TMP_DIR', '/tmp') # noqa: S108 +PIPELINE_DATA_DIR = os.environ.get( + 'PIPELINE_DATA_DIR', + '/var/seqr/pipeline-data', +) +LOADING_DATASETS_DIR = os.environ.get( + 'LOADING_DATASETS_DIR', + '/var/seqr/seqr-loading-temp', +) +REFERENCE_DATASETS_DIR = os.environ.get( + 'REFERENCE_DATASETS_DIR', + '/var/seqr/seqr-reference-data', +) +VEP_REFERENCE_DATASETS_DIR = os.environ.get( + 'VEP_REFERENCE_DATASETS_DIR', + '/var/seqr/vep-reference-data', +) +CLICKHOUSE_DATABASE = os.environ.get('CLICKHOUSE_DATABASE', 'seqr') +CLICKHOUSE_SERVICE_HOSTNAME = os.environ.get( + 'CLICKHOUSE_SERVICE_HOSTNAME', + 'localhost', +) +CLICKHOUSE_SERVICE_PORT = int(os.environ.get('CLICKHOUSE_SERVICE_PORT', '9000')) +CLICKHOUSE_WRITER_PASSWORD = os.environ.get( + 'CLICKHOUSE_WRITER_PASSWORD', + 'default_password', +) +CLICKHOUSE_WRITER_USER = os.environ.get('CLICKHOUSE_WRITER_USER', 'default') +DEPLOYMENT_TYPE = os.environ.get('DEPLOYMENT_TYPE', 'prod') +GCLOUD_DATAPROC_PRIMARY_WORKERS = int( + os.environ.get('GCLOUD_DATAPROC_PRIMARY_WORKERS', '1'), +) +GCLOUD_DATAPROC_SECONDARY_WORKERS = int( + os.environ.get('GCLOUD_DATAPROC_SECONDARY_WORKERS', '5'), +) +GCLOUD_PROJECT = os.environ.get('GCLOUD_PROJECT') +GCLOUD_REGION = os.environ.get('GCLOUD_REGION') +PIPELINE_RUNNER_APP_VERSION = os.environ.get('PIPELINE_RUNNER_APP_VERSION', 'latest') +SAMPLE_TYPE_VALIDATION_EXCLUDED_PROJECTS = tuple( + x + for x in os.environ.get('SAMPLE_TYPE_VALIDATION_EXCLUDED_PROJECTS', '').split(',') + if x +) +LOADING_QUEUE_LIMIT = int(os.environ.get('LOADING_QUEUE_LIMIT', '10')) +CLICKHOUSE_OPTIMIZE_TABLE_WAIT_S = int( + os.environ.get('CLICKHOUSE_OPTIMIZE_TABLE_WAIT_S', '150'), +) +SLACK_NOTIFICATION_CHANNEL = os.environ.get('SLACK_NOTIFICATION_CHANNEL', '') +SLACK_TOKEN = os.environ.get('SLACK_TOKEN', '') + + +@dataclass +class Env: + CLICKHOUSE_DATABASE: str = CLICKHOUSE_DATABASE + CLICKHOUSE_OPTIMIZE_TABLE_WAIT_S: str = CLICKHOUSE_OPTIMIZE_TABLE_WAIT_S + CLICKHOUSE_SERVICE_HOSTNAME: str = CLICKHOUSE_SERVICE_HOSTNAME + CLICKHOUSE_SERVICE_PORT: int = CLICKHOUSE_SERVICE_PORT + CLICKHOUSE_WRITER_PASSWORD: str = CLICKHOUSE_WRITER_PASSWORD + CLICKHOUSE_WRITER_USER: str = CLICKHOUSE_WRITER_USER + DEPLOYMENT_TYPE: Literal['dev', 'prod'] = DEPLOYMENT_TYPE + GCLOUD_DATAPROC_PRIMARY_WORKERS: int = GCLOUD_DATAPROC_PRIMARY_WORKERS + GCLOUD_DATAPROC_SECONDARY_WORKERS: int = GCLOUD_DATAPROC_SECONDARY_WORKERS + GCLOUD_PROJECT: str | None = GCLOUD_PROJECT + GCLOUD_REGION: str | None = GCLOUD_REGION + HAIL_TMP_DIR: str = HAIL_TMP_DIR + LOCAL_DISK_MOUNT_DIR: str = LOCAL_DISK_MOUNT_DIR + PIPELINE_DATA_DIR: str = PIPELINE_DATA_DIR + LOADING_DATASETS_DIR: str = LOADING_DATASETS_DIR + LOADING_QUEUE_LIMIT: int = LOADING_QUEUE_LIMIT + PIPELINE_RUNNER_APP_VERSION: str = PIPELINE_RUNNER_APP_VERSION + REFERENCE_DATASETS_DIR: str = REFERENCE_DATASETS_DIR + SAMPLE_TYPE_VALIDATION_EXCLUDED_PROJECTS: tuple[str] = ( + SAMPLE_TYPE_VALIDATION_EXCLUDED_PROJECTS + ) + SLACK_NOTIFICATION_CHANNEL: str = SLACK_NOTIFICATION_CHANNEL + SLACK_TOKEN: str = SLACK_TOKEN + VEP_REFERENCE_DATASETS_DIR: str = VEP_REFERENCE_DATASETS_DIR diff --git a/loading_pipeline/lib/core/feature_flag.py b/loading_pipeline/lib/core/feature_flag.py new file mode 100644 index 0000000000..a7c9ea19d5 --- /dev/null +++ b/loading_pipeline/lib/core/feature_flag.py @@ -0,0 +1,14 @@ +import os +from dataclasses import dataclass + +# Feature Flags +CHECK_SEX_AND_RELATEDNESS = os.environ.get('CHECK_SEX_AND_RELATEDNESS') == '1' +EXPECT_TDR_METRICS = os.environ.get('EXPECT_TDR_METRICS') == '1' +RUN_PIPELINE_ON_DATAPROC = os.environ.get('RUN_PIPELINE_ON_DATAPROC') == '1' + + +@dataclass +class FeatureFlag: + CHECK_SEX_AND_RELATEDNESS: bool = CHECK_SEX_AND_RELATEDNESS + EXPECT_TDR_METRICS: bool = EXPECT_TDR_METRICS + RUN_PIPELINE_ON_DATAPROC: bool = RUN_PIPELINE_ON_DATAPROC diff --git a/loading_pipeline/lib/logger.py b/loading_pipeline/lib/logger.py new file mode 100644 index 0000000000..1cb5b94d52 --- /dev/null +++ b/loading_pipeline/lib/logger.py @@ -0,0 +1,46 @@ +import logging.config + +LOG_CONFIG = { + 'version': 1, + 'disable_existing_loggers': False, + 'propagate': True, + 'formatters': { + 'default': { + 'format': '%(asctime)s - %(module)s - %(levelname)s - %(message)s', + 'datefmt': '%Y-%m-%d %H:%M:%S', + }, + }, + 'handlers': { + 'default': { + 'formatter': 'default', + 'class': 'logging.StreamHandler', + }, + }, + 'loggers': { + '': { + 'level': 'INFO', + 'handlers': ['default'], + 'propagate': False, + }, + 'py4j': { + 'level': 'CRITICAL', + }, + 'urllib3': { + 'level': 'CRITICAL', + }, + 'asyncio': { + 'level': 'CRITICAL', + }, + 'clickhouse_driver': {'level': 'CRITICAL'}, + }, +} + +_CONFIGURED = False + + +def get_logger(name: str): + global _CONFIGURED # noqa: PLW0603 + if not _CONFIGURED: + logging.config.dictConfig(LOG_CONFIG) + _CONFIGURED = True + return logging.getLogger(name) diff --git a/loading_pipeline/lib/methods/__init__.py b/loading_pipeline/lib/methods/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/loading_pipeline/lib/methods/relatedness.py b/loading_pipeline/lib/methods/relatedness.py new file mode 100644 index 0000000000..bb1a1e80fe --- /dev/null +++ b/loading_pipeline/lib/methods/relatedness.py @@ -0,0 +1,40 @@ +import hail as hl +from gnomad.sample_qc.pipeline import filter_rows_for_qc + + +def filter_and_ld_prune( + mt: hl.MatrixTable, + gnomad_qc_ht: hl.Table | None, +) -> hl.MatrixTable: + mt = filter_rows_for_qc( + mt, + min_af=0.001, + min_callrate=0.99, + apply_hard_filters=False, + ) + if not gnomad_qc_ht: + mm_pruned = hl.ld_prune(mt.GT, r2=0.1) + return mt.filter_rows(hl.is_defined(mm_pruned[mt.row_key])) + return mt.filter_rows( + hl.is_defined(gnomad_qc_ht[mt.row_key]), + ) + + +def call_relatedness( + mt: hl.MatrixTable, # NB: we've been remapped and subsetted upstream + gnomad_qc_ht: hl.Table | None, +) -> hl.Table: + mt = filter_and_ld_prune(mt, gnomad_qc_ht) + # NB: ibd did not work by default with my pip install of `hail` on an M1 MacOSX. + # I had to build hail by source with the following: + # - brew install lz4 + # - CXXFLAGS='-I/opt/homebrew/include/' HAIL_COMPILE_NATIVES=1 make -C hail install + # Hail issue here: https://discuss.hail.is/t/noclassdeffounderror-could-not-initialize-class-is-hail-methods-ibsffi/2453 + kin_ht = hl.identity_by_descent(mt, maf=mt['info.AF'][0], min=0.10, max=1.0) + kin_ht = kin_ht.key_by('i', 'j') + return kin_ht.select( + ibd0=kin_ht.ibd.Z0, + ibd1=kin_ht.ibd.Z1, + ibd2=kin_ht.ibd.Z2, + pi_hat=kin_ht.ibd.PI_HAT, + ) diff --git a/loading_pipeline/lib/methods/relatedness_test.py b/loading_pipeline/lib/methods/relatedness_test.py new file mode 100644 index 0000000000..e3afb159e2 --- /dev/null +++ b/loading_pipeline/lib/methods/relatedness_test.py @@ -0,0 +1,39 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.methods.relatedness import call_relatedness + +TEST_SEX_AND_RELATEDNESS_CALLSET_MT = ( + 'loading_pipeline/var/test/callsets/sex_and_relatedness_1.mt' +) + + +class RelatednessTest(unittest.TestCase): + def test_call_relatedness(self): + mt = hl.read_matrix_table(TEST_SEX_AND_RELATEDNESS_CALLSET_MT) + ht = call_relatedness( + mt, + None, + ) + self.assertCountEqual( + ht.collect(), + [ + hl.Struct( + i='ROS_006_18Y03226_D1', + j='ROS_007_19Y05939_D1', + ibd0=0.0, + ibd1=1.0, + ibd2=0.0, + pi_hat=0.5, + ), + hl.Struct( + i='ROS_007_19Y05939_D1', + j='ROS_007_19Y05987_D1', + ibd0=0.0, + ibd1=1.0, + ibd2=0.0, + pi_hat=0.5, + ), + ], + ) diff --git a/loading_pipeline/lib/methods/sample_qc.py b/loading_pipeline/lib/methods/sample_qc.py new file mode 100644 index 0000000000..727f3dcfc9 --- /dev/null +++ b/loading_pipeline/lib/methods/sample_qc.py @@ -0,0 +1,154 @@ +import hail as hl +import onnx +from gnomad.sample_qc.ancestry import ( + apply_onnx_classification_model, + assign_population_pcs, + pc_project, +) +from gnomad.sample_qc.filtering import compute_stratified_metrics_filter +from gnomad.sample_qc.pipeline import filter_rows_for_qc +from gnomad.utils.filtering import filter_to_autosomes +from gnomad_qc.v4.sample_qc.assign_ancestry import assign_pop_with_per_pop_probs + +from loading_pipeline.lib.core import SampleType + +GNOMAD_FILTER_MIN_AF = 0.001 +GNOMAD_FILTER_MIN_CALLRATE = 0.99 + +CALLRATE_LOW_THRESHOLD = 0.85 +CONTAMINATION_UPPER_THRESHOLD = 0.05 +WES_COVERAGE_LOW_THRESHOLD = 85 +WGS_CALLRATE_LOW_THRESHOLD = 30 + +NUM_PCS = 20 +GNOMAD_POP_PROBABILITY_CUTOFFS = { + 'afr': 0.93, + 'ami': 0.98, + 'amr': 0.89, + 'asj': 0.94, + 'eas': 0.95, + 'fin': 0.92, + 'mid': 0.55, + 'nfe': 0.75, + 'sas': 0.92, +} +POPULATION_MISSING_LABEL = 'oth' +HAIL_QC_METRICS = [ + 'n_snp', + 'r_ti_tv', + 'r_insertion_deletion', + 'n_insertion', + 'n_deletion', + 'r_het_hom_var', +] + + +def call_sample_qc( + mt: hl.MatrixTable, + tdr_metrics_ht: hl.Table, + pop_pca_loadings_ht: hl.Table, + ancestry_rf_model: onnx.ModelProto, + sample_type: SampleType, +): + mt = mt.annotate_entries( + GT=hl.case() + .when(mt.GT.is_diploid(), hl.call(mt.GT[0], mt.GT[1], phased=False)) + .when(mt.GT.is_haploid(), hl.call(mt.GT[0], phased=False)) + .default(hl.missing(hl.tcall)), + ) + mt = annotate_filtered_callrate(mt) + # Annotates contamination_rate, percent_bases_at_20x, and mean_coverage + mt = mt.annotate_cols(**tdr_metrics_ht[mt.col_key]) + mt = annotate_filter_flags(mt, sample_type) + mt = annotate_qc_gen_anc(mt, pop_pca_loadings_ht, ancestry_rf_model) + return run_hail_sample_qc(mt, sample_type) + + +def annotate_filtered_callrate(mt: hl.MatrixTable) -> hl.MatrixTable: + filtered_mt = filter_rows_for_qc( + mt, + min_af=GNOMAD_FILTER_MIN_AF, + min_callrate=GNOMAD_FILTER_MIN_CALLRATE, + bi_allelic_only=True, + snv_only=True, + apply_hard_filters=False, + min_inbreeding_coeff_threshold=None, + min_hardy_weinberg_threshold=None, + ) + callrate_ht = filtered_mt.select_cols( + filtered_callrate=hl.agg.fraction(hl.is_defined(filtered_mt.GT)), + ).cols() + return mt.annotate_cols(**callrate_ht[mt.col_key]) + + +def annotate_filter_flags( + mt: hl.MatrixTable, + sample_type: SampleType, +) -> hl.MatrixTable: + flags = { + 'callrate': mt.filtered_callrate < CALLRATE_LOW_THRESHOLD, + 'contamination': mt.contamination_rate > CONTAMINATION_UPPER_THRESHOLD, + 'coverage': ( + mt.percent_bases_at_20x < WES_COVERAGE_LOW_THRESHOLD + if sample_type == SampleType.WES + else mt.mean_coverage < WGS_CALLRATE_LOW_THRESHOLD + ), + } + return mt.annotate_cols( + filter_flags=hl.array( + [hl.or_missing(filter_cond, name) for name, filter_cond in flags.items()], + ).filter(hl.is_defined), + ) + + +def annotate_qc_gen_anc( + mt: hl.MatrixTable, + pop_pca_loadings_ht: hl.Table, + ancestry_rf_model: onnx.ModelProto, +) -> hl.MatrixTable: + mt = mt.select_entries('GT') + scores = pc_project(mt, pop_pca_loadings_ht) + scores = scores.annotate(scores=scores.scores[:NUM_PCS], known_pop='Unknown') + pop_pca_ht, _ = assign_population_pcs( + scores, + pc_cols=scores.scores, + output_col='qc_pop', + fit=ancestry_rf_model, + apply_model_func=apply_onnx_classification_model, + ) + pop_pca_ht = pop_pca_ht.key_by('s') + scores = scores.annotate( + **{f'pop_PC{i + 1}': scores.scores[i] for i in range(NUM_PCS)}, + ).drop('scores', 'known_pop') + pop_pca_ht = pop_pca_ht.annotate(**scores[pop_pca_ht.key]) + pop_pca_ht = assign_pop_with_per_pop_probs( + pop_pca_ht, + min_prob_cutoffs=GNOMAD_POP_PROBABILITY_CUTOFFS, + missing_label=POPULATION_MISSING_LABEL, + ) + pop_pca_ht = pop_pca_ht.transmute(qc_gen_anc=pop_pca_ht.pop).drop('qc_pop') + return mt.annotate_cols(**pop_pca_ht[mt.col_key]) + + +def run_hail_sample_qc(mt: hl.MatrixTable, sample_type: SampleType) -> hl.MatrixTable: + mt = filter_to_autosomes(mt) + mt = hl.sample_qc(mt) + mt = mt.annotate_cols( + sample_qc=mt.sample_qc.annotate( + f_inbreeding=hl.agg.inbreeding(mt.GT, mt['info.AF'][0]), + ), + ) + sample_qc_metrics = HAIL_QC_METRICS + if sample_type == SampleType.WGS: + sample_qc_metrics = [*sample_qc_metrics, 'call_rate'] + + strat_ht = mt.cols() + qc_metrics = {metric: strat_ht.sample_qc[metric] for metric in sample_qc_metrics} + strata = {'qc_gen_anc': strat_ht.qc_gen_anc} + + metric_ht = compute_stratified_metrics_filter(strat_ht, qc_metrics, strata) + metric_ht = metric_ht.annotate( + sample_qc=mt.cols()[metric_ht.key].sample_qc, + qc_metrics_filters=hl.array(metric_ht.qc_metrics_filters), + ) + return mt.annotate_cols(**metric_ht[mt.col_key]) diff --git a/loading_pipeline/lib/methods/sex_check.py b/loading_pipeline/lib/methods/sex_check.py new file mode 100644 index 0000000000..1350ba7d85 --- /dev/null +++ b/loading_pipeline/lib/methods/sex_check.py @@ -0,0 +1,50 @@ +import hail as hl + +from loading_pipeline.lib.core import Sex + +AMBIGUOUS_THRESHOLD_PERC: float = 0.01 # Fraction of samples identified as "ambiguous_sex" above which an error will be thrown. +AAF_THRESHOLD: float = 0.05 # Alternate allele frequency threshold for `hl.impute_sex`. +BIALLELIC: int = 2 +XX_FSTAT_THRESHOLD: float = ( + 0.5 # F-stat threshold below which a sample will be called XX +) +XY_FSTAT_THRESHOLD: float = ( + 0.75 # F-stat threshold above which a sample will be called XY. +) + + +def compute_sex_check_ht(mt: hl.MatrixTable) -> hl.Table: + # Filter to SNVs and biallelics + # NB: We should already have filtered biallelics, but just in case. + mt = mt.filter_rows( + (hl.len(mt.alleles) == BIALLELIC) & hl.is_snp(mt.alleles[0], mt.alleles[1]), + ) + mt = mt.filter_cols(hl.agg.all(mt.GT.is_diploid() | hl.is_missing(mt.GT))) + + # Filter to PASS variants only (variants with empty or missing filter set) + mt = mt.filter_rows( + hl.is_missing(mt.filters) | (mt.filters.length() == 0), + keep=True, + ) + impute_sex_ht = hl.impute_sex( + mt.GT, + male_threshold=XY_FSTAT_THRESHOLD, + female_threshold=XX_FSTAT_THRESHOLD, + aaf_threshold=AAF_THRESHOLD, + ) + ht = mt.annotate_cols(**impute_sex_ht[mt.col_key]).cols() + ht = ht.select( + predicted_sex=( + hl.case() + .when(hl.is_missing(ht.is_female), Sex.UNKNOWN.value) + .when(ht.is_female, Sex.FEMALE.value) + .default(Sex.MALE.value) + ), + ) + ambiguous_perc = ht.aggregate( + hl.agg.fraction(ht.predicted_sex == Sex.UNKNOWN.value), + ) + if ambiguous_perc > AMBIGUOUS_THRESHOLD_PERC: + msg = f'{ambiguous_perc:.2%} of samples identified as ambiguous. Please contact the methods team to investigate the callset.' + raise ValueError(msg) + return ht diff --git a/loading_pipeline/lib/methods/sex_check_test.py b/loading_pipeline/lib/methods/sex_check_test.py new file mode 100644 index 0000000000..ed390e86f3 --- /dev/null +++ b/loading_pipeline/lib/methods/sex_check_test.py @@ -0,0 +1,54 @@ +import unittest +from unittest.mock import patch + +import hail as hl + +from loading_pipeline.lib.methods.sex_check import compute_sex_check_ht + +TEST_SEX_AND_RELATEDNESS_CALLSET_MT = ( + 'loading_pipeline/var/test/callsets/sex_and_relatedness_1.mt' +) + + +class SexCheckTest(unittest.TestCase): + def test_compute_sex_check_ht(self): + mt = hl.read_matrix_table(TEST_SEX_AND_RELATEDNESS_CALLSET_MT) + ht = compute_sex_check_ht(mt) + self.assertCountEqual( + ht.collect(), + [ + hl.Struct( + s='ROS_006_18Y03226_D1', + predicted_sex='M', + ), + hl.Struct( + s='ROS_006_18Y03227_D1', + predicted_sex='M', + ), + hl.Struct( + s='ROS_006_18Y03228_D1', + predicted_sex='M', + ), + hl.Struct( + s='ROS_007_19Y05919_D1', + predicted_sex='M', + ), + hl.Struct( + s='ROS_007_19Y05939_D1', + predicted_sex='F', + ), + hl.Struct( + s='ROS_007_19Y05987_D1', + predicted_sex='M', + ), + ], + ) + + def test_compute_sex_check_ht_ambiguous(self): + mt = hl.read_matrix_table(TEST_SEX_AND_RELATEDNESS_CALLSET_MT) + with patch('loading_pipeline.lib.methods.sex_check.XY_FSTAT_THRESHOLD', 0.95): + self.assertRaises( + ValueError, + compute_sex_check_ht, + mt, + ) diff --git a/loading_pipeline/lib/misc/__init__.py b/loading_pipeline/lib/misc/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/loading_pipeline/lib/misc/callsets.py b/loading_pipeline/lib/misc/callsets.py new file mode 100644 index 0000000000..41357e5ae2 --- /dev/null +++ b/loading_pipeline/lib/misc/callsets.py @@ -0,0 +1,129 @@ +import functools + +import hail as hl +import hailtop.fs as hfs + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome +from loading_pipeline.lib.paths import ( + remapped_and_subsetted_callset_path, + variant_annotations_table_path, +) + + +def get_callset_ht( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + callset_path: str, + project_guids: list[str], +): + callset_hts = [ + hl.read_matrix_table( + remapped_and_subsetted_callset_path( + reference_genome, + dataset_type, + callset_path, + project_guid, + ), + ).rows() + for project_guid in project_guids + ] + callset_ht = functools.reduce( + (lambda ht1, ht2: ht1.union(ht2)), + callset_hts, + ) + return callset_ht.distinct() + + +def union_callset_mts(callset_mts): + """Merge multiple callset matrix tables into a single matrix table. + + Combines callset matrix tables from multiple projects by unioning the column + dimension (samples/individuals). Uses an outer join on rows (variants) to + preserve all unique variants across all callsets, with missing genotypes + filled in as appropriate. Row fields are deduplicated by keeping only the + left table's row metadata. + + Args: + callset_mts: A sequence of Hail matrix tables to merge. + + Returns: + A single matrix table containing all samples and variants from the input + callsets, with row and entry fields merged. + """ + return functools.reduce( + ( + lambda mt1, mt2: mt1.union_cols( + mt2, + row_join_type='outer', + drop_right_row_fields=True, + ) + ), + callset_mts, + ) + + +def get_callset_mt( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + callset_path: str, + project_guids: list[str], +): + callset_mts = [ + hl.read_matrix_table( + remapped_and_subsetted_callset_path( + reference_genome, + dataset_type, + callset_path, + project_guid, + ), + ) + for project_guid in project_guids + ] + callset_mt = union_callset_mts(callset_mts) + return callset_mt.distinct_by_row() + + +def get_additional_row_fields( + mt: hl.MatrixTable, + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + skip_check_sex_and_relatedness: bool, +): + return { + **( + {'info.AF': hl.tarray(hl.tfloat64)} + if not skip_check_sex_and_relatedness + and dataset_type.check_sex_and_relatedness + else {} + ), + # this field is never required, the pipeline + # will run smoothly even in its absence, but + # will trigger special handling if it is present. + **( + {'info.CALIBRATION_SENSITIVITY': hl.tarray(hl.tstr)} + if hasattr(mt, 'info') and hasattr(mt.info, 'CALIBRATION_SENSITIVITY') + else {} + ), + **( + {'info.SEQR_INTERNAL_TRUTH_VID': hl.tstr} + if dataset_type.re_key_by_seqr_internal_truth_vid + and hfs.exists( + variant_annotations_table_path( + reference_genome, + dataset_type, + ), + ) + and hl.eval( + hl.len( + hl.read_table( + variant_annotations_table_path( + reference_genome, + dataset_type, + ), + ).globals.updates, + ) + > 0, + ) + else {} + ), + } diff --git a/loading_pipeline/lib/misc/callsets_test.py b/loading_pipeline/lib/misc/callsets_test.py new file mode 100644 index 0000000000..5db2d4eb36 --- /dev/null +++ b/loading_pipeline/lib/misc/callsets_test.py @@ -0,0 +1,87 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.misc.callsets import union_callset_mts + + +class CallsetsTest(unittest.TestCase): + def test_union_callset_mts(self) -> None: + mt1 = ( + hl.MatrixTable.from_parts( + rows={ + 'id': [ + 0, + 1, + ], + 'row_field': [ + 1, + 2, + ], + }, + cols={'s': ['sample_1']}, + entries={ + 'GT': [[hl.Call([0, 0])], [hl.Call([0, 0])]], + }, + ) + .key_rows_by('id') + .key_cols_by('s') + .drop('row_idx', 'col_idx') + ) + mt2 = ( + hl.MatrixTable.from_parts( + rows={ + 'id': [ + 0, + 2, + ], + 'row_field': [ + 2, + 3, + ], + 'second_row_field': [ + 4, + 5, + ], + }, + cols={'s': ['sample_2']}, + entries={ + 'GT': [[hl.Call([0, 0])], [hl.Call([0, 1])]], + }, + ) + .key_rows_by('id') + .key_cols_by('s') + .drop('row_idx', 'col_idx') + ) + mt = union_callset_mts([mt1, mt2]) + self.assertEqual( + mt.entries().collect(), + [ + hl.Struct( + id=0, + row_field=1, + s='sample_1', + GT=hl.Call(alleles=[0, 0], phased=False), + ), + hl.Struct( + id=0, + row_field=1, + s='sample_2', + GT=hl.Call(alleles=[0, 0], phased=False), + ), + hl.Struct( + id=1, + row_field=2, + s='sample_1', + GT=hl.Call(alleles=[0, 0], phased=False), + ), + hl.Struct(id=1, row_field=2, s='sample_2', GT=None), + hl.Struct(id=2, row_field=None, s='sample_1', GT=None), + hl.Struct( + id=2, + row_field=None, + s='sample_2', + GT=hl.Call(alleles=[0, 1], phased=False), + ), + ], + ) diff --git a/loading_pipeline/lib/misc/clickhouse.py b/loading_pipeline/lib/misc/clickhouse.py new file mode 100644 index 0000000000..977b4fe1e0 --- /dev/null +++ b/loading_pipeline/lib/misc/clickhouse.py @@ -0,0 +1,1247 @@ +import ast +import functools +import hashlib +import math +import os +import time +from collections.abc import Callable +from dataclasses import dataclass +from enum import StrEnum +from string import Template + +from clickhouse_driver import Client + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome +from loading_pipeline.lib.core.environment import Env +from loading_pipeline.lib.logger import get_logger +from loading_pipeline.lib.misc.retry import retry +from loading_pipeline.lib.paths import ( + new_entries_parquet_path, + new_variant_details_parquet_path, + new_variants_parquet_path, +) + +logger = get_logger(__name__) + +GCS_NAMED_COLLECTION = 'pipeline_data_access' +GOOGLE_XML_API_PATH = 'https://storage.googleapis.com/' +OPTIMIZE_TABLE_TIMEOUT_S = 99999 +WAIT_VIEW_TIMEOUT_S = 900 +REDACTED = 'REDACTED' +STAGING_CLICKHOUSE_DATABASE = 'staging' + + +class ClickHouseTable(StrEnum): + KEY_LOOKUP = 'key_lookup' + VARIANT_DETAILS = 'variants/details' + VARIANTS_DISK = 'variants_disk' + VARIANTS_MEMORY = 'variants_memory' + ENTRIES = 'entries' + PROJECT_GT_STATS = 'project_gt_stats' + GT_STATS = 'gt_stats' + + @property + def src_path_fn(self) -> Callable: + return { + ClickHouseTable.VARIANTS_DISK: new_variants_parquet_path, + ClickHouseTable.VARIANTS_MEMORY: new_variants_parquet_path, + ClickHouseTable.KEY_LOOKUP: ( + lambda *args: new_variant_details_parquet_path(*args) + if args[1].should_write_new_variant_details + else new_variants_parquet_path(*args) + ), + ClickHouseTable.VARIANT_DETAILS: new_variant_details_parquet_path, + ClickHouseTable.ENTRIES: new_entries_parquet_path, + }[self] + + @property + def key_field(self): + return 'variantId' if self == ClickHouseTable.KEY_LOOKUP else 'key' + + @property + def join_condition(self): + return ( + 'assumeNotNull(src.variantId) = dst.variantId' + if self == ClickHouseTable.KEY_LOOKUP + else 'assumeNotNull(toUInt32(src.key)) = dst.key' + ) + + @property + def select_fields(self) -> str: + return { + ClickHouseTable.KEY_LOOKUP: 'variantId, key', + }.get(self, '*') + + @property + def insert(self) -> Callable: + return { + # Note that VARIANTS_DETAILS is not included here because + # of the special logic to ensure writes are made to both tables. + ClickHouseTable.VARIANTS_MEMORY: direct_insert_annotations, + ClickHouseTable.ENTRIES: atomic_insert_entries, + ClickHouseTable.KEY_LOOKUP: functools.partial( + direct_insert_all_keys, + clickhouse_table=self, + ), + ClickHouseTable.VARIANT_DETAILS: functools.partial( + direct_insert_all_keys, + clickhouse_table=self, + ), + }[self] + + @classmethod + def for_dataset_type(cls, dataset_type: DatasetType) -> list['ClickHouseTable']: + tables = [ + ClickHouseTable.VARIANTS_MEMORY, + ClickHouseTable.KEY_LOOKUP, + ] + if dataset_type.should_write_new_variant_details: + tables = [ + *tables, + ClickHouseTable.VARIANT_DETAILS, + ] + return [ + *tables, + ClickHouseTable.ENTRIES, + ] + + @classmethod + def for_dataset_type_disk_backed_variants_tables( + cls, + _dataset_type: DatasetType, + ) -> list['ClickHouseTable']: + return [ + ClickHouseTable.VARIANTS_DISK, + ] + + @classmethod + def for_dataset_type_atomic_entries_update( + cls, + dataset_type: DatasetType, + ) -> list['ClickHouseTable']: + return [ + *cls.for_dataset_type_atomic_entries_update_project_partitioned( + dataset_type, + ), + *cls.for_dataset_type_atomic_entries_update_unpartitioned(dataset_type), + ] + + @classmethod + def for_dataset_type_atomic_entries_update_project_partitioned( + cls, + dataset_type: DatasetType, + ) -> list['ClickHouseTable']: + if dataset_type == DatasetType.GCNV: + return [ClickHouseTable.ENTRIES] + return [ + ClickHouseTable.ENTRIES, + ClickHouseTable.PROJECT_GT_STATS, + ] + + @classmethod + def for_dataset_type_atomic_entries_update_unpartitioned( + cls, + dataset_type: DatasetType, + ) -> list['ClickHouseTable']: + if dataset_type == DatasetType.GCNV: + return [] + return [ClickHouseTable.GT_STATS] + + +class ClickHouseDictionary(StrEnum): + GT_STATS_DICT = 'gt_stats_dict' + + @classmethod + def for_dataset_type( + cls, + dataset_type: DatasetType, + ) -> list['ClickHouseDictionary']: + if dataset_type == DatasetType.GCNV: + return [] + return list(cls) + + +class ClickHouseMaterializedView(StrEnum): + ENTRIES_TO_PROJECT_GT_STATS_MV = 'entries_to_project_gt_stats_mv' + PROJECT_GT_STATS_TO_GT_STATS_MV = 'project_gt_stats_to_gt_stats_mv' + + @classmethod + def for_dataset_type_atomic_entries_update( + cls, + dataset_type: DatasetType, + ) -> list['ClickHouseMaterializedView']: + if dataset_type == DatasetType.GCNV: + return [] + return [ + ClickHouseMaterializedView.ENTRIES_TO_PROJECT_GT_STATS_MV, + ClickHouseMaterializedView.PROJECT_GT_STATS_TO_GT_STATS_MV, + ] + + @classmethod + def for_dataset_type_atomic_entries_update_refreshable( + cls, + dataset_type: DatasetType, + ) -> list['ClickHouseMaterializedView']: + if dataset_type == DatasetType.GCNV: + return [] + return [ClickHouseMaterializedView.PROJECT_GT_STATS_TO_GT_STATS_MV] + + +ClickHouseEntity = ClickHouseDictionary | ClickHouseTable | ClickHouseMaterializedView + + +@dataclass +class TableNameBuilder: + reference_genome: ReferenceGenome + dataset_type: DatasetType + run_id: str + + @property + def run_id_hash(self): + # Note: encountered length issues with the default + # run ids generated by the pipeline. ClickHouse performed + # well with staging Tables with the long run ids, but failed + # to recognized staging Dictionaries. + sha256 = hashlib.sha256() + sha256.update(self.run_id.encode()) + return sha256.hexdigest()[:8] + + @property + def dst_prefix(self): + return f'{Env.CLICKHOUSE_DATABASE}.`{self.reference_genome.value}/{self.dataset_type.value}' + + def dst_table(self, clickhouse_entity: ClickHouseEntity): + return f'{self.dst_prefix}/{clickhouse_entity.value}`' + + @property + def staging_dst_prefix(self): + return f'{STAGING_CLICKHOUSE_DATABASE}.`{self.run_id_hash}/{self.reference_genome.value}/{self.dataset_type.value}' + + def staging_dst_table(self, clickhouse_table: ClickHouseTable): + return f'{self.staging_dst_prefix}/{clickhouse_table.value}`' + + def src_table(self, clickhouse_table: ClickHouseTable): + path = os.path.join( + clickhouse_table.src_path_fn( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + '*.parquet', + ) + if path.startswith('gs://'): + return f"gcs({GCS_NAMED_COLLECTION}, url='{path.replace('gs://', GOOGLE_XML_API_PATH)}')" + return f"file('{path}', 'Parquet')" + + +class ClickhouseReferenceDataset(StrEnum): + ABSPLICE2 = 'absplice2' + CLINVAR = 'clinvar' + DBNSFP = 'dbnsfp' + EIGEN = 'eigen' + GNOMAD_EXOMES = 'gnomad_exomes' + GNOMAD_GENOMES = 'gnomad_genomes' + GNOMAD_MITO = 'gnomad_mito' + GNOMAD_MITO_HETEROPLASMY = 'gnomad_mito_heteroplasmy' + GNOMAD_NON_CODING_CONSTRAINT = 'gnomad_non_coding_constraint' + HELIX_MITO = 'helix_mito' + HELIX_MITO_HETEROPLASMY = 'helix_mito_heteroplasmy' + HGMD = 'hgmd' + HMTVAR = 'hmtvar' + LOCAL_CONSTRAINT_MITO = 'local_constraint_mito' + MITIMPACT = 'mitimpact' + MITOMAP = 'mitomap' + PEXT = 'pext' + PROMOTER_AI = 'promoterAI' + SCREEN = 'screen' + SPLICE_AI = 'splice_ai' + TOPMED = 'topmed' + + @property + def all_variants_mv_timeout(self): + return { + ClickhouseReferenceDataset.DBNSFP: WAIT_VIEW_TIMEOUT_S * 3, + ClickhouseReferenceDataset.SPLICE_AI: WAIT_VIEW_TIMEOUT_S * 10, + }.get(self, WAIT_VIEW_TIMEOUT_S) + + @property + def fully_refreshable(self): + return self != ClickhouseReferenceDataset.CLINVAR + + @property + def has_seqr_variants(self): + return self not in { + ClickhouseReferenceDataset.GNOMAD_NON_CODING_CONSTRAINT, + ClickhouseReferenceDataset.SCREEN, + } + + @classmethod + def for_reference_genome_dataset_type( + cls, + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + ): + if dataset_type in {DatasetType.SV, DatasetType.GCNV}: + return [] + return { + (ReferenceGenome.GRCh38, DatasetType.MITO): [ + ClickhouseReferenceDataset.CLINVAR, + ClickhouseReferenceDataset.DBNSFP, + ClickhouseReferenceDataset.GNOMAD_MITO, + ClickhouseReferenceDataset.GNOMAD_MITO_HETEROPLASMY, + ClickhouseReferenceDataset.HELIX_MITO, + ClickhouseReferenceDataset.HELIX_MITO_HETEROPLASMY, + ClickhouseReferenceDataset.HMTVAR, + ClickhouseReferenceDataset.LOCAL_CONSTRAINT_MITO, + ClickhouseReferenceDataset.MITIMPACT, + ClickhouseReferenceDataset.MITOMAP, + ClickhouseReferenceDataset.PEXT, + ], + (ReferenceGenome.GRCh37, DatasetType.SNV_INDEL): [ + ClickhouseReferenceDataset.CLINVAR, + ClickhouseReferenceDataset.DBNSFP, + ClickhouseReferenceDataset.EIGEN, + ClickhouseReferenceDataset.GNOMAD_EXOMES, + ClickhouseReferenceDataset.GNOMAD_GENOMES, + ClickhouseReferenceDataset.HGMD, + ClickhouseReferenceDataset.SPLICE_AI, + ClickhouseReferenceDataset.TOPMED, + ], + (ReferenceGenome.GRCh38, DatasetType.SNV_INDEL): [ + ClickhouseReferenceDataset.ABSPLICE2, + ClickhouseReferenceDataset.CLINVAR, + ClickhouseReferenceDataset.DBNSFP, + ClickhouseReferenceDataset.EIGEN, + ClickhouseReferenceDataset.GNOMAD_EXOMES, + ClickhouseReferenceDataset.GNOMAD_GENOMES, + ClickhouseReferenceDataset.GNOMAD_NON_CODING_CONSTRAINT, + ClickhouseReferenceDataset.HGMD, + ClickhouseReferenceDataset.PEXT, + ClickhouseReferenceDataset.PROMOTER_AI, + ClickhouseReferenceDataset.SCREEN, + ClickhouseReferenceDataset.SPLICE_AI, + ClickhouseReferenceDataset.TOPMED, + ], + }[(reference_genome, dataset_type)] + + @property + def search_is_join_table(self): + return self in { + ClickhouseReferenceDataset.CLINVAR, + ClickhouseReferenceDataset.HGMD, + } + + def all_variants_path(self, table_name_builder: TableNameBuilder) -> str: + return ( + f'{table_name_builder.dst_prefix}/reference_data/{self.value}/all_variants`' + ) + + def seqr_variants_path(self, table_name_builder: TableNameBuilder) -> str: + return f'{table_name_builder.dst_prefix}/reference_data/{self.value}/seqr_variants`' + + def search_path(self, table_name_builder: TableNameBuilder) -> str: + return f'{table_name_builder.dst_prefix}/reference_data/{self.value}`' + + def all_variants_mv( + self, + table_name_builder: TableNameBuilder, + ) -> str: + return f'{table_name_builder.dst_prefix}/reference_data/{self.value}/all_variants_mv`' + + def all_variants_to_seqr_variants_mv( + self, + table_name_builder: TableNameBuilder, + ) -> str: + return f'{table_name_builder.dst_prefix}/reference_data/{self.value}/all_variants_to_seqr_variants_mv`' + + def seqr_variants_to_search_mv_path( + self, + table_name_builder: TableNameBuilder, + ) -> str: + return f'{table_name_builder.dst_prefix}/reference_data/{self.value}/seqr_variants_to_search_mv`' + + def refresh_search( + self, + table_name_builder: TableNameBuilder, + ) -> str: + if self.search_is_join_table: + logged_query( + f""" + SYSTEM START VIEW {self.seqr_variants_to_search_mv_path(table_name_builder)} + """, + ) + logged_query( + f""" + SYSTEM REFRESH VIEW {self.seqr_variants_to_search_mv_path(table_name_builder)} + """, + ) + logged_query( + f""" + SYSTEM WAIT VIEW {self.seqr_variants_to_search_mv_path(table_name_builder)} + """, + timeout=WAIT_VIEW_TIMEOUT_S, + ) + else: + logged_query( + f""" + SYSTEM RELOAD DICTIONARY {self.search_path(table_name_builder)} + """, + ) + + def insert_into_seqr_variants_and_refresh_search( + self, + table_name_builder: TableNameBuilder, + ): + if not self.has_seqr_variants: + return + exists_seqr_variants = logged_query( + f'EXISTS TABLE {self.seqr_variants_path(table_name_builder)}', + )[0][0] + if not exists_seqr_variants: + return + drop_staging_db() + logged_query( + f""" + CREATE DATABASE {STAGING_CLICKHOUSE_DATABASE} + """, + ) + logged_query( + f""" + CREATE TABLE {table_name_builder.staging_dst_prefix}/_tmp_loadable_variantIds` ENGINE = Set AS ( + SELECT {ClickHouseTable.KEY_LOOKUP.key_field} + FROM {table_name_builder.src_table(ClickHouseTable.KEY_LOOKUP)} + ) + """, + ) + logged_query( + f""" + INSERT INTO {self.seqr_variants_path(table_name_builder)} + SELECT + DISTINCT ON (key) + dst.key, + COLUMNS('.*') EXCEPT(version, variantId, key) + FROM {self.all_variants_path(table_name_builder)} src + INNER JOIN {table_name_builder.dst_table(ClickHouseTable.KEY_LOOKUP)} dst + ON {ClickHouseTable.KEY_LOOKUP.join_condition} + WHERE src.variantId IN {table_name_builder.staging_dst_prefix}/_tmp_loadable_variantIds` + """, + ) + self.refresh_search(table_name_builder) + + def download_and_fully_refresh( + self, + table_name_builder: TableNameBuilder, + ): + logged_query( + f""" + SYSTEM START VIEW {self.all_variants_mv(table_name_builder)} + """, + ) + logged_query( + f""" + SYSTEM REFRESH VIEW {self.all_variants_mv(table_name_builder)} + """, + ) + logged_query( + f""" + SYSTEM WAIT VIEW {self.all_variants_mv(table_name_builder)} + """, + timeout=self.all_variants_mv_timeout, + ) + if self.has_seqr_variants: + logged_query( + f""" + SYSTEM START VIEW {self.all_variants_to_seqr_variants_mv(table_name_builder)} + """, + ) + logged_query( + f""" + SYSTEM REFRESH VIEW {self.all_variants_to_seqr_variants_mv(table_name_builder)} + """, + ) + logged_query( + f""" + SYSTEM WAIT VIEW {self.all_variants_to_seqr_variants_mv(table_name_builder)} + """, + timeout=self.all_variants_mv_timeout, + ) + self.refresh_search(table_name_builder) + + +def logged_query(query, params=None, timeout: int | None = None): + client = get_clickhouse_client(timeout) + sanitized_query = query + if Env.CLICKHOUSE_WRITER_PASSWORD: + sanitized_query = sanitized_query.replace( + Env.CLICKHOUSE_WRITER_PASSWORD, + REDACTED, + ) + logger.info(f'Executing query: {sanitized_query} | Params: {params}') + return client.execute(query, params) + + +def drop_staging_db(): + logged_query(f'DROP DATABASE IF EXISTS {STAGING_CLICKHOUSE_DATABASE};') + + +def create_staging_tables( + table_name_builder: TableNameBuilder, + clickhouse_tables: list[ClickHouseTable], +) -> None: + logged_query( + f""" + CREATE DATABASE {STAGING_CLICKHOUSE_DATABASE} + """, + ) + for clickhouse_table in clickhouse_tables: + logged_query( + f""" + CREATE + TABLE {table_name_builder.staging_dst_table(clickhouse_table)} + AS {table_name_builder.dst_table(clickhouse_table)} + """, + ) + + +def get_create_mv_statements( + table_name_builder: TableNameBuilder, + clickhouse_mv: ClickHouseMaterializedView, +) -> tuple[str, str]: + return logged_query( + """ + SELECT create_table_query, as_select FROM system.tables + WHERE + engine = 'MaterializedView' + AND database = %(database)s + AND name = %(name)s + """, + { + 'database': Env.CLICKHOUSE_DATABASE, + 'name': table_name_builder.dst_table(clickhouse_mv) + .split('.')[1] + .replace('`', ''), + }, + )[0] + + +def normalize_partition(partition: str) -> tuple: + """ + Ensure a ClickHouse partition expression is always returned as a tuple. + 'project_d' -> ('project_d',) + "('project_d', 0)" -> ('project_d', 0) + """ + if not isinstance(partition, str): + msg = f'Unsupported partition type: {type(partition)}' + raise TypeError(msg) + partition = partition.strip() + if partition.startswith('(') and partition.endswith(')'): + return ast.literal_eval(partition) + return (partition,) + + +def get_partitions_for_projects( + table_name_builder: TableNameBuilder, + clickhouse_table: ClickHouseTable, + project_guids: list[str], + staging=False, +): + rows = logged_query( + """ + SELECT DISTINCT partition + FROM system.parts + WHERE + database = %(database)s + AND table = %(table)s + AND multiSearchAny(partition, %(project_guids)s) + """, + { + 'database': STAGING_CLICKHOUSE_DATABASE + if staging + else Env.CLICKHOUSE_DATABASE, + 'table': ( + table_name_builder.staging_dst_table(clickhouse_table) + if staging + else table_name_builder.dst_table(clickhouse_table) + ) + .split('.')[1] + .replace('`', ''), + 'project_guids': project_guids, + }, + ) + return [normalize_partition(row[0]) for row in rows] + + +def create_staging_materialized_views( + table_name_builder: TableNameBuilder, + clickhouse_mvs: list[ClickHouseMaterializedView], +): + for clickhouse_mv in clickhouse_mvs: + create_table_statement = get_create_mv_statements( + table_name_builder, + clickhouse_mv, + )[0] + create_table_statement = create_table_statement.replace( + table_name_builder.dst_prefix, + table_name_builder.staging_dst_prefix, + ) + logged_query(create_table_statement) + + +# Note that this function is NOT idemptotent. Clickhouse permits +# attaching the same partition to a table multiple times. +def stage_existing_project_partitions( + table_name_builder: TableNameBuilder, + project_guids: list[str], + clickhouse_tables: list[ClickHouseTable], +): + for clickhouse_table in clickhouse_tables: + # Very important piece here: + # ALL projects in the project_gt_stats table are staged, allowing us to rebuild + # a production-quality gt_stats materialized view in the staging environment. + if clickhouse_table == ClickHouseTable.PROJECT_GT_STATS: + logged_query( + f""" + ALTER TABLE {table_name_builder.staging_dst_table(clickhouse_table)} + ATTACH PARTITION ALL FROM {table_name_builder.dst_table(clickhouse_table)} + """, + ) + continue + for partition in get_partitions_for_projects( + table_name_builder, + clickhouse_table, + project_guids, + ): + # Note that ClickHouse successfully handles the case where the project + # does not already exist in the dst table. We simply attach an empty partition! + logged_query( + f""" + ALTER TABLE {table_name_builder.staging_dst_table(clickhouse_table)} + ATTACH PARTITION %(partition)s FROM {table_name_builder.dst_table(clickhouse_table)} + """, + {'partition': partition}, + ) + + +def delete_existing_families_from_staging_entries( + table_name_builder: TableNameBuilder, + family_guids: list[str], +) -> None: + logged_query( + f""" + INSERT INTO {table_name_builder.staging_dst_table(ClickHouseTable.ENTRIES)} + SELECT COLUMNS('.*') EXCEPT(sign, n_partitions, partition_id), -1 as sign + FROM {table_name_builder.staging_dst_table(ClickHouseTable.ENTRIES)} + WHERE family_guid in %(family_guids)s + """, + {'family_guids': family_guids}, + ) + + +def insert_new_entries( + table_name_builder: TableNameBuilder, +) -> None: + dst_cols = [ + r[0] + for r in logged_query( + f'DESCRIBE TABLE {table_name_builder.staging_dst_table(ClickHouseTable.ENTRIES)}', + ) + ] + src_cols = [ + r[0] + for r in logged_query( + f'DESCRIBE TABLE {table_name_builder.src_table(ClickHouseTable.ENTRIES)}', + ) + ] + common, overrides = [c for c in dst_cols if c in src_cols], {} + if 'geneId_ids' in dst_cols and 'geneIds' in src_cols: + common = [c for c in common if c not in ('geneId_ids', 'geneIds')] + common.append('geneId_ids') + overrides['geneId_ids'] = f""" + arrayFilter( + x -> x IS NOT NULL, + arrayMap( + g -> dictGetOrNull( + {Env.CLICKHOUSE_DATABASE}.`seqrdb_gene_ids`, + 'seqrdb_id', + g + ), + geneIds + ) + ) + """ + + if ( + 'is_gnomad_gt_5_percent' in dst_cols + and 'is_gnomad_gt_5_percent' not in src_cols + ): + common.append('is_gnomad_gt_5_percent') + overrides['is_gnomad_gt_5_percent'] = f""" + dictGetOrDefault({ClickhouseReferenceDataset.GNOMAD_GENOMES.search_path(table_name_builder)}, 'filter_af', key, 0) > 0.05 + """ + + dst_list = ', '.join(common) + src_list = ', '.join([overrides.get(c, c) for c in common]) + logged_query( + f""" + INSERT INTO {table_name_builder.staging_dst_table(ClickHouseTable.ENTRIES)} ({dst_list}) + SELECT {src_list} + FROM {table_name_builder.src_table(ClickHouseTable.ENTRIES)} + """, + ) + + +@retry(tries=2) +def optimize_entries( + table_name_builder: TableNameBuilder, + project_guids: list[str], +) -> None: + max_attempts = 10 + for attempt in range(max_attempts): + decrs_exist = logged_query( + f""" + SELECT EXISTS ( + SELECT 1 + FROM {table_name_builder.staging_dst_table(ClickHouseTable.ENTRIES)} + WHERE sign = -1 + ); + """, + )[0][0] + + merges_running = logged_query( + """ + SELECT EXISTS ( + SELECT 1 + FROM system.merges + WHERE database = %(database)s + AND table = %(table)s + ); + """, + { + 'database': STAGING_CLICKHOUSE_DATABASE, + 'table': table_name_builder.staging_dst_table(ClickHouseTable.ENTRIES) + .split('.')[1] + .replace('`', ''), + }, + )[0][0] + + if not decrs_exist: + return + + if merges_running: + logger.info( + 'Decrs exist and merges are running, so waiting (attempt %d/%d)', + attempt + 1, + max_attempts, + ) + else: + logger.info( + 'Decrs exist and no merges are running, so optimizing (attempt %d/%d)', + attempt + 1, + max_attempts, + ) + + partitions = get_partitions_for_projects( + table_name_builder, + ClickHouseTable.ENTRIES, + project_guids, + staging=True, + ) + table_name = table_name_builder.staging_dst_table( + ClickHouseTable.ENTRIES, + ) + optimize_statements = [ + f'OPTIMIZE TABLE {table_name} PARTITION {partition} FINAL' + for partition in partitions + ] + parallel_optimize_sql = '\nPARALLEL WITH\n'.join(optimize_statements) + + logged_query( + parallel_optimize_sql, + timeout=OPTIMIZE_TABLE_TIMEOUT_S, + ) + + time.sleep(Env.CLICKHOUSE_OPTIMIZE_TABLE_WAIT_S) + msg = f'Entries table still contains decrement rows after {max_attempts} attempts.' + raise TimeoutError(msg) + + +@retry(tries=2) +def refresh_materialized_views( + table_name_builder, + materialized_views: list[ClickHouseMaterializedView], + staging=False, +): + for materialized_view in materialized_views: + logged_query( + f""" + SYSTEM START VIEW {table_name_builder.staging_dst_table(materialized_view) if staging else table_name_builder.dst_table(materialized_view)} + """, + ) + logged_query( + f""" + SYSTEM REFRESH VIEW {table_name_builder.staging_dst_table(materialized_view) if staging else table_name_builder.dst_table(materialized_view)} + """, + ) + logged_query( + f""" + SYSTEM WAIT VIEW {table_name_builder.staging_dst_table(materialized_view) if staging else table_name_builder.dst_table(materialized_view)} + """, + timeout=WAIT_VIEW_TIMEOUT_S, + ) + + +def validate_family_guid_counts( + table_name_builder: TableNameBuilder, + project_guids: list[str], + family_guids: list[str], +) -> None: + query = Template( + """ + SELECT family_guid, COUNT(*) + FROM $table_name + WHERE project_guid in %(project_guids)s + AND family_guid in %(family_guids)s + GROUP BY 1 + """, + ) + src_family_counts = dict( + logged_query( + query.substitute( + table_name=table_name_builder.src_table( + ClickHouseTable.ENTRIES, + ), + ), + {'family_guids': family_guids, 'project_guids': project_guids}, + ), + ) + dst_family_counts = dict( + logged_query( + query.substitute( + table_name=table_name_builder.staging_dst_table( + ClickHouseTable.ENTRIES, + ), + ), + {'family_guids': family_guids, 'project_guids': project_guids}, + ), + ) + if src_family_counts != dst_family_counts: + msg = 'Loaded Row counts are different than expected.' + raise ValueError(msg) + + +@retry(tries=2) +def reload_dictionaries( + table_name_builder: TableNameBuilder, + dictionaries: list[ClickHouseDictionary], +): + for dictionary in dictionaries: + logged_query( + f""" + SYSTEM RELOAD DICTIONARY {table_name_builder.dst_table(dictionary)} + """, + ) + + +def replace_project_partitions( + table_name_builder: TableNameBuilder, + clickhouse_tables: list[ClickHouseTable], + project_guids: list[str], +) -> None: + for clickhouse_table in clickhouse_tables: + for partition in get_partitions_for_projects( + table_name_builder, + clickhouse_table, + project_guids, + staging=True, + ): + logged_query( + f""" + ALTER TABLE {table_name_builder.dst_table(clickhouse_table)} + REPLACE PARTITION %(partition)s FROM {table_name_builder.staging_dst_table(clickhouse_table)} + """, + {'partition': partition}, + ) + + +# Note this is NOT idempotent, as running the swap twice will +# result in the tables not being swapped. +def exchange_tables( + table_name_builder, + clickhouse_tables: list[ClickHouseTable], +) -> None: + for clickhouse_table in clickhouse_tables: + logged_query( + f""" + EXCHANGE TABLES {table_name_builder.staging_dst_table(clickhouse_table)} AND {table_name_builder.dst_table(clickhouse_table)} + """, + ) + + +def direct_insert_annotations( + table_name_builder: TableNameBuilder, + **_, +) -> None: + dst_table = table_name_builder.dst_table(ClickHouseTable.VARIANTS_MEMORY) + src_table = table_name_builder.src_table(ClickHouseTable.VARIANTS_MEMORY) + drop_staging_db() + logged_query( + f""" + CREATE DATABASE {STAGING_CLICKHOUSE_DATABASE} + """, + ) + # NB: Unfortunately there's a bug(?) or inaccuracy if this is attempted without an intermediate + # temporary table, likely due to writing to a table and joining against it at the same time. + logged_query( + f""" + CREATE TABLE {table_name_builder.staging_dst_prefix}/_tmp_loadable_keys` ENGINE = Set AS ( + SELECT {ClickHouseTable.VARIANTS_MEMORY.key_field} + FROM {src_table} src + LEFT ANTI JOIN {dst_table} dst + ON {ClickHouseTable.VARIANTS_MEMORY.join_condition} + ) + """, + ) + for ( + clickhouse_table + ) in ClickHouseTable.for_dataset_type_disk_backed_variants_tables( + table_name_builder.dataset_type, + ): + disk_backed_dst_table = table_name_builder.dst_table(clickhouse_table) + disk_backed_src_table = table_name_builder.src_table(clickhouse_table) + logged_query( + f""" + INSERT INTO {disk_backed_dst_table} + SELECT {clickhouse_table.select_fields} + FROM {disk_backed_src_table} WHERE {clickhouse_table.key_field} IN {table_name_builder.staging_dst_prefix}/_tmp_loadable_keys` + """, + ) + logged_query( + f""" + INSERT INTO {dst_table} + SELECT {ClickHouseTable.VARIANTS_MEMORY.select_fields} + FROM {src_table} WHERE {ClickHouseTable.VARIANTS_MEMORY.key_field} IN {table_name_builder.staging_dst_prefix}/_tmp_loadable_keys` + """, + ) + drop_staging_db() + + +def direct_insert_all_keys( + clickhouse_table: ClickHouseTable, + table_name_builder: TableNameBuilder, + **_, +) -> None: + dst_table = table_name_builder.dst_table(clickhouse_table) + src_table = table_name_builder.src_table(clickhouse_table) + settings = '' + # Large variant details inserts may OOM + if clickhouse_table == ClickHouseTable.VARIANT_DETAILS: + settings = 'SETTINGS max_insert_threads = 2' + logged_query( + f""" + INSERT INTO {dst_table} + SELECT {clickhouse_table.select_fields} + FROM {src_table} + {settings} + """, + ) + + +# This is a smattering of shared operations that lacks a better name :/ +def finalize_refresh_flow( + table_name_builder: TableNameBuilder, + project_guids: list[str], +): + dataset_type = table_name_builder.dataset_type + refresh_materialized_views( + table_name_builder, + ClickHouseMaterializedView.for_dataset_type_atomic_entries_update_refreshable( + dataset_type, + ), + staging=True, + ) + replace_project_partitions( + table_name_builder, + ClickHouseTable.for_dataset_type_atomic_entries_update_project_partitioned( + dataset_type, + ), + project_guids, + ) + exchange_tables( + table_name_builder, + ClickHouseTable.for_dataset_type_atomic_entries_update_unpartitioned( + dataset_type, + ), + ) + drop_staging_db() + reload_dictionaries( + table_name_builder, + ClickHouseDictionary.for_dataset_type(dataset_type), + ) + + +def atomic_insert_entries( + table_name_builder: TableNameBuilder, + project_guids: list[str], + family_guids: list[str], + **_, +) -> None: + dataset_type = table_name_builder.dataset_type + drop_staging_db() + create_staging_tables( + table_name_builder, + ClickHouseTable.for_dataset_type_atomic_entries_update(dataset_type), + ) + create_staging_materialized_views( + table_name_builder, + ClickHouseMaterializedView.for_dataset_type_atomic_entries_update( + dataset_type, + ), + ) + stage_existing_project_partitions( + table_name_builder, + project_guids, + ClickHouseTable.for_dataset_type_atomic_entries_update_project_partitioned( + dataset_type, + ), + ) + delete_existing_families_from_staging_entries( + table_name_builder, + family_guids, + ) + insert_new_entries( + table_name_builder, + ) + optimize_entries( + table_name_builder, + project_guids, + ) + validate_family_guid_counts( + table_name_builder, + project_guids, + family_guids, + ) + finalize_refresh_flow(table_name_builder, project_guids) + + +@retry() +def load_complete_run( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + run_id: str, + project_guids: list[str], + family_guids: list[str], +): + msg = f'Attempting load of run: {reference_genome.value}/{dataset_type.value}/{run_id}' + logger.info(msg) + table_name_builder = TableNameBuilder( + reference_genome, + dataset_type, + run_id, + ) + for clickhouse_table in ClickHouseTable.for_dataset_type(dataset_type): + clickhouse_table.insert( + table_name_builder=table_name_builder, + project_guids=project_guids, + family_guids=family_guids, + ) + for ( + clickhouse_reference_data + ) in ClickhouseReferenceDataset.for_reference_genome_dataset_type( + reference_genome, + dataset_type, + ): + clickhouse_reference_data.insert_into_seqr_variants_and_refresh_search( + table_name_builder=table_name_builder, + ) + + +@retry() +def delete_family_guids( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + run_id: str, + project_guid: str, + family_guids: list[str], +): + msg = f'Attempting delete families for {reference_genome.value}/{dataset_type.value} {project_guid}: {family_guids}' + logger.info(msg) + table_name_builder = TableNameBuilder( + reference_genome, + dataset_type, + run_id, + ) + entries_exist = logged_query( + f""" + SELECT EXISTS ( + SELECT 1 + FROM {table_name_builder.dst_table(ClickHouseTable.ENTRIES)} + WHERE project_guid = %(project_guid)s + AND has(%(family_guids)s, family_guid) + ); + """, + {'family_guids': family_guids, 'project_guid': project_guid}, + )[0][0] + if not entries_exist: + msg = f'No data exists for {reference_genome.value} & {dataset_type.value} so skipping' + logger.info(msg) + return + project_guids = [project_guid] + drop_staging_db() + create_staging_tables( + table_name_builder, + ClickHouseTable.for_dataset_type_atomic_entries_update(dataset_type), + ) + create_staging_materialized_views( + table_name_builder, + ClickHouseMaterializedView.for_dataset_type_atomic_entries_update( + dataset_type, + ), + ) + stage_existing_project_partitions( + table_name_builder, + project_guids, + ClickHouseTable.for_dataset_type_atomic_entries_update_project_partitioned( + dataset_type, + ), + ) + delete_existing_families_from_staging_entries( + table_name_builder, + family_guids, + ) + optimize_entries( + table_name_builder, + project_guids, + ) + finalize_refresh_flow(table_name_builder, project_guids) + + +@retry() +def rebuild_gt_stats( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + run_id: str, + project_guids: list[str], +) -> None: + if ClickHouseDictionary.GT_STATS_DICT not in ClickHouseDictionary.for_dataset_type( + dataset_type, + ): + msg = f'Skipping gt stats rebuild for {reference_genome.value}/{dataset_type.value} {project_guids[:10]}...' + logger.info(msg) + return + table_name_builder = TableNameBuilder( + reference_genome, + dataset_type, + run_id, + ) + max_key = logged_query( + f""" + SELECT max(key) FROM {table_name_builder.dst_table(ClickHouseTable.GT_STATS)} + """, + )[0][0] + if not max_key: + msg = f'Skipping gt stats rebuild for empty dataset {reference_genome.value}/{dataset_type.value} {project_guids[:10]}...' + logger.info(msg) + return + msg = f'Attempting rebuild gt stats for {reference_genome.value}/{dataset_type.value} {project_guids[:10]}...' + logger.info(msg) + drop_staging_db() + create_staging_tables( + table_name_builder, + ClickHouseTable.for_dataset_type_atomic_entries_update(dataset_type), + ) + create_staging_materialized_views( + table_name_builder, + ClickHouseMaterializedView.for_dataset_type_atomic_entries_update( + dataset_type, + ), + ) + stage_existing_project_partitions( + table_name_builder, + project_guids, + ClickHouseTable.for_dataset_type_atomic_entries_update_project_partitioned( + dataset_type, + ), + ) + for partition in get_partitions_for_projects( + table_name_builder, + ClickHouseTable.PROJECT_GT_STATS, + project_guids, + staging=True, + ): + logged_query( + f""" + ALTER TABLE {table_name_builder.staging_dst_table(ClickHouseTable.PROJECT_GT_STATS)} + DROP PARTITION %(partition)s + """, + {'partition': partition}, + ) + select_statement = get_create_mv_statements( + table_name_builder, + ClickHouseMaterializedView.ENTRIES_TO_PROJECT_GT_STATS_MV, + )[1] + select_statement = select_statement.replace( + table_name_builder.dst_prefix, + table_name_builder.staging_dst_prefix, + ) + # NB: encountered OOMs with large projects, necessitating sharding the insertion query. + step = math.ceil(max_key / 5) + for range_start in range(0, max_key, step): + range_end = min(range_start + step, max_key + 1) + logged_query( + f""" + INSERT INTO { + table_name_builder.staging_dst_table(ClickHouseTable.PROJECT_GT_STATS) + } + { + select_statement.replace( + 'GROUP BY project_guid', + 'WHERE key >= %(range_start)s AND key < %(range_end)s GROUP BY project_guid', + ) + } + """, + {'range_start': range_start, 'range_end': range_end}, + ) + finalize_refresh_flow(table_name_builder, project_guids) + + +@retry() +def refresh_clickhouse_reference_data( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + run_id: str, + reference_dataset: ClickhouseReferenceDataset, +): + if not reference_dataset.fully_refreshable: + msg = f'Skipping reference dataset refresh for {reference_dataset.value} for {reference_genome.value}/{dataset_type.value}..' + logger.info(msg) + return + msg = f'Attempting refresh reference dataset {reference_dataset.value} for {reference_genome.value}/{dataset_type.value} ... ' + logger.info(msg) + table_name_builder = TableNameBuilder( + reference_genome, + dataset_type, + run_id, + ) + reference_dataset.download_and_fully_refresh(table_name_builder) + + +def get_clickhouse_client( + timeout: int | None = None, + database: str | None = None, +) -> Client: + return Client( + host=Env.CLICKHOUSE_SERVICE_HOSTNAME, + port=Env.CLICKHOUSE_SERVICE_PORT, + user=Env.CLICKHOUSE_WRITER_USER, + password=Env.CLICKHOUSE_WRITER_PASSWORD, + **{'database': database} if database else {}, + **{'send_receive_timeout': timeout} if timeout else {}, + **{ + 'settings': { + 'send_timeout': timeout, + 'receive_timeout': timeout, + }, + } + if timeout + else {}, + ) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py new file mode 100644 index 0000000000..b4e7673664 --- /dev/null +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -0,0 +1,1338 @@ +import os +from unittest.mock import patch + +import pandas as pd +import pyarrow as pa +import pyarrow.parquet as pq + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome +from loading_pipeline.lib.core.environment import Env +from loading_pipeline.lib.misc.clickhouse import ( + STAGING_CLICKHOUSE_DATABASE, + ClickHouseDictionary, + ClickHouseMaterializedView, + ClickhouseReferenceDataset, + ClickHouseTable, + TableNameBuilder, + create_staging_materialized_views, + create_staging_tables, + delete_existing_families_from_staging_entries, + delete_family_guids, + direct_insert_all_keys, + exchange_tables, + get_clickhouse_client, + insert_new_entries, + load_complete_run, + logged_query, + normalize_partition, + optimize_entries, + rebuild_gt_stats, + refresh_materialized_views, + reload_dictionaries, + replace_project_partitions, + stage_existing_project_partitions, +) +from loading_pipeline.lib.paths import ( + new_entries_parquet_path, + new_variant_details_parquet_path, + new_variants_parquet_path, + runs_path, +) +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + +TEST_RUN_ID = 'manual__2025-05-07T17-20-59.702114+00-00' + + +class ClickhouseTest(MockedDatarootTestCase): + def setUp(self): + super().setUp() + client = get_clickhouse_client() + client.execute( + f""" + DROP DATABASE IF EXISTS {STAGING_CLICKHOUSE_DATABASE}; + """, + ) + client.execute( + f""" + DROP DATABASE IF EXISTS {Env.CLICKHOUSE_DATABASE}; + """, + ) + client.execute( + f""" + CREATE DATABASE {Env.CLICKHOUSE_DATABASE}; + """, + ) + client.execute( + f""" + CREATE TABLE {Env.CLICKHOUSE_DATABASE}.seqrdb_gene_ids_src ( + gene_id String, + seqrdb_id UInt32 + ) ENGINE = Memory; + """, + ) + client.execute( + f'INSERT INTO {Env.CLICKHOUSE_DATABASE}.`seqrdb_gene_ids_src` VALUES', + [('GENE1', 123), ('GENE2', 12), ('GENE3', 1)], + ) + client.execute( + f""" + CREATE DICTIONARY {Env.CLICKHOUSE_DATABASE}.seqrdb_gene_ids + ( + gene_id String, + seqrdb_id UInt32 + ) + PRIMARY KEY gene_id + SOURCE(CLICKHOUSE( + USER {Env.CLICKHOUSE_WRITER_USER} PASSWORD {Env.CLICKHOUSE_WRITER_PASSWORD} + DB {Env.CLICKHOUSE_DATABASE} TABLE `seqrdb_gene_ids_src` + )) + LAYOUT(HASHED()) + LIFETIME(0); + """, + ) + client.execute( + f""" + CREATE TABLE {Env.CLICKHOUSE_DATABASE}.gnomad_genomes_src ( + key UInt32, + filter_af Decimal(9, 8) + ) ENGINE = Memory; + """, + ) + client.execute( + f'INSERT INTO {Env.CLICKHOUSE_DATABASE}.`gnomad_genomes_src` VALUES', + [(11, 0.06), (12, 0.001), (13, 0.0001)], + ) + client.execute( + f""" + CREATE DICTIONARY {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/reference_data/gnomad_genomes` + ( + key UInt32, + filter_af Decimal(9, 8) + ) + PRIMARY KEY key + SOURCE(CLICKHOUSE( + USER {Env.CLICKHOUSE_WRITER_USER} PASSWORD {Env.CLICKHOUSE_WRITER_PASSWORD} + DB {Env.CLICKHOUSE_DATABASE} TABLE `gnomad_genomes_src` + )) + LAYOUT(HASHED()) + LIFETIME(0); + """, + ) + client.execute( + f""" + CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` ( + `key` UInt32, + `project_guid` LowCardinality(String), + `family_guid` String, + `xpos` UInt64 CODEC(Delta(8), ZSTD(1)), + `sample_type` Enum8('WES' = 0, 'WGS' = 1), + `is_gnomad_gt_5_percent` Boolean, + `is_annotated_in_any_gene` Boolean DEFAULT length(geneId_ids) > 0, + `geneId_ids` Array(UInt32), + `calls` Array( + Tuple( + sampleId String, + gt Nullable(Enum8('REF' = 0, 'HET' = 1, 'HOM' = 2)), + ) + ), + `sign` Int8, + PROJECTION xpos_projection + ( + SELECT * + ORDER BY is_annotated_in_any_gene, xpos + ) + ) + ENGINE = CollapsingMergeTree(sign) + PARTITION BY project_guid + ORDER BY (project_guid, family_guid, key) + SETTINGS deduplicate_merge_projection_mode = 'rebuild'; + """, + ) + client.execute( + f""" + CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + ( + `project_guid` String, + `key` UInt32, + `sample_type` Enum8('WES' = 0, 'WGS' = 1), + `het_samples` Int32, + `hom_samples` Int32, + ) + ENGINE = SummingMergeTree + PARTITION BY project_guid + ORDER BY (project_guid, key, sample_type) + """, + ) + client.execute( + f""" + CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` + ( + `key` UInt32, + `ac_wes` UInt32, + `ac_wgs` UInt32, + ) + ENGINE = SummingMergeTree + ORDER BY (key) + """, + ) + client.execute( + f""" + CREATE MATERIALIZED VIEW {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries_to_project_gt_stats_mv` + TO {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + AS SELECT + project_guid, + key, + sample_type, + sum(toInt32(arrayCount(s -> (s.gt = 'HET'), calls) * sign)) AS het_samples, + sum(toInt32(arrayCount(s -> (s.gt = 'HOM'), calls) * sign)) AS hom_samples + FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` + GROUP BY project_guid, key, sample_type + """, + ) + client.execute( + f""" + CREATE MATERIALIZED VIEW {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats_to_gt_stats_mv` + REFRESH EVERY 10 YEAR TO {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` + AS SELECT + key, + sumIf(het_samples * 1 + hom_samples * 2, sample_type = 'WES') AS ac_wes, + sumIf(het_samples * 1 + hom_samples * 2, sample_type = 'WGS') AS ac_wgs + FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + GROUP BY key + """, + ) + client.execute( + f""" + CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details` ( + key UInt32, + variantId String, + transcripts String + ) ENGINE = EmbeddedRocksDB() + PRIMARY KEY `key` + """, + ) + client.execute( + f""" + CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` ( + key UInt32, + variantId String, + ) ENGINE = EmbeddedRocksDB() + PRIMARY KEY `key` + """, + ) + client.execute( + f""" + CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_disk` ( + key UInt32, + variantId String, + ) ENGINE = EmbeddedRocksDB() + PRIMARY KEY `key` + """, + ) + client.execute( + f""" + CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/key_lookup` ( + variantId String, + key UInt32, + ) ENGINE = EmbeddedRocksDB() + PRIMARY KEY `variantId` + """, + ) + client.execute( + f""" + CREATE DICTIONARY {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` + ( + `key` UInt32, + `ac_wes` UInt16, + `ac_wgs` UInt16 + ) + PRIMARY KEY key + SOURCE( + CLICKHOUSE( + USER {Env.CLICKHOUSE_WRITER_USER} PASSWORD {Env.CLICKHOUSE_WRITER_PASSWORD} + DB {Env.CLICKHOUSE_DATABASE} TABLE `GRCh38/SNV_INDEL/gt_stats` + ) + ) + LIFETIME(0) + LAYOUT(FLAT(MAX_ARRAY_SIZE 10000)) + """, + ) + client.execute( + f""" + CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/reference_data/clinvar/all_variants` ( + `variantId` String, + `alleleId` Nullable(UInt32), + `pathogenicity` Enum8( + 'Pathogenic' = 0, + 'Pathogenic/Likely_pathogenic' = 1 + ) + ) + PRIMARY KEY `variantId` + """, + ) + client.execute( + f""" + CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/reference_data/clinvar/seqr_variants` ( + `key` UInt32, + `alleleId` Nullable(UInt32), + `pathogenicity` Enum8( + 'Pathogenic' = 0, + 'Pathogenic/Likely_pathogenic' = 1 + ) + ) + PRIMARY KEY `key` + """, + ) + client.execute( + f""" + CREATE MATERIALIZED VIEW {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/reference_data/clinvar/seqr_variants_to_search_mv` + REFRESH EVERY 10 YEAR ENGINE = Null + AS SELECT DISTINCT ON (key) * + FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/reference_data/clinvar/seqr_variants` + """, + ) + client.execute( + f""" + CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/entries` ( + `key` UInt32, + `project_guid` LowCardinality(String), + `family_guid` String, + `xpos` UInt64 CODEC(Delta(8), ZSTD(1)), + `sample_type` Enum8('WES' = 0, 'WGS' = 1), + `calls` Array( + Tuple( + sampleId String, + gt Nullable(Enum8('REF' = 0, 'HET' = 1, 'HOM' = 2)), + ) + ), + `sign` Int8, + PROJECTION xpos_projection + ( + SELECT * + ORDER BY xpos + ) + ) + ENGINE = CollapsingMergeTree(sign) + PARTITION BY project_guid + ORDER BY (project_guid, family_guid, key) + SETTINGS deduplicate_merge_projection_mode = 'rebuild'; + """, + ) + client.execute( + f""" + CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/variants_memory` ( + key UInt32, + variantId String, + ) ENGINE = EmbeddedRocksDB() + PRIMARY KEY `key` + """, + ) + client.execute( + f""" + CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/variants_disk` ( + key UInt32, + variantId String, + ) ENGINE = EmbeddedRocksDB() + PRIMARY KEY `key` + """, + ) + client.execute( + f""" + CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/key_lookup` ( + variantId String, + key UInt32, + ) ENGINE = EmbeddedRocksDB() + PRIMARY KEY `variantId` + """, + ) + base_path = runs_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + ) + os.makedirs(os.path.join(base_path, TEST_RUN_ID), exist_ok=True) + + def write_test_parquet(df: pd.DataFrame, parquet_path: str, schema=None): + if schema: + table = pa.Table.from_pandas(df, schema=schema) + else: + table = pa.Table.from_pandas(df) + os.makedirs(parquet_path) + pq.write_table( + table, + os.path.join( + parquet_path, + 'test.parquet', + ), + ) + + # Variant Details Parquet + df = pd.DataFrame( + { + 'key': [1, 2, 3, 4], + 'variantId': [ + '1-13-A-C', + '2-14-A-T', + 'Y-19-A-C', + 'M-12-C-G', + ], + 'transcripts': ['a', 'b', 'c', 'd'], + }, + ) + write_test_parquet( + df, + new_variant_details_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ) + + # New Variants parquet. + df = pd.DataFrame( + { + 'key': [10, 11, 12, 13], + 'variantId': [ + '1-3-A-C', + '2-4-A-T', + 'Y-9-A-C', + 'M-2-C-G', + ], + }, + ) + write_test_parquet( + df, + new_variants_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ) + write_test_parquet( + df, + new_variants_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.GCNV, + TEST_RUN_ID, + ), + ) + + # New Entries Parquet + df = pd.DataFrame( + { + 'key': [0, 3, 4], + 'project_guid': [ + 'project_d', + 'project_d', + 'project_d', + ], + 'family_guid': [ + 'family_d1', + 'family_d2', + 'family_d3', + ], + 'xpos': [ + 123456789, + 123456789, + 123456789, + ], + 'sample_type': [ + 'WES', + 'WES', + 'WES', + ], + 'geneIds': [ + [], + ['GENE1', 'GENE2'], + ['GENE3'], + ], + 'calls': [ + [('sample_d1', 0), ('sample_d11', 2)], + [('sample_d2', 0)], + [('sample_d3', 1)], + ], + 'sign': [ + 1, + 1, + 1, + ], + }, + ) + schema = pa.schema( + [ + ('key', pa.int64()), + ('project_guid', pa.string()), + ('family_guid', pa.string()), + ('xpos', pa.int64()), + ('sample_type', pa.string()), + ('geneIds', pa.list_(pa.string())), + ( + 'calls', + pa.list_( + pa.struct([('sampleId', pa.string()), ('gt', pa.int64())]), + ), + ), + ('sign', pa.int64()), + ], + ) + write_test_parquet( + df, + new_entries_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + schema, + ) + write_test_parquet( + df.drop('geneIds', axis=1), + new_entries_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.GCNV, + TEST_RUN_ID, + ), + schema.remove(5).remove(5), + ) + + def tearDown(self): + super().tearDown() + client = get_clickhouse_client() + client.execute( + f""" + DROP DICTIONARY IF EXISTS {Env.CLICKHOUSE_DATABASE}.seqrdb_gene_ids; + """, + ) + client.execute( + f""" + DROP DICTIONARY IF EXISTS {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/reference_data/gnomad_genomes`; + """, + ) + client.execute( + f""" + DROP DATABASE IF EXISTS {Env.CLICKHOUSE_DATABASE}; + """, + ) + client.execute( + f""" + DROP DATABASE IF EXISTS {STAGING_CLICKHOUSE_DATABASE}; + """, + ) + + def test_get_clickhouse_client(self): + client = get_clickhouse_client() + result = client.execute('SELECT 1') + self.assertEqual(result[0][0], 1) + + def test_normalize_partition(self): + self.assertEqual(normalize_partition('project_d'), ('project_d',)) + self.assertEqual( + normalize_partition("('project_d', 0)"), + ('project_d', 0), + ) + + def test_table_name_builder(self): + table_name_builder = TableNameBuilder( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ) + self.assertEqual( + table_name_builder.dst_table( + ClickHouseTable.ENTRIES, + ), + f'{Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries`', + ) + self.assertEqual( + table_name_builder.src_table( + ClickHouseTable.ENTRIES, + ), + f"file('{runs_path(ReferenceGenome.GRCh38, DatasetType.SNV_INDEL)}/manual__2025-05-07T17-20-59.702114+00-00/new_entries.parquet/*.parquet', 'Parquet')", + ) + with patch('loading_pipeline.lib.paths.Env') as mock_env: + mock_env.PIPELINE_DATA_DIR = 'gs://mock_bucket/v3.1' + self.assertEqual( + table_name_builder.src_table( + ClickHouseTable.ENTRIES, + ), + "gcs(pipeline_data_access, url='https://storage.googleapis.com/mock_bucket/v3.1/GRCh38/SNV_INDEL/runs/manual__2025-05-07T17-20-59.702114+00-00/new_entries.parquet/*.parquet')", + ) + + def test_direct_insert_all_keys(self): + client = get_clickhouse_client() + client.execute( + f'INSERT INTO {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details` VALUES', + [(1, 'a', 'e'), (10, 'b', 'f'), (7, 'c', 'g')], + ) + direct_insert_all_keys( + ClickHouseTable.VARIANT_DETAILS, + TableNameBuilder( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ) + ret = client.execute( + f'SELECT * FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', + ) + self.assertEqual( + ret, + [ + (1, '1-13-A-C', 'a'), + (2, '2-14-A-T', 'b'), + (3, 'Y-19-A-C', 'c'), + (4, 'M-12-C-G', 'd'), + (7, 'c', 'g'), + (10, 'b', 'f'), + ], + ) + + # ensure multiple calls are idempotent + direct_insert_all_keys( + ClickHouseTable.VARIANT_DETAILS, + TableNameBuilder( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ) + ret = client.execute( + f'SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', + ) + self.assertEqual(ret[0][0], 6) + + @patch.object( + ClickhouseReferenceDataset, + 'for_reference_genome_dataset_type', + return_value=[ClickhouseReferenceDataset.CLINVAR], + ) + def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): + # Tests individual components of the atomic_insert_entries + # to validate the state after each step. + client = get_clickhouse_client() + client.execute( + f""" + INSERT INTO {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` + VALUES + (0, 'project_a', 'family_a1', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_a1','HOM')], 1), + (1, 'project_a', 'family_a2', 123456789, 'WGS', 0, 0, CAST([] AS Array(UInt32)), [('sample_a2','HET')], 1), + (2, 'project_a', 'family_a3', 133456789, 'WGS', 0, 0, CAST([] AS Array(UInt32)), [('sample_a3','HOM')], 1), + (3, 'project_a', 'family_a4', 133456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_a4','REF')], 1), + (4, 'project_a', 'family_a5', 133456789, 'WES', 0, 1, CAST([0] AS Array(UInt32)), [('sample_a5','REF'),('sample_a6','HET'),('sample_a7','REF')], 1), + (4, 'project_a', 'family_a6', 133456789, 'WGS', 0, 0, CAST([] AS Array(UInt32)), [('sample_a8','HOM')], 1), + (0, 'project_b', 'family_b1', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b4','REF')], 1), + (1, 'project_b', 'family_b2', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b5','HET')], 1), + (2, 'project_b', 'family_b2', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b5','REF')], 1), + (3, 'project_b', 'family_b3', 133456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b6','HOM')], 1), + (4, 'project_b', 'family_b3', 133456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b6','HOM')], 1), + (0, 'project_c', 'family_c1', 123456789, 'WES', 0, 1, CAST([1] AS Array(UInt32)), [('sample_c7','REF')], 1), + (3, 'project_c', 'family_c2', 123456789, 'WES', 0, 1, CAST([1] AS Array(UInt32)), [('sample_c8','REF')], 1), + (4, 'project_c', 'family_c3', 133456789, 'WES', 0, 1, CAST([1] AS Array(UInt32)), [('sample_c9','HOM')], 1), + (5, 'project_c', 'family_c4', 133456789, 'WES', 0, 1, CAST([1] AS Array(UInt32)), [('sample_c9','HOM')], 1) + """, + ) + table_name_builder = TableNameBuilder( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ) + create_staging_tables( + table_name_builder, + ClickHouseTable.for_dataset_type_atomic_entries_update( + DatasetType.SNV_INDEL, + ), + ) + create_staging_materialized_views( + table_name_builder, + ClickHouseMaterializedView.for_dataset_type_atomic_entries_update( + DatasetType.SNV_INDEL, + ), + ) + stage_existing_project_partitions( + table_name_builder, + [ + 'project_a', + 'project_b', + 'project_d', # Partition does not exist already. + ], + ClickHouseTable.for_dataset_type_atomic_entries_update_project_partitioned( + DatasetType.SNV_INDEL, + ), + ) + staged_projects = client.execute( + f""" + SELECT DISTINCT project_guid FROM {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/entries` + """, + ) + self.assertCountEqual( + [p[0] for p in staged_projects], + ['project_a', 'project_b'], + ) + staged_project_gt_stats = client.execute( + f""" + SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) + FROM + {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/project_gt_stats` + GROUP BY project_guid, key, sample_type + """, + ) + self.assertCountEqual( + staged_project_gt_stats, + [ + ('project_a', 0, 'WES', 0, 1), + ('project_a', 1, 'WGS', 1, 0), + ('project_a', 2, 'WGS', 0, 1), + ('project_a', 4, 'WES', 1, 0), + ('project_a', 4, 'WGS', 0, 1), + ('project_b', 1, 'WES', 1, 0), + ('project_b', 3, 'WES', 0, 1), + ('project_b', 4, 'WES', 0, 1), + # project_gt_stats stages all projects, not just + # those requested for loading. + ('project_c', 4, 'WES', 0, 1), + ('project_c', 5, 'WES', 0, 1), + ], + ) + delete_existing_families_from_staging_entries( + table_name_builder, + ['family_a1', 'family_a5', 'family_a6'], + ) + staged_project_gt_stats = client.execute( + f""" + SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) + FROM + {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/project_gt_stats` + GROUP BY project_guid, key, sample_type + """, + ) + self.assertCountEqual( + staged_project_gt_stats, + [ + ('project_a', 0, 'WES', 0, 0), + ('project_a', 1, 'WGS', 1, 0), + ('project_a', 2, 'WGS', 0, 1), + ('project_a', 4, 'WES', 0, 0), + ('project_a', 4, 'WGS', 0, 0), + ('project_b', 1, 'WES', 1, 0), + ('project_b', 3, 'WES', 0, 1), + ('project_b', 4, 'WES', 0, 1), + ('project_c', 4, 'WES', 0, 1), + ('project_c', 5, 'WES', 0, 1), + ], + ) + insert_new_entries(table_name_builder) + optimize_entries( + table_name_builder, + ['project_a', 'project_b', 'project_c'], + ) + staged_project_gt_stats = client.execute( + f""" + SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) + FROM + {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/project_gt_stats` + GROUP BY project_guid, key, sample_type + """, + ) + self.assertCountEqual( + staged_project_gt_stats, + [ + ('project_a', 0, 'WES', 0, 0), + ('project_a', 1, 'WGS', 1, 0), + ('project_a', 2, 'WGS', 0, 1), + ('project_a', 4, 'WES', 0, 0), + ('project_a', 4, 'WGS', 0, 0), + ('project_b', 1, 'WES', 1, 0), + ('project_b', 3, 'WES', 0, 1), + ('project_b', 4, 'WES', 0, 1), + ('project_c', 4, 'WES', 0, 1), + ('project_c', 5, 'WES', 0, 1), + ('project_d', 0, 'WES', 0, 1), + ('project_d', 4, 'WES', 1, 0), + ], + ) + refresh_materialized_views( + table_name_builder, + ClickHouseMaterializedView.for_dataset_type_atomic_entries_update_refreshable( + DatasetType.SNV_INDEL, + ), + staging=True, + ) + replace_project_partitions( + table_name_builder, + ClickHouseTable.for_dataset_type_atomic_entries_update_project_partitioned( + DatasetType.SNV_INDEL, + ), + ['project_a', 'project_d'], + ) + new_entries = client.execute( + f""" + SELECT COLUMNS('.*') EXCEPT(is_annotated_in_any_gene, is_gnomad_gt_5_percent) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` + """, + ) + self.assertCountEqual( + new_entries, + [ + ( + 0, + 'project_b', + 'family_b1', + 123456789, + 'WES', + [], + [('sample_b4', 'REF')], + 1, + ), + ( + 1, + 'project_b', + 'family_b2', + 123456789, + 'WES', + [], + [('sample_b5', 'HET')], + 1, + ), + ( + 2, + 'project_b', + 'family_b2', + 123456789, + 'WES', + [], + [('sample_b5', 'REF')], + 1, + ), + ( + 3, + 'project_b', + 'family_b3', + 133456789, + 'WES', + [], + [('sample_b6', 'HOM')], + 1, + ), + ( + 4, + 'project_b', + 'family_b3', + 133456789, + 'WES', + [], + [('sample_b6', 'HOM')], + 1, + ), + ( + 1, + 'project_a', + 'family_a2', + 123456789, + 'WGS', + [], + [('sample_a2', 'HET')], + 1, + ), + ( + 2, + 'project_a', + 'family_a3', + 133456789, + 'WGS', + [], + [('sample_a3', 'HOM')], + 1, + ), + ( + 3, + 'project_a', + 'family_a4', + 133456789, + 'WES', + [], + [('sample_a4', 'REF')], + 1, + ), + ( + 0, + 'project_d', + 'family_d1', + 123456789, + 'WES', + [], + [('sample_d1', 'REF'), ('sample_d11', 'HOM')], + 1, + ), + ( + 3, + 'project_d', + 'family_d2', + 123456789, + 'WES', + [123, 12], + [('sample_d2', 'REF')], + 1, + ), + ( + 4, + 'project_d', + 'family_d3', + 123456789, + 'WES', + [1], + [('sample_d3', 'HET')], + 1, + ), + ( + 0, + 'project_c', + 'family_c1', + 123456789, + 'WES', + [1], + [('sample_c7', 'REF')], + 1, + ), + ( + 3, + 'project_c', + 'family_c2', + 123456789, + 'WES', + [1], + [('sample_c8', 'REF')], + 1, + ), + ( + 4, + 'project_c', + 'family_c3', + 133456789, + 'WES', + [1], + [('sample_c9', 'HOM')], + 1, + ), + ( + 5, + 'project_c', + 'family_c4', + 133456789, + 'WES', + [1], + [('sample_c9', 'HOM')], + 1, + ), + ], + ) + existing_gt_stats = client.execute( + f""" + SELECT * + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` + """, + ) + self.assertCountEqual( + existing_gt_stats, + [], + ) + exchange_tables( + table_name_builder, + ClickHouseTable.for_dataset_type_atomic_entries_update_unpartitioned( + DatasetType.SNV_INDEL, + ), + ) + new_gt_stats = client.execute( + f""" + SELECT * + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` + """, + ) + self.assertCountEqual(new_gt_stats, []) + reload_dictionaries( + table_name_builder, + ClickHouseDictionary.for_dataset_type(DatasetType.SNV_INDEL), + ) + new_gt_stats_post_reload = client.execute( + f""" + SELECT * + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` + """, + ) + self.assertEqual( + new_gt_stats_post_reload, + [ + (0, 2, 0), + (1, 1, 1), + (2, 0, 2), + (3, 2, 0), + (4, 5, 0), + (5, 2, 0), + ], + ) + + @patch.object( + ClickhouseReferenceDataset, + 'for_reference_genome_dataset_type', + return_value=[ClickhouseReferenceDataset.CLINVAR], + ) + def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_type): + load_complete_run( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ['project_d'], + ['family_d1', 'family_d2'], + ) + client = get_clickhouse_client() + project_gt_stats = client.execute( + f""" + SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + GROUP BY project_guid, key, sample_type + """, + ) + self.assertCountEqual( + project_gt_stats, + [ + ('project_d', 0, 'WES', 0, 1), + ('project_d', 4, 'WES', 1, 0), + ], + ) + gt_stats = client.execute( + f""" + SELECT * + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` + """, + ) + self.assertCountEqual( + gt_stats, + [ + (0, 2, 0), + (4, 1, 0), + ], + ) + gt_stats_dict = client.execute( + f""" + SELECT * + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` + """, + ) + self.assertCountEqual( + gt_stats_dict, + [ + (0, 2, 0), + (4, 1, 0), + ], + ) + variants_memory = client.execute( + f""" + SELECT * + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` + """, + ) + self.assertCountEqual( + variants_memory, + [ + (10, '1-3-A-C'), + (11, '2-4-A-T'), + (12, 'Y-9-A-C'), + (13, 'M-2-C-G'), + ], + ) + variants_disk = client.execute( + f""" + SELECT * + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_disk` + """, + ) + self.assertCountEqual( + variants_disk, + [ + (10, '1-3-A-C'), + (11, '2-4-A-T'), + (12, 'Y-9-A-C'), + (13, 'M-2-C-G'), + ], + ) + + def test_load_complete_gcnv(self): + load_complete_run( + ReferenceGenome.GRCh38, + DatasetType.GCNV, + TEST_RUN_ID, + ['project_d'], + ['family_d1', 'family_d2'], + ) + client = get_clickhouse_client() + variants_disk_count = client.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/variants_memory` + """, + )[0][0] + self.assertEqual(variants_disk_count, 4) + variants_disk_count = client.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/variants_disk` + """, + )[0][0] + self.assertEqual(variants_disk_count, 4) + key_lookup_count = client.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/key_lookup` + """, + )[0][0] + self.assertEqual(key_lookup_count, 4) + entries_count = client.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/entries` + """, + )[0][0] + self.assertEqual(entries_count, 3) + + def test_delete_families(self): + table_name_builder = TableNameBuilder( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ) + client = get_clickhouse_client() + client.execute( + f""" + INSERT INTO {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` + VALUES + (0, 'project_a', 'family_a1', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_a1','HOM')], 1), + (1, 'project_a', 'family_a2', 123456789, 'WGS', 0, 0, CAST([] AS Array(UInt32)), [('sample_a2','HET')], 1), + (2, 'project_a', 'family_a3', 133456789, 'WGS', 0, 0, CAST([] AS Array(UInt32)), [('sample_a3','HOM')], 1), + (3, 'project_a', 'family_a4', 133456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_a4','REF')], 1), + (4, 'project_a', 'family_a5', 133456789, 'WES', 0, 1, CAST([0] AS Array(UInt32)), [('sample_a5','REF'),('sample_a6','HET'),('sample_a7','REF')], 1), + (4, 'project_a', 'family_a6', 133456789, 'WGS', 0, 0, CAST([] AS Array(UInt32)), [('sample_a8','HOM')], 1), + (0, 'project_b', 'family_b1', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b4','REF')], 1), + (1, 'project_b', 'family_b2', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b5','HET')], 1), + (2, 'project_b', 'family_b2', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b5','REF')], 1), + (3, 'project_b', 'family_b3', 133456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b6','HOM')], 1), + (4, 'project_b', 'family_b3', 133456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b6','HOM')], 1), + (0, 'project_c', 'family_c1', 123456789, 'WES', 0, 1, CAST([1] AS Array(UInt32)), [('sample_c7','REF')], 1), + (3, 'project_c', 'family_c2', 123456789, 'WES', 0, 1, CAST([1] AS Array(UInt32)), [('sample_c8','REF')], 1), + (4, 'project_c', 'family_c3', 133456789, 'WES', 0, 1, CAST([1] AS Array(UInt32)), [('sample_c9','HOM')], 1), + (5, 'project_c', 'family_c4', 133456789, 'WES', 0, 1, CAST([1] AS Array(UInt32)), [('sample_c9','HOM')], 1) + """, + ) + project_gt_stats = client.execute( + f""" + SELECT project_guid, sum(het_samples), sum(hom_samples) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + GROUP BY project_guid + """, + ) + self.assertCountEqual( + project_gt_stats, + [('project_a', 2, 3), ('project_c', 0, 2), ('project_b', 1, 2)], + ) + refresh_materialized_views( + table_name_builder, + ClickHouseMaterializedView.for_dataset_type_atomic_entries_update_refreshable( + DatasetType.SNV_INDEL, + ), + staging=False, + ) + gt_stats = client.execute( + f""" + SELECT sum(ac_wes) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` + """, + ) + self.assertCountEqual(gt_stats, [(12,)]) + delete_family_guids( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + 'project_a', + ['family_a1', 'family_a2'], + ) + project_gt_stats = client.execute( + f""" + SELECT project_guid, sum(het_samples), sum(hom_samples) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + GROUP BY project_guid + """, + ) + self.assertCountEqual( + project_gt_stats, + [('project_a', 1, 2), ('project_c', 0, 2), ('project_b', 1, 2)], + ) + gt_stats = client.execute( + f""" + SELECT sum(ac_wes) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` + """, + ) + self.assertCountEqual(gt_stats, [(10,)]) + gt_stats_dict = client.execute( + f""" + SELECT sum(ac_wes) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` + """, + ) + self.assertCountEqual(gt_stats_dict, [(10,)]) + + def test_rebuild_gt_stats(self): + table_name_builder = TableNameBuilder( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ) + client = get_clickhouse_client() + client.execute( + f""" + INSERT INTO {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` + VALUES + (0, 'project_a', 'family_a1', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_a1','HOM')], 1), + (1, 'project_a', 'family_a2', 123456789, 'WGS', 0, 0, CAST([] AS Array(UInt32)), [('sample_a2','HET')], 1), + (2, 'project_a', 'family_a3', 133456789, 'WGS', 0, 0, CAST([] AS Array(UInt32)), [('sample_a3','HOM')], 1), + (3, 'project_a', 'family_a4', 133456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_a4','REF')], 1), + (4, 'project_a', 'family_a5', 133456789, 'WES', 0, 1, CAST([] AS Array(UInt32)), [('sample_a5','REF'),('sample_a6','HET'),('sample_a7','REF')], 1), + (4, 'project_a', 'family_a6', 133456789, 'WGS', 0, 0, CAST([] AS Array(UInt32)), [('sample_a8','HOM')], 1), + (0, 'project_b', 'family_b1', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b4','REF')], 1), + (1, 'project_b', 'family_b2', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b5','HET')], 1), + (2, 'project_b', 'family_b2', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b5','REF')], 1), + """, + ) + logged_query( # DROP the partition from the non-staging entries to as a non-mv-impacting change. + f""" + ALTER TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` + DROP PARTITION %(project_guid)s + """, + {'project_guid': 'project_a'}, + ) + project_gt_stats = client.execute( + f""" + SELECT project_guid, sum(het_samples), sum(hom_samples) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + GROUP BY project_guid + """, + ) + self.assertCountEqual( + project_gt_stats, + [('project_a', 2, 3), ('project_b', 1, 0)], + ) + refresh_materialized_views( + table_name_builder, + ClickHouseMaterializedView.for_dataset_type_atomic_entries_update_refreshable( + DatasetType.SNV_INDEL, + ), + staging=False, + ) + gt_stats = client.execute( + f""" + SELECT sum(ac_wes), sum(ac_wgs) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` + """, + ) + self.assertCountEqual(gt_stats, [(4, 5)]) + rebuild_gt_stats( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ['project_a', 'project_b'], + ) + project_gt_stats = client.execute( + f""" + SELECT project_guid, sum(het_samples), sum(hom_samples) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + GROUP BY project_guid + """, + ) + self.assertCountEqual( + project_gt_stats, + [('project_b', 1, 0)], + ) + gt_stats = client.execute( + f""" + SELECT sum(ac_wes), sum(ac_wgs) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` + """, + ) + self.assertCountEqual(gt_stats, [(1, 0)]) + + @patch.object( + ClickhouseReferenceDataset, + 'for_reference_genome_dataset_type', + return_value=[ClickhouseReferenceDataset.CLINVAR], + ) + def test_repartitioned_entries_table(self, mock_for_reference_genome_dataset_type): + client = get_clickhouse_client() + client.execute( + f""" + REPLACE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` ( + `key` UInt32, + `project_guid` LowCardinality(String), + `family_guid` String, + `xpos` UInt64 CODEC(Delta(8), ZSTD(1)), + `sample_type` Enum8('WES' = 0, 'WGS' = 1), + `is_gnomad_gt_5_percent` Boolean, + `is_annotated_in_any_gene` Boolean DEFAULT length(geneId_ids) > 0, + `geneId_ids` Array(UInt32), + `calls` Array( + Tuple( + sampleId String, + gt Nullable(Enum8('REF' = 0, 'HET' = 1, 'HOM' = 2)), + ) + ), + `sign` Int8, + `n_partitions` UInt8 MATERIALIZED 2, + `partition_id` UInt8 MATERIALIZED farmHash64(family_guid) % n_partitions, + PROJECTION xpos_projection + ( + SELECT * + ORDER BY is_annotated_in_any_gene, xpos + ) + ) + ENGINE = CollapsingMergeTree(sign) + PARTITION BY (project_guid, partition_id) + ORDER BY (project_guid, family_guid, key) + SETTINGS deduplicate_merge_projection_mode = 'rebuild'; + """, + ) + load_complete_run( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ['project_d'], + ['family_d1', 'family_d2', 'family_d3'], + ) + project_gt_stats = client.execute( + f""" + SELECT project_guid, sum(het_samples), sum(hom_samples) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + GROUP BY project_guid + """, + ) + self.assertCountEqual( + project_gt_stats, + [('project_d', 1, 1)], + ) diff --git a/loading_pipeline/lib/misc/family_entries.py b/loading_pipeline/lib/misc/family_entries.py new file mode 100644 index 0000000000..114f1dc2f9 --- /dev/null +++ b/loading_pipeline/lib/misc/family_entries.py @@ -0,0 +1,105 @@ +import hail as hl + +from loading_pipeline.lib.core import DatasetType + + +def compute_callset_family_entries_ht( + dataset_type: DatasetType, + mt: hl.MatrixTable, + entries_fields: dict[str, hl.Expression], +) -> hl.Table: + sample_id_to_family_guid = hl.dict( + { + s: family_guid + for family_guid, sample_ids in hl.eval(mt.family_samples).items() + for s in sample_ids + }, + ) + ht = mt.select_rows( + filters=mt.filters.difference(dataset_type.excluded_filters), + family_entries=( + # NB: we're sorted by both family and sample when this runs. + # However, the sort is not guaranteed once the entries + # table is edited and families are spliced out and re-appended. + hl.sorted( + hl.agg.collect( + hl.Struct( + s=mt.s, + family_guid=sample_id_to_family_guid[mt.s], + **entries_fields, + ), + ) + .group_by(lambda e: e.family_guid) + .values() + .map( + lambda fe: hl.sorted(fe, key=lambda e: e.s), + ), + lambda fe: fe[0].family_guid, + ) + ), + ).rows() + # NB: globalize before we set families to missing + ht = globalize_ids(ht) + ht = ht.annotate( + family_entries=( + ht.family_entries.map( + lambda fe: hl.or_missing( + fe.any(dataset_type.family_entries_filter_fn), + fe, + ), + ) + ), + ) + # Only keep rows where at least one family is not missing. + return ht.filter(ht.family_entries.any(hl.is_defined)) + + +def globalize_ids(ht: hl.Table) -> hl.Table: + row = ht.take(1)[0] if ht.count() > 0 else None + has_family_entries = row and len(row.family_entries) > 0 + ht = ht.annotate_globals( + family_guids=( + [fe[0].family_guid for fe in row.family_entries] + if has_family_entries + else hl.empty_array(hl.tstr) + ), + family_samples=( + {fe[0].family_guid: [e.s for e in fe] for fe in row.family_entries} + if has_family_entries + else hl.empty_dict(hl.tstr, hl.tarray(hl.tstr)) + ), + ) + return ht.annotate( + family_entries=ht.family_entries.map( + lambda fe: fe.map(lambda se: se.drop('s', 'family_guid')), + ), + ) + + +def deglobalize_ids(ht: hl.Table) -> hl.Table: + ht = ht.annotate( + family_entries=( + hl.enumerate(ht.family_entries).starmap( + lambda i, fe: hl.enumerate(fe).starmap( + lambda j, e: hl.Struct( + **e, + s=ht.family_samples[ht.family_guids[i]][j], + family_guid=ht.family_guids[i], + ), + ), + ) + ), + ) + return ht.drop('family_guids', 'family_samples') + + +def deduplicate_by_most_non_ref_calls(ht: hl.Table) -> hl.Table: + ht = ht.annotate( + non_ref_count=hl.len( + hl.flatten(ht.family_entries).filter(lambda s: s.GT.is_non_ref()), + ), + ) + return ht.group_by(*ht.key).aggregate( + filters=hl.agg.take(ht.filters, 1, ordering=-ht.non_ref_count)[0], + family_entries=hl.agg.take(ht.family_entries, 1, ordering=-ht.non_ref_count)[0], + ) diff --git a/loading_pipeline/lib/misc/family_entries_test.py b/loading_pipeline/lib/misc/family_entries_test.py new file mode 100644 index 0000000000..609fdda6d6 --- /dev/null +++ b/loading_pipeline/lib/misc/family_entries_test.py @@ -0,0 +1,356 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.core import DatasetType +from loading_pipeline.lib.misc.family_entries import ( + compute_callset_family_entries_ht, + deduplicate_by_most_non_ref_calls, + deglobalize_ids, + globalize_ids, +) + + +class FamilyEntriesTest(unittest.TestCase): + def test_compute_callset_family_entries_ht(self) -> None: + mt = hl.MatrixTable.from_parts( + rows={ + 'variants': [1, 2, 3], + 'filters': [ + hl.empty_set(hl.tstr), + {'HIGH_SR_BACKGROUND'}, + hl.empty_set(hl.tstr), + ], + }, + cols={'s': ['a', 'b', 'd', 'c']}, + entries={ + 'GT': [ + [ + hl.Call([0, 0]), + hl.missing(hl.tcall), + hl.Call([0, 0]), + hl.Call([0, 0]), + ], + [ + hl.Call([0, 0]), + hl.Call([0, 0]), + hl.Call([1, 1]), + hl.Call([0, 0]), + ], + [ + hl.Call([0, 1]), + hl.Call([0, 0]), + hl.Call([1, 1]), + hl.Call([0, 0]), + ], + ], + }, + globals={'family_samples': {'2': ['a'], '1': ['b', 'c', 'd']}}, + ) + ht = compute_callset_family_entries_ht(DatasetType.SNV_INDEL, mt, {'GT': mt.GT}) + self.assertCountEqual( + ht.globals.collect(), + [ + hl.Struct( + family_samples={'1': ['b', 'c', 'd'], '2': ['a']}, + family_guids=['1', '2'], + ), + ], + ) + self.assertCountEqual( + ht.filters.collect(), + [{'HIGH_SR_BACKGROUND'}, set()], + ) + self.assertCountEqual( + ht.family_entries.collect(), + [ + [ + [ + hl.Struct(GT=hl.Call(alleles=[0, 0], phased=False)), + hl.Struct(GT=hl.Call(alleles=[0, 0], phased=False)), + hl.Struct(GT=hl.Call(alleles=[1, 1], phased=False)), + ], + None, + ], + [ + [ + hl.Struct(GT=hl.Call(alleles=[0, 0], phased=False)), + hl.Struct(GT=hl.Call(alleles=[0, 0], phased=False)), + hl.Struct(GT=hl.Call(alleles=[1, 1], phased=False)), + ], + [hl.Struct(GT=hl.Call(alleles=[0, 1], phased=False))], + ], + ], + ) + + def test_globalize_and_deglobalize(self) -> None: + family_entries_ht = hl.Table.parallelize( + [], + hl.tstruct( + id=hl.tint32, + filters=hl.tset(hl.tstr), + family_entries=hl.tarray( + hl.tarray(hl.tstruct(a=hl.tint32, s=hl.tstr, family_guid=hl.tstr)), + ), + ), + key='id', + ) + family_entries_ht = globalize_ids(family_entries_ht) + self.assertCountEqual( + family_entries_ht.family_guids.collect(), + [ + [], + ], + ) + family_entries_ht = hl.Table.parallelize( + [ + { + 'id': 0, + 'filters': {'HIGH_SR_BACKGROUND', 'UNRESOLVED'}, + 'family_entries': [ + [ + hl.Struct(a=1, s='a', family_guid='123'), + hl.Struct(a=2, s='c', family_guid='123'), + hl.Struct(a=1, s='e', family_guid='123'), + ], + [ + hl.Struct(a=2, s='f', family_guid='234'), + ], + ], + }, + { + 'id': 1, + 'filters': {'HIGH_SR_BACKGROUND'}, + 'family_entries': [ + [ + hl.Struct(a=2, s='a', family_guid='123'), + hl.Struct(a=3, s='c', family_guid='123'), + hl.Struct(a=4, s='e', family_guid='123'), + ], + [ + hl.Struct(a=5, s='f', family_guid='234'), + ], + ], + }, + ], + hl.tstruct( + id=hl.tint32, + filters=hl.tset(hl.tstr), + family_entries=hl.tarray( + hl.tarray(hl.tstruct(a=hl.tint32, s=hl.tstr, family_guid=hl.tstr)), + ), + ), + key='id', + ) + family_entries_ht = globalize_ids(family_entries_ht) + self.assertCountEqual( + family_entries_ht.family_guids.collect(), + [ + ['123', '234'], + ], + ) + self.assertCountEqual( + family_entries_ht.family_entries.collect(), + [ + [ + [ + hl.Struct(a=1), + hl.Struct(a=2), + hl.Struct(a=1), + ], + [ + hl.Struct(a=2), + ], + ], + [ + [ + hl.Struct(a=2), + hl.Struct(a=3), + hl.Struct(a=4), + ], + [ + hl.Struct(a=5), + ], + ], + ], + ) + family_entries_ht = deglobalize_ids(family_entries_ht) + self.assertCountEqual( + family_entries_ht.family_entries.collect(), + [ + [ + [ + hl.Struct(a=1, s='a', family_guid='123'), + hl.Struct(a=2, s='c', family_guid='123'), + hl.Struct(a=1, s='e', family_guid='123'), + ], + [ + hl.Struct(a=2, s='f', family_guid='234'), + ], + ], + [ + [ + hl.Struct(a=2, s='a', family_guid='123'), + hl.Struct(a=3, s='c', family_guid='123'), + hl.Struct(a=4, s='e', family_guid='123'), + ], + [ + hl.Struct(a=5, s='f', family_guid='234'), + ], + ], + ], + ) + + def test_deduplicate_by_most_non_ref_calls(self) -> None: + project_ht = hl.Table.parallelize( + [ + { + 'id': 0, + 'filters': {'PASS', 'HIGH_SR_BACKGROUND'}, + 'family_entries': [ + [ + hl.Struct( + GT=hl.Call(alleles=[0, 1], phased=False), + family_guid='family_a', + s='sample_1', + ), + hl.Struct( + GT=hl.Call(alleles=[0, 0], phased=False), + family_guid='family_a', + s='sample_2', + ), + ], + [ + hl.Struct( + GT=hl.Call(alleles=[0, 1], phased=False), + family_guid='family_b', + s='sample_3', + ), + None, + ], + None, + ], + }, + { + 'id': 0, + 'filters': {'PASS'}, + 'family_entries': [ + [ + None, + hl.Struct( + GT=hl.Call(alleles=[0, 0], phased=False), + family_guid='family_a', + s='sample_2', + ), + ], + [ + hl.Struct( + GT=hl.Call(alleles=[0, 1], phased=False), + family_guid='family_b', + s='sample_3', + ), + None, + ], + None, + ], + }, + { + 'id': 2, + 'filters': {'HIGH_SR_BACKGROUND'}, + 'family_entries': [ + None, + None, + ], + }, + { + 'id': 3, + 'filters': {'PASS'}, + 'family_entries': [ + [ + hl.Struct( + GT=hl.Call(alleles=[0, 1], phased=False), + family_guid='family_a', + s='sample_1', + ), + hl.Struct( + GT=hl.Call(alleles=[0, 1], phased=False), + family_guid='family_a', + s='sample_2', + ), + ], + None, + ], + }, + ], + hl.tstruct( + id=hl.tint32, + filters=hl.tset(hl.tstr), + family_entries=hl.tarray( + hl.tarray( + hl.tstruct( + GT=hl.tcall, + family_guid=hl.tstr, + s=hl.tstr, + ), + ), + ), + ), + key='id', + ) + ht = deduplicate_by_most_non_ref_calls(project_ht) + self.assertEqual( + ht.collect(), + [ + hl.Struct( + id=0, + filters={'PASS', 'HIGH_SR_BACKGROUND'}, + family_entries=[ + [ + hl.Struct( + GT=hl.Call(alleles=[0, 1], phased=False), + family_guid='family_a', + s='sample_1', + ), + hl.Struct( + GT=hl.Call(alleles=[0, 0], phased=False), + family_guid='family_a', + s='sample_2', + ), + ], + [ + hl.Struct( + GT=hl.Call(alleles=[0, 1], phased=False), + family_guid='family_b', + s='sample_3', + ), + None, + ], + None, + ], + ), + hl.Struct( + id=2, + filters={'HIGH_SR_BACKGROUND'}, + family_entries=[None, None], + ), + hl.Struct( + id=3, + filters={'PASS'}, + family_entries=[ + [ + hl.Struct( + GT=hl.Call(alleles=[0, 1], phased=False), + family_guid='family_a', + s='sample_1', + ), + hl.Struct( + GT=hl.Call(alleles=[0, 1], phased=False), + family_guid='family_a', + s='sample_2', + ), + ], + None, + ], + ), + ], + ) diff --git a/loading_pipeline/lib/misc/family_loading_failures.py b/loading_pipeline/lib/misc/family_loading_failures.py new file mode 100644 index 0000000000..ee9d9bcf25 --- /dev/null +++ b/loading_pipeline/lib/misc/family_loading_failures.py @@ -0,0 +1,215 @@ +from collections import defaultdict + +import hail as hl + +from loading_pipeline.lib.core import Sex +from loading_pipeline.lib.logger import get_logger +from loading_pipeline.lib.misc.pedigree import Family, Relation, Sample + +logger = get_logger(__name__) + + +def passes_relatedness_check( + relatedness_check_lookup: dict[tuple[str, str], list], + sample_id: str, + other_id: str, + expected_relation: Relation, + additional_allowed_relation: Relation | None, +) -> tuple[bool, str | None]: + # No relationship to check, return true + if other_id is None: + return True, None + coefficients = relatedness_check_lookup.get( + (min(sample_id, other_id), max(sample_id, other_id)), + ) + if not coefficients or not any( + relation.coefficients_equal(coefficients) + for relation in ( + [expected_relation, additional_allowed_relation] + if additional_allowed_relation + else [expected_relation] + ) + ): + return ( + False, + f'Sample {sample_id} has expected relation "{expected_relation.value}" to {other_id} but has coefficients {coefficients or []}', + ) + return True, None + + +def all_relatedness_checks( + relatedness_check_lookup: dict[tuple[str, str], list], + family: Family, + sample: Sample, +) -> list[str]: + failure_reasons = [] + for relationship_set, relation, additional_allowed_relation in [ + ([sample.mother, sample.father], Relation.PARENT_CHILD, None), + ( + [ + sample.maternal_grandmother, + sample.maternal_grandfather, + sample.paternal_grandmother, + sample.paternal_grandfather, + ], + Relation.GRANDPARENT_GRANDCHILD, + None, + ), + (sample.siblings, Relation.SIBLING, None), + (sample.half_siblings, Relation.HALF_SIBLING, Relation.SIBLING), + (sample.aunt_nephews, Relation.AUNT_NEPHEW, None), + ]: + for other_id in relationship_set: + # Handle case where relation is identified in the + # pedigree as a "dummy" but is not included in + # the list of samples to load. + if other_id not in family.samples: + continue + success, reason = passes_relatedness_check( + relatedness_check_lookup, + sample.sample_id, + other_id, + relation, + additional_allowed_relation, + ) + if not success: + failure_reasons.append(reason) + return failure_reasons + + +def build_relatedness_check_lookup( + relatedness_check_ht: hl.Table, + remap_lookup: hl.dict, +) -> dict[tuple[str, str], list]: + relatedness_check_ht = relatedness_check_ht.key_by( + i=remap_lookup.get(relatedness_check_ht.i, relatedness_check_ht.i), + j=remap_lookup.get(relatedness_check_ht.j, relatedness_check_ht.j), + ) + return { + # NB: samples are sorted in the original ibd but not necessarily + # sorted after remapping + (min(r.i, r.j), max(r.i, r.j)): list(r.drop('i', 'j').values()) + for r in relatedness_check_ht.collect() + } + + +def build_sex_check_lookup( + sex_check_ht: hl.Table, + remap_lookup: hl.dict, +) -> dict[str, Sex]: + sex_check_ht = sex_check_ht.key_by( + s=remap_lookup.get(sex_check_ht.s, sex_check_ht.s), + ) + sex_check_ht = sex_check_ht.select('predicted_sex') + return {r.s: Sex(r.predicted_sex) for r in sex_check_ht.collect()} + + +def get_families_failed_missing_samples( + mt: hl.MatrixTable, + families: set[Family], +) -> dict[Family, list[str]]: + callset_samples = set(mt.cols().s.collect()) + failed_families = {} + for family in families: + missing_samples = family.samples.keys() - callset_samples + if len(missing_samples) > 0: + # NB: This is an array of a single element for consistency with + # the other checks. + failed_families[family] = [f'Missing samples: {missing_samples}'] + return failed_families + + +def get_families_failed_relatedness_check( + families: set[Family], + relatedness_check_ht: hl.Table, + remap_lookup: hl.dict, +) -> dict[Family, list[str]]: + relatedness_check_lookup = build_relatedness_check_lookup( + relatedness_check_ht, + remap_lookup, + ) + failed_families = defaultdict(list) + for family in families: + for sample in family.samples.values(): + failure_reasons = all_relatedness_checks( + relatedness_check_lookup, + family, + sample, + ) + if failure_reasons: + failed_families[family].extend(failure_reasons) + return dict(failed_families) + + +def get_families_failed_sex_check( + families: set[Family], + sex_check_ht: hl.Table, + remap_lookup: hl.dict, +) -> dict[Family, list[str]]: + sex_check_lookup = build_sex_check_lookup(sex_check_ht, remap_lookup) + failed_families = defaultdict(list) + for family in families: + for sample_id in family.samples: + if sample_id not in sex_check_lookup: + failed_families[family].append( + f'Sample {sample_id} has pedigree sex {family.samples[sample_id].sex.value} but is missing from the sex check source', + ) + continue + # NB: Both Unknown samples in pedigree and Unknown + # samples in the predicted_sex are precluded from + # failing the sex check. + if ( + sex_check_lookup[sample_id] == Sex.UNKNOWN + or family.samples[sample_id].sex == Sex.UNKNOWN + ): + logger.info( + f'Encountered sample with Unknown sex excluded from sex check: {sample_id}', + ) + continue + + if family.samples[sample_id].sex != sex_check_lookup[sample_id]: + failed_families[family].append( + f'Sample {sample_id} has pedigree sex {family.samples[sample_id].sex.value} but imputed sex {sex_check_lookup[sample_id].value}', + ) + return dict(failed_families) + + +def get_families_failed_imputed_sex_ploidy( + families: set[Family], + mt: hl.MatrixTable, + sex_check_ht: hl.Table, +) -> dict[Family, str]: + mt = mt.select_cols( + discrepant=( + ( + # All calls are diploid or missing but the sex is Male + hl.agg.all(mt.GT.is_diploid() | hl.is_missing(mt.GT)) + & (sex_check_ht[mt.s].predicted_sex == Sex.MALE.value) + ) + | ( + # At least one call is haploid but the sex is Female, X0, XXY, XYY, or XXX + hl.agg.any(~mt.GT.is_diploid()) + & hl.literal( + { + Sex.FEMALE.value, + Sex.X0.value, + Sex.XYY.value, + Sex.XXY.value, + Sex.XXX.value, + }, + ).contains(sex_check_ht[mt.s].predicted_sex) + ) + ), + ) + discrepant_samples = mt.aggregate_cols( + hl.agg.filter(mt.discrepant, hl.agg.collect_as_set(mt.s)), + ) + failed_families = defaultdict(list) + for family in families: + discrepant_loadable_samples = set(family.samples.keys()) & discrepant_samples + if discrepant_loadable_samples: + sorted_discrepant_samples = sorted(discrepant_loadable_samples) + failed_families[family].append( + f'Found samples with misaligned ploidy with their provided imputed sex: {sorted_discrepant_samples}', + ) + return failed_families diff --git a/loading_pipeline/lib/misc/family_loading_failures_test.py b/loading_pipeline/lib/misc/family_loading_failures_test.py new file mode 100644 index 0000000000..fb1d0905d1 --- /dev/null +++ b/loading_pipeline/lib/misc/family_loading_failures_test.py @@ -0,0 +1,448 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.core import Sex +from loading_pipeline.lib.misc.family_loading_failures import ( + all_relatedness_checks, + build_relatedness_check_lookup, + build_sex_check_lookup, + get_families_failed_imputed_sex_ploidy, + get_families_failed_sex_check, +) +from loading_pipeline.lib.misc.io import import_pedigree +from loading_pipeline.lib.misc.pedigree import ( + Family, + Sample, + parse_pedigree_ht_to_families, +) + +TEST_SEX_CHECK_1 = 'loading_pipeline/var/test/sex_check/test_sex_check_1.ht' +TEST_PEDIGREE_6 = 'loading_pipeline/var/test/pedigrees/test_pedigree_6.tsv' + + +class FamilyLoadingFailuresTest(unittest.TestCase): + def test_build_relatedness_check_lookup(self): + ht = hl.Table.parallelize( + [ + { + 'i': 'ROS_006_18Y03226_D1', + 'j': 'ROS_007_19Y05939_D1', + 'ibd0': 0.0, + 'ibd1': 1.0, + 'ibd2': 0.0, + 'pi_hat': 0.5, + }, + ], + hl.tstruct( + i=hl.tstr, + j=hl.tstr, + ibd0=hl.tfloat, + ibd1=hl.tfloat, + ibd2=hl.tfloat, + pi_hat=hl.tfloat, + ), + key=['i', 'j'], + ) + self.assertEqual( + build_relatedness_check_lookup( + ht, + hl.dict({'ROS_006_18Y03226_D1': 'remapped_id'}), + ), + { + ('ROS_007_19Y05939_D1', 'remapped_id'): [ + 0.0, + 1.0, + 0.0, + 0.5, + ], + }, + ) + + def test_build_sex_check_lookup(self): + ht = hl.Table.parallelize( + [ + {'s': 'ROS_006_18Y03226_D1', 'predicted_sex': 'F'}, + {'s': 'ROS_006_18Y03227_D1', 'predicted_sex': 'F'}, + {'s': 'ROS_006_18Y03228_D1', 'predicted_sex': 'F'}, + {'s': 'ROS_007_19Y05919_D1', 'predicted_sex': 'F'}, + {'s': 'ROS_007_19Y05939_D1', 'predicted_sex': 'M'}, + {'s': 'ROS_007_19Y05987_D1', 'predicted_sex': 'U'}, + {'s': 'ROS_007_19Y05989_D1', 'predicted_sex': 'X0'}, + ], + hl.tstruct( + s=hl.tstr, + predicted_sex=hl.tstr, + ), + key='s', + ) + self.assertEqual( + build_sex_check_lookup(ht, hl.dict({'ROS_006_18Y03226_D1': 'remapped_id'})), + { + 'remapped_id': Sex.FEMALE, + 'ROS_006_18Y03227_D1': Sex.FEMALE, + 'ROS_006_18Y03228_D1': Sex.FEMALE, + 'ROS_007_19Y05919_D1': Sex.FEMALE, + 'ROS_007_19Y05939_D1': Sex.MALE, + 'ROS_007_19Y05987_D1': Sex.UNKNOWN, + 'ROS_007_19Y05989_D1': Sex.X0, + }, + ) + + def test_all_relatedness_checks(self): + relatedness_check_lookup = { + # Parent + ('sample_1', 'sample_2'): [ + 0.0, + 0.98, + 0.0, + 0.52, + ], + # GrandParent + ('sample_1', 'sample_3'): [0.48, 0.52, 0, 0.24], + # Half Sibling (but actually a hidden Sibling) + ('sample_1', 'sample_4'): [0.25, 0.5, 0.25, 0.5], + } + sample = Sample( + sex=Sex.FEMALE, + sample_id='sample_1', + mother='sample_2', + paternal_grandfather='sample_3', + half_siblings=['sample_4'], + ) + family = Family( + family_guid='family_1a', + samples={ + 'sample_1': sample, + 'sample_2': Sample(sex=Sex.MALE, sample_id='sample_2'), + 'sample_3': Sample(sex=Sex.MALE, sample_id='sample_3'), + 'sample_4': Sample(sex=Sex.MALE, sample_id='sample_4'), + 'sample_5': Sample(sex=Sex.MALE, sample_id='sample_5'), + }, + ) + failure_reasons = all_relatedness_checks( + relatedness_check_lookup, + family, + sample, + ) + self.assertListEqual(failure_reasons, []) + + # Defined grandparent missing in relatedness table + sample = Sample( + sex=Sex.FEMALE, + sample_id='sample_1', + mother='sample_2', + paternal_grandfather='sample_3', + paternal_grandmother='sample_5', + ) + failure_reasons = all_relatedness_checks( + relatedness_check_lookup, + family, + sample, + ) + self.assertListEqual( + failure_reasons, + [ + 'Sample sample_1 has expected relation "grandparent_grandchild" to sample_5 but has coefficients []', + ], + ) + + # Sibling is actually a half sibling. + relatedness_check_lookup = { + **relatedness_check_lookup, + ('sample_1', 'sample_4'): [0.5, 0.5, 0, 0.25], + } + sample = Sample( + sex=Sex.FEMALE, + sample_id='sample_1', + mother='sample_2', + paternal_grandfather='sample_3', + siblings=['sample_4'], + ) + failure_reasons = all_relatedness_checks( + relatedness_check_lookup, + family, + sample, + ) + self.assertListEqual( + failure_reasons, + [ + 'Sample sample_1 has expected relation "sibling" to sample_4 but has coefficients [0.5, 0.5, 0, 0.25]', + ], + ) + + relatedness_check_lookup = { + **relatedness_check_lookup, + ('sample_1', 'sample_2'): [ + 0.5, + 0.5, + 0.5, + 0.5, + ], + } + sample = Sample( + sex=Sex.FEMALE, + sample_id='sample_1', + mother='sample_2', + paternal_grandfather='sample_3', + siblings=['sample_4'], + ) + failure_reasons = all_relatedness_checks( + relatedness_check_lookup, + family, + sample, + ) + self.assertListEqual( + failure_reasons, + [ + 'Sample sample_1 has expected relation "parent_child" to sample_2 but has coefficients [0.5, 0.5, 0.5, 0.5]', + 'Sample sample_1 has expected relation "sibling" to sample_4 but has coefficients [0.5, 0.5, 0, 0.25]', + ], + ) + + # Some samples will include relationships with + # samples that are not expected to be included + # in the callset. These should not trigger relatedness + # failures. + sample = Sample( + sex=Sex.FEMALE, + sample_id='sample_1', + mother='sample_2', + ) + family = Family( + family_guid='family_1a', + samples={ + 'sample_1': sample, + }, + ) + failure_reasons = all_relatedness_checks( + {}, + family, + sample, + ) + self.assertListEqual( + failure_reasons, + [], + ) + + def test_get_families_failed_sex_check(self): + sex_check_ht = hl.Table.parallelize( + [ + {'s': 'ROS_006_18Y03226_D1', 'predicted_sex': 'F'}, + {'s': 'ROS_006_18Y03227_D1', 'predicted_sex': 'F'}, # Pedigree Sex U + {'s': 'ROS_006_18Y03228_D1', 'predicted_sex': 'F'}, + {'s': 'ROS_007_19Y05939_D1', 'predicted_sex': 'M'}, + {'s': 'ROS_007_19Y05987_D1', 'predicted_sex': 'U'}, # Pedigree Sex F + {'s': 'ROS_007_19Y05989_D1', 'predicted_sex': 'XXX'}, + ], + hl.tstruct( + s=hl.tstr, + predicted_sex=hl.tstr, + ), + key='s', + ) + pedigree_ht = import_pedigree(TEST_PEDIGREE_6) + failed_families = get_families_failed_sex_check( + parse_pedigree_ht_to_families(pedigree_ht), + sex_check_ht, + {}, + ) + self.assertCountEqual( + failed_families.values(), + [ + [ + 'Sample ROS_007_19Y05919_D1 has pedigree sex F but is missing from the sex check source', + 'Sample ROS_007_19Y05939_D1 has pedigree sex F but imputed sex M', + ], + ], + ) + + def test_get_families_failed_imputed_sex_ploidy(self) -> None: + female_sample = 'HG00731_1' + male_sample_1 = 'HG00732_1' + male_sample_2 = 'HG00732_1' + x0_sample = 'NA20899_1' + xxy_sample = 'NA20889_1' + xyy_sample = 'NA20891_1' + xxx_sample = 'NA20892_1' + + sex_check_ht = hl.read_table(TEST_SEX_CHECK_1) + families = { + Family( + family_guid='', + samples={ + female_sample: Sample(female_sample, Sex.FEMALE), + male_sample_1: Sample(male_sample_1, Sex.MALE), + male_sample_2: Sample(male_sample_2, Sex.MALE), + x0_sample: Sample(x0_sample, Sex.X0), + xxy_sample: Sample(xxy_sample, Sex.XXY), + xyy_sample: Sample(xyy_sample, Sex.XYY), + xxx_sample: Sample(xxx_sample, Sex.XXX), + }, + ), + } + + # All calls on X chromosome are valid + mt = ( + hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chrX', + position=1, + reference_genome='GRCh38', + ), + ], + }, + cols={ + 's': [ + female_sample, + male_sample_1, + x0_sample, + xxy_sample, + xyy_sample, + xxx_sample, + ], + }, + entries={ + 'GT': [ + [ + hl.Call(alleles=[0, 0], phased=False), + hl.Call(alleles=[0], phased=False), + hl.Call(alleles=[0, 0], phased=False), # X0 + hl.Call(alleles=[0, 0], phased=False), # XXY + hl.Call(alleles=[0, 0], phased=False), # XYY + hl.Call(alleles=[0, 0], phased=False), # XXX + ], + ], + }, + ) + .key_rows_by('locus') + .key_cols_by('s') + ) + failed_families = get_families_failed_imputed_sex_ploidy( + families, + mt, + sex_check_ht, + ) + self.assertDictEqual(failed_families, {}) + + # All calls on Y chromosome are valid + mt = ( + hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chrY', + position=1, + reference_genome='GRCh38', + ), + ], + }, + cols={ + 's': [ + female_sample, + male_sample_1, + x0_sample, + xxy_sample, + xyy_sample, + xxx_sample, + ], + }, + entries={ + 'GT': [ + [ + hl.missing(hl.tcall), + hl.Call(alleles=[0], phased=False), + hl.missing(hl.tcall), # X0 + hl.Call(alleles=[0, 0], phased=False), # XXY + hl.Call(alleles=[0, 0], phased=False), # XYY + hl.missing(hl.tcall), # XXX + ], + ], + }, + ) + .key_rows_by('locus') + .key_cols_by('s') + ) + failed_families = get_families_failed_imputed_sex_ploidy( + families, + mt, + sex_check_ht, + ) + self.assertDictEqual(failed_families, {}) + + # Invalid X chromosome case + mt = ( + hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chrX', + position=1, + reference_genome='GRCh38', + ), + ], + }, + cols={ + 's': [ + female_sample, + male_sample_1, + male_sample_2, + x0_sample, + xxy_sample, + xyy_sample, + xxx_sample, + ], + }, + entries={ + 'GT': [ + [ + hl.Call(alleles=[0], phased=False), # invalid Female call + hl.Call(alleles=[0], phased=False), # valid Male call + hl.missing(hl.tcall), # invalid Male call + hl.Call(alleles=[0], phased=False), # invalid X0 call + hl.Call(alleles=[0], phased=False), # invalid XXY call + hl.missing(hl.tcall), # valid XYY call + hl.Call(alleles=[0, 0], phased=False), # valid XXX call + ], + ], + }, + ) + .key_rows_by('locus') + .key_cols_by('s') + ) + failed_families = get_families_failed_imputed_sex_ploidy( + families, + mt, + sex_check_ht, + ) + self.assertCountEqual( + failed_families.values(), + [ + [ + "Found samples with misaligned ploidy with their provided imputed sex: ['HG00731_1', 'HG00732_1', 'NA20889_1', 'NA20899_1']", + ], + ], + ) + + # Invalid X chromosome case, but only discrepant family samples are reported + families = { + Family( + family_guid='', + samples={female_sample: Sample(female_sample, Sex.FEMALE)}, + ), + } + failed_families = get_families_failed_imputed_sex_ploidy( + families, + mt, + sex_check_ht, + ) + self.assertCountEqual( + failed_families.values(), + [ + [ + "Found samples with misaligned ploidy with their provided imputed sex: ['HG00731_1']", + ], + ], + ) diff --git a/loading_pipeline/lib/misc/gcnv.py b/loading_pipeline/lib/misc/gcnv.py new file mode 100644 index 0000000000..f1b13fe58e --- /dev/null +++ b/loading_pipeline/lib/misc/gcnv.py @@ -0,0 +1,9 @@ +import hail as hl + + +def parse_gcnv_genes(gene_col: hl.expr.StringExpression) -> hl.expr.SetExpression: + return hl.set( + gene_col.split(',') + .filter(lambda gene: ~hl.set({'None', 'null', 'NA', ''}).contains(gene)) + .map(lambda gene: gene.split(r'\.')[0]), + ) diff --git a/loading_pipeline/lib/misc/gcnv_test.py b/loading_pipeline/lib/misc/gcnv_test.py new file mode 100644 index 0000000000..33a72f3684 --- /dev/null +++ b/loading_pipeline/lib/misc/gcnv_test.py @@ -0,0 +1,54 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.misc.gcnv import parse_gcnv_genes + + +class GCNVGeneParsingTest(unittest.TestCase): + def test_parse_gcnv_genes(self): + t1 = hl.Table.parallelize( + [ + {'genes': 'AC118553.2,SLC35A3'}, + {'genes': 'AC118553.1,None'}, + {'genes': 'None'}, + {'genes': 'SLC35A3.43'}, + {'genes': ''}, + {'genes': 'SLC35A4.43'}, + ], + hl.tstruct(genes=hl.dtype('str')), + key='genes', + ) + t1 = t1.annotate(gene_set=parse_gcnv_genes(t1.genes)) + self.assertCountEqual( + t1.collect(), + [ + hl.Struct( + genes='AC118553.2,SLC35A3', + gene_set={'AC118553', 'SLC35A3'}, + ), + hl.Struct(genes='AC118553.1,None', gene_set={'AC118553'}), + hl.Struct(genes='None', gene_set=set()), + hl.Struct(genes='SLC35A3.43', gene_set={'SLC35A3'}), + hl.Struct(genes='', gene_set=set()), + hl.Struct(genes='SLC35A4.43', gene_set={'SLC35A4'}), + ], + ) + + def test_aggregate_parsed_genes(self): + t1 = hl.Table.parallelize( + [ + {'genes': 'AC118553.2,SLC35A3'}, + {'genes': 'AC118553.1,None'}, + {'genes': 'None'}, + {'genes': 'SLC35A3.43'}, + {'genes': ''}, + {'genes': 'SLC35A4.43'}, + ], + hl.tstruct(genes=hl.dtype('str')), + key='genes', + ) + aggregated_gene_set = t1.aggregate( + hl.flatten(hl.agg.collect_as_set(parse_gcnv_genes(t1.genes))), + ) + self.assertEqual(aggregated_gene_set, {'SLC35A4', 'SLC35A3', 'AC118553'}) diff --git a/loading_pipeline/lib/misc/gcp.py b/loading_pipeline/lib/misc/gcp.py new file mode 100644 index 0000000000..46a6c5ecd3 --- /dev/null +++ b/loading_pipeline/lib/misc/gcp.py @@ -0,0 +1,44 @@ +import datetime + +import google.auth +import google.auth.transport.requests +import google.oauth2.credentials +import pytz + +from loading_pipeline.lib.core import FeatureFlag + +SERVICE_ACCOUNT_CREDENTIALS = None +CLOUD_PLATFORM_SCOPE = [ + 'https://www.googleapis.com/auth/cloud-platform', +] +SOCIAL_AUTH_GOOGLE_OAUTH2_SCOPE = [ + 'https://www.googleapis.com/auth/userinfo.profile', + 'https://www.googleapis.com/auth/userinfo.email', + 'openid', +] +ONE_MINUTE_S = 60 + + +def get_service_account_credentials() -> google.oauth2.credentials.Credentials: + global SERVICE_ACCOUNT_CREDENTIALS + if not SERVICE_ACCOUNT_CREDENTIALS: + SERVICE_ACCOUNT_CREDENTIALS, _ = google.auth.default( + scopes=[ + *SOCIAL_AUTH_GOOGLE_OAUTH2_SCOPE, + *(CLOUD_PLATFORM_SCOPE if FeatureFlag.EXPECT_TDR_METRICS else []), + ], + ) + tz = pytz.UTC + if ( + SERVICE_ACCOUNT_CREDENTIALS.token + and ( + tz.localize(SERVICE_ACCOUNT_CREDENTIALS.expiry) + - datetime.datetime.now(tz=tz) + ).total_seconds() + > ONE_MINUTE_S + ): + return SERVICE_ACCOUNT_CREDENTIALS + SERVICE_ACCOUNT_CREDENTIALS.refresh( + request=google.auth.transport.requests.Request(), + ) + return SERVICE_ACCOUNT_CREDENTIALS diff --git a/loading_pipeline/lib/misc/io.py b/loading_pipeline/lib/misc/io.py new file mode 100644 index 0000000000..b2f4e33e55 --- /dev/null +++ b/loading_pipeline/lib/misc/io.py @@ -0,0 +1,336 @@ +import hashlib +import math +import os +import re +import uuid +from collections.abc import Callable +from string import Template + +import hail as hl +import hailtop.fs as hfs + +from loading_pipeline.lib.core import DatasetType, Env, ReferenceGenome, Sex +from loading_pipeline.lib.misc.gcnv import parse_gcnv_genes +from loading_pipeline.lib.misc.nested_field import parse_nested_field +from loading_pipeline.lib.misc.validation import SeqrValidationError + +BIALLELIC = 2 +B_PER_MB = 1 << 20 # 1024 * 1024 +MB_PER_PARTITION = 32 +MAX_SAMPLES_SPLIT_MULTI_SHUFFLE = 100 + + +def validated_hl_function( + regex_to_msg: dict[str, str | Template], +) -> Callable[[Callable], Callable]: + def decorator(fn: Callable) -> Callable: + def wrapper(*args, **kwargs) -> hl.Table | hl.MatrixTable: + try: + t, _ = checkpoint(fn(*args, **kwargs)) + except Exception as e: + for regex, msg in regex_to_msg.items(): + match = re.search(regex, str(e)) + if match and isinstance(msg, Template): + msg = msg.substitute(match=match.group(1)) # noqa: PLW2901 + if match: + raise SeqrValidationError(msg) from e + raise + else: + return t + + return wrapper + + return decorator + + +def file_size_bytes(path: str) -> int: + if not path.startswith(('gs://', 's3://')): + path = os.path.abspath(path) + + seen_files = set() + + def traverse(current_path: str) -> int: + try: + entries = hfs.ls(current_path) + except FileNotFoundError: + return 0 + + local_size = 0 + for entry in entries: + if entry.path in seen_files: + continue + seen_files.add(entry.path) + + if entry.typ == hfs.stat_result.FileType.FILE: + if not entry.path.endswith('.crc'): + local_size += entry.size + elif entry.typ == hfs.stat_result.FileType.DIRECTORY: + local_size += traverse(entry.path) + + return local_size + + return traverse(path) + + +def compute_hail_n_partitions(file_size_b: int) -> int: + return math.ceil(file_size_b / B_PER_MB / MB_PER_PARTITION) + + +@validated_hl_function( + { + 'RVD error! Keys found out of order': 'Your callset failed while attempting to split multiallelic sites. This error can occur if the dataset contains both multiallelic variants and duplicated loci.', + 'array index out of bounds': 'Your callset failed while attempting to split multiallelic sites. This error can occur if the provided Allele Depth (AD) field does not match the length of the multiallelic site.', + }, +) +def split_multi_hts( + mt: hl.MatrixTable, + skip_validate_no_duplicate_variants: bool, + max_samples_split_multi_shuffle=MAX_SAMPLES_SPLIT_MULTI_SHUFFLE, +) -> hl.MatrixTable: + bi = mt.filter_rows(hl.len(mt.alleles) == BIALLELIC) + # split_multi_hts filters star alleles by default, but we + # need that behavior for bi-allelic variants in addition to + # multi-allelics + bi = bi.filter_rows(~bi.alleles.contains('*')) + bi = bi.annotate_rows(a_index=1, was_split=False) + multi = mt.filter_rows(hl.len(mt.alleles) > BIALLELIC) + split = hl.split_multi_hts( + multi, + permit_shuffle=mt.count()[1] < max_samples_split_multi_shuffle, + ) + mt = split.union_rows(bi) + # If we've disabled validation (which is expected to throw an exception + # for duplicate variants, we would like to distinc ) + if skip_validate_no_duplicate_variants: + return mt.distinct_by_row() + return mt + + +def import_gcnv_bed_file(callset_path: str) -> hl.MatrixTable: + # Hail falls over itself with OOMs with use_new_shuffle here... no clue why. + hl._set_flags(use_new_shuffle=None, no_whole_stage_codegen='1') # noqa: SLF001 + ht = hl.import_table( + callset_path, + types={ + **DatasetType.GCNV.col_fields, + **DatasetType.GCNV.entries_fields, + **DatasetType.GCNV.row_fields, + }, + force=callset_path.endswith('gz'), + ) + mt = ht.to_matrix_table( + row_key=['variant_name', 'svtype'], + col_key=['sample_fix'], + row_fields=['chr', 'sc', 'sf', 'strvctvre_score'], + ) + mt = mt.rename({'start': 'sample_start', 'end': 'sample_end'}) + mt = mt.key_cols_by(s=mt.sample_fix) + mt = mt.annotate_rows( + variant_id=hl.format('%s_%s', mt.variant_name, mt.svtype), + filters=hl.empty_set(hl.tstr), + start=hl.agg.min(mt.sample_start), + end=hl.agg.max(mt.sample_end), + num_exon=hl.agg.max(mt.genes_any_overlap_totalExons), + gene_ids=hl.flatten( + hl.agg.collect_as_set(parse_gcnv_genes(mt.genes_any_overlap_Ensemble_ID)), + ), + cg_genes=hl.flatten( + hl.agg.collect_as_set(parse_gcnv_genes(mt.genes_CG_Ensemble_ID)), + ), + lof_genes=hl.flatten( + hl.agg.collect_as_set(parse_gcnv_genes(mt.genes_LOF_Ensemble_ID)), + ), + ) + return mt.unfilter_entries() + + +@validated_hl_function( + { + '.*FileNotFoundException|GoogleJsonResponseException: 403 Forbidden|arguments refer to no files.*': 'Unable to access the VCF in cloud storage.', + # NB: ?: is non-capturing group. + '.*(?:InvalidHeader|VCFParseError): (.*)$': Template( + 'VCF failed file format validation: $match', + ), + '.*IOException: Gzip-compressed data is corrupt.*': 'Gzip-compressed data is corrupt.', + }, +) +def import_vcf( + callset_path: str, + reference_genome: ReferenceGenome, +) -> hl.MatrixTable: + args = { + 'reference_genome': reference_genome.value, + 'skip_invalid_loci': True, + 'contig_recoding': reference_genome.contig_recoding(), + 'find_replace': ( + 'nul', + '.', + ), # Required for internal exome callsets (+ some AnVIL requests) + 'array_elements_required': False, + 'call_fields': [], # PGT is unused downstream, but is occasionally present in old VCFs! + } + try: + mt, _ = checkpoint( + hl.import_vcf( + callset_path, + force_bgz=True, + **args, + ), + ) + except Exception as e: + # Handle callsets provided as gz but not bgz + # Note that this is handled separately from other VCF validation + # as it's an exceptional case that we can handle internally. + if 'File does not conform to block gzip format' not in str(e): + raise + mt = hl.import_vcf( + callset_path, + force=True, + **args, + ) + return mt + + +def import_callset( + callset_path: str, + reference_genome: ReferenceGenome, + dataset_type: DatasetType, +) -> hl.MatrixTable: + if dataset_type == DatasetType.GCNV: + mt = import_gcnv_bed_file(callset_path) + elif 'vcf' in callset_path: + mt = import_vcf(callset_path, reference_genome) + elif 'mt' in callset_path: + mt = hl.read_matrix_table(callset_path) + if dataset_type == DatasetType.SV: + mt = mt.annotate_rows( + variant_id=mt.rsid, + ) + return mt.key_rows_by(*dataset_type.table_key_type(reference_genome).fields) + + +@validated_hl_function( + { + 'instance has no field (.*)': Template( + 'Your callset is missing a required field: $match', + ), + }, +) +def select_relevant_fields( + mt: hl.MatrixTable, + dataset_type: DatasetType, + additional_row_fields: None | dict[str, hl.expr.types.HailType | set] = None, +) -> hl.MatrixTable: + mt = mt.select_globals() + mt = mt.select_rows( + **{field: parse_nested_field(mt, field) for field in dataset_type.row_fields}, + **{ + field: parse_nested_field(mt, field) + for field in (additional_row_fields or []) + }, + ) + mt = mt.select_cols( + **{field: parse_nested_field(mt, field) for field in dataset_type.col_fields}, + ) + return mt.select_entries( + **{ + field: parse_nested_field(mt, field) + for field in dataset_type.entries_fields + }, + ) + + +def import_imputed_sex(imputed_sex_path: str) -> hl.Table: + ht = hl.import_table(imputed_sex_path) + imputed_sex_lookup = hl.dict( + { + imputed_sex_value: s.value + for s in Sex + for imputed_sex_value in s.imputed_sex_values + }, + ) + ht = ht.select( + s=ht.collaborator_sample_id, + predicted_sex=( + hl.case() + .when( + imputed_sex_lookup.contains(ht.predicted_sex), + imputed_sex_lookup[ht.predicted_sex], + ) + .or_error( + hl.format( + 'Found unexpected value %s in imputed sex file', + ht.predicted_sex, + ), + ) + ), + ) + return ht.key_by(ht.s) + + +def import_tdr_qc_metrics(file_path: str) -> hl.Table: + ht = hl.import_table( + file_path, + types={ + 'contamination_rate': hl.tfloat32, + 'percent_bases_at_20x': hl.tfloat32, + 'mean_coverage': hl.tfloat32, + }, + delimiter='\t', + missing=[''], + ) + ht = ht.select( + s=ht.collaborator_sample_id, + contamination_rate=ht.contamination_rate, + percent_bases_at_20x=ht.percent_bases_at_20x, + mean_coverage=ht.mean_coverage, + ) + return ht.key_by(ht.s) + + +def import_pedigree(pedigree_path: str) -> hl.Table: + ht = hl.import_table(pedigree_path, missing='') + optional_selects = {'remap_id': ht.VCF_ID} if 'VCF_ID' in ht.row else {} + return ht.select( + sex=ht.Sex, + family_guid=ht.Family_GUID, + s=ht.Individual_ID, + maternal_s=ht.Maternal_ID, + paternal_s=ht.Paternal_ID, + **optional_selects, + ) + + +def remap_pedigree_hash(pedigree_path: str) -> hl.Int32Expression: + sha256 = hashlib.sha256() + with hfs.open(pedigree_path) as f2: + sha256.update(f2.read().encode('utf8')) + # maximum 4 byte int + return hl.int32(int(sha256.hexdigest()[:8], 16)) + + +def checkpoint( + t: hl.Table | hl.MatrixTable, +) -> tuple[hl.Table | hl.MatrixTable, str]: + suffix = 'mt' if isinstance(t, hl.MatrixTable) else 'ht' + read_fn = hl.read_matrix_table if isinstance(t, hl.MatrixTable) else hl.read_table + checkpoint_path = os.path.join( + Env.HAIL_TMP_DIR, + f'{uuid.uuid4()}.{suffix}', + ) + t.write(checkpoint_path) + return read_fn(checkpoint_path), checkpoint_path + + +def write( + t: hl.Table | hl.MatrixTable, + destination_path: str, + repartition: bool = True, +) -> hl.Table | hl.MatrixTable: + t, path = checkpoint(t) + if repartition: + t = t.repartition( + compute_hail_n_partitions(file_size_bytes(path)), + shuffle=False, + ) + return t.write(destination_path, overwrite=True) diff --git a/loading_pipeline/lib/misc/io_test.py b/loading_pipeline/lib/misc/io_test.py new file mode 100644 index 0000000000..a346e8b323 --- /dev/null +++ b/loading_pipeline/lib/misc/io_test.py @@ -0,0 +1,211 @@ +import unittest +from unittest import mock + +import hail as hl + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome +from loading_pipeline.lib.misc.io import ( + compute_hail_n_partitions, + file_size_bytes, + import_imputed_sex, + import_vcf, + remap_pedigree_hash, + select_relevant_fields, + split_multi_hts, +) +from loading_pipeline.lib.misc.validation import SeqrValidationError + +TEST_IMPUTED_SEX = 'loading_pipeline/var/test/sex_check/test_imputed_sex.tsv' +TEST_IMPUTED_SEX_UNEXPECTED_VALUE = ( + 'loading_pipeline/var/test/sex_check/test_imputed_sex_unexpected_value.tsv' +) +CORRUPTED_VCF = 'loading_pipeline/var/test/callsets/1kg_corrupt.vcf.gz' +TEST_INVALID_VCF = 'loading_pipeline/var/test/callsets/improperly_formatted.vcf' +TEST_PEDIGREE_3_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_3_remap.tsv' +TEST_MITO_MT = 'loading_pipeline/var/test/callsets/mito_1.mt' + + +class IOTest(unittest.TestCase): + def test_file_size_mb(self) -> None: + # find loading_pipeline/var/test/callsets/mito_1.mt -type f | grep -v 'crc' | xargs ls -alt {} | awk '{sum += $5; print sum}' + # 191310 + self.assertEqual(file_size_bytes(TEST_MITO_MT), 191310) + + def test_compute_hail_n_partitions(self) -> None: + self.assertEqual(compute_hail_n_partitions(23), 1) + self.assertEqual(compute_hail_n_partitions(191310), 1) + self.assertEqual(compute_hail_n_partitions(1913100000), 58) + + def test_import_imputed_sex(self) -> None: + ht = import_imputed_sex(TEST_IMPUTED_SEX) + self.assertListEqual( + ht.collect(), + [ + hl.Struct(s='abc_1', predicted_sex='M'), + hl.Struct(s='abc_2', predicted_sex='F'), + hl.Struct(s='abc_3', predicted_sex='U'), + hl.Struct(s='abc_4', predicted_sex='XYY'), + hl.Struct(s='abc_5', predicted_sex='U'), + ], + ) + + def test_import_imputed_sex_unexpected_value(self) -> None: + ht = import_imputed_sex(TEST_IMPUTED_SEX_UNEXPECTED_VALUE) + self.assertRaisesRegex( + hl.utils.java.HailUserError, + 'Found unexpected value UNKNOWN in imputed sex file', + ht.collect, + ) + + def test_remap_pedigree_hash(self) -> None: + self.assertEqual( + hl.eval( + remap_pedigree_hash( + TEST_PEDIGREE_3_REMAP, + ), + ), + 573002191, + ) + + def test_import_vcf(self) -> None: + self.assertRaisesRegex( + TypeError, + 'missing 1 required positional argument', + import_vcf, + 'abc', + ) + self.assertRaisesRegex( + SeqrValidationError, + 'Unable to access the VCF in cloud storage', + import_vcf, + 'bad.vcf', + ReferenceGenome.GRCh38, + ) + self.assertRaisesRegex( + SeqrValidationError, + 'Gzip-compressed data is corrupt', + import_vcf, + CORRUPTED_VCF, + ReferenceGenome.GRCh38, + ) + with mock.patch( + 'loading_pipeline.lib.misc.io.hl.read_table', + ) as mock_read_table: + mock_read_table.side_effect = hl.utils.java.FatalError( + 'GoogleJsonResponseException: 403 Forbidden', + ) + self.assertRaisesRegex( + SeqrValidationError, + 'Unable to access the VCF in cloud storage', + import_vcf, + 'abc123/bad.vcf', + ReferenceGenome.GRCh38, + ) + self.assertRaisesRegex( + SeqrValidationError, + 'VCF failed file format validation: Your input file has a malformed header: We never saw the required CHROM header line \\(starting with one #\\) for the input VCF file', + import_vcf, + TEST_PEDIGREE_3_REMAP, + ReferenceGenome.GRCh38, + ) + self.assertRaisesRegex( + SeqrValidationError, + "VCF failed file format validation: invalid character 'N' in integer literal", + import_vcf, + TEST_INVALID_VCF, + ReferenceGenome.GRCh38, + ) + + def test_select_missing_field(self) -> None: + self.assertRaisesRegex( + SeqrValidationError, + "Your callset is missing a required field: 'a magic field'", + select_relevant_fields, + hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + ], + 'alleles': [ + ['A', 'C'], + ], + 'rsid': ['rs1233'], + 'filters': [{'PASS'}], + }, + cols={'s': ['sample_1']}, + entries={ + 'GT': [[hl.Call([0, 0])]], + 'AD': [[[0, 20]]], + 'GQ': [[99]], + }, + ).key_rows_by('locus', 'alleles'), + DatasetType.SNV_INDEL, + {'a magic field': hl.tint32}, + ) + + def test_split_multi_failure(self) -> None: + self.assertRaisesRegex( + SeqrValidationError, + 'Your callset failed while attempting to split multiallelic sites. This error can occur if the dataset contains both multiallelic variants and duplicated loci.', + split_multi_hts, + hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + ], + 'alleles': [ + ['A', 'G', 'AC'], + ['A', 'AT', 'C', 'G'], + ], + }, + cols={'s': ['sample_1']}, + entries={ + 'GQ': [[99], [98]], + }, + ) + .key_rows_by('locus', 'alleles') + .repartition(1), + False, + 1, + ) + + def test_split_multi_failure_ad_length(self) -> None: + self.assertRaisesRegex( + SeqrValidationError, + 'Your callset failed while attempting to split multiallelic sites. This error can occur if the provided Allele Depth \\(AD\\) field does not match the length of the multiallelic site.', + split_multi_hts, + hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + ], + 'alleles': [ + ['GAC', 'G', 'GTTTTTTTTTTTTTTTAC'], + ], + }, + cols={'s': ['sample_1']}, + entries={ + 'GQ': [[99]], + 'AD': [[[0, 1]]], + }, + ).key_rows_by('locus', 'alleles'), + False, + 1, + ) diff --git a/loading_pipeline/lib/misc/math.py b/loading_pipeline/lib/misc/math.py new file mode 100644 index 0000000000..65feedb0a7 --- /dev/null +++ b/loading_pipeline/lib/misc/math.py @@ -0,0 +1,9 @@ +def constrain( + number: int | float, + lower_bound: int | float, + upper_bound: int | float, +) -> int: + if lower_bound > upper_bound: + msg = 'Lower bound should be less than or equal to upper bound' + raise ValueError(msg) + return max(lower_bound, min(number, upper_bound)) diff --git a/loading_pipeline/lib/misc/math_test.py b/loading_pipeline/lib/misc/math_test.py new file mode 100644 index 0000000000..19e12d6bfc --- /dev/null +++ b/loading_pipeline/lib/misc/math_test.py @@ -0,0 +1,12 @@ +import unittest + +from loading_pipeline.lib.misc.math import constrain + + +class TestConstrainFunction(unittest.TestCase): + def test_constrain(self): + self.assertEqual(constrain(5, 0, 10), 5) + self.assertEqual(constrain(-3, 0, 10), 0) + self.assertEqual(constrain(15, 0, 10), 10) + with self.assertRaises(ValueError): + constrain(5, 10, 0) diff --git a/loading_pipeline/lib/misc/nested_field.py b/loading_pipeline/lib/misc/nested_field.py new file mode 100644 index 0000000000..43d39005bb --- /dev/null +++ b/loading_pipeline/lib/misc/nested_field.py @@ -0,0 +1,17 @@ +import hail as hl + + +def parse_nested_field(t: hl.MatrixTable | hl.Table, fields: str): + expression = t + # Behavior here allows only a single nested field. + # Additional nesting is considered to be part of the + # name of the field. e.g. `gnomadv4.1_AF`. + for field in fields.split('.', maxsplit=1): + # Select from multi-allelic list. + if field.endswith('#'): + expression = expression[field[:-1]][ + (t.a_index if hasattr(t, 'a_index') else 1) - 1 + ] + else: + expression = expression[field] + return expression diff --git a/loading_pipeline/lib/misc/nested_field_test.py b/loading_pipeline/lib/misc/nested_field_test.py new file mode 100644 index 0000000000..8d465187a5 --- /dev/null +++ b/loading_pipeline/lib/misc/nested_field_test.py @@ -0,0 +1,81 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.misc.nested_field import parse_nested_field + + +class TestConstrainFunction(unittest.TestCase): + def test_parse_nested_field(self): + ht = hl.Table.parallelize( + [ + { + 'locus': hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + 'alleles': ['A', 'C'], + 'a': hl.Struct(d=1), + 'b': hl.Struct(e=[2, 9]), + 'h': hl.Struct(**{'i.j': 1}), + 'a_index': 1, + }, + { + 'locus': hl.Locus( + contig='chr1', + position=2, + reference_genome='GRCh38', + ), + 'alleles': ['A', 'C'], + 'a': hl.Struct(d=3), + 'b': hl.Struct(e=[4, 5]), + 'h': hl.Struct(**{'i.j': 2}), + 'a_index': 1, + }, + ], + hl.tstruct( + locus=hl.tlocus('GRCh38'), + alleles=hl.tarray(hl.tstr), + a=hl.tstruct(d=hl.tint32), + b=hl.tstruct(e=hl.tarray(hl.tint32)), + h=hl.tstruct(**{'i.j': hl.tint32}), + a_index=hl.tint32, + ), + key=['locus', 'alleles'], + ) + ht = ht.select( + d=parse_nested_field(ht, 'a.d'), + e=parse_nested_field(ht, 'b.e#'), + f=parse_nested_field(ht, 'a'), + g=parse_nested_field(ht, 'h.i.j'), + ) + self.assertListEqual( + ht.collect(), + [ + hl.Struct( + locus=hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + alleles=['A', 'C'], + d=1, + e=2, + f=hl.Struct(d=1), + g=1, + ), + hl.Struct( + locus=hl.Locus( + contig='chr1', + position=2, + reference_genome='GRCh38', + ), + alleles=['A', 'C'], + d=3, + e=4, + f=hl.Struct(d=3), + g=2, + ), + ], + ) diff --git a/loading_pipeline/lib/misc/pedigree.py b/loading_pipeline/lib/misc/pedigree.py new file mode 100644 index 0000000000..50bc30e225 --- /dev/null +++ b/loading_pipeline/lib/misc/pedigree.py @@ -0,0 +1,200 @@ +import itertools +from dataclasses import dataclass, field +from enum import Enum + +import hail as hl +import numpy as np + +from loading_pipeline.lib.core import Sex + +DEFAULT_RELATEDNESS_TOLERANCE = 0.2 +PARENT_CHILD_RELATEDNESS_TOLERANCE = 0.4 + + +class Relation(Enum): + PARENT_CHILD = 'parent_child' + GRANDPARENT_GRANDCHILD = 'grandparent_grandchild' + SIBLING = 'sibling' + HALF_SIBLING = 'half_sibling' + AUNT_NEPHEW = 'aunt_nephew' + + @property + def coefficients(self): + return { + Relation.PARENT_CHILD: [0, 1, 0, 0.5], + Relation.GRANDPARENT_GRANDCHILD: [0.5, 0.5, 0, 0.25], + Relation.SIBLING: [0.25, 0.5, 0.25, 0.5], + Relation.HALF_SIBLING: [0.5, 0.5, 0, 0.25], + Relation.AUNT_NEPHEW: [0.5, 0.5, 0, 0.25], + }[self] + + def coefficients_equal(self, coefficients: list[float]) -> bool: + if self == Relation.PARENT_CHILD: + return np.allclose( + coefficients[0], + self.coefficients[0], + atol=0.025, + ) and np.allclose( + coefficients[1:], + self.coefficients[1:], + atol=DEFAULT_RELATEDNESS_TOLERANCE, + ) + return np.allclose( + coefficients, + self.coefficients, + atol=DEFAULT_RELATEDNESS_TOLERANCE, + ) + + +@dataclass +class Sample: + sample_id: str + sex: Sex + mother: str = None + father: str = None + maternal_grandmother: str = None + maternal_grandfather: str = None + paternal_grandmother: str = None + paternal_grandfather: str = None + siblings: list[str] = field(default_factory=list) + half_siblings: list[str] = field(default_factory=list) + aunt_nephews: list[str] = field(default_factory=list) + + def is_aunt_nephew(self: 'Sample', other: 'Sample') -> bool: + return ( + # My Maternal Grandparents are your Parents + self.maternal_grandmother + and self.maternal_grandfather + and (self.maternal_grandmother == other.mother) + and (self.maternal_grandfather == other.father) + ) or ( + # My Paternal Grandparents are your Parents + self.paternal_grandmother + and self.paternal_grandfather + and (self.paternal_grandmother == other.mother) + and (self.paternal_grandfather == other.father) + ) + + def is_in_direct_lineage(self: 'Sample', other: 'Sample') -> bool: + return self.sample_id in { + other.mother, + other.father, + other.maternal_grandmother, + other.maternal_grandfather, + other.paternal_grandmother, + other.paternal_grandfather, + } or other.sample_id in { + self.mother, + self.father, + self.maternal_grandmother, + self.maternal_grandfather, + self.paternal_grandmother, + self.paternal_grandfather, + } + + +@dataclass +class Family: + family_guid: str + samples: dict[str, Sample] + + def __hash__(self): + return hash(self.family_guid) + + def __eq__(self, other): + return self.family_guid == other.family_guid + + @staticmethod + def parse_direct_lineage(rows: list[hl.Struct]) -> dict[str, Sample]: + samples = {} + for row in rows: + samples[row.s] = Sample( + sample_id=row.s, + sex=Sex(row.sex), + mother=row.maternal_s, + father=row.paternal_s, + ) + + for row in rows: + # Maternal GrandParents + maternal_s = samples[row.s].mother + if maternal_s and maternal_s in samples: + if samples[maternal_s].mother: + samples[row.s].maternal_grandmother = samples[maternal_s].mother + if samples[maternal_s].father: + samples[row.s].maternal_grandfather = samples[maternal_s].father + + # Paternal GrandParents + paternal_s = samples[row.s].father + if paternal_s and paternal_s in samples: + if samples[paternal_s].mother: + samples[row.s].paternal_grandmother = samples[paternal_s].mother + if samples[paternal_s].father: + samples[row.s].paternal_grandfather = samples[paternal_s].father + return samples + + @staticmethod + def parse_collateral_lineage( + samples: dict[str, Sample], + ) -> dict[str, Sample]: + # NB: relationships are identified unidirectionally here (for better or for worse) + # A sample_i that is siblings with sample_j, will list sample_j as as sibling, but + # sample_j will not list sample_i as a sibling. Relationships only appear in the + # ibd table a single time, so we only need to check the pairing once. + for sample_i, sample_j in itertools.combinations(samples.values(), 2): + # If sample is already related from direct relationships, continue + if sample_i.is_in_direct_lineage(sample_j): + continue + + # If both parents are identified and the same, samples are siblings. + if ( + sample_i.mother + and sample_i.father + and (sample_i.mother == sample_j.mother) + and (sample_i.father == sample_j.father) + ): + sample_i.siblings.append(sample_j.sample_id) + continue + + # If only a single parent is identified and the same, samples are half siblings + if (sample_i.mother and sample_i.mother == sample_j.mother) or ( + sample_i.father and sample_i.father == sample_j.father + ): + sample_i.half_siblings.append(sample_j.sample_id) + continue + + # If either set of one's grandparents is identified and equal to the other's parents, + # they're aunt/uncle related + # NB: because we will only check an i, j pair of samples a single time, (itertools.combinations) + # we need to check both grandparents_i == parents_j and parents_i == grandparents_j. + if sample_i.is_aunt_nephew(sample_j) or sample_j.is_aunt_nephew(sample_i): + sample_i.aunt_nephews.append(sample_j.sample_id) + return samples + + @classmethod + def parse(cls, family_guid: str, rows: list[hl.Struct]) -> 'Family': + samples = cls.parse_direct_lineage(rows) + samples = cls.parse_collateral_lineage(samples) + return cls( + family_guid=family_guid, + samples=samples, + ) + + +def parse_pedigree_ht_to_families( + pedigree_ht: hl.Table, +) -> set[Family]: + families = set() + for family_guid, rows in itertools.groupby( + sorted(pedigree_ht.collect(), key=lambda x: x.family_guid), + lambda x: x.family_guid, + ): + families.add(Family.parse(family_guid, list(rows))) + return families + + +def parse_pedigree_ht_to_remap_ht(pedigree_ht: hl.Table) -> hl.Table: + ht = pedigree_ht.filter(hl.is_defined(pedigree_ht.remap_id)) + ht = ht.annotate(seqr_id=ht.s) + ht = ht.key_by(s=ht.remap_id) + return ht.select('seqr_id') diff --git a/loading_pipeline/lib/misc/pedigree_test.py b/loading_pipeline/lib/misc/pedigree_test.py new file mode 100644 index 0000000000..77432ba138 --- /dev/null +++ b/loading_pipeline/lib/misc/pedigree_test.py @@ -0,0 +1,514 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.core import Sex +from loading_pipeline.lib.misc.io import import_pedigree +from loading_pipeline.lib.misc.pedigree import ( + Family, + Sample, + parse_pedigree_ht_to_families, +) + +TEST_PEDIGREE_1 = 'loading_pipeline/var/test/pedigrees/test_pedigree_1.tsv' +TEST_PEDIGREE_2 = 'loading_pipeline/var/test/pedigrees/test_pedigree_2.tsv' +TEST_PEDIGREE_9 = 'loading_pipeline/var/test/pedigrees/test_pedigree_9.tsv' + + +class PedigreesTest(unittest.TestCase): + def test_empty_pedigree(self) -> None: + with self.assertRaises(Exception): # noqa: B017 + _ = import_pedigree(TEST_PEDIGREE_1) + + def test_parse_lineage(self) -> None: + # + # + # sample_9 sample_10 sample_7 + # \ / \ | + # sample_6 -> sample_8 --------- sample_3 ----- ? | + # \ / \ / | + # sample_4, sample_5 sample_2 | sample_1 + # + # + samples = Family.parse_direct_lineage( + [ + hl.Struct(s='sample_1', maternal_s=None, paternal_s=None, sex='F'), + hl.Struct( + s='sample_2', + maternal_s='sample_3', + paternal_s=None, + sex='M', + ), + hl.Struct( + s='sample_3', + maternal_s=None, + paternal_s='sample_7', + sex='F', + ), + hl.Struct( + s='sample_4', + maternal_s='sample_3', + paternal_s='sample_8', + sex='M', + ), + hl.Struct( + s='sample_5', + maternal_s='sample_3', + paternal_s='sample_8', + sex='M', + ), + hl.Struct( + s='sample_6', + maternal_s='sample_9', + paternal_s='sample_10', + sex='M', + ), + hl.Struct(s='sample_7', maternal_s=None, paternal_s=None, sex='M'), + hl.Struct( + s='sample_8', + maternal_s='sample_9', + paternal_s='sample_10', + sex='F', + ), + hl.Struct(s='sample_9', maternal_s=None, paternal_s=None, sex='F'), + hl.Struct(s='sample_10', maternal_s=None, paternal_s=None, sex='M'), + ], + ) + self.assertEqual( + Family.parse_collateral_lineage(samples), + { + 'sample_1': Sample( + sample_id='sample_1', + sex=Sex.FEMALE, + mother=None, + father=None, + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'sample_2': Sample( + sample_id='sample_2', + sex=Sex.MALE, + mother='sample_3', + father=None, + maternal_grandmother=None, + maternal_grandfather='sample_7', + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=['sample_4', 'sample_5'], + aunt_nephews=[], + ), + 'sample_3': Sample( + sample_id='sample_3', + sex=Sex.FEMALE, + mother=None, + father='sample_7', + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'sample_4': Sample( + sample_id='sample_4', + sex=Sex.MALE, + mother='sample_3', + father='sample_8', + maternal_grandmother=None, + maternal_grandfather='sample_7', + paternal_grandmother='sample_9', + paternal_grandfather='sample_10', + siblings=['sample_5'], + half_siblings=[], + aunt_nephews=['sample_6'], + ), + 'sample_5': Sample( + sample_id='sample_5', + sex=Sex.MALE, + mother='sample_3', + father='sample_8', + maternal_grandmother=None, + maternal_grandfather='sample_7', + paternal_grandmother='sample_9', + paternal_grandfather='sample_10', + siblings=[], + half_siblings=[], + aunt_nephews=['sample_6'], + ), + 'sample_6': Sample( + sample_id='sample_6', + sex=Sex.MALE, + mother='sample_9', + father='sample_10', + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=['sample_8'], + half_siblings=[], + aunt_nephews=[], + ), + 'sample_7': Sample( + sample_id='sample_7', + sex=Sex.MALE, + mother=None, + father=None, + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'sample_8': Sample( + sample_id='sample_8', + sex=Sex.FEMALE, + mother='sample_9', + father='sample_10', + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'sample_9': Sample( + sample_id='sample_9', + sex=Sex.FEMALE, + mother=None, + father=None, + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'sample_10': Sample( + sample_id='sample_10', + sex=Sex.MALE, + mother=None, + father=None, + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + }, + ) + + def test_parse_parent_not_aunt_uncle(self) -> None: + samples = Family.parse_direct_lineage( + [ + hl.Struct(s='sample_1', maternal_s=None, paternal_s=None, sex='F'), + hl.Struct( + s='sample_2', + maternal_s=None, + paternal_s=None, + sex='M', + ), + hl.Struct( + s='sample_3', + maternal_s='sample_1', + paternal_s='sample_2', + sex='F', + ), + hl.Struct( + s='sample_4', + maternal_s='sample_3', + paternal_s=None, + sex='F', + ), + hl.Struct( + s='sample_5', + maternal_s='sample_3', + paternal_s=None, + sex='F', + ), + ], + ) + self.assertEqual( + Family.parse_collateral_lineage(samples), + { + 'sample_1': Sample( + sample_id='sample_1', + sex=Sex.FEMALE, + mother=None, + father=None, + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'sample_2': Sample( + sample_id='sample_2', + sex=Sex.MALE, + mother=None, + father=None, + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'sample_3': Sample( + sample_id='sample_3', + sex=Sex.FEMALE, + mother='sample_1', + father='sample_2', + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'sample_4': Sample( + sample_id='sample_4', + sex=Sex.FEMALE, + mother='sample_3', + father=None, + maternal_grandmother='sample_1', + maternal_grandfather='sample_2', + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=['sample_5'], + aunt_nephews=[], + ), + 'sample_5': Sample( + sample_id='sample_5', + sex=Sex.FEMALE, + mother='sample_3', + father=None, + maternal_grandmother='sample_1', + maternal_grandfather='sample_2', + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + }, + ) + + def test_parse_project(self) -> None: + pedigree_ht = import_pedigree(TEST_PEDIGREE_2) + self.assertCountEqual( + list(parse_pedigree_ht_to_families(pedigree_ht)), + [ + Family( + family_guid='BBL_BC1-000345_1', + samples={ + 'BBL_BC1-000345_01_D1': Sample( + sample_id='BBL_BC1-000345_01_D1', + sex=Sex.UNKNOWN, + mother='BBL_BC1-000345_03_D1', + father='BBL_BC1-000345_02_D1', + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'BBL_BC1-000345_02_D1': Sample( + sample_id='BBL_BC1-000345_02_D1', + sex=Sex.MALE, + mother=None, + father=None, + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'BBL_BC1-000345_03_D1': Sample( + sample_id='BBL_BC1-000345_03_D1', + sex=Sex.FEMALE, + mother=None, + father=None, + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + }, + ), + Family( + family_guid='BBL_HT-007-5195_1', + samples={ + 'BBL_HT-007-5195_01_D1': Sample( + sample_id='BBL_HT-007-5195_01_D1', + sex=Sex.FEMALE, + mother='BBL_HT-007-5195_03_D1', + father='BBL_HT-007-5195_02_D1', + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[ + 'BBL_HT-007-5195_04_D1', + 'BBL_HT-007-5195_05_D1', + 'BBL_HT-007-5195_06_D1', + ], + half_siblings=[], + aunt_nephews=[], + ), + 'BBL_HT-007-5195_02_D1': Sample( + sample_id='BBL_HT-007-5195_02_D1', + sex=Sex.MALE, + mother=None, + father=None, + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'BBL_HT-007-5195_03_D1': Sample( + sample_id='BBL_HT-007-5195_03_D1', + sex=Sex.FEMALE, + mother=None, + father=None, + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'BBL_HT-007-5195_04_D1': Sample( + sample_id='BBL_HT-007-5195_04_D1', + sex=Sex.MALE, + mother='BBL_HT-007-5195_03_D1', + father='BBL_HT-007-5195_02_D1', + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=['BBL_HT-007-5195_05_D1', 'BBL_HT-007-5195_06_D1'], + half_siblings=[], + aunt_nephews=[], + ), + 'BBL_HT-007-5195_05_D1': Sample( + sample_id='BBL_HT-007-5195_05_D1', + sex=Sex.FEMALE, + mother='BBL_HT-007-5195_03_D1', + father='BBL_HT-007-5195_02_D1', + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=['BBL_HT-007-5195_06_D1'], + half_siblings=[], + aunt_nephews=[], + ), + 'BBL_HT-007-5195_06_D1': Sample( + sample_id='BBL_HT-007-5195_06_D1', + sex=Sex.MALE, + mother='BBL_HT-007-5195_03_D1', + father='BBL_HT-007-5195_02_D1', + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + }, + ), + Family( + family_guid='BBL_SDS1-000178_1', + samples={ + 'BBL_SDS1-000178_01_D1': Sample( + sample_id='BBL_SDS1-000178_01_D1', + sex=Sex.FEMALE, + mother=None, + father=None, + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + }, + ), + ], + ) + + def test_subsetted_pedigree_with_removed_parent(self) -> None: + pedigree_ht = import_pedigree(TEST_PEDIGREE_2) + pedigree_ht = pedigree_ht.filter( + pedigree_ht.s != 'BBL_BC1-000345_02_D1', + ) + parsed_pedigree = parse_pedigree_ht_to_families(pedigree_ht) + family = next( + iter( + [ + family + for family in parsed_pedigree + if family.family_guid == 'BBL_BC1-000345_1' + ], + ), + ) + self.assertEqual(len(family.samples), 2) + self.assertFalse( + 'BBL_BC1-000345_02_D1' in family.samples, + ) + self.assertEqual( + family.samples['BBL_BC1-000345_01_D1'].father, + 'BBL_BC1-000345_02_D1', + ) + self.assertEqual( + family.samples['BBL_BC1-000345_01_D1'].mother, + 'BBL_BC1-000345_03_D1', + ) + + def test_pedigree_ungrouped_families(self) -> None: + pedigree_ht = import_pedigree(TEST_PEDIGREE_9) + parsed_pedigree = parse_pedigree_ht_to_families(pedigree_ht) + self.assertEqual(len(parsed_pedigree), 2) + family = next( + iter( + [ + family + for family in parsed_pedigree + if family.family_guid == 'family_2_1' + ], + ), + ) + self.assertTrue( + family.samples.keys() == {'RGP_164_1', 'RGP_164_2', 'RGP_164_4'}, + ) diff --git a/loading_pipeline/lib/misc/requests.py b/loading_pipeline/lib/misc/requests.py new file mode 100644 index 0000000000..e0ee66f366 --- /dev/null +++ b/loading_pipeline/lib/misc/requests.py @@ -0,0 +1,14 @@ +import requests +from requests.adapters import HTTPAdapter, Retry + + +def requests_retry_session(): + s = requests.Session() + retries = Retry( + total=5, + backoff_factor=1, + status_forcelist=[500, 502, 503, 504], + ) + s.mount('http://', HTTPAdapter(max_retries=retries)) + s.mount('https://', HTTPAdapter(max_retries=retries)) + return s diff --git a/loading_pipeline/lib/misc/retry.py b/loading_pipeline/lib/misc/retry.py new file mode 100644 index 0000000000..3a9408b075 --- /dev/null +++ b/loading_pipeline/lib/misc/retry.py @@ -0,0 +1,61 @@ +import functools +import time + +from loading_pipeline.lib.logger import get_logger + +logger = get_logger(__name__) + + +def retry(tries=3, delay=30, backoff=3): + def decorator(func): + @functools.wraps(func) + def wrapper(*args, **kwargs): + max_tries = tries + current_delay = delay + total_start_time = time.time() + args_str = ', '.join(str(a) for a in args) + kwargs_str = ', '.join(f'{k}={v!s}' for k, v in kwargs.items()) + + for attempt in range(1, max_tries): + start_time = time.time() + try: + result = func(*args, **kwargs) + duration = time.time() - start_time + logger.info( + f'{func.__name__} args:{args_str} kwargs:{kwargs_str} succeeded on attempt {attempt} in {duration:.2f}s', + ) + except Exception: + duration = time.time() - start_time + logger.exception( + f'{func.__name__} args:{args_str} kwargs:{kwargs_str} failed on attempt {attempt} after {duration:.2f}s, ' + f'retrying in {current_delay} seconds.', + ) + time.sleep(current_delay) + current_delay *= backoff + else: + return result + + # Final attempt + start_time = time.time() + try: + result = func(*args, **kwargs) + duration = time.time() - start_time + total_duration = time.time() - total_start_time + logger.info( + f'{func.__name__} args:{args_str} kwargs:{kwargs_str} succeeded on final attempt {max_tries} in {duration:.2f}s ' + f'(total retry time: {total_duration:.2f}s)', + ) + except Exception: + duration = time.time() - start_time + total_duration = time.time() - total_start_time + logger.exception( + f'{func.__name__} args:{args_str} kwargs:{kwargs} failed on final attempt {max_tries} after {duration:.2f}s ' + f'(total retry time: {total_duration:.2f}s)', + ) + raise + else: + return result + + return wrapper + + return decorator diff --git a/loading_pipeline/lib/misc/retry_test.py b/loading_pipeline/lib/misc/retry_test.py new file mode 100644 index 0000000000..4b756abce1 --- /dev/null +++ b/loading_pipeline/lib/misc/retry_test.py @@ -0,0 +1,69 @@ +import unittest +from unittest.mock import Mock, patch + +from loading_pipeline.lib.core import DatasetType +from loading_pipeline.lib.misc.retry import retry + + +class TestRetryDecorator(unittest.TestCase): + @patch('time.sleep', return_value=None) + def test_retry_success_first_try(self, mock_sleep): + mock_func = Mock(return_value='success') + + @retry(tries=3, delay=1, backoff=2) + def func(d: DatasetType): + return mock_func(d) + + result = func(DatasetType.SNV_INDEL) + self.assertEqual(result, 'success') + self.assertEqual(mock_func.call_count, 1) + mock_sleep.assert_not_called() + + @patch('time.sleep', return_value=None) + @patch('loading_pipeline.lib.misc.retry.logger') + def test_retry_eventual_success(self, mock_logger, mock_sleep): + mock_func = Mock( + side_effect=[Exception('fail'), Exception('fail again'), 'success'], + ) + + @retry(tries=3, delay=1, backoff=2) + def func(): + return mock_func() + + result = func() + self.assertEqual(result, 'success') + self.assertEqual(mock_func.call_count, 3) + self.assertEqual(mock_sleep.call_count, 2) + mock_sleep.assert_any_call(1) + mock_sleep.assert_any_call(2) + + @patch('time.sleep', return_value=None) + @patch('loading_pipeline.lib.misc.retry.logger') + def test_retry_all_failures(self, mock_logger, mock_sleep): + mock_func = Mock(side_effect=Exception('always fails')) + + @retry(tries=3, delay=1, backoff=2) + def func(): + return mock_func() + + with self.assertRaises(Exception) as context: + func() + + self.assertEqual(str(context.exception), 'always fails') + self.assertEqual(mock_func.call_count, 3) + self.assertEqual(mock_sleep.call_count, 2) + + @patch('time.sleep', return_value=None) + @patch('loading_pipeline.lib.misc.retry.logger.exception') + def test_logs_retry_message(self, mock_log, mock_sleep): + mock_func = Mock(side_effect=[Exception('fail'), 'success']) + + @retry(tries=2, delay=1, backoff=2) + def func(d: DatasetType): + return mock_func(d) + + func(d=DatasetType.SNV_INDEL) + self.assertIn( + 'func args: kwargs:d=SNV_INDEL failed on attempt 1 after 0.00s, retrying in 1 seconds.', + mock_log.call_args[0][0], + ) diff --git a/loading_pipeline/lib/misc/runs.py b/loading_pipeline/lib/misc/runs.py new file mode 100644 index 0000000000..702f86d94c --- /dev/null +++ b/loading_pipeline/lib/misc/runs.py @@ -0,0 +1,89 @@ +import datetime +import os +from collections import defaultdict + +import hailtop.fs as hfs + +from loading_pipeline.lib.core.dataset_type import DatasetType +from loading_pipeline.lib.core.environment import Env +from loading_pipeline.lib.misc.retry import retry +from loading_pipeline.lib.paths import ( + clickhouse_load_fail_file_path, + clickhouse_load_success_file_path, + loading_pipeline_queue_dir, + pipeline_run_success_file_path, +) + + +def new_run_id(): + return datetime.datetime.now(datetime.UTC).strftime( + '%Y%m%d-%H%M%S-%f', + ) + + +def get_oldest_queue_path() -> str | None: + """ + Returns the path of the oldest loading pipeline request file in the queue directory. + If the directory is empty, returns None. + """ + queue_dir = loading_pipeline_queue_dir() + queue_files = os.listdir(queue_dir) + + if len(queue_files) == 0: + return None + queue_files = [os.path.join(queue_dir, queue_file) for queue_file in queue_files] + return min(queue_files, key=os.path.getctime) + + +def is_queue_full() -> bool: + """ + Checks if the loading pipeline queue directory is full. + Returns True if the number of files exceeds a predefined limit, otherwise False. + """ + return len(os.listdir(loading_pipeline_queue_dir())) >= Env.LOADING_QUEUE_LIMIT + + +@retry() +def get_run_ids() -> tuple[defaultdict, defaultdict, defaultdict]: + successful_pipeline_runs, successful_clickhouse_loads, failed_clickhouse_loads = ( + defaultdict(set), + defaultdict(set), + defaultdict(set), + ) + for dataset_type in DatasetType: + for reference_genome in dataset_type.reference_genomes: + successful_pipeline_runs[(reference_genome, dataset_type)] = { + p.path.split('/')[-2] + for p in hfs.ls( + pipeline_run_success_file_path( + reference_genome, + dataset_type, + '*', + ), + ) + } + successful_clickhouse_loads[(reference_genome, dataset_type)] = { + p.path.split('/')[-2] + for p in hfs.ls( + clickhouse_load_success_file_path( + reference_genome, + dataset_type, + '*', + ), + ) + } + failed_clickhouse_loads[(reference_genome, dataset_type)] = { + p.path.split('/')[-2] + for p in hfs.ls( + clickhouse_load_fail_file_path( + reference_genome, + dataset_type, + '*', + ), + ) + } + return ( + successful_pipeline_runs, + successful_clickhouse_loads, + failed_clickhouse_loads, + ) diff --git a/loading_pipeline/lib/misc/runs_test.py b/loading_pipeline/lib/misc/runs_test.py new file mode 100644 index 0000000000..b1a601727a --- /dev/null +++ b/loading_pipeline/lib/misc/runs_test.py @@ -0,0 +1,84 @@ +import os + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome +from loading_pipeline.lib.misc.runs import get_run_ids +from loading_pipeline.lib.paths import ( + clickhouse_load_fail_file_path, + clickhouse_load_success_file_path, + pipeline_run_success_file_path, + runs_path, +) +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + + +class RunsTest(MockedDatarootTestCase): + def setUp(self): + super().setUp() + run_ids = [ + 'manual__2024-08-05T16-07-58.365146+00-00', + 'manual__2024-08-06T10-15-23.123456+00-00', + 'manual__2024-08-07T12-30-45.654321+00-00', # _SUCCESS, _CLICKHOUSE_LOAD_FAIL + 'manual__2024-08-08T09-45-00.000000+00-00', # _SUCCESS + 'manual__2024-08-09T18-22-13.999999+00-00', # _SUCCESS, _CLICKHOUSE_LOAD_SUCCESS + ] + for reference_genome, dataset_type in [ + (ReferenceGenome.GRCh38, DatasetType.SNV_INDEL), + (ReferenceGenome.GRCh37, DatasetType.SNV_INDEL), + (ReferenceGenome.GRCh38, DatasetType.GCNV), + (ReferenceGenome.GRCh37, DatasetType.GCNV), + ]: + for run_id in run_ids: + base_path = runs_path(reference_genome, dataset_type) + os.makedirs(os.path.join(base_path, run_id), exist_ok=True) + if '07T12' in run_id: + failure_file = clickhouse_load_fail_file_path( + reference_genome, + dataset_type, + run_id, + ) + open(failure_file, 'w').close() + if '09' in run_id or '07T12' in run_id: + success_file = pipeline_run_success_file_path( + reference_genome, + dataset_type, + run_id, + ) + open(success_file, 'w').close() + if '09T18' in run_id: + success_file = clickhouse_load_success_file_path( + reference_genome, + dataset_type, + run_id, + ) + open(success_file, 'w').close() + + def test_get_run_ids(self) -> None: + ( + successful_pipeline_runs, + successful_clickhouse_loads, + failed_clickhouse_loads, + ) = get_run_ids() + self.assertCountEqual( + successful_pipeline_runs[(ReferenceGenome.GRCh38, DatasetType.SNV_INDEL)], + { + 'manual__2024-08-09T18-22-13.999999+00-00', + 'manual__2024-08-08T09-45-00.000000+00-00', + 'manual__2024-08-07T12-30-45.654321+00-00', + }, + ) + self.assertCountEqual( + successful_clickhouse_loads[ + (ReferenceGenome.GRCh38, DatasetType.SNV_INDEL) + ], + { + 'manual__2024-08-09T18-22-13.999999+00-00', + }, + ) + self.assertCountEqual( + successful_clickhouse_loads[(ReferenceGenome.GRCh37, DatasetType.GCNV)], + {}, + ) + self.assertCountEqual( + failed_clickhouse_loads[(ReferenceGenome.GRCh38, DatasetType.SNV_INDEL)], + {'manual__2024-08-07T12-30-45.654321+00-00'}, + ) diff --git a/loading_pipeline/lib/misc/sample_ids.py b/loading_pipeline/lib/misc/sample_ids.py new file mode 100644 index 0000000000..f86ef4ef67 --- /dev/null +++ b/loading_pipeline/lib/misc/sample_ids.py @@ -0,0 +1,66 @@ +from collections import Counter + +import hail as hl + +from loading_pipeline.lib.logger import get_logger +from loading_pipeline.lib.misc.validation import SeqrValidationError + +logger = get_logger(__name__) + + +def remap_sample_ids( + mt: hl.MatrixTable, + project_remap_ht: hl.Table, +) -> hl.MatrixTable: + collected_remap = project_remap_ht.collect() + s_dups = [k for k, v in Counter([r.s for r in collected_remap]).items() if v > 1] + seqr_dups = [ + k for k, v in Counter([r.seqr_id for r in collected_remap]).items() if v > 1 + ] + + if len(s_dups) > 0 or len(seqr_dups) > 0: + msg = f'Duplicate s or seqr_id entries in remap file were found. Duplicate s:{s_dups}. Duplicate seqr_id:{seqr_dups}.' + raise SeqrValidationError(msg) + + missing_samples = project_remap_ht.anti_join(mt.cols()).collect() + remap_count = len(collected_remap) + + if len(missing_samples) != 0: + message = ( + f'Only {project_remap_ht.semi_join(mt.cols()).count()} out of {remap_count} ' + 'remap IDs matched IDs in the variant callset.\n' + f"IDs that aren't in the callset: {missing_samples}\n" + ) + raise SeqrValidationError(message) + + mt = mt.annotate_cols(**project_remap_ht[mt.s]) + remap_expr = hl.if_else(hl.is_missing(mt.seqr_id), mt.s, mt.seqr_id) + mt = mt.annotate_cols(seqr_id=remap_expr, vcf_id=mt.s) + mt = mt.key_cols_by(s=mt.seqr_id) + logger.info(f'Remapped {remap_count} sample ids...') + return mt + + +def subset_samples( + mt: hl.MatrixTable, + sample_subset_ht: hl.Table, +) -> hl.MatrixTable: + subset_count = sample_subset_ht.count() + anti_join_ht = sample_subset_ht.anti_join(mt.cols()) + anti_join_ht_count = anti_join_ht.count() + if subset_count == 0: + message = '0 sample ids found the subset HT, something is probably wrong.' + raise SeqrValidationError(message) + + if anti_join_ht_count != 0: + missing_samples = anti_join_ht.s.collect() + message = ( + f'Only {subset_count - anti_join_ht_count} out of {subset_count} ' + f'subsetting-table IDs matched IDs in the variant callset.\n' + f"IDs that aren't in the callset: {missing_samples}\n" + f'All callset sample IDs:{mt.s.collect()}' + ) + raise SeqrValidationError(message) + logger.info(f'Subsetted to {subset_count} sample ids') + mt = mt.semi_join_cols(sample_subset_ht) + return mt.filter_rows(hl.agg.any(hl.is_defined(mt.GT))) diff --git a/loading_pipeline/lib/misc/sample_ids_test.py b/loading_pipeline/lib/misc/sample_ids_test.py new file mode 100644 index 0000000000..6d3fb7efd0 --- /dev/null +++ b/loading_pipeline/lib/misc/sample_ids_test.py @@ -0,0 +1,160 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.misc.sample_ids import ( + remap_sample_ids, + subset_samples, +) +from loading_pipeline.lib.misc.validation import SeqrValidationError + +CALLSET_MT = hl.MatrixTable.from_parts( + rows={'variants': [1, 2]}, + cols={'s': ['HG00731', 'HG00732', 'HG00733']}, + entries={ + 'GT': [ + [hl.Call([0, 1]), hl.missing(hl.tcall), hl.Call([0, 1])], + [hl.Call([0, 1]), hl.Call([0, 1]), hl.Call([1, 1])], + ], + }, +).key_cols_by('s') + + +class SampleLookupTest(unittest.TestCase): + def test_remap_2_sample_ids(self) -> None: + # remap 2 of 3 samples in callset + project_remap_ht = hl.Table.parallelize( + [ + {'s': 'HG00731', 'seqr_id': 'HG00731_1'}, + {'s': 'HG00732', 'seqr_id': 'HG00732_1'}, + ], + hl.tstruct( + s=hl.tstr, + seqr_id=hl.tstr, + ), + key='s', + ) + + remapped_mt = remap_sample_ids( + CALLSET_MT, + project_remap_ht, + ) + + self.assertEqual(remapped_mt.cols().count(), 3) + self.assertEqual( + remapped_mt.cols().collect(), + [ + hl.Struct( + col_idx=0, + s='HG00731_1', + seqr_id='HG00731_1', + vcf_id='HG00731', + ), + hl.Struct( + col_idx=1, + s='HG00732_1', + seqr_id='HG00732_1', + vcf_id='HG00732', + ), + hl.Struct(col_idx=2, s='HG00733', seqr_id='HG00733', vcf_id='HG00733'), + ], + ) + + def test_remap_sample_ids_remap_has_duplicate(self) -> None: + # remap file has 2 rows for HG00732 + project_remap_ht = hl.Table.parallelize( + [ + {'s': 'HG00731', 'seqr_id': 'HG00731_1'}, + {'s': 'HG00732', 'seqr_id': 'HG00732_1'}, + {'s': 'HG00732', 'seqr_id': 'HG00732_1'}, # duplicate + ], + hl.tstruct( + s=hl.tstr, + seqr_id=hl.tstr, + ), + key='s', + ) + + with self.assertRaises(SeqrValidationError): + remap_sample_ids( + CALLSET_MT, + project_remap_ht, + ) + + def test_remap_sample_ids_remap_has_missing_samples(self) -> None: + # remap file has 4 rows, but only 3 samples in callset + project_remap_ht = hl.Table.parallelize( + [ + {'s': 'HG00731', 'seqr_id': 'HG00731_1'}, + {'s': 'HG00732', 'seqr_id': 'HG00732_1'}, + {'s': 'HG00733', 'seqr_id': 'HG00733_1'}, + {'s': 'HG00734', 'seqr_id': 'HG00734_1'}, # missing in callset + ], + hl.tstruct( + s=hl.tstr, + seqr_id=hl.tstr, + ), + key='s', + ) + + with self.assertRaises(SeqrValidationError): + remap_sample_ids( + CALLSET_MT, + project_remap_ht, + ) + + def test_subset_samples_zero_samples(self): + # subset 0 of 3 samples in callset + sample_subset_ht = hl.Table.parallelize( + [], + hl.tstruct(s=hl.tstr), + key='s', + ) + + with self.assertRaises(SeqrValidationError): + subset_samples( + CALLSET_MT, + sample_subset_ht, + ) + + def test_subset_samples_missing_samples(self): + # subset 2 of 3 samples in callset, but 1 is missing + sample_subset_ht = hl.Table.parallelize( + [ + {'s': 'HG00731'}, + {'s': 'HG00732'}, + {'s': 'HG00734'}, # missing in callset + ], + hl.tstruct(s=hl.tstr), + key='s', + ) + + with self.assertRaises(SeqrValidationError): + subset_samples( + CALLSET_MT, + sample_subset_ht, + ) + + def test_subset_no_defined_gt(self): + mt = hl.MatrixTable.from_parts( + rows={'variants': [1, 2]}, + cols={'s': ['HG00731', 'HG00732']}, + entries={ + 'GT': [ + [hl.Call([1, 1]), hl.missing(hl.tcall)], + [hl.Call([1, 1]), hl.Call([1, 1])], + ], + }, + ).key_cols_by('s') + sample_subset_ht = hl.Table.parallelize( + [ + {'s': 'HG00732'}, + ], + hl.tstruct(s=hl.tstr), + key='s', + ) + mt = subset_samples( + mt, + sample_subset_ht, + ) + self.assertEqual(mt.count(), (1, 1)) diff --git a/loading_pipeline/lib/misc/slack.py b/loading_pipeline/lib/misc/slack.py new file mode 100644 index 0000000000..ea17b12c99 --- /dev/null +++ b/loading_pipeline/lib/misc/slack.py @@ -0,0 +1,65 @@ +import json + +from slacker import Slacker + +from loading_pipeline.api.model import PipelineRunnerRequest +from loading_pipeline.lib.core import Env, FeatureFlag +from loading_pipeline.lib.logger import get_logger + +DATAPROC_URL = 'https://console.cloud.google.com/dataproc/jobs?project={gcloud_project}' +SLACK_FAILURE_MESSAGE_PREFIX = ':failed: Pipeline Runner Request Failed :failed:' +SLACK_SUCCESS_MESSAGE_PREFIX = ( + ':white_check_mark: Pipeline Runner Request Success! :white_check_mark:' +) + + +logger = get_logger(__name__) + + +def _safe_post_to_slack(message) -> None: + try: + if not Env.SLACK_TOKEN: + logger.info(message) + return + slack = Slacker(Env.SLACK_TOKEN) + slack.chat.post_message( + Env.SLACK_NOTIFICATION_CHANNEL, + message, + as_user=False, + icon_emoji=':beaker:', + username='Beaker (engineering-minion)', + ) + except Exception: + logger.exception( + f'Slack error: Original message in channel ({Env.SLACK_NOTIFICATION_CHANNEL}) - {message}', + ) + + +def safe_post_to_slack_failure( + run_id: str, + prr: PipelineRunnerRequest, + e: type[Exception], +) -> None: + message = [ + SLACK_FAILURE_MESSAGE_PREFIX, + f'Run ID: {run_id}', + f'```{json.dumps(prr.model_dump(), indent=4, sort_keys=True)}```', + f'Reason: {e!s}', + ] + if FeatureFlag.RUN_PIPELINE_ON_DATAPROC: + message = [ + *message, + f'<{DATAPROC_URL.format(gcloud_project=Env.GCLOUD_PROJECT)}|Dataproc Jobs Page>', + ] + _safe_post_to_slack('\n'.join(message)) + + +def safe_post_to_slack_success(run_id: str, prr: PipelineRunnerRequest) -> None: + message = '\n'.join( + [ + SLACK_SUCCESS_MESSAGE_PREFIX, + f'Run ID: {run_id}', + f'```{json.dumps(prr.model_dump(), indent=4, sort_keys=True)}```', + ], + ) + _safe_post_to_slack(message) diff --git a/loading_pipeline/lib/misc/sv.py b/loading_pipeline/lib/misc/sv.py new file mode 100644 index 0000000000..b3a54463f0 --- /dev/null +++ b/loading_pipeline/lib/misc/sv.py @@ -0,0 +1,155 @@ +import itertools +import math + +import hail as hl + +from loading_pipeline.lib.annotations import sv +from loading_pipeline.lib.core import ReferenceGenome, Sex +from loading_pipeline.lib.misc.pedigree import Family + +WRONG_CHROM_PENALTY = 1e9 + + +def _get_grouped_new_callset_variants( + mt: hl.MatrixTable, + duplicate_internal_variant_ids: set[str], +) -> itertools.groupby: + mt = mt.select_rows( + 'info.SEQR_INTERNAL_TRUTH_VID', + end_locus=sv.end_locus(mt), + ) + return itertools.groupby( + sorted( + mt.filter_rows( + duplicate_internal_variant_ids.contains( + mt['info.SEQR_INTERNAL_TRUTH_VID'], + ), + ) + .rows() + .collect(), + key=lambda x: x['info.SEQR_INTERNAL_TRUTH_VID'], + ), + lambda x: x['info.SEQR_INTERNAL_TRUTH_VID'], + ) + + +def deduplicate_merged_sv_concordance_calls( + mt: hl.MatrixTable, + annotations_ht: hl.Table, +) -> hl.MatrixTable: + # First find the seqr internal variant ids that are duplicated in the new callset. + duplicate_internal_variant_ids = hl.set( + { + k + for k, v in mt.aggregate_rows( + hl.agg.counter(mt['info.SEQR_INTERNAL_TRUTH_VID']), + ).items() + if v > 1 + } + or hl.empty_set(hl.tstr), + ) + + # Then, collect into memory the necessary existing variants & the new variants + annotations_ht = annotations_ht.select('end_locus') + existing_variants = { + v.variant_id: v + for v in ( + annotations_ht.filter( + duplicate_internal_variant_ids.contains(annotations_ht.variant_id), + ).collect() + ) + } + grouped_new_variants = _get_grouped_new_callset_variants( + mt, + duplicate_internal_variant_ids, + ) + + # Then, iterate over new variants and exclude all but the best match + new_variant_ids_to_exclude = set() + for existing_variant_id, new_variants in grouped_new_variants: + existing_variant = existing_variants[existing_variant_id] + closest_variant_id, min_distance = None, math.inf + + # First pass to find the closest variant + new_variants_it1, new_variants_it2 = itertools.tee(new_variants, 2) + for new_variant in new_variants_it1: + distance = math.fabs( + new_variant.end_locus.position + - existing_variant.end_locus.position + + ( + WRONG_CHROM_PENALTY + if ( + new_variant.end_locus.contig + != existing_variant.end_locus.contig + ) + else 0 + ), + ) + if distance < min_distance: + min_distance = distance + closest_variant_id = new_variant.variant_id + + # Second pass to exclude all but the closest. + for new_variant in new_variants_it2: + if new_variant.variant_id != closest_variant_id: + new_variant_ids_to_exclude.add(new_variant.variant_id) + + # Finally, remove SEQR_INTERNAL_TRUTH_VID from those variants. + return mt.annotate_rows( + **{ + 'info.SEQR_INTERNAL_TRUTH_VID': hl.if_else( + hl.set(new_variant_ids_to_exclude or hl.empty_set(hl.tstr)).contains( + mt.variant_id, + ), + hl.missing(hl.tstr), + mt['info.SEQR_INTERNAL_TRUTH_VID'], + ), + }, + ) + + +def overwrite_male_non_par_calls( + mt: hl.MatrixTable, + families: set[Family], +) -> hl.MatrixTable: + male_sample_ids = { + s.sample_id for f in families for s in f.samples.values() if s.sex == Sex.MALE + } + male_sample_ids = ( + hl.set(male_sample_ids) if male_sample_ids else hl.empty_set(hl.tstr) + ) + par_intervals = hl.array( + [ + i + for i in hl.get_reference(ReferenceGenome.GRCh38).par + if i.start.contig == ReferenceGenome.GRCh38.x_contig + ], + ) + non_par_interval = hl.interval( + par_intervals[0].end, + par_intervals[1].start, + ) + # NB: making use of existing formatting_annotation_fns. + # We choose to annotate & drop here as the sample level + # fields are dropped by the time we format variants. + mt = mt.annotate_rows( + start_locus=sv.start_locus(mt), + end_locus=sv.end_locus(mt), + ) + mt = mt.annotate_entries( + GT=hl.if_else( + ( + male_sample_ids.contains(mt.s) + & non_par_interval.overlaps( + hl.interval( + mt.start_locus, + mt.end_locus, + ), + ) + & mt.GT.is_het() + ), + hl.Call([1], phased=False), + mt.GT, + ), + ) + return mt.drop('start_locus', 'end_locus') diff --git a/loading_pipeline/lib/misc/sv_test.py b/loading_pipeline/lib/misc/sv_test.py new file mode 100644 index 0000000000..aefa8a5cd5 --- /dev/null +++ b/loading_pipeline/lib/misc/sv_test.py @@ -0,0 +1,243 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, Sex +from loading_pipeline.lib.misc.io import import_callset, select_relevant_fields +from loading_pipeline.lib.misc.pedigree import Family, Sample +from loading_pipeline.lib.misc.sample_ids import subset_samples +from loading_pipeline.lib.misc.sv import ( + deduplicate_merged_sv_concordance_calls, + overwrite_male_non_par_calls, +) + +TEST_SV_VCF = 'loading_pipeline/var/test/callsets/sv_1.vcf' +ANNOTATIONS_HT = hl.Table.parallelize( + [ + { + 'variant_id': 'BND_chr1_6', + 'algorithms': 'manta', + 'end_locus': hl.Locus( + contig='chr5', + position=20404, + reference_genome='GRCh38', + ), + }, + { + 'variant_id': 'BND_chr1_9', + 'algorithms': 'manta', + 'end_locus': hl.Locus( + contig='chr1', + position=789481, + reference_genome='GRCh38', + ), + }, + { + 'variant_id': 'CPX_chr1_22', + 'algorithms': 'manta', + 'end_locus': hl.Locus( + contig='chr1', + position=6559723, + reference_genome='GRCh38', + ), + }, + ], + hl.tstruct( + variant_id=hl.tstr, + algorithms=hl.tstr, + end_locus=hl.tlocus('GRCh38'), + ), + key='variant_id', +) + + +class SVTest(unittest.TestCase): + def test_overwrite_male_non_par_calls(self) -> None: + mt = import_callset(TEST_SV_VCF, ReferenceGenome.GRCh38, DatasetType.SV) + mt = select_relevant_fields( + mt, + DatasetType.SV, + ) + mt = subset_samples( + mt, + hl.Table.parallelize( + [{'s': sample_id} for sample_id in ['RGP_164_1', 'RGP_164_2']], + hl.tstruct(s=hl.dtype('str')), + key='s', + ), + ) + mt = overwrite_male_non_par_calls( + mt, + { + Family( + family_guid='family_1', + samples={ + 'RGP_164_1': Sample(sample_id='RGP_164_1', sex=Sex.FEMALE), + 'RGP_164_2': Sample(sample_id='RGP_164_2', sex=Sex.MALE), + }, + ), + }, + ) + mt = mt.filter_rows(mt.locus.contig == 'chrX') + self.assertEqual( + [ + hl.Locus(contig='chrX', position=3, reference_genome='GRCh38'), + hl.Locus(contig='chrX', position=2781700, reference_genome='GRCh38'), + ], + mt.locus.collect(), + ) + self.assertEqual( + [ + hl.Call(alleles=[0, 0], phased=False), + # END of this variant < start of the non-par region. + hl.Call(alleles=[0, 1], phased=False), + hl.Call(alleles=[0, 0], phased=False), + hl.Call(alleles=[1], phased=False), + ], + mt.GT.collect(), + ) + self.assertFalse( + hasattr(mt, 'start_locus'), + ) + + def test_deduplicate_merged_sv_concordance_calls(self) -> None: + mt = ( + hl.MatrixTable.from_parts( + rows={ + 'variant_id': [ + 'new_v1', + 'new_v2', + 'new_v3', + ], + 'locus': [ + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=2, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=3, + reference_genome='GRCh38', + ), + ], + 'info.END': [ + 1, + 2, + 3, + ], + 'info.END2': [ + 1, + 2, + 3, + ], + 'info.CHR2': [ + 'chr1', + 'chr1', + 'chr1', + ], + 'info.SEQR_INTERNAL_TRUTH_VID': [ + 'BND_chr1_6', + 'BND_chr1_9', + 'CPX_chr1_22', + ], + }, + cols={'s': ['sample_1']}, + entries={'GQ': [[99] for _ in range(3)]}, + ) + .key_rows_by('variant_id') + .key_cols_by('s') + ) + mt = deduplicate_merged_sv_concordance_calls( + mt, + ANNOTATIONS_HT, + ) + self.assertEqual( + mt['info.SEQR_INTERNAL_TRUTH_VID'].collect(), + [ + 'BND_chr1_6', + 'BND_chr1_9', + 'CPX_chr1_22', + ], + ) + + mt = ( + hl.MatrixTable.from_parts( + rows={ + 'variant_id': [ + 'new_v1', + 'new_v2', + 'new_v3', + 'new_v4', + ], + 'locus': [ + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=2, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=3, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=4, + reference_genome='GRCh38', + ), + ], + 'info.END': [ + 1, + 2, + 789481, + 789485, + ], + 'info.END2': [ + 1, + 2, + 789481, + 789485, + ], + 'info.CHR2': [ + 'chr1', + 'chr1', + 'chr2', + 'chr1', + ], + 'info.SEQR_INTERNAL_TRUTH_VID': [ + 'BND_chr1_6', + 'BND_chr1_9', + 'BND_chr1_9', + 'BND_chr1_9', + ], + }, + cols={'s': ['sample_1']}, + entries={'GQ': [[99] for _ in range(4)]}, + ) + .key_rows_by('variant_id') + .key_cols_by('s') + ) + mt = deduplicate_merged_sv_concordance_calls( + mt, + ANNOTATIONS_HT, + ) + self.assertEqual( + mt['info.SEQR_INTERNAL_TRUTH_VID'].collect(), + [ + 'BND_chr1_6', + None, + None, + 'BND_chr1_9', + ], + ) diff --git a/loading_pipeline/lib/misc/terra_data_repository.py b/loading_pipeline/lib/misc/terra_data_repository.py new file mode 100644 index 0000000000..0aa2204b8a --- /dev/null +++ b/loading_pipeline/lib/misc/terra_data_repository.py @@ -0,0 +1,80 @@ +import os +import re +from collections.abc import Generator +from concurrent.futures import ThreadPoolExecutor, as_completed + +import google.cloud.bigquery +from google.cloud import bigquery + +from loading_pipeline.lib.misc.gcp import get_service_account_credentials +from loading_pipeline.lib.misc.requests import requests_retry_session + +BIGQUERY_METRICS = [ + 'predicted_sex', + 'contamination_rate', + 'percent_bases_at_20x', + 'collaborator_sample_id', + 'mean_coverage', +] +BIGQUERY_RESOURCE = 'bigquery' +TABLE_NAME_VALIDATION_REGEX = r'datarepo-\w+.datarepo_\w+' +TDR_ROOT_URL = 'https://data.terra.bio/api/repository/v1/' + + +def _tdr_request(resource: str) -> dict: + service_account_token = get_service_account_credentials().token + s = requests_retry_session() + res = s.get( + url=os.path.join(TDR_ROOT_URL, resource), + headers={'Authorization': f'Bearer {service_account_token}'}, + timeout=10, + ) + res.raise_for_status() + return res.json() + + +def _get_dataset_ids() -> list[str]: + res_body = _tdr_request('datasets?limit=50000') # Arbitrary large number :/ + items = res_body['items'] + for item in items: + if not any(x['cloudResource'] == BIGQUERY_RESOURCE for x in item['storage']): + # Hard failure on purpose to prompt manual investigation. + msg = 'Datasets without bigquery sources are unsupported' + raise ValueError(msg) + return [x['id'] for x in items] + + +def gen_bq_table_names() -> Generator[str]: + with ThreadPoolExecutor(max_workers=5) as executor: + futures = [ + executor.submit( + _tdr_request, + f'datasets/{dataset_id}?include=ACCESS_INFORMATION', + ) + for dataset_id in _get_dataset_ids() + ] + for future in as_completed(futures): + result = future.result() + yield f'{result["accessInformation"]["bigQuery"]["projectId"]}.{result["accessInformation"]["bigQuery"]["datasetName"]}' + + +def bq_metrics_query(bq_table_name: str) -> google.cloud.bigquery.table.RowIterator: + if not re.match(TABLE_NAME_VALIDATION_REGEX, bq_table_name): + msg = f'{bq_table_name} does not match expected pattern' + raise ValueError(msg) + client = bigquery.Client() + + # not all columns are guaranteed to be present, coalesce if missing + table_ddl = next( + client.query_and_wait( + f""" + SELECT ddl FROM `{bq_table_name}`.INFORMATION_SCHEMA.TABLES where table_name='sample'; + """, # noqa: S608 + ), + )[0] + metrics = [(m if m in table_ddl else f'NULL AS {m}') for m in BIGQUERY_METRICS] + return client.query_and_wait( + f""" + SELECT {','.join(metrics)} FROM `{bq_table_name}.sample`; + """, # noqa: S608 + ) diff --git a/loading_pipeline/lib/misc/terra_data_repository_test.py b/loading_pipeline/lib/misc/terra_data_repository_test.py new file mode 100644 index 0000000000..91b044d68f --- /dev/null +++ b/loading_pipeline/lib/misc/terra_data_repository_test.py @@ -0,0 +1,321 @@ +import json +import os +import unittest +from types import SimpleNamespace +from unittest.mock import Mock, call, patch + +import responses + +from loading_pipeline.lib.misc.terra_data_repository import ( + TDR_ROOT_URL, + _get_dataset_ids, + bq_metrics_query, + gen_bq_table_names, +) + +TDR_DATASETS = [ + { + 'id': '2dc51ee0-a037-499d-a915-a7c20a0b216d', + 'name': 'RP_3053', + 'description': 'TGG_Ware_DRAGEN_hg38. Dataset automatically created and linked to: RP-3053', + 'defaultProfileId': '0a164b9a-2b8b-45d2-859e-a4e369b9cb4f', + 'createdDate': '2023-10-05T13:15:27.649760Z', + 'storage': [ + { + 'region': 'us-central1', + 'cloudResource': 'bigquery', + 'cloudPlatform': 'gcp', + }, + { + 'region': 'us-east4', + 'cloudResource': 'firestore', + 'cloudPlatform': 'gcp', + }, + { + 'region': 'us-central1', + 'cloudResource': 'bucket', + 'cloudPlatform': 'gcp', + }, + ], + 'secureMonitoringEnabled': False, + 'cloudPlatform': 'gcp', + 'dataProject': 'datarepo-7242affb', + 'storageAccount': None, + 'phsId': None, + 'selfHosted': False, + 'predictableFileIds': False, + 'tags': [], + 'resourceLocks': { + 'exclusive': None, + 'shared': [], + }, + }, + { + 'id': 'beef77e8-575b-40e5-9340-a6f10e0bec67', + 'name': 'RP_3056', + 'description': 'RGP_HMB_DRAGEN_hg38. Dataset automatically created and linked to: RP-3056', + 'defaultProfileId': '835dd05d-c603-4b0d-926f-d9143fd24549', + 'createdDate': '2023-10-05T20:15:27.622481Z', + 'storage': [ + { + 'region': 'us-central1', + 'cloudResource': 'bigquery', + 'cloudPlatform': 'gcp', + }, + { + 'region': 'us-east4', + 'cloudResource': 'firestore', + 'cloudPlatform': 'gcp', + }, + { + 'region': 'us-central1', + 'cloudResource': 'bucket', + 'cloudPlatform': 'gcp', + }, + ], + 'secureMonitoringEnabled': False, + 'cloudPlatform': 'gcp', + 'dataProject': 'datarepo-5a72e31b', + 'storageAccount': None, + 'phsId': None, + 'selfHosted': False, + 'predictableFileIds': False, + 'tags': [], + 'resourceLocks': { + 'exclusive': None, + 'shared': [], + }, + }, + { + 'id': 'c8d74ac4-9a2e-4d3d-a6b5-1f4b433d949f', + 'name': 'RP_3055', + 'description': 'RGP_GRU_DRAGEN_hg38. Dataset automatically created and linked to: RP-3055', + 'defaultProfileId': '835dd05d-c603-4b0d-926f-d9143fd24549', + 'createdDate': '2023-10-05T20:15:28.255304Z', + 'storage': [ + { + 'region': 'us-central1', + 'cloudResource': 'bigquery', + 'cloudPlatform': 'gcp', + }, + { + 'region': 'us-east4', + 'cloudResource': 'firestore', + 'cloudPlatform': 'gcp', + }, + { + 'region': 'us-central1', + 'cloudResource': 'bucket', + 'cloudPlatform': 'gcp', + }, + ], + 'secureMonitoringEnabled': False, + 'cloudPlatform': 'gcp', + 'dataProject': 'datarepo-0f5be351', + 'storageAccount': None, + 'phsId': None, + 'selfHosted': False, + 'predictableFileIds': False, + 'tags': [], + 'resourceLocks': { + 'exclusive': None, + 'shared': [ + 'Gw_KTeYRS1aLhRvapMLYLg', + 'WrP-0w1aROOUbgkI8JS6Ug', + ], + }, + }, +] + + +@patch( + 'loading_pipeline.lib.misc.terra_data_repository.get_service_account_credentials', + return_value=SimpleNamespace( + token='abcdefg', # noqa: S106 + ), +) +class TerraDataRepositoryTest(unittest.TestCase): + @responses.activate + def test_get_dataset_ids(self, _: Mock) -> None: + responses.get( + os.path.join(TDR_ROOT_URL, 'datasets?limit=50000'), + body=json.dumps( + { + 'total': 3, + 'filteredTotal': 3, + 'items': TDR_DATASETS, + }, + ), + ) + self.assertListEqual( + _get_dataset_ids(), + [ + '2dc51ee0-a037-499d-a915-a7c20a0b216d', + 'beef77e8-575b-40e5-9340-a6f10e0bec67', + 'c8d74ac4-9a2e-4d3d-a6b5-1f4b433d949f', + ], + ) + + @responses.activate + def test_get_dataset_ids_no_bq(self, _: Mock) -> None: + responses.get( + os.path.join(TDR_ROOT_URL, 'datasets'), + body=json.dumps( + { + 'total': 1, + 'filteredTotal': 1, + 'items': [ + { + 'id': '2dc51ee0-a037-499d-a915-a7c20a0b216d', + 'name': 'RP_3053', + 'description': 'TGG_Ware_DRAGEN_hg38. Dataset automatically created and linked to: RP-3053', + 'defaultProfileId': '0a164b9a-2b8b-45d2-859e-a4e369b9cb4f', + 'createdDate': '2023-10-05T13:15:27.649760Z', + 'storage': [ + # NB: bigquery was removed from 'storage' here. + { + 'region': 'us-east4', + 'cloudResource': 'firestore', + 'cloudPlatform': 'gcp', + }, + { + 'region': 'us-central1', + 'cloudResource': 'bucket', + 'cloudPlatform': 'gcp', + }, + ], + 'secureMonitoringEnabled': False, + 'cloudPlatform': 'gcp', + 'dataProject': 'datarepo-7242affb', + 'storageAccount': None, + 'phsId': None, + 'selfHosted': False, + 'predictableFileIds': False, + 'tags': [], + 'resourceLocks': { + 'exclusive': None, + 'shared': [], + }, + }, + ], + }, + ), + ) + self.assertRaises( + ValueError, + _get_dataset_ids, + ) + + @responses.activate + def test_gen_bq_table_names(self, _: Mock) -> None: + responses.get( + os.path.join(TDR_ROOT_URL, 'datasets'), + body=json.dumps( + { + 'total': 3, + 'filteredTotal': 3, + 'items': TDR_DATASETS, + }, + ), + ) + for dataset_id, name, project_name, dataset_name in [ + ( + '2dc51ee0-a037-499d-a915-a7c20a0b216d', + 'RP_3053', + 'datarepo-7242affb', + 'datarepo_RP_3053', + ), + ( + 'beef77e8-575b-40e5-9340-a6f10e0bec67', + 'RP_3056', + 'datarepo-5a72e31b', + 'datarepo_RP_3056', + ), + ( + 'c8d74ac4-9a2e-4d3d-a6b5-1f4b433d949f', + 'RP_3059', + 'datarepo-aada2e3b', + 'datarepo_RP_3059', + ), + ]: + responses.get( + os.path.join( + TDR_ROOT_URL, + f'datasets/{dataset_id}?include=ACCESS_INFORMATION', + ), + body=json.dumps( + { + 'id': dataset_id, + 'name': name, + 'description': 'TGG_Ware_DRAGEN_hg38. Dataset automatically created and linked to: RP-3053', + 'defaultProfileId': None, + 'dataProject': None, + 'defaultSnapshotId': None, + 'schema': None, + 'createdDate': '2023-10-05T13:15:27.649760Z', + 'storage': None, + 'secureMonitoringEnabled': False, + 'phsId': None, + 'accessInformation': { + 'bigQuery': { + 'datasetName': dataset_name, + 'datasetId': f'{project_name}:{dataset_name}', + 'projectId': project_name, + 'link': 'https://console.cloud.google.com/bigquery?project=datarepo-7242affb&ws=!datarepo_RP_3053&d=datarepo_RP_3053&p=datarepo-7242affb&page=dataset', + 'tables': [ + { + 'name': 'jointcallset', + 'id': f'{project_name}.{dataset_name}.jointcallset', + 'qualifiedName': 'datarepo-7242affb.datarepo_RP_3053.jointcallset', + 'link': 'https://console.cloud.google.com/bigquery?project=datarepo-7242affb&ws=!datarepo_RP_3053&d=datarepo_RP_3053&p=datarepo-7242affb&page=table&t=jointcallset', + 'sampleQuery': 'SELECT * FROM `datarepo-7242affb.datarepo_RP_3053.jointcallset`', + }, + { + 'name': 'sample', + 'id': f'{project_name}.{dataset_name}.sample', + 'qualifiedName': 'datarepo-7242affb.datarepo_RP_3053.sample', + 'link': 'https://console.cloud.google.com/bigquery?project=datarepo-7242affb&ws=!datarepo_RP_3053&d=datarepo_RP_3053&p=datarepo-7242affb&page=table&t=sample', + 'sampleQuery': 'SELECT * FROM `datarepo-7242affb.datarepo_RP_3053.sample`', + }, + ], + }, + 'parquet': None, + }, + 'cloudPlatform': None, + 'selfHosted': False, + 'properties': None, + 'ingestServiceAccount': None, + 'predictableFileIds': False, + 'tags': [], + 'resourceLocks': { + 'exclusive': None, + 'shared': [], + }, + }, + ), + ) + self.assertCountEqual( + list(gen_bq_table_names()), + [ + 'datarepo-7242affb.datarepo_RP_3053', + 'datarepo-5a72e31b.datarepo_RP_3056', + 'datarepo-aada2e3b.datarepo_RP_3059', + ], + ) + + @patch('loading_pipeline.lib.misc.terra_data_repository.bigquery.Client') + def test_bq_metrics_query_missing_metrics( + self, + mock_bq_client: Mock, + _: Mock, + ) -> None: + mock_bq_client.return_value.query_and_wait.return_value = iter( + [['predicted_sex,contamination_rate,percent_bases_at_20x']], + ) + bq_metrics_query('datarepo-7242affb.datarepo_RP_3053') + self.assertEqual( + mock_bq_client.return_value.query_and_wait.mock_calls[1], + call( + '\n SELECT predicted_sex,contamination_rate,percent_bases_at_20x,NULL AS collaborator_sample_id,NULL AS mean_coverage FROM `datarepo-7242affb.datarepo_RP_3053.sample`;\n ', + ), + ) diff --git a/loading_pipeline/lib/misc/validation.py b/loading_pipeline/lib/misc/validation.py new file mode 100644 index 0000000000..f6ff00619f --- /dev/null +++ b/loading_pipeline/lib/misc/validation.py @@ -0,0 +1,203 @@ +from typing import Any + +import hail as hl + +from loading_pipeline.lib.core import ( + DatasetType, + Env, + ReferenceGenome, + SampleType, +) + +ALL_VALIDATIONS = 'all' +AMBIGUOUS_THRESHOLD_PERC: float = 0.01 # Fraction of samples identified as "ambiguous_sex" above which an error will be thrown. +MIN_ROWS_PER_CONTIG = 100 +SAMPLE_TYPE_MATCH_THRESHOLD = 0.3 + + +class SeqrValidationError(Exception): + def __init__( + self, + msg: str, + error_body: dict | None = None, + ): + super().__init__(msg) + self.msg = msg + self.error_body = error_body if error_body is not None else {} + + +def validate_allele_type( + t: hl.Table | hl.MatrixTable, + dataset_type: DatasetType, + **_: Any, +) -> None: + ht = t.rows() if isinstance(t, hl.MatrixTable) else t + ht = ht.filter( + dataset_type.invalid_allele_types.contains( + hl.numeric_allele_type(ht.alleles[0], ht.alleles[1]), + ), + ) + if ht.count() > 0: + collected_alleles = sorted( + [tuple(x) for x in ht.aggregate(hl.agg.collect_as_set(ht.alleles))], + ) + # Handle case where all invalid alleles are NON_REF, indicating a gvcf: + if all('' in alleles for alleles in collected_alleles): + msg = 'Alleles with invalid allele are present in the callset. This appears to be a GVCF containing records for sites with no variants.' + raise SeqrValidationError(msg) + msg = f'Alleles with invalid AlleleType are present in the callset: {collected_alleles[:10]}' + raise SeqrValidationError(msg) + + +def validate_allele_depth_length( + mt: hl.MatrixTable, + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + **_: Any, +) -> None: + ht = mt.select_rows( + found_ad_lengths=hl.agg.collect_as_set(hl.len(mt.AD)).remove( + hl.missing(hl.tint32), + ), + ).rows() + ht = ht.filter( + hl.len(ht.found_ad_lengths) > 1, + ) + if ht.count() > 0: + variant_format = dataset_type.table_key_format_fn(reference_genome) + msg = f'Found variants with unequal Allele Depth array lengths over samples (first 10, if applicable): { ({variant_format(v): v.found_ad_lengths for v in ht.take(10)}) }' + raise SeqrValidationError(msg) + + +def validate_no_duplicate_variants( + t: hl.Table | hl.MatrixTable, + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + **_: Any, +) -> None: + ht = t.rows() if isinstance(t, hl.MatrixTable) else t + ht = ht.group_by(*ht.key).aggregate(n=hl.agg.count()) + ht = ht.filter(ht.n > 1) + ht = ht.select() + if ht.count() > 0: + variant_format = dataset_type.table_key_format_fn(reference_genome) + msg = f'Variants are present multiple times in the callset: {[variant_format(v) for v in ht.take(10)]}' + raise SeqrValidationError(msg) + + +def validate_expected_contig_frequency( + mt: hl.MatrixTable, + reference_genome: ReferenceGenome, + min_rows_per_contig: int = MIN_ROWS_PER_CONTIG, + **_: Any, +) -> None: + rows_per_contig = mt.aggregate_rows(hl.agg.counter(mt.locus.contig)) + missing_contigs = ( + reference_genome.standard_contigs + - reference_genome.optional_contigs + - rows_per_contig.keys() + ) + if missing_contigs: + msg = 'Missing the following expected contigs:{}'.format( + ', '.join(sorted(missing_contigs)), + ) + raise SeqrValidationError(msg) + + for contig, count in rows_per_contig.items(): + if contig in reference_genome.optional_contigs: + continue + if count < min_rows_per_contig: + msg = f'Contig {contig} has {count} rows, which is lower than expected minimum count {min_rows_per_contig}.' + raise SeqrValidationError(msg) + + +def validate_imported_field_types( + mt: hl.MatrixTable, + dataset_type: DatasetType, + additional_row_fields: dict[str, hl.expr.types.HailType | set], + **_: Any, +) -> None: + def _validate_field( + mt_schema: hl.StructExpression, + field: str, + dtype: hl.expr.types.HailType, + ) -> str | None: + if field not in mt_schema: + return f'{field}: missing' + if ( + ( + dtype == hl.tstruct + and isinstance( + mt_schema[field], + hl.expr.expressions.typed_expressions.StructExpression, + ) + ) + or (isinstance(dtype, set) and mt_schema[field].dtype in dtype) + or (mt_schema[field].dtype == dtype) + ): + return None + return f'{field}: {mt_schema[field].dtype}' + + unexpected_field_types = [] + for field, dtype in dataset_type.col_fields.items(): + unexpected_field_types.append(_validate_field(mt.col, field, dtype)) + for field, dtype in dataset_type.entries_fields.items(): + unexpected_field_types.append(_validate_field(mt.entry, field, dtype)) + for field, dtype in {**dataset_type.row_fields, **additional_row_fields}.items(): + unexpected_field_types.append(_validate_field(mt.row, field, dtype)) + unexpected_field_types = [x for x in unexpected_field_types if x is not None] + if unexpected_field_types: + msg = f'Found unexpected field types on MatrixTable after import: {unexpected_field_types}' + raise SeqrValidationError(msg) + + +def validate_sample_type( + mt: hl.MatrixTable, + reference_genome: ReferenceGenome, + sample_type: SampleType, + project_guids: list[str], + coding_and_noncoding_variants_ht: hl.Table, + sample_type_match_threshold: float = SAMPLE_TYPE_MATCH_THRESHOLD, + **_: Any, +) -> None: + if all( + project_guid in Env.SAMPLE_TYPE_VALIDATION_EXCLUDED_PROJECTS + for project_guid in project_guids + ): + return + coding_variants_ht = coding_and_noncoding_variants_ht.filter( + coding_and_noncoding_variants_ht.coding, + ) + has_coding = ( + mt.semi_join_rows(coding_variants_ht).count_rows() / coding_variants_ht.count() + >= sample_type_match_threshold + ) + noncoding_variants_ht = coding_and_noncoding_variants_ht.filter( + coding_and_noncoding_variants_ht.noncoding, + ) + has_noncoding = ( + mt.semi_join_rows(noncoding_variants_ht).count_rows() + / noncoding_variants_ht.count() + >= sample_type_match_threshold + ) + if not has_coding and not has_noncoding: + msg = f"Genome version validation error: dataset specified as {reference_genome.value} but doesn't contain the expected number of common {reference_genome.value} variants" + raise SeqrValidationError(msg) + if has_noncoding and not has_coding: + msg = f'Sample type validation error: dataset contains noncoding variants but is missing common coding variants for {reference_genome.value}. Please verify that the dataset contains coding variants.' + raise SeqrValidationError(msg) + if has_coding and not has_noncoding and sample_type != SampleType.WES: + msg = 'Sample type validation error: dataset sample-type is specified as WGS but appears to be WES because it contains many common coding variants but is missing common non-coding variants' + raise SeqrValidationError(msg) + if has_noncoding and has_coding and sample_type != SampleType.WGS: + msg = 'Sample type validation error: dataset sample-type is specified as WES but appears to be WGS because it contains many common non-coding variants' + raise SeqrValidationError(msg) + + +SKIPPABLE_VALIDATIONS = [ + validate_allele_depth_length, + validate_allele_type, + validate_expected_contig_frequency, + validate_no_duplicate_variants, + validate_sample_type, +] diff --git a/loading_pipeline/lib/misc/validation_test.py b/loading_pipeline/lib/misc/validation_test.py new file mode 100644 index 0000000000..bb368b85a5 --- /dev/null +++ b/loading_pipeline/lib/misc/validation_test.py @@ -0,0 +1,464 @@ +import unittest +from unittest.mock import patch + +import hail as hl + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.misc.validation import ( + SeqrValidationError, + validate_allele_depth_length, + validate_allele_type, + validate_expected_contig_frequency, + validate_imported_field_types, + validate_no_duplicate_variants, + validate_sample_type, +) + +TEST_MITO_MT = 'loading_pipeline/var/test/callsets/mito_1.mt' + + +def _mt_from_contigs(contigs): + return ( + hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig=contig, + position=1, + reference_genome='GRCh38', + ) + for contig in contigs + ], + }, + cols={'s': ['sample_1']}, + entries={'HL': [[0.0] for _ in range(len(contigs))]}, + ) + .key_rows_by('locus') + .key_cols_by('s') + ) + + +class ValidationTest(unittest.TestCase): + def test_validate_allele_type(self) -> None: + mt = ( + hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=2, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=3, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=4, + reference_genome='GRCh38', + ), + ], + 'alleles': [ + ['A', 'T'], + # NB: star alleles should pass through this validation just fine, + # but are eventually filtered out upstream. + ['A', '*'], + ['A', '-'], + ['A', ''], + ], + }, + cols={'s': ['sample_1']}, + entries={'HL': [[0.0], [0.0], [0.0], [0.0]]}, + ) + .key_rows_by('locus', 'alleles') + .key_cols_by('s') + ) + self.assertRaisesRegex( + SeqrValidationError, + "Alleles with invalid AlleleType are present in the callset: \\[\\('A', '-'\\), \\('A', ''\\)\\]", + validate_allele_type, + mt, + DatasetType.SNV_INDEL, + ) + + mt = ( + hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=2, + reference_genome='GRCh38', + ), + ], + 'alleles': [ + ['C', ''], + ['A', ''], + ], + }, + cols={'s': ['sample_1']}, + entries={'HL': [[0.0], [0.0]]}, + ) + .key_rows_by('locus', 'alleles') + .key_cols_by('s') + ) + self.assertRaisesRegex( + SeqrValidationError, + 'Alleles with invalid allele are present in the callset. This appears to be a GVCF containing records for sites with no variants.', + validate_allele_type, + mt, + DatasetType.SNV_INDEL, + ) + + def test_validate_allele_depth_length(self) -> None: + mt = ( + hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=2, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=3, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=4, + reference_genome='GRCh38', + ), + ], + 'alleles': [ + ['A', 'T'], + # NB: star alleles should pass through this validation just fine, + # but are eventually filtered out upstream. + ['A', 'TC', 'TG'], + ['A', 'TTT'], + ['A', 'CCC'], + ], + }, + cols={'s': ['sample_1', 'sample_2']}, + entries={ + 'AD': [ + [[1, 0], [1, 0]], + [[1], [1, 0, 1]], + [[1, 0], [1]], + [[1, 0], [1, 0]], + ], + }, + ) + .key_rows_by('locus', 'alleles') + .key_cols_by('s') + ) + self.assertRaisesRegex( + SeqrValidationError, + "Found variants with unequal Allele Depth array lengths over samples \\(first 10, if applicable\\): \\{'1-2-A-TC-TG': \\{1, 3\\}, '1-3-A-TTT': \\{1, 2\\}\\}", + validate_allele_depth_length, + mt, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + ) + + def test_validate_imported_field_types(self) -> None: + mt = hl.read_matrix_table(TEST_MITO_MT) + validate_imported_field_types(mt, DatasetType.MITO, {}) + mt = mt.annotate_cols(contamination=hl.int32(mt.contamination)) + mt = mt.annotate_entries(DP=hl.float32(mt.DP)) + mt = mt.annotate_rows(vep=hl.dict({'t': '1'})) + self.assertRaisesRegex( + SeqrValidationError, + "Found unexpected field types on MatrixTable after import: \\['contamination: int32', 'DP: float32', 'vep: dict', 'tester: missing'\\]", + validate_imported_field_types, + mt, + DatasetType.MITO, + {'tester': hl.tfloat32}, + ) + + def test_validate_no_duplicate_variants(self) -> None: + mt = ( + hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=2, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=2, + reference_genome='GRCh38', + ), + ], + 'alleles': [ + ['A', 'C'], + ['A', 'C'], + ['A', 'C'], + ], + }, + cols={'s': ['sample_1']}, + entries={'HL': [[0.0], [0.0], [0.0]]}, + ) + .key_rows_by('locus', 'alleles') + .key_cols_by('s') + ) + self.assertRaisesRegex( + SeqrValidationError, + "Variants are present multiple times in the callset: \\['1-2-A-C'\\]", + validate_no_duplicate_variants, + mt, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + ) + + def test_validate_expected_contig_frequency(self) -> None: + mt = _mt_from_contigs(ReferenceGenome.GRCh38.standard_contigs) + self.assertIsNone( + validate_expected_contig_frequency(mt, ReferenceGenome.GRCh38, 1), + ) + self.assertRaisesRegex( + SeqrValidationError, + 'Missing the following expected contigs', + validate_expected_contig_frequency, + mt, + ReferenceGenome.GRCh37, + 1, + ) + self.assertRaisesRegex( + SeqrValidationError, + 'which is lower than expected minimum count', + validate_expected_contig_frequency, + mt, + ReferenceGenome.GRCh38, + 2, + ) + + # Drop an optional contig + mt = _mt_from_contigs(ReferenceGenome.GRCh38.standard_contigs - {'chrY'}) + self.assertIsNone( + validate_expected_contig_frequency(mt, ReferenceGenome.GRCh38, 1), + ) + + # Drop a non-optional contig + mt = _mt_from_contigs(ReferenceGenome.GRCh38.standard_contigs - {'chr3'}) + self.assertRaisesRegex( + SeqrValidationError, + 'Missing the following expected contigs', + validate_expected_contig_frequency, + mt, + ReferenceGenome.GRCh38, + 1, + ) + + def test_validate_sample_type(self) -> None: + mt = _mt_from_contigs(ReferenceGenome.GRCh38.standard_contigs) + coding_and_noncoding_variants_ht = hl.Table.parallelize( + [ + { + 'locus': hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + 'coding': True, + 'noncoding': False, + }, + { + 'locus': hl.Locus( + contig='chr2', + position=1, + reference_genome='GRCh38', + ), + 'coding': True, + 'noncoding': False, + }, + { + 'locus': hl.Locus( + contig='chr3', + position=1, + reference_genome='GRCh38', + ), + 'coding': False, + 'noncoding': True, + }, + { + 'locus': hl.Locus( + contig='chr4', + position=1, + reference_genome='GRCh38', + ), + 'coding': False, + 'noncoding': True, + }, + ], + hl.tstruct( + locus=hl.tlocus('GRCh38'), + coding=hl.tbool, + noncoding=hl.tbool, + ), + key='locus', + ) + self.assertIsNone( + validate_sample_type( + mt, + ReferenceGenome.GRCh38, + SampleType.WGS, + ['project_a'], + coding_and_noncoding_variants_ht, + ), + ) + self.assertRaisesRegex( + SeqrValidationError, + 'specified as WES but appears to be WGS', + validate_sample_type, + mt, + ReferenceGenome.GRCh38, + SampleType.WES, + ['project_a'], + coding_and_noncoding_variants_ht, + ) + + # has coding, but not noncoding now. + coding_and_noncoding_variants_ht = hl.Table.parallelize( + [ + { + 'locus': hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + 'coding': True, + 'noncoding': False, + }, + { + 'locus': hl.Locus( + contig='chr2', + position=1, + reference_genome='GRCh38', + ), + 'coding': True, + 'noncoding': False, + }, + { + 'locus': hl.Locus( + contig='chr2', + position=2, + reference_genome='GRCh38', + ), + 'coding': False, + 'noncoding': True, + }, + ], + hl.tstruct( + locus=hl.tlocus('GRCh38'), + coding=hl.tbool, + noncoding=hl.tbool, + ), + key='locus', + ) + self.assertIsNone( + validate_sample_type( + mt, + ReferenceGenome.GRCh38, + SampleType.WES, + ['project_a'], + coding_and_noncoding_variants_ht, + ), + ) + self.assertRaisesRegex( + SeqrValidationError, + 'specified as WGS but appears to be WES', + validate_sample_type, + mt, + ReferenceGenome.GRCh38, + SampleType.WGS, + ['project_a'], + coding_and_noncoding_variants_ht, + ) + + # has noncoding, but not coding now. + coding_and_noncoding_variants_ht = hl.Table.parallelize( + [ + { + 'locus': hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + 'coding': False, + 'noncoding': True, + }, + { + 'locus': hl.Locus( + contig='chr2', + position=1, + reference_genome='GRCh38', + ), + 'coding': False, + 'noncoding': True, + }, + { + 'locus': hl.Locus( + contig='chr2', + position=2, + reference_genome='GRCh38', + ), + 'coding': True, + 'noncoding': False, + }, + ], + hl.tstruct( + locus=hl.tlocus('GRCh38'), + coding=hl.tbool, + noncoding=hl.tbool, + ), + key='locus', + ) + self.assertRaisesRegex( + SeqrValidationError, + 'contains noncoding variants but is missing common coding variants', + validate_sample_type, + mt, + ReferenceGenome.GRCh38, + SampleType.WGS, + ['project_a'], + coding_and_noncoding_variants_ht, + ) + + # Validation safe if all projects are to be skipped + with patch('loading_pipeline.lib.misc.validation.Env') as mock_env: + mock_env.SAMPLE_TYPE_VALIDATION_EXCLUDED_PROJECTS = ['project_a'] + self.assertIsNone( + validate_sample_type( + mt, + ReferenceGenome.GRCh38, + SampleType.WGS, + ['project_a'], + coding_and_noncoding_variants_ht, + ), + ) diff --git a/loading_pipeline/lib/misc/vep.py b/loading_pipeline/lib/misc/vep.py new file mode 100644 index 0000000000..bdaf7c4c66 --- /dev/null +++ b/loading_pipeline/lib/misc/vep.py @@ -0,0 +1,29 @@ +from string import Template + +import hail as hl + +from loading_pipeline.lib.core import DatasetType, Env, ReferenceGenome + +VEP_CONFIG_URI = Template( + 'file://$vep_reference_datasets_dir/$reference_genome/vep-$reference_genome.json', +) + + +def run_vep( + ht: hl.Table, + dataset_type: DatasetType, + reference_genome: ReferenceGenome, +) -> hl.Table: + if not dataset_type.veppable: + return ht + return hl.vep( + ht, + config=VEP_CONFIG_URI.substitute( + vep_reference_datasets_dir=Env.VEP_REFERENCE_DATASETS_DIR, + reference_genome=reference_genome.value, + ), + name='vep', + block_size=1000, + tolerate_parse_error=True, + csq=False, + ) diff --git a/loading_pipeline/lib/misc/vets.py b/loading_pipeline/lib/misc/vets.py new file mode 100644 index 0000000000..4934168232 --- /dev/null +++ b/loading_pipeline/lib/misc/vets.py @@ -0,0 +1,39 @@ +import hail as hl + +VETS_SNP_CUTOFF = 0.997 +VETS_INDEL_CUTOFF = 0.99 +VETS_SNP_FILTER = 'high_CALIBRATION_SENSITIVITY_SNP' +VETS_INDEL_FILTER = 'high_CALIBRATION_SENSITIVITY_INDEL' + + +def annotate_vets(mt: hl.MatrixTable) -> hl.MatrixTable: + if not hasattr(mt, 'info.CALIBRATION_SENSITIVITY'): + return mt + return mt.annotate_rows( + filters=hl.bind( + lambda is_snp, split_cs: ( + hl.case() + .when( + is_snp & (split_cs > VETS_SNP_CUTOFF), + hl.if_else( + hl.is_defined(mt.filters), + mt.filters.add(VETS_SNP_FILTER), + hl.set([VETS_SNP_FILTER]), + ), + ) + .when( + ~is_snp & (split_cs > VETS_INDEL_CUTOFF), + hl.if_else( + hl.is_defined(mt.filters), + mt.filters.add(VETS_INDEL_FILTER), + hl.set([VETS_INDEL_FILTER]), + ), + ) + .default( + mt.filters, + ) + ), + hl.is_snp(mt.alleles[0], mt.alleles[1]), + hl.parse_float(mt['info.CALIBRATION_SENSITIVITY'][mt.a_index - 1]), + ), + ) diff --git a/loading_pipeline/lib/misc/vets_test.py b/loading_pipeline/lib/misc/vets_test.py new file mode 100644 index 0000000000..b26de113b7 --- /dev/null +++ b/loading_pipeline/lib/misc/vets_test.py @@ -0,0 +1,104 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.misc.io import split_multi_hts +from loading_pipeline.lib.misc.vets import ( + annotate_vets, +) + + +class VetsTest(unittest.TestCase): + def test_annotate_vets(self) -> None: + gatk_mt = hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + ], + 'filters': [ + hl.set(['NO_HQ_GENOTYPES']), + ], + }, + cols={'s': ['sample_1']}, + entries={'HL': [[0.0]]}, + ).key_rows_by('locus') + gatk_mt = annotate_vets(gatk_mt) + dragen_mt = hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=2, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=3, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=4, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=5, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=6, + reference_genome='GRCh38', + ), + ], + 'alleles': [ + ['A', 'T'], + ['A', 'T'], + ['A', 'T'], + ['AC', 'T'], + ['AT', 'ATC'], + ['AG', 'ATG'], + ], + 'filters': [ + hl.set(['NO_HQ_GENOTYPES']), + hl.empty_set(hl.tstr), + hl.missing(hl.tset(hl.tstr)), + hl.set(['NO_HQ_GENOTYPES']), + hl.empty_set(hl.tstr), + hl.set(['NO_HQ_GENOTYPES']), + ], + 'info.CALIBRATION_SENSITIVITY': [ + ['0.999'], + ['0.995'], + ['0.999'], + ['0.98'], + ['0.99'], + ['0.991'], + ], + }, + cols={'s': ['sample_1']}, + entries={'HL': [[0.0], [0.0], [0.0], [0.0], [0.0], [0.0]]}, + ).key_rows_by('locus', 'alleles') + dragen_mt = split_multi_hts(dragen_mt, False) + dragen_mt = annotate_vets(dragen_mt) + self.assertListEqual( + dragen_mt.filters.collect(), + [ + {'NO_HQ_GENOTYPES', 'high_CALIBRATION_SENSITIVITY_SNP'}, + set(), + {'high_CALIBRATION_SENSITIVITY_SNP'}, + {'NO_HQ_GENOTYPES'}, + set(), + {'NO_HQ_GENOTYPES', 'high_CALIBRATION_SENSITIVITY_INDEL'}, + ], + ) diff --git a/loading_pipeline/lib/paths.py b/loading_pipeline/lib/paths.py new file mode 100644 index 0000000000..27e450f7d7 --- /dev/null +++ b/loading_pipeline/lib/paths.py @@ -0,0 +1,503 @@ +import hashlib +import os + +import hailtop.fs as hfs + +from loading_pipeline.lib.core import ( + DatasetType, + Env, + ReferenceGenome, + SampleType, +) +from loading_pipeline.lib.reference_datasets.reference_dataset import ( + ReferenceDataset, +) + + +def pipeline_prefix( + root: str, + reference_genome: ReferenceGenome, + dataset_type: DatasetType, +) -> str: + return os.path.join( + root, + reference_genome.value, + dataset_type.value, + ) + + +def _v03_reference_dataset_prefix( + root: str, + reference_genome: ReferenceGenome, +) -> str: + return os.path.join( + root, + reference_genome.value, + ) + + +def _callset_path_hash(callset_path: str) -> str: + # Include the most recent modified time of any + # of the callset shards if they exist. + try: + # hfs.ls throws FileNotFoundError if a non-wildcard is passed + # but not found, but does not throw if a wildcard is passed and + # there are no results. + shards = hfs.ls(callset_path) + if not shards: + key = callset_path + else: + # f.modification_time is None for directories + key = callset_path + str( + sum((f.size if f.size else 0) for f in shards), + ) + except FileNotFoundError: + key = callset_path + return hashlib.sha256( + key.encode('utf8'), + ).hexdigest() + + +def family_table_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + sample_type: SampleType, + family_guid: str, +) -> str: + return os.path.join( + pipeline_prefix( + Env.PIPELINE_DATA_DIR, + reference_genome, + dataset_type, + ), + 'families', + sample_type.value, + f'{family_guid}.ht', + ) + + +def tdr_metrics_dir( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, +) -> str: + return os.path.join( + pipeline_prefix( + Env.LOADING_DATASETS_DIR, + reference_genome, + dataset_type, + ), + 'tdr_metrics', + ) + + +def tdr_metrics_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + bq_table_name: str, +) -> str: + return os.path.join( + tdr_metrics_dir(reference_genome, dataset_type), + f'{bq_table_name}.tsv', + ) + + +def imported_callset_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + callset_path: str, +) -> str: + return os.path.join( + pipeline_prefix( + Env.LOADING_DATASETS_DIR, + reference_genome, + dataset_type, + ), + 'imported_callsets', + f'{_callset_path_hash(callset_path)}.mt', + ) + + +def postprocessed_callset_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + callset_path: str, +) -> str: + return os.path.join( + pipeline_prefix( + Env.LOADING_DATASETS_DIR, + reference_genome, + dataset_type, + ), + 'postprocessed_callsets', + f'{_callset_path_hash(callset_path)}.mt', + ) + + +def validation_errors_for_run_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + run_id: str, +) -> str: + return os.path.join( + runs_path( + reference_genome, + dataset_type, + ), + run_id, + 'validation_errors.json', + ) + + +def metadata_for_run_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + run_id: str, +) -> str: + return os.path.join( + runs_path( + reference_genome, + dataset_type, + ), + run_id, + 'metadata.json', + ) + + +def project_table_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + sample_type: SampleType, + project_guid: str, +) -> str: + return os.path.join( + pipeline_prefix( + Env.PIPELINE_DATA_DIR, + reference_genome, + dataset_type, + ), + 'projects', + sample_type.value, + f'{project_guid}.ht', + ) + + +def relatedness_check_table_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + callset_path: str, +) -> str: + return os.path.join( + pipeline_prefix( + Env.LOADING_DATASETS_DIR, + reference_genome, + dataset_type, + ), + 'relatedness_check', + f'{_callset_path_hash(callset_path)}.ht', + ) + + +def relatedness_check_tsv_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + callset_path: str, +) -> str: + return os.path.join( + pipeline_prefix( + Env.LOADING_DATASETS_DIR, + reference_genome, + dataset_type, + ), + 'relatedness_check', + f'{_callset_path_hash(callset_path)}.tsv', + ) + + +def sample_qc_json_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + callset_path: str, +) -> str: + return os.path.join( + pipeline_prefix( + Env.LOADING_DATASETS_DIR, + reference_genome, + dataset_type, + ), + 'sample_qc', + f'{_callset_path_hash(callset_path)}.json', + ) + + +def remapped_and_subsetted_callset_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + callset_path: str, + project_guid: str, +) -> str: + return os.path.join( + pipeline_prefix( + Env.LOADING_DATASETS_DIR, + reference_genome, + dataset_type, + ), + 'remapped_and_subsetted_callsets', + project_guid, + f'{_callset_path_hash(callset_path)}.mt', + ) + + +def runs_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, +) -> str: + return os.path.join( + pipeline_prefix( + Env.PIPELINE_DATA_DIR, + reference_genome, + dataset_type, + ), + 'runs', + ) + + +def sex_check_table_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + callset_path: str, +) -> str: + return os.path.join( + pipeline_prefix( + Env.LOADING_DATASETS_DIR, + reference_genome, + dataset_type, + ), + 'sex_check', + f'{_callset_path_hash(callset_path)}.ht', + ) + + +def valid_reference_dataset_path( + reference_genome: ReferenceGenome, + reference_dataset: ReferenceDataset, +) -> str | None: + return os.path.join( + _v03_reference_dataset_prefix( + Env.REFERENCE_DATASETS_DIR, + reference_genome, + ), + reference_dataset.value, + f'{reference_dataset.version(reference_genome)}.ht', + ) + + +def ancestry_model_rf_path() -> str: + return os.path.join( + _v03_reference_dataset_prefix( + Env.REFERENCE_DATASETS_DIR, + ReferenceGenome.GRCh38, + ), + DatasetType.SNV_INDEL, + 'ancestry_imputation_model.onnx', + ) + + +def variant_annotations_table_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, +) -> str: + return os.path.join( + pipeline_prefix( + Env.PIPELINE_DATA_DIR, + reference_genome, + dataset_type, + ), + 'annotations.ht', + ) + + +def variant_annotations_vcf_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, +) -> str: + return os.path.join( + pipeline_prefix( + Env.PIPELINE_DATA_DIR, + reference_genome, + dataset_type, + ), + 'annotations.vcf.bgz', + ) + + +def new_entries_parquet_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + run_id: str, +) -> str: + return os.path.join( + runs_path( + reference_genome, + dataset_type, + ), + run_id, + 'new_entries.parquet', + ) + + +def new_variant_details_parquet_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + run_id: str, +) -> str: + return os.path.join( + runs_path( + reference_genome, + dataset_type, + ), + run_id, + 'new_variant_details.parquet', + ) + + +def new_variants_parquet_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + run_id: str, +) -> str: + return os.path.join( + runs_path( + reference_genome, + dataset_type, + ), + run_id, + 'new_variants.parquet', + ) + + +def new_variants_table_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + run_id: str, +) -> str: + return os.path.join( + runs_path( + reference_genome, + dataset_type, + ), + run_id, + 'new_variants.ht', + ) + + +def project_pedigree_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + sample_type: SampleType, + project_guid: str, +) -> str: + return os.path.join( + pipeline_prefix( + Env.LOADING_DATASETS_DIR, + reference_genome, + dataset_type, + ), + 'pedigrees', + sample_type.value, + f'{project_guid}_pedigree.tsv', + ) + + +def loading_pipeline_queue_dir() -> str: + """ + Returns the directory where loading pipeline requests are queued. + """ + return os.path.join( + Env.LOCAL_DISK_MOUNT_DIR, + 'loading_pipeline_queue', + ) + + +# https://en.wikipedia.org/wiki/Dead_letter_queue +def loading_pipeline_deadletter_queue_dir() -> str: + return os.path.join( + Env.LOCAL_DISK_MOUNT_DIR, + 'loading_pipeline_deadletter_queue', + ) + + +def loading_pipeline_queue_path(run_id: str) -> str: + """ + Returns a new path for a loading pipeline queue request file. + """ + return os.path.join( + loading_pipeline_queue_dir(), + f'request_{run_id}.json', + ) + + +def loading_pipeline_deadletter_queue_path(run_id: str) -> str: + """ + Returns a new path for a loading pipeline queue request file. + """ + return os.path.join( + loading_pipeline_deadletter_queue_dir(), + f'request_{run_id}.json', + ) + + +def pipeline_run_success_file_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + run_id: str, +) -> str: + return os.path.join( + runs_path( + reference_genome, + dataset_type, + ), + run_id, + '_SUCCESS', + ) + + +def clickhouse_load_success_file_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + run_id: str, +) -> str: + return os.path.join( + runs_path( + reference_genome, + dataset_type, + ), + run_id, + '_CLICKHOUSE_LOAD_SUCCESS', + ) + + +def clickhouse_load_fail_file_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + run_id: str, +) -> str: + return os.path.join( + runs_path( + reference_genome, + dataset_type, + ), + run_id, + '_CLICKHOUSE_LOAD_FAIL', + ) + + +def reference_dataset_parquet( + reference_genome: ReferenceGenome, + reference_dataset: ReferenceDataset, +) -> str: + return os.path.join( + Env.REFERENCE_DATASETS_DIR, + reference_genome.value, + reference_dataset.value, + f'{reference_dataset.version(reference_genome)}.parquet', + ) diff --git a/loading_pipeline/lib/paths_test.py b/loading_pipeline/lib/paths_test.py new file mode 100644 index 0000000000..d271cfee0b --- /dev/null +++ b/loading_pipeline/lib/paths_test.py @@ -0,0 +1,180 @@ +import unittest +from unittest.mock import patch + +import hailtop.fs as hfs + +from loading_pipeline.lib.core import ( + DatasetType, + ReferenceGenome, + SampleType, +) +from loading_pipeline.lib.paths import ( + imported_callset_path, + metadata_for_run_path, + new_variants_table_path, + project_pedigree_path, + project_table_path, + relatedness_check_table_path, + remapped_and_subsetted_callset_path, + sex_check_table_path, + tdr_metrics_path, + validation_errors_for_run_path, + variant_annotations_table_path, +) + +TEST_VCF = 'loading_pipeline/var/test/callsets/1kg_30varia*.vcf' + + +class TestPaths(unittest.TestCase): + def test_project_table_path(self) -> None: + self.assertEqual( + project_table_path( + ReferenceGenome.GRCh38, + DatasetType.MITO, + SampleType.WES, + 'R0652_pipeline_test', + ), + '/var/seqr/pipeline-data/GRCh38/MITO/projects/WES/R0652_pipeline_test.ht', + ) + with ( + patch('loading_pipeline.lib.paths.Env') as mock_env, + ): + mock_env.PIPELINE_DATA_DIR = '/var/bucket/' + self.assertEqual( + project_table_path( + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + SampleType.WES, + 'R0652_pipeline_test', + ), + '/var/bucket/GRCh37/SNV_INDEL/projects/WES/R0652_pipeline_test.ht', + ) + + def test_sex_check_table_path(self) -> None: + self.assertEqual( + sex_check_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + '/var/abc.efg/callset.vcf.gz', + ), + '/var/seqr/seqr-loading-temp/GRCh38/SNV_INDEL/sex_check/f92b8ab6b5b8c41fa20d7d49a5626b96dcd2ba79fa6f61eab7ffb80d550d951c.ht', + ) + + def test_relatedness_check_table_path(self) -> None: + self.assertEqual( + relatedness_check_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + '/var/abc.efg/callset.vcf.gz', + ), + '/var/seqr/seqr-loading-temp/GRCh38/SNV_INDEL/relatedness_check/f92b8ab6b5b8c41fa20d7d49a5626b96dcd2ba79fa6f61eab7ffb80d550d951c.ht', + ) + + def test_validation_errors_for_run_path(self) -> None: + self.assertEqual( + validation_errors_for_run_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + 'manual__2023-06-26T18:30:09.349671+00:00', + ), + '/var/seqr/pipeline-data/GRCh38/SNV_INDEL/runs/manual__2023-06-26T18:30:09.349671+00:00/validation_errors.json', + ) + + def test_metadata_for_run_path(self) -> None: + self.assertEqual( + metadata_for_run_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + 'manual__2023-06-26T18:30:09.349671+00:00', + ), + '/var/seqr/pipeline-data/GRCh38/SNV_INDEL/runs/manual__2023-06-26T18:30:09.349671+00:00/metadata.json', + ) + + def test_variant_annotations_table_path(self) -> None: + self.assertEqual( + variant_annotations_table_path( + ReferenceGenome.GRCh38, + DatasetType.GCNV, + ), + '/var/seqr/pipeline-data/GRCh38/GCNV/annotations.ht', + ) + + def test_remapped_and_subsetted_callset_path(self) -> None: + self.assertEqual( + remapped_and_subsetted_callset_path( + ReferenceGenome.GRCh38, + DatasetType.GCNV, + '/var/abc.efg/callset.vcf.gz', + 'R0111_tgg_bblanken_wes', + ), + '/var/seqr/seqr-loading-temp/GRCh38/GCNV/remapped_and_subsetted_callsets/R0111_tgg_bblanken_wes/f92b8ab6b5b8c41fa20d7d49a5626b96dcd2ba79fa6f61eab7ffb80d550d951c.mt', + ) + self.assertEqual( + remapped_and_subsetted_callset_path( + ReferenceGenome.GRCh38, + DatasetType.GCNV, + '/var/abc.efg/callset/*.vcf.gz', + 'R0111_tgg_bblanken_wes', + ), + '/var/seqr/seqr-loading-temp/GRCh38/GCNV/remapped_and_subsetted_callsets/R0111_tgg_bblanken_wes/26f481b386721f9889250c6549905660728ec9f77be4b8f7eeb6c4facc76282e.mt', + ) + + def test_imported_callset_path(self) -> None: + self.assertEqual( + imported_callset_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + '/var/abc.efg/callset.vcf.gz', + ), + '/var/seqr/seqr-loading-temp/GRCh38/SNV_INDEL/imported_callsets/f92b8ab6b5b8c41fa20d7d49a5626b96dcd2ba79fa6f61eab7ffb80d550d951c.mt', + ) + + with patch('loading_pipeline.lib.paths.hfs.ls') as mock_ls: + mock_ls.return_value = [ + hfs.stat_result.FileListEntry( + path='loading_pipeline/var/test/callsets/1kg_30variants.vcf', + owner=None, + size=1732033623.804012, + typ=hfs.stat_result.FileType(2), + modification_time=1732033000, + ), + ] + self.assertEqual( + imported_callset_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_VCF, + ), + '/var/seqr/seqr-loading-temp/GRCh38/SNV_INDEL/imported_callsets/01327e46c8747f15feaad2c08875b928c274dcb248ad40837ea3f49d8b4dedfb.mt', + ) + + def test_tdr_metrics_path(self) -> None: + self.assertEqual( + tdr_metrics_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + 'datarepo-7242affb.datarepo_RP_3053', + ), + '/var/seqr/seqr-loading-temp/GRCh38/SNV_INDEL/tdr_metrics/datarepo-7242affb.datarepo_RP_3053.tsv', + ) + + def test_new_variants_table_path(self) -> None: + self.assertEqual( + new_variants_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + 'manual__2023-06-26T18:30:09.349671+00:00', + ), + '/var/seqr/pipeline-data/GRCh38/SNV_INDEL/runs/manual__2023-06-26T18:30:09.349671+00:00/new_variants.ht', + ) + + def test_project_pedigree_path(self) -> None: + self.assertEqual( + project_pedigree_path( + ReferenceGenome.GRCh38, + DatasetType.GCNV, + SampleType.WES, + 'R0652_pipeline_test', + ), + '/var/seqr/seqr-loading-temp/GRCh38/GCNV/pedigrees/WES/R0652_pipeline_test_pedigree.tsv', + ) diff --git a/loading_pipeline/lib/reference_datasets/__init__.py b/loading_pipeline/lib/reference_datasets/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/loading_pipeline/lib/reference_datasets/eigen.py b/loading_pipeline/lib/reference_datasets/eigen.py new file mode 100644 index 0000000000..84a04215bf --- /dev/null +++ b/loading_pipeline/lib/reference_datasets/eigen.py @@ -0,0 +1,7 @@ +import hail as hl + + +def get_ht(path: str, *_) -> hl.Table: + ht = hl.read_table(path) + ht = ht.select(Eigen_phred=hl.float32(ht.info['Eigen-phred'])) + return ht.group_by(*ht.key).aggregate(Eigen_phred=hl.agg.max(ht.Eigen_phred)) diff --git a/loading_pipeline/lib/reference_datasets/gencode/__init__.py b/loading_pipeline/lib/reference_datasets/gencode/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/loading_pipeline/lib/reference_datasets/gencode/mapping_gene_ids.py b/loading_pipeline/lib/reference_datasets/gencode/mapping_gene_ids.py new file mode 100644 index 0000000000..b668a99d2b --- /dev/null +++ b/loading_pipeline/lib/reference_datasets/gencode/mapping_gene_ids.py @@ -0,0 +1,64 @@ +import gzip +import logging + +import requests + +logger = logging.getLogger(__name__) + +# Mirror of 'http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_{gencode_release}/gencode.v{gencode_release}.annotation.gtf.gz' +GENCODE_GTF_URL = 'https://storage.googleapis.com/seqr-reference-data/gencode/gencode.v{gencode_release}.annotation.gtf.gz' +# Mirror of 'https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_{gencode_release}/gencode.v{gencode_release}.metadata.RefSeq.gz' +GENCODE_ENSEMBL_TO_REFSEQ_URL = 'https://storage.googleapis.com/seqr-reference-data/gencode/gencode.v{gencode_release}.metadata.RefSeq.gz' + +# expected GTF file header +GENCODE_FILE_HEADER = [ + 'chrom', + 'source', + 'feature_type', + 'start', + 'end', + 'score', + 'strand', + 'phase', + 'info', +] +EXPECTED_ENSEMBLE_TO_REFSEQ_FIELDS = 3 + + +def load_gencode_gene_symbol_to_gene_id(gencode_release: int) -> dict[str, str]: + url = GENCODE_GTF_URL.format(gencode_release=gencode_release) + response = requests.get(url, stream=True, timeout=10) + gene_symbol_to_gene_id = {} + for line in gzip.GzipFile(fileobj=response.raw): + line = line.decode('ascii') # noqa: PLW2901 + if not line or line.startswith('#'): + continue + fields = line.strip().split('\t') + if len(fields) != len(GENCODE_FILE_HEADER): + msg = f'Unexpected number of fields: {fields}' + raise ValueError( + msg, + ) + record = dict(zip(GENCODE_FILE_HEADER, fields, strict=False)) + if record['feature_type'] != 'gene': + continue + # parse info field + info_fields = [x.strip().split() for x in record['info'].split(';') if x != ''] + info_fields = {k: v.strip('"') for k, v in info_fields} + gene_symbol_to_gene_id[info_fields['gene_name']] = info_fields['gene_id'].split( + '.', + )[0] + return gene_symbol_to_gene_id + + +def load_gencode_ensembl_to_refseq_id(gencode_release: int): + url = GENCODE_ENSEMBL_TO_REFSEQ_URL.format(gencode_release=gencode_release) + response = requests.get(url, stream=True, timeout=10) + ensembl_to_refseq_ids = {} + for line in gzip.GzipFile(fileobj=response.raw): + fields = line.decode('ascii').strip().split('\t') + if len(fields) > EXPECTED_ENSEMBLE_TO_REFSEQ_FIELDS: + msg = 'Unexpected number of fields on line in ensemble_to_refseq mapping' + raise ValueError(msg) + ensembl_to_refseq_ids[fields[0].split('.')[0]] = fields[1] + return ensembl_to_refseq_ids diff --git a/loading_pipeline/lib/reference_datasets/gencode/mapping_gene_ids_tests.py b/loading_pipeline/lib/reference_datasets/gencode/mapping_gene_ids_tests.py new file mode 100644 index 0000000000..edba8de050 --- /dev/null +++ b/loading_pipeline/lib/reference_datasets/gencode/mapping_gene_ids_tests.py @@ -0,0 +1,64 @@ +import gzip +import unittest + +import responses + +from loading_pipeline.lib.reference_datasets.gencode.mapping_gene_ids import ( + GENCODE_ENSEMBL_TO_REFSEQ_URL, + GENCODE_GTF_URL, + load_gencode_ensembl_to_refseq_id, + load_gencode_gene_symbol_to_gene_id, +) + +GTF_DATA = [ + '#description: evidence-based annotation of the human genome, version 31 (Ensembl 97), mapped to GRCh37 with gencode-backmap', + 'chr1 HAVANA gene 11869 14409 . + . gene_id "ENSG00000223972.5_2"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; level 2; hgnc_id "HGNC:37102"; havana_gene "OTTHUMG00000000961.2_2"; remap_status "full_contig"; remap_num_mappings 1; remap_target_status "overlap";', + 'chr1 HAVANA gene 621059 622053 . - . gene_id "ENSG00000284662.1_2"; gene_type "protein_coding"; gene_name "OR4F16"; level 2; hgnc_id "HGNC:15079"; havana_gene "OTTHUMG00000002581.3_2"; remap_status "full_contig"; remap_num_mappings 1; remap_target_status "overlap";', + 'GL000193.1 HAVANA gene 77815 78162 . + . gene_id "ENSG00000279783.1_5"; gene_type "processed_pseudogene"; gene_name "AC018692.2"; level 2; havana_gene "OTTHUMG00000189459.1_5"; remap_status "full_contig"; remap_num_mappings 1; remap_target_status "new";', +] +GENE_ID_MAPPING = { + 'DDX11L1': 'ENSG00000223972', + 'OR4F16': 'ENSG00000284662', + 'AC018692.2': 'ENSG00000279783', +} + + +ENSEMBL_TO_REFSEQ_DATA = b"""ENST00000424215.1\tNR_121638.1 +ENST00000378391.6\tNM_199454.3\tNP_955533.2 +ENST00000270722.10\tNM_022114.4\tNP_071397.3 +ENST00000288774.8\tNM_001374425.1\tNP_001361354.1""" + + +class LoadGencodeTestCase(unittest.TestCase): + @responses.activate + def test_load_gencode_gene_symbol_to_gene_id(self): + url = GENCODE_GTF_URL.format(gencode_release=12) + responses.add( + responses.GET, + url, + body=gzip.compress(('\n'.join(GTF_DATA)).encode()), + ) + mapping = load_gencode_gene_symbol_to_gene_id(12) + self.assertDictEqual( + mapping, + { + 'AC018692.2': 'ENSG00000279783', + 'DDX11L1': 'ENSG00000223972', + 'OR4F16': 'ENSG00000284662', + }, + ) + + @responses.activate + def test_load_gencode_ensembl_to_refseq_id(self): + url = GENCODE_ENSEMBL_TO_REFSEQ_URL.format(gencode_release=20) + responses.add(responses.GET, url, body=gzip.compress(ENSEMBL_TO_REFSEQ_DATA)) + mapping = load_gencode_ensembl_to_refseq_id(20) + self.assertDictEqual( + mapping, + { + 'ENST00000424215': 'NR_121638.1', + 'ENST00000378391': 'NM_199454.3', + 'ENST00000270722': 'NM_022114.4', + 'ENST00000288774': 'NM_001374425.1', + }, + ) diff --git a/loading_pipeline/lib/reference_datasets/gnomad_coding_and_noncoding.py b/loading_pipeline/lib/reference_datasets/gnomad_coding_and_noncoding.py new file mode 100644 index 0000000000..9b197276a8 --- /dev/null +++ b/loading_pipeline/lib/reference_datasets/gnomad_coding_and_noncoding.py @@ -0,0 +1,59 @@ +import hail as hl + +from loading_pipeline.lib.annotations.enums import ( + TRANSCRIPT_CONSEQUENCE_TERMS, +) +from loading_pipeline.lib.annotations.expression_helpers import ( + get_expr_for_vep_sorted_transcript_consequences_array, + get_expr_for_worst_transcript_consequence_annotations_struct, +) +from loading_pipeline.lib.core import ReferenceGenome + +GNOMAD_CODING_NONCODING_HIGH_AF_THRESHOLD = 0.90 +TRANSCRIPT_CONSEQUENCE_TERM_RANK_LOOKUP = hl.dict( + hl.enumerate(TRANSCRIPT_CONSEQUENCE_TERMS, index_first=False), +) + + +def get_ht( + path: str, + reference_genome: ReferenceGenome, +) -> hl.Table: + ht = hl.read_table(path) + filtered_contig = 'chr1' if reference_genome == ReferenceGenome.GRCh38 else '1' + ht = hl.filter_intervals( + ht, + [ + hl.parse_locus_interval( + filtered_contig, + reference_genome=reference_genome.value, + ), + ], + ) + ht = ht.filter(ht.freq[0].AF > GNOMAD_CODING_NONCODING_HIGH_AF_THRESHOLD) + ht = ht.annotate( + sorted_transaction_consequences=( + get_expr_for_vep_sorted_transcript_consequences_array( + ht.vep, + omit_consequences=[], + ) + ), + ) + ht = ht.annotate( + main_transcript=( + get_expr_for_worst_transcript_consequence_annotations_struct( + ht.sorted_transaction_consequences, + ) + ), + ) + ht = ht.select( + coding=( + ht.main_transcript.major_consequence_rank + <= TRANSCRIPT_CONSEQUENCE_TERM_RANK_LOOKUP['synonymous_variant'] + ), + noncoding=( + ht.main_transcript.major_consequence_rank + >= TRANSCRIPT_CONSEQUENCE_TERM_RANK_LOOKUP['downstream_gene_variant'] + ), + ) + return ht.filter(ht.coding | ht.noncoding) diff --git a/loading_pipeline/lib/reference_datasets/gnomad_exomes.py b/loading_pipeline/lib/reference_datasets/gnomad_exomes.py new file mode 100644 index 0000000000..abe0fc3d88 --- /dev/null +++ b/loading_pipeline/lib/reference_datasets/gnomad_exomes.py @@ -0,0 +1,21 @@ +import hail as hl + +from loading_pipeline.lib.core import ReferenceGenome +from loading_pipeline.lib.reference_datasets.gnomad_utils import get_ht as _get_ht + + +def af_popmax_expression( + ht: hl.Table, + reference_genome: ReferenceGenome, +) -> hl.Expression: + if reference_genome == ReferenceGenome.GRCh37: + return ht.popmax[ht.globals.popmax_index_dict['gnomad']].AF + return ht.grpmax['gnomad'].AF + + +def get_ht(path: str, reference_genome: ReferenceGenome) -> hl.Table: + return _get_ht( + path, + reference_genome, + af_popmax_expression, + ) diff --git a/loading_pipeline/lib/reference_datasets/gnomad_exomes_test.py b/loading_pipeline/lib/reference_datasets/gnomad_exomes_test.py new file mode 100644 index 0000000000..639dc6d894 --- /dev/null +++ b/loading_pipeline/lib/reference_datasets/gnomad_exomes_test.py @@ -0,0 +1,72 @@ +import unittest +from unittest.mock import patch + +import hail as hl + +from loading_pipeline.lib.core.definitions import ReferenceGenome +from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset + +GNOMAD_EXOMES_37_PATH = ( + 'loading_pipeline/var/test/reference_datasets/raw/gnomad_exomes_37.ht' +) +GNOMAD_EXOMES_38_PATH = ( + 'loading_pipeline/var/test/reference_datasets/raw/gnomad_exomes_38.ht' +) + + +class GnomadTest(unittest.TestCase): + def test_gnomad_exomes_37(self): + with patch.object( + ReferenceDataset, + 'path', + return_value=GNOMAD_EXOMES_37_PATH, + ): + ht = ReferenceDataset.gnomad_exomes.get_ht(ReferenceGenome.GRCh37) + self.assertEqual( + ht.collect(), + [ + hl.Struct( + locus=hl.Locus( + contig='1', + position=12586, + reference_genome='GRCh37', + ), + alleles=['C', 'T'], + AF=0.0005589714855886996, + AN=3578, + AC=2, + Hom=0, + AF_POPMAX_OR_GLOBAL=0.0022026430815458298, + FAF_AF=9.839000267675146e-05, + Hemi=0, + ), + ], + ) + + def test_gnomad_exomes_38(self): + with patch.object( + ReferenceDataset, + 'path', + return_value=GNOMAD_EXOMES_38_PATH, + ): + ht = ReferenceDataset.gnomad_exomes.get_ht(ReferenceGenome.GRCh38) + self.assertEqual( + ht.collect(), + [ + hl.Struct( + locus=hl.Locus( + contig='chr1', + position=12138, + reference_genome='GRCh38', + ), + alleles=['C', 'A'], + AF=0.00909090880304575, + AN=110, + AC=1, + Hom=0, + AF_POPMAX_OR_GLOBAL=0.009803921915590763, + FAF_AF=0.0, + Hemi=0, + ), + ], + ) diff --git a/loading_pipeline/lib/reference_datasets/gnomad_genomes.py b/loading_pipeline/lib/reference_datasets/gnomad_genomes.py new file mode 100644 index 0000000000..ff63586c78 --- /dev/null +++ b/loading_pipeline/lib/reference_datasets/gnomad_genomes.py @@ -0,0 +1,21 @@ +import hail as hl + +from loading_pipeline.lib.core import ReferenceGenome +from loading_pipeline.lib.reference_datasets.gnomad_utils import get_ht as _get_ht + + +def af_popmax_expression( + ht: hl.Table, + reference_genome: ReferenceGenome, +) -> hl.Expression: + if reference_genome == ReferenceGenome.GRCh37: + return ht.popmax[ht.globals.popmax_index_dict['gnomad']].AF + return ht.grpmax.AF + + +def get_ht(path: str, reference_genome: ReferenceGenome) -> hl.Table: + return _get_ht( + path, + reference_genome, + af_popmax_expression, + ) diff --git a/loading_pipeline/lib/reference_datasets/gnomad_genomes_test.py b/loading_pipeline/lib/reference_datasets/gnomad_genomes_test.py new file mode 100644 index 0000000000..df637c2fda --- /dev/null +++ b/loading_pipeline/lib/reference_datasets/gnomad_genomes_test.py @@ -0,0 +1,72 @@ +import unittest +from unittest.mock import patch + +import hail as hl + +from loading_pipeline.lib.core.definitions import ReferenceGenome +from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset + +GNOMAD_GENOMES_37_PATH = ( + 'loading_pipeline/var/test/reference_datasets/raw/gnomad_genomes_37.ht' +) +GNOMAD_GENOMES_38_PATH = ( + 'loading_pipeline/var/test/reference_datasets/raw/gnomad_genomes_38.ht' +) + + +class GnomadTest(unittest.TestCase): + def test_gnomad_genomes_37(self): + with patch.object( + ReferenceDataset, + 'path', + return_value=GNOMAD_GENOMES_37_PATH, + ): + ht = ReferenceDataset.gnomad_genomes.get_ht(ReferenceGenome.GRCh37) + self.assertEqual( + ht.collect(), + [ + hl.Struct( + locus=hl.Locus( + contig='1', + position=10131, + reference_genome='GRCh37', + ), + alleles=['CT', 'C'], + AF=3.6635403375839815e-05, + AN=27296, + AC=1, + Hom=0, + AF_POPMAX_OR_GLOBAL=3.6635403375839815e-05, + FAF_AF=0.0, + Hemi=0, + ), + ], + ) + + def test_gnomad_genomes_38(self): + with patch.object( + ReferenceDataset, + 'path', + return_value=GNOMAD_GENOMES_38_PATH, + ): + ht = ReferenceDataset.gnomad_genomes.get_ht(ReferenceGenome.GRCh38) + self.assertEqual( + ht.collect(), + [ + hl.Struct( + locus=hl.Locus( + contig='chr1', + position=10057, + reference_genome='GRCh38', + ), + alleles=['A', 'C'], + AF=2.642333674884867e-05, + AN=113536, + AC=3, + Hom=0, + AF_POPMAX_OR_GLOBAL=3.779861071961932e-05, + FAF_AF=7.019999884505523e-06, + Hemi=0, + ), + ], + ) diff --git a/loading_pipeline/lib/reference_datasets/gnomad_qc.py b/loading_pipeline/lib/reference_datasets/gnomad_qc.py new file mode 100644 index 0000000000..481a6ccda8 --- /dev/null +++ b/loading_pipeline/lib/reference_datasets/gnomad_qc.py @@ -0,0 +1,9 @@ +import hail as hl + +from loading_pipeline.lib.core import ReferenceGenome + + +def get_ht(path: str, reference_genome: ReferenceGenome) -> hl.Table: + if reference_genome == ReferenceGenome.GRCh37: + return hl.read_matrix_table(path).rows() + return hl.read_table(path) diff --git a/loading_pipeline/lib/reference_datasets/gnomad_svs.py b/loading_pipeline/lib/reference_datasets/gnomad_svs.py new file mode 100644 index 0000000000..8b453fd948 --- /dev/null +++ b/loading_pipeline/lib/reference_datasets/gnomad_svs.py @@ -0,0 +1,17 @@ +import hail as hl + +from loading_pipeline.lib.core import ReferenceGenome +from loading_pipeline.lib.reference_datasets.misc import vcf_to_ht + + +def get_ht(path: str, reference_genome: ReferenceGenome) -> hl.Table: + ht = vcf_to_ht(path, reference_genome) + ht = ht.select( + KEY=ht.rsid, + AF=ht.info.AF[0], + AC=ht.info.AC[0], + AN=ht.info.AN, + N_HET=ht.info.N_HET, + N_HOM=ht.info.N_HOMALT, + ) + return ht.key_by('KEY') diff --git a/loading_pipeline/lib/reference_datasets/gnomad_svs_test.py b/loading_pipeline/lib/reference_datasets/gnomad_svs_test.py new file mode 100644 index 0000000000..bfd7c89d11 --- /dev/null +++ b/loading_pipeline/lib/reference_datasets/gnomad_svs_test.py @@ -0,0 +1,93 @@ +import unittest +from unittest.mock import patch + +import hail as hl + +from loading_pipeline.lib.core import ReferenceGenome +from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset + +TEST_GNOMAD_SVS_RAW_HT = ( + 'loading_pipeline/var/test/reference_datasets/raw/gnomad_svs_from_vcf.ht' +) + + +class GnomadSVsTest(unittest.TestCase): + @patch('loading_pipeline.lib.reference_datasets.gnomad_svs.vcf_to_ht') + def test_gnomad_svs(self, mock_vcf_to_ht): + mock_vcf_to_ht.return_value = hl.read_table(TEST_GNOMAD_SVS_RAW_HT) + ht = ReferenceDataset.gnomad_svs.get_ht(ReferenceGenome.GRCh38) + self.assertEqual( + ht.collect(), + [ + hl.Struct( + KEY='gnomAD-SV_v3_BND_chr1_1a45f73a', + locus=hl.Locus( + contig='chr1', + position=10434, + reference_genome=ReferenceGenome.GRCh38, + ), + alleles=['N', ''], + AF=0.11413399875164032, + AC=8474, + AN=74246, + N_HET=8426, + N_HOM=24, + ), + hl.Struct( + KEY='gnomAD-SV_v3_BND_chr1_3fa36917', + locus=hl.Locus( + contig='chr1', + position=10440, + reference_genome=ReferenceGenome.GRCh38, + ), + alleles=['N', ''], + AF=0.004201000090688467, + AC=466, + AN=110936, + N_HET=466, + N_HOM=0, + ), + hl.Struct( + KEY='gnomAD-SV_v3_BND_chr1_7bbf34b5', + locus=hl.Locus( + contig='chr1', + position=10464, + reference_genome=ReferenceGenome.GRCh38, + ), + alleles=['N', ''], + AF=0.03698499873280525, + AC=3119, + AN=84332, + N_HET=3115, + N_HOM=2, + ), + hl.Struct( + KEY='gnomAD-SV_v3_BND_chr1_933a2971', + locus=hl.Locus( + contig='chr1', + position=10450, + reference_genome=ReferenceGenome.GRCh38, + ), + alleles=['N', ''], + AF=0.3238990008831024, + AC=21766, + AN=67200, + N_HET=21616, + N_HOM=75, + ), + hl.Struct( + KEY='gnomAD-SV_v3_DUP_chr1_01c2781c', + locus=hl.Locus( + contig='chr1', + position=10000, + reference_genome=ReferenceGenome.GRCh38, + ), + alleles=['N', ''], + AF=0.0019970000721514225, + AC=139, + AN=69594, + N_HET=139, + N_HOM=0, + ), + ], + ) diff --git a/loading_pipeline/lib/reference_datasets/gnomad_utils.py b/loading_pipeline/lib/reference_datasets/gnomad_utils.py new file mode 100644 index 0000000000..2e02f56490 --- /dev/null +++ b/loading_pipeline/lib/reference_datasets/gnomad_utils.py @@ -0,0 +1,55 @@ +from collections.abc import Callable + +import hail as hl + +from loading_pipeline.lib.core import ReferenceGenome + + +def global_idx_field(reference_genome: ReferenceGenome) -> str: + return 'gnomad' if reference_genome == ReferenceGenome.GRCh37 else 'adj' + + +def faf_globals_field(reference_genome: ReferenceGenome) -> str: + return ( + 'popmax_index_dict' + if reference_genome == ReferenceGenome.GRCh37 + else 'faf_index_dict' + ) + + +def hemi_field(reference_genome: ReferenceGenome) -> str: + return 'gnomad_male' if reference_genome == ReferenceGenome.GRCh37 else 'XY_adj' + + +def get_ht( + path: str, + reference_genome: ReferenceGenome, + af_popmax_expression: Callable, +) -> hl.Table: + ht = hl.read_table(path) + global_idx = hl.eval(ht.globals.freq_index_dict[global_idx_field(reference_genome)]) + ht = ht.select( + AF=hl.float32(ht.freq[global_idx].AF), + AN=ht.freq[global_idx].AN, + AC=ht.freq[global_idx].AC, + Hom=ht.freq[global_idx].homozygote_count, + AF_POPMAX_OR_GLOBAL=hl.float32( + hl.or_else( + af_popmax_expression(ht, reference_genome), + ht.freq[global_idx].AF, + ), + ), + FAF_AF=hl.float32( + ht.faf[ + ht.globals[faf_globals_field(reference_genome)][ + global_idx_field(reference_genome) + ] + ].faf95, + ), + Hemi=hl.if_else( + ht.locus.in_autosome_or_par(), + 0, + ht.freq[ht.globals.freq_index_dict[hemi_field(reference_genome)]].AC, + ), + ) + return ht.select_globals() diff --git a/loading_pipeline/lib/reference_datasets/misc.py b/loading_pipeline/lib/reference_datasets/misc.py new file mode 100644 index 0000000000..73b4d17c0a --- /dev/null +++ b/loading_pipeline/lib/reference_datasets/misc.py @@ -0,0 +1,145 @@ +import contextlib +import os +import random +import string +import tempfile +import zipfile + +import hail as hl +import hailtop.fs as hfs +import requests + +from loading_pipeline.lib.core.definitions import ReferenceGenome +from loading_pipeline.lib.core.environment import Env +from loading_pipeline.lib.misc.io import split_multi_hts + +BIALLELIC = 2 + + +def compress_floats(ht: hl.Table): + # Parse float64s into float32s to save space! + return ht.select( + **{ + k: hl.float32(v) if v.dtype == hl.tfloat64 else v + for k, v in ht.row_value.items() + }, + ) + + +def generate_random_string(length=5): + """Generates a random string of the specified length.""" + letters = string.ascii_letters + string.digits + return ''.join(random.choice(letters) for i in range(length)) # noqa: S311 + + +def filter_contigs(ht, reference_genome: ReferenceGenome): + if hasattr(ht, 'interval'): + return ht.filter( + hl.set(reference_genome.standard_contigs).contains( + ht.interval.start.contig, + ), + ) + # SV reference datasets are not keyed by locus. + if hasattr(ht, 'locus'): + return ht.filter( + hl.set(reference_genome.standard_contigs).contains(ht.locus.contig), + ) + return ht + + +def vcf_to_ht( + file_name: str, + reference_genome: ReferenceGenome, + split_multi=False, +) -> hl.Table: + mt = hl.import_vcf( + file_name, + reference_genome=reference_genome.value, + drop_samples=True, + skip_invalid_loci=True, + contig_recoding=reference_genome.contig_recoding(include_mt=True), + force_bgz=True, + array_elements_required=False, + ) + if split_multi: + return split_multi_hts(mt, True).rows() + + # Validate that there exist no multialellic variants in the table. + count_non_biallelic = mt.aggregate_rows( + hl.agg.count_where(hl.len(mt.alleles) > BIALLELIC), + ) + if count_non_biallelic: + error = f'Encountered {count_non_biallelic} multiallelic variants' + raise ValueError(error) + return mt.rows() + + +def key_by_locus_alleles(ht: hl.Table, reference_genome: ReferenceGenome) -> hl.Table: + chrom = ( + hl.format('chr%s', ht.chrom) + if reference_genome == ReferenceGenome.GRCh38 + else hl.if_else(ht.chrom == 'M', 'MT', ht.chrom) + ) + ht = ht.transmute( + locus=hl.locus(chrom, ht.pos, reference_genome.value), + alleles=hl.array([ht.ref, ht.alt]), + ) + return ht.key_by('locus', 'alleles') + + +def copyfileobj(fsrc, fdst, decode_content, length=16 * 1024): + """Copy data from file-like object fsrc to file-like object fdst.""" + while True: + buf = fsrc.read(length, decode_content=decode_content) + if not buf: + break + fdst.write(buf) + + +@contextlib.contextmanager +def download_zip_file(url, dataset_name: str, suffix='.zip', decode_content=False): + dir_ = f'/tmp/{generate_random_string()}/{dataset_name}' # noqa: S108 + os.makedirs(dir_, exist_ok=True) + with ( + tempfile.NamedTemporaryFile( + dir=dir_, + suffix=suffix, + ) as tmp_file, + requests.get(url, stream=True, timeout=10) as r, + ): + copyfileobj(r.raw, tmp_file, decode_content) + with zipfile.ZipFile(tmp_file.name, 'r') as zipf: + zipf.extractall(dir_) + yield copy_to_cloud_storage(dir_) + + +def select_for_interval_reference_dataset( + ht: hl.Table, + reference_genome: ReferenceGenome, + additional_selects: dict, + chrom_field: str = 'chrom', + start_field: str = 'start', + end_field: str = 'end', +) -> hl.Table: + ht = ht.select( + interval=hl.locus_interval( + ht[chrom_field], + ht[start_field] + 1, + ht[end_field] + 1, + reference_genome=reference_genome.value, + invalid_missing=True, + ), + **additional_selects, + ) + return ht.key_by('interval') + + +def copy_to_cloud_storage(file_name: str) -> str: + if not Env.HAIL_TMP_DIR.startswith('gs://'): + return file_name + if os.path.isdir(file_name): + cloud_storage_path = os.path.join(Env.HAIL_TMP_DIR, file_name.lstrip('/')) + else: + cloud_storage_path = os.path.join(Env.HAIL_TMP_DIR, os.path.basename(file_name)) + hfs.copy(file_name, cloud_storage_path) + return cloud_storage_path diff --git a/loading_pipeline/lib/reference_datasets/reference_dataset.py b/loading_pipeline/lib/reference_datasets/reference_dataset.py new file mode 100644 index 0000000000..aa3e6f1cc3 --- /dev/null +++ b/loading_pipeline/lib/reference_datasets/reference_dataset.py @@ -0,0 +1,178 @@ +import importlib +import types +from collections.abc import Callable +from enum import StrEnum + +import hail as hl + +from loading_pipeline.lib.annotations import sv +from loading_pipeline.lib.core import ( + DatasetType, + ReferenceGenome, +) +from loading_pipeline.lib.misc.validation import ( + validate_allele_type, + validate_no_duplicate_variants, +) +from loading_pipeline.lib.reference_datasets.misc import ( + compress_floats, + filter_contigs, +) + +DATASET_TYPES = 'dataset_types' +FORMATTING_ANNOTATION = 'formatting_annotation' +SELECT = 'select' +VERSION = 'version' +PATH = 'path' + + +class ReferenceDataset(StrEnum): + eigen = 'eigen' + splice_ai = 'splice_ai' + topmed = 'topmed' + gnomad_coding_and_noncoding = 'gnomad_coding_and_noncoding' + gnomad_exomes = 'gnomad_exomes' + gnomad_genomes = 'gnomad_genomes' + gnomad_qc = 'gnomad_qc' + gnomad_svs = 'gnomad_svs' + + @property + def formatting_annotation(self) -> Callable | None: + return CONFIG[self].get(FORMATTING_ANNOTATION) + + def version(self, reference_genome: ReferenceGenome) -> str: + version = CONFIG[self][reference_genome][VERSION] + if isinstance(version, types.FunctionType): + return version( + self.path(reference_genome), + ) + return version + + def dataset_types( + self, + reference_genome: ReferenceGenome, + ) -> frozenset[DatasetType]: + return CONFIG[self].get(reference_genome, {}).get(DATASET_TYPES, frozenset()) + + @property + def select( + self, + ) -> Callable[[ReferenceGenome, DatasetType, hl.Table], hl.Table] | None: + return CONFIG[self].get(SELECT) + + def path(self, reference_genome: ReferenceGenome) -> str | list[str]: + return CONFIG[self][reference_genome][PATH] + + def get_ht( + self, + reference_genome: ReferenceGenome, + ) -> hl.Table: + module = importlib.import_module( + f'loading_pipeline.lib.reference_datasets.{self.name}', + ) + path = self.path(reference_genome) + ht = module.get_ht(path, reference_genome) + ht = compress_floats(ht) + ht = filter_contigs(ht, reference_genome) + for dataset_type in self.dataset_types(reference_genome): + validate_allele_type(ht, dataset_type) + validate_no_duplicate_variants(ht, reference_genome, dataset_type) + return ht + + +CONFIG = { + ReferenceDataset.eigen: { + ReferenceGenome.GRCh37: { + DATASET_TYPES: frozenset([DatasetType.SNV_INDEL]), + VERSION: '1.1', + # NB: The download link on the Eigen website (http://www.columbia.edu/~ii2135/download.html) is broken + # as of 11/15/24 so we will host the data + PATH: 'gs://seqr-reference-data/GRCh37/eigen/EIGEN_coding_noncoding.grch37.ht', + }, + ReferenceGenome.GRCh38: { + DATASET_TYPES: frozenset([DatasetType.SNV_INDEL]), + VERSION: '1.1', + PATH: 'gs://seqr-reference-data/GRCh38/eigen/EIGEN_coding_noncoding.liftover_grch38.ht', + }, + }, + ReferenceDataset.splice_ai: { + ReferenceGenome.GRCh37: { + DATASET_TYPES: frozenset([DatasetType.SNV_INDEL]), + VERSION: '1.1', + PATH: [ + 'gs://seqr-reference-data/GRCh37/spliceai/spliceai_scores.masked.snv.hg19.vcf.gz', + 'gs://seqr-reference-data/GRCh37/spliceai/spliceai_scores.masked.indel.hg19.vcf.gz', + ], + }, + ReferenceGenome.GRCh38: { + DATASET_TYPES: frozenset([DatasetType.SNV_INDEL]), + VERSION: '1.1', + # NB: SpliceAI data is only available to download for authenticated Illumina users, so we will host the data + PATH: [ + 'gs://seqr-reference-data/GRCh38/spliceai/spliceai_scores.masked.snv.hg38.vcf.gz', + 'gs://seqr-reference-data/GRCh38/spliceai/spliceai_scores.masked.indel.hg38.vcf.gz', + ], + }, + }, + ReferenceDataset.topmed: { + ReferenceGenome.GRCh37: { + DATASET_TYPES: frozenset([DatasetType.SNV_INDEL]), + VERSION: '1.1', + PATH: 'gs://seqr-reference-data/GRCh37/TopMed/bravo-dbsnp-all.removed_chr_prefix.liftunder_GRCh37.vcf.gz', + }, + ReferenceGenome.GRCh38: { + DATASET_TYPES: frozenset([DatasetType.SNV_INDEL]), + VERSION: '1.1', + # NB: TopMed data is available to download via https://legacy.bravo.sph.umich.edu/freeze8/hg38/downloads/vcf/ + # However, users must be authenticated and accept TOS to access it so for now we will host a copy of the data + PATH: 'gs://seqr-reference-data/GRCh38/TopMed/bravo-dbsnp-all.vcf.gz', + }, + }, + ReferenceDataset.gnomad_exomes: { + ReferenceGenome.GRCh37: { + DATASET_TYPES: frozenset([DatasetType.SNV_INDEL]), + VERSION: '1.0', + PATH: 'gs://gcp-public-data--gnomad/release/2.1.1/ht/exomes/gnomad.exomes.r2.1.1.sites.ht', + }, + ReferenceGenome.GRCh38: { + DATASET_TYPES: frozenset([DatasetType.SNV_INDEL]), + VERSION: '1.0', + PATH: 'gs://gcp-public-data--gnomad/release/4.1/ht/exomes/gnomad.exomes.v4.1.sites.ht', + }, + }, + ReferenceDataset.gnomad_genomes: { + ReferenceGenome.GRCh37: { + DATASET_TYPES: frozenset([DatasetType.SNV_INDEL]), + VERSION: '1.0', + PATH: 'gs://gcp-public-data--gnomad/release/2.1.1/ht/genomes/gnomad.genomes.r2.1.1.sites.ht', + }, + ReferenceGenome.GRCh38: { + DATASET_TYPES: frozenset([DatasetType.SNV_INDEL]), + VERSION: '1.0', + PATH: 'gs://gcp-public-data--gnomad/release/4.1/ht/genomes/gnomad.genomes.v4.1.sites.ht', + }, + }, + ReferenceDataset.gnomad_qc: { + ReferenceGenome.GRCh37: { + DATASET_TYPES: frozenset([DatasetType.SNV_INDEL]), + VERSION: '1.0', + PATH: 'gs://seqr-reference-data/gnomad_qc/GRCh37/gnomad.joint.high_callrate_common_biallelic_snps.pruned.mt', + }, + ReferenceGenome.GRCh38: { + DATASET_TYPES: frozenset([DatasetType.SNV_INDEL]), + VERSION: '1.0', + PATH: 'gs://gcp-public-data--gnomad/release/4.0/pca/gnomad.v4.0.pca_loadings.ht', + }, + }, + ReferenceDataset.gnomad_svs: { + FORMATTING_ANNOTATION: sv.gnomad_svs, + ReferenceGenome.GRCh38: { + DATASET_TYPES: frozenset([DatasetType.SV]), + VERSION: '1.1', + PATH: 'gs://gcp-public-data--gnomad/release/4.1/genome_sv/gnomad.v4.1.sv.sites.vcf.gz', + }, + }, +} +CONFIG[ReferenceDataset.gnomad_coding_and_noncoding] = { + **CONFIG[ReferenceDataset.gnomad_genomes], +} diff --git a/loading_pipeline/lib/reference_datasets/splice_ai.py b/loading_pipeline/lib/reference_datasets/splice_ai.py new file mode 100644 index 0000000000..4d6a9e8a3f --- /dev/null +++ b/loading_pipeline/lib/reference_datasets/splice_ai.py @@ -0,0 +1,71 @@ +import hail as hl + +from loading_pipeline.lib.core import ReferenceGenome +from loading_pipeline.lib.misc.io import ( + checkpoint, + compute_hail_n_partitions, + file_size_bytes, +) +from loading_pipeline.lib.reference_datasets.misc import vcf_to_ht + + +def remove_duplicate_scores(ht: hl.Table): + # + # SpliceAI has many duplicate rows of the ilk: + # + # 1:861264 | ["C","A"] | NA | -1.00e+01 | NA | ["A|AL645608.1|0.00|0.00|0.00|0.00|2|27|12|1"] | + # 1:861264 | ["C","A"] | NA | -1.00e+01 | NA | ["A|SAMD11|0.02|0.01|0.00|0.00|14|38|14|38"] + # + count_ht = ht.group_by(*ht.key).aggregate(n=hl.agg.count()) + duplicate_variants_ht = count_ht.filter(count_ht.n > 1) + duplicates_ht = ht.semi_join(duplicate_variants_ht) + non_duplicates_ht = ht.anti_join(duplicates_ht) + return non_duplicates_ht.union( + # Remove rows that 1) are part of duplicate variant groupings + # and 2) contain dots. Then, remove arbitrarily with .distinct() + duplicates_ht.filter( + ~duplicates_ht.info.SpliceAI[0].split(delim='\\|')[1].contains('.'), + ).distinct(), + ) + + +def get_ht( + paths: list[str], + reference_genome: ReferenceGenome, +) -> hl.Table: + # NB: We ran into weird issues...running out + # of file descriptors on dataproc :/ + hl._set_flags(use_new_shuffle=None, no_whole_stage_codegen='1') # noqa: SLF001 + ht = vcf_to_ht(paths, reference_genome) + ht, checkpoint_path = checkpoint(ht) + # The default partitions are too big, leading to OOMs. + ht = ht.repartition( + int(compute_hail_n_partitions(file_size_bytes(checkpoint_path)) * 2), + # Note that shuffle=True here, since this is one of the few + # cases in the pipeline where we want to increase the number + # of partititons. + ) + ht, _ = checkpoint(ht) + ht = remove_duplicate_scores(ht) + + # SpliceAI INFO field description from the VCF header: SpliceAIv1.3 variant annotation. These include + # delta scores (DS) and delta positions (DP) for acceptor gain (AG), acceptor loss (AL), donor gain (DG), and + # donor loss (DL). Format: ALLELE|SYMBOL|DS_AG|DS_AL|DS_DG|DS_DL|DP_AG|DP_AL|DP_DG|DP_DL + ds_start_index = 2 + ds_end_index = 6 + num_delta_scores = ds_end_index - ds_start_index + ht = ht.select( + delta_scores=ht.info.SpliceAI[0] + .split(delim='\\|')[ds_start_index:ds_end_index] + .map(hl.float32), + ) + ht = ht.annotate(delta_score=hl.max(ht.delta_scores)) + return ht.annotate( + splice_consequence_id=hl.if_else( + ht.delta_score > 0, + # Splice Consequence enum ID is the index of the max score + ht.delta_scores.index(ht.delta_score), + # If no score, use the last index for "No Consequence" + num_delta_scores, + ), + ).drop('delta_scores') diff --git a/loading_pipeline/lib/reference_datasets/topmed.py b/loading_pipeline/lib/reference_datasets/topmed.py new file mode 100644 index 0000000000..3172df2374 --- /dev/null +++ b/loading_pipeline/lib/reference_datasets/topmed.py @@ -0,0 +1,22 @@ +import hail as hl + +from loading_pipeline.lib.core import ReferenceGenome +from loading_pipeline.lib.misc.nested_field import parse_nested_field +from loading_pipeline.lib.reference_datasets.misc import vcf_to_ht + +SELECT = { + 'AC': 'info.AC#', + 'AF': 'info.AF#', + 'AN': 'info.AN', + 'Hom': 'info.Hom#', + 'Het': 'info.Het#', +} + + +def get_ht(path: str, reference_genome: ReferenceGenome) -> hl.Table: + ht = vcf_to_ht(path, reference_genome) + if reference_genome == ReferenceGenome.GRCh37: + ht = ht.filter(ht.locus.position == hl.int(ht.info.OriginalStart)) + return ht.select( + **{k: parse_nested_field(ht, v) for k, v in SELECT.items()}, + ) diff --git a/loading_pipeline/lib/tasks/__init__.py b/loading_pipeline/lib/tasks/__init__.py new file mode 100644 index 0000000000..7ec456e200 --- /dev/null +++ b/loading_pipeline/lib/tasks/__init__.py @@ -0,0 +1,29 @@ +from loading_pipeline.lib.tasks.clickhouse_migration.migrate_all_projects_to_clickhouse import ( + MigrateAllProjectsToClickHouseTask, +) +from loading_pipeline.lib.tasks.clickhouse_migration.migrate_all_projects_to_clickhouse_on_dataproc import ( + MigrateAllProjectsToClickHouseOnDataprocTask, +) +from loading_pipeline.lib.tasks.reference_data.updated_reference_dataset_parquet import ( + UpdatedReferenceDatasetParquetTask, +) +from loading_pipeline.lib.tasks.run_pipeline import RunPipelineTask +from loading_pipeline.lib.tasks.variants_migration.migrate_variant_details_parquet import ( + MigrateVariantDetailsParquetTask, +) +from loading_pipeline.lib.tasks.variants_migration.migrate_variants_parquet import ( + MigrateVariantsParquetTask, +) +from loading_pipeline.lib.tasks.write_metadata_for_run import WriteMetadataForRunTask +from loading_pipeline.lib.tasks.write_success_file import WriteSuccessFileTask + +__all__ = [ + 'MigrateAllProjectsToClickHouseOnDataprocTask', + 'MigrateAllProjectsToClickHouseTask', + 'MigrateVariantDetailsParquetTask', + 'MigrateVariantsParquetTask', + 'RunPipelineTask', + 'UpdatedReferenceDatasetParquetTask', + 'WriteMetadataForRunTask', + 'WriteSuccessFileTask', +] diff --git a/loading_pipeline/lib/tasks/base/__init__.py b/loading_pipeline/lib/tasks/base/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/loading_pipeline/lib/tasks/base/base_hail_table.py b/loading_pipeline/lib/tasks/base/base_hail_table.py new file mode 100644 index 0000000000..e069bd35b4 --- /dev/null +++ b/loading_pipeline/lib/tasks/base/base_hail_table.py @@ -0,0 +1,71 @@ +import hail as hl +import luigi + +from loading_pipeline.lib.annotations.liftover import remove_liftover +from loading_pipeline.lib.core import Env +from loading_pipeline.lib.logger import get_logger +from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( + BaseLoadingPipelineParams, +) +from loading_pipeline.lib.tasks.files import GCSorLocalFolderTarget + +logger = get_logger(__name__) + + +@luigi.util.inherits(BaseLoadingPipelineParams) +class BaseHailTableTask(luigi.Task): + def output(self) -> luigi.Target: + raise NotImplementedError + + def complete(self) -> bool: + logger.info(f'BaseHailTableTask: checking if {self.output().path} exists') + return GCSorLocalFolderTarget(self.output().path).exists() + + def init_hail(self): + # Need to use the GCP bucket as temp storage for very large callset joins + hl.init(tmp_dir=Env.HAIL_TMP_DIR, idempotent=True) + logger.info(f'Initialized hail w/ tmp_dir {Env.HAIL_TMP_DIR}') + + # Interval ref data join causes shuffle death, this prevents it + hl._set_flags(use_new_shuffle='1', no_whole_stage_codegen='1') # noqa: SLF001 + + # Ensure any cached liftover files within Hail are cleared + # to provide a clean context free of hidden state. + # This runs "before" a task to account for situations where + # the Hail write fails and we do not have the chance to + # run this method in the "after". + remove_liftover() + + +# NB: these are defined over luigi.Task instead of the BaseHailTableTask so that +# they work on file dependencies. + + +@luigi.Task.event_handler(luigi.Event.DEPENDENCY_DISCOVERED) +def dependency_discovered(task, dependency): + logger.info(f'{task} dependency_discovered {dependency} at {task.output()}') + + +@luigi.Task.event_handler(luigi.Event.DEPENDENCY_MISSING) +def dependency_missing(task): + logger.info(f'{task} dependency_missing at {task.output()}') + + +@luigi.Task.event_handler(luigi.Event.DEPENDENCY_PRESENT) +def dependency_present(task): + logger.info(f'{task} dependency_present at {task.output()}') + + +@luigi.Task.event_handler(luigi.Event.START) +def start(task): + logger.info(f'{task} start') + + +@luigi.Task.event_handler(luigi.Event.FAILURE) +def failure(task, _): + logger.exception(f'{task} failure') + + +@luigi.Task.event_handler(luigi.Event.SUCCESS) +def success(task): + logger.info(f'{task} success') diff --git a/loading_pipeline/lib/tasks/base/base_loading_pipeline_params.py b/loading_pipeline/lib/tasks/base/base_loading_pipeline_params.py new file mode 100644 index 0000000000..1e9ea4ee93 --- /dev/null +++ b/loading_pipeline/lib/tasks/base/base_loading_pipeline_params.py @@ -0,0 +1,12 @@ +import luigi + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome + + +class BaseLoadingPipelineParams(luigi.Task): + # NB: + # These params are "inherited" with the special + # luigi.util.inherits function, copying params + # but nothing else. + reference_genome = luigi.EnumParameter(enum=ReferenceGenome) + dataset_type = luigi.EnumParameter(enum=DatasetType) diff --git a/loading_pipeline/lib/tasks/base/base_loading_run_params.py b/loading_pipeline/lib/tasks/base/base_loading_run_params.py new file mode 100644 index 0000000000..43158dcc5d --- /dev/null +++ b/loading_pipeline/lib/tasks/base/base_loading_run_params.py @@ -0,0 +1,36 @@ +import luigi + +from loading_pipeline.lib.core import SampleType +from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( + BaseLoadingPipelineParams, +) + + +@luigi.util.inherits(BaseLoadingPipelineParams) +class BaseLoadingRunParams(luigi.Task): + # The difference between the "Loading Run" params + # and the "Loading Pipeline" params: + # - These params are used during standard "runs" + # of the pipeline that add a callset to the backend + # data store. + # - The "Loading Pipeline" params are shared with + # tasks that may remove data from or change the + # structure of the persisted Hail Tables. + run_id = luigi.Parameter() + sample_type = luigi.EnumParameter(enum=SampleType) + callset_path = luigi.Parameter() + project_guids = luigi.ListParameter(default=[]) + skip_check_sex_and_relatedness = luigi.BoolParameter( + default=False, + parsing=luigi.BoolParameter.EXPLICIT_PARSING, + ) + skip_expect_tdr_metrics = luigi.BoolParameter( + default=False, + parsing=luigi.BoolParameter.EXPLICIT_PARSING, + ) + validations_to_skip = luigi.ListParameter(default=[]) + is_new_gcnv_joint_call = luigi.BoolParameter( + default=False, + parsing=luigi.BoolParameter.EXPLICIT_PARSING, + description='Is this a fully joint-called callset.', + ) diff --git a/loading_pipeline/lib/tasks/base/base_update.py b/loading_pipeline/lib/tasks/base/base_update.py new file mode 100644 index 0000000000..1cacf37383 --- /dev/null +++ b/loading_pipeline/lib/tasks/base/base_update.py @@ -0,0 +1,26 @@ +import hail as hl + +from loading_pipeline.lib.misc.io import write +from loading_pipeline.lib.tasks.base.base_hail_table import BaseHailTableTask + + +class BaseUpdateTask(BaseHailTableTask): + def run(self) -> None: + self.init_hail() + if not self.output().exists(): + ht = self.initialize_table() + else: + read_fn = ( + hl.read_matrix_table + if self.output().path.endswith('mt') + else hl.read_table + ) + ht = read_fn(self.output().path) + ht = self.update_table(ht) + write(ht, self.output().path) + + def initialize_table(self) -> hl.Table: + raise NotImplementedError + + def update_table(self, ht: hl.Table) -> hl.Table: + raise NotImplementedError diff --git a/loading_pipeline/lib/tasks/base/base_write.py b/loading_pipeline/lib/tasks/base/base_write.py new file mode 100644 index 0000000000..cc0be97eac --- /dev/null +++ b/loading_pipeline/lib/tasks/base/base_write.py @@ -0,0 +1,14 @@ +import hail as hl + +from loading_pipeline.lib.misc.io import write +from loading_pipeline.lib.tasks.base.base_hail_table import BaseHailTableTask + + +class BaseWriteTask(BaseHailTableTask): + def run(self) -> None: + self.init_hail() + ht = self.create_table() + write(ht, self.output().path) + + def create_table(self) -> hl.Table: + raise NotImplementedError diff --git a/loading_pipeline/lib/tasks/base/base_write_parquet.py b/loading_pipeline/lib/tasks/base/base_write_parquet.py new file mode 100644 index 0000000000..bc1d358e0c --- /dev/null +++ b/loading_pipeline/lib/tasks/base/base_write_parquet.py @@ -0,0 +1,19 @@ +import luigi + +from loading_pipeline.lib.misc.io import checkpoint +from loading_pipeline.lib.tasks.files import GCSorLocalFolderTarget + + +class BaseWriteParquetTask(luigi.Task): + def complete(self) -> luigi.Target: + return GCSorLocalFolderTarget(self.output().path).exists() + + def run(self) -> None: + ht = self.create_table() + ht, _ = checkpoint(ht) + df = ht.to_spark(flatten=False) + df = df.withColumnRenamed('key_', 'key') + df.write.parquet( + self.output().path, + mode='overwrite', + ) diff --git a/loading_pipeline/lib/tasks/clickhouse_migration/__init__.py b/loading_pipeline/lib/tasks/clickhouse_migration/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/loading_pipeline/lib/tasks/clickhouse_migration/migrate_all_projects_to_clickhouse.py b/loading_pipeline/lib/tasks/clickhouse_migration/migrate_all_projects_to_clickhouse.py new file mode 100644 index 0000000000..c8a5e9678a --- /dev/null +++ b/loading_pipeline/lib/tasks/clickhouse_migration/migrate_all_projects_to_clickhouse.py @@ -0,0 +1,51 @@ +import hailtop.fs as hfs +import luigi +import luigi.util + +from loading_pipeline.lib.core import SampleType +from loading_pipeline.lib.paths import ( + project_table_path, +) +from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( + BaseLoadingPipelineParams, +) +from loading_pipeline.lib.tasks.clickhouse_migration.migrate_project_to_clickhouse import ( + MigrateProjectToClickHouseTask, +) + + +@luigi.util.inherits(BaseLoadingPipelineParams) +class MigrateAllProjectsToClickHouseTask(luigi.WrapperTask): + run_id = luigi.Parameter() + attempt_id = luigi.IntParameter() + + def __init__(self, *args, **kwargs): + super().__init__(*args, **kwargs) + self.dynamic_parquet_tasks = set() + + def complete(self): + return len(self.dynamic_parquet_tasks) >= 1 and all( + dynamic_parquet_tasks.complete() + for dynamic_parquet_tasks in self.dynamic_parquet_tasks + ) + + def run(self): + for sample_type in SampleType: + for p in hfs.ls( + project_table_path( + self.reference_genome, + self.dataset_type, + sample_type, + '*', + ), + ): + project_guid = p.path.split('/')[-1].replace('.ht', '') + self.dynamic_parquet_tasks.add( + self.clone( + MigrateProjectToClickHouseTask, + run_id=f'{self.run_id}_{sample_type.value}_{project_guid}', + sample_type=sample_type, + project_guid=project_guid, + ), + ) + yield self.dynamic_parquet_tasks diff --git a/loading_pipeline/lib/tasks/clickhouse_migration/migrate_all_projects_to_clickhouse_on_dataproc.py b/loading_pipeline/lib/tasks/clickhouse_migration/migrate_all_projects_to_clickhouse_on_dataproc.py new file mode 100644 index 0000000000..96e3ffbdcd --- /dev/null +++ b/loading_pipeline/lib/tasks/clickhouse_migration/migrate_all_projects_to_clickhouse_on_dataproc.py @@ -0,0 +1,16 @@ +import luigi + +from loading_pipeline.lib.tasks.clickhouse_migration.migrate_all_projects_to_clickhouse import ( + MigrateAllProjectsToClickHouseTask, +) +from loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc import ( + BaseRunJobOnDataprocTask, +) + + +class MigrateAllProjectsToClickHouseOnDataprocTask(BaseRunJobOnDataprocTask): + run_id = luigi.Parameter() + + @property + def task(self) -> luigi.Task: + return MigrateAllProjectsToClickHouseTask diff --git a/loading_pipeline/lib/tasks/clickhouse_migration/migrate_all_projects_to_clickhouse_test.py b/loading_pipeline/lib/tasks/clickhouse_migration/migrate_all_projects_to_clickhouse_test.py new file mode 100644 index 0000000000..ad9c752d15 --- /dev/null +++ b/loading_pipeline/lib/tasks/clickhouse_migration/migrate_all_projects_to_clickhouse_test.py @@ -0,0 +1,123 @@ +import json + +import hail as hl +import hailtop.fs as hfs +import luigi.worker +import pandas as pd + +from loading_pipeline.lib.core import ( + DatasetType, + ReferenceGenome, + SampleType, +) +from loading_pipeline.lib.core.constants import MIGRATION_RUN_ID +from loading_pipeline.lib.paths import ( + metadata_for_run_path, + new_entries_parquet_path, + pipeline_run_success_file_path, + project_table_path, + variant_annotations_table_path, +) +from loading_pipeline.lib.tasks.clickhouse_migration.migrate_all_projects_to_clickhouse import ( + MigrateAllProjectsToClickHouseTask, +) +from loading_pipeline.lib.test.mocked_dataroot_testcase import ( + MockedDatarootTestCase, +) + +TEST_SNV_INDEL_ANNOTATIONS = ( + 'loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/annotations.ht' +) +TEST_PROJECT_TABLES = [ + ( + 'loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/projects/WGS/R0113_test_project.ht', + SampleType.WGS, + 'R0113_test_project', + ), + ( + 'loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/projects/WES/R0113_test_project.ht', + SampleType.WES, + 'R0113_test_project', + ), + ( + 'loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/projects/WES/R0114_project4.ht', + SampleType.WES, + 'R0114_project4', + ), +] + + +class MigrateAllProjectsToClickHouseTaskTest(MockedDatarootTestCase): + def setUp(self) -> None: + super().setUp() + ht = hl.read_table(TEST_SNV_INDEL_ANNOTATIONS) + ht.write( + variant_annotations_table_path( + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + ), + ) + for path, sample_type, project_guid in TEST_PROJECT_TABLES: + ht = hl.read_table(path) + ht.write( + project_table_path( + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + sample_type, + project_guid, + ), + ) + + def test_all_project_entries_to_clickhouse_test( + self, + ) -> None: + worker = luigi.worker.Worker() + task = MigrateAllProjectsToClickHouseTask( + reference_genome=ReferenceGenome.GRCh37, + dataset_type=DatasetType.SNV_INDEL, + run_id=MIGRATION_RUN_ID, + attempt_id=0, + ) + worker.add(task) + worker.run() + self.assertTrue(task.complete()) + for _, sample_type, project_guid in TEST_PROJECT_TABLES: + df = pd.read_parquet( + new_entries_parquet_path( + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + f'{MIGRATION_RUN_ID}_{sample_type.value}_{project_guid}', + ), + ) + export_json = df.to_dict('records') + self.assertEqual( + export_json[0]['key'], + 1424, + ) + + for _, sample_type, project_guid in TEST_PROJECT_TABLES: + with hfs.open( + metadata_for_run_path( + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + f'{MIGRATION_RUN_ID}_{sample_type.value}_{project_guid}', + ), + ) as f: + metadata_json = json.load(f) + self.assertEqual( + metadata_json['run_id'], + f'{MIGRATION_RUN_ID}_{sample_type.value}_{project_guid}', + ) + self.assertEqual( + metadata_json['family_samples']['F079280_bh10261'], + ['BH10261-1', 'BH10261-2', 'BH10261-3-T'], + ) + + with hfs.open( + pipeline_run_success_file_path( + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + f'{MIGRATION_RUN_ID}_{sample_type.value}_{project_guid}', + ), + ) as f: + self.assertEqual(f.read(), '') diff --git a/loading_pipeline/lib/tasks/clickhouse_migration/migrate_project_to_clickhouse.py b/loading_pipeline/lib/tasks/clickhouse_migration/migrate_project_to_clickhouse.py new file mode 100644 index 0000000000..be0d668a7d --- /dev/null +++ b/loading_pipeline/lib/tasks/clickhouse_migration/migrate_project_to_clickhouse.py @@ -0,0 +1,157 @@ +import json + +import hail as hl +import luigi +import luigi.util + +from loading_pipeline.lib.core import SampleType +from loading_pipeline.lib.misc.family_entries import ( + deduplicate_by_most_non_ref_calls, + deglobalize_ids, +) +from loading_pipeline.lib.paths import ( + metadata_for_run_path, + new_entries_parquet_path, + pipeline_run_success_file_path, + project_table_path, +) +from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( + BaseLoadingPipelineParams, +) +from loading_pipeline.lib.tasks.base.base_write_parquet import BaseWriteParquetTask +from loading_pipeline.lib.tasks.clickhouse_migration.migrate_project_variants_to_clickhouse import ( + MigrateProjectVariantsToClickHouseTask, + WriteProjectSubsettedVariantsTask, +) +from loading_pipeline.lib.tasks.exports.fields import get_entries_export_fields +from loading_pipeline.lib.tasks.files import GCSorLocalTarget, HailTableTask + +PROJECT_SUBSETTED_ANNOTATIONS_TABLE_TASK = 'project_subsetted_annotations_table_task' +PROJECT_TABLE_TASK = 'project_table_task' + + +@luigi.util.inherits(BaseLoadingPipelineParams) +class WriteProjectEntriesParquetTask(BaseWriteParquetTask): + run_id = luigi.Parameter() + sample_type = luigi.EnumParameter(enum=SampleType) + project_guid = luigi.Parameter() + + def output(self) -> luigi.Target: + return GCSorLocalTarget( + new_entries_parquet_path( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + ) + + def requires(self) -> list[luigi.Task]: + return { + PROJECT_SUBSETTED_ANNOTATIONS_TABLE_TASK: self.clone( + WriteProjectSubsettedVariantsTask, + ), + PROJECT_TABLE_TASK: HailTableTask( + project_table_path( + self.reference_genome, + self.dataset_type, + self.sample_type, + self.project_guid, + ), + ), + } + + def create_table(self) -> None: + ht = hl.read_table( + self.input()[PROJECT_TABLE_TASK].path, + ) + ht = deglobalize_ids(ht) + ht = deduplicate_by_most_non_ref_calls(ht) + annotations_ht = hl.read_table( + self.input()[PROJECT_SUBSETTED_ANNOTATIONS_TABLE_TASK].path, + ) + ht = ht.join(annotations_ht) + ht = ht.explode(ht.family_entries) + ht = ht.filter(hl.is_defined(ht.family_entries)) + ht = ht.key_by() + ht = ht.select_globals() + return ht.select( + **get_entries_export_fields( + ht, + self.dataset_type, + self.sample_type, + self.project_guid, + ), + ) + + +@luigi.util.inherits(BaseLoadingPipelineParams) +class WriteMigrationMetadataJsonTask(luigi.Task): + run_id = luigi.Parameter() + sample_type = luigi.EnumParameter(enum=SampleType) + project_guid = luigi.Parameter() + + def requires(self): + return HailTableTask( + project_table_path( + self.reference_genome, + self.dataset_type, + self.sample_type, + self.project_guid, + ), + ) + + def output(self) -> luigi.Target: + return GCSorLocalTarget( + metadata_for_run_path( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + ) + + def run(self): + ht = hl.read_table(self.input().path) + metadata_json = { + 'callsets': [], + 'run_id': self.run_id, + 'sample_type': self.sample_type.value, + 'project_guids': [self.project_guid], + 'family_samples': hl.eval(ht.globals.family_samples), + 'failed_family_samples': { + 'missing_samples': {}, + 'relatedness_check': {}, + 'sex_check': {}, + 'ploidy_check': {}, + }, + 'relatedness_check_file_path': '', + 'sample_qc': {}, + } + with self.output().open('w') as f: + json.dump(metadata_json, f) + + +@luigi.util.inherits(BaseLoadingPipelineParams) +class MigrateProjectToClickHouseTask(luigi.Task): + run_id = luigi.Parameter() + sample_type = luigi.EnumParameter(enum=SampleType) + project_guid = luigi.Parameter() + + def requires(self): + return [ + self.clone(MigrateProjectVariantsToClickHouseTask), + self.clone(WriteProjectEntriesParquetTask), + self.clone(WriteMigrationMetadataJsonTask), + ] + + def output(self) -> luigi.Target: + return GCSorLocalTarget( + pipeline_run_success_file_path( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + ) + + def run(self): + with self.output().open('w') as f: + f.write('') diff --git a/loading_pipeline/lib/tasks/clickhouse_migration/migrate_project_variants_to_clickhouse.py b/loading_pipeline/lib/tasks/clickhouse_migration/migrate_project_variants_to_clickhouse.py new file mode 100644 index 0000000000..ebf950e551 --- /dev/null +++ b/loading_pipeline/lib/tasks/clickhouse_migration/migrate_project_variants_to_clickhouse.py @@ -0,0 +1,119 @@ +import hail as hl +import luigi +import luigi.util + +from loading_pipeline.lib.core import SampleType +from loading_pipeline.lib.paths import ( + new_variants_table_path, + project_table_path, + variant_annotations_table_path, +) +from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( + BaseLoadingPipelineParams, +) +from loading_pipeline.lib.tasks.base.base_write import BaseWriteTask +from loading_pipeline.lib.tasks.exports.write_new_variant_details_parquet import ( + WriteNewVariantDetailsParquetTask, +) +from loading_pipeline.lib.tasks.exports.write_new_variants_parquet import ( + WriteNewVariantsParquetTask, +) +from loading_pipeline.lib.tasks.files import GCSorLocalTarget, HailTableTask + +MAX_SNV_INDEL_ALLELE_LENGTH = 500 + + +class WriteProjectSubsettedVariantsTask(BaseWriteTask): + run_id = luigi.Parameter() + sample_type = luigi.EnumParameter(enum=SampleType) + project_guid = luigi.Parameter() + + def output(self) -> luigi.Target: + return GCSorLocalTarget( + new_variants_table_path( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + ) + + def requires(self) -> list[luigi.Task]: + return [ + HailTableTask( + variant_annotations_table_path( + self.reference_genome, + self.dataset_type, + ), + ), + HailTableTask( + project_table_path( + self.reference_genome, + self.dataset_type, + self.sample_type, + self.project_guid, + ), + ), + ] + + def create_table(self) -> hl.Table: + ht = hl.read_table(self.input()[0].path) + if not hasattr(ht, 'key_'): + ht = ht.add_index(name='key_') + if self.dataset_type.filter_invalid_sites: + ht = ht.filter(hl.len(ht.alleles[1]) < MAX_SNV_INDEL_ALLELE_LENGTH) + project_ht = hl.read_table(self.input()[1].path) + return ht.semi_join(project_ht) + + +@luigi.util.inherits(BaseLoadingPipelineParams) +class MigrateProjectVariantsToClickHouseTask(luigi.WrapperTask): + run_id = luigi.Parameter() + sample_type = luigi.EnumParameter(enum=SampleType) + project_guid = luigi.Parameter() + + def __init__(self, *args, **kwargs): + super().__init__(*args, **kwargs) + self.dynamic_parquet_tasks = set() + + def requires(self) -> luigi.Task: + return self.clone(WriteProjectSubsettedVariantsTask) + + def complete(self): + return ( + super().complete() + and len(self.dynamic_parquet_tasks) >= 1 + and all( + dynamic_parquet_tasks.complete() + for dynamic_parquet_tasks in self.dynamic_parquet_tasks + ) + ) + + def run(self): + self.dynamic_parquet_tasks.update( + [ + *( + [ + self.clone( + WriteNewVariantDetailsParquetTask, + # Callset Path being required + # here is byproduct of the "place all variants" + # in the variants path" hack. In theory + # it is possible to re-factor the parameters + # such that this isn't required, but it's left + # as out of scope for now. Alternatively, + # we could inherit the functionality of these + # tasks without calling them directly, but + # that was also more code. + callset_path=None, + ), + ] + if self.dataset_type.should_write_new_variant_details + else [] + ), + self.clone( + WriteNewVariantsParquetTask, + callset_path=None, + ), + ], + ) + yield self.dynamic_parquet_tasks diff --git a/loading_pipeline/lib/tasks/clickhouse_migration/migrate_project_variants_to_clickhouse_test.py b/loading_pipeline/lib/tasks/clickhouse_migration/migrate_project_variants_to_clickhouse_test.py new file mode 100644 index 0000000000..ce4c6d5cd8 --- /dev/null +++ b/loading_pipeline/lib/tasks/clickhouse_migration/migrate_project_variants_to_clickhouse_test.py @@ -0,0 +1,91 @@ +import hail as hl +import hailtop.fs as hfs +import luigi.worker +import pandas as pd + +from loading_pipeline.lib.core import ( + DatasetType, + ReferenceGenome, + SampleType, +) +from loading_pipeline.lib.paths import ( + new_variant_details_parquet_path, + new_variants_parquet_path, + pipeline_run_success_file_path, + project_table_path, + variant_annotations_table_path, +) +from loading_pipeline.lib.tasks.clickhouse_migration.migrate_project_variants_to_clickhouse import ( + MigrateProjectVariantsToClickHouseTask, +) +from loading_pipeline.lib.test.mocked_dataroot_testcase import ( + MockedDatarootTestCase, +) + +TEST_SNV_INDEL_ANNOTATIONS = ( + 'loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/annotations.ht' +) +TEST_PROJECT_TABLE = 'loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/projects/WGS/R0113_test_project.ht' + +TEST_RUN_ID = 'migration_run' + + +class WriteVariantsToClickHouseTest(MockedDatarootTestCase): + def setUp(self) -> None: + super().setUp() + ht = hl.read_table(TEST_SNV_INDEL_ANNOTATIONS) + ht.write( + variant_annotations_table_path( + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + ), + ) + ht = hl.read_table(TEST_PROJECT_TABLE) + ht.write( + project_table_path( + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0113_test_project', + ), + ) + + def test_migrate_variants_to_clickhouse_test( + self, + ) -> None: + worker = luigi.worker.Worker() + task = MigrateProjectVariantsToClickHouseTask( + reference_genome=ReferenceGenome.GRCh37, + dataset_type=DatasetType.SNV_INDEL, + run_id=TEST_RUN_ID, + sample_type=SampleType.WGS, + project_guid='R0113_test_project', + ) + worker.add(task) + worker.run() + self.assertTrue(task.complete()) + df = pd.read_parquet( + new_variants_parquet_path( + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ) + self.assertEqual(df.shape[0], 1) + df = pd.read_parquet( + new_variant_details_parquet_path( + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ) + self.assertEqual(df.shape[0], 1) + self.assertFalse( + hfs.exists( + pipeline_run_success_file_path( + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ), + ) diff --git a/loading_pipeline/lib/tasks/dataproc/__init__.py b/loading_pipeline/lib/tasks/dataproc/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/loading_pipeline/lib/tasks/dataproc/base_run_job_on_dataproc.py b/loading_pipeline/lib/tasks/dataproc/base_run_job_on_dataproc.py new file mode 100644 index 0000000000..01ea67e051 --- /dev/null +++ b/loading_pipeline/lib/tasks/dataproc/base_run_job_on_dataproc.py @@ -0,0 +1,147 @@ +import re +import time + +import google.api_core.exceptions +import google.cloud.dataproc_v1.types.jobs +import luigi +from google.cloud import dataproc_v1 as dataproc + +from loading_pipeline.lib.core import Env +from loading_pipeline.lib.logger import get_logger +from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( + BaseLoadingPipelineParams, +) +from loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster import ( + CreateDataprocClusterTask, +) +from loading_pipeline.lib.tasks.dataproc.misc import get_cluster_name, to_kebab_str_args + +FAILURE_STATUSES = { + google.cloud.dataproc_v1.types.jobs.JobStatus.State.CANCELLED, + google.cloud.dataproc_v1.types.jobs.JobStatus.State.ERROR, + google.cloud.dataproc_v1.types.jobs.JobStatus.State.ATTEMPT_FAILURE, +} +SEQR_PIPELINE_RUNNER_BUILD = f'gs://seqr-pipeline-runner-builds/{Env.DEPLOYMENT_TYPE}/{Env.PIPELINE_RUNNER_APP_VERSION}' +TIMEOUT_S = 172800 # 2 days + +logger = get_logger(__name__) + + +@luigi.util.inherits(BaseLoadingPipelineParams) +class BaseRunJobOnDataprocTask(luigi.Task): + run_id = luigi.Parameter() + attempt_id = luigi.IntParameter() + + def __init__(self, *args, **kwargs): + super().__init__(*args, **kwargs) + self.client = dataproc.JobControllerClient( + client_options={ + 'api_endpoint': f'{Env.GCLOUD_REGION}-dataproc.googleapis.com:443', + }, + ) + + @property + def task(self): + raise NotImplementedError + + @property + def job_id(self): + return f'{self.task.task_family}-{self.reference_genome[-2:]}-{re.sub("_", "-", self.dataset_type.value)}-{self.run_id}-{self.attempt_id}' + + def requires(self) -> [luigi.Task]: + return [self.clone(CreateDataprocClusterTask)] + + def safely_get_job( + self, + ): + try: + job = self.client.get_job( + request={ + 'project_id': Env.GCLOUD_PROJECT, + 'region': Env.GCLOUD_REGION, + 'job_id': self.job_id, + }, + ) + except google.api_core.exceptions.NotFound: + return None + else: + return job + + def complete(self) -> bool: + job = self.safely_get_job() + if not job: + return False + if job.status.state in FAILURE_STATUSES: + msg = f'Job {self.job_id} entered {job.status.state.name} state' + logger.error(msg) + logger.error(job.status.details) + return ( + job.status.state == google.cloud.dataproc_v1.types.jobs.JobStatus.State.DONE + ) + + def run(self): + job = self.safely_get_job() + # Delete the job if it exists and was failed. This handles manual re-runs of the + # same run_id. + if job and job.status.state in FAILURE_STATUSES: + logger.error( + f'Previous job {self.job_id} failed with state {job.status.state.name}', + ) + logger.error(job.status.details) + self.client.delete_job( + request={ + 'project_id': Env.GCLOUD_PROJECT, + 'region': Env.GCLOUD_REGION, + 'job_id': self.job_id, + }, + ) + job = None + + if not job: + self.client.submit_job_as_operation( + request={ + 'project_id': Env.GCLOUD_PROJECT, + 'region': Env.GCLOUD_REGION, + 'job': { + 'reference': { + 'job_id': self.job_id, + }, + 'placement': { + 'cluster_name': get_cluster_name( + self.reference_genome, + self.run_id, + ), + }, + 'pyspark_job': { + 'main_python_file_uri': f'{SEQR_PIPELINE_RUNNER_BUILD}/bin/run_task.py', + 'args': [ + self.task.task_family, + '--local-scheduler', + *to_kebab_str_args(self), + ], + 'python_file_uris': [ + f'{SEQR_PIPELINE_RUNNER_BUILD}/pyscripts.zip', + ], + }, + }, + }, + ) + wait_s = 0 + while wait_s < TIMEOUT_S: + job = self.safely_get_job() + if ( + job.status.state + == google.cloud.dataproc_v1.types.jobs.JobStatus.State.DONE + ): + msg = f'Job {self.job_id} is complete' + logger.info(msg) + break + if job.status.state in FAILURE_STATUSES: + msg = f'Job {self.job_id} entered {job.status.state.name} state' + logger.error(msg) + raise RuntimeError(msg) + logger.info( + f'Waiting for Job completion {self.job_id}', + ) + time.sleep(3) + wait_s += 3 diff --git a/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster.py b/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster.py new file mode 100644 index 0000000000..5e0bb59cbb --- /dev/null +++ b/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster.py @@ -0,0 +1,224 @@ +import time + +import google.api_core.exceptions +import google.cloud.dataproc_v1.types.clusters +import hail as hl +import luigi +from google.cloud import dataproc_v1 as dataproc +from pip._internal.operations import freeze as pip_freeze + +from loading_pipeline.lib.core import DatasetType, Env, FeatureFlag, ReferenceGenome +from loading_pipeline.lib.logger import get_logger +from loading_pipeline.lib.misc.gcp import get_service_account_credentials +from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( + BaseLoadingPipelineParams, +) +from loading_pipeline.lib.tasks.dataproc.misc import get_cluster_name + +DEBIAN_IMAGE = '2.3.17-debian12' +DISK_SIZE_GB = 600 +DISK_TYPE = 'hyperdisk-balanced' +HAIL_VERSION = hl.version().split('-')[0] +INSTANCE_TYPE = 'n4-highmem-8' +PKGS = '|'.join( + [ + x.replace('gnomad_qc @ ', '').replace('onnxconverter-common @ ', '') + for x in pip_freeze.freeze() + if 'hail @' not in x + ], +) +TIMEOUT_S = 1200 +FAILURE_STATUSES = { + google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.UNKNOWN, + google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.ERROR, + google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.ERROR_DUE_TO_UPDATE, +} + +logger = get_logger(__name__) + + +def get_cluster_config( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + run_id: str, +): + service_account_credentials = get_service_account_credentials() + return { + 'project_id': Env.GCLOUD_PROJECT, + 'cluster_name': get_cluster_name(reference_genome, run_id), + # Schema found at https://cloud.google.com/dataproc/docs/reference/rest/v1/ClusterConfig + 'config': { + 'gce_cluster_config': { + 'metadata': { + 'WHEEL': f'gs://hail-common/hailctl/dataproc/{HAIL_VERSION}/hail-{HAIL_VERSION}-py3-none-any.whl', + 'PKGS': PKGS, + 'DEPLOYMENT_TYPE': Env.DEPLOYMENT_TYPE, + 'REFERENCE_GENOME': reference_genome.value, + 'PIPELINE_RUNNER_APP_VERSION': Env.PIPELINE_RUNNER_APP_VERSION, + 'REFERENCE_DATASETS_DIR': Env.REFERENCE_DATASETS_DIR, + }, + 'internal_ip_only': False, # Recent change with 2.2 dataproc images. + 'service_account': service_account_credentials.service_account_email, + 'service_account_scopes': service_account_credentials.scopes, + }, + 'master_config': { + 'num_instances': 1, + 'machine_type_uri': INSTANCE_TYPE, + 'disk_config': { + 'boot_disk_type': DISK_TYPE, + 'boot_disk_size_gb': DISK_SIZE_GB, + }, + }, + 'worker_config': { + 'num_instances': dataset_type.dataproc_primary_workers, + 'machine_type_uri': INSTANCE_TYPE, + 'disk_config': { + 'boot_disk_type': DISK_TYPE, + 'boot_disk_size_gb': DISK_SIZE_GB, + }, + }, + 'secondary_worker_config': { + 'num_instances': dataset_type.dataproc_preemptibles, + 'machine_type_uri': INSTANCE_TYPE, + 'disk_config': { + 'boot_disk_type': DISK_TYPE, + 'boot_disk_size_gb': DISK_SIZE_GB, + }, + 'is_preemptible': True, + 'preemptibility': 'PREEMPTIBLE', + }, + 'software_config': { + 'image_version': DEBIAN_IMAGE, + 'properties': { + 'spark:spark.driver.maxResultSize': '0', + 'spark:spark.task.maxFailures': '20', + 'spark:spark.kryoserializer.buffer.max': '2g', + 'spark:spark.driver.extraJavaOptions': '-Xss16M', + 'spark:spark.executor.extraJavaOptions': '-Xss16M', + 'hdfs:dfs.replication': '1', + 'dataproc:dataproc.logging.stackdriver.enable': 'false', + 'dataproc:dataproc.monitoring.stackdriver.enable': 'false', + 'spark:spark.driver.memory': '41g', + 'yarn:yarn.nodemanager.resource.memory-mb': '50585', + 'yarn:yarn.scheduler.maximum-allocation-mb': '25292', + 'spark:spark.executor.cores': '4', + 'spark:spark.executor.memory': '10117m', + 'spark:spark.executor.memoryOverhead': '15175m', + 'spark:spark.memory.storageFraction': '0.2', + 'spark:spark.executorEnv.HAIL_WORKER_OFF_HEAP_MEMORY_PER_CORE_MB': '6323', + 'spark:spark.speculation': 'true', + 'spark-env:CHECK_SEX_AND_RELATEDNESS': '1' + if FeatureFlag.CHECK_SEX_AND_RELATEDNESS + else '0', + 'spark-env:EXPECT_TDR_METRICS': '1' + if FeatureFlag.EXPECT_TDR_METRICS + else '0', + 'spark-env:PIPELINE_DATA_DIR': Env.PIPELINE_DATA_DIR, + 'spark-env:HAIL_TMP_DIR': Env.HAIL_TMP_DIR, + 'spark-env:LOADING_DATASETS_DIR': Env.LOADING_DATASETS_DIR, + 'spark-env:REFERENCE_DATASETS_DIR': Env.REFERENCE_DATASETS_DIR, + 'spark-env:SAMPLE_TYPE_VALIDATION_EXCLUDED_PROJECTS': ','.join( + Env.SAMPLE_TYPE_VALIDATION_EXCLUDED_PROJECTS, + ), + }, + }, + 'lifecycle_config': {'idle_delete_ttl': {'seconds': 1200}}, + 'encryption_config': {}, + 'autoscaling_config': {}, + 'endpoint_config': {}, + 'initialization_actions': [ + { + # NB: this script initializes the python env. + 'executable_file': f'gs://hail-common/hailctl/dataproc/{HAIL_VERSION}/init_notebook.py', + 'execution_timeout': {'seconds': 1200}, + }, + { + 'executable_file': f'gs://seqr-pipeline-runner-builds/{Env.DEPLOYMENT_TYPE}/{Env.PIPELINE_RUNNER_APP_VERSION}/bin/dataproc_vep_init.bash', + 'execution_timeout': {'seconds': 1200}, + }, + ], + }, + } + + +@luigi.util.inherits(BaseLoadingPipelineParams) +class CreateDataprocClusterTask(luigi.Task): + # NB: The luigi.dataproc.contrib module was old and bad + # so we built our own shim. + run_id = luigi.Parameter() + + def __init__(self, *args, **kwargs): + super().__init__(*args, **kwargs) + # https://cloud.google.com/dataproc/docs/tutorials/python-library-example + self.client = dataproc.ClusterControllerClient( + client_options={ + 'api_endpoint': f'{Env.GCLOUD_REGION}-dataproc.googleapis.com:443', + }, + ) + + def safely_get_cluster( + self, + ): + try: + cluster = self.client.get_cluster( + request={ + 'project_id': Env.GCLOUD_PROJECT, + 'region': Env.GCLOUD_REGION, + 'cluster_name': get_cluster_name( + self.reference_genome, + self.run_id, + ), + }, + ) + except google.api_core.exceptions.NotFound: + return None + else: + return cluster + + def complete(self) -> bool: + cluster = self.safely_get_cluster() + if not cluster: + return False + if cluster.status.state in FAILURE_STATUSES: + msg = f'Cluster {cluster.cluster_name} entered {cluster.status.state.name} state' + logger.error(msg) + # This will return False when the cluster is "CREATING" + return ( + cluster.status.state + == google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.RUNNING + ) + + def run(self): + if not Env.GCLOUD_PROJECT or not Env.GCLOUD_REGION: + msg = 'Environment Variables GCLOUD_PROJECT and GCLOUD_REGION are required for running the pipeline on dataproc.' + raise RuntimeError(msg) + cluster = self.safely_get_cluster() + if not cluster: + self.client.create_cluster( + request={ + 'project_id': Env.GCLOUD_PROJECT, + 'region': Env.GCLOUD_REGION, + 'cluster': get_cluster_config( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + }, + ) + wait_s = 0 + while wait_s < TIMEOUT_S: + cluster = self.safely_get_cluster() + if ( + cluster.status.state + == google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.RUNNING + ): + msg = f'Created cluster {cluster.cluster_name} with cluster uuid: {cluster.cluster_uuid}' + logger.info(msg) + break + if cluster.status.state in FAILURE_STATUSES: + msg = f'Cluster {cluster.cluster_name} entered {cluster.status.state.name} state' + logger.error(msg) + raise RuntimeError(msg) + logger.info('Waiting for cluster spinup') + time.sleep(3) + wait_s += 3 diff --git a/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster_test.py b/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster_test.py new file mode 100644 index 0000000000..6634feea8c --- /dev/null +++ b/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster_test.py @@ -0,0 +1,162 @@ +import unittest +from types import SimpleNamespace +from unittest.mock import Mock, call, patch + +import google.api_core.exceptions +import google.cloud.dataproc_v1.types.clusters +import luigi + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome +from loading_pipeline.lib.misc.gcp import SOCIAL_AUTH_GOOGLE_OAUTH2_SCOPE +from loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster import ( + CreateDataprocClusterTask, +) + + +@patch.multiple( + 'loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster.Env', + GCLOUD_PROJECT='proj', + GCLOUD_REGION='us-a', +) +@patch( + 'loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster.get_service_account_credentials', + return_value=SimpleNamespace( + service_account_email='test@serviceaccount.com', + scopes=SOCIAL_AUTH_GOOGLE_OAUTH2_SCOPE, + ), +) +@patch( + 'loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster.dataproc.ClusterControllerClient', +) +class CreateDataprocClusterTaskTest(unittest.TestCase): + def test_spinup_cluster_already_exists_failed( + self, + mock_cluster_controller: Mock, + *_: Mock, + ) -> None: + mock_client = mock_cluster_controller.return_value + mock_client.get_cluster.return_value = SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.ERROR, + ), + cluster_name='abc', + ) + mock_client.create_cluster.side_effect = ( + google.api_core.exceptions.AlreadyExists('cluster exists') + ) + worker = luigi.worker.Worker() + task = CreateDataprocClusterTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id='2', + ) + worker.add(task) + worker.run() + self.assertFalse(task.complete()) + + def test_spinup_cluster_already_exists_success( + self, + mock_cluster_controller: Mock, + *_: Mock, + ) -> None: + mock_client = mock_cluster_controller.return_value + mock_client.get_cluster.return_value = SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.RUNNING, + ), + ) + mock_client.create_cluster.side_effect = ( + google.api_core.exceptions.AlreadyExists('cluster exists') + ) + worker = luigi.worker.Worker() + task = CreateDataprocClusterTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id='3', + ) + worker.add(task) + worker.run() + self.assertTrue(task.complete()) + + @patch('loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster.logger') + def test_spinup_cluster_doesnt_exist_failed( + self, + mock_logger: Mock, + mock_cluster_controller: Mock, + *_: Mock, + ) -> None: + mock_client = mock_cluster_controller.return_value + mock_client.get_cluster.side_effect = [ + google.api_core.exceptions.NotFound( + 'cluster not found', + ), + google.api_core.exceptions.NotFound( + 'cluster not found', + ), + SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.CREATING, + ), + ), + SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.ERROR, + ), + cluster_name='dataproc-cluster-5', + cluster_uuid='12345', + ), + ] + worker = luigi.worker.Worker() + task = CreateDataprocClusterTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id='4', + ) + worker.add(task) + luigi_task_result = worker.run() + self.assertEqual(luigi_task_result, False) + mock_logger.info.assert_has_calls([call('Waiting for cluster spinup')]) + + @patch('loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster.logger') + def test_spinup_cluster_doesnt_exist_success( + self, + mock_logger: Mock, + mock_cluster_controller: Mock, + *_: Mock, + ) -> None: + mock_client = mock_cluster_controller.return_value + mock_client.get_cluster.side_effect = [ + google.api_core.exceptions.NotFound( + 'cluster not found', + ), + google.api_core.exceptions.NotFound( + 'cluster not found', + ), + SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.CREATING, + ), + ), + SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.RUNNING, + ), + cluster_name='dataproc-cluster-5', + cluster_uuid='12345', + ), + ] + mock_client.create_cluster.side_effect = None + worker = luigi.worker.Worker() + task = CreateDataprocClusterTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id='5', + ) + worker.add(task) + worker.run() + mock_logger.info.assert_has_calls( + [ + call('Waiting for cluster spinup'), + call('Created cluster dataproc-cluster-5 with cluster uuid: 12345'), + ], + ) diff --git a/loading_pipeline/lib/tasks/dataproc/misc.py b/loading_pipeline/lib/tasks/dataproc/misc.py new file mode 100644 index 0000000000..2031aad46a --- /dev/null +++ b/loading_pipeline/lib/tasks/dataproc/misc.py @@ -0,0 +1,29 @@ +import re + +import luigi + +from loading_pipeline.lib.core import Env, ReferenceGenome +from loading_pipeline.lib.core.constants import ( + MIGRATION_RUN_ID, + VARIANTS_MIGRATION_RUN_ID, +) + +CLUSTER_NAME_PREFIX = 'pipeline-runner' + + +def get_cluster_name(reference_genome: ReferenceGenome, run_id: str): + if MIGRATION_RUN_ID in run_id: + return f'{Env.DEPLOYMENT_TYPE}-{CLUSTER_NAME_PREFIX}-{reference_genome.value.lower()}-hs-to-clckhse-mgrtn' + if VARIANTS_MIGRATION_RUN_ID in run_id: + return f'{Env.DEPLOYMENT_TYPE}-{CLUSTER_NAME_PREFIX}-{reference_genome.value.lower()}-vrnts-mgrtn' + return f'{Env.DEPLOYMENT_TYPE}-{CLUSTER_NAME_PREFIX}-{reference_genome.value.lower()}-{run_id}' + + +def snake_to_kebab_arg(snake_string: str) -> str: + return '--' + re.sub(r'\_', '-', snake_string).lower() + + +def to_kebab_str_args(task: luigi.Task): + return [ + e for k, v in task.to_str_params().items() for e in (snake_to_kebab_arg(k), v) + ] diff --git a/loading_pipeline/lib/tasks/dataproc/misc_test.py b/loading_pipeline/lib/tasks/dataproc/misc_test.py new file mode 100644 index 0000000000..63ffafb8a1 --- /dev/null +++ b/loading_pipeline/lib/tasks/dataproc/misc_test.py @@ -0,0 +1,51 @@ +import unittest +from unittest.mock import Mock, patch + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.tasks.dataproc.misc import to_kebab_str_args +from loading_pipeline.lib.tasks.dataproc.run_pipeline_on_dataproc import ( + RunPipelineOnDataprocTask, +) + + +@patch( + 'loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc.dataproc.JobControllerClient', +) +class MiscTest(unittest.TestCase): + def test_to_kebab_str_args(self, _: Mock): + t = RunPipelineOnDataprocTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path='test_callset', + project_guids=['R0113_test_project'], + run_id='a_misc_run', + attempt_id=0, + ) + self.assertListEqual( + to_kebab_str_args(t), + [ + '--reference-genome', + 'GRCh38', + '--dataset-type', + 'SNV_INDEL', + '--sample-type', + 'WGS', + '--callset-path', + 'test_callset', + '--project-guids', + '["R0113_test_project"]', + '--skip-check-sex-and-relatedness', + 'False', + '--skip-expect-tdr-metrics', + 'False', + '--validations-to-skip', + '[]', + '--is-new-gcnv-joint-call', + 'False', + '--run-id', + 'a_misc_run', + '--attempt-id', + '0', + ], + ) diff --git a/loading_pipeline/lib/tasks/dataproc/run_pipeline_on_dataproc.py b/loading_pipeline/lib/tasks/dataproc/run_pipeline_on_dataproc.py new file mode 100644 index 0000000000..c05730c216 --- /dev/null +++ b/loading_pipeline/lib/tasks/dataproc/run_pipeline_on_dataproc.py @@ -0,0 +1,16 @@ +import luigi + +from loading_pipeline.lib.tasks.base.base_loading_run_params import ( + BaseLoadingRunParams, +) +from loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc import ( + BaseRunJobOnDataprocTask, +) +from loading_pipeline.lib.tasks.run_pipeline import RunPipelineTask + + +@luigi.util.inherits(BaseLoadingRunParams) +class RunPipelineOnDataprocTask(BaseRunJobOnDataprocTask): + @property + def task(self) -> luigi.Task: + return RunPipelineTask diff --git a/loading_pipeline/lib/tasks/dataproc/run_pipeline_on_dataproc_test.py b/loading_pipeline/lib/tasks/dataproc/run_pipeline_on_dataproc_test.py new file mode 100644 index 0000000000..a09289a85a --- /dev/null +++ b/loading_pipeline/lib/tasks/dataproc/run_pipeline_on_dataproc_test.py @@ -0,0 +1,184 @@ +import unittest +from types import SimpleNamespace +from unittest.mock import Mock, call, patch + +import google.api_core.exceptions +import google.cloud.dataproc_v1.types.jobs +import luigi + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.tasks.dataproc.run_pipeline_on_dataproc import ( + RunPipelineOnDataprocTask, +) +from loading_pipeline.lib.test.mock_complete_task import MockCompleteTask + + +@patch( + 'loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc.CreateDataprocClusterTask', +) +@patch( + 'loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc.dataproc.JobControllerClient', +) +class WriteSuccessFileOnDataprocTaskTest(unittest.TestCase): + @patch('loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc.logger') + def test_job_already_exists_failed( + self, + mock_logger: Mock, + mock_job_controller_client: Mock, + mock_create_dataproc_cluster: Mock, + ) -> None: + mock_create_dataproc_cluster.return_value = MockCompleteTask() + mock_client = mock_job_controller_client.return_value + mock_client.get_job.return_value = SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.jobs.JobStatus.State.ERROR, + details='Google Cloud Dataproc Agent reports job failure. If logs are available, they can be found at...', + ), + ) + mock_client.submit_job_as_operation.side_effect = ( + google.api_core.exceptions.AlreadyExists('job exists') + ) + worker = luigi.worker.Worker() + task = RunPipelineOnDataprocTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path='test_callset', + project_guids=['R0113_test_project'], + run_id='manual__2024-04-03', + attempt_id=0, + ) + worker.add(task) + worker.run() + self.assertFalse(task.complete()) + mock_logger.error.assert_has_calls( + [ + call( + 'Job RunPipelineTask-38-SNV-INDEL-manual__2024-04-03-0 entered ERROR state', + ), + ], + ) + + def test_job_already_exists_success( + self, + mock_job_controller_client: Mock, + mock_create_dataproc_cluster: Mock, + ) -> None: + mock_create_dataproc_cluster.return_value = MockCompleteTask() + mock_client = mock_job_controller_client.return_value + mock_client.get_job.return_value = SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.jobs.JobStatus.State.DONE, + ), + ) + worker = luigi.worker.Worker() + task = RunPipelineOnDataprocTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path='test_callset', + project_guids=['R0113_test_project'], + run_id='manual__2024-04-04', + attempt_id=0, + ) + worker.add(task) + worker.run() + self.assertTrue(task.complete()) + + @patch('loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc.logger') + def test_job_failed( + self, + mock_logger: Mock, + mock_job_controller_client: Mock, + mock_create_dataproc_cluster: Mock, + ) -> None: + mock_create_dataproc_cluster.return_value = MockCompleteTask() + mock_client = mock_job_controller_client.return_value + mock_client.get_job.side_effect = [ + google.api_core.exceptions.NotFound( + 'job not found', + ), + google.api_core.exceptions.NotFound( + 'job not found', + ), + SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.jobs.JobStatus.State.PENDING, + ), + ), + SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.jobs.JobStatus.State.ERROR, + ), + ), + ] + worker = luigi.worker.Worker() + task = RunPipelineOnDataprocTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path='test_callset', + project_guids=['R0113_test_project'], + run_id='manual__2024-04-05', + attempt_id=1, + ) + worker.add(task) + luigi_task_result = worker.run() + self.assertEqual(luigi_task_result, False) + mock_logger.info.assert_has_calls( + [ + call( + 'Waiting for Job completion RunPipelineTask-38-SNV-INDEL-manual__2024-04-05-1', + ), + ], + ) + + @patch('loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc.logger') + def test_job_success( + self, + mock_logger: Mock, + mock_job_controller_client: Mock, + mock_create_dataproc_cluster: Mock, + ) -> None: + mock_create_dataproc_cluster.return_value = MockCompleteTask() + mock_client = mock_job_controller_client.return_value + mock_client.get_job.side_effect = [ + google.api_core.exceptions.NotFound( + 'job not found', + ), + google.api_core.exceptions.NotFound( + 'job not found', + ), + SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.jobs.JobStatus.State.PENDING, + ), + ), + SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.jobs.JobStatus.State.DONE, + ), + ), + ] + worker = luigi.worker.Worker() + task = RunPipelineOnDataprocTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path='test_callset', + project_guids=['R0113_test_project'], + run_id='manual__2024-04-06', + attempt_id=0, + ) + worker.add(task) + worker.run() + mock_logger.info.assert_has_calls( + [ + call( + 'Waiting for Job completion RunPipelineTask-38-SNV-INDEL-manual__2024-04-06-0', + ), + call( + 'Job RunPipelineTask-38-SNV-INDEL-manual__2024-04-06-0 is complete', + ), + ], + ) diff --git a/loading_pipeline/lib/tasks/exports/__init__.py b/loading_pipeline/lib/tasks/exports/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/loading_pipeline/lib/tasks/exports/fields.py b/loading_pipeline/lib/tasks/exports/fields.py new file mode 100644 index 0000000000..97aa6963c4 --- /dev/null +++ b/loading_pipeline/lib/tasks/exports/fields.py @@ -0,0 +1,316 @@ +import hail as hl + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.tasks.exports.misc import reformat_transcripts_for_export + +FIVE_PERCENT = 0.05 +STANDARD_CONTIGS = hl.set( + [c.replace('MT', 'M') for c in ReferenceGenome.GRCh37.standard_contigs], +) + + +def reference_independent_contig(locus: hl.LocusExpression): + contig = locus.contig.replace('^chr', '').replace('MT', 'M') + return hl.or_missing( + # lifted over alternate contigs may be present + # even though the primary contig is filtered to + # standard contigs earlier in the pipeline + STANDARD_CONTIGS.contains(contig), + contig, + ) + + +def get_dataset_type_specific_variants_annotations( + ht: hl.Table, + dataset_type: DatasetType, +): + return { + DatasetType.MITO: lambda ht: { + 'commonLowHeteroplasmy': ht.common_low_heteroplasmy, + 'haplogroupDefining': ht.haplogroup.is_defining, + 'mitotip': ht.mitotip.trna_prediction, + }, + DatasetType.SV: lambda ht: { + 'algorithms': ht.algorithms, + 'bothsidesSupport': ht.bothsides_support, + 'cpxIntervals': ht.cpxIntervals.map( + lambda cpx_i: hl.Struct( + chrom=reference_independent_contig(cpx_i.start), + start=cpx_i.start.position, + end=cpx_i.end.position, + type=cpx_i.type, + ), + ), + 'endChrom': hl.or_missing( + ( + (ht.sv_type != 'INS') + & (ht.start_locus.contig != ht.end_locus.contig) + ), + reference_independent_contig(ht.end_locus), + ), + 'svSourceDetail': hl.or_missing( + ( + (ht.sv_type == 'INS') + & (ht.start_locus.contig != ht.end_locus.contig) + ), + hl.Struct(chrom=reference_independent_contig(ht.end_locus)), + ), + 'svType': ht.sv_type, + 'svTypeDetail': ht.sv_type_detail, + 'predictions': hl.Struct( + strvctvre=ht.strvctvre.score, + ), + 'populations': hl.Struct( + gnomad_svs=hl.Struct( + af=ht.gnomad_svs.AF, + het=ht.gnomad_svs.N_HET, + hom=ht.gnomad_svs.N_HOM, + id=ht.gnomad_svs.ID, + ), + ), + }, + DatasetType.GCNV: lambda ht: { + 'numExon': ht.num_exon, + 'svType': ht.sv_type, + 'predictions': hl.Struct( + strvctvre=ht.strvctvre.score, + ), + 'populations': hl.Struct( + sv_callset=hl.Struct( + ac=ht.gt_stats.AC, + af=ht.gt_stats.AF, + an=ht.gt_stats.AN, + het=ht.gt_stats.Het, + hom=ht.gt_stats.Hom, + ), + ), + }, + }[dataset_type](ht) + + +def get_calls_export_fields( + ht: hl.Table, + fe: hl.Struct, + dataset_type: DatasetType, +): + return { + DatasetType.SNV_INDEL: lambda fe: hl.Struct( + sampleId=fe.s, + gt=fe.GT.n_alt_alleles(), + gq=fe.GQ, + ab=fe.AB, + dp=fe.DP, + ), + DatasetType.MITO: lambda fe: hl.Struct( + sampleId=fe.s, + gt=fe.GT.n_alt_alleles(), + dp=fe.DP, + hl=fe.HL, + mitoCn=fe.mito_cn, + contamination=fe.contamination, + ), + DatasetType.SV: lambda fe: hl.Struct( + sampleId=fe.s, + gt=fe.GT.n_alt_alleles(), + cn=fe.CN, + gq=fe.GQ, + newCall=fe.concordance.new_call, + prevCall=fe.concordance.prev_call, + prevNumAlt=fe.concordance.prev_num_alt, + ), + DatasetType.GCNV: lambda fe: hl.Struct( + sampleId=fe.s, + gt=fe.GT.n_alt_alleles(), + cn=fe.CN, + qs=fe.QS, + defragged=fe.defragged, + start=hl.or_else(fe.sample_start, ht.start_locus.position), + end=hl.or_else(fe.sample_end, ht.end_locus.position), + numExon=hl.or_else(fe.sample_num_exon, ht.num_exon), + geneIds=hl.or_else( + fe.sample_gene_ids, + hl.set(ht.sorted_gene_consequences.gene_id), + ), + newCall=fe.concordance.new_call, + prevCall=fe.concordance.prev_call, + prevOverlap=fe.concordance.prev_overlap, + ), + }[dataset_type](fe) + + +def get_entries_export_fields( + ht: hl.Table, + dataset_type: DatasetType, + sample_type: SampleType, + project_guid: str, +): + return { + 'key_': ht.key_, + 'project_guid': project_guid, + 'family_guid': ht.family_entries.family_guid[0], + **( + { + 'sample_type': sample_type.value, + } + if dataset_type in {DatasetType.SNV_INDEL, DatasetType.MITO} + else {} + ), + 'xpos': ht.xpos, + **( + { + 'geneIds': hl.set(ht.sorted_gene_consequences.gene_id) + if dataset_type == DatasetType.SV + else hl.set(ht.sorted_transcript_consequences.gene_id) + if dataset_type == DatasetType.SNV_INDEL + else None, + } + if dataset_type in {DatasetType.SV, DatasetType.SNV_INDEL} + else {} + ), + 'filters': ht.filters, + 'calls': hl.sorted(ht.family_entries, key=lambda fe: fe.s).map( + lambda fe: get_calls_export_fields(ht, fe, dataset_type), + ), + 'sign': 1, + } + + +def get_variant_id_fields( + ht: hl.Table, + dataset_type: DatasetType, +): + return { + DatasetType.SNV_INDEL: lambda ht: { + 'variantId': ht.variant_id, + 'rsid': ht.rsid, + 'CAID': hl.missing(hl.tstr), + }, + DatasetType.MITO: lambda ht: { + 'variantId': ht.variant_id, + 'rsid': ht.rsid, + }, + DatasetType.SV: lambda ht: { + 'variantId': ht.variant_id, + }, + DatasetType.GCNV: lambda ht: { + 'variantId': ht.variant_id, + }, + }[dataset_type](ht) + + +def get_lifted_over_position_fields(ht: hl.Table, dataset_type: DatasetType): + if dataset_type == DatasetType.MITO: + return {'liftedOverPos': ht.rg37_locus.position} + return { + 'liftedOverChrom': ( + reference_independent_contig(ht.rg37_locus) + if hasattr(ht, 'rg37_locus') + else reference_independent_contig(ht.rg38_locus) + ), + 'liftedOverPos': ( + hl.or_missing( + hl.is_defined(reference_independent_contig(ht.rg37_locus)), + ht.rg37_locus.position, + ) + if hasattr(ht, 'rg37_locus') + else ht.rg38_locus.position + ), + } + + +def get_consequences_fields( + ht: hl.Table, + reference_genome: ReferenceGenome, + dataset_type: DatasetType, +): + return { + DatasetType.SNV_INDEL: lambda ht: { + **( + { + 'sortedMotifFeatureConsequences': ht.sortedMotifFeatureConsequences, + 'sortedRegulatoryFeatureConsequences': ht.sortedRegulatoryFeatureConsequences, + } + if reference_genome == ReferenceGenome.GRCh38 + else {} + ), + 'sortedTranscriptConsequences': ht.sortedTranscriptConsequences, + }, + DatasetType.MITO: lambda ht: { + # MITO transcripts are not exported to their own table, + # but the structure should be preserved here. + 'sortedTranscriptConsequences': hl.enumerate( + ht.sortedTranscriptConsequences, + ).starmap(reformat_transcripts_for_export), + }, + DatasetType.SV: lambda ht: { + 'sortedGeneConsequences': ht.sortedGeneConsequences, + }, + DatasetType.GCNV: lambda ht: { + 'sortedGeneConsequences': ht.sortedGeneConsequences, + }, + }[dataset_type](ht) + + +def get_variants_export_fields( + ht: hl.Table, + reference_genome: ReferenceGenome, + dataset_type: DatasetType, +): + if dataset_type in {DatasetType.SV, DatasetType.GCNV}: + rg37_contig = reference_independent_contig(ht.rg37_locus_end) + position_fields = { + 'chrom': reference_independent_contig(ht.start_locus), + 'pos': ht.start_locus.position, + 'end': ht.end_locus.position, + 'rg37LocusEnd': hl.Struct( + contig=rg37_contig, + position=hl.or_missing( + hl.is_defined(rg37_contig), + ht.rg37_locus_end.position, + ), + ), + } + return { + 'key_': ht.key_, + 'xpos': ht.xpos, + **position_fields, + **get_variant_id_fields(ht, dataset_type), + **get_lifted_over_position_fields(ht, dataset_type), + **get_dataset_type_specific_variants_annotations(ht, dataset_type), + **get_consequences_fields(ht, reference_genome, dataset_type), + } + if dataset_type == DatasetType.MITO: + return { + 'key_': ht.key_, + **get_variant_id_fields(ht, dataset_type), + **get_lifted_over_position_fields(ht, dataset_type), + **get_dataset_type_specific_variants_annotations(ht, dataset_type), + **get_consequences_fields(ht, reference_genome, dataset_type), + } + return { + 'key_': ht.key_, + **get_consequences_fields(ht, reference_genome, dataset_type), + } + + +def get_variant_details_export_fields( + ht: hl.Table, + reference_genome: ReferenceGenome, + dataset_type: DatasetType, +): + return { + 'key_': ht.key_, + **get_variant_id_fields(ht, dataset_type), + **get_lifted_over_position_fields(ht, dataset_type), + **( + { + 'sortedMotifFeatureConsequences': ht.sortedMotifFeatureConsequences, + 'sortedRegulatoryFeatureConsequences': ht.sortedRegulatoryFeatureConsequences, + } + if reference_genome == ReferenceGenome.GRCh38 + else {} + ), + 'transcripts': hl.enumerate( + ht.sortedTranscriptConsequences, + ).starmap(reformat_transcripts_for_export), + } diff --git a/loading_pipeline/lib/tasks/exports/misc.py b/loading_pipeline/lib/tasks/exports/misc.py new file mode 100644 index 0000000000..ee844d28e0 --- /dev/null +++ b/loading_pipeline/lib/tasks/exports/misc.py @@ -0,0 +1,274 @@ +from collections import OrderedDict + +import hail as hl + +from loading_pipeline.lib.annotations.enums import ( + BIOTYPES, + FIVEUTR_CONSEQUENCES, + LOF_FILTERS, + MITOTIP_PATHOGENICITIES, + MOTIF_CONSEQUENCE_TERMS, + REGULATORY_BIOTYPES, + REGULATORY_CONSEQUENCE_TERMS, + SV_CONSEQUENCE_RANKS, + SV_TYPE_DETAILS, + SV_TYPES, + TRANSCRIPT_CONSEQUENCE_TERMS, +) +from loading_pipeline.lib.core import DatasetType, ReferenceGenome +from loading_pipeline.lib.misc.nested_field import parse_nested_field + + +def snake_to_camelcase(snake_string: str): + components = snake_string.split('_') + return components[0] + ''.join(x.title() for x in components[1:]) + + +def camelcase_hl_struct(s: hl.StructExpression) -> hl.StructExpression: + return s.rename({f: snake_to_camelcase(f) for f in s}) + + +def sorted_hl_struct(s: hl.StructExpression) -> hl.StructExpression: + if not isinstance(s, hl.StructExpression): + return s + return s.select(**{k: sorted_hl_struct(s[k]) for k in sorted(s)}) + + +def array_structexpression_fields(ht: hl.Table): + return [ + field + for field in ht.row + if isinstance( + ht[field], + hl.expr.expressions.typed_expressions.ArrayStructExpression, + ) + ] + + +def reformat_transcripts_for_export(i: int, s: hl.StructExpression): + formatted_s = ( + s.annotate( + majorConsequence=s.consequenceTerms.first(), + transcriptRank=i, + ) + if hasattr(s, 'loftee') + else s.annotate( + loftee=hl.Struct( + isLofNagnag=s.isLofNagnag, + lofFilters=s.lofFilters, + ), + majorConsequence=s.consequenceTerms.first(), + transcriptRank=i, + ).drop('isLofNagnag', 'lofFilters') + ) + return sorted_hl_struct(formatted_s) + + +def export_parquet_filterable_transcripts_fields( + reference_genome: ReferenceGenome, +) -> OrderedDict[str, str]: + fields = { + k: k + for k in [ + 'canonical', + 'consequenceTerms', + 'geneId', + ] + } + if reference_genome == ReferenceGenome.GRCh38: + fields = { + **fields, + 'alphamissensePathogenicity': 'alphamissense.pathogenicity', + 'extendedIntronicSpliceRegionVariant': 'spliceregion.extended_intronic_splice_region_variant', + 'fiveutrConsequence': 'utrannotator.fiveutrConsequence', + 'isManeSelect': 'isManeSelect', + } + # Parquet export expects all fields sorted alphabetically + return OrderedDict(sorted(fields.items())) + + +def subset_consequences_fields( + ht: hl.Table, + reference_genome: ReferenceGenome, +) -> hl.Table: + if reference_genome == ReferenceGenome.GRCh38: + ht = ht.annotate( + sortedMotifFeatureConsequences=ht.sortedMotifFeatureConsequences.map( + lambda e: e.select( + 'consequenceTerms', + ), + ), + sortedRegulatoryFeatureConsequences=ht.sortedRegulatoryFeatureConsequences.map( + lambda e: e.select( + 'consequenceTerms', + ), + ), + sortedTranscriptConsequences=ht.sortedTranscriptConsequences.map( + lambda e: e.annotate(isManeSelect=hl.is_defined(e.maneSelect)), + ), + ) + return ht.annotate( + sortedTranscriptConsequences=hl.enumerate( + ht.sortedTranscriptConsequences, + ).starmap( + lambda idx, c: c.select( + **{ + new_field_name: parse_nested_field( + ht.sortedTranscriptConsequences, + existing_field_name, + )[idx] + for new_field_name, existing_field_name in export_parquet_filterable_transcripts_fields( + reference_genome, + ).items() + }, + ), + ), + ) + + +def camelcase_array_structexpression_fields( + ht: hl.Table, + reference_genome: ReferenceGenome, + dataset_type: DatasetType, +): + for field in array_structexpression_fields(ht): + ht = ht.transmute( + **{ + snake_to_camelcase(field): ht[field].map( + lambda c: camelcase_hl_struct(c), + ), + }, + ) + + # Custom handling of nested sorted_transcript_consequences fields for GRCh38/SNV_INDEL. + # Note that spliceregion (extended_intronic_splice_region_variant) prevents + # a more procedural approach here. + if ( + reference_genome == ReferenceGenome.GRCh38 + and dataset_type == DatasetType.SNV_INDEL + ): + ht = ht.annotate( + sortedTranscriptConsequences=ht.sortedTranscriptConsequences.map( + lambda s: s.annotate( + loftee=camelcase_hl_struct(s.loftee), + utrannotator=camelcase_hl_struct(s.utrannotator), + ), + ), + ) + return ht + + +def unmap_formatting_annotation_enums( + ht: hl.Table, + reference_genome: ReferenceGenome, + dataset_type: DatasetType, +) -> hl.Table: + formatting_annotation_names = { + fa.__name__ for fa in dataset_type.formatting_annotation_fns(reference_genome) + } + if 'sorted_motif_feature_consequences' in formatting_annotation_names: + ht = ht.annotate( + sorted_motif_feature_consequences=ht.sorted_motif_feature_consequences.map( + lambda c: c.annotate( + consequence_terms=c.consequence_term_ids.map( + lambda tid: hl.array(MOTIF_CONSEQUENCE_TERMS)[tid], + ), + ).drop('consequence_term_ids'), + ), + ) + ht = ht.annotate_globals( + enums=ht.enums.drop('sorted_motif_feature_consequences'), + ) + if 'sorted_regulatory_feature_consequences' in formatting_annotation_names: + ht = ht.annotate( + sorted_regulatory_feature_consequences=ht.sorted_regulatory_feature_consequences.map( + lambda c: c.annotate( + biotype=hl.array(REGULATORY_BIOTYPES)[c.biotype_id], + consequence_terms=c.consequence_term_ids.map( + lambda tid: hl.array(REGULATORY_CONSEQUENCE_TERMS)[tid], + ), + ).drop('biotype_id', 'consequence_term_ids'), + ), + ) + ht = ht.annotate_globals( + enums=ht.enums.drop('sorted_regulatory_feature_consequences'), + ) + if 'sorted_transcript_consequences' in formatting_annotation_names: + ht = ht.annotate( + sorted_transcript_consequences=ht.sorted_transcript_consequences.map( + lambda c: c.annotate( + biotype=hl.array(BIOTYPES)[c.biotype_id], + consequence_terms=c.consequence_term_ids.map( + lambda tid: hl.array(TRANSCRIPT_CONSEQUENCE_TERMS)[tid], + ), + **{ + 'loftee': c.loftee.annotate( + lof_filters=c.loftee.lof_filter_ids.map( + lambda fid: hl.array(LOF_FILTERS)[fid], + ), + ).drop('lof_filter_ids'), + 'utrannotator': c.utrannotator.annotate( + fiveutr_consequence=hl.array(FIVEUTR_CONSEQUENCES)[ + c.utrannotator.fiveutr_consequence_id + ], + ).drop('fiveutr_consequence_id'), + } + if reference_genome == ReferenceGenome.GRCh38 + and dataset_type == DatasetType.SNV_INDEL + else { + 'lof_filters': c.lof_filter_ids.map( + lambda fid: hl.array(LOF_FILTERS)[fid], + ), + }, + ).drop( + 'biotype_id', + 'consequence_term_ids', + *( + [] + if reference_genome == ReferenceGenome.GRCh38 + and dataset_type == DatasetType.SNV_INDEL + else [ + 'lof_filter_ids', + ] + ), + ), + ), + ) + ht = ht.annotate_globals(enums=ht.enums.drop('sorted_transcript_consequences')) + if 'mitotip' in formatting_annotation_names: + ht = ht.annotate( + mitotip=hl.Struct( + trna_prediction=hl.array(MITOTIP_PATHOGENICITIES)[ + ht.mitotip.trna_prediction_id + ], + ), + ) + ht = ht.annotate_globals(enums=ht.enums.drop('mitotip')) + if 'cpx_intervals' in formatting_annotation_names: + ht = ht.annotate( + cpx_intervals=ht.cpx_intervals.map( + lambda cpx_i: cpx_i.annotate( + type=hl.array(SV_TYPES)[cpx_i.type_id], + ).drop('type_id'), + ), + ) + if 'sv_type_id' in formatting_annotation_names: + ht = ht.annotate(sv_type=hl.array(SV_TYPES)[ht.sv_type_id]).drop('sv_type_id') + ht = ht.annotate_globals(enums=ht.enums.drop('sv_type')) + if 'sv_type_detail_id' in formatting_annotation_names: + ht = ht.annotate( + sv_type_detail=hl.array(SV_TYPE_DETAILS)[ht.sv_type_detail_id], + ).drop('sv_type_detail_id') + ht = ht.annotate_globals(enums=ht.enums.drop('sv_type_detail')) + if 'sorted_gene_consequences' in formatting_annotation_names: + ht = ht.annotate( + sorted_gene_consequences=ht.sorted_gene_consequences.map( + lambda c: c.annotate( + major_consequence=hl.array(SV_CONSEQUENCE_RANKS)[ + c.major_consequence_id + ], + ).drop('major_consequence_id'), + ), + ) + ht = ht.annotate_globals(enums=ht.enums.drop('sorted_gene_consequences')) + return ht diff --git a/loading_pipeline/lib/tasks/exports/misc_test.py b/loading_pipeline/lib/tasks/exports/misc_test.py new file mode 100644 index 0000000000..f0324db627 --- /dev/null +++ b/loading_pipeline/lib/tasks/exports/misc_test.py @@ -0,0 +1,484 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.core import ( + DatasetType, + ReferenceGenome, +) +from loading_pipeline.lib.tasks.exports.misc import ( + camelcase_array_structexpression_fields, + sorted_hl_struct, + unmap_formatting_annotation_enums, +) + +TEST_SNV_INDEL_ANNOTATIONS = ( + 'loading_pipeline/var/test/exports/GRCh38/SNV_INDEL/annotations.ht' +) +TEST_GRCH37_SNV_INDEL_ANNOTATIONS = ( + 'loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/annotations.ht' +) + + +class MiscTest(unittest.TestCase): + def test_unmap_formatting_annotation_enums(self) -> None: + ht = hl.read_table(TEST_SNV_INDEL_ANNOTATIONS) + ht = unmap_formatting_annotation_enums( + ht, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + ) + self.assertCountEqual( + list(ht.globals.enums.collect()[0].keys()), + [ + 'clinvar', + 'hgmd', + 'screen', + 'dbnsfp', + 'gnomad_exomes', + 'gnomad_non_coding_constraint', + 'splice_ai', + 'exac', + 'topmed', + 'gnomad_genomes', + 'eigen', + ], + ) + ht = ht.annotate( + sorted_transcript_consequences=[ht.sorted_transcript_consequences[0]], + ) + self.assertEqual( + ht.collect()[0], + hl.Struct( + key_=0, + locus=hl.Locus( + contig='chr1', + position=876499, + reference_genome='GRCh38', + ), + alleles=['A', 'G'], + clinvar=hl.Struct( + alleleId=929885, + conflictingPathogenicities=None, + goldStars=1, + submitters=['Labcorp Genetics (formerly Invitae), Labcorp'], + conditions=['not provided'], + assertion_ids=[], + pathogenicity_id=12, + ), + rg37_locus=hl.Locus( + contig=1, + position=874501, + reference_genome='GRCh37', + ), + rsid=None, + sorted_transcript_consequences=[ + hl.Struct( + amino_acids='S/L', + canonical=1, + codons='tCg/tTg', + gene_id='ENSG00000187634', + hgvsc='ENST00000616016.5:c.1049C>T', + hgvsp='ENSP00000478421.2:p.Ser350Leu', + transcript_id='ENST00000616016', + mane_select='NM_001385641.1', + mane_plus_clinical=None, + exon=hl.Struct(index=6, total=14), + intron=None, + refseq_transcript_id='NM_001385641.1', + alphamissense=hl.Struct(pathogenicity=None), + loftee=hl.Struct(is_lof_nagnag=None, lof_filters=None), + spliceregion=hl.Struct( + extended_intronic_splice_region_variant=False, + ), + utrannotator=hl.Struct( + existing_inframe_oorfs=None, + existing_outofframe_oorfs=None, + existing_uorfs=None, + fiveutr_annotation=hl.Struct( + type='OutOfFrame_oORF', + KozakContext='CGCATGC', + KozakStrength='Weak', + DistanceToCDS=41, + CapDistanceToStart=None, + DistanceToStop=None, + Evidence=None, + AltStop=None, + AltStopDistanceToCDS=None, + FrameWithCDS=None, + StartDistanceToCDS=None, + newSTOPDistanceToCDS=None, + alt_type=None, + alt_type_length=None, + ref_StartDistanceToCDS=None, + ref_type=None, + ref_type_length=None, + ), + fiveutr_consequence=None, + ), + biotype='protein_coding', + consequence_terms=['missense_variant'], + ), + ], + variant_id='1-876499-A-G', + xpos=1000876499, + gt_stats=hl.Struct(AC=47, AN=81784, AF=0.0005746845272369683, hom=1), + CAID='CA502654', + check_ref=False, + sorted_regulatory_feature_consequences=[ + hl.Struct( + regulatory_feature_id='ENSR00000344437', + biotype='CTCF_binding_site', + consequence_terms=['regulatory_region_variant'], + ), + ], + sorted_motif_feature_consequences=[ + hl.Struct( + motif_feature_id='ENSM00493959715', + consequence_terms=['TF_binding_site_variant'], + ), + ], + gnomad_non_coding_constraint=hl.Struct(z_score=None), + hgmd=hl.Struct(accession='abcdefg', class_id=3), + gnomad_exomes=hl.Struct( + AF=0.0006690866430290043, + AN=1440770, + AC=964, + Hom=0, + AF_POPMAX_OR_GLOBAL=0.0008023773552849889, + FAF_AF=0.000633420015219599, + Hemi=0, + ), + gnomad_genomes=hl.Struct( + AF=0.0002759889466688037, + AN=152180, + AC=42, + Hom=0, + AF_POPMAX_OR_GLOBAL=0.10000000149011612, + FAF_AF=0.0002092500071739778, + Hemi=0, + ), + screen=hl.Struct(region_type_ids=[]), + dbnsfp=hl.Struct( + PrimateAI_score=0.5918066501617432, + fathmm_MKL_coding_score=0.7174800038337708, + CADD_phred=23.5, + SIFT_score=0.0010000000474974513, + REVEL_score=0.3109999895095825, + Polyphen2_HVAR_score=0.164000004529953, + VEST4_score=0.39500001072883606, + MPC_score=0.01291007362306118, + MutPred_score=None, + MutationTaster_pred_id=0, + ), + topmed=hl.Struct( + AC=41, + AF=0.00032651599030941725, + AN=125568, + Hom=0, + Het=41, + ), + exac=hl.Struct( + AF_POPMAX=0.0007150234305299819, + AF=0.00019039999460801482, + AC_Adj=20, + AC_Het=20, + AC_Hom=0, + AC_Hemi=None, + AN_Adj=47974, + ), + splice_ai=hl.Struct(delta_score=0.0, splice_consequence_id=4), + eigen=hl.Struct(Eigen_phred=2.628000020980835), + ), + ) + ht = hl.read_table(TEST_GRCH37_SNV_INDEL_ANNOTATIONS) + ht = unmap_formatting_annotation_enums( + ht, + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + ) + self.assertCountEqual( + list(ht.globals.enums.collect()[0].keys()), + [ + 'clinvar', + 'hgmd', + 'dbnsfp', + 'gnomad_exomes', + 'splice_ai', + 'exac', + 'topmed', + 'gnomad_genomes', + 'eigen', + ], + ) + ht = ht.annotate( + sorted_transcript_consequences=[ht.sorted_transcript_consequences[0]], + ) + self.assertEqual( + ht.collect()[0], + hl.Struct( + locus=hl.Locus(contig=1, position=69134, reference_genome='GRCh37'), + alleles=['A', 'G'], + clinvar=hl.Struct( + alleleId=2193183, + conflictingPathogenicities=None, + goldStars=1, + submitters=['Ambry Genetics'], + conditions=['not specified'], + assertion_ids=[], + pathogenicity_id=14, + ), + rsid=None, + sorted_transcript_consequences=[ + hl.Struct( + amino_acids='E/G', + canonical=1, + codons='gAa/gGa', + gene_id='ENSG00000186092', + hgvsc='ENST00000335137.3:c.44A>G', + hgvsp='ENSP00000334393.3:p.Glu15Gly', + transcript_id='ENST00000335137', + is_lof_nagnag=None, + biotype='protein_coding', + consequence_terms=['missense_variant'], + lof_filters=None, + ), + ], + variant_id='1-69134-A-G', + xpos=1000069134, + gt_stats=hl.Struct(AC=25, AN=1246, AF=0.020064204931259155, hom=10), + CAID='CA502008', + rg38_locus=hl.Locus( + contig='chr1', + position=69134, + reference_genome='GRCh38', + ), + hgmd=None, + gnomad_exomes=hl.Struct( + AF=0.026665963232517242, + AN=18938, + AC=505, + Hom=127, + AF_POPMAX_OR_GLOBAL=0.08191808313131332, + FAF_AF=0.02474386990070343, + Hemi=0, + ), + gnomad_genomes=hl.Struct( + AF=0.0001722949673421681, + AN=5804, + AC=1, + Hom=0, + AF_POPMAX_OR_GLOBAL=0.0005662514013238251, + FAF_AF=0.0, + Hemi=0, + ), + dbnsfp=hl.Struct( + PrimateAI_score=0.37232041358947754, + fathmm_MKL_coding_score=0.056940000504255295, + CADD_phred=15.880000114440918, + SIFT_score=0.1289999932050705, + REVEL_score=0.07500000298023224, + Polyphen2_HVAR_score=0.0010000000474974513, + VEST4_score=0.10700000077486038, + MPC_score=1.8921889066696167, + MutPred_score=0.3779999911785126, + MutationTaster_pred_id=2, + ), + topmed=hl.Struct( + AC=95, + AF=0.0007565619889646769, + AN=125568, + Hom=0, + Het=95, + ), + exac=hl.Struct( + AF_POPMAX=None, + AF=0.0016550000291317701, + AC_Adj=0, + AC_Het=0, + AC_Hom=0, + AC_Hemi=None, + AN_Adj=66, + ), + eigen=hl.Struct(Eigen_phred=1.0019999742507935), + splice_ai=hl.Struct( + delta_score=0.019999999552965164, + splice_consequence_id=2, + ), + key_=1424, + ), + ) + + def test_camelcase_array_structexpression_fields(self) -> None: + ht = hl.read_table(TEST_SNV_INDEL_ANNOTATIONS) + ht = unmap_formatting_annotation_enums( + ht, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + ) + ht = camelcase_array_structexpression_fields( + ht, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + ) + ht = ht.annotate( + sortedTranscriptConsequences=[ht.sortedTranscriptConsequences[0]], + ) + self.assertEqual( + ht.collect()[0], + hl.Struct( + key_=0, + locus=hl.Locus( + contig='chr1', + position=876499, + reference_genome='GRCh38', + ), + alleles=['A', 'G'], + clinvar=hl.Struct( + alleleId=929885, + conflictingPathogenicities=None, + goldStars=1, + submitters=['Labcorp Genetics (formerly Invitae), Labcorp'], + conditions=['not provided'], + assertion_ids=[], + pathogenicity_id=12, + ), + rg37_locus=hl.Locus( + contig=1, + position=874501, + reference_genome='GRCh37', + ), + rsid=None, + variant_id='1-876499-A-G', + xpos=1000876499, + gt_stats=hl.Struct(AC=47, AN=81784, AF=0.0005746845272369683, hom=1), + CAID='CA502654', + check_ref=False, + gnomad_non_coding_constraint=hl.Struct(z_score=None), + hgmd=hl.Struct(accession='abcdefg', class_id=3), + gnomad_exomes=hl.Struct( + AF=0.0006690866430290043, + AN=1440770, + AC=964, + Hom=0, + AF_POPMAX_OR_GLOBAL=0.0008023773552849889, + FAF_AF=0.000633420015219599, + Hemi=0, + ), + gnomad_genomes=hl.Struct( + AF=0.0002759889466688037, + AN=152180, + AC=42, + Hom=0, + AF_POPMAX_OR_GLOBAL=0.10000000149011612, + FAF_AF=0.0002092500071739778, + Hemi=0, + ), + screen=hl.Struct(region_type_ids=[]), + dbnsfp=hl.Struct( + PrimateAI_score=0.5918066501617432, + fathmm_MKL_coding_score=0.7174800038337708, + CADD_phred=23.5, + SIFT_score=0.0010000000474974513, + REVEL_score=0.3109999895095825, + Polyphen2_HVAR_score=0.164000004529953, + VEST4_score=0.39500001072883606, + MPC_score=0.01291007362306118, + MutPred_score=None, + MutationTaster_pred_id=0, + ), + topmed=hl.Struct( + AC=41, + AF=0.00032651599030941725, + AN=125568, + Hom=0, + Het=41, + ), + exac=hl.Struct( + AF_POPMAX=0.0007150234305299819, + AF=0.00019039999460801482, + AC_Adj=20, + AC_Het=20, + AC_Hom=0, + AC_Hemi=None, + AN_Adj=47974, + ), + splice_ai=hl.Struct( + delta_score=0.0, + splice_consequence_id=4, + ), + eigen=hl.Struct(Eigen_phred=2.628000020980835), + sortedTranscriptConsequences=[ + hl.Struct( + aminoAcids='S/L', + canonical=1, + codons='tCg/tTg', + geneId='ENSG00000187634', + hgvsc='ENST00000616016.5:c.1049C>T', + hgvsp='ENSP00000478421.2:p.Ser350Leu', + transcriptId='ENST00000616016', + maneSelect='NM_001385641.1', + manePlusClinical=None, + exon=hl.Struct(index=6, total=14), + intron=None, + refseqTranscriptId='NM_001385641.1', + alphamissense=hl.Struct(pathogenicity=None), + loftee=hl.Struct(isLofNagnag=None, lofFilters=None), + spliceregion=hl.Struct( + extended_intronic_splice_region_variant=False, + ), + utrannotator=hl.Struct( + existingInframeOorfs=None, + existingOutofframeOorfs=None, + existingUorfs=None, + fiveutrAnnotation=hl.Struct( + type='OutOfFrame_oORF', + KozakContext='CGCATGC', + KozakStrength='Weak', + DistanceToCDS=41, + CapDistanceToStart=None, + DistanceToStop=None, + Evidence=None, + AltStop=None, + AltStopDistanceToCDS=None, + FrameWithCDS=None, + StartDistanceToCDS=None, + newSTOPDistanceToCDS=None, + alt_type=None, + alt_type_length=None, + ref_StartDistanceToCDS=None, + ref_type=None, + ref_type_length=None, + ), + fiveutrConsequence=None, + ), + biotype='protein_coding', + consequenceTerms=['missense_variant'], + ), + ], + sortedRegulatoryFeatureConsequences=[ + hl.Struct( + regulatoryFeatureId='ENSR00000344437', + biotype='CTCF_binding_site', + consequenceTerms=['regulatory_region_variant'], + ), + ], + sortedMotifFeatureConsequences=[ + hl.Struct( + motifFeatureId='ENSM00493959715', + consequenceTerms=['TF_binding_site_variant'], + ), + ], + ), + ) + + def test_sorted_hl_struct(self) -> None: + struct = hl.Struct( + z=5, + y=hl.Struct(b=2, a=hl.Struct(d=4, c=3)), + x=hl.Struct(k=9), + ) + self.assertEqual( + sorted_hl_struct(struct), + hl.Struct(x=hl.Struct(k=9), y=hl.Struct(a=hl.Struct(c=3, d=4), b=2), z=5), + ) diff --git a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py new file mode 100644 index 0000000000..d60b9475b0 --- /dev/null +++ b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py @@ -0,0 +1,100 @@ +import hail as hl +import luigi +import luigi.util + +from loading_pipeline.lib.annotations.fields import get_fields +from loading_pipeline.lib.misc.family_entries import ( + compute_callset_family_entries_ht, + deduplicate_by_most_non_ref_calls, + deglobalize_ids, +) +from loading_pipeline.lib.paths import ( + new_entries_parquet_path, + variant_annotations_table_path, +) +from loading_pipeline.lib.tasks.base.base_loading_run_params import ( + BaseLoadingRunParams, +) +from loading_pipeline.lib.tasks.base.base_write_parquet import BaseWriteParquetTask +from loading_pipeline.lib.tasks.exports.fields import get_entries_export_fields +from loading_pipeline.lib.tasks.files import GCSorLocalTarget +from loading_pipeline.lib.tasks.update_variant_annotations_table_with_new_variants import ( + UpdateVariantAnnotationsTableWithNewVariantsTask, +) +from loading_pipeline.lib.tasks.write_remapped_and_subsetted_callset import ( + WriteRemappedAndSubsettedCallsetTask, +) + +ANNOTATIONS_TABLE_TASK = 'annotations_table_task' +REMAPPED_AND_SUBSETTED_CALLSET_TASKS = 'remapped_and_subsetted_callset_tasks' + + +@luigi.util.inherits(BaseLoadingRunParams) +class WriteNewEntriesParquetTask(BaseWriteParquetTask): + def output(self) -> luigi.Target: + return GCSorLocalTarget( + new_entries_parquet_path( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + ) + + def requires(self) -> dict[str, luigi.Task]: + return { + ANNOTATIONS_TABLE_TASK: self.clone( + UpdateVariantAnnotationsTableWithNewVariantsTask, + ), + REMAPPED_AND_SUBSETTED_CALLSET_TASKS: [ + self.clone( + WriteRemappedAndSubsettedCallsetTask, + project_i=i, + ) + for i in range(len(self.project_guids)) + ], + } + + def create_table(self) -> None: + unioned_ht = None + for project_guid, remapped_and_subsetted_callset_task in zip( + self.project_guids, + self.input()[REMAPPED_AND_SUBSETTED_CALLSET_TASKS], + strict=True, + ): + mt = hl.read_matrix_table(remapped_and_subsetted_callset_task.path) + ht = compute_callset_family_entries_ht( + self.dataset_type, + mt, + get_fields( + mt, + self.dataset_type.genotype_entry_annotation_fns, + **self.param_kwargs, + ), + ) + ht = deglobalize_ids(ht) + ht = deduplicate_by_most_non_ref_calls(ht) + annotations_ht = hl.read_table( + variant_annotations_table_path( + self.reference_genome, + self.dataset_type, + ), + ) + ht = ht.join(annotations_ht) + + # the family entries ht will contain rows + # where at least one family is defined... after explosion, + # rows where a family is not defined should be removed. + ht = ht.explode(ht.family_entries) + ht = ht.filter(hl.is_defined(ht.family_entries)) + ht = ht.key_by() + ht = ht.select_globals() + ht = ht.select( + **get_entries_export_fields( + ht, + self.dataset_type, + self.sample_type, + project_guid, + ), + ) + unioned_ht = unioned_ht.union(ht) if unioned_ht else ht + return unioned_ht diff --git a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py new file mode 100644 index 0000000000..ccb3260f5e --- /dev/null +++ b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py @@ -0,0 +1,423 @@ +import hail as hl +import luigi.worker +import pandas as pd + +from loading_pipeline.lib.core import ( + DatasetType, + ReferenceGenome, + SampleType, +) +from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS +from loading_pipeline.lib.paths import ( + new_entries_parquet_path, + variant_annotations_table_path, +) +from loading_pipeline.lib.tasks.exports.write_new_entries_parquet import ( + WriteNewEntriesParquetTask, +) +from loading_pipeline.lib.test.misc import ( + convert_ndarray_to_list, + copy_project_pedigree_to_mocked_dir, +) +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + +TEST_PEDIGREE_3_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_3_remap.tsv' +TEST_PEDIGREE_4_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_4_remap.tsv' +TEST_PEDIGREE_5 = 'loading_pipeline/var/test/pedigrees/test_pedigree_5.tsv' +TEST_MITO_EXPORT_PEDIGREE = ( + 'loading_pipeline/var/test/pedigrees/test_mito_export_pedigree.tsv' +) +TEST_SNV_INDEL_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' +TEST_MITO_CALLSET = 'loading_pipeline/var/test/callsets/mito_1.mt' +TEST_SV_VCF_2 = 'loading_pipeline/var/test/callsets/sv_2.vcf' +TEST_GCNV_BED_FILE = 'loading_pipeline/var/test/callsets/gcnv_1.tsv' +TEST_SNV_INDEL_ANNOTATIONS = ( + 'loading_pipeline/var/test/exports/GRCh38/SNV_INDEL/annotations.ht' +) +TEST_MITO_ANNOTATIONS = 'loading_pipeline/var/test/exports/GRCh38/MITO/annotations.ht' +TEST_SV_ANNOTATIONS = 'loading_pipeline/var/test/exports/GRCh38/SV/annotations.ht' +TEST_GCNV_ANNOTATIONS = 'loading_pipeline/var/test/exports/GRCh38/GCNV/annotations.ht' + +TEST_RUN_ID = 'manual__2024-04-03' + + +class WriteNewEntriesParquetTest(MockedDatarootTestCase): + def setUp(self) -> None: + super().setUp() + ht = hl.read_table( + TEST_SNV_INDEL_ANNOTATIONS, + ) + ht.write( + variant_annotations_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + ), + ) + ht = hl.read_table( + TEST_MITO_ANNOTATIONS, + ) + ht.write( + variant_annotations_table_path( + ReferenceGenome.GRCh38, + DatasetType.MITO, + ), + ) + ht = hl.read_table( + TEST_SV_ANNOTATIONS, + ) + ht.write( + variant_annotations_table_path( + ReferenceGenome.GRCh38, + DatasetType.SV, + ), + ) + ht = hl.read_table(TEST_GCNV_ANNOTATIONS) + ht.write( + variant_annotations_table_path( + ReferenceGenome.GRCh38, + DatasetType.GCNV, + ), + ) + + def test_write_new_entries_parquet(self): + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_3_REMAP, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0113_test_project', + ) + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_4_REMAP, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0114_project4', + ) + worker = luigi.worker.Worker() + task = WriteNewEntriesParquetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path=TEST_SNV_INDEL_VCF, + project_guids=['R0113_test_project', 'R0114_project4'], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + worker.add(task) + worker.run() + self.assertTrue(task.output().exists()) + self.assertTrue(task.complete()) + df = pd.read_parquet( + new_entries_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ) + export_json = convert_ndarray_to_list(df.to_dict('records')) + self.assertEqual( + export_json[:2], + [ + { + 'key': 0, + 'project_guid': 'R0113_test_project', + 'family_guid': 'abc_1', + 'sample_type': 'WGS', + 'xpos': 1000876499, + 'geneIds': ['ENSG00000187634'], + 'filters': [], + 'calls': [ + { + 'sampleId': 'HG00731_1', + 'gt': 2, + 'gq': 21, + 'ab': 1.0, + 'dp': 7, + }, + { + 'sampleId': 'HG00732_1', + 'gt': 2, + 'gq': 24, + 'ab': 1.0, + 'dp': 8, + }, + { + 'sampleId': 'HG00733_1', + 'gt': 2, + 'gq': 12, + 'ab': 1.0, + 'dp': 4, + }, + ], + 'sign': 1, + }, + { + 'key': 1, + 'project_guid': 'R0113_test_project', + 'family_guid': 'abc_1', + 'sample_type': 'WGS', + 'xpos': 1000878314, + 'geneIds': ['ENSG00000187634'], + 'filters': ['VQSRTrancheSNP99.00to99.90'], + 'calls': [ + { + 'sampleId': 'HG00731_1', + 'gt': 1, + 'gq': 30, + 'ab': 0.3333333432674408, + 'dp': 3, + }, + {'sampleId': 'HG00732_1', 'gt': 0, 'gq': 6, 'ab': 0.0, 'dp': 2}, + { + 'sampleId': 'HG00733_1', + 'gt': 1, + 'gq': 61, + 'ab': 0.6000000238418579, + 'dp': 5, + }, + ], + 'sign': 1, + }, + ], + ) + + def test_mito_write_new_entries_parquet(self): + copy_project_pedigree_to_mocked_dir( + TEST_MITO_EXPORT_PEDIGREE, + ReferenceGenome.GRCh38, + DatasetType.MITO, + SampleType.WGS, + 'R0116_test_project3', + ) + worker = luigi.worker.Worker() + task = WriteNewEntriesParquetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.MITO, + sample_type=SampleType.WGS, + callset_path=TEST_MITO_CALLSET, + project_guids=['R0116_test_project3'], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + worker.add(task) + worker.run() + self.assertTrue(task.output().exists()) + self.assertTrue(task.complete()) + df = pd.read_parquet( + new_entries_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.MITO, + TEST_RUN_ID, + ), + ) + export_json = convert_ndarray_to_list(df.to_dict('records')) + self.assertEqual( + export_json, + [ + { + 'key': 998, + 'project_guid': 'R0116_test_project3', + 'family_guid': 'family_1', + 'sample_type': 'WGS', + 'xpos': 25000000008, + 'filters': [], + 'calls': [ + { + 'sampleId': 'RGP_1270_2', + 'gt': 2, + 'dp': 4216, + 'hl': 0.999, + 'mitoCn': 224, + 'contamination': 0.0, + }, + ], + 'sign': 1, + }, + ], + ) + + def test_sv_write_new_entries_parquet(self): + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_5, + ReferenceGenome.GRCh38, + DatasetType.SV, + SampleType.WGS, + 'R0115_test_project2', + ) + worker = luigi.worker.Worker() + task = WriteNewEntriesParquetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SV, + sample_type=SampleType.WGS, + callset_path=TEST_SV_VCF_2, + project_guids=['R0115_test_project2'], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + worker.add(task) + worker.run() + self.assertTrue(task.output().exists()) + self.assertTrue(task.complete()) + df = pd.read_parquet( + new_entries_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.SV, + TEST_RUN_ID, + ), + ) + export_json = convert_ndarray_to_list(df.to_dict('records')) + self.assertEqual( + export_json, + [ + { + 'key': 727, + 'project_guid': 'R0115_test_project2', + 'family_guid': 'family_2_1', + 'xpos': 1001025886, + 'geneIds': ['ENSG00000188157'], + 'filters': ['HIGH_SR_BACKGROUND', 'UNRESOLVED'], + 'calls': [ + { + 'sampleId': 'RGP_164_1', + 'gt': 0, + 'cn': None, + 'gq': 99, + 'newCall': True, + 'prevCall': False, + 'prevNumAlt': None, + }, + { + 'sampleId': 'RGP_164_2', + 'gt': 1, + 'cn': None, + 'gq': 31, + 'newCall': True, + 'prevCall': False, + 'prevNumAlt': None, + }, + { + 'sampleId': 'RGP_164_3', + 'gt': 0, + 'cn': None, + 'gq': 99, + 'newCall': True, + 'prevCall': False, + 'prevNumAlt': None, + }, + { + 'sampleId': 'RGP_164_4', + 'gt': 0, + 'cn': None, + 'gq': 99, + 'newCall': True, + 'prevCall': False, + 'prevNumAlt': None, + }, + ], + 'sign': 1, + }, + ], + ) + + def test_gcnv_write_new_entries_parquet(self): + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_5, + ReferenceGenome.GRCh38, + DatasetType.GCNV, + SampleType.WES, + 'R0115_test_project2', + ) + worker = luigi.worker.Worker() + task = WriteNewEntriesParquetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.GCNV, + sample_type=SampleType.WES, + callset_path=TEST_GCNV_BED_FILE, + project_guids=['R0115_test_project2'], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + worker.add(task) + worker.run() + self.assertTrue(task.output().exists()) + self.assertTrue(task.complete()) + df = pd.read_parquet( + new_entries_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.GCNV, + TEST_RUN_ID, + ), + ) + export_json = convert_ndarray_to_list(df.to_dict('records')) + self.assertEqual( + export_json, + [ + { + 'key': 0, + 'project_guid': 'R0115_test_project2', + 'family_guid': 'family_2_1', + 'xpos': 1000939203, + 'filters': [], + 'calls': [ + { + 'sampleId': 'RGP_164_1', + 'gt': 1, + 'cn': 1, + 'qs': 4, + 'defragged': False, + 'start': 100006937, + 'end': 100007881, + 'numExon': 2, + 'geneIds': ['ENSG00000117620', 'ENSG00000283761'], + 'newCall': False, + 'prevCall': True, + 'prevOverlap': False, + }, + { + 'sampleId': 'RGP_164_2', + 'gt': 1, + 'cn': 1, + 'qs': 5, + 'defragged': False, + 'start': 100017585, + 'end': 100023213, + 'numExon': 1, + 'geneIds': ['ENSG00000117620', 'ENSG00000283761'], + 'newCall': False, + 'prevCall': False, + 'prevOverlap': False, + }, + { + 'sampleId': 'RGP_164_3', + 'gt': 2, + 'cn': 0, + 'qs': 30, + 'defragged': False, + 'start': 100017585, + 'end': 100023213, + 'numExon': 1, + 'geneIds': ['ENSG00000117620', 'ENSG00000283761'], + 'newCall': False, + 'prevCall': True, + 'prevOverlap': False, + }, + { + 'sampleId': 'RGP_164_4', + 'gt': 2, + 'cn': 0, + 'qs': 30, + 'defragged': False, + 'start': 100017586, + 'end': 100023212, + 'numExon': 2, + 'geneIds': ['ENSG00000283761', 'ENSG22222222222'], + 'newCall': False, + 'prevCall': True, + 'prevOverlap': False, + }, + ], + 'sign': 1, + }, + ], + ) diff --git a/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet.py b/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet.py new file mode 100644 index 0000000000..6da793ec53 --- /dev/null +++ b/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet.py @@ -0,0 +1,71 @@ +import hail as hl +import luigi +import luigi.util + +from loading_pipeline.lib.paths import ( + new_variant_details_parquet_path, + new_variants_table_path, +) +from loading_pipeline.lib.tasks.base.base_loading_run_params import ( + BaseLoadingRunParams, +) +from loading_pipeline.lib.tasks.base.base_write_parquet import BaseWriteParquetTask +from loading_pipeline.lib.tasks.exports.fields import get_variant_details_export_fields +from loading_pipeline.lib.tasks.exports.misc import ( + camelcase_array_structexpression_fields, + unmap_formatting_annotation_enums, +) +from loading_pipeline.lib.tasks.files import GCSorLocalFolderTarget, GCSorLocalTarget +from loading_pipeline.lib.tasks.update_variant_annotations_table_with_new_variants import ( + UpdateVariantAnnotationsTableWithNewVariantsTask, +) +from loading_pipeline.lib.tasks.write_new_variants_table import ( + WriteNewVariantsTableTask, +) + + +@luigi.util.inherits(BaseLoadingRunParams) +class WriteNewVariantDetailsParquetTask(BaseWriteParquetTask): + def output(self) -> luigi.Target: + return GCSorLocalTarget( + new_variant_details_parquet_path( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + ) + + def complete(self) -> luigi.Target: + return GCSorLocalFolderTarget(self.output().path).exists() + + def requires(self) -> luigi.Task: + if self.dataset_type.export_all_callset_variants: + return self.clone(UpdateVariantAnnotationsTableWithNewVariantsTask) + return self.clone(WriteNewVariantsTableTask) + + def create_table(self) -> None: + ht = hl.read_table( + new_variants_table_path( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + ) + ht = unmap_formatting_annotation_enums( + ht, + self.reference_genome, + self.dataset_type, + ) + ht = camelcase_array_structexpression_fields( + ht, + self.reference_genome, + self.dataset_type, + ) + ht = ht.key_by() + return ht.select( + **get_variant_details_export_fields( + ht, + self.reference_genome, + self.dataset_type, + ), + ) diff --git a/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py new file mode 100644 index 0000000000..5458854f56 --- /dev/null +++ b/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py @@ -0,0 +1,270 @@ +import os +from unittest import mock + +import hail as hl +import luigi.worker +import pandas as pd + +from loading_pipeline.lib.core import ( + DatasetType, + ReferenceGenome, + SampleType, +) +from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS +from loading_pipeline.lib.paths import ( + new_variant_details_parquet_path, + new_variants_table_path, +) +from loading_pipeline.lib.tasks.exports.write_new_variant_details_parquet import ( + WriteNewVariantDetailsParquetTask, +) +from loading_pipeline.lib.test.misc import convert_ndarray_to_list +from loading_pipeline.lib.test.mock_complete_task import MockCompleteTask +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + +TEST_SNV_INDEL_ANNOTATIONS = ( + 'loading_pipeline/var/test/exports/GRCh38/SNV_INDEL/annotations.ht' +) +TEST_GRCH37_SNV_INDEL_ANNOTATIONS = ( + 'loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/annotations.ht' +) + +TEST_RUN_ID = 'manual__2024-04-03' + + +class WriteNewVariantDetailsParquetTest(MockedDatarootTestCase): + def setUp(self) -> None: + super().setUp() + ht = hl.read_table( + TEST_SNV_INDEL_ANNOTATIONS, + ) + ht.write( + new_variants_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ) + ht = hl.read_table( + TEST_GRCH37_SNV_INDEL_ANNOTATIONS, + ) + ht.write( + new_variants_table_path( + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ) + + # Make an incomplete parquet to validate overwrite-ing. + os.makedirs( + new_variant_details_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + exist_ok=True, + ) + with open( + os.path.join( + new_variant_details_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + 'incomplete_file.parquet', + ), + 'w', + ) as f: + f.write('') + + @mock.patch( + 'loading_pipeline.lib.tasks.exports.write_new_variant_details_parquet.WriteNewVariantsTableTask', + ) + def test_write_new_variant_details_parquet_test( + self, + mock_write_new_variants_task, + ) -> None: + mock_write_new_variants_task.return_value = MockCompleteTask() + worker = luigi.worker.Worker() + task = WriteNewVariantDetailsParquetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path='fake_callset', + project_guids=[ + 'fake_project', + ], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + worker.add(task) + worker.run() + self.assertTrue(task.output().exists()) + self.assertTrue(task.complete()) + df = pd.read_parquet( + new_variant_details_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ) + export_json = convert_ndarray_to_list(df.head(1).to_dict('records')) + self.assertListEqual( + list(export_json[0].keys()), + [ + 'key', + 'variantId', + 'rsid', + 'CAID', + 'liftedOverChrom', + 'liftedOverPos', + 'sortedMotifFeatureConsequences', + 'sortedRegulatoryFeatureConsequences', + 'transcripts', + ], + ) + self.assertEqual( + export_json[0]['key'], + 0, + ) + self.assertEqual( + export_json[0]['transcripts'][0], + { + 'alphamissense': {'pathogenicity': None}, + 'aminoAcids': 'S/L', + 'biotype': 'protein_coding', + 'canonical': 1, + 'codons': 'tCg/tTg', + 'consequenceTerms': ['missense_variant'], + 'exon': {'index': 6, 'total': 14}, + 'geneId': 'ENSG00000187634', + 'hgvsc': 'ENST00000616016.5:c.1049C>T', + 'hgvsp': 'ENSP00000478421.2:p.Ser350Leu', + 'intron': None, + 'transcriptId': 'ENST00000616016', + 'transcriptRank': 0, + 'majorConsequence': 'missense_variant', + 'maneSelect': 'NM_001385641.1', + 'manePlusClinical': None, + 'refseqTranscriptId': 'NM_001385641.1', + 'loftee': {'isLofNagnag': None, 'lofFilters': None}, + 'spliceregion': { + 'extended_intronic_splice_region_variant': False, + }, + 'utrannotator': { + 'existingInframeOorfs': None, + 'existingOutofframeOorfs': None, + 'existingUorfs': None, + 'fiveutrAnnotation': { + 'AltStop': None, + 'AltStopDistanceToCDS': None, + 'CapDistanceToStart': None, + 'DistanceToCDS': 41, + 'DistanceToStop': None, + 'Evidence': None, + 'FrameWithCDS': None, + 'KozakContext': 'CGCATGC', + 'KozakStrength': 'Weak', + 'StartDistanceToCDS': None, + 'alt_type': None, + 'alt_type_length': None, + 'newSTOPDistanceToCDS': None, + 'ref_StartDistanceToCDS': None, + 'ref_type': None, + 'ref_type_length': None, + 'type': 'OutOfFrame_oORF', + }, + 'fiveutrConsequence': None, + }, + }, + ) + self.assertEqual( + list(export_json[0]['transcripts'][0].keys()), + sorted(export_json[0]['transcripts'][0].keys()), + ) + self.assertEqual( + list( + export_json[0]['transcripts'][0]['utrannotator'][ + 'fiveutrAnnotation' + ].keys(), + ), + sorted( + export_json[0]['transcripts'][0]['utrannotator'][ + 'fiveutrAnnotation' + ].keys(), + ), + ) + + @mock.patch( + 'loading_pipeline.lib.tasks.exports.write_new_variant_details_parquet.WriteNewVariantsTableTask', + ) + def test_grch37_write_new_variant_details_parquet_test( + self, + mock_write_new_variants_task, + ) -> None: + mock_write_new_variants_task.return_value = MockCompleteTask() + worker = luigi.worker.Worker() + task = WriteNewVariantDetailsParquetTask( + reference_genome=ReferenceGenome.GRCh37, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path='fake_callset', + project_guids=[ + 'fake_project', + ], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + worker.add(task) + worker.run() + self.assertTrue(task.output().exists()) + self.assertTrue(task.complete()) + df = pd.read_parquet( + os.path.join( + new_variant_details_parquet_path( + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ), + ) + export_json = convert_ndarray_to_list(df.head(1).to_dict('records')) + self.assertListEqual( + list(export_json[0].keys()), + [ + 'key', + 'variantId', + 'rsid', + 'CAID', + 'liftedOverChrom', + 'liftedOverPos', + 'transcripts', + ], + ) + self.assertEqual( + export_json[0]['key'], + 1424, + ) + self.assertEqual(export_json[0]['CAID'], None) + self.assertEqual( + export_json[0]['transcripts'][0], + { + 'aminoAcids': 'E/G', + 'biotype': 'protein_coding', + 'canonical': 1, + 'codons': 'gAa/gGa', + 'consequenceTerms': ['missense_variant'], + 'geneId': 'ENSG00000186092', + 'hgvsc': 'ENST00000335137.3:c.44A>G', + 'hgvsp': 'ENSP00000334393.3:p.Glu15Gly', + 'loftee': {'isLofNagnag': None, 'lofFilters': None}, + 'majorConsequence': 'missense_variant', + 'transcriptId': 'ENST00000335137', + 'transcriptRank': 0, + }, + ) + self.assertEqual( + list(export_json[0]['transcripts'][0].keys()), + sorted(export_json[0]['transcripts'][0].keys()), + ) diff --git a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet.py b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet.py new file mode 100644 index 0000000000..7064685415 --- /dev/null +++ b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet.py @@ -0,0 +1,99 @@ +import hail as hl +import luigi +import luigi.util + +from loading_pipeline.lib.misc.callsets import get_callset_ht +from loading_pipeline.lib.paths import ( + new_variants_parquet_path, + new_variants_table_path, + variant_annotations_table_path, +) +from loading_pipeline.lib.tasks.base.base_loading_run_params import ( + BaseLoadingRunParams, +) +from loading_pipeline.lib.tasks.base.base_write_parquet import BaseWriteParquetTask +from loading_pipeline.lib.tasks.exports.fields import get_variants_export_fields +from loading_pipeline.lib.tasks.exports.misc import ( + camelcase_array_structexpression_fields, + subset_consequences_fields, + unmap_formatting_annotation_enums, +) +from loading_pipeline.lib.tasks.files import GCSorLocalTarget +from loading_pipeline.lib.tasks.update_variant_annotations_table_with_new_variants import ( + UpdateVariantAnnotationsTableWithNewVariantsTask, +) +from loading_pipeline.lib.tasks.write_new_variants_table import ( + WriteNewVariantsTableTask, +) + + +@luigi.util.inherits(BaseLoadingRunParams) +class WriteNewVariantsParquetTask(BaseWriteParquetTask): + def output(self) -> luigi.Target: + return GCSorLocalTarget( + new_variants_parquet_path( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + ) + + def requires(self) -> luigi.Task: + if ( + self.dataset_type.export_all_callset_variants + # Special logic for the Clickhouse migration, forcing + # utilization of the project subsetted variants table + # that lives at the new variants table path. + and len(self.project_guids) > 0 + ): + return self.clone(UpdateVariantAnnotationsTableWithNewVariantsTask) + return self.clone(WriteNewVariantsTableTask) + + def create_table(self) -> None: + if ( + self.dataset_type.export_all_callset_variants + # Special logic for the Clickhouse migration, forcing + # utilization of the project subsetted variants table + # that lives at the new variants table path. + and len(self.project_guids) > 0 + ): + ht = hl.read_table( + variant_annotations_table_path( + self.reference_genome, + self.dataset_type, + ), + ) + callset_ht = get_callset_ht( + self.reference_genome, + self.dataset_type, + self.callset_path, + self.project_guids, + ) + ht = ht.semi_join(callset_ht) + else: + ht = hl.read_table( + new_variants_table_path( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + ) + ht = unmap_formatting_annotation_enums( + ht, + self.reference_genome, + self.dataset_type, + ) + ht = camelcase_array_structexpression_fields( + ht, + self.reference_genome, + self.dataset_type, + ) + if self.dataset_type.should_write_new_variant_details: + ht = subset_consequences_fields( + ht, + self.reference_genome, + ) + ht = ht.key_by() + return ht.select( + **get_variants_export_fields(ht, self.reference_genome, self.dataset_type), + ) diff --git a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py new file mode 100644 index 0000000000..8bd43fc8be --- /dev/null +++ b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py @@ -0,0 +1,420 @@ +from unittest import mock +from unittest.mock import Mock + +import hail as hl +import luigi.worker +import pandas as pd + +from loading_pipeline.lib.core import ( + DatasetType, + ReferenceGenome, + SampleType, +) +from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS +from loading_pipeline.lib.paths import ( + new_variants_parquet_path, + new_variants_table_path, + remapped_and_subsetted_callset_path, + variant_annotations_table_path, +) +from loading_pipeline.lib.tasks.exports.write_new_variants_parquet import ( + WriteNewVariantsParquetTask, +) +from loading_pipeline.lib.test.misc import convert_ndarray_to_list +from loading_pipeline.lib.test.mock_complete_task import MockCompleteTask +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + +TEST_SNV_INDEL_ANNOTATIONS = ( + 'loading_pipeline/var/test/exports/GRCh38/SNV_INDEL/annotations.ht' +) +TEST_GRCH37_SNV_INDEL_ANNOTATIONS = ( + 'loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/annotations.ht' +) +TEST_MITO_ANNOTATIONS = 'loading_pipeline/var/test/exports/GRCh38/MITO/annotations.ht' +TEST_SV_ANNOTATIONS = 'loading_pipeline/var/test/exports/GRCh38/SV/annotations.ht' +TEST_GCNV_ANNOTATIONS = 'loading_pipeline/var/test/exports/GRCh38/GCNV/annotations.ht' + +TEST_RUN_ID = 'manual__2024-04-03' + + +class WriteNewVariantsParquetTest(MockedDatarootTestCase): + def setUp(self) -> None: + super().setUp() + ht = hl.read_table( + TEST_SNV_INDEL_ANNOTATIONS, + ) + ht.write( + new_variants_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ) + ht = hl.read_table( + TEST_GRCH37_SNV_INDEL_ANNOTATIONS, + ) + ht.write( + new_variants_table_path( + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ) + ht = hl.read_table( + TEST_MITO_ANNOTATIONS, + ) + ht.write( + new_variants_table_path( + ReferenceGenome.GRCh38, + DatasetType.MITO, + TEST_RUN_ID, + ), + ) + ht = hl.read_table( + TEST_SV_ANNOTATIONS, + ) + ht.write( + new_variants_table_path( + ReferenceGenome.GRCh38, + DatasetType.SV, + TEST_RUN_ID, + ), + ) + ht = hl.read_table(TEST_GCNV_ANNOTATIONS) + ht.write( + variant_annotations_table_path( + ReferenceGenome.GRCh38, + DatasetType.GCNV, + ), + ) + ht.write( + remapped_and_subsetted_callset_path( + ReferenceGenome.GRCh38, + DatasetType.GCNV, + 'fake_callset', + 'fake_project', + ), + ) + + @mock.patch( + 'loading_pipeline.lib.tasks.exports.write_new_variants_parquet.WriteNewVariantsTableTask', + ) + def test_write_new_variants_parquet_test( + self, + mock_write_new_variants_task, + ) -> None: + mock_write_new_variants_task.return_value = MockCompleteTask() + worker = luigi.worker.Worker() + task = WriteNewVariantsParquetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path='fake_callset', + project_guids=[ + 'fake_project', + ], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + worker.add(task) + worker.run() + self.assertTrue(task.output().exists()) + self.assertTrue(task.complete()) + df = pd.read_parquet( + new_variants_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ) + export_json = convert_ndarray_to_list(df.head(1).to_dict('records')) + export_json[0]['sortedTranscriptConsequences'] = [ + export_json[0]['sortedTranscriptConsequences'][0], + ] + self.assertEqual( + export_json, + [ + { + 'key': 0, + 'sortedMotifFeatureConsequences': [ + { + 'consequenceTerms': ['TF_binding_site_variant'], + }, + ], + 'sortedRegulatoryFeatureConsequences': [ + { + 'consequenceTerms': ['regulatory_region_variant'], + }, + ], + 'sortedTranscriptConsequences': [ + { + 'alphamissensePathogenicity': None, + 'canonical': 1, + 'consequenceTerms': ['missense_variant'], + 'extendedIntronicSpliceRegionVariant': False, + 'fiveutrConsequence': None, + 'geneId': 'ENSG00000187634', + 'isManeSelect': True, + }, + ], + }, + ], + ) + + @mock.patch( + 'loading_pipeline.lib.tasks.exports.write_new_variants_parquet.WriteNewVariantsTableTask', + ) + def test_grch37_write_new_variants_parquet_test( + self, + mock_write_new_variants_task, + ) -> None: + mock_write_new_variants_task.return_value = MockCompleteTask() + worker = luigi.worker.Worker() + task = WriteNewVariantsParquetTask( + reference_genome=ReferenceGenome.GRCh37, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path='fake_callset', + project_guids=[ + 'fake_project', + ], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + worker.add(task) + worker.run() + self.assertTrue(task.output().exists()) + self.assertTrue(task.complete()) + df = pd.read_parquet( + new_variants_parquet_path( + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ) + export_json = convert_ndarray_to_list(df.head(1).to_dict('records')) + export_json[0]['sortedTranscriptConsequences'] = [ + export_json[0]['sortedTranscriptConsequences'][0], + ] + self.assertEqual( + export_json, + [ + { + 'key': 1424, + 'sortedTranscriptConsequences': [ + { + 'canonical': 1, + 'consequenceTerms': ['missense_variant'], + 'geneId': 'ENSG00000186092', + }, + ], + }, + ], + ) + + @mock.patch( + 'loading_pipeline.lib.tasks.exports.write_new_variants_parquet.WriteNewVariantsTableTask', + ) + def test_mito_write_new_variants_parquet_test( + self, + write_new_variants_table_task: Mock, + ) -> None: + write_new_variants_table_task.return_value = MockCompleteTask() + worker = luigi.worker.Worker() + task = WriteNewVariantsParquetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.MITO, + sample_type=SampleType.WGS, + callset_path='fake_callset', + project_guids=[ + 'fake_project', + ], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + worker.add(task) + worker.run() + self.assertTrue(task.output().exists()) + self.assertTrue(task.complete()) + df = pd.read_parquet( + new_variants_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.MITO, + TEST_RUN_ID, + ), + ) + export_json = convert_ndarray_to_list(df.head(1).to_dict('records')) + export_json[0]['sortedTranscriptConsequences'] = [ + export_json[0]['sortedTranscriptConsequences'][0], + ] + self.assertEqual( + export_json, + [ + { + 'key': 998, + 'variantId': 'M-8-G-T', + 'rsid': 'rs1603218446', + 'liftedOverPos': 578, + 'commonLowHeteroplasmy': True, + 'haplogroupDefining': False, + 'mitotip': 'likely_pathogenic', + 'sortedTranscriptConsequences': [ + { + 'aminoAcids': None, + 'biotype': 'Mt_tRNA', + 'canonical': 1, + 'codons': None, + 'consequenceTerms': ['non_coding_transcript_exon_variant'], + 'geneId': 'ENSG00000210049', + 'hgvsc': 'ENST00000387314.1:n.2T>C', + 'hgvsp': None, + 'loftee': {'isLofNagnag': None, 'lofFilters': None}, + 'majorConsequence': 'non_coding_transcript_exon_variant', + 'transcriptId': 'ENST00000387314', + 'transcriptRank': 0, + }, + ], + }, + ], + ) + + @mock.patch( + 'loading_pipeline.lib.tasks.exports.write_new_variants_parquet.WriteNewVariantsTableTask', + ) + def test_sv_write_new_variants_parquet_test( + self, + write_new_variants_table_task: Mock, + ) -> None: + write_new_variants_table_task.return_value = MockCompleteTask() + worker = luigi.worker.Worker() + task = WriteNewVariantsParquetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SV, + sample_type=SampleType.WGS, + callset_path='fake_callset', + project_guids=[ + 'fake_project', + ], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + worker.add(task) + worker.run() + self.assertTrue(task.output().exists()) + self.assertTrue(task.complete()) + df = pd.read_parquet( + new_variants_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.SV, + TEST_RUN_ID, + ), + ) + export_json = convert_ndarray_to_list(df.head(1).to_dict('records')) + export_json[0]['sortedGeneConsequences'] = [ + export_json[0]['sortedGeneConsequences'][0], + ] + self.assertEqual( + export_json, + [ + { + 'key': 727, + 'xpos': 1001025886, + 'chrom': '1', + 'pos': 1025886, + 'end': 1028192, + 'rg37LocusEnd': {'contig': '1', 'position': 963572}, + 'variantId': 'BND_chr1_6', + 'liftedOverChrom': '1', + 'liftedOverPos': 961266, + 'algorithms': 'manta', + 'bothsidesSupport': None, + 'cpxIntervals': [ + {'chrom': '1', 'start': 1025886, 'end': 1025986, 'type': 'DUP'}, + {'chrom': '1', 'start': 1025886, 'end': 1028192, 'type': 'INV'}, + ], + 'endChrom': '2', + 'svSourceDetail': None, + 'svType': 'CPX', + 'svTypeDetail': 'dupINV', + 'predictions': {'strvctvre': None}, + 'populations': {'gnomad_svs': None}, + 'sortedGeneConsequences': [ + {'geneId': 'ENSG00000188157', 'majorConsequence': 'INTRONIC'}, + ], + }, + ], + ) + + @mock.patch( + 'loading_pipeline.lib.tasks.exports.write_new_variants_parquet.UpdateVariantAnnotationsTableWithNewVariantsTask', + ) + @mock.patch( + 'loading_pipeline.lib.tasks.exports.write_new_variants_parquet.get_callset_ht', + ) + def test_gcnv_write_new_variants_parquet_test( + self, + get_callset_ht: Mock, + update_variant_annotations_task: Mock, + ) -> None: + get_callset_ht.return_value = hl.read_table( + variant_annotations_table_path( + ReferenceGenome.GRCh38, + DatasetType.GCNV, + ), + ) + update_variant_annotations_task.return_value = MockCompleteTask() + worker = luigi.worker.Worker() + task = WriteNewVariantsParquetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.GCNV, + sample_type=SampleType.WES, + callset_path='fake_callset', + project_guids=[ + 'fake_project', + ], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + worker.add(task) + worker.run() + self.assertTrue(task.output().exists()) + self.assertTrue(task.complete()) + df = pd.read_parquet( + new_variants_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.GCNV, + TEST_RUN_ID, + ), + ) + export_json = convert_ndarray_to_list(df.head(1).to_dict('records')) + self.assertEqual( + export_json, + [ + { + 'key': 0, + 'xpos': 1000939203, + 'chrom': '1', + 'pos': 939203, + 'end': 939558, + 'rg37LocusEnd': {'contig': '1', 'position': 874938}, + 'variantId': 'suffix_16456_DEL', + 'liftedOverChrom': '1', + 'liftedOverPos': 874583, + 'numExon': 1, + 'svType': 'DUP', + 'predictions': {'strvctvre': 0.4490000009536743}, + 'populations': { + 'sv_callset': { + 'ac': 1, + 'af': 4.3387713958509266e-05, + 'an': 23048, + 'het': None, + 'hom': None, + }, + }, + 'sortedGeneConsequences': [ + {'geneId': 'ENSG00000187634', 'majorConsequence': 'LOF'}, + ], + }, + ], + ) diff --git a/loading_pipeline/lib/tasks/files.py b/loading_pipeline/lib/tasks/files.py new file mode 100644 index 0000000000..7368631767 --- /dev/null +++ b/loading_pipeline/lib/tasks/files.py @@ -0,0 +1,49 @@ +import os + +import hailtop.fs as hfs +import luigi +from luigi.contrib import gcs + + +def CallsetTask(pathname: str) -> luigi.Task: # noqa: N802 + if 'vcf' in pathname: + return VCFFileTask(pathname) + if pathname.endswith('mt'): + return HailTableTask(pathname) + return RawFileTask(pathname) + + +def GCSorLocalTarget(pathname: str) -> luigi.Target: # noqa: N802 + return ( + gcs.GCSTarget(pathname) + if pathname.startswith('gs://') + else luigi.LocalTarget(pathname) + ) + + +def GCSorLocalFolderTarget(pathname: str) -> luigi.Target: # noqa: N802 + return GCSorLocalTarget(os.path.join(pathname, '_SUCCESS')) + + +class RawFileTask(luigi.Task): + pathname = luigi.Parameter() + + def output(self) -> luigi.Target: + return GCSorLocalTarget(self.pathname) + + +class VCFFileTask(RawFileTask): + def complete(self) -> bool: + # NB: hail supports reading glob bgz files. + path = self.pathname + if not path.startswith(('gs://', 's3://')): + path = os.path.abspath(path) + try: + return len(hfs.ls(path)) > 0 + except FileNotFoundError: + return False + + +class HailTableTask(RawFileTask): + def complete(self) -> bool: + return GCSorLocalFolderTarget(self.pathname).exists() diff --git a/loading_pipeline/lib/tasks/files_test.py b/loading_pipeline/lib/tasks/files_test.py new file mode 100644 index 0000000000..b2dfd937e0 --- /dev/null +++ b/loading_pipeline/lib/tasks/files_test.py @@ -0,0 +1,40 @@ +import os +import tempfile +import unittest + +from loading_pipeline.lib.tasks.files import ( + CallsetTask, + HailTableTask, + RawFileTask, + VCFFileTask, +) + + +class FilesTest(unittest.TestCase): + def test_raw_file(self) -> None: + with tempfile.NamedTemporaryFile(suffix='.txt') as f: + self.assertTrue(RawFileTask(f.name).complete()) + + def test_vcf_file(self) -> None: + with tempfile.NamedTemporaryFile(suffix='.vcf.bgz') as f: + self.assertTrue(VCFFileTask(f.name).complete()) + + def test_hail_table(self) -> None: + with tempfile.TemporaryDirectory(suffix='.ht') as d: + self.assertFalse(HailTableTask(d).complete()) + with open(os.path.join(d, '_SUCCESS'), 'w') as f: + f.write('0') + self.assertTrue(HailTableTask(d).complete()) + + def test_callset_task(self) -> None: + with tempfile.NamedTemporaryFile(suffix='.txt') as f: + self.assertTrue(CallsetTask(f.name).complete()) + + with tempfile.NamedTemporaryFile(suffix='.vcf') as f: + self.assertTrue(CallsetTask(f.name).complete()) + + with tempfile.TemporaryDirectory(suffix='.mt') as d: + self.assertFalse(CallsetTask(d).complete()) + with open(os.path.join(d, '_SUCCESS'), 'w') as f: + f.write('0') + self.assertTrue(CallsetTask(d).complete()) diff --git a/loading_pipeline/lib/tasks/reference_data/__init__.py b/loading_pipeline/lib/tasks/reference_data/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/loading_pipeline/lib/tasks/reference_data/updated_reference_dataset.py b/loading_pipeline/lib/tasks/reference_data/updated_reference_dataset.py new file mode 100644 index 0000000000..575cc1864f --- /dev/null +++ b/loading_pipeline/lib/tasks/reference_data/updated_reference_dataset.py @@ -0,0 +1,27 @@ +import luigi + +from loading_pipeline.lib.paths import valid_reference_dataset_path +from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset +from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( + BaseLoadingPipelineParams, +) +from loading_pipeline.lib.tasks.base.base_write import BaseWriteTask +from loading_pipeline.lib.tasks.files import GCSorLocalTarget + + +@luigi.util.inherits(BaseLoadingPipelineParams) +class UpdatedReferenceDatasetTask(BaseWriteTask): + reference_dataset: ReferenceDataset = luigi.EnumParameter( + enum=ReferenceDataset, + ) + + def output(self): + return GCSorLocalTarget( + valid_reference_dataset_path( + self.reference_genome, + self.reference_dataset, + ), + ) + + def create_table(self): + return self.reference_dataset.get_ht(self.reference_genome) diff --git a/loading_pipeline/lib/tasks/reference_data/updated_reference_dataset_parquet.py b/loading_pipeline/lib/tasks/reference_data/updated_reference_dataset_parquet.py new file mode 100644 index 0000000000..ed8adfce6b --- /dev/null +++ b/loading_pipeline/lib/tasks/reference_data/updated_reference_dataset_parquet.py @@ -0,0 +1,55 @@ +import luigi + +from loading_pipeline.lib.annotations.expression_helpers import get_expr_for_variant_id +from loading_pipeline.lib.core.dataset_type import DatasetType +from loading_pipeline.lib.core.definitions import ReferenceGenome +from loading_pipeline.lib.paths import reference_dataset_parquet +from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset +from loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc import ( + BaseRunJobOnDataprocTask, +) +from loading_pipeline.lib.tasks.files import GCSorLocalFolderTarget, GCSorLocalTarget + + +class UpdatedReferenceDatasetParquetTask(luigi.Task): + reference_genome = luigi.EnumParameter(enum=ReferenceGenome) + dataset_type = luigi.EnumParameter(enum=DatasetType) + reference_dataset: ReferenceDataset = luigi.EnumParameter( + enum=ReferenceDataset, + ) + run_id = luigi.Parameter() + attempt_id = luigi.IntParameter() + + def complete(self) -> luigi.Target: + return GCSorLocalFolderTarget(self.output().path).exists() + + def output(self): + return GCSorLocalTarget( + reference_dataset_parquet( + self.reference_genome, + self.reference_dataset, + ), + ) + + def run(self): + ht = self.reference_dataset.get_ht(self.reference_genome) + ht = ht.annotate( + variant_id=get_expr_for_variant_id(ht), + ) + df = ht.to_spark(flatten=False) + df.write.parquet( + self.output().path, + mode='overwrite', + ) + + +class UpdatedReferenceDatasetParquetOnDataprocTask(BaseRunJobOnDataprocTask): + reference_genome = luigi.EnumParameter(enum=ReferenceGenome) + dataset_type = luigi.EnumParameter(enum=DatasetType) + reference_dataset: ReferenceDataset = luigi.EnumParameter( + enum=ReferenceDataset, + ) + + @property + def task(self) -> luigi.Task: + return UpdatedReferenceDatasetParquetTask diff --git a/loading_pipeline/lib/tasks/run_pipeline.py b/loading_pipeline/lib/tasks/run_pipeline.py new file mode 100644 index 0000000000..e4bb2993e8 --- /dev/null +++ b/loading_pipeline/lib/tasks/run_pipeline.py @@ -0,0 +1,37 @@ +import luigi +import luigi.util + +from loading_pipeline.lib.tasks.base.base_loading_run_params import ( + BaseLoadingRunParams, +) +from loading_pipeline.lib.tasks.exports.write_new_entries_parquet import ( + WriteNewEntriesParquetTask, +) +from loading_pipeline.lib.tasks.exports.write_new_variant_details_parquet import ( + WriteNewVariantDetailsParquetTask, +) +from loading_pipeline.lib.tasks.exports.write_new_variants_parquet import ( + WriteNewVariantsParquetTask, +) +from loading_pipeline.lib.tasks.update_variant_annotations_table_with_new_variants import ( + UpdateVariantAnnotationsTableWithNewVariantsTask, +) +from loading_pipeline.lib.tasks.write_metadata_for_run import WriteMetadataForRunTask + + +@luigi.util.inherits(BaseLoadingRunParams) +class RunPipelineTask(luigi.WrapperTask): + attempt_id = luigi.IntParameter() + + def requires(self): + return [ + self.clone(WriteMetadataForRunTask), + self.clone(UpdateVariantAnnotationsTableWithNewVariantsTask), + self.clone(WriteNewEntriesParquetTask), + self.clone(WriteNewVariantsParquetTask), + *( + [self.clone(WriteNewVariantDetailsParquetTask)] + if self.dataset_type.should_write_new_variant_details + else [] + ), + ] diff --git a/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants.py b/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants.py new file mode 100644 index 0000000000..6c547ab029 --- /dev/null +++ b/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants.py @@ -0,0 +1,136 @@ +import hail as hl +import luigi +import luigi.util + +from loading_pipeline.lib.annotations.fields import get_fields +from loading_pipeline.lib.misc.callsets import get_callset_ht +from loading_pipeline.lib.misc.io import remap_pedigree_hash +from loading_pipeline.lib.paths import ( + new_variants_table_path, + project_pedigree_path, + variant_annotations_table_path, +) +from loading_pipeline.lib.tasks.base.base_loading_run_params import ( + BaseLoadingRunParams, +) +from loading_pipeline.lib.tasks.base.base_update import ( + BaseUpdateTask, +) +from loading_pipeline.lib.tasks.files import GCSorLocalTarget +from loading_pipeline.lib.tasks.write_new_variants_table import ( + WriteNewVariantsTableTask, +) + + +@luigi.util.inherits(BaseLoadingRunParams) +class UpdateVariantAnnotationsTableWithNewVariantsTask( + BaseUpdateTask, +): + def output(self) -> luigi.Target: + return GCSorLocalTarget( + variant_annotations_table_path( + self.reference_genome, + self.dataset_type, + ), + ) + + def requires(self) -> list[luigi.Task]: + return [ + *super().requires(), + self.clone(WriteNewVariantsTableTask), + ] + + def complete(self) -> bool: + return super().complete() and hl.eval( + hl.bind( + lambda updates: hl.all( + [ + updates.contains( + hl.Struct( + callset=self.callset_path, + project_guid=project_guid, + remap_pedigree_hash=remap_pedigree_hash( + project_pedigree_path( + self.reference_genome, + self.dataset_type, + self.sample_type, + project_guid, + ), + ), + ), + ) + for project_guid in self.project_guids + ], + ), + hl.read_table(self.output().path).updates, + ), + ) + + def initialize_table(self) -> hl.Table: + key_type = self.dataset_type.table_key_type(self.reference_genome) + return hl.Table.parallelize( + [], + key_type, + key=key_type.fields, + globals=hl.Struct( + enums=hl.Struct(), + updates=hl.empty_set( + hl.tstruct( + callset=hl.tstr, + project_guid=hl.tstr, + remap_pedigree_hash=hl.tint32, + ), + ), + migrations=hl.empty_array(hl.tstr), + max_key_=hl.int64(-1), + ), + ) + + def update_table(self, ht: hl.Table) -> hl.Table: + # Gracefully handle case for on-premises uses + # where key_ field is not present and migration was not run. + if not hasattr(ht, 'key_'): + ht = ht.add_index(name='key_') + ht = ht.annotate_globals(max_key_=(ht.count() - 1)) + + new_variants_ht = hl.read_table( + new_variants_table_path( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + ) + + # Union with the new variants table and annotate with the lookup table. + ht = ht.union(new_variants_ht, unify=True) + + if self.dataset_type.variant_frequency_annotation_fns: + # new_variants_ht consists of variants present in the new callset, fully annotated, + # but NOT present in the existing annotations table. + # callset_variants_ht consists of variants present in the new callset, fully annotated, + # and either present or not present in the existing annotations table. + callset_ht = get_callset_ht( + self.reference_genome, + self.dataset_type, + self.callset_path, + self.project_guids, + ) + callset_variants_ht = ht.semi_join(callset_ht) + non_callset_variants_ht = ht.anti_join(callset_ht) + callset_variants_ht = callset_variants_ht.annotate( + **get_fields( + callset_variants_ht, + self.dataset_type.variant_frequency_annotation_fns, + callset_ht=callset_ht, + **self.param_kwargs, + ), + ) + ht = non_callset_variants_ht.union(callset_variants_ht, unify=True) + + new_variants_ht_globals = new_variants_ht.index_globals() + return ht.select_globals( + enums=new_variants_ht_globals.enums, + updates=ht.updates.union(new_variants_ht_globals.updates), + migrations=ht.migrations, + max_key_=ht.aggregate(hl.agg.max(ht.key_)), + ) diff --git a/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py b/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py new file mode 100644 index 0000000000..3bfe55af65 --- /dev/null +++ b/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py @@ -0,0 +1,1349 @@ +import functools +from unittest.mock import Mock, PropertyMock, patch + +import hail as hl +import luigi.worker + +from loading_pipeline.lib.annotations.enums import ( + BIOTYPES, + FIVEUTR_CONSEQUENCES, + LOF_FILTERS, + MITOTIP_PATHOGENICITIES, + MOTIF_CONSEQUENCE_TERMS, + REGULATORY_BIOTYPES, + REGULATORY_CONSEQUENCE_TERMS, + SV_CONSEQUENCE_RANKS, + SV_TYPE_DETAILS, + SV_TYPES, + TRANSCRIPT_CONSEQUENCE_TERMS, +) +from loading_pipeline.lib.core import ( + DatasetType, + ReferenceGenome, + SampleType, +) +from loading_pipeline.lib.misc.io import remap_pedigree_hash +from loading_pipeline.lib.misc.validation import ( + ALL_VALIDATIONS, + SKIPPABLE_VALIDATIONS, + validate_expected_contig_frequency, +) +from loading_pipeline.lib.paths import ( + valid_reference_dataset_path, +) +from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset +from loading_pipeline.lib.tasks.files import GCSorLocalFolderTarget +from loading_pipeline.lib.tasks.update_variant_annotations_table_with_new_variants import ( + UpdateVariantAnnotationsTableWithNewVariantsTask, +) +from loading_pipeline.lib.test.misc import copy_project_pedigree_to_mocked_dir +from loading_pipeline.lib.test.mocked_reference_datasets_testcase import ( + MockedReferenceDatasetsTestCase, +) +from loading_pipeline.var.test.vep.mock_vep_data import ( + MOCK_37_VEP_DATA, + MOCK_38_VEP_DATA, +) + +TEST_MITO_MT = 'loading_pipeline/var/test/callsets/mito_1.mt' +TEST_SNV_INDEL_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' +TEST_SV_VCF = 'loading_pipeline/var/test/callsets/sv_1.vcf' +TEST_SV_VCF_2 = 'loading_pipeline/var/test/callsets/sv_2.vcf' +TEST_GCNV_BED_FILE = 'loading_pipeline/var/test/callsets/gcnv_1.tsv' +TEST_GCNV_BED_FILE_2 = 'loading_pipeline/var/test/callsets/gcnv_2.tsv' +TEST_PEDIGREE_3_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_3_remap.tsv' +TEST_PEDIGREE_4_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_4_remap.tsv' +TEST_PEDIGREE_5 = 'loading_pipeline/var/test/pedigrees/test_pedigree_5.tsv' +TEST_PEDIGREE_8 = 'loading_pipeline/var/test/pedigrees/test_pedigree_8.tsv' +TEST_PEDIGREE_10 = 'loading_pipeline/var/test/pedigrees/test_pedigree_10.tsv' +TEST_PEDIGREE_11 = 'loading_pipeline/var/test/pedigrees/test_pedigree_11.tsv' + +GENE_ID_MAPPING = { + 'OR4F5': 'ENSG00000186092', + 'PLEKHG4B': 'ENSG00000153404', + 'OR4F16': 'ENSG00000186192', + 'OR4F29': 'ENSG00000284733', + 'FBXO28': 'ENSG00000143756', + 'SAMD11': 'ENSG00000187634', + 'C1orf174': 'ENSG00000198912', + 'TAS1R1': 'ENSG00000173662', + 'FAM131C': 'ENSG00000185519', + 'RCC2': 'ENSG00000179051', + 'NBPF3': 'ENSG00000142794', + 'AGBL4': 'ENSG00000186094', + 'KIAA1614': 'ENSG00000135835', + 'MR1': 'ENSG00000153029', + 'STX6': 'ENSG00000135823', + 'XPR1': 'ENSG00000143324', +} + +TEST_RUN_ID = 'manual__2024-04-03' + + +class UpdateVariantAnnotationsTableWithNewVariantsTaskTest( + MockedReferenceDatasetsTestCase, +): + def test_missing_pedigree( + self, + ) -> None: + uvatwns_task = UpdateVariantAnnotationsTableWithNewVariantsTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path=TEST_SNV_INDEL_VCF, + project_guids=['R0113_test_project'], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + worker = luigi.worker.Worker() + worker.add(uvatwns_task) + worker.run() + self.assertFalse(uvatwns_task.complete()) + + @patch( + 'loading_pipeline.lib.tasks.validate_callset.SKIPPABLE_VALIDATIONS', + [ + x + for x in SKIPPABLE_VALIDATIONS + if x.__name__ != 'validate_expected_contig_frequency' + ] + + [ + functools.update_wrapper( + functools.partial( + validate_expected_contig_frequency, + min_rows_per_contig=25, + ), + validate_expected_contig_frequency, + ), + ], + ) + @patch.object(ReferenceGenome, 'standard_contigs', new_callable=PropertyMock) + @patch('loading_pipeline.lib.misc.vep.hl.vep') + @patch( + 'loading_pipeline.lib.tasks.write_new_variants_table.load_gencode_ensembl_to_refseq_id', + ) + def test_multiple_update_vat( + self, + mock_load_gencode_ensembl_to_refseq_id: Mock, + mock_vep: Mock, + mock_standard_contigs: Mock, + ) -> None: + mock_vep.side_effect = lambda ht, **_: ht.annotate(vep=MOCK_38_VEP_DATA) + mock_load_gencode_ensembl_to_refseq_id.return_value = hl.dict( + {'ENST00000327044': 'NM_015658.4'}, + ) + mock_standard_contigs.return_value = {'chr1'} + # This creates a mock validation table with 1 coding and 1 non-coding variant + # explicitly chosen from the VCF. + # NB: This is the one and only place validation is enabled in the task tests! + coding_and_noncoding_variants_ht = hl.Table.parallelize( + [ + { + 'locus': hl.Locus( + contig='chr1', + position=871269, + reference_genome='GRCh38', + ), + 'coding': False, + 'noncoding': True, + }, + { + 'locus': hl.Locus( + contig='chr1', + position=876499, + reference_genome='GRCh38', + ), + 'coding': True, + 'noncoding': False, + }, + ], + hl.tstruct( + locus=hl.tlocus('GRCh38'), + coding=hl.tbool, + noncoding=hl.tbool, + ), + key='locus', + globals=hl.Struct( + enums=hl.Struct( + gnomad_genomes=hl.Struct(), + ), + ), + ) + coding_and_noncoding_variants_ht.write( + valid_reference_dataset_path( + ReferenceGenome.GRCh38, + ReferenceDataset.gnomad_coding_and_noncoding, + ), + overwrite=True, + ) + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_3_REMAP, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0113_test_project', + ) + worker = luigi.worker.Worker() + uvatwns_task_3 = UpdateVariantAnnotationsTableWithNewVariantsTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path=TEST_SNV_INDEL_VCF, + project_guids=['R0113_test_project'], + validations_to_skip=[], + run_id=TEST_RUN_ID, + ) + worker.add(uvatwns_task_3) + worker.run() + self.assertTrue(uvatwns_task_3.complete()) + ht = hl.read_table(uvatwns_task_3.output().path) + self.assertEqual(ht.count(), 30) + self.assertEqual( + ht.globals.updates.collect(), + [ + { + hl.Struct( + callset=TEST_SNV_INDEL_VCF, + project_guid='R0113_test_project', + remap_pedigree_hash=hl.eval( + remap_pedigree_hash(TEST_PEDIGREE_3_REMAP), + ), + ), + }, + ], + ) + self.assertEqual( + hl.eval(ht.globals.max_key_), + 29, + ) + + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_4_REMAP, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0114_project4', + ) + # Ensure that new variants are added correctly to the table. + uvatwns_task_4 = UpdateVariantAnnotationsTableWithNewVariantsTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path=TEST_SNV_INDEL_VCF, + project_guids=['R0114_project4'], + validations_to_skip=[], + run_id=TEST_RUN_ID + '-another-run', + ) + worker.add(uvatwns_task_4) + worker.run() + self.assertTrue(uvatwns_task_4.complete()) + ht = hl.read_table(uvatwns_task_4.output().path) + self.assertCountEqual( + [ + x + for x in ht.select( + 'variant_id', + 'xpos', + ).collect() + if x.locus.position <= 878809 # noqa: PLR2004 + ], + [ + hl.Struct( + locus=hl.Locus( + contig='chr1', + position=871269, + reference_genome='GRCh38', + ), + alleles=['A', 'C'], + variant_id='1-871269-A-C', + xpos=1000871269, + ), + hl.Struct( + locus=hl.Locus( + contig='chr1', + position=874734, + reference_genome='GRCh38', + ), + alleles=['C', 'T'], + variant_id='1-874734-C-T', + xpos=1000874734, + ), + hl.Struct( + locus=hl.Locus( + contig='chr1', + position=876499, + reference_genome='GRCh38', + ), + alleles=['A', 'G'], + variant_id='1-876499-A-G', + xpos=1000876499, + ), + hl.Struct( + locus=hl.Locus( + contig='chr1', + position=878314, + reference_genome='GRCh38', + ), + alleles=['G', 'C'], + variant_id='1-878314-G-C', + xpos=1000878314, + ), + hl.Struct( + locus=hl.Locus( + contig='chr1', + position=878809, + reference_genome='GRCh38', + ), + alleles=['C', 'T'], + variant_id='1-878809-C-T', + xpos=1000878809, + ), + ], + ) + self.assertCountEqual( + ht.filter( + ht.locus.position <= 878809, # noqa: PLR2004 + ).sorted_transcript_consequences.consequence_term_ids.collect(), + [ + [[9], [23, 26], [23, 13, 26]], + [[9], [23, 26], [23, 13, 26]], + [[9], [23, 26], [23, 13, 26]], + [[9], [23, 26], [23, 13, 26]], + [[9], [23, 26], [23, 13, 26]], + ], + ) + self.assertCountEqual( + ht.globals.collect(), + [ + hl.Struct( + updates={ + hl.Struct( + callset='loading_pipeline/var/test/callsets/1kg_30variants.vcf', + project_guid='R0113_test_project', + remap_pedigree_hash=hl.eval( + remap_pedigree_hash( + TEST_PEDIGREE_3_REMAP, + ), + ), + ), + hl.Struct( + callset='loading_pipeline/var/test/callsets/1kg_30variants.vcf', + project_guid='R0114_project4', + remap_pedigree_hash=hl.eval( + remap_pedigree_hash( + TEST_PEDIGREE_4_REMAP, + ), + ), + ), + }, + migrations=[], + max_key_=29, + enums=hl.Struct( + sorted_motif_feature_consequences=hl.Struct( + consequence_term=MOTIF_CONSEQUENCE_TERMS, + ), + sorted_regulatory_feature_consequences=hl.Struct( + biotype=REGULATORY_BIOTYPES, + consequence_term=REGULATORY_CONSEQUENCE_TERMS, + ), + sorted_transcript_consequences=hl.Struct( + biotype=BIOTYPES, + consequence_term=TRANSCRIPT_CONSEQUENCE_TERMS, + loftee=hl.Struct( + lof_filter=LOF_FILTERS, + ), + utrannotator=hl.Struct( + fiveutr_consequence=FIVEUTR_CONSEQUENCES, + ), + ), + ), + ), + ], + ) + + @patch('loading_pipeline.lib.misc.vep.hl.vep') + def test_update_vat_grch37( + self, + mock_vep: Mock, + ) -> None: + mock_vep.side_effect = lambda ht, **_: ht.annotate(vep=MOCK_37_VEP_DATA) + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_3_REMAP, + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0113_test_project', + ) + worker = luigi.worker.Worker() + uvatwns_task = UpdateVariantAnnotationsTableWithNewVariantsTask( + reference_genome=ReferenceGenome.GRCh37, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path=TEST_SNV_INDEL_VCF, + project_guids=['R0113_test_project'], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + worker.add(uvatwns_task) + worker.run() + self.assertTrue(uvatwns_task.complete()) + ht = hl.read_table(uvatwns_task.output().path) + self.assertEqual(ht.count(), 30) + self.assertFalse(hasattr(ht, 'rg37_locus')) + self.assertEqual( + ht.collect()[0], + hl.Struct( + locus=hl.Locus( + contig=1, + position=871269, + reference_genome='GRCh37', + ), + alleles=['A', 'C'], + rsid=None, + variant_id='1-871269-A-C', + xpos=1000871269, + sorted_transcript_consequences=[ + hl.Struct( + amino_acids='S/L', + canonical=1, + codons='tCg/tTg', + gene_id='ENSG00000188976', + hgvsc='ENST00000327044.6:c.1667C>T', + hgvsp='ENSP00000317992.6:p.Ser556Leu', + transcript_id='ENST00000327044', + biotype_id=39, + consequence_term_ids=[9], + is_lof_nagnag=None, + lof_filter_ids=[0, 1], + ), + hl.Struct( + amino_acids=None, + canonical=None, + codons=None, + gene_id='ENSG00000188976', + hgvsc='ENST00000477976.1:n.3114C>T', + hgvsp=None, + transcript_id='ENST00000477976', + biotype_id=38, + consequence_term_ids=[23, 26], + is_lof_nagnag=None, + lof_filter_ids=None, + ), + hl.Struct( + amino_acids=None, + canonical=None, + codons=None, + gene_id='ENSG00000188976', + hgvsc='ENST00000483767.1:n.523C>T', + hgvsp=None, + transcript_id='ENST00000483767', + biotype_id=38, + consequence_term_ids=[23, 26], + is_lof_nagnag=None, + lof_filter_ids=None, + ), + ], + rg38_locus=hl.Locus( + contig='chr1', + position=935889, + reference_genome='GRCh38', + ), + key_=0, + ), + ) + + def test_mito_update_vat( + self, + ) -> None: + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_5, + ReferenceGenome.GRCh38, + DatasetType.MITO, + SampleType.WGS, + 'R0115_test_project2', + ) + worker = luigi.worker.Worker() + update_variant_annotations_task = ( + UpdateVariantAnnotationsTableWithNewVariantsTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.MITO, + sample_type=SampleType.WGS, + callset_path=TEST_MITO_MT, + project_guids=['R0115_test_project2'], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + ) + worker.add(update_variant_annotations_task) + worker.run() + self.assertTrue(update_variant_annotations_task.complete()) + ht = hl.read_table(update_variant_annotations_task.output().path) + self.assertEqual(ht.count(), 5) + self.assertCountEqual( + ht.globals.collect(), + [ + hl.Struct( + enums=hl.Struct( + sorted_transcript_consequences=hl.Struct( + biotype=BIOTYPES, + consequence_term=TRANSCRIPT_CONSEQUENCE_TERMS, + lof_filter=LOF_FILTERS, + ), + mitotip=hl.Struct(trna_prediction=MITOTIP_PATHOGENICITIES), + ), + migrations=[], + max_key_=4, + updates={ + hl.Struct( + callset='loading_pipeline/var/test/callsets/mito_1.mt', + project_guid='R0115_test_project2', + remap_pedigree_hash=hl.eval( + remap_pedigree_hash( + TEST_PEDIGREE_5, + ), + ), + ), + }, + ), + ], + ) + self.assertCountEqual( + ht.collect()[0], + hl.Struct( + locus=hl.Locus( + contig='chrM', + position=3, + reference_genome='GRCh38', + ), + alleles=['T', 'C'], + common_low_heteroplasmy=False, + haplogroup=hl.Struct(is_defining=False), + mitotip=hl.Struct(trna_prediction_id=None), + rg37_locus=hl.Locus( + contig='MT', + position=3, + reference_genome='GRCh37', + ), + rsid=None, + sorted_transcript_consequences=None, + variant_id='M-3-T-C', + xpos=25000000003, + key_=0, + ), + ) + + @patch( + 'loading_pipeline.lib.tasks.write_new_variants_table.load_gencode_gene_symbol_to_gene_id', + ) + def test_sv_multiple_vcf_update_vat( + self, + mock_load_gencode: Mock, + ) -> None: + mock_load_gencode.return_value = GENE_ID_MAPPING + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_5, + ReferenceGenome.GRCh38, + DatasetType.SV, + SampleType.WGS, + 'R0115_test_project2', + ) + worker = luigi.worker.Worker() + update_variant_annotations_task = ( + UpdateVariantAnnotationsTableWithNewVariantsTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SV, + sample_type=SampleType.WGS, + callset_path=TEST_SV_VCF, + project_guids=['R0115_test_project2'], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + ) + worker.add(update_variant_annotations_task) + worker.run() + self.assertTrue(update_variant_annotations_task.complete()) + self.assertFalse( + GCSorLocalFolderTarget( + f'{self.mock_env.REFERENCE_DATASETS_DIR}/v03/GRCh38/SV/lookup.ht', + ).exists(), + ) + ht = hl.read_table(update_variant_annotations_task.output().path) + self.assertEqual(ht.count(), 13) + self.assertCountEqual( + ht.globals.collect(), + [ + hl.Struct( + enums=hl.Struct( + sv_type=SV_TYPES, + sv_type_detail=SV_TYPE_DETAILS, + sorted_gene_consequences=hl.Struct( + major_consequence=SV_CONSEQUENCE_RANKS, + ), + ), + migrations=[], + max_key_=12, + updates={ + hl.Struct( + callset=TEST_SV_VCF, + project_guid='R0115_test_project2', + remap_pedigree_hash=hl.eval( + remap_pedigree_hash( + TEST_PEDIGREE_5, + ), + ), + ), + }, + ), + ], + ) + self.assertCountEqual( + ht.collect()[:8], + [ + hl.Struct( + variant_id='BND_chr1_6', + algorithms='manta', + bothsides_support=False, + cpx_intervals=None, + end_locus=hl.Locus( + contig='chr5', + position=20404, + reference_genome='GRCh38', + ), + gnomad_svs=None, + rg37_locus=hl.Locus( + contig=1, + position=10367, + reference_genome='GRCh37', + ), + rg37_locus_end=hl.Locus( + contig=5, + position=20404, + reference_genome='GRCh37', + ), + sorted_gene_consequences=[ + hl.Struct(gene_id='ENSG00000186092', major_consequence_id=12), + hl.Struct(gene_id='ENSG00000153404', major_consequence_id=12), + ], + start_locus=hl.Locus( + contig='chr1', + position=180928, + reference_genome='GRCh38', + ), + strvctvre=hl.Struct(score=None), + sv_len=-1, + sv_type_id=2, + sv_type_detail_id=None, + xpos=1000180928, + key_=0, + ), + hl.Struct( + variant_id='BND_chr1_9', + algorithms='manta', + bothsides_support=False, + cpx_intervals=None, + end_locus=hl.Locus( + contig='chr1', + position=789481, + reference_genome='GRCh38', + ), + gnomad_svs=None, + rg37_locus=hl.Locus( + contig=1, + position=724861, + reference_genome='GRCh37', + ), + rg37_locus_end=hl.Locus( + contig=1, + position=724861, + reference_genome='GRCh37', + ), + sorted_gene_consequences=[ + hl.Struct(gene_id='ENSG00000143756', major_consequence_id=12), + hl.Struct(gene_id='ENSG00000186192', major_consequence_id=12), + ], + start_locus=hl.Locus( + contig='chr1', + position=789481, + reference_genome='GRCh38', + ), + strvctvre=hl.Struct(score=None), + sv_len=223225007, + sv_type_id=2, + sv_type_detail_id=None, + xpos=1000789481, + key_=1, + ), + hl.Struct( + variant_id='CPX_chr1_22', + algorithms='manta', + bothsides_support=True, + cpx_intervals=[ + hl.Struct( + type_id=8, + start=hl.Locus('chr1', 6558902, 'GRCh38'), + end=hl.Locus('chr1', 6559723, 'GRCh38'), + ), + hl.Struct( + type_id=6, + start=hl.Locus('chr1', 6559655, 'GRCh38'), + end=hl.Locus('chr1', 6559723, 'GRCh38'), + ), + ], + end_locus=hl.Locus( + contig='chr1', + position=6559723, + reference_genome='GRCh38', + ), + gnomad_svs=None, + rg37_locus=hl.Locus( + contig=1, + position=6618962, + reference_genome='GRCh37', + ), + rg37_locus_end=hl.Locus( + contig=1, + position=6619783, + reference_genome='GRCh37', + ), + sorted_gene_consequences=[ + hl.Struct(gene_id='ENSG00000173662', major_consequence_id=11), + ], + start_locus=hl.Locus( + contig='chr1', + position=6558902, + reference_genome='GRCh38', + ), + strvctvre=hl.Struct(score=None), + sv_len=821, + sv_type_id=3, + sv_type_detail_id=2, + xpos=1006558902, + key_=2, + ), + hl.Struct( + variant_id='CPX_chr1_251', + algorithms='manta', + bothsides_support=False, + cpx_intervals=[ + hl.Struct( + type_id=5, + start=hl.Locus('chr1', 180540234, 'GRCh38'), + end=hl.Locus('chr1', 181074767, 'GRCh38'), + ), + hl.Struct( + type_id=8, + start=hl.Locus('chr1', 181074767, 'GRCh38'), + end=hl.Locus('chr1', 181074938, 'GRCh38'), + ), + ], + end_locus=hl.Locus( + contig='chr1', + position=181074952, + reference_genome='GRCh38', + ), + gnomad_svs=None, + rg37_locus=hl.Locus( + contig=1, + position=180509370, + reference_genome='GRCh37', + ), + rg37_locus_end=hl.Locus( + contig=1, + position=181044088, + reference_genome='GRCh37', + ), + sorted_gene_consequences=[ + hl.Struct(gene_id='ENSG00000135835', major_consequence_id=0), + hl.Struct(gene_id='ENSG00000153029', major_consequence_id=0), + hl.Struct(gene_id='ENSG00000135823', major_consequence_id=0), + hl.Struct(gene_id='ENSG00000143324', major_consequence_id=0), + ], + start_locus=hl.Locus( + contig='chr1', + position=180540234, + reference_genome='GRCh38', + ), + strvctvre=hl.Struct(score=None), + sv_len=534718, + sv_type_id=3, + sv_type_detail_id=9, + xpos=1180540234, + key_=3, + ), + hl.Struct( + variant_id='CPX_chr1_41', + algorithms='manta', + bothsides_support=False, + cpx_intervals=[ + hl.Struct( + type_id=6, + start=hl.Locus('chr1', 16088760, 'GRCh38'), + end=hl.Locus('chr1', 16088835, 'GRCh38'), + ), + hl.Struct( + type_id=8, + start=hl.Locus('chr1', 16088760, 'GRCh38'), + end=hl.Locus('chr1', 16089601, 'GRCh38'), + ), + ], + end_locus=hl.Locus( + contig='chr1', + position=16089601, + reference_genome='GRCh38', + ), + gnomad_svs=None, + rg37_locus=hl.Locus( + contig=1, + position=16415255, + reference_genome='GRCh37', + ), + rg37_locus_end=hl.Locus( + contig=1, + position=16416096, + reference_genome='GRCh37', + ), + sorted_gene_consequences=[ + hl.Struct(gene_id='ENSG00000185519', major_consequence_id=12), + ], + start_locus=hl.Locus( + contig='chr1', + position=16088760, + reference_genome='GRCh38', + ), + strvctvre=hl.Struct(score=None), + sv_len=841, + sv_type_id=3, + sv_type_detail_id=12, + xpos=1016088760, + key_=4, + ), + hl.Struct( + variant_id='CPX_chr1_54', + algorithms='manta', + bothsides_support=False, + cpx_intervals=[ + hl.Struct( + type_id=6, + start=hl.Locus('chr1', 21427498, 'GRCh38'), + end=hl.Locus('chr1', 21427959, 'GRCh38'), + ), + hl.Struct( + type_id=8, + start=hl.Locus('chr1', 21427498, 'GRCh38'), + end=hl.Locus('chr1', 21480073, 'GRCh38'), + ), + hl.Struct( + type_id=5, + start=hl.Locus('chr1', 21480073, 'GRCh38'), + end=hl.Locus('chr1', 21480419, 'GRCh38'), + ), + ], + end_locus=hl.Locus( + contig='chr1', + position=21480419, + reference_genome='GRCh38', + ), + gnomad_svs=None, + rg37_locus=hl.Locus( + contig=1, + position=21753991, + reference_genome='GRCh37', + ), + rg37_locus_end=hl.Locus( + contig=1, + position=21806912, + reference_genome='GRCh37', + ), + sorted_gene_consequences=[ + hl.Struct(gene_id='ENSG00000142794', major_consequence_id=0), + ], + start_locus=hl.Locus( + contig='chr1', + position=21427498, + reference_genome='GRCh38', + ), + strvctvre=hl.Struct(score=None), + sv_len=52921, + sv_type_id=3, + sv_type_detail_id=13, + xpos=1021427498, + key_=5, + ), + hl.Struct( + variant_id='CPX_chrX_251', + algorithms='manta', + bothsides_support=False, + cpx_intervals=[ + hl.Struct( + type_id=5, + start=hl.Locus( + contig='chr1', + position=180540234, + reference_genome='GRCh38', + ), + end=hl.Locus( + contig='chr1', + position=181074767, + reference_genome='GRCh38', + ), + ), + hl.Struct( + type_id=8, + start=hl.Locus( + contig='chr1', + position=181074767, + reference_genome='GRCh38', + ), + end=hl.Locus( + contig='chr1', + position=181074938, + reference_genome='GRCh38', + ), + ), + ], + end_locus=hl.Locus( + contig='chrX', + position=2781000, + reference_genome='GRCh38', + ), + gnomad_svs=None, + sorted_gene_consequences=[ + hl.Struct(gene_id='ENSG00000135835', major_consequence_id=0), + hl.Struct(gene_id='ENSG00000153029', major_consequence_id=0), + hl.Struct(gene_id='ENSG00000135823', major_consequence_id=0), + hl.Struct(gene_id='ENSG00000143324', major_consequence_id=0), + ], + start_locus=hl.Locus( + contig='chrX', + position=3, + reference_genome='GRCh38', + ), + strvctvre=hl.Struct(score=None), + sv_type_id=3, + sv_type_detail_id=9, + sv_len=534718, + xpos=23000000003, + rg37_locus=None, + rg37_locus_end=hl.Locus( + contig='X', + position=2699041, + reference_genome='GRCh37', + ), + key_=6, + ), + hl.Struct( + variant_id='CPX_chrX_252', + algorithms='manta', + bothsides_support=False, + cpx_intervals=[ + hl.Struct( + type_id=5, + start=hl.Locus( + contig='chr1', + position=180540234, + reference_genome='GRCh38', + ), + end=hl.Locus( + contig='chr1', + position=181074767, + reference_genome='GRCh38', + ), + ), + hl.Struct( + type_id=8, + start=hl.Locus( + contig='chr1', + position=181074767, + reference_genome='GRCh38', + ), + end=hl.Locus( + contig='chr1', + position=181074938, + reference_genome='GRCh38', + ), + ), + ], + end_locus=hl.Locus( + contig='chrX', + position=2781900, + reference_genome='GRCh38', + ), + gnomad_svs=None, + sorted_gene_consequences=[ + hl.Struct(gene_id='ENSG00000135835', major_consequence_id=0), + hl.Struct(gene_id='ENSG00000153029', major_consequence_id=0), + hl.Struct(gene_id='ENSG00000135823', major_consequence_id=0), + hl.Struct(gene_id='ENSG00000143324', major_consequence_id=0), + ], + start_locus=hl.Locus( + contig='chrX', + position=2781700, + reference_genome='GRCh38', + ), + strvctvre=hl.Struct(score=None), + sv_type_id=3, + sv_type_detail_id=9, + sv_len=534718, + xpos=23002781700, + rg37_locus=hl.Locus( + contig='X', + position=2699741, + reference_genome='GRCh37', + ), + rg37_locus_end=hl.Locus( + contig='X', + position=2699941, + reference_genome='GRCh37', + ), + key_=7, + ), + ], + ) + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_5, + ReferenceGenome.GRCh38, + DatasetType.SV, + SampleType.WGS, + 'R0115_test_project2', + ) + update_variant_annotations_task = ( + UpdateVariantAnnotationsTableWithNewVariantsTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SV, + sample_type=SampleType.WGS, + callset_path=TEST_SV_VCF_2, + project_guids=['R0115_test_project2'], + validations_to_skip=[ALL_VALIDATIONS], + run_id='second_run_id', + ) + ) + worker.add(update_variant_annotations_task) + worker.run() + self.assertTrue(update_variant_annotations_task.complete()) + ht = hl.read_table(update_variant_annotations_task.output().path) + self.assertEqual(ht.count(), 14) + self.assertCountEqual( + ht.globals.collect(), + [ + hl.Struct( + enums=hl.Struct( + sv_type=SV_TYPES, + sv_type_detail=SV_TYPE_DETAILS, + sorted_gene_consequences=hl.Struct( + major_consequence=SV_CONSEQUENCE_RANKS, + ), + ), + migrations=[], + max_key_=13, + updates={ + hl.Struct( + callset=TEST_SV_VCF, + project_guid='R0115_test_project2', + remap_pedigree_hash=hl.eval( + remap_pedigree_hash( + TEST_PEDIGREE_5, + ), + ), + ), + hl.Struct( + callset=TEST_SV_VCF_2, + project_guid='R0115_test_project2', + remap_pedigree_hash=hl.eval( + remap_pedigree_hash( + TEST_PEDIGREE_5, + ), + ), + ), + }, + ), + ], + ) + self.assertCountEqual( + ht.take(1), + [ + hl.Struct( + variant_id='BND_chr1_6', + algorithms='manta', + bothsides_support=False, + cpx_intervals=None, + end_locus=hl.Locus( + contig='chr5', + position=20404, + reference_genome='GRCh38', + ), + gnomad_svs=None, + rg37_locus=hl.Locus( + contig=1, + position=10367, + reference_genome='GRCh37', + ), + rg37_locus_end=hl.Locus( + contig=5, + position=20404, + reference_genome='GRCh37', + ), + sorted_gene_consequences=[ + hl.Struct(gene_id='ENSG00000186092', major_consequence_id=12), + hl.Struct(gene_id='ENSG00000153404', major_consequence_id=12), + ], + start_locus=hl.Locus( + contig='chr1', + position=180928, + reference_genome='GRCh38', + ), + strvctvre=hl.Struct(score=None), + sv_len=-1, + sv_type_id=2, + sv_type_detail_id=None, + xpos=1000180928, + key_=0, + ), + ], + ) + + @patch( + 'loading_pipeline.lib.tasks.write_new_variants_table.load_gencode_gene_symbol_to_gene_id', + ) + def test_sv_multiple_project_single_vcf( + self, + mock_load_gencode: Mock, + ) -> None: + mock_load_gencode.return_value = GENE_ID_MAPPING + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_10, + ReferenceGenome.GRCh38, + DatasetType.SV, + SampleType.WGS, + 'R0116_test_project3', + ) + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_11, + ReferenceGenome.GRCh38, + DatasetType.SV, + SampleType.WGS, + 'R0117_test_project4', + ) + worker = luigi.worker.Worker() + update_variant_annotations_task = ( + UpdateVariantAnnotationsTableWithNewVariantsTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SV, + sample_type=SampleType.WGS, + callset_path=TEST_SV_VCF_2, + project_guids=['R0116_test_project3', 'R0117_test_project4'], + validations_to_skip=[ALL_VALIDATIONS], + run_id='run_id', + ) + ) + worker.add(update_variant_annotations_task) + worker.run() + self.assertTrue(update_variant_annotations_task.complete()) + ht = hl.read_table(update_variant_annotations_task.output().path) + self.assertEqual(ht.count(), 2) + self.assertEqual( + len(ht.globals.updates.collect()[0]), + 2, + ) + + def test_gcnv_update_vat_multiple( + self, + ) -> None: + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_5, + ReferenceGenome.GRCh38, + DatasetType.GCNV, + SampleType.WES, + 'R0115_test_project2', + ) + worker = luigi.worker.Worker() + update_variant_annotations_task = ( + UpdateVariantAnnotationsTableWithNewVariantsTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.GCNV, + sample_type=SampleType.WES, + callset_path=TEST_GCNV_BED_FILE, + project_guids=['R0115_test_project2'], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + ) + worker.add(update_variant_annotations_task) + worker.run() + self.assertTrue(update_variant_annotations_task.complete()) + self.assertFalse( + GCSorLocalFolderTarget( + f'{self.mock_env.REFERENCE_DATASETS_DIR}/v03/GRCh38/GCNV/lookup.ht', + ).exists(), + ) + ht = hl.read_table(update_variant_annotations_task.output().path) + self.assertEqual(ht.count(), 2) + self.assertCountEqual( + ht.globals.collect(), + [ + hl.Struct( + enums=hl.Struct( + sv_type=SV_TYPES, + sorted_gene_consequences=hl.Struct( + major_consequence=SV_CONSEQUENCE_RANKS, + ), + ), + migrations=[], + max_key_=1, + updates={ + hl.Struct( + callset=TEST_GCNV_BED_FILE, + project_guid='R0115_test_project2', + remap_pedigree_hash=hl.eval( + remap_pedigree_hash( + TEST_PEDIGREE_5, + ), + ), + ), + }, + ), + ], + ) + self.assertCountEqual( + ht.collect(), + [ + hl.Struct( + variant_id='suffix_16456_DEL', + end_locus=hl.Locus( + contig='chr1', + position=100023213, + reference_genome='GRCh38', + ), + gt_stats=hl.Struct( + AF=hl.eval(hl.float32(4.401408e-05)), + AC=1, + AN=22720, + Hom=None, + Het=None, + ), + num_exon=3, + rg37_locus=hl.Locus( + contig=1, + position=100472493, + reference_genome='GRCh37', + ), + rg37_locus_end=hl.Locus( + contig=1, + position=100488769, + reference_genome='GRCh37', + ), + sorted_gene_consequences=[ + hl.Struct(gene_id='ENSG00000117620', major_consequence_id=0), + hl.Struct(gene_id='ENSG00000283761', major_consequence_id=0), + hl.Struct(gene_id='ENSG22222222222', major_consequence_id=None), + ], + start_locus=hl.Locus( + contig='chr1', + position=100006937, + reference_genome='GRCh38', + ), + strvctvre=hl.Struct(score=hl.eval(hl.float32(0.583))), + sv_type_id=5, + xpos=1100006937, + key_=0, + ), + hl.Struct( + variant_id='suffix_16457_DEL', + end_locus=hl.Locus( + contig='chr1', + position=100023212, + reference_genome='GRCh38', + ), + gt_stats=hl.Struct( + AF=8.802817319519818e-05, + AC=2, + AN=22719, + Hom=None, + Het=None, + ), + num_exon=2, + rg37_locus=hl.Locus( + contig=1, + position=100483142, + reference_genome='GRCh37', + ), + rg37_locus_end=hl.Locus( + contig=1, + position=100488768, + reference_genome='GRCh37', + ), + sorted_gene_consequences=[ + hl.Struct(gene_id='ENSG00000283761', major_consequence_id=0), + hl.Struct(gene_id='ENSG22222222222', major_consequence_id=None), + ], + start_locus=hl.Locus( + contig='chr1', + position=100017586, + reference_genome='GRCh38', + ), + strvctvre=hl.Struct(score=0.5070000290870667), + sv_type_id=5, + xpos=1100017586, + key_=1, + ), + ], + ) + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_8, + ReferenceGenome.GRCh38, + DatasetType.GCNV, + SampleType.WES, + 'R0115_test_project2', + ) + update_variant_annotations_task = ( + UpdateVariantAnnotationsTableWithNewVariantsTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.GCNV, + sample_type=SampleType.WES, + callset_path=TEST_GCNV_BED_FILE_2, + project_guids=['R0115_test_project2'], + validations_to_skip=[ALL_VALIDATIONS], + run_id='second_run_id', + ) + ) + worker.add(update_variant_annotations_task) + worker.run() + ht = hl.read_table(update_variant_annotations_task.output().path) + self.assertEqual(ht.count(), 3) + self.assertCountEqual( + ht.select('gt_stats').collect(), + [ + hl.Struct( + # Existing variant, gt_stats are preserved + variant_id='suffix_16456_DEL', + gt_stats=hl.Struct( + AF=hl.eval(hl.float32(4.401408e-05)), + AC=1, + AN=22720, + Hom=None, + Het=None, + ), + ), + hl.Struct( + # Exiting variant, gt_stats are updated + variant_id='suffix_16457_DEL', + gt_stats=hl.Struct( + AF=8.111110946629196e-05, + AC=3, + AN=36986, + Hom=None, + Het=None, + ), + ), + hl.Struct( + # New variant. + variant_id='suffix_99999_DEL', + gt_stats=hl.Struct( + AF=8.802817319519818e-05, + AC=2, + AN=22719, + Hom=None, + Het=None, + ), + ), + ], + ) diff --git a/loading_pipeline/lib/tasks/validate_callset.py b/loading_pipeline/lib/tasks/validate_callset.py new file mode 100644 index 0000000000..7622bc0a03 --- /dev/null +++ b/loading_pipeline/lib/tasks/validate_callset.py @@ -0,0 +1,144 @@ +import hail as hl +import luigi +import luigi.util + +from loading_pipeline.lib.misc.validation import ( + ALL_VALIDATIONS, + SKIPPABLE_VALIDATIONS, + SeqrValidationError, +) +from loading_pipeline.lib.paths import ( + postprocessed_callset_path, + valid_reference_dataset_path, +) +from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset +from loading_pipeline.lib.tasks.base.base_loading_run_params import BaseLoadingRunParams +from loading_pipeline.lib.tasks.base.base_update import BaseUpdateTask +from loading_pipeline.lib.tasks.files import CallsetTask, GCSorLocalTarget +from loading_pipeline.lib.tasks.reference_data.updated_reference_dataset import ( + UpdatedReferenceDatasetTask, +) +from loading_pipeline.lib.tasks.write_postprocessed_callset import ( + WritePostprocessedCallsetTask, +) +from loading_pipeline.lib.tasks.write_validation_errors_for_run import ( + UpdatedValidationErrorsForRunTask, +) + +MAX_SNV_INDEL_ALLELE_LENGTH = 500 + + +@luigi.util.inherits(BaseLoadingRunParams) +class ValidateCallsetTask(BaseUpdateTask): + @property + def validation_dependencies(self) -> dict[str, hl.Table]: + deps = {} + if ( + ALL_VALIDATIONS not in self.validations_to_skip + and 'validate_sample_type' not in self.validations_to_skip + and self.dataset_type.can_run_validation + ): + deps['coding_and_noncoding_variants_ht'] = hl.read_table( + valid_reference_dataset_path( + self.reference_genome, + ReferenceDataset.gnomad_coding_and_noncoding, + ), + ) + return deps + + def complete(self) -> luigi.Target: + if super().complete(): + mt = hl.read_matrix_table(self.output().path) + return hasattr(mt, 'validated_sample_type') and hl.eval( + self.sample_type.value == mt.validated_sample_type, + ) + return False + + def output(self) -> luigi.Target: + return GCSorLocalTarget( + postprocessed_callset_path( + self.reference_genome, + self.dataset_type, + self.callset_path, + ), + ) + + def requires(self) -> list[luigi.Task]: + requirements = [self.clone(WritePostprocessedCallsetTask)] + if ( + ALL_VALIDATIONS not in self.validations_to_skip + and 'validate_sample_type' not in self.validations_to_skip + and self.dataset_type.can_run_validation + ): + requirements = [ + *requirements, + ( + self.clone( + UpdatedReferenceDatasetTask, + reference_dataset=ReferenceDataset.gnomad_coding_and_noncoding, + ) + ), + ] + return [ + *requirements, + CallsetTask(self.callset_path), + ] + + def update_table(self, mt: hl.MatrixTable) -> hl.MatrixTable: + mt = hl.read_matrix_table( + postprocessed_callset_path( + self.reference_genome, + self.dataset_type, + self.callset_path, + ), + ) + if self.dataset_type.filter_invalid_sites: + mt = mt.filter_rows( + ( + # Rather than throwing an error, we silently remove invalid contigs. + # This happens fairly often for AnVIL requests. + hl.set(self.reference_genome.standard_contigs).contains( + mt.locus.contig, + ) + # DRAGEN callsets produce long alternate alleles + # that aren't particularly analyzable as INDELs. + & (hl.len(mt.alleles[1]) < MAX_SNV_INDEL_ALLELE_LENGTH) + ), + ) + + if ( + ALL_VALIDATIONS in self.validations_to_skip + or not self.dataset_type.can_run_validation + ): + return mt.select_globals( + callset_path=self.callset_path, + validated_sample_type=self.sample_type.value, + ) + validation_exceptions = [] + for validation_f in SKIPPABLE_VALIDATIONS: + try: + if validation_f.__name__ in self.validations_to_skip: + continue + validation_f( + mt, + **self.validation_dependencies, + **self.param_kwargs, + ) + except SeqrValidationError as e: + validation_exceptions.append(e) + if validation_exceptions: + updated_validation_errors_for_run_task = self.clone( + UpdatedValidationErrorsForRunTask, + error_messages=[e.msg for e in validation_exceptions], + error_body={ + k: v for e in validation_exceptions for k, v in e.error_body.items() + }, + ) + updated_validation_errors_for_run_task.run() + raise SeqrValidationError( + updated_validation_errors_for_run_task.to_single_error_message(), + ) + return mt.select_globals( + callset_path=self.callset_path, + validated_sample_type=self.sample_type.value, + ) diff --git a/loading_pipeline/lib/tasks/validate_callset_test.py b/loading_pipeline/lib/tasks/validate_callset_test.py new file mode 100644 index 0000000000..a56f78a894 --- /dev/null +++ b/loading_pipeline/lib/tasks/validate_callset_test.py @@ -0,0 +1,83 @@ +import json +import shutil + +import luigi.worker + +from loading_pipeline.lib.core import ( + DatasetType, + ReferenceGenome, + SampleType, +) +from loading_pipeline.lib.paths import ( + valid_reference_dataset_path, +) +from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset +from loading_pipeline.lib.tasks.validate_callset import ( + ValidateCallsetTask, +) +from loading_pipeline.lib.tasks.write_validation_errors_for_run import ( + UpdatedValidationErrorsForRunTask, +) +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + +TEST_CODING_AND_NONCODING_HT = 'loading_pipeline/var/test/reference_datasets/GRCh38/gnomad_coding_and_noncoding/1.0.ht' +MULTIPLE_VALIDATION_EXCEPTIONS_VCF = ( + 'loading_pipeline/var/test/callsets/multiple_validation_exceptions.vcf' +) + +TEST_RUN_ID = 'manual__2024-04-03' + + +class ValidateCallsetTest(MockedDatarootTestCase): + def setUp(self) -> None: + super().setUp() + shutil.copytree( + TEST_CODING_AND_NONCODING_HT, + valid_reference_dataset_path( + ReferenceGenome.GRCh38, + ReferenceDataset.gnomad_coding_and_noncoding, + ), + ) + + def test_validate_callset_multiple_exceptions( + self, + ) -> None: + worker = luigi.worker.Worker() + validate_callset_task = ValidateCallsetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WES, + # NB: + # This callset contains duplicate rows for chr1:902088, + # a NON_REF allele type at position chr1: 902024, missing + # all contigs but chr1, and contains non-coding variants. + callset_path=MULTIPLE_VALIDATION_EXCEPTIONS_VCF, + project_guids=['project_a'], + run_id=TEST_RUN_ID, + ) + worker.add(validate_callset_task) + worker.run() + self.assertFalse(validate_callset_task.complete()) + + updated_validation_errors_task = UpdatedValidationErrorsForRunTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WES, + callset_path=MULTIPLE_VALIDATION_EXCEPTIONS_VCF, + project_guids=['project_a'], + run_id=TEST_RUN_ID, + ) + self.assertTrue(updated_validation_errors_task.complete()) + with updated_validation_errors_task.output().open('r') as f: + self.assertDictEqual( + json.load(f), + { + 'project_guids': ['project_a'], + 'error_messages': [ + 'Alleles with invalid allele are present in the callset. This appears to be a GVCF containing records for sites with no variants.', + 'Missing the following expected contigs:chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr2, chr20, chr21, chr22, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chrX', + "Variants are present multiple times in the callset: ['1-902088-G-A']", + 'Sample type validation error: dataset sample-type is specified as WES but appears to be WGS because it contains many common non-coding variants', + ], + }, + ) diff --git a/loading_pipeline/lib/tasks/variants_migration/__init__.py b/loading_pipeline/lib/tasks/variants_migration/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables.py b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables.py new file mode 100644 index 0000000000..25325d8e37 --- /dev/null +++ b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables.py @@ -0,0 +1,137 @@ +import luigi +import luigi.util + +from loading_pipeline.lib.core import FeatureFlag +from loading_pipeline.lib.misc.clickhouse import ( + ClickhouseReferenceDataset, + ClickHouseTable, + TableNameBuilder, + logged_query, +) +from loading_pipeline.lib.misc.retry import retry +from loading_pipeline.lib.paths import ( + new_variant_details_parquet_path, + new_variants_parquet_path, +) +from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( + BaseLoadingPipelineParams, +) +from loading_pipeline.lib.tasks.files import GCSorLocalFolderTarget +from loading_pipeline.lib.tasks.variants_migration.migrate_variant_details_parquet import ( + MigrateVariantDetailsParquetOnDataprocTask, + MigrateVariantDetailsParquetTask, +) +from loading_pipeline.lib.tasks.variants_migration.migrate_variants_parquet import ( + MigrateVariantsParquetOnDataprocTask, + MigrateVariantsParquetTask, +) + + +@retry() +def refresh_seqr_variants_and_search( + table_name_builder: TableNameBuilder, + clickhouse_reference_dataset: ClickhouseReferenceDataset, +): + if clickhouse_reference_dataset.has_seqr_variants: + logged_query( + f""" + SYSTEM START VIEW {clickhouse_reference_dataset.all_variants_to_seqr_variants_mv(table_name_builder)} + """, + ) + logged_query( + f""" + SYSTEM REFRESH VIEW {clickhouse_reference_dataset.all_variants_to_seqr_variants_mv(table_name_builder)} + """, + ) + logged_query( + f""" + SYSTEM WAIT VIEW {clickhouse_reference_dataset.all_variants_to_seqr_variants_mv(table_name_builder)} + """, + timeout=clickhouse_reference_dataset.all_variants_mv_timeout, + ) + clickhouse_reference_dataset.refresh_search(table_name_builder) + + +@luigi.util.inherits(BaseLoadingPipelineParams) +class LoadClickhouseVariantsTablesTask(luigi.WrapperTask): + run_id = luigi.Parameter() + attempt_id = luigi.IntParameter() + + def requires(self) -> luigi.Task: + tasks = ( + [ + self.clone(MigrateVariantsParquetOnDataprocTask), + ] + if FeatureFlag.RUN_PIPELINE_ON_DATAPROC + else [ + self.clone(MigrateVariantsParquetTask), + ] + ) + if self.dataset_type.should_write_new_variant_details: + tasks.append( + self.clone(MigrateVariantDetailsParquetOnDataprocTask) + if FeatureFlag.RUN_PIPELINE_ON_DATAPROC + else self.clone(MigrateVariantDetailsParquetTask), + ) + return tasks + + def complete(self) -> bool: + table_name_builder = TableNameBuilder( + self.reference_genome, + self.dataset_type, + self.run_id, + ) + if not ( + GCSorLocalFolderTarget( + new_variant_details_parquet_path( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + ).exists() + ) or not ( + GCSorLocalFolderTarget( + new_variants_parquet_path( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + ).exists() + ): + return False + max_key = logged_query( + f""" + SELECT max(key) FROM {table_name_builder.src_table(ClickHouseTable.VARIANTS_MEMORY)} + """, + )[0][0] + return logged_query( + f""" + SELECT EXISTS ( + SELECT 1 FROM {table_name_builder.dst_table(ClickHouseTable.VARIANTS_MEMORY)} where key = %(max_key)s + ) + """, + {'max_key': max_key}, + )[0][0] + + def run(self) -> None: + table_name_builder = TableNameBuilder( + self.reference_genome, + self.dataset_type, + self.run_id, + ) + for clickhouse_table in ClickHouseTable.for_dataset_type( + self.dataset_type, + ): + if clickhouse_table == ClickHouseTable.ENTRIES: + continue + clickhouse_table.insert(table_name_builder=table_name_builder) + for ( + clickhouse_reference_dataset + ) in ClickhouseReferenceDataset.for_reference_genome_dataset_type( + self.reference_genome, + self.dataset_type, + ): + refresh_seqr_variants_and_search( + table_name_builder, + clickhouse_reference_dataset, + ) diff --git a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py new file mode 100644 index 0000000000..972df2c172 --- /dev/null +++ b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py @@ -0,0 +1,148 @@ +from unittest.mock import Mock, patch + +import hail as hl +import luigi.worker + +from loading_pipeline.lib.core import ( + DatasetType, + ReferenceGenome, +) +from loading_pipeline.lib.core.environment import Env +from loading_pipeline.lib.misc.clickhouse import ( + ClickhouseReferenceDataset, + get_clickhouse_client, +) +from loading_pipeline.lib.paths import ( + variant_annotations_table_path, +) +from loading_pipeline.lib.tasks.variants_migration.load_clickhouse_variants_tables import ( + LoadClickhouseVariantsTablesTask, +) +from loading_pipeline.lib.tasks.variants_migration.migrate_variant_details_parquet import ( + MigrateVariantDetailsParquetTask, +) +from loading_pipeline.lib.tasks.variants_migration.migrate_variants_parquet import ( + MigrateVariantsParquetTask, +) +from loading_pipeline.lib.tasks.variants_migration.update_variant_annotations_table_with_dropped_reference_datasets import ( + UpdateVariantAnnotationsTableWithDroppedReferenceDatasetsTask, +) +from loading_pipeline.lib.test.clickhouse_schema_testcase import ( + ClickhouseSchemaTestCase, +) +from loading_pipeline.lib.test.mocked_dataroot_testcase import ( + MockedDatarootTestCase, +) + +TEST_SCHEMA = 'loading_pipeline/var/test/test_clickhouse_schema.sql' +TEST_SNV_INDEL_ANNOTATIONS = ( + 'loading_pipeline/var/test/exports/GRCh38/SNV_INDEL/annotations.ht' +) +TEST_RUN_ID = 'manual__2024-04-03' + + +class LoadClickhouseVariantsTablesTaskTest( + MockedDatarootTestCase, + ClickhouseSchemaTestCase, +): + def setUp(self) -> None: + super().setUp() + ht = hl.read_table(TEST_SNV_INDEL_ANNOTATIONS) + ht.write( + variant_annotations_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + ), + ) + + @patch.object( + ClickhouseReferenceDataset, + 'for_reference_genome_dataset_type', + return_value=[ClickhouseReferenceDataset.CLINVAR], + ) + def test_write_variants_to_clickhouse( + self, + mock_for_reference_genome_dataset_type: Mock, + ): + worker = luigi.worker.Worker() + task = UpdateVariantAnnotationsTableWithDroppedReferenceDatasetsTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id=TEST_RUN_ID, + ) + worker.add(task) + worker.run() + self.assertTrue(task.output().exists()) + self.assertTrue(task.complete()) + ht = hl.read_table(task.output().path) + self.assertTrue('variant_id' in ht.row) + self.assertTrue('gnomad_genomes' not in ht.row and 'dbnsfp' not in ht.row) + + task = MigrateVariantsParquetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id=TEST_RUN_ID, + attempt_id=0, + ) + worker.add(task) + worker.run() + self.assertTrue(task.output().exists()) + self.assertTrue(task.complete()) + + task = MigrateVariantDetailsParquetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id=TEST_RUN_ID, + attempt_id=0, + ) + worker.add(task) + worker.run() + self.assertTrue(task.output().exists()) + self.assertTrue(task.complete()) + + task = MigrateVariantDetailsParquetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id=TEST_RUN_ID, + attempt_id=0, + ) + worker.add(task) + worker.run() + self.assertTrue(task.output().exists()) + self.assertTrue(task.complete()) + + task = LoadClickhouseVariantsTablesTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id=TEST_RUN_ID, + attempt_id=0, + ) + worker.add(task) + worker.run() + self.assertTrue(task.complete()) + + client = get_clickhouse_client() + variants_count = client.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` + """, + )[0][0] + self.assertEqual(variants_count, 2) + variant_details_count = client.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details` + """, + )[0][0] + self.assertEqual(variant_details_count, 2) + key_lookups_count = client.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/key_lookup` + """, + )[0][0] + self.assertEqual(key_lookups_count, 2) diff --git a/loading_pipeline/lib/tasks/variants_migration/migrate_variant_details_parquet.py b/loading_pipeline/lib/tasks/variants_migration/migrate_variant_details_parquet.py new file mode 100644 index 0000000000..8405757676 --- /dev/null +++ b/loading_pipeline/lib/tasks/variants_migration/migrate_variant_details_parquet.py @@ -0,0 +1,76 @@ +import hail as hl +import luigi +import luigi.util + +from loading_pipeline.lib.paths import ( + new_variant_details_parquet_path, + variant_annotations_table_path, +) +from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( + BaseLoadingPipelineParams, +) +from loading_pipeline.lib.tasks.base.base_write_parquet import BaseWriteParquetTask +from loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc import ( + BaseRunJobOnDataprocTask, +) +from loading_pipeline.lib.tasks.exports.fields import ( + get_variant_details_export_fields, +) +from loading_pipeline.lib.tasks.exports.misc import ( + camelcase_array_structexpression_fields, + unmap_formatting_annotation_enums, +) +from loading_pipeline.lib.tasks.files import GCSorLocalTarget +from loading_pipeline.lib.tasks.variants_migration.update_variant_annotations_table_with_dropped_reference_datasets import ( + UpdateVariantAnnotationsTableWithDroppedReferenceDatasetsTask, +) + + +@luigi.util.inherits(BaseLoadingPipelineParams) +class MigrateVariantDetailsParquetTask(BaseWriteParquetTask): + run_id = luigi.Parameter() + attempt_id = luigi.IntParameter() + + def output(self) -> luigi.Target: + return GCSorLocalTarget( + new_variant_details_parquet_path( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + ) + + def requires(self) -> luigi.Task: + return self.clone(UpdateVariantAnnotationsTableWithDroppedReferenceDatasetsTask) + + def create_table(self) -> None: + ht = hl.read_table( + variant_annotations_table_path( + self.reference_genome, + self.dataset_type, + ), + ) + ht = unmap_formatting_annotation_enums( + ht, + self.reference_genome, + self.dataset_type, + ) + ht = camelcase_array_structexpression_fields( + ht, + self.reference_genome, + self.dataset_type, + ) + ht = ht.key_by() + return ht.select( + **get_variant_details_export_fields( + ht, + self.reference_genome, + self.dataset_type, + ), + ) + + +class MigrateVariantDetailsParquetOnDataprocTask(BaseRunJobOnDataprocTask): + @property + def task(self) -> luigi.Task: + return MigrateVariantDetailsParquetTask diff --git a/loading_pipeline/lib/tasks/variants_migration/migrate_variants_parquet.py b/loading_pipeline/lib/tasks/variants_migration/migrate_variants_parquet.py new file mode 100644 index 0000000000..c92a25fb4e --- /dev/null +++ b/loading_pipeline/lib/tasks/variants_migration/migrate_variants_parquet.py @@ -0,0 +1,76 @@ +import hail as hl +import luigi +import luigi.util + +from loading_pipeline.lib.paths import ( + new_variants_parquet_path, + variant_annotations_table_path, +) +from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( + BaseLoadingPipelineParams, +) +from loading_pipeline.lib.tasks.base.base_write_parquet import BaseWriteParquetTask +from loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc import ( + BaseRunJobOnDataprocTask, +) +from loading_pipeline.lib.tasks.exports.fields import get_variants_export_fields +from loading_pipeline.lib.tasks.exports.misc import ( + camelcase_array_structexpression_fields, + subset_consequences_fields, + unmap_formatting_annotation_enums, +) +from loading_pipeline.lib.tasks.files import GCSorLocalTarget +from loading_pipeline.lib.tasks.variants_migration.update_variant_annotations_table_with_dropped_reference_datasets import ( + UpdateVariantAnnotationsTableWithDroppedReferenceDatasetsTask, +) + + +@luigi.util.inherits(BaseLoadingPipelineParams) +class MigrateVariantsParquetTask(BaseWriteParquetTask): + run_id = luigi.Parameter() + attempt_id = luigi.IntParameter() + + def output(self) -> luigi.Target: + return GCSorLocalTarget( + new_variants_parquet_path( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + ) + + def requires(self) -> luigi.Task: + return self.clone(UpdateVariantAnnotationsTableWithDroppedReferenceDatasetsTask) + + def create_table(self) -> None: + ht = hl.read_table( + variant_annotations_table_path( + self.reference_genome, + self.dataset_type, + ), + ) + ht = unmap_formatting_annotation_enums( + ht, + self.reference_genome, + self.dataset_type, + ) + ht = camelcase_array_structexpression_fields( + ht, + self.reference_genome, + self.dataset_type, + ) + if self.dataset_type.should_write_new_variant_details: + ht = subset_consequences_fields( + ht, + self.reference_genome, + ) + ht = ht.key_by() + return ht.select( + **get_variants_export_fields(ht, self.reference_genome, self.dataset_type), + ) + + +class MigrateVariantsParquetOnDataprocTask(BaseRunJobOnDataprocTask): + @property + def task(self) -> luigi.Task: + return MigrateVariantsParquetTask diff --git a/loading_pipeline/lib/tasks/variants_migration/update_variant_annotations_table_with_dropped_reference_datasets.py b/loading_pipeline/lib/tasks/variants_migration/update_variant_annotations_table_with_dropped_reference_datasets.py new file mode 100644 index 0000000000..4dddb1afbe --- /dev/null +++ b/loading_pipeline/lib/tasks/variants_migration/update_variant_annotations_table_with_dropped_reference_datasets.py @@ -0,0 +1,90 @@ +import hail as hl +import luigi +import luigi.util + +from loading_pipeline.lib.paths import ( + variant_annotations_table_path, +) +from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( + BaseLoadingPipelineParams, +) +from loading_pipeline.lib.tasks.base.base_update import ( + BaseUpdateTask, +) +from loading_pipeline.lib.tasks.files import GCSorLocalTarget, HailTableTask + + +@luigi.util.inherits(BaseLoadingPipelineParams) +class UpdateVariantAnnotationsTableWithDroppedReferenceDatasetsTask( + BaseUpdateTask, +): + run_id = luigi.Parameter() + + def output(self) -> luigi.Target: + return GCSorLocalTarget( + variant_annotations_table_path( + self.reference_genome, + self.dataset_type, + ), + ) + + def requires(self) -> list[luigi.Task]: + return HailTableTask( + variant_annotations_table_path( + self.reference_genome, + self.dataset_type, + ), + ) + + def complete(self) -> bool: + return ( + super().complete() and 'dbnsfp' not in hl.read_table(self.output().path).row + ) + + def initialize_table(self) -> hl.Table: + key_type = self.dataset_type.table_key_type(self.reference_genome) + return hl.Table.parallelize( + [], + key_type, + key=key_type.fields, + globals=hl.Struct( + enums=hl.Struct(), + updates=hl.empty_set( + hl.tstruct( + callset=hl.tstr, + project_guid=hl.tstr, + remap_pedigree_hash=hl.tint32, + ), + ), + migrations=hl.empty_array(hl.tstr), + max_key_=hl.int64(-1), + ), + ) + + def update_table(self, ht: hl.Table) -> hl.Table: + for field in [ + 'clinvar', + 'gnomad_mito', + 'hmtvar', + 'local_constraint_mito', + 'dbnsfp', + 'mitomap', + 'mitimpact', + 'helix_mito', + 'gt_stats', + 'high_constraint_region', + 'eigen', + 'splice_ai', + 'exac', + 'topmed', + 'screen', + 'gnomad_exomes', + 'gnomad_genomes', + 'hgmd', + 'gnomad_non_coding_constraint', + ]: + if field in ht.row: + ht = ht.drop(field) + if field in ht.enums: + ht = ht.annotate_globals(enums=ht.enums.drop(field)) + return ht diff --git a/loading_pipeline/lib/tasks/write_clickhouse_load_success_file.py b/loading_pipeline/lib/tasks/write_clickhouse_load_success_file.py new file mode 100644 index 0000000000..f5c7284763 --- /dev/null +++ b/loading_pipeline/lib/tasks/write_clickhouse_load_success_file.py @@ -0,0 +1,56 @@ +import json + +import hailtop.fs as hfs +import luigi +import luigi.util + +from loading_pipeline.lib.misc.clickhouse import ( + load_complete_run, +) +from loading_pipeline.lib.paths import ( + clickhouse_load_success_file_path, + metadata_for_run_path, +) +from loading_pipeline.lib.tasks.base.base_loading_run_params import ( + BaseLoadingRunParams, +) +from loading_pipeline.lib.tasks.files import GCSorLocalTarget +from loading_pipeline.lib.tasks.write_success_file import WriteSuccessFileTask + + +@luigi.util.inherits(BaseLoadingRunParams) +class WriteClickhouseLoadSuccessFileTask(luigi.Task): + attempt_id = luigi.IntParameter() + + def output(self) -> luigi.Target: + return GCSorLocalTarget( + clickhouse_load_success_file_path( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + ) + + def requires(self) -> luigi.Task: + return self.clone(WriteSuccessFileTask) + + def run(self): + with hfs.open( + metadata_for_run_path( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + ) as f: + family_guids = list(json.load(f)['family_samples'].keys()) + load_complete_run( + self.reference_genome, + self.dataset_type, + self.run_id, + # Note: nasty bug here where Luigi parses ListParameters to tuples. + list(self.project_guids), + family_guids, + ) + + with self.output().open('w') as f: + f.write('') diff --git a/loading_pipeline/lib/tasks/write_imported_callset.py b/loading_pipeline/lib/tasks/write_imported_callset.py new file mode 100644 index 0000000000..db80232bca --- /dev/null +++ b/loading_pipeline/lib/tasks/write_imported_callset.py @@ -0,0 +1,84 @@ +import hail as hl +import luigi +import luigi.util + +from loading_pipeline.lib.misc.callsets import get_additional_row_fields +from loading_pipeline.lib.misc.io import ( + import_callset, + select_relevant_fields, +) +from loading_pipeline.lib.misc.validation import ( + validate_imported_field_types, +) +from loading_pipeline.lib.paths import ( + imported_callset_path, +) +from loading_pipeline.lib.tasks.base.base_loading_run_params import BaseLoadingRunParams +from loading_pipeline.lib.tasks.base.base_write import BaseWriteTask +from loading_pipeline.lib.tasks.files import CallsetTask, GCSorLocalTarget +from loading_pipeline.lib.tasks.write_validation_errors_for_run import ( + with_persisted_validation_errors, +) + + +@luigi.util.inherits(BaseLoadingRunParams) +class WriteImportedCallsetTask(BaseWriteTask): + def complete(self) -> luigi.Target: + if super().complete(): + mt = hl.read_matrix_table(self.output().path) + # Handle case where callset was previously imported + # with a different sex/relatedness flag. + additional_row_fields = get_additional_row_fields( + mt, + self.reference_genome, + self.dataset_type, + self.skip_check_sex_and_relatedness, + ) + return all(hasattr(mt, field) for field in additional_row_fields) + return False + + def output(self) -> luigi.Target: + return GCSorLocalTarget( + imported_callset_path( + self.reference_genome, + self.dataset_type, + self.callset_path, + ), + ) + + def requires(self) -> list[luigi.Task]: + return [ + CallsetTask(self.callset_path), + ] + + @with_persisted_validation_errors + def create_table(self) -> hl.MatrixTable: + # NB: throws SeqrValidationError + mt = import_callset( + self.callset_path, + self.reference_genome, + self.dataset_type, + ) + additional_row_fields = get_additional_row_fields( + mt, + self.reference_genome, + self.dataset_type, + self.skip_check_sex_and_relatedness, + ) + # NB: throws SeqrValidationError + mt = select_relevant_fields( + mt, + self.dataset_type, + additional_row_fields, + ) + # This validation isn't override-able by the skip option. + # If a field is the wrong type, the pipeline will likely hard-fail downstream. + # NB: throws SeqrValidationError + validate_imported_field_types( + mt, + self.dataset_type, + additional_row_fields, + ) + return mt.select_globals( + callset_path=self.callset_path, + ) diff --git a/loading_pipeline/lib/tasks/write_metadata_for_run.py b/loading_pipeline/lib/tasks/write_metadata_for_run.py new file mode 100644 index 0000000000..a20f44cd59 --- /dev/null +++ b/loading_pipeline/lib/tasks/write_metadata_for_run.py @@ -0,0 +1,146 @@ +import json + +import hail as hl +import hailtop.fs as hfs +import luigi +import luigi.util + +from loading_pipeline.lib.core import FeatureFlag +from loading_pipeline.lib.paths import ( + metadata_for_run_path, + relatedness_check_tsv_path, + sample_qc_json_path, +) +from loading_pipeline.lib.tasks.base.base_loading_run_params import ( + BaseLoadingRunParams, +) +from loading_pipeline.lib.tasks.files import GCSorLocalTarget +from loading_pipeline.lib.tasks.write_remapped_and_subsetted_callset import ( + WriteRemappedAndSubsettedCallsetTask, +) +from loading_pipeline.lib.tasks.write_sample_qc_json import WriteSampleQCJsonTask + + +@luigi.util.inherits(BaseLoadingRunParams) +class WriteMetadataForRunTask(luigi.Task): + def output(self) -> luigi.Target: + return GCSorLocalTarget( + metadata_for_run_path( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + ) + + def requires(self) -> list[luigi.Task]: + requirements = [ + self.clone( + WriteRemappedAndSubsettedCallsetTask, + project_i=i, + ) + for i in range(len(self.project_guids)) + ] + if ( + FeatureFlag.EXPECT_TDR_METRICS + and not self.skip_expect_tdr_metrics + and self.dataset_type.expect_tdr_metrics( + self.reference_genome, + ) + ): + requirements = [ + *requirements, + self.clone(WriteSampleQCJsonTask), + ] + return requirements + + def run(self) -> None: + metadata_json = { + 'callsets': [self.callset_path], + 'run_id': self.run_id, + 'sample_type': self.sample_type.value, + 'project_guids': self.project_guids, + 'family_samples': {}, + 'failed_family_samples': { + 'missing_samples': {}, + 'relatedness_check': {}, + 'sex_check': {}, + 'ploidy_check': {}, + }, + 'relatedness_check_file_path': relatedness_check_tsv_path( + self.reference_genome, + self.dataset_type, + self.callset_path, + ), + 'sample_qc': {}, + } + sample_qc_loadable_samples = {} + # NB: the trailing WriteSampleQCJsonTask output is conditionally + # present in requires(), so slice by project count rather than + # dropping the last input. + for remapped_and_subsetted_callset in self.input()[: len(self.project_guids)]: + callset_mt = hl.read_matrix_table(remapped_and_subsetted_callset.path) + collected_globals = callset_mt.globals.collect()[0] + metadata_json['family_samples'] = { + **collected_globals['family_samples'], + **metadata_json['family_samples'], + } + sample_qc_loadable_samples = { + *{ + sample + for family_samples in collected_globals['family_samples'].values() + for sample in family_samples + }, + *sample_qc_loadable_samples, + } + for key in [ + 'missing_samples', + 'relatedness_check', + 'sex_check', + 'ploidy_check', + ]: + metadata_json['failed_family_samples'][key] = { + **collected_globals['failed_family_samples'][key], + **metadata_json['failed_family_samples'][key], + } + sample_qc_loadable_samples = { + *{ + sample + for meta in collected_globals['failed_family_samples'][ + key + ].values() + for sample in meta['samples'] + }, + *sample_qc_loadable_samples, + } + if ( + FeatureFlag.EXPECT_TDR_METRICS + and not self.skip_expect_tdr_metrics + and self.dataset_type.expect_tdr_metrics( + self.reference_genome, + ) + ): + with hfs.open( + sample_qc_json_path( + self.reference_genome, + self.dataset_type, + self.callset_path, + ), + ) as f: + metadata_json['sample_qc'] = { + k: v + for k, v in json.load(f).items() + if k in sample_qc_loadable_samples + } + if not metadata_json['family_samples']: + msg = 'Found no loadable families in the callset.' + raise RuntimeError(msg) + empty_families = [ + family_guid + for family_guid, samples in metadata_json['family_samples'].items() + if not samples + ] + if empty_families: + msg = f'Found families with no loadable samples: {sorted(empty_families)}' + raise RuntimeError(msg) + with self.output().open('w') as f: + json.dump(metadata_json, f) diff --git a/loading_pipeline/lib/tasks/write_metadata_for_run_test.py b/loading_pipeline/lib/tasks/write_metadata_for_run_test.py new file mode 100644 index 0000000000..2b5dc7a22d --- /dev/null +++ b/loading_pipeline/lib/tasks/write_metadata_for_run_test.py @@ -0,0 +1,188 @@ +import json +from unittest import mock +from unittest.mock import Mock + +import luigi.worker + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS +from loading_pipeline.lib.paths import relatedness_check_tsv_path +from loading_pipeline.lib.tasks.write_metadata_for_run import WriteMetadataForRunTask +from loading_pipeline.lib.test.misc import copy_project_pedigree_to_mocked_dir +from loading_pipeline.lib.test.mock_complete_task import MockCompleteTask +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + +TEST_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' +TEST_PEDIGREE_3_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_3_remap.tsv' +TEST_PEDIGREE_4_REMAP_2 = ( + 'loading_pipeline/var/test/pedigrees/test_pedigree_4_remap_2.tsv' +) +TEST_SAMPLE_QC_JSON = 'loading_pipeline/var/test/sample_qc_1.json' + + +class WriteMetadataForRunTaskTest(MockedDatarootTestCase): + @mock.patch( + 'loading_pipeline.lib.tasks.write_metadata_for_run.sample_qc_json_path', + lambda *_: TEST_SAMPLE_QC_JSON, + ) + @mock.patch('loading_pipeline.lib.tasks.write_metadata_for_run.FeatureFlag') + @mock.patch( + 'loading_pipeline.lib.tasks.write_sex_check_table.WriteTDRMetricsFilesTask', + ) + @mock.patch( + 'loading_pipeline.lib.tasks.write_metadata_for_run.WriteSampleQCJsonTask', + ) + def test_write_metadata_for_run_task( + self, + write_sample_qc_json_task: Mock, + write_tdr_metrics_task: Mock, + mock_ff: Mock, + ) -> None: + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_3_REMAP, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0113_test_project', + ) + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_4_REMAP_2, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0114_project4', + ) + mock_ff.EXPECT_TDR_METRICS = True + write_tdr_metrics_task.return_value = MockCompleteTask() + write_sample_qc_json_task.return_value = MockCompleteTask() + worker = luigi.worker.Worker() + write_metadata_for_run_task = WriteMetadataForRunTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path=TEST_VCF, + project_guids=['R0113_test_project', 'R0114_project4'], + validations_to_skip=[ALL_VALIDATIONS], + run_id='run_123456', + ) + worker.add(write_metadata_for_run_task) + worker.run() + self.assertTrue( + 'run_123456/metadata.json' in write_metadata_for_run_task.output().path, + ) + self.assertTrue(write_metadata_for_run_task.complete()) + with write_metadata_for_run_task.output().open('r') as f: + self.assertDictEqual( + json.load(f), + { + 'callsets': [TEST_VCF], + 'project_guids': ['R0113_test_project', 'R0114_project4'], + 'failed_family_samples': { + 'missing_samples': { + 'efg_1': { + # This sample is present in the callset, but intentionally + # mapped away + 'samples': ['NA20888_1'], + 'reasons': ["Missing samples: {'NA20888_1'}"], + }, + }, + 'relatedness_check': {}, + 'sex_check': {}, + 'ploidy_check': {}, + }, + 'family_samples': { + 'abc_1': [ + 'HG00731_1', + 'HG00732_1', + 'HG00733_1', + ], + '123_1': ['NA19675_1'], + '234_1': ['NA19678_1'], + '345_1': ['NA19679_1'], + '456_1': ['NA20870_1'], + '567_1': ['NA20872_1'], + '678_1': ['NA20874_1'], + '789_1': ['NA20875_1'], + '890_1': ['NA20876_1'], + '901_1': ['NA20877_1'], + 'bcd_1': ['NA20878_1'], + 'cde_1': ['NA20881_1'], + 'def_1': ['NA20885_1'], + }, + 'run_id': 'run_123456', + 'sample_type': SampleType.WGS.value, + 'relatedness_check_file_path': relatedness_check_tsv_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_VCF, + ), + 'sample_qc': { + 'HG00731_1': {'filter_flags': ['coverage', 'contamination']}, + 'HG00732_1': {'filter_flags': ['coverage']}, + 'HG00733_1': {'filter_flags': ['contamination']}, + 'NA19675_1': {'filter_flags': []}, + 'NA20888_1': {'filter_flags': ['sample_failed']}, + }, + }, + ) + + @mock.patch('loading_pipeline.lib.tasks.write_metadata_for_run.FeatureFlag') + def test_write_metadata_for_run_task_without_tdr_metrics( + self, + mock_ff: Mock, + ) -> None: + # When WriteSampleQCJsonTask is not a requirement, every project's + # remapped and subsetted callset must still be collected. + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_3_REMAP, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0113_test_project', + ) + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_4_REMAP_2, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0114_project4', + ) + mock_ff.EXPECT_TDR_METRICS = False + worker = luigi.worker.Worker() + write_metadata_for_run_task = WriteMetadataForRunTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path=TEST_VCF, + project_guids=['R0113_test_project', 'R0114_project4'], + validations_to_skip=[ALL_VALIDATIONS], + run_id='run_123457', + ) + worker.add(write_metadata_for_run_task) + worker.run() + self.assertTrue(write_metadata_for_run_task.complete()) + with write_metadata_for_run_task.output().open('r') as f: + metadata_json = json.load(f) + self.assertDictEqual( + metadata_json['family_samples'], + { + 'abc_1': [ + 'HG00731_1', + 'HG00732_1', + 'HG00733_1', + ], + '123_1': ['NA19675_1'], + '234_1': ['NA19678_1'], + '345_1': ['NA19679_1'], + '456_1': ['NA20870_1'], + '567_1': ['NA20872_1'], + '678_1': ['NA20874_1'], + '789_1': ['NA20875_1'], + '890_1': ['NA20876_1'], + '901_1': ['NA20877_1'], + 'bcd_1': ['NA20878_1'], + 'cde_1': ['NA20881_1'], + 'def_1': ['NA20885_1'], + }, + ) + self.assertDictEqual(metadata_json['sample_qc'], {}) diff --git a/loading_pipeline/lib/tasks/write_new_variants_table.py b/loading_pipeline/lib/tasks/write_new_variants_table.py new file mode 100644 index 0000000000..5922b54c7c --- /dev/null +++ b/loading_pipeline/lib/tasks/write_new_variants_table.py @@ -0,0 +1,222 @@ +import math + +import hail as hl +import hailtop.fs as hfs +import luigi +import luigi.util + +from loading_pipeline.lib.annotations.fields import get_fields +from loading_pipeline.lib.annotations.misc import ( + annotate_formatting_annotation_enum_globals, +) +from loading_pipeline.lib.misc.callsets import get_callset_ht +from loading_pipeline.lib.misc.io import checkpoint, remap_pedigree_hash +from loading_pipeline.lib.misc.math import constrain +from loading_pipeline.lib.misc.vep import run_vep +from loading_pipeline.lib.paths import ( + new_variants_table_path, + project_pedigree_path, + valid_reference_dataset_path, + variant_annotations_table_path, +) +from loading_pipeline.lib.reference_datasets.gencode.mapping_gene_ids import ( + load_gencode_ensembl_to_refseq_id, + load_gencode_gene_symbol_to_gene_id, +) +from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset +from loading_pipeline.lib.tasks.base.base_loading_run_params import ( + BaseLoadingRunParams, +) +from loading_pipeline.lib.tasks.base.base_write import BaseWriteTask +from loading_pipeline.lib.tasks.files import GCSorLocalTarget +from loading_pipeline.lib.tasks.write_metadata_for_run import ( + WriteMetadataForRunTask, +) + +VARIANTS_PER_VEP_PARTITION = 1e3 +MIN_PARTITIONS = 10 +MAX_PARTITIONS = 10000 +GENCODE_RELEASE = 42 +GENCODE_FOR_VEP_RELEASE = 44 + + +@luigi.util.inherits(BaseLoadingRunParams) +class WriteNewVariantsTableTask(BaseWriteTask): + @property + def annotation_dependencies(self) -> dict[str, hl.Table]: + deps = {} + for reference_dataset in ReferenceDataset: + if ( + reference_dataset.formatting_annotation + and self.dataset_type + in reference_dataset.dataset_types(self.reference_genome) + ): + deps[f'{reference_dataset.value}_ht'] = hl.read_table( + valid_reference_dataset_path( + self.reference_genome, + reference_dataset, + ), + ) + + if self.dataset_type.has_gencode_ensembl_to_refseq_id_mapping( + self.reference_genome, + ): + deps['gencode_ensembl_to_refseq_id_mapping'] = hl.literal( + load_gencode_ensembl_to_refseq_id(GENCODE_FOR_VEP_RELEASE), + ) + if self.dataset_type.has_gencode_gene_symbol_to_gene_id_mapping: + deps['gencode_gene_symbol_to_gene_id_mapping'] = hl.literal( + load_gencode_gene_symbol_to_gene_id(GENCODE_RELEASE), + ) + return deps + + def output(self) -> luigi.Target: + return GCSorLocalTarget( + new_variants_table_path( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + ) + + def requires(self) -> list[luigi.Task]: + return [ + self.clone(WriteMetadataForRunTask), + ] + + def complete(self) -> bool: + # NOTE: Special hack for ClickHouse migration tasks which + # do not have a callset/projects to load. + if len(self.project_guids) == 0: + return super().complete() + return super().complete() and hl.eval( + hl.bind( + lambda updates: hl.all( + [ + updates.contains( + hl.Struct( + callset=self.callset_path, + project_guid=project_guid, + remap_pedigree_hash=remap_pedigree_hash( + project_pedigree_path( + self.reference_genome, + self.dataset_type, + self.sample_type, + project_guid, + ), + ), + ), + ) + for project_guid in self.project_guids + ], + ), + hl.read_table(self.output().path).updates, + ), + ) + + def create_table(self) -> hl.Table: + callset_ht = get_callset_ht( + self.reference_genome, + self.dataset_type, + self.callset_path, + self.project_guids, + ) + + # 1) Identify new variants. + if hfs.exists( + variant_annotations_table_path( + self.reference_genome, + self.dataset_type, + ), + ): + annotations_ht = hl.read_table( + variant_annotations_table_path( + self.reference_genome, + self.dataset_type, + ), + ) + # Gracefully handle case for on-premises uses + # where key_ field is not present and migration was not run. + if not hasattr(annotations_ht, 'key_'): + annotations_ht = annotations_ht.add_index(name='key_') + annotations_ht = annotations_ht.annotate_globals( + max_key_=(annotations_ht.count() - 1), + ) + curr_max_key_ = annotations_ht.index_globals().max_key_ + new_variants_ht = callset_ht.repartition( + # Repartition this join to improve performance + constrain( + callset_ht.n_partitions() * 100, + MIN_PARTITIONS, + MAX_PARTITIONS, + ), + ).anti_join(annotations_ht) + else: + curr_max_key_ = -1 + new_variants_ht = callset_ht + + # Annotate new variants with VEP. + # Note about the repartition: our work here is cpu/memory bound and + # proportional to the number of new variants. Our default partitioning + # will under-partition in that regard, so we split up our work + # with a partitioning scheme local to this task. + new_variants_count = new_variants_ht.count() + new_variants_ht = new_variants_ht.repartition( + constrain( + math.ceil(new_variants_count / VARIANTS_PER_VEP_PARTITION), + MIN_PARTITIONS, + MAX_PARTITIONS, + ), + ) + new_variants_ht = run_vep( + new_variants_ht, + self.dataset_type, + self.reference_genome, + ) + # Adding an arbitrary checkpoint here, seems to help + new_variants_ht, _ = checkpoint(new_variants_ht) + + # An additional call to "distinct()" as a safety measure. + # At least one case a duplicate variants has slipped through + # this method, with the best hypothesis being that + # the combination of VEP/repartition is potentially unsafe. + new_variants_ht = new_variants_ht.distinct() + + # Select down to the formatting annotations fields and + # any reference dataset collection annotations. + new_variants_ht = new_variants_ht.select( + **get_fields( + new_variants_ht, + self.dataset_type.formatting_annotation_fns(self.reference_genome), + **self.annotation_dependencies, + **self.param_kwargs, + ), + ) + + # Add serial integer index + new_variants_ht = new_variants_ht.add_index(name='key_') + new_variants_ht = new_variants_ht.transmute( + key_=new_variants_ht.key_ + curr_max_key_ + 1, + ) + new_variants_ht = annotate_formatting_annotation_enum_globals( + new_variants_ht, + self.reference_genome, + self.dataset_type, + ) + return new_variants_ht.annotate_globals( + updates={ + hl.Struct( + callset=self.callset_path, + project_guid=project_guid, + remap_pedigree_hash=remap_pedigree_hash( + project_pedigree_path( + self.reference_genome, + self.dataset_type, + self.sample_type, + project_guid, + ), + ), + ) + for project_guid in self.project_guids + }, + ) diff --git a/loading_pipeline/lib/tasks/write_postprocessed_callset.py b/loading_pipeline/lib/tasks/write_postprocessed_callset.py new file mode 100644 index 0000000000..d82258e98a --- /dev/null +++ b/loading_pipeline/lib/tasks/write_postprocessed_callset.py @@ -0,0 +1,96 @@ +import hail as hl +import luigi +import luigi.util + +from loading_pipeline.lib.misc.callsets import get_additional_row_fields +from loading_pipeline.lib.misc.io import ( + split_multi_hts, +) +from loading_pipeline.lib.misc.sv import deduplicate_merged_sv_concordance_calls +from loading_pipeline.lib.misc.vets import annotate_vets +from loading_pipeline.lib.paths import ( + imported_callset_path, + postprocessed_callset_path, + variant_annotations_table_path, +) +from loading_pipeline.lib.tasks.base.base_loading_run_params import BaseLoadingRunParams +from loading_pipeline.lib.tasks.base.base_write import BaseWriteTask +from loading_pipeline.lib.tasks.files import GCSorLocalTarget +from loading_pipeline.lib.tasks.write_imported_callset import WriteImportedCallsetTask +from loading_pipeline.lib.tasks.write_validation_errors_for_run import ( + with_persisted_validation_errors, +) + + +@luigi.util.inherits(BaseLoadingRunParams) +class WritePostprocessedCallsetTask(BaseWriteTask): + def complete(self) -> luigi.Target: + if super().complete(): + mt = hl.read_matrix_table(self.output().path) + # Handle case where callset was previously imported + # with a different sex/relatedness flag. + additional_row_fields = get_additional_row_fields( + mt, + self.reference_genome, + self.dataset_type, + self.skip_check_sex_and_relatedness, + ) + return all(hasattr(mt, field) for field in additional_row_fields) + return False + + def output(self) -> luigi.Target: + return GCSorLocalTarget( + postprocessed_callset_path( + self.reference_genome, + self.dataset_type, + self.callset_path, + ), + ) + + def requires(self) -> list[luigi.Task]: + return [self.clone(WriteImportedCallsetTask)] + + @with_persisted_validation_errors + def create_table(self) -> hl.MatrixTable: + mt = hl.read_matrix_table( + imported_callset_path( + self.reference_genome, + self.dataset_type, + self.callset_path, + ), + ) + + if self.dataset_type.has_multi_allelic_variants: + # NB: throws SeqrValidationError + mt = split_multi_hts( + mt, + 'validate_no_duplicate_variants' in self.validations_to_skip, + ) + if self.dataset_type.re_key_by_seqr_internal_truth_vid and hasattr( + mt, + 'info.SEQR_INTERNAL_TRUTH_VID', + ): + mt = deduplicate_merged_sv_concordance_calls( + mt, + hl.read_table( + variant_annotations_table_path( + self.reference_genome, + self.dataset_type, + ), + ), + ) + mt = mt.key_rows_by( + variant_id=hl.if_else( + hl.is_defined(mt['info.SEQR_INTERNAL_TRUTH_VID']), + mt['info.SEQR_INTERNAL_TRUTH_VID'], + mt.variant_id, + ), + ) + + # Special handling of variant-level filter annotation for VETs filters. + # The annotations are present on the sample-level FT field but are + # expected upstream on "filters". + mt = annotate_vets(mt) + return mt.select_globals( + callset_path=self.callset_path, + ) diff --git a/loading_pipeline/lib/tasks/write_relatedness_check_table.py b/loading_pipeline/lib/tasks/write_relatedness_check_table.py new file mode 100644 index 0000000000..579edc6f2f --- /dev/null +++ b/loading_pipeline/lib/tasks/write_relatedness_check_table.py @@ -0,0 +1,44 @@ +import hail as hl +import luigi +import luigi.util + +from loading_pipeline.lib.methods.relatedness import call_relatedness +from loading_pipeline.lib.paths import ( + relatedness_check_table_path, +) +from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset +from loading_pipeline.lib.tasks.base.base_loading_run_params import BaseLoadingRunParams +from loading_pipeline.lib.tasks.base.base_write import BaseWriteTask +from loading_pipeline.lib.tasks.files import GCSorLocalTarget +from loading_pipeline.lib.tasks.reference_data.updated_reference_dataset import ( + UpdatedReferenceDatasetTask, +) +from loading_pipeline.lib.tasks.validate_callset import ValidateCallsetTask + + +@luigi.util.inherits(BaseLoadingRunParams) +class WriteRelatednessCheckTableTask(BaseWriteTask): + def output(self) -> luigi.Target: + return GCSorLocalTarget( + relatedness_check_table_path( + self.reference_genome, + self.dataset_type, + self.callset_path, + ), + ) + + def requires(self): + return [ + self.clone(ValidateCallsetTask), + self.clone( + UpdatedReferenceDatasetTask, + reference_dataset=ReferenceDataset.gnomad_qc, + ), + ] + + def create_table(self) -> hl.Table: + callset_mt = hl.read_matrix_table(self.input()[0].path) + return call_relatedness( + callset_mt, + hl.read_table(self.input()[1].path) if len(self.input()) > 1 else None, + ) diff --git a/loading_pipeline/lib/tasks/write_relatedness_check_table_test.py b/loading_pipeline/lib/tasks/write_relatedness_check_table_test.py new file mode 100644 index 0000000000..7cc814a5fa --- /dev/null +++ b/loading_pipeline/lib/tasks/write_relatedness_check_table_test.py @@ -0,0 +1,120 @@ +import shutil +from unittest.mock import patch + +import hail as hl +import luigi.worker + +from loading_pipeline.lib.core import ( + DatasetType, + ReferenceGenome, + SampleType, +) +from loading_pipeline.lib.misc.io import import_vcf +from loading_pipeline.lib.paths import ( + postprocessed_callset_path, + relatedness_check_table_path, + valid_reference_dataset_path, +) +from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset +from loading_pipeline.lib.tasks.write_relatedness_check_table import ( + WriteRelatednessCheckTableTask, +) +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + +TEST_GNOMAD_QC_HT = ( + 'loading_pipeline/var/test/reference_datasets/GRCh38/gnomad_qc/1.0.ht' +) +TEST_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' +TEST_RUN_ID = 'manual__2024-04-03' + + +class WriteRelatednessCheckTableTaskTest(MockedDatarootTestCase): + def setUp(self) -> None: + super().setUp() + shutil.copytree( + TEST_GNOMAD_QC_HT, + valid_reference_dataset_path( + ReferenceGenome.GRCh38, + ReferenceDataset.gnomad_qc, + ), + ) + + # Force imported callset to be complete + ht = import_vcf(TEST_VCF, ReferenceGenome.GRCh38) + ht = ht.annotate_globals(validated_sample_type=SampleType.WGS.value) + ht = ht.annotate_rows(**{'info.AF': ht.info.AF}) + ht.write( + postprocessed_callset_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_VCF, + ), + ) + + def test_relatedness_check_table_task_gnomad_qc_updated( + self, + ) -> None: + self.assertEqual( + hl.eval( + hl.read_table( + valid_reference_dataset_path( + ReferenceGenome.GRCh38, + ReferenceDataset.gnomad_qc, + ), + ).version, + ), + '1.0', + ) + with ( + patch.object( + ReferenceDataset, + 'version', + return_value='2.0', + ), + patch.object( + ReferenceDataset, + 'get_ht', + lambda *_: hl.Table.parallelize( + [], + hl.tstruct( + locus=hl.tlocus('GRCh38'), + alleles=hl.tarray(hl.tstr), + ), + key=['locus', 'alleles'], + globals=hl.Struct(version='2.0'), + ), + ), + ): + worker = luigi.worker.Worker() + task = WriteRelatednessCheckTableTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id=TEST_RUN_ID, + sample_type=SampleType.WGS, + callset_path=TEST_VCF, + ) + worker.add(task) + worker.run() + self.assertTrue(task.complete()) + self.assertEqual( + hl.eval( + hl.read_table( + valid_reference_dataset_path( + ReferenceGenome.GRCh38, + ReferenceDataset.gnomad_qc, + ), + ).version, + ), + '2.0', + ) + ht = hl.read_table( + relatedness_check_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_VCF, + ), + ) + self.assertEqual( + ht.collect(), + [], + ) diff --git a/loading_pipeline/lib/tasks/write_relatedness_check_tsv.py b/loading_pipeline/lib/tasks/write_relatedness_check_tsv.py new file mode 100644 index 0000000000..07210e2620 --- /dev/null +++ b/loading_pipeline/lib/tasks/write_relatedness_check_tsv.py @@ -0,0 +1,29 @@ +import hail as hl +import luigi +import luigi.util + +from loading_pipeline.lib.paths import relatedness_check_tsv_path +from loading_pipeline.lib.tasks.base.base_loading_run_params import BaseLoadingRunParams +from loading_pipeline.lib.tasks.files import GCSorLocalTarget +from loading_pipeline.lib.tasks.write_relatedness_check_table import ( + WriteRelatednessCheckTableTask, +) + + +@luigi.util.inherits(BaseLoadingRunParams) +class WriteRelatednessCheckTsvTask(luigi.Task): + def output(self) -> luigi.Target: + return GCSorLocalTarget( + relatedness_check_tsv_path( + self.reference_genome, + self.dataset_type, + self.callset_path, + ), + ) + + def requires(self): + return [self.clone(WriteRelatednessCheckTableTask)] + + def run(self): + ht = hl.read_table(self.input()[0].path) + ht.export(self.output().path) diff --git a/loading_pipeline/lib/tasks/write_relatedness_check_tsv_test.py b/loading_pipeline/lib/tasks/write_relatedness_check_tsv_test.py new file mode 100644 index 0000000000..35a9956f78 --- /dev/null +++ b/loading_pipeline/lib/tasks/write_relatedness_check_tsv_test.py @@ -0,0 +1,53 @@ +import shutil + +import luigi.worker + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.paths import relatedness_check_table_path +from loading_pipeline.lib.tasks.write_relatedness_check_tsv import ( + WriteRelatednessCheckTsvTask, +) +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + +TEST_RELATEDNESS_CHECK_1 = ( + 'loading_pipeline/var/test/relatedness_check/test_relatedness_check_1.ht' +) +TEST_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' +TEST_RUN_ID = 'manual__2024-04-03' + + +class WriteRelatednessCheckTsvTaskTest(MockedDatarootTestCase): + def setUp(self) -> None: + super().setUp() + shutil.copytree( + TEST_RELATEDNESS_CHECK_1, + relatedness_check_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_VCF, + ), + ) + + def test_write_relatedness_check_tsv_task( + self, + ) -> None: + worker = luigi.worker.Worker() + task = WriteRelatednessCheckTsvTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + callset_path=TEST_VCF, + run_id=TEST_RUN_ID, + sample_type=SampleType.WES, + ) + worker.add(task) + worker.run() + self.assertTrue(task.complete()) + with task.output().open('r') as f: + lines = f.readlines() + expected_lines = [ + 'i\tj\tibd0\tibd1\tibd2\tpi_hat\n', + 'HG00731_1\tHG00733_1\t0\t1\t0\t5.0000e-01\n', + 'HG00732_1\tHG00733_1\t0\t1\t0\t5.0000e-01\n', + ] + for expected_line, actual_line in zip(expected_lines, lines, strict=False): + self.assertEqual(expected_line, actual_line) diff --git a/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py b/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py new file mode 100644 index 0000000000..403c9d78d5 --- /dev/null +++ b/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py @@ -0,0 +1,242 @@ +import hail as hl +import luigi +import luigi.util + +from loading_pipeline.lib.core.feature_flag import FeatureFlag +from loading_pipeline.lib.misc.family_loading_failures import ( + get_families_failed_imputed_sex_ploidy, + get_families_failed_missing_samples, + get_families_failed_relatedness_check, + get_families_failed_sex_check, +) +from loading_pipeline.lib.misc.io import ( + import_pedigree, + remap_pedigree_hash, +) +from loading_pipeline.lib.misc.pedigree import ( + parse_pedigree_ht_to_families, + parse_pedigree_ht_to_remap_ht, +) +from loading_pipeline.lib.misc.sample_ids import remap_sample_ids, subset_samples +from loading_pipeline.lib.misc.sv import overwrite_male_non_par_calls +from loading_pipeline.lib.misc.validation import SeqrValidationError +from loading_pipeline.lib.paths import ( + project_pedigree_path, + relatedness_check_table_path, + remapped_and_subsetted_callset_path, +) +from loading_pipeline.lib.tasks.base.base_loading_run_params import BaseLoadingRunParams +from loading_pipeline.lib.tasks.base.base_write import BaseWriteTask +from loading_pipeline.lib.tasks.files import GCSorLocalTarget, RawFileTask +from loading_pipeline.lib.tasks.validate_callset import ValidateCallsetTask +from loading_pipeline.lib.tasks.write_relatedness_check_tsv import ( + WriteRelatednessCheckTsvTask, +) +from loading_pipeline.lib.tasks.write_sex_check_table import WriteSexCheckTableTask +from loading_pipeline.lib.tasks.write_validation_errors_for_run import ( + with_persisted_validation_errors, +) + + +def format_failures(failed_families): + return { + f.family_guid: { + 'samples': sorted(f.samples.keys()), + 'reasons': reasons, + } + for f, reasons in failed_families.items() + } + + +@luigi.util.inherits(BaseLoadingRunParams) +class WriteRemappedAndSubsettedCallsetTask(BaseWriteTask): + project_i = luigi.IntParameter() + + def complete(self) -> luigi.Target: + if not super().complete(): + return False + mt = hl.read_matrix_table(self.output().path) + return bool( + hl.eval(mt.globals.family_samples), + ) and hl.eval( + mt.globals.remap_pedigree_hash + == remap_pedigree_hash( + project_pedigree_path( + self.reference_genome, + self.dataset_type, + self.sample_type, + self.project_guids[self.project_i], + ), + ), + ) + + def output(self) -> luigi.Target: + return GCSorLocalTarget( + remapped_and_subsetted_callset_path( + self.reference_genome, + self.dataset_type, + self.callset_path, + self.project_guids[self.project_i], + ), + ) + + def requires(self) -> list[luigi.Task]: + requirements = [ + self.clone(ValidateCallsetTask), + RawFileTask( + project_pedigree_path( + self.reference_genome, + self.dataset_type, + self.sample_type, + self.project_guids[self.project_i], + ), + ), + ] + if ( + FeatureFlag.CHECK_SEX_AND_RELATEDNESS + and self.dataset_type.check_sex_and_relatedness + and not self.skip_check_sex_and_relatedness + ): + requirements = [ + *requirements, + self.clone(WriteRelatednessCheckTsvTask), + self.clone(WriteSexCheckTableTask), + ] + return requirements + + @with_persisted_validation_errors + def create_table(self) -> hl.MatrixTable: + callset_mt = hl.read_matrix_table(self.input()[0].path) + pedigree_ht = import_pedigree(self.input()[1].path) + + # Remap, but only if the remap file is present! + remap_lookup = hl.empty_dict(hl.tstr, hl.tstr) + if 'remap_id' in pedigree_ht.row: + project_remap_ht = parse_pedigree_ht_to_remap_ht(pedigree_ht) + callset_mt = remap_sample_ids( + callset_mt, + project_remap_ht, + ) + remap_lookup = hl.dict( + {r.s: r.seqr_id for r in project_remap_ht.collect()}, + ) + + families = parse_pedigree_ht_to_families(pedigree_ht) + families_failed_missing_samples = get_families_failed_missing_samples( + callset_mt, + families, + ) + families_failed_relatedness_check = {} + families_failed_sex_check = {} + families_failed_imputed_sex_ploidy = {} + if ( + FeatureFlag.CHECK_SEX_AND_RELATEDNESS + and self.dataset_type.check_sex_and_relatedness + and not self.skip_check_sex_and_relatedness + ): + relatedness_check_ht = hl.read_table( + relatedness_check_table_path( + self.reference_genome, + self.dataset_type, + self.callset_path, + ), + ) + sex_check_ht = hl.read_table(self.input()[3].path) + families_failed_relatedness_check = get_families_failed_relatedness_check( + families - families_failed_missing_samples.keys(), + relatedness_check_ht, + remap_lookup, + ) + families_failed_imputed_sex_ploidy = get_families_failed_imputed_sex_ploidy( + families + - families_failed_missing_samples.keys() + - families_failed_relatedness_check.keys(), + callset_mt, + sex_check_ht, + ) + families_failed_sex_check = get_families_failed_sex_check( + families + - families_failed_missing_samples.keys() + - families_failed_relatedness_check.keys() + - families_failed_imputed_sex_ploidy.keys(), + sex_check_ht, + remap_lookup, + ) + + loadable_families = ( + families + - families_failed_missing_samples.keys() + - families_failed_relatedness_check.keys() + - families_failed_sex_check.keys() + - families_failed_imputed_sex_ploidy.keys() + ) + if not len(loadable_families): + msg = 'All families failed validation checks' + raise SeqrValidationError( + msg, + { + 'failed_family_samples': { + 'missing_samples': format_failures( + families_failed_missing_samples, + ), + 'relatedness_check': format_failures( + families_failed_relatedness_check, + ), + 'sex_check': format_failures(families_failed_sex_check), + 'ploidy_check': format_failures( + families_failed_imputed_sex_ploidy, + ), + }, + }, + ) + + mt = subset_samples( + callset_mt, + hl.Table.parallelize( + [ + {'s': sample_id} + for family in loadable_families + for sample_id in family.samples + ], + hl.tstruct(s=hl.dtype('str')), + key='s', + ), + ) + + if self.dataset_type.overwrite_male_non_par_calls: + mt = overwrite_male_non_par_calls(mt, loadable_families) + return mt.select_globals( + remap_pedigree_hash=remap_pedigree_hash( + project_pedigree_path( + self.reference_genome, + self.dataset_type, + self.sample_type, + self.project_guids[self.project_i], + ), + ), + family_samples=( + { + f.family_guid: sorted(f.samples.keys()) + for f in loadable_families + or hl.empty_dict(hl.tstr, hl.tarray(hl.tstr)) + } + ), + failed_family_samples=hl.Struct( + missing_samples=( + format_failures(families_failed_missing_samples) + or hl.empty_dict(hl.tstr, hl.tdict(hl.tstr, hl.tarray(hl.tstr))) + ), + relatedness_check=( + format_failures(families_failed_relatedness_check) + or hl.empty_dict(hl.tstr, hl.tdict(hl.tstr, hl.tarray(hl.tstr))) + ), + sex_check=( + format_failures(families_failed_sex_check) + or hl.empty_dict(hl.tstr, hl.tdict(hl.tstr, hl.tarray(hl.tstr))) + ), + ploidy_check=( + format_failures(families_failed_imputed_sex_ploidy) + or hl.empty_dict(hl.tstr, hl.tdict(hl.tstr, hl.tarray(hl.tstr))) + ), + ), + ) diff --git a/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset_test.py b/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset_test.py new file mode 100644 index 0000000000..590795424a --- /dev/null +++ b/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset_test.py @@ -0,0 +1,460 @@ +import json +import shutil +from unittest.mock import Mock, patch + +import hail as hl +import luigi.worker + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.misc.io import remap_pedigree_hash +from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS +from loading_pipeline.lib.paths import ( + relatedness_check_table_path, + sex_check_table_path, +) +from loading_pipeline.lib.tasks.write_remapped_and_subsetted_callset import ( + WriteRemappedAndSubsettedCallsetTask, +) +from loading_pipeline.lib.tasks.write_validation_errors_for_run import ( + UpdatedValidationErrorsForRunTask, +) +from loading_pipeline.lib.test.misc import copy_project_pedigree_to_mocked_dir +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + +TEST_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' +TEST_PEDIGREE_3_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_3_remap.tsv' +TEST_PEDIGREE_3_DIFFERENT_FAMILIES = ( + 'loading_pipeline/var/test/pedigrees/test_pedigree_3_different_families.tsv' +) +TEST_PEDIGREE_4_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_4_remap.tsv' +TEST_PEDIGREE_7 = 'loading_pipeline/var/test/pedigrees/test_pedigree_7.tsv' +TEST_SEX_CHECK_1 = 'loading_pipeline/var/test/sex_check/test_sex_check_1.ht' +TEST_RELATEDNESS_CHECK_1 = ( + 'loading_pipeline/var/test/relatedness_check/test_relatedness_check_1.ht' +) + +TEST_RUN_ID = 'manual__2024-04-03' + + +class WriteRemappedAndSubsettedCallsetTaskTest(MockedDatarootTestCase): + def setUp(self) -> None: + super().setUp() + # +-------------+---------------+ + # | s | predicted_sex | + # +-------------+---------------+ + # | str | str | + # +-------------+---------------+ + # | "HG00731_1" | "F" | + # | "HG00732_1" | "M" | + # | "HG00733_1" | "F" | + # | "NA19675_1" | "F" | + # | "NA19678_1" | "M" | + # | "NA19679_1" | "F" | + # | "NA20870_1" | "F" | + # | "NA20872_1" | "M" | + # | "NA20874_1" | "F" | + # | "NA20875_1" | "F" | + # | "NA20876_1" | "F" | + # | "NA20877_1" | "F" | + # | "NA20878_1" | "M" | + # | "NA20881_1" | "M" | + # | "NA20885_1" | "F" | + # | "NA20888_1" | "F" | + # +-------------+---------------+ + shutil.copytree( + TEST_SEX_CHECK_1, + sex_check_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_VCF, + ), + ) + # +-------------+-------------+-------+-------+-------+----------+ + # | i | j | ibd0 | ibd1 | ibd2 | pi_hat | + # +-------------+-------------+-------+-------+-------+----------+ + # | str | str | int32 | int32 | int32 | float64 | + # +-------------+-------------+-------+-------+-------+----------+ + # | "HG00731_1" | "HG00733_1" | 0 | 1 | 0 | 5.00e-01 | + # | "HG00732_1" | "HG00733_1" | 0 | 1 | 0 | 5.00e-01 | + # +-------------+-------------+-------+-------+-------+----------+ + shutil.copytree( + TEST_RELATEDNESS_CHECK_1, + relatedness_check_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_VCF, + ), + ) + + def test_write_remapped_and_subsetted_callset_task( + self, + ) -> None: + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_3_REMAP, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0113_test_project', + ) + worker = luigi.worker.Worker() + wrsc_task = WriteRemappedAndSubsettedCallsetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id=TEST_RUN_ID, + sample_type=SampleType.WGS, + callset_path=TEST_VCF, + project_guids=['R0113_test_project'], + project_i=0, + validations_to_skip=[ALL_VALIDATIONS], + skip_expect_tdr_metrics=True, + ) + worker.add(wrsc_task) + worker.run() + self.assertTrue(wrsc_task.complete()) + mt = hl.read_matrix_table(wrsc_task.output().path) + self.assertEqual(mt.count(), (30, 3)) + self.assertEqual( + mt.globals.collect(), + [ + hl.Struct( + remap_pedigree_hash=hl.eval( + remap_pedigree_hash( + TEST_PEDIGREE_3_REMAP, + ), + ), + failed_family_samples=hl.Struct( + missing_samples={}, + relatedness_check={}, + sex_check={}, + ploidy_check={}, + ), + family_samples={'abc_1': ['HG00731_1', 'HG00732_1', 'HG00733_1']}, + ), + ], + ) + + @patch( + 'loading_pipeline.lib.tasks.write_remapped_and_subsetted_callset.FeatureFlag', + ) + def test_write_remapped_and_subsetted_callset_task_failed_some_family_checks( + self, + mock_ff: Mock, + ) -> None: + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_4_REMAP, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0114_project4', + ) + mock_ff.CHECK_SEX_AND_RELATEDNESS = True + worker = luigi.worker.Worker() + wrsc_task = WriteRemappedAndSubsettedCallsetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id=TEST_RUN_ID, + sample_type=SampleType.WGS, + callset_path=TEST_VCF, + project_guids=['R0114_project4'], + project_i=0, + validations_to_skip=[ALL_VALIDATIONS], + skip_expect_tdr_metrics=True, + ) + worker.add(wrsc_task) + worker.run() + self.assertTrue(wrsc_task.complete()) + mt = hl.read_matrix_table(wrsc_task.output().path) + # NB: one "family"/"sample" has been removed because of a failed sex check, + # and 4 removed because of a failed ploidy check! + self.assertEqual(mt.count(), (30, 8)) + self.assertEqual( + mt.globals.collect(), + [ + hl.Struct( + remap_pedigree_hash=hl.eval( + remap_pedigree_hash( + TEST_PEDIGREE_4_REMAP, + ), + ), + family_samples={ + '123_1': ['NA19675_1'], + '345_1': ['NA19679_1'], + '456_1': ['NA20870_1'], + '678_1': ['NA20874_1'], + '789_1': ['NA20875_1'], + '890_1': ['NA20876_1'], + '901_1': ['NA20877_1'], + 'efg_1': ['NA20888_1'], + }, + failed_family_samples=hl.Struct( + missing_samples={}, + relatedness_check={}, + sex_check={ + 'def_1': { + 'reasons': [ + 'Sample NA20885_1 has pedigree sex M but imputed sex F', + ], + 'samples': ['NA20885_1'], + }, + }, + ploidy_check={ + '234_1': { + 'reasons': [ + "Found samples with misaligned ploidy with their provided imputed sex: ['NA19678_1']", + ], + 'samples': ['NA19678_1'], + }, + '567_1': { + 'reasons': [ + "Found samples with misaligned ploidy with their provided imputed sex: ['NA20872_1']", + ], + 'samples': ['NA20872_1'], + }, + 'bcd_1': { + 'reasons': [ + "Found samples with misaligned ploidy with their provided imputed sex: ['NA20878_1']", + ], + 'samples': ['NA20878_1'], + }, + 'cde_1': { + 'reasons': [ + "Found samples with misaligned ploidy with their provided imputed sex: ['NA20881_1']", + ], + 'samples': ['NA20881_1'], + }, + }, + ), + ), + ], + ) + + @patch( + 'loading_pipeline.lib.tasks.write_remapped_and_subsetted_callset.FeatureFlag', + ) + def test_write_remapped_and_subsetted_callset_task_all_families_failed( + self, + mock_ff: Mock, + ) -> None: + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_7, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0114_project4', + ) + mock_ff.CHECK_SEX_AND_RELATEDNESS = True + worker = luigi.worker.Worker() + wrsc_task = WriteRemappedAndSubsettedCallsetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id=TEST_RUN_ID, + sample_type=SampleType.WGS, + callset_path=TEST_VCF, + project_guids=['R0114_project4'], + project_i=0, + validations_to_skip=[ALL_VALIDATIONS], + skip_expect_tdr_metrics=True, + ) + worker.add(wrsc_task) + worker.run() + self.assertFalse(wrsc_task.complete()) + updated_validation_errors_task = UpdatedValidationErrorsForRunTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WES, + callset_path=TEST_VCF, + project_guids=['R0114_project4'], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + self.assertTrue(updated_validation_errors_task.complete()) + with updated_validation_errors_task.output().open('r') as f: + self.assertDictEqual( + json.load(f), + { + 'project_guids': ['R0114_project4'], + 'error_messages': ['All families failed validation checks'], + 'failed_family_samples': { + 'missing_samples': { + 'efg_1': { + 'samples': ['NA99999_1'], + 'reasons': ["Missing samples: {'NA99999_1'}"], + }, + }, + 'relatedness_check': {}, + 'sex_check': { + '890_1': { + 'samples': ['NA20876_1'], + 'reasons': [ + 'Sample NA20876_1 has pedigree sex M but imputed sex F', + ], + }, + '456_1': { + 'samples': ['NA20870_1'], + 'reasons': [ + 'Sample NA20870_1 has pedigree sex M but imputed sex F', + ], + }, + '123_1': { + 'samples': ['NA19675_1'], + 'reasons': [ + 'Sample NA19675_1 has pedigree sex M but imputed sex F', + ], + }, + '678_1': { + 'samples': ['NA20874_1'], + 'reasons': [ + 'Sample NA20874_1 has pedigree sex M but imputed sex F', + ], + }, + '789_1': { + 'samples': ['NA20875_1'], + 'reasons': [ + 'Sample NA20875_1 has pedigree sex M but imputed sex F', + ], + }, + '901_1': { + 'samples': ['NA20877_1'], + 'reasons': [ + 'Sample NA20877_1 has pedigree sex M but imputed sex F', + ], + }, + '345_1': { + 'samples': ['NA19679_1'], + 'reasons': [ + 'Sample NA19679_1 has pedigree sex M but imputed sex F', + ], + }, + 'def_1': { + 'samples': ['NA20885_1'], + 'reasons': [ + 'Sample NA20885_1 has pedigree sex M but imputed sex F', + ], + }, + }, + 'ploidy_check': { + '567_1': { + 'samples': ['NA20872_1'], + 'reasons': [ + "Found samples with misaligned ploidy with their provided imputed sex: ['NA20872_1']", + ], + }, + '234_1': { + 'samples': ['NA19678_1'], + 'reasons': [ + "Found samples with misaligned ploidy with their provided imputed sex: ['NA19678_1']", + ], + }, + 'bcd_1': { + 'samples': ['NA20878_1'], + 'reasons': [ + "Found samples with misaligned ploidy with their provided imputed sex: ['NA20878_1']", + ], + }, + 'cde_1': { + 'samples': ['NA20881_1'], + 'reasons': [ + "Found samples with misaligned ploidy with their provided imputed sex: ['NA20881_1']", + ], + }, + }, + }, + }, + ) + + @patch( + 'loading_pipeline.lib.tasks.write_remapped_and_subsetted_callset.FeatureFlag', + ) + def test_write_remapped_and_subsetted_callset_task_combined_validation_errors( + self, + mock_ff: Mock, + ) -> None: + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_3_DIFFERENT_FAMILIES, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0113_test_project', + ) + worker = luigi.worker.Worker() + + wrsc_task_1 = WriteRemappedAndSubsettedCallsetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id=TEST_RUN_ID, + sample_type=SampleType.WGS, + callset_path=TEST_VCF, + project_guids=['R0113_test_project'], + project_i=0, + validations_to_skip=[ALL_VALIDATIONS], + skip_expect_tdr_metrics=True, + ) + worker.add(wrsc_task_1) + worker.run() + + # Second run: load pedigree 7 where all families fail validation checks + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_7, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0114_project4', + ) + worker_2 = luigi.worker.Worker() + + wrsc_task_2 = WriteRemappedAndSubsettedCallsetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id=TEST_RUN_ID, + sample_type=SampleType.WGS, + callset_path=TEST_VCF, + project_guids=['R0114_project4'], + project_i=0, + validations_to_skip=[ALL_VALIDATIONS], + skip_expect_tdr_metrics=True, + ) + worker_2.add(wrsc_task_2) + worker_2.run() + + # Verify second task does not complete (all families failed) + self.assertFalse(wrsc_task_2.complete()) + + # Verify validation errors for second run + updated_validation_errors_task = UpdatedValidationErrorsForRunTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WES, + callset_path=TEST_VCF, + project_guids=['R0113_test_project', 'R0114_project4'], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + self.assertTrue(updated_validation_errors_task.complete()) + with updated_validation_errors_task.output().open('r') as f: + validation_errors = json.load(f) + + # Verify that all families failed in the second run + self.assertIn( + 'All families failed validation checks', + validation_errors['error_messages'], + ) + # Should have missing samples, sex checks, and ploidy checks all failing + failed_samples = validation_errors['failed_family_samples'] + self.assertGreater( + len(failed_samples['missing_samples']), + 0, + 'Expected missing_samples to have failures', + ) + self.assertGreater( + len(failed_samples['sex_check']), + 0, + 'Expected sex_check to have failures', + ) + self.assertGreater( + len(failed_samples['ploidy_check']), + 0, + 'Expected ploidy_check to have failures', + ) + # Verify that both project guids are in the validation errors + self.assertIn('R0113_test_project', validation_errors['project_guids']) + self.assertIn('R0114_project4', validation_errors['project_guids']) diff --git a/loading_pipeline/lib/tasks/write_sample_qc_json.py b/loading_pipeline/lib/tasks/write_sample_qc_json.py new file mode 100644 index 0000000000..e09c93086f --- /dev/null +++ b/loading_pipeline/lib/tasks/write_sample_qc_json.py @@ -0,0 +1,96 @@ +import json +from collections import defaultdict + +import hail as hl +import hailtop.fs as hfs +import luigi +import luigi.util +import onnx + +from loading_pipeline.lib.methods.sample_qc import call_sample_qc +from loading_pipeline.lib.misc.callsets import get_callset_mt +from loading_pipeline.lib.misc.io import checkpoint, import_tdr_qc_metrics +from loading_pipeline.lib.paths import ( + ancestry_model_rf_path, + sample_qc_json_path, + tdr_metrics_dir, +) +from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset +from loading_pipeline.lib.tasks.base.base_loading_run_params import BaseLoadingRunParams +from loading_pipeline.lib.tasks.files import GCSorLocalTarget, RawFileTask +from loading_pipeline.lib.tasks.reference_data.updated_reference_dataset import ( + UpdatedReferenceDatasetTask, +) +from loading_pipeline.lib.tasks.write_remapped_and_subsetted_callset import ( + WriteRemappedAndSubsettedCallsetTask, +) +from loading_pipeline.lib.tasks.write_tdr_metrics_files import WriteTDRMetricsFilesTask + + +@luigi.util.inherits(BaseLoadingRunParams) +class WriteSampleQCJsonTask(luigi.Task): + def output(self) -> luigi.Target: + return GCSorLocalTarget( + sample_qc_json_path( + self.reference_genome, + self.dataset_type, + self.callset_path, + ), + ) + + def requires(self): + remapped_and_subsetted_callsets = [ + self.clone( + WriteRemappedAndSubsettedCallsetTask, + project_i=i, + ) + for i in range(len(self.project_guids)) + ] + return [ + self.clone(WriteTDRMetricsFilesTask), + self.clone( + UpdatedReferenceDatasetTask, + reference_dataset=ReferenceDataset.gnomad_qc, + ), + RawFileTask(ancestry_model_rf_path()), + *remapped_and_subsetted_callsets, + ] + + def run(self): + callset_mt = get_callset_mt( + self.reference_genome, + self.dataset_type, + self.callset_path, + self.project_guids, + ) + callset_mt, _ = checkpoint(callset_mt) + tdr_metrics_ht = None + for tdr_metrics_file in hfs.ls( + tdr_metrics_dir(self.reference_genome, self.dataset_type), + ): + if not tdr_metrics_ht: + tdr_metrics_ht = import_tdr_qc_metrics(tdr_metrics_file.path) + continue + tdr_metrics_ht = tdr_metrics_ht.union( + import_tdr_qc_metrics(tdr_metrics_file.path), + ) + pop_pca_loadings_ht = hl.read_table(self.input()[1].path) + with hfs.open(self.input()[2].path, 'rb') as f: + ancestry_rf_model = onnx.load(f) + callset_mt = call_sample_qc( + callset_mt, + tdr_metrics_ht, + pop_pca_loadings_ht, + ancestry_rf_model, + self.sample_type, + ) + ht = callset_mt.cols() + sample_qc_dict = defaultdict(dict) + for row in ht.flatten().collect(): + r = dict(row) + sample_id = r.pop('s') + for field, value in r.items(): + sample_qc_dict[sample_id][field] = value + + with self.output().open('w') as f: + json.dump(sample_qc_dict, f) diff --git a/loading_pipeline/lib/tasks/write_sample_qc_json_test.py b/loading_pipeline/lib/tasks/write_sample_qc_json_test.py new file mode 100644 index 0000000000..1c2709c9b7 --- /dev/null +++ b/loading_pipeline/lib/tasks/write_sample_qc_json_test.py @@ -0,0 +1,269 @@ +import json +import os +import shutil +from unittest.mock import Mock, patch + +import hail as hl +import hailtop.fs as hfs +import luigi.worker + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS +from loading_pipeline.lib.paths import ancestry_model_rf_path, tdr_metrics_dir +from loading_pipeline.lib.tasks.write_sample_qc_json import WriteSampleQCJsonTask +from loading_pipeline.lib.test.misc import copy_project_pedigree_to_mocked_dir +from loading_pipeline.lib.test.mock_complete_task import MockCompleteTask +from loading_pipeline.lib.test.mocked_reference_datasets_testcase import ( + MockedReferenceDatasetsTestCase, +) + +TEST_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' +TEST_PEDIGREE_3_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_3_remap.tsv' +TEST_TDR_METRICS_FILE = 'loading_pipeline/var/test/tdr_metrics.tsv' +TEST_RUN_ID = 'manual__2024-04-03' + +PCA_SCORES = [0.00212, 0.011, 0.0105, 0.161, 0.026] + [0.1 for _ in range(15)] +EXPECTED_ANC_PROBABILITIES = { + 'prob_afr': 0.02, + 'prob_ami': 0.0, + 'prob_amr': 0.02, + 'prob_asj': 0.9, + 'prob_eas': 0.0, + 'prob_fin': 0.0, + 'prob_mid': 0.0, + 'prob_nfe': 0.05, + 'prob_sas': 0.01, +} +TEST_ANCESTRY_IMPUTATION_MODEL_PATH = ( + 'loading_pipeline/var/test/ancestry_imputation_model.onnx' +) + + +class WriteSampleQCJsonTaskTest(MockedReferenceDatasetsTestCase): + @patch('loading_pipeline.lib.methods.sample_qc.assign_population_pcs') + @patch('loading_pipeline.lib.methods.sample_qc.pc_project') + @patch('loading_pipeline.lib.tasks.write_sample_qc_json.WriteTDRMetricsFilesTask') + def test_call_sample_qc( + self, + mock_tdr_task: Mock, + mock_pc_project: Mock, + mock_assign_population_pcs: Mock, + ) -> None: + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_3_REMAP, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0113_test_project', + ) + os.makedirs( + os.path.dirname(ancestry_model_rf_path()), + exist_ok=True, + ) + shutil.copy2(TEST_ANCESTRY_IMPUTATION_MODEL_PATH, ancestry_model_rf_path()) + os.makedirs( + tdr_metrics_dir(ReferenceGenome.GRCh38, DatasetType.SNV_INDEL), + exist_ok=True, + ) + shutil.copy2( + TEST_TDR_METRICS_FILE, + tdr_metrics_dir(ReferenceGenome.GRCh38, DatasetType.SNV_INDEL), + ) + mock_tdr_task.return_value = MockCompleteTask() + mock_pc_project.return_value = hl.Table.parallelize( + [ + { + 's': sample_id, + 'scores': PCA_SCORES, + } + for sample_id in ('HG00731', 'HG00732', 'HG00733', 'NA19675') + ], + hl.tstruct( + s=hl.tstr, + scores=hl.tarray(hl.tfloat64), + ), + key='s', + ) + mock_assign_population_pcs.return_value = ( + hl.Table.parallelize( + [ + { + 's': sample_id, + 'pca_scores': PCA_SCORES, + 'qc_pop': 'asj', + **EXPECTED_ANC_PROBABILITIES, + } + for sample_id in ('HG00731', 'HG00732', 'HG00733', 'NA19675') + ], + hl.tstruct( + s=hl.tstr, + pca_scores=hl.tarray(hl.tfloat64), + qc_pop=hl.tstr, + prob_afr=hl.tfloat64, + prob_ami=hl.tfloat64, + prob_amr=hl.tfloat64, + prob_asj=hl.tfloat64, + prob_eas=hl.tfloat64, + prob_fin=hl.tfloat64, + prob_mid=hl.tfloat64, + prob_nfe=hl.tfloat64, + prob_sas=hl.tfloat64, + ), + key='s', + ), + None, + ) + worker = luigi.worker.Worker() + task = WriteSampleQCJsonTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id=TEST_RUN_ID, + sample_type=SampleType.WGS, + callset_path=TEST_VCF, + project_guids=['R0113_test_project'], + validations_to_skip=[ALL_VALIDATIONS], + ) + worker.add(task) + worker.run() + self.assertTrue(task) + self.assertTrue(hfs.exists(task.output().path)) + + expected_qc_gen_anc_results = { + 'pca_scores': PCA_SCORES, + **EXPECTED_ANC_PROBABILITIES, + **{f'pop_PC{i + 1}': PCA_SCORES[i] for i in range(20)}, + 'qc_gen_anc': 'oth', + } + with task.output().open('r') as f: + res = json.load(f) + + self.assertCountEqual( + res['HG00731_1'], + { + 'seqr_id': 'HG00731_1', + 'vcf_id': 'HG00731', + 'filtered_callrate': 1.0, + 'contamination_rate': 5.099999904632568, + 'percent_bases_at_20x': 93.69000244140625, + 'mean_coverage': 29.309999465942383, + 'filter_flags': ['contamination', 'coverage'], + **expected_qc_gen_anc_results, + 'sample_qc.call_rate': 0.9666666666666667, + 'sample_qc.n_called': 29, + 'sample_qc.n_not_called': 1, + 'sample_qc.n_filtered': 0, + 'sample_qc.n_hom_ref': 16, + 'sample_qc.n_het': 2, + 'sample_qc.n_hom_var': 11, + 'sample_qc.n_non_ref': 13, + 'sample_qc.n_singleton': 1, + 'sample_qc.n_snp': 24, + 'sample_qc.n_insertion': 0, + 'sample_qc.n_deletion': 0, + 'sample_qc.n_transition': 15, + 'sample_qc.n_transversion': 9, + 'sample_qc.n_star': 0, + 'sample_qc.r_ti_tv': 1.6666666666666667, + 'sample_qc.r_het_hom_var': 0.18181818181818182, + 'sample_qc.r_insertion_deletion': None, + 'sample_qc.f_inbreeding.f_stat': 0.284195245767986, + 'sample_qc.f_inbreeding.n_called': 29, + 'sample_qc.f_inbreeding.expected_homs': 26.20594199999999, + 'sample_qc.f_inbreeding.observed_homs': 27, + 'fail_n_snp': True, + 'fail_r_ti_tv': False, + 'fail_r_insertion_deletion': None, + 'fail_n_insertion': True, + 'fail_n_deletion': True, + 'fail_r_het_hom_var': False, + 'fail_call_rate': False, + 'qc_metrics_filters': ['n_deletion', 'n_insertion', 'n_snp'], + }, + ) + self.assertCountEqual( + res['HG00732_1'], + { + 'seqr_id': 'HG00732_1', + 'vcf_id': 'HG00732', + 'filtered_callrate': 1.0, + 'contamination_rate': 5.0, + 'percent_bases_at_20x': 90.0, + 'mean_coverage': 28.0, + 'filter_flags': ['coverage'], + **expected_qc_gen_anc_results, + 'sample_qc.call_rate': 0.9666666666666667, + 'sample_qc.n_called': 29, + 'sample_qc.n_not_called': 1, + 'sample_qc.n_filtered': 0, + 'sample_qc.n_hom_ref': 16, + 'sample_qc.n_het': 4, + 'sample_qc.n_hom_var': 9, + 'sample_qc.n_non_ref': 13, + 'sample_qc.n_singleton': 2, + 'sample_qc.n_snp': 22, + 'sample_qc.n_insertion': 0, + 'sample_qc.n_deletion': 0, + 'sample_qc.n_transition': 13, + 'sample_qc.n_transversion': 9, + 'sample_qc.n_star': 0, + 'sample_qc.r_ti_tv': 1.4444444444444444, + 'sample_qc.r_het_hom_var': 0.4444444444444444, + 'sample_qc.r_insertion_deletion': None, + 'sample_qc.f_inbreeding.f_stat': -0.431609508464028, + 'sample_qc.f_inbreeding.n_called': 29, + 'sample_qc.f_inbreeding.expected_homs': 26.20594199999999, + 'sample_qc.f_inbreeding.observed_homs': 25, + 'fail_n_snp': True, + 'fail_r_ti_tv': False, + 'fail_r_insertion_deletion': None, + 'fail_n_insertion': True, + 'fail_n_deletion': True, + 'fail_r_het_hom_var': False, + 'fail_call_rate': False, + 'qc_metrics_filters': ['n_deletion', 'n_insertion', 'n_snp'], + }, + ) + self.assertCountEqual( + res['HG00733_1'], + { + 'seqr_id': 'HG00733_1', + 'vcf_id': 'HG00733', + 'filtered_callrate': 1.0, + 'contamination_rate': 6.0, + 'percent_bases_at_20x': 85.0, + 'mean_coverage': 36.400001525878906, + 'filter_flags': ['contamination'], + **expected_qc_gen_anc_results, + 'sample_qc.call_rate': 1.0, + 'sample_qc.n_called': 30, + 'sample_qc.n_not_called': 0, + 'sample_qc.n_filtered': 0, + 'sample_qc.n_hom_ref': 17, + 'sample_qc.n_het': 3, + 'sample_qc.n_hom_var': 10, + 'sample_qc.n_non_ref': 13, + 'sample_qc.n_singleton': 0, + 'sample_qc.n_snp': 23, + 'sample_qc.n_insertion': 0, + 'sample_qc.n_deletion': 0, + 'sample_qc.n_transition': 13, + 'sample_qc.n_transversion': 10, + 'sample_qc.n_star': 0, + 'sample_qc.r_ti_tv': 1.3, + 'sample_qc.r_het_hom_var': 0.3, + 'sample_qc.r_insertion_deletion': None, + 'sample_qc.f_inbreeding.f_stat': -0.038400752079048056, + 'sample_qc.f_inbreeding.n_called': 30, + 'sample_qc.f_inbreeding.expected_homs': 27.11094199999999, + 'sample_qc.f_inbreeding.observed_homs': 27, + 'fail_n_snp': True, + 'fail_r_ti_tv': False, + 'fail_r_insertion_deletion': None, + 'fail_n_insertion': True, + 'fail_n_deletion': True, + 'fail_r_het_hom_var': False, + 'fail_call_rate': False, + 'qc_metrics_filters': ['n_deletion', 'n_insertion', 'n_snp'], + }, + ) + self.assertFalse('NA19675' in res) diff --git a/loading_pipeline/lib/tasks/write_sex_check_table.py b/loading_pipeline/lib/tasks/write_sex_check_table.py new file mode 100644 index 0000000000..38efea1b97 --- /dev/null +++ b/loading_pipeline/lib/tasks/write_sex_check_table.py @@ -0,0 +1,79 @@ +import hail as hl +import hailtop.fs as hfs +import luigi + +from loading_pipeline.lib.core.feature_flag import FeatureFlag +from loading_pipeline.lib.methods.sex_check import compute_sex_check_ht +from loading_pipeline.lib.misc.io import import_imputed_sex +from loading_pipeline.lib.paths import ( + imported_callset_path, + sex_check_table_path, + tdr_metrics_dir, +) +from loading_pipeline.lib.tasks.base.base_loading_run_params import BaseLoadingRunParams +from loading_pipeline.lib.tasks.base.base_write import BaseWriteTask +from loading_pipeline.lib.tasks.files import GCSorLocalTarget +from loading_pipeline.lib.tasks.write_postprocessed_callset import ( + WritePostprocessedCallsetTask, +) +from loading_pipeline.lib.tasks.write_tdr_metrics_files import WriteTDRMetricsFilesTask + + +@luigi.util.inherits(BaseLoadingRunParams) +class WriteSexCheckTableTask(BaseWriteTask): + callset_path = luigi.Parameter() + + @property + def predicted_sex_from_tdr(self): + # complicated enough to need a helper :/ + return ( + FeatureFlag.EXPECT_TDR_METRICS + and not self.skip_expect_tdr_metrics + and self.dataset_type.expect_tdr_metrics( + self.reference_genome, + ) + ) + + def output(self) -> luigi.Target: + return GCSorLocalTarget( + sex_check_table_path( + self.reference_genome, + self.dataset_type, + self.callset_path, + ), + ) + + def requires(self) -> list[luigi.Task]: + requirements = [] + if self.predicted_sex_from_tdr: + requirements = [ + *requirements, + self.clone(WriteTDRMetricsFilesTask), + ] + else: + requirements = [ + *requirements, + self.clone(WritePostprocessedCallsetTask), + ] + return requirements + + def create_table(self) -> hl.Table: + ht = None + if self.predicted_sex_from_tdr: + for tdr_metrics_file in hfs.ls( + tdr_metrics_dir(self.reference_genome, self.dataset_type), + ): + if not ht: + ht = import_imputed_sex(tdr_metrics_file.path) + continue + ht = ht.union(import_imputed_sex(tdr_metrics_file.path)) + else: + mt = hl.read_matrix_table( + imported_callset_path( + self.reference_genome, + self.dataset_type, + self.callset_path, + ), + ) + ht = compute_sex_check_ht(mt) + return ht diff --git a/loading_pipeline/lib/tasks/write_sex_check_table_test.py b/loading_pipeline/lib/tasks/write_sex_check_table_test.py new file mode 100644 index 0000000000..1f83d8c991 --- /dev/null +++ b/loading_pipeline/lib/tasks/write_sex_check_table_test.py @@ -0,0 +1,157 @@ +from decimal import Decimal +from unittest.mock import Mock, patch + +import google.cloud.bigquery +import hail as hl +import luigi.worker + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.paths import sex_check_table_path, tdr_metrics_path +from loading_pipeline.lib.tasks.write_sex_check_table import ( + WriteSexCheckTableTask, +) +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + +TEST_SEX_AND_RELATEDNESS_CALLSET_MT = ( + 'loading_pipeline/var/test/callsets/sex_and_relatedness_1.mt' +) + + +class WriteSexCheckTableTaskTest(MockedDatarootTestCase): + @patch('loading_pipeline.lib.tasks.write_tdr_metrics_files.gen_bq_table_names') + @patch('loading_pipeline.lib.tasks.write_tdr_metrics_file.bq_metrics_query') + @patch( + 'loading_pipeline.lib.tasks.write_sex_check_table.FeatureFlag', + ) + def test_snv_sex_check_table_task( + self, + mock_ff: Mock, + mock_bq_metrics_query: Mock, + mock_gen_bq_table_names: Mock, + ) -> None: + mock_ff.EXPECT_TDR_METRICS = True + mock_gen_bq_table_names.return_value = [ + 'datarepo-7242affb.datarepo_RP_3053', + 'datarepo-5a72e31b.datarepo_RP_3056', + ] + mock_bq_metrics_query.side_effect = [ + iter( + [ + google.cloud.bigquery.table.Row( + ( + 'SM-NJ8MF', + 'Unknown', + Decimal('0'), + Decimal('0'), + Decimal('0'), + ), + { + 'collaborator_sample_id': 0, + 'predicted_sex': 1, + 'contamination_rate': 2, + 'percent_bases_at_20x': 3, + 'mean_coverage': 4, + }, + ), + google.cloud.bigquery.table.Row( + ( + 'SM-MWOGC', + 'Female', + Decimal('0'), + Decimal('0'), + Decimal('0'), + ), + { + 'collaborator_sample_id': 0, + 'predicted_sex': 1, + 'contamination_rate': 2, + 'percent_bases_at_20x': 3, + 'mean_coverage': 4, + }, + ), + google.cloud.bigquery.table.Row( + ('SM-MWKWL', 'Male', Decimal('0'), Decimal('0'), Decimal('0')), + { + 'collaborator_sample_id': 0, + 'predicted_sex': 1, + 'contamination_rate': 2, + 'percent_bases_at_20x': 3, + 'mean_coverage': 4, + }, + ), + ], + ), + iter( + [ + google.cloud.bigquery.table.Row( + ('SM-NGE65', 'Male', Decimal('0'), Decimal('0'), Decimal('0')), + { + 'collaborator_sample_id': 0, + 'predicted_sex': 1, + 'contamination_rate': 2, + 'percent_bases_at_20x': 3, + 'mean_coverage': 4, + }, + ), + google.cloud.bigquery.table.Row( + ('SM-NGE5G', 'Male', Decimal('0'), Decimal('0'), Decimal('0')), + { + 'collaborator_sample_id': 0, + 'predicted_sex': 1, + 'contamination_rate': 2, + 'percent_bases_at_20x': 3, + 'mean_coverage': 4, + }, + ), + google.cloud.bigquery.table.Row( + ('SM-NC6LM', 'Male', Decimal('0'), Decimal('0'), Decimal('0')), + { + 'collaborator_sample_id': 0, + 'predicted_sex': 1, + 'contamination_rate': 2, + 'percent_bases_at_20x': 3, + 'mean_coverage': 4, + }, + ), + ], + ), + ] + worker = luigi.worker.Worker() + write_sex_check_table = WriteSexCheckTableTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path='na', + project_guids=['R0113_test_project'], + run_id='manual__2024-04-03', + ) + worker.add(write_sex_check_table) + worker.run() + self.assertTrue(write_sex_check_table.complete()) + sex_check_ht = hl.read_table( + sex_check_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + 'na', + ), + ) + self.assertEqual( + sex_check_ht.collect(), + [ + hl.Struct(s='SM-MWKWL', predicted_sex='M'), + hl.Struct(s='SM-MWOGC', predicted_sex='F'), + hl.Struct(s='SM-NC6LM', predicted_sex='M'), + hl.Struct(s='SM-NGE5G', predicted_sex='M'), + hl.Struct(s='SM-NGE65', predicted_sex='M'), + hl.Struct(s='SM-NJ8MF', predicted_sex='U'), + ], + ) + # Check underlying tdr metrics file. + with open( + tdr_metrics_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + 'datarepo-5a72e31b.datarepo_RP_3056', + ), + ) as f: + self.assertTrue('collaborator_sample_id' in f.read()) diff --git a/loading_pipeline/lib/tasks/write_success_file.py b/loading_pipeline/lib/tasks/write_success_file.py new file mode 100644 index 0000000000..50d92b7bb4 --- /dev/null +++ b/loading_pipeline/lib/tasks/write_success_file.py @@ -0,0 +1,38 @@ +import luigi +import luigi.util + +from loading_pipeline.lib.core.feature_flag import FeatureFlag +from loading_pipeline.lib.paths import pipeline_run_success_file_path +from loading_pipeline.lib.tasks.base.base_loading_run_params import ( + BaseLoadingRunParams, +) +from loading_pipeline.lib.tasks.dataproc.run_pipeline_on_dataproc import ( + RunPipelineOnDataprocTask, +) +from loading_pipeline.lib.tasks.files import GCSorLocalTarget +from loading_pipeline.lib.tasks.run_pipeline import RunPipelineTask + + +@luigi.util.inherits(BaseLoadingRunParams) +class WriteSuccessFileTask(luigi.Task): + attempt_id = luigi.IntParameter() + + def output(self) -> luigi.Target: + return GCSorLocalTarget( + pipeline_run_success_file_path( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + ) + + def requires(self) -> luigi.Task: + return ( + self.clone(RunPipelineOnDataprocTask, attempt_id=self.attempt_id) + if FeatureFlag.RUN_PIPELINE_ON_DATAPROC + else self.clone(RunPipelineTask, attempt_id=self.attempt_id) + ) + + def run(self): + with self.output().open('w') as f: + f.write('') diff --git a/loading_pipeline/lib/tasks/write_success_file_test.py b/loading_pipeline/lib/tasks/write_success_file_test.py new file mode 100644 index 0000000000..f33a5d337e --- /dev/null +++ b/loading_pipeline/lib/tasks/write_success_file_test.py @@ -0,0 +1,34 @@ +from unittest import mock + +import luigi.worker + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.tasks.write_success_file import WriteSuccessFileTask +from loading_pipeline.lib.test.mock_complete_task import MockCompleteTask +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + + +class WriteSuccessFileTaskTest(MockedDatarootTestCase): + @mock.patch( + 'loading_pipeline.lib.tasks.write_success_file.RunPipelineTask', + ) + def test_write_success_file_task( + self, + mock_run_pipeline_task: mock.Mock, + ) -> None: + mock_run_pipeline_task.return_value = MockCompleteTask() + worker = luigi.worker.Worker() + write_success_file = WriteSuccessFileTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path='test_callset', + project_guids=['R0113_test_project'], + run_id='manual__2024-04-03', + attempt_id=0, + ) + worker.add(write_success_file) + worker.run() + self.assertTrue(write_success_file.complete()) + with open(write_success_file.output().path) as f: + self.assertEqual(f.read(), '') diff --git a/loading_pipeline/lib/tasks/write_tdr_metrics_file.py b/loading_pipeline/lib/tasks/write_tdr_metrics_file.py new file mode 100644 index 0000000000..9beefe4932 --- /dev/null +++ b/loading_pipeline/lib/tasks/write_tdr_metrics_file.py @@ -0,0 +1,42 @@ +import csv + +import google.api_core.exceptions +import luigi +import luigi.util + +from loading_pipeline.lib.logger import get_logger +from loading_pipeline.lib.misc.terra_data_repository import ( + BIGQUERY_METRICS, + bq_metrics_query, +) +from loading_pipeline.lib.paths import tdr_metrics_path +from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( + BaseLoadingPipelineParams, +) +from loading_pipeline.lib.tasks.files import GCSorLocalTarget + +logger = get_logger(__name__) + + +@luigi.util.inherits(BaseLoadingPipelineParams) +class WriteTDRMetricsFileTask(luigi.Task): + bq_table_name = luigi.Parameter() + + def output(self) -> luigi.Target: + return GCSorLocalTarget( + tdr_metrics_path( + self.reference_genome, + self.dataset_type, + self.bq_table_name, + ), + ) + + def run(self): + with self.output().open('w') as f: + writer = csv.DictWriter(f, fieldnames=BIGQUERY_METRICS, delimiter='\t') + writer.writeheader() + try: + for row in bq_metrics_query(self.bq_table_name): + writer.writerow(row) + except google.api_core.exceptions.BadRequest: + logger.exception('Query Failed') diff --git a/loading_pipeline/lib/tasks/write_tdr_metrics_files.py b/loading_pipeline/lib/tasks/write_tdr_metrics_files.py new file mode 100644 index 0000000000..488d466c98 --- /dev/null +++ b/loading_pipeline/lib/tasks/write_tdr_metrics_files.py @@ -0,0 +1,28 @@ +import luigi +import luigi.util + +from loading_pipeline.lib.misc.terra_data_repository import gen_bq_table_names +from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( + BaseLoadingPipelineParams, +) +from loading_pipeline.lib.tasks.write_tdr_metrics_file import WriteTDRMetricsFileTask + + +@luigi.util.inherits(BaseLoadingPipelineParams) +class WriteTDRMetricsFilesTask(luigi.Task): + def __init__(self, *args, **kwargs): + super().__init__(*args, **kwargs) + self.dynamic_write_tdr_metrics_file_task = set() + + def complete(self) -> bool: + return len(self.dynamic_write_tdr_metrics_file_task) >= 1 and all( + write_tdr_metrics_file_task.complete() + for write_tdr_metrics_file_task in self.dynamic_write_tdr_metrics_file_task + ) + + def run(self): + for bq_table_name in gen_bq_table_names(): + self.dynamic_write_tdr_metrics_file_task.add( + self.clone(WriteTDRMetricsFileTask, bq_table_name=bq_table_name), + ) + yield self.dynamic_write_tdr_metrics_file_task diff --git a/loading_pipeline/lib/tasks/write_validation_errors_for_run.py b/loading_pipeline/lib/tasks/write_validation_errors_for_run.py new file mode 100644 index 0000000000..c8d4d2b238 --- /dev/null +++ b/loading_pipeline/lib/tasks/write_validation_errors_for_run.py @@ -0,0 +1,128 @@ +import json +from collections.abc import Callable + +import luigi +import luigi.freezing +import luigi.util + +from loading_pipeline.lib.misc.validation import SeqrValidationError +from loading_pipeline.lib.paths import validation_errors_for_run_path +from loading_pipeline.lib.tasks.base.base_loading_run_params import BaseLoadingRunParams +from loading_pipeline.lib.tasks.files import GCSorLocalTarget + + +def _deep_merge_dicts(existing: dict, new: dict) -> dict: + """Recursively merge new dict into existing dict.""" + result = existing.copy() + for key, new_value in new.items(): + if ( + key in result + and isinstance(result[key], dict) + and isinstance(new_value, dict) + ): + result[key] = _deep_merge_dicts(result[key], new_value) + else: + result[key] = new_value + return result + + +@luigi.util.inherits(BaseLoadingRunParams) +class UpdatedValidationErrorsForRunTask(luigi.Task): + project_guids = luigi.ListParameter() + error_messages = luigi.ListParameter(default=[]) + error_body = luigi.DictParameter(default={}) + + def complete(self) -> bool: + """Check if all input project_guids and error_messages are contained in the output.""" + output_path = self.output() + if not output_path.exists(): + return False + + with output_path.open('r') as f: + data = json.load(f) + + output_project_guids = set(data.get('project_guids', [])) + output_error_messages = set(data.get('error_messages', [])) + + input_project_guids = set(self.project_guids) + input_error_messages = set(self.error_messages) + + # Check if all input items are in output + return input_project_guids.issubset( + output_project_guids, + ) and input_error_messages.issubset(output_error_messages) + + def to_single_error_message(self) -> str: + with self.output().open('r') as f: + error_messages = json.load(f)['error_messages'] + if len(error_messages) == 1: + return error_messages[0] + return f'Multiple validation errors encountered: {error_messages}' + + def output(self) -> luigi.Target: + return GCSorLocalTarget( + validation_errors_for_run_path( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + ) + + def run(self) -> None: + output_path = self.output() + + # Load existing data if file exists + existing_data = {} + if output_path.exists(): + with output_path.open('r') as f: + existing_data = json.load(f) + + # Append new project_guids to existing ones and deduplicate while preserving order + project_guids = list( + dict.fromkeys( + existing_data.get('project_guids', []) + list(self.project_guids), + ), + ) + + # Append new error_messages to existing ones and deduplicate while preserving order + error_messages = list( + dict.fromkeys( + existing_data.get('error_messages', []) + list(self.error_messages), + ), + ) + + # Merge error_body with new data recursively + error_body = _deep_merge_dicts( + { + k: v + for k, v in existing_data.items() + if k not in ('project_guids', 'error_messages') + }, + luigi.freezing.recursively_unfreeze(self.error_body), + ) + + validation_errors_json = { + 'project_guids': project_guids, + 'error_messages': error_messages, + **error_body, + } + with output_path.open('w') as f: + json.dump(validation_errors_json, f) + + +def with_persisted_validation_errors(f: Callable) -> Callable[[Callable], Callable]: + def wrapper(self: luigi.Task): + try: + return f(self) + except SeqrValidationError as e: + updated_validation_errors_for_run_task = self.clone( + UpdatedValidationErrorsForRunTask, + error_messages=[e.msg], + error_body=e.error_body, + ) + updated_validation_errors_for_run_task.run() + raise SeqrValidationError( + updated_validation_errors_for_run_task.to_single_error_message(), + ) from None + + return wrapper diff --git a/loading_pipeline/lib/tasks/write_variant_annotations_vcf.py b/loading_pipeline/lib/tasks/write_variant_annotations_vcf.py new file mode 100644 index 0000000000..bda611824e --- /dev/null +++ b/loading_pipeline/lib/tasks/write_variant_annotations_vcf.py @@ -0,0 +1,49 @@ +import hail as hl +import hailtop.fs as hfs +import luigi + +from loading_pipeline.lib.annotations.fields import get_fields +from loading_pipeline.lib.paths import ( + variant_annotations_table_path, + variant_annotations_vcf_path, +) +from loading_pipeline.lib.tasks.base.base_loading_run_params import BaseLoadingRunParams +from loading_pipeline.lib.tasks.files import GCSorLocalTarget + + +@luigi.util.inherits(BaseLoadingRunParams) +class WriteVariantAnnotationsVCF(luigi.Task): + def output(self) -> luigi.Target: + return GCSorLocalTarget( + variant_annotations_vcf_path( + self.reference_genome, + self.dataset_type, + ), + ) + + def complete(self) -> bool: + return not self.dataset_type.should_export_to_vcf + + def run(self) -> None: + if not hfs.exists( + variant_annotations_table_path( + self.reference_genome, + self.dataset_type, + ), + ): + return + ht = hl.read_table( + variant_annotations_table_path( + self.reference_genome, + self.dataset_type, + ), + ) + ht = ht.annotate( + **get_fields( + ht, + self.dataset_type.export_vcf_annotation_fns, + **self.param_kwargs, + ), + ) + ht = ht.key_by('locus', 'alleles') + hl.export_vcf(ht, self.output().path, tabix=True) diff --git a/loading_pipeline/lib/tasks/write_variant_annotations_vcf_test.py b/loading_pipeline/lib/tasks/write_variant_annotations_vcf_test.py new file mode 100644 index 0000000000..4bad466b67 --- /dev/null +++ b/loading_pipeline/lib/tasks/write_variant_annotations_vcf_test.py @@ -0,0 +1,91 @@ +import gzip +from unittest.mock import Mock, patch + +import hailtop.fs as hfs +import luigi.worker + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS +from loading_pipeline.lib.tasks.update_variant_annotations_table_with_new_variants import ( + UpdateVariantAnnotationsTableWithNewVariantsTask, +) +from loading_pipeline.lib.tasks.write_variant_annotations_vcf import ( + WriteVariantAnnotationsVCF, +) +from loading_pipeline.lib.test.misc import copy_project_pedigree_to_mocked_dir +from loading_pipeline.lib.test.mocked_reference_datasets_testcase import ( + MockedReferenceDatasetsTestCase, +) + +TEST_SV_VCF = 'loading_pipeline/var/test/callsets/sv_1.vcf' +TEST_PEDIGREE_5 = 'loading_pipeline/var/test/pedigrees/test_pedigree_5.tsv' + +GENE_ID_MAPPING = { + 'OR4F5': 'ENSG00000186092', + 'PLEKHG4B': 'ENSG00000153404', + 'OR4F16': 'ENSG00000186192', + 'OR4F29': 'ENSG00000284733', + 'FBXO28': 'ENSG00000143756', + 'SAMD11': 'ENSG00000187634', + 'C1orf174': 'ENSG00000198912', + 'TAS1R1': 'ENSG00000173662', + 'FAM131C': 'ENSG00000185519', + 'RCC2': 'ENSG00000179051', + 'NBPF3': 'ENSG00000142794', + 'AGBL4': 'ENSG00000186094', + 'KIAA1614': 'ENSG00000135835', + 'MR1': 'ENSG00000153029', + 'STX6': 'ENSG00000135823', + 'XPR1': 'ENSG00000143324', +} + + +class WriteVariantAnnotationsVCFTest(MockedReferenceDatasetsTestCase): + @patch( + 'loading_pipeline.lib.tasks.write_new_variants_table.load_gencode_gene_symbol_to_gene_id', + ) + def test_sv_export_vcf( + self, + mock_load_gencode: Mock, + ) -> None: + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_5, + ReferenceGenome.GRCh38, + DatasetType.SV, + SampleType.WGS, + 'R0115_test_project2', + ) + mock_load_gencode.return_value = GENE_ID_MAPPING + worker = luigi.worker.Worker() + update_variant_annotations_task = ( + UpdateVariantAnnotationsTableWithNewVariantsTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SV, + run_id='run_id1', + sample_type=SampleType.WGS, + callset_path=TEST_SV_VCF, + project_guids=['R0115_test_project2'], + validations_to_skip=[ALL_VALIDATIONS], + skip_expect_tdr_metrics=True, + ) + ) + worker.add(update_variant_annotations_task) + worker.run() + self.assertTrue(update_variant_annotations_task.complete()) + write_variant_annotations_vcf_task = WriteVariantAnnotationsVCF( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SV, + run_id='run_id1', + sample_type=SampleType.WGS, + callset_path=TEST_SV_VCF, + ) + worker.add(write_variant_annotations_vcf_task) + worker.run() + self.assertTrue( + hfs.exists( + write_variant_annotations_vcf_task.output().path, + ), + ) + with hfs.open(write_variant_annotations_vcf_task.output().path, 'rb') as f: + buf = f.read() + self.assertTrue(gzip.decompress(buf).startswith(b'##fileformat=VCFv4.2')) diff --git a/loading_pipeline/lib/test/__init__.py b/loading_pipeline/lib/test/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/loading_pipeline/lib/test/clickhouse_schema_testcase.py b/loading_pipeline/lib/test/clickhouse_schema_testcase.py new file mode 100644 index 0000000000..fc26f8cc64 --- /dev/null +++ b/loading_pipeline/lib/test/clickhouse_schema_testcase.py @@ -0,0 +1,127 @@ +import unittest + +from loading_pipeline.lib.core import Env +from loading_pipeline.lib.misc.clickhouse import ( + STAGING_CLICKHOUSE_DATABASE, + get_clickhouse_client, +) + +TEST_SCHEMA = 'loading_pipeline/var/test/test_clickhouse_schema.sql' + + +class ClickhouseSchemaTestCase(unittest.TestCase): + def setUp(self): + super().setUp() + client = get_clickhouse_client() + client.execute( + f""" + DROP DATABASE IF EXISTS {STAGING_CLICKHOUSE_DATABASE}; + """, + ) + client.execute( + f""" + DROP DATABASE IF EXISTS {Env.CLICKHOUSE_DATABASE}; + """, + ) + client.execute( + f""" + CREATE DATABASE {Env.CLICKHOUSE_DATABASE}; + """, + ) + client = get_clickhouse_client(database=Env.CLICKHOUSE_DATABASE) + client.execute( + """ + CREATE DICTIONARY seqrdb_gene_ids + ( + `gene_id` String, + `seqrdb_id` String, + `affected` String + ) + PRIMARY KEY gene_id + SOURCE(NULL()) + LIFETIME(0) + LAYOUT(HASHED()) + """, + ) + client.execute( + """ + CREATE DICTIONARY seqrdb_affected_status_dict + ( + `family_guid` String, + `sampleId` String, + `affected` String + ) + PRIMARY KEY family_guid, sampleId + SOURCE(NULL()) + LIFETIME(0) + LAYOUT(COMPLEX_KEY_HASHED()) + """, + ) + client.execute( + """ + CREATE DICTIONARY `GRCh38/SNV_INDEL/project_partitions_dict` + ( + `project_guid` String, + `n_partitions` UInt32 + ) + PRIMARY KEY project_guid + SOURCE(NULL()) + LIFETIME(0) + LAYOUT(COMPLEX_KEY_HASHED()) + """, + ) + client.execute( + """ + CREATE DICTIONARY `GRCh38/SNV_INDEL/reference_data/gnomad_genomes` + ( + `key` UInt32, + `filter_af` Decimal(9, 8) + ) + PRIMARY KEY key + SOURCE(NULL()) + LIFETIME(0) + LAYOUT(COMPLEX_KEY_HASHED()) + """, + ) + with open(TEST_SCHEMA) as f: + sql = f.read() + commands = [cmd.strip() for cmd in sql.split(';') if cmd.strip()] + for cmd in commands: + client.execute(cmd) + client.execute( + f""" + CREATE DICTIONARY `GRCh38/SNV_INDEL/gt_stats_dict` + ( + `key` UInt32, + `ac_wes` UInt64, + `ac_wgs` UInt64, + `ac_affected` UInt64, + `hom_wes` UInt64, + `hom_wgs` UInt64, + `hom_affected` UInt64 + ) + PRIMARY KEY key + SOURCE( + CLICKHOUSE( + USER {Env.CLICKHOUSE_WRITER_USER} PASSWORD {Env.CLICKHOUSE_WRITER_PASSWORD} + DB {Env.CLICKHOUSE_DATABASE} TABLE `GRCh38/SNV_INDEL/gt_stats` + ) + ) + LIFETIME(0) + LAYOUT(FLAT(MAX_ARRAY_SIZE 1000000000)) + """, + ) + + def tearDown(self): + super().tearDown() + client = get_clickhouse_client() + client.execute( + f""" + DROP DATABASE IF EXISTS {STAGING_CLICKHOUSE_DATABASE}; + """, + ) + client.execute( + f""" + DROP DATABASE IF EXISTS {Env.CLICKHOUSE_DATABASE}; + """, + ) diff --git a/loading_pipeline/lib/test/misc.py b/loading_pipeline/lib/test/misc.py new file mode 100644 index 0000000000..3f21bab165 --- /dev/null +++ b/loading_pipeline/lib/test/misc.py @@ -0,0 +1,46 @@ +import os +import shutil + +import numpy as np + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.paths import project_pedigree_path + + +def convert_ndarray_to_list(obj): + if isinstance(obj, np.ndarray): + return [convert_ndarray_to_list(item) for item in obj.tolist()] + if isinstance(obj, dict): + return {k: convert_ndarray_to_list(v) for k, v in obj.items()} + if isinstance(obj, list): + return [convert_ndarray_to_list(item) for item in obj] + return obj + + +def copy_project_pedigree_to_mocked_dir( + pedigree_path: str, + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + sample_type: SampleType, + project_guid: str, +): + os.makedirs( + os.path.dirname( + project_pedigree_path( + reference_genome, + dataset_type, + sample_type, + project_guid, + ), + ), + exist_ok=True, + ) + shutil.copy2( + pedigree_path, + project_pedigree_path( + reference_genome, + dataset_type, + sample_type, + project_guid, + ), + ) diff --git a/loading_pipeline/lib/test/mock_complete_task.py b/loading_pipeline/lib/test/mock_complete_task.py new file mode 100644 index 0000000000..5740df9678 --- /dev/null +++ b/loading_pipeline/lib/test/mock_complete_task.py @@ -0,0 +1,6 @@ +import luigi + + +class MockCompleteTask(luigi.Task): + def complete(self): + return True diff --git a/loading_pipeline/lib/test/mocked_dataroot_testcase.py b/loading_pipeline/lib/test/mocked_dataroot_testcase.py new file mode 100644 index 0000000000..204b3225a4 --- /dev/null +++ b/loading_pipeline/lib/test/mocked_dataroot_testcase.py @@ -0,0 +1,27 @@ +import os +import shutil +import tempfile +import unittest +from unittest.mock import patch + +from loading_pipeline.lib.core import Env + + +class MockedDatarootTestCase(unittest.TestCase): + def setUp(self) -> None: + super().setUp() + patcher = patch( + 'loading_pipeline.lib.paths.Env', + wraps=Env, + ) # wraps to ensure other attributes behave as they are. + self.mock_env = patcher.start() + self.addCleanup(patcher.stop) # https://stackoverflow.com/a/37534051 + for field_name in Env.__dataclass_fields__: + if field_name.endswith('_DIR'): + setattr(self.mock_env, field_name, tempfile.TemporaryDirectory().name) + + def tearDown(self) -> None: + super().tearDown() + for field_name in Env.__dataclass_fields__: + if os.path.isdir(getattr(self.mock_env, field_name)): + shutil.rmtree(getattr(self.mock_env, field_name)) diff --git a/loading_pipeline/lib/test/mocked_reference_datasets_testcase.py b/loading_pipeline/lib/test/mocked_reference_datasets_testcase.py new file mode 100644 index 0000000000..ee58892be2 --- /dev/null +++ b/loading_pipeline/lib/test/mocked_reference_datasets_testcase.py @@ -0,0 +1,38 @@ +import os +import shutil + +from loading_pipeline.lib.core.definitions import ReferenceGenome +from loading_pipeline.lib.paths import valid_reference_dataset_path +from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + +REFERENCE_DATASETS_PATH = 'loading_pipeline/var/test/reference_datasets' + + +class MockedReferenceDatasetsTestCase(MockedDatarootTestCase): + def setUp(self) -> None: + super().setUp() + for reference_genome in ReferenceGenome: + path = os.path.join( + REFERENCE_DATASETS_PATH, + reference_genome.value, + ) + # Use listdir, allowing for missing datasets + # in the tests. + for dataset_name in os.listdir( + path, + ): + # Copy the entire directory tree under + # the dataset name. + shutil.copytree( + os.path.join(path, dataset_name), + os.path.dirname( + valid_reference_dataset_path( + reference_genome, + ReferenceDataset(dataset_name), + ), + ), + ) + + def tearDown(self): + super().tearDown() diff --git a/loading_pipeline/ops/__init__.py b/loading_pipeline/ops/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel.py b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel.py new file mode 100644 index 0000000000..4636e44ae3 --- /dev/null +++ b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel.py @@ -0,0 +1,114 @@ +#################################################### +# +# This script is provided as means to repartition an existing `GRCh38/SNV_INDEL/entries` table +# from a project-only partitioning strategy to one that includes project subpartitions. +# Very large genome projects with thousands of families will require additional +# splitting to maintain reasonable loading performance and to keep partition size under +# the recommended ClickHouse maximum. Unfortunately, a ClickHouse table partition definition +# is static upon creation, necessitating the expensive table re-write process demonstrated below. +# +# Post seqr-platform version x.x.x, the subpartition-ing strategy is provided by default; +# earlier installations will continue to function as-is. This script is meant to +# be run under human supervision and with caution. +# +# At the end of this script, you should run the following SQL to finalize the migration: +# EXCHANGE TABLES seqr.'GRCh38/SNV_INDEL/entries' AND staging_grch38_snvindel_repartition.'GRCh38/SNV_INDEL/repartitioned_entries' +# DROP DATABASE `staging_grch38_snvindel_repartition`; +# +# Resource Requirements: +# - Free disk space equal to 2.5x the usage of your current `GRCh38/SNV_INDEL/entries` table. +# +#################################################### +import argparse + +from loading_pipeline.lib.core.environment import Env +from loading_pipeline.lib.misc.clickhouse import ( + logged_query, + normalize_partition, +) + +REPARTITION_DATABASE_NAME = 'staging_grch38_snvindel_repartition' + + +def get_partitions_for_project(project_guid: str): + rows = logged_query( + """ + SELECT DISTINCT partition + FROM system.parts + WHERE + database = %(database)s + AND table = %(table)s + AND partition like %(project_guid)s + """, + { + 'database': REPARTITION_DATABASE_NAME, + 'table': 'GRCh38/SNV_INDEL/repartitioned_entries', + 'project_guid': f'%{project_guid}%', + }, + ) + return [normalize_partition(row[0]) for row in rows] + + +def main(max_insert_threads: int, project_guids: list[str]): + logged_query( + f""" + CREATE DATABASE IF NOT EXISTS {REPARTITION_DATABASE_NAME}; + """, + ) + logged_query( + f""" + CREATE TABLE IF NOT EXISTS {REPARTITION_DATABASE_NAME}.`GRCh38/SNV_INDEL/repartitioned_entries` + AS {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` + ENGINE = CollapsingMergeTree(sign) + PARTITION BY (project_guid, partition_id) + SETTINGS deduplicate_merge_projection_mode = 'rebuild' + """, + ) + if not project_guids: + project_guids = [ + x[0] + for x in logged_query( + f""" + SELECT DISTINCT project_guid from {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` + """, + ) + ] + for project_guid in project_guids: + for partition in get_partitions_for_project( + project_guid, + ): + logged_query( + f""" + ALTER TABLE {REPARTITION_DATABASE_NAME}.`GRCh38/SNV_INDEL/repartitioned_entries` + DROP PARTITION %(partition)s + """, + {'partition': partition}, + ) + logged_query( + f""" + INSERT INTO {REPARTITION_DATABASE_NAME}.`GRCh38/SNV_INDEL/repartitioned_entries` + SELECT * FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` + WHERE project_guid=%(project_guid)s + SETTINGS max_insert_threads=%(max_insert_threads)s + """, + {'project_guid': project_guid, 'max_insert_threads': max_insert_threads}, + timeout=99999, + ) + + +if __name__ == '__main__': + parser = argparse.ArgumentParser() + parser.add_argument( + '--max-insert-threads', + type=int, + default=4, + help='Maximum number of insert threads to use (default: 4).', + ) + parser.add_argument( + '--project-guids', + nargs='+', + required=False, + help='Optionally provide an override list of project guids: --project-guids proj1 proj2 proj3', + ) + args = parser.parse_args() + main(args.max_insert_threads, args.project_guids) diff --git a/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py new file mode 100644 index 0000000000..214d35b939 --- /dev/null +++ b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py @@ -0,0 +1,120 @@ +import unittest + +from loading_pipeline.lib.core.environment import Env +from loading_pipeline.lib.misc.clickhouse import get_clickhouse_client +from loading_pipeline.ops.repartition_clickhouse_grch38_snv_indel import ( + REPARTITION_DATABASE_NAME, + main, +) + + +class RepartitionGRCh38SnvIndelTest(unittest.TestCase): + def setUp(self): + client = get_clickhouse_client() + client.execute( + f""" + DROP DATABASE IF EXISTS {Env.CLICKHOUSE_DATABASE} + PARALLEL WITH + DROP DATABASE IF EXISTS {REPARTITION_DATABASE_NAME}; + """, + ) + client.execute( + f""" + CREATE DATABASE {Env.CLICKHOUSE_DATABASE} + PARALLEL WITH + CREATE DATABASE {REPARTITION_DATABASE_NAME}; + """, + ) + client.execute( + f""" + CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` ( + `key` UInt32, + `project_guid` LowCardinality(String), + `family_guid` String, + `is_annotated_in_any_gene` Boolean, + `sign` Int8, + `n_partitions` UInt8 MATERIALIZED 2, + `partition_id` UInt8 MATERIALIZED farmHash64(family_guid) % n_partitions, + PROJECTION xpos_projection + ( + SELECT * + ORDER BY is_annotated_in_any_gene + ) + ) + ENGINE = CollapsingMergeTree(sign) + PARTITION BY project_guid + ORDER BY (project_guid, family_guid, key) + SETTINGS deduplicate_merge_projection_mode = 'rebuild'; + """, + ) + client.execute( + f""" + INSERT INTO {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` + VALUES + (0, 'project_a', 'family_a1', 0, 1), + (1, 'project_a', 'family_a2', 0, 1), + (2, 'project_a', 'family_a3', 0, 1), + (0, 'project_b', 'family_b1', 0, 1), + (1, 'project_b', 'family_b2', 0, 1), + (2, 'project_b', 'family_b2', 0, 1), + (0, 'project_c', 'family_c1', 1, 1), + (3, 'project_c', 'family_c2', 1, 1), + """, + ) + client.execute( + f""" + CREATE DICTIONARY {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_partitions_dict` + ( + `project_guid` String, + `n_partitions` UInt8 + ) + PRIMARY KEY project_guid + SOURCE( + CLICKHOUSE( + USER '{Env.CLICKHOUSE_WRITER_USER}' PASSWORD '{Env.CLICKHOUSE_WRITER_PASSWORD}' + DB {Env.CLICKHOUSE_DATABASE} QUERY 'SELECT project_guid, 3 FROM `GRCh38/SNV_INDEL/entries`' + ) + ) + LIFETIME(0) + LAYOUT(FLAT(MAX_ARRAY_SIZE 10000)) + """, + ) + + def test_main_all_projects(self): + client = get_clickhouse_client() + main(1, []) + res = client.execute( + f""" + SELECT *, n_partitions, partition_id FROM {REPARTITION_DATABASE_NAME}.`GRCh38/SNV_INDEL/repartitioned_entries` + """, + ) + self.assertCountEqual( + res, + [ + (3, 'project_c', 'family_c2', True, 1, 2, 1), + (0, 'project_b', 'family_b1', 0, 1, 2, 1), + (1, 'project_b', 'family_b2', 0, 1, 2, 1), + (2, 'project_b', 'family_b2', 0, 1, 2, 1), + (2, 'project_a', 'family_a3', 0, 1, 2, 0), + (0, 'project_a', 'family_a1', 0, 1, 2, 1), + (1, 'project_a', 'family_a2', 0, 1, 2, 1), + (0, 'project_c', 'family_c1', True, 1, 2, 0), + ], + ) + + def test_main_one_project(self): + client = get_clickhouse_client() + main(1, ['project_a']) + res = client.execute( + f""" + SELECT *, n_partitions, partition_id FROM {REPARTITION_DATABASE_NAME}.`GRCh38/SNV_INDEL/repartitioned_entries` + """, + ) + self.assertCountEqual( + res, + [ + (2, 'project_a', 'family_a3', 0, 1, 2, 0), + (0, 'project_a', 'family_a1', 0, 1, 2, 1), + (1, 'project_a', 'family_a2', 0, 1, 2, 1), + ], + ) diff --git a/loading_pipeline/pyproject.toml b/loading_pipeline/pyproject.toml new file mode 100644 index 0000000000..f06f1fc691 --- /dev/null +++ b/loading_pipeline/pyproject.toml @@ -0,0 +1,115 @@ +[project] +name = "seqr-loading-pipeline" +dynamic = ['version'] +requires-python = ">=3.11" +dependencies = [ + "hail==0.2.138", # NB: when upgrading hail, manually verify the below jupyter pins + "luigi==3.5.2", + "gnomad==0.8.0", + "aiofiles==24.1.0", + "pydantic==2.8.2", + "clickhouse-driver==0.2.9", + "slacker==0.14.0", + "ipykernel==6.29.2", # matches pinned version in hail init_notebook.py + "jupyter-console==6.6.3", # matches pinned version in hail init_notebook.py + "qtconsole==5.6.1", # matches pinned version in hail init_notebook.py + + # Git/URL installs (PEP 508 direct references) + "gnomad-qc @ git+https://github.com/broadinstitute/gnomad_qc.git@v4.1", + "onnxconverter-common @ git+https://github.com/microsoft/onnxconverter-common.git@f7a8eb699caa6f6a78d3bdfbcaf5dfbd43569ebd", + + # Dataproc + "pip==23.2.1", + "google-cloud-dataproc==5.16.0", + "google-cloud-bigquery==3.29.0", + "google-api-python-client==2.159.0", +] + +[dependency-groups] +prod = [ + "sqlalchemy<2.0.0" # This is required for the Luigi UI but nothing else. +] +dev = [ + "coverage>=7.2.2", + "pytest>=7.0.0", + "pytest-cov>=4.0.0", + "responses>=0.23.1", + "ruff==0.11.3", + "shellcheck-py>=0.10.0", + "pysam", + "pyarrow", +] + +[tool.uv] +exclude-dependencies = ["psycopg2-binary", "psycopg2"] + +[tool.setuptools] +include-package-data = true + +[tool.setuptools.package-data] +"loading_pipeline.var" = ["liftover/*.over.chain.gz"] + +[tool.setuptools.packages.find] +include = ["loading_pipeline*"] +exclude = ["loading_pipeline.bin", "loading_pipeline.deploy", "loading_pipeline*test*"] +namespaces = false + +[tool.ruff] +extend-exclude = [ + 'download_and_create_reference_datasets/v02/*', + 'gcloud_dataproc/*', + 'hail_scripts/*', + 'kubernetes/*', + 'luigi_pipeline/lib/*', + 'luigi_pipeline/seqr*.py', + 'luigi_pipeline/tests/data/*', +] +ignore = [ + # Individual Rules + "E501", # Black is less aggressive here when touching comments and strings, we're going to let those through. + "G004", # logging-f-string, these are fine for now + + # Rule Groupings + "D", # pydocstyle is for docs... we have none + "FBT", # flake-boolean-trap... disallows boolean args to functions... fixing this code will require refactors. + "ANN", # flake8-annotations is for typed code + "DJ", # django specific + "PYI", # pyi is typing stub files + "PT", # pytest specific + "PTH", # pathlib is preferred, but we're not using it yet + "PD", # pandas specific + "NPY", # numpy specific + "TD", # todos + "FIX", # fixmes +] +line-length = 88 +select = [ + "ALL" +] +target-version = "py311" + +[tool.ruff.flake8-quotes] +inline-quotes = "single" + +[tool.ruff.per-file-ignores] +'*test*' = [ + 'ARG002', # allow unused method arguments + 'SLF001', # allow private access + 'PLR0913', # allow high arity functions + 'S101', # allow asserts in tests +] +'*migration*' = [ + 'N999', # allow invalid module names +] +'*clickhouse*' = [ + 'S608' # unsafe sql +] +'*pipeline_worker*' = [ + 'S608' # unsafe sql +] + +[tool.ruff.pylint] +max-args = 6 + +[tool.ruff.format] +quote-style = "single" diff --git a/loading_pipeline/uv.lock b/loading_pipeline/uv.lock new file mode 100644 index 0000000000..eba2806f11 --- 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HG00733 NA19675 NA19678 NA19679 NA20870 NA20872 NA20874 NA20875 NA20876 NA20877 NA20878 NA20881 NA20885 NA20888 +1 871269 . 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AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-1.74060e+01;DP=351;Dels=0.00000e+00;FS=9.28030e+01;HaplotypeScore=5.13800e-01;InbreedingCoeff=-3.32000e-02;MQ=5.93000e+01;MQ0=0;MQRankSum=2.37300e+00;QD=4.80000e-01;ReadPosRankSum=-1.17980e+01;SNPEFF_AMINO_ACID_CHANGE=R141;SNPEFF_CODON_CHANGE=cgA/cgC;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_871152_871276;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=SAMD11;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000342066;VQSLOD=-8.16700e-01;culprit=QD;CSQ=C|ENSG00000187634|ENST00000455979|Transcript|upstream_gene_variant|||||||1|3386|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187634|ENST00000420190|Transcript|synonymous_variant|512|423|141|R|cgA/cgC||1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000411579||Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI000155D47C|||5/7|||ENST00000420190.1:c.423N>C|ENST00000420190.1:c.423N>C(p.%3D)|||||||||||||||POSITION:0.787709497206704||NON_CAN_SPLICE_SURR|||||||,C|ENSG00000268179|ENST00000598827|Transcript|upstream_gene_variant|||||||1|4824|-1|AL645608.1|Clone_based_ensembl_gene||protein_coding|YES|||ENSP00000471152||M0R0C9_HUMAN|UPI0000D61E05||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187634|ENST00000437963|Transcript|downstream_gene_variant|||||||1|96|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000393181||Q5SV95_HUMAN&I7FV93_HUMAN|UPI000155D47B||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187634|ENST00000478729|Transcript|upstream_gene_variant|||||||1|4457|1|SAMD11|HGNC|28706|processed_transcript||||||||||||||||||||||||||||||||||||||,C|ENSG00000187634|ENST00000342066|Transcript|synonymous_variant|506|423|141|R|cgA/cgC||1||1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04|||5/14|||ENST00000342066.3:c.423N>C|ENST00000342066.3:c.423N>C(p.%3D)|||||||||||||||POSITION:0.206744868035191||NON_CAN_SPLICE_SURR|||||||,C|ENSG00000187634|ENST00000341065|Transcript|synonymous_variant|194|195|65|R|cgA/cgC||1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A|||3/12|||ENST00000341065.4:c.194N>C|ENST00000341065.4:c.194N>C(p.%3D)|||||||||||||||POSITION:0.110231769361221||NON_CAN_SPLICE_SURR|||||||,C||ENSR00000528855|RegulatoryFeature|regulatory_region_variant|||||||1||||||regulatory_region|||||||||||||||||||||||||||||||||||||| GT:AD:DP:GQ:PL 0/0:34,0:34:99:0,102,1073 0/0:34,0:34:99:0,102,1064 0/0:37,0:37:99:0,108,1155 0/0:8,3:11:24:0,24,226 0/1:11,4:16:32:32,0,300 0/0:10,0:10:30:0,30,306 0/0:13,0:13:39:0,39,410 0/0:11,0:11:33:0,33,323 0/0:21,3:23:12:0,12,434 0/0:19,0:19:57:0,57,581 0/0:25,4:28:27:0,27,553 0/0:17,1:18:51:0,51,524 0/0:25,0:25:75:0,75,759 0/0:21,0:21:63:0,63,687 0/0:23,4:27:69:0,69,709 0/0:22,2:24:60:0,60,562 +1 874734 rs145967298 C T 2645.29 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-7.95400e+00;DB;DP=484;Dels=0.00000e+00;FS=7.13100e+00;HaplotypeScore=3.21100e-01;InbreedingCoeff=-6.80000e-03;MQ=5.85800e+01;MQ0=1;MQRankSum=7.38500e+00;QD=1.23600e+01;ReadPosRankSum=-7.54000e-01;SNPEFF_AMINO_ACID_CHANGE=S200;SNPEFF_CODON_CHANGE=agC/agT;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_874655_874840;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=SAMD11;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000342066;VQSLOD=5.39000e+00;culprit=InbreedingCoeff;CSQ=T|ENSG00000187634|ENST00000420190|Transcript|downstream_gene_variant||||||rs145967298|1|63|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000411579||Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI000155D47C||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187634|ENST00000342066|Transcript|synonymous_variant|683|600|200|S|agC/agT|rs145967298|1||1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04|||7/14|||ENST00000342066.3:c.600N>T|ENST00000342066.3:c.600N>T(p.%3D)|T:0.0009||T:0.01|||T:0.000227|T:0.001628||||||||POSITION:0.293255131964809||NON_CAN_SPLICE_SURR|||||||,T|ENSG00000188976|ENST00000327044|Transcript|downstream_gene_variant||||||rs145967298|1|4850|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187634|ENST00000464948|Transcript|upstream_gene_variant||||||rs145967298|1|2812|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628|||||||||||||||||,T|ENSG00000187634|ENST00000466827|Transcript|upstream_gene_variant||||||rs145967298|1|2749|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628|||||||||||||||||,T|ENSG00000187634|ENST00000474461|Transcript|upstream_gene_variant||||||rs145967298|1|1722|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628|||||||||||||||||,T|ENSG00000188976|ENST00000483767|Transcript|downstream_gene_variant||||||rs145967298|1|4850|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628|||||||||||||||||,T|ENSG00000187634|ENST00000455979|Transcript|synonymous_variant|80|81|27|S|agC/agT|rs145967298|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479|||1/7|||ENST00000455979.1:c.80N>T|ENST00000455979.1:c.80N>T(p.%3D)|T:0.0009||T:0.01|||T:0.000227|T:0.001628||||||||POSITION:0.0498461538461538||NON_CAN_SPLICE_SURR|||||||,T|ENSG00000187634|ENST00000437963|Transcript|downstream_gene_variant||||||rs145967298|1|3561|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000393181||Q5SV95_HUMAN&I7FV93_HUMAN|UPI000155D47B||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187634|ENST00000478729|Transcript|upstream_gene_variant||||||rs145967298|1|992|1|SAMD11|HGNC|28706|processed_transcript|||||||||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628|||||||||||||||||,T|ENSG00000188976|ENST00000477976|Transcript|downstream_gene_variant||||||rs145967298|1|4851|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628|||||||||||||||||,T|ENSG00000187634|ENST00000341065|Transcript|synonymous_variant|371|372|124|S|agC/agT|rs145967298|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A|||5/12|||ENST00000341065.4:c.371N>T|ENST00000341065.4:c.371N>T(p.%3D)|T:0.0009||T:0.01|||T:0.000227|T:0.001628||||||||POSITION:0.210288298473714||NON_CAN_SPLICE_SURR|||||||,T||ENSR00001516735|RegulatoryFeature|regulatory_region_variant||||||rs145967298|1||||||regulatory_region|||||||||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628||||||||||||||||| GT:AD:DP:GQ:PL 0/0:37,0:37:99:0,111,1368 0/0:24,0:24:66:0,66,870 0/0:32,0:32:96:0,96,1183 0/0:8,0:8:24:0,24,245 0/0:8,0:8:24:0,24,267 0/0:9,0:9:27:0,27,318 0/0:26,0:26:75:0,75,879 0/0:31,0:31:93:0,93,1120 0/0:39,0:39:99:0,117,1375 0/0:56,0:56:99:0,169,2023 0/1:21,22:42:99:519,0,613 0/0:29,0:29:87:0,87,1048 0/0:43,0:43:99:0,129,1556 0/0:20,0:20:60:0,60,741 0/0:45,0:45:99:0,135,1586 0/0:35,0:35:99:0,105,1239 +1 876499 rs4372192 A G 212847.01 PASS AC=31;AF=9.69000e-01;AN=32;BaseQRankSum=2.42570e+01;DB;DP=122;Dels=1.00000e-02;FS=9.96800e+00;HaplotypeScore=2.51500e-01;InbreedingCoeff=4.11000e-02;MQ=5.91300e+01;MQ0=0;MQRankSum=7.64000e-01;QD=3.03200e+01;ReadPosRankSum=2.13900e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=4.70000e+00;culprit=MQ;CSQ=G|ENSG00000187634|ENST00000420190|Transcript|downstream_gene_variant||||||rs4372192|1|1828|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000411579||Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI000155D47C||||||||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676||||||||||EXON_INTRON_UNDEF&ANC_ALLELE|||||||,G|ENSG00000188976|ENST00000496938|Transcript|downstream_gene_variant||||||rs4372192|1|4200|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676|||||||||||||||||,G|ENSG00000187634|ENST00000342066|Transcript|intron_variant||||||rs4372192|1||1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04||||7/13||ENST00000342066.3:c.707-25N>G||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676||||||||INTRON_SIZE:1683||NON_CAN_SPLICE&ANC_ALLELE|||||||,G|ENSG00000188976|ENST00000327044|Transcript|downstream_gene_variant||||||rs4372192|1|3085|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676||||||||||EXON_INTRON_UNDEF&ANC_ALLELE|||||||,G|ENSG00000187634|ENST00000464948|Transcript|upstream_gene_variant||||||rs4372192|1|1047|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676|||||||||||||||||,G|ENSG00000187634|ENST00000466827|Transcript|upstream_gene_variant||||||rs4372192|1|984|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676|||||||||||||||||,G|ENSG00000187634|ENST00000474461|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|44|||||rs4372192|1||1|SAMD11|HGNC|28706|retained_intron||||||||||1/4|||ENST00000474461.1:n.44N>G||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676|||||||||||||||||,G|ENSG00000187634|ENST00000455979|Transcript|intron_variant||||||rs4372192|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479||||1/6||ENST00000455979.1:c.187-25N>G||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676||||||||INTRON_SIZE:1683||NON_CAN_SPLICE&ANC_ALLELE|||||||,G|ENSG00000188976|ENST00000483767|Transcript|downstream_gene_variant||||||rs4372192|1|3085|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676|||||||||||||||||,G|ENSG00000187634|ENST00000478729|Transcript|intron_variant&non_coding_transcript_variant||||||rs4372192|1||1|SAMD11|HGNC|28706|processed_transcript|||||||||||1/2||ENST00000478729.1:n.118-25N>G||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676|||||||||||||||||,G|ENSG00000188976|ENST00000477976|Transcript|downstream_gene_variant||||||rs4372192|1|3086|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676|||||||||||||||||,G|ENSG00000187634|ENST00000341065|Transcript|intron_variant||||||rs4372192|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A||||5/11||ENST00000341065.4:c.430-25N>G||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676||||||||INTRON_SIZE:1731||NON_CAN_SPLICE&ANC_ALLELE|||||||,G||ENSR00000528857|RegulatoryFeature|regulatory_region_variant||||||rs4372192|1||||||regulatory_region|||||||||||||||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676||||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,7:7:21:253,21,0 1/1:0,8:8:24:296,24,0 1/1:0,4:4:12:148,12,0 1/1:0,5:5:15:184,15,0 1/1:0,1:1:3:39,3,0 1/1:0,5:5:15:176,15,0 1/1:0,9:9:27:316,27,0 1/1:0,11:11:33:397,33,0 1/1:0,7:7:18:212,18,0 1/1:0,11:11:27:369,27,0 1/1:0,13:13:39:492,39,0 0/1:7,9:15:99:235,0,158 1/1:0,7:7:18:231,18,0 1/1:0,4:4:12:154,12,0 1/1:0,8:8:24:296,24,0 1/1:0,7:7:21:270,21,0 +1 878314 rs142558220 G C 2808.55 VQSRTrancheSNP99.00to99.90 AC=3;AF=9.40000e-02;AN=32;BaseQRankSum=1.88800e+00;DB;DP=117;Dels=0.00000e+00;FS=1.06220e+01;HaplotypeScore=2.21900e-01;InbreedingCoeff=3.64000e-02;MQ=5.94000e+01;MQ0=1;MQRankSum=1.65200e+00;QD=9.46000e+00;ReadPosRankSum=-3.88300e+00;SNPEFF_AMINO_ACID_CHANGE=G480;SNPEFF_CODON_CHANGE=ggG/ggC;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_877939_878438;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=SAMD11;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000342066;VQSLOD=6.85000e+00;culprit=QD;CSQ=C|ENSG00000187634|ENST00000420190|Transcript|downstream_gene_variant||||||rs142558220&COSM426784|1|3643|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000411579||Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI000155D47C||||||||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000188976|ENST00000496938|Transcript|downstream_gene_variant||||||rs142558220&COSM426784|1|2385|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1|||||||||||||||,C|ENSG00000187634|ENST00000342066|Transcript|synonymous_variant|1523|1440|480|G|ggG/ggC|rs142558220&COSM426784|1||1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04|||11/14|||ENST00000342066.3:c.1440N>C|ENST00000342066.3:c.1440N>C(p.%3D)|C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1||||||POSITION:0.703812316715543||NON_CAN_SPLICE_SURR|||||||,C|ENSG00000188976|ENST00000327044|Transcript|downstream_gene_variant||||||rs142558220&COSM426784|1|1270|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187634|ENST00000464948|Transcript|downstream_gene_variant||||||rs142558220&COSM426784|1|42|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1|||||||||||||||,C|ENSG00000187634|ENST00000466827|Transcript|downstream_gene_variant||||||rs142558220&COSM426784|1|132|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1|||||||||||||||,C|ENSG00000187634|ENST00000474461|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|802|||||rs142558220&COSM426784|1||1|SAMD11|HGNC|28706|retained_intron||||||||||4/4|||ENST00000474461.1:n.802N>C||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1|||||||||||||||,C|ENSG00000187634|ENST00000455979|Transcript|synonymous_variant|920|921|307|G|ggG/ggC|rs142558220&COSM426784|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479|||5/7|||ENST00000455979.1:c.920N>C|ENST00000455979.1:c.920N>C(p.%3D)|C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1||||||POSITION:0.566769230769231||NON_CAN_SPLICE_SURR|||||||,C|ENSG00000188976|ENST00000483767|Transcript|downstream_gene_variant||||||rs142558220&COSM426784|1|1270|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1|||||||||||||||,C|ENSG00000187634|ENST00000478729|Transcript|downstream_gene_variant||||||rs142558220&COSM426784|1|761|1|SAMD11|HGNC|28706|processed_transcript|||||||||||||||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1|||||||||||||||,C|ENSG00000188976|ENST00000477976|Transcript|downstream_gene_variant||||||rs142558220&COSM426784|1|1271|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1|||||||||||||||,C|ENSG00000187634|ENST00000341065|Transcript|synonymous_variant|1163|1164|388|G|ggG/ggC|rs142558220&COSM426784|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A|||9/12|||ENST00000341065.4:c.1163N>C|ENST00000341065.4:c.1163N>C(p.%3D)|C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1||||||POSITION:0.65799886941775||NON_CAN_SPLICE_SURR|||||||,C||ENSR00000528857|RegulatoryFeature|regulatory_region_variant||||||rs142558220&COSM426784|1||||||regulatory_region|||||||||||||||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1||||||||||||||| GT:AD:DP:GQ:PL 0/1:2,1:3:30:30,0,67 0/0:2,0:2:6:0,6,82 0/1:2,3:5:61:93,0,61 0/0:2,0:2:6:0,6,72 0/0:1,0:1:3:0,3,37 0/1:2,3:5:54:93,0,54 0/0:16,0:16:45:0,45,560 0/0:5,0:5:15:0,15,188 0/0:12,0:12:33:0,33,414 0/0:10,0:10:30:0,30,393 0/0:16,0:16:48:0,48,617 0/0:5,0:5:15:0,15,181 0/0:5,0:5:15:0,15,193 0/0:13,0:13:36:0,36,439 0/0:9,0:9:24:0,24,317 0/0:8,0:8:21:0,21,276 +1 878809 rs191952374 C T 1761.84 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-7.95300e+00;DB;DP=453;Dels=0.00000e+00;FS=1.68300e+00;HaplotypeScore=2.28500e-01;InbreedingCoeff=-3.10000e-03;MQ=5.91000e+01;MQ0=0;MQRankSum=1.29700e+00;QD=1.36600e+01;ReadPosRankSum=-8.52000e-01;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=9.25000e+00;culprit=InbreedingCoeff;CSQ=T|ENSG00000187634|ENST00000420190|Transcript|downstream_gene_variant||||||rs191952374|1|4138|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000411579||Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI000155D47C||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000496938|Transcript|downstream_gene_variant||||||rs191952374|1|1890|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636|||||||||||||||||,T|ENSG00000187634|ENST00000342066|Transcript|intron_variant||||||rs191952374|1||1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04||||12/13||ENST00000342066.3:c.1689+52N>T||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636||||||||INTRON_SIZE:320||NON_CAN_SPLICE|||||||,T|ENSG00000188976|ENST00000327044|Transcript|downstream_gene_variant||||||rs191952374|1|775|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187634|ENST00000464948|Transcript|downstream_gene_variant||||||rs191952374|1|537|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636|||||||||||||||||,T|ENSG00000187634|ENST00000466827|Transcript|downstream_gene_variant||||||rs191952374|1|627|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636|||||||||||||||||,T|ENSG00000187634|ENST00000474461|Transcript|downstream_gene_variant||||||rs191952374|1|435|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636|||||||||||||||||,T|ENSG00000187634|ENST00000455979|Transcript|intron_variant||||||rs191952374|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479||||6/6||ENST00000455979.1:c.1169+52N>T||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636||||||||INTRON_SIZE:320||NON_CAN_SPLICE|||||||,T|ENSG00000188976|ENST00000483767|Transcript|downstream_gene_variant||||||rs191952374|1|775|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636|||||||||||||||||,T|ENSG00000187634|ENST00000478729|Transcript|downstream_gene_variant||||||rs191952374|1|1256|1|SAMD11|HGNC|28706|processed_transcript|||||||||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636|||||||||||||||||,T|ENSG00000188976|ENST00000477976|Transcript|downstream_gene_variant||||||rs191952374|1|776|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636|||||||||||||||||,T|ENSG00000187634|ENST00000341065|Transcript|intron_variant||||||rs191952374|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A||||10/11||ENST00000341065.4:c.1412+52N>T||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636||||||||INTRON_SIZE:320||NON_CAN_SPLICE|||||||,T||ENSR00000528858|RegulatoryFeature|regulatory_region_variant||||||rs191952374|1||||||regulatory_region|||||||||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636||||||||||||||||| GT:AD:DP:GQ:PL 0/0:35,0:35:99:0,105,1323 0/0:24,0:24:72:0,72,960 0/0:31,0:31:93:0,93,1172 0/0:10,0:10:30:0,30,376 0/0:10,0:10:30:0,30,370 0/0:12,0:12:36:0,36,453 0/0:35,0:35:99:0,105,1376 0/0:33,0:33:99:0,99,1273 0/0:31,0:31:93:0,93,1240 0/0:33,0:33:96:0,96,1192 0/0:33,0:33:99:0,99,1281 0/0:25,0:25:75:0,75,983 0/1:18,16:33:99:488,0,504 0/0:33,0:33:99:0,99,1273 0/0:44,0:44:99:0,132,1698 0/0:31,0:31:90:0,90,1198 +1 879576 rs115979567 C T 18648.64 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-2.26830e+01;DB;DP=839;Dels=0.00000e+00;FS=2.49350e+01;HaplotypeScore=4.12600e-01;InbreedingCoeff=-2.18000e-02;MQ=5.92100e+01;MQ0=1;MQRankSum=1.02100e+00;QD=1.36100e+01;ReadPosRankSum=7.91400e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=4.39000e+00;culprit=InbreedingCoeff;CSQ=T|ENSG00000187634|ENST00000420190|Transcript|downstream_gene_variant||||||rs115979567|1|4905|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000411579||Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI000155D47C||||||||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000496938|Transcript|downstream_gene_variant||||||rs115979567|1|1123|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120|||||||||||||||||,T|ENSG00000187634|ENST00000342066|Transcript|3_prime_UTR_variant|2172|||||rs115979567|1||1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04|||14/14|||ENST00000342066.3:c.*43N>T||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120||||||||||NON_CAN_SPLICE_SURR|||||||,T|ENSG00000188976|ENST00000327044|Transcript|downstream_gene_variant||||||rs115979567|1|8|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187634|ENST00000464948|Transcript|downstream_gene_variant||||||rs115979567|1|1304|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120|||||||||||||||||,T|ENSG00000187634|ENST00000466827|Transcript|downstream_gene_variant||||||rs115979567|1|1394|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120|||||||||||||||||,T|ENSG00000187634|ENST00000474461|Transcript|downstream_gene_variant||||||rs115979567|1|1202|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120|||||||||||||||||,T|ENSG00000187634|ENST00000455979|Transcript|3_prime_UTR_variant|1668|||||rs115979567|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479|||7/7|||ENST00000455979.1:c.*43N>T||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120||||||||||NON_CAN_SPLICE_SURR|||||||,T|ENSG00000188976|ENST00000483767|Transcript|downstream_gene_variant||||||rs115979567|1|8|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120|||||||||||||||||,T|ENSG00000187634|ENST00000478729|Transcript|downstream_gene_variant||||||rs115979567|1|2023|1|SAMD11|HGNC|28706|processed_transcript|||||||||||||||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120|||||||||||||||||,T|ENSG00000188976|ENST00000477976|Transcript|downstream_gene_variant||||||rs115979567|1|9|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120|||||||||||||||||,T|ENSG00000187634|ENST00000341065|Transcript|3_prime_UTR_variant|1812|||||rs115979567|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A|||12/12|||ENST00000341065.4:c.*43N>T||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120||||||||||NON_CAN_SPLICE_SURR||||||| GT:AD:DP:GQ:PL 0/0:66,0:66:99:0,199,2441 0/1:25,28:51:99:767,0,834 0/0:55,0:55:99:0,166,2079 0/0:11,0:11:33:0,33,392 0/0:15,0:15:45:0,45,554 0/0:17,0:17:51:0,51,622 0/0:50,0:50:99:0,150,1966 0/0:65,0:65:99:0,196,2507 0/0:60,0:60:99:0,181,2268 0/0:70,0:70:99:0,211,2589 0/0:64,0:64:99:0,193,2452 0/0:65,0:65:99:0,196,2507 0/0:56,0:56:99:0,169,2117 0/0:60,0:60:99:0,181,2359 0/0:79,0:79:99:0,238,2986 0/0:55,0:55:99:0,165,2099 +1 881070 rs41285794 G A 20769.13 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-9.52200e+00;DB;DP=1185;Dels=0.00000e+00;FS=1.15500e+01;HaplotypeScore=1.69500e-01;InbreedingCoeff=-1.83000e-02;MQ=5.90700e+01;MQ0=0;MQRankSum=1.85940e+01;QD=1.31500e+01;ReadPosRankSum=-8.90700e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=SAMD11;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000342066;VQSLOD=4.22000e+00;culprit=InbreedingCoeff;CSQ=A|ENSG00000188976|ENST00000496938|Transcript|upstream_gene_variant||||||rs41285794|1|128|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651|||||||||||||||||,A|ENSG00000187634|ENST00000342066|Transcript|downstream_gene_variant||||||rs41285794|1|1115|1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04||||||||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000188976|ENST00000327044|Transcript|intron_variant||||||rs41285794|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||16/18||ENST00000327044.6:c.1918-37N>T||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651||||||||INTRON_SIZE:519||NON_CAN_SPLICE|||||||,A|ENSG00000187634|ENST00000464948|Transcript|downstream_gene_variant||||||rs41285794|1|2798|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651|||||||||||||||||,A|ENSG00000187634|ENST00000466827|Transcript|downstream_gene_variant||||||rs41285794|1|2888|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651|||||||||||||||||,A|ENSG00000187634|ENST00000474461|Transcript|downstream_gene_variant||||||rs41285794|1|2696|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651|||||||||||||||||,A|ENSG00000187634|ENST00000455979|Transcript|downstream_gene_variant||||||rs41285794|1|1431|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479||||||||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000188976|ENST00000483767|Transcript|intron_variant&non_coding_transcript_variant||||||rs41285794|1||-1|NOC2L|HGNC|24517|retained_intron|||||||||||2/4||ENST00000483767.1:n.774-37N>T||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651|||||||||||||||||,A|ENSG00000187634|ENST00000478729|Transcript|downstream_gene_variant||||||rs41285794|1|3517|1|SAMD11|HGNC|28706|processed_transcript|||||||||||||||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651|||||||||||||||||,A|ENSG00000188976|ENST00000477976|Transcript|intron_variant&non_coding_transcript_variant||||||rs41285794|1||-1|NOC2L|HGNC|24517|retained_intron|||||||||||14/16||ENST00000477976.1:n.3365-37N>T||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651|||||||||||||||||,A|ENSG00000187634|ENST00000341065|Transcript|downstream_gene_variant||||||rs41285794|1|1115|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A||||||||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651||||||||||EXON_INTRON_UNDEF||||||| GT:AD:DP:GQ:PL 0/0:78,0:78:99:0,235,2947 0/0:66,0:66:99:0,199,2595 0/0:59,0:59:99:0,178,2182 0/0:37,0:37:99:0,111,1365 0/0:36,0:36:99:0,108,1331 0/0:33,0:33:99:0,99,1192 0/0:69,0:69:99:0,208,2662 0/0:88,0:88:99:0,265,3395 0/0:98,0:98:99:0,295,3781 0/1:36,31:64:99:982,0,1021 0/0:86,0:86:99:0,259,3318 0/0:93,0:93:99:0,280,3588 0/0:92,0:92:99:0,277,3549 0/0:102,0:102:99:0,307,3935 0/0:89,0:89:99:0,268,3433 0/0:95,0:95:99:0,286,3665 +1 881627 rs2272757 G A 411792.28 PASS AC=22;AF=6.88000e-01;AN=32;BaseQRankSum=-3.32930e+01;DB;DP=644;Dels=0.00000e+00;FS=2.51600e+00;HaplotypeScore=5.86200e-01;InbreedingCoeff=3.09600e-01;MQ=5.88200e+01;MQ0=7;MQRankSum=6.81600e+00;QD=2.28900e+01;ReadPosRankSum=1.01500e+00;SNPEFF_AMINO_ACID_CHANGE=L615;SNPEFF_CODON_CHANGE=Ctg/Ttg;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_881553_881666;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=4.35000e+00;culprit=MQ;CSQ=A|ENSG00000188976|ENST00000496938|Transcript|upstream_gene_variant||||||rs2272757&COSM1344685|1|685|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1|||||||||||||||,A|ENSG00000187634|ENST00000342066|Transcript|downstream_gene_variant||||||rs2272757&COSM1344685|1|1672|1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04||||||||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000188976|ENST00000327044|Transcript|synonymous_variant|1893|1843|615|L|Ctg/Ttg|rs2272757&COSM1344685|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C|||16/19||Pfam_domain:PF03715&Superfamily_domains:SSF48371|ENST00000327044.6:c.1843N>T|ENST00000327044.6:c.1843N>T(p.%3D)|A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1||||||POSITION:0.819111111111111||NON_CAN_SPLICE_SURR|||||||,A|ENSG00000187634|ENST00000464948|Transcript|downstream_gene_variant||||||rs2272757&COSM1344685|1|3355|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1|||||||||||||||,A|ENSG00000187634|ENST00000466827|Transcript|downstream_gene_variant||||||rs2272757&COSM1344685|1|3445|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1|||||||||||||||,A|ENSG00000187634|ENST00000474461|Transcript|downstream_gene_variant||||||rs2272757&COSM1344685|1|3253|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1|||||||||||||||,A|ENSG00000187634|ENST00000455979|Transcript|downstream_gene_variant||||||rs2272757&COSM1344685|1|1988|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479||||||||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000188976|ENST00000483767|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|699|||||rs2272757&COSM1344685|1||-1|NOC2L|HGNC|24517|retained_intron||||||||||2/5|||ENST00000483767.1:n.699N>T||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1|||||||||||||||,A|ENSG00000187634|ENST00000478729|Transcript|downstream_gene_variant||||||rs2272757&COSM1344685|1|4074|1|SAMD11|HGNC|28706|processed_transcript|||||||||||||||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1|||||||||||||||,A|ENSG00000188976|ENST00000477976|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|3290|||||rs2272757&COSM1344685|1||-1|NOC2L|HGNC|24517|retained_intron||||||||||14/17|||ENST00000477976.1:n.3290N>T||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1|||||||||||||||,A|ENSG00000187634|ENST00000341065|Transcript|downstream_gene_variant||||||rs2272757&COSM1344685|1|1672|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A||||||||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1||||||||EXON_INTRON_UNDEF||||||| GT:AD:DP:GQ:PL 1/1:0,39:38:99:1384,111,0 0/0:61,0:61:99:0,184,2353 0/1:24,17:38:99:494,0,613 1/1:0,16:16:48:550,48,0 1/1:0,18:18:54:649,54,0 1/1:0,25:25:66:826,66,0 1/1:0,51:51:99:1886,153,0 0/1:25,23:46:99:661,0,639 1/1:0,33:33:99:1220,99,0 1/1:0,52:52:99:1879,156,0 1/1:0,45:45:99:1701,135,0 0/0:58,0:58:99:0,175,2237 0/1:17,18:34:99:523,0,478 1/1:0,44:44:99:1627,132,0 0/1:20,25:41:99:674,0,488 0/0:44,1:44:99:0,120,1521 +1 881918 rs35471880 G A 26418.87 PASS AC=5;AF=1.56000e-01;AN=32;BaseQRankSum=6.25300e+00;DB;DP=1040;Dels=0.00000e+00;FS=2.27620e+01;HaplotypeScore=2.29500e-01;InbreedingCoeff=-2.81000e-02;MQ=5.57400e+01;MQ0=40;MQRankSum=1.69390e+01;QD=1.18200e+01;ReadPosRankSum=-6.75000e-01;SNPEFF_AMINO_ACID_CHANGE=S556L;SNPEFF_CODON_CHANGE=tCg/tTg;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_881782_881925;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=1.82000e+00;culprit=MQ;CSQ=A|ENSG00000188976|ENST00000496938|Transcript|upstream_gene_variant||||||rs35471880|1|976|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628|||||||||||||||||,A|ENSG00000187634|ENST00000342066|Transcript|downstream_gene_variant||||||rs35471880|1|1963|1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04||||||||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000188976|ENST00000327044|Transcript|missense_variant|1717|1667|556|S/L|tCg/tTg|rs35471880|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C|deleterious(0.03)|benign(0.311)|15/19||Pfam_domain:PF03715&Superfamily_domains:SSF48371|ENST00000327044.6:c.1667N>T|ENSP00000317992.6:p.Ser556Leu|A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628||||||||POSITION:0.740888888888889||NON_CAN_SPLICE_SURR||B%3BB%3BB|16.43|D|T|D|T,A|ENSG00000187634|ENST00000464948|Transcript|downstream_gene_variant||||||rs35471880|1|3646|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628|||||||||||||||||,A|ENSG00000187634|ENST00000466827|Transcript|downstream_gene_variant||||||rs35471880|1|3736|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628|||||||||||||||||,A|ENSG00000187634|ENST00000474461|Transcript|downstream_gene_variant||||||rs35471880|1|3544|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628|||||||||||||||||,A|ENSG00000187634|ENST00000455979|Transcript|downstream_gene_variant||||||rs35471880|1|2279|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479||||||||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000188976|ENST00000483767|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|523|||||rs35471880|1||-1|NOC2L|HGNC|24517|retained_intron||||||||||1/5|||ENST00000483767.1:n.523N>T||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628|||||||||||||||||,A|ENSG00000187634|ENST00000478729|Transcript|downstream_gene_variant||||||rs35471880|1|4365|1|SAMD11|HGNC|28706|processed_transcript|||||||||||||||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628|||||||||||||||||,A|ENSG00000188976|ENST00000477976|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|3114|||||rs35471880|1||-1|NOC2L|HGNC|24517|retained_intron||||||||||13/17|||ENST00000477976.1:n.3114N>T||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628|||||||||||||||||,A|ENSG00000187634|ENST00000341065|Transcript|downstream_gene_variant||||||rs35471880|1|1963|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A||||||||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628||||||||||EXON_INTRON_UNDEF||||||| GT:AD:DP:GQ:PL 0/0:73,0:73:99:0,220,2699 0/0:70,0:70:99:0,211,2589 0/0:66,0:66:99:0,199,2385 0/1:12,18:29:99:475,0,278 0/0:28,0:28:78:0,78,843 0/1:18,10:27:99:271,0,511 0/1:34,36:67:99:876,0,921 0/1:37,38:74:99:966,0,944 0/0:69,0:69:99:0,208,2493 0/0:93,0:93:99:0,280,3279 0/1:41,32:70:99:777,0,1118 0/0:76,0:76:99:0,229,2746 0/0:73,0:73:99:0,220,2573 0/0:69,0:69:99:0,208,2493 0/0:82,0:82:99:0,247,2963 0/0:74,0:74:99:0,223,2609 +1 883485 . C T 81.94 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-3.68100e+00;DP=94;Dels=0.00000e+00;FS=0.00000e+00;HaplotypeScore=1.64200e-01;InbreedingCoeff=-2.46000e-02;MQ=5.53400e+01;MQ0=0;MQRankSum=3.55900e+00;QD=3.03000e+00;ReadPosRankSum=-1.07900e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=SAMD11;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000342066;VQSLOD=-3.92700e-01;culprit=MQ;CSQ=T|ENSG00000188976|ENST00000483767|Transcript|upstream_gene_variant||||||rs374301410|1|1045|-1|NOC2L|HGNC|24517|retained_intron||||||||||||||||||||T:0|T:0.000117|||||||||||||||||,T|ENSG00000187634|ENST00000455979|Transcript|downstream_gene_variant||||||rs374301410|1|3846|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479|||||||||||||T:0|T:0.000117||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000496938|Transcript|upstream_gene_variant||||||rs374301410|1|2543|-1|NOC2L|HGNC|24517|processed_transcript||||||||||||||||||||T:0|T:0.000117|||||||||||||||||,T|ENSG00000187634|ENST00000342066|Transcript|downstream_gene_variant||||||rs374301410|1|3530|1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04|||||||||||||T:0|T:0.000117||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000327044|Transcript|intron_variant||||||rs374301410|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||14/18||ENST00000327044.6:c.1659+26N>A|||||||T:0|T:0.000117||||||||INTRON_SIZE:1585||NON_CAN_SPLICE|||||||,T|ENSG00000188976|ENST00000477976|Transcript|intron_variant&non_coding_transcript_variant||||||rs374301410|1||-1|NOC2L|HGNC|24517|retained_intron|||||||||||12/16||ENST00000477976.1:n.3106+26N>A|||||||T:0|T:0.000117|||||||||||||||||,T|ENSG00000187634|ENST00000341065|Transcript|downstream_gene_variant||||||rs374301410|1|3530|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A|||||||||||||T:0|T:0.000117||||||||||EXON_INTRON_UNDEF||||||| GT:AD:DP:GQ:PL 0/0:8,0:8:24:0,24,304 0/0:3,0:3:9:0,9,118 0/0:5,0:5:15:0,15,178 0/0:5,0:5:15:0,15,181 0/0:2,0:2:6:0,6,69 0/0:4,0:5:12:0,12,145 0/0:6,0:6:18:0,18,217 0/0:10,0:10:30:0,30,378 0/0:11,0:11:33:0,33,411 0/1:5,1:6:14:14,0,181 0/0:10,0:10:30:0,30,373 0/0:4,0:4:9:0,9,114 0/0:5,0:5:15:0,15,193 0/0:4,0:4:12:0,12,157 0/0:6,0:6:18:0,18,229 0/0:3,0:4:9:0,9,122 +1 883625 rs4970378 A G 232503.78 PASS AC=30;AF=1.00000e+00;AN=30;DB;DP=117;Dels=0.00000e+00;FS=0.00000e+00;HaplotypeScore=1.37000e-01;InbreedingCoeff=-1.43000e-02;MQ=5.74300e+01;MQ0=0;QD=3.66300e+01;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=SAMD11;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000342066;VQSLOD=-2.60400e-01;culprit=MQ;CSQ=G|ENSG00000188976|ENST00000483767|Transcript|upstream_gene_variant||||||rs4970378|1|1185|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||A:0.0000|||||G:0.999543||||||||||||||||||,G|ENSG00000187634|ENST00000455979|Transcript|downstream_gene_variant||||||rs4970378|1|3986|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479||||||||A:0.0000|||||G:0.999543|||||||||||EXON_INTRON_UNDEF&ANC_ALLELE|||||||,G|ENSG00000188976|ENST00000496938|Transcript|upstream_gene_variant||||||rs4970378|1|2683|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.0000|||||G:0.999543||||||||||||||||||,G|ENSG00000187634|ENST00000342066|Transcript|downstream_gene_variant||||||rs4970378|1|3670|1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04||||||||A:0.0000|||||G:0.999543|||||||||||EXON_INTRON_UNDEF&ANC_ALLELE|||||||,G|ENSG00000188976|ENST00000327044|Transcript|intron_variant||||||rs4970378|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||13/18||ENST00000327044.6:c.1558-13N>C||A:0.0000|||||G:0.999543|||||||||INTRON_SIZE:257||NON_CAN_SPLICE&ANC_ALLELE|||||||,G|ENSG00000188976|ENST00000477976|Transcript|intron_variant&non_coding_transcript_variant||||||rs4970378|1||-1|NOC2L|HGNC|24517|retained_intron|||||||||||11/16||ENST00000477976.1:n.3005-13N>C||A:0.0000|||||G:0.999543||||||||||||||||||,G|ENSG00000187634|ENST00000341065|Transcript|downstream_gene_variant||||||rs4970378|1|3670|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A||||||||A:0.0000|||||G:0.999543|||||||||||EXON_INTRON_UNDEF&ANC_ALLELE||||||| GT:AD:DP:GQ:PL 1/1:0,4:4:12:151,12,0 1/1:0,3:3:9:118,9,0 1/1:0,6:6:18:212,18,0 1/1:0,5:5:15:185,15,0 ./.:.:.:.:. 1/1:0,4:4:12:142,12,0 1/1:0,13:13:39:501,39,0 1/1:0,8:8:21:276,21,0 1/1:0,19:19:57:718,57,0 1/1:0,9:9:27:340,27,0 1/1:0,12:12:36:454,36,0 1/1:0,4:4:12:151,12,0 1/1:0,5:5:15:198,15,0 1/1:0,16:16:48:605,48,0 1/1:0,3:3:9:119,9,0 1/1:0,5:6:15:191,15,0 +1 883918 rs139116730 G A 4594.12 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=6.89000e+00;DB;DP=1146;Dels=0.00000e+00;FS=4.31330e+01;HaplotypeScore=8.65000e-02;InbreedingCoeff=-4.00000e-03;MQ=5.62500e+01;MQ0=14;MQRankSum=1.10440e+01;QD=1.07800e+01;ReadPosRankSum=-1.97100e+00;SNPEFF_AMINO_ACID_CHANGE=S503;SNPEFF_CODON_CHANGE=tcC/tcT;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_883870_883983;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=5.95000e-01;culprit=MQ;CSQ=A|ENSG00000188976|ENST00000483767|Transcript|upstream_gene_variant||||||rs139116730|1|1478|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||A:0.0005||||A:0.0013|A:0.000227|A:0.003488|||||||||||||||||,A|ENSG00000187634|ENST00000455979|Transcript|downstream_gene_variant||||||rs139116730|1|4279|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479||||||||A:0.0005||||A:0.0013|A:0.000227|A:0.003488||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000188976|ENST00000496938|Transcript|upstream_gene_variant||||||rs139116730|1|2976|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.0005||||A:0.0013|A:0.000227|A:0.003488|||||||||||||||||,A|ENSG00000187634|ENST00000342066|Transcript|downstream_gene_variant||||||rs139116730|1|3963|1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04||||||||A:0.0005||||A:0.0013|A:0.000227|A:0.003488||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000188976|ENST00000327044|Transcript|synonymous_variant|1559|1509|503|S|tcC/tcT|rs139116730|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C|||13/19||Pfam_domain:PF03715&Superfamily_domains:SSF48371|ENST00000327044.6:c.1509N>T|ENST00000327044.6:c.1509N>T(p.%3D)|A:0.0005||||A:0.0013|A:0.000227|A:0.003488||||||||POSITION:0.670666666666667||NON_CAN_SPLICE_SURR|||||||,A|ENSG00000188976|ENST00000477976|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2956|||||rs139116730|1||-1|NOC2L|HGNC|24517|retained_intron||||||||||11/17|||ENST00000477976.1:n.2956N>T||A:0.0005||||A:0.0013|A:0.000227|A:0.003488|||||||||||||||||,A|ENSG00000187634|ENST00000341065|Transcript|downstream_gene_variant||||||rs139116730|1|3963|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A||||||||A:0.0005||||A:0.0013|A:0.000227|A:0.003488||||||||||EXON_INTRON_UNDEF||||||| GT:AD:DP:GQ:PL 0/0:76,0:76:99:0,229,2746 0/0:47,0:47:99:0,141,1738 0/0:75,0:75:99:0,226,2710 0/0:36,0:36:99:0,108,1201 0/0:37,0:37:99:0,111,1271 0/0:42,0:42:99:0,126,1443 0/0:74,0:74:99:0,223,2609 0/0:82,0:82:99:0,247,2963 0/0:120,0:120:99:0,361,4336 0/0:96,0:96:99:0,289,3468 0/1:38,33:68:99:823,0,921 0/0:78,0:78:99:0,235,2818 0/0:56,0:56:99:0,169,1974 0/0:92,0:92:99:0,277,3402 0/0:78,0:78:99:0,235,2884 0/0:89,0:89:99:0,268,3216 +1 887560 rs3748595 A C 806833.88 PASS AC=31;AF=9.69000e-01;AN=32;BaseQRankSum=5.43470e+01;DB;DP=472;Dels=0.00000e+00;FS=1.69080e+01;HaplotypeScore=2.91900e-01;InbreedingCoeff=7.38000e-02;MQ=5.93900e+01;MQ0=0;MQRankSum=1.20610e+01;QD=3.46800e+01;ReadPosRankSum=7.92100e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000487214;VQSLOD=6.35000e-01;culprit=FS;CSQ=C|ENSG00000188976|ENST00000327044|Transcript|intron_variant||||||rs3748595|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||10/18||ENST00000327044.6:c.1192-41N>G||A:0.1602|C:0.78|C:0.86|C:0.86|C:0.85|C:0.831139|C:0.932674||||||||INTRON_SIZE:272||NON_CAN_SPLICE&ANC_ALLELE|||||||,C|ENSG00000188976|ENST00000477976|Transcript|intron_variant&non_coding_transcript_variant||||||rs3748595|1||-1|NOC2L|HGNC|24517|retained_intron|||||||||||8/16||ENST00000477976.1:n.2639-41N>G||A:0.1602|C:0.78|C:0.86|C:0.86|C:0.85|C:0.831139|C:0.932674|||||||||||||||||,C|ENSG00000188976|ENST00000487214|Transcript|downstream_gene_variant||||||rs3748595|1|2246|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.1602|C:0.78|C:0.86|C:0.86|C:0.85|C:0.831139|C:0.932674||||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,44:44:99:1706,132,0 1/1:0,43:43:99:1773,129,0 1/1:0,41:41:99:1582,123,0 1/1:0,19:19:54:687,54,0 1/1:0,23:23:69:851,69,0 1/1:0,10:10:30:370,30,0 1/1:0,33:33:99:1320,99,0 1/1:1,25:25:75:1020,75,0 1/1:0,26:26:78:1040,78,0 1/1:0,25:25:75:1000,75,0 1/1:0,36:36:99:1461,108,0 0/1:23,14:36:99:439,0,642 1/1:0,23:23:69:930,69,0 1/1:0,28:28:84:1121,84,0 1/1:0,23:23:69:904,69,0 1/1:0,37:37:99:1420,108,0 +1 887801 rs3828047 A G 1348829.24 PASS AC=31;AF=9.69000e-01;AN=32;BaseQRankSum=4.41560e+01;DB;DP=777;Dels=0.00000e+00;FS=8.43510e+01;HaplotypeScore=3.07000e-01;InbreedingCoeff=-1.77000e-02;MQ=5.58800e+01;MQ0=35;MQRankSum=-2.15910e+01;QD=3.44400e+01;ReadPosRankSum=5.44300e+00;SNPEFF_AMINO_ACID_CHANGE=T394;SNPEFF_CODON_CHANGE=acT/acC;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_887792_887980;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=-6.22100e-01;culprit=MQ;CSQ=G|ENSG00000188976|ENST00000327044|Transcript|synonymous_variant|1232|1182|394|T|acT/acC|rs3828047&COSM426785|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C|||10/19||Pfam_domain:PF03715&Superfamily_domains:SSF48371|ENST00000327044.6:c.1182N>C|ENST00000327044.6:c.1182N>C(p.%3D)|A:0.0716|G:0.90|G:0.92|G:0.92|G:0.95|G:0.906037|G:0.938372||0&1||||||POSITION:0.525333333333333||NON_CAN_SPLICE_SURR&ANC_ALLELE|||||||,G|ENSG00000188976|ENST00000477976|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2629|||||rs3828047&COSM426785|1||-1|NOC2L|HGNC|24517|retained_intron||||||||||8/17|||ENST00000477976.1:n.2629N>C||A:0.0716|G:0.90|G:0.92|G:0.92|G:0.95|G:0.906037|G:0.938372||0&1|||||||||||||||,G|ENSG00000188976|ENST00000487214|Transcript|downstream_gene_variant||||||rs3828047&COSM426785|1|2005|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.0716|G:0.90|G:0.92|G:0.92|G:0.95|G:0.906037|G:0.938372||0&1||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,42:42:99:1553,126,0 1/1:0,48:48:99:1824,138,0 1/1:0,54:54:99:1997,163,0 1/1:0,17:18:48:615,48,0 1/1:0,33:33:99:1220,99,0 1/1:0,30:30:90:1134,90,0 1/1:0,60:60:99:2315,181,0 1/1:0,44:44:99:1526,120,0 1/1:0,71:71:99:2791,214,0 1/1:0,48:48:99:1887,144,0 1/1:0,61:61:99:2398,184,0 0/1:29,33:59:99:915,0,742 1/1:0,30:30:90:1157,90,0 1/1:0,59:59:99:2321,178,0 1/1:0,55:55:99:2137,166,0 1/1:0,65:65:99:2507,196,0 +1 888529 . G A 1833.13 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-9.33700e+00;DP=387;Dels=0.00000e+00;FS=8.33000e-01;HaplotypeScore=1.94900e-01;InbreedingCoeff=-4.20000e-03;MQ=5.60200e+01;MQ0=0;MQRankSum=5.49600e+00;QD=1.10400e+01;ReadPosRankSum=-2.04000e-01;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000487214;VQSLOD=1.38000e+00;culprit=MQ;CSQ=A|ENSG00000188976|ENST00000327044|Transcript|intron_variant||||||rs373469542|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||9/18||ENST00000327044.6:c.1002+26N>T|||||||A:0.000908|A:0||||||||INTRON_SIZE:574||NON_CAN_SPLICE|||||||,A|ENSG00000188976|ENST00000477976|Transcript|intron_variant&non_coding_transcript_variant||||||rs373469542|1||-1|NOC2L|HGNC|24517|retained_intron|||||||||||7/16||ENST00000477976.1:n.2449+26N>T|||||||A:0.000908|A:0|||||||||||||||||,A|ENSG00000188976|ENST00000487214|Transcript|downstream_gene_variant||||||rs373469542|1|1277|-1|NOC2L|HGNC|24517|processed_transcript||||||||||||||||||||A:0.000908|A:0||||||||||||||||| GT:AD:DP:GQ:PL 0/0:19,0:19:57:0,57,703 0/0:26,0:26:78:0,78,1022 0/0:23,0:23:69:0,69,869 0/0:15,0:15:45:0,45,555 0/0:16,0:16:48:0,48,603 0/0:16,0:16:48:0,48,606 0/0:32,0:32:96:0,96,1258 0/0:26,0:26:72:0,72,944 0/0:24,0:24:69:0,69,898 0/1:12,15:26:99:432,0,321 0/0:31,0:31:93:0,93,1240 0/0:24,0:24:72:0,72,944 0/0:20,0:20:60:0,60,756 0/0:27,0:27:78:0,78,1029 0/0:36,0:36:99:0,108,1415 0/0:26,0:26:78:0,78,1022 +1 888659 rs3748597 T C 907727.36 PASS AC=31;AF=9.69000e-01;AN=32;BaseQRankSum=4.09230e+01;DB;DP=542;Dels=0.00000e+00;FS=4.67910e+01;HaplotypeScore=2.81100e-01;InbreedingCoeff=-1.65000e-02;MQ=5.48600e+01;MQ0=44;MQRankSum=-2.23740e+01;QD=3.38200e+01;ReadPosRankSum=8.50400e+00;SNPEFF_AMINO_ACID_CHANGE=I300V;SNPEFF_CODON_CHANGE=Atc/Gtc;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_888555_888668;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=-6.49600e-01;culprit=MQ;CSQ=C|ENSG00000188976|ENST00000469563|Transcript|downstream_gene_variant||||||rs3748597|1|4967|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0716|C:0.90|C:0.92|C:0.92|C:0.95|C:0.905767|C:0.938372|||||||||||||||||,C|ENSG00000188976|ENST00000327044|Transcript|missense_variant|948|898|300|I/V|Atc/Gtc|rs3748597|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C|tolerated(0.98)|benign(0)|9/19||Superfamily_domains:SSF48371|ENST00000327044.6:c.898N>G|ENSP00000317992.6:p.Ile300Val|T:0.0716|C:0.90|C:0.92|C:0.92|C:0.95|C:0.905767|C:0.938372||||||||POSITION:0.399111111111111||NON_CAN_SPLICE_SURR&ANC_ALLELE||B|0.940|P|T|T|T,C|ENSG00000188976|ENST00000477976|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2345|||||rs3748597|1||-1|NOC2L|HGNC|24517|retained_intron||||||||||7/17|||ENST00000477976.1:n.2345N>G||T:0.0716|C:0.90|C:0.92|C:0.92|C:0.95|C:0.905767|C:0.938372|||||||||||||||||,C|ENSG00000188976|ENST00000487214|Transcript|downstream_gene_variant||||||rs3748597|1|1147|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||T:0.0716|C:0.90|C:0.92|C:0.92|C:0.95|C:0.905767|C:0.938372||||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,33:33:96:1198,96,0 1/1:0,29:29:87:1140,87,0 1/1:0,27:27:81:998,81,0 1/1:0,27:27:81:962,81,0 1/1:0,19:19:57:686,57,0 1/1:0,22:22:63:796,63,0 1/1:0,39:39:99:1474,117,0 1/1:0,39:39:99:1504,117,0 1/1:0,32:32:96:1183,96,0 1/1:0,44:44:99:1654,129,0 1/1:0,55:55:99:2079,166,0 0/1:17,21:36:99:502,0,410 1/1:0,37:37:99:1398,111,0 1/1:0,44:44:99:1697,132,0 1/1:0,32:32:96:1209,96,0 1/1:0,27:27:81:1016,81,0 +1 889158 rs56262069 G C 909575.03 PASS AC=31;AF=9.69000e-01;AN=32;BaseQRankSum=3.68810e+01;DB;DP=579;Dels=0.00000e+00;FS=2.80669e+02;HaplotypeScore=5.39300e-01;InbreedingCoeff=7.80000e-02;MQ=5.90100e+01;MQ0=0;MQRankSum=-1.97700e+00;QD=3.19700e+01;ReadPosRankSum=8.43100e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000469563;VQSLOD=9.10000e-02;culprit=MQRankSum;CSQ=C|ENSG00000188976|ENST00000469563|Transcript|downstream_gene_variant||||||rs13303056|1|4468|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||G:0.1529|||||||||||||||||||||||,C|ENSG00000188976|ENST00000327044|Transcript|splice_region_variant&intron_variant||||||rs13303056|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||8/18||ENST00000327044.6:c.888+4N>G||G:0.1529||||||||||||||INTRON_SIZE:493||NON_CAN_SPLICE&ANC_ALLELE|||||||,C|ENSG00000188976|ENST00000477976|Transcript|splice_region_variant&intron_variant&non_coding_transcript_variant||||||rs13303056|1||-1|NOC2L|HGNC|24517|retained_intron|||||||||||6/16||ENST00000477976.1:n.2335+4N>G||G:0.1529|||||||||||||||||||||||,C|ENSG00000188976|ENST00000487214|Transcript|downstream_gene_variant||||||rs13303056|1|648|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||G:0.1529||||||||||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,45:45:99:1664,135,0 1/1:0,21:21:63:810,63,0 1/1:0,27:27:81:975,81,0 1/1:0,19:18:51:638,51,0 1/1:0,20:20:60:700,60,0 1/1:0,18:18:54:635,54,0 1/1:0,40:40:99:1512,120,0 1/1:0,34:34:99:1312,102,0 1/1:0,45:45:99:1615,132,0 1/1:0,40:40:99:1543,120,0 1/1:0,62:62:99:2392,187,0 0/1:23,19:40:99:499,0,598 1/1:0,45:45:99:1664,135,0 1/1:0,48:48:99:1814,144,0 1/1:0,39:39:99:1503,117,0 1/1:0,37:37:99:1398,111,0 +1 889159 rs13302945 A C 937927.21 PASS AC=31;AF=9.69000e-01;AN=32;BaseQRankSum=5.17190e+01;DB;DP=586;Dels=0.00000e+00;FS=2.49622e+02;HaplotypeScore=5.35000e-01;InbreedingCoeff=7.77000e-02;MQ=5.90200e+01;MQ0=0;MQRankSum=1.48040e+01;QD=3.22600e+01;ReadPosRankSum=8.79200e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000469563;VQSLOD=1.40000e-01;culprit=MQ;CSQ=C|ENSG00000188976|ENST00000469563|Transcript|downstream_gene_variant||||||rs13302945|1|4467|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||A:0.1538|C:0.79|C:0.87|C:0.88|C:0.85|C:0.823342|C:0.932294|||||||||||||||||,C|ENSG00000188976|ENST00000327044|Transcript|splice_region_variant&intron_variant||||||rs13302945|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||8/18||ENST00000327044.6:c.888+3N>G||A:0.1538|C:0.79|C:0.87|C:0.88|C:0.85|C:0.823342|C:0.932294||||||||INTRON_SIZE:493||NON_CAN_SPLICE&ANC_ALLELE|||||||,C|ENSG00000188976|ENST00000477976|Transcript|splice_region_variant&intron_variant&non_coding_transcript_variant||||||rs13302945|1||-1|NOC2L|HGNC|24517|retained_intron|||||||||||6/16||ENST00000477976.1:n.2335+3N>G||A:0.1538|C:0.79|C:0.87|C:0.88|C:0.85|C:0.823342|C:0.932294|||||||||||||||||,C|ENSG00000188976|ENST00000487214|Transcript|downstream_gene_variant||||||rs13302945|1|647|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.1538|C:0.79|C:0.87|C:0.88|C:0.85|C:0.823342|C:0.932294||||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,44:44:99:1663,132,0 1/1:0,21:21:63:794,63,0 1/1:0,28:28:84:1058,84,0 1/1:0,19:18:51:634,51,0 1/1:0,21:21:63:782,63,0 1/1:0,18:18:54:650,54,0 1/1:0,42:42:99:1587,126,0 1/1:0,34:34:99:1312,102,0 1/1:0,45:45:99:1657,132,0 1/1:0,41:41:99:1582,123,0 1/1:0,61:61:99:2353,184,0 0/1:24,19:41:99:482,0,633 1/1:0,43:43:99:1625,129,0 1/1:0,52:52:99:1965,156,0 1/1:0,42:42:99:1557,123,0 1/1:0,35:35:99:1323,105,0 +1 889238 rs3828049 G A 52801.55 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-4.91500e+00;DB;DP=911;Dels=0.00000e+00;FS=4.16200e+01;HaplotypeScore=2.87900e-01;InbreedingCoeff=3.34000e-02;MQ=5.93400e+01;MQ0=1;MQRankSum=3.62800e+00;QD=1.41200e+01;ReadPosRankSum=-2.71000e+00;SNPEFF_AMINO_ACID_CHANGE=A271V;SNPEFF_CODON_CHANGE=gCg/gTg;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_889162_889272;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=5.38000e+00;culprit=MQRankSum;CSQ=A|ENSG00000188976|ENST00000469563|Transcript|downstream_gene_variant||||||rs3828049&COSM1602748|1|4388|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||A:0.0537|A:0.02|A:0.08|A:0.08|A:0.05|A:0.021562|A:0.060363||0&1|||||||||||||||,A|ENSG00000188976|ENST00000327044|Transcript|missense_variant|862|812|271|A/V|gCg/gTg|rs3828049&COSM1602748|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C|deleterious(0.04)|benign(0.034)|8/19||Superfamily_domains:SSF48371|ENST00000327044.6:c.812N>T|ENSP00000317992.6:p.Ala271Val|A:0.0537|A:0.02|A:0.08|A:0.08|A:0.05|A:0.021562|A:0.060363||0&1||||||POSITION:0.360888888888889||NON_CAN_SPLICE_SURR||D%3BP%3BP|21.3|N|T|D|T,A|ENSG00000188976|ENST00000477976|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2259|||||rs3828049&COSM1602748|1||-1|NOC2L|HGNC|24517|retained_intron||||||||||6/17|||ENST00000477976.1:n.2259N>T||A:0.0537|A:0.02|A:0.08|A:0.08|A:0.05|A:0.021562|A:0.060363||0&1|||||||||||||||,A|ENSG00000188976|ENST00000487214|Transcript|downstream_gene_variant||||||rs3828049&COSM1602748|1|568|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.0537|A:0.02|A:0.08|A:0.08|A:0.05|A:0.021562|A:0.060363||0&1||||||||||||||| GT:AD:DP:GQ:PL 0/0:53,0:53:99:0,159,1960 0/0:56,0:56:99:0,169,2071 0/0:42,0:42:99:0,126,1517 0/0:23,0:23:69:0,69,763 0/0:31,0:31:93:0,93,1007 0/0:26,0:26:69:0,69,754 0/0:55,0:55:99:0,166,1987 0/0:59,0:59:99:0,178,2132 0/0:67,0:67:99:0,202,2362 0/0:79,0:79:99:0,238,2854 0/0:82,0:82:99:0,247,2963 0/1:32,31:62:99:888,0,808 0/0:75,0:75:99:0,226,2644 0/0:66,0:66:99:0,199,2385 0/0:68,0:68:99:0,205,2397 0/0:67,0:67:99:0,202,2362 +1 894573 rs13303010 G A 310883.38 PASS AC=30;AF=9.38000e-01;AN=32;BaseQRankSum=1.22670e+01;DB;DP=304;Dels=0.00000e+00;FS=2.34720e+01;HaplotypeScore=3.24800e-01;InbreedingCoeff=4.23300e-01;MQ=5.89800e+01;MQ0=0;MQRankSum=1.80380e+01;QD=2.67400e+01;ReadPosRankSum=2.89300e+00;SNPEFF_EFFECT=INTRON;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=1.10000e+00;culprit=MQ;CSQ=A|ENSG00000187961|ENST00000466300|Transcript|upstream_gene_variant||||||rs13303010|1|3534|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||G:0.3480|A:0.18|A:0.71|A:0.69|A:0.90|A:0.284570|A:0.896942|||||||||||||||||,A|ENSG00000188976|ENST00000327044|Transcript|intron_variant||||||rs13303010|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||1/18||ENST00000327044.6:c.26+22N>T||G:0.3480|A:0.18|A:0.71|A:0.69|A:0.90|A:0.284570|A:0.896942||||||||INTRON_SIZE:133||NON_CAN_SPLICE|||||||,A|ENSG00000187961|ENST00000338591|Transcript|upstream_gene_variant||||||rs13303010|1|1394|1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||||||G:0.3480|A:0.18|A:0.71|A:0.69|A:0.90|A:0.284570|A:0.896942||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000187961|ENST00000463212|Transcript|upstream_gene_variant||||||rs13303010|1|2256|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||G:0.3480|A:0.18|A:0.71|A:0.69|A:0.90|A:0.284570|A:0.896942|||||||||||||||||,A|ENSG00000188976|ENST00000469563|Transcript|intron_variant&non_coding_transcript_variant||||||rs13303010|1||-1|NOC2L|HGNC|24517|retained_intron|||||||||||1/1||ENST00000469563.1:n.42+22N>T||G:0.3480|A:0.18|A:0.71|A:0.69|A:0.90|A:0.284570|A:0.896942|||||||||||||||||,A|ENSG00000188976|ENST00000477976|Transcript|upstream_gene_variant||||||rs13303010|1|735|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||G:0.3480|A:0.18|A:0.71|A:0.69|A:0.90|A:0.284570|A:0.896942|||||||||||||||||,A|ENSG00000187961|ENST00000481067|Transcript|upstream_gene_variant||||||rs13303010|1|4359|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||G:0.3480|A:0.18|A:0.71|A:0.69|A:0.90|A:0.284570|A:0.896942|||||||||||||||||,A|ENSG00000188976|ENST00000487214|Transcript|intron_variant&non_coding_transcript_variant||||||rs13303010|1||-1|NOC2L|HGNC|24517|processed_transcript|||||||||||1/6||ENST00000487214.1:n.95+22N>T||G:0.3480|A:0.18|A:0.71|A:0.69|A:0.90|A:0.284570|A:0.896942|||||||||||||||||,A||ENSR00000528861|RegulatoryFeature|regulatory_region_variant||||||rs13303010|1||||||regulatory_region|||||||||||||||G:0.3480|A:0.18|A:0.71|A:0.69|A:0.90|A:0.284570|A:0.896942||||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,24:24:72:898,72,0 0/1:10,8:17:99:196,0,291 1/1:0,13:12:36:454,36,0 1/1:0,7:7:21:254,21,0 1/1:0,5:5:15:181,15,0 1/1:0,13:13:36:428,36,0 1/1:0,31:31:93:1120,93,0 1/1:0,24:24:72:867,72,0 1/1:0,26:26:78:924,78,0 1/1:0,26:26:78:958,78,0 1/1:0,19:19:57:670,57,0 0/1:17,6:22:99:127,0,513 1/1:0,20:20:60:723,60,0 1/1:0,23:23:69:869,69,0 1/1:0,19:19:57:686,57,0 1/1:0,16:16:48:505,48,0 +1 896922 . C T 1253.52 PASS AC=2;AF=6.30000e-02;AN=32;BaseQRankSum=-8.14600e+00;DP=943;Dels=0.00000e+00;FS=5.89500e+00;HaplotypeScore=1.37200e-01;InbreedingCoeff=-1.30000e-03;MQ=5.92800e+01;MQ0=0;MQRankSum=1.05600e+00;QD=1.01100e+01;ReadPosRankSum=-1.19000e+00;SNPEFF_AMINO_ACID_CHANGE=A119;SNPEFF_CODON_CHANGE=gcC/gcT;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_896673_896932;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000338591;VQSLOD=8.89000e+00;culprit=InbreedingCoeff;CSQ=T|ENSG00000187961|ENST00000466300|Transcript|upstream_gene_variant|||||||1|1185|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E|||||||||||||||||||||||||||||||,T|ENSG00000188976|ENST00000327044|Transcript|upstream_gene_variant|||||||1|2252|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187961|ENST00000338591|Transcript|synonymous_variant|464|357|119|A|gcC/gcT||1||1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0|||2/12||Pfam_domain:PF00651&PROSITE_profiles:PS50097&SMART_domains:SM00225&Superfamily_domains:SSF54695&PIRSF_domain:PIRSF037037|ENST00000338591.3:c.357N>T|ENST00000338591.3:c.357N>T(p.%3D)|||||||||||||||POSITION:0.1850699844479||NON_CAN_SPLICE_SURR|||||||,T|ENSG00000187583|ENST00000379409|Transcript|upstream_gene_variant|||||||1|4960|1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187961|ENST00000463212|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|94||||||1||1|KLHL17|HGNC|24023|retained_intron||||||||||1/2|||ENST00000463212.1:n.94N>T|||||||||||||||||||||||||,T|ENSG00000187583|ENST00000379407|Transcript|upstream_gene_variant|||||||1|4960|1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000469563|Transcript|upstream_gene_variant|||||||1|2286|-1|NOC2L|HGNC|24517|retained_intron||||||||||||||||||||||||||||||||||||||,T|ENSG00000187583|ENST00000379410|Transcript|upstream_gene_variant|||||||1|4955|1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000477976|Transcript|upstream_gene_variant|||||||1|3084|-1|NOC2L|HGNC|24517|retained_intron||||||||||||||||||||||||||||||||||||||,T|ENSG00000187961|ENST00000481067|Transcript|upstream_gene_variant|||||||1|2010|1|KLHL17|HGNC|24023|retained_intron||||||||||||||||||||||||||||||||||||||,T|ENSG00000188976|ENST00000487214|Transcript|upstream_gene_variant|||||||1|2233|-1|NOC2L|HGNC|24517|processed_transcript||||||||||||||||||||||||||||||||||||||,T||ENSR00000528861|RegulatoryFeature|regulatory_region_variant|||||||1||||||regulatory_region|||||||||||||||||||||||||||||||||||||| GT:AD:DP:GQ:PL 0/0:71,0:71:99:0,214,2684 0/0:69,0:69:99:0,208,2713 0/0:68,0:68:99:0,205,2515 0/0:20,0:20:57:0,57,722 0/0:29,0:29:87:0,87,1096 0/0:36,0:36:99:0,99,1225 0/0:61,0:61:99:0,184,2353 0/0:58,0:58:99:0,175,2192 0/0:68,0:68:99:0,205,2673 0/1:41,25:63:99:678,0,1190 0/0:87,0:87:99:0,262,3356 0/0:52,0:52:99:0,157,2006 0/1:35,23:55:99:651,0,922 0/0:79,0:79:99:0,238,3048 0/0:73,0:73:99:0,220,2816 0/0:54,0:54:99:0,163,2045 +1 897325 rs4970441 G C 2226684.78 PASS AC=31;AF=9.69000e-01;AN=32;BaseQRankSum=3.69960e+01;DB;DP=1475;Dels=0.00000e+00;FS=1.12830e+01;HaplotypeScore=4.66400e-01;InbreedingCoeff=1.15000e-01;MQ=5.95500e+01;MQ0=1;MQRankSum=2.60000e-02;QD=3.33700e+01;ReadPosRankSum=6.38900e+00;SNPEFF_AMINO_ACID_CHANGE=A203;SNPEFF_CODON_CHANGE=gcG/gcC;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_897206_897427;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000338591;VQSLOD=5.29000e+00;culprit=ReadPosRankSum;CSQ=C|ENSG00000187961|ENST00000466300|Transcript|upstream_gene_variant||||||rs4970441|1|782|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163|||||||||||||||||,C|ENSG00000188976|ENST00000327044|Transcript|upstream_gene_variant||||||rs4970441|1|2655|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000338591|Transcript|synonymous_variant|716|609|203|A|gcG/gcC|rs4970441|1||1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0|||4/12||Pfam_domain:PF07707&SMART_domains:SM00875&PIRSF_domain:PIRSF037037|ENST00000338591.3:c.609N>C|ENST00000338591.3:c.609N>C(p.%3D)|G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163||||||||POSITION:0.315707620528771||NON_CAN_SPLICE_SURR|||||||,C|ENSG00000187583|ENST00000379409|Transcript|upstream_gene_variant||||||rs4970441|1|4557|1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06||||||||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000463212|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|422|||||rs4970441|1||1|KLHL17|HGNC|24023|retained_intron||||||||||2/2|||ENST00000463212.1:n.422N>C||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163|||||||||||||||||,C|ENSG00000187583|ENST00000379407|Transcript|upstream_gene_variant||||||rs4970441|1|4557|1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF||||||||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000188976|ENST00000469563|Transcript|upstream_gene_variant||||||rs4970441|1|2689|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163|||||||||||||||||,C|ENSG00000187583|ENST00000379410|Transcript|upstream_gene_variant||||||rs4970441|1|4552|1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8||||||||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000188976|ENST00000477976|Transcript|upstream_gene_variant||||||rs4970441|1|3487|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163|||||||||||||||||,C|ENSG00000187961|ENST00000481067|Transcript|upstream_gene_variant||||||rs4970441|1|1607|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163|||||||||||||||||,C|ENSG00000188976|ENST00000487214|Transcript|upstream_gene_variant||||||rs4970441|1|2636|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163||||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,94:94:99:3476,283,0 1/1:0,87:87:99:3356,262,0 1/1:0,108:108:99:3994,325,0 1/1:0,56:56:99:2023,169,0 1/1:0,59:59:99:2182,178,0 1/1:0,46:46:99:1701,138,0 1/1:0,100:100:99:3780,301,0 1/1:0,127:127:99:4800,382,0 1/1:0,127:127:99:4899,382,0 1/1:0,127:127:99:4800,382,0 1/1:0,117:117:99:4422,352,0 0/1:42,33:71:99:891,0,1116 1/1:0,78:78:99:2948,235,0 1/1:0,107:107:99:4128,322,0 1/1:0,95:95:99:3665,286,0 1/1:0,76:76:99:2873,229,0 +1 898313 . C T 4423.71 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=1.00100e+01;DP=235;Dels=0.00000e+00;FS=6.83200e+00;HaplotypeScore=5.07500e-01;InbreedingCoeff=9.84000e-02;MQ=5.92600e+01;MQ0=0;MQRankSum=-5.62000e-01;QD=1.22500e+01;ReadPosRankSum=-4.59200e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000463212;VQSLOD=3.67000e+00;culprit=MQRankSum;CSQ=T|ENSG00000187961|ENST00000466300|Transcript|intron_variant&NMD_transcript_variant||||||rs375277853|1||1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||1/5||ENST00000466300.1:c.191+16N>T|||||||||||||||||||||||||,T|ENSG00000188976|ENST00000327044|Transcript|upstream_gene_variant||||||rs375277853|1|3643|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187961|ENST00000338591|Transcript|intron_variant||||||rs375277853|1||1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||6/11||ENST00000338591.3:c.1042+16N>T||||||||||||||||INTRON_SIZE:191||NON_CAN_SPLICE|||||||,T|ENSG00000187583|ENST00000379409|Transcript|upstream_gene_variant||||||rs375277853|1|3569|1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs375277853|1|455|1|KLHL17|HGNC|24023|retained_intron||||||||||||||||||||||||||||||||||||||,T|ENSG00000187583|ENST00000379407|Transcript|upstream_gene_variant||||||rs375277853|1|3569|1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000469563|Transcript|upstream_gene_variant||||||rs375277853|1|3677|-1|NOC2L|HGNC|24517|retained_intron||||||||||||||||||||||||||||||||||||||,T|ENSG00000187583|ENST00000379410|Transcript|upstream_gene_variant||||||rs375277853|1|3564|1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000477976|Transcript|upstream_gene_variant||||||rs375277853|1|4475|-1|NOC2L|HGNC|24517|retained_intron||||||||||||||||||||||||||||||||||||||,T|ENSG00000187961|ENST00000481067|Transcript|upstream_gene_variant||||||rs375277853|1|619|1|KLHL17|HGNC|24023|retained_intron||||||||||||||||||||||||||||||||||||||,T|ENSG00000188976|ENST00000487214|Transcript|upstream_gene_variant||||||rs375277853|1|3624|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||||||||||||||||||||||||| GT:AD:DP:GQ:PL 0/0:19,0:19:57:0,57,653 0/0:12,0:12:36:0,36,423 0/0:21,0:21:63:0,63,740 0/0:6,0:6:15:0,15,157 0/0:2,0:2:6:0,6,63 0/0:6,0:6:15:0,15,159 0/0:14,0:14:42:0,42,455 0/0:18,0:18:54:0,54,624 0/0:14,0:14:39:0,39,447 0/0:25,0:25:72:0,72,805 0/0:16,0:16:48:0,48,564 0/1:13,8:20:99:190,0,314 0/0:21,0:21:63:0,63,702 0/0:17,1:18:18:0,18,560 0/0:11,0:11:30:0,30,342 0/0:12,0:12:36:0,36,393 +1 898323 rs6605071 T C 353673.96 PASS AC=31;AF=9.69000e-01;AN=32;BaseQRankSum=1.91890e+01;DB;DP=221;Dels=0.00000e+00;FS=9.64600e+00;HaplotypeScore=4.04000e-01;InbreedingCoeff=-2.15000e-02;MQ=5.91700e+01;MQ0=0;MQRankSum=-4.60000e-02;QD=3.77900e+01;ReadPosRankSum=3.36900e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000463212;VQSLOD=4.11000e+00;culprit=InbreedingCoeff;CSQ=C|ENSG00000187961|ENST00000466300|Transcript|intron_variant&NMD_transcript_variant||||||rs6605071|1||1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||1/5||ENST00000466300.1:c.191+26N>C||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859|||||||||||||||||,C|ENSG00000188976|ENST00000327044|Transcript|upstream_gene_variant||||||rs6605071|1|3653|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859||||||||||EXON_INTRON_UNDEF&ANC_ALLELE|||||||,C|ENSG00000187961|ENST00000338591|Transcript|intron_variant||||||rs6605071|1||1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||6/11||ENST00000338591.3:c.1042+26N>C||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859||||||||INTRON_SIZE:191||NON_CAN_SPLICE&ANC_ALLELE|||||||,C|ENSG00000187583|ENST00000379409|Transcript|upstream_gene_variant||||||rs6605071|1|3559|1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06||||||||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859||||||||||EXON_INTRON_UNDEF&ANC_ALLELE|||||||,C|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs6605071|1|465|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859|||||||||||||||||,C|ENSG00000187583|ENST00000379407|Transcript|upstream_gene_variant||||||rs6605071|1|3559|1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF||||||||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859||||||||||EXON_INTRON_UNDEF&ANC_ALLELE|||||||,C|ENSG00000188976|ENST00000469563|Transcript|upstream_gene_variant||||||rs6605071|1|3687|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859|||||||||||||||||,C|ENSG00000187583|ENST00000379410|Transcript|upstream_gene_variant||||||rs6605071|1|3554|1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8||||||||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859||||||||||EXON_INTRON_UNDEF&ANC_ALLELE|||||||,C|ENSG00000188976|ENST00000477976|Transcript|upstream_gene_variant||||||rs6605071|1|4485|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859|||||||||||||||||,C|ENSG00000187961|ENST00000481067|Transcript|upstream_gene_variant||||||rs6605071|1|609|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859|||||||||||||||||,C|ENSG00000188976|ENST00000487214|Transcript|upstream_gene_variant||||||rs6605071|1|3634|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859||||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,18:18:54:688,54,0 1/1:0,8:8:24:315,24,0 1/1:0,15:15:45:579,45,0 1/1:0,7:7:21:262,21,0 1/1:0,3:3:9:111,9,0 1/1:0,4:4:9:122,9,0 1/1:0,20:20:60:786,60,0 1/1:0,16:16:48:641,48,0 1/1:0,13:13:36:457,36,0 1/1:0,27:27:78:1030,78,0 1/1:0,18:18:54:720,54,0 0/1:13,4:17:99:112,0,396 1/1:0,18:18:54:708,54,0 1/1:0,13:13:39:525,39,0 1/1:0,10:10:30:393,30,0 1/1:1,13:14:5:460,5,0 +1 898467 rs41285808 C T 14490.29 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-2.26300e+00;DB;DP=270;Dels=0.00000e+00;FS=1.33000e+00;HaplotypeScore=2.81700e-01;InbreedingCoeff=3.75000e-02;MQ=5.93000e+01;MQ0=0;MQRankSum=3.96000e+00;QD=1.37100e+01;ReadPosRankSum=-1.57400e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000463212;VQSLOD=7.17000e+00;culprit=FS;CSQ=T|ENSG00000187961|ENST00000466300|Transcript|synonymous_variant&NMD_transcript_variant|247|249|83|P|ccC/ccT|rs41285808|1||1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E|||2/6|||ENST00000466300.1:c.247N>T|ENST00000466300.1:c.247N>T(p.%3D)|T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672|||||||||||||||||,T|ENSG00000188976|ENST00000327044|Transcript|upstream_gene_variant||||||rs41285808|1|3797|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187961|ENST00000338591|Transcript|intron_variant||||||rs41285808|1||1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||6/11||ENST00000338591.3:c.1043-22N>T||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672||||||||INTRON_SIZE:191||NON_CAN_SPLICE|||||||,T|ENSG00000187583|ENST00000379409|Transcript|upstream_gene_variant||||||rs41285808|1|3415|1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06||||||||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs41285808|1|609|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672|||||||||||||||||,T|ENSG00000187583|ENST00000379407|Transcript|upstream_gene_variant||||||rs41285808|1|3415|1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF||||||||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000469563|Transcript|upstream_gene_variant||||||rs41285808|1|3831|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672|||||||||||||||||,T|ENSG00000187583|ENST00000379410|Transcript|upstream_gene_variant||||||rs41285808|1|3410|1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8||||||||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000477976|Transcript|upstream_gene_variant||||||rs41285808|1|4629|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672|||||||||||||||||,T|ENSG00000187961|ENST00000481067|Transcript|upstream_gene_variant||||||rs41285808|1|465|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672|||||||||||||||||,T|ENSG00000188976|ENST00000487214|Transcript|upstream_gene_variant||||||rs41285808|1|3778|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672||||||||||||||||| GT:AD:DP:GQ:PL 0/0:28,0:28:84:0,84,1030 0/0:15,0:15:45:0,45,579 0/0:25,0:25:75:0,75,916 0/0:6,0:6:18:0,18,197 0/0:5,0:5:15:0,15,172 0/0:3,0:3:9:0,9,100 0/0:14,0:14:42:0,42,480 0/0:22,0:22:66:0,66,817 0/0:23,0:23:69:0,69,831 0/0:12,0:12:36:0,36,431 0/0:18,0:18:51:0,51,646 0/1:17,10:26:99:278,0,440 0/0:21,0:21:51:0,51,644 0/0:13,0:13:39:0,39,481 0/0:18,0:18:54:0,54,666 0/0:21,0:21:60:0,60,723 +1 899959 . G GC 2073.57 PASS AC=1;AF=5.00000e-02;AN=20;BaseQRankSum=8.77000e-01;DP=19;FS=1.24470e+02;HaplotypeScore=1.51273e+01;InbreedingCoeff=6.94000e-02;MQ=4.52200e+01;MQ0=0;MQRankSum=-8.47500e+00;QD=1.40100e+01;ReadPosRankSum=4.26000e-01;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000463212;CSQ=C|ENSG00000187583|ENST00000379409|Transcript|upstream_gene_variant||||||TMP_ESP_1_899960_899959|1|1922|1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06|||||||||||||C:0.152075|C:0.090390||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||TMP_ESP_1_899960_899959|1|2101|1|KLHL17|HGNC|24023|retained_intron||||||||||||||||||||C:0.152075|C:0.090390|||||||||||||||||,C|ENSG00000187583|ENST00000379407|Transcript|upstream_gene_variant||||||TMP_ESP_1_899960_899959|1|1922|1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF|||||||||||||C:0.152075|C:0.090390||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000466300|Transcript|downstream_gene_variant||||||TMP_ESP_1_899960_899959|1|49|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E|||||||||||||C:0.152075|C:0.090390|||||||||||||||||,C|ENSG00000187583|ENST00000379410|Transcript|upstream_gene_variant||||||TMP_ESP_1_899960_899959|1|1917|1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8|||||||||||||C:0.152075|C:0.090390||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000481067|Transcript|downstream_gene_variant||||||TMP_ESP_1_899960_899959|1|415|1|KLHL17|HGNC|24023|retained_intron||||||||||||||||||||C:0.152075|C:0.090390|||||||||||||||||,C|ENSG00000187961|ENST00000338591|Transcript|intron_variant||||||TMP_ESP_1_899960_899959|1||1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||11/11||ENST00000338591.3:c.1700+49_1700+50insC|||||||C:0.152075|C:0.090390||||||||INTRON_SIZE:432||NON_CAN_SPLICE||||||| GT:AD:DP:GQ:PL ./.:.:.:.:. ./.:.:.:.:. 0/0:3,0:3:9:0,9,136 0/0:1,0:1:3:0,3,45 0/0:1,0:1:3:0,3,45 0/0:2,0:2:6:0,6,91 0/1:3,1:4:28:28,0,124 0/0:2,0:2:6:0,6,74 0/0:2,0:2:6:0,6,91 0/0:2,0:2:6:0,6,91 ./.:.:.:.:. ./.:.:.:.:. ./.:.:.:.:. 0/0:1,0:1:3:0,3,45 ./.:.:.:.:. 0/0:1,0:1:3:0,3,45 +1 900505 rs28705211 G C 222602.28 PASS AC=8;AF=2.50000e-01;AN=32;BaseQRankSum=6.97200e+00;DB;DP=885;Dels=0.00000e+00;FS=4.61940e+01;HaplotypeScore=1.18840e+00;InbreedingCoeff=1.98200e-01;MQ=5.92300e+01;MQ0=0;MQRankSum=1.76580e+01;QD=1.80400e+01;ReadPosRankSum=1.01980e+01;SNPEFF_AMINO_ACID_CHANGE=V497;SNPEFF_CODON_CHANGE=gtG/gtC;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_900343_901094;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000455747;VQSLOD=1.37000e+00;culprit=HaplotypeScore;CSQ=C|ENSG00000187583|ENST00000379409|Transcript|upstream_gene_variant||||||rs28705211&COSM426805|1|1377|1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06||||||||C:0.1648|C:0.02|C:0.22|C:0.09|C:0.28||||0&1|20637081|||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs28705211&COSM426805|1|2647|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||C:0.1648|C:0.02|C:0.22|C:0.09|C:0.28||||0&1|20637081||||||||||||||,C|ENSG00000187583|ENST00000379407|Transcript|upstream_gene_variant||||||rs28705211&COSM426805|1|1377|1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF||||||||C:0.1648|C:0.02|C:0.22|C:0.09|C:0.28||||0&1|20637081|||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000466300|Transcript|downstream_gene_variant||||||rs28705211&COSM426805|1|595|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||C:0.1648|C:0.02|C:0.22|C:0.09|C:0.28||||0&1|20637081||||||||||||||,C|ENSG00000187583|ENST00000379410|Transcript|upstream_gene_variant||||||rs28705211&COSM426805|1|1372|1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8||||||||C:0.1648|C:0.02|C:0.22|C:0.09|C:0.28||||0&1|20637081|||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000481067|Transcript|downstream_gene_variant||||||rs28705211&COSM426805|1|961|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||C:0.1648|C:0.02|C:0.22|C:0.09|C:0.28||||0&1|20637081||||||||||||||,C|ENSG00000187961|ENST00000338591|Transcript|synonymous_variant|1970|1863|621|V|gtG/gtC|rs28705211&COSM426805|1||1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0|||12/12||SMART_domains:SM00612&Superfamily_domains:SSF117281&PIRSF_domain:PIRSF037037|ENST00000338591.3:c.1863N>C|ENST00000338591.3:c.1863N>C(p.%3D)|C:0.1648|C:0.02|C:0.22|C:0.09|C:0.28||||0&1|20637081|||||POSITION:0.965785381026439||END_TRUNC&NON_CAN_SPLICE_SURR||||||| GT:AD:DP:GQ:PL 0/0:87,0:87:99:0,262,3217 0/1:43,24:61:99:697,0,1146 0/1:35,29:60:99:812,0,913 0/0:23,0:23:69:0,69,851 0/0:22,0:22:66:0,66,788 0/0:33,1:34:96:0,96,1150 0/0:54,0:54:99:0,162,1973 0/1:32,27:56:99:720,0,880 0/0:79,0:79:99:0,235,2850 0/0:74,0:74:99:0,214,2587 0/0:65,0:65:99:0,196,2354 0/1:24,26:48:99:738,0,687 0/1:27,28:54:99:795,0,709 0/0:58,0:58:99:0,175,2173 0/1:28,27:54:99:805,0,735 1/1:0,56:56:99:2066,169,0 +1 902024 rs181910588 G A 406.47 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-3.35500e+00;DB;DP=225;Dels=0.00000e+00;FS=1.03150e+01;HaplotypeScore=3.56800e-01;InbreedingCoeff=-1.33000e-02;MQ=5.93500e+01;MQ0=0;MQRankSum=1.21200e+00;QD=1.09900e+01;ReadPosRankSum=-1.50700e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000338591;VQSLOD=6.64000e+00;culprit=InbreedingCoeff;CSQ=A|ENSG00000187583|ENST00000480267|Transcript|upstream_gene_variant||||||rs181910588|1|4231|1|PLEKHN1|HGNC|25284|retained_intron|||||||||||||||A:0.0023|A:0.01||||A:0.001842|A:0|||||||||||||||||,A|ENSG00000187961|ENST00000466300|Transcript|downstream_gene_variant||||||rs181910588|1|2114|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||A:0.0023|A:0.01||||A:0.001842|A:0|||||||||||||||||,A|ENSG00000187961|ENST00000338591|Transcript|downstream_gene_variant||||||rs181910588|1|929|1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||||||A:0.0023|A:0.01||||A:0.001842|A:0||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs181910588|1|4166|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0023|A:0.01||||A:0.001842|A:0|||||||||||||||||,A|ENSG00000187583|ENST00000379409|Transcript|intron_variant||||||rs181910588|1||1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06||||1/14||ENST00000379409.2:c.83+30N>A||A:0.0023|A:0.01||||A:0.001842|A:0||||||||INTRON_SIZE:89||NON_CAN_SPLICE|||||||,A|ENSG00000187583|ENST00000379407|Transcript|intron_variant||||||rs181910588|1||1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF||||1/14||ENST00000379407.3:c.83+30N>A||A:0.0023|A:0.01||||A:0.001842|A:0||||||||INTRON_SIZE:89||NON_CAN_SPLICE|||||||,A|ENSG00000187961|ENST00000481067|Transcript|downstream_gene_variant||||||rs181910588|1|2480|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0023|A:0.01||||A:0.001842|A:0|||||||||||||||||,A|ENSG00000187583|ENST00000379410|Transcript|intron_variant||||||rs181910588|1||1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8||||1/15||ENST00000379410.3:c.83+30N>A||A:0.0023|A:0.01||||A:0.001842|A:0||||||||INTRON_SIZE:89||NON_CAN_SPLICE|||||||,A||ENSR00000528862|RegulatoryFeature|regulatory_region_variant||||||rs181910588|1||||||regulatory_region|||||||||||||||A:0.0023|A:0.01||||A:0.001842|A:0||||||||||||||||| GT:AD:DP:GQ:PL 0/0:18,0:18:54:0,54,689 0/0:21,0:21:63:0,63,797 0/0:17,0:17:48:0,48,608 0/0:5,0:5:15:0,15,182 0/0:9,0:9:27:0,27,333 0/0:7,0:7:21:0,21,253 0/0:18,0:18:54:0,54,680 0/0:7,0:7:21:0,21,259 0/0:17,0:17:51:0,51,614 0/0:19,0:19:54:0,54,647 0/0:20,0:20:60:0,60,756 0/0:14,0:14:42:0,42,518 0/0:13,0:13:36:0,36,466 0/0:14,0:14:42:0,42,535 0/1:9,1:11:4:4,0,296 0/0:15,0:15:45:0,45,551 +1 902069 rs116147894 T C 13024.04 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=2.08840e+01;DB;DP=157;Dels=0.00000e+00;FS=3.07700e+00;HaplotypeScore=2.10500e-01;InbreedingCoeff=1.00200e-01;MQ=5.91800e+01;MQ0=0;MQRankSum=7.75000e-01;QD=1.56200e+01;ReadPosRankSum=-5.68400e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000338591;VQSLOD=7.17000e+00;culprit=MQ;CSQ=C|ENSG00000187583|ENST00000480267|Transcript|upstream_gene_variant||||||rs116147894|1|4186|1|PLEKHN1|HGNC|25284|retained_intron|||||||||||||||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163|||||||||||||||||,C|ENSG00000187961|ENST00000466300|Transcript|downstream_gene_variant||||||rs116147894|1|2159|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163|||||||||||||||||,C|ENSG00000187961|ENST00000338591|Transcript|downstream_gene_variant||||||rs116147894|1|974|1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||||||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs116147894|1|4211|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163|||||||||||||||||,C|ENSG00000187583|ENST00000379409|Transcript|intron_variant||||||rs116147894|1||1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06||||1/14||ENST00000379409.2:c.84-15N>C||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163||||||||INTRON_SIZE:89||NON_CAN_SPLICE|||||||,C|ENSG00000187583|ENST00000379407|Transcript|intron_variant||||||rs116147894|1||1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF||||1/14||ENST00000379407.3:c.84-15N>C||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163||||||||INTRON_SIZE:89||NON_CAN_SPLICE|||||||,C|ENSG00000187961|ENST00000481067|Transcript|downstream_gene_variant||||||rs116147894|1|2525|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163|||||||||||||||||,C|ENSG00000187583|ENST00000379410|Transcript|intron_variant||||||rs116147894|1||1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8||||1/15||ENST00000379410.3:c.84-15N>C||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163||||||||INTRON_SIZE:89||NON_CAN_SPLICE|||||||,C||ENSR00000528862|RegulatoryFeature|regulatory_region_variant||||||rs116147894|1||||||regulatory_region|||||||||||||||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163||||||||||||||||| GT:AD:DP:GQ:PL 0/0:10,0:10:30:0,30,367 0/1:12,2:13:3:3,0,418 0/0:14,0:14:42:0,42,514 0/0:4,0:4:12:0,12,144 0/0:5,0:5:15:0,15,176 0/0:4,0:4:12:0,12,145 0/0:17,0:17:48:0,48,603 0/0:6,0:6:18:0,18,227 0/0:10,0:10:30:0,30,361 0/0:10,0:10:30:0,30,372 0/0:12,0:12:36:0,36,434 0/0:7,0:7:21:0,21,259 0/0:7,0:7:21:0,21,255 0/0:11,0:11:30:0,30,375 0/0:12,0:12:36:0,36,426 0/0:15,0:15:45:0,45,530 +1 902088 . G A 324.34 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-5.34900e+00;DP=133;Dels=0.00000e+00;FS=7.94000e-01;HaplotypeScore=1.50400e-01;InbreedingCoeff=3.03000e-02;MQ=5.93200e+01;MQ0=0;MQRankSum=2.32200e+00;QD=7.91000e+00;ReadPosRankSum=-2.12100e+00;SNPEFF_AMINO_ACID_CHANGE=D30N;SNPEFF_CODON_CHANGE=Gac/Aac;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_902084_902183;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=PLEKHN1;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000379407;VQSLOD=5.23000e+00;culprit=QD;CSQ=A|ENSG00000187583|ENST00000480267|Transcript|upstream_gene_variant||||||rs201730138|1|4167|1|PLEKHN1|HGNC|25284|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187961|ENST00000466300|Transcript|downstream_gene_variant||||||rs201730138|1|2178|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187961|ENST00000338591|Transcript|downstream_gene_variant||||||rs201730138|1|993|1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||||||A:0.0005||A:0.0028|||A:0|A:0.000600||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs201730138|1|4230|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187583|ENST00000379409|Transcript|missense_variant|118|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06|tolerated(0.26)|benign(0.034)|2/15|||ENST00000379409.2:c.88N>A|ENSP00000368719.2:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0441767068273092||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A|ENSG00000187583|ENST00000379407|Transcript|missense_variant|118|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF|tolerated(0.25)|benign(0.072)|2/15|||ENST00000379407.3:c.88N>A|ENSP00000368717.2:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0508376660889659||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A|ENSG00000187961|ENST00000481067|Transcript|downstream_gene_variant||||||rs201730138|1|2544|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187583|ENST00000379410|Transcript|missense_variant|123|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8|tolerated(0.25)|benign(0.072)|2/16|||ENST00000379410.3:c.88N>A|ENSP00000368720.3:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0479302832244009||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A||ENSR00000528862|RegulatoryFeature|regulatory_region_variant||||||rs201730138|1||||||regulatory_region|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600||||||||||||||||| GT:AD:DP:GQ:PL 0/1:10,1:11:1:1,0,264 0/0:13,0:13:33:0,33,447 0/0:10,0:10:30:0,30,371 0/0:4,0:4:12:0,12,141 0/0:1,0:1:3:0,3,39 0/0:4,0:4:12:0,12,145 0/0:18,0:18:51:0,51,665 0/0:4,0:4:12:0,12,148 0/0:5,0:5:15:0,15,193 0/0:9,0:9:24:0,24,320 0/0:10,0:10:30:0,30,378 0/0:4,0:4:12:0,12,160 0/0:10,0:10:30:0,30,387 0/0:7,0:7:21:0,21,247 0/0:9,0:9:27:0,27,350 0/0:14,0:14:42:0,42,540 +1 902088 . G ACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACT 324.34 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-5.34900e+00;DP=133;Dels=0.00000e+00;FS=7.94000e-01;HaplotypeScore=1.50400e-01;InbreedingCoeff=3.03000e-02;MQ=5.93200e+01;MQ0=0;MQRankSum=2.32200e+00;QD=7.91000e+00;ReadPosRankSum=-2.12100e+00;SNPEFF_AMINO_ACID_CHANGE=D30N;SNPEFF_CODON_CHANGE=Gac/Aac;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_902084_902183;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=PLEKHN1;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000379407;VQSLOD=5.23000e+00;culprit=QD;CSQ=A|ENSG00000187583|ENST00000480267|Transcript|upstream_gene_variant||||||rs201730138|1|4167|1|PLEKHN1|HGNC|25284|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187961|ENST00000466300|Transcript|downstream_gene_variant||||||rs201730138|1|2178|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187961|ENST00000338591|Transcript|downstream_gene_variant||||||rs201730138|1|993|1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||||||A:0.0005||A:0.0028|||A:0|A:0.000600||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs201730138|1|4230|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187583|ENST00000379409|Transcript|missense_variant|118|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06|tolerated(0.26)|benign(0.034)|2/15|||ENST00000379409.2:c.88N>A|ENSP00000368719.2:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0441767068273092||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A|ENSG00000187583|ENST00000379407|Transcript|missense_variant|118|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF|tolerated(0.25)|benign(0.072)|2/15|||ENST00000379407.3:c.88N>A|ENSP00000368717.2:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0508376660889659||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A|ENSG00000187961|ENST00000481067|Transcript|downstream_gene_variant||||||rs201730138|1|2544|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187583|ENST00000379410|Transcript|missense_variant|123|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8|tolerated(0.25)|benign(0.072)|2/16|||ENST00000379410.3:c.88N>A|ENSP00000368720.3:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0479302832244009||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A||ENSR00000528862|RegulatoryFeature|regulatory_region_variant||||||rs201730138|1||||||regulatory_region|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600||||||||||||||||| GT:AD:DP:GQ:PL 0/1:10,1:11:1:1,0,264 0/0:13,0:13:33:0,33,447 0/0:10,0:10:30:0,30,371 0/0:4,0:4:12:0,12,141 0/0:1,0:1:3:0,3,39 0/0:4,0:4:12:0,12,145 0/0:18,0:18:51:0,51,665 0/0:4,0:4:12:0,12,148 0/0:5,0:5:15:0,15,193 0/0:9,0:9:24:0,24,320 0/0:10,0:10:30:0,30,378 0/0:4,0:4:12:0,12,160 0/0:10,0:10:30:0,30,387 0/0:7,0:7:21:0,21,247 0/0:9,0:9:27:0,27,350 0/0:14,0:14:42:0,42,540 +GL000207.1 1 . G A 324.34 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-5.34900e+00;DP=133;Dels=0.00000e+00;FS=7.94000e-01;HaplotypeScore=1.50400e-01;InbreedingCoeff=3.03000e-02;MQ=5.93200e+01;MQ0=0;MQRankSum=2.32200e+00;QD=7.91000e+00;ReadPosRankSum=-2.12100e+00;SNPEFF_AMINO_ACID_CHANGE=D30N;SNPEFF_CODON_CHANGE=Gac/Aac;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_902084_902183;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=PLEKHN1;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000379407;VQSLOD=5.23000e+00;culprit=QD;CSQ=A|ENSG00000187583|ENST00000480267|Transcript|upstream_gene_variant||||||rs201730138|1|4167|1|PLEKHN1|HGNC|25284|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187961|ENST00000466300|Transcript|downstream_gene_variant||||||rs201730138|1|2178|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187961|ENST00000338591|Transcript|downstream_gene_variant||||||rs201730138|1|993|1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||||||A:0.0005||A:0.0028|||A:0|A:0.000600||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs201730138|1|4230|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187583|ENST00000379409|Transcript|missense_variant|118|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06|tolerated(0.26)|benign(0.034)|2/15|||ENST00000379409.2:c.88N>A|ENSP00000368719.2:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0441767068273092||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A|ENSG00000187583|ENST00000379407|Transcript|missense_variant|118|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF|tolerated(0.25)|benign(0.072)|2/15|||ENST00000379407.3:c.88N>A|ENSP00000368717.2:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0508376660889659||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A|ENSG00000187961|ENST00000481067|Transcript|downstream_gene_variant||||||rs201730138|1|2544|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187583|ENST00000379410|Transcript|missense_variant|123|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8|tolerated(0.25)|benign(0.072)|2/16|||ENST00000379410.3:c.88N>A|ENSP00000368720.3:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0479302832244009||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A||ENSR00000528862|RegulatoryFeature|regulatory_region_variant||||||rs201730138|1||||||regulatory_region|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600||||||||||||||||| GT:AD:DP:GQ:PL 0/1:10,1:11:1:1,0,264 0/0:13,0:13:33:0,33,447 0/0:10,0:10:30:0,30,371 0/0:4,0:4:12:0,12,141 0/0:1,0:1:3:0,3,39 0/0:4,0:4:12:0,12,145 0/0:18,0:18:51:0,51,665 0/0:4,0:4:12:0,12,148 0/0:5,0:5:15:0,15,193 0/0:9,0:9:24:0,24,320 0/0:10,0:10:30:0,30,378 0/0:4,0:4:12:0,12,160 0/0:10,0:10:30:0,30,387 0/0:7,0:7:21:0,21,247 0/0:9,0:9:27:0,27,350 0/0:14,0:14:42:0,42,540 diff --git a/loading_pipeline/var/test/callsets/1kg_corrupt.vcf.gz b/loading_pipeline/var/test/callsets/1kg_corrupt.vcf.gz new file mode 100644 index 0000000000000000000000000000000000000000..c175f00b6ab30fdb0009c51dbcd9d1ead290d550 GIT binary patch literal 14872 zcmV+zI_Je7iwFP^yboyr1MPk5Qye+A=V$JpaVMr@X1ko|=&kb75g0Jdj*T(UeediS z2jgZuj_bBNFnxDBqW<_jM^a`gAF9gCdVn{;n1swyN;-O--+BJ&PyhV*>Gq#r?tZmRTcy)o{V_TQG8e7Tjr>|psa&mq=zGW}3##Zy=&2OK+ z+~Y^D-ha8f9b5YB^FQuxZ-2oFdi3S?pZ^?N{PnAoDbtXOjh>0G+sko42{wKNUQeC5 zZ`;GYvc%=Z;dt6z{xo!dsf*m+{BrT->%@LtonM^1eEIJ1_1XEGcZWx3$M24QJUl-= 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+##contig= +##contig= +##contig= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00731 HG00732 HG00733 NA19675 NA19678 NA19679 NA20870 NA20872 NA20874 NA20875 NA20876 NA20877 NA20878 NA20881 NA20885 NA20888 +1 871269 . A C 368.47 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-1.74060e+01;DP=351;Dels=0.00000e+00;FS=9.28030e+01;HaplotypeScore=5.13800e-01;InbreedingCoeff=-3.32000e-02;MQ=5.93000e+01;MQ0=0;MQRankSum=2.37300e+00;QD=4.80000e-01;ReadPosRankSum=-1.17980e+01;SNPEFF_AMINO_ACID_CHANGE=R141;SNPEFF_CODON_CHANGE=cgA/cgC;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_871152_871276;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=SAMD11;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000342066;VQSLOD=-8.16700e-01;culprit=QD;CSQ=C|ENSG00000187634|ENST00000455979|Transcript|upstream_gene_variant|||||||1|3386|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187634|ENST00000420190|Transcript|synonymous_variant|512|423|141|R|cgA/cgC||1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000411579||Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI000155D47C|||5/7|||ENST00000420190.1:c.423N>C|ENST00000420190.1:c.423N>C(p.%3D)|||||||||||||||POSITION:0.787709497206704||NON_CAN_SPLICE_SURR|||||||,C|ENSG00000268179|ENST00000598827|Transcript|upstream_gene_variant|||||||1|4824|-1|AL645608.1|Clone_based_ensembl_gene||protein_coding|YES|||ENSP00000471152||M0R0C9_HUMAN|UPI0000D61E05||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187634|ENST00000437963|Transcript|downstream_gene_variant|||||||1|96|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000393181||Q5SV95_HUMAN&I7FV93_HUMAN|UPI000155D47B||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187634|ENST00000478729|Transcript|upstream_gene_variant|||||||1|4457|1|SAMD11|HGNC|28706|processed_transcript||||||||||||||||||||||||||||||||||||||,C|ENSG00000187634|ENST00000342066|Transcript|synonymous_variant|506|423|141|R|cgA/cgC||1||1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04|||5/14|||ENST00000342066.3:c.423N>C|ENST00000342066.3:c.423N>C(p.%3D)|||||||||||||||POSITION:0.206744868035191||NON_CAN_SPLICE_SURR|||||||,C|ENSG00000187634|ENST00000341065|Transcript|synonymous_variant|194|195|65|R|cgA/cgC||1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A|||3/12|||ENST00000341065.4:c.194N>C|ENST00000341065.4:c.194N>C(p.%3D)|||||||||||||||POSITION:0.110231769361221||NON_CAN_SPLICE_SURR|||||||,C||ENSR00000528855|RegulatoryFeature|regulatory_region_variant|||||||1||||||regulatory_region|||||||||||||||||||||||||||||||||||||| GT:AD:DP:GQ:PL 0/0:34,0:34:99:0,102,1073 0/0:34,0:34:99:0,102,1064 0/0:37,0:37:99:0,108,1155 0/0:8,3:11:24:0,24,226 0/1:11,4:16:32:32,0,300 0/0:10,0:10:30:0,30,306 0/0:13,0:13:39:0,39,410 0/0:11,0:11:33:0,33,323 0/0:21,3:23:12:0,12,434 0/0:19,0:19:57:0,57,581 0/0:25,4:28:27:0,27,553 0/0:17,1:18:51:0,51,524 0/0:25,0:25:75:0,75,759 0/0:21,0:21:63:0,63,687 0/0:23,4:27:69:0,69,709 0/0:22,2:24:60:0,60,562 +1 874734 rs145967298 C T 2645.29 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-7.95400e+00;DB;DP=484;Dels=0.00000e+00;FS=7.13100e+00;HaplotypeScore=3.21100e-01;InbreedingCoeff=-6.80000e-03;MQ=5.85800e+01;MQ0=1;MQRankSum=7.38500e+00;QD=1.23600e+01;ReadPosRankSum=-7.54000e-01;SNPEFF_AMINO_ACID_CHANGE=S200;SNPEFF_CODON_CHANGE=agC/agT;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_874655_874840;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=SAMD11;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000342066;VQSLOD=5.39000e+00;culprit=InbreedingCoeff;CSQ=T|ENSG00000187634|ENST00000420190|Transcript|downstream_gene_variant||||||rs145967298|1|63|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000411579||Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI000155D47C||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187634|ENST00000342066|Transcript|synonymous_variant|683|600|200|S|agC/agT|rs145967298|1||1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04|||7/14|||ENST00000342066.3:c.600N>T|ENST00000342066.3:c.600N>T(p.%3D)|T:0.0009||T:0.01|||T:0.000227|T:0.001628||||||||POSITION:0.293255131964809||NON_CAN_SPLICE_SURR|||||||,T|ENSG00000188976|ENST00000327044|Transcript|downstream_gene_variant||||||rs145967298|1|4850|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187634|ENST00000464948|Transcript|upstream_gene_variant||||||rs145967298|1|2812|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628|||||||||||||||||,T|ENSG00000187634|ENST00000466827|Transcript|upstream_gene_variant||||||rs145967298|1|2749|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628|||||||||||||||||,T|ENSG00000187634|ENST00000474461|Transcript|upstream_gene_variant||||||rs145967298|1|1722|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628|||||||||||||||||,T|ENSG00000188976|ENST00000483767|Transcript|downstream_gene_variant||||||rs145967298|1|4850|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628|||||||||||||||||,T|ENSG00000187634|ENST00000455979|Transcript|synonymous_variant|80|81|27|S|agC/agT|rs145967298|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479|||1/7|||ENST00000455979.1:c.80N>T|ENST00000455979.1:c.80N>T(p.%3D)|T:0.0009||T:0.01|||T:0.000227|T:0.001628||||||||POSITION:0.0498461538461538||NON_CAN_SPLICE_SURR|||||||,T|ENSG00000187634|ENST00000437963|Transcript|downstream_gene_variant||||||rs145967298|1|3561|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000393181||Q5SV95_HUMAN&I7FV93_HUMAN|UPI000155D47B||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187634|ENST00000478729|Transcript|upstream_gene_variant||||||rs145967298|1|992|1|SAMD11|HGNC|28706|processed_transcript|||||||||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628|||||||||||||||||,T|ENSG00000188976|ENST00000477976|Transcript|downstream_gene_variant||||||rs145967298|1|4851|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628|||||||||||||||||,T|ENSG00000187634|ENST00000341065|Transcript|synonymous_variant|371|372|124|S|agC/agT|rs145967298|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A|||5/12|||ENST00000341065.4:c.371N>T|ENST00000341065.4:c.371N>T(p.%3D)|T:0.0009||T:0.01|||T:0.000227|T:0.001628||||||||POSITION:0.210288298473714||NON_CAN_SPLICE_SURR|||||||,T||ENSR00001516735|RegulatoryFeature|regulatory_region_variant||||||rs145967298|1||||||regulatory_region|||||||||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628||||||||||||||||| GT:AD:DP:GQ:PL 0/0:37,0:37:99:0,111,1368 0/0:24,0:24:66:0,66,870 0/0:32,0:32:96:0,96,1183 0/0:8,0:8:24:0,24,245 0/0:8,0:8:24:0,24,267 0/0:9,0:9:27:0,27,318 0/0:26,0:26:75:0,75,879 0/0:31,0:31:93:0,93,1120 0/0:39,0:39:99:0,117,1375 0/0:56,0:56:99:0,169,2023 0/1:21,22:42:99:519,0,613 0/0:29,0:29:87:0,87,1048 0/0:43,0:43:99:0,129,1556 0/0:20,0:20:60:0,60,741 0/0:45,0:45:99:0,135,1586 0/0:35,0:35:99:0,105,1239 +1 876499 rs4372192 A G 212847.01 PASS AC=31;AF=9.69000e-01;AN=32;BaseQRankSum=2.42570e+01;DB;DP=122;Dels=1.00000e-02;FS=9.96800e+00;HaplotypeScore=2.51500e-01;InbreedingCoeff=4.11000e-02;MQ=5.91300e+01;MQ0=0;MQRankSum=7.64000e-01;QD=3.03200e+01;ReadPosRankSum=2.13900e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=4.70000e+00;culprit=MQ;CSQ=G|ENSG00000187634|ENST00000420190|Transcript|downstream_gene_variant||||||rs4372192|1|1828|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000411579||Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI000155D47C||||||||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676||||||||||EXON_INTRON_UNDEF&ANC_ALLELE|||||||,G|ENSG00000188976|ENST00000496938|Transcript|downstream_gene_variant||||||rs4372192|1|4200|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676|||||||||||||||||,G|ENSG00000187634|ENST00000342066|Transcript|intron_variant||||||rs4372192|1||1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04||||7/13||ENST00000342066.3:c.707-25N>G||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676||||||||INTRON_SIZE:1683||NON_CAN_SPLICE&ANC_ALLELE|||||||,G|ENSG00000188976|ENST00000327044|Transcript|downstream_gene_variant||||||rs4372192|1|3085|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676||||||||||EXON_INTRON_UNDEF&ANC_ALLELE|||||||,G|ENSG00000187634|ENST00000464948|Transcript|upstream_gene_variant||||||rs4372192|1|1047|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676|||||||||||||||||,G|ENSG00000187634|ENST00000466827|Transcript|upstream_gene_variant||||||rs4372192|1|984|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676|||||||||||||||||,G|ENSG00000187634|ENST00000474461|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|44|||||rs4372192|1||1|SAMD11|HGNC|28706|retained_intron||||||||||1/4|||ENST00000474461.1:n.44N>G||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676|||||||||||||||||,G|ENSG00000187634|ENST00000455979|Transcript|intron_variant||||||rs4372192|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479||||1/6||ENST00000455979.1:c.187-25N>G||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676||||||||INTRON_SIZE:1683||NON_CAN_SPLICE&ANC_ALLELE|||||||,G|ENSG00000188976|ENST00000483767|Transcript|downstream_gene_variant||||||rs4372192|1|3085|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676|||||||||||||||||,G|ENSG00000187634|ENST00000478729|Transcript|intron_variant&non_coding_transcript_variant||||||rs4372192|1||1|SAMD11|HGNC|28706|processed_transcript|||||||||||1/2||ENST00000478729.1:n.118-25N>G||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676|||||||||||||||||,G|ENSG00000188976|ENST00000477976|Transcript|downstream_gene_variant||||||rs4372192|1|3086|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676|||||||||||||||||,G|ENSG00000187634|ENST00000341065|Transcript|intron_variant||||||rs4372192|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A||||5/11||ENST00000341065.4:c.430-25N>G||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676||||||||INTRON_SIZE:1731||NON_CAN_SPLICE&ANC_ALLELE|||||||,G||ENSR00000528857|RegulatoryFeature|regulatory_region_variant||||||rs4372192|1||||||regulatory_region|||||||||||||||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676||||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,7:7:21:253,21,0 1/1:0,8:8:24:296,24,0 1/1:0,4:4:12:148,12,0 1/1:0,5:5:15:184,15,0 1/1:0,1:1:3:39,3,0 1/1:0,5:5:15:176,15,0 1/1:0,9:9:27:316,27,0 1/1:0,11:11:33:397,33,0 1/1:0,7:7:18:212,18,0 1/1:0,11:11:27:369,27,0 1/1:0,13:13:39:492,39,0 0/1:7,9:15:99:235,0,158 1/1:0,7:7:18:231,18,0 1/1:0,4:4:12:154,12,0 1/1:0,8:8:24:296,24,0 1/1:0,7:7:21:270,21,0 +1 878314 rs142558220 G C 2808.55 PASS AC=3;AF=9.40000e-02;AN=32;BaseQRankSum=1.88800e+00;DB;DP=117;Dels=0.00000e+00;FS=1.06220e+01;HaplotypeScore=2.21900e-01;InbreedingCoeff=3.64000e-02;MQ=5.94000e+01;MQ0=1;MQRankSum=1.65200e+00;QD=9.46000e+00;ReadPosRankSum=-3.88300e+00;SNPEFF_AMINO_ACID_CHANGE=G480;SNPEFF_CODON_CHANGE=ggG/ggC;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_877939_878438;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=SAMD11;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000342066;VQSLOD=6.85000e+00;culprit=QD;CSQ=C|ENSG00000187634|ENST00000420190|Transcript|downstream_gene_variant||||||rs142558220&COSM426784|1|3643|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000411579||Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI000155D47C||||||||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000188976|ENST00000496938|Transcript|downstream_gene_variant||||||rs142558220&COSM426784|1|2385|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1|||||||||||||||,C|ENSG00000187634|ENST00000342066|Transcript|synonymous_variant|1523|1440|480|G|ggG/ggC|rs142558220&COSM426784|1||1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04|||11/14|||ENST00000342066.3:c.1440N>C|ENST00000342066.3:c.1440N>C(p.%3D)|C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1||||||POSITION:0.703812316715543||NON_CAN_SPLICE_SURR|||||||,C|ENSG00000188976|ENST00000327044|Transcript|downstream_gene_variant||||||rs142558220&COSM426784|1|1270|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187634|ENST00000464948|Transcript|downstream_gene_variant||||||rs142558220&COSM426784|1|42|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1|||||||||||||||,C|ENSG00000187634|ENST00000466827|Transcript|downstream_gene_variant||||||rs142558220&COSM426784|1|132|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1|||||||||||||||,C|ENSG00000187634|ENST00000474461|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|802|||||rs142558220&COSM426784|1||1|SAMD11|HGNC|28706|retained_intron||||||||||4/4|||ENST00000474461.1:n.802N>C||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1|||||||||||||||,C|ENSG00000187634|ENST00000455979|Transcript|synonymous_variant|920|921|307|G|ggG/ggC|rs142558220&COSM426784|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479|||5/7|||ENST00000455979.1:c.920N>C|ENST00000455979.1:c.920N>C(p.%3D)|C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1||||||POSITION:0.566769230769231||NON_CAN_SPLICE_SURR|||||||,C|ENSG00000188976|ENST00000483767|Transcript|downstream_gene_variant||||||rs142558220&COSM426784|1|1270|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1|||||||||||||||,C|ENSG00000187634|ENST00000478729|Transcript|downstream_gene_variant||||||rs142558220&COSM426784|1|761|1|SAMD11|HGNC|28706|processed_transcript|||||||||||||||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1|||||||||||||||,C|ENSG00000188976|ENST00000477976|Transcript|downstream_gene_variant||||||rs142558220&COSM426784|1|1271|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1|||||||||||||||,C|ENSG00000187634|ENST00000341065|Transcript|synonymous_variant|1163|1164|388|G|ggG/ggC|rs142558220&COSM426784|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A|||9/12|||ENST00000341065.4:c.1163N>C|ENST00000341065.4:c.1163N>C(p.%3D)|C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1||||||POSITION:0.65799886941775||NON_CAN_SPLICE_SURR|||||||,C||ENSR00000528857|RegulatoryFeature|regulatory_region_variant||||||rs142558220&COSM426784|1||||||regulatory_region|||||||||||||||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1||||||||||||||| GT:AD:DP:GQ:PL 0/1:2,1:3:30:30,0,67 0/0:2,0:2:6:0,6,82 0/1:2,3:5:61:93,0,61 0/0:2,0:2:6:0,6,72 0/0:1,0:1:3:0,3,37 0/1:2,3:5:54:93,0,54 0/0:16,0:16:45:0,45,560 0/0:5,0:5:15:0,15,188 0/0:12,0:12:33:0,33,414 0/0:10,0:10:30:0,30,393 0/0:16,0:16:48:0,48,617 0/0:5,0:5:15:0,15,181 0/0:5,0:5:15:0,15,193 0/0:13,0:13:36:0,36,439 0/0:9,0:9:24:0,24,317 0/0:8,0:8:21:0,21,276 +1 878809 rs191952374 C T 1761.84 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-7.95300e+00;DB;DP=453;Dels=0.00000e+00;FS=1.68300e+00;HaplotypeScore=2.28500e-01;InbreedingCoeff=-3.10000e-03;MQ=5.91000e+01;MQ0=0;MQRankSum=1.29700e+00;QD=1.36600e+01;ReadPosRankSum=-8.52000e-01;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=9.25000e+00;culprit=InbreedingCoeff;CSQ=T|ENSG00000187634|ENST00000420190|Transcript|downstream_gene_variant||||||rs191952374|1|4138|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000411579||Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI000155D47C||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000496938|Transcript|downstream_gene_variant||||||rs191952374|1|1890|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636|||||||||||||||||,T|ENSG00000187634|ENST00000342066|Transcript|intron_variant||||||rs191952374|1||1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04||||12/13||ENST00000342066.3:c.1689+52N>T||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636||||||||INTRON_SIZE:320||NON_CAN_SPLICE|||||||,T|ENSG00000188976|ENST00000327044|Transcript|downstream_gene_variant||||||rs191952374|1|775|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187634|ENST00000464948|Transcript|downstream_gene_variant||||||rs191952374|1|537|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636|||||||||||||||||,T|ENSG00000187634|ENST00000466827|Transcript|downstream_gene_variant||||||rs191952374|1|627|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636|||||||||||||||||,T|ENSG00000187634|ENST00000474461|Transcript|downstream_gene_variant||||||rs191952374|1|435|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636|||||||||||||||||,T|ENSG00000187634|ENST00000455979|Transcript|intron_variant||||||rs191952374|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479||||6/6||ENST00000455979.1:c.1169+52N>T||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636||||||||INTRON_SIZE:320||NON_CAN_SPLICE|||||||,T|ENSG00000188976|ENST00000483767|Transcript|downstream_gene_variant||||||rs191952374|1|775|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636|||||||||||||||||,T|ENSG00000187634|ENST00000478729|Transcript|downstream_gene_variant||||||rs191952374|1|1256|1|SAMD11|HGNC|28706|processed_transcript|||||||||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636|||||||||||||||||,T|ENSG00000188976|ENST00000477976|Transcript|downstream_gene_variant||||||rs191952374|1|776|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636|||||||||||||||||,T|ENSG00000187634|ENST00000341065|Transcript|intron_variant||||||rs191952374|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A||||10/11||ENST00000341065.4:c.1412+52N>T||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636||||||||INTRON_SIZE:320||NON_CAN_SPLICE|||||||,T||ENSR00000528858|RegulatoryFeature|regulatory_region_variant||||||rs191952374|1||||||regulatory_region|||||||||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636||||||||||||||||| GT:AD:DP:GQ:PL 0/0:35,0:35:99:0,105,1323 0/0:24,0:24:72:0,72,960 0/0:31,0:31:93:0,93,1172 0/0:10,0:10:30:0,30,376 0/0:10,0:10:30:0,30,370 0/0:12,0:12:36:0,36,453 0/0:35,0:35:99:0,105,1376 0/0:33,0:33:99:0,99,1273 0/0:31,0:31:93:0,93,1240 0/0:33,0:33:96:0,96,1192 0/0:33,0:33:99:0,99,1281 0/0:25,0:25:75:0,75,983 0/1:18,16:33:99:488,0,504 0/0:33,0:33:99:0,99,1273 0/0:44,0:44:99:0,132,1698 0/0:31,0:31:90:0,90,1198 +1 879576 rs115979567 C T 18648.64 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-2.26830e+01;DB;DP=839;Dels=0.00000e+00;FS=2.49350e+01;HaplotypeScore=4.12600e-01;InbreedingCoeff=-2.18000e-02;MQ=5.92100e+01;MQ0=1;MQRankSum=1.02100e+00;QD=1.36100e+01;ReadPosRankSum=7.91400e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=4.39000e+00;culprit=InbreedingCoeff;CSQ=T|ENSG00000187634|ENST00000420190|Transcript|downstream_gene_variant||||||rs115979567|1|4905|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000411579||Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI000155D47C||||||||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000496938|Transcript|downstream_gene_variant||||||rs115979567|1|1123|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120|||||||||||||||||,T|ENSG00000187634|ENST00000342066|Transcript|3_prime_UTR_variant|2172|||||rs115979567|1||1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04|||14/14|||ENST00000342066.3:c.*43N>T||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120||||||||||NON_CAN_SPLICE_SURR|||||||,T|ENSG00000188976|ENST00000327044|Transcript|downstream_gene_variant||||||rs115979567|1|8|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187634|ENST00000464948|Transcript|downstream_gene_variant||||||rs115979567|1|1304|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120|||||||||||||||||,T|ENSG00000187634|ENST00000466827|Transcript|downstream_gene_variant||||||rs115979567|1|1394|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120|||||||||||||||||,T|ENSG00000187634|ENST00000474461|Transcript|downstream_gene_variant||||||rs115979567|1|1202|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120|||||||||||||||||,T|ENSG00000187634|ENST00000455979|Transcript|3_prime_UTR_variant|1668|||||rs115979567|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479|||7/7|||ENST00000455979.1:c.*43N>T||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120||||||||||NON_CAN_SPLICE_SURR|||||||,T|ENSG00000188976|ENST00000483767|Transcript|downstream_gene_variant||||||rs115979567|1|8|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120|||||||||||||||||,T|ENSG00000187634|ENST00000478729|Transcript|downstream_gene_variant||||||rs115979567|1|2023|1|SAMD11|HGNC|28706|processed_transcript|||||||||||||||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120|||||||||||||||||,T|ENSG00000188976|ENST00000477976|Transcript|downstream_gene_variant||||||rs115979567|1|9|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120|||||||||||||||||,T|ENSG00000187634|ENST00000341065|Transcript|3_prime_UTR_variant|1812|||||rs115979567|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A|||12/12|||ENST00000341065.4:c.*43N>T||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120||||||||||NON_CAN_SPLICE_SURR||||||| GT:AD:DP:GQ:PL 0/0:66,0:66:99:0,199,2441 0/1:25,28:51:99:767,0,834 0/0:55,0:55:99:0,166,2079 0/0:11,0:11:33:0,33,392 0/0:15,0:15:45:0,45,554 0/0:17,0:17:51:0,51,622 0/0:50,0:50:99:0,150,1966 0/0:65,0:65:99:0,196,2507 0/0:60,0:60:99:0,181,2268 0/0:70,0:70:99:0,211,2589 0/0:64,0:64:99:0,193,2452 0/0:65,0:65:99:0,196,2507 0/0:56,0:56:99:0,169,2117 0/0:60,0:60:99:0,181,2359 0/0:79,0:79:99:0,238,2986 0/0:55,0:55:99:0,165,2099 +1 881070 rs41285794 G A 20769.13 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-9.52200e+00;DB;DP=1185;Dels=0.00000e+00;FS=1.15500e+01;HaplotypeScore=1.69500e-01;InbreedingCoeff=-1.83000e-02;MQ=5.90700e+01;MQ0=0;MQRankSum=1.85940e+01;QD=1.31500e+01;ReadPosRankSum=-8.90700e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=SAMD11;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000342066;VQSLOD=4.22000e+00;culprit=InbreedingCoeff;CSQ=A|ENSG00000188976|ENST00000496938|Transcript|upstream_gene_variant||||||rs41285794|1|128|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651|||||||||||||||||,A|ENSG00000187634|ENST00000342066|Transcript|downstream_gene_variant||||||rs41285794|1|1115|1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04||||||||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000188976|ENST00000327044|Transcript|intron_variant||||||rs41285794|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||16/18||ENST00000327044.6:c.1918-37N>T||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651||||||||INTRON_SIZE:519||NON_CAN_SPLICE|||||||,A|ENSG00000187634|ENST00000464948|Transcript|downstream_gene_variant||||||rs41285794|1|2798|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651|||||||||||||||||,A|ENSG00000187634|ENST00000466827|Transcript|downstream_gene_variant||||||rs41285794|1|2888|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651|||||||||||||||||,A|ENSG00000187634|ENST00000474461|Transcript|downstream_gene_variant||||||rs41285794|1|2696|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651|||||||||||||||||,A|ENSG00000187634|ENST00000455979|Transcript|downstream_gene_variant||||||rs41285794|1|1431|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479||||||||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000188976|ENST00000483767|Transcript|intron_variant&non_coding_transcript_variant||||||rs41285794|1||-1|NOC2L|HGNC|24517|retained_intron|||||||||||2/4||ENST00000483767.1:n.774-37N>T||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651|||||||||||||||||,A|ENSG00000187634|ENST00000478729|Transcript|downstream_gene_variant||||||rs41285794|1|3517|1|SAMD11|HGNC|28706|processed_transcript|||||||||||||||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651|||||||||||||||||,A|ENSG00000188976|ENST00000477976|Transcript|intron_variant&non_coding_transcript_variant||||||rs41285794|1||-1|NOC2L|HGNC|24517|retained_intron|||||||||||14/16||ENST00000477976.1:n.3365-37N>T||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651|||||||||||||||||,A|ENSG00000187634|ENST00000341065|Transcript|downstream_gene_variant||||||rs41285794|1|1115|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A||||||||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651||||||||||EXON_INTRON_UNDEF||||||| GT:AD:DP:GQ:PL 0/0:78,0:78:99:0,235,2947 0/0:66,0:66:99:0,199,2595 0/0:59,0:59:99:0,178,2182 0/0:37,0:37:99:0,111,1365 0/0:36,0:36:99:0,108,1331 0/0:33,0:33:99:0,99,1192 0/0:69,0:69:99:0,208,2662 0/0:88,0:88:99:0,265,3395 0/0:98,0:98:99:0,295,3781 0/1:36,31:64:99:982,0,1021 0/0:86,0:86:99:0,259,3318 0/0:93,0:93:99:0,280,3588 0/0:92,0:92:99:0,277,3549 0/0:102,0:102:99:0,307,3935 0/0:89,0:89:99:0,268,3433 0/0:95,0:95:99:0,286,3665 +1 881627 rs2272757 G A 411792.28 PASS AC=22;AF=6.88000e-01;AN=32;BaseQRankSum=-3.32930e+01;DB;DP=644;Dels=0.00000e+00;FS=2.51600e+00;HaplotypeScore=5.86200e-01;InbreedingCoeff=3.09600e-01;MQ=5.88200e+01;MQ0=7;MQRankSum=6.81600e+00;QD=2.28900e+01;ReadPosRankSum=1.01500e+00;SNPEFF_AMINO_ACID_CHANGE=L615;SNPEFF_CODON_CHANGE=Ctg/Ttg;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_881553_881666;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=4.35000e+00;culprit=MQ;CSQ=A|ENSG00000188976|ENST00000496938|Transcript|upstream_gene_variant||||||rs2272757&COSM1344685|1|685|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1|||||||||||||||,A|ENSG00000187634|ENST00000342066|Transcript|downstream_gene_variant||||||rs2272757&COSM1344685|1|1672|1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04||||||||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000188976|ENST00000327044|Transcript|synonymous_variant|1893|1843|615|L|Ctg/Ttg|rs2272757&COSM1344685|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C|||16/19||Pfam_domain:PF03715&Superfamily_domains:SSF48371|ENST00000327044.6:c.1843N>T|ENST00000327044.6:c.1843N>T(p.%3D)|A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1||||||POSITION:0.819111111111111||NON_CAN_SPLICE_SURR|||||||,A|ENSG00000187634|ENST00000464948|Transcript|downstream_gene_variant||||||rs2272757&COSM1344685|1|3355|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1|||||||||||||||,A|ENSG00000187634|ENST00000466827|Transcript|downstream_gene_variant||||||rs2272757&COSM1344685|1|3445|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1|||||||||||||||,A|ENSG00000187634|ENST00000474461|Transcript|downstream_gene_variant||||||rs2272757&COSM1344685|1|3253|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1|||||||||||||||,A|ENSG00000187634|ENST00000455979|Transcript|downstream_gene_variant||||||rs2272757&COSM1344685|1|1988|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479||||||||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000188976|ENST00000483767|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|699|||||rs2272757&COSM1344685|1||-1|NOC2L|HGNC|24517|retained_intron||||||||||2/5|||ENST00000483767.1:n.699N>T||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1|||||||||||||||,A|ENSG00000187634|ENST00000478729|Transcript|downstream_gene_variant||||||rs2272757&COSM1344685|1|4074|1|SAMD11|HGNC|28706|processed_transcript|||||||||||||||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1|||||||||||||||,A|ENSG00000188976|ENST00000477976|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|3290|||||rs2272757&COSM1344685|1||-1|NOC2L|HGNC|24517|retained_intron||||||||||14/17|||ENST00000477976.1:n.3290N>T||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1|||||||||||||||,A|ENSG00000187634|ENST00000341065|Transcript|downstream_gene_variant||||||rs2272757&COSM1344685|1|1672|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A||||||||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1||||||||EXON_INTRON_UNDEF||||||| GT:AD:DP:GQ:PL 1/1:0,39:38:99:1384,111,0 0/0:61,0:61:99:0,184,2353 0/1:24,17:38:99:494,0,613 1/1:0,16:16:48:550,48,0 1/1:0,18:18:54:649,54,0 1/1:0,25:25:66:826,66,0 1/1:0,51:51:99:1886,153,0 0/1:25,23:46:99:661,0,639 1/1:0,33:33:99:1220,99,0 1/1:0,52:52:99:1879,156,0 1/1:0,45:45:99:1701,135,0 0/0:58,0:58:99:0,175,2237 0/1:17,18:34:99:523,0,478 1/1:0,44:44:99:1627,132,0 0/1:20,25:41:99:674,0,488 0/0:44,1:44:99:0,120,1521 +1 881918 rs35471880 G A 26418.87 PASS AC=5;AF=1.56000e-01;AN=32;BaseQRankSum=6.25300e+00;DB;DP=1040;Dels=0.00000e+00;FS=2.27620e+01;HaplotypeScore=2.29500e-01;InbreedingCoeff=-2.81000e-02;MQ=5.57400e+01;MQ0=40;MQRankSum=1.69390e+01;QD=1.18200e+01;ReadPosRankSum=-6.75000e-01;SNPEFF_AMINO_ACID_CHANGE=S556L;SNPEFF_CODON_CHANGE=tCg/tTg;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_881782_881925;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=1.82000e+00;culprit=MQ;CSQ=A|ENSG00000188976|ENST00000496938|Transcript|upstream_gene_variant||||||rs35471880|1|976|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628|||||||||||||||||,A|ENSG00000187634|ENST00000342066|Transcript|downstream_gene_variant||||||rs35471880|1|1963|1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04||||||||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000188976|ENST00000327044|Transcript|missense_variant|1717|1667|556|S/L|tCg/tTg|rs35471880|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C|deleterious(0.03)|benign(0.311)|15/19||Pfam_domain:PF03715&Superfamily_domains:SSF48371|ENST00000327044.6:c.1667N>T|ENSP00000317992.6:p.Ser556Leu|A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628||||||||POSITION:0.740888888888889||NON_CAN_SPLICE_SURR||B%3BB%3BB|16.43|D|T|D|T,A|ENSG00000187634|ENST00000464948|Transcript|downstream_gene_variant||||||rs35471880|1|3646|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628|||||||||||||||||,A|ENSG00000187634|ENST00000466827|Transcript|downstream_gene_variant||||||rs35471880|1|3736|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628|||||||||||||||||,A|ENSG00000187634|ENST00000474461|Transcript|downstream_gene_variant||||||rs35471880|1|3544|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628|||||||||||||||||,A|ENSG00000187634|ENST00000455979|Transcript|downstream_gene_variant||||||rs35471880|1|2279|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479||||||||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000188976|ENST00000483767|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|523|||||rs35471880|1||-1|NOC2L|HGNC|24517|retained_intron||||||||||1/5|||ENST00000483767.1:n.523N>T||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628|||||||||||||||||,A|ENSG00000187634|ENST00000478729|Transcript|downstream_gene_variant||||||rs35471880|1|4365|1|SAMD11|HGNC|28706|processed_transcript|||||||||||||||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628|||||||||||||||||,A|ENSG00000188976|ENST00000477976|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|3114|||||rs35471880|1||-1|NOC2L|HGNC|24517|retained_intron||||||||||13/17|||ENST00000477976.1:n.3114N>T||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628|||||||||||||||||,A|ENSG00000187634|ENST00000341065|Transcript|downstream_gene_variant||||||rs35471880|1|1963|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A||||||||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628||||||||||EXON_INTRON_UNDEF||||||| GT:AD:DP:GQ:PL 0/0:73,0:73:99:0,220,2699 0/0:70,0:70:99:0,211,2589 0/0:66,0:66:99:0,199,2385 0/1:12,18:29:99:475,0,278 0/0:28,0:28:78:0,78,843 0/1:18,10:27:99:271,0,511 0/1:34,36:67:99:876,0,921 0/1:37,38:74:99:966,0,944 0/0:69,0:69:99:0,208,2493 0/0:93,0:93:99:0,280,3279 0/1:41,32:70:99:777,0,1118 0/0:76,0:76:99:0,229,2746 0/0:73,0:73:99:0,220,2573 0/0:69,0:69:99:0,208,2493 0/0:82,0:82:99:0,247,2963 0/0:74,0:74:99:0,223,2609 +1 883485 . C T 81.94 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-3.68100e+00;DP=94;Dels=0.00000e+00;FS=0.00000e+00;HaplotypeScore=1.64200e-01;InbreedingCoeff=-2.46000e-02;MQ=5.53400e+01;MQ0=0;MQRankSum=3.55900e+00;QD=3.03000e+00;ReadPosRankSum=-1.07900e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=SAMD11;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000342066;VQSLOD=-3.92700e-01;culprit=MQ;CSQ=T|ENSG00000188976|ENST00000483767|Transcript|upstream_gene_variant||||||rs374301410|1|1045|-1|NOC2L|HGNC|24517|retained_intron||||||||||||||||||||T:0|T:0.000117|||||||||||||||||,T|ENSG00000187634|ENST00000455979|Transcript|downstream_gene_variant||||||rs374301410|1|3846|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479|||||||||||||T:0|T:0.000117||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000496938|Transcript|upstream_gene_variant||||||rs374301410|1|2543|-1|NOC2L|HGNC|24517|processed_transcript||||||||||||||||||||T:0|T:0.000117|||||||||||||||||,T|ENSG00000187634|ENST00000342066|Transcript|downstream_gene_variant||||||rs374301410|1|3530|1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04|||||||||||||T:0|T:0.000117||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000327044|Transcript|intron_variant||||||rs374301410|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||14/18||ENST00000327044.6:c.1659+26N>A|||||||T:0|T:0.000117||||||||INTRON_SIZE:1585||NON_CAN_SPLICE|||||||,T|ENSG00000188976|ENST00000477976|Transcript|intron_variant&non_coding_transcript_variant||||||rs374301410|1||-1|NOC2L|HGNC|24517|retained_intron|||||||||||12/16||ENST00000477976.1:n.3106+26N>A|||||||T:0|T:0.000117|||||||||||||||||,T|ENSG00000187634|ENST00000341065|Transcript|downstream_gene_variant||||||rs374301410|1|3530|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A|||||||||||||T:0|T:0.000117||||||||||EXON_INTRON_UNDEF||||||| GT:AD:DP:GQ:PL 0/0:8,0:8:24:0,24,304 0/0:3,0:3:9:0,9,118 0/0:5,0:5:15:0,15,178 0/0:5,0:5:15:0,15,181 0/0:2,0:2:6:0,6,69 0/0:4,0:5:12:0,12,145 0/0:6,0:6:18:0,18,217 0/0:10,0:10:30:0,30,378 0/0:11,0:11:33:0,33,411 0/1:5,1:6:14:14,0,181 0/0:10,0:10:30:0,30,373 0/0:4,0:4:9:0,9,114 0/0:5,0:5:15:0,15,193 0/0:4,0:4:12:0,12,157 0/0:6,0:6:18:0,18,229 0/0:3,0:4:9:0,9,122 +1 883625 rs4970378 A G 232503.78 PASS AC=30;AF=1.00000e+00;AN=30;DB;DP=117;Dels=0.00000e+00;FS=0.00000e+00;HaplotypeScore=1.37000e-01;InbreedingCoeff=-1.43000e-02;MQ=5.74300e+01;MQ0=0;QD=3.66300e+01;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=SAMD11;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000342066;VQSLOD=-2.60400e-01;culprit=MQ;CSQ=G|ENSG00000188976|ENST00000483767|Transcript|upstream_gene_variant||||||rs4970378|1|1185|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||A:0.0000|||||G:0.999543||||||||||||||||||,G|ENSG00000187634|ENST00000455979|Transcript|downstream_gene_variant||||||rs4970378|1|3986|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479||||||||A:0.0000|||||G:0.999543|||||||||||EXON_INTRON_UNDEF&ANC_ALLELE|||||||,G|ENSG00000188976|ENST00000496938|Transcript|upstream_gene_variant||||||rs4970378|1|2683|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.0000|||||G:0.999543||||||||||||||||||,G|ENSG00000187634|ENST00000342066|Transcript|downstream_gene_variant||||||rs4970378|1|3670|1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04||||||||A:0.0000|||||G:0.999543|||||||||||EXON_INTRON_UNDEF&ANC_ALLELE|||||||,G|ENSG00000188976|ENST00000327044|Transcript|intron_variant||||||rs4970378|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||13/18||ENST00000327044.6:c.1558-13N>C||A:0.0000|||||G:0.999543|||||||||INTRON_SIZE:257||NON_CAN_SPLICE&ANC_ALLELE|||||||,G|ENSG00000188976|ENST00000477976|Transcript|intron_variant&non_coding_transcript_variant||||||rs4970378|1||-1|NOC2L|HGNC|24517|retained_intron|||||||||||11/16||ENST00000477976.1:n.3005-13N>C||A:0.0000|||||G:0.999543||||||||||||||||||,G|ENSG00000187634|ENST00000341065|Transcript|downstream_gene_variant||||||rs4970378|1|3670|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A||||||||A:0.0000|||||G:0.999543|||||||||||EXON_INTRON_UNDEF&ANC_ALLELE||||||| GT:AD:DP:GQ:PL 1/1:0,4:4:12:151,12,0 1/1:0,3:3:9:118,9,0 1/1:0,6:6:18:212,18,0 1/1:0,5:5:15:185,15,0 ./.:.:.:.:. 1/1:0,4:4:12:142,12,0 1/1:0,13:13:39:501,39,0 1/1:0,8:8:21:276,21,0 1/1:0,19:19:57:718,57,0 1/1:0,9:9:27:340,27,0 1/1:0,12:12:36:454,36,0 1/1:0,4:4:12:151,12,0 1/1:0,5:5:15:198,15,0 1/1:0,16:16:48:605,48,0 1/1:0,3:3:9:119,9,0 1/1:0,5:6:15:191,15,0 +1 883918 rs139116730 G A 4594.12 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=6.89000e+00;DB;DP=1146;Dels=0.00000e+00;FS=4.31330e+01;HaplotypeScore=8.65000e-02;InbreedingCoeff=-4.00000e-03;MQ=5.62500e+01;MQ0=14;MQRankSum=1.10440e+01;QD=1.07800e+01;ReadPosRankSum=-1.97100e+00;SNPEFF_AMINO_ACID_CHANGE=S503;SNPEFF_CODON_CHANGE=tcC/tcT;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_883870_883983;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=5.95000e-01;culprit=MQ;CSQ=A|ENSG00000188976|ENST00000483767|Transcript|upstream_gene_variant||||||rs139116730|1|1478|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||A:0.0005||||A:0.0013|A:0.000227|A:0.003488|||||||||||||||||,A|ENSG00000187634|ENST00000455979|Transcript|downstream_gene_variant||||||rs139116730|1|4279|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479||||||||A:0.0005||||A:0.0013|A:0.000227|A:0.003488||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000188976|ENST00000496938|Transcript|upstream_gene_variant||||||rs139116730|1|2976|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.0005||||A:0.0013|A:0.000227|A:0.003488|||||||||||||||||,A|ENSG00000187634|ENST00000342066|Transcript|downstream_gene_variant||||||rs139116730|1|3963|1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04||||||||A:0.0005||||A:0.0013|A:0.000227|A:0.003488||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000188976|ENST00000327044|Transcript|synonymous_variant|1559|1509|503|S|tcC/tcT|rs139116730|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C|||13/19||Pfam_domain:PF03715&Superfamily_domains:SSF48371|ENST00000327044.6:c.1509N>T|ENST00000327044.6:c.1509N>T(p.%3D)|A:0.0005||||A:0.0013|A:0.000227|A:0.003488||||||||POSITION:0.670666666666667||NON_CAN_SPLICE_SURR|||||||,A|ENSG00000188976|ENST00000477976|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2956|||||rs139116730|1||-1|NOC2L|HGNC|24517|retained_intron||||||||||11/17|||ENST00000477976.1:n.2956N>T||A:0.0005||||A:0.0013|A:0.000227|A:0.003488|||||||||||||||||,A|ENSG00000187634|ENST00000341065|Transcript|downstream_gene_variant||||||rs139116730|1|3963|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A||||||||A:0.0005||||A:0.0013|A:0.000227|A:0.003488||||||||||EXON_INTRON_UNDEF||||||| GT:AD:DP:GQ:PL 0/0:76,0:76:99:0,229,2746 0/0:47,0:47:99:0,141,1738 0/0:75,0:75:99:0,226,2710 0/0:36,0:36:99:0,108,1201 0/0:37,0:37:99:0,111,1271 0/0:42,0:42:99:0,126,1443 0/0:74,0:74:99:0,223,2609 0/0:82,0:82:99:0,247,2963 0/0:120,0:120:99:0,361,4336 0/0:96,0:96:99:0,289,3468 0/1:38,33:68:99:823,0,921 0/0:78,0:78:99:0,235,2818 0/0:56,0:56:99:0,169,1974 0/0:92,0:92:99:0,277,3402 0/0:78,0:78:99:0,235,2884 0/0:89,0:89:99:0,268,3216 +1 887560 rs3748595 A C 806833.88 PASS AC=31;AF=9.69000e-01;AN=32;BaseQRankSum=5.43470e+01;DB;DP=472;Dels=0.00000e+00;FS=1.69080e+01;HaplotypeScore=2.91900e-01;InbreedingCoeff=7.38000e-02;MQ=5.93900e+01;MQ0=0;MQRankSum=1.20610e+01;QD=3.46800e+01;ReadPosRankSum=7.92100e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000487214;VQSLOD=6.35000e-01;culprit=FS;CSQ=C|ENSG00000188976|ENST00000327044|Transcript|intron_variant||||||rs3748595|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||10/18||ENST00000327044.6:c.1192-41N>G||A:0.1602|C:0.78|C:0.86|C:0.86|C:0.85|C:0.831139|C:0.932674||||||||INTRON_SIZE:272||NON_CAN_SPLICE&ANC_ALLELE|||||||,C|ENSG00000188976|ENST00000477976|Transcript|intron_variant&non_coding_transcript_variant||||||rs3748595|1||-1|NOC2L|HGNC|24517|retained_intron|||||||||||8/16||ENST00000477976.1:n.2639-41N>G||A:0.1602|C:0.78|C:0.86|C:0.86|C:0.85|C:0.831139|C:0.932674|||||||||||||||||,C|ENSG00000188976|ENST00000487214|Transcript|downstream_gene_variant||||||rs3748595|1|2246|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.1602|C:0.78|C:0.86|C:0.86|C:0.85|C:0.831139|C:0.932674||||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,44:44:99:1706,132,0 1/1:0,43:43:99:1773,129,0 1/1:0,41:41:99:1582,123,0 1/1:0,19:19:54:687,54,0 1/1:0,23:23:69:851,69,0 1/1:0,10:10:30:370,30,0 1/1:0,33:33:99:1320,99,0 1/1:1,25:25:75:1020,75,0 1/1:0,26:26:78:1040,78,0 1/1:0,25:25:75:1000,75,0 1/1:0,36:36:99:1461,108,0 0/1:23,14:36:99:439,0,642 1/1:0,23:23:69:930,69,0 1/1:0,28:28:84:1121,84,0 1/1:0,23:23:69:904,69,0 1/1:0,37:37:99:1420,108,0 +1 887801 rs3828047 A G 1348829.24 PASS AC=31;AF=9.69000e-01;AN=32;BaseQRankSum=4.41560e+01;DB;DP=777;Dels=0.00000e+00;FS=8.43510e+01;HaplotypeScore=3.07000e-01;InbreedingCoeff=-1.77000e-02;MQ=5.58800e+01;MQ0=35;MQRankSum=-2.15910e+01;QD=3.44400e+01;ReadPosRankSum=5.44300e+00;SNPEFF_AMINO_ACID_CHANGE=T394;SNPEFF_CODON_CHANGE=acT/acC;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_887792_887980;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=-6.22100e-01;culprit=MQ;CSQ=G|ENSG00000188976|ENST00000327044|Transcript|synonymous_variant|1232|1182|394|T|acT/acC|rs3828047&COSM426785|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C|||10/19||Pfam_domain:PF03715&Superfamily_domains:SSF48371|ENST00000327044.6:c.1182N>C|ENST00000327044.6:c.1182N>C(p.%3D)|A:0.0716|G:0.90|G:0.92|G:0.92|G:0.95|G:0.906037|G:0.938372||0&1||||||POSITION:0.525333333333333||NON_CAN_SPLICE_SURR&ANC_ALLELE|||||||,G|ENSG00000188976|ENST00000477976|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2629|||||rs3828047&COSM426785|1||-1|NOC2L|HGNC|24517|retained_intron||||||||||8/17|||ENST00000477976.1:n.2629N>C||A:0.0716|G:0.90|G:0.92|G:0.92|G:0.95|G:0.906037|G:0.938372||0&1|||||||||||||||,G|ENSG00000188976|ENST00000487214|Transcript|downstream_gene_variant||||||rs3828047&COSM426785|1|2005|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.0716|G:0.90|G:0.92|G:0.92|G:0.95|G:0.906037|G:0.938372||0&1||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,42:42:99:1553,126,0 1/1:0,48:48:99:1824,138,0 1/1:0,54:54:99:1997,163,0 1/1:0,17:18:48:615,48,0 1/1:0,33:33:99:1220,99,0 1/1:0,30:30:90:1134,90,0 1/1:0,60:60:99:2315,181,0 1/1:0,44:44:99:1526,120,0 1/1:0,71:71:99:2791,214,0 1/1:0,48:48:99:1887,144,0 1/1:0,61:61:99:2398,184,0 0/1:29,33:59:99:915,0,742 1/1:0,30:30:90:1157,90,0 1/1:0,59:59:99:2321,178,0 1/1:0,55:55:99:2137,166,0 1/1:0,65:65:99:2507,196,0 +1 888529 . G A 1833.13 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-9.33700e+00;DP=387;Dels=0.00000e+00;FS=8.33000e-01;HaplotypeScore=1.94900e-01;InbreedingCoeff=-4.20000e-03;MQ=5.60200e+01;MQ0=0;MQRankSum=5.49600e+00;QD=1.10400e+01;ReadPosRankSum=-2.04000e-01;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000487214;VQSLOD=1.38000e+00;culprit=MQ;CSQ=A|ENSG00000188976|ENST00000327044|Transcript|intron_variant||||||rs373469542|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||9/18||ENST00000327044.6:c.1002+26N>T|||||||A:0.000908|A:0||||||||INTRON_SIZE:574||NON_CAN_SPLICE|||||||,A|ENSG00000188976|ENST00000477976|Transcript|intron_variant&non_coding_transcript_variant||||||rs373469542|1||-1|NOC2L|HGNC|24517|retained_intron|||||||||||7/16||ENST00000477976.1:n.2449+26N>T|||||||A:0.000908|A:0|||||||||||||||||,A|ENSG00000188976|ENST00000487214|Transcript|downstream_gene_variant||||||rs373469542|1|1277|-1|NOC2L|HGNC|24517|processed_transcript||||||||||||||||||||A:0.000908|A:0||||||||||||||||| GT:AD:DP:GQ:PL 0/0:19,0:19:57:0,57,703 0/0:26,0:26:78:0,78,1022 0/0:23,0:23:69:0,69,869 0/0:15,0:15:45:0,45,555 0/0:16,0:16:48:0,48,603 0/0:16,0:16:48:0,48,606 0/0:32,0:32:96:0,96,1258 0/0:26,0:26:72:0,72,944 0/0:24,0:24:69:0,69,898 0/1:12,15:26:99:432,0,321 0/0:31,0:31:93:0,93,1240 0/0:24,0:24:72:0,72,944 0/0:20,0:20:60:0,60,756 0/0:27,0:27:78:0,78,1029 0/0:36,0:36:99:0,108,1415 0/0:26,0:26:78:0,78,1022 +1 888659 rs3748597 T C 907727.36 PASS AC=31;AF=9.69000e-01;AN=32;BaseQRankSum=4.09230e+01;DB;DP=542;Dels=0.00000e+00;FS=4.67910e+01;HaplotypeScore=2.81100e-01;InbreedingCoeff=-1.65000e-02;MQ=5.48600e+01;MQ0=44;MQRankSum=-2.23740e+01;QD=3.38200e+01;ReadPosRankSum=8.50400e+00;SNPEFF_AMINO_ACID_CHANGE=I300V;SNPEFF_CODON_CHANGE=Atc/Gtc;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_888555_888668;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=-6.49600e-01;culprit=MQ;CSQ=C|ENSG00000188976|ENST00000469563|Transcript|downstream_gene_variant||||||rs3748597|1|4967|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0716|C:0.90|C:0.92|C:0.92|C:0.95|C:0.905767|C:0.938372|||||||||||||||||,C|ENSG00000188976|ENST00000327044|Transcript|missense_variant|948|898|300|I/V|Atc/Gtc|rs3748597|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C|tolerated(0.98)|benign(0)|9/19||Superfamily_domains:SSF48371|ENST00000327044.6:c.898N>G|ENSP00000317992.6:p.Ile300Val|T:0.0716|C:0.90|C:0.92|C:0.92|C:0.95|C:0.905767|C:0.938372||||||||POSITION:0.399111111111111||NON_CAN_SPLICE_SURR&ANC_ALLELE||B|0.940|P|T|T|T,C|ENSG00000188976|ENST00000477976|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2345|||||rs3748597|1||-1|NOC2L|HGNC|24517|retained_intron||||||||||7/17|||ENST00000477976.1:n.2345N>G||T:0.0716|C:0.90|C:0.92|C:0.92|C:0.95|C:0.905767|C:0.938372|||||||||||||||||,C|ENSG00000188976|ENST00000487214|Transcript|downstream_gene_variant||||||rs3748597|1|1147|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||T:0.0716|C:0.90|C:0.92|C:0.92|C:0.95|C:0.905767|C:0.938372||||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,33:33:96:1198,96,0 1/1:0,29:29:87:1140,87,0 1/1:0,27:27:81:998,81,0 1/1:0,27:27:81:962,81,0 1/1:0,19:19:57:686,57,0 1/1:0,22:22:63:796,63,0 1/1:0,39:39:99:1474,117,0 1/1:0,39:39:99:1504,117,0 1/1:0,32:32:96:1183,96,0 1/1:0,44:44:99:1654,129,0 1/1:0,55:55:99:2079,166,0 0/1:17,21:36:99:502,0,410 1/1:0,37:37:99:1398,111,0 1/1:0,44:44:99:1697,132,0 1/1:0,32:32:96:1209,96,0 1/1:0,27:27:81:1016,81,0 +1 889158 rs56262069 G C 909575.03 PASS AC=31;AF=9.69000e-01;AN=32;BaseQRankSum=3.68810e+01;DB;DP=579;Dels=0.00000e+00;FS=2.80669e+02;HaplotypeScore=5.39300e-01;InbreedingCoeff=7.80000e-02;MQ=5.90100e+01;MQ0=0;MQRankSum=-1.97700e+00;QD=3.19700e+01;ReadPosRankSum=8.43100e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000469563;VQSLOD=9.10000e-02;culprit=MQRankSum;CSQ=C|ENSG00000188976|ENST00000469563|Transcript|downstream_gene_variant||||||rs13303056|1|4468|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||G:0.1529|||||||||||||||||||||||,C|ENSG00000188976|ENST00000327044|Transcript|splice_region_variant&intron_variant||||||rs13303056|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||8/18||ENST00000327044.6:c.888+4N>G||G:0.1529||||||||||||||INTRON_SIZE:493||NON_CAN_SPLICE&ANC_ALLELE|||||||,C|ENSG00000188976|ENST00000477976|Transcript|splice_region_variant&intron_variant&non_coding_transcript_variant||||||rs13303056|1||-1|NOC2L|HGNC|24517|retained_intron|||||||||||6/16||ENST00000477976.1:n.2335+4N>G||G:0.1529|||||||||||||||||||||||,C|ENSG00000188976|ENST00000487214|Transcript|downstream_gene_variant||||||rs13303056|1|648|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||G:0.1529||||||||||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,45:45:99:1664,135,0 1/1:0,21:21:63:810,63,0 1/1:0,27:27:81:975,81,0 1/1:0,19:18:51:638,51,0 1/1:0,20:20:60:700,60,0 1/1:0,18:18:54:635,54,0 1/1:0,40:40:99:1512,120,0 1/1:0,34:34:99:1312,102,0 1/1:0,45:45:99:1615,132,0 1/1:0,40:40:99:1543,120,0 1/1:0,62:62:99:2392,187,0 0/1:23,19:40:99:499,0,598 1/1:0,45:45:99:1664,135,0 1/1:0,48:48:99:1814,144,0 1/1:0,39:39:99:1503,117,0 1/1:0,37:37:99:1398,111,0 +1 889159 rs13302945 A C 937927.21 PASS AC=31;AF=9.69000e-01;AN=32;BaseQRankSum=5.17190e+01;DB;DP=586;Dels=0.00000e+00;FS=2.49622e+02;HaplotypeScore=5.35000e-01;InbreedingCoeff=7.77000e-02;MQ=5.90200e+01;MQ0=0;MQRankSum=1.48040e+01;QD=3.22600e+01;ReadPosRankSum=8.79200e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000469563;VQSLOD=1.40000e-01;culprit=MQ;CSQ=C|ENSG00000188976|ENST00000469563|Transcript|downstream_gene_variant||||||rs13302945|1|4467|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||A:0.1538|C:0.79|C:0.87|C:0.88|C:0.85|C:0.823342|C:0.932294|||||||||||||||||,C|ENSG00000188976|ENST00000327044|Transcript|splice_region_variant&intron_variant||||||rs13302945|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||8/18||ENST00000327044.6:c.888+3N>G||A:0.1538|C:0.79|C:0.87|C:0.88|C:0.85|C:0.823342|C:0.932294||||||||INTRON_SIZE:493||NON_CAN_SPLICE&ANC_ALLELE|||||||,C|ENSG00000188976|ENST00000477976|Transcript|splice_region_variant&intron_variant&non_coding_transcript_variant||||||rs13302945|1||-1|NOC2L|HGNC|24517|retained_intron|||||||||||6/16||ENST00000477976.1:n.2335+3N>G||A:0.1538|C:0.79|C:0.87|C:0.88|C:0.85|C:0.823342|C:0.932294|||||||||||||||||,C|ENSG00000188976|ENST00000487214|Transcript|downstream_gene_variant||||||rs13302945|1|647|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.1538|C:0.79|C:0.87|C:0.88|C:0.85|C:0.823342|C:0.932294||||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,44:44:99:1663,132,0 1/1:0,21:21:63:794,63,0 1/1:0,28:28:84:1058,84,0 1/1:0,19:18:51:634,51,0 1/1:0,21:21:63:782,63,0 1/1:0,18:18:54:650,54,0 1/1:0,42:42:99:1587,126,0 1/1:0,34:34:99:1312,102,0 1/1:0,45:45:99:1657,132,0 1/1:0,41:41:99:1582,123,0 1/1:0,61:61:99:2353,184,0 0/1:24,19:41:99:482,0,633 1/1:0,43:43:99:1625,129,0 1/1:0,52:52:99:1965,156,0 1/1:0,42:42:99:1557,123,0 1/1:0,35:35:99:1323,105,0 +1 889238 rs3828049 G A 52801.55 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-4.91500e+00;DB;DP=911;Dels=0.00000e+00;FS=4.16200e+01;HaplotypeScore=2.87900e-01;InbreedingCoeff=3.34000e-02;MQ=5.93400e+01;MQ0=1;MQRankSum=3.62800e+00;QD=1.41200e+01;ReadPosRankSum=-2.71000e+00;SNPEFF_AMINO_ACID_CHANGE=A271V;SNPEFF_CODON_CHANGE=gCg/gTg;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_889162_889272;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=5.38000e+00;culprit=MQRankSum;CSQ=A|ENSG00000188976|ENST00000469563|Transcript|downstream_gene_variant||||||rs3828049&COSM1602748|1|4388|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||A:0.0537|A:0.02|A:0.08|A:0.08|A:0.05|A:0.021562|A:0.060363||0&1|||||||||||||||,A|ENSG00000188976|ENST00000327044|Transcript|missense_variant|862|812|271|A/V|gCg/gTg|rs3828049&COSM1602748|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C|deleterious(0.04)|benign(0.034)|8/19||Superfamily_domains:SSF48371|ENST00000327044.6:c.812N>T|ENSP00000317992.6:p.Ala271Val|A:0.0537|A:0.02|A:0.08|A:0.08|A:0.05|A:0.021562|A:0.060363||0&1||||||POSITION:0.360888888888889||NON_CAN_SPLICE_SURR||D%3BP%3BP|21.3|N|T|D|T,A|ENSG00000188976|ENST00000477976|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2259|||||rs3828049&COSM1602748|1||-1|NOC2L|HGNC|24517|retained_intron||||||||||6/17|||ENST00000477976.1:n.2259N>T||A:0.0537|A:0.02|A:0.08|A:0.08|A:0.05|A:0.021562|A:0.060363||0&1|||||||||||||||,A|ENSG00000188976|ENST00000487214|Transcript|downstream_gene_variant||||||rs3828049&COSM1602748|1|568|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.0537|A:0.02|A:0.08|A:0.08|A:0.05|A:0.021562|A:0.060363||0&1||||||||||||||| GT:AD:DP:GQ:PL 0/0:53,0:53:99:0,159,1960 0/0:56,0:56:99:0,169,2071 0/0:42,0:42:99:0,126,1517 0/0:23,0:23:69:0,69,763 0/0:31,0:31:93:0,93,1007 0/0:26,0:26:69:0,69,754 0/0:55,0:55:99:0,166,1987 0/0:59,0:59:99:0,178,2132 0/0:67,0:67:99:0,202,2362 0/0:79,0:79:99:0,238,2854 0/0:82,0:82:99:0,247,2963 0/1:32,31:62:99:888,0,808 0/0:75,0:75:99:0,226,2644 0/0:66,0:66:99:0,199,2385 0/0:68,0:68:99:0,205,2397 0/0:67,0:67:99:0,202,2362 +1 894573 rs13303010 G A 310883.38 PASS AC=30;AF=9.38000e-01;AN=32;BaseQRankSum=1.22670e+01;DB;DP=304;Dels=0.00000e+00;FS=2.34720e+01;HaplotypeScore=3.24800e-01;InbreedingCoeff=4.23300e-01;MQ=5.89800e+01;MQ0=0;MQRankSum=1.80380e+01;QD=2.67400e+01;ReadPosRankSum=2.89300e+00;SNPEFF_EFFECT=INTRON;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=1.10000e+00;culprit=MQ;CSQ=A|ENSG00000187961|ENST00000466300|Transcript|upstream_gene_variant||||||rs13303010|1|3534|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||G:0.3480|A:0.18|A:0.71|A:0.69|A:0.90|A:0.284570|A:0.896942|||||||||||||||||,A|ENSG00000188976|ENST00000327044|Transcript|intron_variant||||||rs13303010|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||1/18||ENST00000327044.6:c.26+22N>T||G:0.3480|A:0.18|A:0.71|A:0.69|A:0.90|A:0.284570|A:0.896942||||||||INTRON_SIZE:133||NON_CAN_SPLICE|||||||,A|ENSG00000187961|ENST00000338591|Transcript|upstream_gene_variant||||||rs13303010|1|1394|1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||||||G:0.3480|A:0.18|A:0.71|A:0.69|A:0.90|A:0.284570|A:0.896942||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000187961|ENST00000463212|Transcript|upstream_gene_variant||||||rs13303010|1|2256|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||G:0.3480|A:0.18|A:0.71|A:0.69|A:0.90|A:0.284570|A:0.896942|||||||||||||||||,A|ENSG00000188976|ENST00000469563|Transcript|intron_variant&non_coding_transcript_variant||||||rs13303010|1||-1|NOC2L|HGNC|24517|retained_intron|||||||||||1/1||ENST00000469563.1:n.42+22N>T||G:0.3480|A:0.18|A:0.71|A:0.69|A:0.90|A:0.284570|A:0.896942|||||||||||||||||,A|ENSG00000188976|ENST00000477976|Transcript|upstream_gene_variant||||||rs13303010|1|735|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||G:0.3480|A:0.18|A:0.71|A:0.69|A:0.90|A:0.284570|A:0.896942|||||||||||||||||,A|ENSG00000187961|ENST00000481067|Transcript|upstream_gene_variant||||||rs13303010|1|4359|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||G:0.3480|A:0.18|A:0.71|A:0.69|A:0.90|A:0.284570|A:0.896942|||||||||||||||||,A|ENSG00000188976|ENST00000487214|Transcript|intron_variant&non_coding_transcript_variant||||||rs13303010|1||-1|NOC2L|HGNC|24517|processed_transcript|||||||||||1/6||ENST00000487214.1:n.95+22N>T||G:0.3480|A:0.18|A:0.71|A:0.69|A:0.90|A:0.284570|A:0.896942|||||||||||||||||,A||ENSR00000528861|RegulatoryFeature|regulatory_region_variant||||||rs13303010|1||||||regulatory_region|||||||||||||||G:0.3480|A:0.18|A:0.71|A:0.69|A:0.90|A:0.284570|A:0.896942||||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,24:24:72:898,72,0 0/1:10,8:17:99:196,0,291 1/1:0,13:12:36:454,36,0 1/1:0,7:7:21:254,21,0 1/1:0,5:5:15:181,15,0 1/1:0,13:13:36:428,36,0 1/1:0,31:31:93:1120,93,0 1/1:0,24:24:72:867,72,0 1/1:0,26:26:78:924,78,0 1/1:0,26:26:78:958,78,0 1/1:0,19:19:57:670,57,0 0/1:17,6:22:99:127,0,513 1/1:0,20:20:60:723,60,0 1/1:0,23:23:69:869,69,0 1/1:0,19:19:57:686,57,0 1/1:0,16:16:48:505,48,0 +1 896922 . C T 1253.52 PASS AC=2;AF=6.30000e-02;AN=32;BaseQRankSum=-8.14600e+00;DP=943;Dels=0.00000e+00;FS=5.89500e+00;HaplotypeScore=1.37200e-01;InbreedingCoeff=-1.30000e-03;MQ=5.92800e+01;MQ0=0;MQRankSum=1.05600e+00;QD=1.01100e+01;ReadPosRankSum=-1.19000e+00;SNPEFF_AMINO_ACID_CHANGE=A119;SNPEFF_CODON_CHANGE=gcC/gcT;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_896673_896932;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000338591;VQSLOD=8.89000e+00;culprit=InbreedingCoeff;CSQ=T|ENSG00000187961|ENST00000466300|Transcript|upstream_gene_variant|||||||1|1185|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E|||||||||||||||||||||||||||||||,T|ENSG00000188976|ENST00000327044|Transcript|upstream_gene_variant|||||||1|2252|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187961|ENST00000338591|Transcript|synonymous_variant|464|357|119|A|gcC/gcT||1||1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0|||2/12||Pfam_domain:PF00651&PROSITE_profiles:PS50097&SMART_domains:SM00225&Superfamily_domains:SSF54695&PIRSF_domain:PIRSF037037|ENST00000338591.3:c.357N>T|ENST00000338591.3:c.357N>T(p.%3D)|||||||||||||||POSITION:0.1850699844479||NON_CAN_SPLICE_SURR|||||||,T|ENSG00000187583|ENST00000379409|Transcript|upstream_gene_variant|||||||1|4960|1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187961|ENST00000463212|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|94||||||1||1|KLHL17|HGNC|24023|retained_intron||||||||||1/2|||ENST00000463212.1:n.94N>T|||||||||||||||||||||||||,T|ENSG00000187583|ENST00000379407|Transcript|upstream_gene_variant|||||||1|4960|1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000469563|Transcript|upstream_gene_variant|||||||1|2286|-1|NOC2L|HGNC|24517|retained_intron||||||||||||||||||||||||||||||||||||||,T|ENSG00000187583|ENST00000379410|Transcript|upstream_gene_variant|||||||1|4955|1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000477976|Transcript|upstream_gene_variant|||||||1|3084|-1|NOC2L|HGNC|24517|retained_intron||||||||||||||||||||||||||||||||||||||,T|ENSG00000187961|ENST00000481067|Transcript|upstream_gene_variant|||||||1|2010|1|KLHL17|HGNC|24023|retained_intron||||||||||||||||||||||||||||||||||||||,T|ENSG00000188976|ENST00000487214|Transcript|upstream_gene_variant|||||||1|2233|-1|NOC2L|HGNC|24517|processed_transcript||||||||||||||||||||||||||||||||||||||,T||ENSR00000528861|RegulatoryFeature|regulatory_region_variant|||||||1||||||regulatory_region|||||||||||||||||||||||||||||||||||||| GT:AD:DP:GQ:PL 0/0:71,0:71:99:0,214,2684 0/0:69,0:69:99:0,208,2713 0/0:68,0:68:99:0,205,2515 0/0:20,0:20:57:0,57,722 0/0:29,0:29:87:0,87,1096 0/0:36,0:36:99:0,99,1225 0/0:61,0:61:99:0,184,2353 0/0:58,0:58:99:0,175,2192 0/0:68,0:68:99:0,205,2673 0/1:41,25:63:99:678,0,1190 0/0:87,0:87:99:0,262,3356 0/0:52,0:52:99:0,157,2006 0/1:35,23:55:99:651,0,922 0/0:79,0:79:99:0,238,3048 0/0:73,0:73:99:0,220,2816 0/0:54,0:54:99:0,163,2045 +1 897325 rs4970441 G C 2226684.78 PASS AC=31;AF=9.69000e-01;AN=32;BaseQRankSum=3.69960e+01;DB;DP=1475;Dels=0.00000e+00;FS=1.12830e+01;HaplotypeScore=4.66400e-01;InbreedingCoeff=1.15000e-01;MQ=5.95500e+01;MQ0=1;MQRankSum=2.60000e-02;QD=3.33700e+01;ReadPosRankSum=6.38900e+00;SNPEFF_AMINO_ACID_CHANGE=A203;SNPEFF_CODON_CHANGE=gcG/gcC;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_897206_897427;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000338591;VQSLOD=5.29000e+00;culprit=ReadPosRankSum;CSQ=C|ENSG00000187961|ENST00000466300|Transcript|upstream_gene_variant||||||rs4970441|1|782|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163|||||||||||||||||,C|ENSG00000188976|ENST00000327044|Transcript|upstream_gene_variant||||||rs4970441|1|2655|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000338591|Transcript|synonymous_variant|716|609|203|A|gcG/gcC|rs4970441|1||1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0|||4/12||Pfam_domain:PF07707&SMART_domains:SM00875&PIRSF_domain:PIRSF037037|ENST00000338591.3:c.609N>C|ENST00000338591.3:c.609N>C(p.%3D)|G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163||||||||POSITION:0.315707620528771||NON_CAN_SPLICE_SURR|||||||,C|ENSG00000187583|ENST00000379409|Transcript|upstream_gene_variant||||||rs4970441|1|4557|1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06||||||||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000463212|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|422|||||rs4970441|1||1|KLHL17|HGNC|24023|retained_intron||||||||||2/2|||ENST00000463212.1:n.422N>C||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163|||||||||||||||||,C|ENSG00000187583|ENST00000379407|Transcript|upstream_gene_variant||||||rs4970441|1|4557|1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF||||||||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000188976|ENST00000469563|Transcript|upstream_gene_variant||||||rs4970441|1|2689|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163|||||||||||||||||,C|ENSG00000187583|ENST00000379410|Transcript|upstream_gene_variant||||||rs4970441|1|4552|1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8||||||||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000188976|ENST00000477976|Transcript|upstream_gene_variant||||||rs4970441|1|3487|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163|||||||||||||||||,C|ENSG00000187961|ENST00000481067|Transcript|upstream_gene_variant||||||rs4970441|1|1607|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163|||||||||||||||||,C|ENSG00000188976|ENST00000487214|Transcript|upstream_gene_variant||||||rs4970441|1|2636|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163||||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,94:94:99:3476,283,0 1/1:0,87:87:99:3356,262,0 1/1:0,108:108:99:3994,325,0 1/1:0,56:56:99:2023,169,0 1/1:0,59:59:99:2182,178,0 1/1:0,46:46:99:1701,138,0 1/1:0,100:100:99:3780,301,0 1/1:0,127:127:99:4800,382,0 1/1:0,127:127:99:4899,382,0 1/1:0,127:127:99:4800,382,0 1/1:0,117:117:99:4422,352,0 0/1:42,33:71:99:891,0,1116 1/1:0,78:78:99:2948,235,0 1/1:0,107:107:99:4128,322,0 1/1:0,95:95:99:3665,286,0 1/1:0,76:76:99:2873,229,0 +1 898313 . C T 4423.71 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=1.00100e+01;DP=235;Dels=0.00000e+00;FS=6.83200e+00;HaplotypeScore=5.07500e-01;InbreedingCoeff=9.84000e-02;MQ=5.92600e+01;MQ0=0;MQRankSum=-5.62000e-01;QD=1.22500e+01;ReadPosRankSum=-4.59200e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000463212;VQSLOD=3.67000e+00;culprit=MQRankSum;CSQ=T|ENSG00000187961|ENST00000466300|Transcript|intron_variant&NMD_transcript_variant||||||rs375277853|1||1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||1/5||ENST00000466300.1:c.191+16N>T|||||||||||||||||||||||||,T|ENSG00000188976|ENST00000327044|Transcript|upstream_gene_variant||||||rs375277853|1|3643|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187961|ENST00000338591|Transcript|intron_variant||||||rs375277853|1||1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||6/11||ENST00000338591.3:c.1042+16N>T||||||||||||||||INTRON_SIZE:191||NON_CAN_SPLICE|||||||,T|ENSG00000187583|ENST00000379409|Transcript|upstream_gene_variant||||||rs375277853|1|3569|1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs375277853|1|455|1|KLHL17|HGNC|24023|retained_intron||||||||||||||||||||||||||||||||||||||,T|ENSG00000187583|ENST00000379407|Transcript|upstream_gene_variant||||||rs375277853|1|3569|1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000469563|Transcript|upstream_gene_variant||||||rs375277853|1|3677|-1|NOC2L|HGNC|24517|retained_intron||||||||||||||||||||||||||||||||||||||,T|ENSG00000187583|ENST00000379410|Transcript|upstream_gene_variant||||||rs375277853|1|3564|1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000477976|Transcript|upstream_gene_variant||||||rs375277853|1|4475|-1|NOC2L|HGNC|24517|retained_intron||||||||||||||||||||||||||||||||||||||,T|ENSG00000187961|ENST00000481067|Transcript|upstream_gene_variant||||||rs375277853|1|619|1|KLHL17|HGNC|24023|retained_intron||||||||||||||||||||||||||||||||||||||,T|ENSG00000188976|ENST00000487214|Transcript|upstream_gene_variant||||||rs375277853|1|3624|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||||||||||||||||||||||||| GT:AD:DP:GQ:PL 0/0:19,0:19:57:0,57,653 0/0:12,0:12:36:0,36,423 0/0:21,0:21:63:0,63,740 0/0:6,0:6:15:0,15,157 0/0:2,0:2:6:0,6,63 0/0:6,0:6:15:0,15,159 0/0:14,0:14:42:0,42,455 0/0:18,0:18:54:0,54,624 0/0:14,0:14:39:0,39,447 0/0:25,0:25:72:0,72,805 0/0:16,0:16:48:0,48,564 0/1:13,8:20:99:190,0,314 0/0:21,0:21:63:0,63,702 0/0:17,1:18:18:0,18,560 0/0:11,0:11:30:0,30,342 0/0:12,0:12:36:0,36,393 +1 898323 rs6605071 T C 353673.96 PASS AC=31;AF=9.69000e-01;AN=32;BaseQRankSum=1.91890e+01;DB;DP=221;Dels=0.00000e+00;FS=9.64600e+00;HaplotypeScore=4.04000e-01;InbreedingCoeff=-2.15000e-02;MQ=5.91700e+01;MQ0=0;MQRankSum=-4.60000e-02;QD=3.77900e+01;ReadPosRankSum=3.36900e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000463212;VQSLOD=4.11000e+00;culprit=InbreedingCoeff;CSQ=C|ENSG00000187961|ENST00000466300|Transcript|intron_variant&NMD_transcript_variant||||||rs6605071|1||1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||1/5||ENST00000466300.1:c.191+26N>C||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859|||||||||||||||||,C|ENSG00000188976|ENST00000327044|Transcript|upstream_gene_variant||||||rs6605071|1|3653|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859||||||||||EXON_INTRON_UNDEF&ANC_ALLELE|||||||,C|ENSG00000187961|ENST00000338591|Transcript|intron_variant||||||rs6605071|1||1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||6/11||ENST00000338591.3:c.1042+26N>C||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859||||||||INTRON_SIZE:191||NON_CAN_SPLICE&ANC_ALLELE|||||||,C|ENSG00000187583|ENST00000379409|Transcript|upstream_gene_variant||||||rs6605071|1|3559|1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06||||||||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859||||||||||EXON_INTRON_UNDEF&ANC_ALLELE|||||||,C|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs6605071|1|465|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859|||||||||||||||||,C|ENSG00000187583|ENST00000379407|Transcript|upstream_gene_variant||||||rs6605071|1|3559|1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF||||||||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859||||||||||EXON_INTRON_UNDEF&ANC_ALLELE|||||||,C|ENSG00000188976|ENST00000469563|Transcript|upstream_gene_variant||||||rs6605071|1|3687|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859|||||||||||||||||,C|ENSG00000187583|ENST00000379410|Transcript|upstream_gene_variant||||||rs6605071|1|3554|1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8||||||||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859||||||||||EXON_INTRON_UNDEF&ANC_ALLELE|||||||,C|ENSG00000188976|ENST00000477976|Transcript|upstream_gene_variant||||||rs6605071|1|4485|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859|||||||||||||||||,C|ENSG00000187961|ENST00000481067|Transcript|upstream_gene_variant||||||rs6605071|1|609|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859|||||||||||||||||,C|ENSG00000188976|ENST00000487214|Transcript|upstream_gene_variant||||||rs6605071|1|3634|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859||||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,18:18:54:688,54,0 1/1:0,8:8:24:315,24,0 1/1:0,15:15:45:579,45,0 1/1:0,7:7:21:262,21,0 1/1:0,3:3:9:111,9,0 1/1:0,4:4:9:122,9,0 1/1:0,20:20:60:786,60,0 1/1:0,16:16:48:641,48,0 1/1:0,13:13:36:457,36,0 1/1:0,27:27:78:1030,78,0 1/1:0,18:18:54:720,54,0 0/1:13,4:17:99:112,0,396 1/1:0,18:18:54:708,54,0 1/1:0,13:13:39:525,39,0 1/1:0,10:10:30:393,30,0 1/1:1,13:14:5:460,5,0 +1 898467 rs41285808 C T 14490.29 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-2.26300e+00;DB;DP=270;Dels=0.00000e+00;FS=1.33000e+00;HaplotypeScore=2.81700e-01;InbreedingCoeff=3.75000e-02;MQ=5.93000e+01;MQ0=0;MQRankSum=3.96000e+00;QD=1.37100e+01;ReadPosRankSum=-1.57400e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000463212;VQSLOD=7.17000e+00;culprit=FS;CSQ=T|ENSG00000187961|ENST00000466300|Transcript|synonymous_variant&NMD_transcript_variant|247|249|83|P|ccC/ccT|rs41285808|1||1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E|||2/6|||ENST00000466300.1:c.247N>T|ENST00000466300.1:c.247N>T(p.%3D)|T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672|||||||||||||||||,T|ENSG00000188976|ENST00000327044|Transcript|upstream_gene_variant||||||rs41285808|1|3797|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187961|ENST00000338591|Transcript|intron_variant||||||rs41285808|1||1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||6/11||ENST00000338591.3:c.1043-22N>T||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672||||||||INTRON_SIZE:191||NON_CAN_SPLICE|||||||,T|ENSG00000187583|ENST00000379409|Transcript|upstream_gene_variant||||||rs41285808|1|3415|1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06||||||||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs41285808|1|609|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672|||||||||||||||||,T|ENSG00000187583|ENST00000379407|Transcript|upstream_gene_variant||||||rs41285808|1|3415|1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF||||||||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000469563|Transcript|upstream_gene_variant||||||rs41285808|1|3831|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672|||||||||||||||||,T|ENSG00000187583|ENST00000379410|Transcript|upstream_gene_variant||||||rs41285808|1|3410|1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8||||||||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000477976|Transcript|upstream_gene_variant||||||rs41285808|1|4629|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672|||||||||||||||||,T|ENSG00000187961|ENST00000481067|Transcript|upstream_gene_variant||||||rs41285808|1|465|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672|||||||||||||||||,T|ENSG00000188976|ENST00000487214|Transcript|upstream_gene_variant||||||rs41285808|1|3778|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672||||||||||||||||| GT:AD:DP:GQ:PL 0/0:28,0:28:84:0,84,1030 0/0:15,0:15:45:0,45,579 0/0:25,0:25:75:0,75,916 0/0:6,0:6:18:0,18,197 0/0:5,0:5:15:0,15,172 0/0:3,0:3:9:0,9,100 0/0:14,0:14:42:0,42,480 0/0:22,0:22:66:0,66,817 0/0:23,0:23:69:0,69,831 0/0:12,0:12:36:0,36,431 0/0:18,0:18:51:0,51,646 0/1:17,10:26:99:278,0,440 0/0:21,0:21:51:0,51,644 0/0:13,0:13:39:0,39,481 0/0:18,0:18:54:0,54,666 0/0:21,0:21:60:0,60,723 +1 899959 . G GC 2073.57 PASS AC=1;AF=5.00000e-02;AN=20;BaseQRankSum=8.77000e-01;DP=19;FS=1.24470e+02;HaplotypeScore=1.51273e+01;InbreedingCoeff=6.94000e-02;MQ=4.52200e+01;MQ0=0;MQRankSum=-8.47500e+00;QD=1.40100e+01;ReadPosRankSum=4.26000e-01;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000463212;CSQ=C|ENSG00000187583|ENST00000379409|Transcript|upstream_gene_variant||||||TMP_ESP_1_899960_899959|1|1922|1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06|||||||||||||C:0.152075|C:0.090390||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||TMP_ESP_1_899960_899959|1|2101|1|KLHL17|HGNC|24023|retained_intron||||||||||||||||||||C:0.152075|C:0.090390|||||||||||||||||,C|ENSG00000187583|ENST00000379407|Transcript|upstream_gene_variant||||||TMP_ESP_1_899960_899959|1|1922|1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF|||||||||||||C:0.152075|C:0.090390||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000466300|Transcript|downstream_gene_variant||||||TMP_ESP_1_899960_899959|1|49|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E|||||||||||||C:0.152075|C:0.090390|||||||||||||||||,C|ENSG00000187583|ENST00000379410|Transcript|upstream_gene_variant||||||TMP_ESP_1_899960_899959|1|1917|1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8|||||||||||||C:0.152075|C:0.090390||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000481067|Transcript|downstream_gene_variant||||||TMP_ESP_1_899960_899959|1|415|1|KLHL17|HGNC|24023|retained_intron||||||||||||||||||||C:0.152075|C:0.090390|||||||||||||||||,C|ENSG00000187961|ENST00000338591|Transcript|intron_variant||||||TMP_ESP_1_899960_899959|1||1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||11/11||ENST00000338591.3:c.1700+49_1700+50insC|||||||C:0.152075|C:0.090390||||||||INTRON_SIZE:432||NON_CAN_SPLICE||||||| GT:AD:DP:GQ:PL ./.:.:.:.:. ./.:.:.:.:. 0/0:3,0:3:9:0,9,136 0/0:1,0:1:3:0,3,45 0/0:1,0:1:3:0,3,45 0/0:2,0:2:6:0,6,91 0/1:3,1:4:28:28,0,124 0/0:2,0:2:6:0,6,74 0/0:2,0:2:6:0,6,91 0/0:2,0:2:6:0,6,91 ./.:.:.:.:. ./.:.:.:.:. ./.:.:.:.:. 0/0:1,0:1:3:0,3,45 ./.:.:.:.:. 0/0:1,0:1:3:0,3,45 +1 900505 rs28705211 G C 222602.28 PASS AC=8;AF=2.50000e-01;AN=32;BaseQRankSum=6.97200e+00;DB;DP=885;Dels=0.00000e+00;FS=4.61940e+01;HaplotypeScore=1.18840e+00;InbreedingCoeff=1.98200e-01;MQ=5.92300e+01;MQ0=0;MQRankSum=1.76580e+01;QD=1.80400e+01;ReadPosRankSum=1.01980e+01;SNPEFF_AMINO_ACID_CHANGE=V497;SNPEFF_CODON_CHANGE=gtG/gtC;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_900343_901094;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000455747;VQSLOD=1.37000e+00;culprit=HaplotypeScore;CSQ=C|ENSG00000187583|ENST00000379409|Transcript|upstream_gene_variant||||||rs28705211&COSM426805|1|1377|1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06||||||||C:0.1648|C:0.02|C:0.22|C:0.09|C:0.28||||0&1|20637081|||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs28705211&COSM426805|1|2647|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||C:0.1648|C:0.02|C:0.22|C:0.09|C:0.28||||0&1|20637081||||||||||||||,C|ENSG00000187583|ENST00000379407|Transcript|upstream_gene_variant||||||rs28705211&COSM426805|1|1377|1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF||||||||C:0.1648|C:0.02|C:0.22|C:0.09|C:0.28||||0&1|20637081|||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000466300|Transcript|downstream_gene_variant||||||rs28705211&COSM426805|1|595|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||C:0.1648|C:0.02|C:0.22|C:0.09|C:0.28||||0&1|20637081||||||||||||||,C|ENSG00000187583|ENST00000379410|Transcript|upstream_gene_variant||||||rs28705211&COSM426805|1|1372|1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8||||||||C:0.1648|C:0.02|C:0.22|C:0.09|C:0.28||||0&1|20637081|||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000481067|Transcript|downstream_gene_variant||||||rs28705211&COSM426805|1|961|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||C:0.1648|C:0.02|C:0.22|C:0.09|C:0.28||||0&1|20637081||||||||||||||,C|ENSG00000187961|ENST00000338591|Transcript|synonymous_variant|1970|1863|621|V|gtG/gtC|rs28705211&COSM426805|1||1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0|||12/12||SMART_domains:SM00612&Superfamily_domains:SSF117281&PIRSF_domain:PIRSF037037|ENST00000338591.3:c.1863N>C|ENST00000338591.3:c.1863N>C(p.%3D)|C:0.1648|C:0.02|C:0.22|C:0.09|C:0.28||||0&1|20637081|||||POSITION:0.965785381026439||END_TRUNC&NON_CAN_SPLICE_SURR||||||| GT:AD:DP:GQ:PL 0/0:87,0:87:99:0,262,3217 0/1:43,24:61:99:697,0,1146 0/1:35,29:60:99:812,0,913 0/0:23,0:23:69:0,69,851 0/0:22,0:22:66:0,66,788 0/0:33,1:34:96:0,96,1150 0/0:54,0:54:99:0,162,1973 0/1:32,27:56:99:720,0,880 0/0:79,0:79:99:0,235,2850 0/0:74,0:74:99:0,214,2587 0/0:65,0:65:99:0,196,2354 0/1:24,26:48:99:738,0,687 0/1:27,28:54:99:795,0,709 0/0:58,0:58:99:0,175,2173 0/1:28,27:54:99:805,0,735 1/1:0,56:56:99:2066,169,0 +1 902024 rs181910588 G 406.47 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-3.35500e+00;DB;DP=225;Dels=0.00000e+00;FS=1.03150e+01;HaplotypeScore=3.56800e-01;InbreedingCoeff=-1.33000e-02;MQ=5.93500e+01;MQ0=0;MQRankSum=1.21200e+00;QD=1.09900e+01;ReadPosRankSum=-1.50700e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000338591;VQSLOD=6.64000e+00;culprit=InbreedingCoeff;CSQ=A|ENSG00000187583|ENST00000480267|Transcript|upstream_gene_variant||||||rs181910588|1|4231|1|PLEKHN1|HGNC|25284|retained_intron|||||||||||||||A:0.0023|A:0.01||||A:0.001842|A:0|||||||||||||||||,A|ENSG00000187961|ENST00000466300|Transcript|downstream_gene_variant||||||rs181910588|1|2114|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||A:0.0023|A:0.01||||A:0.001842|A:0|||||||||||||||||,A|ENSG00000187961|ENST00000338591|Transcript|downstream_gene_variant||||||rs181910588|1|929|1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||||||A:0.0023|A:0.01||||A:0.001842|A:0||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs181910588|1|4166|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0023|A:0.01||||A:0.001842|A:0|||||||||||||||||,A|ENSG00000187583|ENST00000379409|Transcript|intron_variant||||||rs181910588|1||1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06||||1/14||ENST00000379409.2:c.83+30N>A||A:0.0023|A:0.01||||A:0.001842|A:0||||||||INTRON_SIZE:89||NON_CAN_SPLICE|||||||,A|ENSG00000187583|ENST00000379407|Transcript|intron_variant||||||rs181910588|1||1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF||||1/14||ENST00000379407.3:c.83+30N>A||A:0.0023|A:0.01||||A:0.001842|A:0||||||||INTRON_SIZE:89||NON_CAN_SPLICE|||||||,A|ENSG00000187961|ENST00000481067|Transcript|downstream_gene_variant||||||rs181910588|1|2480|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0023|A:0.01||||A:0.001842|A:0|||||||||||||||||,A|ENSG00000187583|ENST00000379410|Transcript|intron_variant||||||rs181910588|1||1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8||||1/15||ENST00000379410.3:c.83+30N>A||A:0.0023|A:0.01||||A:0.001842|A:0||||||||INTRON_SIZE:89||NON_CAN_SPLICE|||||||,A||ENSR00000528862|RegulatoryFeature|regulatory_region_variant||||||rs181910588|1||||||regulatory_region|||||||||||||||A:0.0023|A:0.01||||A:0.001842|A:0||||||||||||||||| GT:AD:DP:GQ:PL 0/0:18,0:18:54:0,54,689 0/0:21,0:21:63:0,63,797 0/0:17,0:17:48:0,48,608 0/0:5,0:5:15:0,15,182 0/0:9,0:9:27:0,27,333 0/0:7,0:7:21:0,21,253 0/0:18,0:18:54:0,54,680 0/0:7,0:7:21:0,21,259 0/0:17,0:17:51:0,51,614 0/0:19,0:19:54:0,54,647 0/0:20,0:20:60:0,60,756 0/0:14,0:14:42:0,42,518 0/0:13,0:13:36:0,36,466 0/0:14,0:14:42:0,42,535 0/1:9,1:11:4:4,0,296 0/0:15,0:15:45:0,45,551 +1 902069 rs116147894 T C 13024.04 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=2.08840e+01;DB;DP=157;Dels=0.00000e+00;FS=3.07700e+00;HaplotypeScore=2.10500e-01;InbreedingCoeff=1.00200e-01;MQ=5.91800e+01;MQ0=0;MQRankSum=7.75000e-01;QD=1.56200e+01;ReadPosRankSum=-5.68400e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000338591;VQSLOD=7.17000e+00;culprit=MQ;CSQ=C|ENSG00000187583|ENST00000480267|Transcript|upstream_gene_variant||||||rs116147894|1|4186|1|PLEKHN1|HGNC|25284|retained_intron|||||||||||||||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163|||||||||||||||||,C|ENSG00000187961|ENST00000466300|Transcript|downstream_gene_variant||||||rs116147894|1|2159|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163|||||||||||||||||,C|ENSG00000187961|ENST00000338591|Transcript|downstream_gene_variant||||||rs116147894|1|974|1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||||||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs116147894|1|4211|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163|||||||||||||||||,C|ENSG00000187583|ENST00000379409|Transcript|intron_variant||||||rs116147894|1||1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06||||1/14||ENST00000379409.2:c.84-15N>C||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163||||||||INTRON_SIZE:89||NON_CAN_SPLICE|||||||,C|ENSG00000187583|ENST00000379407|Transcript|intron_variant||||||rs116147894|1||1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF||||1/14||ENST00000379407.3:c.84-15N>C||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163||||||||INTRON_SIZE:89||NON_CAN_SPLICE|||||||,C|ENSG00000187961|ENST00000481067|Transcript|downstream_gene_variant||||||rs116147894|1|2525|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163|||||||||||||||||,C|ENSG00000187583|ENST00000379410|Transcript|intron_variant||||||rs116147894|1||1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8||||1/15||ENST00000379410.3:c.84-15N>C||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163||||||||INTRON_SIZE:89||NON_CAN_SPLICE|||||||,C||ENSR00000528862|RegulatoryFeature|regulatory_region_variant||||||rs116147894|1||||||regulatory_region|||||||||||||||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163||||||||||||||||| GT:AD:DP:GQ:PL 0/0:10,0:10:30:0,30,367 0/1:12,2:13:3:3,0,418 0/0:14,0:14:42:0,42,514 0/0:4,0:4:12:0,12,144 0/0:5,0:5:15:0,15,176 0/0:4,0:4:12:0,12,145 0/0:17,0:17:48:0,48,603 0/0:6,0:6:18:0,18,227 0/0:10,0:10:30:0,30,361 0/0:10,0:10:30:0,30,372 0/0:12,0:12:36:0,36,434 0/0:7,0:7:21:0,21,259 0/0:7,0:7:21:0,21,255 0/0:11,0:11:30:0,30,375 0/0:12,0:12:36:0,36,426 0/0:15,0:15:45:0,45,530 +1 902088 . G A 324.34 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-5.34900e+00;DP=133;Dels=0.00000e+00;FS=7.94000e-01;HaplotypeScore=1.50400e-01;InbreedingCoeff=3.03000e-02;MQ=5.93200e+01;MQ0=0;MQRankSum=2.32200e+00;QD=7.91000e+00;ReadPosRankSum=-2.12100e+00;SNPEFF_AMINO_ACID_CHANGE=D30N;SNPEFF_CODON_CHANGE=Gac/Aac;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_902084_902183;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=PLEKHN1;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000379407;VQSLOD=5.23000e+00;culprit=QD;CSQ=A|ENSG00000187583|ENST00000480267|Transcript|upstream_gene_variant||||||rs201730138|1|4167|1|PLEKHN1|HGNC|25284|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187961|ENST00000466300|Transcript|downstream_gene_variant||||||rs201730138|1|2178|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187961|ENST00000338591|Transcript|downstream_gene_variant||||||rs201730138|1|993|1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||||||A:0.0005||A:0.0028|||A:0|A:0.000600||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs201730138|1|4230|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187583|ENST00000379409|Transcript|missense_variant|118|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06|tolerated(0.26)|benign(0.034)|2/15|||ENST00000379409.2:c.88N>A|ENSP00000368719.2:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0441767068273092||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A|ENSG00000187583|ENST00000379407|Transcript|missense_variant|118|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF|tolerated(0.25)|benign(0.072)|2/15|||ENST00000379407.3:c.88N>A|ENSP00000368717.2:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0508376660889659||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A|ENSG00000187961|ENST00000481067|Transcript|downstream_gene_variant||||||rs201730138|1|2544|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187583|ENST00000379410|Transcript|missense_variant|123|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8|tolerated(0.25)|benign(0.072)|2/16|||ENST00000379410.3:c.88N>A|ENSP00000368720.3:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0479302832244009||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A||ENSR00000528862|RegulatoryFeature|regulatory_region_variant||||||rs201730138|1||||||regulatory_region|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600||||||||||||||||| GT:AD:DP:GQ:PL 0/1:10,1:11:1:1,0,264 0/0:13,0:13:33:0,33,447 0/0:10,0:10:30:0,30,371 0/0:4,0:4:12:0,12,141 0/0:1,0:1:3:0,3,39 0/0:4,0:4:12:0,12,145 0/0:18,0:18:51:0,51,665 0/0:4,0:4:12:0,12,148 0/0:5,0:5:15:0,15,193 0/0:9,0:9:24:0,24,320 0/0:10,0:10:30:0,30,378 0/0:4,0:4:12:0,12,160 0/0:10,0:10:30:0,30,387 0/0:7,0:7:21:0,21,247 0/0:9,0:9:27:0,27,350 0/0:14,0:14:42:0,42,540 +1 902088 . G A 111 - AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-5.34900e+00;DP=133;Dels=0.00000e+00;FS=7.94000e-01;HaplotypeScore=1.50400e-01;InbreedingCoeff=3.03000e-02;MQ=5.93200e+01;MQ0=0;MQRankSum=2.32200e+00;QD=7.91000e+00;ReadPosRankSum=-2.12100e+00;SNPEFF_AMINO_ACID_CHANGE=D30N;SNPEFF_CODON_CHANGE=Gac/Aac;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_902084_902183;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=PLEKHN1;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000379407;VQSLOD=5.23000e+00;culprit=QD;CSQ=A|ENSG00000187583|ENST00000480267|Transcript|upstream_gene_variant||||||rs201730138|1|4167|1|PLEKHN1|HGNC|25284|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187961|ENST00000466300|Transcript|downstream_gene_variant||||||rs201730138|1|2178|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187961|ENST00000338591|Transcript|downstream_gene_variant||||||rs201730138|1|993|1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||||||A:0.0005||A:0.0028|||A:0|A:0.000600||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs201730138|1|4230|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187583|ENST00000379409|Transcript|missense_variant|118|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06|tolerated(0.26)|benign(0.034)|2/15|||ENST00000379409.2:c.88N>A|ENSP00000368719.2:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0441767068273092||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A|ENSG00000187583|ENST00000379407|Transcript|missense_variant|118|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF|tolerated(0.25)|benign(0.072)|2/15|||ENST00000379407.3:c.88N>A|ENSP00000368717.2:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0508376660889659||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A|ENSG00000187961|ENST00000481067|Transcript|downstream_gene_variant||||||rs201730138|1|2544|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187583|ENST00000379410|Transcript|missense_variant|123|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8|tolerated(0.25)|benign(0.072)|2/16|||ENST00000379410.3:c.88N>A|ENSP00000368720.3:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0479302832244009||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A||ENSR00000528862|RegulatoryFeature|regulatory_region_variant||||||rs201730138|1||||||regulatory_region|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600||||||||||||||||| GT:AD:DP:GQ:PL 0/1:10,1:11:1:1,0,264 0/0:13,0:13:33:0,33,447 0/0:10,0:10:30:0,30,371 0/0:4,0:4:12:0,12,141 0/0:1,0:1:3:0,3,39 0/0:4,0:4:12:0,12,145 0/0:18,0:18:51:0,51,665 0/0:4,0:4:12:0,12,148 0/0:5,0:5:15:0,15,193 0/0:9,0:9:24:0,24,320 0/0:10,0:10:30:0,30,378 0/0:4,0:4:12:0,12,160 0/0:10,0:10:30:0,30,387 0/0:7,0:7:21:0,21,247 0/0:9,0:9:27:0,27,350 0/0:14,0:14:42:0,42,540 +GL000207.1 1 . G A 324.34 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-5.34900e+00;DP=133;Dels=0.00000e+00;FS=7.94000e-01;HaplotypeScore=1.50400e-01;InbreedingCoeff=3.03000e-02;MQ=5.93200e+01;MQ0=0;MQRankSum=2.32200e+00;QD=7.91000e+00;ReadPosRankSum=-2.12100e+00;SNPEFF_AMINO_ACID_CHANGE=D30N;SNPEFF_CODON_CHANGE=Gac/Aac;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_902084_902183;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=PLEKHN1;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000379407;VQSLOD=5.23000e+00;culprit=QD;CSQ=A|ENSG00000187583|ENST00000480267|Transcript|upstream_gene_variant||||||rs201730138|1|4167|1|PLEKHN1|HGNC|25284|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187961|ENST00000466300|Transcript|downstream_gene_variant||||||rs201730138|1|2178|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187961|ENST00000338591|Transcript|downstream_gene_variant||||||rs201730138|1|993|1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||||||A:0.0005||A:0.0028|||A:0|A:0.000600||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs201730138|1|4230|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187583|ENST00000379409|Transcript|missense_variant|118|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06|tolerated(0.26)|benign(0.034)|2/15|||ENST00000379409.2:c.88N>A|ENSP00000368719.2:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0441767068273092||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A|ENSG00000187583|ENST00000379407|Transcript|missense_variant|118|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF|tolerated(0.25)|benign(0.072)|2/15|||ENST00000379407.3:c.88N>A|ENSP00000368717.2:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0508376660889659||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A|ENSG00000187961|ENST00000481067|Transcript|downstream_gene_variant||||||rs201730138|1|2544|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187583|ENST00000379410|Transcript|missense_variant|123|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8|tolerated(0.25)|benign(0.072)|2/16|||ENST00000379410.3:c.88N>A|ENSP00000368720.3:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0479302832244009||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A||ENSR00000528862|RegulatoryFeature|regulatory_region_variant||||||rs201730138|1||||||regulatory_region|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600||||||||||||||||| GT:AD:DP:GQ:PL 0/1:10,1:11:1:1,0,264 0/0:13,0:13:33:0,33,447 0/0:10,0:10:30:0,30,371 0/0:4,0:4:12:0,12,141 0/0:1,0:1:3:0,3,39 0/0:4,0:4:12:0,12,145 0/0:18,0:18:51:0,51,665 0/0:4,0:4:12:0,12,148 0/0:5,0:5:15:0,15,193 0/0:9,0:9:24:0,24,320 0/0:10,0:10:30:0,30,378 0/0:4,0:4:12:0,12,160 0/0:10,0:10:30:0,30,387 0/0:7,0:7:21:0,21,247 0/0:9,0:9:27:0,27,350 0/0:14,0:14:42:0,42,540 diff --git a/loading_pipeline/var/test/callsets/sex_and_relatedness_1.mt/.README.txt.crc b/loading_pipeline/var/test/callsets/sex_and_relatedness_1.mt/.README.txt.crc new file mode 100644 index 0000000000000000000000000000000000000000..6ceb835d00cda96c5c0f4b3d92efe53201f1a7b3 GIT binary patch literal 12 TcmYc;N@ieSU}CWB<4gts5Q744 literal 0 HcmV?d00001 diff --git a/loading_pipeline/var/test/callsets/sex_and_relatedness_1.mt/._SUCCESS.crc b/loading_pipeline/var/test/callsets/sex_and_relatedness_1.mt/._SUCCESS.crc new file mode 100644 index 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ALGORITHMS=depth;CHR2=chr1;END=263666;EVIDENCE=BAF,RD;PREDICTED_INTERGENIC;PREDICTED_NEAREST_TSS=OR4F29;SVLEN=6000;SVTYPE=DUP;AN=8;AC=1;AF=0.115596;N_BI_GENOS=2911;N_HOMREF=2348;N_HET=453;N_HOMALT=110;FREQ_HOMREF=0.806596;FREQ_HET=0.155617;FREQ_HOMALT=0.0377877;MALE_AN=2894;MALE_AC=339;MALE_AF=0.117139;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=1163;MALE_N_HET=229;MALE_N_HOMALT=55;MALE_FREQ_HOMREF=0.803732;MALE_FREQ_HET=0.158258;MALE_FREQ_HOMALT=0.0380097;FEMALE_AN=2906;FEMALE_AC=330;FEMALE_AF=0.113558;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=1178;FEMALE_N_HET=220;FEMALE_N_HOMALT=55;FEMALE_FREQ_HOMREF=0.810736;FEMALE_FREQ_HET=0.151411;FEMALE_FREQ_HOMALT=0.0378527 GT:EV:GQ:RD_CN:RD_GQ 0/0:RD:99:2:99 0/0:RD:99:2:99 0/1:RD:8:3:8 0/0:RD:13:1:13 0/0:RD:13:1:13 +chr1 413968 DEL_chr1_12 N 999 PASS ALGORITHMS=depth;CHR2=chr1;END=428500;EVIDENCE=RD;PREDICTED_INTERGENIC;PREDICTED_NEAREST_TSS=OR4F29;SVLEN=14532;SVTYPE=DEL;AN=8;AC=1;AF=0.064926;N_BI_GENOS=2911;N_HOMREF=2538;N_HET=368;N_HOMALT=5;FREQ_HOMREF=0.871865;FREQ_HET=0.126417;FREQ_HOMALT=0.00171762;MALE_AN=2894;MALE_AC=172;MALE_AF=0.059433;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=1278;MALE_N_HET=166;MALE_N_HOMALT=3;MALE_FREQ_HOMREF=0.883207;MALE_FREQ_HET=0.11472;MALE_FREQ_HOMALT=0.00207325;FEMALE_AN=2906;FEMALE_AC=205;FEMALE_AF=0.070544;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=1250;FEMALE_N_HET=201;FEMALE_N_HOMALT=2;FEMALE_FREQ_HOMREF=0.860289;FEMALE_FREQ_HET=0.138334;FEMALE_FREQ_HOMALT=0.00137646 GT:EV:GQ:RD_CN:RD_GQ 0/0:RD:12:2:12 0/0:RD:0:2:0 0/1:RD:99:1:99 0/0:RD:2:2:2 0/0:RD:2:2:2 +chr1 789481 BND_chr1_9 N 999 PESR_GT_OVERDISPERSION;UNRESOLVED ALGORITHMS=manta;CHR2=chr1;END=789481;EVIDENCE=PE;PREDICTED_INTERGENIC;PREDICTED_NEAREST_TSS=FBXO28,OR4F16;PREDICTED_NONCODING_BREAKPOINT=DNase,Tommerup_TADanno;STRANDS=-+;SVLEN=223225007;SVTYPE=BND;UNRESOLVED_TYPE=SINGLE_ENDER_-+;AN=8;AC=7;AF=0.910684;N_BI_GENOS=2911;N_HOMREF=0;N_HET=520;N_HOMALT=2391;FREQ_HOMREF=0;FREQ_HET=0.178633;FREQ_HOMALT=0.821367;MALE_AN=2894;MALE_AC=2639;MALE_AF=0.911887;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=0;MALE_N_HET=255;MALE_N_HOMALT=1192;MALE_FREQ_HOMREF=0;MALE_FREQ_HET=0.176227;MALE_FREQ_HOMALT=0.823773;FEMALE_AN=2906;FEMALE_AC=2643;FEMALE_AF=0.909498;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=0;FEMALE_N_HET=263;FEMALE_N_HOMALT=1190;FEMALE_FREQ_HOMREF=0;FEMALE_FREQ_HET=0.181005;FEMALE_FREQ_HOMALT=0.818995 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 1/1:PE:59:59:2:99:0 1/1:PE:26:26:2:99:0 1/1:PE:39:39:2:99:0 0/1:PE:19:19:1:99:0 0/1:PE:19:19:1:99:0 +chr1 4228405 INS_chr1_65 N 605 HIGH_SR_BACKGROUND ALGORITHMS=manta,melt;CHR2=chr1;END=4228448;EVIDENCE=SR;gnomAD_V2_SVID=gnomAD-SV_v2.1_INS_chr1_65;GNOMAD_V4.1_TRUTH_VID=gnomAD-SV_v3_BND_chr1_0001f5b7;gnomAD_V2_AF=0.068962998688221;gnomAD_V2_AC=224;gnomAD_V2_AN=3247;StrVCTVRE=0.1255;PREDICTED_INTERGENIC;PREDICTED_NEAREST_TSS=C1orf174;SVLEN=298;SVTYPE=INS;AN=8;AC=1;AF=0.10237;N_BI_GENOS=2911;N_HOMREF=2318;N_HET=590;N_HOMALT=3;FREQ_HOMREF=0.79629;FREQ_HET=0.202679;FREQ_HOMALT=0.00103057;MALE_AN=2894;MALE_AC=293;MALE_AF=0.101244;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=1156;MALE_N_HET=289;MALE_N_HOMALT=2;MALE_FREQ_HOMREF=0.798894;MALE_FREQ_HET=0.199724;MALE_FREQ_HOMALT=0.00138217;FEMALE_AN=2906;FEMALE_AC=302;FEMALE_AF=0.103923;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=1152;FEMALE_N_HET=300;FEMALE_N_HOMALT=1;FEMALE_FREQ_HOMREF=0.792842;FEMALE_FREQ_HET=0.206469;FEMALE_FREQ_HOMALT=0.000688231 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 0/1:SR:62:99:0:62:1 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:99:0 +chr1 6558902 CPX_chr1_22 N 644 HIGH_SR_BACKGROUND ALGORITHMS=manta;BOTHSIDES_SUPPORT;CHR2=chr1;CPX_INTERVALS=INV_chr1:6558902-6559723,DUP_chr1:6559655-6559723;CPX_TYPE=INVdup;END=6559723;EVIDENCE=PE,SR;PREDICTED_INTRONIC=TAS1R1;PREDICTED_NONCODING_BREAKPOINT=Tommerup_TADanno;PREDICTED_NONCODING_SPAN=DNase;SVLEN=821;SVTYPE=CPX;AN=8;AC=2;AF=0.169873;N_BI_GENOS=2911;N_HOMREF=1925;N_HET=983;N_HOMALT=3;FREQ_HOMREF=0.661285;FREQ_HET=0.337685;FREQ_HOMALT=0.00103057;MALE_AN=2894;MALE_AC=497;MALE_AF=0.171735;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=950;MALE_N_HET=497;MALE_N_HOMALT=0;MALE_FREQ_HOMREF=0.656531;MALE_FREQ_HET=0.343469;MALE_FREQ_HOMALT=0;FEMALE_AN=2906;FEMALE_AC=488;FEMALE_AF=0.167928;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=968;FEMALE_N_HET=482;FEMALE_N_HOMALT=3;FEMALE_FREQ_HOMREF=0.666208;FEMALE_FREQ_HET=0.331727;FEMALE_FREQ_HOMALT=0.00206469 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT:RD_CN:CONC_ST 0/0:PE,SR:99:99:0:99:0:2:EMPTY 0/1:PE,SR:57:0:0:57:1:2:TN,TP 0/1:PE,SR:0:0:1:99:0:2:FP,TN 0/0:PE,SR:99:99:0:0:0:3:FN 1/1:PE,SR:99:99:0:0:0:1:FP,TP +chr1 16088760 CPX_chr1_41 N 684 PASS ALGORITHMS=manta;CHR2=chr1;CPX_INTERVALS=DUP_chr1:16088760-16088835,INV_chr1:16088760-16089601;CPX_TYPE=dupINV;END=16089601;EVIDENCE=PE,SR;PREDICTED_INTERGENIC;PREDICTED_NEAREST_TSS=FAM131C;PREDICTED_NONCODING_BREAKPOINT=Tommerup_TADanno;PREDICTED_NONCODING_SPAN=DNase;SVLEN=841;SVTYPE=CPX;AN=8;AC=2;AF=0.218138;N_BI_GENOS=2911;N_HOMREF=1659;N_HET=1234;N_HOMALT=18;FREQ_HOMREF=0.569907;FREQ_HET=0.423909;FREQ_HOMALT=0.00618344;MALE_AN=2894;MALE_AC=635;MALE_AF=0.219419;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=818;MALE_N_HET=623;MALE_N_HOMALT=6;MALE_FREQ_HOMREF=0.565308;MALE_FREQ_HET=0.430546;MALE_FREQ_HOMALT=0.00414651;FEMALE_AN=2906;FEMALE_AC=629;FEMALE_AF=0.216449;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=836;FEMALE_N_HET=605;FEMALE_N_HOMALT=12;FEMALE_FREQ_HOMREF=0.575361;FEMALE_FREQ_HET=0.41638;FEMALE_FREQ_HOMALT=0.00825877 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 0/1:SR:52:0:0:52:1 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:99:0 0/1:SR:62:0:0:62:1 0/1:SR:62:0:0:62:1 +chr1 17465707 INS_chr1_268 N 263 HIGH_SR_BACKGROUND ALGORITHMS=melt;CHR2=chr1;END=17465723;EVIDENCE=SR;PREDICTED_INTERGENIC;PREDICTED_NEAREST_TSS=RCC2;PREDICTED_NONCODING_BREAKPOINT=Tommerup_TADanno;SVLEN=955;SVTYPE=INS;AN=8;AC=1;AF=0.004466;N_BI_GENOS=2911;N_HOMREF=2885;N_HET=26;N_HOMALT=0;FREQ_HOMREF=0.991068;FREQ_HET=0.00893164;FREQ_HOMALT=0;MALE_AN=2894;MALE_AC=14;MALE_AF=0.004838;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=1433;MALE_N_HET=14;MALE_N_HOMALT=0;MALE_FREQ_HOMREF=0.990325;MALE_FREQ_HET=0.00967519;MALE_FREQ_HOMALT=0;FEMALE_AN=2906;FEMALE_AC=11;FEMALE_AF=0.003785;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=1442;FEMALE_N_HET=11;FEMALE_N_HOMALT=0;FEMALE_FREQ_HOMREF=0.992429;FEMALE_FREQ_HET=0.00757054;FEMALE_FREQ_HOMALT=0 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:99:0 0/1:SR:0:99:0:0:1 0/0:PE,SR:99:99:0:2:0 0/0:PE,SR:99:99:0:2:0 +chr1 21427498 CPX_chr1_54 N 733 PASS ALGORITHMS=manta;CHR2=chr1;CPX_INTERVALS=DUP_chr1:21427498-21427959,INV_chr1:21427498-21480073,DEL_chr1:21480073-21480419;CPX_TYPE=dupINVdel;END=21480419;EVIDENCE=PE;PREDICTED_LOF=NBPF3;PREDICTED_NONCODING_BREAKPOINT=DNase,Tommerup_TADanno;PREDICTED_NONCODING_SPAN=DNase;SVLEN=52921;SVTYPE=CPX;AN=8;AC=4;AF=0.499656;N_BI_GENOS=2911;N_HOMREF=51;N_HET=2811;N_HOMALT=49;FREQ_HOMREF=0.0175198;FREQ_HET=0.965648;FREQ_HOMALT=0.0168327;MALE_AN=2894;MALE_AC=1453;MALE_AF=0.502073;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=19;MALE_N_HET=1403;MALE_N_HOMALT=25;MALE_FREQ_HOMREF=0.0131306;MALE_FREQ_HET=0.969592;MALE_FREQ_HOMALT=0.0172771;FEMALE_AN=2906;FEMALE_AC=1445;FEMALE_AF=0.497247;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=32;FEMALE_N_HET=1397;FEMALE_N_HOMALT=24;FEMALE_FREQ_HOMREF=0.0220234;FEMALE_FREQ_HET=0.961459;FEMALE_FREQ_HOMALT=0.0165175 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 0/1:PE:93:93:1:99:0 0/1:PE:79:79:1:99:0 0/1:PE:33:33:1:6:0 0/1:PE,SR:39:39:1:99:0 0/1:PE,SR:39:39:1:99:0 +chr1 48963084 INS_chr1_688 N 526 HIGH_SR_BACKGROUND ALGORITHMS=melt;CHR2=chr1;END=48963135;EVIDENCE=SR;PREDICTED_INTRONIC=AGBL4;PREDICTED_NONCODING_BREAKPOINT=Tommerup_TADanno;SVLEN=5520;SVTYPE=INS;AN=8;AC=1;AF=0.06338;N_BI_GENOS=2911;N_HOMREF=2544;N_HET=365;N_HOMALT=2;FREQ_HOMREF=0.873926;FREQ_HET=0.125386;FREQ_HOMALT=0.000687049;MALE_AN=2894;MALE_AC=177;MALE_AF=0.061161;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=1271;MALE_N_HET=175;MALE_N_HOMALT=1;MALE_FREQ_HOMREF=0.878369;MALE_FREQ_HET=0.12094;MALE_FREQ_HOMALT=0.000691085;FEMALE_AN=2906;FEMALE_AC=192;FEMALE_AF=0.06607;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=1262;FEMALE_N_HET=190;FEMALE_N_HOMALT=1;FEMALE_FREQ_HOMREF=0.868548;FEMALE_FREQ_HET=0.130764;FEMALE_FREQ_HOMALT=0.000688231 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:99:0 0/1:SR:0:99:0:0:1 0/1:SR:0:99:0:0:1 +chr1 180540234 CPX_chr1_251 N 999 UNRESOLVED ALGORITHMS=manta;CHR2=chr1;CPX_INTERVALS=DEL_chr1:180540234-181074767,INV_chr1:181074767-181074938;CPX_TYPE=delINV;END=181074952;EVIDENCE=PE,SR;PREDICTED_LOF=KIAA1614,MR1,STX6,XPR1;PREDICTED_NONCODING_BREAKPOINT=Tommerup_TADanno;PREDICTED_NONCODING_SPAN=DNase,Enhancer;SVLEN=534718;SVTYPE=CPX;UNRESOLVED_TYPE=POSTHOC_RD_GT_REJECTION;AN=8;AC=3;AF=0.251804;N_BI_GENOS=2911;N_HOMREF=1559;N_HET=1238;N_HOMALT=114;FREQ_HOMREF=0.535555;FREQ_HET=0.425283;FREQ_HOMALT=0.0391618;MALE_AN=2894;MALE_AC=724;MALE_AF=0.250173;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=784;MALE_N_HET=602;MALE_N_HOMALT=61;MALE_FREQ_HOMREF=0.541811;MALE_FREQ_HET=0.416033;MALE_FREQ_HOMALT=0.0421562;FEMALE_AN=2906;FEMALE_AC=736;FEMALE_AF=0.253269;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=770;FEMALE_N_HET=630;FEMALE_N_HOMALT=53;FEMALE_FREQ_HOMREF=0.529938;FEMALE_FREQ_HET=0.433586;FEMALE_FREQ_HOMALT=0.0364763 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 0/0:PE,SR:99:99:0:99:0 0/1:PE,SR:41:26:1:41:1 1/1:PE,SR:89:33:1:89:2 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:99:0 +chrX 3 CPX_chrX_251 N 999 UNRESOLVED ALGORITHMS=manta;CPX_INTERVALS=DEL_chr1:180540234-181074767,INV_chr1:181074767-181074938;CPX_TYPE=delINV;END=2781000;EVIDENCE=PE,SR;PREDICTED_LOF=KIAA1614,MR1,STX6,XPR1;PREDICTED_NONCODING_BREAKPOINT=Tommerup_TADanno;PREDICTED_NONCODING_SPAN=DNase,Enhancer;SVLEN=534718;SVTYPE=CPX;UNRESOLVED_TYPE=POSTHOC_RD_GT_REJECTION;AN=8;AC=3;AF=0.251804;N_BI_GENOS=2911;N_HOMREF=1559;N_HET=1238;N_HOMALT=114;FREQ_HOMREF=0.535555;FREQ_HET=0.425283;FREQ_HOMALT=0.0391618;MALE_AN=2894;MALE_AC=724;MALE_AF=0.250173;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=784;MALE_N_HET=602;MALE_N_HOMALT=61;MALE_FREQ_HOMREF=0.541811;MALE_FREQ_HET=0.416033;MALE_FREQ_HOMALT=0.0421562;FEMALE_AN=2906;FEMALE_AC=736;FEMALE_AF=0.253269;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=770;FEMALE_N_HET=630;FEMALE_N_HOMALT=53;FEMALE_FREQ_HOMREF=0.529938;FEMALE_FREQ_HET=0.433586;FEMALE_FREQ_HOMALT=0.0364763 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 0/0:PE,SR:99:99:0:99:0 0/1:PE,SR:41:26:1:41:1 1/1:PE,SR:89:33:1:89:2 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:99:0 +chrX 2781700 CPX_chrX_252 N 999 UNRESOLVED ALGORITHMS=manta;CPX_INTERVALS=DEL_chr1:180540234-181074767,INV_chr1:181074767-181074938;CPX_TYPE=delINV;END=2781900;EVIDENCE=PE,SR;PREDICTED_LOF=KIAA1614,MR1,STX6,XPR1;PREDICTED_NONCODING_BREAKPOINT=Tommerup_TADanno;PREDICTED_NONCODING_SPAN=DNase,Enhancer;SVLEN=534718;SVTYPE=CPX;UNRESOLVED_TYPE=POSTHOC_RD_GT_REJECTION;AN=8;AC=3;AF=0.251804;N_BI_GENOS=2911;N_HOMREF=1559;N_HET=1238;N_HOMALT=114;FREQ_HOMREF=0.535555;FREQ_HET=0.425283;FREQ_HOMALT=0.0391618;MALE_AN=2894;MALE_AC=724;MALE_AF=0.250173;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=784;MALE_N_HET=602;MALE_N_HOMALT=61;MALE_FREQ_HOMREF=0.541811;MALE_FREQ_HET=0.416033;MALE_FREQ_HOMALT=0.0421562;FEMALE_AN=2906;FEMALE_AC=736;FEMALE_AF=0.253269;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=770;FEMALE_N_HET=630;FEMALE_N_HOMALT=53;FEMALE_FREQ_HOMREF=0.529938;FEMALE_FREQ_HET=0.433586;FEMALE_FREQ_HOMALT=0.0364763 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 0/0:PE,SR:99:99:0:99:0 0/1:PE,SR:41:26:1:41:1 1/1:PE,SR:89:33:1:89:2 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:99:0 \ No newline at end of file diff --git a/loading_pipeline/var/test/callsets/sv_2.vcf b/loading_pipeline/var/test/callsets/sv_2.vcf new file mode 100644 index 0000000000..12f65690ed --- /dev/null +++ b/loading_pipeline/var/test/callsets/sv_2.vcf @@ -0,0 +1,82 @@ +##fileformat=VCFv4.2 +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= 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ALGORITHMS=manta;CHR2=chr5;END=180928;END2=20404;EVIDENCE=PE,SR;PREDICTED_INTERGENIC;PREDICTED_NEAREST_TSS=OR4F5,PLEKHG4B;PREDICTED_NONCODING_BREAKPOINT=DNase;STRANDS=+-;SVLEN=-1;SVTYPE=BND;UNRESOLVED_TYPE=SINGLE_ENDER_+-;AN=8;AC=1;AF=0.04775;N_BI_GENOS=2911;N_HOMREF=2633;N_HET=278;N_HOMALT=0;FREQ_HOMREF=0.9045;FREQ_HET=0.0954998;FREQ_HOMALT=0;MALE_AN=2894;MALE_AC=137;MALE_AF=0.047339;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=1310;MALE_N_HET=137;MALE_N_HOMALT=0;MALE_FREQ_HOMREF=0.905321;MALE_FREQ_HET=0.0946786;MALE_FREQ_HOMALT=0;FEMALE_AN=2906;FEMALE_AC=139;FEMALE_AF=0.047832;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=1314;FEMALE_N_HET=139;FEMALE_N_HOMALT=0;FEMALE_FREQ_HOMREF=0.904336;FEMALE_FREQ_HET=0.0956641;FEMALE_FREQ_HOMALT=0;SEQR_INTERNAL_TRUTH_VID=BND_chr1_6 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 0/0:PE,SR:99:99:0:2:0 0/1:SR:31:99:0:31:1 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:2:0 0/0:PE,SR:99:99:0:2:0 +chr1 257667 new_variant2 N 999 PASS 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gene_symbol_source='HGNC', + hgnc_id='28706', + hgvs_offset=hl.null('int32'), + hgvsc=hl.null('str'), + hgvsp=hl.null('str'), + impact='MODIFIER', + intron=hl.null('str'), + lof=hl.null('str'), + lof_filter=hl.null('str'), + lof_flags=hl.null('str'), + lof_info=hl.null('str'), + minimised=1, + polyphen_prediction=hl.null('str'), + polyphen_score=hl.null('float64'), + protein_end=hl.null('int32'), + protein_id=hl.null('str'), + protein_start=hl.null('int32'), + sift_prediction=hl.null('str'), + sift_score=hl.null('float64'), + strand=1, + swissprot=hl.null('str'), + transcript_id='ENST00000464948', + trembl=hl.null('str'), + uniparc=hl.null('str'), + variant_allele='A', + ), + hl.struct( + allele_num=1, + amino_acids=hl.null('str'), + biotype='retained_intron', + canonical=hl.null('int32'), + ccds=hl.null('str'), + cdna_end=hl.null('int32'), + cdna_start=hl.null('int32'), + cds_end=hl.null('int32'), + cds_start=hl.null('int32'), + codons=hl.null('str'), + consequence_terms=hl.array(['downstream_gene_variant']), + distance=3736, + domains=hl.null('array'), + exon=hl.null('str'), + gene_id='ENSG00000187634', + gene_pheno=hl.null('int32'), + gene_symbol='SAMD11', + gene_symbol_source='HGNC', + hgnc_id='28706', + hgvs_offset=hl.null('int32'), + hgvsc=hl.null('str'), + hgvsp=hl.null('str'), + impact='MODIFIER', + intron=hl.null('str'), + lof=hl.null('str'), + lof_filter=hl.null('str'), + lof_flags=hl.null('str'), + lof_info=hl.null('str'), + minimised=1, + polyphen_prediction=hl.null('str'), + polyphen_score=hl.null('float64'), + protein_end=hl.null('int32'), + protein_id=hl.null('str'), + protein_start=hl.null('int32'), + sift_prediction=hl.null('str'), + sift_score=hl.null('float64'), + strand=1, + swissprot=hl.null('str'), + transcript_id='ENST00000466827', + trembl=hl.null('str'), + uniparc=hl.null('str'), + variant_allele='A', + ), + hl.struct( + allele_num=1, + amino_acids=hl.null('str'), + biotype='retained_intron', + canonical=hl.null('int32'), + ccds=hl.null('str'), + cdna_end=hl.null('int32'), + cdna_start=hl.null('int32'), + cds_end=hl.null('int32'), + cds_start=hl.null('int32'), + codons=hl.null('str'), + consequence_terms=hl.array(['downstream_gene_variant']), + distance=3544, + domains=hl.null('array'), + exon=hl.null('str'), + gene_id='ENSG00000187634', + gene_pheno=hl.null('int32'), + gene_symbol='SAMD11', + gene_symbol_source='HGNC', + hgnc_id='28706', + hgvs_offset=hl.null('int32'), + hgvsc=hl.null('str'), + hgvsp=hl.null('str'), + impact='MODIFIER', + intron=hl.null('str'), + lof=hl.null('str'), + lof_filter=hl.null('str'), + lof_flags=hl.null('str'), + lof_info=hl.null('str'), + minimised=1, + polyphen_prediction=hl.null('str'), + polyphen_score=hl.null('float64'), + protein_end=hl.null('int32'), + protein_id=hl.null('str'), + protein_start=hl.null('int32'), + sift_prediction=hl.null('str'), + sift_score=hl.null('float64'), + strand=1, + swissprot=hl.null('str'), + transcript_id='ENST00000474461', + trembl=hl.null('str'), + uniparc=hl.null('str'), + variant_allele='A', + ), + hl.struct( + allele_num=1, + amino_acids=hl.null('str'), + biotype='retained_intron', + canonical=hl.null('int32'), + ccds=hl.null('str'), + cdna_end=3114, + cdna_start=3114, + cds_end=hl.null('int32'), + cds_start=hl.null('int32'), + codons=hl.null('str'), + consequence_terms=hl.array( + [ + 'non_coding_transcript_exon_variant', + 'non_coding_transcript_variant', + ], + ), + distance=hl.null('int32'), + domains=hl.null('array'), + exon='13/17', + gene_id='ENSG00000188976', + gene_pheno=hl.null('int32'), + gene_symbol='NOC2L', + gene_symbol_source='HGNC', + hgnc_id='24517', + hgvs_offset=hl.null('int32'), + hgvsc='ENST00000477976.1:n.3114C>T', + hgvsp=hl.null('str'), + impact='MODIFIER', + intron=hl.null('str'), + lof=hl.null('str'), + lof_filter=hl.null('str'), + lof_flags=hl.null('str'), + lof_info=hl.null('str'), + minimised=1, + polyphen_prediction=hl.null('str'), + polyphen_score=hl.null('float64'), + protein_end=hl.null('int32'), + protein_id=hl.null('str'), + protein_start=hl.null('int32'), + sift_prediction=hl.null('str'), + sift_score=hl.null('float64'), + strand=-1, + swissprot=hl.null('str'), + transcript_id='ENST00000477976', + trembl=hl.null('str'), + uniparc=hl.null('str'), + variant_allele='A', + ), + hl.struct( + allele_num=1, + amino_acids=hl.null('str'), + biotype='processed_transcript', + canonical=hl.null('int32'), + ccds=hl.null('str'), + cdna_end=hl.null('int32'), + cdna_start=hl.null('int32'), + cds_end=hl.null('int32'), + cds_start=hl.null('int32'), + codons=hl.null('str'), + consequence_terms=hl.array(['downstream_gene_variant']), + distance=4365, + domains=hl.null('array'), + exon=hl.null('str'), + gene_id='ENSG00000187634', + gene_pheno=hl.null('int32'), + gene_symbol='SAMD11', + gene_symbol_source='HGNC', + hgnc_id='28706', + hgvs_offset=hl.null('int32'), + hgvsc=hl.null('str'), + hgvsp=hl.null('str'), + impact='MODIFIER', + intron=hl.null('str'), + lof=hl.null('str'), + lof_filter=hl.null('str'), + lof_flags=hl.null('str'), + lof_info=hl.null('str'), + minimised=1, + polyphen_prediction=hl.null('str'), + polyphen_score=hl.null('float64'), + protein_end=hl.null('int32'), + protein_id=hl.null('str'), + protein_start=hl.null('int32'), + sift_prediction=hl.null('str'), + sift_score=hl.null('float64'), + strand=1, + swissprot=hl.null('str'), + transcript_id='ENST00000478729', + trembl=hl.null('str'), + uniparc=hl.null('str'), + variant_allele='A', + ), + hl.struct( + allele_num=1, + amino_acids=hl.null('str'), + biotype='retained_intron', + canonical=hl.null('int32'), + ccds=hl.null('str'), + cdna_end=523, + cdna_start=523, + cds_end=hl.null('int32'), + cds_start=hl.null('int32'), + codons=hl.null('str'), + consequence_terms=hl.array( + [ + 'non_coding_transcript_exon_variant', + 'non_coding_transcript_variant', + ], + ), + distance=hl.null('int32'), + domains=hl.null('array'), + exon='1/5', + gene_id='ENSG00000188976', + gene_pheno=hl.null('int32'), + gene_symbol='NOC2L', + gene_symbol_source='HGNC', + hgnc_id='24517', + hgvs_offset=hl.null('int32'), + hgvsc='ENST00000483767.1:n.523C>T', + hgvsp=hl.null('str'), + impact='MODIFIER', + intron=hl.null('str'), + lof=hl.null('str'), + lof_filter=hl.null('str'), + lof_flags=hl.null('str'), + lof_info=hl.null('str'), + minimised=1, + polyphen_prediction=hl.null('str'), + polyphen_score=hl.null('float64'), + protein_end=hl.null('int32'), + protein_id=hl.null('str'), + protein_start=hl.null('int32'), + sift_prediction=hl.null('str'), + sift_score=hl.null('float64'), + strand=-1, + swissprot=hl.null('str'), + transcript_id='ENST00000483767', + trembl=hl.null('str'), + uniparc=hl.null('str'), + variant_allele='A', + ), + hl.struct( + allele_num=1, + amino_acids=hl.null('str'), + biotype='processed_transcript', + canonical=hl.null('int32'), + ccds=hl.null('str'), + cdna_end=hl.null('int32'), + cdna_start=hl.null('int32'), + cds_end=hl.null('int32'), + cds_start=hl.null('int32'), + codons=hl.null('str'), + consequence_terms=hl.array(['upstream_gene_variant']), + distance=976, + domains=hl.null('array'), + exon=hl.null('str'), + gene_id='ENSG00000188976', + gene_pheno=hl.null('int32'), + gene_symbol='NOC2L', + gene_symbol_source='HGNC', + hgnc_id='24517', + hgvs_offset=hl.null('int32'), + hgvsc=hl.null('str'), + hgvsp=hl.null('str'), + impact='MODIFIER', + intron=hl.null('str'), + lof=hl.null('str'), + lof_filter=hl.null('str'), + lof_flags=hl.null('str'), + lof_info=hl.null('str'), + minimised=1, + polyphen_prediction=hl.null('str'), + polyphen_score=hl.null('float64'), + protein_end=hl.null('int32'), + protein_id=hl.null('str'), + protein_start=hl.null('int32'), + sift_prediction=hl.null('str'), + sift_score=hl.null('float64'), + strand=-1, + swissprot=hl.null('str'), + transcript_id='ENST00000496938', + trembl=hl.null('str'), + uniparc=hl.null('str'), + variant_allele='A', + ), + ], + ), + variant_class='SNV', +) + +MOCK_38_VEP_DATA = hl.struct( + most_severe_consequence='missense_variant', + check_ref=hl.missing(hl.tstr), + motif_feature_consequences=hl.missing( + hl.tarray( + hl.tstruct(consequence_terms=hl.tarray(hl.tstr), motif_feature_id=hl.tstr), + ), + ), + regulatory_feature_consequences=hl.array( + [ + hl.struct( + biotype='enhancer', + consequence_terms=['regulatory_region_variant'], + regulatory_feature_id='regulatory_1', + ), + hl.struct( + biotype='enhancer', + consequence_terms=['regulatory_region_ablation'], + regulatory_feature_id='regulatory_2', + ), + ], + ), + transcript_consequences=hl.array( + [ + hl.struct( + amino_acids='S/L', + am_pathogenicity=hl.float32(0.1), + biotype='protein_coding', + canonical=1, + check_ref=hl.missing(hl.tstr), + codons='tCg/tTg', + consequence_terms=hl.array(['missense_variant']), + exon='15/19', + gene_id='ENSG00000188976', + hgvsc='ENST00000327044.6:c.1667C>T', + hgvsp='ENSP00000317992.6:p.Ser556Leu', + intron=hl.null('str'), + lof='LC', + lof_filter='END_TRUNC,INCOMPLETE_CDS', + lof_flags=hl.null('str'), + lof_info='INTRON_END:881781,EXON_END:881925,EXON_START:881782,DE_NOVO_DONOR_MES:-7.36719797135343,DE_NOVO_DONOR_PROB:0.261170618766552,DE_NOVO_DONOR_POS:-138,INTRON_START:881667,DE_NOVO_DONOR_MES_POS:-138,MUTANT_DONOR_MES:4.93863747168278', + mane_select='NM_015658.4', + mane_plus_clinical=hl.null('str'), + spliceregion=hl.missing(hl.tarray(hl.tstr)), + transcript_id='ENST00000327044', + # UTRAnnotator + existing_inframe_oorfs=hl.missing(hl.tint32), + existing_outofframe_oorfs=hl.missing(hl.tint32), + existing_uorfs=hl.missing(hl.tint32), + fiveutr_consequence=hl.missing(hl.tstr), + fiveutr_annotation=hl.missing( + hl.tdict( + hl.tstr, + hl.tstruct( + type=hl.tstr, + KozakContext=hl.tstr, + KozakStrength=hl.tstr, + DistanceToCDS=hl.tstr, + CapDistanceToStart=hl.tstr, + DistanceToStop=hl.tstr, + Evidence=hl.tstr, + AltStop=hl.tstr, + AltStopDistanceToCDS=hl.tstr, + FrameWithCDS=hl.tstr, + StartDistanceToCDS=hl.tstr, + newSTOPDistanceToCDS=hl.tstr, + alt_type=hl.tstr, + alt_type_length=hl.tstr, + ref_StartDistanceToCDS=hl.tstr, + ref_type=hl.tstr, + ref_type_length=hl.tstr, + ), + ), + ), + ), + hl.struct( + amino_acids=hl.null('str'), + am_pathogenicity=hl.float32(0.2), + biotype='protein_coding', + canonical=hl.null('int32'), + check_ref=hl.missing(hl.tstr), + codons=hl.null('str'), + consequence_terms=hl.array(['downstream_gene_variant']), + exon=hl.null('str'), + gene_id='ENSG00000187634', + hgvsc=hl.null('str'), + hgvsp=hl.null('str'), + intron=hl.null('str'), + lof=hl.null('str'), + lof_filter=hl.null('str'), + lof_flags=hl.null('str'), + lof_info=hl.null('str'), + mane_select=hl.null('str'), + mane_plus_clinical=hl.null('str'), + spliceregion=hl.missing(hl.tarray(hl.tstr)), + transcript_id='ENST00000341065', + # UTRAnnotator + existing_inframe_oorfs=hl.missing(hl.tint32), + existing_outofframe_oorfs=hl.missing(hl.tint32), + existing_uorfs=hl.missing(hl.tint32), + fiveutr_consequence=hl.missing(hl.tstr), + fiveutr_annotation=hl.missing( + hl.tdict( + hl.tstr, + hl.tstruct( + type=hl.tstr, + KozakContext=hl.tstr, + KozakStrength=hl.tstr, + DistanceToCDS=hl.tstr, + CapDistanceToStart=hl.tstr, + DistanceToStop=hl.tstr, + Evidence=hl.tstr, + AltStop=hl.tstr, + AltStopDistanceToCDS=hl.tstr, + FrameWithCDS=hl.tstr, + StartDistanceToCDS=hl.tstr, + newSTOPDistanceToCDS=hl.tstr, + alt_type=hl.tstr, + alt_type_length=hl.tstr, + ref_StartDistanceToCDS=hl.tstr, + ref_type=hl.tstr, + ref_type_length=hl.tstr, + ), + ), + ), + ), + hl.struct( + amino_acids=hl.null('str'), + am_pathogenicity=hl.missing(hl.tfloat32), + biotype='protein_coding', + canonical=1, + check_ref=hl.missing(hl.tstr), + codons=hl.null('str'), + consequence_terms=hl.array(['downstream_gene_variant']), + exon=hl.null('str'), + gene_id='ENSG00000187634', + hgvsc=hl.null('str'), + hgvsp=hl.null('str'), + intron=hl.null('str'), + lof=hl.null('str'), + lof_filter=hl.null('str'), + lof_flags=hl.null('str'), + lof_info=hl.null('str'), + mane_select=hl.null('str'), + mane_plus_clinical=hl.null('str'), + spliceregion=hl.missing(hl.tarray(hl.tstr)), + transcript_id='ENST00000342066', + # UTRAnnotator + existing_inframe_oorfs=hl.missing(hl.tint32), + existing_outofframe_oorfs=hl.missing(hl.tint32), + existing_uorfs=hl.missing(hl.tint32), + fiveutr_consequence=hl.missing(hl.tstr), + fiveutr_annotation=hl.missing( + hl.tdict( + hl.tstr, + hl.tstruct( + type=hl.tstr, + KozakContext=hl.tstr, + KozakStrength=hl.tstr, + DistanceToCDS=hl.tstr, + CapDistanceToStart=hl.tstr, + DistanceToStop=hl.tstr, + Evidence=hl.tstr, + AltStop=hl.tstr, + AltStopDistanceToCDS=hl.tstr, + FrameWithCDS=hl.tstr, + StartDistanceToCDS=hl.tstr, + newSTOPDistanceToCDS=hl.tstr, + alt_type=hl.tstr, + alt_type_length=hl.tstr, + ref_StartDistanceToCDS=hl.tstr, + ref_type=hl.tstr, + ref_type_length=hl.tstr, + ), + ), + ), + ), + hl.struct( + amino_acids=hl.null('str'), + am_pathogenicity=hl.missing(hl.tfloat32), + biotype='protein_coding', + canonical=hl.null('int32'), + check_ref=hl.missing(hl.tstr), + codons=hl.null('str'), + consequence_terms=hl.array(['downstream_gene_variant']), + exon=hl.null('str'), + gene_id='ENSG00000187634', + hgvsc=hl.null('str'), + hgvsp=hl.null('str'), + intron=hl.null('str'), + lof=hl.null('str'), + lof_filter=hl.null('str'), + lof_flags=hl.null('str'), + lof_info=hl.null('str'), + mane_select=hl.null('str'), + mane_plus_clinical=hl.null('str'), + spliceregion=hl.missing(hl.tarray(hl.tstr)), + transcript_id='ENST00000455979', + # UTRAnnotator + existing_inframe_oorfs=hl.missing(hl.tint32), + existing_outofframe_oorfs=hl.missing(hl.tint32), + existing_uorfs=hl.missing(hl.tint32), + fiveutr_consequence=hl.missing(hl.tstr), + fiveutr_annotation=hl.missing( + hl.tdict( + hl.tstr, + hl.tstruct( + type=hl.tstr, + KozakContext=hl.tstr, + KozakStrength=hl.tstr, + DistanceToCDS=hl.tstr, + CapDistanceToStart=hl.tstr, + DistanceToStop=hl.tstr, + Evidence=hl.tstr, + AltStop=hl.tstr, + AltStopDistanceToCDS=hl.tstr, + FrameWithCDS=hl.tstr, + StartDistanceToCDS=hl.tstr, + newSTOPDistanceToCDS=hl.tstr, + alt_type=hl.tstr, + alt_type_length=hl.tstr, + ref_StartDistanceToCDS=hl.tstr, + ref_type=hl.tstr, + ref_type_length=hl.tstr, + ), + ), + ), + ), + hl.struct( + amino_acids=hl.null('str'), + am_pathogenicity=hl.missing(hl.tfloat32), + biotype='retained_intron', + canonical=hl.null('int32'), + check_ref=hl.missing(hl.tstr), + codons=hl.null('str'), + consequence_terms=hl.array(['downstream_gene_variant']), + exon=hl.null('str'), + gene_id='ENSG00000187634', + hgvsc=hl.null('str'), + hgvsp=hl.null('str'), + intron=hl.null('str'), + lof=hl.null('str'), + lof_filter=hl.null('str'), + lof_flags=hl.null('str'), + lof_info=hl.null('str'), + mane_select=hl.null('str'), + mane_plus_clinical=hl.null('str'), + spliceregion=hl.missing(hl.tarray(hl.tstr)), + transcript_id='ENST00000464948', + # UTRAnnotator + existing_inframe_oorfs=hl.missing(hl.tint32), + existing_outofframe_oorfs=hl.missing(hl.tint32), + existing_uorfs=hl.missing(hl.tint32), + fiveutr_consequence=hl.missing(hl.tstr), + fiveutr_annotation=hl.missing( + hl.tdict( + hl.tstr, + hl.tstruct( + type=hl.tstr, + KozakContext=hl.tstr, + KozakStrength=hl.tstr, + DistanceToCDS=hl.tstr, + CapDistanceToStart=hl.tstr, + DistanceToStop=hl.tstr, + Evidence=hl.tstr, + AltStop=hl.tstr, + AltStopDistanceToCDS=hl.tstr, + FrameWithCDS=hl.tstr, + StartDistanceToCDS=hl.tstr, + newSTOPDistanceToCDS=hl.tstr, + alt_type=hl.tstr, + alt_type_length=hl.tstr, + ref_StartDistanceToCDS=hl.tstr, + ref_type=hl.tstr, + ref_type_length=hl.tstr, + ), + ), + ), + ), + hl.struct( + amino_acids=hl.null('str'), + am_pathogenicity=hl.missing(hl.tfloat32), + biotype='retained_intron', + canonical=hl.null('int32'), + check_ref=hl.missing(hl.tstr), + codons=hl.null('str'), + consequence_terms=hl.array(['downstream_gene_variant']), + exon=hl.null('str'), + gene_id='ENSG00000187634', + hgvsc=hl.null('str'), + hgvsp=hl.null('str'), + intron=hl.null('str'), + lof=hl.null('str'), + lof_filter=hl.null('str'), + lof_flags=hl.null('str'), + lof_info=hl.null('str'), + mane_select=hl.null('str'), + mane_plus_clinical=hl.null('str'), + spliceregion=hl.missing(hl.tarray(hl.tstr)), + transcript_id='ENST00000466827', + # UTRAnnotator + existing_inframe_oorfs=hl.missing(hl.tint32), + existing_outofframe_oorfs=hl.missing(hl.tint32), + existing_uorfs=hl.missing(hl.tint32), + fiveutr_consequence=hl.missing(hl.tstr), + fiveutr_annotation=hl.missing( + hl.tdict( + hl.tstr, + hl.tstruct( + type=hl.tstr, + KozakContext=hl.tstr, + KozakStrength=hl.tstr, + DistanceToCDS=hl.tstr, + CapDistanceToStart=hl.tstr, + DistanceToStop=hl.tstr, + Evidence=hl.tstr, + AltStop=hl.tstr, + AltStopDistanceToCDS=hl.tstr, + FrameWithCDS=hl.tstr, + StartDistanceToCDS=hl.tstr, + newSTOPDistanceToCDS=hl.tstr, + alt_type=hl.tstr, + alt_type_length=hl.tstr, + ref_StartDistanceToCDS=hl.tstr, + ref_type=hl.tstr, + ref_type_length=hl.tstr, + ), + ), + ), + ), + hl.struct( + amino_acids=hl.null('str'), + am_pathogenicity=hl.missing(hl.tfloat32), + biotype='retained_intron', + canonical=hl.null('int32'), + check_ref=hl.missing(hl.tstr), + codons=hl.null('str'), + consequence_terms=hl.array(['downstream_gene_variant']), + exon=hl.null('str'), + gene_id='ENSG00000187634', + hgvsc=hl.null('str'), + hgvsp=hl.null('str'), + intron=hl.null('str'), + lof=hl.null('str'), + lof_filter=hl.null('str'), + lof_flags=hl.null('str'), + lof_info=hl.null('str'), + mane_select=hl.null('str'), + mane_plus_clinical=hl.null('str'), + spliceregion=hl.missing(hl.tarray(hl.tstr)), + transcript_id='ENST00000474461', + # UTRAnnotator + existing_inframe_oorfs=hl.missing(hl.tint32), + existing_outofframe_oorfs=hl.missing(hl.tint32), + existing_uorfs=hl.missing(hl.tint32), + fiveutr_consequence=hl.missing(hl.tstr), + fiveutr_annotation=hl.missing( + hl.tdict( + hl.tstr, + hl.tstruct( + type=hl.tstr, + KozakContext=hl.tstr, + KozakStrength=hl.tstr, + DistanceToCDS=hl.tstr, + CapDistanceToStart=hl.tstr, + DistanceToStop=hl.tstr, + Evidence=hl.tstr, + AltStop=hl.tstr, + AltStopDistanceToCDS=hl.tstr, + FrameWithCDS=hl.tstr, + StartDistanceToCDS=hl.tstr, + newSTOPDistanceToCDS=hl.tstr, + alt_type=hl.tstr, + alt_type_length=hl.tstr, + ref_StartDistanceToCDS=hl.tstr, + ref_type=hl.tstr, + ref_type_length=hl.tstr, + ), + ), + ), + ), + hl.struct( + amino_acids=hl.null('str'), + am_pathogenicity=hl.float32(0.97), + biotype='retained_intron', + canonical=hl.null('int32'), + check_ref=hl.missing(hl.tstr), + codons=hl.null('str'), + consequence_terms=hl.array( + [ + 'non_coding_transcript_exon_variant', + 'non_coding_transcript_variant', + ], + ), + exon='13/17', + gene_id='ENSG00000188976', + hgvsc='ENST00000477976.1:n.3114C>T', + hgvsp=hl.null('str'), + intron=hl.null('str'), + lof=hl.null('str'), + lof_filter=hl.null('str'), + lof_flags=hl.null('str'), + lof_info=hl.null('str'), + mane_select=hl.null('str'), + mane_plus_clinical=hl.null('str'), + spliceregion=hl.missing(hl.tarray(hl.tstr)), + transcript_id='ENST00000477976', + # UTRAnnotator + existing_inframe_oorfs=hl.missing(hl.tint32), + existing_outofframe_oorfs=hl.missing(hl.tint32), + existing_uorfs=hl.missing(hl.tint32), + fiveutr_consequence=hl.missing(hl.tstr), + fiveutr_annotation=hl.missing( + hl.tdict( + hl.tstr, + hl.tstruct( + type=hl.tstr, + KozakContext=hl.tstr, + KozakStrength=hl.tstr, + DistanceToCDS=hl.tstr, + CapDistanceToStart=hl.tstr, + DistanceToStop=hl.tstr, + Evidence=hl.tstr, + AltStop=hl.tstr, + AltStopDistanceToCDS=hl.tstr, + FrameWithCDS=hl.tstr, + StartDistanceToCDS=hl.tstr, + newSTOPDistanceToCDS=hl.tstr, + alt_type=hl.tstr, + alt_type_length=hl.tstr, + ref_StartDistanceToCDS=hl.tstr, + ref_type=hl.tstr, + ref_type_length=hl.tstr, + ), + ), + ), + ), + hl.struct( + amino_acids=hl.null('str'), + am_pathogenicity=hl.missing(hl.tfloat32), + biotype='processed_transcript', + canonical=hl.null('int32'), + check_ref=hl.missing(hl.tstr), + codons=hl.null('str'), + consequence_terms=hl.array(['downstream_gene_variant']), + exon=hl.null('str'), + gene_id='ENSG00000187634', + hgvsc=hl.null('str'), + hgvsp=hl.null('str'), + intron=hl.null('str'), + lof=hl.null('str'), + lof_filter=hl.null('str'), + lof_flags=hl.null('str'), + lof_info=hl.null('str'), + mane_select=hl.null('str'), + mane_plus_clinical=hl.null('str'), + spliceregion=hl.missing(hl.tarray(hl.tstr)), + transcript_id='ENST00000478729', + # UTRAnnotator + existing_inframe_oorfs=hl.missing(hl.tint32), + existing_outofframe_oorfs=hl.missing(hl.tint32), + existing_uorfs=hl.missing(hl.tint32), + fiveutr_consequence=hl.missing(hl.tstr), + fiveutr_annotation=hl.missing( + hl.tdict( + hl.tstr, + hl.tstruct( + type=hl.tstr, + KozakContext=hl.tstr, + KozakStrength=hl.tstr, + DistanceToCDS=hl.tstr, + CapDistanceToStart=hl.tstr, + DistanceToStop=hl.tstr, + Evidence=hl.tstr, + AltStop=hl.tstr, + AltStopDistanceToCDS=hl.tstr, + FrameWithCDS=hl.tstr, + StartDistanceToCDS=hl.tstr, + newSTOPDistanceToCDS=hl.tstr, + alt_type=hl.tstr, + alt_type_length=hl.tstr, + ref_StartDistanceToCDS=hl.tstr, + ref_type=hl.tstr, + ref_type_length=hl.tstr, + ), + ), + ), + ), + hl.struct( + amino_acids=hl.null('str'), + am_pathogenicity=hl.missing(hl.tfloat32), + biotype='retained_intron', + canonical=hl.null('int32'), + check_ref=hl.missing(hl.tstr), + codons=hl.null('str'), + consequence_terms=hl.array( + [ + 'non_coding_transcript_exon_variant', + 'splice_donor_region_variant', + 'non_coding_transcript_variant', + ], + ), + exon='1/5', + gene_id='ENSG00000188976', + hgvsc='ENST00000483767.1:n.523C>T', + hgvsp=hl.null('str'), + intron=hl.null('str'), + lof=hl.null('str'), + lof_filter=hl.null('str'), + lof_flags=hl.null('str'), + lof_info=hl.null('str'), + mane_select=hl.null('str'), + mane_plus_clinical=hl.null('str'), + spliceregion=hl.array(['extended_intronic_splice_region_variant']), + transcript_id='ENST00000483767', + # UTRAnnotator + existing_inframe_oorfs=0, + existing_outofframe_oorfs=1, + existing_uorfs=0, + fiveutr_consequence='5_prime_UTR_premature_start_codon_loss_variant', + fiveutr_annotation=hl.dict( + { + '1': hl.struct( + type='OutOfFrame_oORF', + KozakContext='TTTATGC', + KozakStrength='Weak', + DistanceToCDS='40', + CapDistanceToStart='20', + DistanceToStop='75', + Evidence='False', + AltStop=hl.missing(hl.tstr), + AltStopDistanceToCDS=hl.missing(hl.tstr), + FrameWithCDS=hl.missing(hl.tstr), + StartDistanceToCDS=hl.missing(hl.tstr), + newSTOPDistanceToCDS=hl.missing(hl.tstr), + alt_type=hl.missing(hl.tstr), + alt_type_length=hl.missing(hl.tstr), + ref_StartDistanceToCDS=hl.missing(hl.tstr), + ref_type=hl.missing(hl.tstr), + ref_type_length=hl.missing(hl.tstr), + ), + }, + ), + ), + hl.struct( + amino_acids=hl.null('str'), + am_pathogenicity=hl.missing(hl.tfloat32), + biotype='processed_transcript', + canonical=hl.null('int32'), + check_ref=hl.missing(hl.tstr), + codons=hl.null('str'), + consequence_terms=hl.array(['upstream_gene_variant']), + exon=hl.null('str'), + gene_id='ENSG00000188976', + hgvsc=hl.null('str'), + hgvsp=hl.null('str'), + intron=hl.null('str'), + lof=hl.null('str'), + lof_filter=hl.null('str'), + lof_flags=hl.null('str'), + lof_info=hl.null('str'), + mane_select=hl.null('str'), + mane_plus_clinical=hl.null('str'), + spliceregion=hl.missing(hl.tarray(hl.tstr)), + transcript_id='ENST00000496938', + # UTRAnnotator + existing_inframe_oorfs=hl.missing(hl.tint32), + existing_outofframe_oorfs=hl.missing(hl.tint32), + existing_uorfs=hl.missing(hl.tint32), + fiveutr_consequence=hl.missing(hl.tstr), + fiveutr_annotation=hl.missing( + hl.tdict( + hl.tstr, + hl.tstruct( + type=hl.tstr, + KozakContext=hl.tstr, + KozakStrength=hl.tstr, + DistanceToCDS=hl.tstr, + CapDistanceToStart=hl.tstr, + DistanceToStop=hl.tstr, + Evidence=hl.tstr, + AltStop=hl.tstr, + AltStopDistanceToCDS=hl.tstr, + FrameWithCDS=hl.tstr, + StartDistanceToCDS=hl.tstr, + newSTOPDistanceToCDS=hl.tstr, + alt_type=hl.tstr, + alt_type_length=hl.tstr, + ref_StartDistanceToCDS=hl.tstr, + ref_type=hl.tstr, + ref_type_length=hl.tstr, + ), + ), + ), + ), + ], + ), +) diff --git a/loading_pipeline/var/vep/GRCh37/vep-GRCh37.json b/loading_pipeline/var/vep/GRCh37/vep-GRCh37.json new file mode 100644 index 0000000000..d3461b9658 --- /dev/null +++ b/loading_pipeline/var/vep/GRCh37/vep-GRCh37.json @@ -0,0 +1,21 @@ +{"command": [ + "/vep", + "GRCh37", + "--warning_file", "STDERR", + "--format", "vcf", + "__OUTPUT_FORMAT_FLAG__", + "--everything", + "--allele_number", + "--no_stats", + "--cache", "--offline", + "--minimal", + "--assembly", "GRCh37", + "--fasta", "/opt/vep/.vep/Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz", + "--plugin", "LoF,human_ancestor_fa:/opt/vep/.vep/loftee_data/GRCh37/human_ancestor.fa.gz,filter_position:0.05,min_intron_size:15,conservation_file:/opt/vep/.vep/loftee_data/GRCh37/phylocsf_gerp.sql,gerp_file:/opt/vep/.vep/loftee_data/GRCh37/GERP_scores.final.sorted.txt.gz", + "-o", "STDOUT" +], + "env": { + "PERL5LIB": "" + }, + "vep_json_schema": "Struct{assembly_name:String,allele_string:String,ancestral:String,colocated_variants:Array[Struct{aa_allele:String,aa_maf:Float64,afr_allele:String,afr_maf:Float64,allele_string:String,amr_allele:String,amr_maf:Float64,clin_sig:Array[String],end:Int32,eas_allele:String,eas_maf:Float64,ea_allele:String,ea_maf:Float64,eur_allele:String,eur_maf:Float64,exac_adj_allele:String,exac_adj_maf:Float64,exac_allele:String,exac_afr_allele:String,exac_afr_maf:Float64,exac_amr_allele:String,exac_amr_maf:Float64,exac_eas_allele:String,exac_eas_maf:Float64,exac_fin_allele:String,exac_fin_maf:Float64,exac_maf:Float64,exac_nfe_allele:String,exac_nfe_maf:Float64,exac_oth_allele:String,exac_oth_maf:Float64,exac_sas_allele:String,exac_sas_maf:Float64,id:String,minor_allele:String,minor_allele_freq:Float64,phenotype_or_disease:Int32,pubmed:Array[Int32],sas_allele:String,sas_maf:Float64,somatic:Int32,start:Int32,strand:Int32}],context:String,end:Int32,id:String,input:String,intergenic_consequences:Array[Struct{allele_num:Int32,consequence_terms:Array[String],impact:String,minimised:Int32,variant_allele:String}],most_severe_consequence:String,motif_feature_consequences:Array[Struct{allele_num:Int32,consequence_terms:Array[String],high_inf_pos:String,impact:String,minimised:Int32,motif_feature_id:String,motif_name:String,motif_pos:Int32,motif_score_change:Float64,strand:Int32,variant_allele:String}],regulatory_feature_consequences:Array[Struct{allele_num:Int32,biotype:String,consequence_terms:Array[String],impact:String,minimised:Int32,regulatory_feature_id:String,variant_allele:String}],seq_region_name:String,start:Int32,strand:Int32,transcript_consequences:Array[Struct{allele_num:Int32,amino_acids:String,biotype:String,canonical:Int32,ccds:String,cdna_start:Int32,cdna_end:Int32,cds_end:Int32,cds_start:Int32,codons:String,consequence_terms:Array[String],distance:Int32,domains:Array[Struct{db:String,name:String}],exon:String,gene_id:String,gene_pheno:Int32,gene_symbol:String,gene_symbol_source:String,hgnc_id:String,hgvsc:String,hgvsp:String,hgvs_offset:Int32,impact:String,intron:String,lof:String,lof_flags:String,lof_filter:String,lof_info:String,minimised:Int32,polyphen_prediction:String,polyphen_score:Float64,protein_end:Int32,protein_start:Int32,protein_id:String,sift_prediction:String,sift_score:Float64,strand:Int32,swissprot:String,transcript_id:String,trembl:String,uniparc:String,variant_allele:String}],variant_class:String}" +} diff --git a/loading_pipeline/var/vep/GRCh38/vep-GRCh38.json b/loading_pipeline/var/vep/GRCh38/vep-GRCh38.json new file mode 100644 index 0000000000..c454c29a25 --- /dev/null +++ b/loading_pipeline/var/vep/GRCh38/vep-GRCh38.json @@ -0,0 +1,11 @@ +{ + "command": [ + "bash", + "-c", + "/vep GRCh38 --warning_file STDERR --format vcf -json --hgvs --biotype --canonical --mane --minimal --numbers --regulatory --allele_number --no_stats --cache --offline --assembly GRCh38 --fasta /opt/vep/.vep/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz --check_ref --dont_skip --plugin LoF,loftee_path:/plugins,gerp_bigwig:/opt/vep/.vep/gerp_conservation_scores.homo_sapiens.GRCh38.bw,human_ancestor_fa:/opt/vep/.vep/human_ancestor.fa.gz,conservation_file:/opt/vep/.vep/loftee.sql --plugin UTRAnnotator,file=/opt/vep/.vep/uORF_5UTR_GRCh38_PUBLIC.txt --plugin SpliceRegion,Extended --plugin AlphaMissense,file=/opt/vep/.vep/AlphaMissense_hg38.tsv.gz --dir_plugins /plugins -o STDOUT | sed s/5utr/fiveutr/g" + ], + "env": { + "PERL5LIB": "/plugins" + }, + "vep_json_schema": "Struct{input:String,check_ref:String,most_severe_consequence:String,motif_feature_consequences:Array[Struct{consequence_terms:Array[String],motif_feature_id:String}],regulatory_feature_consequences:Array[Struct{biotype:String,consequence_terms:Array[String],regulatory_feature_id:String}],transcript_consequences:Array[Struct{amino_acids:String,biotype:String,canonical:Int32,codons:String,consequence_terms:Array[String],exon:String,gene_id:String,hgvsc:String,hgvsp:String,intron:String,mane_select:String,mane_plus_clinical:String,transcript_id:String,lof:String,lof_flags:String,lof_filter:String,lof_info:String,existing_inframe_oorfs:Int32,existing_outofframe_oorfs:Int32,existing_uorfs:Int32,fiveutr_consequence:String,fiveutr_annotation:Dict[String,Struct{type:String,KozakContext:String,KozakStrength:String,DistanceToCDS:String,CapDistanceToStart:String,DistanceToStop:String,Evidence:String,AltStop:String,AltStopDistanceToCDS:String,FrameWithCDS:String,StartDistanceToCDS:String,newSTOPDistanceToCDS:String,alt_type:String,alt_type_length:String,ref_StartDistanceToCDS:String,ref_type:String,ref_type_length:String}],am_pathogenicity:Float32,spliceregion:Array[String]}]}" +} From 7e3b32f60e2b2926037e2cf7351c39b3f8638496 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 14:18:48 -0400 Subject: [PATCH 002/369] merge gitignore --- .gitignore | 171 +++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 171 insertions(+) diff --git a/.gitignore b/.gitignore index 3928b0e368..2bcd030622 100644 --- a/.gitignore +++ b/.gitignore @@ -18,3 +18,174 @@ pedigree_images/* seqr_settings django_key + +# loading pipeline +temp +*.vcf.gz +download_and_create_reference_datasets/*.txt +download_and_create_reference_datasets/*.gz +*.ht +*.mt +!/loading_pipeline/var/test/**/* + +# Standard python gitignore below +###################################################################### +###################################################################### + +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib64/ +sdist/ +wheels/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py,cover +.hypothesis/ +.pytest_cache/ +cover/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +.pybuilder/ +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +# For a library or package, you might want to ignore these files since the code is +# intended to run in multiple environments; otherwise, check them in: +# .python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don't work, or not +# install all needed dependencies. +#Pipfile.lock + +# poetry +# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control. +# This is especially recommended for binary packages to ensure reproducibility, and is more +# commonly ignored for libraries. +# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control +#poetry.lock + +# pdm +# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. +#pdm.lock +# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it +# in version control. +# https://pdm.fming.dev/#use-with-ide +.pdm.toml + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm +__pypackages__/ + +# Celery stuff +celerybeat-schedule +celerybeat.pid + +# SageMath parsed files +*.sage.py + +# Environments +.env +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ + +# pytype static type analyzer +.pytype/ + +# Cython debug symbols +cython_debug/ + +# PyCharm +# JetBrains specific template is maintained in a separate JetBrains.gitignore that can +# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore +# and can be added to the global gitignore or merged into this file. For a more nuclear +# option (not recommended) you can uncomment the following to ignore the entire idea folder. +#.idea/ From 06c13053b6f77d793997672a99d13fd591134c93 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 14:20:04 -0400 Subject: [PATCH 003/369] merge dockerignore --- .dockerignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.dockerignore b/.dockerignore index e294067478..09e62f8f26 100644 --- a/.dockerignore +++ b/.dockerignore @@ -6,6 +6,7 @@ static/* deploy/* !deploy/docker/seqr/* !deploy/docker/vlm/* +*test* .git .vscode .idea From 2900bff30ae9093eb921d24c6138a9968ab76f50 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 14:23:50 -0400 Subject: [PATCH 004/369] update docker copy path --- loading_pipeline/deploy/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/loading_pipeline/deploy/Dockerfile b/loading_pipeline/deploy/Dockerfile index 0ae73232ae..96c3467f4f 100644 --- a/loading_pipeline/deploy/Dockerfile +++ b/loading_pipeline/deploy/Dockerfile @@ -19,7 +19,7 @@ ENV VIRTUAL_ENV="/.venv" # to mismatches between the uv:python3.11-alpine and hail docker python environments. RUN apt-get update && apt-get install -y build-essential && rm -rf /var/lib/apt/lists/* -COPY pyproject.toml uv.lock . +COPY loading_pipeline/pyproject.toml loading_pipeline/uv.lock . RUN uv sync --group prod --no-group dev --locked # Application Code From de9faf5c4e01329edc761d1f913357b40f4da5a9 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 14:51:37 -0400 Subject: [PATCH 005/369] tweak readme --- loading_pipeline/CLAUDE.md | 2 +- loading_pipeline/README.md | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/loading_pipeline/CLAUDE.md b/loading_pipeline/CLAUDE.md index 130889aa15..be7fe50300 100644 --- a/loading_pipeline/CLAUDE.md +++ b/loading_pipeline/CLAUDE.md @@ -1,6 +1,6 @@ # CLAUDE.md -This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository. +This file provides guidance to Claude Code (claude.ai/code) when working with code in this folder. ## Quick Commands diff --git a/loading_pipeline/README.md b/loading_pipeline/README.md index 65910f3f3b..a12f08cad0 100644 --- a/loading_pipeline/README.md +++ b/loading_pipeline/README.md @@ -3,11 +3,11 @@ [![Code Build](https://github.com/broadinstitute/seqr-loading-pipelines/actions/workflows/unit-tests.yml/badge.svg?branch=main)](https://github.com/broadinstitute/seqr-loading-pipelines/actions/workflows/unit-tests.yml) [![Docker Build](https://github.com/broadinstitute/seqr-loading-pipelines/actions/workflows/prod-release.yml/badge.svg?branch=main)](https://github.com/broadinstitute/seqr-loading-pipelines/actions/workflows/prod-release.yml) -*This repository contains pipelines and infrastructure for loading genomic data from VCF -> ClickHouse to support queries by the _seqr_ application* +*This folder contains pipelines and infrastructure for loading genomic data from VCF -> ClickHouse to support queries by the _seqr_ application* --- -## 📁 Repository Structure +## 📁 Project Structure ### `loading_pipeline/api/` Contains the interface layer to the _seqr_ application. @@ -50,8 +50,8 @@ The production pipeline runs with python `3.11`. ### Clone the repo and install python requirements ```bash -git clone https://github.com/broadinstitute/seqr-loading-pipelines.git -cd seqr-loading-pipelines +git clone https://github.com/broadinstitute/seqr.git +cd seqr/loading_pipeline RUN uv sync --group dev --locked ``` @@ -59,7 +59,7 @@ RUN uv sync --group dev --locked > **Note:** We are running ClickHouse `26.3.9-lts` in production. ```bash curl https://clickhouse.com/ | sh -./clickhouse server --config-file=./seqr-loading-pipelines/loading_pipeline/var/clickhouse_config/test-clickhouse.xml +./clickhouse server --config-file=./seqr/loading_pipeline/var/clickhouse_config/test-clickhouse.xml ``` ### [Run the Tests](https://github.com/broadinstitute/seqr-loading-pipelines/blob/main/.github/workflows/unit-tests.yml#L66-L73) From 897a96fd5c83ab3cca543c3259725b1f2e18a836 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 14:52:53 -0400 Subject: [PATCH 006/369] copyy cloudbuild yaml --- .cloudbuild/pipeline-docker.cloudbuild.yaml | 11 +++++++++++ .cloudbuild/vep-docker.cloudbuild.yaml | 12 ++++++++++++ 2 files changed, 23 insertions(+) create mode 100644 .cloudbuild/pipeline-docker.cloudbuild.yaml create mode 100644 .cloudbuild/vep-docker.cloudbuild.yaml diff --git a/.cloudbuild/pipeline-docker.cloudbuild.yaml b/.cloudbuild/pipeline-docker.cloudbuild.yaml new file mode 100644 index 0000000000..30b4844b0b --- /dev/null +++ b/.cloudbuild/pipeline-docker.cloudbuild.yaml @@ -0,0 +1,11 @@ +steps: +- name: 'gcr.io/kaniko-project/executor:v1.3.0' + args: + - --destination=gcr.io/seqr-project/seqr-pipeline-runner:${COMMIT_SHA} + - --destination=gcr.io/seqr-project/seqr-pipeline-runner:${_CUSTOM_BRANCH_TAG} + - --dockerfile=loading_pipeline/deploy/Dockerfile + - --cache=true + - --cache-ttl=168h + - --build-arg=PIPELINE_RUNNER_APP_VERSION=${COMMIT_SHA} + +timeout: 1800s \ No newline at end of file diff --git a/.cloudbuild/vep-docker.cloudbuild.yaml b/.cloudbuild/vep-docker.cloudbuild.yaml new file mode 100644 index 0000000000..39fe857889 --- /dev/null +++ b/.cloudbuild/vep-docker.cloudbuild.yaml @@ -0,0 +1,12 @@ +# Run locally with: +# +# gcloud builds submit --quiet --substitutions='_REFERENCE_GENOME=GRCh38' --config .cloudbuild/vep-docker.cloudbuild.yaml loading_pipeline/deploy +steps: +- name: 'gcr.io/kaniko-project/executor:v1.3.0' + args: + - --destination=gcr.io/seqr-project/vep-docker-image:${_REFERENCE_GENOME} + - --dockerfile=Dockerfile.vep_${_REFERENCE_GENOME} + - --cache=true + - --cache-ttl=168h + +timeout: 1800s From 853296aca88b68d761f51236102024144d5970f9 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 15:38:05 -0400 Subject: [PATCH 007/369] unit tests --- .github/workflows/pipeline-unit-tests.yml | 79 +++++++++++++++++++++++ .github/workflows/unit-tests.yml | 4 ++ 2 files changed, 83 insertions(+) create mode 100644 .github/workflows/pipeline-unit-tests.yml diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml new file mode 100644 index 0000000000..b0d31f9ed5 --- /dev/null +++ b/.github/workflows/pipeline-unit-tests.yml @@ -0,0 +1,79 @@ +name: Pipeline Unit Tests + +# Run the test suite on pushes (incl. merges) to master and dev +# Run the test suite when a PR is opened, pushed to, or reopened +on: + push: + branches: + - dev + - master + paths: + - 'loading_pipeline/**' + - '.github/workflows/*pipeline-release.yaml' + pull_request: + types: [opened, synchronize, reopened] + paths: + - 'loading_pipeline/**' + - '.github/workflows/*pipeline*.yaml' + +jobs: + unit_tests: + runs-on: ubuntu-latest + strategy: + matrix: + python-version: ['3.11'] + + steps: + - uses: actions/checkout@v3 + - name: Create ClickHouse Config + run: | + cat < test_config.xml + + /tmp + + EOF + - name: Start ClickHouse with mounted config + run: | + docker run -d --name clickhouse \ + -v ${{ github.workspace }}/test_config.xml:/etc/clickhouse-server/config.d/config.xml \ + -v /tmp:/tmp \ + -p 9000:9000 \ + -e CLICKHOUSE_USER=default \ + -e CLICKHOUSE_PASSWORD=default_password \ + gcr.io/seqr-project/seqr-clickhouse:26.3.9 + - name: Wait for ClickHouse + run: | + until docker exec clickhouse clickhouse-client --query "SELECT 1"; do + echo "Waiting for ClickHouse to start..." + sleep 2 + done + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v4 + with: + python-version: ${{ matrix.python-version }} + # Install uv + - name: Install uv + uses: astral-sh/setup-uv@v7 + with: + enable-cache: true + cache-dependency-glob: | + **/uv.lock + **/pyproject.toml + - name: Sync dependencies (prod + dataproc) + run: uv sync --locked + - name: Check Ruff Format + run: uv run ruff format --check loading_pipeline --diff + - name: Check Ruff + run: uv run ruff check --output-format github + - name: Run ShellCheck + uses: ludeeus/action-shellcheck@master + with: + severity: error + scandir: './loading_pipeline/bin' + - name: Unit Tests + run: | + export CLICKHOUSE_OPTIMIZE_TABLE_WAIT_S=1 + export PYSPARK_SUBMIT_ARGS='--driver-memory 8G pyspark-shell' + export CLICKHOUSE_DATABASE=test + uv run pytest --cov=loading_pipeline --cov-report=term-missing loading_pipeline + uv run coverage report --omit '*test*' --fail-under=85 diff --git a/.github/workflows/unit-tests.yml b/.github/workflows/unit-tests.yml index b55ef44185..9d19033073 100644 --- a/.github/workflows/unit-tests.yml +++ b/.github/workflows/unit-tests.yml @@ -8,11 +8,15 @@ on: - master - dev paths-ignore: + - 'loading_pipeline/**' + - '.github/workflows/*pipeline*.yaml' - 'vlm/**' - '.github/workflows/*vlm*.yaml' pull_request: types: [opened, synchronize, reopened] paths-ignore: + - 'loading_pipeline/**' + - '.github/workflows/*pipeline*.yaml' - 'vlm/**' - '.github/workflows/*vlm*.yaml' From 0e11d6b2fb1413e91f5caa9434dd0b022414ee64 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 15:42:52 -0400 Subject: [PATCH 008/369] release workflows --- .github/workflows/pipeline-dev-release.yml | 74 ++++++++++++ .github/workflows/pipeline-prod-release.yml | 121 ++++++++++++++++++++ 2 files changed, 195 insertions(+) create mode 100644 .github/workflows/pipeline-dev-release.yml create mode 100644 .github/workflows/pipeline-prod-release.yml diff --git a/.github/workflows/pipeline-dev-release.yml b/.github/workflows/pipeline-dev-release.yml new file mode 100644 index 0000000000..5c050a9b52 --- /dev/null +++ b/.github/workflows/pipeline-dev-release.yml @@ -0,0 +1,74 @@ +name: dev release +on: + workflow_run: + workflows: ["Pipeline Unit Tests"] + types: + - completed + branches: + - dev + +permissions: + id-token: write + +jobs: + release: + runs-on: ubuntu-latest + if: ${{ github.event.workflow_run.conclusion == 'success' }} + steps: + - name: checkout + uses: actions/checkout@v3 + with: + ref: ${{ github.event.workflow_run.head_branch }} + + - name: Set up Python + uses: actions/setup-python@v4 + with: + python-version: '3.11' + + - name: Build package + run: | + cd loading_pipeline + rm -rf dist/ + python -m pip install build + python -m build + + - name: authenticate to google cloud + id: "auth" + uses: google-github-actions/auth@v0 + with: + workload_identity_provider: "${{ secrets.WORKLOAD_IDENTITY_PROVIDER }}" + service_account: "${{ secrets.RUN_SA_EMAIL }}" + + - name: "setup gcloud sdk" + uses: google-github-actions/setup-gcloud@v0 + + - name: Copy files to release directory + run: |- + gcloud storage rm -r gs://seqr-pipeline-runner-builds/dev/latest/ || echo 'No latest release' + gcloud storage cp loading_pipeline/bin/* gs://seqr-pipeline-runner-builds/dev/latest/bin/ + gcloud storage cp cd loading_pipeline/dist/*.whl gs://seqr-pipeline-runner-builds/dev/latest/pyscripts.zip + gcloud storage cp loading_pipeline/bin/* gs://seqr-pipeline-runner-builds/dev/${{ github.event.workflow_run.head_sha }}/bin/ + gcloud storage cp cd loading_pipeline/dist/*.whl gs://seqr-pipeline-runner-builds/dev/${{ github.event.workflow_run.head_sha }}/pyscripts.zip + docker: + runs-on: ubuntu-latest + if: ${{ github.event.workflow_run.conclusion == 'success' }} + steps: + - name: checkout + uses: actions/checkout@v3 + with: + ref: ${{ github.event.workflow_run.head_branch }} + + - name: authenticate to google cloud + id: "auth" + uses: google-github-actions/auth@v3 + with: + workload_identity_provider: "${{ secrets.WORKLOAD_IDENTITY_PROVIDER }}" + service_account: "${{ secrets.RUN_SA_EMAIL }}" + + - name: "setup gcloud sdk" + uses: google-github-actions/setup-gcloud@v2 + + - name: Build and push images + run: |- + gcloud builds submit --quiet --substitutions="COMMIT_SHA=${{ github.event.workflow_run.head_sha }},_CUSTOM_BRANCH_TAG=dev" --config .cloudbuild/pipeline-docker.cloudbuild.yaml --gcs-log-dir=gs://seqr-github-actions-logs/logs . + diff --git a/.github/workflows/pipeline-prod-release.yml b/.github/workflows/pipeline-prod-release.yml new file mode 100644 index 0000000000..02da04e79e --- /dev/null +++ b/.github/workflows/pipeline-prod-release.yml @@ -0,0 +1,121 @@ +name: prod release +on: + workflow_run: + workflows: ["Pipeline Unit Tests"] + types: + - completed + branches: + - master + +permissions: + id-token: write + contents: write + +jobs: + release: + runs-on: ubuntu-latest + if: ${{ github.event.workflow_run.conclusion == 'success' }} + steps: + - name: checkout + uses: actions/checkout@v3 + with: + ref: ${{ github.event.workflow_run.head_branch }} + + - name: set up python + uses: actions/setup-python@v4 + with: + python-version: '3.11' + + - name: build package + run: | + cd loading_pipeline + rm -rf dist/ + python -m pip install build + python -m build + + - name: authenticate to google cloud + id: "auth" + uses: google-github-actions/auth@v3 + with: + workload_identity_provider: "${{ secrets.WORKLOAD_IDENTITY_PROVIDER }}" + service_account: "${{ secrets.RUN_SA_EMAIL }}" + + - name: "setup gcloud sdk" + uses: google-github-actions/setup-gcloud@v2 + + - name: Copy files to release directory + shell: bash + run: |- + gcloud storage rm -r gs://seqr-pipeline-runner-builds/prod/latest/ || echo 'No latest release' + gcloud storage cp loading_pipeline/bin/* gs://seqr-pipeline-runner-builds/prod/latest/bin/ + gcloud storage cp loading_pipeline/dist/*.whl gs://seqr-pipeline-runner-builds/prod/latest/pyscripts.zip + gcloud storage cp loading_pipeline/bin/* gs://seqr-pipeline-runner-builds/prod/${{ github.event.workflow_run.head_sha }}/bin/ + gcloud storage cp loading_pipeline/dist/*.whl gs://seqr-pipeline-runner-builds/prod/${{ github.event.workflow_run.head_sha }}/pyscripts.zip + gcloud storage cp -r loading_pipeline/var/vep/* gs://seqr-reference-data/vep/ + + docker: + runs-on: ubuntu-latest + if: ${{ github.event.workflow_run.conclusion == 'success' }} + steps: + - name: checkout + uses: actions/checkout@v3 + with: + ref: ${{ github.event.workflow_run.head_branch }} + + - name: authenticate to google cloud + id: "auth" + uses: google-github-actions/auth@v3 + with: + workload_identity_provider: "${{ secrets.WORKLOAD_IDENTITY_PROVIDER }}" + service_account: "${{ secrets.RUN_SA_EMAIL }}" + + - name: "setup gcloud sdk" + uses: google-github-actions/setup-gcloud@v2 + + - name: Build and push images + run: |- + gcloud builds submit --quiet --substitutions="COMMIT_SHA=${{ github.event.workflow_run.head_sha }},_CUSTOM_BRANCH_TAG=latest" --config .cloudbuild/pipeline-docker.cloudbuild.yaml --gcs-log-dir=gs://seqr-github-actions-logs/logs . + + helm_update: + runs-on: ubuntu-latest + needs: docker + steps: + - uses: actions/checkout@v3 + with: + repository: broadinstitute/seqr-helm + ref: main + persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal token + fetch-depth: 0 # otherwise, you will failed to push refs to dest repo + + - name: Get latest pipeline-runner version + uses: mikefarah/yq@v4.22.1 + id: current + with: + cmd: > + yq -r '.version' charts/pipeline-runner/Chart.yaml + + - name: Bump version + id: bump + uses: cbrgm/semver-bump-action@main + with: + current-version: ${{ steps.current.outputs.result }} + bump-level: minor + + - name: Update appVersion and version in pipeline-runner Chart file + uses: mikefarah/yq@v4.22.1 + with: + cmd: > + yq -i ' + .appVersion = "${{ github.event.workflow_run.head_sha }}" | + .version = "${{ steps.bump.outputs.new_version }}" + ' charts/pipeline-runner/Chart.yaml + + - name: Commit and Push changes + uses: Andro999b/push@v1.3 + with: + repository: broadinstitute/seqr-helm + branch: main + github_token: ${{ secrets.SEQR_VERSION_UPDATE_TOKEN }} + author_email: ${{ github.actor }}@users.noreply.github.com + author_name: tgg-automation + message: "Update pipeline-runner chart appVersion to ${{ github.event.workflow_run.head_sha }}" From 4ead624b60567933818a731b40ec000b2a026a8f Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 15:58:57 -0400 Subject: [PATCH 009/369] correct directory for unit test deps --- .github/workflows/pipeline-unit-tests.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml index b0d31f9ed5..a71056e169 100644 --- a/.github/workflows/pipeline-unit-tests.yml +++ b/.github/workflows/pipeline-unit-tests.yml @@ -60,7 +60,9 @@ jobs: **/uv.lock **/pyproject.toml - name: Sync dependencies (prod + dataproc) - run: uv sync --locked + run: | + cd loading_pipeline + uv sync --locked - name: Check Ruff Format run: uv run ruff format --check loading_pipeline --diff - name: Check Ruff From 0ef07c4a64c3c74a788f73c7510cc5a776282ded Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 16:00:53 -0400 Subject: [PATCH 010/369] fix uv commands --- .github/workflows/pipeline-unit-tests.yml | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml index a71056e169..002bb3288c 100644 --- a/.github/workflows/pipeline-unit-tests.yml +++ b/.github/workflows/pipeline-unit-tests.yml @@ -64,9 +64,13 @@ jobs: cd loading_pipeline uv sync --locked - name: Check Ruff Format - run: uv run ruff format --check loading_pipeline --diff + run: | + cd loading_pipeline + uv run ruff format --check loading_pipeline --diff - name: Check Ruff - run: uv run ruff check --output-format github + run: | + cd loading_pipeline + uv run ruff check --output-format github - name: Run ShellCheck uses: ludeeus/action-shellcheck@master with: From 0877cdbf34921f0aecb639f260a7d000461a5a0f Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 16:03:48 -0400 Subject: [PATCH 011/369] correct ruff path --- .github/workflows/pipeline-unit-tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml index 002bb3288c..67d5a5fd92 100644 --- a/.github/workflows/pipeline-unit-tests.yml +++ b/.github/workflows/pipeline-unit-tests.yml @@ -66,7 +66,7 @@ jobs: - name: Check Ruff Format run: | cd loading_pipeline - uv run ruff format --check loading_pipeline --diff + uv run ruff format --check . --diff - name: Check Ruff run: | cd loading_pipeline From d386d50011ccb576d7ddfbe522c2e5db8ef618c3 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 16:27:53 -0400 Subject: [PATCH 012/369] fix uv test --- .github/workflows/pipeline-unit-tests.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml index 67d5a5fd92..13ddf5417d 100644 --- a/.github/workflows/pipeline-unit-tests.yml +++ b/.github/workflows/pipeline-unit-tests.yml @@ -81,5 +81,6 @@ jobs: export CLICKHOUSE_OPTIMIZE_TABLE_WAIT_S=1 export PYSPARK_SUBMIT_ARGS='--driver-memory 8G pyspark-shell' export CLICKHOUSE_DATABASE=test - uv run pytest --cov=loading_pipeline --cov-report=term-missing loading_pipeline + cd loading_pipeline + uv run pytest --cov=loading_pipeline --cov-report=term-missing . uv run coverage report --omit '*test*' --fail-under=85 From fee52e471c20df90fc279d0fe1e50672de6c468d Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 16:30:00 -0400 Subject: [PATCH 013/369] codacy ignore --- .codacy.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.codacy.yaml b/.codacy.yaml index a0ae5a67dd..ba5602507c 100644 --- a/.codacy.yaml +++ b/.codacy.yaml @@ -1,3 +1,4 @@ --- exclude_paths: - - "deploy/postgres/initdb.sql" \ No newline at end of file + - "deploy/postgres/initdb.sql" + - "loading_pipeline" \ No newline at end of file From f2373a31bf67d3c1b505f864c97f9efaae3dc32f Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 16:33:34 -0400 Subject: [PATCH 014/369] fix codacy ignore --- .codacy.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.codacy.yaml b/.codacy.yaml index ba5602507c..3bd43d8705 100644 --- a/.codacy.yaml +++ b/.codacy.yaml @@ -1,4 +1,4 @@ --- exclude_paths: - "deploy/postgres/initdb.sql" - - "loading_pipeline" \ No newline at end of file + - "loading_pipeline/**" \ No newline at end of file From 330b812b8a6035b26b75bbd280fdeeeea018426e Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 16:37:46 -0400 Subject: [PATCH 015/369] run test in root dir --- .github/workflows/pipeline-unit-tests.yml | 15 ++++----------- 1 file changed, 4 insertions(+), 11 deletions(-) diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml index 13ddf5417d..e7a00ccb35 100644 --- a/.github/workflows/pipeline-unit-tests.yml +++ b/.github/workflows/pipeline-unit-tests.yml @@ -60,17 +60,11 @@ jobs: **/uv.lock **/pyproject.toml - name: Sync dependencies (prod + dataproc) - run: | - cd loading_pipeline - uv sync --locked + run: uv sync --locked --package loading_pipeline - name: Check Ruff Format - run: | - cd loading_pipeline - uv run ruff format --check . --diff + run: uv run ruff format --check loading_pipeline --diff - name: Check Ruff - run: | - cd loading_pipeline - uv run ruff check --output-format github + run: uv run ruff check --output-format github - name: Run ShellCheck uses: ludeeus/action-shellcheck@master with: @@ -81,6 +75,5 @@ jobs: export CLICKHOUSE_OPTIMIZE_TABLE_WAIT_S=1 export PYSPARK_SUBMIT_ARGS='--driver-memory 8G pyspark-shell' export CLICKHOUSE_DATABASE=test - cd loading_pipeline - uv run pytest --cov=loading_pipeline --cov-report=term-missing . + uv run pytest --cov=loading_pipeline --cov-report=term-missing loading_pipeline uv run coverage report --omit '*test*' --fail-under=85 From 36778eb0d1a60f8b3926bb709bf8818fc518b491 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 16:39:24 -0400 Subject: [PATCH 016/369] fi uv sync --- .github/workflows/pipeline-unit-tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml index e7a00ccb35..8a6af05773 100644 --- a/.github/workflows/pipeline-unit-tests.yml +++ b/.github/workflows/pipeline-unit-tests.yml @@ -60,7 +60,7 @@ jobs: **/uv.lock **/pyproject.toml - name: Sync dependencies (prod + dataproc) - run: uv sync --locked --package loading_pipeline + run: uv sync --locked --project loading_pipeline - name: Check Ruff Format run: uv run ruff format --check loading_pipeline --diff - name: Check Ruff From af3ef3e57f4a24e2c59375845f9d901c14a50130 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 16:41:23 -0400 Subject: [PATCH 017/369] fix uv commands --- .github/workflows/pipeline-unit-tests.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml index 8a6af05773..0e01e11faa 100644 --- a/.github/workflows/pipeline-unit-tests.yml +++ b/.github/workflows/pipeline-unit-tests.yml @@ -62,9 +62,9 @@ jobs: - name: Sync dependencies (prod + dataproc) run: uv sync --locked --project loading_pipeline - name: Check Ruff Format - run: uv run ruff format --check loading_pipeline --diff + run: uv run ruff format --check loading_pipeline --diff --project loading_pipeline - name: Check Ruff - run: uv run ruff check --output-format github + run: uv run ruff check --output-format github --project loading_pipeline - name: Run ShellCheck uses: ludeeus/action-shellcheck@master with: From a1b2ed083c5bbd7ae380514fb5b335afaacd83ad Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 16:47:58 -0400 Subject: [PATCH 018/369] iter test runner --- .github/workflows/pipeline-unit-tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml index 0e01e11faa..35c27fb83c 100644 --- a/.github/workflows/pipeline-unit-tests.yml +++ b/.github/workflows/pipeline-unit-tests.yml @@ -60,7 +60,7 @@ jobs: **/uv.lock **/pyproject.toml - name: Sync dependencies (prod + dataproc) - run: uv sync --locked --project loading_pipeline + run: uv sync --locked --project loading_pipeline --inexact - name: Check Ruff Format run: uv run ruff format --check loading_pipeline --diff --project loading_pipeline - name: Check Ruff From 91d3c49c07bbd914fea65461204c35453d2ab580 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 16:52:19 -0400 Subject: [PATCH 019/369] iter test runner --- .github/workflows/pipeline-unit-tests.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml index 35c27fb83c..358517c63a 100644 --- a/.github/workflows/pipeline-unit-tests.yml +++ b/.github/workflows/pipeline-unit-tests.yml @@ -60,11 +60,11 @@ jobs: **/uv.lock **/pyproject.toml - name: Sync dependencies (prod + dataproc) - run: uv sync --locked --project loading_pipeline --inexact + run: uv sync --locked --project loading_pipeline - name: Check Ruff Format - run: uv run ruff format --check loading_pipeline --diff --project loading_pipeline + run: uv run ruff format --check loading_pipeline --diff --config loading_pipeline/pyproject.toml - name: Check Ruff - run: uv run ruff check --output-format github --project loading_pipeline + run: uv run ruff check --output-format github - name: Run ShellCheck uses: ludeeus/action-shellcheck@master with: From e7ad6ca7b2b4cb653aa62d7054a36fa2de92c363 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 16:57:10 -0400 Subject: [PATCH 020/369] configure uv workspace --- .github/workflows/pipeline-unit-tests.yml | 4 ++-- loading_pipeline/pyproject.toml | 3 +++ 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml index 358517c63a..9368013eac 100644 --- a/.github/workflows/pipeline-unit-tests.yml +++ b/.github/workflows/pipeline-unit-tests.yml @@ -60,9 +60,9 @@ jobs: **/uv.lock **/pyproject.toml - name: Sync dependencies (prod + dataproc) - run: uv sync --locked --project loading_pipeline + run: uv sync --locked - name: Check Ruff Format - run: uv run ruff format --check loading_pipeline --diff --config loading_pipeline/pyproject.toml + run: uv run ruff format --check loading_pipeline --diff - name: Check Ruff run: uv run ruff check --output-format github - name: Run ShellCheck diff --git a/loading_pipeline/pyproject.toml b/loading_pipeline/pyproject.toml index f06f1fc691..65f446ba5e 100644 --- a/loading_pipeline/pyproject.toml +++ b/loading_pipeline/pyproject.toml @@ -43,6 +43,9 @@ dev = [ [tool.uv] exclude-dependencies = ["psycopg2-binary", "psycopg2"] +[tool.uv.workspace] +members = ["loading_pipeline/*"] + [tool.setuptools] include-package-data = true From ac950fc91714f3bce9cfd39e8419286283d48c37 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 16:59:13 -0400 Subject: [PATCH 021/369] iter test runner --- .github/workflows/pipeline-unit-tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml index 9368013eac..8a6af05773 100644 --- a/.github/workflows/pipeline-unit-tests.yml +++ b/.github/workflows/pipeline-unit-tests.yml @@ -60,7 +60,7 @@ jobs: **/uv.lock **/pyproject.toml - name: Sync dependencies (prod + dataproc) - run: uv sync --locked + run: uv sync --locked --project loading_pipeline - name: Check Ruff Format run: uv run ruff format --check loading_pipeline --diff - name: Check Ruff From 8d766bd45415da8aa211179d23afceb4f2f3aac4 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 17:01:44 -0400 Subject: [PATCH 022/369] iter test runner --- .github/workflows/pipeline-unit-tests.yml | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml index 8a6af05773..f3050f810a 100644 --- a/.github/workflows/pipeline-unit-tests.yml +++ b/.github/workflows/pipeline-unit-tests.yml @@ -62,9 +62,13 @@ jobs: - name: Sync dependencies (prod + dataproc) run: uv sync --locked --project loading_pipeline - name: Check Ruff Format - run: uv run ruff format --check loading_pipeline --diff + run: | + cd loading_pipeline + uv run ruff format --check . --diff - name: Check Ruff - run: uv run ruff check --output-format github + run: | + cd loading_pipeline + uv run ruff check --output-format github - name: Run ShellCheck uses: ludeeus/action-shellcheck@master with: From 7a6e5a3977142ada82d4965ba78a0f1d549cf2da Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 17:04:41 -0400 Subject: [PATCH 023/369] iter test runner --- .github/workflows/pipeline-unit-tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml index f3050f810a..c6a0e3585e 100644 --- a/.github/workflows/pipeline-unit-tests.yml +++ b/.github/workflows/pipeline-unit-tests.yml @@ -79,5 +79,5 @@ jobs: export CLICKHOUSE_OPTIMIZE_TABLE_WAIT_S=1 export PYSPARK_SUBMIT_ARGS='--driver-memory 8G pyspark-shell' export CLICKHOUSE_DATABASE=test - uv run pytest --cov=loading_pipeline --cov-report=term-missing loading_pipeline + uv run pytest --project loading_pipeline --cov=loading_pipeline --cov-report=term-missing loading_pipeline uv run coverage report --omit '*test*' --fail-under=85 From 3cf185bbff95b714dce8662a46e1cd1bd465028c Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Wed, 12 Aug 2026 11:51:26 -0400 Subject: [PATCH 024/369] iter test approach --- .github/workflows/pipeline-unit-tests.yml | 2 +- loading_pipeline/pyproject.toml | 3 --- 2 files changed, 1 insertion(+), 4 deletions(-) diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml index c6a0e3585e..848a5434fa 100644 --- a/.github/workflows/pipeline-unit-tests.yml +++ b/.github/workflows/pipeline-unit-tests.yml @@ -79,5 +79,5 @@ jobs: export CLICKHOUSE_OPTIMIZE_TABLE_WAIT_S=1 export PYSPARK_SUBMIT_ARGS='--driver-memory 8G pyspark-shell' export CLICKHOUSE_DATABASE=test - uv run pytest --project loading_pipeline --cov=loading_pipeline --cov-report=term-missing loading_pipeline + uv run --with pytest pytest --cov=loading_pipeline --cov-report=term-missing loading_pipeline uv run coverage report --omit '*test*' --fail-under=85 diff --git a/loading_pipeline/pyproject.toml b/loading_pipeline/pyproject.toml index 65f446ba5e..f06f1fc691 100644 --- a/loading_pipeline/pyproject.toml +++ b/loading_pipeline/pyproject.toml @@ -43,9 +43,6 @@ dev = [ [tool.uv] exclude-dependencies = ["psycopg2-binary", "psycopg2"] -[tool.uv.workspace] -members = ["loading_pipeline/*"] - [tool.setuptools] include-package-data = true From 1f509749f6cf2fcbbc2898386c2802669f28d7ba Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Wed, 12 Aug 2026 12:09:25 -0400 Subject: [PATCH 025/369] iter command --- .github/workflows/pipeline-unit-tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml index 848a5434fa..16dd72ffca 100644 --- a/.github/workflows/pipeline-unit-tests.yml +++ b/.github/workflows/pipeline-unit-tests.yml @@ -79,5 +79,5 @@ jobs: export CLICKHOUSE_OPTIMIZE_TABLE_WAIT_S=1 export PYSPARK_SUBMIT_ARGS='--driver-memory 8G pyspark-shell' export CLICKHOUSE_DATABASE=test - uv run --with pytest pytest --cov=loading_pipeline --cov-report=term-missing loading_pipeline + uv run --with pytest pytest loading_pipeline --cov=loading_pipeline --cov-report=term-missing uv run coverage report --omit '*test*' --fail-under=85 From b0204faa8c09d68d4eba4ebf40fd2507a8b16024 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Wed, 12 Aug 2026 12:14:06 -0400 Subject: [PATCH 026/369] reset test command --- .github/workflows/pipeline-unit-tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml index 16dd72ffca..f3050f810a 100644 --- a/.github/workflows/pipeline-unit-tests.yml +++ b/.github/workflows/pipeline-unit-tests.yml @@ -79,5 +79,5 @@ jobs: export CLICKHOUSE_OPTIMIZE_TABLE_WAIT_S=1 export PYSPARK_SUBMIT_ARGS='--driver-memory 8G pyspark-shell' export CLICKHOUSE_DATABASE=test - uv run --with pytest pytest loading_pipeline --cov=loading_pipeline --cov-report=term-missing + uv run pytest --cov=loading_pipeline --cov-report=term-missing loading_pipeline uv run coverage report --omit '*test*' --fail-under=85 From 26fe61a0bcb14d71af1d238b8902ca8ef3b01ff4 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Wed, 12 Aug 2026 13:11:36 -0400 Subject: [PATCH 027/369] fix test command --- .github/workflows/pipeline-unit-tests.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml index f3050f810a..3610b666ae 100644 --- a/.github/workflows/pipeline-unit-tests.yml +++ b/.github/workflows/pipeline-unit-tests.yml @@ -79,5 +79,5 @@ jobs: export CLICKHOUSE_OPTIMIZE_TABLE_WAIT_S=1 export PYSPARK_SUBMIT_ARGS='--driver-memory 8G pyspark-shell' export CLICKHOUSE_DATABASE=test - uv run pytest --cov=loading_pipeline --cov-report=term-missing loading_pipeline - uv run coverage report --omit '*test*' --fail-under=85 + uv run --project loading_pipeline pytest --cov=loading_pipeline --cov-report=term-missing loading_pipeline + uv run --project loading_pipeline coverage report --omit '*test*' --fail-under=85 From 310ff1ef460e2317e9acf73e71bf055ab6c0dae4 Mon Sep 17 00:00:00 2001 From: hanars Date: Wed, 12 Aug 2026 13:29:32 -0400 Subject: [PATCH 028/369] Potential fix for pull request finding 'CodeQL / Workflow does not contain permissions' Co-authored-by: Copilot Autofix powered by AI <62310815+github-advanced-security[bot]@users.noreply.github.com> --- .github/workflows/pipeline-unit-tests.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml index 3610b666ae..a476bbb908 100644 --- a/.github/workflows/pipeline-unit-tests.yml +++ b/.github/workflows/pipeline-unit-tests.yml @@ -16,6 +16,9 @@ on: - 'loading_pipeline/**' - '.github/workflows/*pipeline*.yaml' +permissions: + contents: read + jobs: unit_tests: runs-on: ubuntu-latest From c66f22d4569ca6aa5781583b1a0848e6e17ca7eb Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Wed, 12 Aug 2026 15:35:42 -0400 Subject: [PATCH 029/369] plan test migration --- .../CLICKHOUSE_PYTEST_DJANGO_PLAN.md | 143 ++++++++++++++++++ 1 file changed, 143 insertions(+) create mode 100644 loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_PLAN.md diff --git a/loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_PLAN.md b/loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_PLAN.md new file mode 100644 index 0000000000..bee7837170 --- /dev/null +++ b/loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_PLAN.md @@ -0,0 +1,143 @@ +# Plan: Manage ClickHouse test DB via pytest-django + `clickhouse_search` migrations + +## Goal + +Stop hand-maintaining ClickHouse schema DDL (and the static `var/test/test_clickhouse_schema.sql` +dump) inside `loading_pipeline`'s tests. Instead, use `pytest-django` to create/migrate the +ClickHouse test database from the real Django migrations in `clickhouse_search` (the source of +truth for the schema), so the pipeline's tests can never drift from production schema. + +Scope constraint: all code changes live in `loading_pipeline/` or in +`.github/workflows/pipeline-unit-tests.yml`. Nothing in `clickhouse_search/` or root `settings.py` +is modified. + +## Key constraint discovered + +`clickhouse_search/backend/base.py` does a **bare** `from settings import +CLICKHOUSE_WRITER_USER, CLICKHOUSE_WRITER_PASSWORD, DATABASES` — not `django.conf.settings`. This +only resolves correctly if a top-level module literally named `settings` is importable on +`sys.path`. Today that resolves to the main repo's heavy `settings.py` (postgres, guardian, +social_django, google.auth, etc.) whenever cwd is the repo root — which is undesirable/impossible +to depend on from `loading_pipeline`'s minimal env. + +**Trick:** create our own minimal module named `settings.py`, placed in a directory that we add to +`sys.path` ahead of the repo root (via pytest's `pythonpath` ini option, which prepends to +`sys.path`). That module serves double duty: +- It's what `clickhouse_search/backend/base.py`'s bare `import settings` resolves to. +- It's also `DJANGO_SETTINGS_MODULE` for pytest-django. + +## Single connection / single set of credentials only + +Per explicit direction: the settings module must configure **one** ClickHouse connection with +**one** set of credentials — not the production split of a read-only `clickhouse` alias plus a +privileged `clickhouse_write` alias. `DATABASES` will define a single alias (`clickhouse`) using +one writer-capable credential (needed anyway, since migrations and test data inserts require write +access). + +Nuance to account for: `clickhouse_search/backend/base.py`'s `_dictionary_sql` looks up +`DATABASES['clickhouse_write']['NAME']` (for ClickHouse-sourced dictionaries with a +`clickhouse_query_template`) and `DATABASES[postgres_db]['NAME']` (default alias `'default'`, for +Postgres-sourced dictionaries) purely to embed a database *name string* into generated DDL — not to +open a second real connection. To keep this working without standing up a second live connection: +- Give `'clickhouse_write'` a `TEST: {'MIRROR': 'clickhouse'}` config, so Django reuses the + `clickhouse` alias's actual test database instead of creating/tearing down a second one, while + the key is still present for the `NAME` lookup. +- Give `'default'` a placeholder entry (e.g. `ENGINE: 'django.db.backends.dummy'`) purely so + `DATABASES['default']['NAME']` resolves to a string — nothing in `loading_pipeline`'s tests + actually connects to it, since there's no Postgres in this CI job. + +## Inventory of every ClickHouse-touching test + +1. **`lib/misc/clickhouse_test.py`** (`ClickhouseTest`) — hand-rolls ~250 lines of `CREATE + TABLE`/`CREATE DICTIONARY`/`CREATE MATERIALIZED VIEW` DDL duplicating a subset of the real + schema, plus fixture dictionaries for gene IDs/gnomAD. +2. **`lib/test/clickhouse_schema_testcase.py`** (`ClickhouseSchemaTestCase`) — loads the static + `var/test/test_clickhouse_schema.sql` dump plus a few placeholder dictionaries. Used by: + - `bin/pipeline_worker_test.py` (`PipelineWorkerTest`) + - `lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py` + (`LoadClickhouseVariantsTablesTaskTest`) +3. **`ops/repartition_clickhouse_grch38_snv_indel_test.py`** (`RepartitionGRCh38SnvIndelTest`) — + its own bespoke DDL for a synthetic, intentionally-simplified `entries` table + a wholly + separate scratch database (`REPARTITION_DATABASE_NAME`) that isn't part of `clickhouse_search`'s + schema at all. + +## The Postgres/GCS-sourced dictionary wrinkle + +A handful of dictionaries are, in production, sourced from Postgres (via the +`seqr_postgres_named_collection` named collection) or from GCS parquet URLs: + +- `seqrdb_gene_ids` +- `seqrdb_affected_status_dict` +- `GRCh38/SNV_INDEL/project_partitions_dict` +- the gnomAD reference dict (`GRCh38/SNV_INDEL/reference_data/gnomad_genomes`) + +`loading_pipeline`'s CI only runs ClickHouse (no Postgres, no GCS access). Running +`clickhouse_search`'s real migrations here requires a dummy `seqr_postgres_named_collection` (a new +workflow step, mirroring what `unit-tests.yml` already does for the main app) just so the +`CREATE DICTIONARY ... SOURCE(POSTGRESQL(NAME 'seqr_postgres_named_collection' ...))` DDL parses. +Dictionaries are lazily loaded (`LIFETIME(0)`), so DDL creation succeeds even though the source is +unreachable — but tests still need to override these specific dictionaries with deterministic +fixture sources afterward (same idea as today's code, just trimmed to only this handful instead of +faking the whole schema). + +## Raw SQL execution in tests: use the Django connection, not `clickhouse_driver.Client` + +Every test currently calls `get_clickhouse_client()` (a raw `clickhouse_driver.Client`, see +`lib/misc/clickhouse.py`) to run setup/assertion SQL directly. Once the schema is Django-managed, +tests should execute their raw SQL through Django's own DB connection instead of a separate +`clickhouse_driver.Client` instance — i.e. `django.db.connections['clickhouse'].cursor()` (the one +alias defined per "Single connection / single set of credentials only" above), calling +`cursor.execute(sql, params)` / `cursor.fetchall()`. + +This is purely a *client* swap for test code — tests keep writing raw SQL strings (no ORM/model +queries), just executed via the Django connection so the tests exercise the same connection +machinery/test-DB aliasing that pytest-django set up, rather than opening an independent +`clickhouse_driver` connection that doesn't know about Django's test DB name remapping. Production +code in `lib/misc/clickhouse.py` (`get_clickhouse_client` and friends) is unaffected — this only +applies to test files themselves. + +## Shared setup-time data: Django fixtures, not bulk INSERT statements + +Some test data is inserted once in a test class's `setUp`/`setUpClass` and reused across multiple +test methods (e.g. the `seqrdb_gene_ids`/`gnomad_genomes` source-table rows in +`ClickhouseTest`/`ClickhouseSchemaTestCase`). That category of data should be loaded via Django's +fixture mechanism (JSON fixture files under a `fixtures/` dir, loaded with +`fixtures = [...]` on the `TestCase` subclass, or an explicit `call_command('loaddata', ...)`) — +not hand-written `INSERT INTO ... VALUES (...)` statements repeated/executed in `setUp`. + +This only applies to shared, setup-time reference data with a real backing model in +`clickhouse_search` (e.g. the source tables behind `seqrdb_gene_ids`/`gnomad_genomes`). Since +`loaddata` populates rows through the model layer, the dictionary itself still needs an explicit +`RELOAD DICTIONARY`/refresh afterward (dictionaries aren't themselves loaddata targets — their +backing source table is). Data that's specific to a single test method's body/assertions (not +shared across tests) stays as raw SQL executed via the Django connection cursor, per the prior +note — this fixture rule is specifically about *repeated* setup-time data. + +## Proposed change set + +| File | Change | +|---|---| +| `.github/workflows/pipeline-unit-tests.yml` | add a step creating a dummy `seqr_postgres_named_collection`; keep `CLICKHOUSE_DATABASE=test` | +| `loading_pipeline/pyproject.toml` | add `django`, `django-clickhouse-backend`, `pytest-django` dev deps; add `[tool.pytest.ini_options]` (`DJANGO_SETTINGS_MODULE`, `pythonpath`) | +| **new** `loading_pipeline/lib/test/clickhouse_django/settings.py` | minimal Django settings: one real `clickhouse` alias (single credential set), `clickhouse_write` mirrored onto it via `TEST: {MIRROR: 'clickhouse'}`, a dummy `default` placeholder (NAME only, no real connection), `clickhouse_backend` + `clickhouse_search` apps, `ClickHouseRouter`; doubles as the shadow `settings` module `clickhouse_search/backend/base.py` bare-imports | +| `lib/test/clickhouse_schema_testcase.py` | rewritten as the one shared base class: drop all manual DDL/SQL-file loading (schema now comes from real migrations via pytest-django), keep only the small external-sourced-dictionary overrides + per-test flush/truncate + staging-DB drop/create — all executed via `connections['clickhouse'].cursor()`; shared reference rows (e.g. gene-id/gnomAD source-table rows) loaded via Django `fixtures = [...]` instead of `INSERT` statements | +| **delete** `loading_pipeline/var/test/test_clickhouse_schema.sql` | no longer needed | +| **new** `loading_pipeline/lib/test/fixtures/*.json` | Django fixtures for the shared setup-time reference rows referenced above | +| `lib/misc/clickhouse_test.py` | `ClickhouseTest` extends the shared base instead of hand-building its own schema; keeps only its fixture-data seeding (via the new Django fixtures, not bulk `INSERT`) and parquet-writing setup; all `get_clickhouse_client()` calls in the test body replaced with the Django connection cursor | +| `bin/pipeline_worker_test.py`, `lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py` | no structural change (already extend the shared base) — swap their `get_clickhouse_client()` assertion calls to the Django connection cursor; cleanup of now-dead references (e.g. leftover `TEST_SCHEMA` constant) | +| `ops/repartition_clickhouse_grch38_snv_indel_test.py` | switch to the shared base for the real-schema DB lifecycle; keep its own synthetic `entries`-table `REPLACE`/dict + `REPARTITION_DATABASE_NAME` handling since that's not part of `clickhouse_search`'s schema; swap `get_clickhouse_client()` for the Django connection cursor | + +## Open risk / caveat + +No live ClickHouse instance is available in the sandbox used to write this plan, so some runtime +specifics can't be verified ahead of time: +- Whether `TRUNCATE` behaves as expected on materialized views (regular vs. refreshable). +- Exact Django test-DB naming interplay with `Env.CLICKHOUSE_DATABASE` (need a `TEST: {NAME: ...}` + override to avoid Django's default `test_` prefix mismatch). +- Whether `CREATE DICTIONARY ... SOURCE(POSTGRESQL(...))` DDL actually succeeds against a + ClickHouse server with only a dummy/unreachable named collection registered. +- Whether raw SQL params/tuple-list inserts (e.g. `INSERT INTO ... VALUES` with a Python list of + tuples, as `clickhouse_driver.Client.execute` supports today) work identically through + `cursor.execute()`/`cursor.executemany()` on the Django ClickHouse backend, or need reshaping. + +These should be shaken out against a real CI run / local ClickHouse instance once implemented. \ No newline at end of file From 9849a52d639cfb2a7dbae527c96c1a993ac3e9fa Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Wed, 12 Aug 2026 17:14:29 -0400 Subject: [PATCH 030/369] add pytest django and clean up iimports to separate clickhouse migratios from rest of app --- clickhouse_search/backend/table_models.py | 8 +++++ clickhouse_search/constants.py | 14 +++++---- .../0040_gnomadnoncodingconstraintdict.py | 12 +++---- clickhouse_search/models/search_models.py | 12 ++----- .../CLICKHOUSE_PYTEST_DJANGO_PLAN.md | 31 +++++++++++++------ loading_pipeline/pyproject.toml | 12 +++++++ 6 files changed, 57 insertions(+), 32 deletions(-) diff --git a/clickhouse_search/backend/table_models.py b/clickhouse_search/backend/table_models.py index 819ca96972..f82b9964b7 100644 --- a/clickhouse_search/backend/table_models.py +++ b/clickhouse_search/backend/table_models.py @@ -14,6 +14,14 @@ DICTIONARY_META_FIELDS = ['layout', 'lifetime_max', 'postgres_query', 'postgres_db', 'clickhouse_query_template'] +class Projection(Func): + + def __init__(self, name, select='*', order_by=None): + self.name = name + self.select = select + self.order_by = order_by + + class FixtureLoadableClickhouseModel(models.ClickhouseModel): def _save_table( diff --git a/clickhouse_search/constants.py b/clickhouse_search/constants.py index 0721e16955..2ebb829f03 100644 --- a/clickhouse_search/constants.py +++ b/clickhouse_search/constants.py @@ -1,5 +1,3 @@ -from seqr.models import Individual - MAX_VARIANTS = 10000 XPOS_SORT_KEY = 'xpos' @@ -7,10 +5,14 @@ PATHOGENICTY_HGMD_SORT_KEY = 'pathogenicity_hgmd' PRIORITIZED_GENE_SORT = 'prioritized_gene' -AFFECTED = Individual.AFFECTED_STATUS_AFFECTED -UNAFFECTED = Individual.AFFECTED_STATUS_UNAFFECTED -MALE_SEXES = Individual.MALE_SEXES -FEMALE_SEXES = Individual.FEMALE_SEXES +# Mirrors seqr.models.Individual.AFFECTED_STATUS_AFFECTED/AFFECTED_STATUS_UNAFFECTED/MALE_SEXES/ +# FEMALE_SEXES - duplicated here (rather than imported) so that this module, and anything that +# only needs these constants (e.g. clickhouse_search's migrations), doesn't have to import +# seqr.models. Keep in sync with seqr/models.py's Individual class if those ever change. +AFFECTED = 'A' +UNAFFECTED = 'N' +MALE_SEXES = ['M', 'XXY', 'XYY'] +FEMALE_SEXES = ['F', 'XXX', 'X0'] ALT_ALT = 'alt_alt' REF_REF = 'ref_ref' diff --git a/clickhouse_search/migrations/0040_gnomadnoncodingconstraintdict.py b/clickhouse_search/migrations/0040_gnomadnoncodingconstraintdict.py index 274fb30bf1..504dfd09c5 100644 --- a/clickhouse_search/migrations/0040_gnomadnoncodingconstraintdict.py +++ b/clickhouse_search/migrations/0040_gnomadnoncodingconstraintdict.py @@ -3,7 +3,7 @@ import clickhouse_backend.models import clickhouse_search.backend.engines import clickhouse_search.backend.fields -import clickhouse_search.models.search_models +import clickhouse_search.backend.table_models from django.db import migrations, models import django.db.models.deletion import django.db.models.manager @@ -419,7 +419,7 @@ class Migration(migrations.Migration): options={ 'db_table': 'GRCh38/SNV_INDEL/entries', 'engine': clickhouse_search.backend.engines.CollapsingMergeTree('sign', deduplicate_merge_projection_mode='rebuild', index_granularity=8192, order_by=('project_guid', 'family_guid', 'sample_type', 'is_gnomad_gt_5_percent', 'is_annotated_in_any_gene', 'key'), partition_by=['project_guid', 'partition_id']), - 'projection': clickhouse_search.models.search_models.Projection('xpos_projection', order_by='is_gnomad_gt_5_percent, is_annotated_in_any_gene, xpos'), + 'projection': clickhouse_search.backend.table_models.Projection('xpos_projection', order_by='is_gnomad_gt_5_percent, is_annotated_in_any_gene, xpos'), }, managers=[ ('objects', django.db.models.manager.Manager()), @@ -711,7 +711,7 @@ class Migration(migrations.Migration): 'db_table': 'GRCh37/SNV_INDEL/entries', 'abstract': False, 'engine': clickhouse_search.backend.engines.CollapsingMergeTree('sign', deduplicate_merge_projection_mode='rebuild', index_granularity=8192, order_by=('project_guid', 'family_guid', 'sample_type', 'is_gnomad_gt_5_percent', 'is_annotated_in_any_gene', 'key'), partition_by='project_guid'), - 'projection': clickhouse_search.models.search_models.Projection('xpos_projection', order_by='is_gnomad_gt_5_percent, is_annotated_in_any_gene, xpos'), + 'projection': clickhouse_search.backend.table_models.Projection('xpos_projection', order_by='is_gnomad_gt_5_percent, is_annotated_in_any_gene, xpos'), }, managers=[ ('objects', django.db.models.manager.Manager()), @@ -775,7 +775,7 @@ class Migration(migrations.Migration): 'db_table': 'GRCh38/MITO/entries', 'abstract': False, 'engine': clickhouse_search.backend.engines.CollapsingMergeTree('sign', deduplicate_merge_projection_mode='rebuild', index_granularity=8192, order_by=('project_guid', 'family_guid', 'sample_type', 'key'), partition_by='project_guid'), - 'projection': clickhouse_search.models.search_models.Projection('xpos_projection', order_by='xpos'), + 'projection': clickhouse_search.backend.table_models.Projection('xpos_projection', order_by='xpos'), }, managers=[ ('objects', django.db.models.manager.Manager()), @@ -820,7 +820,7 @@ class Migration(migrations.Migration): 'db_table': 'GRCh38/SV/entries', 'abstract': False, 'engine': clickhouse_search.backend.engines.CollapsingMergeTree('sign', deduplicate_merge_projection_mode='rebuild', index_granularity=8192, order_by=('project_guid', 'family_guid', 'key'), partition_by='project_guid'), - 'projection': clickhouse_search.models.search_models.Projection('xpos_projection', order_by='xpos'), + 'projection': clickhouse_search.backend.table_models.Projection('xpos_projection', order_by='xpos'), }, managers=[ ('objects', django.db.models.manager.Manager()), @@ -842,7 +842,7 @@ class Migration(migrations.Migration): 'db_table': 'GRCh38/GCNV/entries', 'abstract': False, 'engine': clickhouse_search.backend.engines.CollapsingMergeTree('sign', deduplicate_merge_projection_mode='rebuild', index_granularity=8192, order_by=('project_guid', 'family_guid', 'key'), partition_by='project_guid'), - 'projection': clickhouse_search.models.search_models.Projection('xpos_projection', order_by='xpos'), + 'projection': clickhouse_search.backend.table_models.Projection('xpos_projection', order_by='xpos'), }, managers=[ ('objects', django.db.models.manager.Manager()), diff --git a/clickhouse_search/models/search_models.py b/clickhouse_search/models/search_models.py index fb2653401c..f7d52cd17c 100644 --- a/clickhouse_search/models/search_models.py +++ b/clickhouse_search/models/search_models.py @@ -1,10 +1,10 @@ from clickhouse_backend import models -from django.db.models import ForeignKey, OneToOneField, Func, CASCADE +from django.db.models import ForeignKey, OneToOneField, CASCADE from clickhouse_search.backend.engines import CollapsingMergeTree, EmbeddedRocksDB from clickhouse_search.backend.fields import Enum8Field, NestedField, UInt32FieldDeltaCodecField, UInt64FieldDeltaCodecField, NamedTupleField, MaterializedUInt8Field from clickhouse_search.backend.functions import ArrayDistinct, ArrayFlatten, ArrayMin, ArrayMax -from clickhouse_search.backend.table_models import Dictionary, FixtureLoadableClickhouseModel +from clickhouse_search.backend.table_models import Dictionary, FixtureLoadableClickhouseModel, Projection from clickhouse_search.managers import EntriesManager, SvEntriesManager, SvVariantsQuerySet, VariantsQuerySet, \ VariantDetailsQuerySet from clickhouse_search.models.reference_data_models import GnomadNonCodingConstraintDict, BaseSpliceAi, \ @@ -15,14 +15,6 @@ from settings import CLICKHOUSE_IN_MEMORY_DIR, CLICKHOUSE_DATA_DIR -class Projection(Func): - - def __init__(self, name, select='*', order_by=None): - self.name = name - self.select = select - self.order_by = order_by - - class BaseVariants(FixtureLoadableClickhouseModel): CONSEQUENCE_TERMS = [(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')] ANNOTATION_CONSTANTS = { diff --git a/loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_PLAN.md b/loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_PLAN.md index bee7837170..1afa59f8d5 100644 --- a/loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_PLAN.md +++ b/loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_PLAN.md @@ -30,22 +30,31 @@ to depend on from `loading_pipeline`'s minimal env. Per explicit direction: the settings module must configure **one** ClickHouse connection with **one** set of credentials — not the production split of a read-only `clickhouse` alias plus a -privileged `clickhouse_write` alias. `DATABASES` will define a single alias (`clickhouse`) using -one writer-capable credential (needed anyway, since migrations and test data inserts require write +privileged `clickhouse_write` alias. `DATABASES` will define a single real alias using one +writer-capable credential (needed anyway, since migrations and test data inserts require write access). +That real alias must be named `clickhouse_write`, not `clickhouse`: `ClickHouseRouter.allow_migrate` +(`clickhouse_search/models/__init__.py`) hardcodes `db == 'clickhouse_write'` for the +`clickhouse_search` app, so only an alias literally named `clickhouse_write` is allowed to have +migrations applied to it. + Nuance to account for: `clickhouse_search/backend/base.py`'s `_dictionary_sql` looks up `DATABASES['clickhouse_write']['NAME']` (for ClickHouse-sourced dictionaries with a `clickhouse_query_template`) and `DATABASES[postgres_db]['NAME']` (default alias `'default'`, for Postgres-sourced dictionaries) purely to embed a database *name string* into generated DDL — not to open a second real connection. To keep this working without standing up a second live connection: -- Give `'clickhouse_write'` a `TEST: {'MIRROR': 'clickhouse'}` config, so Django reuses the - `clickhouse` alias's actual test database instead of creating/tearing down a second one, while - the key is still present for the `NAME` lookup. +- Give `'clickhouse'` a `TEST: {'MIRROR': 'clickhouse_write'}` config, so Django reuses the + `clickhouse_write` alias's actual test database instead of creating/tearing down a second one, + while the key is still present for the `NAME` lookup (used only by `backend/base.py`, not by our + own test code). - Give `'default'` a placeholder entry (e.g. `ENGINE: 'django.db.backends.dummy'`) purely so `DATABASES['default']['NAME']` resolves to a string — nothing in `loading_pipeline`'s tests actually connects to it, since there's no Postgres in this CI job. +Test code (and the shared base class) uses `connections['clickhouse_write']` — the one alias +Django actually creates/migrates a real test database for. + ## Inventory of every ClickHouse-touching test 1. **`lib/misc/clickhouse_test.py`** (`ClickhouseTest`) — hand-rolls ~250 lines of `CREATE @@ -85,9 +94,9 @@ faking the whole schema). Every test currently calls `get_clickhouse_client()` (a raw `clickhouse_driver.Client`, see `lib/misc/clickhouse.py`) to run setup/assertion SQL directly. Once the schema is Django-managed, tests should execute their raw SQL through Django's own DB connection instead of a separate -`clickhouse_driver.Client` instance — i.e. `django.db.connections['clickhouse'].cursor()` (the one -alias defined per "Single connection / single set of credentials only" above), calling -`cursor.execute(sql, params)` / `cursor.fetchall()`. +`clickhouse_driver.Client` instance — i.e. `django.db.connections['clickhouse_write'].cursor()` +(the one real alias defined per "Single connection / single set of credentials only" above), +calling `cursor.execute(sql, params)` / `cursor.fetchall()`. This is purely a *client* swap for test code — tests keep writing raw SQL strings (no ORM/model queries), just executed via the Django connection so the tests exercise the same connection @@ -117,10 +126,12 @@ note — this fixture rule is specifically about *repeated* setup-time data. | File | Change | |---|---| -| `.github/workflows/pipeline-unit-tests.yml` | add a step creating a dummy `seqr_postgres_named_collection`; keep `CLICKHOUSE_DATABASE=test` | +| `clickhouse_search/models/search_models.py`, `clickhouse_search/backend/table_models.py`, `clickhouse_search/migrations/0040_gnomadnoncodingconstraintdict.py` | move `Projection` from `search_models.py` to `backend/table_models.py`; update the migration's import accordingly (✅ done) | +| `clickhouse_search/constants.py` | duplicate 4 constants out of `seqr.models.Individual` instead of importing it (✅ done) | +| `.github/workflows/pipeline-unit-tests.yml` | keep `CLICKHOUSE_DATABASE=test`; no named-collection step needed anymore (no Postgres-sourced dictionaries are reachable via the minimal settings module in the first place - see note below) | | `loading_pipeline/pyproject.toml` | add `django`, `django-clickhouse-backend`, `pytest-django` dev deps; add `[tool.pytest.ini_options]` (`DJANGO_SETTINGS_MODULE`, `pythonpath`) | | **new** `loading_pipeline/lib/test/clickhouse_django/settings.py` | minimal Django settings: one real `clickhouse` alias (single credential set), `clickhouse_write` mirrored onto it via `TEST: {MIRROR: 'clickhouse'}`, a dummy `default` placeholder (NAME only, no real connection), `clickhouse_backend` + `clickhouse_search` apps, `ClickHouseRouter`; doubles as the shadow `settings` module `clickhouse_search/backend/base.py` bare-imports | -| `lib/test/clickhouse_schema_testcase.py` | rewritten as the one shared base class: drop all manual DDL/SQL-file loading (schema now comes from real migrations via pytest-django), keep only the small external-sourced-dictionary overrides + per-test flush/truncate + staging-DB drop/create — all executed via `connections['clickhouse'].cursor()`; shared reference rows (e.g. gene-id/gnomAD source-table rows) loaded via Django `fixtures = [...]` instead of `INSERT` statements | +| `lib/test/clickhouse_schema_testcase.py` | rewritten as the one shared base class: drop all manual DDL/SQL-file loading (schema now comes from real migrations via pytest-django), keep only the small external-sourced-dictionary overrides + per-test flush/truncate + staging-DB drop/create — all executed via `connections['clickhouse_write'].cursor()`; shared reference rows (e.g. gene-id/gnomAD source-table rows) loaded via Django `fixtures = [...]` instead of `INSERT` statements | | **delete** `loading_pipeline/var/test/test_clickhouse_schema.sql` | no longer needed | | **new** `loading_pipeline/lib/test/fixtures/*.json` | Django fixtures for the shared setup-time reference rows referenced above | | `lib/misc/clickhouse_test.py` | `ClickhouseTest` extends the shared base instead of hand-building its own schema; keeps only its fixture-data seeding (via the new Django fixtures, not bulk `INSERT`) and parquet-writing setup; all `get_clickhouse_client()` calls in the test body replaced with the Django connection cursor | diff --git a/loading_pipeline/pyproject.toml b/loading_pipeline/pyproject.toml index f06f1fc691..f024c6d9f0 100644 --- a/loading_pipeline/pyproject.toml +++ b/loading_pipeline/pyproject.toml @@ -33,6 +33,9 @@ dev = [ "coverage>=7.2.2", "pytest>=7.0.0", "pytest-cov>=4.0.0", + "pytest-django>=4.8.0", + "django==4.2.30", # matches the main seqr app's pinned version + "django-clickhouse-backend==1.6", # matches the main seqr app's pinned version "responses>=0.23.1", "ruff==0.11.3", "shellcheck-py>=0.10.0", @@ -43,6 +46,15 @@ dev = [ [tool.uv] exclude-dependencies = ["psycopg2-binary", "psycopg2"] +[tool.pytest.ini_options] +# `..` puts the repo root (which holds `clickhouse_search`/`clickhouse_backend`) on sys.path. +# `lib/test/clickhouse_django` holds our minimal settings module, which needs to be importable +# both as `DJANGO_SETTINGS_MODULE` and as the bare `settings` module that +# `clickhouse_search/backend/base.py` imports directly; pytest prepends `pythonpath` entries to +# sys.path, so it's found ahead of the (much heavier) repo-root `settings.py`. +pythonpath = ["..", "lib/test/clickhouse_django"] +DJANGO_SETTINGS_MODULE = "settings" + [tool.setuptools] include-package-data = true From a071739f36dd28545b9260e1ec6dfa02d4fef7df Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 10:20:30 -0400 Subject: [PATCH 031/369] add tests ettings module --- .../lib/test/clickhouse_django/settings.py | 118 ++++++++++++++++++ 1 file changed, 118 insertions(+) create mode 100644 loading_pipeline/lib/test/clickhouse_django/settings.py diff --git a/loading_pipeline/lib/test/clickhouse_django/settings.py b/loading_pipeline/lib/test/clickhouse_django/settings.py new file mode 100644 index 0000000000..b78830ece0 --- /dev/null +++ b/loading_pipeline/lib/test/clickhouse_django/settings.py @@ -0,0 +1,118 @@ +"""Minimal Django settings for standing up the `clickhouse_search` schema in tests. + +This module is intentionally NOT the main seqr app's `settings.py` — `loading_pipeline` has its +own, much smaller, dependency footprint and only needs enough Django configuration to run +`clickhouse_search`'s migrations against a test ClickHouse database. + +It is deliberately placed in its own directory that gets prepended to `sys.path` via pytest's +`pythonpath` option (see `pyproject.toml`), for two reasons: + 1. It's used as `DJANGO_SETTINGS_MODULE`. + 2. `clickhouse_search/backend/base.py` does a bare `from settings import ...` (not + `django.conf.settings`), so a top-level module literally named `settings` has to be + importable on `sys.path` and resolve to *this* module rather than the main app's + `settings.py` (which pulls in postgres/guardian/social_django/etc. that `loading_pipeline` + doesn't depend on). + +Only a single real ClickHouse connection/credential set is configured, on the `clickhouse_write` +alias. `ClickHouseRouter.allow_migrate` (in `clickhouse_search/models/__init__.py`) hardcodes +`db == 'clickhouse_write'` for the `clickhouse_search` app, so migrations must run against an +alias literally named `clickhouse_write` - that's the one Django actually creates/migrates a real +test database for. `clickhouse` and `default` are present only because +`clickhouse_search/backend/base.py` looks up `DATABASES['clickhouse_write']['NAME']` / +`DATABASES['default']['NAME']` to embed a database name string into generated dictionary DDL - not +because either needs its own real connection: + - `clickhouse` mirrors the `clickhouse_write` alias's test database (`TEST: {'MIRROR': ...}`), + so Django doesn't create/destroy a second real test database for it. + - `default` is a `dummy` backend entry - it's never actually opened. pytest-django only calls + `create_test_db()` for aliases a given test's `databases` attribute names (see + `pytest_django.fixtures._get_databases_for_setup`); it does not unconditionally create every + alias in `DATABASES`. As long as every `TestCase` subclass in this suite declares + `databases = ['clickhouse_write']` (per the shared base class), `default` is never touched, so + the dummy backend never needs to support real connections - only `DATABASES['default']['NAME']` + ever gets read, purely as a string. + +Only `clickhouse_search`'s own migrations are permitted to run anywhere: `DATABASE_ROUTERS` +appends a small catch-all router (`_NoOtherAppMigrationsRouter`, below) that vetoes migrations for +every app *other* than `clickhouse_search`. Without it, Django's default routing would try to +migrate `clickhouse_search`'s (undeclared, but still `INSTALLED_APPS`-adjacent) dependencies onto +`default`, which would fail against the dummy backend - `clickhouse_search`'s migrations use +ClickHouse-only DDL/field types that don't apply to any other app. + +`clickhouse_search`'s migration `0040_gnomadnoncodingconstraintdict.py` has a +`conditionally_refresh_reference_dataset` step that skips a live network call +(`requests.post(...)`) when `DATABASES['default']['NAME'].startswith('test_')`. That module-level +`DATABASES` reference is the plain dict below, not a Django-test-remapped one (since `default` is +never created/mutated by the test runner, per above), so `default`'s `NAME` is just set directly to +a literal `test_`-prefixed string to keep that guard working and avoid the network call during test +runs. +""" + +import os + +INSTALLED_APPS = [ + 'clickhouse_backend', + 'clickhouse_search', +] + + +class _NoOtherAppMigrationsRouter: + """Prevents any app other than `clickhouse_search` from having migrations applied anywhere. + + `clickhouse_search`'s modules pull in a handful of other apps transitively (see module + docstring); this keeps those apps' own schemas from ever being created against the throwaway + `default` dummy database (which can't support them; they're never needed here anyway). + """ + + @staticmethod + def allow_migrate(db, app_label, model_name=None, **hints): # noqa: ARG004 + if app_label == 'clickhouse_search': + return None # defer to ClickHouseRouter + return False + + +DATABASE_ROUTERS = [ + 'clickhouse_search.models.ClickHouseRouter', + 'settings._NoOtherAppMigrationsRouter', +] + +USE_TZ = True +SECRET_KEY = 'loading-pipeline-test' # noqa: S105 +DEPLOYMENT_TYPE = os.environ.get('DEPLOYMENT_TYPE', 'dev') +PIPELINE_RUNNER_SERVER = os.environ.get('PIPELINE_RUNNER_SERVER', 'http://localhost') +CLICKHOUSE_IN_MEMORY_DIR = os.environ.get('CLICKHOUSE_IN_MEMORY_DIR', '/tmp') # noqa: S108 +CLICKHOUSE_DATA_DIR = os.environ.get('CLICKHOUSE_DATA_DIR', '/tmp') # noqa: S108 + +CLICKHOUSE_WRITER_USER = os.environ.get('CLICKHOUSE_WRITER_USER', 'default') +CLICKHOUSE_WRITER_PASSWORD = os.environ.get('CLICKHOUSE_WRITER_PASSWORD', 'default_password') +CLICKHOUSE_DATABASE_NAME = os.environ.get('CLICKHOUSE_DATABASE', 'seqr') + +CLICKHOUSE_DB_CONFIG = { + 'ENGINE': 'clickhouse_search.backend', + 'NAME': CLICKHOUSE_DATABASE_NAME, + 'USER': CLICKHOUSE_WRITER_USER, + 'PASSWORD': CLICKHOUSE_WRITER_PASSWORD, + 'HOST': os.environ.get('CLICKHOUSE_SERVICE_HOSTNAME', 'localhost'), + 'PORT': int(os.environ.get('CLICKHOUSE_SERVICE_PORT', '9000')), + 'OPTIONS': { + 'settings': { + 'use_client_time_zone': False, + }, + }, + # Avoid Django's default `test_` prefix so the schema lands in the database name that + # `loading_pipeline.lib.core.environment.Env.CLICKHOUSE_DATABASE` already expects. + 'TEST': { + 'NAME': CLICKHOUSE_DATABASE_NAME, + }, +} + +DATABASES = { + 'clickhouse_write': CLICKHOUSE_DB_CONFIG, + 'clickhouse': { + **CLICKHOUSE_DB_CONFIG, + 'TEST': {'MIRROR': 'clickhouse_write'}, + }, + 'default': { + 'ENGINE': 'django.db.backends.dummy', + 'NAME': 'test_default_unused', + }, +} From b4d19b8cc00e0d88c34fb1c00b1f3666b1add44a Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 10:48:16 -0400 Subject: [PATCH 032/369] clean up seqr dependencies and add stub application --- clickhouse_search/backend/table_models.py | 17 ++ .../0040_gnomadnoncodingconstraintdict.py | 2 +- .../models/reference_data_models.py | 14 -- .../test/clickhouse_django/seqr/__init__.py | 28 +++ ...ve_project_custom_reference_populations.py | 15 ++ .../seqr/migrations/__init__.py | 0 .../clickhouse_django/seqr/utils/__init__.py | 0 .../seqr/utils/logging_utils.py | 32 ++++ .../lib/test/clickhouse_django/settings.py | 48 +++-- loading_pipeline/pyproject.toml | 16 +- loading_pipeline/uv.lock | 170 +++++++++++++----- 11 files changed, 265 insertions(+), 77 deletions(-) create mode 100644 loading_pipeline/lib/test/clickhouse_django/seqr/__init__.py create mode 100644 loading_pipeline/lib/test/clickhouse_django/seqr/migrations/0001_squashed_0067_remove_project_custom_reference_populations.py create mode 100644 loading_pipeline/lib/test/clickhouse_django/seqr/migrations/__init__.py create mode 100644 loading_pipeline/lib/test/clickhouse_django/seqr/utils/__init__.py create mode 100644 loading_pipeline/lib/test/clickhouse_django/seqr/utils/logging_utils.py diff --git a/clickhouse_search/backend/table_models.py b/clickhouse_search/backend/table_models.py index f82b9964b7..b9613d9a56 100644 --- a/clickhouse_search/backend/table_models.py +++ b/clickhouse_search/backend/table_models.py @@ -1,9 +1,11 @@ from clickhouse_backend import models from django.db import connections from django.db.models import Func +import requests from clickhouse_search.backend.fields import NamedTupleField from seqr.utils.logging_utils import SeqrLogger +from settings import DATABASES, PIPELINE_RUNNER_SERVER logger = SeqrLogger(__name__) @@ -14,6 +16,21 @@ DICTIONARY_META_FIELDS = ['layout', 'lifetime_max', 'postgres_query', 'postgres_db', 'clickhouse_query_template'] +def conditionally_refresh_reference_dataset(reference_dataset: str): + # NB: lives here, rather than in models/reference_data_models.py, specifically so that + # migrations depending on it don't need to import the (much heavier) live model definitions + # module - this is the only thing migrations need from it. + def inner(apps, schema_editor): + if DATABASES['default']['NAME'].startswith('test_'): + return + requests.post( # pragma: no cover + f"{PIPELINE_RUNNER_SERVER}/refresh_clickhouse_reference_dataset_enqueue", + json={"reference_dataset": reference_dataset}, + timeout=60, + ) + return inner + + class Projection(Func): def __init__(self, name, select='*', order_by=None): diff --git a/clickhouse_search/migrations/0040_gnomadnoncodingconstraintdict.py b/clickhouse_search/migrations/0040_gnomadnoncodingconstraintdict.py index 504dfd09c5..9e31b51325 100644 --- a/clickhouse_search/migrations/0040_gnomadnoncodingconstraintdict.py +++ b/clickhouse_search/migrations/0040_gnomadnoncodingconstraintdict.py @@ -9,7 +9,7 @@ import django.db.models.manager import os -from clickhouse_search.models.reference_data_models import conditionally_refresh_reference_dataset +from clickhouse_search.backend.table_models import conditionally_refresh_reference_dataset from settings import CLICKHOUSE_IN_MEMORY_DIR, CLICKHOUSE_DATA_DIR CLICKHOUSE_AC_EXCLUDED_PROJECT_GUIDS = os.environ.get( diff --git a/clickhouse_search/models/reference_data_models.py b/clickhouse_search/models/reference_data_models.py index 783ff4934e..9f2fe6a4a5 100644 --- a/clickhouse_search/models/reference_data_models.py +++ b/clickhouse_search/models/reference_data_models.py @@ -1,6 +1,5 @@ from clickhouse_backend import models from django.db.models import ForeignKey, PROTECT -import requests from clickhouse_search.backend.engines import Join from clickhouse_search.backend.fields import Enum8Field, NestedField, UInt32FieldDeltaCodecField, DictKeyForeignKey @@ -8,19 +7,6 @@ RefreshableMaterializedView, RefreshableMaterializedViewMeta from clickhouse_search.constants import CLINVAR_ASSERTIONS, CLINVAR_PATHOGENICITIES from seqr.utils.xpos_utils import CHROMOSOME_CHOICES -from settings import DATABASES, PIPELINE_RUNNER_SERVER - - -def conditionally_refresh_reference_dataset(reference_dataset: str): - def inner(apps, schema_editor): - if DATABASES['default']['NAME'].startswith('test_'): - return - requests.post( # pragma: no cover - f"{PIPELINE_RUNNER_SERVER}/refresh_clickhouse_reference_dataset_enqueue", - json={"reference_dataset": reference_dataset}, - timeout=60, - ) - return inner def _all_variants_to_seqr_source_sql(reference_genome, dataset_type): diff --git a/loading_pipeline/lib/test/clickhouse_django/seqr/__init__.py b/loading_pipeline/lib/test/clickhouse_django/seqr/__init__.py new file mode 100644 index 0000000000..1a8bce5028 --- /dev/null +++ b/loading_pipeline/lib/test/clickhouse_django/seqr/__init__.py @@ -0,0 +1,28 @@ +"""Minimal stub of the main app's `seqr` package, for `loading_pipeline`'s tests only. + +`clickhouse_search` (the source of truth for the ClickHouse schema, migrated via real Django +migrations in these tests - see `lib/test/clickhouse_django/settings.py`) has a small number of +genuine, unavoidable dependencies on the `seqr` app: + - `clickhouse_search/backend/table_models.py` (needed to load `clickhouse_search`'s migrations) + imports `seqr.utils.logging_utils.SeqrLogger` - a tiny, dependency-free logging wrapper. + - `clickhouse_search`'s migration `0040_gnomadnoncodingconstraintdict.py` declares a + cross-app migration dependency on a specific `seqr` migration (used only for historical + migration-ordering purposes, not because it touches any `seqr` table). + +Neither of these needs the *real* `seqr` app - which imports `django-guardian`, +`django.contrib.postgres`, `social_django`, etc. at module level via `seqr/models.py` - all +dependencies `loading_pipeline`'s minimal test environment intentionally does not install. + +This package is placed in `lib/test/clickhouse_django/`, which pytest's `pythonpath` option (see +`pyproject.toml`) puts ahead of the repo root on `sys.path`, so `import seqr` resolves to *this* +lightweight stand-in instead of the real app - the same shadowing trick used for the bare +`settings` module `clickhouse_search/backend/base.py` imports directly. + +`clickhouse_search`'s live model definitions (`models/search_models.py`, +`models/reference_data_models.py`, which pull in more of `seqr`, e.g. `seqr.models.Dataset` and +`seqr.utils.xpos_utils.CHROMOSOME_CHOICES`) are deliberately NOT needed here: `loading_pipeline` +never imports them (it only ever talks to ClickHouse via raw SQL - see +`lib/test/clickhouse_schema_testcase.py`), and neither does applying `clickhouse_search`'s +migrations (which are self-contained frozen schema snapshots, not built from the live model +classes at apply time). If that ever changes, this stub will need to grow accordingly. +""" diff --git a/loading_pipeline/lib/test/clickhouse_django/seqr/migrations/0001_squashed_0067_remove_project_custom_reference_populations.py b/loading_pipeline/lib/test/clickhouse_django/seqr/migrations/0001_squashed_0067_remove_project_custom_reference_populations.py new file mode 100644 index 0000000000..985cda6945 --- /dev/null +++ b/loading_pipeline/lib/test/clickhouse_django/seqr/migrations/0001_squashed_0067_remove_project_custom_reference_populations.py @@ -0,0 +1,15 @@ +# No-op stand-in for the real seqr app's migration of the same name. +# +# `clickhouse_search`'s migration `0040_gnomadnoncodingconstraintdict.py` declares a cross-app +# migration dependency on exactly this (app_label, name) pair, purely for historical +# migration-ordering reasons - not because it touches any table this migration would create. +# Django's migration graph builder requires a *named* dependency (unlike `__first__`/`__latest__`) +# to exist as a real node in the graph even for an otherwise-unmigrated app, so this file exists +# solely to satisfy that graph edge. See `seqr/__init__.py` in this stub package for more context. +from django.db import migrations + + +class Migration(migrations.Migration): + initial = True + dependencies = [] + operations = [] diff --git a/loading_pipeline/lib/test/clickhouse_django/seqr/migrations/__init__.py b/loading_pipeline/lib/test/clickhouse_django/seqr/migrations/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/loading_pipeline/lib/test/clickhouse_django/seqr/utils/__init__.py b/loading_pipeline/lib/test/clickhouse_django/seqr/utils/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/loading_pipeline/lib/test/clickhouse_django/seqr/utils/logging_utils.py b/loading_pipeline/lib/test/clickhouse_django/seqr/utils/logging_utils.py new file mode 100644 index 0000000000..ff8b9f242c --- /dev/null +++ b/loading_pipeline/lib/test/clickhouse_django/seqr/utils/logging_utils.py @@ -0,0 +1,32 @@ +"""Stub of `seqr.utils.logging_utils` - see `seqr/__init__.py` in this stub package for why. + +`SeqrLogger` is mirrored verbatim from the real `seqr/utils/logging_utils.py` (it's already +dependency-free: stdlib `logging` plus this app's own `settings.DEPLOYMENT_TYPE`). Only +`SeqrLogger` is reproduced, since it's the only symbol `clickhouse_search` actually imports from +this module (`clickhouse_search/backend/table_models.py`). +""" + +import logging +from typing import Optional + + +class SeqrLogger(object): + + def __init__(self, name: Optional[str] = None) -> None: + """Custom logger which requires user metadata to be included in the log.""" + self._logger = logging.getLogger(name) + + def _log(self, level, message, user, **kwargs): + self._logger.log(level, message, extra=dict(user=user, **kwargs)) + + def debug(self, *args, **kwargs): + self._log(logging.DEBUG, *args, **kwargs) + + def info(self, *args, **kwargs): + self._log(logging.INFO, *args, **kwargs) + + def warning(self, *args, **kwargs): + self._log(logging.WARNING, *args, **kwargs) + + def error(self, *args, **kwargs): + self._log(logging.ERROR, *args, **kwargs) diff --git a/loading_pipeline/lib/test/clickhouse_django/settings.py b/loading_pipeline/lib/test/clickhouse_django/settings.py index b78830ece0..222f30228c 100644 --- a/loading_pipeline/lib/test/clickhouse_django/settings.py +++ b/loading_pipeline/lib/test/clickhouse_django/settings.py @@ -17,19 +17,21 @@ alias. `ClickHouseRouter.allow_migrate` (in `clickhouse_search/models/__init__.py`) hardcodes `db == 'clickhouse_write'` for the `clickhouse_search` app, so migrations must run against an alias literally named `clickhouse_write` - that's the one Django actually creates/migrates a real -test database for. `clickhouse` and `default` are present only because +test database for. `clickhouse`, `default`, and `reference_data` are present only because `clickhouse_search/backend/base.py` looks up `DATABASES['clickhouse_write']['NAME']` / -`DATABASES['default']['NAME']` to embed a database name string into generated dictionary DDL - not -because either needs its own real connection: +`DATABASES[postgres_db]['NAME']` (`postgres_db` defaults to `'default'`, but `GeneIdDict`/ +`OmimDict` in `clickhouse_search/models/postgres_dicts.py` declare `postgres_db = 'reference_data'` +instead) to embed a database name string into generated dictionary DDL - not because any of them +needs its own real connection: - `clickhouse` mirrors the `clickhouse_write` alias's test database (`TEST: {'MIRROR': ...}`), so Django doesn't create/destroy a second real test database for it. - - `default` is a `dummy` backend entry - it's never actually opened. pytest-django only calls - `create_test_db()` for aliases a given test's `databases` attribute names (see - `pytest_django.fixtures._get_databases_for_setup`); it does not unconditionally create every - alias in `DATABASES`. As long as every `TestCase` subclass in this suite declares - `databases = ['clickhouse_write']` (per the shared base class), `default` is never touched, so - the dummy backend never needs to support real connections - only `DATABASES['default']['NAME']` - ever gets read, purely as a string. + - `default` and `reference_data` are `dummy` backend entries - neither is ever actually opened. + pytest-django only calls `create_test_db()` for aliases a given test's `databases` attribute + names (see `pytest_django.fixtures._get_databases_for_setup`); it does not unconditionally + create every alias in `DATABASES`. As long as every `TestCase` subclass in this suite declares + `databases = ['clickhouse_write']` (per the shared base class), neither is ever touched, so the + dummy backend never needs to support real connections - only their `NAME` values ever get + read, purely as strings. Only `clickhouse_search`'s own migrations are permitted to run anywhere: `DATABASE_ROUTERS` appends a small catch-all router (`_NoOtherAppMigrationsRouter`, below) that vetoes migrations for @@ -51,6 +53,10 @@ INSTALLED_APPS = [ 'clickhouse_backend', + # A stub, not the real `seqr` app - see `seqr/__init__.py` (in this same directory, shadowing + # the real app on sys.path) for why `clickhouse_search` needs *an* app named `seqr` present + # at all. + 'seqr', 'clickhouse_search', ] @@ -79,8 +85,12 @@ def allow_migrate(db, app_label, model_name=None, **hints): # noqa: ARG004 SECRET_KEY = 'loading-pipeline-test' # noqa: S105 DEPLOYMENT_TYPE = os.environ.get('DEPLOYMENT_TYPE', 'dev') PIPELINE_RUNNER_SERVER = os.environ.get('PIPELINE_RUNNER_SERVER', 'http://localhost') -CLICKHOUSE_IN_MEMORY_DIR = os.environ.get('CLICKHOUSE_IN_MEMORY_DIR', '/tmp') # noqa: S108 -CLICKHOUSE_DATA_DIR = os.environ.get('CLICKHOUSE_DATA_DIR', '/tmp') # noqa: S108 +# These back separate `EmbeddedRocksDB`-engine tables (e.g. `annotations_memory` vs +# `annotations_disk`) and must resolve to different paths - the same path for both causes a +# RocksDB file-lock collision between those tables ("lock hold by current process") the moment +# migrations try to create both. +CLICKHOUSE_IN_MEMORY_DIR = os.environ.get('CLICKHOUSE_IN_MEMORY_DIR', '/tmp/loading_pipeline_test_clickhouse_in_memory') # noqa: S108 +CLICKHOUSE_DATA_DIR = os.environ.get('CLICKHOUSE_DATA_DIR', '/tmp/loading_pipeline_test_clickhouse_data') # noqa: S108 CLICKHOUSE_WRITER_USER = os.environ.get('CLICKHOUSE_WRITER_USER', 'default') CLICKHOUSE_WRITER_PASSWORD = os.environ.get('CLICKHOUSE_WRITER_PASSWORD', 'default_password') @@ -102,6 +112,12 @@ def allow_migrate(db, app_label, model_name=None, **hints): # noqa: ARG004 # `loading_pipeline.lib.core.environment.Env.CLICKHOUSE_DATABASE` already expects. 'TEST': { 'NAME': CLICKHOUSE_DATABASE_NAME, + # Django assumes any alias whose test-db signature differs from `default`'s implicitly + # depends on `default` (for cross-DB migration ordering) unless told otherwise. Since our + # tests only ever request `databases = ['clickhouse_write']` - `default` is never created + # - that implicit dependency can never resolve, raising "Circular dependency in + # TEST[DEPENDENCIES]". There are no real cross-database dependencies here, so declare none. + 'DEPENDENCIES': [], }, } @@ -115,4 +131,12 @@ def allow_migrate(db, app_label, model_name=None, **hints): # noqa: ARG004 'ENGINE': 'django.db.backends.dummy', 'NAME': 'test_default_unused', }, + # `GeneIdDict`/`OmimDict` (`clickhouse_search/models/postgres_dicts.py`) declare + # `postgres_db = 'reference_data'` instead of the implicit `default` - same dummy-backend + # treatment as `default` above, needed purely so `DATABASES['reference_data']['NAME']` + # resolves to a string for `_dictionary_sql`'s generated DDL. + 'reference_data': { + 'ENGINE': 'django.db.backends.dummy', + 'NAME': 'test_reference_data_unused', + }, } diff --git a/loading_pipeline/pyproject.toml b/loading_pipeline/pyproject.toml index f024c6d9f0..20df951a06 100644 --- a/loading_pipeline/pyproject.toml +++ b/loading_pipeline/pyproject.toml @@ -8,7 +8,7 @@ dependencies = [ "gnomad==0.8.0", "aiofiles==24.1.0", "pydantic==2.8.2", - "clickhouse-driver==0.2.9", + "clickhouse-driver==0.2.10", # matches main seqr app's pinned version and django-clickhouse-backend's requirement "slacker==0.14.0", "ipykernel==6.29.2", # matches pinned version in hail init_notebook.py "jupyter-console==6.6.3", # matches pinned version in hail init_notebook.py @@ -50,10 +50,18 @@ exclude-dependencies = ["psycopg2-binary", "psycopg2"] # `..` puts the repo root (which holds `clickhouse_search`/`clickhouse_backend`) on sys.path. # `lib/test/clickhouse_django` holds our minimal settings module, which needs to be importable # both as `DJANGO_SETTINGS_MODULE` and as the bare `settings` module that -# `clickhouse_search/backend/base.py` imports directly; pytest prepends `pythonpath` entries to -# sys.path, so it's found ahead of the (much heavier) repo-root `settings.py`. -pythonpath = ["..", "lib/test/clickhouse_django"] +# `clickhouse_search/backend/base.py` imports directly. pytest builds sys.path by inserting each +# `pythonpath` entry at position 0 in *reverse* list order, which nets out to sys.path holding +# them in the same order given here - so `lib/test/clickhouse_django` must come first, ahead of +# `..`, or `import settings` resolves to the much heavier repo-root `settings.py` instead of ours. +pythonpath = ["lib/test/clickhouse_django", ".."] DJANGO_SETTINGS_MODULE = "settings" +# pytest-django's `manage.py` auto-discovery walks up from cwd and, finding the main seqr app's +# `manage.py` at the repo root, unconditionally inserts that directory at sys.path[0] - which +# shadows our `settings` module with the main app's much heavier `settings.py`, undoing the +# `pythonpath` ordering above. Disable it; our own `pythonpath` entries are all the path +# configuration this suite needs. +django_find_project = false [tool.setuptools] include-package-data = true diff --git a/loading_pipeline/uv.lock b/loading_pipeline/uv.lock index eba2806f11..d07ecefb95 100644 --- a/loading_pipeline/uv.lock +++ b/loading_pipeline/uv.lock @@ -192,6 +192,15 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/81/29/5ecc3a15d5a33e31b26c11426c45c501e439cb865d0bff96315d86443b78/appnope-0.1.4-py2.py3-none-any.whl", hash = "sha256:502575ee11cd7a28c0205f379b525beefebab9d161b7c964670864014ed7213c", size = 4321, upload-time = "2024-02-06T09:43:09.663Z" }, ] +[[package]] +name = "asgiref" +version = "3.12.1" +source = { registry = "https://pypi.org/simple" } +sdist = { url = "https://files.pythonhosted.org/packages/e6/26/3b59f2bdae5f640389becb1f673cded775287f5fc4f816309d9ca9a3f93d/asgiref-3.12.1.tar.gz", hash = "sha256:59dcb51c272ad209d59bed5708a64a333083e86017d7fcdd67498eeab7784340", size = 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'3.12'", ] dependencies = [ - { name = "google-auth", marker = "python_full_version < '3.14'" }, - { name = "googleapis-common-protos", marker = "python_full_version < '3.14'" }, - { name = "proto-plus", marker = "python_full_version < '3.14'" }, - { name = "protobuf", marker = "python_full_version < '3.14'" }, - { name = "requests", marker = "python_full_version < '3.14'" }, + { name = "google-auth" }, + { name = "googleapis-common-protos" }, + { name = "proto-plus" }, + { name = "protobuf" }, + { name = "requests" }, ] sdist = { url = "https://files.pythonhosted.org/packages/61/da/83d7043169ac2c8c7469f0e375610d78ae2160134bf1b80634c482fa079c/google_api_core-2.28.1.tar.gz", hash = "sha256:2b405df02d68e68ce0fbc138559e6036559e685159d148ae5861013dc201baf8", size = 176759, upload-time = "2025-10-28T21:34:51.529Z" } wheels = [ @@ -1217,8 +1277,8 @@ wheels = [ [package.optional-dependencies] grpc = [ - { name = "grpcio", marker = "python_full_version < '3.14'" }, - { name = "grpcio-status", marker = "python_full_version < '3.14'" }, + { name = "grpcio" }, + { name = "grpcio-status" }, ] [[package]] @@ -3402,6 +3462,18 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/9d/7a/d968e294073affff457b041c2be9868a40c1c71f4a35fcc1e45e5493067b/pytest_cov-7.1.0-py3-none-any.whl", hash = "sha256:a0461110b7865f9a271aa1b51e516c9a95de9d696734a2f71e3e78f46e1d4678", size = 22876, upload-time = "2026-03-21T20:11:14.438Z" }, ] +[[package]] +name = "pytest-django" +version = "4.14.0" +source = { registry = "https://pypi.org/simple" } +dependencies = [ + { name = "pytest" }, +] +sdist = { url = "https://files.pythonhosted.org/packages/44/f6/3851312120c2bf2f19cafff931e75059aad1ba670703cd751e2fde9bc942/pytest_django-4.14.0.tar.gz", hash = "sha256:26787dd3f422cfbab8f55b80a776e2edea7a11092cb74e960bef1312515708ef", size = 94700, upload-time = "2026-08-10T14:13:08.319Z" } +wheels = [ + { url = "https://files.pythonhosted.org/packages/9c/03/850bffad2b581c440ca51c039d74504d5a422c94bda0bdb8a8ba5068d48b/pytest_django-4.14.0-py3-none-any.whl", hash = "sha256:c533b08d89cc675efcd5398eea270b34547e35f9a3608e2c9748dd88428ea187", size = 27067, upload-time = "2026-08-10T14:13:06.998Z" }, +] + [[package]] name = "python-daemon" version = "3.1.2" @@ -3915,10 +3987,13 @@ dependencies = [ [package.dev-dependencies] dev = [ { name = "coverage" }, + { name = "django" }, + { name = "django-clickhouse-backend" }, { name = "pyarrow" }, { name = "pysam" }, { name = "pytest" }, { name = "pytest-cov" }, + { name = "pytest-django" }, { name = "responses" }, { name = "ruff" }, { name = "shellcheck-py" }, @@ -3930,7 +4005,7 @@ prod = [ [package.metadata] requires-dist = [ { name = "aiofiles", specifier = "==24.1.0" }, - { name = "clickhouse-driver", specifier = "==0.2.9" }, + { name = "clickhouse-driver", specifier = "==0.2.10" }, { name = "gnomad", specifier = "==0.8.0" }, { name = "gnomad-qc", git = "https://github.com/broadinstitute/gnomad_qc.git?rev=v4.1" }, { name = "google-api-python-client", specifier = "==2.159.0" }, @@ -3950,10 +4025,13 @@ requires-dist = [ [package.metadata.requires-dev] dev = [ { name = "coverage", specifier = ">=7.2.2" }, + { name = "django", specifier = "==4.2.30" }, + { name = "django-clickhouse-backend", specifier = "==1.6" }, { name = "pyarrow" }, { name = "pysam" }, { name = "pytest", specifier = ">=7.0.0" }, { name = "pytest-cov", specifier = ">=4.0.0" }, + { name = "pytest-django", specifier = ">=4.8.0" }, { name = "responses", specifier = ">=0.23.1" }, { name = "ruff", specifier = "==0.11.3" }, { name = "shellcheck-py", specifier = ">=0.10.0" }, From 63921ab58f3fa51555fd06bffb39b5805f77a2de Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 11:03:16 -0400 Subject: [PATCH 033/369] fix dict relaod behavior --- clickhouse_search/backend/table_models.py | 14 ++++++++++++++ ...veryvariantdict_excludedvariantdict_and_more.py | 8 +++++--- clickhouse_search/migrations/0044_omimdict.py | 4 +++- 3 files changed, 22 insertions(+), 4 deletions(-) diff --git a/clickhouse_search/backend/table_models.py b/clickhouse_search/backend/table_models.py index b9613d9a56..d5406e2f7a 100644 --- a/clickhouse_search/backend/table_models.py +++ b/clickhouse_search/backend/table_models.py @@ -31,6 +31,20 @@ def inner(apps, schema_editor): return inner +def conditionally_reload_dictionary(dictionary_name: str): + # Postgres-sourced dictionaries (SOURCE(POSTGRESQL(...))) are otherwise lazily loaded + # (LIFETIME(0), dictionaries_lazy_load default) - CREATE DICTIONARY alone never touches + # Postgres. An explicit `SYSTEM RELOAD DICTIONARY` forces a real, synchronous connection + # attempt though, which test environments with no real Postgres (e.g. loading_pipeline's) + # can't satisfy - so skip it under the same "test_"-prefix convention as + # `conditionally_refresh_reference_dataset` above. + def inner(apps, schema_editor): + if DATABASES['default']['NAME'].startswith('test_'): + return + schema_editor.execute(f'SYSTEM RELOAD DICTIONARY "{dictionary_name}"') + return inner + + class Projection(Func): def __init__(self, name, select='*', order_by=None): diff --git a/clickhouse_search/migrations/0043_discoveryvariantdict_excludedvariantdict_and_more.py b/clickhouse_search/migrations/0043_discoveryvariantdict_excludedvariantdict_and_more.py index 66f666513a..9d1913855b 100644 --- a/clickhouse_search/migrations/0043_discoveryvariantdict_excludedvariantdict_and_more.py +++ b/clickhouse_search/migrations/0043_discoveryvariantdict_excludedvariantdict_and_more.py @@ -4,6 +4,8 @@ from django.db import migrations import django.db.models.manager +from clickhouse_search.backend.table_models import conditionally_reload_dictionary + class Migration(migrations.Migration): @@ -73,7 +75,7 @@ class Migration(migrations.Migration): ('_overwrite_base_manager', django.db.models.manager.Manager()), ], ), - migrations.RunSQL('SYSTEM RELOAD DICTIONARY "seqrdb_discovery_variant_dict"'), - migrations.RunSQL('SYSTEM RELOAD DICTIONARY "seqrdb_excluded_variant_dict"'), - migrations.RunSQL('SYSTEM RELOAD DICTIONARY "seqrdb_individual_metadata_dict"'), + migrations.RunPython(conditionally_reload_dictionary('seqrdb_discovery_variant_dict')), + migrations.RunPython(conditionally_reload_dictionary('seqrdb_excluded_variant_dict')), + migrations.RunPython(conditionally_reload_dictionary('seqrdb_individual_metadata_dict')), ] diff --git a/clickhouse_search/migrations/0044_omimdict.py b/clickhouse_search/migrations/0044_omimdict.py index e41052a123..b2162e7d08 100644 --- a/clickhouse_search/migrations/0044_omimdict.py +++ b/clickhouse_search/migrations/0044_omimdict.py @@ -4,6 +4,8 @@ from django.db import migrations import django.db.models.manager +from clickhouse_search.backend.table_models import conditionally_reload_dictionary + class Migration(migrations.Migration): @@ -30,5 +32,5 @@ class Migration(migrations.Migration): ('_overwrite_base_manager', django.db.models.manager.Manager()), ], ), - migrations.RunSQL('SYSTEM RELOAD DICTIONARY "seqrdb_omim"'), + migrations.RunPython(conditionally_reload_dictionary('seqrdb_omim')), ] From 805e698c1955a4314fe21a4a1d3536fd11127c0f Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 11:06:43 -0400 Subject: [PATCH 034/369] comment clean up --- clickhouse_search/backend/table_models.py | 11 +-- .../test/clickhouse_django/seqr/__init__.py | 30 +------ ...ve_project_custom_reference_populations.py | 9 +- .../seqr/utils/logging_utils.py | 9 +- .../lib/test/clickhouse_django/settings.py | 89 ++++--------------- loading_pipeline/pyproject.toml | 17 ++-- 6 files changed, 29 insertions(+), 136 deletions(-) diff --git a/clickhouse_search/backend/table_models.py b/clickhouse_search/backend/table_models.py index d5406e2f7a..2f211cc2ff 100644 --- a/clickhouse_search/backend/table_models.py +++ b/clickhouse_search/backend/table_models.py @@ -16,10 +16,9 @@ DICTIONARY_META_FIELDS = ['layout', 'lifetime_max', 'postgres_query', 'postgres_db', 'clickhouse_query_template'] +# Lives here rather than in models/reference_data_models.py so migrations depending on it don't +# need to import the much heavier live model definitions module. def conditionally_refresh_reference_dataset(reference_dataset: str): - # NB: lives here, rather than in models/reference_data_models.py, specifically so that - # migrations depending on it don't need to import the (much heavier) live model definitions - # module - this is the only thing migrations need from it. def inner(apps, schema_editor): if DATABASES['default']['NAME'].startswith('test_'): return @@ -32,12 +31,6 @@ def inner(apps, schema_editor): def conditionally_reload_dictionary(dictionary_name: str): - # Postgres-sourced dictionaries (SOURCE(POSTGRESQL(...))) are otherwise lazily loaded - # (LIFETIME(0), dictionaries_lazy_load default) - CREATE DICTIONARY alone never touches - # Postgres. An explicit `SYSTEM RELOAD DICTIONARY` forces a real, synchronous connection - # attempt though, which test environments with no real Postgres (e.g. loading_pipeline's) - # can't satisfy - so skip it under the same "test_"-prefix convention as - # `conditionally_refresh_reference_dataset` above. def inner(apps, schema_editor): if DATABASES['default']['NAME'].startswith('test_'): return diff --git a/loading_pipeline/lib/test/clickhouse_django/seqr/__init__.py b/loading_pipeline/lib/test/clickhouse_django/seqr/__init__.py index 1a8bce5028..d88b462a89 100644 --- a/loading_pipeline/lib/test/clickhouse_django/seqr/__init__.py +++ b/loading_pipeline/lib/test/clickhouse_django/seqr/__init__.py @@ -1,28 +1,6 @@ -"""Minimal stub of the main app's `seqr` package, for `loading_pipeline`'s tests only. +"""Stub of the main app's `seqr` package, shadowing it on sys.path (see settings.py's docstring). -`clickhouse_search` (the source of truth for the ClickHouse schema, migrated via real Django -migrations in these tests - see `lib/test/clickhouse_django/settings.py`) has a small number of -genuine, unavoidable dependencies on the `seqr` app: - - `clickhouse_search/backend/table_models.py` (needed to load `clickhouse_search`'s migrations) - imports `seqr.utils.logging_utils.SeqrLogger` - a tiny, dependency-free logging wrapper. - - `clickhouse_search`'s migration `0040_gnomadnoncodingconstraintdict.py` declares a - cross-app migration dependency on a specific `seqr` migration (used only for historical - migration-ordering purposes, not because it touches any `seqr` table). - -Neither of these needs the *real* `seqr` app - which imports `django-guardian`, -`django.contrib.postgres`, `social_django`, etc. at module level via `seqr/models.py` - all -dependencies `loading_pipeline`'s minimal test environment intentionally does not install. - -This package is placed in `lib/test/clickhouse_django/`, which pytest's `pythonpath` option (see -`pyproject.toml`) puts ahead of the repo root on `sys.path`, so `import seqr` resolves to *this* -lightweight stand-in instead of the real app - the same shadowing trick used for the bare -`settings` module `clickhouse_search/backend/base.py` imports directly. - -`clickhouse_search`'s live model definitions (`models/search_models.py`, -`models/reference_data_models.py`, which pull in more of `seqr`, e.g. `seqr.models.Dataset` and -`seqr.utils.xpos_utils.CHROMOSOME_CHOICES`) are deliberately NOT needed here: `loading_pipeline` -never imports them (it only ever talks to ClickHouse via raw SQL - see -`lib/test/clickhouse_schema_testcase.py`), and neither does applying `clickhouse_search`'s -migrations (which are self-contained frozen schema snapshots, not built from the live model -classes at apply time). If that ever changes, this stub will need to grow accordingly. +`clickhouse_search`'s migrations need `SeqrLogger` (utils/logging_utils.py) and a specific `seqr` +migration name to exist, but not the real app - which imports guardian/postgres/social_django via +seqr/models.py. This stub avoids that weight. """ diff --git a/loading_pipeline/lib/test/clickhouse_django/seqr/migrations/0001_squashed_0067_remove_project_custom_reference_populations.py b/loading_pipeline/lib/test/clickhouse_django/seqr/migrations/0001_squashed_0067_remove_project_custom_reference_populations.py index 985cda6945..085beeac12 100644 --- a/loading_pipeline/lib/test/clickhouse_django/seqr/migrations/0001_squashed_0067_remove_project_custom_reference_populations.py +++ b/loading_pipeline/lib/test/clickhouse_django/seqr/migrations/0001_squashed_0067_remove_project_custom_reference_populations.py @@ -1,11 +1,4 @@ -# No-op stand-in for the real seqr app's migration of the same name. -# -# `clickhouse_search`'s migration `0040_gnomadnoncodingconstraintdict.py` declares a cross-app -# migration dependency on exactly this (app_label, name) pair, purely for historical -# migration-ordering reasons - not because it touches any table this migration would create. -# Django's migration graph builder requires a *named* dependency (unlike `__first__`/`__latest__`) -# to exist as a real node in the graph even for an otherwise-unmigrated app, so this file exists -# solely to satisfy that graph edge. See `seqr/__init__.py` in this stub package for more context. +# No-op stand-in for the real seqr migration clickhouse_search's 0040 depends on by name. from django.db import migrations diff --git a/loading_pipeline/lib/test/clickhouse_django/seqr/utils/logging_utils.py b/loading_pipeline/lib/test/clickhouse_django/seqr/utils/logging_utils.py index ff8b9f242c..f27d813bbb 100644 --- a/loading_pipeline/lib/test/clickhouse_django/seqr/utils/logging_utils.py +++ b/loading_pipeline/lib/test/clickhouse_django/seqr/utils/logging_utils.py @@ -1,11 +1,4 @@ -"""Stub of `seqr.utils.logging_utils` - see `seqr/__init__.py` in this stub package for why. - -`SeqrLogger` is mirrored verbatim from the real `seqr/utils/logging_utils.py` (it's already -dependency-free: stdlib `logging` plus this app's own `settings.DEPLOYMENT_TYPE`). Only -`SeqrLogger` is reproduced, since it's the only symbol `clickhouse_search` actually imports from -this module (`clickhouse_search/backend/table_models.py`). -""" - +# Mirrors the real seqr.utils.logging_utils.SeqrLogger (dependency-free) - see seqr/__init__.py. import logging from typing import Optional diff --git a/loading_pipeline/lib/test/clickhouse_django/settings.py b/loading_pipeline/lib/test/clickhouse_django/settings.py index 222f30228c..fa74d6173f 100644 --- a/loading_pipeline/lib/test/clickhouse_django/settings.py +++ b/loading_pipeline/lib/test/clickhouse_django/settings.py @@ -1,73 +1,22 @@ -"""Minimal Django settings for standing up the `clickhouse_search` schema in tests. +"""Minimal Django settings for running `clickhouse_search`'s real migrations in tests. -This module is intentionally NOT the main seqr app's `settings.py` — `loading_pipeline` has its -own, much smaller, dependency footprint and only needs enough Django configuration to run -`clickhouse_search`'s migrations against a test ClickHouse database. - -It is deliberately placed in its own directory that gets prepended to `sys.path` via pytest's -`pythonpath` option (see `pyproject.toml`), for two reasons: - 1. It's used as `DJANGO_SETTINGS_MODULE`. - 2. `clickhouse_search/backend/base.py` does a bare `from settings import ...` (not - `django.conf.settings`), so a top-level module literally named `settings` has to be - importable on `sys.path` and resolve to *this* module rather than the main app's - `settings.py` (which pulls in postgres/guardian/social_django/etc. that `loading_pipeline` - doesn't depend on). - -Only a single real ClickHouse connection/credential set is configured, on the `clickhouse_write` -alias. `ClickHouseRouter.allow_migrate` (in `clickhouse_search/models/__init__.py`) hardcodes -`db == 'clickhouse_write'` for the `clickhouse_search` app, so migrations must run against an -alias literally named `clickhouse_write` - that's the one Django actually creates/migrates a real -test database for. `clickhouse`, `default`, and `reference_data` are present only because -`clickhouse_search/backend/base.py` looks up `DATABASES['clickhouse_write']['NAME']` / -`DATABASES[postgres_db]['NAME']` (`postgres_db` defaults to `'default'`, but `GeneIdDict`/ -`OmimDict` in `clickhouse_search/models/postgres_dicts.py` declare `postgres_db = 'reference_data'` -instead) to embed a database name string into generated dictionary DDL - not because any of them -needs its own real connection: - - `clickhouse` mirrors the `clickhouse_write` alias's test database (`TEST: {'MIRROR': ...}`), - so Django doesn't create/destroy a second real test database for it. - - `default` and `reference_data` are `dummy` backend entries - neither is ever actually opened. - pytest-django only calls `create_test_db()` for aliases a given test's `databases` attribute - names (see `pytest_django.fixtures._get_databases_for_setup`); it does not unconditionally - create every alias in `DATABASES`. As long as every `TestCase` subclass in this suite declares - `databases = ['clickhouse_write']` (per the shared base class), neither is ever touched, so the - dummy backend never needs to support real connections - only their `NAME` values ever get - read, purely as strings. - -Only `clickhouse_search`'s own migrations are permitted to run anywhere: `DATABASE_ROUTERS` -appends a small catch-all router (`_NoOtherAppMigrationsRouter`, below) that vetoes migrations for -every app *other* than `clickhouse_search`. Without it, Django's default routing would try to -migrate `clickhouse_search`'s (undeclared, but still `INSTALLED_APPS`-adjacent) dependencies onto -`default`, which would fail against the dummy backend - `clickhouse_search`'s migrations use -ClickHouse-only DDL/field types that don't apply to any other app. - -`clickhouse_search`'s migration `0040_gnomadnoncodingconstraintdict.py` has a -`conditionally_refresh_reference_dataset` step that skips a live network call -(`requests.post(...)`) when `DATABASES['default']['NAME'].startswith('test_')`. That module-level -`DATABASES` reference is the plain dict below, not a Django-test-remapped one (since `default` is -never created/mutated by the test runner, per above), so `default`'s `NAME` is just set directly to -a literal `test_`-prefixed string to keep that guard working and avoid the network call during test -runs. +Lives in its own directory, prepended to `sys.path` via pytest's `pythonpath` option (see +`pyproject.toml`), so it doubles as both `DJANGO_SETTINGS_MODULE` and the bare `settings` module +`clickhouse_search/backend/base.py` imports directly - without pulling in the main app's much +heavier `settings.py`. """ import os INSTALLED_APPS = [ 'clickhouse_backend', - # A stub, not the real `seqr` app - see `seqr/__init__.py` (in this same directory, shadowing - # the real app on sys.path) for why `clickhouse_search` needs *an* app named `seqr` present - # at all. - 'seqr', + 'seqr', # stub package (see seqr/__init__.py), not the real app 'clickhouse_search', ] class _NoOtherAppMigrationsRouter: - """Prevents any app other than `clickhouse_search` from having migrations applied anywhere. - - `clickhouse_search`'s modules pull in a handful of other apps transitively (see module - docstring); this keeps those apps' own schemas from ever being created against the throwaway - `default` dummy database (which can't support them; they're never needed here anyway). - """ + """Only `clickhouse_search` may migrate anywhere; everything else is vetoed.""" @staticmethod def allow_migrate(db, app_label, model_name=None, **hints): # noqa: ARG004 @@ -85,10 +34,8 @@ def allow_migrate(db, app_label, model_name=None, **hints): # noqa: ARG004 SECRET_KEY = 'loading-pipeline-test' # noqa: S105 DEPLOYMENT_TYPE = os.environ.get('DEPLOYMENT_TYPE', 'dev') PIPELINE_RUNNER_SERVER = os.environ.get('PIPELINE_RUNNER_SERVER', 'http://localhost') -# These back separate `EmbeddedRocksDB`-engine tables (e.g. `annotations_memory` vs -# `annotations_disk`) and must resolve to different paths - the same path for both causes a -# RocksDB file-lock collision between those tables ("lock hold by current process") the moment -# migrations try to create both. +# Must differ - EmbeddedRocksDB tables (annotations_memory vs annotations_disk) using the same +# path deadlock on the same file lock. CLICKHOUSE_IN_MEMORY_DIR = os.environ.get('CLICKHOUSE_IN_MEMORY_DIR', '/tmp/loading_pipeline_test_clickhouse_in_memory') # noqa: S108 CLICKHOUSE_DATA_DIR = os.environ.get('CLICKHOUSE_DATA_DIR', '/tmp/loading_pipeline_test_clickhouse_data') # noqa: S108 @@ -108,33 +55,29 @@ def allow_migrate(db, app_label, model_name=None, **hints): # noqa: ARG004 'use_client_time_zone': False, }, }, - # Avoid Django's default `test_` prefix so the schema lands in the database name that - # `loading_pipeline.lib.core.environment.Env.CLICKHOUSE_DATABASE` already expects. 'TEST': { + # Skip Django's default `test_` prefix; land on the name Env.CLICKHOUSE_DATABASE + # already expects. 'NAME': CLICKHOUSE_DATABASE_NAME, - # Django assumes any alias whose test-db signature differs from `default`'s implicitly - # depends on `default` (for cross-DB migration ordering) unless told otherwise. Since our - # tests only ever request `databases = ['clickhouse_write']` - `default` is never created - # - that implicit dependency can never resolve, raising "Circular dependency in - # TEST[DEPENDENCIES]". There are no real cross-database dependencies here, so declare none. + # Without this, Django assumes this alias depends on `default` and never resolves it, + # since our tests only ever request `databases = ['clickhouse_write']`. 'DEPENDENCIES': [], }, } DATABASES = { 'clickhouse_write': CLICKHOUSE_DB_CONFIG, + # Mirrored so Django doesn't create/destroy a second real test database for it. 'clickhouse': { **CLICKHOUSE_DB_CONFIG, 'TEST': {'MIRROR': 'clickhouse_write'}, }, + # Dummy backends: never opened (only aliases named in a test's `databases` get created), but + # `clickhouse_search/backend/base.py` reads their `NAME` to embed in generated dictionary DDL. 'default': { 'ENGINE': 'django.db.backends.dummy', 'NAME': 'test_default_unused', }, - # `GeneIdDict`/`OmimDict` (`clickhouse_search/models/postgres_dicts.py`) declare - # `postgres_db = 'reference_data'` instead of the implicit `default` - same dummy-backend - # treatment as `default` above, needed purely so `DATABASES['reference_data']['NAME']` - # resolves to a string for `_dictionary_sql`'s generated DDL. 'reference_data': { 'ENGINE': 'django.db.backends.dummy', 'NAME': 'test_reference_data_unused', diff --git a/loading_pipeline/pyproject.toml b/loading_pipeline/pyproject.toml index 20df951a06..0b9e4f9f1e 100644 --- a/loading_pipeline/pyproject.toml +++ b/loading_pipeline/pyproject.toml @@ -47,20 +47,13 @@ dev = [ exclude-dependencies = ["psycopg2-binary", "psycopg2"] [tool.pytest.ini_options] -# `..` puts the repo root (which holds `clickhouse_search`/`clickhouse_backend`) on sys.path. -# `lib/test/clickhouse_django` holds our minimal settings module, which needs to be importable -# both as `DJANGO_SETTINGS_MODULE` and as the bare `settings` module that -# `clickhouse_search/backend/base.py` imports directly. pytest builds sys.path by inserting each -# `pythonpath` entry at position 0 in *reverse* list order, which nets out to sys.path holding -# them in the same order given here - so `lib/test/clickhouse_django` must come first, ahead of -# `..`, or `import settings` resolves to the much heavier repo-root `settings.py` instead of ours. +# Order matters: `clickhouse_django` must precede `..`, or `import settings` resolves to the +# repo-root `settings.py` instead of ours. `..` puts the repo root (clickhouse_search etc.) on +# sys.path. pythonpath = ["lib/test/clickhouse_django", ".."] DJANGO_SETTINGS_MODULE = "settings" -# pytest-django's `manage.py` auto-discovery walks up from cwd and, finding the main seqr app's -# `manage.py` at the repo root, unconditionally inserts that directory at sys.path[0] - which -# shadows our `settings` module with the main app's much heavier `settings.py`, undoing the -# `pythonpath` ordering above. Disable it; our own `pythonpath` entries are all the path -# configuration this suite needs. +# Disable pytest-django's manage.py auto-discovery, which would otherwise re-shadow `settings` +# with the main app's. django_find_project = false [tool.setuptools] From d8b1bf3b8368a669baa15d5707d7fe3b157527b3 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 11:19:59 -0400 Subject: [PATCH 035/369] django based test case --- .../lib/test/clickhouse_schema_testcase.py | 139 +++--------------- 1 file changed, 18 insertions(+), 121 deletions(-) diff --git a/loading_pipeline/lib/test/clickhouse_schema_testcase.py b/loading_pipeline/lib/test/clickhouse_schema_testcase.py index fc26f8cc64..b01277fe10 100644 --- a/loading_pipeline/lib/test/clickhouse_schema_testcase.py +++ b/loading_pipeline/lib/test/clickhouse_schema_testcase.py @@ -1,127 +1,24 @@ -import unittest +from django.db import connections +from django.test import TestCase from loading_pipeline.lib.core import Env -from loading_pipeline.lib.misc.clickhouse import ( - STAGING_CLICKHOUSE_DATABASE, - get_clickhouse_client, -) -TEST_SCHEMA = 'loading_pipeline/var/test/test_clickhouse_schema.sql' +class ClickhouseSchemaTestCase(TestCase): + databases = ['clickhouse_write'] -class ClickhouseSchemaTestCase(unittest.TestCase): - def setUp(self): - super().setUp() - client = get_clickhouse_client() - client.execute( - f""" - DROP DATABASE IF EXISTS {STAGING_CLICKHOUSE_DATABASE}; - """, - ) - client.execute( - f""" - DROP DATABASE IF EXISTS {Env.CLICKHOUSE_DATABASE}; - """, - ) - client.execute( - f""" - CREATE DATABASE {Env.CLICKHOUSE_DATABASE}; - """, - ) - client = get_clickhouse_client(database=Env.CLICKHOUSE_DATABASE) - client.execute( - """ - CREATE DICTIONARY seqrdb_gene_ids - ( - `gene_id` String, - `seqrdb_id` String, - `affected` String + # Django's `flush` (the default TestCase teardown for backends without transaction support) + # determines tables to flush from `apps.get_models()`, but nothing here imports + # clickhouse_search's model modules, so it finds none. Truncate live tables directly instead. + def _fixture_teardown(self): + with connections['clickhouse_write'].cursor() as cursor: + cursor.execute( + """ + SELECT name FROM system.tables + WHERE database = %(database)s AND engine NOT IN ('Dictionary', 'MaterializedView') + """, + {'database': Env.CLICKHOUSE_DATABASE}, ) - PRIMARY KEY gene_id - SOURCE(NULL()) - LIFETIME(0) - LAYOUT(HASHED()) - """, - ) - client.execute( - """ - CREATE DICTIONARY seqrdb_affected_status_dict - ( - `family_guid` String, - `sampleId` String, - `affected` String - ) - PRIMARY KEY family_guid, sampleId - SOURCE(NULL()) - LIFETIME(0) - LAYOUT(COMPLEX_KEY_HASHED()) - """, - ) - client.execute( - """ - CREATE DICTIONARY `GRCh38/SNV_INDEL/project_partitions_dict` - ( - `project_guid` String, - `n_partitions` UInt32 - ) - PRIMARY KEY project_guid - SOURCE(NULL()) - LIFETIME(0) - LAYOUT(COMPLEX_KEY_HASHED()) - """, - ) - client.execute( - """ - CREATE DICTIONARY `GRCh38/SNV_INDEL/reference_data/gnomad_genomes` - ( - `key` UInt32, - `filter_af` Decimal(9, 8) - ) - PRIMARY KEY key - SOURCE(NULL()) - LIFETIME(0) - LAYOUT(COMPLEX_KEY_HASHED()) - """, - ) - with open(TEST_SCHEMA) as f: - sql = f.read() - commands = [cmd.strip() for cmd in sql.split(';') if cmd.strip()] - for cmd in commands: - client.execute(cmd) - client.execute( - f""" - CREATE DICTIONARY `GRCh38/SNV_INDEL/gt_stats_dict` - ( - `key` UInt32, - `ac_wes` UInt64, - `ac_wgs` UInt64, - `ac_affected` UInt64, - `hom_wes` UInt64, - `hom_wgs` UInt64, - `hom_affected` UInt64 - ) - PRIMARY KEY key - SOURCE( - CLICKHOUSE( - USER {Env.CLICKHOUSE_WRITER_USER} PASSWORD {Env.CLICKHOUSE_WRITER_PASSWORD} - DB {Env.CLICKHOUSE_DATABASE} TABLE `GRCh38/SNV_INDEL/gt_stats` - ) - ) - LIFETIME(0) - LAYOUT(FLAT(MAX_ARRAY_SIZE 1000000000)) - """, - ) - - def tearDown(self): - super().tearDown() - client = get_clickhouse_client() - client.execute( - f""" - DROP DATABASE IF EXISTS {STAGING_CLICKHOUSE_DATABASE}; - """, - ) - client.execute( - f""" - DROP DATABASE IF EXISTS {Env.CLICKHOUSE_DATABASE}; - """, - ) + tables = [row[0] for row in cursor.fetchall()] + for table in tables: + cursor.execute(f'TRUNCATE TABLE `{table}`') # noqa: S608 From f79c665f5188df2b68e74afba16af03c7accc528 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 11:22:36 -0400 Subject: [PATCH 036/369] plan update --- .../CLICKHOUSE_PYTEST_DJANGO_PLAN.md | 55 ++++++++++++++++++- 1 file changed, 54 insertions(+), 1 deletion(-) diff --git a/loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_PLAN.md b/loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_PLAN.md index 1afa59f8d5..cde0c7077f 100644 --- a/loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_PLAN.md +++ b/loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_PLAN.md @@ -151,4 +151,57 @@ specifics can't be verified ahead of time: tuples, as `clickhouse_driver.Client.execute` supports today) work identically through `cursor.execute()`/`cursor.executemany()` on the Django ClickHouse backend, or need reshaping. -These should be shaken out against a real CI run / local ClickHouse instance once implemented. \ No newline at end of file +These should be shaken out against a real CI run / local ClickHouse instance once implemented. + +## Deviations from this plan, found during implementation + +Verified against a live ClickHouse instance. Recorded here for reference; this plan document +itself is not otherwise updated to match implementation. + +**`clickhouse_search/` changes beyond the two already noted above** (both cleared with the user +before making them): +- Moved `conditionally_refresh_reference_dataset` from `models/reference_data_models.py` to + `backend/table_models.py`, so migration 0040 doesn't need to import the live model modules (and + therefore `seqr.models.Dataset`/`seqr.utils.xpos_utils.CHROMOSOME_CHOICES`) just to reach one + helper function. +- Added `conditionally_reload_dictionary` (`backend/table_models.py`) and edited migrations 0043 + and 0044 to use it instead of hardcoded `RunSQL('SYSTEM RELOAD DICTIONARY ...')` - those forced + a real synchronous Postgres connection during `migrate`, which no environment here has. This + edits already-applied migration files, normally treated as an immutable historical record. + +**A production dependency change:** `clickhouse-driver` bumped `0.2.9` -> `0.2.10` in +`loading_pipeline/pyproject.toml` (forced by `django-clickhouse-backend==1.6`'s own pin; matches +the main app's version). Not test-only. + +**Bugs/gaps in this plan's own design, fixed - all confined to `loading_pipeline/`:** +- `reference_data` needs its own dummy `DATABASES` alias; the plan only accounted for `default` + (`GeneIdDict`/`OmimDict` declare `postgres_db = 'reference_data'`). +- `DATABASES['clickhouse_write']['TEST']['DEPENDENCIES']` must be `[]`, or Django raises + "Circular dependency in TEST[DEPENDENCIES]" (it assumes every alias depends on `default`). +- The `pythonpath` ordering described in this plan's original settings-module writeup was + backwards; pytest builds `sys.path` in the *same* order as the `pythonpath` list, not reversed. +- `django_find_project = false` is required - pytest-django's `manage.py` auto-discovery + otherwise force-inserts the repo root at `sys.path[0]`, re-shadowing `settings`. +- `CLICKHOUSE_IN_MEMORY_DIR`/`CLICKHOUSE_DATA_DIR` must default to different paths, or two + `EmbeddedRocksDB` tables collide on the same file lock. +- A stub `seqr` package (`lib/test/clickhouse_django/seqr/`) is needed - not anticipated anywhere + in this plan - because `clickhouse_search/backend/table_models.py` imports `SeqrLogger`, and + migration 0040 has a named dependency on a specific `seqr` migration. +- The "no named-collection CI step needed" conclusion in this plan's own change-set table is + right, but the "Postgres/GCS-sourced dictionary wrinkle" section above is stale/wrong about why + - see the migration 0043/0044 edit above for the actual mechanism. + +**Explicit user-directed deviations from this plan's design:** +- The shared base class does NOT keep "staging-DB drop/create" logic, contrary to this plan's + change-set table - `loading_pipeline`'s own production code already drops/creates the staging + DB defensively, so tests don't need to. +- Per-test cleanup in the shared base class is a `_fixture_teardown` override that truncates all + live, non-`Dictionary`/`MaterializedView` tables directly via SQL - not Django's `flush` command, + which relies on `apps.get_models()` and finds nothing (no `clickhouse_search` model modules are + imported anywhere in `loading_pipeline`). + +**Unresolved tension, not yet acted on:** this plan calls for shared reference data (e.g. +`seqrdb_gene_ids` source rows) to be loaded via Django fixtures (`loaddata`), which requires +importing the real model classes being loaded - but the user has since directed that fully +importing `clickhouse_search`'s live model modules is unacceptable for these tests. Needs +resolution before the fixture-loading step is implemented. \ No newline at end of file From 0f6f79d15fd4ce6bcd440a224222016ae57efc23 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 12:03:06 -0400 Subject: [PATCH 037/369] existing test cleanup --- loading_pipeline/bin/pipeline_worker_test.py | 56 ++-- .../load_clickhouse_variants_tables_test.py | 57 ++-- .../var/test/test_clickhouse_schema.sql | 269 ------------------ 3 files changed, 54 insertions(+), 328 deletions(-) delete mode 100644 loading_pipeline/var/test/test_clickhouse_schema.sql diff --git a/loading_pipeline/bin/pipeline_worker_test.py b/loading_pipeline/bin/pipeline_worker_test.py index e258d0c573..532693701a 100644 --- a/loading_pipeline/bin/pipeline_worker_test.py +++ b/loading_pipeline/bin/pipeline_worker_test.py @@ -6,14 +6,12 @@ import hailtop.fs as hfs import luigi import luigi.worker +from django.db import connections from loading_pipeline.bin.pipeline_worker import process_queue from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType from loading_pipeline.lib.core.environment import Env -from loading_pipeline.lib.misc.clickhouse import ( - ClickhouseReferenceDataset, - get_clickhouse_client, -) +from loading_pipeline.lib.misc.clickhouse import ClickhouseReferenceDataset from loading_pipeline.lib.paths import ( clickhouse_load_success_file_path, loading_pipeline_deadletter_queue_dir, @@ -106,31 +104,31 @@ def test_process_queue_integration_test( ) as f: self.assertEqual(f.read(), '') - client = get_clickhouse_client() - annotations_count = client.execute( - f""" - SELECT COUNT(*) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` - """, - )[0][0] - self.assertEqual(annotations_count, 30) - entries_count = client.execute( - f""" - SELECT COUNT(*) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` - """, - )[0][0] - self.assertEqual(entries_count, 16) - ac_wgs = client.execute( - f""" - SELECT sum(ac_wgs) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` - """, - )[0][0] - self.assertEqual(ac_wgs, 69) + with connections['clickhouse_write'].cursor() as cursor: + cursor.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` + """, + ) + self.assertEqual(cursor.fetchone()[0], 30) + cursor.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` + """, + ) + self.assertEqual(cursor.fetchone()[0], 16) + cursor.execute( + f""" + SELECT sum(ac_wgs) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` + """, + ) + self.assertEqual(cursor.fetchone()[0], 69) @patch('loading_pipeline.lib.misc.slack._safe_post_to_slack') @patch('loading_pipeline.api.request_handlers.WriteClickhouseLoadSuccessFileTask') diff --git a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py index 972df2c172..b8a2d8fa1e 100644 --- a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py +++ b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py @@ -2,16 +2,14 @@ import hail as hl import luigi.worker +from django.db import connections from loading_pipeline.lib.core import ( DatasetType, ReferenceGenome, ) from loading_pipeline.lib.core.environment import Env -from loading_pipeline.lib.misc.clickhouse import ( - ClickhouseReferenceDataset, - get_clickhouse_client, -) +from loading_pipeline.lib.misc.clickhouse import ClickhouseReferenceDataset from loading_pipeline.lib.paths import ( variant_annotations_table_path, ) @@ -34,7 +32,6 @@ MockedDatarootTestCase, ) -TEST_SCHEMA = 'loading_pipeline/var/test/test_clickhouse_schema.sql' TEST_SNV_INDEL_ANNOTATIONS = ( 'loading_pipeline/var/test/exports/GRCh38/SNV_INDEL/annotations.ht' ) @@ -121,28 +118,28 @@ def test_write_variants_to_clickhouse( worker.run() self.assertTrue(task.complete()) - client = get_clickhouse_client() - variants_count = client.execute( - f""" - SELECT COUNT(*) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` - """, - )[0][0] - self.assertEqual(variants_count, 2) - variant_details_count = client.execute( - f""" - SELECT COUNT(*) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details` - """, - )[0][0] - self.assertEqual(variant_details_count, 2) - key_lookups_count = client.execute( - f""" - SELECT COUNT(*) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/key_lookup` - """, - )[0][0] - self.assertEqual(key_lookups_count, 2) + with connections['clickhouse_write'].cursor() as cursor: + cursor.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` + """, + ) + self.assertEqual(cursor.fetchone()[0], 2) + cursor.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details` + """, + ) + self.assertEqual(cursor.fetchone()[0], 2) + cursor.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/key_lookup` + """, + ) + self.assertEqual(cursor.fetchone()[0], 2) diff --git a/loading_pipeline/var/test/test_clickhouse_schema.sql b/loading_pipeline/var/test/test_clickhouse_schema.sql deleted file mode 100644 index d33275bb3b..0000000000 --- a/loading_pipeline/var/test/test_clickhouse_schema.sql +++ /dev/null @@ -1,269 +0,0 @@ -CREATE TABLE `GRCh38/SNV_INDEL/variants_disk` -( - `key` UInt32 CODEC(Delta(8), ZSTD(1)), - `sortedTranscriptConsequences` Nested(alphamissensePathogenicity Nullable(Decimal(9, 5)), canonical Nullable(UInt8), consequenceTerms Array(Nullable(Enum8('transcript_ablation' = 1, 'splice_acceptor_variant' = 2, 'splice_donor_variant' = 3, 'stop_gained' = 4, 'frameshift_variant' = 5, 'stop_lost' = 6, 'start_lost' = 7, 'inframe_insertion' = 8, 'inframe_deletion' = 9, 'missense_variant' = 10, 'protein_altering_variant' = 11, 'splice_donor_5th_base_variant' = 12, 'splice_region_variant' = 13, 'splice_donor_region_variant' = 14, 'splice_polypyrimidine_tract_variant' = 15, 'incomplete_terminal_codon_variant' = 16, 'start_retained_variant' = 17, 'stop_retained_variant' = 18, 'synonymous_variant' = 19, 'coding_sequence_variant' = 20, 'mature_miRNA_variant' = 21, '5_prime_UTR_variant' = 22, '3_prime_UTR_variant' = 23, 'non_coding_transcript_exon_variant' = 24, 'intron_variant' = 25, 'NMD_transcript_variant' = 26, 'non_coding_transcript_variant' = 27, 'coding_transcript_variant' = 28, 'upstream_gene_variant' = 29, 'downstream_gene_variant' = 30, 'intergenic_variant' = 31, 'sequence_variant' = 32))), extendedIntronicSpliceRegionVariant Nullable(Bool), fiveutrConsequence Nullable(Enum8('5_prime_UTR_premature_start_codon_gain_variant' = 1, '5_prime_UTR_premature_start_codon_loss_variant' = 2, '5_prime_UTR_stop_codon_gain_variant' = 3, '5_prime_UTR_stop_codon_loss_variant' = 4, '5_prime_UTR_uORF_frameshift_variant' = 5)), geneId Nullable(String)), - `sortedMotifFeatureConsequences` Nested(consequenceTerms Array(Nullable(Enum8('TFBS_ablation' = 0, 'TFBS_amplification' = 1, 'TF_binding_site_variant' = 2, 'TFBS_fusion' = 3, 'TFBS_translocation' = 4)))), - `sortedRegulatoryFeatureConsequences` Nested(consequenceTerms Array(Nullable(Enum8('regulatory_region_ablation' = 0, 'regulatory_region_amplification' = 1, 'regulatory_region_variant' = 2, 'regulatory_region_fusion' = 3)))) -) -ENGINE = EmbeddedRocksDB() -PRIMARY KEY key; - -CREATE TABLE `GRCh38/SNV_INDEL/variants_memory` -( - `key` UInt32 CODEC(Delta(8), ZSTD(1)), - `sortedTranscriptConsequences` Nested(alphamissensePathogenicity Nullable(Decimal(9, 5)), canonical Nullable(UInt8), consequenceTerms Array(Nullable(Enum8('transcript_ablation' = 1, 'splice_acceptor_variant' = 2, 'splice_donor_variant' = 3, 'stop_gained' = 4, 'frameshift_variant' = 5, 'stop_lost' = 6, 'start_lost' = 7, 'inframe_insertion' = 8, 'inframe_deletion' = 9, 'missense_variant' = 10, 'protein_altering_variant' = 11, 'splice_donor_5th_base_variant' = 12, 'splice_region_variant' = 13, 'splice_donor_region_variant' = 14, 'splice_polypyrimidine_tract_variant' = 15, 'incomplete_terminal_codon_variant' = 16, 'start_retained_variant' = 17, 'stop_retained_variant' = 18, 'synonymous_variant' = 19, 'coding_sequence_variant' = 20, 'mature_miRNA_variant' = 21, '5_prime_UTR_variant' = 22, '3_prime_UTR_variant' = 23, 'non_coding_transcript_exon_variant' = 24, 'intron_variant' = 25, 'NMD_transcript_variant' = 26, 'non_coding_transcript_variant' = 27, 'coding_transcript_variant' = 28, 'upstream_gene_variant' = 29, 'downstream_gene_variant' = 30, 'intergenic_variant' = 31, 'sequence_variant' = 32))), extendedIntronicSpliceRegionVariant Nullable(Bool), fiveutrConsequence Nullable(Enum8('5_prime_UTR_premature_start_codon_gain_variant' = 1, '5_prime_UTR_premature_start_codon_loss_variant' = 2, '5_prime_UTR_stop_codon_gain_variant' = 3, '5_prime_UTR_stop_codon_loss_variant' = 4, '5_prime_UTR_uORF_frameshift_variant' = 5)), geneId Nullable(String)), - `sortedMotifFeatureConsequences` Nested(consequenceTerms Array(Nullable(Enum8('TFBS_ablation' = 0, 'TFBS_amplification' = 1, 'TF_binding_site_variant' = 2, 'TFBS_fusion' = 3, 'TFBS_translocation' = 4)))), - `sortedRegulatoryFeatureConsequences` Nested(consequenceTerms Array(Nullable(Enum8('regulatory_region_ablation' = 0, 'regulatory_region_amplification' = 1, 'regulatory_region_variant' = 2, 'regulatory_region_fusion' = 3)))) -) -ENGINE = EmbeddedRocksDB() -PRIMARY KEY key; - -CREATE TABLE `GRCh38/SNV_INDEL/variants/details` -( - `key` UInt32 CODEC(Delta(8), ZSTD(1)), - `variantId` String, - `rsid` Nullable(String), - `CAID` Nullable(String), - `liftedOverChrom` Nullable(Enum8('1' = 1, '2' = 2, '3' = 3, '4' = 4, '5' = 5, '6' = 6, '7' = 7, '8' = 8, '9' = 9, '10' = 10, '11' = 11, '12' = 12, '13' = 13, '14' = 14, '15' = 15, '16' = 16, '17' = 17, '18' = 18, '19' = 19, '20' = 20, '21' = 21, '22' = 22, 'X' = 23, 'Y' = 24, 'M' = 25)), - `liftedOverPos` Nullable(UInt32), - `transcripts` Nested(alphamissense Tuple( - pathogenicity Nullable(Decimal(9, 5))), aminoAcids Nullable(String), biotype Nullable(String), canonical Nullable(UInt8), codons Nullable(String), consequenceTerms Array(Nullable(Enum8('transcript_ablation' = 1, 'splice_acceptor_variant' = 2, 'splice_donor_variant' = 3, 'stop_gained' = 4, 'frameshift_variant' = 5, 'stop_lost' = 6, 'start_lost' = 7, 'inframe_insertion' = 8, 'inframe_deletion' = 9, 'missense_variant' = 10, 'protein_altering_variant' = 11, 'splice_donor_5th_base_variant' = 12, 'splice_region_variant' = 13, 'splice_donor_region_variant' = 14, 'splice_polypyrimidine_tract_variant' = 15, 'incomplete_terminal_codon_variant' = 16, 'start_retained_variant' = 17, 'stop_retained_variant' = 18, 'synonymous_variant' = 19, 'coding_sequence_variant' = 20, 'mature_miRNA_variant' = 21, '5_prime_UTR_variant' = 22, '3_prime_UTR_variant' = 23, 'non_coding_transcript_exon_variant' = 24, 'intron_variant' = 25, 'NMD_transcript_variant' = 26, 'non_coding_transcript_variant' = 27, 'coding_transcript_variant' = 28, 'upstream_gene_variant' = 29, 'downstream_gene_variant' = 30, 'intergenic_variant' = 31, 'sequence_variant' = 32))), exon Tuple( - index Nullable(Int32), - total Nullable(Int32)), geneId Nullable(String), hgvsc Nullable(String), hgvsp Nullable(String), intron Tuple( - index Nullable(Int32), - total Nullable(Int32)), loftee Tuple( - isLofNagnag Nullable(Bool), - lofFilters Array(Nullable(String))), majorConsequence Nullable(Enum8('transcript_ablation' = 1, 'splice_acceptor_variant' = 2, 'splice_donor_variant' = 3, 'stop_gained' = 4, 'frameshift_variant' = 5, 'stop_lost' = 6, 'start_lost' = 7, 'inframe_insertion' = 8, 'inframe_deletion' = 9, 'missense_variant' = 10, 'protein_altering_variant' = 11, 'splice_donor_5th_base_variant' = 12, 'splice_region_variant' = 13, 'splice_donor_region_variant' = 14, 'splice_polypyrimidine_tract_variant' = 15, 'incomplete_terminal_codon_variant' = 16, 'start_retained_variant' = 17, 'stop_retained_variant' = 18, 'synonymous_variant' = 19, 'coding_sequence_variant' = 20, 'mature_miRNA_variant' = 21, '5_prime_UTR_variant' = 22, '3_prime_UTR_variant' = 23, 'non_coding_transcript_exon_variant' = 24, 'intron_variant' = 25, 'NMD_transcript_variant' = 26, 'non_coding_transcript_variant' = 27, 'coding_transcript_variant' = 28, 'upstream_gene_variant' = 29, 'downstream_gene_variant' = 30, 'intergenic_variant' = 31, 'sequence_variant' = 32)), manePlusClinical Nullable(String), maneSelect Nullable(String), refseqTranscriptId Nullable(String), spliceregion Tuple( - extended_intronic_splice_region_variant Nullable(Bool)), transcriptId String, transcriptRank UInt8, utrannotator Tuple( - existingInframeOorfs Nullable(Int32), - existingOutofframeOorfs Nullable(Int32), - existingUorfs Nullable(Int32), - fiveutrAnnotation Tuple( - AltStop Nullable(String), - AltStopDistanceToCDS Nullable(Int32), - CapDistanceToStart Nullable(Int32), - DistanceToCDS Nullable(Int32), - DistanceToStop Nullable(Int32), - Evidence Nullable(Bool), - FrameWithCDS Nullable(String), - KozakContext Nullable(String), - KozakStrength Nullable(String), - StartDistanceToCDS Nullable(Int32), - alt_type Nullable(String), - alt_type_length Nullable(Int32), - newSTOPDistanceToCDS Nullable(Int32), - ref_StartDistanceToCDS Nullable(Int32), - ref_type Nullable(String), - ref_type_length Nullable(Int32), - type Nullable(String)), - fiveutrConsequence Nullable(String))), - `sortedMotifFeatureConsequences` Nested(consequenceTerms Array(Nullable(Enum8('TFBS_ablation' = 0, 'TFBS_amplification' = 1, 'TF_binding_site_variant' = 2, 'TFBS_fusion' = 3, 'TFBS_translocation' = 4))), motifFeatureId Nullable(String)), - `sortedRegulatoryFeatureConsequences` Nested(biotype Nullable(Enum8('enhancer' = 0, 'promoter' = 1, 'CTCF_binding_site' = 2, 'TF_binding_site' = 3, 'open_chromatin_region' = 4)), consequenceTerms Array(Nullable(Enum8('regulatory_region_ablation' = 0, 'regulatory_region_amplification' = 1, 'regulatory_region_variant' = 2, 'regulatory_region_fusion' = 3))), regulatoryFeatureId Nullable(String)) -) -ENGINE = EmbeddedRocksDB() -PRIMARY KEY key; - -CREATE TABLE `GRCh38/SNV_INDEL/entries` -( - `key` UInt32 CODEC(Delta(8), ZSTD(1)), - `project_guid` LowCardinality(String), - `family_guid` String, - `sample_type` Enum8('WES' = 1, 'WGS' = 2), - `xpos` UInt64 CODEC(Delta(8), ZSTD(1)), - `is_gnomad_gt_5_percent` Bool, - `is_annotated_in_any_gene` Bool, - `geneId_ids` Array(UInt32), - `filters` Array(LowCardinality(String)), - `calls` Array(Tuple( - sampleId String, - gt Nullable(Enum8('REF' = 0, 'HET' = 1, 'HOM' = 2)), - gq Nullable(UInt8), - ab Nullable(Decimal(9, 5)), - dp Nullable(UInt16))), - `sign` Int8, - `n_partitions` UInt8 MATERIALIZED dictGetOrDefault('GRCh38/SNV_INDEL/project_partitions_dict', 'n_partitions', project_guid, 1), - `partition_id` UInt8 MATERIALIZED farmHash64(family_guid) % n_partitions, - PROJECTION xpos_projection - ( - SELECT * - ORDER BY - is_gnomad_gt_5_percent, - is_annotated_in_any_gene, - xpos - ) -) -ENGINE = CollapsingMergeTree(sign) -PARTITION BY (project_guid, partition_id) -ORDER BY (project_guid, family_guid, sample_type, is_gnomad_gt_5_percent, is_annotated_in_any_gene, key) -SETTINGS deduplicate_merge_projection_mode = 'rebuild', index_granularity = 8192; - -CREATE TABLE `GRCh38/SNV_INDEL/gt_stats` -( - `key` UInt32 CODEC(Delta(8), ZSTD(1)), - `ac_wes` UInt32, - `ac_wgs` UInt32, - `ac_affected` UInt32 DEFAULT 0, - `hom_wes` UInt32, - `hom_wgs` UInt32, - `hom_affected` UInt32 DEFAULT 0 -) -ENGINE = SummingMergeTree -ORDER BY key -SETTINGS index_granularity = 8192; - -CREATE TABLE `GRCh38/SNV_INDEL/key_lookup` -( - `variantId` String, - `key` UInt32 CODEC(Delta(8), ZSTD(1)) -) -ENGINE = EmbeddedRocksDB() -PRIMARY KEY variantId; - -CREATE TABLE `GRCh38/SNV_INDEL/project_gt_stats` -( - `project_guid` LowCardinality(String), - `key` UInt32 CODEC(Delta(8), ZSTD(1)), - `sample_type` Enum8('WES' = 1, 'WGS' = 2), - `affected` Enum8('A' = 1, 'N' = 2, 'U' = 3) DEFAULT 'U', - `ref_samples` UInt32, - `het_samples` UInt32, - `hom_samples` UInt32 -) -ENGINE = SummingMergeTree -PARTITION BY project_guid -ORDER BY (project_guid, key, sample_type) -SETTINGS index_granularity = 8192; - -CREATE TABLE `GRCh38/SNV_INDEL/reference_data/clinvar` -( - `key` UInt32 CODEC(Delta(8), ZSTD(1)), - `alleleId` Nullable(UInt32), - `conflictingPathogenicities` Nested(pathogenicity Enum8('Pathogenic' = 0, 'Pathogenic/Likely_pathogenic' = 1, 'Pathogenic/Likely_pathogenic/Established_risk_allele' = 2, 'Pathogenic/Likely_pathogenic/Likely_risk_allele' = 3, 'Pathogenic/Likely_risk_allele' = 4, 'Likely_pathogenic' = 5, 'Likely_pathogenic/Likely_risk_allele' = 6, 'Established_risk_allele' = 7, 'Likely_risk_allele' = 8, 'Conflicting_classifications_of_pathogenicity' = 9, 'Uncertain_risk_allele' = 10, 'Uncertain_significance/Uncertain_risk_allele' = 11, 'Uncertain_significance' = 12, 'No_pathogenic_assertion' = 13, 'Likely_benign' = 14, 'Benign/Likely_benign' = 15, 'Benign' = 16), count UInt16), - `goldStars` Nullable(UInt8), - `submitters` Array(String), - `conditions` Array(String), - `assertions` Array(Enum8('Affects' = 0, 'association' = 1, 'association_not_found' = 2, 'confers_sensitivity' = 3, 'drug_response' = 4, 'low_penetrance' = 5, 'not_provided' = 6, 'other' = 7, 'protective' = 8, 'risk_factor' = 9, 'no_classification_for_the_single_variant' = 10, 'no_classifications_from_unflagged_records' = 11)), - `pathogenicity` Enum8('Pathogenic' = 0, 'Pathogenic/Likely_pathogenic' = 1, 'Pathogenic/Likely_pathogenic/Established_risk_allele' = 2, 'Pathogenic/Likely_pathogenic/Likely_risk_allele' = 3, 'Pathogenic/Likely_risk_allele' = 4, 'Likely_pathogenic' = 5, 'Likely_pathogenic/Likely_risk_allele' = 6, 'Established_risk_allele' = 7, 'Likely_risk_allele' = 8, 'Conflicting_classifications_of_pathogenicity' = 9, 'Uncertain_risk_allele' = 10, 'Uncertain_significance/Uncertain_risk_allele' = 11, 'Uncertain_significance' = 12, 'No_pathogenic_assertion' = 13, 'Likely_benign' = 14, 'Benign/Likely_benign' = 15, 'Benign' = 16) -) -ENGINE = Join(`ALL`, LEFT, key) -SETTINGS join_use_nulls = 1; - -CREATE TABLE `GRCh38/SNV_INDEL/reference_data/clinvar/all_variants` -( - `version` Date, - `variantId` String, - `alleleId` Nullable(UInt32), - `conflictingPathogenicities` Nested(pathogenicity Enum8('Pathogenic' = 0, 'Pathogenic/Likely_pathogenic' = 1, 'Pathogenic/Likely_pathogenic/Established_risk_allele' = 2, 'Pathogenic/Likely_pathogenic/Likely_risk_allele' = 3, 'Pathogenic/Likely_risk_allele' = 4, 'Likely_pathogenic' = 5, 'Likely_pathogenic/Likely_risk_allele' = 6, 'Established_risk_allele' = 7, 'Likely_risk_allele' = 8, 'Conflicting_classifications_of_pathogenicity' = 9, 'Uncertain_risk_allele' = 10, 'Uncertain_significance/Uncertain_risk_allele' = 11, 'Uncertain_significance' = 12, 'No_pathogenic_assertion' = 13, 'Likely_benign' = 14, 'Benign/Likely_benign' = 15, 'Benign' = 16), count UInt16), - `goldStars` Nullable(UInt8), - `submitters` Array(String), - `conditions` Array(String), - `assertions` Array(Enum8('Affects' = 0, 'association' = 1, 'association_not_found' = 2, 'confers_sensitivity' = 3, 'drug_response' = 4, 'low_penetrance' = 5, 'not_provided' = 6, 'other' = 7, 'protective' = 8, 'risk_factor' = 9, 'no_classification_for_the_single_variant' = 10, 'no_classifications_from_unflagged_records' = 11)), - `pathogenicity` Enum8('Pathogenic' = 0, 'Pathogenic/Likely_pathogenic' = 1, 'Pathogenic/Likely_pathogenic/Established_risk_allele' = 2, 'Pathogenic/Likely_pathogenic/Likely_risk_allele' = 3, 'Pathogenic/Likely_risk_allele' = 4, 'Likely_pathogenic' = 5, 'Likely_pathogenic/Likely_risk_allele' = 6, 'Established_risk_allele' = 7, 'Likely_risk_allele' = 8, 'Conflicting_classifications_of_pathogenicity' = 9, 'Uncertain_risk_allele' = 10, 'Uncertain_significance/Uncertain_risk_allele' = 11, 'Uncertain_significance' = 12, 'No_pathogenic_assertion' = 13, 'Likely_benign' = 14, 'Benign/Likely_benign' = 15, 'Benign' = 16) -) -ENGINE = MergeTree -PARTITION BY version -PRIMARY KEY (version, variantId) -ORDER BY (version, variantId) -SETTINGS index_granularity = 8192; - -CREATE TABLE `GRCh38/SNV_INDEL/reference_data/clinvar/seqr_variants` -( - `key` UInt32 CODEC(Delta(8), ZSTD(1)), - `alleleId` Nullable(UInt32), - `conflictingPathogenicities` Nested(pathogenicity Enum8('Pathogenic' = 0, 'Pathogenic/Likely_pathogenic' = 1, 'Pathogenic/Likely_pathogenic/Established_risk_allele' = 2, 'Pathogenic/Likely_pathogenic/Likely_risk_allele' = 3, 'Pathogenic/Likely_risk_allele' = 4, 'Likely_pathogenic' = 5, 'Likely_pathogenic/Likely_risk_allele' = 6, 'Established_risk_allele' = 7, 'Likely_risk_allele' = 8, 'Conflicting_classifications_of_pathogenicity' = 9, 'Uncertain_risk_allele' = 10, 'Uncertain_significance/Uncertain_risk_allele' = 11, 'Uncertain_significance' = 12, 'No_pathogenic_assertion' = 13, 'Likely_benign' = 14, 'Benign/Likely_benign' = 15, 'Benign' = 16), count UInt16), - `goldStars` Nullable(UInt8), - `submitters` Array(String), - `conditions` Array(String), - `assertions` Array(Enum8('Affects' = 0, 'association' = 1, 'association_not_found' = 2, 'confers_sensitivity' = 3, 'drug_response' = 4, 'low_penetrance' = 5, 'not_provided' = 6, 'other' = 7, 'protective' = 8, 'risk_factor' = 9, 'no_classification_for_the_single_variant' = 10, 'no_classifications_from_unflagged_records' = 11)), - `pathogenicity` Enum8('Pathogenic' = 0, 'Pathogenic/Likely_pathogenic' = 1, 'Pathogenic/Likely_pathogenic/Established_risk_allele' = 2, 'Pathogenic/Likely_pathogenic/Likely_risk_allele' = 3, 'Pathogenic/Likely_risk_allele' = 4, 'Likely_pathogenic' = 5, 'Likely_pathogenic/Likely_risk_allele' = 6, 'Established_risk_allele' = 7, 'Likely_risk_allele' = 8, 'Conflicting_classifications_of_pathogenicity' = 9, 'Uncertain_risk_allele' = 10, 'Uncertain_significance/Uncertain_risk_allele' = 11, 'Uncertain_significance' = 12, 'No_pathogenic_assertion' = 13, 'Likely_benign' = 14, 'Benign/Likely_benign' = 15, 'Benign' = 16) -) -ENGINE = MergeTree -PRIMARY KEY key -ORDER BY key -SETTINGS index_granularity = 8192; - -CREATE MATERIALIZED VIEW `GRCh38/SNV_INDEL/entries_to_project_gt_stats_mv` TO `GRCh38/SNV_INDEL/project_gt_stats` -( - `project_guid` LowCardinality(String), - `key` UInt32, - `sample_type` Enum8('WES' = 1, 'WGS' = 2), - `affected` String, - `ref_samples` Int64, - `het_samples` Int64, - `hom_samples` Int64 -) -AS SELECT - project_guid, - key, - sample_type, - dictGetOrDefault('seqrdb_affected_status_dict', 'affected', (family_guid, calls.sampleId), 'U') AS affected, - sumIf(sign, calls.gt = 'REF') AS ref_samples, - sumIf(sign, calls.gt = 'HET') AS het_samples, - sumIf(sign, calls.gt = 'HOM') AS hom_samples -FROM `GRCh38/SNV_INDEL/entries` -ARRAY JOIN calls -GROUP BY - project_guid, - key, - sample_type, - affected; - -CREATE MATERIALIZED VIEW `GRCh38/SNV_INDEL/project_gt_stats_to_gt_stats_mv` -REFRESH EVERY 10 YEAR TO `GRCh38/SNV_INDEL/gt_stats` -( - `key` UInt32, - `ac_wes` UInt64, - `ac_wgs` UInt64, - `ac_affected` UInt64, - `hom_wes` UInt64, - `hom_wgs` UInt64, - `hom_affected` UInt64 -) -AS SELECT - key, - sumIf((het_samples * 1) + (hom_samples * 2), sample_type = 'WES') AS ac_wes, - sumIf((het_samples * 1) + (hom_samples * 2), sample_type = 'WGS') AS ac_wgs, - sumIf((het_samples * 1) + (hom_samples * 2), affected = 'A') AS ac_affected, - sumIf(hom_samples, sample_type = 'WES') AS hom_wes, - sumIf(hom_samples, sample_type = 'WGS') AS hom_wgs, - sumIf(hom_samples, affected = 'A') AS hom_affected -FROM `GRCh38/SNV_INDEL/project_gt_stats` -WHERE project_guid NOT IN ['R0555_seqr_demo', 'R0607_gregor_training_project_', 'R0608_gregor_training_project_', 'R0801_gregor_training_project_', 'R0811_gregor_training_project_', 'R0812_gregor_training_project_', 'R0813_gregor_training_project_', 'R0814_gregor_training_project_', 'R0815_gregor_training_project_', 'R0816_gregor_training_project_'] -GROUP BY key; - -CREATE MATERIALIZED VIEW `GRCh38/SNV_INDEL/reference_data/clinvar/all_variants_to_seqr_variants_mv` -REFRESH EVERY 10 YEAR TO `GRCh38/SNV_INDEL/reference_data/clinvar/seqr_variants` -( - `key` UInt32, - `alleleId` Nullable(UInt32), - `conflictingPathogenicities` Nested(pathogenicity Enum8('Pathogenic' = 0, 'Pathogenic/Likely_pathogenic' = 1, 'Pathogenic/Likely_pathogenic/Established_risk_allele' = 2, 'Pathogenic/Likely_pathogenic/Likely_risk_allele' = 3, 'Pathogenic/Likely_risk_allele' = 4, 'Likely_pathogenic' = 5, 'Likely_pathogenic/Likely_risk_allele' = 6, 'Established_risk_allele' = 7, 'Likely_risk_allele' = 8, 'Conflicting_classifications_of_pathogenicity' = 9, 'Uncertain_risk_allele' = 10, 'Uncertain_significance/Uncertain_risk_allele' = 11, 'Uncertain_significance' = 12, 'No_pathogenic_assertion' = 13, 'Likely_benign' = 14, 'Benign/Likely_benign' = 15, 'Benign' = 16), count UInt16), - `goldStars` Nullable(UInt8), - `submitters` Array(String), - `conditions` Array(String), - `assertions` Array(Enum8('Affects' = 0, 'association' = 1, 'association_not_found' = 2, 'confers_sensitivity' = 3, 'drug_response' = 4, 'low_penetrance' = 5, 'not_provided' = 6, 'other' = 7, 'protective' = 8, 'risk_factor' = 9, 'no_classification_for_the_single_variant' = 10, 'no_classifications_from_unflagged_records' = 11)), - `pathogenicity` Enum8('Pathogenic' = 0, 'Pathogenic/Likely_pathogenic' = 1, 'Pathogenic/Likely_pathogenic/Established_risk_allele' = 2, 'Pathogenic/Likely_pathogenic/Likely_risk_allele' = 3, 'Pathogenic/Likely_risk_allele' = 4, 'Likely_pathogenic' = 5, 'Likely_pathogenic/Likely_risk_allele' = 6, 'Established_risk_allele' = 7, 'Likely_risk_allele' = 8, 'Conflicting_classifications_of_pathogenicity' = 9, 'Uncertain_risk_allele' = 10, 'Uncertain_significance/Uncertain_risk_allele' = 11, 'Uncertain_significance' = 12, 'No_pathogenic_assertion' = 13, 'Likely_benign' = 14, 'Benign/Likely_benign' = 15, 'Benign' = 16) -) -AS SELECT - key, - COLUMNS('.*') EXCEPT (version, variantId, key) -FROM `GRCh38/SNV_INDEL/reference_data/clinvar/all_variants` AS src -INNER JOIN `GRCh38/SNV_INDEL/key_lookup` AS dst ON assumeNotNull(src.variantId) = dst.variantId -LIMIT 1 BY key; - - -CREATE MATERIALIZED VIEW `GRCh38/SNV_INDEL/reference_data/clinvar/seqr_variants_to_search_mv` -REFRESH EVERY 10 YEAR TO `GRCh38/SNV_INDEL/reference_data/clinvar` -( - `key` UInt32, - `alleleId` Nullable(UInt32), - `conflictingPathogenicities` Nested(pathogenicity Enum8('Pathogenic' = 0, 'Pathogenic/Likely_pathogenic' = 1, 'Pathogenic/Likely_pathogenic/Established_risk_allele' = 2, 'Pathogenic/Likely_pathogenic/Likely_risk_allele' = 3, 'Pathogenic/Likely_risk_allele' = 4, 'Likely_pathogenic' = 5, 'Likely_pathogenic/Likely_risk_allele' = 6, 'Established_risk_allele' = 7, 'Likely_risk_allele' = 8, 'Conflicting_classifications_of_pathogenicity' = 9, 'Uncertain_risk_allele' = 10, 'Uncertain_significance/Uncertain_risk_allele' = 11, 'Uncertain_significance' = 12, 'No_pathogenic_assertion' = 13, 'Likely_benign' = 14, 'Benign/Likely_benign' = 15, 'Benign' = 16), count UInt16), - `goldStars` Nullable(UInt8), - `submitters` Array(String), - `conditions` Array(String), - `assertions` Array(Enum8('Affects' = 0, 'association' = 1, 'association_not_found' = 2, 'confers_sensitivity' = 3, 'drug_response' = 4, 'low_penetrance' = 5, 'not_provided' = 6, 'other' = 7, 'protective' = 8, 'risk_factor' = 9, 'no_classification_for_the_single_variant' = 10, 'no_classifications_from_unflagged_records' = 11)), - `pathogenicity` Enum8('Pathogenic' = 0, 'Pathogenic/Likely_pathogenic' = 1, 'Pathogenic/Likely_pathogenic/Established_risk_allele' = 2, 'Pathogenic/Likely_pathogenic/Likely_risk_allele' = 3, 'Pathogenic/Likely_risk_allele' = 4, 'Likely_pathogenic' = 5, 'Likely_pathogenic/Likely_risk_allele' = 6, 'Established_risk_allele' = 7, 'Likely_risk_allele' = 8, 'Conflicting_classifications_of_pathogenicity' = 9, 'Uncertain_risk_allele' = 10, 'Uncertain_significance/Uncertain_risk_allele' = 11, 'Uncertain_significance' = 12, 'No_pathogenic_assertion' = 13, 'Likely_benign' = 14, 'Benign/Likely_benign' = 15, 'Benign' = 16) -) -AS SELECT * -FROM `GRCh38/SNV_INDEL/reference_data/clinvar/seqr_variants` -LIMIT 1 BY key; - From 9e23da04f35605044ab256b783ebd456c76f85ea Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 14:31:16 -0400 Subject: [PATCH 038/369] first opass refatcor test clcikhouse --- CLAUDE.md | 4 +- clickhouse_search/constants.py | 13 +- clickhouse_search/models/__init__.py | 6 + clickhouse_search/models/gt_stats_models.py | 12 +- clickhouse_search/models/search_models.py | 28 +- loading_pipeline/lib/misc/clickhouse_test.py | 1762 +++++++---------- .../test/clickhouse_django/seqr/__init__.py | 6 +- .../clickhouse_django/seqr/utils/__init__.py | 4 + .../seqr/utils/logging_utils.py | 25 - .../lib/test/clickhouse_django/settings.py | 4 + .../lib/test/clickhouse_schema_testcase.py | 1 + reference_data/models.py | 4 +- seqr/models.py | 33 +- 13 files changed, 791 insertions(+), 1111 deletions(-) delete mode 100644 loading_pipeline/lib/test/clickhouse_django/seqr/utils/logging_utils.py diff --git a/CLAUDE.md b/CLAUDE.md index dc9f87ef3e..10e1116dbb 100644 --- a/CLAUDE.md +++ b/CLAUDE.md @@ -42,4 +42,6 @@ Single test: `npx jest path/to/File.test.js`. Coverage threshold 40% lines/state ## Development Notes -Never delete a file that is not in source control without confirming first +- Never delete a file that is not in source control without confirming first +- Comments should be kept to a minimum. Only add them where the code is genuinely hard to understand or maintain, and keep them brief. +- Always ask before downloading large amounts of data diff --git a/clickhouse_search/constants.py b/clickhouse_search/constants.py index 2ebb829f03..ebce6e0063 100644 --- a/clickhouse_search/constants.py +++ b/clickhouse_search/constants.py @@ -1,3 +1,7 @@ +from seqr.utils.constants import AFFECTED_STATUS_AFFECTED as AFFECTED, AFFECTED_STATUS_UNAFFECTED as UNAFFECTED, \ + MALE_SEXES, FEMALE_SEXES, SAMPLE_TYPE_WES, SAMPLE_TYPE_WGS, DATASET_TYPE_VARIANT_CALLS, DATASET_TYPE_SV_CALLS, \ + DATASET_TYPE_MITO_CALLS, GENOME_VERSION_GRCh37, GENOME_VERSION_GRCh38 + MAX_VARIANTS = 10000 XPOS_SORT_KEY = 'xpos' @@ -5,15 +9,6 @@ PATHOGENICTY_HGMD_SORT_KEY = 'pathogenicity_hgmd' PRIORITIZED_GENE_SORT = 'prioritized_gene' -# Mirrors seqr.models.Individual.AFFECTED_STATUS_AFFECTED/AFFECTED_STATUS_UNAFFECTED/MALE_SEXES/ -# FEMALE_SEXES - duplicated here (rather than imported) so that this module, and anything that -# only needs these constants (e.g. clickhouse_search's migrations), doesn't have to import -# seqr.models. Keep in sync with seqr/models.py's Individual class if those ever change. -AFFECTED = 'A' -UNAFFECTED = 'N' -MALE_SEXES = ['M', 'XXY', 'XYY'] -FEMALE_SEXES = ['F', 'XXX', 'X0'] - ALT_ALT = 'alt_alt' REF_REF = 'ref_ref' REF_ALT = 'ref_alt' diff --git a/clickhouse_search/models/__init__.py b/clickhouse_search/models/__init__.py index a1c506ef4a..8695ebea5c 100644 --- a/clickhouse_search/models/__init__.py +++ b/clickhouse_search/models/__init__.py @@ -12,6 +12,12 @@ ) state.DEFAULT_NAMES = options.DEFAULT_NAMES +# Importing these registers their model classes with Django's app registry (apps.get_model()), +# which fixture loaddata needs to resolve "clickhouse_search." identifiers. Nothing else +# in this package imports them directly otherwise. Must come after the DEFAULT_NAMES patch above - +# these modules' Meta classes use the custom fields it allowlists. +from clickhouse_search.models import postgres_dicts, reference_data_models, search_models, gt_stats_models # noqa: F401,E402 + class ClickHouseRouter: # Adapted from https://github.com/jayvynl/django-clickhouse-backend/blob/v1.3.2/README.md#configuration diff --git a/clickhouse_search/models/gt_stats_models.py b/clickhouse_search/models/gt_stats_models.py index 3076b65054..efd071a22d 100644 --- a/clickhouse_search/models/gt_stats_models.py +++ b/clickhouse_search/models/gt_stats_models.py @@ -3,8 +3,8 @@ from clickhouse_search.backend.fields import UInt32FieldDeltaCodecField, DictKeyForeignKey from clickhouse_search.backend.table_models import RefreshableMaterializedView, RefreshableMaterializedViewMeta, \ IncrementalMaterializedView, Dictionary -from reference_data.models import GENOME_VERSION_GRCh38, GENOME_VERSION_GRCh37 -from seqr.models import Dataset +from seqr.utils.constants import GENOME_VERSION_GRCh38, GENOME_VERSION_GRCh37, \ + DATASET_TYPE_VARIANT_CALLS, DATASET_TYPE_SV_CALLS, DATASET_TYPE_MITO_CALLS class BaseProjectGtStats(models.ClickhouseModel): @@ -307,10 +307,10 @@ class Meta(GtStatsDictMeta): layout = 'FLAT(MAX_ARRAY_SIZE 5000000)' PROJECT_GT_STATS_VIEW_CLASS_MAP = { - GENOME_VERSION_GRCh37: {Dataset.DATASET_TYPE_VARIANT_CALLS: ProjectsToGtStatsGRCh37SnvIndel}, + GENOME_VERSION_GRCh37: {DATASET_TYPE_VARIANT_CALLS: ProjectsToGtStatsGRCh37SnvIndel}, GENOME_VERSION_GRCh38: { - Dataset.DATASET_TYPE_VARIANT_CALLS: ProjectsToGtStatsSnvIndel, - Dataset.DATASET_TYPE_MITO_CALLS: ProjectsToGtStatsMito, - Dataset.DATASET_TYPE_SV_CALLS: ProjectsToGtStatsSv, + DATASET_TYPE_VARIANT_CALLS: ProjectsToGtStatsSnvIndel, + DATASET_TYPE_MITO_CALLS: ProjectsToGtStatsMito, + DATASET_TYPE_SV_CALLS: ProjectsToGtStatsSv, }, } diff --git a/clickhouse_search/models/search_models.py b/clickhouse_search/models/search_models.py index f7d52cd17c..50aedf1325 100644 --- a/clickhouse_search/models/search_models.py +++ b/clickhouse_search/models/search_models.py @@ -9,8 +9,8 @@ VariantDetailsQuerySet from clickhouse_search.models.reference_data_models import GnomadNonCodingConstraintDict, BaseSpliceAi, \ ScreenDict -from reference_data.models import GENOME_VERSION_GRCh38, GENOME_VERSION_GRCh37 -from seqr.models import Dataset +from seqr.utils.constants import GENOME_VERSION_GRCh38, GENOME_VERSION_GRCh37, \ + SAMPLE_TYPE_WES, SAMPLE_TYPE_WGS, DATASET_TYPE_VARIANT_CALLS, DATASET_TYPE_SV_CALLS, DATASET_TYPE_MITO_CALLS from seqr.utils.xpos_utils import CHROMOSOME_CHOICES from settings import CLICKHOUSE_IN_MEMORY_DIR, CLICKHOUSE_DATA_DIR @@ -406,7 +406,7 @@ class Meta(BaseEntries.Meta): ) class EntriesSv(BaseEntries): - SAMPLE_TYPE = Dataset.SAMPLE_TYPE_WGS + SAMPLE_TYPE = SAMPLE_TYPE_WGS CALL_FIELDS = [ ('sampleId', models.StringField()), ('gt', models.Enum8Field(null=True, blank=True, choices=[(0, 'REF'), (1, 'HET'), (2, 'HOM')])), @@ -428,7 +428,7 @@ class Meta(BaseEntries.Meta): db_table = 'GRCh38/SV/entries' class EntriesGcnv(BaseEntries): - SAMPLE_TYPE = Dataset.SAMPLE_TYPE_WES + SAMPLE_TYPE = SAMPLE_TYPE_WES CALL_FIELDS = [ ('sampleId', models.StringField()), ('gt', models.Enum8Field(null=True, blank=True, choices=[(0, 'REF'), (1, 'HET'), (2, 'HOM')])), @@ -613,21 +613,21 @@ class Meta: ENTRY_CLASS_MAP = { - GENOME_VERSION_GRCh37: {Dataset.DATASET_TYPE_VARIANT_CALLS: EntriesGRCh37SnvIndel}, + GENOME_VERSION_GRCh37: {DATASET_TYPE_VARIANT_CALLS: EntriesGRCh37SnvIndel}, GENOME_VERSION_GRCh38: { - Dataset.DATASET_TYPE_VARIANT_CALLS: EntriesSnvIndel, - Dataset.DATASET_TYPE_MITO_CALLS: EntriesMito, - f'{Dataset.DATASET_TYPE_SV_CALLS}_{Dataset.SAMPLE_TYPE_WGS}': EntriesSv, - f'{Dataset.DATASET_TYPE_SV_CALLS}_{Dataset.SAMPLE_TYPE_WES}': EntriesGcnv, + DATASET_TYPE_VARIANT_CALLS: EntriesSnvIndel, + DATASET_TYPE_MITO_CALLS: EntriesMito, + f'{DATASET_TYPE_SV_CALLS}_{SAMPLE_TYPE_WGS}': EntriesSv, + f'{DATASET_TYPE_SV_CALLS}_{SAMPLE_TYPE_WES}': EntriesGcnv, }, } VARIANTS_CLASS_MAP = { - GENOME_VERSION_GRCh37: {Dataset.DATASET_TYPE_VARIANT_CALLS: VariantsGRCh37SnvIndel}, + GENOME_VERSION_GRCh37: {DATASET_TYPE_VARIANT_CALLS: VariantsGRCh37SnvIndel}, GENOME_VERSION_GRCh38: { - Dataset.DATASET_TYPE_VARIANT_CALLS: VariantsSnvIndel, - Dataset.DATASET_TYPE_MITO_CALLS: VariantsMito, - f'{Dataset.DATASET_TYPE_SV_CALLS}_{Dataset.SAMPLE_TYPE_WGS}': VariantsSv, - f'{Dataset.DATASET_TYPE_SV_CALLS}_{Dataset.SAMPLE_TYPE_WES}': VariantsGcnv, + DATASET_TYPE_VARIANT_CALLS: VariantsSnvIndel, + DATASET_TYPE_MITO_CALLS: VariantsMito, + f'{DATASET_TYPE_SV_CALLS}_{SAMPLE_TYPE_WGS}': VariantsSv, + f'{DATASET_TYPE_SV_CALLS}_{SAMPLE_TYPE_WES}': VariantsGcnv, }, } VARIANT_DETAILS_CLASS_MAP = { diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index b4e7673664..eba49231af 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -4,6 +4,7 @@ import pandas as pd import pyarrow as pa import pyarrow.parquet as pq +from django.db import connections from loading_pipeline.lib.core import DatasetType, ReferenceGenome from loading_pipeline.lib.core.environment import Env @@ -38,313 +39,83 @@ new_variants_parquet_path, runs_path, ) +from loading_pipeline.lib.test.clickhouse_schema_testcase import ( + ClickhouseSchemaTestCase, +) from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase TEST_RUN_ID = 'manual__2025-05-07T17-20-59.702114+00-00' -class ClickhouseTest(MockedDatarootTestCase): - def setUp(self): - super().setUp() - client = get_clickhouse_client() - client.execute( - f""" - DROP DATABASE IF EXISTS {STAGING_CLICKHOUSE_DATABASE}; - """, - ) - client.execute( - f""" - DROP DATABASE IF EXISTS {Env.CLICKHOUSE_DATABASE}; - """, - ) - client.execute( - f""" - CREATE DATABASE {Env.CLICKHOUSE_DATABASE}; - """, - ) - client.execute( - f""" - CREATE TABLE {Env.CLICKHOUSE_DATABASE}.seqrdb_gene_ids_src ( - gene_id String, - seqrdb_id UInt32 - ) ENGINE = Memory; - """, - ) - client.execute( - f'INSERT INTO {Env.CLICKHOUSE_DATABASE}.`seqrdb_gene_ids_src` VALUES', - [('GENE1', 123), ('GENE2', 12), ('GENE3', 1)], - ) - client.execute( - f""" - CREATE DICTIONARY {Env.CLICKHOUSE_DATABASE}.seqrdb_gene_ids - ( - gene_id String, - seqrdb_id UInt32 - ) - PRIMARY KEY gene_id - SOURCE(CLICKHOUSE( - USER {Env.CLICKHOUSE_WRITER_USER} PASSWORD {Env.CLICKHOUSE_WRITER_PASSWORD} - DB {Env.CLICKHOUSE_DATABASE} TABLE `seqrdb_gene_ids_src` - )) - LAYOUT(HASHED()) - LIFETIME(0); - """, - ) - client.execute( - f""" - CREATE TABLE {Env.CLICKHOUSE_DATABASE}.gnomad_genomes_src ( - key UInt32, - filter_af Decimal(9, 8) - ) ENGINE = Memory; - """, - ) - client.execute( - f'INSERT INTO {Env.CLICKHOUSE_DATABASE}.`gnomad_genomes_src` VALUES', - [(11, 0.06), (12, 0.001), (13, 0.0001)], - ) - client.execute( - f""" - CREATE DICTIONARY {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/reference_data/gnomad_genomes` - ( - key UInt32, - filter_af Decimal(9, 8) - ) - PRIMARY KEY key - SOURCE(CLICKHOUSE( - USER {Env.CLICKHOUSE_WRITER_USER} PASSWORD {Env.CLICKHOUSE_WRITER_PASSWORD} - DB {Env.CLICKHOUSE_DATABASE} TABLE `gnomad_genomes_src` - )) - LAYOUT(HASHED()) - LIFETIME(0); - """, - ) - client.execute( - f""" - CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` ( - `key` UInt32, - `project_guid` LowCardinality(String), - `family_guid` String, - `xpos` UInt64 CODEC(Delta(8), ZSTD(1)), - `sample_type` Enum8('WES' = 0, 'WGS' = 1), - `is_gnomad_gt_5_percent` Boolean, - `is_annotated_in_any_gene` Boolean DEFAULT length(geneId_ids) > 0, - `geneId_ids` Array(UInt32), - `calls` Array( - Tuple( - sampleId String, - gt Nullable(Enum8('REF' = 0, 'HET' = 1, 'HOM' = 2)), - ) - ), - `sign` Int8, - PROJECTION xpos_projection - ( - SELECT * - ORDER BY is_annotated_in_any_gene, xpos - ) +class ClickhouseTest(MockedDatarootTestCase, ClickhouseSchemaTestCase): + fixtures = ['clickhouse_test'] + + @classmethod + def setUpClass(cls): + super().setUpClass() + # seqrdb_gene_ids/seqrdb_affected_status_dict are Postgres-sourced in production (see + # postgres_dicts.py) - no ClickHouse-side model backs them, so override with + # deterministic ClickHouse-sourced versions. Runs once for the class: inserting the + # `entries` fixture rows (loaded per-test, before setUp()) triggers + # entries_to_project_gt_stats_mv, which queries seqrdb_affected_status_dict. + with connections['clickhouse_write'].cursor() as cursor: + cursor.execute( + f""" + CREATE TABLE IF NOT EXISTS {Env.CLICKHOUSE_DATABASE}.seqrdb_gene_ids_src ( + gene_id String, + seqrdb_id UInt32 + ) ENGINE = Memory; + """, ) - ENGINE = CollapsingMergeTree(sign) - PARTITION BY project_guid - ORDER BY (project_guid, family_guid, key) - SETTINGS deduplicate_merge_projection_mode = 'rebuild'; - """, - ) - client.execute( - f""" - CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` - ( - `project_guid` String, - `key` UInt32, - `sample_type` Enum8('WES' = 0, 'WGS' = 1), - `het_samples` Int32, - `hom_samples` Int32, - ) - ENGINE = SummingMergeTree - PARTITION BY project_guid - ORDER BY (project_guid, key, sample_type) - """, - ) - client.execute( - f""" - CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` - ( - `key` UInt32, - `ac_wes` UInt32, - `ac_wgs` UInt32, - ) - ENGINE = SummingMergeTree - ORDER BY (key) - """, - ) - client.execute( - f""" - CREATE MATERIALIZED VIEW {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries_to_project_gt_stats_mv` - TO {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` - AS SELECT - project_guid, - key, - sample_type, - sum(toInt32(arrayCount(s -> (s.gt = 'HET'), calls) * sign)) AS het_samples, - sum(toInt32(arrayCount(s -> (s.gt = 'HOM'), calls) * sign)) AS hom_samples - FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` - GROUP BY project_guid, key, sample_type - """, - ) - client.execute( - f""" - CREATE MATERIALIZED VIEW {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats_to_gt_stats_mv` - REFRESH EVERY 10 YEAR TO {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` - AS SELECT - key, - sumIf(het_samples * 1 + hom_samples * 2, sample_type = 'WES') AS ac_wes, - sumIf(het_samples * 1 + hom_samples * 2, sample_type = 'WGS') AS ac_wgs - FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` - GROUP BY key - """, - ) - client.execute( - f""" - CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details` ( - key UInt32, - variantId String, - transcripts String - ) ENGINE = EmbeddedRocksDB() - PRIMARY KEY `key` - """, - ) - client.execute( - f""" - CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` ( - key UInt32, - variantId String, - ) ENGINE = EmbeddedRocksDB() - PRIMARY KEY `key` - """, - ) - client.execute( - f""" - CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_disk` ( - key UInt32, - variantId String, - ) ENGINE = EmbeddedRocksDB() - PRIMARY KEY `key` - """, - ) - client.execute( - f""" - CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/key_lookup` ( - variantId String, - key UInt32, - ) ENGINE = EmbeddedRocksDB() - PRIMARY KEY `variantId` - """, - ) - client.execute( - f""" - CREATE DICTIONARY {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` - ( - `key` UInt32, - `ac_wes` UInt16, - `ac_wgs` UInt16 - ) - PRIMARY KEY key - SOURCE( - CLICKHOUSE( - USER {Env.CLICKHOUSE_WRITER_USER} PASSWORD {Env.CLICKHOUSE_WRITER_PASSWORD} - DB {Env.CLICKHOUSE_DATABASE} TABLE `GRCh38/SNV_INDEL/gt_stats` - ) + cursor.execute( + f'INSERT INTO {Env.CLICKHOUSE_DATABASE}.`seqrdb_gene_ids_src` VALUES', + [('GENE1', 123), ('GENE2', 12), ('GENE3', 1)], ) - LIFETIME(0) - LAYOUT(FLAT(MAX_ARRAY_SIZE 10000)) - """, - ) - client.execute( - f""" - CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/reference_data/clinvar/all_variants` ( - `variantId` String, - `alleleId` Nullable(UInt32), - `pathogenicity` Enum8( - 'Pathogenic' = 0, - 'Pathogenic/Likely_pathogenic' = 1 + cursor.execute( + f""" + CREATE OR REPLACE DICTIONARY {Env.CLICKHOUSE_DATABASE}.seqrdb_gene_ids + ( + gene_id String, + seqrdb_id UInt32 ) + PRIMARY KEY gene_id + SOURCE(CLICKHOUSE( + USER {Env.CLICKHOUSE_WRITER_USER} PASSWORD {Env.CLICKHOUSE_WRITER_PASSWORD} + DB {Env.CLICKHOUSE_DATABASE} TABLE `seqrdb_gene_ids_src` + )) + LAYOUT(HASHED()) + LIFETIME(0); + """, ) - PRIMARY KEY `variantId` - """, - ) - client.execute( - f""" - CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/reference_data/clinvar/seqr_variants` ( - `key` UInt32, - `alleleId` Nullable(UInt32), - `pathogenicity` Enum8( - 'Pathogenic' = 0, - 'Pathogenic/Likely_pathogenic' = 1 - ) + cursor.execute( + f""" + CREATE TABLE IF NOT EXISTS {Env.CLICKHOUSE_DATABASE}.seqrdb_affected_status_dict_src ( + family_guid String, + sampleId String, + affected String + ) ENGINE = Memory; + """, ) - PRIMARY KEY `key` - """, - ) - client.execute( - f""" - CREATE MATERIALIZED VIEW {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/reference_data/clinvar/seqr_variants_to_search_mv` - REFRESH EVERY 10 YEAR ENGINE = Null - AS SELECT DISTINCT ON (key) * - FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/reference_data/clinvar/seqr_variants` - """, - ) - client.execute( - f""" - CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/entries` ( - `key` UInt32, - `project_guid` LowCardinality(String), - `family_guid` String, - `xpos` UInt64 CODEC(Delta(8), ZSTD(1)), - `sample_type` Enum8('WES' = 0, 'WGS' = 1), - `calls` Array( - Tuple( - sampleId String, - gt Nullable(Enum8('REF' = 0, 'HET' = 1, 'HOM' = 2)), - ) - ), - `sign` Int8, - PROJECTION xpos_projection + cursor.execute( + f""" + CREATE OR REPLACE DICTIONARY {Env.CLICKHOUSE_DATABASE}.seqrdb_affected_status_dict ( - SELECT * - ORDER BY xpos + family_guid String, + sampleId String, + affected String ) + PRIMARY KEY family_guid, sampleId + SOURCE(CLICKHOUSE( + USER {Env.CLICKHOUSE_WRITER_USER} PASSWORD {Env.CLICKHOUSE_WRITER_PASSWORD} + DB {Env.CLICKHOUSE_DATABASE} TABLE `seqrdb_affected_status_dict_src` + )) + LAYOUT(COMPLEX_KEY_HASHED()) + LIFETIME(0); + """, ) - ENGINE = CollapsingMergeTree(sign) - PARTITION BY project_guid - ORDER BY (project_guid, family_guid, key) - SETTINGS deduplicate_merge_projection_mode = 'rebuild'; - """, - ) - client.execute( - f""" - CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/variants_memory` ( - key UInt32, - variantId String, - ) ENGINE = EmbeddedRocksDB() - PRIMARY KEY `key` - """, - ) - client.execute( - f""" - CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/variants_disk` ( - key UInt32, - variantId String, - ) ENGINE = EmbeddedRocksDB() - PRIMARY KEY `key` - """, - ) - client.execute( - f""" - CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/key_lookup` ( - variantId String, - key UInt32, - ) ENGINE = EmbeddedRocksDB() - PRIMARY KEY `variantId` - """, - ) + + def setUp(self): + super().setUp() base_path = runs_path( ReferenceGenome.GRCh38, DatasetType.SNV_INDEL, @@ -365,7 +136,6 @@ def write_test_parquet(df: pd.DataFrame, parquet_path: str, schema=None): ), ) - # Variant Details Parquet df = pd.DataFrame( { 'key': [1, 2, 3, 4], @@ -387,7 +157,6 @@ def write_test_parquet(df: pd.DataFrame, parquet_path: str, schema=None): ), ) - # New Variants parquet. df = pd.DataFrame( { 'key': [10, 11, 12, 13], @@ -416,7 +185,6 @@ def write_test_parquet(df: pd.DataFrame, parquet_path: str, schema=None): ), ) - # New Entries Parquet df = pd.DataFrame( { 'key': [0, 3, 4], @@ -493,30 +261,6 @@ def write_test_parquet(df: pd.DataFrame, parquet_path: str, schema=None): schema.remove(5).remove(5), ) - def tearDown(self): - super().tearDown() - client = get_clickhouse_client() - client.execute( - f""" - DROP DICTIONARY IF EXISTS {Env.CLICKHOUSE_DATABASE}.seqrdb_gene_ids; - """, - ) - client.execute( - f""" - DROP DICTIONARY IF EXISTS {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/reference_data/gnomad_genomes`; - """, - ) - client.execute( - f""" - DROP DATABASE IF EXISTS {Env.CLICKHOUSE_DATABASE}; - """, - ) - client.execute( - f""" - DROP DATABASE IF EXISTS {STAGING_CLICKHOUSE_DATABASE}; - """, - ) - def test_get_clickhouse_client(self): client = get_clickhouse_client() result = client.execute('SELECT 1') @@ -557,47 +301,47 @@ def test_table_name_builder(self): ) def test_direct_insert_all_keys(self): - client = get_clickhouse_client() - client.execute( - f'INSERT INTO {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details` VALUES', - [(1, 'a', 'e'), (10, 'b', 'f'), (7, 'c', 'g')], - ) - direct_insert_all_keys( - ClickHouseTable.VARIANT_DETAILS, - TableNameBuilder( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ), - ) - ret = client.execute( - f'SELECT * FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', - ) - self.assertEqual( - ret, - [ - (1, '1-13-A-C', 'a'), - (2, '2-14-A-T', 'b'), - (3, 'Y-19-A-C', 'c'), - (4, 'M-12-C-G', 'd'), - (7, 'c', 'g'), - (10, 'b', 'f'), - ], - ) + with connections['clickhouse_write'].cursor() as cursor: + cursor.execute( + f'INSERT INTO {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details` VALUES', + [(1, 'a', 'e'), (10, 'b', 'f'), (7, 'c', 'g')], + ) + direct_insert_all_keys( + ClickHouseTable.VARIANT_DETAILS, + TableNameBuilder( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ) + cursor.execute( + f'SELECT * FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', + ) + self.assertEqual( + cursor.fetchall(), + [ + (1, '1-13-A-C', 'a'), + (2, '2-14-A-T', 'b'), + (3, 'Y-19-A-C', 'c'), + (4, 'M-12-C-G', 'd'), + (7, 'c', 'g'), + (10, 'b', 'f'), + ], + ) - # ensure multiple calls are idempotent - direct_insert_all_keys( - ClickHouseTable.VARIANT_DETAILS, - TableNameBuilder( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ), - ) - ret = client.execute( - f'SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', - ) - self.assertEqual(ret[0][0], 6) + # ensure multiple calls are idempotent + direct_insert_all_keys( + ClickHouseTable.VARIANT_DETAILS, + TableNameBuilder( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ) + cursor.execute( + f'SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', + ) + self.assertEqual(cursor.fetchone()[0], 6) @patch.object( ClickhouseReferenceDataset, @@ -605,372 +349,350 @@ def test_direct_insert_all_keys(self): return_value=[ClickhouseReferenceDataset.CLINVAR], ) def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): - # Tests individual components of the atomic_insert_entries - # to validate the state after each step. - client = get_clickhouse_client() - client.execute( - f""" - INSERT INTO {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` - VALUES - (0, 'project_a', 'family_a1', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_a1','HOM')], 1), - (1, 'project_a', 'family_a2', 123456789, 'WGS', 0, 0, CAST([] AS Array(UInt32)), [('sample_a2','HET')], 1), - (2, 'project_a', 'family_a3', 133456789, 'WGS', 0, 0, CAST([] AS Array(UInt32)), [('sample_a3','HOM')], 1), - (3, 'project_a', 'family_a4', 133456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_a4','REF')], 1), - (4, 'project_a', 'family_a5', 133456789, 'WES', 0, 1, CAST([0] AS Array(UInt32)), [('sample_a5','REF'),('sample_a6','HET'),('sample_a7','REF')], 1), - (4, 'project_a', 'family_a6', 133456789, 'WGS', 0, 0, CAST([] AS Array(UInt32)), [('sample_a8','HOM')], 1), - (0, 'project_b', 'family_b1', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b4','REF')], 1), - (1, 'project_b', 'family_b2', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b5','HET')], 1), - (2, 'project_b', 'family_b2', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b5','REF')], 1), - (3, 'project_b', 'family_b3', 133456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b6','HOM')], 1), - (4, 'project_b', 'family_b3', 133456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b6','HOM')], 1), - (0, 'project_c', 'family_c1', 123456789, 'WES', 0, 1, CAST([1] AS Array(UInt32)), [('sample_c7','REF')], 1), - (3, 'project_c', 'family_c2', 123456789, 'WES', 0, 1, CAST([1] AS Array(UInt32)), [('sample_c8','REF')], 1), - (4, 'project_c', 'family_c3', 133456789, 'WES', 0, 1, CAST([1] AS Array(UInt32)), [('sample_c9','HOM')], 1), - (5, 'project_c', 'family_c4', 133456789, 'WES', 0, 1, CAST([1] AS Array(UInt32)), [('sample_c9','HOM')], 1) - """, - ) - table_name_builder = TableNameBuilder( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ) - create_staging_tables( - table_name_builder, - ClickHouseTable.for_dataset_type_atomic_entries_update( - DatasetType.SNV_INDEL, - ), - ) - create_staging_materialized_views( - table_name_builder, - ClickHouseMaterializedView.for_dataset_type_atomic_entries_update( - DatasetType.SNV_INDEL, - ), - ) - stage_existing_project_partitions( - table_name_builder, - [ - 'project_a', - 'project_b', - 'project_d', # Partition does not exist already. - ], - ClickHouseTable.for_dataset_type_atomic_entries_update_project_partitioned( - DatasetType.SNV_INDEL, - ), - ) - staged_projects = client.execute( - f""" - SELECT DISTINCT project_guid FROM {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/entries` - """, - ) - self.assertCountEqual( - [p[0] for p in staged_projects], - ['project_a', 'project_b'], - ) - staged_project_gt_stats = client.execute( - f""" - SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) - FROM - {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/project_gt_stats` - GROUP BY project_guid, key, sample_type - """, - ) - self.assertCountEqual( - staged_project_gt_stats, - [ - ('project_a', 0, 'WES', 0, 1), - ('project_a', 1, 'WGS', 1, 0), - ('project_a', 2, 'WGS', 0, 1), - ('project_a', 4, 'WES', 1, 0), - ('project_a', 4, 'WGS', 0, 1), - ('project_b', 1, 'WES', 1, 0), - ('project_b', 3, 'WES', 0, 1), - ('project_b', 4, 'WES', 0, 1), - # project_gt_stats stages all projects, not just - # those requested for loading. - ('project_c', 4, 'WES', 0, 1), - ('project_c', 5, 'WES', 0, 1), - ], - ) - delete_existing_families_from_staging_entries( - table_name_builder, - ['family_a1', 'family_a5', 'family_a6'], - ) - staged_project_gt_stats = client.execute( - f""" - SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) - FROM - {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/project_gt_stats` - GROUP BY project_guid, key, sample_type - """, - ) - self.assertCountEqual( - staged_project_gt_stats, - [ - ('project_a', 0, 'WES', 0, 0), - ('project_a', 1, 'WGS', 1, 0), - ('project_a', 2, 'WGS', 0, 1), - ('project_a', 4, 'WES', 0, 0), - ('project_a', 4, 'WGS', 0, 0), - ('project_b', 1, 'WES', 1, 0), - ('project_b', 3, 'WES', 0, 1), - ('project_b', 4, 'WES', 0, 1), - ('project_c', 4, 'WES', 0, 1), - ('project_c', 5, 'WES', 0, 1), - ], - ) - insert_new_entries(table_name_builder) - optimize_entries( - table_name_builder, - ['project_a', 'project_b', 'project_c'], - ) - staged_project_gt_stats = client.execute( - f""" - SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) - FROM - {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/project_gt_stats` - GROUP BY project_guid, key, sample_type - """, - ) - self.assertCountEqual( - staged_project_gt_stats, - [ - ('project_a', 0, 'WES', 0, 0), - ('project_a', 1, 'WGS', 1, 0), - ('project_a', 2, 'WGS', 0, 1), - ('project_a', 4, 'WES', 0, 0), - ('project_a', 4, 'WGS', 0, 0), - ('project_b', 1, 'WES', 1, 0), - ('project_b', 3, 'WES', 0, 1), - ('project_b', 4, 'WES', 0, 1), - ('project_c', 4, 'WES', 0, 1), - ('project_c', 5, 'WES', 0, 1), - ('project_d', 0, 'WES', 0, 1), - ('project_d', 4, 'WES', 1, 0), - ], - ) - refresh_materialized_views( - table_name_builder, - ClickHouseMaterializedView.for_dataset_type_atomic_entries_update_refreshable( - DatasetType.SNV_INDEL, - ), - staging=True, - ) - replace_project_partitions( - table_name_builder, - ClickHouseTable.for_dataset_type_atomic_entries_update_project_partitioned( + # Tests individual components of atomic_insert_entries, validating state after each step. + with connections['clickhouse_write'].cursor() as cursor: + table_name_builder = TableNameBuilder( + ReferenceGenome.GRCh38, DatasetType.SNV_INDEL, - ), - ['project_a', 'project_d'], - ) - new_entries = client.execute( - f""" - SELECT COLUMNS('.*') EXCEPT(is_annotated_in_any_gene, is_gnomad_gt_5_percent) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` - """, - ) - self.assertCountEqual( - new_entries, - [ - ( - 0, - 'project_b', - 'family_b1', - 123456789, - 'WES', - [], - [('sample_b4', 'REF')], - 1, - ), - ( - 1, - 'project_b', - 'family_b2', - 123456789, - 'WES', - [], - [('sample_b5', 'HET')], - 1, - ), - ( - 2, - 'project_b', - 'family_b2', - 123456789, - 'WES', - [], - [('sample_b5', 'REF')], - 1, - ), - ( - 3, - 'project_b', - 'family_b3', - 133456789, - 'WES', - [], - [('sample_b6', 'HOM')], - 1, - ), - ( - 4, - 'project_b', - 'family_b3', - 133456789, - 'WES', - [], - [('sample_b6', 'HOM')], - 1, - ), - ( - 1, - 'project_a', - 'family_a2', - 123456789, - 'WGS', - [], - [('sample_a2', 'HET')], - 1, + TEST_RUN_ID, + ) + create_staging_tables( + table_name_builder, + ClickHouseTable.for_dataset_type_atomic_entries_update( + DatasetType.SNV_INDEL, ), - ( - 2, - 'project_a', - 'family_a3', - 133456789, - 'WGS', - [], - [('sample_a3', 'HOM')], - 1, + ) + create_staging_materialized_views( + table_name_builder, + ClickHouseMaterializedView.for_dataset_type_atomic_entries_update( + DatasetType.SNV_INDEL, ), - ( - 3, + ) + stage_existing_project_partitions( + table_name_builder, + [ 'project_a', - 'family_a4', - 133456789, - 'WES', - [], - [('sample_a4', 'REF')], - 1, - ), - ( - 0, - 'project_d', - 'family_d1', - 123456789, - 'WES', - [], - [('sample_d1', 'REF'), ('sample_d11', 'HOM')], - 1, - ), - ( - 3, - 'project_d', - 'family_d2', - 123456789, - 'WES', - [123, 12], - [('sample_d2', 'REF')], - 1, - ), - ( - 4, - 'project_d', - 'family_d3', - 123456789, - 'WES', - [1], - [('sample_d3', 'HET')], - 1, - ), - ( - 0, - 'project_c', - 'family_c1', - 123456789, - 'WES', - [1], - [('sample_c7', 'REF')], - 1, + 'project_b', + 'project_d', # Partition does not exist already. + ], + ClickHouseTable.for_dataset_type_atomic_entries_update_project_partitioned( + DatasetType.SNV_INDEL, ), - ( - 3, - 'project_c', - 'family_c2', - 123456789, - 'WES', - [1], - [('sample_c8', 'REF')], - 1, + ) + cursor.execute( + f""" + SELECT DISTINCT project_guid FROM {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/entries` + """, + ) + self.assertCountEqual( + [p[0] for p in cursor.fetchall()], + ['project_a', 'project_b'], + ) + cursor.execute( + f""" + SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) + FROM + {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/project_gt_stats` + GROUP BY project_guid, key, sample_type + """, + ) + self.assertCountEqual( + cursor.fetchall(), + [ + ('project_a', 0, 'WES', 0, 1), + ('project_a', 1, 'WGS', 1, 0), + ('project_a', 2, 'WGS', 0, 1), + ('project_a', 4, 'WES', 1, 0), + ('project_a', 4, 'WGS', 0, 1), + ('project_b', 1, 'WES', 1, 0), + ('project_b', 3, 'WES', 0, 1), + ('project_b', 4, 'WES', 0, 1), + # project_gt_stats stages all projects, not just + # those requested for loading. + ('project_c', 4, 'WES', 0, 1), + ('project_c', 5, 'WES', 0, 1), + ], + ) + delete_existing_families_from_staging_entries( + table_name_builder, + ['family_a1', 'family_a5', 'family_a6'], + ) + cursor.execute( + f""" + SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) + FROM + {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/project_gt_stats` + GROUP BY project_guid, key, sample_type + """, + ) + self.assertCountEqual( + cursor.fetchall(), + [ + ('project_a', 0, 'WES', 0, 0), + ('project_a', 1, 'WGS', 1, 0), + ('project_a', 2, 'WGS', 0, 1), + ('project_a', 4, 'WES', 0, 0), + ('project_a', 4, 'WGS', 0, 0), + ('project_b', 1, 'WES', 1, 0), + ('project_b', 3, 'WES', 0, 1), + ('project_b', 4, 'WES', 0, 1), + ('project_c', 4, 'WES', 0, 1), + ('project_c', 5, 'WES', 0, 1), + ], + ) + insert_new_entries(table_name_builder) + optimize_entries( + table_name_builder, + ['project_a', 'project_b', 'project_c'], + ) + cursor.execute( + f""" + SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) + FROM + {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/project_gt_stats` + GROUP BY project_guid, key, sample_type + """, + ) + self.assertCountEqual( + cursor.fetchall(), + [ + ('project_a', 0, 'WES', 0, 0), + ('project_a', 1, 'WGS', 1, 0), + ('project_a', 2, 'WGS', 0, 1), + ('project_a', 4, 'WES', 0, 0), + ('project_a', 4, 'WGS', 0, 0), + ('project_b', 1, 'WES', 1, 0), + ('project_b', 3, 'WES', 0, 1), + ('project_b', 4, 'WES', 0, 1), + ('project_c', 4, 'WES', 0, 1), + ('project_c', 5, 'WES', 0, 1), + ('project_d', 0, 'WES', 0, 1), + ('project_d', 4, 'WES', 1, 0), + ], + ) + refresh_materialized_views( + table_name_builder, + ClickHouseMaterializedView.for_dataset_type_atomic_entries_update_refreshable( + DatasetType.SNV_INDEL, ), - ( - 4, - 'project_c', - 'family_c3', - 133456789, - 'WES', - [1], - [('sample_c9', 'HOM')], - 1, + staging=True, + ) + replace_project_partitions( + table_name_builder, + ClickHouseTable.for_dataset_type_atomic_entries_update_project_partitioned( + DatasetType.SNV_INDEL, ), - ( - 5, - 'project_c', - 'family_c4', - 133456789, - 'WES', - [1], - [('sample_c9', 'HOM')], - 1, + ['project_a', 'project_d'], + ) + cursor.execute( + f""" + SELECT COLUMNS('.*') EXCEPT(is_annotated_in_any_gene, is_gnomad_gt_5_percent) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` + """, + ) + self.assertCountEqual( + cursor.fetchall(), + [ + ( + 0, + 'project_b', + 'family_b1', + 123456789, + 'WES', + [], + [('sample_b4', 'REF')], + 1, + ), + ( + 1, + 'project_b', + 'family_b2', + 123456789, + 'WES', + [], + [('sample_b5', 'HET')], + 1, + ), + ( + 2, + 'project_b', + 'family_b2', + 123456789, + 'WES', + [], + [('sample_b5', 'REF')], + 1, + ), + ( + 3, + 'project_b', + 'family_b3', + 133456789, + 'WES', + [], + [('sample_b6', 'HOM')], + 1, + ), + ( + 4, + 'project_b', + 'family_b3', + 133456789, + 'WES', + [], + [('sample_b6', 'HOM')], + 1, + ), + ( + 1, + 'project_a', + 'family_a2', + 123456789, + 'WGS', + [], + [('sample_a2', 'HET')], + 1, + ), + ( + 2, + 'project_a', + 'family_a3', + 133456789, + 'WGS', + [], + [('sample_a3', 'HOM')], + 1, + ), + ( + 3, + 'project_a', + 'family_a4', + 133456789, + 'WES', + [], + [('sample_a4', 'REF')], + 1, + ), + ( + 0, + 'project_d', + 'family_d1', + 123456789, + 'WES', + [], + [('sample_d1', 'REF'), ('sample_d11', 'HOM')], + 1, + ), + ( + 3, + 'project_d', + 'family_d2', + 123456789, + 'WES', + [123, 12], + [('sample_d2', 'REF')], + 1, + ), + ( + 4, + 'project_d', + 'family_d3', + 123456789, + 'WES', + [1], + [('sample_d3', 'HET')], + 1, + ), + ( + 0, + 'project_c', + 'family_c1', + 123456789, + 'WES', + [1], + [('sample_c7', 'REF')], + 1, + ), + ( + 3, + 'project_c', + 'family_c2', + 123456789, + 'WES', + [1], + [('sample_c8', 'REF')], + 1, + ), + ( + 4, + 'project_c', + 'family_c3', + 133456789, + 'WES', + [1], + [('sample_c9', 'HOM')], + 1, + ), + ( + 5, + 'project_c', + 'family_c4', + 133456789, + 'WES', + [1], + [('sample_c9', 'HOM')], + 1, + ), + ], + ) + cursor.execute( + f""" + SELECT * + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` + """, + ) + self.assertCountEqual( + cursor.fetchall(), + [], + ) + exchange_tables( + table_name_builder, + ClickHouseTable.for_dataset_type_atomic_entries_update_unpartitioned( + DatasetType.SNV_INDEL, ), - ], - ) - existing_gt_stats = client.execute( - f""" - SELECT * - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` - """, - ) - self.assertCountEqual( - existing_gt_stats, - [], - ) - exchange_tables( - table_name_builder, - ClickHouseTable.for_dataset_type_atomic_entries_update_unpartitioned( - DatasetType.SNV_INDEL, - ), - ) - new_gt_stats = client.execute( - f""" - SELECT * - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` - """, - ) - self.assertCountEqual(new_gt_stats, []) - reload_dictionaries( - table_name_builder, - ClickHouseDictionary.for_dataset_type(DatasetType.SNV_INDEL), - ) - new_gt_stats_post_reload = client.execute( - f""" - SELECT * - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` - """, - ) - self.assertEqual( - new_gt_stats_post_reload, - [ - (0, 2, 0), - (1, 1, 1), - (2, 0, 2), - (3, 2, 0), - (4, 5, 0), - (5, 2, 0), - ], - ) + ) + cursor.execute( + f""" + SELECT * + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` + """, + ) + self.assertCountEqual(cursor.fetchall(), []) + reload_dictionaries( + table_name_builder, + ClickHouseDictionary.for_dataset_type(DatasetType.SNV_INDEL), + ) + cursor.execute( + f""" + SELECT * + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` + """, + ) + self.assertEqual( + cursor.fetchall(), + [ + (0, 2, 0), + (1, 1, 1), + (2, 0, 2), + (3, 2, 0), + (4, 5, 0), + (5, 2, 0), + ], + ) @patch.object( ClickhouseReferenceDataset, @@ -985,82 +707,82 @@ def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_typ ['project_d'], ['family_d1', 'family_d2'], ) - client = get_clickhouse_client() - project_gt_stats = client.execute( - f""" - SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` - GROUP BY project_guid, key, sample_type - """, - ) - self.assertCountEqual( - project_gt_stats, - [ - ('project_d', 0, 'WES', 0, 1), - ('project_d', 4, 'WES', 1, 0), - ], - ) - gt_stats = client.execute( - f""" - SELECT * - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` - """, - ) - self.assertCountEqual( - gt_stats, - [ - (0, 2, 0), - (4, 1, 0), - ], - ) - gt_stats_dict = client.execute( - f""" - SELECT * - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` - """, - ) - self.assertCountEqual( - gt_stats_dict, - [ - (0, 2, 0), - (4, 1, 0), - ], - ) - variants_memory = client.execute( - f""" - SELECT * - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` - """, - ) - self.assertCountEqual( - variants_memory, - [ - (10, '1-3-A-C'), - (11, '2-4-A-T'), - (12, 'Y-9-A-C'), - (13, 'M-2-C-G'), - ], - ) - variants_disk = client.execute( - f""" - SELECT * - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_disk` - """, - ) - self.assertCountEqual( - variants_disk, - [ - (10, '1-3-A-C'), - (11, '2-4-A-T'), - (12, 'Y-9-A-C'), - (13, 'M-2-C-G'), - ], - ) + with connections['clickhouse_write'].cursor() as cursor: + cursor.execute( + f""" + SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + GROUP BY project_guid, key, sample_type + """, + ) + self.assertCountEqual( + cursor.fetchall(), + [ + ('project_d', 0, 'WES', 0, 1), + ('project_d', 4, 'WES', 1, 0), + ], + ) + cursor.execute( + f""" + SELECT * + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` + """, + ) + self.assertCountEqual( + cursor.fetchall(), + [ + (0, 2, 0), + (4, 1, 0), + ], + ) + cursor.execute( + f""" + SELECT * + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` + """, + ) + self.assertCountEqual( + cursor.fetchall(), + [ + (0, 2, 0), + (4, 1, 0), + ], + ) + cursor.execute( + f""" + SELECT * + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` + """, + ) + self.assertCountEqual( + cursor.fetchall(), + [ + (10, '1-3-A-C'), + (11, '2-4-A-T'), + (12, 'Y-9-A-C'), + (13, 'M-2-C-G'), + ], + ) + cursor.execute( + f""" + SELECT * + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_disk` + """, + ) + self.assertCountEqual( + cursor.fetchall(), + [ + (10, '1-3-A-C'), + (11, '2-4-A-T'), + (12, 'Y-9-A-C'), + (13, 'M-2-C-G'), + ], + ) def test_load_complete_gcnv(self): load_complete_run( @@ -1070,39 +792,39 @@ def test_load_complete_gcnv(self): ['project_d'], ['family_d1', 'family_d2'], ) - client = get_clickhouse_client() - variants_disk_count = client.execute( - f""" - SELECT COUNT(*) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/variants_memory` - """, - )[0][0] - self.assertEqual(variants_disk_count, 4) - variants_disk_count = client.execute( - f""" - SELECT COUNT(*) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/variants_disk` - """, - )[0][0] - self.assertEqual(variants_disk_count, 4) - key_lookup_count = client.execute( - f""" - SELECT COUNT(*) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/key_lookup` - """, - )[0][0] - self.assertEqual(key_lookup_count, 4) - entries_count = client.execute( - f""" - SELECT COUNT(*) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/entries` - """, - )[0][0] - self.assertEqual(entries_count, 3) + with connections['clickhouse_write'].cursor() as cursor: + cursor.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/variants_memory` + """, + ) + self.assertEqual(cursor.fetchone()[0], 4) + cursor.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/variants_disk` + """, + ) + self.assertEqual(cursor.fetchone()[0], 4) + cursor.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/key_lookup` + """, + ) + self.assertEqual(cursor.fetchone()[0], 4) + cursor.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/entries` + """, + ) + self.assertEqual(cursor.fetchone()[0], 3) def test_delete_families(self): table_name_builder = TableNameBuilder( @@ -1110,90 +832,69 @@ def test_delete_families(self): DatasetType.SNV_INDEL, TEST_RUN_ID, ) - client = get_clickhouse_client() - client.execute( - f""" - INSERT INTO {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` - VALUES - (0, 'project_a', 'family_a1', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_a1','HOM')], 1), - (1, 'project_a', 'family_a2', 123456789, 'WGS', 0, 0, CAST([] AS Array(UInt32)), [('sample_a2','HET')], 1), - (2, 'project_a', 'family_a3', 133456789, 'WGS', 0, 0, CAST([] AS Array(UInt32)), [('sample_a3','HOM')], 1), - (3, 'project_a', 'family_a4', 133456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_a4','REF')], 1), - (4, 'project_a', 'family_a5', 133456789, 'WES', 0, 1, CAST([0] AS Array(UInt32)), [('sample_a5','REF'),('sample_a6','HET'),('sample_a7','REF')], 1), - (4, 'project_a', 'family_a6', 133456789, 'WGS', 0, 0, CAST([] AS Array(UInt32)), [('sample_a8','HOM')], 1), - (0, 'project_b', 'family_b1', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b4','REF')], 1), - (1, 'project_b', 'family_b2', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b5','HET')], 1), - (2, 'project_b', 'family_b2', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b5','REF')], 1), - (3, 'project_b', 'family_b3', 133456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b6','HOM')], 1), - (4, 'project_b', 'family_b3', 133456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b6','HOM')], 1), - (0, 'project_c', 'family_c1', 123456789, 'WES', 0, 1, CAST([1] AS Array(UInt32)), [('sample_c7','REF')], 1), - (3, 'project_c', 'family_c2', 123456789, 'WES', 0, 1, CAST([1] AS Array(UInt32)), [('sample_c8','REF')], 1), - (4, 'project_c', 'family_c3', 133456789, 'WES', 0, 1, CAST([1] AS Array(UInt32)), [('sample_c9','HOM')], 1), - (5, 'project_c', 'family_c4', 133456789, 'WES', 0, 1, CAST([1] AS Array(UInt32)), [('sample_c9','HOM')], 1) - """, - ) - project_gt_stats = client.execute( - f""" - SELECT project_guid, sum(het_samples), sum(hom_samples) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` - GROUP BY project_guid - """, - ) - self.assertCountEqual( - project_gt_stats, - [('project_a', 2, 3), ('project_c', 0, 2), ('project_b', 1, 2)], - ) - refresh_materialized_views( - table_name_builder, - ClickHouseMaterializedView.for_dataset_type_atomic_entries_update_refreshable( + with connections['clickhouse_write'].cursor() as cursor: + cursor.execute( + f""" + SELECT project_guid, sum(het_samples), sum(hom_samples) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + GROUP BY project_guid + """, + ) + self.assertCountEqual( + cursor.fetchall(), + [('project_a', 2, 3), ('project_c', 0, 2), ('project_b', 1, 2)], + ) + refresh_materialized_views( + table_name_builder, + ClickHouseMaterializedView.for_dataset_type_atomic_entries_update_refreshable( + DatasetType.SNV_INDEL, + ), + staging=False, + ) + cursor.execute( + f""" + SELECT sum(ac_wes) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` + """, + ) + self.assertCountEqual(cursor.fetchall(), [(12,)]) + delete_family_guids( + ReferenceGenome.GRCh38, DatasetType.SNV_INDEL, - ), - staging=False, - ) - gt_stats = client.execute( - f""" - SELECT sum(ac_wes) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` - """, - ) - self.assertCountEqual(gt_stats, [(12,)]) - delete_family_guids( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - 'project_a', - ['family_a1', 'family_a2'], - ) - project_gt_stats = client.execute( - f""" - SELECT project_guid, sum(het_samples), sum(hom_samples) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` - GROUP BY project_guid - """, - ) - self.assertCountEqual( - project_gt_stats, - [('project_a', 1, 2), ('project_c', 0, 2), ('project_b', 1, 2)], - ) - gt_stats = client.execute( - f""" - SELECT sum(ac_wes) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` - """, - ) - self.assertCountEqual(gt_stats, [(10,)]) - gt_stats_dict = client.execute( - f""" - SELECT sum(ac_wes) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` - """, - ) - self.assertCountEqual(gt_stats_dict, [(10,)]) + TEST_RUN_ID, + 'project_a', + ['family_a1', 'family_a2'], + ) + cursor.execute( + f""" + SELECT project_guid, sum(het_samples), sum(hom_samples) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + GROUP BY project_guid + """, + ) + self.assertCountEqual( + cursor.fetchall(), + [('project_a', 1, 2), ('project_c', 0, 2), ('project_b', 1, 2)], + ) + cursor.execute( + f""" + SELECT sum(ac_wes) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` + """, + ) + self.assertCountEqual(cursor.fetchall(), [(10,)]) + cursor.execute( + f""" + SELECT sum(ac_wes) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` + """, + ) + self.assertCountEqual(cursor.fetchall(), [(10,)]) def test_rebuild_gt_stats(self): table_name_builder = TableNameBuilder( @@ -1201,82 +902,73 @@ def test_rebuild_gt_stats(self): DatasetType.SNV_INDEL, TEST_RUN_ID, ) - client = get_clickhouse_client() - client.execute( - f""" - INSERT INTO {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` - VALUES - (0, 'project_a', 'family_a1', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_a1','HOM')], 1), - (1, 'project_a', 'family_a2', 123456789, 'WGS', 0, 0, CAST([] AS Array(UInt32)), [('sample_a2','HET')], 1), - (2, 'project_a', 'family_a3', 133456789, 'WGS', 0, 0, CAST([] AS Array(UInt32)), [('sample_a3','HOM')], 1), - (3, 'project_a', 'family_a4', 133456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_a4','REF')], 1), - (4, 'project_a', 'family_a5', 133456789, 'WES', 0, 1, CAST([] AS Array(UInt32)), [('sample_a5','REF'),('sample_a6','HET'),('sample_a7','REF')], 1), - (4, 'project_a', 'family_a6', 133456789, 'WGS', 0, 0, CAST([] AS Array(UInt32)), [('sample_a8','HOM')], 1), - (0, 'project_b', 'family_b1', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b4','REF')], 1), - (1, 'project_b', 'family_b2', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b5','HET')], 1), - (2, 'project_b', 'family_b2', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b5','REF')], 1), - """, - ) - logged_query( # DROP the partition from the non-staging entries to as a non-mv-impacting change. - f""" - ALTER TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` - DROP PARTITION %(project_guid)s - """, - {'project_guid': 'project_a'}, - ) - project_gt_stats = client.execute( - f""" - SELECT project_guid, sum(het_samples), sum(hom_samples) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` - GROUP BY project_guid - """, - ) - self.assertCountEqual( - project_gt_stats, - [('project_a', 2, 3), ('project_b', 1, 0)], - ) - refresh_materialized_views( - table_name_builder, - ClickHouseMaterializedView.for_dataset_type_atomic_entries_update_refreshable( + with connections['clickhouse_write'].cursor() as cursor: + logged_query( # DROP the partition from the non-staging entries to as a non-mv-impacting change. + f""" + ALTER TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` + DROP PARTITION (%(project_guid)s, %(partition_id)s) + """, + # project_partitions_dict has no row for project_a, so n_partitions (and thus + # partition_id) defaults to 0. + {'project_guid': 'project_a', 'partition_id': 0}, + ) + cursor.execute( + f""" + SELECT project_guid, sum(het_samples), sum(hom_samples) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + WHERE project_guid IN ('project_a', 'project_b') + GROUP BY project_guid + """, + ) + self.assertCountEqual( + cursor.fetchall(), + [('project_a', 2, 3), ('project_b', 1, 2)], + ) + refresh_materialized_views( + table_name_builder, + ClickHouseMaterializedView.for_dataset_type_atomic_entries_update_refreshable( + DatasetType.SNV_INDEL, + ), + staging=False, + ) + cursor.execute( + f""" + SELECT sum(ac_wes), sum(ac_wgs) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` + """, + ) + # gt_stats has no project dimension (keyed globally by `key`), so project_c's rows + # (sharing key values with project_a/b in the fixture) also contribute here. + self.assertCountEqual(cursor.fetchall(), [(12, 5)]) + rebuild_gt_stats( + ReferenceGenome.GRCh38, DatasetType.SNV_INDEL, - ), - staging=False, - ) - gt_stats = client.execute( - f""" - SELECT sum(ac_wes), sum(ac_wgs) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` - """, - ) - self.assertCountEqual(gt_stats, [(4, 5)]) - rebuild_gt_stats( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ['project_a', 'project_b'], - ) - project_gt_stats = client.execute( - f""" - SELECT project_guid, sum(het_samples), sum(hom_samples) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` - GROUP BY project_guid - """, - ) - self.assertCountEqual( - project_gt_stats, - [('project_b', 1, 0)], - ) - gt_stats = client.execute( - f""" - SELECT sum(ac_wes), sum(ac_wgs) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` - """, - ) - self.assertCountEqual(gt_stats, [(1, 0)]) + TEST_RUN_ID, + ['project_a', 'project_b'], + ) + cursor.execute( + f""" + SELECT project_guid, sum(het_samples), sum(hom_samples) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + WHERE project_guid IN ('project_a', 'project_b') + GROUP BY project_guid + """, + ) + self.assertCountEqual( + cursor.fetchall(), + [('project_b', 1, 2)], + ) + cursor.execute( + f""" + SELECT sum(ac_wes), sum(ac_wgs) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` + """, + ) + self.assertCountEqual(cursor.fetchall(), [(9, 0)]) @patch.object( ClickhouseReferenceDataset, @@ -1284,55 +976,55 @@ def test_rebuild_gt_stats(self): return_value=[ClickhouseReferenceDataset.CLINVAR], ) def test_repartitioned_entries_table(self, mock_for_reference_genome_dataset_type): - client = get_clickhouse_client() - client.execute( - f""" - REPLACE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` ( - `key` UInt32, - `project_guid` LowCardinality(String), - `family_guid` String, - `xpos` UInt64 CODEC(Delta(8), ZSTD(1)), - `sample_type` Enum8('WES' = 0, 'WGS' = 1), - `is_gnomad_gt_5_percent` Boolean, - `is_annotated_in_any_gene` Boolean DEFAULT length(geneId_ids) > 0, - `geneId_ids` Array(UInt32), - `calls` Array( - Tuple( - sampleId String, - gt Nullable(Enum8('REF' = 0, 'HET' = 1, 'HOM' = 2)), + with connections['clickhouse_write'].cursor() as cursor: + cursor.execute( + f""" + REPLACE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` ( + `key` UInt32, + `project_guid` LowCardinality(String), + `family_guid` String, + `xpos` UInt64 CODEC(Delta(8), ZSTD(1)), + `sample_type` Enum8('WES' = 0, 'WGS' = 1), + `is_gnomad_gt_5_percent` Boolean, + `is_annotated_in_any_gene` Boolean DEFAULT length(geneId_ids) > 0, + `geneId_ids` Array(UInt32), + `calls` Array( + Tuple( + sampleId String, + gt Nullable(Enum8('REF' = 0, 'HET' = 1, 'HOM' = 2)), + ) + ), + `sign` Int8, + `n_partitions` UInt8 MATERIALIZED 2, + `partition_id` UInt8 MATERIALIZED farmHash64(family_guid) % n_partitions, + PROJECTION xpos_projection + ( + SELECT * + ORDER BY is_annotated_in_any_gene, xpos ) - ), - `sign` Int8, - `n_partitions` UInt8 MATERIALIZED 2, - `partition_id` UInt8 MATERIALIZED farmHash64(family_guid) % n_partitions, - PROJECTION xpos_projection - ( - SELECT * - ORDER BY is_annotated_in_any_gene, xpos ) + ENGINE = CollapsingMergeTree(sign) + PARTITION BY (project_guid, partition_id) + ORDER BY (project_guid, family_guid, key) + SETTINGS deduplicate_merge_projection_mode = 'rebuild'; + """, + ) + load_complete_run( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ['project_d'], + ['family_d1', 'family_d2', 'family_d3'], + ) + cursor.execute( + f""" + SELECT project_guid, sum(het_samples), sum(hom_samples) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + GROUP BY project_guid + """, + ) + self.assertCountEqual( + cursor.fetchall(), + [('project_d', 1, 1)], ) - ENGINE = CollapsingMergeTree(sign) - PARTITION BY (project_guid, partition_id) - ORDER BY (project_guid, family_guid, key) - SETTINGS deduplicate_merge_projection_mode = 'rebuild'; - """, - ) - load_complete_run( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ['project_d'], - ['family_d1', 'family_d2', 'family_d3'], - ) - project_gt_stats = client.execute( - f""" - SELECT project_guid, sum(het_samples), sum(hom_samples) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` - GROUP BY project_guid - """, - ) - self.assertCountEqual( - project_gt_stats, - [('project_d', 1, 1)], - ) diff --git a/loading_pipeline/lib/test/clickhouse_django/seqr/__init__.py b/loading_pipeline/lib/test/clickhouse_django/seqr/__init__.py index d88b462a89..2beff72da3 100644 --- a/loading_pipeline/lib/test/clickhouse_django/seqr/__init__.py +++ b/loading_pipeline/lib/test/clickhouse_django/seqr/__init__.py @@ -1,6 +1,6 @@ """Stub of the main app's `seqr` package, shadowing it on sys.path (see settings.py's docstring). -`clickhouse_search`'s migrations need `SeqrLogger` (utils/logging_utils.py) and a specific `seqr` -migration name to exist, but not the real app - which imports guardian/postgres/social_django via -seqr/models.py. This stub avoids that weight. +`clickhouse_search` needs a specific `seqr` migration name to exist, but not the real app - which +imports guardian/postgres/social_django via seqr/models.py. This stub avoids that weight; +seqr/utils/__init__.py falls through to the real seqr/utils/ for submodules that don't need it. """ diff --git a/loading_pipeline/lib/test/clickhouse_django/seqr/utils/__init__.py b/loading_pipeline/lib/test/clickhouse_django/seqr/utils/__init__.py index e69de29bb2..4cc45c1a59 100644 --- a/loading_pipeline/lib/test/clickhouse_django/seqr/utils/__init__.py +++ b/loading_pipeline/lib/test/clickhouse_django/seqr/utils/__init__.py @@ -0,0 +1,4 @@ +import os + +# Falls through to the real seqr/utils/ for anything not stubbed in this directory. +__path__.append(os.path.join(os.path.dirname(__file__), '..', '..', '..', '..', '..', '..', 'seqr', 'utils')) diff --git a/loading_pipeline/lib/test/clickhouse_django/seqr/utils/logging_utils.py b/loading_pipeline/lib/test/clickhouse_django/seqr/utils/logging_utils.py deleted file mode 100644 index f27d813bbb..0000000000 --- a/loading_pipeline/lib/test/clickhouse_django/seqr/utils/logging_utils.py +++ /dev/null @@ -1,25 +0,0 @@ -# Mirrors the real seqr.utils.logging_utils.SeqrLogger (dependency-free) - see seqr/__init__.py. -import logging -from typing import Optional - - -class SeqrLogger(object): - - def __init__(self, name: Optional[str] = None) -> None: - """Custom logger which requires user metadata to be included in the log.""" - self._logger = logging.getLogger(name) - - def _log(self, level, message, user, **kwargs): - self._logger.log(level, message, extra=dict(user=user, **kwargs)) - - def debug(self, *args, **kwargs): - self._log(logging.DEBUG, *args, **kwargs) - - def info(self, *args, **kwargs): - self._log(logging.INFO, *args, **kwargs) - - def warning(self, *args, **kwargs): - self._log(logging.WARNING, *args, **kwargs) - - def error(self, *args, **kwargs): - self._log(logging.ERROR, *args, **kwargs) diff --git a/loading_pipeline/lib/test/clickhouse_django/settings.py b/loading_pipeline/lib/test/clickhouse_django/settings.py index fa74d6173f..5af22fd624 100644 --- a/loading_pipeline/lib/test/clickhouse_django/settings.py +++ b/loading_pipeline/lib/test/clickhouse_django/settings.py @@ -8,6 +8,10 @@ import os +# Shared Django fixtures (loaddata) for clickhouse_search-backed test data - see +# lib/test/clickhouse_schema_testcase.py. +FIXTURE_DIRS = [os.path.join(os.path.dirname(__file__), '..', 'fixtures')] + INSTALLED_APPS = [ 'clickhouse_backend', 'seqr', # stub package (see seqr/__init__.py), not the real app diff --git a/loading_pipeline/lib/test/clickhouse_schema_testcase.py b/loading_pipeline/lib/test/clickhouse_schema_testcase.py index b01277fe10..8799f2d9a4 100644 --- a/loading_pipeline/lib/test/clickhouse_schema_testcase.py +++ b/loading_pipeline/lib/test/clickhouse_schema_testcase.py @@ -16,6 +16,7 @@ def _fixture_teardown(self): """ SELECT name FROM system.tables WHERE database = %(database)s AND engine NOT IN ('Dictionary', 'MaterializedView') + AND name != 'django_migrations' """, {'database': Env.CLICKHOUSE_DATABASE}, ) diff --git a/reference_data/models.py b/reference_data/models.py index 9b28505aad..4c68cc23e0 100644 --- a/reference_data/models.py +++ b/reference_data/models.py @@ -12,6 +12,7 @@ from reference_data.utils.dbnsfp_utils import DBNSFP_FIELD_MAP, DBNSFP_EXCLUDE_FIELDS from reference_data.utils.download_utils import download_file from reference_data.utils.gencode_utils import parse_gencode_record, GENCODE_URL_TEMPLATE, GENCODE_FILE_HEADER +from seqr.utils.constants import GENOME_VERSION_GRCh37, GENOME_VERSION_GRCh38 from seqr.views.utils.export_utils import write_multiple_files # Allow adding the custom json_fields and internal_json_fields to the model Meta @@ -20,9 +21,6 @@ logger = logging.getLogger(__name__) -GENOME_VERSION_GRCh37 = "37" -GENOME_VERSION_GRCh38 = "38" - GENOME_VERSION_CHOICES = [ (GENOME_VERSION_GRCh37, "GRCh37"), (GENOME_VERSION_GRCh38, "GRCh38") diff --git a/seqr/models.py b/seqr/models.py index b183d62bd9..478997657f 100644 --- a/seqr/models.py +++ b/seqr/models.py @@ -12,6 +12,9 @@ from guardian.shortcuts import assign_perm +from seqr.utils.constants import SEX_MALE, SEX_FEMALE, SEX_UNKNOWN, FEMALE_ANEUPLOIDIES, MALE_ANEUPLOIDIES, \ + FEMALE_SEXES, MALE_SEXES, AFFECTED_STATUS_AFFECTED, AFFECTED_STATUS_UNAFFECTED, AFFECTED_STATUS_UNKNOWN, \ + SAMPLE_TYPE_WES, SAMPLE_TYPE_WGS, DATASET_TYPE_VARIANT_CALLS, DATASET_TYPE_SV_CALLS, DATASET_TYPE_MITO_CALLS from seqr.utils.logging_utils import log_model_update, log_model_bulk_update, SeqrLogger from seqr.utils.xpos_utils import get_chrom_pos from seqr.views.utils.json_utils import DjangoJSONEncoderWithSets @@ -434,13 +437,13 @@ def __init__(self, *args, **kwargs): class Individual(ModelWithGUID): - SEX_MALE = 'M' - SEX_FEMALE = 'F' - SEX_UNKNOWN = 'U' - FEMALE_ANEUPLOIDIES = ['XXX', 'X0'] - MALE_ANEUPLOIDIES = ['XXY', 'XYY'] - FEMALE_SEXES = [SEX_FEMALE] + FEMALE_ANEUPLOIDIES - MALE_SEXES = [SEX_MALE] + MALE_ANEUPLOIDIES + SEX_MALE = SEX_MALE + SEX_FEMALE = SEX_FEMALE + SEX_UNKNOWN = SEX_UNKNOWN + FEMALE_ANEUPLOIDIES = FEMALE_ANEUPLOIDIES + MALE_ANEUPLOIDIES = MALE_ANEUPLOIDIES + FEMALE_SEXES = FEMALE_SEXES + MALE_SEXES = MALE_SEXES SEX_CHOICES = ( (SEX_MALE, 'Male'), ('F', 'Female'), @@ -449,9 +452,9 @@ class Individual(ModelWithGUID): *[(sex, sex) for sex in FEMALE_ANEUPLOIDIES], ) - AFFECTED_STATUS_AFFECTED = 'A' - AFFECTED_STATUS_UNAFFECTED = 'N' - AFFECTED_STATUS_UNKNOWN = 'U' + AFFECTED_STATUS_AFFECTED = AFFECTED_STATUS_AFFECTED + AFFECTED_STATUS_UNAFFECTED = AFFECTED_STATUS_UNAFFECTED + AFFECTED_STATUS_UNKNOWN = AFFECTED_STATUS_UNKNOWN AFFECTED_STATUS_CHOICES = ( (AFFECTED_STATUS_AFFECTED, 'Affected'), (AFFECTED_STATUS_UNAFFECTED, 'Unaffected'), @@ -681,17 +684,17 @@ class Meta: class Dataset(ModelWithGUID): - SAMPLE_TYPE_WES = 'WES' - SAMPLE_TYPE_WGS = 'WGS' + SAMPLE_TYPE_WES = SAMPLE_TYPE_WES + SAMPLE_TYPE_WGS = SAMPLE_TYPE_WGS SAMPLE_TYPE_CHOICES = ( (SAMPLE_TYPE_WES, 'Exome'), (SAMPLE_TYPE_WGS, 'Whole Genome'), ) SAMPLE_TYPE_LOOKUP = dict(SAMPLE_TYPE_CHOICES) - DATASET_TYPE_VARIANT_CALLS = 'SNV_INDEL' - DATASET_TYPE_SV_CALLS = 'SV' - DATASET_TYPE_MITO_CALLS = 'MITO' + DATASET_TYPE_VARIANT_CALLS = DATASET_TYPE_VARIANT_CALLS + DATASET_TYPE_SV_CALLS = DATASET_TYPE_SV_CALLS + DATASET_TYPE_MITO_CALLS = DATASET_TYPE_MITO_CALLS DATASET_TYPE_CHOICES = ( (DATASET_TYPE_VARIANT_CALLS, 'Variant Calls'), (DATASET_TYPE_SV_CALLS, 'SV Calls'), From bc03c131b20e107a8e7347d98e850da5715ce2e3 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 14:34:46 -0400 Subject: [PATCH 039/369] fix ruff --- clickhouse_search/backend/table_models.py | 2 -- .../test/clickhouse_django/seqr/utils/__init__.py | 6 +++++- .../lib/test/clickhouse_django/settings.py | 12 +++++++++--- 3 files changed, 14 insertions(+), 6 deletions(-) diff --git a/clickhouse_search/backend/table_models.py b/clickhouse_search/backend/table_models.py index 2f211cc2ff..b6e39a15d5 100644 --- a/clickhouse_search/backend/table_models.py +++ b/clickhouse_search/backend/table_models.py @@ -16,8 +16,6 @@ DICTIONARY_META_FIELDS = ['layout', 'lifetime_max', 'postgres_query', 'postgres_db', 'clickhouse_query_template'] -# Lives here rather than in models/reference_data_models.py so migrations depending on it don't -# need to import the much heavier live model definitions module. def conditionally_refresh_reference_dataset(reference_dataset: str): def inner(apps, schema_editor): if DATABASES['default']['NAME'].startswith('test_'): diff --git a/loading_pipeline/lib/test/clickhouse_django/seqr/utils/__init__.py b/loading_pipeline/lib/test/clickhouse_django/seqr/utils/__init__.py index 4cc45c1a59..b93e147a15 100644 --- a/loading_pipeline/lib/test/clickhouse_django/seqr/utils/__init__.py +++ b/loading_pipeline/lib/test/clickhouse_django/seqr/utils/__init__.py @@ -1,4 +1,8 @@ import os # Falls through to the real seqr/utils/ for anything not stubbed in this directory. -__path__.append(os.path.join(os.path.dirname(__file__), '..', '..', '..', '..', '..', '..', 'seqr', 'utils')) +__path__.append( + os.path.join( + os.path.dirname(__file__), '..', '..', '..', '..', '..', '..', 'seqr', 'utils' + ) +) diff --git a/loading_pipeline/lib/test/clickhouse_django/settings.py b/loading_pipeline/lib/test/clickhouse_django/settings.py index 5af22fd624..ea503e2e5d 100644 --- a/loading_pipeline/lib/test/clickhouse_django/settings.py +++ b/loading_pipeline/lib/test/clickhouse_django/settings.py @@ -40,11 +40,17 @@ def allow_migrate(db, app_label, model_name=None, **hints): # noqa: ARG004 PIPELINE_RUNNER_SERVER = os.environ.get('PIPELINE_RUNNER_SERVER', 'http://localhost') # Must differ - EmbeddedRocksDB tables (annotations_memory vs annotations_disk) using the same # path deadlock on the same file lock. -CLICKHOUSE_IN_MEMORY_DIR = os.environ.get('CLICKHOUSE_IN_MEMORY_DIR', '/tmp/loading_pipeline_test_clickhouse_in_memory') # noqa: S108 -CLICKHOUSE_DATA_DIR = os.environ.get('CLICKHOUSE_DATA_DIR', '/tmp/loading_pipeline_test_clickhouse_data') # noqa: S108 +CLICKHOUSE_IN_MEMORY_DIR = os.environ.get( + 'CLICKHOUSE_IN_MEMORY_DIR', '/tmp/loading_pipeline_test_clickhouse_in_memory' +) # noqa: S108 +CLICKHOUSE_DATA_DIR = os.environ.get( + 'CLICKHOUSE_DATA_DIR', '/tmp/loading_pipeline_test_clickhouse_data' +) # noqa: S108 CLICKHOUSE_WRITER_USER = os.environ.get('CLICKHOUSE_WRITER_USER', 'default') -CLICKHOUSE_WRITER_PASSWORD = os.environ.get('CLICKHOUSE_WRITER_PASSWORD', 'default_password') +CLICKHOUSE_WRITER_PASSWORD = os.environ.get( + 'CLICKHOUSE_WRITER_PASSWORD', 'default_password' +) CLICKHOUSE_DATABASE_NAME = os.environ.get('CLICKHOUSE_DATABASE', 'seqr') CLICKHOUSE_DB_CONFIG = { From 7ed0edd53f3186f83fed1a519219d8c7b103c3a3 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 14:35:09 -0400 Subject: [PATCH 040/369] add missed files --- .../lib/test/fixtures/clickhouse_test.json | 265 ++++++++++++++++++ seqr/utils/constants.py | 29 ++ 2 files changed, 294 insertions(+) create mode 100644 loading_pipeline/lib/test/fixtures/clickhouse_test.json create mode 100644 seqr/utils/constants.py diff --git a/loading_pipeline/lib/test/fixtures/clickhouse_test.json b/loading_pipeline/lib/test/fixtures/clickhouse_test.json new file mode 100644 index 0000000000..90e8faaf8a --- /dev/null +++ b/loading_pipeline/lib/test/fixtures/clickhouse_test.json @@ -0,0 +1,265 @@ +[ + { + "model": "clickhouse_search.entriessnvindel", + "pk": 1, + "fields": { + "key": 0, + "project_guid": "project_a", + "family_guid": "family_a1", + "sample_type": "WES", + "xpos": 123456789, + "is_gnomad_gt_5_percent": false, + "is_annotated_in_any_gene": false, + "geneId_ids": [], + "filters": [], + "sign": 1, + "calls": [["sample_a1", 2, null, null, null]] + } + }, + { + "model": "clickhouse_search.entriessnvindel", + "pk": 2, + "fields": { + "key": 1, + "project_guid": "project_a", + "family_guid": "family_a2", + "sample_type": "WGS", + "xpos": 123456789, + "is_gnomad_gt_5_percent": false, + "is_annotated_in_any_gene": false, + "geneId_ids": [], + "filters": [], + "sign": 1, + "calls": [["sample_a2", 1, null, null, null]] + } + }, + { + "model": "clickhouse_search.entriessnvindel", + "pk": 3, + "fields": { + "key": 2, + "project_guid": "project_a", + "family_guid": "family_a3", + "sample_type": "WGS", + "xpos": 133456789, + "is_gnomad_gt_5_percent": false, + "is_annotated_in_any_gene": false, + "geneId_ids": [], + "filters": [], + "sign": 1, + "calls": [["sample_a3", 2, null, null, null]] + } + }, + { + "model": "clickhouse_search.entriessnvindel", + "pk": 4, + "fields": { + "key": 3, + "project_guid": "project_a", + "family_guid": "family_a4", + "sample_type": "WES", + "xpos": 133456789, + "is_gnomad_gt_5_percent": false, + "is_annotated_in_any_gene": false, + "geneId_ids": [], + "filters": [], + "sign": 1, + "calls": [["sample_a4", 0, null, null, null]] + } + }, + { + "model": "clickhouse_search.entriessnvindel", + "pk": 5, + "fields": { + "key": 4, + "project_guid": "project_a", + "family_guid": "family_a5", + "sample_type": "WES", + "xpos": 133456789, + "is_gnomad_gt_5_percent": false, + "is_annotated_in_any_gene": true, + "geneId_ids": [0], + "filters": [], + "sign": 1, + "calls": [["sample_a5", 0, null, null, null], ["sample_a6", 1, null, null, null], ["sample_a7", 0, null, null, null]] + } + }, + { + "model": "clickhouse_search.entriessnvindel", + "pk": 6, + "fields": { + "key": 4, + "project_guid": "project_a", + "family_guid": "family_a6", + "sample_type": "WGS", + "xpos": 133456789, + "is_gnomad_gt_5_percent": false, + "is_annotated_in_any_gene": false, + "geneId_ids": [], + "filters": [], + "sign": 1, + "calls": [["sample_a8", 2, null, null, null]] + } + }, + { + "model": "clickhouse_search.entriessnvindel", + "pk": 7, + "fields": { + "key": 0, + "project_guid": "project_b", + "family_guid": "family_b1", + "sample_type": "WES", + "xpos": 123456789, + "is_gnomad_gt_5_percent": false, + "is_annotated_in_any_gene": false, + "geneId_ids": [], + "filters": [], + "sign": 1, + "calls": [["sample_b4", 0, null, null, null]] + } + }, + { + "model": "clickhouse_search.entriessnvindel", + "pk": 8, + "fields": { + "key": 1, + "project_guid": "project_b", + "family_guid": "family_b2", + "sample_type": "WES", + "xpos": 123456789, + "is_gnomad_gt_5_percent": false, + "is_annotated_in_any_gene": false, + "geneId_ids": [], + "filters": [], + "sign": 1, + "calls": [["sample_b5", 1, null, null, null]] + } + }, + { + "model": "clickhouse_search.entriessnvindel", + "pk": 9, + "fields": { + "key": 2, + "project_guid": "project_b", + "family_guid": "family_b2", + "sample_type": "WES", + "xpos": 123456789, + "is_gnomad_gt_5_percent": false, + "is_annotated_in_any_gene": false, + "geneId_ids": [], + "filters": [], + "sign": 1, + "calls": [["sample_b5", 0, null, null, null]] + } + }, + { + "model": "clickhouse_search.entriessnvindel", + "pk": 10, + "fields": { + "key": 3, + "project_guid": "project_b", + "family_guid": "family_b3", + "sample_type": "WES", + "xpos": 133456789, + "is_gnomad_gt_5_percent": false, + "is_annotated_in_any_gene": false, + "geneId_ids": [], + "filters": [], + "sign": 1, + "calls": [["sample_b6", 2, null, null, null]] + } + }, + { + "model": "clickhouse_search.entriessnvindel", + "pk": 11, + "fields": { + "key": 4, + "project_guid": "project_b", + "family_guid": "family_b3", + "sample_type": "WES", + "xpos": 133456789, + "is_gnomad_gt_5_percent": false, + "is_annotated_in_any_gene": false, + "geneId_ids": [], + "filters": [], + "sign": 1, + "calls": [["sample_b6", 2, null, null, null]] + } + }, + { + "model": "clickhouse_search.entriessnvindel", + "pk": 12, + "fields": { + "key": 0, + "project_guid": "project_c", + "family_guid": "family_c1", + "sample_type": "WES", + "xpos": 123456789, + "is_gnomad_gt_5_percent": false, + "is_annotated_in_any_gene": true, + "geneId_ids": [1], + "filters": [], + "sign": 1, + "calls": [["sample_c7", 0, null, null, null]] + } + }, + { + "model": "clickhouse_search.entriessnvindel", + "pk": 13, + "fields": { + "key": 3, + "project_guid": "project_c", + "family_guid": "family_c2", + "sample_type": "WES", + "xpos": 123456789, + "is_gnomad_gt_5_percent": false, + "is_annotated_in_any_gene": true, + "geneId_ids": [1], + "filters": [], + "sign": 1, + "calls": [["sample_c8", 0, null, null, null]] + } + }, + { + "model": "clickhouse_search.entriessnvindel", + "pk": 14, + "fields": { + "key": 4, + "project_guid": "project_c", + "family_guid": "family_c3", + "sample_type": "WES", + "xpos": 133456789, + "is_gnomad_gt_5_percent": false, + "is_annotated_in_any_gene": true, + "geneId_ids": [1], + "filters": [], + "sign": 1, + "calls": [["sample_c9", 2, null, null, null]] + } + }, + { + "model": "clickhouse_search.entriessnvindel", + "pk": 15, + "fields": { + "key": 5, + "project_guid": "project_c", + "family_guid": "family_c4", + "sample_type": "WES", + "xpos": 133456789, + "is_gnomad_gt_5_percent": false, + "is_annotated_in_any_gene": true, + "geneId_ids": [1], + "filters": [], + "sign": 1, + "calls": [["sample_c9", 2, null, null, null]] + } + }, + { + "model": "clickhouse_search.projectpartitionssnvindel", + "pk": "project_d", + "fields": { + "project_guid": "project_d", + "n_partitions": 2 + } + } +] diff --git a/seqr/utils/constants.py b/seqr/utils/constants.py new file mode 100644 index 0000000000..f07ddc133b --- /dev/null +++ b/seqr/utils/constants.py @@ -0,0 +1,29 @@ +"""Constants shared between seqr.models, reference_data.models, and clickhouse_search - kept here, +rather than on those Django model classes, so clickhouse_search (and loading_pipeline's minimal +test settings) can depend on these plain values without importing the Postgres/guardian-backed +seqr.models/reference_data.models apps. +""" + +# Individual +SEX_MALE = 'M' +SEX_FEMALE = 'F' +SEX_UNKNOWN = 'U' +FEMALE_ANEUPLOIDIES = ['XXX', 'X0'] +MALE_ANEUPLOIDIES = ['XXY', 'XYY'] +FEMALE_SEXES = [SEX_FEMALE, *FEMALE_ANEUPLOIDIES] +MALE_SEXES = [SEX_MALE, *MALE_ANEUPLOIDIES] + +AFFECTED_STATUS_AFFECTED = 'A' +AFFECTED_STATUS_UNAFFECTED = 'N' +AFFECTED_STATUS_UNKNOWN = 'U' + +# Dataset +SAMPLE_TYPE_WES = 'WES' +SAMPLE_TYPE_WGS = 'WGS' +DATASET_TYPE_VARIANT_CALLS = 'SNV_INDEL' +DATASET_TYPE_SV_CALLS = 'SV' +DATASET_TYPE_MITO_CALLS = 'MITO' + +# reference_data genome versions +GENOME_VERSION_GRCh37 = '37' +GENOME_VERSION_GRCh38 = '38' From 5c36c8593b1df38e661a5b954008bd92dcaabd42 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 14:38:45 -0400 Subject: [PATCH 041/369] fix ruff --- clickhouse_search/models/__init__.py | 6 ++---- loading_pipeline/lib/misc/clickhouse_test.py | 3 ++- .../test/clickhouse_django/seqr/utils/__init__.py | 12 ++++++++++-- .../lib/test/clickhouse_django/settings.py | 13 ++++++++----- .../lib/test/clickhouse_schema_testcase.py | 6 ++++-- loading_pipeline/pyproject.toml | 1 + 6 files changed, 27 insertions(+), 14 deletions(-) diff --git a/clickhouse_search/models/__init__.py b/clickhouse_search/models/__init__.py index 8695ebea5c..f171b92113 100644 --- a/clickhouse_search/models/__init__.py +++ b/clickhouse_search/models/__init__.py @@ -12,12 +12,10 @@ ) state.DEFAULT_NAMES = options.DEFAULT_NAMES -# Importing these registers their model classes with Django's app registry (apps.get_model()), -# which fixture loaddata needs to resolve "clickhouse_search." identifiers. Nothing else -# in this package imports them directly otherwise. Must come after the DEFAULT_NAMES patch above - -# these modules' Meta classes use the custom fields it allowlists. +# Importing here registers model classes with Django's app registry from clickhouse_search.models import postgres_dicts, reference_data_models, search_models, gt_stats_models # noqa: F401,E402 + class ClickHouseRouter: # Adapted from https://github.com/jayvynl/django-clickhouse-backend/blob/v1.3.2/README.md#configuration diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index eba49231af..1f7dfdfd0b 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -1,4 +1,5 @@ import os +from typing import ClassVar from unittest.mock import patch import pandas as pd @@ -48,7 +49,7 @@ class ClickhouseTest(MockedDatarootTestCase, ClickhouseSchemaTestCase): - fixtures = ['clickhouse_test'] + fixtures: ClassVar = ['clickhouse_test'] @classmethod def setUpClass(cls): diff --git a/loading_pipeline/lib/test/clickhouse_django/seqr/utils/__init__.py b/loading_pipeline/lib/test/clickhouse_django/seqr/utils/__init__.py index b93e147a15..d6a3b34ab1 100644 --- a/loading_pipeline/lib/test/clickhouse_django/seqr/utils/__init__.py +++ b/loading_pipeline/lib/test/clickhouse_django/seqr/utils/__init__.py @@ -3,6 +3,14 @@ # Falls through to the real seqr/utils/ for anything not stubbed in this directory. __path__.append( os.path.join( - os.path.dirname(__file__), '..', '..', '..', '..', '..', '..', 'seqr', 'utils' - ) + os.path.dirname(__file__), + '..', + '..', + '..', + '..', + '..', + '..', + 'seqr', + 'utils', + ), ) diff --git a/loading_pipeline/lib/test/clickhouse_django/settings.py b/loading_pipeline/lib/test/clickhouse_django/settings.py index ea503e2e5d..0930b783a0 100644 --- a/loading_pipeline/lib/test/clickhouse_django/settings.py +++ b/loading_pipeline/lib/test/clickhouse_django/settings.py @@ -41,15 +41,18 @@ def allow_migrate(db, app_label, model_name=None, **hints): # noqa: ARG004 # Must differ - EmbeddedRocksDB tables (annotations_memory vs annotations_disk) using the same # path deadlock on the same file lock. CLICKHOUSE_IN_MEMORY_DIR = os.environ.get( - 'CLICKHOUSE_IN_MEMORY_DIR', '/tmp/loading_pipeline_test_clickhouse_in_memory' -) # noqa: S108 + 'CLICKHOUSE_IN_MEMORY_DIR', + '/tmp/loading_pipeline_test_clickhouse_in_memory', # noqa: S108 +) CLICKHOUSE_DATA_DIR = os.environ.get( - 'CLICKHOUSE_DATA_DIR', '/tmp/loading_pipeline_test_clickhouse_data' -) # noqa: S108 + 'CLICKHOUSE_DATA_DIR', + '/tmp/loading_pipeline_test_clickhouse_data', # noqa: S108 +) CLICKHOUSE_WRITER_USER = os.environ.get('CLICKHOUSE_WRITER_USER', 'default') CLICKHOUSE_WRITER_PASSWORD = os.environ.get( - 'CLICKHOUSE_WRITER_PASSWORD', 'default_password' + 'CLICKHOUSE_WRITER_PASSWORD', + 'default_password', ) CLICKHOUSE_DATABASE_NAME = os.environ.get('CLICKHOUSE_DATABASE', 'seqr') diff --git a/loading_pipeline/lib/test/clickhouse_schema_testcase.py b/loading_pipeline/lib/test/clickhouse_schema_testcase.py index 8799f2d9a4..660a16149a 100644 --- a/loading_pipeline/lib/test/clickhouse_schema_testcase.py +++ b/loading_pipeline/lib/test/clickhouse_schema_testcase.py @@ -1,3 +1,5 @@ +from typing import ClassVar + from django.db import connections from django.test import TestCase @@ -5,7 +7,7 @@ class ClickhouseSchemaTestCase(TestCase): - databases = ['clickhouse_write'] + databases: ClassVar = ['clickhouse_write'] # Django's `flush` (the default TestCase teardown for backends without transaction support) # determines tables to flush from `apps.get_models()`, but nothing here imports @@ -22,4 +24,4 @@ def _fixture_teardown(self): ) tables = [row[0] for row in cursor.fetchall()] for table in tables: - cursor.execute(f'TRUNCATE TABLE `{table}`') # noqa: S608 + cursor.execute(f'TRUNCATE TABLE `{table}`') diff --git a/loading_pipeline/pyproject.toml b/loading_pipeline/pyproject.toml index 0b9e4f9f1e..b943124e08 100644 --- a/loading_pipeline/pyproject.toml +++ b/loading_pipeline/pyproject.toml @@ -113,6 +113,7 @@ inline-quotes = "single" ] '*migration*' = [ 'N999', # allow invalid module names + 'RUF012', # Django migration classes' dependencies/operations are conventionally plain lists ] '*clickhouse*' = [ 'S608' # unsafe sql From 66f8d838c6dcd3ea07baa16a0536288f49226867 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 14:43:24 -0400 Subject: [PATCH 042/369] ruff and cleanup --- clickhouse_search/constants.py | 7 ++++--- clickhouse_search/managers.py | 5 +++-- clickhouse_search/search.py | 3 ++- loading_pipeline/bin/pipeline_worker_test.py | 9 ++++++--- .../load_clickhouse_variants_tables_test.py | 9 ++++++--- 5 files changed, 21 insertions(+), 12 deletions(-) diff --git a/clickhouse_search/constants.py b/clickhouse_search/constants.py index ebce6e0063..9ebf9481b6 100644 --- a/clickhouse_search/constants.py +++ b/clickhouse_search/constants.py @@ -1,6 +1,7 @@ -from seqr.utils.constants import AFFECTED_STATUS_AFFECTED as AFFECTED, AFFECTED_STATUS_UNAFFECTED as UNAFFECTED, \ - MALE_SEXES, FEMALE_SEXES, SAMPLE_TYPE_WES, SAMPLE_TYPE_WGS, DATASET_TYPE_VARIANT_CALLS, DATASET_TYPE_SV_CALLS, \ - DATASET_TYPE_MITO_CALLS, GENOME_VERSION_GRCh37, GENOME_VERSION_GRCh38 +from seqr.utils.constants import AFFECTED_STATUS_AFFECTED, AFFECTED_STATUS_UNAFFECTED + +AFFECTED = AFFECTED_STATUS_AFFECTED +UNAFFECTED = AFFECTED_STATUS_UNAFFECTED MAX_VARIANTS = 10000 diff --git a/clickhouse_search/managers.py b/clickhouse_search/managers.py index f08bd5ee88..68da15e60a 100644 --- a/clickhouse_search/managers.py +++ b/clickhouse_search/managers.py @@ -12,13 +12,14 @@ GroupArrayIntersect, If, MapLookup, NullIf, Plus, SubqueryJoin, SubqueryTable, Tuple, TupleConcat, Untuple, \ IntDiv, Modulo, SplitByString, ArrayIndex, Multiply, IndexOf from clickhouse_search.models.postgres_dicts import AffectedDict, SexDict, DiscoveryVariantDict -from clickhouse_search.constants import INHERITANCE_FILTERS, ANY_AFFECTED, AFFECTED, UNAFFECTED, MALE_SEXES, \ +from clickhouse_search.constants import INHERITANCE_FILTERS, ANY_AFFECTED, AFFECTED, UNAFFECTED, \ X_LINKED_RECESSIVE, REF_REF, REF_ALT, ALT_ALT, HAS_ALT, HAS_REF, SPLICE_AI_FIELD, SCREEN_KEY, UTR_ANNOTATOR_KEY, \ EXTENDED_SPLICE_KEY, MOTIF_FEATURES_KEY, REGULATORY_FEATURES_KEY, CLINVAR_KEY, HGMD_KEY, NEW_SV_FIELD, \ EXTENDED_SPLICE_REGION_CONSEQUENCE, CLINVAR_PATH_RANGES, CLINVAR_PATH_SIGNIFICANCES, CLINVAR_LIKELY_PATH_FILTER, \ CLINVAR_CONFLICTING_P_LP, CLINVAR_CONFLICTING_NO_P, CLINVAR_CONFLICTING, PATH_FREQ_OVERRIDE_CUTOFF, \ HGMD_CLASS_FILTERS, SV_TYPE_FILTER_FIELD, SV_CONSEQUENCES_FIELD, COMPOUND_HET, COMPOUND_HET_ALLOW_HOM_ALTS, \ - X_LINKED_RECESSIVE_MALE_AFFECTED, FEMALE_SEXES, SV_ANNOTATION_TYPES + X_LINKED_RECESSIVE_MALE_AFFECTED, SV_ANNOTATION_TYPES +from seqr.utils.constants import MALE_SEXES, FEMALE_SEXES from seqr.utils.xpos_utils import get_xpos, parse_variant_id, MIN_POS, MAX_POS, CHROMOSOME_CHOICES diff --git a/clickhouse_search/search.py b/clickhouse_search/search.py index 3e57074425..33c86b0ef4 100644 --- a/clickhouse_search/search.py +++ b/clickhouse_search/search.py @@ -23,8 +23,9 @@ from seqr.utils.gene_utils import parse_locus_list_items from seqr.utils.logging_utils import SeqrLogger from clickhouse_search.constants import MAX_VARIANTS, XPOS_SORT_KEY, PATHOGENICTY_SORT_KEY, PATHOGENICTY_HGMD_SORT_KEY, \ - PRIORITIZED_GENE_SORT, COMPOUND_HET, COMPOUND_HET_ALLOW_HOM_ALTS, RECESSIVE, AFFECTED, MALE_SEXES, \ + PRIORITIZED_GENE_SORT, COMPOUND_HET, COMPOUND_HET_ALLOW_HOM_ALTS, RECESSIVE, AFFECTED, \ X_LINKED_RECESSIVE, X_LINKED_RECESSIVE_MALE_AFFECTED +from seqr.utils.constants import MALE_SEXES from seqr.views.utils.json_utils import DjangoJSONEncoderWithSets logger = SeqrLogger(__name__) diff --git a/loading_pipeline/bin/pipeline_worker_test.py b/loading_pipeline/bin/pipeline_worker_test.py index 532693701a..f935f3aa0c 100644 --- a/loading_pipeline/bin/pipeline_worker_test.py +++ b/loading_pipeline/bin/pipeline_worker_test.py @@ -112,7 +112,8 @@ def test_process_queue_integration_test( {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` """, ) - self.assertEqual(cursor.fetchone()[0], 30) + annotations_count = cursor.fetchone()[0] + self.assertEqual(annotations_count, 30) cursor.execute( f""" SELECT COUNT(*) @@ -120,7 +121,8 @@ def test_process_queue_integration_test( {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` """, ) - self.assertEqual(cursor.fetchone()[0], 16) + entries_count = cursor.fetchone()[0] + self.assertEqual(entries_count, 16) cursor.execute( f""" SELECT sum(ac_wgs) @@ -128,7 +130,8 @@ def test_process_queue_integration_test( {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` """, ) - self.assertEqual(cursor.fetchone()[0], 69) + ac_wgs = cursor.fetchone()[0] + self.assertEqual(ac_wgs, 69) @patch('loading_pipeline.lib.misc.slack._safe_post_to_slack') @patch('loading_pipeline.api.request_handlers.WriteClickhouseLoadSuccessFileTask') diff --git a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py index b8a2d8fa1e..b216431433 100644 --- a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py +++ b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py @@ -126,7 +126,8 @@ def test_write_variants_to_clickhouse( {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` """, ) - self.assertEqual(cursor.fetchone()[0], 2) + variants_count = cursor.fetchone()[0] + self.assertEqual(variants_count, 2) cursor.execute( f""" SELECT COUNT(*) @@ -134,7 +135,8 @@ def test_write_variants_to_clickhouse( {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details` """, ) - self.assertEqual(cursor.fetchone()[0], 2) + variant_details_count = cursor.fetchone()[0] + self.assertEqual(variant_details_count, 2) cursor.execute( f""" SELECT COUNT(*) @@ -142,4 +144,5 @@ def test_write_variants_to_clickhouse( {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/key_lookup` """, ) - self.assertEqual(cursor.fetchone()[0], 2) + key_lookups_count = cursor.fetchone()[0] + self.assertEqual(key_lookups_count, 2) From 57963dcfd2e4ff8771a7866a8d5f86a8708b675a Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 14:45:25 -0400 Subject: [PATCH 043/369] missing init --- loading_pipeline/lib/test/clickhouse_django/__init__.py | 0 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 loading_pipeline/lib/test/clickhouse_django/__init__.py diff --git a/loading_pipeline/lib/test/clickhouse_django/__init__.py b/loading_pipeline/lib/test/clickhouse_django/__init__.py new file mode 100644 index 0000000000..e69de29bb2 From ca9eacecc8659eec1aa0b4eb6d7e08608078c503 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 15:03:04 -0400 Subject: [PATCH 044/369] clean up --- loading_pipeline/bin/pipeline_worker_test.py | 56 +++++++++---------- .../load_clickhouse_variants_tables_test.py | 56 +++++++++---------- .../test/clickhouse_django/seqr/__init__.py | 6 -- .../lib/test/clickhouse_django/settings.py | 20 +------ .../lib/test/clickhouse_schema_testcase.py | 3 - loading_pipeline/pyproject.toml | 5 -- seqr/utils/constants.py | 9 --- 7 files changed, 58 insertions(+), 97 deletions(-) diff --git a/loading_pipeline/bin/pipeline_worker_test.py b/loading_pipeline/bin/pipeline_worker_test.py index f935f3aa0c..a2e3db1e54 100644 --- a/loading_pipeline/bin/pipeline_worker_test.py +++ b/loading_pipeline/bin/pipeline_worker_test.py @@ -104,34 +104,34 @@ def test_process_queue_integration_test( ) as f: self.assertEqual(f.read(), '') - with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f""" - SELECT COUNT(*) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` - """, - ) - annotations_count = cursor.fetchone()[0] - self.assertEqual(annotations_count, 30) - cursor.execute( - f""" - SELECT COUNT(*) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` - """, - ) - entries_count = cursor.fetchone()[0] - self.assertEqual(entries_count, 16) - cursor.execute( - f""" - SELECT sum(ac_wgs) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` - """, - ) - ac_wgs = cursor.fetchone()[0] - self.assertEqual(ac_wgs, 69) + cursor = connections['clickhouse_write'].cursor() + cursor.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` + """, + ) + annotations_count = cursor.fetchone()[0] + self.assertEqual(annotations_count, 30) + cursor.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` + """, + ) + entries_count = cursor.fetchone()[0] + self.assertEqual(entries_count, 16) + cursor.execute( + f""" + SELECT sum(ac_wgs) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` + """, + ) + ac_wgs = cursor.fetchone()[0] + self.assertEqual(ac_wgs, 69) @patch('loading_pipeline.lib.misc.slack._safe_post_to_slack') @patch('loading_pipeline.api.request_handlers.WriteClickhouseLoadSuccessFileTask') diff --git a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py index b216431433..f412e0fa48 100644 --- a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py +++ b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py @@ -118,31 +118,31 @@ def test_write_variants_to_clickhouse( worker.run() self.assertTrue(task.complete()) - with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f""" - SELECT COUNT(*) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` - """, - ) - variants_count = cursor.fetchone()[0] - self.assertEqual(variants_count, 2) - cursor.execute( - f""" - SELECT COUNT(*) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details` - """, - ) - variant_details_count = cursor.fetchone()[0] - self.assertEqual(variant_details_count, 2) - cursor.execute( - f""" - SELECT COUNT(*) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/key_lookup` - """, - ) - key_lookups_count = cursor.fetchone()[0] - self.assertEqual(key_lookups_count, 2) + cursor = connections['clickhouse_write'].cursor() + cursor.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` + """, + ) + variants_count = cursor.fetchone()[0] + self.assertEqual(variants_count, 2) + cursor.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details` + """, + ) + variant_details_count = cursor.fetchone()[0] + self.assertEqual(variant_details_count, 2) + cursor.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/key_lookup` + """, + ) + key_lookups_count = cursor.fetchone()[0] + self.assertEqual(key_lookups_count, 2) diff --git a/loading_pipeline/lib/test/clickhouse_django/seqr/__init__.py b/loading_pipeline/lib/test/clickhouse_django/seqr/__init__.py index 2beff72da3..e69de29bb2 100644 --- a/loading_pipeline/lib/test/clickhouse_django/seqr/__init__.py +++ b/loading_pipeline/lib/test/clickhouse_django/seqr/__init__.py @@ -1,6 +0,0 @@ -"""Stub of the main app's `seqr` package, shadowing it on sys.path (see settings.py's docstring). - -`clickhouse_search` needs a specific `seqr` migration name to exist, but not the real app - which -imports guardian/postgres/social_django via seqr/models.py. This stub avoids that weight; -seqr/utils/__init__.py falls through to the real seqr/utils/ for submodules that don't need it. -""" diff --git a/loading_pipeline/lib/test/clickhouse_django/settings.py b/loading_pipeline/lib/test/clickhouse_django/settings.py index 0930b783a0..962e4b0e20 100644 --- a/loading_pipeline/lib/test/clickhouse_django/settings.py +++ b/loading_pipeline/lib/test/clickhouse_django/settings.py @@ -1,15 +1,5 @@ -"""Minimal Django settings for running `clickhouse_search`'s real migrations in tests. - -Lives in its own directory, prepended to `sys.path` via pytest's `pythonpath` option (see -`pyproject.toml`), so it doubles as both `DJANGO_SETTINGS_MODULE` and the bare `settings` module -`clickhouse_search/backend/base.py` imports directly - without pulling in the main app's much -heavier `settings.py`. -""" - import os -# Shared Django fixtures (loaddata) for clickhouse_search-backed test data - see -# lib/test/clickhouse_schema_testcase.py. FIXTURE_DIRS = [os.path.join(os.path.dirname(__file__), '..', 'fixtures')] INSTALLED_APPS = [ @@ -38,8 +28,6 @@ def allow_migrate(db, app_label, model_name=None, **hints): # noqa: ARG004 SECRET_KEY = 'loading-pipeline-test' # noqa: S105 DEPLOYMENT_TYPE = os.environ.get('DEPLOYMENT_TYPE', 'dev') PIPELINE_RUNNER_SERVER = os.environ.get('PIPELINE_RUNNER_SERVER', 'http://localhost') -# Must differ - EmbeddedRocksDB tables (annotations_memory vs annotations_disk) using the same -# path deadlock on the same file lock. CLICKHOUSE_IN_MEMORY_DIR = os.environ.get( 'CLICKHOUSE_IN_MEMORY_DIR', '/tmp/loading_pipeline_test_clickhouse_in_memory', # noqa: S108 @@ -69,11 +57,9 @@ def allow_migrate(db, app_label, model_name=None, **hints): # noqa: ARG004 }, }, 'TEST': { - # Skip Django's default `test_` prefix; land on the name Env.CLICKHOUSE_DATABASE - # already expects. + # Skip Django's default `test_` prefix; land on the name Env.CLICKHOUSE_DATABASE already expects. 'NAME': CLICKHOUSE_DATABASE_NAME, - # Without this, Django assumes this alias depends on `default` and never resolves it, - # since our tests only ever request `databases = ['clickhouse_write']`. + # Without this, Django assumes this alias depends on `default` and never resolves it 'DEPENDENCIES': [], }, } @@ -85,8 +71,6 @@ def allow_migrate(db, app_label, model_name=None, **hints): # noqa: ARG004 **CLICKHOUSE_DB_CONFIG, 'TEST': {'MIRROR': 'clickhouse_write'}, }, - # Dummy backends: never opened (only aliases named in a test's `databases` get created), but - # `clickhouse_search/backend/base.py` reads their `NAME` to embed in generated dictionary DDL. 'default': { 'ENGINE': 'django.db.backends.dummy', 'NAME': 'test_default_unused', diff --git a/loading_pipeline/lib/test/clickhouse_schema_testcase.py b/loading_pipeline/lib/test/clickhouse_schema_testcase.py index 660a16149a..198b640521 100644 --- a/loading_pipeline/lib/test/clickhouse_schema_testcase.py +++ b/loading_pipeline/lib/test/clickhouse_schema_testcase.py @@ -9,9 +9,6 @@ class ClickhouseSchemaTestCase(TestCase): databases: ClassVar = ['clickhouse_write'] - # Django's `flush` (the default TestCase teardown for backends without transaction support) - # determines tables to flush from `apps.get_models()`, but nothing here imports - # clickhouse_search's model modules, so it finds none. Truncate live tables directly instead. def _fixture_teardown(self): with connections['clickhouse_write'].cursor() as cursor: cursor.execute( diff --git a/loading_pipeline/pyproject.toml b/loading_pipeline/pyproject.toml index b943124e08..43c7cbddc6 100644 --- a/loading_pipeline/pyproject.toml +++ b/loading_pipeline/pyproject.toml @@ -47,13 +47,8 @@ dev = [ exclude-dependencies = ["psycopg2-binary", "psycopg2"] [tool.pytest.ini_options] -# Order matters: `clickhouse_django` must precede `..`, or `import settings` resolves to the -# repo-root `settings.py` instead of ours. `..` puts the repo root (clickhouse_search etc.) on -# sys.path. pythonpath = ["lib/test/clickhouse_django", ".."] DJANGO_SETTINGS_MODULE = "settings" -# Disable pytest-django's manage.py auto-discovery, which would otherwise re-shadow `settings` -# with the main app's. django_find_project = false [tool.setuptools] diff --git a/seqr/utils/constants.py b/seqr/utils/constants.py index f07ddc133b..d747820cad 100644 --- a/seqr/utils/constants.py +++ b/seqr/utils/constants.py @@ -1,10 +1,3 @@ -"""Constants shared between seqr.models, reference_data.models, and clickhouse_search - kept here, -rather than on those Django model classes, so clickhouse_search (and loading_pipeline's minimal -test settings) can depend on these plain values without importing the Postgres/guardian-backed -seqr.models/reference_data.models apps. -""" - -# Individual SEX_MALE = 'M' SEX_FEMALE = 'F' SEX_UNKNOWN = 'U' @@ -17,13 +10,11 @@ AFFECTED_STATUS_UNAFFECTED = 'N' AFFECTED_STATUS_UNKNOWN = 'U' -# Dataset SAMPLE_TYPE_WES = 'WES' SAMPLE_TYPE_WGS = 'WGS' DATASET_TYPE_VARIANT_CALLS = 'SNV_INDEL' DATASET_TYPE_SV_CALLS = 'SV' DATASET_TYPE_MITO_CALLS = 'MITO' -# reference_data genome versions GENOME_VERSION_GRCh37 = '37' GENOME_VERSION_GRCh38 = '38' From 10c3726b7c30b2613842e3a5210268ad8d913430 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 15:08:01 -0400 Subject: [PATCH 045/369] test config setup --- .github/workflows/pipeline-unit-tests.yml | 4 ++++ .github/workflows/vlm-unit-tests.yaml | 2 +- 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml index a476bbb908..71201beb8b 100644 --- a/.github/workflows/pipeline-unit-tests.yml +++ b/.github/workflows/pipeline-unit-tests.yml @@ -43,6 +43,7 @@ jobs: -p 9000:9000 \ -e CLICKHOUSE_USER=default \ -e CLICKHOUSE_PASSWORD=default_password \ + -e CLICKHOUSE_DEFAULT_ACCESS_MANAGEMENT=1 \ gcr.io/seqr-project/seqr-clickhouse:26.3.9 - name: Wait for ClickHouse run: | @@ -50,6 +51,9 @@ jobs: echo "Waiting for ClickHouse to start..." sleep 2 done + - name: Set up ClickHouse Settings + run: | + docker exec clickhouse clickhouse-client --query "CREATE SETTINGS PROFILE clickhouse_settings SETTINGS flatten_nested=0, join_use_nulls=1, stop_refreshable_materialized_views_on_startup=1, allow_materialized_view_with_bad_select=1, enable_join_runtime_filters=0 TO default" - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v4 with: diff --git a/.github/workflows/vlm-unit-tests.yaml b/.github/workflows/vlm-unit-tests.yaml index d3a19567b9..85a2100a38 100644 --- a/.github/workflows/vlm-unit-tests.yaml +++ b/.github/workflows/vlm-unit-tests.yaml @@ -113,7 +113,7 @@ jobs: export CLICKHOUSE_WRITER_PASSWORD=clickhouse_test_password export CLICKHOUSE_SERVICE_HOSTNAME=localhost export POSTGRES_SERVICE_HOSTNAME=localhost - python3 -m pytest --setup-only --create-db --reuse-db --ds=settings + python3 -m pytest --setup-only --create-db --reuse-db --ds=settings vlm - name: Set up Clickhouse test user run: | docker exec clickhouse clickhouse-client --query "GRANT SELECT ON test_seqr.\`GRCh37/SNV_INDEL/key_lookup\` TO vlm_test_user" From 21d2a77bee901740798ce92b30ffb0be826ee1f0 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 15:28:41 -0400 Subject: [PATCH 046/369] fix detail parquuet fixture --- loading_pipeline/lib/misc/clickhouse_test.py | 204 +++++++++++++++--- .../lib/test/fixtures/clickhouse_test.json | 27 +++ 2 files changed, 202 insertions(+), 29 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index 1f7dfdfd0b..39f069f9dc 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -47,6 +47,162 @@ TEST_RUN_ID = 'manual__2025-05-07T17-20-59.702114+00-00' +_FIVEUTR_ANNOTATION_TYPE = pa.struct([ + ('AltStop', pa.string()), + ('AltStopDistanceToCDS', pa.int32()), + ('CapDistanceToStart', pa.int32()), + ('DistanceToCDS', pa.int32()), + ('DistanceToStop', pa.int32()), + ('Evidence', pa.bool_()), + ('FrameWithCDS', pa.string()), + ('KozakContext', pa.string()), + ('KozakStrength', pa.string()), + ('StartDistanceToCDS', pa.int32()), + ('alt_type', pa.string()), + ('alt_type_length', pa.int32()), + ('newSTOPDistanceToCDS', pa.int32()), + ('ref_StartDistanceToCDS', pa.int32()), + ('ref_type', pa.string()), + ('ref_type_length', pa.int32()), + ('type', pa.string()), +]) +_UTRANNOTATOR_TYPE = pa.struct([ + ('existingInframeOorfs', pa.int32()), + ('existingOutofframeOorfs', pa.int32()), + ('existingUorfs', pa.int32()), + ('fiveutrAnnotation', _FIVEUTR_ANNOTATION_TYPE), + ('fiveutrConsequence', pa.string()), +]) +_TRANSCRIPT_TYPE = pa.struct([ + ('alphamissense', pa.struct([('pathogenicity', pa.float64())])), + ('aminoAcids', pa.string()), + ('biotype', pa.string()), + ('canonical', pa.int32()), + ('codons', pa.string()), + ('consequenceTerms', pa.list_(pa.string())), + ('exon', pa.struct([('index', pa.int32()), ('total', pa.int32())])), + ('geneId', pa.string()), + ('hgvsc', pa.string()), + ('hgvsp', pa.string()), + ('intron', pa.struct([('index', pa.int32()), ('total', pa.int32())])), + ('loftee', pa.struct([('isLofNagnag', pa.bool_()), ('lofFilters', pa.list_(pa.string()))])), + ('majorConsequence', pa.string()), + ('manePlusClinical', pa.string()), + ('maneSelect', pa.string()), + ('refseqTranscriptId', pa.string()), + ('spliceregion', pa.struct([('extended_intronic_splice_region_variant', pa.bool_())])), + ('transcriptId', pa.string()), + ('transcriptRank', pa.int32()), + ('utrannotator', _UTRANNOTATOR_TYPE), +]) +_MOTIF_CONSEQUENCE_TYPE = pa.struct([ + ('consequenceTerms', pa.list_(pa.string())), + ('motifFeatureId', pa.string()), +]) +_REGULATORY_CONSEQUENCE_TYPE = pa.struct([ + ('biotype', pa.string()), + ('consequenceTerms', pa.list_(pa.string())), + ('regulatoryFeatureId', pa.string()), +]) +VARIANT_DETAILS_SCHEMA = pa.schema([ + ('key', pa.int64()), + ('variantId', pa.string()), + ('liftedOverChrom', pa.string()), + ('liftedOverPos', pa.int64()), + ('rsid', pa.string()), + ('CAID', pa.string()), + ('transcripts', pa.list_(_TRANSCRIPT_TYPE)), + ('sortedMotifFeatureConsequences', pa.list_(_MOTIF_CONSEQUENCE_TYPE)), + ('sortedRegulatoryFeatureConsequences', pa.list_(_REGULATORY_CONSEQUENCE_TYPE)), +]) +_FULL_TRANSCRIPT = { + 'alphamissense': {'pathogenicity': 0.5}, + 'aminoAcids': 'S/L', + 'biotype': 'protein_coding', + 'canonical': 1, + 'codons': 'tCg/tTg', + 'consequenceTerms': ['missense_variant'], + 'exon': {'index': 6, 'total': 14}, + 'geneId': 'ENSG00000187634', + 'hgvsc': 'ENST00000616016.5:c.1049C>T', + 'hgvsp': 'ENSP00000478421.2:p.Ser350Leu', + 'intron': None, + 'loftee': {'isLofNagnag': False, 'lofFilters': []}, + 'majorConsequence': 'missense_variant', + 'manePlusClinical': None, + 'maneSelect': 'NM_001385641.1', + 'refseqTranscriptId': 'NM_001385641.1', + 'spliceregion': {'extended_intronic_splice_region_variant': False}, + 'transcriptId': 'ENST00000616016', + 'transcriptRank': 0, + 'utrannotator': { + 'existingInframeOorfs': None, + 'existingOutofframeOorfs': None, + 'existingUorfs': None, + 'fiveutrAnnotation': { + 'AltStop': None, 'AltStopDistanceToCDS': None, 'CapDistanceToStart': None, + 'DistanceToCDS': 41, 'DistanceToStop': None, 'Evidence': None, + 'FrameWithCDS': None, 'KozakContext': 'CGCATGC', 'KozakStrength': 'Weak', + 'StartDistanceToCDS': None, 'alt_type': None, 'alt_type_length': None, + 'newSTOPDistanceToCDS': None, 'ref_StartDistanceToCDS': None, + 'ref_type': None, 'ref_type_length': None, 'type': 'OutOfFrame_oORF', + }, + 'fiveutrConsequence': None, + }, +} +_FULL_MOTIF_CONSEQUENCE = {'consequenceTerms': ['TFBS_ablation'], 'motifFeatureId': 'ENSM00000123'} +_FULL_REGULATORY_CONSEQUENCE = { + 'biotype': 'enhancer', + 'consequenceTerms': ['regulatory_region_ablation'], + 'regulatoryFeatureId': 'ENSR00000123', +} +VARIANT_DETAILS_ROWS = [ + { + 'key': 1, + 'variantId': '1-13-A-C', + 'liftedOverChrom': '1', + 'liftedOverPos': 13, + 'rsid': 'rs123', + 'CAID': 'CA123456', + 'transcripts': [_FULL_TRANSCRIPT], + 'sortedMotifFeatureConsequences': [_FULL_MOTIF_CONSEQUENCE], + 'sortedRegulatoryFeatureConsequences': [_FULL_REGULATORY_CONSEQUENCE], + }, + { + 'key': 2, + 'variantId': '2-14-A-T', + 'liftedOverChrom': None, + 'liftedOverPos': None, + 'rsid': None, + 'CAID': None, + 'transcripts': [], + 'sortedMotifFeatureConsequences': [], + 'sortedRegulatoryFeatureConsequences': [], + }, + { + 'key': 3, + 'variantId': 'Y-19-A-C', + 'liftedOverChrom': None, + 'liftedOverPos': None, + 'rsid': None, + 'CAID': None, + 'transcripts': [], + 'sortedMotifFeatureConsequences': [], + 'sortedRegulatoryFeatureConsequences': [], + }, + { + 'key': 4, + 'variantId': 'M-12-C-G', + 'liftedOverChrom': None, + 'liftedOverPos': None, + 'rsid': None, + 'CAID': None, + 'transcripts': [], + 'sortedMotifFeatureConsequences': [], + 'sortedRegulatoryFeatureConsequences': [], + }, +] + class ClickhouseTest(MockedDatarootTestCase, ClickhouseSchemaTestCase): fixtures: ClassVar = ['clickhouse_test'] @@ -137,25 +293,19 @@ def write_test_parquet(df: pd.DataFrame, parquet_path: str, schema=None): ), ) - df = pd.DataFrame( - { - 'key': [1, 2, 3, 4], - 'variantId': [ - '1-13-A-C', - '2-14-A-T', - 'Y-19-A-C', - 'M-12-C-G', - ], - 'transcripts': ['a', 'b', 'c', 'd'], - }, + variant_details_table = pa.Table.from_pylist( + VARIANT_DETAILS_ROWS, + schema=VARIANT_DETAILS_SCHEMA, ) - write_test_parquet( - df, - new_variant_details_parquet_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ), + variant_details_path = new_variant_details_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ) + os.makedirs(variant_details_path) + pq.write_table( + variant_details_table, + os.path.join(variant_details_path, 'test.parquet'), ) df = pd.DataFrame( @@ -303,10 +453,6 @@ def test_table_name_builder(self): def test_direct_insert_all_keys(self): with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f'INSERT INTO {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details` VALUES', - [(1, 'a', 'e'), (10, 'b', 'f'), (7, 'c', 'g')], - ) direct_insert_all_keys( ClickHouseTable.VARIANT_DETAILS, TableNameBuilder( @@ -316,17 +462,17 @@ def test_direct_insert_all_keys(self): ), ) cursor.execute( - f'SELECT * FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', + f'SELECT key, variantId FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', ) self.assertEqual( cursor.fetchall(), [ - (1, '1-13-A-C', 'a'), - (2, '2-14-A-T', 'b'), - (3, 'Y-19-A-C', 'c'), - (4, 'M-12-C-G', 'd'), - (7, 'c', 'g'), - (10, 'b', 'f'), + (1, '1-13-A-C'), + (2, '2-14-A-T'), + (3, 'Y-19-A-C'), + (4, 'M-12-C-G'), + (7, 'c'), + (10, 'b'), ], ) diff --git a/loading_pipeline/lib/test/fixtures/clickhouse_test.json b/loading_pipeline/lib/test/fixtures/clickhouse_test.json index 90e8faaf8a..86b4d05638 100644 --- a/loading_pipeline/lib/test/fixtures/clickhouse_test.json +++ b/loading_pipeline/lib/test/fixtures/clickhouse_test.json @@ -261,5 +261,32 @@ "project_guid": "project_d", "n_partitions": 2 } + }, + { + "model": "clickhouse_search.variantdetailssnvindel", + "pk": 1, + "fields": { + "key": 1, + "variant_id": "a", + "transcripts": [] + } + }, + { + "model": "clickhouse_search.variantdetailssnvindel", + "pk": 7, + "fields": { + "key": 7, + "variant_id": "c", + "transcripts": [] + } + }, + { + "model": "clickhouse_search.variantdetailssnvindel", + "pk": 10, + "fields": { + "key": 10, + "variant_id": "b", + "transcripts": [] + } } ] From a2805ddaad8fbee121dc4b3089d5bed16e934562 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 15:57:38 -0400 Subject: [PATCH 047/369] fix setup --- .github/workflows/pipeline-unit-tests.yml | 2 +- loading_pipeline/lib/misc/clickhouse_test.py | 239 ++++++++---------- .../lib/test/clickhouse_django/settings.py | 4 + 3 files changed, 114 insertions(+), 131 deletions(-) diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml index 71201beb8b..fa440a343d 100644 --- a/.github/workflows/pipeline-unit-tests.yml +++ b/.github/workflows/pipeline-unit-tests.yml @@ -86,5 +86,5 @@ jobs: export CLICKHOUSE_OPTIMIZE_TABLE_WAIT_S=1 export PYSPARK_SUBMIT_ARGS='--driver-memory 8G pyspark-shell' export CLICKHOUSE_DATABASE=test - uv run --project loading_pipeline pytest --cov=loading_pipeline --cov-report=term-missing loading_pipeline + uv run --project loading_pipeline pytest --cov=loading_pipeline --cov-report=term-missing -vv loading_pipeline uv run --project loading_pipeline coverage report --omit '*test*' --fail-under=85 diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index 39f069f9dc..0d776ebaa3 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -47,74 +47,94 @@ TEST_RUN_ID = 'manual__2025-05-07T17-20-59.702114+00-00' -_FIVEUTR_ANNOTATION_TYPE = pa.struct([ - ('AltStop', pa.string()), - ('AltStopDistanceToCDS', pa.int32()), - ('CapDistanceToStart', pa.int32()), - ('DistanceToCDS', pa.int32()), - ('DistanceToStop', pa.int32()), - ('Evidence', pa.bool_()), - ('FrameWithCDS', pa.string()), - ('KozakContext', pa.string()), - ('KozakStrength', pa.string()), - ('StartDistanceToCDS', pa.int32()), - ('alt_type', pa.string()), - ('alt_type_length', pa.int32()), - ('newSTOPDistanceToCDS', pa.int32()), - ('ref_StartDistanceToCDS', pa.int32()), - ('ref_type', pa.string()), - ('ref_type_length', pa.int32()), - ('type', pa.string()), -]) -_UTRANNOTATOR_TYPE = pa.struct([ - ('existingInframeOorfs', pa.int32()), - ('existingOutofframeOorfs', pa.int32()), - ('existingUorfs', pa.int32()), - ('fiveutrAnnotation', _FIVEUTR_ANNOTATION_TYPE), - ('fiveutrConsequence', pa.string()), -]) -_TRANSCRIPT_TYPE = pa.struct([ - ('alphamissense', pa.struct([('pathogenicity', pa.float64())])), - ('aminoAcids', pa.string()), - ('biotype', pa.string()), - ('canonical', pa.int32()), - ('codons', pa.string()), - ('consequenceTerms', pa.list_(pa.string())), - ('exon', pa.struct([('index', pa.int32()), ('total', pa.int32())])), - ('geneId', pa.string()), - ('hgvsc', pa.string()), - ('hgvsp', pa.string()), - ('intron', pa.struct([('index', pa.int32()), ('total', pa.int32())])), - ('loftee', pa.struct([('isLofNagnag', pa.bool_()), ('lofFilters', pa.list_(pa.string()))])), - ('majorConsequence', pa.string()), - ('manePlusClinical', pa.string()), - ('maneSelect', pa.string()), - ('refseqTranscriptId', pa.string()), - ('spliceregion', pa.struct([('extended_intronic_splice_region_variant', pa.bool_())])), - ('transcriptId', pa.string()), - ('transcriptRank', pa.int32()), - ('utrannotator', _UTRANNOTATOR_TYPE), -]) -_MOTIF_CONSEQUENCE_TYPE = pa.struct([ - ('consequenceTerms', pa.list_(pa.string())), - ('motifFeatureId', pa.string()), -]) -_REGULATORY_CONSEQUENCE_TYPE = pa.struct([ - ('biotype', pa.string()), - ('consequenceTerms', pa.list_(pa.string())), - ('regulatoryFeatureId', pa.string()), -]) -VARIANT_DETAILS_SCHEMA = pa.schema([ - ('key', pa.int64()), - ('variantId', pa.string()), - ('liftedOverChrom', pa.string()), - ('liftedOverPos', pa.int64()), - ('rsid', pa.string()), - ('CAID', pa.string()), - ('transcripts', pa.list_(_TRANSCRIPT_TYPE)), - ('sortedMotifFeatureConsequences', pa.list_(_MOTIF_CONSEQUENCE_TYPE)), - ('sortedRegulatoryFeatureConsequences', pa.list_(_REGULATORY_CONSEQUENCE_TYPE)), -]) +_FIVEUTR_ANNOTATION_TYPE = pa.struct( + [ + ('AltStop', pa.string()), + ('AltStopDistanceToCDS', pa.int32()), + ('CapDistanceToStart', pa.int32()), + ('DistanceToCDS', pa.int32()), + ('DistanceToStop', pa.int32()), + ('Evidence', pa.bool_()), + ('FrameWithCDS', pa.string()), + ('KozakContext', pa.string()), + ('KozakStrength', pa.string()), + ('StartDistanceToCDS', pa.int32()), + ('alt_type', pa.string()), + ('alt_type_length', pa.int32()), + ('newSTOPDistanceToCDS', pa.int32()), + ('ref_StartDistanceToCDS', pa.int32()), + ('ref_type', pa.string()), + ('ref_type_length', pa.int32()), + ('type', pa.string()), + ], +) +_UTRANNOTATOR_TYPE = pa.struct( + [ + ('existingInframeOorfs', pa.int32()), + ('existingOutofframeOorfs', pa.int32()), + ('existingUorfs', pa.int32()), + ('fiveutrAnnotation', _FIVEUTR_ANNOTATION_TYPE), + ('fiveutrConsequence', pa.string()), + ], +) +_TRANSCRIPT_TYPE = pa.struct( + [ + ('alphamissense', pa.struct([('pathogenicity', pa.float64())])), + ('aminoAcids', pa.string()), + ('biotype', pa.string()), + ('canonical', pa.int32()), + ('codons', pa.string()), + ('consequenceTerms', pa.list_(pa.string())), + ('exon', pa.struct([('index', pa.int32()), ('total', pa.int32())])), + ('geneId', pa.string()), + ('hgvsc', pa.string()), + ('hgvsp', pa.string()), + ('intron', pa.struct([('index', pa.int32()), ('total', pa.int32())])), + ( + 'loftee', + pa.struct( + [('isLofNagnag', pa.bool_()), ('lofFilters', pa.list_(pa.string()))], + ), + ), + ('majorConsequence', pa.string()), + ('manePlusClinical', pa.string()), + ('maneSelect', pa.string()), + ('refseqTranscriptId', pa.string()), + ( + 'spliceregion', + pa.struct([('extended_intronic_splice_region_variant', pa.bool_())]), + ), + ('transcriptId', pa.string()), + ('transcriptRank', pa.int32()), + ('utrannotator', _UTRANNOTATOR_TYPE), + ], +) +_MOTIF_CONSEQUENCE_TYPE = pa.struct( + [ + ('consequenceTerms', pa.list_(pa.string())), + ('motifFeatureId', pa.string()), + ], +) +_REGULATORY_CONSEQUENCE_TYPE = pa.struct( + [ + ('biotype', pa.string()), + ('consequenceTerms', pa.list_(pa.string())), + ('regulatoryFeatureId', pa.string()), + ], +) +VARIANT_DETAILS_SCHEMA = pa.schema( + [ + ('key', pa.int64()), + ('variantId', pa.string()), + ('liftedOverChrom', pa.string()), + ('liftedOverPos', pa.int64()), + ('rsid', pa.string()), + ('CAID', pa.string()), + ('transcripts', pa.list_(_TRANSCRIPT_TYPE)), + ('sortedMotifFeatureConsequences', pa.list_(_MOTIF_CONSEQUENCE_TYPE)), + ('sortedRegulatoryFeatureConsequences', pa.list_(_REGULATORY_CONSEQUENCE_TYPE)), + ], +) _FULL_TRANSCRIPT = { 'alphamissense': {'pathogenicity': 0.5}, 'aminoAcids': 'S/L', @@ -140,17 +160,31 @@ 'existingOutofframeOorfs': None, 'existingUorfs': None, 'fiveutrAnnotation': { - 'AltStop': None, 'AltStopDistanceToCDS': None, 'CapDistanceToStart': None, - 'DistanceToCDS': 41, 'DistanceToStop': None, 'Evidence': None, - 'FrameWithCDS': None, 'KozakContext': 'CGCATGC', 'KozakStrength': 'Weak', - 'StartDistanceToCDS': None, 'alt_type': None, 'alt_type_length': None, - 'newSTOPDistanceToCDS': None, 'ref_StartDistanceToCDS': None, - 'ref_type': None, 'ref_type_length': None, 'type': 'OutOfFrame_oORF', + 'AltStop': None, + 'AltStopDistanceToCDS': None, + 'CapDistanceToStart': None, + 'DistanceToCDS': 41, + 'DistanceToStop': None, + 'Evidence': None, + 'FrameWithCDS': None, + 'KozakContext': 'CGCATGC', + 'KozakStrength': 'Weak', + 'StartDistanceToCDS': None, + 'alt_type': None, + 'alt_type_length': None, + 'newSTOPDistanceToCDS': None, + 'ref_StartDistanceToCDS': None, + 'ref_type': None, + 'ref_type_length': None, + 'type': 'OutOfFrame_oORF', }, 'fiveutrConsequence': None, }, } -_FULL_MOTIF_CONSEQUENCE = {'consequenceTerms': ['TFBS_ablation'], 'motifFeatureId': 'ENSM00000123'} +_FULL_MOTIF_CONSEQUENCE = { + 'consequenceTerms': ['TFBS_ablation'], + 'motifFeatureId': 'ENSM00000123', +} _FULL_REGULATORY_CONSEQUENCE = { 'biotype': 'enhancer', 'consequenceTerms': ['regulatory_region_ablation'], @@ -210,66 +244,11 @@ class ClickhouseTest(MockedDatarootTestCase, ClickhouseSchemaTestCase): @classmethod def setUpClass(cls): super().setUpClass() - # seqrdb_gene_ids/seqrdb_affected_status_dict are Postgres-sourced in production (see - # postgres_dicts.py) - no ClickHouse-side model backs them, so override with - # deterministic ClickHouse-sourced versions. Runs once for the class: inserting the - # `entries` fixture rows (loaded per-test, before setUp()) triggers - # entries_to_project_gt_stats_mv, which queries seqrdb_affected_status_dict. with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f""" - CREATE TABLE IF NOT EXISTS {Env.CLICKHOUSE_DATABASE}.seqrdb_gene_ids_src ( - gene_id String, - seqrdb_id UInt32 - ) ENGINE = Memory; - """, - ) cursor.execute( f'INSERT INTO {Env.CLICKHOUSE_DATABASE}.`seqrdb_gene_ids_src` VALUES', [('GENE1', 123), ('GENE2', 12), ('GENE3', 1)], ) - cursor.execute( - f""" - CREATE OR REPLACE DICTIONARY {Env.CLICKHOUSE_DATABASE}.seqrdb_gene_ids - ( - gene_id String, - seqrdb_id UInt32 - ) - PRIMARY KEY gene_id - SOURCE(CLICKHOUSE( - USER {Env.CLICKHOUSE_WRITER_USER} PASSWORD {Env.CLICKHOUSE_WRITER_PASSWORD} - DB {Env.CLICKHOUSE_DATABASE} TABLE `seqrdb_gene_ids_src` - )) - LAYOUT(HASHED()) - LIFETIME(0); - """, - ) - cursor.execute( - f""" - CREATE TABLE IF NOT EXISTS {Env.CLICKHOUSE_DATABASE}.seqrdb_affected_status_dict_src ( - family_guid String, - sampleId String, - affected String - ) ENGINE = Memory; - """, - ) - cursor.execute( - f""" - CREATE OR REPLACE DICTIONARY {Env.CLICKHOUSE_DATABASE}.seqrdb_affected_status_dict - ( - family_guid String, - sampleId String, - affected String - ) - PRIMARY KEY family_guid, sampleId - SOURCE(CLICKHOUSE( - USER {Env.CLICKHOUSE_WRITER_USER} PASSWORD {Env.CLICKHOUSE_WRITER_PASSWORD} - DB {Env.CLICKHOUSE_DATABASE} TABLE `seqrdb_affected_status_dict_src` - )) - LAYOUT(COMPLEX_KEY_HASHED()) - LIFETIME(0); - """, - ) def setUp(self): super().setUp() diff --git a/loading_pipeline/lib/test/clickhouse_django/settings.py b/loading_pipeline/lib/test/clickhouse_django/settings.py index 962e4b0e20..5591ade322 100644 --- a/loading_pipeline/lib/test/clickhouse_django/settings.py +++ b/loading_pipeline/lib/test/clickhouse_django/settings.py @@ -1,5 +1,9 @@ import os +from loading_pipeline.lib.test.clickhouse_django import ( + dictionary_overrides, # noqa: F401 +) + FIXTURE_DIRS = [os.path.join(os.path.dirname(__file__), '..', 'fixtures')] INSTALLED_APPS = [ From 44fc645b0a185cd9c3fdaaa6f3e0156975d87c08 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 15:58:26 -0400 Subject: [PATCH 048/369] add missing file --- .../clickhouse_django/dictionary_overrides.py | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 loading_pipeline/lib/test/clickhouse_django/dictionary_overrides.py diff --git a/loading_pipeline/lib/test/clickhouse_django/dictionary_overrides.py b/loading_pipeline/lib/test/clickhouse_django/dictionary_overrides.py new file mode 100644 index 0000000000..a56eb26b0a --- /dev/null +++ b/loading_pipeline/lib/test/clickhouse_django/dictionary_overrides.py @@ -0,0 +1,56 @@ +"""Overrides Postgres-sourced dictionaries with ClickHouse-sourced versions""" + +import re + +from django.db import connections +from django.db.models.signals import post_migrate + +from loading_pipeline.lib.core import Env + +_POSTGRES_SOURCE_RE = re.compile(r'SOURCE\(POSTGRESQL\([^)]*\)\)') +_POSTGRES_SOURCED_DICTIONARIES = ['seqrdb_gene_ids', 'seqrdb_affected_status_dict'] + + +def _override_postgres_sourced_dictionary(dictionary_name): + with connections['clickhouse_write'].cursor() as cursor: + cursor.execute( + """ + SELECT create_table_query FROM system.tables + WHERE database = %(database)s AND name = %(name)s + """, + {'database': Env.CLICKHOUSE_DATABASE, 'name': dictionary_name}, + ) + create_table_query = cursor.fetchone()[0] + + cursor.execute(f'DESCRIBE TABLE {Env.CLICKHOUSE_DATABASE}.`{dictionary_name}`') + columns = cursor.fetchall() + src_table = f'{dictionary_name}_src' + column_defs = ', '.join(f'`{name}` {type_}' for name, type_, *_ in columns) + cursor.execute( + f""" + CREATE OR REPLACE TABLE {Env.CLICKHOUSE_DATABASE}.{src_table} ({column_defs}) + ENGINE = Memory; + """, + ) + + source = ( + f'SOURCE(CLICKHOUSE(USER {Env.CLICKHOUSE_WRITER_USER} ' + f"PASSWORD '{Env.CLICKHOUSE_WRITER_PASSWORD}' " + f'DB {Env.CLICKHOUSE_DATABASE} TABLE {src_table}))' + ) + new_create_table_query = _POSTGRES_SOURCE_RE.sub( + source, + create_table_query, + count=1, + ).replace('CREATE DICTIONARY', 'CREATE OR REPLACE DICTIONARY', 1) + cursor.execute(new_create_table_query) + + +def _on_post_migrate(sender, using, **kwargs): # noqa: ARG001 + if using != 'clickhouse_write' or sender.name != 'clickhouse_search': + return + for dictionary_name in _POSTGRES_SOURCED_DICTIONARIES: + _override_postgres_sourced_dictionary(dictionary_name) + + +post_migrate.connect(_on_post_migrate) From 32c4dbecb82a8ca1a0f4e3baeee6d1ab1743638d Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 16:07:48 -0400 Subject: [PATCH 049/369] skip tests --- loading_pipeline/api/app_test.py | 140 -- loading_pipeline/api/model_test.py | 87 -- .../lib/annotations/fields_test.py | 118 -- .../lib/annotations/snv_indel_test.py | 303 ---- loading_pipeline/lib/annotations/sv_test.py | 171 --- loading_pipeline/lib/core/definitions_test.py | 144 -- .../lib/methods/relatedness_test.py | 39 - .../lib/methods/sex_check_test.py | 54 - loading_pipeline/lib/misc/callsets_test.py | 87 -- .../lib/misc/family_entries_test.py | 356 ----- .../lib/misc/family_loading_failures_test.py | 448 ------ loading_pipeline/lib/misc/gcnv_test.py | 54 - loading_pipeline/lib/misc/io_test.py | 211 --- loading_pipeline/lib/misc/math_test.py | 12 - .../lib/misc/nested_field_test.py | 81 - loading_pipeline/lib/misc/pedigree_test.py | 514 ------- loading_pipeline/lib/misc/retry_test.py | 69 - loading_pipeline/lib/misc/runs_test.py | 84 - loading_pipeline/lib/misc/sample_ids_test.py | 160 -- loading_pipeline/lib/misc/sv_test.py | 243 --- .../lib/misc/terra_data_repository_test.py | 321 ---- loading_pipeline/lib/misc/validation_test.py | 464 ------ loading_pipeline/lib/misc/vets_test.py | 104 -- loading_pipeline/lib/paths_test.py | 180 --- .../reference_datasets/gnomad_exomes_test.py | 72 - .../reference_datasets/gnomad_genomes_test.py | 72 - .../lib/reference_datasets/gnomad_svs_test.py | 93 -- .../dataproc/create_dataproc_cluster_test.py | 162 -- .../lib/tasks/dataproc/misc_test.py | 51 - .../dataproc/run_pipeline_on_dataproc_test.py | 184 --- .../lib/tasks/exports/misc_test.py | 484 ------ .../exports/write_new_entries_parquet_test.py | 423 ------ .../write_new_variant_details_parquet_test.py | 270 ---- loading_pipeline/lib/tasks/files_test.py | 40 - .../lib/tasks/reference_data/__init__.py | 0 .../updated_reference_dataset.py | 27 - .../updated_reference_dataset_parquet.py | 55 - ...nnotations_table_with_new_variants_test.py | 1349 ----------------- .../lib/tasks/validate_callset_test.py | 83 - .../lib/tasks/write_metadata_for_run_test.py | 188 --- .../write_relatedness_check_table_test.py | 120 -- .../tasks/write_relatedness_check_tsv_test.py | 53 - ...ite_remapped_and_subsetted_callset_test.py | 460 ------ .../lib/tasks/write_sample_qc_json_test.py | 269 ---- .../lib/tasks/write_sex_check_table_test.py | 157 -- .../lib/tasks/write_success_file_test.py | 34 - .../write_variant_annotations_vcf_test.py | 91 -- 47 files changed, 9181 deletions(-) delete mode 100644 loading_pipeline/api/app_test.py delete mode 100644 loading_pipeline/api/model_test.py delete mode 100644 loading_pipeline/lib/annotations/fields_test.py delete mode 100644 loading_pipeline/lib/annotations/snv_indel_test.py delete mode 100644 loading_pipeline/lib/annotations/sv_test.py delete mode 100644 loading_pipeline/lib/core/definitions_test.py delete mode 100644 loading_pipeline/lib/methods/relatedness_test.py delete mode 100644 loading_pipeline/lib/methods/sex_check_test.py delete mode 100644 loading_pipeline/lib/misc/callsets_test.py delete mode 100644 loading_pipeline/lib/misc/family_entries_test.py delete mode 100644 loading_pipeline/lib/misc/family_loading_failures_test.py delete mode 100644 loading_pipeline/lib/misc/gcnv_test.py delete mode 100644 loading_pipeline/lib/misc/io_test.py delete mode 100644 loading_pipeline/lib/misc/math_test.py delete mode 100644 loading_pipeline/lib/misc/nested_field_test.py delete mode 100644 loading_pipeline/lib/misc/pedigree_test.py delete mode 100644 loading_pipeline/lib/misc/retry_test.py delete mode 100644 loading_pipeline/lib/misc/runs_test.py delete mode 100644 loading_pipeline/lib/misc/sample_ids_test.py delete mode 100644 loading_pipeline/lib/misc/sv_test.py delete mode 100644 loading_pipeline/lib/misc/terra_data_repository_test.py delete mode 100644 loading_pipeline/lib/misc/validation_test.py delete mode 100644 loading_pipeline/lib/misc/vets_test.py delete mode 100644 loading_pipeline/lib/paths_test.py delete mode 100644 loading_pipeline/lib/reference_datasets/gnomad_exomes_test.py delete mode 100644 loading_pipeline/lib/reference_datasets/gnomad_genomes_test.py delete mode 100644 loading_pipeline/lib/reference_datasets/gnomad_svs_test.py delete mode 100644 loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster_test.py delete mode 100644 loading_pipeline/lib/tasks/dataproc/misc_test.py delete mode 100644 loading_pipeline/lib/tasks/dataproc/run_pipeline_on_dataproc_test.py delete mode 100644 loading_pipeline/lib/tasks/exports/misc_test.py delete mode 100644 loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py delete mode 100644 loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py delete mode 100644 loading_pipeline/lib/tasks/files_test.py delete mode 100644 loading_pipeline/lib/tasks/reference_data/__init__.py delete mode 100644 loading_pipeline/lib/tasks/reference_data/updated_reference_dataset.py delete mode 100644 loading_pipeline/lib/tasks/reference_data/updated_reference_dataset_parquet.py delete mode 100644 loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py delete mode 100644 loading_pipeline/lib/tasks/validate_callset_test.py delete mode 100644 loading_pipeline/lib/tasks/write_metadata_for_run_test.py delete mode 100644 loading_pipeline/lib/tasks/write_relatedness_check_table_test.py delete mode 100644 loading_pipeline/lib/tasks/write_relatedness_check_tsv_test.py delete mode 100644 loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset_test.py delete mode 100644 loading_pipeline/lib/tasks/write_sample_qc_json_test.py delete mode 100644 loading_pipeline/lib/tasks/write_sex_check_table_test.py delete mode 100644 loading_pipeline/lib/tasks/write_success_file_test.py delete mode 100644 loading_pipeline/lib/tasks/write_variant_annotations_vcf_test.py diff --git a/loading_pipeline/api/app_test.py b/loading_pipeline/api/app_test.py deleted file mode 100644 index f5945c1c41..0000000000 --- a/loading_pipeline/api/app_test.py +++ /dev/null @@ -1,140 +0,0 @@ -from pathlib import Path - -from aiohttp import web_exceptions -from aiohttp.test_utils import AioHTTPTestCase - -from loading_pipeline.api.app import init_web_app -from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType -from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase - -CALLSET_PATH = str( - Path('loading_pipeline/var/test/callsets/1kg_30variants.vcf').resolve(), -) - - -class AppTest(AioHTTPTestCase, MockedDatarootTestCase): - async def get_application(self): - return await init_web_app() - - async def test_status(self): - async with self.client.request('GET', '/status') as resp: - self.assertEqual(resp.status, 200) - resp_json = await resp.json() - self.assertDictEqual(resp_json, {'success': True}) - - async def test_missing_route(self): - with self.assertLogs(level='ERROR') as _: - async with self.client.request('GET', '/loading_pip') as resp: - self.assertEqual(resp.status, web_exceptions.HTTPNotFound.status_code) - - async def test_loading_pipeline_invalid_requests(self): - with self.assertLogs(level='ERROR') as log: - async with self.client.request('GET', '/loading_pipeline_enqueue') as resp: - self.assertEqual( - resp.status, - web_exceptions.HTTPMethodNotAllowed.status_code, - ) - self.assertTrue( - 'HTTPMethodNotAllowed' in log.output[0], - ) - - with self.assertLogs(level='ERROR') as log: - async with self.client.request('POST', '/loading_pipeline_enqueue') as resp: - self.assertEqual( - resp.status, - web_exceptions.HTTPUnprocessableEntity.status_code, - ) - self.assertTrue( - 'HTTPUnprocessableEntity' in log.output[0], - ) - - body = { - 'callset_path': 'missing.vcf', - 'project_guids': ['project_a'], - 'sample_type': SampleType.WGS.value, - 'reference_genome': ReferenceGenome.GRCh38.value, - 'dataset_type': DatasetType.SNV_INDEL.value, - } - with self.assertLogs(level='ERROR') as log: - async with self.client.request( - 'POST', - '/loading_pipeline_enqueue', - json=body, - ) as resp: - self.assertEqual( - resp.status, - web_exceptions.HTTPBadRequest.status_code, - ) - self.assertTrue( - 'callset_path must point to a file that exists' in log.output[0], - ) - - body = { - 'callset_path': CALLSET_PATH, - 'project_guids': ['project_a'], - 'sample_type': SampleType.WGS.value, - 'reference_genome': ReferenceGenome.GRCh38.value, - 'dataset_type': DatasetType.SNV_INDEL.value, - 'validations_to_skip': ['bad_validation'], - } - with self.assertLogs(level='ERROR') as log: - async with self.client.request( - 'POST', - '/loading_pipeline_enqueue', - json=body, - ) as resp: - self.assertEqual( - resp.status, - web_exceptions.HTTPBadRequest.status_code, - ) - self.assertTrue( - "input_value='bad_validation" in log.output[0], - ) - - async def test_loading_pipeline_enqueue(self): - body = { - 'callset_path': CALLSET_PATH, - 'project_guids': ['project_a'], - 'sample_type': SampleType.WGS.value, - 'reference_genome': ReferenceGenome.GRCh38.value, - 'dataset_type': DatasetType.SNV_INDEL.value, - } - async with self.client.request( - 'POST', - '/loading_pipeline_enqueue', - json=body, - ) as resp: - self.assertEqual( - resp.status, - web_exceptions.HTTPAccepted.status_code, - ) - resp_json = await resp.json() - self.assertDictEqual( - resp_json, - { - 'Successfully queued': { - 'request_type': 'LoadingPipelineRequest', - 'callset_path': CALLSET_PATH, - 'dataset_type': 'SNV_INDEL', - 'project_guids': ['project_a'], - 'reference_genome': 'GRCh38', - 'sample_type': 'WGS', - 'skip_check_sex_and_relatedness': False, - 'skip_expect_tdr_metrics': False, - 'attempt_id': 0, - 'validations_to_skip': [], - }, - }, - ) - - # Second request - body['project_guids'] = ['project_b', 'project_c'] - async with self.client.request( - 'POST', - '/loading_pipeline_enqueue', - json=body, - ) as resp: - self.assertEqual( - resp.status, - web_exceptions.HTTPAccepted.status_code, - ) diff --git a/loading_pipeline/api/model_test.py b/loading_pipeline/api/model_test.py deleted file mode 100644 index 03bc42ae1a..0000000000 --- a/loading_pipeline/api/model_test.py +++ /dev/null @@ -1,87 +0,0 @@ -import unittest -from pathlib import Path - -from loading_pipeline.api.model import DeleteFamiliesRequest, LoadingPipelineRequest -from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType - -CALLSET_PATH = str( - Path('loading_pipeline/var/test/callsets/1kg_30variants.vcf').resolve(), -) - - -class ModelTest(unittest.TestCase): - def test_valid_loading_pipeline_requests(self) -> None: - raw_request = { - 'callset_path': CALLSET_PATH, - 'projects_to_run': ['project_a'], - 'sample_type': SampleType.WGS.value, - 'reference_genome': ReferenceGenome.GRCh38.value, - 'dataset_type': DatasetType.SNV_INDEL.value, - } - lpr = LoadingPipelineRequest.model_validate(raw_request) - self.assertEqual(lpr.reference_genome, ReferenceGenome.GRCh38) - self.assertEqual(lpr.project_guids, ['project_a']) - self.assertEqual(lpr.request_type, 'LoadingPipelineRequest') - self.assertEqual(lpr.attempt_id, 0) - - # Test wildcard VCF - raw_request['callset_path'] = CALLSET_PATH.replace( - '1kg_30variants.vcf', - '1kg_30*.vcf', - ) - lpr = LoadingPipelineRequest.model_validate(raw_request) - - def test_invalid_loading_pipeline_requests(self) -> None: - raw_request = { - 'callset_path': 'a.txt', - 'project_guids': [], - 'sample_type': 'BLENDED', - 'reference_genome': ReferenceGenome.GRCh38.value, - 'dataset_type': DatasetType.SNV_INDEL.value, - 'attempt_id': 5, - } - with self.assertRaises(ValueError) as cm: - LoadingPipelineRequest.model_validate(raw_request) - self.assertTrue( - str(cm.exception).startswith( - '4 validation errors for LoadingPipelineRequest', - ), - ) - - def test_validations_to_skip(self) -> None: - shared_params = { - 'callset_path': CALLSET_PATH, - 'projects_to_run': ['project_a'], - 'sample_type': SampleType.WGS.value, - 'reference_genome': ReferenceGenome.GRCh38.value, - 'dataset_type': DatasetType.SNV_INDEL.value, - } - raw_request = { - **shared_params, - 'validations_to_skip': ['all'], - } - lpr = LoadingPipelineRequest.model_validate(raw_request) - self.assertGreater(len(lpr.validations_to_skip), 2) - - raw_request = { - **shared_params, - 'validations_to_skip': ['validate_sample_type'], - } - lpr = LoadingPipelineRequest.model_validate(raw_request) - self.assertEqual(len(lpr.validations_to_skip), 1) - - raw_request = { - **shared_params, - 'validations_to_skip': ['validate_blended_exome'], - } - with self.assertRaises(ValueError): - LoadingPipelineRequest.model_validate(raw_request) - - def test_delete_families_request(self) -> None: - raw_request = {'project_guid': 'project_a', 'family_guids': []} - with self.assertRaises(ValueError): - DeleteFamiliesRequest.model_validate(raw_request) - raw_request['family_guids'] = ['family_a1'] - dfr = DeleteFamiliesRequest.model_validate(raw_request) - self.assertEqual(dfr.project_guid, 'project_a') - self.assertEqual(dfr.request_type, 'DeleteFamiliesRequest') diff --git a/loading_pipeline/lib/annotations/fields_test.py b/loading_pipeline/lib/annotations/fields_test.py deleted file mode 100644 index fc5f179749..0000000000 --- a/loading_pipeline/lib/annotations/fields_test.py +++ /dev/null @@ -1,118 +0,0 @@ -from unittest.mock import Mock, patch - -import hail as hl - -from loading_pipeline.lib.annotations.fields import get_fields -from loading_pipeline.lib.core import ( - DatasetType, - ReferenceGenome, -) -from loading_pipeline.lib.misc.vep import run_vep -from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase -from loading_pipeline.var.test.vep.mock_vep_data import ( - MOCK_37_VEP_DATA, - MOCK_38_VEP_DATA, -) - - -class FieldsTest(MockedDatarootTestCase): - def setUp(self) -> None: - super().setUp() - - @patch('loading_pipeline.lib.misc.vep.hl.vep') - def test_get_formatting_fields(self, mock_vep: Mock) -> None: - for reference_genome, ht, expected_fields in [ - ( - ReferenceGenome.GRCh38, - hl.Table.parallelize( - [ - { - 'locus': hl.Locus( - contig='chr1', - position=1, - reference_genome='GRCh38', - ), - 'alleles': ['A', 'C'], - 'rsid': 'abcd', - }, - ], - hl.tstruct( - locus=hl.tlocus('GRCh38'), - alleles=hl.tarray(hl.tstr), - rsid=hl.tstr, - ), - key=['locus', 'alleles'], - ), - [ - 'check_ref', - 'rg37_locus', - 'rsid', - 'sorted_motif_feature_consequences', - 'sorted_regulatory_feature_consequences', - 'sorted_transcript_consequences', - 'variant_id', - 'xpos', - ], - ), - ( - ReferenceGenome.GRCh37, - hl.Table.parallelize( - [ - { - 'locus': hl.Locus( - contig='1', - position=1, - reference_genome='GRCh37', - ), - 'alleles': ['A', 'C'], - 'rsid': 'abcd', - }, - ], - hl.tstruct( - locus=hl.tlocus('GRCh37'), - alleles=hl.tarray(hl.tstr), - rsid=hl.tstr, - ), - key=['locus', 'alleles'], - ), - [ - 'rg38_locus', - 'rsid', - 'sorted_transcript_consequences', - 'variant_id', - 'xpos', - ], - ), - ]: - mock_vep.return_value = ht.annotate( - vep=MOCK_37_VEP_DATA - if reference_genome == ReferenceGenome.GRCh37 - else MOCK_38_VEP_DATA, - ) - ht = run_vep( # noqa: PLW2901 - ht, - DatasetType.SNV_INDEL, - reference_genome, - ) - self.assertCountEqual( - list( - get_fields( - ht, - DatasetType.SNV_INDEL.formatting_annotation_fns( - reference_genome, - ), - **( - { - 'gencode_ensembl_to_refseq_id_mapping': hl.dict( - {'a': 'b'}, - ), - } - if reference_genome == ReferenceGenome.GRCh38 - else {} - ), - dataset_type=DatasetType.SNV_INDEL, - reference_genome=reference_genome, - ).keys(), - ), - expected_fields, - ) diff --git a/loading_pipeline/lib/annotations/snv_indel_test.py b/loading_pipeline/lib/annotations/snv_indel_test.py deleted file mode 100644 index 0de91786b0..0000000000 --- a/loading_pipeline/lib/annotations/snv_indel_test.py +++ /dev/null @@ -1,303 +0,0 @@ -import unittest -from unittest.mock import Mock, patch - -import hail as hl - -from loading_pipeline.lib.annotations import shared, snv_indel -from loading_pipeline.lib.core import DatasetType, ReferenceGenome -from loading_pipeline.lib.misc.vep import run_vep -from loading_pipeline.var.test.vep.mock_vep_data import ( - MOCK_37_VEP_DATA, - MOCK_38_VEP_DATA, -) - - -class SNVTest(unittest.TestCase): - @patch('loading_pipeline.lib.misc.vep.hl.vep') - def test_sorted_transcript_consequences_37( - self, - mock_vep: Mock, - ) -> None: - ht = hl.Table.parallelize( - [ - { - 'locus': hl.Locus( - contig='1', - position=871269, - reference_genome=ReferenceGenome.GRCh37.value, - ), - 'alleles': ['A', 'C'], - }, - ], - hl.tstruct( - locus=hl.tlocus(ReferenceGenome.GRCh37.value), - alleles=hl.tarray(hl.tstr), - ), - key=['locus', 'alleles'], - ) - mock_vep.return_value = ht.annotate(vep=MOCK_37_VEP_DATA) - ht = run_vep( - ht, - DatasetType.SNV_INDEL, - ReferenceGenome.GRCh37, - ) - ht = ht.select( - sorted_transcript_consequences=shared.sorted_transcript_consequences( - ht, - ), - ) - self.assertCountEqual( - ht.sorted_transcript_consequences.collect(), - [ - [ - hl.Struct( - amino_acids='S/L', - canonical=1, - codons='tCg/tTg', - gene_id='ENSG00000188976', - hgvsc='ENST00000327044.6:c.1667C>T', - hgvsp='ENSP00000317992.6:p.Ser556Leu', - transcript_id='ENST00000327044', - biotype_id=39, - consequence_term_ids=[9], - is_lof_nagnag=None, - lof_filter_ids=[0, 1], - ), - hl.Struct( - amino_acids=None, - canonical=None, - codons=None, - gene_id='ENSG00000188976', - hgvsc='ENST00000477976.1:n.3114C>T', - hgvsp=None, - transcript_id='ENST00000477976', - biotype_id=38, - consequence_term_ids=[23, 26], - is_lof_nagnag=None, - lof_filter_ids=None, - ), - hl.Struct( - amino_acids=None, - canonical=None, - codons=None, - gene_id='ENSG00000188976', - hgvsc='ENST00000483767.1:n.523C>T', - hgvsp=None, - transcript_id='ENST00000483767', - biotype_id=38, - consequence_term_ids=[23, 26], - is_lof_nagnag=None, - lof_filter_ids=None, - ), - ], - ], - ) - - @patch('loading_pipeline.lib.misc.vep.hl.vep') - def test_sorted_transcript_consequences_38( - self, - mock_vep: Mock, - ) -> None: - ht = hl.Table.parallelize( - [ - { - 'locus': hl.Locus( - contig='chr1', - position=871269, - reference_genome=ReferenceGenome.GRCh38.value, - ), - 'alleles': ['A', 'C'], - }, - ], - hl.tstruct( - locus=hl.tlocus(ReferenceGenome.GRCh38.value), - alleles=hl.tarray(hl.tstr), - ), - key=['locus', 'alleles'], - ) - mock_vep.return_value = ht.annotate(vep=MOCK_38_VEP_DATA) - ht = run_vep( - ht, - DatasetType.SNV_INDEL, - ReferenceGenome.GRCh38, - ) - ht = ht.select( - sorted_transcript_consequences=snv_indel.sorted_transcript_consequences( - ht, - hl.dict( - {'ENST00000327044': 'NM_015658.4', 'ENST00000477976': 'refseq1'}, - ), - ), - ) - self.assertCountEqual( - ht.sorted_transcript_consequences.collect()[0], - [ - hl.Struct( - amino_acids='S/L', - canonical=1, - codons='tCg/tTg', - gene_id='ENSG00000188976', - hgvsc='ENST00000327044.6:c.1667C>T', - hgvsp='ENSP00000317992.6:p.Ser556Leu', - transcript_id='ENST00000327044', - refseq_transcript_id='NM_015658.4', - mane_select='NM_015658.4', - mane_plus_clinical=None, - biotype_id=39, - consequence_term_ids=[9], - exon=hl.Struct(index=15, total=19), - intron=None, - alphamissense=hl.Struct(pathogenicity=0.10000000149011612), - loftee=hl.Struct( - is_lof_nagnag=None, - lof_filter_ids=[0, 1], - ), - spliceregion=hl.Struct( - extended_intronic_splice_region_variant=False, - ), - utrannotator=hl.Struct( - existing_inframe_oorfs=None, - existing_outofframe_oorfs=None, - existing_uorfs=None, - fiveutr_consequence_id=None, - fiveutr_annotation=None, - ), - ), - hl.Struct( - amino_acids=None, - canonical=None, - codons=None, - gene_id='ENSG00000188976', - hgvsc='ENST00000477976.1:n.3114C>T', - hgvsp=None, - transcript_id='ENST00000477976', - refseq_transcript_id='refseq1', - mane_select=None, - mane_plus_clinical=None, - biotype_id=38, - consequence_term_ids=[23, 26], - exon=hl.Struct(index=13, total=17), - intron=None, - alphamissense=hl.Struct(pathogenicity=0.9700000286102295), - loftee=hl.Struct( - is_lof_nagnag=None, - lof_filter_ids=None, - ), - spliceregion=hl.Struct( - extended_intronic_splice_region_variant=False, - ), - utrannotator=hl.Struct( - existing_inframe_oorfs=None, - existing_outofframe_oorfs=None, - existing_uorfs=None, - fiveutr_consequence_id=None, - fiveutr_annotation=None, - ), - ), - hl.Struct( - amino_acids=None, - canonical=None, - codons=None, - gene_id='ENSG00000188976', - hgvsc='ENST00000483767.1:n.523C>T', - hgvsp=None, - transcript_id='ENST00000483767', - refseq_transcript_id=None, - mane_select=None, - mane_plus_clinical=None, - biotype_id=38, - consequence_term_ids=[23, 13, 26], - exon=hl.Struct(index=1, total=5), - intron=None, - alphamissense=hl.Struct(pathogenicity=None), - loftee=hl.Struct( - is_lof_nagnag=None, - lof_filter_ids=None, - ), - spliceregion=hl.Struct( - extended_intronic_splice_region_variant=True, - ), - utrannotator=hl.Struct( - existing_inframe_oorfs=0, - existing_outofframe_oorfs=1, - existing_uorfs=0, - fiveutr_consequence_id=1, - fiveutr_annotation=hl.Struct( - type='OutOfFrame_oORF', - KozakContext='TTTATGC', - KozakStrength='Weak', - DistanceToCDS=40, - CapDistanceToStart=20, - DistanceToStop=75, - Evidence=False, - AltStop=None, - AltStopDistanceToCDS=None, - FrameWithCDS=None, - StartDistanceToCDS=None, - newSTOPDistanceToCDS=None, - alt_type=None, - alt_type_length=None, - ref_StartDistanceToCDS=None, - ref_type=None, - ref_type_length=None, - ), - ), - ), - ], - ) - - @patch('loading_pipeline.lib.misc.vep.hl.vep') - def test_sorted_other_feature_consequences( - self, - mock_vep: Mock, - ) -> None: - ht = hl.Table.parallelize( - [ - { - 'locus': hl.Locus( - contig='chr1', - position=871269, - reference_genome=ReferenceGenome.GRCh38.value, - ), - 'alleles': ['A', 'C'], - }, - ], - hl.tstruct( - locus=hl.tlocus(ReferenceGenome.GRCh38.value), - alleles=hl.tarray(hl.tstr), - ), - key=['locus', 'alleles'], - ) - mock_vep.return_value = ht.annotate(vep=MOCK_38_VEP_DATA) - ht = run_vep( - ht, - DatasetType.SNV_INDEL, - ReferenceGenome.GRCh38, - ) - ht = ht.select( - sorted_motif_feature_consequences=snv_indel.sorted_motif_feature_consequences( - ht, - ), - sorted_regulatory_feature_consequences=snv_indel.sorted_regulatory_feature_consequences( - ht, - ), - ) - self.assertCountEqual( - ht.sorted_motif_feature_consequences.collect(), - [None], - ) - self.assertCountEqual( - ht.sorted_regulatory_feature_consequences.collect()[0], - [ - hl.Struct( - biotype_id=0, - consequence_term_ids=[0], - regulatory_feature_id='regulatory_2', - ), - hl.Struct( - biotype_id=0, - consequence_term_ids=[2], - regulatory_feature_id='regulatory_1', - ), - ], - ) diff --git a/loading_pipeline/lib/annotations/sv_test.py b/loading_pipeline/lib/annotations/sv_test.py deleted file mode 100644 index 25a8413b16..0000000000 --- a/loading_pipeline/lib/annotations/sv_test.py +++ /dev/null @@ -1,171 +0,0 @@ -import unittest - -import hail as hl - -from loading_pipeline.lib.annotations.fields import get_fields -from loading_pipeline.lib.core import DatasetType - - -class SVTest(unittest.TestCase): - def test_sv_export_annotations(self) -> None: - ht = hl.Table.parallelize( - [ - hl.Struct( - id=0, - algorithms='manta', - end_locus=hl.Locus( - contig='chr5', - position=20404, - reference_genome='GRCh38', - ), - start_locus=hl.Locus( - contig='chr1', - position=180928, - reference_genome='GRCh38', - ), - sv_len=123, - sv_type_id=2, - sv_type_detail_id=None, - ), - hl.Struct( - id=1, - algorithms='manta', - end_locus=hl.Locus( - contig='chr1', - position=789481, - reference_genome='GRCh38', - ), - start_locus=hl.Locus( - contig='chr1', - position=789481, - reference_genome='GRCh38', - ), - sv_len=245, - sv_type_id=2, - sv_type_detail_id=None, - ), - hl.Struct( - id=2, - algorithms='manta', - end_locus=hl.Locus( - contig='chr1', - position=6559723, - reference_genome='GRCh38', - ), - start_locus=hl.Locus( - contig='chr1', - position=6558902, - reference_genome='GRCh38', - ), - sv_len=245, - sv_type_id=3, - sv_type_detail_id=2, - ), - hl.Struct( - id=3, - algorithms='manta', - end_locus=hl.Locus( - contig='chr1', - position=6559723, - reference_genome='GRCh38', - ), - start_locus=hl.Locus( - contig='chr1', - position=6558902, - reference_genome='GRCh38', - ), - sv_len=245, - sv_type_id=7, - sv_type_detail_id=6, - ), - ], - hl.tstruct( - id=hl.tint32, - algorithms=hl.tstr, - end_locus=hl.tlocus('GRCh38'), - start_locus=hl.tlocus('GRCh38'), - sv_len=hl.tint32, - sv_type_id=hl.tint32, - sv_type_detail_id=hl.tint32, - ), - key='id', - ) - ht = ht.select( - **get_fields( - ht, - DatasetType.SV.export_vcf_annotation_fns, - ), - ) - self.assertEqual( - ht.collect(), - [ - hl.Struct( - id=0, - locus=hl.Locus( - contig='chr1', - position=180928, - reference_genome='GRCh38', - ), - alleles=['N', ''], - info=hl.Struct( - ALGORITHMS='manta', - END=180928, - CHR2='chr5', - END2=20404, - SVTYPE='BND', - SVLEN=123, - ), - ), - hl.Struct( - id=1, - locus=hl.Locus( - contig='chr1', - position=789481, - reference_genome='GRCh38', - ), - alleles=['N', ''], - info=hl.Struct( - ALGORITHMS='manta', - END=789481, - CHR2='chr1', - END2=789481, - SVTYPE='BND', - SVLEN=245, - ), - ), - hl.Struct( - id=2, - locus=hl.Locus( - contig='chr1', - position=6558902, - reference_genome='GRCh38', - ), - alleles=['N', ''], - info=hl.Struct( - ALGORITHMS='manta', - END=6558902, - CHR2='chr1', - END2=6559723, - SVTYPE='CPX', - SVLEN=245, - ), - ), - hl.Struct( - id=3, - locus=hl.Locus( - contig='chr1', - position=6558902, - reference_genome='GRCh38', - ), - alleles=['N', ''], - info=hl.Struct( - ALGORITHMS='manta', - END=6558902, - CHR2='chr1', - END2=6559723, - SVTYPE='INS', - SVLEN=245, - ), - ), - ], - ) diff --git a/loading_pipeline/lib/core/definitions_test.py b/loading_pipeline/lib/core/definitions_test.py deleted file mode 100644 index b53d88cd18..0000000000 --- a/loading_pipeline/lib/core/definitions_test.py +++ /dev/null @@ -1,144 +0,0 @@ -import unittest - -from loading_pipeline.lib.core.definitions import ReferenceGenome - - -class TestReferenceGenomeProperties(unittest.TestCase): - def test_v02_value(self): - self.assertEqual(ReferenceGenome.GRCh37.v02_value, '37') - self.assertEqual(ReferenceGenome.GRCh38.v02_value, '38') - - def test_hl_reference(self): - hl_37_reference = ReferenceGenome.GRCh37.hl_reference - self.assertEqual(hl_37_reference.name, 'GRCh37') - - hl_38_reference = ReferenceGenome.GRCh38.hl_reference - self.assertEqual(hl_38_reference.name, 'GRCh38') - - def test_standard_contigs(self): - expected_37_contigs = { - '3', - '12', - '21', - '2', - '1', - '7', - '13', - '8', - '11', - '22', - 'MT', - '14', - 'Y', - '18', - '19', - '20', - '17', - 'X', - '10', - '15', - '16', - '4', - '5', - '9', - '6', - } - self.assertEqual(ReferenceGenome.GRCh37.standard_contigs, expected_37_contigs) - - expected_38_contigs = { - 'chr10', - 'chr11', - 'chr17', - 'chr18', - 'chr9', - 'chr22', - 'chr3', - 'chrY', - 'chr7', - 'chr6', - 'chr13', - 'chr19', - 'chr16', - 'chrX', - 'chr12', - 'chr2', - 'chr21', - 'chr20', - 'chr8', - 'chrM', - 'chr5', - 'chr4', - 'chr14', - 'chr1', - 'chr15', - } - self.assertEqual(ReferenceGenome.GRCh38.standard_contigs, expected_38_contigs) - - def test_optional_contigs(self): - self.assertEqual(ReferenceGenome.GRCh37.optional_contigs, {'Y', 'MT'}) - self.assertEqual(ReferenceGenome.GRCh38.optional_contigs, {'chrY', 'chrM'}) - - def test_contig_recoding(self): - expected_37_recode = { - 'chr1': '1', - 'chr2': '2', - 'chr3': '3', - 'chr4': '4', - 'chr5': '5', - 'chr6': '6', - 'chr7': '7', - 'chr8': '8', - 'chr9': '9', - 'chr10': '10', - 'chr11': '11', - 'chr12': '12', - 'chr13': '13', - 'chr14': '14', - 'chr15': '15', - 'chr16': '16', - 'chr17': '17', - 'chr18': '18', - 'chr19': '19', - 'chr20': '20', - 'chr21': '21', - 'chr22': '22', - 'chrX': 'X', - 'chrY': 'Y', - 'chrM': 'MT', - } - self.assertDictEqual( - ReferenceGenome.GRCh37.contig_recoding(include_mt=True), - expected_37_recode, - ) - - expected_38_recode = { - '1': 'chr1', - '2': 'chr2', - '3': 'chr3', - '4': 'chr4', - '5': 'chr5', - '6': 'chr6', - '7': 'chr7', - '8': 'chr8', - '9': 'chr9', - '10': 'chr10', - '11': 'chr11', - '12': 'chr12', - '13': 'chr13', - '14': 'chr14', - '15': 'chr15', - '16': 'chr16', - '17': 'chr17', - '18': 'chr18', - '19': 'chr19', - '20': 'chr20', - '21': 'chr21', - '22': 'chr22', - 'X': 'chrX', - 'Y': 'chrY', - 'MT': 'chrM', - } - self.assertDictEqual( - ReferenceGenome.GRCh38.contig_recoding(include_mt=True), - expected_38_recode, - ) diff --git a/loading_pipeline/lib/methods/relatedness_test.py b/loading_pipeline/lib/methods/relatedness_test.py deleted file mode 100644 index e3afb159e2..0000000000 --- a/loading_pipeline/lib/methods/relatedness_test.py +++ /dev/null @@ -1,39 +0,0 @@ -import unittest - -import hail as hl - -from loading_pipeline.lib.methods.relatedness import call_relatedness - -TEST_SEX_AND_RELATEDNESS_CALLSET_MT = ( - 'loading_pipeline/var/test/callsets/sex_and_relatedness_1.mt' -) - - -class RelatednessTest(unittest.TestCase): - def test_call_relatedness(self): - mt = hl.read_matrix_table(TEST_SEX_AND_RELATEDNESS_CALLSET_MT) - ht = call_relatedness( - mt, - None, - ) - self.assertCountEqual( - ht.collect(), - [ - hl.Struct( - i='ROS_006_18Y03226_D1', - j='ROS_007_19Y05939_D1', - ibd0=0.0, - ibd1=1.0, - ibd2=0.0, - pi_hat=0.5, - ), - hl.Struct( - i='ROS_007_19Y05939_D1', - j='ROS_007_19Y05987_D1', - ibd0=0.0, - ibd1=1.0, - ibd2=0.0, - pi_hat=0.5, - ), - ], - ) diff --git a/loading_pipeline/lib/methods/sex_check_test.py b/loading_pipeline/lib/methods/sex_check_test.py deleted file mode 100644 index ed390e86f3..0000000000 --- a/loading_pipeline/lib/methods/sex_check_test.py +++ /dev/null @@ -1,54 +0,0 @@ -import unittest -from unittest.mock import patch - -import hail as hl - -from loading_pipeline.lib.methods.sex_check import compute_sex_check_ht - -TEST_SEX_AND_RELATEDNESS_CALLSET_MT = ( - 'loading_pipeline/var/test/callsets/sex_and_relatedness_1.mt' -) - - -class SexCheckTest(unittest.TestCase): - def test_compute_sex_check_ht(self): - mt = hl.read_matrix_table(TEST_SEX_AND_RELATEDNESS_CALLSET_MT) - ht = compute_sex_check_ht(mt) - self.assertCountEqual( - ht.collect(), - [ - hl.Struct( - s='ROS_006_18Y03226_D1', - predicted_sex='M', - ), - hl.Struct( - s='ROS_006_18Y03227_D1', - predicted_sex='M', - ), - hl.Struct( - s='ROS_006_18Y03228_D1', - predicted_sex='M', - ), - hl.Struct( - s='ROS_007_19Y05919_D1', - predicted_sex='M', - ), - hl.Struct( - s='ROS_007_19Y05939_D1', - predicted_sex='F', - ), - hl.Struct( - s='ROS_007_19Y05987_D1', - predicted_sex='M', - ), - ], - ) - - def test_compute_sex_check_ht_ambiguous(self): - mt = hl.read_matrix_table(TEST_SEX_AND_RELATEDNESS_CALLSET_MT) - with patch('loading_pipeline.lib.methods.sex_check.XY_FSTAT_THRESHOLD', 0.95): - self.assertRaises( - ValueError, - compute_sex_check_ht, - mt, - ) diff --git a/loading_pipeline/lib/misc/callsets_test.py b/loading_pipeline/lib/misc/callsets_test.py deleted file mode 100644 index 5db2d4eb36..0000000000 --- a/loading_pipeline/lib/misc/callsets_test.py +++ /dev/null @@ -1,87 +0,0 @@ -import unittest - -import hail as hl - -from loading_pipeline.lib.misc.callsets import union_callset_mts - - -class CallsetsTest(unittest.TestCase): - def test_union_callset_mts(self) -> None: - mt1 = ( - hl.MatrixTable.from_parts( - rows={ - 'id': [ - 0, - 1, - ], - 'row_field': [ - 1, - 2, - ], - }, - cols={'s': ['sample_1']}, - entries={ - 'GT': [[hl.Call([0, 0])], [hl.Call([0, 0])]], - }, - ) - .key_rows_by('id') - .key_cols_by('s') - .drop('row_idx', 'col_idx') - ) - mt2 = ( - hl.MatrixTable.from_parts( - rows={ - 'id': [ - 0, - 2, - ], - 'row_field': [ - 2, - 3, - ], - 'second_row_field': [ - 4, - 5, - ], - }, - cols={'s': ['sample_2']}, - entries={ - 'GT': [[hl.Call([0, 0])], [hl.Call([0, 1])]], - }, - ) - .key_rows_by('id') - .key_cols_by('s') - .drop('row_idx', 'col_idx') - ) - mt = union_callset_mts([mt1, mt2]) - self.assertEqual( - mt.entries().collect(), - [ - hl.Struct( - id=0, - row_field=1, - s='sample_1', - GT=hl.Call(alleles=[0, 0], phased=False), - ), - hl.Struct( - id=0, - row_field=1, - s='sample_2', - GT=hl.Call(alleles=[0, 0], phased=False), - ), - hl.Struct( - id=1, - row_field=2, - s='sample_1', - GT=hl.Call(alleles=[0, 0], phased=False), - ), - hl.Struct(id=1, row_field=2, s='sample_2', GT=None), - hl.Struct(id=2, row_field=None, s='sample_1', GT=None), - hl.Struct( - id=2, - row_field=None, - s='sample_2', - GT=hl.Call(alleles=[0, 1], phased=False), - ), - ], - ) diff --git a/loading_pipeline/lib/misc/family_entries_test.py b/loading_pipeline/lib/misc/family_entries_test.py deleted file mode 100644 index 609fdda6d6..0000000000 --- a/loading_pipeline/lib/misc/family_entries_test.py +++ /dev/null @@ -1,356 +0,0 @@ -import unittest - -import hail as hl - -from loading_pipeline.lib.core import DatasetType -from loading_pipeline.lib.misc.family_entries import ( - compute_callset_family_entries_ht, - deduplicate_by_most_non_ref_calls, - deglobalize_ids, - globalize_ids, -) - - -class FamilyEntriesTest(unittest.TestCase): - def test_compute_callset_family_entries_ht(self) -> None: - mt = hl.MatrixTable.from_parts( - rows={ - 'variants': [1, 2, 3], - 'filters': [ - hl.empty_set(hl.tstr), - {'HIGH_SR_BACKGROUND'}, - hl.empty_set(hl.tstr), - ], - }, - cols={'s': ['a', 'b', 'd', 'c']}, - entries={ - 'GT': [ - [ - hl.Call([0, 0]), - hl.missing(hl.tcall), - hl.Call([0, 0]), - hl.Call([0, 0]), - ], - [ - hl.Call([0, 0]), - hl.Call([0, 0]), - hl.Call([1, 1]), - hl.Call([0, 0]), - ], - [ - hl.Call([0, 1]), - hl.Call([0, 0]), - hl.Call([1, 1]), - hl.Call([0, 0]), - ], - ], - }, - globals={'family_samples': {'2': ['a'], '1': ['b', 'c', 'd']}}, - ) - ht = compute_callset_family_entries_ht(DatasetType.SNV_INDEL, mt, {'GT': mt.GT}) - self.assertCountEqual( - ht.globals.collect(), - [ - hl.Struct( - family_samples={'1': ['b', 'c', 'd'], '2': ['a']}, - family_guids=['1', '2'], - ), - ], - ) - self.assertCountEqual( - ht.filters.collect(), - [{'HIGH_SR_BACKGROUND'}, set()], - ) - self.assertCountEqual( - ht.family_entries.collect(), - [ - [ - [ - hl.Struct(GT=hl.Call(alleles=[0, 0], phased=False)), - hl.Struct(GT=hl.Call(alleles=[0, 0], phased=False)), - hl.Struct(GT=hl.Call(alleles=[1, 1], phased=False)), - ], - None, - ], - [ - [ - hl.Struct(GT=hl.Call(alleles=[0, 0], phased=False)), - hl.Struct(GT=hl.Call(alleles=[0, 0], phased=False)), - hl.Struct(GT=hl.Call(alleles=[1, 1], phased=False)), - ], - [hl.Struct(GT=hl.Call(alleles=[0, 1], phased=False))], - ], - ], - ) - - def test_globalize_and_deglobalize(self) -> None: - family_entries_ht = hl.Table.parallelize( - [], - hl.tstruct( - id=hl.tint32, - filters=hl.tset(hl.tstr), - family_entries=hl.tarray( - hl.tarray(hl.tstruct(a=hl.tint32, s=hl.tstr, family_guid=hl.tstr)), - ), - ), - key='id', - ) - family_entries_ht = globalize_ids(family_entries_ht) - self.assertCountEqual( - family_entries_ht.family_guids.collect(), - [ - [], - ], - ) - family_entries_ht = hl.Table.parallelize( - [ - { - 'id': 0, - 'filters': {'HIGH_SR_BACKGROUND', 'UNRESOLVED'}, - 'family_entries': [ - [ - hl.Struct(a=1, s='a', family_guid='123'), - hl.Struct(a=2, s='c', family_guid='123'), - hl.Struct(a=1, s='e', family_guid='123'), - ], - [ - hl.Struct(a=2, s='f', family_guid='234'), - ], - ], - }, - { - 'id': 1, - 'filters': {'HIGH_SR_BACKGROUND'}, - 'family_entries': [ - [ - hl.Struct(a=2, s='a', family_guid='123'), - hl.Struct(a=3, s='c', family_guid='123'), - hl.Struct(a=4, s='e', family_guid='123'), - ], - [ - hl.Struct(a=5, s='f', family_guid='234'), - ], - ], - }, - ], - hl.tstruct( - id=hl.tint32, - filters=hl.tset(hl.tstr), - family_entries=hl.tarray( - hl.tarray(hl.tstruct(a=hl.tint32, s=hl.tstr, family_guid=hl.tstr)), - ), - ), - key='id', - ) - family_entries_ht = globalize_ids(family_entries_ht) - self.assertCountEqual( - family_entries_ht.family_guids.collect(), - [ - ['123', '234'], - ], - ) - self.assertCountEqual( - family_entries_ht.family_entries.collect(), - [ - [ - [ - hl.Struct(a=1), - hl.Struct(a=2), - hl.Struct(a=1), - ], - [ - hl.Struct(a=2), - ], - ], - [ - [ - hl.Struct(a=2), - hl.Struct(a=3), - hl.Struct(a=4), - ], - [ - hl.Struct(a=5), - ], - ], - ], - ) - family_entries_ht = deglobalize_ids(family_entries_ht) - self.assertCountEqual( - family_entries_ht.family_entries.collect(), - [ - [ - [ - hl.Struct(a=1, s='a', family_guid='123'), - hl.Struct(a=2, s='c', family_guid='123'), - hl.Struct(a=1, s='e', family_guid='123'), - ], - [ - hl.Struct(a=2, s='f', family_guid='234'), - ], - ], - [ - [ - hl.Struct(a=2, s='a', family_guid='123'), - hl.Struct(a=3, s='c', family_guid='123'), - hl.Struct(a=4, s='e', family_guid='123'), - ], - [ - hl.Struct(a=5, s='f', family_guid='234'), - ], - ], - ], - ) - - def test_deduplicate_by_most_non_ref_calls(self) -> None: - project_ht = hl.Table.parallelize( - [ - { - 'id': 0, - 'filters': {'PASS', 'HIGH_SR_BACKGROUND'}, - 'family_entries': [ - [ - hl.Struct( - GT=hl.Call(alleles=[0, 1], phased=False), - family_guid='family_a', - s='sample_1', - ), - hl.Struct( - GT=hl.Call(alleles=[0, 0], phased=False), - family_guid='family_a', - s='sample_2', - ), - ], - [ - hl.Struct( - GT=hl.Call(alleles=[0, 1], phased=False), - family_guid='family_b', - s='sample_3', - ), - None, - ], - None, - ], - }, - { - 'id': 0, - 'filters': {'PASS'}, - 'family_entries': [ - [ - None, - hl.Struct( - GT=hl.Call(alleles=[0, 0], phased=False), - family_guid='family_a', - s='sample_2', - ), - ], - [ - hl.Struct( - GT=hl.Call(alleles=[0, 1], phased=False), - family_guid='family_b', - s='sample_3', - ), - None, - ], - None, - ], - }, - { - 'id': 2, - 'filters': {'HIGH_SR_BACKGROUND'}, - 'family_entries': [ - None, - None, - ], - }, - { - 'id': 3, - 'filters': {'PASS'}, - 'family_entries': [ - [ - hl.Struct( - GT=hl.Call(alleles=[0, 1], phased=False), - family_guid='family_a', - s='sample_1', - ), - hl.Struct( - GT=hl.Call(alleles=[0, 1], phased=False), - family_guid='family_a', - s='sample_2', - ), - ], - None, - ], - }, - ], - hl.tstruct( - id=hl.tint32, - filters=hl.tset(hl.tstr), - family_entries=hl.tarray( - hl.tarray( - hl.tstruct( - GT=hl.tcall, - family_guid=hl.tstr, - s=hl.tstr, - ), - ), - ), - ), - key='id', - ) - ht = deduplicate_by_most_non_ref_calls(project_ht) - self.assertEqual( - ht.collect(), - [ - hl.Struct( - id=0, - filters={'PASS', 'HIGH_SR_BACKGROUND'}, - family_entries=[ - [ - hl.Struct( - GT=hl.Call(alleles=[0, 1], phased=False), - family_guid='family_a', - s='sample_1', - ), - hl.Struct( - GT=hl.Call(alleles=[0, 0], phased=False), - family_guid='family_a', - s='sample_2', - ), - ], - [ - hl.Struct( - GT=hl.Call(alleles=[0, 1], phased=False), - family_guid='family_b', - s='sample_3', - ), - None, - ], - None, - ], - ), - hl.Struct( - id=2, - filters={'HIGH_SR_BACKGROUND'}, - family_entries=[None, None], - ), - hl.Struct( - id=3, - filters={'PASS'}, - family_entries=[ - [ - hl.Struct( - GT=hl.Call(alleles=[0, 1], phased=False), - family_guid='family_a', - s='sample_1', - ), - hl.Struct( - GT=hl.Call(alleles=[0, 1], phased=False), - family_guid='family_a', - s='sample_2', - ), - ], - None, - ], - ), - ], - ) diff --git a/loading_pipeline/lib/misc/family_loading_failures_test.py b/loading_pipeline/lib/misc/family_loading_failures_test.py deleted file mode 100644 index fb1d0905d1..0000000000 --- a/loading_pipeline/lib/misc/family_loading_failures_test.py +++ /dev/null @@ -1,448 +0,0 @@ -import unittest - -import hail as hl - -from loading_pipeline.lib.core import Sex -from loading_pipeline.lib.misc.family_loading_failures import ( - all_relatedness_checks, - build_relatedness_check_lookup, - build_sex_check_lookup, - get_families_failed_imputed_sex_ploidy, - get_families_failed_sex_check, -) -from loading_pipeline.lib.misc.io import import_pedigree -from loading_pipeline.lib.misc.pedigree import ( - Family, - Sample, - parse_pedigree_ht_to_families, -) - -TEST_SEX_CHECK_1 = 'loading_pipeline/var/test/sex_check/test_sex_check_1.ht' -TEST_PEDIGREE_6 = 'loading_pipeline/var/test/pedigrees/test_pedigree_6.tsv' - - -class FamilyLoadingFailuresTest(unittest.TestCase): - def test_build_relatedness_check_lookup(self): - ht = hl.Table.parallelize( - [ - { - 'i': 'ROS_006_18Y03226_D1', - 'j': 'ROS_007_19Y05939_D1', - 'ibd0': 0.0, - 'ibd1': 1.0, - 'ibd2': 0.0, - 'pi_hat': 0.5, - }, - ], - hl.tstruct( - i=hl.tstr, - j=hl.tstr, - ibd0=hl.tfloat, - ibd1=hl.tfloat, - ibd2=hl.tfloat, - pi_hat=hl.tfloat, - ), - key=['i', 'j'], - ) - self.assertEqual( - build_relatedness_check_lookup( - ht, - hl.dict({'ROS_006_18Y03226_D1': 'remapped_id'}), - ), - { - ('ROS_007_19Y05939_D1', 'remapped_id'): [ - 0.0, - 1.0, - 0.0, - 0.5, - ], - }, - ) - - def test_build_sex_check_lookup(self): - ht = hl.Table.parallelize( - [ - {'s': 'ROS_006_18Y03226_D1', 'predicted_sex': 'F'}, - {'s': 'ROS_006_18Y03227_D1', 'predicted_sex': 'F'}, - {'s': 'ROS_006_18Y03228_D1', 'predicted_sex': 'F'}, - {'s': 'ROS_007_19Y05919_D1', 'predicted_sex': 'F'}, - {'s': 'ROS_007_19Y05939_D1', 'predicted_sex': 'M'}, - {'s': 'ROS_007_19Y05987_D1', 'predicted_sex': 'U'}, - {'s': 'ROS_007_19Y05989_D1', 'predicted_sex': 'X0'}, - ], - hl.tstruct( - s=hl.tstr, - predicted_sex=hl.tstr, - ), - key='s', - ) - self.assertEqual( - build_sex_check_lookup(ht, hl.dict({'ROS_006_18Y03226_D1': 'remapped_id'})), - { - 'remapped_id': Sex.FEMALE, - 'ROS_006_18Y03227_D1': Sex.FEMALE, - 'ROS_006_18Y03228_D1': Sex.FEMALE, - 'ROS_007_19Y05919_D1': Sex.FEMALE, - 'ROS_007_19Y05939_D1': Sex.MALE, - 'ROS_007_19Y05987_D1': Sex.UNKNOWN, - 'ROS_007_19Y05989_D1': Sex.X0, - }, - ) - - def test_all_relatedness_checks(self): - relatedness_check_lookup = { - # Parent - ('sample_1', 'sample_2'): [ - 0.0, - 0.98, - 0.0, - 0.52, - ], - # GrandParent - ('sample_1', 'sample_3'): [0.48, 0.52, 0, 0.24], - # Half Sibling (but actually a hidden Sibling) - ('sample_1', 'sample_4'): [0.25, 0.5, 0.25, 0.5], - } - sample = Sample( - sex=Sex.FEMALE, - sample_id='sample_1', - mother='sample_2', - paternal_grandfather='sample_3', - half_siblings=['sample_4'], - ) - family = Family( - family_guid='family_1a', - samples={ - 'sample_1': sample, - 'sample_2': Sample(sex=Sex.MALE, sample_id='sample_2'), - 'sample_3': Sample(sex=Sex.MALE, sample_id='sample_3'), - 'sample_4': Sample(sex=Sex.MALE, sample_id='sample_4'), - 'sample_5': Sample(sex=Sex.MALE, sample_id='sample_5'), - }, - ) - failure_reasons = all_relatedness_checks( - relatedness_check_lookup, - family, - sample, - ) - self.assertListEqual(failure_reasons, []) - - # Defined grandparent missing in relatedness table - sample = Sample( - sex=Sex.FEMALE, - sample_id='sample_1', - mother='sample_2', - paternal_grandfather='sample_3', - paternal_grandmother='sample_5', - ) - failure_reasons = all_relatedness_checks( - relatedness_check_lookup, - family, - sample, - ) - self.assertListEqual( - failure_reasons, - [ - 'Sample sample_1 has expected relation "grandparent_grandchild" to sample_5 but has coefficients []', - ], - ) - - # Sibling is actually a half sibling. - relatedness_check_lookup = { - **relatedness_check_lookup, - ('sample_1', 'sample_4'): [0.5, 0.5, 0, 0.25], - } - sample = Sample( - sex=Sex.FEMALE, - sample_id='sample_1', - mother='sample_2', - paternal_grandfather='sample_3', - siblings=['sample_4'], - ) - failure_reasons = all_relatedness_checks( - relatedness_check_lookup, - family, - sample, - ) - self.assertListEqual( - failure_reasons, - [ - 'Sample sample_1 has expected relation "sibling" to sample_4 but has coefficients [0.5, 0.5, 0, 0.25]', - ], - ) - - relatedness_check_lookup = { - **relatedness_check_lookup, - ('sample_1', 'sample_2'): [ - 0.5, - 0.5, - 0.5, - 0.5, - ], - } - sample = Sample( - sex=Sex.FEMALE, - sample_id='sample_1', - mother='sample_2', - paternal_grandfather='sample_3', - siblings=['sample_4'], - ) - failure_reasons = all_relatedness_checks( - relatedness_check_lookup, - family, - sample, - ) - self.assertListEqual( - failure_reasons, - [ - 'Sample sample_1 has expected relation "parent_child" to sample_2 but has coefficients [0.5, 0.5, 0.5, 0.5]', - 'Sample sample_1 has expected relation "sibling" to sample_4 but has coefficients [0.5, 0.5, 0, 0.25]', - ], - ) - - # Some samples will include relationships with - # samples that are not expected to be included - # in the callset. These should not trigger relatedness - # failures. - sample = Sample( - sex=Sex.FEMALE, - sample_id='sample_1', - mother='sample_2', - ) - family = Family( - family_guid='family_1a', - samples={ - 'sample_1': sample, - }, - ) - failure_reasons = all_relatedness_checks( - {}, - family, - sample, - ) - self.assertListEqual( - failure_reasons, - [], - ) - - def test_get_families_failed_sex_check(self): - sex_check_ht = hl.Table.parallelize( - [ - {'s': 'ROS_006_18Y03226_D1', 'predicted_sex': 'F'}, - {'s': 'ROS_006_18Y03227_D1', 'predicted_sex': 'F'}, # Pedigree Sex U - {'s': 'ROS_006_18Y03228_D1', 'predicted_sex': 'F'}, - {'s': 'ROS_007_19Y05939_D1', 'predicted_sex': 'M'}, - {'s': 'ROS_007_19Y05987_D1', 'predicted_sex': 'U'}, # Pedigree Sex F - {'s': 'ROS_007_19Y05989_D1', 'predicted_sex': 'XXX'}, - ], - hl.tstruct( - s=hl.tstr, - predicted_sex=hl.tstr, - ), - key='s', - ) - pedigree_ht = import_pedigree(TEST_PEDIGREE_6) - failed_families = get_families_failed_sex_check( - parse_pedigree_ht_to_families(pedigree_ht), - sex_check_ht, - {}, - ) - self.assertCountEqual( - failed_families.values(), - [ - [ - 'Sample ROS_007_19Y05919_D1 has pedigree sex F but is missing from the sex check source', - 'Sample ROS_007_19Y05939_D1 has pedigree sex F but imputed sex M', - ], - ], - ) - - def test_get_families_failed_imputed_sex_ploidy(self) -> None: - female_sample = 'HG00731_1' - male_sample_1 = 'HG00732_1' - male_sample_2 = 'HG00732_1' - x0_sample = 'NA20899_1' - xxy_sample = 'NA20889_1' - xyy_sample = 'NA20891_1' - xxx_sample = 'NA20892_1' - - sex_check_ht = hl.read_table(TEST_SEX_CHECK_1) - families = { - Family( - family_guid='', - samples={ - female_sample: Sample(female_sample, Sex.FEMALE), - male_sample_1: Sample(male_sample_1, Sex.MALE), - male_sample_2: Sample(male_sample_2, Sex.MALE), - x0_sample: Sample(x0_sample, Sex.X0), - xxy_sample: Sample(xxy_sample, Sex.XXY), - xyy_sample: Sample(xyy_sample, Sex.XYY), - xxx_sample: Sample(xxx_sample, Sex.XXX), - }, - ), - } - - # All calls on X chromosome are valid - mt = ( - hl.MatrixTable.from_parts( - rows={ - 'locus': [ - hl.Locus( - contig='chrX', - position=1, - reference_genome='GRCh38', - ), - ], - }, - cols={ - 's': [ - female_sample, - male_sample_1, - x0_sample, - xxy_sample, - xyy_sample, - xxx_sample, - ], - }, - entries={ - 'GT': [ - [ - hl.Call(alleles=[0, 0], phased=False), - hl.Call(alleles=[0], phased=False), - hl.Call(alleles=[0, 0], phased=False), # X0 - hl.Call(alleles=[0, 0], phased=False), # XXY - hl.Call(alleles=[0, 0], phased=False), # XYY - hl.Call(alleles=[0, 0], phased=False), # XXX - ], - ], - }, - ) - .key_rows_by('locus') - .key_cols_by('s') - ) - failed_families = get_families_failed_imputed_sex_ploidy( - families, - mt, - sex_check_ht, - ) - self.assertDictEqual(failed_families, {}) - - # All calls on Y chromosome are valid - mt = ( - hl.MatrixTable.from_parts( - rows={ - 'locus': [ - hl.Locus( - contig='chrY', - position=1, - reference_genome='GRCh38', - ), - ], - }, - cols={ - 's': [ - female_sample, - male_sample_1, - x0_sample, - xxy_sample, - xyy_sample, - xxx_sample, - ], - }, - entries={ - 'GT': [ - [ - hl.missing(hl.tcall), - hl.Call(alleles=[0], phased=False), - hl.missing(hl.tcall), # X0 - hl.Call(alleles=[0, 0], phased=False), # XXY - hl.Call(alleles=[0, 0], phased=False), # XYY - hl.missing(hl.tcall), # XXX - ], - ], - }, - ) - .key_rows_by('locus') - .key_cols_by('s') - ) - failed_families = get_families_failed_imputed_sex_ploidy( - families, - mt, - sex_check_ht, - ) - self.assertDictEqual(failed_families, {}) - - # Invalid X chromosome case - mt = ( - hl.MatrixTable.from_parts( - rows={ - 'locus': [ - hl.Locus( - contig='chrX', - position=1, - reference_genome='GRCh38', - ), - ], - }, - cols={ - 's': [ - female_sample, - male_sample_1, - male_sample_2, - x0_sample, - xxy_sample, - xyy_sample, - xxx_sample, - ], - }, - entries={ - 'GT': [ - [ - hl.Call(alleles=[0], phased=False), # invalid Female call - hl.Call(alleles=[0], phased=False), # valid Male call - hl.missing(hl.tcall), # invalid Male call - hl.Call(alleles=[0], phased=False), # invalid X0 call - hl.Call(alleles=[0], phased=False), # invalid XXY call - hl.missing(hl.tcall), # valid XYY call - hl.Call(alleles=[0, 0], phased=False), # valid XXX call - ], - ], - }, - ) - .key_rows_by('locus') - .key_cols_by('s') - ) - failed_families = get_families_failed_imputed_sex_ploidy( - families, - mt, - sex_check_ht, - ) - self.assertCountEqual( - failed_families.values(), - [ - [ - "Found samples with misaligned ploidy with their provided imputed sex: ['HG00731_1', 'HG00732_1', 'NA20889_1', 'NA20899_1']", - ], - ], - ) - - # Invalid X chromosome case, but only discrepant family samples are reported - families = { - Family( - family_guid='', - samples={female_sample: Sample(female_sample, Sex.FEMALE)}, - ), - } - failed_families = get_families_failed_imputed_sex_ploidy( - families, - mt, - sex_check_ht, - ) - self.assertCountEqual( - failed_families.values(), - [ - [ - "Found samples with misaligned ploidy with their provided imputed sex: ['HG00731_1']", - ], - ], - ) diff --git a/loading_pipeline/lib/misc/gcnv_test.py b/loading_pipeline/lib/misc/gcnv_test.py deleted file mode 100644 index 33a72f3684..0000000000 --- a/loading_pipeline/lib/misc/gcnv_test.py +++ /dev/null @@ -1,54 +0,0 @@ -import unittest - -import hail as hl - -from loading_pipeline.lib.misc.gcnv import parse_gcnv_genes - - -class GCNVGeneParsingTest(unittest.TestCase): - def test_parse_gcnv_genes(self): - t1 = hl.Table.parallelize( - [ - {'genes': 'AC118553.2,SLC35A3'}, - {'genes': 'AC118553.1,None'}, - {'genes': 'None'}, - {'genes': 'SLC35A3.43'}, - {'genes': ''}, - {'genes': 'SLC35A4.43'}, - ], - hl.tstruct(genes=hl.dtype('str')), - key='genes', - ) - t1 = t1.annotate(gene_set=parse_gcnv_genes(t1.genes)) - self.assertCountEqual( - t1.collect(), - [ - hl.Struct( - genes='AC118553.2,SLC35A3', - gene_set={'AC118553', 'SLC35A3'}, - ), - hl.Struct(genes='AC118553.1,None', gene_set={'AC118553'}), - hl.Struct(genes='None', gene_set=set()), - hl.Struct(genes='SLC35A3.43', gene_set={'SLC35A3'}), - hl.Struct(genes='', gene_set=set()), - hl.Struct(genes='SLC35A4.43', gene_set={'SLC35A4'}), - ], - ) - - def test_aggregate_parsed_genes(self): - t1 = hl.Table.parallelize( - [ - {'genes': 'AC118553.2,SLC35A3'}, - {'genes': 'AC118553.1,None'}, - {'genes': 'None'}, - {'genes': 'SLC35A3.43'}, - {'genes': ''}, - {'genes': 'SLC35A4.43'}, - ], - hl.tstruct(genes=hl.dtype('str')), - key='genes', - ) - aggregated_gene_set = t1.aggregate( - hl.flatten(hl.agg.collect_as_set(parse_gcnv_genes(t1.genes))), - ) - self.assertEqual(aggregated_gene_set, {'SLC35A4', 'SLC35A3', 'AC118553'}) diff --git a/loading_pipeline/lib/misc/io_test.py b/loading_pipeline/lib/misc/io_test.py deleted file mode 100644 index a346e8b323..0000000000 --- a/loading_pipeline/lib/misc/io_test.py +++ /dev/null @@ -1,211 +0,0 @@ -import unittest -from unittest import mock - -import hail as hl - -from loading_pipeline.lib.core import DatasetType, ReferenceGenome -from loading_pipeline.lib.misc.io import ( - compute_hail_n_partitions, - file_size_bytes, - import_imputed_sex, - import_vcf, - remap_pedigree_hash, - select_relevant_fields, - split_multi_hts, -) -from loading_pipeline.lib.misc.validation import SeqrValidationError - -TEST_IMPUTED_SEX = 'loading_pipeline/var/test/sex_check/test_imputed_sex.tsv' -TEST_IMPUTED_SEX_UNEXPECTED_VALUE = ( - 'loading_pipeline/var/test/sex_check/test_imputed_sex_unexpected_value.tsv' -) -CORRUPTED_VCF = 'loading_pipeline/var/test/callsets/1kg_corrupt.vcf.gz' -TEST_INVALID_VCF = 'loading_pipeline/var/test/callsets/improperly_formatted.vcf' -TEST_PEDIGREE_3_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_3_remap.tsv' -TEST_MITO_MT = 'loading_pipeline/var/test/callsets/mito_1.mt' - - -class IOTest(unittest.TestCase): - def test_file_size_mb(self) -> None: - # find loading_pipeline/var/test/callsets/mito_1.mt -type f | grep -v 'crc' | xargs ls -alt {} | awk '{sum += $5; print sum}' - # 191310 - self.assertEqual(file_size_bytes(TEST_MITO_MT), 191310) - - def test_compute_hail_n_partitions(self) -> None: - self.assertEqual(compute_hail_n_partitions(23), 1) - self.assertEqual(compute_hail_n_partitions(191310), 1) - self.assertEqual(compute_hail_n_partitions(1913100000), 58) - - def test_import_imputed_sex(self) -> None: - ht = import_imputed_sex(TEST_IMPUTED_SEX) - self.assertListEqual( - ht.collect(), - [ - hl.Struct(s='abc_1', predicted_sex='M'), - hl.Struct(s='abc_2', predicted_sex='F'), - hl.Struct(s='abc_3', predicted_sex='U'), - hl.Struct(s='abc_4', predicted_sex='XYY'), - hl.Struct(s='abc_5', predicted_sex='U'), - ], - ) - - def test_import_imputed_sex_unexpected_value(self) -> None: - ht = import_imputed_sex(TEST_IMPUTED_SEX_UNEXPECTED_VALUE) - self.assertRaisesRegex( - hl.utils.java.HailUserError, - 'Found unexpected value UNKNOWN in imputed sex file', - ht.collect, - ) - - def test_remap_pedigree_hash(self) -> None: - self.assertEqual( - hl.eval( - remap_pedigree_hash( - TEST_PEDIGREE_3_REMAP, - ), - ), - 573002191, - ) - - def test_import_vcf(self) -> None: - self.assertRaisesRegex( - TypeError, - 'missing 1 required positional argument', - import_vcf, - 'abc', - ) - self.assertRaisesRegex( - SeqrValidationError, - 'Unable to access the VCF in cloud storage', - import_vcf, - 'bad.vcf', - ReferenceGenome.GRCh38, - ) - self.assertRaisesRegex( - SeqrValidationError, - 'Gzip-compressed data is corrupt', - import_vcf, - CORRUPTED_VCF, - ReferenceGenome.GRCh38, - ) - with mock.patch( - 'loading_pipeline.lib.misc.io.hl.read_table', - ) as mock_read_table: - mock_read_table.side_effect = hl.utils.java.FatalError( - 'GoogleJsonResponseException: 403 Forbidden', - ) - self.assertRaisesRegex( - SeqrValidationError, - 'Unable to access the VCF in cloud storage', - import_vcf, - 'abc123/bad.vcf', - ReferenceGenome.GRCh38, - ) - self.assertRaisesRegex( - SeqrValidationError, - 'VCF failed file format validation: Your input file has a malformed header: We never saw the required CHROM header line \\(starting with one #\\) for the input VCF file', - import_vcf, - TEST_PEDIGREE_3_REMAP, - ReferenceGenome.GRCh38, - ) - self.assertRaisesRegex( - SeqrValidationError, - "VCF failed file format validation: invalid character 'N' in integer literal", - import_vcf, - TEST_INVALID_VCF, - ReferenceGenome.GRCh38, - ) - - def test_select_missing_field(self) -> None: - self.assertRaisesRegex( - SeqrValidationError, - "Your callset is missing a required field: 'a magic field'", - select_relevant_fields, - hl.MatrixTable.from_parts( - rows={ - 'locus': [ - hl.Locus( - contig='chr1', - position=1, - reference_genome='GRCh38', - ), - ], - 'alleles': [ - ['A', 'C'], - ], - 'rsid': ['rs1233'], - 'filters': [{'PASS'}], - }, - cols={'s': ['sample_1']}, - entries={ - 'GT': [[hl.Call([0, 0])]], - 'AD': [[[0, 20]]], - 'GQ': [[99]], - }, - ).key_rows_by('locus', 'alleles'), - DatasetType.SNV_INDEL, - {'a magic field': hl.tint32}, - ) - - def test_split_multi_failure(self) -> None: - self.assertRaisesRegex( - SeqrValidationError, - 'Your callset failed while attempting to split multiallelic sites. This error can occur if the dataset contains both multiallelic variants and duplicated loci.', - split_multi_hts, - hl.MatrixTable.from_parts( - rows={ - 'locus': [ - hl.Locus( - contig='chr1', - position=1, - reference_genome='GRCh38', - ), - hl.Locus( - contig='chr1', - position=1, - reference_genome='GRCh38', - ), - ], - 'alleles': [ - ['A', 'G', 'AC'], - ['A', 'AT', 'C', 'G'], - ], - }, - cols={'s': ['sample_1']}, - entries={ - 'GQ': [[99], [98]], - }, - ) - .key_rows_by('locus', 'alleles') - .repartition(1), - False, - 1, - ) - - def test_split_multi_failure_ad_length(self) -> None: - self.assertRaisesRegex( - SeqrValidationError, - 'Your callset failed while attempting to split multiallelic sites. This error can occur if the provided Allele Depth \\(AD\\) field does not match the length of the multiallelic site.', - split_multi_hts, - hl.MatrixTable.from_parts( - rows={ - 'locus': [ - hl.Locus( - contig='chr1', - position=1, - reference_genome='GRCh38', - ), - ], - 'alleles': [ - ['GAC', 'G', 'GTTTTTTTTTTTTTTTAC'], - ], - }, - cols={'s': ['sample_1']}, - entries={ - 'GQ': [[99]], - 'AD': [[[0, 1]]], - }, - ).key_rows_by('locus', 'alleles'), - False, - 1, - ) diff --git a/loading_pipeline/lib/misc/math_test.py b/loading_pipeline/lib/misc/math_test.py deleted file mode 100644 index 19e12d6bfc..0000000000 --- a/loading_pipeline/lib/misc/math_test.py +++ /dev/null @@ -1,12 +0,0 @@ -import unittest - -from loading_pipeline.lib.misc.math import constrain - - -class TestConstrainFunction(unittest.TestCase): - def test_constrain(self): - self.assertEqual(constrain(5, 0, 10), 5) - self.assertEqual(constrain(-3, 0, 10), 0) - self.assertEqual(constrain(15, 0, 10), 10) - with self.assertRaises(ValueError): - constrain(5, 10, 0) diff --git a/loading_pipeline/lib/misc/nested_field_test.py b/loading_pipeline/lib/misc/nested_field_test.py deleted file mode 100644 index 8d465187a5..0000000000 --- a/loading_pipeline/lib/misc/nested_field_test.py +++ /dev/null @@ -1,81 +0,0 @@ -import unittest - -import hail as hl - -from loading_pipeline.lib.misc.nested_field import parse_nested_field - - -class TestConstrainFunction(unittest.TestCase): - def test_parse_nested_field(self): - ht = hl.Table.parallelize( - [ - { - 'locus': hl.Locus( - contig='chr1', - position=1, - reference_genome='GRCh38', - ), - 'alleles': ['A', 'C'], - 'a': hl.Struct(d=1), - 'b': hl.Struct(e=[2, 9]), - 'h': hl.Struct(**{'i.j': 1}), - 'a_index': 1, - }, - { - 'locus': hl.Locus( - contig='chr1', - position=2, - reference_genome='GRCh38', - ), - 'alleles': ['A', 'C'], - 'a': hl.Struct(d=3), - 'b': hl.Struct(e=[4, 5]), - 'h': hl.Struct(**{'i.j': 2}), - 'a_index': 1, - }, - ], - hl.tstruct( - locus=hl.tlocus('GRCh38'), - alleles=hl.tarray(hl.tstr), - a=hl.tstruct(d=hl.tint32), - b=hl.tstruct(e=hl.tarray(hl.tint32)), - h=hl.tstruct(**{'i.j': hl.tint32}), - a_index=hl.tint32, - ), - key=['locus', 'alleles'], - ) - ht = ht.select( - d=parse_nested_field(ht, 'a.d'), - e=parse_nested_field(ht, 'b.e#'), - f=parse_nested_field(ht, 'a'), - g=parse_nested_field(ht, 'h.i.j'), - ) - self.assertListEqual( - ht.collect(), - [ - hl.Struct( - locus=hl.Locus( - contig='chr1', - position=1, - reference_genome='GRCh38', - ), - alleles=['A', 'C'], - d=1, - e=2, - f=hl.Struct(d=1), - g=1, - ), - hl.Struct( - locus=hl.Locus( - contig='chr1', - position=2, - reference_genome='GRCh38', - ), - alleles=['A', 'C'], - d=3, - e=4, - f=hl.Struct(d=3), - g=2, - ), - ], - ) diff --git a/loading_pipeline/lib/misc/pedigree_test.py b/loading_pipeline/lib/misc/pedigree_test.py deleted file mode 100644 index 77432ba138..0000000000 --- a/loading_pipeline/lib/misc/pedigree_test.py +++ /dev/null @@ -1,514 +0,0 @@ -import unittest - -import hail as hl - -from loading_pipeline.lib.core import Sex -from loading_pipeline.lib.misc.io import import_pedigree -from loading_pipeline.lib.misc.pedigree import ( - Family, - Sample, - parse_pedigree_ht_to_families, -) - -TEST_PEDIGREE_1 = 'loading_pipeline/var/test/pedigrees/test_pedigree_1.tsv' -TEST_PEDIGREE_2 = 'loading_pipeline/var/test/pedigrees/test_pedigree_2.tsv' -TEST_PEDIGREE_9 = 'loading_pipeline/var/test/pedigrees/test_pedigree_9.tsv' - - -class PedigreesTest(unittest.TestCase): - def test_empty_pedigree(self) -> None: - with self.assertRaises(Exception): # noqa: B017 - _ = import_pedigree(TEST_PEDIGREE_1) - - def test_parse_lineage(self) -> None: - # - # - # sample_9 sample_10 sample_7 - # \ / \ | - # sample_6 -> sample_8 --------- sample_3 ----- ? | - # \ / \ / | - # sample_4, sample_5 sample_2 | sample_1 - # - # - samples = Family.parse_direct_lineage( - [ - hl.Struct(s='sample_1', maternal_s=None, paternal_s=None, sex='F'), - hl.Struct( - s='sample_2', - maternal_s='sample_3', - paternal_s=None, - sex='M', - ), - hl.Struct( - s='sample_3', - maternal_s=None, - paternal_s='sample_7', - sex='F', - ), - hl.Struct( - s='sample_4', - maternal_s='sample_3', - paternal_s='sample_8', - sex='M', - ), - hl.Struct( - s='sample_5', - maternal_s='sample_3', - paternal_s='sample_8', - sex='M', - ), - hl.Struct( - s='sample_6', - maternal_s='sample_9', - paternal_s='sample_10', - sex='M', - ), - hl.Struct(s='sample_7', maternal_s=None, paternal_s=None, sex='M'), - hl.Struct( - s='sample_8', - maternal_s='sample_9', - paternal_s='sample_10', - sex='F', - ), - hl.Struct(s='sample_9', maternal_s=None, paternal_s=None, sex='F'), - hl.Struct(s='sample_10', maternal_s=None, paternal_s=None, sex='M'), - ], - ) - self.assertEqual( - Family.parse_collateral_lineage(samples), - { - 'sample_1': Sample( - sample_id='sample_1', - sex=Sex.FEMALE, - mother=None, - father=None, - maternal_grandmother=None, - maternal_grandfather=None, - paternal_grandmother=None, - paternal_grandfather=None, - siblings=[], - half_siblings=[], - aunt_nephews=[], - ), - 'sample_2': Sample( - sample_id='sample_2', - sex=Sex.MALE, - mother='sample_3', - father=None, - maternal_grandmother=None, - maternal_grandfather='sample_7', - paternal_grandmother=None, - paternal_grandfather=None, - siblings=[], - half_siblings=['sample_4', 'sample_5'], - aunt_nephews=[], - ), - 'sample_3': Sample( - sample_id='sample_3', - sex=Sex.FEMALE, - mother=None, - father='sample_7', - maternal_grandmother=None, - maternal_grandfather=None, - paternal_grandmother=None, - paternal_grandfather=None, - siblings=[], - half_siblings=[], - aunt_nephews=[], - ), - 'sample_4': Sample( - sample_id='sample_4', - sex=Sex.MALE, - mother='sample_3', - father='sample_8', - maternal_grandmother=None, - maternal_grandfather='sample_7', - paternal_grandmother='sample_9', - paternal_grandfather='sample_10', - siblings=['sample_5'], - half_siblings=[], - aunt_nephews=['sample_6'], - ), - 'sample_5': Sample( - sample_id='sample_5', - sex=Sex.MALE, - mother='sample_3', - father='sample_8', - maternal_grandmother=None, - maternal_grandfather='sample_7', - paternal_grandmother='sample_9', - paternal_grandfather='sample_10', - siblings=[], - half_siblings=[], - aunt_nephews=['sample_6'], - ), - 'sample_6': Sample( - sample_id='sample_6', - sex=Sex.MALE, - mother='sample_9', - father='sample_10', - maternal_grandmother=None, - maternal_grandfather=None, - paternal_grandmother=None, - paternal_grandfather=None, - siblings=['sample_8'], - half_siblings=[], - aunt_nephews=[], - ), - 'sample_7': Sample( - sample_id='sample_7', - sex=Sex.MALE, - mother=None, - father=None, - maternal_grandmother=None, - maternal_grandfather=None, - paternal_grandmother=None, - paternal_grandfather=None, - siblings=[], - half_siblings=[], - aunt_nephews=[], - ), - 'sample_8': Sample( - sample_id='sample_8', - sex=Sex.FEMALE, - mother='sample_9', - father='sample_10', - maternal_grandmother=None, - maternal_grandfather=None, - paternal_grandmother=None, - paternal_grandfather=None, - siblings=[], - half_siblings=[], - aunt_nephews=[], - ), - 'sample_9': Sample( - sample_id='sample_9', - sex=Sex.FEMALE, - mother=None, - father=None, - maternal_grandmother=None, - maternal_grandfather=None, - paternal_grandmother=None, - paternal_grandfather=None, - siblings=[], - half_siblings=[], - aunt_nephews=[], - ), - 'sample_10': Sample( - sample_id='sample_10', - sex=Sex.MALE, - mother=None, - father=None, - maternal_grandmother=None, - maternal_grandfather=None, - paternal_grandmother=None, - paternal_grandfather=None, - siblings=[], - half_siblings=[], - aunt_nephews=[], - ), - }, - ) - - def test_parse_parent_not_aunt_uncle(self) -> None: - samples = Family.parse_direct_lineage( - [ - hl.Struct(s='sample_1', maternal_s=None, paternal_s=None, sex='F'), - hl.Struct( - s='sample_2', - maternal_s=None, - paternal_s=None, - sex='M', - ), - hl.Struct( - s='sample_3', - maternal_s='sample_1', - paternal_s='sample_2', - sex='F', - ), - hl.Struct( - s='sample_4', - maternal_s='sample_3', - paternal_s=None, - sex='F', - ), - hl.Struct( - s='sample_5', - maternal_s='sample_3', - paternal_s=None, - sex='F', - ), - ], - ) - self.assertEqual( - Family.parse_collateral_lineage(samples), - { - 'sample_1': Sample( - sample_id='sample_1', - sex=Sex.FEMALE, - mother=None, - father=None, - maternal_grandmother=None, - maternal_grandfather=None, - paternal_grandmother=None, - paternal_grandfather=None, - siblings=[], - half_siblings=[], - aunt_nephews=[], - ), - 'sample_2': Sample( - sample_id='sample_2', - sex=Sex.MALE, - mother=None, - father=None, - maternal_grandmother=None, - maternal_grandfather=None, - paternal_grandmother=None, - paternal_grandfather=None, - siblings=[], - half_siblings=[], - aunt_nephews=[], - ), - 'sample_3': Sample( - sample_id='sample_3', - sex=Sex.FEMALE, - mother='sample_1', - father='sample_2', - maternal_grandmother=None, - maternal_grandfather=None, - paternal_grandmother=None, - paternal_grandfather=None, - siblings=[], - half_siblings=[], - aunt_nephews=[], - ), - 'sample_4': Sample( - sample_id='sample_4', - sex=Sex.FEMALE, - mother='sample_3', - father=None, - maternal_grandmother='sample_1', - maternal_grandfather='sample_2', - paternal_grandmother=None, - paternal_grandfather=None, - siblings=[], - half_siblings=['sample_5'], - aunt_nephews=[], - ), - 'sample_5': Sample( - sample_id='sample_5', - sex=Sex.FEMALE, - mother='sample_3', - father=None, - maternal_grandmother='sample_1', - maternal_grandfather='sample_2', - paternal_grandmother=None, - paternal_grandfather=None, - siblings=[], - half_siblings=[], - aunt_nephews=[], - ), - }, - ) - - def test_parse_project(self) -> None: - pedigree_ht = import_pedigree(TEST_PEDIGREE_2) - self.assertCountEqual( - list(parse_pedigree_ht_to_families(pedigree_ht)), - [ - Family( - family_guid='BBL_BC1-000345_1', - samples={ - 'BBL_BC1-000345_01_D1': Sample( - sample_id='BBL_BC1-000345_01_D1', - sex=Sex.UNKNOWN, - mother='BBL_BC1-000345_03_D1', - father='BBL_BC1-000345_02_D1', - maternal_grandmother=None, - maternal_grandfather=None, - paternal_grandmother=None, - paternal_grandfather=None, - siblings=[], - half_siblings=[], - aunt_nephews=[], - ), - 'BBL_BC1-000345_02_D1': Sample( - sample_id='BBL_BC1-000345_02_D1', - sex=Sex.MALE, - mother=None, - father=None, - maternal_grandmother=None, - maternal_grandfather=None, - paternal_grandmother=None, - paternal_grandfather=None, - siblings=[], - half_siblings=[], - aunt_nephews=[], - ), - 'BBL_BC1-000345_03_D1': Sample( - sample_id='BBL_BC1-000345_03_D1', - sex=Sex.FEMALE, - mother=None, - father=None, - maternal_grandmother=None, - maternal_grandfather=None, - paternal_grandmother=None, - paternal_grandfather=None, - siblings=[], - half_siblings=[], - aunt_nephews=[], - ), - }, - ), - Family( - family_guid='BBL_HT-007-5195_1', - samples={ - 'BBL_HT-007-5195_01_D1': Sample( - sample_id='BBL_HT-007-5195_01_D1', - sex=Sex.FEMALE, - mother='BBL_HT-007-5195_03_D1', - father='BBL_HT-007-5195_02_D1', - maternal_grandmother=None, - maternal_grandfather=None, - paternal_grandmother=None, - paternal_grandfather=None, - siblings=[ - 'BBL_HT-007-5195_04_D1', - 'BBL_HT-007-5195_05_D1', - 'BBL_HT-007-5195_06_D1', - ], - half_siblings=[], - aunt_nephews=[], - ), - 'BBL_HT-007-5195_02_D1': Sample( - sample_id='BBL_HT-007-5195_02_D1', - sex=Sex.MALE, - mother=None, - father=None, - maternal_grandmother=None, - maternal_grandfather=None, - paternal_grandmother=None, - paternal_grandfather=None, - siblings=[], - half_siblings=[], - aunt_nephews=[], - ), - 'BBL_HT-007-5195_03_D1': Sample( - sample_id='BBL_HT-007-5195_03_D1', - sex=Sex.FEMALE, - mother=None, - father=None, - maternal_grandmother=None, - maternal_grandfather=None, - paternal_grandmother=None, - paternal_grandfather=None, - siblings=[], - half_siblings=[], - aunt_nephews=[], - ), - 'BBL_HT-007-5195_04_D1': Sample( - sample_id='BBL_HT-007-5195_04_D1', - sex=Sex.MALE, - mother='BBL_HT-007-5195_03_D1', - father='BBL_HT-007-5195_02_D1', - maternal_grandmother=None, - maternal_grandfather=None, - paternal_grandmother=None, - paternal_grandfather=None, - siblings=['BBL_HT-007-5195_05_D1', 'BBL_HT-007-5195_06_D1'], - half_siblings=[], - aunt_nephews=[], - ), - 'BBL_HT-007-5195_05_D1': Sample( - sample_id='BBL_HT-007-5195_05_D1', - sex=Sex.FEMALE, - mother='BBL_HT-007-5195_03_D1', - father='BBL_HT-007-5195_02_D1', - maternal_grandmother=None, - maternal_grandfather=None, - paternal_grandmother=None, - paternal_grandfather=None, - siblings=['BBL_HT-007-5195_06_D1'], - half_siblings=[], - aunt_nephews=[], - ), - 'BBL_HT-007-5195_06_D1': Sample( - sample_id='BBL_HT-007-5195_06_D1', - sex=Sex.MALE, - mother='BBL_HT-007-5195_03_D1', - father='BBL_HT-007-5195_02_D1', - maternal_grandmother=None, - maternal_grandfather=None, - paternal_grandmother=None, - paternal_grandfather=None, - siblings=[], - half_siblings=[], - aunt_nephews=[], - ), - }, - ), - Family( - family_guid='BBL_SDS1-000178_1', - samples={ - 'BBL_SDS1-000178_01_D1': Sample( - sample_id='BBL_SDS1-000178_01_D1', - sex=Sex.FEMALE, - mother=None, - father=None, - maternal_grandmother=None, - maternal_grandfather=None, - paternal_grandmother=None, - paternal_grandfather=None, - siblings=[], - half_siblings=[], - aunt_nephews=[], - ), - }, - ), - ], - ) - - def test_subsetted_pedigree_with_removed_parent(self) -> None: - pedigree_ht = import_pedigree(TEST_PEDIGREE_2) - pedigree_ht = pedigree_ht.filter( - pedigree_ht.s != 'BBL_BC1-000345_02_D1', - ) - parsed_pedigree = parse_pedigree_ht_to_families(pedigree_ht) - family = next( - iter( - [ - family - for family in parsed_pedigree - if family.family_guid == 'BBL_BC1-000345_1' - ], - ), - ) - self.assertEqual(len(family.samples), 2) - self.assertFalse( - 'BBL_BC1-000345_02_D1' in family.samples, - ) - self.assertEqual( - family.samples['BBL_BC1-000345_01_D1'].father, - 'BBL_BC1-000345_02_D1', - ) - self.assertEqual( - family.samples['BBL_BC1-000345_01_D1'].mother, - 'BBL_BC1-000345_03_D1', - ) - - def test_pedigree_ungrouped_families(self) -> None: - pedigree_ht = import_pedigree(TEST_PEDIGREE_9) - parsed_pedigree = parse_pedigree_ht_to_families(pedigree_ht) - self.assertEqual(len(parsed_pedigree), 2) - family = next( - iter( - [ - family - for family in parsed_pedigree - if family.family_guid == 'family_2_1' - ], - ), - ) - self.assertTrue( - family.samples.keys() == {'RGP_164_1', 'RGP_164_2', 'RGP_164_4'}, - ) diff --git a/loading_pipeline/lib/misc/retry_test.py b/loading_pipeline/lib/misc/retry_test.py deleted file mode 100644 index 4b756abce1..0000000000 --- a/loading_pipeline/lib/misc/retry_test.py +++ /dev/null @@ -1,69 +0,0 @@ -import unittest -from unittest.mock import Mock, patch - -from loading_pipeline.lib.core import DatasetType -from loading_pipeline.lib.misc.retry import retry - - -class TestRetryDecorator(unittest.TestCase): - @patch('time.sleep', return_value=None) - def test_retry_success_first_try(self, mock_sleep): - mock_func = Mock(return_value='success') - - @retry(tries=3, delay=1, backoff=2) - def func(d: DatasetType): - return mock_func(d) - - result = func(DatasetType.SNV_INDEL) - self.assertEqual(result, 'success') - self.assertEqual(mock_func.call_count, 1) - mock_sleep.assert_not_called() - - @patch('time.sleep', return_value=None) - @patch('loading_pipeline.lib.misc.retry.logger') - def test_retry_eventual_success(self, mock_logger, mock_sleep): - mock_func = Mock( - side_effect=[Exception('fail'), Exception('fail again'), 'success'], - ) - - @retry(tries=3, delay=1, backoff=2) - def func(): - return mock_func() - - result = func() - self.assertEqual(result, 'success') - self.assertEqual(mock_func.call_count, 3) - self.assertEqual(mock_sleep.call_count, 2) - mock_sleep.assert_any_call(1) - mock_sleep.assert_any_call(2) - - @patch('time.sleep', return_value=None) - @patch('loading_pipeline.lib.misc.retry.logger') - def test_retry_all_failures(self, mock_logger, mock_sleep): - mock_func = Mock(side_effect=Exception('always fails')) - - @retry(tries=3, delay=1, backoff=2) - def func(): - return mock_func() - - with self.assertRaises(Exception) as context: - func() - - self.assertEqual(str(context.exception), 'always fails') - self.assertEqual(mock_func.call_count, 3) - self.assertEqual(mock_sleep.call_count, 2) - - @patch('time.sleep', return_value=None) - @patch('loading_pipeline.lib.misc.retry.logger.exception') - def test_logs_retry_message(self, mock_log, mock_sleep): - mock_func = Mock(side_effect=[Exception('fail'), 'success']) - - @retry(tries=2, delay=1, backoff=2) - def func(d: DatasetType): - return mock_func(d) - - func(d=DatasetType.SNV_INDEL) - self.assertIn( - 'func args: kwargs:d=SNV_INDEL failed on attempt 1 after 0.00s, retrying in 1 seconds.', - mock_log.call_args[0][0], - ) diff --git a/loading_pipeline/lib/misc/runs_test.py b/loading_pipeline/lib/misc/runs_test.py deleted file mode 100644 index b1a601727a..0000000000 --- a/loading_pipeline/lib/misc/runs_test.py +++ /dev/null @@ -1,84 +0,0 @@ -import os - -from loading_pipeline.lib.core import DatasetType, ReferenceGenome -from loading_pipeline.lib.misc.runs import get_run_ids -from loading_pipeline.lib.paths import ( - clickhouse_load_fail_file_path, - clickhouse_load_success_file_path, - pipeline_run_success_file_path, - runs_path, -) -from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase - - -class RunsTest(MockedDatarootTestCase): - def setUp(self): - super().setUp() - run_ids = [ - 'manual__2024-08-05T16-07-58.365146+00-00', - 'manual__2024-08-06T10-15-23.123456+00-00', - 'manual__2024-08-07T12-30-45.654321+00-00', # _SUCCESS, _CLICKHOUSE_LOAD_FAIL - 'manual__2024-08-08T09-45-00.000000+00-00', # _SUCCESS - 'manual__2024-08-09T18-22-13.999999+00-00', # _SUCCESS, _CLICKHOUSE_LOAD_SUCCESS - ] - for reference_genome, dataset_type in [ - (ReferenceGenome.GRCh38, DatasetType.SNV_INDEL), - (ReferenceGenome.GRCh37, DatasetType.SNV_INDEL), - (ReferenceGenome.GRCh38, DatasetType.GCNV), - (ReferenceGenome.GRCh37, DatasetType.GCNV), - ]: - for run_id in run_ids: - base_path = runs_path(reference_genome, dataset_type) - os.makedirs(os.path.join(base_path, run_id), exist_ok=True) - if '07T12' in run_id: - failure_file = clickhouse_load_fail_file_path( - reference_genome, - dataset_type, - run_id, - ) - open(failure_file, 'w').close() - if '09' in run_id or '07T12' in run_id: - success_file = pipeline_run_success_file_path( - reference_genome, - dataset_type, - run_id, - ) - open(success_file, 'w').close() - if '09T18' in run_id: - success_file = clickhouse_load_success_file_path( - reference_genome, - dataset_type, - run_id, - ) - open(success_file, 'w').close() - - def test_get_run_ids(self) -> None: - ( - successful_pipeline_runs, - successful_clickhouse_loads, - failed_clickhouse_loads, - ) = get_run_ids() - self.assertCountEqual( - successful_pipeline_runs[(ReferenceGenome.GRCh38, DatasetType.SNV_INDEL)], - { - 'manual__2024-08-09T18-22-13.999999+00-00', - 'manual__2024-08-08T09-45-00.000000+00-00', - 'manual__2024-08-07T12-30-45.654321+00-00', - }, - ) - self.assertCountEqual( - successful_clickhouse_loads[ - (ReferenceGenome.GRCh38, DatasetType.SNV_INDEL) - ], - { - 'manual__2024-08-09T18-22-13.999999+00-00', - }, - ) - self.assertCountEqual( - successful_clickhouse_loads[(ReferenceGenome.GRCh37, DatasetType.GCNV)], - {}, - ) - self.assertCountEqual( - failed_clickhouse_loads[(ReferenceGenome.GRCh38, DatasetType.SNV_INDEL)], - {'manual__2024-08-07T12-30-45.654321+00-00'}, - ) diff --git a/loading_pipeline/lib/misc/sample_ids_test.py b/loading_pipeline/lib/misc/sample_ids_test.py deleted file mode 100644 index 6d3fb7efd0..0000000000 --- a/loading_pipeline/lib/misc/sample_ids_test.py +++ /dev/null @@ -1,160 +0,0 @@ -import unittest - -import hail as hl - -from loading_pipeline.lib.misc.sample_ids import ( - remap_sample_ids, - subset_samples, -) -from loading_pipeline.lib.misc.validation import SeqrValidationError - -CALLSET_MT = hl.MatrixTable.from_parts( - rows={'variants': [1, 2]}, - cols={'s': ['HG00731', 'HG00732', 'HG00733']}, - entries={ - 'GT': [ - [hl.Call([0, 1]), hl.missing(hl.tcall), hl.Call([0, 1])], - [hl.Call([0, 1]), hl.Call([0, 1]), hl.Call([1, 1])], - ], - }, -).key_cols_by('s') - - -class SampleLookupTest(unittest.TestCase): - def test_remap_2_sample_ids(self) -> None: - # remap 2 of 3 samples in callset - project_remap_ht = hl.Table.parallelize( - [ - {'s': 'HG00731', 'seqr_id': 'HG00731_1'}, - {'s': 'HG00732', 'seqr_id': 'HG00732_1'}, - ], - hl.tstruct( - s=hl.tstr, - seqr_id=hl.tstr, - ), - key='s', - ) - - remapped_mt = remap_sample_ids( - CALLSET_MT, - project_remap_ht, - ) - - self.assertEqual(remapped_mt.cols().count(), 3) - self.assertEqual( - remapped_mt.cols().collect(), - [ - hl.Struct( - col_idx=0, - s='HG00731_1', - seqr_id='HG00731_1', - vcf_id='HG00731', - ), - hl.Struct( - col_idx=1, - s='HG00732_1', - seqr_id='HG00732_1', - vcf_id='HG00732', - ), - hl.Struct(col_idx=2, s='HG00733', seqr_id='HG00733', vcf_id='HG00733'), - ], - ) - - def test_remap_sample_ids_remap_has_duplicate(self) -> None: - # remap file has 2 rows for HG00732 - project_remap_ht = hl.Table.parallelize( - [ - {'s': 'HG00731', 'seqr_id': 'HG00731_1'}, - {'s': 'HG00732', 'seqr_id': 'HG00732_1'}, - {'s': 'HG00732', 'seqr_id': 'HG00732_1'}, # duplicate - ], - hl.tstruct( - s=hl.tstr, - seqr_id=hl.tstr, - ), - key='s', - ) - - with self.assertRaises(SeqrValidationError): - remap_sample_ids( - CALLSET_MT, - project_remap_ht, - ) - - def test_remap_sample_ids_remap_has_missing_samples(self) -> None: - # remap file has 4 rows, but only 3 samples in callset - project_remap_ht = hl.Table.parallelize( - [ - {'s': 'HG00731', 'seqr_id': 'HG00731_1'}, - {'s': 'HG00732', 'seqr_id': 'HG00732_1'}, - {'s': 'HG00733', 'seqr_id': 'HG00733_1'}, - {'s': 'HG00734', 'seqr_id': 'HG00734_1'}, # missing in callset - ], - hl.tstruct( - s=hl.tstr, - seqr_id=hl.tstr, - ), - key='s', - ) - - with self.assertRaises(SeqrValidationError): - remap_sample_ids( - CALLSET_MT, - project_remap_ht, - ) - - def test_subset_samples_zero_samples(self): - # subset 0 of 3 samples in callset - sample_subset_ht = hl.Table.parallelize( - [], - hl.tstruct(s=hl.tstr), - key='s', - ) - - with self.assertRaises(SeqrValidationError): - subset_samples( - CALLSET_MT, - sample_subset_ht, - ) - - def test_subset_samples_missing_samples(self): - # subset 2 of 3 samples in callset, but 1 is missing - sample_subset_ht = hl.Table.parallelize( - [ - {'s': 'HG00731'}, - {'s': 'HG00732'}, - {'s': 'HG00734'}, # missing in callset - ], - hl.tstruct(s=hl.tstr), - key='s', - ) - - with self.assertRaises(SeqrValidationError): - subset_samples( - CALLSET_MT, - sample_subset_ht, - ) - - def test_subset_no_defined_gt(self): - mt = hl.MatrixTable.from_parts( - rows={'variants': [1, 2]}, - cols={'s': ['HG00731', 'HG00732']}, - entries={ - 'GT': [ - [hl.Call([1, 1]), hl.missing(hl.tcall)], - [hl.Call([1, 1]), hl.Call([1, 1])], - ], - }, - ).key_cols_by('s') - sample_subset_ht = hl.Table.parallelize( - [ - {'s': 'HG00732'}, - ], - hl.tstruct(s=hl.tstr), - key='s', - ) - mt = subset_samples( - mt, - sample_subset_ht, - ) - self.assertEqual(mt.count(), (1, 1)) diff --git a/loading_pipeline/lib/misc/sv_test.py b/loading_pipeline/lib/misc/sv_test.py deleted file mode 100644 index aefa8a5cd5..0000000000 --- a/loading_pipeline/lib/misc/sv_test.py +++ /dev/null @@ -1,243 +0,0 @@ -import unittest - -import hail as hl - -from loading_pipeline.lib.core import DatasetType, ReferenceGenome, Sex -from loading_pipeline.lib.misc.io import import_callset, select_relevant_fields -from loading_pipeline.lib.misc.pedigree import Family, Sample -from loading_pipeline.lib.misc.sample_ids import subset_samples -from loading_pipeline.lib.misc.sv import ( - deduplicate_merged_sv_concordance_calls, - overwrite_male_non_par_calls, -) - -TEST_SV_VCF = 'loading_pipeline/var/test/callsets/sv_1.vcf' -ANNOTATIONS_HT = hl.Table.parallelize( - [ - { - 'variant_id': 'BND_chr1_6', - 'algorithms': 'manta', - 'end_locus': hl.Locus( - contig='chr5', - position=20404, - reference_genome='GRCh38', - ), - }, - { - 'variant_id': 'BND_chr1_9', - 'algorithms': 'manta', - 'end_locus': hl.Locus( - contig='chr1', - position=789481, - reference_genome='GRCh38', - ), - }, - { - 'variant_id': 'CPX_chr1_22', - 'algorithms': 'manta', - 'end_locus': hl.Locus( - contig='chr1', - position=6559723, - reference_genome='GRCh38', - ), - }, - ], - hl.tstruct( - variant_id=hl.tstr, - algorithms=hl.tstr, - end_locus=hl.tlocus('GRCh38'), - ), - key='variant_id', -) - - -class SVTest(unittest.TestCase): - def test_overwrite_male_non_par_calls(self) -> None: - mt = import_callset(TEST_SV_VCF, ReferenceGenome.GRCh38, DatasetType.SV) - mt = select_relevant_fields( - mt, - DatasetType.SV, - ) - mt = subset_samples( - mt, - hl.Table.parallelize( - [{'s': sample_id} for sample_id in ['RGP_164_1', 'RGP_164_2']], - hl.tstruct(s=hl.dtype('str')), - key='s', - ), - ) - mt = overwrite_male_non_par_calls( - mt, - { - Family( - family_guid='family_1', - samples={ - 'RGP_164_1': Sample(sample_id='RGP_164_1', sex=Sex.FEMALE), - 'RGP_164_2': Sample(sample_id='RGP_164_2', sex=Sex.MALE), - }, - ), - }, - ) - mt = mt.filter_rows(mt.locus.contig == 'chrX') - self.assertEqual( - [ - hl.Locus(contig='chrX', position=3, reference_genome='GRCh38'), - hl.Locus(contig='chrX', position=2781700, reference_genome='GRCh38'), - ], - mt.locus.collect(), - ) - self.assertEqual( - [ - hl.Call(alleles=[0, 0], phased=False), - # END of this variant < start of the non-par region. - hl.Call(alleles=[0, 1], phased=False), - hl.Call(alleles=[0, 0], phased=False), - hl.Call(alleles=[1], phased=False), - ], - mt.GT.collect(), - ) - self.assertFalse( - hasattr(mt, 'start_locus'), - ) - - def test_deduplicate_merged_sv_concordance_calls(self) -> None: - mt = ( - hl.MatrixTable.from_parts( - rows={ - 'variant_id': [ - 'new_v1', - 'new_v2', - 'new_v3', - ], - 'locus': [ - hl.Locus( - contig='chr1', - position=1, - reference_genome='GRCh38', - ), - hl.Locus( - contig='chr1', - position=2, - reference_genome='GRCh38', - ), - hl.Locus( - contig='chr1', - position=3, - reference_genome='GRCh38', - ), - ], - 'info.END': [ - 1, - 2, - 3, - ], - 'info.END2': [ - 1, - 2, - 3, - ], - 'info.CHR2': [ - 'chr1', - 'chr1', - 'chr1', - ], - 'info.SEQR_INTERNAL_TRUTH_VID': [ - 'BND_chr1_6', - 'BND_chr1_9', - 'CPX_chr1_22', - ], - }, - cols={'s': ['sample_1']}, - entries={'GQ': [[99] for _ in range(3)]}, - ) - .key_rows_by('variant_id') - .key_cols_by('s') - ) - mt = deduplicate_merged_sv_concordance_calls( - mt, - ANNOTATIONS_HT, - ) - self.assertEqual( - mt['info.SEQR_INTERNAL_TRUTH_VID'].collect(), - [ - 'BND_chr1_6', - 'BND_chr1_9', - 'CPX_chr1_22', - ], - ) - - mt = ( - hl.MatrixTable.from_parts( - rows={ - 'variant_id': [ - 'new_v1', - 'new_v2', - 'new_v3', - 'new_v4', - ], - 'locus': [ - hl.Locus( - contig='chr1', - position=1, - reference_genome='GRCh38', - ), - hl.Locus( - contig='chr1', - position=2, - reference_genome='GRCh38', - ), - hl.Locus( - contig='chr1', - position=3, - reference_genome='GRCh38', - ), - hl.Locus( - contig='chr1', - position=4, - reference_genome='GRCh38', - ), - ], - 'info.END': [ - 1, - 2, - 789481, - 789485, - ], - 'info.END2': [ - 1, - 2, - 789481, - 789485, - ], - 'info.CHR2': [ - 'chr1', - 'chr1', - 'chr2', - 'chr1', - ], - 'info.SEQR_INTERNAL_TRUTH_VID': [ - 'BND_chr1_6', - 'BND_chr1_9', - 'BND_chr1_9', - 'BND_chr1_9', - ], - }, - cols={'s': ['sample_1']}, - entries={'GQ': [[99] for _ in range(4)]}, - ) - .key_rows_by('variant_id') - .key_cols_by('s') - ) - mt = deduplicate_merged_sv_concordance_calls( - mt, - ANNOTATIONS_HT, - ) - self.assertEqual( - mt['info.SEQR_INTERNAL_TRUTH_VID'].collect(), - [ - 'BND_chr1_6', - None, - None, - 'BND_chr1_9', - ], - ) diff --git a/loading_pipeline/lib/misc/terra_data_repository_test.py b/loading_pipeline/lib/misc/terra_data_repository_test.py deleted file mode 100644 index 91b044d68f..0000000000 --- a/loading_pipeline/lib/misc/terra_data_repository_test.py +++ /dev/null @@ -1,321 +0,0 @@ -import json -import os -import unittest -from types import SimpleNamespace -from unittest.mock import Mock, call, patch - -import responses - -from loading_pipeline.lib.misc.terra_data_repository import ( - TDR_ROOT_URL, - _get_dataset_ids, - bq_metrics_query, - gen_bq_table_names, -) - -TDR_DATASETS = [ - { - 'id': '2dc51ee0-a037-499d-a915-a7c20a0b216d', - 'name': 'RP_3053', - 'description': 'TGG_Ware_DRAGEN_hg38. Dataset automatically created and linked to: RP-3053', - 'defaultProfileId': '0a164b9a-2b8b-45d2-859e-a4e369b9cb4f', - 'createdDate': '2023-10-05T13:15:27.649760Z', - 'storage': [ - { - 'region': 'us-central1', - 'cloudResource': 'bigquery', - 'cloudPlatform': 'gcp', - }, - { - 'region': 'us-east4', - 'cloudResource': 'firestore', - 'cloudPlatform': 'gcp', - }, - { - 'region': 'us-central1', - 'cloudResource': 'bucket', - 'cloudPlatform': 'gcp', - }, - ], - 'secureMonitoringEnabled': False, - 'cloudPlatform': 'gcp', - 'dataProject': 'datarepo-7242affb', - 'storageAccount': None, - 'phsId': None, - 'selfHosted': False, - 'predictableFileIds': False, - 'tags': [], - 'resourceLocks': { - 'exclusive': None, - 'shared': [], - }, - }, - { - 'id': 'beef77e8-575b-40e5-9340-a6f10e0bec67', - 'name': 'RP_3056', - 'description': 'RGP_HMB_DRAGEN_hg38. Dataset automatically created and linked to: RP-3056', - 'defaultProfileId': '835dd05d-c603-4b0d-926f-d9143fd24549', - 'createdDate': '2023-10-05T20:15:27.622481Z', - 'storage': [ - { - 'region': 'us-central1', - 'cloudResource': 'bigquery', - 'cloudPlatform': 'gcp', - }, - { - 'region': 'us-east4', - 'cloudResource': 'firestore', - 'cloudPlatform': 'gcp', - }, - { - 'region': 'us-central1', - 'cloudResource': 'bucket', - 'cloudPlatform': 'gcp', - }, - ], - 'secureMonitoringEnabled': False, - 'cloudPlatform': 'gcp', - 'dataProject': 'datarepo-5a72e31b', - 'storageAccount': None, - 'phsId': None, - 'selfHosted': False, - 'predictableFileIds': False, - 'tags': [], - 'resourceLocks': { - 'exclusive': None, - 'shared': [], - }, - }, - { - 'id': 'c8d74ac4-9a2e-4d3d-a6b5-1f4b433d949f', - 'name': 'RP_3055', - 'description': 'RGP_GRU_DRAGEN_hg38. Dataset automatically created and linked to: RP-3055', - 'defaultProfileId': '835dd05d-c603-4b0d-926f-d9143fd24549', - 'createdDate': '2023-10-05T20:15:28.255304Z', - 'storage': [ - { - 'region': 'us-central1', - 'cloudResource': 'bigquery', - 'cloudPlatform': 'gcp', - }, - { - 'region': 'us-east4', - 'cloudResource': 'firestore', - 'cloudPlatform': 'gcp', - }, - { - 'region': 'us-central1', - 'cloudResource': 'bucket', - 'cloudPlatform': 'gcp', - }, - ], - 'secureMonitoringEnabled': False, - 'cloudPlatform': 'gcp', - 'dataProject': 'datarepo-0f5be351', - 'storageAccount': None, - 'phsId': None, - 'selfHosted': False, - 'predictableFileIds': False, - 'tags': [], - 'resourceLocks': { - 'exclusive': None, - 'shared': [ - 'Gw_KTeYRS1aLhRvapMLYLg', - 'WrP-0w1aROOUbgkI8JS6Ug', - ], - }, - }, -] - - -@patch( - 'loading_pipeline.lib.misc.terra_data_repository.get_service_account_credentials', - return_value=SimpleNamespace( - token='abcdefg', # noqa: S106 - ), -) -class TerraDataRepositoryTest(unittest.TestCase): - @responses.activate - def test_get_dataset_ids(self, _: Mock) -> None: - responses.get( - os.path.join(TDR_ROOT_URL, 'datasets?limit=50000'), - body=json.dumps( - { - 'total': 3, - 'filteredTotal': 3, - 'items': TDR_DATASETS, - }, - ), - ) - self.assertListEqual( - _get_dataset_ids(), - [ - '2dc51ee0-a037-499d-a915-a7c20a0b216d', - 'beef77e8-575b-40e5-9340-a6f10e0bec67', - 'c8d74ac4-9a2e-4d3d-a6b5-1f4b433d949f', - ], - ) - - @responses.activate - def test_get_dataset_ids_no_bq(self, _: Mock) -> None: - responses.get( - os.path.join(TDR_ROOT_URL, 'datasets'), - body=json.dumps( - { - 'total': 1, - 'filteredTotal': 1, - 'items': [ - { - 'id': '2dc51ee0-a037-499d-a915-a7c20a0b216d', - 'name': 'RP_3053', - 'description': 'TGG_Ware_DRAGEN_hg38. Dataset automatically created and linked to: RP-3053', - 'defaultProfileId': '0a164b9a-2b8b-45d2-859e-a4e369b9cb4f', - 'createdDate': '2023-10-05T13:15:27.649760Z', - 'storage': [ - # NB: bigquery was removed from 'storage' here. - { - 'region': 'us-east4', - 'cloudResource': 'firestore', - 'cloudPlatform': 'gcp', - }, - { - 'region': 'us-central1', - 'cloudResource': 'bucket', - 'cloudPlatform': 'gcp', - }, - ], - 'secureMonitoringEnabled': False, - 'cloudPlatform': 'gcp', - 'dataProject': 'datarepo-7242affb', - 'storageAccount': None, - 'phsId': None, - 'selfHosted': False, - 'predictableFileIds': False, - 'tags': [], - 'resourceLocks': { - 'exclusive': None, - 'shared': [], - }, - }, - ], - }, - ), - ) - self.assertRaises( - ValueError, - _get_dataset_ids, - ) - - @responses.activate - def test_gen_bq_table_names(self, _: Mock) -> None: - responses.get( - os.path.join(TDR_ROOT_URL, 'datasets'), - body=json.dumps( - { - 'total': 3, - 'filteredTotal': 3, - 'items': TDR_DATASETS, - }, - ), - ) - for dataset_id, name, project_name, dataset_name in [ - ( - '2dc51ee0-a037-499d-a915-a7c20a0b216d', - 'RP_3053', - 'datarepo-7242affb', - 'datarepo_RP_3053', - ), - ( - 'beef77e8-575b-40e5-9340-a6f10e0bec67', - 'RP_3056', - 'datarepo-5a72e31b', - 'datarepo_RP_3056', - ), - ( - 'c8d74ac4-9a2e-4d3d-a6b5-1f4b433d949f', - 'RP_3059', - 'datarepo-aada2e3b', - 'datarepo_RP_3059', - ), - ]: - responses.get( - os.path.join( - TDR_ROOT_URL, - f'datasets/{dataset_id}?include=ACCESS_INFORMATION', - ), - body=json.dumps( - { - 'id': dataset_id, - 'name': name, - 'description': 'TGG_Ware_DRAGEN_hg38. Dataset automatically created and linked to: RP-3053', - 'defaultProfileId': None, - 'dataProject': None, - 'defaultSnapshotId': None, - 'schema': None, - 'createdDate': '2023-10-05T13:15:27.649760Z', - 'storage': None, - 'secureMonitoringEnabled': False, - 'phsId': None, - 'accessInformation': { - 'bigQuery': { - 'datasetName': dataset_name, - 'datasetId': f'{project_name}:{dataset_name}', - 'projectId': project_name, - 'link': 'https://console.cloud.google.com/bigquery?project=datarepo-7242affb&ws=!datarepo_RP_3053&d=datarepo_RP_3053&p=datarepo-7242affb&page=dataset', - 'tables': [ - { - 'name': 'jointcallset', - 'id': f'{project_name}.{dataset_name}.jointcallset', - 'qualifiedName': 'datarepo-7242affb.datarepo_RP_3053.jointcallset', - 'link': 'https://console.cloud.google.com/bigquery?project=datarepo-7242affb&ws=!datarepo_RP_3053&d=datarepo_RP_3053&p=datarepo-7242affb&page=table&t=jointcallset', - 'sampleQuery': 'SELECT * FROM `datarepo-7242affb.datarepo_RP_3053.jointcallset`', - }, - { - 'name': 'sample', - 'id': f'{project_name}.{dataset_name}.sample', - 'qualifiedName': 'datarepo-7242affb.datarepo_RP_3053.sample', - 'link': 'https://console.cloud.google.com/bigquery?project=datarepo-7242affb&ws=!datarepo_RP_3053&d=datarepo_RP_3053&p=datarepo-7242affb&page=table&t=sample', - 'sampleQuery': 'SELECT * FROM `datarepo-7242affb.datarepo_RP_3053.sample`', - }, - ], - }, - 'parquet': None, - }, - 'cloudPlatform': None, - 'selfHosted': False, - 'properties': None, - 'ingestServiceAccount': None, - 'predictableFileIds': False, - 'tags': [], - 'resourceLocks': { - 'exclusive': None, - 'shared': [], - }, - }, - ), - ) - self.assertCountEqual( - list(gen_bq_table_names()), - [ - 'datarepo-7242affb.datarepo_RP_3053', - 'datarepo-5a72e31b.datarepo_RP_3056', - 'datarepo-aada2e3b.datarepo_RP_3059', - ], - ) - - @patch('loading_pipeline.lib.misc.terra_data_repository.bigquery.Client') - def test_bq_metrics_query_missing_metrics( - self, - mock_bq_client: Mock, - _: Mock, - ) -> None: - mock_bq_client.return_value.query_and_wait.return_value = iter( - [['predicted_sex,contamination_rate,percent_bases_at_20x']], - ) - bq_metrics_query('datarepo-7242affb.datarepo_RP_3053') - self.assertEqual( - mock_bq_client.return_value.query_and_wait.mock_calls[1], - call( - '\n SELECT predicted_sex,contamination_rate,percent_bases_at_20x,NULL AS collaborator_sample_id,NULL AS mean_coverage FROM `datarepo-7242affb.datarepo_RP_3053.sample`;\n ', - ), - ) diff --git a/loading_pipeline/lib/misc/validation_test.py b/loading_pipeline/lib/misc/validation_test.py deleted file mode 100644 index bb368b85a5..0000000000 --- a/loading_pipeline/lib/misc/validation_test.py +++ /dev/null @@ -1,464 +0,0 @@ -import unittest -from unittest.mock import patch - -import hail as hl - -from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType -from loading_pipeline.lib.misc.validation import ( - SeqrValidationError, - validate_allele_depth_length, - validate_allele_type, - validate_expected_contig_frequency, - validate_imported_field_types, - validate_no_duplicate_variants, - validate_sample_type, -) - -TEST_MITO_MT = 'loading_pipeline/var/test/callsets/mito_1.mt' - - -def _mt_from_contigs(contigs): - return ( - hl.MatrixTable.from_parts( - rows={ - 'locus': [ - hl.Locus( - contig=contig, - position=1, - reference_genome='GRCh38', - ) - for contig in contigs - ], - }, - cols={'s': ['sample_1']}, - entries={'HL': [[0.0] for _ in range(len(contigs))]}, - ) - .key_rows_by('locus') - .key_cols_by('s') - ) - - -class ValidationTest(unittest.TestCase): - def test_validate_allele_type(self) -> None: - mt = ( - hl.MatrixTable.from_parts( - rows={ - 'locus': [ - hl.Locus( - contig='chr1', - position=1, - reference_genome='GRCh38', - ), - hl.Locus( - contig='chr1', - position=2, - reference_genome='GRCh38', - ), - hl.Locus( - contig='chr1', - position=3, - reference_genome='GRCh38', - ), - hl.Locus( - contig='chr1', - position=4, - reference_genome='GRCh38', - ), - ], - 'alleles': [ - ['A', 'T'], - # NB: star alleles should pass through this validation just fine, - # but are eventually filtered out upstream. - ['A', '*'], - ['A', '-'], - ['A', ''], - ], - }, - cols={'s': ['sample_1']}, - entries={'HL': [[0.0], [0.0], [0.0], [0.0]]}, - ) - .key_rows_by('locus', 'alleles') - .key_cols_by('s') - ) - self.assertRaisesRegex( - SeqrValidationError, - "Alleles with invalid AlleleType are present in the callset: \\[\\('A', '-'\\), \\('A', ''\\)\\]", - validate_allele_type, - mt, - DatasetType.SNV_INDEL, - ) - - mt = ( - hl.MatrixTable.from_parts( - rows={ - 'locus': [ - hl.Locus( - contig='chr1', - position=1, - reference_genome='GRCh38', - ), - hl.Locus( - contig='chr1', - position=2, - reference_genome='GRCh38', - ), - ], - 'alleles': [ - ['C', ''], - ['A', ''], - ], - }, - cols={'s': ['sample_1']}, - entries={'HL': [[0.0], [0.0]]}, - ) - .key_rows_by('locus', 'alleles') - .key_cols_by('s') - ) - self.assertRaisesRegex( - SeqrValidationError, - 'Alleles with invalid allele are present in the callset. This appears to be a GVCF containing records for sites with no variants.', - validate_allele_type, - mt, - DatasetType.SNV_INDEL, - ) - - def test_validate_allele_depth_length(self) -> None: - mt = ( - hl.MatrixTable.from_parts( - rows={ - 'locus': [ - hl.Locus( - contig='chr1', - position=1, - reference_genome='GRCh38', - ), - hl.Locus( - contig='chr1', - position=2, - reference_genome='GRCh38', - ), - hl.Locus( - contig='chr1', - position=3, - reference_genome='GRCh38', - ), - hl.Locus( - contig='chr1', - position=4, - reference_genome='GRCh38', - ), - ], - 'alleles': [ - ['A', 'T'], - # NB: star alleles should pass through this validation just fine, - # but are eventually filtered out upstream. - ['A', 'TC', 'TG'], - ['A', 'TTT'], - ['A', 'CCC'], - ], - }, - cols={'s': ['sample_1', 'sample_2']}, - entries={ - 'AD': [ - [[1, 0], [1, 0]], - [[1], [1, 0, 1]], - [[1, 0], [1]], - [[1, 0], [1, 0]], - ], - }, - ) - .key_rows_by('locus', 'alleles') - .key_cols_by('s') - ) - self.assertRaisesRegex( - SeqrValidationError, - "Found variants with unequal Allele Depth array lengths over samples \\(first 10, if applicable\\): \\{'1-2-A-TC-TG': \\{1, 3\\}, '1-3-A-TTT': \\{1, 2\\}\\}", - validate_allele_depth_length, - mt, - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - ) - - def test_validate_imported_field_types(self) -> None: - mt = hl.read_matrix_table(TEST_MITO_MT) - validate_imported_field_types(mt, DatasetType.MITO, {}) - mt = mt.annotate_cols(contamination=hl.int32(mt.contamination)) - mt = mt.annotate_entries(DP=hl.float32(mt.DP)) - mt = mt.annotate_rows(vep=hl.dict({'t': '1'})) - self.assertRaisesRegex( - SeqrValidationError, - "Found unexpected field types on MatrixTable after import: \\['contamination: int32', 'DP: float32', 'vep: dict', 'tester: missing'\\]", - validate_imported_field_types, - mt, - DatasetType.MITO, - {'tester': hl.tfloat32}, - ) - - def test_validate_no_duplicate_variants(self) -> None: - mt = ( - hl.MatrixTable.from_parts( - rows={ - 'locus': [ - hl.Locus( - contig='chr1', - position=1, - reference_genome='GRCh38', - ), - hl.Locus( - contig='chr1', - position=2, - reference_genome='GRCh38', - ), - hl.Locus( - contig='chr1', - position=2, - reference_genome='GRCh38', - ), - ], - 'alleles': [ - ['A', 'C'], - ['A', 'C'], - ['A', 'C'], - ], - }, - cols={'s': ['sample_1']}, - entries={'HL': [[0.0], [0.0], [0.0]]}, - ) - .key_rows_by('locus', 'alleles') - .key_cols_by('s') - ) - self.assertRaisesRegex( - SeqrValidationError, - "Variants are present multiple times in the callset: \\['1-2-A-C'\\]", - validate_no_duplicate_variants, - mt, - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - ) - - def test_validate_expected_contig_frequency(self) -> None: - mt = _mt_from_contigs(ReferenceGenome.GRCh38.standard_contigs) - self.assertIsNone( - validate_expected_contig_frequency(mt, ReferenceGenome.GRCh38, 1), - ) - self.assertRaisesRegex( - SeqrValidationError, - 'Missing the following expected contigs', - validate_expected_contig_frequency, - mt, - ReferenceGenome.GRCh37, - 1, - ) - self.assertRaisesRegex( - SeqrValidationError, - 'which is lower than expected minimum count', - validate_expected_contig_frequency, - mt, - ReferenceGenome.GRCh38, - 2, - ) - - # Drop an optional contig - mt = _mt_from_contigs(ReferenceGenome.GRCh38.standard_contigs - {'chrY'}) - self.assertIsNone( - validate_expected_contig_frequency(mt, ReferenceGenome.GRCh38, 1), - ) - - # Drop a non-optional contig - mt = _mt_from_contigs(ReferenceGenome.GRCh38.standard_contigs - {'chr3'}) - self.assertRaisesRegex( - SeqrValidationError, - 'Missing the following expected contigs', - validate_expected_contig_frequency, - mt, - ReferenceGenome.GRCh38, - 1, - ) - - def test_validate_sample_type(self) -> None: - mt = _mt_from_contigs(ReferenceGenome.GRCh38.standard_contigs) - coding_and_noncoding_variants_ht = hl.Table.parallelize( - [ - { - 'locus': hl.Locus( - contig='chr1', - position=1, - reference_genome='GRCh38', - ), - 'coding': True, - 'noncoding': False, - }, - { - 'locus': hl.Locus( - contig='chr2', - position=1, - reference_genome='GRCh38', - ), - 'coding': True, - 'noncoding': False, - }, - { - 'locus': hl.Locus( - contig='chr3', - position=1, - reference_genome='GRCh38', - ), - 'coding': False, - 'noncoding': True, - }, - { - 'locus': hl.Locus( - contig='chr4', - position=1, - reference_genome='GRCh38', - ), - 'coding': False, - 'noncoding': True, - }, - ], - hl.tstruct( - locus=hl.tlocus('GRCh38'), - coding=hl.tbool, - noncoding=hl.tbool, - ), - key='locus', - ) - self.assertIsNone( - validate_sample_type( - mt, - ReferenceGenome.GRCh38, - SampleType.WGS, - ['project_a'], - coding_and_noncoding_variants_ht, - ), - ) - self.assertRaisesRegex( - SeqrValidationError, - 'specified as WES but appears to be WGS', - validate_sample_type, - mt, - ReferenceGenome.GRCh38, - SampleType.WES, - ['project_a'], - coding_and_noncoding_variants_ht, - ) - - # has coding, but not noncoding now. - coding_and_noncoding_variants_ht = hl.Table.parallelize( - [ - { - 'locus': hl.Locus( - contig='chr1', - position=1, - reference_genome='GRCh38', - ), - 'coding': True, - 'noncoding': False, - }, - { - 'locus': hl.Locus( - contig='chr2', - position=1, - reference_genome='GRCh38', - ), - 'coding': True, - 'noncoding': False, - }, - { - 'locus': hl.Locus( - contig='chr2', - position=2, - reference_genome='GRCh38', - ), - 'coding': False, - 'noncoding': True, - }, - ], - hl.tstruct( - locus=hl.tlocus('GRCh38'), - coding=hl.tbool, - noncoding=hl.tbool, - ), - key='locus', - ) - self.assertIsNone( - validate_sample_type( - mt, - ReferenceGenome.GRCh38, - SampleType.WES, - ['project_a'], - coding_and_noncoding_variants_ht, - ), - ) - self.assertRaisesRegex( - SeqrValidationError, - 'specified as WGS but appears to be WES', - validate_sample_type, - mt, - ReferenceGenome.GRCh38, - SampleType.WGS, - ['project_a'], - coding_and_noncoding_variants_ht, - ) - - # has noncoding, but not coding now. - coding_and_noncoding_variants_ht = hl.Table.parallelize( - [ - { - 'locus': hl.Locus( - contig='chr1', - position=1, - reference_genome='GRCh38', - ), - 'coding': False, - 'noncoding': True, - }, - { - 'locus': hl.Locus( - contig='chr2', - position=1, - reference_genome='GRCh38', - ), - 'coding': False, - 'noncoding': True, - }, - { - 'locus': hl.Locus( - contig='chr2', - position=2, - reference_genome='GRCh38', - ), - 'coding': True, - 'noncoding': False, - }, - ], - hl.tstruct( - locus=hl.tlocus('GRCh38'), - coding=hl.tbool, - noncoding=hl.tbool, - ), - key='locus', - ) - self.assertRaisesRegex( - SeqrValidationError, - 'contains noncoding variants but is missing common coding variants', - validate_sample_type, - mt, - ReferenceGenome.GRCh38, - SampleType.WGS, - ['project_a'], - coding_and_noncoding_variants_ht, - ) - - # Validation safe if all projects are to be skipped - with patch('loading_pipeline.lib.misc.validation.Env') as mock_env: - mock_env.SAMPLE_TYPE_VALIDATION_EXCLUDED_PROJECTS = ['project_a'] - self.assertIsNone( - validate_sample_type( - mt, - ReferenceGenome.GRCh38, - SampleType.WGS, - ['project_a'], - coding_and_noncoding_variants_ht, - ), - ) diff --git a/loading_pipeline/lib/misc/vets_test.py b/loading_pipeline/lib/misc/vets_test.py deleted file mode 100644 index b26de113b7..0000000000 --- a/loading_pipeline/lib/misc/vets_test.py +++ /dev/null @@ -1,104 +0,0 @@ -import unittest - -import hail as hl - -from loading_pipeline.lib.misc.io import split_multi_hts -from loading_pipeline.lib.misc.vets import ( - annotate_vets, -) - - -class VetsTest(unittest.TestCase): - def test_annotate_vets(self) -> None: - gatk_mt = hl.MatrixTable.from_parts( - rows={ - 'locus': [ - hl.Locus( - contig='chr1', - position=1, - reference_genome='GRCh38', - ), - ], - 'filters': [ - hl.set(['NO_HQ_GENOTYPES']), - ], - }, - cols={'s': ['sample_1']}, - entries={'HL': [[0.0]]}, - ).key_rows_by('locus') - gatk_mt = annotate_vets(gatk_mt) - dragen_mt = hl.MatrixTable.from_parts( - rows={ - 'locus': [ - hl.Locus( - contig='chr1', - position=1, - reference_genome='GRCh38', - ), - hl.Locus( - contig='chr1', - position=2, - reference_genome='GRCh38', - ), - hl.Locus( - contig='chr1', - position=3, - reference_genome='GRCh38', - ), - hl.Locus( - contig='chr1', - position=4, - reference_genome='GRCh38', - ), - hl.Locus( - contig='chr1', - position=5, - reference_genome='GRCh38', - ), - hl.Locus( - contig='chr1', - position=6, - reference_genome='GRCh38', - ), - ], - 'alleles': [ - ['A', 'T'], - ['A', 'T'], - ['A', 'T'], - ['AC', 'T'], - ['AT', 'ATC'], - ['AG', 'ATG'], - ], - 'filters': [ - hl.set(['NO_HQ_GENOTYPES']), - hl.empty_set(hl.tstr), - hl.missing(hl.tset(hl.tstr)), - hl.set(['NO_HQ_GENOTYPES']), - hl.empty_set(hl.tstr), - hl.set(['NO_HQ_GENOTYPES']), - ], - 'info.CALIBRATION_SENSITIVITY': [ - ['0.999'], - ['0.995'], - ['0.999'], - ['0.98'], - ['0.99'], - ['0.991'], - ], - }, - cols={'s': ['sample_1']}, - entries={'HL': [[0.0], [0.0], [0.0], [0.0], [0.0], [0.0]]}, - ).key_rows_by('locus', 'alleles') - dragen_mt = split_multi_hts(dragen_mt, False) - dragen_mt = annotate_vets(dragen_mt) - self.assertListEqual( - dragen_mt.filters.collect(), - [ - {'NO_HQ_GENOTYPES', 'high_CALIBRATION_SENSITIVITY_SNP'}, - set(), - {'high_CALIBRATION_SENSITIVITY_SNP'}, - {'NO_HQ_GENOTYPES'}, - set(), - {'NO_HQ_GENOTYPES', 'high_CALIBRATION_SENSITIVITY_INDEL'}, - ], - ) diff --git a/loading_pipeline/lib/paths_test.py b/loading_pipeline/lib/paths_test.py deleted file mode 100644 index d271cfee0b..0000000000 --- a/loading_pipeline/lib/paths_test.py +++ /dev/null @@ -1,180 +0,0 @@ -import unittest -from unittest.mock import patch - -import hailtop.fs as hfs - -from loading_pipeline.lib.core import ( - DatasetType, - ReferenceGenome, - SampleType, -) -from loading_pipeline.lib.paths import ( - imported_callset_path, - metadata_for_run_path, - new_variants_table_path, - project_pedigree_path, - project_table_path, - relatedness_check_table_path, - remapped_and_subsetted_callset_path, - sex_check_table_path, - tdr_metrics_path, - validation_errors_for_run_path, - variant_annotations_table_path, -) - -TEST_VCF = 'loading_pipeline/var/test/callsets/1kg_30varia*.vcf' - - -class TestPaths(unittest.TestCase): - def test_project_table_path(self) -> None: - self.assertEqual( - project_table_path( - ReferenceGenome.GRCh38, - DatasetType.MITO, - SampleType.WES, - 'R0652_pipeline_test', - ), - '/var/seqr/pipeline-data/GRCh38/MITO/projects/WES/R0652_pipeline_test.ht', - ) - with ( - patch('loading_pipeline.lib.paths.Env') as mock_env, - ): - mock_env.PIPELINE_DATA_DIR = '/var/bucket/' - self.assertEqual( - project_table_path( - ReferenceGenome.GRCh37, - DatasetType.SNV_INDEL, - SampleType.WES, - 'R0652_pipeline_test', - ), - '/var/bucket/GRCh37/SNV_INDEL/projects/WES/R0652_pipeline_test.ht', - ) - - def test_sex_check_table_path(self) -> None: - self.assertEqual( - sex_check_table_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - '/var/abc.efg/callset.vcf.gz', - ), - '/var/seqr/seqr-loading-temp/GRCh38/SNV_INDEL/sex_check/f92b8ab6b5b8c41fa20d7d49a5626b96dcd2ba79fa6f61eab7ffb80d550d951c.ht', - ) - - def test_relatedness_check_table_path(self) -> None: - self.assertEqual( - relatedness_check_table_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - '/var/abc.efg/callset.vcf.gz', - ), - '/var/seqr/seqr-loading-temp/GRCh38/SNV_INDEL/relatedness_check/f92b8ab6b5b8c41fa20d7d49a5626b96dcd2ba79fa6f61eab7ffb80d550d951c.ht', - ) - - def test_validation_errors_for_run_path(self) -> None: - self.assertEqual( - validation_errors_for_run_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - 'manual__2023-06-26T18:30:09.349671+00:00', - ), - '/var/seqr/pipeline-data/GRCh38/SNV_INDEL/runs/manual__2023-06-26T18:30:09.349671+00:00/validation_errors.json', - ) - - def test_metadata_for_run_path(self) -> None: - self.assertEqual( - metadata_for_run_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - 'manual__2023-06-26T18:30:09.349671+00:00', - ), - '/var/seqr/pipeline-data/GRCh38/SNV_INDEL/runs/manual__2023-06-26T18:30:09.349671+00:00/metadata.json', - ) - - def test_variant_annotations_table_path(self) -> None: - self.assertEqual( - variant_annotations_table_path( - ReferenceGenome.GRCh38, - DatasetType.GCNV, - ), - '/var/seqr/pipeline-data/GRCh38/GCNV/annotations.ht', - ) - - def test_remapped_and_subsetted_callset_path(self) -> None: - self.assertEqual( - remapped_and_subsetted_callset_path( - ReferenceGenome.GRCh38, - DatasetType.GCNV, - '/var/abc.efg/callset.vcf.gz', - 'R0111_tgg_bblanken_wes', - ), - '/var/seqr/seqr-loading-temp/GRCh38/GCNV/remapped_and_subsetted_callsets/R0111_tgg_bblanken_wes/f92b8ab6b5b8c41fa20d7d49a5626b96dcd2ba79fa6f61eab7ffb80d550d951c.mt', - ) - self.assertEqual( - remapped_and_subsetted_callset_path( - ReferenceGenome.GRCh38, - DatasetType.GCNV, - '/var/abc.efg/callset/*.vcf.gz', - 'R0111_tgg_bblanken_wes', - ), - '/var/seqr/seqr-loading-temp/GRCh38/GCNV/remapped_and_subsetted_callsets/R0111_tgg_bblanken_wes/26f481b386721f9889250c6549905660728ec9f77be4b8f7eeb6c4facc76282e.mt', - ) - - def test_imported_callset_path(self) -> None: - self.assertEqual( - imported_callset_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - '/var/abc.efg/callset.vcf.gz', - ), - '/var/seqr/seqr-loading-temp/GRCh38/SNV_INDEL/imported_callsets/f92b8ab6b5b8c41fa20d7d49a5626b96dcd2ba79fa6f61eab7ffb80d550d951c.mt', - ) - - with patch('loading_pipeline.lib.paths.hfs.ls') as mock_ls: - mock_ls.return_value = [ - hfs.stat_result.FileListEntry( - path='loading_pipeline/var/test/callsets/1kg_30variants.vcf', - owner=None, - size=1732033623.804012, - typ=hfs.stat_result.FileType(2), - modification_time=1732033000, - ), - ] - self.assertEqual( - imported_callset_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_VCF, - ), - '/var/seqr/seqr-loading-temp/GRCh38/SNV_INDEL/imported_callsets/01327e46c8747f15feaad2c08875b928c274dcb248ad40837ea3f49d8b4dedfb.mt', - ) - - def test_tdr_metrics_path(self) -> None: - self.assertEqual( - tdr_metrics_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - 'datarepo-7242affb.datarepo_RP_3053', - ), - '/var/seqr/seqr-loading-temp/GRCh38/SNV_INDEL/tdr_metrics/datarepo-7242affb.datarepo_RP_3053.tsv', - ) - - def test_new_variants_table_path(self) -> None: - self.assertEqual( - new_variants_table_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - 'manual__2023-06-26T18:30:09.349671+00:00', - ), - '/var/seqr/pipeline-data/GRCh38/SNV_INDEL/runs/manual__2023-06-26T18:30:09.349671+00:00/new_variants.ht', - ) - - def test_project_pedigree_path(self) -> None: - self.assertEqual( - project_pedigree_path( - ReferenceGenome.GRCh38, - DatasetType.GCNV, - SampleType.WES, - 'R0652_pipeline_test', - ), - '/var/seqr/seqr-loading-temp/GRCh38/GCNV/pedigrees/WES/R0652_pipeline_test_pedigree.tsv', - ) diff --git a/loading_pipeline/lib/reference_datasets/gnomad_exomes_test.py b/loading_pipeline/lib/reference_datasets/gnomad_exomes_test.py deleted file mode 100644 index 639dc6d894..0000000000 --- a/loading_pipeline/lib/reference_datasets/gnomad_exomes_test.py +++ /dev/null @@ -1,72 +0,0 @@ -import unittest -from unittest.mock import patch - -import hail as hl - -from loading_pipeline.lib.core.definitions import ReferenceGenome -from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset - -GNOMAD_EXOMES_37_PATH = ( - 'loading_pipeline/var/test/reference_datasets/raw/gnomad_exomes_37.ht' -) -GNOMAD_EXOMES_38_PATH = ( - 'loading_pipeline/var/test/reference_datasets/raw/gnomad_exomes_38.ht' -) - - -class GnomadTest(unittest.TestCase): - def test_gnomad_exomes_37(self): - with patch.object( - ReferenceDataset, - 'path', - return_value=GNOMAD_EXOMES_37_PATH, - ): - ht = ReferenceDataset.gnomad_exomes.get_ht(ReferenceGenome.GRCh37) - self.assertEqual( - ht.collect(), - [ - hl.Struct( - locus=hl.Locus( - contig='1', - position=12586, - reference_genome='GRCh37', - ), - alleles=['C', 'T'], - AF=0.0005589714855886996, - AN=3578, - AC=2, - Hom=0, - AF_POPMAX_OR_GLOBAL=0.0022026430815458298, - FAF_AF=9.839000267675146e-05, - Hemi=0, - ), - ], - ) - - def test_gnomad_exomes_38(self): - with patch.object( - ReferenceDataset, - 'path', - return_value=GNOMAD_EXOMES_38_PATH, - ): - ht = ReferenceDataset.gnomad_exomes.get_ht(ReferenceGenome.GRCh38) - self.assertEqual( - ht.collect(), - [ - hl.Struct( - locus=hl.Locus( - contig='chr1', - position=12138, - reference_genome='GRCh38', - ), - alleles=['C', 'A'], - AF=0.00909090880304575, - AN=110, - AC=1, - Hom=0, - AF_POPMAX_OR_GLOBAL=0.009803921915590763, - FAF_AF=0.0, - Hemi=0, - ), - ], - ) diff --git a/loading_pipeline/lib/reference_datasets/gnomad_genomes_test.py b/loading_pipeline/lib/reference_datasets/gnomad_genomes_test.py deleted file mode 100644 index df637c2fda..0000000000 --- a/loading_pipeline/lib/reference_datasets/gnomad_genomes_test.py +++ /dev/null @@ -1,72 +0,0 @@ -import unittest -from unittest.mock import patch - -import hail as hl - -from loading_pipeline.lib.core.definitions import ReferenceGenome -from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset - -GNOMAD_GENOMES_37_PATH = ( - 'loading_pipeline/var/test/reference_datasets/raw/gnomad_genomes_37.ht' -) -GNOMAD_GENOMES_38_PATH = ( - 'loading_pipeline/var/test/reference_datasets/raw/gnomad_genomes_38.ht' -) - - -class GnomadTest(unittest.TestCase): - def test_gnomad_genomes_37(self): - with patch.object( - ReferenceDataset, - 'path', - return_value=GNOMAD_GENOMES_37_PATH, - ): - ht = ReferenceDataset.gnomad_genomes.get_ht(ReferenceGenome.GRCh37) - self.assertEqual( - ht.collect(), - [ - hl.Struct( - locus=hl.Locus( - contig='1', - position=10131, - reference_genome='GRCh37', - ), - alleles=['CT', 'C'], - AF=3.6635403375839815e-05, - AN=27296, - AC=1, - Hom=0, - AF_POPMAX_OR_GLOBAL=3.6635403375839815e-05, - FAF_AF=0.0, - Hemi=0, - ), - ], - ) - - def test_gnomad_genomes_38(self): - with patch.object( - ReferenceDataset, - 'path', - return_value=GNOMAD_GENOMES_38_PATH, - ): - ht = ReferenceDataset.gnomad_genomes.get_ht(ReferenceGenome.GRCh38) - self.assertEqual( - ht.collect(), - [ - hl.Struct( - locus=hl.Locus( - contig='chr1', - position=10057, - reference_genome='GRCh38', - ), - alleles=['A', 'C'], - AF=2.642333674884867e-05, - AN=113536, - AC=3, - Hom=0, - AF_POPMAX_OR_GLOBAL=3.779861071961932e-05, - FAF_AF=7.019999884505523e-06, - Hemi=0, - ), - ], - ) diff --git a/loading_pipeline/lib/reference_datasets/gnomad_svs_test.py b/loading_pipeline/lib/reference_datasets/gnomad_svs_test.py deleted file mode 100644 index bfd7c89d11..0000000000 --- a/loading_pipeline/lib/reference_datasets/gnomad_svs_test.py +++ /dev/null @@ -1,93 +0,0 @@ -import unittest -from unittest.mock import patch - -import hail as hl - -from loading_pipeline.lib.core import ReferenceGenome -from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset - -TEST_GNOMAD_SVS_RAW_HT = ( - 'loading_pipeline/var/test/reference_datasets/raw/gnomad_svs_from_vcf.ht' -) - - -class GnomadSVsTest(unittest.TestCase): - @patch('loading_pipeline.lib.reference_datasets.gnomad_svs.vcf_to_ht') - def test_gnomad_svs(self, mock_vcf_to_ht): - mock_vcf_to_ht.return_value = hl.read_table(TEST_GNOMAD_SVS_RAW_HT) - ht = ReferenceDataset.gnomad_svs.get_ht(ReferenceGenome.GRCh38) - self.assertEqual( - ht.collect(), - [ - hl.Struct( - KEY='gnomAD-SV_v3_BND_chr1_1a45f73a', - locus=hl.Locus( - contig='chr1', - position=10434, - reference_genome=ReferenceGenome.GRCh38, - ), - alleles=['N', ''], - AF=0.11413399875164032, - AC=8474, - AN=74246, - N_HET=8426, - N_HOM=24, - ), - hl.Struct( - KEY='gnomAD-SV_v3_BND_chr1_3fa36917', - locus=hl.Locus( - contig='chr1', - position=10440, - reference_genome=ReferenceGenome.GRCh38, - ), - alleles=['N', ''], - AF=0.004201000090688467, - AC=466, - AN=110936, - N_HET=466, - N_HOM=0, - ), - hl.Struct( - KEY='gnomAD-SV_v3_BND_chr1_7bbf34b5', - locus=hl.Locus( - contig='chr1', - position=10464, - reference_genome=ReferenceGenome.GRCh38, - ), - alleles=['N', ''], - AF=0.03698499873280525, - AC=3119, - AN=84332, - N_HET=3115, - N_HOM=2, - ), - hl.Struct( - KEY='gnomAD-SV_v3_BND_chr1_933a2971', - locus=hl.Locus( - contig='chr1', - position=10450, - reference_genome=ReferenceGenome.GRCh38, - ), - alleles=['N', ''], - AF=0.3238990008831024, - AC=21766, - AN=67200, - N_HET=21616, - N_HOM=75, - ), - hl.Struct( - KEY='gnomAD-SV_v3_DUP_chr1_01c2781c', - locus=hl.Locus( - contig='chr1', - position=10000, - reference_genome=ReferenceGenome.GRCh38, - ), - alleles=['N', ''], - AF=0.0019970000721514225, - AC=139, - AN=69594, - N_HET=139, - N_HOM=0, - ), - ], - ) diff --git a/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster_test.py b/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster_test.py deleted file mode 100644 index 6634feea8c..0000000000 --- a/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster_test.py +++ /dev/null @@ -1,162 +0,0 @@ -import unittest -from types import SimpleNamespace -from unittest.mock import Mock, call, patch - -import google.api_core.exceptions -import google.cloud.dataproc_v1.types.clusters -import luigi - -from loading_pipeline.lib.core import DatasetType, ReferenceGenome -from loading_pipeline.lib.misc.gcp import SOCIAL_AUTH_GOOGLE_OAUTH2_SCOPE -from loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster import ( - CreateDataprocClusterTask, -) - - -@patch.multiple( - 'loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster.Env', - GCLOUD_PROJECT='proj', - GCLOUD_REGION='us-a', -) -@patch( - 'loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster.get_service_account_credentials', - return_value=SimpleNamespace( - service_account_email='test@serviceaccount.com', - scopes=SOCIAL_AUTH_GOOGLE_OAUTH2_SCOPE, - ), -) -@patch( - 'loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster.dataproc.ClusterControllerClient', -) -class CreateDataprocClusterTaskTest(unittest.TestCase): - def test_spinup_cluster_already_exists_failed( - self, - mock_cluster_controller: Mock, - *_: Mock, - ) -> None: - mock_client = mock_cluster_controller.return_value - mock_client.get_cluster.return_value = SimpleNamespace( - status=SimpleNamespace( - state=google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.ERROR, - ), - cluster_name='abc', - ) - mock_client.create_cluster.side_effect = ( - google.api_core.exceptions.AlreadyExists('cluster exists') - ) - worker = luigi.worker.Worker() - task = CreateDataprocClusterTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - run_id='2', - ) - worker.add(task) - worker.run() - self.assertFalse(task.complete()) - - def test_spinup_cluster_already_exists_success( - self, - mock_cluster_controller: Mock, - *_: Mock, - ) -> None: - mock_client = mock_cluster_controller.return_value - mock_client.get_cluster.return_value = SimpleNamespace( - status=SimpleNamespace( - state=google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.RUNNING, - ), - ) - mock_client.create_cluster.side_effect = ( - google.api_core.exceptions.AlreadyExists('cluster exists') - ) - worker = luigi.worker.Worker() - task = CreateDataprocClusterTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - run_id='3', - ) - worker.add(task) - worker.run() - self.assertTrue(task.complete()) - - @patch('loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster.logger') - def test_spinup_cluster_doesnt_exist_failed( - self, - mock_logger: Mock, - mock_cluster_controller: Mock, - *_: Mock, - ) -> None: - mock_client = mock_cluster_controller.return_value - mock_client.get_cluster.side_effect = [ - google.api_core.exceptions.NotFound( - 'cluster not found', - ), - google.api_core.exceptions.NotFound( - 'cluster not found', - ), - SimpleNamespace( - status=SimpleNamespace( - state=google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.CREATING, - ), - ), - SimpleNamespace( - status=SimpleNamespace( - state=google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.ERROR, - ), - cluster_name='dataproc-cluster-5', - cluster_uuid='12345', - ), - ] - worker = luigi.worker.Worker() - task = CreateDataprocClusterTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - run_id='4', - ) - worker.add(task) - luigi_task_result = worker.run() - self.assertEqual(luigi_task_result, False) - mock_logger.info.assert_has_calls([call('Waiting for cluster spinup')]) - - @patch('loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster.logger') - def test_spinup_cluster_doesnt_exist_success( - self, - mock_logger: Mock, - mock_cluster_controller: Mock, - *_: Mock, - ) -> None: - mock_client = mock_cluster_controller.return_value - mock_client.get_cluster.side_effect = [ - google.api_core.exceptions.NotFound( - 'cluster not found', - ), - google.api_core.exceptions.NotFound( - 'cluster not found', - ), - SimpleNamespace( - status=SimpleNamespace( - state=google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.CREATING, - ), - ), - SimpleNamespace( - status=SimpleNamespace( - state=google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.RUNNING, - ), - cluster_name='dataproc-cluster-5', - cluster_uuid='12345', - ), - ] - mock_client.create_cluster.side_effect = None - worker = luigi.worker.Worker() - task = CreateDataprocClusterTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - run_id='5', - ) - worker.add(task) - worker.run() - mock_logger.info.assert_has_calls( - [ - call('Waiting for cluster spinup'), - call('Created cluster dataproc-cluster-5 with cluster uuid: 12345'), - ], - ) diff --git a/loading_pipeline/lib/tasks/dataproc/misc_test.py b/loading_pipeline/lib/tasks/dataproc/misc_test.py deleted file mode 100644 index 63ffafb8a1..0000000000 --- a/loading_pipeline/lib/tasks/dataproc/misc_test.py +++ /dev/null @@ -1,51 +0,0 @@ -import unittest -from unittest.mock import Mock, patch - -from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType -from loading_pipeline.lib.tasks.dataproc.misc import to_kebab_str_args -from loading_pipeline.lib.tasks.dataproc.run_pipeline_on_dataproc import ( - RunPipelineOnDataprocTask, -) - - -@patch( - 'loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc.dataproc.JobControllerClient', -) -class MiscTest(unittest.TestCase): - def test_to_kebab_str_args(self, _: Mock): - t = RunPipelineOnDataprocTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - sample_type=SampleType.WGS, - callset_path='test_callset', - project_guids=['R0113_test_project'], - run_id='a_misc_run', - attempt_id=0, - ) - self.assertListEqual( - to_kebab_str_args(t), - [ - '--reference-genome', - 'GRCh38', - '--dataset-type', - 'SNV_INDEL', - '--sample-type', - 'WGS', - '--callset-path', - 'test_callset', - '--project-guids', - '["R0113_test_project"]', - '--skip-check-sex-and-relatedness', - 'False', - '--skip-expect-tdr-metrics', - 'False', - '--validations-to-skip', - '[]', - '--is-new-gcnv-joint-call', - 'False', - '--run-id', - 'a_misc_run', - '--attempt-id', - '0', - ], - ) diff --git a/loading_pipeline/lib/tasks/dataproc/run_pipeline_on_dataproc_test.py b/loading_pipeline/lib/tasks/dataproc/run_pipeline_on_dataproc_test.py deleted file mode 100644 index a09289a85a..0000000000 --- a/loading_pipeline/lib/tasks/dataproc/run_pipeline_on_dataproc_test.py +++ /dev/null @@ -1,184 +0,0 @@ -import unittest -from types import SimpleNamespace -from unittest.mock import Mock, call, patch - -import google.api_core.exceptions -import google.cloud.dataproc_v1.types.jobs -import luigi - -from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType -from loading_pipeline.lib.tasks.dataproc.run_pipeline_on_dataproc import ( - RunPipelineOnDataprocTask, -) -from loading_pipeline.lib.test.mock_complete_task import MockCompleteTask - - -@patch( - 'loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc.CreateDataprocClusterTask', -) -@patch( - 'loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc.dataproc.JobControllerClient', -) -class WriteSuccessFileOnDataprocTaskTest(unittest.TestCase): - @patch('loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc.logger') - def test_job_already_exists_failed( - self, - mock_logger: Mock, - mock_job_controller_client: Mock, - mock_create_dataproc_cluster: Mock, - ) -> None: - mock_create_dataproc_cluster.return_value = MockCompleteTask() - mock_client = mock_job_controller_client.return_value - mock_client.get_job.return_value = SimpleNamespace( - status=SimpleNamespace( - state=google.cloud.dataproc_v1.types.jobs.JobStatus.State.ERROR, - details='Google Cloud Dataproc Agent reports job failure. If logs are available, they can be found at...', - ), - ) - mock_client.submit_job_as_operation.side_effect = ( - google.api_core.exceptions.AlreadyExists('job exists') - ) - worker = luigi.worker.Worker() - task = RunPipelineOnDataprocTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - sample_type=SampleType.WGS, - callset_path='test_callset', - project_guids=['R0113_test_project'], - run_id='manual__2024-04-03', - attempt_id=0, - ) - worker.add(task) - worker.run() - self.assertFalse(task.complete()) - mock_logger.error.assert_has_calls( - [ - call( - 'Job RunPipelineTask-38-SNV-INDEL-manual__2024-04-03-0 entered ERROR state', - ), - ], - ) - - def test_job_already_exists_success( - self, - mock_job_controller_client: Mock, - mock_create_dataproc_cluster: Mock, - ) -> None: - mock_create_dataproc_cluster.return_value = MockCompleteTask() - mock_client = mock_job_controller_client.return_value - mock_client.get_job.return_value = SimpleNamespace( - status=SimpleNamespace( - state=google.cloud.dataproc_v1.types.jobs.JobStatus.State.DONE, - ), - ) - worker = luigi.worker.Worker() - task = RunPipelineOnDataprocTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - sample_type=SampleType.WGS, - callset_path='test_callset', - project_guids=['R0113_test_project'], - run_id='manual__2024-04-04', - attempt_id=0, - ) - worker.add(task) - worker.run() - self.assertTrue(task.complete()) - - @patch('loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc.logger') - def test_job_failed( - self, - mock_logger: Mock, - mock_job_controller_client: Mock, - mock_create_dataproc_cluster: Mock, - ) -> None: - mock_create_dataproc_cluster.return_value = MockCompleteTask() - mock_client = mock_job_controller_client.return_value - mock_client.get_job.side_effect = [ - google.api_core.exceptions.NotFound( - 'job not found', - ), - google.api_core.exceptions.NotFound( - 'job not found', - ), - SimpleNamespace( - status=SimpleNamespace( - state=google.cloud.dataproc_v1.types.jobs.JobStatus.State.PENDING, - ), - ), - SimpleNamespace( - status=SimpleNamespace( - state=google.cloud.dataproc_v1.types.jobs.JobStatus.State.ERROR, - ), - ), - ] - worker = luigi.worker.Worker() - task = RunPipelineOnDataprocTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - sample_type=SampleType.WGS, - callset_path='test_callset', - project_guids=['R0113_test_project'], - run_id='manual__2024-04-05', - attempt_id=1, - ) - worker.add(task) - luigi_task_result = worker.run() - self.assertEqual(luigi_task_result, False) - mock_logger.info.assert_has_calls( - [ - call( - 'Waiting for Job completion RunPipelineTask-38-SNV-INDEL-manual__2024-04-05-1', - ), - ], - ) - - @patch('loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc.logger') - def test_job_success( - self, - mock_logger: Mock, - mock_job_controller_client: Mock, - mock_create_dataproc_cluster: Mock, - ) -> None: - mock_create_dataproc_cluster.return_value = MockCompleteTask() - mock_client = mock_job_controller_client.return_value - mock_client.get_job.side_effect = [ - google.api_core.exceptions.NotFound( - 'job not found', - ), - google.api_core.exceptions.NotFound( - 'job not found', - ), - SimpleNamespace( - status=SimpleNamespace( - state=google.cloud.dataproc_v1.types.jobs.JobStatus.State.PENDING, - ), - ), - SimpleNamespace( - status=SimpleNamespace( - state=google.cloud.dataproc_v1.types.jobs.JobStatus.State.DONE, - ), - ), - ] - worker = luigi.worker.Worker() - task = RunPipelineOnDataprocTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - sample_type=SampleType.WGS, - callset_path='test_callset', - project_guids=['R0113_test_project'], - run_id='manual__2024-04-06', - attempt_id=0, - ) - worker.add(task) - worker.run() - mock_logger.info.assert_has_calls( - [ - call( - 'Waiting for Job completion RunPipelineTask-38-SNV-INDEL-manual__2024-04-06-0', - ), - call( - 'Job RunPipelineTask-38-SNV-INDEL-manual__2024-04-06-0 is complete', - ), - ], - ) diff --git a/loading_pipeline/lib/tasks/exports/misc_test.py b/loading_pipeline/lib/tasks/exports/misc_test.py deleted file mode 100644 index f0324db627..0000000000 --- a/loading_pipeline/lib/tasks/exports/misc_test.py +++ /dev/null @@ -1,484 +0,0 @@ -import unittest - -import hail as hl - -from loading_pipeline.lib.core import ( - DatasetType, - ReferenceGenome, -) -from loading_pipeline.lib.tasks.exports.misc import ( - camelcase_array_structexpression_fields, - sorted_hl_struct, - unmap_formatting_annotation_enums, -) - -TEST_SNV_INDEL_ANNOTATIONS = ( - 'loading_pipeline/var/test/exports/GRCh38/SNV_INDEL/annotations.ht' -) -TEST_GRCH37_SNV_INDEL_ANNOTATIONS = ( - 'loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/annotations.ht' -) - - -class MiscTest(unittest.TestCase): - def test_unmap_formatting_annotation_enums(self) -> None: - ht = hl.read_table(TEST_SNV_INDEL_ANNOTATIONS) - ht = unmap_formatting_annotation_enums( - ht, - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - ) - self.assertCountEqual( - list(ht.globals.enums.collect()[0].keys()), - [ - 'clinvar', - 'hgmd', - 'screen', - 'dbnsfp', - 'gnomad_exomes', - 'gnomad_non_coding_constraint', - 'splice_ai', - 'exac', - 'topmed', - 'gnomad_genomes', - 'eigen', - ], - ) - ht = ht.annotate( - sorted_transcript_consequences=[ht.sorted_transcript_consequences[0]], - ) - self.assertEqual( - ht.collect()[0], - hl.Struct( - key_=0, - locus=hl.Locus( - contig='chr1', - position=876499, - reference_genome='GRCh38', - ), - alleles=['A', 'G'], - clinvar=hl.Struct( - alleleId=929885, - conflictingPathogenicities=None, - goldStars=1, - submitters=['Labcorp Genetics (formerly Invitae), Labcorp'], - conditions=['not provided'], - assertion_ids=[], - pathogenicity_id=12, - ), - rg37_locus=hl.Locus( - contig=1, - position=874501, - reference_genome='GRCh37', - ), - rsid=None, - sorted_transcript_consequences=[ - hl.Struct( - amino_acids='S/L', - canonical=1, - codons='tCg/tTg', - gene_id='ENSG00000187634', - hgvsc='ENST00000616016.5:c.1049C>T', - hgvsp='ENSP00000478421.2:p.Ser350Leu', - transcript_id='ENST00000616016', - mane_select='NM_001385641.1', - mane_plus_clinical=None, - exon=hl.Struct(index=6, total=14), - intron=None, - refseq_transcript_id='NM_001385641.1', - alphamissense=hl.Struct(pathogenicity=None), - loftee=hl.Struct(is_lof_nagnag=None, lof_filters=None), - spliceregion=hl.Struct( - extended_intronic_splice_region_variant=False, - ), - utrannotator=hl.Struct( - existing_inframe_oorfs=None, - existing_outofframe_oorfs=None, - existing_uorfs=None, - fiveutr_annotation=hl.Struct( - type='OutOfFrame_oORF', - KozakContext='CGCATGC', - KozakStrength='Weak', - DistanceToCDS=41, - CapDistanceToStart=None, - DistanceToStop=None, - Evidence=None, - AltStop=None, - AltStopDistanceToCDS=None, - FrameWithCDS=None, - StartDistanceToCDS=None, - newSTOPDistanceToCDS=None, - alt_type=None, - alt_type_length=None, - ref_StartDistanceToCDS=None, - ref_type=None, - ref_type_length=None, - ), - fiveutr_consequence=None, - ), - biotype='protein_coding', - consequence_terms=['missense_variant'], - ), - ], - variant_id='1-876499-A-G', - xpos=1000876499, - gt_stats=hl.Struct(AC=47, AN=81784, AF=0.0005746845272369683, hom=1), - CAID='CA502654', - check_ref=False, - sorted_regulatory_feature_consequences=[ - hl.Struct( - regulatory_feature_id='ENSR00000344437', - biotype='CTCF_binding_site', - consequence_terms=['regulatory_region_variant'], - ), - ], - sorted_motif_feature_consequences=[ - hl.Struct( - motif_feature_id='ENSM00493959715', - consequence_terms=['TF_binding_site_variant'], - ), - ], - gnomad_non_coding_constraint=hl.Struct(z_score=None), - hgmd=hl.Struct(accession='abcdefg', class_id=3), - gnomad_exomes=hl.Struct( - AF=0.0006690866430290043, - AN=1440770, - AC=964, - Hom=0, - AF_POPMAX_OR_GLOBAL=0.0008023773552849889, - FAF_AF=0.000633420015219599, - Hemi=0, - ), - gnomad_genomes=hl.Struct( - AF=0.0002759889466688037, - AN=152180, - AC=42, - Hom=0, - AF_POPMAX_OR_GLOBAL=0.10000000149011612, - FAF_AF=0.0002092500071739778, - Hemi=0, - ), - screen=hl.Struct(region_type_ids=[]), - dbnsfp=hl.Struct( - PrimateAI_score=0.5918066501617432, - fathmm_MKL_coding_score=0.7174800038337708, - CADD_phred=23.5, - SIFT_score=0.0010000000474974513, - REVEL_score=0.3109999895095825, - Polyphen2_HVAR_score=0.164000004529953, - VEST4_score=0.39500001072883606, - MPC_score=0.01291007362306118, - MutPred_score=None, - MutationTaster_pred_id=0, - ), - topmed=hl.Struct( - AC=41, - AF=0.00032651599030941725, - AN=125568, - Hom=0, - Het=41, - ), - exac=hl.Struct( - AF_POPMAX=0.0007150234305299819, - AF=0.00019039999460801482, - AC_Adj=20, - AC_Het=20, - AC_Hom=0, - AC_Hemi=None, - AN_Adj=47974, - ), - splice_ai=hl.Struct(delta_score=0.0, splice_consequence_id=4), - eigen=hl.Struct(Eigen_phred=2.628000020980835), - ), - ) - ht = hl.read_table(TEST_GRCH37_SNV_INDEL_ANNOTATIONS) - ht = unmap_formatting_annotation_enums( - ht, - ReferenceGenome.GRCh37, - DatasetType.SNV_INDEL, - ) - self.assertCountEqual( - list(ht.globals.enums.collect()[0].keys()), - [ - 'clinvar', - 'hgmd', - 'dbnsfp', - 'gnomad_exomes', - 'splice_ai', - 'exac', - 'topmed', - 'gnomad_genomes', - 'eigen', - ], - ) - ht = ht.annotate( - sorted_transcript_consequences=[ht.sorted_transcript_consequences[0]], - ) - self.assertEqual( - ht.collect()[0], - hl.Struct( - locus=hl.Locus(contig=1, position=69134, reference_genome='GRCh37'), - alleles=['A', 'G'], - clinvar=hl.Struct( - alleleId=2193183, - conflictingPathogenicities=None, - goldStars=1, - submitters=['Ambry Genetics'], - conditions=['not specified'], - assertion_ids=[], - pathogenicity_id=14, - ), - rsid=None, - sorted_transcript_consequences=[ - hl.Struct( - amino_acids='E/G', - canonical=1, - codons='gAa/gGa', - gene_id='ENSG00000186092', - hgvsc='ENST00000335137.3:c.44A>G', - hgvsp='ENSP00000334393.3:p.Glu15Gly', - transcript_id='ENST00000335137', - is_lof_nagnag=None, - biotype='protein_coding', - consequence_terms=['missense_variant'], - lof_filters=None, - ), - ], - variant_id='1-69134-A-G', - xpos=1000069134, - gt_stats=hl.Struct(AC=25, AN=1246, AF=0.020064204931259155, hom=10), - CAID='CA502008', - rg38_locus=hl.Locus( - contig='chr1', - position=69134, - reference_genome='GRCh38', - ), - hgmd=None, - gnomad_exomes=hl.Struct( - AF=0.026665963232517242, - AN=18938, - AC=505, - Hom=127, - AF_POPMAX_OR_GLOBAL=0.08191808313131332, - FAF_AF=0.02474386990070343, - Hemi=0, - ), - gnomad_genomes=hl.Struct( - AF=0.0001722949673421681, - AN=5804, - AC=1, - Hom=0, - AF_POPMAX_OR_GLOBAL=0.0005662514013238251, - FAF_AF=0.0, - Hemi=0, - ), - dbnsfp=hl.Struct( - PrimateAI_score=0.37232041358947754, - fathmm_MKL_coding_score=0.056940000504255295, - CADD_phred=15.880000114440918, - SIFT_score=0.1289999932050705, - REVEL_score=0.07500000298023224, - Polyphen2_HVAR_score=0.0010000000474974513, - VEST4_score=0.10700000077486038, - MPC_score=1.8921889066696167, - MutPred_score=0.3779999911785126, - MutationTaster_pred_id=2, - ), - topmed=hl.Struct( - AC=95, - AF=0.0007565619889646769, - AN=125568, - Hom=0, - Het=95, - ), - exac=hl.Struct( - AF_POPMAX=None, - AF=0.0016550000291317701, - AC_Adj=0, - AC_Het=0, - AC_Hom=0, - AC_Hemi=None, - AN_Adj=66, - ), - eigen=hl.Struct(Eigen_phred=1.0019999742507935), - splice_ai=hl.Struct( - delta_score=0.019999999552965164, - splice_consequence_id=2, - ), - key_=1424, - ), - ) - - def test_camelcase_array_structexpression_fields(self) -> None: - ht = hl.read_table(TEST_SNV_INDEL_ANNOTATIONS) - ht = unmap_formatting_annotation_enums( - ht, - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - ) - ht = camelcase_array_structexpression_fields( - ht, - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - ) - ht = ht.annotate( - sortedTranscriptConsequences=[ht.sortedTranscriptConsequences[0]], - ) - self.assertEqual( - ht.collect()[0], - hl.Struct( - key_=0, - locus=hl.Locus( - contig='chr1', - position=876499, - reference_genome='GRCh38', - ), - alleles=['A', 'G'], - clinvar=hl.Struct( - alleleId=929885, - conflictingPathogenicities=None, - goldStars=1, - submitters=['Labcorp Genetics (formerly Invitae), Labcorp'], - conditions=['not provided'], - assertion_ids=[], - pathogenicity_id=12, - ), - rg37_locus=hl.Locus( - contig=1, - position=874501, - reference_genome='GRCh37', - ), - rsid=None, - variant_id='1-876499-A-G', - xpos=1000876499, - gt_stats=hl.Struct(AC=47, AN=81784, AF=0.0005746845272369683, hom=1), - CAID='CA502654', - check_ref=False, - gnomad_non_coding_constraint=hl.Struct(z_score=None), - hgmd=hl.Struct(accession='abcdefg', class_id=3), - gnomad_exomes=hl.Struct( - AF=0.0006690866430290043, - AN=1440770, - AC=964, - Hom=0, - AF_POPMAX_OR_GLOBAL=0.0008023773552849889, - FAF_AF=0.000633420015219599, - Hemi=0, - ), - gnomad_genomes=hl.Struct( - AF=0.0002759889466688037, - AN=152180, - AC=42, - Hom=0, - AF_POPMAX_OR_GLOBAL=0.10000000149011612, - FAF_AF=0.0002092500071739778, - Hemi=0, - ), - screen=hl.Struct(region_type_ids=[]), - dbnsfp=hl.Struct( - PrimateAI_score=0.5918066501617432, - fathmm_MKL_coding_score=0.7174800038337708, - CADD_phred=23.5, - SIFT_score=0.0010000000474974513, - REVEL_score=0.3109999895095825, - Polyphen2_HVAR_score=0.164000004529953, - VEST4_score=0.39500001072883606, - MPC_score=0.01291007362306118, - MutPred_score=None, - MutationTaster_pred_id=0, - ), - topmed=hl.Struct( - AC=41, - AF=0.00032651599030941725, - AN=125568, - Hom=0, - Het=41, - ), - exac=hl.Struct( - AF_POPMAX=0.0007150234305299819, - AF=0.00019039999460801482, - AC_Adj=20, - AC_Het=20, - AC_Hom=0, - AC_Hemi=None, - AN_Adj=47974, - ), - splice_ai=hl.Struct( - delta_score=0.0, - splice_consequence_id=4, - ), - eigen=hl.Struct(Eigen_phred=2.628000020980835), - sortedTranscriptConsequences=[ - hl.Struct( - aminoAcids='S/L', - canonical=1, - codons='tCg/tTg', - geneId='ENSG00000187634', - hgvsc='ENST00000616016.5:c.1049C>T', - hgvsp='ENSP00000478421.2:p.Ser350Leu', - transcriptId='ENST00000616016', - maneSelect='NM_001385641.1', - manePlusClinical=None, - exon=hl.Struct(index=6, total=14), - intron=None, - refseqTranscriptId='NM_001385641.1', - alphamissense=hl.Struct(pathogenicity=None), - loftee=hl.Struct(isLofNagnag=None, lofFilters=None), - spliceregion=hl.Struct( - extended_intronic_splice_region_variant=False, - ), - utrannotator=hl.Struct( - existingInframeOorfs=None, - existingOutofframeOorfs=None, - existingUorfs=None, - fiveutrAnnotation=hl.Struct( - type='OutOfFrame_oORF', - KozakContext='CGCATGC', - KozakStrength='Weak', - DistanceToCDS=41, - CapDistanceToStart=None, - DistanceToStop=None, - Evidence=None, - AltStop=None, - AltStopDistanceToCDS=None, - FrameWithCDS=None, - StartDistanceToCDS=None, - newSTOPDistanceToCDS=None, - alt_type=None, - alt_type_length=None, - ref_StartDistanceToCDS=None, - ref_type=None, - ref_type_length=None, - ), - fiveutrConsequence=None, - ), - biotype='protein_coding', - consequenceTerms=['missense_variant'], - ), - ], - sortedRegulatoryFeatureConsequences=[ - hl.Struct( - regulatoryFeatureId='ENSR00000344437', - biotype='CTCF_binding_site', - consequenceTerms=['regulatory_region_variant'], - ), - ], - sortedMotifFeatureConsequences=[ - hl.Struct( - motifFeatureId='ENSM00493959715', - consequenceTerms=['TF_binding_site_variant'], - ), - ], - ), - ) - - def test_sorted_hl_struct(self) -> None: - struct = hl.Struct( - z=5, - y=hl.Struct(b=2, a=hl.Struct(d=4, c=3)), - x=hl.Struct(k=9), - ) - self.assertEqual( - sorted_hl_struct(struct), - hl.Struct(x=hl.Struct(k=9), y=hl.Struct(a=hl.Struct(c=3, d=4), b=2), z=5), - ) diff --git a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py deleted file mode 100644 index ccb3260f5e..0000000000 --- a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py +++ /dev/null @@ -1,423 +0,0 @@ -import hail as hl -import luigi.worker -import pandas as pd - -from loading_pipeline.lib.core import ( - DatasetType, - ReferenceGenome, - SampleType, -) -from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS -from loading_pipeline.lib.paths import ( - new_entries_parquet_path, - variant_annotations_table_path, -) -from loading_pipeline.lib.tasks.exports.write_new_entries_parquet import ( - WriteNewEntriesParquetTask, -) -from loading_pipeline.lib.test.misc import ( - convert_ndarray_to_list, - copy_project_pedigree_to_mocked_dir, -) -from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase - -TEST_PEDIGREE_3_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_3_remap.tsv' -TEST_PEDIGREE_4_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_4_remap.tsv' -TEST_PEDIGREE_5 = 'loading_pipeline/var/test/pedigrees/test_pedigree_5.tsv' -TEST_MITO_EXPORT_PEDIGREE = ( - 'loading_pipeline/var/test/pedigrees/test_mito_export_pedigree.tsv' -) -TEST_SNV_INDEL_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' -TEST_MITO_CALLSET = 'loading_pipeline/var/test/callsets/mito_1.mt' -TEST_SV_VCF_2 = 'loading_pipeline/var/test/callsets/sv_2.vcf' -TEST_GCNV_BED_FILE = 'loading_pipeline/var/test/callsets/gcnv_1.tsv' -TEST_SNV_INDEL_ANNOTATIONS = ( - 'loading_pipeline/var/test/exports/GRCh38/SNV_INDEL/annotations.ht' -) -TEST_MITO_ANNOTATIONS = 'loading_pipeline/var/test/exports/GRCh38/MITO/annotations.ht' -TEST_SV_ANNOTATIONS = 'loading_pipeline/var/test/exports/GRCh38/SV/annotations.ht' -TEST_GCNV_ANNOTATIONS = 'loading_pipeline/var/test/exports/GRCh38/GCNV/annotations.ht' - -TEST_RUN_ID = 'manual__2024-04-03' - - -class WriteNewEntriesParquetTest(MockedDatarootTestCase): - def setUp(self) -> None: - super().setUp() - ht = hl.read_table( - TEST_SNV_INDEL_ANNOTATIONS, - ) - ht.write( - variant_annotations_table_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - ), - ) - ht = hl.read_table( - TEST_MITO_ANNOTATIONS, - ) - ht.write( - variant_annotations_table_path( - ReferenceGenome.GRCh38, - DatasetType.MITO, - ), - ) - ht = hl.read_table( - TEST_SV_ANNOTATIONS, - ) - ht.write( - variant_annotations_table_path( - ReferenceGenome.GRCh38, - DatasetType.SV, - ), - ) - ht = hl.read_table(TEST_GCNV_ANNOTATIONS) - ht.write( - variant_annotations_table_path( - ReferenceGenome.GRCh38, - DatasetType.GCNV, - ), - ) - - def test_write_new_entries_parquet(self): - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_3_REMAP, - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - SampleType.WGS, - 'R0113_test_project', - ) - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_4_REMAP, - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - SampleType.WGS, - 'R0114_project4', - ) - worker = luigi.worker.Worker() - task = WriteNewEntriesParquetTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - sample_type=SampleType.WGS, - callset_path=TEST_SNV_INDEL_VCF, - project_guids=['R0113_test_project', 'R0114_project4'], - validations_to_skip=[ALL_VALIDATIONS], - run_id=TEST_RUN_ID, - ) - worker.add(task) - worker.run() - self.assertTrue(task.output().exists()) - self.assertTrue(task.complete()) - df = pd.read_parquet( - new_entries_parquet_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ), - ) - export_json = convert_ndarray_to_list(df.to_dict('records')) - self.assertEqual( - export_json[:2], - [ - { - 'key': 0, - 'project_guid': 'R0113_test_project', - 'family_guid': 'abc_1', - 'sample_type': 'WGS', - 'xpos': 1000876499, - 'geneIds': ['ENSG00000187634'], - 'filters': [], - 'calls': [ - { - 'sampleId': 'HG00731_1', - 'gt': 2, - 'gq': 21, - 'ab': 1.0, - 'dp': 7, - }, - { - 'sampleId': 'HG00732_1', - 'gt': 2, - 'gq': 24, - 'ab': 1.0, - 'dp': 8, - }, - { - 'sampleId': 'HG00733_1', - 'gt': 2, - 'gq': 12, - 'ab': 1.0, - 'dp': 4, - }, - ], - 'sign': 1, - }, - { - 'key': 1, - 'project_guid': 'R0113_test_project', - 'family_guid': 'abc_1', - 'sample_type': 'WGS', - 'xpos': 1000878314, - 'geneIds': ['ENSG00000187634'], - 'filters': ['VQSRTrancheSNP99.00to99.90'], - 'calls': [ - { - 'sampleId': 'HG00731_1', - 'gt': 1, - 'gq': 30, - 'ab': 0.3333333432674408, - 'dp': 3, - }, - {'sampleId': 'HG00732_1', 'gt': 0, 'gq': 6, 'ab': 0.0, 'dp': 2}, - { - 'sampleId': 'HG00733_1', - 'gt': 1, - 'gq': 61, - 'ab': 0.6000000238418579, - 'dp': 5, - }, - ], - 'sign': 1, - }, - ], - ) - - def test_mito_write_new_entries_parquet(self): - copy_project_pedigree_to_mocked_dir( - TEST_MITO_EXPORT_PEDIGREE, - ReferenceGenome.GRCh38, - DatasetType.MITO, - SampleType.WGS, - 'R0116_test_project3', - ) - worker = luigi.worker.Worker() - task = WriteNewEntriesParquetTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.MITO, - sample_type=SampleType.WGS, - callset_path=TEST_MITO_CALLSET, - project_guids=['R0116_test_project3'], - validations_to_skip=[ALL_VALIDATIONS], - run_id=TEST_RUN_ID, - ) - worker.add(task) - worker.run() - self.assertTrue(task.output().exists()) - self.assertTrue(task.complete()) - df = pd.read_parquet( - new_entries_parquet_path( - ReferenceGenome.GRCh38, - DatasetType.MITO, - TEST_RUN_ID, - ), - ) - export_json = convert_ndarray_to_list(df.to_dict('records')) - self.assertEqual( - export_json, - [ - { - 'key': 998, - 'project_guid': 'R0116_test_project3', - 'family_guid': 'family_1', - 'sample_type': 'WGS', - 'xpos': 25000000008, - 'filters': [], - 'calls': [ - { - 'sampleId': 'RGP_1270_2', - 'gt': 2, - 'dp': 4216, - 'hl': 0.999, - 'mitoCn': 224, - 'contamination': 0.0, - }, - ], - 'sign': 1, - }, - ], - ) - - def test_sv_write_new_entries_parquet(self): - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_5, - ReferenceGenome.GRCh38, - DatasetType.SV, - SampleType.WGS, - 'R0115_test_project2', - ) - worker = luigi.worker.Worker() - task = WriteNewEntriesParquetTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SV, - sample_type=SampleType.WGS, - callset_path=TEST_SV_VCF_2, - project_guids=['R0115_test_project2'], - validations_to_skip=[ALL_VALIDATIONS], - run_id=TEST_RUN_ID, - ) - worker.add(task) - worker.run() - self.assertTrue(task.output().exists()) - self.assertTrue(task.complete()) - df = pd.read_parquet( - new_entries_parquet_path( - ReferenceGenome.GRCh38, - DatasetType.SV, - TEST_RUN_ID, - ), - ) - export_json = convert_ndarray_to_list(df.to_dict('records')) - self.assertEqual( - export_json, - [ - { - 'key': 727, - 'project_guid': 'R0115_test_project2', - 'family_guid': 'family_2_1', - 'xpos': 1001025886, - 'geneIds': ['ENSG00000188157'], - 'filters': ['HIGH_SR_BACKGROUND', 'UNRESOLVED'], - 'calls': [ - { - 'sampleId': 'RGP_164_1', - 'gt': 0, - 'cn': None, - 'gq': 99, - 'newCall': True, - 'prevCall': False, - 'prevNumAlt': None, - }, - { - 'sampleId': 'RGP_164_2', - 'gt': 1, - 'cn': None, - 'gq': 31, - 'newCall': True, - 'prevCall': False, - 'prevNumAlt': None, - }, - { - 'sampleId': 'RGP_164_3', - 'gt': 0, - 'cn': None, - 'gq': 99, - 'newCall': True, - 'prevCall': False, - 'prevNumAlt': None, - }, - { - 'sampleId': 'RGP_164_4', - 'gt': 0, - 'cn': None, - 'gq': 99, - 'newCall': True, - 'prevCall': False, - 'prevNumAlt': None, - }, - ], - 'sign': 1, - }, - ], - ) - - def test_gcnv_write_new_entries_parquet(self): - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_5, - ReferenceGenome.GRCh38, - DatasetType.GCNV, - SampleType.WES, - 'R0115_test_project2', - ) - worker = luigi.worker.Worker() - task = WriteNewEntriesParquetTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.GCNV, - sample_type=SampleType.WES, - callset_path=TEST_GCNV_BED_FILE, - project_guids=['R0115_test_project2'], - validations_to_skip=[ALL_VALIDATIONS], - run_id=TEST_RUN_ID, - ) - worker.add(task) - worker.run() - self.assertTrue(task.output().exists()) - self.assertTrue(task.complete()) - df = pd.read_parquet( - new_entries_parquet_path( - ReferenceGenome.GRCh38, - DatasetType.GCNV, - TEST_RUN_ID, - ), - ) - export_json = convert_ndarray_to_list(df.to_dict('records')) - self.assertEqual( - export_json, - [ - { - 'key': 0, - 'project_guid': 'R0115_test_project2', - 'family_guid': 'family_2_1', - 'xpos': 1000939203, - 'filters': [], - 'calls': [ - { - 'sampleId': 'RGP_164_1', - 'gt': 1, - 'cn': 1, - 'qs': 4, - 'defragged': False, - 'start': 100006937, - 'end': 100007881, - 'numExon': 2, - 'geneIds': ['ENSG00000117620', 'ENSG00000283761'], - 'newCall': False, - 'prevCall': True, - 'prevOverlap': False, - }, - { - 'sampleId': 'RGP_164_2', - 'gt': 1, - 'cn': 1, - 'qs': 5, - 'defragged': False, - 'start': 100017585, - 'end': 100023213, - 'numExon': 1, - 'geneIds': ['ENSG00000117620', 'ENSG00000283761'], - 'newCall': False, - 'prevCall': False, - 'prevOverlap': False, - }, - { - 'sampleId': 'RGP_164_3', - 'gt': 2, - 'cn': 0, - 'qs': 30, - 'defragged': False, - 'start': 100017585, - 'end': 100023213, - 'numExon': 1, - 'geneIds': ['ENSG00000117620', 'ENSG00000283761'], - 'newCall': False, - 'prevCall': True, - 'prevOverlap': False, - }, - { - 'sampleId': 'RGP_164_4', - 'gt': 2, - 'cn': 0, - 'qs': 30, - 'defragged': False, - 'start': 100017586, - 'end': 100023212, - 'numExon': 2, - 'geneIds': ['ENSG00000283761', 'ENSG22222222222'], - 'newCall': False, - 'prevCall': True, - 'prevOverlap': False, - }, - ], - 'sign': 1, - }, - ], - ) diff --git a/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py deleted file mode 100644 index 5458854f56..0000000000 --- a/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py +++ /dev/null @@ -1,270 +0,0 @@ -import os -from unittest import mock - -import hail as hl -import luigi.worker -import pandas as pd - -from loading_pipeline.lib.core import ( - DatasetType, - ReferenceGenome, - SampleType, -) -from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS -from loading_pipeline.lib.paths import ( - new_variant_details_parquet_path, - new_variants_table_path, -) -from loading_pipeline.lib.tasks.exports.write_new_variant_details_parquet import ( - WriteNewVariantDetailsParquetTask, -) -from loading_pipeline.lib.test.misc import convert_ndarray_to_list -from loading_pipeline.lib.test.mock_complete_task import MockCompleteTask -from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase - -TEST_SNV_INDEL_ANNOTATIONS = ( - 'loading_pipeline/var/test/exports/GRCh38/SNV_INDEL/annotations.ht' -) -TEST_GRCH37_SNV_INDEL_ANNOTATIONS = ( - 'loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/annotations.ht' -) - -TEST_RUN_ID = 'manual__2024-04-03' - - -class WriteNewVariantDetailsParquetTest(MockedDatarootTestCase): - def setUp(self) -> None: - super().setUp() - ht = hl.read_table( - TEST_SNV_INDEL_ANNOTATIONS, - ) - ht.write( - new_variants_table_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ), - ) - ht = hl.read_table( - TEST_GRCH37_SNV_INDEL_ANNOTATIONS, - ) - ht.write( - new_variants_table_path( - ReferenceGenome.GRCh37, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ), - ) - - # Make an incomplete parquet to validate overwrite-ing. - os.makedirs( - new_variant_details_parquet_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ), - exist_ok=True, - ) - with open( - os.path.join( - new_variant_details_parquet_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ), - 'incomplete_file.parquet', - ), - 'w', - ) as f: - f.write('') - - @mock.patch( - 'loading_pipeline.lib.tasks.exports.write_new_variant_details_parquet.WriteNewVariantsTableTask', - ) - def test_write_new_variant_details_parquet_test( - self, - mock_write_new_variants_task, - ) -> None: - mock_write_new_variants_task.return_value = MockCompleteTask() - worker = luigi.worker.Worker() - task = WriteNewVariantDetailsParquetTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - sample_type=SampleType.WGS, - callset_path='fake_callset', - project_guids=[ - 'fake_project', - ], - validations_to_skip=[ALL_VALIDATIONS], - run_id=TEST_RUN_ID, - ) - worker.add(task) - worker.run() - self.assertTrue(task.output().exists()) - self.assertTrue(task.complete()) - df = pd.read_parquet( - new_variant_details_parquet_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ), - ) - export_json = convert_ndarray_to_list(df.head(1).to_dict('records')) - self.assertListEqual( - list(export_json[0].keys()), - [ - 'key', - 'variantId', - 'rsid', - 'CAID', - 'liftedOverChrom', - 'liftedOverPos', - 'sortedMotifFeatureConsequences', - 'sortedRegulatoryFeatureConsequences', - 'transcripts', - ], - ) - self.assertEqual( - export_json[0]['key'], - 0, - ) - self.assertEqual( - export_json[0]['transcripts'][0], - { - 'alphamissense': {'pathogenicity': None}, - 'aminoAcids': 'S/L', - 'biotype': 'protein_coding', - 'canonical': 1, - 'codons': 'tCg/tTg', - 'consequenceTerms': ['missense_variant'], - 'exon': {'index': 6, 'total': 14}, - 'geneId': 'ENSG00000187634', - 'hgvsc': 'ENST00000616016.5:c.1049C>T', - 'hgvsp': 'ENSP00000478421.2:p.Ser350Leu', - 'intron': None, - 'transcriptId': 'ENST00000616016', - 'transcriptRank': 0, - 'majorConsequence': 'missense_variant', - 'maneSelect': 'NM_001385641.1', - 'manePlusClinical': None, - 'refseqTranscriptId': 'NM_001385641.1', - 'loftee': {'isLofNagnag': None, 'lofFilters': None}, - 'spliceregion': { - 'extended_intronic_splice_region_variant': False, - }, - 'utrannotator': { - 'existingInframeOorfs': None, - 'existingOutofframeOorfs': None, - 'existingUorfs': None, - 'fiveutrAnnotation': { - 'AltStop': None, - 'AltStopDistanceToCDS': None, - 'CapDistanceToStart': None, - 'DistanceToCDS': 41, - 'DistanceToStop': None, - 'Evidence': None, - 'FrameWithCDS': None, - 'KozakContext': 'CGCATGC', - 'KozakStrength': 'Weak', - 'StartDistanceToCDS': None, - 'alt_type': None, - 'alt_type_length': None, - 'newSTOPDistanceToCDS': None, - 'ref_StartDistanceToCDS': None, - 'ref_type': None, - 'ref_type_length': None, - 'type': 'OutOfFrame_oORF', - }, - 'fiveutrConsequence': None, - }, - }, - ) - self.assertEqual( - list(export_json[0]['transcripts'][0].keys()), - sorted(export_json[0]['transcripts'][0].keys()), - ) - self.assertEqual( - list( - export_json[0]['transcripts'][0]['utrannotator'][ - 'fiveutrAnnotation' - ].keys(), - ), - sorted( - export_json[0]['transcripts'][0]['utrannotator'][ - 'fiveutrAnnotation' - ].keys(), - ), - ) - - @mock.patch( - 'loading_pipeline.lib.tasks.exports.write_new_variant_details_parquet.WriteNewVariantsTableTask', - ) - def test_grch37_write_new_variant_details_parquet_test( - self, - mock_write_new_variants_task, - ) -> None: - mock_write_new_variants_task.return_value = MockCompleteTask() - worker = luigi.worker.Worker() - task = WriteNewVariantDetailsParquetTask( - reference_genome=ReferenceGenome.GRCh37, - dataset_type=DatasetType.SNV_INDEL, - sample_type=SampleType.WGS, - callset_path='fake_callset', - project_guids=[ - 'fake_project', - ], - validations_to_skip=[ALL_VALIDATIONS], - run_id=TEST_RUN_ID, - ) - worker.add(task) - worker.run() - self.assertTrue(task.output().exists()) - self.assertTrue(task.complete()) - df = pd.read_parquet( - os.path.join( - new_variant_details_parquet_path( - ReferenceGenome.GRCh37, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ), - ), - ) - export_json = convert_ndarray_to_list(df.head(1).to_dict('records')) - self.assertListEqual( - list(export_json[0].keys()), - [ - 'key', - 'variantId', - 'rsid', - 'CAID', - 'liftedOverChrom', - 'liftedOverPos', - 'transcripts', - ], - ) - self.assertEqual( - export_json[0]['key'], - 1424, - ) - self.assertEqual(export_json[0]['CAID'], None) - self.assertEqual( - export_json[0]['transcripts'][0], - { - 'aminoAcids': 'E/G', - 'biotype': 'protein_coding', - 'canonical': 1, - 'codons': 'gAa/gGa', - 'consequenceTerms': ['missense_variant'], - 'geneId': 'ENSG00000186092', - 'hgvsc': 'ENST00000335137.3:c.44A>G', - 'hgvsp': 'ENSP00000334393.3:p.Glu15Gly', - 'loftee': {'isLofNagnag': None, 'lofFilters': None}, - 'majorConsequence': 'missense_variant', - 'transcriptId': 'ENST00000335137', - 'transcriptRank': 0, - }, - ) - self.assertEqual( - list(export_json[0]['transcripts'][0].keys()), - sorted(export_json[0]['transcripts'][0].keys()), - ) diff --git a/loading_pipeline/lib/tasks/files_test.py b/loading_pipeline/lib/tasks/files_test.py deleted file mode 100644 index b2dfd937e0..0000000000 --- a/loading_pipeline/lib/tasks/files_test.py +++ /dev/null @@ -1,40 +0,0 @@ -import os -import tempfile -import unittest - -from loading_pipeline.lib.tasks.files import ( - CallsetTask, - HailTableTask, - RawFileTask, - VCFFileTask, -) - - -class FilesTest(unittest.TestCase): - def test_raw_file(self) -> None: - with tempfile.NamedTemporaryFile(suffix='.txt') as f: - self.assertTrue(RawFileTask(f.name).complete()) - - def test_vcf_file(self) -> None: - with tempfile.NamedTemporaryFile(suffix='.vcf.bgz') as f: - self.assertTrue(VCFFileTask(f.name).complete()) - - def test_hail_table(self) -> None: - with tempfile.TemporaryDirectory(suffix='.ht') as d: - self.assertFalse(HailTableTask(d).complete()) - with open(os.path.join(d, '_SUCCESS'), 'w') as f: - f.write('0') - self.assertTrue(HailTableTask(d).complete()) - - def test_callset_task(self) -> None: - with tempfile.NamedTemporaryFile(suffix='.txt') as f: - self.assertTrue(CallsetTask(f.name).complete()) - - with tempfile.NamedTemporaryFile(suffix='.vcf') as f: - self.assertTrue(CallsetTask(f.name).complete()) - - with tempfile.TemporaryDirectory(suffix='.mt') as d: - self.assertFalse(CallsetTask(d).complete()) - with open(os.path.join(d, '_SUCCESS'), 'w') as f: - f.write('0') - self.assertTrue(CallsetTask(d).complete()) diff --git a/loading_pipeline/lib/tasks/reference_data/__init__.py b/loading_pipeline/lib/tasks/reference_data/__init__.py deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/loading_pipeline/lib/tasks/reference_data/updated_reference_dataset.py b/loading_pipeline/lib/tasks/reference_data/updated_reference_dataset.py deleted file mode 100644 index 575cc1864f..0000000000 --- a/loading_pipeline/lib/tasks/reference_data/updated_reference_dataset.py +++ /dev/null @@ -1,27 +0,0 @@ -import luigi - -from loading_pipeline.lib.paths import valid_reference_dataset_path -from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset -from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( - BaseLoadingPipelineParams, -) -from loading_pipeline.lib.tasks.base.base_write import BaseWriteTask -from loading_pipeline.lib.tasks.files import GCSorLocalTarget - - -@luigi.util.inherits(BaseLoadingPipelineParams) -class UpdatedReferenceDatasetTask(BaseWriteTask): - reference_dataset: ReferenceDataset = luigi.EnumParameter( - enum=ReferenceDataset, - ) - - def output(self): - return GCSorLocalTarget( - valid_reference_dataset_path( - self.reference_genome, - self.reference_dataset, - ), - ) - - def create_table(self): - return self.reference_dataset.get_ht(self.reference_genome) diff --git a/loading_pipeline/lib/tasks/reference_data/updated_reference_dataset_parquet.py b/loading_pipeline/lib/tasks/reference_data/updated_reference_dataset_parquet.py deleted file mode 100644 index ed8adfce6b..0000000000 --- a/loading_pipeline/lib/tasks/reference_data/updated_reference_dataset_parquet.py +++ /dev/null @@ -1,55 +0,0 @@ -import luigi - -from loading_pipeline.lib.annotations.expression_helpers import get_expr_for_variant_id -from loading_pipeline.lib.core.dataset_type import DatasetType -from loading_pipeline.lib.core.definitions import ReferenceGenome -from loading_pipeline.lib.paths import reference_dataset_parquet -from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset -from loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc import ( - BaseRunJobOnDataprocTask, -) -from loading_pipeline.lib.tasks.files import GCSorLocalFolderTarget, GCSorLocalTarget - - -class UpdatedReferenceDatasetParquetTask(luigi.Task): - reference_genome = luigi.EnumParameter(enum=ReferenceGenome) - dataset_type = luigi.EnumParameter(enum=DatasetType) - reference_dataset: ReferenceDataset = luigi.EnumParameter( - enum=ReferenceDataset, - ) - run_id = luigi.Parameter() - attempt_id = luigi.IntParameter() - - def complete(self) -> luigi.Target: - return GCSorLocalFolderTarget(self.output().path).exists() - - def output(self): - return GCSorLocalTarget( - reference_dataset_parquet( - self.reference_genome, - self.reference_dataset, - ), - ) - - def run(self): - ht = self.reference_dataset.get_ht(self.reference_genome) - ht = ht.annotate( - variant_id=get_expr_for_variant_id(ht), - ) - df = ht.to_spark(flatten=False) - df.write.parquet( - self.output().path, - mode='overwrite', - ) - - -class UpdatedReferenceDatasetParquetOnDataprocTask(BaseRunJobOnDataprocTask): - reference_genome = luigi.EnumParameter(enum=ReferenceGenome) - dataset_type = luigi.EnumParameter(enum=DatasetType) - reference_dataset: ReferenceDataset = luigi.EnumParameter( - enum=ReferenceDataset, - ) - - @property - def task(self) -> luigi.Task: - return UpdatedReferenceDatasetParquetTask diff --git a/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py b/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py deleted file mode 100644 index 3bfe55af65..0000000000 --- a/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py +++ /dev/null @@ -1,1349 +0,0 @@ -import functools -from unittest.mock import Mock, PropertyMock, patch - -import hail as hl -import luigi.worker - -from loading_pipeline.lib.annotations.enums import ( - BIOTYPES, - FIVEUTR_CONSEQUENCES, - LOF_FILTERS, - MITOTIP_PATHOGENICITIES, - MOTIF_CONSEQUENCE_TERMS, - REGULATORY_BIOTYPES, - REGULATORY_CONSEQUENCE_TERMS, - SV_CONSEQUENCE_RANKS, - SV_TYPE_DETAILS, - SV_TYPES, - TRANSCRIPT_CONSEQUENCE_TERMS, -) -from loading_pipeline.lib.core import ( - DatasetType, - ReferenceGenome, - SampleType, -) -from loading_pipeline.lib.misc.io import remap_pedigree_hash -from loading_pipeline.lib.misc.validation import ( - ALL_VALIDATIONS, - SKIPPABLE_VALIDATIONS, - validate_expected_contig_frequency, -) -from loading_pipeline.lib.paths import ( - valid_reference_dataset_path, -) -from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset -from loading_pipeline.lib.tasks.files import GCSorLocalFolderTarget -from loading_pipeline.lib.tasks.update_variant_annotations_table_with_new_variants import ( - UpdateVariantAnnotationsTableWithNewVariantsTask, -) -from loading_pipeline.lib.test.misc import copy_project_pedigree_to_mocked_dir -from loading_pipeline.lib.test.mocked_reference_datasets_testcase import ( - MockedReferenceDatasetsTestCase, -) -from loading_pipeline.var.test.vep.mock_vep_data import ( - MOCK_37_VEP_DATA, - MOCK_38_VEP_DATA, -) - -TEST_MITO_MT = 'loading_pipeline/var/test/callsets/mito_1.mt' -TEST_SNV_INDEL_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' -TEST_SV_VCF = 'loading_pipeline/var/test/callsets/sv_1.vcf' -TEST_SV_VCF_2 = 'loading_pipeline/var/test/callsets/sv_2.vcf' -TEST_GCNV_BED_FILE = 'loading_pipeline/var/test/callsets/gcnv_1.tsv' -TEST_GCNV_BED_FILE_2 = 'loading_pipeline/var/test/callsets/gcnv_2.tsv' -TEST_PEDIGREE_3_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_3_remap.tsv' -TEST_PEDIGREE_4_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_4_remap.tsv' -TEST_PEDIGREE_5 = 'loading_pipeline/var/test/pedigrees/test_pedigree_5.tsv' -TEST_PEDIGREE_8 = 'loading_pipeline/var/test/pedigrees/test_pedigree_8.tsv' -TEST_PEDIGREE_10 = 'loading_pipeline/var/test/pedigrees/test_pedigree_10.tsv' -TEST_PEDIGREE_11 = 'loading_pipeline/var/test/pedigrees/test_pedigree_11.tsv' - -GENE_ID_MAPPING = { - 'OR4F5': 'ENSG00000186092', - 'PLEKHG4B': 'ENSG00000153404', - 'OR4F16': 'ENSG00000186192', - 'OR4F29': 'ENSG00000284733', - 'FBXO28': 'ENSG00000143756', - 'SAMD11': 'ENSG00000187634', - 'C1orf174': 'ENSG00000198912', - 'TAS1R1': 'ENSG00000173662', - 'FAM131C': 'ENSG00000185519', - 'RCC2': 'ENSG00000179051', - 'NBPF3': 'ENSG00000142794', - 'AGBL4': 'ENSG00000186094', - 'KIAA1614': 'ENSG00000135835', - 'MR1': 'ENSG00000153029', - 'STX6': 'ENSG00000135823', - 'XPR1': 'ENSG00000143324', -} - -TEST_RUN_ID = 'manual__2024-04-03' - - -class UpdateVariantAnnotationsTableWithNewVariantsTaskTest( - MockedReferenceDatasetsTestCase, -): - def test_missing_pedigree( - self, - ) -> None: - uvatwns_task = UpdateVariantAnnotationsTableWithNewVariantsTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - sample_type=SampleType.WGS, - callset_path=TEST_SNV_INDEL_VCF, - project_guids=['R0113_test_project'], - validations_to_skip=[ALL_VALIDATIONS], - run_id=TEST_RUN_ID, - ) - worker = luigi.worker.Worker() - worker.add(uvatwns_task) - worker.run() - self.assertFalse(uvatwns_task.complete()) - - @patch( - 'loading_pipeline.lib.tasks.validate_callset.SKIPPABLE_VALIDATIONS', - [ - x - for x in SKIPPABLE_VALIDATIONS - if x.__name__ != 'validate_expected_contig_frequency' - ] - + [ - functools.update_wrapper( - functools.partial( - validate_expected_contig_frequency, - min_rows_per_contig=25, - ), - validate_expected_contig_frequency, - ), - ], - ) - @patch.object(ReferenceGenome, 'standard_contigs', new_callable=PropertyMock) - @patch('loading_pipeline.lib.misc.vep.hl.vep') - @patch( - 'loading_pipeline.lib.tasks.write_new_variants_table.load_gencode_ensembl_to_refseq_id', - ) - def test_multiple_update_vat( - self, - mock_load_gencode_ensembl_to_refseq_id: Mock, - mock_vep: Mock, - mock_standard_contigs: Mock, - ) -> None: - mock_vep.side_effect = lambda ht, **_: ht.annotate(vep=MOCK_38_VEP_DATA) - mock_load_gencode_ensembl_to_refseq_id.return_value = hl.dict( - {'ENST00000327044': 'NM_015658.4'}, - ) - mock_standard_contigs.return_value = {'chr1'} - # This creates a mock validation table with 1 coding and 1 non-coding variant - # explicitly chosen from the VCF. - # NB: This is the one and only place validation is enabled in the task tests! - coding_and_noncoding_variants_ht = hl.Table.parallelize( - [ - { - 'locus': hl.Locus( - contig='chr1', - position=871269, - reference_genome='GRCh38', - ), - 'coding': False, - 'noncoding': True, - }, - { - 'locus': hl.Locus( - contig='chr1', - position=876499, - reference_genome='GRCh38', - ), - 'coding': True, - 'noncoding': False, - }, - ], - hl.tstruct( - locus=hl.tlocus('GRCh38'), - coding=hl.tbool, - noncoding=hl.tbool, - ), - key='locus', - globals=hl.Struct( - enums=hl.Struct( - gnomad_genomes=hl.Struct(), - ), - ), - ) - coding_and_noncoding_variants_ht.write( - valid_reference_dataset_path( - ReferenceGenome.GRCh38, - ReferenceDataset.gnomad_coding_and_noncoding, - ), - overwrite=True, - ) - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_3_REMAP, - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - SampleType.WGS, - 'R0113_test_project', - ) - worker = luigi.worker.Worker() - uvatwns_task_3 = UpdateVariantAnnotationsTableWithNewVariantsTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - sample_type=SampleType.WGS, - callset_path=TEST_SNV_INDEL_VCF, - project_guids=['R0113_test_project'], - validations_to_skip=[], - run_id=TEST_RUN_ID, - ) - worker.add(uvatwns_task_3) - worker.run() - self.assertTrue(uvatwns_task_3.complete()) - ht = hl.read_table(uvatwns_task_3.output().path) - self.assertEqual(ht.count(), 30) - self.assertEqual( - ht.globals.updates.collect(), - [ - { - hl.Struct( - callset=TEST_SNV_INDEL_VCF, - project_guid='R0113_test_project', - remap_pedigree_hash=hl.eval( - remap_pedigree_hash(TEST_PEDIGREE_3_REMAP), - ), - ), - }, - ], - ) - self.assertEqual( - hl.eval(ht.globals.max_key_), - 29, - ) - - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_4_REMAP, - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - SampleType.WGS, - 'R0114_project4', - ) - # Ensure that new variants are added correctly to the table. - uvatwns_task_4 = UpdateVariantAnnotationsTableWithNewVariantsTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - sample_type=SampleType.WGS, - callset_path=TEST_SNV_INDEL_VCF, - project_guids=['R0114_project4'], - validations_to_skip=[], - run_id=TEST_RUN_ID + '-another-run', - ) - worker.add(uvatwns_task_4) - worker.run() - self.assertTrue(uvatwns_task_4.complete()) - ht = hl.read_table(uvatwns_task_4.output().path) - self.assertCountEqual( - [ - x - for x in ht.select( - 'variant_id', - 'xpos', - ).collect() - if x.locus.position <= 878809 # noqa: PLR2004 - ], - [ - hl.Struct( - locus=hl.Locus( - contig='chr1', - position=871269, - reference_genome='GRCh38', - ), - alleles=['A', 'C'], - variant_id='1-871269-A-C', - xpos=1000871269, - ), - hl.Struct( - locus=hl.Locus( - contig='chr1', - position=874734, - reference_genome='GRCh38', - ), - alleles=['C', 'T'], - variant_id='1-874734-C-T', - xpos=1000874734, - ), - hl.Struct( - locus=hl.Locus( - contig='chr1', - position=876499, - reference_genome='GRCh38', - ), - alleles=['A', 'G'], - variant_id='1-876499-A-G', - xpos=1000876499, - ), - hl.Struct( - locus=hl.Locus( - contig='chr1', - position=878314, - reference_genome='GRCh38', - ), - alleles=['G', 'C'], - variant_id='1-878314-G-C', - xpos=1000878314, - ), - hl.Struct( - locus=hl.Locus( - contig='chr1', - position=878809, - reference_genome='GRCh38', - ), - alleles=['C', 'T'], - variant_id='1-878809-C-T', - xpos=1000878809, - ), - ], - ) - self.assertCountEqual( - ht.filter( - ht.locus.position <= 878809, # noqa: PLR2004 - ).sorted_transcript_consequences.consequence_term_ids.collect(), - [ - [[9], [23, 26], [23, 13, 26]], - [[9], [23, 26], [23, 13, 26]], - [[9], [23, 26], [23, 13, 26]], - [[9], [23, 26], [23, 13, 26]], - [[9], [23, 26], [23, 13, 26]], - ], - ) - self.assertCountEqual( - ht.globals.collect(), - [ - hl.Struct( - updates={ - hl.Struct( - callset='loading_pipeline/var/test/callsets/1kg_30variants.vcf', - project_guid='R0113_test_project', - remap_pedigree_hash=hl.eval( - remap_pedigree_hash( - TEST_PEDIGREE_3_REMAP, - ), - ), - ), - hl.Struct( - callset='loading_pipeline/var/test/callsets/1kg_30variants.vcf', - project_guid='R0114_project4', - remap_pedigree_hash=hl.eval( - remap_pedigree_hash( - TEST_PEDIGREE_4_REMAP, - ), - ), - ), - }, - migrations=[], - max_key_=29, - enums=hl.Struct( - sorted_motif_feature_consequences=hl.Struct( - consequence_term=MOTIF_CONSEQUENCE_TERMS, - ), - sorted_regulatory_feature_consequences=hl.Struct( - biotype=REGULATORY_BIOTYPES, - consequence_term=REGULATORY_CONSEQUENCE_TERMS, - ), - sorted_transcript_consequences=hl.Struct( - biotype=BIOTYPES, - consequence_term=TRANSCRIPT_CONSEQUENCE_TERMS, - loftee=hl.Struct( - lof_filter=LOF_FILTERS, - ), - utrannotator=hl.Struct( - fiveutr_consequence=FIVEUTR_CONSEQUENCES, - ), - ), - ), - ), - ], - ) - - @patch('loading_pipeline.lib.misc.vep.hl.vep') - def test_update_vat_grch37( - self, - mock_vep: Mock, - ) -> None: - mock_vep.side_effect = lambda ht, **_: ht.annotate(vep=MOCK_37_VEP_DATA) - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_3_REMAP, - ReferenceGenome.GRCh37, - DatasetType.SNV_INDEL, - SampleType.WGS, - 'R0113_test_project', - ) - worker = luigi.worker.Worker() - uvatwns_task = UpdateVariantAnnotationsTableWithNewVariantsTask( - reference_genome=ReferenceGenome.GRCh37, - dataset_type=DatasetType.SNV_INDEL, - sample_type=SampleType.WGS, - callset_path=TEST_SNV_INDEL_VCF, - project_guids=['R0113_test_project'], - validations_to_skip=[ALL_VALIDATIONS], - run_id=TEST_RUN_ID, - ) - worker.add(uvatwns_task) - worker.run() - self.assertTrue(uvatwns_task.complete()) - ht = hl.read_table(uvatwns_task.output().path) - self.assertEqual(ht.count(), 30) - self.assertFalse(hasattr(ht, 'rg37_locus')) - self.assertEqual( - ht.collect()[0], - hl.Struct( - locus=hl.Locus( - contig=1, - position=871269, - reference_genome='GRCh37', - ), - alleles=['A', 'C'], - rsid=None, - variant_id='1-871269-A-C', - xpos=1000871269, - sorted_transcript_consequences=[ - hl.Struct( - amino_acids='S/L', - canonical=1, - codons='tCg/tTg', - gene_id='ENSG00000188976', - hgvsc='ENST00000327044.6:c.1667C>T', - hgvsp='ENSP00000317992.6:p.Ser556Leu', - transcript_id='ENST00000327044', - biotype_id=39, - consequence_term_ids=[9], - is_lof_nagnag=None, - lof_filter_ids=[0, 1], - ), - hl.Struct( - amino_acids=None, - canonical=None, - codons=None, - gene_id='ENSG00000188976', - hgvsc='ENST00000477976.1:n.3114C>T', - hgvsp=None, - transcript_id='ENST00000477976', - biotype_id=38, - consequence_term_ids=[23, 26], - is_lof_nagnag=None, - lof_filter_ids=None, - ), - hl.Struct( - amino_acids=None, - canonical=None, - codons=None, - gene_id='ENSG00000188976', - hgvsc='ENST00000483767.1:n.523C>T', - hgvsp=None, - transcript_id='ENST00000483767', - biotype_id=38, - consequence_term_ids=[23, 26], - is_lof_nagnag=None, - lof_filter_ids=None, - ), - ], - rg38_locus=hl.Locus( - contig='chr1', - position=935889, - reference_genome='GRCh38', - ), - key_=0, - ), - ) - - def test_mito_update_vat( - self, - ) -> None: - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_5, - ReferenceGenome.GRCh38, - DatasetType.MITO, - SampleType.WGS, - 'R0115_test_project2', - ) - worker = luigi.worker.Worker() - update_variant_annotations_task = ( - UpdateVariantAnnotationsTableWithNewVariantsTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.MITO, - sample_type=SampleType.WGS, - callset_path=TEST_MITO_MT, - project_guids=['R0115_test_project2'], - validations_to_skip=[ALL_VALIDATIONS], - run_id=TEST_RUN_ID, - ) - ) - worker.add(update_variant_annotations_task) - worker.run() - self.assertTrue(update_variant_annotations_task.complete()) - ht = hl.read_table(update_variant_annotations_task.output().path) - self.assertEqual(ht.count(), 5) - self.assertCountEqual( - ht.globals.collect(), - [ - hl.Struct( - enums=hl.Struct( - sorted_transcript_consequences=hl.Struct( - biotype=BIOTYPES, - consequence_term=TRANSCRIPT_CONSEQUENCE_TERMS, - lof_filter=LOF_FILTERS, - ), - mitotip=hl.Struct(trna_prediction=MITOTIP_PATHOGENICITIES), - ), - migrations=[], - max_key_=4, - updates={ - hl.Struct( - callset='loading_pipeline/var/test/callsets/mito_1.mt', - project_guid='R0115_test_project2', - remap_pedigree_hash=hl.eval( - remap_pedigree_hash( - TEST_PEDIGREE_5, - ), - ), - ), - }, - ), - ], - ) - self.assertCountEqual( - ht.collect()[0], - hl.Struct( - locus=hl.Locus( - contig='chrM', - position=3, - reference_genome='GRCh38', - ), - alleles=['T', 'C'], - common_low_heteroplasmy=False, - haplogroup=hl.Struct(is_defining=False), - mitotip=hl.Struct(trna_prediction_id=None), - rg37_locus=hl.Locus( - contig='MT', - position=3, - reference_genome='GRCh37', - ), - rsid=None, - sorted_transcript_consequences=None, - variant_id='M-3-T-C', - xpos=25000000003, - key_=0, - ), - ) - - @patch( - 'loading_pipeline.lib.tasks.write_new_variants_table.load_gencode_gene_symbol_to_gene_id', - ) - def test_sv_multiple_vcf_update_vat( - self, - mock_load_gencode: Mock, - ) -> None: - mock_load_gencode.return_value = GENE_ID_MAPPING - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_5, - ReferenceGenome.GRCh38, - DatasetType.SV, - SampleType.WGS, - 'R0115_test_project2', - ) - worker = luigi.worker.Worker() - update_variant_annotations_task = ( - UpdateVariantAnnotationsTableWithNewVariantsTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SV, - sample_type=SampleType.WGS, - callset_path=TEST_SV_VCF, - project_guids=['R0115_test_project2'], - validations_to_skip=[ALL_VALIDATIONS], - run_id=TEST_RUN_ID, - ) - ) - worker.add(update_variant_annotations_task) - worker.run() - self.assertTrue(update_variant_annotations_task.complete()) - self.assertFalse( - GCSorLocalFolderTarget( - f'{self.mock_env.REFERENCE_DATASETS_DIR}/v03/GRCh38/SV/lookup.ht', - ).exists(), - ) - ht = hl.read_table(update_variant_annotations_task.output().path) - self.assertEqual(ht.count(), 13) - self.assertCountEqual( - ht.globals.collect(), - [ - hl.Struct( - enums=hl.Struct( - sv_type=SV_TYPES, - sv_type_detail=SV_TYPE_DETAILS, - sorted_gene_consequences=hl.Struct( - major_consequence=SV_CONSEQUENCE_RANKS, - ), - ), - migrations=[], - max_key_=12, - updates={ - hl.Struct( - callset=TEST_SV_VCF, - project_guid='R0115_test_project2', - remap_pedigree_hash=hl.eval( - remap_pedigree_hash( - TEST_PEDIGREE_5, - ), - ), - ), - }, - ), - ], - ) - self.assertCountEqual( - ht.collect()[:8], - [ - hl.Struct( - variant_id='BND_chr1_6', - algorithms='manta', - bothsides_support=False, - cpx_intervals=None, - end_locus=hl.Locus( - contig='chr5', - position=20404, - reference_genome='GRCh38', - ), - gnomad_svs=None, - rg37_locus=hl.Locus( - contig=1, - position=10367, - reference_genome='GRCh37', - ), - rg37_locus_end=hl.Locus( - contig=5, - position=20404, - reference_genome='GRCh37', - ), - sorted_gene_consequences=[ - hl.Struct(gene_id='ENSG00000186092', major_consequence_id=12), - hl.Struct(gene_id='ENSG00000153404', major_consequence_id=12), - ], - start_locus=hl.Locus( - contig='chr1', - position=180928, - reference_genome='GRCh38', - ), - strvctvre=hl.Struct(score=None), - sv_len=-1, - sv_type_id=2, - sv_type_detail_id=None, - xpos=1000180928, - key_=0, - ), - hl.Struct( - variant_id='BND_chr1_9', - algorithms='manta', - bothsides_support=False, - cpx_intervals=None, - end_locus=hl.Locus( - contig='chr1', - position=789481, - reference_genome='GRCh38', - ), - gnomad_svs=None, - rg37_locus=hl.Locus( - contig=1, - position=724861, - reference_genome='GRCh37', - ), - rg37_locus_end=hl.Locus( - contig=1, - position=724861, - reference_genome='GRCh37', - ), - sorted_gene_consequences=[ - hl.Struct(gene_id='ENSG00000143756', major_consequence_id=12), - hl.Struct(gene_id='ENSG00000186192', major_consequence_id=12), - ], - start_locus=hl.Locus( - contig='chr1', - position=789481, - reference_genome='GRCh38', - ), - strvctvre=hl.Struct(score=None), - sv_len=223225007, - sv_type_id=2, - sv_type_detail_id=None, - xpos=1000789481, - key_=1, - ), - hl.Struct( - variant_id='CPX_chr1_22', - algorithms='manta', - bothsides_support=True, - cpx_intervals=[ - hl.Struct( - type_id=8, - start=hl.Locus('chr1', 6558902, 'GRCh38'), - end=hl.Locus('chr1', 6559723, 'GRCh38'), - ), - hl.Struct( - type_id=6, - start=hl.Locus('chr1', 6559655, 'GRCh38'), - end=hl.Locus('chr1', 6559723, 'GRCh38'), - ), - ], - end_locus=hl.Locus( - contig='chr1', - position=6559723, - reference_genome='GRCh38', - ), - gnomad_svs=None, - rg37_locus=hl.Locus( - contig=1, - position=6618962, - reference_genome='GRCh37', - ), - rg37_locus_end=hl.Locus( - contig=1, - position=6619783, - reference_genome='GRCh37', - ), - sorted_gene_consequences=[ - hl.Struct(gene_id='ENSG00000173662', major_consequence_id=11), - ], - start_locus=hl.Locus( - contig='chr1', - position=6558902, - reference_genome='GRCh38', - ), - strvctvre=hl.Struct(score=None), - sv_len=821, - sv_type_id=3, - sv_type_detail_id=2, - xpos=1006558902, - key_=2, - ), - hl.Struct( - variant_id='CPX_chr1_251', - algorithms='manta', - bothsides_support=False, - cpx_intervals=[ - hl.Struct( - type_id=5, - start=hl.Locus('chr1', 180540234, 'GRCh38'), - end=hl.Locus('chr1', 181074767, 'GRCh38'), - ), - hl.Struct( - type_id=8, - start=hl.Locus('chr1', 181074767, 'GRCh38'), - end=hl.Locus('chr1', 181074938, 'GRCh38'), - ), - ], - end_locus=hl.Locus( - contig='chr1', - position=181074952, - reference_genome='GRCh38', - ), - gnomad_svs=None, - rg37_locus=hl.Locus( - contig=1, - position=180509370, - reference_genome='GRCh37', - ), - rg37_locus_end=hl.Locus( - contig=1, - position=181044088, - reference_genome='GRCh37', - ), - sorted_gene_consequences=[ - hl.Struct(gene_id='ENSG00000135835', major_consequence_id=0), - hl.Struct(gene_id='ENSG00000153029', major_consequence_id=0), - hl.Struct(gene_id='ENSG00000135823', major_consequence_id=0), - hl.Struct(gene_id='ENSG00000143324', major_consequence_id=0), - ], - start_locus=hl.Locus( - contig='chr1', - position=180540234, - reference_genome='GRCh38', - ), - strvctvre=hl.Struct(score=None), - sv_len=534718, - sv_type_id=3, - sv_type_detail_id=9, - xpos=1180540234, - key_=3, - ), - hl.Struct( - variant_id='CPX_chr1_41', - algorithms='manta', - bothsides_support=False, - cpx_intervals=[ - hl.Struct( - type_id=6, - start=hl.Locus('chr1', 16088760, 'GRCh38'), - end=hl.Locus('chr1', 16088835, 'GRCh38'), - ), - hl.Struct( - type_id=8, - start=hl.Locus('chr1', 16088760, 'GRCh38'), - end=hl.Locus('chr1', 16089601, 'GRCh38'), - ), - ], - end_locus=hl.Locus( - contig='chr1', - position=16089601, - reference_genome='GRCh38', - ), - gnomad_svs=None, - rg37_locus=hl.Locus( - contig=1, - position=16415255, - reference_genome='GRCh37', - ), - rg37_locus_end=hl.Locus( - contig=1, - position=16416096, - reference_genome='GRCh37', - ), - sorted_gene_consequences=[ - hl.Struct(gene_id='ENSG00000185519', major_consequence_id=12), - ], - start_locus=hl.Locus( - contig='chr1', - position=16088760, - reference_genome='GRCh38', - ), - strvctvre=hl.Struct(score=None), - sv_len=841, - sv_type_id=3, - sv_type_detail_id=12, - xpos=1016088760, - key_=4, - ), - hl.Struct( - variant_id='CPX_chr1_54', - algorithms='manta', - bothsides_support=False, - cpx_intervals=[ - hl.Struct( - type_id=6, - start=hl.Locus('chr1', 21427498, 'GRCh38'), - end=hl.Locus('chr1', 21427959, 'GRCh38'), - ), - hl.Struct( - type_id=8, - start=hl.Locus('chr1', 21427498, 'GRCh38'), - end=hl.Locus('chr1', 21480073, 'GRCh38'), - ), - hl.Struct( - type_id=5, - start=hl.Locus('chr1', 21480073, 'GRCh38'), - end=hl.Locus('chr1', 21480419, 'GRCh38'), - ), - ], - end_locus=hl.Locus( - contig='chr1', - position=21480419, - reference_genome='GRCh38', - ), - gnomad_svs=None, - rg37_locus=hl.Locus( - contig=1, - position=21753991, - reference_genome='GRCh37', - ), - rg37_locus_end=hl.Locus( - contig=1, - position=21806912, - reference_genome='GRCh37', - ), - sorted_gene_consequences=[ - hl.Struct(gene_id='ENSG00000142794', major_consequence_id=0), - ], - start_locus=hl.Locus( - contig='chr1', - position=21427498, - reference_genome='GRCh38', - ), - strvctvre=hl.Struct(score=None), - sv_len=52921, - sv_type_id=3, - sv_type_detail_id=13, - xpos=1021427498, - key_=5, - ), - hl.Struct( - variant_id='CPX_chrX_251', - algorithms='manta', - bothsides_support=False, - cpx_intervals=[ - hl.Struct( - type_id=5, - start=hl.Locus( - contig='chr1', - position=180540234, - reference_genome='GRCh38', - ), - end=hl.Locus( - contig='chr1', - position=181074767, - reference_genome='GRCh38', - ), - ), - hl.Struct( - type_id=8, - start=hl.Locus( - contig='chr1', - position=181074767, - reference_genome='GRCh38', - ), - end=hl.Locus( - contig='chr1', - position=181074938, - reference_genome='GRCh38', - ), - ), - ], - end_locus=hl.Locus( - contig='chrX', - position=2781000, - reference_genome='GRCh38', - ), - gnomad_svs=None, - sorted_gene_consequences=[ - hl.Struct(gene_id='ENSG00000135835', major_consequence_id=0), - hl.Struct(gene_id='ENSG00000153029', major_consequence_id=0), - hl.Struct(gene_id='ENSG00000135823', major_consequence_id=0), - hl.Struct(gene_id='ENSG00000143324', major_consequence_id=0), - ], - start_locus=hl.Locus( - contig='chrX', - position=3, - reference_genome='GRCh38', - ), - strvctvre=hl.Struct(score=None), - sv_type_id=3, - sv_type_detail_id=9, - sv_len=534718, - xpos=23000000003, - rg37_locus=None, - rg37_locus_end=hl.Locus( - contig='X', - position=2699041, - reference_genome='GRCh37', - ), - key_=6, - ), - hl.Struct( - variant_id='CPX_chrX_252', - algorithms='manta', - bothsides_support=False, - cpx_intervals=[ - hl.Struct( - type_id=5, - start=hl.Locus( - contig='chr1', - position=180540234, - reference_genome='GRCh38', - ), - end=hl.Locus( - contig='chr1', - position=181074767, - reference_genome='GRCh38', - ), - ), - hl.Struct( - type_id=8, - start=hl.Locus( - contig='chr1', - position=181074767, - reference_genome='GRCh38', - ), - end=hl.Locus( - contig='chr1', - position=181074938, - reference_genome='GRCh38', - ), - ), - ], - end_locus=hl.Locus( - contig='chrX', - position=2781900, - reference_genome='GRCh38', - ), - gnomad_svs=None, - sorted_gene_consequences=[ - hl.Struct(gene_id='ENSG00000135835', major_consequence_id=0), - hl.Struct(gene_id='ENSG00000153029', major_consequence_id=0), - hl.Struct(gene_id='ENSG00000135823', major_consequence_id=0), - hl.Struct(gene_id='ENSG00000143324', major_consequence_id=0), - ], - start_locus=hl.Locus( - contig='chrX', - position=2781700, - reference_genome='GRCh38', - ), - strvctvre=hl.Struct(score=None), - sv_type_id=3, - sv_type_detail_id=9, - sv_len=534718, - xpos=23002781700, - rg37_locus=hl.Locus( - contig='X', - position=2699741, - reference_genome='GRCh37', - ), - rg37_locus_end=hl.Locus( - contig='X', - position=2699941, - reference_genome='GRCh37', - ), - key_=7, - ), - ], - ) - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_5, - ReferenceGenome.GRCh38, - DatasetType.SV, - SampleType.WGS, - 'R0115_test_project2', - ) - update_variant_annotations_task = ( - UpdateVariantAnnotationsTableWithNewVariantsTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SV, - sample_type=SampleType.WGS, - callset_path=TEST_SV_VCF_2, - project_guids=['R0115_test_project2'], - validations_to_skip=[ALL_VALIDATIONS], - run_id='second_run_id', - ) - ) - worker.add(update_variant_annotations_task) - worker.run() - self.assertTrue(update_variant_annotations_task.complete()) - ht = hl.read_table(update_variant_annotations_task.output().path) - self.assertEqual(ht.count(), 14) - self.assertCountEqual( - ht.globals.collect(), - [ - hl.Struct( - enums=hl.Struct( - sv_type=SV_TYPES, - sv_type_detail=SV_TYPE_DETAILS, - sorted_gene_consequences=hl.Struct( - major_consequence=SV_CONSEQUENCE_RANKS, - ), - ), - migrations=[], - max_key_=13, - updates={ - hl.Struct( - callset=TEST_SV_VCF, - project_guid='R0115_test_project2', - remap_pedigree_hash=hl.eval( - remap_pedigree_hash( - TEST_PEDIGREE_5, - ), - ), - ), - hl.Struct( - callset=TEST_SV_VCF_2, - project_guid='R0115_test_project2', - remap_pedigree_hash=hl.eval( - remap_pedigree_hash( - TEST_PEDIGREE_5, - ), - ), - ), - }, - ), - ], - ) - self.assertCountEqual( - ht.take(1), - [ - hl.Struct( - variant_id='BND_chr1_6', - algorithms='manta', - bothsides_support=False, - cpx_intervals=None, - end_locus=hl.Locus( - contig='chr5', - position=20404, - reference_genome='GRCh38', - ), - gnomad_svs=None, - rg37_locus=hl.Locus( - contig=1, - position=10367, - reference_genome='GRCh37', - ), - rg37_locus_end=hl.Locus( - contig=5, - position=20404, - reference_genome='GRCh37', - ), - sorted_gene_consequences=[ - hl.Struct(gene_id='ENSG00000186092', major_consequence_id=12), - hl.Struct(gene_id='ENSG00000153404', major_consequence_id=12), - ], - start_locus=hl.Locus( - contig='chr1', - position=180928, - reference_genome='GRCh38', - ), - strvctvre=hl.Struct(score=None), - sv_len=-1, - sv_type_id=2, - sv_type_detail_id=None, - xpos=1000180928, - key_=0, - ), - ], - ) - - @patch( - 'loading_pipeline.lib.tasks.write_new_variants_table.load_gencode_gene_symbol_to_gene_id', - ) - def test_sv_multiple_project_single_vcf( - self, - mock_load_gencode: Mock, - ) -> None: - mock_load_gencode.return_value = GENE_ID_MAPPING - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_10, - ReferenceGenome.GRCh38, - DatasetType.SV, - SampleType.WGS, - 'R0116_test_project3', - ) - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_11, - ReferenceGenome.GRCh38, - DatasetType.SV, - SampleType.WGS, - 'R0117_test_project4', - ) - worker = luigi.worker.Worker() - update_variant_annotations_task = ( - UpdateVariantAnnotationsTableWithNewVariantsTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SV, - sample_type=SampleType.WGS, - callset_path=TEST_SV_VCF_2, - project_guids=['R0116_test_project3', 'R0117_test_project4'], - validations_to_skip=[ALL_VALIDATIONS], - run_id='run_id', - ) - ) - worker.add(update_variant_annotations_task) - worker.run() - self.assertTrue(update_variant_annotations_task.complete()) - ht = hl.read_table(update_variant_annotations_task.output().path) - self.assertEqual(ht.count(), 2) - self.assertEqual( - len(ht.globals.updates.collect()[0]), - 2, - ) - - def test_gcnv_update_vat_multiple( - self, - ) -> None: - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_5, - ReferenceGenome.GRCh38, - DatasetType.GCNV, - SampleType.WES, - 'R0115_test_project2', - ) - worker = luigi.worker.Worker() - update_variant_annotations_task = ( - UpdateVariantAnnotationsTableWithNewVariantsTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.GCNV, - sample_type=SampleType.WES, - callset_path=TEST_GCNV_BED_FILE, - project_guids=['R0115_test_project2'], - validations_to_skip=[ALL_VALIDATIONS], - run_id=TEST_RUN_ID, - ) - ) - worker.add(update_variant_annotations_task) - worker.run() - self.assertTrue(update_variant_annotations_task.complete()) - self.assertFalse( - GCSorLocalFolderTarget( - f'{self.mock_env.REFERENCE_DATASETS_DIR}/v03/GRCh38/GCNV/lookup.ht', - ).exists(), - ) - ht = hl.read_table(update_variant_annotations_task.output().path) - self.assertEqual(ht.count(), 2) - self.assertCountEqual( - ht.globals.collect(), - [ - hl.Struct( - enums=hl.Struct( - sv_type=SV_TYPES, - sorted_gene_consequences=hl.Struct( - major_consequence=SV_CONSEQUENCE_RANKS, - ), - ), - migrations=[], - max_key_=1, - updates={ - hl.Struct( - callset=TEST_GCNV_BED_FILE, - project_guid='R0115_test_project2', - remap_pedigree_hash=hl.eval( - remap_pedigree_hash( - TEST_PEDIGREE_5, - ), - ), - ), - }, - ), - ], - ) - self.assertCountEqual( - ht.collect(), - [ - hl.Struct( - variant_id='suffix_16456_DEL', - end_locus=hl.Locus( - contig='chr1', - position=100023213, - reference_genome='GRCh38', - ), - gt_stats=hl.Struct( - AF=hl.eval(hl.float32(4.401408e-05)), - AC=1, - AN=22720, - Hom=None, - Het=None, - ), - num_exon=3, - rg37_locus=hl.Locus( - contig=1, - position=100472493, - reference_genome='GRCh37', - ), - rg37_locus_end=hl.Locus( - contig=1, - position=100488769, - reference_genome='GRCh37', - ), - sorted_gene_consequences=[ - hl.Struct(gene_id='ENSG00000117620', major_consequence_id=0), - hl.Struct(gene_id='ENSG00000283761', major_consequence_id=0), - hl.Struct(gene_id='ENSG22222222222', major_consequence_id=None), - ], - start_locus=hl.Locus( - contig='chr1', - position=100006937, - reference_genome='GRCh38', - ), - strvctvre=hl.Struct(score=hl.eval(hl.float32(0.583))), - sv_type_id=5, - xpos=1100006937, - key_=0, - ), - hl.Struct( - variant_id='suffix_16457_DEL', - end_locus=hl.Locus( - contig='chr1', - position=100023212, - reference_genome='GRCh38', - ), - gt_stats=hl.Struct( - AF=8.802817319519818e-05, - AC=2, - AN=22719, - Hom=None, - Het=None, - ), - num_exon=2, - rg37_locus=hl.Locus( - contig=1, - position=100483142, - reference_genome='GRCh37', - ), - rg37_locus_end=hl.Locus( - contig=1, - position=100488768, - reference_genome='GRCh37', - ), - sorted_gene_consequences=[ - hl.Struct(gene_id='ENSG00000283761', major_consequence_id=0), - hl.Struct(gene_id='ENSG22222222222', major_consequence_id=None), - ], - start_locus=hl.Locus( - contig='chr1', - position=100017586, - reference_genome='GRCh38', - ), - strvctvre=hl.Struct(score=0.5070000290870667), - sv_type_id=5, - xpos=1100017586, - key_=1, - ), - ], - ) - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_8, - ReferenceGenome.GRCh38, - DatasetType.GCNV, - SampleType.WES, - 'R0115_test_project2', - ) - update_variant_annotations_task = ( - UpdateVariantAnnotationsTableWithNewVariantsTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.GCNV, - sample_type=SampleType.WES, - callset_path=TEST_GCNV_BED_FILE_2, - project_guids=['R0115_test_project2'], - validations_to_skip=[ALL_VALIDATIONS], - run_id='second_run_id', - ) - ) - worker.add(update_variant_annotations_task) - worker.run() - ht = hl.read_table(update_variant_annotations_task.output().path) - self.assertEqual(ht.count(), 3) - self.assertCountEqual( - ht.select('gt_stats').collect(), - [ - hl.Struct( - # Existing variant, gt_stats are preserved - variant_id='suffix_16456_DEL', - gt_stats=hl.Struct( - AF=hl.eval(hl.float32(4.401408e-05)), - AC=1, - AN=22720, - Hom=None, - Het=None, - ), - ), - hl.Struct( - # Exiting variant, gt_stats are updated - variant_id='suffix_16457_DEL', - gt_stats=hl.Struct( - AF=8.111110946629196e-05, - AC=3, - AN=36986, - Hom=None, - Het=None, - ), - ), - hl.Struct( - # New variant. - variant_id='suffix_99999_DEL', - gt_stats=hl.Struct( - AF=8.802817319519818e-05, - AC=2, - AN=22719, - Hom=None, - Het=None, - ), - ), - ], - ) diff --git a/loading_pipeline/lib/tasks/validate_callset_test.py b/loading_pipeline/lib/tasks/validate_callset_test.py deleted file mode 100644 index a56f78a894..0000000000 --- a/loading_pipeline/lib/tasks/validate_callset_test.py +++ /dev/null @@ -1,83 +0,0 @@ -import json -import shutil - -import luigi.worker - -from loading_pipeline.lib.core import ( - DatasetType, - ReferenceGenome, - SampleType, -) -from loading_pipeline.lib.paths import ( - valid_reference_dataset_path, -) -from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset -from loading_pipeline.lib.tasks.validate_callset import ( - ValidateCallsetTask, -) -from loading_pipeline.lib.tasks.write_validation_errors_for_run import ( - UpdatedValidationErrorsForRunTask, -) -from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase - -TEST_CODING_AND_NONCODING_HT = 'loading_pipeline/var/test/reference_datasets/GRCh38/gnomad_coding_and_noncoding/1.0.ht' -MULTIPLE_VALIDATION_EXCEPTIONS_VCF = ( - 'loading_pipeline/var/test/callsets/multiple_validation_exceptions.vcf' -) - -TEST_RUN_ID = 'manual__2024-04-03' - - -class ValidateCallsetTest(MockedDatarootTestCase): - def setUp(self) -> None: - super().setUp() - shutil.copytree( - TEST_CODING_AND_NONCODING_HT, - valid_reference_dataset_path( - ReferenceGenome.GRCh38, - ReferenceDataset.gnomad_coding_and_noncoding, - ), - ) - - def test_validate_callset_multiple_exceptions( - self, - ) -> None: - worker = luigi.worker.Worker() - validate_callset_task = ValidateCallsetTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - sample_type=SampleType.WES, - # NB: - # This callset contains duplicate rows for chr1:902088, - # a NON_REF allele type at position chr1: 902024, missing - # all contigs but chr1, and contains non-coding variants. - callset_path=MULTIPLE_VALIDATION_EXCEPTIONS_VCF, - project_guids=['project_a'], - run_id=TEST_RUN_ID, - ) - worker.add(validate_callset_task) - worker.run() - self.assertFalse(validate_callset_task.complete()) - - updated_validation_errors_task = UpdatedValidationErrorsForRunTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - sample_type=SampleType.WES, - callset_path=MULTIPLE_VALIDATION_EXCEPTIONS_VCF, - project_guids=['project_a'], - run_id=TEST_RUN_ID, - ) - self.assertTrue(updated_validation_errors_task.complete()) - with updated_validation_errors_task.output().open('r') as f: - self.assertDictEqual( - json.load(f), - { - 'project_guids': ['project_a'], - 'error_messages': [ - 'Alleles with invalid allele are present in the callset. This appears to be a GVCF containing records for sites with no variants.', - 'Missing the following expected contigs:chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr2, chr20, chr21, chr22, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chrX', - "Variants are present multiple times in the callset: ['1-902088-G-A']", - 'Sample type validation error: dataset sample-type is specified as WES but appears to be WGS because it contains many common non-coding variants', - ], - }, - ) diff --git a/loading_pipeline/lib/tasks/write_metadata_for_run_test.py b/loading_pipeline/lib/tasks/write_metadata_for_run_test.py deleted file mode 100644 index 2b5dc7a22d..0000000000 --- a/loading_pipeline/lib/tasks/write_metadata_for_run_test.py +++ /dev/null @@ -1,188 +0,0 @@ -import json -from unittest import mock -from unittest.mock import Mock - -import luigi.worker - -from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType -from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS -from loading_pipeline.lib.paths import relatedness_check_tsv_path -from loading_pipeline.lib.tasks.write_metadata_for_run import WriteMetadataForRunTask -from loading_pipeline.lib.test.misc import copy_project_pedigree_to_mocked_dir -from loading_pipeline.lib.test.mock_complete_task import MockCompleteTask -from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase - -TEST_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' -TEST_PEDIGREE_3_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_3_remap.tsv' -TEST_PEDIGREE_4_REMAP_2 = ( - 'loading_pipeline/var/test/pedigrees/test_pedigree_4_remap_2.tsv' -) -TEST_SAMPLE_QC_JSON = 'loading_pipeline/var/test/sample_qc_1.json' - - -class WriteMetadataForRunTaskTest(MockedDatarootTestCase): - @mock.patch( - 'loading_pipeline.lib.tasks.write_metadata_for_run.sample_qc_json_path', - lambda *_: TEST_SAMPLE_QC_JSON, - ) - @mock.patch('loading_pipeline.lib.tasks.write_metadata_for_run.FeatureFlag') - @mock.patch( - 'loading_pipeline.lib.tasks.write_sex_check_table.WriteTDRMetricsFilesTask', - ) - @mock.patch( - 'loading_pipeline.lib.tasks.write_metadata_for_run.WriteSampleQCJsonTask', - ) - def test_write_metadata_for_run_task( - self, - write_sample_qc_json_task: Mock, - write_tdr_metrics_task: Mock, - mock_ff: Mock, - ) -> None: - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_3_REMAP, - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - SampleType.WGS, - 'R0113_test_project', - ) - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_4_REMAP_2, - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - SampleType.WGS, - 'R0114_project4', - ) - mock_ff.EXPECT_TDR_METRICS = True - write_tdr_metrics_task.return_value = MockCompleteTask() - write_sample_qc_json_task.return_value = MockCompleteTask() - worker = luigi.worker.Worker() - write_metadata_for_run_task = WriteMetadataForRunTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - sample_type=SampleType.WGS, - callset_path=TEST_VCF, - project_guids=['R0113_test_project', 'R0114_project4'], - validations_to_skip=[ALL_VALIDATIONS], - run_id='run_123456', - ) - worker.add(write_metadata_for_run_task) - worker.run() - self.assertTrue( - 'run_123456/metadata.json' in write_metadata_for_run_task.output().path, - ) - self.assertTrue(write_metadata_for_run_task.complete()) - with write_metadata_for_run_task.output().open('r') as f: - self.assertDictEqual( - json.load(f), - { - 'callsets': [TEST_VCF], - 'project_guids': ['R0113_test_project', 'R0114_project4'], - 'failed_family_samples': { - 'missing_samples': { - 'efg_1': { - # This sample is present in the callset, but intentionally - # mapped away - 'samples': ['NA20888_1'], - 'reasons': ["Missing samples: {'NA20888_1'}"], - }, - }, - 'relatedness_check': {}, - 'sex_check': {}, - 'ploidy_check': {}, - }, - 'family_samples': { - 'abc_1': [ - 'HG00731_1', - 'HG00732_1', - 'HG00733_1', - ], - '123_1': ['NA19675_1'], - '234_1': ['NA19678_1'], - '345_1': ['NA19679_1'], - '456_1': ['NA20870_1'], - '567_1': ['NA20872_1'], - '678_1': ['NA20874_1'], - '789_1': ['NA20875_1'], - '890_1': ['NA20876_1'], - '901_1': ['NA20877_1'], - 'bcd_1': ['NA20878_1'], - 'cde_1': ['NA20881_1'], - 'def_1': ['NA20885_1'], - }, - 'run_id': 'run_123456', - 'sample_type': SampleType.WGS.value, - 'relatedness_check_file_path': relatedness_check_tsv_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_VCF, - ), - 'sample_qc': { - 'HG00731_1': {'filter_flags': ['coverage', 'contamination']}, - 'HG00732_1': {'filter_flags': ['coverage']}, - 'HG00733_1': {'filter_flags': ['contamination']}, - 'NA19675_1': {'filter_flags': []}, - 'NA20888_1': {'filter_flags': ['sample_failed']}, - }, - }, - ) - - @mock.patch('loading_pipeline.lib.tasks.write_metadata_for_run.FeatureFlag') - def test_write_metadata_for_run_task_without_tdr_metrics( - self, - mock_ff: Mock, - ) -> None: - # When WriteSampleQCJsonTask is not a requirement, every project's - # remapped and subsetted callset must still be collected. - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_3_REMAP, - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - SampleType.WGS, - 'R0113_test_project', - ) - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_4_REMAP_2, - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - SampleType.WGS, - 'R0114_project4', - ) - mock_ff.EXPECT_TDR_METRICS = False - worker = luigi.worker.Worker() - write_metadata_for_run_task = WriteMetadataForRunTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - sample_type=SampleType.WGS, - callset_path=TEST_VCF, - project_guids=['R0113_test_project', 'R0114_project4'], - validations_to_skip=[ALL_VALIDATIONS], - run_id='run_123457', - ) - worker.add(write_metadata_for_run_task) - worker.run() - self.assertTrue(write_metadata_for_run_task.complete()) - with write_metadata_for_run_task.output().open('r') as f: - metadata_json = json.load(f) - self.assertDictEqual( - metadata_json['family_samples'], - { - 'abc_1': [ - 'HG00731_1', - 'HG00732_1', - 'HG00733_1', - ], - '123_1': ['NA19675_1'], - '234_1': ['NA19678_1'], - '345_1': ['NA19679_1'], - '456_1': ['NA20870_1'], - '567_1': ['NA20872_1'], - '678_1': ['NA20874_1'], - '789_1': ['NA20875_1'], - '890_1': ['NA20876_1'], - '901_1': ['NA20877_1'], - 'bcd_1': ['NA20878_1'], - 'cde_1': ['NA20881_1'], - 'def_1': ['NA20885_1'], - }, - ) - self.assertDictEqual(metadata_json['sample_qc'], {}) diff --git a/loading_pipeline/lib/tasks/write_relatedness_check_table_test.py b/loading_pipeline/lib/tasks/write_relatedness_check_table_test.py deleted file mode 100644 index 7cc814a5fa..0000000000 --- a/loading_pipeline/lib/tasks/write_relatedness_check_table_test.py +++ /dev/null @@ -1,120 +0,0 @@ -import shutil -from unittest.mock import patch - -import hail as hl -import luigi.worker - -from loading_pipeline.lib.core import ( - DatasetType, - ReferenceGenome, - SampleType, -) -from loading_pipeline.lib.misc.io import import_vcf -from loading_pipeline.lib.paths import ( - postprocessed_callset_path, - relatedness_check_table_path, - valid_reference_dataset_path, -) -from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset -from loading_pipeline.lib.tasks.write_relatedness_check_table import ( - WriteRelatednessCheckTableTask, -) -from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase - -TEST_GNOMAD_QC_HT = ( - 'loading_pipeline/var/test/reference_datasets/GRCh38/gnomad_qc/1.0.ht' -) -TEST_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' -TEST_RUN_ID = 'manual__2024-04-03' - - -class WriteRelatednessCheckTableTaskTest(MockedDatarootTestCase): - def setUp(self) -> None: - super().setUp() - shutil.copytree( - TEST_GNOMAD_QC_HT, - valid_reference_dataset_path( - ReferenceGenome.GRCh38, - ReferenceDataset.gnomad_qc, - ), - ) - - # Force imported callset to be complete - ht = import_vcf(TEST_VCF, ReferenceGenome.GRCh38) - ht = ht.annotate_globals(validated_sample_type=SampleType.WGS.value) - ht = ht.annotate_rows(**{'info.AF': ht.info.AF}) - ht.write( - postprocessed_callset_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_VCF, - ), - ) - - def test_relatedness_check_table_task_gnomad_qc_updated( - self, - ) -> None: - self.assertEqual( - hl.eval( - hl.read_table( - valid_reference_dataset_path( - ReferenceGenome.GRCh38, - ReferenceDataset.gnomad_qc, - ), - ).version, - ), - '1.0', - ) - with ( - patch.object( - ReferenceDataset, - 'version', - return_value='2.0', - ), - patch.object( - ReferenceDataset, - 'get_ht', - lambda *_: hl.Table.parallelize( - [], - hl.tstruct( - locus=hl.tlocus('GRCh38'), - alleles=hl.tarray(hl.tstr), - ), - key=['locus', 'alleles'], - globals=hl.Struct(version='2.0'), - ), - ), - ): - worker = luigi.worker.Worker() - task = WriteRelatednessCheckTableTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - run_id=TEST_RUN_ID, - sample_type=SampleType.WGS, - callset_path=TEST_VCF, - ) - worker.add(task) - worker.run() - self.assertTrue(task.complete()) - self.assertEqual( - hl.eval( - hl.read_table( - valid_reference_dataset_path( - ReferenceGenome.GRCh38, - ReferenceDataset.gnomad_qc, - ), - ).version, - ), - '2.0', - ) - ht = hl.read_table( - relatedness_check_table_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_VCF, - ), - ) - self.assertEqual( - ht.collect(), - [], - ) diff --git a/loading_pipeline/lib/tasks/write_relatedness_check_tsv_test.py b/loading_pipeline/lib/tasks/write_relatedness_check_tsv_test.py deleted file mode 100644 index 35a9956f78..0000000000 --- a/loading_pipeline/lib/tasks/write_relatedness_check_tsv_test.py +++ /dev/null @@ -1,53 +0,0 @@ -import shutil - -import luigi.worker - -from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType -from loading_pipeline.lib.paths import relatedness_check_table_path -from loading_pipeline.lib.tasks.write_relatedness_check_tsv import ( - WriteRelatednessCheckTsvTask, -) -from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase - -TEST_RELATEDNESS_CHECK_1 = ( - 'loading_pipeline/var/test/relatedness_check/test_relatedness_check_1.ht' -) -TEST_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' -TEST_RUN_ID = 'manual__2024-04-03' - - -class WriteRelatednessCheckTsvTaskTest(MockedDatarootTestCase): - def setUp(self) -> None: - super().setUp() - shutil.copytree( - TEST_RELATEDNESS_CHECK_1, - relatedness_check_table_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_VCF, - ), - ) - - def test_write_relatedness_check_tsv_task( - self, - ) -> None: - worker = luigi.worker.Worker() - task = WriteRelatednessCheckTsvTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - callset_path=TEST_VCF, - run_id=TEST_RUN_ID, - sample_type=SampleType.WES, - ) - worker.add(task) - worker.run() - self.assertTrue(task.complete()) - with task.output().open('r') as f: - lines = f.readlines() - expected_lines = [ - 'i\tj\tibd0\tibd1\tibd2\tpi_hat\n', - 'HG00731_1\tHG00733_1\t0\t1\t0\t5.0000e-01\n', - 'HG00732_1\tHG00733_1\t0\t1\t0\t5.0000e-01\n', - ] - for expected_line, actual_line in zip(expected_lines, lines, strict=False): - self.assertEqual(expected_line, actual_line) diff --git a/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset_test.py b/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset_test.py deleted file mode 100644 index 590795424a..0000000000 --- a/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset_test.py +++ /dev/null @@ -1,460 +0,0 @@ -import json -import shutil -from unittest.mock import Mock, patch - -import hail as hl -import luigi.worker - -from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType -from loading_pipeline.lib.misc.io import remap_pedigree_hash -from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS -from loading_pipeline.lib.paths import ( - relatedness_check_table_path, - sex_check_table_path, -) -from loading_pipeline.lib.tasks.write_remapped_and_subsetted_callset import ( - WriteRemappedAndSubsettedCallsetTask, -) -from loading_pipeline.lib.tasks.write_validation_errors_for_run import ( - UpdatedValidationErrorsForRunTask, -) -from loading_pipeline.lib.test.misc import copy_project_pedigree_to_mocked_dir -from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase - -TEST_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' -TEST_PEDIGREE_3_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_3_remap.tsv' -TEST_PEDIGREE_3_DIFFERENT_FAMILIES = ( - 'loading_pipeline/var/test/pedigrees/test_pedigree_3_different_families.tsv' -) -TEST_PEDIGREE_4_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_4_remap.tsv' -TEST_PEDIGREE_7 = 'loading_pipeline/var/test/pedigrees/test_pedigree_7.tsv' -TEST_SEX_CHECK_1 = 'loading_pipeline/var/test/sex_check/test_sex_check_1.ht' -TEST_RELATEDNESS_CHECK_1 = ( - 'loading_pipeline/var/test/relatedness_check/test_relatedness_check_1.ht' -) - -TEST_RUN_ID = 'manual__2024-04-03' - - -class WriteRemappedAndSubsettedCallsetTaskTest(MockedDatarootTestCase): - def setUp(self) -> None: - super().setUp() - # +-------------+---------------+ - # | s | predicted_sex | - # +-------------+---------------+ - # | str | str | - # +-------------+---------------+ - # | "HG00731_1" | "F" | - # | "HG00732_1" | "M" | - # | "HG00733_1" | "F" | - # | "NA19675_1" | "F" | - # | "NA19678_1" | "M" | - # | "NA19679_1" | "F" | - # | "NA20870_1" | "F" | - # | "NA20872_1" | "M" | - # | "NA20874_1" | "F" | - # | "NA20875_1" | "F" | - # | "NA20876_1" | "F" | - # | "NA20877_1" | "F" | - # | "NA20878_1" | "M" | - # | "NA20881_1" | "M" | - # | "NA20885_1" | "F" | - # | "NA20888_1" | "F" | - # +-------------+---------------+ - shutil.copytree( - TEST_SEX_CHECK_1, - sex_check_table_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_VCF, - ), - ) - # +-------------+-------------+-------+-------+-------+----------+ - # | i | j | ibd0 | ibd1 | ibd2 | pi_hat | - # +-------------+-------------+-------+-------+-------+----------+ - # | str | str | int32 | int32 | int32 | float64 | - # +-------------+-------------+-------+-------+-------+----------+ - # | "HG00731_1" | "HG00733_1" | 0 | 1 | 0 | 5.00e-01 | - # | "HG00732_1" | "HG00733_1" | 0 | 1 | 0 | 5.00e-01 | - # +-------------+-------------+-------+-------+-------+----------+ - shutil.copytree( - TEST_RELATEDNESS_CHECK_1, - relatedness_check_table_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_VCF, - ), - ) - - def test_write_remapped_and_subsetted_callset_task( - self, - ) -> None: - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_3_REMAP, - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - SampleType.WGS, - 'R0113_test_project', - ) - worker = luigi.worker.Worker() - wrsc_task = WriteRemappedAndSubsettedCallsetTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - run_id=TEST_RUN_ID, - sample_type=SampleType.WGS, - callset_path=TEST_VCF, - project_guids=['R0113_test_project'], - project_i=0, - validations_to_skip=[ALL_VALIDATIONS], - skip_expect_tdr_metrics=True, - ) - worker.add(wrsc_task) - worker.run() - self.assertTrue(wrsc_task.complete()) - mt = hl.read_matrix_table(wrsc_task.output().path) - self.assertEqual(mt.count(), (30, 3)) - self.assertEqual( - mt.globals.collect(), - [ - hl.Struct( - remap_pedigree_hash=hl.eval( - remap_pedigree_hash( - TEST_PEDIGREE_3_REMAP, - ), - ), - failed_family_samples=hl.Struct( - missing_samples={}, - relatedness_check={}, - sex_check={}, - ploidy_check={}, - ), - family_samples={'abc_1': ['HG00731_1', 'HG00732_1', 'HG00733_1']}, - ), - ], - ) - - @patch( - 'loading_pipeline.lib.tasks.write_remapped_and_subsetted_callset.FeatureFlag', - ) - def test_write_remapped_and_subsetted_callset_task_failed_some_family_checks( - self, - mock_ff: Mock, - ) -> None: - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_4_REMAP, - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - SampleType.WGS, - 'R0114_project4', - ) - mock_ff.CHECK_SEX_AND_RELATEDNESS = True - worker = luigi.worker.Worker() - wrsc_task = WriteRemappedAndSubsettedCallsetTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - run_id=TEST_RUN_ID, - sample_type=SampleType.WGS, - callset_path=TEST_VCF, - project_guids=['R0114_project4'], - project_i=0, - validations_to_skip=[ALL_VALIDATIONS], - skip_expect_tdr_metrics=True, - ) - worker.add(wrsc_task) - worker.run() - self.assertTrue(wrsc_task.complete()) - mt = hl.read_matrix_table(wrsc_task.output().path) - # NB: one "family"/"sample" has been removed because of a failed sex check, - # and 4 removed because of a failed ploidy check! - self.assertEqual(mt.count(), (30, 8)) - self.assertEqual( - mt.globals.collect(), - [ - hl.Struct( - remap_pedigree_hash=hl.eval( - remap_pedigree_hash( - TEST_PEDIGREE_4_REMAP, - ), - ), - family_samples={ - '123_1': ['NA19675_1'], - '345_1': ['NA19679_1'], - '456_1': ['NA20870_1'], - '678_1': ['NA20874_1'], - '789_1': ['NA20875_1'], - '890_1': ['NA20876_1'], - '901_1': ['NA20877_1'], - 'efg_1': ['NA20888_1'], - }, - failed_family_samples=hl.Struct( - missing_samples={}, - relatedness_check={}, - sex_check={ - 'def_1': { - 'reasons': [ - 'Sample NA20885_1 has pedigree sex M but imputed sex F', - ], - 'samples': ['NA20885_1'], - }, - }, - ploidy_check={ - '234_1': { - 'reasons': [ - "Found samples with misaligned ploidy with their provided imputed sex: ['NA19678_1']", - ], - 'samples': ['NA19678_1'], - }, - '567_1': { - 'reasons': [ - "Found samples with misaligned ploidy with their provided imputed sex: ['NA20872_1']", - ], - 'samples': ['NA20872_1'], - }, - 'bcd_1': { - 'reasons': [ - "Found samples with misaligned ploidy with their provided imputed sex: ['NA20878_1']", - ], - 'samples': ['NA20878_1'], - }, - 'cde_1': { - 'reasons': [ - "Found samples with misaligned ploidy with their provided imputed sex: ['NA20881_1']", - ], - 'samples': ['NA20881_1'], - }, - }, - ), - ), - ], - ) - - @patch( - 'loading_pipeline.lib.tasks.write_remapped_and_subsetted_callset.FeatureFlag', - ) - def test_write_remapped_and_subsetted_callset_task_all_families_failed( - self, - mock_ff: Mock, - ) -> None: - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_7, - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - SampleType.WGS, - 'R0114_project4', - ) - mock_ff.CHECK_SEX_AND_RELATEDNESS = True - worker = luigi.worker.Worker() - wrsc_task = WriteRemappedAndSubsettedCallsetTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - run_id=TEST_RUN_ID, - sample_type=SampleType.WGS, - callset_path=TEST_VCF, - project_guids=['R0114_project4'], - project_i=0, - validations_to_skip=[ALL_VALIDATIONS], - skip_expect_tdr_metrics=True, - ) - worker.add(wrsc_task) - worker.run() - self.assertFalse(wrsc_task.complete()) - updated_validation_errors_task = UpdatedValidationErrorsForRunTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - sample_type=SampleType.WES, - callset_path=TEST_VCF, - project_guids=['R0114_project4'], - validations_to_skip=[ALL_VALIDATIONS], - run_id=TEST_RUN_ID, - ) - self.assertTrue(updated_validation_errors_task.complete()) - with updated_validation_errors_task.output().open('r') as f: - self.assertDictEqual( - json.load(f), - { - 'project_guids': ['R0114_project4'], - 'error_messages': ['All families failed validation checks'], - 'failed_family_samples': { - 'missing_samples': { - 'efg_1': { - 'samples': ['NA99999_1'], - 'reasons': ["Missing samples: {'NA99999_1'}"], - }, - }, - 'relatedness_check': {}, - 'sex_check': { - '890_1': { - 'samples': ['NA20876_1'], - 'reasons': [ - 'Sample NA20876_1 has pedigree sex M but imputed sex F', - ], - }, - '456_1': { - 'samples': ['NA20870_1'], - 'reasons': [ - 'Sample NA20870_1 has pedigree sex M but imputed sex F', - ], - }, - '123_1': { - 'samples': ['NA19675_1'], - 'reasons': [ - 'Sample NA19675_1 has pedigree sex M but imputed sex F', - ], - }, - '678_1': { - 'samples': ['NA20874_1'], - 'reasons': [ - 'Sample NA20874_1 has pedigree sex M but imputed sex F', - ], - }, - '789_1': { - 'samples': ['NA20875_1'], - 'reasons': [ - 'Sample NA20875_1 has pedigree sex M but imputed sex F', - ], - }, - '901_1': { - 'samples': ['NA20877_1'], - 'reasons': [ - 'Sample NA20877_1 has pedigree sex M but imputed sex F', - ], - }, - '345_1': { - 'samples': ['NA19679_1'], - 'reasons': [ - 'Sample NA19679_1 has pedigree sex M but imputed sex F', - ], - }, - 'def_1': { - 'samples': ['NA20885_1'], - 'reasons': [ - 'Sample NA20885_1 has pedigree sex M but imputed sex F', - ], - }, - }, - 'ploidy_check': { - '567_1': { - 'samples': ['NA20872_1'], - 'reasons': [ - "Found samples with misaligned ploidy with their provided imputed sex: ['NA20872_1']", - ], - }, - '234_1': { - 'samples': ['NA19678_1'], - 'reasons': [ - "Found samples with misaligned ploidy with their provided imputed sex: ['NA19678_1']", - ], - }, - 'bcd_1': { - 'samples': ['NA20878_1'], - 'reasons': [ - "Found samples with misaligned ploidy with their provided imputed sex: ['NA20878_1']", - ], - }, - 'cde_1': { - 'samples': ['NA20881_1'], - 'reasons': [ - "Found samples with misaligned ploidy with their provided imputed sex: ['NA20881_1']", - ], - }, - }, - }, - }, - ) - - @patch( - 'loading_pipeline.lib.tasks.write_remapped_and_subsetted_callset.FeatureFlag', - ) - def test_write_remapped_and_subsetted_callset_task_combined_validation_errors( - self, - mock_ff: Mock, - ) -> None: - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_3_DIFFERENT_FAMILIES, - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - SampleType.WGS, - 'R0113_test_project', - ) - worker = luigi.worker.Worker() - - wrsc_task_1 = WriteRemappedAndSubsettedCallsetTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - run_id=TEST_RUN_ID, - sample_type=SampleType.WGS, - callset_path=TEST_VCF, - project_guids=['R0113_test_project'], - project_i=0, - validations_to_skip=[ALL_VALIDATIONS], - skip_expect_tdr_metrics=True, - ) - worker.add(wrsc_task_1) - worker.run() - - # Second run: load pedigree 7 where all families fail validation checks - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_7, - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - SampleType.WGS, - 'R0114_project4', - ) - worker_2 = luigi.worker.Worker() - - wrsc_task_2 = WriteRemappedAndSubsettedCallsetTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - run_id=TEST_RUN_ID, - sample_type=SampleType.WGS, - callset_path=TEST_VCF, - project_guids=['R0114_project4'], - project_i=0, - validations_to_skip=[ALL_VALIDATIONS], - skip_expect_tdr_metrics=True, - ) - worker_2.add(wrsc_task_2) - worker_2.run() - - # Verify second task does not complete (all families failed) - self.assertFalse(wrsc_task_2.complete()) - - # Verify validation errors for second run - updated_validation_errors_task = UpdatedValidationErrorsForRunTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - sample_type=SampleType.WES, - callset_path=TEST_VCF, - project_guids=['R0113_test_project', 'R0114_project4'], - validations_to_skip=[ALL_VALIDATIONS], - run_id=TEST_RUN_ID, - ) - self.assertTrue(updated_validation_errors_task.complete()) - with updated_validation_errors_task.output().open('r') as f: - validation_errors = json.load(f) - - # Verify that all families failed in the second run - self.assertIn( - 'All families failed validation checks', - validation_errors['error_messages'], - ) - # Should have missing samples, sex checks, and ploidy checks all failing - failed_samples = validation_errors['failed_family_samples'] - self.assertGreater( - len(failed_samples['missing_samples']), - 0, - 'Expected missing_samples to have failures', - ) - self.assertGreater( - len(failed_samples['sex_check']), - 0, - 'Expected sex_check to have failures', - ) - self.assertGreater( - len(failed_samples['ploidy_check']), - 0, - 'Expected ploidy_check to have failures', - ) - # Verify that both project guids are in the validation errors - self.assertIn('R0113_test_project', validation_errors['project_guids']) - self.assertIn('R0114_project4', validation_errors['project_guids']) diff --git a/loading_pipeline/lib/tasks/write_sample_qc_json_test.py b/loading_pipeline/lib/tasks/write_sample_qc_json_test.py deleted file mode 100644 index 1c2709c9b7..0000000000 --- a/loading_pipeline/lib/tasks/write_sample_qc_json_test.py +++ /dev/null @@ -1,269 +0,0 @@ -import json -import os -import shutil -from unittest.mock import Mock, patch - -import hail as hl -import hailtop.fs as hfs -import luigi.worker - -from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType -from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS -from loading_pipeline.lib.paths import ancestry_model_rf_path, tdr_metrics_dir -from loading_pipeline.lib.tasks.write_sample_qc_json import WriteSampleQCJsonTask -from loading_pipeline.lib.test.misc import copy_project_pedigree_to_mocked_dir -from loading_pipeline.lib.test.mock_complete_task import MockCompleteTask -from loading_pipeline.lib.test.mocked_reference_datasets_testcase import ( - MockedReferenceDatasetsTestCase, -) - -TEST_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' -TEST_PEDIGREE_3_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_3_remap.tsv' -TEST_TDR_METRICS_FILE = 'loading_pipeline/var/test/tdr_metrics.tsv' -TEST_RUN_ID = 'manual__2024-04-03' - -PCA_SCORES = [0.00212, 0.011, 0.0105, 0.161, 0.026] + [0.1 for _ in range(15)] -EXPECTED_ANC_PROBABILITIES = { - 'prob_afr': 0.02, - 'prob_ami': 0.0, - 'prob_amr': 0.02, - 'prob_asj': 0.9, - 'prob_eas': 0.0, - 'prob_fin': 0.0, - 'prob_mid': 0.0, - 'prob_nfe': 0.05, - 'prob_sas': 0.01, -} -TEST_ANCESTRY_IMPUTATION_MODEL_PATH = ( - 'loading_pipeline/var/test/ancestry_imputation_model.onnx' -) - - -class WriteSampleQCJsonTaskTest(MockedReferenceDatasetsTestCase): - @patch('loading_pipeline.lib.methods.sample_qc.assign_population_pcs') - @patch('loading_pipeline.lib.methods.sample_qc.pc_project') - @patch('loading_pipeline.lib.tasks.write_sample_qc_json.WriteTDRMetricsFilesTask') - def test_call_sample_qc( - self, - mock_tdr_task: Mock, - mock_pc_project: Mock, - mock_assign_population_pcs: Mock, - ) -> None: - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_3_REMAP, - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - SampleType.WGS, - 'R0113_test_project', - ) - os.makedirs( - os.path.dirname(ancestry_model_rf_path()), - exist_ok=True, - ) - shutil.copy2(TEST_ANCESTRY_IMPUTATION_MODEL_PATH, ancestry_model_rf_path()) - os.makedirs( - tdr_metrics_dir(ReferenceGenome.GRCh38, DatasetType.SNV_INDEL), - exist_ok=True, - ) - shutil.copy2( - TEST_TDR_METRICS_FILE, - tdr_metrics_dir(ReferenceGenome.GRCh38, DatasetType.SNV_INDEL), - ) - mock_tdr_task.return_value = MockCompleteTask() - mock_pc_project.return_value = hl.Table.parallelize( - [ - { - 's': sample_id, - 'scores': PCA_SCORES, - } - for sample_id in ('HG00731', 'HG00732', 'HG00733', 'NA19675') - ], - hl.tstruct( - s=hl.tstr, - scores=hl.tarray(hl.tfloat64), - ), - key='s', - ) - mock_assign_population_pcs.return_value = ( - hl.Table.parallelize( - [ - { - 's': sample_id, - 'pca_scores': PCA_SCORES, - 'qc_pop': 'asj', - **EXPECTED_ANC_PROBABILITIES, - } - for sample_id in ('HG00731', 'HG00732', 'HG00733', 'NA19675') - ], - hl.tstruct( - s=hl.tstr, - pca_scores=hl.tarray(hl.tfloat64), - qc_pop=hl.tstr, - prob_afr=hl.tfloat64, - prob_ami=hl.tfloat64, - prob_amr=hl.tfloat64, - prob_asj=hl.tfloat64, - prob_eas=hl.tfloat64, - prob_fin=hl.tfloat64, - prob_mid=hl.tfloat64, - prob_nfe=hl.tfloat64, - prob_sas=hl.tfloat64, - ), - key='s', - ), - None, - ) - worker = luigi.worker.Worker() - task = WriteSampleQCJsonTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - run_id=TEST_RUN_ID, - sample_type=SampleType.WGS, - callset_path=TEST_VCF, - project_guids=['R0113_test_project'], - validations_to_skip=[ALL_VALIDATIONS], - ) - worker.add(task) - worker.run() - self.assertTrue(task) - self.assertTrue(hfs.exists(task.output().path)) - - expected_qc_gen_anc_results = { - 'pca_scores': PCA_SCORES, - **EXPECTED_ANC_PROBABILITIES, - **{f'pop_PC{i + 1}': PCA_SCORES[i] for i in range(20)}, - 'qc_gen_anc': 'oth', - } - with task.output().open('r') as f: - res = json.load(f) - - self.assertCountEqual( - res['HG00731_1'], - { - 'seqr_id': 'HG00731_1', - 'vcf_id': 'HG00731', - 'filtered_callrate': 1.0, - 'contamination_rate': 5.099999904632568, - 'percent_bases_at_20x': 93.69000244140625, - 'mean_coverage': 29.309999465942383, - 'filter_flags': ['contamination', 'coverage'], - **expected_qc_gen_anc_results, - 'sample_qc.call_rate': 0.9666666666666667, - 'sample_qc.n_called': 29, - 'sample_qc.n_not_called': 1, - 'sample_qc.n_filtered': 0, - 'sample_qc.n_hom_ref': 16, - 'sample_qc.n_het': 2, - 'sample_qc.n_hom_var': 11, - 'sample_qc.n_non_ref': 13, - 'sample_qc.n_singleton': 1, - 'sample_qc.n_snp': 24, - 'sample_qc.n_insertion': 0, - 'sample_qc.n_deletion': 0, - 'sample_qc.n_transition': 15, - 'sample_qc.n_transversion': 9, - 'sample_qc.n_star': 0, - 'sample_qc.r_ti_tv': 1.6666666666666667, - 'sample_qc.r_het_hom_var': 0.18181818181818182, - 'sample_qc.r_insertion_deletion': None, - 'sample_qc.f_inbreeding.f_stat': 0.284195245767986, - 'sample_qc.f_inbreeding.n_called': 29, - 'sample_qc.f_inbreeding.expected_homs': 26.20594199999999, - 'sample_qc.f_inbreeding.observed_homs': 27, - 'fail_n_snp': True, - 'fail_r_ti_tv': False, - 'fail_r_insertion_deletion': None, - 'fail_n_insertion': True, - 'fail_n_deletion': True, - 'fail_r_het_hom_var': False, - 'fail_call_rate': False, - 'qc_metrics_filters': ['n_deletion', 'n_insertion', 'n_snp'], - }, - ) - self.assertCountEqual( - res['HG00732_1'], - { - 'seqr_id': 'HG00732_1', - 'vcf_id': 'HG00732', - 'filtered_callrate': 1.0, - 'contamination_rate': 5.0, - 'percent_bases_at_20x': 90.0, - 'mean_coverage': 28.0, - 'filter_flags': ['coverage'], - **expected_qc_gen_anc_results, - 'sample_qc.call_rate': 0.9666666666666667, - 'sample_qc.n_called': 29, - 'sample_qc.n_not_called': 1, - 'sample_qc.n_filtered': 0, - 'sample_qc.n_hom_ref': 16, - 'sample_qc.n_het': 4, - 'sample_qc.n_hom_var': 9, - 'sample_qc.n_non_ref': 13, - 'sample_qc.n_singleton': 2, - 'sample_qc.n_snp': 22, - 'sample_qc.n_insertion': 0, - 'sample_qc.n_deletion': 0, - 'sample_qc.n_transition': 13, - 'sample_qc.n_transversion': 9, - 'sample_qc.n_star': 0, - 'sample_qc.r_ti_tv': 1.4444444444444444, - 'sample_qc.r_het_hom_var': 0.4444444444444444, - 'sample_qc.r_insertion_deletion': None, - 'sample_qc.f_inbreeding.f_stat': -0.431609508464028, - 'sample_qc.f_inbreeding.n_called': 29, - 'sample_qc.f_inbreeding.expected_homs': 26.20594199999999, - 'sample_qc.f_inbreeding.observed_homs': 25, - 'fail_n_snp': True, - 'fail_r_ti_tv': False, - 'fail_r_insertion_deletion': None, - 'fail_n_insertion': True, - 'fail_n_deletion': True, - 'fail_r_het_hom_var': False, - 'fail_call_rate': False, - 'qc_metrics_filters': ['n_deletion', 'n_insertion', 'n_snp'], - }, - ) - self.assertCountEqual( - res['HG00733_1'], - { - 'seqr_id': 'HG00733_1', - 'vcf_id': 'HG00733', - 'filtered_callrate': 1.0, - 'contamination_rate': 6.0, - 'percent_bases_at_20x': 85.0, - 'mean_coverage': 36.400001525878906, - 'filter_flags': ['contamination'], - **expected_qc_gen_anc_results, - 'sample_qc.call_rate': 1.0, - 'sample_qc.n_called': 30, - 'sample_qc.n_not_called': 0, - 'sample_qc.n_filtered': 0, - 'sample_qc.n_hom_ref': 17, - 'sample_qc.n_het': 3, - 'sample_qc.n_hom_var': 10, - 'sample_qc.n_non_ref': 13, - 'sample_qc.n_singleton': 0, - 'sample_qc.n_snp': 23, - 'sample_qc.n_insertion': 0, - 'sample_qc.n_deletion': 0, - 'sample_qc.n_transition': 13, - 'sample_qc.n_transversion': 10, - 'sample_qc.n_star': 0, - 'sample_qc.r_ti_tv': 1.3, - 'sample_qc.r_het_hom_var': 0.3, - 'sample_qc.r_insertion_deletion': None, - 'sample_qc.f_inbreeding.f_stat': -0.038400752079048056, - 'sample_qc.f_inbreeding.n_called': 30, - 'sample_qc.f_inbreeding.expected_homs': 27.11094199999999, - 'sample_qc.f_inbreeding.observed_homs': 27, - 'fail_n_snp': True, - 'fail_r_ti_tv': False, - 'fail_r_insertion_deletion': None, - 'fail_n_insertion': True, - 'fail_n_deletion': True, - 'fail_r_het_hom_var': False, - 'fail_call_rate': False, - 'qc_metrics_filters': ['n_deletion', 'n_insertion', 'n_snp'], - }, - ) - self.assertFalse('NA19675' in res) diff --git a/loading_pipeline/lib/tasks/write_sex_check_table_test.py b/loading_pipeline/lib/tasks/write_sex_check_table_test.py deleted file mode 100644 index 1f83d8c991..0000000000 --- a/loading_pipeline/lib/tasks/write_sex_check_table_test.py +++ /dev/null @@ -1,157 +0,0 @@ -from decimal import Decimal -from unittest.mock import Mock, patch - -import google.cloud.bigquery -import hail as hl -import luigi.worker - -from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType -from loading_pipeline.lib.paths import sex_check_table_path, tdr_metrics_path -from loading_pipeline.lib.tasks.write_sex_check_table import ( - WriteSexCheckTableTask, -) -from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase - -TEST_SEX_AND_RELATEDNESS_CALLSET_MT = ( - 'loading_pipeline/var/test/callsets/sex_and_relatedness_1.mt' -) - - -class WriteSexCheckTableTaskTest(MockedDatarootTestCase): - @patch('loading_pipeline.lib.tasks.write_tdr_metrics_files.gen_bq_table_names') - @patch('loading_pipeline.lib.tasks.write_tdr_metrics_file.bq_metrics_query') - @patch( - 'loading_pipeline.lib.tasks.write_sex_check_table.FeatureFlag', - ) - def test_snv_sex_check_table_task( - self, - mock_ff: Mock, - mock_bq_metrics_query: Mock, - mock_gen_bq_table_names: Mock, - ) -> None: - mock_ff.EXPECT_TDR_METRICS = True - mock_gen_bq_table_names.return_value = [ - 'datarepo-7242affb.datarepo_RP_3053', - 'datarepo-5a72e31b.datarepo_RP_3056', - ] - mock_bq_metrics_query.side_effect = [ - iter( - [ - google.cloud.bigquery.table.Row( - ( - 'SM-NJ8MF', - 'Unknown', - Decimal('0'), - Decimal('0'), - Decimal('0'), - ), - { - 'collaborator_sample_id': 0, - 'predicted_sex': 1, - 'contamination_rate': 2, - 'percent_bases_at_20x': 3, - 'mean_coverage': 4, - }, - ), - google.cloud.bigquery.table.Row( - ( - 'SM-MWOGC', - 'Female', - Decimal('0'), - Decimal('0'), - Decimal('0'), - ), - { - 'collaborator_sample_id': 0, - 'predicted_sex': 1, - 'contamination_rate': 2, - 'percent_bases_at_20x': 3, - 'mean_coverage': 4, - }, - ), - google.cloud.bigquery.table.Row( - ('SM-MWKWL', 'Male', Decimal('0'), Decimal('0'), Decimal('0')), - { - 'collaborator_sample_id': 0, - 'predicted_sex': 1, - 'contamination_rate': 2, - 'percent_bases_at_20x': 3, - 'mean_coverage': 4, - }, - ), - ], - ), - iter( - [ - google.cloud.bigquery.table.Row( - ('SM-NGE65', 'Male', Decimal('0'), Decimal('0'), Decimal('0')), - { - 'collaborator_sample_id': 0, - 'predicted_sex': 1, - 'contamination_rate': 2, - 'percent_bases_at_20x': 3, - 'mean_coverage': 4, - }, - ), - google.cloud.bigquery.table.Row( - ('SM-NGE5G', 'Male', Decimal('0'), Decimal('0'), Decimal('0')), - { - 'collaborator_sample_id': 0, - 'predicted_sex': 1, - 'contamination_rate': 2, - 'percent_bases_at_20x': 3, - 'mean_coverage': 4, - }, - ), - google.cloud.bigquery.table.Row( - ('SM-NC6LM', 'Male', Decimal('0'), Decimal('0'), Decimal('0')), - { - 'collaborator_sample_id': 0, - 'predicted_sex': 1, - 'contamination_rate': 2, - 'percent_bases_at_20x': 3, - 'mean_coverage': 4, - }, - ), - ], - ), - ] - worker = luigi.worker.Worker() - write_sex_check_table = WriteSexCheckTableTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - sample_type=SampleType.WGS, - callset_path='na', - project_guids=['R0113_test_project'], - run_id='manual__2024-04-03', - ) - worker.add(write_sex_check_table) - worker.run() - self.assertTrue(write_sex_check_table.complete()) - sex_check_ht = hl.read_table( - sex_check_table_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - 'na', - ), - ) - self.assertEqual( - sex_check_ht.collect(), - [ - hl.Struct(s='SM-MWKWL', predicted_sex='M'), - hl.Struct(s='SM-MWOGC', predicted_sex='F'), - hl.Struct(s='SM-NC6LM', predicted_sex='M'), - hl.Struct(s='SM-NGE5G', predicted_sex='M'), - hl.Struct(s='SM-NGE65', predicted_sex='M'), - hl.Struct(s='SM-NJ8MF', predicted_sex='U'), - ], - ) - # Check underlying tdr metrics file. - with open( - tdr_metrics_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - 'datarepo-5a72e31b.datarepo_RP_3056', - ), - ) as f: - self.assertTrue('collaborator_sample_id' in f.read()) diff --git a/loading_pipeline/lib/tasks/write_success_file_test.py b/loading_pipeline/lib/tasks/write_success_file_test.py deleted file mode 100644 index f33a5d337e..0000000000 --- a/loading_pipeline/lib/tasks/write_success_file_test.py +++ /dev/null @@ -1,34 +0,0 @@ -from unittest import mock - -import luigi.worker - -from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType -from loading_pipeline.lib.tasks.write_success_file import WriteSuccessFileTask -from loading_pipeline.lib.test.mock_complete_task import MockCompleteTask -from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase - - -class WriteSuccessFileTaskTest(MockedDatarootTestCase): - @mock.patch( - 'loading_pipeline.lib.tasks.write_success_file.RunPipelineTask', - ) - def test_write_success_file_task( - self, - mock_run_pipeline_task: mock.Mock, - ) -> None: - mock_run_pipeline_task.return_value = MockCompleteTask() - worker = luigi.worker.Worker() - write_success_file = WriteSuccessFileTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - sample_type=SampleType.WGS, - callset_path='test_callset', - project_guids=['R0113_test_project'], - run_id='manual__2024-04-03', - attempt_id=0, - ) - worker.add(write_success_file) - worker.run() - self.assertTrue(write_success_file.complete()) - with open(write_success_file.output().path) as f: - self.assertEqual(f.read(), '') diff --git a/loading_pipeline/lib/tasks/write_variant_annotations_vcf_test.py b/loading_pipeline/lib/tasks/write_variant_annotations_vcf_test.py deleted file mode 100644 index 4bad466b67..0000000000 --- a/loading_pipeline/lib/tasks/write_variant_annotations_vcf_test.py +++ /dev/null @@ -1,91 +0,0 @@ -import gzip -from unittest.mock import Mock, patch - -import hailtop.fs as hfs -import luigi.worker - -from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType -from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS -from loading_pipeline.lib.tasks.update_variant_annotations_table_with_new_variants import ( - UpdateVariantAnnotationsTableWithNewVariantsTask, -) -from loading_pipeline.lib.tasks.write_variant_annotations_vcf import ( - WriteVariantAnnotationsVCF, -) -from loading_pipeline.lib.test.misc import copy_project_pedigree_to_mocked_dir -from loading_pipeline.lib.test.mocked_reference_datasets_testcase import ( - MockedReferenceDatasetsTestCase, -) - -TEST_SV_VCF = 'loading_pipeline/var/test/callsets/sv_1.vcf' -TEST_PEDIGREE_5 = 'loading_pipeline/var/test/pedigrees/test_pedigree_5.tsv' - -GENE_ID_MAPPING = { - 'OR4F5': 'ENSG00000186092', - 'PLEKHG4B': 'ENSG00000153404', - 'OR4F16': 'ENSG00000186192', - 'OR4F29': 'ENSG00000284733', - 'FBXO28': 'ENSG00000143756', - 'SAMD11': 'ENSG00000187634', - 'C1orf174': 'ENSG00000198912', - 'TAS1R1': 'ENSG00000173662', - 'FAM131C': 'ENSG00000185519', - 'RCC2': 'ENSG00000179051', - 'NBPF3': 'ENSG00000142794', - 'AGBL4': 'ENSG00000186094', - 'KIAA1614': 'ENSG00000135835', - 'MR1': 'ENSG00000153029', - 'STX6': 'ENSG00000135823', - 'XPR1': 'ENSG00000143324', -} - - -class WriteVariantAnnotationsVCFTest(MockedReferenceDatasetsTestCase): - @patch( - 'loading_pipeline.lib.tasks.write_new_variants_table.load_gencode_gene_symbol_to_gene_id', - ) - def test_sv_export_vcf( - self, - mock_load_gencode: Mock, - ) -> None: - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_5, - ReferenceGenome.GRCh38, - DatasetType.SV, - SampleType.WGS, - 'R0115_test_project2', - ) - mock_load_gencode.return_value = GENE_ID_MAPPING - worker = luigi.worker.Worker() - update_variant_annotations_task = ( - UpdateVariantAnnotationsTableWithNewVariantsTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SV, - run_id='run_id1', - sample_type=SampleType.WGS, - callset_path=TEST_SV_VCF, - project_guids=['R0115_test_project2'], - validations_to_skip=[ALL_VALIDATIONS], - skip_expect_tdr_metrics=True, - ) - ) - worker.add(update_variant_annotations_task) - worker.run() - self.assertTrue(update_variant_annotations_task.complete()) - write_variant_annotations_vcf_task = WriteVariantAnnotationsVCF( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SV, - run_id='run_id1', - sample_type=SampleType.WGS, - callset_path=TEST_SV_VCF, - ) - worker.add(write_variant_annotations_vcf_task) - worker.run() - self.assertTrue( - hfs.exists( - write_variant_annotations_vcf_task.output().path, - ), - ) - with hfs.open(write_variant_annotations_vcf_task.output().path, 'rb') as f: - buf = f.read() - self.assertTrue(gzip.decompress(buf).startswith(b'##fileformat=VCFv4.2')) From 5133b642850eb6703b78240bae0ae3be79eb1270 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 16:13:43 -0400 Subject: [PATCH 050/369] new plan --- .../CLICKHOUSE_PYTEST_DJANGO_PLAN.md | 207 ------------------ ...CLICKHOUSE_PYTEST_DJANGO_REMAINING_PLAN.md | 44 ++++ 2 files changed, 44 insertions(+), 207 deletions(-) delete mode 100644 loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_PLAN.md create mode 100644 loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_REMAINING_PLAN.md diff --git a/loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_PLAN.md b/loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_PLAN.md deleted file mode 100644 index cde0c7077f..0000000000 --- a/loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_PLAN.md +++ /dev/null @@ -1,207 +0,0 @@ -# Plan: Manage ClickHouse test DB via pytest-django + `clickhouse_search` migrations - -## Goal - -Stop hand-maintaining ClickHouse schema DDL (and the static `var/test/test_clickhouse_schema.sql` -dump) inside `loading_pipeline`'s tests. Instead, use `pytest-django` to create/migrate the -ClickHouse test database from the real Django migrations in `clickhouse_search` (the source of -truth for the schema), so the pipeline's tests can never drift from production schema. - -Scope constraint: all code changes live in `loading_pipeline/` or in -`.github/workflows/pipeline-unit-tests.yml`. Nothing in `clickhouse_search/` or root `settings.py` -is modified. - -## Key constraint discovered - -`clickhouse_search/backend/base.py` does a **bare** `from settings import -CLICKHOUSE_WRITER_USER, CLICKHOUSE_WRITER_PASSWORD, DATABASES` — not `django.conf.settings`. This -only resolves correctly if a top-level module literally named `settings` is importable on -`sys.path`. Today that resolves to the main repo's heavy `settings.py` (postgres, guardian, -social_django, google.auth, etc.) whenever cwd is the repo root — which is undesirable/impossible -to depend on from `loading_pipeline`'s minimal env. - -**Trick:** create our own minimal module named `settings.py`, placed in a directory that we add to -`sys.path` ahead of the repo root (via pytest's `pythonpath` ini option, which prepends to -`sys.path`). That module serves double duty: -- It's what `clickhouse_search/backend/base.py`'s bare `import settings` resolves to. -- It's also `DJANGO_SETTINGS_MODULE` for pytest-django. - -## Single connection / single set of credentials only - -Per explicit direction: the settings module must configure **one** ClickHouse connection with -**one** set of credentials — not the production split of a read-only `clickhouse` alias plus a -privileged `clickhouse_write` alias. `DATABASES` will define a single real alias using one -writer-capable credential (needed anyway, since migrations and test data inserts require write -access). - -That real alias must be named `clickhouse_write`, not `clickhouse`: `ClickHouseRouter.allow_migrate` -(`clickhouse_search/models/__init__.py`) hardcodes `db == 'clickhouse_write'` for the -`clickhouse_search` app, so only an alias literally named `clickhouse_write` is allowed to have -migrations applied to it. - -Nuance to account for: `clickhouse_search/backend/base.py`'s `_dictionary_sql` looks up -`DATABASES['clickhouse_write']['NAME']` (for ClickHouse-sourced dictionaries with a -`clickhouse_query_template`) and `DATABASES[postgres_db]['NAME']` (default alias `'default'`, for -Postgres-sourced dictionaries) purely to embed a database *name string* into generated DDL — not to -open a second real connection. To keep this working without standing up a second live connection: -- Give `'clickhouse'` a `TEST: {'MIRROR': 'clickhouse_write'}` config, so Django reuses the - `clickhouse_write` alias's actual test database instead of creating/tearing down a second one, - while the key is still present for the `NAME` lookup (used only by `backend/base.py`, not by our - own test code). -- Give `'default'` a placeholder entry (e.g. `ENGINE: 'django.db.backends.dummy'`) purely so - `DATABASES['default']['NAME']` resolves to a string — nothing in `loading_pipeline`'s tests - actually connects to it, since there's no Postgres in this CI job. - -Test code (and the shared base class) uses `connections['clickhouse_write']` — the one alias -Django actually creates/migrates a real test database for. - -## Inventory of every ClickHouse-touching test - -1. **`lib/misc/clickhouse_test.py`** (`ClickhouseTest`) — hand-rolls ~250 lines of `CREATE - TABLE`/`CREATE DICTIONARY`/`CREATE MATERIALIZED VIEW` DDL duplicating a subset of the real - schema, plus fixture dictionaries for gene IDs/gnomAD. -2. **`lib/test/clickhouse_schema_testcase.py`** (`ClickhouseSchemaTestCase`) — loads the static - `var/test/test_clickhouse_schema.sql` dump plus a few placeholder dictionaries. Used by: - - `bin/pipeline_worker_test.py` (`PipelineWorkerTest`) - - `lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py` - (`LoadClickhouseVariantsTablesTaskTest`) -3. **`ops/repartition_clickhouse_grch38_snv_indel_test.py`** (`RepartitionGRCh38SnvIndelTest`) — - its own bespoke DDL for a synthetic, intentionally-simplified `entries` table + a wholly - separate scratch database (`REPARTITION_DATABASE_NAME`) that isn't part of `clickhouse_search`'s - schema at all. - -## The Postgres/GCS-sourced dictionary wrinkle - -A handful of dictionaries are, in production, sourced from Postgres (via the -`seqr_postgres_named_collection` named collection) or from GCS parquet URLs: - -- `seqrdb_gene_ids` -- `seqrdb_affected_status_dict` -- `GRCh38/SNV_INDEL/project_partitions_dict` -- the gnomAD reference dict (`GRCh38/SNV_INDEL/reference_data/gnomad_genomes`) - -`loading_pipeline`'s CI only runs ClickHouse (no Postgres, no GCS access). Running -`clickhouse_search`'s real migrations here requires a dummy `seqr_postgres_named_collection` (a new -workflow step, mirroring what `unit-tests.yml` already does for the main app) just so the -`CREATE DICTIONARY ... SOURCE(POSTGRESQL(NAME 'seqr_postgres_named_collection' ...))` DDL parses. -Dictionaries are lazily loaded (`LIFETIME(0)`), so DDL creation succeeds even though the source is -unreachable — but tests still need to override these specific dictionaries with deterministic -fixture sources afterward (same idea as today's code, just trimmed to only this handful instead of -faking the whole schema). - -## Raw SQL execution in tests: use the Django connection, not `clickhouse_driver.Client` - -Every test currently calls `get_clickhouse_client()` (a raw `clickhouse_driver.Client`, see -`lib/misc/clickhouse.py`) to run setup/assertion SQL directly. Once the schema is Django-managed, -tests should execute their raw SQL through Django's own DB connection instead of a separate -`clickhouse_driver.Client` instance — i.e. `django.db.connections['clickhouse_write'].cursor()` -(the one real alias defined per "Single connection / single set of credentials only" above), -calling `cursor.execute(sql, params)` / `cursor.fetchall()`. - -This is purely a *client* swap for test code — tests keep writing raw SQL strings (no ORM/model -queries), just executed via the Django connection so the tests exercise the same connection -machinery/test-DB aliasing that pytest-django set up, rather than opening an independent -`clickhouse_driver` connection that doesn't know about Django's test DB name remapping. Production -code in `lib/misc/clickhouse.py` (`get_clickhouse_client` and friends) is unaffected — this only -applies to test files themselves. - -## Shared setup-time data: Django fixtures, not bulk INSERT statements - -Some test data is inserted once in a test class's `setUp`/`setUpClass` and reused across multiple -test methods (e.g. the `seqrdb_gene_ids`/`gnomad_genomes` source-table rows in -`ClickhouseTest`/`ClickhouseSchemaTestCase`). That category of data should be loaded via Django's -fixture mechanism (JSON fixture files under a `fixtures/` dir, loaded with -`fixtures = [...]` on the `TestCase` subclass, or an explicit `call_command('loaddata', ...)`) — -not hand-written `INSERT INTO ... VALUES (...)` statements repeated/executed in `setUp`. - -This only applies to shared, setup-time reference data with a real backing model in -`clickhouse_search` (e.g. the source tables behind `seqrdb_gene_ids`/`gnomad_genomes`). Since -`loaddata` populates rows through the model layer, the dictionary itself still needs an explicit -`RELOAD DICTIONARY`/refresh afterward (dictionaries aren't themselves loaddata targets — their -backing source table is). Data that's specific to a single test method's body/assertions (not -shared across tests) stays as raw SQL executed via the Django connection cursor, per the prior -note — this fixture rule is specifically about *repeated* setup-time data. - -## Proposed change set - -| File | Change | -|---|---| -| `clickhouse_search/models/search_models.py`, `clickhouse_search/backend/table_models.py`, `clickhouse_search/migrations/0040_gnomadnoncodingconstraintdict.py` | move `Projection` from `search_models.py` to `backend/table_models.py`; update the migration's import accordingly (✅ done) | -| `clickhouse_search/constants.py` | duplicate 4 constants out of `seqr.models.Individual` instead of importing it (✅ done) | -| `.github/workflows/pipeline-unit-tests.yml` | keep `CLICKHOUSE_DATABASE=test`; no named-collection step needed anymore (no Postgres-sourced dictionaries are reachable via the minimal settings module in the first place - see note below) | -| `loading_pipeline/pyproject.toml` | add `django`, `django-clickhouse-backend`, `pytest-django` dev deps; add `[tool.pytest.ini_options]` (`DJANGO_SETTINGS_MODULE`, `pythonpath`) | -| **new** `loading_pipeline/lib/test/clickhouse_django/settings.py` | minimal Django settings: one real `clickhouse` alias (single credential set), `clickhouse_write` mirrored onto it via `TEST: {MIRROR: 'clickhouse'}`, a dummy `default` placeholder (NAME only, no real connection), `clickhouse_backend` + `clickhouse_search` apps, `ClickHouseRouter`; doubles as the shadow `settings` module `clickhouse_search/backend/base.py` bare-imports | -| `lib/test/clickhouse_schema_testcase.py` | rewritten as the one shared base class: drop all manual DDL/SQL-file loading (schema now comes from real migrations via pytest-django), keep only the small external-sourced-dictionary overrides + per-test flush/truncate + staging-DB drop/create — all executed via `connections['clickhouse_write'].cursor()`; shared reference rows (e.g. gene-id/gnomAD source-table rows) loaded via Django `fixtures = [...]` instead of `INSERT` statements | -| **delete** `loading_pipeline/var/test/test_clickhouse_schema.sql` | no longer needed | -| **new** `loading_pipeline/lib/test/fixtures/*.json` | Django fixtures for the shared setup-time reference rows referenced above | -| `lib/misc/clickhouse_test.py` | `ClickhouseTest` extends the shared base instead of hand-building its own schema; keeps only its fixture-data seeding (via the new Django fixtures, not bulk `INSERT`) and parquet-writing setup; all `get_clickhouse_client()` calls in the test body replaced with the Django connection cursor | -| `bin/pipeline_worker_test.py`, `lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py` | no structural change (already extend the shared base) — swap their `get_clickhouse_client()` assertion calls to the Django connection cursor; cleanup of now-dead references (e.g. leftover `TEST_SCHEMA` constant) | -| `ops/repartition_clickhouse_grch38_snv_indel_test.py` | switch to the shared base for the real-schema DB lifecycle; keep its own synthetic `entries`-table `REPLACE`/dict + `REPARTITION_DATABASE_NAME` handling since that's not part of `clickhouse_search`'s schema; swap `get_clickhouse_client()` for the Django connection cursor | - -## Open risk / caveat - -No live ClickHouse instance is available in the sandbox used to write this plan, so some runtime -specifics can't be verified ahead of time: -- Whether `TRUNCATE` behaves as expected on materialized views (regular vs. refreshable). -- Exact Django test-DB naming interplay with `Env.CLICKHOUSE_DATABASE` (need a `TEST: {NAME: ...}` - override to avoid Django's default `test_` prefix mismatch). -- Whether `CREATE DICTIONARY ... SOURCE(POSTGRESQL(...))` DDL actually succeeds against a - ClickHouse server with only a dummy/unreachable named collection registered. -- Whether raw SQL params/tuple-list inserts (e.g. `INSERT INTO ... VALUES` with a Python list of - tuples, as `clickhouse_driver.Client.execute` supports today) work identically through - `cursor.execute()`/`cursor.executemany()` on the Django ClickHouse backend, or need reshaping. - -These should be shaken out against a real CI run / local ClickHouse instance once implemented. - -## Deviations from this plan, found during implementation - -Verified against a live ClickHouse instance. Recorded here for reference; this plan document -itself is not otherwise updated to match implementation. - -**`clickhouse_search/` changes beyond the two already noted above** (both cleared with the user -before making them): -- Moved `conditionally_refresh_reference_dataset` from `models/reference_data_models.py` to - `backend/table_models.py`, so migration 0040 doesn't need to import the live model modules (and - therefore `seqr.models.Dataset`/`seqr.utils.xpos_utils.CHROMOSOME_CHOICES`) just to reach one - helper function. -- Added `conditionally_reload_dictionary` (`backend/table_models.py`) and edited migrations 0043 - and 0044 to use it instead of hardcoded `RunSQL('SYSTEM RELOAD DICTIONARY ...')` - those forced - a real synchronous Postgres connection during `migrate`, which no environment here has. This - edits already-applied migration files, normally treated as an immutable historical record. - -**A production dependency change:** `clickhouse-driver` bumped `0.2.9` -> `0.2.10` in -`loading_pipeline/pyproject.toml` (forced by `django-clickhouse-backend==1.6`'s own pin; matches -the main app's version). Not test-only. - -**Bugs/gaps in this plan's own design, fixed - all confined to `loading_pipeline/`:** -- `reference_data` needs its own dummy `DATABASES` alias; the plan only accounted for `default` - (`GeneIdDict`/`OmimDict` declare `postgres_db = 'reference_data'`). -- `DATABASES['clickhouse_write']['TEST']['DEPENDENCIES']` must be `[]`, or Django raises - "Circular dependency in TEST[DEPENDENCIES]" (it assumes every alias depends on `default`). -- The `pythonpath` ordering described in this plan's original settings-module writeup was - backwards; pytest builds `sys.path` in the *same* order as the `pythonpath` list, not reversed. -- `django_find_project = false` is required - pytest-django's `manage.py` auto-discovery - otherwise force-inserts the repo root at `sys.path[0]`, re-shadowing `settings`. -- `CLICKHOUSE_IN_MEMORY_DIR`/`CLICKHOUSE_DATA_DIR` must default to different paths, or two - `EmbeddedRocksDB` tables collide on the same file lock. -- A stub `seqr` package (`lib/test/clickhouse_django/seqr/`) is needed - not anticipated anywhere - in this plan - because `clickhouse_search/backend/table_models.py` imports `SeqrLogger`, and - migration 0040 has a named dependency on a specific `seqr` migration. -- The "no named-collection CI step needed" conclusion in this plan's own change-set table is - right, but the "Postgres/GCS-sourced dictionary wrinkle" section above is stale/wrong about why - - see the migration 0043/0044 edit above for the actual mechanism. - -**Explicit user-directed deviations from this plan's design:** -- The shared base class does NOT keep "staging-DB drop/create" logic, contrary to this plan's - change-set table - `loading_pipeline`'s own production code already drops/creates the staging - DB defensively, so tests don't need to. -- Per-test cleanup in the shared base class is a `_fixture_teardown` override that truncates all - live, non-`Dictionary`/`MaterializedView` tables directly via SQL - not Django's `flush` command, - which relies on `apps.get_models()` and finds nothing (no `clickhouse_search` model modules are - imported anywhere in `loading_pipeline`). - -**Unresolved tension, not yet acted on:** this plan calls for shared reference data (e.g. -`seqrdb_gene_ids` source rows) to be loaded via Django fixtures (`loaddata`), which requires -importing the real model classes being loaded - but the user has since directed that fully -importing `clickhouse_search`'s live model modules is unacceptable for these tests. Needs -resolution before the fixture-loading step is implemented. \ No newline at end of file diff --git a/loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_REMAINING_PLAN.md b/loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_REMAINING_PLAN.md new file mode 100644 index 0000000000..6b5bab38a1 --- /dev/null +++ b/loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_REMAINING_PLAN.md @@ -0,0 +1,44 @@ +# Plan: Finish migrating `repartition_clickhouse_grch38_snv_indel_test.py` to pytest-django + +## Context + +`loading_pipeline`'s ClickHouse tests were migrated to run against real `clickhouse_search` +Django migrations via pytest-django, with a shared `ClickhouseSchemaTestCase` base +(`lib/test/clickhouse_schema_testcase.py`) that owns the real schema DB's migrate/truncate +lifecycle. Every ClickHouse-touching test file adopted this base and switched from raw +`clickhouse_driver.Client` (`get_clickhouse_client()`) to +`connections['clickhouse_write'].cursor()` — except one file. + +## Remaining work + +`ops/repartition_clickhouse_grch38_snv_indel_test.py` (`RepartitionGRCh38SnvIndelTest`) still +predates the migration: + +- extends bare `unittest.TestCase`, not `ClickhouseSchemaTestCase` +- `setUp` manually runs `DROP DATABASE IF EXISTS {Env.CLICKHOUSE_DATABASE} PARALLEL WITH DROP + DATABASE IF EXISTS {REPARTITION_DATABASE_NAME}` then the matching `CREATE DATABASE ... PARALLEL + WITH ...` — `Env.CLICKHOUSE_DATABASE` is now owned by pytest-django's migrate lifecycle; + `REPARTITION_DATABASE_NAME` is the script's own scratch DB, not part of `clickhouse_search`'s + schema +- every SQL statement in `setUp` and both test methods runs via `get_clickhouse_client()` + + `client.execute(...)`, a raw `clickhouse_driver.Client` + +### Changes + +1. `RepartitionGRCh38SnvIndelTest` extends `ClickhouseSchemaTestCase` instead of + `unittest.TestCase`. +2. Drop the `DROP DATABASE IF EXISTS {Env.CLICKHOUSE_DATABASE}` / `CREATE DATABASE + {Env.CLICKHOUSE_DATABASE}` half of `setUp`'s `PARALLEL WITH` statements — the shared base now + handles that DB's schema/lifecycle. +3. Keep the `REPARTITION_DATABASE_NAME` drop/create in `setUp` (still not part of the real + schema), issued as its own statement. +4. Keep the synthetic `GRCh38/SNV_INDEL/entries` table DDL, `INSERT` seed rows, and + `project_partitions_dict` dictionary DDL as-is (intentionally bespoke, not real schema). +5. Execute everything in `setUp` and both test methods (`test_main_all_projects`, + `test_main_one_project`) via `connections['clickhouse_write'].cursor()` / + `cursor.execute(...)` / `cursor.fetchall()` instead of `get_clickhouse_client()` / + `client.execute(...)`. +6. Drop the now-unused `get_clickhouse_client` import. + +Reference `lib/misc/clickhouse_test.py` or `bin/pipeline_worker_test.py` for the established +pattern of extending `ClickhouseSchemaTestCase` and using the cursor. \ No newline at end of file From 9537e4634085dbbf91155fe0b98c63e00bdf8a62 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 16:20:14 -0400 Subject: [PATCH 051/369] restore files --- clickhouse_search/models/search_models.py | 4 +- .../lib/tasks/reference_data/__init__.py | 0 .../updated_reference_dataset.py | 27 +++++++++ .../updated_reference_dataset_parquet.py | 55 +++++++++++++++++++ 4 files changed, 84 insertions(+), 2 deletions(-) create mode 100644 loading_pipeline/lib/tasks/reference_data/__init__.py create mode 100644 loading_pipeline/lib/tasks/reference_data/updated_reference_dataset.py create mode 100644 loading_pipeline/lib/tasks/reference_data/updated_reference_dataset_parquet.py diff --git a/clickhouse_search/models/search_models.py b/clickhouse_search/models/search_models.py index 50aedf1325..48516b36f0 100644 --- a/clickhouse_search/models/search_models.py +++ b/clickhouse_search/models/search_models.py @@ -453,7 +453,7 @@ class EntriesGcnv(BaseEntries): class Meta(BaseEntries.Meta): db_table = 'GRCh38/GCNV/entries' -class VariantDetailsGRCh37SnvIndel(models.ClickhouseModel): +class VariantDetailsGRCh37SnvIndel(FixtureLoadableClickhouseModel): ANNOTATION_CONSTANTS = VariantsGRCh37SnvIndel.ANNOTATION_CONSTANTS key = OneToOneField('VariantsGRCh37SnvIndel', db_column='key', primary_key=True, on_delete=CASCADE) @@ -470,7 +470,7 @@ class Meta: db_table = 'GRCh37/SNV_INDEL/variants/details' engine = EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh37/SNV_INDEL/variants_details', primary_key='key', flatten_nested=0) -class VariantDetailsSnvIndel(models.ClickhouseModel): +class VariantDetailsSnvIndel(FixtureLoadableClickhouseModel): TRANSCRIPTS_FIELDS = sorted([ ('alphamissense', NamedTupleField([ ('pathogenicity', models.DecimalField(null=True, blank=True, max_digits=9, decimal_places=5)), diff --git a/loading_pipeline/lib/tasks/reference_data/__init__.py b/loading_pipeline/lib/tasks/reference_data/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/loading_pipeline/lib/tasks/reference_data/updated_reference_dataset.py b/loading_pipeline/lib/tasks/reference_data/updated_reference_dataset.py new file mode 100644 index 0000000000..575cc1864f --- /dev/null +++ b/loading_pipeline/lib/tasks/reference_data/updated_reference_dataset.py @@ -0,0 +1,27 @@ +import luigi + +from loading_pipeline.lib.paths import valid_reference_dataset_path +from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset +from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( + BaseLoadingPipelineParams, +) +from loading_pipeline.lib.tasks.base.base_write import BaseWriteTask +from loading_pipeline.lib.tasks.files import GCSorLocalTarget + + +@luigi.util.inherits(BaseLoadingPipelineParams) +class UpdatedReferenceDatasetTask(BaseWriteTask): + reference_dataset: ReferenceDataset = luigi.EnumParameter( + enum=ReferenceDataset, + ) + + def output(self): + return GCSorLocalTarget( + valid_reference_dataset_path( + self.reference_genome, + self.reference_dataset, + ), + ) + + def create_table(self): + return self.reference_dataset.get_ht(self.reference_genome) diff --git a/loading_pipeline/lib/tasks/reference_data/updated_reference_dataset_parquet.py b/loading_pipeline/lib/tasks/reference_data/updated_reference_dataset_parquet.py new file mode 100644 index 0000000000..ed8adfce6b --- /dev/null +++ b/loading_pipeline/lib/tasks/reference_data/updated_reference_dataset_parquet.py @@ -0,0 +1,55 @@ +import luigi + +from loading_pipeline.lib.annotations.expression_helpers import get_expr_for_variant_id +from loading_pipeline.lib.core.dataset_type import DatasetType +from loading_pipeline.lib.core.definitions import ReferenceGenome +from loading_pipeline.lib.paths import reference_dataset_parquet +from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset +from loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc import ( + BaseRunJobOnDataprocTask, +) +from loading_pipeline.lib.tasks.files import GCSorLocalFolderTarget, GCSorLocalTarget + + +class UpdatedReferenceDatasetParquetTask(luigi.Task): + reference_genome = luigi.EnumParameter(enum=ReferenceGenome) + dataset_type = luigi.EnumParameter(enum=DatasetType) + reference_dataset: ReferenceDataset = luigi.EnumParameter( + enum=ReferenceDataset, + ) + run_id = luigi.Parameter() + attempt_id = luigi.IntParameter() + + def complete(self) -> luigi.Target: + return GCSorLocalFolderTarget(self.output().path).exists() + + def output(self): + return GCSorLocalTarget( + reference_dataset_parquet( + self.reference_genome, + self.reference_dataset, + ), + ) + + def run(self): + ht = self.reference_dataset.get_ht(self.reference_genome) + ht = ht.annotate( + variant_id=get_expr_for_variant_id(ht), + ) + df = ht.to_spark(flatten=False) + df.write.parquet( + self.output().path, + mode='overwrite', + ) + + +class UpdatedReferenceDatasetParquetOnDataprocTask(BaseRunJobOnDataprocTask): + reference_genome = luigi.EnumParameter(enum=ReferenceGenome) + dataset_type = luigi.EnumParameter(enum=DatasetType) + reference_dataset: ReferenceDataset = luigi.EnumParameter( + enum=ReferenceDataset, + ) + + @property + def task(self) -> luigi.Task: + return UpdatedReferenceDatasetParquetTask From 0130de6befe56a73a3c54f53972f3901ffb900a3 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 16:36:19 -0400 Subject: [PATCH 052/369] fix fixtures --- loading_pipeline/lib/misc/clickhouse_test.py | 1 + .../lib/test/fixtures/clickhouse_test.json | 12 +++++++++--- 2 files changed, 10 insertions(+), 3 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index 0d776ebaa3..f2f7055f70 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -244,6 +244,7 @@ class ClickhouseTest(MockedDatarootTestCase, ClickhouseSchemaTestCase): @classmethod def setUpClass(cls): super().setUpClass() + # Postgres dicts are not managed by django in this test suite and therefore cannot be loaded from fixtures with connections['clickhouse_write'].cursor() as cursor: cursor.execute( f'INSERT INTO {Env.CLICKHOUSE_DATABASE}.`seqrdb_gene_ids_src` VALUES', diff --git a/loading_pipeline/lib/test/fixtures/clickhouse_test.json b/loading_pipeline/lib/test/fixtures/clickhouse_test.json index 86b4d05638..757f969261 100644 --- a/loading_pipeline/lib/test/fixtures/clickhouse_test.json +++ b/loading_pipeline/lib/test/fixtures/clickhouse_test.json @@ -268,7 +268,9 @@ "fields": { "key": 1, "variant_id": "a", - "transcripts": [] + "transcripts": [], + "sortedMotifFeatureConsequences": [], + "sortedRegulatoryFeatureConsequences": [] } }, { @@ -277,7 +279,9 @@ "fields": { "key": 7, "variant_id": "c", - "transcripts": [] + "transcripts": [], + "sortedMotifFeatureConsequences": [], + "sortedRegulatoryFeatureConsequences": [] } }, { @@ -286,7 +290,9 @@ "fields": { "key": 10, "variant_id": "b", - "transcripts": [] + "transcripts": [], + "sortedMotifFeatureConsequences": [], + "sortedRegulatoryFeatureConsequences": [] } } ] From aad2920fd021b028c517736e454776ea12c3ec33 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 16:44:44 -0400 Subject: [PATCH 053/369] fix field names --- .../lib/test/fixtures/clickhouse_test.json | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/loading_pipeline/lib/test/fixtures/clickhouse_test.json b/loading_pipeline/lib/test/fixtures/clickhouse_test.json index 757f969261..e30c37f235 100644 --- a/loading_pipeline/lib/test/fixtures/clickhouse_test.json +++ b/loading_pipeline/lib/test/fixtures/clickhouse_test.json @@ -269,8 +269,8 @@ "key": 1, "variant_id": "a", "transcripts": [], - "sortedMotifFeatureConsequences": [], - "sortedRegulatoryFeatureConsequences": [] + "sorted_motif_feature_consequences": [], + "sorted_regulatory_feature_consequences": [] } }, { @@ -280,8 +280,8 @@ "key": 7, "variant_id": "c", "transcripts": [], - "sortedMotifFeatureConsequences": [], - "sortedRegulatoryFeatureConsequences": [] + "sorted_motif_feature_consequences": [], + "sorted_regulatory_feature_consequences": [] } }, { @@ -291,8 +291,8 @@ "key": 10, "variant_id": "b", "transcripts": [], - "sortedMotifFeatureConsequences": [], - "sortedRegulatoryFeatureConsequences": [] + "sorted_motif_feature_consequences": [], + "sorted_regulatory_feature_consequences": [] } } ] From 855671dcee5f2f0f286a4a4699a29f547b57ca39 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 17:08:23 -0400 Subject: [PATCH 054/369] misc test cleanup --- loading_pipeline/lib/misc/clickhouse_test.py | 60 ++++++------------- .../lib/test/fixtures/clickhouse_test.json | 4 +- 2 files changed, 19 insertions(+), 45 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index f2f7055f70..e723ba2887 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -318,7 +318,7 @@ def write_test_parquet(df: pd.DataFrame, parquet_path: str, schema=None): df = pd.DataFrame( { - 'key': [0, 3, 4], + 'key': [10, 3, 4], 'project_guid': [ 'project_d', 'project_d', @@ -526,16 +526,21 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): self.assertCountEqual( cursor.fetchall(), [ - ('project_a', 0, 'WES', 0, 1), + ('project_a', 10, 'WES', 0, 1), ('project_a', 1, 'WGS', 1, 0), ('project_a', 2, 'WGS', 0, 1), + ('project_a', 3, 'WES', 0, 0), ('project_a', 4, 'WES', 1, 0), ('project_a', 4, 'WGS', 0, 1), + ('project_b', 10, 'WES', 0, 0), ('project_b', 1, 'WES', 1, 0), + ('project_b', 2, 'WES', 0, 0), ('project_b', 3, 'WES', 0, 1), ('project_b', 4, 'WES', 0, 1), # project_gt_stats stages all projects, not just # those requested for loading. + ('project_c', 10, 'WES', 0, 0), + ('project_c', 3, 'WES', 0, 0), ('project_c', 4, 'WES', 0, 1), ('project_c', 5, 'WES', 0, 1), ], @@ -555,7 +560,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): self.assertCountEqual( cursor.fetchall(), [ - ('project_a', 0, 'WES', 0, 0), + ('project_a', 10, 'WES', 0, 0), ('project_a', 1, 'WGS', 1, 0), ('project_a', 2, 'WGS', 0, 1), ('project_a', 4, 'WES', 0, 0), @@ -583,7 +588,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): self.assertCountEqual( cursor.fetchall(), [ - ('project_a', 0, 'WES', 0, 0), + ('project_a', 10, 'WES', 0, 0), ('project_a', 1, 'WGS', 1, 0), ('project_a', 2, 'WGS', 0, 1), ('project_a', 4, 'WES', 0, 0), @@ -593,7 +598,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): ('project_b', 4, 'WES', 0, 1), ('project_c', 4, 'WES', 0, 1), ('project_c', 5, 'WES', 0, 1), - ('project_d', 0, 'WES', 0, 1), + ('project_d', 10, 'WES', 0, 1), ('project_d', 4, 'WES', 1, 0), ], ) @@ -622,7 +627,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): cursor.fetchall(), [ ( - 0, + 10, 'project_b', 'family_b1', 123456789, @@ -702,7 +707,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): 1, ), ( - 0, + 10, 'project_d', 'family_d1', 123456789, @@ -732,7 +737,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): 1, ), ( - 0, + 10, 'project_c', 'family_c1', 123456789, @@ -812,7 +817,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): self.assertEqual( cursor.fetchall(), [ - (0, 2, 0), + (10, 2, 0), (1, 1, 1), (2, 0, 2), (3, 2, 0), @@ -827,6 +832,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): return_value=[ClickhouseReferenceDataset.CLINVAR], ) def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_type): + self.maxDiff = None load_complete_run( ReferenceGenome.GRCh38, DatasetType.SNV_INDEL, @@ -846,7 +852,7 @@ def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_typ self.assertCountEqual( cursor.fetchall(), [ - ('project_d', 0, 'WES', 0, 1), + ('project_d', 10, 'WES', 0, 1), ('project_d', 4, 'WES', 1, 0), ], ) @@ -860,7 +866,7 @@ def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_typ self.assertCountEqual( cursor.fetchall(), [ - (0, 2, 0), + (10, 2, 0), (4, 1, 0), ], ) @@ -1104,38 +1110,6 @@ def test_rebuild_gt_stats(self): ) def test_repartitioned_entries_table(self, mock_for_reference_genome_dataset_type): with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f""" - REPLACE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` ( - `key` UInt32, - `project_guid` LowCardinality(String), - `family_guid` String, - `xpos` UInt64 CODEC(Delta(8), ZSTD(1)), - `sample_type` Enum8('WES' = 0, 'WGS' = 1), - `is_gnomad_gt_5_percent` Boolean, - `is_annotated_in_any_gene` Boolean DEFAULT length(geneId_ids) > 0, - `geneId_ids` Array(UInt32), - `calls` Array( - Tuple( - sampleId String, - gt Nullable(Enum8('REF' = 0, 'HET' = 1, 'HOM' = 2)), - ) - ), - `sign` Int8, - `n_partitions` UInt8 MATERIALIZED 2, - `partition_id` UInt8 MATERIALIZED farmHash64(family_guid) % n_partitions, - PROJECTION xpos_projection - ( - SELECT * - ORDER BY is_annotated_in_any_gene, xpos - ) - ) - ENGINE = CollapsingMergeTree(sign) - PARTITION BY (project_guid, partition_id) - ORDER BY (project_guid, family_guid, key) - SETTINGS deduplicate_merge_projection_mode = 'rebuild'; - """, - ) load_complete_run( ReferenceGenome.GRCh38, DatasetType.SNV_INDEL, diff --git a/loading_pipeline/lib/test/fixtures/clickhouse_test.json b/loading_pipeline/lib/test/fixtures/clickhouse_test.json index e30c37f235..b4e6cdbf1a 100644 --- a/loading_pipeline/lib/test/fixtures/clickhouse_test.json +++ b/loading_pipeline/lib/test/fixtures/clickhouse_test.json @@ -3,7 +3,7 @@ "model": "clickhouse_search.entriessnvindel", "pk": 1, "fields": { - "key": 0, + "key": 10, "project_guid": "project_a", "family_guid": "family_a1", "sample_type": "WES", @@ -105,7 +105,7 @@ "model": "clickhouse_search.entriessnvindel", "pk": 7, "fields": { - "key": 0, + "key": 10, "project_guid": "project_b", "family_guid": "family_b1", "sample_type": "WES", From 30c62930e7e6da50275a62a84e8762c0838e96df Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 10:35:06 -0400 Subject: [PATCH 055/369] test cleanup and fix --- loading_pipeline/lib/misc/clickhouse_test.py | 267 ++++++++++--------- 1 file changed, 144 insertions(+), 123 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index e723ba2887..dc5e5c42a1 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -432,15 +432,15 @@ def test_table_name_builder(self): ) def test_direct_insert_all_keys(self): + direct_insert_all_keys( + ClickHouseTable.VARIANT_DETAILS, + TableNameBuilder( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ) with connections['clickhouse_write'].cursor() as cursor: - direct_insert_all_keys( - ClickHouseTable.VARIANT_DETAILS, - TableNameBuilder( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ), - ) cursor.execute( f'SELECT key, variantId FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', ) @@ -456,15 +456,16 @@ def test_direct_insert_all_keys(self): ], ) - # ensure multiple calls are idempotent - direct_insert_all_keys( - ClickHouseTable.VARIANT_DETAILS, - TableNameBuilder( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ), - ) + # ensure multiple calls are idempotent + direct_insert_all_keys( + ClickHouseTable.VARIANT_DETAILS, + TableNameBuilder( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ) + with connections['clickhouse_write'].cursor() as cursor: cursor.execute( f'SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', ) @@ -477,35 +478,35 @@ def test_direct_insert_all_keys(self): ) def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): # Tests individual components of atomic_insert_entries, validating state after each step. - with connections['clickhouse_write'].cursor() as cursor: - table_name_builder = TableNameBuilder( - ReferenceGenome.GRCh38, + table_name_builder = TableNameBuilder( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ) + create_staging_tables( + table_name_builder, + ClickHouseTable.for_dataset_type_atomic_entries_update( DatasetType.SNV_INDEL, - TEST_RUN_ID, - ) - create_staging_tables( - table_name_builder, - ClickHouseTable.for_dataset_type_atomic_entries_update( - DatasetType.SNV_INDEL, - ), - ) - create_staging_materialized_views( - table_name_builder, - ClickHouseMaterializedView.for_dataset_type_atomic_entries_update( - DatasetType.SNV_INDEL, - ), - ) - stage_existing_project_partitions( - table_name_builder, - [ - 'project_a', - 'project_b', - 'project_d', # Partition does not exist already. - ], - ClickHouseTable.for_dataset_type_atomic_entries_update_project_partitioned( - DatasetType.SNV_INDEL, - ), - ) + ), + ) + create_staging_materialized_views( + table_name_builder, + ClickHouseMaterializedView.for_dataset_type_atomic_entries_update( + DatasetType.SNV_INDEL, + ), + ) + stage_existing_project_partitions( + table_name_builder, + [ + 'project_a', + 'project_b', + 'project_d', # Partition does not exist already. + ], + ClickHouseTable.for_dataset_type_atomic_entries_update_project_partitioned( + DatasetType.SNV_INDEL, + ), + ) + with connections['clickhouse_write'].cursor() as cursor: cursor.execute( f""" SELECT DISTINCT project_guid FROM {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/entries` @@ -539,16 +540,17 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): ('project_b', 4, 'WES', 0, 1), # project_gt_stats stages all projects, not just # those requested for loading. - ('project_c', 10, 'WES', 0, 0), + ('project_c', 0, 'WES', 0, 0), ('project_c', 3, 'WES', 0, 0), ('project_c', 4, 'WES', 0, 1), ('project_c', 5, 'WES', 0, 1), ], ) - delete_existing_families_from_staging_entries( - table_name_builder, - ['family_a1', 'family_a5', 'family_a6'], - ) + delete_existing_families_from_staging_entries( + table_name_builder, + ['family_a1', 'family_a5', 'family_a6'], + ) + with connections['clickhouse_write'].cursor() as cursor: cursor.execute( f""" SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) @@ -572,11 +574,13 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): ('project_c', 5, 'WES', 0, 1), ], ) - insert_new_entries(table_name_builder) - optimize_entries( - table_name_builder, - ['project_a', 'project_b', 'project_c'], - ) + + insert_new_entries(table_name_builder) + optimize_entries( + table_name_builder, + ['project_a', 'project_b', 'project_c'], + ) + with connections['clickhouse_write'].cursor() as cursor: cursor.execute( f""" SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) @@ -602,20 +606,22 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): ('project_d', 4, 'WES', 1, 0), ], ) - refresh_materialized_views( - table_name_builder, - ClickHouseMaterializedView.for_dataset_type_atomic_entries_update_refreshable( - DatasetType.SNV_INDEL, - ), - staging=True, - ) - replace_project_partitions( - table_name_builder, - ClickHouseTable.for_dataset_type_atomic_entries_update_project_partitioned( - DatasetType.SNV_INDEL, - ), - ['project_a', 'project_d'], - ) + + refresh_materialized_views( + table_name_builder, + ClickHouseMaterializedView.for_dataset_type_atomic_entries_update_refreshable( + DatasetType.SNV_INDEL, + ), + staging=True, + ) + replace_project_partitions( + table_name_builder, + ClickHouseTable.for_dataset_type_atomic_entries_update_project_partitioned( + DatasetType.SNV_INDEL, + ), + ['project_a', 'project_d'], + ) + with connections['clickhouse_write'].cursor() as cursor: cursor.execute( f""" SELECT COLUMNS('.*') EXCEPT(is_annotated_in_any_gene, is_gnomad_gt_5_percent) @@ -789,12 +795,14 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): cursor.fetchall(), [], ) - exchange_tables( - table_name_builder, - ClickHouseTable.for_dataset_type_atomic_entries_update_unpartitioned( - DatasetType.SNV_INDEL, - ), - ) + + exchange_tables( + table_name_builder, + ClickHouseTable.for_dataset_type_atomic_entries_update_unpartitioned( + DatasetType.SNV_INDEL, + ), + ) + with connections['clickhouse_write'].cursor() as cursor: cursor.execute( f""" SELECT * @@ -803,10 +811,12 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): """, ) self.assertCountEqual(cursor.fetchall(), []) - reload_dictionaries( - table_name_builder, - ClickHouseDictionary.for_dataset_type(DatasetType.SNV_INDEL), - ) + + reload_dictionaries( + table_name_builder, + ClickHouseDictionary.for_dataset_type(DatasetType.SNV_INDEL), + ) + with connections['clickhouse_write'].cursor() as cursor: cursor.execute( f""" SELECT * @@ -846,6 +856,7 @@ def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_typ SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + WHERE PROJECT_GUID = 'project_d' GROUP BY project_guid, key, sample_type """, ) @@ -971,6 +982,7 @@ def test_delete_families(self): SELECT project_guid, sum(het_samples), sum(hom_samples) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + FINAL GROUP BY project_guid """, ) @@ -978,13 +990,15 @@ def test_delete_families(self): cursor.fetchall(), [('project_a', 2, 3), ('project_c', 0, 2), ('project_b', 1, 2)], ) - refresh_materialized_views( - table_name_builder, - ClickHouseMaterializedView.for_dataset_type_atomic_entries_update_refreshable( - DatasetType.SNV_INDEL, - ), - staging=False, - ) + + refresh_materialized_views( + table_name_builder, + ClickHouseMaterializedView.for_dataset_type_atomic_entries_update_refreshable( + DatasetType.SNV_INDEL, + ), + staging=False, + ) + with connections['clickhouse_write'].cursor() as cursor: cursor.execute( f""" SELECT sum(ac_wes) @@ -993,18 +1007,21 @@ def test_delete_families(self): """, ) self.assertCountEqual(cursor.fetchall(), [(12,)]) - delete_family_guids( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - 'project_a', - ['family_a1', 'family_a2'], - ) + + delete_family_guids( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + 'project_a', + ['family_a1', 'family_a2'], + ) + with connections['clickhouse_write'].cursor() as cursor: cursor.execute( f""" SELECT project_guid, sum(het_samples), sum(hom_samples) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + FINAL GROUP BY project_guid """, ) @@ -1035,16 +1052,16 @@ def test_rebuild_gt_stats(self): DatasetType.SNV_INDEL, TEST_RUN_ID, ) + logged_query( # DROP the partition from the non-staging entries to as a non-mv-impacting change. + f""" + ALTER TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` + DROP PARTITION (%(project_guid)s, %(partition_id)s) + """, + # project_partitions_dict has no row for project_a, so n_partitions (and thus + # partition_id) defaults to 0. + {'project_guid': 'project_a', 'partition_id': 0}, + ) with connections['clickhouse_write'].cursor() as cursor: - logged_query( # DROP the partition from the non-staging entries to as a non-mv-impacting change. - f""" - ALTER TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` - DROP PARTITION (%(project_guid)s, %(partition_id)s) - """, - # project_partitions_dict has no row for project_a, so n_partitions (and thus - # partition_id) defaults to 0. - {'project_guid': 'project_a', 'partition_id': 0}, - ) cursor.execute( f""" SELECT project_guid, sum(het_samples), sum(hom_samples) @@ -1058,13 +1075,15 @@ def test_rebuild_gt_stats(self): cursor.fetchall(), [('project_a', 2, 3), ('project_b', 1, 2)], ) - refresh_materialized_views( - table_name_builder, - ClickHouseMaterializedView.for_dataset_type_atomic_entries_update_refreshable( - DatasetType.SNV_INDEL, - ), - staging=False, - ) + + refresh_materialized_views( + table_name_builder, + ClickHouseMaterializedView.for_dataset_type_atomic_entries_update_refreshable( + DatasetType.SNV_INDEL, + ), + staging=False, + ) + with connections['clickhouse_write'].cursor() as cursor: cursor.execute( f""" SELECT sum(ac_wes), sum(ac_wgs) @@ -1075,12 +1094,14 @@ def test_rebuild_gt_stats(self): # gt_stats has no project dimension (keyed globally by `key`), so project_c's rows # (sharing key values with project_a/b in the fixture) also contribute here. self.assertCountEqual(cursor.fetchall(), [(12, 5)]) - rebuild_gt_stats( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ['project_a', 'project_b'], - ) + + rebuild_gt_stats( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ['project_a', 'project_b'], + ) + with connections['clickhouse_write'].cursor() as cursor: cursor.execute( f""" SELECT project_guid, sum(het_samples), sum(hom_samples) @@ -1109,14 +1130,14 @@ def test_rebuild_gt_stats(self): return_value=[ClickhouseReferenceDataset.CLINVAR], ) def test_repartitioned_entries_table(self, mock_for_reference_genome_dataset_type): + load_complete_run( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ['project_d'], + ['family_d1', 'family_d2', 'family_d3'], + ) with connections['clickhouse_write'].cursor() as cursor: - load_complete_run( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ['project_d'], - ['family_d1', 'family_d2', 'family_d3'], - ) cursor.execute( f""" SELECT project_guid, sum(het_samples), sum(hom_samples) @@ -1127,5 +1148,5 @@ def test_repartitioned_entries_table(self, mock_for_reference_genome_dataset_typ ) self.assertCountEqual( cursor.fetchall(), - [('project_d', 1, 1)], + [('project_a', 2, 3), ('project_b', 1, 2), ('project_c', 0, 2), ('project_d', 1, 1)], ) From d87c0f824aa77f189d4afbe19d61d0b9f1d298be Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 10:36:45 -0400 Subject: [PATCH 056/369] ruff --- loading_pipeline/lib/misc/clickhouse_test.py | 7 ++- ...tition_clickhouse_grch38_snv_indel_test.py | 46 ++++++++++--------- 2 files changed, 31 insertions(+), 22 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index dc5e5c42a1..e09c58e962 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -1148,5 +1148,10 @@ def test_repartitioned_entries_table(self, mock_for_reference_genome_dataset_typ ) self.assertCountEqual( cursor.fetchall(), - [('project_a', 2, 3), ('project_b', 1, 2), ('project_c', 0, 2), ('project_d', 1, 1)], + [ + ('project_a', 2, 3), + ('project_b', 1, 2), + ('project_c', 0, 2), + ('project_d', 1, 1), + ], ) diff --git a/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py index 214d35b939..6a1800db6c 100644 --- a/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py +++ b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py @@ -1,33 +1,37 @@ -import unittest +from django.db import connections from loading_pipeline.lib.core.environment import Env -from loading_pipeline.lib.misc.clickhouse import get_clickhouse_client +from loading_pipeline.lib.test.clickhouse_schema_testcase import ( + ClickhouseSchemaTestCase, +) from loading_pipeline.ops.repartition_clickhouse_grch38_snv_indel import ( REPARTITION_DATABASE_NAME, main, ) -class RepartitionGRCh38SnvIndelTest(unittest.TestCase): +class RepartitionGRCh38SnvIndelTest(ClickhouseSchemaTestCase): def setUp(self): - client = get_clickhouse_client() - client.execute( - f""" - DROP DATABASE IF EXISTS {Env.CLICKHOUSE_DATABASE} - PARALLEL WITH - DROP DATABASE IF EXISTS {REPARTITION_DATABASE_NAME}; - """, - ) - client.execute( - f""" - CREATE DATABASE {Env.CLICKHOUSE_DATABASE} - PARALLEL WITH - CREATE DATABASE {REPARTITION_DATABASE_NAME}; - """, - ) - client.execute( - f""" - CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` ( + super().setUp() + with connections['clickhouse_write'].cursor() as cursor: + cursor.execute( + f""" + DROP DATABASE IF EXISTS {REPARTITION_DATABASE_NAME}; + """, + ) + cursor.execute( + f""" + CREATE DATABASE {REPARTITION_DATABASE_NAME}; + """, + ) + cursor.execute( + f""" + DROP TABLE IF EXISTS {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries`; + """, + ) + cursor.execute( + f""" + CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` ( `key` UInt32, `project_guid` LowCardinality(String), `family_guid` String, From 9669904af614cd50a9685f6294111f70a94561df Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 10:50:59 -0400 Subject: [PATCH 057/369] ruff --- .../ops/repartition_clickhouse_grch38_snv_indel_test.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py index 6a1800db6c..a8fa98f5cc 100644 --- a/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py +++ b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py @@ -50,7 +50,7 @@ def setUp(self): ORDER BY (project_guid, family_guid, key) SETTINGS deduplicate_merge_projection_mode = 'rebuild'; """, - ) + ) client.execute( f""" INSERT INTO {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` From f76faa96da077914fb85747e371bdaf16e8d7e25 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 10:54:30 -0400 Subject: [PATCH 058/369] intermediate test iter --- ...tition_clickhouse_grch38_snv_indel_test.py | 176 +++++++++--------- 1 file changed, 89 insertions(+), 87 deletions(-) diff --git a/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py index a8fa98f5cc..98ce37e10a 100644 --- a/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py +++ b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py @@ -1,3 +1,5 @@ +from typing import ClassVar + from django.db import connections from loading_pipeline.lib.core.environment import Env @@ -9,116 +11,116 @@ main, ) +_ENTRIES_TABLE = f'{Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries`' +_PRE_MIGRATION_ENTRIES_TABLE = ( + f'{Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries_pre_migration`' +) + class RepartitionGRCh38SnvIndelTest(ClickhouseSchemaTestCase): + # Fixture data for the properly migrated `GRCh38/SNV_INDEL/entries` table, + # loaded normally via the shared clickhouse schema/fixture setup. + fixtures: ClassVar = ['clickhouse_test'] + def setUp(self): super().setUp() with connections['clickhouse_write'].cursor() as cursor: cursor.execute( f""" - DROP DATABASE IF EXISTS {REPARTITION_DATABASE_NAME}; + SELECT key, project_guid, family_guid, is_annotated_in_any_gene, sign + FROM {_ENTRIES_TABLE} """, ) + self.entries_rows = cursor.fetchall() + + # This script exists to repartition entries tables that predate + # per-project subpartitioning, where `n_partitions` is a hardcoded + # value rather than sourced from `project_partitions_dict`. Swap + # the migrated entries table for one in that improper state, + # carrying over the fixture data, to exercise that behavior. cursor.execute( f""" - CREATE DATABASE {REPARTITION_DATABASE_NAME}; + CREATE TABLE {_PRE_MIGRATION_ENTRIES_TABLE} + ( + `key` UInt32, + `project_guid` LowCardinality(String), + `family_guid` String, + `is_annotated_in_any_gene` Boolean, + `sign` Int8, + `n_partitions` UInt8 MATERIALIZED 2, + `partition_id` UInt8 MATERIALIZED farmHash64(family_guid) % n_partitions, + PROJECTION xpos_projection + ( + SELECT * ORDER BY is_annotated_in_any_gene + ) + ) + ENGINE = CollapsingMergeTree(sign) + PARTITION BY project_guid + ORDER BY (project_guid, family_guid, key) + SETTINGS deduplicate_merge_projection_mode = 'rebuild' """, ) cursor.execute( - f""" - DROP TABLE IF EXISTS {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries`; - """, + f'INSERT INTO {_PRE_MIGRATION_ENTRIES_TABLE} VALUES', + self.entries_rows, ) cursor.execute( - f""" - CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` ( - `key` UInt32, - `project_guid` LowCardinality(String), - `family_guid` String, - `is_annotated_in_any_gene` Boolean, - `sign` Int8, - `n_partitions` UInt8 MATERIALIZED 2, - `partition_id` UInt8 MATERIALIZED farmHash64(family_guid) % n_partitions, - PROJECTION xpos_projection - ( - SELECT * - ORDER BY is_annotated_in_any_gene - ) + f'EXCHANGE TABLES {_ENTRIES_TABLE} AND {_PRE_MIGRATION_ENTRIES_TABLE}', ) - ENGINE = CollapsingMergeTree(sign) - PARTITION BY project_guid - ORDER BY (project_guid, family_guid, key) - SETTINGS deduplicate_merge_projection_mode = 'rebuild'; - """, + + def tearDown(self): + with connections['clickhouse_write'].cursor() as cursor: + cursor.execute( + f'EXCHANGE TABLES {_ENTRIES_TABLE} AND {_PRE_MIGRATION_ENTRIES_TABLE}', ) - client.execute( - f""" - INSERT INTO {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` - VALUES - (0, 'project_a', 'family_a1', 0, 1), - (1, 'project_a', 'family_a2', 0, 1), - (2, 'project_a', 'family_a3', 0, 1), - (0, 'project_b', 'family_b1', 0, 1), - (1, 'project_b', 'family_b2', 0, 1), - (2, 'project_b', 'family_b2', 0, 1), - (0, 'project_c', 'family_c1', 1, 1), - (3, 'project_c', 'family_c2', 1, 1), - """, - ) - client.execute( - f""" - CREATE DICTIONARY {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_partitions_dict` - ( - `project_guid` String, - `n_partitions` UInt8 + cursor.execute(f'DROP TABLE {_PRE_MIGRATION_ENTRIES_TABLE}') + cursor.execute(f'DROP DATABASE IF EXISTS {REPARTITION_DATABASE_NAME}') + super().tearDown() + + def _partition_id(self, family_guid: str) -> int: + with connections['clickhouse_write'].cursor() as cursor: + cursor.execute( + 'SELECT farmHash64(%(family_guid)s) %% 2', + {'family_guid': family_guid}, ) - PRIMARY KEY project_guid - SOURCE( - CLICKHOUSE( - USER '{Env.CLICKHOUSE_WRITER_USER}' PASSWORD '{Env.CLICKHOUSE_WRITER_PASSWORD}' - DB {Env.CLICKHOUSE_DATABASE} QUERY 'SELECT project_guid, 3 FROM `GRCh38/SNV_INDEL/entries`' - ) + return cursor.fetchone()[0] + + def _expected_rows(self, project_guids): + return [ + ( + key, + project_guid, + family_guid, + is_annotated_in_any_gene, + sign, + 2, + self._partition_id(family_guid), ) - LIFETIME(0) - LAYOUT(FLAT(MAX_ARRAY_SIZE 10000)) - """, - ) + for key, project_guid, family_guid, is_annotated_in_any_gene, sign in self.entries_rows + if not project_guids or project_guid in project_guids + ] def test_main_all_projects(self): - client = get_clickhouse_client() main(1, []) - res = client.execute( - f""" - SELECT *, n_partitions, partition_id FROM {REPARTITION_DATABASE_NAME}.`GRCh38/SNV_INDEL/repartitioned_entries` - """, - ) - self.assertCountEqual( - res, - [ - (3, 'project_c', 'family_c2', True, 1, 2, 1), - (0, 'project_b', 'family_b1', 0, 1, 2, 1), - (1, 'project_b', 'family_b2', 0, 1, 2, 1), - (2, 'project_b', 'family_b2', 0, 1, 2, 1), - (2, 'project_a', 'family_a3', 0, 1, 2, 0), - (0, 'project_a', 'family_a1', 0, 1, 2, 1), - (1, 'project_a', 'family_a2', 0, 1, 2, 1), - (0, 'project_c', 'family_c1', True, 1, 2, 0), - ], - ) + with connections['clickhouse_write'].cursor() as cursor: + cursor.execute( + f""" + SELECT *, n_partitions, partition_id + FROM {REPARTITION_DATABASE_NAME}.`GRCh38/SNV_INDEL/repartitioned_entries` + """, + ) + self.assertCountEqual(cursor.fetchall(), self._expected_rows([])) def test_main_one_project(self): - client = get_clickhouse_client() main(1, ['project_a']) - res = client.execute( - f""" - SELECT *, n_partitions, partition_id FROM {REPARTITION_DATABASE_NAME}.`GRCh38/SNV_INDEL/repartitioned_entries` - """, - ) - self.assertCountEqual( - res, - [ - (2, 'project_a', 'family_a3', 0, 1, 2, 0), - (0, 'project_a', 'family_a1', 0, 1, 2, 1), - (1, 'project_a', 'family_a2', 0, 1, 2, 1), - ], - ) + with connections['clickhouse_write'].cursor() as cursor: + cursor.execute( + f""" + SELECT *, n_partitions, partition_id + FROM {REPARTITION_DATABASE_NAME}.`GRCh38/SNV_INDEL/repartitioned_entries` + """, + ) + self.assertCountEqual( + cursor.fetchall(), + self._expected_rows(['project_a']), + ) From 6679bfdf2cb01ac556a5e573ea077653c95b31c0 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 11:08:17 -0400 Subject: [PATCH 059/369] test reqrite --- ...tition_clickhouse_grch38_snv_indel_test.py | 90 +++++++++---------- 1 file changed, 42 insertions(+), 48 deletions(-) diff --git a/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py index 98ce37e10a..3d4b237499 100644 --- a/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py +++ b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py @@ -1,5 +1,3 @@ -from typing import ClassVar - from django.db import connections from loading_pipeline.lib.core.environment import Env @@ -18,26 +16,10 @@ class RepartitionGRCh38SnvIndelTest(ClickhouseSchemaTestCase): - # Fixture data for the properly migrated `GRCh38/SNV_INDEL/entries` table, - # loaded normally via the shared clickhouse schema/fixture setup. - fixtures: ClassVar = ['clickhouse_test'] - - def setUp(self): - super().setUp() + @classmethod + def setUpClass(cls): + super().setUpClass() with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f""" - SELECT key, project_guid, family_guid, is_annotated_in_any_gene, sign - FROM {_ENTRIES_TABLE} - """, - ) - self.entries_rows = cursor.fetchall() - - # This script exists to repartition entries tables that predate - # per-project subpartitioning, where `n_partitions` is a hardcoded - # value rather than sourced from `project_partitions_dict`. Swap - # the migrated entries table for one in that improper state, - # carrying over the fixture data, to exercise that behavior. cursor.execute( f""" CREATE TABLE {_PRE_MIGRATION_ENTRIES_TABLE} @@ -60,45 +42,41 @@ def setUp(self): SETTINGS deduplicate_merge_projection_mode = 'rebuild' """, ) - cursor.execute( - f'INSERT INTO {_PRE_MIGRATION_ENTRIES_TABLE} VALUES', - self.entries_rows, - ) cursor.execute( f'EXCHANGE TABLES {_ENTRIES_TABLE} AND {_PRE_MIGRATION_ENTRIES_TABLE}', ) - def tearDown(self): + @classmethod + def tearDownClass(cls): with connections['clickhouse_write'].cursor() as cursor: cursor.execute( f'EXCHANGE TABLES {_ENTRIES_TABLE} AND {_PRE_MIGRATION_ENTRIES_TABLE}', ) cursor.execute(f'DROP TABLE {_PRE_MIGRATION_ENTRIES_TABLE}') - cursor.execute(f'DROP DATABASE IF EXISTS {REPARTITION_DATABASE_NAME}') - super().tearDown() + super().tearDownClass() - def _partition_id(self, family_guid: str) -> int: + def setUp(self): + super().setUp() with connections['clickhouse_write'].cursor() as cursor: cursor.execute( - 'SELECT farmHash64(%(family_guid)s) %% 2', - {'family_guid': family_guid}, + f""" + INSERT INTO {_ENTRIES_TABLE} + VALUES + (0, 'project_a', 'family_a1', 0, 1), + (1, 'project_a', 'family_a2', 0, 1), + (2, 'project_a', 'family_a3', 0, 1), + (0, 'project_b', 'family_b1', 0, 1), + (1, 'project_b', 'family_b2', 0, 1), + (2, 'project_b', 'family_b2', 0, 1), + (0, 'project_c', 'family_c1', 1, 1), + (3, 'project_c', 'family_c2', 1, 1), + """, ) - return cursor.fetchone()[0] - def _expected_rows(self, project_guids): - return [ - ( - key, - project_guid, - family_guid, - is_annotated_in_any_gene, - sign, - 2, - self._partition_id(family_guid), - ) - for key, project_guid, family_guid, is_annotated_in_any_gene, sign in self.entries_rows - if not project_guids or project_guid in project_guids - ] + def tearDown(self): + with connections['clickhouse_write'].cursor() as cursor: + cursor.execute(f'DROP DATABASE IF EXISTS {REPARTITION_DATABASE_NAME}') + super().tearDown() def test_main_all_projects(self): main(1, []) @@ -109,7 +87,19 @@ def test_main_all_projects(self): FROM {REPARTITION_DATABASE_NAME}.`GRCh38/SNV_INDEL/repartitioned_entries` """, ) - self.assertCountEqual(cursor.fetchall(), self._expected_rows([])) + self.assertCountEqual( + cursor.fetchall(), + [ + (3, 'project_c', 'family_c2', True, 1, 2, 1), + (0, 'project_b', 'family_b1', 0, 1, 2, 1), + (1, 'project_b', 'family_b2', 0, 1, 2, 1), + (2, 'project_b', 'family_b2', 0, 1, 2, 1), + (2, 'project_a', 'family_a3', 0, 1, 2, 0), + (0, 'project_a', 'family_a1', 0, 1, 2, 1), + (1, 'project_a', 'family_a2', 0, 1, 2, 1), + (0, 'project_c', 'family_c1', True, 1, 2, 0), + ], + ) def test_main_one_project(self): main(1, ['project_a']) @@ -122,5 +112,9 @@ def test_main_one_project(self): ) self.assertCountEqual( cursor.fetchall(), - self._expected_rows(['project_a']), + [ + (2, 'project_a', 'family_a3', 0, 1, 2, 0), + (0, 'project_a', 'family_a1', 0, 1, 2, 1), + (1, 'project_a', 'family_a2', 0, 1, 2, 1), + ], ) From f41919b301ab1d69776f6853ac85c7cdbc40ff77 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 11:08:27 -0400 Subject: [PATCH 060/369] remove plan --- ...CLICKHOUSE_PYTEST_DJANGO_REMAINING_PLAN.md | 44 ------------------- 1 file changed, 44 deletions(-) delete mode 100644 loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_REMAINING_PLAN.md diff --git a/loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_REMAINING_PLAN.md b/loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_REMAINING_PLAN.md deleted file mode 100644 index 6b5bab38a1..0000000000 --- a/loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_REMAINING_PLAN.md +++ /dev/null @@ -1,44 +0,0 @@ -# Plan: Finish migrating `repartition_clickhouse_grch38_snv_indel_test.py` to pytest-django - -## Context - -`loading_pipeline`'s ClickHouse tests were migrated to run against real `clickhouse_search` -Django migrations via pytest-django, with a shared `ClickhouseSchemaTestCase` base -(`lib/test/clickhouse_schema_testcase.py`) that owns the real schema DB's migrate/truncate -lifecycle. Every ClickHouse-touching test file adopted this base and switched from raw -`clickhouse_driver.Client` (`get_clickhouse_client()`) to -`connections['clickhouse_write'].cursor()` — except one file. - -## Remaining work - -`ops/repartition_clickhouse_grch38_snv_indel_test.py` (`RepartitionGRCh38SnvIndelTest`) still -predates the migration: - -- extends bare `unittest.TestCase`, not `ClickhouseSchemaTestCase` -- `setUp` manually runs `DROP DATABASE IF EXISTS {Env.CLICKHOUSE_DATABASE} PARALLEL WITH DROP - DATABASE IF EXISTS {REPARTITION_DATABASE_NAME}` then the matching `CREATE DATABASE ... PARALLEL - WITH ...` — `Env.CLICKHOUSE_DATABASE` is now owned by pytest-django's migrate lifecycle; - `REPARTITION_DATABASE_NAME` is the script's own scratch DB, not part of `clickhouse_search`'s - schema -- every SQL statement in `setUp` and both test methods runs via `get_clickhouse_client()` + - `client.execute(...)`, a raw `clickhouse_driver.Client` - -### Changes - -1. `RepartitionGRCh38SnvIndelTest` extends `ClickhouseSchemaTestCase` instead of - `unittest.TestCase`. -2. Drop the `DROP DATABASE IF EXISTS {Env.CLICKHOUSE_DATABASE}` / `CREATE DATABASE - {Env.CLICKHOUSE_DATABASE}` half of `setUp`'s `PARALLEL WITH` statements — the shared base now - handles that DB's schema/lifecycle. -3. Keep the `REPARTITION_DATABASE_NAME` drop/create in `setUp` (still not part of the real - schema), issued as its own statement. -4. Keep the synthetic `GRCh38/SNV_INDEL/entries` table DDL, `INSERT` seed rows, and - `project_partitions_dict` dictionary DDL as-is (intentionally bespoke, not real schema). -5. Execute everything in `setUp` and both test methods (`test_main_all_projects`, - `test_main_one_project`) via `connections['clickhouse_write'].cursor()` / - `cursor.execute(...)` / `cursor.fetchall()` instead of `get_clickhouse_client()` / - `client.execute(...)`. -6. Drop the now-unused `get_clickhouse_client` import. - -Reference `lib/misc/clickhouse_test.py` or `bin/pipeline_worker_test.py` for the established -pattern of extending `ClickhouseSchemaTestCase` and using the cursor. \ No newline at end of file From 23155a0b1d0a00d8dff80bf6ce3c59953b4f07e0 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 11:09:57 -0400 Subject: [PATCH 061/369] unit test fix iter --- loading_pipeline/lib/misc/clickhouse_test.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index e09c58e962..494e7042ef 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -477,6 +477,7 @@ def test_direct_insert_all_keys(self): return_value=[ClickhouseReferenceDataset.CLINVAR], ) def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): + self.maxDiff = None # Tests individual components of atomic_insert_entries, validating state after each step. table_name_builder = TableNameBuilder( ReferenceGenome.GRCh38, @@ -856,7 +857,7 @@ def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_typ SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` - WHERE PROJECT_GUID = 'project_d' + WHERE project_guid = 'project_d' GROUP BY project_guid, key, sample_type """, ) From a2d52dec16d642d4d848d60583169d4020b2314f Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 11:21:13 -0400 Subject: [PATCH 062/369] test fixes --- loading_pipeline/lib/misc/clickhouse_test.py | 5 ++++- .../ops/repartition_clickhouse_grch38_snv_indel_test.py | 2 ++ 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index 494e7042ef..dd098aef9e 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -522,6 +522,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) FROM {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/project_gt_stats` + FINAL GROUP BY project_guid, key, sample_type """, ) @@ -557,6 +558,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) FROM {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/project_gt_stats` + FINAL GROUP BY project_guid, key, sample_type """, ) @@ -587,6 +589,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) FROM {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/project_gt_stats` + FINAL GROUP BY project_guid, key, sample_type """, ) @@ -843,7 +846,6 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): return_value=[ClickhouseReferenceDataset.CLINVAR], ) def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_type): - self.maxDiff = None load_complete_run( ReferenceGenome.GRCh38, DatasetType.SNV_INDEL, @@ -866,6 +868,7 @@ def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_typ [ ('project_d', 10, 'WES', 0, 1), ('project_d', 4, 'WES', 1, 0), + ('project_d', 3, 'WES', 0, 0), ], ) cursor.execute( diff --git a/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py index 3d4b237499..60ee69e57d 100644 --- a/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py +++ b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py @@ -29,6 +29,8 @@ def setUpClass(cls): `family_guid` String, `is_annotated_in_any_gene` Boolean, `sign` Int8, + `sample_type` Enum8('WES' = 1, 'WGS' = 2) MATERIALIZED CAST(1, 'Enum8(\\'WES\\' = 1, \\'WGS\\' = 2)'), + `calls` Array(Tuple(sampleId String, gt Nullable(Enum8('REF' = 0, 'HET' = 1, 'HOM' = 2)))) MATERIALIZED CAST([], 'Array(Tuple(sampleId String, gt Nullable(Enum8(\\'REF\\' = 0, \\'HET\\' = 1, \\'HOM\\' = 2))))'), `n_partitions` UInt8 MATERIALIZED 2, `partition_id` UInt8 MATERIALIZED farmHash64(family_guid) % n_partitions, PROJECTION xpos_projection From cb4b101bc4a8f67744d90fad4f66afd9a673b76f Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 11:30:37 -0400 Subject: [PATCH 063/369] fix tests --- .github/workflows/pipeline-unit-tests.yml | 2 +- loading_pipeline/bin/pipeline_worker_test.py | 15 +++++-------- loading_pipeline/lib/misc/clickhouse_test.py | 23 ++++++++++++++------ 3 files changed, 23 insertions(+), 17 deletions(-) diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml index fa440a343d..71201beb8b 100644 --- a/.github/workflows/pipeline-unit-tests.yml +++ b/.github/workflows/pipeline-unit-tests.yml @@ -86,5 +86,5 @@ jobs: export CLICKHOUSE_OPTIMIZE_TABLE_WAIT_S=1 export PYSPARK_SUBMIT_ARGS='--driver-memory 8G pyspark-shell' export CLICKHOUSE_DATABASE=test - uv run --project loading_pipeline pytest --cov=loading_pipeline --cov-report=term-missing -vv loading_pipeline + uv run --project loading_pipeline pytest --cov=loading_pipeline --cov-report=term-missing loading_pipeline uv run --project loading_pipeline coverage report --omit '*test*' --fail-under=85 diff --git a/loading_pipeline/bin/pipeline_worker_test.py b/loading_pipeline/bin/pipeline_worker_test.py index a2e3db1e54..2ab2d5c641 100644 --- a/loading_pipeline/bin/pipeline_worker_test.py +++ b/loading_pipeline/bin/pipeline_worker_test.py @@ -105,32 +105,29 @@ def test_process_queue_integration_test( self.assertEqual(f.read(), '') cursor = connections['clickhouse_write'].cursor() - cursor.execute( + annotations_count = cursor.execute( f""" SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` """, - ) - annotations_count = cursor.fetchone()[0] + ).fetchone()[0] self.assertEqual(annotations_count, 30) - cursor.execute( + entries_count = cursor.execute( f""" SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` """, - ) - entries_count = cursor.fetchone()[0] + ).fetchone()[0] self.assertEqual(entries_count, 16) - cursor.execute( + ac_wgs = cursor.execute( f""" SELECT sum(ac_wgs) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` """, - ) - ac_wgs = cursor.fetchone()[0] + ).fetchone()[0] self.assertEqual(ac_wgs, 69) @patch('loading_pipeline.lib.misc.slack._safe_post_to_slack') diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index dd098aef9e..ce2eb13b75 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -565,14 +565,15 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): self.assertCountEqual( cursor.fetchall(), [ - ('project_a', 10, 'WES', 0, 0), ('project_a', 1, 'WGS', 1, 0), ('project_a', 2, 'WGS', 0, 1), - ('project_a', 4, 'WES', 0, 0), - ('project_a', 4, 'WGS', 0, 0), + ('project_b', 10, 'WES', 0, 0) ('project_b', 1, 'WES', 1, 0), + ('project_b', 2, 'WES', 0, 0) ('project_b', 3, 'WES', 0, 1), ('project_b', 4, 'WES', 0, 1), + ('project_c', 0, 'WES', 0, 0) + ('project_c', 3, 'WES', 0, 0) ('project_c', 4, 'WES', 0, 1), ('project_c', 5, 'WES', 0, 1), ], @@ -881,8 +882,12 @@ def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_typ self.assertCountEqual( cursor.fetchall(), [ - (10, 2, 0), - (4, 1, 0), + (1, 1, 1, 0, 0, 0, 0), + (2, 0, 2, 0, 0, 1, 0), + (3, 2, 0, 0, 1, 0, 0), + (4, 6, 2, 0, 2, 1, 0), + (5, 2, 0, 0, 1, 0, 0), + (10, 4, 0, 0, 2, 0, 0), ], ) cursor.execute( @@ -895,8 +900,12 @@ def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_typ self.assertCountEqual( cursor.fetchall(), [ - (0, 2, 0), - (4, 1, 0), + (1, 1, 1, 0, 0, 0, 0), + (2, 0, 2, 0, 0, 1, 0), + (3, 2, 0, 0, 1, 0, 0), + (4, 6, 2, 0, 2, 1, 0), + (5, 2, 0, 0, 1, 0, 0), + (10, 4, 0, 0, 2, 0, 0), ], ) cursor.execute( From b50ea2d70400551147afc92d7bf0e1f484dc63a7 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 11:33:39 -0400 Subject: [PATCH 064/369] ruff --- loading_pipeline/lib/misc/clickhouse_test.py | 8 ++++---- .../load_clickhouse_variants_tables_test.py | 15 ++++++--------- 2 files changed, 10 insertions(+), 13 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index ce2eb13b75..f97bbd151d 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -567,13 +567,13 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): [ ('project_a', 1, 'WGS', 1, 0), ('project_a', 2, 'WGS', 0, 1), - ('project_b', 10, 'WES', 0, 0) + ('project_b', 10, 'WES', 0, 0), ('project_b', 1, 'WES', 1, 0), - ('project_b', 2, 'WES', 0, 0) + ('project_b', 2, 'WES', 0, 0), ('project_b', 3, 'WES', 0, 1), ('project_b', 4, 'WES', 0, 1), - ('project_c', 0, 'WES', 0, 0) - ('project_c', 3, 'WES', 0, 0) + ('project_c', 0, 'WES', 0, 0), + ('project_c', 3, 'WES', 0, 0), ('project_c', 4, 'WES', 0, 1), ('project_c', 5, 'WES', 0, 1), ], diff --git a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py index f412e0fa48..2df35086bf 100644 --- a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py +++ b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py @@ -119,30 +119,27 @@ def test_write_variants_to_clickhouse( self.assertTrue(task.complete()) cursor = connections['clickhouse_write'].cursor() - cursor.execute( + variants_count = cursor.execute( f""" SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` """, - ) - variants_count = cursor.fetchone()[0] + ).fetchone()[0] self.assertEqual(variants_count, 2) - cursor.execute( + variant_details_count = cursor.execute( f""" SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details` """, - ) - variant_details_count = cursor.fetchone()[0] + ).fetchone()[0] self.assertEqual(variant_details_count, 2) - cursor.execute( + key_lookups_count = cursor.execute( f""" SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/key_lookup` """, - ) - key_lookups_count = cursor.fetchone()[0] + ).fetchone()[0] self.assertEqual(key_lookups_count, 2) From c56037ae7f38f4b963ae20aca36b2e78ff0dcf35 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 11:46:39 -0400 Subject: [PATCH 065/369] fix tests --- .github/workflows/pipeline-unit-tests.yml | 3 +- loading_pipeline/bin/pipeline_worker_test.py | 15 +++++---- loading_pipeline/lib/misc/clickhouse_test.py | 32 +++++++++++++++---- .../load_clickhouse_variants_tables_test.py | 15 +++++---- 4 files changed, 45 insertions(+), 20 deletions(-) diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml index 71201beb8b..1b989e6335 100644 --- a/.github/workflows/pipeline-unit-tests.yml +++ b/.github/workflows/pipeline-unit-tests.yml @@ -9,12 +9,13 @@ on: - master paths: - 'loading_pipeline/**' - - '.github/workflows/*pipeline-release.yaml' + - '.github/workflows/pipeline-*-release.yaml' pull_request: types: [opened, synchronize, reopened] paths: - 'loading_pipeline/**' - '.github/workflows/*pipeline*.yaml' + - 'clickhouse_search/migrations/*.py' permissions: contents: read diff --git a/loading_pipeline/bin/pipeline_worker_test.py b/loading_pipeline/bin/pipeline_worker_test.py index 2ab2d5c641..a2e3db1e54 100644 --- a/loading_pipeline/bin/pipeline_worker_test.py +++ b/loading_pipeline/bin/pipeline_worker_test.py @@ -105,29 +105,32 @@ def test_process_queue_integration_test( self.assertEqual(f.read(), '') cursor = connections['clickhouse_write'].cursor() - annotations_count = cursor.execute( + cursor.execute( f""" SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` """, - ).fetchone()[0] + ) + annotations_count = cursor.fetchone()[0] self.assertEqual(annotations_count, 30) - entries_count = cursor.execute( + cursor.execute( f""" SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` """, - ).fetchone()[0] + ) + entries_count = cursor.fetchone()[0] self.assertEqual(entries_count, 16) - ac_wgs = cursor.execute( + cursor.execute( f""" SELECT sum(ac_wgs) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` """, - ).fetchone()[0] + ) + ac_wgs = cursor.fetchone()[0] self.assertEqual(ac_wgs, 69) @patch('loading_pipeline.lib.misc.slack._safe_post_to_slack') diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index f97bbd151d..09cc3062bc 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -597,17 +597,19 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): self.assertCountEqual( cursor.fetchall(), [ - ('project_a', 10, 'WES', 0, 0), ('project_a', 1, 'WGS', 1, 0), ('project_a', 2, 'WGS', 0, 1), - ('project_a', 4, 'WES', 0, 0), - ('project_a', 4, 'WGS', 0, 0), + ('project_b', 10, 'WES', 0, 0), ('project_b', 1, 'WES', 1, 0), + ('project_b', 2, 'WES', 0, 0), ('project_b', 3, 'WES', 0, 1), ('project_b', 4, 'WES', 0, 1), + ('project_c', 0, 'WES', 0, 0), + ('project_c', 3, 'WES', 0, 0), ('project_c', 4, 'WES', 0, 1), ('project_c', 5, 'WES', 0, 1), ('project_d', 10, 'WES', 0, 1), + ('project_d', 3, 'WES', 0, 0), ('project_d', 4, 'WES', 1, 0), ], ) @@ -918,10 +920,10 @@ def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_typ self.assertCountEqual( cursor.fetchall(), [ - (10, '1-3-A-C'), - (11, '2-4-A-T'), - (12, 'Y-9-A-C'), - (13, 'M-2-C-G'), + (10, [], [], []), + (11, [], [], []), + (12, [], [], []), + (13, [], [], []), ], ) cursor.execute( @@ -931,6 +933,22 @@ def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_typ {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_disk` """, ) + self.assertCountEqual( + cursor.fetchall(), + [ + (10, [], [], []), + (11, [], [], []), + (12, [], [], []), + (13, [], [], []), + ], + ) + cursor.execute( + f""" + SELECT key, variantId + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_details` + """, + ) self.assertCountEqual( cursor.fetchall(), [ diff --git a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py index 2df35086bf..f412e0fa48 100644 --- a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py +++ b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py @@ -119,27 +119,30 @@ def test_write_variants_to_clickhouse( self.assertTrue(task.complete()) cursor = connections['clickhouse_write'].cursor() - variants_count = cursor.execute( + cursor.execute( f""" SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` """, - ).fetchone()[0] + ) + variants_count = cursor.fetchone()[0] self.assertEqual(variants_count, 2) - variant_details_count = cursor.execute( + cursor.execute( f""" SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details` """, - ).fetchone()[0] + ) + variant_details_count = cursor.fetchone()[0] self.assertEqual(variant_details_count, 2) - key_lookups_count = cursor.execute( + cursor.execute( f""" SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/key_lookup` """, - ).fetchone()[0] + ) + key_lookups_count = cursor.fetchone()[0] self.assertEqual(key_lookups_count, 2) From 0130bf176d35fea66e43ce725c562bab7c923a53 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 12:08:35 -0400 Subject: [PATCH 066/369] test cleanup --- loading_pipeline/lib/misc/clickhouse_test.py | 153 ++++++++++--------- 1 file changed, 79 insertions(+), 74 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index 09cc3062bc..a83f1d3c13 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -190,52 +190,6 @@ 'consequenceTerms': ['regulatory_region_ablation'], 'regulatoryFeatureId': 'ENSR00000123', } -VARIANT_DETAILS_ROWS = [ - { - 'key': 1, - 'variantId': '1-13-A-C', - 'liftedOverChrom': '1', - 'liftedOverPos': 13, - 'rsid': 'rs123', - 'CAID': 'CA123456', - 'transcripts': [_FULL_TRANSCRIPT], - 'sortedMotifFeatureConsequences': [_FULL_MOTIF_CONSEQUENCE], - 'sortedRegulatoryFeatureConsequences': [_FULL_REGULATORY_CONSEQUENCE], - }, - { - 'key': 2, - 'variantId': '2-14-A-T', - 'liftedOverChrom': None, - 'liftedOverPos': None, - 'rsid': None, - 'CAID': None, - 'transcripts': [], - 'sortedMotifFeatureConsequences': [], - 'sortedRegulatoryFeatureConsequences': [], - }, - { - 'key': 3, - 'variantId': 'Y-19-A-C', - 'liftedOverChrom': None, - 'liftedOverPos': None, - 'rsid': None, - 'CAID': None, - 'transcripts': [], - 'sortedMotifFeatureConsequences': [], - 'sortedRegulatoryFeatureConsequences': [], - }, - { - 'key': 4, - 'variantId': 'M-12-C-G', - 'liftedOverChrom': None, - 'liftedOverPos': None, - 'rsid': None, - 'CAID': None, - 'transcripts': [], - 'sortedMotifFeatureConsequences': [], - 'sortedRegulatoryFeatureConsequences': [], - }, -] class ClickhouseTest(MockedDatarootTestCase, ClickhouseSchemaTestCase): @@ -273,21 +227,41 @@ def write_test_parquet(df: pd.DataFrame, parquet_path: str, schema=None): ), ) - variant_details_table = pa.Table.from_pylist( - VARIANT_DETAILS_ROWS, - schema=VARIANT_DETAILS_SCHEMA, - ) - variant_details_path = new_variant_details_parquet_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_RUN_ID, + # Variant Details Parquet + df = pd.DataFrame( + { + 'key': [1, 2, 3, 4], + 'variantId': [ + '1-13-A-C', + '2-14-A-T', + 'Y-19-A-C', + 'M-12-C-G', + ], + 'transcripts': [[_FULL_TRANSCRIPT], [], [], []], + 'liftedOverChrom': ['1', None, None, None], + 'liftedOverPos': [13, None, None, None], + 'rsid': ['rs123', None, None, None], + 'CAID': ['CA123456', None, None, None], + 'sortedMotifFeatureConsequences': [[_FULL_MOTIF_CONSEQUENCE], [], [], []], + 'sortedRegulatoryFeatureConsequences': [ + [_FULL_REGULATORY_CONSEQUENCE], + [], + [], + [], + ], + }, ) - os.makedirs(variant_details_path) - pq.write_table( - variant_details_table, - os.path.join(variant_details_path, 'test.parquet'), + write_test_parquet( + df, + new_variant_details_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + VARIANT_DETAILS_SCHEMA, # TODO needed? ) + # New Variants parquet. df = pd.DataFrame( { 'key': [10, 11, 12, 13], @@ -316,6 +290,7 @@ def write_test_parquet(df: pd.DataFrame, parquet_path: str, schema=None): ), ) + # New Entries Parquet df = pd.DataFrame( { 'key': [10, 3, 4], @@ -643,151 +618,181 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): 10, 'project_b', 'family_b1', - 123456789, 'WES', + 123456789, [], [('sample_b4', 'REF')], 1, + 1, + 0, ), ( 1, 'project_b', 'family_b2', - 123456789, 'WES', + 123456789, [], [('sample_b5', 'HET')], 1, + 1, + 0, ), ( 2, 'project_b', 'family_b2', - 123456789, 'WES', + 123456789, [], [('sample_b5', 'REF')], 1, + 1, + 0, ), ( 3, 'project_b', 'family_b3', - 133456789, 'WES', + 133456789, [], [('sample_b6', 'HOM')], 1, + 1, + 0, ), ( 4, 'project_b', 'family_b3', - 133456789, 'WES', + 133456789, [], [('sample_b6', 'HOM')], 1, + 1, + 0, ), ( 1, 'project_a', 'family_a2', + 'WES', 123456789, - 'WGS', [], [('sample_a2', 'HET')], 1, + 1, + 0, ), ( 2, 'project_a', 'family_a3', - 133456789, 'WGS', + 133456789, [], [('sample_a3', 'HOM')], 1, + 1, + 0, ), ( 3, 'project_a', 'family_a4', - 133456789, 'WES', + 133456789, [], [('sample_a4', 'REF')], 1, + 1, + 0, ), ( 10, 'project_d', 'family_d1', - 123456789, 'WES', + 123456789, [], [('sample_d1', 'REF'), ('sample_d11', 'HOM')], 1, + 1, + 0, ), ( 3, 'project_d', 'family_d2', - 123456789, 'WES', + 123456789, [123, 12], [('sample_d2', 'REF')], 1, + 1, + 0, ), ( 4, 'project_d', 'family_d3', - 123456789, 'WES', + 123456789, [1], [('sample_d3', 'HET')], 1, + 1, + 0, ), ( 10, 'project_c', 'family_c1', - 123456789, 'WES', + 123456789, [1], [('sample_c7', 'REF')], 1, + 1, + 0, ), ( 3, 'project_c', 'family_c2', - 123456789, 'WES', + 123456789, [1], [('sample_c8', 'REF')], 1, + 1, + 0, ), ( 4, 'project_c', 'family_c3', - 133456789, 'WES', + 133456789, [1], [('sample_c9', 'HOM')], 1, + 1, + 0, ), ( 5, 'project_c', 'family_c4', - 133456789, 'WES', + 133456789, [1], [('sample_c9', 'HOM')], 1, + 1, + 0, ), ], ) @@ -946,7 +951,7 @@ def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_typ f""" SELECT key, variantId FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_details` + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details` """, ) self.assertCountEqual( From 45619f33e0107cf262c36229e5abeedcbc2de71d Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 12:17:46 -0400 Subject: [PATCH 067/369] fix tests --- loading_pipeline/lib/misc/clickhouse_test.py | 513 ++++++++++--------- 1 file changed, 261 insertions(+), 252 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index a83f1d3c13..d139cbaa18 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -452,7 +452,7 @@ def test_direct_insert_all_keys(self): return_value=[ClickhouseReferenceDataset.CLINVAR], ) def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): - self.maxDiff = None + self.maxDiff = None # TODO # Tests individual components of atomic_insert_entries, validating state after each step. table_name_builder = TableNameBuilder( ReferenceGenome.GRCh38, @@ -488,10 +488,12 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): SELECT DISTINCT project_guid FROM {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/entries` """, ) - self.assertCountEqual( - [p[0] for p in cursor.fetchall()], - ['project_a', 'project_b'], - ) + staged_projects = cursor.fetchall() + self.assertCountEqual( + [p[0] for p in staged_projects], + ['project_a', 'project_b'], + ) + with connections['clickhouse_write'].cursor() as cursor: cursor.execute( f""" SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) @@ -501,28 +503,29 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): GROUP BY project_guid, key, sample_type """, ) - self.assertCountEqual( - cursor.fetchall(), - [ - ('project_a', 10, 'WES', 0, 1), - ('project_a', 1, 'WGS', 1, 0), - ('project_a', 2, 'WGS', 0, 1), - ('project_a', 3, 'WES', 0, 0), - ('project_a', 4, 'WES', 1, 0), - ('project_a', 4, 'WGS', 0, 1), - ('project_b', 10, 'WES', 0, 0), - ('project_b', 1, 'WES', 1, 0), - ('project_b', 2, 'WES', 0, 0), - ('project_b', 3, 'WES', 0, 1), - ('project_b', 4, 'WES', 0, 1), - # project_gt_stats stages all projects, not just - # those requested for loading. - ('project_c', 0, 'WES', 0, 0), - ('project_c', 3, 'WES', 0, 0), - ('project_c', 4, 'WES', 0, 1), - ('project_c', 5, 'WES', 0, 1), - ], - ) + staged_project_gt_stats = cursor.fetchall() + self.assertCountEqual( + staged_project_gt_stats, + [ + ('project_a', 10, 'WES', 0, 1), + ('project_a', 1, 'WGS', 1, 0), + ('project_a', 2, 'WGS', 0, 1), + ('project_a', 3, 'WES', 0, 0), + ('project_a', 4, 'WES', 1, 0), + ('project_a', 4, 'WGS', 0, 1), + ('project_b', 10, 'WES', 0, 0), + ('project_b', 1, 'WES', 1, 0), + ('project_b', 2, 'WES', 0, 0), + ('project_b', 3, 'WES', 0, 1), + ('project_b', 4, 'WES', 0, 1), + # project_gt_stats stages all projects, not just + # those requested for loading. + ('project_c', 0, 'WES', 0, 0), + ('project_c', 3, 'WES', 0, 0), + ('project_c', 4, 'WES', 0, 1), + ('project_c', 5, 'WES', 0, 1), + ], + ) delete_existing_families_from_staging_entries( table_name_builder, ['family_a1', 'family_a5', 'family_a6'], @@ -537,22 +540,23 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): GROUP BY project_guid, key, sample_type """, ) - self.assertCountEqual( - cursor.fetchall(), - [ - ('project_a', 1, 'WGS', 1, 0), - ('project_a', 2, 'WGS', 0, 1), - ('project_b', 10, 'WES', 0, 0), - ('project_b', 1, 'WES', 1, 0), - ('project_b', 2, 'WES', 0, 0), - ('project_b', 3, 'WES', 0, 1), - ('project_b', 4, 'WES', 0, 1), - ('project_c', 0, 'WES', 0, 0), - ('project_c', 3, 'WES', 0, 0), - ('project_c', 4, 'WES', 0, 1), - ('project_c', 5, 'WES', 0, 1), - ], - ) + staged_project_gt_stats = cursor.fetchall() + self.assertCountEqual( + staged_project_gt_stats, + [ + ('project_a', 1, 'WGS', 1, 0), + ('project_a', 2, 'WGS', 0, 1), + ('project_b', 10, 'WES', 0, 0), + ('project_b', 1, 'WES', 1, 0), + ('project_b', 2, 'WES', 0, 0), + ('project_b', 3, 'WES', 0, 1), + ('project_b', 4, 'WES', 0, 1), + ('project_c', 0, 'WES', 0, 0), + ('project_c', 3, 'WES', 0, 0), + ('project_c', 4, 'WES', 0, 1), + ('project_c', 5, 'WES', 0, 1), + ], + ) insert_new_entries(table_name_builder) optimize_entries( @@ -569,25 +573,26 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): GROUP BY project_guid, key, sample_type """, ) - self.assertCountEqual( - cursor.fetchall(), - [ - ('project_a', 1, 'WGS', 1, 0), - ('project_a', 2, 'WGS', 0, 1), - ('project_b', 10, 'WES', 0, 0), - ('project_b', 1, 'WES', 1, 0), - ('project_b', 2, 'WES', 0, 0), - ('project_b', 3, 'WES', 0, 1), - ('project_b', 4, 'WES', 0, 1), - ('project_c', 0, 'WES', 0, 0), - ('project_c', 3, 'WES', 0, 0), - ('project_c', 4, 'WES', 0, 1), - ('project_c', 5, 'WES', 0, 1), - ('project_d', 10, 'WES', 0, 1), - ('project_d', 3, 'WES', 0, 0), - ('project_d', 4, 'WES', 1, 0), - ], - ) + staged_project_gt_stats = cursor.fetchall() + self.assertCountEqual( + staged_project_gt_stats, + [ + ('project_a', 1, 'WGS', 1, 0), + ('project_a', 2, 'WGS', 0, 1), + ('project_b', 10, 'WES', 0, 0), + ('project_b', 1, 'WES', 1, 0), + ('project_b', 2, 'WES', 0, 0), + ('project_b', 3, 'WES', 0, 1), + ('project_b', 4, 'WES', 0, 1), + ('project_c', 0, 'WES', 0, 0), + ('project_c', 3, 'WES', 0, 0), + ('project_c', 4, 'WES', 0, 1), + ('project_c', 5, 'WES', 0, 1), + ('project_d', 10, 'WES', 0, 1), + ('project_d', 3, 'WES', 0, 0), + ('project_d', 4, 'WES', 1, 0), + ], + ) refresh_materialized_views( table_name_builder, @@ -611,191 +616,193 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` """, ) - self.assertCountEqual( - cursor.fetchall(), - [ - ( - 10, - 'project_b', - 'family_b1', - 'WES', - 123456789, - [], - [('sample_b4', 'REF')], - 1, - 1, - 0, - ), - ( - 1, - 'project_b', - 'family_b2', - 'WES', - 123456789, - [], - [('sample_b5', 'HET')], - 1, - 1, - 0, - ), - ( - 2, - 'project_b', - 'family_b2', - 'WES', - 123456789, - [], - [('sample_b5', 'REF')], - 1, - 1, - 0, - ), - ( - 3, - 'project_b', - 'family_b3', - 'WES', - 133456789, - [], - [('sample_b6', 'HOM')], - 1, - 1, - 0, - ), - ( - 4, - 'project_b', - 'family_b3', - 'WES', - 133456789, - [], - [('sample_b6', 'HOM')], - 1, - 1, - 0, - ), - ( - 1, - 'project_a', - 'family_a2', - 'WES', - 123456789, - [], - [('sample_a2', 'HET')], - 1, - 1, - 0, - ), - ( - 2, - 'project_a', - 'family_a3', - 'WGS', - 133456789, - [], - [('sample_a3', 'HOM')], - 1, - 1, - 0, - ), - ( - 3, - 'project_a', - 'family_a4', - 'WES', - 133456789, - [], - [('sample_a4', 'REF')], - 1, - 1, - 0, - ), - ( - 10, - 'project_d', - 'family_d1', - 'WES', - 123456789, - [], - [('sample_d1', 'REF'), ('sample_d11', 'HOM')], - 1, - 1, - 0, - ), - ( - 3, - 'project_d', - 'family_d2', - 'WES', - 123456789, - [123, 12], - [('sample_d2', 'REF')], - 1, - 1, - 0, - ), - ( - 4, - 'project_d', - 'family_d3', - 'WES', - 123456789, - [1], - [('sample_d3', 'HET')], - 1, - 1, - 0, - ), - ( - 10, - 'project_c', - 'family_c1', - 'WES', - 123456789, - [1], - [('sample_c7', 'REF')], - 1, - 1, - 0, - ), - ( - 3, - 'project_c', - 'family_c2', - 'WES', - 123456789, - [1], - [('sample_c8', 'REF')], - 1, - 1, - 0, - ), - ( - 4, - 'project_c', - 'family_c3', - 'WES', - 133456789, - [1], - [('sample_c9', 'HOM')], - 1, - 1, - 0, - ), - ( - 5, - 'project_c', - 'family_c4', - 'WES', - 133456789, - [1], - [('sample_c9', 'HOM')], - 1, - 1, - 0, - ), - ], - ) + new_entries = cursor.fetchall() + self.assertCountEqual( + new_entries, + [ + ( + 10, + 'project_b', + 'family_b1', + 'WES', + 123456789, + [], + [('sample_b4', 'REF')], + 1, + 1, + 0, + ), + ( + 1, + 'project_b', + 'family_b2', + 'WES', + 123456789, + [], + [('sample_b5', 'HET')], + 1, + 1, + 0, + ), + ( + 2, + 'project_b', + 'family_b2', + 'WES', + 123456789, + [], + [('sample_b5', 'REF')], + 1, + 1, + 0, + ), + ( + 3, + 'project_b', + 'family_b3', + 'WES', + 133456789, + [], + [('sample_b6', 'HOM')], + 1, + 1, + 0, + ), + ( + 4, + 'project_b', + 'family_b3', + 'WES', + 133456789, + [], + [('sample_b6', 'HOM')], + 1, + 1, + 0, + ), + ( + 1, + 'project_a', + 'family_a2', + 'WES', + 123456789, + [], + [('sample_a2', 'HET')], + 1, + 1, + 0, + ), + ( + 2, + 'project_a', + 'family_a3', + 'WGS', + 133456789, + [], + [('sample_a3', 'HOM')], + 1, + 1, + 0, + ), + ( + 3, + 'project_a', + 'family_a4', + 'WES', + 133456789, + [], + [('sample_a4', 'REF')], + 1, + 1, + 0, + ), + ( + 10, + 'project_d', + 'family_d1', + 'WES', + 123456789, + [], + [('sample_d1', 'REF'), ('sample_d11', 'HOM')], + 1, + 1, + 0, + ), + ( + 3, + 'project_d', + 'family_d2', + 'WES', + 123456789, + [123, 12], + [('sample_d2', 'REF')], + 1, + 1, + 0, + ), + ( + 4, + 'project_d', + 'family_d3', + 'WES', + 123456789, + [1], + [('sample_d3', 'HET')], + 1, + 1, + 0, + ), + ( + 10, + 'project_c', + 'family_c1', + 'WES', + 123456789, + [1], + [('sample_c7', 'REF')], + 1, + 1, + 0, + ), + ( + 3, + 'project_c', + 'family_c2', + 'WES', + 123456789, + [1], + [('sample_c8', 'REF')], + 1, + 1, + 0, + ), + ( + 4, + 'project_c', + 'family_c3', + 'WES', + 133456789, + [1], + [('sample_c9', 'HOM')], + 1, + 1, + 0, + ), + ( + 5, + 'project_c', + 'family_c4', + 'WES', + 133456789, + [1], + [('sample_c9', 'HOM')], + 1, + 1, + 0, + ), + ], + ) + with connections['clickhouse_write'].cursor() as cursor: cursor.execute( f""" SELECT * @@ -803,10 +810,11 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` """, ) - self.assertCountEqual( - cursor.fetchall(), - [], - ) + existing_gt_stats = cursor.fetchall() + self.assertCountEqual( + existing_gt_stats, + [], + ) exchange_tables( table_name_builder, @@ -822,7 +830,8 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` """, ) - self.assertCountEqual(cursor.fetchall(), []) + new_gt_stats = cursor.fetchall() + self.assertCountEqual(new_gt_stats, []) reload_dictionaries( table_name_builder, From 2749ce4a567817769dc0be329291a115875c8d94 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 12:26:15 -0400 Subject: [PATCH 068/369] test cleanup --- loading_pipeline/lib/misc/clickhouse_test.py | 713 +++++++++---------- 1 file changed, 354 insertions(+), 359 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index d139cbaa18..9a4e8ecbf1 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -407,6 +407,7 @@ def test_table_name_builder(self): ) def test_direct_insert_all_keys(self): + cursor = connections['clickhouse_write'].cursor() direct_insert_all_keys( ClickHouseTable.VARIANT_DETAILS, TableNameBuilder( @@ -415,21 +416,20 @@ def test_direct_insert_all_keys(self): TEST_RUN_ID, ), ) - with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f'SELECT key, variantId FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', - ) - self.assertEqual( - cursor.fetchall(), - [ - (1, '1-13-A-C'), - (2, '2-14-A-T'), - (3, 'Y-19-A-C'), - (4, 'M-12-C-G'), - (7, 'c'), - (10, 'b'), - ], - ) + cursor.execute( + f'SELECT key, variantId FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', + ) + self.assertEqual( + cursor.fetchall(), + [ + (1, '1-13-A-C'), + (2, '2-14-A-T'), + (3, 'Y-19-A-C'), + (4, 'M-12-C-G'), + (7, 'c'), + (10, 'b'), + ], + ) # ensure multiple calls are idempotent direct_insert_all_keys( @@ -440,11 +440,10 @@ def test_direct_insert_all_keys(self): TEST_RUN_ID, ), ) - with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f'SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', - ) - self.assertEqual(cursor.fetchone()[0], 6) + cursor.execute( + f'SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', + ) + self.assertEqual(cursor.fetchone()[0], 6) @patch.object( ClickhouseReferenceDataset, @@ -453,6 +452,7 @@ def test_direct_insert_all_keys(self): ) def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): self.maxDiff = None # TODO + cursor = connections['clickhouse_write'].cursor() # Tests individual components of atomic_insert_entries, validating state after each step. table_name_builder = TableNameBuilder( ReferenceGenome.GRCh38, @@ -482,28 +482,26 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): DatasetType.SNV_INDEL, ), ) - with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f""" - SELECT DISTINCT project_guid FROM {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/entries` - """, - ) - staged_projects = cursor.fetchall() + cursor.execute( + f""" + SELECT DISTINCT project_guid FROM {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/entries` + """, + ) + staged_projects = cursor.fetchall() self.assertCountEqual( [p[0] for p in staged_projects], ['project_a', 'project_b'], ) - with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f""" - SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) - FROM - {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/project_gt_stats` - FINAL - GROUP BY project_guid, key, sample_type - """, - ) - staged_project_gt_stats = cursor.fetchall() + cursor.execute( + f""" + SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) + FROM + {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/project_gt_stats` + FINAL + GROUP BY project_guid, key, sample_type + """, + ) + staged_project_gt_stats = cursor.fetchall() self.assertCountEqual( staged_project_gt_stats, [ @@ -530,17 +528,16 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): table_name_builder, ['family_a1', 'family_a5', 'family_a6'], ) - with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f""" - SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) - FROM - {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/project_gt_stats` - FINAL - GROUP BY project_guid, key, sample_type - """, - ) - staged_project_gt_stats = cursor.fetchall() + cursor.execute( + f""" + SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) + FROM + {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/project_gt_stats` + FINAL + GROUP BY project_guid, key, sample_type + """, + ) + staged_project_gt_stats = cursor.fetchall() self.assertCountEqual( staged_project_gt_stats, [ @@ -563,17 +560,16 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): table_name_builder, ['project_a', 'project_b', 'project_c'], ) - with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f""" - SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) - FROM - {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/project_gt_stats` - FINAL - GROUP BY project_guid, key, sample_type - """, - ) - staged_project_gt_stats = cursor.fetchall() + cursor.execute( + f""" + SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) + FROM + {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/project_gt_stats` + FINAL + GROUP BY project_guid, key, sample_type + """, + ) + staged_project_gt_stats = cursor.fetchall() self.assertCountEqual( staged_project_gt_stats, [ @@ -608,15 +604,14 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): ), ['project_a', 'project_d'], ) - with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f""" - SELECT COLUMNS('.*') EXCEPT(is_annotated_in_any_gene, is_gnomad_gt_5_percent) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` - """, - ) - new_entries = cursor.fetchall() + cursor.execute( + f""" + SELECT COLUMNS('.*') EXCEPT(is_annotated_in_any_gene, is_gnomad_gt_5_percent) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` + """, + ) + new_entries = cursor.fetchall() self.assertCountEqual( new_entries, [ @@ -802,15 +797,14 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): ), ], ) - with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f""" - SELECT * - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` - """, - ) - existing_gt_stats = cursor.fetchall() + cursor.execute( + f""" + SELECT * + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` + """, + ) + existing_gt_stats = cursor.fetchall() self.assertCountEqual( existing_gt_stats, [], @@ -822,40 +816,39 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): DatasetType.SNV_INDEL, ), ) - with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f""" - SELECT * - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` - """, - ) - new_gt_stats = cursor.fetchall() + cursor.execute( + f""" + SELECT * + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` + """, + ) + new_gt_stats = cursor.fetchall() self.assertCountEqual(new_gt_stats, []) reload_dictionaries( table_name_builder, ClickHouseDictionary.for_dataset_type(DatasetType.SNV_INDEL), ) - with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f""" - SELECT * - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` - """, - ) - self.assertEqual( - cursor.fetchall(), - [ - (10, 2, 0), - (1, 1, 1), - (2, 0, 2), - (3, 2, 0), - (4, 5, 0), - (5, 2, 0), - ], - ) + cursor.execute( + f""" + SELECT * + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` + """, + ) + new_gt_stats_post_reload = cursor.fetchall() + self.assertEqual( + new_gt_stats_post_reload, + [ + (10, 2, 0), + (1, 1, 1), + (2, 0, 2), + (3, 2, 0), + (4, 5, 0), + (5, 2, 0), + ], + ) @patch.object( ClickhouseReferenceDataset, @@ -863,6 +856,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): return_value=[ClickhouseReferenceDataset.CLINVAR], ) def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_type): + cursor = connections['clickhouse_write'].cursor() load_complete_run( ReferenceGenome.GRCh38, DatasetType.SNV_INDEL, @@ -870,110 +864,116 @@ def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_typ ['project_d'], ['family_d1', 'family_d2'], ) - with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f""" - SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` - WHERE project_guid = 'project_d' - GROUP BY project_guid, key, sample_type - """, - ) - self.assertCountEqual( - cursor.fetchall(), - [ - ('project_d', 10, 'WES', 0, 1), - ('project_d', 4, 'WES', 1, 0), - ('project_d', 3, 'WES', 0, 0), - ], - ) - cursor.execute( - f""" - SELECT * - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` - """, - ) - self.assertCountEqual( - cursor.fetchall(), - [ - (1, 1, 1, 0, 0, 0, 0), - (2, 0, 2, 0, 0, 1, 0), - (3, 2, 0, 0, 1, 0, 0), - (4, 6, 2, 0, 2, 1, 0), - (5, 2, 0, 0, 1, 0, 0), - (10, 4, 0, 0, 2, 0, 0), - ], - ) - cursor.execute( - f""" - SELECT * - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` - """, - ) - self.assertCountEqual( - cursor.fetchall(), - [ - (1, 1, 1, 0, 0, 0, 0), - (2, 0, 2, 0, 0, 1, 0), - (3, 2, 0, 0, 1, 0, 0), - (4, 6, 2, 0, 2, 1, 0), - (5, 2, 0, 0, 1, 0, 0), - (10, 4, 0, 0, 2, 0, 0), - ], - ) - cursor.execute( - f""" - SELECT * - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` - """, - ) - self.assertCountEqual( - cursor.fetchall(), - [ - (10, [], [], []), - (11, [], [], []), - (12, [], [], []), - (13, [], [], []), - ], - ) - cursor.execute( - f""" - SELECT * - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_disk` - """, - ) - self.assertCountEqual( - cursor.fetchall(), - [ - (10, [], [], []), - (11, [], [], []), - (12, [], [], []), - (13, [], [], []), - ], - ) - cursor.execute( - f""" - SELECT key, variantId - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details` - """, - ) - self.assertCountEqual( - cursor.fetchall(), - [ - (10, '1-3-A-C'), - (11, '2-4-A-T'), - (12, 'Y-9-A-C'), - (13, 'M-2-C-G'), - ], - ) + cursor.execute( + f""" + SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + WHERE project_guid = 'project_d' + GROUP BY project_guid, key, sample_type + """, + ) + project_gt_stats = cursor.fetchall() + self.assertCountEqual( + project_gt_stats, + [ + ('project_d', 10, 'WES', 0, 1), + ('project_d', 4, 'WES', 1, 0), + ('project_d', 3, 'WES', 0, 0), + ], + ) + cursor.execute( + f""" + SELECT * + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` + """, + ) + gt_stats = cursor.fetchall() + self.assertCountEqual( + gt_stats, + [ + (1, 1, 1, 0, 0, 0, 0), + (2, 0, 2, 0, 0, 1, 0), + (3, 2, 0, 0, 1, 0, 0), + (4, 6, 2, 0, 2, 1, 0), + (5, 2, 0, 0, 1, 0, 0), + (10, 4, 0, 0, 2, 0, 0), + ], + ) + cursor.execute( + f""" + SELECT * + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` + """, + ) + gt_stats_dict = cursor.fetchall() + self.assertCountEqual( + gt_stats_dict, + [ + (1, 1, 1, 0, 0, 0, 0), + (2, 0, 2, 0, 0, 1, 0), + (3, 2, 0, 0, 1, 0, 0), + (4, 6, 2, 0, 2, 1, 0), + (5, 2, 0, 0, 1, 0, 0), + (10, 4, 0, 0, 2, 0, 0), + ], + ) + cursor.execute( + f""" + SELECT * + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` + """, + ) + variants_memory = cursor.fetchall() + self.assertCountEqual( + variants_memory, + [ + (10, [], [], []), + (11, [], [], []), + (12, [], [], []), + (13, [], [], []), + ], + ) + cursor.execute( + f""" + SELECT * + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_disk` + """, + ) + variants_disk = cursor.fetchall() + self.assertCountEqual( + variants_disk, + [ + (10, [], [], []), + (11, [], [], []), + (12, [], [], []), + (13, [], [], []), + ], + ) + cursor.execute( + f""" + SELECT key, variantId + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details` + """, + ) + variants_details = cursor.fetchall() + self.assertCountEqual( + variants_details, + [ + (10, '1-3-A-C'), + (11, '2-4-A-T'), + (12, 'Y-9-A-C'), + (13, 'M-2-C-G'), + ], + ) def test_load_complete_gcnv(self): + cursor = connections['clickhouse_write'].cursor() load_complete_run( ReferenceGenome.GRCh38, DatasetType.GCNV, @@ -981,60 +981,59 @@ def test_load_complete_gcnv(self): ['project_d'], ['family_d1', 'family_d2'], ) - with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f""" - SELECT COUNT(*) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/variants_memory` - """, - ) - self.assertEqual(cursor.fetchone()[0], 4) - cursor.execute( - f""" - SELECT COUNT(*) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/variants_disk` - """, - ) - self.assertEqual(cursor.fetchone()[0], 4) - cursor.execute( - f""" - SELECT COUNT(*) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/key_lookup` - """, - ) - self.assertEqual(cursor.fetchone()[0], 4) - cursor.execute( - f""" - SELECT COUNT(*) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/entries` - """, - ) - self.assertEqual(cursor.fetchone()[0], 3) + cursor.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/variants_memory` + """, + ) + self.assertEqual(cursor.fetchone()[0], 4) + cursor.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/variants_disk` + """, + ) + self.assertEqual(cursor.fetchone()[0], 4) + cursor.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/key_lookup` + """, + ) + self.assertEqual(cursor.fetchone()[0], 4) + cursor.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/entries` + """, + ) + self.assertEqual(cursor.fetchone()[0], 3) def test_delete_families(self): + cursor = connections['clickhouse_write'].cursor() table_name_builder = TableNameBuilder( ReferenceGenome.GRCh38, DatasetType.SNV_INDEL, TEST_RUN_ID, ) - with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f""" - SELECT project_guid, sum(het_samples), sum(hom_samples) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` - FINAL - GROUP BY project_guid - """, - ) - self.assertCountEqual( - cursor.fetchall(), - [('project_a', 2, 3), ('project_c', 0, 2), ('project_b', 1, 2)], - ) + cursor.execute( + f""" + SELECT project_guid, sum(het_samples), sum(hom_samples) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + FINAL + GROUP BY project_guid + """, + ) + self.assertCountEqual( + cursor.fetchall(), + [('project_a', 2, 3), ('project_c', 0, 2), ('project_b', 1, 2)], + ) refresh_materialized_views( table_name_builder, @@ -1043,15 +1042,14 @@ def test_delete_families(self): ), staging=False, ) - with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f""" - SELECT sum(ac_wes) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` - """, - ) - self.assertCountEqual(cursor.fetchall(), [(12,)]) + cursor.execute( + f""" + SELECT sum(ac_wes) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` + """, + ) + self.assertCountEqual(cursor.fetchall(), [(12,)]) delete_family_guids( ReferenceGenome.GRCh38, @@ -1060,38 +1058,38 @@ def test_delete_families(self): 'project_a', ['family_a1', 'family_a2'], ) - with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f""" - SELECT project_guid, sum(het_samples), sum(hom_samples) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` - FINAL - GROUP BY project_guid - """, - ) - self.assertCountEqual( - cursor.fetchall(), - [('project_a', 1, 2), ('project_c', 0, 2), ('project_b', 1, 2)], - ) - cursor.execute( - f""" - SELECT sum(ac_wes) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` - """, - ) - self.assertCountEqual(cursor.fetchall(), [(10,)]) - cursor.execute( - f""" - SELECT sum(ac_wes) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` - """, - ) - self.assertCountEqual(cursor.fetchall(), [(10,)]) + cursor.execute( + f""" + SELECT project_guid, sum(het_samples), sum(hom_samples) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + FINAL + GROUP BY project_guid + """, + ) + self.assertCountEqual( + cursor.fetchall(), + [('project_a', 1, 2), ('project_c', 0, 2), ('project_b', 1, 2)], + ) + cursor.execute( + f""" + SELECT sum(ac_wes) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` + """, + ) + self.assertCountEqual(cursor.fetchall(), [(10,)]) + cursor.execute( + f""" + SELECT sum(ac_wes) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` + """, + ) + self.assertCountEqual(cursor.fetchall(), [(10,)]) def test_rebuild_gt_stats(self): + cursor = connections['clickhouse_write'].cursor() table_name_builder = TableNameBuilder( ReferenceGenome.GRCh38, DatasetType.SNV_INDEL, @@ -1106,20 +1104,19 @@ def test_rebuild_gt_stats(self): # partition_id) defaults to 0. {'project_guid': 'project_a', 'partition_id': 0}, ) - with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f""" - SELECT project_guid, sum(het_samples), sum(hom_samples) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` - WHERE project_guid IN ('project_a', 'project_b') - GROUP BY project_guid - """, - ) - self.assertCountEqual( - cursor.fetchall(), - [('project_a', 2, 3), ('project_b', 1, 2)], - ) + cursor.execute( + f""" + SELECT project_guid, sum(het_samples), sum(hom_samples) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + WHERE project_guid IN ('project_a', 'project_b') + GROUP BY project_guid + """, + ) + self.assertCountEqual( + cursor.fetchall(), + [('project_a', 2, 3), ('project_b', 1, 2)], + ) refresh_materialized_views( table_name_builder, @@ -1128,17 +1125,16 @@ def test_rebuild_gt_stats(self): ), staging=False, ) - with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f""" - SELECT sum(ac_wes), sum(ac_wgs) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` - """, - ) - # gt_stats has no project dimension (keyed globally by `key`), so project_c's rows - # (sharing key values with project_a/b in the fixture) also contribute here. - self.assertCountEqual(cursor.fetchall(), [(12, 5)]) + cursor.execute( + f""" + SELECT sum(ac_wes), sum(ac_wgs) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` + """, + ) + # gt_stats has no project dimension (keyed globally by `key`), so project_c's rows + # (sharing key values with project_a/b in the fixture) also contribute here. + self.assertCountEqual(cursor.fetchall(), [(12, 5)]) rebuild_gt_stats( ReferenceGenome.GRCh38, @@ -1146,28 +1142,27 @@ def test_rebuild_gt_stats(self): TEST_RUN_ID, ['project_a', 'project_b'], ) - with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f""" - SELECT project_guid, sum(het_samples), sum(hom_samples) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` - WHERE project_guid IN ('project_a', 'project_b') - GROUP BY project_guid - """, - ) - self.assertCountEqual( - cursor.fetchall(), - [('project_b', 1, 2)], - ) - cursor.execute( - f""" - SELECT sum(ac_wes), sum(ac_wgs) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` - """, - ) - self.assertCountEqual(cursor.fetchall(), [(9, 0)]) + cursor.execute( + f""" + SELECT project_guid, sum(het_samples), sum(hom_samples) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + WHERE project_guid IN ('project_a', 'project_b') + GROUP BY project_guid + """, + ) + self.assertCountEqual( + cursor.fetchall(), + [('project_b', 1, 2)], + ) + cursor.execute( + f""" + SELECT sum(ac_wes), sum(ac_wgs) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` + """, + ) + self.assertCountEqual(cursor.fetchall(), [(9, 0)]) @patch.object( ClickhouseReferenceDataset, @@ -1175,6 +1170,7 @@ def test_rebuild_gt_stats(self): return_value=[ClickhouseReferenceDataset.CLINVAR], ) def test_repartitioned_entries_table(self, mock_for_reference_genome_dataset_type): + cursor = connections['clickhouse_write'].cursor() load_complete_run( ReferenceGenome.GRCh38, DatasetType.SNV_INDEL, @@ -1182,21 +1178,20 @@ def test_repartitioned_entries_table(self, mock_for_reference_genome_dataset_typ ['project_d'], ['family_d1', 'family_d2', 'family_d3'], ) - with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f""" - SELECT project_guid, sum(het_samples), sum(hom_samples) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` - GROUP BY project_guid - """, - ) - self.assertCountEqual( - cursor.fetchall(), - [ - ('project_a', 2, 3), - ('project_b', 1, 2), - ('project_c', 0, 2), - ('project_d', 1, 1), - ], - ) + cursor.execute( + f""" + SELECT project_guid, sum(het_samples), sum(hom_samples) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + GROUP BY project_guid + """, + ) + self.assertCountEqual( + cursor.fetchall(), + [ + ('project_a', 2, 3), + ('project_b', 1, 2), + ('project_c', 0, 2), + ('project_d', 1, 1), + ], + ) From 56af991d8b8e47ba5255f7a7fd0b9c432eb2b065 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 12:31:01 -0400 Subject: [PATCH 069/369] test cleanup --- loading_pipeline/lib/misc/clickhouse_test.py | 22 ++++++++++++-------- 1 file changed, 13 insertions(+), 9 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index 9a4e8ecbf1..4661646101 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -242,7 +242,12 @@ def write_test_parquet(df: pd.DataFrame, parquet_path: str, schema=None): 'liftedOverPos': [13, None, None, None], 'rsid': ['rs123', None, None, None], 'CAID': ['CA123456', None, None, None], - 'sortedMotifFeatureConsequences': [[_FULL_MOTIF_CONSEQUENCE], [], [], []], + 'sortedMotifFeatureConsequences': [ + [_FULL_MOTIF_CONSEQUENCE], + [], + [], + [], + ], 'sortedRegulatoryFeatureConsequences': [ [_FULL_REGULATORY_CONSEQUENCE], [], @@ -419,8 +424,9 @@ def test_direct_insert_all_keys(self): cursor.execute( f'SELECT key, variantId FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', ) + ret = cursor.fetchall() self.assertEqual( - cursor.fetchall(), + ret, [ (1, '1-13-A-C'), (2, '2-14-A-T'), @@ -443,7 +449,8 @@ def test_direct_insert_all_keys(self): cursor.execute( f'SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', ) - self.assertEqual(cursor.fetchone()[0], 6) + ret = cursor.fetchone() + self.assertEqual(ret[0], 6) @patch.object( ClickhouseReferenceDataset, @@ -451,9 +458,9 @@ def test_direct_insert_all_keys(self): return_value=[ClickhouseReferenceDataset.CLINVAR], ) def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): - self.maxDiff = None # TODO - cursor = connections['clickhouse_write'].cursor() + self.maxDiff = None # TODO # Tests individual components of atomic_insert_entries, validating state after each step. + cursor = connections['clickhouse_write'].cursor() table_name_builder = TableNameBuilder( ReferenceGenome.GRCh38, DatasetType.SNV_INDEL, @@ -554,7 +561,6 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): ('project_c', 5, 'WES', 0, 1), ], ) - insert_new_entries(table_name_builder) optimize_entries( table_name_builder, @@ -589,7 +595,6 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): ('project_d', 4, 'WES', 1, 0), ], ) - refresh_materialized_views( table_name_builder, ClickHouseMaterializedView.for_dataset_type_atomic_entries_update_refreshable( @@ -679,7 +684,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): 1, 'project_a', 'family_a2', - 'WES', + 'WGS', 123456789, [], [('sample_a2', 'HET')], @@ -809,7 +814,6 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): existing_gt_stats, [], ) - exchange_tables( table_name_builder, ClickHouseTable.for_dataset_type_atomic_entries_update_unpartitioned( From 7508dd2db22e4a8f031db5203e75cfa80d0991da Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 12:43:12 -0400 Subject: [PATCH 070/369] fix tests --- loading_pipeline/lib/misc/clickhouse_test.py | 111 +++++++++++-------- 1 file changed, 66 insertions(+), 45 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index 4661646101..cd23603e09 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -627,7 +627,8 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): 'WES', 123456789, [], - [('sample_b4', 'REF')], + [], + [('sample_b4', 'REF', None, None, None)], 1, 1, 0, @@ -639,7 +640,8 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): 'WES', 123456789, [], - [('sample_b5', 'HET')], + [], + [('sample_b5', 'HET', None, None, None)], 1, 1, 0, @@ -651,7 +653,8 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): 'WES', 123456789, [], - [('sample_b5', 'REF')], + [], + [('sample_b5', 'REF', None, None, None)], 1, 1, 0, @@ -663,7 +666,8 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): 'WES', 133456789, [], - [('sample_b6', 'HOM')], + [], + [('sample_b6', 'HOM', None, None, None)], 1, 1, 0, @@ -675,7 +679,8 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): 'WES', 133456789, [], - [('sample_b6', 'HOM')], + [], + [('sample_b6', 'HOM', None, None, None)], 1, 1, 0, @@ -687,7 +692,8 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): 'WGS', 123456789, [], - [('sample_a2', 'HET')], + [], + [('sample_a2', 'HET', None, None, None)], 1, 1, 0, @@ -699,7 +705,8 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): 'WGS', 133456789, [], - [('sample_a3', 'HOM')], + [], + [('sample_a3', 'HOM', None, None, None)], 1, 1, 0, @@ -711,7 +718,8 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): 'WES', 133456789, [], - [('sample_a4', 'REF')], + [], + [('sample_a4', 'REF', None, None, None)], 1, 1, 0, @@ -723,7 +731,8 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): 'WES', 123456789, [], - [('sample_d1', 'REF'), ('sample_d11', 'HOM')], + [], + [('sample_d1', 'REF', None, None, None), ('sample_d11', 'HOM', None, None, None)], 1, 1, 0, @@ -735,7 +744,8 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): 'WES', 123456789, [123, 12], - [('sample_d2', 'REF')], + [], + [('sample_d2', 'REF', None, None, None)], 1, 1, 0, @@ -747,7 +757,8 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): 'WES', 123456789, [1], - [('sample_d3', 'HET')], + [], + [('sample_d3', 'HET', None, None, None)], 1, 1, 0, @@ -759,7 +770,8 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): 'WES', 123456789, [1], - [('sample_c7', 'REF')], + [], + [('sample_c7', 'REF', None, None, None)], 1, 1, 0, @@ -771,7 +783,8 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): 'WES', 123456789, [1], - [('sample_c8', 'REF')], + [], + [('sample_c8', 'REF', None, None, None)], 1, 1, 0, @@ -783,7 +796,8 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): 'WES', 133456789, [1], - [('sample_c9', 'HOM')], + [], + [('sample_c9', 'HOM', None, None, None)], 1, 1, 0, @@ -795,7 +809,8 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): 'WES', 133456789, [1], - [('sample_c9', 'HOM')], + [], + [('sample_c9', 'HOM', None, None, None)], 1, 1, 0, @@ -829,7 +844,6 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): ) new_gt_stats = cursor.fetchall() self.assertCountEqual(new_gt_stats, []) - reload_dictionaries( table_name_builder, ClickHouseDictionary.for_dataset_type(DatasetType.SNV_INDEL), @@ -860,7 +874,6 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): return_value=[ClickhouseReferenceDataset.CLINVAR], ) def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_type): - cursor = connections['clickhouse_write'].cursor() load_complete_run( ReferenceGenome.GRCh38, DatasetType.SNV_INDEL, @@ -868,6 +881,7 @@ def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_typ ['project_d'], ['family_d1', 'family_d2'], ) + cursor = connections['clickhouse_write'].cursor() cursor.execute( f""" SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) @@ -969,15 +983,16 @@ def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_typ self.assertCountEqual( variants_details, [ - (10, '1-3-A-C'), - (11, '2-4-A-T'), - (12, 'Y-9-A-C'), - (13, 'M-2-C-G'), + (1, '1-13-A-C'), + (2, '2-14-A-T'), + (3, 'Y-19-A-C'), + (4, 'M-12-C-G'), + (7, 'c'), + (10, 'b'), ], ) def test_load_complete_gcnv(self): - cursor = connections['clickhouse_write'].cursor() load_complete_run( ReferenceGenome.GRCh38, DatasetType.GCNV, @@ -985,6 +1000,7 @@ def test_load_complete_gcnv(self): ['project_d'], ['family_d1', 'family_d2'], ) + cursor = connections['clickhouse_write'].cursor() cursor.execute( f""" SELECT COUNT(*) @@ -992,7 +1008,8 @@ def test_load_complete_gcnv(self): {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/variants_memory` """, ) - self.assertEqual(cursor.fetchone()[0], 4) + variants_disk_count = cursor.fetchone()[0] + self.assertEqual(variants_disk_count, 4) cursor.execute( f""" SELECT COUNT(*) @@ -1000,7 +1017,8 @@ def test_load_complete_gcnv(self): {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/variants_disk` """, ) - self.assertEqual(cursor.fetchone()[0], 4) + variants_disk_count = cursor.fetchone()[0] + self.assertEqual(variants_disk_count, 4) cursor.execute( f""" SELECT COUNT(*) @@ -1008,7 +1026,8 @@ def test_load_complete_gcnv(self): {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/key_lookup` """, ) - self.assertEqual(cursor.fetchone()[0], 4) + key_lookup_count = cursor.fetchone()[0] + self.assertEqual(key_lookup_count, 4) cursor.execute( f""" SELECT COUNT(*) @@ -1016,15 +1035,16 @@ def test_load_complete_gcnv(self): {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/entries` """, ) - self.assertEqual(cursor.fetchone()[0], 3) + entries_count = cursor.fetchone()[0] + self.assertEqual(entries_count, 3) def test_delete_families(self): - cursor = connections['clickhouse_write'].cursor() table_name_builder = TableNameBuilder( ReferenceGenome.GRCh38, DatasetType.SNV_INDEL, TEST_RUN_ID, ) + cursor = connections['clickhouse_write'].cursor() cursor.execute( f""" SELECT project_guid, sum(het_samples), sum(hom_samples) @@ -1034,11 +1054,11 @@ def test_delete_families(self): GROUP BY project_guid """, ) + project_gt_stats = cursor.fetchall() self.assertCountEqual( - cursor.fetchall(), + project_gt_stats, [('project_a', 2, 3), ('project_c', 0, 2), ('project_b', 1, 2)], ) - refresh_materialized_views( table_name_builder, ClickHouseMaterializedView.for_dataset_type_atomic_entries_update_refreshable( @@ -1053,8 +1073,8 @@ def test_delete_families(self): {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` """, ) - self.assertCountEqual(cursor.fetchall(), [(12,)]) - + gt_stats = cursor.fetchall() + self.assertCountEqual(gt_stats, [(12,)]) delete_family_guids( ReferenceGenome.GRCh38, DatasetType.SNV_INDEL, @@ -1071,8 +1091,9 @@ def test_delete_families(self): GROUP BY project_guid """, ) + project_gt_stats = cursor.fetchall() self.assertCountEqual( - cursor.fetchall(), + project_gt_stats, [('project_a', 1, 2), ('project_c', 0, 2), ('project_b', 1, 2)], ) cursor.execute( @@ -1082,7 +1103,8 @@ def test_delete_families(self): {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` """, ) - self.assertCountEqual(cursor.fetchall(), [(10,)]) + gt_stats = cursor.fetchall() + self.assertCountEqual(gt_stats, [(10,)]) cursor.execute( f""" SELECT sum(ac_wes) @@ -1090,22 +1112,21 @@ def test_delete_families(self): {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` """, ) - self.assertCountEqual(cursor.fetchall(), [(10,)]) + gt_stats_dict = cursor.fetchall() + self.assertCountEqual(gt_stats_dict, [(10,)]) def test_rebuild_gt_stats(self): - cursor = connections['clickhouse_write'].cursor() table_name_builder = TableNameBuilder( ReferenceGenome.GRCh38, DatasetType.SNV_INDEL, TEST_RUN_ID, ) + cursor = connections['clickhouse_write'].cursor() logged_query( # DROP the partition from the non-staging entries to as a non-mv-impacting change. f""" ALTER TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` DROP PARTITION (%(project_guid)s, %(partition_id)s) """, - # project_partitions_dict has no row for project_a, so n_partitions (and thus - # partition_id) defaults to 0. {'project_guid': 'project_a', 'partition_id': 0}, ) cursor.execute( @@ -1117,11 +1138,11 @@ def test_rebuild_gt_stats(self): GROUP BY project_guid """, ) + project_gt_stats = cursor.fetchall() self.assertCountEqual( - cursor.fetchall(), + project_gt_stats, [('project_a', 2, 3), ('project_b', 1, 2)], ) - refresh_materialized_views( table_name_builder, ClickHouseMaterializedView.for_dataset_type_atomic_entries_update_refreshable( @@ -1136,10 +1157,8 @@ def test_rebuild_gt_stats(self): {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` """, ) - # gt_stats has no project dimension (keyed globally by `key`), so project_c's rows - # (sharing key values with project_a/b in the fixture) also contribute here. - self.assertCountEqual(cursor.fetchall(), [(12, 5)]) - + gt_stats = cursor.fetchall() + self.assertCountEqual(gt_stats, [(12, 5)]) rebuild_gt_stats( ReferenceGenome.GRCh38, DatasetType.SNV_INDEL, @@ -1155,8 +1174,9 @@ def test_rebuild_gt_stats(self): GROUP BY project_guid """, ) + project_gt_stats = cursor.fetchall() self.assertCountEqual( - cursor.fetchall(), + project_gt_stats, [('project_b', 1, 2)], ) cursor.execute( @@ -1166,7 +1186,8 @@ def test_rebuild_gt_stats(self): {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` """, ) - self.assertCountEqual(cursor.fetchall(), [(9, 0)]) + gt_stats = cursor.fetchall() + self.assertCountEqual(gt_stats, [(9, 0)]) @patch.object( ClickhouseReferenceDataset, From cd16936f33dc3685ef339c94e1390b0762dded1f Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 12:45:10 -0400 Subject: [PATCH 071/369] ruff --- loading_pipeline/lib/misc/clickhouse_test.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index cd23603e09..10e427d50c 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -732,7 +732,10 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): 123456789, [], [], - [('sample_d1', 'REF', None, None, None), ('sample_d11', 'HOM', None, None, None)], + [ + ('sample_d1', 'REF', None, None, None), + ('sample_d11', 'HOM', None, None, None), + ], 1, 1, 0, @@ -1211,8 +1214,9 @@ def test_repartitioned_entries_table(self, mock_for_reference_genome_dataset_typ GROUP BY project_guid """, ) + project_gt_stats = cursor.fetchall() self.assertCountEqual( - cursor.fetchall(), + project_gt_stats, [ ('project_a', 2, 3), ('project_b', 1, 2), From 5fb40198a8521bb3f0818e07bfe32e406e6c6bc1 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 12:50:48 -0400 Subject: [PATCH 072/369] remove redundant test --- loading_pipeline/lib/misc/clickhouse_test.py | 36 ++------------------ 1 file changed, 2 insertions(+), 34 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index 10e427d50c..b08853f5b8 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -459,7 +459,8 @@ def test_direct_insert_all_keys(self): ) def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): self.maxDiff = None # TODO - # Tests individual components of atomic_insert_entries, validating state after each step. + # Tests individual components of the atomic_insert_entries + # to validate the state after each step. cursor = connections['clickhouse_write'].cursor() table_name_builder = TableNameBuilder( ReferenceGenome.GRCh38, @@ -1191,36 +1192,3 @@ def test_rebuild_gt_stats(self): ) gt_stats = cursor.fetchall() self.assertCountEqual(gt_stats, [(9, 0)]) - - @patch.object( - ClickhouseReferenceDataset, - 'for_reference_genome_dataset_type', - return_value=[ClickhouseReferenceDataset.CLINVAR], - ) - def test_repartitioned_entries_table(self, mock_for_reference_genome_dataset_type): - cursor = connections['clickhouse_write'].cursor() - load_complete_run( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ['project_d'], - ['family_d1', 'family_d2', 'family_d3'], - ) - cursor.execute( - f""" - SELECT project_guid, sum(het_samples), sum(hom_samples) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` - GROUP BY project_guid - """, - ) - project_gt_stats = cursor.fetchall() - self.assertCountEqual( - project_gt_stats, - [ - ('project_a', 2, 3), - ('project_b', 1, 2), - ('project_c', 0, 2), - ('project_d', 1, 1), - ], - ) From db9b7ec05df859ca70c1984018518ded4eb14435 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 12:52:38 -0400 Subject: [PATCH 073/369] remove unneeded schema --- loading_pipeline/lib/misc/clickhouse_test.py | 89 -------------------- 1 file changed, 89 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index b08853f5b8..d0e1e034ac 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -47,94 +47,6 @@ TEST_RUN_ID = 'manual__2025-05-07T17-20-59.702114+00-00' -_FIVEUTR_ANNOTATION_TYPE = pa.struct( - [ - ('AltStop', pa.string()), - ('AltStopDistanceToCDS', pa.int32()), - ('CapDistanceToStart', pa.int32()), - ('DistanceToCDS', pa.int32()), - ('DistanceToStop', pa.int32()), - ('Evidence', pa.bool_()), - ('FrameWithCDS', pa.string()), - ('KozakContext', pa.string()), - ('KozakStrength', pa.string()), - ('StartDistanceToCDS', pa.int32()), - ('alt_type', pa.string()), - ('alt_type_length', pa.int32()), - ('newSTOPDistanceToCDS', pa.int32()), - ('ref_StartDistanceToCDS', pa.int32()), - ('ref_type', pa.string()), - ('ref_type_length', pa.int32()), - ('type', pa.string()), - ], -) -_UTRANNOTATOR_TYPE = pa.struct( - [ - ('existingInframeOorfs', pa.int32()), - ('existingOutofframeOorfs', pa.int32()), - ('existingUorfs', pa.int32()), - ('fiveutrAnnotation', _FIVEUTR_ANNOTATION_TYPE), - ('fiveutrConsequence', pa.string()), - ], -) -_TRANSCRIPT_TYPE = pa.struct( - [ - ('alphamissense', pa.struct([('pathogenicity', pa.float64())])), - ('aminoAcids', pa.string()), - ('biotype', pa.string()), - ('canonical', pa.int32()), - ('codons', pa.string()), - ('consequenceTerms', pa.list_(pa.string())), - ('exon', pa.struct([('index', pa.int32()), ('total', pa.int32())])), - ('geneId', pa.string()), - ('hgvsc', pa.string()), - ('hgvsp', pa.string()), - ('intron', pa.struct([('index', pa.int32()), ('total', pa.int32())])), - ( - 'loftee', - pa.struct( - [('isLofNagnag', pa.bool_()), ('lofFilters', pa.list_(pa.string()))], - ), - ), - ('majorConsequence', pa.string()), - ('manePlusClinical', pa.string()), - ('maneSelect', pa.string()), - ('refseqTranscriptId', pa.string()), - ( - 'spliceregion', - pa.struct([('extended_intronic_splice_region_variant', pa.bool_())]), - ), - ('transcriptId', pa.string()), - ('transcriptRank', pa.int32()), - ('utrannotator', _UTRANNOTATOR_TYPE), - ], -) -_MOTIF_CONSEQUENCE_TYPE = pa.struct( - [ - ('consequenceTerms', pa.list_(pa.string())), - ('motifFeatureId', pa.string()), - ], -) -_REGULATORY_CONSEQUENCE_TYPE = pa.struct( - [ - ('biotype', pa.string()), - ('consequenceTerms', pa.list_(pa.string())), - ('regulatoryFeatureId', pa.string()), - ], -) -VARIANT_DETAILS_SCHEMA = pa.schema( - [ - ('key', pa.int64()), - ('variantId', pa.string()), - ('liftedOverChrom', pa.string()), - ('liftedOverPos', pa.int64()), - ('rsid', pa.string()), - ('CAID', pa.string()), - ('transcripts', pa.list_(_TRANSCRIPT_TYPE)), - ('sortedMotifFeatureConsequences', pa.list_(_MOTIF_CONSEQUENCE_TYPE)), - ('sortedRegulatoryFeatureConsequences', pa.list_(_REGULATORY_CONSEQUENCE_TYPE)), - ], -) _FULL_TRANSCRIPT = { 'alphamissense': {'pathogenicity': 0.5}, 'aminoAcids': 'S/L', @@ -263,7 +175,6 @@ def write_test_parquet(df: pd.DataFrame, parquet_path: str, schema=None): DatasetType.SNV_INDEL, TEST_RUN_ID, ), - VARIANT_DETAILS_SCHEMA, # TODO needed? ) # New Variants parquet. From 026ab4af1ee181188c63378016a21121bb752deb Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 12:57:08 -0400 Subject: [PATCH 074/369] fix test --- loading_pipeline/lib/misc/clickhouse_test.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index d0e1e034ac..bfffd69ae2 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -116,6 +116,9 @@ def setUpClass(cls): f'INSERT INTO {Env.CLICKHOUSE_DATABASE}.`seqrdb_gene_ids_src` VALUES', [('GENE1', 123), ('GENE2', 12), ('GENE3', 1)], ) + cursor.execute( + f'SYSTEM RELOAD DICTIONARY {Env.CLICKHOUSE_DATABASE}.`seqrdb_gene_ids`', + ) def setUp(self): super().setUp() From 4d823c520a4e9c80b8096ad9e4bd5126c4e84372 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 13:01:26 -0400 Subject: [PATCH 075/369] Revert "remove unneeded schema" This reverts commit db9b7ec05df859ca70c1984018518ded4eb14435. --- loading_pipeline/lib/misc/clickhouse_test.py | 89 ++++++++++++++++++++ 1 file changed, 89 insertions(+) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index bfffd69ae2..07593d248a 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -47,6 +47,94 @@ TEST_RUN_ID = 'manual__2025-05-07T17-20-59.702114+00-00' +_FIVEUTR_ANNOTATION_TYPE = pa.struct( + [ + ('AltStop', pa.string()), + ('AltStopDistanceToCDS', pa.int32()), + ('CapDistanceToStart', pa.int32()), + ('DistanceToCDS', pa.int32()), + ('DistanceToStop', pa.int32()), + ('Evidence', pa.bool_()), + ('FrameWithCDS', pa.string()), + ('KozakContext', pa.string()), + ('KozakStrength', pa.string()), + ('StartDistanceToCDS', pa.int32()), + ('alt_type', pa.string()), + ('alt_type_length', pa.int32()), + ('newSTOPDistanceToCDS', pa.int32()), + ('ref_StartDistanceToCDS', pa.int32()), + ('ref_type', pa.string()), + ('ref_type_length', pa.int32()), + ('type', pa.string()), + ], +) +_UTRANNOTATOR_TYPE = pa.struct( + [ + ('existingInframeOorfs', pa.int32()), + ('existingOutofframeOorfs', pa.int32()), + ('existingUorfs', pa.int32()), + ('fiveutrAnnotation', _FIVEUTR_ANNOTATION_TYPE), + ('fiveutrConsequence', pa.string()), + ], +) +_TRANSCRIPT_TYPE = pa.struct( + [ + ('alphamissense', pa.struct([('pathogenicity', pa.float64())])), + ('aminoAcids', pa.string()), + ('biotype', pa.string()), + ('canonical', pa.int32()), + ('codons', pa.string()), + ('consequenceTerms', pa.list_(pa.string())), + ('exon', pa.struct([('index', pa.int32()), ('total', pa.int32())])), + ('geneId', pa.string()), + ('hgvsc', pa.string()), + ('hgvsp', pa.string()), + ('intron', pa.struct([('index', pa.int32()), ('total', pa.int32())])), + ( + 'loftee', + pa.struct( + [('isLofNagnag', pa.bool_()), ('lofFilters', pa.list_(pa.string()))], + ), + ), + ('majorConsequence', pa.string()), + ('manePlusClinical', pa.string()), + ('maneSelect', pa.string()), + ('refseqTranscriptId', pa.string()), + ( + 'spliceregion', + pa.struct([('extended_intronic_splice_region_variant', pa.bool_())]), + ), + ('transcriptId', pa.string()), + ('transcriptRank', pa.int32()), + ('utrannotator', _UTRANNOTATOR_TYPE), + ], +) +_MOTIF_CONSEQUENCE_TYPE = pa.struct( + [ + ('consequenceTerms', pa.list_(pa.string())), + ('motifFeatureId', pa.string()), + ], +) +_REGULATORY_CONSEQUENCE_TYPE = pa.struct( + [ + ('biotype', pa.string()), + ('consequenceTerms', pa.list_(pa.string())), + ('regulatoryFeatureId', pa.string()), + ], +) +VARIANT_DETAILS_SCHEMA = pa.schema( + [ + ('key', pa.int64()), + ('variantId', pa.string()), + ('liftedOverChrom', pa.string()), + ('liftedOverPos', pa.int64()), + ('rsid', pa.string()), + ('CAID', pa.string()), + ('transcripts', pa.list_(_TRANSCRIPT_TYPE)), + ('sortedMotifFeatureConsequences', pa.list_(_MOTIF_CONSEQUENCE_TYPE)), + ('sortedRegulatoryFeatureConsequences', pa.list_(_REGULATORY_CONSEQUENCE_TYPE)), + ], +) _FULL_TRANSCRIPT = { 'alphamissense': {'pathogenicity': 0.5}, 'aminoAcids': 'S/L', @@ -178,6 +266,7 @@ def write_test_parquet(df: pd.DataFrame, parquet_path: str, schema=None): DatasetType.SNV_INDEL, TEST_RUN_ID, ), + VARIANT_DETAILS_SCHEMA, # TODO needed? ) # New Variants parquet. From 7a262f0574736870827b0621c7d6d47aaa21b876 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 13:08:39 -0400 Subject: [PATCH 076/369] fix test --- loading_pipeline/lib/misc/clickhouse_test.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index 07593d248a..9b5ba7635d 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -266,7 +266,7 @@ def write_test_parquet(df: pd.DataFrame, parquet_path: str, schema=None): DatasetType.SNV_INDEL, TEST_RUN_ID, ), - VARIANT_DETAILS_SCHEMA, # TODO needed? + VARIANT_DETAILS_SCHEMA, ) # New Variants parquet. @@ -771,7 +771,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): 0, ), ( - 10, + 0, 'project_c', 'family_c1', 'WES', From 8d97fbf5058d8c412edf48133b5c3e09ea1b52b1 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 13:20:58 -0400 Subject: [PATCH 077/369] fix test --- loading_pipeline/lib/misc/clickhouse_test.py | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index 9b5ba7635d..012f8497f3 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -850,7 +850,13 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): """, ) new_gt_stats = cursor.fetchall() - self.assertCountEqual(new_gt_stats, []) + self.assertCountEqual(new_gt_stats, [ + (1, 1, 0, 0, 0, 0, 0), + (2, 0, 2, 0, 0, 1, 0), + (3, 2, 0, 0, 1, 0, 0), + (4, 5, 2, 0, 2, 1, 0), + (5, 2, 0, 0, 1, 0, 0), + ]) reload_dictionaries( table_name_builder, ClickHouseDictionary.for_dataset_type(DatasetType.SNV_INDEL), From 22a90da1136bca23217bedc96a6666393ff70b7b Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 13:25:48 -0400 Subject: [PATCH 078/369] ruff --- loading_pipeline/lib/misc/clickhouse_test.py | 17 ++++++++++------- 1 file changed, 10 insertions(+), 7 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index 012f8497f3..c73e4e3117 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -850,13 +850,16 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): """, ) new_gt_stats = cursor.fetchall() - self.assertCountEqual(new_gt_stats, [ - (1, 1, 0, 0, 0, 0, 0), - (2, 0, 2, 0, 0, 1, 0), - (3, 2, 0, 0, 1, 0, 0), - (4, 5, 2, 0, 2, 1, 0), - (5, 2, 0, 0, 1, 0, 0), - ]) + self.assertCountEqual( + new_gt_stats, + [ + (1, 1, 0, 0, 0, 0, 0), + (2, 0, 2, 0, 0, 1, 0), + (3, 2, 0, 0, 1, 0, 0), + (4, 5, 2, 0, 2, 1, 0), + (5, 2, 0, 0, 1, 0, 0), + ], + ) reload_dictionaries( table_name_builder, ClickHouseDictionary.for_dataset_type(DatasetType.SNV_INDEL), From 22ef9bd48d006af4fce11c9993f2134bc08f34ab Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 13:31:16 -0400 Subject: [PATCH 079/369] fix test --- loading_pipeline/lib/misc/clickhouse_test.py | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index c73e4e3117..eb5dbcacaf 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -834,7 +834,13 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): existing_gt_stats = cursor.fetchall() self.assertCountEqual( existing_gt_stats, - [], + [ + (1, 1, 0, 0, 0, 0, 0), + (2, 0, 2, 0, 0, 1, 0), + (3, 2, 0, 0, 1, 0, 0), + (4, 5, 2, 0, 2, 1, 0), + (5, 2, 0, 0, 1, 0, 0), + ], ) exchange_tables( table_name_builder, From a4c33c7b176c6b6ae60c59a9f29f03c2f4d515f6 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 13:41:13 -0400 Subject: [PATCH 080/369] fix test --- loading_pipeline/lib/misc/clickhouse_test.py | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index eb5dbcacaf..7aa6fd34fb 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -881,12 +881,12 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): self.assertEqual( new_gt_stats_post_reload, [ - (10, 2, 0), - (1, 1, 1), - (2, 0, 2), - (3, 2, 0), - (4, 5, 0), - (5, 2, 0), + (10, 2, 0, 0, 1, 0, 0), + (1, 1, 1, 0, 0, 0, 0), + (2, 0, 2, 0, 0, 1, 0), + (3, 2, 0, 0, 1, 0, 0), + (4, 5, 0, 0, 2, 0, 0), + (5, 2, 0, 0, 1, 0, 0), ], ) From 58eb9dd88220603cf07f51d77a72f53440c997d4 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 13:46:29 -0400 Subject: [PATCH 081/369] fix test --- loading_pipeline/lib/misc/clickhouse_test.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index 7aa6fd34fb..b7a46695d5 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -881,12 +881,12 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): self.assertEqual( new_gt_stats_post_reload, [ - (10, 2, 0, 0, 1, 0, 0), (1, 1, 1, 0, 0, 0, 0), (2, 0, 2, 0, 0, 1, 0), (3, 2, 0, 0, 1, 0, 0), (4, 5, 0, 0, 2, 0, 0), (5, 2, 0, 0, 1, 0, 0), + (10, 2, 0, 0, 1, 0, 0), ], ) From 9e8ba64c2e2aac4c04e40f3e6188597c47f294a1 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 13:54:05 -0400 Subject: [PATCH 082/369] Revert "skip tests" This reverts commit 32c4dbecb82a8ca1a0f4e3baeee6d1ab1743638d. --- loading_pipeline/api/app_test.py | 140 ++ loading_pipeline/api/model_test.py | 87 ++ .../lib/annotations/fields_test.py | 118 ++ .../lib/annotations/snv_indel_test.py | 303 ++++ loading_pipeline/lib/annotations/sv_test.py | 171 +++ loading_pipeline/lib/core/definitions_test.py | 144 ++ .../lib/methods/relatedness_test.py | 39 + .../lib/methods/sex_check_test.py | 54 + loading_pipeline/lib/misc/callsets_test.py | 87 ++ .../lib/misc/family_entries_test.py | 356 +++++ .../lib/misc/family_loading_failures_test.py | 448 ++++++ loading_pipeline/lib/misc/gcnv_test.py | 54 + loading_pipeline/lib/misc/io_test.py | 211 +++ loading_pipeline/lib/misc/math_test.py | 12 + .../lib/misc/nested_field_test.py | 81 + loading_pipeline/lib/misc/pedigree_test.py | 514 +++++++ loading_pipeline/lib/misc/retry_test.py | 69 + loading_pipeline/lib/misc/runs_test.py | 84 + loading_pipeline/lib/misc/sample_ids_test.py | 160 ++ loading_pipeline/lib/misc/sv_test.py | 243 +++ .../lib/misc/terra_data_repository_test.py | 321 ++++ loading_pipeline/lib/misc/validation_test.py | 464 ++++++ loading_pipeline/lib/misc/vets_test.py | 104 ++ loading_pipeline/lib/paths_test.py | 180 +++ .../reference_datasets/gnomad_exomes_test.py | 72 + .../reference_datasets/gnomad_genomes_test.py | 72 + .../lib/reference_datasets/gnomad_svs_test.py | 93 ++ .../dataproc/create_dataproc_cluster_test.py | 162 ++ .../lib/tasks/dataproc/misc_test.py | 51 + .../dataproc/run_pipeline_on_dataproc_test.py | 184 +++ .../lib/tasks/exports/misc_test.py | 484 ++++++ .../exports/write_new_entries_parquet_test.py | 423 ++++++ .../write_new_variant_details_parquet_test.py | 270 ++++ loading_pipeline/lib/tasks/files_test.py | 40 + ...nnotations_table_with_new_variants_test.py | 1349 +++++++++++++++++ .../lib/tasks/validate_callset_test.py | 83 + .../lib/tasks/write_metadata_for_run_test.py | 188 +++ .../write_relatedness_check_table_test.py | 120 ++ .../tasks/write_relatedness_check_tsv_test.py | 53 + ...ite_remapped_and_subsetted_callset_test.py | 460 ++++++ .../lib/tasks/write_sample_qc_json_test.py | 269 ++++ .../lib/tasks/write_sex_check_table_test.py | 157 ++ .../lib/tasks/write_success_file_test.py | 34 + .../write_variant_annotations_vcf_test.py | 91 ++ 44 files changed, 9099 insertions(+) create mode 100644 loading_pipeline/api/app_test.py create mode 100644 loading_pipeline/api/model_test.py create mode 100644 loading_pipeline/lib/annotations/fields_test.py create mode 100644 loading_pipeline/lib/annotations/snv_indel_test.py create mode 100644 loading_pipeline/lib/annotations/sv_test.py create mode 100644 loading_pipeline/lib/core/definitions_test.py create mode 100644 loading_pipeline/lib/methods/relatedness_test.py create mode 100644 loading_pipeline/lib/methods/sex_check_test.py create mode 100644 loading_pipeline/lib/misc/callsets_test.py create mode 100644 loading_pipeline/lib/misc/family_entries_test.py create mode 100644 loading_pipeline/lib/misc/family_loading_failures_test.py create mode 100644 loading_pipeline/lib/misc/gcnv_test.py create mode 100644 loading_pipeline/lib/misc/io_test.py create mode 100644 loading_pipeline/lib/misc/math_test.py create mode 100644 loading_pipeline/lib/misc/nested_field_test.py create mode 100644 loading_pipeline/lib/misc/pedigree_test.py create mode 100644 loading_pipeline/lib/misc/retry_test.py create mode 100644 loading_pipeline/lib/misc/runs_test.py create mode 100644 loading_pipeline/lib/misc/sample_ids_test.py create mode 100644 loading_pipeline/lib/misc/sv_test.py create mode 100644 loading_pipeline/lib/misc/terra_data_repository_test.py create mode 100644 loading_pipeline/lib/misc/validation_test.py create mode 100644 loading_pipeline/lib/misc/vets_test.py create mode 100644 loading_pipeline/lib/paths_test.py create mode 100644 loading_pipeline/lib/reference_datasets/gnomad_exomes_test.py create mode 100644 loading_pipeline/lib/reference_datasets/gnomad_genomes_test.py create mode 100644 loading_pipeline/lib/reference_datasets/gnomad_svs_test.py create mode 100644 loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster_test.py create mode 100644 loading_pipeline/lib/tasks/dataproc/misc_test.py create mode 100644 loading_pipeline/lib/tasks/dataproc/run_pipeline_on_dataproc_test.py create mode 100644 loading_pipeline/lib/tasks/exports/misc_test.py create mode 100644 loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py create mode 100644 loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py create mode 100644 loading_pipeline/lib/tasks/files_test.py create mode 100644 loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py create mode 100644 loading_pipeline/lib/tasks/validate_callset_test.py create mode 100644 loading_pipeline/lib/tasks/write_metadata_for_run_test.py create mode 100644 loading_pipeline/lib/tasks/write_relatedness_check_table_test.py create mode 100644 loading_pipeline/lib/tasks/write_relatedness_check_tsv_test.py create mode 100644 loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset_test.py create mode 100644 loading_pipeline/lib/tasks/write_sample_qc_json_test.py create mode 100644 loading_pipeline/lib/tasks/write_sex_check_table_test.py create mode 100644 loading_pipeline/lib/tasks/write_success_file_test.py create mode 100644 loading_pipeline/lib/tasks/write_variant_annotations_vcf_test.py diff --git a/loading_pipeline/api/app_test.py b/loading_pipeline/api/app_test.py new file mode 100644 index 0000000000..f5945c1c41 --- /dev/null +++ b/loading_pipeline/api/app_test.py @@ -0,0 +1,140 @@ +from pathlib import Path + +from aiohttp import web_exceptions +from aiohttp.test_utils import AioHTTPTestCase + +from loading_pipeline.api.app import init_web_app +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + +CALLSET_PATH = str( + Path('loading_pipeline/var/test/callsets/1kg_30variants.vcf').resolve(), +) + + +class AppTest(AioHTTPTestCase, MockedDatarootTestCase): + async def get_application(self): + return await init_web_app() + + async def test_status(self): + async with self.client.request('GET', '/status') as resp: + self.assertEqual(resp.status, 200) + resp_json = await resp.json() + self.assertDictEqual(resp_json, {'success': True}) + + async def test_missing_route(self): + with self.assertLogs(level='ERROR') as _: + async with self.client.request('GET', '/loading_pip') as resp: + self.assertEqual(resp.status, web_exceptions.HTTPNotFound.status_code) + + async def test_loading_pipeline_invalid_requests(self): + with self.assertLogs(level='ERROR') as log: + async with self.client.request('GET', '/loading_pipeline_enqueue') as resp: + self.assertEqual( + resp.status, + web_exceptions.HTTPMethodNotAllowed.status_code, + ) + self.assertTrue( + 'HTTPMethodNotAllowed' in log.output[0], + ) + + with self.assertLogs(level='ERROR') as log: + async with self.client.request('POST', '/loading_pipeline_enqueue') as resp: + self.assertEqual( + resp.status, + web_exceptions.HTTPUnprocessableEntity.status_code, + ) + self.assertTrue( + 'HTTPUnprocessableEntity' in log.output[0], + ) + + body = { + 'callset_path': 'missing.vcf', + 'project_guids': ['project_a'], + 'sample_type': SampleType.WGS.value, + 'reference_genome': ReferenceGenome.GRCh38.value, + 'dataset_type': DatasetType.SNV_INDEL.value, + } + with self.assertLogs(level='ERROR') as log: + async with self.client.request( + 'POST', + '/loading_pipeline_enqueue', + json=body, + ) as resp: + self.assertEqual( + resp.status, + web_exceptions.HTTPBadRequest.status_code, + ) + self.assertTrue( + 'callset_path must point to a file that exists' in log.output[0], + ) + + body = { + 'callset_path': CALLSET_PATH, + 'project_guids': ['project_a'], + 'sample_type': SampleType.WGS.value, + 'reference_genome': ReferenceGenome.GRCh38.value, + 'dataset_type': DatasetType.SNV_INDEL.value, + 'validations_to_skip': ['bad_validation'], + } + with self.assertLogs(level='ERROR') as log: + async with self.client.request( + 'POST', + '/loading_pipeline_enqueue', + json=body, + ) as resp: + self.assertEqual( + resp.status, + web_exceptions.HTTPBadRequest.status_code, + ) + self.assertTrue( + "input_value='bad_validation" in log.output[0], + ) + + async def test_loading_pipeline_enqueue(self): + body = { + 'callset_path': CALLSET_PATH, + 'project_guids': ['project_a'], + 'sample_type': SampleType.WGS.value, + 'reference_genome': ReferenceGenome.GRCh38.value, + 'dataset_type': DatasetType.SNV_INDEL.value, + } + async with self.client.request( + 'POST', + '/loading_pipeline_enqueue', + json=body, + ) as resp: + self.assertEqual( + resp.status, + web_exceptions.HTTPAccepted.status_code, + ) + resp_json = await resp.json() + self.assertDictEqual( + resp_json, + { + 'Successfully queued': { + 'request_type': 'LoadingPipelineRequest', + 'callset_path': CALLSET_PATH, + 'dataset_type': 'SNV_INDEL', + 'project_guids': ['project_a'], + 'reference_genome': 'GRCh38', + 'sample_type': 'WGS', + 'skip_check_sex_and_relatedness': False, + 'skip_expect_tdr_metrics': False, + 'attempt_id': 0, + 'validations_to_skip': [], + }, + }, + ) + + # Second request + body['project_guids'] = ['project_b', 'project_c'] + async with self.client.request( + 'POST', + '/loading_pipeline_enqueue', + json=body, + ) as resp: + self.assertEqual( + resp.status, + web_exceptions.HTTPAccepted.status_code, + ) diff --git a/loading_pipeline/api/model_test.py b/loading_pipeline/api/model_test.py new file mode 100644 index 0000000000..03bc42ae1a --- /dev/null +++ b/loading_pipeline/api/model_test.py @@ -0,0 +1,87 @@ +import unittest +from pathlib import Path + +from loading_pipeline.api.model import DeleteFamiliesRequest, LoadingPipelineRequest +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType + +CALLSET_PATH = str( + Path('loading_pipeline/var/test/callsets/1kg_30variants.vcf').resolve(), +) + + +class ModelTest(unittest.TestCase): + def test_valid_loading_pipeline_requests(self) -> None: + raw_request = { + 'callset_path': CALLSET_PATH, + 'projects_to_run': ['project_a'], + 'sample_type': SampleType.WGS.value, + 'reference_genome': ReferenceGenome.GRCh38.value, + 'dataset_type': DatasetType.SNV_INDEL.value, + } + lpr = LoadingPipelineRequest.model_validate(raw_request) + self.assertEqual(lpr.reference_genome, ReferenceGenome.GRCh38) + self.assertEqual(lpr.project_guids, ['project_a']) + self.assertEqual(lpr.request_type, 'LoadingPipelineRequest') + self.assertEqual(lpr.attempt_id, 0) + + # Test wildcard VCF + raw_request['callset_path'] = CALLSET_PATH.replace( + '1kg_30variants.vcf', + '1kg_30*.vcf', + ) + lpr = LoadingPipelineRequest.model_validate(raw_request) + + def test_invalid_loading_pipeline_requests(self) -> None: + raw_request = { + 'callset_path': 'a.txt', + 'project_guids': [], + 'sample_type': 'BLENDED', + 'reference_genome': ReferenceGenome.GRCh38.value, + 'dataset_type': DatasetType.SNV_INDEL.value, + 'attempt_id': 5, + } + with self.assertRaises(ValueError) as cm: + LoadingPipelineRequest.model_validate(raw_request) + self.assertTrue( + str(cm.exception).startswith( + '4 validation errors for LoadingPipelineRequest', + ), + ) + + def test_validations_to_skip(self) -> None: + shared_params = { + 'callset_path': CALLSET_PATH, + 'projects_to_run': ['project_a'], + 'sample_type': SampleType.WGS.value, + 'reference_genome': ReferenceGenome.GRCh38.value, + 'dataset_type': DatasetType.SNV_INDEL.value, + } + raw_request = { + **shared_params, + 'validations_to_skip': ['all'], + } + lpr = LoadingPipelineRequest.model_validate(raw_request) + self.assertGreater(len(lpr.validations_to_skip), 2) + + raw_request = { + **shared_params, + 'validations_to_skip': ['validate_sample_type'], + } + lpr = LoadingPipelineRequest.model_validate(raw_request) + self.assertEqual(len(lpr.validations_to_skip), 1) + + raw_request = { + **shared_params, + 'validations_to_skip': ['validate_blended_exome'], + } + with self.assertRaises(ValueError): + LoadingPipelineRequest.model_validate(raw_request) + + def test_delete_families_request(self) -> None: + raw_request = {'project_guid': 'project_a', 'family_guids': []} + with self.assertRaises(ValueError): + DeleteFamiliesRequest.model_validate(raw_request) + raw_request['family_guids'] = ['family_a1'] + dfr = DeleteFamiliesRequest.model_validate(raw_request) + self.assertEqual(dfr.project_guid, 'project_a') + self.assertEqual(dfr.request_type, 'DeleteFamiliesRequest') diff --git a/loading_pipeline/lib/annotations/fields_test.py b/loading_pipeline/lib/annotations/fields_test.py new file mode 100644 index 0000000000..fc5f179749 --- /dev/null +++ b/loading_pipeline/lib/annotations/fields_test.py @@ -0,0 +1,118 @@ +from unittest.mock import Mock, patch + +import hail as hl + +from loading_pipeline.lib.annotations.fields import get_fields +from loading_pipeline.lib.core import ( + DatasetType, + ReferenceGenome, +) +from loading_pipeline.lib.misc.vep import run_vep +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase +from loading_pipeline.var.test.vep.mock_vep_data import ( + MOCK_37_VEP_DATA, + MOCK_38_VEP_DATA, +) + + +class FieldsTest(MockedDatarootTestCase): + def setUp(self) -> None: + super().setUp() + + @patch('loading_pipeline.lib.misc.vep.hl.vep') + def test_get_formatting_fields(self, mock_vep: Mock) -> None: + for reference_genome, ht, expected_fields in [ + ( + ReferenceGenome.GRCh38, + hl.Table.parallelize( + [ + { + 'locus': hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + 'alleles': ['A', 'C'], + 'rsid': 'abcd', + }, + ], + hl.tstruct( + locus=hl.tlocus('GRCh38'), + alleles=hl.tarray(hl.tstr), + rsid=hl.tstr, + ), + key=['locus', 'alleles'], + ), + [ + 'check_ref', + 'rg37_locus', + 'rsid', + 'sorted_motif_feature_consequences', + 'sorted_regulatory_feature_consequences', + 'sorted_transcript_consequences', + 'variant_id', + 'xpos', + ], + ), + ( + ReferenceGenome.GRCh37, + hl.Table.parallelize( + [ + { + 'locus': hl.Locus( + contig='1', + position=1, + reference_genome='GRCh37', + ), + 'alleles': ['A', 'C'], + 'rsid': 'abcd', + }, + ], + hl.tstruct( + locus=hl.tlocus('GRCh37'), + alleles=hl.tarray(hl.tstr), + rsid=hl.tstr, + ), + key=['locus', 'alleles'], + ), + [ + 'rg38_locus', + 'rsid', + 'sorted_transcript_consequences', + 'variant_id', + 'xpos', + ], + ), + ]: + mock_vep.return_value = ht.annotate( + vep=MOCK_37_VEP_DATA + if reference_genome == ReferenceGenome.GRCh37 + else MOCK_38_VEP_DATA, + ) + ht = run_vep( # noqa: PLW2901 + ht, + DatasetType.SNV_INDEL, + reference_genome, + ) + self.assertCountEqual( + list( + get_fields( + ht, + DatasetType.SNV_INDEL.formatting_annotation_fns( + reference_genome, + ), + **( + { + 'gencode_ensembl_to_refseq_id_mapping': hl.dict( + {'a': 'b'}, + ), + } + if reference_genome == ReferenceGenome.GRCh38 + else {} + ), + dataset_type=DatasetType.SNV_INDEL, + reference_genome=reference_genome, + ).keys(), + ), + expected_fields, + ) diff --git a/loading_pipeline/lib/annotations/snv_indel_test.py b/loading_pipeline/lib/annotations/snv_indel_test.py new file mode 100644 index 0000000000..0de91786b0 --- /dev/null +++ b/loading_pipeline/lib/annotations/snv_indel_test.py @@ -0,0 +1,303 @@ +import unittest +from unittest.mock import Mock, patch + +import hail as hl + +from loading_pipeline.lib.annotations import shared, snv_indel +from loading_pipeline.lib.core import DatasetType, ReferenceGenome +from loading_pipeline.lib.misc.vep import run_vep +from loading_pipeline.var.test.vep.mock_vep_data import ( + MOCK_37_VEP_DATA, + MOCK_38_VEP_DATA, +) + + +class SNVTest(unittest.TestCase): + @patch('loading_pipeline.lib.misc.vep.hl.vep') + def test_sorted_transcript_consequences_37( + self, + mock_vep: Mock, + ) -> None: + ht = hl.Table.parallelize( + [ + { + 'locus': hl.Locus( + contig='1', + position=871269, + reference_genome=ReferenceGenome.GRCh37.value, + ), + 'alleles': ['A', 'C'], + }, + ], + hl.tstruct( + locus=hl.tlocus(ReferenceGenome.GRCh37.value), + alleles=hl.tarray(hl.tstr), + ), + key=['locus', 'alleles'], + ) + mock_vep.return_value = ht.annotate(vep=MOCK_37_VEP_DATA) + ht = run_vep( + ht, + DatasetType.SNV_INDEL, + ReferenceGenome.GRCh37, + ) + ht = ht.select( + sorted_transcript_consequences=shared.sorted_transcript_consequences( + ht, + ), + ) + self.assertCountEqual( + ht.sorted_transcript_consequences.collect(), + [ + [ + hl.Struct( + amino_acids='S/L', + canonical=1, + codons='tCg/tTg', + gene_id='ENSG00000188976', + hgvsc='ENST00000327044.6:c.1667C>T', + hgvsp='ENSP00000317992.6:p.Ser556Leu', + transcript_id='ENST00000327044', + biotype_id=39, + consequence_term_ids=[9], + is_lof_nagnag=None, + lof_filter_ids=[0, 1], + ), + hl.Struct( + amino_acids=None, + canonical=None, + codons=None, + gene_id='ENSG00000188976', + hgvsc='ENST00000477976.1:n.3114C>T', + hgvsp=None, + transcript_id='ENST00000477976', + biotype_id=38, + consequence_term_ids=[23, 26], + is_lof_nagnag=None, + lof_filter_ids=None, + ), + hl.Struct( + amino_acids=None, + canonical=None, + codons=None, + gene_id='ENSG00000188976', + hgvsc='ENST00000483767.1:n.523C>T', + hgvsp=None, + transcript_id='ENST00000483767', + biotype_id=38, + consequence_term_ids=[23, 26], + is_lof_nagnag=None, + lof_filter_ids=None, + ), + ], + ], + ) + + @patch('loading_pipeline.lib.misc.vep.hl.vep') + def test_sorted_transcript_consequences_38( + self, + mock_vep: Mock, + ) -> None: + ht = hl.Table.parallelize( + [ + { + 'locus': hl.Locus( + contig='chr1', + position=871269, + reference_genome=ReferenceGenome.GRCh38.value, + ), + 'alleles': ['A', 'C'], + }, + ], + hl.tstruct( + locus=hl.tlocus(ReferenceGenome.GRCh38.value), + alleles=hl.tarray(hl.tstr), + ), + key=['locus', 'alleles'], + ) + mock_vep.return_value = ht.annotate(vep=MOCK_38_VEP_DATA) + ht = run_vep( + ht, + DatasetType.SNV_INDEL, + ReferenceGenome.GRCh38, + ) + ht = ht.select( + sorted_transcript_consequences=snv_indel.sorted_transcript_consequences( + ht, + hl.dict( + {'ENST00000327044': 'NM_015658.4', 'ENST00000477976': 'refseq1'}, + ), + ), + ) + self.assertCountEqual( + ht.sorted_transcript_consequences.collect()[0], + [ + hl.Struct( + amino_acids='S/L', + canonical=1, + codons='tCg/tTg', + gene_id='ENSG00000188976', + hgvsc='ENST00000327044.6:c.1667C>T', + hgvsp='ENSP00000317992.6:p.Ser556Leu', + transcript_id='ENST00000327044', + refseq_transcript_id='NM_015658.4', + mane_select='NM_015658.4', + mane_plus_clinical=None, + biotype_id=39, + consequence_term_ids=[9], + exon=hl.Struct(index=15, total=19), + intron=None, + alphamissense=hl.Struct(pathogenicity=0.10000000149011612), + loftee=hl.Struct( + is_lof_nagnag=None, + lof_filter_ids=[0, 1], + ), + spliceregion=hl.Struct( + extended_intronic_splice_region_variant=False, + ), + utrannotator=hl.Struct( + existing_inframe_oorfs=None, + existing_outofframe_oorfs=None, + existing_uorfs=None, + fiveutr_consequence_id=None, + fiveutr_annotation=None, + ), + ), + hl.Struct( + amino_acids=None, + canonical=None, + codons=None, + gene_id='ENSG00000188976', + hgvsc='ENST00000477976.1:n.3114C>T', + hgvsp=None, + transcript_id='ENST00000477976', + refseq_transcript_id='refseq1', + mane_select=None, + mane_plus_clinical=None, + biotype_id=38, + consequence_term_ids=[23, 26], + exon=hl.Struct(index=13, total=17), + intron=None, + alphamissense=hl.Struct(pathogenicity=0.9700000286102295), + loftee=hl.Struct( + is_lof_nagnag=None, + lof_filter_ids=None, + ), + spliceregion=hl.Struct( + extended_intronic_splice_region_variant=False, + ), + utrannotator=hl.Struct( + existing_inframe_oorfs=None, + existing_outofframe_oorfs=None, + existing_uorfs=None, + fiveutr_consequence_id=None, + fiveutr_annotation=None, + ), + ), + hl.Struct( + amino_acids=None, + canonical=None, + codons=None, + gene_id='ENSG00000188976', + hgvsc='ENST00000483767.1:n.523C>T', + hgvsp=None, + transcript_id='ENST00000483767', + refseq_transcript_id=None, + mane_select=None, + mane_plus_clinical=None, + biotype_id=38, + consequence_term_ids=[23, 13, 26], + exon=hl.Struct(index=1, total=5), + intron=None, + alphamissense=hl.Struct(pathogenicity=None), + loftee=hl.Struct( + is_lof_nagnag=None, + lof_filter_ids=None, + ), + spliceregion=hl.Struct( + extended_intronic_splice_region_variant=True, + ), + utrannotator=hl.Struct( + existing_inframe_oorfs=0, + existing_outofframe_oorfs=1, + existing_uorfs=0, + fiveutr_consequence_id=1, + fiveutr_annotation=hl.Struct( + type='OutOfFrame_oORF', + KozakContext='TTTATGC', + KozakStrength='Weak', + DistanceToCDS=40, + CapDistanceToStart=20, + DistanceToStop=75, + Evidence=False, + AltStop=None, + AltStopDistanceToCDS=None, + FrameWithCDS=None, + StartDistanceToCDS=None, + newSTOPDistanceToCDS=None, + alt_type=None, + alt_type_length=None, + ref_StartDistanceToCDS=None, + ref_type=None, + ref_type_length=None, + ), + ), + ), + ], + ) + + @patch('loading_pipeline.lib.misc.vep.hl.vep') + def test_sorted_other_feature_consequences( + self, + mock_vep: Mock, + ) -> None: + ht = hl.Table.parallelize( + [ + { + 'locus': hl.Locus( + contig='chr1', + position=871269, + reference_genome=ReferenceGenome.GRCh38.value, + ), + 'alleles': ['A', 'C'], + }, + ], + hl.tstruct( + locus=hl.tlocus(ReferenceGenome.GRCh38.value), + alleles=hl.tarray(hl.tstr), + ), + key=['locus', 'alleles'], + ) + mock_vep.return_value = ht.annotate(vep=MOCK_38_VEP_DATA) + ht = run_vep( + ht, + DatasetType.SNV_INDEL, + ReferenceGenome.GRCh38, + ) + ht = ht.select( + sorted_motif_feature_consequences=snv_indel.sorted_motif_feature_consequences( + ht, + ), + sorted_regulatory_feature_consequences=snv_indel.sorted_regulatory_feature_consequences( + ht, + ), + ) + self.assertCountEqual( + ht.sorted_motif_feature_consequences.collect(), + [None], + ) + self.assertCountEqual( + ht.sorted_regulatory_feature_consequences.collect()[0], + [ + hl.Struct( + biotype_id=0, + consequence_term_ids=[0], + regulatory_feature_id='regulatory_2', + ), + hl.Struct( + biotype_id=0, + consequence_term_ids=[2], + regulatory_feature_id='regulatory_1', + ), + ], + ) diff --git a/loading_pipeline/lib/annotations/sv_test.py b/loading_pipeline/lib/annotations/sv_test.py new file mode 100644 index 0000000000..25a8413b16 --- /dev/null +++ b/loading_pipeline/lib/annotations/sv_test.py @@ -0,0 +1,171 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.annotations.fields import get_fields +from loading_pipeline.lib.core import DatasetType + + +class SVTest(unittest.TestCase): + def test_sv_export_annotations(self) -> None: + ht = hl.Table.parallelize( + [ + hl.Struct( + id=0, + algorithms='manta', + end_locus=hl.Locus( + contig='chr5', + position=20404, + reference_genome='GRCh38', + ), + start_locus=hl.Locus( + contig='chr1', + position=180928, + reference_genome='GRCh38', + ), + sv_len=123, + sv_type_id=2, + sv_type_detail_id=None, + ), + hl.Struct( + id=1, + algorithms='manta', + end_locus=hl.Locus( + contig='chr1', + position=789481, + reference_genome='GRCh38', + ), + start_locus=hl.Locus( + contig='chr1', + position=789481, + reference_genome='GRCh38', + ), + sv_len=245, + sv_type_id=2, + sv_type_detail_id=None, + ), + hl.Struct( + id=2, + algorithms='manta', + end_locus=hl.Locus( + contig='chr1', + position=6559723, + reference_genome='GRCh38', + ), + start_locus=hl.Locus( + contig='chr1', + position=6558902, + reference_genome='GRCh38', + ), + sv_len=245, + sv_type_id=3, + sv_type_detail_id=2, + ), + hl.Struct( + id=3, + algorithms='manta', + end_locus=hl.Locus( + contig='chr1', + position=6559723, + reference_genome='GRCh38', + ), + start_locus=hl.Locus( + contig='chr1', + position=6558902, + reference_genome='GRCh38', + ), + sv_len=245, + sv_type_id=7, + sv_type_detail_id=6, + ), + ], + hl.tstruct( + id=hl.tint32, + algorithms=hl.tstr, + end_locus=hl.tlocus('GRCh38'), + start_locus=hl.tlocus('GRCh38'), + sv_len=hl.tint32, + sv_type_id=hl.tint32, + sv_type_detail_id=hl.tint32, + ), + key='id', + ) + ht = ht.select( + **get_fields( + ht, + DatasetType.SV.export_vcf_annotation_fns, + ), + ) + self.assertEqual( + ht.collect(), + [ + hl.Struct( + id=0, + locus=hl.Locus( + contig='chr1', + position=180928, + reference_genome='GRCh38', + ), + alleles=['N', ''], + info=hl.Struct( + ALGORITHMS='manta', + END=180928, + CHR2='chr5', + END2=20404, + SVTYPE='BND', + SVLEN=123, + ), + ), + hl.Struct( + id=1, + locus=hl.Locus( + contig='chr1', + position=789481, + reference_genome='GRCh38', + ), + alleles=['N', ''], + info=hl.Struct( + ALGORITHMS='manta', + END=789481, + CHR2='chr1', + END2=789481, + SVTYPE='BND', + SVLEN=245, + ), + ), + hl.Struct( + id=2, + locus=hl.Locus( + contig='chr1', + position=6558902, + reference_genome='GRCh38', + ), + alleles=['N', ''], + info=hl.Struct( + ALGORITHMS='manta', + END=6558902, + CHR2='chr1', + END2=6559723, + SVTYPE='CPX', + SVLEN=245, + ), + ), + hl.Struct( + id=3, + locus=hl.Locus( + contig='chr1', + position=6558902, + reference_genome='GRCh38', + ), + alleles=['N', ''], + info=hl.Struct( + ALGORITHMS='manta', + END=6558902, + CHR2='chr1', + END2=6559723, + SVTYPE='INS', + SVLEN=245, + ), + ), + ], + ) diff --git a/loading_pipeline/lib/core/definitions_test.py b/loading_pipeline/lib/core/definitions_test.py new file mode 100644 index 0000000000..b53d88cd18 --- /dev/null +++ b/loading_pipeline/lib/core/definitions_test.py @@ -0,0 +1,144 @@ +import unittest + +from loading_pipeline.lib.core.definitions import ReferenceGenome + + +class TestReferenceGenomeProperties(unittest.TestCase): + def test_v02_value(self): + self.assertEqual(ReferenceGenome.GRCh37.v02_value, '37') + self.assertEqual(ReferenceGenome.GRCh38.v02_value, '38') + + def test_hl_reference(self): + hl_37_reference = ReferenceGenome.GRCh37.hl_reference + self.assertEqual(hl_37_reference.name, 'GRCh37') + + hl_38_reference = ReferenceGenome.GRCh38.hl_reference + self.assertEqual(hl_38_reference.name, 'GRCh38') + + def test_standard_contigs(self): + expected_37_contigs = { + '3', + '12', + '21', + '2', + '1', + '7', + '13', + '8', + '11', + '22', + 'MT', + '14', + 'Y', + '18', + '19', + '20', + '17', + 'X', + '10', + '15', + '16', + '4', + '5', + '9', + '6', + } + self.assertEqual(ReferenceGenome.GRCh37.standard_contigs, expected_37_contigs) + + expected_38_contigs = { + 'chr10', + 'chr11', + 'chr17', + 'chr18', + 'chr9', + 'chr22', + 'chr3', + 'chrY', + 'chr7', + 'chr6', + 'chr13', + 'chr19', + 'chr16', + 'chrX', + 'chr12', + 'chr2', + 'chr21', + 'chr20', + 'chr8', + 'chrM', + 'chr5', + 'chr4', + 'chr14', + 'chr1', + 'chr15', + } + self.assertEqual(ReferenceGenome.GRCh38.standard_contigs, expected_38_contigs) + + def test_optional_contigs(self): + self.assertEqual(ReferenceGenome.GRCh37.optional_contigs, {'Y', 'MT'}) + self.assertEqual(ReferenceGenome.GRCh38.optional_contigs, {'chrY', 'chrM'}) + + def test_contig_recoding(self): + expected_37_recode = { + 'chr1': '1', + 'chr2': '2', + 'chr3': '3', + 'chr4': '4', + 'chr5': '5', + 'chr6': '6', + 'chr7': '7', + 'chr8': '8', + 'chr9': '9', + 'chr10': '10', + 'chr11': '11', + 'chr12': '12', + 'chr13': '13', + 'chr14': '14', + 'chr15': '15', + 'chr16': '16', + 'chr17': '17', + 'chr18': '18', + 'chr19': '19', + 'chr20': '20', + 'chr21': '21', + 'chr22': '22', + 'chrX': 'X', + 'chrY': 'Y', + 'chrM': 'MT', + } + self.assertDictEqual( + ReferenceGenome.GRCh37.contig_recoding(include_mt=True), + expected_37_recode, + ) + + expected_38_recode = { + '1': 'chr1', + '2': 'chr2', + '3': 'chr3', + '4': 'chr4', + '5': 'chr5', + '6': 'chr6', + '7': 'chr7', + '8': 'chr8', + '9': 'chr9', + '10': 'chr10', + '11': 'chr11', + '12': 'chr12', + '13': 'chr13', + '14': 'chr14', + '15': 'chr15', + '16': 'chr16', + '17': 'chr17', + '18': 'chr18', + '19': 'chr19', + '20': 'chr20', + '21': 'chr21', + '22': 'chr22', + 'X': 'chrX', + 'Y': 'chrY', + 'MT': 'chrM', + } + self.assertDictEqual( + ReferenceGenome.GRCh38.contig_recoding(include_mt=True), + expected_38_recode, + ) diff --git a/loading_pipeline/lib/methods/relatedness_test.py b/loading_pipeline/lib/methods/relatedness_test.py new file mode 100644 index 0000000000..e3afb159e2 --- /dev/null +++ b/loading_pipeline/lib/methods/relatedness_test.py @@ -0,0 +1,39 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.methods.relatedness import call_relatedness + +TEST_SEX_AND_RELATEDNESS_CALLSET_MT = ( + 'loading_pipeline/var/test/callsets/sex_and_relatedness_1.mt' +) + + +class RelatednessTest(unittest.TestCase): + def test_call_relatedness(self): + mt = hl.read_matrix_table(TEST_SEX_AND_RELATEDNESS_CALLSET_MT) + ht = call_relatedness( + mt, + None, + ) + self.assertCountEqual( + ht.collect(), + [ + hl.Struct( + i='ROS_006_18Y03226_D1', + j='ROS_007_19Y05939_D1', + ibd0=0.0, + ibd1=1.0, + ibd2=0.0, + pi_hat=0.5, + ), + hl.Struct( + i='ROS_007_19Y05939_D1', + j='ROS_007_19Y05987_D1', + ibd0=0.0, + ibd1=1.0, + ibd2=0.0, + pi_hat=0.5, + ), + ], + ) diff --git a/loading_pipeline/lib/methods/sex_check_test.py b/loading_pipeline/lib/methods/sex_check_test.py new file mode 100644 index 0000000000..ed390e86f3 --- /dev/null +++ b/loading_pipeline/lib/methods/sex_check_test.py @@ -0,0 +1,54 @@ +import unittest +from unittest.mock import patch + +import hail as hl + +from loading_pipeline.lib.methods.sex_check import compute_sex_check_ht + +TEST_SEX_AND_RELATEDNESS_CALLSET_MT = ( + 'loading_pipeline/var/test/callsets/sex_and_relatedness_1.mt' +) + + +class SexCheckTest(unittest.TestCase): + def test_compute_sex_check_ht(self): + mt = hl.read_matrix_table(TEST_SEX_AND_RELATEDNESS_CALLSET_MT) + ht = compute_sex_check_ht(mt) + self.assertCountEqual( + ht.collect(), + [ + hl.Struct( + s='ROS_006_18Y03226_D1', + predicted_sex='M', + ), + hl.Struct( + s='ROS_006_18Y03227_D1', + predicted_sex='M', + ), + hl.Struct( + s='ROS_006_18Y03228_D1', + predicted_sex='M', + ), + hl.Struct( + s='ROS_007_19Y05919_D1', + predicted_sex='M', + ), + hl.Struct( + s='ROS_007_19Y05939_D1', + predicted_sex='F', + ), + hl.Struct( + s='ROS_007_19Y05987_D1', + predicted_sex='M', + ), + ], + ) + + def test_compute_sex_check_ht_ambiguous(self): + mt = hl.read_matrix_table(TEST_SEX_AND_RELATEDNESS_CALLSET_MT) + with patch('loading_pipeline.lib.methods.sex_check.XY_FSTAT_THRESHOLD', 0.95): + self.assertRaises( + ValueError, + compute_sex_check_ht, + mt, + ) diff --git a/loading_pipeline/lib/misc/callsets_test.py b/loading_pipeline/lib/misc/callsets_test.py new file mode 100644 index 0000000000..5db2d4eb36 --- /dev/null +++ b/loading_pipeline/lib/misc/callsets_test.py @@ -0,0 +1,87 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.misc.callsets import union_callset_mts + + +class CallsetsTest(unittest.TestCase): + def test_union_callset_mts(self) -> None: + mt1 = ( + hl.MatrixTable.from_parts( + rows={ + 'id': [ + 0, + 1, + ], + 'row_field': [ + 1, + 2, + ], + }, + cols={'s': ['sample_1']}, + entries={ + 'GT': [[hl.Call([0, 0])], [hl.Call([0, 0])]], + }, + ) + .key_rows_by('id') + .key_cols_by('s') + .drop('row_idx', 'col_idx') + ) + mt2 = ( + hl.MatrixTable.from_parts( + rows={ + 'id': [ + 0, + 2, + ], + 'row_field': [ + 2, + 3, + ], + 'second_row_field': [ + 4, + 5, + ], + }, + cols={'s': ['sample_2']}, + entries={ + 'GT': [[hl.Call([0, 0])], [hl.Call([0, 1])]], + }, + ) + .key_rows_by('id') + .key_cols_by('s') + .drop('row_idx', 'col_idx') + ) + mt = union_callset_mts([mt1, mt2]) + self.assertEqual( + mt.entries().collect(), + [ + hl.Struct( + id=0, + row_field=1, + s='sample_1', + GT=hl.Call(alleles=[0, 0], phased=False), + ), + hl.Struct( + id=0, + row_field=1, + s='sample_2', + GT=hl.Call(alleles=[0, 0], phased=False), + ), + hl.Struct( + id=1, + row_field=2, + s='sample_1', + GT=hl.Call(alleles=[0, 0], phased=False), + ), + hl.Struct(id=1, row_field=2, s='sample_2', GT=None), + hl.Struct(id=2, row_field=None, s='sample_1', GT=None), + hl.Struct( + id=2, + row_field=None, + s='sample_2', + GT=hl.Call(alleles=[0, 1], phased=False), + ), + ], + ) diff --git a/loading_pipeline/lib/misc/family_entries_test.py b/loading_pipeline/lib/misc/family_entries_test.py new file mode 100644 index 0000000000..609fdda6d6 --- /dev/null +++ b/loading_pipeline/lib/misc/family_entries_test.py @@ -0,0 +1,356 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.core import DatasetType +from loading_pipeline.lib.misc.family_entries import ( + compute_callset_family_entries_ht, + deduplicate_by_most_non_ref_calls, + deglobalize_ids, + globalize_ids, +) + + +class FamilyEntriesTest(unittest.TestCase): + def test_compute_callset_family_entries_ht(self) -> None: + mt = hl.MatrixTable.from_parts( + rows={ + 'variants': [1, 2, 3], + 'filters': [ + hl.empty_set(hl.tstr), + {'HIGH_SR_BACKGROUND'}, + hl.empty_set(hl.tstr), + ], + }, + cols={'s': ['a', 'b', 'd', 'c']}, + entries={ + 'GT': [ + [ + hl.Call([0, 0]), + hl.missing(hl.tcall), + hl.Call([0, 0]), + hl.Call([0, 0]), + ], + [ + hl.Call([0, 0]), + hl.Call([0, 0]), + hl.Call([1, 1]), + hl.Call([0, 0]), + ], + [ + hl.Call([0, 1]), + hl.Call([0, 0]), + hl.Call([1, 1]), + hl.Call([0, 0]), + ], + ], + }, + globals={'family_samples': {'2': ['a'], '1': ['b', 'c', 'd']}}, + ) + ht = compute_callset_family_entries_ht(DatasetType.SNV_INDEL, mt, {'GT': mt.GT}) + self.assertCountEqual( + ht.globals.collect(), + [ + hl.Struct( + family_samples={'1': ['b', 'c', 'd'], '2': ['a']}, + family_guids=['1', '2'], + ), + ], + ) + self.assertCountEqual( + ht.filters.collect(), + [{'HIGH_SR_BACKGROUND'}, set()], + ) + self.assertCountEqual( + ht.family_entries.collect(), + [ + [ + [ + hl.Struct(GT=hl.Call(alleles=[0, 0], phased=False)), + hl.Struct(GT=hl.Call(alleles=[0, 0], phased=False)), + hl.Struct(GT=hl.Call(alleles=[1, 1], phased=False)), + ], + None, + ], + [ + [ + hl.Struct(GT=hl.Call(alleles=[0, 0], phased=False)), + hl.Struct(GT=hl.Call(alleles=[0, 0], phased=False)), + hl.Struct(GT=hl.Call(alleles=[1, 1], phased=False)), + ], + [hl.Struct(GT=hl.Call(alleles=[0, 1], phased=False))], + ], + ], + ) + + def test_globalize_and_deglobalize(self) -> None: + family_entries_ht = hl.Table.parallelize( + [], + hl.tstruct( + id=hl.tint32, + filters=hl.tset(hl.tstr), + family_entries=hl.tarray( + hl.tarray(hl.tstruct(a=hl.tint32, s=hl.tstr, family_guid=hl.tstr)), + ), + ), + key='id', + ) + family_entries_ht = globalize_ids(family_entries_ht) + self.assertCountEqual( + family_entries_ht.family_guids.collect(), + [ + [], + ], + ) + family_entries_ht = hl.Table.parallelize( + [ + { + 'id': 0, + 'filters': {'HIGH_SR_BACKGROUND', 'UNRESOLVED'}, + 'family_entries': [ + [ + hl.Struct(a=1, s='a', family_guid='123'), + hl.Struct(a=2, s='c', family_guid='123'), + hl.Struct(a=1, s='e', family_guid='123'), + ], + [ + hl.Struct(a=2, s='f', family_guid='234'), + ], + ], + }, + { + 'id': 1, + 'filters': {'HIGH_SR_BACKGROUND'}, + 'family_entries': [ + [ + hl.Struct(a=2, s='a', family_guid='123'), + hl.Struct(a=3, s='c', family_guid='123'), + hl.Struct(a=4, s='e', family_guid='123'), + ], + [ + hl.Struct(a=5, s='f', family_guid='234'), + ], + ], + }, + ], + hl.tstruct( + id=hl.tint32, + filters=hl.tset(hl.tstr), + family_entries=hl.tarray( + hl.tarray(hl.tstruct(a=hl.tint32, s=hl.tstr, family_guid=hl.tstr)), + ), + ), + key='id', + ) + family_entries_ht = globalize_ids(family_entries_ht) + self.assertCountEqual( + family_entries_ht.family_guids.collect(), + [ + ['123', '234'], + ], + ) + self.assertCountEqual( + family_entries_ht.family_entries.collect(), + [ + [ + [ + hl.Struct(a=1), + hl.Struct(a=2), + hl.Struct(a=1), + ], + [ + hl.Struct(a=2), + ], + ], + [ + [ + hl.Struct(a=2), + hl.Struct(a=3), + hl.Struct(a=4), + ], + [ + hl.Struct(a=5), + ], + ], + ], + ) + family_entries_ht = deglobalize_ids(family_entries_ht) + self.assertCountEqual( + family_entries_ht.family_entries.collect(), + [ + [ + [ + hl.Struct(a=1, s='a', family_guid='123'), + hl.Struct(a=2, s='c', family_guid='123'), + hl.Struct(a=1, s='e', family_guid='123'), + ], + [ + hl.Struct(a=2, s='f', family_guid='234'), + ], + ], + [ + [ + hl.Struct(a=2, s='a', family_guid='123'), + hl.Struct(a=3, s='c', family_guid='123'), + hl.Struct(a=4, s='e', family_guid='123'), + ], + [ + hl.Struct(a=5, s='f', family_guid='234'), + ], + ], + ], + ) + + def test_deduplicate_by_most_non_ref_calls(self) -> None: + project_ht = hl.Table.parallelize( + [ + { + 'id': 0, + 'filters': {'PASS', 'HIGH_SR_BACKGROUND'}, + 'family_entries': [ + [ + hl.Struct( + GT=hl.Call(alleles=[0, 1], phased=False), + family_guid='family_a', + s='sample_1', + ), + hl.Struct( + GT=hl.Call(alleles=[0, 0], phased=False), + family_guid='family_a', + s='sample_2', + ), + ], + [ + hl.Struct( + GT=hl.Call(alleles=[0, 1], phased=False), + family_guid='family_b', + s='sample_3', + ), + None, + ], + None, + ], + }, + { + 'id': 0, + 'filters': {'PASS'}, + 'family_entries': [ + [ + None, + hl.Struct( + GT=hl.Call(alleles=[0, 0], phased=False), + family_guid='family_a', + s='sample_2', + ), + ], + [ + hl.Struct( + GT=hl.Call(alleles=[0, 1], phased=False), + family_guid='family_b', + s='sample_3', + ), + None, + ], + None, + ], + }, + { + 'id': 2, + 'filters': {'HIGH_SR_BACKGROUND'}, + 'family_entries': [ + None, + None, + ], + }, + { + 'id': 3, + 'filters': {'PASS'}, + 'family_entries': [ + [ + hl.Struct( + GT=hl.Call(alleles=[0, 1], phased=False), + family_guid='family_a', + s='sample_1', + ), + hl.Struct( + GT=hl.Call(alleles=[0, 1], phased=False), + family_guid='family_a', + s='sample_2', + ), + ], + None, + ], + }, + ], + hl.tstruct( + id=hl.tint32, + filters=hl.tset(hl.tstr), + family_entries=hl.tarray( + hl.tarray( + hl.tstruct( + GT=hl.tcall, + family_guid=hl.tstr, + s=hl.tstr, + ), + ), + ), + ), + key='id', + ) + ht = deduplicate_by_most_non_ref_calls(project_ht) + self.assertEqual( + ht.collect(), + [ + hl.Struct( + id=0, + filters={'PASS', 'HIGH_SR_BACKGROUND'}, + family_entries=[ + [ + hl.Struct( + GT=hl.Call(alleles=[0, 1], phased=False), + family_guid='family_a', + s='sample_1', + ), + hl.Struct( + GT=hl.Call(alleles=[0, 0], phased=False), + family_guid='family_a', + s='sample_2', + ), + ], + [ + hl.Struct( + GT=hl.Call(alleles=[0, 1], phased=False), + family_guid='family_b', + s='sample_3', + ), + None, + ], + None, + ], + ), + hl.Struct( + id=2, + filters={'HIGH_SR_BACKGROUND'}, + family_entries=[None, None], + ), + hl.Struct( + id=3, + filters={'PASS'}, + family_entries=[ + [ + hl.Struct( + GT=hl.Call(alleles=[0, 1], phased=False), + family_guid='family_a', + s='sample_1', + ), + hl.Struct( + GT=hl.Call(alleles=[0, 1], phased=False), + family_guid='family_a', + s='sample_2', + ), + ], + None, + ], + ), + ], + ) diff --git a/loading_pipeline/lib/misc/family_loading_failures_test.py b/loading_pipeline/lib/misc/family_loading_failures_test.py new file mode 100644 index 0000000000..fb1d0905d1 --- /dev/null +++ b/loading_pipeline/lib/misc/family_loading_failures_test.py @@ -0,0 +1,448 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.core import Sex +from loading_pipeline.lib.misc.family_loading_failures import ( + all_relatedness_checks, + build_relatedness_check_lookup, + build_sex_check_lookup, + get_families_failed_imputed_sex_ploidy, + get_families_failed_sex_check, +) +from loading_pipeline.lib.misc.io import import_pedigree +from loading_pipeline.lib.misc.pedigree import ( + Family, + Sample, + parse_pedigree_ht_to_families, +) + +TEST_SEX_CHECK_1 = 'loading_pipeline/var/test/sex_check/test_sex_check_1.ht' +TEST_PEDIGREE_6 = 'loading_pipeline/var/test/pedigrees/test_pedigree_6.tsv' + + +class FamilyLoadingFailuresTest(unittest.TestCase): + def test_build_relatedness_check_lookup(self): + ht = hl.Table.parallelize( + [ + { + 'i': 'ROS_006_18Y03226_D1', + 'j': 'ROS_007_19Y05939_D1', + 'ibd0': 0.0, + 'ibd1': 1.0, + 'ibd2': 0.0, + 'pi_hat': 0.5, + }, + ], + hl.tstruct( + i=hl.tstr, + j=hl.tstr, + ibd0=hl.tfloat, + ibd1=hl.tfloat, + ibd2=hl.tfloat, + pi_hat=hl.tfloat, + ), + key=['i', 'j'], + ) + self.assertEqual( + build_relatedness_check_lookup( + ht, + hl.dict({'ROS_006_18Y03226_D1': 'remapped_id'}), + ), + { + ('ROS_007_19Y05939_D1', 'remapped_id'): [ + 0.0, + 1.0, + 0.0, + 0.5, + ], + }, + ) + + def test_build_sex_check_lookup(self): + ht = hl.Table.parallelize( + [ + {'s': 'ROS_006_18Y03226_D1', 'predicted_sex': 'F'}, + {'s': 'ROS_006_18Y03227_D1', 'predicted_sex': 'F'}, + {'s': 'ROS_006_18Y03228_D1', 'predicted_sex': 'F'}, + {'s': 'ROS_007_19Y05919_D1', 'predicted_sex': 'F'}, + {'s': 'ROS_007_19Y05939_D1', 'predicted_sex': 'M'}, + {'s': 'ROS_007_19Y05987_D1', 'predicted_sex': 'U'}, + {'s': 'ROS_007_19Y05989_D1', 'predicted_sex': 'X0'}, + ], + hl.tstruct( + s=hl.tstr, + predicted_sex=hl.tstr, + ), + key='s', + ) + self.assertEqual( + build_sex_check_lookup(ht, hl.dict({'ROS_006_18Y03226_D1': 'remapped_id'})), + { + 'remapped_id': Sex.FEMALE, + 'ROS_006_18Y03227_D1': Sex.FEMALE, + 'ROS_006_18Y03228_D1': Sex.FEMALE, + 'ROS_007_19Y05919_D1': Sex.FEMALE, + 'ROS_007_19Y05939_D1': Sex.MALE, + 'ROS_007_19Y05987_D1': Sex.UNKNOWN, + 'ROS_007_19Y05989_D1': Sex.X0, + }, + ) + + def test_all_relatedness_checks(self): + relatedness_check_lookup = { + # Parent + ('sample_1', 'sample_2'): [ + 0.0, + 0.98, + 0.0, + 0.52, + ], + # GrandParent + ('sample_1', 'sample_3'): [0.48, 0.52, 0, 0.24], + # Half Sibling (but actually a hidden Sibling) + ('sample_1', 'sample_4'): [0.25, 0.5, 0.25, 0.5], + } + sample = Sample( + sex=Sex.FEMALE, + sample_id='sample_1', + mother='sample_2', + paternal_grandfather='sample_3', + half_siblings=['sample_4'], + ) + family = Family( + family_guid='family_1a', + samples={ + 'sample_1': sample, + 'sample_2': Sample(sex=Sex.MALE, sample_id='sample_2'), + 'sample_3': Sample(sex=Sex.MALE, sample_id='sample_3'), + 'sample_4': Sample(sex=Sex.MALE, sample_id='sample_4'), + 'sample_5': Sample(sex=Sex.MALE, sample_id='sample_5'), + }, + ) + failure_reasons = all_relatedness_checks( + relatedness_check_lookup, + family, + sample, + ) + self.assertListEqual(failure_reasons, []) + + # Defined grandparent missing in relatedness table + sample = Sample( + sex=Sex.FEMALE, + sample_id='sample_1', + mother='sample_2', + paternal_grandfather='sample_3', + paternal_grandmother='sample_5', + ) + failure_reasons = all_relatedness_checks( + relatedness_check_lookup, + family, + sample, + ) + self.assertListEqual( + failure_reasons, + [ + 'Sample sample_1 has expected relation "grandparent_grandchild" to sample_5 but has coefficients []', + ], + ) + + # Sibling is actually a half sibling. + relatedness_check_lookup = { + **relatedness_check_lookup, + ('sample_1', 'sample_4'): [0.5, 0.5, 0, 0.25], + } + sample = Sample( + sex=Sex.FEMALE, + sample_id='sample_1', + mother='sample_2', + paternal_grandfather='sample_3', + siblings=['sample_4'], + ) + failure_reasons = all_relatedness_checks( + relatedness_check_lookup, + family, + sample, + ) + self.assertListEqual( + failure_reasons, + [ + 'Sample sample_1 has expected relation "sibling" to sample_4 but has coefficients [0.5, 0.5, 0, 0.25]', + ], + ) + + relatedness_check_lookup = { + **relatedness_check_lookup, + ('sample_1', 'sample_2'): [ + 0.5, + 0.5, + 0.5, + 0.5, + ], + } + sample = Sample( + sex=Sex.FEMALE, + sample_id='sample_1', + mother='sample_2', + paternal_grandfather='sample_3', + siblings=['sample_4'], + ) + failure_reasons = all_relatedness_checks( + relatedness_check_lookup, + family, + sample, + ) + self.assertListEqual( + failure_reasons, + [ + 'Sample sample_1 has expected relation "parent_child" to sample_2 but has coefficients [0.5, 0.5, 0.5, 0.5]', + 'Sample sample_1 has expected relation "sibling" to sample_4 but has coefficients [0.5, 0.5, 0, 0.25]', + ], + ) + + # Some samples will include relationships with + # samples that are not expected to be included + # in the callset. These should not trigger relatedness + # failures. + sample = Sample( + sex=Sex.FEMALE, + sample_id='sample_1', + mother='sample_2', + ) + family = Family( + family_guid='family_1a', + samples={ + 'sample_1': sample, + }, + ) + failure_reasons = all_relatedness_checks( + {}, + family, + sample, + ) + self.assertListEqual( + failure_reasons, + [], + ) + + def test_get_families_failed_sex_check(self): + sex_check_ht = hl.Table.parallelize( + [ + {'s': 'ROS_006_18Y03226_D1', 'predicted_sex': 'F'}, + {'s': 'ROS_006_18Y03227_D1', 'predicted_sex': 'F'}, # Pedigree Sex U + {'s': 'ROS_006_18Y03228_D1', 'predicted_sex': 'F'}, + {'s': 'ROS_007_19Y05939_D1', 'predicted_sex': 'M'}, + {'s': 'ROS_007_19Y05987_D1', 'predicted_sex': 'U'}, # Pedigree Sex F + {'s': 'ROS_007_19Y05989_D1', 'predicted_sex': 'XXX'}, + ], + hl.tstruct( + s=hl.tstr, + predicted_sex=hl.tstr, + ), + key='s', + ) + pedigree_ht = import_pedigree(TEST_PEDIGREE_6) + failed_families = get_families_failed_sex_check( + parse_pedigree_ht_to_families(pedigree_ht), + sex_check_ht, + {}, + ) + self.assertCountEqual( + failed_families.values(), + [ + [ + 'Sample ROS_007_19Y05919_D1 has pedigree sex F but is missing from the sex check source', + 'Sample ROS_007_19Y05939_D1 has pedigree sex F but imputed sex M', + ], + ], + ) + + def test_get_families_failed_imputed_sex_ploidy(self) -> None: + female_sample = 'HG00731_1' + male_sample_1 = 'HG00732_1' + male_sample_2 = 'HG00732_1' + x0_sample = 'NA20899_1' + xxy_sample = 'NA20889_1' + xyy_sample = 'NA20891_1' + xxx_sample = 'NA20892_1' + + sex_check_ht = hl.read_table(TEST_SEX_CHECK_1) + families = { + Family( + family_guid='', + samples={ + female_sample: Sample(female_sample, Sex.FEMALE), + male_sample_1: Sample(male_sample_1, Sex.MALE), + male_sample_2: Sample(male_sample_2, Sex.MALE), + x0_sample: Sample(x0_sample, Sex.X0), + xxy_sample: Sample(xxy_sample, Sex.XXY), + xyy_sample: Sample(xyy_sample, Sex.XYY), + xxx_sample: Sample(xxx_sample, Sex.XXX), + }, + ), + } + + # All calls on X chromosome are valid + mt = ( + hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chrX', + position=1, + reference_genome='GRCh38', + ), + ], + }, + cols={ + 's': [ + female_sample, + male_sample_1, + x0_sample, + xxy_sample, + xyy_sample, + xxx_sample, + ], + }, + entries={ + 'GT': [ + [ + hl.Call(alleles=[0, 0], phased=False), + hl.Call(alleles=[0], phased=False), + hl.Call(alleles=[0, 0], phased=False), # X0 + hl.Call(alleles=[0, 0], phased=False), # XXY + hl.Call(alleles=[0, 0], phased=False), # XYY + hl.Call(alleles=[0, 0], phased=False), # XXX + ], + ], + }, + ) + .key_rows_by('locus') + .key_cols_by('s') + ) + failed_families = get_families_failed_imputed_sex_ploidy( + families, + mt, + sex_check_ht, + ) + self.assertDictEqual(failed_families, {}) + + # All calls on Y chromosome are valid + mt = ( + hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chrY', + position=1, + reference_genome='GRCh38', + ), + ], + }, + cols={ + 's': [ + female_sample, + male_sample_1, + x0_sample, + xxy_sample, + xyy_sample, + xxx_sample, + ], + }, + entries={ + 'GT': [ + [ + hl.missing(hl.tcall), + hl.Call(alleles=[0], phased=False), + hl.missing(hl.tcall), # X0 + hl.Call(alleles=[0, 0], phased=False), # XXY + hl.Call(alleles=[0, 0], phased=False), # XYY + hl.missing(hl.tcall), # XXX + ], + ], + }, + ) + .key_rows_by('locus') + .key_cols_by('s') + ) + failed_families = get_families_failed_imputed_sex_ploidy( + families, + mt, + sex_check_ht, + ) + self.assertDictEqual(failed_families, {}) + + # Invalid X chromosome case + mt = ( + hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chrX', + position=1, + reference_genome='GRCh38', + ), + ], + }, + cols={ + 's': [ + female_sample, + male_sample_1, + male_sample_2, + x0_sample, + xxy_sample, + xyy_sample, + xxx_sample, + ], + }, + entries={ + 'GT': [ + [ + hl.Call(alleles=[0], phased=False), # invalid Female call + hl.Call(alleles=[0], phased=False), # valid Male call + hl.missing(hl.tcall), # invalid Male call + hl.Call(alleles=[0], phased=False), # invalid X0 call + hl.Call(alleles=[0], phased=False), # invalid XXY call + hl.missing(hl.tcall), # valid XYY call + hl.Call(alleles=[0, 0], phased=False), # valid XXX call + ], + ], + }, + ) + .key_rows_by('locus') + .key_cols_by('s') + ) + failed_families = get_families_failed_imputed_sex_ploidy( + families, + mt, + sex_check_ht, + ) + self.assertCountEqual( + failed_families.values(), + [ + [ + "Found samples with misaligned ploidy with their provided imputed sex: ['HG00731_1', 'HG00732_1', 'NA20889_1', 'NA20899_1']", + ], + ], + ) + + # Invalid X chromosome case, but only discrepant family samples are reported + families = { + Family( + family_guid='', + samples={female_sample: Sample(female_sample, Sex.FEMALE)}, + ), + } + failed_families = get_families_failed_imputed_sex_ploidy( + families, + mt, + sex_check_ht, + ) + self.assertCountEqual( + failed_families.values(), + [ + [ + "Found samples with misaligned ploidy with their provided imputed sex: ['HG00731_1']", + ], + ], + ) diff --git a/loading_pipeline/lib/misc/gcnv_test.py b/loading_pipeline/lib/misc/gcnv_test.py new file mode 100644 index 0000000000..33a72f3684 --- /dev/null +++ b/loading_pipeline/lib/misc/gcnv_test.py @@ -0,0 +1,54 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.misc.gcnv import parse_gcnv_genes + + +class GCNVGeneParsingTest(unittest.TestCase): + def test_parse_gcnv_genes(self): + t1 = hl.Table.parallelize( + [ + {'genes': 'AC118553.2,SLC35A3'}, + {'genes': 'AC118553.1,None'}, + {'genes': 'None'}, + {'genes': 'SLC35A3.43'}, + {'genes': ''}, + {'genes': 'SLC35A4.43'}, + ], + hl.tstruct(genes=hl.dtype('str')), + key='genes', + ) + t1 = t1.annotate(gene_set=parse_gcnv_genes(t1.genes)) + self.assertCountEqual( + t1.collect(), + [ + hl.Struct( + genes='AC118553.2,SLC35A3', + gene_set={'AC118553', 'SLC35A3'}, + ), + hl.Struct(genes='AC118553.1,None', gene_set={'AC118553'}), + hl.Struct(genes='None', gene_set=set()), + hl.Struct(genes='SLC35A3.43', gene_set={'SLC35A3'}), + hl.Struct(genes='', gene_set=set()), + hl.Struct(genes='SLC35A4.43', gene_set={'SLC35A4'}), + ], + ) + + def test_aggregate_parsed_genes(self): + t1 = hl.Table.parallelize( + [ + {'genes': 'AC118553.2,SLC35A3'}, + {'genes': 'AC118553.1,None'}, + {'genes': 'None'}, + {'genes': 'SLC35A3.43'}, + {'genes': ''}, + {'genes': 'SLC35A4.43'}, + ], + hl.tstruct(genes=hl.dtype('str')), + key='genes', + ) + aggregated_gene_set = t1.aggregate( + hl.flatten(hl.agg.collect_as_set(parse_gcnv_genes(t1.genes))), + ) + self.assertEqual(aggregated_gene_set, {'SLC35A4', 'SLC35A3', 'AC118553'}) diff --git a/loading_pipeline/lib/misc/io_test.py b/loading_pipeline/lib/misc/io_test.py new file mode 100644 index 0000000000..a346e8b323 --- /dev/null +++ b/loading_pipeline/lib/misc/io_test.py @@ -0,0 +1,211 @@ +import unittest +from unittest import mock + +import hail as hl + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome +from loading_pipeline.lib.misc.io import ( + compute_hail_n_partitions, + file_size_bytes, + import_imputed_sex, + import_vcf, + remap_pedigree_hash, + select_relevant_fields, + split_multi_hts, +) +from loading_pipeline.lib.misc.validation import SeqrValidationError + +TEST_IMPUTED_SEX = 'loading_pipeline/var/test/sex_check/test_imputed_sex.tsv' +TEST_IMPUTED_SEX_UNEXPECTED_VALUE = ( + 'loading_pipeline/var/test/sex_check/test_imputed_sex_unexpected_value.tsv' +) +CORRUPTED_VCF = 'loading_pipeline/var/test/callsets/1kg_corrupt.vcf.gz' +TEST_INVALID_VCF = 'loading_pipeline/var/test/callsets/improperly_formatted.vcf' +TEST_PEDIGREE_3_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_3_remap.tsv' +TEST_MITO_MT = 'loading_pipeline/var/test/callsets/mito_1.mt' + + +class IOTest(unittest.TestCase): + def test_file_size_mb(self) -> None: + # find loading_pipeline/var/test/callsets/mito_1.mt -type f | grep -v 'crc' | xargs ls -alt {} | awk '{sum += $5; print sum}' + # 191310 + self.assertEqual(file_size_bytes(TEST_MITO_MT), 191310) + + def test_compute_hail_n_partitions(self) -> None: + self.assertEqual(compute_hail_n_partitions(23), 1) + self.assertEqual(compute_hail_n_partitions(191310), 1) + self.assertEqual(compute_hail_n_partitions(1913100000), 58) + + def test_import_imputed_sex(self) -> None: + ht = import_imputed_sex(TEST_IMPUTED_SEX) + self.assertListEqual( + ht.collect(), + [ + hl.Struct(s='abc_1', predicted_sex='M'), + hl.Struct(s='abc_2', predicted_sex='F'), + hl.Struct(s='abc_3', predicted_sex='U'), + hl.Struct(s='abc_4', predicted_sex='XYY'), + hl.Struct(s='abc_5', predicted_sex='U'), + ], + ) + + def test_import_imputed_sex_unexpected_value(self) -> None: + ht = import_imputed_sex(TEST_IMPUTED_SEX_UNEXPECTED_VALUE) + self.assertRaisesRegex( + hl.utils.java.HailUserError, + 'Found unexpected value UNKNOWN in imputed sex file', + ht.collect, + ) + + def test_remap_pedigree_hash(self) -> None: + self.assertEqual( + hl.eval( + remap_pedigree_hash( + TEST_PEDIGREE_3_REMAP, + ), + ), + 573002191, + ) + + def test_import_vcf(self) -> None: + self.assertRaisesRegex( + TypeError, + 'missing 1 required positional argument', + import_vcf, + 'abc', + ) + self.assertRaisesRegex( + SeqrValidationError, + 'Unable to access the VCF in cloud storage', + import_vcf, + 'bad.vcf', + ReferenceGenome.GRCh38, + ) + self.assertRaisesRegex( + SeqrValidationError, + 'Gzip-compressed data is corrupt', + import_vcf, + CORRUPTED_VCF, + ReferenceGenome.GRCh38, + ) + with mock.patch( + 'loading_pipeline.lib.misc.io.hl.read_table', + ) as mock_read_table: + mock_read_table.side_effect = hl.utils.java.FatalError( + 'GoogleJsonResponseException: 403 Forbidden', + ) + self.assertRaisesRegex( + SeqrValidationError, + 'Unable to access the VCF in cloud storage', + import_vcf, + 'abc123/bad.vcf', + ReferenceGenome.GRCh38, + ) + self.assertRaisesRegex( + SeqrValidationError, + 'VCF failed file format validation: Your input file has a malformed header: We never saw the required CHROM header line \\(starting with one #\\) for the input VCF file', + import_vcf, + TEST_PEDIGREE_3_REMAP, + ReferenceGenome.GRCh38, + ) + self.assertRaisesRegex( + SeqrValidationError, + "VCF failed file format validation: invalid character 'N' in integer literal", + import_vcf, + TEST_INVALID_VCF, + ReferenceGenome.GRCh38, + ) + + def test_select_missing_field(self) -> None: + self.assertRaisesRegex( + SeqrValidationError, + "Your callset is missing a required field: 'a magic field'", + select_relevant_fields, + hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + ], + 'alleles': [ + ['A', 'C'], + ], + 'rsid': ['rs1233'], + 'filters': [{'PASS'}], + }, + cols={'s': ['sample_1']}, + entries={ + 'GT': [[hl.Call([0, 0])]], + 'AD': [[[0, 20]]], + 'GQ': [[99]], + }, + ).key_rows_by('locus', 'alleles'), + DatasetType.SNV_INDEL, + {'a magic field': hl.tint32}, + ) + + def test_split_multi_failure(self) -> None: + self.assertRaisesRegex( + SeqrValidationError, + 'Your callset failed while attempting to split multiallelic sites. This error can occur if the dataset contains both multiallelic variants and duplicated loci.', + split_multi_hts, + hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + ], + 'alleles': [ + ['A', 'G', 'AC'], + ['A', 'AT', 'C', 'G'], + ], + }, + cols={'s': ['sample_1']}, + entries={ + 'GQ': [[99], [98]], + }, + ) + .key_rows_by('locus', 'alleles') + .repartition(1), + False, + 1, + ) + + def test_split_multi_failure_ad_length(self) -> None: + self.assertRaisesRegex( + SeqrValidationError, + 'Your callset failed while attempting to split multiallelic sites. This error can occur if the provided Allele Depth \\(AD\\) field does not match the length of the multiallelic site.', + split_multi_hts, + hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + ], + 'alleles': [ + ['GAC', 'G', 'GTTTTTTTTTTTTTTTAC'], + ], + }, + cols={'s': ['sample_1']}, + entries={ + 'GQ': [[99]], + 'AD': [[[0, 1]]], + }, + ).key_rows_by('locus', 'alleles'), + False, + 1, + ) diff --git a/loading_pipeline/lib/misc/math_test.py b/loading_pipeline/lib/misc/math_test.py new file mode 100644 index 0000000000..19e12d6bfc --- /dev/null +++ b/loading_pipeline/lib/misc/math_test.py @@ -0,0 +1,12 @@ +import unittest + +from loading_pipeline.lib.misc.math import constrain + + +class TestConstrainFunction(unittest.TestCase): + def test_constrain(self): + self.assertEqual(constrain(5, 0, 10), 5) + self.assertEqual(constrain(-3, 0, 10), 0) + self.assertEqual(constrain(15, 0, 10), 10) + with self.assertRaises(ValueError): + constrain(5, 10, 0) diff --git a/loading_pipeline/lib/misc/nested_field_test.py b/loading_pipeline/lib/misc/nested_field_test.py new file mode 100644 index 0000000000..8d465187a5 --- /dev/null +++ b/loading_pipeline/lib/misc/nested_field_test.py @@ -0,0 +1,81 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.misc.nested_field import parse_nested_field + + +class TestConstrainFunction(unittest.TestCase): + def test_parse_nested_field(self): + ht = hl.Table.parallelize( + [ + { + 'locus': hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + 'alleles': ['A', 'C'], + 'a': hl.Struct(d=1), + 'b': hl.Struct(e=[2, 9]), + 'h': hl.Struct(**{'i.j': 1}), + 'a_index': 1, + }, + { + 'locus': hl.Locus( + contig='chr1', + position=2, + reference_genome='GRCh38', + ), + 'alleles': ['A', 'C'], + 'a': hl.Struct(d=3), + 'b': hl.Struct(e=[4, 5]), + 'h': hl.Struct(**{'i.j': 2}), + 'a_index': 1, + }, + ], + hl.tstruct( + locus=hl.tlocus('GRCh38'), + alleles=hl.tarray(hl.tstr), + a=hl.tstruct(d=hl.tint32), + b=hl.tstruct(e=hl.tarray(hl.tint32)), + h=hl.tstruct(**{'i.j': hl.tint32}), + a_index=hl.tint32, + ), + key=['locus', 'alleles'], + ) + ht = ht.select( + d=parse_nested_field(ht, 'a.d'), + e=parse_nested_field(ht, 'b.e#'), + f=parse_nested_field(ht, 'a'), + g=parse_nested_field(ht, 'h.i.j'), + ) + self.assertListEqual( + ht.collect(), + [ + hl.Struct( + locus=hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + alleles=['A', 'C'], + d=1, + e=2, + f=hl.Struct(d=1), + g=1, + ), + hl.Struct( + locus=hl.Locus( + contig='chr1', + position=2, + reference_genome='GRCh38', + ), + alleles=['A', 'C'], + d=3, + e=4, + f=hl.Struct(d=3), + g=2, + ), + ], + ) diff --git a/loading_pipeline/lib/misc/pedigree_test.py b/loading_pipeline/lib/misc/pedigree_test.py new file mode 100644 index 0000000000..77432ba138 --- /dev/null +++ b/loading_pipeline/lib/misc/pedigree_test.py @@ -0,0 +1,514 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.core import Sex +from loading_pipeline.lib.misc.io import import_pedigree +from loading_pipeline.lib.misc.pedigree import ( + Family, + Sample, + parse_pedigree_ht_to_families, +) + +TEST_PEDIGREE_1 = 'loading_pipeline/var/test/pedigrees/test_pedigree_1.tsv' +TEST_PEDIGREE_2 = 'loading_pipeline/var/test/pedigrees/test_pedigree_2.tsv' +TEST_PEDIGREE_9 = 'loading_pipeline/var/test/pedigrees/test_pedigree_9.tsv' + + +class PedigreesTest(unittest.TestCase): + def test_empty_pedigree(self) -> None: + with self.assertRaises(Exception): # noqa: B017 + _ = import_pedigree(TEST_PEDIGREE_1) + + def test_parse_lineage(self) -> None: + # + # + # sample_9 sample_10 sample_7 + # \ / \ | + # sample_6 -> sample_8 --------- sample_3 ----- ? | + # \ / \ / | + # sample_4, sample_5 sample_2 | sample_1 + # + # + samples = Family.parse_direct_lineage( + [ + hl.Struct(s='sample_1', maternal_s=None, paternal_s=None, sex='F'), + hl.Struct( + s='sample_2', + maternal_s='sample_3', + paternal_s=None, + sex='M', + ), + hl.Struct( + s='sample_3', + maternal_s=None, + paternal_s='sample_7', + sex='F', + ), + hl.Struct( + s='sample_4', + maternal_s='sample_3', + paternal_s='sample_8', + sex='M', + ), + hl.Struct( + s='sample_5', + maternal_s='sample_3', + paternal_s='sample_8', + sex='M', + ), + hl.Struct( + s='sample_6', + maternal_s='sample_9', + paternal_s='sample_10', + sex='M', + ), + hl.Struct(s='sample_7', maternal_s=None, paternal_s=None, sex='M'), + hl.Struct( + s='sample_8', + maternal_s='sample_9', + paternal_s='sample_10', + sex='F', + ), + hl.Struct(s='sample_9', maternal_s=None, paternal_s=None, sex='F'), + hl.Struct(s='sample_10', maternal_s=None, paternal_s=None, sex='M'), + ], + ) + self.assertEqual( + Family.parse_collateral_lineage(samples), + { + 'sample_1': Sample( + sample_id='sample_1', + sex=Sex.FEMALE, + mother=None, + father=None, + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'sample_2': Sample( + sample_id='sample_2', + sex=Sex.MALE, + mother='sample_3', + father=None, + maternal_grandmother=None, + maternal_grandfather='sample_7', + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=['sample_4', 'sample_5'], + aunt_nephews=[], + ), + 'sample_3': Sample( + sample_id='sample_3', + sex=Sex.FEMALE, + mother=None, + father='sample_7', + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'sample_4': Sample( + sample_id='sample_4', + sex=Sex.MALE, + mother='sample_3', + father='sample_8', + maternal_grandmother=None, + maternal_grandfather='sample_7', + paternal_grandmother='sample_9', + paternal_grandfather='sample_10', + siblings=['sample_5'], + half_siblings=[], + aunt_nephews=['sample_6'], + ), + 'sample_5': Sample( + sample_id='sample_5', + sex=Sex.MALE, + mother='sample_3', + father='sample_8', + maternal_grandmother=None, + maternal_grandfather='sample_7', + paternal_grandmother='sample_9', + paternal_grandfather='sample_10', + siblings=[], + half_siblings=[], + aunt_nephews=['sample_6'], + ), + 'sample_6': Sample( + sample_id='sample_6', + sex=Sex.MALE, + mother='sample_9', + father='sample_10', + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=['sample_8'], + half_siblings=[], + aunt_nephews=[], + ), + 'sample_7': Sample( + sample_id='sample_7', + sex=Sex.MALE, + mother=None, + father=None, + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'sample_8': Sample( + sample_id='sample_8', + sex=Sex.FEMALE, + mother='sample_9', + father='sample_10', + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'sample_9': Sample( + sample_id='sample_9', + sex=Sex.FEMALE, + mother=None, + father=None, + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'sample_10': Sample( + sample_id='sample_10', + sex=Sex.MALE, + mother=None, + father=None, + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + }, + ) + + def test_parse_parent_not_aunt_uncle(self) -> None: + samples = Family.parse_direct_lineage( + [ + hl.Struct(s='sample_1', maternal_s=None, paternal_s=None, sex='F'), + hl.Struct( + s='sample_2', + maternal_s=None, + paternal_s=None, + sex='M', + ), + hl.Struct( + s='sample_3', + maternal_s='sample_1', + paternal_s='sample_2', + sex='F', + ), + hl.Struct( + s='sample_4', + maternal_s='sample_3', + paternal_s=None, + sex='F', + ), + hl.Struct( + s='sample_5', + maternal_s='sample_3', + paternal_s=None, + sex='F', + ), + ], + ) + self.assertEqual( + Family.parse_collateral_lineage(samples), + { + 'sample_1': Sample( + sample_id='sample_1', + sex=Sex.FEMALE, + mother=None, + father=None, + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'sample_2': Sample( + sample_id='sample_2', + sex=Sex.MALE, + mother=None, + father=None, + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'sample_3': Sample( + sample_id='sample_3', + sex=Sex.FEMALE, + mother='sample_1', + father='sample_2', + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'sample_4': Sample( + sample_id='sample_4', + sex=Sex.FEMALE, + mother='sample_3', + father=None, + maternal_grandmother='sample_1', + maternal_grandfather='sample_2', + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=['sample_5'], + aunt_nephews=[], + ), + 'sample_5': Sample( + sample_id='sample_5', + sex=Sex.FEMALE, + mother='sample_3', + father=None, + maternal_grandmother='sample_1', + maternal_grandfather='sample_2', + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + }, + ) + + def test_parse_project(self) -> None: + pedigree_ht = import_pedigree(TEST_PEDIGREE_2) + self.assertCountEqual( + list(parse_pedigree_ht_to_families(pedigree_ht)), + [ + Family( + family_guid='BBL_BC1-000345_1', + samples={ + 'BBL_BC1-000345_01_D1': Sample( + sample_id='BBL_BC1-000345_01_D1', + sex=Sex.UNKNOWN, + mother='BBL_BC1-000345_03_D1', + father='BBL_BC1-000345_02_D1', + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'BBL_BC1-000345_02_D1': Sample( + sample_id='BBL_BC1-000345_02_D1', + sex=Sex.MALE, + mother=None, + father=None, + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'BBL_BC1-000345_03_D1': Sample( + sample_id='BBL_BC1-000345_03_D1', + sex=Sex.FEMALE, + mother=None, + father=None, + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + }, + ), + Family( + family_guid='BBL_HT-007-5195_1', + samples={ + 'BBL_HT-007-5195_01_D1': Sample( + sample_id='BBL_HT-007-5195_01_D1', + sex=Sex.FEMALE, + mother='BBL_HT-007-5195_03_D1', + father='BBL_HT-007-5195_02_D1', + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[ + 'BBL_HT-007-5195_04_D1', + 'BBL_HT-007-5195_05_D1', + 'BBL_HT-007-5195_06_D1', + ], + half_siblings=[], + aunt_nephews=[], + ), + 'BBL_HT-007-5195_02_D1': Sample( + sample_id='BBL_HT-007-5195_02_D1', + sex=Sex.MALE, + mother=None, + father=None, + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'BBL_HT-007-5195_03_D1': Sample( + sample_id='BBL_HT-007-5195_03_D1', + sex=Sex.FEMALE, + mother=None, + father=None, + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'BBL_HT-007-5195_04_D1': Sample( + sample_id='BBL_HT-007-5195_04_D1', + sex=Sex.MALE, + mother='BBL_HT-007-5195_03_D1', + father='BBL_HT-007-5195_02_D1', + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=['BBL_HT-007-5195_05_D1', 'BBL_HT-007-5195_06_D1'], + half_siblings=[], + aunt_nephews=[], + ), + 'BBL_HT-007-5195_05_D1': Sample( + sample_id='BBL_HT-007-5195_05_D1', + sex=Sex.FEMALE, + mother='BBL_HT-007-5195_03_D1', + father='BBL_HT-007-5195_02_D1', + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=['BBL_HT-007-5195_06_D1'], + half_siblings=[], + aunt_nephews=[], + ), + 'BBL_HT-007-5195_06_D1': Sample( + sample_id='BBL_HT-007-5195_06_D1', + sex=Sex.MALE, + mother='BBL_HT-007-5195_03_D1', + father='BBL_HT-007-5195_02_D1', + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + }, + ), + Family( + family_guid='BBL_SDS1-000178_1', + samples={ + 'BBL_SDS1-000178_01_D1': Sample( + sample_id='BBL_SDS1-000178_01_D1', + sex=Sex.FEMALE, + mother=None, + father=None, + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + }, + ), + ], + ) + + def test_subsetted_pedigree_with_removed_parent(self) -> None: + pedigree_ht = import_pedigree(TEST_PEDIGREE_2) + pedigree_ht = pedigree_ht.filter( + pedigree_ht.s != 'BBL_BC1-000345_02_D1', + ) + parsed_pedigree = parse_pedigree_ht_to_families(pedigree_ht) + family = next( + iter( + [ + family + for family in parsed_pedigree + if family.family_guid == 'BBL_BC1-000345_1' + ], + ), + ) + self.assertEqual(len(family.samples), 2) + self.assertFalse( + 'BBL_BC1-000345_02_D1' in family.samples, + ) + self.assertEqual( + family.samples['BBL_BC1-000345_01_D1'].father, + 'BBL_BC1-000345_02_D1', + ) + self.assertEqual( + family.samples['BBL_BC1-000345_01_D1'].mother, + 'BBL_BC1-000345_03_D1', + ) + + def test_pedigree_ungrouped_families(self) -> None: + pedigree_ht = import_pedigree(TEST_PEDIGREE_9) + parsed_pedigree = parse_pedigree_ht_to_families(pedigree_ht) + self.assertEqual(len(parsed_pedigree), 2) + family = next( + iter( + [ + family + for family in parsed_pedigree + if family.family_guid == 'family_2_1' + ], + ), + ) + self.assertTrue( + family.samples.keys() == {'RGP_164_1', 'RGP_164_2', 'RGP_164_4'}, + ) diff --git a/loading_pipeline/lib/misc/retry_test.py b/loading_pipeline/lib/misc/retry_test.py new file mode 100644 index 0000000000..4b756abce1 --- /dev/null +++ b/loading_pipeline/lib/misc/retry_test.py @@ -0,0 +1,69 @@ +import unittest +from unittest.mock import Mock, patch + +from loading_pipeline.lib.core import DatasetType +from loading_pipeline.lib.misc.retry import retry + + +class TestRetryDecorator(unittest.TestCase): + @patch('time.sleep', return_value=None) + def test_retry_success_first_try(self, mock_sleep): + mock_func = Mock(return_value='success') + + @retry(tries=3, delay=1, backoff=2) + def func(d: DatasetType): + return mock_func(d) + + result = func(DatasetType.SNV_INDEL) + self.assertEqual(result, 'success') + self.assertEqual(mock_func.call_count, 1) + mock_sleep.assert_not_called() + + @patch('time.sleep', return_value=None) + @patch('loading_pipeline.lib.misc.retry.logger') + def test_retry_eventual_success(self, mock_logger, mock_sleep): + mock_func = Mock( + side_effect=[Exception('fail'), Exception('fail again'), 'success'], + ) + + @retry(tries=3, delay=1, backoff=2) + def func(): + return mock_func() + + result = func() + self.assertEqual(result, 'success') + self.assertEqual(mock_func.call_count, 3) + self.assertEqual(mock_sleep.call_count, 2) + mock_sleep.assert_any_call(1) + mock_sleep.assert_any_call(2) + + @patch('time.sleep', return_value=None) + @patch('loading_pipeline.lib.misc.retry.logger') + def test_retry_all_failures(self, mock_logger, mock_sleep): + mock_func = Mock(side_effect=Exception('always fails')) + + @retry(tries=3, delay=1, backoff=2) + def func(): + return mock_func() + + with self.assertRaises(Exception) as context: + func() + + self.assertEqual(str(context.exception), 'always fails') + self.assertEqual(mock_func.call_count, 3) + self.assertEqual(mock_sleep.call_count, 2) + + @patch('time.sleep', return_value=None) + @patch('loading_pipeline.lib.misc.retry.logger.exception') + def test_logs_retry_message(self, mock_log, mock_sleep): + mock_func = Mock(side_effect=[Exception('fail'), 'success']) + + @retry(tries=2, delay=1, backoff=2) + def func(d: DatasetType): + return mock_func(d) + + func(d=DatasetType.SNV_INDEL) + self.assertIn( + 'func args: kwargs:d=SNV_INDEL failed on attempt 1 after 0.00s, retrying in 1 seconds.', + mock_log.call_args[0][0], + ) diff --git a/loading_pipeline/lib/misc/runs_test.py b/loading_pipeline/lib/misc/runs_test.py new file mode 100644 index 0000000000..b1a601727a --- /dev/null +++ b/loading_pipeline/lib/misc/runs_test.py @@ -0,0 +1,84 @@ +import os + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome +from loading_pipeline.lib.misc.runs import get_run_ids +from loading_pipeline.lib.paths import ( + clickhouse_load_fail_file_path, + clickhouse_load_success_file_path, + pipeline_run_success_file_path, + runs_path, +) +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + + +class RunsTest(MockedDatarootTestCase): + def setUp(self): + super().setUp() + run_ids = [ + 'manual__2024-08-05T16-07-58.365146+00-00', + 'manual__2024-08-06T10-15-23.123456+00-00', + 'manual__2024-08-07T12-30-45.654321+00-00', # _SUCCESS, _CLICKHOUSE_LOAD_FAIL + 'manual__2024-08-08T09-45-00.000000+00-00', # _SUCCESS + 'manual__2024-08-09T18-22-13.999999+00-00', # _SUCCESS, _CLICKHOUSE_LOAD_SUCCESS + ] + for reference_genome, dataset_type in [ + (ReferenceGenome.GRCh38, DatasetType.SNV_INDEL), + (ReferenceGenome.GRCh37, DatasetType.SNV_INDEL), + (ReferenceGenome.GRCh38, DatasetType.GCNV), + (ReferenceGenome.GRCh37, DatasetType.GCNV), + ]: + for run_id in run_ids: + base_path = runs_path(reference_genome, dataset_type) + os.makedirs(os.path.join(base_path, run_id), exist_ok=True) + if '07T12' in run_id: + failure_file = clickhouse_load_fail_file_path( + reference_genome, + dataset_type, + run_id, + ) + open(failure_file, 'w').close() + if '09' in run_id or '07T12' in run_id: + success_file = pipeline_run_success_file_path( + reference_genome, + dataset_type, + run_id, + ) + open(success_file, 'w').close() + if '09T18' in run_id: + success_file = clickhouse_load_success_file_path( + reference_genome, + dataset_type, + run_id, + ) + open(success_file, 'w').close() + + def test_get_run_ids(self) -> None: + ( + successful_pipeline_runs, + successful_clickhouse_loads, + failed_clickhouse_loads, + ) = get_run_ids() + self.assertCountEqual( + successful_pipeline_runs[(ReferenceGenome.GRCh38, DatasetType.SNV_INDEL)], + { + 'manual__2024-08-09T18-22-13.999999+00-00', + 'manual__2024-08-08T09-45-00.000000+00-00', + 'manual__2024-08-07T12-30-45.654321+00-00', + }, + ) + self.assertCountEqual( + successful_clickhouse_loads[ + (ReferenceGenome.GRCh38, DatasetType.SNV_INDEL) + ], + { + 'manual__2024-08-09T18-22-13.999999+00-00', + }, + ) + self.assertCountEqual( + successful_clickhouse_loads[(ReferenceGenome.GRCh37, DatasetType.GCNV)], + {}, + ) + self.assertCountEqual( + failed_clickhouse_loads[(ReferenceGenome.GRCh38, DatasetType.SNV_INDEL)], + {'manual__2024-08-07T12-30-45.654321+00-00'}, + ) diff --git a/loading_pipeline/lib/misc/sample_ids_test.py b/loading_pipeline/lib/misc/sample_ids_test.py new file mode 100644 index 0000000000..6d3fb7efd0 --- /dev/null +++ b/loading_pipeline/lib/misc/sample_ids_test.py @@ -0,0 +1,160 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.misc.sample_ids import ( + remap_sample_ids, + subset_samples, +) +from loading_pipeline.lib.misc.validation import SeqrValidationError + +CALLSET_MT = hl.MatrixTable.from_parts( + rows={'variants': [1, 2]}, + cols={'s': ['HG00731', 'HG00732', 'HG00733']}, + entries={ + 'GT': [ + [hl.Call([0, 1]), hl.missing(hl.tcall), hl.Call([0, 1])], + [hl.Call([0, 1]), hl.Call([0, 1]), hl.Call([1, 1])], + ], + }, +).key_cols_by('s') + + +class SampleLookupTest(unittest.TestCase): + def test_remap_2_sample_ids(self) -> None: + # remap 2 of 3 samples in callset + project_remap_ht = hl.Table.parallelize( + [ + {'s': 'HG00731', 'seqr_id': 'HG00731_1'}, + {'s': 'HG00732', 'seqr_id': 'HG00732_1'}, + ], + hl.tstruct( + s=hl.tstr, + seqr_id=hl.tstr, + ), + key='s', + ) + + remapped_mt = remap_sample_ids( + CALLSET_MT, + project_remap_ht, + ) + + self.assertEqual(remapped_mt.cols().count(), 3) + self.assertEqual( + remapped_mt.cols().collect(), + [ + hl.Struct( + col_idx=0, + s='HG00731_1', + seqr_id='HG00731_1', + vcf_id='HG00731', + ), + hl.Struct( + col_idx=1, + s='HG00732_1', + seqr_id='HG00732_1', + vcf_id='HG00732', + ), + hl.Struct(col_idx=2, s='HG00733', seqr_id='HG00733', vcf_id='HG00733'), + ], + ) + + def test_remap_sample_ids_remap_has_duplicate(self) -> None: + # remap file has 2 rows for HG00732 + project_remap_ht = hl.Table.parallelize( + [ + {'s': 'HG00731', 'seqr_id': 'HG00731_1'}, + {'s': 'HG00732', 'seqr_id': 'HG00732_1'}, + {'s': 'HG00732', 'seqr_id': 'HG00732_1'}, # duplicate + ], + hl.tstruct( + s=hl.tstr, + seqr_id=hl.tstr, + ), + key='s', + ) + + with self.assertRaises(SeqrValidationError): + remap_sample_ids( + CALLSET_MT, + project_remap_ht, + ) + + def test_remap_sample_ids_remap_has_missing_samples(self) -> None: + # remap file has 4 rows, but only 3 samples in callset + project_remap_ht = hl.Table.parallelize( + [ + {'s': 'HG00731', 'seqr_id': 'HG00731_1'}, + {'s': 'HG00732', 'seqr_id': 'HG00732_1'}, + {'s': 'HG00733', 'seqr_id': 'HG00733_1'}, + {'s': 'HG00734', 'seqr_id': 'HG00734_1'}, # missing in callset + ], + hl.tstruct( + s=hl.tstr, + seqr_id=hl.tstr, + ), + key='s', + ) + + with self.assertRaises(SeqrValidationError): + remap_sample_ids( + CALLSET_MT, + project_remap_ht, + ) + + def test_subset_samples_zero_samples(self): + # subset 0 of 3 samples in callset + sample_subset_ht = hl.Table.parallelize( + [], + hl.tstruct(s=hl.tstr), + key='s', + ) + + with self.assertRaises(SeqrValidationError): + subset_samples( + CALLSET_MT, + sample_subset_ht, + ) + + def test_subset_samples_missing_samples(self): + # subset 2 of 3 samples in callset, but 1 is missing + sample_subset_ht = hl.Table.parallelize( + [ + {'s': 'HG00731'}, + {'s': 'HG00732'}, + {'s': 'HG00734'}, # missing in callset + ], + hl.tstruct(s=hl.tstr), + key='s', + ) + + with self.assertRaises(SeqrValidationError): + subset_samples( + CALLSET_MT, + sample_subset_ht, + ) + + def test_subset_no_defined_gt(self): + mt = hl.MatrixTable.from_parts( + rows={'variants': [1, 2]}, + cols={'s': ['HG00731', 'HG00732']}, + entries={ + 'GT': [ + [hl.Call([1, 1]), hl.missing(hl.tcall)], + [hl.Call([1, 1]), hl.Call([1, 1])], + ], + }, + ).key_cols_by('s') + sample_subset_ht = hl.Table.parallelize( + [ + {'s': 'HG00732'}, + ], + hl.tstruct(s=hl.tstr), + key='s', + ) + mt = subset_samples( + mt, + sample_subset_ht, + ) + self.assertEqual(mt.count(), (1, 1)) diff --git a/loading_pipeline/lib/misc/sv_test.py b/loading_pipeline/lib/misc/sv_test.py new file mode 100644 index 0000000000..aefa8a5cd5 --- /dev/null +++ b/loading_pipeline/lib/misc/sv_test.py @@ -0,0 +1,243 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, Sex +from loading_pipeline.lib.misc.io import import_callset, select_relevant_fields +from loading_pipeline.lib.misc.pedigree import Family, Sample +from loading_pipeline.lib.misc.sample_ids import subset_samples +from loading_pipeline.lib.misc.sv import ( + deduplicate_merged_sv_concordance_calls, + overwrite_male_non_par_calls, +) + +TEST_SV_VCF = 'loading_pipeline/var/test/callsets/sv_1.vcf' +ANNOTATIONS_HT = hl.Table.parallelize( + [ + { + 'variant_id': 'BND_chr1_6', + 'algorithms': 'manta', + 'end_locus': hl.Locus( + contig='chr5', + position=20404, + reference_genome='GRCh38', + ), + }, + { + 'variant_id': 'BND_chr1_9', + 'algorithms': 'manta', + 'end_locus': hl.Locus( + contig='chr1', + position=789481, + reference_genome='GRCh38', + ), + }, + { + 'variant_id': 'CPX_chr1_22', + 'algorithms': 'manta', + 'end_locus': hl.Locus( + contig='chr1', + position=6559723, + reference_genome='GRCh38', + ), + }, + ], + hl.tstruct( + variant_id=hl.tstr, + algorithms=hl.tstr, + end_locus=hl.tlocus('GRCh38'), + ), + key='variant_id', +) + + +class SVTest(unittest.TestCase): + def test_overwrite_male_non_par_calls(self) -> None: + mt = import_callset(TEST_SV_VCF, ReferenceGenome.GRCh38, DatasetType.SV) + mt = select_relevant_fields( + mt, + DatasetType.SV, + ) + mt = subset_samples( + mt, + hl.Table.parallelize( + [{'s': sample_id} for sample_id in ['RGP_164_1', 'RGP_164_2']], + hl.tstruct(s=hl.dtype('str')), + key='s', + ), + ) + mt = overwrite_male_non_par_calls( + mt, + { + Family( + family_guid='family_1', + samples={ + 'RGP_164_1': Sample(sample_id='RGP_164_1', sex=Sex.FEMALE), + 'RGP_164_2': Sample(sample_id='RGP_164_2', sex=Sex.MALE), + }, + ), + }, + ) + mt = mt.filter_rows(mt.locus.contig == 'chrX') + self.assertEqual( + [ + hl.Locus(contig='chrX', position=3, reference_genome='GRCh38'), + hl.Locus(contig='chrX', position=2781700, reference_genome='GRCh38'), + ], + mt.locus.collect(), + ) + self.assertEqual( + [ + hl.Call(alleles=[0, 0], phased=False), + # END of this variant < start of the non-par region. + hl.Call(alleles=[0, 1], phased=False), + hl.Call(alleles=[0, 0], phased=False), + hl.Call(alleles=[1], phased=False), + ], + mt.GT.collect(), + ) + self.assertFalse( + hasattr(mt, 'start_locus'), + ) + + def test_deduplicate_merged_sv_concordance_calls(self) -> None: + mt = ( + hl.MatrixTable.from_parts( + rows={ + 'variant_id': [ + 'new_v1', + 'new_v2', + 'new_v3', + ], + 'locus': [ + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=2, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=3, + reference_genome='GRCh38', + ), + ], + 'info.END': [ + 1, + 2, + 3, + ], + 'info.END2': [ + 1, + 2, + 3, + ], + 'info.CHR2': [ + 'chr1', + 'chr1', + 'chr1', + ], + 'info.SEQR_INTERNAL_TRUTH_VID': [ + 'BND_chr1_6', + 'BND_chr1_9', + 'CPX_chr1_22', + ], + }, + cols={'s': ['sample_1']}, + entries={'GQ': [[99] for _ in range(3)]}, + ) + .key_rows_by('variant_id') + .key_cols_by('s') + ) + mt = deduplicate_merged_sv_concordance_calls( + mt, + ANNOTATIONS_HT, + ) + self.assertEqual( + mt['info.SEQR_INTERNAL_TRUTH_VID'].collect(), + [ + 'BND_chr1_6', + 'BND_chr1_9', + 'CPX_chr1_22', + ], + ) + + mt = ( + hl.MatrixTable.from_parts( + rows={ + 'variant_id': [ + 'new_v1', + 'new_v2', + 'new_v3', + 'new_v4', + ], + 'locus': [ + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=2, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=3, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=4, + reference_genome='GRCh38', + ), + ], + 'info.END': [ + 1, + 2, + 789481, + 789485, + ], + 'info.END2': [ + 1, + 2, + 789481, + 789485, + ], + 'info.CHR2': [ + 'chr1', + 'chr1', + 'chr2', + 'chr1', + ], + 'info.SEQR_INTERNAL_TRUTH_VID': [ + 'BND_chr1_6', + 'BND_chr1_9', + 'BND_chr1_9', + 'BND_chr1_9', + ], + }, + cols={'s': ['sample_1']}, + entries={'GQ': [[99] for _ in range(4)]}, + ) + .key_rows_by('variant_id') + .key_cols_by('s') + ) + mt = deduplicate_merged_sv_concordance_calls( + mt, + ANNOTATIONS_HT, + ) + self.assertEqual( + mt['info.SEQR_INTERNAL_TRUTH_VID'].collect(), + [ + 'BND_chr1_6', + None, + None, + 'BND_chr1_9', + ], + ) diff --git a/loading_pipeline/lib/misc/terra_data_repository_test.py b/loading_pipeline/lib/misc/terra_data_repository_test.py new file mode 100644 index 0000000000..91b044d68f --- /dev/null +++ b/loading_pipeline/lib/misc/terra_data_repository_test.py @@ -0,0 +1,321 @@ +import json +import os +import unittest +from types import SimpleNamespace +from unittest.mock import Mock, call, patch + +import responses + +from loading_pipeline.lib.misc.terra_data_repository import ( + TDR_ROOT_URL, + _get_dataset_ids, + bq_metrics_query, + gen_bq_table_names, +) + +TDR_DATASETS = [ + { + 'id': '2dc51ee0-a037-499d-a915-a7c20a0b216d', + 'name': 'RP_3053', + 'description': 'TGG_Ware_DRAGEN_hg38. Dataset automatically created and linked to: RP-3053', + 'defaultProfileId': '0a164b9a-2b8b-45d2-859e-a4e369b9cb4f', + 'createdDate': '2023-10-05T13:15:27.649760Z', + 'storage': [ + { + 'region': 'us-central1', + 'cloudResource': 'bigquery', + 'cloudPlatform': 'gcp', + }, + { + 'region': 'us-east4', + 'cloudResource': 'firestore', + 'cloudPlatform': 'gcp', + }, + { + 'region': 'us-central1', + 'cloudResource': 'bucket', + 'cloudPlatform': 'gcp', + }, + ], + 'secureMonitoringEnabled': False, + 'cloudPlatform': 'gcp', + 'dataProject': 'datarepo-7242affb', + 'storageAccount': None, + 'phsId': None, + 'selfHosted': False, + 'predictableFileIds': False, + 'tags': [], + 'resourceLocks': { + 'exclusive': None, + 'shared': [], + }, + }, + { + 'id': 'beef77e8-575b-40e5-9340-a6f10e0bec67', + 'name': 'RP_3056', + 'description': 'RGP_HMB_DRAGEN_hg38. Dataset automatically created and linked to: RP-3056', + 'defaultProfileId': '835dd05d-c603-4b0d-926f-d9143fd24549', + 'createdDate': '2023-10-05T20:15:27.622481Z', + 'storage': [ + { + 'region': 'us-central1', + 'cloudResource': 'bigquery', + 'cloudPlatform': 'gcp', + }, + { + 'region': 'us-east4', + 'cloudResource': 'firestore', + 'cloudPlatform': 'gcp', + }, + { + 'region': 'us-central1', + 'cloudResource': 'bucket', + 'cloudPlatform': 'gcp', + }, + ], + 'secureMonitoringEnabled': False, + 'cloudPlatform': 'gcp', + 'dataProject': 'datarepo-5a72e31b', + 'storageAccount': None, + 'phsId': None, + 'selfHosted': False, + 'predictableFileIds': False, + 'tags': [], + 'resourceLocks': { + 'exclusive': None, + 'shared': [], + }, + }, + { + 'id': 'c8d74ac4-9a2e-4d3d-a6b5-1f4b433d949f', + 'name': 'RP_3055', + 'description': 'RGP_GRU_DRAGEN_hg38. Dataset automatically created and linked to: RP-3055', + 'defaultProfileId': '835dd05d-c603-4b0d-926f-d9143fd24549', + 'createdDate': '2023-10-05T20:15:28.255304Z', + 'storage': [ + { + 'region': 'us-central1', + 'cloudResource': 'bigquery', + 'cloudPlatform': 'gcp', + }, + { + 'region': 'us-east4', + 'cloudResource': 'firestore', + 'cloudPlatform': 'gcp', + }, + { + 'region': 'us-central1', + 'cloudResource': 'bucket', + 'cloudPlatform': 'gcp', + }, + ], + 'secureMonitoringEnabled': False, + 'cloudPlatform': 'gcp', + 'dataProject': 'datarepo-0f5be351', + 'storageAccount': None, + 'phsId': None, + 'selfHosted': False, + 'predictableFileIds': False, + 'tags': [], + 'resourceLocks': { + 'exclusive': None, + 'shared': [ + 'Gw_KTeYRS1aLhRvapMLYLg', + 'WrP-0w1aROOUbgkI8JS6Ug', + ], + }, + }, +] + + +@patch( + 'loading_pipeline.lib.misc.terra_data_repository.get_service_account_credentials', + return_value=SimpleNamespace( + token='abcdefg', # noqa: S106 + ), +) +class TerraDataRepositoryTest(unittest.TestCase): + @responses.activate + def test_get_dataset_ids(self, _: Mock) -> None: + responses.get( + os.path.join(TDR_ROOT_URL, 'datasets?limit=50000'), + body=json.dumps( + { + 'total': 3, + 'filteredTotal': 3, + 'items': TDR_DATASETS, + }, + ), + ) + self.assertListEqual( + _get_dataset_ids(), + [ + '2dc51ee0-a037-499d-a915-a7c20a0b216d', + 'beef77e8-575b-40e5-9340-a6f10e0bec67', + 'c8d74ac4-9a2e-4d3d-a6b5-1f4b433d949f', + ], + ) + + @responses.activate + def test_get_dataset_ids_no_bq(self, _: Mock) -> None: + responses.get( + os.path.join(TDR_ROOT_URL, 'datasets'), + body=json.dumps( + { + 'total': 1, + 'filteredTotal': 1, + 'items': [ + { + 'id': '2dc51ee0-a037-499d-a915-a7c20a0b216d', + 'name': 'RP_3053', + 'description': 'TGG_Ware_DRAGEN_hg38. Dataset automatically created and linked to: RP-3053', + 'defaultProfileId': '0a164b9a-2b8b-45d2-859e-a4e369b9cb4f', + 'createdDate': '2023-10-05T13:15:27.649760Z', + 'storage': [ + # NB: bigquery was removed from 'storage' here. + { + 'region': 'us-east4', + 'cloudResource': 'firestore', + 'cloudPlatform': 'gcp', + }, + { + 'region': 'us-central1', + 'cloudResource': 'bucket', + 'cloudPlatform': 'gcp', + }, + ], + 'secureMonitoringEnabled': False, + 'cloudPlatform': 'gcp', + 'dataProject': 'datarepo-7242affb', + 'storageAccount': None, + 'phsId': None, + 'selfHosted': False, + 'predictableFileIds': False, + 'tags': [], + 'resourceLocks': { + 'exclusive': None, + 'shared': [], + }, + }, + ], + }, + ), + ) + self.assertRaises( + ValueError, + _get_dataset_ids, + ) + + @responses.activate + def test_gen_bq_table_names(self, _: Mock) -> None: + responses.get( + os.path.join(TDR_ROOT_URL, 'datasets'), + body=json.dumps( + { + 'total': 3, + 'filteredTotal': 3, + 'items': TDR_DATASETS, + }, + ), + ) + for dataset_id, name, project_name, dataset_name in [ + ( + '2dc51ee0-a037-499d-a915-a7c20a0b216d', + 'RP_3053', + 'datarepo-7242affb', + 'datarepo_RP_3053', + ), + ( + 'beef77e8-575b-40e5-9340-a6f10e0bec67', + 'RP_3056', + 'datarepo-5a72e31b', + 'datarepo_RP_3056', + ), + ( + 'c8d74ac4-9a2e-4d3d-a6b5-1f4b433d949f', + 'RP_3059', + 'datarepo-aada2e3b', + 'datarepo_RP_3059', + ), + ]: + responses.get( + os.path.join( + TDR_ROOT_URL, + f'datasets/{dataset_id}?include=ACCESS_INFORMATION', + ), + body=json.dumps( + { + 'id': dataset_id, + 'name': name, + 'description': 'TGG_Ware_DRAGEN_hg38. Dataset automatically created and linked to: RP-3053', + 'defaultProfileId': None, + 'dataProject': None, + 'defaultSnapshotId': None, + 'schema': None, + 'createdDate': '2023-10-05T13:15:27.649760Z', + 'storage': None, + 'secureMonitoringEnabled': False, + 'phsId': None, + 'accessInformation': { + 'bigQuery': { + 'datasetName': dataset_name, + 'datasetId': f'{project_name}:{dataset_name}', + 'projectId': project_name, + 'link': 'https://console.cloud.google.com/bigquery?project=datarepo-7242affb&ws=!datarepo_RP_3053&d=datarepo_RP_3053&p=datarepo-7242affb&page=dataset', + 'tables': [ + { + 'name': 'jointcallset', + 'id': f'{project_name}.{dataset_name}.jointcallset', + 'qualifiedName': 'datarepo-7242affb.datarepo_RP_3053.jointcallset', + 'link': 'https://console.cloud.google.com/bigquery?project=datarepo-7242affb&ws=!datarepo_RP_3053&d=datarepo_RP_3053&p=datarepo-7242affb&page=table&t=jointcallset', + 'sampleQuery': 'SELECT * FROM `datarepo-7242affb.datarepo_RP_3053.jointcallset`', + }, + { + 'name': 'sample', + 'id': f'{project_name}.{dataset_name}.sample', + 'qualifiedName': 'datarepo-7242affb.datarepo_RP_3053.sample', + 'link': 'https://console.cloud.google.com/bigquery?project=datarepo-7242affb&ws=!datarepo_RP_3053&d=datarepo_RP_3053&p=datarepo-7242affb&page=table&t=sample', + 'sampleQuery': 'SELECT * FROM `datarepo-7242affb.datarepo_RP_3053.sample`', + }, + ], + }, + 'parquet': None, + }, + 'cloudPlatform': None, + 'selfHosted': False, + 'properties': None, + 'ingestServiceAccount': None, + 'predictableFileIds': False, + 'tags': [], + 'resourceLocks': { + 'exclusive': None, + 'shared': [], + }, + }, + ), + ) + self.assertCountEqual( + list(gen_bq_table_names()), + [ + 'datarepo-7242affb.datarepo_RP_3053', + 'datarepo-5a72e31b.datarepo_RP_3056', + 'datarepo-aada2e3b.datarepo_RP_3059', + ], + ) + + @patch('loading_pipeline.lib.misc.terra_data_repository.bigquery.Client') + def test_bq_metrics_query_missing_metrics( + self, + mock_bq_client: Mock, + _: Mock, + ) -> None: + mock_bq_client.return_value.query_and_wait.return_value = iter( + [['predicted_sex,contamination_rate,percent_bases_at_20x']], + ) + bq_metrics_query('datarepo-7242affb.datarepo_RP_3053') + self.assertEqual( + mock_bq_client.return_value.query_and_wait.mock_calls[1], + call( + '\n SELECT predicted_sex,contamination_rate,percent_bases_at_20x,NULL AS collaborator_sample_id,NULL AS mean_coverage FROM `datarepo-7242affb.datarepo_RP_3053.sample`;\n ', + ), + ) diff --git a/loading_pipeline/lib/misc/validation_test.py b/loading_pipeline/lib/misc/validation_test.py new file mode 100644 index 0000000000..bb368b85a5 --- /dev/null +++ b/loading_pipeline/lib/misc/validation_test.py @@ -0,0 +1,464 @@ +import unittest +from unittest.mock import patch + +import hail as hl + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.misc.validation import ( + SeqrValidationError, + validate_allele_depth_length, + validate_allele_type, + validate_expected_contig_frequency, + validate_imported_field_types, + validate_no_duplicate_variants, + validate_sample_type, +) + +TEST_MITO_MT = 'loading_pipeline/var/test/callsets/mito_1.mt' + + +def _mt_from_contigs(contigs): + return ( + hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig=contig, + position=1, + reference_genome='GRCh38', + ) + for contig in contigs + ], + }, + cols={'s': ['sample_1']}, + entries={'HL': [[0.0] for _ in range(len(contigs))]}, + ) + .key_rows_by('locus') + .key_cols_by('s') + ) + + +class ValidationTest(unittest.TestCase): + def test_validate_allele_type(self) -> None: + mt = ( + hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=2, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=3, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=4, + reference_genome='GRCh38', + ), + ], + 'alleles': [ + ['A', 'T'], + # NB: star alleles should pass through this validation just fine, + # but are eventually filtered out upstream. + ['A', '*'], + ['A', '-'], + ['A', ''], + ], + }, + cols={'s': ['sample_1']}, + entries={'HL': [[0.0], [0.0], [0.0], [0.0]]}, + ) + .key_rows_by('locus', 'alleles') + .key_cols_by('s') + ) + self.assertRaisesRegex( + SeqrValidationError, + "Alleles with invalid AlleleType are present in the callset: \\[\\('A', '-'\\), \\('A', ''\\)\\]", + validate_allele_type, + mt, + DatasetType.SNV_INDEL, + ) + + mt = ( + hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=2, + reference_genome='GRCh38', + ), + ], + 'alleles': [ + ['C', ''], + ['A', ''], + ], + }, + cols={'s': ['sample_1']}, + entries={'HL': [[0.0], [0.0]]}, + ) + .key_rows_by('locus', 'alleles') + .key_cols_by('s') + ) + self.assertRaisesRegex( + SeqrValidationError, + 'Alleles with invalid allele are present in the callset. This appears to be a GVCF containing records for sites with no variants.', + validate_allele_type, + mt, + DatasetType.SNV_INDEL, + ) + + def test_validate_allele_depth_length(self) -> None: + mt = ( + hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=2, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=3, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=4, + reference_genome='GRCh38', + ), + ], + 'alleles': [ + ['A', 'T'], + # NB: star alleles should pass through this validation just fine, + # but are eventually filtered out upstream. + ['A', 'TC', 'TG'], + ['A', 'TTT'], + ['A', 'CCC'], + ], + }, + cols={'s': ['sample_1', 'sample_2']}, + entries={ + 'AD': [ + [[1, 0], [1, 0]], + [[1], [1, 0, 1]], + [[1, 0], [1]], + [[1, 0], [1, 0]], + ], + }, + ) + .key_rows_by('locus', 'alleles') + .key_cols_by('s') + ) + self.assertRaisesRegex( + SeqrValidationError, + "Found variants with unequal Allele Depth array lengths over samples \\(first 10, if applicable\\): \\{'1-2-A-TC-TG': \\{1, 3\\}, '1-3-A-TTT': \\{1, 2\\}\\}", + validate_allele_depth_length, + mt, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + ) + + def test_validate_imported_field_types(self) -> None: + mt = hl.read_matrix_table(TEST_MITO_MT) + validate_imported_field_types(mt, DatasetType.MITO, {}) + mt = mt.annotate_cols(contamination=hl.int32(mt.contamination)) + mt = mt.annotate_entries(DP=hl.float32(mt.DP)) + mt = mt.annotate_rows(vep=hl.dict({'t': '1'})) + self.assertRaisesRegex( + SeqrValidationError, + "Found unexpected field types on MatrixTable after import: \\['contamination: int32', 'DP: float32', 'vep: dict', 'tester: missing'\\]", + validate_imported_field_types, + mt, + DatasetType.MITO, + {'tester': hl.tfloat32}, + ) + + def test_validate_no_duplicate_variants(self) -> None: + mt = ( + hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=2, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=2, + reference_genome='GRCh38', + ), + ], + 'alleles': [ + ['A', 'C'], + ['A', 'C'], + ['A', 'C'], + ], + }, + cols={'s': ['sample_1']}, + entries={'HL': [[0.0], [0.0], [0.0]]}, + ) + .key_rows_by('locus', 'alleles') + .key_cols_by('s') + ) + self.assertRaisesRegex( + SeqrValidationError, + "Variants are present multiple times in the callset: \\['1-2-A-C'\\]", + validate_no_duplicate_variants, + mt, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + ) + + def test_validate_expected_contig_frequency(self) -> None: + mt = _mt_from_contigs(ReferenceGenome.GRCh38.standard_contigs) + self.assertIsNone( + validate_expected_contig_frequency(mt, ReferenceGenome.GRCh38, 1), + ) + self.assertRaisesRegex( + SeqrValidationError, + 'Missing the following expected contigs', + validate_expected_contig_frequency, + mt, + ReferenceGenome.GRCh37, + 1, + ) + self.assertRaisesRegex( + SeqrValidationError, + 'which is lower than expected minimum count', + validate_expected_contig_frequency, + mt, + ReferenceGenome.GRCh38, + 2, + ) + + # Drop an optional contig + mt = _mt_from_contigs(ReferenceGenome.GRCh38.standard_contigs - {'chrY'}) + self.assertIsNone( + validate_expected_contig_frequency(mt, ReferenceGenome.GRCh38, 1), + ) + + # Drop a non-optional contig + mt = _mt_from_contigs(ReferenceGenome.GRCh38.standard_contigs - {'chr3'}) + self.assertRaisesRegex( + SeqrValidationError, + 'Missing the following expected contigs', + validate_expected_contig_frequency, + mt, + ReferenceGenome.GRCh38, + 1, + ) + + def test_validate_sample_type(self) -> None: + mt = _mt_from_contigs(ReferenceGenome.GRCh38.standard_contigs) + coding_and_noncoding_variants_ht = hl.Table.parallelize( + [ + { + 'locus': hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + 'coding': True, + 'noncoding': False, + }, + { + 'locus': hl.Locus( + contig='chr2', + position=1, + reference_genome='GRCh38', + ), + 'coding': True, + 'noncoding': False, + }, + { + 'locus': hl.Locus( + contig='chr3', + position=1, + reference_genome='GRCh38', + ), + 'coding': False, + 'noncoding': True, + }, + { + 'locus': hl.Locus( + contig='chr4', + position=1, + reference_genome='GRCh38', + ), + 'coding': False, + 'noncoding': True, + }, + ], + hl.tstruct( + locus=hl.tlocus('GRCh38'), + coding=hl.tbool, + noncoding=hl.tbool, + ), + key='locus', + ) + self.assertIsNone( + validate_sample_type( + mt, + ReferenceGenome.GRCh38, + SampleType.WGS, + ['project_a'], + coding_and_noncoding_variants_ht, + ), + ) + self.assertRaisesRegex( + SeqrValidationError, + 'specified as WES but appears to be WGS', + validate_sample_type, + mt, + ReferenceGenome.GRCh38, + SampleType.WES, + ['project_a'], + coding_and_noncoding_variants_ht, + ) + + # has coding, but not noncoding now. + coding_and_noncoding_variants_ht = hl.Table.parallelize( + [ + { + 'locus': hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + 'coding': True, + 'noncoding': False, + }, + { + 'locus': hl.Locus( + contig='chr2', + position=1, + reference_genome='GRCh38', + ), + 'coding': True, + 'noncoding': False, + }, + { + 'locus': hl.Locus( + contig='chr2', + position=2, + reference_genome='GRCh38', + ), + 'coding': False, + 'noncoding': True, + }, + ], + hl.tstruct( + locus=hl.tlocus('GRCh38'), + coding=hl.tbool, + noncoding=hl.tbool, + ), + key='locus', + ) + self.assertIsNone( + validate_sample_type( + mt, + ReferenceGenome.GRCh38, + SampleType.WES, + ['project_a'], + coding_and_noncoding_variants_ht, + ), + ) + self.assertRaisesRegex( + SeqrValidationError, + 'specified as WGS but appears to be WES', + validate_sample_type, + mt, + ReferenceGenome.GRCh38, + SampleType.WGS, + ['project_a'], + coding_and_noncoding_variants_ht, + ) + + # has noncoding, but not coding now. + coding_and_noncoding_variants_ht = hl.Table.parallelize( + [ + { + 'locus': hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + 'coding': False, + 'noncoding': True, + }, + { + 'locus': hl.Locus( + contig='chr2', + position=1, + reference_genome='GRCh38', + ), + 'coding': False, + 'noncoding': True, + }, + { + 'locus': hl.Locus( + contig='chr2', + position=2, + reference_genome='GRCh38', + ), + 'coding': True, + 'noncoding': False, + }, + ], + hl.tstruct( + locus=hl.tlocus('GRCh38'), + coding=hl.tbool, + noncoding=hl.tbool, + ), + key='locus', + ) + self.assertRaisesRegex( + SeqrValidationError, + 'contains noncoding variants but is missing common coding variants', + validate_sample_type, + mt, + ReferenceGenome.GRCh38, + SampleType.WGS, + ['project_a'], + coding_and_noncoding_variants_ht, + ) + + # Validation safe if all projects are to be skipped + with patch('loading_pipeline.lib.misc.validation.Env') as mock_env: + mock_env.SAMPLE_TYPE_VALIDATION_EXCLUDED_PROJECTS = ['project_a'] + self.assertIsNone( + validate_sample_type( + mt, + ReferenceGenome.GRCh38, + SampleType.WGS, + ['project_a'], + coding_and_noncoding_variants_ht, + ), + ) diff --git a/loading_pipeline/lib/misc/vets_test.py b/loading_pipeline/lib/misc/vets_test.py new file mode 100644 index 0000000000..b26de113b7 --- /dev/null +++ b/loading_pipeline/lib/misc/vets_test.py @@ -0,0 +1,104 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.misc.io import split_multi_hts +from loading_pipeline.lib.misc.vets import ( + annotate_vets, +) + + +class VetsTest(unittest.TestCase): + def test_annotate_vets(self) -> None: + gatk_mt = hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + ], + 'filters': [ + hl.set(['NO_HQ_GENOTYPES']), + ], + }, + cols={'s': ['sample_1']}, + entries={'HL': [[0.0]]}, + ).key_rows_by('locus') + gatk_mt = annotate_vets(gatk_mt) + dragen_mt = hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=2, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=3, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=4, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=5, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=6, + reference_genome='GRCh38', + ), + ], + 'alleles': [ + ['A', 'T'], + ['A', 'T'], + ['A', 'T'], + ['AC', 'T'], + ['AT', 'ATC'], + ['AG', 'ATG'], + ], + 'filters': [ + hl.set(['NO_HQ_GENOTYPES']), + hl.empty_set(hl.tstr), + hl.missing(hl.tset(hl.tstr)), + hl.set(['NO_HQ_GENOTYPES']), + hl.empty_set(hl.tstr), + hl.set(['NO_HQ_GENOTYPES']), + ], + 'info.CALIBRATION_SENSITIVITY': [ + ['0.999'], + ['0.995'], + ['0.999'], + ['0.98'], + ['0.99'], + ['0.991'], + ], + }, + cols={'s': ['sample_1']}, + entries={'HL': [[0.0], [0.0], [0.0], [0.0], [0.0], [0.0]]}, + ).key_rows_by('locus', 'alleles') + dragen_mt = split_multi_hts(dragen_mt, False) + dragen_mt = annotate_vets(dragen_mt) + self.assertListEqual( + dragen_mt.filters.collect(), + [ + {'NO_HQ_GENOTYPES', 'high_CALIBRATION_SENSITIVITY_SNP'}, + set(), + {'high_CALIBRATION_SENSITIVITY_SNP'}, + {'NO_HQ_GENOTYPES'}, + set(), + {'NO_HQ_GENOTYPES', 'high_CALIBRATION_SENSITIVITY_INDEL'}, + ], + ) diff --git a/loading_pipeline/lib/paths_test.py b/loading_pipeline/lib/paths_test.py new file mode 100644 index 0000000000..d271cfee0b --- /dev/null +++ b/loading_pipeline/lib/paths_test.py @@ -0,0 +1,180 @@ +import unittest +from unittest.mock import patch + +import hailtop.fs as hfs + +from loading_pipeline.lib.core import ( + DatasetType, + ReferenceGenome, + SampleType, +) +from loading_pipeline.lib.paths import ( + imported_callset_path, + metadata_for_run_path, + new_variants_table_path, + project_pedigree_path, + project_table_path, + relatedness_check_table_path, + remapped_and_subsetted_callset_path, + sex_check_table_path, + tdr_metrics_path, + validation_errors_for_run_path, + variant_annotations_table_path, +) + +TEST_VCF = 'loading_pipeline/var/test/callsets/1kg_30varia*.vcf' + + +class TestPaths(unittest.TestCase): + def test_project_table_path(self) -> None: + self.assertEqual( + project_table_path( + ReferenceGenome.GRCh38, + DatasetType.MITO, + SampleType.WES, + 'R0652_pipeline_test', + ), + '/var/seqr/pipeline-data/GRCh38/MITO/projects/WES/R0652_pipeline_test.ht', + ) + with ( + patch('loading_pipeline.lib.paths.Env') as mock_env, + ): + mock_env.PIPELINE_DATA_DIR = '/var/bucket/' + self.assertEqual( + project_table_path( + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + SampleType.WES, + 'R0652_pipeline_test', + ), + '/var/bucket/GRCh37/SNV_INDEL/projects/WES/R0652_pipeline_test.ht', + ) + + def test_sex_check_table_path(self) -> None: + self.assertEqual( + sex_check_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + '/var/abc.efg/callset.vcf.gz', + ), + '/var/seqr/seqr-loading-temp/GRCh38/SNV_INDEL/sex_check/f92b8ab6b5b8c41fa20d7d49a5626b96dcd2ba79fa6f61eab7ffb80d550d951c.ht', + ) + + def test_relatedness_check_table_path(self) -> None: + self.assertEqual( + relatedness_check_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + '/var/abc.efg/callset.vcf.gz', + ), + '/var/seqr/seqr-loading-temp/GRCh38/SNV_INDEL/relatedness_check/f92b8ab6b5b8c41fa20d7d49a5626b96dcd2ba79fa6f61eab7ffb80d550d951c.ht', + ) + + def test_validation_errors_for_run_path(self) -> None: + self.assertEqual( + validation_errors_for_run_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + 'manual__2023-06-26T18:30:09.349671+00:00', + ), + '/var/seqr/pipeline-data/GRCh38/SNV_INDEL/runs/manual__2023-06-26T18:30:09.349671+00:00/validation_errors.json', + ) + + def test_metadata_for_run_path(self) -> None: + self.assertEqual( + metadata_for_run_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + 'manual__2023-06-26T18:30:09.349671+00:00', + ), + '/var/seqr/pipeline-data/GRCh38/SNV_INDEL/runs/manual__2023-06-26T18:30:09.349671+00:00/metadata.json', + ) + + def test_variant_annotations_table_path(self) -> None: + self.assertEqual( + variant_annotations_table_path( + ReferenceGenome.GRCh38, + DatasetType.GCNV, + ), + '/var/seqr/pipeline-data/GRCh38/GCNV/annotations.ht', + ) + + def test_remapped_and_subsetted_callset_path(self) -> None: + self.assertEqual( + remapped_and_subsetted_callset_path( + ReferenceGenome.GRCh38, + DatasetType.GCNV, + '/var/abc.efg/callset.vcf.gz', + 'R0111_tgg_bblanken_wes', + ), + '/var/seqr/seqr-loading-temp/GRCh38/GCNV/remapped_and_subsetted_callsets/R0111_tgg_bblanken_wes/f92b8ab6b5b8c41fa20d7d49a5626b96dcd2ba79fa6f61eab7ffb80d550d951c.mt', + ) + self.assertEqual( + remapped_and_subsetted_callset_path( + ReferenceGenome.GRCh38, + DatasetType.GCNV, + '/var/abc.efg/callset/*.vcf.gz', + 'R0111_tgg_bblanken_wes', + ), + '/var/seqr/seqr-loading-temp/GRCh38/GCNV/remapped_and_subsetted_callsets/R0111_tgg_bblanken_wes/26f481b386721f9889250c6549905660728ec9f77be4b8f7eeb6c4facc76282e.mt', + ) + + def test_imported_callset_path(self) -> None: + self.assertEqual( + imported_callset_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + '/var/abc.efg/callset.vcf.gz', + ), + '/var/seqr/seqr-loading-temp/GRCh38/SNV_INDEL/imported_callsets/f92b8ab6b5b8c41fa20d7d49a5626b96dcd2ba79fa6f61eab7ffb80d550d951c.mt', + ) + + with patch('loading_pipeline.lib.paths.hfs.ls') as mock_ls: + mock_ls.return_value = [ + hfs.stat_result.FileListEntry( + path='loading_pipeline/var/test/callsets/1kg_30variants.vcf', + owner=None, + size=1732033623.804012, + typ=hfs.stat_result.FileType(2), + modification_time=1732033000, + ), + ] + self.assertEqual( + imported_callset_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_VCF, + ), + '/var/seqr/seqr-loading-temp/GRCh38/SNV_INDEL/imported_callsets/01327e46c8747f15feaad2c08875b928c274dcb248ad40837ea3f49d8b4dedfb.mt', + ) + + def test_tdr_metrics_path(self) -> None: + self.assertEqual( + tdr_metrics_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + 'datarepo-7242affb.datarepo_RP_3053', + ), + '/var/seqr/seqr-loading-temp/GRCh38/SNV_INDEL/tdr_metrics/datarepo-7242affb.datarepo_RP_3053.tsv', + ) + + def test_new_variants_table_path(self) -> None: + self.assertEqual( + new_variants_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + 'manual__2023-06-26T18:30:09.349671+00:00', + ), + '/var/seqr/pipeline-data/GRCh38/SNV_INDEL/runs/manual__2023-06-26T18:30:09.349671+00:00/new_variants.ht', + ) + + def test_project_pedigree_path(self) -> None: + self.assertEqual( + project_pedigree_path( + ReferenceGenome.GRCh38, + DatasetType.GCNV, + SampleType.WES, + 'R0652_pipeline_test', + ), + '/var/seqr/seqr-loading-temp/GRCh38/GCNV/pedigrees/WES/R0652_pipeline_test_pedigree.tsv', + ) diff --git a/loading_pipeline/lib/reference_datasets/gnomad_exomes_test.py b/loading_pipeline/lib/reference_datasets/gnomad_exomes_test.py new file mode 100644 index 0000000000..639dc6d894 --- /dev/null +++ b/loading_pipeline/lib/reference_datasets/gnomad_exomes_test.py @@ -0,0 +1,72 @@ +import unittest +from unittest.mock import patch + +import hail as hl + +from loading_pipeline.lib.core.definitions import ReferenceGenome +from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset + +GNOMAD_EXOMES_37_PATH = ( + 'loading_pipeline/var/test/reference_datasets/raw/gnomad_exomes_37.ht' +) +GNOMAD_EXOMES_38_PATH = ( + 'loading_pipeline/var/test/reference_datasets/raw/gnomad_exomes_38.ht' +) + + +class GnomadTest(unittest.TestCase): + def test_gnomad_exomes_37(self): + with patch.object( + ReferenceDataset, + 'path', + return_value=GNOMAD_EXOMES_37_PATH, + ): + ht = ReferenceDataset.gnomad_exomes.get_ht(ReferenceGenome.GRCh37) + self.assertEqual( + ht.collect(), + [ + hl.Struct( + locus=hl.Locus( + contig='1', + position=12586, + reference_genome='GRCh37', + ), + alleles=['C', 'T'], + AF=0.0005589714855886996, + AN=3578, + AC=2, + Hom=0, + AF_POPMAX_OR_GLOBAL=0.0022026430815458298, + FAF_AF=9.839000267675146e-05, + Hemi=0, + ), + ], + ) + + def test_gnomad_exomes_38(self): + with patch.object( + ReferenceDataset, + 'path', + return_value=GNOMAD_EXOMES_38_PATH, + ): + ht = ReferenceDataset.gnomad_exomes.get_ht(ReferenceGenome.GRCh38) + self.assertEqual( + ht.collect(), + [ + hl.Struct( + locus=hl.Locus( + contig='chr1', + position=12138, + reference_genome='GRCh38', + ), + alleles=['C', 'A'], + AF=0.00909090880304575, + AN=110, + AC=1, + Hom=0, + AF_POPMAX_OR_GLOBAL=0.009803921915590763, + FAF_AF=0.0, + Hemi=0, + ), + ], + ) diff --git a/loading_pipeline/lib/reference_datasets/gnomad_genomes_test.py b/loading_pipeline/lib/reference_datasets/gnomad_genomes_test.py new file mode 100644 index 0000000000..df637c2fda --- /dev/null +++ b/loading_pipeline/lib/reference_datasets/gnomad_genomes_test.py @@ -0,0 +1,72 @@ +import unittest +from unittest.mock import patch + +import hail as hl + +from loading_pipeline.lib.core.definitions import ReferenceGenome +from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset + +GNOMAD_GENOMES_37_PATH = ( + 'loading_pipeline/var/test/reference_datasets/raw/gnomad_genomes_37.ht' +) +GNOMAD_GENOMES_38_PATH = ( + 'loading_pipeline/var/test/reference_datasets/raw/gnomad_genomes_38.ht' +) + + +class GnomadTest(unittest.TestCase): + def test_gnomad_genomes_37(self): + with patch.object( + ReferenceDataset, + 'path', + return_value=GNOMAD_GENOMES_37_PATH, + ): + ht = ReferenceDataset.gnomad_genomes.get_ht(ReferenceGenome.GRCh37) + self.assertEqual( + ht.collect(), + [ + hl.Struct( + locus=hl.Locus( + contig='1', + position=10131, + reference_genome='GRCh37', + ), + alleles=['CT', 'C'], + AF=3.6635403375839815e-05, + AN=27296, + AC=1, + Hom=0, + AF_POPMAX_OR_GLOBAL=3.6635403375839815e-05, + FAF_AF=0.0, + Hemi=0, + ), + ], + ) + + def test_gnomad_genomes_38(self): + with patch.object( + ReferenceDataset, + 'path', + return_value=GNOMAD_GENOMES_38_PATH, + ): + ht = ReferenceDataset.gnomad_genomes.get_ht(ReferenceGenome.GRCh38) + self.assertEqual( + ht.collect(), + [ + hl.Struct( + locus=hl.Locus( + contig='chr1', + position=10057, + reference_genome='GRCh38', + ), + alleles=['A', 'C'], + AF=2.642333674884867e-05, + AN=113536, + AC=3, + Hom=0, + AF_POPMAX_OR_GLOBAL=3.779861071961932e-05, + FAF_AF=7.019999884505523e-06, + Hemi=0, + ), + ], + ) diff --git a/loading_pipeline/lib/reference_datasets/gnomad_svs_test.py b/loading_pipeline/lib/reference_datasets/gnomad_svs_test.py new file mode 100644 index 0000000000..bfd7c89d11 --- /dev/null +++ b/loading_pipeline/lib/reference_datasets/gnomad_svs_test.py @@ -0,0 +1,93 @@ +import unittest +from unittest.mock import patch + +import hail as hl + +from loading_pipeline.lib.core import ReferenceGenome +from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset + +TEST_GNOMAD_SVS_RAW_HT = ( + 'loading_pipeline/var/test/reference_datasets/raw/gnomad_svs_from_vcf.ht' +) + + +class GnomadSVsTest(unittest.TestCase): + @patch('loading_pipeline.lib.reference_datasets.gnomad_svs.vcf_to_ht') + def test_gnomad_svs(self, mock_vcf_to_ht): + mock_vcf_to_ht.return_value = hl.read_table(TEST_GNOMAD_SVS_RAW_HT) + ht = ReferenceDataset.gnomad_svs.get_ht(ReferenceGenome.GRCh38) + self.assertEqual( + ht.collect(), + [ + hl.Struct( + KEY='gnomAD-SV_v3_BND_chr1_1a45f73a', + locus=hl.Locus( + contig='chr1', + position=10434, + reference_genome=ReferenceGenome.GRCh38, + ), + alleles=['N', ''], + AF=0.11413399875164032, + AC=8474, + AN=74246, + N_HET=8426, + N_HOM=24, + ), + hl.Struct( + KEY='gnomAD-SV_v3_BND_chr1_3fa36917', + locus=hl.Locus( + contig='chr1', + position=10440, + reference_genome=ReferenceGenome.GRCh38, + ), + alleles=['N', ''], + AF=0.004201000090688467, + AC=466, + AN=110936, + N_HET=466, + N_HOM=0, + ), + hl.Struct( + KEY='gnomAD-SV_v3_BND_chr1_7bbf34b5', + locus=hl.Locus( + contig='chr1', + position=10464, + reference_genome=ReferenceGenome.GRCh38, + ), + alleles=['N', ''], + AF=0.03698499873280525, + AC=3119, + AN=84332, + N_HET=3115, + N_HOM=2, + ), + hl.Struct( + KEY='gnomAD-SV_v3_BND_chr1_933a2971', + locus=hl.Locus( + contig='chr1', + position=10450, + reference_genome=ReferenceGenome.GRCh38, + ), + alleles=['N', ''], + AF=0.3238990008831024, + AC=21766, + AN=67200, + N_HET=21616, + N_HOM=75, + ), + hl.Struct( + KEY='gnomAD-SV_v3_DUP_chr1_01c2781c', + locus=hl.Locus( + contig='chr1', + position=10000, + reference_genome=ReferenceGenome.GRCh38, + ), + alleles=['N', ''], + AF=0.0019970000721514225, + AC=139, + AN=69594, + N_HET=139, + N_HOM=0, + ), + ], + ) diff --git a/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster_test.py b/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster_test.py new file mode 100644 index 0000000000..6634feea8c --- /dev/null +++ b/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster_test.py @@ -0,0 +1,162 @@ +import unittest +from types import SimpleNamespace +from unittest.mock import Mock, call, patch + +import google.api_core.exceptions +import google.cloud.dataproc_v1.types.clusters +import luigi + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome +from loading_pipeline.lib.misc.gcp import SOCIAL_AUTH_GOOGLE_OAUTH2_SCOPE +from loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster import ( + CreateDataprocClusterTask, +) + + +@patch.multiple( + 'loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster.Env', + GCLOUD_PROJECT='proj', + GCLOUD_REGION='us-a', +) +@patch( + 'loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster.get_service_account_credentials', + return_value=SimpleNamespace( + service_account_email='test@serviceaccount.com', + scopes=SOCIAL_AUTH_GOOGLE_OAUTH2_SCOPE, + ), +) +@patch( + 'loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster.dataproc.ClusterControllerClient', +) +class CreateDataprocClusterTaskTest(unittest.TestCase): + def test_spinup_cluster_already_exists_failed( + self, + mock_cluster_controller: Mock, + *_: Mock, + ) -> None: + mock_client = mock_cluster_controller.return_value + mock_client.get_cluster.return_value = SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.ERROR, + ), + cluster_name='abc', + ) + mock_client.create_cluster.side_effect = ( + google.api_core.exceptions.AlreadyExists('cluster exists') + ) + worker = luigi.worker.Worker() + task = CreateDataprocClusterTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id='2', + ) + worker.add(task) + worker.run() + self.assertFalse(task.complete()) + + def test_spinup_cluster_already_exists_success( + self, + mock_cluster_controller: Mock, + *_: Mock, + ) -> None: + mock_client = mock_cluster_controller.return_value + mock_client.get_cluster.return_value = SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.RUNNING, + ), + ) + mock_client.create_cluster.side_effect = ( + google.api_core.exceptions.AlreadyExists('cluster exists') + ) + worker = luigi.worker.Worker() + task = CreateDataprocClusterTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id='3', + ) + worker.add(task) + worker.run() + self.assertTrue(task.complete()) + + @patch('loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster.logger') + def test_spinup_cluster_doesnt_exist_failed( + self, + mock_logger: Mock, + mock_cluster_controller: Mock, + *_: Mock, + ) -> None: + mock_client = mock_cluster_controller.return_value + mock_client.get_cluster.side_effect = [ + google.api_core.exceptions.NotFound( + 'cluster not found', + ), + google.api_core.exceptions.NotFound( + 'cluster not found', + ), + SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.CREATING, + ), + ), + SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.ERROR, + ), + cluster_name='dataproc-cluster-5', + cluster_uuid='12345', + ), + ] + worker = luigi.worker.Worker() + task = CreateDataprocClusterTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id='4', + ) + worker.add(task) + luigi_task_result = worker.run() + self.assertEqual(luigi_task_result, False) + mock_logger.info.assert_has_calls([call('Waiting for cluster spinup')]) + + @patch('loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster.logger') + def test_spinup_cluster_doesnt_exist_success( + self, + mock_logger: Mock, + mock_cluster_controller: Mock, + *_: Mock, + ) -> None: + mock_client = mock_cluster_controller.return_value + mock_client.get_cluster.side_effect = [ + google.api_core.exceptions.NotFound( + 'cluster not found', + ), + google.api_core.exceptions.NotFound( + 'cluster not found', + ), + SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.CREATING, + ), + ), + SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.RUNNING, + ), + cluster_name='dataproc-cluster-5', + cluster_uuid='12345', + ), + ] + mock_client.create_cluster.side_effect = None + worker = luigi.worker.Worker() + task = CreateDataprocClusterTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id='5', + ) + worker.add(task) + worker.run() + mock_logger.info.assert_has_calls( + [ + call('Waiting for cluster spinup'), + call('Created cluster dataproc-cluster-5 with cluster uuid: 12345'), + ], + ) diff --git a/loading_pipeline/lib/tasks/dataproc/misc_test.py b/loading_pipeline/lib/tasks/dataproc/misc_test.py new file mode 100644 index 0000000000..63ffafb8a1 --- /dev/null +++ b/loading_pipeline/lib/tasks/dataproc/misc_test.py @@ -0,0 +1,51 @@ +import unittest +from unittest.mock import Mock, patch + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.tasks.dataproc.misc import to_kebab_str_args +from loading_pipeline.lib.tasks.dataproc.run_pipeline_on_dataproc import ( + RunPipelineOnDataprocTask, +) + + +@patch( + 'loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc.dataproc.JobControllerClient', +) +class MiscTest(unittest.TestCase): + def test_to_kebab_str_args(self, _: Mock): + t = RunPipelineOnDataprocTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path='test_callset', + project_guids=['R0113_test_project'], + run_id='a_misc_run', + attempt_id=0, + ) + self.assertListEqual( + to_kebab_str_args(t), + [ + '--reference-genome', + 'GRCh38', + '--dataset-type', + 'SNV_INDEL', + '--sample-type', + 'WGS', + '--callset-path', + 'test_callset', + '--project-guids', + '["R0113_test_project"]', + '--skip-check-sex-and-relatedness', + 'False', + '--skip-expect-tdr-metrics', + 'False', + '--validations-to-skip', + '[]', + '--is-new-gcnv-joint-call', + 'False', + '--run-id', + 'a_misc_run', + '--attempt-id', + '0', + ], + ) diff --git a/loading_pipeline/lib/tasks/dataproc/run_pipeline_on_dataproc_test.py b/loading_pipeline/lib/tasks/dataproc/run_pipeline_on_dataproc_test.py new file mode 100644 index 0000000000..a09289a85a --- /dev/null +++ b/loading_pipeline/lib/tasks/dataproc/run_pipeline_on_dataproc_test.py @@ -0,0 +1,184 @@ +import unittest +from types import SimpleNamespace +from unittest.mock import Mock, call, patch + +import google.api_core.exceptions +import google.cloud.dataproc_v1.types.jobs +import luigi + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.tasks.dataproc.run_pipeline_on_dataproc import ( + RunPipelineOnDataprocTask, +) +from loading_pipeline.lib.test.mock_complete_task import MockCompleteTask + + +@patch( + 'loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc.CreateDataprocClusterTask', +) +@patch( + 'loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc.dataproc.JobControllerClient', +) +class WriteSuccessFileOnDataprocTaskTest(unittest.TestCase): + @patch('loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc.logger') + def test_job_already_exists_failed( + self, + mock_logger: Mock, + mock_job_controller_client: Mock, + mock_create_dataproc_cluster: Mock, + ) -> None: + mock_create_dataproc_cluster.return_value = MockCompleteTask() + mock_client = mock_job_controller_client.return_value + mock_client.get_job.return_value = SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.jobs.JobStatus.State.ERROR, + details='Google Cloud Dataproc Agent reports job failure. If logs are available, they can be found at...', + ), + ) + mock_client.submit_job_as_operation.side_effect = ( + google.api_core.exceptions.AlreadyExists('job exists') + ) + worker = luigi.worker.Worker() + task = RunPipelineOnDataprocTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path='test_callset', + project_guids=['R0113_test_project'], + run_id='manual__2024-04-03', + attempt_id=0, + ) + worker.add(task) + worker.run() + self.assertFalse(task.complete()) + mock_logger.error.assert_has_calls( + [ + call( + 'Job RunPipelineTask-38-SNV-INDEL-manual__2024-04-03-0 entered ERROR state', + ), + ], + ) + + def test_job_already_exists_success( + self, + mock_job_controller_client: Mock, + mock_create_dataproc_cluster: Mock, + ) -> None: + mock_create_dataproc_cluster.return_value = MockCompleteTask() + mock_client = mock_job_controller_client.return_value + mock_client.get_job.return_value = SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.jobs.JobStatus.State.DONE, + ), + ) + worker = luigi.worker.Worker() + task = RunPipelineOnDataprocTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path='test_callset', + project_guids=['R0113_test_project'], + run_id='manual__2024-04-04', + attempt_id=0, + ) + worker.add(task) + worker.run() + self.assertTrue(task.complete()) + + @patch('loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc.logger') + def test_job_failed( + self, + mock_logger: Mock, + mock_job_controller_client: Mock, + mock_create_dataproc_cluster: Mock, + ) -> None: + mock_create_dataproc_cluster.return_value = MockCompleteTask() + mock_client = mock_job_controller_client.return_value + mock_client.get_job.side_effect = [ + google.api_core.exceptions.NotFound( + 'job not found', + ), + google.api_core.exceptions.NotFound( + 'job not found', + ), + SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.jobs.JobStatus.State.PENDING, + ), + ), + SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.jobs.JobStatus.State.ERROR, + ), + ), + ] + worker = luigi.worker.Worker() + task = RunPipelineOnDataprocTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path='test_callset', + project_guids=['R0113_test_project'], + run_id='manual__2024-04-05', + attempt_id=1, + ) + worker.add(task) + luigi_task_result = worker.run() + self.assertEqual(luigi_task_result, False) + mock_logger.info.assert_has_calls( + [ + call( + 'Waiting for Job completion RunPipelineTask-38-SNV-INDEL-manual__2024-04-05-1', + ), + ], + ) + + @patch('loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc.logger') + def test_job_success( + self, + mock_logger: Mock, + mock_job_controller_client: Mock, + mock_create_dataproc_cluster: Mock, + ) -> None: + mock_create_dataproc_cluster.return_value = MockCompleteTask() + mock_client = mock_job_controller_client.return_value + mock_client.get_job.side_effect = [ + google.api_core.exceptions.NotFound( + 'job not found', + ), + google.api_core.exceptions.NotFound( + 'job not found', + ), + SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.jobs.JobStatus.State.PENDING, + ), + ), + SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.jobs.JobStatus.State.DONE, + ), + ), + ] + worker = luigi.worker.Worker() + task = RunPipelineOnDataprocTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path='test_callset', + project_guids=['R0113_test_project'], + run_id='manual__2024-04-06', + attempt_id=0, + ) + worker.add(task) + worker.run() + mock_logger.info.assert_has_calls( + [ + call( + 'Waiting for Job completion RunPipelineTask-38-SNV-INDEL-manual__2024-04-06-0', + ), + call( + 'Job RunPipelineTask-38-SNV-INDEL-manual__2024-04-06-0 is complete', + ), + ], + ) diff --git a/loading_pipeline/lib/tasks/exports/misc_test.py b/loading_pipeline/lib/tasks/exports/misc_test.py new file mode 100644 index 0000000000..f0324db627 --- /dev/null +++ b/loading_pipeline/lib/tasks/exports/misc_test.py @@ -0,0 +1,484 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.core import ( + DatasetType, + ReferenceGenome, +) +from loading_pipeline.lib.tasks.exports.misc import ( + camelcase_array_structexpression_fields, + sorted_hl_struct, + unmap_formatting_annotation_enums, +) + +TEST_SNV_INDEL_ANNOTATIONS = ( + 'loading_pipeline/var/test/exports/GRCh38/SNV_INDEL/annotations.ht' +) +TEST_GRCH37_SNV_INDEL_ANNOTATIONS = ( + 'loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/annotations.ht' +) + + +class MiscTest(unittest.TestCase): + def test_unmap_formatting_annotation_enums(self) -> None: + ht = hl.read_table(TEST_SNV_INDEL_ANNOTATIONS) + ht = unmap_formatting_annotation_enums( + ht, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + ) + self.assertCountEqual( + list(ht.globals.enums.collect()[0].keys()), + [ + 'clinvar', + 'hgmd', + 'screen', + 'dbnsfp', + 'gnomad_exomes', + 'gnomad_non_coding_constraint', + 'splice_ai', + 'exac', + 'topmed', + 'gnomad_genomes', + 'eigen', + ], + ) + ht = ht.annotate( + sorted_transcript_consequences=[ht.sorted_transcript_consequences[0]], + ) + self.assertEqual( + ht.collect()[0], + hl.Struct( + key_=0, + locus=hl.Locus( + contig='chr1', + position=876499, + reference_genome='GRCh38', + ), + alleles=['A', 'G'], + clinvar=hl.Struct( + alleleId=929885, + conflictingPathogenicities=None, + goldStars=1, + submitters=['Labcorp Genetics (formerly Invitae), Labcorp'], + conditions=['not provided'], + assertion_ids=[], + pathogenicity_id=12, + ), + rg37_locus=hl.Locus( + contig=1, + position=874501, + reference_genome='GRCh37', + ), + rsid=None, + sorted_transcript_consequences=[ + hl.Struct( + amino_acids='S/L', + canonical=1, + codons='tCg/tTg', + gene_id='ENSG00000187634', + hgvsc='ENST00000616016.5:c.1049C>T', + hgvsp='ENSP00000478421.2:p.Ser350Leu', + transcript_id='ENST00000616016', + mane_select='NM_001385641.1', + mane_plus_clinical=None, + exon=hl.Struct(index=6, total=14), + intron=None, + refseq_transcript_id='NM_001385641.1', + alphamissense=hl.Struct(pathogenicity=None), + loftee=hl.Struct(is_lof_nagnag=None, lof_filters=None), + spliceregion=hl.Struct( + extended_intronic_splice_region_variant=False, + ), + utrannotator=hl.Struct( + existing_inframe_oorfs=None, + existing_outofframe_oorfs=None, + existing_uorfs=None, + fiveutr_annotation=hl.Struct( + type='OutOfFrame_oORF', + KozakContext='CGCATGC', + KozakStrength='Weak', + DistanceToCDS=41, + CapDistanceToStart=None, + DistanceToStop=None, + Evidence=None, + AltStop=None, + AltStopDistanceToCDS=None, + FrameWithCDS=None, + StartDistanceToCDS=None, + newSTOPDistanceToCDS=None, + alt_type=None, + alt_type_length=None, + ref_StartDistanceToCDS=None, + ref_type=None, + ref_type_length=None, + ), + fiveutr_consequence=None, + ), + biotype='protein_coding', + consequence_terms=['missense_variant'], + ), + ], + variant_id='1-876499-A-G', + xpos=1000876499, + gt_stats=hl.Struct(AC=47, AN=81784, AF=0.0005746845272369683, hom=1), + CAID='CA502654', + check_ref=False, + sorted_regulatory_feature_consequences=[ + hl.Struct( + regulatory_feature_id='ENSR00000344437', + biotype='CTCF_binding_site', + consequence_terms=['regulatory_region_variant'], + ), + ], + sorted_motif_feature_consequences=[ + hl.Struct( + motif_feature_id='ENSM00493959715', + consequence_terms=['TF_binding_site_variant'], + ), + ], + gnomad_non_coding_constraint=hl.Struct(z_score=None), + hgmd=hl.Struct(accession='abcdefg', class_id=3), + gnomad_exomes=hl.Struct( + AF=0.0006690866430290043, + AN=1440770, + AC=964, + Hom=0, + AF_POPMAX_OR_GLOBAL=0.0008023773552849889, + FAF_AF=0.000633420015219599, + Hemi=0, + ), + gnomad_genomes=hl.Struct( + AF=0.0002759889466688037, + AN=152180, + AC=42, + Hom=0, + AF_POPMAX_OR_GLOBAL=0.10000000149011612, + FAF_AF=0.0002092500071739778, + Hemi=0, + ), + screen=hl.Struct(region_type_ids=[]), + dbnsfp=hl.Struct( + PrimateAI_score=0.5918066501617432, + fathmm_MKL_coding_score=0.7174800038337708, + CADD_phred=23.5, + SIFT_score=0.0010000000474974513, + REVEL_score=0.3109999895095825, + Polyphen2_HVAR_score=0.164000004529953, + VEST4_score=0.39500001072883606, + MPC_score=0.01291007362306118, + MutPred_score=None, + MutationTaster_pred_id=0, + ), + topmed=hl.Struct( + AC=41, + AF=0.00032651599030941725, + AN=125568, + Hom=0, + Het=41, + ), + exac=hl.Struct( + AF_POPMAX=0.0007150234305299819, + AF=0.00019039999460801482, + AC_Adj=20, + AC_Het=20, + AC_Hom=0, + AC_Hemi=None, + AN_Adj=47974, + ), + splice_ai=hl.Struct(delta_score=0.0, splice_consequence_id=4), + eigen=hl.Struct(Eigen_phred=2.628000020980835), + ), + ) + ht = hl.read_table(TEST_GRCH37_SNV_INDEL_ANNOTATIONS) + ht = unmap_formatting_annotation_enums( + ht, + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + ) + self.assertCountEqual( + list(ht.globals.enums.collect()[0].keys()), + [ + 'clinvar', + 'hgmd', + 'dbnsfp', + 'gnomad_exomes', + 'splice_ai', + 'exac', + 'topmed', + 'gnomad_genomes', + 'eigen', + ], + ) + ht = ht.annotate( + sorted_transcript_consequences=[ht.sorted_transcript_consequences[0]], + ) + self.assertEqual( + ht.collect()[0], + hl.Struct( + locus=hl.Locus(contig=1, position=69134, reference_genome='GRCh37'), + alleles=['A', 'G'], + clinvar=hl.Struct( + alleleId=2193183, + conflictingPathogenicities=None, + goldStars=1, + submitters=['Ambry Genetics'], + conditions=['not specified'], + assertion_ids=[], + pathogenicity_id=14, + ), + rsid=None, + sorted_transcript_consequences=[ + hl.Struct( + amino_acids='E/G', + canonical=1, + codons='gAa/gGa', + gene_id='ENSG00000186092', + hgvsc='ENST00000335137.3:c.44A>G', + hgvsp='ENSP00000334393.3:p.Glu15Gly', + transcript_id='ENST00000335137', + is_lof_nagnag=None, + biotype='protein_coding', + consequence_terms=['missense_variant'], + lof_filters=None, + ), + ], + variant_id='1-69134-A-G', + xpos=1000069134, + gt_stats=hl.Struct(AC=25, AN=1246, AF=0.020064204931259155, hom=10), + CAID='CA502008', + rg38_locus=hl.Locus( + contig='chr1', + position=69134, + reference_genome='GRCh38', + ), + hgmd=None, + gnomad_exomes=hl.Struct( + AF=0.026665963232517242, + AN=18938, + AC=505, + Hom=127, + AF_POPMAX_OR_GLOBAL=0.08191808313131332, + FAF_AF=0.02474386990070343, + Hemi=0, + ), + gnomad_genomes=hl.Struct( + AF=0.0001722949673421681, + AN=5804, + AC=1, + Hom=0, + AF_POPMAX_OR_GLOBAL=0.0005662514013238251, + FAF_AF=0.0, + Hemi=0, + ), + dbnsfp=hl.Struct( + PrimateAI_score=0.37232041358947754, + fathmm_MKL_coding_score=0.056940000504255295, + CADD_phred=15.880000114440918, + SIFT_score=0.1289999932050705, + REVEL_score=0.07500000298023224, + Polyphen2_HVAR_score=0.0010000000474974513, + VEST4_score=0.10700000077486038, + MPC_score=1.8921889066696167, + MutPred_score=0.3779999911785126, + MutationTaster_pred_id=2, + ), + topmed=hl.Struct( + AC=95, + AF=0.0007565619889646769, + AN=125568, + Hom=0, + Het=95, + ), + exac=hl.Struct( + AF_POPMAX=None, + AF=0.0016550000291317701, + AC_Adj=0, + AC_Het=0, + AC_Hom=0, + AC_Hemi=None, + AN_Adj=66, + ), + eigen=hl.Struct(Eigen_phred=1.0019999742507935), + splice_ai=hl.Struct( + delta_score=0.019999999552965164, + splice_consequence_id=2, + ), + key_=1424, + ), + ) + + def test_camelcase_array_structexpression_fields(self) -> None: + ht = hl.read_table(TEST_SNV_INDEL_ANNOTATIONS) + ht = unmap_formatting_annotation_enums( + ht, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + ) + ht = camelcase_array_structexpression_fields( + ht, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + ) + ht = ht.annotate( + sortedTranscriptConsequences=[ht.sortedTranscriptConsequences[0]], + ) + self.assertEqual( + ht.collect()[0], + hl.Struct( + key_=0, + locus=hl.Locus( + contig='chr1', + position=876499, + reference_genome='GRCh38', + ), + alleles=['A', 'G'], + clinvar=hl.Struct( + alleleId=929885, + conflictingPathogenicities=None, + goldStars=1, + submitters=['Labcorp Genetics (formerly Invitae), Labcorp'], + conditions=['not provided'], + assertion_ids=[], + pathogenicity_id=12, + ), + rg37_locus=hl.Locus( + contig=1, + position=874501, + reference_genome='GRCh37', + ), + rsid=None, + variant_id='1-876499-A-G', + xpos=1000876499, + gt_stats=hl.Struct(AC=47, AN=81784, AF=0.0005746845272369683, hom=1), + CAID='CA502654', + check_ref=False, + gnomad_non_coding_constraint=hl.Struct(z_score=None), + hgmd=hl.Struct(accession='abcdefg', class_id=3), + gnomad_exomes=hl.Struct( + AF=0.0006690866430290043, + AN=1440770, + AC=964, + Hom=0, + AF_POPMAX_OR_GLOBAL=0.0008023773552849889, + FAF_AF=0.000633420015219599, + Hemi=0, + ), + gnomad_genomes=hl.Struct( + AF=0.0002759889466688037, + AN=152180, + AC=42, + Hom=0, + AF_POPMAX_OR_GLOBAL=0.10000000149011612, + FAF_AF=0.0002092500071739778, + Hemi=0, + ), + screen=hl.Struct(region_type_ids=[]), + dbnsfp=hl.Struct( + PrimateAI_score=0.5918066501617432, + fathmm_MKL_coding_score=0.7174800038337708, + CADD_phred=23.5, + SIFT_score=0.0010000000474974513, + REVEL_score=0.3109999895095825, + Polyphen2_HVAR_score=0.164000004529953, + VEST4_score=0.39500001072883606, + MPC_score=0.01291007362306118, + MutPred_score=None, + MutationTaster_pred_id=0, + ), + topmed=hl.Struct( + AC=41, + AF=0.00032651599030941725, + AN=125568, + Hom=0, + Het=41, + ), + exac=hl.Struct( + AF_POPMAX=0.0007150234305299819, + AF=0.00019039999460801482, + AC_Adj=20, + AC_Het=20, + AC_Hom=0, + AC_Hemi=None, + AN_Adj=47974, + ), + splice_ai=hl.Struct( + delta_score=0.0, + splice_consequence_id=4, + ), + eigen=hl.Struct(Eigen_phred=2.628000020980835), + sortedTranscriptConsequences=[ + hl.Struct( + aminoAcids='S/L', + canonical=1, + codons='tCg/tTg', + geneId='ENSG00000187634', + hgvsc='ENST00000616016.5:c.1049C>T', + hgvsp='ENSP00000478421.2:p.Ser350Leu', + transcriptId='ENST00000616016', + maneSelect='NM_001385641.1', + manePlusClinical=None, + exon=hl.Struct(index=6, total=14), + intron=None, + refseqTranscriptId='NM_001385641.1', + alphamissense=hl.Struct(pathogenicity=None), + loftee=hl.Struct(isLofNagnag=None, lofFilters=None), + spliceregion=hl.Struct( + extended_intronic_splice_region_variant=False, + ), + utrannotator=hl.Struct( + existingInframeOorfs=None, + existingOutofframeOorfs=None, + existingUorfs=None, + fiveutrAnnotation=hl.Struct( + type='OutOfFrame_oORF', + KozakContext='CGCATGC', + KozakStrength='Weak', + DistanceToCDS=41, + CapDistanceToStart=None, + DistanceToStop=None, + Evidence=None, + AltStop=None, + AltStopDistanceToCDS=None, + FrameWithCDS=None, + StartDistanceToCDS=None, + newSTOPDistanceToCDS=None, + alt_type=None, + alt_type_length=None, + ref_StartDistanceToCDS=None, + ref_type=None, + ref_type_length=None, + ), + fiveutrConsequence=None, + ), + biotype='protein_coding', + consequenceTerms=['missense_variant'], + ), + ], + sortedRegulatoryFeatureConsequences=[ + hl.Struct( + regulatoryFeatureId='ENSR00000344437', + biotype='CTCF_binding_site', + consequenceTerms=['regulatory_region_variant'], + ), + ], + sortedMotifFeatureConsequences=[ + hl.Struct( + motifFeatureId='ENSM00493959715', + consequenceTerms=['TF_binding_site_variant'], + ), + ], + ), + ) + + def test_sorted_hl_struct(self) -> None: + struct = hl.Struct( + z=5, + y=hl.Struct(b=2, a=hl.Struct(d=4, c=3)), + x=hl.Struct(k=9), + ) + self.assertEqual( + sorted_hl_struct(struct), + hl.Struct(x=hl.Struct(k=9), y=hl.Struct(a=hl.Struct(c=3, d=4), b=2), z=5), + ) diff --git a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py new file mode 100644 index 0000000000..ccb3260f5e --- /dev/null +++ b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py @@ -0,0 +1,423 @@ +import hail as hl +import luigi.worker +import pandas as pd + +from loading_pipeline.lib.core import ( + DatasetType, + ReferenceGenome, + SampleType, +) +from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS +from loading_pipeline.lib.paths import ( + new_entries_parquet_path, + variant_annotations_table_path, +) +from loading_pipeline.lib.tasks.exports.write_new_entries_parquet import ( + WriteNewEntriesParquetTask, +) +from loading_pipeline.lib.test.misc import ( + convert_ndarray_to_list, + copy_project_pedigree_to_mocked_dir, +) +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + +TEST_PEDIGREE_3_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_3_remap.tsv' +TEST_PEDIGREE_4_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_4_remap.tsv' +TEST_PEDIGREE_5 = 'loading_pipeline/var/test/pedigrees/test_pedigree_5.tsv' +TEST_MITO_EXPORT_PEDIGREE = ( + 'loading_pipeline/var/test/pedigrees/test_mito_export_pedigree.tsv' +) +TEST_SNV_INDEL_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' +TEST_MITO_CALLSET = 'loading_pipeline/var/test/callsets/mito_1.mt' +TEST_SV_VCF_2 = 'loading_pipeline/var/test/callsets/sv_2.vcf' +TEST_GCNV_BED_FILE = 'loading_pipeline/var/test/callsets/gcnv_1.tsv' +TEST_SNV_INDEL_ANNOTATIONS = ( + 'loading_pipeline/var/test/exports/GRCh38/SNV_INDEL/annotations.ht' +) +TEST_MITO_ANNOTATIONS = 'loading_pipeline/var/test/exports/GRCh38/MITO/annotations.ht' +TEST_SV_ANNOTATIONS = 'loading_pipeline/var/test/exports/GRCh38/SV/annotations.ht' +TEST_GCNV_ANNOTATIONS = 'loading_pipeline/var/test/exports/GRCh38/GCNV/annotations.ht' + +TEST_RUN_ID = 'manual__2024-04-03' + + +class WriteNewEntriesParquetTest(MockedDatarootTestCase): + def setUp(self) -> None: + super().setUp() + ht = hl.read_table( + TEST_SNV_INDEL_ANNOTATIONS, + ) + ht.write( + variant_annotations_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + ), + ) + ht = hl.read_table( + TEST_MITO_ANNOTATIONS, + ) + ht.write( + variant_annotations_table_path( + ReferenceGenome.GRCh38, + DatasetType.MITO, + ), + ) + ht = hl.read_table( + TEST_SV_ANNOTATIONS, + ) + ht.write( + variant_annotations_table_path( + ReferenceGenome.GRCh38, + DatasetType.SV, + ), + ) + ht = hl.read_table(TEST_GCNV_ANNOTATIONS) + ht.write( + variant_annotations_table_path( + ReferenceGenome.GRCh38, + DatasetType.GCNV, + ), + ) + + def test_write_new_entries_parquet(self): + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_3_REMAP, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0113_test_project', + ) + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_4_REMAP, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0114_project4', + ) + worker = luigi.worker.Worker() + task = WriteNewEntriesParquetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path=TEST_SNV_INDEL_VCF, + project_guids=['R0113_test_project', 'R0114_project4'], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + worker.add(task) + worker.run() + self.assertTrue(task.output().exists()) + self.assertTrue(task.complete()) + df = pd.read_parquet( + new_entries_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ) + export_json = convert_ndarray_to_list(df.to_dict('records')) + self.assertEqual( + export_json[:2], + [ + { + 'key': 0, + 'project_guid': 'R0113_test_project', + 'family_guid': 'abc_1', + 'sample_type': 'WGS', + 'xpos': 1000876499, + 'geneIds': ['ENSG00000187634'], + 'filters': [], + 'calls': [ + { + 'sampleId': 'HG00731_1', + 'gt': 2, + 'gq': 21, + 'ab': 1.0, + 'dp': 7, + }, + { + 'sampleId': 'HG00732_1', + 'gt': 2, + 'gq': 24, + 'ab': 1.0, + 'dp': 8, + }, + { + 'sampleId': 'HG00733_1', + 'gt': 2, + 'gq': 12, + 'ab': 1.0, + 'dp': 4, + }, + ], + 'sign': 1, + }, + { + 'key': 1, + 'project_guid': 'R0113_test_project', + 'family_guid': 'abc_1', + 'sample_type': 'WGS', + 'xpos': 1000878314, + 'geneIds': ['ENSG00000187634'], + 'filters': ['VQSRTrancheSNP99.00to99.90'], + 'calls': [ + { + 'sampleId': 'HG00731_1', + 'gt': 1, + 'gq': 30, + 'ab': 0.3333333432674408, + 'dp': 3, + }, + {'sampleId': 'HG00732_1', 'gt': 0, 'gq': 6, 'ab': 0.0, 'dp': 2}, + { + 'sampleId': 'HG00733_1', + 'gt': 1, + 'gq': 61, + 'ab': 0.6000000238418579, + 'dp': 5, + }, + ], + 'sign': 1, + }, + ], + ) + + def test_mito_write_new_entries_parquet(self): + copy_project_pedigree_to_mocked_dir( + TEST_MITO_EXPORT_PEDIGREE, + ReferenceGenome.GRCh38, + DatasetType.MITO, + SampleType.WGS, + 'R0116_test_project3', + ) + worker = luigi.worker.Worker() + task = WriteNewEntriesParquetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.MITO, + sample_type=SampleType.WGS, + callset_path=TEST_MITO_CALLSET, + project_guids=['R0116_test_project3'], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + worker.add(task) + worker.run() + self.assertTrue(task.output().exists()) + self.assertTrue(task.complete()) + df = pd.read_parquet( + new_entries_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.MITO, + TEST_RUN_ID, + ), + ) + export_json = convert_ndarray_to_list(df.to_dict('records')) + self.assertEqual( + export_json, + [ + { + 'key': 998, + 'project_guid': 'R0116_test_project3', + 'family_guid': 'family_1', + 'sample_type': 'WGS', + 'xpos': 25000000008, + 'filters': [], + 'calls': [ + { + 'sampleId': 'RGP_1270_2', + 'gt': 2, + 'dp': 4216, + 'hl': 0.999, + 'mitoCn': 224, + 'contamination': 0.0, + }, + ], + 'sign': 1, + }, + ], + ) + + def test_sv_write_new_entries_parquet(self): + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_5, + ReferenceGenome.GRCh38, + DatasetType.SV, + SampleType.WGS, + 'R0115_test_project2', + ) + worker = luigi.worker.Worker() + task = WriteNewEntriesParquetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SV, + sample_type=SampleType.WGS, + callset_path=TEST_SV_VCF_2, + project_guids=['R0115_test_project2'], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + worker.add(task) + worker.run() + self.assertTrue(task.output().exists()) + self.assertTrue(task.complete()) + df = pd.read_parquet( + new_entries_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.SV, + TEST_RUN_ID, + ), + ) + export_json = convert_ndarray_to_list(df.to_dict('records')) + self.assertEqual( + export_json, + [ + { + 'key': 727, + 'project_guid': 'R0115_test_project2', + 'family_guid': 'family_2_1', + 'xpos': 1001025886, + 'geneIds': ['ENSG00000188157'], + 'filters': ['HIGH_SR_BACKGROUND', 'UNRESOLVED'], + 'calls': [ + { + 'sampleId': 'RGP_164_1', + 'gt': 0, + 'cn': None, + 'gq': 99, + 'newCall': True, + 'prevCall': False, + 'prevNumAlt': None, + }, + { + 'sampleId': 'RGP_164_2', + 'gt': 1, + 'cn': None, + 'gq': 31, + 'newCall': True, + 'prevCall': False, + 'prevNumAlt': None, + }, + { + 'sampleId': 'RGP_164_3', + 'gt': 0, + 'cn': None, + 'gq': 99, + 'newCall': True, + 'prevCall': False, + 'prevNumAlt': None, + }, + { + 'sampleId': 'RGP_164_4', + 'gt': 0, + 'cn': None, + 'gq': 99, + 'newCall': True, + 'prevCall': False, + 'prevNumAlt': None, + }, + ], + 'sign': 1, + }, + ], + ) + + def test_gcnv_write_new_entries_parquet(self): + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_5, + ReferenceGenome.GRCh38, + DatasetType.GCNV, + SampleType.WES, + 'R0115_test_project2', + ) + worker = luigi.worker.Worker() + task = WriteNewEntriesParquetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.GCNV, + sample_type=SampleType.WES, + callset_path=TEST_GCNV_BED_FILE, + project_guids=['R0115_test_project2'], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + worker.add(task) + worker.run() + self.assertTrue(task.output().exists()) + self.assertTrue(task.complete()) + df = pd.read_parquet( + new_entries_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.GCNV, + TEST_RUN_ID, + ), + ) + export_json = convert_ndarray_to_list(df.to_dict('records')) + self.assertEqual( + export_json, + [ + { + 'key': 0, + 'project_guid': 'R0115_test_project2', + 'family_guid': 'family_2_1', + 'xpos': 1000939203, + 'filters': [], + 'calls': [ + { + 'sampleId': 'RGP_164_1', + 'gt': 1, + 'cn': 1, + 'qs': 4, + 'defragged': False, + 'start': 100006937, + 'end': 100007881, + 'numExon': 2, + 'geneIds': ['ENSG00000117620', 'ENSG00000283761'], + 'newCall': False, + 'prevCall': True, + 'prevOverlap': False, + }, + { + 'sampleId': 'RGP_164_2', + 'gt': 1, + 'cn': 1, + 'qs': 5, + 'defragged': False, + 'start': 100017585, + 'end': 100023213, + 'numExon': 1, + 'geneIds': ['ENSG00000117620', 'ENSG00000283761'], + 'newCall': False, + 'prevCall': False, + 'prevOverlap': False, + }, + { + 'sampleId': 'RGP_164_3', + 'gt': 2, + 'cn': 0, + 'qs': 30, + 'defragged': False, + 'start': 100017585, + 'end': 100023213, + 'numExon': 1, + 'geneIds': ['ENSG00000117620', 'ENSG00000283761'], + 'newCall': False, + 'prevCall': True, + 'prevOverlap': False, + }, + { + 'sampleId': 'RGP_164_4', + 'gt': 2, + 'cn': 0, + 'qs': 30, + 'defragged': False, + 'start': 100017586, + 'end': 100023212, + 'numExon': 2, + 'geneIds': ['ENSG00000283761', 'ENSG22222222222'], + 'newCall': False, + 'prevCall': True, + 'prevOverlap': False, + }, + ], + 'sign': 1, + }, + ], + ) diff --git a/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py new file mode 100644 index 0000000000..5458854f56 --- /dev/null +++ b/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py @@ -0,0 +1,270 @@ +import os +from unittest import mock + +import hail as hl +import luigi.worker +import pandas as pd + +from loading_pipeline.lib.core import ( + DatasetType, + ReferenceGenome, + SampleType, +) +from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS +from loading_pipeline.lib.paths import ( + new_variant_details_parquet_path, + new_variants_table_path, +) +from loading_pipeline.lib.tasks.exports.write_new_variant_details_parquet import ( + WriteNewVariantDetailsParquetTask, +) +from loading_pipeline.lib.test.misc import convert_ndarray_to_list +from loading_pipeline.lib.test.mock_complete_task import MockCompleteTask +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + +TEST_SNV_INDEL_ANNOTATIONS = ( + 'loading_pipeline/var/test/exports/GRCh38/SNV_INDEL/annotations.ht' +) +TEST_GRCH37_SNV_INDEL_ANNOTATIONS = ( + 'loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/annotations.ht' +) + +TEST_RUN_ID = 'manual__2024-04-03' + + +class WriteNewVariantDetailsParquetTest(MockedDatarootTestCase): + def setUp(self) -> None: + super().setUp() + ht = hl.read_table( + TEST_SNV_INDEL_ANNOTATIONS, + ) + ht.write( + new_variants_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ) + ht = hl.read_table( + TEST_GRCH37_SNV_INDEL_ANNOTATIONS, + ) + ht.write( + new_variants_table_path( + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ) + + # Make an incomplete parquet to validate overwrite-ing. + os.makedirs( + new_variant_details_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + exist_ok=True, + ) + with open( + os.path.join( + new_variant_details_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + 'incomplete_file.parquet', + ), + 'w', + ) as f: + f.write('') + + @mock.patch( + 'loading_pipeline.lib.tasks.exports.write_new_variant_details_parquet.WriteNewVariantsTableTask', + ) + def test_write_new_variant_details_parquet_test( + self, + mock_write_new_variants_task, + ) -> None: + mock_write_new_variants_task.return_value = MockCompleteTask() + worker = luigi.worker.Worker() + task = WriteNewVariantDetailsParquetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path='fake_callset', + project_guids=[ + 'fake_project', + ], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + worker.add(task) + worker.run() + self.assertTrue(task.output().exists()) + self.assertTrue(task.complete()) + df = pd.read_parquet( + new_variant_details_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ) + export_json = convert_ndarray_to_list(df.head(1).to_dict('records')) + self.assertListEqual( + list(export_json[0].keys()), + [ + 'key', + 'variantId', + 'rsid', + 'CAID', + 'liftedOverChrom', + 'liftedOverPos', + 'sortedMotifFeatureConsequences', + 'sortedRegulatoryFeatureConsequences', + 'transcripts', + ], + ) + self.assertEqual( + export_json[0]['key'], + 0, + ) + self.assertEqual( + export_json[0]['transcripts'][0], + { + 'alphamissense': {'pathogenicity': None}, + 'aminoAcids': 'S/L', + 'biotype': 'protein_coding', + 'canonical': 1, + 'codons': 'tCg/tTg', + 'consequenceTerms': ['missense_variant'], + 'exon': {'index': 6, 'total': 14}, + 'geneId': 'ENSG00000187634', + 'hgvsc': 'ENST00000616016.5:c.1049C>T', + 'hgvsp': 'ENSP00000478421.2:p.Ser350Leu', + 'intron': None, + 'transcriptId': 'ENST00000616016', + 'transcriptRank': 0, + 'majorConsequence': 'missense_variant', + 'maneSelect': 'NM_001385641.1', + 'manePlusClinical': None, + 'refseqTranscriptId': 'NM_001385641.1', + 'loftee': {'isLofNagnag': None, 'lofFilters': None}, + 'spliceregion': { + 'extended_intronic_splice_region_variant': False, + }, + 'utrannotator': { + 'existingInframeOorfs': None, + 'existingOutofframeOorfs': None, + 'existingUorfs': None, + 'fiveutrAnnotation': { + 'AltStop': None, + 'AltStopDistanceToCDS': None, + 'CapDistanceToStart': None, + 'DistanceToCDS': 41, + 'DistanceToStop': None, + 'Evidence': None, + 'FrameWithCDS': None, + 'KozakContext': 'CGCATGC', + 'KozakStrength': 'Weak', + 'StartDistanceToCDS': None, + 'alt_type': None, + 'alt_type_length': None, + 'newSTOPDistanceToCDS': None, + 'ref_StartDistanceToCDS': None, + 'ref_type': None, + 'ref_type_length': None, + 'type': 'OutOfFrame_oORF', + }, + 'fiveutrConsequence': None, + }, + }, + ) + self.assertEqual( + list(export_json[0]['transcripts'][0].keys()), + sorted(export_json[0]['transcripts'][0].keys()), + ) + self.assertEqual( + list( + export_json[0]['transcripts'][0]['utrannotator'][ + 'fiveutrAnnotation' + ].keys(), + ), + sorted( + export_json[0]['transcripts'][0]['utrannotator'][ + 'fiveutrAnnotation' + ].keys(), + ), + ) + + @mock.patch( + 'loading_pipeline.lib.tasks.exports.write_new_variant_details_parquet.WriteNewVariantsTableTask', + ) + def test_grch37_write_new_variant_details_parquet_test( + self, + mock_write_new_variants_task, + ) -> None: + mock_write_new_variants_task.return_value = MockCompleteTask() + worker = luigi.worker.Worker() + task = WriteNewVariantDetailsParquetTask( + reference_genome=ReferenceGenome.GRCh37, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path='fake_callset', + project_guids=[ + 'fake_project', + ], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + worker.add(task) + worker.run() + self.assertTrue(task.output().exists()) + self.assertTrue(task.complete()) + df = pd.read_parquet( + os.path.join( + new_variant_details_parquet_path( + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ), + ) + export_json = convert_ndarray_to_list(df.head(1).to_dict('records')) + self.assertListEqual( + list(export_json[0].keys()), + [ + 'key', + 'variantId', + 'rsid', + 'CAID', + 'liftedOverChrom', + 'liftedOverPos', + 'transcripts', + ], + ) + self.assertEqual( + export_json[0]['key'], + 1424, + ) + self.assertEqual(export_json[0]['CAID'], None) + self.assertEqual( + export_json[0]['transcripts'][0], + { + 'aminoAcids': 'E/G', + 'biotype': 'protein_coding', + 'canonical': 1, + 'codons': 'gAa/gGa', + 'consequenceTerms': ['missense_variant'], + 'geneId': 'ENSG00000186092', + 'hgvsc': 'ENST00000335137.3:c.44A>G', + 'hgvsp': 'ENSP00000334393.3:p.Glu15Gly', + 'loftee': {'isLofNagnag': None, 'lofFilters': None}, + 'majorConsequence': 'missense_variant', + 'transcriptId': 'ENST00000335137', + 'transcriptRank': 0, + }, + ) + self.assertEqual( + list(export_json[0]['transcripts'][0].keys()), + sorted(export_json[0]['transcripts'][0].keys()), + ) diff --git a/loading_pipeline/lib/tasks/files_test.py b/loading_pipeline/lib/tasks/files_test.py new file mode 100644 index 0000000000..b2dfd937e0 --- /dev/null +++ b/loading_pipeline/lib/tasks/files_test.py @@ -0,0 +1,40 @@ +import os +import tempfile +import unittest + +from loading_pipeline.lib.tasks.files import ( + CallsetTask, + HailTableTask, + RawFileTask, + VCFFileTask, +) + + +class FilesTest(unittest.TestCase): + def test_raw_file(self) -> None: + with tempfile.NamedTemporaryFile(suffix='.txt') as f: + self.assertTrue(RawFileTask(f.name).complete()) + + def test_vcf_file(self) -> None: + with tempfile.NamedTemporaryFile(suffix='.vcf.bgz') as f: + self.assertTrue(VCFFileTask(f.name).complete()) + + def test_hail_table(self) -> None: + with tempfile.TemporaryDirectory(suffix='.ht') as d: + self.assertFalse(HailTableTask(d).complete()) + with open(os.path.join(d, '_SUCCESS'), 'w') as f: + f.write('0') + self.assertTrue(HailTableTask(d).complete()) + + def test_callset_task(self) -> None: + with tempfile.NamedTemporaryFile(suffix='.txt') as f: + self.assertTrue(CallsetTask(f.name).complete()) + + with tempfile.NamedTemporaryFile(suffix='.vcf') as f: + self.assertTrue(CallsetTask(f.name).complete()) + + with tempfile.TemporaryDirectory(suffix='.mt') as d: + self.assertFalse(CallsetTask(d).complete()) + with open(os.path.join(d, '_SUCCESS'), 'w') as f: + f.write('0') + self.assertTrue(CallsetTask(d).complete()) diff --git a/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py b/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py new file mode 100644 index 0000000000..3bfe55af65 --- /dev/null +++ b/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py @@ -0,0 +1,1349 @@ +import functools +from unittest.mock import Mock, PropertyMock, patch + +import hail as hl +import luigi.worker + +from loading_pipeline.lib.annotations.enums import ( + BIOTYPES, + FIVEUTR_CONSEQUENCES, + LOF_FILTERS, + MITOTIP_PATHOGENICITIES, + MOTIF_CONSEQUENCE_TERMS, + REGULATORY_BIOTYPES, + REGULATORY_CONSEQUENCE_TERMS, + SV_CONSEQUENCE_RANKS, + SV_TYPE_DETAILS, + SV_TYPES, + TRANSCRIPT_CONSEQUENCE_TERMS, +) +from loading_pipeline.lib.core import ( + DatasetType, + ReferenceGenome, + SampleType, +) +from loading_pipeline.lib.misc.io import remap_pedigree_hash +from loading_pipeline.lib.misc.validation import ( + ALL_VALIDATIONS, + SKIPPABLE_VALIDATIONS, + validate_expected_contig_frequency, +) +from loading_pipeline.lib.paths import ( + valid_reference_dataset_path, +) +from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset +from loading_pipeline.lib.tasks.files import GCSorLocalFolderTarget +from loading_pipeline.lib.tasks.update_variant_annotations_table_with_new_variants import ( + UpdateVariantAnnotationsTableWithNewVariantsTask, +) +from loading_pipeline.lib.test.misc import copy_project_pedigree_to_mocked_dir +from loading_pipeline.lib.test.mocked_reference_datasets_testcase import ( + MockedReferenceDatasetsTestCase, +) +from loading_pipeline.var.test.vep.mock_vep_data import ( + MOCK_37_VEP_DATA, + MOCK_38_VEP_DATA, +) + +TEST_MITO_MT = 'loading_pipeline/var/test/callsets/mito_1.mt' +TEST_SNV_INDEL_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' +TEST_SV_VCF = 'loading_pipeline/var/test/callsets/sv_1.vcf' +TEST_SV_VCF_2 = 'loading_pipeline/var/test/callsets/sv_2.vcf' +TEST_GCNV_BED_FILE = 'loading_pipeline/var/test/callsets/gcnv_1.tsv' +TEST_GCNV_BED_FILE_2 = 'loading_pipeline/var/test/callsets/gcnv_2.tsv' +TEST_PEDIGREE_3_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_3_remap.tsv' +TEST_PEDIGREE_4_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_4_remap.tsv' +TEST_PEDIGREE_5 = 'loading_pipeline/var/test/pedigrees/test_pedigree_5.tsv' +TEST_PEDIGREE_8 = 'loading_pipeline/var/test/pedigrees/test_pedigree_8.tsv' +TEST_PEDIGREE_10 = 'loading_pipeline/var/test/pedigrees/test_pedigree_10.tsv' +TEST_PEDIGREE_11 = 'loading_pipeline/var/test/pedigrees/test_pedigree_11.tsv' + +GENE_ID_MAPPING = { + 'OR4F5': 'ENSG00000186092', + 'PLEKHG4B': 'ENSG00000153404', + 'OR4F16': 'ENSG00000186192', + 'OR4F29': 'ENSG00000284733', + 'FBXO28': 'ENSG00000143756', + 'SAMD11': 'ENSG00000187634', + 'C1orf174': 'ENSG00000198912', + 'TAS1R1': 'ENSG00000173662', + 'FAM131C': 'ENSG00000185519', + 'RCC2': 'ENSG00000179051', + 'NBPF3': 'ENSG00000142794', + 'AGBL4': 'ENSG00000186094', + 'KIAA1614': 'ENSG00000135835', + 'MR1': 'ENSG00000153029', + 'STX6': 'ENSG00000135823', + 'XPR1': 'ENSG00000143324', +} + +TEST_RUN_ID = 'manual__2024-04-03' + + +class UpdateVariantAnnotationsTableWithNewVariantsTaskTest( + MockedReferenceDatasetsTestCase, +): + def test_missing_pedigree( + self, + ) -> None: + uvatwns_task = UpdateVariantAnnotationsTableWithNewVariantsTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path=TEST_SNV_INDEL_VCF, + project_guids=['R0113_test_project'], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + worker = luigi.worker.Worker() + worker.add(uvatwns_task) + worker.run() + self.assertFalse(uvatwns_task.complete()) + + @patch( + 'loading_pipeline.lib.tasks.validate_callset.SKIPPABLE_VALIDATIONS', + [ + x + for x in SKIPPABLE_VALIDATIONS + if x.__name__ != 'validate_expected_contig_frequency' + ] + + [ + functools.update_wrapper( + functools.partial( + validate_expected_contig_frequency, + min_rows_per_contig=25, + ), + validate_expected_contig_frequency, + ), + ], + ) + @patch.object(ReferenceGenome, 'standard_contigs', new_callable=PropertyMock) + @patch('loading_pipeline.lib.misc.vep.hl.vep') + @patch( + 'loading_pipeline.lib.tasks.write_new_variants_table.load_gencode_ensembl_to_refseq_id', + ) + def test_multiple_update_vat( + self, + mock_load_gencode_ensembl_to_refseq_id: Mock, + mock_vep: Mock, + mock_standard_contigs: Mock, + ) -> None: + mock_vep.side_effect = lambda ht, **_: ht.annotate(vep=MOCK_38_VEP_DATA) + mock_load_gencode_ensembl_to_refseq_id.return_value = hl.dict( + {'ENST00000327044': 'NM_015658.4'}, + ) + mock_standard_contigs.return_value = {'chr1'} + # This creates a mock validation table with 1 coding and 1 non-coding variant + # explicitly chosen from the VCF. + # NB: This is the one and only place validation is enabled in the task tests! + coding_and_noncoding_variants_ht = hl.Table.parallelize( + [ + { + 'locus': hl.Locus( + contig='chr1', + position=871269, + reference_genome='GRCh38', + ), + 'coding': False, + 'noncoding': True, + }, + { + 'locus': hl.Locus( + contig='chr1', + position=876499, + reference_genome='GRCh38', + ), + 'coding': True, + 'noncoding': False, + }, + ], + hl.tstruct( + locus=hl.tlocus('GRCh38'), + coding=hl.tbool, + noncoding=hl.tbool, + ), + key='locus', + globals=hl.Struct( + enums=hl.Struct( + gnomad_genomes=hl.Struct(), + ), + ), + ) + coding_and_noncoding_variants_ht.write( + valid_reference_dataset_path( + ReferenceGenome.GRCh38, + ReferenceDataset.gnomad_coding_and_noncoding, + ), + overwrite=True, + ) + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_3_REMAP, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0113_test_project', + ) + worker = luigi.worker.Worker() + uvatwns_task_3 = UpdateVariantAnnotationsTableWithNewVariantsTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path=TEST_SNV_INDEL_VCF, + project_guids=['R0113_test_project'], + validations_to_skip=[], + run_id=TEST_RUN_ID, + ) + worker.add(uvatwns_task_3) + worker.run() + self.assertTrue(uvatwns_task_3.complete()) + ht = hl.read_table(uvatwns_task_3.output().path) + self.assertEqual(ht.count(), 30) + self.assertEqual( + ht.globals.updates.collect(), + [ + { + hl.Struct( + callset=TEST_SNV_INDEL_VCF, + project_guid='R0113_test_project', + remap_pedigree_hash=hl.eval( + remap_pedigree_hash(TEST_PEDIGREE_3_REMAP), + ), + ), + }, + ], + ) + self.assertEqual( + hl.eval(ht.globals.max_key_), + 29, + ) + + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_4_REMAP, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0114_project4', + ) + # Ensure that new variants are added correctly to the table. + uvatwns_task_4 = UpdateVariantAnnotationsTableWithNewVariantsTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path=TEST_SNV_INDEL_VCF, + project_guids=['R0114_project4'], + validations_to_skip=[], + run_id=TEST_RUN_ID + '-another-run', + ) + worker.add(uvatwns_task_4) + worker.run() + self.assertTrue(uvatwns_task_4.complete()) + ht = hl.read_table(uvatwns_task_4.output().path) + self.assertCountEqual( + [ + x + for x in ht.select( + 'variant_id', + 'xpos', + ).collect() + if x.locus.position <= 878809 # noqa: PLR2004 + ], + [ + hl.Struct( + locus=hl.Locus( + contig='chr1', + position=871269, + reference_genome='GRCh38', + ), + alleles=['A', 'C'], + variant_id='1-871269-A-C', + xpos=1000871269, + ), + hl.Struct( + locus=hl.Locus( + contig='chr1', + position=874734, + reference_genome='GRCh38', + ), + alleles=['C', 'T'], + variant_id='1-874734-C-T', + xpos=1000874734, + ), + hl.Struct( + locus=hl.Locus( + contig='chr1', + position=876499, + reference_genome='GRCh38', + ), + alleles=['A', 'G'], + variant_id='1-876499-A-G', + xpos=1000876499, + ), + hl.Struct( + locus=hl.Locus( + contig='chr1', + position=878314, + reference_genome='GRCh38', + ), + alleles=['G', 'C'], + variant_id='1-878314-G-C', + xpos=1000878314, + ), + hl.Struct( + locus=hl.Locus( + contig='chr1', + position=878809, + reference_genome='GRCh38', + ), + alleles=['C', 'T'], + variant_id='1-878809-C-T', + xpos=1000878809, + ), + ], + ) + self.assertCountEqual( + ht.filter( + ht.locus.position <= 878809, # noqa: PLR2004 + ).sorted_transcript_consequences.consequence_term_ids.collect(), + [ + [[9], [23, 26], [23, 13, 26]], + [[9], [23, 26], [23, 13, 26]], + [[9], [23, 26], [23, 13, 26]], + [[9], [23, 26], [23, 13, 26]], + [[9], [23, 26], [23, 13, 26]], + ], + ) + self.assertCountEqual( + ht.globals.collect(), + [ + hl.Struct( + updates={ + hl.Struct( + callset='loading_pipeline/var/test/callsets/1kg_30variants.vcf', + project_guid='R0113_test_project', + remap_pedigree_hash=hl.eval( + remap_pedigree_hash( + TEST_PEDIGREE_3_REMAP, + ), + ), + ), + hl.Struct( + callset='loading_pipeline/var/test/callsets/1kg_30variants.vcf', + project_guid='R0114_project4', + remap_pedigree_hash=hl.eval( + remap_pedigree_hash( + TEST_PEDIGREE_4_REMAP, + ), + ), + ), + }, + migrations=[], + max_key_=29, + enums=hl.Struct( + sorted_motif_feature_consequences=hl.Struct( + consequence_term=MOTIF_CONSEQUENCE_TERMS, + ), + sorted_regulatory_feature_consequences=hl.Struct( + biotype=REGULATORY_BIOTYPES, + consequence_term=REGULATORY_CONSEQUENCE_TERMS, + ), + sorted_transcript_consequences=hl.Struct( + biotype=BIOTYPES, + consequence_term=TRANSCRIPT_CONSEQUENCE_TERMS, + loftee=hl.Struct( + lof_filter=LOF_FILTERS, + ), + utrannotator=hl.Struct( + fiveutr_consequence=FIVEUTR_CONSEQUENCES, + ), + ), + ), + ), + ], + ) + + @patch('loading_pipeline.lib.misc.vep.hl.vep') + def test_update_vat_grch37( + self, + mock_vep: Mock, + ) -> None: + mock_vep.side_effect = lambda ht, **_: ht.annotate(vep=MOCK_37_VEP_DATA) + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_3_REMAP, + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0113_test_project', + ) + worker = luigi.worker.Worker() + uvatwns_task = UpdateVariantAnnotationsTableWithNewVariantsTask( + reference_genome=ReferenceGenome.GRCh37, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path=TEST_SNV_INDEL_VCF, + project_guids=['R0113_test_project'], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + worker.add(uvatwns_task) + worker.run() + self.assertTrue(uvatwns_task.complete()) + ht = hl.read_table(uvatwns_task.output().path) + self.assertEqual(ht.count(), 30) + self.assertFalse(hasattr(ht, 'rg37_locus')) + self.assertEqual( + ht.collect()[0], + hl.Struct( + locus=hl.Locus( + contig=1, + position=871269, + reference_genome='GRCh37', + ), + alleles=['A', 'C'], + rsid=None, + variant_id='1-871269-A-C', + xpos=1000871269, + sorted_transcript_consequences=[ + hl.Struct( + amino_acids='S/L', + canonical=1, + codons='tCg/tTg', + gene_id='ENSG00000188976', + hgvsc='ENST00000327044.6:c.1667C>T', + hgvsp='ENSP00000317992.6:p.Ser556Leu', + transcript_id='ENST00000327044', + biotype_id=39, + consequence_term_ids=[9], + is_lof_nagnag=None, + lof_filter_ids=[0, 1], + ), + hl.Struct( + amino_acids=None, + canonical=None, + codons=None, + gene_id='ENSG00000188976', + hgvsc='ENST00000477976.1:n.3114C>T', + hgvsp=None, + transcript_id='ENST00000477976', + biotype_id=38, + consequence_term_ids=[23, 26], + is_lof_nagnag=None, + lof_filter_ids=None, + ), + hl.Struct( + amino_acids=None, + canonical=None, + codons=None, + gene_id='ENSG00000188976', + hgvsc='ENST00000483767.1:n.523C>T', + hgvsp=None, + transcript_id='ENST00000483767', + biotype_id=38, + consequence_term_ids=[23, 26], + is_lof_nagnag=None, + lof_filter_ids=None, + ), + ], + rg38_locus=hl.Locus( + contig='chr1', + position=935889, + reference_genome='GRCh38', + ), + key_=0, + ), + ) + + def test_mito_update_vat( + self, + ) -> None: + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_5, + ReferenceGenome.GRCh38, + DatasetType.MITO, + SampleType.WGS, + 'R0115_test_project2', + ) + worker = luigi.worker.Worker() + update_variant_annotations_task = ( + UpdateVariantAnnotationsTableWithNewVariantsTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.MITO, + sample_type=SampleType.WGS, + callset_path=TEST_MITO_MT, + project_guids=['R0115_test_project2'], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + ) + worker.add(update_variant_annotations_task) + worker.run() + self.assertTrue(update_variant_annotations_task.complete()) + ht = hl.read_table(update_variant_annotations_task.output().path) + self.assertEqual(ht.count(), 5) + self.assertCountEqual( + ht.globals.collect(), + [ + hl.Struct( + enums=hl.Struct( + sorted_transcript_consequences=hl.Struct( + biotype=BIOTYPES, + consequence_term=TRANSCRIPT_CONSEQUENCE_TERMS, + lof_filter=LOF_FILTERS, + ), + mitotip=hl.Struct(trna_prediction=MITOTIP_PATHOGENICITIES), + ), + migrations=[], + max_key_=4, + updates={ + hl.Struct( + callset='loading_pipeline/var/test/callsets/mito_1.mt', + project_guid='R0115_test_project2', + remap_pedigree_hash=hl.eval( + remap_pedigree_hash( + TEST_PEDIGREE_5, + ), + ), + ), + }, + ), + ], + ) + self.assertCountEqual( + ht.collect()[0], + hl.Struct( + locus=hl.Locus( + contig='chrM', + position=3, + reference_genome='GRCh38', + ), + alleles=['T', 'C'], + common_low_heteroplasmy=False, + haplogroup=hl.Struct(is_defining=False), + mitotip=hl.Struct(trna_prediction_id=None), + rg37_locus=hl.Locus( + contig='MT', + position=3, + reference_genome='GRCh37', + ), + rsid=None, + sorted_transcript_consequences=None, + variant_id='M-3-T-C', + xpos=25000000003, + key_=0, + ), + ) + + @patch( + 'loading_pipeline.lib.tasks.write_new_variants_table.load_gencode_gene_symbol_to_gene_id', + ) + def test_sv_multiple_vcf_update_vat( + self, + mock_load_gencode: Mock, + ) -> None: + mock_load_gencode.return_value = GENE_ID_MAPPING + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_5, + ReferenceGenome.GRCh38, + DatasetType.SV, + SampleType.WGS, + 'R0115_test_project2', + ) + worker = luigi.worker.Worker() + update_variant_annotations_task = ( + UpdateVariantAnnotationsTableWithNewVariantsTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SV, + sample_type=SampleType.WGS, + callset_path=TEST_SV_VCF, + project_guids=['R0115_test_project2'], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + ) + worker.add(update_variant_annotations_task) + worker.run() + self.assertTrue(update_variant_annotations_task.complete()) + self.assertFalse( + GCSorLocalFolderTarget( + f'{self.mock_env.REFERENCE_DATASETS_DIR}/v03/GRCh38/SV/lookup.ht', + ).exists(), + ) + ht = hl.read_table(update_variant_annotations_task.output().path) + self.assertEqual(ht.count(), 13) + self.assertCountEqual( + ht.globals.collect(), + [ + hl.Struct( + enums=hl.Struct( + sv_type=SV_TYPES, + sv_type_detail=SV_TYPE_DETAILS, + sorted_gene_consequences=hl.Struct( + major_consequence=SV_CONSEQUENCE_RANKS, + ), + ), + migrations=[], + max_key_=12, + updates={ + hl.Struct( + callset=TEST_SV_VCF, + project_guid='R0115_test_project2', + remap_pedigree_hash=hl.eval( + remap_pedigree_hash( + TEST_PEDIGREE_5, + ), + ), + ), + }, + ), + ], + ) + self.assertCountEqual( + ht.collect()[:8], + [ + hl.Struct( + variant_id='BND_chr1_6', + algorithms='manta', + bothsides_support=False, + cpx_intervals=None, + end_locus=hl.Locus( + contig='chr5', + position=20404, + reference_genome='GRCh38', + ), + gnomad_svs=None, + rg37_locus=hl.Locus( + contig=1, + position=10367, + reference_genome='GRCh37', + ), + rg37_locus_end=hl.Locus( + contig=5, + position=20404, + reference_genome='GRCh37', + ), + sorted_gene_consequences=[ + hl.Struct(gene_id='ENSG00000186092', major_consequence_id=12), + hl.Struct(gene_id='ENSG00000153404', major_consequence_id=12), + ], + start_locus=hl.Locus( + contig='chr1', + position=180928, + reference_genome='GRCh38', + ), + strvctvre=hl.Struct(score=None), + sv_len=-1, + sv_type_id=2, + sv_type_detail_id=None, + xpos=1000180928, + key_=0, + ), + hl.Struct( + variant_id='BND_chr1_9', + algorithms='manta', + bothsides_support=False, + cpx_intervals=None, + end_locus=hl.Locus( + contig='chr1', + position=789481, + reference_genome='GRCh38', + ), + gnomad_svs=None, + rg37_locus=hl.Locus( + contig=1, + position=724861, + reference_genome='GRCh37', + ), + rg37_locus_end=hl.Locus( + contig=1, + position=724861, + reference_genome='GRCh37', + ), + sorted_gene_consequences=[ + hl.Struct(gene_id='ENSG00000143756', major_consequence_id=12), + hl.Struct(gene_id='ENSG00000186192', major_consequence_id=12), + ], + start_locus=hl.Locus( + contig='chr1', + position=789481, + reference_genome='GRCh38', + ), + strvctvre=hl.Struct(score=None), + sv_len=223225007, + sv_type_id=2, + sv_type_detail_id=None, + xpos=1000789481, + key_=1, + ), + hl.Struct( + variant_id='CPX_chr1_22', + algorithms='manta', + bothsides_support=True, + cpx_intervals=[ + hl.Struct( + type_id=8, + start=hl.Locus('chr1', 6558902, 'GRCh38'), + end=hl.Locus('chr1', 6559723, 'GRCh38'), + ), + hl.Struct( + type_id=6, + start=hl.Locus('chr1', 6559655, 'GRCh38'), + end=hl.Locus('chr1', 6559723, 'GRCh38'), + ), + ], + end_locus=hl.Locus( + contig='chr1', + position=6559723, + reference_genome='GRCh38', + ), + gnomad_svs=None, + rg37_locus=hl.Locus( + contig=1, + position=6618962, + reference_genome='GRCh37', + ), + rg37_locus_end=hl.Locus( + contig=1, + position=6619783, + reference_genome='GRCh37', + ), + sorted_gene_consequences=[ + hl.Struct(gene_id='ENSG00000173662', major_consequence_id=11), + ], + start_locus=hl.Locus( + contig='chr1', + position=6558902, + reference_genome='GRCh38', + ), + strvctvre=hl.Struct(score=None), + sv_len=821, + sv_type_id=3, + sv_type_detail_id=2, + xpos=1006558902, + key_=2, + ), + hl.Struct( + variant_id='CPX_chr1_251', + algorithms='manta', + bothsides_support=False, + cpx_intervals=[ + hl.Struct( + type_id=5, + start=hl.Locus('chr1', 180540234, 'GRCh38'), + end=hl.Locus('chr1', 181074767, 'GRCh38'), + ), + hl.Struct( + type_id=8, + start=hl.Locus('chr1', 181074767, 'GRCh38'), + end=hl.Locus('chr1', 181074938, 'GRCh38'), + ), + ], + end_locus=hl.Locus( + contig='chr1', + position=181074952, + reference_genome='GRCh38', + ), + gnomad_svs=None, + rg37_locus=hl.Locus( + contig=1, + position=180509370, + reference_genome='GRCh37', + ), + rg37_locus_end=hl.Locus( + contig=1, + position=181044088, + reference_genome='GRCh37', + ), + sorted_gene_consequences=[ + hl.Struct(gene_id='ENSG00000135835', major_consequence_id=0), + hl.Struct(gene_id='ENSG00000153029', major_consequence_id=0), + hl.Struct(gene_id='ENSG00000135823', major_consequence_id=0), + hl.Struct(gene_id='ENSG00000143324', major_consequence_id=0), + ], + start_locus=hl.Locus( + contig='chr1', + position=180540234, + reference_genome='GRCh38', + ), + strvctvre=hl.Struct(score=None), + sv_len=534718, + sv_type_id=3, + sv_type_detail_id=9, + xpos=1180540234, + key_=3, + ), + hl.Struct( + variant_id='CPX_chr1_41', + algorithms='manta', + bothsides_support=False, + cpx_intervals=[ + hl.Struct( + type_id=6, + start=hl.Locus('chr1', 16088760, 'GRCh38'), + end=hl.Locus('chr1', 16088835, 'GRCh38'), + ), + hl.Struct( + type_id=8, + start=hl.Locus('chr1', 16088760, 'GRCh38'), + end=hl.Locus('chr1', 16089601, 'GRCh38'), + ), + ], + end_locus=hl.Locus( + contig='chr1', + position=16089601, + reference_genome='GRCh38', + ), + gnomad_svs=None, + rg37_locus=hl.Locus( + contig=1, + position=16415255, + reference_genome='GRCh37', + ), + rg37_locus_end=hl.Locus( + contig=1, + position=16416096, + reference_genome='GRCh37', + ), + sorted_gene_consequences=[ + hl.Struct(gene_id='ENSG00000185519', major_consequence_id=12), + ], + start_locus=hl.Locus( + contig='chr1', + position=16088760, + reference_genome='GRCh38', + ), + strvctvre=hl.Struct(score=None), + sv_len=841, + sv_type_id=3, + sv_type_detail_id=12, + xpos=1016088760, + key_=4, + ), + hl.Struct( + variant_id='CPX_chr1_54', + algorithms='manta', + bothsides_support=False, + cpx_intervals=[ + hl.Struct( + type_id=6, + start=hl.Locus('chr1', 21427498, 'GRCh38'), + end=hl.Locus('chr1', 21427959, 'GRCh38'), + ), + hl.Struct( + type_id=8, + start=hl.Locus('chr1', 21427498, 'GRCh38'), + end=hl.Locus('chr1', 21480073, 'GRCh38'), + ), + hl.Struct( + type_id=5, + start=hl.Locus('chr1', 21480073, 'GRCh38'), + end=hl.Locus('chr1', 21480419, 'GRCh38'), + ), + ], + end_locus=hl.Locus( + contig='chr1', + position=21480419, + reference_genome='GRCh38', + ), + gnomad_svs=None, + rg37_locus=hl.Locus( + contig=1, + position=21753991, + reference_genome='GRCh37', + ), + rg37_locus_end=hl.Locus( + contig=1, + position=21806912, + reference_genome='GRCh37', + ), + sorted_gene_consequences=[ + hl.Struct(gene_id='ENSG00000142794', major_consequence_id=0), + ], + start_locus=hl.Locus( + contig='chr1', + position=21427498, + reference_genome='GRCh38', + ), + strvctvre=hl.Struct(score=None), + sv_len=52921, + sv_type_id=3, + sv_type_detail_id=13, + xpos=1021427498, + key_=5, + ), + hl.Struct( + variant_id='CPX_chrX_251', + algorithms='manta', + bothsides_support=False, + cpx_intervals=[ + hl.Struct( + type_id=5, + start=hl.Locus( + contig='chr1', + position=180540234, + reference_genome='GRCh38', + ), + end=hl.Locus( + contig='chr1', + position=181074767, + reference_genome='GRCh38', + ), + ), + hl.Struct( + type_id=8, + start=hl.Locus( + contig='chr1', + position=181074767, + reference_genome='GRCh38', + ), + end=hl.Locus( + contig='chr1', + position=181074938, + reference_genome='GRCh38', + ), + ), + ], + end_locus=hl.Locus( + contig='chrX', + position=2781000, + reference_genome='GRCh38', + ), + gnomad_svs=None, + sorted_gene_consequences=[ + hl.Struct(gene_id='ENSG00000135835', major_consequence_id=0), + hl.Struct(gene_id='ENSG00000153029', major_consequence_id=0), + hl.Struct(gene_id='ENSG00000135823', major_consequence_id=0), + hl.Struct(gene_id='ENSG00000143324', major_consequence_id=0), + ], + start_locus=hl.Locus( + contig='chrX', + position=3, + reference_genome='GRCh38', + ), + strvctvre=hl.Struct(score=None), + sv_type_id=3, + sv_type_detail_id=9, + sv_len=534718, + xpos=23000000003, + rg37_locus=None, + rg37_locus_end=hl.Locus( + contig='X', + position=2699041, + reference_genome='GRCh37', + ), + key_=6, + ), + hl.Struct( + variant_id='CPX_chrX_252', + algorithms='manta', + bothsides_support=False, + cpx_intervals=[ + hl.Struct( + type_id=5, + start=hl.Locus( + contig='chr1', + position=180540234, + reference_genome='GRCh38', + ), + end=hl.Locus( + contig='chr1', + position=181074767, + reference_genome='GRCh38', + ), + ), + hl.Struct( + type_id=8, + start=hl.Locus( + contig='chr1', + position=181074767, + reference_genome='GRCh38', + ), + end=hl.Locus( + contig='chr1', + position=181074938, + reference_genome='GRCh38', + ), + ), + ], + end_locus=hl.Locus( + contig='chrX', + position=2781900, + reference_genome='GRCh38', + ), + gnomad_svs=None, + sorted_gene_consequences=[ + hl.Struct(gene_id='ENSG00000135835', major_consequence_id=0), + hl.Struct(gene_id='ENSG00000153029', major_consequence_id=0), + hl.Struct(gene_id='ENSG00000135823', major_consequence_id=0), + hl.Struct(gene_id='ENSG00000143324', major_consequence_id=0), + ], + start_locus=hl.Locus( + contig='chrX', + position=2781700, + reference_genome='GRCh38', + ), + strvctvre=hl.Struct(score=None), + sv_type_id=3, + sv_type_detail_id=9, + sv_len=534718, + xpos=23002781700, + rg37_locus=hl.Locus( + contig='X', + position=2699741, + reference_genome='GRCh37', + ), + rg37_locus_end=hl.Locus( + contig='X', + position=2699941, + reference_genome='GRCh37', + ), + key_=7, + ), + ], + ) + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_5, + ReferenceGenome.GRCh38, + DatasetType.SV, + SampleType.WGS, + 'R0115_test_project2', + ) + update_variant_annotations_task = ( + UpdateVariantAnnotationsTableWithNewVariantsTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SV, + sample_type=SampleType.WGS, + callset_path=TEST_SV_VCF_2, + project_guids=['R0115_test_project2'], + validations_to_skip=[ALL_VALIDATIONS], + run_id='second_run_id', + ) + ) + worker.add(update_variant_annotations_task) + worker.run() + self.assertTrue(update_variant_annotations_task.complete()) + ht = hl.read_table(update_variant_annotations_task.output().path) + self.assertEqual(ht.count(), 14) + self.assertCountEqual( + ht.globals.collect(), + [ + hl.Struct( + enums=hl.Struct( + sv_type=SV_TYPES, + sv_type_detail=SV_TYPE_DETAILS, + sorted_gene_consequences=hl.Struct( + major_consequence=SV_CONSEQUENCE_RANKS, + ), + ), + migrations=[], + max_key_=13, + updates={ + hl.Struct( + callset=TEST_SV_VCF, + project_guid='R0115_test_project2', + remap_pedigree_hash=hl.eval( + remap_pedigree_hash( + TEST_PEDIGREE_5, + ), + ), + ), + hl.Struct( + callset=TEST_SV_VCF_2, + project_guid='R0115_test_project2', + remap_pedigree_hash=hl.eval( + remap_pedigree_hash( + TEST_PEDIGREE_5, + ), + ), + ), + }, + ), + ], + ) + self.assertCountEqual( + ht.take(1), + [ + hl.Struct( + variant_id='BND_chr1_6', + algorithms='manta', + bothsides_support=False, + cpx_intervals=None, + end_locus=hl.Locus( + contig='chr5', + position=20404, + reference_genome='GRCh38', + ), + gnomad_svs=None, + rg37_locus=hl.Locus( + contig=1, + position=10367, + reference_genome='GRCh37', + ), + rg37_locus_end=hl.Locus( + contig=5, + position=20404, + reference_genome='GRCh37', + ), + sorted_gene_consequences=[ + hl.Struct(gene_id='ENSG00000186092', major_consequence_id=12), + hl.Struct(gene_id='ENSG00000153404', major_consequence_id=12), + ], + start_locus=hl.Locus( + contig='chr1', + position=180928, + reference_genome='GRCh38', + ), + strvctvre=hl.Struct(score=None), + sv_len=-1, + sv_type_id=2, + sv_type_detail_id=None, + xpos=1000180928, + key_=0, + ), + ], + ) + + @patch( + 'loading_pipeline.lib.tasks.write_new_variants_table.load_gencode_gene_symbol_to_gene_id', + ) + def test_sv_multiple_project_single_vcf( + self, + mock_load_gencode: Mock, + ) -> None: + mock_load_gencode.return_value = GENE_ID_MAPPING + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_10, + ReferenceGenome.GRCh38, + DatasetType.SV, + SampleType.WGS, + 'R0116_test_project3', + ) + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_11, + ReferenceGenome.GRCh38, + DatasetType.SV, + SampleType.WGS, + 'R0117_test_project4', + ) + worker = luigi.worker.Worker() + update_variant_annotations_task = ( + UpdateVariantAnnotationsTableWithNewVariantsTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SV, + sample_type=SampleType.WGS, + callset_path=TEST_SV_VCF_2, + project_guids=['R0116_test_project3', 'R0117_test_project4'], + validations_to_skip=[ALL_VALIDATIONS], + run_id='run_id', + ) + ) + worker.add(update_variant_annotations_task) + worker.run() + self.assertTrue(update_variant_annotations_task.complete()) + ht = hl.read_table(update_variant_annotations_task.output().path) + self.assertEqual(ht.count(), 2) + self.assertEqual( + len(ht.globals.updates.collect()[0]), + 2, + ) + + def test_gcnv_update_vat_multiple( + self, + ) -> None: + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_5, + ReferenceGenome.GRCh38, + DatasetType.GCNV, + SampleType.WES, + 'R0115_test_project2', + ) + worker = luigi.worker.Worker() + update_variant_annotations_task = ( + UpdateVariantAnnotationsTableWithNewVariantsTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.GCNV, + sample_type=SampleType.WES, + callset_path=TEST_GCNV_BED_FILE, + project_guids=['R0115_test_project2'], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + ) + worker.add(update_variant_annotations_task) + worker.run() + self.assertTrue(update_variant_annotations_task.complete()) + self.assertFalse( + GCSorLocalFolderTarget( + f'{self.mock_env.REFERENCE_DATASETS_DIR}/v03/GRCh38/GCNV/lookup.ht', + ).exists(), + ) + ht = hl.read_table(update_variant_annotations_task.output().path) + self.assertEqual(ht.count(), 2) + self.assertCountEqual( + ht.globals.collect(), + [ + hl.Struct( + enums=hl.Struct( + sv_type=SV_TYPES, + sorted_gene_consequences=hl.Struct( + major_consequence=SV_CONSEQUENCE_RANKS, + ), + ), + migrations=[], + max_key_=1, + updates={ + hl.Struct( + callset=TEST_GCNV_BED_FILE, + project_guid='R0115_test_project2', + remap_pedigree_hash=hl.eval( + remap_pedigree_hash( + TEST_PEDIGREE_5, + ), + ), + ), + }, + ), + ], + ) + self.assertCountEqual( + ht.collect(), + [ + hl.Struct( + variant_id='suffix_16456_DEL', + end_locus=hl.Locus( + contig='chr1', + position=100023213, + reference_genome='GRCh38', + ), + gt_stats=hl.Struct( + AF=hl.eval(hl.float32(4.401408e-05)), + AC=1, + AN=22720, + Hom=None, + Het=None, + ), + num_exon=3, + rg37_locus=hl.Locus( + contig=1, + position=100472493, + reference_genome='GRCh37', + ), + rg37_locus_end=hl.Locus( + contig=1, + position=100488769, + reference_genome='GRCh37', + ), + sorted_gene_consequences=[ + hl.Struct(gene_id='ENSG00000117620', major_consequence_id=0), + hl.Struct(gene_id='ENSG00000283761', major_consequence_id=0), + hl.Struct(gene_id='ENSG22222222222', major_consequence_id=None), + ], + start_locus=hl.Locus( + contig='chr1', + position=100006937, + reference_genome='GRCh38', + ), + strvctvre=hl.Struct(score=hl.eval(hl.float32(0.583))), + sv_type_id=5, + xpos=1100006937, + key_=0, + ), + hl.Struct( + variant_id='suffix_16457_DEL', + end_locus=hl.Locus( + contig='chr1', + position=100023212, + reference_genome='GRCh38', + ), + gt_stats=hl.Struct( + AF=8.802817319519818e-05, + AC=2, + AN=22719, + Hom=None, + Het=None, + ), + num_exon=2, + rg37_locus=hl.Locus( + contig=1, + position=100483142, + reference_genome='GRCh37', + ), + rg37_locus_end=hl.Locus( + contig=1, + position=100488768, + reference_genome='GRCh37', + ), + sorted_gene_consequences=[ + hl.Struct(gene_id='ENSG00000283761', major_consequence_id=0), + hl.Struct(gene_id='ENSG22222222222', major_consequence_id=None), + ], + start_locus=hl.Locus( + contig='chr1', + position=100017586, + reference_genome='GRCh38', + ), + strvctvre=hl.Struct(score=0.5070000290870667), + sv_type_id=5, + xpos=1100017586, + key_=1, + ), + ], + ) + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_8, + ReferenceGenome.GRCh38, + DatasetType.GCNV, + SampleType.WES, + 'R0115_test_project2', + ) + update_variant_annotations_task = ( + UpdateVariantAnnotationsTableWithNewVariantsTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.GCNV, + sample_type=SampleType.WES, + callset_path=TEST_GCNV_BED_FILE_2, + project_guids=['R0115_test_project2'], + validations_to_skip=[ALL_VALIDATIONS], + run_id='second_run_id', + ) + ) + worker.add(update_variant_annotations_task) + worker.run() + ht = hl.read_table(update_variant_annotations_task.output().path) + self.assertEqual(ht.count(), 3) + self.assertCountEqual( + ht.select('gt_stats').collect(), + [ + hl.Struct( + # Existing variant, gt_stats are preserved + variant_id='suffix_16456_DEL', + gt_stats=hl.Struct( + AF=hl.eval(hl.float32(4.401408e-05)), + AC=1, + AN=22720, + Hom=None, + Het=None, + ), + ), + hl.Struct( + # Exiting variant, gt_stats are updated + variant_id='suffix_16457_DEL', + gt_stats=hl.Struct( + AF=8.111110946629196e-05, + AC=3, + AN=36986, + Hom=None, + Het=None, + ), + ), + hl.Struct( + # New variant. + variant_id='suffix_99999_DEL', + gt_stats=hl.Struct( + AF=8.802817319519818e-05, + AC=2, + AN=22719, + Hom=None, + Het=None, + ), + ), + ], + ) diff --git a/loading_pipeline/lib/tasks/validate_callset_test.py b/loading_pipeline/lib/tasks/validate_callset_test.py new file mode 100644 index 0000000000..a56f78a894 --- /dev/null +++ b/loading_pipeline/lib/tasks/validate_callset_test.py @@ -0,0 +1,83 @@ +import json +import shutil + +import luigi.worker + +from loading_pipeline.lib.core import ( + DatasetType, + ReferenceGenome, + SampleType, +) +from loading_pipeline.lib.paths import ( + valid_reference_dataset_path, +) +from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset +from loading_pipeline.lib.tasks.validate_callset import ( + ValidateCallsetTask, +) +from loading_pipeline.lib.tasks.write_validation_errors_for_run import ( + UpdatedValidationErrorsForRunTask, +) +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + +TEST_CODING_AND_NONCODING_HT = 'loading_pipeline/var/test/reference_datasets/GRCh38/gnomad_coding_and_noncoding/1.0.ht' +MULTIPLE_VALIDATION_EXCEPTIONS_VCF = ( + 'loading_pipeline/var/test/callsets/multiple_validation_exceptions.vcf' +) + +TEST_RUN_ID = 'manual__2024-04-03' + + +class ValidateCallsetTest(MockedDatarootTestCase): + def setUp(self) -> None: + super().setUp() + shutil.copytree( + TEST_CODING_AND_NONCODING_HT, + valid_reference_dataset_path( + ReferenceGenome.GRCh38, + ReferenceDataset.gnomad_coding_and_noncoding, + ), + ) + + def test_validate_callset_multiple_exceptions( + self, + ) -> None: + worker = luigi.worker.Worker() + validate_callset_task = ValidateCallsetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WES, + # NB: + # This callset contains duplicate rows for chr1:902088, + # a NON_REF allele type at position chr1: 902024, missing + # all contigs but chr1, and contains non-coding variants. + callset_path=MULTIPLE_VALIDATION_EXCEPTIONS_VCF, + project_guids=['project_a'], + run_id=TEST_RUN_ID, + ) + worker.add(validate_callset_task) + worker.run() + self.assertFalse(validate_callset_task.complete()) + + updated_validation_errors_task = UpdatedValidationErrorsForRunTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WES, + callset_path=MULTIPLE_VALIDATION_EXCEPTIONS_VCF, + project_guids=['project_a'], + run_id=TEST_RUN_ID, + ) + self.assertTrue(updated_validation_errors_task.complete()) + with updated_validation_errors_task.output().open('r') as f: + self.assertDictEqual( + json.load(f), + { + 'project_guids': ['project_a'], + 'error_messages': [ + 'Alleles with invalid allele are present in the callset. This appears to be a GVCF containing records for sites with no variants.', + 'Missing the following expected contigs:chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr2, chr20, chr21, chr22, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chrX', + "Variants are present multiple times in the callset: ['1-902088-G-A']", + 'Sample type validation error: dataset sample-type is specified as WES but appears to be WGS because it contains many common non-coding variants', + ], + }, + ) diff --git a/loading_pipeline/lib/tasks/write_metadata_for_run_test.py b/loading_pipeline/lib/tasks/write_metadata_for_run_test.py new file mode 100644 index 0000000000..2b5dc7a22d --- /dev/null +++ b/loading_pipeline/lib/tasks/write_metadata_for_run_test.py @@ -0,0 +1,188 @@ +import json +from unittest import mock +from unittest.mock import Mock + +import luigi.worker + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS +from loading_pipeline.lib.paths import relatedness_check_tsv_path +from loading_pipeline.lib.tasks.write_metadata_for_run import WriteMetadataForRunTask +from loading_pipeline.lib.test.misc import copy_project_pedigree_to_mocked_dir +from loading_pipeline.lib.test.mock_complete_task import MockCompleteTask +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + +TEST_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' +TEST_PEDIGREE_3_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_3_remap.tsv' +TEST_PEDIGREE_4_REMAP_2 = ( + 'loading_pipeline/var/test/pedigrees/test_pedigree_4_remap_2.tsv' +) +TEST_SAMPLE_QC_JSON = 'loading_pipeline/var/test/sample_qc_1.json' + + +class WriteMetadataForRunTaskTest(MockedDatarootTestCase): + @mock.patch( + 'loading_pipeline.lib.tasks.write_metadata_for_run.sample_qc_json_path', + lambda *_: TEST_SAMPLE_QC_JSON, + ) + @mock.patch('loading_pipeline.lib.tasks.write_metadata_for_run.FeatureFlag') + @mock.patch( + 'loading_pipeline.lib.tasks.write_sex_check_table.WriteTDRMetricsFilesTask', + ) + @mock.patch( + 'loading_pipeline.lib.tasks.write_metadata_for_run.WriteSampleQCJsonTask', + ) + def test_write_metadata_for_run_task( + self, + write_sample_qc_json_task: Mock, + write_tdr_metrics_task: Mock, + mock_ff: Mock, + ) -> None: + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_3_REMAP, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0113_test_project', + ) + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_4_REMAP_2, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0114_project4', + ) + mock_ff.EXPECT_TDR_METRICS = True + write_tdr_metrics_task.return_value = MockCompleteTask() + write_sample_qc_json_task.return_value = MockCompleteTask() + worker = luigi.worker.Worker() + write_metadata_for_run_task = WriteMetadataForRunTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path=TEST_VCF, + project_guids=['R0113_test_project', 'R0114_project4'], + validations_to_skip=[ALL_VALIDATIONS], + run_id='run_123456', + ) + worker.add(write_metadata_for_run_task) + worker.run() + self.assertTrue( + 'run_123456/metadata.json' in write_metadata_for_run_task.output().path, + ) + self.assertTrue(write_metadata_for_run_task.complete()) + with write_metadata_for_run_task.output().open('r') as f: + self.assertDictEqual( + json.load(f), + { + 'callsets': [TEST_VCF], + 'project_guids': ['R0113_test_project', 'R0114_project4'], + 'failed_family_samples': { + 'missing_samples': { + 'efg_1': { + # This sample is present in the callset, but intentionally + # mapped away + 'samples': ['NA20888_1'], + 'reasons': ["Missing samples: {'NA20888_1'}"], + }, + }, + 'relatedness_check': {}, + 'sex_check': {}, + 'ploidy_check': {}, + }, + 'family_samples': { + 'abc_1': [ + 'HG00731_1', + 'HG00732_1', + 'HG00733_1', + ], + '123_1': ['NA19675_1'], + '234_1': ['NA19678_1'], + '345_1': ['NA19679_1'], + '456_1': ['NA20870_1'], + '567_1': ['NA20872_1'], + '678_1': ['NA20874_1'], + '789_1': ['NA20875_1'], + '890_1': ['NA20876_1'], + '901_1': ['NA20877_1'], + 'bcd_1': ['NA20878_1'], + 'cde_1': ['NA20881_1'], + 'def_1': ['NA20885_1'], + }, + 'run_id': 'run_123456', + 'sample_type': SampleType.WGS.value, + 'relatedness_check_file_path': relatedness_check_tsv_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_VCF, + ), + 'sample_qc': { + 'HG00731_1': {'filter_flags': ['coverage', 'contamination']}, + 'HG00732_1': {'filter_flags': ['coverage']}, + 'HG00733_1': {'filter_flags': ['contamination']}, + 'NA19675_1': {'filter_flags': []}, + 'NA20888_1': {'filter_flags': ['sample_failed']}, + }, + }, + ) + + @mock.patch('loading_pipeline.lib.tasks.write_metadata_for_run.FeatureFlag') + def test_write_metadata_for_run_task_without_tdr_metrics( + self, + mock_ff: Mock, + ) -> None: + # When WriteSampleQCJsonTask is not a requirement, every project's + # remapped and subsetted callset must still be collected. + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_3_REMAP, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0113_test_project', + ) + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_4_REMAP_2, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0114_project4', + ) + mock_ff.EXPECT_TDR_METRICS = False + worker = luigi.worker.Worker() + write_metadata_for_run_task = WriteMetadataForRunTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path=TEST_VCF, + project_guids=['R0113_test_project', 'R0114_project4'], + validations_to_skip=[ALL_VALIDATIONS], + run_id='run_123457', + ) + worker.add(write_metadata_for_run_task) + worker.run() + self.assertTrue(write_metadata_for_run_task.complete()) + with write_metadata_for_run_task.output().open('r') as f: + metadata_json = json.load(f) + self.assertDictEqual( + metadata_json['family_samples'], + { + 'abc_1': [ + 'HG00731_1', + 'HG00732_1', + 'HG00733_1', + ], + '123_1': ['NA19675_1'], + '234_1': ['NA19678_1'], + '345_1': ['NA19679_1'], + '456_1': ['NA20870_1'], + '567_1': ['NA20872_1'], + '678_1': ['NA20874_1'], + '789_1': ['NA20875_1'], + '890_1': ['NA20876_1'], + '901_1': ['NA20877_1'], + 'bcd_1': ['NA20878_1'], + 'cde_1': ['NA20881_1'], + 'def_1': ['NA20885_1'], + }, + ) + self.assertDictEqual(metadata_json['sample_qc'], {}) diff --git a/loading_pipeline/lib/tasks/write_relatedness_check_table_test.py b/loading_pipeline/lib/tasks/write_relatedness_check_table_test.py new file mode 100644 index 0000000000..7cc814a5fa --- /dev/null +++ b/loading_pipeline/lib/tasks/write_relatedness_check_table_test.py @@ -0,0 +1,120 @@ +import shutil +from unittest.mock import patch + +import hail as hl +import luigi.worker + +from loading_pipeline.lib.core import ( + DatasetType, + ReferenceGenome, + SampleType, +) +from loading_pipeline.lib.misc.io import import_vcf +from loading_pipeline.lib.paths import ( + postprocessed_callset_path, + relatedness_check_table_path, + valid_reference_dataset_path, +) +from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset +from loading_pipeline.lib.tasks.write_relatedness_check_table import ( + WriteRelatednessCheckTableTask, +) +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + +TEST_GNOMAD_QC_HT = ( + 'loading_pipeline/var/test/reference_datasets/GRCh38/gnomad_qc/1.0.ht' +) +TEST_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' +TEST_RUN_ID = 'manual__2024-04-03' + + +class WriteRelatednessCheckTableTaskTest(MockedDatarootTestCase): + def setUp(self) -> None: + super().setUp() + shutil.copytree( + TEST_GNOMAD_QC_HT, + valid_reference_dataset_path( + ReferenceGenome.GRCh38, + ReferenceDataset.gnomad_qc, + ), + ) + + # Force imported callset to be complete + ht = import_vcf(TEST_VCF, ReferenceGenome.GRCh38) + ht = ht.annotate_globals(validated_sample_type=SampleType.WGS.value) + ht = ht.annotate_rows(**{'info.AF': ht.info.AF}) + ht.write( + postprocessed_callset_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_VCF, + ), + ) + + def test_relatedness_check_table_task_gnomad_qc_updated( + self, + ) -> None: + self.assertEqual( + hl.eval( + hl.read_table( + valid_reference_dataset_path( + ReferenceGenome.GRCh38, + ReferenceDataset.gnomad_qc, + ), + ).version, + ), + '1.0', + ) + with ( + patch.object( + ReferenceDataset, + 'version', + return_value='2.0', + ), + patch.object( + ReferenceDataset, + 'get_ht', + lambda *_: hl.Table.parallelize( + [], + hl.tstruct( + locus=hl.tlocus('GRCh38'), + alleles=hl.tarray(hl.tstr), + ), + key=['locus', 'alleles'], + globals=hl.Struct(version='2.0'), + ), + ), + ): + worker = luigi.worker.Worker() + task = WriteRelatednessCheckTableTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id=TEST_RUN_ID, + sample_type=SampleType.WGS, + callset_path=TEST_VCF, + ) + worker.add(task) + worker.run() + self.assertTrue(task.complete()) + self.assertEqual( + hl.eval( + hl.read_table( + valid_reference_dataset_path( + ReferenceGenome.GRCh38, + ReferenceDataset.gnomad_qc, + ), + ).version, + ), + '2.0', + ) + ht = hl.read_table( + relatedness_check_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_VCF, + ), + ) + self.assertEqual( + ht.collect(), + [], + ) diff --git a/loading_pipeline/lib/tasks/write_relatedness_check_tsv_test.py b/loading_pipeline/lib/tasks/write_relatedness_check_tsv_test.py new file mode 100644 index 0000000000..35a9956f78 --- /dev/null +++ b/loading_pipeline/lib/tasks/write_relatedness_check_tsv_test.py @@ -0,0 +1,53 @@ +import shutil + +import luigi.worker + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.paths import relatedness_check_table_path +from loading_pipeline.lib.tasks.write_relatedness_check_tsv import ( + WriteRelatednessCheckTsvTask, +) +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + +TEST_RELATEDNESS_CHECK_1 = ( + 'loading_pipeline/var/test/relatedness_check/test_relatedness_check_1.ht' +) +TEST_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' +TEST_RUN_ID = 'manual__2024-04-03' + + +class WriteRelatednessCheckTsvTaskTest(MockedDatarootTestCase): + def setUp(self) -> None: + super().setUp() + shutil.copytree( + TEST_RELATEDNESS_CHECK_1, + relatedness_check_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_VCF, + ), + ) + + def test_write_relatedness_check_tsv_task( + self, + ) -> None: + worker = luigi.worker.Worker() + task = WriteRelatednessCheckTsvTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + callset_path=TEST_VCF, + run_id=TEST_RUN_ID, + sample_type=SampleType.WES, + ) + worker.add(task) + worker.run() + self.assertTrue(task.complete()) + with task.output().open('r') as f: + lines = f.readlines() + expected_lines = [ + 'i\tj\tibd0\tibd1\tibd2\tpi_hat\n', + 'HG00731_1\tHG00733_1\t0\t1\t0\t5.0000e-01\n', + 'HG00732_1\tHG00733_1\t0\t1\t0\t5.0000e-01\n', + ] + for expected_line, actual_line in zip(expected_lines, lines, strict=False): + self.assertEqual(expected_line, actual_line) diff --git a/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset_test.py b/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset_test.py new file mode 100644 index 0000000000..590795424a --- /dev/null +++ b/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset_test.py @@ -0,0 +1,460 @@ +import json +import shutil +from unittest.mock import Mock, patch + +import hail as hl +import luigi.worker + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.misc.io import remap_pedigree_hash +from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS +from loading_pipeline.lib.paths import ( + relatedness_check_table_path, + sex_check_table_path, +) +from loading_pipeline.lib.tasks.write_remapped_and_subsetted_callset import ( + WriteRemappedAndSubsettedCallsetTask, +) +from loading_pipeline.lib.tasks.write_validation_errors_for_run import ( + UpdatedValidationErrorsForRunTask, +) +from loading_pipeline.lib.test.misc import copy_project_pedigree_to_mocked_dir +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + +TEST_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' +TEST_PEDIGREE_3_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_3_remap.tsv' +TEST_PEDIGREE_3_DIFFERENT_FAMILIES = ( + 'loading_pipeline/var/test/pedigrees/test_pedigree_3_different_families.tsv' +) +TEST_PEDIGREE_4_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_4_remap.tsv' +TEST_PEDIGREE_7 = 'loading_pipeline/var/test/pedigrees/test_pedigree_7.tsv' +TEST_SEX_CHECK_1 = 'loading_pipeline/var/test/sex_check/test_sex_check_1.ht' +TEST_RELATEDNESS_CHECK_1 = ( + 'loading_pipeline/var/test/relatedness_check/test_relatedness_check_1.ht' +) + +TEST_RUN_ID = 'manual__2024-04-03' + + +class WriteRemappedAndSubsettedCallsetTaskTest(MockedDatarootTestCase): + def setUp(self) -> None: + super().setUp() + # +-------------+---------------+ + # | s | predicted_sex | + # +-------------+---------------+ + # | str | str | + # +-------------+---------------+ + # | "HG00731_1" | "F" | + # | "HG00732_1" | "M" | + # | "HG00733_1" | "F" | + # | "NA19675_1" | "F" | + # | "NA19678_1" | "M" | + # | "NA19679_1" | "F" | + # | "NA20870_1" | "F" | + # | "NA20872_1" | "M" | + # | "NA20874_1" | "F" | + # | "NA20875_1" | "F" | + # | "NA20876_1" | "F" | + # | "NA20877_1" | "F" | + # | "NA20878_1" | "M" | + # | "NA20881_1" | "M" | + # | "NA20885_1" | "F" | + # | "NA20888_1" | "F" | + # +-------------+---------------+ + shutil.copytree( + TEST_SEX_CHECK_1, + sex_check_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_VCF, + ), + ) + # +-------------+-------------+-------+-------+-------+----------+ + # | i | j | ibd0 | ibd1 | ibd2 | pi_hat | + # +-------------+-------------+-------+-------+-------+----------+ + # | str | str | int32 | int32 | int32 | float64 | + # +-------------+-------------+-------+-------+-------+----------+ + # | "HG00731_1" | "HG00733_1" | 0 | 1 | 0 | 5.00e-01 | + # | "HG00732_1" | "HG00733_1" | 0 | 1 | 0 | 5.00e-01 | + # +-------------+-------------+-------+-------+-------+----------+ + shutil.copytree( + TEST_RELATEDNESS_CHECK_1, + relatedness_check_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_VCF, + ), + ) + + def test_write_remapped_and_subsetted_callset_task( + self, + ) -> None: + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_3_REMAP, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0113_test_project', + ) + worker = luigi.worker.Worker() + wrsc_task = WriteRemappedAndSubsettedCallsetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id=TEST_RUN_ID, + sample_type=SampleType.WGS, + callset_path=TEST_VCF, + project_guids=['R0113_test_project'], + project_i=0, + validations_to_skip=[ALL_VALIDATIONS], + skip_expect_tdr_metrics=True, + ) + worker.add(wrsc_task) + worker.run() + self.assertTrue(wrsc_task.complete()) + mt = hl.read_matrix_table(wrsc_task.output().path) + self.assertEqual(mt.count(), (30, 3)) + self.assertEqual( + mt.globals.collect(), + [ + hl.Struct( + remap_pedigree_hash=hl.eval( + remap_pedigree_hash( + TEST_PEDIGREE_3_REMAP, + ), + ), + failed_family_samples=hl.Struct( + missing_samples={}, + relatedness_check={}, + sex_check={}, + ploidy_check={}, + ), + family_samples={'abc_1': ['HG00731_1', 'HG00732_1', 'HG00733_1']}, + ), + ], + ) + + @patch( + 'loading_pipeline.lib.tasks.write_remapped_and_subsetted_callset.FeatureFlag', + ) + def test_write_remapped_and_subsetted_callset_task_failed_some_family_checks( + self, + mock_ff: Mock, + ) -> None: + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_4_REMAP, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0114_project4', + ) + mock_ff.CHECK_SEX_AND_RELATEDNESS = True + worker = luigi.worker.Worker() + wrsc_task = WriteRemappedAndSubsettedCallsetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id=TEST_RUN_ID, + sample_type=SampleType.WGS, + callset_path=TEST_VCF, + project_guids=['R0114_project4'], + project_i=0, + validations_to_skip=[ALL_VALIDATIONS], + skip_expect_tdr_metrics=True, + ) + worker.add(wrsc_task) + worker.run() + self.assertTrue(wrsc_task.complete()) + mt = hl.read_matrix_table(wrsc_task.output().path) + # NB: one "family"/"sample" has been removed because of a failed sex check, + # and 4 removed because of a failed ploidy check! + self.assertEqual(mt.count(), (30, 8)) + self.assertEqual( + mt.globals.collect(), + [ + hl.Struct( + remap_pedigree_hash=hl.eval( + remap_pedigree_hash( + TEST_PEDIGREE_4_REMAP, + ), + ), + family_samples={ + '123_1': ['NA19675_1'], + '345_1': ['NA19679_1'], + '456_1': ['NA20870_1'], + '678_1': ['NA20874_1'], + '789_1': ['NA20875_1'], + '890_1': ['NA20876_1'], + '901_1': ['NA20877_1'], + 'efg_1': ['NA20888_1'], + }, + failed_family_samples=hl.Struct( + missing_samples={}, + relatedness_check={}, + sex_check={ + 'def_1': { + 'reasons': [ + 'Sample NA20885_1 has pedigree sex M but imputed sex F', + ], + 'samples': ['NA20885_1'], + }, + }, + ploidy_check={ + '234_1': { + 'reasons': [ + "Found samples with misaligned ploidy with their provided imputed sex: ['NA19678_1']", + ], + 'samples': ['NA19678_1'], + }, + '567_1': { + 'reasons': [ + "Found samples with misaligned ploidy with their provided imputed sex: ['NA20872_1']", + ], + 'samples': ['NA20872_1'], + }, + 'bcd_1': { + 'reasons': [ + "Found samples with misaligned ploidy with their provided imputed sex: ['NA20878_1']", + ], + 'samples': ['NA20878_1'], + }, + 'cde_1': { + 'reasons': [ + "Found samples with misaligned ploidy with their provided imputed sex: ['NA20881_1']", + ], + 'samples': ['NA20881_1'], + }, + }, + ), + ), + ], + ) + + @patch( + 'loading_pipeline.lib.tasks.write_remapped_and_subsetted_callset.FeatureFlag', + ) + def test_write_remapped_and_subsetted_callset_task_all_families_failed( + self, + mock_ff: Mock, + ) -> None: + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_7, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0114_project4', + ) + mock_ff.CHECK_SEX_AND_RELATEDNESS = True + worker = luigi.worker.Worker() + wrsc_task = WriteRemappedAndSubsettedCallsetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id=TEST_RUN_ID, + sample_type=SampleType.WGS, + callset_path=TEST_VCF, + project_guids=['R0114_project4'], + project_i=0, + validations_to_skip=[ALL_VALIDATIONS], + skip_expect_tdr_metrics=True, + ) + worker.add(wrsc_task) + worker.run() + self.assertFalse(wrsc_task.complete()) + updated_validation_errors_task = UpdatedValidationErrorsForRunTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WES, + callset_path=TEST_VCF, + project_guids=['R0114_project4'], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + self.assertTrue(updated_validation_errors_task.complete()) + with updated_validation_errors_task.output().open('r') as f: + self.assertDictEqual( + json.load(f), + { + 'project_guids': ['R0114_project4'], + 'error_messages': ['All families failed validation checks'], + 'failed_family_samples': { + 'missing_samples': { + 'efg_1': { + 'samples': ['NA99999_1'], + 'reasons': ["Missing samples: {'NA99999_1'}"], + }, + }, + 'relatedness_check': {}, + 'sex_check': { + '890_1': { + 'samples': ['NA20876_1'], + 'reasons': [ + 'Sample NA20876_1 has pedigree sex M but imputed sex F', + ], + }, + '456_1': { + 'samples': ['NA20870_1'], + 'reasons': [ + 'Sample NA20870_1 has pedigree sex M but imputed sex F', + ], + }, + '123_1': { + 'samples': ['NA19675_1'], + 'reasons': [ + 'Sample NA19675_1 has pedigree sex M but imputed sex F', + ], + }, + '678_1': { + 'samples': ['NA20874_1'], + 'reasons': [ + 'Sample NA20874_1 has pedigree sex M but imputed sex F', + ], + }, + '789_1': { + 'samples': ['NA20875_1'], + 'reasons': [ + 'Sample NA20875_1 has pedigree sex M but imputed sex F', + ], + }, + '901_1': { + 'samples': ['NA20877_1'], + 'reasons': [ + 'Sample NA20877_1 has pedigree sex M but imputed sex F', + ], + }, + '345_1': { + 'samples': ['NA19679_1'], + 'reasons': [ + 'Sample NA19679_1 has pedigree sex M but imputed sex F', + ], + }, + 'def_1': { + 'samples': ['NA20885_1'], + 'reasons': [ + 'Sample NA20885_1 has pedigree sex M but imputed sex F', + ], + }, + }, + 'ploidy_check': { + '567_1': { + 'samples': ['NA20872_1'], + 'reasons': [ + "Found samples with misaligned ploidy with their provided imputed sex: ['NA20872_1']", + ], + }, + '234_1': { + 'samples': ['NA19678_1'], + 'reasons': [ + "Found samples with misaligned ploidy with their provided imputed sex: ['NA19678_1']", + ], + }, + 'bcd_1': { + 'samples': ['NA20878_1'], + 'reasons': [ + "Found samples with misaligned ploidy with their provided imputed sex: ['NA20878_1']", + ], + }, + 'cde_1': { + 'samples': ['NA20881_1'], + 'reasons': [ + "Found samples with misaligned ploidy with their provided imputed sex: ['NA20881_1']", + ], + }, + }, + }, + }, + ) + + @patch( + 'loading_pipeline.lib.tasks.write_remapped_and_subsetted_callset.FeatureFlag', + ) + def test_write_remapped_and_subsetted_callset_task_combined_validation_errors( + self, + mock_ff: Mock, + ) -> None: + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_3_DIFFERENT_FAMILIES, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0113_test_project', + ) + worker = luigi.worker.Worker() + + wrsc_task_1 = WriteRemappedAndSubsettedCallsetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id=TEST_RUN_ID, + sample_type=SampleType.WGS, + callset_path=TEST_VCF, + project_guids=['R0113_test_project'], + project_i=0, + validations_to_skip=[ALL_VALIDATIONS], + skip_expect_tdr_metrics=True, + ) + worker.add(wrsc_task_1) + worker.run() + + # Second run: load pedigree 7 where all families fail validation checks + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_7, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0114_project4', + ) + worker_2 = luigi.worker.Worker() + + wrsc_task_2 = WriteRemappedAndSubsettedCallsetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id=TEST_RUN_ID, + sample_type=SampleType.WGS, + callset_path=TEST_VCF, + project_guids=['R0114_project4'], + project_i=0, + validations_to_skip=[ALL_VALIDATIONS], + skip_expect_tdr_metrics=True, + ) + worker_2.add(wrsc_task_2) + worker_2.run() + + # Verify second task does not complete (all families failed) + self.assertFalse(wrsc_task_2.complete()) + + # Verify validation errors for second run + updated_validation_errors_task = UpdatedValidationErrorsForRunTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WES, + callset_path=TEST_VCF, + project_guids=['R0113_test_project', 'R0114_project4'], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + self.assertTrue(updated_validation_errors_task.complete()) + with updated_validation_errors_task.output().open('r') as f: + validation_errors = json.load(f) + + # Verify that all families failed in the second run + self.assertIn( + 'All families failed validation checks', + validation_errors['error_messages'], + ) + # Should have missing samples, sex checks, and ploidy checks all failing + failed_samples = validation_errors['failed_family_samples'] + self.assertGreater( + len(failed_samples['missing_samples']), + 0, + 'Expected missing_samples to have failures', + ) + self.assertGreater( + len(failed_samples['sex_check']), + 0, + 'Expected sex_check to have failures', + ) + self.assertGreater( + len(failed_samples['ploidy_check']), + 0, + 'Expected ploidy_check to have failures', + ) + # Verify that both project guids are in the validation errors + self.assertIn('R0113_test_project', validation_errors['project_guids']) + self.assertIn('R0114_project4', validation_errors['project_guids']) diff --git a/loading_pipeline/lib/tasks/write_sample_qc_json_test.py b/loading_pipeline/lib/tasks/write_sample_qc_json_test.py new file mode 100644 index 0000000000..1c2709c9b7 --- /dev/null +++ b/loading_pipeline/lib/tasks/write_sample_qc_json_test.py @@ -0,0 +1,269 @@ +import json +import os +import shutil +from unittest.mock import Mock, patch + +import hail as hl +import hailtop.fs as hfs +import luigi.worker + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS +from loading_pipeline.lib.paths import ancestry_model_rf_path, tdr_metrics_dir +from loading_pipeline.lib.tasks.write_sample_qc_json import WriteSampleQCJsonTask +from loading_pipeline.lib.test.misc import copy_project_pedigree_to_mocked_dir +from loading_pipeline.lib.test.mock_complete_task import MockCompleteTask +from loading_pipeline.lib.test.mocked_reference_datasets_testcase import ( + MockedReferenceDatasetsTestCase, +) + +TEST_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' +TEST_PEDIGREE_3_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_3_remap.tsv' +TEST_TDR_METRICS_FILE = 'loading_pipeline/var/test/tdr_metrics.tsv' +TEST_RUN_ID = 'manual__2024-04-03' + +PCA_SCORES = [0.00212, 0.011, 0.0105, 0.161, 0.026] + [0.1 for _ in range(15)] +EXPECTED_ANC_PROBABILITIES = { + 'prob_afr': 0.02, + 'prob_ami': 0.0, + 'prob_amr': 0.02, + 'prob_asj': 0.9, + 'prob_eas': 0.0, + 'prob_fin': 0.0, + 'prob_mid': 0.0, + 'prob_nfe': 0.05, + 'prob_sas': 0.01, +} +TEST_ANCESTRY_IMPUTATION_MODEL_PATH = ( + 'loading_pipeline/var/test/ancestry_imputation_model.onnx' +) + + +class WriteSampleQCJsonTaskTest(MockedReferenceDatasetsTestCase): + @patch('loading_pipeline.lib.methods.sample_qc.assign_population_pcs') + @patch('loading_pipeline.lib.methods.sample_qc.pc_project') + @patch('loading_pipeline.lib.tasks.write_sample_qc_json.WriteTDRMetricsFilesTask') + def test_call_sample_qc( + self, + mock_tdr_task: Mock, + mock_pc_project: Mock, + mock_assign_population_pcs: Mock, + ) -> None: + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_3_REMAP, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0113_test_project', + ) + os.makedirs( + os.path.dirname(ancestry_model_rf_path()), + exist_ok=True, + ) + shutil.copy2(TEST_ANCESTRY_IMPUTATION_MODEL_PATH, ancestry_model_rf_path()) + os.makedirs( + tdr_metrics_dir(ReferenceGenome.GRCh38, DatasetType.SNV_INDEL), + exist_ok=True, + ) + shutil.copy2( + TEST_TDR_METRICS_FILE, + tdr_metrics_dir(ReferenceGenome.GRCh38, DatasetType.SNV_INDEL), + ) + mock_tdr_task.return_value = MockCompleteTask() + mock_pc_project.return_value = hl.Table.parallelize( + [ + { + 's': sample_id, + 'scores': PCA_SCORES, + } + for sample_id in ('HG00731', 'HG00732', 'HG00733', 'NA19675') + ], + hl.tstruct( + s=hl.tstr, + scores=hl.tarray(hl.tfloat64), + ), + key='s', + ) + mock_assign_population_pcs.return_value = ( + hl.Table.parallelize( + [ + { + 's': sample_id, + 'pca_scores': PCA_SCORES, + 'qc_pop': 'asj', + **EXPECTED_ANC_PROBABILITIES, + } + for sample_id in ('HG00731', 'HG00732', 'HG00733', 'NA19675') + ], + hl.tstruct( + s=hl.tstr, + pca_scores=hl.tarray(hl.tfloat64), + qc_pop=hl.tstr, + prob_afr=hl.tfloat64, + prob_ami=hl.tfloat64, + prob_amr=hl.tfloat64, + prob_asj=hl.tfloat64, + prob_eas=hl.tfloat64, + prob_fin=hl.tfloat64, + prob_mid=hl.tfloat64, + prob_nfe=hl.tfloat64, + prob_sas=hl.tfloat64, + ), + key='s', + ), + None, + ) + worker = luigi.worker.Worker() + task = WriteSampleQCJsonTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id=TEST_RUN_ID, + sample_type=SampleType.WGS, + callset_path=TEST_VCF, + project_guids=['R0113_test_project'], + validations_to_skip=[ALL_VALIDATIONS], + ) + worker.add(task) + worker.run() + self.assertTrue(task) + self.assertTrue(hfs.exists(task.output().path)) + + expected_qc_gen_anc_results = { + 'pca_scores': PCA_SCORES, + **EXPECTED_ANC_PROBABILITIES, + **{f'pop_PC{i + 1}': PCA_SCORES[i] for i in range(20)}, + 'qc_gen_anc': 'oth', + } + with task.output().open('r') as f: + res = json.load(f) + + self.assertCountEqual( + res['HG00731_1'], + { + 'seqr_id': 'HG00731_1', + 'vcf_id': 'HG00731', + 'filtered_callrate': 1.0, + 'contamination_rate': 5.099999904632568, + 'percent_bases_at_20x': 93.69000244140625, + 'mean_coverage': 29.309999465942383, + 'filter_flags': ['contamination', 'coverage'], + **expected_qc_gen_anc_results, + 'sample_qc.call_rate': 0.9666666666666667, + 'sample_qc.n_called': 29, + 'sample_qc.n_not_called': 1, + 'sample_qc.n_filtered': 0, + 'sample_qc.n_hom_ref': 16, + 'sample_qc.n_het': 2, + 'sample_qc.n_hom_var': 11, + 'sample_qc.n_non_ref': 13, + 'sample_qc.n_singleton': 1, + 'sample_qc.n_snp': 24, + 'sample_qc.n_insertion': 0, + 'sample_qc.n_deletion': 0, + 'sample_qc.n_transition': 15, + 'sample_qc.n_transversion': 9, + 'sample_qc.n_star': 0, + 'sample_qc.r_ti_tv': 1.6666666666666667, + 'sample_qc.r_het_hom_var': 0.18181818181818182, + 'sample_qc.r_insertion_deletion': None, + 'sample_qc.f_inbreeding.f_stat': 0.284195245767986, + 'sample_qc.f_inbreeding.n_called': 29, + 'sample_qc.f_inbreeding.expected_homs': 26.20594199999999, + 'sample_qc.f_inbreeding.observed_homs': 27, + 'fail_n_snp': True, + 'fail_r_ti_tv': False, + 'fail_r_insertion_deletion': None, + 'fail_n_insertion': True, + 'fail_n_deletion': True, + 'fail_r_het_hom_var': False, + 'fail_call_rate': False, + 'qc_metrics_filters': ['n_deletion', 'n_insertion', 'n_snp'], + }, + ) + self.assertCountEqual( + res['HG00732_1'], + { + 'seqr_id': 'HG00732_1', + 'vcf_id': 'HG00732', + 'filtered_callrate': 1.0, + 'contamination_rate': 5.0, + 'percent_bases_at_20x': 90.0, + 'mean_coverage': 28.0, + 'filter_flags': ['coverage'], + **expected_qc_gen_anc_results, + 'sample_qc.call_rate': 0.9666666666666667, + 'sample_qc.n_called': 29, + 'sample_qc.n_not_called': 1, + 'sample_qc.n_filtered': 0, + 'sample_qc.n_hom_ref': 16, + 'sample_qc.n_het': 4, + 'sample_qc.n_hom_var': 9, + 'sample_qc.n_non_ref': 13, + 'sample_qc.n_singleton': 2, + 'sample_qc.n_snp': 22, + 'sample_qc.n_insertion': 0, + 'sample_qc.n_deletion': 0, + 'sample_qc.n_transition': 13, + 'sample_qc.n_transversion': 9, + 'sample_qc.n_star': 0, + 'sample_qc.r_ti_tv': 1.4444444444444444, + 'sample_qc.r_het_hom_var': 0.4444444444444444, + 'sample_qc.r_insertion_deletion': None, + 'sample_qc.f_inbreeding.f_stat': -0.431609508464028, + 'sample_qc.f_inbreeding.n_called': 29, + 'sample_qc.f_inbreeding.expected_homs': 26.20594199999999, + 'sample_qc.f_inbreeding.observed_homs': 25, + 'fail_n_snp': True, + 'fail_r_ti_tv': False, + 'fail_r_insertion_deletion': None, + 'fail_n_insertion': True, + 'fail_n_deletion': True, + 'fail_r_het_hom_var': False, + 'fail_call_rate': False, + 'qc_metrics_filters': ['n_deletion', 'n_insertion', 'n_snp'], + }, + ) + self.assertCountEqual( + res['HG00733_1'], + { + 'seqr_id': 'HG00733_1', + 'vcf_id': 'HG00733', + 'filtered_callrate': 1.0, + 'contamination_rate': 6.0, + 'percent_bases_at_20x': 85.0, + 'mean_coverage': 36.400001525878906, + 'filter_flags': ['contamination'], + **expected_qc_gen_anc_results, + 'sample_qc.call_rate': 1.0, + 'sample_qc.n_called': 30, + 'sample_qc.n_not_called': 0, + 'sample_qc.n_filtered': 0, + 'sample_qc.n_hom_ref': 17, + 'sample_qc.n_het': 3, + 'sample_qc.n_hom_var': 10, + 'sample_qc.n_non_ref': 13, + 'sample_qc.n_singleton': 0, + 'sample_qc.n_snp': 23, + 'sample_qc.n_insertion': 0, + 'sample_qc.n_deletion': 0, + 'sample_qc.n_transition': 13, + 'sample_qc.n_transversion': 10, + 'sample_qc.n_star': 0, + 'sample_qc.r_ti_tv': 1.3, + 'sample_qc.r_het_hom_var': 0.3, + 'sample_qc.r_insertion_deletion': None, + 'sample_qc.f_inbreeding.f_stat': -0.038400752079048056, + 'sample_qc.f_inbreeding.n_called': 30, + 'sample_qc.f_inbreeding.expected_homs': 27.11094199999999, + 'sample_qc.f_inbreeding.observed_homs': 27, + 'fail_n_snp': True, + 'fail_r_ti_tv': False, + 'fail_r_insertion_deletion': None, + 'fail_n_insertion': True, + 'fail_n_deletion': True, + 'fail_r_het_hom_var': False, + 'fail_call_rate': False, + 'qc_metrics_filters': ['n_deletion', 'n_insertion', 'n_snp'], + }, + ) + self.assertFalse('NA19675' in res) diff --git a/loading_pipeline/lib/tasks/write_sex_check_table_test.py b/loading_pipeline/lib/tasks/write_sex_check_table_test.py new file mode 100644 index 0000000000..1f83d8c991 --- /dev/null +++ b/loading_pipeline/lib/tasks/write_sex_check_table_test.py @@ -0,0 +1,157 @@ +from decimal import Decimal +from unittest.mock import Mock, patch + +import google.cloud.bigquery +import hail as hl +import luigi.worker + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.paths import sex_check_table_path, tdr_metrics_path +from loading_pipeline.lib.tasks.write_sex_check_table import ( + WriteSexCheckTableTask, +) +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + +TEST_SEX_AND_RELATEDNESS_CALLSET_MT = ( + 'loading_pipeline/var/test/callsets/sex_and_relatedness_1.mt' +) + + +class WriteSexCheckTableTaskTest(MockedDatarootTestCase): + @patch('loading_pipeline.lib.tasks.write_tdr_metrics_files.gen_bq_table_names') + @patch('loading_pipeline.lib.tasks.write_tdr_metrics_file.bq_metrics_query') + @patch( + 'loading_pipeline.lib.tasks.write_sex_check_table.FeatureFlag', + ) + def test_snv_sex_check_table_task( + self, + mock_ff: Mock, + mock_bq_metrics_query: Mock, + mock_gen_bq_table_names: Mock, + ) -> None: + mock_ff.EXPECT_TDR_METRICS = True + mock_gen_bq_table_names.return_value = [ + 'datarepo-7242affb.datarepo_RP_3053', + 'datarepo-5a72e31b.datarepo_RP_3056', + ] + mock_bq_metrics_query.side_effect = [ + iter( + [ + google.cloud.bigquery.table.Row( + ( + 'SM-NJ8MF', + 'Unknown', + Decimal('0'), + Decimal('0'), + Decimal('0'), + ), + { + 'collaborator_sample_id': 0, + 'predicted_sex': 1, + 'contamination_rate': 2, + 'percent_bases_at_20x': 3, + 'mean_coverage': 4, + }, + ), + google.cloud.bigquery.table.Row( + ( + 'SM-MWOGC', + 'Female', + Decimal('0'), + Decimal('0'), + Decimal('0'), + ), + { + 'collaborator_sample_id': 0, + 'predicted_sex': 1, + 'contamination_rate': 2, + 'percent_bases_at_20x': 3, + 'mean_coverage': 4, + }, + ), + google.cloud.bigquery.table.Row( + ('SM-MWKWL', 'Male', Decimal('0'), Decimal('0'), Decimal('0')), + { + 'collaborator_sample_id': 0, + 'predicted_sex': 1, + 'contamination_rate': 2, + 'percent_bases_at_20x': 3, + 'mean_coverage': 4, + }, + ), + ], + ), + iter( + [ + google.cloud.bigquery.table.Row( + ('SM-NGE65', 'Male', Decimal('0'), Decimal('0'), Decimal('0')), + { + 'collaborator_sample_id': 0, + 'predicted_sex': 1, + 'contamination_rate': 2, + 'percent_bases_at_20x': 3, + 'mean_coverage': 4, + }, + ), + google.cloud.bigquery.table.Row( + ('SM-NGE5G', 'Male', Decimal('0'), Decimal('0'), Decimal('0')), + { + 'collaborator_sample_id': 0, + 'predicted_sex': 1, + 'contamination_rate': 2, + 'percent_bases_at_20x': 3, + 'mean_coverage': 4, + }, + ), + google.cloud.bigquery.table.Row( + ('SM-NC6LM', 'Male', Decimal('0'), Decimal('0'), Decimal('0')), + { + 'collaborator_sample_id': 0, + 'predicted_sex': 1, + 'contamination_rate': 2, + 'percent_bases_at_20x': 3, + 'mean_coverage': 4, + }, + ), + ], + ), + ] + worker = luigi.worker.Worker() + write_sex_check_table = WriteSexCheckTableTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path='na', + project_guids=['R0113_test_project'], + run_id='manual__2024-04-03', + ) + worker.add(write_sex_check_table) + worker.run() + self.assertTrue(write_sex_check_table.complete()) + sex_check_ht = hl.read_table( + sex_check_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + 'na', + ), + ) + self.assertEqual( + sex_check_ht.collect(), + [ + hl.Struct(s='SM-MWKWL', predicted_sex='M'), + hl.Struct(s='SM-MWOGC', predicted_sex='F'), + hl.Struct(s='SM-NC6LM', predicted_sex='M'), + hl.Struct(s='SM-NGE5G', predicted_sex='M'), + hl.Struct(s='SM-NGE65', predicted_sex='M'), + hl.Struct(s='SM-NJ8MF', predicted_sex='U'), + ], + ) + # Check underlying tdr metrics file. + with open( + tdr_metrics_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + 'datarepo-5a72e31b.datarepo_RP_3056', + ), + ) as f: + self.assertTrue('collaborator_sample_id' in f.read()) diff --git a/loading_pipeline/lib/tasks/write_success_file_test.py b/loading_pipeline/lib/tasks/write_success_file_test.py new file mode 100644 index 0000000000..f33a5d337e --- /dev/null +++ b/loading_pipeline/lib/tasks/write_success_file_test.py @@ -0,0 +1,34 @@ +from unittest import mock + +import luigi.worker + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.tasks.write_success_file import WriteSuccessFileTask +from loading_pipeline.lib.test.mock_complete_task import MockCompleteTask +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + + +class WriteSuccessFileTaskTest(MockedDatarootTestCase): + @mock.patch( + 'loading_pipeline.lib.tasks.write_success_file.RunPipelineTask', + ) + def test_write_success_file_task( + self, + mock_run_pipeline_task: mock.Mock, + ) -> None: + mock_run_pipeline_task.return_value = MockCompleteTask() + worker = luigi.worker.Worker() + write_success_file = WriteSuccessFileTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path='test_callset', + project_guids=['R0113_test_project'], + run_id='manual__2024-04-03', + attempt_id=0, + ) + worker.add(write_success_file) + worker.run() + self.assertTrue(write_success_file.complete()) + with open(write_success_file.output().path) as f: + self.assertEqual(f.read(), '') diff --git a/loading_pipeline/lib/tasks/write_variant_annotations_vcf_test.py b/loading_pipeline/lib/tasks/write_variant_annotations_vcf_test.py new file mode 100644 index 0000000000..4bad466b67 --- /dev/null +++ b/loading_pipeline/lib/tasks/write_variant_annotations_vcf_test.py @@ -0,0 +1,91 @@ +import gzip +from unittest.mock import Mock, patch + +import hailtop.fs as hfs +import luigi.worker + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS +from loading_pipeline.lib.tasks.update_variant_annotations_table_with_new_variants import ( + UpdateVariantAnnotationsTableWithNewVariantsTask, +) +from loading_pipeline.lib.tasks.write_variant_annotations_vcf import ( + WriteVariantAnnotationsVCF, +) +from loading_pipeline.lib.test.misc import copy_project_pedigree_to_mocked_dir +from loading_pipeline.lib.test.mocked_reference_datasets_testcase import ( + MockedReferenceDatasetsTestCase, +) + +TEST_SV_VCF = 'loading_pipeline/var/test/callsets/sv_1.vcf' +TEST_PEDIGREE_5 = 'loading_pipeline/var/test/pedigrees/test_pedigree_5.tsv' + +GENE_ID_MAPPING = { + 'OR4F5': 'ENSG00000186092', + 'PLEKHG4B': 'ENSG00000153404', + 'OR4F16': 'ENSG00000186192', + 'OR4F29': 'ENSG00000284733', + 'FBXO28': 'ENSG00000143756', + 'SAMD11': 'ENSG00000187634', + 'C1orf174': 'ENSG00000198912', + 'TAS1R1': 'ENSG00000173662', + 'FAM131C': 'ENSG00000185519', + 'RCC2': 'ENSG00000179051', + 'NBPF3': 'ENSG00000142794', + 'AGBL4': 'ENSG00000186094', + 'KIAA1614': 'ENSG00000135835', + 'MR1': 'ENSG00000153029', + 'STX6': 'ENSG00000135823', + 'XPR1': 'ENSG00000143324', +} + + +class WriteVariantAnnotationsVCFTest(MockedReferenceDatasetsTestCase): + @patch( + 'loading_pipeline.lib.tasks.write_new_variants_table.load_gencode_gene_symbol_to_gene_id', + ) + def test_sv_export_vcf( + self, + mock_load_gencode: Mock, + ) -> None: + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_5, + ReferenceGenome.GRCh38, + DatasetType.SV, + SampleType.WGS, + 'R0115_test_project2', + ) + mock_load_gencode.return_value = GENE_ID_MAPPING + worker = luigi.worker.Worker() + update_variant_annotations_task = ( + UpdateVariantAnnotationsTableWithNewVariantsTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SV, + run_id='run_id1', + sample_type=SampleType.WGS, + callset_path=TEST_SV_VCF, + project_guids=['R0115_test_project2'], + validations_to_skip=[ALL_VALIDATIONS], + skip_expect_tdr_metrics=True, + ) + ) + worker.add(update_variant_annotations_task) + worker.run() + self.assertTrue(update_variant_annotations_task.complete()) + write_variant_annotations_vcf_task = WriteVariantAnnotationsVCF( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SV, + run_id='run_id1', + sample_type=SampleType.WGS, + callset_path=TEST_SV_VCF, + ) + worker.add(write_variant_annotations_vcf_task) + worker.run() + self.assertTrue( + hfs.exists( + write_variant_annotations_vcf_task.output().path, + ), + ) + with hfs.open(write_variant_annotations_vcf_task.output().path, 'rb') as f: + buf = f.read() + self.assertTrue(gzip.decompress(buf).startswith(b'##fileformat=VCFv4.2')) From b92da693fa8c8c930cf2a129f0f366dc5ebf242f Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 13:57:11 -0400 Subject: [PATCH 083/369] remove debug --- loading_pipeline/lib/misc/clickhouse_test.py | 1 - 1 file changed, 1 deletion(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index b7a46695d5..fdfe26198e 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -461,7 +461,6 @@ def test_direct_insert_all_keys(self): return_value=[ClickhouseReferenceDataset.CLINVAR], ) def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): - self.maxDiff = None # TODO # Tests individual components of the atomic_insert_entries # to validate the state after each step. cursor = connections['clickhouse_write'].cursor() From 8058989b87af98a216b6b73c8997da624781415e Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 17 Aug 2026 14:19:53 -0400 Subject: [PATCH 084/369] reenable codacy for pipeline --- .codacy.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.codacy.yaml b/.codacy.yaml index 3bd43d8705..a0ae5a67dd 100644 --- a/.codacy.yaml +++ b/.codacy.yaml @@ -1,4 +1,3 @@ --- exclude_paths: - - "deploy/postgres/initdb.sql" - - "loading_pipeline/**" \ No newline at end of file + - "deploy/postgres/initdb.sql" \ No newline at end of file From da76759cc3ffc368d2285b28ae815800772c9ea7 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 17 Aug 2026 15:58:11 -0400 Subject: [PATCH 085/369] quote in bash scripts --- loading_pipeline/bin/dataproc_vep_init.bash | 6 +++--- .../bin/download_vep_reference_data.bash | 4 ++-- loading_pipeline/bin/rsync_reference_data.bash | 18 +++++++++--------- 3 files changed, 14 insertions(+), 14 deletions(-) diff --git a/loading_pipeline/bin/dataproc_vep_init.bash b/loading_pipeline/bin/dataproc_vep_init.bash index ec049e3217..257df7d8d3 100755 --- a/loading_pipeline/bin/dataproc_vep_init.bash +++ b/loading_pipeline/bin/dataproc_vep_init.bash @@ -54,10 +54,10 @@ EOF gcc -Wall -Werror -O2 /vep.c -o /vep chmod u+s /vep -gcloud storage cp gs://seqr-pipeline-runner-builds/$DEPLOYMENT_TYPE/$PIPELINE_RUNNER_APP_VERSION/bin/download_vep_reference_data.bash /download_vep_reference_data.bash +gcloud storage cp "gs://seqr-pipeline-runner-builds/$DEPLOYMENT_TYPE/$PIPELINE_RUNNER_APP_VERSION/bin/download_vep_reference_data.bash" /download_vep_reference_data.bash chmod +x /download_vep_reference_data.bash -./download_vep_reference_data.bash $REFERENCE_GENOME +./download_vep_reference_data.bash "$REFERENCE_GENOME" -gcloud storage cp gs://seqr-pipeline-runner-builds/$DEPLOYMENT_TYPE/$PIPELINE_RUNNER_APP_VERSION/bin/vep /vep.bash +gcloud storage cp "gs://seqr-pipeline-runner-builds/$DEPLOYMENT_TYPE/$PIPELINE_RUNNER_APP_VERSION/bin/vep" /vep.bash chmod +x /vep.bash diff --git a/loading_pipeline/bin/download_vep_reference_data.bash b/loading_pipeline/bin/download_vep_reference_data.bash index c1784d80ac..653dd459c0 100755 --- a/loading_pipeline/bin/download_vep_reference_data.bash +++ b/loading_pipeline/bin/download_vep_reference_data.bash @@ -2,7 +2,7 @@ set -eux -REFERENCE_GENOME=$1 +REFERENCE_GENOME="$1" VEP_REFERENCE_DATASETS_DIR=${VEP_REFERENCE_DATASETS_DIR:-/var/seqr/vep-reference-data} DEFAULT_REFERENCE_DATASETS_DIR="gs://seqr-reference-data" if [[ -n "${REFERENCE_DATASETS_DIR:-}" && "$REFERENCE_DATASETS_DIR" == gs://* ]]; then @@ -12,7 +12,7 @@ else echo "Using default GCS path: $REFERENCE_DATASETS_DIR" fi -case $REFERENCE_GENOME in +case "$REFERENCE_GENOME" in GRCh38) VEP_REFERENCE_DATA_FILES=( "$REFERENCE_DATASETS_DIR/vep_data/loftee-beta/GRCh38.tar.gz" diff --git a/loading_pipeline/bin/rsync_reference_data.bash b/loading_pipeline/bin/rsync_reference_data.bash index 360a6d6e1a..6577392745 100755 --- a/loading_pipeline/bin/rsync_reference_data.bash +++ b/loading_pipeline/bin/rsync_reference_data.bash @@ -2,11 +2,11 @@ set -eux -REFERENCE_GENOME=$1 +REFERENCE_GENOME="$1" REFERENCE_DATASETS_DIR=${REFERENCE_DATASETS_DIR:-/var/seqr/seqr-reference-data} -case $REFERENCE_GENOME in +case "$REFERENCE_GENOME" in GRCh38) ;; GRCh37) @@ -16,7 +16,7 @@ case $REFERENCE_GENOME in exit 1 esac -case $REFERENCE_DATASETS_DIR in +case "$REFERENCE_DATASETS_DIR" in "gs://seqr-reference-data") echo "Cannot rsync to the authoritative source" exit 1 @@ -26,26 +26,26 @@ case $REFERENCE_DATASETS_DIR in esac if ! [[ "$REFERENCE_DATASETS_DIR" =~ gs://* ]]; then - mkdir -p $REFERENCE_DATASETS_DIR/$REFERENCE_GENOME; + mkdir -p "$REFERENCE_DATASETS_DIR"/"$REFERENCE_GENOME"; if [ -f "$REFERENCE_DATASETS_DIR"/"$REFERENCE_GENOME"/_SUCCESS ]; then echo "Skipping rsync because already successful" exit 0; fi else result=$(gsutil -q stat "$REFERENCE_DATASETS_DIR"/"$REFERENCE_GENOME"/_SUCCESS || echo 1) - if [[ $result != 1 ]]; then + if [[ "$result" != 1 ]]; then echo "Skipping rsync because already successful" exit 0; fi fi -gsutil -m rsync -rd -x '.*\.parquet.*' "gs://seqr-reference-data/v3.2/$REFERENCE_GENOME" $REFERENCE_DATASETS_DIR/$REFERENCE_GENOME -if ! [[ $REFERENCE_DATASETS_DIR =~ gs://* ]]; then +gsutil -m rsync -rd -x '.*\.parquet.*' "gs://seqr-reference-data/v3.2/$REFERENCE_GENOME" "$REFERENCE_DATASETS_DIR"/"$REFERENCE_GENOME" +if ! [[ "$REFERENCE_DATASETS_DIR" =~ gs://* ]]; then touch "$REFERENCE_DATASETS_DIR"/"$REFERENCE_GENOME"/_SUCCESS else # If a different reference datasets dir is provided, sync vep data to the provided bucket. - gsutil cp "gs://seqr-reference-data/vep_data/loftee-beta/$REFERENCE_GENOME.tar.gz" $REFERENCE_DATASETS_DIR/vep_data/loftee-beta/$REFERENCE_GENOME.tar.gz - gsutil -m rsync -rd "gs://seqr-reference-data/vep/$REFERENCE_GENOME" $REFERENCE_DATASETS_DIR/vep/$REFERENCE_GENOME + gsutil cp "gs://seqr-reference-data/vep_data/loftee-beta/$REFERENCE_GENOME.tar.gz" "$REFERENCE_DATASETS_DIR"/vep_data/loftee-beta/"$REFERENCE_GENOME".tar.gz + gsutil -m rsync -rd "gs://seqr-reference-data/vep/$REFERENCE_GENOME" "$REFERENCE_DATASETS_DIR"/vep/"$REFERENCE_GENOME" touch _SUCCESS gsutil cp _SUCCESS "$REFERENCE_DATASETS_DIR"/"$REFERENCE_GENOME"/_SUCCESS rm -rf _SUCCESS From 3e2f280bb6c168a5b953a249d0d098b7c0edb8e0 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 17 Aug 2026 16:18:11 -0400 Subject: [PATCH 086/369] disable errors --- .codacy.yaml | 3 ++- loading_pipeline/api/__main__.py | 2 +- loading_pipeline/bin/pipeline_worker_test.py | 2 +- loading_pipeline/lib/core/environment.py | 2 +- loading_pipeline/lib/misc/clickhouse.py | 2 +- loading_pipeline/lib/misc/clickhouse_test.py | 6 +++--- loading_pipeline/lib/misc/terra_data_repository.py | 4 ++-- loading_pipeline/lib/reference_datasets/misc.py | 4 ++-- .../variants_migration/load_clickhouse_variants_tables.py | 2 +- .../load_clickhouse_variants_tables_test.py | 2 +- loading_pipeline/lib/test/clickhouse_django/settings.py | 6 +++--- .../ops/repartition_clickhouse_grch38_snv_indel.py | 4 ++-- .../ops/repartition_clickhouse_grch38_snv_indel_test.py | 2 +- 13 files changed, 21 insertions(+), 20 deletions(-) diff --git a/.codacy.yaml b/.codacy.yaml index a0ae5a67dd..121f658884 100644 --- a/.codacy.yaml +++ b/.codacy.yaml @@ -1,3 +1,4 @@ --- exclude_paths: - - "deploy/postgres/initdb.sql" \ No newline at end of file + - "deploy/postgres/initdb.sql" + - "loading_pipeline/deploy/Dockerfile" \ No newline at end of file diff --git a/loading_pipeline/api/__main__.py b/loading_pipeline/api/__main__.py index 38b30d74ef..5d5926f7cb 100644 --- a/loading_pipeline/api/__main__.py +++ b/loading_pipeline/api/__main__.py @@ -9,7 +9,7 @@ def run(): logger = get_logger(__name__) web.run_app( app, - host='0.0.0.0', # noqa: S104 + host='0.0.0.0', # noqa: S104 # nosec B104 port=6000, access_log=logger, ) diff --git a/loading_pipeline/bin/pipeline_worker_test.py b/loading_pipeline/bin/pipeline_worker_test.py index a2e3db1e54..b8b1233989 100644 --- a/loading_pipeline/bin/pipeline_worker_test.py +++ b/loading_pipeline/bin/pipeline_worker_test.py @@ -110,7 +110,7 @@ def test_process_queue_integration_test( SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` - """, + """, # nosec B608 ) annotations_count = cursor.fetchone()[0] self.assertEqual(annotations_count, 30) diff --git a/loading_pipeline/lib/core/environment.py b/loading_pipeline/lib/core/environment.py index 87d81e46d4..5a7d9611b1 100644 --- a/loading_pipeline/lib/core/environment.py +++ b/loading_pipeline/lib/core/environment.py @@ -4,7 +4,7 @@ # NB: using os.environ.get inside the dataclass defaults gives a lint error. LOCAL_DISK_MOUNT_DIR = os.environ.get('LOCAL_DISK_MOUNT_DIR', '/var/seqr') -HAIL_TMP_DIR = os.environ.get('HAIL_TMP_DIR', '/tmp') # noqa: S108 +HAIL_TMP_DIR = os.environ.get('HAIL_TMP_DIR', '/tmp') # noqa: S108 # nosec B108 PIPELINE_DATA_DIR = os.environ.get( 'PIPELINE_DATA_DIR', '/var/seqr/pipeline-data', diff --git a/loading_pipeline/lib/misc/clickhouse.py b/loading_pipeline/lib/misc/clickhouse.py index 977b4fe1e0..7eca49e931 100644 --- a/loading_pipeline/lib/misc/clickhouse.py +++ b/loading_pipeline/lib/misc/clickhouse.py @@ -411,7 +411,7 @@ def insert_into_seqr_variants_and_refresh_search( SELECT {ClickHouseTable.KEY_LOOKUP.key_field} FROM {table_name_builder.src_table(ClickHouseTable.KEY_LOOKUP)} ) - """, + """, # nosec B608 ) logged_query( f""" diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index fdfe26198e..487626e86d 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -425,7 +425,7 @@ def test_direct_insert_all_keys(self): ), ) cursor.execute( - f'SELECT key, variantId FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', + f'SELECT key, variantId FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', # nosec B608 ) ret = cursor.fetchall() self.assertEqual( @@ -450,7 +450,7 @@ def test_direct_insert_all_keys(self): ), ) cursor.execute( - f'SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', + f'SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', # nosec B608 ) ret = cursor.fetchone() self.assertEqual(ret[0], 6) @@ -495,7 +495,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): cursor.execute( f""" SELECT DISTINCT project_guid FROM {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/entries` - """, + """, # nosec B608 ) staged_projects = cursor.fetchall() self.assertCountEqual( diff --git a/loading_pipeline/lib/misc/terra_data_repository.py b/loading_pipeline/lib/misc/terra_data_repository.py index 0aa2204b8a..115a765c69 100644 --- a/loading_pipeline/lib/misc/terra_data_repository.py +++ b/loading_pipeline/lib/misc/terra_data_repository.py @@ -69,12 +69,12 @@ def bq_metrics_query(bq_table_name: str) -> google.cloud.bigquery.table.RowItera client.query_and_wait( f""" SELECT ddl FROM `{bq_table_name}`.INFORMATION_SCHEMA.TABLES where table_name='sample'; - """, # noqa: S608 + """, # noqa: S608 # nosec B608 ), )[0] metrics = [(m if m in table_ddl else f'NULL AS {m}') for m in BIGQUERY_METRICS] return client.query_and_wait( f""" SELECT {','.join(metrics)} FROM `{bq_table_name}.sample`; - """, # noqa: S608 + """, # noqa: S608 # nosec B608 ) diff --git a/loading_pipeline/lib/reference_datasets/misc.py b/loading_pipeline/lib/reference_datasets/misc.py index 73b4d17c0a..cf9fe37680 100644 --- a/loading_pipeline/lib/reference_datasets/misc.py +++ b/loading_pipeline/lib/reference_datasets/misc.py @@ -29,7 +29,7 @@ def compress_floats(ht: hl.Table): def generate_random_string(length=5): """Generates a random string of the specified length.""" letters = string.ascii_letters + string.digits - return ''.join(random.choice(letters) for i in range(length)) # noqa: S311 + return ''.join(random.choice(letters) for i in range(length)) # noqa: S311 # nosec B311 def filter_contigs(ht, reference_genome: ReferenceGenome): @@ -98,7 +98,7 @@ def copyfileobj(fsrc, fdst, decode_content, length=16 * 1024): @contextlib.contextmanager def download_zip_file(url, dataset_name: str, suffix='.zip', decode_content=False): - dir_ = f'/tmp/{generate_random_string()}/{dataset_name}' # noqa: S108 + dir_ = f'/tmp/{generate_random_string()}/{dataset_name}' # noqa: S108 # nosec B108 os.makedirs(dir_, exist_ok=True) with ( tempfile.NamedTemporaryFile( diff --git a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables.py b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables.py index 25325d8e37..c39d1383d0 100644 --- a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables.py +++ b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables.py @@ -102,7 +102,7 @@ def complete(self) -> bool: max_key = logged_query( f""" SELECT max(key) FROM {table_name_builder.src_table(ClickHouseTable.VARIANTS_MEMORY)} - """, + """, # nosec B608 )[0][0] return logged_query( f""" diff --git a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py index f412e0fa48..5751ec39d9 100644 --- a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py +++ b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py @@ -124,7 +124,7 @@ def test_write_variants_to_clickhouse( SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` - """, + """, # nosec B608 ) variants_count = cursor.fetchone()[0] self.assertEqual(variants_count, 2) diff --git a/loading_pipeline/lib/test/clickhouse_django/settings.py b/loading_pipeline/lib/test/clickhouse_django/settings.py index 5591ade322..78f7a6cf4d 100644 --- a/loading_pipeline/lib/test/clickhouse_django/settings.py +++ b/loading_pipeline/lib/test/clickhouse_django/settings.py @@ -29,16 +29,16 @@ def allow_migrate(db, app_label, model_name=None, **hints): # noqa: ARG004 ] USE_TZ = True -SECRET_KEY = 'loading-pipeline-test' # noqa: S105 +SECRET_KEY = 'loading-pipeline-test' # noqa: S105 # nosec B105 DEPLOYMENT_TYPE = os.environ.get('DEPLOYMENT_TYPE', 'dev') PIPELINE_RUNNER_SERVER = os.environ.get('PIPELINE_RUNNER_SERVER', 'http://localhost') CLICKHOUSE_IN_MEMORY_DIR = os.environ.get( 'CLICKHOUSE_IN_MEMORY_DIR', - '/tmp/loading_pipeline_test_clickhouse_in_memory', # noqa: S108 + '/tmp/loading_pipeline_test_clickhouse_in_memory', # noqa: S108 # nosec B108 ) CLICKHOUSE_DATA_DIR = os.environ.get( 'CLICKHOUSE_DATA_DIR', - '/tmp/loading_pipeline_test_clickhouse_data', # noqa: S108 + '/tmp/loading_pipeline_test_clickhouse_data', # noqa: S108 # nosec B108 ) CLICKHOUSE_WRITER_USER = os.environ.get('CLICKHOUSE_WRITER_USER', 'default') diff --git a/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel.py b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel.py index 4636e44ae3..30f0067425 100644 --- a/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel.py +++ b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel.py @@ -62,7 +62,7 @@ def main(max_insert_threads: int, project_guids: list[str]): ENGINE = CollapsingMergeTree(sign) PARTITION BY (project_guid, partition_id) SETTINGS deduplicate_merge_projection_mode = 'rebuild' - """, + """, # nosec B608 ) if not project_guids: project_guids = [ @@ -70,7 +70,7 @@ def main(max_insert_threads: int, project_guids: list[str]): for x in logged_query( f""" SELECT DISTINCT project_guid from {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` - """, + """, # nosec B608 ) ] for project_guid in project_guids: diff --git a/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py index 60ee69e57d..8781305e8a 100644 --- a/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py +++ b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py @@ -72,7 +72,7 @@ def setUp(self): (2, 'project_b', 'family_b2', 0, 1), (0, 'project_c', 'family_c1', 1, 1), (3, 'project_c', 'family_c2', 1, 1), - """, + """, # nosec B608 ) def tearDown(self): From 9192d0e8afa69983b1c56ee50b66a8ac592dfb69 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 17 Aug 2026 16:31:18 -0400 Subject: [PATCH 087/369] more disable rules --- loading_pipeline/bin/pipeline_worker_test.py | 4 ++-- loading_pipeline/bin/run_task.py | 4 ++-- loading_pipeline/lib/misc/clickhouse.py | 4 ++-- loading_pipeline/lib/misc/clickhouse_test.py | 8 ++++---- loading_pipeline/lib/misc/terra_data_repository_test.py | 2 +- .../variants_migration/load_clickhouse_variants_tables.py | 4 ++-- .../load_clickhouse_variants_tables_test.py | 4 ++-- .../ops/repartition_clickhouse_grch38_snv_indel.py | 6 +++--- .../ops/repartition_clickhouse_grch38_snv_indel_test.py | 4 ++-- 9 files changed, 20 insertions(+), 20 deletions(-) diff --git a/loading_pipeline/bin/pipeline_worker_test.py b/loading_pipeline/bin/pipeline_worker_test.py index b8b1233989..4bb8691908 100644 --- a/loading_pipeline/bin/pipeline_worker_test.py +++ b/loading_pipeline/bin/pipeline_worker_test.py @@ -110,7 +110,7 @@ def test_process_queue_integration_test( SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` - """, # nosec B608 + """, # nosec B608 ) annotations_count = cursor.fetchone()[0] self.assertEqual(annotations_count, 30) @@ -119,7 +119,7 @@ def test_process_queue_integration_test( SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` - """, + """, # nosec B608 ) entries_count = cursor.fetchone()[0] self.assertEqual(entries_count, 16) diff --git a/loading_pipeline/bin/run_task.py b/loading_pipeline/bin/run_task.py index 37b96c4fb7..18dc77e839 100755 --- a/loading_pipeline/bin/run_task.py +++ b/loading_pipeline/bin/run_task.py @@ -3,8 +3,8 @@ import luigi -from loading_pipeline.lib.tasks import * # noqa: F403 +from loading_pipeline.lib.tasks import * # noqa: F403 # nosec F403 if __name__ == '__main__': # If run does not succeed, exit with 1 status code. - luigi.run() or sys.exit(1) + luigi.run() or sys.exit(1) # pylint: disable=W0106 diff --git a/loading_pipeline/lib/misc/clickhouse.py b/loading_pipeline/lib/misc/clickhouse.py index 7eca49e931..44facc59ca 100644 --- a/loading_pipeline/lib/misc/clickhouse.py +++ b/loading_pipeline/lib/misc/clickhouse.py @@ -411,7 +411,7 @@ def insert_into_seqr_variants_and_refresh_search( SELECT {ClickHouseTable.KEY_LOOKUP.key_field} FROM {table_name_builder.src_table(ClickHouseTable.KEY_LOOKUP)} ) - """, # nosec B608 + """, # nosec B608 ) logged_query( f""" @@ -424,7 +424,7 @@ def insert_into_seqr_variants_and_refresh_search( INNER JOIN {table_name_builder.dst_table(ClickHouseTable.KEY_LOOKUP)} dst ON {ClickHouseTable.KEY_LOOKUP.join_condition} WHERE src.variantId IN {table_name_builder.staging_dst_prefix}/_tmp_loadable_variantIds` - """, + """, # nosec B608 ) self.refresh_search(table_name_builder) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index 487626e86d..4e250af66b 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -425,7 +425,7 @@ def test_direct_insert_all_keys(self): ), ) cursor.execute( - f'SELECT key, variantId FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', # nosec B608 + f'SELECT key, variantId FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', # nosec B608 ) ret = cursor.fetchall() self.assertEqual( @@ -450,7 +450,7 @@ def test_direct_insert_all_keys(self): ), ) cursor.execute( - f'SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', # nosec B608 + f'SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', # nosec B608 ) ret = cursor.fetchone() self.assertEqual(ret[0], 6) @@ -495,7 +495,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): cursor.execute( f""" SELECT DISTINCT project_guid FROM {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/entries` - """, # nosec B608 + """, # nosec B608 ) staged_projects = cursor.fetchall() self.assertCountEqual( @@ -509,7 +509,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/project_gt_stats` FINAL GROUP BY project_guid, key, sample_type - """, + """, # nosec B608 ) staged_project_gt_stats = cursor.fetchall() self.assertCountEqual( diff --git a/loading_pipeline/lib/misc/terra_data_repository_test.py b/loading_pipeline/lib/misc/terra_data_repository_test.py index 91b044d68f..d798b5bcef 100644 --- a/loading_pipeline/lib/misc/terra_data_repository_test.py +++ b/loading_pipeline/lib/misc/terra_data_repository_test.py @@ -131,7 +131,7 @@ @patch( 'loading_pipeline.lib.misc.terra_data_repository.get_service_account_credentials', return_value=SimpleNamespace( - token='abcdefg', # noqa: S106 + token='abcdefg', # noqa: S106 # nosec B106 ), ) class TerraDataRepositoryTest(unittest.TestCase): diff --git a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables.py b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables.py index c39d1383d0..85ce9f0e10 100644 --- a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables.py +++ b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables.py @@ -102,14 +102,14 @@ def complete(self) -> bool: max_key = logged_query( f""" SELECT max(key) FROM {table_name_builder.src_table(ClickHouseTable.VARIANTS_MEMORY)} - """, # nosec B608 + """, # nosec B608 )[0][0] return logged_query( f""" SELECT EXISTS ( SELECT 1 FROM {table_name_builder.dst_table(ClickHouseTable.VARIANTS_MEMORY)} where key = %(max_key)s ) - """, + """, # nosec B608 {'max_key': max_key}, )[0][0] diff --git a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py index 5751ec39d9..e009a6d177 100644 --- a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py +++ b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py @@ -124,7 +124,7 @@ def test_write_variants_to_clickhouse( SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` - """, # nosec B608 + """, # nosec B608 ) variants_count = cursor.fetchone()[0] self.assertEqual(variants_count, 2) @@ -133,7 +133,7 @@ def test_write_variants_to_clickhouse( SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details` - """, + """, # nosec B608 ) variant_details_count = cursor.fetchone()[0] self.assertEqual(variant_details_count, 2) diff --git a/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel.py b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel.py index 30f0067425..053e9f71c8 100644 --- a/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel.py +++ b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel.py @@ -62,7 +62,7 @@ def main(max_insert_threads: int, project_guids: list[str]): ENGINE = CollapsingMergeTree(sign) PARTITION BY (project_guid, partition_id) SETTINGS deduplicate_merge_projection_mode = 'rebuild' - """, # nosec B608 + """, # nosec B608 ) if not project_guids: project_guids = [ @@ -70,7 +70,7 @@ def main(max_insert_threads: int, project_guids: list[str]): for x in logged_query( f""" SELECT DISTINCT project_guid from {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` - """, # nosec B608 + """, # nosec B608 ) ] for project_guid in project_guids: @@ -90,7 +90,7 @@ def main(max_insert_threads: int, project_guids: list[str]): SELECT * FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` WHERE project_guid=%(project_guid)s SETTINGS max_insert_threads=%(max_insert_threads)s - """, + """, # nosec B608 {'project_guid': project_guid, 'max_insert_threads': max_insert_threads}, timeout=99999, ) diff --git a/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py index 8781305e8a..ec8f7f93b2 100644 --- a/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py +++ b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py @@ -72,7 +72,7 @@ def setUp(self): (2, 'project_b', 'family_b2', 0, 1), (0, 'project_c', 'family_c1', 1, 1), (3, 'project_c', 'family_c2', 1, 1), - """, # nosec B608 + """, # nosec B608 ) def tearDown(self): @@ -87,7 +87,7 @@ def test_main_all_projects(self): f""" SELECT *, n_partitions, partition_id FROM {REPARTITION_DATABASE_NAME}.`GRCh38/SNV_INDEL/repartitioned_entries` - """, + """, # nosec B608 ) self.assertCountEqual( cursor.fetchall(), From 32e59ae8d23be51bdc649df6947be84fa5a63190 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 17 Aug 2026 16:38:43 -0400 Subject: [PATCH 088/369] more disable rules --- loading_pipeline/bin/pipeline_worker_test.py | 2 +- loading_pipeline/lib/misc/clickhouse.py | 2 +- loading_pipeline/lib/misc/clickhouse_test.py | 2 +- .../variants_migration/load_clickhouse_variants_tables_test.py | 2 +- .../ops/repartition_clickhouse_grch38_snv_indel_test.py | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/loading_pipeline/bin/pipeline_worker_test.py b/loading_pipeline/bin/pipeline_worker_test.py index 4bb8691908..e1fcefd710 100644 --- a/loading_pipeline/bin/pipeline_worker_test.py +++ b/loading_pipeline/bin/pipeline_worker_test.py @@ -128,7 +128,7 @@ def test_process_queue_integration_test( SELECT sum(ac_wgs) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` - """, + """, # nosec B608 ) ac_wgs = cursor.fetchone()[0] self.assertEqual(ac_wgs, 69) diff --git a/loading_pipeline/lib/misc/clickhouse.py b/loading_pipeline/lib/misc/clickhouse.py index 44facc59ca..936bfb59c5 100644 --- a/loading_pipeline/lib/misc/clickhouse.py +++ b/loading_pipeline/lib/misc/clickhouse.py @@ -632,7 +632,7 @@ def delete_existing_families_from_staging_entries( SELECT COLUMNS('.*') EXCEPT(sign, n_partitions, partition_id), -1 as sign FROM {table_name_builder.staging_dst_table(ClickHouseTable.ENTRIES)} WHERE family_guid in %(family_guids)s - """, + """, # nosec B608 {'family_guids': family_guids}, ) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index 4e250af66b..9a9a4c43bc 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -545,7 +545,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/project_gt_stats` FINAL GROUP BY project_guid, key, sample_type - """, + """, # nosec B608 ) staged_project_gt_stats = cursor.fetchall() self.assertCountEqual( diff --git a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py index e009a6d177..704f45d9c9 100644 --- a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py +++ b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py @@ -142,7 +142,7 @@ def test_write_variants_to_clickhouse( SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/key_lookup` - """, + """, # nosec B608 ) key_lookups_count = cursor.fetchone()[0] self.assertEqual(key_lookups_count, 2) diff --git a/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py index ec8f7f93b2..dca4e702af 100644 --- a/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py +++ b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py @@ -110,7 +110,7 @@ def test_main_one_project(self): f""" SELECT *, n_partitions, partition_id FROM {REPARTITION_DATABASE_NAME}.`GRCh38/SNV_INDEL/repartitioned_entries` - """, + """, # nosec B608 ) self.assertCountEqual( cursor.fetchall(), From 80d98463d6795a5fade9753946a48d1ceb7de270 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 17 Aug 2026 16:48:47 -0400 Subject: [PATCH 089/369] codacy clean up --- loading_pipeline/lib/annotations/expression_helpers.py | 4 ++-- loading_pipeline/lib/annotations/mito.py | 2 +- loading_pipeline/lib/misc/clickhouse.py | 2 +- loading_pipeline/lib/misc/clickhouse_test.py | 2 +- loading_pipeline/lib/misc/terra_data_repository.py | 3 +-- loading_pipeline/lib/tasks/exports/misc.py | 2 +- 6 files changed, 7 insertions(+), 8 deletions(-) diff --git a/loading_pipeline/lib/annotations/expression_helpers.py b/loading_pipeline/lib/annotations/expression_helpers.py index ab0b34c25f..221c4054bf 100644 --- a/loading_pipeline/lib/annotations/expression_helpers.py +++ b/loading_pipeline/lib/annotations/expression_helpers.py @@ -79,7 +79,7 @@ def _get_expr_for_formatted_hgvs(csq): + protein_letters, hl.delimit( csq.amino_acids.split('').map( - lambda pl: PROTEIN_LETTERS_1TO3.get(pl), + PROTEIN_LETTERS_1TO3.get, ), '', ), @@ -193,7 +193,7 @@ def get_expr_for_vep_sorted_transcript_consequences_array( c.consequence_terms.size() > 0, hl.sorted( c.consequence_terms, - key=lambda t: TRANSCRIPT_CONSEQUENCE_TERM_RANK_LOOKUP.get(t), + key=TRANSCRIPT_CONSEQUENCE_TERM_RANK_LOOKUP.get, )[0], hl.null(hl.tstr), ), diff --git a/loading_pipeline/lib/annotations/mito.py b/loading_pipeline/lib/annotations/mito.py index 85b65ce75c..fd367ba946 100644 --- a/loading_pipeline/lib/annotations/mito.py +++ b/loading_pipeline/lib/annotations/mito.py @@ -58,4 +58,4 @@ def mitotip(ht: hl.Table, **_: Any) -> hl.Expression: def rsid(ht: hl.Table, **_: Any) -> hl.Expression: - return ht.rsid.find(lambda x: hl.is_defined(x)) + return ht.rsid.find(hl.is_defined) diff --git a/loading_pipeline/lib/misc/clickhouse.py b/loading_pipeline/lib/misc/clickhouse.py index 936bfb59c5..68f0991978 100644 --- a/loading_pipeline/lib/misc/clickhouse.py +++ b/loading_pipeline/lib/misc/clickhouse.py @@ -686,7 +686,7 @@ def insert_new_entries( INSERT INTO {table_name_builder.staging_dst_table(ClickHouseTable.ENTRIES)} ({dst_list}) SELECT {src_list} FROM {table_name_builder.src_table(ClickHouseTable.ENTRIES)} - """, + """, # nosec B608 ) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index 9a9a4c43bc..3190b9af5e 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -576,7 +576,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/project_gt_stats` FINAL GROUP BY project_guid, key, sample_type - """, + """, # nosec B608 ) staged_project_gt_stats = cursor.fetchall() self.assertCountEqual( diff --git a/loading_pipeline/lib/misc/terra_data_repository.py b/loading_pipeline/lib/misc/terra_data_repository.py index 115a765c69..b4af9b7341 100644 --- a/loading_pipeline/lib/misc/terra_data_repository.py +++ b/loading_pipeline/lib/misc/terra_data_repository.py @@ -3,7 +3,6 @@ from collections.abc import Generator from concurrent.futures import ThreadPoolExecutor, as_completed -import google.cloud.bigquery from google.cloud import bigquery from loading_pipeline.lib.misc.gcp import get_service_account_credentials @@ -58,7 +57,7 @@ def gen_bq_table_names() -> Generator[str]: yield f'{result["accessInformation"]["bigQuery"]["projectId"]}.{result["accessInformation"]["bigQuery"]["datasetName"]}' -def bq_metrics_query(bq_table_name: str) -> google.cloud.bigquery.table.RowIterator: +def bq_metrics_query(bq_table_name: str) -> bigquery.table.RowIterator: if not re.match(TABLE_NAME_VALIDATION_REGEX, bq_table_name): msg = f'{bq_table_name} does not match expected pattern' raise ValueError(msg) diff --git a/loading_pipeline/lib/tasks/exports/misc.py b/loading_pipeline/lib/tasks/exports/misc.py index ee844d28e0..bbc45b4271 100644 --- a/loading_pipeline/lib/tasks/exports/misc.py +++ b/loading_pipeline/lib/tasks/exports/misc.py @@ -135,7 +135,7 @@ def camelcase_array_structexpression_fields( ht = ht.transmute( **{ snake_to_camelcase(field): ht[field].map( - lambda c: camelcase_hl_struct(c), + camelcase_hl_struct, ), }, ) From 7066d501eabdda5dc73adfd964d6fec1fba2c905 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 17 Aug 2026 16:53:41 -0400 Subject: [PATCH 090/369] remove deprecated param --- .../lib/annotations/expression_helpers.py | 13 +------------ .../gnomad_coding_and_noncoding.py | 1 - 2 files changed, 1 insertion(+), 13 deletions(-) diff --git a/loading_pipeline/lib/annotations/expression_helpers.py b/loading_pipeline/lib/annotations/expression_helpers.py index 221c4054bf..13a6f027e8 100644 --- a/loading_pipeline/lib/annotations/expression_helpers.py +++ b/loading_pipeline/lib/annotations/expression_helpers.py @@ -8,10 +8,6 @@ HGVSC_CONSEQUENCES = hl.set( ['splice_donor_variant', 'splice_acceptor_variant', 'splice_region_variant'], ) -OMIT_TRANSCRIPT_CONSEQUENCE_TERMS = [ - 'upstream_gene_variant', - 'downstream_gene_variant', -] PROTEIN_LETTERS_1TO3 = hl.dict( { 'A': 'Ala', @@ -124,7 +120,6 @@ def get_expr_for_xpos(locus: hl.expr.LocusExpression) -> hl.expr.Int64Expression def get_expr_for_vep_sorted_transcript_consequences_array( vep_root, include_coding_annotations=True, - omit_consequences=OMIT_TRANSCRIPT_CONSEQUENCE_TERMS, ): """Sort transcripts by 3 properties: @@ -177,17 +172,11 @@ def get_expr_for_vep_sorted_transcript_consequences_array( ], ) - omit_consequence_terms = ( - hl.set(omit_consequences) if omit_consequences else hl.empty_set(hl.tstr) - ) - result = hl.sorted( vep_root.transcript_consequences.map( lambda c: c.select( *selected_annotations, - consequence_terms=c.consequence_terms.filter( - lambda t: ~omit_consequence_terms.contains(t), - ), + consequence_terms=c.consequence_terms, domains=c.domains.map(lambda domain: domain.db + ':' + domain.name), major_consequence=hl.cond( c.consequence_terms.size() > 0, diff --git a/loading_pipeline/lib/reference_datasets/gnomad_coding_and_noncoding.py b/loading_pipeline/lib/reference_datasets/gnomad_coding_and_noncoding.py index 9b197276a8..fcb137d2b2 100644 --- a/loading_pipeline/lib/reference_datasets/gnomad_coding_and_noncoding.py +++ b/loading_pipeline/lib/reference_datasets/gnomad_coding_and_noncoding.py @@ -35,7 +35,6 @@ def get_ht( sorted_transaction_consequences=( get_expr_for_vep_sorted_transcript_consequences_array( ht.vep, - omit_consequences=[], ) ), ) From 7b37200811fb5615b42ef4da2d63cb0c629912a7 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 17 Aug 2026 17:11:42 -0400 Subject: [PATCH 091/369] disable codacy errors --- loading_pipeline/lib/misc/clickhouse.py | 24 ++++++++-------- loading_pipeline/lib/misc/clickhouse_test.py | 30 ++++++++++---------- 2 files changed, 27 insertions(+), 27 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse.py b/loading_pipeline/lib/misc/clickhouse.py index 68f0991978..d214f601bf 100644 --- a/loading_pipeline/lib/misc/clickhouse.py +++ b/loading_pipeline/lib/misc/clickhouse.py @@ -704,7 +704,7 @@ def optimize_entries( FROM {table_name_builder.staging_dst_table(ClickHouseTable.ENTRIES)} WHERE sign = -1 ); - """, + """, # nosec B608 )[0][0] merges_running = logged_query( @@ -838,7 +838,7 @@ def reload_dictionaries( logged_query( f""" SYSTEM RELOAD DICTIONARY {table_name_builder.dst_table(dictionary)} - """, + """, # nosec B608 ) @@ -858,7 +858,7 @@ def replace_project_partitions( f""" ALTER TABLE {table_name_builder.dst_table(clickhouse_table)} REPLACE PARTITION %(partition)s FROM {table_name_builder.staging_dst_table(clickhouse_table)} - """, + """, # nosec B608 {'partition': partition}, ) @@ -873,7 +873,7 @@ def exchange_tables( logged_query( f""" EXCHANGE TABLES {table_name_builder.staging_dst_table(clickhouse_table)} AND {table_name_builder.dst_table(clickhouse_table)} - """, + """, # nosec B608 ) @@ -887,7 +887,7 @@ def direct_insert_annotations( logged_query( f""" CREATE DATABASE {STAGING_CLICKHOUSE_DATABASE} - """, + """, # nosec B608 ) # NB: Unfortunately there's a bug(?) or inaccuracy if this is attempted without an intermediate # temporary table, likely due to writing to a table and joining against it at the same time. @@ -899,7 +899,7 @@ def direct_insert_annotations( LEFT ANTI JOIN {dst_table} dst ON {ClickHouseTable.VARIANTS_MEMORY.join_condition} ) - """, + """, # nosec B608 ) for ( clickhouse_table @@ -913,14 +913,14 @@ def direct_insert_annotations( INSERT INTO {disk_backed_dst_table} SELECT {clickhouse_table.select_fields} FROM {disk_backed_src_table} WHERE {clickhouse_table.key_field} IN {table_name_builder.staging_dst_prefix}/_tmp_loadable_keys` - """, + """, # nosec B608 ) logged_query( f""" INSERT INTO {dst_table} SELECT {ClickHouseTable.VARIANTS_MEMORY.select_fields} FROM {src_table} WHERE {ClickHouseTable.VARIANTS_MEMORY.key_field} IN {table_name_builder.staging_dst_prefix}/_tmp_loadable_keys` - """, + """, # nosec B608 ) drop_staging_db() @@ -942,7 +942,7 @@ def direct_insert_all_keys( SELECT {clickhouse_table.select_fields} FROM {src_table} {settings} - """, + """, # nosec B608 ) @@ -1078,7 +1078,7 @@ def delete_family_guids( WHERE project_guid = %(project_guid)s AND has(%(family_guids)s, family_guid) ); - """, + """, # nosec B608 {'family_guids': family_guids, 'project_guid': project_guid}, )[0][0] if not entries_exist: @@ -1136,7 +1136,7 @@ def rebuild_gt_stats( max_key = logged_query( f""" SELECT max(key) FROM {table_name_builder.dst_table(ClickHouseTable.GT_STATS)} - """, + """, # nosec B608 )[0][0] if not max_key: msg = f'Skipping gt stats rebuild for empty dataset {reference_genome.value}/{dataset_type.value} {project_guids[:10]}...' @@ -1172,7 +1172,7 @@ def rebuild_gt_stats( f""" ALTER TABLE {table_name_builder.staging_dst_table(ClickHouseTable.PROJECT_GT_STATS)} DROP PARTITION %(partition)s - """, + """, # nosec B608 {'partition': partition}, ) select_statement = get_create_mv_statements( diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index 3190b9af5e..e29fc3e901 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -617,7 +617,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): SELECT COLUMNS('.*') EXCEPT(is_annotated_in_any_gene, is_gnomad_gt_5_percent) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` - """, + """, # nosec B608 ) new_entries = cursor.fetchall() self.assertCountEqual( @@ -998,7 +998,7 @@ def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_typ SELECT key, variantId FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details` - """, + """, # nosec B608 ) variants_details = cursor.fetchall() self.assertCountEqual( @@ -1027,7 +1027,7 @@ def test_load_complete_gcnv(self): SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/variants_memory` - """, + """, # nosec B608 ) variants_disk_count = cursor.fetchone()[0] self.assertEqual(variants_disk_count, 4) @@ -1036,7 +1036,7 @@ def test_load_complete_gcnv(self): SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/variants_disk` - """, + """, # nosec B608 ) variants_disk_count = cursor.fetchone()[0] self.assertEqual(variants_disk_count, 4) @@ -1045,7 +1045,7 @@ def test_load_complete_gcnv(self): SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/key_lookup` - """, + """, # nosec B608 ) key_lookup_count = cursor.fetchone()[0] self.assertEqual(key_lookup_count, 4) @@ -1054,7 +1054,7 @@ def test_load_complete_gcnv(self): SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/entries` - """, + """, # nosec B608 ) entries_count = cursor.fetchone()[0] self.assertEqual(entries_count, 3) @@ -1073,7 +1073,7 @@ def test_delete_families(self): {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` FINAL GROUP BY project_guid - """, + """, # nosec B608 ) project_gt_stats = cursor.fetchall() self.assertCountEqual( @@ -1092,7 +1092,7 @@ def test_delete_families(self): SELECT sum(ac_wes) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` - """, + """, # nosec B608 ) gt_stats = cursor.fetchall() self.assertCountEqual(gt_stats, [(12,)]) @@ -1110,7 +1110,7 @@ def test_delete_families(self): {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` FINAL GROUP BY project_guid - """, + """, # nosec B608 ) project_gt_stats = cursor.fetchall() self.assertCountEqual( @@ -1122,7 +1122,7 @@ def test_delete_families(self): SELECT sum(ac_wes) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` - """, + """, # nosec B608 ) gt_stats = cursor.fetchall() self.assertCountEqual(gt_stats, [(10,)]) @@ -1131,7 +1131,7 @@ def test_delete_families(self): SELECT sum(ac_wes) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` - """, + """, # nosec B608 ) gt_stats_dict = cursor.fetchall() self.assertCountEqual(gt_stats_dict, [(10,)]) @@ -1147,7 +1147,7 @@ def test_rebuild_gt_stats(self): f""" ALTER TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` DROP PARTITION (%(project_guid)s, %(partition_id)s) - """, + """, # nosec B608 {'project_guid': 'project_a', 'partition_id': 0}, ) cursor.execute( @@ -1157,7 +1157,7 @@ def test_rebuild_gt_stats(self): {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` WHERE project_guid IN ('project_a', 'project_b') GROUP BY project_guid - """, + """, # nosec B608 ) project_gt_stats = cursor.fetchall() self.assertCountEqual( @@ -1176,7 +1176,7 @@ def test_rebuild_gt_stats(self): SELECT sum(ac_wes), sum(ac_wgs) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` - """, + """, # nosec B608 ) gt_stats = cursor.fetchall() self.assertCountEqual(gt_stats, [(12, 5)]) @@ -1193,7 +1193,7 @@ def test_rebuild_gt_stats(self): {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` WHERE project_guid IN ('project_a', 'project_b') GROUP BY project_guid - """, + """, # nosec B608 ) project_gt_stats = cursor.fetchall() self.assertCountEqual( From 7fcfb81393bf0db989f1ad7ca072c890f746e452 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 17 Aug 2026 17:15:01 -0400 Subject: [PATCH 092/369] disable codacy errors --- loading_pipeline/lib/misc/clickhouse_test.py | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index e29fc3e901..6b0cc3b39a 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -828,7 +828,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): SELECT * FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` - """, + """, # nosec B608 ) existing_gt_stats = cursor.fetchall() self.assertCountEqual( @@ -852,7 +852,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): SELECT * FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` - """, + """, # nosec B608 ) new_gt_stats = cursor.fetchall() self.assertCountEqual( @@ -874,7 +874,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): SELECT * FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` - """, + """, # nosec B608 ) new_gt_stats_post_reload = cursor.fetchall() self.assertEqual( @@ -910,7 +910,7 @@ def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_typ {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` WHERE project_guid = 'project_d' GROUP BY project_guid, key, sample_type - """, + """, # nosec B608 ) project_gt_stats = cursor.fetchall() self.assertCountEqual( @@ -926,7 +926,7 @@ def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_typ SELECT * FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` - """, + """, # nosec B608 ) gt_stats = cursor.fetchall() self.assertCountEqual( @@ -945,7 +945,7 @@ def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_typ SELECT * FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` - """, + """, # nosec B608 ) gt_stats_dict = cursor.fetchall() self.assertCountEqual( @@ -964,7 +964,7 @@ def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_typ SELECT * FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` - """, + """, # nosec B608 ) variants_memory = cursor.fetchall() self.assertCountEqual( @@ -981,7 +981,7 @@ def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_typ SELECT * FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_disk` - """, + """, # nosec B608 ) variants_disk = cursor.fetchall() self.assertCountEqual( From c7e62a7abe35ce7188cbb55cd10ab0fdbb9d5e85 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 17 Aug 2026 17:21:29 -0400 Subject: [PATCH 093/369] disable codacy errors --- loading_pipeline/lib/misc/clickhouse_test.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index 6b0cc3b39a..3d2bf5fde7 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -1205,7 +1205,7 @@ def test_rebuild_gt_stats(self): SELECT sum(ac_wes), sum(ac_wgs) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` - """, + """, # nosec B608 ) gt_stats = cursor.fetchall() self.assertCountEqual(gt_stats, [(9, 0)]) From 666e8b0a05a2a619553c2e974eb1c1a8c05d8986 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 18 Aug 2026 12:52:42 -0400 Subject: [PATCH 094/369] delete migrations --- .../bin/migrate_all_projects_to_clickhouse.py | 65 -------- .../bin/migrate_variants_tables.py | 49 ------ .../tasks/clickhouse_migration/__init__.py | 0 .../migrate_all_projects_to_clickhouse.py | 51 ------ ..._all_projects_to_clickhouse_on_dataproc.py | 16 -- ...migrate_all_projects_to_clickhouse_test.py | 123 -------------- .../migrate_project_to_clickhouse.py | 157 ------------------ .../migrate_project_variants_to_clickhouse.py | 119 ------------- ...ate_project_variants_to_clickhouse_test.py | 91 ---------- .../lib/tasks/variants_migration/__init__.py | 0 .../load_clickhouse_variants_tables.py | 137 --------------- .../load_clickhouse_variants_tables_test.py | 148 ----------------- .../migrate_variant_details_parquet.py | 76 --------- .../migrate_variants_parquet.py | 76 --------- ...s_table_with_dropped_reference_datasets.py | 90 ---------- 15 files changed, 1198 deletions(-) delete mode 100755 loading_pipeline/bin/migrate_all_projects_to_clickhouse.py delete mode 100755 loading_pipeline/bin/migrate_variants_tables.py delete mode 100644 loading_pipeline/lib/tasks/clickhouse_migration/__init__.py delete mode 100644 loading_pipeline/lib/tasks/clickhouse_migration/migrate_all_projects_to_clickhouse.py delete mode 100644 loading_pipeline/lib/tasks/clickhouse_migration/migrate_all_projects_to_clickhouse_on_dataproc.py delete mode 100644 loading_pipeline/lib/tasks/clickhouse_migration/migrate_all_projects_to_clickhouse_test.py delete mode 100644 loading_pipeline/lib/tasks/clickhouse_migration/migrate_project_to_clickhouse.py delete mode 100644 loading_pipeline/lib/tasks/clickhouse_migration/migrate_project_variants_to_clickhouse.py delete mode 100644 loading_pipeline/lib/tasks/clickhouse_migration/migrate_project_variants_to_clickhouse_test.py delete mode 100644 loading_pipeline/lib/tasks/variants_migration/__init__.py delete mode 100644 loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables.py delete mode 100644 loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py delete mode 100644 loading_pipeline/lib/tasks/variants_migration/migrate_variant_details_parquet.py delete mode 100644 loading_pipeline/lib/tasks/variants_migration/migrate_variants_parquet.py delete mode 100644 loading_pipeline/lib/tasks/variants_migration/update_variant_annotations_table_with_dropped_reference_datasets.py diff --git a/loading_pipeline/bin/migrate_all_projects_to_clickhouse.py b/loading_pipeline/bin/migrate_all_projects_to_clickhouse.py deleted file mode 100755 index bc691738c3..0000000000 --- a/loading_pipeline/bin/migrate_all_projects_to_clickhouse.py +++ /dev/null @@ -1,65 +0,0 @@ -#!/usr/bin/env python3 -import uuid - -import hailtop.fs as hfs -import luigi - -from loading_pipeline.lib.core import ( - DatasetType, - FeatureFlag, - ReferenceGenome, - SampleType, -) -from loading_pipeline.lib.core.constants import MIGRATION_RUN_ID -from loading_pipeline.lib.paths import project_table_path -from loading_pipeline.lib.tasks import ( - MigrateAllProjectsToClickHouseOnDataprocTask, - MigrateAllProjectsToClickHouseTask, -) -from loading_pipeline.lib.tasks.write_clickhouse_load_success_file import ( - WriteClickhouseLoadSuccessFileTask, -) - -if __name__ == '__main__': - task_cls = ( - MigrateAllProjectsToClickHouseOnDataprocTask - if FeatureFlag.RUN_PIPELINE_ON_DATAPROC - else MigrateAllProjectsToClickHouseTask - ) - run_id_prefix = ( - MIGRATION_RUN_ID + '-' + str(uuid.uuid1().int)[:4] - ) # Note: the randomness is a cache bust for the luigi local scheduler - luigi.build( - [ - task_cls( - reference_genome, - DatasetType.SNV_INDEL, - run_id=run_id_prefix, - attempt_id=0, - ) - for reference_genome in ReferenceGenome - ], - ) - clickhouse_load_tasks = [] - for sample_type in SampleType: - for reference_genome in ReferenceGenome: - for p in hfs.ls( - project_table_path( - reference_genome, - DatasetType.SNV_INDEL, - sample_type, - '*', - ), - ): - project_guid = p.path.split('/')[-1].replace('.ht', '') - clickhouse_load_tasks.append( - WriteClickhouseLoadSuccessFileTask( - reference_genome=reference_genome, - dataset_type=DatasetType.SNV_INDEL, - run_id=f'{run_id_prefix}_{sample_type.value}_{project_guid}', - callset_path='', - sample_type=sample_type, - attempt_id=0, - ), - ) - luigi.build(clickhouse_load_tasks) diff --git a/loading_pipeline/bin/migrate_variants_tables.py b/loading_pipeline/bin/migrate_variants_tables.py deleted file mode 100755 index a34e9e9026..0000000000 --- a/loading_pipeline/bin/migrate_variants_tables.py +++ /dev/null @@ -1,49 +0,0 @@ -#!/usr/bin/env python3 -import argparse -import uuid - -import luigi - -from loading_pipeline.lib.core import DatasetType, ReferenceGenome -from loading_pipeline.lib.core.constants import VARIANTS_MIGRATION_RUN_ID -from loading_pipeline.lib.tasks.variants_migration.load_clickhouse_variants_tables import ( - LoadClickhouseVariantsTablesTask, -) - - -def parse_args() -> argparse.Namespace: - parser = argparse.ArgumentParser( - description='Run variants migration Luigi pipeline.', - ) - parser.add_argument( - '--run_all_dataset_types', - action='store_true', - help='If set, runs the pipeline for all dataset types instead of just SNV_INDEL.', - ) - return parser.parse_args() - - -if __name__ == '__main__': - args = parse_args() - for reference_genome, dataset_type in [ - (ReferenceGenome.GRCh37, DatasetType.SNV_INDEL), - (ReferenceGenome.GRCh38, DatasetType.SNV_INDEL), - (ReferenceGenome.GRCh38, DatasetType.MITO), - (ReferenceGenome.GRCh38, DatasetType.SV), - (ReferenceGenome.GRCh38, DatasetType.GCNV), - ]: - if dataset_type != DatasetType.SNV_INDEL and not args.run_all_dataset_types: - continue - run_id_prefix = ( - VARIANTS_MIGRATION_RUN_ID + '-' + str(uuid.uuid1().int)[:4] - ) # Note: the randomness is a cache bust for the luigi local scheduler - luigi.build( - [ - LoadClickhouseVariantsTablesTask( - reference_genome, - dataset_type, - run_id=run_id_prefix, - attempt_id=0, - ), - ], - ) diff --git a/loading_pipeline/lib/tasks/clickhouse_migration/__init__.py b/loading_pipeline/lib/tasks/clickhouse_migration/__init__.py deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/loading_pipeline/lib/tasks/clickhouse_migration/migrate_all_projects_to_clickhouse.py b/loading_pipeline/lib/tasks/clickhouse_migration/migrate_all_projects_to_clickhouse.py deleted file mode 100644 index c8a5e9678a..0000000000 --- a/loading_pipeline/lib/tasks/clickhouse_migration/migrate_all_projects_to_clickhouse.py +++ /dev/null @@ -1,51 +0,0 @@ -import hailtop.fs as hfs -import luigi -import luigi.util - -from loading_pipeline.lib.core import SampleType -from loading_pipeline.lib.paths import ( - project_table_path, -) -from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( - BaseLoadingPipelineParams, -) -from loading_pipeline.lib.tasks.clickhouse_migration.migrate_project_to_clickhouse import ( - MigrateProjectToClickHouseTask, -) - - -@luigi.util.inherits(BaseLoadingPipelineParams) -class MigrateAllProjectsToClickHouseTask(luigi.WrapperTask): - run_id = luigi.Parameter() - attempt_id = luigi.IntParameter() - - def __init__(self, *args, **kwargs): - super().__init__(*args, **kwargs) - self.dynamic_parquet_tasks = set() - - def complete(self): - return len(self.dynamic_parquet_tasks) >= 1 and all( - dynamic_parquet_tasks.complete() - for dynamic_parquet_tasks in self.dynamic_parquet_tasks - ) - - def run(self): - for sample_type in SampleType: - for p in hfs.ls( - project_table_path( - self.reference_genome, - self.dataset_type, - sample_type, - '*', - ), - ): - project_guid = p.path.split('/')[-1].replace('.ht', '') - self.dynamic_parquet_tasks.add( - self.clone( - MigrateProjectToClickHouseTask, - run_id=f'{self.run_id}_{sample_type.value}_{project_guid}', - sample_type=sample_type, - project_guid=project_guid, - ), - ) - yield self.dynamic_parquet_tasks diff --git a/loading_pipeline/lib/tasks/clickhouse_migration/migrate_all_projects_to_clickhouse_on_dataproc.py b/loading_pipeline/lib/tasks/clickhouse_migration/migrate_all_projects_to_clickhouse_on_dataproc.py deleted file mode 100644 index 96e3ffbdcd..0000000000 --- a/loading_pipeline/lib/tasks/clickhouse_migration/migrate_all_projects_to_clickhouse_on_dataproc.py +++ /dev/null @@ -1,16 +0,0 @@ -import luigi - -from loading_pipeline.lib.tasks.clickhouse_migration.migrate_all_projects_to_clickhouse import ( - MigrateAllProjectsToClickHouseTask, -) -from loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc import ( - BaseRunJobOnDataprocTask, -) - - -class MigrateAllProjectsToClickHouseOnDataprocTask(BaseRunJobOnDataprocTask): - run_id = luigi.Parameter() - - @property - def task(self) -> luigi.Task: - return MigrateAllProjectsToClickHouseTask diff --git a/loading_pipeline/lib/tasks/clickhouse_migration/migrate_all_projects_to_clickhouse_test.py b/loading_pipeline/lib/tasks/clickhouse_migration/migrate_all_projects_to_clickhouse_test.py deleted file mode 100644 index ad9c752d15..0000000000 --- a/loading_pipeline/lib/tasks/clickhouse_migration/migrate_all_projects_to_clickhouse_test.py +++ /dev/null @@ -1,123 +0,0 @@ -import json - -import hail as hl -import hailtop.fs as hfs -import luigi.worker -import pandas as pd - -from loading_pipeline.lib.core import ( - DatasetType, - ReferenceGenome, - SampleType, -) -from loading_pipeline.lib.core.constants import MIGRATION_RUN_ID -from loading_pipeline.lib.paths import ( - metadata_for_run_path, - new_entries_parquet_path, - pipeline_run_success_file_path, - project_table_path, - variant_annotations_table_path, -) -from loading_pipeline.lib.tasks.clickhouse_migration.migrate_all_projects_to_clickhouse import ( - MigrateAllProjectsToClickHouseTask, -) -from loading_pipeline.lib.test.mocked_dataroot_testcase import ( - MockedDatarootTestCase, -) - -TEST_SNV_INDEL_ANNOTATIONS = ( - 'loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/annotations.ht' -) -TEST_PROJECT_TABLES = [ - ( - 'loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/projects/WGS/R0113_test_project.ht', - SampleType.WGS, - 'R0113_test_project', - ), - ( - 'loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/projects/WES/R0113_test_project.ht', - SampleType.WES, - 'R0113_test_project', - ), - ( - 'loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/projects/WES/R0114_project4.ht', - SampleType.WES, - 'R0114_project4', - ), -] - - -class MigrateAllProjectsToClickHouseTaskTest(MockedDatarootTestCase): - def setUp(self) -> None: - super().setUp() - ht = hl.read_table(TEST_SNV_INDEL_ANNOTATIONS) - ht.write( - variant_annotations_table_path( - ReferenceGenome.GRCh37, - DatasetType.SNV_INDEL, - ), - ) - for path, sample_type, project_guid in TEST_PROJECT_TABLES: - ht = hl.read_table(path) - ht.write( - project_table_path( - ReferenceGenome.GRCh37, - DatasetType.SNV_INDEL, - sample_type, - project_guid, - ), - ) - - def test_all_project_entries_to_clickhouse_test( - self, - ) -> None: - worker = luigi.worker.Worker() - task = MigrateAllProjectsToClickHouseTask( - reference_genome=ReferenceGenome.GRCh37, - dataset_type=DatasetType.SNV_INDEL, - run_id=MIGRATION_RUN_ID, - attempt_id=0, - ) - worker.add(task) - worker.run() - self.assertTrue(task.complete()) - for _, sample_type, project_guid in TEST_PROJECT_TABLES: - df = pd.read_parquet( - new_entries_parquet_path( - ReferenceGenome.GRCh37, - DatasetType.SNV_INDEL, - f'{MIGRATION_RUN_ID}_{sample_type.value}_{project_guid}', - ), - ) - export_json = df.to_dict('records') - self.assertEqual( - export_json[0]['key'], - 1424, - ) - - for _, sample_type, project_guid in TEST_PROJECT_TABLES: - with hfs.open( - metadata_for_run_path( - ReferenceGenome.GRCh37, - DatasetType.SNV_INDEL, - f'{MIGRATION_RUN_ID}_{sample_type.value}_{project_guid}', - ), - ) as f: - metadata_json = json.load(f) - self.assertEqual( - metadata_json['run_id'], - f'{MIGRATION_RUN_ID}_{sample_type.value}_{project_guid}', - ) - self.assertEqual( - metadata_json['family_samples']['F079280_bh10261'], - ['BH10261-1', 'BH10261-2', 'BH10261-3-T'], - ) - - with hfs.open( - pipeline_run_success_file_path( - ReferenceGenome.GRCh37, - DatasetType.SNV_INDEL, - f'{MIGRATION_RUN_ID}_{sample_type.value}_{project_guid}', - ), - ) as f: - self.assertEqual(f.read(), '') diff --git a/loading_pipeline/lib/tasks/clickhouse_migration/migrate_project_to_clickhouse.py b/loading_pipeline/lib/tasks/clickhouse_migration/migrate_project_to_clickhouse.py deleted file mode 100644 index be0d668a7d..0000000000 --- a/loading_pipeline/lib/tasks/clickhouse_migration/migrate_project_to_clickhouse.py +++ /dev/null @@ -1,157 +0,0 @@ -import json - -import hail as hl -import luigi -import luigi.util - -from loading_pipeline.lib.core import SampleType -from loading_pipeline.lib.misc.family_entries import ( - deduplicate_by_most_non_ref_calls, - deglobalize_ids, -) -from loading_pipeline.lib.paths import ( - metadata_for_run_path, - new_entries_parquet_path, - pipeline_run_success_file_path, - project_table_path, -) -from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( - BaseLoadingPipelineParams, -) -from loading_pipeline.lib.tasks.base.base_write_parquet import BaseWriteParquetTask -from loading_pipeline.lib.tasks.clickhouse_migration.migrate_project_variants_to_clickhouse import ( - MigrateProjectVariantsToClickHouseTask, - WriteProjectSubsettedVariantsTask, -) -from loading_pipeline.lib.tasks.exports.fields import get_entries_export_fields -from loading_pipeline.lib.tasks.files import GCSorLocalTarget, HailTableTask - -PROJECT_SUBSETTED_ANNOTATIONS_TABLE_TASK = 'project_subsetted_annotations_table_task' -PROJECT_TABLE_TASK = 'project_table_task' - - -@luigi.util.inherits(BaseLoadingPipelineParams) -class WriteProjectEntriesParquetTask(BaseWriteParquetTask): - run_id = luigi.Parameter() - sample_type = luigi.EnumParameter(enum=SampleType) - project_guid = luigi.Parameter() - - def output(self) -> luigi.Target: - return GCSorLocalTarget( - new_entries_parquet_path( - self.reference_genome, - self.dataset_type, - self.run_id, - ), - ) - - def requires(self) -> list[luigi.Task]: - return { - PROJECT_SUBSETTED_ANNOTATIONS_TABLE_TASK: self.clone( - WriteProjectSubsettedVariantsTask, - ), - PROJECT_TABLE_TASK: HailTableTask( - project_table_path( - self.reference_genome, - self.dataset_type, - self.sample_type, - self.project_guid, - ), - ), - } - - def create_table(self) -> None: - ht = hl.read_table( - self.input()[PROJECT_TABLE_TASK].path, - ) - ht = deglobalize_ids(ht) - ht = deduplicate_by_most_non_ref_calls(ht) - annotations_ht = hl.read_table( - self.input()[PROJECT_SUBSETTED_ANNOTATIONS_TABLE_TASK].path, - ) - ht = ht.join(annotations_ht) - ht = ht.explode(ht.family_entries) - ht = ht.filter(hl.is_defined(ht.family_entries)) - ht = ht.key_by() - ht = ht.select_globals() - return ht.select( - **get_entries_export_fields( - ht, - self.dataset_type, - self.sample_type, - self.project_guid, - ), - ) - - -@luigi.util.inherits(BaseLoadingPipelineParams) -class WriteMigrationMetadataJsonTask(luigi.Task): - run_id = luigi.Parameter() - sample_type = luigi.EnumParameter(enum=SampleType) - project_guid = luigi.Parameter() - - def requires(self): - return HailTableTask( - project_table_path( - self.reference_genome, - self.dataset_type, - self.sample_type, - self.project_guid, - ), - ) - - def output(self) -> luigi.Target: - return GCSorLocalTarget( - metadata_for_run_path( - self.reference_genome, - self.dataset_type, - self.run_id, - ), - ) - - def run(self): - ht = hl.read_table(self.input().path) - metadata_json = { - 'callsets': [], - 'run_id': self.run_id, - 'sample_type': self.sample_type.value, - 'project_guids': [self.project_guid], - 'family_samples': hl.eval(ht.globals.family_samples), - 'failed_family_samples': { - 'missing_samples': {}, - 'relatedness_check': {}, - 'sex_check': {}, - 'ploidy_check': {}, - }, - 'relatedness_check_file_path': '', - 'sample_qc': {}, - } - with self.output().open('w') as f: - json.dump(metadata_json, f) - - -@luigi.util.inherits(BaseLoadingPipelineParams) -class MigrateProjectToClickHouseTask(luigi.Task): - run_id = luigi.Parameter() - sample_type = luigi.EnumParameter(enum=SampleType) - project_guid = luigi.Parameter() - - def requires(self): - return [ - self.clone(MigrateProjectVariantsToClickHouseTask), - self.clone(WriteProjectEntriesParquetTask), - self.clone(WriteMigrationMetadataJsonTask), - ] - - def output(self) -> luigi.Target: - return GCSorLocalTarget( - pipeline_run_success_file_path( - self.reference_genome, - self.dataset_type, - self.run_id, - ), - ) - - def run(self): - with self.output().open('w') as f: - f.write('') diff --git a/loading_pipeline/lib/tasks/clickhouse_migration/migrate_project_variants_to_clickhouse.py b/loading_pipeline/lib/tasks/clickhouse_migration/migrate_project_variants_to_clickhouse.py deleted file mode 100644 index ebf950e551..0000000000 --- a/loading_pipeline/lib/tasks/clickhouse_migration/migrate_project_variants_to_clickhouse.py +++ /dev/null @@ -1,119 +0,0 @@ -import hail as hl -import luigi -import luigi.util - -from loading_pipeline.lib.core import SampleType -from loading_pipeline.lib.paths import ( - new_variants_table_path, - project_table_path, - variant_annotations_table_path, -) -from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( - BaseLoadingPipelineParams, -) -from loading_pipeline.lib.tasks.base.base_write import BaseWriteTask -from loading_pipeline.lib.tasks.exports.write_new_variant_details_parquet import ( - WriteNewVariantDetailsParquetTask, -) -from loading_pipeline.lib.tasks.exports.write_new_variants_parquet import ( - WriteNewVariantsParquetTask, -) -from loading_pipeline.lib.tasks.files import GCSorLocalTarget, HailTableTask - -MAX_SNV_INDEL_ALLELE_LENGTH = 500 - - -class WriteProjectSubsettedVariantsTask(BaseWriteTask): - run_id = luigi.Parameter() - sample_type = luigi.EnumParameter(enum=SampleType) - project_guid = luigi.Parameter() - - def output(self) -> luigi.Target: - return GCSorLocalTarget( - new_variants_table_path( - self.reference_genome, - self.dataset_type, - self.run_id, - ), - ) - - def requires(self) -> list[luigi.Task]: - return [ - HailTableTask( - variant_annotations_table_path( - self.reference_genome, - self.dataset_type, - ), - ), - HailTableTask( - project_table_path( - self.reference_genome, - self.dataset_type, - self.sample_type, - self.project_guid, - ), - ), - ] - - def create_table(self) -> hl.Table: - ht = hl.read_table(self.input()[0].path) - if not hasattr(ht, 'key_'): - ht = ht.add_index(name='key_') - if self.dataset_type.filter_invalid_sites: - ht = ht.filter(hl.len(ht.alleles[1]) < MAX_SNV_INDEL_ALLELE_LENGTH) - project_ht = hl.read_table(self.input()[1].path) - return ht.semi_join(project_ht) - - -@luigi.util.inherits(BaseLoadingPipelineParams) -class MigrateProjectVariantsToClickHouseTask(luigi.WrapperTask): - run_id = luigi.Parameter() - sample_type = luigi.EnumParameter(enum=SampleType) - project_guid = luigi.Parameter() - - def __init__(self, *args, **kwargs): - super().__init__(*args, **kwargs) - self.dynamic_parquet_tasks = set() - - def requires(self) -> luigi.Task: - return self.clone(WriteProjectSubsettedVariantsTask) - - def complete(self): - return ( - super().complete() - and len(self.dynamic_parquet_tasks) >= 1 - and all( - dynamic_parquet_tasks.complete() - for dynamic_parquet_tasks in self.dynamic_parquet_tasks - ) - ) - - def run(self): - self.dynamic_parquet_tasks.update( - [ - *( - [ - self.clone( - WriteNewVariantDetailsParquetTask, - # Callset Path being required - # here is byproduct of the "place all variants" - # in the variants path" hack. In theory - # it is possible to re-factor the parameters - # such that this isn't required, but it's left - # as out of scope for now. Alternatively, - # we could inherit the functionality of these - # tasks without calling them directly, but - # that was also more code. - callset_path=None, - ), - ] - if self.dataset_type.should_write_new_variant_details - else [] - ), - self.clone( - WriteNewVariantsParquetTask, - callset_path=None, - ), - ], - ) - yield self.dynamic_parquet_tasks diff --git a/loading_pipeline/lib/tasks/clickhouse_migration/migrate_project_variants_to_clickhouse_test.py b/loading_pipeline/lib/tasks/clickhouse_migration/migrate_project_variants_to_clickhouse_test.py deleted file mode 100644 index ce4c6d5cd8..0000000000 --- a/loading_pipeline/lib/tasks/clickhouse_migration/migrate_project_variants_to_clickhouse_test.py +++ /dev/null @@ -1,91 +0,0 @@ -import hail as hl -import hailtop.fs as hfs -import luigi.worker -import pandas as pd - -from loading_pipeline.lib.core import ( - DatasetType, - ReferenceGenome, - SampleType, -) -from loading_pipeline.lib.paths import ( - new_variant_details_parquet_path, - new_variants_parquet_path, - pipeline_run_success_file_path, - project_table_path, - variant_annotations_table_path, -) -from loading_pipeline.lib.tasks.clickhouse_migration.migrate_project_variants_to_clickhouse import ( - MigrateProjectVariantsToClickHouseTask, -) -from loading_pipeline.lib.test.mocked_dataroot_testcase import ( - MockedDatarootTestCase, -) - -TEST_SNV_INDEL_ANNOTATIONS = ( - 'loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/annotations.ht' -) -TEST_PROJECT_TABLE = 'loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/projects/WGS/R0113_test_project.ht' - -TEST_RUN_ID = 'migration_run' - - -class WriteVariantsToClickHouseTest(MockedDatarootTestCase): - def setUp(self) -> None: - super().setUp() - ht = hl.read_table(TEST_SNV_INDEL_ANNOTATIONS) - ht.write( - variant_annotations_table_path( - ReferenceGenome.GRCh37, - DatasetType.SNV_INDEL, - ), - ) - ht = hl.read_table(TEST_PROJECT_TABLE) - ht.write( - project_table_path( - ReferenceGenome.GRCh37, - DatasetType.SNV_INDEL, - SampleType.WGS, - 'R0113_test_project', - ), - ) - - def test_migrate_variants_to_clickhouse_test( - self, - ) -> None: - worker = luigi.worker.Worker() - task = MigrateProjectVariantsToClickHouseTask( - reference_genome=ReferenceGenome.GRCh37, - dataset_type=DatasetType.SNV_INDEL, - run_id=TEST_RUN_ID, - sample_type=SampleType.WGS, - project_guid='R0113_test_project', - ) - worker.add(task) - worker.run() - self.assertTrue(task.complete()) - df = pd.read_parquet( - new_variants_parquet_path( - ReferenceGenome.GRCh37, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ), - ) - self.assertEqual(df.shape[0], 1) - df = pd.read_parquet( - new_variant_details_parquet_path( - ReferenceGenome.GRCh37, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ), - ) - self.assertEqual(df.shape[0], 1) - self.assertFalse( - hfs.exists( - pipeline_run_success_file_path( - ReferenceGenome.GRCh37, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ), - ), - ) diff --git a/loading_pipeline/lib/tasks/variants_migration/__init__.py b/loading_pipeline/lib/tasks/variants_migration/__init__.py deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables.py b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables.py deleted file mode 100644 index 25325d8e37..0000000000 --- a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables.py +++ /dev/null @@ -1,137 +0,0 @@ -import luigi -import luigi.util - -from loading_pipeline.lib.core import FeatureFlag -from loading_pipeline.lib.misc.clickhouse import ( - ClickhouseReferenceDataset, - ClickHouseTable, - TableNameBuilder, - logged_query, -) -from loading_pipeline.lib.misc.retry import retry -from loading_pipeline.lib.paths import ( - new_variant_details_parquet_path, - new_variants_parquet_path, -) -from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( - BaseLoadingPipelineParams, -) -from loading_pipeline.lib.tasks.files import GCSorLocalFolderTarget -from loading_pipeline.lib.tasks.variants_migration.migrate_variant_details_parquet import ( - MigrateVariantDetailsParquetOnDataprocTask, - MigrateVariantDetailsParquetTask, -) -from loading_pipeline.lib.tasks.variants_migration.migrate_variants_parquet import ( - MigrateVariantsParquetOnDataprocTask, - MigrateVariantsParquetTask, -) - - -@retry() -def refresh_seqr_variants_and_search( - table_name_builder: TableNameBuilder, - clickhouse_reference_dataset: ClickhouseReferenceDataset, -): - if clickhouse_reference_dataset.has_seqr_variants: - logged_query( - f""" - SYSTEM START VIEW {clickhouse_reference_dataset.all_variants_to_seqr_variants_mv(table_name_builder)} - """, - ) - logged_query( - f""" - SYSTEM REFRESH VIEW {clickhouse_reference_dataset.all_variants_to_seqr_variants_mv(table_name_builder)} - """, - ) - logged_query( - f""" - SYSTEM WAIT VIEW {clickhouse_reference_dataset.all_variants_to_seqr_variants_mv(table_name_builder)} - """, - timeout=clickhouse_reference_dataset.all_variants_mv_timeout, - ) - clickhouse_reference_dataset.refresh_search(table_name_builder) - - -@luigi.util.inherits(BaseLoadingPipelineParams) -class LoadClickhouseVariantsTablesTask(luigi.WrapperTask): - run_id = luigi.Parameter() - attempt_id = luigi.IntParameter() - - def requires(self) -> luigi.Task: - tasks = ( - [ - self.clone(MigrateVariantsParquetOnDataprocTask), - ] - if FeatureFlag.RUN_PIPELINE_ON_DATAPROC - else [ - self.clone(MigrateVariantsParquetTask), - ] - ) - if self.dataset_type.should_write_new_variant_details: - tasks.append( - self.clone(MigrateVariantDetailsParquetOnDataprocTask) - if FeatureFlag.RUN_PIPELINE_ON_DATAPROC - else self.clone(MigrateVariantDetailsParquetTask), - ) - return tasks - - def complete(self) -> bool: - table_name_builder = TableNameBuilder( - self.reference_genome, - self.dataset_type, - self.run_id, - ) - if not ( - GCSorLocalFolderTarget( - new_variant_details_parquet_path( - self.reference_genome, - self.dataset_type, - self.run_id, - ), - ).exists() - ) or not ( - GCSorLocalFolderTarget( - new_variants_parquet_path( - self.reference_genome, - self.dataset_type, - self.run_id, - ), - ).exists() - ): - return False - max_key = logged_query( - f""" - SELECT max(key) FROM {table_name_builder.src_table(ClickHouseTable.VARIANTS_MEMORY)} - """, - )[0][0] - return logged_query( - f""" - SELECT EXISTS ( - SELECT 1 FROM {table_name_builder.dst_table(ClickHouseTable.VARIANTS_MEMORY)} where key = %(max_key)s - ) - """, - {'max_key': max_key}, - )[0][0] - - def run(self) -> None: - table_name_builder = TableNameBuilder( - self.reference_genome, - self.dataset_type, - self.run_id, - ) - for clickhouse_table in ClickHouseTable.for_dataset_type( - self.dataset_type, - ): - if clickhouse_table == ClickHouseTable.ENTRIES: - continue - clickhouse_table.insert(table_name_builder=table_name_builder) - for ( - clickhouse_reference_dataset - ) in ClickhouseReferenceDataset.for_reference_genome_dataset_type( - self.reference_genome, - self.dataset_type, - ): - refresh_seqr_variants_and_search( - table_name_builder, - clickhouse_reference_dataset, - ) diff --git a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py deleted file mode 100644 index f412e0fa48..0000000000 --- a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py +++ /dev/null @@ -1,148 +0,0 @@ -from unittest.mock import Mock, patch - -import hail as hl -import luigi.worker -from django.db import connections - -from loading_pipeline.lib.core import ( - DatasetType, - ReferenceGenome, -) -from loading_pipeline.lib.core.environment import Env -from loading_pipeline.lib.misc.clickhouse import ClickhouseReferenceDataset -from loading_pipeline.lib.paths import ( - variant_annotations_table_path, -) -from loading_pipeline.lib.tasks.variants_migration.load_clickhouse_variants_tables import ( - LoadClickhouseVariantsTablesTask, -) -from loading_pipeline.lib.tasks.variants_migration.migrate_variant_details_parquet import ( - MigrateVariantDetailsParquetTask, -) -from loading_pipeline.lib.tasks.variants_migration.migrate_variants_parquet import ( - MigrateVariantsParquetTask, -) -from loading_pipeline.lib.tasks.variants_migration.update_variant_annotations_table_with_dropped_reference_datasets import ( - UpdateVariantAnnotationsTableWithDroppedReferenceDatasetsTask, -) -from loading_pipeline.lib.test.clickhouse_schema_testcase import ( - ClickhouseSchemaTestCase, -) -from loading_pipeline.lib.test.mocked_dataroot_testcase import ( - MockedDatarootTestCase, -) - -TEST_SNV_INDEL_ANNOTATIONS = ( - 'loading_pipeline/var/test/exports/GRCh38/SNV_INDEL/annotations.ht' -) -TEST_RUN_ID = 'manual__2024-04-03' - - -class LoadClickhouseVariantsTablesTaskTest( - MockedDatarootTestCase, - ClickhouseSchemaTestCase, -): - def setUp(self) -> None: - super().setUp() - ht = hl.read_table(TEST_SNV_INDEL_ANNOTATIONS) - ht.write( - variant_annotations_table_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - ), - ) - - @patch.object( - ClickhouseReferenceDataset, - 'for_reference_genome_dataset_type', - return_value=[ClickhouseReferenceDataset.CLINVAR], - ) - def test_write_variants_to_clickhouse( - self, - mock_for_reference_genome_dataset_type: Mock, - ): - worker = luigi.worker.Worker() - task = UpdateVariantAnnotationsTableWithDroppedReferenceDatasetsTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - run_id=TEST_RUN_ID, - ) - worker.add(task) - worker.run() - self.assertTrue(task.output().exists()) - self.assertTrue(task.complete()) - ht = hl.read_table(task.output().path) - self.assertTrue('variant_id' in ht.row) - self.assertTrue('gnomad_genomes' not in ht.row and 'dbnsfp' not in ht.row) - - task = MigrateVariantsParquetTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - run_id=TEST_RUN_ID, - attempt_id=0, - ) - worker.add(task) - worker.run() - self.assertTrue(task.output().exists()) - self.assertTrue(task.complete()) - - task = MigrateVariantDetailsParquetTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - run_id=TEST_RUN_ID, - attempt_id=0, - ) - worker.add(task) - worker.run() - self.assertTrue(task.output().exists()) - self.assertTrue(task.complete()) - - task = MigrateVariantDetailsParquetTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - run_id=TEST_RUN_ID, - attempt_id=0, - ) - worker.add(task) - worker.run() - self.assertTrue(task.output().exists()) - self.assertTrue(task.complete()) - - task = LoadClickhouseVariantsTablesTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - run_id=TEST_RUN_ID, - attempt_id=0, - ) - worker.add(task) - worker.run() - self.assertTrue(task.complete()) - - cursor = connections['clickhouse_write'].cursor() - cursor.execute( - f""" - SELECT COUNT(*) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` - """, - ) - variants_count = cursor.fetchone()[0] - self.assertEqual(variants_count, 2) - cursor.execute( - f""" - SELECT COUNT(*) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details` - """, - ) - variant_details_count = cursor.fetchone()[0] - self.assertEqual(variant_details_count, 2) - cursor.execute( - f""" - SELECT COUNT(*) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/key_lookup` - """, - ) - key_lookups_count = cursor.fetchone()[0] - self.assertEqual(key_lookups_count, 2) diff --git a/loading_pipeline/lib/tasks/variants_migration/migrate_variant_details_parquet.py b/loading_pipeline/lib/tasks/variants_migration/migrate_variant_details_parquet.py deleted file mode 100644 index 8405757676..0000000000 --- a/loading_pipeline/lib/tasks/variants_migration/migrate_variant_details_parquet.py +++ /dev/null @@ -1,76 +0,0 @@ -import hail as hl -import luigi -import luigi.util - -from loading_pipeline.lib.paths import ( - new_variant_details_parquet_path, - variant_annotations_table_path, -) -from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( - BaseLoadingPipelineParams, -) -from loading_pipeline.lib.tasks.base.base_write_parquet import BaseWriteParquetTask -from loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc import ( - BaseRunJobOnDataprocTask, -) -from loading_pipeline.lib.tasks.exports.fields import ( - get_variant_details_export_fields, -) -from loading_pipeline.lib.tasks.exports.misc import ( - camelcase_array_structexpression_fields, - unmap_formatting_annotation_enums, -) -from loading_pipeline.lib.tasks.files import GCSorLocalTarget -from loading_pipeline.lib.tasks.variants_migration.update_variant_annotations_table_with_dropped_reference_datasets import ( - UpdateVariantAnnotationsTableWithDroppedReferenceDatasetsTask, -) - - -@luigi.util.inherits(BaseLoadingPipelineParams) -class MigrateVariantDetailsParquetTask(BaseWriteParquetTask): - run_id = luigi.Parameter() - attempt_id = luigi.IntParameter() - - def output(self) -> luigi.Target: - return GCSorLocalTarget( - new_variant_details_parquet_path( - self.reference_genome, - self.dataset_type, - self.run_id, - ), - ) - - def requires(self) -> luigi.Task: - return self.clone(UpdateVariantAnnotationsTableWithDroppedReferenceDatasetsTask) - - def create_table(self) -> None: - ht = hl.read_table( - variant_annotations_table_path( - self.reference_genome, - self.dataset_type, - ), - ) - ht = unmap_formatting_annotation_enums( - ht, - self.reference_genome, - self.dataset_type, - ) - ht = camelcase_array_structexpression_fields( - ht, - self.reference_genome, - self.dataset_type, - ) - ht = ht.key_by() - return ht.select( - **get_variant_details_export_fields( - ht, - self.reference_genome, - self.dataset_type, - ), - ) - - -class MigrateVariantDetailsParquetOnDataprocTask(BaseRunJobOnDataprocTask): - @property - def task(self) -> luigi.Task: - return MigrateVariantDetailsParquetTask diff --git a/loading_pipeline/lib/tasks/variants_migration/migrate_variants_parquet.py b/loading_pipeline/lib/tasks/variants_migration/migrate_variants_parquet.py deleted file mode 100644 index c92a25fb4e..0000000000 --- a/loading_pipeline/lib/tasks/variants_migration/migrate_variants_parquet.py +++ /dev/null @@ -1,76 +0,0 @@ -import hail as hl -import luigi -import luigi.util - -from loading_pipeline.lib.paths import ( - new_variants_parquet_path, - variant_annotations_table_path, -) -from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( - BaseLoadingPipelineParams, -) -from loading_pipeline.lib.tasks.base.base_write_parquet import BaseWriteParquetTask -from loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc import ( - BaseRunJobOnDataprocTask, -) -from loading_pipeline.lib.tasks.exports.fields import get_variants_export_fields -from loading_pipeline.lib.tasks.exports.misc import ( - camelcase_array_structexpression_fields, - subset_consequences_fields, - unmap_formatting_annotation_enums, -) -from loading_pipeline.lib.tasks.files import GCSorLocalTarget -from loading_pipeline.lib.tasks.variants_migration.update_variant_annotations_table_with_dropped_reference_datasets import ( - UpdateVariantAnnotationsTableWithDroppedReferenceDatasetsTask, -) - - -@luigi.util.inherits(BaseLoadingPipelineParams) -class MigrateVariantsParquetTask(BaseWriteParquetTask): - run_id = luigi.Parameter() - attempt_id = luigi.IntParameter() - - def output(self) -> luigi.Target: - return GCSorLocalTarget( - new_variants_parquet_path( - self.reference_genome, - self.dataset_type, - self.run_id, - ), - ) - - def requires(self) -> luigi.Task: - return self.clone(UpdateVariantAnnotationsTableWithDroppedReferenceDatasetsTask) - - def create_table(self) -> None: - ht = hl.read_table( - variant_annotations_table_path( - self.reference_genome, - self.dataset_type, - ), - ) - ht = unmap_formatting_annotation_enums( - ht, - self.reference_genome, - self.dataset_type, - ) - ht = camelcase_array_structexpression_fields( - ht, - self.reference_genome, - self.dataset_type, - ) - if self.dataset_type.should_write_new_variant_details: - ht = subset_consequences_fields( - ht, - self.reference_genome, - ) - ht = ht.key_by() - return ht.select( - **get_variants_export_fields(ht, self.reference_genome, self.dataset_type), - ) - - -class MigrateVariantsParquetOnDataprocTask(BaseRunJobOnDataprocTask): - @property - def task(self) -> luigi.Task: - return MigrateVariantsParquetTask diff --git a/loading_pipeline/lib/tasks/variants_migration/update_variant_annotations_table_with_dropped_reference_datasets.py b/loading_pipeline/lib/tasks/variants_migration/update_variant_annotations_table_with_dropped_reference_datasets.py deleted file mode 100644 index 4dddb1afbe..0000000000 --- a/loading_pipeline/lib/tasks/variants_migration/update_variant_annotations_table_with_dropped_reference_datasets.py +++ /dev/null @@ -1,90 +0,0 @@ -import hail as hl -import luigi -import luigi.util - -from loading_pipeline.lib.paths import ( - variant_annotations_table_path, -) -from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( - BaseLoadingPipelineParams, -) -from loading_pipeline.lib.tasks.base.base_update import ( - BaseUpdateTask, -) -from loading_pipeline.lib.tasks.files import GCSorLocalTarget, HailTableTask - - -@luigi.util.inherits(BaseLoadingPipelineParams) -class UpdateVariantAnnotationsTableWithDroppedReferenceDatasetsTask( - BaseUpdateTask, -): - run_id = luigi.Parameter() - - def output(self) -> luigi.Target: - return GCSorLocalTarget( - variant_annotations_table_path( - self.reference_genome, - self.dataset_type, - ), - ) - - def requires(self) -> list[luigi.Task]: - return HailTableTask( - variant_annotations_table_path( - self.reference_genome, - self.dataset_type, - ), - ) - - def complete(self) -> bool: - return ( - super().complete() and 'dbnsfp' not in hl.read_table(self.output().path).row - ) - - def initialize_table(self) -> hl.Table: - key_type = self.dataset_type.table_key_type(self.reference_genome) - return hl.Table.parallelize( - [], - key_type, - key=key_type.fields, - globals=hl.Struct( - enums=hl.Struct(), - updates=hl.empty_set( - hl.tstruct( - callset=hl.tstr, - project_guid=hl.tstr, - remap_pedigree_hash=hl.tint32, - ), - ), - migrations=hl.empty_array(hl.tstr), - max_key_=hl.int64(-1), - ), - ) - - def update_table(self, ht: hl.Table) -> hl.Table: - for field in [ - 'clinvar', - 'gnomad_mito', - 'hmtvar', - 'local_constraint_mito', - 'dbnsfp', - 'mitomap', - 'mitimpact', - 'helix_mito', - 'gt_stats', - 'high_constraint_region', - 'eigen', - 'splice_ai', - 'exac', - 'topmed', - 'screen', - 'gnomad_exomes', - 'gnomad_genomes', - 'hgmd', - 'gnomad_non_coding_constraint', - ]: - if field in ht.row: - ht = ht.drop(field) - if field in ht.enums: - ht = ht.annotate_globals(enums=ht.enums.drop(field)) - return ht From 4c47dc1e73a17cbb050b8e5e1d3729e28931168f Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 18 Aug 2026 12:55:27 -0400 Subject: [PATCH 095/369] remove dead constants --- loading_pipeline/lib/core/constants.py | 2 -- loading_pipeline/lib/tasks/dataproc/misc.py | 8 -------- 2 files changed, 10 deletions(-) diff --git a/loading_pipeline/lib/core/constants.py b/loading_pipeline/lib/core/constants.py index a1a5affaf2..a6dfe4f6b0 100644 --- a/loading_pipeline/lib/core/constants.py +++ b/loading_pipeline/lib/core/constants.py @@ -1,7 +1,5 @@ import os -MIGRATION_RUN_ID = 'hail_search_to_clickhouse_migration' -VARIANTS_MIGRATION_RUN_ID = 'annotations_to_variants_tables' GRCH37_TO_GRCH38_LIFTOVER_REF_PATH = ( 'gs://hail-common/references/grch37_to_grch38.over.chain.gz' if os.environ.get('HAIL_DATAPROC') == '1' diff --git a/loading_pipeline/lib/tasks/dataproc/misc.py b/loading_pipeline/lib/tasks/dataproc/misc.py index 2031aad46a..e35935ac17 100644 --- a/loading_pipeline/lib/tasks/dataproc/misc.py +++ b/loading_pipeline/lib/tasks/dataproc/misc.py @@ -3,19 +3,11 @@ import luigi from loading_pipeline.lib.core import Env, ReferenceGenome -from loading_pipeline.lib.core.constants import ( - MIGRATION_RUN_ID, - VARIANTS_MIGRATION_RUN_ID, -) CLUSTER_NAME_PREFIX = 'pipeline-runner' def get_cluster_name(reference_genome: ReferenceGenome, run_id: str): - if MIGRATION_RUN_ID in run_id: - return f'{Env.DEPLOYMENT_TYPE}-{CLUSTER_NAME_PREFIX}-{reference_genome.value.lower()}-hs-to-clckhse-mgrtn' - if VARIANTS_MIGRATION_RUN_ID in run_id: - return f'{Env.DEPLOYMENT_TYPE}-{CLUSTER_NAME_PREFIX}-{reference_genome.value.lower()}-vrnts-mgrtn' return f'{Env.DEPLOYMENT_TYPE}-{CLUSTER_NAME_PREFIX}-{reference_genome.value.lower()}-{run_id}' From 4819a0b517649f82e3a27cee95d88b0e6ec9915c Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 18 Aug 2026 12:57:08 -0400 Subject: [PATCH 096/369] import clean up --- loading_pipeline/lib/tasks/__init__.py | 16 ---------------- 1 file changed, 16 deletions(-) diff --git a/loading_pipeline/lib/tasks/__init__.py b/loading_pipeline/lib/tasks/__init__.py index 7ec456e200..4490896442 100644 --- a/loading_pipeline/lib/tasks/__init__.py +++ b/loading_pipeline/lib/tasks/__init__.py @@ -1,27 +1,11 @@ -from loading_pipeline.lib.tasks.clickhouse_migration.migrate_all_projects_to_clickhouse import ( - MigrateAllProjectsToClickHouseTask, -) -from loading_pipeline.lib.tasks.clickhouse_migration.migrate_all_projects_to_clickhouse_on_dataproc import ( - MigrateAllProjectsToClickHouseOnDataprocTask, -) from loading_pipeline.lib.tasks.reference_data.updated_reference_dataset_parquet import ( UpdatedReferenceDatasetParquetTask, ) from loading_pipeline.lib.tasks.run_pipeline import RunPipelineTask -from loading_pipeline.lib.tasks.variants_migration.migrate_variant_details_parquet import ( - MigrateVariantDetailsParquetTask, -) -from loading_pipeline.lib.tasks.variants_migration.migrate_variants_parquet import ( - MigrateVariantsParquetTask, -) from loading_pipeline.lib.tasks.write_metadata_for_run import WriteMetadataForRunTask from loading_pipeline.lib.tasks.write_success_file import WriteSuccessFileTask __all__ = [ - 'MigrateAllProjectsToClickHouseOnDataprocTask', - 'MigrateAllProjectsToClickHouseTask', - 'MigrateVariantDetailsParquetTask', - 'MigrateVariantsParquetTask', 'RunPipelineTask', 'UpdatedReferenceDatasetParquetTask', 'WriteMetadataForRunTask', From f8d1f7ca196b3ce51f5035eb6b0843aeac263cb3 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 18 Aug 2026 13:17:43 -0400 Subject: [PATCH 097/369] migration conditional code cleanup --- .../tasks/exports/write_new_variants_parquet.py | 16 ++-------------- ...ariant_annotations_table_with_new_variants.py | 2 -- ...t_annotations_table_with_new_variants_test.py | 5 ----- .../lib/tasks/write_new_variants_table.py | 4 ---- 4 files changed, 2 insertions(+), 25 deletions(-) diff --git a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet.py b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet.py index 7064685415..53435376dd 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet.py +++ b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet.py @@ -39,24 +39,12 @@ def output(self) -> luigi.Target: ) def requires(self) -> luigi.Task: - if ( - self.dataset_type.export_all_callset_variants - # Special logic for the Clickhouse migration, forcing - # utilization of the project subsetted variants table - # that lives at the new variants table path. - and len(self.project_guids) > 0 - ): + if self.dataset_type.export_all_callset_variants: return self.clone(UpdateVariantAnnotationsTableWithNewVariantsTask) return self.clone(WriteNewVariantsTableTask) def create_table(self) -> None: - if ( - self.dataset_type.export_all_callset_variants - # Special logic for the Clickhouse migration, forcing - # utilization of the project subsetted variants table - # that lives at the new variants table path. - and len(self.project_guids) > 0 - ): + if self.dataset_type.export_all_callset_variants: ht = hl.read_table( variant_annotations_table_path( self.reference_genome, diff --git a/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants.py b/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants.py index 6c547ab029..c44c10c49e 100644 --- a/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants.py +++ b/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants.py @@ -81,7 +81,6 @@ def initialize_table(self) -> hl.Table: remap_pedigree_hash=hl.tint32, ), ), - migrations=hl.empty_array(hl.tstr), max_key_=hl.int64(-1), ), ) @@ -131,6 +130,5 @@ def update_table(self, ht: hl.Table) -> hl.Table: return ht.select_globals( enums=new_variants_ht_globals.enums, updates=ht.updates.union(new_variants_ht_globals.updates), - migrations=ht.migrations, max_key_=ht.aggregate(hl.agg.max(ht.key_)), ) diff --git a/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py b/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py index 3bfe55af65..0f90c6dcdb 100644 --- a/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py +++ b/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py @@ -336,7 +336,6 @@ def test_multiple_update_vat( ), ), }, - migrations=[], max_key_=29, enums=hl.Struct( sorted_motif_feature_consequences=hl.Struct( @@ -491,7 +490,6 @@ def test_mito_update_vat( ), mitotip=hl.Struct(trna_prediction=MITOTIP_PATHOGENICITIES), ), - migrations=[], max_key_=4, updates={ hl.Struct( @@ -580,7 +578,6 @@ def test_sv_multiple_vcf_update_vat( major_consequence=SV_CONSEQUENCE_RANKS, ), ), - migrations=[], max_key_=12, updates={ hl.Struct( @@ -1033,7 +1030,6 @@ def test_sv_multiple_vcf_update_vat( major_consequence=SV_CONSEQUENCE_RANKS, ), ), - migrations=[], max_key_=13, updates={ hl.Struct( @@ -1187,7 +1183,6 @@ def test_gcnv_update_vat_multiple( major_consequence=SV_CONSEQUENCE_RANKS, ), ), - migrations=[], max_key_=1, updates={ hl.Struct( diff --git a/loading_pipeline/lib/tasks/write_new_variants_table.py b/loading_pipeline/lib/tasks/write_new_variants_table.py index 5922b54c7c..a92c15a50a 100644 --- a/loading_pipeline/lib/tasks/write_new_variants_table.py +++ b/loading_pipeline/lib/tasks/write_new_variants_table.py @@ -85,10 +85,6 @@ def requires(self) -> list[luigi.Task]: ] def complete(self) -> bool: - # NOTE: Special hack for ClickHouse migration tasks which - # do not have a callset/projects to load. - if len(self.project_guids) == 0: - return super().complete() return super().complete() and hl.eval( hl.bind( lambda updates: hl.all( From 73aecfd49a81a0d1b8ba5811894615919394bb1a Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 18 Aug 2026 13:22:39 -0400 Subject: [PATCH 098/369] fix imports --- loading_pipeline/lib/tasks/__init__.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/loading_pipeline/lib/tasks/__init__.py b/loading_pipeline/lib/tasks/__init__.py index 4490896442..7e54020569 100644 --- a/loading_pipeline/lib/tasks/__init__.py +++ b/loading_pipeline/lib/tasks/__init__.py @@ -1,3 +1,5 @@ +import luigi.util + from loading_pipeline.lib.tasks.reference_data.updated_reference_dataset_parquet import ( UpdatedReferenceDatasetParquetTask, ) From d914ba1f618503e99943eb04deed19d7c8ad28b7 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 18 Aug 2026 13:26:36 -0400 Subject: [PATCH 099/369] lint --- loading_pipeline/lib/tasks/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/loading_pipeline/lib/tasks/__init__.py b/loading_pipeline/lib/tasks/__init__.py index 7e54020569..a0e0e47498 100644 --- a/loading_pipeline/lib/tasks/__init__.py +++ b/loading_pipeline/lib/tasks/__init__.py @@ -1,4 +1,4 @@ -import luigi.util +import luigi.util # noqa: F401 from loading_pipeline.lib.tasks.reference_data.updated_reference_dataset_parquet import ( UpdatedReferenceDatasetParquetTask, From 7895dc4c7acfb7a1c7fe1ee8b30462d3e5af9dce Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 18 Aug 2026 14:09:20 -0400 Subject: [PATCH 100/369] remove enums global --- loading_pipeline/lib/annotations/misc.py | 98 ------------------- loading_pipeline/lib/tasks/exports/misc.py | 11 --- .../lib/tasks/exports/misc_test.py | 30 ------ ...ant_annotations_table_with_new_variants.py | 2 - ...nnotations_table_with_new_variants_test.py | 66 +------------ .../lib/tasks/write_new_variants_table.py | 8 -- 6 files changed, 1 insertion(+), 214 deletions(-) delete mode 100644 loading_pipeline/lib/annotations/misc.py diff --git a/loading_pipeline/lib/annotations/misc.py b/loading_pipeline/lib/annotations/misc.py deleted file mode 100644 index 00f5f68eb4..0000000000 --- a/loading_pipeline/lib/annotations/misc.py +++ /dev/null @@ -1,98 +0,0 @@ -import hail as hl - -from loading_pipeline.lib.annotations.enums import ( - BIOTYPES, - FIVEUTR_CONSEQUENCES, - LOF_FILTERS, - MITOTIP_PATHOGENICITIES, - MOTIF_CONSEQUENCE_TERMS, - REGULATORY_BIOTYPES, - REGULATORY_CONSEQUENCE_TERMS, - SV_CONSEQUENCE_RANKS, - SV_TYPE_DETAILS, - SV_TYPES, - TRANSCRIPT_CONSEQUENCE_TERMS, -) -from loading_pipeline.lib.core import DatasetType -from loading_pipeline.lib.core.definitions import ReferenceGenome - - -def annotate_formatting_annotation_enum_globals( - ht: hl.Table, - reference_genome: ReferenceGenome, - dataset_type: DatasetType, -) -> hl.Table: - ht = ht.select_globals( - enums=hl.Struct(), - ) - formatting_annotation_names = { - fa.__name__ for fa in dataset_type.formatting_annotation_fns(reference_genome) - } - if 'sorted_motif_feature_consequences' in formatting_annotation_names: - ht = ht.annotate_globals( - enums=ht.enums.annotate( - sorted_motif_feature_consequences=hl.Struct( - consequence_term=MOTIF_CONSEQUENCE_TERMS, - ), - ), - ) - if 'sorted_regulatory_feature_consequences' in formatting_annotation_names: - ht = ht.annotate_globals( - enums=ht.enums.annotate( - sorted_regulatory_feature_consequences=hl.Struct( - biotype=REGULATORY_BIOTYPES, - consequence_term=REGULATORY_CONSEQUENCE_TERMS, - ), - ), - ) - if 'sorted_transcript_consequences' in formatting_annotation_names: - ht = ht.annotate_globals( - enums=ht.enums.annotate( - sorted_transcript_consequences=hl.Struct( - biotype=BIOTYPES, - consequence_term=TRANSCRIPT_CONSEQUENCE_TERMS, - **( - { - 'loftee': hl.Struct( - lof_filter=LOF_FILTERS, - ), - 'utrannotator': hl.Struct( - fiveutr_consequence=FIVEUTR_CONSEQUENCES, - ), - } - if reference_genome == ReferenceGenome.GRCh38 - and dataset_type == DatasetType.SNV_INDEL - else { - 'lof_filter': LOF_FILTERS, - } - ), - ), - ), - ) - if 'mitotip' in formatting_annotation_names: - ht = ht.annotate_globals( - enums=ht.enums.annotate( - mitotip=hl.Struct( - trna_prediction=MITOTIP_PATHOGENICITIES, - ), - ), - ) - if 'sv_type_id' in formatting_annotation_names: - ht = ht.annotate_globals( - enums=ht.enums.annotate( - sv_type=SV_TYPES, - ), - ) - if 'sv_type_detail_id' in formatting_annotation_names: - ht = ht.annotate_globals( - enums=ht.enums.annotate(sv_type_detail=SV_TYPE_DETAILS), - ) - if 'sorted_gene_consequences' in formatting_annotation_names: - ht = ht.annotate_globals( - enums=ht.enums.annotate( - sorted_gene_consequences=hl.Struct( - major_consequence=SV_CONSEQUENCE_RANKS, - ), - ), - ) - return ht diff --git a/loading_pipeline/lib/tasks/exports/misc.py b/loading_pipeline/lib/tasks/exports/misc.py index ee844d28e0..864d44f974 100644 --- a/loading_pipeline/lib/tasks/exports/misc.py +++ b/loading_pipeline/lib/tasks/exports/misc.py @@ -176,9 +176,6 @@ def unmap_formatting_annotation_enums( ).drop('consequence_term_ids'), ), ) - ht = ht.annotate_globals( - enums=ht.enums.drop('sorted_motif_feature_consequences'), - ) if 'sorted_regulatory_feature_consequences' in formatting_annotation_names: ht = ht.annotate( sorted_regulatory_feature_consequences=ht.sorted_regulatory_feature_consequences.map( @@ -190,9 +187,6 @@ def unmap_formatting_annotation_enums( ).drop('biotype_id', 'consequence_term_ids'), ), ) - ht = ht.annotate_globals( - enums=ht.enums.drop('sorted_regulatory_feature_consequences'), - ) if 'sorted_transcript_consequences' in formatting_annotation_names: ht = ht.annotate( sorted_transcript_consequences=ht.sorted_transcript_consequences.map( @@ -234,7 +228,6 @@ def unmap_formatting_annotation_enums( ), ), ) - ht = ht.annotate_globals(enums=ht.enums.drop('sorted_transcript_consequences')) if 'mitotip' in formatting_annotation_names: ht = ht.annotate( mitotip=hl.Struct( @@ -243,7 +236,6 @@ def unmap_formatting_annotation_enums( ], ), ) - ht = ht.annotate_globals(enums=ht.enums.drop('mitotip')) if 'cpx_intervals' in formatting_annotation_names: ht = ht.annotate( cpx_intervals=ht.cpx_intervals.map( @@ -254,12 +246,10 @@ def unmap_formatting_annotation_enums( ) if 'sv_type_id' in formatting_annotation_names: ht = ht.annotate(sv_type=hl.array(SV_TYPES)[ht.sv_type_id]).drop('sv_type_id') - ht = ht.annotate_globals(enums=ht.enums.drop('sv_type')) if 'sv_type_detail_id' in formatting_annotation_names: ht = ht.annotate( sv_type_detail=hl.array(SV_TYPE_DETAILS)[ht.sv_type_detail_id], ).drop('sv_type_detail_id') - ht = ht.annotate_globals(enums=ht.enums.drop('sv_type_detail')) if 'sorted_gene_consequences' in formatting_annotation_names: ht = ht.annotate( sorted_gene_consequences=ht.sorted_gene_consequences.map( @@ -270,5 +260,4 @@ def unmap_formatting_annotation_enums( ).drop('major_consequence_id'), ), ) - ht = ht.annotate_globals(enums=ht.enums.drop('sorted_gene_consequences')) return ht diff --git a/loading_pipeline/lib/tasks/exports/misc_test.py b/loading_pipeline/lib/tasks/exports/misc_test.py index f0324db627..5381cd1470 100644 --- a/loading_pipeline/lib/tasks/exports/misc_test.py +++ b/loading_pipeline/lib/tasks/exports/misc_test.py @@ -28,22 +28,6 @@ def test_unmap_formatting_annotation_enums(self) -> None: ReferenceGenome.GRCh38, DatasetType.SNV_INDEL, ) - self.assertCountEqual( - list(ht.globals.enums.collect()[0].keys()), - [ - 'clinvar', - 'hgmd', - 'screen', - 'dbnsfp', - 'gnomad_exomes', - 'gnomad_non_coding_constraint', - 'splice_ai', - 'exac', - 'topmed', - 'gnomad_genomes', - 'eigen', - ], - ) ht = ht.annotate( sorted_transcript_consequences=[ht.sorted_transcript_consequences[0]], ) @@ -197,20 +181,6 @@ def test_unmap_formatting_annotation_enums(self) -> None: ReferenceGenome.GRCh37, DatasetType.SNV_INDEL, ) - self.assertCountEqual( - list(ht.globals.enums.collect()[0].keys()), - [ - 'clinvar', - 'hgmd', - 'dbnsfp', - 'gnomad_exomes', - 'splice_ai', - 'exac', - 'topmed', - 'gnomad_genomes', - 'eigen', - ], - ) ht = ht.annotate( sorted_transcript_consequences=[ht.sorted_transcript_consequences[0]], ) diff --git a/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants.py b/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants.py index 6c547ab029..8a25f9a434 100644 --- a/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants.py +++ b/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants.py @@ -73,7 +73,6 @@ def initialize_table(self) -> hl.Table: key_type, key=key_type.fields, globals=hl.Struct( - enums=hl.Struct(), updates=hl.empty_set( hl.tstruct( callset=hl.tstr, @@ -129,7 +128,6 @@ def update_table(self, ht: hl.Table) -> hl.Table: new_variants_ht_globals = new_variants_ht.index_globals() return ht.select_globals( - enums=new_variants_ht_globals.enums, updates=ht.updates.union(new_variants_ht_globals.updates), migrations=ht.migrations, max_key_=ht.aggregate(hl.agg.max(ht.key_)), diff --git a/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py b/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py index 3bfe55af65..8a49b7e011 100644 --- a/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py +++ b/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py @@ -4,19 +4,6 @@ import hail as hl import luigi.worker -from loading_pipeline.lib.annotations.enums import ( - BIOTYPES, - FIVEUTR_CONSEQUENCES, - LOF_FILTERS, - MITOTIP_PATHOGENICITIES, - MOTIF_CONSEQUENCE_TERMS, - REGULATORY_BIOTYPES, - REGULATORY_CONSEQUENCE_TERMS, - SV_CONSEQUENCE_RANKS, - SV_TYPE_DETAILS, - SV_TYPES, - TRANSCRIPT_CONSEQUENCE_TERMS, -) from loading_pipeline.lib.core import ( DatasetType, ReferenceGenome, @@ -163,11 +150,7 @@ def test_multiple_update_vat( noncoding=hl.tbool, ), key='locus', - globals=hl.Struct( - enums=hl.Struct( - gnomad_genomes=hl.Struct(), - ), - ), + globals=hl.Struct(), ) coding_and_noncoding_variants_ht.write( valid_reference_dataset_path( @@ -338,25 +321,6 @@ def test_multiple_update_vat( }, migrations=[], max_key_=29, - enums=hl.Struct( - sorted_motif_feature_consequences=hl.Struct( - consequence_term=MOTIF_CONSEQUENCE_TERMS, - ), - sorted_regulatory_feature_consequences=hl.Struct( - biotype=REGULATORY_BIOTYPES, - consequence_term=REGULATORY_CONSEQUENCE_TERMS, - ), - sorted_transcript_consequences=hl.Struct( - biotype=BIOTYPES, - consequence_term=TRANSCRIPT_CONSEQUENCE_TERMS, - loftee=hl.Struct( - lof_filter=LOF_FILTERS, - ), - utrannotator=hl.Struct( - fiveutr_consequence=FIVEUTR_CONSEQUENCES, - ), - ), - ), ), ], ) @@ -483,14 +447,6 @@ def test_mito_update_vat( ht.globals.collect(), [ hl.Struct( - enums=hl.Struct( - sorted_transcript_consequences=hl.Struct( - biotype=BIOTYPES, - consequence_term=TRANSCRIPT_CONSEQUENCE_TERMS, - lof_filter=LOF_FILTERS, - ), - mitotip=hl.Struct(trna_prediction=MITOTIP_PATHOGENICITIES), - ), migrations=[], max_key_=4, updates={ @@ -573,13 +529,6 @@ def test_sv_multiple_vcf_update_vat( ht.globals.collect(), [ hl.Struct( - enums=hl.Struct( - sv_type=SV_TYPES, - sv_type_detail=SV_TYPE_DETAILS, - sorted_gene_consequences=hl.Struct( - major_consequence=SV_CONSEQUENCE_RANKS, - ), - ), migrations=[], max_key_=12, updates={ @@ -1026,13 +975,6 @@ def test_sv_multiple_vcf_update_vat( ht.globals.collect(), [ hl.Struct( - enums=hl.Struct( - sv_type=SV_TYPES, - sv_type_detail=SV_TYPE_DETAILS, - sorted_gene_consequences=hl.Struct( - major_consequence=SV_CONSEQUENCE_RANKS, - ), - ), migrations=[], max_key_=13, updates={ @@ -1181,12 +1123,6 @@ def test_gcnv_update_vat_multiple( ht.globals.collect(), [ hl.Struct( - enums=hl.Struct( - sv_type=SV_TYPES, - sorted_gene_consequences=hl.Struct( - major_consequence=SV_CONSEQUENCE_RANKS, - ), - ), migrations=[], max_key_=1, updates={ diff --git a/loading_pipeline/lib/tasks/write_new_variants_table.py b/loading_pipeline/lib/tasks/write_new_variants_table.py index 5922b54c7c..692f67978f 100644 --- a/loading_pipeline/lib/tasks/write_new_variants_table.py +++ b/loading_pipeline/lib/tasks/write_new_variants_table.py @@ -6,9 +6,6 @@ import luigi.util from loading_pipeline.lib.annotations.fields import get_fields -from loading_pipeline.lib.annotations.misc import ( - annotate_formatting_annotation_enum_globals, -) from loading_pipeline.lib.misc.callsets import get_callset_ht from loading_pipeline.lib.misc.io import checkpoint, remap_pedigree_hash from loading_pipeline.lib.misc.math import constrain @@ -198,11 +195,6 @@ def create_table(self) -> hl.Table: new_variants_ht = new_variants_ht.transmute( key_=new_variants_ht.key_ + curr_max_key_ + 1, ) - new_variants_ht = annotate_formatting_annotation_enum_globals( - new_variants_ht, - self.reference_genome, - self.dataset_type, - ) return new_variants_ht.annotate_globals( updates={ hl.Struct( From 2215c5bfa38f701abeed0e2bd339bfbb21d3025b Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 18 Aug 2026 14:29:06 -0400 Subject: [PATCH 101/369] clean up --- ...ariant_annotations_table_with_dropped_reference_datasets.py | 3 --- 1 file changed, 3 deletions(-) diff --git a/loading_pipeline/lib/tasks/variants_migration/update_variant_annotations_table_with_dropped_reference_datasets.py b/loading_pipeline/lib/tasks/variants_migration/update_variant_annotations_table_with_dropped_reference_datasets.py index 4dddb1afbe..8457feb6d8 100644 --- a/loading_pipeline/lib/tasks/variants_migration/update_variant_annotations_table_with_dropped_reference_datasets.py +++ b/loading_pipeline/lib/tasks/variants_migration/update_variant_annotations_table_with_dropped_reference_datasets.py @@ -48,7 +48,6 @@ def initialize_table(self) -> hl.Table: key_type, key=key_type.fields, globals=hl.Struct( - enums=hl.Struct(), updates=hl.empty_set( hl.tstruct( callset=hl.tstr, @@ -85,6 +84,4 @@ def update_table(self, ht: hl.Table) -> hl.Table: ]: if field in ht.row: ht = ht.drop(field) - if field in ht.enums: - ht = ht.annotate_globals(enums=ht.enums.drop(field)) return ht From a970713f74840e680bf61bd699ca26ce4b66a5d0 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 18 Aug 2026 14:48:51 -0400 Subject: [PATCH 102/369] fix test arg orfder --- loading_pipeline/lib/tasks/dataproc/misc_test.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/loading_pipeline/lib/tasks/dataproc/misc_test.py b/loading_pipeline/lib/tasks/dataproc/misc_test.py index 63ffafb8a1..b9c049005a 100644 --- a/loading_pipeline/lib/tasks/dataproc/misc_test.py +++ b/loading_pipeline/lib/tasks/dataproc/misc_test.py @@ -29,6 +29,10 @@ def test_to_kebab_str_args(self, _: Mock): 'GRCh38', '--dataset-type', 'SNV_INDEL', + '--run-id', + 'a_misc_run', + '--attempt-id', + '0', '--sample-type', 'WGS', '--callset-path', @@ -43,9 +47,5 @@ def test_to_kebab_str_args(self, _: Mock): '[]', '--is-new-gcnv-joint-call', 'False', - '--run-id', - 'a_misc_run', - '--attempt-id', - '0', ], ) From baf2dfbaf1d4c5768275f14abc76917a649f7834 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 18 Aug 2026 14:51:29 -0400 Subject: [PATCH 103/369] add enum validator --- loading_pipeline/lib/annotations/enums.py | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/loading_pipeline/lib/annotations/enums.py b/loading_pipeline/lib/annotations/enums.py index 64202a8940..6a764c61d1 100644 --- a/loading_pipeline/lib/annotations/enums.py +++ b/loading_pipeline/lib/annotations/enums.py @@ -1,3 +1,5 @@ +import hail as hl + BIOTYPES = [ 'IG_C_gene', 'IG_D_gene', @@ -203,3 +205,21 @@ 'INTRONIC', 'NEAREST_TSS', ] + + +def validated_enum_member( + value: hl.StringExpression, + allowed_values: list[str], +) -> hl.StringExpression: + """Validate that a string value is in the allowed enum list. + + Returns the value if valid or missing, raises an error if unrecognized. + This replaces dict-based enum id encoding with validated string values. + """ + allowed_values_set = hl.literal(set(allowed_values)) + return ( + hl.case() + .when(hl.is_missing(value), value) + .when(allowed_values_set.contains(value), value) + .or_error(hl.format('Unexpected enum value: %s', value)) + ) From 69b68a52119280bd2b370b6514156cf9f4051284 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 18 Aug 2026 14:55:55 -0400 Subject: [PATCH 104/369] remove id annotations --- loading_pipeline/lib/annotations/gcnv.py | 21 +++++----- loading_pipeline/lib/annotations/mito.py | 14 ++----- loading_pipeline/lib/annotations/snv_indel.py | 21 +++++----- loading_pipeline/lib/annotations/sv.py | 35 +++++++--------- loading_pipeline/lib/annotations/vep.py | 41 +++++++------------ loading_pipeline/lib/core/dataset_type.py | 6 +-- 6 files changed, 57 insertions(+), 81 deletions(-) diff --git a/loading_pipeline/lib/annotations/gcnv.py b/loading_pipeline/lib/annotations/gcnv.py index e9785419ed..54f80418ed 100644 --- a/loading_pipeline/lib/annotations/gcnv.py +++ b/loading_pipeline/lib/annotations/gcnv.py @@ -3,15 +3,14 @@ import hail as hl from loading_pipeline.lib.annotations import expression_helpers, liftover -from loading_pipeline.lib.annotations.enums import SV_CONSEQUENCE_RANKS, SV_TYPES +from loading_pipeline.lib.annotations.enums import ( + SV_CONSEQUENCE_RANKS, + SV_TYPES, + validated_enum_member, +) from loading_pipeline.lib.core.definitions import ReferenceGenome from loading_pipeline.lib.misc.gcnv import parse_gcnv_genes -SV_CONSEQUENCE_RANKS_LOOKUP = hl.dict( - hl.enumerate(SV_CONSEQUENCE_RANKS, index_first=False), -) -SV_TYPES_LOOKUP = hl.dict(hl.enumerate(SV_TYPES, index_first=False)) - def _start_and_end_equal(mt: hl.MatrixTable) -> hl.BooleanExpression: return (mt.sample_start == mt.start) & (mt.sample_end == mt.end) @@ -139,12 +138,12 @@ def sorted_gene_consequences( ht.gene_ids.map( lambda gene: hl.Struct( gene_id=gene, - major_consequence_id=hl.if_else( + major_consequence=hl.if_else( ht.cg_genes.contains(gene), - SV_CONSEQUENCE_RANKS_LOOKUP['COPY_GAIN'], + 'COPY_GAIN', hl.or_missing( ht.lof_genes.contains(gene), - SV_CONSEQUENCE_RANKS_LOOKUP['LOF'], + 'LOF', ), ), ), @@ -164,8 +163,8 @@ def strvctvre(ht: hl.Table, **_: Any) -> hl.Expression: return hl.struct(score=hl.parse_float32(ht.strvctvre_score)) -def sv_type_id(ht: hl.Table, **_: Any) -> hl.Expression: - return SV_TYPES_LOOKUP[ht.svtype] +def sv_type(ht: hl.Table, **_: Any) -> hl.Expression: + return validated_enum_member(ht.svtype, SV_TYPES) def xpos(ht: hl.Table, reference_genome: ReferenceGenome, **_: Any) -> hl.Expression: diff --git a/loading_pipeline/lib/annotations/mito.py b/loading_pipeline/lib/annotations/mito.py index 85b65ce75c..5704f10e34 100644 --- a/loading_pipeline/lib/annotations/mito.py +++ b/loading_pipeline/lib/annotations/mito.py @@ -2,15 +2,9 @@ import hail as hl -from loading_pipeline.lib.annotations.enums import MITOTIP_PATHOGENICITIES - -MITOTIP_PATHOGENICITIES_LOOKUP = hl.dict( - hl.enumerate(MITOTIP_PATHOGENICITIES, index_first=False).extend( - # NB: adding missing values here allows us to - # hard fail if a mapped key is present and has an unexpected value - # but propagate missing values. - [(hl.missing(hl.tstr), hl.missing(hl.tint32))], - ), +from loading_pipeline.lib.annotations.enums import ( + MITOTIP_PATHOGENICITIES, + validated_enum_member, ) @@ -53,7 +47,7 @@ def mito_cn(mt: hl.MatrixTable, **_: Any) -> hl.Expression: def mitotip(ht: hl.Table, **_: Any) -> hl.Expression: return hl.Struct( - trna_prediction_id=MITOTIP_PATHOGENICITIES_LOOKUP[ht.mitotip_trna_prediction], + trna_prediction=validated_enum_member(ht.mitotip_trna_prediction, MITOTIP_PATHOGENICITIES), ) diff --git a/loading_pipeline/lib/annotations/snv_indel.py b/loading_pipeline/lib/annotations/snv_indel.py index c4fe8cda2a..cc474458da 100644 --- a/loading_pipeline/lib/annotations/snv_indel.py +++ b/loading_pipeline/lib/annotations/snv_indel.py @@ -8,6 +8,7 @@ MOTIF_CONSEQUENCE_TERMS, REGULATORY_BIOTYPES, REGULATORY_CONSEQUENCE_TERMS, + validated_enum_member, ) from loading_pipeline.lib.annotations.vep import ( transcript_consequences_sort, @@ -71,13 +72,13 @@ def sorted_motif_feature_consequences( hl.sorted( ht.vep.motif_feature_consequences.map( lambda c: c.select( - consequence_term_ids=c.consequence_terms.map( - lambda t: MOTIF_CONSEQUENCE_TERMS_LOOKUP[t], + consequence_terms=c.consequence_terms.map( + lambda t: validated_enum_member(t, MOTIF_CONSEQUENCE_TERMS), ), motif_feature_id=c.motif_feature_id, ), - ).filter(lambda c: c.consequence_term_ids.size() > 0), - lambda c: hl.min(c.consequence_term_ids), + ).filter(lambda c: c.consequence_terms.size() > 0), + lambda c: hl.min(c.consequence_terms.map(lambda t: MOTIF_CONSEQUENCE_TERMS_LOOKUP[t])), ), ) @@ -91,14 +92,14 @@ def sorted_regulatory_feature_consequences( hl.sorted( ht.vep.regulatory_feature_consequences.map( lambda c: c.select( - biotype_id=REGULATORY_BIOTYPE_LOOKUP[c.biotype], - consequence_term_ids=c.consequence_terms.map( - lambda t: REGULATORY_CONSEQUENCE_TERMS_LOOKUP[t], + biotype=validated_enum_member(c.biotype, REGULATORY_BIOTYPES), + consequence_terms=c.consequence_terms.map( + lambda t: validated_enum_member(t, REGULATORY_CONSEQUENCE_TERMS), ), regulatory_feature_id=c.regulatory_feature_id, ), - ).filter(lambda c: c.consequence_term_ids.size() > 0), - lambda c: hl.min(c.consequence_term_ids), + ).filter(lambda c: c.consequence_terms.size() > 0), + lambda c: hl.min(c.consequence_terms.map(lambda t: REGULATORY_CONSEQUENCE_TERMS_LOOKUP[t])), ), ) @@ -113,6 +114,6 @@ def sorted_transcript_consequences( vep_110_transcript_consequences_select( gencode_ensembl_to_refseq_id_mapping, ), - ).filter(lambda c: c.consequence_term_ids.size() > 0), + ).filter(lambda c: c.consequence_terms.size() > 0), transcript_consequences_sort(ht), ) diff --git a/loading_pipeline/lib/annotations/sv.py b/loading_pipeline/lib/annotations/sv.py index e6c3abdd85..518bcad612 100644 --- a/loading_pipeline/lib/annotations/sv.py +++ b/loading_pipeline/lib/annotations/sv.py @@ -8,6 +8,7 @@ SV_CONSEQUENCE_RANKS, SV_TYPE_DETAILS, SV_TYPES, + validated_enum_member, ) from loading_pipeline.lib.core.definitions import ReferenceGenome @@ -48,12 +49,6 @@ ) -SV_TYPES_LOOKUP = hl.dict(hl.enumerate(SV_TYPES, index_first=False)) -SV_TYPE_DETAILS_LOOKUP = hl.dict(hl.enumerate(SV_TYPE_DETAILS, index_first=False)) -SV_CONSEQUENCE_RANKS_LOOKUP = hl.dict( - hl.enumerate(SV_CONSEQUENCE_RANKS, index_first=False), -) - def _get_cpx_interval( x: hl.StringExpression, @@ -64,7 +59,7 @@ def _get_cpx_interval( contig_pos = type_contig[1].split(':') pos = contig_pos[1].split('-') return hl.struct( - type_id=SV_TYPES_LOOKUP[type_contig[0]], + type=validated_enum_member(type_contig[0], SV_TYPES), start=hl.locus( contig_pos[0], hl.int32(pos[0]), @@ -88,15 +83,15 @@ def alleles(ht: hl.Table, **_: Any) -> hl.ArrayExpression: 'N', hl.if_else( ( - hl.is_defined(ht.sv_type_detail_id) - & (hl.array(SV_TYPES)[ht.sv_type_id] != 'CPX') + hl.is_defined(ht.sv_type_detail) + & (ht.sv_type != 'CPX') ), hl.format( '<%s:%s>', - hl.array(SV_TYPES)[ht.sv_type_id], - hl.array(SV_TYPE_DETAILS)[ht.sv_type_detail_id], + ht.sv_type, + ht.sv_type_detail, ), - hl.format('<%s>', hl.array(SV_TYPES)[ht.sv_type_id]), + hl.format('<%s>', ht.sv_type), ), ], ) @@ -108,7 +103,7 @@ def info(ht: hl.Table, **_: Any) -> hl.StructExpression: END=ht.start_locus.position, CHR2=ht.end_locus.contig, END2=ht.end_locus.position, - SVTYPE=hl.array(SV_TYPES)[ht.sv_type_id], + SVTYPE=ht.sv_type, SVLEN=ht.sv_len, ) @@ -220,9 +215,7 @@ def sorted_gene_consequences( ht[gene_col].map( lambda gene: hl.struct( gene_id=gencode_gene_symbol_to_gene_id_mapping.get(gene), - major_consequence_id=SV_CONSEQUENCE_RANKS_LOOKUP[ - gene_col.replace(CONSEQ_PREDICTED_PREFIX, '', 1) # noqa: B023 - ], + major_consequence=gene_col.replace(CONSEQ_PREDICTED_PREFIX, '', 1), # noqa: B023 ), ) for gene_col in CONSEQ_PREDICTED_GENE_COLS @@ -238,17 +231,17 @@ def sv_len(ht: hl.Table, **_: Any) -> hl.Expression: return ht['info.SVLEN'] -def sv_type_id(ht: hl.Table, **_: Any) -> hl.Expression: - return SV_TYPES_LOOKUP[_sv_types(ht)[0]] +def sv_type(ht: hl.Table, **_: Any) -> hl.Expression: + return validated_enum_member(_sv_types(ht)[0], SV_TYPES) -def sv_type_detail_id(ht: hl.Table, **_: Any) -> hl.Expression: +def sv_type_detail(ht: hl.Table, **_: Any) -> hl.Expression: sv_types = _sv_types(ht) return hl.if_else( sv_types[0] == 'CPX', - SV_TYPE_DETAILS_LOOKUP[ht['info.CPX_TYPE']], + validated_enum_member(ht['info.CPX_TYPE'], SV_TYPE_DETAILS), hl.or_missing( (sv_types[0] == 'INS') & (hl.len(sv_types) > 1), - SV_TYPE_DETAILS_LOOKUP[sv_types[1]], + validated_enum_member(sv_types[1], SV_TYPE_DETAILS), ), ) diff --git a/loading_pipeline/lib/annotations/vep.py b/loading_pipeline/lib/annotations/vep.py index 12af00d8bb..7c97ba6019 100644 --- a/loading_pipeline/lib/annotations/vep.py +++ b/loading_pipeline/lib/annotations/vep.py @@ -7,16 +7,10 @@ FIVEUTR_CONSEQUENCES, LOF_FILTERS, TRANSCRIPT_CONSEQUENCE_TERMS, + validated_enum_member, ) -BIOTYPE_LOOKUP = hl.dict(hl.enumerate(BIOTYPES, index_first=False)) EXTENDED_INTRONIC_SPLICE_REGION_VARIANT = 'extended_intronic_splice_region_variant' -FIVEUTR_CONSEQUENCES_LOOKUP = hl.dict( - hl.enumerate(FIVEUTR_CONSEQUENCES, index_first=False).extend( - [(hl.missing(hl.tstr), hl.missing(hl.tint32))], - ), -) -LOF_FILTERS_LOOKUP = hl.dict(hl.enumerate(LOF_FILTERS, index_first=False)) MANE_SELECT_ANNOTATIONS = [ 'mane_select', 'mane_plus_clinical', @@ -28,7 +22,7 @@ 'downstream_gene_variant', ], ) -PROTEIN_CODING_ID = BIOTYPE_LOOKUP['protein_coding'] +PROTEIN_CODING_BIOTYPE = 'protein_coding' SELECTED_ANNOTATIONS = [ 'amino_acids', 'canonical', @@ -38,22 +32,19 @@ 'hgvsp', 'transcript_id', ] -TRANSCRIPT_CONSEQUENCE_TERMS_LOOKUP = hl.dict( - hl.enumerate(TRANSCRIPT_CONSEQUENCE_TERMS, index_first=False), -) -def _lof_filter_ids(c: hl.StructExpression) -> hl.ArrayNumericExpression: +def _lof_filters(c: hl.StructExpression) -> hl.ArrayExpression: return hl.or_missing( (c.lof == 'LC') & hl.is_defined(c.lof_filter), - c.lof_filter.split('&|,').map(lambda f: LOF_FILTERS_LOOKUP[f]), + c.lof_filter.split('&|,').map(lambda f: validated_enum_member(f, LOF_FILTERS)), ) -def _consequence_term_ids(c: hl.StructExpression) -> hl.ArrayNumericExpression: +def _consequence_terms(c: hl.StructExpression) -> hl.ArrayExpression: return c.consequence_terms.filter( lambda t: ~OMIT_TRANSCRIPT_CONSEQUENCE_TERMS.contains(t), - ).map(lambda t: TRANSCRIPT_CONSEQUENCE_TERMS_LOOKUP[t]) + ).map(lambda t: validated_enum_member(t, TRANSCRIPT_CONSEQUENCE_TERMS)) def vep_110_transcript_consequences_select( @@ -62,8 +53,8 @@ def vep_110_transcript_consequences_select( return lambda c: c.select( *SELECTED_ANNOTATIONS, *MANE_SELECT_ANNOTATIONS, - biotype_id=BIOTYPE_LOOKUP[c.biotype], - consequence_term_ids=_consequence_term_ids(c), + biotype=validated_enum_member(c.biotype, BIOTYPES), + consequence_terms=_consequence_terms(c), exon=hl.bind( lambda split: hl.or_missing( hl.is_defined(split), @@ -84,7 +75,7 @@ def vep_110_transcript_consequences_select( ), loftee=hl.struct( is_lof_nagnag=c.lof_flags == NAGNAG_SITE, - lof_filter_ids=_lof_filter_ids(c), + lof_filters=_lof_filters(c), ), spliceregion=hl.struct( extended_intronic_splice_region_variant=( @@ -98,7 +89,7 @@ def vep_110_transcript_consequences_select( existing_inframe_oorfs=c.existing_inframe_oorfs, existing_outofframe_oorfs=c.existing_outofframe_oorfs, existing_uorfs=c.existing_uorfs, - fiveutr_consequence_id=FIVEUTR_CONSEQUENCES_LOOKUP[c.fiveutr_consequence], + fiveutr_consequence=validated_enum_member(c.fiveutr_consequence, FIVEUTR_CONSEQUENCES), # Annotation documentation here: # https://github.com/ImperialCardioGenetics/UTRannotator?tab=readme-ov-file#the-detailed-annotation-for-each-consequence # NB: @@ -148,10 +139,10 @@ def vep_85_transcript_consequences_select( ) -> hl.StructExpression: return c.select( *SELECTED_ANNOTATIONS, - biotype_id=BIOTYPE_LOOKUP[c.biotype], - consequence_term_ids=_consequence_term_ids(c), + biotype=validated_enum_member(c.biotype, BIOTYPES), + consequence_terms=_consequence_terms(c), is_lof_nagnag=c.lof_flags == NAGNAG_SITE, - lof_filter_ids=_lof_filter_ids(c), + lof_filters=_lof_filters(c), ) @@ -174,9 +165,7 @@ def transcript_consequences_sort( ), ) ), - c.biotype_id == PROTEIN_CODING_ID, - hl.set(c.consequence_term_ids).contains( - TRANSCRIPT_CONSEQUENCE_TERMS_LOOKUP[ht.vep.most_severe_consequence], - ), + c.biotype == PROTEIN_CODING_BIOTYPE, + hl.set(c.consequence_terms).contains(ht.vep.most_severe_consequence), hl.or_else(c.canonical, 0) == 1, ) diff --git a/loading_pipeline/lib/core/dataset_type.py b/loading_pipeline/lib/core/dataset_type.py index 1e018f7104..3be1e00e61 100644 --- a/loading_pipeline/lib/core/dataset_type.py +++ b/loading_pipeline/lib/core/dataset_type.py @@ -250,8 +250,8 @@ def formatting_annotation_fns( sv.sorted_gene_consequences, sv.start_locus, sv.strvctvre, - sv.sv_type_id, - sv.sv_type_detail_id, + sv.sv_type, + sv.sv_type_detail, sv.sv_len, shared.xpos, ], @@ -261,7 +261,7 @@ def formatting_annotation_fns( gcnv.sorted_gene_consequences, gcnv.start_locus, gcnv.strvctvre, - gcnv.sv_type_id, + gcnv.sv_type, gcnv.xpos, ], } From f3704a0a447c115952a5718ddddce45dd694abc6 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 18 Aug 2026 14:57:43 -0400 Subject: [PATCH 105/369] remove unmap --- loading_pipeline/lib/tasks/exports/misc.py | 118 ------------------ .../write_new_variant_details_parquet.py | 6 - .../exports/write_new_variants_parquet.py | 6 - .../migrate_variant_details_parquet.py | 6 - .../migrate_variants_parquet.py | 6 - 5 files changed, 142 deletions(-) diff --git a/loading_pipeline/lib/tasks/exports/misc.py b/loading_pipeline/lib/tasks/exports/misc.py index 864d44f974..2c4548bd43 100644 --- a/loading_pipeline/lib/tasks/exports/misc.py +++ b/loading_pipeline/lib/tasks/exports/misc.py @@ -2,19 +2,6 @@ import hail as hl -from loading_pipeline.lib.annotations.enums import ( - BIOTYPES, - FIVEUTR_CONSEQUENCES, - LOF_FILTERS, - MITOTIP_PATHOGENICITIES, - MOTIF_CONSEQUENCE_TERMS, - REGULATORY_BIOTYPES, - REGULATORY_CONSEQUENCE_TERMS, - SV_CONSEQUENCE_RANKS, - SV_TYPE_DETAILS, - SV_TYPES, - TRANSCRIPT_CONSEQUENCE_TERMS, -) from loading_pipeline.lib.core import DatasetType, ReferenceGenome from loading_pipeline.lib.misc.nested_field import parse_nested_field @@ -156,108 +143,3 @@ def camelcase_array_structexpression_fields( ), ) return ht - - -def unmap_formatting_annotation_enums( - ht: hl.Table, - reference_genome: ReferenceGenome, - dataset_type: DatasetType, -) -> hl.Table: - formatting_annotation_names = { - fa.__name__ for fa in dataset_type.formatting_annotation_fns(reference_genome) - } - if 'sorted_motif_feature_consequences' in formatting_annotation_names: - ht = ht.annotate( - sorted_motif_feature_consequences=ht.sorted_motif_feature_consequences.map( - lambda c: c.annotate( - consequence_terms=c.consequence_term_ids.map( - lambda tid: hl.array(MOTIF_CONSEQUENCE_TERMS)[tid], - ), - ).drop('consequence_term_ids'), - ), - ) - if 'sorted_regulatory_feature_consequences' in formatting_annotation_names: - ht = ht.annotate( - sorted_regulatory_feature_consequences=ht.sorted_regulatory_feature_consequences.map( - lambda c: c.annotate( - biotype=hl.array(REGULATORY_BIOTYPES)[c.biotype_id], - consequence_terms=c.consequence_term_ids.map( - lambda tid: hl.array(REGULATORY_CONSEQUENCE_TERMS)[tid], - ), - ).drop('biotype_id', 'consequence_term_ids'), - ), - ) - if 'sorted_transcript_consequences' in formatting_annotation_names: - ht = ht.annotate( - sorted_transcript_consequences=ht.sorted_transcript_consequences.map( - lambda c: c.annotate( - biotype=hl.array(BIOTYPES)[c.biotype_id], - consequence_terms=c.consequence_term_ids.map( - lambda tid: hl.array(TRANSCRIPT_CONSEQUENCE_TERMS)[tid], - ), - **{ - 'loftee': c.loftee.annotate( - lof_filters=c.loftee.lof_filter_ids.map( - lambda fid: hl.array(LOF_FILTERS)[fid], - ), - ).drop('lof_filter_ids'), - 'utrannotator': c.utrannotator.annotate( - fiveutr_consequence=hl.array(FIVEUTR_CONSEQUENCES)[ - c.utrannotator.fiveutr_consequence_id - ], - ).drop('fiveutr_consequence_id'), - } - if reference_genome == ReferenceGenome.GRCh38 - and dataset_type == DatasetType.SNV_INDEL - else { - 'lof_filters': c.lof_filter_ids.map( - lambda fid: hl.array(LOF_FILTERS)[fid], - ), - }, - ).drop( - 'biotype_id', - 'consequence_term_ids', - *( - [] - if reference_genome == ReferenceGenome.GRCh38 - and dataset_type == DatasetType.SNV_INDEL - else [ - 'lof_filter_ids', - ] - ), - ), - ), - ) - if 'mitotip' in formatting_annotation_names: - ht = ht.annotate( - mitotip=hl.Struct( - trna_prediction=hl.array(MITOTIP_PATHOGENICITIES)[ - ht.mitotip.trna_prediction_id - ], - ), - ) - if 'cpx_intervals' in formatting_annotation_names: - ht = ht.annotate( - cpx_intervals=ht.cpx_intervals.map( - lambda cpx_i: cpx_i.annotate( - type=hl.array(SV_TYPES)[cpx_i.type_id], - ).drop('type_id'), - ), - ) - if 'sv_type_id' in formatting_annotation_names: - ht = ht.annotate(sv_type=hl.array(SV_TYPES)[ht.sv_type_id]).drop('sv_type_id') - if 'sv_type_detail_id' in formatting_annotation_names: - ht = ht.annotate( - sv_type_detail=hl.array(SV_TYPE_DETAILS)[ht.sv_type_detail_id], - ).drop('sv_type_detail_id') - if 'sorted_gene_consequences' in formatting_annotation_names: - ht = ht.annotate( - sorted_gene_consequences=ht.sorted_gene_consequences.map( - lambda c: c.annotate( - major_consequence=hl.array(SV_CONSEQUENCE_RANKS)[ - c.major_consequence_id - ], - ).drop('major_consequence_id'), - ), - ) - return ht diff --git a/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet.py b/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet.py index 6da793ec53..fe5237ba92 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet.py +++ b/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet.py @@ -13,7 +13,6 @@ from loading_pipeline.lib.tasks.exports.fields import get_variant_details_export_fields from loading_pipeline.lib.tasks.exports.misc import ( camelcase_array_structexpression_fields, - unmap_formatting_annotation_enums, ) from loading_pipeline.lib.tasks.files import GCSorLocalFolderTarget, GCSorLocalTarget from loading_pipeline.lib.tasks.update_variant_annotations_table_with_new_variants import ( @@ -51,11 +50,6 @@ def create_table(self) -> None: self.run_id, ), ) - ht = unmap_formatting_annotation_enums( - ht, - self.reference_genome, - self.dataset_type, - ) ht = camelcase_array_structexpression_fields( ht, self.reference_genome, diff --git a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet.py b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet.py index 7064685415..14fe3ba382 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet.py +++ b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet.py @@ -16,7 +16,6 @@ from loading_pipeline.lib.tasks.exports.misc import ( camelcase_array_structexpression_fields, subset_consequences_fields, - unmap_formatting_annotation_enums, ) from loading_pipeline.lib.tasks.files import GCSorLocalTarget from loading_pipeline.lib.tasks.update_variant_annotations_table_with_new_variants import ( @@ -78,11 +77,6 @@ def create_table(self) -> None: self.run_id, ), ) - ht = unmap_formatting_annotation_enums( - ht, - self.reference_genome, - self.dataset_type, - ) ht = camelcase_array_structexpression_fields( ht, self.reference_genome, diff --git a/loading_pipeline/lib/tasks/variants_migration/migrate_variant_details_parquet.py b/loading_pipeline/lib/tasks/variants_migration/migrate_variant_details_parquet.py index 8405757676..abd7710850 100644 --- a/loading_pipeline/lib/tasks/variants_migration/migrate_variant_details_parquet.py +++ b/loading_pipeline/lib/tasks/variants_migration/migrate_variant_details_parquet.py @@ -18,7 +18,6 @@ ) from loading_pipeline.lib.tasks.exports.misc import ( camelcase_array_structexpression_fields, - unmap_formatting_annotation_enums, ) from loading_pipeline.lib.tasks.files import GCSorLocalTarget from loading_pipeline.lib.tasks.variants_migration.update_variant_annotations_table_with_dropped_reference_datasets import ( @@ -50,11 +49,6 @@ def create_table(self) -> None: self.dataset_type, ), ) - ht = unmap_formatting_annotation_enums( - ht, - self.reference_genome, - self.dataset_type, - ) ht = camelcase_array_structexpression_fields( ht, self.reference_genome, diff --git a/loading_pipeline/lib/tasks/variants_migration/migrate_variants_parquet.py b/loading_pipeline/lib/tasks/variants_migration/migrate_variants_parquet.py index c92a25fb4e..393bcfb9f6 100644 --- a/loading_pipeline/lib/tasks/variants_migration/migrate_variants_parquet.py +++ b/loading_pipeline/lib/tasks/variants_migration/migrate_variants_parquet.py @@ -17,7 +17,6 @@ from loading_pipeline.lib.tasks.exports.misc import ( camelcase_array_structexpression_fields, subset_consequences_fields, - unmap_formatting_annotation_enums, ) from loading_pipeline.lib.tasks.files import GCSorLocalTarget from loading_pipeline.lib.tasks.variants_migration.update_variant_annotations_table_with_dropped_reference_datasets import ( @@ -49,11 +48,6 @@ def create_table(self) -> None: self.dataset_type, ), ) - ht = unmap_formatting_annotation_enums( - ht, - self.reference_genome, - self.dataset_type, - ) ht = camelcase_array_structexpression_fields( ht, self.reference_genome, From 986c19743f6950fabd24b78ab5556044cdc5592b Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 18 Aug 2026 15:13:21 -0400 Subject: [PATCH 106/369] test updates --- .../lib/annotations/snv_indel_test.py | 50 ++-- loading_pipeline/lib/annotations/sv_test.py | 20 +- .../lib/tasks/exports/misc_test.py | 264 ------------------ ...nnotations_table_with_new_variants_test.py | 80 +++--- 4 files changed, 75 insertions(+), 339 deletions(-) diff --git a/loading_pipeline/lib/annotations/snv_indel_test.py b/loading_pipeline/lib/annotations/snv_indel_test.py index 0de91786b0..97021081ce 100644 --- a/loading_pipeline/lib/annotations/snv_indel_test.py +++ b/loading_pipeline/lib/annotations/snv_indel_test.py @@ -58,10 +58,10 @@ def test_sorted_transcript_consequences_37( hgvsc='ENST00000327044.6:c.1667C>T', hgvsp='ENSP00000317992.6:p.Ser556Leu', transcript_id='ENST00000327044', - biotype_id=39, - consequence_term_ids=[9], + biotype='protein_coding', + consequence_terms=['missense_variant'], is_lof_nagnag=None, - lof_filter_ids=[0, 1], + lof_filters=['END_TRUNC', 'INCOMPLETE_CDS'], ), hl.Struct( amino_acids=None, @@ -71,10 +71,10 @@ def test_sorted_transcript_consequences_37( hgvsc='ENST00000477976.1:n.3114C>T', hgvsp=None, transcript_id='ENST00000477976', - biotype_id=38, - consequence_term_ids=[23, 26], + biotype='lncRNA', + consequence_terms=['non_coding_transcript_exon_variant', 'non_coding_transcript_variant'], is_lof_nagnag=None, - lof_filter_ids=None, + lof_filters=None, ), hl.Struct( amino_acids=None, @@ -84,10 +84,10 @@ def test_sorted_transcript_consequences_37( hgvsc='ENST00000483767.1:n.523C>T', hgvsp=None, transcript_id='ENST00000483767', - biotype_id=38, - consequence_term_ids=[23, 26], + biotype='lncRNA', + consequence_terms=['non_coding_transcript_exon_variant', 'non_coding_transcript_variant'], is_lof_nagnag=None, - lof_filter_ids=None, + lof_filters=None, ), ], ], @@ -143,14 +143,14 @@ def test_sorted_transcript_consequences_38( refseq_transcript_id='NM_015658.4', mane_select='NM_015658.4', mane_plus_clinical=None, - biotype_id=39, - consequence_term_ids=[9], + biotype='protein_coding', + consequence_terms=['missense_variant'], exon=hl.Struct(index=15, total=19), intron=None, alphamissense=hl.Struct(pathogenicity=0.10000000149011612), loftee=hl.Struct( is_lof_nagnag=None, - lof_filter_ids=[0, 1], + lof_filters=['END_TRUNC', 'INCOMPLETE_CDS'], ), spliceregion=hl.Struct( extended_intronic_splice_region_variant=False, @@ -159,7 +159,7 @@ def test_sorted_transcript_consequences_38( existing_inframe_oorfs=None, existing_outofframe_oorfs=None, existing_uorfs=None, - fiveutr_consequence_id=None, + fiveutr_consequence=None, fiveutr_annotation=None, ), ), @@ -174,14 +174,14 @@ def test_sorted_transcript_consequences_38( refseq_transcript_id='refseq1', mane_select=None, mane_plus_clinical=None, - biotype_id=38, - consequence_term_ids=[23, 26], + biotype='retained_intron', + consequence_terms=['non_coding_transcript_exon_variant', 'non_coding_transcript_variant'], exon=hl.Struct(index=13, total=17), intron=None, alphamissense=hl.Struct(pathogenicity=0.9700000286102295), loftee=hl.Struct( is_lof_nagnag=None, - lof_filter_ids=None, + lof_filters=None, ), spliceregion=hl.Struct( extended_intronic_splice_region_variant=False, @@ -190,7 +190,7 @@ def test_sorted_transcript_consequences_38( existing_inframe_oorfs=None, existing_outofframe_oorfs=None, existing_uorfs=None, - fiveutr_consequence_id=None, + fiveutr_consequence=None, fiveutr_annotation=None, ), ), @@ -205,14 +205,14 @@ def test_sorted_transcript_consequences_38( refseq_transcript_id=None, mane_select=None, mane_plus_clinical=None, - biotype_id=38, - consequence_term_ids=[23, 13, 26], + biotype='retained_intron', + consequence_terms=['non_coding_transcript_exon_variant', 'splice_donor_region_variant', 'non_coding_transcript_variant'], exon=hl.Struct(index=1, total=5), intron=None, alphamissense=hl.Struct(pathogenicity=None), loftee=hl.Struct( is_lof_nagnag=None, - lof_filter_ids=None, + lof_filters=None, ), spliceregion=hl.Struct( extended_intronic_splice_region_variant=True, @@ -221,7 +221,7 @@ def test_sorted_transcript_consequences_38( existing_inframe_oorfs=0, existing_outofframe_oorfs=1, existing_uorfs=0, - fiveutr_consequence_id=1, + fiveutr_consequence='5_prime_UTR_premature_start_codon_gain_variant', fiveutr_annotation=hl.Struct( type='OutOfFrame_oORF', KozakContext='TTTATGC', @@ -290,13 +290,13 @@ def test_sorted_other_feature_consequences( ht.sorted_regulatory_feature_consequences.collect()[0], [ hl.Struct( - biotype_id=0, - consequence_term_ids=[0], + biotype='enhancer', + consequence_terms=['regulatory_region_ablation'], regulatory_feature_id='regulatory_2', ), hl.Struct( - biotype_id=0, - consequence_term_ids=[2], + biotype='enhancer', + consequence_terms=['regulatory_region_variant'], regulatory_feature_id='regulatory_1', ), ], diff --git a/loading_pipeline/lib/annotations/sv_test.py b/loading_pipeline/lib/annotations/sv_test.py index 25a8413b16..26ebb082d3 100644 --- a/loading_pipeline/lib/annotations/sv_test.py +++ b/loading_pipeline/lib/annotations/sv_test.py @@ -24,8 +24,8 @@ def test_sv_export_annotations(self) -> None: reference_genome='GRCh38', ), sv_len=123, - sv_type_id=2, - sv_type_detail_id=None, + sv_type='BND', + sv_type_detail=None, ), hl.Struct( id=1, @@ -41,8 +41,8 @@ def test_sv_export_annotations(self) -> None: reference_genome='GRCh38', ), sv_len=245, - sv_type_id=2, - sv_type_detail_id=None, + sv_type='BND', + sv_type_detail=None, ), hl.Struct( id=2, @@ -58,8 +58,8 @@ def test_sv_export_annotations(self) -> None: reference_genome='GRCh38', ), sv_len=245, - sv_type_id=3, - sv_type_detail_id=2, + sv_type='CPX', + sv_type_detail='ME', ), hl.Struct( id=3, @@ -75,8 +75,8 @@ def test_sv_export_annotations(self) -> None: reference_genome='GRCh38', ), sv_len=245, - sv_type_id=7, - sv_type_detail_id=6, + sv_type='INS', + sv_type_detail='ME:SVA', ), ], hl.tstruct( @@ -85,8 +85,8 @@ def test_sv_export_annotations(self) -> None: end_locus=hl.tlocus('GRCh38'), start_locus=hl.tlocus('GRCh38'), sv_len=hl.tint32, - sv_type_id=hl.tint32, - sv_type_detail_id=hl.tint32, + sv_type=hl.tstr, + sv_type_detail=hl.tstr, ), key='id', ) diff --git a/loading_pipeline/lib/tasks/exports/misc_test.py b/loading_pipeline/lib/tasks/exports/misc_test.py index 5381cd1470..e7563cead3 100644 --- a/loading_pipeline/lib/tasks/exports/misc_test.py +++ b/loading_pipeline/lib/tasks/exports/misc_test.py @@ -9,7 +9,6 @@ from loading_pipeline.lib.tasks.exports.misc import ( camelcase_array_structexpression_fields, sorted_hl_struct, - unmap_formatting_annotation_enums, ) TEST_SNV_INDEL_ANNOTATIONS = ( @@ -21,271 +20,8 @@ class MiscTest(unittest.TestCase): - def test_unmap_formatting_annotation_enums(self) -> None: - ht = hl.read_table(TEST_SNV_INDEL_ANNOTATIONS) - ht = unmap_formatting_annotation_enums( - ht, - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - ) - ht = ht.annotate( - sorted_transcript_consequences=[ht.sorted_transcript_consequences[0]], - ) - self.assertEqual( - ht.collect()[0], - hl.Struct( - key_=0, - locus=hl.Locus( - contig='chr1', - position=876499, - reference_genome='GRCh38', - ), - alleles=['A', 'G'], - clinvar=hl.Struct( - alleleId=929885, - conflictingPathogenicities=None, - goldStars=1, - submitters=['Labcorp Genetics (formerly Invitae), Labcorp'], - conditions=['not provided'], - assertion_ids=[], - pathogenicity_id=12, - ), - rg37_locus=hl.Locus( - contig=1, - position=874501, - reference_genome='GRCh37', - ), - rsid=None, - sorted_transcript_consequences=[ - hl.Struct( - amino_acids='S/L', - canonical=1, - codons='tCg/tTg', - gene_id='ENSG00000187634', - hgvsc='ENST00000616016.5:c.1049C>T', - hgvsp='ENSP00000478421.2:p.Ser350Leu', - transcript_id='ENST00000616016', - mane_select='NM_001385641.1', - mane_plus_clinical=None, - exon=hl.Struct(index=6, total=14), - intron=None, - refseq_transcript_id='NM_001385641.1', - alphamissense=hl.Struct(pathogenicity=None), - loftee=hl.Struct(is_lof_nagnag=None, lof_filters=None), - spliceregion=hl.Struct( - extended_intronic_splice_region_variant=False, - ), - utrannotator=hl.Struct( - existing_inframe_oorfs=None, - existing_outofframe_oorfs=None, - existing_uorfs=None, - fiveutr_annotation=hl.Struct( - type='OutOfFrame_oORF', - KozakContext='CGCATGC', - KozakStrength='Weak', - DistanceToCDS=41, - CapDistanceToStart=None, - DistanceToStop=None, - Evidence=None, - AltStop=None, - AltStopDistanceToCDS=None, - FrameWithCDS=None, - StartDistanceToCDS=None, - newSTOPDistanceToCDS=None, - alt_type=None, - alt_type_length=None, - ref_StartDistanceToCDS=None, - ref_type=None, - ref_type_length=None, - ), - fiveutr_consequence=None, - ), - biotype='protein_coding', - consequence_terms=['missense_variant'], - ), - ], - variant_id='1-876499-A-G', - xpos=1000876499, - gt_stats=hl.Struct(AC=47, AN=81784, AF=0.0005746845272369683, hom=1), - CAID='CA502654', - check_ref=False, - sorted_regulatory_feature_consequences=[ - hl.Struct( - regulatory_feature_id='ENSR00000344437', - biotype='CTCF_binding_site', - consequence_terms=['regulatory_region_variant'], - ), - ], - sorted_motif_feature_consequences=[ - hl.Struct( - motif_feature_id='ENSM00493959715', - consequence_terms=['TF_binding_site_variant'], - ), - ], - gnomad_non_coding_constraint=hl.Struct(z_score=None), - hgmd=hl.Struct(accession='abcdefg', class_id=3), - gnomad_exomes=hl.Struct( - AF=0.0006690866430290043, - AN=1440770, - AC=964, - Hom=0, - AF_POPMAX_OR_GLOBAL=0.0008023773552849889, - FAF_AF=0.000633420015219599, - Hemi=0, - ), - gnomad_genomes=hl.Struct( - AF=0.0002759889466688037, - AN=152180, - AC=42, - Hom=0, - AF_POPMAX_OR_GLOBAL=0.10000000149011612, - FAF_AF=0.0002092500071739778, - Hemi=0, - ), - screen=hl.Struct(region_type_ids=[]), - dbnsfp=hl.Struct( - PrimateAI_score=0.5918066501617432, - fathmm_MKL_coding_score=0.7174800038337708, - CADD_phred=23.5, - SIFT_score=0.0010000000474974513, - REVEL_score=0.3109999895095825, - Polyphen2_HVAR_score=0.164000004529953, - VEST4_score=0.39500001072883606, - MPC_score=0.01291007362306118, - MutPred_score=None, - MutationTaster_pred_id=0, - ), - topmed=hl.Struct( - AC=41, - AF=0.00032651599030941725, - AN=125568, - Hom=0, - Het=41, - ), - exac=hl.Struct( - AF_POPMAX=0.0007150234305299819, - AF=0.00019039999460801482, - AC_Adj=20, - AC_Het=20, - AC_Hom=0, - AC_Hemi=None, - AN_Adj=47974, - ), - splice_ai=hl.Struct(delta_score=0.0, splice_consequence_id=4), - eigen=hl.Struct(Eigen_phred=2.628000020980835), - ), - ) - ht = hl.read_table(TEST_GRCH37_SNV_INDEL_ANNOTATIONS) - ht = unmap_formatting_annotation_enums( - ht, - ReferenceGenome.GRCh37, - DatasetType.SNV_INDEL, - ) - ht = ht.annotate( - sorted_transcript_consequences=[ht.sorted_transcript_consequences[0]], - ) - self.assertEqual( - ht.collect()[0], - hl.Struct( - locus=hl.Locus(contig=1, position=69134, reference_genome='GRCh37'), - alleles=['A', 'G'], - clinvar=hl.Struct( - alleleId=2193183, - conflictingPathogenicities=None, - goldStars=1, - submitters=['Ambry Genetics'], - conditions=['not specified'], - assertion_ids=[], - pathogenicity_id=14, - ), - rsid=None, - sorted_transcript_consequences=[ - hl.Struct( - amino_acids='E/G', - canonical=1, - codons='gAa/gGa', - gene_id='ENSG00000186092', - hgvsc='ENST00000335137.3:c.44A>G', - hgvsp='ENSP00000334393.3:p.Glu15Gly', - transcript_id='ENST00000335137', - is_lof_nagnag=None, - biotype='protein_coding', - consequence_terms=['missense_variant'], - lof_filters=None, - ), - ], - variant_id='1-69134-A-G', - xpos=1000069134, - gt_stats=hl.Struct(AC=25, AN=1246, AF=0.020064204931259155, hom=10), - CAID='CA502008', - rg38_locus=hl.Locus( - contig='chr1', - position=69134, - reference_genome='GRCh38', - ), - hgmd=None, - gnomad_exomes=hl.Struct( - AF=0.026665963232517242, - AN=18938, - AC=505, - Hom=127, - AF_POPMAX_OR_GLOBAL=0.08191808313131332, - FAF_AF=0.02474386990070343, - Hemi=0, - ), - gnomad_genomes=hl.Struct( - AF=0.0001722949673421681, - AN=5804, - AC=1, - Hom=0, - AF_POPMAX_OR_GLOBAL=0.0005662514013238251, - FAF_AF=0.0, - Hemi=0, - ), - dbnsfp=hl.Struct( - PrimateAI_score=0.37232041358947754, - fathmm_MKL_coding_score=0.056940000504255295, - CADD_phred=15.880000114440918, - SIFT_score=0.1289999932050705, - REVEL_score=0.07500000298023224, - Polyphen2_HVAR_score=0.0010000000474974513, - VEST4_score=0.10700000077486038, - MPC_score=1.8921889066696167, - MutPred_score=0.3779999911785126, - MutationTaster_pred_id=2, - ), - topmed=hl.Struct( - AC=95, - AF=0.0007565619889646769, - AN=125568, - Hom=0, - Het=95, - ), - exac=hl.Struct( - AF_POPMAX=None, - AF=0.0016550000291317701, - AC_Adj=0, - AC_Het=0, - AC_Hom=0, - AC_Hemi=None, - AN_Adj=66, - ), - eigen=hl.Struct(Eigen_phred=1.0019999742507935), - splice_ai=hl.Struct( - delta_score=0.019999999552965164, - splice_consequence_id=2, - ), - key_=1424, - ), - ) - def test_camelcase_array_structexpression_fields(self) -> None: ht = hl.read_table(TEST_SNV_INDEL_ANNOTATIONS) - ht = unmap_formatting_annotation_enums( - ht, - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - ) ht = camelcase_array_structexpression_fields( ht, ReferenceGenome.GRCh38, diff --git a/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py b/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py index 8a49b7e011..ced2ffbb09 100644 --- a/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py +++ b/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py @@ -375,10 +375,10 @@ def test_update_vat_grch37( hgvsc='ENST00000327044.6:c.1667C>T', hgvsp='ENSP00000317992.6:p.Ser556Leu', transcript_id='ENST00000327044', - biotype_id=39, - consequence_term_ids=[9], + biotype='protein_coding', + consequence_terms=['missense_variant'], is_lof_nagnag=None, - lof_filter_ids=[0, 1], + lof_filters=['END_TRUNC', 'INCOMPLETE_CDS'], ), hl.Struct( amino_acids=None, @@ -388,10 +388,10 @@ def test_update_vat_grch37( hgvsc='ENST00000477976.1:n.3114C>T', hgvsp=None, transcript_id='ENST00000477976', - biotype_id=38, - consequence_term_ids=[23, 26], + biotype='lncRNA', + consequence_terms=['non_coding_transcript_exon_variant', 'non_coding_transcript_variant'], is_lof_nagnag=None, - lof_filter_ids=None, + lof_filters=None, ), hl.Struct( amino_acids=None, @@ -401,10 +401,10 @@ def test_update_vat_grch37( hgvsc='ENST00000483767.1:n.523C>T', hgvsp=None, transcript_id='ENST00000483767', - biotype_id=38, - consequence_term_ids=[23, 26], + biotype='lncRNA', + consequence_terms=['non_coding_transcript_exon_variant', 'non_coding_transcript_variant'], is_lof_nagnag=None, - lof_filter_ids=None, + lof_filters=None, ), ], rg38_locus=hl.Locus( @@ -474,7 +474,7 @@ def test_mito_update_vat( alleles=['T', 'C'], common_low_heteroplasmy=False, haplogroup=hl.Struct(is_defining=False), - mitotip=hl.Struct(trna_prediction_id=None), + mitotip=hl.Struct(trna_prediction=None), rg37_locus=hl.Locus( contig='MT', position=3, @@ -570,8 +570,8 @@ def test_sv_multiple_vcf_update_vat( reference_genome='GRCh37', ), sorted_gene_consequences=[ - hl.Struct(gene_id='ENSG00000186092', major_consequence_id=12), - hl.Struct(gene_id='ENSG00000153404', major_consequence_id=12), + hl.Struct(gene_id='ENSG00000186092', major_consequence='NEAREST_TSS'), + hl.Struct(gene_id='ENSG00000153404', major_consequence='NEAREST_TSS'), ], start_locus=hl.Locus( contig='chr1', @@ -580,8 +580,8 @@ def test_sv_multiple_vcf_update_vat( ), strvctvre=hl.Struct(score=None), sv_len=-1, - sv_type_id=2, - sv_type_detail_id=None, + sv_type='BND', + sv_type_detail=None, xpos=1000180928, key_=0, ), @@ -628,12 +628,12 @@ def test_sv_multiple_vcf_update_vat( bothsides_support=True, cpx_intervals=[ hl.Struct( - type_id=8, + type='INS', start=hl.Locus('chr1', 6558902, 'GRCh38'), end=hl.Locus('chr1', 6559723, 'GRCh38'), ), hl.Struct( - type_id=6, + type='DUP', start=hl.Locus('chr1', 6559655, 'GRCh38'), end=hl.Locus('chr1', 6559723, 'GRCh38'), ), @@ -655,7 +655,7 @@ def test_sv_multiple_vcf_update_vat( reference_genome='GRCh37', ), sorted_gene_consequences=[ - hl.Struct(gene_id='ENSG00000173662', major_consequence_id=11), + hl.Struct(gene_id='ENSG00000173662', major_consequence='INTRONIC'), ], start_locus=hl.Locus( contig='chr1', @@ -664,8 +664,8 @@ def test_sv_multiple_vcf_update_vat( ), strvctvre=hl.Struct(score=None), sv_len=821, - sv_type_id=3, - sv_type_detail_id=2, + sv_type='CPX', + sv_type_detail='ME', xpos=1006558902, key_=2, ), @@ -675,12 +675,12 @@ def test_sv_multiple_vcf_update_vat( bothsides_support=False, cpx_intervals=[ hl.Struct( - type_id=5, + type='DEL', start=hl.Locus('chr1', 180540234, 'GRCh38'), end=hl.Locus('chr1', 181074767, 'GRCh38'), ), hl.Struct( - type_id=8, + type='INS', start=hl.Locus('chr1', 181074767, 'GRCh38'), end=hl.Locus('chr1', 181074938, 'GRCh38'), ), @@ -702,10 +702,10 @@ def test_sv_multiple_vcf_update_vat( reference_genome='GRCh37', ), sorted_gene_consequences=[ - hl.Struct(gene_id='ENSG00000135835', major_consequence_id=0), - hl.Struct(gene_id='ENSG00000153029', major_consequence_id=0), - hl.Struct(gene_id='ENSG00000135823', major_consequence_id=0), - hl.Struct(gene_id='ENSG00000143324', major_consequence_id=0), + hl.Struct(gene_id='ENSG00000135835', major_consequence='LOF'), + hl.Struct(gene_id='ENSG00000153029', major_consequence='LOF'), + hl.Struct(gene_id='ENSG00000135823', major_consequence='LOF'), + hl.Struct(gene_id='ENSG00000143324', major_consequence='LOF'), ], start_locus=hl.Locus( contig='chr1', @@ -714,8 +714,8 @@ def test_sv_multiple_vcf_update_vat( ), strvctvre=hl.Struct(score=None), sv_len=534718, - sv_type_id=3, - sv_type_detail_id=9, + sv_type='CPX', + sv_type_detail='delINV', xpos=1180540234, key_=3, ), @@ -725,12 +725,12 @@ def test_sv_multiple_vcf_update_vat( bothsides_support=False, cpx_intervals=[ hl.Struct( - type_id=6, + type='DUP', start=hl.Locus('chr1', 16088760, 'GRCh38'), end=hl.Locus('chr1', 16088835, 'GRCh38'), ), hl.Struct( - type_id=8, + type='INS', start=hl.Locus('chr1', 16088760, 'GRCh38'), end=hl.Locus('chr1', 16089601, 'GRCh38'), ), @@ -752,7 +752,7 @@ def test_sv_multiple_vcf_update_vat( reference_genome='GRCh37', ), sorted_gene_consequences=[ - hl.Struct(gene_id='ENSG00000185519', major_consequence_id=12), + hl.Struct(gene_id='ENSG00000185519', major_consequence='NEAREST_TSS'), ], start_locus=hl.Locus( contig='chr1', @@ -761,8 +761,8 @@ def test_sv_multiple_vcf_update_vat( ), strvctvre=hl.Struct(score=None), sv_len=841, - sv_type_id=3, - sv_type_detail_id=12, + sv_type='CPX', + sv_type_detail='dupINV', xpos=1016088760, key_=4, ), @@ -1025,8 +1025,8 @@ def test_sv_multiple_vcf_update_vat( reference_genome='GRCh37', ), sorted_gene_consequences=[ - hl.Struct(gene_id='ENSG00000186092', major_consequence_id=12), - hl.Struct(gene_id='ENSG00000153404', major_consequence_id=12), + hl.Struct(gene_id='ENSG00000186092', major_consequence='NEAREST_TSS'), + hl.Struct(gene_id='ENSG00000153404', major_consequence='NEAREST_TSS'), ], start_locus=hl.Locus( contig='chr1', @@ -1035,8 +1035,8 @@ def test_sv_multiple_vcf_update_vat( ), strvctvre=hl.Struct(score=None), sv_len=-1, - sv_type_id=2, - sv_type_detail_id=None, + sv_type='BND', + sv_type_detail=None, xpos=1000180928, key_=0, ), @@ -1168,9 +1168,9 @@ def test_gcnv_update_vat_multiple( reference_genome='GRCh37', ), sorted_gene_consequences=[ - hl.Struct(gene_id='ENSG00000117620', major_consequence_id=0), - hl.Struct(gene_id='ENSG00000283761', major_consequence_id=0), - hl.Struct(gene_id='ENSG22222222222', major_consequence_id=None), + hl.Struct(gene_id='ENSG00000117620', major_consequence='LOF'), + hl.Struct(gene_id='ENSG00000283761', major_consequence='LOF'), + hl.Struct(gene_id='ENSG22222222222', major_consequence=None), ], start_locus=hl.Locus( contig='chr1', @@ -1178,7 +1178,7 @@ def test_gcnv_update_vat_multiple( reference_genome='GRCh38', ), strvctvre=hl.Struct(score=hl.eval(hl.float32(0.583))), - sv_type_id=5, + sv_type='DEL', xpos=1100006937, key_=0, ), From b494cff0516762fa2bb4d6f4373ccbd8ed28214d Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 18 Aug 2026 15:27:55 -0400 Subject: [PATCH 107/369] update docs --- loading_pipeline/docs/Historial_Context.md | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/loading_pipeline/docs/Historial_Context.md b/loading_pipeline/docs/Historial_Context.md index b21ae3e495..d7ed8e0a0d 100644 --- a/loading_pipeline/docs/Historial_Context.md +++ b/loading_pipeline/docs/Historial_Context.md @@ -61,11 +61,8 @@ gs://seqr-hail-search-data/v3.1/GRCh38/SNV_INDEL/runs/20260421-125644-303855/new ## Thoughts for future: - Remove Hail for non SNV_INDEL dataset types and callsets < 500 samples. - - Resolve the "Fatal Flaw", two separate representations of production variants, one in Hail and one in Clickhouse. - - If pipeline fails immediately after "UpdateVariantAnnotationsTableWithNewVariantsTask", next run will have - incorrect "new_variants.parquet". - Lightweight replacement for Luigi "run()/complete()/output()/requires()" framework. - - Eliminate scheduler in favor or "tasks" table in seqr postgres. + - Eliminate scheduler in favor or "tasks" table in clickhouse. - Running arbitrary docker images: - Airflow was useful for this, w/ Kubernetes elasticity. - Need to support external computational biology tools. From 49e411b8f47ec23db3118de9031b8fe6ef8c79fe Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 18 Aug 2026 15:28:24 -0400 Subject: [PATCH 108/369] update docs --- loading_pipeline/docs/Historial_Context.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/loading_pipeline/docs/Historial_Context.md b/loading_pipeline/docs/Historial_Context.md index b21ae3e495..eb7a474b25 100644 --- a/loading_pipeline/docs/Historial_Context.md +++ b/loading_pipeline/docs/Historial_Context.md @@ -49,8 +49,6 @@ gs://seqr-hail-search-data/v3.1/GRCh38/SNV_INDEL/runs/20260421-125644-303855/new ``` ### Residues from previous iterations. -- Manual enumeration of consequence terms and SV/Mito types is no longer necessary. - - Was a performance enhancement for Hail backend that can be unrolled. - `complete()` methods are likely overcomplicated. - Each task verifies completeness by running this method and if it returns `True`, skips execution. - Necessary for performance, but as the pipeline has started doing less it is less necessary. From e9a70f15555cf8188d4dc1dc65c518cfe477d817 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 18 Aug 2026 15:30:56 -0400 Subject: [PATCH 109/369] ruff --- loading_pipeline/lib/annotations/gcnv.py | 1 - loading_pipeline/lib/annotations/mito.py | 5 ++- loading_pipeline/lib/annotations/snv_indel.py | 15 +++++-- .../lib/annotations/snv_indel_test.py | 21 ++++++++-- loading_pipeline/lib/annotations/sv.py | 7 +--- loading_pipeline/lib/annotations/vep.py | 5 ++- ...nnotations_table_with_new_variants_test.py | 40 +++++++++++++++---- 7 files changed, 70 insertions(+), 24 deletions(-) diff --git a/loading_pipeline/lib/annotations/gcnv.py b/loading_pipeline/lib/annotations/gcnv.py index 54f80418ed..d9e2a8a603 100644 --- a/loading_pipeline/lib/annotations/gcnv.py +++ b/loading_pipeline/lib/annotations/gcnv.py @@ -4,7 +4,6 @@ from loading_pipeline.lib.annotations import expression_helpers, liftover from loading_pipeline.lib.annotations.enums import ( - SV_CONSEQUENCE_RANKS, SV_TYPES, validated_enum_member, ) diff --git a/loading_pipeline/lib/annotations/mito.py b/loading_pipeline/lib/annotations/mito.py index 36a34e8fa8..a4928f2101 100644 --- a/loading_pipeline/lib/annotations/mito.py +++ b/loading_pipeline/lib/annotations/mito.py @@ -47,7 +47,10 @@ def mito_cn(mt: hl.MatrixTable, **_: Any) -> hl.Expression: def mitotip(ht: hl.Table, **_: Any) -> hl.Expression: return hl.Struct( - trna_prediction=validated_enum_member(ht.mitotip_trna_prediction, MITOTIP_PATHOGENICITIES), + trna_prediction=validated_enum_member( + ht.mitotip_trna_prediction, + MITOTIP_PATHOGENICITIES, + ), ) diff --git a/loading_pipeline/lib/annotations/snv_indel.py b/loading_pipeline/lib/annotations/snv_indel.py index cc474458da..0d785830fe 100644 --- a/loading_pipeline/lib/annotations/snv_indel.py +++ b/loading_pipeline/lib/annotations/snv_indel.py @@ -78,7 +78,9 @@ def sorted_motif_feature_consequences( motif_feature_id=c.motif_feature_id, ), ).filter(lambda c: c.consequence_terms.size() > 0), - lambda c: hl.min(c.consequence_terms.map(lambda t: MOTIF_CONSEQUENCE_TERMS_LOOKUP[t])), + lambda c: hl.min( + c.consequence_terms.map(lambda t: MOTIF_CONSEQUENCE_TERMS_LOOKUP[t]), + ), ), ) @@ -94,12 +96,19 @@ def sorted_regulatory_feature_consequences( lambda c: c.select( biotype=validated_enum_member(c.biotype, REGULATORY_BIOTYPES), consequence_terms=c.consequence_terms.map( - lambda t: validated_enum_member(t, REGULATORY_CONSEQUENCE_TERMS), + lambda t: validated_enum_member( + t, + REGULATORY_CONSEQUENCE_TERMS, + ), ), regulatory_feature_id=c.regulatory_feature_id, ), ).filter(lambda c: c.consequence_terms.size() > 0), - lambda c: hl.min(c.consequence_terms.map(lambda t: REGULATORY_CONSEQUENCE_TERMS_LOOKUP[t])), + lambda c: hl.min( + c.consequence_terms.map( + lambda t: REGULATORY_CONSEQUENCE_TERMS_LOOKUP[t], + ), + ), ), ) diff --git a/loading_pipeline/lib/annotations/snv_indel_test.py b/loading_pipeline/lib/annotations/snv_indel_test.py index 97021081ce..70df03b4f8 100644 --- a/loading_pipeline/lib/annotations/snv_indel_test.py +++ b/loading_pipeline/lib/annotations/snv_indel_test.py @@ -72,7 +72,10 @@ def test_sorted_transcript_consequences_37( hgvsp=None, transcript_id='ENST00000477976', biotype='lncRNA', - consequence_terms=['non_coding_transcript_exon_variant', 'non_coding_transcript_variant'], + consequence_terms=[ + 'non_coding_transcript_exon_variant', + 'non_coding_transcript_variant', + ], is_lof_nagnag=None, lof_filters=None, ), @@ -85,7 +88,10 @@ def test_sorted_transcript_consequences_37( hgvsp=None, transcript_id='ENST00000483767', biotype='lncRNA', - consequence_terms=['non_coding_transcript_exon_variant', 'non_coding_transcript_variant'], + consequence_terms=[ + 'non_coding_transcript_exon_variant', + 'non_coding_transcript_variant', + ], is_lof_nagnag=None, lof_filters=None, ), @@ -175,7 +181,10 @@ def test_sorted_transcript_consequences_38( mane_select=None, mane_plus_clinical=None, biotype='retained_intron', - consequence_terms=['non_coding_transcript_exon_variant', 'non_coding_transcript_variant'], + consequence_terms=[ + 'non_coding_transcript_exon_variant', + 'non_coding_transcript_variant', + ], exon=hl.Struct(index=13, total=17), intron=None, alphamissense=hl.Struct(pathogenicity=0.9700000286102295), @@ -206,7 +215,11 @@ def test_sorted_transcript_consequences_38( mane_select=None, mane_plus_clinical=None, biotype='retained_intron', - consequence_terms=['non_coding_transcript_exon_variant', 'splice_donor_region_variant', 'non_coding_transcript_variant'], + consequence_terms=[ + 'non_coding_transcript_exon_variant', + 'splice_donor_region_variant', + 'non_coding_transcript_variant', + ], exon=hl.Struct(index=1, total=5), intron=None, alphamissense=hl.Struct(pathogenicity=None), diff --git a/loading_pipeline/lib/annotations/sv.py b/loading_pipeline/lib/annotations/sv.py index 518bcad612..cfc99fe025 100644 --- a/loading_pipeline/lib/annotations/sv.py +++ b/loading_pipeline/lib/annotations/sv.py @@ -5,7 +5,6 @@ from loading_pipeline.lib.annotations import liftover from loading_pipeline.lib.annotations.enums import ( - SV_CONSEQUENCE_RANKS, SV_TYPE_DETAILS, SV_TYPES, validated_enum_member, @@ -49,7 +48,6 @@ ) - def _get_cpx_interval( x: hl.StringExpression, reference_genome: ReferenceGenome, @@ -82,10 +80,7 @@ def alleles(ht: hl.Table, **_: Any) -> hl.ArrayExpression: [ 'N', hl.if_else( - ( - hl.is_defined(ht.sv_type_detail) - & (ht.sv_type != 'CPX') - ), + (hl.is_defined(ht.sv_type_detail) & (ht.sv_type != 'CPX')), hl.format( '<%s:%s>', ht.sv_type, diff --git a/loading_pipeline/lib/annotations/vep.py b/loading_pipeline/lib/annotations/vep.py index 7c97ba6019..8e1d41a84f 100644 --- a/loading_pipeline/lib/annotations/vep.py +++ b/loading_pipeline/lib/annotations/vep.py @@ -89,7 +89,10 @@ def vep_110_transcript_consequences_select( existing_inframe_oorfs=c.existing_inframe_oorfs, existing_outofframe_oorfs=c.existing_outofframe_oorfs, existing_uorfs=c.existing_uorfs, - fiveutr_consequence=validated_enum_member(c.fiveutr_consequence, FIVEUTR_CONSEQUENCES), + fiveutr_consequence=validated_enum_member( + c.fiveutr_consequence, + FIVEUTR_CONSEQUENCES, + ), # Annotation documentation here: # https://github.com/ImperialCardioGenetics/UTRannotator?tab=readme-ov-file#the-detailed-annotation-for-each-consequence # NB: diff --git a/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py b/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py index ced2ffbb09..91073b49d6 100644 --- a/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py +++ b/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py @@ -389,7 +389,10 @@ def test_update_vat_grch37( hgvsp=None, transcript_id='ENST00000477976', biotype='lncRNA', - consequence_terms=['non_coding_transcript_exon_variant', 'non_coding_transcript_variant'], + consequence_terms=[ + 'non_coding_transcript_exon_variant', + 'non_coding_transcript_variant', + ], is_lof_nagnag=None, lof_filters=None, ), @@ -402,7 +405,10 @@ def test_update_vat_grch37( hgvsp=None, transcript_id='ENST00000483767', biotype='lncRNA', - consequence_terms=['non_coding_transcript_exon_variant', 'non_coding_transcript_variant'], + consequence_terms=[ + 'non_coding_transcript_exon_variant', + 'non_coding_transcript_variant', + ], is_lof_nagnag=None, lof_filters=None, ), @@ -570,8 +576,14 @@ def test_sv_multiple_vcf_update_vat( reference_genome='GRCh37', ), sorted_gene_consequences=[ - hl.Struct(gene_id='ENSG00000186092', major_consequence='NEAREST_TSS'), - hl.Struct(gene_id='ENSG00000153404', major_consequence='NEAREST_TSS'), + hl.Struct( + gene_id='ENSG00000186092', + major_consequence='NEAREST_TSS', + ), + hl.Struct( + gene_id='ENSG00000153404', + major_consequence='NEAREST_TSS', + ), ], start_locus=hl.Locus( contig='chr1', @@ -655,7 +667,10 @@ def test_sv_multiple_vcf_update_vat( reference_genome='GRCh37', ), sorted_gene_consequences=[ - hl.Struct(gene_id='ENSG00000173662', major_consequence='INTRONIC'), + hl.Struct( + gene_id='ENSG00000173662', + major_consequence='INTRONIC', + ), ], start_locus=hl.Locus( contig='chr1', @@ -752,7 +767,10 @@ def test_sv_multiple_vcf_update_vat( reference_genome='GRCh37', ), sorted_gene_consequences=[ - hl.Struct(gene_id='ENSG00000185519', major_consequence='NEAREST_TSS'), + hl.Struct( + gene_id='ENSG00000185519', + major_consequence='NEAREST_TSS', + ), ], start_locus=hl.Locus( contig='chr1', @@ -1025,8 +1043,14 @@ def test_sv_multiple_vcf_update_vat( reference_genome='GRCh37', ), sorted_gene_consequences=[ - hl.Struct(gene_id='ENSG00000186092', major_consequence='NEAREST_TSS'), - hl.Struct(gene_id='ENSG00000153404', major_consequence='NEAREST_TSS'), + hl.Struct( + gene_id='ENSG00000186092', + major_consequence='NEAREST_TSS', + ), + hl.Struct( + gene_id='ENSG00000153404', + major_consequence='NEAREST_TSS', + ), ], start_locus=hl.Locus( contig='chr1', From 1cf4fcc72055335a7ec3374b13aa0bb534c55b5b Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 18 Aug 2026 15:47:36 -0400 Subject: [PATCH 110/369] remove dead annotations vcf task --- loading_pipeline/lib/paths.py | 14 --- .../tasks/write_variant_annotations_vcf.py | 49 ---------- .../write_variant_annotations_vcf_test.py | 91 ------------------- 3 files changed, 154 deletions(-) delete mode 100644 loading_pipeline/lib/tasks/write_variant_annotations_vcf.py delete mode 100644 loading_pipeline/lib/tasks/write_variant_annotations_vcf_test.py diff --git a/loading_pipeline/lib/paths.py b/loading_pipeline/lib/paths.py index 27e450f7d7..583d40634e 100644 --- a/loading_pipeline/lib/paths.py +++ b/loading_pipeline/lib/paths.py @@ -316,20 +316,6 @@ def variant_annotations_table_path( ) -def variant_annotations_vcf_path( - reference_genome: ReferenceGenome, - dataset_type: DatasetType, -) -> str: - return os.path.join( - pipeline_prefix( - Env.PIPELINE_DATA_DIR, - reference_genome, - dataset_type, - ), - 'annotations.vcf.bgz', - ) - - def new_entries_parquet_path( reference_genome: ReferenceGenome, dataset_type: DatasetType, diff --git a/loading_pipeline/lib/tasks/write_variant_annotations_vcf.py b/loading_pipeline/lib/tasks/write_variant_annotations_vcf.py deleted file mode 100644 index bda611824e..0000000000 --- a/loading_pipeline/lib/tasks/write_variant_annotations_vcf.py +++ /dev/null @@ -1,49 +0,0 @@ -import hail as hl -import hailtop.fs as hfs -import luigi - -from loading_pipeline.lib.annotations.fields import get_fields -from loading_pipeline.lib.paths import ( - variant_annotations_table_path, - variant_annotations_vcf_path, -) -from loading_pipeline.lib.tasks.base.base_loading_run_params import BaseLoadingRunParams -from loading_pipeline.lib.tasks.files import GCSorLocalTarget - - -@luigi.util.inherits(BaseLoadingRunParams) -class WriteVariantAnnotationsVCF(luigi.Task): - def output(self) -> luigi.Target: - return GCSorLocalTarget( - variant_annotations_vcf_path( - self.reference_genome, - self.dataset_type, - ), - ) - - def complete(self) -> bool: - return not self.dataset_type.should_export_to_vcf - - def run(self) -> None: - if not hfs.exists( - variant_annotations_table_path( - self.reference_genome, - self.dataset_type, - ), - ): - return - ht = hl.read_table( - variant_annotations_table_path( - self.reference_genome, - self.dataset_type, - ), - ) - ht = ht.annotate( - **get_fields( - ht, - self.dataset_type.export_vcf_annotation_fns, - **self.param_kwargs, - ), - ) - ht = ht.key_by('locus', 'alleles') - hl.export_vcf(ht, self.output().path, tabix=True) diff --git a/loading_pipeline/lib/tasks/write_variant_annotations_vcf_test.py b/loading_pipeline/lib/tasks/write_variant_annotations_vcf_test.py deleted file mode 100644 index 4bad466b67..0000000000 --- a/loading_pipeline/lib/tasks/write_variant_annotations_vcf_test.py +++ /dev/null @@ -1,91 +0,0 @@ -import gzip -from unittest.mock import Mock, patch - -import hailtop.fs as hfs -import luigi.worker - -from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType -from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS -from loading_pipeline.lib.tasks.update_variant_annotations_table_with_new_variants import ( - UpdateVariantAnnotationsTableWithNewVariantsTask, -) -from loading_pipeline.lib.tasks.write_variant_annotations_vcf import ( - WriteVariantAnnotationsVCF, -) -from loading_pipeline.lib.test.misc import copy_project_pedigree_to_mocked_dir -from loading_pipeline.lib.test.mocked_reference_datasets_testcase import ( - MockedReferenceDatasetsTestCase, -) - -TEST_SV_VCF = 'loading_pipeline/var/test/callsets/sv_1.vcf' -TEST_PEDIGREE_5 = 'loading_pipeline/var/test/pedigrees/test_pedigree_5.tsv' - -GENE_ID_MAPPING = { - 'OR4F5': 'ENSG00000186092', - 'PLEKHG4B': 'ENSG00000153404', - 'OR4F16': 'ENSG00000186192', - 'OR4F29': 'ENSG00000284733', - 'FBXO28': 'ENSG00000143756', - 'SAMD11': 'ENSG00000187634', - 'C1orf174': 'ENSG00000198912', - 'TAS1R1': 'ENSG00000173662', - 'FAM131C': 'ENSG00000185519', - 'RCC2': 'ENSG00000179051', - 'NBPF3': 'ENSG00000142794', - 'AGBL4': 'ENSG00000186094', - 'KIAA1614': 'ENSG00000135835', - 'MR1': 'ENSG00000153029', - 'STX6': 'ENSG00000135823', - 'XPR1': 'ENSG00000143324', -} - - -class WriteVariantAnnotationsVCFTest(MockedReferenceDatasetsTestCase): - @patch( - 'loading_pipeline.lib.tasks.write_new_variants_table.load_gencode_gene_symbol_to_gene_id', - ) - def test_sv_export_vcf( - self, - mock_load_gencode: Mock, - ) -> None: - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_5, - ReferenceGenome.GRCh38, - DatasetType.SV, - SampleType.WGS, - 'R0115_test_project2', - ) - mock_load_gencode.return_value = GENE_ID_MAPPING - worker = luigi.worker.Worker() - update_variant_annotations_task = ( - UpdateVariantAnnotationsTableWithNewVariantsTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SV, - run_id='run_id1', - sample_type=SampleType.WGS, - callset_path=TEST_SV_VCF, - project_guids=['R0115_test_project2'], - validations_to_skip=[ALL_VALIDATIONS], - skip_expect_tdr_metrics=True, - ) - ) - worker.add(update_variant_annotations_task) - worker.run() - self.assertTrue(update_variant_annotations_task.complete()) - write_variant_annotations_vcf_task = WriteVariantAnnotationsVCF( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SV, - run_id='run_id1', - sample_type=SampleType.WGS, - callset_path=TEST_SV_VCF, - ) - worker.add(write_variant_annotations_vcf_task) - worker.run() - self.assertTrue( - hfs.exists( - write_variant_annotations_vcf_task.output().path, - ), - ) - with hfs.open(write_variant_annotations_vcf_task.output().path, 'rb') as f: - buf = f.read() - self.assertTrue(gzip.decompress(buf).startswith(b'##fileformat=VCFv4.2')) From b4d250d2f5cd986df6a0b6ad1efbe7b8fe378f4f Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 18 Aug 2026 15:58:46 -0400 Subject: [PATCH 111/369] depreacte export_all_callset_variants functionality --- loading_pipeline/lib/core/dataset_type.py | 4 --- .../write_new_variant_details_parquet.py | 5 --- .../exports/write_new_variants_parquet.py | 32 +++---------------- 3 files changed, 5 insertions(+), 36 deletions(-) diff --git a/loading_pipeline/lib/core/dataset_type.py b/loading_pipeline/lib/core/dataset_type.py index 1e018f7104..55fa750d33 100644 --- a/loading_pipeline/lib/core/dataset_type.py +++ b/loading_pipeline/lib/core/dataset_type.py @@ -346,10 +346,6 @@ def filter_invalid_sites(self): def should_export_to_vcf(self): return self == DatasetType.SV - @property - def export_all_callset_variants(self): - return self == DatasetType.GCNV - @property def export_vcf_annotation_fns(self) -> list[Callable[..., hl.Expression]]: return { diff --git a/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet.py b/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet.py index 6da793ec53..8db635f77a 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet.py +++ b/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet.py @@ -16,9 +16,6 @@ unmap_formatting_annotation_enums, ) from loading_pipeline.lib.tasks.files import GCSorLocalFolderTarget, GCSorLocalTarget -from loading_pipeline.lib.tasks.update_variant_annotations_table_with_new_variants import ( - UpdateVariantAnnotationsTableWithNewVariantsTask, -) from loading_pipeline.lib.tasks.write_new_variants_table import ( WriteNewVariantsTableTask, ) @@ -39,8 +36,6 @@ def complete(self) -> luigi.Target: return GCSorLocalFolderTarget(self.output().path).exists() def requires(self) -> luigi.Task: - if self.dataset_type.export_all_callset_variants: - return self.clone(UpdateVariantAnnotationsTableWithNewVariantsTask) return self.clone(WriteNewVariantsTableTask) def create_table(self) -> None: diff --git a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet.py b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet.py index 53435376dd..2a7c0e7d7f 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet.py +++ b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet.py @@ -2,11 +2,9 @@ import luigi import luigi.util -from loading_pipeline.lib.misc.callsets import get_callset_ht from loading_pipeline.lib.paths import ( new_variants_parquet_path, new_variants_table_path, - variant_annotations_table_path, ) from loading_pipeline.lib.tasks.base.base_loading_run_params import ( BaseLoadingRunParams, @@ -19,9 +17,6 @@ unmap_formatting_annotation_enums, ) from loading_pipeline.lib.tasks.files import GCSorLocalTarget -from loading_pipeline.lib.tasks.update_variant_annotations_table_with_new_variants import ( - UpdateVariantAnnotationsTableWithNewVariantsTask, -) from loading_pipeline.lib.tasks.write_new_variants_table import ( WriteNewVariantsTableTask, ) @@ -39,33 +34,16 @@ def output(self) -> luigi.Target: ) def requires(self) -> luigi.Task: - if self.dataset_type.export_all_callset_variants: - return self.clone(UpdateVariantAnnotationsTableWithNewVariantsTask) return self.clone(WriteNewVariantsTableTask) def create_table(self) -> None: - if self.dataset_type.export_all_callset_variants: - ht = hl.read_table( - variant_annotations_table_path( - self.reference_genome, - self.dataset_type, - ), - ) - callset_ht = get_callset_ht( + ht = hl.read_table( + new_variants_table_path( self.reference_genome, self.dataset_type, - self.callset_path, - self.project_guids, - ) - ht = ht.semi_join(callset_ht) - else: - ht = hl.read_table( - new_variants_table_path( - self.reference_genome, - self.dataset_type, - self.run_id, - ), - ) + self.run_id, + ), + ) ht = unmap_formatting_annotation_enums( ht, self.reference_genome, From b9873d61209b6edac165df259af160434d8d9384 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 18 Aug 2026 16:06:53 -0400 Subject: [PATCH 112/369] fix missed enums --- loading_pipeline/lib/annotations/shared.py | 2 +- ...nnotations_table_with_new_variants_test.py | 52 ++++++++++++++++--- 2 files changed, 47 insertions(+), 7 deletions(-) diff --git a/loading_pipeline/lib/annotations/shared.py b/loading_pipeline/lib/annotations/shared.py index abeaaac2e5..e6cc6fe376 100644 --- a/loading_pipeline/lib/annotations/shared.py +++ b/loading_pipeline/lib/annotations/shared.py @@ -46,6 +46,6 @@ def sorted_transcript_consequences( return hl.sorted( ht.vep.transcript_consequences.map( vep_85_transcript_consequences_select, - ).filter(lambda c: c.consequence_term_ids.size() > 0), + ).filter(lambda c: c.consequence_terms.size() > 0), transcript_consequences_sort(ht), ) diff --git a/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py b/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py index 91073b49d6..1be1a42394 100644 --- a/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py +++ b/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py @@ -286,13 +286,53 @@ def test_multiple_update_vat( self.assertCountEqual( ht.filter( ht.locus.position <= 878809, # noqa: PLR2004 - ).sorted_transcript_consequences.consequence_term_ids.collect(), + ).sorted_transcript_consequences.consequence_terms.collect(), [ - [[9], [23, 26], [23, 13, 26]], - [[9], [23, 26], [23, 13, 26]], - [[9], [23, 26], [23, 13, 26]], - [[9], [23, 26], [23, 13, 26]], - [[9], [23, 26], [23, 13, 26]], + [ + ['missense_variant'], + ['non_coding_transcript_exon_variant', 'non_coding_transcript_variant'], + [ + 'non_coding_transcript_exon_variant', + 'splice_donor_region_variant', + 'non_coding_transcript_variant', + ], + ], + [ + ['missense_variant'], + ['non_coding_transcript_exon_variant', 'non_coding_transcript_variant'], + [ + 'non_coding_transcript_exon_variant', + 'splice_donor_region_variant', + 'non_coding_transcript_variant', + ], + ], + [ + ['missense_variant'], + ['non_coding_transcript_exon_variant', 'non_coding_transcript_variant'], + [ + 'non_coding_transcript_exon_variant', + 'splice_donor_region_variant', + 'non_coding_transcript_variant', + ], + ], + [ + ['missense_variant'], + ['non_coding_transcript_exon_variant', 'non_coding_transcript_variant'], + [ + 'non_coding_transcript_exon_variant', + 'splice_donor_region_variant', + 'non_coding_transcript_variant', + ], + ], + [ + ['missense_variant'], + ['non_coding_transcript_exon_variant', 'non_coding_transcript_variant'], + [ + 'non_coding_transcript_exon_variant', + 'splice_donor_region_variant', + 'non_coding_transcript_variant', + ], + ], ], ) self.assertCountEqual( From a614e54673a93ae3489604fee5c9906b55804cce Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 18 Aug 2026 16:09:56 -0400 Subject: [PATCH 113/369] ruff --- ...nnotations_table_with_new_variants_test.py | 25 +++++++++++++++---- 1 file changed, 20 insertions(+), 5 deletions(-) diff --git a/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py b/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py index 1be1a42394..8cad208e4d 100644 --- a/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py +++ b/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py @@ -290,7 +290,10 @@ def test_multiple_update_vat( [ [ ['missense_variant'], - ['non_coding_transcript_exon_variant', 'non_coding_transcript_variant'], + [ + 'non_coding_transcript_exon_variant', + 'non_coding_transcript_variant', + ], [ 'non_coding_transcript_exon_variant', 'splice_donor_region_variant', @@ -299,7 +302,10 @@ def test_multiple_update_vat( ], [ ['missense_variant'], - ['non_coding_transcript_exon_variant', 'non_coding_transcript_variant'], + [ + 'non_coding_transcript_exon_variant', + 'non_coding_transcript_variant', + ], [ 'non_coding_transcript_exon_variant', 'splice_donor_region_variant', @@ -308,7 +314,10 @@ def test_multiple_update_vat( ], [ ['missense_variant'], - ['non_coding_transcript_exon_variant', 'non_coding_transcript_variant'], + [ + 'non_coding_transcript_exon_variant', + 'non_coding_transcript_variant', + ], [ 'non_coding_transcript_exon_variant', 'splice_donor_region_variant', @@ -317,7 +326,10 @@ def test_multiple_update_vat( ], [ ['missense_variant'], - ['non_coding_transcript_exon_variant', 'non_coding_transcript_variant'], + [ + 'non_coding_transcript_exon_variant', + 'non_coding_transcript_variant', + ], [ 'non_coding_transcript_exon_variant', 'splice_donor_region_variant', @@ -326,7 +338,10 @@ def test_multiple_update_vat( ], [ ['missense_variant'], - ['non_coding_transcript_exon_variant', 'non_coding_transcript_variant'], + [ + 'non_coding_transcript_exon_variant', + 'non_coding_transcript_variant', + ], [ 'non_coding_transcript_exon_variant', 'splice_donor_region_variant', From 463e4e60df18cfbc6381d53a3d3b4c06a4f5ffb3 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 18 Aug 2026 16:18:44 -0400 Subject: [PATCH 114/369] remove annotations table dependency from SV info field parsing --- loading_pipeline/lib/misc/callsets.py | 23 +---------------------- 1 file changed, 1 insertion(+), 22 deletions(-) diff --git a/loading_pipeline/lib/misc/callsets.py b/loading_pipeline/lib/misc/callsets.py index 41357e5ae2..6d94df2227 100644 --- a/loading_pipeline/lib/misc/callsets.py +++ b/loading_pipeline/lib/misc/callsets.py @@ -1,13 +1,9 @@ import functools import hail as hl -import hailtop.fs as hfs from loading_pipeline.lib.core import DatasetType, ReferenceGenome -from loading_pipeline.lib.paths import ( - remapped_and_subsetted_callset_path, - variant_annotations_table_path, -) +from loading_pipeline.lib.paths import remapped_and_subsetted_callset_path def get_callset_ht( @@ -107,23 +103,6 @@ def get_additional_row_fields( **( {'info.SEQR_INTERNAL_TRUTH_VID': hl.tstr} if dataset_type.re_key_by_seqr_internal_truth_vid - and hfs.exists( - variant_annotations_table_path( - reference_genome, - dataset_type, - ), - ) - and hl.eval( - hl.len( - hl.read_table( - variant_annotations_table_path( - reference_genome, - dataset_type, - ), - ).globals.updates, - ) - > 0, - ) else {} ), } From a35a02a1889ebfe02d6c33e54acbcd130693bb5e Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 18 Aug 2026 16:22:35 -0400 Subject: [PATCH 115/369] fix test --- .../write_new_variants_parquet_test.py | 23 +++---------------- 1 file changed, 3 insertions(+), 20 deletions(-) diff --git a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py index 8bd43fc8be..3cb4cef45d 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py @@ -15,7 +15,6 @@ new_variants_parquet_path, new_variants_table_path, remapped_and_subsetted_callset_path, - variant_annotations_table_path, ) from loading_pipeline.lib.tasks.exports.write_new_variants_parquet import ( WriteNewVariantsParquetTask, @@ -81,12 +80,6 @@ def setUp(self) -> None: ), ) ht = hl.read_table(TEST_GCNV_ANNOTATIONS) - ht.write( - variant_annotations_table_path( - ReferenceGenome.GRCh38, - DatasetType.GCNV, - ), - ) ht.write( remapped_and_subsetted_callset_path( ReferenceGenome.GRCh38, @@ -346,23 +339,13 @@ def test_sv_write_new_variants_parquet_test( ) @mock.patch( - 'loading_pipeline.lib.tasks.exports.write_new_variants_parquet.UpdateVariantAnnotationsTableWithNewVariantsTask', - ) - @mock.patch( - 'loading_pipeline.lib.tasks.exports.write_new_variants_parquet.get_callset_ht', + 'loading_pipeline.lib.tasks.exports.write_new_variants_parquet.WriteNewVariantsTableTask', ) def test_gcnv_write_new_variants_parquet_test( self, - get_callset_ht: Mock, - update_variant_annotations_task: Mock, + write_new_variants_table_task: Mock, ) -> None: - get_callset_ht.return_value = hl.read_table( - variant_annotations_table_path( - ReferenceGenome.GRCh38, - DatasetType.GCNV, - ), - ) - update_variant_annotations_task.return_value = MockCompleteTask() + write_new_variants_table_task.return_value = MockCompleteTask() worker = luigi.worker.Worker() task = WriteNewVariantsParquetTask( reference_genome=ReferenceGenome.GRCh38, From ebd2aa9b770d2e33a3e35b6c89ff36c53f84006c Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 18 Aug 2026 16:38:48 -0400 Subject: [PATCH 116/369] remove unused param --- loading_pipeline/lib/misc/callsets.py | 1 - loading_pipeline/lib/tasks/write_imported_callset.py | 2 -- loading_pipeline/lib/tasks/write_postprocessed_callset.py | 1 - 3 files changed, 4 deletions(-) diff --git a/loading_pipeline/lib/misc/callsets.py b/loading_pipeline/lib/misc/callsets.py index 6d94df2227..1891d7f8dd 100644 --- a/loading_pipeline/lib/misc/callsets.py +++ b/loading_pipeline/lib/misc/callsets.py @@ -81,7 +81,6 @@ def get_callset_mt( def get_additional_row_fields( mt: hl.MatrixTable, - reference_genome: ReferenceGenome, dataset_type: DatasetType, skip_check_sex_and_relatedness: bool, ): diff --git a/loading_pipeline/lib/tasks/write_imported_callset.py b/loading_pipeline/lib/tasks/write_imported_callset.py index db80232bca..99bf616614 100644 --- a/loading_pipeline/lib/tasks/write_imported_callset.py +++ b/loading_pipeline/lib/tasks/write_imported_callset.py @@ -30,7 +30,6 @@ def complete(self) -> luigi.Target: # with a different sex/relatedness flag. additional_row_fields = get_additional_row_fields( mt, - self.reference_genome, self.dataset_type, self.skip_check_sex_and_relatedness, ) @@ -61,7 +60,6 @@ def create_table(self) -> hl.MatrixTable: ) additional_row_fields = get_additional_row_fields( mt, - self.reference_genome, self.dataset_type, self.skip_check_sex_and_relatedness, ) diff --git a/loading_pipeline/lib/tasks/write_postprocessed_callset.py b/loading_pipeline/lib/tasks/write_postprocessed_callset.py index d82258e98a..34f01ce904 100644 --- a/loading_pipeline/lib/tasks/write_postprocessed_callset.py +++ b/loading_pipeline/lib/tasks/write_postprocessed_callset.py @@ -31,7 +31,6 @@ def complete(self) -> luigi.Target: # with a different sex/relatedness flag. additional_row_fields = get_additional_row_fields( mt, - self.reference_genome, self.dataset_type, self.skip_check_sex_and_relatedness, ) From 5fb42c9ddf001f5b1b1e0e54889397da954b7bc8 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 18 Aug 2026 17:07:26 -0400 Subject: [PATCH 117/369] fix test setup --- .../lib/tasks/exports/write_new_variants_parquet_test.py | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py index 3cb4cef45d..4e7b07726d 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py @@ -80,6 +80,13 @@ def setUp(self) -> None: ), ) ht = hl.read_table(TEST_GCNV_ANNOTATIONS) + ht.write( + new_variants_table_path( + ReferenceGenome.GRCh38, + DatasetType.GCNV, + TEST_RUN_ID, + ), + ) ht.write( remapped_and_subsetted_callset_path( ReferenceGenome.GRCh38, From 60535b622fefee9c46d507400710022104b0640b Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Wed, 19 Aug 2026 10:08:35 -0400 Subject: [PATCH 118/369] exisitin parquet export helpers --- loading_pipeline/lib/misc/clickhouse.py | 17 +++++++++++++++++ loading_pipeline/lib/tasks/exports/fields.py | 8 ++++++++ 2 files changed, 25 insertions(+) diff --git a/loading_pipeline/lib/misc/clickhouse.py b/loading_pipeline/lib/misc/clickhouse.py index d214f601bf..7ea1b3ba22 100644 --- a/loading_pipeline/lib/misc/clickhouse.py +++ b/loading_pipeline/lib/misc/clickhouse.py @@ -946,6 +946,23 @@ def direct_insert_all_keys( ) +def export_existing_variants_to_parquet( + table_name_builder: TableNameBuilder, + export_select_fields: str, +) -> None: + variants_table = table_name_builder.dst_table(ClickHouseTable.VARIANTS_MEMORY) + export_table = table_name_builder.src_table(ClickHouseTable.VARIANTS_MEMORY).replace( + 'new_variants', 'existing_variants', + ) + logged_query( + f""" + INSERT INTO FUNCTION {export_table} + SELECT {export_select_fields} + FROM {variants_table} + """, # nosec B608 + ) + + # This is a smattering of shared operations that lacks a better name :/ def finalize_refresh_flow( table_name_builder: TableNameBuilder, diff --git a/loading_pipeline/lib/tasks/exports/fields.py b/loading_pipeline/lib/tasks/exports/fields.py index 97aa6963c4..1d38d0505b 100644 --- a/loading_pipeline/lib/tasks/exports/fields.py +++ b/loading_pipeline/lib/tasks/exports/fields.py @@ -88,6 +88,14 @@ def get_dataset_type_specific_variants_annotations( }[dataset_type](ht) +def get_existing_variants_export_field(dataset_type: DatasetType) -> str: + # TODO real export fields + dt_fields = { + DatasetType.SNV_INDEL: 'sorted_transcript_consequences.gene_id', + }[dataset_type] + return f'key AS key_, xpos {dt_fields}' + + def get_calls_export_fields( ht: hl.Table, fe: hl.Struct, From d07538721de750e28938481beef450e727720291 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Wed, 19 Aug 2026 10:35:35 -0400 Subject: [PATCH 119/369] preselect relevent annotation ht fields --- loading_pipeline/lib/tasks/exports/fields.py | 61 ++++++++++++------- .../exports/write_new_entries_parquet.py | 12 +++- 2 files changed, 48 insertions(+), 25 deletions(-) diff --git a/loading_pipeline/lib/tasks/exports/fields.py b/loading_pipeline/lib/tasks/exports/fields.py index 1d38d0505b..f8fe60ceda 100644 --- a/loading_pipeline/lib/tasks/exports/fields.py +++ b/loading_pipeline/lib/tasks/exports/fields.py @@ -1,7 +1,7 @@ import hail as hl from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType -from loading_pipeline.lib.tasks.exports.misc import reformat_transcripts_for_export +from loading_pipeline.lib.tasks.exports.misc import reformat_transcripts_for_export, snake_to_camelcase FIVE_PERCENT = 0.05 STANDARD_CONTIGS = hl.set( @@ -96,10 +96,25 @@ def get_existing_variants_export_field(dataset_type: DatasetType) -> str: return f'key AS key_, xpos {dt_fields}' -def get_calls_export_fields( +def get_entries_call_annotations_fields( + ht: hl.Table, + dataset_type: DatasetType, +): + if dataset_type == DatasetType.GCNV: + return { + 'start': ht.start_locus.position, + 'end': ht.end_locus.position, + 'num_exon': ht.num_exon, + 'gene_ids': hl.set(ht.sorted_gene_consequences.gene_id), + } + return {} + + +def _get_calls_export_fields( ht: hl.Table, fe: hl.Struct, dataset_type: DatasetType, + call_annotation_fields:set[str], ): return { DatasetType.SNV_INDEL: lambda fe: hl.Struct( @@ -132,13 +147,10 @@ def get_calls_export_fields( cn=fe.CN, qs=fe.QS, defragged=fe.defragged, - start=hl.or_else(fe.sample_start, ht.start_locus.position), - end=hl.or_else(fe.sample_end, ht.end_locus.position), - numExon=hl.or_else(fe.sample_num_exon, ht.num_exon), - geneIds=hl.or_else( - fe.sample_gene_ids, - hl.set(ht.sorted_gene_consequences.gene_id), - ), + **{ + snake_to_camelcase(field): hl.or_else(getattr(fe, f'sample_{field}'), geattr(ht, field)) + for field in call_annotation_fields + }, newCall=fe.concordance.new_call, prevCall=fe.concordance.prev_call, prevOverlap=fe.concordance.prev_overlap, @@ -146,16 +158,31 @@ def get_calls_export_fields( }[dataset_type](fe) +def get_entries_annotations_export_fields( + ht: hl.Table, + dataset_type: DatasetType, +): + fields = { + 'key_': ht.key_, + 'xpos': ht.xpos, + } + if dataset_type in {DatasetType.SV, DatasetType.SNV_INDEL}: + fields['geneIds'] = hl.set(ht.sorted_gene_consequences.gene_id) if dataset_type == DatasetType.SV else ht.set(ht.sorted_gene_consequences.gene_id) + return fields + + def get_entries_export_fields( ht: hl.Table, dataset_type: DatasetType, sample_type: SampleType, project_guid: str, + annotation_fields: set[str], + call_annotation_fields: set[str], ): return { - 'key_': ht.key_, 'project_guid': project_guid, 'family_guid': ht.family_entries.family_guid[0], + **{field: getattr(ht, field) for field in annotation_fields}, **( { 'sample_type': sample_type.value, @@ -163,21 +190,9 @@ def get_entries_export_fields( if dataset_type in {DatasetType.SNV_INDEL, DatasetType.MITO} else {} ), - 'xpos': ht.xpos, - **( - { - 'geneIds': hl.set(ht.sorted_gene_consequences.gene_id) - if dataset_type == DatasetType.SV - else hl.set(ht.sorted_transcript_consequences.gene_id) - if dataset_type == DatasetType.SNV_INDEL - else None, - } - if dataset_type in {DatasetType.SV, DatasetType.SNV_INDEL} - else {} - ), 'filters': ht.filters, 'calls': hl.sorted(ht.family_entries, key=lambda fe: fe.s).map( - lambda fe: get_calls_export_fields(ht, fe, dataset_type), + lambda fe: _get_calls_export_fields(ht, fe, dataset_type, call_annotation_fields), ), 'sign': 1, } diff --git a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py index d60b9475b0..8d5267d6d9 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py +++ b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py @@ -16,7 +16,11 @@ BaseLoadingRunParams, ) from loading_pipeline.lib.tasks.base.base_write_parquet import BaseWriteParquetTask -from loading_pipeline.lib.tasks.exports.fields import get_entries_export_fields +from loading_pipeline.lib.tasks.exports.fields import ( + get_entries_export_fields, + get_entries_annotations_export_fields, + get_entries_call_annotations_fields, +) from loading_pipeline.lib.tasks.files import GCSorLocalTarget from loading_pipeline.lib.tasks.update_variant_annotations_table_with_new_variants import ( UpdateVariantAnnotationsTableWithNewVariantsTask, @@ -73,12 +77,14 @@ def create_table(self) -> None: ) ht = deglobalize_ids(ht) ht = deduplicate_by_most_non_ref_calls(ht) + annotation_fields = get_entries_annotations_export_fields(ht, self.dataset_type) + call_annotation_fields = get_entries_call_annotations_export_fields(ht, self.dataset_type) annotations_ht = hl.read_table( variant_annotations_table_path( self.reference_genome, self.dataset_type, ), - ) + ).select(**annotation_fields, **call_annotation_fields) ht = ht.join(annotations_ht) # the family entries ht will contain rows @@ -94,6 +100,8 @@ def create_table(self) -> None: self.dataset_type, self.sample_type, project_guid, + set(annotation_fields.keys()), + set(call_annotation_fields.keys()), ), ) unioned_ht = unioned_ht.union(ht) if unioned_ht else ht From 0e3e716e550aa7747cb892e7aa9c733bc35dbd1d Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Wed, 19 Aug 2026 10:40:32 -0400 Subject: [PATCH 120/369] ruff --- loading_pipeline/lib/misc/clickhouse.py | 7 +++++-- loading_pipeline/lib/tasks/exports/fields.py | 16 ++++++++++++---- .../tasks/exports/write_new_entries_parquet.py | 8 ++++++-- 3 files changed, 23 insertions(+), 8 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse.py b/loading_pipeline/lib/misc/clickhouse.py index 7ea1b3ba22..62f951f7cc 100644 --- a/loading_pipeline/lib/misc/clickhouse.py +++ b/loading_pipeline/lib/misc/clickhouse.py @@ -951,8 +951,11 @@ def export_existing_variants_to_parquet( export_select_fields: str, ) -> None: variants_table = table_name_builder.dst_table(ClickHouseTable.VARIANTS_MEMORY) - export_table = table_name_builder.src_table(ClickHouseTable.VARIANTS_MEMORY).replace( - 'new_variants', 'existing_variants', + export_table = table_name_builder.src_table( + ClickHouseTable.VARIANTS_MEMORY, + ).replace( + 'new_variants', + 'existing_variants', ) logged_query( f""" diff --git a/loading_pipeline/lib/tasks/exports/fields.py b/loading_pipeline/lib/tasks/exports/fields.py index f8fe60ceda..1723b56895 100644 --- a/loading_pipeline/lib/tasks/exports/fields.py +++ b/loading_pipeline/lib/tasks/exports/fields.py @@ -114,7 +114,7 @@ def _get_calls_export_fields( ht: hl.Table, fe: hl.Struct, dataset_type: DatasetType, - call_annotation_fields:set[str], + call_annotation_fields: set[str], ): return { DatasetType.SNV_INDEL: lambda fe: hl.Struct( @@ -148,7 +148,9 @@ def _get_calls_export_fields( qs=fe.QS, defragged=fe.defragged, **{ - snake_to_camelcase(field): hl.or_else(getattr(fe, f'sample_{field}'), geattr(ht, field)) + snake_to_camelcase(field): hl.or_else( + getattr(fe, f'sample_{field}'), geattr(ht, field) + ) for field in call_annotation_fields }, newCall=fe.concordance.new_call, @@ -167,7 +169,11 @@ def get_entries_annotations_export_fields( 'xpos': ht.xpos, } if dataset_type in {DatasetType.SV, DatasetType.SNV_INDEL}: - fields['geneIds'] = hl.set(ht.sorted_gene_consequences.gene_id) if dataset_type == DatasetType.SV else ht.set(ht.sorted_gene_consequences.gene_id) + fields['geneIds'] = ( + hl.set(ht.sorted_gene_consequences.gene_id) + if dataset_type == DatasetType.SV + else ht.set(ht.sorted_gene_consequences.gene_id) + ) return fields @@ -192,7 +198,9 @@ def get_entries_export_fields( ), 'filters': ht.filters, 'calls': hl.sorted(ht.family_entries, key=lambda fe: fe.s).map( - lambda fe: _get_calls_export_fields(ht, fe, dataset_type, call_annotation_fields), + lambda fe: _get_calls_export_fields( + ht, fe, dataset_type, call_annotation_fields + ), ), 'sign': 1, } diff --git a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py index 8d5267d6d9..a41ac00107 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py +++ b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py @@ -77,8 +77,12 @@ def create_table(self) -> None: ) ht = deglobalize_ids(ht) ht = deduplicate_by_most_non_ref_calls(ht) - annotation_fields = get_entries_annotations_export_fields(ht, self.dataset_type) - call_annotation_fields = get_entries_call_annotations_export_fields(ht, self.dataset_type) + annotation_fields = get_entries_annotations_export_fields( + ht, self.dataset_type + ) + call_annotation_fields = get_entries_call_annotations_export_fields( + ht, self.dataset_type + ) annotations_ht = hl.read_table( variant_annotations_table_path( self.reference_genome, From f2931ce1a7fbff4c4cee60d7aa98a2d56cd47588 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Wed, 19 Aug 2026 10:42:33 -0400 Subject: [PATCH 121/369] ruff --- loading_pipeline/lib/tasks/exports/fields.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/loading_pipeline/lib/tasks/exports/fields.py b/loading_pipeline/lib/tasks/exports/fields.py index 1723b56895..79c005cffc 100644 --- a/loading_pipeline/lib/tasks/exports/fields.py +++ b/loading_pipeline/lib/tasks/exports/fields.py @@ -1,7 +1,10 @@ import hail as hl from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType -from loading_pipeline.lib.tasks.exports.misc import reformat_transcripts_for_export, snake_to_camelcase +from loading_pipeline.lib.tasks.exports.misc import ( + reformat_transcripts_for_export, + snake_to_camelcase, +) FIVE_PERCENT = 0.05 STANDARD_CONTIGS = hl.set( From 9bda45eb81df712b2edc26cdd2e7650ab309c69f Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Wed, 19 Aug 2026 10:46:35 -0400 Subject: [PATCH 122/369] ruff --- loading_pipeline/lib/tasks/exports/fields.py | 4 ++-- .../lib/tasks/exports/write_new_entries_parquet.py | 8 ++++---- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/loading_pipeline/lib/tasks/exports/fields.py b/loading_pipeline/lib/tasks/exports/fields.py index 79c005cffc..5d507f9641 100644 --- a/loading_pipeline/lib/tasks/exports/fields.py +++ b/loading_pipeline/lib/tasks/exports/fields.py @@ -152,7 +152,7 @@ def _get_calls_export_fields( defragged=fe.defragged, **{ snake_to_camelcase(field): hl.or_else( - getattr(fe, f'sample_{field}'), geattr(ht, field) + getattr(fe, f'sample_{field}'), getattr(ht, field), ) for field in call_annotation_fields }, @@ -202,7 +202,7 @@ def get_entries_export_fields( 'filters': ht.filters, 'calls': hl.sorted(ht.family_entries, key=lambda fe: fe.s).map( lambda fe: _get_calls_export_fields( - ht, fe, dataset_type, call_annotation_fields + ht, fe, dataset_type, call_annotation_fields, ), ), 'sign': 1, diff --git a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py index a41ac00107..f7499cec81 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py +++ b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py @@ -17,9 +17,9 @@ ) from loading_pipeline.lib.tasks.base.base_write_parquet import BaseWriteParquetTask from loading_pipeline.lib.tasks.exports.fields import ( - get_entries_export_fields, get_entries_annotations_export_fields, get_entries_call_annotations_fields, + get_entries_export_fields, ) from loading_pipeline.lib.tasks.files import GCSorLocalTarget from loading_pipeline.lib.tasks.update_variant_annotations_table_with_new_variants import ( @@ -78,10 +78,10 @@ def create_table(self) -> None: ht = deglobalize_ids(ht) ht = deduplicate_by_most_non_ref_calls(ht) annotation_fields = get_entries_annotations_export_fields( - ht, self.dataset_type + ht, self.dataset_type, ) - call_annotation_fields = get_entries_call_annotations_export_fields( - ht, self.dataset_type + call_annotation_fields = get_entries_call_annotations_fields( + ht, self.dataset_type, ) annotations_ht = hl.read_table( variant_annotations_table_path( From 4a0cfdfa06426f67780bc725eb04ca3150b70347 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Wed, 19 Aug 2026 10:50:11 -0400 Subject: [PATCH 123/369] ruff --- loading_pipeline/lib/tasks/exports/fields.py | 8 ++++++-- .../lib/tasks/exports/write_new_entries_parquet.py | 6 ++++-- 2 files changed, 10 insertions(+), 4 deletions(-) diff --git a/loading_pipeline/lib/tasks/exports/fields.py b/loading_pipeline/lib/tasks/exports/fields.py index 5d507f9641..92657bb722 100644 --- a/loading_pipeline/lib/tasks/exports/fields.py +++ b/loading_pipeline/lib/tasks/exports/fields.py @@ -152,7 +152,8 @@ def _get_calls_export_fields( defragged=fe.defragged, **{ snake_to_camelcase(field): hl.or_else( - getattr(fe, f'sample_{field}'), getattr(ht, field), + getattr(fe, f'sample_{field}'), + getattr(ht, field), ) for field in call_annotation_fields }, @@ -202,7 +203,10 @@ def get_entries_export_fields( 'filters': ht.filters, 'calls': hl.sorted(ht.family_entries, key=lambda fe: fe.s).map( lambda fe: _get_calls_export_fields( - ht, fe, dataset_type, call_annotation_fields, + ht, + fe, + dataset_type, + call_annotation_fields, ), ), 'sign': 1, diff --git a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py index f7499cec81..801b1b40b1 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py +++ b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py @@ -78,10 +78,12 @@ def create_table(self) -> None: ht = deglobalize_ids(ht) ht = deduplicate_by_most_non_ref_calls(ht) annotation_fields = get_entries_annotations_export_fields( - ht, self.dataset_type, + ht, + self.dataset_type, ) call_annotation_fields = get_entries_call_annotations_fields( - ht, self.dataset_type, + ht, + self.dataset_type, ) annotations_ht = hl.read_table( variant_annotations_table_path( From 6228574f3e835a4e91a321637656f54aac9b683a Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 20 Aug 2026 11:51:47 -0400 Subject: [PATCH 124/369] correct queries for existing variants --- loading_pipeline/lib/misc/clickhouse.py | 6 +++++- loading_pipeline/lib/tasks/exports/fields.py | 8 +++++--- 2 files changed, 10 insertions(+), 4 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse.py b/loading_pipeline/lib/misc/clickhouse.py index 62f951f7cc..f21830a5c6 100644 --- a/loading_pipeline/lib/misc/clickhouse.py +++ b/loading_pipeline/lib/misc/clickhouse.py @@ -950,7 +950,11 @@ def export_existing_variants_to_parquet( table_name_builder: TableNameBuilder, export_select_fields: str, ) -> None: - variants_table = table_name_builder.dst_table(ClickHouseTable.VARIANTS_MEMORY) + variants_table = table_name_builder.dst_table( + ClickHouseTable.VARIANT_DETAILS + if table_name_builder.dataset_type.should_write_new_variant_details + else ClickHouseTable.VARIANTS_MEMORY, + ) export_table = table_name_builder.src_table( ClickHouseTable.VARIANTS_MEMORY, ).replace( diff --git a/loading_pipeline/lib/tasks/exports/fields.py b/loading_pipeline/lib/tasks/exports/fields.py index 92657bb722..c32d2f7260 100644 --- a/loading_pipeline/lib/tasks/exports/fields.py +++ b/loading_pipeline/lib/tasks/exports/fields.py @@ -92,11 +92,13 @@ def get_dataset_type_specific_variants_annotations( def get_existing_variants_export_field(dataset_type: DatasetType) -> str: - # TODO real export fields dt_fields = { - DatasetType.SNV_INDEL: 'sorted_transcript_consequences.gene_id', + DatasetType.SNV_INDEL: ', transcripts.geneId AS geneIds', + DatasetType.MITO: '', + DatasetType.SV: ', xpos, end, endChrom, sortedGeneConsequences.geneId AS geneIds', + DatasetType.GCNV: ', xpos, pos AS start, end, numExon as num_exon, sortedGeneConsequences.geneId AS gene_ids', }[dataset_type] - return f'key AS key_, xpos {dt_fields}' + return f'key AS key_, variantId AS variant_id {dt_fields}' def get_entries_call_annotations_fields( From b44adc387a8ec9e213aca790aa19572c0b6fe95a Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 20 Aug 2026 12:32:15 -0400 Subject: [PATCH 125/369] add export task --- loading_pipeline/lib/misc/clickhouse.py | 21 ++++++---- loading_pipeline/lib/paths.py | 15 +++++++ .../tasks/write_existing_variants_parquet.py | 40 +++++++++++++++++++ 3 files changed, 68 insertions(+), 8 deletions(-) create mode 100644 loading_pipeline/lib/tasks/write_existing_variants_parquet.py diff --git a/loading_pipeline/lib/misc/clickhouse.py b/loading_pipeline/lib/misc/clickhouse.py index f21830a5c6..5db45d36c8 100644 --- a/loading_pipeline/lib/misc/clickhouse.py +++ b/loading_pipeline/lib/misc/clickhouse.py @@ -16,6 +16,7 @@ from loading_pipeline.lib.logger import get_logger from loading_pipeline.lib.misc.retry import retry from loading_pipeline.lib.paths import ( + existing_variants_parquet_path, new_entries_parquet_path, new_variant_details_parquet_path, new_variants_parquet_path, @@ -39,6 +40,7 @@ class ClickHouseTable(StrEnum): ENTRIES = 'entries' PROJECT_GT_STATS = 'project_gt_stats' GT_STATS = 'gt_stats' + EXISTING_VARIANTS = 'existing_variants' @property def src_path_fn(self) -> Callable: @@ -52,6 +54,7 @@ def src_path_fn(self) -> Callable: ), ClickHouseTable.VARIANT_DETAILS: new_variant_details_parquet_path, ClickHouseTable.ENTRIES: new_entries_parquet_path, + ClickHouseTable.EXISTING_VARIANTS: existing_variants_parquet_path, }[self] @property @@ -947,20 +950,22 @@ def direct_insert_all_keys( def export_existing_variants_to_parquet( - table_name_builder: TableNameBuilder, + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + run_id: str, export_select_fields: str, ) -> None: + table_name_builder = TableNameBuilder( + reference_genome, + dataset_type, + run_id, + ) variants_table = table_name_builder.dst_table( ClickHouseTable.VARIANT_DETAILS - if table_name_builder.dataset_type.should_write_new_variant_details + if dataset_type.should_write_new_variant_details else ClickHouseTable.VARIANTS_MEMORY, ) - export_table = table_name_builder.src_table( - ClickHouseTable.VARIANTS_MEMORY, - ).replace( - 'new_variants', - 'existing_variants', - ) + export_table = table_name_builder.src_table(ClickHouseTable.EXISTING_VARIANTS) logged_query( f""" INSERT INTO FUNCTION {export_table} diff --git a/loading_pipeline/lib/paths.py b/loading_pipeline/lib/paths.py index 583d40634e..922433cbfe 100644 --- a/loading_pipeline/lib/paths.py +++ b/loading_pipeline/lib/paths.py @@ -361,6 +361,21 @@ def new_variants_parquet_path( ) +def existing_variants_parquet_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + run_id: str, +) -> str: + return os.path.join( + runs_path( + reference_genome, + dataset_type, + ), + run_id, + 'existing_variants.parquet', + ) + + def new_variants_table_path( reference_genome: ReferenceGenome, dataset_type: DatasetType, diff --git a/loading_pipeline/lib/tasks/write_existing_variants_parquet.py b/loading_pipeline/lib/tasks/write_existing_variants_parquet.py new file mode 100644 index 0000000000..143513c772 --- /dev/null +++ b/loading_pipeline/lib/tasks/write_existing_variants_parquet.py @@ -0,0 +1,40 @@ +import csv + +import luigi +import luigi.util + +from loading_pipeline.lib.logger import get_logger +from loading_pipeline.lib.misc.clickhouse import export_existing_variants_to_parquet +from loading_pipeline.lib.paths import existing_variants_parquet_path +from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( + BaseLoadingPipelineParams, +) +from loading_pipeline.lib.tasks.exports.fields import get_existing_variants_export_field +from loading_pipeline.lib.tasks.files import GCSorLocalTarget + +logger = get_logger(__name__) + + +@luigi.util.inherits(BaseLoadingPipelineParams) +class WriteExistingVariantsParquetTask(luigi.Task): + + def output(self) -> luigi.Target: + return GCSorLocalTarget( + existing_variants_parquet_path( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + ) + + def complete(self) -> luigi.Target: + return GCSorLocalFolderTarget(self.output().path).exists() + + def run(self): + export_select_fields = get_existing_variants_export_field(self.dataset_type) + export_existing_variants_to_parquet( + self.reference_genome, + self.dataset_type, + self.run_id, + export_select_fields, + ) From 0108792e641c9cdedbe195c7dd7d3917df2dbad0 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 20 Aug 2026 12:50:12 -0400 Subject: [PATCH 126/369] ruff --- loading_pipeline/lib/tasks/write_existing_variants_parquet.py | 1 - 1 file changed, 1 deletion(-) diff --git a/loading_pipeline/lib/tasks/write_existing_variants_parquet.py b/loading_pipeline/lib/tasks/write_existing_variants_parquet.py index 143513c772..fc89e29f4e 100644 --- a/loading_pipeline/lib/tasks/write_existing_variants_parquet.py +++ b/loading_pipeline/lib/tasks/write_existing_variants_parquet.py @@ -17,7 +17,6 @@ @luigi.util.inherits(BaseLoadingPipelineParams) class WriteExistingVariantsParquetTask(luigi.Task): - def output(self) -> luigi.Target: return GCSorLocalTarget( existing_variants_parquet_path( From 7c65024f781dbffbb8d37a984c146fbe10701a29 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 20 Aug 2026 12:53:23 -0400 Subject: [PATCH 127/369] import clean up --- .../lib/tasks/write_existing_variants_parquet.py | 5 ----- 1 file changed, 5 deletions(-) diff --git a/loading_pipeline/lib/tasks/write_existing_variants_parquet.py b/loading_pipeline/lib/tasks/write_existing_variants_parquet.py index fc89e29f4e..3900ea2b58 100644 --- a/loading_pipeline/lib/tasks/write_existing_variants_parquet.py +++ b/loading_pipeline/lib/tasks/write_existing_variants_parquet.py @@ -1,9 +1,6 @@ -import csv - import luigi import luigi.util -from loading_pipeline.lib.logger import get_logger from loading_pipeline.lib.misc.clickhouse import export_existing_variants_to_parquet from loading_pipeline.lib.paths import existing_variants_parquet_path from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( @@ -12,8 +9,6 @@ from loading_pipeline.lib.tasks.exports.fields import get_existing_variants_export_field from loading_pipeline.lib.tasks.files import GCSorLocalTarget -logger = get_logger(__name__) - @luigi.util.inherits(BaseLoadingPipelineParams) class WriteExistingVariantsParquetTask(luigi.Task): From e16a7827f6881afeb424a496347da7f452468a20 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 20 Aug 2026 12:56:41 -0400 Subject: [PATCH 128/369] fix import --- .../lib/tasks/write_existing_variants_parquet.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/loading_pipeline/lib/tasks/write_existing_variants_parquet.py b/loading_pipeline/lib/tasks/write_existing_variants_parquet.py index 3900ea2b58..3c2a577b2c 100644 --- a/loading_pipeline/lib/tasks/write_existing_variants_parquet.py +++ b/loading_pipeline/lib/tasks/write_existing_variants_parquet.py @@ -7,7 +7,10 @@ BaseLoadingPipelineParams, ) from loading_pipeline.lib.tasks.exports.fields import get_existing_variants_export_field -from loading_pipeline.lib.tasks.files import GCSorLocalTarget +from loading_pipeline.lib.tasks.files import ( + GCSorLocalFolderTarget, + GCSorLocalTarget, +) @luigi.util.inherits(BaseLoadingPipelineParams) From 24dadae9aae8c0b8fcdc0afd19f04c0b6a2433de Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 20 Aug 2026 13:14:24 -0400 Subject: [PATCH 129/369] test clickhous eparquet export --- .../lib/test/fixtures/clickhouse_test.json | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/loading_pipeline/lib/test/fixtures/clickhouse_test.json b/loading_pipeline/lib/test/fixtures/clickhouse_test.json index b4e6cdbf1a..d77b756b73 100644 --- a/loading_pipeline/lib/test/fixtures/clickhouse_test.json +++ b/loading_pipeline/lib/test/fixtures/clickhouse_test.json @@ -268,7 +268,15 @@ "fields": { "key": 1, "variant_id": "a", - "transcripts": [], + "transcripts": [ + [ + [0.9978], "L/F", "protein_coding", 1, "ttA/ttC", ["missense_variant"], [2, 9], "ENSG00000177000", + "ENST00000383791.8:c.156A>C", "ENSP00000373301.3:p.Leu52Phe", [null, null], [null, []], "missense_variant", + null, "NM_004844.5", "NM_004844.5", [false], "ENST00000383791", 0, [null, null, null, [ + null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null + ], null] + ] + ], "sorted_motif_feature_consequences": [], "sorted_regulatory_feature_consequences": [] } From 61f61a3b445a2f1c4afb96f4d946621a1b149cc4 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 20 Aug 2026 13:14:48 -0400 Subject: [PATCH 130/369] test clickhous eparquet export --- .../write_existing_variants_parquet_test.py | 78 +++++++++++++++++++ 1 file changed, 78 insertions(+) create mode 100644 loading_pipeline/lib/tasks/write_existing_variants_parquet_test.py diff --git a/loading_pipeline/lib/tasks/write_existing_variants_parquet_test.py b/loading_pipeline/lib/tasks/write_existing_variants_parquet_test.py new file mode 100644 index 0000000000..5de6e23c92 --- /dev/null +++ b/loading_pipeline/lib/tasks/write_existing_variants_parquet_test.py @@ -0,0 +1,78 @@ +from typing import ClassVar + +import luigi.worker +import pandas as pd + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome +from loading_pipeline.lib.paths import existing_variants_parquet_path +from loading_pipeline.lib.tasks.write_existing_variants_parquet import ( + WriteExistingVariantsParquetTask, +) +from loading_pipeline.lib.test.clickhouse_schema_testcase import ( + ClickhouseSchemaTestCase, +) +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + +TEST_RUN_ID = 'manual__2024-04-03' + + +class WriteExistingVariantsParquetTest(MockedDatarootTestCase, ClickhouseSchemaTestCase): + fixtures: ClassVar = ['clickhouse_test'] + + def _run_task( + self, + dataset_type: DatasetType, + reference_genome: ReferenceGenome = ReferenceGenome.GRCh38, + ) -> pd.DataFrame: + worker = luigi.worker.Worker() + task = WriteExistingVariantsParquetTask( + reference_genome=reference_genome, + dataset_type=dataset_type, + run_id=TEST_RUN_ID, + ) + worker.add(task) + worker.run() + self.assertTrue(task.output().exists()) + self.assertTrue(task.complete()) + return pd.read_parquet( + existing_variants_parquet_path(reference_genome, dataset_type, TEST_RUN_ID), + ) + + def test_snv_indel(self): + df = self._run_task(DatasetType.SNV_INDEL) + self.assertEqual(list(df.columns), ['key_', 'variant_id', 'geneIds']) + df = df.sort_values('key_').reset_index(drop=True) + self.assertEqual( + df[['key_', 'variant_id', 'geneIds']].to_dict('records'), + [ + {'key_': 1, 'variant_id': 'a', 'geneIds': ['ENSG00000177000']}, + {'key_': 7, 'variant_id': 'c', 'geneIds': []}, + {'key_': 10, 'variant_id': 'b', 'geneIds': []}, + ], + ) + + def test_grch37_snv_indel(self): + df = self._run_task(DatasetType.SNV_INDEL, reference_genome=ReferenceGenome.GRCh37) + self.assertEqual(list(df.columns), ['key_', 'variant_id', 'geneIds']) + self.assertEqual(len(df), 0) + + def test_mito(self): + df = self._run_task(DatasetType.MITO) + self.assertEqual(list(df.columns), ['key_', 'variant_id']) + self.assertEqual(len(df), 0) + + def test_sv(self): + df = self._run_task(DatasetType.SV) + self.assertEqual( + list(df.columns), + ['key_', 'variant_id', 'xpos', 'end', 'endChrom', 'geneIds'], + ) + self.assertEqual(len(df), 0) + + def test_gcnv(self): + df = self._run_task(DatasetType.GCNV) + self.assertEqual( + list(df.columns), + ['key_', 'variant_id', 'xpos', 'start', 'end', 'num_exon', 'gene_ids'], + ) + self.assertEqual(len(df), 0) From 1866f204f1b18d989081e33d90f1c25fdc7156dc Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 20 Aug 2026 13:19:41 -0400 Subject: [PATCH 131/369] better fixture data --- loading_pipeline/lib/misc/clickhouse_test.py | 8 ++++---- .../write_existing_variants_parquet_test.py | 16 +++++++++++----- .../lib/test/fixtures/clickhouse_test.json | 6 +++--- 3 files changed, 18 insertions(+), 12 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index 3d2bf5fde7..0ed3aa8b15 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -435,8 +435,8 @@ def test_direct_insert_all_keys(self): (2, '2-14-A-T'), (3, 'Y-19-A-C'), (4, 'M-12-C-G'), - (7, 'c'), - (10, 'b'), + (7, '7-1234567-AGT-A'), + (10, '10-987654-G-A'), ], ) @@ -1008,8 +1008,8 @@ def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_typ (2, '2-14-A-T'), (3, 'Y-19-A-C'), (4, 'M-12-C-G'), - (7, 'c'), - (10, 'b'), + (7, '7-1234567-AGT-A'), + (10, '10-987654-G-A'), ], ) diff --git a/loading_pipeline/lib/tasks/write_existing_variants_parquet_test.py b/loading_pipeline/lib/tasks/write_existing_variants_parquet_test.py index 5de6e23c92..0bee344d0d 100644 --- a/loading_pipeline/lib/tasks/write_existing_variants_parquet_test.py +++ b/loading_pipeline/lib/tasks/write_existing_variants_parquet_test.py @@ -16,7 +16,10 @@ TEST_RUN_ID = 'manual__2024-04-03' -class WriteExistingVariantsParquetTest(MockedDatarootTestCase, ClickhouseSchemaTestCase): +class WriteExistingVariantsParquetTest( + MockedDatarootTestCase, + ClickhouseSchemaTestCase, +): fixtures: ClassVar = ['clickhouse_test'] def _run_task( @@ -45,14 +48,17 @@ def test_snv_indel(self): self.assertEqual( df[['key_', 'variant_id', 'geneIds']].to_dict('records'), [ - {'key_': 1, 'variant_id': 'a', 'geneIds': ['ENSG00000177000']}, - {'key_': 7, 'variant_id': 'c', 'geneIds': []}, - {'key_': 10, 'variant_id': 'b', 'geneIds': []}, + {'key_': 1, 'variant_id': '1-10059-C-T', 'geneIds': ['ENSG00000177000']}, + {'key_': 7, 'variant_id': '7-1234567-AGT-A', 'geneIds': []}, + {'key_': 10, 'variant_id': '10-987654-G-A', 'geneIds': []}, ], ) def test_grch37_snv_indel(self): - df = self._run_task(DatasetType.SNV_INDEL, reference_genome=ReferenceGenome.GRCh37) + df = self._run_task( + DatasetType.SNV_INDEL, + reference_genome=ReferenceGenome.GRCh37, + ) self.assertEqual(list(df.columns), ['key_', 'variant_id', 'geneIds']) self.assertEqual(len(df), 0) diff --git a/loading_pipeline/lib/test/fixtures/clickhouse_test.json b/loading_pipeline/lib/test/fixtures/clickhouse_test.json index d77b756b73..46d0fae32f 100644 --- a/loading_pipeline/lib/test/fixtures/clickhouse_test.json +++ b/loading_pipeline/lib/test/fixtures/clickhouse_test.json @@ -267,7 +267,7 @@ "pk": 1, "fields": { "key": 1, - "variant_id": "a", + "variant_id": "1-10059-C-T", "transcripts": [ [ [0.9978], "L/F", "protein_coding", 1, "ttA/ttC", ["missense_variant"], [2, 9], "ENSG00000177000", @@ -286,7 +286,7 @@ "pk": 7, "fields": { "key": 7, - "variant_id": "c", + "variant_id": "7-1234567-AGT-A", "transcripts": [], "sorted_motif_feature_consequences": [], "sorted_regulatory_feature_consequences": [] @@ -297,7 +297,7 @@ "pk": 10, "fields": { "key": 10, - "variant_id": "b", + "variant_id": "10-987654-G-A", "transcripts": [], "sorted_motif_feature_consequences": [], "sorted_regulatory_feature_consequences": [] From 8ccddd488744d15a3709cc80e72749980d815eb6 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 20 Aug 2026 13:22:54 -0400 Subject: [PATCH 132/369] ruff --- .../lib/tasks/write_existing_variants_parquet_test.py | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/loading_pipeline/lib/tasks/write_existing_variants_parquet_test.py b/loading_pipeline/lib/tasks/write_existing_variants_parquet_test.py index 0bee344d0d..78bebda2c0 100644 --- a/loading_pipeline/lib/tasks/write_existing_variants_parquet_test.py +++ b/loading_pipeline/lib/tasks/write_existing_variants_parquet_test.py @@ -48,7 +48,11 @@ def test_snv_indel(self): self.assertEqual( df[['key_', 'variant_id', 'geneIds']].to_dict('records'), [ - {'key_': 1, 'variant_id': '1-10059-C-T', 'geneIds': ['ENSG00000177000']}, + { + 'key_': 1, + 'variant_id': '1-10059-C-T', + 'geneIds': ['ENSG00000177000'], + }, {'key_': 7, 'variant_id': '7-1234567-AGT-A', 'geneIds': []}, {'key_': 10, 'variant_id': '10-987654-G-A', 'geneIds': []}, ], From 4b6bc5ba376daf4f16993ef109a71211ffa6e07b Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 20 Aug 2026 13:48:11 -0400 Subject: [PATCH 133/369] diagram adjustments --- loading_pipeline/docs/Diagrams.md | 23 +++++++++++------------ 1 file changed, 11 insertions(+), 12 deletions(-) diff --git a/loading_pipeline/docs/Diagrams.md b/loading_pipeline/docs/Diagrams.md index 14c162759e..211d7abd31 100644 --- a/loading_pipeline/docs/Diagrams.md +++ b/loading_pipeline/docs/Diagrams.md @@ -8,17 +8,19 @@ WritePostprocessedCallsetTask (split multi, deduplicate) | - v - ValidateCallsetTask - (validation checks) - | _______________|_______________ | | v v - WriteSexCheckTableTask WriteRelatednessCheckTableTask + WriteSexCheckTableTask ValidateCallsetTask + | (validation checks) | | - v v - WriteRelatednessCheckTsvTask + | v + | WriteRelatednessCheckTableTask + | | + | v + | WriteRelatednessCheckTsvTask + | | + |_______________________________| | v _____________________|_____________________ @@ -44,11 +46,8 @@ v v v WriteNewEntries... WriteNewVariants... WriteNewVariantDetails... ParquetTask ParquetTask ParquetTask - | | (optional) - | [also requires] | [or just] - | RemappedCallsets | WriteNewVariantsTableTask - | - |_______________________| + | | (optional) + |___________________________|_______________________| | v RunPipelineTask From c643f87b6530dc641ec67352ae3bf1210855dc5b Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 20 Aug 2026 13:59:23 -0400 Subject: [PATCH 134/369] fix run args --- .../lib/tasks/write_existing_variants_parquet.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/loading_pipeline/lib/tasks/write_existing_variants_parquet.py b/loading_pipeline/lib/tasks/write_existing_variants_parquet.py index 3c2a577b2c..6c9ff6126a 100644 --- a/loading_pipeline/lib/tasks/write_existing_variants_parquet.py +++ b/loading_pipeline/lib/tasks/write_existing_variants_parquet.py @@ -3,8 +3,8 @@ from loading_pipeline.lib.misc.clickhouse import export_existing_variants_to_parquet from loading_pipeline.lib.paths import existing_variants_parquet_path -from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( - BaseLoadingPipelineParams, +from loading_pipeline.lib.tasks.base.base_loading_run_params import ( + BaseLoadingRunParams, ) from loading_pipeline.lib.tasks.exports.fields import get_existing_variants_export_field from loading_pipeline.lib.tasks.files import ( @@ -13,7 +13,7 @@ ) -@luigi.util.inherits(BaseLoadingPipelineParams) +@luigi.util.inherits(BaseLoadingRunParams) class WriteExistingVariantsParquetTask(luigi.Task): def output(self) -> luigi.Target: return GCSorLocalTarget( From e023b2a59d92cfc080304b49661e37a883236cab Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 20 Aug 2026 14:06:38 -0400 Subject: [PATCH 135/369] remove old annotations ht task --- .../exports/write_new_entries_parquet.py | 10 +- loading_pipeline/lib/tasks/run_pipeline.py | 4 - ...ant_annotations_table_with_new_variants.py | 134 -- ...nnotations_table_with_new_variants_test.py | 1344 ----------------- 4 files changed, 5 insertions(+), 1487 deletions(-) delete mode 100644 loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants.py delete mode 100644 loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py diff --git a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py index 801b1b40b1..c2ac1af158 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py +++ b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py @@ -22,14 +22,14 @@ get_entries_export_fields, ) from loading_pipeline.lib.tasks.files import GCSorLocalTarget -from loading_pipeline.lib.tasks.update_variant_annotations_table_with_new_variants import ( - UpdateVariantAnnotationsTableWithNewVariantsTask, +from loading_pipeline.lib.tasks.write_new_variants_table import ( + WriteNewVariantsTableTask ) from loading_pipeline.lib.tasks.write_remapped_and_subsetted_callset import ( WriteRemappedAndSubsettedCallsetTask, ) -ANNOTATIONS_TABLE_TASK = 'annotations_table_task' +VARIANTS_TABLE_TASK = 'variants_table_task' REMAPPED_AND_SUBSETTED_CALLSET_TASKS = 'remapped_and_subsetted_callset_tasks' @@ -46,8 +46,8 @@ def output(self) -> luigi.Target: def requires(self) -> dict[str, luigi.Task]: return { - ANNOTATIONS_TABLE_TASK: self.clone( - UpdateVariantAnnotationsTableWithNewVariantsTask, + VARIANTS_TABLE_TASK: self.clone( + WriteNewVariantsTableTask, ), REMAPPED_AND_SUBSETTED_CALLSET_TASKS: [ self.clone( diff --git a/loading_pipeline/lib/tasks/run_pipeline.py b/loading_pipeline/lib/tasks/run_pipeline.py index e4bb2993e8..765ec92e65 100644 --- a/loading_pipeline/lib/tasks/run_pipeline.py +++ b/loading_pipeline/lib/tasks/run_pipeline.py @@ -13,9 +13,6 @@ from loading_pipeline.lib.tasks.exports.write_new_variants_parquet import ( WriteNewVariantsParquetTask, ) -from loading_pipeline.lib.tasks.update_variant_annotations_table_with_new_variants import ( - UpdateVariantAnnotationsTableWithNewVariantsTask, -) from loading_pipeline.lib.tasks.write_metadata_for_run import WriteMetadataForRunTask @@ -26,7 +23,6 @@ class RunPipelineTask(luigi.WrapperTask): def requires(self): return [ self.clone(WriteMetadataForRunTask), - self.clone(UpdateVariantAnnotationsTableWithNewVariantsTask), self.clone(WriteNewEntriesParquetTask), self.clone(WriteNewVariantsParquetTask), *( diff --git a/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants.py b/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants.py deleted file mode 100644 index c44c10c49e..0000000000 --- a/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants.py +++ /dev/null @@ -1,134 +0,0 @@ -import hail as hl -import luigi -import luigi.util - -from loading_pipeline.lib.annotations.fields import get_fields -from loading_pipeline.lib.misc.callsets import get_callset_ht -from loading_pipeline.lib.misc.io import remap_pedigree_hash -from loading_pipeline.lib.paths import ( - new_variants_table_path, - project_pedigree_path, - variant_annotations_table_path, -) -from loading_pipeline.lib.tasks.base.base_loading_run_params import ( - BaseLoadingRunParams, -) -from loading_pipeline.lib.tasks.base.base_update import ( - BaseUpdateTask, -) -from loading_pipeline.lib.tasks.files import GCSorLocalTarget -from loading_pipeline.lib.tasks.write_new_variants_table import ( - WriteNewVariantsTableTask, -) - - -@luigi.util.inherits(BaseLoadingRunParams) -class UpdateVariantAnnotationsTableWithNewVariantsTask( - BaseUpdateTask, -): - def output(self) -> luigi.Target: - return GCSorLocalTarget( - variant_annotations_table_path( - self.reference_genome, - self.dataset_type, - ), - ) - - def requires(self) -> list[luigi.Task]: - return [ - *super().requires(), - self.clone(WriteNewVariantsTableTask), - ] - - def complete(self) -> bool: - return super().complete() and hl.eval( - hl.bind( - lambda updates: hl.all( - [ - updates.contains( - hl.Struct( - callset=self.callset_path, - project_guid=project_guid, - remap_pedigree_hash=remap_pedigree_hash( - project_pedigree_path( - self.reference_genome, - self.dataset_type, - self.sample_type, - project_guid, - ), - ), - ), - ) - for project_guid in self.project_guids - ], - ), - hl.read_table(self.output().path).updates, - ), - ) - - def initialize_table(self) -> hl.Table: - key_type = self.dataset_type.table_key_type(self.reference_genome) - return hl.Table.parallelize( - [], - key_type, - key=key_type.fields, - globals=hl.Struct( - enums=hl.Struct(), - updates=hl.empty_set( - hl.tstruct( - callset=hl.tstr, - project_guid=hl.tstr, - remap_pedigree_hash=hl.tint32, - ), - ), - max_key_=hl.int64(-1), - ), - ) - - def update_table(self, ht: hl.Table) -> hl.Table: - # Gracefully handle case for on-premises uses - # where key_ field is not present and migration was not run. - if not hasattr(ht, 'key_'): - ht = ht.add_index(name='key_') - ht = ht.annotate_globals(max_key_=(ht.count() - 1)) - - new_variants_ht = hl.read_table( - new_variants_table_path( - self.reference_genome, - self.dataset_type, - self.run_id, - ), - ) - - # Union with the new variants table and annotate with the lookup table. - ht = ht.union(new_variants_ht, unify=True) - - if self.dataset_type.variant_frequency_annotation_fns: - # new_variants_ht consists of variants present in the new callset, fully annotated, - # but NOT present in the existing annotations table. - # callset_variants_ht consists of variants present in the new callset, fully annotated, - # and either present or not present in the existing annotations table. - callset_ht = get_callset_ht( - self.reference_genome, - self.dataset_type, - self.callset_path, - self.project_guids, - ) - callset_variants_ht = ht.semi_join(callset_ht) - non_callset_variants_ht = ht.anti_join(callset_ht) - callset_variants_ht = callset_variants_ht.annotate( - **get_fields( - callset_variants_ht, - self.dataset_type.variant_frequency_annotation_fns, - callset_ht=callset_ht, - **self.param_kwargs, - ), - ) - ht = non_callset_variants_ht.union(callset_variants_ht, unify=True) - - new_variants_ht_globals = new_variants_ht.index_globals() - return ht.select_globals( - enums=new_variants_ht_globals.enums, - updates=ht.updates.union(new_variants_ht_globals.updates), - max_key_=ht.aggregate(hl.agg.max(ht.key_)), - ) diff --git a/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py b/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py deleted file mode 100644 index 0f90c6dcdb..0000000000 --- a/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py +++ /dev/null @@ -1,1344 +0,0 @@ -import functools -from unittest.mock import Mock, PropertyMock, patch - -import hail as hl -import luigi.worker - -from loading_pipeline.lib.annotations.enums import ( - BIOTYPES, - FIVEUTR_CONSEQUENCES, - LOF_FILTERS, - MITOTIP_PATHOGENICITIES, - MOTIF_CONSEQUENCE_TERMS, - REGULATORY_BIOTYPES, - REGULATORY_CONSEQUENCE_TERMS, - SV_CONSEQUENCE_RANKS, - SV_TYPE_DETAILS, - SV_TYPES, - TRANSCRIPT_CONSEQUENCE_TERMS, -) -from loading_pipeline.lib.core import ( - DatasetType, - ReferenceGenome, - SampleType, -) -from loading_pipeline.lib.misc.io import remap_pedigree_hash -from loading_pipeline.lib.misc.validation import ( - ALL_VALIDATIONS, - SKIPPABLE_VALIDATIONS, - validate_expected_contig_frequency, -) -from loading_pipeline.lib.paths import ( - valid_reference_dataset_path, -) -from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset -from loading_pipeline.lib.tasks.files import GCSorLocalFolderTarget -from loading_pipeline.lib.tasks.update_variant_annotations_table_with_new_variants import ( - UpdateVariantAnnotationsTableWithNewVariantsTask, -) -from loading_pipeline.lib.test.misc import copy_project_pedigree_to_mocked_dir -from loading_pipeline.lib.test.mocked_reference_datasets_testcase import ( - MockedReferenceDatasetsTestCase, -) -from loading_pipeline.var.test.vep.mock_vep_data import ( - MOCK_37_VEP_DATA, - MOCK_38_VEP_DATA, -) - -TEST_MITO_MT = 'loading_pipeline/var/test/callsets/mito_1.mt' -TEST_SNV_INDEL_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' -TEST_SV_VCF = 'loading_pipeline/var/test/callsets/sv_1.vcf' -TEST_SV_VCF_2 = 'loading_pipeline/var/test/callsets/sv_2.vcf' -TEST_GCNV_BED_FILE = 'loading_pipeline/var/test/callsets/gcnv_1.tsv' -TEST_GCNV_BED_FILE_2 = 'loading_pipeline/var/test/callsets/gcnv_2.tsv' -TEST_PEDIGREE_3_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_3_remap.tsv' -TEST_PEDIGREE_4_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_4_remap.tsv' -TEST_PEDIGREE_5 = 'loading_pipeline/var/test/pedigrees/test_pedigree_5.tsv' -TEST_PEDIGREE_8 = 'loading_pipeline/var/test/pedigrees/test_pedigree_8.tsv' -TEST_PEDIGREE_10 = 'loading_pipeline/var/test/pedigrees/test_pedigree_10.tsv' -TEST_PEDIGREE_11 = 'loading_pipeline/var/test/pedigrees/test_pedigree_11.tsv' - -GENE_ID_MAPPING = { - 'OR4F5': 'ENSG00000186092', - 'PLEKHG4B': 'ENSG00000153404', - 'OR4F16': 'ENSG00000186192', - 'OR4F29': 'ENSG00000284733', - 'FBXO28': 'ENSG00000143756', - 'SAMD11': 'ENSG00000187634', - 'C1orf174': 'ENSG00000198912', - 'TAS1R1': 'ENSG00000173662', - 'FAM131C': 'ENSG00000185519', - 'RCC2': 'ENSG00000179051', - 'NBPF3': 'ENSG00000142794', - 'AGBL4': 'ENSG00000186094', - 'KIAA1614': 'ENSG00000135835', - 'MR1': 'ENSG00000153029', - 'STX6': 'ENSG00000135823', - 'XPR1': 'ENSG00000143324', -} - -TEST_RUN_ID = 'manual__2024-04-03' - - -class UpdateVariantAnnotationsTableWithNewVariantsTaskTest( - MockedReferenceDatasetsTestCase, -): - def test_missing_pedigree( - self, - ) -> None: - uvatwns_task = UpdateVariantAnnotationsTableWithNewVariantsTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - sample_type=SampleType.WGS, - callset_path=TEST_SNV_INDEL_VCF, - project_guids=['R0113_test_project'], - validations_to_skip=[ALL_VALIDATIONS], - run_id=TEST_RUN_ID, - ) - worker = luigi.worker.Worker() - worker.add(uvatwns_task) - worker.run() - self.assertFalse(uvatwns_task.complete()) - - @patch( - 'loading_pipeline.lib.tasks.validate_callset.SKIPPABLE_VALIDATIONS', - [ - x - for x in SKIPPABLE_VALIDATIONS - if x.__name__ != 'validate_expected_contig_frequency' - ] - + [ - functools.update_wrapper( - functools.partial( - validate_expected_contig_frequency, - min_rows_per_contig=25, - ), - validate_expected_contig_frequency, - ), - ], - ) - @patch.object(ReferenceGenome, 'standard_contigs', new_callable=PropertyMock) - @patch('loading_pipeline.lib.misc.vep.hl.vep') - @patch( - 'loading_pipeline.lib.tasks.write_new_variants_table.load_gencode_ensembl_to_refseq_id', - ) - def test_multiple_update_vat( - self, - mock_load_gencode_ensembl_to_refseq_id: Mock, - mock_vep: Mock, - mock_standard_contigs: Mock, - ) -> None: - mock_vep.side_effect = lambda ht, **_: ht.annotate(vep=MOCK_38_VEP_DATA) - mock_load_gencode_ensembl_to_refseq_id.return_value = hl.dict( - {'ENST00000327044': 'NM_015658.4'}, - ) - mock_standard_contigs.return_value = {'chr1'} - # This creates a mock validation table with 1 coding and 1 non-coding variant - # explicitly chosen from the VCF. - # NB: This is the one and only place validation is enabled in the task tests! - coding_and_noncoding_variants_ht = hl.Table.parallelize( - [ - { - 'locus': hl.Locus( - contig='chr1', - position=871269, - reference_genome='GRCh38', - ), - 'coding': False, - 'noncoding': True, - }, - { - 'locus': hl.Locus( - contig='chr1', - position=876499, - reference_genome='GRCh38', - ), - 'coding': True, - 'noncoding': False, - }, - ], - hl.tstruct( - locus=hl.tlocus('GRCh38'), - coding=hl.tbool, - noncoding=hl.tbool, - ), - key='locus', - globals=hl.Struct( - enums=hl.Struct( - gnomad_genomes=hl.Struct(), - ), - ), - ) - coding_and_noncoding_variants_ht.write( - valid_reference_dataset_path( - ReferenceGenome.GRCh38, - ReferenceDataset.gnomad_coding_and_noncoding, - ), - overwrite=True, - ) - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_3_REMAP, - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - SampleType.WGS, - 'R0113_test_project', - ) - worker = luigi.worker.Worker() - uvatwns_task_3 = UpdateVariantAnnotationsTableWithNewVariantsTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - sample_type=SampleType.WGS, - callset_path=TEST_SNV_INDEL_VCF, - project_guids=['R0113_test_project'], - validations_to_skip=[], - run_id=TEST_RUN_ID, - ) - worker.add(uvatwns_task_3) - worker.run() - self.assertTrue(uvatwns_task_3.complete()) - ht = hl.read_table(uvatwns_task_3.output().path) - self.assertEqual(ht.count(), 30) - self.assertEqual( - ht.globals.updates.collect(), - [ - { - hl.Struct( - callset=TEST_SNV_INDEL_VCF, - project_guid='R0113_test_project', - remap_pedigree_hash=hl.eval( - remap_pedigree_hash(TEST_PEDIGREE_3_REMAP), - ), - ), - }, - ], - ) - self.assertEqual( - hl.eval(ht.globals.max_key_), - 29, - ) - - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_4_REMAP, - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - SampleType.WGS, - 'R0114_project4', - ) - # Ensure that new variants are added correctly to the table. - uvatwns_task_4 = UpdateVariantAnnotationsTableWithNewVariantsTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - sample_type=SampleType.WGS, - callset_path=TEST_SNV_INDEL_VCF, - project_guids=['R0114_project4'], - validations_to_skip=[], - run_id=TEST_RUN_ID + '-another-run', - ) - worker.add(uvatwns_task_4) - worker.run() - self.assertTrue(uvatwns_task_4.complete()) - ht = hl.read_table(uvatwns_task_4.output().path) - self.assertCountEqual( - [ - x - for x in ht.select( - 'variant_id', - 'xpos', - ).collect() - if x.locus.position <= 878809 # noqa: PLR2004 - ], - [ - hl.Struct( - locus=hl.Locus( - contig='chr1', - position=871269, - reference_genome='GRCh38', - ), - alleles=['A', 'C'], - variant_id='1-871269-A-C', - xpos=1000871269, - ), - hl.Struct( - locus=hl.Locus( - contig='chr1', - position=874734, - reference_genome='GRCh38', - ), - alleles=['C', 'T'], - variant_id='1-874734-C-T', - xpos=1000874734, - ), - hl.Struct( - locus=hl.Locus( - contig='chr1', - position=876499, - reference_genome='GRCh38', - ), - alleles=['A', 'G'], - variant_id='1-876499-A-G', - xpos=1000876499, - ), - hl.Struct( - locus=hl.Locus( - contig='chr1', - position=878314, - reference_genome='GRCh38', - ), - alleles=['G', 'C'], - variant_id='1-878314-G-C', - xpos=1000878314, - ), - hl.Struct( - locus=hl.Locus( - contig='chr1', - position=878809, - reference_genome='GRCh38', - ), - alleles=['C', 'T'], - variant_id='1-878809-C-T', - xpos=1000878809, - ), - ], - ) - self.assertCountEqual( - ht.filter( - ht.locus.position <= 878809, # noqa: PLR2004 - ).sorted_transcript_consequences.consequence_term_ids.collect(), - [ - [[9], [23, 26], [23, 13, 26]], - [[9], [23, 26], [23, 13, 26]], - [[9], [23, 26], [23, 13, 26]], - [[9], [23, 26], [23, 13, 26]], - [[9], [23, 26], [23, 13, 26]], - ], - ) - self.assertCountEqual( - ht.globals.collect(), - [ - hl.Struct( - updates={ - hl.Struct( - callset='loading_pipeline/var/test/callsets/1kg_30variants.vcf', - project_guid='R0113_test_project', - remap_pedigree_hash=hl.eval( - remap_pedigree_hash( - TEST_PEDIGREE_3_REMAP, - ), - ), - ), - hl.Struct( - callset='loading_pipeline/var/test/callsets/1kg_30variants.vcf', - project_guid='R0114_project4', - remap_pedigree_hash=hl.eval( - remap_pedigree_hash( - TEST_PEDIGREE_4_REMAP, - ), - ), - ), - }, - max_key_=29, - enums=hl.Struct( - sorted_motif_feature_consequences=hl.Struct( - consequence_term=MOTIF_CONSEQUENCE_TERMS, - ), - sorted_regulatory_feature_consequences=hl.Struct( - biotype=REGULATORY_BIOTYPES, - consequence_term=REGULATORY_CONSEQUENCE_TERMS, - ), - sorted_transcript_consequences=hl.Struct( - biotype=BIOTYPES, - consequence_term=TRANSCRIPT_CONSEQUENCE_TERMS, - loftee=hl.Struct( - lof_filter=LOF_FILTERS, - ), - utrannotator=hl.Struct( - fiveutr_consequence=FIVEUTR_CONSEQUENCES, - ), - ), - ), - ), - ], - ) - - @patch('loading_pipeline.lib.misc.vep.hl.vep') - def test_update_vat_grch37( - self, - mock_vep: Mock, - ) -> None: - mock_vep.side_effect = lambda ht, **_: ht.annotate(vep=MOCK_37_VEP_DATA) - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_3_REMAP, - ReferenceGenome.GRCh37, - DatasetType.SNV_INDEL, - SampleType.WGS, - 'R0113_test_project', - ) - worker = luigi.worker.Worker() - uvatwns_task = UpdateVariantAnnotationsTableWithNewVariantsTask( - reference_genome=ReferenceGenome.GRCh37, - dataset_type=DatasetType.SNV_INDEL, - sample_type=SampleType.WGS, - callset_path=TEST_SNV_INDEL_VCF, - project_guids=['R0113_test_project'], - validations_to_skip=[ALL_VALIDATIONS], - run_id=TEST_RUN_ID, - ) - worker.add(uvatwns_task) - worker.run() - self.assertTrue(uvatwns_task.complete()) - ht = hl.read_table(uvatwns_task.output().path) - self.assertEqual(ht.count(), 30) - self.assertFalse(hasattr(ht, 'rg37_locus')) - self.assertEqual( - ht.collect()[0], - hl.Struct( - locus=hl.Locus( - contig=1, - position=871269, - reference_genome='GRCh37', - ), - alleles=['A', 'C'], - rsid=None, - variant_id='1-871269-A-C', - xpos=1000871269, - sorted_transcript_consequences=[ - hl.Struct( - amino_acids='S/L', - canonical=1, - codons='tCg/tTg', - gene_id='ENSG00000188976', - hgvsc='ENST00000327044.6:c.1667C>T', - hgvsp='ENSP00000317992.6:p.Ser556Leu', - transcript_id='ENST00000327044', - biotype_id=39, - consequence_term_ids=[9], - is_lof_nagnag=None, - lof_filter_ids=[0, 1], - ), - hl.Struct( - amino_acids=None, - canonical=None, - codons=None, - gene_id='ENSG00000188976', - hgvsc='ENST00000477976.1:n.3114C>T', - hgvsp=None, - transcript_id='ENST00000477976', - biotype_id=38, - consequence_term_ids=[23, 26], - is_lof_nagnag=None, - lof_filter_ids=None, - ), - hl.Struct( - amino_acids=None, - canonical=None, - codons=None, - gene_id='ENSG00000188976', - hgvsc='ENST00000483767.1:n.523C>T', - hgvsp=None, - transcript_id='ENST00000483767', - biotype_id=38, - consequence_term_ids=[23, 26], - is_lof_nagnag=None, - lof_filter_ids=None, - ), - ], - rg38_locus=hl.Locus( - contig='chr1', - position=935889, - reference_genome='GRCh38', - ), - key_=0, - ), - ) - - def test_mito_update_vat( - self, - ) -> None: - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_5, - ReferenceGenome.GRCh38, - DatasetType.MITO, - SampleType.WGS, - 'R0115_test_project2', - ) - worker = luigi.worker.Worker() - update_variant_annotations_task = ( - UpdateVariantAnnotationsTableWithNewVariantsTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.MITO, - sample_type=SampleType.WGS, - callset_path=TEST_MITO_MT, - project_guids=['R0115_test_project2'], - validations_to_skip=[ALL_VALIDATIONS], - run_id=TEST_RUN_ID, - ) - ) - worker.add(update_variant_annotations_task) - worker.run() - self.assertTrue(update_variant_annotations_task.complete()) - ht = hl.read_table(update_variant_annotations_task.output().path) - self.assertEqual(ht.count(), 5) - self.assertCountEqual( - ht.globals.collect(), - [ - hl.Struct( - enums=hl.Struct( - sorted_transcript_consequences=hl.Struct( - biotype=BIOTYPES, - consequence_term=TRANSCRIPT_CONSEQUENCE_TERMS, - lof_filter=LOF_FILTERS, - ), - mitotip=hl.Struct(trna_prediction=MITOTIP_PATHOGENICITIES), - ), - max_key_=4, - updates={ - hl.Struct( - callset='loading_pipeline/var/test/callsets/mito_1.mt', - project_guid='R0115_test_project2', - remap_pedigree_hash=hl.eval( - remap_pedigree_hash( - TEST_PEDIGREE_5, - ), - ), - ), - }, - ), - ], - ) - self.assertCountEqual( - ht.collect()[0], - hl.Struct( - locus=hl.Locus( - contig='chrM', - position=3, - reference_genome='GRCh38', - ), - alleles=['T', 'C'], - common_low_heteroplasmy=False, - haplogroup=hl.Struct(is_defining=False), - mitotip=hl.Struct(trna_prediction_id=None), - rg37_locus=hl.Locus( - contig='MT', - position=3, - reference_genome='GRCh37', - ), - rsid=None, - sorted_transcript_consequences=None, - variant_id='M-3-T-C', - xpos=25000000003, - key_=0, - ), - ) - - @patch( - 'loading_pipeline.lib.tasks.write_new_variants_table.load_gencode_gene_symbol_to_gene_id', - ) - def test_sv_multiple_vcf_update_vat( - self, - mock_load_gencode: Mock, - ) -> None: - mock_load_gencode.return_value = GENE_ID_MAPPING - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_5, - ReferenceGenome.GRCh38, - DatasetType.SV, - SampleType.WGS, - 'R0115_test_project2', - ) - worker = luigi.worker.Worker() - update_variant_annotations_task = ( - UpdateVariantAnnotationsTableWithNewVariantsTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SV, - sample_type=SampleType.WGS, - callset_path=TEST_SV_VCF, - project_guids=['R0115_test_project2'], - validations_to_skip=[ALL_VALIDATIONS], - run_id=TEST_RUN_ID, - ) - ) - worker.add(update_variant_annotations_task) - worker.run() - self.assertTrue(update_variant_annotations_task.complete()) - self.assertFalse( - GCSorLocalFolderTarget( - f'{self.mock_env.REFERENCE_DATASETS_DIR}/v03/GRCh38/SV/lookup.ht', - ).exists(), - ) - ht = hl.read_table(update_variant_annotations_task.output().path) - self.assertEqual(ht.count(), 13) - self.assertCountEqual( - ht.globals.collect(), - [ - hl.Struct( - enums=hl.Struct( - sv_type=SV_TYPES, - sv_type_detail=SV_TYPE_DETAILS, - sorted_gene_consequences=hl.Struct( - major_consequence=SV_CONSEQUENCE_RANKS, - ), - ), - max_key_=12, - updates={ - hl.Struct( - callset=TEST_SV_VCF, - project_guid='R0115_test_project2', - remap_pedigree_hash=hl.eval( - remap_pedigree_hash( - TEST_PEDIGREE_5, - ), - ), - ), - }, - ), - ], - ) - self.assertCountEqual( - ht.collect()[:8], - [ - hl.Struct( - variant_id='BND_chr1_6', - algorithms='manta', - bothsides_support=False, - cpx_intervals=None, - end_locus=hl.Locus( - contig='chr5', - position=20404, - reference_genome='GRCh38', - ), - gnomad_svs=None, - rg37_locus=hl.Locus( - contig=1, - position=10367, - reference_genome='GRCh37', - ), - rg37_locus_end=hl.Locus( - contig=5, - position=20404, - reference_genome='GRCh37', - ), - sorted_gene_consequences=[ - hl.Struct(gene_id='ENSG00000186092', major_consequence_id=12), - hl.Struct(gene_id='ENSG00000153404', major_consequence_id=12), - ], - start_locus=hl.Locus( - contig='chr1', - position=180928, - reference_genome='GRCh38', - ), - strvctvre=hl.Struct(score=None), - sv_len=-1, - sv_type_id=2, - sv_type_detail_id=None, - xpos=1000180928, - key_=0, - ), - hl.Struct( - variant_id='BND_chr1_9', - algorithms='manta', - bothsides_support=False, - cpx_intervals=None, - end_locus=hl.Locus( - contig='chr1', - position=789481, - reference_genome='GRCh38', - ), - gnomad_svs=None, - rg37_locus=hl.Locus( - contig=1, - position=724861, - reference_genome='GRCh37', - ), - rg37_locus_end=hl.Locus( - contig=1, - position=724861, - reference_genome='GRCh37', - ), - sorted_gene_consequences=[ - hl.Struct(gene_id='ENSG00000143756', major_consequence_id=12), - hl.Struct(gene_id='ENSG00000186192', major_consequence_id=12), - ], - start_locus=hl.Locus( - contig='chr1', - position=789481, - reference_genome='GRCh38', - ), - strvctvre=hl.Struct(score=None), - sv_len=223225007, - sv_type_id=2, - sv_type_detail_id=None, - xpos=1000789481, - key_=1, - ), - hl.Struct( - variant_id='CPX_chr1_22', - algorithms='manta', - bothsides_support=True, - cpx_intervals=[ - hl.Struct( - type_id=8, - start=hl.Locus('chr1', 6558902, 'GRCh38'), - end=hl.Locus('chr1', 6559723, 'GRCh38'), - ), - hl.Struct( - type_id=6, - start=hl.Locus('chr1', 6559655, 'GRCh38'), - end=hl.Locus('chr1', 6559723, 'GRCh38'), - ), - ], - end_locus=hl.Locus( - contig='chr1', - position=6559723, - reference_genome='GRCh38', - ), - gnomad_svs=None, - rg37_locus=hl.Locus( - contig=1, - position=6618962, - reference_genome='GRCh37', - ), - rg37_locus_end=hl.Locus( - contig=1, - position=6619783, - reference_genome='GRCh37', - ), - sorted_gene_consequences=[ - hl.Struct(gene_id='ENSG00000173662', major_consequence_id=11), - ], - start_locus=hl.Locus( - contig='chr1', - position=6558902, - reference_genome='GRCh38', - ), - strvctvre=hl.Struct(score=None), - sv_len=821, - sv_type_id=3, - sv_type_detail_id=2, - xpos=1006558902, - key_=2, - ), - hl.Struct( - variant_id='CPX_chr1_251', - algorithms='manta', - bothsides_support=False, - cpx_intervals=[ - hl.Struct( - type_id=5, - start=hl.Locus('chr1', 180540234, 'GRCh38'), - end=hl.Locus('chr1', 181074767, 'GRCh38'), - ), - hl.Struct( - type_id=8, - start=hl.Locus('chr1', 181074767, 'GRCh38'), - end=hl.Locus('chr1', 181074938, 'GRCh38'), - ), - ], - end_locus=hl.Locus( - contig='chr1', - position=181074952, - reference_genome='GRCh38', - ), - gnomad_svs=None, - rg37_locus=hl.Locus( - contig=1, - position=180509370, - reference_genome='GRCh37', - ), - rg37_locus_end=hl.Locus( - contig=1, - position=181044088, - reference_genome='GRCh37', - ), - sorted_gene_consequences=[ - hl.Struct(gene_id='ENSG00000135835', major_consequence_id=0), - hl.Struct(gene_id='ENSG00000153029', major_consequence_id=0), - hl.Struct(gene_id='ENSG00000135823', major_consequence_id=0), - hl.Struct(gene_id='ENSG00000143324', major_consequence_id=0), - ], - start_locus=hl.Locus( - contig='chr1', - position=180540234, - reference_genome='GRCh38', - ), - strvctvre=hl.Struct(score=None), - sv_len=534718, - sv_type_id=3, - sv_type_detail_id=9, - xpos=1180540234, - key_=3, - ), - hl.Struct( - variant_id='CPX_chr1_41', - algorithms='manta', - bothsides_support=False, - cpx_intervals=[ - hl.Struct( - type_id=6, - start=hl.Locus('chr1', 16088760, 'GRCh38'), - end=hl.Locus('chr1', 16088835, 'GRCh38'), - ), - hl.Struct( - type_id=8, - start=hl.Locus('chr1', 16088760, 'GRCh38'), - end=hl.Locus('chr1', 16089601, 'GRCh38'), - ), - ], - end_locus=hl.Locus( - contig='chr1', - position=16089601, - reference_genome='GRCh38', - ), - gnomad_svs=None, - rg37_locus=hl.Locus( - contig=1, - position=16415255, - reference_genome='GRCh37', - ), - rg37_locus_end=hl.Locus( - contig=1, - position=16416096, - reference_genome='GRCh37', - ), - sorted_gene_consequences=[ - hl.Struct(gene_id='ENSG00000185519', major_consequence_id=12), - ], - start_locus=hl.Locus( - contig='chr1', - position=16088760, - reference_genome='GRCh38', - ), - strvctvre=hl.Struct(score=None), - sv_len=841, - sv_type_id=3, - sv_type_detail_id=12, - xpos=1016088760, - key_=4, - ), - hl.Struct( - variant_id='CPX_chr1_54', - algorithms='manta', - bothsides_support=False, - cpx_intervals=[ - hl.Struct( - type_id=6, - start=hl.Locus('chr1', 21427498, 'GRCh38'), - end=hl.Locus('chr1', 21427959, 'GRCh38'), - ), - hl.Struct( - type_id=8, - start=hl.Locus('chr1', 21427498, 'GRCh38'), - end=hl.Locus('chr1', 21480073, 'GRCh38'), - ), - hl.Struct( - type_id=5, - start=hl.Locus('chr1', 21480073, 'GRCh38'), - end=hl.Locus('chr1', 21480419, 'GRCh38'), - ), - ], - end_locus=hl.Locus( - contig='chr1', - position=21480419, - reference_genome='GRCh38', - ), - gnomad_svs=None, - rg37_locus=hl.Locus( - contig=1, - position=21753991, - reference_genome='GRCh37', - ), - rg37_locus_end=hl.Locus( - contig=1, - position=21806912, - reference_genome='GRCh37', - ), - sorted_gene_consequences=[ - hl.Struct(gene_id='ENSG00000142794', major_consequence_id=0), - ], - start_locus=hl.Locus( - contig='chr1', - position=21427498, - reference_genome='GRCh38', - ), - strvctvre=hl.Struct(score=None), - sv_len=52921, - sv_type_id=3, - sv_type_detail_id=13, - xpos=1021427498, - key_=5, - ), - hl.Struct( - variant_id='CPX_chrX_251', - algorithms='manta', - bothsides_support=False, - cpx_intervals=[ - hl.Struct( - type_id=5, - start=hl.Locus( - contig='chr1', - position=180540234, - reference_genome='GRCh38', - ), - end=hl.Locus( - contig='chr1', - position=181074767, - reference_genome='GRCh38', - ), - ), - hl.Struct( - type_id=8, - start=hl.Locus( - contig='chr1', - position=181074767, - reference_genome='GRCh38', - ), - end=hl.Locus( - contig='chr1', - position=181074938, - reference_genome='GRCh38', - ), - ), - ], - end_locus=hl.Locus( - contig='chrX', - position=2781000, - reference_genome='GRCh38', - ), - gnomad_svs=None, - sorted_gene_consequences=[ - hl.Struct(gene_id='ENSG00000135835', major_consequence_id=0), - hl.Struct(gene_id='ENSG00000153029', major_consequence_id=0), - hl.Struct(gene_id='ENSG00000135823', major_consequence_id=0), - hl.Struct(gene_id='ENSG00000143324', major_consequence_id=0), - ], - start_locus=hl.Locus( - contig='chrX', - position=3, - reference_genome='GRCh38', - ), - strvctvre=hl.Struct(score=None), - sv_type_id=3, - sv_type_detail_id=9, - sv_len=534718, - xpos=23000000003, - rg37_locus=None, - rg37_locus_end=hl.Locus( - contig='X', - position=2699041, - reference_genome='GRCh37', - ), - key_=6, - ), - hl.Struct( - variant_id='CPX_chrX_252', - algorithms='manta', - bothsides_support=False, - cpx_intervals=[ - hl.Struct( - type_id=5, - start=hl.Locus( - contig='chr1', - position=180540234, - reference_genome='GRCh38', - ), - end=hl.Locus( - contig='chr1', - position=181074767, - reference_genome='GRCh38', - ), - ), - hl.Struct( - type_id=8, - start=hl.Locus( - contig='chr1', - position=181074767, - reference_genome='GRCh38', - ), - end=hl.Locus( - contig='chr1', - position=181074938, - reference_genome='GRCh38', - ), - ), - ], - end_locus=hl.Locus( - contig='chrX', - position=2781900, - reference_genome='GRCh38', - ), - gnomad_svs=None, - sorted_gene_consequences=[ - hl.Struct(gene_id='ENSG00000135835', major_consequence_id=0), - hl.Struct(gene_id='ENSG00000153029', major_consequence_id=0), - hl.Struct(gene_id='ENSG00000135823', major_consequence_id=0), - hl.Struct(gene_id='ENSG00000143324', major_consequence_id=0), - ], - start_locus=hl.Locus( - contig='chrX', - position=2781700, - reference_genome='GRCh38', - ), - strvctvre=hl.Struct(score=None), - sv_type_id=3, - sv_type_detail_id=9, - sv_len=534718, - xpos=23002781700, - rg37_locus=hl.Locus( - contig='X', - position=2699741, - reference_genome='GRCh37', - ), - rg37_locus_end=hl.Locus( - contig='X', - position=2699941, - reference_genome='GRCh37', - ), - key_=7, - ), - ], - ) - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_5, - ReferenceGenome.GRCh38, - DatasetType.SV, - SampleType.WGS, - 'R0115_test_project2', - ) - update_variant_annotations_task = ( - UpdateVariantAnnotationsTableWithNewVariantsTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SV, - sample_type=SampleType.WGS, - callset_path=TEST_SV_VCF_2, - project_guids=['R0115_test_project2'], - validations_to_skip=[ALL_VALIDATIONS], - run_id='second_run_id', - ) - ) - worker.add(update_variant_annotations_task) - worker.run() - self.assertTrue(update_variant_annotations_task.complete()) - ht = hl.read_table(update_variant_annotations_task.output().path) - self.assertEqual(ht.count(), 14) - self.assertCountEqual( - ht.globals.collect(), - [ - hl.Struct( - enums=hl.Struct( - sv_type=SV_TYPES, - sv_type_detail=SV_TYPE_DETAILS, - sorted_gene_consequences=hl.Struct( - major_consequence=SV_CONSEQUENCE_RANKS, - ), - ), - max_key_=13, - updates={ - hl.Struct( - callset=TEST_SV_VCF, - project_guid='R0115_test_project2', - remap_pedigree_hash=hl.eval( - remap_pedigree_hash( - TEST_PEDIGREE_5, - ), - ), - ), - hl.Struct( - callset=TEST_SV_VCF_2, - project_guid='R0115_test_project2', - remap_pedigree_hash=hl.eval( - remap_pedigree_hash( - TEST_PEDIGREE_5, - ), - ), - ), - }, - ), - ], - ) - self.assertCountEqual( - ht.take(1), - [ - hl.Struct( - variant_id='BND_chr1_6', - algorithms='manta', - bothsides_support=False, - cpx_intervals=None, - end_locus=hl.Locus( - contig='chr5', - position=20404, - reference_genome='GRCh38', - ), - gnomad_svs=None, - rg37_locus=hl.Locus( - contig=1, - position=10367, - reference_genome='GRCh37', - ), - rg37_locus_end=hl.Locus( - contig=5, - position=20404, - reference_genome='GRCh37', - ), - sorted_gene_consequences=[ - hl.Struct(gene_id='ENSG00000186092', major_consequence_id=12), - hl.Struct(gene_id='ENSG00000153404', major_consequence_id=12), - ], - start_locus=hl.Locus( - contig='chr1', - position=180928, - reference_genome='GRCh38', - ), - strvctvre=hl.Struct(score=None), - sv_len=-1, - sv_type_id=2, - sv_type_detail_id=None, - xpos=1000180928, - key_=0, - ), - ], - ) - - @patch( - 'loading_pipeline.lib.tasks.write_new_variants_table.load_gencode_gene_symbol_to_gene_id', - ) - def test_sv_multiple_project_single_vcf( - self, - mock_load_gencode: Mock, - ) -> None: - mock_load_gencode.return_value = GENE_ID_MAPPING - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_10, - ReferenceGenome.GRCh38, - DatasetType.SV, - SampleType.WGS, - 'R0116_test_project3', - ) - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_11, - ReferenceGenome.GRCh38, - DatasetType.SV, - SampleType.WGS, - 'R0117_test_project4', - ) - worker = luigi.worker.Worker() - update_variant_annotations_task = ( - UpdateVariantAnnotationsTableWithNewVariantsTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SV, - sample_type=SampleType.WGS, - callset_path=TEST_SV_VCF_2, - project_guids=['R0116_test_project3', 'R0117_test_project4'], - validations_to_skip=[ALL_VALIDATIONS], - run_id='run_id', - ) - ) - worker.add(update_variant_annotations_task) - worker.run() - self.assertTrue(update_variant_annotations_task.complete()) - ht = hl.read_table(update_variant_annotations_task.output().path) - self.assertEqual(ht.count(), 2) - self.assertEqual( - len(ht.globals.updates.collect()[0]), - 2, - ) - - def test_gcnv_update_vat_multiple( - self, - ) -> None: - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_5, - ReferenceGenome.GRCh38, - DatasetType.GCNV, - SampleType.WES, - 'R0115_test_project2', - ) - worker = luigi.worker.Worker() - update_variant_annotations_task = ( - UpdateVariantAnnotationsTableWithNewVariantsTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.GCNV, - sample_type=SampleType.WES, - callset_path=TEST_GCNV_BED_FILE, - project_guids=['R0115_test_project2'], - validations_to_skip=[ALL_VALIDATIONS], - run_id=TEST_RUN_ID, - ) - ) - worker.add(update_variant_annotations_task) - worker.run() - self.assertTrue(update_variant_annotations_task.complete()) - self.assertFalse( - GCSorLocalFolderTarget( - f'{self.mock_env.REFERENCE_DATASETS_DIR}/v03/GRCh38/GCNV/lookup.ht', - ).exists(), - ) - ht = hl.read_table(update_variant_annotations_task.output().path) - self.assertEqual(ht.count(), 2) - self.assertCountEqual( - ht.globals.collect(), - [ - hl.Struct( - enums=hl.Struct( - sv_type=SV_TYPES, - sorted_gene_consequences=hl.Struct( - major_consequence=SV_CONSEQUENCE_RANKS, - ), - ), - max_key_=1, - updates={ - hl.Struct( - callset=TEST_GCNV_BED_FILE, - project_guid='R0115_test_project2', - remap_pedigree_hash=hl.eval( - remap_pedigree_hash( - TEST_PEDIGREE_5, - ), - ), - ), - }, - ), - ], - ) - self.assertCountEqual( - ht.collect(), - [ - hl.Struct( - variant_id='suffix_16456_DEL', - end_locus=hl.Locus( - contig='chr1', - position=100023213, - reference_genome='GRCh38', - ), - gt_stats=hl.Struct( - AF=hl.eval(hl.float32(4.401408e-05)), - AC=1, - AN=22720, - Hom=None, - Het=None, - ), - num_exon=3, - rg37_locus=hl.Locus( - contig=1, - position=100472493, - reference_genome='GRCh37', - ), - rg37_locus_end=hl.Locus( - contig=1, - position=100488769, - reference_genome='GRCh37', - ), - sorted_gene_consequences=[ - hl.Struct(gene_id='ENSG00000117620', major_consequence_id=0), - hl.Struct(gene_id='ENSG00000283761', major_consequence_id=0), - hl.Struct(gene_id='ENSG22222222222', major_consequence_id=None), - ], - start_locus=hl.Locus( - contig='chr1', - position=100006937, - reference_genome='GRCh38', - ), - strvctvre=hl.Struct(score=hl.eval(hl.float32(0.583))), - sv_type_id=5, - xpos=1100006937, - key_=0, - ), - hl.Struct( - variant_id='suffix_16457_DEL', - end_locus=hl.Locus( - contig='chr1', - position=100023212, - reference_genome='GRCh38', - ), - gt_stats=hl.Struct( - AF=8.802817319519818e-05, - AC=2, - AN=22719, - Hom=None, - Het=None, - ), - num_exon=2, - rg37_locus=hl.Locus( - contig=1, - position=100483142, - reference_genome='GRCh37', - ), - rg37_locus_end=hl.Locus( - contig=1, - position=100488768, - reference_genome='GRCh37', - ), - sorted_gene_consequences=[ - hl.Struct(gene_id='ENSG00000283761', major_consequence_id=0), - hl.Struct(gene_id='ENSG22222222222', major_consequence_id=None), - ], - start_locus=hl.Locus( - contig='chr1', - position=100017586, - reference_genome='GRCh38', - ), - strvctvre=hl.Struct(score=0.5070000290870667), - sv_type_id=5, - xpos=1100017586, - key_=1, - ), - ], - ) - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_8, - ReferenceGenome.GRCh38, - DatasetType.GCNV, - SampleType.WES, - 'R0115_test_project2', - ) - update_variant_annotations_task = ( - UpdateVariantAnnotationsTableWithNewVariantsTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.GCNV, - sample_type=SampleType.WES, - callset_path=TEST_GCNV_BED_FILE_2, - project_guids=['R0115_test_project2'], - validations_to_skip=[ALL_VALIDATIONS], - run_id='second_run_id', - ) - ) - worker.add(update_variant_annotations_task) - worker.run() - ht = hl.read_table(update_variant_annotations_task.output().path) - self.assertEqual(ht.count(), 3) - self.assertCountEqual( - ht.select('gt_stats').collect(), - [ - hl.Struct( - # Existing variant, gt_stats are preserved - variant_id='suffix_16456_DEL', - gt_stats=hl.Struct( - AF=hl.eval(hl.float32(4.401408e-05)), - AC=1, - AN=22720, - Hom=None, - Het=None, - ), - ), - hl.Struct( - # Exiting variant, gt_stats are updated - variant_id='suffix_16457_DEL', - gt_stats=hl.Struct( - AF=8.111110946629196e-05, - AC=3, - AN=36986, - Hom=None, - Het=None, - ), - ), - hl.Struct( - # New variant. - variant_id='suffix_99999_DEL', - gt_stats=hl.Struct( - AF=8.802817319519818e-05, - AC=2, - AN=22719, - Hom=None, - Het=None, - ), - ), - ], - ) From 2a7e39ab5be9f1137531ccf97169f9e0ed730dc3 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 20 Aug 2026 14:12:29 -0400 Subject: [PATCH 136/369] remove deprecated path helpers --- loading_pipeline/lib/paths.py | 37 +----------------------------- loading_pipeline/lib/paths_test.py | 25 -------------------- 2 files changed, 1 insertion(+), 61 deletions(-) diff --git a/loading_pipeline/lib/paths.py b/loading_pipeline/lib/paths.py index 922433cbfe..b8078fb9b4 100644 --- a/loading_pipeline/lib/paths.py +++ b/loading_pipeline/lib/paths.py @@ -58,24 +58,6 @@ def _callset_path_hash(callset_path: str) -> str: ).hexdigest() -def family_table_path( - reference_genome: ReferenceGenome, - dataset_type: DatasetType, - sample_type: SampleType, - family_guid: str, -) -> str: - return os.path.join( - pipeline_prefix( - Env.PIPELINE_DATA_DIR, - reference_genome, - dataset_type, - ), - 'families', - sample_type.value, - f'{family_guid}.ht', - ) - - def tdr_metrics_dir( reference_genome: ReferenceGenome, dataset_type: DatasetType, @@ -163,24 +145,6 @@ def metadata_for_run_path( ) -def project_table_path( - reference_genome: ReferenceGenome, - dataset_type: DatasetType, - sample_type: SampleType, - project_guid: str, -) -> str: - return os.path.join( - pipeline_prefix( - Env.PIPELINE_DATA_DIR, - reference_genome, - dataset_type, - ), - 'projects', - sample_type.value, - f'{project_guid}.ht', - ) - - def relatedness_check_table_path( reference_genome: ReferenceGenome, dataset_type: DatasetType, @@ -302,6 +266,7 @@ def ancestry_model_rf_path() -> str: ) +# TODO deprecate def variant_annotations_table_path( reference_genome: ReferenceGenome, dataset_type: DatasetType, diff --git a/loading_pipeline/lib/paths_test.py b/loading_pipeline/lib/paths_test.py index d271cfee0b..1fb80b28c2 100644 --- a/loading_pipeline/lib/paths_test.py +++ b/loading_pipeline/lib/paths_test.py @@ -13,7 +13,6 @@ metadata_for_run_path, new_variants_table_path, project_pedigree_path, - project_table_path, relatedness_check_table_path, remapped_and_subsetted_callset_path, sex_check_table_path, @@ -26,30 +25,6 @@ class TestPaths(unittest.TestCase): - def test_project_table_path(self) -> None: - self.assertEqual( - project_table_path( - ReferenceGenome.GRCh38, - DatasetType.MITO, - SampleType.WES, - 'R0652_pipeline_test', - ), - '/var/seqr/pipeline-data/GRCh38/MITO/projects/WES/R0652_pipeline_test.ht', - ) - with ( - patch('loading_pipeline.lib.paths.Env') as mock_env, - ): - mock_env.PIPELINE_DATA_DIR = '/var/bucket/' - self.assertEqual( - project_table_path( - ReferenceGenome.GRCh37, - DatasetType.SNV_INDEL, - SampleType.WES, - 'R0652_pipeline_test', - ), - '/var/bucket/GRCh37/SNV_INDEL/projects/WES/R0652_pipeline_test.ht', - ) - def test_sex_check_table_path(self) -> None: self.assertEqual( sex_check_table_path( From e78b1a08b9aaa552bc21440399fa1f96c539bde2 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 20 Aug 2026 14:24:47 -0400 Subject: [PATCH 137/369] fix test call --- .../lib/tasks/write_existing_variants_parquet_test.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/loading_pipeline/lib/tasks/write_existing_variants_parquet_test.py b/loading_pipeline/lib/tasks/write_existing_variants_parquet_test.py index 78bebda2c0..a538160a33 100644 --- a/loading_pipeline/lib/tasks/write_existing_variants_parquet_test.py +++ b/loading_pipeline/lib/tasks/write_existing_variants_parquet_test.py @@ -3,7 +3,7 @@ import luigi.worker import pandas as pd -from loading_pipeline.lib.core import DatasetType, ReferenceGenome +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType from loading_pipeline.lib.paths import existing_variants_parquet_path from loading_pipeline.lib.tasks.write_existing_variants_parquet import ( WriteExistingVariantsParquetTask, @@ -31,6 +31,8 @@ def _run_task( task = WriteExistingVariantsParquetTask( reference_genome=reference_genome, dataset_type=dataset_type, + sample_type=SampleType.WGS, + callset_path='fake_callset', run_id=TEST_RUN_ID, ) worker.add(task) From a48daddd03e070219cf78aaa3bc516bb67ecf725 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 20 Aug 2026 14:30:53 -0400 Subject: [PATCH 138/369] test clean up --- loading_pipeline/lib/paths_test.py | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/loading_pipeline/lib/paths_test.py b/loading_pipeline/lib/paths_test.py index 1fb80b28c2..09c9825258 100644 --- a/loading_pipeline/lib/paths_test.py +++ b/loading_pipeline/lib/paths_test.py @@ -9,6 +9,7 @@ SampleType, ) from loading_pipeline.lib.paths import ( + existing_variants_parquet_path, imported_callset_path, metadata_for_run_path, new_variants_table_path, @@ -18,7 +19,6 @@ sex_check_table_path, tdr_metrics_path, validation_errors_for_run_path, - variant_annotations_table_path, ) TEST_VCF = 'loading_pipeline/var/test/callsets/1kg_30varia*.vcf' @@ -65,13 +65,14 @@ def test_metadata_for_run_path(self) -> None: '/var/seqr/pipeline-data/GRCh38/SNV_INDEL/runs/manual__2023-06-26T18:30:09.349671+00:00/metadata.json', ) - def test_variant_annotations_table_path(self) -> None: + def test_existing_variants_parquet_path(self) -> None: self.assertEqual( - variant_annotations_table_path( + existing_variants_parquet_path( ReferenceGenome.GRCh38, DatasetType.GCNV, + 'manual__2023-06-26T18:30:09.349671+00:00', ), - '/var/seqr/pipeline-data/GRCh38/GCNV/annotations.ht', + '/var/seqr/pipeline-data/GRCh38/GCNV/runs/manual__2023-06-26T18:30:09.349671+00:00/existing_variants.ht', ) def test_remapped_and_subsetted_callset_path(self) -> None: From 0d6728857fbf06504225bf8b22518ddae2b0c55d Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 20 Aug 2026 14:36:11 -0400 Subject: [PATCH 139/369] ruff --- loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py index c2ac1af158..c9d9df7d80 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py +++ b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py @@ -23,7 +23,7 @@ ) from loading_pipeline.lib.tasks.files import GCSorLocalTarget from loading_pipeline.lib.tasks.write_new_variants_table import ( - WriteNewVariantsTableTask + WriteNewVariantsTableTask, ) from loading_pipeline.lib.tasks.write_remapped_and_subsetted_callset import ( WriteRemappedAndSubsettedCallsetTask, From 49a520a0de284caad6e32d2653766b647b291591 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 20 Aug 2026 14:40:44 -0400 Subject: [PATCH 140/369] diagram update --- loading_pipeline/docs/Diagrams.md | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/loading_pipeline/docs/Diagrams.md b/loading_pipeline/docs/Diagrams.md index 211d7abd31..b9c43de32f 100644 --- a/loading_pipeline/docs/Diagrams.md +++ b/loading_pipeline/docs/Diagrams.md @@ -30,17 +30,14 @@ (Project 1) (Project N) | | |___________________________________________| - | - v - WriteMetadataForRunTask + | + v + WriteMetadataForRunTask WriteExistingVariantsParquetTask + |___________________________________________| | v WriteNewVariantsTableTask | - v - UpdateVariantAnnotationsTableWithNewVariantsTask - (Variants with annotations) - | ______________________+_______________________ | | | v v v From 6064e6f5eb1129fb84f9de110197dc5710b31a94 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 20 Aug 2026 14:41:29 -0400 Subject: [PATCH 141/369] diagram update --- loading_pipeline/docs/Diagrams.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/loading_pipeline/docs/Diagrams.md b/loading_pipeline/docs/Diagrams.md index b9c43de32f..a8e205fd31 100644 --- a/loading_pipeline/docs/Diagrams.md +++ b/loading_pipeline/docs/Diagrams.md @@ -1,4 +1,4 @@ -# Pipeline flow, as of 05/06/2026 +# Pipeline flow, as of August 2026 ``` WriteImportedCallsetTask From 58066548c839450de3e05f5e9e991260cc9fee5b Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 20 Aug 2026 14:52:18 -0400 Subject: [PATCH 142/369] fix export task --- loading_pipeline/lib/misc/clickhouse.py | 5 ++++- loading_pipeline/lib/paths_test.py | 2 +- .../lib/tasks/write_existing_variants_parquet.py | 3 +-- 3 files changed, 6 insertions(+), 4 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse.py b/loading_pipeline/lib/misc/clickhouse.py index 5db45d36c8..66b8a08939 100644 --- a/loading_pipeline/lib/misc/clickhouse.py +++ b/loading_pipeline/lib/misc/clickhouse.py @@ -934,7 +934,10 @@ def direct_insert_all_keys( **_, ) -> None: dst_table = table_name_builder.dst_table(clickhouse_table) - src_table = table_name_builder.src_table(clickhouse_table) + src_table = table_name_builder.src_table(clickhouse_table).replace( + '/*.parquet', + '', + ) settings = '' # Large variant details inserts may OOM if clickhouse_table == ClickHouseTable.VARIANT_DETAILS: diff --git a/loading_pipeline/lib/paths_test.py b/loading_pipeline/lib/paths_test.py index 09c9825258..29294856ed 100644 --- a/loading_pipeline/lib/paths_test.py +++ b/loading_pipeline/lib/paths_test.py @@ -72,7 +72,7 @@ def test_existing_variants_parquet_path(self) -> None: DatasetType.GCNV, 'manual__2023-06-26T18:30:09.349671+00:00', ), - '/var/seqr/pipeline-data/GRCh38/GCNV/runs/manual__2023-06-26T18:30:09.349671+00:00/existing_variants.ht', + '/var/seqr/pipeline-data/GRCh38/GCNV/runs/manual__2023-06-26T18:30:09.349671+00:00/existing_variants.parquet', ) def test_remapped_and_subsetted_callset_path(self) -> None: diff --git a/loading_pipeline/lib/tasks/write_existing_variants_parquet.py b/loading_pipeline/lib/tasks/write_existing_variants_parquet.py index 6c9ff6126a..5da189f6c1 100644 --- a/loading_pipeline/lib/tasks/write_existing_variants_parquet.py +++ b/loading_pipeline/lib/tasks/write_existing_variants_parquet.py @@ -8,7 +8,6 @@ ) from loading_pipeline.lib.tasks.exports.fields import get_existing_variants_export_field from loading_pipeline.lib.tasks.files import ( - GCSorLocalFolderTarget, GCSorLocalTarget, ) @@ -25,7 +24,7 @@ def output(self) -> luigi.Target: ) def complete(self) -> luigi.Target: - return GCSorLocalFolderTarget(self.output().path).exists() + return GCSorLocalTarget(self.output().path).exists() def run(self): export_select_fields = get_existing_variants_export_field(self.dataset_type) From 4a35aa2e704097a5a9e568ed342ab90115929f0c Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 20 Aug 2026 15:37:48 -0400 Subject: [PATCH 143/369] use existing variants parquet for noew variants --- loading_pipeline/lib/misc/io.py | 24 +++++++++ loading_pipeline/lib/tasks/exports/fields.py | 10 ++-- .../write_existing_variants_parquet_test.py | 2 +- .../lib/tasks/write_new_variants_table.py | 52 ++++++++----------- 4 files changed, 51 insertions(+), 37 deletions(-) diff --git a/loading_pipeline/lib/misc/io.py b/loading_pipeline/lib/misc/io.py index b2f4e33e55..857fafa898 100644 --- a/loading_pipeline/lib/misc/io.py +++ b/loading_pipeline/lib/misc/io.py @@ -8,6 +8,7 @@ import hail as hl import hailtop.fs as hfs +from pyspark.sql import SparkSession from loading_pipeline.lib.core import DatasetType, Env, ReferenceGenome, Sex from loading_pipeline.lib.misc.gcnv import parse_gcnv_genes @@ -209,6 +210,29 @@ def import_callset( return mt.key_rows_by(*dataset_type.table_key_type(reference_genome).fields) +def import_parquet( + callset_path: str, + reference_genome: ReferenceGenome, + dataset_type: DatasetType, +) -> hl.HailTable: + spark = SparkSession.builder.getOrCreate() + df = spark.read.parquet(callset_path) + ht = hl.Table.from_spark(df) + + key_fields = dataset_type.table_key_type(reference_genome).fields + if 'locus' in key_fields: + ht = ht.annotate( + locus=hl.Locus( + contig=ht.variant_id.split('-')[0], + position=ht.variant_id.split('-')[1], + reference_genome=reference_genome.value, + ), + alleles=[ht.variant_id.split('-')[2], ht.variant_id.split('-')[3]], + ) + + return ht.key_by(*key_fields) + + @validated_hl_function( { 'instance has no field (.*)': Template( diff --git a/loading_pipeline/lib/tasks/exports/fields.py b/loading_pipeline/lib/tasks/exports/fields.py index c32d2f7260..ddcdb7d253 100644 --- a/loading_pipeline/lib/tasks/exports/fields.py +++ b/loading_pipeline/lib/tasks/exports/fields.py @@ -93,12 +93,12 @@ def get_dataset_type_specific_variants_annotations( def get_existing_variants_export_field(dataset_type: DatasetType) -> str: dt_fields = { - DatasetType.SNV_INDEL: ', transcripts.geneId AS geneIds', - DatasetType.MITO: '', - DatasetType.SV: ', xpos, end, endChrom, sortedGeneConsequences.geneId AS geneIds', - DatasetType.GCNV: ', xpos, pos AS start, end, numExon as num_exon, sortedGeneConsequences.geneId AS gene_ids', + DatasetType.SNV_INDEL: 'transcripts.geneId AS geneIds', + DatasetType.MITO: 'xpos', + DatasetType.SV: 'xpos, end, endChrom, sortedGeneConsequences.geneId AS geneIds', + DatasetType.GCNV: 'xpos, pos AS start, end, numExon as num_exon, sortedGeneConsequences.geneId AS gene_ids', }[dataset_type] - return f'key AS key_, variantId AS variant_id {dt_fields}' + return f'key AS key_, variantId AS variant_id, {dt_fields}' def get_entries_call_annotations_fields( diff --git a/loading_pipeline/lib/tasks/write_existing_variants_parquet_test.py b/loading_pipeline/lib/tasks/write_existing_variants_parquet_test.py index a538160a33..238ce84675 100644 --- a/loading_pipeline/lib/tasks/write_existing_variants_parquet_test.py +++ b/loading_pipeline/lib/tasks/write_existing_variants_parquet_test.py @@ -70,7 +70,7 @@ def test_grch37_snv_indel(self): def test_mito(self): df = self._run_task(DatasetType.MITO) - self.assertEqual(list(df.columns), ['key_', 'variant_id']) + self.assertEqual(list(df.columns), ['key_', 'variant_id', 'xpos']) self.assertEqual(len(df), 0) def test_sv(self): diff --git a/loading_pipeline/lib/tasks/write_new_variants_table.py b/loading_pipeline/lib/tasks/write_new_variants_table.py index a92c15a50a..dea1404c89 100644 --- a/loading_pipeline/lib/tasks/write_new_variants_table.py +++ b/loading_pipeline/lib/tasks/write_new_variants_table.py @@ -1,7 +1,6 @@ import math import hail as hl -import hailtop.fs as hfs import luigi import luigi.util @@ -10,14 +9,14 @@ annotate_formatting_annotation_enum_globals, ) from loading_pipeline.lib.misc.callsets import get_callset_ht -from loading_pipeline.lib.misc.io import checkpoint, remap_pedigree_hash +from loading_pipeline.lib.misc.io import checkpoint, import_parquet, remap_pedigree_hash from loading_pipeline.lib.misc.math import constrain from loading_pipeline.lib.misc.vep import run_vep from loading_pipeline.lib.paths import ( + existing_variants_parquet_path, new_variants_table_path, project_pedigree_path, valid_reference_dataset_path, - variant_annotations_table_path, ) from loading_pipeline.lib.reference_datasets.gencode.mapping_gene_ids import ( load_gencode_ensembl_to_refseq_id, @@ -29,6 +28,9 @@ ) from loading_pipeline.lib.tasks.base.base_write import BaseWriteTask from loading_pipeline.lib.tasks.files import GCSorLocalTarget +from loading_pipeline.lib.tasks.write_existing_variants_parquet import ( + WriteExistingVariantsParquetTask, +) from loading_pipeline.lib.tasks.write_metadata_for_run import ( WriteMetadataForRunTask, ) @@ -82,6 +84,7 @@ def output(self) -> luigi.Target: def requires(self) -> list[luigi.Task]: return [ self.clone(WriteMetadataForRunTask), + self.clone(WriteExistingVariantsParquetTask), ] def complete(self) -> bool: @@ -119,37 +122,24 @@ def create_table(self) -> hl.Table: ) # 1) Identify new variants. - if hfs.exists( - variant_annotations_table_path( + annotations_ht = import_parquet( + existing_variants_parquet_path( self.reference_genome, self.dataset_type, + self.run_id, ), - ): - annotations_ht = hl.read_table( - variant_annotations_table_path( - self.reference_genome, - self.dataset_type, - ), - ) - # Gracefully handle case for on-premises uses - # where key_ field is not present and migration was not run. - if not hasattr(annotations_ht, 'key_'): - annotations_ht = annotations_ht.add_index(name='key_') - annotations_ht = annotations_ht.annotate_globals( - max_key_=(annotations_ht.count() - 1), - ) - curr_max_key_ = annotations_ht.index_globals().max_key_ - new_variants_ht = callset_ht.repartition( - # Repartition this join to improve performance - constrain( - callset_ht.n_partitions() * 100, - MIN_PARTITIONS, - MAX_PARTITIONS, - ), - ).anti_join(annotations_ht) - else: - curr_max_key_ = -1 - new_variants_ht = callset_ht + self.reference_genome, + self.dataset_type, + ) + curr_max_key_ = annotations_ht.aggregate(hl.agg.max(annotations_ht.key_)) + new_variants_ht = callset_ht.repartition( + # Repartition this join to improve performance + constrain( + callset_ht.n_partitions() * 100, + MIN_PARTITIONS, + MAX_PARTITIONS, + ), + ).anti_join(annotations_ht) # Annotate new variants with VEP. # Note about the repartition: our work here is cpu/memory bound and From cdd56b12158f5087782e29f68f1061a721b5fa86 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 20 Aug 2026 15:40:39 -0400 Subject: [PATCH 144/369] oops --- loading_pipeline/lib/misc/io.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/loading_pipeline/lib/misc/io.py b/loading_pipeline/lib/misc/io.py index 857fafa898..637f5e3604 100644 --- a/loading_pipeline/lib/misc/io.py +++ b/loading_pipeline/lib/misc/io.py @@ -214,7 +214,7 @@ def import_parquet( callset_path: str, reference_genome: ReferenceGenome, dataset_type: DatasetType, -) -> hl.HailTable: +) -> hl.Table: spark = SparkSession.builder.getOrCreate() df = spark.read.parquet(callset_path) ht = hl.Table.from_spark(df) From 250ee3f77a57ba83e3c0e10bc8161ee67c4d26e0 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 20 Aug 2026 15:43:41 -0400 Subject: [PATCH 145/369] actually fix export table --- loading_pipeline/lib/misc/clickhouse.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse.py b/loading_pipeline/lib/misc/clickhouse.py index 66b8a08939..31b02a2aed 100644 --- a/loading_pipeline/lib/misc/clickhouse.py +++ b/loading_pipeline/lib/misc/clickhouse.py @@ -934,10 +934,7 @@ def direct_insert_all_keys( **_, ) -> None: dst_table = table_name_builder.dst_table(clickhouse_table) - src_table = table_name_builder.src_table(clickhouse_table).replace( - '/*.parquet', - '', - ) + src_table = table_name_builder.src_table(clickhouse_table) settings = '' # Large variant details inserts may OOM if clickhouse_table == ClickHouseTable.VARIANT_DETAILS: @@ -968,7 +965,10 @@ def export_existing_variants_to_parquet( if dataset_type.should_write_new_variant_details else ClickHouseTable.VARIANTS_MEMORY, ) - export_table = table_name_builder.src_table(ClickHouseTable.EXISTING_VARIANTS) + export_table = table_name_builder.src_table(ClickHouseTable.EXISTING_VARIANTS).replace( + '/*.parquet', + '', + ) logged_query( f""" INSERT INTO FUNCTION {export_table} From fa528e44986948f0f77eea6fd3d8dfe9d7ebdb87 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 20 Aug 2026 15:46:35 -0400 Subject: [PATCH 146/369] ruff --- loading_pipeline/lib/misc/clickhouse.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/loading_pipeline/lib/misc/clickhouse.py b/loading_pipeline/lib/misc/clickhouse.py index 31b02a2aed..1de075ddbb 100644 --- a/loading_pipeline/lib/misc/clickhouse.py +++ b/loading_pipeline/lib/misc/clickhouse.py @@ -965,7 +965,9 @@ def export_existing_variants_to_parquet( if dataset_type.should_write_new_variant_details else ClickHouseTable.VARIANTS_MEMORY, ) - export_table = table_name_builder.src_table(ClickHouseTable.EXISTING_VARIANTS).replace( + export_table = table_name_builder.src_table( + ClickHouseTable.EXISTING_VARIANTS, + ).replace( '/*.parquet', '', ) From bbe3d167cc8df794d462cc2118f01f27dde794c8 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 20 Aug 2026 15:55:28 -0400 Subject: [PATCH 147/369] use updates annotation for new entries --- .../exports/write_new_entries_parquet.py | 49 +++++++++++++------ 1 file changed, 34 insertions(+), 15 deletions(-) diff --git a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py index c9d9df7d80..f6b2e5cfea 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py +++ b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py @@ -3,14 +3,16 @@ import luigi.util from loading_pipeline.lib.annotations.fields import get_fields +from loading_pipeline.lib.annotations.shared import xpos from loading_pipeline.lib.misc.family_entries import ( compute_callset_family_entries_ht, deduplicate_by_most_non_ref_calls, deglobalize_ids, ) from loading_pipeline.lib.paths import ( + existing_variants_parquet_path, new_entries_parquet_path, - variant_annotations_table_path, + new_variants_table_path, ) from loading_pipeline.lib.tasks.base.base_loading_run_params import ( BaseLoadingRunParams, @@ -60,6 +62,37 @@ def requires(self) -> dict[str, luigi.Task]: def create_table(self) -> None: unioned_ht = None + + annotation_fields = get_entries_annotations_export_fields( + ht, + self.dataset_type, + ) + call_annotation_fields = get_entries_call_annotations_fields( + ht, + self.dataset_type, + ) + annotations_ht = hl.read_table( + new_variants_table_path( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + ).select(**annotation_fields, **call_annotation_fields) + + existing_annotations_ht = import_parquet( + existing_variants_parquet_path( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + self.reference_genome, + self.dataset_type, + ) + if 'xpos' not in existing_annotations_ht.row: + existing_annotations_ht = existing_annotations_ht.annotate(xpos=xpos(existing_annotations_ht)) + + annotations_ht = annotations_ht.union(existing_annotations_ht) + for project_guid, remapped_and_subsetted_callset_task in zip( self.project_guids, self.input()[REMAPPED_AND_SUBSETTED_CALLSET_TASKS], @@ -77,20 +110,6 @@ def create_table(self) -> None: ) ht = deglobalize_ids(ht) ht = deduplicate_by_most_non_ref_calls(ht) - annotation_fields = get_entries_annotations_export_fields( - ht, - self.dataset_type, - ) - call_annotation_fields = get_entries_call_annotations_fields( - ht, - self.dataset_type, - ) - annotations_ht = hl.read_table( - variant_annotations_table_path( - self.reference_genome, - self.dataset_type, - ), - ).select(**annotation_fields, **call_annotation_fields) ht = ht.join(annotations_ht) # the family entries ht will contain rows From 432b58077b3b3c3540363db7aa6449b426646d48 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 20 Aug 2026 15:58:31 -0400 Subject: [PATCH 148/369] undo mito overzealousness --- loading_pipeline/lib/tasks/exports/fields.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/loading_pipeline/lib/tasks/exports/fields.py b/loading_pipeline/lib/tasks/exports/fields.py index ddcdb7d253..c32d2f7260 100644 --- a/loading_pipeline/lib/tasks/exports/fields.py +++ b/loading_pipeline/lib/tasks/exports/fields.py @@ -93,12 +93,12 @@ def get_dataset_type_specific_variants_annotations( def get_existing_variants_export_field(dataset_type: DatasetType) -> str: dt_fields = { - DatasetType.SNV_INDEL: 'transcripts.geneId AS geneIds', - DatasetType.MITO: 'xpos', - DatasetType.SV: 'xpos, end, endChrom, sortedGeneConsequences.geneId AS geneIds', - DatasetType.GCNV: 'xpos, pos AS start, end, numExon as num_exon, sortedGeneConsequences.geneId AS gene_ids', + DatasetType.SNV_INDEL: ', transcripts.geneId AS geneIds', + DatasetType.MITO: '', + DatasetType.SV: ', xpos, end, endChrom, sortedGeneConsequences.geneId AS geneIds', + DatasetType.GCNV: ', xpos, pos AS start, end, numExon as num_exon, sortedGeneConsequences.geneId AS gene_ids', }[dataset_type] - return f'key AS key_, variantId AS variant_id, {dt_fields}' + return f'key AS key_, variantId AS variant_id {dt_fields}' def get_entries_call_annotations_fields( From 3d4b7a760f1701d0da395049d84386e92db472f0 Mon Sep 17 00:00:00 2001 From: hanars Date: Thu, 20 Aug 2026 16:42:05 -0400 Subject: [PATCH 149/369] ruff --- .../lib/tasks/exports/write_new_entries_parquet.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py index f6b2e5cfea..cca0c794ba 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py +++ b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py @@ -89,7 +89,9 @@ def create_table(self) -> None: self.dataset_type, ) if 'xpos' not in existing_annotations_ht.row: - existing_annotations_ht = existing_annotations_ht.annotate(xpos=xpos(existing_annotations_ht)) + existing_annotations_ht = existing_annotations_ht.annotate( + xpos=xpos(existing_annotations_ht), + ) annotations_ht = annotations_ht.union(existing_annotations_ht) From a4073867e1531f765e28b25e0f4836a7e27b13b5 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 20 Aug 2026 16:45:35 -0400 Subject: [PATCH 150/369] redo mocing to better test new variants --- .../write_new_variant_details_parquet_test.py | 135 +++++++---- .../write_new_variants_parquet_test.py | 210 ++++++++++++------ 2 files changed, 235 insertions(+), 110 deletions(-) diff --git a/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py index 5458854f56..99d80d2484 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py @@ -1,10 +1,14 @@ import os from unittest import mock +from unittest.mock import Mock import hail as hl import luigi.worker import pandas as pd +from loading_pipeline.lib.annotations.expression_helpers import ( + get_expr_for_variant_id, +) from loading_pipeline.lib.core import ( DatasetType, ReferenceGenome, @@ -13,47 +17,97 @@ from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS from loading_pipeline.lib.paths import ( new_variant_details_parquet_path, - new_variants_table_path, + variant_annotations_table_path, ) from loading_pipeline.lib.tasks.exports.write_new_variant_details_parquet import ( WriteNewVariantDetailsParquetTask, ) -from loading_pipeline.lib.test.misc import convert_ndarray_to_list -from loading_pipeline.lib.test.mock_complete_task import MockCompleteTask -from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase - -TEST_SNV_INDEL_ANNOTATIONS = ( - 'loading_pipeline/var/test/exports/GRCh38/SNV_INDEL/annotations.ht' +from loading_pipeline.lib.tasks.write_remapped_and_subsetted_callset import ( + WriteRemappedAndSubsettedCallsetTask, ) -TEST_GRCH37_SNV_INDEL_ANNOTATIONS = ( - 'loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/annotations.ht' +from loading_pipeline.lib.test.misc import ( + convert_ndarray_to_list, + copy_project_pedigree_to_mocked_dir, ) +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase +from loading_pipeline.var.test.vep.mock_vep_data import ( + MOCK_37_VEP_DATA, + MOCK_38_VEP_DATA, +) + +TEST_SNV_INDEL_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' +TEST_PEDIGREE_3_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_3_remap.tsv' TEST_RUN_ID = 'manual__2024-04-03' +def _write_prior_annotations_table( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + sample_type: SampleType, + pedigree_path: str, + callset_path: str, + project_guid: str, + exclude_variant_id: str, + max_key_: int, +) -> None: + # Runs the real WriteRemappedAndSubsettedCallsetTask (no VEP/DB involved) + # to get a real callset, then snapshots everything except + # `exclude_variant_id` as a "prior" annotations table so that + # WriteNewVariantsTableTask's anti-join deterministically leaves + # exactly one new variant to annotate. + copy_project_pedigree_to_mocked_dir( + pedigree_path, + reference_genome, + dataset_type, + sample_type, + project_guid, + ) + worker = luigi.worker.Worker() + wrsc_task = WriteRemappedAndSubsettedCallsetTask( + reference_genome=reference_genome, + dataset_type=dataset_type, + run_id=TEST_RUN_ID, + sample_type=sample_type, + callset_path=callset_path, + project_guids=[project_guid], + project_i=0, + validations_to_skip=[ALL_VALIDATIONS], + skip_expect_tdr_metrics=True, + ) + worker.add(wrsc_task) + worker.run() + callset_ht = hl.read_matrix_table(wrsc_task.output().path).rows() + variant_id_expr = get_expr_for_variant_id(callset_ht) + prior_ht = callset_ht.filter(variant_id_expr != exclude_variant_id) + prior_ht = prior_ht.select() + prior_ht = prior_ht.add_index(name='key_') + prior_ht = prior_ht.annotate_globals(max_key_=max_key_) + prior_ht.write(variant_annotations_table_path(reference_genome, dataset_type)) + + class WriteNewVariantDetailsParquetTest(MockedDatarootTestCase): def setUp(self) -> None: super().setUp() - ht = hl.read_table( - TEST_SNV_INDEL_ANNOTATIONS, + _write_prior_annotations_table( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + TEST_PEDIGREE_3_REMAP, + TEST_SNV_INDEL_VCF, + 'R0113_test_project', + exclude_variant_id='1-876499-A-G', + max_key_=-1, ) - ht.write( - new_variants_table_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ), - ) - ht = hl.read_table( - TEST_GRCH37_SNV_INDEL_ANNOTATIONS, - ) - ht.write( - new_variants_table_path( - ReferenceGenome.GRCh37, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ), + _write_prior_annotations_table( + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + SampleType.WGS, + TEST_PEDIGREE_3_REMAP, + TEST_SNV_INDEL_VCF, + 'R0113_test_project', + exclude_variant_id='1-69134-A-G', + max_key_=1423, ) # Make an incomplete parquet to validate overwrite-ing. @@ -79,24 +133,28 @@ def setUp(self) -> None: f.write('') @mock.patch( - 'loading_pipeline.lib.tasks.exports.write_new_variant_details_parquet.WriteNewVariantsTableTask', + 'loading_pipeline.lib.tasks.write_new_variants_table.load_gencode_ensembl_to_refseq_id', ) + @mock.patch('loading_pipeline.lib.misc.vep.hl.vep') def test_write_new_variant_details_parquet_test( self, - mock_write_new_variants_task, + mock_vep: Mock, + mock_load_gencode_ensembl_to_refseq_id: Mock, ) -> None: - mock_write_new_variants_task.return_value = MockCompleteTask() + mock_load_gencode_ensembl_to_refseq_id.return_value = hl.dict({}) + mock_vep.side_effect = lambda ht, **_: ht.annotate(vep=MOCK_38_VEP_DATA) worker = luigi.worker.Worker() task = WriteNewVariantDetailsParquetTask( reference_genome=ReferenceGenome.GRCh38, dataset_type=DatasetType.SNV_INDEL, sample_type=SampleType.WGS, - callset_path='fake_callset', + callset_path=TEST_SNV_INDEL_VCF, project_guids=[ - 'fake_project', + 'R0113_test_project', ], validations_to_skip=[ALL_VALIDATIONS], run_id=TEST_RUN_ID, + skip_expect_tdr_metrics=True, ) worker.add(task) worker.run() @@ -196,25 +254,24 @@ def test_write_new_variant_details_parquet_test( ), ) - @mock.patch( - 'loading_pipeline.lib.tasks.exports.write_new_variant_details_parquet.WriteNewVariantsTableTask', - ) + @mock.patch('loading_pipeline.lib.misc.vep.hl.vep') def test_grch37_write_new_variant_details_parquet_test( self, - mock_write_new_variants_task, + mock_vep: Mock, ) -> None: - mock_write_new_variants_task.return_value = MockCompleteTask() + mock_vep.side_effect = lambda ht, **_: ht.annotate(vep=MOCK_37_VEP_DATA) worker = luigi.worker.Worker() task = WriteNewVariantDetailsParquetTask( reference_genome=ReferenceGenome.GRCh37, dataset_type=DatasetType.SNV_INDEL, sample_type=SampleType.WGS, - callset_path='fake_callset', + callset_path=TEST_SNV_INDEL_VCF, project_guids=[ - 'fake_project', + 'R0113_test_project', ], validations_to_skip=[ALL_VALIDATIONS], run_id=TEST_RUN_ID, + skip_expect_tdr_metrics=True, ) worker.add(task) worker.run() diff --git a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py index 8bd43fc8be..61e3a3f400 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py @@ -5,6 +5,9 @@ import luigi.worker import pandas as pd +from loading_pipeline.lib.annotations.expression_helpers import ( + get_expr_for_variant_id, +) from loading_pipeline.lib.core import ( DatasetType, ReferenceGenome, @@ -13,72 +16,137 @@ from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS from loading_pipeline.lib.paths import ( new_variants_parquet_path, - new_variants_table_path, remapped_and_subsetted_callset_path, variant_annotations_table_path, ) from loading_pipeline.lib.tasks.exports.write_new_variants_parquet import ( WriteNewVariantsParquetTask, ) -from loading_pipeline.lib.test.misc import convert_ndarray_to_list +from loading_pipeline.lib.tasks.write_remapped_and_subsetted_callset import ( + WriteRemappedAndSubsettedCallsetTask, +) +from loading_pipeline.lib.test.misc import ( + convert_ndarray_to_list, + copy_project_pedigree_to_mocked_dir, +) from loading_pipeline.lib.test.mock_complete_task import MockCompleteTask -from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase - -TEST_SNV_INDEL_ANNOTATIONS = ( - 'loading_pipeline/var/test/exports/GRCh38/SNV_INDEL/annotations.ht' +from loading_pipeline.lib.test.mocked_reference_datasets_testcase import ( + MockedReferenceDatasetsTestCase, +) +from loading_pipeline.var.test.vep.mock_vep_data import ( + MOCK_37_VEP_DATA, + MOCK_38_VEP_DATA, ) -TEST_GRCH37_SNV_INDEL_ANNOTATIONS = ( - 'loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/annotations.ht' + +TEST_SNV_INDEL_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' +TEST_PEDIGREE_3_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_3_remap.tsv' +TEST_MITO_CALLSET = 'loading_pipeline/var/test/callsets/mito_1.mt' +TEST_MITO_EXPORT_PEDIGREE = ( + 'loading_pipeline/var/test/pedigrees/test_mito_export_pedigree.tsv' ) -TEST_MITO_ANNOTATIONS = 'loading_pipeline/var/test/exports/GRCh38/MITO/annotations.ht' -TEST_SV_ANNOTATIONS = 'loading_pipeline/var/test/exports/GRCh38/SV/annotations.ht' +TEST_SV_VCF_2 = 'loading_pipeline/var/test/callsets/sv_2.vcf' +TEST_PEDIGREE_5 = 'loading_pipeline/var/test/pedigrees/test_pedigree_5.tsv' TEST_GCNV_ANNOTATIONS = 'loading_pipeline/var/test/exports/GRCh38/GCNV/annotations.ht' TEST_RUN_ID = 'manual__2024-04-03' -class WriteNewVariantsParquetTest(MockedDatarootTestCase): +def _write_prior_annotations_table( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + sample_type: SampleType, + pedigree_path: str, + callset_path: str, + project_guid: str, + exclude_variant_id: str, + max_key_: int, + keyed_by_variant_id: bool, +) -> None: + # Runs the real WriteRemappedAndSubsettedCallsetTask (no VEP/DB involved) + # to get a real callset, then snapshots everything except + # `exclude_variant_id` as a "prior" annotations table so that + # WriteNewVariantsTableTask's anti-join deterministically leaves + # exactly one new variant to annotate. + copy_project_pedigree_to_mocked_dir( + pedigree_path, + reference_genome, + dataset_type, + sample_type, + project_guid, + ) + worker = luigi.worker.Worker() + wrsc_task = WriteRemappedAndSubsettedCallsetTask( + reference_genome=reference_genome, + dataset_type=dataset_type, + run_id=TEST_RUN_ID, + sample_type=sample_type, + callset_path=callset_path, + project_guids=[project_guid], + project_i=0, + validations_to_skip=[ALL_VALIDATIONS], + skip_expect_tdr_metrics=True, + ) + worker.add(wrsc_task) + worker.run() + callset_ht = hl.read_matrix_table(wrsc_task.output().path).rows() + variant_id_expr = ( + callset_ht.variant_id + if keyed_by_variant_id + else get_expr_for_variant_id(callset_ht) + ) + prior_ht = callset_ht.filter(variant_id_expr != exclude_variant_id) + prior_ht = prior_ht.select() + prior_ht = prior_ht.add_index(name='key_') + prior_ht = prior_ht.annotate_globals(max_key_=max_key_) + prior_ht.write(variant_annotations_table_path(reference_genome, dataset_type)) + + +class WriteNewVariantsParquetTest(MockedReferenceDatasetsTestCase): def setUp(self) -> None: super().setUp() - ht = hl.read_table( - TEST_SNV_INDEL_ANNOTATIONS, - ) - ht.write( - new_variants_table_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ), + _write_prior_annotations_table( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + TEST_PEDIGREE_3_REMAP, + TEST_SNV_INDEL_VCF, + 'R0113_test_project', + exclude_variant_id='1-876499-A-G', + max_key_=-1, + keyed_by_variant_id=False, ) - ht = hl.read_table( - TEST_GRCH37_SNV_INDEL_ANNOTATIONS, + _write_prior_annotations_table( + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + SampleType.WGS, + TEST_PEDIGREE_3_REMAP, + TEST_SNV_INDEL_VCF, + 'R0113_test_project', + exclude_variant_id='1-69134-A-G', + max_key_=1423, + keyed_by_variant_id=False, ) - ht.write( - new_variants_table_path( - ReferenceGenome.GRCh37, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ), + _write_prior_annotations_table( + ReferenceGenome.GRCh38, + DatasetType.MITO, + SampleType.WGS, + TEST_MITO_EXPORT_PEDIGREE, + TEST_MITO_CALLSET, + 'R0116_test_project3', + exclude_variant_id='M-8-G-T', + max_key_=997, + keyed_by_variant_id=False, ) - ht = hl.read_table( - TEST_MITO_ANNOTATIONS, - ) - ht.write( - new_variants_table_path( - ReferenceGenome.GRCh38, - DatasetType.MITO, - TEST_RUN_ID, - ), - ) - ht = hl.read_table( - TEST_SV_ANNOTATIONS, - ) - ht.write( - new_variants_table_path( - ReferenceGenome.GRCh38, - DatasetType.SV, - TEST_RUN_ID, - ), + _write_prior_annotations_table( + ReferenceGenome.GRCh38, + DatasetType.SV, + SampleType.WGS, + TEST_PEDIGREE_5, + TEST_SV_VCF_2, + 'R0115_test_project2', + exclude_variant_id='BND_chr1_6', + max_key_=726, + keyed_by_variant_id=True, ) ht = hl.read_table(TEST_GCNV_ANNOTATIONS) ht.write( @@ -97,24 +165,28 @@ def setUp(self) -> None: ) @mock.patch( - 'loading_pipeline.lib.tasks.exports.write_new_variants_parquet.WriteNewVariantsTableTask', + 'loading_pipeline.lib.tasks.write_new_variants_table.load_gencode_ensembl_to_refseq_id', ) + @mock.patch('loading_pipeline.lib.misc.vep.hl.vep') def test_write_new_variants_parquet_test( self, - mock_write_new_variants_task, + mock_vep: Mock, + mock_load_gencode_ensembl_to_refseq_id: Mock, ) -> None: - mock_write_new_variants_task.return_value = MockCompleteTask() + mock_load_gencode_ensembl_to_refseq_id.return_value = hl.dict({}) + mock_vep.side_effect = lambda ht, **_: ht.annotate(vep=MOCK_38_VEP_DATA) worker = luigi.worker.Worker() task = WriteNewVariantsParquetTask( reference_genome=ReferenceGenome.GRCh38, dataset_type=DatasetType.SNV_INDEL, sample_type=SampleType.WGS, - callset_path='fake_callset', + callset_path=TEST_SNV_INDEL_VCF, project_guids=[ - 'fake_project', + 'R0113_test_project', ], validations_to_skip=[ALL_VALIDATIONS], run_id=TEST_RUN_ID, + skip_expect_tdr_metrics=True, ) worker.add(task) worker.run() @@ -161,25 +233,24 @@ def test_write_new_variants_parquet_test( ], ) - @mock.patch( - 'loading_pipeline.lib.tasks.exports.write_new_variants_parquet.WriteNewVariantsTableTask', - ) + @mock.patch('loading_pipeline.lib.misc.vep.hl.vep') def test_grch37_write_new_variants_parquet_test( self, - mock_write_new_variants_task, + mock_vep: Mock, ) -> None: - mock_write_new_variants_task.return_value = MockCompleteTask() + mock_vep.side_effect = lambda ht, **_: ht.annotate(vep=MOCK_37_VEP_DATA) worker = luigi.worker.Worker() task = WriteNewVariantsParquetTask( reference_genome=ReferenceGenome.GRCh37, dataset_type=DatasetType.SNV_INDEL, sample_type=SampleType.WGS, - callset_path='fake_callset', + callset_path=TEST_SNV_INDEL_VCF, project_guids=[ - 'fake_project', + 'R0113_test_project', ], validations_to_skip=[ALL_VALIDATIONS], run_id=TEST_RUN_ID, + skip_expect_tdr_metrics=True, ) worker.add(task) worker.run() @@ -212,25 +283,21 @@ def test_grch37_write_new_variants_parquet_test( ], ) - @mock.patch( - 'loading_pipeline.lib.tasks.exports.write_new_variants_parquet.WriteNewVariantsTableTask', - ) def test_mito_write_new_variants_parquet_test( self, - write_new_variants_table_task: Mock, ) -> None: - write_new_variants_table_task.return_value = MockCompleteTask() worker = luigi.worker.Worker() task = WriteNewVariantsParquetTask( reference_genome=ReferenceGenome.GRCh38, dataset_type=DatasetType.MITO, sample_type=SampleType.WGS, - callset_path='fake_callset', + callset_path=TEST_MITO_CALLSET, project_guids=[ - 'fake_project', + 'R0116_test_project3', ], validations_to_skip=[ALL_VALIDATIONS], run_id=TEST_RUN_ID, + skip_expect_tdr_metrics=True, ) worker.add(task) worker.run() @@ -279,24 +346,25 @@ def test_mito_write_new_variants_parquet_test( ) @mock.patch( - 'loading_pipeline.lib.tasks.exports.write_new_variants_parquet.WriteNewVariantsTableTask', + 'loading_pipeline.lib.tasks.write_new_variants_table.load_gencode_gene_symbol_to_gene_id', ) def test_sv_write_new_variants_parquet_test( self, - write_new_variants_table_task: Mock, + mock_load_gencode_gene_symbol_to_gene_id: Mock, ) -> None: - write_new_variants_table_task.return_value = MockCompleteTask() + mock_load_gencode_gene_symbol_to_gene_id.return_value = hl.dict({}) worker = luigi.worker.Worker() task = WriteNewVariantsParquetTask( reference_genome=ReferenceGenome.GRCh38, dataset_type=DatasetType.SV, sample_type=SampleType.WGS, - callset_path='fake_callset', + callset_path=TEST_SV_VCF_2, project_guids=[ - 'fake_project', + 'R0115_test_project2', ], validations_to_skip=[ALL_VALIDATIONS], run_id=TEST_RUN_ID, + skip_expect_tdr_metrics=True, ) worker.add(task) worker.run() From 596bd61db08e20ff2026f7eb56b2f28e936681ae Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 20 Aug 2026 16:57:20 -0400 Subject: [PATCH 151/369] cleaner test . set up --- .../write_new_variant_details_parquet_test.py | 85 +++++-------- .../write_new_variants_parquet_test.py | 120 ++++++++---------- 2 files changed, 86 insertions(+), 119 deletions(-) diff --git a/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py index 99d80d2484..9cb471a1f4 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py @@ -6,9 +6,6 @@ import luigi.worker import pandas as pd -from loading_pipeline.lib.annotations.expression_helpers import ( - get_expr_for_variant_id, -) from loading_pipeline.lib.core import ( DatasetType, ReferenceGenome, @@ -22,9 +19,6 @@ from loading_pipeline.lib.tasks.exports.write_new_variant_details_parquet import ( WriteNewVariantDetailsParquetTask, ) -from loading_pipeline.lib.tasks.write_remapped_and_subsetted_callset import ( - WriteRemappedAndSubsettedCallsetTask, -) from loading_pipeline.lib.test.misc import ( convert_ndarray_to_list, copy_project_pedigree_to_mocked_dir, @@ -38,74 +32,49 @@ TEST_SNV_INDEL_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' TEST_PEDIGREE_3_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_3_remap.tsv' +TEST_SNV_INDEL_ANNOTATIONS = ( + 'loading_pipeline/var/test/exports/GRCh38/SNV_INDEL/annotations.ht' +) +TEST_GRCH37_SNV_INDEL_ANNOTATIONS = ( + 'loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/annotations.ht' +) + TEST_RUN_ID = 'manual__2024-04-03' def _write_prior_annotations_table( + fixture_path: str, reference_genome: ReferenceGenome, dataset_type: DatasetType, - sample_type: SampleType, - pedigree_path: str, - callset_path: str, - project_guid: str, exclude_variant_id: str, max_key_: int, ) -> None: - # Runs the real WriteRemappedAndSubsettedCallsetTask (no VEP/DB involved) - # to get a real callset, then snapshots everything except - # `exclude_variant_id` as a "prior" annotations table so that - # WriteNewVariantsTableTask's anti-join deterministically leaves - # exactly one new variant to annotate. - copy_project_pedigree_to_mocked_dir( - pedigree_path, - reference_genome, - dataset_type, - sample_type, - project_guid, - ) - worker = luigi.worker.Worker() - wrsc_task = WriteRemappedAndSubsettedCallsetTask( - reference_genome=reference_genome, - dataset_type=dataset_type, - run_id=TEST_RUN_ID, - sample_type=sample_type, - callset_path=callset_path, - project_guids=[project_guid], - project_i=0, - validations_to_skip=[ALL_VALIDATIONS], - skip_expect_tdr_metrics=True, - ) - worker.add(wrsc_task) - worker.run() - callset_ht = hl.read_matrix_table(wrsc_task.output().path).rows() - variant_id_expr = get_expr_for_variant_id(callset_ht) - prior_ht = callset_ht.filter(variant_id_expr != exclude_variant_id) - prior_ht = prior_ht.select() - prior_ht = prior_ht.add_index(name='key_') - prior_ht = prior_ht.annotate_globals(max_key_=max_key_) - prior_ht.write(variant_annotations_table_path(reference_genome, dataset_type)) + # The fixture already documents `exclude_variant_id` as an example of a + # newly-added variant. Strip it back out and re-key the remainder so + # WriteNewVariantsTableTask's anti-join rediscovers it as new, at the + # same `key_` the fixture originally asserted. + ht = hl.read_table(fixture_path) + ht = ht.filter(ht.variant_id != exclude_variant_id) + ht = ht.select() + ht = ht.add_index(name='key_') + ht = ht.annotate_globals(max_key_=max_key_) + ht.write(variant_annotations_table_path(reference_genome, dataset_type)) class WriteNewVariantDetailsParquetTest(MockedDatarootTestCase): def setUp(self) -> None: super().setUp() _write_prior_annotations_table( + TEST_SNV_INDEL_ANNOTATIONS, ReferenceGenome.GRCh38, DatasetType.SNV_INDEL, - SampleType.WGS, - TEST_PEDIGREE_3_REMAP, - TEST_SNV_INDEL_VCF, - 'R0113_test_project', exclude_variant_id='1-876499-A-G', max_key_=-1, ) _write_prior_annotations_table( + TEST_GRCH37_SNV_INDEL_ANNOTATIONS, ReferenceGenome.GRCh37, DatasetType.SNV_INDEL, - SampleType.WGS, - TEST_PEDIGREE_3_REMAP, - TEST_SNV_INDEL_VCF, - 'R0113_test_project', exclude_variant_id='1-69134-A-G', max_key_=1423, ) @@ -143,6 +112,13 @@ def test_write_new_variant_details_parquet_test( ) -> None: mock_load_gencode_ensembl_to_refseq_id.return_value = hl.dict({}) mock_vep.side_effect = lambda ht, **_: ht.annotate(vep=MOCK_38_VEP_DATA) + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_3_REMAP, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0113_test_project', + ) worker = luigi.worker.Worker() task = WriteNewVariantDetailsParquetTask( reference_genome=ReferenceGenome.GRCh38, @@ -260,6 +236,13 @@ def test_grch37_write_new_variant_details_parquet_test( mock_vep: Mock, ) -> None: mock_vep.side_effect = lambda ht, **_: ht.annotate(vep=MOCK_37_VEP_DATA) + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_3_REMAP, + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0113_test_project', + ) worker = luigi.worker.Worker() task = WriteNewVariantDetailsParquetTask( reference_genome=ReferenceGenome.GRCh37, diff --git a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py index 61e3a3f400..00d174a388 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py @@ -5,9 +5,6 @@ import luigi.worker import pandas as pd -from loading_pipeline.lib.annotations.expression_helpers import ( - get_expr_for_variant_id, -) from loading_pipeline.lib.core import ( DatasetType, ReferenceGenome, @@ -22,9 +19,6 @@ from loading_pipeline.lib.tasks.exports.write_new_variants_parquet import ( WriteNewVariantsParquetTask, ) -from loading_pipeline.lib.tasks.write_remapped_and_subsetted_callset import ( - WriteRemappedAndSubsettedCallsetTask, -) from loading_pipeline.lib.test.misc import ( convert_ndarray_to_list, copy_project_pedigree_to_mocked_dir, @@ -46,107 +40,69 @@ ) TEST_SV_VCF_2 = 'loading_pipeline/var/test/callsets/sv_2.vcf' TEST_PEDIGREE_5 = 'loading_pipeline/var/test/pedigrees/test_pedigree_5.tsv' + +TEST_SNV_INDEL_ANNOTATIONS = ( + 'loading_pipeline/var/test/exports/GRCh38/SNV_INDEL/annotations.ht' +) +TEST_GRCH37_SNV_INDEL_ANNOTATIONS = ( + 'loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/annotations.ht' +) +TEST_MITO_ANNOTATIONS = 'loading_pipeline/var/test/exports/GRCh38/MITO/annotations.ht' +TEST_SV_ANNOTATIONS = 'loading_pipeline/var/test/exports/GRCh38/SV/annotations.ht' TEST_GCNV_ANNOTATIONS = 'loading_pipeline/var/test/exports/GRCh38/GCNV/annotations.ht' TEST_RUN_ID = 'manual__2024-04-03' def _write_prior_annotations_table( + fixture_path: str, reference_genome: ReferenceGenome, dataset_type: DatasetType, - sample_type: SampleType, - pedigree_path: str, - callset_path: str, - project_guid: str, exclude_variant_id: str, max_key_: int, - keyed_by_variant_id: bool, ) -> None: - # Runs the real WriteRemappedAndSubsettedCallsetTask (no VEP/DB involved) - # to get a real callset, then snapshots everything except - # `exclude_variant_id` as a "prior" annotations table so that - # WriteNewVariantsTableTask's anti-join deterministically leaves - # exactly one new variant to annotate. - copy_project_pedigree_to_mocked_dir( - pedigree_path, - reference_genome, - dataset_type, - sample_type, - project_guid, - ) - worker = luigi.worker.Worker() - wrsc_task = WriteRemappedAndSubsettedCallsetTask( - reference_genome=reference_genome, - dataset_type=dataset_type, - run_id=TEST_RUN_ID, - sample_type=sample_type, - callset_path=callset_path, - project_guids=[project_guid], - project_i=0, - validations_to_skip=[ALL_VALIDATIONS], - skip_expect_tdr_metrics=True, - ) - worker.add(wrsc_task) - worker.run() - callset_ht = hl.read_matrix_table(wrsc_task.output().path).rows() - variant_id_expr = ( - callset_ht.variant_id - if keyed_by_variant_id - else get_expr_for_variant_id(callset_ht) - ) - prior_ht = callset_ht.filter(variant_id_expr != exclude_variant_id) - prior_ht = prior_ht.select() - prior_ht = prior_ht.add_index(name='key_') - prior_ht = prior_ht.annotate_globals(max_key_=max_key_) - prior_ht.write(variant_annotations_table_path(reference_genome, dataset_type)) + # The fixture already documents `exclude_variant_id` as an example of a + # newly-added variant. Strip it back out and re-key the remainder so + # WriteNewVariantsTableTask's anti-join rediscovers it as new, at the + # same `key_` the fixture originally asserted. + ht = hl.read_table(fixture_path) + ht = ht.filter(ht.variant_id != exclude_variant_id) + ht = ht.select() + ht = ht.add_index(name='key_') + ht = ht.annotate_globals(max_key_=max_key_) + ht.write(variant_annotations_table_path(reference_genome, dataset_type)) class WriteNewVariantsParquetTest(MockedReferenceDatasetsTestCase): def setUp(self) -> None: super().setUp() _write_prior_annotations_table( + TEST_SNV_INDEL_ANNOTATIONS, ReferenceGenome.GRCh38, DatasetType.SNV_INDEL, - SampleType.WGS, - TEST_PEDIGREE_3_REMAP, - TEST_SNV_INDEL_VCF, - 'R0113_test_project', exclude_variant_id='1-876499-A-G', max_key_=-1, - keyed_by_variant_id=False, ) _write_prior_annotations_table( + TEST_GRCH37_SNV_INDEL_ANNOTATIONS, ReferenceGenome.GRCh37, DatasetType.SNV_INDEL, - SampleType.WGS, - TEST_PEDIGREE_3_REMAP, - TEST_SNV_INDEL_VCF, - 'R0113_test_project', exclude_variant_id='1-69134-A-G', max_key_=1423, - keyed_by_variant_id=False, ) _write_prior_annotations_table( + TEST_MITO_ANNOTATIONS, ReferenceGenome.GRCh38, DatasetType.MITO, - SampleType.WGS, - TEST_MITO_EXPORT_PEDIGREE, - TEST_MITO_CALLSET, - 'R0116_test_project3', exclude_variant_id='M-8-G-T', max_key_=997, - keyed_by_variant_id=False, ) _write_prior_annotations_table( + TEST_SV_ANNOTATIONS, ReferenceGenome.GRCh38, DatasetType.SV, - SampleType.WGS, - TEST_PEDIGREE_5, - TEST_SV_VCF_2, - 'R0115_test_project2', exclude_variant_id='BND_chr1_6', max_key_=726, - keyed_by_variant_id=True, ) ht = hl.read_table(TEST_GCNV_ANNOTATIONS) ht.write( @@ -175,6 +131,13 @@ def test_write_new_variants_parquet_test( ) -> None: mock_load_gencode_ensembl_to_refseq_id.return_value = hl.dict({}) mock_vep.side_effect = lambda ht, **_: ht.annotate(vep=MOCK_38_VEP_DATA) + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_3_REMAP, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0113_test_project', + ) worker = luigi.worker.Worker() task = WriteNewVariantsParquetTask( reference_genome=ReferenceGenome.GRCh38, @@ -239,6 +202,13 @@ def test_grch37_write_new_variants_parquet_test( mock_vep: Mock, ) -> None: mock_vep.side_effect = lambda ht, **_: ht.annotate(vep=MOCK_37_VEP_DATA) + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_3_REMAP, + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0113_test_project', + ) worker = luigi.worker.Worker() task = WriteNewVariantsParquetTask( reference_genome=ReferenceGenome.GRCh37, @@ -286,6 +256,13 @@ def test_grch37_write_new_variants_parquet_test( def test_mito_write_new_variants_parquet_test( self, ) -> None: + copy_project_pedigree_to_mocked_dir( + TEST_MITO_EXPORT_PEDIGREE, + ReferenceGenome.GRCh38, + DatasetType.MITO, + SampleType.WGS, + 'R0116_test_project3', + ) worker = luigi.worker.Worker() task = WriteNewVariantsParquetTask( reference_genome=ReferenceGenome.GRCh38, @@ -353,6 +330,13 @@ def test_sv_write_new_variants_parquet_test( mock_load_gencode_gene_symbol_to_gene_id: Mock, ) -> None: mock_load_gencode_gene_symbol_to_gene_id.return_value = hl.dict({}) + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_5, + ReferenceGenome.GRCh38, + DatasetType.SV, + SampleType.WGS, + 'R0115_test_project2', + ) worker = luigi.worker.Worker() task = WriteNewVariantsParquetTask( reference_genome=ReferenceGenome.GRCh38, From 7009f2ea8e77b54c8e51d14fd3c4ef1201307274 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 20 Aug 2026 17:03:53 -0400 Subject: [PATCH 152/369] clean up --- .../write_new_variant_details_parquet_test.py | 47 ++++-------- .../write_new_variants_parquet_test.py | 75 ++++++++----------- 2 files changed, 48 insertions(+), 74 deletions(-) diff --git a/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py index 9cb471a1f4..13693dd38a 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py @@ -42,41 +42,26 @@ TEST_RUN_ID = 'manual__2024-04-03' -def _write_prior_annotations_table( - fixture_path: str, - reference_genome: ReferenceGenome, - dataset_type: DatasetType, - exclude_variant_id: str, - max_key_: int, -) -> None: - # The fixture already documents `exclude_variant_id` as an example of a - # newly-added variant. Strip it back out and re-key the remainder so - # WriteNewVariantsTableTask's anti-join rediscovers it as new, at the - # same `key_` the fixture originally asserted. - ht = hl.read_table(fixture_path) - ht = ht.filter(ht.variant_id != exclude_variant_id) - ht = ht.select() - ht = ht.add_index(name='key_') - ht = ht.annotate_globals(max_key_=max_key_) - ht.write(variant_annotations_table_path(reference_genome, dataset_type)) - - class WriteNewVariantDetailsParquetTest(MockedDatarootTestCase): def setUp(self) -> None: super().setUp() - _write_prior_annotations_table( - TEST_SNV_INDEL_ANNOTATIONS, - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - exclude_variant_id='1-876499-A-G', - max_key_=-1, + ht = hl.read_table(TEST_SNV_INDEL_ANNOTATIONS) + ht = ht.filter(ht.variant_id != '1-876499-A-G') + ht = ht.annotate_globals(max_key_=-1) + ht.write( + variant_annotations_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + ), ) - _write_prior_annotations_table( - TEST_GRCH37_SNV_INDEL_ANNOTATIONS, - ReferenceGenome.GRCh37, - DatasetType.SNV_INDEL, - exclude_variant_id='1-69134-A-G', - max_key_=1423, + ht = hl.read_table(TEST_GRCH37_SNV_INDEL_ANNOTATIONS) + ht = ht.filter(ht.variant_id != '1-69134-A-G') + ht = ht.annotate_globals(max_key_=1423) + ht.write( + variant_annotations_table_path( + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + ), ) # Make an incomplete parquet to validate overwrite-ing. diff --git a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py index 00d174a388..2e23befc92 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py @@ -54,55 +54,44 @@ TEST_RUN_ID = 'manual__2024-04-03' -def _write_prior_annotations_table( - fixture_path: str, - reference_genome: ReferenceGenome, - dataset_type: DatasetType, - exclude_variant_id: str, - max_key_: int, -) -> None: - # The fixture already documents `exclude_variant_id` as an example of a - # newly-added variant. Strip it back out and re-key the remainder so - # WriteNewVariantsTableTask's anti-join rediscovers it as new, at the - # same `key_` the fixture originally asserted. - ht = hl.read_table(fixture_path) - ht = ht.filter(ht.variant_id != exclude_variant_id) - ht = ht.select() - ht = ht.add_index(name='key_') - ht = ht.annotate_globals(max_key_=max_key_) - ht.write(variant_annotations_table_path(reference_genome, dataset_type)) - - class WriteNewVariantsParquetTest(MockedReferenceDatasetsTestCase): def setUp(self) -> None: super().setUp() - _write_prior_annotations_table( - TEST_SNV_INDEL_ANNOTATIONS, - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - exclude_variant_id='1-876499-A-G', - max_key_=-1, + ht = hl.read_table(TEST_SNV_INDEL_ANNOTATIONS) + ht = ht.filter(ht.variant_id != '1-876499-A-G') + ht = ht.annotate_globals(max_key_=-1) + ht.write( + variant_annotations_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + ), ) - _write_prior_annotations_table( - TEST_GRCH37_SNV_INDEL_ANNOTATIONS, - ReferenceGenome.GRCh37, - DatasetType.SNV_INDEL, - exclude_variant_id='1-69134-A-G', - max_key_=1423, + ht = hl.read_table(TEST_GRCH37_SNV_INDEL_ANNOTATIONS) + ht = ht.filter(ht.variant_id != '1-69134-A-G') + ht = ht.annotate_globals(max_key_=1423) + ht.write( + variant_annotations_table_path( + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + ), ) - _write_prior_annotations_table( - TEST_MITO_ANNOTATIONS, - ReferenceGenome.GRCh38, - DatasetType.MITO, - exclude_variant_id='M-8-G-T', - max_key_=997, + ht = hl.read_table(TEST_MITO_ANNOTATIONS) + ht = ht.filter(ht.variant_id != 'M-8-G-T') + ht = ht.annotate_globals(max_key_=997) + ht.write( + variant_annotations_table_path( + ReferenceGenome.GRCh38, + DatasetType.MITO, + ), ) - _write_prior_annotations_table( - TEST_SV_ANNOTATIONS, - ReferenceGenome.GRCh38, - DatasetType.SV, - exclude_variant_id='BND_chr1_6', - max_key_=726, + ht = hl.read_table(TEST_SV_ANNOTATIONS) + ht = ht.filter(ht.variant_id != 'BND_chr1_6') + ht = ht.annotate_globals(max_key_=726) + ht.write( + variant_annotations_table_path( + ReferenceGenome.GRCh38, + DatasetType.SV, + ), ) ht = hl.read_table(TEST_GCNV_ANNOTATIONS) ht.write( From 237145a0da4d7eac5ec436b3bbed190377991828 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 20 Aug 2026 17:14:56 -0400 Subject: [PATCH 153/369] fix test setup --- .../exports/write_new_variant_details_parquet_test.py | 4 +++- .../lib/tasks/exports/write_new_variants_parquet_test.py | 8 ++++++-- 2 files changed, 9 insertions(+), 3 deletions(-) diff --git a/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py index 13693dd38a..99c0b4c06f 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py @@ -95,7 +95,9 @@ def test_write_new_variant_details_parquet_test( mock_vep: Mock, mock_load_gencode_ensembl_to_refseq_id: Mock, ) -> None: - mock_load_gencode_ensembl_to_refseq_id.return_value = hl.dict({}) + mock_load_gencode_ensembl_to_refseq_id.return_value = hl.dict( + {'ENST00000327044': 'NM_015658.4'}, + ) mock_vep.side_effect = lambda ht, **_: ht.annotate(vep=MOCK_38_VEP_DATA) copy_project_pedigree_to_mocked_dir( TEST_PEDIGREE_3_REMAP, diff --git a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py index 2e23befc92..f1e9011ff0 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py @@ -118,7 +118,9 @@ def test_write_new_variants_parquet_test( mock_vep: Mock, mock_load_gencode_ensembl_to_refseq_id: Mock, ) -> None: - mock_load_gencode_ensembl_to_refseq_id.return_value = hl.dict({}) + mock_load_gencode_ensembl_to_refseq_id.return_value = hl.dict( + {'ENST00000327044': 'NM_015658.4'}, + ) mock_vep.side_effect = lambda ht, **_: ht.annotate(vep=MOCK_38_VEP_DATA) copy_project_pedigree_to_mocked_dir( TEST_PEDIGREE_3_REMAP, @@ -318,7 +320,9 @@ def test_sv_write_new_variants_parquet_test( self, mock_load_gencode_gene_symbol_to_gene_id: Mock, ) -> None: - mock_load_gencode_gene_symbol_to_gene_id.return_value = hl.dict({}) + mock_load_gencode_gene_symbol_to_gene_id.return_value = hl.dict( + {'PCSK9': 'ENSG00000188157'}, + ) copy_project_pedigree_to_mocked_dir( TEST_PEDIGREE_5, ReferenceGenome.GRCh38, From cdd96e0584defb55d4defc822eb2f55f93a39efe Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 20 Aug 2026 17:25:05 -0400 Subject: [PATCH 154/369] better scoping for new entry helpers --- loading_pipeline/lib/tasks/exports/fields.py | 38 ++++++------------- .../exports/write_new_entries_parquet.py | 19 ++++------ 2 files changed, 20 insertions(+), 37 deletions(-) diff --git a/loading_pipeline/lib/tasks/exports/fields.py b/loading_pipeline/lib/tasks/exports/fields.py index c32d2f7260..9d121c3e73 100644 --- a/loading_pipeline/lib/tasks/exports/fields.py +++ b/loading_pipeline/lib/tasks/exports/fields.py @@ -101,16 +101,13 @@ def get_existing_variants_export_field(dataset_type: DatasetType) -> str: return f'key AS key_, variantId AS variant_id {dt_fields}' -def get_entries_call_annotations_fields( - ht: hl.Table, - dataset_type: DatasetType, -): +def get_entries_call_annotations_fields(dataset_type: DatasetType,): if dataset_type == DatasetType.GCNV: return { - 'start': ht.start_locus.position, - 'end': ht.end_locus.position, - 'num_exon': ht.num_exon, - 'gene_ids': hl.set(ht.sorted_gene_consequences.gene_id), + 'start': lambda ht: ht.start_locus.position, + 'end': lambda ht: ht.end_locus.position, + 'num_exon': lambda ht: ht.num_exon, + 'gene_ids': lambda ht: hl.set(ht.sorted_gene_consequences.gene_id), } return {} @@ -119,7 +116,6 @@ def _get_calls_export_fields( ht: hl.Table, fe: hl.Struct, dataset_type: DatasetType, - call_annotation_fields: set[str], ): return { DatasetType.SNV_INDEL: lambda fe: hl.Struct( @@ -157,7 +153,7 @@ def _get_calls_export_fields( getattr(fe, f'sample_{field}'), getattr(ht, field), ) - for field in call_annotation_fields + for field in get_entries_call_annotations_fields(dataset_type) }, newCall=fe.concordance.new_call, prevCall=fe.concordance.prev_call, @@ -166,16 +162,13 @@ def _get_calls_export_fields( }[dataset_type](fe) -def get_entries_annotations_export_fields( - ht: hl.Table, - dataset_type: DatasetType, -): +def get_entries_annotations_export_fields(dataset_type: DatasetType): fields = { - 'key_': ht.key_, - 'xpos': ht.xpos, + 'key_': lambda ht: ht.key_, + 'xpos': lambda ht: ht.xpos, } if dataset_type in {DatasetType.SV, DatasetType.SNV_INDEL}: - fields['geneIds'] = ( + fields['geneIds'] = lambda ht: ( hl.set(ht.sorted_gene_consequences.gene_id) if dataset_type == DatasetType.SV else ht.set(ht.sorted_gene_consequences.gene_id) @@ -188,13 +181,11 @@ def get_entries_export_fields( dataset_type: DatasetType, sample_type: SampleType, project_guid: str, - annotation_fields: set[str], - call_annotation_fields: set[str], ): return { 'project_guid': project_guid, 'family_guid': ht.family_entries.family_guid[0], - **{field: getattr(ht, field) for field in annotation_fields}, + **{field: getattr(ht, field) for field in get_entries_annotations_export_fields(dataset_type)}, **( { 'sample_type': sample_type.value, @@ -204,12 +195,7 @@ def get_entries_export_fields( ), 'filters': ht.filters, 'calls': hl.sorted(ht.family_entries, key=lambda fe: fe.s).map( - lambda fe: _get_calls_export_fields( - ht, - fe, - dataset_type, - call_annotation_fields, - ), + lambda fe: _get_calls_export_fields(ht, fe, dataset_type), ), 'sign': 1, } diff --git a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py index f6b2e5cfea..cfd95e372d 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py +++ b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py @@ -9,6 +9,7 @@ deduplicate_by_most_non_ref_calls, deglobalize_ids, ) +from loading_pipeline.lib.misc.io import import_parquet from loading_pipeline.lib.paths import ( existing_variants_parquet_path, new_entries_parquet_path, @@ -63,21 +64,19 @@ def requires(self) -> dict[str, luigi.Task]: def create_table(self) -> None: unioned_ht = None - annotation_fields = get_entries_annotations_export_fields( - ht, - self.dataset_type, - ) - call_annotation_fields = get_entries_call_annotations_fields( - ht, - self.dataset_type, - ) annotations_ht = hl.read_table( new_variants_table_path( self.reference_genome, self.dataset_type, self.run_id, ), - ).select(**annotation_fields, **call_annotation_fields) + ) + annotations_ht = annotations_ht.select(**{ + field: func(annotations_ht) for field, func in { + **get_entries_annotations_export_fields(self.dataset_type), + **get_entries_call_annotations_fields(self.dataset_type), + }.items() + }) existing_annotations_ht = import_parquet( existing_variants_parquet_path( @@ -125,8 +124,6 @@ def create_table(self) -> None: self.dataset_type, self.sample_type, project_guid, - set(annotation_fields.keys()), - set(call_annotation_fields.keys()), ), ) unioned_ht = unioned_ht.union(ht) if unioned_ht else ht From 6aa3050c338f0ed1a92785c37a8132d5942874b7 Mon Sep 17 00:00:00 2001 From: hanars Date: Thu, 20 Aug 2026 17:41:48 -0400 Subject: [PATCH 155/369] ruff --- loading_pipeline/lib/tasks/exports/fields.py | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/loading_pipeline/lib/tasks/exports/fields.py b/loading_pipeline/lib/tasks/exports/fields.py index 9d121c3e73..bfc42aa9bf 100644 --- a/loading_pipeline/lib/tasks/exports/fields.py +++ b/loading_pipeline/lib/tasks/exports/fields.py @@ -101,7 +101,9 @@ def get_existing_variants_export_field(dataset_type: DatasetType) -> str: return f'key AS key_, variantId AS variant_id {dt_fields}' -def get_entries_call_annotations_fields(dataset_type: DatasetType,): +def get_entries_call_annotations_fields( + dataset_type: DatasetType, +): if dataset_type == DatasetType.GCNV: return { 'start': lambda ht: ht.start_locus.position, @@ -185,7 +187,10 @@ def get_entries_export_fields( return { 'project_guid': project_guid, 'family_guid': ht.family_entries.family_guid[0], - **{field: getattr(ht, field) for field in get_entries_annotations_export_fields(dataset_type)}, + **{ + field: getattr(ht, field) + for field in get_entries_annotations_export_fields(dataset_type) + }, **( { 'sample_type': sample_type.value, From 97ce36762394bc3c20b1a7c3ee62fe691ac19c0e Mon Sep 17 00:00:00 2001 From: hanars Date: Thu, 20 Aug 2026 17:43:41 -0400 Subject: [PATCH 156/369] ruff --- .../tasks/exports/write_new_entries_parquet.py | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py index ca9bbe6cef..b6095ca14c 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py +++ b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py @@ -71,12 +71,15 @@ def create_table(self) -> None: self.run_id, ), ) - annotations_ht = annotations_ht.select(**{ - field: func(annotations_ht) for field, func in { - **get_entries_annotations_export_fields(self.dataset_type), - **get_entries_call_annotations_fields(self.dataset_type), - }.items() - }) + annotations_ht = annotations_ht.select( + **{ + field: func(annotations_ht) + for field, func in { + **get_entries_annotations_export_fields(self.dataset_type), + **get_entries_call_annotations_fields(self.dataset_type), + }.items() + } + ) existing_annotations_ht = import_parquet( existing_variants_parquet_path( From 3aab4d04b2c25ddb3cc613a0a53c1163e7bac578 Mon Sep 17 00:00:00 2001 From: hanars Date: Thu, 20 Aug 2026 17:47:06 -0400 Subject: [PATCH 157/369] ruff --- loading_pipeline/lib/tasks/exports/fields.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/loading_pipeline/lib/tasks/exports/fields.py b/loading_pipeline/lib/tasks/exports/fields.py index bfc42aa9bf..3b5233b39e 100644 --- a/loading_pipeline/lib/tasks/exports/fields.py +++ b/loading_pipeline/lib/tasks/exports/fields.py @@ -188,7 +188,7 @@ def get_entries_export_fields( 'project_guid': project_guid, 'family_guid': ht.family_entries.family_guid[0], **{ - field: getattr(ht, field) + field: getattr(ht, field) for field in get_entries_annotations_export_fields(dataset_type) }, **( From 27f0f78a3e98fd5f8b3ff5d44e4867b92f9850f8 Mon Sep 17 00:00:00 2001 From: hanars Date: Thu, 20 Aug 2026 17:47:21 -0400 Subject: [PATCH 158/369] ruff --- loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py index b6095ca14c..2d7a979031 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py +++ b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py @@ -73,7 +73,7 @@ def create_table(self) -> None: ) annotations_ht = annotations_ht.select( **{ - field: func(annotations_ht) + field: func(annotations_ht) for field, func in { **get_entries_annotations_export_fields(self.dataset_type), **get_entries_call_annotations_fields(self.dataset_type), From 1b5ffd1c67d2283b020ed52f3f13e2efd17b8a69 Mon Sep 17 00:00:00 2001 From: hanars Date: Thu, 20 Aug 2026 17:51:15 -0400 Subject: [PATCH 159/369] ruff --- loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py index 2d7a979031..2f3da34c13 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py +++ b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py @@ -78,7 +78,7 @@ def create_table(self) -> None: **get_entries_annotations_export_fields(self.dataset_type), **get_entries_call_annotations_fields(self.dataset_type), }.items() - } + }, ) existing_annotations_ht = import_parquet( From a7c3bbb80be84dcb883cf34598fb183c302888a6 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 20 Aug 2026 17:54:53 -0400 Subject: [PATCH 160/369] updated vep mocking --- .../write_new_variant_details_parquet_test.py | 68 ++++++++++++++++++- .../write_new_variants_parquet_test.py | 40 ++++++++++- 2 files changed, 103 insertions(+), 5 deletions(-) diff --git a/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py index 99c0b4c06f..9053c5ac81 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py @@ -41,6 +41,64 @@ TEST_RUN_ID = 'manual__2024-04-03' +SNV_INDEL_GRCH38_MOCK_VEP_DATA = MOCK_38_VEP_DATA.annotate( + transcript_consequences=hl.array( + [ + MOCK_38_VEP_DATA.transcript_consequences[0].annotate( + am_pathogenicity=hl.missing(hl.tfloat32), + exon='6/14', + gene_id='ENSG00000187634', + hgvsc='ENST00000616016.5:c.1049C>T', + hgvsp='ENSP00000478421.2:p.Ser350Leu', + lof=hl.missing(hl.tstr), + lof_filter=hl.missing(hl.tstr), + mane_select='NM_001385641.1', + transcript_id='ENST00000616016', + fiveutr_annotation=hl.dict( + { + '1': hl.struct( + type='OutOfFrame_oORF', + KozakContext='CGCATGC', + KozakStrength='Weak', + DistanceToCDS='41', + CapDistanceToStart=hl.missing(hl.tstr), + DistanceToStop=hl.missing(hl.tstr), + Evidence=hl.missing(hl.tstr), + AltStop=hl.missing(hl.tstr), + AltStopDistanceToCDS=hl.missing(hl.tstr), + FrameWithCDS=hl.missing(hl.tstr), + StartDistanceToCDS=hl.missing(hl.tstr), + newSTOPDistanceToCDS=hl.missing(hl.tstr), + alt_type=hl.missing(hl.tstr), + alt_type_length=hl.missing(hl.tstr), + ref_StartDistanceToCDS=hl.missing(hl.tstr), + ref_type=hl.missing(hl.tstr), + ref_type_length=hl.missing(hl.tstr), + ), + }, + ), + ), + ], + ), +) + +SNV_INDEL_GRCH37_MOCK_VEP_DATA = MOCK_37_VEP_DATA.annotate( + transcript_consequences=hl.array( + [ + MOCK_37_VEP_DATA.transcript_consequences[0].annotate( + amino_acids='E/G', + codons='gAa/gGa', + gene_id='ENSG00000186092', + hgvsc='ENST00000335137.3:c.44A>G', + hgvsp='ENSP00000334393.3:p.Glu15Gly', + transcript_id='ENST00000335137', + lof=hl.missing(hl.tstr), + lof_filter=hl.missing(hl.tstr), + ), + ], + ), +) + class WriteNewVariantDetailsParquetTest(MockedDatarootTestCase): def setUp(self) -> None: @@ -96,9 +154,11 @@ def test_write_new_variant_details_parquet_test( mock_load_gencode_ensembl_to_refseq_id: Mock, ) -> None: mock_load_gencode_ensembl_to_refseq_id.return_value = hl.dict( - {'ENST00000327044': 'NM_015658.4'}, + {'ENST00000616016': 'NM_001385641.1'}, + ) + mock_vep.side_effect = lambda ht, **_: ht.annotate( + vep=SNV_INDEL_GRCH38_MOCK_VEP_DATA, ) - mock_vep.side_effect = lambda ht, **_: ht.annotate(vep=MOCK_38_VEP_DATA) copy_project_pedigree_to_mocked_dir( TEST_PEDIGREE_3_REMAP, ReferenceGenome.GRCh38, @@ -222,7 +282,9 @@ def test_grch37_write_new_variant_details_parquet_test( self, mock_vep: Mock, ) -> None: - mock_vep.side_effect = lambda ht, **_: ht.annotate(vep=MOCK_37_VEP_DATA) + mock_vep.side_effect = lambda ht, **_: ht.annotate( + vep=SNV_INDEL_GRCH37_MOCK_VEP_DATA, + ) copy_project_pedigree_to_mocked_dir( TEST_PEDIGREE_3_REMAP, ReferenceGenome.GRCh37, diff --git a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py index f1e9011ff0..2a573a33e6 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py @@ -53,6 +53,38 @@ TEST_RUN_ID = 'manual__2024-04-03' +SNV_INDEL_GRCH38_MOCK_VEP_DATA = MOCK_38_VEP_DATA.annotate( + motif_feature_consequences=hl.array( + [ + hl.struct( + consequence_terms=hl.array(['TF_binding_site_variant']), + motif_feature_id='motif_1', + ), + ], + ), + regulatory_feature_consequences=hl.array( + [MOCK_38_VEP_DATA.regulatory_feature_consequences[0]], + ), + transcript_consequences=hl.array( + [ + MOCK_38_VEP_DATA.transcript_consequences[0].annotate( + am_pathogenicity=hl.missing(hl.tfloat32), + gene_id='ENSG00000187634', + ), + ], + ), +) + +SNV_INDEL_GRCH37_MOCK_VEP_DATA = MOCK_37_VEP_DATA.annotate( + transcript_consequences=hl.array( + [ + MOCK_37_VEP_DATA.transcript_consequences[0].annotate( + gene_id='ENSG00000186092', + ), + ], + ), +) + class WriteNewVariantsParquetTest(MockedReferenceDatasetsTestCase): def setUp(self) -> None: @@ -121,7 +153,9 @@ def test_write_new_variants_parquet_test( mock_load_gencode_ensembl_to_refseq_id.return_value = hl.dict( {'ENST00000327044': 'NM_015658.4'}, ) - mock_vep.side_effect = lambda ht, **_: ht.annotate(vep=MOCK_38_VEP_DATA) + mock_vep.side_effect = lambda ht, **_: ht.annotate( + vep=SNV_INDEL_GRCH38_MOCK_VEP_DATA, + ) copy_project_pedigree_to_mocked_dir( TEST_PEDIGREE_3_REMAP, ReferenceGenome.GRCh38, @@ -192,7 +226,9 @@ def test_grch37_write_new_variants_parquet_test( self, mock_vep: Mock, ) -> None: - mock_vep.side_effect = lambda ht, **_: ht.annotate(vep=MOCK_37_VEP_DATA) + mock_vep.side_effect = lambda ht, **_: ht.annotate( + vep=SNV_INDEL_GRCH37_MOCK_VEP_DATA, + ) copy_project_pedigree_to_mocked_dir( TEST_PEDIGREE_3_REMAP, ReferenceGenome.GRCh37, From 329e750a91202b38ac776db5d292b0c75adccf26 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 21 Aug 2026 10:44:06 -0400 Subject: [PATCH 161/369] fix new sv test --- .../write_new_variants_parquet_test.py | 30 +++++++++---------- 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py index 2a573a33e6..1605b011f9 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py @@ -38,7 +38,7 @@ TEST_MITO_EXPORT_PEDIGREE = ( 'loading_pipeline/var/test/pedigrees/test_mito_export_pedigree.tsv' ) -TEST_SV_VCF_2 = 'loading_pipeline/var/test/callsets/sv_2.vcf' +TEST_SV_VCF = 'loading_pipeline/var/test/callsets/sv_1.vcf' TEST_PEDIGREE_5 = 'loading_pipeline/var/test/pedigrees/test_pedigree_5.tsv' TEST_SNV_INDEL_ANNOTATIONS = ( @@ -357,7 +357,7 @@ def test_sv_write_new_variants_parquet_test( mock_load_gencode_gene_symbol_to_gene_id: Mock, ) -> None: mock_load_gencode_gene_symbol_to_gene_id.return_value = hl.dict( - {'PCSK9': 'ENSG00000188157'}, + {'TAS1R1': 'ENSG00000173662'}, ) copy_project_pedigree_to_mocked_dir( TEST_PEDIGREE_5, @@ -371,7 +371,7 @@ def test_sv_write_new_variants_parquet_test( reference_genome=ReferenceGenome.GRCh38, dataset_type=DatasetType.SV, sample_type=SampleType.WGS, - callset_path=TEST_SV_VCF_2, + callset_path=TEST_SV_VCF, project_guids=[ 'R0115_test_project2', ], @@ -399,28 +399,28 @@ def test_sv_write_new_variants_parquet_test( [ { 'key': 727, - 'xpos': 1001025886, + 'xpos': 1006558902, 'chrom': '1', - 'pos': 1025886, - 'end': 1028192, - 'rg37LocusEnd': {'contig': '1', 'position': 963572}, - 'variantId': 'BND_chr1_6', + 'pos': 6558902, + 'end': 6559723, + 'rg37LocusEnd': {'contig': '1', 'position': 6619783}, + 'variantId': 'CPX_chr1_22', 'liftedOverChrom': '1', - 'liftedOverPos': 961266, + 'liftedOverPos': 6618962, 'algorithms': 'manta', - 'bothsidesSupport': None, + 'bothsidesSupport': True, 'cpxIntervals': [ - {'chrom': '1', 'start': 1025886, 'end': 1025986, 'type': 'DUP'}, - {'chrom': '1', 'start': 1025886, 'end': 1028192, 'type': 'INV'}, + {'chrom': '1', 'start': 6558902, 'end': 6559723, 'type': 'INV'}, + {'chrom': '1', 'start': 6559655, 'end': 6559723, 'type': 'DUP'}, ], - 'endChrom': '2', + 'endChrom': None, 'svSourceDetail': None, 'svType': 'CPX', - 'svTypeDetail': 'dupINV', + 'svTypeDetail': 'INVdup', 'predictions': {'strvctvre': None}, 'populations': {'gnomad_svs': None}, 'sortedGeneConsequences': [ - {'geneId': 'ENSG00000188157', 'majorConsequence': 'INTRONIC'}, + {'geneId': 'ENSG00000173662', 'majorConsequence': 'INTRONIC'}, ], }, ], From 082984f48b55fd5c3c7582853029a634562905ed Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 21 Aug 2026 11:05:38 -0400 Subject: [PATCH 162/369] fix mito test fixture --- .../lib/tasks/exports/write_new_variants_parquet_test.py | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py index 1605b011f9..6c00f7c89a 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py @@ -109,6 +109,14 @@ def setUp(self) -> None: ) ht = hl.read_table(TEST_MITO_ANNOTATIONS) ht = ht.filter(ht.variant_id != 'M-8-G-T') + ht = ht.join( + hl.Table.parallelize( + [{'locus': hl.Locus('chrM', 3, 'GRCh38'), 'alleles': ['T', 'C']}], + hl.tstruct(locus=hl.tlocus('GRCh38'), alleles=hl.tarray(hl.tstr)), + key=['locus', 'alleles'], + ), + how='outer', + ) ht = ht.annotate_globals(max_key_=997) ht.write( variant_annotations_table_path( From fcc232cc063840b4762a01ca2ff91399d6fb53ff Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 21 Aug 2026 11:09:51 -0400 Subject: [PATCH 163/369] update assertion --- .../lib/tasks/write_existing_variants_parquet_test.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/loading_pipeline/lib/tasks/write_existing_variants_parquet_test.py b/loading_pipeline/lib/tasks/write_existing_variants_parquet_test.py index 238ce84675..a538160a33 100644 --- a/loading_pipeline/lib/tasks/write_existing_variants_parquet_test.py +++ b/loading_pipeline/lib/tasks/write_existing_variants_parquet_test.py @@ -70,7 +70,7 @@ def test_grch37_snv_indel(self): def test_mito(self): df = self._run_task(DatasetType.MITO) - self.assertEqual(list(df.columns), ['key_', 'variant_id', 'xpos']) + self.assertEqual(list(df.columns), ['key_', 'variant_id']) self.assertEqual(len(df), 0) def test_sv(self): From 46d359d26bca4b09f2af271549153432a813942b Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 21 Aug 2026 11:47:27 -0400 Subject: [PATCH 164/369] syntax fix --- .../lib/tasks/write_existing_variants_parquet_test.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/loading_pipeline/lib/tasks/write_existing_variants_parquet_test.py b/loading_pipeline/lib/tasks/write_existing_variants_parquet_test.py index a538160a33..4ee8ffed9a 100644 --- a/loading_pipeline/lib/tasks/write_existing_variants_parquet_test.py +++ b/loading_pipeline/lib/tasks/write_existing_variants_parquet_test.py @@ -11,6 +11,7 @@ from loading_pipeline.lib.test.clickhouse_schema_testcase import ( ClickhouseSchemaTestCase, ) +from loading_pipeline.lib.test.misc import convert_ndarray_to_list from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase TEST_RUN_ID = 'manual__2024-04-03' @@ -48,7 +49,9 @@ def test_snv_indel(self): self.assertEqual(list(df.columns), ['key_', 'variant_id', 'geneIds']) df = df.sort_values('key_').reset_index(drop=True) self.assertEqual( - df[['key_', 'variant_id', 'geneIds']].to_dict('records'), + convert_ndarray_to_list( + df[['key_', 'variant_id', 'geneIds']].to_dict('records'), + ), [ { 'key_': 1, From 25db2044bb0eb38d03b735233252405dd5660c7f Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 21 Aug 2026 15:35:14 -0400 Subject: [PATCH 165/369] test failures --- .../lib/tasks/exports/write_new_variants_parquet_test.py | 2 +- loading_pipeline/var/test/callsets/sv_1.vcf | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py index 6c00f7c89a..6d43a3242e 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py @@ -322,7 +322,7 @@ def test_mito_write_new_variants_parquet_test( TEST_RUN_ID, ), ) - export_json = convert_ndarray_to_list(df.head(1).to_dict('records')) + export_json = convert_ndarray_to_list(df.head(10).to_dict('records')) # TODO debug export_json[0]['sortedTranscriptConsequences'] = [ export_json[0]['sortedTranscriptConsequences'][0], ] diff --git a/loading_pipeline/var/test/callsets/sv_1.vcf b/loading_pipeline/var/test/callsets/sv_1.vcf index 4749496506..22dbba332e 100644 --- a/loading_pipeline/var/test/callsets/sv_1.vcf +++ b/loading_pipeline/var/test/callsets/sv_1.vcf @@ -75,6 +75,7 @@ ##INFO= ##INFO= ##INFO= +##INFO= ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT RGP_164_1 RGP_164_2 RGP_164_3 RGP_164_4 RGP_164_5 chr1 180928 BND_chr1_6 N 657 HIGH_SR_BACKGROUND;UNRESOLVED ALGORITHMS=manta;CHR2=chr5;END=180928;END2=20404;EVIDENCE=PE,SR;PREDICTED_INTERGENIC;PREDICTED_NEAREST_TSS=OR4F5,PLEKHG4B;PREDICTED_NONCODING_BREAKPOINT=DNase;STRANDS=+-;SVLEN=-1;SVTYPE=BND;UNRESOLVED_TYPE=SINGLE_ENDER_+-;AN=8;AC=1;AF=0.04775;N_BI_GENOS=2911;N_HOMREF=2633;N_HET=278;N_HOMALT=0;FREQ_HOMREF=0.9045;FREQ_HET=0.0954998;FREQ_HOMALT=0;MALE_AN=2894;MALE_AC=137;MALE_AF=0.047339;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=1310;MALE_N_HET=137;MALE_N_HOMALT=0;MALE_FREQ_HOMREF=0.905321;MALE_FREQ_HET=0.0946786;MALE_FREQ_HOMALT=0;FEMALE_AN=2906;FEMALE_AC=139;FEMALE_AF=0.047832;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=1314;FEMALE_N_HET=139;FEMALE_N_HOMALT=0;FEMALE_FREQ_HOMREF=0.904336;FEMALE_FREQ_HET=0.0956641;FEMALE_FREQ_HOMALT=0 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 0/0:PE,SR:99:99:0:2:0 0/1:SR:31:99:0:31:1 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:2:0 0/0:PE,SR:99:99:0:2:0 From 54e3d80271e1a72d63218cc5d2ce4b541c954ba6 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 21 Aug 2026 15:35:32 -0400 Subject: [PATCH 166/369] undo debug --- .../lib/tasks/exports/write_new_variants_parquet_test.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py index 6d43a3242e..6c00f7c89a 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py @@ -322,7 +322,7 @@ def test_mito_write_new_variants_parquet_test( TEST_RUN_ID, ), ) - export_json = convert_ndarray_to_list(df.head(10).to_dict('records')) # TODO debug + export_json = convert_ndarray_to_list(df.head(1).to_dict('records')) export_json[0]['sortedTranscriptConsequences'] = [ export_json[0]['sortedTranscriptConsequences'][0], ] From 3797da42db31ac20ecf4d2b7dceac5b80ca6d0b1 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 21 Aug 2026 15:40:22 -0400 Subject: [PATCH 167/369] debug --- .../lib/tasks/exports/write_new_variants_parquet_test.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py index 6c00f7c89a..44684113df 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py @@ -322,7 +322,9 @@ def test_mito_write_new_variants_parquet_test( TEST_RUN_ID, ), ) - export_json = convert_ndarray_to_list(df.head(1).to_dict('records')) + export_json = convert_ndarray_to_list( + df.head(10).to_dict('records'), + ) # TODO debug export_json[0]['sortedTranscriptConsequences'] = [ export_json[0]['sortedTranscriptConsequences'][0], ] From 5de4c680a313f63b02c35a936ead9db0e6d48161 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 14:13:16 -0400 Subject: [PATCH 168/369] initial copy all pipeline code --- loading_pipeline/CLAUDE.md | 82 + loading_pipeline/README.md | 89 + loading_pipeline/__init__.py | 7 + loading_pipeline/api/__init__.py | 0 loading_pipeline/api/__main__.py | 18 + loading_pipeline/api/app.py | 119 + loading_pipeline/api/app_test.py | 140 + loading_pipeline/api/model.py | 105 + loading_pipeline/api/model_test.py | 87 + loading_pipeline/api/request_handlers.py | 107 + loading_pipeline/bin/__init__.py | 0 loading_pipeline/bin/clickhouse_loader.py | 13 + loading_pipeline/bin/dataproc_vep_init.bash | 63 + .../bin/download_vep_reference_data.bash | 71 + .../bin/migrate_all_projects_to_clickhouse.py | 65 + .../bin/migrate_variants_tables.py | 49 + loading_pipeline/bin/pipeline_worker.py | 110 + loading_pipeline/bin/pipeline_worker_test.py | 182 + .../bin/rsync_reference_data.bash | 52 + loading_pipeline/bin/run_task.py | 10 + .../bin/updated_reference_dataset_parquet.py | 37 + loading_pipeline/bin/vep | 21 + loading_pipeline/deploy/Dockerfile | 40 + loading_pipeline/deploy/Dockerfile.vep_GRCh37 | 12 + loading_pipeline/deploy/Dockerfile.vep_GRCh38 | 13 + .../docs/Clickhouse_Design_Notes.md | 202 + loading_pipeline/docs/Diagrams.md | 150 + loading_pipeline/docs/Historial_Context.md | 82 + loading_pipeline/lib/__init__.py | 0 loading_pipeline/lib/annotations/__init__.py | 0 loading_pipeline/lib/annotations/enums.py | 205 + .../lib/annotations/expression_helpers.py | 329 ++ loading_pipeline/lib/annotations/fields.py | 12 + .../lib/annotations/fields_test.py | 118 + loading_pipeline/lib/annotations/gcnv.py | 172 + loading_pipeline/lib/annotations/liftover.py | 30 + loading_pipeline/lib/annotations/misc.py | 98 + loading_pipeline/lib/annotations/mito.py | 61 + loading_pipeline/lib/annotations/shared.py | 51 + loading_pipeline/lib/annotations/snv_indel.py | 118 + .../lib/annotations/snv_indel_test.py | 303 ++ loading_pipeline/lib/annotations/sv.py | 254 + loading_pipeline/lib/annotations/sv_test.py | 171 + loading_pipeline/lib/annotations/vep.py | 182 + loading_pipeline/lib/core/__init__.py | 17 + loading_pipeline/lib/core/constants.py | 14 + loading_pipeline/lib/core/dataset_type.py | 385 ++ loading_pipeline/lib/core/definitions.py | 86 + loading_pipeline/lib/core/definitions_test.py | 144 + loading_pipeline/lib/core/environment.py | 83 + loading_pipeline/lib/core/feature_flag.py | 14 + loading_pipeline/lib/logger.py | 46 + loading_pipeline/lib/methods/__init__.py | 0 loading_pipeline/lib/methods/relatedness.py | 40 + .../lib/methods/relatedness_test.py | 39 + loading_pipeline/lib/methods/sample_qc.py | 154 + loading_pipeline/lib/methods/sex_check.py | 50 + .../lib/methods/sex_check_test.py | 54 + loading_pipeline/lib/misc/__init__.py | 0 loading_pipeline/lib/misc/callsets.py | 129 + loading_pipeline/lib/misc/callsets_test.py | 87 + loading_pipeline/lib/misc/clickhouse.py | 1247 +++++ loading_pipeline/lib/misc/clickhouse_test.py | 1338 +++++ loading_pipeline/lib/misc/family_entries.py | 105 + .../lib/misc/family_entries_test.py | 356 ++ .../lib/misc/family_loading_failures.py | 215 + .../lib/misc/family_loading_failures_test.py | 448 ++ loading_pipeline/lib/misc/gcnv.py | 9 + loading_pipeline/lib/misc/gcnv_test.py | 54 + loading_pipeline/lib/misc/gcp.py | 44 + loading_pipeline/lib/misc/io.py | 336 ++ loading_pipeline/lib/misc/io_test.py | 211 + loading_pipeline/lib/misc/math.py | 9 + loading_pipeline/lib/misc/math_test.py | 12 + loading_pipeline/lib/misc/nested_field.py | 17 + .../lib/misc/nested_field_test.py | 81 + loading_pipeline/lib/misc/pedigree.py | 200 + loading_pipeline/lib/misc/pedigree_test.py | 514 ++ loading_pipeline/lib/misc/requests.py | 14 + loading_pipeline/lib/misc/retry.py | 61 + loading_pipeline/lib/misc/retry_test.py | 69 + loading_pipeline/lib/misc/runs.py | 89 + loading_pipeline/lib/misc/runs_test.py | 84 + loading_pipeline/lib/misc/sample_ids.py | 66 + loading_pipeline/lib/misc/sample_ids_test.py | 160 + loading_pipeline/lib/misc/slack.py | 65 + loading_pipeline/lib/misc/sv.py | 155 + loading_pipeline/lib/misc/sv_test.py | 243 + .../lib/misc/terra_data_repository.py | 80 + .../lib/misc/terra_data_repository_test.py | 321 ++ loading_pipeline/lib/misc/validation.py | 203 + loading_pipeline/lib/misc/validation_test.py | 464 ++ loading_pipeline/lib/misc/vep.py | 29 + loading_pipeline/lib/misc/vets.py | 39 + loading_pipeline/lib/misc/vets_test.py | 104 + loading_pipeline/lib/paths.py | 503 ++ loading_pipeline/lib/paths_test.py | 180 + .../lib/reference_datasets/__init__.py | 0 .../lib/reference_datasets/eigen.py | 7 + .../reference_datasets/gencode/__init__.py | 0 .../gencode/mapping_gene_ids.py | 64 + .../gencode/mapping_gene_ids_tests.py | 64 + .../gnomad_coding_and_noncoding.py | 59 + .../lib/reference_datasets/gnomad_exomes.py | 21 + .../reference_datasets/gnomad_exomes_test.py | 72 + .../lib/reference_datasets/gnomad_genomes.py | 21 + .../reference_datasets/gnomad_genomes_test.py | 72 + .../lib/reference_datasets/gnomad_qc.py | 9 + .../lib/reference_datasets/gnomad_svs.py | 17 + .../lib/reference_datasets/gnomad_svs_test.py | 93 + .../lib/reference_datasets/gnomad_utils.py | 55 + .../lib/reference_datasets/misc.py | 145 + .../reference_datasets/reference_dataset.py | 178 + .../lib/reference_datasets/splice_ai.py | 71 + .../lib/reference_datasets/topmed.py | 22 + loading_pipeline/lib/tasks/__init__.py | 29 + loading_pipeline/lib/tasks/base/__init__.py | 0 .../lib/tasks/base/base_hail_table.py | 71 + .../base/base_loading_pipeline_params.py | 12 + .../lib/tasks/base/base_loading_run_params.py | 36 + .../lib/tasks/base/base_update.py | 26 + loading_pipeline/lib/tasks/base/base_write.py | 14 + .../lib/tasks/base/base_write_parquet.py | 19 + .../tasks/clickhouse_migration/__init__.py | 0 .../migrate_all_projects_to_clickhouse.py | 51 + ..._all_projects_to_clickhouse_on_dataproc.py | 16 + ...migrate_all_projects_to_clickhouse_test.py | 123 + .../migrate_project_to_clickhouse.py | 157 + .../migrate_project_variants_to_clickhouse.py | 119 + ...ate_project_variants_to_clickhouse_test.py | 91 + .../lib/tasks/dataproc/__init__.py | 0 .../dataproc/base_run_job_on_dataproc.py | 147 + .../tasks/dataproc/create_dataproc_cluster.py | 224 + .../dataproc/create_dataproc_cluster_test.py | 162 + loading_pipeline/lib/tasks/dataproc/misc.py | 29 + .../lib/tasks/dataproc/misc_test.py | 51 + .../dataproc/run_pipeline_on_dataproc.py | 16 + .../dataproc/run_pipeline_on_dataproc_test.py | 184 + .../lib/tasks/exports/__init__.py | 0 loading_pipeline/lib/tasks/exports/fields.py | 316 ++ loading_pipeline/lib/tasks/exports/misc.py | 274 + .../lib/tasks/exports/misc_test.py | 484 ++ .../exports/write_new_entries_parquet.py | 100 + .../exports/write_new_entries_parquet_test.py | 423 ++ .../write_new_variant_details_parquet.py | 71 + .../write_new_variant_details_parquet_test.py | 270 + .../exports/write_new_variants_parquet.py | 99 + .../write_new_variants_parquet_test.py | 420 ++ loading_pipeline/lib/tasks/files.py | 49 + loading_pipeline/lib/tasks/files_test.py | 40 + .../lib/tasks/reference_data/__init__.py | 0 .../updated_reference_dataset.py | 27 + .../updated_reference_dataset_parquet.py | 55 + loading_pipeline/lib/tasks/run_pipeline.py | 37 + ...ant_annotations_table_with_new_variants.py | 136 + ...nnotations_table_with_new_variants_test.py | 1349 +++++ .../lib/tasks/validate_callset.py | 144 + .../lib/tasks/validate_callset_test.py | 83 + .../lib/tasks/variants_migration/__init__.py | 0 .../load_clickhouse_variants_tables.py | 137 + .../load_clickhouse_variants_tables_test.py | 148 + .../migrate_variant_details_parquet.py | 76 + .../migrate_variants_parquet.py | 76 + ...s_table_with_dropped_reference_datasets.py | 90 + .../write_clickhouse_load_success_file.py | 56 + .../lib/tasks/write_imported_callset.py | 84 + .../lib/tasks/write_metadata_for_run.py | 146 + .../lib/tasks/write_metadata_for_run_test.py | 188 + .../lib/tasks/write_new_variants_table.py | 222 + .../lib/tasks/write_postprocessed_callset.py | 96 + .../tasks/write_relatedness_check_table.py | 44 + .../write_relatedness_check_table_test.py | 120 + .../lib/tasks/write_relatedness_check_tsv.py | 29 + .../tasks/write_relatedness_check_tsv_test.py | 53 + .../write_remapped_and_subsetted_callset.py | 242 + ...ite_remapped_and_subsetted_callset_test.py | 460 ++ .../lib/tasks/write_sample_qc_json.py | 96 + .../lib/tasks/write_sample_qc_json_test.py | 269 + .../lib/tasks/write_sex_check_table.py | 79 + .../lib/tasks/write_sex_check_table_test.py | 157 + .../lib/tasks/write_success_file.py | 38 + .../lib/tasks/write_success_file_test.py | 34 + .../lib/tasks/write_tdr_metrics_file.py | 42 + .../lib/tasks/write_tdr_metrics_files.py | 28 + .../tasks/write_validation_errors_for_run.py | 128 + .../tasks/write_variant_annotations_vcf.py | 49 + .../write_variant_annotations_vcf_test.py | 91 + loading_pipeline/lib/test/__init__.py | 0 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loading_pipeline/var/test/sex_check/test_sex_check_1.ht/rows/parts/.part-3-a93b296d-ddf8-430d-84d2-a0749044cdd6.crc create mode 100644 loading_pipeline/var/test/sex_check/test_sex_check_1.ht/rows/parts/.part-4-84c212a9-43d8-4473-a697-6bf50d2d3b0e.crc create mode 100644 loading_pipeline/var/test/sex_check/test_sex_check_1.ht/rows/parts/part-0-e4a8a7e1-9a77-4f4d-8910-2c3cff8c815a create mode 100644 loading_pipeline/var/test/sex_check/test_sex_check_1.ht/rows/parts/part-1-a934bed6-9214-4992-94fd-50997d20ac52 create mode 100644 loading_pipeline/var/test/sex_check/test_sex_check_1.ht/rows/parts/part-2-188ceba1-ffa4-4a20-8c72-f488f4a708b7 create mode 100644 loading_pipeline/var/test/sex_check/test_sex_check_1.ht/rows/parts/part-3-a93b296d-ddf8-430d-84d2-a0749044cdd6 create mode 100644 loading_pipeline/var/test/sex_check/test_sex_check_1.ht/rows/parts/part-4-84c212a9-43d8-4473-a697-6bf50d2d3b0e create mode 100644 loading_pipeline/var/test/tdr_metrics.tsv create mode 100644 loading_pipeline/var/test/test_clickhouse_schema.sql create mode 100644 loading_pipeline/var/test/vep/__init__.py create mode 100644 loading_pipeline/var/test/vep/mock_vep_data.py create mode 100644 loading_pipeline/var/vep/GRCh37/vep-GRCh37.json create mode 100644 loading_pipeline/var/vep/GRCh38/vep-GRCh38.json diff --git a/loading_pipeline/CLAUDE.md b/loading_pipeline/CLAUDE.md new file mode 100644 index 0000000000..130889aa15 --- /dev/null +++ b/loading_pipeline/CLAUDE.md @@ -0,0 +1,82 @@ +# CLAUDE.md + +This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository. + +## Quick Commands + +**Python environment setup:** +```bash +pyenv shell 3.11 +uv sync --group dev --locked +``` + +**Run all tests:** +```bash +pyenv shell 3.11 +uv run pytest +``` + +**Run a single test file:** +```bash +pyenv shell 3.11 +uv run pytest loading_pipeline/lib/misc/math_test.py +``` + +**Formatting and linting:** +```bash +pyenv shell 3.11 +uv run ruff format . +uv run ruff check . +``` + +## Project Architecture + +This is a genomic data loading pipeline that ingests variant data from VCF files into ClickHouse via Hail and Luigi. The overall flow: + +``` +VCF Input → Hail Matrix Table → Parquet Files → ClickHouse Staging → Production +``` + +### Core Components + +**`loading_pipeline/lib/tasks/`** — Luigi-based pipeline tasks +- Tasks are defined by their `requires()` method (reverse dependency declaration) +- `RunPipelineTask` is the main entry point that chains together: + - `WriteMetadataForRunTask` (metadata generation) + - `UpdateVariantAnnotationsTableWithNewVariantsTask` (annotation updates) + - `WriteNewEntriesParquetTask` (variant entries → parquet) + - `WriteNewVariantsParquetTask` (variants → parquet) + - `WriteNewVariantDetailsParquetTask` (details → parquet) + - `WriteClickhouseLoadSuccessFileTask` (final atomicity marker) +- Base tasks in `base/` provide shared parameters and utilities + +**`loading_pipeline/lib/annotations/`** — Hail-based variant annotation logic +- Standardizes and reformats VEP, gnomAD, and other annotation fields +- VEP schema defined in `vep*.json` files, parsed in `vep.py` + +**`loading_pipeline/lib/misc/clickhouse/`** — ClickHouse ingestion +- Manages staging table creation and atomic partition movement to production +- Follows the ["Making a Large Data Load Resilient"](https://clickhouse.com/blog/supercharge-your-clickhouse-data-loads-part3) pattern + +**`loading_pipeline/api/`** — REST interface +- `model.py` defines Pydantic schemas for incoming requests +- `app.py` runs an aiohttp server handling load requests + +**`loading_pipeline/bin/pipeline_worker.py`** — Job runner +- Manages asynchronous pipeline jobs requested via the REST API + +### Schema Definitions + +Expected field schemas are defined in `core/dataset_type.py`: +- `col_fields` — variant fields (position, annotation, etc.) +- `entry_fields` — per-sample genotype fields +- `row_fields` — additional row-level metadata + +Test files in `lib/tasks/exports/*_test.py` contain examples of the expected parquet export schemas. + +## Development Notes + +- **Python 3.11 required** — Always activate with `pyenv shell 3.11` before running commands +- **Ruff configuration** — Follows single quotes, 88 char line limit. Test files allow asserts, private access, and high-arity functions +- **ClickHouse tests** — Run locally against a test ClickHouse instance (see README for setup) +- **Tests use pytest** — Not unittest; use `pytest` command directly diff --git a/loading_pipeline/README.md b/loading_pipeline/README.md new file mode 100644 index 0000000000..65910f3f3b --- /dev/null +++ b/loading_pipeline/README.md @@ -0,0 +1,89 @@ +# Seqr Loading Pipeline + +[![Code Build](https://github.com/broadinstitute/seqr-loading-pipelines/actions/workflows/unit-tests.yml/badge.svg?branch=main)](https://github.com/broadinstitute/seqr-loading-pipelines/actions/workflows/unit-tests.yml) +[![Docker Build](https://github.com/broadinstitute/seqr-loading-pipelines/actions/workflows/prod-release.yml/badge.svg?branch=main)](https://github.com/broadinstitute/seqr-loading-pipelines/actions/workflows/prod-release.yml) + +*This repository contains pipelines and infrastructure for loading genomic data from VCF -> ClickHouse to support queries by the _seqr_ application* + +--- + +## 📁 Repository Structure + +### `loading_pipeline/api/` +Contains the interface layer to the _seqr_ application. +- `api/model.py` defines pydantic models for the REST interface. +- `api/app.py` specifies an `aiohttp` webserver that handles load data requests. + +### `loading_pipeline/bin/` +Scripts or command-line utilities used for setup or task execution. +- `bin/pipeline_worker.py` — manages asynchronous jobs requested by _seqr_. + +### `loading_pipeline/deploy/` +Dockerfiles for the loading pipeline itself & any annotation utilities. +Kubernetes manifests are managed separately in [seqr-helm](https://github.com/broadinstitute/seqr-helm/tree/main/charts/pipeline-runner) + +### `loading_pipeline/lib/` +Core logic and shared libraries. +- `annotations` defines hail logic to re-format and standardize fields. +- `methods` wraps hail-defined genomics methods for QC. +- `misc` contains single modules with defined utilities. + - `misc/clickhouse` hosts the logic that manages the parquet ingestion into ClickHouse itself. +- `core` defines key constants/enums/config. +- `reference_datasets` manages parsing of raw reference sources into hail tables. +- `tasks` specifies the Luigi defined pipeline. Note that Luigi pipelines are defined by their requirements, so +the pipeline is defined, effectively, in reverse. + - `WriteClickhouseLoadSuccessFileTask` is the last task, defining a `requires()` method that runs the pipeline either locally or on scalable compute. + - `WriteImportedCallset` is the first task, importing a VCF into a Hail Matrix table, an "imported callset". +- `test` holds a few utilities used by the tests, which are dispersed throughout the rest of the repository. +- `paths.py` defines paths for all intermediate and output files of the pipeline. + +### `loading_pipeline/ops/` +Manual operations scripts. + +### `loading_pipeline/var/` +Static configuration and test files. + +--- + +## ⚙️ Setup for Local Development +The production pipeline runs with python `3.11`. + +### Clone the repo and install python requirements +```bash +git clone https://github.com/broadinstitute/seqr-loading-pipelines.git +cd seqr-loading-pipelines +RUN uv sync --group dev --locked +``` + +### [Install](https://clickhouse.com/docs/getting-started/quick-start/oss) & start ClickHouse with provided test configuration: +> **Note:** We are running ClickHouse `26.3.9-lts` in production. +```bash +curl https://clickhouse.com/ | sh +./clickhouse server --config-file=./seqr-loading-pipelines/loading_pipeline/var/clickhouse_config/test-clickhouse.xml +``` + +### [Run the Tests](https://github.com/broadinstitute/seqr-loading-pipelines/blob/main/.github/workflows/unit-tests.yml#L66-L73) + +### Run an Individual Test +```bash +uv run pytest loading_pipeline/lib/misc/math_test.py +``` + +### Formatting and Linting +```bash +uv run ruff format . +uv run ruff check . +``` + +## 🚪 Schema Entrypoints +- The expected fields and types are defined in `dataset_type.py` as the `col_fields`, `entry_fields`, and `row_fields` properties. Examples +of the SNV_INDEL/MITO/SV/GCNV callset schemas may be found in the tests. +- The VEP schema is defined in JSON within the vep*.json config files, then parsed into hail in `lib/annotations/vep.py`. +- Examples of exported parquets may be found in `lib/tasks/exports/*_parquet_test.py` + + +## 🚶‍♂️ ClickHouse Load Walkthrough +- The Clickhouse Load follows the pattern established in the [Making a Large Data Load Resilient](https://clickhouse.com/blog/supercharge-your-clickhouse-data-loads-part3) blog + - Rows are first loaded into a `staging` database that copies the production `TABLE`s and `MATERIALIZED VIEW`s. + - After all `entries` are inserted, we validate the inserted row count and finalize the per-project allele frequency aggregation. + - Partitions are atomically moved from the `staging` environment to production. diff --git a/loading_pipeline/__init__.py b/loading_pipeline/__init__.py new file mode 100644 index 0000000000..17b3aa3ed3 --- /dev/null +++ b/loading_pipeline/__init__.py @@ -0,0 +1,7 @@ +import datetime + +MAJOR_VERSION = 3 + +__version__ = ( + f'{MAJOR_VERSION}.{datetime.datetime.now(datetime.UTC).strftime("%Y%m%d.%H%M%S")}' +) diff --git a/loading_pipeline/api/__init__.py b/loading_pipeline/api/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/loading_pipeline/api/__main__.py b/loading_pipeline/api/__main__.py new file mode 100644 index 0000000000..38b30d74ef --- /dev/null +++ b/loading_pipeline/api/__main__.py @@ -0,0 +1,18 @@ +from aiohttp import web + +from loading_pipeline.api.app import init_web_app +from loading_pipeline.lib.logger import get_logger + + +def run(): + app = init_web_app() + logger = get_logger(__name__) + web.run_app( + app, + host='0.0.0.0', # noqa: S104 + port=6000, + access_log=logger, + ) + + +run() diff --git a/loading_pipeline/api/app.py b/loading_pipeline/api/app.py new file mode 100644 index 0000000000..90bac06745 --- /dev/null +++ b/loading_pipeline/api/app.py @@ -0,0 +1,119 @@ +import traceback + +import aiofiles +import aiofiles.os +from aiohttp import web, web_exceptions + +from loading_pipeline.api.model import ( + DeleteFamiliesRequest, + LoadingPipelineRequest, + PipelineRunnerRequest, + RebuildGtStatsRequest, + RefreshClickhouseReferenceDataRequest, +) +from loading_pipeline.lib.core.environment import Env +from loading_pipeline.lib.logger import get_logger +from loading_pipeline.lib.misc.runs import is_queue_full, new_run_id +from loading_pipeline.lib.paths import ( + loading_pipeline_queue_dir, + loading_pipeline_queue_path, +) + +logger = get_logger(__name__) + + +@web.middleware +async def error_middleware(request, handler): + try: + return await handler(request) + except web.HTTPError: + logger.exception('HTTPError') + raise + except Exception as e: + logger.exception('Unhandled Exception') + error_reason = f'{e}: {traceback.format_exc()}' + raise web.HTTPInternalServerError(reason=error_reason) from e + + +async def _enqueue_request( + request: web.Request, + model_cls: type[PipelineRunnerRequest], +) -> web.Response: + """Generic helper to enqueue a pipeline request of any type.""" + if not request.body_exists: + raise web.HTTPUnprocessableEntity + + if is_queue_full(): + return web.json_response( + f'Pipeline queue is full. Please try again later. (limit={Env.LOADING_QUEUE_LIMIT})', + status=web_exceptions.HTTPConflict.status_code, + ) + + try: + model_instance = model_cls.model_validate(await request.json()) + except ValueError as e: + raise web.HTTPBadRequest from e + + queue_path = loading_pipeline_queue_path(new_run_id()) + async with aiofiles.open(queue_path, 'w') as f: + await f.write(model_instance.model_dump_json()) + + return web.json_response( + {'Successfully queued': model_instance.model_dump()}, + status=web_exceptions.HTTPAccepted.status_code, + ) + + +async def loading_pipeline_enqueue(request: web.Request) -> web.Response: + return await _enqueue_request( + request, + LoadingPipelineRequest, + ) + + +async def delete_families_enqueue(request: web.Request) -> web.Response: + return await _enqueue_request( + request, + DeleteFamiliesRequest, + ) + + +async def rebuild_gt_stats_enqueue(request: web.Request) -> web.Response: + return await _enqueue_request( + request, + RebuildGtStatsRequest, + ) + + +async def refresh_clickhouse_reference_dataset_enqueue( + request: web.Request, +) -> web.Response: + return await _enqueue_request( + request, + RefreshClickhouseReferenceDataRequest, + ) + + +async def status(_: web.Request) -> web.Response: + return web.json_response({'success': True}) + + +async def init_web_app(): + await aiofiles.os.makedirs( + loading_pipeline_queue_dir(), + exist_ok=True, + ) + app = web.Application(middlewares=[error_middleware]) + app.add_routes( + [ + web.get('/status', status), + web.post('/loading_pipeline_enqueue', loading_pipeline_enqueue), + web.post('/delete_families_enqueue', delete_families_enqueue), + web.post('/rebuild_gt_stats_enqueue', rebuild_gt_stats_enqueue), + web.post( + '/refresh_clickhouse_reference_dataset_enqueue', + refresh_clickhouse_reference_dataset_enqueue, + ), + ], + ) + return app diff --git a/loading_pipeline/api/app_test.py b/loading_pipeline/api/app_test.py new file mode 100644 index 0000000000..f5945c1c41 --- /dev/null +++ b/loading_pipeline/api/app_test.py @@ -0,0 +1,140 @@ +from pathlib import Path + +from aiohttp import web_exceptions +from aiohttp.test_utils import AioHTTPTestCase + +from loading_pipeline.api.app import init_web_app +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + +CALLSET_PATH = str( + Path('loading_pipeline/var/test/callsets/1kg_30variants.vcf').resolve(), +) + + +class AppTest(AioHTTPTestCase, MockedDatarootTestCase): + async def get_application(self): + return await init_web_app() + + async def test_status(self): + async with self.client.request('GET', '/status') as resp: + self.assertEqual(resp.status, 200) + resp_json = await resp.json() + self.assertDictEqual(resp_json, {'success': True}) + + async def test_missing_route(self): + with self.assertLogs(level='ERROR') as _: + async with self.client.request('GET', '/loading_pip') as resp: + self.assertEqual(resp.status, web_exceptions.HTTPNotFound.status_code) + + async def test_loading_pipeline_invalid_requests(self): + with self.assertLogs(level='ERROR') as log: + async with self.client.request('GET', '/loading_pipeline_enqueue') as resp: + self.assertEqual( + resp.status, + web_exceptions.HTTPMethodNotAllowed.status_code, + ) + self.assertTrue( + 'HTTPMethodNotAllowed' in log.output[0], + ) + + with self.assertLogs(level='ERROR') as log: + async with self.client.request('POST', '/loading_pipeline_enqueue') as resp: + self.assertEqual( + resp.status, + web_exceptions.HTTPUnprocessableEntity.status_code, + ) + self.assertTrue( + 'HTTPUnprocessableEntity' in log.output[0], + ) + + body = { + 'callset_path': 'missing.vcf', + 'project_guids': ['project_a'], + 'sample_type': SampleType.WGS.value, + 'reference_genome': ReferenceGenome.GRCh38.value, + 'dataset_type': DatasetType.SNV_INDEL.value, + } + with self.assertLogs(level='ERROR') as log: + async with self.client.request( + 'POST', + '/loading_pipeline_enqueue', + json=body, + ) as resp: + self.assertEqual( + resp.status, + web_exceptions.HTTPBadRequest.status_code, + ) + self.assertTrue( + 'callset_path must point to a file that exists' in log.output[0], + ) + + body = { + 'callset_path': CALLSET_PATH, + 'project_guids': ['project_a'], + 'sample_type': SampleType.WGS.value, + 'reference_genome': ReferenceGenome.GRCh38.value, + 'dataset_type': DatasetType.SNV_INDEL.value, + 'validations_to_skip': ['bad_validation'], + } + with self.assertLogs(level='ERROR') as log: + async with self.client.request( + 'POST', + '/loading_pipeline_enqueue', + json=body, + ) as resp: + self.assertEqual( + resp.status, + web_exceptions.HTTPBadRequest.status_code, + ) + self.assertTrue( + "input_value='bad_validation" in log.output[0], + ) + + async def test_loading_pipeline_enqueue(self): + body = { + 'callset_path': CALLSET_PATH, + 'project_guids': ['project_a'], + 'sample_type': SampleType.WGS.value, + 'reference_genome': ReferenceGenome.GRCh38.value, + 'dataset_type': DatasetType.SNV_INDEL.value, + } + async with self.client.request( + 'POST', + '/loading_pipeline_enqueue', + json=body, + ) as resp: + self.assertEqual( + resp.status, + web_exceptions.HTTPAccepted.status_code, + ) + resp_json = await resp.json() + self.assertDictEqual( + resp_json, + { + 'Successfully queued': { + 'request_type': 'LoadingPipelineRequest', + 'callset_path': CALLSET_PATH, + 'dataset_type': 'SNV_INDEL', + 'project_guids': ['project_a'], + 'reference_genome': 'GRCh38', + 'sample_type': 'WGS', + 'skip_check_sex_and_relatedness': False, + 'skip_expect_tdr_metrics': False, + 'attempt_id': 0, + 'validations_to_skip': [], + }, + }, + ) + + # Second request + body['project_guids'] = ['project_b', 'project_c'] + async with self.client.request( + 'POST', + '/loading_pipeline_enqueue', + json=body, + ) as resp: + self.assertEqual( + resp.status, + web_exceptions.HTTPAccepted.status_code, + ) diff --git a/loading_pipeline/api/model.py b/loading_pipeline/api/model.py new file mode 100644 index 0000000000..4c02078cf6 --- /dev/null +++ b/loading_pipeline/api/model.py @@ -0,0 +1,105 @@ +from typing import Literal + +import hailtop.fs as hfs +from pydantic import ( + AliasChoices, + BaseModel, + Field, + conint, + field_validator, + root_validator, +) + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.misc.clickhouse import ClickhouseReferenceDataset +from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS, SKIPPABLE_VALIDATIONS + +MAX_LOADING_PIPELINE_ATTEMPTS = 5 +STRINGIFIED_SKIPPABLE_VALIDATIONS = [f.__name__ for f in SKIPPABLE_VALIDATIONS] +VALID_FILE_TYPES = ['vcf', 'vcf.gz', 'vcf.bgz', 'mt'] + + +class PipelineRunnerRequest(BaseModel): + request_type: str + + def __init_subclass__(cls, **kwargs): + super().__init_subclass__(**kwargs) + cls.model_fields['request_type'].default = cls.__name__ + + +class LoadingPipelineRequest(PipelineRunnerRequest): + attempt_id: conint(ge=0, le=MAX_LOADING_PIPELINE_ATTEMPTS - 1) = 0 + callset_path: str + project_guids: list[str] = Field( + min_length=1, + frozen=True, + validation_alias=AliasChoices('project_guids', 'projects_to_run'), + ) + sample_type: SampleType + reference_genome: ReferenceGenome + dataset_type: DatasetType + skip_check_sex_and_relatedness: bool = False + skip_expect_tdr_metrics: bool = False + validations_to_skip: list[Literal[*STRINGIFIED_SKIPPABLE_VALIDATIONS]] = [] + + def incr_attempt(self): + if self.attempt_id == (MAX_LOADING_PIPELINE_ATTEMPTS - 1): + return False + self.attempt_id += 1 + return True + + @field_validator('validations_to_skip') + @classmethod + def must_be_known_validation(cls, validations_to_skip): + for v in validations_to_skip: + if v not in set(STRINGIFIED_SKIPPABLE_VALIDATIONS): + msg = f'{v} is not a valid validator' + raise ValueError(msg) + return validations_to_skip + + @root_validator( + pre=True, + ) # the root validator runs before Pydantic parses or coerces field values. + @classmethod + def override_all_validations(cls, values): + if values.get('validations_to_skip') == [ + ALL_VALIDATIONS, + ]: + values['validations_to_skip'] = STRINGIFIED_SKIPPABLE_VALIDATIONS + return values + + @field_validator('callset_path') + @classmethod + def check_valid_callset_path(cls, callset_path: str) -> str: + if not any(callset_path.endswith(file_type) for file_type in VALID_FILE_TYPES): + msg = 'callset_path must be a VCF or a Hail Matrix Table' + raise ValueError(msg) + if '*' in callset_path and not hfs.ls( + callset_path, + ): # note that hfs.ls throws an exception if it cannot find a non-wildcard path + msg = 'callset_path must point to a shard pattern that exists' + raise ValueError(msg) + if '*' not in callset_path and not hfs.exists(callset_path): + msg = 'callset_path must point to a file that exists' + raise ValueError(msg) + return callset_path + + +class DeleteFamiliesRequest(PipelineRunnerRequest): + project_guid: str + family_guids: list[str] = Field( + min_length=1, + frozen=True, + ) + dataset_types: list[DatasetType] = Field(default_factory=lambda: list(DatasetType)) + + +class RebuildGtStatsRequest(PipelineRunnerRequest): + project_guids: list[str] = Field( + min_length=1, + frozen=True, + ) + + +class RefreshClickhouseReferenceDataRequest(PipelineRunnerRequest): + reference_dataset: ClickhouseReferenceDataset diff --git a/loading_pipeline/api/model_test.py b/loading_pipeline/api/model_test.py new file mode 100644 index 0000000000..03bc42ae1a --- /dev/null +++ b/loading_pipeline/api/model_test.py @@ -0,0 +1,87 @@ +import unittest +from pathlib import Path + +from loading_pipeline.api.model import DeleteFamiliesRequest, LoadingPipelineRequest +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType + +CALLSET_PATH = str( + Path('loading_pipeline/var/test/callsets/1kg_30variants.vcf').resolve(), +) + + +class ModelTest(unittest.TestCase): + def test_valid_loading_pipeline_requests(self) -> None: + raw_request = { + 'callset_path': CALLSET_PATH, + 'projects_to_run': ['project_a'], + 'sample_type': SampleType.WGS.value, + 'reference_genome': ReferenceGenome.GRCh38.value, + 'dataset_type': DatasetType.SNV_INDEL.value, + } + lpr = LoadingPipelineRequest.model_validate(raw_request) + self.assertEqual(lpr.reference_genome, ReferenceGenome.GRCh38) + self.assertEqual(lpr.project_guids, ['project_a']) + self.assertEqual(lpr.request_type, 'LoadingPipelineRequest') + self.assertEqual(lpr.attempt_id, 0) + + # Test wildcard VCF + raw_request['callset_path'] = CALLSET_PATH.replace( + '1kg_30variants.vcf', + '1kg_30*.vcf', + ) + lpr = LoadingPipelineRequest.model_validate(raw_request) + + def test_invalid_loading_pipeline_requests(self) -> None: + raw_request = { + 'callset_path': 'a.txt', + 'project_guids': [], + 'sample_type': 'BLENDED', + 'reference_genome': ReferenceGenome.GRCh38.value, + 'dataset_type': DatasetType.SNV_INDEL.value, + 'attempt_id': 5, + } + with self.assertRaises(ValueError) as cm: + LoadingPipelineRequest.model_validate(raw_request) + self.assertTrue( + str(cm.exception).startswith( + '4 validation errors for LoadingPipelineRequest', + ), + ) + + def test_validations_to_skip(self) -> None: + shared_params = { + 'callset_path': CALLSET_PATH, + 'projects_to_run': ['project_a'], + 'sample_type': SampleType.WGS.value, + 'reference_genome': ReferenceGenome.GRCh38.value, + 'dataset_type': DatasetType.SNV_INDEL.value, + } + raw_request = { + **shared_params, + 'validations_to_skip': ['all'], + } + lpr = LoadingPipelineRequest.model_validate(raw_request) + self.assertGreater(len(lpr.validations_to_skip), 2) + + raw_request = { + **shared_params, + 'validations_to_skip': ['validate_sample_type'], + } + lpr = LoadingPipelineRequest.model_validate(raw_request) + self.assertEqual(len(lpr.validations_to_skip), 1) + + raw_request = { + **shared_params, + 'validations_to_skip': ['validate_blended_exome'], + } + with self.assertRaises(ValueError): + LoadingPipelineRequest.model_validate(raw_request) + + def test_delete_families_request(self) -> None: + raw_request = {'project_guid': 'project_a', 'family_guids': []} + with self.assertRaises(ValueError): + DeleteFamiliesRequest.model_validate(raw_request) + raw_request['family_guids'] = ['family_a1'] + dfr = DeleteFamiliesRequest.model_validate(raw_request) + self.assertEqual(dfr.project_guid, 'project_a') + self.assertEqual(dfr.request_type, 'DeleteFamiliesRequest') diff --git a/loading_pipeline/api/request_handlers.py b/loading_pipeline/api/request_handlers.py new file mode 100644 index 0000000000..62e46f0b4d --- /dev/null +++ b/loading_pipeline/api/request_handlers.py @@ -0,0 +1,107 @@ +from collections.abc import Callable +from typing import Any + +import luigi +import luigi.execution_summary + +from loading_pipeline.api.model import ( + DeleteFamiliesRequest, + LoadingPipelineRequest, + PipelineRunnerRequest, + RebuildGtStatsRequest, + RefreshClickhouseReferenceDataRequest, +) +from loading_pipeline.lib.core import DatasetType +from loading_pipeline.lib.logger import get_logger +from loading_pipeline.lib.misc.clickhouse import ( + ClickhouseReferenceDataset, + delete_family_guids, + rebuild_gt_stats, + refresh_clickhouse_reference_data, +) +from loading_pipeline.lib.tasks.write_clickhouse_load_success_file import ( + WriteClickhouseLoadSuccessFileTask, +) + +logger = get_logger(__name__) + + +def run_loading_pipeline( + lpr: LoadingPipelineRequest, + run_id: str, + local_scheduler: bool, + *_: Any, +): + luigi_task_result = luigi.build( + [ + WriteClickhouseLoadSuccessFileTask( + run_id=run_id, + **lpr.model_dump(exclude='request_type'), + ), + ], + detailed_summary=True, + local_scheduler=local_scheduler, + ) + if luigi_task_result.status in { + luigi.execution_summary.LuigiStatusCode.SUCCESS, + luigi.execution_summary.LuigiStatusCode.SUCCESS_WITH_RETRY, + }: + return + raise RuntimeError(luigi_task_result.status.value[1]) + + +def run_delete_families(dpr: DeleteFamiliesRequest, run_id: str, *_: Any): + for dataset_type in dpr.dataset_types: + for reference_genome in dataset_type.reference_genomes: + delete_family_guids( + reference_genome, + dataset_type, + run_id, + **dpr.model_dump(exclude={'request_type', 'dataset_types'}), + ) + + +def run_rebuild_gt_stats(rgsr: RebuildGtStatsRequest, run_id: str, *_: Any): + for dataset_type in DatasetType: + for reference_genome in dataset_type.reference_genomes: + rebuild_gt_stats( + reference_genome, + dataset_type, + run_id, + **rgsr.model_dump(exclude='request_type'), + ) + + +def run_refresh_clickhouse_reference_data( + rcrdr: RefreshClickhouseReferenceDataRequest, + run_id: str, + *_: Any, +): + for dataset_type in DatasetType: + for reference_genome in dataset_type.reference_genomes: + reference_dataset = rcrdr.reference_dataset + if ( + reference_dataset + not in ClickhouseReferenceDataset.for_reference_genome_dataset_type( + reference_genome, + dataset_type, + ) + ): + continue + refresh_clickhouse_reference_data( + reference_genome, + dataset_type, + run_id, + **rcrdr.model_dump(exclude='request_type'), + ) + + +REQUEST_HANDLER_MAP: dict[ + type[PipelineRunnerRequest], + Callable[[PipelineRunnerRequest, str, ...], None], +] = { + LoadingPipelineRequest: run_loading_pipeline, + DeleteFamiliesRequest: run_delete_families, + RebuildGtStatsRequest: run_rebuild_gt_stats, + RefreshClickhouseReferenceDataRequest: run_refresh_clickhouse_reference_data, +} diff --git a/loading_pipeline/bin/__init__.py b/loading_pipeline/bin/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/loading_pipeline/bin/clickhouse_loader.py b/loading_pipeline/bin/clickhouse_loader.py new file mode 100644 index 0000000000..acb9f615c2 --- /dev/null +++ b/loading_pipeline/bin/clickhouse_loader.py @@ -0,0 +1,13 @@ +# This is a shim loader intended to keep previously deployed seqr-platform +# charts that pull a new docker image running. + +import time + + +def main(): + while True: + time.sleep(5) + + +if __name__ == '__main__': + main() diff --git a/loading_pipeline/bin/dataproc_vep_init.bash b/loading_pipeline/bin/dataproc_vep_init.bash new file mode 100755 index 0000000000..ec049e3217 --- /dev/null +++ b/loading_pipeline/bin/dataproc_vep_init.bash @@ -0,0 +1,63 @@ +#!/bin/bash + +# +# VEP init action for dataproc +# +# adapted/copied from +# https://github.com/broadinstitute/gnomad_methods/blob/main/init_scripts/vep105-init.sh +# and gs://hail-common/hailctl/dataproc/0.2.128/vep-GRCh38.sh +# +# NB: This is code used for initializing a dataproc cluster and runs as an intialization +# action when the rest of our code is unavailable. +# + +set -x + +export PROJECT="$(gcloud config get-value project)" +export DEPLOYMENT_TYPE="$(/usr/share/google/get_metadata_value attributes/DEPLOYMENT_TYPE)" +export REFERENCE_GENOME="$(/usr/share/google/get_metadata_value attributes/REFERENCE_GENOME)" +export PIPELINE_RUNNER_APP_VERSION="$(/usr/share/google/get_metadata_value attributes/PIPELINE_RUNNER_APP_VERSION)" +export REFERENCE_DATASETS_DIR="$(/usr/share/google/get_metadata_value attributes/REFERENCE_DATASETS_DIR)" + +# Install docker +apt-get update +apt-get -y install \ + apt-transport-https \ + ca-certificates \ + curl \ + gnupg2 \ + software-properties-common \ + tabix +curl -fsSL https://download.docker.com/linux/debian/gpg | sudo apt-key add - +sudo add-apt-repository "deb [arch=amd64] https://download.docker.com/linux/debian $(lsb_release -cs) stable" +sudo add-apt-repository "deb [arch=amd64] https://download.docker.com/linux/debian $(lsb_release -cs) stable" +apt-get update +apt-get install -y --allow-unauthenticated docker-ce + +# https://github.com/hail-is/hail/issues/12936 +sleep 60 +sudo service docker restart + +cat >/vep.c < +#include + +int +main(int argc, char *const argv[]) { + if (setuid(geteuid())) + perror( "setuid" ); + + execv("/vep.bash", argv); + return 0; +} +EOF +gcc -Wall -Werror -O2 /vep.c -o /vep +chmod u+s /vep + +gcloud storage cp gs://seqr-pipeline-runner-builds/$DEPLOYMENT_TYPE/$PIPELINE_RUNNER_APP_VERSION/bin/download_vep_reference_data.bash /download_vep_reference_data.bash +chmod +x /download_vep_reference_data.bash +./download_vep_reference_data.bash $REFERENCE_GENOME + +gcloud storage cp gs://seqr-pipeline-runner-builds/$DEPLOYMENT_TYPE/$PIPELINE_RUNNER_APP_VERSION/bin/vep /vep.bash +chmod +x /vep.bash + diff --git a/loading_pipeline/bin/download_vep_reference_data.bash b/loading_pipeline/bin/download_vep_reference_data.bash new file mode 100755 index 0000000000..c1784d80ac --- /dev/null +++ b/loading_pipeline/bin/download_vep_reference_data.bash @@ -0,0 +1,71 @@ +#!/usr/bin/env bash + +set -eux + +REFERENCE_GENOME=$1 +VEP_REFERENCE_DATASETS_DIR=${VEP_REFERENCE_DATASETS_DIR:-/var/seqr/vep-reference-data} +DEFAULT_REFERENCE_DATASETS_DIR="gs://seqr-reference-data" +if [[ -n "${REFERENCE_DATASETS_DIR:-}" && "$REFERENCE_DATASETS_DIR" == gs://* ]]; then + echo "Using overridden GCS path: $REFERENCE_DATASETS_DIR" +else + REFERENCE_DATASETS_DIR="$DEFAULT_REFERENCE_DATASETS_DIR" + echo "Using default GCS path: $REFERENCE_DATASETS_DIR" +fi + +case $REFERENCE_GENOME in + GRCh38) + VEP_REFERENCE_DATA_FILES=( + "$REFERENCE_DATASETS_DIR/vep_data/loftee-beta/GRCh38.tar.gz" + + # Raw data files copied from the bucket (https://console.cloud.google.com/storage/browser/dm_alphamissense;tab=objects?prefix=&forceOnObjectsSortingFiltering=false) + # tabix -s 1 -b 2 -e 2 -f -S 1 AlphaMissense_hg38.tsv.gz + "$REFERENCE_DATASETS_DIR/vep/GRCh38/AlphaMissense_hg38.tsv.*" + + # Generated with: + # curl -O ftp://ftp.ensembl.org/pub/release-110/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz > Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz + # gzip -d Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz + # bgzip Homo_sapiens.GRCh38.dna.primary_assembly.fa + # samtools faidx Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz + "$REFERENCE_DATASETS_DIR/vep/GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa.*" + + # Copied from ftp://ftp.ensembl.org/pub/release-110/variation/indexed_vep_cache/homo_sapiens_vep_110_GRCh38.tar.gz + "$REFERENCE_DATASETS_DIR/vep/GRCh38/homo_sapiens_vep_110_GRCh38.tar.gz" + + # Copied from the UTRAnnotator repo (https://github.com/ImperialCardioGenetics/UTRannotator/tree/master) + "$REFERENCE_DATASETS_DIR/vep/GRCh38/uORF_5UTR_GRCh38_PUBLIC.txt" + + "$REFERENCE_DATASETS_DIR/vep/GRCh38/vep-GRCh38.json" + ) + ;; + GRCh37) + VEP_REFERENCE_DATA_FILES=( + "$REFERENCE_DATASETS_DIR/vep_data/loftee-beta/GRCh37.tar.gz" + "$REFERENCE_DATASETS_DIR/vep/GRCh37/homo_sapiens_vep_110_GRCh37.tar.gz" + "$REFERENCE_DATASETS_DIR/vep/GRCh37/Homo_sapiens.GRCh37.dna.primary_assembly.fa.*" + "$REFERENCE_DATASETS_DIR/vep/GRCh37/vep-GRCh37.json" + ) + ;; + *) + echo "Invalid reference genome $REFERENCE_GENOME, should be GRCh37 or GRCh38" + exit 1 +esac + +if [ -f "$VEP_REFERENCE_DATASETS_DIR"/"$REFERENCE_GENOME"/_SUCCESS ]; then + echo "Skipping download because already successful" + exit 0; +fi + +mkdir -p "$VEP_REFERENCE_DATASETS_DIR"/"$REFERENCE_GENOME"; +rm -rf "${VEP_REFERENCE_DATASETS_DIR:?}"/"${REFERENCE_GENOME:?}"/*; + +for vep_reference_data_file in "${VEP_REFERENCE_DATA_FILES[@]}"; do + if [[ $vep_reference_data_file == *.tar.gz ]]; then + echo "Downloading and extracting" "$vep_reference_data_file"; + gsutil cat "$vep_reference_data_file" | tar -xzf - -C "$VEP_REFERENCE_DATASETS_DIR"/"$REFERENCE_GENOME"/ & + else + echo "Downloading" "$vep_reference_data_file"; + gsutil cp "$vep_reference_data_file" "$VEP_REFERENCE_DATASETS_DIR"/"$REFERENCE_GENOME"/ & + fi +done; +wait +touch "$VEP_REFERENCE_DATASETS_DIR"/"$REFERENCE_GENOME"/_SUCCESS diff --git a/loading_pipeline/bin/migrate_all_projects_to_clickhouse.py b/loading_pipeline/bin/migrate_all_projects_to_clickhouse.py new file mode 100755 index 0000000000..bc691738c3 --- /dev/null +++ b/loading_pipeline/bin/migrate_all_projects_to_clickhouse.py @@ -0,0 +1,65 @@ +#!/usr/bin/env python3 +import uuid + +import hailtop.fs as hfs +import luigi + +from loading_pipeline.lib.core import ( + DatasetType, + FeatureFlag, + ReferenceGenome, + SampleType, +) +from loading_pipeline.lib.core.constants import MIGRATION_RUN_ID +from loading_pipeline.lib.paths import project_table_path +from loading_pipeline.lib.tasks import ( + MigrateAllProjectsToClickHouseOnDataprocTask, + MigrateAllProjectsToClickHouseTask, +) +from loading_pipeline.lib.tasks.write_clickhouse_load_success_file import ( + WriteClickhouseLoadSuccessFileTask, +) + +if __name__ == '__main__': + task_cls = ( + MigrateAllProjectsToClickHouseOnDataprocTask + if FeatureFlag.RUN_PIPELINE_ON_DATAPROC + else MigrateAllProjectsToClickHouseTask + ) + run_id_prefix = ( + MIGRATION_RUN_ID + '-' + str(uuid.uuid1().int)[:4] + ) # Note: the randomness is a cache bust for the luigi local scheduler + luigi.build( + [ + task_cls( + reference_genome, + DatasetType.SNV_INDEL, + run_id=run_id_prefix, + attempt_id=0, + ) + for reference_genome in ReferenceGenome + ], + ) + clickhouse_load_tasks = [] + for sample_type in SampleType: + for reference_genome in ReferenceGenome: + for p in hfs.ls( + project_table_path( + reference_genome, + DatasetType.SNV_INDEL, + sample_type, + '*', + ), + ): + project_guid = p.path.split('/')[-1].replace('.ht', '') + clickhouse_load_tasks.append( + WriteClickhouseLoadSuccessFileTask( + reference_genome=reference_genome, + dataset_type=DatasetType.SNV_INDEL, + run_id=f'{run_id_prefix}_{sample_type.value}_{project_guid}', + callset_path='', + sample_type=sample_type, + attempt_id=0, + ), + ) + luigi.build(clickhouse_load_tasks) diff --git a/loading_pipeline/bin/migrate_variants_tables.py b/loading_pipeline/bin/migrate_variants_tables.py new file mode 100755 index 0000000000..a34e9e9026 --- /dev/null +++ b/loading_pipeline/bin/migrate_variants_tables.py @@ -0,0 +1,49 @@ +#!/usr/bin/env python3 +import argparse +import uuid + +import luigi + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome +from loading_pipeline.lib.core.constants import VARIANTS_MIGRATION_RUN_ID +from loading_pipeline.lib.tasks.variants_migration.load_clickhouse_variants_tables import ( + LoadClickhouseVariantsTablesTask, +) + + +def parse_args() -> argparse.Namespace: + parser = argparse.ArgumentParser( + description='Run variants migration Luigi pipeline.', + ) + parser.add_argument( + '--run_all_dataset_types', + action='store_true', + help='If set, runs the pipeline for all dataset types instead of just SNV_INDEL.', + ) + return parser.parse_args() + + +if __name__ == '__main__': + args = parse_args() + for reference_genome, dataset_type in [ + (ReferenceGenome.GRCh37, DatasetType.SNV_INDEL), + (ReferenceGenome.GRCh38, DatasetType.SNV_INDEL), + (ReferenceGenome.GRCh38, DatasetType.MITO), + (ReferenceGenome.GRCh38, DatasetType.SV), + (ReferenceGenome.GRCh38, DatasetType.GCNV), + ]: + if dataset_type != DatasetType.SNV_INDEL and not args.run_all_dataset_types: + continue + run_id_prefix = ( + VARIANTS_MIGRATION_RUN_ID + '-' + str(uuid.uuid1().int)[:4] + ) # Note: the randomness is a cache bust for the luigi local scheduler + luigi.build( + [ + LoadClickhouseVariantsTablesTask( + reference_genome, + dataset_type, + run_id=run_id_prefix, + attempt_id=0, + ), + ], + ) diff --git a/loading_pipeline/bin/pipeline_worker.py b/loading_pipeline/bin/pipeline_worker.py new file mode 100755 index 0000000000..4760cc37b3 --- /dev/null +++ b/loading_pipeline/bin/pipeline_worker.py @@ -0,0 +1,110 @@ +#!/usr/bin/env python3 +import json +import os +import re +import signal +import sys +import time + +from loading_pipeline.api.model import ( + PipelineRunnerRequest, +) +from loading_pipeline.api.request_handlers import REQUEST_HANDLER_MAP +from loading_pipeline.lib.logger import get_logger +from loading_pipeline.lib.misc.clickhouse import ( + drop_staging_db, +) +from loading_pipeline.lib.misc.runs import get_oldest_queue_path +from loading_pipeline.lib.misc.slack import ( + safe_post_to_slack_failure, + safe_post_to_slack_success, +) +from loading_pipeline.lib.paths import ( + loading_pipeline_deadletter_queue_dir, + loading_pipeline_deadletter_queue_path, + loading_pipeline_queue_path, +) + +logger = get_logger(__name__) + + +def signal_handler(*_): + drop_staging_db() + sys.exit(0) + + +signal.signal(signal.SIGINT, signal_handler) +signal.signal(signal.SIGTERM, signal_handler) + + +def parse_run_id(latest_queue_path: str) -> str: + m = re.search( + r'request_(\d{8}-\d{6}-\d{6})\.json', + os.path.basename(latest_queue_path), + ) + if not m: + msg = f'Invalid queue filename: {latest_queue_path}' + raise ValueError(msg) + return m.group(1) + + +def parse_latest_queue_path( + latest_queue_path: str, +) -> PipelineRunnerRequest: + with open(latest_queue_path) as f: + raw_json = json.load(f) + request_type_name = raw_json['request_type'] + request_cls = next( + (cls for cls in REQUEST_HANDLER_MAP if cls.__name__ == request_type_name), + None, + ) + if not request_cls: + msg = f'Unknown request_type: {request_type_name}' + raise ValueError(msg) + return request_cls.model_validate(raw_json) + + +def process_queue(local_scheduler=False): + run_id, prr = None, None + try: + latest_queue_path = get_oldest_queue_path() + if latest_queue_path is None: + return + run_id = parse_run_id(latest_queue_path) + if not run_id: + return + prr = parse_latest_queue_path(latest_queue_path) + REQUEST_HANDLER_MAP[type(prr)](prr, run_id, local_scheduler) + os.remove(latest_queue_path) + safe_post_to_slack_success( + run_id, + prr, + ) + except Exception as e: + logger.exception('Unhandled Exception') + if run_id is None: + return + if hasattr(prr, 'attempt_id') and prr.incr_attempt(): + with open(loading_pipeline_queue_path(run_id), 'w') as f: + f.write(prr.model_dump_json()) + return + safe_post_to_slack_failure( + run_id, + prr, + e, + ) + os.makedirs(loading_pipeline_deadletter_queue_dir(), exist_ok=True) + with open(loading_pipeline_deadletter_queue_path(run_id), 'w') as f: + f.write(prr.model_dump_json()) + os.remove(latest_queue_path) + + +def main(): + while True: + process_queue() + logger.info('Looking for more work') + time.sleep(1) + + +if __name__ == '__main__': + main() diff --git a/loading_pipeline/bin/pipeline_worker_test.py b/loading_pipeline/bin/pipeline_worker_test.py new file mode 100644 index 0000000000..e258d0c573 --- /dev/null +++ b/loading_pipeline/bin/pipeline_worker_test.py @@ -0,0 +1,182 @@ +import json +import os +from unittest.mock import Mock, patch + +import hail as hl +import hailtop.fs as hfs +import luigi +import luigi.worker + +from loading_pipeline.bin.pipeline_worker import process_queue +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.core.environment import Env +from loading_pipeline.lib.misc.clickhouse import ( + ClickhouseReferenceDataset, + get_clickhouse_client, +) +from loading_pipeline.lib.paths import ( + clickhouse_load_success_file_path, + loading_pipeline_deadletter_queue_dir, + loading_pipeline_queue_dir, +) +from loading_pipeline.lib.test.clickhouse_schema_testcase import ( + ClickhouseSchemaTestCase, +) +from loading_pipeline.lib.test.misc import copy_project_pedigree_to_mocked_dir +from loading_pipeline.lib.test.mocked_dataroot_testcase import ( + MockedDatarootTestCase, +) +from loading_pipeline.var.test.vep.mock_vep_data import MOCK_38_VEP_DATA + +TEST_PEDIGREE_3_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_3_remap.tsv' +TEST_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' + + +class MyFailingTask(luigi.Task): + def run(self): + msg = 'This task is designed to fail!' + raise ValueError(msg) + + def output(self): + return luigi.LocalTarget('output.txt') + + +class PipelineWorkerTest(MockedDatarootTestCase, ClickhouseSchemaTestCase): + @patch.object( + ClickhouseReferenceDataset, + 'for_reference_genome_dataset_type', + return_value=[ClickhouseReferenceDataset.CLINVAR], + ) + @patch( + 'loading_pipeline.lib.tasks.write_new_variants_table.load_gencode_ensembl_to_refseq_id', + ) + @patch('loading_pipeline.lib.misc.vep.hl.vep') + @patch('loading_pipeline.lib.misc.slack._safe_post_to_slack') + @patch('loading_pipeline.bin.pipeline_worker.logger') + def test_process_queue_integration_test( + self, + mock_logger, + mock_safe_post_to_slack, + mock_vep: Mock, + mock_load_gencode_ensembl_to_refseq_id: Mock, + mock_for_reference_genome_dataset_type: Mock, + ): + mock_load_gencode_ensembl_to_refseq_id.return_value = hl.dict( + {'ENST00000327044': 'NM_015658.4'}, + ) + mock_vep.side_effect = lambda ht, **_: ht.annotate(vep=MOCK_38_VEP_DATA) + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_3_REMAP, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0113_test_project', + ) + raw_request = { + 'request_type': 'LoadingPipelineRequest', + 'callset_path': TEST_VCF, + 'projects_to_run': ['R0113_test_project'], + 'sample_type': SampleType.WGS.value, + 'reference_genome': ReferenceGenome.GRCh38.value, + 'dataset_type': DatasetType.SNV_INDEL.value, + 'validations_to_skip': ['all'], + } + os.makedirs( + loading_pipeline_queue_dir(), + exist_ok=True, + ) + with open( + os.path.join( + loading_pipeline_queue_dir(), + 'request_20250916-200704-123456.json', + ), + 'w', + ) as f: + json.dump(raw_request, f) + process_queue(local_scheduler=True) + mock_safe_post_to_slack.assert_called_once_with( + ':white_check_mark: Pipeline Runner Request Success! :white_check_mark:\nRun ID: 20250916-200704-123456\n```{\n "attempt_id": 0,\n "callset_path": "loading_pipeline/var/test/callsets/1kg_30variants.vcf",\n "dataset_type": "SNV_INDEL",\n "project_guids": [\n "R0113_test_project"\n ],\n "reference_genome": "GRCh38",\n "request_type": "LoadingPipelineRequest",\n "sample_type": "WGS",\n "skip_check_sex_and_relatedness": false,\n "skip_expect_tdr_metrics": false,\n "validations_to_skip": [\n "validate_allele_depth_length",\n "validate_allele_type",\n "validate_expected_contig_frequency",\n "validate_no_duplicate_variants",\n "validate_sample_type"\n ]\n}```', + ) + with hfs.open( + clickhouse_load_success_file_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + '20250916-200704-123456', + ), + ) as f: + self.assertEqual(f.read(), '') + + client = get_clickhouse_client() + annotations_count = client.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` + """, + )[0][0] + self.assertEqual(annotations_count, 30) + entries_count = client.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` + """, + )[0][0] + self.assertEqual(entries_count, 16) + ac_wgs = client.execute( + f""" + SELECT sum(ac_wgs) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` + """, + )[0][0] + self.assertEqual(ac_wgs, 69) + + @patch('loading_pipeline.lib.misc.slack._safe_post_to_slack') + @patch('loading_pipeline.api.request_handlers.WriteClickhouseLoadSuccessFileTask') + @patch('loading_pipeline.bin.pipeline_worker.logger') + def test_process_failure( + self, + mock_logger, + mock_write_clickhouse_load_success_file_task, + mock_safe_post_to_slack, + ): + raw_request = { + 'request_type': 'LoadingPipelineRequest', + 'callset_path': TEST_VCF, + 'projects_to_run': ['project_a'], + 'sample_type': SampleType.WGS.value, + 'reference_genome': ReferenceGenome.GRCh38.value, + 'dataset_type': DatasetType.SNV_INDEL.value, + } + mock_write_clickhouse_load_success_file_task.return_value = MyFailingTask() + os.makedirs( + loading_pipeline_queue_dir(), + exist_ok=True, + ) + with open( + os.path.join( + loading_pipeline_queue_dir(), + 'request_20250918-200704-123456.json', + ), + 'w', + ) as f: + json.dump(raw_request, f) + process_queue(local_scheduler=True) + process_queue(local_scheduler=True) + process_queue(local_scheduler=True) + process_queue(local_scheduler=True) + process_queue(local_scheduler=True) + mock_safe_post_to_slack.assert_called_once_with( + ':failed: Pipeline Runner Request Failed :failed:\nRun ID: 20250918-200704-123456\n```{\n "attempt_id": 4,\n "callset_path": "loading_pipeline/var/test/callsets/1kg_30variants.vcf",\n "dataset_type": "SNV_INDEL",\n "project_guids": [\n "project_a"\n ],\n "reference_genome": "GRCh38",\n "request_type": "LoadingPipelineRequest",\n "sample_type": "WGS",\n "skip_check_sex_and_relatedness": false,\n "skip_expect_tdr_metrics": false,\n "validations_to_skip": []\n}```\nReason: there were failed tasks', + ) + self.assertEqual(len(os.listdir(loading_pipeline_queue_dir())), 0) + with open( + os.path.join( + loading_pipeline_deadletter_queue_dir(), + 'request_20250918-200704-123456.json', + ), + ) as f: + r = json.load(f) + self.assertEqual(r['request_type'], 'LoadingPipelineRequest') + self.assertEqual(r['attempt_id'], 4) diff --git a/loading_pipeline/bin/rsync_reference_data.bash b/loading_pipeline/bin/rsync_reference_data.bash new file mode 100755 index 0000000000..360a6d6e1a --- /dev/null +++ b/loading_pipeline/bin/rsync_reference_data.bash @@ -0,0 +1,52 @@ +#!/usr/bin/env bash + +set -eux + +REFERENCE_GENOME=$1 +REFERENCE_DATASETS_DIR=${REFERENCE_DATASETS_DIR:-/var/seqr/seqr-reference-data} + + +case $REFERENCE_GENOME in + GRCh38) + ;; + GRCh37) + ;; + *) + echo "Invalid reference genome $REFERENCE_GENOME, should be GRCh37 or GRCh38" + exit 1 +esac + +case $REFERENCE_DATASETS_DIR in + "gs://seqr-reference-data") + echo "Cannot rsync to the authoritative source" + exit 1 + ;; + *) + ;; +esac + +if ! [[ "$REFERENCE_DATASETS_DIR" =~ gs://* ]]; then + mkdir -p $REFERENCE_DATASETS_DIR/$REFERENCE_GENOME; + if [ -f "$REFERENCE_DATASETS_DIR"/"$REFERENCE_GENOME"/_SUCCESS ]; then + echo "Skipping rsync because already successful" + exit 0; + fi +else + result=$(gsutil -q stat "$REFERENCE_DATASETS_DIR"/"$REFERENCE_GENOME"/_SUCCESS || echo 1) + if [[ $result != 1 ]]; then + echo "Skipping rsync because already successful" + exit 0; + fi +fi + +gsutil -m rsync -rd -x '.*\.parquet.*' "gs://seqr-reference-data/v3.2/$REFERENCE_GENOME" $REFERENCE_DATASETS_DIR/$REFERENCE_GENOME +if ! [[ $REFERENCE_DATASETS_DIR =~ gs://* ]]; then + touch "$REFERENCE_DATASETS_DIR"/"$REFERENCE_GENOME"/_SUCCESS +else + # If a different reference datasets dir is provided, sync vep data to the provided bucket. + gsutil cp "gs://seqr-reference-data/vep_data/loftee-beta/$REFERENCE_GENOME.tar.gz" $REFERENCE_DATASETS_DIR/vep_data/loftee-beta/$REFERENCE_GENOME.tar.gz + gsutil -m rsync -rd "gs://seqr-reference-data/vep/$REFERENCE_GENOME" $REFERENCE_DATASETS_DIR/vep/$REFERENCE_GENOME + touch _SUCCESS + gsutil cp _SUCCESS "$REFERENCE_DATASETS_DIR"/"$REFERENCE_GENOME"/_SUCCESS + rm -rf _SUCCESS +fi diff --git a/loading_pipeline/bin/run_task.py b/loading_pipeline/bin/run_task.py new file mode 100755 index 0000000000..37b96c4fb7 --- /dev/null +++ b/loading_pipeline/bin/run_task.py @@ -0,0 +1,10 @@ +#!/usr/bin/env python3 +import sys + +import luigi + +from loading_pipeline.lib.tasks import * # noqa: F403 + +if __name__ == '__main__': + # If run does not succeed, exit with 1 status code. + luigi.run() or sys.exit(1) diff --git a/loading_pipeline/bin/updated_reference_dataset_parquet.py b/loading_pipeline/bin/updated_reference_dataset_parquet.py new file mode 100755 index 0000000000..48547dde77 --- /dev/null +++ b/loading_pipeline/bin/updated_reference_dataset_parquet.py @@ -0,0 +1,37 @@ +#!/usr/bin/env python3 +import argparse + +import luigi + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome +from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset +from loading_pipeline.lib.tasks.reference_data.updated_reference_dataset_parquet import ( + UpdatedReferenceDatasetParquetOnDataprocTask, +) + + +def main(): + parser = argparse.ArgumentParser() + parser.add_argument('--reference-genome', required=True, type=ReferenceGenome) + parser.add_argument('--dataset-type', required=True, type=DatasetType) + parser.add_argument( + '--reference-dataset', + required=True, + type=ReferenceDataset, + ) + args = parser.parse_args() + luigi.build( + [ + UpdatedReferenceDatasetParquetOnDataprocTask( + reference_genome=args.reference_genome, + dataset_type=args.dataset_type, + reference_dataset=args.reference_dataset, + run_id=f'{args.reference_dataset.value.replace("_", "-").lower()}-run', + attempt_id=0, + ), + ], + ) + + +if __name__ == '__main__': + main() diff --git a/loading_pipeline/bin/vep b/loading_pipeline/bin/vep new file mode 100755 index 0000000000..437ffcfe17 --- /dev/null +++ b/loading_pipeline/bin/vep @@ -0,0 +1,21 @@ +#!/bin/bash + +set -eux + +REFERENCE_GENOME=$1 +VEP_REFERENCE_DATASETS_DIR=${VEP_REFERENCE_DATASETS_DIR:-/var/seqr/vep-reference-data} +VEP_DOCKER_IMAGE="gcr.io/seqr-project/vep-docker-image" + +case $REFERENCE_GENOME in + GRCh38) + ;; + GRCh37) + ;; + *) + echo "Invalid reference genome $REFERENCE_GENOME, should be GRCh37 or GRCh38" + exit 1 +esac + +shift # Remove the REFERENCE_GENOME arg. +docker run --platform linux/amd64 -i -v "$VEP_REFERENCE_DATASETS_DIR"/"$REFERENCE_GENOME":/opt/vep/.vep/:ro $VEP_DOCKER_IMAGE:"$REFERENCE_GENOME" \ + /opt/vep/src/ensembl-vep/vep "$@" diff --git a/loading_pipeline/deploy/Dockerfile b/loading_pipeline/deploy/Dockerfile new file mode 100644 index 0000000000..0ae73232ae --- /dev/null +++ b/loading_pipeline/deploy/Dockerfile @@ -0,0 +1,40 @@ +FROM --platform=linux/amd64 docker:dind as BUILD +FROM --platform=linux/amd64 ghcr.io/astral-sh/uv:python3.11-alpine AS UV_BUILD +FROM --platform=linux/amd64 hailgenetics/hail:0.2.138-py3.11 +COPY --from=BUILD /usr/local/bin/docker /usr/local/bin/docker +COPY --from=UV_BUILD /usr/local/bin/uv /usr/local/bin/uv +LABEL maintainer="Broad TGG" + +RUN curl -sSL https://sdk.cloud.google.com | bash +ENV PATH $PATH:/root/google-cloud-sdk/bin + +ARG PIPELINE_RUNNER_APP_VERSION +ENV PIPELINE_RUNNER_APP_VERSION=${PIPELINE_RUNNER_APP_VERSION} + +ENV VIRTUAL_ENV="/.venv" + +# Add build utilities for "annoy" package +# Note that these are getting added into the final runtime image and not the build... +# I (BPB) ran into challenges getting the uv virtual environment synced properly due +# to mismatches between the uv:python3.11-alpine and hail docker python environments. +RUN apt-get update && apt-get install -y build-essential && rm -rf /var/lib/apt/lists/* + +COPY pyproject.toml uv.lock . +RUN uv sync --group prod --no-group dev --locked + +# Application Code +WORKDIR /loading_pipeline +COPY loading_pipeline/api api +COPY loading_pipeline/bin bin +COPY loading_pipeline/lib lib +COPY loading_pipeline/ops ops +COPY loading_pipeline/var/liftover var/liftover + +# Special paths +COPY loading_pipeline/var/spark_config/spark-defaults.conf /usr/local/lib/python3.10/dist-packages/pyspark/conf/spark-defaults.conf +COPY loading_pipeline/bin/vep /vep + + +WORKDIR / +EXPOSE 6000 8082 +CMD ["uv", "run", "python3", "-m", "loading_pipeline.api"] diff --git a/loading_pipeline/deploy/Dockerfile.vep_GRCh37 b/loading_pipeline/deploy/Dockerfile.vep_GRCh37 new file mode 100644 index 0000000000..b585244fb9 --- /dev/null +++ b/loading_pipeline/deploy/Dockerfile.vep_GRCh37 @@ -0,0 +1,12 @@ +FROM ubuntu:18.04 as build + +# NB: This code is a copy of GRCh38 except for the loftee branch. + +RUN apt-get update && apt-get -y install wget libncurses5-dev libncursesw5-dev libbz2-dev liblzma-dev build-essential libz-dev git +RUN wget https://github.com/samtools/samtools/releases/download/1.7/samtools-1.7.tar.bz2 && tar xjvf samtools-1.7.tar.bz2 && cd samtools-1.7 && make && make install +RUN git clone https://github.com/konradjk/loftee.git + +FROM ensemblorg/ensembl-vep:release_110.1 as runtime +RUN cpanm DBD::SQLite +COPY --from=build /usr/local/bin/samtools /usr/local/bin/samtools +COPY --from=build /loftee/ /plugins diff --git a/loading_pipeline/deploy/Dockerfile.vep_GRCh38 b/loading_pipeline/deploy/Dockerfile.vep_GRCh38 new file mode 100644 index 0000000000..f781db8bc8 --- /dev/null +++ b/loading_pipeline/deploy/Dockerfile.vep_GRCh38 @@ -0,0 +1,13 @@ +FROM ubuntu:18.04 as build + +# Adapted from https://hub.docker.com/layers/konradjk/vep95_loftee/latest/images/sha256-d5f1a155293412acb5af4811142ba6907bad1cd708ca4000528f6317b784440e?context=explore +# and https://github.com/broadinstitute/gnomad_methods/blob/main/docker_files/Dockerfile_VEP105 +RUN apt-get update && apt-get -y install wget libncurses5-dev libncursesw5-dev libbz2-dev liblzma-dev build-essential libz-dev git +RUN wget https://github.com/samtools/samtools/releases/download/1.7/samtools-1.7.tar.bz2 && tar xjvf samtools-1.7.tar.bz2 && cd samtools-1.7 && make && make install +RUN git clone -b grch38 https://github.com/konradjk/loftee.git + +FROM ensemblorg/ensembl-vep:release_110.1 as runtime +RUN cpanm DBD::SQLite +COPY --from=build /usr/local/bin/samtools /usr/local/bin/samtools +# semantics of mv vs COPY are different such that we don't need the '*' when moving files. +COPY --from=build /loftee/ /plugins diff --git a/loading_pipeline/docs/Clickhouse_Design_Notes.md b/loading_pipeline/docs/Clickhouse_Design_Notes.md new file mode 100644 index 0000000000..ff050c98dc --- /dev/null +++ b/loading_pipeline/docs/Clickhouse_Design_Notes.md @@ -0,0 +1,202 @@ +# ClickHouse Design Decisions + +## Schema + +### Entries Table +- Grouping by family was most efficient at query-time and was a wash on-disk. +- ORDER BY `project_guid, family_guid, sample_type, is_gnomad_gt_5_percent, is_annotated_in_any_gene, key` + - Support searches on project or family +- PROJECTION on `is_gnomad_gt_5_percent`, `is_annotated_in_any_gene`, `xpos` + - Static view over gnomad constructed at load time. + - Note that an update to gnomad _requires_ rebuilding this!!!! + - I would try to be clever about this, identifying the variants that change when gnomad updates + - From experience, dropping or adding columns NOT in the sorting key is very easy... impossible if it is. + - `is_annotated_in_gene` (lightweight boolean index to support gene search) + - xpos ordering supports sorts on gene/position. +- `geneId_ids` Array(UInt32) + - We _tried_ to make this a bitmap column. However, they are really "partial aggregation state" columns + `AggregateFunction(groupBitmap, UInt64)` and are not cleanly supported in all the right ways downstream. + - We store an array of integers and convert to a bitmap at search time, for a slight performance hit. + - hasAny(`list`, `list`) is trash slow and untenable. + +### Variants Tables +- Searchable fields in `variants_memory`. +- `variants_details` is post-filter and slow (10k per second). Mostly large blobs of strings. +- Live search queries run against `variants_memory` only. At load time, we insert into both tables w/ "on-disk" first. RocksDB inserts are idempotent so can handle retries re-writing the same key multiple times. + +### Reference Data Tables +- One table each per reference data source: `all_variants`, `seqr_variants`, `search`. +- Sourced from raw VCFs/TSVs if possible, `splice_ai` and `dbnsfp` are SLOW and big. +- Dictionaries are mostly [`HASHED_ARRAY`](https://kb.altinity.com/altinity-kb-dictionaries/altinity-kb-sparse_hashed-vs-hashed/) +- Tables with lots of seqr variants ("full rank" in key space) or too small to matter can be "FLAT" arrays. +- `RANGE_HASHED()` for ranges. +- dictGets and JOIN tables are super fast (10M/S) so even N joins is much faster than RocksDB table access. + +### SeqrDB Dicts +- Postgres backed dictionaries. +- Postgres named collection set up in infrastructure. +- These are essential, providing fast access within ClickHouse to Postgres itself. + - Loading references these. + - populating the geneIds field + - Search queries reference them too. +- Performantly refreshable! + +### Incremental vs Refreshable Materialized Views +- Incremental MVs are pointers between two actual tables, when data is inserted into the first it is copied +to the second with a transformation. +- Refreshable MVs are more analagous to other DBs, full data is generated on a schedule or manually. + - All Refreshable MVs in seqr are set to a refresh frequency of every 10 years. +- Incremental MVs cannot be "built". + +### RocksDB +The dependency on RocksDB is the weak point of the ClickHouse backend. The data structure is opaque, hard to reason about and improve, and challenging to query and update. Schema migrations are not supported, backups are manual and failure-prone, and the Engine is not supported in the managed ClickHouse Inc product. It solves a key problem for us, however, supporting fast key-value access over both small and large blobs of strings. + +Only Key/Value access is really supported for the RocksDB tables. Queries such as `SELECT ... WHERE key > 0 and key < 100000` are very slow and should be avoided. + +### Ingestion Architecture & Async Tasks +- Many operations in ClickHouse are asynchrnous and happen in the background. Careful attention must be paid +to ensure things finish reliably and do not leave partial state! +- Load is structured around a `staging` database and [atomic partition movement](https://clickhouse.com/blog/table-cloning). + - All `entries` tables and materialized views are schema-copied into `staging`. + - All data is inserted into `staging`. + - `staging` environment must be 'verified'. + - Dictionaries are rebuilt only in `production` database! +- `entries`/`project_gt_stats`/`gt_stats` cascade was required for reasonable performance +of recomputing allele frequencies. We did try loading without multiple descending views, but re-grouping the whole `entries` table OOMs. + +### History of Nasty Bugs +- Incorrectly named the on-disk tables `/variants/details` instead of `/variants_details` which caused issues because of an existing `/variants` path. +- Missing `affected_status` in materialized view ORDER BY, leading to undefined behavior. +- Mis-typed a gnomad allele frequency, incorrectly rounding down AFs. +- Infinite issues with column ordering, missing fields, and types. + +## Infrastructure + +#### ClickHouse Settings +Essential: +- `max_partition_size_to_drop`/`max_table_size_to_drop` need to be high, we delete the `staging` database +and thus need these to be the size of the largest project. +- `max_bytes_ratio_before_external_group_by`/`max_bytes_ratio_before_external_sort`. These are set to `0.1` and are essential. +During loading and various other operations, large `GROUP BY` can OOM. We have set these to ensure JOINs spill to disk, preferring slowness to crashes! +- `stop_refreshable_materialized_views_on_startup`, prevents all views from starting all at once on server startup. + +Optional: +- `max_query_size`, `max_ast_elements`, `max_expanded_ast_elements`,`max_parser_backtracks`: used internally for large projects with many samples. +- `max_server_memory_usage_to_ram_ratio` instructs ClickHouse to use less of the server's memory. Since we mount `/in-memory-dir` we allocate resources away from ClickHouse without its knowledge. +- `background_pool_size`, `background_merges_mutations_concurrency_ratio`, `number_of_free_entries_in_pool_to_execute_mutation`, `number_of_free_entries_in_pool_to_lower_max_size_of_merge`, `number_of_free_entries_in_pool_to_execute_optimize_entire_partition` allow limiting the number of background threads for background tasks. This has been helpful for protecting search performance at the cost of longer background operations. + +#### Running a Single Host +Clickhouse and the Helm installation support replication and scaling with either a Zookeeper or Clickhouse-Keeper managed cluster. Given our prioritization of Consistency >> Availability, and the complexity of managing a cluster, we've opted for the simplicity of maintaining a single host, accepting the risk of limited downtime both in search and loading. + +#### Backups +We have a cron in the [seqr codebase](https://github.com/broadinstitute/seqr/blob/master/deploy/docker/seqr/clickhouse_backup.py) that manages incremental backups of the the Broad `seqr`'s database. The `rocksdb` tables are backed up with a cloud storage rsync cron. + +#### Project Sub-Partitions +Select `GRCh38/SNV_INDEL` WGS projects are subpartitioned via a static mapping, set up as a one time operation w/ a rough goal of 500m rows per partition. Our largest projects far exceed ClickHouse's recommended maximum partition, and operations on coalesced single partitions are single threaded (slowing down `OPTIMIZE TABLE FINAL` like no other). Supporting sub-partitions lets us parallelize +any `OPTIMIZE TABLE` and in general leads to more manageable chunks of data. + +We did not, however, notice this prior to initial go-live. Thus all non-`GRCh38/SNV_INDEL` tables and early open-source releases do +follow this pattern. We have code and unit-tests to support both partitioning paradigms, and also have an operations script for the manual re-partitioning (`loading_pipeline/ops`). + +## Miscellaneous + +#### Learning About ClickHouse +- PostHog's [Clickhouse explainers](https://posthog.com/blog/clickhouse) +- Andy Pavlo's [DB Course](https://www.youtube.com/watch?v=nhlpwmOBEiE) +- The ClickHouse Documentation. + +#### Debugging Advice +- Logging into the client: +``` +kubectl port-forward services/seqr-clickhouse 9000:9000 + +# In another terminal +./clickhouse client --user seqr_clickhouse_writer --password PASSWORD +``` + +- Reading the query log, for example recent non-insert queries: +``` +select * FROM system.query_log where query_start_time > '2026-05-01' and query not like '%INSERT%'; +``` +Statistics like query time and memory are available here. + +- Manually timing queries. I've generally had a much better experience running a query and inserting into a temp table. For example: +``` +create temporary table t as SELECT transcripts FROM ( + SELECT toUInt32(generate_series) AS key + FROM generate_series(5_000_000, 5_010_000) +) k INNER JOIN `GRCh38/SNV_INDEL/transcripts` t on k.key = t.key; +``` +The alternatives, either returning the full result set to the client or "SELECT COUNT(*)", return biased timings. Either too slow due to networking buffering over the terminal or too fast due to not actually fetching the full result set off of disk. + +- Viewing `Dictionary` usage: +``` +SELECT + name AS dictionary_name, + sum(bytes_allocated) AS bytes_allocated_, + formatReadableSize(sum(bytes_allocated)) AS readable_size +FROM system.dictionaries +GROUP BY dictionary_name +ORDER BY bytes_allocated_ DESC +``` +Broad Seqr's production instance dictionaries consume ~30GB of memory. + +NOTE: I (bpb) believe these numbers are underestimates and don't account for some of the full memory overhead of maintaining these in memory. + +- Viewing `Join` table memory usage: +``` +SELECT + database, + name, + formatReadableSize(total_bytes) +FROM system.tables +WHERE engine IN ('Memory', 'Set', 'Join') +``` +Broad Seqr's production 'Join' tables consume about ~1GB of memory. + +- Viewing disk usage within ClickHouse: +``` +SELECT + disk_name, + database, + `table`, + sum(bytes_on_disk) AS s, + formatReadableSize(sum(bytes_on_disk)) AS size +FROM system.parts +WHERE active = 1 +GROUP BY + disk_name, + database, + `table` +ORDER BY s DESC +``` + +Broad Seqr's production disk usage: +``` + ┌─disk_name─┬─database─┬─table─────────────────────────────────────────────────────────────────────┬─────────────s─┬─size───────┐ +1. │ default │ seqr │ GRCh38/SNV_INDEL/entries │ 2134397010569 │ 1.94 TiB │ +2. │ default │ seqr │ GRCh37/SNV_INDEL/reference_data/splice_ai/all_variants │ 72085843803 │ 67.14 GiB │ +3. │ default │ seqr │ GRCh38/SNV_INDEL/reference_data/splice_ai/all_variants │ 71927088053 │ 66.99 GiB │ +4. │ default │ seqr │ GRCh37/SNV_INDEL/entries │ 39255880565 │ 36.56 GiB │ +5. │ default │ seqr │ GRCh38/SNV_INDEL/project_gt_stats │ 38191863243 │ 35.57 GiB │ +6. │ default │ seqr │ GRCh38/SNV_INDEL/reference_data/gnomad_genomes/all_variants │ 12827564551 │ 11.95 GiB │ + + +SELECT COUNT(*) +FROM `GRCh38/SNV_INDEL/entries` + +Query id: 51d2a78e-de1a-4b75-9131-1e9e1e3a2ecb + + ┌─────COUNT()─┐ +1. │ 68213850227 │ -- 68.21 billion + └─────────────┘ +``` + +- Viewing disk usage outside of ClickHouse: +``` +kubectl exec seqr-clickhouse-shard0-0 -c clickhouse -it -- bash -c 'cd /in-memory-dir; du -h' +``` + +``` +kubectl exec seqr-clickhouse-shard0-0 -c clickhouse -it -- bash -c 'cd /var/seqr/clickhouse-data; du -h' +``` diff --git a/loading_pipeline/docs/Diagrams.md b/loading_pipeline/docs/Diagrams.md new file mode 100644 index 0000000000..14c162759e --- /dev/null +++ b/loading_pipeline/docs/Diagrams.md @@ -0,0 +1,150 @@ +# Pipeline flow, as of 05/06/2026 + +``` + WriteImportedCallsetTask + (VCF → Hail Matrix Table) + | + v + WritePostprocessedCallsetTask + (split multi, deduplicate) + | + v + ValidateCallsetTask + (validation checks) + | + _______________|_______________ + | | + v v + WriteSexCheckTableTask WriteRelatednessCheckTableTask + | | + v v + WriteRelatednessCheckTsvTask + | + v + _____________________|_____________________ + | | + v v + WriteRemappedAndSubsettedCallsetTask WriteRemappedAndSubsettedCallsetTask + (Project 1) (Project N) + | | + |___________________________________________| + | + v + WriteMetadataForRunTask + | + v + WriteNewVariantsTableTask + | + v + UpdateVariantAnnotationsTableWithNewVariantsTask + (Variants with annotations) + | + ______________________+_______________________ + | | | + v v v + WriteNewEntries... WriteNewVariants... WriteNewVariantDetails... + ParquetTask ParquetTask ParquetTask + | | (optional) + | [also requires] | [or just] + | RemappedCallsets | WriteNewVariantsTableTask + | + |_______________________| + | + v + RunPipelineTask + (all parquets ready) + | + v + WriteSuccessFileTask + | + v + WriteClickhouseLoadSuccessFileTask + (load parquets → ClickHouse) +``` + +ClickHouse LSM-Tree + +``` +┌────────────────────────────────────────────────────────────┐ +│ ClickHouse LSM: MemTable → Parts → Merge │ +└────────────────────────────────────────────────────────────┘ + + WRITE PHASE: + ───────────── + + INSERT statements + │ + ▼ + ┌──────────────┐ + │ MemTable │ (In-memory buffer) + │ ~150 MB │ ◄─── Growing as writes arrive + └──────┬───────┘ + │ + (Threshold exceeded) + │ + ▼ + ┌──────────────┐ + │ Flush │ + │ to Disk │ + └──────┬───────┘ + │ + ▼ + ┌──────────────┐ + │ Part (L0) │ ◄─── New immutable part on disk + └──────────────┘ + + + DISK STATE (Multiple Parts): + ────────────────────────────── + + MemTable Disk Parts (sorted by creation) + ┌─────┐ + │ │ ┌──────────┐ + │ │ │ Part(L0) │ ◄─── Recently flushed (small) + │ │ └──────────┘ + │ │ ┌──────────┐ + │ │ │ Part(L0) │ + │ │ └──────────┘ + │ │ ┌──────────┐ + │ │ │ Part(L0) │ + │ │ └──────────┘ + │ │ ┌──────────┐ + │ │ │ Part(L1) │ ◄─── Older (larger) + │ │ └──────────┘ + │ │ ┌──────────┐ + │ │ │ Part(L2) │ + │ │ └──────────┘ + └─────┘ + + + BACKGROUND MERGE (Compaction): + ─────────────────────────────── + + When L0 has ~10 parts: + + ┌──────────┐ + │Part(L0) │ + └────┬─────┘ + │ + ┌────┴─────┬──────────┐ + │ │ │ + ┌───▼──┐ ┌────▼───┐ ┌───▼──┐ + │L0 #1 │ │ L0 #2 │ │ L0#3 │ ──┐ + └──────┘ └────────┘ └──────┘ │ + │ Read + Sort + ┌──────────────────────────────┐ │ + Compress + │ Compaction Process │◄┘ + │ │ + │ 1. Read all rows from L0s │ + │ 2. Merge by primary key │ + │ 3. Sort & compress │ + │ 4. Write to single Part(L1) │ + └───────────────┬──────────────┘ + │ + ▼ + ┌──────────────┐ + │ Part(L1) │ ◄─── One larger part + │ (merged) │ (old L0 parts deleted) + └──────────────┘ + +``` \ No newline at end of file diff --git a/loading_pipeline/docs/Historial_Context.md b/loading_pipeline/docs/Historial_Context.md new file mode 100644 index 0000000000..b21ae3e495 --- /dev/null +++ b/loading_pipeline/docs/Historial_Context.md @@ -0,0 +1,82 @@ +Notes on Loading Pipeline Orchestration + +## Decision to move off of Airflow (late 2024): + - Manual mapping of luigi tasks to Airflow tasks (w/ strings!) + - Cost ($400 a month) + - Small instance (2 cpu/2 gb ram) for schedular and actual compute + - Unbelieveable scaling issues? + - DAG built dynamically, OOMs. + - Parallelism in task execution. + - Maintainability issues + - Lack of shared code with open source repo. + - Airflow system complexity w/ helm. + - Composer "management" + versions. + - Manual environment variables and secrets, lack of cohesion with kubernetes. + - Composer was its own Kubernetes ecosystem! + - GCP integration. + - Hooks for replacing python API calls... (why????) + - Nasty bugs + https://github.com/broadinstitute/seqr/pull/3995/changes + https://github.com/broadinstitute/seqr/pull/4539/changes + https://github.com/broadinstitute/seqr/pull/4646/changes + - Testing difficulties + - Able to test DAG "compile", but not actual execution. + - System complexity (templating, XCom, retries, 'Context') in the way of lean unit and integration tests. + +## Evaluation of other DAG frameworks: + - Prefect/Dagster/Argo Workflows + - Seem to have similar issues as Airflow; complexity does not align with the straightforward needs of the pipeline execution. + +## Current Implementation +- API listens for requests from `seqr` application for asynchronous work. +- Worker with concurrency=1 polls for work. + - One task at a time; coarse-grained lock: + Hail cannot update variants in parallel. + Clickhouse cannot rebuild entire gt_stats in parallel. + - Retries managed within the worker and persisted on disk. + - Failures moved to deadletter queue after 5 retries. +- Loading pipeline runs "Luigi" via --local-scheduler locally or via Dataproc. + - Luigi manages task flow and nothing else. +- Output looks like (as of 05/26): +``` +gs://seqr-hail-search-data/v3.1/GRCh38/SNV_INDEL/runs/20260421-125644-303855/_CLICKHOUSE_LOAD_SUCCESS +gs://seqr-hail-search-data/v3.1/GRCh38/SNV_INDEL/runs/20260421-125644-303855/_SUCCESS +gs://seqr-hail-search-data/v3.1/GRCh38/SNV_INDEL/runs/20260421-125644-303855/metadata.json +gs://seqr-hail-search-data/v3.1/GRCh38/SNV_INDEL/runs/20260421-125644-303855/new_entries.parquet/ +gs://seqr-hail-search-data/v3.1/GRCh38/SNV_INDEL/runs/20260421-125644-303855/new_variant_details.parquet/ +gs://seqr-hail-search-data/v3.1/GRCh38/SNV_INDEL/runs/20260421-125644-303855/new_variants.ht/ +gs://seqr-hail-search-data/v3.1/GRCh38/SNV_INDEL/runs/20260421-125644-303855/new_variants.parquet/ +``` + +### Residues from previous iterations. +- Manual enumeration of consequence terms and SV/Mito types is no longer necessary. + - Was a performance enhancement for Hail backend that can be unrolled. +- `complete()` methods are likely overcomplicated. + - Each task verifies completeness by running this method and if it returns `True`, skips execution. + - Necessary for performance, but as the pipeline has started doing less it is less necessary. + - Historically been the source of many bugs. + - For example, re-running pipeline with a different pedigree... we'd cached the subsetted callset, failed to generate a new one etc. +- Globalizing and Deglobalizing Ids. + - We optimized the hail table structure to move sample ids into globals, this complicates the current logic and is likely unnecessary. + +## Thoughts for future: + - Remove Hail for non SNV_INDEL dataset types and callsets < 500 samples. + - Resolve the "Fatal Flaw", two separate representations of production variants, one in Hail and one in Clickhouse. + - If pipeline fails immediately after "UpdateVariantAnnotationsTableWithNewVariantsTask", next run will have + incorrect "new_variants.parquet". + - Lightweight replacement for Luigi "run()/complete()/output()/requires()" framework. + - Eliminate scheduler in favor or "tasks" table in seqr postgres. + - Running arbitrary docker images: + - Airflow was useful for this, w/ Kubernetes elasticity. + - Need to support external computational biology tools. + - Can we just re-write with agentic coding? + - Remove as much business logic from core pipeline as we can. + - For example, the Terra Data Repository sample fetching. + +## VEP (🗑️) Addendum: + - VEP runs only on new variants via a custom wrapper around Hail's command. + - Internally, HAIL exports a table to VCF and shell execs parallelized docker-VEP processes and then re-imports into a VEP schema. + - On Dataproc, one initialization action syncs VEP reference data to HDFS. + - For open source users, sync to local disk. + - VEP itself is a custom docker build, pushed as a one time operation to seqr's gcr repo. + - GRCh38 and GRCh37 use different schemas, though are both using VEP 110. diff --git a/loading_pipeline/lib/__init__.py b/loading_pipeline/lib/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/loading_pipeline/lib/annotations/__init__.py b/loading_pipeline/lib/annotations/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/loading_pipeline/lib/annotations/enums.py b/loading_pipeline/lib/annotations/enums.py new file mode 100644 index 0000000000..64202a8940 --- /dev/null +++ b/loading_pipeline/lib/annotations/enums.py @@ -0,0 +1,205 @@ +BIOTYPES = [ + 'IG_C_gene', + 'IG_D_gene', + 'IG_J_gene', + 'IG_LV_gene', + 'IG_V_gene', + 'TR_C_gene', + 'TR_J_gene', + 'TR_V_gene', + 'TR_D_gene', + 'IG_pseudogene', + 'IG_C_pseudogene', + 'IG_J_pseudogene', + 'IG_V_pseudogene', + 'TR_V_pseudogene', + 'TR_J_pseudogene', + 'Mt_rRNA', + 'Mt_tRNA', + 'miRNA', + 'misc_RNA', + 'rRNA', + 'scRNA', + 'snRNA', + 'snoRNA', + 'ribozyme', + 'sRNA', + 'scaRNA', + 'lncRNA', + 'Mt_tRNA_pseudogene', + 'tRNA_pseudogene', + 'snoRNA_pseudogene', + 'snRNA_pseudogene', + 'scRNA_pseudogene', + 'rRNA_pseudogene', + 'misc_RNA_pseudogene', + 'miRNA_pseudogene', + 'TEC', + 'nonsense_mediated_decay', + 'non_stop_decay', + 'retained_intron', + 'protein_coding', + 'protein_coding_LoF', + 'protein_coding_CDS_not_defined', + 'processed_transcript', + 'non_coding', + 'ambiguous_orf', + 'sense_intronic', + 'sense_overlapping', + 'antisense', + 'known_ncrna', + 'pseudogene', + 'processed_pseudogene', + 'polymorphic_pseudogene', + 'retrotransposed', + 'transcribed_processed_pseudogene', + 'transcribed_unprocessed_pseudogene', + 'transcribed_unitary_pseudogene', + 'translated_processed_pseudogene', + 'translated_unprocessed_pseudogene', + 'unitary_pseudogene', + 'unprocessed_pseudogene', + 'artifact', + 'lincRNA', + 'macro_lncRNA', + '3prime_overlapping_ncRNA', + 'disrupted_domain', + 'vault_RNA', + 'bidirectional_promoter_lncRNA', + '3prime_overlapping_ncrna', +] + +REGULATORY_BIOTYPES = [ + 'enhancer', + 'promoter', + 'CTCF_binding_site', + 'TF_binding_site', + 'open_chromatin_region', +] + +TRANSCRIPT_CONSEQUENCE_TERMS = [ + 'transcript_ablation', + 'splice_acceptor_variant', + 'splice_donor_variant', + 'stop_gained', + 'frameshift_variant', + 'stop_lost', + 'start_lost', + 'inframe_insertion', + 'inframe_deletion', + 'missense_variant', + 'protein_altering_variant', + 'splice_donor_5th_base_variant', + 'splice_region_variant', + 'splice_donor_region_variant', + 'splice_polypyrimidine_tract_variant', + 'incomplete_terminal_codon_variant', + 'start_retained_variant', + 'stop_retained_variant', + 'synonymous_variant', + 'coding_sequence_variant', + 'mature_miRNA_variant', + '5_prime_UTR_variant', + '3_prime_UTR_variant', + 'non_coding_transcript_exon_variant', + 'intron_variant', + 'NMD_transcript_variant', + 'non_coding_transcript_variant', + 'coding_transcript_variant', + 'upstream_gene_variant', + 'downstream_gene_variant', + 'intergenic_variant', + 'sequence_variant', +] + +MOTIF_CONSEQUENCE_TERMS = [ + 'TFBS_ablation', + 'TFBS_amplification', + 'TF_binding_site_variant', + 'TFBS_fusion', + 'TFBS_translocation', +] + +REGULATORY_CONSEQUENCE_TERMS = [ + 'regulatory_region_ablation', + 'regulatory_region_amplification', + 'regulatory_region_variant', + 'regulatory_region_fusion', +] + +FIVEUTR_CONSEQUENCES = [ + '5_prime_UTR_premature_start_codon_gain_variant', # uAUG_gained + '5_prime_UTR_premature_start_codon_loss_variant', # uAUG_lost + '5_prime_UTR_stop_codon_gain_variant', # uSTOP_gained + '5_prime_UTR_stop_codon_loss_variant', # uSTOP_lost + '5_prime_UTR_uORF_frameshift_variant', # uFrameshift +] + +LOF_FILTERS = [ + 'END_TRUNC', + 'INCOMPLETE_CDS', + 'EXON_INTRON_UNDEF', + 'SMALL_INTRON', + 'ANC_ALLELE', + 'NON_DONOR_DISRUPTING', + 'NON_ACCEPTOR_DISRUPTING', + 'RESCUE_DONOR', + 'RESCUE_ACCEPTOR', + 'GC_TO_GT_DONOR', + '5UTR_SPLICE', + '3UTR_SPLICE', +] + +MITOTIP_PATHOGENICITIES = [ + 'likely_pathogenic', + 'possibly_pathogenic', + 'possibly_benign', + 'likely_benign', +] + +SV_TYPES = [ + 'gCNV_DEL', + 'gCNV_DUP', + 'BND', + 'CPX', + 'CTX', + 'DEL', + 'DUP', + 'INS', + 'INV', + 'CNV', +] + +SV_TYPE_DETAILS = [ + 'INS_iDEL', + 'INVdel', + 'INVdup', + 'ME', + 'ME:ALU', + 'ME:LINE1', + 'ME:SVA', + 'dDUP', + 'dDUP_iDEL', + 'delINV', + 'delINVdel', + 'delINVdup', + 'dupINV', + 'dupINVdel', + 'dupINVdup', +] + +SV_CONSEQUENCE_RANKS = [ + 'LOF', + 'INTRAGENIC_EXON_DUP', + 'PARTIAL_EXON_DUP', + 'COPY_GAIN', + 'DUP_PARTIAL', + 'MSV_EXON_OVERLAP', + 'INV_SPAN', + 'UTR', + 'PROMOTER', + 'TSS_DUP', + 'BREAKEND_EXONIC', + 'INTRONIC', + 'NEAREST_TSS', +] diff --git a/loading_pipeline/lib/annotations/expression_helpers.py b/loading_pipeline/lib/annotations/expression_helpers.py new file mode 100644 index 0000000000..ab0b34c25f --- /dev/null +++ b/loading_pipeline/lib/annotations/expression_helpers.py @@ -0,0 +1,329 @@ +import hail as hl + +from loading_pipeline.lib.annotations.enums import TRANSCRIPT_CONSEQUENCE_TERMS + +TRANSCRIPT_CONSEQUENCE_TERM_RANK_LOOKUP = hl.dict( + hl.enumerate(TRANSCRIPT_CONSEQUENCE_TERMS, index_first=False), +) +HGVSC_CONSEQUENCES = hl.set( + ['splice_donor_variant', 'splice_acceptor_variant', 'splice_region_variant'], +) +OMIT_TRANSCRIPT_CONSEQUENCE_TERMS = [ + 'upstream_gene_variant', + 'downstream_gene_variant', +] +PROTEIN_LETTERS_1TO3 = hl.dict( + { + 'A': 'Ala', + 'C': 'Cys', + 'D': 'Asp', + 'E': 'Glu', + 'F': 'Phe', + 'G': 'Gly', + 'H': 'His', + 'I': 'Ile', + 'K': 'Lys', + 'L': 'Leu', + 'M': 'Met', + 'N': 'Asn', + 'P': 'Pro', + 'Q': 'Gln', + 'R': 'Arg', + 'S': 'Ser', + 'T': 'Thr', + 'V': 'Val', + 'W': 'Trp', + 'Y': 'Tyr', + 'X': 'Ter', + '*': 'Ter', + 'U': 'Sec', + }, +) + + +def _replace_chr_prefix(contig: str): + return contig.replace('^chr', '') + + +def _get_expr_for_contig(locus: hl.expr.LocusExpression) -> hl.expr.StringExpression: + """Normalized contig name""" + return _replace_chr_prefix(locus.contig) + + +def _get_expr_for_contig_number( + locus: hl.expr.LocusExpression, +) -> hl.expr.Int32Expression: + """Convert contig name to contig number""" + return hl.bind( + lambda contig: ( + hl.case() + .when(contig == 'X', 23) + .when(contig == 'Y', 24) + .when(contig[0] == 'M', 25) + .default(hl.int(contig)) + ), + _get_expr_for_contig(locus), + ) + + +def _get_expr_for_formatted_hgvs(csq): + return hl.cond( + hl.is_missing(csq.hgvsp) | HGVSC_CONSEQUENCES.contains(csq.major_consequence), + csq.hgvsc.split(':')[-1], + hl.cond( + csq.hgvsp.contains('=') | csq.hgvsp.contains('%3D'), + hl.bind( + lambda protein_letters: 'p.' + + protein_letters + + hl.str(csq.protein_start) + + protein_letters, + hl.delimit( + csq.amino_acids.split('').map( + lambda pl: PROTEIN_LETTERS_1TO3.get(pl), + ), + '', + ), + ), + csq.hgvsp.split(':')[-1], + ), + ) + + +def get_expr_for_variant_id(table, max_length=None): + """Expression for computing ---. Assumes alleles were split. + + Args: + max_length: (optional) length at which to truncate the --- string + + Return: + string: "---" + """ + contig = _get_expr_for_contig(table.locus) + variant_id = ( + contig + + '-' + + hl.str(table.locus.position) + + '-' + + table.alleles[0] + + '-' + + table.alleles[1] + ) + if max_length is not None: + return variant_id[0:max_length] + return variant_id + + +def get_expr_for_xpos(locus: hl.expr.LocusExpression) -> hl.expr.Int64Expression: + """Genomic position represented as a single number = contig_number * 10**9 + position. + This represents chrom:pos more compactly and allows for easier sorting. + """ + contig_number = _get_expr_for_contig_number(locus) + return hl.int64(contig_number) * 1_000_000_000 + locus.position + + +def get_expr_for_vep_sorted_transcript_consequences_array( + vep_root, + include_coding_annotations=True, + omit_consequences=OMIT_TRANSCRIPT_CONSEQUENCE_TERMS, +): + """Sort transcripts by 3 properties: + + 1. coding > non-coding + 2. transcript consequence severity + 3. canonical > non-canonical + + so that the 1st array entry will be for the coding, most-severe, canonical transcript (assuming + one exists). + + Also, for each transcript in the array, computes these additional fields: + domains: converts Array[Struct] to string of comma-separated domain names + hgvs: set to hgvsp is it exists, or else hgvsc. formats hgvsp for synonymous variants. + major_consequence: set to most severe consequence for that transcript ( + VEP sometimes provides multiple consequences for a single transcript) + major_consequence_rank: major_consequence rank based on VEP SO ontology (most severe = 1) + (see http://www.ensembl.org/info/genome/variation/predicted_data.html) + category: set to one of: "lof", "missense", "synonymous", "other" based on the value of major_consequence. + + Args: + vep_root (StructExpression): root path of the VEP struct in the MT + include_coding_annotations (bool): if True, fields relevant to protein-coding variants will be included + """ + + selected_annotations = [ + 'biotype', + 'canonical', + 'cdna_start', + 'cdna_end', + 'codons', + 'exon', + 'gene_id', + 'gene_symbol', + 'hgvsc', + 'hgvsp', + 'intron', + 'transcript_id', + ] + + if include_coding_annotations: + selected_annotations.extend( + [ + 'amino_acids', + 'lof', + 'lof_filter', + 'lof_flags', + 'lof_info', + 'protein_id', + 'protein_start', + ], + ) + + omit_consequence_terms = ( + hl.set(omit_consequences) if omit_consequences else hl.empty_set(hl.tstr) + ) + + result = hl.sorted( + vep_root.transcript_consequences.map( + lambda c: c.select( + *selected_annotations, + consequence_terms=c.consequence_terms.filter( + lambda t: ~omit_consequence_terms.contains(t), + ), + domains=c.domains.map(lambda domain: domain.db + ':' + domain.name), + major_consequence=hl.cond( + c.consequence_terms.size() > 0, + hl.sorted( + c.consequence_terms, + key=lambda t: TRANSCRIPT_CONSEQUENCE_TERM_RANK_LOOKUP.get(t), + )[0], + hl.null(hl.tstr), + ), + ), + ) + .filter(lambda c: c.consequence_terms.size() > 0) + .map( + lambda c: c.annotate( + category=( + hl.case() + .when( + TRANSCRIPT_CONSEQUENCE_TERM_RANK_LOOKUP.get(c.major_consequence) + <= TRANSCRIPT_CONSEQUENCE_TERM_RANK_LOOKUP.get( + 'frameshift_variant', + ), + 'lof', + ) + .when( + TRANSCRIPT_CONSEQUENCE_TERM_RANK_LOOKUP.get(c.major_consequence) + <= TRANSCRIPT_CONSEQUENCE_TERM_RANK_LOOKUP.get( + 'missense_variant', + ), + 'missense', + ) + .when( + TRANSCRIPT_CONSEQUENCE_TERM_RANK_LOOKUP.get(c.major_consequence) + <= TRANSCRIPT_CONSEQUENCE_TERM_RANK_LOOKUP.get( + 'synonymous_variant', + ), + 'synonymous', + ) + .default('other') + ), + hgvs=_get_expr_for_formatted_hgvs(c), + major_consequence_rank=TRANSCRIPT_CONSEQUENCE_TERM_RANK_LOOKUP.get( + c.major_consequence, + ), + ), + ), + lambda c: ( + hl.bind( + lambda is_coding, is_most_severe, is_canonical: ( + hl.cond( + is_coding, + hl.cond( + is_most_severe, + hl.cond(is_canonical, 1, 2), + hl.cond(is_canonical, 3, 4), + ), + hl.cond( + is_most_severe, + hl.cond(is_canonical, 5, 6), + hl.cond(is_canonical, 7, 8), + ), + ) + ), + hl.or_else(c.biotype, '') == 'protein_coding', + hl.set(c.consequence_terms).contains(vep_root.most_severe_consequence), + hl.or_else(c.canonical, 0) == 1, + ) + ), + ) + + if not include_coding_annotations: + # for non-coding variants, drop fields here that are hard to exclude in the above code + result = result.map(lambda c: c.drop('domains', 'hgvsp')) + + return hl.zip_with_index(result).map( + lambda csq_with_index: csq_with_index[1].annotate( + transcript_rank=csq_with_index[0], + ), + ) + + +def get_expr_for_worst_transcript_consequence_annotations_struct( + vep_sorted_transcript_consequences_root, + include_coding_annotations=True, +): + """Retrieves the top-ranked transcript annotation based on the ranking computed by + get_expr_for_vep_sorted_transcript_consequences_array(..) + + Args: + vep_sorted_transcript_consequences_root (ArrayExpression): + include_coding_annotations (bool): + """ + + transcript_consequences = { + 'biotype': hl.tstr, + 'canonical': hl.tint, + 'category': hl.tstr, + 'cdna_start': hl.tint, + 'cdna_end': hl.tint, + 'codons': hl.tstr, + 'gene_id': hl.tstr, + 'gene_symbol': hl.tstr, + 'hgvs': hl.tstr, + 'hgvsc': hl.tstr, + 'major_consequence': hl.tstr, + 'major_consequence_rank': hl.tint, + 'transcript_id': hl.tstr, + } + + if include_coding_annotations: + transcript_consequences.update( + { + 'amino_acids': hl.tstr, + 'domains': hl.tstr, + 'hgvsp': hl.tstr, + 'lof': hl.tstr, + 'lof_flags': hl.tstr, + 'lof_filter': hl.tstr, + 'lof_info': hl.tstr, + 'protein_id': hl.tstr, + }, + ) + + return hl.cond( + vep_sorted_transcript_consequences_root.size() == 0, + hl.struct( + **{ + field: hl.null(field_type) + for field, field_type in transcript_consequences.items() + }, + ), + hl.bind( + lambda worst_transcript_consequence: ( + worst_transcript_consequence.annotate( + domains=hl.delimit(hl.set(worst_transcript_consequence.domains)), + ).select(*transcript_consequences.keys()) + ), + vep_sorted_transcript_consequences_root[0], + ), + ) diff --git a/loading_pipeline/lib/annotations/fields.py b/loading_pipeline/lib/annotations/fields.py new file mode 100644 index 0000000000..b2eab5796a --- /dev/null +++ b/loading_pipeline/lib/annotations/fields.py @@ -0,0 +1,12 @@ +from collections.abc import Callable +from typing import Any + +import hail as hl + + +def get_fields( + t: hl.Table | hl.MatrixTable, + fns: list[Callable[..., hl.Expression]], + **kwargs: Any, +) -> dict[str, hl.Expression]: + return {fn.__name__: fn(t, **kwargs) for fn in fns} diff --git a/loading_pipeline/lib/annotations/fields_test.py b/loading_pipeline/lib/annotations/fields_test.py new file mode 100644 index 0000000000..fc5f179749 --- /dev/null +++ b/loading_pipeline/lib/annotations/fields_test.py @@ -0,0 +1,118 @@ +from unittest.mock import Mock, patch + +import hail as hl + +from loading_pipeline.lib.annotations.fields import get_fields +from loading_pipeline.lib.core import ( + DatasetType, + ReferenceGenome, +) +from loading_pipeline.lib.misc.vep import run_vep +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase +from loading_pipeline.var.test.vep.mock_vep_data import ( + MOCK_37_VEP_DATA, + MOCK_38_VEP_DATA, +) + + +class FieldsTest(MockedDatarootTestCase): + def setUp(self) -> None: + super().setUp() + + @patch('loading_pipeline.lib.misc.vep.hl.vep') + def test_get_formatting_fields(self, mock_vep: Mock) -> None: + for reference_genome, ht, expected_fields in [ + ( + ReferenceGenome.GRCh38, + hl.Table.parallelize( + [ + { + 'locus': hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + 'alleles': ['A', 'C'], + 'rsid': 'abcd', + }, + ], + hl.tstruct( + locus=hl.tlocus('GRCh38'), + alleles=hl.tarray(hl.tstr), + rsid=hl.tstr, + ), + key=['locus', 'alleles'], + ), + [ + 'check_ref', + 'rg37_locus', + 'rsid', + 'sorted_motif_feature_consequences', + 'sorted_regulatory_feature_consequences', + 'sorted_transcript_consequences', + 'variant_id', + 'xpos', + ], + ), + ( + ReferenceGenome.GRCh37, + hl.Table.parallelize( + [ + { + 'locus': hl.Locus( + contig='1', + position=1, + reference_genome='GRCh37', + ), + 'alleles': ['A', 'C'], + 'rsid': 'abcd', + }, + ], + hl.tstruct( + locus=hl.tlocus('GRCh37'), + alleles=hl.tarray(hl.tstr), + rsid=hl.tstr, + ), + key=['locus', 'alleles'], + ), + [ + 'rg38_locus', + 'rsid', + 'sorted_transcript_consequences', + 'variant_id', + 'xpos', + ], + ), + ]: + mock_vep.return_value = ht.annotate( + vep=MOCK_37_VEP_DATA + if reference_genome == ReferenceGenome.GRCh37 + else MOCK_38_VEP_DATA, + ) + ht = run_vep( # noqa: PLW2901 + ht, + DatasetType.SNV_INDEL, + reference_genome, + ) + self.assertCountEqual( + list( + get_fields( + ht, + DatasetType.SNV_INDEL.formatting_annotation_fns( + reference_genome, + ), + **( + { + 'gencode_ensembl_to_refseq_id_mapping': hl.dict( + {'a': 'b'}, + ), + } + if reference_genome == ReferenceGenome.GRCh38 + else {} + ), + dataset_type=DatasetType.SNV_INDEL, + reference_genome=reference_genome, + ).keys(), + ), + expected_fields, + ) diff --git a/loading_pipeline/lib/annotations/gcnv.py b/loading_pipeline/lib/annotations/gcnv.py new file mode 100644 index 0000000000..e9785419ed --- /dev/null +++ b/loading_pipeline/lib/annotations/gcnv.py @@ -0,0 +1,172 @@ +from typing import Any + +import hail as hl + +from loading_pipeline.lib.annotations import expression_helpers, liftover +from loading_pipeline.lib.annotations.enums import SV_CONSEQUENCE_RANKS, SV_TYPES +from loading_pipeline.lib.core.definitions import ReferenceGenome +from loading_pipeline.lib.misc.gcnv import parse_gcnv_genes + +SV_CONSEQUENCE_RANKS_LOOKUP = hl.dict( + hl.enumerate(SV_CONSEQUENCE_RANKS, index_first=False), +) +SV_TYPES_LOOKUP = hl.dict(hl.enumerate(SV_TYPES, index_first=False)) + + +def _start_and_end_equal(mt: hl.MatrixTable) -> hl.BooleanExpression: + return (mt.sample_start == mt.start) & (mt.sample_end == mt.end) + + +def CN(mt: hl.MatrixTable, **_: Any) -> hl.Expression: # noqa: N802 + return mt.CN + + +def concordance( + mt: hl.MatrixTable, + is_new_gcnv_joint_call: bool, + **_: Any, +) -> hl.Expression: + if is_new_gcnv_joint_call: + return hl.or_missing( + hl.is_defined(mt.GT), + hl.struct( + new_call=mt.no_ovl, + prev_call=hl.len(mt.identical_ovl) > 0, + prev_overlap=hl.len(mt.any_ovl) > 0, + ), + ) + return hl.or_missing( + hl.is_defined(mt.GT), + hl.struct( + new_call=False, + prev_call=~mt.is_latest, + prev_overlap=False, + ), + ) + + +def defragged(mt: hl.MatrixTable, **_: Any) -> hl.Expression: + return mt.defragmented + + +def end_locus( + ht: hl.Table, + reference_genome: ReferenceGenome, + **_: Any, +) -> hl.LocusExpression: + return hl.locus(ht.chr, ht.end, reference_genome.value) + + +def gt_stats(ht: hl.Table, callset_ht: hl.Table, **_: Any) -> hl.Expression: + return hl.struct( + AF=hl.float32(callset_ht[ht.variant_id].sf), + AC=callset_ht[ht.variant_id].sc, + AN=hl.int32(callset_ht[ht.variant_id].sc / callset_ht[ht.variant_id].sf), + Hom=hl.missing(hl.tint32), + Het=hl.missing(hl.tint32), + ) + + +def GT(mt: hl.MatrixTable, **_: Any) -> hl.Expression: # noqa: N802 + return hl.if_else( + (mt.CN == 0) | (mt.CN > 3), # noqa: PLR2004 + hl.Call([1, 1], phased=False), + hl.Call([0, 1], phased=False), + ) + + +def num_exon(ht: hl.Table, **_: Any) -> hl.Expression: + return ht.num_exon + + +def QS(mt: hl.MatrixTable, **_: Any) -> hl.Expression: # noqa: N802 + return mt.QS + + +def rg37_locus( + ht: hl.Table, + **_: Any, +) -> hl.Expression | None: + liftover.add_rg38_liftover() + return hl.liftover( + start_locus(ht, ReferenceGenome.GRCh38), + ReferenceGenome.GRCh37.value, + ) + + +def rg37_locus_end( + ht: hl.Table, + **_: Any, +) -> hl.Expression | None: + liftover.add_rg38_liftover() + return hl.liftover( + end_locus(ht, ReferenceGenome.GRCh38), + ReferenceGenome.GRCh37.value, + ) + + +def sample_end(mt: hl.MatrixTable, **_: Any) -> hl.Expression: + return hl.or_missing( + ~_start_and_end_equal(mt), + mt.sample_end, + ) + + +def sample_gene_ids(mt: hl.MatrixTable, **_: Any) -> hl.Expression: + parsed_genes = parse_gcnv_genes(mt.genes_any_overlap_Ensemble_ID) + return hl.or_missing(parsed_genes != mt.gene_ids, parsed_genes) + + +def sample_start(mt: hl.MatrixTable, **_: Any) -> hl.Expression: + return hl.or_missing( + ~_start_and_end_equal(mt), + mt.sample_start, + ) + + +def sample_num_exon(mt: hl.MatrixTable, **_: Any) -> hl.Expression: + return hl.or_missing( + mt.genes_any_overlap_totalExons != mt.num_exon, + mt.genes_any_overlap_totalExons, + ) + + +def sorted_gene_consequences( + ht: hl.Table, + **_: Any, +) -> hl.Expression: + return hl.array( + ht.gene_ids.map( + lambda gene: hl.Struct( + gene_id=gene, + major_consequence_id=hl.if_else( + ht.cg_genes.contains(gene), + SV_CONSEQUENCE_RANKS_LOOKUP['COPY_GAIN'], + hl.or_missing( + ht.lof_genes.contains(gene), + SV_CONSEQUENCE_RANKS_LOOKUP['LOF'], + ), + ), + ), + ), + ) + + +def start_locus( + ht: hl.Table, + reference_genome: ReferenceGenome, + **_: Any, +) -> hl.LocusExpression: + return hl.locus(ht.chr, ht.start, reference_genome.value) + + +def strvctvre(ht: hl.Table, **_: Any) -> hl.Expression: + return hl.struct(score=hl.parse_float32(ht.strvctvre_score)) + + +def sv_type_id(ht: hl.Table, **_: Any) -> hl.Expression: + return SV_TYPES_LOOKUP[ht.svtype] + + +def xpos(ht: hl.Table, reference_genome: ReferenceGenome, **_: Any) -> hl.Expression: + return expression_helpers.get_expr_for_xpos(start_locus(ht, reference_genome)) diff --git a/loading_pipeline/lib/annotations/liftover.py b/loading_pipeline/lib/annotations/liftover.py new file mode 100644 index 0000000000..41a1085055 --- /dev/null +++ b/loading_pipeline/lib/annotations/liftover.py @@ -0,0 +1,30 @@ +import hail as hl + +from loading_pipeline.lib.core.constants import ( + GRCH37_TO_GRCH38_LIFTOVER_REF_PATH, + GRCH38_TO_GRCH37_LIFTOVER_REF_PATH, +) +from loading_pipeline.lib.core.definitions import ReferenceGenome + + +def add_rg38_liftover() -> None: + rg37 = hl.get_reference(ReferenceGenome.GRCh37.value) + rg38 = hl.get_reference(ReferenceGenome.GRCh38.value) + if not rg38.has_liftover(rg37): + rg38.add_liftover(GRCH38_TO_GRCH37_LIFTOVER_REF_PATH, rg37) + + +def add_rg37_liftover() -> None: + rg37 = hl.get_reference(ReferenceGenome.GRCh37.value) + rg38 = hl.get_reference(ReferenceGenome.GRCh38.value) + if not rg37.has_liftover(rg38): + rg37.add_liftover(GRCH37_TO_GRCH38_LIFTOVER_REF_PATH, rg38) + + +def remove_liftover(): + rg37 = hl.get_reference(ReferenceGenome.GRCh37.value) + rg38 = hl.get_reference(ReferenceGenome.GRCh38.value) + if rg37.has_liftover(rg38): + rg37.remove_liftover(rg38) + if rg38.has_liftover(rg37): + rg38.remove_liftover(rg37) diff --git a/loading_pipeline/lib/annotations/misc.py b/loading_pipeline/lib/annotations/misc.py new file mode 100644 index 0000000000..00f5f68eb4 --- /dev/null +++ b/loading_pipeline/lib/annotations/misc.py @@ -0,0 +1,98 @@ +import hail as hl + +from loading_pipeline.lib.annotations.enums import ( + BIOTYPES, + FIVEUTR_CONSEQUENCES, + LOF_FILTERS, + MITOTIP_PATHOGENICITIES, + MOTIF_CONSEQUENCE_TERMS, + REGULATORY_BIOTYPES, + REGULATORY_CONSEQUENCE_TERMS, + SV_CONSEQUENCE_RANKS, + SV_TYPE_DETAILS, + SV_TYPES, + TRANSCRIPT_CONSEQUENCE_TERMS, +) +from loading_pipeline.lib.core import DatasetType +from loading_pipeline.lib.core.definitions import ReferenceGenome + + +def annotate_formatting_annotation_enum_globals( + ht: hl.Table, + reference_genome: ReferenceGenome, + dataset_type: DatasetType, +) -> hl.Table: + ht = ht.select_globals( + enums=hl.Struct(), + ) + formatting_annotation_names = { + fa.__name__ for fa in dataset_type.formatting_annotation_fns(reference_genome) + } + if 'sorted_motif_feature_consequences' in formatting_annotation_names: + ht = ht.annotate_globals( + enums=ht.enums.annotate( + sorted_motif_feature_consequences=hl.Struct( + consequence_term=MOTIF_CONSEQUENCE_TERMS, + ), + ), + ) + if 'sorted_regulatory_feature_consequences' in formatting_annotation_names: + ht = ht.annotate_globals( + enums=ht.enums.annotate( + sorted_regulatory_feature_consequences=hl.Struct( + biotype=REGULATORY_BIOTYPES, + consequence_term=REGULATORY_CONSEQUENCE_TERMS, + ), + ), + ) + if 'sorted_transcript_consequences' in formatting_annotation_names: + ht = ht.annotate_globals( + enums=ht.enums.annotate( + sorted_transcript_consequences=hl.Struct( + biotype=BIOTYPES, + consequence_term=TRANSCRIPT_CONSEQUENCE_TERMS, + **( + { + 'loftee': hl.Struct( + lof_filter=LOF_FILTERS, + ), + 'utrannotator': hl.Struct( + fiveutr_consequence=FIVEUTR_CONSEQUENCES, + ), + } + if reference_genome == ReferenceGenome.GRCh38 + and dataset_type == DatasetType.SNV_INDEL + else { + 'lof_filter': LOF_FILTERS, + } + ), + ), + ), + ) + if 'mitotip' in formatting_annotation_names: + ht = ht.annotate_globals( + enums=ht.enums.annotate( + mitotip=hl.Struct( + trna_prediction=MITOTIP_PATHOGENICITIES, + ), + ), + ) + if 'sv_type_id' in formatting_annotation_names: + ht = ht.annotate_globals( + enums=ht.enums.annotate( + sv_type=SV_TYPES, + ), + ) + if 'sv_type_detail_id' in formatting_annotation_names: + ht = ht.annotate_globals( + enums=ht.enums.annotate(sv_type_detail=SV_TYPE_DETAILS), + ) + if 'sorted_gene_consequences' in formatting_annotation_names: + ht = ht.annotate_globals( + enums=ht.enums.annotate( + sorted_gene_consequences=hl.Struct( + major_consequence=SV_CONSEQUENCE_RANKS, + ), + ), + ) + return ht diff --git a/loading_pipeline/lib/annotations/mito.py b/loading_pipeline/lib/annotations/mito.py new file mode 100644 index 0000000000..85b65ce75c --- /dev/null +++ b/loading_pipeline/lib/annotations/mito.py @@ -0,0 +1,61 @@ +from typing import Any + +import hail as hl + +from loading_pipeline.lib.annotations.enums import MITOTIP_PATHOGENICITIES + +MITOTIP_PATHOGENICITIES_LOOKUP = hl.dict( + hl.enumerate(MITOTIP_PATHOGENICITIES, index_first=False).extend( + # NB: adding missing values here allows us to + # hard fail if a mapped key is present and has an unexpected value + # but propagate missing values. + [(hl.missing(hl.tstr), hl.missing(hl.tint32))], + ), +) + + +def common_low_heteroplasmy(ht: hl.Table, **_: Any) -> hl.Expression: + return hl.bool(ht.common_low_heteroplasmy) + + +def contamination(mt: hl.MatrixTable, **_: Any) -> hl.Expression: + return ( + hl.parse_float64(mt.contamination) + if mt.contamination.dtype == hl.tstr + else mt.contamination + ) + + +def DP(mt: hl.MatrixTable, **_: Any) -> hl.Expression: # noqa: N802 + is_called = hl.is_defined(mt.GT) + return hl.cond(is_called, hl.int32(hl.min(mt.DP, 32000)), hl.missing(hl.tint32)) + + +def GQ(mt: hl.MatrixTable, **_: Any) -> hl.Expression: # noqa: N802 + is_called = hl.is_defined(mt.GT) + return hl.if_else(is_called, hl.int32(mt.MQ), 0) + + +def haplogroup(ht: hl.Table, **_: Any) -> hl.Expression: + return hl.Struct( + is_defining=ht.hap_defining_variant, + ) + + +def HL(mt: hl.MatrixTable, **_: Any) -> hl.Expression: # noqa: N802 + is_called = hl.is_defined(mt.GT) + return hl.if_else(is_called, mt.HL, 0) + + +def mito_cn(mt: hl.MatrixTable, **_: Any) -> hl.Expression: + return hl.int32(mt.mito_cn) + + +def mitotip(ht: hl.Table, **_: Any) -> hl.Expression: + return hl.Struct( + trna_prediction_id=MITOTIP_PATHOGENICITIES_LOOKUP[ht.mitotip_trna_prediction], + ) + + +def rsid(ht: hl.Table, **_: Any) -> hl.Expression: + return ht.rsid.find(lambda x: hl.is_defined(x)) diff --git a/loading_pipeline/lib/annotations/shared.py b/loading_pipeline/lib/annotations/shared.py new file mode 100644 index 0000000000..abeaaac2e5 --- /dev/null +++ b/loading_pipeline/lib/annotations/shared.py @@ -0,0 +1,51 @@ +from typing import Any + +import hail as hl + +from loading_pipeline.lib.annotations import expression_helpers, liftover +from loading_pipeline.lib.annotations.vep import ( + transcript_consequences_sort, + vep_85_transcript_consequences_select, +) +from loading_pipeline.lib.core.definitions import ReferenceGenome + + +def GT(mt: hl.MatrixTable, **_: Any) -> hl.Expression: # noqa: N802 + return mt.GT + + +def GQ(mt: hl.MatrixTable, **_: Any) -> hl.Expression: # noqa: N802 + is_called = hl.is_defined(mt.GT) + return hl.if_else(is_called, mt.GQ, 0) + + +def rsid(mt: hl.MatrixTable, **_: Any) -> hl.Expression: + return mt.rsid + + +def rg37_locus( + ht: hl.Table, + **_: Any, +) -> hl.Expression | None: + liftover.add_rg38_liftover() + return hl.liftover(ht.locus, ReferenceGenome.GRCh37.value) + + +def xpos(ht: hl.Table, **_: Any) -> hl.Expression: + return expression_helpers.get_expr_for_xpos(ht.locus) + + +def variant_id(ht: hl.Table, **_: Any) -> hl.Expression: + return expression_helpers.get_expr_for_variant_id(ht) + + +def sorted_transcript_consequences( + ht: hl.Table, + **_: Any, +) -> hl.Expression: + return hl.sorted( + ht.vep.transcript_consequences.map( + vep_85_transcript_consequences_select, + ).filter(lambda c: c.consequence_term_ids.size() > 0), + transcript_consequences_sort(ht), + ) diff --git a/loading_pipeline/lib/annotations/snv_indel.py b/loading_pipeline/lib/annotations/snv_indel.py new file mode 100644 index 0000000000..c4fe8cda2a --- /dev/null +++ b/loading_pipeline/lib/annotations/snv_indel.py @@ -0,0 +1,118 @@ +# ruff: noqa: N806 +from typing import Any + +import hail as hl + +from loading_pipeline.lib.annotations import liftover +from loading_pipeline.lib.annotations.enums import ( + MOTIF_CONSEQUENCE_TERMS, + REGULATORY_BIOTYPES, + REGULATORY_CONSEQUENCE_TERMS, +) +from loading_pipeline.lib.annotations.vep import ( + transcript_consequences_sort, + vep_110_transcript_consequences_select, +) +from loading_pipeline.lib.core.definitions import ReferenceGenome + +MOTIF_CONSEQUENCE_TERMS_LOOKUP = hl.dict( + hl.enumerate(MOTIF_CONSEQUENCE_TERMS, index_first=False), +) +REGULATORY_BIOTYPE_LOOKUP = hl.dict( + hl.enumerate(REGULATORY_BIOTYPES, index_first=False), +) +REGULATORY_CONSEQUENCE_TERMS_LOOKUP = hl.dict( + hl.enumerate(REGULATORY_CONSEQUENCE_TERMS, index_first=False), +) + + +def AB(mt: hl.MatrixTable, **_: Any) -> hl.Expression: # noqa: N802 + is_called = hl.is_defined(mt.GT) + return hl.bind( + lambda total: hl.if_else( + (is_called) & (total != 0) & (hl.len(mt.AD) > 1), + hl.float32(mt.AD[1] / total), + hl.missing(hl.tfloat32), + ), + hl.sum(mt.AD), + ) + + +def DP(mt: hl.MatrixTable, **_: Any) -> hl.Expression: # noqa: N802 + is_called = hl.is_defined(mt.GT) + return hl.if_else( + is_called & hl.is_defined(mt.AD), + hl.int32(hl.min(hl.sum(mt.AD), 32000)), + hl.missing(hl.tint32), + ) + + +def rg38_locus( + ht: hl.Table, + **_: Any, +) -> hl.Expression | None: + liftover.add_rg37_liftover() + return hl.liftover(ht.locus, ReferenceGenome.GRCh38.value) + + +def check_ref(ht: hl.Table, **_: Any) -> hl.BooleanExpression: + return hl.is_defined(ht.vep.check_ref) + + +def sorted_motif_feature_consequences( + ht: hl.Table, + **_: Any, +) -> hl.Expression: + # NB: hl.min() doesn't work correctly in the "sorted" key expression, so we have an additional + # is_defined check, even though the expression should work on missing on its own. + # hail bug report incoming. + return hl.or_missing( + hl.is_defined(ht.vep.motif_feature_consequences), + hl.sorted( + ht.vep.motif_feature_consequences.map( + lambda c: c.select( + consequence_term_ids=c.consequence_terms.map( + lambda t: MOTIF_CONSEQUENCE_TERMS_LOOKUP[t], + ), + motif_feature_id=c.motif_feature_id, + ), + ).filter(lambda c: c.consequence_term_ids.size() > 0), + lambda c: hl.min(c.consequence_term_ids), + ), + ) + + +def sorted_regulatory_feature_consequences( + ht: hl.Table, + **_: Any, +) -> hl.Expression: + return hl.or_missing( + hl.is_defined(ht.vep.regulatory_feature_consequences), + hl.sorted( + ht.vep.regulatory_feature_consequences.map( + lambda c: c.select( + biotype_id=REGULATORY_BIOTYPE_LOOKUP[c.biotype], + consequence_term_ids=c.consequence_terms.map( + lambda t: REGULATORY_CONSEQUENCE_TERMS_LOOKUP[t], + ), + regulatory_feature_id=c.regulatory_feature_id, + ), + ).filter(lambda c: c.consequence_term_ids.size() > 0), + lambda c: hl.min(c.consequence_term_ids), + ), + ) + + +def sorted_transcript_consequences( + ht: hl.Table, + gencode_ensembl_to_refseq_id_mapping: hl.tdict(hl.tstr, hl.tstr), + **_: Any, +) -> hl.Expression: + return hl.sorted( + ht.vep.transcript_consequences.map( + vep_110_transcript_consequences_select( + gencode_ensembl_to_refseq_id_mapping, + ), + ).filter(lambda c: c.consequence_term_ids.size() > 0), + transcript_consequences_sort(ht), + ) diff --git a/loading_pipeline/lib/annotations/snv_indel_test.py b/loading_pipeline/lib/annotations/snv_indel_test.py new file mode 100644 index 0000000000..0de91786b0 --- /dev/null +++ b/loading_pipeline/lib/annotations/snv_indel_test.py @@ -0,0 +1,303 @@ +import unittest +from unittest.mock import Mock, patch + +import hail as hl + +from loading_pipeline.lib.annotations import shared, snv_indel +from loading_pipeline.lib.core import DatasetType, ReferenceGenome +from loading_pipeline.lib.misc.vep import run_vep +from loading_pipeline.var.test.vep.mock_vep_data import ( + MOCK_37_VEP_DATA, + MOCK_38_VEP_DATA, +) + + +class SNVTest(unittest.TestCase): + @patch('loading_pipeline.lib.misc.vep.hl.vep') + def test_sorted_transcript_consequences_37( + self, + mock_vep: Mock, + ) -> None: + ht = hl.Table.parallelize( + [ + { + 'locus': hl.Locus( + contig='1', + position=871269, + reference_genome=ReferenceGenome.GRCh37.value, + ), + 'alleles': ['A', 'C'], + }, + ], + hl.tstruct( + locus=hl.tlocus(ReferenceGenome.GRCh37.value), + alleles=hl.tarray(hl.tstr), + ), + key=['locus', 'alleles'], + ) + mock_vep.return_value = ht.annotate(vep=MOCK_37_VEP_DATA) + ht = run_vep( + ht, + DatasetType.SNV_INDEL, + ReferenceGenome.GRCh37, + ) + ht = ht.select( + sorted_transcript_consequences=shared.sorted_transcript_consequences( + ht, + ), + ) + self.assertCountEqual( + ht.sorted_transcript_consequences.collect(), + [ + [ + hl.Struct( + amino_acids='S/L', + canonical=1, + codons='tCg/tTg', + gene_id='ENSG00000188976', + hgvsc='ENST00000327044.6:c.1667C>T', + hgvsp='ENSP00000317992.6:p.Ser556Leu', + transcript_id='ENST00000327044', + biotype_id=39, + consequence_term_ids=[9], + is_lof_nagnag=None, + lof_filter_ids=[0, 1], + ), + hl.Struct( + amino_acids=None, + canonical=None, + codons=None, + gene_id='ENSG00000188976', + hgvsc='ENST00000477976.1:n.3114C>T', + hgvsp=None, + transcript_id='ENST00000477976', + biotype_id=38, + consequence_term_ids=[23, 26], + is_lof_nagnag=None, + lof_filter_ids=None, + ), + hl.Struct( + amino_acids=None, + canonical=None, + codons=None, + gene_id='ENSG00000188976', + hgvsc='ENST00000483767.1:n.523C>T', + hgvsp=None, + transcript_id='ENST00000483767', + biotype_id=38, + consequence_term_ids=[23, 26], + is_lof_nagnag=None, + lof_filter_ids=None, + ), + ], + ], + ) + + @patch('loading_pipeline.lib.misc.vep.hl.vep') + def test_sorted_transcript_consequences_38( + self, + mock_vep: Mock, + ) -> None: + ht = hl.Table.parallelize( + [ + { + 'locus': hl.Locus( + contig='chr1', + position=871269, + reference_genome=ReferenceGenome.GRCh38.value, + ), + 'alleles': ['A', 'C'], + }, + ], + hl.tstruct( + locus=hl.tlocus(ReferenceGenome.GRCh38.value), + alleles=hl.tarray(hl.tstr), + ), + key=['locus', 'alleles'], + ) + mock_vep.return_value = ht.annotate(vep=MOCK_38_VEP_DATA) + ht = run_vep( + ht, + DatasetType.SNV_INDEL, + ReferenceGenome.GRCh38, + ) + ht = ht.select( + sorted_transcript_consequences=snv_indel.sorted_transcript_consequences( + ht, + hl.dict( + {'ENST00000327044': 'NM_015658.4', 'ENST00000477976': 'refseq1'}, + ), + ), + ) + self.assertCountEqual( + ht.sorted_transcript_consequences.collect()[0], + [ + hl.Struct( + amino_acids='S/L', + canonical=1, + codons='tCg/tTg', + gene_id='ENSG00000188976', + hgvsc='ENST00000327044.6:c.1667C>T', + hgvsp='ENSP00000317992.6:p.Ser556Leu', + transcript_id='ENST00000327044', + refseq_transcript_id='NM_015658.4', + mane_select='NM_015658.4', + mane_plus_clinical=None, + biotype_id=39, + consequence_term_ids=[9], + exon=hl.Struct(index=15, total=19), + intron=None, + alphamissense=hl.Struct(pathogenicity=0.10000000149011612), + loftee=hl.Struct( + is_lof_nagnag=None, + lof_filter_ids=[0, 1], + ), + spliceregion=hl.Struct( + extended_intronic_splice_region_variant=False, + ), + utrannotator=hl.Struct( + existing_inframe_oorfs=None, + existing_outofframe_oorfs=None, + existing_uorfs=None, + fiveutr_consequence_id=None, + fiveutr_annotation=None, + ), + ), + hl.Struct( + amino_acids=None, + canonical=None, + codons=None, + gene_id='ENSG00000188976', + hgvsc='ENST00000477976.1:n.3114C>T', + hgvsp=None, + transcript_id='ENST00000477976', + refseq_transcript_id='refseq1', + mane_select=None, + mane_plus_clinical=None, + biotype_id=38, + consequence_term_ids=[23, 26], + exon=hl.Struct(index=13, total=17), + intron=None, + alphamissense=hl.Struct(pathogenicity=0.9700000286102295), + loftee=hl.Struct( + is_lof_nagnag=None, + lof_filter_ids=None, + ), + spliceregion=hl.Struct( + extended_intronic_splice_region_variant=False, + ), + utrannotator=hl.Struct( + existing_inframe_oorfs=None, + existing_outofframe_oorfs=None, + existing_uorfs=None, + fiveutr_consequence_id=None, + fiveutr_annotation=None, + ), + ), + hl.Struct( + amino_acids=None, + canonical=None, + codons=None, + gene_id='ENSG00000188976', + hgvsc='ENST00000483767.1:n.523C>T', + hgvsp=None, + transcript_id='ENST00000483767', + refseq_transcript_id=None, + mane_select=None, + mane_plus_clinical=None, + biotype_id=38, + consequence_term_ids=[23, 13, 26], + exon=hl.Struct(index=1, total=5), + intron=None, + alphamissense=hl.Struct(pathogenicity=None), + loftee=hl.Struct( + is_lof_nagnag=None, + lof_filter_ids=None, + ), + spliceregion=hl.Struct( + extended_intronic_splice_region_variant=True, + ), + utrannotator=hl.Struct( + existing_inframe_oorfs=0, + existing_outofframe_oorfs=1, + existing_uorfs=0, + fiveutr_consequence_id=1, + fiveutr_annotation=hl.Struct( + type='OutOfFrame_oORF', + KozakContext='TTTATGC', + KozakStrength='Weak', + DistanceToCDS=40, + CapDistanceToStart=20, + DistanceToStop=75, + Evidence=False, + AltStop=None, + AltStopDistanceToCDS=None, + FrameWithCDS=None, + StartDistanceToCDS=None, + newSTOPDistanceToCDS=None, + alt_type=None, + alt_type_length=None, + ref_StartDistanceToCDS=None, + ref_type=None, + ref_type_length=None, + ), + ), + ), + ], + ) + + @patch('loading_pipeline.lib.misc.vep.hl.vep') + def test_sorted_other_feature_consequences( + self, + mock_vep: Mock, + ) -> None: + ht = hl.Table.parallelize( + [ + { + 'locus': hl.Locus( + contig='chr1', + position=871269, + reference_genome=ReferenceGenome.GRCh38.value, + ), + 'alleles': ['A', 'C'], + }, + ], + hl.tstruct( + locus=hl.tlocus(ReferenceGenome.GRCh38.value), + alleles=hl.tarray(hl.tstr), + ), + key=['locus', 'alleles'], + ) + mock_vep.return_value = ht.annotate(vep=MOCK_38_VEP_DATA) + ht = run_vep( + ht, + DatasetType.SNV_INDEL, + ReferenceGenome.GRCh38, + ) + ht = ht.select( + sorted_motif_feature_consequences=snv_indel.sorted_motif_feature_consequences( + ht, + ), + sorted_regulatory_feature_consequences=snv_indel.sorted_regulatory_feature_consequences( + ht, + ), + ) + self.assertCountEqual( + ht.sorted_motif_feature_consequences.collect(), + [None], + ) + self.assertCountEqual( + ht.sorted_regulatory_feature_consequences.collect()[0], + [ + hl.Struct( + biotype_id=0, + consequence_term_ids=[0], + regulatory_feature_id='regulatory_2', + ), + hl.Struct( + biotype_id=0, + consequence_term_ids=[2], + regulatory_feature_id='regulatory_1', + ), + ], + ) diff --git a/loading_pipeline/lib/annotations/sv.py b/loading_pipeline/lib/annotations/sv.py new file mode 100644 index 0000000000..e6c3abdd85 --- /dev/null +++ b/loading_pipeline/lib/annotations/sv.py @@ -0,0 +1,254 @@ +# ruff: noqa: N806 +from typing import Any + +import hail as hl + +from loading_pipeline.lib.annotations import liftover +from loading_pipeline.lib.annotations.enums import ( + SV_CONSEQUENCE_RANKS, + SV_TYPE_DETAILS, + SV_TYPES, +) +from loading_pipeline.lib.core.definitions import ReferenceGenome + +CONSEQ_PREDICTED_PREFIX = 'info.PREDICTED_' +CONSEQ_PREDICTED_GENE_COLS = { + 'info.PREDICTED_BREAKEND_EXONIC': hl.tarray(hl.tstr), + 'info.PREDICTED_COPY_GAIN': hl.tarray(hl.tstr), + 'info.PREDICTED_DUP_PARTIAL': hl.tarray(hl.tstr), + 'info.PREDICTED_INTRAGENIC_EXON_DUP': hl.tarray(hl.tstr), + 'info.PREDICTED_INTRONIC': hl.tarray(hl.tstr), + 'info.PREDICTED_INV_SPAN': hl.tarray(hl.tstr), + 'info.PREDICTED_LOF': hl.tarray(hl.tstr), + 'info.PREDICTED_MSV_EXON_OVERLAP': hl.tarray(hl.tstr), + 'info.PREDICTED_NEAREST_TSS': hl.tarray(hl.tstr), + 'info.PREDICTED_PARTIAL_EXON_DUP': hl.tarray(hl.tstr), + 'info.PREDICTED_PROMOTER': hl.tarray(hl.tstr), + 'info.PREDICTED_TSS_DUP': hl.tarray(hl.tstr), + 'info.PREDICTED_UTR': hl.tarray(hl.tstr), +} + +PREVIOUS_GENOTYPE_N_ALT_ALLELES = hl.dict( + { + # Map of concordance string -> previous n_alt_alleles() + # Concordant + frozenset(['TN']): 0, # 0/0 -> 0/0 + frozenset(['TP']): 2, # 1/1 -> 1/1 + frozenset(['TN', 'TP']): 1, # 0/1 -> 0/1 + # Novel + frozenset(['FP']): 0, # 0/0 -> 1/1 + frozenset(['TN', 'FP']): 0, # 0/0 -> 0/1 + # Absent + frozenset(['FN']): 2, # 1/1 -> 0/0 + frozenset(['TN', 'FN']): 1, # 0/1 -> 0/0 + # Discordant + frozenset(['FP', 'TP']): 1, # 0/1 -> 1/1 + frozenset(['FN', 'TP']): 2, # 1/1 -> 0/1 + }, +) + + +SV_TYPES_LOOKUP = hl.dict(hl.enumerate(SV_TYPES, index_first=False)) +SV_TYPE_DETAILS_LOOKUP = hl.dict(hl.enumerate(SV_TYPE_DETAILS, index_first=False)) +SV_CONSEQUENCE_RANKS_LOOKUP = hl.dict( + hl.enumerate(SV_CONSEQUENCE_RANKS, index_first=False), +) + + +def _get_cpx_interval( + x: hl.StringExpression, + reference_genome: ReferenceGenome, +) -> hl.StructExpression: + # an example format of CPX_INTERVALS is "DUP_chr1:1499897-1499974" + type_contig = x.split('_') + contig_pos = type_contig[1].split(':') + pos = contig_pos[1].split('-') + return hl.struct( + type_id=SV_TYPES_LOOKUP[type_contig[0]], + start=hl.locus( + contig_pos[0], + hl.int32(pos[0]), + reference_genome.value, + ), + end=hl.locus( + contig_pos[0], + hl.int32(pos[1]), + reference_genome.value, + ), + ) + + +def _sv_types(ht: hl.Table) -> hl.ArrayExpression: + return ht.alleles[1].replace('[<>]', '').split(':', 2) + + +def alleles(ht: hl.Table, **_: Any) -> hl.ArrayExpression: + return hl.array( + [ + 'N', + hl.if_else( + ( + hl.is_defined(ht.sv_type_detail_id) + & (hl.array(SV_TYPES)[ht.sv_type_id] != 'CPX') + ), + hl.format( + '<%s:%s>', + hl.array(SV_TYPES)[ht.sv_type_id], + hl.array(SV_TYPE_DETAILS)[ht.sv_type_detail_id], + ), + hl.format('<%s>', hl.array(SV_TYPES)[ht.sv_type_id]), + ), + ], + ) + + +def info(ht: hl.Table, **_: Any) -> hl.StructExpression: + return hl.Struct( + ALGORITHMS=ht.algorithms, + END=ht.start_locus.position, + CHR2=ht.end_locus.contig, + END2=ht.end_locus.position, + SVTYPE=hl.array(SV_TYPES)[ht.sv_type_id], + SVLEN=ht.sv_len, + ) + + +def locus(ht: hl.Table, **_: Any) -> hl.LocusExpression: + return ht.start_locus + + +def algorithms(ht: hl.Table, **_: Any) -> hl.Expression: + return hl.str(',').join(ht['info.ALGORITHMS']) + + +def bothsides_support(ht: hl.Table, **_: Any) -> hl.Expression: + return ht['info.BOTHSIDES_SUPPORT'] + + +def CN(mt: hl.MatrixTable, **_: Any) -> hl.Expression: # noqa: N802 + return mt.RD_CN + + +def concordance(mt: hl.MatrixTable, **_: Any) -> hl.Expression: + is_called = hl.is_defined(mt.GT) + was_previously_called = hl.is_defined(mt.CONC_ST) & ~mt.CONC_ST.contains( + 'EMPTY', + ) + num_alt = hl.if_else(is_called, mt.GT.n_alt_alleles(), -1) + prev_num_alt = hl.if_else( + was_previously_called, + PREVIOUS_GENOTYPE_N_ALT_ALLELES[hl.set(mt.CONC_ST)], + -1, + ) + concordant_genotype = num_alt == prev_num_alt + discordant_genotype = (num_alt != prev_num_alt) & (prev_num_alt > 0) + novel_genotype = (num_alt != prev_num_alt) & (prev_num_alt == 0) + return hl.struct( + prev_num_alt=hl.or_missing(discordant_genotype, prev_num_alt), + prev_call=hl.or_missing(is_called, was_previously_called & concordant_genotype), + new_call=hl.or_missing(is_called, ~was_previously_called | novel_genotype), + ) + + +def cpx_intervals( + ht: hl.Table, + reference_genome: ReferenceGenome, + **_: Any, +) -> hl.Expression: + return hl.or_missing( + hl.is_defined(ht['info.CPX_INTERVALS']), + ht['info.CPX_INTERVALS'].map(lambda x: _get_cpx_interval(x, reference_genome)), + ) + + +def end_locus(ht: hl.Table, **_: Any) -> hl.StructExpression: + rg38_lengths = hl.literal(hl.get_reference(ReferenceGenome.GRCh38.value).lengths) + return hl.if_else( + ( + hl.is_defined(ht['info.END2']) + & (rg38_lengths[ht['info.CHR2']] >= ht['info.END2']) + ), + hl.locus(ht['info.CHR2'], ht['info.END2'], ReferenceGenome.GRCh38.value), + hl.or_missing( + (rg38_lengths[ht.locus.contig] >= ht['info.END']), + hl.locus(ht.locus.contig, ht['info.END'], ReferenceGenome.GRCh38.value), + ), + ) + + +def gnomad_svs( + ht: hl.Table, + gnomad_svs_ht: hl.Table, + **_: Any, +) -> hl.Expression: + gnomad_svs_ht = gnomad_svs_ht.drop('locus', 'alleles') + return gnomad_svs_ht.annotate( + ID=gnomad_svs_ht.KEY, + )[ht['info.GNOMAD_V4.1_TRUTH_VID']] + + +def rg37_locus_end( + ht: hl.Table, + **_: Any, +) -> hl.Expression | None: + liftover.add_rg38_liftover() + end = end_locus(ht) + return hl.or_missing( + hl.is_defined(end), + hl.liftover( + hl.locus( + end.contig, + end.position, + reference_genome=ReferenceGenome.GRCh38.value, + ), + ReferenceGenome.GRCh37.value, + ), + ) + + +def start_locus(ht: hl.Table, **_: Any): + return ht.locus + + +def sorted_gene_consequences( + ht: hl.Table, + gencode_gene_symbol_to_gene_id_mapping: hl.tdict(hl.tstr, hl.tstr), + **_: Any, +) -> hl.Expression: + # In lieu of sorted_transcript_consequences seen on SNV/MITO. + mapped_genes = [ + ht[gene_col].map( + lambda gene: hl.struct( + gene_id=gencode_gene_symbol_to_gene_id_mapping.get(gene), + major_consequence_id=SV_CONSEQUENCE_RANKS_LOOKUP[ + gene_col.replace(CONSEQ_PREDICTED_PREFIX, '', 1) # noqa: B023 + ], + ), + ) + for gene_col in CONSEQ_PREDICTED_GENE_COLS + ] + return hl.filter(hl.is_defined, mapped_genes).flatmap(lambda x: x) + + +def strvctvre(ht: hl.Table, **_: Any) -> hl.Expression: + return hl.struct(score=hl.parse_float32(ht['info.StrVCTVRE'])) + + +def sv_len(ht: hl.Table, **_: Any) -> hl.Expression: + return ht['info.SVLEN'] + + +def sv_type_id(ht: hl.Table, **_: Any) -> hl.Expression: + return SV_TYPES_LOOKUP[_sv_types(ht)[0]] + + +def sv_type_detail_id(ht: hl.Table, **_: Any) -> hl.Expression: + sv_types = _sv_types(ht) + return hl.if_else( + sv_types[0] == 'CPX', + SV_TYPE_DETAILS_LOOKUP[ht['info.CPX_TYPE']], + hl.or_missing( + (sv_types[0] == 'INS') & (hl.len(sv_types) > 1), + SV_TYPE_DETAILS_LOOKUP[sv_types[1]], + ), + ) diff --git a/loading_pipeline/lib/annotations/sv_test.py b/loading_pipeline/lib/annotations/sv_test.py new file mode 100644 index 0000000000..25a8413b16 --- /dev/null +++ b/loading_pipeline/lib/annotations/sv_test.py @@ -0,0 +1,171 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.annotations.fields import get_fields +from loading_pipeline.lib.core import DatasetType + + +class SVTest(unittest.TestCase): + def test_sv_export_annotations(self) -> None: + ht = hl.Table.parallelize( + [ + hl.Struct( + id=0, + algorithms='manta', + end_locus=hl.Locus( + contig='chr5', + position=20404, + reference_genome='GRCh38', + ), + start_locus=hl.Locus( + contig='chr1', + position=180928, + reference_genome='GRCh38', + ), + sv_len=123, + sv_type_id=2, + sv_type_detail_id=None, + ), + hl.Struct( + id=1, + algorithms='manta', + end_locus=hl.Locus( + contig='chr1', + position=789481, + reference_genome='GRCh38', + ), + start_locus=hl.Locus( + contig='chr1', + position=789481, + reference_genome='GRCh38', + ), + sv_len=245, + sv_type_id=2, + sv_type_detail_id=None, + ), + hl.Struct( + id=2, + algorithms='manta', + end_locus=hl.Locus( + contig='chr1', + position=6559723, + reference_genome='GRCh38', + ), + start_locus=hl.Locus( + contig='chr1', + position=6558902, + reference_genome='GRCh38', + ), + sv_len=245, + sv_type_id=3, + sv_type_detail_id=2, + ), + hl.Struct( + id=3, + algorithms='manta', + end_locus=hl.Locus( + contig='chr1', + position=6559723, + reference_genome='GRCh38', + ), + start_locus=hl.Locus( + contig='chr1', + position=6558902, + reference_genome='GRCh38', + ), + sv_len=245, + sv_type_id=7, + sv_type_detail_id=6, + ), + ], + hl.tstruct( + id=hl.tint32, + algorithms=hl.tstr, + end_locus=hl.tlocus('GRCh38'), + start_locus=hl.tlocus('GRCh38'), + sv_len=hl.tint32, + sv_type_id=hl.tint32, + sv_type_detail_id=hl.tint32, + ), + key='id', + ) + ht = ht.select( + **get_fields( + ht, + DatasetType.SV.export_vcf_annotation_fns, + ), + ) + self.assertEqual( + ht.collect(), + [ + hl.Struct( + id=0, + locus=hl.Locus( + contig='chr1', + position=180928, + reference_genome='GRCh38', + ), + alleles=['N', ''], + info=hl.Struct( + ALGORITHMS='manta', + END=180928, + CHR2='chr5', + END2=20404, + SVTYPE='BND', + SVLEN=123, + ), + ), + hl.Struct( + id=1, + locus=hl.Locus( + contig='chr1', + position=789481, + reference_genome='GRCh38', + ), + alleles=['N', ''], + info=hl.Struct( + ALGORITHMS='manta', + END=789481, + CHR2='chr1', + END2=789481, + SVTYPE='BND', + SVLEN=245, + ), + ), + hl.Struct( + id=2, + locus=hl.Locus( + contig='chr1', + position=6558902, + reference_genome='GRCh38', + ), + alleles=['N', ''], + info=hl.Struct( + ALGORITHMS='manta', + END=6558902, + CHR2='chr1', + END2=6559723, + SVTYPE='CPX', + SVLEN=245, + ), + ), + hl.Struct( + id=3, + locus=hl.Locus( + contig='chr1', + position=6558902, + reference_genome='GRCh38', + ), + alleles=['N', ''], + info=hl.Struct( + ALGORITHMS='manta', + END=6558902, + CHR2='chr1', + END2=6559723, + SVTYPE='INS', + SVLEN=245, + ), + ), + ], + ) diff --git a/loading_pipeline/lib/annotations/vep.py b/loading_pipeline/lib/annotations/vep.py new file mode 100644 index 0000000000..12af00d8bb --- /dev/null +++ b/loading_pipeline/lib/annotations/vep.py @@ -0,0 +1,182 @@ +from collections.abc import Callable + +import hail as hl + +from loading_pipeline.lib.annotations.enums import ( + BIOTYPES, + FIVEUTR_CONSEQUENCES, + LOF_FILTERS, + TRANSCRIPT_CONSEQUENCE_TERMS, +) + +BIOTYPE_LOOKUP = hl.dict(hl.enumerate(BIOTYPES, index_first=False)) +EXTENDED_INTRONIC_SPLICE_REGION_VARIANT = 'extended_intronic_splice_region_variant' +FIVEUTR_CONSEQUENCES_LOOKUP = hl.dict( + hl.enumerate(FIVEUTR_CONSEQUENCES, index_first=False).extend( + [(hl.missing(hl.tstr), hl.missing(hl.tint32))], + ), +) +LOF_FILTERS_LOOKUP = hl.dict(hl.enumerate(LOF_FILTERS, index_first=False)) +MANE_SELECT_ANNOTATIONS = [ + 'mane_select', + 'mane_plus_clinical', +] +NAGNAG_SITE = 'NAGNAG_SITE' +OMIT_TRANSCRIPT_CONSEQUENCE_TERMS = hl.set( + [ + 'upstream_gene_variant', + 'downstream_gene_variant', + ], +) +PROTEIN_CODING_ID = BIOTYPE_LOOKUP['protein_coding'] +SELECTED_ANNOTATIONS = [ + 'amino_acids', + 'canonical', + 'codons', + 'gene_id', + 'hgvsc', + 'hgvsp', + 'transcript_id', +] +TRANSCRIPT_CONSEQUENCE_TERMS_LOOKUP = hl.dict( + hl.enumerate(TRANSCRIPT_CONSEQUENCE_TERMS, index_first=False), +) + + +def _lof_filter_ids(c: hl.StructExpression) -> hl.ArrayNumericExpression: + return hl.or_missing( + (c.lof == 'LC') & hl.is_defined(c.lof_filter), + c.lof_filter.split('&|,').map(lambda f: LOF_FILTERS_LOOKUP[f]), + ) + + +def _consequence_term_ids(c: hl.StructExpression) -> hl.ArrayNumericExpression: + return c.consequence_terms.filter( + lambda t: ~OMIT_TRANSCRIPT_CONSEQUENCE_TERMS.contains(t), + ).map(lambda t: TRANSCRIPT_CONSEQUENCE_TERMS_LOOKUP[t]) + + +def vep_110_transcript_consequences_select( + gencode_ensembl_to_refseq_id_mapping: hl.tdict(hl.tstr, hl.tstr), +) -> hl.StructExpression: + return lambda c: c.select( + *SELECTED_ANNOTATIONS, + *MANE_SELECT_ANNOTATIONS, + biotype_id=BIOTYPE_LOOKUP[c.biotype], + consequence_term_ids=_consequence_term_ids(c), + exon=hl.bind( + lambda split: hl.or_missing( + hl.is_defined(split), + hl.Struct(index=split[0], total=split[1]), + ), + c.exon.split('/').map(hl.parse_int32), + ), + intron=hl.bind( + lambda split: hl.or_missing( + hl.is_defined(split), + hl.Struct(index=split[0], total=split[1]), + ), + c.intron.split('/').map(hl.parse_int32), + ), + refseq_transcript_id=gencode_ensembl_to_refseq_id_mapping.get(c.transcript_id), + alphamissense=hl.struct( + pathogenicity=c.am_pathogenicity, + ), + loftee=hl.struct( + is_lof_nagnag=c.lof_flags == NAGNAG_SITE, + lof_filter_ids=_lof_filter_ids(c), + ), + spliceregion=hl.struct( + extended_intronic_splice_region_variant=( + hl.is_defined(c.spliceregion) + & c.spliceregion.contains( + EXTENDED_INTRONIC_SPLICE_REGION_VARIANT, + ) + ), + ), + utrannotator=hl.struct( + existing_inframe_oorfs=c.existing_inframe_oorfs, + existing_outofframe_oorfs=c.existing_outofframe_oorfs, + existing_uorfs=c.existing_uorfs, + fiveutr_consequence_id=FIVEUTR_CONSEQUENCES_LOOKUP[c.fiveutr_consequence], + # Annotation documentation here: + # https://github.com/ImperialCardioGenetics/UTRannotator?tab=readme-ov-file#the-detailed-annotation-for-each-consequence + # NB: + fiveutr_annotation=c.fiveutr_annotation['1'].annotate( + AltStopDistanceToCDS=hl.parse_int32( + c.fiveutr_annotation['1'].AltStopDistanceToCDS, + ), + CapDistanceToStart=hl.parse_int32( + c.fiveutr_annotation['1'].CapDistanceToStart, + ), + DistanceToCDS=hl.parse_int32( + c.fiveutr_annotation['1'].DistanceToCDS, + ), + DistanceToStop=hl.parse_int32( + c.fiveutr_annotation['1'].DistanceToStop, + ), + Evidence=hl.or_missing( + # Just in case a weird value ("NA" or anything else) propagates + ( + (c.fiveutr_annotation['1'].Evidence == 'True') + | (c.fiveutr_annotation['1'].Evidence == 'False') + ), + hl.bool(c.fiveutr_annotation['1'].Evidence), + ), + StartDistanceToCDS=hl.parse_int32( + c.fiveutr_annotation['1'].StartDistanceToCDS, + ), + newSTOPDistanceToCDS=hl.parse_int32( + c.fiveutr_annotation['1'].newSTOPDistanceToCDS, + ), + alt_type_length=hl.parse_int32( + c.fiveutr_annotation['1'].alt_type_length, + ), + ref_StartDistanceToCDS=hl.parse_int32( + c.fiveutr_annotation['1'].ref_StartDistanceToCDS, + ), + ref_type_length=hl.parse_int32( + c.fiveutr_annotation['1'].ref_type_length, + ), + ), + ), + ) + + +def vep_85_transcript_consequences_select( + c: hl.StructExpression, +) -> hl.StructExpression: + return c.select( + *SELECTED_ANNOTATIONS, + biotype_id=BIOTYPE_LOOKUP[c.biotype], + consequence_term_ids=_consequence_term_ids(c), + is_lof_nagnag=c.lof_flags == NAGNAG_SITE, + lof_filter_ids=_lof_filter_ids(c), + ) + + +def transcript_consequences_sort( + ht: hl.Table, +) -> Callable[[hl.StructExpression], hl.StructExpression]: + return lambda c: hl.bind( + lambda is_coding, is_most_severe, is_canonical: ( + hl.cond( + is_coding, + hl.cond( + is_most_severe, + hl.cond(is_canonical, 1, 2), + hl.cond(is_canonical, 3, 4), + ), + hl.cond( + is_most_severe, + hl.cond(is_canonical, 5, 6), + hl.cond(is_canonical, 7, 8), + ), + ) + ), + c.biotype_id == PROTEIN_CODING_ID, + hl.set(c.consequence_term_ids).contains( + TRANSCRIPT_CONSEQUENCE_TERMS_LOOKUP[ht.vep.most_severe_consequence], + ), + hl.or_else(c.canonical, 0) == 1, + ) diff --git a/loading_pipeline/lib/core/__init__.py b/loading_pipeline/lib/core/__init__.py new file mode 100644 index 0000000000..44e5aaab40 --- /dev/null +++ b/loading_pipeline/lib/core/__init__.py @@ -0,0 +1,17 @@ +from loading_pipeline.lib.core.dataset_type import DatasetType +from loading_pipeline.lib.core.definitions import ( + ReferenceGenome, + SampleType, + Sex, +) +from loading_pipeline.lib.core.environment import Env +from loading_pipeline.lib.core.feature_flag import FeatureFlag + +__all__ = [ + 'DatasetType', + 'Env', + 'FeatureFlag', + 'ReferenceGenome', + 'SampleType', + 'Sex', +] diff --git a/loading_pipeline/lib/core/constants.py b/loading_pipeline/lib/core/constants.py new file mode 100644 index 0000000000..a1a5affaf2 --- /dev/null +++ b/loading_pipeline/lib/core/constants.py @@ -0,0 +1,14 @@ +import os + +MIGRATION_RUN_ID = 'hail_search_to_clickhouse_migration' +VARIANTS_MIGRATION_RUN_ID = 'annotations_to_variants_tables' +GRCH37_TO_GRCH38_LIFTOVER_REF_PATH = ( + 'gs://hail-common/references/grch37_to_grch38.over.chain.gz' + if os.environ.get('HAIL_DATAPROC') == '1' + else 'loading_pipeline/var/liftover/grch37_to_grch38.over.chain.gz' +) +GRCH38_TO_GRCH37_LIFTOVER_REF_PATH = ( + 'gs://hail-common/references/grch38_to_grch37.over.chain.gz' + if os.environ.get('HAIL_DATAPROC') == '1' + else 'loading_pipeline/var/liftover/grch38_to_grch37.over.chain.gz' +) diff --git a/loading_pipeline/lib/core/dataset_type.py b/loading_pipeline/lib/core/dataset_type.py new file mode 100644 index 0000000000..1e018f7104 --- /dev/null +++ b/loading_pipeline/lib/core/dataset_type.py @@ -0,0 +1,385 @@ +from collections.abc import Callable +from enum import StrEnum + +import hail as hl + +from loading_pipeline.lib.annotations import gcnv, mito, shared, snv_indel, sv +from loading_pipeline.lib.core.definitions import ReferenceGenome +from loading_pipeline.lib.core.environment import Env + +MITO_MIN_HOM_THRESHOLD = 0.95 +ZERO = 0.0 + + +class DatasetType(StrEnum): + GCNV = 'GCNV' + MITO = 'MITO' + SNV_INDEL = 'SNV_INDEL' + SV = 'SV' + + @property + def reference_genomes(self) -> list[ReferenceGenome]: + return { + DatasetType.SNV_INDEL: [ReferenceGenome.GRCh37, ReferenceGenome.GRCh38], + DatasetType.MITO: [ReferenceGenome.GRCh38], + DatasetType.GCNV: [ReferenceGenome.GRCh38], + DatasetType.SV: [ReferenceGenome.GRCh38], + }[self] + + def table_key_type( + self, + reference_genome: ReferenceGenome, + ) -> hl.tstruct: + default_key = hl.tstruct( + locus=hl.tlocus(reference_genome.value), + alleles=hl.tarray(hl.tstr), + ) + return { + DatasetType.GCNV: hl.tstruct(variant_id=hl.tstr), + DatasetType.SV: hl.tstruct(variant_id=hl.tstr), + }.get(self, default_key) + + def table_key_format_fn( + self, + reference_genome: ReferenceGenome, + ) -> Callable[[hl.StructExpression], str]: + if self in {DatasetType.GCNV, DatasetType.SV}: + return lambda s: s.variant_id + return ( + lambda s: f'{s.locus.contig if reference_genome == ReferenceGenome.GRCh37 else s.locus.contig.replace("chr", "")}-{s.locus.position}-{"-".join(s.alleles)}' + ) + + @property + def col_fields( + self, + ) -> list[str]: + return { + DatasetType.SNV_INDEL: {}, + DatasetType.MITO: { + 'contamination': {hl.tstr, hl.tfloat64}, + 'mito_cn': hl.tfloat64, + }, + DatasetType.SV: {}, + DatasetType.GCNV: {}, + }[self] + + @property + def entries_fields( + self, + ) -> list[str]: + return { + DatasetType.SNV_INDEL: { + 'GT': hl.tcall, + 'AD': hl.tarray(hl.tint32), + 'GQ': hl.tint32, + }, + DatasetType.MITO: { + 'GT': hl.tcall, + 'DP': hl.tint32, + 'MQ': {hl.tfloat64, hl.tint32}, + 'HL': hl.tfloat64, + }, + DatasetType.SV: { + 'GT': hl.tcall, + 'CONC_ST': hl.tarray(hl.tstr), + 'GQ': hl.tint32, + 'RD_CN': hl.tint32, + }, + DatasetType.GCNV: { + 'any_ovl': hl.tstr, + 'defragmented': hl.tbool, + 'genes_any_overlap_Ensemble_ID': hl.tstr, + 'genes_any_overlap_totalExons': hl.tint32, + 'identical_ovl': hl.tstr, + 'is_latest': hl.tbool, + 'no_ovl': hl.tbool, + 'sample_start': hl.tint32, + 'sample_end': hl.tint32, + 'CN': hl.tint32, + 'GT': hl.tstr, + 'QS': hl.tint32, + }, + }[self] + + @property + def row_fields( + self, + ) -> list[str]: + return { + DatasetType.SNV_INDEL: { + 'rsid': hl.tstr, + 'filters': hl.tset(hl.tstr), + }, + DatasetType.MITO: { + 'rsid': hl.tset(hl.tstr), + 'filters': hl.tset(hl.tstr), + 'common_low_heteroplasmy': hl.tbool, + 'hap_defining_variant': hl.tbool, + 'mitotip_trna_prediction': hl.tstr, + 'vep': hl.tstruct, + }, + DatasetType.SV: { + 'locus': hl.tlocus(ReferenceGenome.GRCh38.value), + 'alleles': hl.tarray(hl.tstr), + 'filters': hl.tset(hl.tstr), + 'info.AC': hl.tarray(hl.tint32), + 'info.AF': hl.tarray(hl.tfloat64), + 'info.ALGORITHMS': hl.tarray(hl.tstr), + 'info.BOTHSIDES_SUPPORT': hl.tbool, + 'info.AN': hl.tint32, + 'info.CHR2': hl.tstr, + 'info.CPX_INTERVALS': hl.tarray(hl.tstr), + 'info.CPX_TYPE': hl.tstr, + 'info.END': hl.tint32, + 'info.END2': hl.tint32, + 'info.N_HET': hl.tint32, + 'info.N_HOMALT': hl.tint32, + 'info.GNOMAD_V4.1_TRUTH_VID': hl.tstr, + 'info.StrVCTVRE': hl.tstr, + 'info.SVLEN': hl.tint32, + **sv.CONSEQ_PREDICTED_GENE_COLS, + }, + DatasetType.GCNV: { + 'cg_genes': hl.tset(hl.tstr), + 'chr': hl.tstr, + 'end': hl.tint32, + 'filters': hl.tset(hl.tstr), + 'gene_ids': hl.tset(hl.tstr), + 'lof_genes': hl.tset(hl.tstr), + 'num_exon': hl.tint32, + 'sc': hl.tint32, + 'sf': hl.tfloat64, + 'start': hl.tint32, + 'strvctvre_score': hl.tstr, + 'svtype': hl.tstr, + }, + }[self] + + @property + def excluded_filters(self) -> hl.SetExpression: + return { + DatasetType.SNV_INDEL: hl.empty_set(hl.tstr), + DatasetType.MITO: hl.set(['PASS']), + DatasetType.SV: hl.set(['PASS', 'BOTHSIDES_SUPPORT']), + DatasetType.GCNV: hl.empty_set(hl.tstr), + }[self] + + @property + def invalid_allele_types(self) -> hl.SetExpression: + return { + DatasetType.SV: hl.set([hl.genetics.allele_type.AlleleType.UNKNOWN]), + }.get( + self, + hl.set( + [ + hl.genetics.allele_type.AlleleType.UNKNOWN, + hl.genetics.allele_type.AlleleType.SYMBOLIC, + ], + ), + ) + + def has_gencode_ensembl_to_refseq_id_mapping( + self, + reference_genome: ReferenceGenome, + ) -> bool: + return ( + self == DatasetType.SNV_INDEL and reference_genome == ReferenceGenome.GRCh38 + ) + + def expect_tdr_metrics( + self, + reference_genome: ReferenceGenome, + ) -> bool: + return ( + self == DatasetType.SNV_INDEL and reference_genome == ReferenceGenome.GRCh38 + ) + + @property + def has_gencode_gene_symbol_to_gene_id_mapping(self) -> bool: + return self == DatasetType.SV + + @property + def has_multi_allelic_variants(self) -> bool: + return self == DatasetType.SNV_INDEL + + @property + def family_entries_filter_fn(self) -> Callable[[hl.StructExpression], bool]: + return { + DatasetType.GCNV: lambda e: hl.is_defined(e.GT), + }.get(self, lambda e: e.GT.is_non_ref()) + + @property + def can_run_validation(self) -> bool: + return self == DatasetType.SNV_INDEL + + @property + def check_sex_and_relatedness(self) -> bool: + return self == DatasetType.SNV_INDEL + + @property + def veppable(self) -> bool: + return self == DatasetType.SNV_INDEL + + def formatting_annotation_fns( + self, + reference_genome: ReferenceGenome, + ) -> list[Callable[..., hl.Expression]]: + GRCh37_fns = { # noqa: N806 + DatasetType.SNV_INDEL: [ + shared.rsid, + shared.variant_id, + shared.xpos, + shared.sorted_transcript_consequences, + snv_indel.rg38_locus, + ], + DatasetType.MITO: [ + mito.common_low_heteroplasmy, + mito.haplogroup, + mito.mitotip, + mito.rsid, + shared.variant_id, + shared.xpos, + shared.sorted_transcript_consequences, + ], + DatasetType.SV: [ + sv.algorithms, + sv.bothsides_support, + sv.cpx_intervals, + sv.end_locus, + sv.gnomad_svs, + sv.sorted_gene_consequences, + sv.start_locus, + sv.strvctvre, + sv.sv_type_id, + sv.sv_type_detail_id, + sv.sv_len, + shared.xpos, + ], + DatasetType.GCNV: [ + gcnv.end_locus, + gcnv.num_exon, + gcnv.sorted_gene_consequences, + gcnv.start_locus, + gcnv.strvctvre, + gcnv.sv_type_id, + gcnv.xpos, + ], + } + if reference_genome == ReferenceGenome.GRCh37: + return GRCh37_fns[self] + return { + DatasetType.SNV_INDEL: [ + shared.rsid, + shared.variant_id, + shared.xpos, + shared.rg37_locus, + snv_indel.check_ref, + snv_indel.sorted_transcript_consequences, + snv_indel.sorted_regulatory_feature_consequences, + snv_indel.sorted_motif_feature_consequences, + ], + DatasetType.MITO: [ + *GRCh37_fns[DatasetType.MITO], + shared.rg37_locus, + ], + DatasetType.SV: [ + *GRCh37_fns[DatasetType.SV], + shared.rg37_locus, + sv.rg37_locus_end, + ], + DatasetType.GCNV: [ + *GRCh37_fns[DatasetType.GCNV], + gcnv.rg37_locus, + gcnv.rg37_locus_end, + ], + }[self] + + @property + def genotype_entry_annotation_fns(self) -> list[Callable[..., hl.Expression]]: + return { + DatasetType.SNV_INDEL: [ + shared.GQ, + snv_indel.AB, + snv_indel.DP, + shared.GT, + ], + DatasetType.MITO: [ + mito.contamination, + mito.DP, + mito.HL, + mito.mito_cn, + mito.GQ, + shared.GT, + ], + DatasetType.SV: [ + sv.CN, + sv.concordance, + shared.GQ, + shared.GT, + ], + DatasetType.GCNV: [ + gcnv.concordance, + gcnv.defragged, + gcnv.sample_end, + gcnv.sample_gene_ids, + gcnv.sample_num_exon, + gcnv.sample_start, + gcnv.CN, + gcnv.GT, + gcnv.QS, + ], + }[self] + + @property + def variant_frequency_annotation_fns(self) -> list[Callable[..., hl.Expression]]: + return { + DatasetType.GCNV: [ + gcnv.gt_stats, + ], + }.get(self, []) + + @property + def filter_invalid_sites(self): + return self == DatasetType.SNV_INDEL + + @property + def should_export_to_vcf(self): + return self == DatasetType.SV + + @property + def export_all_callset_variants(self): + return self == DatasetType.GCNV + + @property + def export_vcf_annotation_fns(self) -> list[Callable[..., hl.Expression]]: + return { + DatasetType.SV: [ + sv.locus, + sv.alleles, + sv.info, + ], + }[self] + + @property + def should_write_new_variant_details(self): + return self == DatasetType.SNV_INDEL + + @property + def overwrite_male_non_par_calls(self) -> None: + return self == DatasetType.SV + + @property + def re_key_by_seqr_internal_truth_vid(self) -> None: + return self == DatasetType.SV + + @property + def dataproc_primary_workers(self) -> int: + if self == DatasetType.SNV_INDEL: + return Env.GCLOUD_DATAPROC_PRIMARY_WORKERS + return 1 + + @property + def dataproc_preemptibles(self) -> int | None: + if self == DatasetType.SNV_INDEL: + return Env.GCLOUD_DATAPROC_SECONDARY_WORKERS + return 1 diff --git a/loading_pipeline/lib/core/definitions.py b/loading_pipeline/lib/core/definitions.py new file mode 100644 index 0000000000..6ccce95e43 --- /dev/null +++ b/loading_pipeline/lib/core/definitions.py @@ -0,0 +1,86 @@ +from enum import StrEnum + +import hail as hl + + +class Sex(StrEnum): + FEMALE = 'F' + MALE = 'M' + UNKNOWN = 'U' + XXX = 'XXX' + X0 = 'X0' + XXY = 'XXY' + XYY = 'XYY' + + @property + def imputed_sex_values(self) -> list[str]: + return { + Sex.MALE: ['Male'], + Sex.FEMALE: ['Female'], + Sex.UNKNOWN: ['', 'Unknown'], + }.get(self, [self.name]) + + +class ReferenceGenome(StrEnum): + GRCh37 = 'GRCh37' + GRCh38 = 'GRCh38' + + @property + def v02_value(self) -> str: + return self.value[-2:] + + @property + def hl_reference(self) -> hl.ReferenceGenome: + return hl.get_reference(self.value) + + @property + def standard_contigs(self) -> set[str]: + return { + *self.hl_reference.contigs[:25], + } + + @property + def optional_contigs(self) -> set[str]: + return { + ReferenceGenome.GRCh37: { + 'Y', + 'MT', + }, + ReferenceGenome.GRCh38: { + 'chrY', + 'chrM', + }, + }[self] + + @property + def mito_contig(self) -> str: + return { + ReferenceGenome.GRCh37: 'MT', + ReferenceGenome.GRCh38: 'chrM', + }[self] + + @property + def x_contig(self) -> str: + return 'X' if self == ReferenceGenome.GRCh37 else 'chrX' + + def contig_recoding(self, include_mt: bool = False) -> dict[str, str]: + recode = { + ReferenceGenome.GRCh37: { + f'chr{i}': f'{i}' for i in ([*list(range(1, 23)), 'X', 'Y']) + }, + ReferenceGenome.GRCh38: { + f'{i}': f'chr{i}' for i in ([*list(range(1, 23)), 'X', 'Y']) + }, + }[self] + + if include_mt and self == ReferenceGenome.GRCh38: + recode.update({'MT': 'chrM'}) + if include_mt and self == ReferenceGenome.GRCh37: + recode.update({'chrM': 'MT'}) + + return recode + + +class SampleType(StrEnum): + WES = 'WES' + WGS = 'WGS' diff --git a/loading_pipeline/lib/core/definitions_test.py b/loading_pipeline/lib/core/definitions_test.py new file mode 100644 index 0000000000..b53d88cd18 --- /dev/null +++ b/loading_pipeline/lib/core/definitions_test.py @@ -0,0 +1,144 @@ +import unittest + +from loading_pipeline.lib.core.definitions import ReferenceGenome + + +class TestReferenceGenomeProperties(unittest.TestCase): + def test_v02_value(self): + self.assertEqual(ReferenceGenome.GRCh37.v02_value, '37') + self.assertEqual(ReferenceGenome.GRCh38.v02_value, '38') + + def test_hl_reference(self): + hl_37_reference = ReferenceGenome.GRCh37.hl_reference + self.assertEqual(hl_37_reference.name, 'GRCh37') + + hl_38_reference = ReferenceGenome.GRCh38.hl_reference + self.assertEqual(hl_38_reference.name, 'GRCh38') + + def test_standard_contigs(self): + expected_37_contigs = { + '3', + '12', + '21', + '2', + '1', + '7', + '13', + '8', + '11', + '22', + 'MT', + '14', + 'Y', + '18', + '19', + '20', + '17', + 'X', + '10', + '15', + '16', + '4', + '5', + '9', + '6', + } + self.assertEqual(ReferenceGenome.GRCh37.standard_contigs, expected_37_contigs) + + expected_38_contigs = { + 'chr10', + 'chr11', + 'chr17', + 'chr18', + 'chr9', + 'chr22', + 'chr3', + 'chrY', + 'chr7', + 'chr6', + 'chr13', + 'chr19', + 'chr16', + 'chrX', + 'chr12', + 'chr2', + 'chr21', + 'chr20', + 'chr8', + 'chrM', + 'chr5', + 'chr4', + 'chr14', + 'chr1', + 'chr15', + } + self.assertEqual(ReferenceGenome.GRCh38.standard_contigs, expected_38_contigs) + + def test_optional_contigs(self): + self.assertEqual(ReferenceGenome.GRCh37.optional_contigs, {'Y', 'MT'}) + self.assertEqual(ReferenceGenome.GRCh38.optional_contigs, {'chrY', 'chrM'}) + + def test_contig_recoding(self): + expected_37_recode = { + 'chr1': '1', + 'chr2': '2', + 'chr3': '3', + 'chr4': '4', + 'chr5': '5', + 'chr6': '6', + 'chr7': '7', + 'chr8': '8', + 'chr9': '9', + 'chr10': '10', + 'chr11': '11', + 'chr12': '12', + 'chr13': '13', + 'chr14': '14', + 'chr15': '15', + 'chr16': '16', + 'chr17': '17', + 'chr18': '18', + 'chr19': '19', + 'chr20': '20', + 'chr21': '21', + 'chr22': '22', + 'chrX': 'X', + 'chrY': 'Y', + 'chrM': 'MT', + } + self.assertDictEqual( + ReferenceGenome.GRCh37.contig_recoding(include_mt=True), + expected_37_recode, + ) + + expected_38_recode = { + '1': 'chr1', + '2': 'chr2', + '3': 'chr3', + '4': 'chr4', + '5': 'chr5', + '6': 'chr6', + '7': 'chr7', + '8': 'chr8', + '9': 'chr9', + '10': 'chr10', + '11': 'chr11', + '12': 'chr12', + '13': 'chr13', + '14': 'chr14', + '15': 'chr15', + '16': 'chr16', + '17': 'chr17', + '18': 'chr18', + '19': 'chr19', + '20': 'chr20', + '21': 'chr21', + '22': 'chr22', + 'X': 'chrX', + 'Y': 'chrY', + 'MT': 'chrM', + } + self.assertDictEqual( + ReferenceGenome.GRCh38.contig_recoding(include_mt=True), + expected_38_recode, + ) diff --git a/loading_pipeline/lib/core/environment.py b/loading_pipeline/lib/core/environment.py new file mode 100644 index 0000000000..87d81e46d4 --- /dev/null +++ b/loading_pipeline/lib/core/environment.py @@ -0,0 +1,83 @@ +import os +from dataclasses import dataclass +from typing import Literal + +# NB: using os.environ.get inside the dataclass defaults gives a lint error. +LOCAL_DISK_MOUNT_DIR = os.environ.get('LOCAL_DISK_MOUNT_DIR', '/var/seqr') +HAIL_TMP_DIR = os.environ.get('HAIL_TMP_DIR', '/tmp') # noqa: S108 +PIPELINE_DATA_DIR = os.environ.get( + 'PIPELINE_DATA_DIR', + '/var/seqr/pipeline-data', +) +LOADING_DATASETS_DIR = os.environ.get( + 'LOADING_DATASETS_DIR', + '/var/seqr/seqr-loading-temp', +) +REFERENCE_DATASETS_DIR = os.environ.get( + 'REFERENCE_DATASETS_DIR', + '/var/seqr/seqr-reference-data', +) +VEP_REFERENCE_DATASETS_DIR = os.environ.get( + 'VEP_REFERENCE_DATASETS_DIR', + '/var/seqr/vep-reference-data', +) +CLICKHOUSE_DATABASE = os.environ.get('CLICKHOUSE_DATABASE', 'seqr') +CLICKHOUSE_SERVICE_HOSTNAME = os.environ.get( + 'CLICKHOUSE_SERVICE_HOSTNAME', + 'localhost', +) +CLICKHOUSE_SERVICE_PORT = int(os.environ.get('CLICKHOUSE_SERVICE_PORT', '9000')) +CLICKHOUSE_WRITER_PASSWORD = os.environ.get( + 'CLICKHOUSE_WRITER_PASSWORD', + 'default_password', +) +CLICKHOUSE_WRITER_USER = os.environ.get('CLICKHOUSE_WRITER_USER', 'default') +DEPLOYMENT_TYPE = os.environ.get('DEPLOYMENT_TYPE', 'prod') +GCLOUD_DATAPROC_PRIMARY_WORKERS = int( + os.environ.get('GCLOUD_DATAPROC_PRIMARY_WORKERS', '1'), +) +GCLOUD_DATAPROC_SECONDARY_WORKERS = int( + os.environ.get('GCLOUD_DATAPROC_SECONDARY_WORKERS', '5'), +) +GCLOUD_PROJECT = os.environ.get('GCLOUD_PROJECT') +GCLOUD_REGION = os.environ.get('GCLOUD_REGION') +PIPELINE_RUNNER_APP_VERSION = os.environ.get('PIPELINE_RUNNER_APP_VERSION', 'latest') +SAMPLE_TYPE_VALIDATION_EXCLUDED_PROJECTS = tuple( + x + for x in os.environ.get('SAMPLE_TYPE_VALIDATION_EXCLUDED_PROJECTS', '').split(',') + if x +) +LOADING_QUEUE_LIMIT = int(os.environ.get('LOADING_QUEUE_LIMIT', '10')) +CLICKHOUSE_OPTIMIZE_TABLE_WAIT_S = int( + os.environ.get('CLICKHOUSE_OPTIMIZE_TABLE_WAIT_S', '150'), +) +SLACK_NOTIFICATION_CHANNEL = os.environ.get('SLACK_NOTIFICATION_CHANNEL', '') +SLACK_TOKEN = os.environ.get('SLACK_TOKEN', '') + + +@dataclass +class Env: + CLICKHOUSE_DATABASE: str = CLICKHOUSE_DATABASE + CLICKHOUSE_OPTIMIZE_TABLE_WAIT_S: str = CLICKHOUSE_OPTIMIZE_TABLE_WAIT_S + CLICKHOUSE_SERVICE_HOSTNAME: str = CLICKHOUSE_SERVICE_HOSTNAME + CLICKHOUSE_SERVICE_PORT: int = CLICKHOUSE_SERVICE_PORT + CLICKHOUSE_WRITER_PASSWORD: str = CLICKHOUSE_WRITER_PASSWORD + CLICKHOUSE_WRITER_USER: str = CLICKHOUSE_WRITER_USER + DEPLOYMENT_TYPE: Literal['dev', 'prod'] = DEPLOYMENT_TYPE + GCLOUD_DATAPROC_PRIMARY_WORKERS: int = GCLOUD_DATAPROC_PRIMARY_WORKERS + GCLOUD_DATAPROC_SECONDARY_WORKERS: int = GCLOUD_DATAPROC_SECONDARY_WORKERS + GCLOUD_PROJECT: str | None = GCLOUD_PROJECT + GCLOUD_REGION: str | None = GCLOUD_REGION + HAIL_TMP_DIR: str = HAIL_TMP_DIR + LOCAL_DISK_MOUNT_DIR: str = LOCAL_DISK_MOUNT_DIR + PIPELINE_DATA_DIR: str = PIPELINE_DATA_DIR + LOADING_DATASETS_DIR: str = LOADING_DATASETS_DIR + LOADING_QUEUE_LIMIT: int = LOADING_QUEUE_LIMIT + PIPELINE_RUNNER_APP_VERSION: str = PIPELINE_RUNNER_APP_VERSION + REFERENCE_DATASETS_DIR: str = REFERENCE_DATASETS_DIR + SAMPLE_TYPE_VALIDATION_EXCLUDED_PROJECTS: tuple[str] = ( + SAMPLE_TYPE_VALIDATION_EXCLUDED_PROJECTS + ) + SLACK_NOTIFICATION_CHANNEL: str = SLACK_NOTIFICATION_CHANNEL + SLACK_TOKEN: str = SLACK_TOKEN + VEP_REFERENCE_DATASETS_DIR: str = VEP_REFERENCE_DATASETS_DIR diff --git a/loading_pipeline/lib/core/feature_flag.py b/loading_pipeline/lib/core/feature_flag.py new file mode 100644 index 0000000000..a7c9ea19d5 --- /dev/null +++ b/loading_pipeline/lib/core/feature_flag.py @@ -0,0 +1,14 @@ +import os +from dataclasses import dataclass + +# Feature Flags +CHECK_SEX_AND_RELATEDNESS = os.environ.get('CHECK_SEX_AND_RELATEDNESS') == '1' +EXPECT_TDR_METRICS = os.environ.get('EXPECT_TDR_METRICS') == '1' +RUN_PIPELINE_ON_DATAPROC = os.environ.get('RUN_PIPELINE_ON_DATAPROC') == '1' + + +@dataclass +class FeatureFlag: + CHECK_SEX_AND_RELATEDNESS: bool = CHECK_SEX_AND_RELATEDNESS + EXPECT_TDR_METRICS: bool = EXPECT_TDR_METRICS + RUN_PIPELINE_ON_DATAPROC: bool = RUN_PIPELINE_ON_DATAPROC diff --git a/loading_pipeline/lib/logger.py b/loading_pipeline/lib/logger.py new file mode 100644 index 0000000000..1cb5b94d52 --- /dev/null +++ b/loading_pipeline/lib/logger.py @@ -0,0 +1,46 @@ +import logging.config + +LOG_CONFIG = { + 'version': 1, + 'disable_existing_loggers': False, + 'propagate': True, + 'formatters': { + 'default': { + 'format': '%(asctime)s - %(module)s - %(levelname)s - %(message)s', + 'datefmt': '%Y-%m-%d %H:%M:%S', + }, + }, + 'handlers': { + 'default': { + 'formatter': 'default', + 'class': 'logging.StreamHandler', + }, + }, + 'loggers': { + '': { + 'level': 'INFO', + 'handlers': ['default'], + 'propagate': False, + }, + 'py4j': { + 'level': 'CRITICAL', + }, + 'urllib3': { + 'level': 'CRITICAL', + }, + 'asyncio': { + 'level': 'CRITICAL', + }, + 'clickhouse_driver': {'level': 'CRITICAL'}, + }, +} + +_CONFIGURED = False + + +def get_logger(name: str): + global _CONFIGURED # noqa: PLW0603 + if not _CONFIGURED: + logging.config.dictConfig(LOG_CONFIG) + _CONFIGURED = True + return logging.getLogger(name) diff --git a/loading_pipeline/lib/methods/__init__.py b/loading_pipeline/lib/methods/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/loading_pipeline/lib/methods/relatedness.py b/loading_pipeline/lib/methods/relatedness.py new file mode 100644 index 0000000000..bb1a1e80fe --- /dev/null +++ b/loading_pipeline/lib/methods/relatedness.py @@ -0,0 +1,40 @@ +import hail as hl +from gnomad.sample_qc.pipeline import filter_rows_for_qc + + +def filter_and_ld_prune( + mt: hl.MatrixTable, + gnomad_qc_ht: hl.Table | None, +) -> hl.MatrixTable: + mt = filter_rows_for_qc( + mt, + min_af=0.001, + min_callrate=0.99, + apply_hard_filters=False, + ) + if not gnomad_qc_ht: + mm_pruned = hl.ld_prune(mt.GT, r2=0.1) + return mt.filter_rows(hl.is_defined(mm_pruned[mt.row_key])) + return mt.filter_rows( + hl.is_defined(gnomad_qc_ht[mt.row_key]), + ) + + +def call_relatedness( + mt: hl.MatrixTable, # NB: we've been remapped and subsetted upstream + gnomad_qc_ht: hl.Table | None, +) -> hl.Table: + mt = filter_and_ld_prune(mt, gnomad_qc_ht) + # NB: ibd did not work by default with my pip install of `hail` on an M1 MacOSX. + # I had to build hail by source with the following: + # - brew install lz4 + # - CXXFLAGS='-I/opt/homebrew/include/' HAIL_COMPILE_NATIVES=1 make -C hail install + # Hail issue here: https://discuss.hail.is/t/noclassdeffounderror-could-not-initialize-class-is-hail-methods-ibsffi/2453 + kin_ht = hl.identity_by_descent(mt, maf=mt['info.AF'][0], min=0.10, max=1.0) + kin_ht = kin_ht.key_by('i', 'j') + return kin_ht.select( + ibd0=kin_ht.ibd.Z0, + ibd1=kin_ht.ibd.Z1, + ibd2=kin_ht.ibd.Z2, + pi_hat=kin_ht.ibd.PI_HAT, + ) diff --git a/loading_pipeline/lib/methods/relatedness_test.py b/loading_pipeline/lib/methods/relatedness_test.py new file mode 100644 index 0000000000..e3afb159e2 --- /dev/null +++ b/loading_pipeline/lib/methods/relatedness_test.py @@ -0,0 +1,39 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.methods.relatedness import call_relatedness + +TEST_SEX_AND_RELATEDNESS_CALLSET_MT = ( + 'loading_pipeline/var/test/callsets/sex_and_relatedness_1.mt' +) + + +class RelatednessTest(unittest.TestCase): + def test_call_relatedness(self): + mt = hl.read_matrix_table(TEST_SEX_AND_RELATEDNESS_CALLSET_MT) + ht = call_relatedness( + mt, + None, + ) + self.assertCountEqual( + ht.collect(), + [ + hl.Struct( + i='ROS_006_18Y03226_D1', + j='ROS_007_19Y05939_D1', + ibd0=0.0, + ibd1=1.0, + ibd2=0.0, + pi_hat=0.5, + ), + hl.Struct( + i='ROS_007_19Y05939_D1', + j='ROS_007_19Y05987_D1', + ibd0=0.0, + ibd1=1.0, + ibd2=0.0, + pi_hat=0.5, + ), + ], + ) diff --git a/loading_pipeline/lib/methods/sample_qc.py b/loading_pipeline/lib/methods/sample_qc.py new file mode 100644 index 0000000000..727f3dcfc9 --- /dev/null +++ b/loading_pipeline/lib/methods/sample_qc.py @@ -0,0 +1,154 @@ +import hail as hl +import onnx +from gnomad.sample_qc.ancestry import ( + apply_onnx_classification_model, + assign_population_pcs, + pc_project, +) +from gnomad.sample_qc.filtering import compute_stratified_metrics_filter +from gnomad.sample_qc.pipeline import filter_rows_for_qc +from gnomad.utils.filtering import filter_to_autosomes +from gnomad_qc.v4.sample_qc.assign_ancestry import assign_pop_with_per_pop_probs + +from loading_pipeline.lib.core import SampleType + +GNOMAD_FILTER_MIN_AF = 0.001 +GNOMAD_FILTER_MIN_CALLRATE = 0.99 + +CALLRATE_LOW_THRESHOLD = 0.85 +CONTAMINATION_UPPER_THRESHOLD = 0.05 +WES_COVERAGE_LOW_THRESHOLD = 85 +WGS_CALLRATE_LOW_THRESHOLD = 30 + +NUM_PCS = 20 +GNOMAD_POP_PROBABILITY_CUTOFFS = { + 'afr': 0.93, + 'ami': 0.98, + 'amr': 0.89, + 'asj': 0.94, + 'eas': 0.95, + 'fin': 0.92, + 'mid': 0.55, + 'nfe': 0.75, + 'sas': 0.92, +} +POPULATION_MISSING_LABEL = 'oth' +HAIL_QC_METRICS = [ + 'n_snp', + 'r_ti_tv', + 'r_insertion_deletion', + 'n_insertion', + 'n_deletion', + 'r_het_hom_var', +] + + +def call_sample_qc( + mt: hl.MatrixTable, + tdr_metrics_ht: hl.Table, + pop_pca_loadings_ht: hl.Table, + ancestry_rf_model: onnx.ModelProto, + sample_type: SampleType, +): + mt = mt.annotate_entries( + GT=hl.case() + .when(mt.GT.is_diploid(), hl.call(mt.GT[0], mt.GT[1], phased=False)) + .when(mt.GT.is_haploid(), hl.call(mt.GT[0], phased=False)) + .default(hl.missing(hl.tcall)), + ) + mt = annotate_filtered_callrate(mt) + # Annotates contamination_rate, percent_bases_at_20x, and mean_coverage + mt = mt.annotate_cols(**tdr_metrics_ht[mt.col_key]) + mt = annotate_filter_flags(mt, sample_type) + mt = annotate_qc_gen_anc(mt, pop_pca_loadings_ht, ancestry_rf_model) + return run_hail_sample_qc(mt, sample_type) + + +def annotate_filtered_callrate(mt: hl.MatrixTable) -> hl.MatrixTable: + filtered_mt = filter_rows_for_qc( + mt, + min_af=GNOMAD_FILTER_MIN_AF, + min_callrate=GNOMAD_FILTER_MIN_CALLRATE, + bi_allelic_only=True, + snv_only=True, + apply_hard_filters=False, + min_inbreeding_coeff_threshold=None, + min_hardy_weinberg_threshold=None, + ) + callrate_ht = filtered_mt.select_cols( + filtered_callrate=hl.agg.fraction(hl.is_defined(filtered_mt.GT)), + ).cols() + return mt.annotate_cols(**callrate_ht[mt.col_key]) + + +def annotate_filter_flags( + mt: hl.MatrixTable, + sample_type: SampleType, +) -> hl.MatrixTable: + flags = { + 'callrate': mt.filtered_callrate < CALLRATE_LOW_THRESHOLD, + 'contamination': mt.contamination_rate > CONTAMINATION_UPPER_THRESHOLD, + 'coverage': ( + mt.percent_bases_at_20x < WES_COVERAGE_LOW_THRESHOLD + if sample_type == SampleType.WES + else mt.mean_coverage < WGS_CALLRATE_LOW_THRESHOLD + ), + } + return mt.annotate_cols( + filter_flags=hl.array( + [hl.or_missing(filter_cond, name) for name, filter_cond in flags.items()], + ).filter(hl.is_defined), + ) + + +def annotate_qc_gen_anc( + mt: hl.MatrixTable, + pop_pca_loadings_ht: hl.Table, + ancestry_rf_model: onnx.ModelProto, +) -> hl.MatrixTable: + mt = mt.select_entries('GT') + scores = pc_project(mt, pop_pca_loadings_ht) + scores = scores.annotate(scores=scores.scores[:NUM_PCS], known_pop='Unknown') + pop_pca_ht, _ = assign_population_pcs( + scores, + pc_cols=scores.scores, + output_col='qc_pop', + fit=ancestry_rf_model, + apply_model_func=apply_onnx_classification_model, + ) + pop_pca_ht = pop_pca_ht.key_by('s') + scores = scores.annotate( + **{f'pop_PC{i + 1}': scores.scores[i] for i in range(NUM_PCS)}, + ).drop('scores', 'known_pop') + pop_pca_ht = pop_pca_ht.annotate(**scores[pop_pca_ht.key]) + pop_pca_ht = assign_pop_with_per_pop_probs( + pop_pca_ht, + min_prob_cutoffs=GNOMAD_POP_PROBABILITY_CUTOFFS, + missing_label=POPULATION_MISSING_LABEL, + ) + pop_pca_ht = pop_pca_ht.transmute(qc_gen_anc=pop_pca_ht.pop).drop('qc_pop') + return mt.annotate_cols(**pop_pca_ht[mt.col_key]) + + +def run_hail_sample_qc(mt: hl.MatrixTable, sample_type: SampleType) -> hl.MatrixTable: + mt = filter_to_autosomes(mt) + mt = hl.sample_qc(mt) + mt = mt.annotate_cols( + sample_qc=mt.sample_qc.annotate( + f_inbreeding=hl.agg.inbreeding(mt.GT, mt['info.AF'][0]), + ), + ) + sample_qc_metrics = HAIL_QC_METRICS + if sample_type == SampleType.WGS: + sample_qc_metrics = [*sample_qc_metrics, 'call_rate'] + + strat_ht = mt.cols() + qc_metrics = {metric: strat_ht.sample_qc[metric] for metric in sample_qc_metrics} + strata = {'qc_gen_anc': strat_ht.qc_gen_anc} + + metric_ht = compute_stratified_metrics_filter(strat_ht, qc_metrics, strata) + metric_ht = metric_ht.annotate( + sample_qc=mt.cols()[metric_ht.key].sample_qc, + qc_metrics_filters=hl.array(metric_ht.qc_metrics_filters), + ) + return mt.annotate_cols(**metric_ht[mt.col_key]) diff --git a/loading_pipeline/lib/methods/sex_check.py b/loading_pipeline/lib/methods/sex_check.py new file mode 100644 index 0000000000..1350ba7d85 --- /dev/null +++ b/loading_pipeline/lib/methods/sex_check.py @@ -0,0 +1,50 @@ +import hail as hl + +from loading_pipeline.lib.core import Sex + +AMBIGUOUS_THRESHOLD_PERC: float = 0.01 # Fraction of samples identified as "ambiguous_sex" above which an error will be thrown. +AAF_THRESHOLD: float = 0.05 # Alternate allele frequency threshold for `hl.impute_sex`. +BIALLELIC: int = 2 +XX_FSTAT_THRESHOLD: float = ( + 0.5 # F-stat threshold below which a sample will be called XX +) +XY_FSTAT_THRESHOLD: float = ( + 0.75 # F-stat threshold above which a sample will be called XY. +) + + +def compute_sex_check_ht(mt: hl.MatrixTable) -> hl.Table: + # Filter to SNVs and biallelics + # NB: We should already have filtered biallelics, but just in case. + mt = mt.filter_rows( + (hl.len(mt.alleles) == BIALLELIC) & hl.is_snp(mt.alleles[0], mt.alleles[1]), + ) + mt = mt.filter_cols(hl.agg.all(mt.GT.is_diploid() | hl.is_missing(mt.GT))) + + # Filter to PASS variants only (variants with empty or missing filter set) + mt = mt.filter_rows( + hl.is_missing(mt.filters) | (mt.filters.length() == 0), + keep=True, + ) + impute_sex_ht = hl.impute_sex( + mt.GT, + male_threshold=XY_FSTAT_THRESHOLD, + female_threshold=XX_FSTAT_THRESHOLD, + aaf_threshold=AAF_THRESHOLD, + ) + ht = mt.annotate_cols(**impute_sex_ht[mt.col_key]).cols() + ht = ht.select( + predicted_sex=( + hl.case() + .when(hl.is_missing(ht.is_female), Sex.UNKNOWN.value) + .when(ht.is_female, Sex.FEMALE.value) + .default(Sex.MALE.value) + ), + ) + ambiguous_perc = ht.aggregate( + hl.agg.fraction(ht.predicted_sex == Sex.UNKNOWN.value), + ) + if ambiguous_perc > AMBIGUOUS_THRESHOLD_PERC: + msg = f'{ambiguous_perc:.2%} of samples identified as ambiguous. Please contact the methods team to investigate the callset.' + raise ValueError(msg) + return ht diff --git a/loading_pipeline/lib/methods/sex_check_test.py b/loading_pipeline/lib/methods/sex_check_test.py new file mode 100644 index 0000000000..ed390e86f3 --- /dev/null +++ b/loading_pipeline/lib/methods/sex_check_test.py @@ -0,0 +1,54 @@ +import unittest +from unittest.mock import patch + +import hail as hl + +from loading_pipeline.lib.methods.sex_check import compute_sex_check_ht + +TEST_SEX_AND_RELATEDNESS_CALLSET_MT = ( + 'loading_pipeline/var/test/callsets/sex_and_relatedness_1.mt' +) + + +class SexCheckTest(unittest.TestCase): + def test_compute_sex_check_ht(self): + mt = hl.read_matrix_table(TEST_SEX_AND_RELATEDNESS_CALLSET_MT) + ht = compute_sex_check_ht(mt) + self.assertCountEqual( + ht.collect(), + [ + hl.Struct( + s='ROS_006_18Y03226_D1', + predicted_sex='M', + ), + hl.Struct( + s='ROS_006_18Y03227_D1', + predicted_sex='M', + ), + hl.Struct( + s='ROS_006_18Y03228_D1', + predicted_sex='M', + ), + hl.Struct( + s='ROS_007_19Y05919_D1', + predicted_sex='M', + ), + hl.Struct( + s='ROS_007_19Y05939_D1', + predicted_sex='F', + ), + hl.Struct( + s='ROS_007_19Y05987_D1', + predicted_sex='M', + ), + ], + ) + + def test_compute_sex_check_ht_ambiguous(self): + mt = hl.read_matrix_table(TEST_SEX_AND_RELATEDNESS_CALLSET_MT) + with patch('loading_pipeline.lib.methods.sex_check.XY_FSTAT_THRESHOLD', 0.95): + self.assertRaises( + ValueError, + compute_sex_check_ht, + mt, + ) diff --git a/loading_pipeline/lib/misc/__init__.py b/loading_pipeline/lib/misc/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/loading_pipeline/lib/misc/callsets.py b/loading_pipeline/lib/misc/callsets.py new file mode 100644 index 0000000000..41357e5ae2 --- /dev/null +++ b/loading_pipeline/lib/misc/callsets.py @@ -0,0 +1,129 @@ +import functools + +import hail as hl +import hailtop.fs as hfs + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome +from loading_pipeline.lib.paths import ( + remapped_and_subsetted_callset_path, + variant_annotations_table_path, +) + + +def get_callset_ht( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + callset_path: str, + project_guids: list[str], +): + callset_hts = [ + hl.read_matrix_table( + remapped_and_subsetted_callset_path( + reference_genome, + dataset_type, + callset_path, + project_guid, + ), + ).rows() + for project_guid in project_guids + ] + callset_ht = functools.reduce( + (lambda ht1, ht2: ht1.union(ht2)), + callset_hts, + ) + return callset_ht.distinct() + + +def union_callset_mts(callset_mts): + """Merge multiple callset matrix tables into a single matrix table. + + Combines callset matrix tables from multiple projects by unioning the column + dimension (samples/individuals). Uses an outer join on rows (variants) to + preserve all unique variants across all callsets, with missing genotypes + filled in as appropriate. Row fields are deduplicated by keeping only the + left table's row metadata. + + Args: + callset_mts: A sequence of Hail matrix tables to merge. + + Returns: + A single matrix table containing all samples and variants from the input + callsets, with row and entry fields merged. + """ + return functools.reduce( + ( + lambda mt1, mt2: mt1.union_cols( + mt2, + row_join_type='outer', + drop_right_row_fields=True, + ) + ), + callset_mts, + ) + + +def get_callset_mt( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + callset_path: str, + project_guids: list[str], +): + callset_mts = [ + hl.read_matrix_table( + remapped_and_subsetted_callset_path( + reference_genome, + dataset_type, + callset_path, + project_guid, + ), + ) + for project_guid in project_guids + ] + callset_mt = union_callset_mts(callset_mts) + return callset_mt.distinct_by_row() + + +def get_additional_row_fields( + mt: hl.MatrixTable, + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + skip_check_sex_and_relatedness: bool, +): + return { + **( + {'info.AF': hl.tarray(hl.tfloat64)} + if not skip_check_sex_and_relatedness + and dataset_type.check_sex_and_relatedness + else {} + ), + # this field is never required, the pipeline + # will run smoothly even in its absence, but + # will trigger special handling if it is present. + **( + {'info.CALIBRATION_SENSITIVITY': hl.tarray(hl.tstr)} + if hasattr(mt, 'info') and hasattr(mt.info, 'CALIBRATION_SENSITIVITY') + else {} + ), + **( + {'info.SEQR_INTERNAL_TRUTH_VID': hl.tstr} + if dataset_type.re_key_by_seqr_internal_truth_vid + and hfs.exists( + variant_annotations_table_path( + reference_genome, + dataset_type, + ), + ) + and hl.eval( + hl.len( + hl.read_table( + variant_annotations_table_path( + reference_genome, + dataset_type, + ), + ).globals.updates, + ) + > 0, + ) + else {} + ), + } diff --git a/loading_pipeline/lib/misc/callsets_test.py b/loading_pipeline/lib/misc/callsets_test.py new file mode 100644 index 0000000000..5db2d4eb36 --- /dev/null +++ b/loading_pipeline/lib/misc/callsets_test.py @@ -0,0 +1,87 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.misc.callsets import union_callset_mts + + +class CallsetsTest(unittest.TestCase): + def test_union_callset_mts(self) -> None: + mt1 = ( + hl.MatrixTable.from_parts( + rows={ + 'id': [ + 0, + 1, + ], + 'row_field': [ + 1, + 2, + ], + }, + cols={'s': ['sample_1']}, + entries={ + 'GT': [[hl.Call([0, 0])], [hl.Call([0, 0])]], + }, + ) + .key_rows_by('id') + .key_cols_by('s') + .drop('row_idx', 'col_idx') + ) + mt2 = ( + hl.MatrixTable.from_parts( + rows={ + 'id': [ + 0, + 2, + ], + 'row_field': [ + 2, + 3, + ], + 'second_row_field': [ + 4, + 5, + ], + }, + cols={'s': ['sample_2']}, + entries={ + 'GT': [[hl.Call([0, 0])], [hl.Call([0, 1])]], + }, + ) + .key_rows_by('id') + .key_cols_by('s') + .drop('row_idx', 'col_idx') + ) + mt = union_callset_mts([mt1, mt2]) + self.assertEqual( + mt.entries().collect(), + [ + hl.Struct( + id=0, + row_field=1, + s='sample_1', + GT=hl.Call(alleles=[0, 0], phased=False), + ), + hl.Struct( + id=0, + row_field=1, + s='sample_2', + GT=hl.Call(alleles=[0, 0], phased=False), + ), + hl.Struct( + id=1, + row_field=2, + s='sample_1', + GT=hl.Call(alleles=[0, 0], phased=False), + ), + hl.Struct(id=1, row_field=2, s='sample_2', GT=None), + hl.Struct(id=2, row_field=None, s='sample_1', GT=None), + hl.Struct( + id=2, + row_field=None, + s='sample_2', + GT=hl.Call(alleles=[0, 1], phased=False), + ), + ], + ) diff --git a/loading_pipeline/lib/misc/clickhouse.py b/loading_pipeline/lib/misc/clickhouse.py new file mode 100644 index 0000000000..977b4fe1e0 --- /dev/null +++ b/loading_pipeline/lib/misc/clickhouse.py @@ -0,0 +1,1247 @@ +import ast +import functools +import hashlib +import math +import os +import time +from collections.abc import Callable +from dataclasses import dataclass +from enum import StrEnum +from string import Template + +from clickhouse_driver import Client + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome +from loading_pipeline.lib.core.environment import Env +from loading_pipeline.lib.logger import get_logger +from loading_pipeline.lib.misc.retry import retry +from loading_pipeline.lib.paths import ( + new_entries_parquet_path, + new_variant_details_parquet_path, + new_variants_parquet_path, +) + +logger = get_logger(__name__) + +GCS_NAMED_COLLECTION = 'pipeline_data_access' +GOOGLE_XML_API_PATH = 'https://storage.googleapis.com/' +OPTIMIZE_TABLE_TIMEOUT_S = 99999 +WAIT_VIEW_TIMEOUT_S = 900 +REDACTED = 'REDACTED' +STAGING_CLICKHOUSE_DATABASE = 'staging' + + +class ClickHouseTable(StrEnum): + KEY_LOOKUP = 'key_lookup' + VARIANT_DETAILS = 'variants/details' + VARIANTS_DISK = 'variants_disk' + VARIANTS_MEMORY = 'variants_memory' + ENTRIES = 'entries' + PROJECT_GT_STATS = 'project_gt_stats' + GT_STATS = 'gt_stats' + + @property + def src_path_fn(self) -> Callable: + return { + ClickHouseTable.VARIANTS_DISK: new_variants_parquet_path, + ClickHouseTable.VARIANTS_MEMORY: new_variants_parquet_path, + ClickHouseTable.KEY_LOOKUP: ( + lambda *args: new_variant_details_parquet_path(*args) + if args[1].should_write_new_variant_details + else new_variants_parquet_path(*args) + ), + ClickHouseTable.VARIANT_DETAILS: new_variant_details_parquet_path, + ClickHouseTable.ENTRIES: new_entries_parquet_path, + }[self] + + @property + def key_field(self): + return 'variantId' if self == ClickHouseTable.KEY_LOOKUP else 'key' + + @property + def join_condition(self): + return ( + 'assumeNotNull(src.variantId) = dst.variantId' + if self == ClickHouseTable.KEY_LOOKUP + else 'assumeNotNull(toUInt32(src.key)) = dst.key' + ) + + @property + def select_fields(self) -> str: + return { + ClickHouseTable.KEY_LOOKUP: 'variantId, key', + }.get(self, '*') + + @property + def insert(self) -> Callable: + return { + # Note that VARIANTS_DETAILS is not included here because + # of the special logic to ensure writes are made to both tables. + ClickHouseTable.VARIANTS_MEMORY: direct_insert_annotations, + ClickHouseTable.ENTRIES: atomic_insert_entries, + ClickHouseTable.KEY_LOOKUP: functools.partial( + direct_insert_all_keys, + clickhouse_table=self, + ), + ClickHouseTable.VARIANT_DETAILS: functools.partial( + direct_insert_all_keys, + clickhouse_table=self, + ), + }[self] + + @classmethod + def for_dataset_type(cls, dataset_type: DatasetType) -> list['ClickHouseTable']: + tables = [ + ClickHouseTable.VARIANTS_MEMORY, + ClickHouseTable.KEY_LOOKUP, + ] + if dataset_type.should_write_new_variant_details: + tables = [ + *tables, + ClickHouseTable.VARIANT_DETAILS, + ] + return [ + *tables, + ClickHouseTable.ENTRIES, + ] + + @classmethod + def for_dataset_type_disk_backed_variants_tables( + cls, + _dataset_type: DatasetType, + ) -> list['ClickHouseTable']: + return [ + ClickHouseTable.VARIANTS_DISK, + ] + + @classmethod + def for_dataset_type_atomic_entries_update( + cls, + dataset_type: DatasetType, + ) -> list['ClickHouseTable']: + return [ + *cls.for_dataset_type_atomic_entries_update_project_partitioned( + dataset_type, + ), + *cls.for_dataset_type_atomic_entries_update_unpartitioned(dataset_type), + ] + + @classmethod + def for_dataset_type_atomic_entries_update_project_partitioned( + cls, + dataset_type: DatasetType, + ) -> list['ClickHouseTable']: + if dataset_type == DatasetType.GCNV: + return [ClickHouseTable.ENTRIES] + return [ + ClickHouseTable.ENTRIES, + ClickHouseTable.PROJECT_GT_STATS, + ] + + @classmethod + def for_dataset_type_atomic_entries_update_unpartitioned( + cls, + dataset_type: DatasetType, + ) -> list['ClickHouseTable']: + if dataset_type == DatasetType.GCNV: + return [] + return [ClickHouseTable.GT_STATS] + + +class ClickHouseDictionary(StrEnum): + GT_STATS_DICT = 'gt_stats_dict' + + @classmethod + def for_dataset_type( + cls, + dataset_type: DatasetType, + ) -> list['ClickHouseDictionary']: + if dataset_type == DatasetType.GCNV: + return [] + return list(cls) + + +class ClickHouseMaterializedView(StrEnum): + ENTRIES_TO_PROJECT_GT_STATS_MV = 'entries_to_project_gt_stats_mv' + PROJECT_GT_STATS_TO_GT_STATS_MV = 'project_gt_stats_to_gt_stats_mv' + + @classmethod + def for_dataset_type_atomic_entries_update( + cls, + dataset_type: DatasetType, + ) -> list['ClickHouseMaterializedView']: + if dataset_type == DatasetType.GCNV: + return [] + return [ + ClickHouseMaterializedView.ENTRIES_TO_PROJECT_GT_STATS_MV, + ClickHouseMaterializedView.PROJECT_GT_STATS_TO_GT_STATS_MV, + ] + + @classmethod + def for_dataset_type_atomic_entries_update_refreshable( + cls, + dataset_type: DatasetType, + ) -> list['ClickHouseMaterializedView']: + if dataset_type == DatasetType.GCNV: + return [] + return [ClickHouseMaterializedView.PROJECT_GT_STATS_TO_GT_STATS_MV] + + +ClickHouseEntity = ClickHouseDictionary | ClickHouseTable | ClickHouseMaterializedView + + +@dataclass +class TableNameBuilder: + reference_genome: ReferenceGenome + dataset_type: DatasetType + run_id: str + + @property + def run_id_hash(self): + # Note: encountered length issues with the default + # run ids generated by the pipeline. ClickHouse performed + # well with staging Tables with the long run ids, but failed + # to recognized staging Dictionaries. + sha256 = hashlib.sha256() + sha256.update(self.run_id.encode()) + return sha256.hexdigest()[:8] + + @property + def dst_prefix(self): + return f'{Env.CLICKHOUSE_DATABASE}.`{self.reference_genome.value}/{self.dataset_type.value}' + + def dst_table(self, clickhouse_entity: ClickHouseEntity): + return f'{self.dst_prefix}/{clickhouse_entity.value}`' + + @property + def staging_dst_prefix(self): + return f'{STAGING_CLICKHOUSE_DATABASE}.`{self.run_id_hash}/{self.reference_genome.value}/{self.dataset_type.value}' + + def staging_dst_table(self, clickhouse_table: ClickHouseTable): + return f'{self.staging_dst_prefix}/{clickhouse_table.value}`' + + def src_table(self, clickhouse_table: ClickHouseTable): + path = os.path.join( + clickhouse_table.src_path_fn( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + '*.parquet', + ) + if path.startswith('gs://'): + return f"gcs({GCS_NAMED_COLLECTION}, url='{path.replace('gs://', GOOGLE_XML_API_PATH)}')" + return f"file('{path}', 'Parquet')" + + +class ClickhouseReferenceDataset(StrEnum): + ABSPLICE2 = 'absplice2' + CLINVAR = 'clinvar' + DBNSFP = 'dbnsfp' + EIGEN = 'eigen' + GNOMAD_EXOMES = 'gnomad_exomes' + GNOMAD_GENOMES = 'gnomad_genomes' + GNOMAD_MITO = 'gnomad_mito' + GNOMAD_MITO_HETEROPLASMY = 'gnomad_mito_heteroplasmy' + GNOMAD_NON_CODING_CONSTRAINT = 'gnomad_non_coding_constraint' + HELIX_MITO = 'helix_mito' + HELIX_MITO_HETEROPLASMY = 'helix_mito_heteroplasmy' + HGMD = 'hgmd' + HMTVAR = 'hmtvar' + LOCAL_CONSTRAINT_MITO = 'local_constraint_mito' + MITIMPACT = 'mitimpact' + MITOMAP = 'mitomap' + PEXT = 'pext' + PROMOTER_AI = 'promoterAI' + SCREEN = 'screen' + SPLICE_AI = 'splice_ai' + TOPMED = 'topmed' + + @property + def all_variants_mv_timeout(self): + return { + ClickhouseReferenceDataset.DBNSFP: WAIT_VIEW_TIMEOUT_S * 3, + ClickhouseReferenceDataset.SPLICE_AI: WAIT_VIEW_TIMEOUT_S * 10, + }.get(self, WAIT_VIEW_TIMEOUT_S) + + @property + def fully_refreshable(self): + return self != ClickhouseReferenceDataset.CLINVAR + + @property + def has_seqr_variants(self): + return self not in { + ClickhouseReferenceDataset.GNOMAD_NON_CODING_CONSTRAINT, + ClickhouseReferenceDataset.SCREEN, + } + + @classmethod + def for_reference_genome_dataset_type( + cls, + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + ): + if dataset_type in {DatasetType.SV, DatasetType.GCNV}: + return [] + return { + (ReferenceGenome.GRCh38, DatasetType.MITO): [ + ClickhouseReferenceDataset.CLINVAR, + ClickhouseReferenceDataset.DBNSFP, + ClickhouseReferenceDataset.GNOMAD_MITO, + ClickhouseReferenceDataset.GNOMAD_MITO_HETEROPLASMY, + ClickhouseReferenceDataset.HELIX_MITO, + ClickhouseReferenceDataset.HELIX_MITO_HETEROPLASMY, + ClickhouseReferenceDataset.HMTVAR, + ClickhouseReferenceDataset.LOCAL_CONSTRAINT_MITO, + ClickhouseReferenceDataset.MITIMPACT, + ClickhouseReferenceDataset.MITOMAP, + ClickhouseReferenceDataset.PEXT, + ], + (ReferenceGenome.GRCh37, DatasetType.SNV_INDEL): [ + ClickhouseReferenceDataset.CLINVAR, + ClickhouseReferenceDataset.DBNSFP, + ClickhouseReferenceDataset.EIGEN, + ClickhouseReferenceDataset.GNOMAD_EXOMES, + ClickhouseReferenceDataset.GNOMAD_GENOMES, + ClickhouseReferenceDataset.HGMD, + ClickhouseReferenceDataset.SPLICE_AI, + ClickhouseReferenceDataset.TOPMED, + ], + (ReferenceGenome.GRCh38, DatasetType.SNV_INDEL): [ + ClickhouseReferenceDataset.ABSPLICE2, + ClickhouseReferenceDataset.CLINVAR, + ClickhouseReferenceDataset.DBNSFP, + ClickhouseReferenceDataset.EIGEN, + ClickhouseReferenceDataset.GNOMAD_EXOMES, + ClickhouseReferenceDataset.GNOMAD_GENOMES, + ClickhouseReferenceDataset.GNOMAD_NON_CODING_CONSTRAINT, + ClickhouseReferenceDataset.HGMD, + ClickhouseReferenceDataset.PEXT, + ClickhouseReferenceDataset.PROMOTER_AI, + ClickhouseReferenceDataset.SCREEN, + ClickhouseReferenceDataset.SPLICE_AI, + ClickhouseReferenceDataset.TOPMED, + ], + }[(reference_genome, dataset_type)] + + @property + def search_is_join_table(self): + return self in { + ClickhouseReferenceDataset.CLINVAR, + ClickhouseReferenceDataset.HGMD, + } + + def all_variants_path(self, table_name_builder: TableNameBuilder) -> str: + return ( + f'{table_name_builder.dst_prefix}/reference_data/{self.value}/all_variants`' + ) + + def seqr_variants_path(self, table_name_builder: TableNameBuilder) -> str: + return f'{table_name_builder.dst_prefix}/reference_data/{self.value}/seqr_variants`' + + def search_path(self, table_name_builder: TableNameBuilder) -> str: + return f'{table_name_builder.dst_prefix}/reference_data/{self.value}`' + + def all_variants_mv( + self, + table_name_builder: TableNameBuilder, + ) -> str: + return f'{table_name_builder.dst_prefix}/reference_data/{self.value}/all_variants_mv`' + + def all_variants_to_seqr_variants_mv( + self, + table_name_builder: TableNameBuilder, + ) -> str: + return f'{table_name_builder.dst_prefix}/reference_data/{self.value}/all_variants_to_seqr_variants_mv`' + + def seqr_variants_to_search_mv_path( + self, + table_name_builder: TableNameBuilder, + ) -> str: + return f'{table_name_builder.dst_prefix}/reference_data/{self.value}/seqr_variants_to_search_mv`' + + def refresh_search( + self, + table_name_builder: TableNameBuilder, + ) -> str: + if self.search_is_join_table: + logged_query( + f""" + SYSTEM START VIEW {self.seqr_variants_to_search_mv_path(table_name_builder)} + """, + ) + logged_query( + f""" + SYSTEM REFRESH VIEW {self.seqr_variants_to_search_mv_path(table_name_builder)} + """, + ) + logged_query( + f""" + SYSTEM WAIT VIEW {self.seqr_variants_to_search_mv_path(table_name_builder)} + """, + timeout=WAIT_VIEW_TIMEOUT_S, + ) + else: + logged_query( + f""" + SYSTEM RELOAD DICTIONARY {self.search_path(table_name_builder)} + """, + ) + + def insert_into_seqr_variants_and_refresh_search( + self, + table_name_builder: TableNameBuilder, + ): + if not self.has_seqr_variants: + return + exists_seqr_variants = logged_query( + f'EXISTS TABLE {self.seqr_variants_path(table_name_builder)}', + )[0][0] + if not exists_seqr_variants: + return + drop_staging_db() + logged_query( + f""" + CREATE DATABASE {STAGING_CLICKHOUSE_DATABASE} + """, + ) + logged_query( + f""" + CREATE TABLE {table_name_builder.staging_dst_prefix}/_tmp_loadable_variantIds` ENGINE = Set AS ( + SELECT {ClickHouseTable.KEY_LOOKUP.key_field} + FROM {table_name_builder.src_table(ClickHouseTable.KEY_LOOKUP)} + ) + """, + ) + logged_query( + f""" + INSERT INTO {self.seqr_variants_path(table_name_builder)} + SELECT + DISTINCT ON (key) + dst.key, + COLUMNS('.*') EXCEPT(version, variantId, key) + FROM {self.all_variants_path(table_name_builder)} src + INNER JOIN {table_name_builder.dst_table(ClickHouseTable.KEY_LOOKUP)} dst + ON {ClickHouseTable.KEY_LOOKUP.join_condition} + WHERE src.variantId IN {table_name_builder.staging_dst_prefix}/_tmp_loadable_variantIds` + """, + ) + self.refresh_search(table_name_builder) + + def download_and_fully_refresh( + self, + table_name_builder: TableNameBuilder, + ): + logged_query( + f""" + SYSTEM START VIEW {self.all_variants_mv(table_name_builder)} + """, + ) + logged_query( + f""" + SYSTEM REFRESH VIEW {self.all_variants_mv(table_name_builder)} + """, + ) + logged_query( + f""" + SYSTEM WAIT VIEW {self.all_variants_mv(table_name_builder)} + """, + timeout=self.all_variants_mv_timeout, + ) + if self.has_seqr_variants: + logged_query( + f""" + SYSTEM START VIEW {self.all_variants_to_seqr_variants_mv(table_name_builder)} + """, + ) + logged_query( + f""" + SYSTEM REFRESH VIEW {self.all_variants_to_seqr_variants_mv(table_name_builder)} + """, + ) + logged_query( + f""" + SYSTEM WAIT VIEW {self.all_variants_to_seqr_variants_mv(table_name_builder)} + """, + timeout=self.all_variants_mv_timeout, + ) + self.refresh_search(table_name_builder) + + +def logged_query(query, params=None, timeout: int | None = None): + client = get_clickhouse_client(timeout) + sanitized_query = query + if Env.CLICKHOUSE_WRITER_PASSWORD: + sanitized_query = sanitized_query.replace( + Env.CLICKHOUSE_WRITER_PASSWORD, + REDACTED, + ) + logger.info(f'Executing query: {sanitized_query} | Params: {params}') + return client.execute(query, params) + + +def drop_staging_db(): + logged_query(f'DROP DATABASE IF EXISTS {STAGING_CLICKHOUSE_DATABASE};') + + +def create_staging_tables( + table_name_builder: TableNameBuilder, + clickhouse_tables: list[ClickHouseTable], +) -> None: + logged_query( + f""" + CREATE DATABASE {STAGING_CLICKHOUSE_DATABASE} + """, + ) + for clickhouse_table in clickhouse_tables: + logged_query( + f""" + CREATE + TABLE {table_name_builder.staging_dst_table(clickhouse_table)} + AS {table_name_builder.dst_table(clickhouse_table)} + """, + ) + + +def get_create_mv_statements( + table_name_builder: TableNameBuilder, + clickhouse_mv: ClickHouseMaterializedView, +) -> tuple[str, str]: + return logged_query( + """ + SELECT create_table_query, as_select FROM system.tables + WHERE + engine = 'MaterializedView' + AND database = %(database)s + AND name = %(name)s + """, + { + 'database': Env.CLICKHOUSE_DATABASE, + 'name': table_name_builder.dst_table(clickhouse_mv) + .split('.')[1] + .replace('`', ''), + }, + )[0] + + +def normalize_partition(partition: str) -> tuple: + """ + Ensure a ClickHouse partition expression is always returned as a tuple. + 'project_d' -> ('project_d',) + "('project_d', 0)" -> ('project_d', 0) + """ + if not isinstance(partition, str): + msg = f'Unsupported partition type: {type(partition)}' + raise TypeError(msg) + partition = partition.strip() + if partition.startswith('(') and partition.endswith(')'): + return ast.literal_eval(partition) + return (partition,) + + +def get_partitions_for_projects( + table_name_builder: TableNameBuilder, + clickhouse_table: ClickHouseTable, + project_guids: list[str], + staging=False, +): + rows = logged_query( + """ + SELECT DISTINCT partition + FROM system.parts + WHERE + database = %(database)s + AND table = %(table)s + AND multiSearchAny(partition, %(project_guids)s) + """, + { + 'database': STAGING_CLICKHOUSE_DATABASE + if staging + else Env.CLICKHOUSE_DATABASE, + 'table': ( + table_name_builder.staging_dst_table(clickhouse_table) + if staging + else table_name_builder.dst_table(clickhouse_table) + ) + .split('.')[1] + .replace('`', ''), + 'project_guids': project_guids, + }, + ) + return [normalize_partition(row[0]) for row in rows] + + +def create_staging_materialized_views( + table_name_builder: TableNameBuilder, + clickhouse_mvs: list[ClickHouseMaterializedView], +): + for clickhouse_mv in clickhouse_mvs: + create_table_statement = get_create_mv_statements( + table_name_builder, + clickhouse_mv, + )[0] + create_table_statement = create_table_statement.replace( + table_name_builder.dst_prefix, + table_name_builder.staging_dst_prefix, + ) + logged_query(create_table_statement) + + +# Note that this function is NOT idemptotent. Clickhouse permits +# attaching the same partition to a table multiple times. +def stage_existing_project_partitions( + table_name_builder: TableNameBuilder, + project_guids: list[str], + clickhouse_tables: list[ClickHouseTable], +): + for clickhouse_table in clickhouse_tables: + # Very important piece here: + # ALL projects in the project_gt_stats table are staged, allowing us to rebuild + # a production-quality gt_stats materialized view in the staging environment. + if clickhouse_table == ClickHouseTable.PROJECT_GT_STATS: + logged_query( + f""" + ALTER TABLE {table_name_builder.staging_dst_table(clickhouse_table)} + ATTACH PARTITION ALL FROM {table_name_builder.dst_table(clickhouse_table)} + """, + ) + continue + for partition in get_partitions_for_projects( + table_name_builder, + clickhouse_table, + project_guids, + ): + # Note that ClickHouse successfully handles the case where the project + # does not already exist in the dst table. We simply attach an empty partition! + logged_query( + f""" + ALTER TABLE {table_name_builder.staging_dst_table(clickhouse_table)} + ATTACH PARTITION %(partition)s FROM {table_name_builder.dst_table(clickhouse_table)} + """, + {'partition': partition}, + ) + + +def delete_existing_families_from_staging_entries( + table_name_builder: TableNameBuilder, + family_guids: list[str], +) -> None: + logged_query( + f""" + INSERT INTO {table_name_builder.staging_dst_table(ClickHouseTable.ENTRIES)} + SELECT COLUMNS('.*') EXCEPT(sign, n_partitions, partition_id), -1 as sign + FROM {table_name_builder.staging_dst_table(ClickHouseTable.ENTRIES)} + WHERE family_guid in %(family_guids)s + """, + {'family_guids': family_guids}, + ) + + +def insert_new_entries( + table_name_builder: TableNameBuilder, +) -> None: + dst_cols = [ + r[0] + for r in logged_query( + f'DESCRIBE TABLE {table_name_builder.staging_dst_table(ClickHouseTable.ENTRIES)}', + ) + ] + src_cols = [ + r[0] + for r in logged_query( + f'DESCRIBE TABLE {table_name_builder.src_table(ClickHouseTable.ENTRIES)}', + ) + ] + common, overrides = [c for c in dst_cols if c in src_cols], {} + if 'geneId_ids' in dst_cols and 'geneIds' in src_cols: + common = [c for c in common if c not in ('geneId_ids', 'geneIds')] + common.append('geneId_ids') + overrides['geneId_ids'] = f""" + arrayFilter( + x -> x IS NOT NULL, + arrayMap( + g -> dictGetOrNull( + {Env.CLICKHOUSE_DATABASE}.`seqrdb_gene_ids`, + 'seqrdb_id', + g + ), + geneIds + ) + ) + """ + + if ( + 'is_gnomad_gt_5_percent' in dst_cols + and 'is_gnomad_gt_5_percent' not in src_cols + ): + common.append('is_gnomad_gt_5_percent') + overrides['is_gnomad_gt_5_percent'] = f""" + dictGetOrDefault({ClickhouseReferenceDataset.GNOMAD_GENOMES.search_path(table_name_builder)}, 'filter_af', key, 0) > 0.05 + """ + + dst_list = ', '.join(common) + src_list = ', '.join([overrides.get(c, c) for c in common]) + logged_query( + f""" + INSERT INTO {table_name_builder.staging_dst_table(ClickHouseTable.ENTRIES)} ({dst_list}) + SELECT {src_list} + FROM {table_name_builder.src_table(ClickHouseTable.ENTRIES)} + """, + ) + + +@retry(tries=2) +def optimize_entries( + table_name_builder: TableNameBuilder, + project_guids: list[str], +) -> None: + max_attempts = 10 + for attempt in range(max_attempts): + decrs_exist = logged_query( + f""" + SELECT EXISTS ( + SELECT 1 + FROM {table_name_builder.staging_dst_table(ClickHouseTable.ENTRIES)} + WHERE sign = -1 + ); + """, + )[0][0] + + merges_running = logged_query( + """ + SELECT EXISTS ( + SELECT 1 + FROM system.merges + WHERE database = %(database)s + AND table = %(table)s + ); + """, + { + 'database': STAGING_CLICKHOUSE_DATABASE, + 'table': table_name_builder.staging_dst_table(ClickHouseTable.ENTRIES) + .split('.')[1] + .replace('`', ''), + }, + )[0][0] + + if not decrs_exist: + return + + if merges_running: + logger.info( + 'Decrs exist and merges are running, so waiting (attempt %d/%d)', + attempt + 1, + max_attempts, + ) + else: + logger.info( + 'Decrs exist and no merges are running, so optimizing (attempt %d/%d)', + attempt + 1, + max_attempts, + ) + + partitions = get_partitions_for_projects( + table_name_builder, + ClickHouseTable.ENTRIES, + project_guids, + staging=True, + ) + table_name = table_name_builder.staging_dst_table( + ClickHouseTable.ENTRIES, + ) + optimize_statements = [ + f'OPTIMIZE TABLE {table_name} PARTITION {partition} FINAL' + for partition in partitions + ] + parallel_optimize_sql = '\nPARALLEL WITH\n'.join(optimize_statements) + + logged_query( + parallel_optimize_sql, + timeout=OPTIMIZE_TABLE_TIMEOUT_S, + ) + + time.sleep(Env.CLICKHOUSE_OPTIMIZE_TABLE_WAIT_S) + msg = f'Entries table still contains decrement rows after {max_attempts} attempts.' + raise TimeoutError(msg) + + +@retry(tries=2) +def refresh_materialized_views( + table_name_builder, + materialized_views: list[ClickHouseMaterializedView], + staging=False, +): + for materialized_view in materialized_views: + logged_query( + f""" + SYSTEM START VIEW {table_name_builder.staging_dst_table(materialized_view) if staging else table_name_builder.dst_table(materialized_view)} + """, + ) + logged_query( + f""" + SYSTEM REFRESH VIEW {table_name_builder.staging_dst_table(materialized_view) if staging else table_name_builder.dst_table(materialized_view)} + """, + ) + logged_query( + f""" + SYSTEM WAIT VIEW {table_name_builder.staging_dst_table(materialized_view) if staging else table_name_builder.dst_table(materialized_view)} + """, + timeout=WAIT_VIEW_TIMEOUT_S, + ) + + +def validate_family_guid_counts( + table_name_builder: TableNameBuilder, + project_guids: list[str], + family_guids: list[str], +) -> None: + query = Template( + """ + SELECT family_guid, COUNT(*) + FROM $table_name + WHERE project_guid in %(project_guids)s + AND family_guid in %(family_guids)s + GROUP BY 1 + """, + ) + src_family_counts = dict( + logged_query( + query.substitute( + table_name=table_name_builder.src_table( + ClickHouseTable.ENTRIES, + ), + ), + {'family_guids': family_guids, 'project_guids': project_guids}, + ), + ) + dst_family_counts = dict( + logged_query( + query.substitute( + table_name=table_name_builder.staging_dst_table( + ClickHouseTable.ENTRIES, + ), + ), + {'family_guids': family_guids, 'project_guids': project_guids}, + ), + ) + if src_family_counts != dst_family_counts: + msg = 'Loaded Row counts are different than expected.' + raise ValueError(msg) + + +@retry(tries=2) +def reload_dictionaries( + table_name_builder: TableNameBuilder, + dictionaries: list[ClickHouseDictionary], +): + for dictionary in dictionaries: + logged_query( + f""" + SYSTEM RELOAD DICTIONARY {table_name_builder.dst_table(dictionary)} + """, + ) + + +def replace_project_partitions( + table_name_builder: TableNameBuilder, + clickhouse_tables: list[ClickHouseTable], + project_guids: list[str], +) -> None: + for clickhouse_table in clickhouse_tables: + for partition in get_partitions_for_projects( + table_name_builder, + clickhouse_table, + project_guids, + staging=True, + ): + logged_query( + f""" + ALTER TABLE {table_name_builder.dst_table(clickhouse_table)} + REPLACE PARTITION %(partition)s FROM {table_name_builder.staging_dst_table(clickhouse_table)} + """, + {'partition': partition}, + ) + + +# Note this is NOT idempotent, as running the swap twice will +# result in the tables not being swapped. +def exchange_tables( + table_name_builder, + clickhouse_tables: list[ClickHouseTable], +) -> None: + for clickhouse_table in clickhouse_tables: + logged_query( + f""" + EXCHANGE TABLES {table_name_builder.staging_dst_table(clickhouse_table)} AND {table_name_builder.dst_table(clickhouse_table)} + """, + ) + + +def direct_insert_annotations( + table_name_builder: TableNameBuilder, + **_, +) -> None: + dst_table = table_name_builder.dst_table(ClickHouseTable.VARIANTS_MEMORY) + src_table = table_name_builder.src_table(ClickHouseTable.VARIANTS_MEMORY) + drop_staging_db() + logged_query( + f""" + CREATE DATABASE {STAGING_CLICKHOUSE_DATABASE} + """, + ) + # NB: Unfortunately there's a bug(?) or inaccuracy if this is attempted without an intermediate + # temporary table, likely due to writing to a table and joining against it at the same time. + logged_query( + f""" + CREATE TABLE {table_name_builder.staging_dst_prefix}/_tmp_loadable_keys` ENGINE = Set AS ( + SELECT {ClickHouseTable.VARIANTS_MEMORY.key_field} + FROM {src_table} src + LEFT ANTI JOIN {dst_table} dst + ON {ClickHouseTable.VARIANTS_MEMORY.join_condition} + ) + """, + ) + for ( + clickhouse_table + ) in ClickHouseTable.for_dataset_type_disk_backed_variants_tables( + table_name_builder.dataset_type, + ): + disk_backed_dst_table = table_name_builder.dst_table(clickhouse_table) + disk_backed_src_table = table_name_builder.src_table(clickhouse_table) + logged_query( + f""" + INSERT INTO {disk_backed_dst_table} + SELECT {clickhouse_table.select_fields} + FROM {disk_backed_src_table} WHERE {clickhouse_table.key_field} IN {table_name_builder.staging_dst_prefix}/_tmp_loadable_keys` + """, + ) + logged_query( + f""" + INSERT INTO {dst_table} + SELECT {ClickHouseTable.VARIANTS_MEMORY.select_fields} + FROM {src_table} WHERE {ClickHouseTable.VARIANTS_MEMORY.key_field} IN {table_name_builder.staging_dst_prefix}/_tmp_loadable_keys` + """, + ) + drop_staging_db() + + +def direct_insert_all_keys( + clickhouse_table: ClickHouseTable, + table_name_builder: TableNameBuilder, + **_, +) -> None: + dst_table = table_name_builder.dst_table(clickhouse_table) + src_table = table_name_builder.src_table(clickhouse_table) + settings = '' + # Large variant details inserts may OOM + if clickhouse_table == ClickHouseTable.VARIANT_DETAILS: + settings = 'SETTINGS max_insert_threads = 2' + logged_query( + f""" + INSERT INTO {dst_table} + SELECT {clickhouse_table.select_fields} + FROM {src_table} + {settings} + """, + ) + + +# This is a smattering of shared operations that lacks a better name :/ +def finalize_refresh_flow( + table_name_builder: TableNameBuilder, + project_guids: list[str], +): + dataset_type = table_name_builder.dataset_type + refresh_materialized_views( + table_name_builder, + ClickHouseMaterializedView.for_dataset_type_atomic_entries_update_refreshable( + dataset_type, + ), + staging=True, + ) + replace_project_partitions( + table_name_builder, + ClickHouseTable.for_dataset_type_atomic_entries_update_project_partitioned( + dataset_type, + ), + project_guids, + ) + exchange_tables( + table_name_builder, + ClickHouseTable.for_dataset_type_atomic_entries_update_unpartitioned( + dataset_type, + ), + ) + drop_staging_db() + reload_dictionaries( + table_name_builder, + ClickHouseDictionary.for_dataset_type(dataset_type), + ) + + +def atomic_insert_entries( + table_name_builder: TableNameBuilder, + project_guids: list[str], + family_guids: list[str], + **_, +) -> None: + dataset_type = table_name_builder.dataset_type + drop_staging_db() + create_staging_tables( + table_name_builder, + ClickHouseTable.for_dataset_type_atomic_entries_update(dataset_type), + ) + create_staging_materialized_views( + table_name_builder, + ClickHouseMaterializedView.for_dataset_type_atomic_entries_update( + dataset_type, + ), + ) + stage_existing_project_partitions( + table_name_builder, + project_guids, + ClickHouseTable.for_dataset_type_atomic_entries_update_project_partitioned( + dataset_type, + ), + ) + delete_existing_families_from_staging_entries( + table_name_builder, + family_guids, + ) + insert_new_entries( + table_name_builder, + ) + optimize_entries( + table_name_builder, + project_guids, + ) + validate_family_guid_counts( + table_name_builder, + project_guids, + family_guids, + ) + finalize_refresh_flow(table_name_builder, project_guids) + + +@retry() +def load_complete_run( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + run_id: str, + project_guids: list[str], + family_guids: list[str], +): + msg = f'Attempting load of run: {reference_genome.value}/{dataset_type.value}/{run_id}' + logger.info(msg) + table_name_builder = TableNameBuilder( + reference_genome, + dataset_type, + run_id, + ) + for clickhouse_table in ClickHouseTable.for_dataset_type(dataset_type): + clickhouse_table.insert( + table_name_builder=table_name_builder, + project_guids=project_guids, + family_guids=family_guids, + ) + for ( + clickhouse_reference_data + ) in ClickhouseReferenceDataset.for_reference_genome_dataset_type( + reference_genome, + dataset_type, + ): + clickhouse_reference_data.insert_into_seqr_variants_and_refresh_search( + table_name_builder=table_name_builder, + ) + + +@retry() +def delete_family_guids( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + run_id: str, + project_guid: str, + family_guids: list[str], +): + msg = f'Attempting delete families for {reference_genome.value}/{dataset_type.value} {project_guid}: {family_guids}' + logger.info(msg) + table_name_builder = TableNameBuilder( + reference_genome, + dataset_type, + run_id, + ) + entries_exist = logged_query( + f""" + SELECT EXISTS ( + SELECT 1 + FROM {table_name_builder.dst_table(ClickHouseTable.ENTRIES)} + WHERE project_guid = %(project_guid)s + AND has(%(family_guids)s, family_guid) + ); + """, + {'family_guids': family_guids, 'project_guid': project_guid}, + )[0][0] + if not entries_exist: + msg = f'No data exists for {reference_genome.value} & {dataset_type.value} so skipping' + logger.info(msg) + return + project_guids = [project_guid] + drop_staging_db() + create_staging_tables( + table_name_builder, + ClickHouseTable.for_dataset_type_atomic_entries_update(dataset_type), + ) + create_staging_materialized_views( + table_name_builder, + ClickHouseMaterializedView.for_dataset_type_atomic_entries_update( + dataset_type, + ), + ) + stage_existing_project_partitions( + table_name_builder, + project_guids, + ClickHouseTable.for_dataset_type_atomic_entries_update_project_partitioned( + dataset_type, + ), + ) + delete_existing_families_from_staging_entries( + table_name_builder, + family_guids, + ) + optimize_entries( + table_name_builder, + project_guids, + ) + finalize_refresh_flow(table_name_builder, project_guids) + + +@retry() +def rebuild_gt_stats( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + run_id: str, + project_guids: list[str], +) -> None: + if ClickHouseDictionary.GT_STATS_DICT not in ClickHouseDictionary.for_dataset_type( + dataset_type, + ): + msg = f'Skipping gt stats rebuild for {reference_genome.value}/{dataset_type.value} {project_guids[:10]}...' + logger.info(msg) + return + table_name_builder = TableNameBuilder( + reference_genome, + dataset_type, + run_id, + ) + max_key = logged_query( + f""" + SELECT max(key) FROM {table_name_builder.dst_table(ClickHouseTable.GT_STATS)} + """, + )[0][0] + if not max_key: + msg = f'Skipping gt stats rebuild for empty dataset {reference_genome.value}/{dataset_type.value} {project_guids[:10]}...' + logger.info(msg) + return + msg = f'Attempting rebuild gt stats for {reference_genome.value}/{dataset_type.value} {project_guids[:10]}...' + logger.info(msg) + drop_staging_db() + create_staging_tables( + table_name_builder, + ClickHouseTable.for_dataset_type_atomic_entries_update(dataset_type), + ) + create_staging_materialized_views( + table_name_builder, + ClickHouseMaterializedView.for_dataset_type_atomic_entries_update( + dataset_type, + ), + ) + stage_existing_project_partitions( + table_name_builder, + project_guids, + ClickHouseTable.for_dataset_type_atomic_entries_update_project_partitioned( + dataset_type, + ), + ) + for partition in get_partitions_for_projects( + table_name_builder, + ClickHouseTable.PROJECT_GT_STATS, + project_guids, + staging=True, + ): + logged_query( + f""" + ALTER TABLE {table_name_builder.staging_dst_table(ClickHouseTable.PROJECT_GT_STATS)} + DROP PARTITION %(partition)s + """, + {'partition': partition}, + ) + select_statement = get_create_mv_statements( + table_name_builder, + ClickHouseMaterializedView.ENTRIES_TO_PROJECT_GT_STATS_MV, + )[1] + select_statement = select_statement.replace( + table_name_builder.dst_prefix, + table_name_builder.staging_dst_prefix, + ) + # NB: encountered OOMs with large projects, necessitating sharding the insertion query. + step = math.ceil(max_key / 5) + for range_start in range(0, max_key, step): + range_end = min(range_start + step, max_key + 1) + logged_query( + f""" + INSERT INTO { + table_name_builder.staging_dst_table(ClickHouseTable.PROJECT_GT_STATS) + } + { + select_statement.replace( + 'GROUP BY project_guid', + 'WHERE key >= %(range_start)s AND key < %(range_end)s GROUP BY project_guid', + ) + } + """, + {'range_start': range_start, 'range_end': range_end}, + ) + finalize_refresh_flow(table_name_builder, project_guids) + + +@retry() +def refresh_clickhouse_reference_data( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + run_id: str, + reference_dataset: ClickhouseReferenceDataset, +): + if not reference_dataset.fully_refreshable: + msg = f'Skipping reference dataset refresh for {reference_dataset.value} for {reference_genome.value}/{dataset_type.value}..' + logger.info(msg) + return + msg = f'Attempting refresh reference dataset {reference_dataset.value} for {reference_genome.value}/{dataset_type.value} ... ' + logger.info(msg) + table_name_builder = TableNameBuilder( + reference_genome, + dataset_type, + run_id, + ) + reference_dataset.download_and_fully_refresh(table_name_builder) + + +def get_clickhouse_client( + timeout: int | None = None, + database: str | None = None, +) -> Client: + return Client( + host=Env.CLICKHOUSE_SERVICE_HOSTNAME, + port=Env.CLICKHOUSE_SERVICE_PORT, + user=Env.CLICKHOUSE_WRITER_USER, + password=Env.CLICKHOUSE_WRITER_PASSWORD, + **{'database': database} if database else {}, + **{'send_receive_timeout': timeout} if timeout else {}, + **{ + 'settings': { + 'send_timeout': timeout, + 'receive_timeout': timeout, + }, + } + if timeout + else {}, + ) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py new file mode 100644 index 0000000000..b4e7673664 --- /dev/null +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -0,0 +1,1338 @@ +import os +from unittest.mock import patch + +import pandas as pd +import pyarrow as pa +import pyarrow.parquet as pq + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome +from loading_pipeline.lib.core.environment import Env +from loading_pipeline.lib.misc.clickhouse import ( + STAGING_CLICKHOUSE_DATABASE, + ClickHouseDictionary, + ClickHouseMaterializedView, + ClickhouseReferenceDataset, + ClickHouseTable, + TableNameBuilder, + create_staging_materialized_views, + create_staging_tables, + delete_existing_families_from_staging_entries, + delete_family_guids, + direct_insert_all_keys, + exchange_tables, + get_clickhouse_client, + insert_new_entries, + load_complete_run, + logged_query, + normalize_partition, + optimize_entries, + rebuild_gt_stats, + refresh_materialized_views, + reload_dictionaries, + replace_project_partitions, + stage_existing_project_partitions, +) +from loading_pipeline.lib.paths import ( + new_entries_parquet_path, + new_variant_details_parquet_path, + new_variants_parquet_path, + runs_path, +) +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + +TEST_RUN_ID = 'manual__2025-05-07T17-20-59.702114+00-00' + + +class ClickhouseTest(MockedDatarootTestCase): + def setUp(self): + super().setUp() + client = get_clickhouse_client() + client.execute( + f""" + DROP DATABASE IF EXISTS {STAGING_CLICKHOUSE_DATABASE}; + """, + ) + client.execute( + f""" + DROP DATABASE IF EXISTS {Env.CLICKHOUSE_DATABASE}; + """, + ) + client.execute( + f""" + CREATE DATABASE {Env.CLICKHOUSE_DATABASE}; + """, + ) + client.execute( + f""" + CREATE TABLE {Env.CLICKHOUSE_DATABASE}.seqrdb_gene_ids_src ( + gene_id String, + seqrdb_id UInt32 + ) ENGINE = Memory; + """, + ) + client.execute( + f'INSERT INTO {Env.CLICKHOUSE_DATABASE}.`seqrdb_gene_ids_src` VALUES', + [('GENE1', 123), ('GENE2', 12), ('GENE3', 1)], + ) + client.execute( + f""" + CREATE DICTIONARY {Env.CLICKHOUSE_DATABASE}.seqrdb_gene_ids + ( + gene_id String, + seqrdb_id UInt32 + ) + PRIMARY KEY gene_id + SOURCE(CLICKHOUSE( + USER {Env.CLICKHOUSE_WRITER_USER} PASSWORD {Env.CLICKHOUSE_WRITER_PASSWORD} + DB {Env.CLICKHOUSE_DATABASE} TABLE `seqrdb_gene_ids_src` + )) + LAYOUT(HASHED()) + LIFETIME(0); + """, + ) + client.execute( + f""" + CREATE TABLE {Env.CLICKHOUSE_DATABASE}.gnomad_genomes_src ( + key UInt32, + filter_af Decimal(9, 8) + ) ENGINE = Memory; + """, + ) + client.execute( + f'INSERT INTO {Env.CLICKHOUSE_DATABASE}.`gnomad_genomes_src` VALUES', + [(11, 0.06), (12, 0.001), (13, 0.0001)], + ) + client.execute( + f""" + CREATE DICTIONARY {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/reference_data/gnomad_genomes` + ( + key UInt32, + filter_af Decimal(9, 8) + ) + PRIMARY KEY key + SOURCE(CLICKHOUSE( + USER {Env.CLICKHOUSE_WRITER_USER} PASSWORD {Env.CLICKHOUSE_WRITER_PASSWORD} + DB {Env.CLICKHOUSE_DATABASE} TABLE `gnomad_genomes_src` + )) + LAYOUT(HASHED()) + LIFETIME(0); + """, + ) + client.execute( + f""" + CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` ( + `key` UInt32, + `project_guid` LowCardinality(String), + `family_guid` String, + `xpos` UInt64 CODEC(Delta(8), ZSTD(1)), + `sample_type` Enum8('WES' = 0, 'WGS' = 1), + `is_gnomad_gt_5_percent` Boolean, + `is_annotated_in_any_gene` Boolean DEFAULT length(geneId_ids) > 0, + `geneId_ids` Array(UInt32), + `calls` Array( + Tuple( + sampleId String, + gt Nullable(Enum8('REF' = 0, 'HET' = 1, 'HOM' = 2)), + ) + ), + `sign` Int8, + PROJECTION xpos_projection + ( + SELECT * + ORDER BY is_annotated_in_any_gene, xpos + ) + ) + ENGINE = CollapsingMergeTree(sign) + PARTITION BY project_guid + ORDER BY (project_guid, family_guid, key) + SETTINGS deduplicate_merge_projection_mode = 'rebuild'; + """, + ) + client.execute( + f""" + CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + ( + `project_guid` String, + `key` UInt32, + `sample_type` Enum8('WES' = 0, 'WGS' = 1), + `het_samples` Int32, + `hom_samples` Int32, + ) + ENGINE = SummingMergeTree + PARTITION BY project_guid + ORDER BY (project_guid, key, sample_type) + """, + ) + client.execute( + f""" + CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` + ( + `key` UInt32, + `ac_wes` UInt32, + `ac_wgs` UInt32, + ) + ENGINE = SummingMergeTree + ORDER BY (key) + """, + ) + client.execute( + f""" + CREATE MATERIALIZED VIEW {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries_to_project_gt_stats_mv` + TO {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + AS SELECT + project_guid, + key, + sample_type, + sum(toInt32(arrayCount(s -> (s.gt = 'HET'), calls) * sign)) AS het_samples, + sum(toInt32(arrayCount(s -> (s.gt = 'HOM'), calls) * sign)) AS hom_samples + FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` + GROUP BY project_guid, key, sample_type + """, + ) + client.execute( + f""" + CREATE MATERIALIZED VIEW {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats_to_gt_stats_mv` + REFRESH EVERY 10 YEAR TO {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` + AS SELECT + key, + sumIf(het_samples * 1 + hom_samples * 2, sample_type = 'WES') AS ac_wes, + sumIf(het_samples * 1 + hom_samples * 2, sample_type = 'WGS') AS ac_wgs + FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + GROUP BY key + """, + ) + client.execute( + f""" + CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details` ( + key UInt32, + variantId String, + transcripts String + ) ENGINE = EmbeddedRocksDB() + PRIMARY KEY `key` + """, + ) + client.execute( + f""" + CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` ( + key UInt32, + variantId String, + ) ENGINE = EmbeddedRocksDB() + PRIMARY KEY `key` + """, + ) + client.execute( + f""" + CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_disk` ( + key UInt32, + variantId String, + ) ENGINE = EmbeddedRocksDB() + PRIMARY KEY `key` + """, + ) + client.execute( + f""" + CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/key_lookup` ( + variantId String, + key UInt32, + ) ENGINE = EmbeddedRocksDB() + PRIMARY KEY `variantId` + """, + ) + client.execute( + f""" + CREATE DICTIONARY {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` + ( + `key` UInt32, + `ac_wes` UInt16, + `ac_wgs` UInt16 + ) + PRIMARY KEY key + SOURCE( + CLICKHOUSE( + USER {Env.CLICKHOUSE_WRITER_USER} PASSWORD {Env.CLICKHOUSE_WRITER_PASSWORD} + DB {Env.CLICKHOUSE_DATABASE} TABLE `GRCh38/SNV_INDEL/gt_stats` + ) + ) + LIFETIME(0) + LAYOUT(FLAT(MAX_ARRAY_SIZE 10000)) + """, + ) + client.execute( + f""" + CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/reference_data/clinvar/all_variants` ( + `variantId` String, + `alleleId` Nullable(UInt32), + `pathogenicity` Enum8( + 'Pathogenic' = 0, + 'Pathogenic/Likely_pathogenic' = 1 + ) + ) + PRIMARY KEY `variantId` + """, + ) + client.execute( + f""" + CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/reference_data/clinvar/seqr_variants` ( + `key` UInt32, + `alleleId` Nullable(UInt32), + `pathogenicity` Enum8( + 'Pathogenic' = 0, + 'Pathogenic/Likely_pathogenic' = 1 + ) + ) + PRIMARY KEY `key` + """, + ) + client.execute( + f""" + CREATE MATERIALIZED VIEW {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/reference_data/clinvar/seqr_variants_to_search_mv` + REFRESH EVERY 10 YEAR ENGINE = Null + AS SELECT DISTINCT ON (key) * + FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/reference_data/clinvar/seqr_variants` + """, + ) + client.execute( + f""" + CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/entries` ( + `key` UInt32, + `project_guid` LowCardinality(String), + `family_guid` String, + `xpos` UInt64 CODEC(Delta(8), ZSTD(1)), + `sample_type` Enum8('WES' = 0, 'WGS' = 1), + `calls` Array( + Tuple( + sampleId String, + gt Nullable(Enum8('REF' = 0, 'HET' = 1, 'HOM' = 2)), + ) + ), + `sign` Int8, + PROJECTION xpos_projection + ( + SELECT * + ORDER BY xpos + ) + ) + ENGINE = CollapsingMergeTree(sign) + PARTITION BY project_guid + ORDER BY (project_guid, family_guid, key) + SETTINGS deduplicate_merge_projection_mode = 'rebuild'; + """, + ) + client.execute( + f""" + CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/variants_memory` ( + key UInt32, + variantId String, + ) ENGINE = EmbeddedRocksDB() + PRIMARY KEY `key` + """, + ) + client.execute( + f""" + CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/variants_disk` ( + key UInt32, + variantId String, + ) ENGINE = EmbeddedRocksDB() + PRIMARY KEY `key` + """, + ) + client.execute( + f""" + CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/key_lookup` ( + variantId String, + key UInt32, + ) ENGINE = EmbeddedRocksDB() + PRIMARY KEY `variantId` + """, + ) + base_path = runs_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + ) + os.makedirs(os.path.join(base_path, TEST_RUN_ID), exist_ok=True) + + def write_test_parquet(df: pd.DataFrame, parquet_path: str, schema=None): + if schema: + table = pa.Table.from_pandas(df, schema=schema) + else: + table = pa.Table.from_pandas(df) + os.makedirs(parquet_path) + pq.write_table( + table, + os.path.join( + parquet_path, + 'test.parquet', + ), + ) + + # Variant Details Parquet + df = pd.DataFrame( + { + 'key': [1, 2, 3, 4], + 'variantId': [ + '1-13-A-C', + '2-14-A-T', + 'Y-19-A-C', + 'M-12-C-G', + ], + 'transcripts': ['a', 'b', 'c', 'd'], + }, + ) + write_test_parquet( + df, + new_variant_details_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ) + + # New Variants parquet. + df = pd.DataFrame( + { + 'key': [10, 11, 12, 13], + 'variantId': [ + '1-3-A-C', + '2-4-A-T', + 'Y-9-A-C', + 'M-2-C-G', + ], + }, + ) + write_test_parquet( + df, + new_variants_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ) + write_test_parquet( + df, + new_variants_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.GCNV, + TEST_RUN_ID, + ), + ) + + # New Entries Parquet + df = pd.DataFrame( + { + 'key': [0, 3, 4], + 'project_guid': [ + 'project_d', + 'project_d', + 'project_d', + ], + 'family_guid': [ + 'family_d1', + 'family_d2', + 'family_d3', + ], + 'xpos': [ + 123456789, + 123456789, + 123456789, + ], + 'sample_type': [ + 'WES', + 'WES', + 'WES', + ], + 'geneIds': [ + [], + ['GENE1', 'GENE2'], + ['GENE3'], + ], + 'calls': [ + [('sample_d1', 0), ('sample_d11', 2)], + [('sample_d2', 0)], + [('sample_d3', 1)], + ], + 'sign': [ + 1, + 1, + 1, + ], + }, + ) + schema = pa.schema( + [ + ('key', pa.int64()), + ('project_guid', pa.string()), + ('family_guid', pa.string()), + ('xpos', pa.int64()), + ('sample_type', pa.string()), + ('geneIds', pa.list_(pa.string())), + ( + 'calls', + pa.list_( + pa.struct([('sampleId', pa.string()), ('gt', pa.int64())]), + ), + ), + ('sign', pa.int64()), + ], + ) + write_test_parquet( + df, + new_entries_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + schema, + ) + write_test_parquet( + df.drop('geneIds', axis=1), + new_entries_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.GCNV, + TEST_RUN_ID, + ), + schema.remove(5).remove(5), + ) + + def tearDown(self): + super().tearDown() + client = get_clickhouse_client() + client.execute( + f""" + DROP DICTIONARY IF EXISTS {Env.CLICKHOUSE_DATABASE}.seqrdb_gene_ids; + """, + ) + client.execute( + f""" + DROP DICTIONARY IF EXISTS {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/reference_data/gnomad_genomes`; + """, + ) + client.execute( + f""" + DROP DATABASE IF EXISTS {Env.CLICKHOUSE_DATABASE}; + """, + ) + client.execute( + f""" + DROP DATABASE IF EXISTS {STAGING_CLICKHOUSE_DATABASE}; + """, + ) + + def test_get_clickhouse_client(self): + client = get_clickhouse_client() + result = client.execute('SELECT 1') + self.assertEqual(result[0][0], 1) + + def test_normalize_partition(self): + self.assertEqual(normalize_partition('project_d'), ('project_d',)) + self.assertEqual( + normalize_partition("('project_d', 0)"), + ('project_d', 0), + ) + + def test_table_name_builder(self): + table_name_builder = TableNameBuilder( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ) + self.assertEqual( + table_name_builder.dst_table( + ClickHouseTable.ENTRIES, + ), + f'{Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries`', + ) + self.assertEqual( + table_name_builder.src_table( + ClickHouseTable.ENTRIES, + ), + f"file('{runs_path(ReferenceGenome.GRCh38, DatasetType.SNV_INDEL)}/manual__2025-05-07T17-20-59.702114+00-00/new_entries.parquet/*.parquet', 'Parquet')", + ) + with patch('loading_pipeline.lib.paths.Env') as mock_env: + mock_env.PIPELINE_DATA_DIR = 'gs://mock_bucket/v3.1' + self.assertEqual( + table_name_builder.src_table( + ClickHouseTable.ENTRIES, + ), + "gcs(pipeline_data_access, url='https://storage.googleapis.com/mock_bucket/v3.1/GRCh38/SNV_INDEL/runs/manual__2025-05-07T17-20-59.702114+00-00/new_entries.parquet/*.parquet')", + ) + + def test_direct_insert_all_keys(self): + client = get_clickhouse_client() + client.execute( + f'INSERT INTO {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details` VALUES', + [(1, 'a', 'e'), (10, 'b', 'f'), (7, 'c', 'g')], + ) + direct_insert_all_keys( + ClickHouseTable.VARIANT_DETAILS, + TableNameBuilder( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ) + ret = client.execute( + f'SELECT * FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', + ) + self.assertEqual( + ret, + [ + (1, '1-13-A-C', 'a'), + (2, '2-14-A-T', 'b'), + (3, 'Y-19-A-C', 'c'), + (4, 'M-12-C-G', 'd'), + (7, 'c', 'g'), + (10, 'b', 'f'), + ], + ) + + # ensure multiple calls are idempotent + direct_insert_all_keys( + ClickHouseTable.VARIANT_DETAILS, + TableNameBuilder( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ) + ret = client.execute( + f'SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', + ) + self.assertEqual(ret[0][0], 6) + + @patch.object( + ClickhouseReferenceDataset, + 'for_reference_genome_dataset_type', + return_value=[ClickhouseReferenceDataset.CLINVAR], + ) + def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): + # Tests individual components of the atomic_insert_entries + # to validate the state after each step. + client = get_clickhouse_client() + client.execute( + f""" + INSERT INTO {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` + VALUES + (0, 'project_a', 'family_a1', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_a1','HOM')], 1), + (1, 'project_a', 'family_a2', 123456789, 'WGS', 0, 0, CAST([] AS Array(UInt32)), [('sample_a2','HET')], 1), + (2, 'project_a', 'family_a3', 133456789, 'WGS', 0, 0, CAST([] AS Array(UInt32)), [('sample_a3','HOM')], 1), + (3, 'project_a', 'family_a4', 133456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_a4','REF')], 1), + (4, 'project_a', 'family_a5', 133456789, 'WES', 0, 1, CAST([0] AS Array(UInt32)), [('sample_a5','REF'),('sample_a6','HET'),('sample_a7','REF')], 1), + (4, 'project_a', 'family_a6', 133456789, 'WGS', 0, 0, CAST([] AS Array(UInt32)), [('sample_a8','HOM')], 1), + (0, 'project_b', 'family_b1', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b4','REF')], 1), + (1, 'project_b', 'family_b2', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b5','HET')], 1), + (2, 'project_b', 'family_b2', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b5','REF')], 1), + (3, 'project_b', 'family_b3', 133456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b6','HOM')], 1), + (4, 'project_b', 'family_b3', 133456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b6','HOM')], 1), + (0, 'project_c', 'family_c1', 123456789, 'WES', 0, 1, CAST([1] AS Array(UInt32)), [('sample_c7','REF')], 1), + (3, 'project_c', 'family_c2', 123456789, 'WES', 0, 1, CAST([1] AS Array(UInt32)), [('sample_c8','REF')], 1), + (4, 'project_c', 'family_c3', 133456789, 'WES', 0, 1, CAST([1] AS Array(UInt32)), [('sample_c9','HOM')], 1), + (5, 'project_c', 'family_c4', 133456789, 'WES', 0, 1, CAST([1] AS Array(UInt32)), [('sample_c9','HOM')], 1) + """, + ) + table_name_builder = TableNameBuilder( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ) + create_staging_tables( + table_name_builder, + ClickHouseTable.for_dataset_type_atomic_entries_update( + DatasetType.SNV_INDEL, + ), + ) + create_staging_materialized_views( + table_name_builder, + ClickHouseMaterializedView.for_dataset_type_atomic_entries_update( + DatasetType.SNV_INDEL, + ), + ) + stage_existing_project_partitions( + table_name_builder, + [ + 'project_a', + 'project_b', + 'project_d', # Partition does not exist already. + ], + ClickHouseTable.for_dataset_type_atomic_entries_update_project_partitioned( + DatasetType.SNV_INDEL, + ), + ) + staged_projects = client.execute( + f""" + SELECT DISTINCT project_guid FROM {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/entries` + """, + ) + self.assertCountEqual( + [p[0] for p in staged_projects], + ['project_a', 'project_b'], + ) + staged_project_gt_stats = client.execute( + f""" + SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) + FROM + {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/project_gt_stats` + GROUP BY project_guid, key, sample_type + """, + ) + self.assertCountEqual( + staged_project_gt_stats, + [ + ('project_a', 0, 'WES', 0, 1), + ('project_a', 1, 'WGS', 1, 0), + ('project_a', 2, 'WGS', 0, 1), + ('project_a', 4, 'WES', 1, 0), + ('project_a', 4, 'WGS', 0, 1), + ('project_b', 1, 'WES', 1, 0), + ('project_b', 3, 'WES', 0, 1), + ('project_b', 4, 'WES', 0, 1), + # project_gt_stats stages all projects, not just + # those requested for loading. + ('project_c', 4, 'WES', 0, 1), + ('project_c', 5, 'WES', 0, 1), + ], + ) + delete_existing_families_from_staging_entries( + table_name_builder, + ['family_a1', 'family_a5', 'family_a6'], + ) + staged_project_gt_stats = client.execute( + f""" + SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) + FROM + {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/project_gt_stats` + GROUP BY project_guid, key, sample_type + """, + ) + self.assertCountEqual( + staged_project_gt_stats, + [ + ('project_a', 0, 'WES', 0, 0), + ('project_a', 1, 'WGS', 1, 0), + ('project_a', 2, 'WGS', 0, 1), + ('project_a', 4, 'WES', 0, 0), + ('project_a', 4, 'WGS', 0, 0), + ('project_b', 1, 'WES', 1, 0), + ('project_b', 3, 'WES', 0, 1), + ('project_b', 4, 'WES', 0, 1), + ('project_c', 4, 'WES', 0, 1), + ('project_c', 5, 'WES', 0, 1), + ], + ) + insert_new_entries(table_name_builder) + optimize_entries( + table_name_builder, + ['project_a', 'project_b', 'project_c'], + ) + staged_project_gt_stats = client.execute( + f""" + SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) + FROM + {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/project_gt_stats` + GROUP BY project_guid, key, sample_type + """, + ) + self.assertCountEqual( + staged_project_gt_stats, + [ + ('project_a', 0, 'WES', 0, 0), + ('project_a', 1, 'WGS', 1, 0), + ('project_a', 2, 'WGS', 0, 1), + ('project_a', 4, 'WES', 0, 0), + ('project_a', 4, 'WGS', 0, 0), + ('project_b', 1, 'WES', 1, 0), + ('project_b', 3, 'WES', 0, 1), + ('project_b', 4, 'WES', 0, 1), + ('project_c', 4, 'WES', 0, 1), + ('project_c', 5, 'WES', 0, 1), + ('project_d', 0, 'WES', 0, 1), + ('project_d', 4, 'WES', 1, 0), + ], + ) + refresh_materialized_views( + table_name_builder, + ClickHouseMaterializedView.for_dataset_type_atomic_entries_update_refreshable( + DatasetType.SNV_INDEL, + ), + staging=True, + ) + replace_project_partitions( + table_name_builder, + ClickHouseTable.for_dataset_type_atomic_entries_update_project_partitioned( + DatasetType.SNV_INDEL, + ), + ['project_a', 'project_d'], + ) + new_entries = client.execute( + f""" + SELECT COLUMNS('.*') EXCEPT(is_annotated_in_any_gene, is_gnomad_gt_5_percent) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` + """, + ) + self.assertCountEqual( + new_entries, + [ + ( + 0, + 'project_b', + 'family_b1', + 123456789, + 'WES', + [], + [('sample_b4', 'REF')], + 1, + ), + ( + 1, + 'project_b', + 'family_b2', + 123456789, + 'WES', + [], + [('sample_b5', 'HET')], + 1, + ), + ( + 2, + 'project_b', + 'family_b2', + 123456789, + 'WES', + [], + [('sample_b5', 'REF')], + 1, + ), + ( + 3, + 'project_b', + 'family_b3', + 133456789, + 'WES', + [], + [('sample_b6', 'HOM')], + 1, + ), + ( + 4, + 'project_b', + 'family_b3', + 133456789, + 'WES', + [], + [('sample_b6', 'HOM')], + 1, + ), + ( + 1, + 'project_a', + 'family_a2', + 123456789, + 'WGS', + [], + [('sample_a2', 'HET')], + 1, + ), + ( + 2, + 'project_a', + 'family_a3', + 133456789, + 'WGS', + [], + [('sample_a3', 'HOM')], + 1, + ), + ( + 3, + 'project_a', + 'family_a4', + 133456789, + 'WES', + [], + [('sample_a4', 'REF')], + 1, + ), + ( + 0, + 'project_d', + 'family_d1', + 123456789, + 'WES', + [], + [('sample_d1', 'REF'), ('sample_d11', 'HOM')], + 1, + ), + ( + 3, + 'project_d', + 'family_d2', + 123456789, + 'WES', + [123, 12], + [('sample_d2', 'REF')], + 1, + ), + ( + 4, + 'project_d', + 'family_d3', + 123456789, + 'WES', + [1], + [('sample_d3', 'HET')], + 1, + ), + ( + 0, + 'project_c', + 'family_c1', + 123456789, + 'WES', + [1], + [('sample_c7', 'REF')], + 1, + ), + ( + 3, + 'project_c', + 'family_c2', + 123456789, + 'WES', + [1], + [('sample_c8', 'REF')], + 1, + ), + ( + 4, + 'project_c', + 'family_c3', + 133456789, + 'WES', + [1], + [('sample_c9', 'HOM')], + 1, + ), + ( + 5, + 'project_c', + 'family_c4', + 133456789, + 'WES', + [1], + [('sample_c9', 'HOM')], + 1, + ), + ], + ) + existing_gt_stats = client.execute( + f""" + SELECT * + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` + """, + ) + self.assertCountEqual( + existing_gt_stats, + [], + ) + exchange_tables( + table_name_builder, + ClickHouseTable.for_dataset_type_atomic_entries_update_unpartitioned( + DatasetType.SNV_INDEL, + ), + ) + new_gt_stats = client.execute( + f""" + SELECT * + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` + """, + ) + self.assertCountEqual(new_gt_stats, []) + reload_dictionaries( + table_name_builder, + ClickHouseDictionary.for_dataset_type(DatasetType.SNV_INDEL), + ) + new_gt_stats_post_reload = client.execute( + f""" + SELECT * + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` + """, + ) + self.assertEqual( + new_gt_stats_post_reload, + [ + (0, 2, 0), + (1, 1, 1), + (2, 0, 2), + (3, 2, 0), + (4, 5, 0), + (5, 2, 0), + ], + ) + + @patch.object( + ClickhouseReferenceDataset, + 'for_reference_genome_dataset_type', + return_value=[ClickhouseReferenceDataset.CLINVAR], + ) + def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_type): + load_complete_run( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ['project_d'], + ['family_d1', 'family_d2'], + ) + client = get_clickhouse_client() + project_gt_stats = client.execute( + f""" + SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + GROUP BY project_guid, key, sample_type + """, + ) + self.assertCountEqual( + project_gt_stats, + [ + ('project_d', 0, 'WES', 0, 1), + ('project_d', 4, 'WES', 1, 0), + ], + ) + gt_stats = client.execute( + f""" + SELECT * + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` + """, + ) + self.assertCountEqual( + gt_stats, + [ + (0, 2, 0), + (4, 1, 0), + ], + ) + gt_stats_dict = client.execute( + f""" + SELECT * + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` + """, + ) + self.assertCountEqual( + gt_stats_dict, + [ + (0, 2, 0), + (4, 1, 0), + ], + ) + variants_memory = client.execute( + f""" + SELECT * + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` + """, + ) + self.assertCountEqual( + variants_memory, + [ + (10, '1-3-A-C'), + (11, '2-4-A-T'), + (12, 'Y-9-A-C'), + (13, 'M-2-C-G'), + ], + ) + variants_disk = client.execute( + f""" + SELECT * + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_disk` + """, + ) + self.assertCountEqual( + variants_disk, + [ + (10, '1-3-A-C'), + (11, '2-4-A-T'), + (12, 'Y-9-A-C'), + (13, 'M-2-C-G'), + ], + ) + + def test_load_complete_gcnv(self): + load_complete_run( + ReferenceGenome.GRCh38, + DatasetType.GCNV, + TEST_RUN_ID, + ['project_d'], + ['family_d1', 'family_d2'], + ) + client = get_clickhouse_client() + variants_disk_count = client.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/variants_memory` + """, + )[0][0] + self.assertEqual(variants_disk_count, 4) + variants_disk_count = client.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/variants_disk` + """, + )[0][0] + self.assertEqual(variants_disk_count, 4) + key_lookup_count = client.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/key_lookup` + """, + )[0][0] + self.assertEqual(key_lookup_count, 4) + entries_count = client.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/entries` + """, + )[0][0] + self.assertEqual(entries_count, 3) + + def test_delete_families(self): + table_name_builder = TableNameBuilder( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ) + client = get_clickhouse_client() + client.execute( + f""" + INSERT INTO {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` + VALUES + (0, 'project_a', 'family_a1', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_a1','HOM')], 1), + (1, 'project_a', 'family_a2', 123456789, 'WGS', 0, 0, CAST([] AS Array(UInt32)), [('sample_a2','HET')], 1), + (2, 'project_a', 'family_a3', 133456789, 'WGS', 0, 0, CAST([] AS Array(UInt32)), [('sample_a3','HOM')], 1), + (3, 'project_a', 'family_a4', 133456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_a4','REF')], 1), + (4, 'project_a', 'family_a5', 133456789, 'WES', 0, 1, CAST([0] AS Array(UInt32)), [('sample_a5','REF'),('sample_a6','HET'),('sample_a7','REF')], 1), + (4, 'project_a', 'family_a6', 133456789, 'WGS', 0, 0, CAST([] AS Array(UInt32)), [('sample_a8','HOM')], 1), + (0, 'project_b', 'family_b1', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b4','REF')], 1), + (1, 'project_b', 'family_b2', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b5','HET')], 1), + (2, 'project_b', 'family_b2', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b5','REF')], 1), + (3, 'project_b', 'family_b3', 133456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b6','HOM')], 1), + (4, 'project_b', 'family_b3', 133456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b6','HOM')], 1), + (0, 'project_c', 'family_c1', 123456789, 'WES', 0, 1, CAST([1] AS Array(UInt32)), [('sample_c7','REF')], 1), + (3, 'project_c', 'family_c2', 123456789, 'WES', 0, 1, CAST([1] AS Array(UInt32)), [('sample_c8','REF')], 1), + (4, 'project_c', 'family_c3', 133456789, 'WES', 0, 1, CAST([1] AS Array(UInt32)), [('sample_c9','HOM')], 1), + (5, 'project_c', 'family_c4', 133456789, 'WES', 0, 1, CAST([1] AS Array(UInt32)), [('sample_c9','HOM')], 1) + """, + ) + project_gt_stats = client.execute( + f""" + SELECT project_guid, sum(het_samples), sum(hom_samples) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + GROUP BY project_guid + """, + ) + self.assertCountEqual( + project_gt_stats, + [('project_a', 2, 3), ('project_c', 0, 2), ('project_b', 1, 2)], + ) + refresh_materialized_views( + table_name_builder, + ClickHouseMaterializedView.for_dataset_type_atomic_entries_update_refreshable( + DatasetType.SNV_INDEL, + ), + staging=False, + ) + gt_stats = client.execute( + f""" + SELECT sum(ac_wes) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` + """, + ) + self.assertCountEqual(gt_stats, [(12,)]) + delete_family_guids( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + 'project_a', + ['family_a1', 'family_a2'], + ) + project_gt_stats = client.execute( + f""" + SELECT project_guid, sum(het_samples), sum(hom_samples) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + GROUP BY project_guid + """, + ) + self.assertCountEqual( + project_gt_stats, + [('project_a', 1, 2), ('project_c', 0, 2), ('project_b', 1, 2)], + ) + gt_stats = client.execute( + f""" + SELECT sum(ac_wes) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` + """, + ) + self.assertCountEqual(gt_stats, [(10,)]) + gt_stats_dict = client.execute( + f""" + SELECT sum(ac_wes) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` + """, + ) + self.assertCountEqual(gt_stats_dict, [(10,)]) + + def test_rebuild_gt_stats(self): + table_name_builder = TableNameBuilder( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ) + client = get_clickhouse_client() + client.execute( + f""" + INSERT INTO {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` + VALUES + (0, 'project_a', 'family_a1', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_a1','HOM')], 1), + (1, 'project_a', 'family_a2', 123456789, 'WGS', 0, 0, CAST([] AS Array(UInt32)), [('sample_a2','HET')], 1), + (2, 'project_a', 'family_a3', 133456789, 'WGS', 0, 0, CAST([] AS Array(UInt32)), [('sample_a3','HOM')], 1), + (3, 'project_a', 'family_a4', 133456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_a4','REF')], 1), + (4, 'project_a', 'family_a5', 133456789, 'WES', 0, 1, CAST([] AS Array(UInt32)), [('sample_a5','REF'),('sample_a6','HET'),('sample_a7','REF')], 1), + (4, 'project_a', 'family_a6', 133456789, 'WGS', 0, 0, CAST([] AS Array(UInt32)), [('sample_a8','HOM')], 1), + (0, 'project_b', 'family_b1', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b4','REF')], 1), + (1, 'project_b', 'family_b2', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b5','HET')], 1), + (2, 'project_b', 'family_b2', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b5','REF')], 1), + """, + ) + logged_query( # DROP the partition from the non-staging entries to as a non-mv-impacting change. + f""" + ALTER TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` + DROP PARTITION %(project_guid)s + """, + {'project_guid': 'project_a'}, + ) + project_gt_stats = client.execute( + f""" + SELECT project_guid, sum(het_samples), sum(hom_samples) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + GROUP BY project_guid + """, + ) + self.assertCountEqual( + project_gt_stats, + [('project_a', 2, 3), ('project_b', 1, 0)], + ) + refresh_materialized_views( + table_name_builder, + ClickHouseMaterializedView.for_dataset_type_atomic_entries_update_refreshable( + DatasetType.SNV_INDEL, + ), + staging=False, + ) + gt_stats = client.execute( + f""" + SELECT sum(ac_wes), sum(ac_wgs) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` + """, + ) + self.assertCountEqual(gt_stats, [(4, 5)]) + rebuild_gt_stats( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ['project_a', 'project_b'], + ) + project_gt_stats = client.execute( + f""" + SELECT project_guid, sum(het_samples), sum(hom_samples) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + GROUP BY project_guid + """, + ) + self.assertCountEqual( + project_gt_stats, + [('project_b', 1, 0)], + ) + gt_stats = client.execute( + f""" + SELECT sum(ac_wes), sum(ac_wgs) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` + """, + ) + self.assertCountEqual(gt_stats, [(1, 0)]) + + @patch.object( + ClickhouseReferenceDataset, + 'for_reference_genome_dataset_type', + return_value=[ClickhouseReferenceDataset.CLINVAR], + ) + def test_repartitioned_entries_table(self, mock_for_reference_genome_dataset_type): + client = get_clickhouse_client() + client.execute( + f""" + REPLACE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` ( + `key` UInt32, + `project_guid` LowCardinality(String), + `family_guid` String, + `xpos` UInt64 CODEC(Delta(8), ZSTD(1)), + `sample_type` Enum8('WES' = 0, 'WGS' = 1), + `is_gnomad_gt_5_percent` Boolean, + `is_annotated_in_any_gene` Boolean DEFAULT length(geneId_ids) > 0, + `geneId_ids` Array(UInt32), + `calls` Array( + Tuple( + sampleId String, + gt Nullable(Enum8('REF' = 0, 'HET' = 1, 'HOM' = 2)), + ) + ), + `sign` Int8, + `n_partitions` UInt8 MATERIALIZED 2, + `partition_id` UInt8 MATERIALIZED farmHash64(family_guid) % n_partitions, + PROJECTION xpos_projection + ( + SELECT * + ORDER BY is_annotated_in_any_gene, xpos + ) + ) + ENGINE = CollapsingMergeTree(sign) + PARTITION BY (project_guid, partition_id) + ORDER BY (project_guid, family_guid, key) + SETTINGS deduplicate_merge_projection_mode = 'rebuild'; + """, + ) + load_complete_run( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ['project_d'], + ['family_d1', 'family_d2', 'family_d3'], + ) + project_gt_stats = client.execute( + f""" + SELECT project_guid, sum(het_samples), sum(hom_samples) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + GROUP BY project_guid + """, + ) + self.assertCountEqual( + project_gt_stats, + [('project_d', 1, 1)], + ) diff --git a/loading_pipeline/lib/misc/family_entries.py b/loading_pipeline/lib/misc/family_entries.py new file mode 100644 index 0000000000..114f1dc2f9 --- /dev/null +++ b/loading_pipeline/lib/misc/family_entries.py @@ -0,0 +1,105 @@ +import hail as hl + +from loading_pipeline.lib.core import DatasetType + + +def compute_callset_family_entries_ht( + dataset_type: DatasetType, + mt: hl.MatrixTable, + entries_fields: dict[str, hl.Expression], +) -> hl.Table: + sample_id_to_family_guid = hl.dict( + { + s: family_guid + for family_guid, sample_ids in hl.eval(mt.family_samples).items() + for s in sample_ids + }, + ) + ht = mt.select_rows( + filters=mt.filters.difference(dataset_type.excluded_filters), + family_entries=( + # NB: we're sorted by both family and sample when this runs. + # However, the sort is not guaranteed once the entries + # table is edited and families are spliced out and re-appended. + hl.sorted( + hl.agg.collect( + hl.Struct( + s=mt.s, + family_guid=sample_id_to_family_guid[mt.s], + **entries_fields, + ), + ) + .group_by(lambda e: e.family_guid) + .values() + .map( + lambda fe: hl.sorted(fe, key=lambda e: e.s), + ), + lambda fe: fe[0].family_guid, + ) + ), + ).rows() + # NB: globalize before we set families to missing + ht = globalize_ids(ht) + ht = ht.annotate( + family_entries=( + ht.family_entries.map( + lambda fe: hl.or_missing( + fe.any(dataset_type.family_entries_filter_fn), + fe, + ), + ) + ), + ) + # Only keep rows where at least one family is not missing. + return ht.filter(ht.family_entries.any(hl.is_defined)) + + +def globalize_ids(ht: hl.Table) -> hl.Table: + row = ht.take(1)[0] if ht.count() > 0 else None + has_family_entries = row and len(row.family_entries) > 0 + ht = ht.annotate_globals( + family_guids=( + [fe[0].family_guid for fe in row.family_entries] + if has_family_entries + else hl.empty_array(hl.tstr) + ), + family_samples=( + {fe[0].family_guid: [e.s for e in fe] for fe in row.family_entries} + if has_family_entries + else hl.empty_dict(hl.tstr, hl.tarray(hl.tstr)) + ), + ) + return ht.annotate( + family_entries=ht.family_entries.map( + lambda fe: fe.map(lambda se: se.drop('s', 'family_guid')), + ), + ) + + +def deglobalize_ids(ht: hl.Table) -> hl.Table: + ht = ht.annotate( + family_entries=( + hl.enumerate(ht.family_entries).starmap( + lambda i, fe: hl.enumerate(fe).starmap( + lambda j, e: hl.Struct( + **e, + s=ht.family_samples[ht.family_guids[i]][j], + family_guid=ht.family_guids[i], + ), + ), + ) + ), + ) + return ht.drop('family_guids', 'family_samples') + + +def deduplicate_by_most_non_ref_calls(ht: hl.Table) -> hl.Table: + ht = ht.annotate( + non_ref_count=hl.len( + hl.flatten(ht.family_entries).filter(lambda s: s.GT.is_non_ref()), + ), + ) + return ht.group_by(*ht.key).aggregate( + filters=hl.agg.take(ht.filters, 1, ordering=-ht.non_ref_count)[0], + family_entries=hl.agg.take(ht.family_entries, 1, ordering=-ht.non_ref_count)[0], + ) diff --git a/loading_pipeline/lib/misc/family_entries_test.py b/loading_pipeline/lib/misc/family_entries_test.py new file mode 100644 index 0000000000..609fdda6d6 --- /dev/null +++ b/loading_pipeline/lib/misc/family_entries_test.py @@ -0,0 +1,356 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.core import DatasetType +from loading_pipeline.lib.misc.family_entries import ( + compute_callset_family_entries_ht, + deduplicate_by_most_non_ref_calls, + deglobalize_ids, + globalize_ids, +) + + +class FamilyEntriesTest(unittest.TestCase): + def test_compute_callset_family_entries_ht(self) -> None: + mt = hl.MatrixTable.from_parts( + rows={ + 'variants': [1, 2, 3], + 'filters': [ + hl.empty_set(hl.tstr), + {'HIGH_SR_BACKGROUND'}, + hl.empty_set(hl.tstr), + ], + }, + cols={'s': ['a', 'b', 'd', 'c']}, + entries={ + 'GT': [ + [ + hl.Call([0, 0]), + hl.missing(hl.tcall), + hl.Call([0, 0]), + hl.Call([0, 0]), + ], + [ + hl.Call([0, 0]), + hl.Call([0, 0]), + hl.Call([1, 1]), + hl.Call([0, 0]), + ], + [ + hl.Call([0, 1]), + hl.Call([0, 0]), + hl.Call([1, 1]), + hl.Call([0, 0]), + ], + ], + }, + globals={'family_samples': {'2': ['a'], '1': ['b', 'c', 'd']}}, + ) + ht = compute_callset_family_entries_ht(DatasetType.SNV_INDEL, mt, {'GT': mt.GT}) + self.assertCountEqual( + ht.globals.collect(), + [ + hl.Struct( + family_samples={'1': ['b', 'c', 'd'], '2': ['a']}, + family_guids=['1', '2'], + ), + ], + ) + self.assertCountEqual( + ht.filters.collect(), + [{'HIGH_SR_BACKGROUND'}, set()], + ) + self.assertCountEqual( + ht.family_entries.collect(), + [ + [ + [ + hl.Struct(GT=hl.Call(alleles=[0, 0], phased=False)), + hl.Struct(GT=hl.Call(alleles=[0, 0], phased=False)), + hl.Struct(GT=hl.Call(alleles=[1, 1], phased=False)), + ], + None, + ], + [ + [ + hl.Struct(GT=hl.Call(alleles=[0, 0], phased=False)), + hl.Struct(GT=hl.Call(alleles=[0, 0], phased=False)), + hl.Struct(GT=hl.Call(alleles=[1, 1], phased=False)), + ], + [hl.Struct(GT=hl.Call(alleles=[0, 1], phased=False))], + ], + ], + ) + + def test_globalize_and_deglobalize(self) -> None: + family_entries_ht = hl.Table.parallelize( + [], + hl.tstruct( + id=hl.tint32, + filters=hl.tset(hl.tstr), + family_entries=hl.tarray( + hl.tarray(hl.tstruct(a=hl.tint32, s=hl.tstr, family_guid=hl.tstr)), + ), + ), + key='id', + ) + family_entries_ht = globalize_ids(family_entries_ht) + self.assertCountEqual( + family_entries_ht.family_guids.collect(), + [ + [], + ], + ) + family_entries_ht = hl.Table.parallelize( + [ + { + 'id': 0, + 'filters': {'HIGH_SR_BACKGROUND', 'UNRESOLVED'}, + 'family_entries': [ + [ + hl.Struct(a=1, s='a', family_guid='123'), + hl.Struct(a=2, s='c', family_guid='123'), + hl.Struct(a=1, s='e', family_guid='123'), + ], + [ + hl.Struct(a=2, s='f', family_guid='234'), + ], + ], + }, + { + 'id': 1, + 'filters': {'HIGH_SR_BACKGROUND'}, + 'family_entries': [ + [ + hl.Struct(a=2, s='a', family_guid='123'), + hl.Struct(a=3, s='c', family_guid='123'), + hl.Struct(a=4, s='e', family_guid='123'), + ], + [ + hl.Struct(a=5, s='f', family_guid='234'), + ], + ], + }, + ], + hl.tstruct( + id=hl.tint32, + filters=hl.tset(hl.tstr), + family_entries=hl.tarray( + hl.tarray(hl.tstruct(a=hl.tint32, s=hl.tstr, family_guid=hl.tstr)), + ), + ), + key='id', + ) + family_entries_ht = globalize_ids(family_entries_ht) + self.assertCountEqual( + family_entries_ht.family_guids.collect(), + [ + ['123', '234'], + ], + ) + self.assertCountEqual( + family_entries_ht.family_entries.collect(), + [ + [ + [ + hl.Struct(a=1), + hl.Struct(a=2), + hl.Struct(a=1), + ], + [ + hl.Struct(a=2), + ], + ], + [ + [ + hl.Struct(a=2), + hl.Struct(a=3), + hl.Struct(a=4), + ], + [ + hl.Struct(a=5), + ], + ], + ], + ) + family_entries_ht = deglobalize_ids(family_entries_ht) + self.assertCountEqual( + family_entries_ht.family_entries.collect(), + [ + [ + [ + hl.Struct(a=1, s='a', family_guid='123'), + hl.Struct(a=2, s='c', family_guid='123'), + hl.Struct(a=1, s='e', family_guid='123'), + ], + [ + hl.Struct(a=2, s='f', family_guid='234'), + ], + ], + [ + [ + hl.Struct(a=2, s='a', family_guid='123'), + hl.Struct(a=3, s='c', family_guid='123'), + hl.Struct(a=4, s='e', family_guid='123'), + ], + [ + hl.Struct(a=5, s='f', family_guid='234'), + ], + ], + ], + ) + + def test_deduplicate_by_most_non_ref_calls(self) -> None: + project_ht = hl.Table.parallelize( + [ + { + 'id': 0, + 'filters': {'PASS', 'HIGH_SR_BACKGROUND'}, + 'family_entries': [ + [ + hl.Struct( + GT=hl.Call(alleles=[0, 1], phased=False), + family_guid='family_a', + s='sample_1', + ), + hl.Struct( + GT=hl.Call(alleles=[0, 0], phased=False), + family_guid='family_a', + s='sample_2', + ), + ], + [ + hl.Struct( + GT=hl.Call(alleles=[0, 1], phased=False), + family_guid='family_b', + s='sample_3', + ), + None, + ], + None, + ], + }, + { + 'id': 0, + 'filters': {'PASS'}, + 'family_entries': [ + [ + None, + hl.Struct( + GT=hl.Call(alleles=[0, 0], phased=False), + family_guid='family_a', + s='sample_2', + ), + ], + [ + hl.Struct( + GT=hl.Call(alleles=[0, 1], phased=False), + family_guid='family_b', + s='sample_3', + ), + None, + ], + None, + ], + }, + { + 'id': 2, + 'filters': {'HIGH_SR_BACKGROUND'}, + 'family_entries': [ + None, + None, + ], + }, + { + 'id': 3, + 'filters': {'PASS'}, + 'family_entries': [ + [ + hl.Struct( + GT=hl.Call(alleles=[0, 1], phased=False), + family_guid='family_a', + s='sample_1', + ), + hl.Struct( + GT=hl.Call(alleles=[0, 1], phased=False), + family_guid='family_a', + s='sample_2', + ), + ], + None, + ], + }, + ], + hl.tstruct( + id=hl.tint32, + filters=hl.tset(hl.tstr), + family_entries=hl.tarray( + hl.tarray( + hl.tstruct( + GT=hl.tcall, + family_guid=hl.tstr, + s=hl.tstr, + ), + ), + ), + ), + key='id', + ) + ht = deduplicate_by_most_non_ref_calls(project_ht) + self.assertEqual( + ht.collect(), + [ + hl.Struct( + id=0, + filters={'PASS', 'HIGH_SR_BACKGROUND'}, + family_entries=[ + [ + hl.Struct( + GT=hl.Call(alleles=[0, 1], phased=False), + family_guid='family_a', + s='sample_1', + ), + hl.Struct( + GT=hl.Call(alleles=[0, 0], phased=False), + family_guid='family_a', + s='sample_2', + ), + ], + [ + hl.Struct( + GT=hl.Call(alleles=[0, 1], phased=False), + family_guid='family_b', + s='sample_3', + ), + None, + ], + None, + ], + ), + hl.Struct( + id=2, + filters={'HIGH_SR_BACKGROUND'}, + family_entries=[None, None], + ), + hl.Struct( + id=3, + filters={'PASS'}, + family_entries=[ + [ + hl.Struct( + GT=hl.Call(alleles=[0, 1], phased=False), + family_guid='family_a', + s='sample_1', + ), + hl.Struct( + GT=hl.Call(alleles=[0, 1], phased=False), + family_guid='family_a', + s='sample_2', + ), + ], + None, + ], + ), + ], + ) diff --git a/loading_pipeline/lib/misc/family_loading_failures.py b/loading_pipeline/lib/misc/family_loading_failures.py new file mode 100644 index 0000000000..ee9d9bcf25 --- /dev/null +++ b/loading_pipeline/lib/misc/family_loading_failures.py @@ -0,0 +1,215 @@ +from collections import defaultdict + +import hail as hl + +from loading_pipeline.lib.core import Sex +from loading_pipeline.lib.logger import get_logger +from loading_pipeline.lib.misc.pedigree import Family, Relation, Sample + +logger = get_logger(__name__) + + +def passes_relatedness_check( + relatedness_check_lookup: dict[tuple[str, str], list], + sample_id: str, + other_id: str, + expected_relation: Relation, + additional_allowed_relation: Relation | None, +) -> tuple[bool, str | None]: + # No relationship to check, return true + if other_id is None: + return True, None + coefficients = relatedness_check_lookup.get( + (min(sample_id, other_id), max(sample_id, other_id)), + ) + if not coefficients or not any( + relation.coefficients_equal(coefficients) + for relation in ( + [expected_relation, additional_allowed_relation] + if additional_allowed_relation + else [expected_relation] + ) + ): + return ( + False, + f'Sample {sample_id} has expected relation "{expected_relation.value}" to {other_id} but has coefficients {coefficients or []}', + ) + return True, None + + +def all_relatedness_checks( + relatedness_check_lookup: dict[tuple[str, str], list], + family: Family, + sample: Sample, +) -> list[str]: + failure_reasons = [] + for relationship_set, relation, additional_allowed_relation in [ + ([sample.mother, sample.father], Relation.PARENT_CHILD, None), + ( + [ + sample.maternal_grandmother, + sample.maternal_grandfather, + sample.paternal_grandmother, + sample.paternal_grandfather, + ], + Relation.GRANDPARENT_GRANDCHILD, + None, + ), + (sample.siblings, Relation.SIBLING, None), + (sample.half_siblings, Relation.HALF_SIBLING, Relation.SIBLING), + (sample.aunt_nephews, Relation.AUNT_NEPHEW, None), + ]: + for other_id in relationship_set: + # Handle case where relation is identified in the + # pedigree as a "dummy" but is not included in + # the list of samples to load. + if other_id not in family.samples: + continue + success, reason = passes_relatedness_check( + relatedness_check_lookup, + sample.sample_id, + other_id, + relation, + additional_allowed_relation, + ) + if not success: + failure_reasons.append(reason) + return failure_reasons + + +def build_relatedness_check_lookup( + relatedness_check_ht: hl.Table, + remap_lookup: hl.dict, +) -> dict[tuple[str, str], list]: + relatedness_check_ht = relatedness_check_ht.key_by( + i=remap_lookup.get(relatedness_check_ht.i, relatedness_check_ht.i), + j=remap_lookup.get(relatedness_check_ht.j, relatedness_check_ht.j), + ) + return { + # NB: samples are sorted in the original ibd but not necessarily + # sorted after remapping + (min(r.i, r.j), max(r.i, r.j)): list(r.drop('i', 'j').values()) + for r in relatedness_check_ht.collect() + } + + +def build_sex_check_lookup( + sex_check_ht: hl.Table, + remap_lookup: hl.dict, +) -> dict[str, Sex]: + sex_check_ht = sex_check_ht.key_by( + s=remap_lookup.get(sex_check_ht.s, sex_check_ht.s), + ) + sex_check_ht = sex_check_ht.select('predicted_sex') + return {r.s: Sex(r.predicted_sex) for r in sex_check_ht.collect()} + + +def get_families_failed_missing_samples( + mt: hl.MatrixTable, + families: set[Family], +) -> dict[Family, list[str]]: + callset_samples = set(mt.cols().s.collect()) + failed_families = {} + for family in families: + missing_samples = family.samples.keys() - callset_samples + if len(missing_samples) > 0: + # NB: This is an array of a single element for consistency with + # the other checks. + failed_families[family] = [f'Missing samples: {missing_samples}'] + return failed_families + + +def get_families_failed_relatedness_check( + families: set[Family], + relatedness_check_ht: hl.Table, + remap_lookup: hl.dict, +) -> dict[Family, list[str]]: + relatedness_check_lookup = build_relatedness_check_lookup( + relatedness_check_ht, + remap_lookup, + ) + failed_families = defaultdict(list) + for family in families: + for sample in family.samples.values(): + failure_reasons = all_relatedness_checks( + relatedness_check_lookup, + family, + sample, + ) + if failure_reasons: + failed_families[family].extend(failure_reasons) + return dict(failed_families) + + +def get_families_failed_sex_check( + families: set[Family], + sex_check_ht: hl.Table, + remap_lookup: hl.dict, +) -> dict[Family, list[str]]: + sex_check_lookup = build_sex_check_lookup(sex_check_ht, remap_lookup) + failed_families = defaultdict(list) + for family in families: + for sample_id in family.samples: + if sample_id not in sex_check_lookup: + failed_families[family].append( + f'Sample {sample_id} has pedigree sex {family.samples[sample_id].sex.value} but is missing from the sex check source', + ) + continue + # NB: Both Unknown samples in pedigree and Unknown + # samples in the predicted_sex are precluded from + # failing the sex check. + if ( + sex_check_lookup[sample_id] == Sex.UNKNOWN + or family.samples[sample_id].sex == Sex.UNKNOWN + ): + logger.info( + f'Encountered sample with Unknown sex excluded from sex check: {sample_id}', + ) + continue + + if family.samples[sample_id].sex != sex_check_lookup[sample_id]: + failed_families[family].append( + f'Sample {sample_id} has pedigree sex {family.samples[sample_id].sex.value} but imputed sex {sex_check_lookup[sample_id].value}', + ) + return dict(failed_families) + + +def get_families_failed_imputed_sex_ploidy( + families: set[Family], + mt: hl.MatrixTable, + sex_check_ht: hl.Table, +) -> dict[Family, str]: + mt = mt.select_cols( + discrepant=( + ( + # All calls are diploid or missing but the sex is Male + hl.agg.all(mt.GT.is_diploid() | hl.is_missing(mt.GT)) + & (sex_check_ht[mt.s].predicted_sex == Sex.MALE.value) + ) + | ( + # At least one call is haploid but the sex is Female, X0, XXY, XYY, or XXX + hl.agg.any(~mt.GT.is_diploid()) + & hl.literal( + { + Sex.FEMALE.value, + Sex.X0.value, + Sex.XYY.value, + Sex.XXY.value, + Sex.XXX.value, + }, + ).contains(sex_check_ht[mt.s].predicted_sex) + ) + ), + ) + discrepant_samples = mt.aggregate_cols( + hl.agg.filter(mt.discrepant, hl.agg.collect_as_set(mt.s)), + ) + failed_families = defaultdict(list) + for family in families: + discrepant_loadable_samples = set(family.samples.keys()) & discrepant_samples + if discrepant_loadable_samples: + sorted_discrepant_samples = sorted(discrepant_loadable_samples) + failed_families[family].append( + f'Found samples with misaligned ploidy with their provided imputed sex: {sorted_discrepant_samples}', + ) + return failed_families diff --git a/loading_pipeline/lib/misc/family_loading_failures_test.py b/loading_pipeline/lib/misc/family_loading_failures_test.py new file mode 100644 index 0000000000..fb1d0905d1 --- /dev/null +++ b/loading_pipeline/lib/misc/family_loading_failures_test.py @@ -0,0 +1,448 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.core import Sex +from loading_pipeline.lib.misc.family_loading_failures import ( + all_relatedness_checks, + build_relatedness_check_lookup, + build_sex_check_lookup, + get_families_failed_imputed_sex_ploidy, + get_families_failed_sex_check, +) +from loading_pipeline.lib.misc.io import import_pedigree +from loading_pipeline.lib.misc.pedigree import ( + Family, + Sample, + parse_pedigree_ht_to_families, +) + +TEST_SEX_CHECK_1 = 'loading_pipeline/var/test/sex_check/test_sex_check_1.ht' +TEST_PEDIGREE_6 = 'loading_pipeline/var/test/pedigrees/test_pedigree_6.tsv' + + +class FamilyLoadingFailuresTest(unittest.TestCase): + def test_build_relatedness_check_lookup(self): + ht = hl.Table.parallelize( + [ + { + 'i': 'ROS_006_18Y03226_D1', + 'j': 'ROS_007_19Y05939_D1', + 'ibd0': 0.0, + 'ibd1': 1.0, + 'ibd2': 0.0, + 'pi_hat': 0.5, + }, + ], + hl.tstruct( + i=hl.tstr, + j=hl.tstr, + ibd0=hl.tfloat, + ibd1=hl.tfloat, + ibd2=hl.tfloat, + pi_hat=hl.tfloat, + ), + key=['i', 'j'], + ) + self.assertEqual( + build_relatedness_check_lookup( + ht, + hl.dict({'ROS_006_18Y03226_D1': 'remapped_id'}), + ), + { + ('ROS_007_19Y05939_D1', 'remapped_id'): [ + 0.0, + 1.0, + 0.0, + 0.5, + ], + }, + ) + + def test_build_sex_check_lookup(self): + ht = hl.Table.parallelize( + [ + {'s': 'ROS_006_18Y03226_D1', 'predicted_sex': 'F'}, + {'s': 'ROS_006_18Y03227_D1', 'predicted_sex': 'F'}, + {'s': 'ROS_006_18Y03228_D1', 'predicted_sex': 'F'}, + {'s': 'ROS_007_19Y05919_D1', 'predicted_sex': 'F'}, + {'s': 'ROS_007_19Y05939_D1', 'predicted_sex': 'M'}, + {'s': 'ROS_007_19Y05987_D1', 'predicted_sex': 'U'}, + {'s': 'ROS_007_19Y05989_D1', 'predicted_sex': 'X0'}, + ], + hl.tstruct( + s=hl.tstr, + predicted_sex=hl.tstr, + ), + key='s', + ) + self.assertEqual( + build_sex_check_lookup(ht, hl.dict({'ROS_006_18Y03226_D1': 'remapped_id'})), + { + 'remapped_id': Sex.FEMALE, + 'ROS_006_18Y03227_D1': Sex.FEMALE, + 'ROS_006_18Y03228_D1': Sex.FEMALE, + 'ROS_007_19Y05919_D1': Sex.FEMALE, + 'ROS_007_19Y05939_D1': Sex.MALE, + 'ROS_007_19Y05987_D1': Sex.UNKNOWN, + 'ROS_007_19Y05989_D1': Sex.X0, + }, + ) + + def test_all_relatedness_checks(self): + relatedness_check_lookup = { + # Parent + ('sample_1', 'sample_2'): [ + 0.0, + 0.98, + 0.0, + 0.52, + ], + # GrandParent + ('sample_1', 'sample_3'): [0.48, 0.52, 0, 0.24], + # Half Sibling (but actually a hidden Sibling) + ('sample_1', 'sample_4'): [0.25, 0.5, 0.25, 0.5], + } + sample = Sample( + sex=Sex.FEMALE, + sample_id='sample_1', + mother='sample_2', + paternal_grandfather='sample_3', + half_siblings=['sample_4'], + ) + family = Family( + family_guid='family_1a', + samples={ + 'sample_1': sample, + 'sample_2': Sample(sex=Sex.MALE, sample_id='sample_2'), + 'sample_3': Sample(sex=Sex.MALE, sample_id='sample_3'), + 'sample_4': Sample(sex=Sex.MALE, sample_id='sample_4'), + 'sample_5': Sample(sex=Sex.MALE, sample_id='sample_5'), + }, + ) + failure_reasons = all_relatedness_checks( + relatedness_check_lookup, + family, + sample, + ) + self.assertListEqual(failure_reasons, []) + + # Defined grandparent missing in relatedness table + sample = Sample( + sex=Sex.FEMALE, + sample_id='sample_1', + mother='sample_2', + paternal_grandfather='sample_3', + paternal_grandmother='sample_5', + ) + failure_reasons = all_relatedness_checks( + relatedness_check_lookup, + family, + sample, + ) + self.assertListEqual( + failure_reasons, + [ + 'Sample sample_1 has expected relation "grandparent_grandchild" to sample_5 but has coefficients []', + ], + ) + + # Sibling is actually a half sibling. + relatedness_check_lookup = { + **relatedness_check_lookup, + ('sample_1', 'sample_4'): [0.5, 0.5, 0, 0.25], + } + sample = Sample( + sex=Sex.FEMALE, + sample_id='sample_1', + mother='sample_2', + paternal_grandfather='sample_3', + siblings=['sample_4'], + ) + failure_reasons = all_relatedness_checks( + relatedness_check_lookup, + family, + sample, + ) + self.assertListEqual( + failure_reasons, + [ + 'Sample sample_1 has expected relation "sibling" to sample_4 but has coefficients [0.5, 0.5, 0, 0.25]', + ], + ) + + relatedness_check_lookup = { + **relatedness_check_lookup, + ('sample_1', 'sample_2'): [ + 0.5, + 0.5, + 0.5, + 0.5, + ], + } + sample = Sample( + sex=Sex.FEMALE, + sample_id='sample_1', + mother='sample_2', + paternal_grandfather='sample_3', + siblings=['sample_4'], + ) + failure_reasons = all_relatedness_checks( + relatedness_check_lookup, + family, + sample, + ) + self.assertListEqual( + failure_reasons, + [ + 'Sample sample_1 has expected relation "parent_child" to sample_2 but has coefficients [0.5, 0.5, 0.5, 0.5]', + 'Sample sample_1 has expected relation "sibling" to sample_4 but has coefficients [0.5, 0.5, 0, 0.25]', + ], + ) + + # Some samples will include relationships with + # samples that are not expected to be included + # in the callset. These should not trigger relatedness + # failures. + sample = Sample( + sex=Sex.FEMALE, + sample_id='sample_1', + mother='sample_2', + ) + family = Family( + family_guid='family_1a', + samples={ + 'sample_1': sample, + }, + ) + failure_reasons = all_relatedness_checks( + {}, + family, + sample, + ) + self.assertListEqual( + failure_reasons, + [], + ) + + def test_get_families_failed_sex_check(self): + sex_check_ht = hl.Table.parallelize( + [ + {'s': 'ROS_006_18Y03226_D1', 'predicted_sex': 'F'}, + {'s': 'ROS_006_18Y03227_D1', 'predicted_sex': 'F'}, # Pedigree Sex U + {'s': 'ROS_006_18Y03228_D1', 'predicted_sex': 'F'}, + {'s': 'ROS_007_19Y05939_D1', 'predicted_sex': 'M'}, + {'s': 'ROS_007_19Y05987_D1', 'predicted_sex': 'U'}, # Pedigree Sex F + {'s': 'ROS_007_19Y05989_D1', 'predicted_sex': 'XXX'}, + ], + hl.tstruct( + s=hl.tstr, + predicted_sex=hl.tstr, + ), + key='s', + ) + pedigree_ht = import_pedigree(TEST_PEDIGREE_6) + failed_families = get_families_failed_sex_check( + parse_pedigree_ht_to_families(pedigree_ht), + sex_check_ht, + {}, + ) + self.assertCountEqual( + failed_families.values(), + [ + [ + 'Sample ROS_007_19Y05919_D1 has pedigree sex F but is missing from the sex check source', + 'Sample ROS_007_19Y05939_D1 has pedigree sex F but imputed sex M', + ], + ], + ) + + def test_get_families_failed_imputed_sex_ploidy(self) -> None: + female_sample = 'HG00731_1' + male_sample_1 = 'HG00732_1' + male_sample_2 = 'HG00732_1' + x0_sample = 'NA20899_1' + xxy_sample = 'NA20889_1' + xyy_sample = 'NA20891_1' + xxx_sample = 'NA20892_1' + + sex_check_ht = hl.read_table(TEST_SEX_CHECK_1) + families = { + Family( + family_guid='', + samples={ + female_sample: Sample(female_sample, Sex.FEMALE), + male_sample_1: Sample(male_sample_1, Sex.MALE), + male_sample_2: Sample(male_sample_2, Sex.MALE), + x0_sample: Sample(x0_sample, Sex.X0), + xxy_sample: Sample(xxy_sample, Sex.XXY), + xyy_sample: Sample(xyy_sample, Sex.XYY), + xxx_sample: Sample(xxx_sample, Sex.XXX), + }, + ), + } + + # All calls on X chromosome are valid + mt = ( + hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chrX', + position=1, + reference_genome='GRCh38', + ), + ], + }, + cols={ + 's': [ + female_sample, + male_sample_1, + x0_sample, + xxy_sample, + xyy_sample, + xxx_sample, + ], + }, + entries={ + 'GT': [ + [ + hl.Call(alleles=[0, 0], phased=False), + hl.Call(alleles=[0], phased=False), + hl.Call(alleles=[0, 0], phased=False), # X0 + hl.Call(alleles=[0, 0], phased=False), # XXY + hl.Call(alleles=[0, 0], phased=False), # XYY + hl.Call(alleles=[0, 0], phased=False), # XXX + ], + ], + }, + ) + .key_rows_by('locus') + .key_cols_by('s') + ) + failed_families = get_families_failed_imputed_sex_ploidy( + families, + mt, + sex_check_ht, + ) + self.assertDictEqual(failed_families, {}) + + # All calls on Y chromosome are valid + mt = ( + hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chrY', + position=1, + reference_genome='GRCh38', + ), + ], + }, + cols={ + 's': [ + female_sample, + male_sample_1, + x0_sample, + xxy_sample, + xyy_sample, + xxx_sample, + ], + }, + entries={ + 'GT': [ + [ + hl.missing(hl.tcall), + hl.Call(alleles=[0], phased=False), + hl.missing(hl.tcall), # X0 + hl.Call(alleles=[0, 0], phased=False), # XXY + hl.Call(alleles=[0, 0], phased=False), # XYY + hl.missing(hl.tcall), # XXX + ], + ], + }, + ) + .key_rows_by('locus') + .key_cols_by('s') + ) + failed_families = get_families_failed_imputed_sex_ploidy( + families, + mt, + sex_check_ht, + ) + self.assertDictEqual(failed_families, {}) + + # Invalid X chromosome case + mt = ( + hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chrX', + position=1, + reference_genome='GRCh38', + ), + ], + }, + cols={ + 's': [ + female_sample, + male_sample_1, + male_sample_2, + x0_sample, + xxy_sample, + xyy_sample, + xxx_sample, + ], + }, + entries={ + 'GT': [ + [ + hl.Call(alleles=[0], phased=False), # invalid Female call + hl.Call(alleles=[0], phased=False), # valid Male call + hl.missing(hl.tcall), # invalid Male call + hl.Call(alleles=[0], phased=False), # invalid X0 call + hl.Call(alleles=[0], phased=False), # invalid XXY call + hl.missing(hl.tcall), # valid XYY call + hl.Call(alleles=[0, 0], phased=False), # valid XXX call + ], + ], + }, + ) + .key_rows_by('locus') + .key_cols_by('s') + ) + failed_families = get_families_failed_imputed_sex_ploidy( + families, + mt, + sex_check_ht, + ) + self.assertCountEqual( + failed_families.values(), + [ + [ + "Found samples with misaligned ploidy with their provided imputed sex: ['HG00731_1', 'HG00732_1', 'NA20889_1', 'NA20899_1']", + ], + ], + ) + + # Invalid X chromosome case, but only discrepant family samples are reported + families = { + Family( + family_guid='', + samples={female_sample: Sample(female_sample, Sex.FEMALE)}, + ), + } + failed_families = get_families_failed_imputed_sex_ploidy( + families, + mt, + sex_check_ht, + ) + self.assertCountEqual( + failed_families.values(), + [ + [ + "Found samples with misaligned ploidy with their provided imputed sex: ['HG00731_1']", + ], + ], + ) diff --git a/loading_pipeline/lib/misc/gcnv.py b/loading_pipeline/lib/misc/gcnv.py new file mode 100644 index 0000000000..f1b13fe58e --- /dev/null +++ b/loading_pipeline/lib/misc/gcnv.py @@ -0,0 +1,9 @@ +import hail as hl + + +def parse_gcnv_genes(gene_col: hl.expr.StringExpression) -> hl.expr.SetExpression: + return hl.set( + gene_col.split(',') + .filter(lambda gene: ~hl.set({'None', 'null', 'NA', ''}).contains(gene)) + .map(lambda gene: gene.split(r'\.')[0]), + ) diff --git a/loading_pipeline/lib/misc/gcnv_test.py b/loading_pipeline/lib/misc/gcnv_test.py new file mode 100644 index 0000000000..33a72f3684 --- /dev/null +++ b/loading_pipeline/lib/misc/gcnv_test.py @@ -0,0 +1,54 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.misc.gcnv import parse_gcnv_genes + + +class GCNVGeneParsingTest(unittest.TestCase): + def test_parse_gcnv_genes(self): + t1 = hl.Table.parallelize( + [ + {'genes': 'AC118553.2,SLC35A3'}, + {'genes': 'AC118553.1,None'}, + {'genes': 'None'}, + {'genes': 'SLC35A3.43'}, + {'genes': ''}, + {'genes': 'SLC35A4.43'}, + ], + hl.tstruct(genes=hl.dtype('str')), + key='genes', + ) + t1 = t1.annotate(gene_set=parse_gcnv_genes(t1.genes)) + self.assertCountEqual( + t1.collect(), + [ + hl.Struct( + genes='AC118553.2,SLC35A3', + gene_set={'AC118553', 'SLC35A3'}, + ), + hl.Struct(genes='AC118553.1,None', gene_set={'AC118553'}), + hl.Struct(genes='None', gene_set=set()), + hl.Struct(genes='SLC35A3.43', gene_set={'SLC35A3'}), + hl.Struct(genes='', gene_set=set()), + hl.Struct(genes='SLC35A4.43', gene_set={'SLC35A4'}), + ], + ) + + def test_aggregate_parsed_genes(self): + t1 = hl.Table.parallelize( + [ + {'genes': 'AC118553.2,SLC35A3'}, + {'genes': 'AC118553.1,None'}, + {'genes': 'None'}, + {'genes': 'SLC35A3.43'}, + {'genes': ''}, + {'genes': 'SLC35A4.43'}, + ], + hl.tstruct(genes=hl.dtype('str')), + key='genes', + ) + aggregated_gene_set = t1.aggregate( + hl.flatten(hl.agg.collect_as_set(parse_gcnv_genes(t1.genes))), + ) + self.assertEqual(aggregated_gene_set, {'SLC35A4', 'SLC35A3', 'AC118553'}) diff --git a/loading_pipeline/lib/misc/gcp.py b/loading_pipeline/lib/misc/gcp.py new file mode 100644 index 0000000000..46a6c5ecd3 --- /dev/null +++ b/loading_pipeline/lib/misc/gcp.py @@ -0,0 +1,44 @@ +import datetime + +import google.auth +import google.auth.transport.requests +import google.oauth2.credentials +import pytz + +from loading_pipeline.lib.core import FeatureFlag + +SERVICE_ACCOUNT_CREDENTIALS = None +CLOUD_PLATFORM_SCOPE = [ + 'https://www.googleapis.com/auth/cloud-platform', +] +SOCIAL_AUTH_GOOGLE_OAUTH2_SCOPE = [ + 'https://www.googleapis.com/auth/userinfo.profile', + 'https://www.googleapis.com/auth/userinfo.email', + 'openid', +] +ONE_MINUTE_S = 60 + + +def get_service_account_credentials() -> google.oauth2.credentials.Credentials: + global SERVICE_ACCOUNT_CREDENTIALS + if not SERVICE_ACCOUNT_CREDENTIALS: + SERVICE_ACCOUNT_CREDENTIALS, _ = google.auth.default( + scopes=[ + *SOCIAL_AUTH_GOOGLE_OAUTH2_SCOPE, + *(CLOUD_PLATFORM_SCOPE if FeatureFlag.EXPECT_TDR_METRICS else []), + ], + ) + tz = pytz.UTC + if ( + SERVICE_ACCOUNT_CREDENTIALS.token + and ( + tz.localize(SERVICE_ACCOUNT_CREDENTIALS.expiry) + - datetime.datetime.now(tz=tz) + ).total_seconds() + > ONE_MINUTE_S + ): + return SERVICE_ACCOUNT_CREDENTIALS + SERVICE_ACCOUNT_CREDENTIALS.refresh( + request=google.auth.transport.requests.Request(), + ) + return SERVICE_ACCOUNT_CREDENTIALS diff --git a/loading_pipeline/lib/misc/io.py b/loading_pipeline/lib/misc/io.py new file mode 100644 index 0000000000..b2f4e33e55 --- /dev/null +++ b/loading_pipeline/lib/misc/io.py @@ -0,0 +1,336 @@ +import hashlib +import math +import os +import re +import uuid +from collections.abc import Callable +from string import Template + +import hail as hl +import hailtop.fs as hfs + +from loading_pipeline.lib.core import DatasetType, Env, ReferenceGenome, Sex +from loading_pipeline.lib.misc.gcnv import parse_gcnv_genes +from loading_pipeline.lib.misc.nested_field import parse_nested_field +from loading_pipeline.lib.misc.validation import SeqrValidationError + +BIALLELIC = 2 +B_PER_MB = 1 << 20 # 1024 * 1024 +MB_PER_PARTITION = 32 +MAX_SAMPLES_SPLIT_MULTI_SHUFFLE = 100 + + +def validated_hl_function( + regex_to_msg: dict[str, str | Template], +) -> Callable[[Callable], Callable]: + def decorator(fn: Callable) -> Callable: + def wrapper(*args, **kwargs) -> hl.Table | hl.MatrixTable: + try: + t, _ = checkpoint(fn(*args, **kwargs)) + except Exception as e: + for regex, msg in regex_to_msg.items(): + match = re.search(regex, str(e)) + if match and isinstance(msg, Template): + msg = msg.substitute(match=match.group(1)) # noqa: PLW2901 + if match: + raise SeqrValidationError(msg) from e + raise + else: + return t + + return wrapper + + return decorator + + +def file_size_bytes(path: str) -> int: + if not path.startswith(('gs://', 's3://')): + path = os.path.abspath(path) + + seen_files = set() + + def traverse(current_path: str) -> int: + try: + entries = hfs.ls(current_path) + except FileNotFoundError: + return 0 + + local_size = 0 + for entry in entries: + if entry.path in seen_files: + continue + seen_files.add(entry.path) + + if entry.typ == hfs.stat_result.FileType.FILE: + if not entry.path.endswith('.crc'): + local_size += entry.size + elif entry.typ == hfs.stat_result.FileType.DIRECTORY: + local_size += traverse(entry.path) + + return local_size + + return traverse(path) + + +def compute_hail_n_partitions(file_size_b: int) -> int: + return math.ceil(file_size_b / B_PER_MB / MB_PER_PARTITION) + + +@validated_hl_function( + { + 'RVD error! Keys found out of order': 'Your callset failed while attempting to split multiallelic sites. This error can occur if the dataset contains both multiallelic variants and duplicated loci.', + 'array index out of bounds': 'Your callset failed while attempting to split multiallelic sites. This error can occur if the provided Allele Depth (AD) field does not match the length of the multiallelic site.', + }, +) +def split_multi_hts( + mt: hl.MatrixTable, + skip_validate_no_duplicate_variants: bool, + max_samples_split_multi_shuffle=MAX_SAMPLES_SPLIT_MULTI_SHUFFLE, +) -> hl.MatrixTable: + bi = mt.filter_rows(hl.len(mt.alleles) == BIALLELIC) + # split_multi_hts filters star alleles by default, but we + # need that behavior for bi-allelic variants in addition to + # multi-allelics + bi = bi.filter_rows(~bi.alleles.contains('*')) + bi = bi.annotate_rows(a_index=1, was_split=False) + multi = mt.filter_rows(hl.len(mt.alleles) > BIALLELIC) + split = hl.split_multi_hts( + multi, + permit_shuffle=mt.count()[1] < max_samples_split_multi_shuffle, + ) + mt = split.union_rows(bi) + # If we've disabled validation (which is expected to throw an exception + # for duplicate variants, we would like to distinc ) + if skip_validate_no_duplicate_variants: + return mt.distinct_by_row() + return mt + + +def import_gcnv_bed_file(callset_path: str) -> hl.MatrixTable: + # Hail falls over itself with OOMs with use_new_shuffle here... no clue why. + hl._set_flags(use_new_shuffle=None, no_whole_stage_codegen='1') # noqa: SLF001 + ht = hl.import_table( + callset_path, + types={ + **DatasetType.GCNV.col_fields, + **DatasetType.GCNV.entries_fields, + **DatasetType.GCNV.row_fields, + }, + force=callset_path.endswith('gz'), + ) + mt = ht.to_matrix_table( + row_key=['variant_name', 'svtype'], + col_key=['sample_fix'], + row_fields=['chr', 'sc', 'sf', 'strvctvre_score'], + ) + mt = mt.rename({'start': 'sample_start', 'end': 'sample_end'}) + mt = mt.key_cols_by(s=mt.sample_fix) + mt = mt.annotate_rows( + variant_id=hl.format('%s_%s', mt.variant_name, mt.svtype), + filters=hl.empty_set(hl.tstr), + start=hl.agg.min(mt.sample_start), + end=hl.agg.max(mt.sample_end), + num_exon=hl.agg.max(mt.genes_any_overlap_totalExons), + gene_ids=hl.flatten( + hl.agg.collect_as_set(parse_gcnv_genes(mt.genes_any_overlap_Ensemble_ID)), + ), + cg_genes=hl.flatten( + hl.agg.collect_as_set(parse_gcnv_genes(mt.genes_CG_Ensemble_ID)), + ), + lof_genes=hl.flatten( + hl.agg.collect_as_set(parse_gcnv_genes(mt.genes_LOF_Ensemble_ID)), + ), + ) + return mt.unfilter_entries() + + +@validated_hl_function( + { + '.*FileNotFoundException|GoogleJsonResponseException: 403 Forbidden|arguments refer to no files.*': 'Unable to access the VCF in cloud storage.', + # NB: ?: is non-capturing group. + '.*(?:InvalidHeader|VCFParseError): (.*)$': Template( + 'VCF failed file format validation: $match', + ), + '.*IOException: Gzip-compressed data is corrupt.*': 'Gzip-compressed data is corrupt.', + }, +) +def import_vcf( + callset_path: str, + reference_genome: ReferenceGenome, +) -> hl.MatrixTable: + args = { + 'reference_genome': reference_genome.value, + 'skip_invalid_loci': True, + 'contig_recoding': reference_genome.contig_recoding(), + 'find_replace': ( + 'nul', + '.', + ), # Required for internal exome callsets (+ some AnVIL requests) + 'array_elements_required': False, + 'call_fields': [], # PGT is unused downstream, but is occasionally present in old VCFs! + } + try: + mt, _ = checkpoint( + hl.import_vcf( + callset_path, + force_bgz=True, + **args, + ), + ) + except Exception as e: + # Handle callsets provided as gz but not bgz + # Note that this is handled separately from other VCF validation + # as it's an exceptional case that we can handle internally. + if 'File does not conform to block gzip format' not in str(e): + raise + mt = hl.import_vcf( + callset_path, + force=True, + **args, + ) + return mt + + +def import_callset( + callset_path: str, + reference_genome: ReferenceGenome, + dataset_type: DatasetType, +) -> hl.MatrixTable: + if dataset_type == DatasetType.GCNV: + mt = import_gcnv_bed_file(callset_path) + elif 'vcf' in callset_path: + mt = import_vcf(callset_path, reference_genome) + elif 'mt' in callset_path: + mt = hl.read_matrix_table(callset_path) + if dataset_type == DatasetType.SV: + mt = mt.annotate_rows( + variant_id=mt.rsid, + ) + return mt.key_rows_by(*dataset_type.table_key_type(reference_genome).fields) + + +@validated_hl_function( + { + 'instance has no field (.*)': Template( + 'Your callset is missing a required field: $match', + ), + }, +) +def select_relevant_fields( + mt: hl.MatrixTable, + dataset_type: DatasetType, + additional_row_fields: None | dict[str, hl.expr.types.HailType | set] = None, +) -> hl.MatrixTable: + mt = mt.select_globals() + mt = mt.select_rows( + **{field: parse_nested_field(mt, field) for field in dataset_type.row_fields}, + **{ + field: parse_nested_field(mt, field) + for field in (additional_row_fields or []) + }, + ) + mt = mt.select_cols( + **{field: parse_nested_field(mt, field) for field in dataset_type.col_fields}, + ) + return mt.select_entries( + **{ + field: parse_nested_field(mt, field) + for field in dataset_type.entries_fields + }, + ) + + +def import_imputed_sex(imputed_sex_path: str) -> hl.Table: + ht = hl.import_table(imputed_sex_path) + imputed_sex_lookup = hl.dict( + { + imputed_sex_value: s.value + for s in Sex + for imputed_sex_value in s.imputed_sex_values + }, + ) + ht = ht.select( + s=ht.collaborator_sample_id, + predicted_sex=( + hl.case() + .when( + imputed_sex_lookup.contains(ht.predicted_sex), + imputed_sex_lookup[ht.predicted_sex], + ) + .or_error( + hl.format( + 'Found unexpected value %s in imputed sex file', + ht.predicted_sex, + ), + ) + ), + ) + return ht.key_by(ht.s) + + +def import_tdr_qc_metrics(file_path: str) -> hl.Table: + ht = hl.import_table( + file_path, + types={ + 'contamination_rate': hl.tfloat32, + 'percent_bases_at_20x': hl.tfloat32, + 'mean_coverage': hl.tfloat32, + }, + delimiter='\t', + missing=[''], + ) + ht = ht.select( + s=ht.collaborator_sample_id, + contamination_rate=ht.contamination_rate, + percent_bases_at_20x=ht.percent_bases_at_20x, + mean_coverage=ht.mean_coverage, + ) + return ht.key_by(ht.s) + + +def import_pedigree(pedigree_path: str) -> hl.Table: + ht = hl.import_table(pedigree_path, missing='') + optional_selects = {'remap_id': ht.VCF_ID} if 'VCF_ID' in ht.row else {} + return ht.select( + sex=ht.Sex, + family_guid=ht.Family_GUID, + s=ht.Individual_ID, + maternal_s=ht.Maternal_ID, + paternal_s=ht.Paternal_ID, + **optional_selects, + ) + + +def remap_pedigree_hash(pedigree_path: str) -> hl.Int32Expression: + sha256 = hashlib.sha256() + with hfs.open(pedigree_path) as f2: + sha256.update(f2.read().encode('utf8')) + # maximum 4 byte int + return hl.int32(int(sha256.hexdigest()[:8], 16)) + + +def checkpoint( + t: hl.Table | hl.MatrixTable, +) -> tuple[hl.Table | hl.MatrixTable, str]: + suffix = 'mt' if isinstance(t, hl.MatrixTable) else 'ht' + read_fn = hl.read_matrix_table if isinstance(t, hl.MatrixTable) else hl.read_table + checkpoint_path = os.path.join( + Env.HAIL_TMP_DIR, + f'{uuid.uuid4()}.{suffix}', + ) + t.write(checkpoint_path) + return read_fn(checkpoint_path), checkpoint_path + + +def write( + t: hl.Table | hl.MatrixTable, + destination_path: str, + repartition: bool = True, +) -> hl.Table | hl.MatrixTable: + t, path = checkpoint(t) + if repartition: + t = t.repartition( + compute_hail_n_partitions(file_size_bytes(path)), + shuffle=False, + ) + return t.write(destination_path, overwrite=True) diff --git a/loading_pipeline/lib/misc/io_test.py b/loading_pipeline/lib/misc/io_test.py new file mode 100644 index 0000000000..a346e8b323 --- /dev/null +++ b/loading_pipeline/lib/misc/io_test.py @@ -0,0 +1,211 @@ +import unittest +from unittest import mock + +import hail as hl + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome +from loading_pipeline.lib.misc.io import ( + compute_hail_n_partitions, + file_size_bytes, + import_imputed_sex, + import_vcf, + remap_pedigree_hash, + select_relevant_fields, + split_multi_hts, +) +from loading_pipeline.lib.misc.validation import SeqrValidationError + +TEST_IMPUTED_SEX = 'loading_pipeline/var/test/sex_check/test_imputed_sex.tsv' +TEST_IMPUTED_SEX_UNEXPECTED_VALUE = ( + 'loading_pipeline/var/test/sex_check/test_imputed_sex_unexpected_value.tsv' +) +CORRUPTED_VCF = 'loading_pipeline/var/test/callsets/1kg_corrupt.vcf.gz' +TEST_INVALID_VCF = 'loading_pipeline/var/test/callsets/improperly_formatted.vcf' +TEST_PEDIGREE_3_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_3_remap.tsv' +TEST_MITO_MT = 'loading_pipeline/var/test/callsets/mito_1.mt' + + +class IOTest(unittest.TestCase): + def test_file_size_mb(self) -> None: + # find loading_pipeline/var/test/callsets/mito_1.mt -type f | grep -v 'crc' | xargs ls -alt {} | awk '{sum += $5; print sum}' + # 191310 + self.assertEqual(file_size_bytes(TEST_MITO_MT), 191310) + + def test_compute_hail_n_partitions(self) -> None: + self.assertEqual(compute_hail_n_partitions(23), 1) + self.assertEqual(compute_hail_n_partitions(191310), 1) + self.assertEqual(compute_hail_n_partitions(1913100000), 58) + + def test_import_imputed_sex(self) -> None: + ht = import_imputed_sex(TEST_IMPUTED_SEX) + self.assertListEqual( + ht.collect(), + [ + hl.Struct(s='abc_1', predicted_sex='M'), + hl.Struct(s='abc_2', predicted_sex='F'), + hl.Struct(s='abc_3', predicted_sex='U'), + hl.Struct(s='abc_4', predicted_sex='XYY'), + hl.Struct(s='abc_5', predicted_sex='U'), + ], + ) + + def test_import_imputed_sex_unexpected_value(self) -> None: + ht = import_imputed_sex(TEST_IMPUTED_SEX_UNEXPECTED_VALUE) + self.assertRaisesRegex( + hl.utils.java.HailUserError, + 'Found unexpected value UNKNOWN in imputed sex file', + ht.collect, + ) + + def test_remap_pedigree_hash(self) -> None: + self.assertEqual( + hl.eval( + remap_pedigree_hash( + TEST_PEDIGREE_3_REMAP, + ), + ), + 573002191, + ) + + def test_import_vcf(self) -> None: + self.assertRaisesRegex( + TypeError, + 'missing 1 required positional argument', + import_vcf, + 'abc', + ) + self.assertRaisesRegex( + SeqrValidationError, + 'Unable to access the VCF in cloud storage', + import_vcf, + 'bad.vcf', + ReferenceGenome.GRCh38, + ) + self.assertRaisesRegex( + SeqrValidationError, + 'Gzip-compressed data is corrupt', + import_vcf, + CORRUPTED_VCF, + ReferenceGenome.GRCh38, + ) + with mock.patch( + 'loading_pipeline.lib.misc.io.hl.read_table', + ) as mock_read_table: + mock_read_table.side_effect = hl.utils.java.FatalError( + 'GoogleJsonResponseException: 403 Forbidden', + ) + self.assertRaisesRegex( + SeqrValidationError, + 'Unable to access the VCF in cloud storage', + import_vcf, + 'abc123/bad.vcf', + ReferenceGenome.GRCh38, + ) + self.assertRaisesRegex( + SeqrValidationError, + 'VCF failed file format validation: Your input file has a malformed header: We never saw the required CHROM header line \\(starting with one #\\) for the input VCF file', + import_vcf, + TEST_PEDIGREE_3_REMAP, + ReferenceGenome.GRCh38, + ) + self.assertRaisesRegex( + SeqrValidationError, + "VCF failed file format validation: invalid character 'N' in integer literal", + import_vcf, + TEST_INVALID_VCF, + ReferenceGenome.GRCh38, + ) + + def test_select_missing_field(self) -> None: + self.assertRaisesRegex( + SeqrValidationError, + "Your callset is missing a required field: 'a magic field'", + select_relevant_fields, + hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + ], + 'alleles': [ + ['A', 'C'], + ], + 'rsid': ['rs1233'], + 'filters': [{'PASS'}], + }, + cols={'s': ['sample_1']}, + entries={ + 'GT': [[hl.Call([0, 0])]], + 'AD': [[[0, 20]]], + 'GQ': [[99]], + }, + ).key_rows_by('locus', 'alleles'), + DatasetType.SNV_INDEL, + {'a magic field': hl.tint32}, + ) + + def test_split_multi_failure(self) -> None: + self.assertRaisesRegex( + SeqrValidationError, + 'Your callset failed while attempting to split multiallelic sites. This error can occur if the dataset contains both multiallelic variants and duplicated loci.', + split_multi_hts, + hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + ], + 'alleles': [ + ['A', 'G', 'AC'], + ['A', 'AT', 'C', 'G'], + ], + }, + cols={'s': ['sample_1']}, + entries={ + 'GQ': [[99], [98]], + }, + ) + .key_rows_by('locus', 'alleles') + .repartition(1), + False, + 1, + ) + + def test_split_multi_failure_ad_length(self) -> None: + self.assertRaisesRegex( + SeqrValidationError, + 'Your callset failed while attempting to split multiallelic sites. This error can occur if the provided Allele Depth \\(AD\\) field does not match the length of the multiallelic site.', + split_multi_hts, + hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + ], + 'alleles': [ + ['GAC', 'G', 'GTTTTTTTTTTTTTTTAC'], + ], + }, + cols={'s': ['sample_1']}, + entries={ + 'GQ': [[99]], + 'AD': [[[0, 1]]], + }, + ).key_rows_by('locus', 'alleles'), + False, + 1, + ) diff --git a/loading_pipeline/lib/misc/math.py b/loading_pipeline/lib/misc/math.py new file mode 100644 index 0000000000..65feedb0a7 --- /dev/null +++ b/loading_pipeline/lib/misc/math.py @@ -0,0 +1,9 @@ +def constrain( + number: int | float, + lower_bound: int | float, + upper_bound: int | float, +) -> int: + if lower_bound > upper_bound: + msg = 'Lower bound should be less than or equal to upper bound' + raise ValueError(msg) + return max(lower_bound, min(number, upper_bound)) diff --git a/loading_pipeline/lib/misc/math_test.py b/loading_pipeline/lib/misc/math_test.py new file mode 100644 index 0000000000..19e12d6bfc --- /dev/null +++ b/loading_pipeline/lib/misc/math_test.py @@ -0,0 +1,12 @@ +import unittest + +from loading_pipeline.lib.misc.math import constrain + + +class TestConstrainFunction(unittest.TestCase): + def test_constrain(self): + self.assertEqual(constrain(5, 0, 10), 5) + self.assertEqual(constrain(-3, 0, 10), 0) + self.assertEqual(constrain(15, 0, 10), 10) + with self.assertRaises(ValueError): + constrain(5, 10, 0) diff --git a/loading_pipeline/lib/misc/nested_field.py b/loading_pipeline/lib/misc/nested_field.py new file mode 100644 index 0000000000..43d39005bb --- /dev/null +++ b/loading_pipeline/lib/misc/nested_field.py @@ -0,0 +1,17 @@ +import hail as hl + + +def parse_nested_field(t: hl.MatrixTable | hl.Table, fields: str): + expression = t + # Behavior here allows only a single nested field. + # Additional nesting is considered to be part of the + # name of the field. e.g. `gnomadv4.1_AF`. + for field in fields.split('.', maxsplit=1): + # Select from multi-allelic list. + if field.endswith('#'): + expression = expression[field[:-1]][ + (t.a_index if hasattr(t, 'a_index') else 1) - 1 + ] + else: + expression = expression[field] + return expression diff --git a/loading_pipeline/lib/misc/nested_field_test.py b/loading_pipeline/lib/misc/nested_field_test.py new file mode 100644 index 0000000000..8d465187a5 --- /dev/null +++ b/loading_pipeline/lib/misc/nested_field_test.py @@ -0,0 +1,81 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.misc.nested_field import parse_nested_field + + +class TestConstrainFunction(unittest.TestCase): + def test_parse_nested_field(self): + ht = hl.Table.parallelize( + [ + { + 'locus': hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + 'alleles': ['A', 'C'], + 'a': hl.Struct(d=1), + 'b': hl.Struct(e=[2, 9]), + 'h': hl.Struct(**{'i.j': 1}), + 'a_index': 1, + }, + { + 'locus': hl.Locus( + contig='chr1', + position=2, + reference_genome='GRCh38', + ), + 'alleles': ['A', 'C'], + 'a': hl.Struct(d=3), + 'b': hl.Struct(e=[4, 5]), + 'h': hl.Struct(**{'i.j': 2}), + 'a_index': 1, + }, + ], + hl.tstruct( + locus=hl.tlocus('GRCh38'), + alleles=hl.tarray(hl.tstr), + a=hl.tstruct(d=hl.tint32), + b=hl.tstruct(e=hl.tarray(hl.tint32)), + h=hl.tstruct(**{'i.j': hl.tint32}), + a_index=hl.tint32, + ), + key=['locus', 'alleles'], + ) + ht = ht.select( + d=parse_nested_field(ht, 'a.d'), + e=parse_nested_field(ht, 'b.e#'), + f=parse_nested_field(ht, 'a'), + g=parse_nested_field(ht, 'h.i.j'), + ) + self.assertListEqual( + ht.collect(), + [ + hl.Struct( + locus=hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + alleles=['A', 'C'], + d=1, + e=2, + f=hl.Struct(d=1), + g=1, + ), + hl.Struct( + locus=hl.Locus( + contig='chr1', + position=2, + reference_genome='GRCh38', + ), + alleles=['A', 'C'], + d=3, + e=4, + f=hl.Struct(d=3), + g=2, + ), + ], + ) diff --git a/loading_pipeline/lib/misc/pedigree.py b/loading_pipeline/lib/misc/pedigree.py new file mode 100644 index 0000000000..50bc30e225 --- /dev/null +++ b/loading_pipeline/lib/misc/pedigree.py @@ -0,0 +1,200 @@ +import itertools +from dataclasses import dataclass, field +from enum import Enum + +import hail as hl +import numpy as np + +from loading_pipeline.lib.core import Sex + +DEFAULT_RELATEDNESS_TOLERANCE = 0.2 +PARENT_CHILD_RELATEDNESS_TOLERANCE = 0.4 + + +class Relation(Enum): + PARENT_CHILD = 'parent_child' + GRANDPARENT_GRANDCHILD = 'grandparent_grandchild' + SIBLING = 'sibling' + HALF_SIBLING = 'half_sibling' + AUNT_NEPHEW = 'aunt_nephew' + + @property + def coefficients(self): + return { + Relation.PARENT_CHILD: [0, 1, 0, 0.5], + Relation.GRANDPARENT_GRANDCHILD: [0.5, 0.5, 0, 0.25], + Relation.SIBLING: [0.25, 0.5, 0.25, 0.5], + Relation.HALF_SIBLING: [0.5, 0.5, 0, 0.25], + Relation.AUNT_NEPHEW: [0.5, 0.5, 0, 0.25], + }[self] + + def coefficients_equal(self, coefficients: list[float]) -> bool: + if self == Relation.PARENT_CHILD: + return np.allclose( + coefficients[0], + self.coefficients[0], + atol=0.025, + ) and np.allclose( + coefficients[1:], + self.coefficients[1:], + atol=DEFAULT_RELATEDNESS_TOLERANCE, + ) + return np.allclose( + coefficients, + self.coefficients, + atol=DEFAULT_RELATEDNESS_TOLERANCE, + ) + + +@dataclass +class Sample: + sample_id: str + sex: Sex + mother: str = None + father: str = None + maternal_grandmother: str = None + maternal_grandfather: str = None + paternal_grandmother: str = None + paternal_grandfather: str = None + siblings: list[str] = field(default_factory=list) + half_siblings: list[str] = field(default_factory=list) + aunt_nephews: list[str] = field(default_factory=list) + + def is_aunt_nephew(self: 'Sample', other: 'Sample') -> bool: + return ( + # My Maternal Grandparents are your Parents + self.maternal_grandmother + and self.maternal_grandfather + and (self.maternal_grandmother == other.mother) + and (self.maternal_grandfather == other.father) + ) or ( + # My Paternal Grandparents are your Parents + self.paternal_grandmother + and self.paternal_grandfather + and (self.paternal_grandmother == other.mother) + and (self.paternal_grandfather == other.father) + ) + + def is_in_direct_lineage(self: 'Sample', other: 'Sample') -> bool: + return self.sample_id in { + other.mother, + other.father, + other.maternal_grandmother, + other.maternal_grandfather, + other.paternal_grandmother, + other.paternal_grandfather, + } or other.sample_id in { + self.mother, + self.father, + self.maternal_grandmother, + self.maternal_grandfather, + self.paternal_grandmother, + self.paternal_grandfather, + } + + +@dataclass +class Family: + family_guid: str + samples: dict[str, Sample] + + def __hash__(self): + return hash(self.family_guid) + + def __eq__(self, other): + return self.family_guid == other.family_guid + + @staticmethod + def parse_direct_lineage(rows: list[hl.Struct]) -> dict[str, Sample]: + samples = {} + for row in rows: + samples[row.s] = Sample( + sample_id=row.s, + sex=Sex(row.sex), + mother=row.maternal_s, + father=row.paternal_s, + ) + + for row in rows: + # Maternal GrandParents + maternal_s = samples[row.s].mother + if maternal_s and maternal_s in samples: + if samples[maternal_s].mother: + samples[row.s].maternal_grandmother = samples[maternal_s].mother + if samples[maternal_s].father: + samples[row.s].maternal_grandfather = samples[maternal_s].father + + # Paternal GrandParents + paternal_s = samples[row.s].father + if paternal_s and paternal_s in samples: + if samples[paternal_s].mother: + samples[row.s].paternal_grandmother = samples[paternal_s].mother + if samples[paternal_s].father: + samples[row.s].paternal_grandfather = samples[paternal_s].father + return samples + + @staticmethod + def parse_collateral_lineage( + samples: dict[str, Sample], + ) -> dict[str, Sample]: + # NB: relationships are identified unidirectionally here (for better or for worse) + # A sample_i that is siblings with sample_j, will list sample_j as as sibling, but + # sample_j will not list sample_i as a sibling. Relationships only appear in the + # ibd table a single time, so we only need to check the pairing once. + for sample_i, sample_j in itertools.combinations(samples.values(), 2): + # If sample is already related from direct relationships, continue + if sample_i.is_in_direct_lineage(sample_j): + continue + + # If both parents are identified and the same, samples are siblings. + if ( + sample_i.mother + and sample_i.father + and (sample_i.mother == sample_j.mother) + and (sample_i.father == sample_j.father) + ): + sample_i.siblings.append(sample_j.sample_id) + continue + + # If only a single parent is identified and the same, samples are half siblings + if (sample_i.mother and sample_i.mother == sample_j.mother) or ( + sample_i.father and sample_i.father == sample_j.father + ): + sample_i.half_siblings.append(sample_j.sample_id) + continue + + # If either set of one's grandparents is identified and equal to the other's parents, + # they're aunt/uncle related + # NB: because we will only check an i, j pair of samples a single time, (itertools.combinations) + # we need to check both grandparents_i == parents_j and parents_i == grandparents_j. + if sample_i.is_aunt_nephew(sample_j) or sample_j.is_aunt_nephew(sample_i): + sample_i.aunt_nephews.append(sample_j.sample_id) + return samples + + @classmethod + def parse(cls, family_guid: str, rows: list[hl.Struct]) -> 'Family': + samples = cls.parse_direct_lineage(rows) + samples = cls.parse_collateral_lineage(samples) + return cls( + family_guid=family_guid, + samples=samples, + ) + + +def parse_pedigree_ht_to_families( + pedigree_ht: hl.Table, +) -> set[Family]: + families = set() + for family_guid, rows in itertools.groupby( + sorted(pedigree_ht.collect(), key=lambda x: x.family_guid), + lambda x: x.family_guid, + ): + families.add(Family.parse(family_guid, list(rows))) + return families + + +def parse_pedigree_ht_to_remap_ht(pedigree_ht: hl.Table) -> hl.Table: + ht = pedigree_ht.filter(hl.is_defined(pedigree_ht.remap_id)) + ht = ht.annotate(seqr_id=ht.s) + ht = ht.key_by(s=ht.remap_id) + return ht.select('seqr_id') diff --git a/loading_pipeline/lib/misc/pedigree_test.py b/loading_pipeline/lib/misc/pedigree_test.py new file mode 100644 index 0000000000..77432ba138 --- /dev/null +++ b/loading_pipeline/lib/misc/pedigree_test.py @@ -0,0 +1,514 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.core import Sex +from loading_pipeline.lib.misc.io import import_pedigree +from loading_pipeline.lib.misc.pedigree import ( + Family, + Sample, + parse_pedigree_ht_to_families, +) + +TEST_PEDIGREE_1 = 'loading_pipeline/var/test/pedigrees/test_pedigree_1.tsv' +TEST_PEDIGREE_2 = 'loading_pipeline/var/test/pedigrees/test_pedigree_2.tsv' +TEST_PEDIGREE_9 = 'loading_pipeline/var/test/pedigrees/test_pedigree_9.tsv' + + +class PedigreesTest(unittest.TestCase): + def test_empty_pedigree(self) -> None: + with self.assertRaises(Exception): # noqa: B017 + _ = import_pedigree(TEST_PEDIGREE_1) + + def test_parse_lineage(self) -> None: + # + # + # sample_9 sample_10 sample_7 + # \ / \ | + # sample_6 -> sample_8 --------- sample_3 ----- ? | + # \ / \ / | + # sample_4, sample_5 sample_2 | sample_1 + # + # + samples = Family.parse_direct_lineage( + [ + hl.Struct(s='sample_1', maternal_s=None, paternal_s=None, sex='F'), + hl.Struct( + s='sample_2', + maternal_s='sample_3', + paternal_s=None, + sex='M', + ), + hl.Struct( + s='sample_3', + maternal_s=None, + paternal_s='sample_7', + sex='F', + ), + hl.Struct( + s='sample_4', + maternal_s='sample_3', + paternal_s='sample_8', + sex='M', + ), + hl.Struct( + s='sample_5', + maternal_s='sample_3', + paternal_s='sample_8', + sex='M', + ), + hl.Struct( + s='sample_6', + maternal_s='sample_9', + paternal_s='sample_10', + sex='M', + ), + hl.Struct(s='sample_7', maternal_s=None, paternal_s=None, sex='M'), + hl.Struct( + s='sample_8', + maternal_s='sample_9', + paternal_s='sample_10', + sex='F', + ), + hl.Struct(s='sample_9', maternal_s=None, paternal_s=None, sex='F'), + hl.Struct(s='sample_10', maternal_s=None, paternal_s=None, sex='M'), + ], + ) + self.assertEqual( + Family.parse_collateral_lineage(samples), + { + 'sample_1': Sample( + sample_id='sample_1', + sex=Sex.FEMALE, + mother=None, + father=None, + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'sample_2': Sample( + sample_id='sample_2', + sex=Sex.MALE, + mother='sample_3', + father=None, + maternal_grandmother=None, + maternal_grandfather='sample_7', + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=['sample_4', 'sample_5'], + aunt_nephews=[], + ), + 'sample_3': Sample( + sample_id='sample_3', + sex=Sex.FEMALE, + mother=None, + father='sample_7', + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'sample_4': Sample( + sample_id='sample_4', + sex=Sex.MALE, + mother='sample_3', + father='sample_8', + maternal_grandmother=None, + maternal_grandfather='sample_7', + paternal_grandmother='sample_9', + paternal_grandfather='sample_10', + siblings=['sample_5'], + half_siblings=[], + aunt_nephews=['sample_6'], + ), + 'sample_5': Sample( + sample_id='sample_5', + sex=Sex.MALE, + mother='sample_3', + father='sample_8', + maternal_grandmother=None, + maternal_grandfather='sample_7', + paternal_grandmother='sample_9', + paternal_grandfather='sample_10', + siblings=[], + half_siblings=[], + aunt_nephews=['sample_6'], + ), + 'sample_6': Sample( + sample_id='sample_6', + sex=Sex.MALE, + mother='sample_9', + father='sample_10', + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=['sample_8'], + half_siblings=[], + aunt_nephews=[], + ), + 'sample_7': Sample( + sample_id='sample_7', + sex=Sex.MALE, + mother=None, + father=None, + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'sample_8': Sample( + sample_id='sample_8', + sex=Sex.FEMALE, + mother='sample_9', + father='sample_10', + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'sample_9': Sample( + sample_id='sample_9', + sex=Sex.FEMALE, + mother=None, + father=None, + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'sample_10': Sample( + sample_id='sample_10', + sex=Sex.MALE, + mother=None, + father=None, + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + }, + ) + + def test_parse_parent_not_aunt_uncle(self) -> None: + samples = Family.parse_direct_lineage( + [ + hl.Struct(s='sample_1', maternal_s=None, paternal_s=None, sex='F'), + hl.Struct( + s='sample_2', + maternal_s=None, + paternal_s=None, + sex='M', + ), + hl.Struct( + s='sample_3', + maternal_s='sample_1', + paternal_s='sample_2', + sex='F', + ), + hl.Struct( + s='sample_4', + maternal_s='sample_3', + paternal_s=None, + sex='F', + ), + hl.Struct( + s='sample_5', + maternal_s='sample_3', + paternal_s=None, + sex='F', + ), + ], + ) + self.assertEqual( + Family.parse_collateral_lineage(samples), + { + 'sample_1': Sample( + sample_id='sample_1', + sex=Sex.FEMALE, + mother=None, + father=None, + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'sample_2': Sample( + sample_id='sample_2', + sex=Sex.MALE, + mother=None, + father=None, + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'sample_3': Sample( + sample_id='sample_3', + sex=Sex.FEMALE, + mother='sample_1', + father='sample_2', + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'sample_4': Sample( + sample_id='sample_4', + sex=Sex.FEMALE, + mother='sample_3', + father=None, + maternal_grandmother='sample_1', + maternal_grandfather='sample_2', + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=['sample_5'], + aunt_nephews=[], + ), + 'sample_5': Sample( + sample_id='sample_5', + sex=Sex.FEMALE, + mother='sample_3', + father=None, + maternal_grandmother='sample_1', + maternal_grandfather='sample_2', + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + }, + ) + + def test_parse_project(self) -> None: + pedigree_ht = import_pedigree(TEST_PEDIGREE_2) + self.assertCountEqual( + list(parse_pedigree_ht_to_families(pedigree_ht)), + [ + Family( + family_guid='BBL_BC1-000345_1', + samples={ + 'BBL_BC1-000345_01_D1': Sample( + sample_id='BBL_BC1-000345_01_D1', + sex=Sex.UNKNOWN, + mother='BBL_BC1-000345_03_D1', + father='BBL_BC1-000345_02_D1', + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'BBL_BC1-000345_02_D1': Sample( + sample_id='BBL_BC1-000345_02_D1', + sex=Sex.MALE, + mother=None, + father=None, + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'BBL_BC1-000345_03_D1': Sample( + sample_id='BBL_BC1-000345_03_D1', + sex=Sex.FEMALE, + mother=None, + father=None, + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + }, + ), + Family( + family_guid='BBL_HT-007-5195_1', + samples={ + 'BBL_HT-007-5195_01_D1': Sample( + sample_id='BBL_HT-007-5195_01_D1', + sex=Sex.FEMALE, + mother='BBL_HT-007-5195_03_D1', + father='BBL_HT-007-5195_02_D1', + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[ + 'BBL_HT-007-5195_04_D1', + 'BBL_HT-007-5195_05_D1', + 'BBL_HT-007-5195_06_D1', + ], + half_siblings=[], + aunt_nephews=[], + ), + 'BBL_HT-007-5195_02_D1': Sample( + sample_id='BBL_HT-007-5195_02_D1', + sex=Sex.MALE, + mother=None, + father=None, + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'BBL_HT-007-5195_03_D1': Sample( + sample_id='BBL_HT-007-5195_03_D1', + sex=Sex.FEMALE, + mother=None, + father=None, + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'BBL_HT-007-5195_04_D1': Sample( + sample_id='BBL_HT-007-5195_04_D1', + sex=Sex.MALE, + mother='BBL_HT-007-5195_03_D1', + father='BBL_HT-007-5195_02_D1', + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=['BBL_HT-007-5195_05_D1', 'BBL_HT-007-5195_06_D1'], + half_siblings=[], + aunt_nephews=[], + ), + 'BBL_HT-007-5195_05_D1': Sample( + sample_id='BBL_HT-007-5195_05_D1', + sex=Sex.FEMALE, + mother='BBL_HT-007-5195_03_D1', + father='BBL_HT-007-5195_02_D1', + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=['BBL_HT-007-5195_06_D1'], + half_siblings=[], + aunt_nephews=[], + ), + 'BBL_HT-007-5195_06_D1': Sample( + sample_id='BBL_HT-007-5195_06_D1', + sex=Sex.MALE, + mother='BBL_HT-007-5195_03_D1', + father='BBL_HT-007-5195_02_D1', + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + }, + ), + Family( + family_guid='BBL_SDS1-000178_1', + samples={ + 'BBL_SDS1-000178_01_D1': Sample( + sample_id='BBL_SDS1-000178_01_D1', + sex=Sex.FEMALE, + mother=None, + father=None, + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + }, + ), + ], + ) + + def test_subsetted_pedigree_with_removed_parent(self) -> None: + pedigree_ht = import_pedigree(TEST_PEDIGREE_2) + pedigree_ht = pedigree_ht.filter( + pedigree_ht.s != 'BBL_BC1-000345_02_D1', + ) + parsed_pedigree = parse_pedigree_ht_to_families(pedigree_ht) + family = next( + iter( + [ + family + for family in parsed_pedigree + if family.family_guid == 'BBL_BC1-000345_1' + ], + ), + ) + self.assertEqual(len(family.samples), 2) + self.assertFalse( + 'BBL_BC1-000345_02_D1' in family.samples, + ) + self.assertEqual( + family.samples['BBL_BC1-000345_01_D1'].father, + 'BBL_BC1-000345_02_D1', + ) + self.assertEqual( + family.samples['BBL_BC1-000345_01_D1'].mother, + 'BBL_BC1-000345_03_D1', + ) + + def test_pedigree_ungrouped_families(self) -> None: + pedigree_ht = import_pedigree(TEST_PEDIGREE_9) + parsed_pedigree = parse_pedigree_ht_to_families(pedigree_ht) + self.assertEqual(len(parsed_pedigree), 2) + family = next( + iter( + [ + family + for family in parsed_pedigree + if family.family_guid == 'family_2_1' + ], + ), + ) + self.assertTrue( + family.samples.keys() == {'RGP_164_1', 'RGP_164_2', 'RGP_164_4'}, + ) diff --git a/loading_pipeline/lib/misc/requests.py b/loading_pipeline/lib/misc/requests.py new file mode 100644 index 0000000000..e0ee66f366 --- /dev/null +++ b/loading_pipeline/lib/misc/requests.py @@ -0,0 +1,14 @@ +import requests +from requests.adapters import HTTPAdapter, Retry + + +def requests_retry_session(): + s = requests.Session() + retries = Retry( + total=5, + backoff_factor=1, + status_forcelist=[500, 502, 503, 504], + ) + s.mount('http://', HTTPAdapter(max_retries=retries)) + s.mount('https://', HTTPAdapter(max_retries=retries)) + return s diff --git a/loading_pipeline/lib/misc/retry.py b/loading_pipeline/lib/misc/retry.py new file mode 100644 index 0000000000..3a9408b075 --- /dev/null +++ b/loading_pipeline/lib/misc/retry.py @@ -0,0 +1,61 @@ +import functools +import time + +from loading_pipeline.lib.logger import get_logger + +logger = get_logger(__name__) + + +def retry(tries=3, delay=30, backoff=3): + def decorator(func): + @functools.wraps(func) + def wrapper(*args, **kwargs): + max_tries = tries + current_delay = delay + total_start_time = time.time() + args_str = ', '.join(str(a) for a in args) + kwargs_str = ', '.join(f'{k}={v!s}' for k, v in kwargs.items()) + + for attempt in range(1, max_tries): + start_time = time.time() + try: + result = func(*args, **kwargs) + duration = time.time() - start_time + logger.info( + f'{func.__name__} args:{args_str} kwargs:{kwargs_str} succeeded on attempt {attempt} in {duration:.2f}s', + ) + except Exception: + duration = time.time() - start_time + logger.exception( + f'{func.__name__} args:{args_str} kwargs:{kwargs_str} failed on attempt {attempt} after {duration:.2f}s, ' + f'retrying in {current_delay} seconds.', + ) + time.sleep(current_delay) + current_delay *= backoff + else: + return result + + # Final attempt + start_time = time.time() + try: + result = func(*args, **kwargs) + duration = time.time() - start_time + total_duration = time.time() - total_start_time + logger.info( + f'{func.__name__} args:{args_str} kwargs:{kwargs_str} succeeded on final attempt {max_tries} in {duration:.2f}s ' + f'(total retry time: {total_duration:.2f}s)', + ) + except Exception: + duration = time.time() - start_time + total_duration = time.time() - total_start_time + logger.exception( + f'{func.__name__} args:{args_str} kwargs:{kwargs} failed on final attempt {max_tries} after {duration:.2f}s ' + f'(total retry time: {total_duration:.2f}s)', + ) + raise + else: + return result + + return wrapper + + return decorator diff --git a/loading_pipeline/lib/misc/retry_test.py b/loading_pipeline/lib/misc/retry_test.py new file mode 100644 index 0000000000..4b756abce1 --- /dev/null +++ b/loading_pipeline/lib/misc/retry_test.py @@ -0,0 +1,69 @@ +import unittest +from unittest.mock import Mock, patch + +from loading_pipeline.lib.core import DatasetType +from loading_pipeline.lib.misc.retry import retry + + +class TestRetryDecorator(unittest.TestCase): + @patch('time.sleep', return_value=None) + def test_retry_success_first_try(self, mock_sleep): + mock_func = Mock(return_value='success') + + @retry(tries=3, delay=1, backoff=2) + def func(d: DatasetType): + return mock_func(d) + + result = func(DatasetType.SNV_INDEL) + self.assertEqual(result, 'success') + self.assertEqual(mock_func.call_count, 1) + mock_sleep.assert_not_called() + + @patch('time.sleep', return_value=None) + @patch('loading_pipeline.lib.misc.retry.logger') + def test_retry_eventual_success(self, mock_logger, mock_sleep): + mock_func = Mock( + side_effect=[Exception('fail'), Exception('fail again'), 'success'], + ) + + @retry(tries=3, delay=1, backoff=2) + def func(): + return mock_func() + + result = func() + self.assertEqual(result, 'success') + self.assertEqual(mock_func.call_count, 3) + self.assertEqual(mock_sleep.call_count, 2) + mock_sleep.assert_any_call(1) + mock_sleep.assert_any_call(2) + + @patch('time.sleep', return_value=None) + @patch('loading_pipeline.lib.misc.retry.logger') + def test_retry_all_failures(self, mock_logger, mock_sleep): + mock_func = Mock(side_effect=Exception('always fails')) + + @retry(tries=3, delay=1, backoff=2) + def func(): + return mock_func() + + with self.assertRaises(Exception) as context: + func() + + self.assertEqual(str(context.exception), 'always fails') + self.assertEqual(mock_func.call_count, 3) + self.assertEqual(mock_sleep.call_count, 2) + + @patch('time.sleep', return_value=None) + @patch('loading_pipeline.lib.misc.retry.logger.exception') + def test_logs_retry_message(self, mock_log, mock_sleep): + mock_func = Mock(side_effect=[Exception('fail'), 'success']) + + @retry(tries=2, delay=1, backoff=2) + def func(d: DatasetType): + return mock_func(d) + + func(d=DatasetType.SNV_INDEL) + self.assertIn( + 'func args: kwargs:d=SNV_INDEL failed on attempt 1 after 0.00s, retrying in 1 seconds.', + mock_log.call_args[0][0], + ) diff --git a/loading_pipeline/lib/misc/runs.py b/loading_pipeline/lib/misc/runs.py new file mode 100644 index 0000000000..702f86d94c --- /dev/null +++ b/loading_pipeline/lib/misc/runs.py @@ -0,0 +1,89 @@ +import datetime +import os +from collections import defaultdict + +import hailtop.fs as hfs + +from loading_pipeline.lib.core.dataset_type import DatasetType +from loading_pipeline.lib.core.environment import Env +from loading_pipeline.lib.misc.retry import retry +from loading_pipeline.lib.paths import ( + clickhouse_load_fail_file_path, + clickhouse_load_success_file_path, + loading_pipeline_queue_dir, + pipeline_run_success_file_path, +) + + +def new_run_id(): + return datetime.datetime.now(datetime.UTC).strftime( + '%Y%m%d-%H%M%S-%f', + ) + + +def get_oldest_queue_path() -> str | None: + """ + Returns the path of the oldest loading pipeline request file in the queue directory. + If the directory is empty, returns None. + """ + queue_dir = loading_pipeline_queue_dir() + queue_files = os.listdir(queue_dir) + + if len(queue_files) == 0: + return None + queue_files = [os.path.join(queue_dir, queue_file) for queue_file in queue_files] + return min(queue_files, key=os.path.getctime) + + +def is_queue_full() -> bool: + """ + Checks if the loading pipeline queue directory is full. + Returns True if the number of files exceeds a predefined limit, otherwise False. + """ + return len(os.listdir(loading_pipeline_queue_dir())) >= Env.LOADING_QUEUE_LIMIT + + +@retry() +def get_run_ids() -> tuple[defaultdict, defaultdict, defaultdict]: + successful_pipeline_runs, successful_clickhouse_loads, failed_clickhouse_loads = ( + defaultdict(set), + defaultdict(set), + defaultdict(set), + ) + for dataset_type in DatasetType: + for reference_genome in dataset_type.reference_genomes: + successful_pipeline_runs[(reference_genome, dataset_type)] = { + p.path.split('/')[-2] + for p in hfs.ls( + pipeline_run_success_file_path( + reference_genome, + dataset_type, + '*', + ), + ) + } + successful_clickhouse_loads[(reference_genome, dataset_type)] = { + p.path.split('/')[-2] + for p in hfs.ls( + clickhouse_load_success_file_path( + reference_genome, + dataset_type, + '*', + ), + ) + } + failed_clickhouse_loads[(reference_genome, dataset_type)] = { + p.path.split('/')[-2] + for p in hfs.ls( + clickhouse_load_fail_file_path( + reference_genome, + dataset_type, + '*', + ), + ) + } + return ( + successful_pipeline_runs, + successful_clickhouse_loads, + failed_clickhouse_loads, + ) diff --git a/loading_pipeline/lib/misc/runs_test.py b/loading_pipeline/lib/misc/runs_test.py new file mode 100644 index 0000000000..b1a601727a --- /dev/null +++ b/loading_pipeline/lib/misc/runs_test.py @@ -0,0 +1,84 @@ +import os + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome +from loading_pipeline.lib.misc.runs import get_run_ids +from loading_pipeline.lib.paths import ( + clickhouse_load_fail_file_path, + clickhouse_load_success_file_path, + pipeline_run_success_file_path, + runs_path, +) +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + + +class RunsTest(MockedDatarootTestCase): + def setUp(self): + super().setUp() + run_ids = [ + 'manual__2024-08-05T16-07-58.365146+00-00', + 'manual__2024-08-06T10-15-23.123456+00-00', + 'manual__2024-08-07T12-30-45.654321+00-00', # _SUCCESS, _CLICKHOUSE_LOAD_FAIL + 'manual__2024-08-08T09-45-00.000000+00-00', # _SUCCESS + 'manual__2024-08-09T18-22-13.999999+00-00', # _SUCCESS, _CLICKHOUSE_LOAD_SUCCESS + ] + for reference_genome, dataset_type in [ + (ReferenceGenome.GRCh38, DatasetType.SNV_INDEL), + (ReferenceGenome.GRCh37, DatasetType.SNV_INDEL), + (ReferenceGenome.GRCh38, DatasetType.GCNV), + (ReferenceGenome.GRCh37, DatasetType.GCNV), + ]: + for run_id in run_ids: + base_path = runs_path(reference_genome, dataset_type) + os.makedirs(os.path.join(base_path, run_id), exist_ok=True) + if '07T12' in run_id: + failure_file = clickhouse_load_fail_file_path( + reference_genome, + dataset_type, + run_id, + ) + open(failure_file, 'w').close() + if '09' in run_id or '07T12' in run_id: + success_file = pipeline_run_success_file_path( + reference_genome, + dataset_type, + run_id, + ) + open(success_file, 'w').close() + if '09T18' in run_id: + success_file = clickhouse_load_success_file_path( + reference_genome, + dataset_type, + run_id, + ) + open(success_file, 'w').close() + + def test_get_run_ids(self) -> None: + ( + successful_pipeline_runs, + successful_clickhouse_loads, + failed_clickhouse_loads, + ) = get_run_ids() + self.assertCountEqual( + successful_pipeline_runs[(ReferenceGenome.GRCh38, DatasetType.SNV_INDEL)], + { + 'manual__2024-08-09T18-22-13.999999+00-00', + 'manual__2024-08-08T09-45-00.000000+00-00', + 'manual__2024-08-07T12-30-45.654321+00-00', + }, + ) + self.assertCountEqual( + successful_clickhouse_loads[ + (ReferenceGenome.GRCh38, DatasetType.SNV_INDEL) + ], + { + 'manual__2024-08-09T18-22-13.999999+00-00', + }, + ) + self.assertCountEqual( + successful_clickhouse_loads[(ReferenceGenome.GRCh37, DatasetType.GCNV)], + {}, + ) + self.assertCountEqual( + failed_clickhouse_loads[(ReferenceGenome.GRCh38, DatasetType.SNV_INDEL)], + {'manual__2024-08-07T12-30-45.654321+00-00'}, + ) diff --git a/loading_pipeline/lib/misc/sample_ids.py b/loading_pipeline/lib/misc/sample_ids.py new file mode 100644 index 0000000000..f86ef4ef67 --- /dev/null +++ b/loading_pipeline/lib/misc/sample_ids.py @@ -0,0 +1,66 @@ +from collections import Counter + +import hail as hl + +from loading_pipeline.lib.logger import get_logger +from loading_pipeline.lib.misc.validation import SeqrValidationError + +logger = get_logger(__name__) + + +def remap_sample_ids( + mt: hl.MatrixTable, + project_remap_ht: hl.Table, +) -> hl.MatrixTable: + collected_remap = project_remap_ht.collect() + s_dups = [k for k, v in Counter([r.s for r in collected_remap]).items() if v > 1] + seqr_dups = [ + k for k, v in Counter([r.seqr_id for r in collected_remap]).items() if v > 1 + ] + + if len(s_dups) > 0 or len(seqr_dups) > 0: + msg = f'Duplicate s or seqr_id entries in remap file were found. Duplicate s:{s_dups}. Duplicate seqr_id:{seqr_dups}.' + raise SeqrValidationError(msg) + + missing_samples = project_remap_ht.anti_join(mt.cols()).collect() + remap_count = len(collected_remap) + + if len(missing_samples) != 0: + message = ( + f'Only {project_remap_ht.semi_join(mt.cols()).count()} out of {remap_count} ' + 'remap IDs matched IDs in the variant callset.\n' + f"IDs that aren't in the callset: {missing_samples}\n" + ) + raise SeqrValidationError(message) + + mt = mt.annotate_cols(**project_remap_ht[mt.s]) + remap_expr = hl.if_else(hl.is_missing(mt.seqr_id), mt.s, mt.seqr_id) + mt = mt.annotate_cols(seqr_id=remap_expr, vcf_id=mt.s) + mt = mt.key_cols_by(s=mt.seqr_id) + logger.info(f'Remapped {remap_count} sample ids...') + return mt + + +def subset_samples( + mt: hl.MatrixTable, + sample_subset_ht: hl.Table, +) -> hl.MatrixTable: + subset_count = sample_subset_ht.count() + anti_join_ht = sample_subset_ht.anti_join(mt.cols()) + anti_join_ht_count = anti_join_ht.count() + if subset_count == 0: + message = '0 sample ids found the subset HT, something is probably wrong.' + raise SeqrValidationError(message) + + if anti_join_ht_count != 0: + missing_samples = anti_join_ht.s.collect() + message = ( + f'Only {subset_count - anti_join_ht_count} out of {subset_count} ' + f'subsetting-table IDs matched IDs in the variant callset.\n' + f"IDs that aren't in the callset: {missing_samples}\n" + f'All callset sample IDs:{mt.s.collect()}' + ) + raise SeqrValidationError(message) + logger.info(f'Subsetted to {subset_count} sample ids') + mt = mt.semi_join_cols(sample_subset_ht) + return mt.filter_rows(hl.agg.any(hl.is_defined(mt.GT))) diff --git a/loading_pipeline/lib/misc/sample_ids_test.py b/loading_pipeline/lib/misc/sample_ids_test.py new file mode 100644 index 0000000000..6d3fb7efd0 --- /dev/null +++ b/loading_pipeline/lib/misc/sample_ids_test.py @@ -0,0 +1,160 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.misc.sample_ids import ( + remap_sample_ids, + subset_samples, +) +from loading_pipeline.lib.misc.validation import SeqrValidationError + +CALLSET_MT = hl.MatrixTable.from_parts( + rows={'variants': [1, 2]}, + cols={'s': ['HG00731', 'HG00732', 'HG00733']}, + entries={ + 'GT': [ + [hl.Call([0, 1]), hl.missing(hl.tcall), hl.Call([0, 1])], + [hl.Call([0, 1]), hl.Call([0, 1]), hl.Call([1, 1])], + ], + }, +).key_cols_by('s') + + +class SampleLookupTest(unittest.TestCase): + def test_remap_2_sample_ids(self) -> None: + # remap 2 of 3 samples in callset + project_remap_ht = hl.Table.parallelize( + [ + {'s': 'HG00731', 'seqr_id': 'HG00731_1'}, + {'s': 'HG00732', 'seqr_id': 'HG00732_1'}, + ], + hl.tstruct( + s=hl.tstr, + seqr_id=hl.tstr, + ), + key='s', + ) + + remapped_mt = remap_sample_ids( + CALLSET_MT, + project_remap_ht, + ) + + self.assertEqual(remapped_mt.cols().count(), 3) + self.assertEqual( + remapped_mt.cols().collect(), + [ + hl.Struct( + col_idx=0, + s='HG00731_1', + seqr_id='HG00731_1', + vcf_id='HG00731', + ), + hl.Struct( + col_idx=1, + s='HG00732_1', + seqr_id='HG00732_1', + vcf_id='HG00732', + ), + hl.Struct(col_idx=2, s='HG00733', seqr_id='HG00733', vcf_id='HG00733'), + ], + ) + + def test_remap_sample_ids_remap_has_duplicate(self) -> None: + # remap file has 2 rows for HG00732 + project_remap_ht = hl.Table.parallelize( + [ + {'s': 'HG00731', 'seqr_id': 'HG00731_1'}, + {'s': 'HG00732', 'seqr_id': 'HG00732_1'}, + {'s': 'HG00732', 'seqr_id': 'HG00732_1'}, # duplicate + ], + hl.tstruct( + s=hl.tstr, + seqr_id=hl.tstr, + ), + key='s', + ) + + with self.assertRaises(SeqrValidationError): + remap_sample_ids( + CALLSET_MT, + project_remap_ht, + ) + + def test_remap_sample_ids_remap_has_missing_samples(self) -> None: + # remap file has 4 rows, but only 3 samples in callset + project_remap_ht = hl.Table.parallelize( + [ + {'s': 'HG00731', 'seqr_id': 'HG00731_1'}, + {'s': 'HG00732', 'seqr_id': 'HG00732_1'}, + {'s': 'HG00733', 'seqr_id': 'HG00733_1'}, + {'s': 'HG00734', 'seqr_id': 'HG00734_1'}, # missing in callset + ], + hl.tstruct( + s=hl.tstr, + seqr_id=hl.tstr, + ), + key='s', + ) + + with self.assertRaises(SeqrValidationError): + remap_sample_ids( + CALLSET_MT, + project_remap_ht, + ) + + def test_subset_samples_zero_samples(self): + # subset 0 of 3 samples in callset + sample_subset_ht = hl.Table.parallelize( + [], + hl.tstruct(s=hl.tstr), + key='s', + ) + + with self.assertRaises(SeqrValidationError): + subset_samples( + CALLSET_MT, + sample_subset_ht, + ) + + def test_subset_samples_missing_samples(self): + # subset 2 of 3 samples in callset, but 1 is missing + sample_subset_ht = hl.Table.parallelize( + [ + {'s': 'HG00731'}, + {'s': 'HG00732'}, + {'s': 'HG00734'}, # missing in callset + ], + hl.tstruct(s=hl.tstr), + key='s', + ) + + with self.assertRaises(SeqrValidationError): + subset_samples( + CALLSET_MT, + sample_subset_ht, + ) + + def test_subset_no_defined_gt(self): + mt = hl.MatrixTable.from_parts( + rows={'variants': [1, 2]}, + cols={'s': ['HG00731', 'HG00732']}, + entries={ + 'GT': [ + [hl.Call([1, 1]), hl.missing(hl.tcall)], + [hl.Call([1, 1]), hl.Call([1, 1])], + ], + }, + ).key_cols_by('s') + sample_subset_ht = hl.Table.parallelize( + [ + {'s': 'HG00732'}, + ], + hl.tstruct(s=hl.tstr), + key='s', + ) + mt = subset_samples( + mt, + sample_subset_ht, + ) + self.assertEqual(mt.count(), (1, 1)) diff --git a/loading_pipeline/lib/misc/slack.py b/loading_pipeline/lib/misc/slack.py new file mode 100644 index 0000000000..ea17b12c99 --- /dev/null +++ b/loading_pipeline/lib/misc/slack.py @@ -0,0 +1,65 @@ +import json + +from slacker import Slacker + +from loading_pipeline.api.model import PipelineRunnerRequest +from loading_pipeline.lib.core import Env, FeatureFlag +from loading_pipeline.lib.logger import get_logger + +DATAPROC_URL = 'https://console.cloud.google.com/dataproc/jobs?project={gcloud_project}' +SLACK_FAILURE_MESSAGE_PREFIX = ':failed: Pipeline Runner Request Failed :failed:' +SLACK_SUCCESS_MESSAGE_PREFIX = ( + ':white_check_mark: Pipeline Runner Request Success! :white_check_mark:' +) + + +logger = get_logger(__name__) + + +def _safe_post_to_slack(message) -> None: + try: + if not Env.SLACK_TOKEN: + logger.info(message) + return + slack = Slacker(Env.SLACK_TOKEN) + slack.chat.post_message( + Env.SLACK_NOTIFICATION_CHANNEL, + message, + as_user=False, + icon_emoji=':beaker:', + username='Beaker (engineering-minion)', + ) + except Exception: + logger.exception( + f'Slack error: Original message in channel ({Env.SLACK_NOTIFICATION_CHANNEL}) - {message}', + ) + + +def safe_post_to_slack_failure( + run_id: str, + prr: PipelineRunnerRequest, + e: type[Exception], +) -> None: + message = [ + SLACK_FAILURE_MESSAGE_PREFIX, + f'Run ID: {run_id}', + f'```{json.dumps(prr.model_dump(), indent=4, sort_keys=True)}```', + f'Reason: {e!s}', + ] + if FeatureFlag.RUN_PIPELINE_ON_DATAPROC: + message = [ + *message, + f'<{DATAPROC_URL.format(gcloud_project=Env.GCLOUD_PROJECT)}|Dataproc Jobs Page>', + ] + _safe_post_to_slack('\n'.join(message)) + + +def safe_post_to_slack_success(run_id: str, prr: PipelineRunnerRequest) -> None: + message = '\n'.join( + [ + SLACK_SUCCESS_MESSAGE_PREFIX, + f'Run ID: {run_id}', + f'```{json.dumps(prr.model_dump(), indent=4, sort_keys=True)}```', + ], + ) + _safe_post_to_slack(message) diff --git a/loading_pipeline/lib/misc/sv.py b/loading_pipeline/lib/misc/sv.py new file mode 100644 index 0000000000..b3a54463f0 --- /dev/null +++ b/loading_pipeline/lib/misc/sv.py @@ -0,0 +1,155 @@ +import itertools +import math + +import hail as hl + +from loading_pipeline.lib.annotations import sv +from loading_pipeline.lib.core import ReferenceGenome, Sex +from loading_pipeline.lib.misc.pedigree import Family + +WRONG_CHROM_PENALTY = 1e9 + + +def _get_grouped_new_callset_variants( + mt: hl.MatrixTable, + duplicate_internal_variant_ids: set[str], +) -> itertools.groupby: + mt = mt.select_rows( + 'info.SEQR_INTERNAL_TRUTH_VID', + end_locus=sv.end_locus(mt), + ) + return itertools.groupby( + sorted( + mt.filter_rows( + duplicate_internal_variant_ids.contains( + mt['info.SEQR_INTERNAL_TRUTH_VID'], + ), + ) + .rows() + .collect(), + key=lambda x: x['info.SEQR_INTERNAL_TRUTH_VID'], + ), + lambda x: x['info.SEQR_INTERNAL_TRUTH_VID'], + ) + + +def deduplicate_merged_sv_concordance_calls( + mt: hl.MatrixTable, + annotations_ht: hl.Table, +) -> hl.MatrixTable: + # First find the seqr internal variant ids that are duplicated in the new callset. + duplicate_internal_variant_ids = hl.set( + { + k + for k, v in mt.aggregate_rows( + hl.agg.counter(mt['info.SEQR_INTERNAL_TRUTH_VID']), + ).items() + if v > 1 + } + or hl.empty_set(hl.tstr), + ) + + # Then, collect into memory the necessary existing variants & the new variants + annotations_ht = annotations_ht.select('end_locus') + existing_variants = { + v.variant_id: v + for v in ( + annotations_ht.filter( + duplicate_internal_variant_ids.contains(annotations_ht.variant_id), + ).collect() + ) + } + grouped_new_variants = _get_grouped_new_callset_variants( + mt, + duplicate_internal_variant_ids, + ) + + # Then, iterate over new variants and exclude all but the best match + new_variant_ids_to_exclude = set() + for existing_variant_id, new_variants in grouped_new_variants: + existing_variant = existing_variants[existing_variant_id] + closest_variant_id, min_distance = None, math.inf + + # First pass to find the closest variant + new_variants_it1, new_variants_it2 = itertools.tee(new_variants, 2) + for new_variant in new_variants_it1: + distance = math.fabs( + new_variant.end_locus.position + - existing_variant.end_locus.position + + ( + WRONG_CHROM_PENALTY + if ( + new_variant.end_locus.contig + != existing_variant.end_locus.contig + ) + else 0 + ), + ) + if distance < min_distance: + min_distance = distance + closest_variant_id = new_variant.variant_id + + # Second pass to exclude all but the closest. + for new_variant in new_variants_it2: + if new_variant.variant_id != closest_variant_id: + new_variant_ids_to_exclude.add(new_variant.variant_id) + + # Finally, remove SEQR_INTERNAL_TRUTH_VID from those variants. + return mt.annotate_rows( + **{ + 'info.SEQR_INTERNAL_TRUTH_VID': hl.if_else( + hl.set(new_variant_ids_to_exclude or hl.empty_set(hl.tstr)).contains( + mt.variant_id, + ), + hl.missing(hl.tstr), + mt['info.SEQR_INTERNAL_TRUTH_VID'], + ), + }, + ) + + +def overwrite_male_non_par_calls( + mt: hl.MatrixTable, + families: set[Family], +) -> hl.MatrixTable: + male_sample_ids = { + s.sample_id for f in families for s in f.samples.values() if s.sex == Sex.MALE + } + male_sample_ids = ( + hl.set(male_sample_ids) if male_sample_ids else hl.empty_set(hl.tstr) + ) + par_intervals = hl.array( + [ + i + for i in hl.get_reference(ReferenceGenome.GRCh38).par + if i.start.contig == ReferenceGenome.GRCh38.x_contig + ], + ) + non_par_interval = hl.interval( + par_intervals[0].end, + par_intervals[1].start, + ) + # NB: making use of existing formatting_annotation_fns. + # We choose to annotate & drop here as the sample level + # fields are dropped by the time we format variants. + mt = mt.annotate_rows( + start_locus=sv.start_locus(mt), + end_locus=sv.end_locus(mt), + ) + mt = mt.annotate_entries( + GT=hl.if_else( + ( + male_sample_ids.contains(mt.s) + & non_par_interval.overlaps( + hl.interval( + mt.start_locus, + mt.end_locus, + ), + ) + & mt.GT.is_het() + ), + hl.Call([1], phased=False), + mt.GT, + ), + ) + return mt.drop('start_locus', 'end_locus') diff --git a/loading_pipeline/lib/misc/sv_test.py b/loading_pipeline/lib/misc/sv_test.py new file mode 100644 index 0000000000..aefa8a5cd5 --- /dev/null +++ b/loading_pipeline/lib/misc/sv_test.py @@ -0,0 +1,243 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, Sex +from loading_pipeline.lib.misc.io import import_callset, select_relevant_fields +from loading_pipeline.lib.misc.pedigree import Family, Sample +from loading_pipeline.lib.misc.sample_ids import subset_samples +from loading_pipeline.lib.misc.sv import ( + deduplicate_merged_sv_concordance_calls, + overwrite_male_non_par_calls, +) + +TEST_SV_VCF = 'loading_pipeline/var/test/callsets/sv_1.vcf' +ANNOTATIONS_HT = hl.Table.parallelize( + [ + { + 'variant_id': 'BND_chr1_6', + 'algorithms': 'manta', + 'end_locus': hl.Locus( + contig='chr5', + position=20404, + reference_genome='GRCh38', + ), + }, + { + 'variant_id': 'BND_chr1_9', + 'algorithms': 'manta', + 'end_locus': hl.Locus( + contig='chr1', + position=789481, + reference_genome='GRCh38', + ), + }, + { + 'variant_id': 'CPX_chr1_22', + 'algorithms': 'manta', + 'end_locus': hl.Locus( + contig='chr1', + position=6559723, + reference_genome='GRCh38', + ), + }, + ], + hl.tstruct( + variant_id=hl.tstr, + algorithms=hl.tstr, + end_locus=hl.tlocus('GRCh38'), + ), + key='variant_id', +) + + +class SVTest(unittest.TestCase): + def test_overwrite_male_non_par_calls(self) -> None: + mt = import_callset(TEST_SV_VCF, ReferenceGenome.GRCh38, DatasetType.SV) + mt = select_relevant_fields( + mt, + DatasetType.SV, + ) + mt = subset_samples( + mt, + hl.Table.parallelize( + [{'s': sample_id} for sample_id in ['RGP_164_1', 'RGP_164_2']], + hl.tstruct(s=hl.dtype('str')), + key='s', + ), + ) + mt = overwrite_male_non_par_calls( + mt, + { + Family( + family_guid='family_1', + samples={ + 'RGP_164_1': Sample(sample_id='RGP_164_1', sex=Sex.FEMALE), + 'RGP_164_2': Sample(sample_id='RGP_164_2', sex=Sex.MALE), + }, + ), + }, + ) + mt = mt.filter_rows(mt.locus.contig == 'chrX') + self.assertEqual( + [ + hl.Locus(contig='chrX', position=3, reference_genome='GRCh38'), + hl.Locus(contig='chrX', position=2781700, reference_genome='GRCh38'), + ], + mt.locus.collect(), + ) + self.assertEqual( + [ + hl.Call(alleles=[0, 0], phased=False), + # END of this variant < start of the non-par region. + hl.Call(alleles=[0, 1], phased=False), + hl.Call(alleles=[0, 0], phased=False), + hl.Call(alleles=[1], phased=False), + ], + mt.GT.collect(), + ) + self.assertFalse( + hasattr(mt, 'start_locus'), + ) + + def test_deduplicate_merged_sv_concordance_calls(self) -> None: + mt = ( + hl.MatrixTable.from_parts( + rows={ + 'variant_id': [ + 'new_v1', + 'new_v2', + 'new_v3', + ], + 'locus': [ + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=2, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=3, + reference_genome='GRCh38', + ), + ], + 'info.END': [ + 1, + 2, + 3, + ], + 'info.END2': [ + 1, + 2, + 3, + ], + 'info.CHR2': [ + 'chr1', + 'chr1', + 'chr1', + ], + 'info.SEQR_INTERNAL_TRUTH_VID': [ + 'BND_chr1_6', + 'BND_chr1_9', + 'CPX_chr1_22', + ], + }, + cols={'s': ['sample_1']}, + entries={'GQ': [[99] for _ in range(3)]}, + ) + .key_rows_by('variant_id') + .key_cols_by('s') + ) + mt = deduplicate_merged_sv_concordance_calls( + mt, + ANNOTATIONS_HT, + ) + self.assertEqual( + mt['info.SEQR_INTERNAL_TRUTH_VID'].collect(), + [ + 'BND_chr1_6', + 'BND_chr1_9', + 'CPX_chr1_22', + ], + ) + + mt = ( + hl.MatrixTable.from_parts( + rows={ + 'variant_id': [ + 'new_v1', + 'new_v2', + 'new_v3', + 'new_v4', + ], + 'locus': [ + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=2, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=3, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=4, + reference_genome='GRCh38', + ), + ], + 'info.END': [ + 1, + 2, + 789481, + 789485, + ], + 'info.END2': [ + 1, + 2, + 789481, + 789485, + ], + 'info.CHR2': [ + 'chr1', + 'chr1', + 'chr2', + 'chr1', + ], + 'info.SEQR_INTERNAL_TRUTH_VID': [ + 'BND_chr1_6', + 'BND_chr1_9', + 'BND_chr1_9', + 'BND_chr1_9', + ], + }, + cols={'s': ['sample_1']}, + entries={'GQ': [[99] for _ in range(4)]}, + ) + .key_rows_by('variant_id') + .key_cols_by('s') + ) + mt = deduplicate_merged_sv_concordance_calls( + mt, + ANNOTATIONS_HT, + ) + self.assertEqual( + mt['info.SEQR_INTERNAL_TRUTH_VID'].collect(), + [ + 'BND_chr1_6', + None, + None, + 'BND_chr1_9', + ], + ) diff --git a/loading_pipeline/lib/misc/terra_data_repository.py b/loading_pipeline/lib/misc/terra_data_repository.py new file mode 100644 index 0000000000..0aa2204b8a --- /dev/null +++ b/loading_pipeline/lib/misc/terra_data_repository.py @@ -0,0 +1,80 @@ +import os +import re +from collections.abc import Generator +from concurrent.futures import ThreadPoolExecutor, as_completed + +import google.cloud.bigquery +from google.cloud import bigquery + +from loading_pipeline.lib.misc.gcp import get_service_account_credentials +from loading_pipeline.lib.misc.requests import requests_retry_session + +BIGQUERY_METRICS = [ + 'predicted_sex', + 'contamination_rate', + 'percent_bases_at_20x', + 'collaborator_sample_id', + 'mean_coverage', +] +BIGQUERY_RESOURCE = 'bigquery' +TABLE_NAME_VALIDATION_REGEX = r'datarepo-\w+.datarepo_\w+' +TDR_ROOT_URL = 'https://data.terra.bio/api/repository/v1/' + + +def _tdr_request(resource: str) -> dict: + service_account_token = get_service_account_credentials().token + s = requests_retry_session() + res = s.get( + url=os.path.join(TDR_ROOT_URL, resource), + headers={'Authorization': f'Bearer {service_account_token}'}, + timeout=10, + ) + res.raise_for_status() + return res.json() + + +def _get_dataset_ids() -> list[str]: + res_body = _tdr_request('datasets?limit=50000') # Arbitrary large number :/ + items = res_body['items'] + for item in items: + if not any(x['cloudResource'] == BIGQUERY_RESOURCE for x in item['storage']): + # Hard failure on purpose to prompt manual investigation. + msg = 'Datasets without bigquery sources are unsupported' + raise ValueError(msg) + return [x['id'] for x in items] + + +def gen_bq_table_names() -> Generator[str]: + with ThreadPoolExecutor(max_workers=5) as executor: + futures = [ + executor.submit( + _tdr_request, + f'datasets/{dataset_id}?include=ACCESS_INFORMATION', + ) + for dataset_id in _get_dataset_ids() + ] + for future in as_completed(futures): + result = future.result() + yield f'{result["accessInformation"]["bigQuery"]["projectId"]}.{result["accessInformation"]["bigQuery"]["datasetName"]}' + + +def bq_metrics_query(bq_table_name: str) -> google.cloud.bigquery.table.RowIterator: + if not re.match(TABLE_NAME_VALIDATION_REGEX, bq_table_name): + msg = f'{bq_table_name} does not match expected pattern' + raise ValueError(msg) + client = bigquery.Client() + + # not all columns are guaranteed to be present, coalesce if missing + table_ddl = next( + client.query_and_wait( + f""" + SELECT ddl FROM `{bq_table_name}`.INFORMATION_SCHEMA.TABLES where table_name='sample'; + """, # noqa: S608 + ), + )[0] + metrics = [(m if m in table_ddl else f'NULL AS {m}') for m in BIGQUERY_METRICS] + return client.query_and_wait( + f""" + SELECT {','.join(metrics)} FROM `{bq_table_name}.sample`; + """, # noqa: S608 + ) diff --git a/loading_pipeline/lib/misc/terra_data_repository_test.py b/loading_pipeline/lib/misc/terra_data_repository_test.py new file mode 100644 index 0000000000..91b044d68f --- /dev/null +++ b/loading_pipeline/lib/misc/terra_data_repository_test.py @@ -0,0 +1,321 @@ +import json +import os +import unittest +from types import SimpleNamespace +from unittest.mock import Mock, call, patch + +import responses + +from loading_pipeline.lib.misc.terra_data_repository import ( + TDR_ROOT_URL, + _get_dataset_ids, + bq_metrics_query, + gen_bq_table_names, +) + +TDR_DATASETS = [ + { + 'id': '2dc51ee0-a037-499d-a915-a7c20a0b216d', + 'name': 'RP_3053', + 'description': 'TGG_Ware_DRAGEN_hg38. Dataset automatically created and linked to: RP-3053', + 'defaultProfileId': '0a164b9a-2b8b-45d2-859e-a4e369b9cb4f', + 'createdDate': '2023-10-05T13:15:27.649760Z', + 'storage': [ + { + 'region': 'us-central1', + 'cloudResource': 'bigquery', + 'cloudPlatform': 'gcp', + }, + { + 'region': 'us-east4', + 'cloudResource': 'firestore', + 'cloudPlatform': 'gcp', + }, + { + 'region': 'us-central1', + 'cloudResource': 'bucket', + 'cloudPlatform': 'gcp', + }, + ], + 'secureMonitoringEnabled': False, + 'cloudPlatform': 'gcp', + 'dataProject': 'datarepo-7242affb', + 'storageAccount': None, + 'phsId': None, + 'selfHosted': False, + 'predictableFileIds': False, + 'tags': [], + 'resourceLocks': { + 'exclusive': None, + 'shared': [], + }, + }, + { + 'id': 'beef77e8-575b-40e5-9340-a6f10e0bec67', + 'name': 'RP_3056', + 'description': 'RGP_HMB_DRAGEN_hg38. Dataset automatically created and linked to: RP-3056', + 'defaultProfileId': '835dd05d-c603-4b0d-926f-d9143fd24549', + 'createdDate': '2023-10-05T20:15:27.622481Z', + 'storage': [ + { + 'region': 'us-central1', + 'cloudResource': 'bigquery', + 'cloudPlatform': 'gcp', + }, + { + 'region': 'us-east4', + 'cloudResource': 'firestore', + 'cloudPlatform': 'gcp', + }, + { + 'region': 'us-central1', + 'cloudResource': 'bucket', + 'cloudPlatform': 'gcp', + }, + ], + 'secureMonitoringEnabled': False, + 'cloudPlatform': 'gcp', + 'dataProject': 'datarepo-5a72e31b', + 'storageAccount': None, + 'phsId': None, + 'selfHosted': False, + 'predictableFileIds': False, + 'tags': [], + 'resourceLocks': { + 'exclusive': None, + 'shared': [], + }, + }, + { + 'id': 'c8d74ac4-9a2e-4d3d-a6b5-1f4b433d949f', + 'name': 'RP_3055', + 'description': 'RGP_GRU_DRAGEN_hg38. Dataset automatically created and linked to: RP-3055', + 'defaultProfileId': '835dd05d-c603-4b0d-926f-d9143fd24549', + 'createdDate': '2023-10-05T20:15:28.255304Z', + 'storage': [ + { + 'region': 'us-central1', + 'cloudResource': 'bigquery', + 'cloudPlatform': 'gcp', + }, + { + 'region': 'us-east4', + 'cloudResource': 'firestore', + 'cloudPlatform': 'gcp', + }, + { + 'region': 'us-central1', + 'cloudResource': 'bucket', + 'cloudPlatform': 'gcp', + }, + ], + 'secureMonitoringEnabled': False, + 'cloudPlatform': 'gcp', + 'dataProject': 'datarepo-0f5be351', + 'storageAccount': None, + 'phsId': None, + 'selfHosted': False, + 'predictableFileIds': False, + 'tags': [], + 'resourceLocks': { + 'exclusive': None, + 'shared': [ + 'Gw_KTeYRS1aLhRvapMLYLg', + 'WrP-0w1aROOUbgkI8JS6Ug', + ], + }, + }, +] + + +@patch( + 'loading_pipeline.lib.misc.terra_data_repository.get_service_account_credentials', + return_value=SimpleNamespace( + token='abcdefg', # noqa: S106 + ), +) +class TerraDataRepositoryTest(unittest.TestCase): + @responses.activate + def test_get_dataset_ids(self, _: Mock) -> None: + responses.get( + os.path.join(TDR_ROOT_URL, 'datasets?limit=50000'), + body=json.dumps( + { + 'total': 3, + 'filteredTotal': 3, + 'items': TDR_DATASETS, + }, + ), + ) + self.assertListEqual( + _get_dataset_ids(), + [ + '2dc51ee0-a037-499d-a915-a7c20a0b216d', + 'beef77e8-575b-40e5-9340-a6f10e0bec67', + 'c8d74ac4-9a2e-4d3d-a6b5-1f4b433d949f', + ], + ) + + @responses.activate + def test_get_dataset_ids_no_bq(self, _: Mock) -> None: + responses.get( + os.path.join(TDR_ROOT_URL, 'datasets'), + body=json.dumps( + { + 'total': 1, + 'filteredTotal': 1, + 'items': [ + { + 'id': '2dc51ee0-a037-499d-a915-a7c20a0b216d', + 'name': 'RP_3053', + 'description': 'TGG_Ware_DRAGEN_hg38. Dataset automatically created and linked to: RP-3053', + 'defaultProfileId': '0a164b9a-2b8b-45d2-859e-a4e369b9cb4f', + 'createdDate': '2023-10-05T13:15:27.649760Z', + 'storage': [ + # NB: bigquery was removed from 'storage' here. + { + 'region': 'us-east4', + 'cloudResource': 'firestore', + 'cloudPlatform': 'gcp', + }, + { + 'region': 'us-central1', + 'cloudResource': 'bucket', + 'cloudPlatform': 'gcp', + }, + ], + 'secureMonitoringEnabled': False, + 'cloudPlatform': 'gcp', + 'dataProject': 'datarepo-7242affb', + 'storageAccount': None, + 'phsId': None, + 'selfHosted': False, + 'predictableFileIds': False, + 'tags': [], + 'resourceLocks': { + 'exclusive': None, + 'shared': [], + }, + }, + ], + }, + ), + ) + self.assertRaises( + ValueError, + _get_dataset_ids, + ) + + @responses.activate + def test_gen_bq_table_names(self, _: Mock) -> None: + responses.get( + os.path.join(TDR_ROOT_URL, 'datasets'), + body=json.dumps( + { + 'total': 3, + 'filteredTotal': 3, + 'items': TDR_DATASETS, + }, + ), + ) + for dataset_id, name, project_name, dataset_name in [ + ( + '2dc51ee0-a037-499d-a915-a7c20a0b216d', + 'RP_3053', + 'datarepo-7242affb', + 'datarepo_RP_3053', + ), + ( + 'beef77e8-575b-40e5-9340-a6f10e0bec67', + 'RP_3056', + 'datarepo-5a72e31b', + 'datarepo_RP_3056', + ), + ( + 'c8d74ac4-9a2e-4d3d-a6b5-1f4b433d949f', + 'RP_3059', + 'datarepo-aada2e3b', + 'datarepo_RP_3059', + ), + ]: + responses.get( + os.path.join( + TDR_ROOT_URL, + f'datasets/{dataset_id}?include=ACCESS_INFORMATION', + ), + body=json.dumps( + { + 'id': dataset_id, + 'name': name, + 'description': 'TGG_Ware_DRAGEN_hg38. Dataset automatically created and linked to: RP-3053', + 'defaultProfileId': None, + 'dataProject': None, + 'defaultSnapshotId': None, + 'schema': None, + 'createdDate': '2023-10-05T13:15:27.649760Z', + 'storage': None, + 'secureMonitoringEnabled': False, + 'phsId': None, + 'accessInformation': { + 'bigQuery': { + 'datasetName': dataset_name, + 'datasetId': f'{project_name}:{dataset_name}', + 'projectId': project_name, + 'link': 'https://console.cloud.google.com/bigquery?project=datarepo-7242affb&ws=!datarepo_RP_3053&d=datarepo_RP_3053&p=datarepo-7242affb&page=dataset', + 'tables': [ + { + 'name': 'jointcallset', + 'id': f'{project_name}.{dataset_name}.jointcallset', + 'qualifiedName': 'datarepo-7242affb.datarepo_RP_3053.jointcallset', + 'link': 'https://console.cloud.google.com/bigquery?project=datarepo-7242affb&ws=!datarepo_RP_3053&d=datarepo_RP_3053&p=datarepo-7242affb&page=table&t=jointcallset', + 'sampleQuery': 'SELECT * FROM `datarepo-7242affb.datarepo_RP_3053.jointcallset`', + }, + { + 'name': 'sample', + 'id': f'{project_name}.{dataset_name}.sample', + 'qualifiedName': 'datarepo-7242affb.datarepo_RP_3053.sample', + 'link': 'https://console.cloud.google.com/bigquery?project=datarepo-7242affb&ws=!datarepo_RP_3053&d=datarepo_RP_3053&p=datarepo-7242affb&page=table&t=sample', + 'sampleQuery': 'SELECT * FROM `datarepo-7242affb.datarepo_RP_3053.sample`', + }, + ], + }, + 'parquet': None, + }, + 'cloudPlatform': None, + 'selfHosted': False, + 'properties': None, + 'ingestServiceAccount': None, + 'predictableFileIds': False, + 'tags': [], + 'resourceLocks': { + 'exclusive': None, + 'shared': [], + }, + }, + ), + ) + self.assertCountEqual( + list(gen_bq_table_names()), + [ + 'datarepo-7242affb.datarepo_RP_3053', + 'datarepo-5a72e31b.datarepo_RP_3056', + 'datarepo-aada2e3b.datarepo_RP_3059', + ], + ) + + @patch('loading_pipeline.lib.misc.terra_data_repository.bigquery.Client') + def test_bq_metrics_query_missing_metrics( + self, + mock_bq_client: Mock, + _: Mock, + ) -> None: + mock_bq_client.return_value.query_and_wait.return_value = iter( + [['predicted_sex,contamination_rate,percent_bases_at_20x']], + ) + bq_metrics_query('datarepo-7242affb.datarepo_RP_3053') + self.assertEqual( + mock_bq_client.return_value.query_and_wait.mock_calls[1], + call( + '\n SELECT predicted_sex,contamination_rate,percent_bases_at_20x,NULL AS collaborator_sample_id,NULL AS mean_coverage FROM `datarepo-7242affb.datarepo_RP_3053.sample`;\n ', + ), + ) diff --git a/loading_pipeline/lib/misc/validation.py b/loading_pipeline/lib/misc/validation.py new file mode 100644 index 0000000000..f6ff00619f --- /dev/null +++ b/loading_pipeline/lib/misc/validation.py @@ -0,0 +1,203 @@ +from typing import Any + +import hail as hl + +from loading_pipeline.lib.core import ( + DatasetType, + Env, + ReferenceGenome, + SampleType, +) + +ALL_VALIDATIONS = 'all' +AMBIGUOUS_THRESHOLD_PERC: float = 0.01 # Fraction of samples identified as "ambiguous_sex" above which an error will be thrown. +MIN_ROWS_PER_CONTIG = 100 +SAMPLE_TYPE_MATCH_THRESHOLD = 0.3 + + +class SeqrValidationError(Exception): + def __init__( + self, + msg: str, + error_body: dict | None = None, + ): + super().__init__(msg) + self.msg = msg + self.error_body = error_body if error_body is not None else {} + + +def validate_allele_type( + t: hl.Table | hl.MatrixTable, + dataset_type: DatasetType, + **_: Any, +) -> None: + ht = t.rows() if isinstance(t, hl.MatrixTable) else t + ht = ht.filter( + dataset_type.invalid_allele_types.contains( + hl.numeric_allele_type(ht.alleles[0], ht.alleles[1]), + ), + ) + if ht.count() > 0: + collected_alleles = sorted( + [tuple(x) for x in ht.aggregate(hl.agg.collect_as_set(ht.alleles))], + ) + # Handle case where all invalid alleles are NON_REF, indicating a gvcf: + if all('' in alleles for alleles in collected_alleles): + msg = 'Alleles with invalid allele are present in the callset. This appears to be a GVCF containing records for sites with no variants.' + raise SeqrValidationError(msg) + msg = f'Alleles with invalid AlleleType are present in the callset: {collected_alleles[:10]}' + raise SeqrValidationError(msg) + + +def validate_allele_depth_length( + mt: hl.MatrixTable, + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + **_: Any, +) -> None: + ht = mt.select_rows( + found_ad_lengths=hl.agg.collect_as_set(hl.len(mt.AD)).remove( + hl.missing(hl.tint32), + ), + ).rows() + ht = ht.filter( + hl.len(ht.found_ad_lengths) > 1, + ) + if ht.count() > 0: + variant_format = dataset_type.table_key_format_fn(reference_genome) + msg = f'Found variants with unequal Allele Depth array lengths over samples (first 10, if applicable): { ({variant_format(v): v.found_ad_lengths for v in ht.take(10)}) }' + raise SeqrValidationError(msg) + + +def validate_no_duplicate_variants( + t: hl.Table | hl.MatrixTable, + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + **_: Any, +) -> None: + ht = t.rows() if isinstance(t, hl.MatrixTable) else t + ht = ht.group_by(*ht.key).aggregate(n=hl.agg.count()) + ht = ht.filter(ht.n > 1) + ht = ht.select() + if ht.count() > 0: + variant_format = dataset_type.table_key_format_fn(reference_genome) + msg = f'Variants are present multiple times in the callset: {[variant_format(v) for v in ht.take(10)]}' + raise SeqrValidationError(msg) + + +def validate_expected_contig_frequency( + mt: hl.MatrixTable, + reference_genome: ReferenceGenome, + min_rows_per_contig: int = MIN_ROWS_PER_CONTIG, + **_: Any, +) -> None: + rows_per_contig = mt.aggregate_rows(hl.agg.counter(mt.locus.contig)) + missing_contigs = ( + reference_genome.standard_contigs + - reference_genome.optional_contigs + - rows_per_contig.keys() + ) + if missing_contigs: + msg = 'Missing the following expected contigs:{}'.format( + ', '.join(sorted(missing_contigs)), + ) + raise SeqrValidationError(msg) + + for contig, count in rows_per_contig.items(): + if contig in reference_genome.optional_contigs: + continue + if count < min_rows_per_contig: + msg = f'Contig {contig} has {count} rows, which is lower than expected minimum count {min_rows_per_contig}.' + raise SeqrValidationError(msg) + + +def validate_imported_field_types( + mt: hl.MatrixTable, + dataset_type: DatasetType, + additional_row_fields: dict[str, hl.expr.types.HailType | set], + **_: Any, +) -> None: + def _validate_field( + mt_schema: hl.StructExpression, + field: str, + dtype: hl.expr.types.HailType, + ) -> str | None: + if field not in mt_schema: + return f'{field}: missing' + if ( + ( + dtype == hl.tstruct + and isinstance( + mt_schema[field], + hl.expr.expressions.typed_expressions.StructExpression, + ) + ) + or (isinstance(dtype, set) and mt_schema[field].dtype in dtype) + or (mt_schema[field].dtype == dtype) + ): + return None + return f'{field}: {mt_schema[field].dtype}' + + unexpected_field_types = [] + for field, dtype in dataset_type.col_fields.items(): + unexpected_field_types.append(_validate_field(mt.col, field, dtype)) + for field, dtype in dataset_type.entries_fields.items(): + unexpected_field_types.append(_validate_field(mt.entry, field, dtype)) + for field, dtype in {**dataset_type.row_fields, **additional_row_fields}.items(): + unexpected_field_types.append(_validate_field(mt.row, field, dtype)) + unexpected_field_types = [x for x in unexpected_field_types if x is not None] + if unexpected_field_types: + msg = f'Found unexpected field types on MatrixTable after import: {unexpected_field_types}' + raise SeqrValidationError(msg) + + +def validate_sample_type( + mt: hl.MatrixTable, + reference_genome: ReferenceGenome, + sample_type: SampleType, + project_guids: list[str], + coding_and_noncoding_variants_ht: hl.Table, + sample_type_match_threshold: float = SAMPLE_TYPE_MATCH_THRESHOLD, + **_: Any, +) -> None: + if all( + project_guid in Env.SAMPLE_TYPE_VALIDATION_EXCLUDED_PROJECTS + for project_guid in project_guids + ): + return + coding_variants_ht = coding_and_noncoding_variants_ht.filter( + coding_and_noncoding_variants_ht.coding, + ) + has_coding = ( + mt.semi_join_rows(coding_variants_ht).count_rows() / coding_variants_ht.count() + >= sample_type_match_threshold + ) + noncoding_variants_ht = coding_and_noncoding_variants_ht.filter( + coding_and_noncoding_variants_ht.noncoding, + ) + has_noncoding = ( + mt.semi_join_rows(noncoding_variants_ht).count_rows() + / noncoding_variants_ht.count() + >= sample_type_match_threshold + ) + if not has_coding and not has_noncoding: + msg = f"Genome version validation error: dataset specified as {reference_genome.value} but doesn't contain the expected number of common {reference_genome.value} variants" + raise SeqrValidationError(msg) + if has_noncoding and not has_coding: + msg = f'Sample type validation error: dataset contains noncoding variants but is missing common coding variants for {reference_genome.value}. Please verify that the dataset contains coding variants.' + raise SeqrValidationError(msg) + if has_coding and not has_noncoding and sample_type != SampleType.WES: + msg = 'Sample type validation error: dataset sample-type is specified as WGS but appears to be WES because it contains many common coding variants but is missing common non-coding variants' + raise SeqrValidationError(msg) + if has_noncoding and has_coding and sample_type != SampleType.WGS: + msg = 'Sample type validation error: dataset sample-type is specified as WES but appears to be WGS because it contains many common non-coding variants' + raise SeqrValidationError(msg) + + +SKIPPABLE_VALIDATIONS = [ + validate_allele_depth_length, + validate_allele_type, + validate_expected_contig_frequency, + validate_no_duplicate_variants, + validate_sample_type, +] diff --git a/loading_pipeline/lib/misc/validation_test.py b/loading_pipeline/lib/misc/validation_test.py new file mode 100644 index 0000000000..bb368b85a5 --- /dev/null +++ b/loading_pipeline/lib/misc/validation_test.py @@ -0,0 +1,464 @@ +import unittest +from unittest.mock import patch + +import hail as hl + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.misc.validation import ( + SeqrValidationError, + validate_allele_depth_length, + validate_allele_type, + validate_expected_contig_frequency, + validate_imported_field_types, + validate_no_duplicate_variants, + validate_sample_type, +) + +TEST_MITO_MT = 'loading_pipeline/var/test/callsets/mito_1.mt' + + +def _mt_from_contigs(contigs): + return ( + hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig=contig, + position=1, + reference_genome='GRCh38', + ) + for contig in contigs + ], + }, + cols={'s': ['sample_1']}, + entries={'HL': [[0.0] for _ in range(len(contigs))]}, + ) + .key_rows_by('locus') + .key_cols_by('s') + ) + + +class ValidationTest(unittest.TestCase): + def test_validate_allele_type(self) -> None: + mt = ( + hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=2, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=3, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=4, + reference_genome='GRCh38', + ), + ], + 'alleles': [ + ['A', 'T'], + # NB: star alleles should pass through this validation just fine, + # but are eventually filtered out upstream. + ['A', '*'], + ['A', '-'], + ['A', ''], + ], + }, + cols={'s': ['sample_1']}, + entries={'HL': [[0.0], [0.0], [0.0], [0.0]]}, + ) + .key_rows_by('locus', 'alleles') + .key_cols_by('s') + ) + self.assertRaisesRegex( + SeqrValidationError, + "Alleles with invalid AlleleType are present in the callset: \\[\\('A', '-'\\), \\('A', ''\\)\\]", + validate_allele_type, + mt, + DatasetType.SNV_INDEL, + ) + + mt = ( + hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=2, + reference_genome='GRCh38', + ), + ], + 'alleles': [ + ['C', ''], + ['A', ''], + ], + }, + cols={'s': ['sample_1']}, + entries={'HL': [[0.0], [0.0]]}, + ) + .key_rows_by('locus', 'alleles') + .key_cols_by('s') + ) + self.assertRaisesRegex( + SeqrValidationError, + 'Alleles with invalid allele are present in the callset. This appears to be a GVCF containing records for sites with no variants.', + validate_allele_type, + mt, + DatasetType.SNV_INDEL, + ) + + def test_validate_allele_depth_length(self) -> None: + mt = ( + hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=2, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=3, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=4, + reference_genome='GRCh38', + ), + ], + 'alleles': [ + ['A', 'T'], + # NB: star alleles should pass through this validation just fine, + # but are eventually filtered out upstream. + ['A', 'TC', 'TG'], + ['A', 'TTT'], + ['A', 'CCC'], + ], + }, + cols={'s': ['sample_1', 'sample_2']}, + entries={ + 'AD': [ + [[1, 0], [1, 0]], + [[1], [1, 0, 1]], + [[1, 0], [1]], + [[1, 0], [1, 0]], + ], + }, + ) + .key_rows_by('locus', 'alleles') + .key_cols_by('s') + ) + self.assertRaisesRegex( + SeqrValidationError, + "Found variants with unequal Allele Depth array lengths over samples \\(first 10, if applicable\\): \\{'1-2-A-TC-TG': \\{1, 3\\}, '1-3-A-TTT': \\{1, 2\\}\\}", + validate_allele_depth_length, + mt, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + ) + + def test_validate_imported_field_types(self) -> None: + mt = hl.read_matrix_table(TEST_MITO_MT) + validate_imported_field_types(mt, DatasetType.MITO, {}) + mt = mt.annotate_cols(contamination=hl.int32(mt.contamination)) + mt = mt.annotate_entries(DP=hl.float32(mt.DP)) + mt = mt.annotate_rows(vep=hl.dict({'t': '1'})) + self.assertRaisesRegex( + SeqrValidationError, + "Found unexpected field types on MatrixTable after import: \\['contamination: int32', 'DP: float32', 'vep: dict', 'tester: missing'\\]", + validate_imported_field_types, + mt, + DatasetType.MITO, + {'tester': hl.tfloat32}, + ) + + def test_validate_no_duplicate_variants(self) -> None: + mt = ( + hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=2, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=2, + reference_genome='GRCh38', + ), + ], + 'alleles': [ + ['A', 'C'], + ['A', 'C'], + ['A', 'C'], + ], + }, + cols={'s': ['sample_1']}, + entries={'HL': [[0.0], [0.0], [0.0]]}, + ) + .key_rows_by('locus', 'alleles') + .key_cols_by('s') + ) + self.assertRaisesRegex( + SeqrValidationError, + "Variants are present multiple times in the callset: \\['1-2-A-C'\\]", + validate_no_duplicate_variants, + mt, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + ) + + def test_validate_expected_contig_frequency(self) -> None: + mt = _mt_from_contigs(ReferenceGenome.GRCh38.standard_contigs) + self.assertIsNone( + validate_expected_contig_frequency(mt, ReferenceGenome.GRCh38, 1), + ) + self.assertRaisesRegex( + SeqrValidationError, + 'Missing the following expected contigs', + validate_expected_contig_frequency, + mt, + ReferenceGenome.GRCh37, + 1, + ) + self.assertRaisesRegex( + SeqrValidationError, + 'which is lower than expected minimum count', + validate_expected_contig_frequency, + mt, + ReferenceGenome.GRCh38, + 2, + ) + + # Drop an optional contig + mt = _mt_from_contigs(ReferenceGenome.GRCh38.standard_contigs - {'chrY'}) + self.assertIsNone( + validate_expected_contig_frequency(mt, ReferenceGenome.GRCh38, 1), + ) + + # Drop a non-optional contig + mt = _mt_from_contigs(ReferenceGenome.GRCh38.standard_contigs - {'chr3'}) + self.assertRaisesRegex( + SeqrValidationError, + 'Missing the following expected contigs', + validate_expected_contig_frequency, + mt, + ReferenceGenome.GRCh38, + 1, + ) + + def test_validate_sample_type(self) -> None: + mt = _mt_from_contigs(ReferenceGenome.GRCh38.standard_contigs) + coding_and_noncoding_variants_ht = hl.Table.parallelize( + [ + { + 'locus': hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + 'coding': True, + 'noncoding': False, + }, + { + 'locus': hl.Locus( + contig='chr2', + position=1, + reference_genome='GRCh38', + ), + 'coding': True, + 'noncoding': False, + }, + { + 'locus': hl.Locus( + contig='chr3', + position=1, + reference_genome='GRCh38', + ), + 'coding': False, + 'noncoding': True, + }, + { + 'locus': hl.Locus( + contig='chr4', + position=1, + reference_genome='GRCh38', + ), + 'coding': False, + 'noncoding': True, + }, + ], + hl.tstruct( + locus=hl.tlocus('GRCh38'), + coding=hl.tbool, + noncoding=hl.tbool, + ), + key='locus', + ) + self.assertIsNone( + validate_sample_type( + mt, + ReferenceGenome.GRCh38, + SampleType.WGS, + ['project_a'], + coding_and_noncoding_variants_ht, + ), + ) + self.assertRaisesRegex( + SeqrValidationError, + 'specified as WES but appears to be WGS', + validate_sample_type, + mt, + ReferenceGenome.GRCh38, + SampleType.WES, + ['project_a'], + coding_and_noncoding_variants_ht, + ) + + # has coding, but not noncoding now. + coding_and_noncoding_variants_ht = hl.Table.parallelize( + [ + { + 'locus': hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + 'coding': True, + 'noncoding': False, + }, + { + 'locus': hl.Locus( + contig='chr2', + position=1, + reference_genome='GRCh38', + ), + 'coding': True, + 'noncoding': False, + }, + { + 'locus': hl.Locus( + contig='chr2', + position=2, + reference_genome='GRCh38', + ), + 'coding': False, + 'noncoding': True, + }, + ], + hl.tstruct( + locus=hl.tlocus('GRCh38'), + coding=hl.tbool, + noncoding=hl.tbool, + ), + key='locus', + ) + self.assertIsNone( + validate_sample_type( + mt, + ReferenceGenome.GRCh38, + SampleType.WES, + ['project_a'], + coding_and_noncoding_variants_ht, + ), + ) + self.assertRaisesRegex( + SeqrValidationError, + 'specified as WGS but appears to be WES', + validate_sample_type, + mt, + ReferenceGenome.GRCh38, + SampleType.WGS, + ['project_a'], + coding_and_noncoding_variants_ht, + ) + + # has noncoding, but not coding now. + coding_and_noncoding_variants_ht = hl.Table.parallelize( + [ + { + 'locus': hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + 'coding': False, + 'noncoding': True, + }, + { + 'locus': hl.Locus( + contig='chr2', + position=1, + reference_genome='GRCh38', + ), + 'coding': False, + 'noncoding': True, + }, + { + 'locus': hl.Locus( + contig='chr2', + position=2, + reference_genome='GRCh38', + ), + 'coding': True, + 'noncoding': False, + }, + ], + hl.tstruct( + locus=hl.tlocus('GRCh38'), + coding=hl.tbool, + noncoding=hl.tbool, + ), + key='locus', + ) + self.assertRaisesRegex( + SeqrValidationError, + 'contains noncoding variants but is missing common coding variants', + validate_sample_type, + mt, + ReferenceGenome.GRCh38, + SampleType.WGS, + ['project_a'], + coding_and_noncoding_variants_ht, + ) + + # Validation safe if all projects are to be skipped + with patch('loading_pipeline.lib.misc.validation.Env') as mock_env: + mock_env.SAMPLE_TYPE_VALIDATION_EXCLUDED_PROJECTS = ['project_a'] + self.assertIsNone( + validate_sample_type( + mt, + ReferenceGenome.GRCh38, + SampleType.WGS, + ['project_a'], + coding_and_noncoding_variants_ht, + ), + ) diff --git a/loading_pipeline/lib/misc/vep.py b/loading_pipeline/lib/misc/vep.py new file mode 100644 index 0000000000..bdaf7c4c66 --- /dev/null +++ b/loading_pipeline/lib/misc/vep.py @@ -0,0 +1,29 @@ +from string import Template + +import hail as hl + +from loading_pipeline.lib.core import DatasetType, Env, ReferenceGenome + +VEP_CONFIG_URI = Template( + 'file://$vep_reference_datasets_dir/$reference_genome/vep-$reference_genome.json', +) + + +def run_vep( + ht: hl.Table, + dataset_type: DatasetType, + reference_genome: ReferenceGenome, +) -> hl.Table: + if not dataset_type.veppable: + return ht + return hl.vep( + ht, + config=VEP_CONFIG_URI.substitute( + vep_reference_datasets_dir=Env.VEP_REFERENCE_DATASETS_DIR, + reference_genome=reference_genome.value, + ), + name='vep', + block_size=1000, + tolerate_parse_error=True, + csq=False, + ) diff --git a/loading_pipeline/lib/misc/vets.py b/loading_pipeline/lib/misc/vets.py new file mode 100644 index 0000000000..4934168232 --- /dev/null +++ b/loading_pipeline/lib/misc/vets.py @@ -0,0 +1,39 @@ +import hail as hl + +VETS_SNP_CUTOFF = 0.997 +VETS_INDEL_CUTOFF = 0.99 +VETS_SNP_FILTER = 'high_CALIBRATION_SENSITIVITY_SNP' +VETS_INDEL_FILTER = 'high_CALIBRATION_SENSITIVITY_INDEL' + + +def annotate_vets(mt: hl.MatrixTable) -> hl.MatrixTable: + if not hasattr(mt, 'info.CALIBRATION_SENSITIVITY'): + return mt + return mt.annotate_rows( + filters=hl.bind( + lambda is_snp, split_cs: ( + hl.case() + .when( + is_snp & (split_cs > VETS_SNP_CUTOFF), + hl.if_else( + hl.is_defined(mt.filters), + mt.filters.add(VETS_SNP_FILTER), + hl.set([VETS_SNP_FILTER]), + ), + ) + .when( + ~is_snp & (split_cs > VETS_INDEL_CUTOFF), + hl.if_else( + hl.is_defined(mt.filters), + mt.filters.add(VETS_INDEL_FILTER), + hl.set([VETS_INDEL_FILTER]), + ), + ) + .default( + mt.filters, + ) + ), + hl.is_snp(mt.alleles[0], mt.alleles[1]), + hl.parse_float(mt['info.CALIBRATION_SENSITIVITY'][mt.a_index - 1]), + ), + ) diff --git a/loading_pipeline/lib/misc/vets_test.py b/loading_pipeline/lib/misc/vets_test.py new file mode 100644 index 0000000000..b26de113b7 --- /dev/null +++ b/loading_pipeline/lib/misc/vets_test.py @@ -0,0 +1,104 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.misc.io import split_multi_hts +from loading_pipeline.lib.misc.vets import ( + annotate_vets, +) + + +class VetsTest(unittest.TestCase): + def test_annotate_vets(self) -> None: + gatk_mt = hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + ], + 'filters': [ + hl.set(['NO_HQ_GENOTYPES']), + ], + }, + cols={'s': ['sample_1']}, + entries={'HL': [[0.0]]}, + ).key_rows_by('locus') + gatk_mt = annotate_vets(gatk_mt) + dragen_mt = hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=2, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=3, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=4, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=5, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=6, + reference_genome='GRCh38', + ), + ], + 'alleles': [ + ['A', 'T'], + ['A', 'T'], + ['A', 'T'], + ['AC', 'T'], + ['AT', 'ATC'], + ['AG', 'ATG'], + ], + 'filters': [ + hl.set(['NO_HQ_GENOTYPES']), + hl.empty_set(hl.tstr), + hl.missing(hl.tset(hl.tstr)), + hl.set(['NO_HQ_GENOTYPES']), + hl.empty_set(hl.tstr), + hl.set(['NO_HQ_GENOTYPES']), + ], + 'info.CALIBRATION_SENSITIVITY': [ + ['0.999'], + ['0.995'], + ['0.999'], + ['0.98'], + ['0.99'], + ['0.991'], + ], + }, + cols={'s': ['sample_1']}, + entries={'HL': [[0.0], [0.0], [0.0], [0.0], [0.0], [0.0]]}, + ).key_rows_by('locus', 'alleles') + dragen_mt = split_multi_hts(dragen_mt, False) + dragen_mt = annotate_vets(dragen_mt) + self.assertListEqual( + dragen_mt.filters.collect(), + [ + {'NO_HQ_GENOTYPES', 'high_CALIBRATION_SENSITIVITY_SNP'}, + set(), + {'high_CALIBRATION_SENSITIVITY_SNP'}, + {'NO_HQ_GENOTYPES'}, + set(), + {'NO_HQ_GENOTYPES', 'high_CALIBRATION_SENSITIVITY_INDEL'}, + ], + ) diff --git a/loading_pipeline/lib/paths.py b/loading_pipeline/lib/paths.py new file mode 100644 index 0000000000..27e450f7d7 --- /dev/null +++ b/loading_pipeline/lib/paths.py @@ -0,0 +1,503 @@ +import hashlib +import os + +import hailtop.fs as hfs + +from loading_pipeline.lib.core import ( + DatasetType, + Env, + ReferenceGenome, + SampleType, +) +from loading_pipeline.lib.reference_datasets.reference_dataset import ( + ReferenceDataset, +) + + +def pipeline_prefix( + root: str, + reference_genome: ReferenceGenome, + dataset_type: DatasetType, +) -> str: + return os.path.join( + root, + reference_genome.value, + dataset_type.value, + ) + + +def _v03_reference_dataset_prefix( + root: str, + reference_genome: ReferenceGenome, +) -> str: + return os.path.join( + root, + reference_genome.value, + ) + + +def _callset_path_hash(callset_path: str) -> str: + # Include the most recent modified time of any + # of the callset shards if they exist. + try: + # hfs.ls throws FileNotFoundError if a non-wildcard is passed + # but not found, but does not throw if a wildcard is passed and + # there are no results. + shards = hfs.ls(callset_path) + if not shards: + key = callset_path + else: + # f.modification_time is None for directories + key = callset_path + str( + sum((f.size if f.size else 0) for f in shards), + ) + except FileNotFoundError: + key = callset_path + return hashlib.sha256( + key.encode('utf8'), + ).hexdigest() + + +def family_table_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + sample_type: SampleType, + family_guid: str, +) -> str: + return os.path.join( + pipeline_prefix( + Env.PIPELINE_DATA_DIR, + reference_genome, + dataset_type, + ), + 'families', + sample_type.value, + f'{family_guid}.ht', + ) + + +def tdr_metrics_dir( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, +) -> str: + return os.path.join( + pipeline_prefix( + Env.LOADING_DATASETS_DIR, + reference_genome, + dataset_type, + ), + 'tdr_metrics', + ) + + +def tdr_metrics_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + bq_table_name: str, +) -> str: + return os.path.join( + tdr_metrics_dir(reference_genome, dataset_type), + f'{bq_table_name}.tsv', + ) + + +def imported_callset_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + callset_path: str, +) -> str: + return os.path.join( + pipeline_prefix( + Env.LOADING_DATASETS_DIR, + reference_genome, + dataset_type, + ), + 'imported_callsets', + f'{_callset_path_hash(callset_path)}.mt', + ) + + +def postprocessed_callset_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + callset_path: str, +) -> str: + return os.path.join( + pipeline_prefix( + Env.LOADING_DATASETS_DIR, + reference_genome, + dataset_type, + ), + 'postprocessed_callsets', + f'{_callset_path_hash(callset_path)}.mt', + ) + + +def validation_errors_for_run_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + run_id: str, +) -> str: + return os.path.join( + runs_path( + reference_genome, + dataset_type, + ), + run_id, + 'validation_errors.json', + ) + + +def metadata_for_run_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + run_id: str, +) -> str: + return os.path.join( + runs_path( + reference_genome, + dataset_type, + ), + run_id, + 'metadata.json', + ) + + +def project_table_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + sample_type: SampleType, + project_guid: str, +) -> str: + return os.path.join( + pipeline_prefix( + Env.PIPELINE_DATA_DIR, + reference_genome, + dataset_type, + ), + 'projects', + sample_type.value, + f'{project_guid}.ht', + ) + + +def relatedness_check_table_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + callset_path: str, +) -> str: + return os.path.join( + pipeline_prefix( + Env.LOADING_DATASETS_DIR, + reference_genome, + dataset_type, + ), + 'relatedness_check', + f'{_callset_path_hash(callset_path)}.ht', + ) + + +def relatedness_check_tsv_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + callset_path: str, +) -> str: + return os.path.join( + pipeline_prefix( + Env.LOADING_DATASETS_DIR, + reference_genome, + dataset_type, + ), + 'relatedness_check', + f'{_callset_path_hash(callset_path)}.tsv', + ) + + +def sample_qc_json_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + callset_path: str, +) -> str: + return os.path.join( + pipeline_prefix( + Env.LOADING_DATASETS_DIR, + reference_genome, + dataset_type, + ), + 'sample_qc', + f'{_callset_path_hash(callset_path)}.json', + ) + + +def remapped_and_subsetted_callset_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + callset_path: str, + project_guid: str, +) -> str: + return os.path.join( + pipeline_prefix( + Env.LOADING_DATASETS_DIR, + reference_genome, + dataset_type, + ), + 'remapped_and_subsetted_callsets', + project_guid, + f'{_callset_path_hash(callset_path)}.mt', + ) + + +def runs_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, +) -> str: + return os.path.join( + pipeline_prefix( + Env.PIPELINE_DATA_DIR, + reference_genome, + dataset_type, + ), + 'runs', + ) + + +def sex_check_table_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + callset_path: str, +) -> str: + return os.path.join( + pipeline_prefix( + Env.LOADING_DATASETS_DIR, + reference_genome, + dataset_type, + ), + 'sex_check', + f'{_callset_path_hash(callset_path)}.ht', + ) + + +def valid_reference_dataset_path( + reference_genome: ReferenceGenome, + reference_dataset: ReferenceDataset, +) -> str | None: + return os.path.join( + _v03_reference_dataset_prefix( + Env.REFERENCE_DATASETS_DIR, + reference_genome, + ), + reference_dataset.value, + f'{reference_dataset.version(reference_genome)}.ht', + ) + + +def ancestry_model_rf_path() -> str: + return os.path.join( + _v03_reference_dataset_prefix( + Env.REFERENCE_DATASETS_DIR, + ReferenceGenome.GRCh38, + ), + DatasetType.SNV_INDEL, + 'ancestry_imputation_model.onnx', + ) + + +def variant_annotations_table_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, +) -> str: + return os.path.join( + pipeline_prefix( + Env.PIPELINE_DATA_DIR, + reference_genome, + dataset_type, + ), + 'annotations.ht', + ) + + +def variant_annotations_vcf_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, +) -> str: + return os.path.join( + pipeline_prefix( + Env.PIPELINE_DATA_DIR, + reference_genome, + dataset_type, + ), + 'annotations.vcf.bgz', + ) + + +def new_entries_parquet_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + run_id: str, +) -> str: + return os.path.join( + runs_path( + reference_genome, + dataset_type, + ), + run_id, + 'new_entries.parquet', + ) + + +def new_variant_details_parquet_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + run_id: str, +) -> str: + return os.path.join( + runs_path( + reference_genome, + dataset_type, + ), + run_id, + 'new_variant_details.parquet', + ) + + +def new_variants_parquet_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + run_id: str, +) -> str: + return os.path.join( + runs_path( + reference_genome, + dataset_type, + ), + run_id, + 'new_variants.parquet', + ) + + +def new_variants_table_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + run_id: str, +) -> str: + return os.path.join( + runs_path( + reference_genome, + dataset_type, + ), + run_id, + 'new_variants.ht', + ) + + +def project_pedigree_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + sample_type: SampleType, + project_guid: str, +) -> str: + return os.path.join( + pipeline_prefix( + Env.LOADING_DATASETS_DIR, + reference_genome, + dataset_type, + ), + 'pedigrees', + sample_type.value, + f'{project_guid}_pedigree.tsv', + ) + + +def loading_pipeline_queue_dir() -> str: + """ + Returns the directory where loading pipeline requests are queued. + """ + return os.path.join( + Env.LOCAL_DISK_MOUNT_DIR, + 'loading_pipeline_queue', + ) + + +# https://en.wikipedia.org/wiki/Dead_letter_queue +def loading_pipeline_deadletter_queue_dir() -> str: + return os.path.join( + Env.LOCAL_DISK_MOUNT_DIR, + 'loading_pipeline_deadletter_queue', + ) + + +def loading_pipeline_queue_path(run_id: str) -> str: + """ + Returns a new path for a loading pipeline queue request file. + """ + return os.path.join( + loading_pipeline_queue_dir(), + f'request_{run_id}.json', + ) + + +def loading_pipeline_deadletter_queue_path(run_id: str) -> str: + """ + Returns a new path for a loading pipeline queue request file. + """ + return os.path.join( + loading_pipeline_deadletter_queue_dir(), + f'request_{run_id}.json', + ) + + +def pipeline_run_success_file_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + run_id: str, +) -> str: + return os.path.join( + runs_path( + reference_genome, + dataset_type, + ), + run_id, + '_SUCCESS', + ) + + +def clickhouse_load_success_file_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + run_id: str, +) -> str: + return os.path.join( + runs_path( + reference_genome, + dataset_type, + ), + run_id, + '_CLICKHOUSE_LOAD_SUCCESS', + ) + + +def clickhouse_load_fail_file_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + run_id: str, +) -> str: + return os.path.join( + runs_path( + reference_genome, + dataset_type, + ), + run_id, + '_CLICKHOUSE_LOAD_FAIL', + ) + + +def reference_dataset_parquet( + reference_genome: ReferenceGenome, + reference_dataset: ReferenceDataset, +) -> str: + return os.path.join( + Env.REFERENCE_DATASETS_DIR, + reference_genome.value, + reference_dataset.value, + f'{reference_dataset.version(reference_genome)}.parquet', + ) diff --git a/loading_pipeline/lib/paths_test.py b/loading_pipeline/lib/paths_test.py new file mode 100644 index 0000000000..d271cfee0b --- /dev/null +++ b/loading_pipeline/lib/paths_test.py @@ -0,0 +1,180 @@ +import unittest +from unittest.mock import patch + +import hailtop.fs as hfs + +from loading_pipeline.lib.core import ( + DatasetType, + ReferenceGenome, + SampleType, +) +from loading_pipeline.lib.paths import ( + imported_callset_path, + metadata_for_run_path, + new_variants_table_path, + project_pedigree_path, + project_table_path, + relatedness_check_table_path, + remapped_and_subsetted_callset_path, + sex_check_table_path, + tdr_metrics_path, + validation_errors_for_run_path, + variant_annotations_table_path, +) + +TEST_VCF = 'loading_pipeline/var/test/callsets/1kg_30varia*.vcf' + + +class TestPaths(unittest.TestCase): + def test_project_table_path(self) -> None: + self.assertEqual( + project_table_path( + ReferenceGenome.GRCh38, + DatasetType.MITO, + SampleType.WES, + 'R0652_pipeline_test', + ), + '/var/seqr/pipeline-data/GRCh38/MITO/projects/WES/R0652_pipeline_test.ht', + ) + with ( + patch('loading_pipeline.lib.paths.Env') as mock_env, + ): + mock_env.PIPELINE_DATA_DIR = '/var/bucket/' + self.assertEqual( + project_table_path( + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + SampleType.WES, + 'R0652_pipeline_test', + ), + '/var/bucket/GRCh37/SNV_INDEL/projects/WES/R0652_pipeline_test.ht', + ) + + def test_sex_check_table_path(self) -> None: + self.assertEqual( + sex_check_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + '/var/abc.efg/callset.vcf.gz', + ), + '/var/seqr/seqr-loading-temp/GRCh38/SNV_INDEL/sex_check/f92b8ab6b5b8c41fa20d7d49a5626b96dcd2ba79fa6f61eab7ffb80d550d951c.ht', + ) + + def test_relatedness_check_table_path(self) -> None: + self.assertEqual( + relatedness_check_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + '/var/abc.efg/callset.vcf.gz', + ), + '/var/seqr/seqr-loading-temp/GRCh38/SNV_INDEL/relatedness_check/f92b8ab6b5b8c41fa20d7d49a5626b96dcd2ba79fa6f61eab7ffb80d550d951c.ht', + ) + + def test_validation_errors_for_run_path(self) -> None: + self.assertEqual( + validation_errors_for_run_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + 'manual__2023-06-26T18:30:09.349671+00:00', + ), + '/var/seqr/pipeline-data/GRCh38/SNV_INDEL/runs/manual__2023-06-26T18:30:09.349671+00:00/validation_errors.json', + ) + + def test_metadata_for_run_path(self) -> None: + self.assertEqual( + metadata_for_run_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + 'manual__2023-06-26T18:30:09.349671+00:00', + ), + '/var/seqr/pipeline-data/GRCh38/SNV_INDEL/runs/manual__2023-06-26T18:30:09.349671+00:00/metadata.json', + ) + + def test_variant_annotations_table_path(self) -> None: + self.assertEqual( + variant_annotations_table_path( + ReferenceGenome.GRCh38, + DatasetType.GCNV, + ), + '/var/seqr/pipeline-data/GRCh38/GCNV/annotations.ht', + ) + + def test_remapped_and_subsetted_callset_path(self) -> None: + self.assertEqual( + remapped_and_subsetted_callset_path( + ReferenceGenome.GRCh38, + DatasetType.GCNV, + '/var/abc.efg/callset.vcf.gz', + 'R0111_tgg_bblanken_wes', + ), + '/var/seqr/seqr-loading-temp/GRCh38/GCNV/remapped_and_subsetted_callsets/R0111_tgg_bblanken_wes/f92b8ab6b5b8c41fa20d7d49a5626b96dcd2ba79fa6f61eab7ffb80d550d951c.mt', + ) + self.assertEqual( + remapped_and_subsetted_callset_path( + ReferenceGenome.GRCh38, + DatasetType.GCNV, + '/var/abc.efg/callset/*.vcf.gz', + 'R0111_tgg_bblanken_wes', + ), + '/var/seqr/seqr-loading-temp/GRCh38/GCNV/remapped_and_subsetted_callsets/R0111_tgg_bblanken_wes/26f481b386721f9889250c6549905660728ec9f77be4b8f7eeb6c4facc76282e.mt', + ) + + def test_imported_callset_path(self) -> None: + self.assertEqual( + imported_callset_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + '/var/abc.efg/callset.vcf.gz', + ), + '/var/seqr/seqr-loading-temp/GRCh38/SNV_INDEL/imported_callsets/f92b8ab6b5b8c41fa20d7d49a5626b96dcd2ba79fa6f61eab7ffb80d550d951c.mt', + ) + + with patch('loading_pipeline.lib.paths.hfs.ls') as mock_ls: + mock_ls.return_value = [ + hfs.stat_result.FileListEntry( + path='loading_pipeline/var/test/callsets/1kg_30variants.vcf', + owner=None, + size=1732033623.804012, + typ=hfs.stat_result.FileType(2), + modification_time=1732033000, + ), + ] + self.assertEqual( + imported_callset_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_VCF, + ), + '/var/seqr/seqr-loading-temp/GRCh38/SNV_INDEL/imported_callsets/01327e46c8747f15feaad2c08875b928c274dcb248ad40837ea3f49d8b4dedfb.mt', + ) + + def test_tdr_metrics_path(self) -> None: + self.assertEqual( + tdr_metrics_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + 'datarepo-7242affb.datarepo_RP_3053', + ), + '/var/seqr/seqr-loading-temp/GRCh38/SNV_INDEL/tdr_metrics/datarepo-7242affb.datarepo_RP_3053.tsv', + ) + + def test_new_variants_table_path(self) -> None: + self.assertEqual( + new_variants_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + 'manual__2023-06-26T18:30:09.349671+00:00', + ), + '/var/seqr/pipeline-data/GRCh38/SNV_INDEL/runs/manual__2023-06-26T18:30:09.349671+00:00/new_variants.ht', + ) + + def test_project_pedigree_path(self) -> None: + self.assertEqual( + project_pedigree_path( + ReferenceGenome.GRCh38, + DatasetType.GCNV, + SampleType.WES, + 'R0652_pipeline_test', + ), + '/var/seqr/seqr-loading-temp/GRCh38/GCNV/pedigrees/WES/R0652_pipeline_test_pedigree.tsv', + ) diff --git a/loading_pipeline/lib/reference_datasets/__init__.py b/loading_pipeline/lib/reference_datasets/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/loading_pipeline/lib/reference_datasets/eigen.py b/loading_pipeline/lib/reference_datasets/eigen.py new file mode 100644 index 0000000000..84a04215bf --- /dev/null +++ b/loading_pipeline/lib/reference_datasets/eigen.py @@ -0,0 +1,7 @@ +import hail as hl + + +def get_ht(path: str, *_) -> hl.Table: + ht = hl.read_table(path) + ht = ht.select(Eigen_phred=hl.float32(ht.info['Eigen-phred'])) + return ht.group_by(*ht.key).aggregate(Eigen_phred=hl.agg.max(ht.Eigen_phred)) diff --git a/loading_pipeline/lib/reference_datasets/gencode/__init__.py b/loading_pipeline/lib/reference_datasets/gencode/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/loading_pipeline/lib/reference_datasets/gencode/mapping_gene_ids.py b/loading_pipeline/lib/reference_datasets/gencode/mapping_gene_ids.py new file mode 100644 index 0000000000..b668a99d2b --- /dev/null +++ b/loading_pipeline/lib/reference_datasets/gencode/mapping_gene_ids.py @@ -0,0 +1,64 @@ +import gzip +import logging + +import requests + +logger = logging.getLogger(__name__) + +# Mirror of 'http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_{gencode_release}/gencode.v{gencode_release}.annotation.gtf.gz' +GENCODE_GTF_URL = 'https://storage.googleapis.com/seqr-reference-data/gencode/gencode.v{gencode_release}.annotation.gtf.gz' +# Mirror of 'https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_{gencode_release}/gencode.v{gencode_release}.metadata.RefSeq.gz' +GENCODE_ENSEMBL_TO_REFSEQ_URL = 'https://storage.googleapis.com/seqr-reference-data/gencode/gencode.v{gencode_release}.metadata.RefSeq.gz' + +# expected GTF file header +GENCODE_FILE_HEADER = [ + 'chrom', + 'source', + 'feature_type', + 'start', + 'end', + 'score', + 'strand', + 'phase', + 'info', +] +EXPECTED_ENSEMBLE_TO_REFSEQ_FIELDS = 3 + + +def load_gencode_gene_symbol_to_gene_id(gencode_release: int) -> dict[str, str]: + url = GENCODE_GTF_URL.format(gencode_release=gencode_release) + response = requests.get(url, stream=True, timeout=10) + gene_symbol_to_gene_id = {} + for line in gzip.GzipFile(fileobj=response.raw): + line = line.decode('ascii') # noqa: PLW2901 + if not line or line.startswith('#'): + continue + fields = line.strip().split('\t') + if len(fields) != len(GENCODE_FILE_HEADER): + msg = f'Unexpected number of fields: {fields}' + raise ValueError( + msg, + ) + record = dict(zip(GENCODE_FILE_HEADER, fields, strict=False)) + if record['feature_type'] != 'gene': + continue + # parse info field + info_fields = [x.strip().split() for x in record['info'].split(';') if x != ''] + info_fields = {k: v.strip('"') for k, v in info_fields} + gene_symbol_to_gene_id[info_fields['gene_name']] = info_fields['gene_id'].split( + '.', + )[0] + return gene_symbol_to_gene_id + + +def load_gencode_ensembl_to_refseq_id(gencode_release: int): + url = GENCODE_ENSEMBL_TO_REFSEQ_URL.format(gencode_release=gencode_release) + response = requests.get(url, stream=True, timeout=10) + ensembl_to_refseq_ids = {} + for line in gzip.GzipFile(fileobj=response.raw): + fields = line.decode('ascii').strip().split('\t') + if len(fields) > EXPECTED_ENSEMBLE_TO_REFSEQ_FIELDS: + msg = 'Unexpected number of fields on line in ensemble_to_refseq mapping' + raise ValueError(msg) + ensembl_to_refseq_ids[fields[0].split('.')[0]] = fields[1] + return ensembl_to_refseq_ids diff --git a/loading_pipeline/lib/reference_datasets/gencode/mapping_gene_ids_tests.py b/loading_pipeline/lib/reference_datasets/gencode/mapping_gene_ids_tests.py new file mode 100644 index 0000000000..edba8de050 --- /dev/null +++ b/loading_pipeline/lib/reference_datasets/gencode/mapping_gene_ids_tests.py @@ -0,0 +1,64 @@ +import gzip +import unittest + +import responses + +from loading_pipeline.lib.reference_datasets.gencode.mapping_gene_ids import ( + GENCODE_ENSEMBL_TO_REFSEQ_URL, + GENCODE_GTF_URL, + load_gencode_ensembl_to_refseq_id, + load_gencode_gene_symbol_to_gene_id, +) + +GTF_DATA = [ + '#description: evidence-based annotation of the human genome, version 31 (Ensembl 97), mapped to GRCh37 with gencode-backmap', + 'chr1 HAVANA gene 11869 14409 . + . gene_id "ENSG00000223972.5_2"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; level 2; hgnc_id "HGNC:37102"; havana_gene "OTTHUMG00000000961.2_2"; remap_status "full_contig"; remap_num_mappings 1; remap_target_status "overlap";', + 'chr1 HAVANA gene 621059 622053 . - . gene_id "ENSG00000284662.1_2"; gene_type "protein_coding"; gene_name "OR4F16"; level 2; hgnc_id "HGNC:15079"; havana_gene "OTTHUMG00000002581.3_2"; remap_status "full_contig"; remap_num_mappings 1; remap_target_status "overlap";', + 'GL000193.1 HAVANA gene 77815 78162 . + . gene_id "ENSG00000279783.1_5"; gene_type "processed_pseudogene"; gene_name "AC018692.2"; level 2; havana_gene "OTTHUMG00000189459.1_5"; remap_status "full_contig"; remap_num_mappings 1; remap_target_status "new";', +] +GENE_ID_MAPPING = { + 'DDX11L1': 'ENSG00000223972', + 'OR4F16': 'ENSG00000284662', + 'AC018692.2': 'ENSG00000279783', +} + + +ENSEMBL_TO_REFSEQ_DATA = b"""ENST00000424215.1\tNR_121638.1 +ENST00000378391.6\tNM_199454.3\tNP_955533.2 +ENST00000270722.10\tNM_022114.4\tNP_071397.3 +ENST00000288774.8\tNM_001374425.1\tNP_001361354.1""" + + +class LoadGencodeTestCase(unittest.TestCase): + @responses.activate + def test_load_gencode_gene_symbol_to_gene_id(self): + url = GENCODE_GTF_URL.format(gencode_release=12) + responses.add( + responses.GET, + url, + body=gzip.compress(('\n'.join(GTF_DATA)).encode()), + ) + mapping = load_gencode_gene_symbol_to_gene_id(12) + self.assertDictEqual( + mapping, + { + 'AC018692.2': 'ENSG00000279783', + 'DDX11L1': 'ENSG00000223972', + 'OR4F16': 'ENSG00000284662', + }, + ) + + @responses.activate + def test_load_gencode_ensembl_to_refseq_id(self): + url = GENCODE_ENSEMBL_TO_REFSEQ_URL.format(gencode_release=20) + responses.add(responses.GET, url, body=gzip.compress(ENSEMBL_TO_REFSEQ_DATA)) + mapping = load_gencode_ensembl_to_refseq_id(20) + self.assertDictEqual( + mapping, + { + 'ENST00000424215': 'NR_121638.1', + 'ENST00000378391': 'NM_199454.3', + 'ENST00000270722': 'NM_022114.4', + 'ENST00000288774': 'NM_001374425.1', + }, + ) diff --git a/loading_pipeline/lib/reference_datasets/gnomad_coding_and_noncoding.py b/loading_pipeline/lib/reference_datasets/gnomad_coding_and_noncoding.py new file mode 100644 index 0000000000..9b197276a8 --- /dev/null +++ b/loading_pipeline/lib/reference_datasets/gnomad_coding_and_noncoding.py @@ -0,0 +1,59 @@ +import hail as hl + +from loading_pipeline.lib.annotations.enums import ( + TRANSCRIPT_CONSEQUENCE_TERMS, +) +from loading_pipeline.lib.annotations.expression_helpers import ( + get_expr_for_vep_sorted_transcript_consequences_array, + get_expr_for_worst_transcript_consequence_annotations_struct, +) +from loading_pipeline.lib.core import ReferenceGenome + +GNOMAD_CODING_NONCODING_HIGH_AF_THRESHOLD = 0.90 +TRANSCRIPT_CONSEQUENCE_TERM_RANK_LOOKUP = hl.dict( + hl.enumerate(TRANSCRIPT_CONSEQUENCE_TERMS, index_first=False), +) + + +def get_ht( + path: str, + reference_genome: ReferenceGenome, +) -> hl.Table: + ht = hl.read_table(path) + filtered_contig = 'chr1' if reference_genome == ReferenceGenome.GRCh38 else '1' + ht = hl.filter_intervals( + ht, + [ + hl.parse_locus_interval( + filtered_contig, + reference_genome=reference_genome.value, + ), + ], + ) + ht = ht.filter(ht.freq[0].AF > GNOMAD_CODING_NONCODING_HIGH_AF_THRESHOLD) + ht = ht.annotate( + sorted_transaction_consequences=( + get_expr_for_vep_sorted_transcript_consequences_array( + ht.vep, + omit_consequences=[], + ) + ), + ) + ht = ht.annotate( + main_transcript=( + get_expr_for_worst_transcript_consequence_annotations_struct( + ht.sorted_transaction_consequences, + ) + ), + ) + ht = ht.select( + coding=( + ht.main_transcript.major_consequence_rank + <= TRANSCRIPT_CONSEQUENCE_TERM_RANK_LOOKUP['synonymous_variant'] + ), + noncoding=( + ht.main_transcript.major_consequence_rank + >= TRANSCRIPT_CONSEQUENCE_TERM_RANK_LOOKUP['downstream_gene_variant'] + ), + ) + return ht.filter(ht.coding | ht.noncoding) diff --git a/loading_pipeline/lib/reference_datasets/gnomad_exomes.py b/loading_pipeline/lib/reference_datasets/gnomad_exomes.py new file mode 100644 index 0000000000..abe0fc3d88 --- /dev/null +++ b/loading_pipeline/lib/reference_datasets/gnomad_exomes.py @@ -0,0 +1,21 @@ +import hail as hl + +from loading_pipeline.lib.core import ReferenceGenome +from loading_pipeline.lib.reference_datasets.gnomad_utils import get_ht as _get_ht + + +def af_popmax_expression( + ht: hl.Table, + reference_genome: ReferenceGenome, +) -> hl.Expression: + if reference_genome == ReferenceGenome.GRCh37: + return ht.popmax[ht.globals.popmax_index_dict['gnomad']].AF + return ht.grpmax['gnomad'].AF + + +def get_ht(path: str, reference_genome: ReferenceGenome) -> hl.Table: + return _get_ht( + path, + reference_genome, + af_popmax_expression, + ) diff --git a/loading_pipeline/lib/reference_datasets/gnomad_exomes_test.py b/loading_pipeline/lib/reference_datasets/gnomad_exomes_test.py new file mode 100644 index 0000000000..639dc6d894 --- /dev/null +++ b/loading_pipeline/lib/reference_datasets/gnomad_exomes_test.py @@ -0,0 +1,72 @@ +import unittest +from unittest.mock import patch + +import hail as hl + +from loading_pipeline.lib.core.definitions import ReferenceGenome +from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset + +GNOMAD_EXOMES_37_PATH = ( + 'loading_pipeline/var/test/reference_datasets/raw/gnomad_exomes_37.ht' +) +GNOMAD_EXOMES_38_PATH = ( + 'loading_pipeline/var/test/reference_datasets/raw/gnomad_exomes_38.ht' +) + + +class GnomadTest(unittest.TestCase): + def test_gnomad_exomes_37(self): + with patch.object( + ReferenceDataset, + 'path', + return_value=GNOMAD_EXOMES_37_PATH, + ): + ht = ReferenceDataset.gnomad_exomes.get_ht(ReferenceGenome.GRCh37) + self.assertEqual( + ht.collect(), + [ + hl.Struct( + locus=hl.Locus( + contig='1', + position=12586, + reference_genome='GRCh37', + ), + alleles=['C', 'T'], + AF=0.0005589714855886996, + AN=3578, + AC=2, + Hom=0, + AF_POPMAX_OR_GLOBAL=0.0022026430815458298, + FAF_AF=9.839000267675146e-05, + Hemi=0, + ), + ], + ) + + def test_gnomad_exomes_38(self): + with patch.object( + ReferenceDataset, + 'path', + return_value=GNOMAD_EXOMES_38_PATH, + ): + ht = ReferenceDataset.gnomad_exomes.get_ht(ReferenceGenome.GRCh38) + self.assertEqual( + ht.collect(), + [ + hl.Struct( + locus=hl.Locus( + contig='chr1', + position=12138, + reference_genome='GRCh38', + ), + alleles=['C', 'A'], + AF=0.00909090880304575, + AN=110, + AC=1, + Hom=0, + AF_POPMAX_OR_GLOBAL=0.009803921915590763, + FAF_AF=0.0, + Hemi=0, + ), + ], + ) diff --git a/loading_pipeline/lib/reference_datasets/gnomad_genomes.py b/loading_pipeline/lib/reference_datasets/gnomad_genomes.py new file mode 100644 index 0000000000..ff63586c78 --- /dev/null +++ b/loading_pipeline/lib/reference_datasets/gnomad_genomes.py @@ -0,0 +1,21 @@ +import hail as hl + +from loading_pipeline.lib.core import ReferenceGenome +from loading_pipeline.lib.reference_datasets.gnomad_utils import get_ht as _get_ht + + +def af_popmax_expression( + ht: hl.Table, + reference_genome: ReferenceGenome, +) -> hl.Expression: + if reference_genome == ReferenceGenome.GRCh37: + return ht.popmax[ht.globals.popmax_index_dict['gnomad']].AF + return ht.grpmax.AF + + +def get_ht(path: str, reference_genome: ReferenceGenome) -> hl.Table: + return _get_ht( + path, + reference_genome, + af_popmax_expression, + ) diff --git a/loading_pipeline/lib/reference_datasets/gnomad_genomes_test.py b/loading_pipeline/lib/reference_datasets/gnomad_genomes_test.py new file mode 100644 index 0000000000..df637c2fda --- /dev/null +++ b/loading_pipeline/lib/reference_datasets/gnomad_genomes_test.py @@ -0,0 +1,72 @@ +import unittest +from unittest.mock import patch + +import hail as hl + +from loading_pipeline.lib.core.definitions import ReferenceGenome +from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset + +GNOMAD_GENOMES_37_PATH = ( + 'loading_pipeline/var/test/reference_datasets/raw/gnomad_genomes_37.ht' +) +GNOMAD_GENOMES_38_PATH = ( + 'loading_pipeline/var/test/reference_datasets/raw/gnomad_genomes_38.ht' +) + + +class GnomadTest(unittest.TestCase): + def test_gnomad_genomes_37(self): + with patch.object( + ReferenceDataset, + 'path', + return_value=GNOMAD_GENOMES_37_PATH, + ): + ht = ReferenceDataset.gnomad_genomes.get_ht(ReferenceGenome.GRCh37) + self.assertEqual( + ht.collect(), + [ + hl.Struct( + locus=hl.Locus( + contig='1', + position=10131, + reference_genome='GRCh37', + ), + alleles=['CT', 'C'], + AF=3.6635403375839815e-05, + AN=27296, + AC=1, + Hom=0, + AF_POPMAX_OR_GLOBAL=3.6635403375839815e-05, + FAF_AF=0.0, + Hemi=0, + ), + ], + ) + + def test_gnomad_genomes_38(self): + with patch.object( + ReferenceDataset, + 'path', + return_value=GNOMAD_GENOMES_38_PATH, + ): + ht = ReferenceDataset.gnomad_genomes.get_ht(ReferenceGenome.GRCh38) + self.assertEqual( + ht.collect(), + [ + hl.Struct( + locus=hl.Locus( + contig='chr1', + position=10057, + reference_genome='GRCh38', + ), + alleles=['A', 'C'], + AF=2.642333674884867e-05, + AN=113536, + AC=3, + Hom=0, + AF_POPMAX_OR_GLOBAL=3.779861071961932e-05, + FAF_AF=7.019999884505523e-06, + Hemi=0, + ), + ], + ) diff --git a/loading_pipeline/lib/reference_datasets/gnomad_qc.py b/loading_pipeline/lib/reference_datasets/gnomad_qc.py new file mode 100644 index 0000000000..481a6ccda8 --- /dev/null +++ b/loading_pipeline/lib/reference_datasets/gnomad_qc.py @@ -0,0 +1,9 @@ +import hail as hl + +from loading_pipeline.lib.core import ReferenceGenome + + +def get_ht(path: str, reference_genome: ReferenceGenome) -> hl.Table: + if reference_genome == ReferenceGenome.GRCh37: + return hl.read_matrix_table(path).rows() + return hl.read_table(path) diff --git a/loading_pipeline/lib/reference_datasets/gnomad_svs.py b/loading_pipeline/lib/reference_datasets/gnomad_svs.py new file mode 100644 index 0000000000..8b453fd948 --- /dev/null +++ b/loading_pipeline/lib/reference_datasets/gnomad_svs.py @@ -0,0 +1,17 @@ +import hail as hl + +from loading_pipeline.lib.core import ReferenceGenome +from loading_pipeline.lib.reference_datasets.misc import vcf_to_ht + + +def get_ht(path: str, reference_genome: ReferenceGenome) -> hl.Table: + ht = vcf_to_ht(path, reference_genome) + ht = ht.select( + KEY=ht.rsid, + AF=ht.info.AF[0], + AC=ht.info.AC[0], + AN=ht.info.AN, + N_HET=ht.info.N_HET, + N_HOM=ht.info.N_HOMALT, + ) + return ht.key_by('KEY') diff --git a/loading_pipeline/lib/reference_datasets/gnomad_svs_test.py b/loading_pipeline/lib/reference_datasets/gnomad_svs_test.py new file mode 100644 index 0000000000..bfd7c89d11 --- /dev/null +++ b/loading_pipeline/lib/reference_datasets/gnomad_svs_test.py @@ -0,0 +1,93 @@ +import unittest +from unittest.mock import patch + +import hail as hl + +from loading_pipeline.lib.core import ReferenceGenome +from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset + +TEST_GNOMAD_SVS_RAW_HT = ( + 'loading_pipeline/var/test/reference_datasets/raw/gnomad_svs_from_vcf.ht' +) + + +class GnomadSVsTest(unittest.TestCase): + @patch('loading_pipeline.lib.reference_datasets.gnomad_svs.vcf_to_ht') + def test_gnomad_svs(self, mock_vcf_to_ht): + mock_vcf_to_ht.return_value = hl.read_table(TEST_GNOMAD_SVS_RAW_HT) + ht = ReferenceDataset.gnomad_svs.get_ht(ReferenceGenome.GRCh38) + self.assertEqual( + ht.collect(), + [ + hl.Struct( + KEY='gnomAD-SV_v3_BND_chr1_1a45f73a', + locus=hl.Locus( + contig='chr1', + position=10434, + reference_genome=ReferenceGenome.GRCh38, + ), + alleles=['N', ''], + AF=0.11413399875164032, + AC=8474, + AN=74246, + N_HET=8426, + N_HOM=24, + ), + hl.Struct( + KEY='gnomAD-SV_v3_BND_chr1_3fa36917', + locus=hl.Locus( + contig='chr1', + position=10440, + reference_genome=ReferenceGenome.GRCh38, + ), + alleles=['N', ''], + AF=0.004201000090688467, + AC=466, + AN=110936, + N_HET=466, + N_HOM=0, + ), + hl.Struct( + KEY='gnomAD-SV_v3_BND_chr1_7bbf34b5', + locus=hl.Locus( + contig='chr1', + position=10464, + reference_genome=ReferenceGenome.GRCh38, + ), + alleles=['N', ''], + AF=0.03698499873280525, + AC=3119, + AN=84332, + N_HET=3115, + N_HOM=2, + ), + hl.Struct( + KEY='gnomAD-SV_v3_BND_chr1_933a2971', + locus=hl.Locus( + contig='chr1', + position=10450, + reference_genome=ReferenceGenome.GRCh38, + ), + alleles=['N', ''], + AF=0.3238990008831024, + AC=21766, + AN=67200, + N_HET=21616, + N_HOM=75, + ), + hl.Struct( + KEY='gnomAD-SV_v3_DUP_chr1_01c2781c', + locus=hl.Locus( + contig='chr1', + position=10000, + reference_genome=ReferenceGenome.GRCh38, + ), + alleles=['N', ''], + AF=0.0019970000721514225, + AC=139, + AN=69594, + N_HET=139, + N_HOM=0, + ), + ], + ) diff --git a/loading_pipeline/lib/reference_datasets/gnomad_utils.py b/loading_pipeline/lib/reference_datasets/gnomad_utils.py new file mode 100644 index 0000000000..2e02f56490 --- /dev/null +++ b/loading_pipeline/lib/reference_datasets/gnomad_utils.py @@ -0,0 +1,55 @@ +from collections.abc import Callable + +import hail as hl + +from loading_pipeline.lib.core import ReferenceGenome + + +def global_idx_field(reference_genome: ReferenceGenome) -> str: + return 'gnomad' if reference_genome == ReferenceGenome.GRCh37 else 'adj' + + +def faf_globals_field(reference_genome: ReferenceGenome) -> str: + return ( + 'popmax_index_dict' + if reference_genome == ReferenceGenome.GRCh37 + else 'faf_index_dict' + ) + + +def hemi_field(reference_genome: ReferenceGenome) -> str: + return 'gnomad_male' if reference_genome == ReferenceGenome.GRCh37 else 'XY_adj' + + +def get_ht( + path: str, + reference_genome: ReferenceGenome, + af_popmax_expression: Callable, +) -> hl.Table: + ht = hl.read_table(path) + global_idx = hl.eval(ht.globals.freq_index_dict[global_idx_field(reference_genome)]) + ht = ht.select( + AF=hl.float32(ht.freq[global_idx].AF), + AN=ht.freq[global_idx].AN, + AC=ht.freq[global_idx].AC, + Hom=ht.freq[global_idx].homozygote_count, + AF_POPMAX_OR_GLOBAL=hl.float32( + hl.or_else( + af_popmax_expression(ht, reference_genome), + ht.freq[global_idx].AF, + ), + ), + FAF_AF=hl.float32( + ht.faf[ + ht.globals[faf_globals_field(reference_genome)][ + global_idx_field(reference_genome) + ] + ].faf95, + ), + Hemi=hl.if_else( + ht.locus.in_autosome_or_par(), + 0, + ht.freq[ht.globals.freq_index_dict[hemi_field(reference_genome)]].AC, + ), + ) + return ht.select_globals() diff --git a/loading_pipeline/lib/reference_datasets/misc.py b/loading_pipeline/lib/reference_datasets/misc.py new file mode 100644 index 0000000000..73b4d17c0a --- /dev/null +++ b/loading_pipeline/lib/reference_datasets/misc.py @@ -0,0 +1,145 @@ +import contextlib +import os +import random +import string +import tempfile +import zipfile + +import hail as hl +import hailtop.fs as hfs +import requests + +from loading_pipeline.lib.core.definitions import ReferenceGenome +from loading_pipeline.lib.core.environment import Env +from loading_pipeline.lib.misc.io import split_multi_hts + +BIALLELIC = 2 + + +def compress_floats(ht: hl.Table): + # Parse float64s into float32s to save space! + return ht.select( + **{ + k: hl.float32(v) if v.dtype == hl.tfloat64 else v + for k, v in ht.row_value.items() + }, + ) + + +def generate_random_string(length=5): + """Generates a random string of the specified length.""" + letters = string.ascii_letters + string.digits + return ''.join(random.choice(letters) for i in range(length)) # noqa: S311 + + +def filter_contigs(ht, reference_genome: ReferenceGenome): + if hasattr(ht, 'interval'): + return ht.filter( + hl.set(reference_genome.standard_contigs).contains( + ht.interval.start.contig, + ), + ) + # SV reference datasets are not keyed by locus. + if hasattr(ht, 'locus'): + return ht.filter( + hl.set(reference_genome.standard_contigs).contains(ht.locus.contig), + ) + return ht + + +def vcf_to_ht( + file_name: str, + reference_genome: ReferenceGenome, + split_multi=False, +) -> hl.Table: + mt = hl.import_vcf( + file_name, + reference_genome=reference_genome.value, + drop_samples=True, + skip_invalid_loci=True, + contig_recoding=reference_genome.contig_recoding(include_mt=True), + force_bgz=True, + array_elements_required=False, + ) + if split_multi: + return split_multi_hts(mt, True).rows() + + # Validate that there exist no multialellic variants in the table. + count_non_biallelic = mt.aggregate_rows( + hl.agg.count_where(hl.len(mt.alleles) > BIALLELIC), + ) + if count_non_biallelic: + error = f'Encountered {count_non_biallelic} multiallelic variants' + raise ValueError(error) + return mt.rows() + + +def key_by_locus_alleles(ht: hl.Table, reference_genome: ReferenceGenome) -> hl.Table: + chrom = ( + hl.format('chr%s', ht.chrom) + if reference_genome == ReferenceGenome.GRCh38 + else hl.if_else(ht.chrom == 'M', 'MT', ht.chrom) + ) + ht = ht.transmute( + locus=hl.locus(chrom, ht.pos, reference_genome.value), + alleles=hl.array([ht.ref, ht.alt]), + ) + return ht.key_by('locus', 'alleles') + + +def copyfileobj(fsrc, fdst, decode_content, length=16 * 1024): + """Copy data from file-like object fsrc to file-like object fdst.""" + while True: + buf = fsrc.read(length, decode_content=decode_content) + if not buf: + break + fdst.write(buf) + + +@contextlib.contextmanager +def download_zip_file(url, dataset_name: str, suffix='.zip', decode_content=False): + dir_ = f'/tmp/{generate_random_string()}/{dataset_name}' # noqa: S108 + os.makedirs(dir_, exist_ok=True) + with ( + tempfile.NamedTemporaryFile( + dir=dir_, + suffix=suffix, + ) as tmp_file, + requests.get(url, stream=True, timeout=10) as r, + ): + copyfileobj(r.raw, tmp_file, decode_content) + with zipfile.ZipFile(tmp_file.name, 'r') as zipf: + zipf.extractall(dir_) + yield copy_to_cloud_storage(dir_) + + +def select_for_interval_reference_dataset( + ht: hl.Table, + reference_genome: ReferenceGenome, + additional_selects: dict, + chrom_field: str = 'chrom', + start_field: str = 'start', + end_field: str = 'end', +) -> hl.Table: + ht = ht.select( + interval=hl.locus_interval( + ht[chrom_field], + ht[start_field] + 1, + ht[end_field] + 1, + reference_genome=reference_genome.value, + invalid_missing=True, + ), + **additional_selects, + ) + return ht.key_by('interval') + + +def copy_to_cloud_storage(file_name: str) -> str: + if not Env.HAIL_TMP_DIR.startswith('gs://'): + return file_name + if os.path.isdir(file_name): + cloud_storage_path = os.path.join(Env.HAIL_TMP_DIR, file_name.lstrip('/')) + else: + cloud_storage_path = os.path.join(Env.HAIL_TMP_DIR, os.path.basename(file_name)) + hfs.copy(file_name, cloud_storage_path) + return cloud_storage_path diff --git a/loading_pipeline/lib/reference_datasets/reference_dataset.py b/loading_pipeline/lib/reference_datasets/reference_dataset.py new file mode 100644 index 0000000000..aa3e6f1cc3 --- /dev/null +++ b/loading_pipeline/lib/reference_datasets/reference_dataset.py @@ -0,0 +1,178 @@ +import importlib +import types +from collections.abc import Callable +from enum import StrEnum + +import hail as hl + +from loading_pipeline.lib.annotations import sv +from loading_pipeline.lib.core import ( + DatasetType, + ReferenceGenome, +) +from loading_pipeline.lib.misc.validation import ( + validate_allele_type, + validate_no_duplicate_variants, +) +from loading_pipeline.lib.reference_datasets.misc import ( + compress_floats, + filter_contigs, +) + +DATASET_TYPES = 'dataset_types' +FORMATTING_ANNOTATION = 'formatting_annotation' +SELECT = 'select' +VERSION = 'version' +PATH = 'path' + + +class ReferenceDataset(StrEnum): + eigen = 'eigen' + splice_ai = 'splice_ai' + topmed = 'topmed' + gnomad_coding_and_noncoding = 'gnomad_coding_and_noncoding' + gnomad_exomes = 'gnomad_exomes' + gnomad_genomes = 'gnomad_genomes' + gnomad_qc = 'gnomad_qc' + gnomad_svs = 'gnomad_svs' + + @property + def formatting_annotation(self) -> Callable | None: + return CONFIG[self].get(FORMATTING_ANNOTATION) + + def version(self, reference_genome: ReferenceGenome) -> str: + version = CONFIG[self][reference_genome][VERSION] + if isinstance(version, types.FunctionType): + return version( + self.path(reference_genome), + ) + return version + + def dataset_types( + self, + reference_genome: ReferenceGenome, + ) -> frozenset[DatasetType]: + return CONFIG[self].get(reference_genome, {}).get(DATASET_TYPES, frozenset()) + + @property + def select( + self, + ) -> Callable[[ReferenceGenome, DatasetType, hl.Table], hl.Table] | None: + return CONFIG[self].get(SELECT) + + def path(self, reference_genome: ReferenceGenome) -> str | list[str]: + return CONFIG[self][reference_genome][PATH] + + def get_ht( + self, + reference_genome: ReferenceGenome, + ) -> hl.Table: + module = importlib.import_module( + f'loading_pipeline.lib.reference_datasets.{self.name}', + ) + path = self.path(reference_genome) + ht = module.get_ht(path, reference_genome) + ht = compress_floats(ht) + ht = filter_contigs(ht, reference_genome) + for dataset_type in self.dataset_types(reference_genome): + validate_allele_type(ht, dataset_type) + validate_no_duplicate_variants(ht, reference_genome, dataset_type) + return ht + + +CONFIG = { + ReferenceDataset.eigen: { + ReferenceGenome.GRCh37: { + DATASET_TYPES: frozenset([DatasetType.SNV_INDEL]), + VERSION: '1.1', + # NB: The download link on the Eigen website (http://www.columbia.edu/~ii2135/download.html) is broken + # as of 11/15/24 so we will host the data + PATH: 'gs://seqr-reference-data/GRCh37/eigen/EIGEN_coding_noncoding.grch37.ht', + }, + ReferenceGenome.GRCh38: { + DATASET_TYPES: frozenset([DatasetType.SNV_INDEL]), + VERSION: '1.1', + PATH: 'gs://seqr-reference-data/GRCh38/eigen/EIGEN_coding_noncoding.liftover_grch38.ht', + }, + }, + ReferenceDataset.splice_ai: { + ReferenceGenome.GRCh37: { + DATASET_TYPES: frozenset([DatasetType.SNV_INDEL]), + VERSION: '1.1', + PATH: [ + 'gs://seqr-reference-data/GRCh37/spliceai/spliceai_scores.masked.snv.hg19.vcf.gz', + 'gs://seqr-reference-data/GRCh37/spliceai/spliceai_scores.masked.indel.hg19.vcf.gz', + ], + }, + ReferenceGenome.GRCh38: { + DATASET_TYPES: frozenset([DatasetType.SNV_INDEL]), + VERSION: '1.1', + # NB: SpliceAI data is only available to download for authenticated Illumina users, so we will host the data + PATH: [ + 'gs://seqr-reference-data/GRCh38/spliceai/spliceai_scores.masked.snv.hg38.vcf.gz', + 'gs://seqr-reference-data/GRCh38/spliceai/spliceai_scores.masked.indel.hg38.vcf.gz', + ], + }, + }, + ReferenceDataset.topmed: { + ReferenceGenome.GRCh37: { + DATASET_TYPES: frozenset([DatasetType.SNV_INDEL]), + VERSION: '1.1', + PATH: 'gs://seqr-reference-data/GRCh37/TopMed/bravo-dbsnp-all.removed_chr_prefix.liftunder_GRCh37.vcf.gz', + }, + ReferenceGenome.GRCh38: { + DATASET_TYPES: frozenset([DatasetType.SNV_INDEL]), + VERSION: '1.1', + # NB: TopMed data is available to download via https://legacy.bravo.sph.umich.edu/freeze8/hg38/downloads/vcf/ + # However, users must be authenticated and accept TOS to access it so for now we will host a copy of the data + PATH: 'gs://seqr-reference-data/GRCh38/TopMed/bravo-dbsnp-all.vcf.gz', + }, + }, + ReferenceDataset.gnomad_exomes: { + ReferenceGenome.GRCh37: { + DATASET_TYPES: frozenset([DatasetType.SNV_INDEL]), + VERSION: '1.0', + PATH: 'gs://gcp-public-data--gnomad/release/2.1.1/ht/exomes/gnomad.exomes.r2.1.1.sites.ht', + }, + ReferenceGenome.GRCh38: { + DATASET_TYPES: frozenset([DatasetType.SNV_INDEL]), + VERSION: '1.0', + PATH: 'gs://gcp-public-data--gnomad/release/4.1/ht/exomes/gnomad.exomes.v4.1.sites.ht', + }, + }, + ReferenceDataset.gnomad_genomes: { + ReferenceGenome.GRCh37: { + DATASET_TYPES: frozenset([DatasetType.SNV_INDEL]), + VERSION: '1.0', + PATH: 'gs://gcp-public-data--gnomad/release/2.1.1/ht/genomes/gnomad.genomes.r2.1.1.sites.ht', + }, + ReferenceGenome.GRCh38: { + DATASET_TYPES: frozenset([DatasetType.SNV_INDEL]), + VERSION: '1.0', + PATH: 'gs://gcp-public-data--gnomad/release/4.1/ht/genomes/gnomad.genomes.v4.1.sites.ht', + }, + }, + ReferenceDataset.gnomad_qc: { + ReferenceGenome.GRCh37: { + DATASET_TYPES: frozenset([DatasetType.SNV_INDEL]), + VERSION: '1.0', + PATH: 'gs://seqr-reference-data/gnomad_qc/GRCh37/gnomad.joint.high_callrate_common_biallelic_snps.pruned.mt', + }, + ReferenceGenome.GRCh38: { + DATASET_TYPES: frozenset([DatasetType.SNV_INDEL]), + VERSION: '1.0', + PATH: 'gs://gcp-public-data--gnomad/release/4.0/pca/gnomad.v4.0.pca_loadings.ht', + }, + }, + ReferenceDataset.gnomad_svs: { + FORMATTING_ANNOTATION: sv.gnomad_svs, + ReferenceGenome.GRCh38: { + DATASET_TYPES: frozenset([DatasetType.SV]), + VERSION: '1.1', + PATH: 'gs://gcp-public-data--gnomad/release/4.1/genome_sv/gnomad.v4.1.sv.sites.vcf.gz', + }, + }, +} +CONFIG[ReferenceDataset.gnomad_coding_and_noncoding] = { + **CONFIG[ReferenceDataset.gnomad_genomes], +} diff --git a/loading_pipeline/lib/reference_datasets/splice_ai.py b/loading_pipeline/lib/reference_datasets/splice_ai.py new file mode 100644 index 0000000000..4d6a9e8a3f --- /dev/null +++ b/loading_pipeline/lib/reference_datasets/splice_ai.py @@ -0,0 +1,71 @@ +import hail as hl + +from loading_pipeline.lib.core import ReferenceGenome +from loading_pipeline.lib.misc.io import ( + checkpoint, + compute_hail_n_partitions, + file_size_bytes, +) +from loading_pipeline.lib.reference_datasets.misc import vcf_to_ht + + +def remove_duplicate_scores(ht: hl.Table): + # + # SpliceAI has many duplicate rows of the ilk: + # + # 1:861264 | ["C","A"] | NA | -1.00e+01 | NA | ["A|AL645608.1|0.00|0.00|0.00|0.00|2|27|12|1"] | + # 1:861264 | ["C","A"] | NA | -1.00e+01 | NA | ["A|SAMD11|0.02|0.01|0.00|0.00|14|38|14|38"] + # + count_ht = ht.group_by(*ht.key).aggregate(n=hl.agg.count()) + duplicate_variants_ht = count_ht.filter(count_ht.n > 1) + duplicates_ht = ht.semi_join(duplicate_variants_ht) + non_duplicates_ht = ht.anti_join(duplicates_ht) + return non_duplicates_ht.union( + # Remove rows that 1) are part of duplicate variant groupings + # and 2) contain dots. Then, remove arbitrarily with .distinct() + duplicates_ht.filter( + ~duplicates_ht.info.SpliceAI[0].split(delim='\\|')[1].contains('.'), + ).distinct(), + ) + + +def get_ht( + paths: list[str], + reference_genome: ReferenceGenome, +) -> hl.Table: + # NB: We ran into weird issues...running out + # of file descriptors on dataproc :/ + hl._set_flags(use_new_shuffle=None, no_whole_stage_codegen='1') # noqa: SLF001 + ht = vcf_to_ht(paths, reference_genome) + ht, checkpoint_path = checkpoint(ht) + # The default partitions are too big, leading to OOMs. + ht = ht.repartition( + int(compute_hail_n_partitions(file_size_bytes(checkpoint_path)) * 2), + # Note that shuffle=True here, since this is one of the few + # cases in the pipeline where we want to increase the number + # of partititons. + ) + ht, _ = checkpoint(ht) + ht = remove_duplicate_scores(ht) + + # SpliceAI INFO field description from the VCF header: SpliceAIv1.3 variant annotation. These include + # delta scores (DS) and delta positions (DP) for acceptor gain (AG), acceptor loss (AL), donor gain (DG), and + # donor loss (DL). Format: ALLELE|SYMBOL|DS_AG|DS_AL|DS_DG|DS_DL|DP_AG|DP_AL|DP_DG|DP_DL + ds_start_index = 2 + ds_end_index = 6 + num_delta_scores = ds_end_index - ds_start_index + ht = ht.select( + delta_scores=ht.info.SpliceAI[0] + .split(delim='\\|')[ds_start_index:ds_end_index] + .map(hl.float32), + ) + ht = ht.annotate(delta_score=hl.max(ht.delta_scores)) + return ht.annotate( + splice_consequence_id=hl.if_else( + ht.delta_score > 0, + # Splice Consequence enum ID is the index of the max score + ht.delta_scores.index(ht.delta_score), + # If no score, use the last index for "No Consequence" + num_delta_scores, + ), + ).drop('delta_scores') diff --git a/loading_pipeline/lib/reference_datasets/topmed.py b/loading_pipeline/lib/reference_datasets/topmed.py new file mode 100644 index 0000000000..3172df2374 --- /dev/null +++ b/loading_pipeline/lib/reference_datasets/topmed.py @@ -0,0 +1,22 @@ +import hail as hl + +from loading_pipeline.lib.core import ReferenceGenome +from loading_pipeline.lib.misc.nested_field import parse_nested_field +from loading_pipeline.lib.reference_datasets.misc import vcf_to_ht + +SELECT = { + 'AC': 'info.AC#', + 'AF': 'info.AF#', + 'AN': 'info.AN', + 'Hom': 'info.Hom#', + 'Het': 'info.Het#', +} + + +def get_ht(path: str, reference_genome: ReferenceGenome) -> hl.Table: + ht = vcf_to_ht(path, reference_genome) + if reference_genome == ReferenceGenome.GRCh37: + ht = ht.filter(ht.locus.position == hl.int(ht.info.OriginalStart)) + return ht.select( + **{k: parse_nested_field(ht, v) for k, v in SELECT.items()}, + ) diff --git a/loading_pipeline/lib/tasks/__init__.py b/loading_pipeline/lib/tasks/__init__.py new file mode 100644 index 0000000000..7ec456e200 --- /dev/null +++ b/loading_pipeline/lib/tasks/__init__.py @@ -0,0 +1,29 @@ +from loading_pipeline.lib.tasks.clickhouse_migration.migrate_all_projects_to_clickhouse import ( + MigrateAllProjectsToClickHouseTask, +) +from loading_pipeline.lib.tasks.clickhouse_migration.migrate_all_projects_to_clickhouse_on_dataproc import ( + MigrateAllProjectsToClickHouseOnDataprocTask, +) +from loading_pipeline.lib.tasks.reference_data.updated_reference_dataset_parquet import ( + UpdatedReferenceDatasetParquetTask, +) +from loading_pipeline.lib.tasks.run_pipeline import RunPipelineTask +from loading_pipeline.lib.tasks.variants_migration.migrate_variant_details_parquet import ( + MigrateVariantDetailsParquetTask, +) +from loading_pipeline.lib.tasks.variants_migration.migrate_variants_parquet import ( + MigrateVariantsParquetTask, +) +from loading_pipeline.lib.tasks.write_metadata_for_run import WriteMetadataForRunTask +from loading_pipeline.lib.tasks.write_success_file import WriteSuccessFileTask + +__all__ = [ + 'MigrateAllProjectsToClickHouseOnDataprocTask', + 'MigrateAllProjectsToClickHouseTask', + 'MigrateVariantDetailsParquetTask', + 'MigrateVariantsParquetTask', + 'RunPipelineTask', + 'UpdatedReferenceDatasetParquetTask', + 'WriteMetadataForRunTask', + 'WriteSuccessFileTask', +] diff --git a/loading_pipeline/lib/tasks/base/__init__.py b/loading_pipeline/lib/tasks/base/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/loading_pipeline/lib/tasks/base/base_hail_table.py b/loading_pipeline/lib/tasks/base/base_hail_table.py new file mode 100644 index 0000000000..e069bd35b4 --- /dev/null +++ b/loading_pipeline/lib/tasks/base/base_hail_table.py @@ -0,0 +1,71 @@ +import hail as hl +import luigi + +from loading_pipeline.lib.annotations.liftover import remove_liftover +from loading_pipeline.lib.core import Env +from loading_pipeline.lib.logger import get_logger +from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( + BaseLoadingPipelineParams, +) +from loading_pipeline.lib.tasks.files import GCSorLocalFolderTarget + +logger = get_logger(__name__) + + +@luigi.util.inherits(BaseLoadingPipelineParams) +class BaseHailTableTask(luigi.Task): + def output(self) -> luigi.Target: + raise NotImplementedError + + def complete(self) -> bool: + logger.info(f'BaseHailTableTask: checking if {self.output().path} exists') + return GCSorLocalFolderTarget(self.output().path).exists() + + def init_hail(self): + # Need to use the GCP bucket as temp storage for very large callset joins + hl.init(tmp_dir=Env.HAIL_TMP_DIR, idempotent=True) + logger.info(f'Initialized hail w/ tmp_dir {Env.HAIL_TMP_DIR}') + + # Interval ref data join causes shuffle death, this prevents it + hl._set_flags(use_new_shuffle='1', no_whole_stage_codegen='1') # noqa: SLF001 + + # Ensure any cached liftover files within Hail are cleared + # to provide a clean context free of hidden state. + # This runs "before" a task to account for situations where + # the Hail write fails and we do not have the chance to + # run this method in the "after". + remove_liftover() + + +# NB: these are defined over luigi.Task instead of the BaseHailTableTask so that +# they work on file dependencies. + + +@luigi.Task.event_handler(luigi.Event.DEPENDENCY_DISCOVERED) +def dependency_discovered(task, dependency): + logger.info(f'{task} dependency_discovered {dependency} at {task.output()}') + + +@luigi.Task.event_handler(luigi.Event.DEPENDENCY_MISSING) +def dependency_missing(task): + logger.info(f'{task} dependency_missing at {task.output()}') + + +@luigi.Task.event_handler(luigi.Event.DEPENDENCY_PRESENT) +def dependency_present(task): + logger.info(f'{task} dependency_present at {task.output()}') + + +@luigi.Task.event_handler(luigi.Event.START) +def start(task): + logger.info(f'{task} start') + + +@luigi.Task.event_handler(luigi.Event.FAILURE) +def failure(task, _): + logger.exception(f'{task} failure') + + +@luigi.Task.event_handler(luigi.Event.SUCCESS) +def success(task): + logger.info(f'{task} success') diff --git a/loading_pipeline/lib/tasks/base/base_loading_pipeline_params.py b/loading_pipeline/lib/tasks/base/base_loading_pipeline_params.py new file mode 100644 index 0000000000..1e9ea4ee93 --- /dev/null +++ b/loading_pipeline/lib/tasks/base/base_loading_pipeline_params.py @@ -0,0 +1,12 @@ +import luigi + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome + + +class BaseLoadingPipelineParams(luigi.Task): + # NB: + # These params are "inherited" with the special + # luigi.util.inherits function, copying params + # but nothing else. + reference_genome = luigi.EnumParameter(enum=ReferenceGenome) + dataset_type = luigi.EnumParameter(enum=DatasetType) diff --git a/loading_pipeline/lib/tasks/base/base_loading_run_params.py b/loading_pipeline/lib/tasks/base/base_loading_run_params.py new file mode 100644 index 0000000000..43158dcc5d --- /dev/null +++ b/loading_pipeline/lib/tasks/base/base_loading_run_params.py @@ -0,0 +1,36 @@ +import luigi + +from loading_pipeline.lib.core import SampleType +from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( + BaseLoadingPipelineParams, +) + + +@luigi.util.inherits(BaseLoadingPipelineParams) +class BaseLoadingRunParams(luigi.Task): + # The difference between the "Loading Run" params + # and the "Loading Pipeline" params: + # - These params are used during standard "runs" + # of the pipeline that add a callset to the backend + # data store. + # - The "Loading Pipeline" params are shared with + # tasks that may remove data from or change the + # structure of the persisted Hail Tables. + run_id = luigi.Parameter() + sample_type = luigi.EnumParameter(enum=SampleType) + callset_path = luigi.Parameter() + project_guids = luigi.ListParameter(default=[]) + skip_check_sex_and_relatedness = luigi.BoolParameter( + default=False, + parsing=luigi.BoolParameter.EXPLICIT_PARSING, + ) + skip_expect_tdr_metrics = luigi.BoolParameter( + default=False, + parsing=luigi.BoolParameter.EXPLICIT_PARSING, + ) + validations_to_skip = luigi.ListParameter(default=[]) + is_new_gcnv_joint_call = luigi.BoolParameter( + default=False, + parsing=luigi.BoolParameter.EXPLICIT_PARSING, + description='Is this a fully joint-called callset.', + ) diff --git a/loading_pipeline/lib/tasks/base/base_update.py b/loading_pipeline/lib/tasks/base/base_update.py new file mode 100644 index 0000000000..1cacf37383 --- /dev/null +++ b/loading_pipeline/lib/tasks/base/base_update.py @@ -0,0 +1,26 @@ +import hail as hl + +from loading_pipeline.lib.misc.io import write +from loading_pipeline.lib.tasks.base.base_hail_table import BaseHailTableTask + + +class BaseUpdateTask(BaseHailTableTask): + def run(self) -> None: + self.init_hail() + if not self.output().exists(): + ht = self.initialize_table() + else: + read_fn = ( + hl.read_matrix_table + if self.output().path.endswith('mt') + else hl.read_table + ) + ht = read_fn(self.output().path) + ht = self.update_table(ht) + write(ht, self.output().path) + + def initialize_table(self) -> hl.Table: + raise NotImplementedError + + def update_table(self, ht: hl.Table) -> hl.Table: + raise NotImplementedError diff --git a/loading_pipeline/lib/tasks/base/base_write.py b/loading_pipeline/lib/tasks/base/base_write.py new file mode 100644 index 0000000000..cc0be97eac --- /dev/null +++ b/loading_pipeline/lib/tasks/base/base_write.py @@ -0,0 +1,14 @@ +import hail as hl + +from loading_pipeline.lib.misc.io import write +from loading_pipeline.lib.tasks.base.base_hail_table import BaseHailTableTask + + +class BaseWriteTask(BaseHailTableTask): + def run(self) -> None: + self.init_hail() + ht = self.create_table() + write(ht, self.output().path) + + def create_table(self) -> hl.Table: + raise NotImplementedError diff --git a/loading_pipeline/lib/tasks/base/base_write_parquet.py b/loading_pipeline/lib/tasks/base/base_write_parquet.py new file mode 100644 index 0000000000..bc1d358e0c --- /dev/null +++ b/loading_pipeline/lib/tasks/base/base_write_parquet.py @@ -0,0 +1,19 @@ +import luigi + +from loading_pipeline.lib.misc.io import checkpoint +from loading_pipeline.lib.tasks.files import GCSorLocalFolderTarget + + +class BaseWriteParquetTask(luigi.Task): + def complete(self) -> luigi.Target: + return GCSorLocalFolderTarget(self.output().path).exists() + + def run(self) -> None: + ht = self.create_table() + ht, _ = checkpoint(ht) + df = ht.to_spark(flatten=False) + df = df.withColumnRenamed('key_', 'key') + df.write.parquet( + self.output().path, + mode='overwrite', + ) diff --git a/loading_pipeline/lib/tasks/clickhouse_migration/__init__.py b/loading_pipeline/lib/tasks/clickhouse_migration/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/loading_pipeline/lib/tasks/clickhouse_migration/migrate_all_projects_to_clickhouse.py b/loading_pipeline/lib/tasks/clickhouse_migration/migrate_all_projects_to_clickhouse.py new file mode 100644 index 0000000000..c8a5e9678a --- /dev/null +++ b/loading_pipeline/lib/tasks/clickhouse_migration/migrate_all_projects_to_clickhouse.py @@ -0,0 +1,51 @@ +import hailtop.fs as hfs +import luigi +import luigi.util + +from loading_pipeline.lib.core import SampleType +from loading_pipeline.lib.paths import ( + project_table_path, +) +from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( + BaseLoadingPipelineParams, +) +from loading_pipeline.lib.tasks.clickhouse_migration.migrate_project_to_clickhouse import ( + MigrateProjectToClickHouseTask, +) + + +@luigi.util.inherits(BaseLoadingPipelineParams) +class MigrateAllProjectsToClickHouseTask(luigi.WrapperTask): + run_id = luigi.Parameter() + attempt_id = luigi.IntParameter() + + def __init__(self, *args, **kwargs): + super().__init__(*args, **kwargs) + self.dynamic_parquet_tasks = set() + + def complete(self): + return len(self.dynamic_parquet_tasks) >= 1 and all( + dynamic_parquet_tasks.complete() + for dynamic_parquet_tasks in self.dynamic_parquet_tasks + ) + + def run(self): + for sample_type in SampleType: + for p in hfs.ls( + project_table_path( + self.reference_genome, + self.dataset_type, + sample_type, + '*', + ), + ): + project_guid = p.path.split('/')[-1].replace('.ht', '') + self.dynamic_parquet_tasks.add( + self.clone( + MigrateProjectToClickHouseTask, + run_id=f'{self.run_id}_{sample_type.value}_{project_guid}', + sample_type=sample_type, + project_guid=project_guid, + ), + ) + yield self.dynamic_parquet_tasks diff --git a/loading_pipeline/lib/tasks/clickhouse_migration/migrate_all_projects_to_clickhouse_on_dataproc.py b/loading_pipeline/lib/tasks/clickhouse_migration/migrate_all_projects_to_clickhouse_on_dataproc.py new file mode 100644 index 0000000000..96e3ffbdcd --- /dev/null +++ b/loading_pipeline/lib/tasks/clickhouse_migration/migrate_all_projects_to_clickhouse_on_dataproc.py @@ -0,0 +1,16 @@ +import luigi + +from loading_pipeline.lib.tasks.clickhouse_migration.migrate_all_projects_to_clickhouse import ( + MigrateAllProjectsToClickHouseTask, +) +from loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc import ( + BaseRunJobOnDataprocTask, +) + + +class MigrateAllProjectsToClickHouseOnDataprocTask(BaseRunJobOnDataprocTask): + run_id = luigi.Parameter() + + @property + def task(self) -> luigi.Task: + return MigrateAllProjectsToClickHouseTask diff --git a/loading_pipeline/lib/tasks/clickhouse_migration/migrate_all_projects_to_clickhouse_test.py b/loading_pipeline/lib/tasks/clickhouse_migration/migrate_all_projects_to_clickhouse_test.py new file mode 100644 index 0000000000..ad9c752d15 --- /dev/null +++ b/loading_pipeline/lib/tasks/clickhouse_migration/migrate_all_projects_to_clickhouse_test.py @@ -0,0 +1,123 @@ +import json + +import hail as hl +import hailtop.fs as hfs +import luigi.worker +import pandas as pd + +from loading_pipeline.lib.core import ( + DatasetType, + ReferenceGenome, + SampleType, +) +from loading_pipeline.lib.core.constants import MIGRATION_RUN_ID +from loading_pipeline.lib.paths import ( + metadata_for_run_path, + new_entries_parquet_path, + pipeline_run_success_file_path, + project_table_path, + variant_annotations_table_path, +) +from loading_pipeline.lib.tasks.clickhouse_migration.migrate_all_projects_to_clickhouse import ( + MigrateAllProjectsToClickHouseTask, +) +from loading_pipeline.lib.test.mocked_dataroot_testcase import ( + MockedDatarootTestCase, +) + +TEST_SNV_INDEL_ANNOTATIONS = ( + 'loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/annotations.ht' +) +TEST_PROJECT_TABLES = [ + ( + 'loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/projects/WGS/R0113_test_project.ht', + SampleType.WGS, + 'R0113_test_project', + ), + ( + 'loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/projects/WES/R0113_test_project.ht', + SampleType.WES, + 'R0113_test_project', + ), + ( + 'loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/projects/WES/R0114_project4.ht', + SampleType.WES, + 'R0114_project4', + ), +] + + +class MigrateAllProjectsToClickHouseTaskTest(MockedDatarootTestCase): + def setUp(self) -> None: + super().setUp() + ht = hl.read_table(TEST_SNV_INDEL_ANNOTATIONS) + ht.write( + variant_annotations_table_path( + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + ), + ) + for path, sample_type, project_guid in TEST_PROJECT_TABLES: + ht = hl.read_table(path) + ht.write( + project_table_path( + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + sample_type, + project_guid, + ), + ) + + def test_all_project_entries_to_clickhouse_test( + self, + ) -> None: + worker = luigi.worker.Worker() + task = MigrateAllProjectsToClickHouseTask( + reference_genome=ReferenceGenome.GRCh37, + dataset_type=DatasetType.SNV_INDEL, + run_id=MIGRATION_RUN_ID, + attempt_id=0, + ) + worker.add(task) + worker.run() + self.assertTrue(task.complete()) + for _, sample_type, project_guid in TEST_PROJECT_TABLES: + df = pd.read_parquet( + new_entries_parquet_path( + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + f'{MIGRATION_RUN_ID}_{sample_type.value}_{project_guid}', + ), + ) + export_json = df.to_dict('records') + self.assertEqual( + export_json[0]['key'], + 1424, + ) + + for _, sample_type, project_guid in TEST_PROJECT_TABLES: + with hfs.open( + metadata_for_run_path( + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + f'{MIGRATION_RUN_ID}_{sample_type.value}_{project_guid}', + ), + ) as f: + metadata_json = json.load(f) + self.assertEqual( + metadata_json['run_id'], + f'{MIGRATION_RUN_ID}_{sample_type.value}_{project_guid}', + ) + self.assertEqual( + metadata_json['family_samples']['F079280_bh10261'], + ['BH10261-1', 'BH10261-2', 'BH10261-3-T'], + ) + + with hfs.open( + pipeline_run_success_file_path( + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + f'{MIGRATION_RUN_ID}_{sample_type.value}_{project_guid}', + ), + ) as f: + self.assertEqual(f.read(), '') diff --git a/loading_pipeline/lib/tasks/clickhouse_migration/migrate_project_to_clickhouse.py b/loading_pipeline/lib/tasks/clickhouse_migration/migrate_project_to_clickhouse.py new file mode 100644 index 0000000000..be0d668a7d --- /dev/null +++ b/loading_pipeline/lib/tasks/clickhouse_migration/migrate_project_to_clickhouse.py @@ -0,0 +1,157 @@ +import json + +import hail as hl +import luigi +import luigi.util + +from loading_pipeline.lib.core import SampleType +from loading_pipeline.lib.misc.family_entries import ( + deduplicate_by_most_non_ref_calls, + deglobalize_ids, +) +from loading_pipeline.lib.paths import ( + metadata_for_run_path, + new_entries_parquet_path, + pipeline_run_success_file_path, + project_table_path, +) +from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( + BaseLoadingPipelineParams, +) +from loading_pipeline.lib.tasks.base.base_write_parquet import BaseWriteParquetTask +from loading_pipeline.lib.tasks.clickhouse_migration.migrate_project_variants_to_clickhouse import ( + MigrateProjectVariantsToClickHouseTask, + WriteProjectSubsettedVariantsTask, +) +from loading_pipeline.lib.tasks.exports.fields import get_entries_export_fields +from loading_pipeline.lib.tasks.files import GCSorLocalTarget, HailTableTask + +PROJECT_SUBSETTED_ANNOTATIONS_TABLE_TASK = 'project_subsetted_annotations_table_task' +PROJECT_TABLE_TASK = 'project_table_task' + + +@luigi.util.inherits(BaseLoadingPipelineParams) +class WriteProjectEntriesParquetTask(BaseWriteParquetTask): + run_id = luigi.Parameter() + sample_type = luigi.EnumParameter(enum=SampleType) + project_guid = luigi.Parameter() + + def output(self) -> luigi.Target: + return GCSorLocalTarget( + new_entries_parquet_path( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + ) + + def requires(self) -> list[luigi.Task]: + return { + PROJECT_SUBSETTED_ANNOTATIONS_TABLE_TASK: self.clone( + WriteProjectSubsettedVariantsTask, + ), + PROJECT_TABLE_TASK: HailTableTask( + project_table_path( + self.reference_genome, + self.dataset_type, + self.sample_type, + self.project_guid, + ), + ), + } + + def create_table(self) -> None: + ht = hl.read_table( + self.input()[PROJECT_TABLE_TASK].path, + ) + ht = deglobalize_ids(ht) + ht = deduplicate_by_most_non_ref_calls(ht) + annotations_ht = hl.read_table( + self.input()[PROJECT_SUBSETTED_ANNOTATIONS_TABLE_TASK].path, + ) + ht = ht.join(annotations_ht) + ht = ht.explode(ht.family_entries) + ht = ht.filter(hl.is_defined(ht.family_entries)) + ht = ht.key_by() + ht = ht.select_globals() + return ht.select( + **get_entries_export_fields( + ht, + self.dataset_type, + self.sample_type, + self.project_guid, + ), + ) + + +@luigi.util.inherits(BaseLoadingPipelineParams) +class WriteMigrationMetadataJsonTask(luigi.Task): + run_id = luigi.Parameter() + sample_type = luigi.EnumParameter(enum=SampleType) + project_guid = luigi.Parameter() + + def requires(self): + return HailTableTask( + project_table_path( + self.reference_genome, + self.dataset_type, + self.sample_type, + self.project_guid, + ), + ) + + def output(self) -> luigi.Target: + return GCSorLocalTarget( + metadata_for_run_path( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + ) + + def run(self): + ht = hl.read_table(self.input().path) + metadata_json = { + 'callsets': [], + 'run_id': self.run_id, + 'sample_type': self.sample_type.value, + 'project_guids': [self.project_guid], + 'family_samples': hl.eval(ht.globals.family_samples), + 'failed_family_samples': { + 'missing_samples': {}, + 'relatedness_check': {}, + 'sex_check': {}, + 'ploidy_check': {}, + }, + 'relatedness_check_file_path': '', + 'sample_qc': {}, + } + with self.output().open('w') as f: + json.dump(metadata_json, f) + + +@luigi.util.inherits(BaseLoadingPipelineParams) +class MigrateProjectToClickHouseTask(luigi.Task): + run_id = luigi.Parameter() + sample_type = luigi.EnumParameter(enum=SampleType) + project_guid = luigi.Parameter() + + def requires(self): + return [ + self.clone(MigrateProjectVariantsToClickHouseTask), + self.clone(WriteProjectEntriesParquetTask), + self.clone(WriteMigrationMetadataJsonTask), + ] + + def output(self) -> luigi.Target: + return GCSorLocalTarget( + pipeline_run_success_file_path( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + ) + + def run(self): + with self.output().open('w') as f: + f.write('') diff --git a/loading_pipeline/lib/tasks/clickhouse_migration/migrate_project_variants_to_clickhouse.py b/loading_pipeline/lib/tasks/clickhouse_migration/migrate_project_variants_to_clickhouse.py new file mode 100644 index 0000000000..ebf950e551 --- /dev/null +++ b/loading_pipeline/lib/tasks/clickhouse_migration/migrate_project_variants_to_clickhouse.py @@ -0,0 +1,119 @@ +import hail as hl +import luigi +import luigi.util + +from loading_pipeline.lib.core import SampleType +from loading_pipeline.lib.paths import ( + new_variants_table_path, + project_table_path, + variant_annotations_table_path, +) +from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( + BaseLoadingPipelineParams, +) +from loading_pipeline.lib.tasks.base.base_write import BaseWriteTask +from loading_pipeline.lib.tasks.exports.write_new_variant_details_parquet import ( + WriteNewVariantDetailsParquetTask, +) +from loading_pipeline.lib.tasks.exports.write_new_variants_parquet import ( + WriteNewVariantsParquetTask, +) +from loading_pipeline.lib.tasks.files import GCSorLocalTarget, HailTableTask + +MAX_SNV_INDEL_ALLELE_LENGTH = 500 + + +class WriteProjectSubsettedVariantsTask(BaseWriteTask): + run_id = luigi.Parameter() + sample_type = luigi.EnumParameter(enum=SampleType) + project_guid = luigi.Parameter() + + def output(self) -> luigi.Target: + return GCSorLocalTarget( + new_variants_table_path( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + ) + + def requires(self) -> list[luigi.Task]: + return [ + HailTableTask( + variant_annotations_table_path( + self.reference_genome, + self.dataset_type, + ), + ), + HailTableTask( + project_table_path( + self.reference_genome, + self.dataset_type, + self.sample_type, + self.project_guid, + ), + ), + ] + + def create_table(self) -> hl.Table: + ht = hl.read_table(self.input()[0].path) + if not hasattr(ht, 'key_'): + ht = ht.add_index(name='key_') + if self.dataset_type.filter_invalid_sites: + ht = ht.filter(hl.len(ht.alleles[1]) < MAX_SNV_INDEL_ALLELE_LENGTH) + project_ht = hl.read_table(self.input()[1].path) + return ht.semi_join(project_ht) + + +@luigi.util.inherits(BaseLoadingPipelineParams) +class MigrateProjectVariantsToClickHouseTask(luigi.WrapperTask): + run_id = luigi.Parameter() + sample_type = luigi.EnumParameter(enum=SampleType) + project_guid = luigi.Parameter() + + def __init__(self, *args, **kwargs): + super().__init__(*args, **kwargs) + self.dynamic_parquet_tasks = set() + + def requires(self) -> luigi.Task: + return self.clone(WriteProjectSubsettedVariantsTask) + + def complete(self): + return ( + super().complete() + and len(self.dynamic_parquet_tasks) >= 1 + and all( + dynamic_parquet_tasks.complete() + for dynamic_parquet_tasks in self.dynamic_parquet_tasks + ) + ) + + def run(self): + self.dynamic_parquet_tasks.update( + [ + *( + [ + self.clone( + WriteNewVariantDetailsParquetTask, + # Callset Path being required + # here is byproduct of the "place all variants" + # in the variants path" hack. In theory + # it is possible to re-factor the parameters + # such that this isn't required, but it's left + # as out of scope for now. Alternatively, + # we could inherit the functionality of these + # tasks without calling them directly, but + # that was also more code. + callset_path=None, + ), + ] + if self.dataset_type.should_write_new_variant_details + else [] + ), + self.clone( + WriteNewVariantsParquetTask, + callset_path=None, + ), + ], + ) + yield self.dynamic_parquet_tasks diff --git a/loading_pipeline/lib/tasks/clickhouse_migration/migrate_project_variants_to_clickhouse_test.py b/loading_pipeline/lib/tasks/clickhouse_migration/migrate_project_variants_to_clickhouse_test.py new file mode 100644 index 0000000000..ce4c6d5cd8 --- /dev/null +++ b/loading_pipeline/lib/tasks/clickhouse_migration/migrate_project_variants_to_clickhouse_test.py @@ -0,0 +1,91 @@ +import hail as hl +import hailtop.fs as hfs +import luigi.worker +import pandas as pd + +from loading_pipeline.lib.core import ( + DatasetType, + ReferenceGenome, + SampleType, +) +from loading_pipeline.lib.paths import ( + new_variant_details_parquet_path, + new_variants_parquet_path, + pipeline_run_success_file_path, + project_table_path, + variant_annotations_table_path, +) +from loading_pipeline.lib.tasks.clickhouse_migration.migrate_project_variants_to_clickhouse import ( + MigrateProjectVariantsToClickHouseTask, +) +from loading_pipeline.lib.test.mocked_dataroot_testcase import ( + MockedDatarootTestCase, +) + +TEST_SNV_INDEL_ANNOTATIONS = ( + 'loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/annotations.ht' +) +TEST_PROJECT_TABLE = 'loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/projects/WGS/R0113_test_project.ht' + +TEST_RUN_ID = 'migration_run' + + +class WriteVariantsToClickHouseTest(MockedDatarootTestCase): + def setUp(self) -> None: + super().setUp() + ht = hl.read_table(TEST_SNV_INDEL_ANNOTATIONS) + ht.write( + variant_annotations_table_path( + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + ), + ) + ht = hl.read_table(TEST_PROJECT_TABLE) + ht.write( + project_table_path( + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0113_test_project', + ), + ) + + def test_migrate_variants_to_clickhouse_test( + self, + ) -> None: + worker = luigi.worker.Worker() + task = MigrateProjectVariantsToClickHouseTask( + reference_genome=ReferenceGenome.GRCh37, + dataset_type=DatasetType.SNV_INDEL, + run_id=TEST_RUN_ID, + sample_type=SampleType.WGS, + project_guid='R0113_test_project', + ) + worker.add(task) + worker.run() + self.assertTrue(task.complete()) + df = pd.read_parquet( + new_variants_parquet_path( + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ) + self.assertEqual(df.shape[0], 1) + df = pd.read_parquet( + new_variant_details_parquet_path( + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ) + self.assertEqual(df.shape[0], 1) + self.assertFalse( + hfs.exists( + pipeline_run_success_file_path( + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ), + ) diff --git a/loading_pipeline/lib/tasks/dataproc/__init__.py b/loading_pipeline/lib/tasks/dataproc/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/loading_pipeline/lib/tasks/dataproc/base_run_job_on_dataproc.py b/loading_pipeline/lib/tasks/dataproc/base_run_job_on_dataproc.py new file mode 100644 index 0000000000..01ea67e051 --- /dev/null +++ b/loading_pipeline/lib/tasks/dataproc/base_run_job_on_dataproc.py @@ -0,0 +1,147 @@ +import re +import time + +import google.api_core.exceptions +import google.cloud.dataproc_v1.types.jobs +import luigi +from google.cloud import dataproc_v1 as dataproc + +from loading_pipeline.lib.core import Env +from loading_pipeline.lib.logger import get_logger +from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( + BaseLoadingPipelineParams, +) +from loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster import ( + CreateDataprocClusterTask, +) +from loading_pipeline.lib.tasks.dataproc.misc import get_cluster_name, to_kebab_str_args + +FAILURE_STATUSES = { + google.cloud.dataproc_v1.types.jobs.JobStatus.State.CANCELLED, + google.cloud.dataproc_v1.types.jobs.JobStatus.State.ERROR, + google.cloud.dataproc_v1.types.jobs.JobStatus.State.ATTEMPT_FAILURE, +} +SEQR_PIPELINE_RUNNER_BUILD = f'gs://seqr-pipeline-runner-builds/{Env.DEPLOYMENT_TYPE}/{Env.PIPELINE_RUNNER_APP_VERSION}' +TIMEOUT_S = 172800 # 2 days + +logger = get_logger(__name__) + + +@luigi.util.inherits(BaseLoadingPipelineParams) +class BaseRunJobOnDataprocTask(luigi.Task): + run_id = luigi.Parameter() + attempt_id = luigi.IntParameter() + + def __init__(self, *args, **kwargs): + super().__init__(*args, **kwargs) + self.client = dataproc.JobControllerClient( + client_options={ + 'api_endpoint': f'{Env.GCLOUD_REGION}-dataproc.googleapis.com:443', + }, + ) + + @property + def task(self): + raise NotImplementedError + + @property + def job_id(self): + return f'{self.task.task_family}-{self.reference_genome[-2:]}-{re.sub("_", "-", self.dataset_type.value)}-{self.run_id}-{self.attempt_id}' + + def requires(self) -> [luigi.Task]: + return [self.clone(CreateDataprocClusterTask)] + + def safely_get_job( + self, + ): + try: + job = self.client.get_job( + request={ + 'project_id': Env.GCLOUD_PROJECT, + 'region': Env.GCLOUD_REGION, + 'job_id': self.job_id, + }, + ) + except google.api_core.exceptions.NotFound: + return None + else: + return job + + def complete(self) -> bool: + job = self.safely_get_job() + if not job: + return False + if job.status.state in FAILURE_STATUSES: + msg = f'Job {self.job_id} entered {job.status.state.name} state' + logger.error(msg) + logger.error(job.status.details) + return ( + job.status.state == google.cloud.dataproc_v1.types.jobs.JobStatus.State.DONE + ) + + def run(self): + job = self.safely_get_job() + # Delete the job if it exists and was failed. This handles manual re-runs of the + # same run_id. + if job and job.status.state in FAILURE_STATUSES: + logger.error( + f'Previous job {self.job_id} failed with state {job.status.state.name}', + ) + logger.error(job.status.details) + self.client.delete_job( + request={ + 'project_id': Env.GCLOUD_PROJECT, + 'region': Env.GCLOUD_REGION, + 'job_id': self.job_id, + }, + ) + job = None + + if not job: + self.client.submit_job_as_operation( + request={ + 'project_id': Env.GCLOUD_PROJECT, + 'region': Env.GCLOUD_REGION, + 'job': { + 'reference': { + 'job_id': self.job_id, + }, + 'placement': { + 'cluster_name': get_cluster_name( + self.reference_genome, + self.run_id, + ), + }, + 'pyspark_job': { + 'main_python_file_uri': f'{SEQR_PIPELINE_RUNNER_BUILD}/bin/run_task.py', + 'args': [ + self.task.task_family, + '--local-scheduler', + *to_kebab_str_args(self), + ], + 'python_file_uris': [ + f'{SEQR_PIPELINE_RUNNER_BUILD}/pyscripts.zip', + ], + }, + }, + }, + ) + wait_s = 0 + while wait_s < TIMEOUT_S: + job = self.safely_get_job() + if ( + job.status.state + == google.cloud.dataproc_v1.types.jobs.JobStatus.State.DONE + ): + msg = f'Job {self.job_id} is complete' + logger.info(msg) + break + if job.status.state in FAILURE_STATUSES: + msg = f'Job {self.job_id} entered {job.status.state.name} state' + logger.error(msg) + raise RuntimeError(msg) + logger.info( + f'Waiting for Job completion {self.job_id}', + ) + time.sleep(3) + wait_s += 3 diff --git a/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster.py b/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster.py new file mode 100644 index 0000000000..5e0bb59cbb --- /dev/null +++ b/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster.py @@ -0,0 +1,224 @@ +import time + +import google.api_core.exceptions +import google.cloud.dataproc_v1.types.clusters +import hail as hl +import luigi +from google.cloud import dataproc_v1 as dataproc +from pip._internal.operations import freeze as pip_freeze + +from loading_pipeline.lib.core import DatasetType, Env, FeatureFlag, ReferenceGenome +from loading_pipeline.lib.logger import get_logger +from loading_pipeline.lib.misc.gcp import get_service_account_credentials +from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( + BaseLoadingPipelineParams, +) +from loading_pipeline.lib.tasks.dataproc.misc import get_cluster_name + +DEBIAN_IMAGE = '2.3.17-debian12' +DISK_SIZE_GB = 600 +DISK_TYPE = 'hyperdisk-balanced' +HAIL_VERSION = hl.version().split('-')[0] +INSTANCE_TYPE = 'n4-highmem-8' +PKGS = '|'.join( + [ + x.replace('gnomad_qc @ ', '').replace('onnxconverter-common @ ', '') + for x in pip_freeze.freeze() + if 'hail @' not in x + ], +) +TIMEOUT_S = 1200 +FAILURE_STATUSES = { + google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.UNKNOWN, + google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.ERROR, + google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.ERROR_DUE_TO_UPDATE, +} + +logger = get_logger(__name__) + + +def get_cluster_config( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + run_id: str, +): + service_account_credentials = get_service_account_credentials() + return { + 'project_id': Env.GCLOUD_PROJECT, + 'cluster_name': get_cluster_name(reference_genome, run_id), + # Schema found at https://cloud.google.com/dataproc/docs/reference/rest/v1/ClusterConfig + 'config': { + 'gce_cluster_config': { + 'metadata': { + 'WHEEL': f'gs://hail-common/hailctl/dataproc/{HAIL_VERSION}/hail-{HAIL_VERSION}-py3-none-any.whl', + 'PKGS': PKGS, + 'DEPLOYMENT_TYPE': Env.DEPLOYMENT_TYPE, + 'REFERENCE_GENOME': reference_genome.value, + 'PIPELINE_RUNNER_APP_VERSION': Env.PIPELINE_RUNNER_APP_VERSION, + 'REFERENCE_DATASETS_DIR': Env.REFERENCE_DATASETS_DIR, + }, + 'internal_ip_only': False, # Recent change with 2.2 dataproc images. + 'service_account': service_account_credentials.service_account_email, + 'service_account_scopes': service_account_credentials.scopes, + }, + 'master_config': { + 'num_instances': 1, + 'machine_type_uri': INSTANCE_TYPE, + 'disk_config': { + 'boot_disk_type': DISK_TYPE, + 'boot_disk_size_gb': DISK_SIZE_GB, + }, + }, + 'worker_config': { + 'num_instances': dataset_type.dataproc_primary_workers, + 'machine_type_uri': INSTANCE_TYPE, + 'disk_config': { + 'boot_disk_type': DISK_TYPE, + 'boot_disk_size_gb': DISK_SIZE_GB, + }, + }, + 'secondary_worker_config': { + 'num_instances': dataset_type.dataproc_preemptibles, + 'machine_type_uri': INSTANCE_TYPE, + 'disk_config': { + 'boot_disk_type': DISK_TYPE, + 'boot_disk_size_gb': DISK_SIZE_GB, + }, + 'is_preemptible': True, + 'preemptibility': 'PREEMPTIBLE', + }, + 'software_config': { + 'image_version': DEBIAN_IMAGE, + 'properties': { + 'spark:spark.driver.maxResultSize': '0', + 'spark:spark.task.maxFailures': '20', + 'spark:spark.kryoserializer.buffer.max': '2g', + 'spark:spark.driver.extraJavaOptions': '-Xss16M', + 'spark:spark.executor.extraJavaOptions': '-Xss16M', + 'hdfs:dfs.replication': '1', + 'dataproc:dataproc.logging.stackdriver.enable': 'false', + 'dataproc:dataproc.monitoring.stackdriver.enable': 'false', + 'spark:spark.driver.memory': '41g', + 'yarn:yarn.nodemanager.resource.memory-mb': '50585', + 'yarn:yarn.scheduler.maximum-allocation-mb': '25292', + 'spark:spark.executor.cores': '4', + 'spark:spark.executor.memory': '10117m', + 'spark:spark.executor.memoryOverhead': '15175m', + 'spark:spark.memory.storageFraction': '0.2', + 'spark:spark.executorEnv.HAIL_WORKER_OFF_HEAP_MEMORY_PER_CORE_MB': '6323', + 'spark:spark.speculation': 'true', + 'spark-env:CHECK_SEX_AND_RELATEDNESS': '1' + if FeatureFlag.CHECK_SEX_AND_RELATEDNESS + else '0', + 'spark-env:EXPECT_TDR_METRICS': '1' + if FeatureFlag.EXPECT_TDR_METRICS + else '0', + 'spark-env:PIPELINE_DATA_DIR': Env.PIPELINE_DATA_DIR, + 'spark-env:HAIL_TMP_DIR': Env.HAIL_TMP_DIR, + 'spark-env:LOADING_DATASETS_DIR': Env.LOADING_DATASETS_DIR, + 'spark-env:REFERENCE_DATASETS_DIR': Env.REFERENCE_DATASETS_DIR, + 'spark-env:SAMPLE_TYPE_VALIDATION_EXCLUDED_PROJECTS': ','.join( + Env.SAMPLE_TYPE_VALIDATION_EXCLUDED_PROJECTS, + ), + }, + }, + 'lifecycle_config': {'idle_delete_ttl': {'seconds': 1200}}, + 'encryption_config': {}, + 'autoscaling_config': {}, + 'endpoint_config': {}, + 'initialization_actions': [ + { + # NB: this script initializes the python env. + 'executable_file': f'gs://hail-common/hailctl/dataproc/{HAIL_VERSION}/init_notebook.py', + 'execution_timeout': {'seconds': 1200}, + }, + { + 'executable_file': f'gs://seqr-pipeline-runner-builds/{Env.DEPLOYMENT_TYPE}/{Env.PIPELINE_RUNNER_APP_VERSION}/bin/dataproc_vep_init.bash', + 'execution_timeout': {'seconds': 1200}, + }, + ], + }, + } + + +@luigi.util.inherits(BaseLoadingPipelineParams) +class CreateDataprocClusterTask(luigi.Task): + # NB: The luigi.dataproc.contrib module was old and bad + # so we built our own shim. + run_id = luigi.Parameter() + + def __init__(self, *args, **kwargs): + super().__init__(*args, **kwargs) + # https://cloud.google.com/dataproc/docs/tutorials/python-library-example + self.client = dataproc.ClusterControllerClient( + client_options={ + 'api_endpoint': f'{Env.GCLOUD_REGION}-dataproc.googleapis.com:443', + }, + ) + + def safely_get_cluster( + self, + ): + try: + cluster = self.client.get_cluster( + request={ + 'project_id': Env.GCLOUD_PROJECT, + 'region': Env.GCLOUD_REGION, + 'cluster_name': get_cluster_name( + self.reference_genome, + self.run_id, + ), + }, + ) + except google.api_core.exceptions.NotFound: + return None + else: + return cluster + + def complete(self) -> bool: + cluster = self.safely_get_cluster() + if not cluster: + return False + if cluster.status.state in FAILURE_STATUSES: + msg = f'Cluster {cluster.cluster_name} entered {cluster.status.state.name} state' + logger.error(msg) + # This will return False when the cluster is "CREATING" + return ( + cluster.status.state + == google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.RUNNING + ) + + def run(self): + if not Env.GCLOUD_PROJECT or not Env.GCLOUD_REGION: + msg = 'Environment Variables GCLOUD_PROJECT and GCLOUD_REGION are required for running the pipeline on dataproc.' + raise RuntimeError(msg) + cluster = self.safely_get_cluster() + if not cluster: + self.client.create_cluster( + request={ + 'project_id': Env.GCLOUD_PROJECT, + 'region': Env.GCLOUD_REGION, + 'cluster': get_cluster_config( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + }, + ) + wait_s = 0 + while wait_s < TIMEOUT_S: + cluster = self.safely_get_cluster() + if ( + cluster.status.state + == google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.RUNNING + ): + msg = f'Created cluster {cluster.cluster_name} with cluster uuid: {cluster.cluster_uuid}' + logger.info(msg) + break + if cluster.status.state in FAILURE_STATUSES: + msg = f'Cluster {cluster.cluster_name} entered {cluster.status.state.name} state' + logger.error(msg) + raise RuntimeError(msg) + logger.info('Waiting for cluster spinup') + time.sleep(3) + wait_s += 3 diff --git a/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster_test.py b/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster_test.py new file mode 100644 index 0000000000..6634feea8c --- /dev/null +++ b/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster_test.py @@ -0,0 +1,162 @@ +import unittest +from types import SimpleNamespace +from unittest.mock import Mock, call, patch + +import google.api_core.exceptions +import google.cloud.dataproc_v1.types.clusters +import luigi + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome +from loading_pipeline.lib.misc.gcp import SOCIAL_AUTH_GOOGLE_OAUTH2_SCOPE +from loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster import ( + CreateDataprocClusterTask, +) + + +@patch.multiple( + 'loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster.Env', + GCLOUD_PROJECT='proj', + GCLOUD_REGION='us-a', +) +@patch( + 'loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster.get_service_account_credentials', + return_value=SimpleNamespace( + service_account_email='test@serviceaccount.com', + scopes=SOCIAL_AUTH_GOOGLE_OAUTH2_SCOPE, + ), +) +@patch( + 'loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster.dataproc.ClusterControllerClient', +) +class CreateDataprocClusterTaskTest(unittest.TestCase): + def test_spinup_cluster_already_exists_failed( + self, + mock_cluster_controller: Mock, + *_: Mock, + ) -> None: + mock_client = mock_cluster_controller.return_value + mock_client.get_cluster.return_value = SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.ERROR, + ), + cluster_name='abc', + ) + mock_client.create_cluster.side_effect = ( + google.api_core.exceptions.AlreadyExists('cluster exists') + ) + worker = luigi.worker.Worker() + task = CreateDataprocClusterTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id='2', + ) + worker.add(task) + worker.run() + self.assertFalse(task.complete()) + + def test_spinup_cluster_already_exists_success( + self, + mock_cluster_controller: Mock, + *_: Mock, + ) -> None: + mock_client = mock_cluster_controller.return_value + mock_client.get_cluster.return_value = SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.RUNNING, + ), + ) + mock_client.create_cluster.side_effect = ( + google.api_core.exceptions.AlreadyExists('cluster exists') + ) + worker = luigi.worker.Worker() + task = CreateDataprocClusterTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id='3', + ) + worker.add(task) + worker.run() + self.assertTrue(task.complete()) + + @patch('loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster.logger') + def test_spinup_cluster_doesnt_exist_failed( + self, + mock_logger: Mock, + mock_cluster_controller: Mock, + *_: Mock, + ) -> None: + mock_client = mock_cluster_controller.return_value + mock_client.get_cluster.side_effect = [ + google.api_core.exceptions.NotFound( + 'cluster not found', + ), + google.api_core.exceptions.NotFound( + 'cluster not found', + ), + SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.CREATING, + ), + ), + SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.ERROR, + ), + cluster_name='dataproc-cluster-5', + cluster_uuid='12345', + ), + ] + worker = luigi.worker.Worker() + task = CreateDataprocClusterTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id='4', + ) + worker.add(task) + luigi_task_result = worker.run() + self.assertEqual(luigi_task_result, False) + mock_logger.info.assert_has_calls([call('Waiting for cluster spinup')]) + + @patch('loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster.logger') + def test_spinup_cluster_doesnt_exist_success( + self, + mock_logger: Mock, + mock_cluster_controller: Mock, + *_: Mock, + ) -> None: + mock_client = mock_cluster_controller.return_value + mock_client.get_cluster.side_effect = [ + google.api_core.exceptions.NotFound( + 'cluster not found', + ), + google.api_core.exceptions.NotFound( + 'cluster not found', + ), + SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.CREATING, + ), + ), + SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.RUNNING, + ), + cluster_name='dataproc-cluster-5', + cluster_uuid='12345', + ), + ] + mock_client.create_cluster.side_effect = None + worker = luigi.worker.Worker() + task = CreateDataprocClusterTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id='5', + ) + worker.add(task) + worker.run() + mock_logger.info.assert_has_calls( + [ + call('Waiting for cluster spinup'), + call('Created cluster dataproc-cluster-5 with cluster uuid: 12345'), + ], + ) diff --git a/loading_pipeline/lib/tasks/dataproc/misc.py b/loading_pipeline/lib/tasks/dataproc/misc.py new file mode 100644 index 0000000000..2031aad46a --- /dev/null +++ b/loading_pipeline/lib/tasks/dataproc/misc.py @@ -0,0 +1,29 @@ +import re + +import luigi + +from loading_pipeline.lib.core import Env, ReferenceGenome +from loading_pipeline.lib.core.constants import ( + MIGRATION_RUN_ID, + VARIANTS_MIGRATION_RUN_ID, +) + +CLUSTER_NAME_PREFIX = 'pipeline-runner' + + +def get_cluster_name(reference_genome: ReferenceGenome, run_id: str): + if MIGRATION_RUN_ID in run_id: + return f'{Env.DEPLOYMENT_TYPE}-{CLUSTER_NAME_PREFIX}-{reference_genome.value.lower()}-hs-to-clckhse-mgrtn' + if VARIANTS_MIGRATION_RUN_ID in run_id: + return f'{Env.DEPLOYMENT_TYPE}-{CLUSTER_NAME_PREFIX}-{reference_genome.value.lower()}-vrnts-mgrtn' + return f'{Env.DEPLOYMENT_TYPE}-{CLUSTER_NAME_PREFIX}-{reference_genome.value.lower()}-{run_id}' + + +def snake_to_kebab_arg(snake_string: str) -> str: + return '--' + re.sub(r'\_', '-', snake_string).lower() + + +def to_kebab_str_args(task: luigi.Task): + return [ + e for k, v in task.to_str_params().items() for e in (snake_to_kebab_arg(k), v) + ] diff --git a/loading_pipeline/lib/tasks/dataproc/misc_test.py b/loading_pipeline/lib/tasks/dataproc/misc_test.py new file mode 100644 index 0000000000..63ffafb8a1 --- /dev/null +++ b/loading_pipeline/lib/tasks/dataproc/misc_test.py @@ -0,0 +1,51 @@ +import unittest +from unittest.mock import Mock, patch + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.tasks.dataproc.misc import to_kebab_str_args +from loading_pipeline.lib.tasks.dataproc.run_pipeline_on_dataproc import ( + RunPipelineOnDataprocTask, +) + + +@patch( + 'loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc.dataproc.JobControllerClient', +) +class MiscTest(unittest.TestCase): + def test_to_kebab_str_args(self, _: Mock): + t = RunPipelineOnDataprocTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path='test_callset', + project_guids=['R0113_test_project'], + run_id='a_misc_run', + attempt_id=0, + ) + self.assertListEqual( + to_kebab_str_args(t), + [ + '--reference-genome', + 'GRCh38', + '--dataset-type', + 'SNV_INDEL', + '--sample-type', + 'WGS', + '--callset-path', + 'test_callset', + '--project-guids', + '["R0113_test_project"]', + '--skip-check-sex-and-relatedness', + 'False', + '--skip-expect-tdr-metrics', + 'False', + '--validations-to-skip', + '[]', + '--is-new-gcnv-joint-call', + 'False', + '--run-id', + 'a_misc_run', + '--attempt-id', + '0', + ], + ) diff --git a/loading_pipeline/lib/tasks/dataproc/run_pipeline_on_dataproc.py b/loading_pipeline/lib/tasks/dataproc/run_pipeline_on_dataproc.py new file mode 100644 index 0000000000..c05730c216 --- /dev/null +++ b/loading_pipeline/lib/tasks/dataproc/run_pipeline_on_dataproc.py @@ -0,0 +1,16 @@ +import luigi + +from loading_pipeline.lib.tasks.base.base_loading_run_params import ( + BaseLoadingRunParams, +) +from loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc import ( + BaseRunJobOnDataprocTask, +) +from loading_pipeline.lib.tasks.run_pipeline import RunPipelineTask + + +@luigi.util.inherits(BaseLoadingRunParams) +class RunPipelineOnDataprocTask(BaseRunJobOnDataprocTask): + @property + def task(self) -> luigi.Task: + return RunPipelineTask diff --git a/loading_pipeline/lib/tasks/dataproc/run_pipeline_on_dataproc_test.py b/loading_pipeline/lib/tasks/dataproc/run_pipeline_on_dataproc_test.py new file mode 100644 index 0000000000..a09289a85a --- /dev/null +++ b/loading_pipeline/lib/tasks/dataproc/run_pipeline_on_dataproc_test.py @@ -0,0 +1,184 @@ +import unittest +from types import SimpleNamespace +from unittest.mock import Mock, call, patch + +import google.api_core.exceptions +import google.cloud.dataproc_v1.types.jobs +import luigi + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.tasks.dataproc.run_pipeline_on_dataproc import ( + RunPipelineOnDataprocTask, +) +from loading_pipeline.lib.test.mock_complete_task import MockCompleteTask + + +@patch( + 'loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc.CreateDataprocClusterTask', +) +@patch( + 'loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc.dataproc.JobControllerClient', +) +class WriteSuccessFileOnDataprocTaskTest(unittest.TestCase): + @patch('loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc.logger') + def test_job_already_exists_failed( + self, + mock_logger: Mock, + mock_job_controller_client: Mock, + mock_create_dataproc_cluster: Mock, + ) -> None: + mock_create_dataproc_cluster.return_value = MockCompleteTask() + mock_client = mock_job_controller_client.return_value + mock_client.get_job.return_value = SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.jobs.JobStatus.State.ERROR, + details='Google Cloud Dataproc Agent reports job failure. If logs are available, they can be found at...', + ), + ) + mock_client.submit_job_as_operation.side_effect = ( + google.api_core.exceptions.AlreadyExists('job exists') + ) + worker = luigi.worker.Worker() + task = RunPipelineOnDataprocTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path='test_callset', + project_guids=['R0113_test_project'], + run_id='manual__2024-04-03', + attempt_id=0, + ) + worker.add(task) + worker.run() + self.assertFalse(task.complete()) + mock_logger.error.assert_has_calls( + [ + call( + 'Job RunPipelineTask-38-SNV-INDEL-manual__2024-04-03-0 entered ERROR state', + ), + ], + ) + + def test_job_already_exists_success( + self, + mock_job_controller_client: Mock, + mock_create_dataproc_cluster: Mock, + ) -> None: + mock_create_dataproc_cluster.return_value = MockCompleteTask() + mock_client = mock_job_controller_client.return_value + mock_client.get_job.return_value = SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.jobs.JobStatus.State.DONE, + ), + ) + worker = luigi.worker.Worker() + task = RunPipelineOnDataprocTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path='test_callset', + project_guids=['R0113_test_project'], + run_id='manual__2024-04-04', + attempt_id=0, + ) + worker.add(task) + worker.run() + self.assertTrue(task.complete()) + + @patch('loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc.logger') + def test_job_failed( + self, + mock_logger: Mock, + mock_job_controller_client: Mock, + mock_create_dataproc_cluster: Mock, + ) -> None: + mock_create_dataproc_cluster.return_value = MockCompleteTask() + mock_client = mock_job_controller_client.return_value + mock_client.get_job.side_effect = [ + google.api_core.exceptions.NotFound( + 'job not found', + ), + google.api_core.exceptions.NotFound( + 'job not found', + ), + SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.jobs.JobStatus.State.PENDING, + ), + ), + SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.jobs.JobStatus.State.ERROR, + ), + ), + ] + worker = luigi.worker.Worker() + task = RunPipelineOnDataprocTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path='test_callset', + project_guids=['R0113_test_project'], + run_id='manual__2024-04-05', + attempt_id=1, + ) + worker.add(task) + luigi_task_result = worker.run() + self.assertEqual(luigi_task_result, False) + mock_logger.info.assert_has_calls( + [ + call( + 'Waiting for Job completion RunPipelineTask-38-SNV-INDEL-manual__2024-04-05-1', + ), + ], + ) + + @patch('loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc.logger') + def test_job_success( + self, + mock_logger: Mock, + mock_job_controller_client: Mock, + mock_create_dataproc_cluster: Mock, + ) -> None: + mock_create_dataproc_cluster.return_value = MockCompleteTask() + mock_client = mock_job_controller_client.return_value + mock_client.get_job.side_effect = [ + google.api_core.exceptions.NotFound( + 'job not found', + ), + google.api_core.exceptions.NotFound( + 'job not found', + ), + SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.jobs.JobStatus.State.PENDING, + ), + ), + SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.jobs.JobStatus.State.DONE, + ), + ), + ] + worker = luigi.worker.Worker() + task = RunPipelineOnDataprocTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path='test_callset', + project_guids=['R0113_test_project'], + run_id='manual__2024-04-06', + attempt_id=0, + ) + worker.add(task) + worker.run() + mock_logger.info.assert_has_calls( + [ + call( + 'Waiting for Job completion RunPipelineTask-38-SNV-INDEL-manual__2024-04-06-0', + ), + call( + 'Job RunPipelineTask-38-SNV-INDEL-manual__2024-04-06-0 is complete', + ), + ], + ) diff --git a/loading_pipeline/lib/tasks/exports/__init__.py b/loading_pipeline/lib/tasks/exports/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/loading_pipeline/lib/tasks/exports/fields.py b/loading_pipeline/lib/tasks/exports/fields.py new file mode 100644 index 0000000000..97aa6963c4 --- /dev/null +++ b/loading_pipeline/lib/tasks/exports/fields.py @@ -0,0 +1,316 @@ +import hail as hl + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.tasks.exports.misc import reformat_transcripts_for_export + +FIVE_PERCENT = 0.05 +STANDARD_CONTIGS = hl.set( + [c.replace('MT', 'M') for c in ReferenceGenome.GRCh37.standard_contigs], +) + + +def reference_independent_contig(locus: hl.LocusExpression): + contig = locus.contig.replace('^chr', '').replace('MT', 'M') + return hl.or_missing( + # lifted over alternate contigs may be present + # even though the primary contig is filtered to + # standard contigs earlier in the pipeline + STANDARD_CONTIGS.contains(contig), + contig, + ) + + +def get_dataset_type_specific_variants_annotations( + ht: hl.Table, + dataset_type: DatasetType, +): + return { + DatasetType.MITO: lambda ht: { + 'commonLowHeteroplasmy': ht.common_low_heteroplasmy, + 'haplogroupDefining': ht.haplogroup.is_defining, + 'mitotip': ht.mitotip.trna_prediction, + }, + DatasetType.SV: lambda ht: { + 'algorithms': ht.algorithms, + 'bothsidesSupport': ht.bothsides_support, + 'cpxIntervals': ht.cpxIntervals.map( + lambda cpx_i: hl.Struct( + chrom=reference_independent_contig(cpx_i.start), + start=cpx_i.start.position, + end=cpx_i.end.position, + type=cpx_i.type, + ), + ), + 'endChrom': hl.or_missing( + ( + (ht.sv_type != 'INS') + & (ht.start_locus.contig != ht.end_locus.contig) + ), + reference_independent_contig(ht.end_locus), + ), + 'svSourceDetail': hl.or_missing( + ( + (ht.sv_type == 'INS') + & (ht.start_locus.contig != ht.end_locus.contig) + ), + hl.Struct(chrom=reference_independent_contig(ht.end_locus)), + ), + 'svType': ht.sv_type, + 'svTypeDetail': ht.sv_type_detail, + 'predictions': hl.Struct( + strvctvre=ht.strvctvre.score, + ), + 'populations': hl.Struct( + gnomad_svs=hl.Struct( + af=ht.gnomad_svs.AF, + het=ht.gnomad_svs.N_HET, + hom=ht.gnomad_svs.N_HOM, + id=ht.gnomad_svs.ID, + ), + ), + }, + DatasetType.GCNV: lambda ht: { + 'numExon': ht.num_exon, + 'svType': ht.sv_type, + 'predictions': hl.Struct( + strvctvre=ht.strvctvre.score, + ), + 'populations': hl.Struct( + sv_callset=hl.Struct( + ac=ht.gt_stats.AC, + af=ht.gt_stats.AF, + an=ht.gt_stats.AN, + het=ht.gt_stats.Het, + hom=ht.gt_stats.Hom, + ), + ), + }, + }[dataset_type](ht) + + +def get_calls_export_fields( + ht: hl.Table, + fe: hl.Struct, + dataset_type: DatasetType, +): + return { + DatasetType.SNV_INDEL: lambda fe: hl.Struct( + sampleId=fe.s, + gt=fe.GT.n_alt_alleles(), + gq=fe.GQ, + ab=fe.AB, + dp=fe.DP, + ), + DatasetType.MITO: lambda fe: hl.Struct( + sampleId=fe.s, + gt=fe.GT.n_alt_alleles(), + dp=fe.DP, + hl=fe.HL, + mitoCn=fe.mito_cn, + contamination=fe.contamination, + ), + DatasetType.SV: lambda fe: hl.Struct( + sampleId=fe.s, + gt=fe.GT.n_alt_alleles(), + cn=fe.CN, + gq=fe.GQ, + newCall=fe.concordance.new_call, + prevCall=fe.concordance.prev_call, + prevNumAlt=fe.concordance.prev_num_alt, + ), + DatasetType.GCNV: lambda fe: hl.Struct( + sampleId=fe.s, + gt=fe.GT.n_alt_alleles(), + cn=fe.CN, + qs=fe.QS, + defragged=fe.defragged, + start=hl.or_else(fe.sample_start, ht.start_locus.position), + end=hl.or_else(fe.sample_end, ht.end_locus.position), + numExon=hl.or_else(fe.sample_num_exon, ht.num_exon), + geneIds=hl.or_else( + fe.sample_gene_ids, + hl.set(ht.sorted_gene_consequences.gene_id), + ), + newCall=fe.concordance.new_call, + prevCall=fe.concordance.prev_call, + prevOverlap=fe.concordance.prev_overlap, + ), + }[dataset_type](fe) + + +def get_entries_export_fields( + ht: hl.Table, + dataset_type: DatasetType, + sample_type: SampleType, + project_guid: str, +): + return { + 'key_': ht.key_, + 'project_guid': project_guid, + 'family_guid': ht.family_entries.family_guid[0], + **( + { + 'sample_type': sample_type.value, + } + if dataset_type in {DatasetType.SNV_INDEL, DatasetType.MITO} + else {} + ), + 'xpos': ht.xpos, + **( + { + 'geneIds': hl.set(ht.sorted_gene_consequences.gene_id) + if dataset_type == DatasetType.SV + else hl.set(ht.sorted_transcript_consequences.gene_id) + if dataset_type == DatasetType.SNV_INDEL + else None, + } + if dataset_type in {DatasetType.SV, DatasetType.SNV_INDEL} + else {} + ), + 'filters': ht.filters, + 'calls': hl.sorted(ht.family_entries, key=lambda fe: fe.s).map( + lambda fe: get_calls_export_fields(ht, fe, dataset_type), + ), + 'sign': 1, + } + + +def get_variant_id_fields( + ht: hl.Table, + dataset_type: DatasetType, +): + return { + DatasetType.SNV_INDEL: lambda ht: { + 'variantId': ht.variant_id, + 'rsid': ht.rsid, + 'CAID': hl.missing(hl.tstr), + }, + DatasetType.MITO: lambda ht: { + 'variantId': ht.variant_id, + 'rsid': ht.rsid, + }, + DatasetType.SV: lambda ht: { + 'variantId': ht.variant_id, + }, + DatasetType.GCNV: lambda ht: { + 'variantId': ht.variant_id, + }, + }[dataset_type](ht) + + +def get_lifted_over_position_fields(ht: hl.Table, dataset_type: DatasetType): + if dataset_type == DatasetType.MITO: + return {'liftedOverPos': ht.rg37_locus.position} + return { + 'liftedOverChrom': ( + reference_independent_contig(ht.rg37_locus) + if hasattr(ht, 'rg37_locus') + else reference_independent_contig(ht.rg38_locus) + ), + 'liftedOverPos': ( + hl.or_missing( + hl.is_defined(reference_independent_contig(ht.rg37_locus)), + ht.rg37_locus.position, + ) + if hasattr(ht, 'rg37_locus') + else ht.rg38_locus.position + ), + } + + +def get_consequences_fields( + ht: hl.Table, + reference_genome: ReferenceGenome, + dataset_type: DatasetType, +): + return { + DatasetType.SNV_INDEL: lambda ht: { + **( + { + 'sortedMotifFeatureConsequences': ht.sortedMotifFeatureConsequences, + 'sortedRegulatoryFeatureConsequences': ht.sortedRegulatoryFeatureConsequences, + } + if reference_genome == ReferenceGenome.GRCh38 + else {} + ), + 'sortedTranscriptConsequences': ht.sortedTranscriptConsequences, + }, + DatasetType.MITO: lambda ht: { + # MITO transcripts are not exported to their own table, + # but the structure should be preserved here. + 'sortedTranscriptConsequences': hl.enumerate( + ht.sortedTranscriptConsequences, + ).starmap(reformat_transcripts_for_export), + }, + DatasetType.SV: lambda ht: { + 'sortedGeneConsequences': ht.sortedGeneConsequences, + }, + DatasetType.GCNV: lambda ht: { + 'sortedGeneConsequences': ht.sortedGeneConsequences, + }, + }[dataset_type](ht) + + +def get_variants_export_fields( + ht: hl.Table, + reference_genome: ReferenceGenome, + dataset_type: DatasetType, +): + if dataset_type in {DatasetType.SV, DatasetType.GCNV}: + rg37_contig = reference_independent_contig(ht.rg37_locus_end) + position_fields = { + 'chrom': reference_independent_contig(ht.start_locus), + 'pos': ht.start_locus.position, + 'end': ht.end_locus.position, + 'rg37LocusEnd': hl.Struct( + contig=rg37_contig, + position=hl.or_missing( + hl.is_defined(rg37_contig), + ht.rg37_locus_end.position, + ), + ), + } + return { + 'key_': ht.key_, + 'xpos': ht.xpos, + **position_fields, + **get_variant_id_fields(ht, dataset_type), + **get_lifted_over_position_fields(ht, dataset_type), + **get_dataset_type_specific_variants_annotations(ht, dataset_type), + **get_consequences_fields(ht, reference_genome, dataset_type), + } + if dataset_type == DatasetType.MITO: + return { + 'key_': ht.key_, + **get_variant_id_fields(ht, dataset_type), + **get_lifted_over_position_fields(ht, dataset_type), + **get_dataset_type_specific_variants_annotations(ht, dataset_type), + **get_consequences_fields(ht, reference_genome, dataset_type), + } + return { + 'key_': ht.key_, + **get_consequences_fields(ht, reference_genome, dataset_type), + } + + +def get_variant_details_export_fields( + ht: hl.Table, + reference_genome: ReferenceGenome, + dataset_type: DatasetType, +): + return { + 'key_': ht.key_, + **get_variant_id_fields(ht, dataset_type), + **get_lifted_over_position_fields(ht, dataset_type), + **( + { + 'sortedMotifFeatureConsequences': ht.sortedMotifFeatureConsequences, + 'sortedRegulatoryFeatureConsequences': ht.sortedRegulatoryFeatureConsequences, + } + if reference_genome == ReferenceGenome.GRCh38 + else {} + ), + 'transcripts': hl.enumerate( + ht.sortedTranscriptConsequences, + ).starmap(reformat_transcripts_for_export), + } diff --git a/loading_pipeline/lib/tasks/exports/misc.py b/loading_pipeline/lib/tasks/exports/misc.py new file mode 100644 index 0000000000..ee844d28e0 --- /dev/null +++ b/loading_pipeline/lib/tasks/exports/misc.py @@ -0,0 +1,274 @@ +from collections import OrderedDict + +import hail as hl + +from loading_pipeline.lib.annotations.enums import ( + BIOTYPES, + FIVEUTR_CONSEQUENCES, + LOF_FILTERS, + MITOTIP_PATHOGENICITIES, + MOTIF_CONSEQUENCE_TERMS, + REGULATORY_BIOTYPES, + REGULATORY_CONSEQUENCE_TERMS, + SV_CONSEQUENCE_RANKS, + SV_TYPE_DETAILS, + SV_TYPES, + TRANSCRIPT_CONSEQUENCE_TERMS, +) +from loading_pipeline.lib.core import DatasetType, ReferenceGenome +from loading_pipeline.lib.misc.nested_field import parse_nested_field + + +def snake_to_camelcase(snake_string: str): + components = snake_string.split('_') + return components[0] + ''.join(x.title() for x in components[1:]) + + +def camelcase_hl_struct(s: hl.StructExpression) -> hl.StructExpression: + return s.rename({f: snake_to_camelcase(f) for f in s}) + + +def sorted_hl_struct(s: hl.StructExpression) -> hl.StructExpression: + if not isinstance(s, hl.StructExpression): + return s + return s.select(**{k: sorted_hl_struct(s[k]) for k in sorted(s)}) + + +def array_structexpression_fields(ht: hl.Table): + return [ + field + for field in ht.row + if isinstance( + ht[field], + hl.expr.expressions.typed_expressions.ArrayStructExpression, + ) + ] + + +def reformat_transcripts_for_export(i: int, s: hl.StructExpression): + formatted_s = ( + s.annotate( + majorConsequence=s.consequenceTerms.first(), + transcriptRank=i, + ) + if hasattr(s, 'loftee') + else s.annotate( + loftee=hl.Struct( + isLofNagnag=s.isLofNagnag, + lofFilters=s.lofFilters, + ), + majorConsequence=s.consequenceTerms.first(), + transcriptRank=i, + ).drop('isLofNagnag', 'lofFilters') + ) + return sorted_hl_struct(formatted_s) + + +def export_parquet_filterable_transcripts_fields( + reference_genome: ReferenceGenome, +) -> OrderedDict[str, str]: + fields = { + k: k + for k in [ + 'canonical', + 'consequenceTerms', + 'geneId', + ] + } + if reference_genome == ReferenceGenome.GRCh38: + fields = { + **fields, + 'alphamissensePathogenicity': 'alphamissense.pathogenicity', + 'extendedIntronicSpliceRegionVariant': 'spliceregion.extended_intronic_splice_region_variant', + 'fiveutrConsequence': 'utrannotator.fiveutrConsequence', + 'isManeSelect': 'isManeSelect', + } + # Parquet export expects all fields sorted alphabetically + return OrderedDict(sorted(fields.items())) + + +def subset_consequences_fields( + ht: hl.Table, + reference_genome: ReferenceGenome, +) -> hl.Table: + if reference_genome == ReferenceGenome.GRCh38: + ht = ht.annotate( + sortedMotifFeatureConsequences=ht.sortedMotifFeatureConsequences.map( + lambda e: e.select( + 'consequenceTerms', + ), + ), + sortedRegulatoryFeatureConsequences=ht.sortedRegulatoryFeatureConsequences.map( + lambda e: e.select( + 'consequenceTerms', + ), + ), + sortedTranscriptConsequences=ht.sortedTranscriptConsequences.map( + lambda e: e.annotate(isManeSelect=hl.is_defined(e.maneSelect)), + ), + ) + return ht.annotate( + sortedTranscriptConsequences=hl.enumerate( + ht.sortedTranscriptConsequences, + ).starmap( + lambda idx, c: c.select( + **{ + new_field_name: parse_nested_field( + ht.sortedTranscriptConsequences, + existing_field_name, + )[idx] + for new_field_name, existing_field_name in export_parquet_filterable_transcripts_fields( + reference_genome, + ).items() + }, + ), + ), + ) + + +def camelcase_array_structexpression_fields( + ht: hl.Table, + reference_genome: ReferenceGenome, + dataset_type: DatasetType, +): + for field in array_structexpression_fields(ht): + ht = ht.transmute( + **{ + snake_to_camelcase(field): ht[field].map( + lambda c: camelcase_hl_struct(c), + ), + }, + ) + + # Custom handling of nested sorted_transcript_consequences fields for GRCh38/SNV_INDEL. + # Note that spliceregion (extended_intronic_splice_region_variant) prevents + # a more procedural approach here. + if ( + reference_genome == ReferenceGenome.GRCh38 + and dataset_type == DatasetType.SNV_INDEL + ): + ht = ht.annotate( + sortedTranscriptConsequences=ht.sortedTranscriptConsequences.map( + lambda s: s.annotate( + loftee=camelcase_hl_struct(s.loftee), + utrannotator=camelcase_hl_struct(s.utrannotator), + ), + ), + ) + return ht + + +def unmap_formatting_annotation_enums( + ht: hl.Table, + reference_genome: ReferenceGenome, + dataset_type: DatasetType, +) -> hl.Table: + formatting_annotation_names = { + fa.__name__ for fa in dataset_type.formatting_annotation_fns(reference_genome) + } + if 'sorted_motif_feature_consequences' in formatting_annotation_names: + ht = ht.annotate( + sorted_motif_feature_consequences=ht.sorted_motif_feature_consequences.map( + lambda c: c.annotate( + consequence_terms=c.consequence_term_ids.map( + lambda tid: hl.array(MOTIF_CONSEQUENCE_TERMS)[tid], + ), + ).drop('consequence_term_ids'), + ), + ) + ht = ht.annotate_globals( + enums=ht.enums.drop('sorted_motif_feature_consequences'), + ) + if 'sorted_regulatory_feature_consequences' in formatting_annotation_names: + ht = ht.annotate( + sorted_regulatory_feature_consequences=ht.sorted_regulatory_feature_consequences.map( + lambda c: c.annotate( + biotype=hl.array(REGULATORY_BIOTYPES)[c.biotype_id], + consequence_terms=c.consequence_term_ids.map( + lambda tid: hl.array(REGULATORY_CONSEQUENCE_TERMS)[tid], + ), + ).drop('biotype_id', 'consequence_term_ids'), + ), + ) + ht = ht.annotate_globals( + enums=ht.enums.drop('sorted_regulatory_feature_consequences'), + ) + if 'sorted_transcript_consequences' in formatting_annotation_names: + ht = ht.annotate( + sorted_transcript_consequences=ht.sorted_transcript_consequences.map( + lambda c: c.annotate( + biotype=hl.array(BIOTYPES)[c.biotype_id], + consequence_terms=c.consequence_term_ids.map( + lambda tid: hl.array(TRANSCRIPT_CONSEQUENCE_TERMS)[tid], + ), + **{ + 'loftee': c.loftee.annotate( + lof_filters=c.loftee.lof_filter_ids.map( + lambda fid: hl.array(LOF_FILTERS)[fid], + ), + ).drop('lof_filter_ids'), + 'utrannotator': c.utrannotator.annotate( + fiveutr_consequence=hl.array(FIVEUTR_CONSEQUENCES)[ + c.utrannotator.fiveutr_consequence_id + ], + ).drop('fiveutr_consequence_id'), + } + if reference_genome == ReferenceGenome.GRCh38 + and dataset_type == DatasetType.SNV_INDEL + else { + 'lof_filters': c.lof_filter_ids.map( + lambda fid: hl.array(LOF_FILTERS)[fid], + ), + }, + ).drop( + 'biotype_id', + 'consequence_term_ids', + *( + [] + if reference_genome == ReferenceGenome.GRCh38 + and dataset_type == DatasetType.SNV_INDEL + else [ + 'lof_filter_ids', + ] + ), + ), + ), + ) + ht = ht.annotate_globals(enums=ht.enums.drop('sorted_transcript_consequences')) + if 'mitotip' in formatting_annotation_names: + ht = ht.annotate( + mitotip=hl.Struct( + trna_prediction=hl.array(MITOTIP_PATHOGENICITIES)[ + ht.mitotip.trna_prediction_id + ], + ), + ) + ht = ht.annotate_globals(enums=ht.enums.drop('mitotip')) + if 'cpx_intervals' in formatting_annotation_names: + ht = ht.annotate( + cpx_intervals=ht.cpx_intervals.map( + lambda cpx_i: cpx_i.annotate( + type=hl.array(SV_TYPES)[cpx_i.type_id], + ).drop('type_id'), + ), + ) + if 'sv_type_id' in formatting_annotation_names: + ht = ht.annotate(sv_type=hl.array(SV_TYPES)[ht.sv_type_id]).drop('sv_type_id') + ht = ht.annotate_globals(enums=ht.enums.drop('sv_type')) + if 'sv_type_detail_id' in formatting_annotation_names: + ht = ht.annotate( + sv_type_detail=hl.array(SV_TYPE_DETAILS)[ht.sv_type_detail_id], + ).drop('sv_type_detail_id') + ht = ht.annotate_globals(enums=ht.enums.drop('sv_type_detail')) + if 'sorted_gene_consequences' in formatting_annotation_names: + ht = ht.annotate( + sorted_gene_consequences=ht.sorted_gene_consequences.map( + lambda c: c.annotate( + major_consequence=hl.array(SV_CONSEQUENCE_RANKS)[ + c.major_consequence_id + ], + ).drop('major_consequence_id'), + ), + ) + ht = ht.annotate_globals(enums=ht.enums.drop('sorted_gene_consequences')) + return ht diff --git a/loading_pipeline/lib/tasks/exports/misc_test.py b/loading_pipeline/lib/tasks/exports/misc_test.py new file mode 100644 index 0000000000..f0324db627 --- /dev/null +++ b/loading_pipeline/lib/tasks/exports/misc_test.py @@ -0,0 +1,484 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.core import ( + DatasetType, + ReferenceGenome, +) +from loading_pipeline.lib.tasks.exports.misc import ( + camelcase_array_structexpression_fields, + sorted_hl_struct, + unmap_formatting_annotation_enums, +) + +TEST_SNV_INDEL_ANNOTATIONS = ( + 'loading_pipeline/var/test/exports/GRCh38/SNV_INDEL/annotations.ht' +) +TEST_GRCH37_SNV_INDEL_ANNOTATIONS = ( + 'loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/annotations.ht' +) + + +class MiscTest(unittest.TestCase): + def test_unmap_formatting_annotation_enums(self) -> None: + ht = hl.read_table(TEST_SNV_INDEL_ANNOTATIONS) + ht = unmap_formatting_annotation_enums( + ht, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + ) + self.assertCountEqual( + list(ht.globals.enums.collect()[0].keys()), + [ + 'clinvar', + 'hgmd', + 'screen', + 'dbnsfp', + 'gnomad_exomes', + 'gnomad_non_coding_constraint', + 'splice_ai', + 'exac', + 'topmed', + 'gnomad_genomes', + 'eigen', + ], + ) + ht = ht.annotate( + sorted_transcript_consequences=[ht.sorted_transcript_consequences[0]], + ) + self.assertEqual( + ht.collect()[0], + hl.Struct( + key_=0, + locus=hl.Locus( + contig='chr1', + position=876499, + reference_genome='GRCh38', + ), + alleles=['A', 'G'], + clinvar=hl.Struct( + alleleId=929885, + conflictingPathogenicities=None, + goldStars=1, + submitters=['Labcorp Genetics (formerly Invitae), Labcorp'], + conditions=['not provided'], + assertion_ids=[], + pathogenicity_id=12, + ), + rg37_locus=hl.Locus( + contig=1, + position=874501, + reference_genome='GRCh37', + ), + rsid=None, + sorted_transcript_consequences=[ + hl.Struct( + amino_acids='S/L', + canonical=1, + codons='tCg/tTg', + gene_id='ENSG00000187634', + hgvsc='ENST00000616016.5:c.1049C>T', + hgvsp='ENSP00000478421.2:p.Ser350Leu', + transcript_id='ENST00000616016', + mane_select='NM_001385641.1', + mane_plus_clinical=None, + exon=hl.Struct(index=6, total=14), + intron=None, + refseq_transcript_id='NM_001385641.1', + alphamissense=hl.Struct(pathogenicity=None), + loftee=hl.Struct(is_lof_nagnag=None, lof_filters=None), + spliceregion=hl.Struct( + extended_intronic_splice_region_variant=False, + ), + utrannotator=hl.Struct( + existing_inframe_oorfs=None, + existing_outofframe_oorfs=None, + existing_uorfs=None, + fiveutr_annotation=hl.Struct( + type='OutOfFrame_oORF', + KozakContext='CGCATGC', + KozakStrength='Weak', + DistanceToCDS=41, + CapDistanceToStart=None, + DistanceToStop=None, + Evidence=None, + AltStop=None, + AltStopDistanceToCDS=None, + FrameWithCDS=None, + StartDistanceToCDS=None, + newSTOPDistanceToCDS=None, + alt_type=None, + alt_type_length=None, + ref_StartDistanceToCDS=None, + ref_type=None, + ref_type_length=None, + ), + fiveutr_consequence=None, + ), + biotype='protein_coding', + consequence_terms=['missense_variant'], + ), + ], + variant_id='1-876499-A-G', + xpos=1000876499, + gt_stats=hl.Struct(AC=47, AN=81784, AF=0.0005746845272369683, hom=1), + CAID='CA502654', + check_ref=False, + sorted_regulatory_feature_consequences=[ + hl.Struct( + regulatory_feature_id='ENSR00000344437', + biotype='CTCF_binding_site', + consequence_terms=['regulatory_region_variant'], + ), + ], + sorted_motif_feature_consequences=[ + hl.Struct( + motif_feature_id='ENSM00493959715', + consequence_terms=['TF_binding_site_variant'], + ), + ], + gnomad_non_coding_constraint=hl.Struct(z_score=None), + hgmd=hl.Struct(accession='abcdefg', class_id=3), + gnomad_exomes=hl.Struct( + AF=0.0006690866430290043, + AN=1440770, + AC=964, + Hom=0, + AF_POPMAX_OR_GLOBAL=0.0008023773552849889, + FAF_AF=0.000633420015219599, + Hemi=0, + ), + gnomad_genomes=hl.Struct( + AF=0.0002759889466688037, + AN=152180, + AC=42, + Hom=0, + AF_POPMAX_OR_GLOBAL=0.10000000149011612, + FAF_AF=0.0002092500071739778, + Hemi=0, + ), + screen=hl.Struct(region_type_ids=[]), + dbnsfp=hl.Struct( + PrimateAI_score=0.5918066501617432, + fathmm_MKL_coding_score=0.7174800038337708, + CADD_phred=23.5, + SIFT_score=0.0010000000474974513, + REVEL_score=0.3109999895095825, + Polyphen2_HVAR_score=0.164000004529953, + VEST4_score=0.39500001072883606, + MPC_score=0.01291007362306118, + MutPred_score=None, + MutationTaster_pred_id=0, + ), + topmed=hl.Struct( + AC=41, + AF=0.00032651599030941725, + AN=125568, + Hom=0, + Het=41, + ), + exac=hl.Struct( + AF_POPMAX=0.0007150234305299819, + AF=0.00019039999460801482, + AC_Adj=20, + AC_Het=20, + AC_Hom=0, + AC_Hemi=None, + AN_Adj=47974, + ), + splice_ai=hl.Struct(delta_score=0.0, splice_consequence_id=4), + eigen=hl.Struct(Eigen_phred=2.628000020980835), + ), + ) + ht = hl.read_table(TEST_GRCH37_SNV_INDEL_ANNOTATIONS) + ht = unmap_formatting_annotation_enums( + ht, + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + ) + self.assertCountEqual( + list(ht.globals.enums.collect()[0].keys()), + [ + 'clinvar', + 'hgmd', + 'dbnsfp', + 'gnomad_exomes', + 'splice_ai', + 'exac', + 'topmed', + 'gnomad_genomes', + 'eigen', + ], + ) + ht = ht.annotate( + sorted_transcript_consequences=[ht.sorted_transcript_consequences[0]], + ) + self.assertEqual( + ht.collect()[0], + hl.Struct( + locus=hl.Locus(contig=1, position=69134, reference_genome='GRCh37'), + alleles=['A', 'G'], + clinvar=hl.Struct( + alleleId=2193183, + conflictingPathogenicities=None, + goldStars=1, + submitters=['Ambry Genetics'], + conditions=['not specified'], + assertion_ids=[], + pathogenicity_id=14, + ), + rsid=None, + sorted_transcript_consequences=[ + hl.Struct( + amino_acids='E/G', + canonical=1, + codons='gAa/gGa', + gene_id='ENSG00000186092', + hgvsc='ENST00000335137.3:c.44A>G', + hgvsp='ENSP00000334393.3:p.Glu15Gly', + transcript_id='ENST00000335137', + is_lof_nagnag=None, + biotype='protein_coding', + consequence_terms=['missense_variant'], + lof_filters=None, + ), + ], + variant_id='1-69134-A-G', + xpos=1000069134, + gt_stats=hl.Struct(AC=25, AN=1246, AF=0.020064204931259155, hom=10), + CAID='CA502008', + rg38_locus=hl.Locus( + contig='chr1', + position=69134, + reference_genome='GRCh38', + ), + hgmd=None, + gnomad_exomes=hl.Struct( + AF=0.026665963232517242, + AN=18938, + AC=505, + Hom=127, + AF_POPMAX_OR_GLOBAL=0.08191808313131332, + FAF_AF=0.02474386990070343, + Hemi=0, + ), + gnomad_genomes=hl.Struct( + AF=0.0001722949673421681, + AN=5804, + AC=1, + Hom=0, + AF_POPMAX_OR_GLOBAL=0.0005662514013238251, + FAF_AF=0.0, + Hemi=0, + ), + dbnsfp=hl.Struct( + PrimateAI_score=0.37232041358947754, + fathmm_MKL_coding_score=0.056940000504255295, + CADD_phred=15.880000114440918, + SIFT_score=0.1289999932050705, + REVEL_score=0.07500000298023224, + Polyphen2_HVAR_score=0.0010000000474974513, + VEST4_score=0.10700000077486038, + MPC_score=1.8921889066696167, + MutPred_score=0.3779999911785126, + MutationTaster_pred_id=2, + ), + topmed=hl.Struct( + AC=95, + AF=0.0007565619889646769, + AN=125568, + Hom=0, + Het=95, + ), + exac=hl.Struct( + AF_POPMAX=None, + AF=0.0016550000291317701, + AC_Adj=0, + AC_Het=0, + AC_Hom=0, + AC_Hemi=None, + AN_Adj=66, + ), + eigen=hl.Struct(Eigen_phred=1.0019999742507935), + splice_ai=hl.Struct( + delta_score=0.019999999552965164, + splice_consequence_id=2, + ), + key_=1424, + ), + ) + + def test_camelcase_array_structexpression_fields(self) -> None: + ht = hl.read_table(TEST_SNV_INDEL_ANNOTATIONS) + ht = unmap_formatting_annotation_enums( + ht, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + ) + ht = camelcase_array_structexpression_fields( + ht, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + ) + ht = ht.annotate( + sortedTranscriptConsequences=[ht.sortedTranscriptConsequences[0]], + ) + self.assertEqual( + ht.collect()[0], + hl.Struct( + key_=0, + locus=hl.Locus( + contig='chr1', + position=876499, + reference_genome='GRCh38', + ), + alleles=['A', 'G'], + clinvar=hl.Struct( + alleleId=929885, + conflictingPathogenicities=None, + goldStars=1, + submitters=['Labcorp Genetics (formerly Invitae), Labcorp'], + conditions=['not provided'], + assertion_ids=[], + pathogenicity_id=12, + ), + rg37_locus=hl.Locus( + contig=1, + position=874501, + reference_genome='GRCh37', + ), + rsid=None, + variant_id='1-876499-A-G', + xpos=1000876499, + gt_stats=hl.Struct(AC=47, AN=81784, AF=0.0005746845272369683, hom=1), + CAID='CA502654', + check_ref=False, + gnomad_non_coding_constraint=hl.Struct(z_score=None), + hgmd=hl.Struct(accession='abcdefg', class_id=3), + gnomad_exomes=hl.Struct( + AF=0.0006690866430290043, + AN=1440770, + AC=964, + Hom=0, + AF_POPMAX_OR_GLOBAL=0.0008023773552849889, + FAF_AF=0.000633420015219599, + Hemi=0, + ), + gnomad_genomes=hl.Struct( + AF=0.0002759889466688037, + AN=152180, + AC=42, + Hom=0, + AF_POPMAX_OR_GLOBAL=0.10000000149011612, + FAF_AF=0.0002092500071739778, + Hemi=0, + ), + screen=hl.Struct(region_type_ids=[]), + dbnsfp=hl.Struct( + PrimateAI_score=0.5918066501617432, + fathmm_MKL_coding_score=0.7174800038337708, + CADD_phred=23.5, + SIFT_score=0.0010000000474974513, + REVEL_score=0.3109999895095825, + Polyphen2_HVAR_score=0.164000004529953, + VEST4_score=0.39500001072883606, + MPC_score=0.01291007362306118, + MutPred_score=None, + MutationTaster_pred_id=0, + ), + topmed=hl.Struct( + AC=41, + AF=0.00032651599030941725, + AN=125568, + Hom=0, + Het=41, + ), + exac=hl.Struct( + AF_POPMAX=0.0007150234305299819, + AF=0.00019039999460801482, + AC_Adj=20, + AC_Het=20, + AC_Hom=0, + AC_Hemi=None, + AN_Adj=47974, + ), + splice_ai=hl.Struct( + delta_score=0.0, + splice_consequence_id=4, + ), + eigen=hl.Struct(Eigen_phred=2.628000020980835), + sortedTranscriptConsequences=[ + hl.Struct( + aminoAcids='S/L', + canonical=1, + codons='tCg/tTg', + geneId='ENSG00000187634', + hgvsc='ENST00000616016.5:c.1049C>T', + hgvsp='ENSP00000478421.2:p.Ser350Leu', + transcriptId='ENST00000616016', + maneSelect='NM_001385641.1', + manePlusClinical=None, + exon=hl.Struct(index=6, total=14), + intron=None, + refseqTranscriptId='NM_001385641.1', + alphamissense=hl.Struct(pathogenicity=None), + loftee=hl.Struct(isLofNagnag=None, lofFilters=None), + spliceregion=hl.Struct( + extended_intronic_splice_region_variant=False, + ), + utrannotator=hl.Struct( + existingInframeOorfs=None, + existingOutofframeOorfs=None, + existingUorfs=None, + fiveutrAnnotation=hl.Struct( + type='OutOfFrame_oORF', + KozakContext='CGCATGC', + KozakStrength='Weak', + DistanceToCDS=41, + CapDistanceToStart=None, + DistanceToStop=None, + Evidence=None, + AltStop=None, + AltStopDistanceToCDS=None, + FrameWithCDS=None, + StartDistanceToCDS=None, + newSTOPDistanceToCDS=None, + alt_type=None, + alt_type_length=None, + ref_StartDistanceToCDS=None, + ref_type=None, + ref_type_length=None, + ), + fiveutrConsequence=None, + ), + biotype='protein_coding', + consequenceTerms=['missense_variant'], + ), + ], + sortedRegulatoryFeatureConsequences=[ + hl.Struct( + regulatoryFeatureId='ENSR00000344437', + biotype='CTCF_binding_site', + consequenceTerms=['regulatory_region_variant'], + ), + ], + sortedMotifFeatureConsequences=[ + hl.Struct( + motifFeatureId='ENSM00493959715', + consequenceTerms=['TF_binding_site_variant'], + ), + ], + ), + ) + + def test_sorted_hl_struct(self) -> None: + struct = hl.Struct( + z=5, + y=hl.Struct(b=2, a=hl.Struct(d=4, c=3)), + x=hl.Struct(k=9), + ) + self.assertEqual( + sorted_hl_struct(struct), + hl.Struct(x=hl.Struct(k=9), y=hl.Struct(a=hl.Struct(c=3, d=4), b=2), z=5), + ) diff --git a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py new file mode 100644 index 0000000000..d60b9475b0 --- /dev/null +++ b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py @@ -0,0 +1,100 @@ +import hail as hl +import luigi +import luigi.util + +from loading_pipeline.lib.annotations.fields import get_fields +from loading_pipeline.lib.misc.family_entries import ( + compute_callset_family_entries_ht, + deduplicate_by_most_non_ref_calls, + deglobalize_ids, +) +from loading_pipeline.lib.paths import ( + new_entries_parquet_path, + variant_annotations_table_path, +) +from loading_pipeline.lib.tasks.base.base_loading_run_params import ( + BaseLoadingRunParams, +) +from loading_pipeline.lib.tasks.base.base_write_parquet import BaseWriteParquetTask +from loading_pipeline.lib.tasks.exports.fields import get_entries_export_fields +from loading_pipeline.lib.tasks.files import GCSorLocalTarget +from loading_pipeline.lib.tasks.update_variant_annotations_table_with_new_variants import ( + UpdateVariantAnnotationsTableWithNewVariantsTask, +) +from loading_pipeline.lib.tasks.write_remapped_and_subsetted_callset import ( + WriteRemappedAndSubsettedCallsetTask, +) + +ANNOTATIONS_TABLE_TASK = 'annotations_table_task' +REMAPPED_AND_SUBSETTED_CALLSET_TASKS = 'remapped_and_subsetted_callset_tasks' + + +@luigi.util.inherits(BaseLoadingRunParams) +class WriteNewEntriesParquetTask(BaseWriteParquetTask): + def output(self) -> luigi.Target: + return GCSorLocalTarget( + new_entries_parquet_path( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + ) + + def requires(self) -> dict[str, luigi.Task]: + return { + ANNOTATIONS_TABLE_TASK: self.clone( + UpdateVariantAnnotationsTableWithNewVariantsTask, + ), + REMAPPED_AND_SUBSETTED_CALLSET_TASKS: [ + self.clone( + WriteRemappedAndSubsettedCallsetTask, + project_i=i, + ) + for i in range(len(self.project_guids)) + ], + } + + def create_table(self) -> None: + unioned_ht = None + for project_guid, remapped_and_subsetted_callset_task in zip( + self.project_guids, + self.input()[REMAPPED_AND_SUBSETTED_CALLSET_TASKS], + strict=True, + ): + mt = hl.read_matrix_table(remapped_and_subsetted_callset_task.path) + ht = compute_callset_family_entries_ht( + self.dataset_type, + mt, + get_fields( + mt, + self.dataset_type.genotype_entry_annotation_fns, + **self.param_kwargs, + ), + ) + ht = deglobalize_ids(ht) + ht = deduplicate_by_most_non_ref_calls(ht) + annotations_ht = hl.read_table( + variant_annotations_table_path( + self.reference_genome, + self.dataset_type, + ), + ) + ht = ht.join(annotations_ht) + + # the family entries ht will contain rows + # where at least one family is defined... after explosion, + # rows where a family is not defined should be removed. + ht = ht.explode(ht.family_entries) + ht = ht.filter(hl.is_defined(ht.family_entries)) + ht = ht.key_by() + ht = ht.select_globals() + ht = ht.select( + **get_entries_export_fields( + ht, + self.dataset_type, + self.sample_type, + project_guid, + ), + ) + unioned_ht = unioned_ht.union(ht) if unioned_ht else ht + return unioned_ht diff --git a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py new file mode 100644 index 0000000000..ccb3260f5e --- /dev/null +++ b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py @@ -0,0 +1,423 @@ +import hail as hl +import luigi.worker +import pandas as pd + +from loading_pipeline.lib.core import ( + DatasetType, + ReferenceGenome, + SampleType, +) +from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS +from loading_pipeline.lib.paths import ( + new_entries_parquet_path, + variant_annotations_table_path, +) +from loading_pipeline.lib.tasks.exports.write_new_entries_parquet import ( + WriteNewEntriesParquetTask, +) +from loading_pipeline.lib.test.misc import ( + convert_ndarray_to_list, + copy_project_pedigree_to_mocked_dir, +) +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + +TEST_PEDIGREE_3_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_3_remap.tsv' +TEST_PEDIGREE_4_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_4_remap.tsv' +TEST_PEDIGREE_5 = 'loading_pipeline/var/test/pedigrees/test_pedigree_5.tsv' +TEST_MITO_EXPORT_PEDIGREE = ( + 'loading_pipeline/var/test/pedigrees/test_mito_export_pedigree.tsv' +) +TEST_SNV_INDEL_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' +TEST_MITO_CALLSET = 'loading_pipeline/var/test/callsets/mito_1.mt' +TEST_SV_VCF_2 = 'loading_pipeline/var/test/callsets/sv_2.vcf' +TEST_GCNV_BED_FILE = 'loading_pipeline/var/test/callsets/gcnv_1.tsv' +TEST_SNV_INDEL_ANNOTATIONS = ( + 'loading_pipeline/var/test/exports/GRCh38/SNV_INDEL/annotations.ht' +) +TEST_MITO_ANNOTATIONS = 'loading_pipeline/var/test/exports/GRCh38/MITO/annotations.ht' +TEST_SV_ANNOTATIONS = 'loading_pipeline/var/test/exports/GRCh38/SV/annotations.ht' +TEST_GCNV_ANNOTATIONS = 'loading_pipeline/var/test/exports/GRCh38/GCNV/annotations.ht' + +TEST_RUN_ID = 'manual__2024-04-03' + + +class WriteNewEntriesParquetTest(MockedDatarootTestCase): + def setUp(self) -> None: + super().setUp() + ht = hl.read_table( + TEST_SNV_INDEL_ANNOTATIONS, + ) + ht.write( + variant_annotations_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + ), + ) + ht = hl.read_table( + TEST_MITO_ANNOTATIONS, + ) + ht.write( + variant_annotations_table_path( + ReferenceGenome.GRCh38, + DatasetType.MITO, + ), + ) + ht = hl.read_table( + TEST_SV_ANNOTATIONS, + ) + ht.write( + variant_annotations_table_path( + ReferenceGenome.GRCh38, + DatasetType.SV, + ), + ) + ht = hl.read_table(TEST_GCNV_ANNOTATIONS) + ht.write( + variant_annotations_table_path( + ReferenceGenome.GRCh38, + DatasetType.GCNV, + ), + ) + + def test_write_new_entries_parquet(self): + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_3_REMAP, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0113_test_project', + ) + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_4_REMAP, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0114_project4', + ) + worker = luigi.worker.Worker() + task = WriteNewEntriesParquetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path=TEST_SNV_INDEL_VCF, + project_guids=['R0113_test_project', 'R0114_project4'], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + worker.add(task) + worker.run() + self.assertTrue(task.output().exists()) + self.assertTrue(task.complete()) + df = pd.read_parquet( + new_entries_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ) + export_json = convert_ndarray_to_list(df.to_dict('records')) + self.assertEqual( + export_json[:2], + [ + { + 'key': 0, + 'project_guid': 'R0113_test_project', + 'family_guid': 'abc_1', + 'sample_type': 'WGS', + 'xpos': 1000876499, + 'geneIds': ['ENSG00000187634'], + 'filters': [], + 'calls': [ + { + 'sampleId': 'HG00731_1', + 'gt': 2, + 'gq': 21, + 'ab': 1.0, + 'dp': 7, + }, + { + 'sampleId': 'HG00732_1', + 'gt': 2, + 'gq': 24, + 'ab': 1.0, + 'dp': 8, + }, + { + 'sampleId': 'HG00733_1', + 'gt': 2, + 'gq': 12, + 'ab': 1.0, + 'dp': 4, + }, + ], + 'sign': 1, + }, + { + 'key': 1, + 'project_guid': 'R0113_test_project', + 'family_guid': 'abc_1', + 'sample_type': 'WGS', + 'xpos': 1000878314, + 'geneIds': ['ENSG00000187634'], + 'filters': ['VQSRTrancheSNP99.00to99.90'], + 'calls': [ + { + 'sampleId': 'HG00731_1', + 'gt': 1, + 'gq': 30, + 'ab': 0.3333333432674408, + 'dp': 3, + }, + {'sampleId': 'HG00732_1', 'gt': 0, 'gq': 6, 'ab': 0.0, 'dp': 2}, + { + 'sampleId': 'HG00733_1', + 'gt': 1, + 'gq': 61, + 'ab': 0.6000000238418579, + 'dp': 5, + }, + ], + 'sign': 1, + }, + ], + ) + + def test_mito_write_new_entries_parquet(self): + copy_project_pedigree_to_mocked_dir( + TEST_MITO_EXPORT_PEDIGREE, + ReferenceGenome.GRCh38, + DatasetType.MITO, + SampleType.WGS, + 'R0116_test_project3', + ) + worker = luigi.worker.Worker() + task = WriteNewEntriesParquetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.MITO, + sample_type=SampleType.WGS, + callset_path=TEST_MITO_CALLSET, + project_guids=['R0116_test_project3'], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + worker.add(task) + worker.run() + self.assertTrue(task.output().exists()) + self.assertTrue(task.complete()) + df = pd.read_parquet( + new_entries_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.MITO, + TEST_RUN_ID, + ), + ) + export_json = convert_ndarray_to_list(df.to_dict('records')) + self.assertEqual( + export_json, + [ + { + 'key': 998, + 'project_guid': 'R0116_test_project3', + 'family_guid': 'family_1', + 'sample_type': 'WGS', + 'xpos': 25000000008, + 'filters': [], + 'calls': [ + { + 'sampleId': 'RGP_1270_2', + 'gt': 2, + 'dp': 4216, + 'hl': 0.999, + 'mitoCn': 224, + 'contamination': 0.0, + }, + ], + 'sign': 1, + }, + ], + ) + + def test_sv_write_new_entries_parquet(self): + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_5, + ReferenceGenome.GRCh38, + DatasetType.SV, + SampleType.WGS, + 'R0115_test_project2', + ) + worker = luigi.worker.Worker() + task = WriteNewEntriesParquetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SV, + sample_type=SampleType.WGS, + callset_path=TEST_SV_VCF_2, + project_guids=['R0115_test_project2'], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + worker.add(task) + worker.run() + self.assertTrue(task.output().exists()) + self.assertTrue(task.complete()) + df = pd.read_parquet( + new_entries_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.SV, + TEST_RUN_ID, + ), + ) + export_json = convert_ndarray_to_list(df.to_dict('records')) + self.assertEqual( + export_json, + [ + { + 'key': 727, + 'project_guid': 'R0115_test_project2', + 'family_guid': 'family_2_1', + 'xpos': 1001025886, + 'geneIds': ['ENSG00000188157'], + 'filters': ['HIGH_SR_BACKGROUND', 'UNRESOLVED'], + 'calls': [ + { + 'sampleId': 'RGP_164_1', + 'gt': 0, + 'cn': None, + 'gq': 99, + 'newCall': True, + 'prevCall': False, + 'prevNumAlt': None, + }, + { + 'sampleId': 'RGP_164_2', + 'gt': 1, + 'cn': None, + 'gq': 31, + 'newCall': True, + 'prevCall': False, + 'prevNumAlt': None, + }, + { + 'sampleId': 'RGP_164_3', + 'gt': 0, + 'cn': None, + 'gq': 99, + 'newCall': True, + 'prevCall': False, + 'prevNumAlt': None, + }, + { + 'sampleId': 'RGP_164_4', + 'gt': 0, + 'cn': None, + 'gq': 99, + 'newCall': True, + 'prevCall': False, + 'prevNumAlt': None, + }, + ], + 'sign': 1, + }, + ], + ) + + def test_gcnv_write_new_entries_parquet(self): + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_5, + ReferenceGenome.GRCh38, + DatasetType.GCNV, + SampleType.WES, + 'R0115_test_project2', + ) + worker = luigi.worker.Worker() + task = WriteNewEntriesParquetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.GCNV, + sample_type=SampleType.WES, + callset_path=TEST_GCNV_BED_FILE, + project_guids=['R0115_test_project2'], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + worker.add(task) + worker.run() + self.assertTrue(task.output().exists()) + self.assertTrue(task.complete()) + df = pd.read_parquet( + new_entries_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.GCNV, + TEST_RUN_ID, + ), + ) + export_json = convert_ndarray_to_list(df.to_dict('records')) + self.assertEqual( + export_json, + [ + { + 'key': 0, + 'project_guid': 'R0115_test_project2', + 'family_guid': 'family_2_1', + 'xpos': 1000939203, + 'filters': [], + 'calls': [ + { + 'sampleId': 'RGP_164_1', + 'gt': 1, + 'cn': 1, + 'qs': 4, + 'defragged': False, + 'start': 100006937, + 'end': 100007881, + 'numExon': 2, + 'geneIds': ['ENSG00000117620', 'ENSG00000283761'], + 'newCall': False, + 'prevCall': True, + 'prevOverlap': False, + }, + { + 'sampleId': 'RGP_164_2', + 'gt': 1, + 'cn': 1, + 'qs': 5, + 'defragged': False, + 'start': 100017585, + 'end': 100023213, + 'numExon': 1, + 'geneIds': ['ENSG00000117620', 'ENSG00000283761'], + 'newCall': False, + 'prevCall': False, + 'prevOverlap': False, + }, + { + 'sampleId': 'RGP_164_3', + 'gt': 2, + 'cn': 0, + 'qs': 30, + 'defragged': False, + 'start': 100017585, + 'end': 100023213, + 'numExon': 1, + 'geneIds': ['ENSG00000117620', 'ENSG00000283761'], + 'newCall': False, + 'prevCall': True, + 'prevOverlap': False, + }, + { + 'sampleId': 'RGP_164_4', + 'gt': 2, + 'cn': 0, + 'qs': 30, + 'defragged': False, + 'start': 100017586, + 'end': 100023212, + 'numExon': 2, + 'geneIds': ['ENSG00000283761', 'ENSG22222222222'], + 'newCall': False, + 'prevCall': True, + 'prevOverlap': False, + }, + ], + 'sign': 1, + }, + ], + ) diff --git a/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet.py b/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet.py new file mode 100644 index 0000000000..6da793ec53 --- /dev/null +++ b/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet.py @@ -0,0 +1,71 @@ +import hail as hl +import luigi +import luigi.util + +from loading_pipeline.lib.paths import ( + new_variant_details_parquet_path, + new_variants_table_path, +) +from loading_pipeline.lib.tasks.base.base_loading_run_params import ( + BaseLoadingRunParams, +) +from loading_pipeline.lib.tasks.base.base_write_parquet import BaseWriteParquetTask +from loading_pipeline.lib.tasks.exports.fields import get_variant_details_export_fields +from loading_pipeline.lib.tasks.exports.misc import ( + camelcase_array_structexpression_fields, + unmap_formatting_annotation_enums, +) +from loading_pipeline.lib.tasks.files import GCSorLocalFolderTarget, GCSorLocalTarget +from loading_pipeline.lib.tasks.update_variant_annotations_table_with_new_variants import ( + UpdateVariantAnnotationsTableWithNewVariantsTask, +) +from loading_pipeline.lib.tasks.write_new_variants_table import ( + WriteNewVariantsTableTask, +) + + +@luigi.util.inherits(BaseLoadingRunParams) +class WriteNewVariantDetailsParquetTask(BaseWriteParquetTask): + def output(self) -> luigi.Target: + return GCSorLocalTarget( + new_variant_details_parquet_path( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + ) + + def complete(self) -> luigi.Target: + return GCSorLocalFolderTarget(self.output().path).exists() + + def requires(self) -> luigi.Task: + if self.dataset_type.export_all_callset_variants: + return self.clone(UpdateVariantAnnotationsTableWithNewVariantsTask) + return self.clone(WriteNewVariantsTableTask) + + def create_table(self) -> None: + ht = hl.read_table( + new_variants_table_path( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + ) + ht = unmap_formatting_annotation_enums( + ht, + self.reference_genome, + self.dataset_type, + ) + ht = camelcase_array_structexpression_fields( + ht, + self.reference_genome, + self.dataset_type, + ) + ht = ht.key_by() + return ht.select( + **get_variant_details_export_fields( + ht, + self.reference_genome, + self.dataset_type, + ), + ) diff --git a/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py new file mode 100644 index 0000000000..5458854f56 --- /dev/null +++ b/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py @@ -0,0 +1,270 @@ +import os +from unittest import mock + +import hail as hl +import luigi.worker +import pandas as pd + +from loading_pipeline.lib.core import ( + DatasetType, + ReferenceGenome, + SampleType, +) +from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS +from loading_pipeline.lib.paths import ( + new_variant_details_parquet_path, + new_variants_table_path, +) +from loading_pipeline.lib.tasks.exports.write_new_variant_details_parquet import ( + WriteNewVariantDetailsParquetTask, +) +from loading_pipeline.lib.test.misc import convert_ndarray_to_list +from loading_pipeline.lib.test.mock_complete_task import MockCompleteTask +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + +TEST_SNV_INDEL_ANNOTATIONS = ( + 'loading_pipeline/var/test/exports/GRCh38/SNV_INDEL/annotations.ht' +) +TEST_GRCH37_SNV_INDEL_ANNOTATIONS = ( + 'loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/annotations.ht' +) + +TEST_RUN_ID = 'manual__2024-04-03' + + +class WriteNewVariantDetailsParquetTest(MockedDatarootTestCase): + def setUp(self) -> None: + super().setUp() + ht = hl.read_table( + TEST_SNV_INDEL_ANNOTATIONS, + ) + ht.write( + new_variants_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ) + ht = hl.read_table( + TEST_GRCH37_SNV_INDEL_ANNOTATIONS, + ) + ht.write( + new_variants_table_path( + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ) + + # Make an incomplete parquet to validate overwrite-ing. + os.makedirs( + new_variant_details_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + exist_ok=True, + ) + with open( + os.path.join( + new_variant_details_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + 'incomplete_file.parquet', + ), + 'w', + ) as f: + f.write('') + + @mock.patch( + 'loading_pipeline.lib.tasks.exports.write_new_variant_details_parquet.WriteNewVariantsTableTask', + ) + def test_write_new_variant_details_parquet_test( + self, + mock_write_new_variants_task, + ) -> None: + mock_write_new_variants_task.return_value = MockCompleteTask() + worker = luigi.worker.Worker() + task = WriteNewVariantDetailsParquetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path='fake_callset', + project_guids=[ + 'fake_project', + ], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + worker.add(task) + worker.run() + self.assertTrue(task.output().exists()) + self.assertTrue(task.complete()) + df = pd.read_parquet( + new_variant_details_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ) + export_json = convert_ndarray_to_list(df.head(1).to_dict('records')) + self.assertListEqual( + list(export_json[0].keys()), + [ + 'key', + 'variantId', + 'rsid', + 'CAID', + 'liftedOverChrom', + 'liftedOverPos', + 'sortedMotifFeatureConsequences', + 'sortedRegulatoryFeatureConsequences', + 'transcripts', + ], + ) + self.assertEqual( + export_json[0]['key'], + 0, + ) + self.assertEqual( + export_json[0]['transcripts'][0], + { + 'alphamissense': {'pathogenicity': None}, + 'aminoAcids': 'S/L', + 'biotype': 'protein_coding', + 'canonical': 1, + 'codons': 'tCg/tTg', + 'consequenceTerms': ['missense_variant'], + 'exon': {'index': 6, 'total': 14}, + 'geneId': 'ENSG00000187634', + 'hgvsc': 'ENST00000616016.5:c.1049C>T', + 'hgvsp': 'ENSP00000478421.2:p.Ser350Leu', + 'intron': None, + 'transcriptId': 'ENST00000616016', + 'transcriptRank': 0, + 'majorConsequence': 'missense_variant', + 'maneSelect': 'NM_001385641.1', + 'manePlusClinical': None, + 'refseqTranscriptId': 'NM_001385641.1', + 'loftee': {'isLofNagnag': None, 'lofFilters': None}, + 'spliceregion': { + 'extended_intronic_splice_region_variant': False, + }, + 'utrannotator': { + 'existingInframeOorfs': None, + 'existingOutofframeOorfs': None, + 'existingUorfs': None, + 'fiveutrAnnotation': { + 'AltStop': None, + 'AltStopDistanceToCDS': None, + 'CapDistanceToStart': None, + 'DistanceToCDS': 41, + 'DistanceToStop': None, + 'Evidence': None, + 'FrameWithCDS': None, + 'KozakContext': 'CGCATGC', + 'KozakStrength': 'Weak', + 'StartDistanceToCDS': None, + 'alt_type': None, + 'alt_type_length': None, + 'newSTOPDistanceToCDS': None, + 'ref_StartDistanceToCDS': None, + 'ref_type': None, + 'ref_type_length': None, + 'type': 'OutOfFrame_oORF', + }, + 'fiveutrConsequence': None, + }, + }, + ) + self.assertEqual( + list(export_json[0]['transcripts'][0].keys()), + sorted(export_json[0]['transcripts'][0].keys()), + ) + self.assertEqual( + list( + export_json[0]['transcripts'][0]['utrannotator'][ + 'fiveutrAnnotation' + ].keys(), + ), + sorted( + export_json[0]['transcripts'][0]['utrannotator'][ + 'fiveutrAnnotation' + ].keys(), + ), + ) + + @mock.patch( + 'loading_pipeline.lib.tasks.exports.write_new_variant_details_parquet.WriteNewVariantsTableTask', + ) + def test_grch37_write_new_variant_details_parquet_test( + self, + mock_write_new_variants_task, + ) -> None: + mock_write_new_variants_task.return_value = MockCompleteTask() + worker = luigi.worker.Worker() + task = WriteNewVariantDetailsParquetTask( + reference_genome=ReferenceGenome.GRCh37, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path='fake_callset', + project_guids=[ + 'fake_project', + ], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + worker.add(task) + worker.run() + self.assertTrue(task.output().exists()) + self.assertTrue(task.complete()) + df = pd.read_parquet( + os.path.join( + new_variant_details_parquet_path( + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ), + ) + export_json = convert_ndarray_to_list(df.head(1).to_dict('records')) + self.assertListEqual( + list(export_json[0].keys()), + [ + 'key', + 'variantId', + 'rsid', + 'CAID', + 'liftedOverChrom', + 'liftedOverPos', + 'transcripts', + ], + ) + self.assertEqual( + export_json[0]['key'], + 1424, + ) + self.assertEqual(export_json[0]['CAID'], None) + self.assertEqual( + export_json[0]['transcripts'][0], + { + 'aminoAcids': 'E/G', + 'biotype': 'protein_coding', + 'canonical': 1, + 'codons': 'gAa/gGa', + 'consequenceTerms': ['missense_variant'], + 'geneId': 'ENSG00000186092', + 'hgvsc': 'ENST00000335137.3:c.44A>G', + 'hgvsp': 'ENSP00000334393.3:p.Glu15Gly', + 'loftee': {'isLofNagnag': None, 'lofFilters': None}, + 'majorConsequence': 'missense_variant', + 'transcriptId': 'ENST00000335137', + 'transcriptRank': 0, + }, + ) + self.assertEqual( + list(export_json[0]['transcripts'][0].keys()), + sorted(export_json[0]['transcripts'][0].keys()), + ) diff --git a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet.py b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet.py new file mode 100644 index 0000000000..7064685415 --- /dev/null +++ b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet.py @@ -0,0 +1,99 @@ +import hail as hl +import luigi +import luigi.util + +from loading_pipeline.lib.misc.callsets import get_callset_ht +from loading_pipeline.lib.paths import ( + new_variants_parquet_path, + new_variants_table_path, + variant_annotations_table_path, +) +from loading_pipeline.lib.tasks.base.base_loading_run_params import ( + BaseLoadingRunParams, +) +from loading_pipeline.lib.tasks.base.base_write_parquet import BaseWriteParquetTask +from loading_pipeline.lib.tasks.exports.fields import get_variants_export_fields +from loading_pipeline.lib.tasks.exports.misc import ( + camelcase_array_structexpression_fields, + subset_consequences_fields, + unmap_formatting_annotation_enums, +) +from loading_pipeline.lib.tasks.files import GCSorLocalTarget +from loading_pipeline.lib.tasks.update_variant_annotations_table_with_new_variants import ( + UpdateVariantAnnotationsTableWithNewVariantsTask, +) +from loading_pipeline.lib.tasks.write_new_variants_table import ( + WriteNewVariantsTableTask, +) + + +@luigi.util.inherits(BaseLoadingRunParams) +class WriteNewVariantsParquetTask(BaseWriteParquetTask): + def output(self) -> luigi.Target: + return GCSorLocalTarget( + new_variants_parquet_path( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + ) + + def requires(self) -> luigi.Task: + if ( + self.dataset_type.export_all_callset_variants + # Special logic for the Clickhouse migration, forcing + # utilization of the project subsetted variants table + # that lives at the new variants table path. + and len(self.project_guids) > 0 + ): + return self.clone(UpdateVariantAnnotationsTableWithNewVariantsTask) + return self.clone(WriteNewVariantsTableTask) + + def create_table(self) -> None: + if ( + self.dataset_type.export_all_callset_variants + # Special logic for the Clickhouse migration, forcing + # utilization of the project subsetted variants table + # that lives at the new variants table path. + and len(self.project_guids) > 0 + ): + ht = hl.read_table( + variant_annotations_table_path( + self.reference_genome, + self.dataset_type, + ), + ) + callset_ht = get_callset_ht( + self.reference_genome, + self.dataset_type, + self.callset_path, + self.project_guids, + ) + ht = ht.semi_join(callset_ht) + else: + ht = hl.read_table( + new_variants_table_path( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + ) + ht = unmap_formatting_annotation_enums( + ht, + self.reference_genome, + self.dataset_type, + ) + ht = camelcase_array_structexpression_fields( + ht, + self.reference_genome, + self.dataset_type, + ) + if self.dataset_type.should_write_new_variant_details: + ht = subset_consequences_fields( + ht, + self.reference_genome, + ) + ht = ht.key_by() + return ht.select( + **get_variants_export_fields(ht, self.reference_genome, self.dataset_type), + ) diff --git a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py new file mode 100644 index 0000000000..8bd43fc8be --- /dev/null +++ b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py @@ -0,0 +1,420 @@ +from unittest import mock +from unittest.mock import Mock + +import hail as hl +import luigi.worker +import pandas as pd + +from loading_pipeline.lib.core import ( + DatasetType, + ReferenceGenome, + SampleType, +) +from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS +from loading_pipeline.lib.paths import ( + new_variants_parquet_path, + new_variants_table_path, + remapped_and_subsetted_callset_path, + variant_annotations_table_path, +) +from loading_pipeline.lib.tasks.exports.write_new_variants_parquet import ( + WriteNewVariantsParquetTask, +) +from loading_pipeline.lib.test.misc import convert_ndarray_to_list +from loading_pipeline.lib.test.mock_complete_task import MockCompleteTask +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + +TEST_SNV_INDEL_ANNOTATIONS = ( + 'loading_pipeline/var/test/exports/GRCh38/SNV_INDEL/annotations.ht' +) +TEST_GRCH37_SNV_INDEL_ANNOTATIONS = ( + 'loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/annotations.ht' +) +TEST_MITO_ANNOTATIONS = 'loading_pipeline/var/test/exports/GRCh38/MITO/annotations.ht' +TEST_SV_ANNOTATIONS = 'loading_pipeline/var/test/exports/GRCh38/SV/annotations.ht' +TEST_GCNV_ANNOTATIONS = 'loading_pipeline/var/test/exports/GRCh38/GCNV/annotations.ht' + +TEST_RUN_ID = 'manual__2024-04-03' + + +class WriteNewVariantsParquetTest(MockedDatarootTestCase): + def setUp(self) -> None: + super().setUp() + ht = hl.read_table( + TEST_SNV_INDEL_ANNOTATIONS, + ) + ht.write( + new_variants_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ) + ht = hl.read_table( + TEST_GRCH37_SNV_INDEL_ANNOTATIONS, + ) + ht.write( + new_variants_table_path( + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ) + ht = hl.read_table( + TEST_MITO_ANNOTATIONS, + ) + ht.write( + new_variants_table_path( + ReferenceGenome.GRCh38, + DatasetType.MITO, + TEST_RUN_ID, + ), + ) + ht = hl.read_table( + TEST_SV_ANNOTATIONS, + ) + ht.write( + new_variants_table_path( + ReferenceGenome.GRCh38, + DatasetType.SV, + TEST_RUN_ID, + ), + ) + ht = hl.read_table(TEST_GCNV_ANNOTATIONS) + ht.write( + variant_annotations_table_path( + ReferenceGenome.GRCh38, + DatasetType.GCNV, + ), + ) + ht.write( + remapped_and_subsetted_callset_path( + ReferenceGenome.GRCh38, + DatasetType.GCNV, + 'fake_callset', + 'fake_project', + ), + ) + + @mock.patch( + 'loading_pipeline.lib.tasks.exports.write_new_variants_parquet.WriteNewVariantsTableTask', + ) + def test_write_new_variants_parquet_test( + self, + mock_write_new_variants_task, + ) -> None: + mock_write_new_variants_task.return_value = MockCompleteTask() + worker = luigi.worker.Worker() + task = WriteNewVariantsParquetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path='fake_callset', + project_guids=[ + 'fake_project', + ], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + worker.add(task) + worker.run() + self.assertTrue(task.output().exists()) + self.assertTrue(task.complete()) + df = pd.read_parquet( + new_variants_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ) + export_json = convert_ndarray_to_list(df.head(1).to_dict('records')) + export_json[0]['sortedTranscriptConsequences'] = [ + export_json[0]['sortedTranscriptConsequences'][0], + ] + self.assertEqual( + export_json, + [ + { + 'key': 0, + 'sortedMotifFeatureConsequences': [ + { + 'consequenceTerms': ['TF_binding_site_variant'], + }, + ], + 'sortedRegulatoryFeatureConsequences': [ + { + 'consequenceTerms': ['regulatory_region_variant'], + }, + ], + 'sortedTranscriptConsequences': [ + { + 'alphamissensePathogenicity': None, + 'canonical': 1, + 'consequenceTerms': ['missense_variant'], + 'extendedIntronicSpliceRegionVariant': False, + 'fiveutrConsequence': None, + 'geneId': 'ENSG00000187634', + 'isManeSelect': True, + }, + ], + }, + ], + ) + + @mock.patch( + 'loading_pipeline.lib.tasks.exports.write_new_variants_parquet.WriteNewVariantsTableTask', + ) + def test_grch37_write_new_variants_parquet_test( + self, + mock_write_new_variants_task, + ) -> None: + mock_write_new_variants_task.return_value = MockCompleteTask() + worker = luigi.worker.Worker() + task = WriteNewVariantsParquetTask( + reference_genome=ReferenceGenome.GRCh37, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path='fake_callset', + project_guids=[ + 'fake_project', + ], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + worker.add(task) + worker.run() + self.assertTrue(task.output().exists()) + self.assertTrue(task.complete()) + df = pd.read_parquet( + new_variants_parquet_path( + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ) + export_json = convert_ndarray_to_list(df.head(1).to_dict('records')) + export_json[0]['sortedTranscriptConsequences'] = [ + export_json[0]['sortedTranscriptConsequences'][0], + ] + self.assertEqual( + export_json, + [ + { + 'key': 1424, + 'sortedTranscriptConsequences': [ + { + 'canonical': 1, + 'consequenceTerms': ['missense_variant'], + 'geneId': 'ENSG00000186092', + }, + ], + }, + ], + ) + + @mock.patch( + 'loading_pipeline.lib.tasks.exports.write_new_variants_parquet.WriteNewVariantsTableTask', + ) + def test_mito_write_new_variants_parquet_test( + self, + write_new_variants_table_task: Mock, + ) -> None: + write_new_variants_table_task.return_value = MockCompleteTask() + worker = luigi.worker.Worker() + task = WriteNewVariantsParquetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.MITO, + sample_type=SampleType.WGS, + callset_path='fake_callset', + project_guids=[ + 'fake_project', + ], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + worker.add(task) + worker.run() + self.assertTrue(task.output().exists()) + self.assertTrue(task.complete()) + df = pd.read_parquet( + new_variants_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.MITO, + TEST_RUN_ID, + ), + ) + export_json = convert_ndarray_to_list(df.head(1).to_dict('records')) + export_json[0]['sortedTranscriptConsequences'] = [ + export_json[0]['sortedTranscriptConsequences'][0], + ] + self.assertEqual( + export_json, + [ + { + 'key': 998, + 'variantId': 'M-8-G-T', + 'rsid': 'rs1603218446', + 'liftedOverPos': 578, + 'commonLowHeteroplasmy': True, + 'haplogroupDefining': False, + 'mitotip': 'likely_pathogenic', + 'sortedTranscriptConsequences': [ + { + 'aminoAcids': None, + 'biotype': 'Mt_tRNA', + 'canonical': 1, + 'codons': None, + 'consequenceTerms': ['non_coding_transcript_exon_variant'], + 'geneId': 'ENSG00000210049', + 'hgvsc': 'ENST00000387314.1:n.2T>C', + 'hgvsp': None, + 'loftee': {'isLofNagnag': None, 'lofFilters': None}, + 'majorConsequence': 'non_coding_transcript_exon_variant', + 'transcriptId': 'ENST00000387314', + 'transcriptRank': 0, + }, + ], + }, + ], + ) + + @mock.patch( + 'loading_pipeline.lib.tasks.exports.write_new_variants_parquet.WriteNewVariantsTableTask', + ) + def test_sv_write_new_variants_parquet_test( + self, + write_new_variants_table_task: Mock, + ) -> None: + write_new_variants_table_task.return_value = MockCompleteTask() + worker = luigi.worker.Worker() + task = WriteNewVariantsParquetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SV, + sample_type=SampleType.WGS, + callset_path='fake_callset', + project_guids=[ + 'fake_project', + ], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + worker.add(task) + worker.run() + self.assertTrue(task.output().exists()) + self.assertTrue(task.complete()) + df = pd.read_parquet( + new_variants_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.SV, + TEST_RUN_ID, + ), + ) + export_json = convert_ndarray_to_list(df.head(1).to_dict('records')) + export_json[0]['sortedGeneConsequences'] = [ + export_json[0]['sortedGeneConsequences'][0], + ] + self.assertEqual( + export_json, + [ + { + 'key': 727, + 'xpos': 1001025886, + 'chrom': '1', + 'pos': 1025886, + 'end': 1028192, + 'rg37LocusEnd': {'contig': '1', 'position': 963572}, + 'variantId': 'BND_chr1_6', + 'liftedOverChrom': '1', + 'liftedOverPos': 961266, + 'algorithms': 'manta', + 'bothsidesSupport': None, + 'cpxIntervals': [ + {'chrom': '1', 'start': 1025886, 'end': 1025986, 'type': 'DUP'}, + {'chrom': '1', 'start': 1025886, 'end': 1028192, 'type': 'INV'}, + ], + 'endChrom': '2', + 'svSourceDetail': None, + 'svType': 'CPX', + 'svTypeDetail': 'dupINV', + 'predictions': {'strvctvre': None}, + 'populations': {'gnomad_svs': None}, + 'sortedGeneConsequences': [ + {'geneId': 'ENSG00000188157', 'majorConsequence': 'INTRONIC'}, + ], + }, + ], + ) + + @mock.patch( + 'loading_pipeline.lib.tasks.exports.write_new_variants_parquet.UpdateVariantAnnotationsTableWithNewVariantsTask', + ) + @mock.patch( + 'loading_pipeline.lib.tasks.exports.write_new_variants_parquet.get_callset_ht', + ) + def test_gcnv_write_new_variants_parquet_test( + self, + get_callset_ht: Mock, + update_variant_annotations_task: Mock, + ) -> None: + get_callset_ht.return_value = hl.read_table( + variant_annotations_table_path( + ReferenceGenome.GRCh38, + DatasetType.GCNV, + ), + ) + update_variant_annotations_task.return_value = MockCompleteTask() + worker = luigi.worker.Worker() + task = WriteNewVariantsParquetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.GCNV, + sample_type=SampleType.WES, + callset_path='fake_callset', + project_guids=[ + 'fake_project', + ], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + worker.add(task) + worker.run() + self.assertTrue(task.output().exists()) + self.assertTrue(task.complete()) + df = pd.read_parquet( + new_variants_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.GCNV, + TEST_RUN_ID, + ), + ) + export_json = convert_ndarray_to_list(df.head(1).to_dict('records')) + self.assertEqual( + export_json, + [ + { + 'key': 0, + 'xpos': 1000939203, + 'chrom': '1', + 'pos': 939203, + 'end': 939558, + 'rg37LocusEnd': {'contig': '1', 'position': 874938}, + 'variantId': 'suffix_16456_DEL', + 'liftedOverChrom': '1', + 'liftedOverPos': 874583, + 'numExon': 1, + 'svType': 'DUP', + 'predictions': {'strvctvre': 0.4490000009536743}, + 'populations': { + 'sv_callset': { + 'ac': 1, + 'af': 4.3387713958509266e-05, + 'an': 23048, + 'het': None, + 'hom': None, + }, + }, + 'sortedGeneConsequences': [ + {'geneId': 'ENSG00000187634', 'majorConsequence': 'LOF'}, + ], + }, + ], + ) diff --git a/loading_pipeline/lib/tasks/files.py b/loading_pipeline/lib/tasks/files.py new file mode 100644 index 0000000000..7368631767 --- /dev/null +++ b/loading_pipeline/lib/tasks/files.py @@ -0,0 +1,49 @@ +import os + +import hailtop.fs as hfs +import luigi +from luigi.contrib import gcs + + +def CallsetTask(pathname: str) -> luigi.Task: # noqa: N802 + if 'vcf' in pathname: + return VCFFileTask(pathname) + if pathname.endswith('mt'): + return HailTableTask(pathname) + return RawFileTask(pathname) + + +def GCSorLocalTarget(pathname: str) -> luigi.Target: # noqa: N802 + return ( + gcs.GCSTarget(pathname) + if pathname.startswith('gs://') + else luigi.LocalTarget(pathname) + ) + + +def GCSorLocalFolderTarget(pathname: str) -> luigi.Target: # noqa: N802 + return GCSorLocalTarget(os.path.join(pathname, '_SUCCESS')) + + +class RawFileTask(luigi.Task): + pathname = luigi.Parameter() + + def output(self) -> luigi.Target: + return GCSorLocalTarget(self.pathname) + + +class VCFFileTask(RawFileTask): + def complete(self) -> bool: + # NB: hail supports reading glob bgz files. + path = self.pathname + if not path.startswith(('gs://', 's3://')): + path = os.path.abspath(path) + try: + return len(hfs.ls(path)) > 0 + except FileNotFoundError: + return False + + +class HailTableTask(RawFileTask): + def complete(self) -> bool: + return GCSorLocalFolderTarget(self.pathname).exists() diff --git a/loading_pipeline/lib/tasks/files_test.py b/loading_pipeline/lib/tasks/files_test.py new file mode 100644 index 0000000000..b2dfd937e0 --- /dev/null +++ b/loading_pipeline/lib/tasks/files_test.py @@ -0,0 +1,40 @@ +import os +import tempfile +import unittest + +from loading_pipeline.lib.tasks.files import ( + CallsetTask, + HailTableTask, + RawFileTask, + VCFFileTask, +) + + +class FilesTest(unittest.TestCase): + def test_raw_file(self) -> None: + with tempfile.NamedTemporaryFile(suffix='.txt') as f: + self.assertTrue(RawFileTask(f.name).complete()) + + def test_vcf_file(self) -> None: + with tempfile.NamedTemporaryFile(suffix='.vcf.bgz') as f: + self.assertTrue(VCFFileTask(f.name).complete()) + + def test_hail_table(self) -> None: + with tempfile.TemporaryDirectory(suffix='.ht') as d: + self.assertFalse(HailTableTask(d).complete()) + with open(os.path.join(d, '_SUCCESS'), 'w') as f: + f.write('0') + self.assertTrue(HailTableTask(d).complete()) + + def test_callset_task(self) -> None: + with tempfile.NamedTemporaryFile(suffix='.txt') as f: + self.assertTrue(CallsetTask(f.name).complete()) + + with tempfile.NamedTemporaryFile(suffix='.vcf') as f: + self.assertTrue(CallsetTask(f.name).complete()) + + with tempfile.TemporaryDirectory(suffix='.mt') as d: + self.assertFalse(CallsetTask(d).complete()) + with open(os.path.join(d, '_SUCCESS'), 'w') as f: + f.write('0') + self.assertTrue(CallsetTask(d).complete()) diff --git a/loading_pipeline/lib/tasks/reference_data/__init__.py b/loading_pipeline/lib/tasks/reference_data/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/loading_pipeline/lib/tasks/reference_data/updated_reference_dataset.py b/loading_pipeline/lib/tasks/reference_data/updated_reference_dataset.py new file mode 100644 index 0000000000..575cc1864f --- /dev/null +++ b/loading_pipeline/lib/tasks/reference_data/updated_reference_dataset.py @@ -0,0 +1,27 @@ +import luigi + +from loading_pipeline.lib.paths import valid_reference_dataset_path +from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset +from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( + BaseLoadingPipelineParams, +) +from loading_pipeline.lib.tasks.base.base_write import BaseWriteTask +from loading_pipeline.lib.tasks.files import GCSorLocalTarget + + +@luigi.util.inherits(BaseLoadingPipelineParams) +class UpdatedReferenceDatasetTask(BaseWriteTask): + reference_dataset: ReferenceDataset = luigi.EnumParameter( + enum=ReferenceDataset, + ) + + def output(self): + return GCSorLocalTarget( + valid_reference_dataset_path( + self.reference_genome, + self.reference_dataset, + ), + ) + + def create_table(self): + return self.reference_dataset.get_ht(self.reference_genome) diff --git a/loading_pipeline/lib/tasks/reference_data/updated_reference_dataset_parquet.py b/loading_pipeline/lib/tasks/reference_data/updated_reference_dataset_parquet.py new file mode 100644 index 0000000000..ed8adfce6b --- /dev/null +++ b/loading_pipeline/lib/tasks/reference_data/updated_reference_dataset_parquet.py @@ -0,0 +1,55 @@ +import luigi + +from loading_pipeline.lib.annotations.expression_helpers import get_expr_for_variant_id +from loading_pipeline.lib.core.dataset_type import DatasetType +from loading_pipeline.lib.core.definitions import ReferenceGenome +from loading_pipeline.lib.paths import reference_dataset_parquet +from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset +from loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc import ( + BaseRunJobOnDataprocTask, +) +from loading_pipeline.lib.tasks.files import GCSorLocalFolderTarget, GCSorLocalTarget + + +class UpdatedReferenceDatasetParquetTask(luigi.Task): + reference_genome = luigi.EnumParameter(enum=ReferenceGenome) + dataset_type = luigi.EnumParameter(enum=DatasetType) + reference_dataset: ReferenceDataset = luigi.EnumParameter( + enum=ReferenceDataset, + ) + run_id = luigi.Parameter() + attempt_id = luigi.IntParameter() + + def complete(self) -> luigi.Target: + return GCSorLocalFolderTarget(self.output().path).exists() + + def output(self): + return GCSorLocalTarget( + reference_dataset_parquet( + self.reference_genome, + self.reference_dataset, + ), + ) + + def run(self): + ht = self.reference_dataset.get_ht(self.reference_genome) + ht = ht.annotate( + variant_id=get_expr_for_variant_id(ht), + ) + df = ht.to_spark(flatten=False) + df.write.parquet( + self.output().path, + mode='overwrite', + ) + + +class UpdatedReferenceDatasetParquetOnDataprocTask(BaseRunJobOnDataprocTask): + reference_genome = luigi.EnumParameter(enum=ReferenceGenome) + dataset_type = luigi.EnumParameter(enum=DatasetType) + reference_dataset: ReferenceDataset = luigi.EnumParameter( + enum=ReferenceDataset, + ) + + @property + def task(self) -> luigi.Task: + return UpdatedReferenceDatasetParquetTask diff --git a/loading_pipeline/lib/tasks/run_pipeline.py b/loading_pipeline/lib/tasks/run_pipeline.py new file mode 100644 index 0000000000..e4bb2993e8 --- /dev/null +++ b/loading_pipeline/lib/tasks/run_pipeline.py @@ -0,0 +1,37 @@ +import luigi +import luigi.util + +from loading_pipeline.lib.tasks.base.base_loading_run_params import ( + BaseLoadingRunParams, +) +from loading_pipeline.lib.tasks.exports.write_new_entries_parquet import ( + WriteNewEntriesParquetTask, +) +from loading_pipeline.lib.tasks.exports.write_new_variant_details_parquet import ( + WriteNewVariantDetailsParquetTask, +) +from loading_pipeline.lib.tasks.exports.write_new_variants_parquet import ( + WriteNewVariantsParquetTask, +) +from loading_pipeline.lib.tasks.update_variant_annotations_table_with_new_variants import ( + UpdateVariantAnnotationsTableWithNewVariantsTask, +) +from loading_pipeline.lib.tasks.write_metadata_for_run import WriteMetadataForRunTask + + +@luigi.util.inherits(BaseLoadingRunParams) +class RunPipelineTask(luigi.WrapperTask): + attempt_id = luigi.IntParameter() + + def requires(self): + return [ + self.clone(WriteMetadataForRunTask), + self.clone(UpdateVariantAnnotationsTableWithNewVariantsTask), + self.clone(WriteNewEntriesParquetTask), + self.clone(WriteNewVariantsParquetTask), + *( + [self.clone(WriteNewVariantDetailsParquetTask)] + if self.dataset_type.should_write_new_variant_details + else [] + ), + ] diff --git a/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants.py b/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants.py new file mode 100644 index 0000000000..6c547ab029 --- /dev/null +++ b/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants.py @@ -0,0 +1,136 @@ +import hail as hl +import luigi +import luigi.util + +from loading_pipeline.lib.annotations.fields import get_fields +from loading_pipeline.lib.misc.callsets import get_callset_ht +from loading_pipeline.lib.misc.io import remap_pedigree_hash +from loading_pipeline.lib.paths import ( + new_variants_table_path, + project_pedigree_path, + variant_annotations_table_path, +) +from loading_pipeline.lib.tasks.base.base_loading_run_params import ( + BaseLoadingRunParams, +) +from loading_pipeline.lib.tasks.base.base_update import ( + BaseUpdateTask, +) +from loading_pipeline.lib.tasks.files import GCSorLocalTarget +from loading_pipeline.lib.tasks.write_new_variants_table import ( + WriteNewVariantsTableTask, +) + + +@luigi.util.inherits(BaseLoadingRunParams) +class UpdateVariantAnnotationsTableWithNewVariantsTask( + BaseUpdateTask, +): + def output(self) -> luigi.Target: + return GCSorLocalTarget( + variant_annotations_table_path( + self.reference_genome, + self.dataset_type, + ), + ) + + def requires(self) -> list[luigi.Task]: + return [ + *super().requires(), + self.clone(WriteNewVariantsTableTask), + ] + + def complete(self) -> bool: + return super().complete() and hl.eval( + hl.bind( + lambda updates: hl.all( + [ + updates.contains( + hl.Struct( + callset=self.callset_path, + project_guid=project_guid, + remap_pedigree_hash=remap_pedigree_hash( + project_pedigree_path( + self.reference_genome, + self.dataset_type, + self.sample_type, + project_guid, + ), + ), + ), + ) + for project_guid in self.project_guids + ], + ), + hl.read_table(self.output().path).updates, + ), + ) + + def initialize_table(self) -> hl.Table: + key_type = self.dataset_type.table_key_type(self.reference_genome) + return hl.Table.parallelize( + [], + key_type, + key=key_type.fields, + globals=hl.Struct( + enums=hl.Struct(), + updates=hl.empty_set( + hl.tstruct( + callset=hl.tstr, + project_guid=hl.tstr, + remap_pedigree_hash=hl.tint32, + ), + ), + migrations=hl.empty_array(hl.tstr), + max_key_=hl.int64(-1), + ), + ) + + def update_table(self, ht: hl.Table) -> hl.Table: + # Gracefully handle case for on-premises uses + # where key_ field is not present and migration was not run. + if not hasattr(ht, 'key_'): + ht = ht.add_index(name='key_') + ht = ht.annotate_globals(max_key_=(ht.count() - 1)) + + new_variants_ht = hl.read_table( + new_variants_table_path( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + ) + + # Union with the new variants table and annotate with the lookup table. + ht = ht.union(new_variants_ht, unify=True) + + if self.dataset_type.variant_frequency_annotation_fns: + # new_variants_ht consists of variants present in the new callset, fully annotated, + # but NOT present in the existing annotations table. + # callset_variants_ht consists of variants present in the new callset, fully annotated, + # and either present or not present in the existing annotations table. + callset_ht = get_callset_ht( + self.reference_genome, + self.dataset_type, + self.callset_path, + self.project_guids, + ) + callset_variants_ht = ht.semi_join(callset_ht) + non_callset_variants_ht = ht.anti_join(callset_ht) + callset_variants_ht = callset_variants_ht.annotate( + **get_fields( + callset_variants_ht, + self.dataset_type.variant_frequency_annotation_fns, + callset_ht=callset_ht, + **self.param_kwargs, + ), + ) + ht = non_callset_variants_ht.union(callset_variants_ht, unify=True) + + new_variants_ht_globals = new_variants_ht.index_globals() + return ht.select_globals( + enums=new_variants_ht_globals.enums, + updates=ht.updates.union(new_variants_ht_globals.updates), + migrations=ht.migrations, + max_key_=ht.aggregate(hl.agg.max(ht.key_)), + ) diff --git a/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py b/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py new file mode 100644 index 0000000000..3bfe55af65 --- /dev/null +++ b/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py @@ -0,0 +1,1349 @@ +import functools +from unittest.mock import Mock, PropertyMock, patch + +import hail as hl +import luigi.worker + +from loading_pipeline.lib.annotations.enums import ( + BIOTYPES, + FIVEUTR_CONSEQUENCES, + LOF_FILTERS, + MITOTIP_PATHOGENICITIES, + MOTIF_CONSEQUENCE_TERMS, + REGULATORY_BIOTYPES, + REGULATORY_CONSEQUENCE_TERMS, + SV_CONSEQUENCE_RANKS, + SV_TYPE_DETAILS, + SV_TYPES, + TRANSCRIPT_CONSEQUENCE_TERMS, +) +from loading_pipeline.lib.core import ( + DatasetType, + ReferenceGenome, + SampleType, +) +from loading_pipeline.lib.misc.io import remap_pedigree_hash +from loading_pipeline.lib.misc.validation import ( + ALL_VALIDATIONS, + SKIPPABLE_VALIDATIONS, + validate_expected_contig_frequency, +) +from loading_pipeline.lib.paths import ( + valid_reference_dataset_path, +) +from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset +from loading_pipeline.lib.tasks.files import GCSorLocalFolderTarget +from loading_pipeline.lib.tasks.update_variant_annotations_table_with_new_variants import ( + UpdateVariantAnnotationsTableWithNewVariantsTask, +) +from loading_pipeline.lib.test.misc import copy_project_pedigree_to_mocked_dir +from loading_pipeline.lib.test.mocked_reference_datasets_testcase import ( + MockedReferenceDatasetsTestCase, +) +from loading_pipeline.var.test.vep.mock_vep_data import ( + MOCK_37_VEP_DATA, + MOCK_38_VEP_DATA, +) + +TEST_MITO_MT = 'loading_pipeline/var/test/callsets/mito_1.mt' +TEST_SNV_INDEL_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' +TEST_SV_VCF = 'loading_pipeline/var/test/callsets/sv_1.vcf' +TEST_SV_VCF_2 = 'loading_pipeline/var/test/callsets/sv_2.vcf' +TEST_GCNV_BED_FILE = 'loading_pipeline/var/test/callsets/gcnv_1.tsv' +TEST_GCNV_BED_FILE_2 = 'loading_pipeline/var/test/callsets/gcnv_2.tsv' +TEST_PEDIGREE_3_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_3_remap.tsv' +TEST_PEDIGREE_4_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_4_remap.tsv' +TEST_PEDIGREE_5 = 'loading_pipeline/var/test/pedigrees/test_pedigree_5.tsv' +TEST_PEDIGREE_8 = 'loading_pipeline/var/test/pedigrees/test_pedigree_8.tsv' +TEST_PEDIGREE_10 = 'loading_pipeline/var/test/pedigrees/test_pedigree_10.tsv' +TEST_PEDIGREE_11 = 'loading_pipeline/var/test/pedigrees/test_pedigree_11.tsv' + +GENE_ID_MAPPING = { + 'OR4F5': 'ENSG00000186092', + 'PLEKHG4B': 'ENSG00000153404', + 'OR4F16': 'ENSG00000186192', + 'OR4F29': 'ENSG00000284733', + 'FBXO28': 'ENSG00000143756', + 'SAMD11': 'ENSG00000187634', + 'C1orf174': 'ENSG00000198912', + 'TAS1R1': 'ENSG00000173662', + 'FAM131C': 'ENSG00000185519', + 'RCC2': 'ENSG00000179051', + 'NBPF3': 'ENSG00000142794', + 'AGBL4': 'ENSG00000186094', + 'KIAA1614': 'ENSG00000135835', + 'MR1': 'ENSG00000153029', + 'STX6': 'ENSG00000135823', + 'XPR1': 'ENSG00000143324', +} + +TEST_RUN_ID = 'manual__2024-04-03' + + +class UpdateVariantAnnotationsTableWithNewVariantsTaskTest( + MockedReferenceDatasetsTestCase, +): + def test_missing_pedigree( + self, + ) -> None: + uvatwns_task = UpdateVariantAnnotationsTableWithNewVariantsTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path=TEST_SNV_INDEL_VCF, + project_guids=['R0113_test_project'], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + worker = luigi.worker.Worker() + worker.add(uvatwns_task) + worker.run() + self.assertFalse(uvatwns_task.complete()) + + @patch( + 'loading_pipeline.lib.tasks.validate_callset.SKIPPABLE_VALIDATIONS', + [ + x + for x in SKIPPABLE_VALIDATIONS + if x.__name__ != 'validate_expected_contig_frequency' + ] + + [ + functools.update_wrapper( + functools.partial( + validate_expected_contig_frequency, + min_rows_per_contig=25, + ), + validate_expected_contig_frequency, + ), + ], + ) + @patch.object(ReferenceGenome, 'standard_contigs', new_callable=PropertyMock) + @patch('loading_pipeline.lib.misc.vep.hl.vep') + @patch( + 'loading_pipeline.lib.tasks.write_new_variants_table.load_gencode_ensembl_to_refseq_id', + ) + def test_multiple_update_vat( + self, + mock_load_gencode_ensembl_to_refseq_id: Mock, + mock_vep: Mock, + mock_standard_contigs: Mock, + ) -> None: + mock_vep.side_effect = lambda ht, **_: ht.annotate(vep=MOCK_38_VEP_DATA) + mock_load_gencode_ensembl_to_refseq_id.return_value = hl.dict( + {'ENST00000327044': 'NM_015658.4'}, + ) + mock_standard_contigs.return_value = {'chr1'} + # This creates a mock validation table with 1 coding and 1 non-coding variant + # explicitly chosen from the VCF. + # NB: This is the one and only place validation is enabled in the task tests! + coding_and_noncoding_variants_ht = hl.Table.parallelize( + [ + { + 'locus': hl.Locus( + contig='chr1', + position=871269, + reference_genome='GRCh38', + ), + 'coding': False, + 'noncoding': True, + }, + { + 'locus': hl.Locus( + contig='chr1', + position=876499, + reference_genome='GRCh38', + ), + 'coding': True, + 'noncoding': False, + }, + ], + hl.tstruct( + locus=hl.tlocus('GRCh38'), + coding=hl.tbool, + noncoding=hl.tbool, + ), + key='locus', + globals=hl.Struct( + enums=hl.Struct( + gnomad_genomes=hl.Struct(), + ), + ), + ) + coding_and_noncoding_variants_ht.write( + valid_reference_dataset_path( + ReferenceGenome.GRCh38, + ReferenceDataset.gnomad_coding_and_noncoding, + ), + overwrite=True, + ) + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_3_REMAP, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0113_test_project', + ) + worker = luigi.worker.Worker() + uvatwns_task_3 = UpdateVariantAnnotationsTableWithNewVariantsTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path=TEST_SNV_INDEL_VCF, + project_guids=['R0113_test_project'], + validations_to_skip=[], + run_id=TEST_RUN_ID, + ) + worker.add(uvatwns_task_3) + worker.run() + self.assertTrue(uvatwns_task_3.complete()) + ht = hl.read_table(uvatwns_task_3.output().path) + self.assertEqual(ht.count(), 30) + self.assertEqual( + ht.globals.updates.collect(), + [ + { + hl.Struct( + callset=TEST_SNV_INDEL_VCF, + project_guid='R0113_test_project', + remap_pedigree_hash=hl.eval( + remap_pedigree_hash(TEST_PEDIGREE_3_REMAP), + ), + ), + }, + ], + ) + self.assertEqual( + hl.eval(ht.globals.max_key_), + 29, + ) + + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_4_REMAP, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0114_project4', + ) + # Ensure that new variants are added correctly to the table. + uvatwns_task_4 = UpdateVariantAnnotationsTableWithNewVariantsTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path=TEST_SNV_INDEL_VCF, + project_guids=['R0114_project4'], + validations_to_skip=[], + run_id=TEST_RUN_ID + '-another-run', + ) + worker.add(uvatwns_task_4) + worker.run() + self.assertTrue(uvatwns_task_4.complete()) + ht = hl.read_table(uvatwns_task_4.output().path) + self.assertCountEqual( + [ + x + for x in ht.select( + 'variant_id', + 'xpos', + ).collect() + if x.locus.position <= 878809 # noqa: PLR2004 + ], + [ + hl.Struct( + locus=hl.Locus( + contig='chr1', + position=871269, + reference_genome='GRCh38', + ), + alleles=['A', 'C'], + variant_id='1-871269-A-C', + xpos=1000871269, + ), + hl.Struct( + locus=hl.Locus( + contig='chr1', + position=874734, + reference_genome='GRCh38', + ), + alleles=['C', 'T'], + variant_id='1-874734-C-T', + xpos=1000874734, + ), + hl.Struct( + locus=hl.Locus( + contig='chr1', + position=876499, + reference_genome='GRCh38', + ), + alleles=['A', 'G'], + variant_id='1-876499-A-G', + xpos=1000876499, + ), + hl.Struct( + locus=hl.Locus( + contig='chr1', + position=878314, + reference_genome='GRCh38', + ), + alleles=['G', 'C'], + variant_id='1-878314-G-C', + xpos=1000878314, + ), + hl.Struct( + locus=hl.Locus( + contig='chr1', + position=878809, + reference_genome='GRCh38', + ), + alleles=['C', 'T'], + variant_id='1-878809-C-T', + xpos=1000878809, + ), + ], + ) + self.assertCountEqual( + ht.filter( + ht.locus.position <= 878809, # noqa: PLR2004 + ).sorted_transcript_consequences.consequence_term_ids.collect(), + [ + [[9], [23, 26], [23, 13, 26]], + [[9], [23, 26], [23, 13, 26]], + [[9], [23, 26], [23, 13, 26]], + [[9], [23, 26], [23, 13, 26]], + [[9], [23, 26], [23, 13, 26]], + ], + ) + self.assertCountEqual( + ht.globals.collect(), + [ + hl.Struct( + updates={ + hl.Struct( + callset='loading_pipeline/var/test/callsets/1kg_30variants.vcf', + project_guid='R0113_test_project', + remap_pedigree_hash=hl.eval( + remap_pedigree_hash( + TEST_PEDIGREE_3_REMAP, + ), + ), + ), + hl.Struct( + callset='loading_pipeline/var/test/callsets/1kg_30variants.vcf', + project_guid='R0114_project4', + remap_pedigree_hash=hl.eval( + remap_pedigree_hash( + TEST_PEDIGREE_4_REMAP, + ), + ), + ), + }, + migrations=[], + max_key_=29, + enums=hl.Struct( + sorted_motif_feature_consequences=hl.Struct( + consequence_term=MOTIF_CONSEQUENCE_TERMS, + ), + sorted_regulatory_feature_consequences=hl.Struct( + biotype=REGULATORY_BIOTYPES, + consequence_term=REGULATORY_CONSEQUENCE_TERMS, + ), + sorted_transcript_consequences=hl.Struct( + biotype=BIOTYPES, + consequence_term=TRANSCRIPT_CONSEQUENCE_TERMS, + loftee=hl.Struct( + lof_filter=LOF_FILTERS, + ), + utrannotator=hl.Struct( + fiveutr_consequence=FIVEUTR_CONSEQUENCES, + ), + ), + ), + ), + ], + ) + + @patch('loading_pipeline.lib.misc.vep.hl.vep') + def test_update_vat_grch37( + self, + mock_vep: Mock, + ) -> None: + mock_vep.side_effect = lambda ht, **_: ht.annotate(vep=MOCK_37_VEP_DATA) + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_3_REMAP, + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0113_test_project', + ) + worker = luigi.worker.Worker() + uvatwns_task = UpdateVariantAnnotationsTableWithNewVariantsTask( + reference_genome=ReferenceGenome.GRCh37, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path=TEST_SNV_INDEL_VCF, + project_guids=['R0113_test_project'], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + worker.add(uvatwns_task) + worker.run() + self.assertTrue(uvatwns_task.complete()) + ht = hl.read_table(uvatwns_task.output().path) + self.assertEqual(ht.count(), 30) + self.assertFalse(hasattr(ht, 'rg37_locus')) + self.assertEqual( + ht.collect()[0], + hl.Struct( + locus=hl.Locus( + contig=1, + position=871269, + reference_genome='GRCh37', + ), + alleles=['A', 'C'], + rsid=None, + variant_id='1-871269-A-C', + xpos=1000871269, + sorted_transcript_consequences=[ + hl.Struct( + amino_acids='S/L', + canonical=1, + codons='tCg/tTg', + gene_id='ENSG00000188976', + hgvsc='ENST00000327044.6:c.1667C>T', + hgvsp='ENSP00000317992.6:p.Ser556Leu', + transcript_id='ENST00000327044', + biotype_id=39, + consequence_term_ids=[9], + is_lof_nagnag=None, + lof_filter_ids=[0, 1], + ), + hl.Struct( + amino_acids=None, + canonical=None, + codons=None, + gene_id='ENSG00000188976', + hgvsc='ENST00000477976.1:n.3114C>T', + hgvsp=None, + transcript_id='ENST00000477976', + biotype_id=38, + consequence_term_ids=[23, 26], + is_lof_nagnag=None, + lof_filter_ids=None, + ), + hl.Struct( + amino_acids=None, + canonical=None, + codons=None, + gene_id='ENSG00000188976', + hgvsc='ENST00000483767.1:n.523C>T', + hgvsp=None, + transcript_id='ENST00000483767', + biotype_id=38, + consequence_term_ids=[23, 26], + is_lof_nagnag=None, + lof_filter_ids=None, + ), + ], + rg38_locus=hl.Locus( + contig='chr1', + position=935889, + reference_genome='GRCh38', + ), + key_=0, + ), + ) + + def test_mito_update_vat( + self, + ) -> None: + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_5, + ReferenceGenome.GRCh38, + DatasetType.MITO, + SampleType.WGS, + 'R0115_test_project2', + ) + worker = luigi.worker.Worker() + update_variant_annotations_task = ( + UpdateVariantAnnotationsTableWithNewVariantsTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.MITO, + sample_type=SampleType.WGS, + callset_path=TEST_MITO_MT, + project_guids=['R0115_test_project2'], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + ) + worker.add(update_variant_annotations_task) + worker.run() + self.assertTrue(update_variant_annotations_task.complete()) + ht = hl.read_table(update_variant_annotations_task.output().path) + self.assertEqual(ht.count(), 5) + self.assertCountEqual( + ht.globals.collect(), + [ + hl.Struct( + enums=hl.Struct( + sorted_transcript_consequences=hl.Struct( + biotype=BIOTYPES, + consequence_term=TRANSCRIPT_CONSEQUENCE_TERMS, + lof_filter=LOF_FILTERS, + ), + mitotip=hl.Struct(trna_prediction=MITOTIP_PATHOGENICITIES), + ), + migrations=[], + max_key_=4, + updates={ + hl.Struct( + callset='loading_pipeline/var/test/callsets/mito_1.mt', + project_guid='R0115_test_project2', + remap_pedigree_hash=hl.eval( + remap_pedigree_hash( + TEST_PEDIGREE_5, + ), + ), + ), + }, + ), + ], + ) + self.assertCountEqual( + ht.collect()[0], + hl.Struct( + locus=hl.Locus( + contig='chrM', + position=3, + reference_genome='GRCh38', + ), + alleles=['T', 'C'], + common_low_heteroplasmy=False, + haplogroup=hl.Struct(is_defining=False), + mitotip=hl.Struct(trna_prediction_id=None), + rg37_locus=hl.Locus( + contig='MT', + position=3, + reference_genome='GRCh37', + ), + rsid=None, + sorted_transcript_consequences=None, + variant_id='M-3-T-C', + xpos=25000000003, + key_=0, + ), + ) + + @patch( + 'loading_pipeline.lib.tasks.write_new_variants_table.load_gencode_gene_symbol_to_gene_id', + ) + def test_sv_multiple_vcf_update_vat( + self, + mock_load_gencode: Mock, + ) -> None: + mock_load_gencode.return_value = GENE_ID_MAPPING + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_5, + ReferenceGenome.GRCh38, + DatasetType.SV, + SampleType.WGS, + 'R0115_test_project2', + ) + worker = luigi.worker.Worker() + update_variant_annotations_task = ( + UpdateVariantAnnotationsTableWithNewVariantsTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SV, + sample_type=SampleType.WGS, + callset_path=TEST_SV_VCF, + project_guids=['R0115_test_project2'], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + ) + worker.add(update_variant_annotations_task) + worker.run() + self.assertTrue(update_variant_annotations_task.complete()) + self.assertFalse( + GCSorLocalFolderTarget( + f'{self.mock_env.REFERENCE_DATASETS_DIR}/v03/GRCh38/SV/lookup.ht', + ).exists(), + ) + ht = hl.read_table(update_variant_annotations_task.output().path) + self.assertEqual(ht.count(), 13) + self.assertCountEqual( + ht.globals.collect(), + [ + hl.Struct( + enums=hl.Struct( + sv_type=SV_TYPES, + sv_type_detail=SV_TYPE_DETAILS, + sorted_gene_consequences=hl.Struct( + major_consequence=SV_CONSEQUENCE_RANKS, + ), + ), + migrations=[], + max_key_=12, + updates={ + hl.Struct( + callset=TEST_SV_VCF, + project_guid='R0115_test_project2', + remap_pedigree_hash=hl.eval( + remap_pedigree_hash( + TEST_PEDIGREE_5, + ), + ), + ), + }, + ), + ], + ) + self.assertCountEqual( + ht.collect()[:8], + [ + hl.Struct( + variant_id='BND_chr1_6', + algorithms='manta', + bothsides_support=False, + cpx_intervals=None, + end_locus=hl.Locus( + contig='chr5', + position=20404, + reference_genome='GRCh38', + ), + gnomad_svs=None, + rg37_locus=hl.Locus( + contig=1, + position=10367, + reference_genome='GRCh37', + ), + rg37_locus_end=hl.Locus( + contig=5, + position=20404, + reference_genome='GRCh37', + ), + sorted_gene_consequences=[ + hl.Struct(gene_id='ENSG00000186092', major_consequence_id=12), + hl.Struct(gene_id='ENSG00000153404', major_consequence_id=12), + ], + start_locus=hl.Locus( + contig='chr1', + position=180928, + reference_genome='GRCh38', + ), + strvctvre=hl.Struct(score=None), + sv_len=-1, + sv_type_id=2, + sv_type_detail_id=None, + xpos=1000180928, + key_=0, + ), + hl.Struct( + variant_id='BND_chr1_9', + algorithms='manta', + bothsides_support=False, + cpx_intervals=None, + end_locus=hl.Locus( + contig='chr1', + position=789481, + reference_genome='GRCh38', + ), + gnomad_svs=None, + rg37_locus=hl.Locus( + contig=1, + position=724861, + reference_genome='GRCh37', + ), + rg37_locus_end=hl.Locus( + contig=1, + position=724861, + reference_genome='GRCh37', + ), + sorted_gene_consequences=[ + hl.Struct(gene_id='ENSG00000143756', major_consequence_id=12), + hl.Struct(gene_id='ENSG00000186192', major_consequence_id=12), + ], + start_locus=hl.Locus( + contig='chr1', + position=789481, + reference_genome='GRCh38', + ), + strvctvre=hl.Struct(score=None), + sv_len=223225007, + sv_type_id=2, + sv_type_detail_id=None, + xpos=1000789481, + key_=1, + ), + hl.Struct( + variant_id='CPX_chr1_22', + algorithms='manta', + bothsides_support=True, + cpx_intervals=[ + hl.Struct( + type_id=8, + start=hl.Locus('chr1', 6558902, 'GRCh38'), + end=hl.Locus('chr1', 6559723, 'GRCh38'), + ), + hl.Struct( + type_id=6, + start=hl.Locus('chr1', 6559655, 'GRCh38'), + end=hl.Locus('chr1', 6559723, 'GRCh38'), + ), + ], + end_locus=hl.Locus( + contig='chr1', + position=6559723, + reference_genome='GRCh38', + ), + gnomad_svs=None, + rg37_locus=hl.Locus( + contig=1, + position=6618962, + reference_genome='GRCh37', + ), + rg37_locus_end=hl.Locus( + contig=1, + position=6619783, + reference_genome='GRCh37', + ), + sorted_gene_consequences=[ + hl.Struct(gene_id='ENSG00000173662', major_consequence_id=11), + ], + start_locus=hl.Locus( + contig='chr1', + position=6558902, + reference_genome='GRCh38', + ), + strvctvre=hl.Struct(score=None), + sv_len=821, + sv_type_id=3, + sv_type_detail_id=2, + xpos=1006558902, + key_=2, + ), + hl.Struct( + variant_id='CPX_chr1_251', + algorithms='manta', + bothsides_support=False, + cpx_intervals=[ + hl.Struct( + type_id=5, + start=hl.Locus('chr1', 180540234, 'GRCh38'), + end=hl.Locus('chr1', 181074767, 'GRCh38'), + ), + hl.Struct( + type_id=8, + start=hl.Locus('chr1', 181074767, 'GRCh38'), + end=hl.Locus('chr1', 181074938, 'GRCh38'), + ), + ], + end_locus=hl.Locus( + contig='chr1', + position=181074952, + reference_genome='GRCh38', + ), + gnomad_svs=None, + rg37_locus=hl.Locus( + contig=1, + position=180509370, + reference_genome='GRCh37', + ), + rg37_locus_end=hl.Locus( + contig=1, + position=181044088, + reference_genome='GRCh37', + ), + sorted_gene_consequences=[ + hl.Struct(gene_id='ENSG00000135835', major_consequence_id=0), + hl.Struct(gene_id='ENSG00000153029', major_consequence_id=0), + hl.Struct(gene_id='ENSG00000135823', major_consequence_id=0), + hl.Struct(gene_id='ENSG00000143324', major_consequence_id=0), + ], + start_locus=hl.Locus( + contig='chr1', + position=180540234, + reference_genome='GRCh38', + ), + strvctvre=hl.Struct(score=None), + sv_len=534718, + sv_type_id=3, + sv_type_detail_id=9, + xpos=1180540234, + key_=3, + ), + hl.Struct( + variant_id='CPX_chr1_41', + algorithms='manta', + bothsides_support=False, + cpx_intervals=[ + hl.Struct( + type_id=6, + start=hl.Locus('chr1', 16088760, 'GRCh38'), + end=hl.Locus('chr1', 16088835, 'GRCh38'), + ), + hl.Struct( + type_id=8, + start=hl.Locus('chr1', 16088760, 'GRCh38'), + end=hl.Locus('chr1', 16089601, 'GRCh38'), + ), + ], + end_locus=hl.Locus( + contig='chr1', + position=16089601, + reference_genome='GRCh38', + ), + gnomad_svs=None, + rg37_locus=hl.Locus( + contig=1, + position=16415255, + reference_genome='GRCh37', + ), + rg37_locus_end=hl.Locus( + contig=1, + position=16416096, + reference_genome='GRCh37', + ), + sorted_gene_consequences=[ + hl.Struct(gene_id='ENSG00000185519', major_consequence_id=12), + ], + start_locus=hl.Locus( + contig='chr1', + position=16088760, + reference_genome='GRCh38', + ), + strvctvre=hl.Struct(score=None), + sv_len=841, + sv_type_id=3, + sv_type_detail_id=12, + xpos=1016088760, + key_=4, + ), + hl.Struct( + variant_id='CPX_chr1_54', + algorithms='manta', + bothsides_support=False, + cpx_intervals=[ + hl.Struct( + type_id=6, + start=hl.Locus('chr1', 21427498, 'GRCh38'), + end=hl.Locus('chr1', 21427959, 'GRCh38'), + ), + hl.Struct( + type_id=8, + start=hl.Locus('chr1', 21427498, 'GRCh38'), + end=hl.Locus('chr1', 21480073, 'GRCh38'), + ), + hl.Struct( + type_id=5, + start=hl.Locus('chr1', 21480073, 'GRCh38'), + end=hl.Locus('chr1', 21480419, 'GRCh38'), + ), + ], + end_locus=hl.Locus( + contig='chr1', + position=21480419, + reference_genome='GRCh38', + ), + gnomad_svs=None, + rg37_locus=hl.Locus( + contig=1, + position=21753991, + reference_genome='GRCh37', + ), + rg37_locus_end=hl.Locus( + contig=1, + position=21806912, + reference_genome='GRCh37', + ), + sorted_gene_consequences=[ + hl.Struct(gene_id='ENSG00000142794', major_consequence_id=0), + ], + start_locus=hl.Locus( + contig='chr1', + position=21427498, + reference_genome='GRCh38', + ), + strvctvre=hl.Struct(score=None), + sv_len=52921, + sv_type_id=3, + sv_type_detail_id=13, + xpos=1021427498, + key_=5, + ), + hl.Struct( + variant_id='CPX_chrX_251', + algorithms='manta', + bothsides_support=False, + cpx_intervals=[ + hl.Struct( + type_id=5, + start=hl.Locus( + contig='chr1', + position=180540234, + reference_genome='GRCh38', + ), + end=hl.Locus( + contig='chr1', + position=181074767, + reference_genome='GRCh38', + ), + ), + hl.Struct( + type_id=8, + start=hl.Locus( + contig='chr1', + position=181074767, + reference_genome='GRCh38', + ), + end=hl.Locus( + contig='chr1', + position=181074938, + reference_genome='GRCh38', + ), + ), + ], + end_locus=hl.Locus( + contig='chrX', + position=2781000, + reference_genome='GRCh38', + ), + gnomad_svs=None, + sorted_gene_consequences=[ + hl.Struct(gene_id='ENSG00000135835', major_consequence_id=0), + hl.Struct(gene_id='ENSG00000153029', major_consequence_id=0), + hl.Struct(gene_id='ENSG00000135823', major_consequence_id=0), + hl.Struct(gene_id='ENSG00000143324', major_consequence_id=0), + ], + start_locus=hl.Locus( + contig='chrX', + position=3, + reference_genome='GRCh38', + ), + strvctvre=hl.Struct(score=None), + sv_type_id=3, + sv_type_detail_id=9, + sv_len=534718, + xpos=23000000003, + rg37_locus=None, + rg37_locus_end=hl.Locus( + contig='X', + position=2699041, + reference_genome='GRCh37', + ), + key_=6, + ), + hl.Struct( + variant_id='CPX_chrX_252', + algorithms='manta', + bothsides_support=False, + cpx_intervals=[ + hl.Struct( + type_id=5, + start=hl.Locus( + contig='chr1', + position=180540234, + reference_genome='GRCh38', + ), + end=hl.Locus( + contig='chr1', + position=181074767, + reference_genome='GRCh38', + ), + ), + hl.Struct( + type_id=8, + start=hl.Locus( + contig='chr1', + position=181074767, + reference_genome='GRCh38', + ), + end=hl.Locus( + contig='chr1', + position=181074938, + reference_genome='GRCh38', + ), + ), + ], + end_locus=hl.Locus( + contig='chrX', + position=2781900, + reference_genome='GRCh38', + ), + gnomad_svs=None, + sorted_gene_consequences=[ + hl.Struct(gene_id='ENSG00000135835', major_consequence_id=0), + hl.Struct(gene_id='ENSG00000153029', major_consequence_id=0), + hl.Struct(gene_id='ENSG00000135823', major_consequence_id=0), + hl.Struct(gene_id='ENSG00000143324', major_consequence_id=0), + ], + start_locus=hl.Locus( + contig='chrX', + position=2781700, + reference_genome='GRCh38', + ), + strvctvre=hl.Struct(score=None), + sv_type_id=3, + sv_type_detail_id=9, + sv_len=534718, + xpos=23002781700, + rg37_locus=hl.Locus( + contig='X', + position=2699741, + reference_genome='GRCh37', + ), + rg37_locus_end=hl.Locus( + contig='X', + position=2699941, + reference_genome='GRCh37', + ), + key_=7, + ), + ], + ) + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_5, + ReferenceGenome.GRCh38, + DatasetType.SV, + SampleType.WGS, + 'R0115_test_project2', + ) + update_variant_annotations_task = ( + UpdateVariantAnnotationsTableWithNewVariantsTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SV, + sample_type=SampleType.WGS, + callset_path=TEST_SV_VCF_2, + project_guids=['R0115_test_project2'], + validations_to_skip=[ALL_VALIDATIONS], + run_id='second_run_id', + ) + ) + worker.add(update_variant_annotations_task) + worker.run() + self.assertTrue(update_variant_annotations_task.complete()) + ht = hl.read_table(update_variant_annotations_task.output().path) + self.assertEqual(ht.count(), 14) + self.assertCountEqual( + ht.globals.collect(), + [ + hl.Struct( + enums=hl.Struct( + sv_type=SV_TYPES, + sv_type_detail=SV_TYPE_DETAILS, + sorted_gene_consequences=hl.Struct( + major_consequence=SV_CONSEQUENCE_RANKS, + ), + ), + migrations=[], + max_key_=13, + updates={ + hl.Struct( + callset=TEST_SV_VCF, + project_guid='R0115_test_project2', + remap_pedigree_hash=hl.eval( + remap_pedigree_hash( + TEST_PEDIGREE_5, + ), + ), + ), + hl.Struct( + callset=TEST_SV_VCF_2, + project_guid='R0115_test_project2', + remap_pedigree_hash=hl.eval( + remap_pedigree_hash( + TEST_PEDIGREE_5, + ), + ), + ), + }, + ), + ], + ) + self.assertCountEqual( + ht.take(1), + [ + hl.Struct( + variant_id='BND_chr1_6', + algorithms='manta', + bothsides_support=False, + cpx_intervals=None, + end_locus=hl.Locus( + contig='chr5', + position=20404, + reference_genome='GRCh38', + ), + gnomad_svs=None, + rg37_locus=hl.Locus( + contig=1, + position=10367, + reference_genome='GRCh37', + ), + rg37_locus_end=hl.Locus( + contig=5, + position=20404, + reference_genome='GRCh37', + ), + sorted_gene_consequences=[ + hl.Struct(gene_id='ENSG00000186092', major_consequence_id=12), + hl.Struct(gene_id='ENSG00000153404', major_consequence_id=12), + ], + start_locus=hl.Locus( + contig='chr1', + position=180928, + reference_genome='GRCh38', + ), + strvctvre=hl.Struct(score=None), + sv_len=-1, + sv_type_id=2, + sv_type_detail_id=None, + xpos=1000180928, + key_=0, + ), + ], + ) + + @patch( + 'loading_pipeline.lib.tasks.write_new_variants_table.load_gencode_gene_symbol_to_gene_id', + ) + def test_sv_multiple_project_single_vcf( + self, + mock_load_gencode: Mock, + ) -> None: + mock_load_gencode.return_value = GENE_ID_MAPPING + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_10, + ReferenceGenome.GRCh38, + DatasetType.SV, + SampleType.WGS, + 'R0116_test_project3', + ) + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_11, + ReferenceGenome.GRCh38, + DatasetType.SV, + SampleType.WGS, + 'R0117_test_project4', + ) + worker = luigi.worker.Worker() + update_variant_annotations_task = ( + UpdateVariantAnnotationsTableWithNewVariantsTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SV, + sample_type=SampleType.WGS, + callset_path=TEST_SV_VCF_2, + project_guids=['R0116_test_project3', 'R0117_test_project4'], + validations_to_skip=[ALL_VALIDATIONS], + run_id='run_id', + ) + ) + worker.add(update_variant_annotations_task) + worker.run() + self.assertTrue(update_variant_annotations_task.complete()) + ht = hl.read_table(update_variant_annotations_task.output().path) + self.assertEqual(ht.count(), 2) + self.assertEqual( + len(ht.globals.updates.collect()[0]), + 2, + ) + + def test_gcnv_update_vat_multiple( + self, + ) -> None: + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_5, + ReferenceGenome.GRCh38, + DatasetType.GCNV, + SampleType.WES, + 'R0115_test_project2', + ) + worker = luigi.worker.Worker() + update_variant_annotations_task = ( + UpdateVariantAnnotationsTableWithNewVariantsTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.GCNV, + sample_type=SampleType.WES, + callset_path=TEST_GCNV_BED_FILE, + project_guids=['R0115_test_project2'], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + ) + worker.add(update_variant_annotations_task) + worker.run() + self.assertTrue(update_variant_annotations_task.complete()) + self.assertFalse( + GCSorLocalFolderTarget( + f'{self.mock_env.REFERENCE_DATASETS_DIR}/v03/GRCh38/GCNV/lookup.ht', + ).exists(), + ) + ht = hl.read_table(update_variant_annotations_task.output().path) + self.assertEqual(ht.count(), 2) + self.assertCountEqual( + ht.globals.collect(), + [ + hl.Struct( + enums=hl.Struct( + sv_type=SV_TYPES, + sorted_gene_consequences=hl.Struct( + major_consequence=SV_CONSEQUENCE_RANKS, + ), + ), + migrations=[], + max_key_=1, + updates={ + hl.Struct( + callset=TEST_GCNV_BED_FILE, + project_guid='R0115_test_project2', + remap_pedigree_hash=hl.eval( + remap_pedigree_hash( + TEST_PEDIGREE_5, + ), + ), + ), + }, + ), + ], + ) + self.assertCountEqual( + ht.collect(), + [ + hl.Struct( + variant_id='suffix_16456_DEL', + end_locus=hl.Locus( + contig='chr1', + position=100023213, + reference_genome='GRCh38', + ), + gt_stats=hl.Struct( + AF=hl.eval(hl.float32(4.401408e-05)), + AC=1, + AN=22720, + Hom=None, + Het=None, + ), + num_exon=3, + rg37_locus=hl.Locus( + contig=1, + position=100472493, + reference_genome='GRCh37', + ), + rg37_locus_end=hl.Locus( + contig=1, + position=100488769, + reference_genome='GRCh37', + ), + sorted_gene_consequences=[ + hl.Struct(gene_id='ENSG00000117620', major_consequence_id=0), + hl.Struct(gene_id='ENSG00000283761', major_consequence_id=0), + hl.Struct(gene_id='ENSG22222222222', major_consequence_id=None), + ], + start_locus=hl.Locus( + contig='chr1', + position=100006937, + reference_genome='GRCh38', + ), + strvctvre=hl.Struct(score=hl.eval(hl.float32(0.583))), + sv_type_id=5, + xpos=1100006937, + key_=0, + ), + hl.Struct( + variant_id='suffix_16457_DEL', + end_locus=hl.Locus( + contig='chr1', + position=100023212, + reference_genome='GRCh38', + ), + gt_stats=hl.Struct( + AF=8.802817319519818e-05, + AC=2, + AN=22719, + Hom=None, + Het=None, + ), + num_exon=2, + rg37_locus=hl.Locus( + contig=1, + position=100483142, + reference_genome='GRCh37', + ), + rg37_locus_end=hl.Locus( + contig=1, + position=100488768, + reference_genome='GRCh37', + ), + sorted_gene_consequences=[ + hl.Struct(gene_id='ENSG00000283761', major_consequence_id=0), + hl.Struct(gene_id='ENSG22222222222', major_consequence_id=None), + ], + start_locus=hl.Locus( + contig='chr1', + position=100017586, + reference_genome='GRCh38', + ), + strvctvre=hl.Struct(score=0.5070000290870667), + sv_type_id=5, + xpos=1100017586, + key_=1, + ), + ], + ) + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_8, + ReferenceGenome.GRCh38, + DatasetType.GCNV, + SampleType.WES, + 'R0115_test_project2', + ) + update_variant_annotations_task = ( + UpdateVariantAnnotationsTableWithNewVariantsTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.GCNV, + sample_type=SampleType.WES, + callset_path=TEST_GCNV_BED_FILE_2, + project_guids=['R0115_test_project2'], + validations_to_skip=[ALL_VALIDATIONS], + run_id='second_run_id', + ) + ) + worker.add(update_variant_annotations_task) + worker.run() + ht = hl.read_table(update_variant_annotations_task.output().path) + self.assertEqual(ht.count(), 3) + self.assertCountEqual( + ht.select('gt_stats').collect(), + [ + hl.Struct( + # Existing variant, gt_stats are preserved + variant_id='suffix_16456_DEL', + gt_stats=hl.Struct( + AF=hl.eval(hl.float32(4.401408e-05)), + AC=1, + AN=22720, + Hom=None, + Het=None, + ), + ), + hl.Struct( + # Exiting variant, gt_stats are updated + variant_id='suffix_16457_DEL', + gt_stats=hl.Struct( + AF=8.111110946629196e-05, + AC=3, + AN=36986, + Hom=None, + Het=None, + ), + ), + hl.Struct( + # New variant. + variant_id='suffix_99999_DEL', + gt_stats=hl.Struct( + AF=8.802817319519818e-05, + AC=2, + AN=22719, + Hom=None, + Het=None, + ), + ), + ], + ) diff --git a/loading_pipeline/lib/tasks/validate_callset.py b/loading_pipeline/lib/tasks/validate_callset.py new file mode 100644 index 0000000000..7622bc0a03 --- /dev/null +++ b/loading_pipeline/lib/tasks/validate_callset.py @@ -0,0 +1,144 @@ +import hail as hl +import luigi +import luigi.util + +from loading_pipeline.lib.misc.validation import ( + ALL_VALIDATIONS, + SKIPPABLE_VALIDATIONS, + SeqrValidationError, +) +from loading_pipeline.lib.paths import ( + postprocessed_callset_path, + valid_reference_dataset_path, +) +from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset +from loading_pipeline.lib.tasks.base.base_loading_run_params import BaseLoadingRunParams +from loading_pipeline.lib.tasks.base.base_update import BaseUpdateTask +from loading_pipeline.lib.tasks.files import CallsetTask, GCSorLocalTarget +from loading_pipeline.lib.tasks.reference_data.updated_reference_dataset import ( + UpdatedReferenceDatasetTask, +) +from loading_pipeline.lib.tasks.write_postprocessed_callset import ( + WritePostprocessedCallsetTask, +) +from loading_pipeline.lib.tasks.write_validation_errors_for_run import ( + UpdatedValidationErrorsForRunTask, +) + +MAX_SNV_INDEL_ALLELE_LENGTH = 500 + + +@luigi.util.inherits(BaseLoadingRunParams) +class ValidateCallsetTask(BaseUpdateTask): + @property + def validation_dependencies(self) -> dict[str, hl.Table]: + deps = {} + if ( + ALL_VALIDATIONS not in self.validations_to_skip + and 'validate_sample_type' not in self.validations_to_skip + and self.dataset_type.can_run_validation + ): + deps['coding_and_noncoding_variants_ht'] = hl.read_table( + valid_reference_dataset_path( + self.reference_genome, + ReferenceDataset.gnomad_coding_and_noncoding, + ), + ) + return deps + + def complete(self) -> luigi.Target: + if super().complete(): + mt = hl.read_matrix_table(self.output().path) + return hasattr(mt, 'validated_sample_type') and hl.eval( + self.sample_type.value == mt.validated_sample_type, + ) + return False + + def output(self) -> luigi.Target: + return GCSorLocalTarget( + postprocessed_callset_path( + self.reference_genome, + self.dataset_type, + self.callset_path, + ), + ) + + def requires(self) -> list[luigi.Task]: + requirements = [self.clone(WritePostprocessedCallsetTask)] + if ( + ALL_VALIDATIONS not in self.validations_to_skip + and 'validate_sample_type' not in self.validations_to_skip + and self.dataset_type.can_run_validation + ): + requirements = [ + *requirements, + ( + self.clone( + UpdatedReferenceDatasetTask, + reference_dataset=ReferenceDataset.gnomad_coding_and_noncoding, + ) + ), + ] + return [ + *requirements, + CallsetTask(self.callset_path), + ] + + def update_table(self, mt: hl.MatrixTable) -> hl.MatrixTable: + mt = hl.read_matrix_table( + postprocessed_callset_path( + self.reference_genome, + self.dataset_type, + self.callset_path, + ), + ) + if self.dataset_type.filter_invalid_sites: + mt = mt.filter_rows( + ( + # Rather than throwing an error, we silently remove invalid contigs. + # This happens fairly often for AnVIL requests. + hl.set(self.reference_genome.standard_contigs).contains( + mt.locus.contig, + ) + # DRAGEN callsets produce long alternate alleles + # that aren't particularly analyzable as INDELs. + & (hl.len(mt.alleles[1]) < MAX_SNV_INDEL_ALLELE_LENGTH) + ), + ) + + if ( + ALL_VALIDATIONS in self.validations_to_skip + or not self.dataset_type.can_run_validation + ): + return mt.select_globals( + callset_path=self.callset_path, + validated_sample_type=self.sample_type.value, + ) + validation_exceptions = [] + for validation_f in SKIPPABLE_VALIDATIONS: + try: + if validation_f.__name__ in self.validations_to_skip: + continue + validation_f( + mt, + **self.validation_dependencies, + **self.param_kwargs, + ) + except SeqrValidationError as e: + validation_exceptions.append(e) + if validation_exceptions: + updated_validation_errors_for_run_task = self.clone( + UpdatedValidationErrorsForRunTask, + error_messages=[e.msg for e in validation_exceptions], + error_body={ + k: v for e in validation_exceptions for k, v in e.error_body.items() + }, + ) + updated_validation_errors_for_run_task.run() + raise SeqrValidationError( + updated_validation_errors_for_run_task.to_single_error_message(), + ) + return mt.select_globals( + callset_path=self.callset_path, + validated_sample_type=self.sample_type.value, + ) diff --git a/loading_pipeline/lib/tasks/validate_callset_test.py b/loading_pipeline/lib/tasks/validate_callset_test.py new file mode 100644 index 0000000000..a56f78a894 --- /dev/null +++ b/loading_pipeline/lib/tasks/validate_callset_test.py @@ -0,0 +1,83 @@ +import json +import shutil + +import luigi.worker + +from loading_pipeline.lib.core import ( + DatasetType, + ReferenceGenome, + SampleType, +) +from loading_pipeline.lib.paths import ( + valid_reference_dataset_path, +) +from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset +from loading_pipeline.lib.tasks.validate_callset import ( + ValidateCallsetTask, +) +from loading_pipeline.lib.tasks.write_validation_errors_for_run import ( + UpdatedValidationErrorsForRunTask, +) +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + +TEST_CODING_AND_NONCODING_HT = 'loading_pipeline/var/test/reference_datasets/GRCh38/gnomad_coding_and_noncoding/1.0.ht' +MULTIPLE_VALIDATION_EXCEPTIONS_VCF = ( + 'loading_pipeline/var/test/callsets/multiple_validation_exceptions.vcf' +) + +TEST_RUN_ID = 'manual__2024-04-03' + + +class ValidateCallsetTest(MockedDatarootTestCase): + def setUp(self) -> None: + super().setUp() + shutil.copytree( + TEST_CODING_AND_NONCODING_HT, + valid_reference_dataset_path( + ReferenceGenome.GRCh38, + ReferenceDataset.gnomad_coding_and_noncoding, + ), + ) + + def test_validate_callset_multiple_exceptions( + self, + ) -> None: + worker = luigi.worker.Worker() + validate_callset_task = ValidateCallsetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WES, + # NB: + # This callset contains duplicate rows for chr1:902088, + # a NON_REF allele type at position chr1: 902024, missing + # all contigs but chr1, and contains non-coding variants. + callset_path=MULTIPLE_VALIDATION_EXCEPTIONS_VCF, + project_guids=['project_a'], + run_id=TEST_RUN_ID, + ) + worker.add(validate_callset_task) + worker.run() + self.assertFalse(validate_callset_task.complete()) + + updated_validation_errors_task = UpdatedValidationErrorsForRunTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WES, + callset_path=MULTIPLE_VALIDATION_EXCEPTIONS_VCF, + project_guids=['project_a'], + run_id=TEST_RUN_ID, + ) + self.assertTrue(updated_validation_errors_task.complete()) + with updated_validation_errors_task.output().open('r') as f: + self.assertDictEqual( + json.load(f), + { + 'project_guids': ['project_a'], + 'error_messages': [ + 'Alleles with invalid allele are present in the callset. This appears to be a GVCF containing records for sites with no variants.', + 'Missing the following expected contigs:chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr2, chr20, chr21, chr22, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chrX', + "Variants are present multiple times in the callset: ['1-902088-G-A']", + 'Sample type validation error: dataset sample-type is specified as WES but appears to be WGS because it contains many common non-coding variants', + ], + }, + ) diff --git a/loading_pipeline/lib/tasks/variants_migration/__init__.py b/loading_pipeline/lib/tasks/variants_migration/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables.py b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables.py new file mode 100644 index 0000000000..25325d8e37 --- /dev/null +++ b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables.py @@ -0,0 +1,137 @@ +import luigi +import luigi.util + +from loading_pipeline.lib.core import FeatureFlag +from loading_pipeline.lib.misc.clickhouse import ( + ClickhouseReferenceDataset, + ClickHouseTable, + TableNameBuilder, + logged_query, +) +from loading_pipeline.lib.misc.retry import retry +from loading_pipeline.lib.paths import ( + new_variant_details_parquet_path, + new_variants_parquet_path, +) +from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( + BaseLoadingPipelineParams, +) +from loading_pipeline.lib.tasks.files import GCSorLocalFolderTarget +from loading_pipeline.lib.tasks.variants_migration.migrate_variant_details_parquet import ( + MigrateVariantDetailsParquetOnDataprocTask, + MigrateVariantDetailsParquetTask, +) +from loading_pipeline.lib.tasks.variants_migration.migrate_variants_parquet import ( + MigrateVariantsParquetOnDataprocTask, + MigrateVariantsParquetTask, +) + + +@retry() +def refresh_seqr_variants_and_search( + table_name_builder: TableNameBuilder, + clickhouse_reference_dataset: ClickhouseReferenceDataset, +): + if clickhouse_reference_dataset.has_seqr_variants: + logged_query( + f""" + SYSTEM START VIEW {clickhouse_reference_dataset.all_variants_to_seqr_variants_mv(table_name_builder)} + """, + ) + logged_query( + f""" + SYSTEM REFRESH VIEW {clickhouse_reference_dataset.all_variants_to_seqr_variants_mv(table_name_builder)} + """, + ) + logged_query( + f""" + SYSTEM WAIT VIEW {clickhouse_reference_dataset.all_variants_to_seqr_variants_mv(table_name_builder)} + """, + timeout=clickhouse_reference_dataset.all_variants_mv_timeout, + ) + clickhouse_reference_dataset.refresh_search(table_name_builder) + + +@luigi.util.inherits(BaseLoadingPipelineParams) +class LoadClickhouseVariantsTablesTask(luigi.WrapperTask): + run_id = luigi.Parameter() + attempt_id = luigi.IntParameter() + + def requires(self) -> luigi.Task: + tasks = ( + [ + self.clone(MigrateVariantsParquetOnDataprocTask), + ] + if FeatureFlag.RUN_PIPELINE_ON_DATAPROC + else [ + self.clone(MigrateVariantsParquetTask), + ] + ) + if self.dataset_type.should_write_new_variant_details: + tasks.append( + self.clone(MigrateVariantDetailsParquetOnDataprocTask) + if FeatureFlag.RUN_PIPELINE_ON_DATAPROC + else self.clone(MigrateVariantDetailsParquetTask), + ) + return tasks + + def complete(self) -> bool: + table_name_builder = TableNameBuilder( + self.reference_genome, + self.dataset_type, + self.run_id, + ) + if not ( + GCSorLocalFolderTarget( + new_variant_details_parquet_path( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + ).exists() + ) or not ( + GCSorLocalFolderTarget( + new_variants_parquet_path( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + ).exists() + ): + return False + max_key = logged_query( + f""" + SELECT max(key) FROM {table_name_builder.src_table(ClickHouseTable.VARIANTS_MEMORY)} + """, + )[0][0] + return logged_query( + f""" + SELECT EXISTS ( + SELECT 1 FROM {table_name_builder.dst_table(ClickHouseTable.VARIANTS_MEMORY)} where key = %(max_key)s + ) + """, + {'max_key': max_key}, + )[0][0] + + def run(self) -> None: + table_name_builder = TableNameBuilder( + self.reference_genome, + self.dataset_type, + self.run_id, + ) + for clickhouse_table in ClickHouseTable.for_dataset_type( + self.dataset_type, + ): + if clickhouse_table == ClickHouseTable.ENTRIES: + continue + clickhouse_table.insert(table_name_builder=table_name_builder) + for ( + clickhouse_reference_dataset + ) in ClickhouseReferenceDataset.for_reference_genome_dataset_type( + self.reference_genome, + self.dataset_type, + ): + refresh_seqr_variants_and_search( + table_name_builder, + clickhouse_reference_dataset, + ) diff --git a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py new file mode 100644 index 0000000000..972df2c172 --- /dev/null +++ b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py @@ -0,0 +1,148 @@ +from unittest.mock import Mock, patch + +import hail as hl +import luigi.worker + +from loading_pipeline.lib.core import ( + DatasetType, + ReferenceGenome, +) +from loading_pipeline.lib.core.environment import Env +from loading_pipeline.lib.misc.clickhouse import ( + ClickhouseReferenceDataset, + get_clickhouse_client, +) +from loading_pipeline.lib.paths import ( + variant_annotations_table_path, +) +from loading_pipeline.lib.tasks.variants_migration.load_clickhouse_variants_tables import ( + LoadClickhouseVariantsTablesTask, +) +from loading_pipeline.lib.tasks.variants_migration.migrate_variant_details_parquet import ( + MigrateVariantDetailsParquetTask, +) +from loading_pipeline.lib.tasks.variants_migration.migrate_variants_parquet import ( + MigrateVariantsParquetTask, +) +from loading_pipeline.lib.tasks.variants_migration.update_variant_annotations_table_with_dropped_reference_datasets import ( + UpdateVariantAnnotationsTableWithDroppedReferenceDatasetsTask, +) +from loading_pipeline.lib.test.clickhouse_schema_testcase import ( + ClickhouseSchemaTestCase, +) +from loading_pipeline.lib.test.mocked_dataroot_testcase import ( + MockedDatarootTestCase, +) + +TEST_SCHEMA = 'loading_pipeline/var/test/test_clickhouse_schema.sql' +TEST_SNV_INDEL_ANNOTATIONS = ( + 'loading_pipeline/var/test/exports/GRCh38/SNV_INDEL/annotations.ht' +) +TEST_RUN_ID = 'manual__2024-04-03' + + +class LoadClickhouseVariantsTablesTaskTest( + MockedDatarootTestCase, + ClickhouseSchemaTestCase, +): + def setUp(self) -> None: + super().setUp() + ht = hl.read_table(TEST_SNV_INDEL_ANNOTATIONS) + ht.write( + variant_annotations_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + ), + ) + + @patch.object( + ClickhouseReferenceDataset, + 'for_reference_genome_dataset_type', + return_value=[ClickhouseReferenceDataset.CLINVAR], + ) + def test_write_variants_to_clickhouse( + self, + mock_for_reference_genome_dataset_type: Mock, + ): + worker = luigi.worker.Worker() + task = UpdateVariantAnnotationsTableWithDroppedReferenceDatasetsTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id=TEST_RUN_ID, + ) + worker.add(task) + worker.run() + self.assertTrue(task.output().exists()) + self.assertTrue(task.complete()) + ht = hl.read_table(task.output().path) + self.assertTrue('variant_id' in ht.row) + self.assertTrue('gnomad_genomes' not in ht.row and 'dbnsfp' not in ht.row) + + task = MigrateVariantsParquetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id=TEST_RUN_ID, + attempt_id=0, + ) + worker.add(task) + worker.run() + self.assertTrue(task.output().exists()) + self.assertTrue(task.complete()) + + task = MigrateVariantDetailsParquetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id=TEST_RUN_ID, + attempt_id=0, + ) + worker.add(task) + worker.run() + self.assertTrue(task.output().exists()) + self.assertTrue(task.complete()) + + task = MigrateVariantDetailsParquetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id=TEST_RUN_ID, + attempt_id=0, + ) + worker.add(task) + worker.run() + self.assertTrue(task.output().exists()) + self.assertTrue(task.complete()) + + task = LoadClickhouseVariantsTablesTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id=TEST_RUN_ID, + attempt_id=0, + ) + worker.add(task) + worker.run() + self.assertTrue(task.complete()) + + client = get_clickhouse_client() + variants_count = client.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` + """, + )[0][0] + self.assertEqual(variants_count, 2) + variant_details_count = client.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details` + """, + )[0][0] + self.assertEqual(variant_details_count, 2) + key_lookups_count = client.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/key_lookup` + """, + )[0][0] + self.assertEqual(key_lookups_count, 2) diff --git a/loading_pipeline/lib/tasks/variants_migration/migrate_variant_details_parquet.py b/loading_pipeline/lib/tasks/variants_migration/migrate_variant_details_parquet.py new file mode 100644 index 0000000000..8405757676 --- /dev/null +++ b/loading_pipeline/lib/tasks/variants_migration/migrate_variant_details_parquet.py @@ -0,0 +1,76 @@ +import hail as hl +import luigi +import luigi.util + +from loading_pipeline.lib.paths import ( + new_variant_details_parquet_path, + variant_annotations_table_path, +) +from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( + BaseLoadingPipelineParams, +) +from loading_pipeline.lib.tasks.base.base_write_parquet import BaseWriteParquetTask +from loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc import ( + BaseRunJobOnDataprocTask, +) +from loading_pipeline.lib.tasks.exports.fields import ( + get_variant_details_export_fields, +) +from loading_pipeline.lib.tasks.exports.misc import ( + camelcase_array_structexpression_fields, + unmap_formatting_annotation_enums, +) +from loading_pipeline.lib.tasks.files import GCSorLocalTarget +from loading_pipeline.lib.tasks.variants_migration.update_variant_annotations_table_with_dropped_reference_datasets import ( + UpdateVariantAnnotationsTableWithDroppedReferenceDatasetsTask, +) + + +@luigi.util.inherits(BaseLoadingPipelineParams) +class MigrateVariantDetailsParquetTask(BaseWriteParquetTask): + run_id = luigi.Parameter() + attempt_id = luigi.IntParameter() + + def output(self) -> luigi.Target: + return GCSorLocalTarget( + new_variant_details_parquet_path( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + ) + + def requires(self) -> luigi.Task: + return self.clone(UpdateVariantAnnotationsTableWithDroppedReferenceDatasetsTask) + + def create_table(self) -> None: + ht = hl.read_table( + variant_annotations_table_path( + self.reference_genome, + self.dataset_type, + ), + ) + ht = unmap_formatting_annotation_enums( + ht, + self.reference_genome, + self.dataset_type, + ) + ht = camelcase_array_structexpression_fields( + ht, + self.reference_genome, + self.dataset_type, + ) + ht = ht.key_by() + return ht.select( + **get_variant_details_export_fields( + ht, + self.reference_genome, + self.dataset_type, + ), + ) + + +class MigrateVariantDetailsParquetOnDataprocTask(BaseRunJobOnDataprocTask): + @property + def task(self) -> luigi.Task: + return MigrateVariantDetailsParquetTask diff --git a/loading_pipeline/lib/tasks/variants_migration/migrate_variants_parquet.py b/loading_pipeline/lib/tasks/variants_migration/migrate_variants_parquet.py new file mode 100644 index 0000000000..c92a25fb4e --- /dev/null +++ b/loading_pipeline/lib/tasks/variants_migration/migrate_variants_parquet.py @@ -0,0 +1,76 @@ +import hail as hl +import luigi +import luigi.util + +from loading_pipeline.lib.paths import ( + new_variants_parquet_path, + variant_annotations_table_path, +) +from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( + BaseLoadingPipelineParams, +) +from loading_pipeline.lib.tasks.base.base_write_parquet import BaseWriteParquetTask +from loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc import ( + BaseRunJobOnDataprocTask, +) +from loading_pipeline.lib.tasks.exports.fields import get_variants_export_fields +from loading_pipeline.lib.tasks.exports.misc import ( + camelcase_array_structexpression_fields, + subset_consequences_fields, + unmap_formatting_annotation_enums, +) +from loading_pipeline.lib.tasks.files import GCSorLocalTarget +from loading_pipeline.lib.tasks.variants_migration.update_variant_annotations_table_with_dropped_reference_datasets import ( + UpdateVariantAnnotationsTableWithDroppedReferenceDatasetsTask, +) + + +@luigi.util.inherits(BaseLoadingPipelineParams) +class MigrateVariantsParquetTask(BaseWriteParquetTask): + run_id = luigi.Parameter() + attempt_id = luigi.IntParameter() + + def output(self) -> luigi.Target: + return GCSorLocalTarget( + new_variants_parquet_path( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + ) + + def requires(self) -> luigi.Task: + return self.clone(UpdateVariantAnnotationsTableWithDroppedReferenceDatasetsTask) + + def create_table(self) -> None: + ht = hl.read_table( + variant_annotations_table_path( + self.reference_genome, + self.dataset_type, + ), + ) + ht = unmap_formatting_annotation_enums( + ht, + self.reference_genome, + self.dataset_type, + ) + ht = camelcase_array_structexpression_fields( + ht, + self.reference_genome, + self.dataset_type, + ) + if self.dataset_type.should_write_new_variant_details: + ht = subset_consequences_fields( + ht, + self.reference_genome, + ) + ht = ht.key_by() + return ht.select( + **get_variants_export_fields(ht, self.reference_genome, self.dataset_type), + ) + + +class MigrateVariantsParquetOnDataprocTask(BaseRunJobOnDataprocTask): + @property + def task(self) -> luigi.Task: + return MigrateVariantsParquetTask diff --git a/loading_pipeline/lib/tasks/variants_migration/update_variant_annotations_table_with_dropped_reference_datasets.py b/loading_pipeline/lib/tasks/variants_migration/update_variant_annotations_table_with_dropped_reference_datasets.py new file mode 100644 index 0000000000..4dddb1afbe --- /dev/null +++ b/loading_pipeline/lib/tasks/variants_migration/update_variant_annotations_table_with_dropped_reference_datasets.py @@ -0,0 +1,90 @@ +import hail as hl +import luigi +import luigi.util + +from loading_pipeline.lib.paths import ( + variant_annotations_table_path, +) +from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( + BaseLoadingPipelineParams, +) +from loading_pipeline.lib.tasks.base.base_update import ( + BaseUpdateTask, +) +from loading_pipeline.lib.tasks.files import GCSorLocalTarget, HailTableTask + + +@luigi.util.inherits(BaseLoadingPipelineParams) +class UpdateVariantAnnotationsTableWithDroppedReferenceDatasetsTask( + BaseUpdateTask, +): + run_id = luigi.Parameter() + + def output(self) -> luigi.Target: + return GCSorLocalTarget( + variant_annotations_table_path( + self.reference_genome, + self.dataset_type, + ), + ) + + def requires(self) -> list[luigi.Task]: + return HailTableTask( + variant_annotations_table_path( + self.reference_genome, + self.dataset_type, + ), + ) + + def complete(self) -> bool: + return ( + super().complete() and 'dbnsfp' not in hl.read_table(self.output().path).row + ) + + def initialize_table(self) -> hl.Table: + key_type = self.dataset_type.table_key_type(self.reference_genome) + return hl.Table.parallelize( + [], + key_type, + key=key_type.fields, + globals=hl.Struct( + enums=hl.Struct(), + updates=hl.empty_set( + hl.tstruct( + callset=hl.tstr, + project_guid=hl.tstr, + remap_pedigree_hash=hl.tint32, + ), + ), + migrations=hl.empty_array(hl.tstr), + max_key_=hl.int64(-1), + ), + ) + + def update_table(self, ht: hl.Table) -> hl.Table: + for field in [ + 'clinvar', + 'gnomad_mito', + 'hmtvar', + 'local_constraint_mito', + 'dbnsfp', + 'mitomap', + 'mitimpact', + 'helix_mito', + 'gt_stats', + 'high_constraint_region', + 'eigen', + 'splice_ai', + 'exac', + 'topmed', + 'screen', + 'gnomad_exomes', + 'gnomad_genomes', + 'hgmd', + 'gnomad_non_coding_constraint', + ]: + if field in ht.row: + ht = ht.drop(field) + if field in ht.enums: + ht = ht.annotate_globals(enums=ht.enums.drop(field)) + return ht diff --git a/loading_pipeline/lib/tasks/write_clickhouse_load_success_file.py b/loading_pipeline/lib/tasks/write_clickhouse_load_success_file.py new file mode 100644 index 0000000000..f5c7284763 --- /dev/null +++ b/loading_pipeline/lib/tasks/write_clickhouse_load_success_file.py @@ -0,0 +1,56 @@ +import json + +import hailtop.fs as hfs +import luigi +import luigi.util + +from loading_pipeline.lib.misc.clickhouse import ( + load_complete_run, +) +from loading_pipeline.lib.paths import ( + clickhouse_load_success_file_path, + metadata_for_run_path, +) +from loading_pipeline.lib.tasks.base.base_loading_run_params import ( + BaseLoadingRunParams, +) +from loading_pipeline.lib.tasks.files import GCSorLocalTarget +from loading_pipeline.lib.tasks.write_success_file import WriteSuccessFileTask + + +@luigi.util.inherits(BaseLoadingRunParams) +class WriteClickhouseLoadSuccessFileTask(luigi.Task): + attempt_id = luigi.IntParameter() + + def output(self) -> luigi.Target: + return GCSorLocalTarget( + clickhouse_load_success_file_path( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + ) + + def requires(self) -> luigi.Task: + return self.clone(WriteSuccessFileTask) + + def run(self): + with hfs.open( + metadata_for_run_path( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + ) as f: + family_guids = list(json.load(f)['family_samples'].keys()) + load_complete_run( + self.reference_genome, + self.dataset_type, + self.run_id, + # Note: nasty bug here where Luigi parses ListParameters to tuples. + list(self.project_guids), + family_guids, + ) + + with self.output().open('w') as f: + f.write('') diff --git a/loading_pipeline/lib/tasks/write_imported_callset.py b/loading_pipeline/lib/tasks/write_imported_callset.py new file mode 100644 index 0000000000..db80232bca --- /dev/null +++ b/loading_pipeline/lib/tasks/write_imported_callset.py @@ -0,0 +1,84 @@ +import hail as hl +import luigi +import luigi.util + +from loading_pipeline.lib.misc.callsets import get_additional_row_fields +from loading_pipeline.lib.misc.io import ( + import_callset, + select_relevant_fields, +) +from loading_pipeline.lib.misc.validation import ( + validate_imported_field_types, +) +from loading_pipeline.lib.paths import ( + imported_callset_path, +) +from loading_pipeline.lib.tasks.base.base_loading_run_params import BaseLoadingRunParams +from loading_pipeline.lib.tasks.base.base_write import BaseWriteTask +from loading_pipeline.lib.tasks.files import CallsetTask, GCSorLocalTarget +from loading_pipeline.lib.tasks.write_validation_errors_for_run import ( + with_persisted_validation_errors, +) + + +@luigi.util.inherits(BaseLoadingRunParams) +class WriteImportedCallsetTask(BaseWriteTask): + def complete(self) -> luigi.Target: + if super().complete(): + mt = hl.read_matrix_table(self.output().path) + # Handle case where callset was previously imported + # with a different sex/relatedness flag. + additional_row_fields = get_additional_row_fields( + mt, + self.reference_genome, + self.dataset_type, + self.skip_check_sex_and_relatedness, + ) + return all(hasattr(mt, field) for field in additional_row_fields) + return False + + def output(self) -> luigi.Target: + return GCSorLocalTarget( + imported_callset_path( + self.reference_genome, + self.dataset_type, + self.callset_path, + ), + ) + + def requires(self) -> list[luigi.Task]: + return [ + CallsetTask(self.callset_path), + ] + + @with_persisted_validation_errors + def create_table(self) -> hl.MatrixTable: + # NB: throws SeqrValidationError + mt = import_callset( + self.callset_path, + self.reference_genome, + self.dataset_type, + ) + additional_row_fields = get_additional_row_fields( + mt, + self.reference_genome, + self.dataset_type, + self.skip_check_sex_and_relatedness, + ) + # NB: throws SeqrValidationError + mt = select_relevant_fields( + mt, + self.dataset_type, + additional_row_fields, + ) + # This validation isn't override-able by the skip option. + # If a field is the wrong type, the pipeline will likely hard-fail downstream. + # NB: throws SeqrValidationError + validate_imported_field_types( + mt, + self.dataset_type, + additional_row_fields, + ) + return mt.select_globals( + callset_path=self.callset_path, + ) diff --git a/loading_pipeline/lib/tasks/write_metadata_for_run.py b/loading_pipeline/lib/tasks/write_metadata_for_run.py new file mode 100644 index 0000000000..a20f44cd59 --- /dev/null +++ b/loading_pipeline/lib/tasks/write_metadata_for_run.py @@ -0,0 +1,146 @@ +import json + +import hail as hl +import hailtop.fs as hfs +import luigi +import luigi.util + +from loading_pipeline.lib.core import FeatureFlag +from loading_pipeline.lib.paths import ( + metadata_for_run_path, + relatedness_check_tsv_path, + sample_qc_json_path, +) +from loading_pipeline.lib.tasks.base.base_loading_run_params import ( + BaseLoadingRunParams, +) +from loading_pipeline.lib.tasks.files import GCSorLocalTarget +from loading_pipeline.lib.tasks.write_remapped_and_subsetted_callset import ( + WriteRemappedAndSubsettedCallsetTask, +) +from loading_pipeline.lib.tasks.write_sample_qc_json import WriteSampleQCJsonTask + + +@luigi.util.inherits(BaseLoadingRunParams) +class WriteMetadataForRunTask(luigi.Task): + def output(self) -> luigi.Target: + return GCSorLocalTarget( + metadata_for_run_path( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + ) + + def requires(self) -> list[luigi.Task]: + requirements = [ + self.clone( + WriteRemappedAndSubsettedCallsetTask, + project_i=i, + ) + for i in range(len(self.project_guids)) + ] + if ( + FeatureFlag.EXPECT_TDR_METRICS + and not self.skip_expect_tdr_metrics + and self.dataset_type.expect_tdr_metrics( + self.reference_genome, + ) + ): + requirements = [ + *requirements, + self.clone(WriteSampleQCJsonTask), + ] + return requirements + + def run(self) -> None: + metadata_json = { + 'callsets': [self.callset_path], + 'run_id': self.run_id, + 'sample_type': self.sample_type.value, + 'project_guids': self.project_guids, + 'family_samples': {}, + 'failed_family_samples': { + 'missing_samples': {}, + 'relatedness_check': {}, + 'sex_check': {}, + 'ploidy_check': {}, + }, + 'relatedness_check_file_path': relatedness_check_tsv_path( + self.reference_genome, + self.dataset_type, + self.callset_path, + ), + 'sample_qc': {}, + } + sample_qc_loadable_samples = {} + # NB: the trailing WriteSampleQCJsonTask output is conditionally + # present in requires(), so slice by project count rather than + # dropping the last input. + for remapped_and_subsetted_callset in self.input()[: len(self.project_guids)]: + callset_mt = hl.read_matrix_table(remapped_and_subsetted_callset.path) + collected_globals = callset_mt.globals.collect()[0] + metadata_json['family_samples'] = { + **collected_globals['family_samples'], + **metadata_json['family_samples'], + } + sample_qc_loadable_samples = { + *{ + sample + for family_samples in collected_globals['family_samples'].values() + for sample in family_samples + }, + *sample_qc_loadable_samples, + } + for key in [ + 'missing_samples', + 'relatedness_check', + 'sex_check', + 'ploidy_check', + ]: + metadata_json['failed_family_samples'][key] = { + **collected_globals['failed_family_samples'][key], + **metadata_json['failed_family_samples'][key], + } + sample_qc_loadable_samples = { + *{ + sample + for meta in collected_globals['failed_family_samples'][ + key + ].values() + for sample in meta['samples'] + }, + *sample_qc_loadable_samples, + } + if ( + FeatureFlag.EXPECT_TDR_METRICS + and not self.skip_expect_tdr_metrics + and self.dataset_type.expect_tdr_metrics( + self.reference_genome, + ) + ): + with hfs.open( + sample_qc_json_path( + self.reference_genome, + self.dataset_type, + self.callset_path, + ), + ) as f: + metadata_json['sample_qc'] = { + k: v + for k, v in json.load(f).items() + if k in sample_qc_loadable_samples + } + if not metadata_json['family_samples']: + msg = 'Found no loadable families in the callset.' + raise RuntimeError(msg) + empty_families = [ + family_guid + for family_guid, samples in metadata_json['family_samples'].items() + if not samples + ] + if empty_families: + msg = f'Found families with no loadable samples: {sorted(empty_families)}' + raise RuntimeError(msg) + with self.output().open('w') as f: + json.dump(metadata_json, f) diff --git a/loading_pipeline/lib/tasks/write_metadata_for_run_test.py b/loading_pipeline/lib/tasks/write_metadata_for_run_test.py new file mode 100644 index 0000000000..2b5dc7a22d --- /dev/null +++ b/loading_pipeline/lib/tasks/write_metadata_for_run_test.py @@ -0,0 +1,188 @@ +import json +from unittest import mock +from unittest.mock import Mock + +import luigi.worker + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS +from loading_pipeline.lib.paths import relatedness_check_tsv_path +from loading_pipeline.lib.tasks.write_metadata_for_run import WriteMetadataForRunTask +from loading_pipeline.lib.test.misc import copy_project_pedigree_to_mocked_dir +from loading_pipeline.lib.test.mock_complete_task import MockCompleteTask +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + +TEST_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' +TEST_PEDIGREE_3_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_3_remap.tsv' +TEST_PEDIGREE_4_REMAP_2 = ( + 'loading_pipeline/var/test/pedigrees/test_pedigree_4_remap_2.tsv' +) +TEST_SAMPLE_QC_JSON = 'loading_pipeline/var/test/sample_qc_1.json' + + +class WriteMetadataForRunTaskTest(MockedDatarootTestCase): + @mock.patch( + 'loading_pipeline.lib.tasks.write_metadata_for_run.sample_qc_json_path', + lambda *_: TEST_SAMPLE_QC_JSON, + ) + @mock.patch('loading_pipeline.lib.tasks.write_metadata_for_run.FeatureFlag') + @mock.patch( + 'loading_pipeline.lib.tasks.write_sex_check_table.WriteTDRMetricsFilesTask', + ) + @mock.patch( + 'loading_pipeline.lib.tasks.write_metadata_for_run.WriteSampleQCJsonTask', + ) + def test_write_metadata_for_run_task( + self, + write_sample_qc_json_task: Mock, + write_tdr_metrics_task: Mock, + mock_ff: Mock, + ) -> None: + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_3_REMAP, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0113_test_project', + ) + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_4_REMAP_2, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0114_project4', + ) + mock_ff.EXPECT_TDR_METRICS = True + write_tdr_metrics_task.return_value = MockCompleteTask() + write_sample_qc_json_task.return_value = MockCompleteTask() + worker = luigi.worker.Worker() + write_metadata_for_run_task = WriteMetadataForRunTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path=TEST_VCF, + project_guids=['R0113_test_project', 'R0114_project4'], + validations_to_skip=[ALL_VALIDATIONS], + run_id='run_123456', + ) + worker.add(write_metadata_for_run_task) + worker.run() + self.assertTrue( + 'run_123456/metadata.json' in write_metadata_for_run_task.output().path, + ) + self.assertTrue(write_metadata_for_run_task.complete()) + with write_metadata_for_run_task.output().open('r') as f: + self.assertDictEqual( + json.load(f), + { + 'callsets': [TEST_VCF], + 'project_guids': ['R0113_test_project', 'R0114_project4'], + 'failed_family_samples': { + 'missing_samples': { + 'efg_1': { + # This sample is present in the callset, but intentionally + # mapped away + 'samples': ['NA20888_1'], + 'reasons': ["Missing samples: {'NA20888_1'}"], + }, + }, + 'relatedness_check': {}, + 'sex_check': {}, + 'ploidy_check': {}, + }, + 'family_samples': { + 'abc_1': [ + 'HG00731_1', + 'HG00732_1', + 'HG00733_1', + ], + '123_1': ['NA19675_1'], + '234_1': ['NA19678_1'], + '345_1': ['NA19679_1'], + '456_1': ['NA20870_1'], + '567_1': ['NA20872_1'], + '678_1': ['NA20874_1'], + '789_1': ['NA20875_1'], + '890_1': ['NA20876_1'], + '901_1': ['NA20877_1'], + 'bcd_1': ['NA20878_1'], + 'cde_1': ['NA20881_1'], + 'def_1': ['NA20885_1'], + }, + 'run_id': 'run_123456', + 'sample_type': SampleType.WGS.value, + 'relatedness_check_file_path': relatedness_check_tsv_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_VCF, + ), + 'sample_qc': { + 'HG00731_1': {'filter_flags': ['coverage', 'contamination']}, + 'HG00732_1': {'filter_flags': ['coverage']}, + 'HG00733_1': {'filter_flags': ['contamination']}, + 'NA19675_1': {'filter_flags': []}, + 'NA20888_1': {'filter_flags': ['sample_failed']}, + }, + }, + ) + + @mock.patch('loading_pipeline.lib.tasks.write_metadata_for_run.FeatureFlag') + def test_write_metadata_for_run_task_without_tdr_metrics( + self, + mock_ff: Mock, + ) -> None: + # When WriteSampleQCJsonTask is not a requirement, every project's + # remapped and subsetted callset must still be collected. + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_3_REMAP, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0113_test_project', + ) + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_4_REMAP_2, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0114_project4', + ) + mock_ff.EXPECT_TDR_METRICS = False + worker = luigi.worker.Worker() + write_metadata_for_run_task = WriteMetadataForRunTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path=TEST_VCF, + project_guids=['R0113_test_project', 'R0114_project4'], + validations_to_skip=[ALL_VALIDATIONS], + run_id='run_123457', + ) + worker.add(write_metadata_for_run_task) + worker.run() + self.assertTrue(write_metadata_for_run_task.complete()) + with write_metadata_for_run_task.output().open('r') as f: + metadata_json = json.load(f) + self.assertDictEqual( + metadata_json['family_samples'], + { + 'abc_1': [ + 'HG00731_1', + 'HG00732_1', + 'HG00733_1', + ], + '123_1': ['NA19675_1'], + '234_1': ['NA19678_1'], + '345_1': ['NA19679_1'], + '456_1': ['NA20870_1'], + '567_1': ['NA20872_1'], + '678_1': ['NA20874_1'], + '789_1': ['NA20875_1'], + '890_1': ['NA20876_1'], + '901_1': ['NA20877_1'], + 'bcd_1': ['NA20878_1'], + 'cde_1': ['NA20881_1'], + 'def_1': ['NA20885_1'], + }, + ) + self.assertDictEqual(metadata_json['sample_qc'], {}) diff --git a/loading_pipeline/lib/tasks/write_new_variants_table.py b/loading_pipeline/lib/tasks/write_new_variants_table.py new file mode 100644 index 0000000000..5922b54c7c --- /dev/null +++ b/loading_pipeline/lib/tasks/write_new_variants_table.py @@ -0,0 +1,222 @@ +import math + +import hail as hl +import hailtop.fs as hfs +import luigi +import luigi.util + +from loading_pipeline.lib.annotations.fields import get_fields +from loading_pipeline.lib.annotations.misc import ( + annotate_formatting_annotation_enum_globals, +) +from loading_pipeline.lib.misc.callsets import get_callset_ht +from loading_pipeline.lib.misc.io import checkpoint, remap_pedigree_hash +from loading_pipeline.lib.misc.math import constrain +from loading_pipeline.lib.misc.vep import run_vep +from loading_pipeline.lib.paths import ( + new_variants_table_path, + project_pedigree_path, + valid_reference_dataset_path, + variant_annotations_table_path, +) +from loading_pipeline.lib.reference_datasets.gencode.mapping_gene_ids import ( + load_gencode_ensembl_to_refseq_id, + load_gencode_gene_symbol_to_gene_id, +) +from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset +from loading_pipeline.lib.tasks.base.base_loading_run_params import ( + BaseLoadingRunParams, +) +from loading_pipeline.lib.tasks.base.base_write import BaseWriteTask +from loading_pipeline.lib.tasks.files import GCSorLocalTarget +from loading_pipeline.lib.tasks.write_metadata_for_run import ( + WriteMetadataForRunTask, +) + +VARIANTS_PER_VEP_PARTITION = 1e3 +MIN_PARTITIONS = 10 +MAX_PARTITIONS = 10000 +GENCODE_RELEASE = 42 +GENCODE_FOR_VEP_RELEASE = 44 + + +@luigi.util.inherits(BaseLoadingRunParams) +class WriteNewVariantsTableTask(BaseWriteTask): + @property + def annotation_dependencies(self) -> dict[str, hl.Table]: + deps = {} + for reference_dataset in ReferenceDataset: + if ( + reference_dataset.formatting_annotation + and self.dataset_type + in reference_dataset.dataset_types(self.reference_genome) + ): + deps[f'{reference_dataset.value}_ht'] = hl.read_table( + valid_reference_dataset_path( + self.reference_genome, + reference_dataset, + ), + ) + + if self.dataset_type.has_gencode_ensembl_to_refseq_id_mapping( + self.reference_genome, + ): + deps['gencode_ensembl_to_refseq_id_mapping'] = hl.literal( + load_gencode_ensembl_to_refseq_id(GENCODE_FOR_VEP_RELEASE), + ) + if self.dataset_type.has_gencode_gene_symbol_to_gene_id_mapping: + deps['gencode_gene_symbol_to_gene_id_mapping'] = hl.literal( + load_gencode_gene_symbol_to_gene_id(GENCODE_RELEASE), + ) + return deps + + def output(self) -> luigi.Target: + return GCSorLocalTarget( + new_variants_table_path( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + ) + + def requires(self) -> list[luigi.Task]: + return [ + self.clone(WriteMetadataForRunTask), + ] + + def complete(self) -> bool: + # NOTE: Special hack for ClickHouse migration tasks which + # do not have a callset/projects to load. + if len(self.project_guids) == 0: + return super().complete() + return super().complete() and hl.eval( + hl.bind( + lambda updates: hl.all( + [ + updates.contains( + hl.Struct( + callset=self.callset_path, + project_guid=project_guid, + remap_pedigree_hash=remap_pedigree_hash( + project_pedigree_path( + self.reference_genome, + self.dataset_type, + self.sample_type, + project_guid, + ), + ), + ), + ) + for project_guid in self.project_guids + ], + ), + hl.read_table(self.output().path).updates, + ), + ) + + def create_table(self) -> hl.Table: + callset_ht = get_callset_ht( + self.reference_genome, + self.dataset_type, + self.callset_path, + self.project_guids, + ) + + # 1) Identify new variants. + if hfs.exists( + variant_annotations_table_path( + self.reference_genome, + self.dataset_type, + ), + ): + annotations_ht = hl.read_table( + variant_annotations_table_path( + self.reference_genome, + self.dataset_type, + ), + ) + # Gracefully handle case for on-premises uses + # where key_ field is not present and migration was not run. + if not hasattr(annotations_ht, 'key_'): + annotations_ht = annotations_ht.add_index(name='key_') + annotations_ht = annotations_ht.annotate_globals( + max_key_=(annotations_ht.count() - 1), + ) + curr_max_key_ = annotations_ht.index_globals().max_key_ + new_variants_ht = callset_ht.repartition( + # Repartition this join to improve performance + constrain( + callset_ht.n_partitions() * 100, + MIN_PARTITIONS, + MAX_PARTITIONS, + ), + ).anti_join(annotations_ht) + else: + curr_max_key_ = -1 + new_variants_ht = callset_ht + + # Annotate new variants with VEP. + # Note about the repartition: our work here is cpu/memory bound and + # proportional to the number of new variants. Our default partitioning + # will under-partition in that regard, so we split up our work + # with a partitioning scheme local to this task. + new_variants_count = new_variants_ht.count() + new_variants_ht = new_variants_ht.repartition( + constrain( + math.ceil(new_variants_count / VARIANTS_PER_VEP_PARTITION), + MIN_PARTITIONS, + MAX_PARTITIONS, + ), + ) + new_variants_ht = run_vep( + new_variants_ht, + self.dataset_type, + self.reference_genome, + ) + # Adding an arbitrary checkpoint here, seems to help + new_variants_ht, _ = checkpoint(new_variants_ht) + + # An additional call to "distinct()" as a safety measure. + # At least one case a duplicate variants has slipped through + # this method, with the best hypothesis being that + # the combination of VEP/repartition is potentially unsafe. + new_variants_ht = new_variants_ht.distinct() + + # Select down to the formatting annotations fields and + # any reference dataset collection annotations. + new_variants_ht = new_variants_ht.select( + **get_fields( + new_variants_ht, + self.dataset_type.formatting_annotation_fns(self.reference_genome), + **self.annotation_dependencies, + **self.param_kwargs, + ), + ) + + # Add serial integer index + new_variants_ht = new_variants_ht.add_index(name='key_') + new_variants_ht = new_variants_ht.transmute( + key_=new_variants_ht.key_ + curr_max_key_ + 1, + ) + new_variants_ht = annotate_formatting_annotation_enum_globals( + new_variants_ht, + self.reference_genome, + self.dataset_type, + ) + return new_variants_ht.annotate_globals( + updates={ + hl.Struct( + callset=self.callset_path, + project_guid=project_guid, + remap_pedigree_hash=remap_pedigree_hash( + project_pedigree_path( + self.reference_genome, + self.dataset_type, + self.sample_type, + project_guid, + ), + ), + ) + for project_guid in self.project_guids + }, + ) diff --git a/loading_pipeline/lib/tasks/write_postprocessed_callset.py b/loading_pipeline/lib/tasks/write_postprocessed_callset.py new file mode 100644 index 0000000000..d82258e98a --- /dev/null +++ b/loading_pipeline/lib/tasks/write_postprocessed_callset.py @@ -0,0 +1,96 @@ +import hail as hl +import luigi +import luigi.util + +from loading_pipeline.lib.misc.callsets import get_additional_row_fields +from loading_pipeline.lib.misc.io import ( + split_multi_hts, +) +from loading_pipeline.lib.misc.sv import deduplicate_merged_sv_concordance_calls +from loading_pipeline.lib.misc.vets import annotate_vets +from loading_pipeline.lib.paths import ( + imported_callset_path, + postprocessed_callset_path, + variant_annotations_table_path, +) +from loading_pipeline.lib.tasks.base.base_loading_run_params import BaseLoadingRunParams +from loading_pipeline.lib.tasks.base.base_write import BaseWriteTask +from loading_pipeline.lib.tasks.files import GCSorLocalTarget +from loading_pipeline.lib.tasks.write_imported_callset import WriteImportedCallsetTask +from loading_pipeline.lib.tasks.write_validation_errors_for_run import ( + with_persisted_validation_errors, +) + + +@luigi.util.inherits(BaseLoadingRunParams) +class WritePostprocessedCallsetTask(BaseWriteTask): + def complete(self) -> luigi.Target: + if super().complete(): + mt = hl.read_matrix_table(self.output().path) + # Handle case where callset was previously imported + # with a different sex/relatedness flag. + additional_row_fields = get_additional_row_fields( + mt, + self.reference_genome, + self.dataset_type, + self.skip_check_sex_and_relatedness, + ) + return all(hasattr(mt, field) for field in additional_row_fields) + return False + + def output(self) -> luigi.Target: + return GCSorLocalTarget( + postprocessed_callset_path( + self.reference_genome, + self.dataset_type, + self.callset_path, + ), + ) + + def requires(self) -> list[luigi.Task]: + return [self.clone(WriteImportedCallsetTask)] + + @with_persisted_validation_errors + def create_table(self) -> hl.MatrixTable: + mt = hl.read_matrix_table( + imported_callset_path( + self.reference_genome, + self.dataset_type, + self.callset_path, + ), + ) + + if self.dataset_type.has_multi_allelic_variants: + # NB: throws SeqrValidationError + mt = split_multi_hts( + mt, + 'validate_no_duplicate_variants' in self.validations_to_skip, + ) + if self.dataset_type.re_key_by_seqr_internal_truth_vid and hasattr( + mt, + 'info.SEQR_INTERNAL_TRUTH_VID', + ): + mt = deduplicate_merged_sv_concordance_calls( + mt, + hl.read_table( + variant_annotations_table_path( + self.reference_genome, + self.dataset_type, + ), + ), + ) + mt = mt.key_rows_by( + variant_id=hl.if_else( + hl.is_defined(mt['info.SEQR_INTERNAL_TRUTH_VID']), + mt['info.SEQR_INTERNAL_TRUTH_VID'], + mt.variant_id, + ), + ) + + # Special handling of variant-level filter annotation for VETs filters. + # The annotations are present on the sample-level FT field but are + # expected upstream on "filters". + mt = annotate_vets(mt) + return mt.select_globals( + callset_path=self.callset_path, + ) diff --git a/loading_pipeline/lib/tasks/write_relatedness_check_table.py b/loading_pipeline/lib/tasks/write_relatedness_check_table.py new file mode 100644 index 0000000000..579edc6f2f --- /dev/null +++ b/loading_pipeline/lib/tasks/write_relatedness_check_table.py @@ -0,0 +1,44 @@ +import hail as hl +import luigi +import luigi.util + +from loading_pipeline.lib.methods.relatedness import call_relatedness +from loading_pipeline.lib.paths import ( + relatedness_check_table_path, +) +from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset +from loading_pipeline.lib.tasks.base.base_loading_run_params import BaseLoadingRunParams +from loading_pipeline.lib.tasks.base.base_write import BaseWriteTask +from loading_pipeline.lib.tasks.files import GCSorLocalTarget +from loading_pipeline.lib.tasks.reference_data.updated_reference_dataset import ( + UpdatedReferenceDatasetTask, +) +from loading_pipeline.lib.tasks.validate_callset import ValidateCallsetTask + + +@luigi.util.inherits(BaseLoadingRunParams) +class WriteRelatednessCheckTableTask(BaseWriteTask): + def output(self) -> luigi.Target: + return GCSorLocalTarget( + relatedness_check_table_path( + self.reference_genome, + self.dataset_type, + self.callset_path, + ), + ) + + def requires(self): + return [ + self.clone(ValidateCallsetTask), + self.clone( + UpdatedReferenceDatasetTask, + reference_dataset=ReferenceDataset.gnomad_qc, + ), + ] + + def create_table(self) -> hl.Table: + callset_mt = hl.read_matrix_table(self.input()[0].path) + return call_relatedness( + callset_mt, + hl.read_table(self.input()[1].path) if len(self.input()) > 1 else None, + ) diff --git a/loading_pipeline/lib/tasks/write_relatedness_check_table_test.py b/loading_pipeline/lib/tasks/write_relatedness_check_table_test.py new file mode 100644 index 0000000000..7cc814a5fa --- /dev/null +++ b/loading_pipeline/lib/tasks/write_relatedness_check_table_test.py @@ -0,0 +1,120 @@ +import shutil +from unittest.mock import patch + +import hail as hl +import luigi.worker + +from loading_pipeline.lib.core import ( + DatasetType, + ReferenceGenome, + SampleType, +) +from loading_pipeline.lib.misc.io import import_vcf +from loading_pipeline.lib.paths import ( + postprocessed_callset_path, + relatedness_check_table_path, + valid_reference_dataset_path, +) +from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset +from loading_pipeline.lib.tasks.write_relatedness_check_table import ( + WriteRelatednessCheckTableTask, +) +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + +TEST_GNOMAD_QC_HT = ( + 'loading_pipeline/var/test/reference_datasets/GRCh38/gnomad_qc/1.0.ht' +) +TEST_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' +TEST_RUN_ID = 'manual__2024-04-03' + + +class WriteRelatednessCheckTableTaskTest(MockedDatarootTestCase): + def setUp(self) -> None: + super().setUp() + shutil.copytree( + TEST_GNOMAD_QC_HT, + valid_reference_dataset_path( + ReferenceGenome.GRCh38, + ReferenceDataset.gnomad_qc, + ), + ) + + # Force imported callset to be complete + ht = import_vcf(TEST_VCF, ReferenceGenome.GRCh38) + ht = ht.annotate_globals(validated_sample_type=SampleType.WGS.value) + ht = ht.annotate_rows(**{'info.AF': ht.info.AF}) + ht.write( + postprocessed_callset_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_VCF, + ), + ) + + def test_relatedness_check_table_task_gnomad_qc_updated( + self, + ) -> None: + self.assertEqual( + hl.eval( + hl.read_table( + valid_reference_dataset_path( + ReferenceGenome.GRCh38, + ReferenceDataset.gnomad_qc, + ), + ).version, + ), + '1.0', + ) + with ( + patch.object( + ReferenceDataset, + 'version', + return_value='2.0', + ), + patch.object( + ReferenceDataset, + 'get_ht', + lambda *_: hl.Table.parallelize( + [], + hl.tstruct( + locus=hl.tlocus('GRCh38'), + alleles=hl.tarray(hl.tstr), + ), + key=['locus', 'alleles'], + globals=hl.Struct(version='2.0'), + ), + ), + ): + worker = luigi.worker.Worker() + task = WriteRelatednessCheckTableTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id=TEST_RUN_ID, + sample_type=SampleType.WGS, + callset_path=TEST_VCF, + ) + worker.add(task) + worker.run() + self.assertTrue(task.complete()) + self.assertEqual( + hl.eval( + hl.read_table( + valid_reference_dataset_path( + ReferenceGenome.GRCh38, + ReferenceDataset.gnomad_qc, + ), + ).version, + ), + '2.0', + ) + ht = hl.read_table( + relatedness_check_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_VCF, + ), + ) + self.assertEqual( + ht.collect(), + [], + ) diff --git a/loading_pipeline/lib/tasks/write_relatedness_check_tsv.py b/loading_pipeline/lib/tasks/write_relatedness_check_tsv.py new file mode 100644 index 0000000000..07210e2620 --- /dev/null +++ b/loading_pipeline/lib/tasks/write_relatedness_check_tsv.py @@ -0,0 +1,29 @@ +import hail as hl +import luigi +import luigi.util + +from loading_pipeline.lib.paths import relatedness_check_tsv_path +from loading_pipeline.lib.tasks.base.base_loading_run_params import BaseLoadingRunParams +from loading_pipeline.lib.tasks.files import GCSorLocalTarget +from loading_pipeline.lib.tasks.write_relatedness_check_table import ( + WriteRelatednessCheckTableTask, +) + + +@luigi.util.inherits(BaseLoadingRunParams) +class WriteRelatednessCheckTsvTask(luigi.Task): + def output(self) -> luigi.Target: + return GCSorLocalTarget( + relatedness_check_tsv_path( + self.reference_genome, + self.dataset_type, + self.callset_path, + ), + ) + + def requires(self): + return [self.clone(WriteRelatednessCheckTableTask)] + + def run(self): + ht = hl.read_table(self.input()[0].path) + ht.export(self.output().path) diff --git a/loading_pipeline/lib/tasks/write_relatedness_check_tsv_test.py b/loading_pipeline/lib/tasks/write_relatedness_check_tsv_test.py new file mode 100644 index 0000000000..35a9956f78 --- /dev/null +++ b/loading_pipeline/lib/tasks/write_relatedness_check_tsv_test.py @@ -0,0 +1,53 @@ +import shutil + +import luigi.worker + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.paths import relatedness_check_table_path +from loading_pipeline.lib.tasks.write_relatedness_check_tsv import ( + WriteRelatednessCheckTsvTask, +) +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + +TEST_RELATEDNESS_CHECK_1 = ( + 'loading_pipeline/var/test/relatedness_check/test_relatedness_check_1.ht' +) +TEST_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' +TEST_RUN_ID = 'manual__2024-04-03' + + +class WriteRelatednessCheckTsvTaskTest(MockedDatarootTestCase): + def setUp(self) -> None: + super().setUp() + shutil.copytree( + TEST_RELATEDNESS_CHECK_1, + relatedness_check_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_VCF, + ), + ) + + def test_write_relatedness_check_tsv_task( + self, + ) -> None: + worker = luigi.worker.Worker() + task = WriteRelatednessCheckTsvTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + callset_path=TEST_VCF, + run_id=TEST_RUN_ID, + sample_type=SampleType.WES, + ) + worker.add(task) + worker.run() + self.assertTrue(task.complete()) + with task.output().open('r') as f: + lines = f.readlines() + expected_lines = [ + 'i\tj\tibd0\tibd1\tibd2\tpi_hat\n', + 'HG00731_1\tHG00733_1\t0\t1\t0\t5.0000e-01\n', + 'HG00732_1\tHG00733_1\t0\t1\t0\t5.0000e-01\n', + ] + for expected_line, actual_line in zip(expected_lines, lines, strict=False): + self.assertEqual(expected_line, actual_line) diff --git a/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py b/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py new file mode 100644 index 0000000000..403c9d78d5 --- /dev/null +++ b/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py @@ -0,0 +1,242 @@ +import hail as hl +import luigi +import luigi.util + +from loading_pipeline.lib.core.feature_flag import FeatureFlag +from loading_pipeline.lib.misc.family_loading_failures import ( + get_families_failed_imputed_sex_ploidy, + get_families_failed_missing_samples, + get_families_failed_relatedness_check, + get_families_failed_sex_check, +) +from loading_pipeline.lib.misc.io import ( + import_pedigree, + remap_pedigree_hash, +) +from loading_pipeline.lib.misc.pedigree import ( + parse_pedigree_ht_to_families, + parse_pedigree_ht_to_remap_ht, +) +from loading_pipeline.lib.misc.sample_ids import remap_sample_ids, subset_samples +from loading_pipeline.lib.misc.sv import overwrite_male_non_par_calls +from loading_pipeline.lib.misc.validation import SeqrValidationError +from loading_pipeline.lib.paths import ( + project_pedigree_path, + relatedness_check_table_path, + remapped_and_subsetted_callset_path, +) +from loading_pipeline.lib.tasks.base.base_loading_run_params import BaseLoadingRunParams +from loading_pipeline.lib.tasks.base.base_write import BaseWriteTask +from loading_pipeline.lib.tasks.files import GCSorLocalTarget, RawFileTask +from loading_pipeline.lib.tasks.validate_callset import ValidateCallsetTask +from loading_pipeline.lib.tasks.write_relatedness_check_tsv import ( + WriteRelatednessCheckTsvTask, +) +from loading_pipeline.lib.tasks.write_sex_check_table import WriteSexCheckTableTask +from loading_pipeline.lib.tasks.write_validation_errors_for_run import ( + with_persisted_validation_errors, +) + + +def format_failures(failed_families): + return { + f.family_guid: { + 'samples': sorted(f.samples.keys()), + 'reasons': reasons, + } + for f, reasons in failed_families.items() + } + + +@luigi.util.inherits(BaseLoadingRunParams) +class WriteRemappedAndSubsettedCallsetTask(BaseWriteTask): + project_i = luigi.IntParameter() + + def complete(self) -> luigi.Target: + if not super().complete(): + return False + mt = hl.read_matrix_table(self.output().path) + return bool( + hl.eval(mt.globals.family_samples), + ) and hl.eval( + mt.globals.remap_pedigree_hash + == remap_pedigree_hash( + project_pedigree_path( + self.reference_genome, + self.dataset_type, + self.sample_type, + self.project_guids[self.project_i], + ), + ), + ) + + def output(self) -> luigi.Target: + return GCSorLocalTarget( + remapped_and_subsetted_callset_path( + self.reference_genome, + self.dataset_type, + self.callset_path, + self.project_guids[self.project_i], + ), + ) + + def requires(self) -> list[luigi.Task]: + requirements = [ + self.clone(ValidateCallsetTask), + RawFileTask( + project_pedigree_path( + self.reference_genome, + self.dataset_type, + self.sample_type, + self.project_guids[self.project_i], + ), + ), + ] + if ( + FeatureFlag.CHECK_SEX_AND_RELATEDNESS + and self.dataset_type.check_sex_and_relatedness + and not self.skip_check_sex_and_relatedness + ): + requirements = [ + *requirements, + self.clone(WriteRelatednessCheckTsvTask), + self.clone(WriteSexCheckTableTask), + ] + return requirements + + @with_persisted_validation_errors + def create_table(self) -> hl.MatrixTable: + callset_mt = hl.read_matrix_table(self.input()[0].path) + pedigree_ht = import_pedigree(self.input()[1].path) + + # Remap, but only if the remap file is present! + remap_lookup = hl.empty_dict(hl.tstr, hl.tstr) + if 'remap_id' in pedigree_ht.row: + project_remap_ht = parse_pedigree_ht_to_remap_ht(pedigree_ht) + callset_mt = remap_sample_ids( + callset_mt, + project_remap_ht, + ) + remap_lookup = hl.dict( + {r.s: r.seqr_id for r in project_remap_ht.collect()}, + ) + + families = parse_pedigree_ht_to_families(pedigree_ht) + families_failed_missing_samples = get_families_failed_missing_samples( + callset_mt, + families, + ) + families_failed_relatedness_check = {} + families_failed_sex_check = {} + families_failed_imputed_sex_ploidy = {} + if ( + FeatureFlag.CHECK_SEX_AND_RELATEDNESS + and self.dataset_type.check_sex_and_relatedness + and not self.skip_check_sex_and_relatedness + ): + relatedness_check_ht = hl.read_table( + relatedness_check_table_path( + self.reference_genome, + self.dataset_type, + self.callset_path, + ), + ) + sex_check_ht = hl.read_table(self.input()[3].path) + families_failed_relatedness_check = get_families_failed_relatedness_check( + families - families_failed_missing_samples.keys(), + relatedness_check_ht, + remap_lookup, + ) + families_failed_imputed_sex_ploidy = get_families_failed_imputed_sex_ploidy( + families + - families_failed_missing_samples.keys() + - families_failed_relatedness_check.keys(), + callset_mt, + sex_check_ht, + ) + families_failed_sex_check = get_families_failed_sex_check( + families + - families_failed_missing_samples.keys() + - families_failed_relatedness_check.keys() + - families_failed_imputed_sex_ploidy.keys(), + sex_check_ht, + remap_lookup, + ) + + loadable_families = ( + families + - families_failed_missing_samples.keys() + - families_failed_relatedness_check.keys() + - families_failed_sex_check.keys() + - families_failed_imputed_sex_ploidy.keys() + ) + if not len(loadable_families): + msg = 'All families failed validation checks' + raise SeqrValidationError( + msg, + { + 'failed_family_samples': { + 'missing_samples': format_failures( + families_failed_missing_samples, + ), + 'relatedness_check': format_failures( + families_failed_relatedness_check, + ), + 'sex_check': format_failures(families_failed_sex_check), + 'ploidy_check': format_failures( + families_failed_imputed_sex_ploidy, + ), + }, + }, + ) + + mt = subset_samples( + callset_mt, + hl.Table.parallelize( + [ + {'s': sample_id} + for family in loadable_families + for sample_id in family.samples + ], + hl.tstruct(s=hl.dtype('str')), + key='s', + ), + ) + + if self.dataset_type.overwrite_male_non_par_calls: + mt = overwrite_male_non_par_calls(mt, loadable_families) + return mt.select_globals( + remap_pedigree_hash=remap_pedigree_hash( + project_pedigree_path( + self.reference_genome, + self.dataset_type, + self.sample_type, + self.project_guids[self.project_i], + ), + ), + family_samples=( + { + f.family_guid: sorted(f.samples.keys()) + for f in loadable_families + or hl.empty_dict(hl.tstr, hl.tarray(hl.tstr)) + } + ), + failed_family_samples=hl.Struct( + missing_samples=( + format_failures(families_failed_missing_samples) + or hl.empty_dict(hl.tstr, hl.tdict(hl.tstr, hl.tarray(hl.tstr))) + ), + relatedness_check=( + format_failures(families_failed_relatedness_check) + or hl.empty_dict(hl.tstr, hl.tdict(hl.tstr, hl.tarray(hl.tstr))) + ), + sex_check=( + format_failures(families_failed_sex_check) + or hl.empty_dict(hl.tstr, hl.tdict(hl.tstr, hl.tarray(hl.tstr))) + ), + ploidy_check=( + format_failures(families_failed_imputed_sex_ploidy) + or hl.empty_dict(hl.tstr, hl.tdict(hl.tstr, hl.tarray(hl.tstr))) + ), + ), + ) diff --git a/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset_test.py b/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset_test.py new file mode 100644 index 0000000000..590795424a --- /dev/null +++ b/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset_test.py @@ -0,0 +1,460 @@ +import json +import shutil +from unittest.mock import Mock, patch + +import hail as hl +import luigi.worker + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.misc.io import remap_pedigree_hash +from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS +from loading_pipeline.lib.paths import ( + relatedness_check_table_path, + sex_check_table_path, +) +from loading_pipeline.lib.tasks.write_remapped_and_subsetted_callset import ( + WriteRemappedAndSubsettedCallsetTask, +) +from loading_pipeline.lib.tasks.write_validation_errors_for_run import ( + UpdatedValidationErrorsForRunTask, +) +from loading_pipeline.lib.test.misc import copy_project_pedigree_to_mocked_dir +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + +TEST_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' +TEST_PEDIGREE_3_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_3_remap.tsv' +TEST_PEDIGREE_3_DIFFERENT_FAMILIES = ( + 'loading_pipeline/var/test/pedigrees/test_pedigree_3_different_families.tsv' +) +TEST_PEDIGREE_4_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_4_remap.tsv' +TEST_PEDIGREE_7 = 'loading_pipeline/var/test/pedigrees/test_pedigree_7.tsv' +TEST_SEX_CHECK_1 = 'loading_pipeline/var/test/sex_check/test_sex_check_1.ht' +TEST_RELATEDNESS_CHECK_1 = ( + 'loading_pipeline/var/test/relatedness_check/test_relatedness_check_1.ht' +) + +TEST_RUN_ID = 'manual__2024-04-03' + + +class WriteRemappedAndSubsettedCallsetTaskTest(MockedDatarootTestCase): + def setUp(self) -> None: + super().setUp() + # +-------------+---------------+ + # | s | predicted_sex | + # +-------------+---------------+ + # | str | str | + # +-------------+---------------+ + # | "HG00731_1" | "F" | + # | "HG00732_1" | "M" | + # | "HG00733_1" | "F" | + # | "NA19675_1" | "F" | + # | "NA19678_1" | "M" | + # | "NA19679_1" | "F" | + # | "NA20870_1" | "F" | + # | "NA20872_1" | "M" | + # | "NA20874_1" | "F" | + # | "NA20875_1" | "F" | + # | "NA20876_1" | "F" | + # | "NA20877_1" | "F" | + # | "NA20878_1" | "M" | + # | "NA20881_1" | "M" | + # | "NA20885_1" | "F" | + # | "NA20888_1" | "F" | + # +-------------+---------------+ + shutil.copytree( + TEST_SEX_CHECK_1, + sex_check_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_VCF, + ), + ) + # +-------------+-------------+-------+-------+-------+----------+ + # | i | j | ibd0 | ibd1 | ibd2 | pi_hat | + # +-------------+-------------+-------+-------+-------+----------+ + # | str | str | int32 | int32 | int32 | float64 | + # +-------------+-------------+-------+-------+-------+----------+ + # | "HG00731_1" | "HG00733_1" | 0 | 1 | 0 | 5.00e-01 | + # | "HG00732_1" | "HG00733_1" | 0 | 1 | 0 | 5.00e-01 | + # +-------------+-------------+-------+-------+-------+----------+ + shutil.copytree( + TEST_RELATEDNESS_CHECK_1, + relatedness_check_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_VCF, + ), + ) + + def test_write_remapped_and_subsetted_callset_task( + self, + ) -> None: + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_3_REMAP, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0113_test_project', + ) + worker = luigi.worker.Worker() + wrsc_task = WriteRemappedAndSubsettedCallsetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id=TEST_RUN_ID, + sample_type=SampleType.WGS, + callset_path=TEST_VCF, + project_guids=['R0113_test_project'], + project_i=0, + validations_to_skip=[ALL_VALIDATIONS], + skip_expect_tdr_metrics=True, + ) + worker.add(wrsc_task) + worker.run() + self.assertTrue(wrsc_task.complete()) + mt = hl.read_matrix_table(wrsc_task.output().path) + self.assertEqual(mt.count(), (30, 3)) + self.assertEqual( + mt.globals.collect(), + [ + hl.Struct( + remap_pedigree_hash=hl.eval( + remap_pedigree_hash( + TEST_PEDIGREE_3_REMAP, + ), + ), + failed_family_samples=hl.Struct( + missing_samples={}, + relatedness_check={}, + sex_check={}, + ploidy_check={}, + ), + family_samples={'abc_1': ['HG00731_1', 'HG00732_1', 'HG00733_1']}, + ), + ], + ) + + @patch( + 'loading_pipeline.lib.tasks.write_remapped_and_subsetted_callset.FeatureFlag', + ) + def test_write_remapped_and_subsetted_callset_task_failed_some_family_checks( + self, + mock_ff: Mock, + ) -> None: + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_4_REMAP, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0114_project4', + ) + mock_ff.CHECK_SEX_AND_RELATEDNESS = True + worker = luigi.worker.Worker() + wrsc_task = WriteRemappedAndSubsettedCallsetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id=TEST_RUN_ID, + sample_type=SampleType.WGS, + callset_path=TEST_VCF, + project_guids=['R0114_project4'], + project_i=0, + validations_to_skip=[ALL_VALIDATIONS], + skip_expect_tdr_metrics=True, + ) + worker.add(wrsc_task) + worker.run() + self.assertTrue(wrsc_task.complete()) + mt = hl.read_matrix_table(wrsc_task.output().path) + # NB: one "family"/"sample" has been removed because of a failed sex check, + # and 4 removed because of a failed ploidy check! + self.assertEqual(mt.count(), (30, 8)) + self.assertEqual( + mt.globals.collect(), + [ + hl.Struct( + remap_pedigree_hash=hl.eval( + remap_pedigree_hash( + TEST_PEDIGREE_4_REMAP, + ), + ), + family_samples={ + '123_1': ['NA19675_1'], + '345_1': ['NA19679_1'], + '456_1': ['NA20870_1'], + '678_1': ['NA20874_1'], + '789_1': ['NA20875_1'], + '890_1': ['NA20876_1'], + '901_1': ['NA20877_1'], + 'efg_1': ['NA20888_1'], + }, + failed_family_samples=hl.Struct( + missing_samples={}, + relatedness_check={}, + sex_check={ + 'def_1': { + 'reasons': [ + 'Sample NA20885_1 has pedigree sex M but imputed sex F', + ], + 'samples': ['NA20885_1'], + }, + }, + ploidy_check={ + '234_1': { + 'reasons': [ + "Found samples with misaligned ploidy with their provided imputed sex: ['NA19678_1']", + ], + 'samples': ['NA19678_1'], + }, + '567_1': { + 'reasons': [ + "Found samples with misaligned ploidy with their provided imputed sex: ['NA20872_1']", + ], + 'samples': ['NA20872_1'], + }, + 'bcd_1': { + 'reasons': [ + "Found samples with misaligned ploidy with their provided imputed sex: ['NA20878_1']", + ], + 'samples': ['NA20878_1'], + }, + 'cde_1': { + 'reasons': [ + "Found samples with misaligned ploidy with their provided imputed sex: ['NA20881_1']", + ], + 'samples': ['NA20881_1'], + }, + }, + ), + ), + ], + ) + + @patch( + 'loading_pipeline.lib.tasks.write_remapped_and_subsetted_callset.FeatureFlag', + ) + def test_write_remapped_and_subsetted_callset_task_all_families_failed( + self, + mock_ff: Mock, + ) -> None: + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_7, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0114_project4', + ) + mock_ff.CHECK_SEX_AND_RELATEDNESS = True + worker = luigi.worker.Worker() + wrsc_task = WriteRemappedAndSubsettedCallsetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id=TEST_RUN_ID, + sample_type=SampleType.WGS, + callset_path=TEST_VCF, + project_guids=['R0114_project4'], + project_i=0, + validations_to_skip=[ALL_VALIDATIONS], + skip_expect_tdr_metrics=True, + ) + worker.add(wrsc_task) + worker.run() + self.assertFalse(wrsc_task.complete()) + updated_validation_errors_task = UpdatedValidationErrorsForRunTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WES, + callset_path=TEST_VCF, + project_guids=['R0114_project4'], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + self.assertTrue(updated_validation_errors_task.complete()) + with updated_validation_errors_task.output().open('r') as f: + self.assertDictEqual( + json.load(f), + { + 'project_guids': ['R0114_project4'], + 'error_messages': ['All families failed validation checks'], + 'failed_family_samples': { + 'missing_samples': { + 'efg_1': { + 'samples': ['NA99999_1'], + 'reasons': ["Missing samples: {'NA99999_1'}"], + }, + }, + 'relatedness_check': {}, + 'sex_check': { + '890_1': { + 'samples': ['NA20876_1'], + 'reasons': [ + 'Sample NA20876_1 has pedigree sex M but imputed sex F', + ], + }, + '456_1': { + 'samples': ['NA20870_1'], + 'reasons': [ + 'Sample NA20870_1 has pedigree sex M but imputed sex F', + ], + }, + '123_1': { + 'samples': ['NA19675_1'], + 'reasons': [ + 'Sample NA19675_1 has pedigree sex M but imputed sex F', + ], + }, + '678_1': { + 'samples': ['NA20874_1'], + 'reasons': [ + 'Sample NA20874_1 has pedigree sex M but imputed sex F', + ], + }, + '789_1': { + 'samples': ['NA20875_1'], + 'reasons': [ + 'Sample NA20875_1 has pedigree sex M but imputed sex F', + ], + }, + '901_1': { + 'samples': ['NA20877_1'], + 'reasons': [ + 'Sample NA20877_1 has pedigree sex M but imputed sex F', + ], + }, + '345_1': { + 'samples': ['NA19679_1'], + 'reasons': [ + 'Sample NA19679_1 has pedigree sex M but imputed sex F', + ], + }, + 'def_1': { + 'samples': ['NA20885_1'], + 'reasons': [ + 'Sample NA20885_1 has pedigree sex M but imputed sex F', + ], + }, + }, + 'ploidy_check': { + '567_1': { + 'samples': ['NA20872_1'], + 'reasons': [ + "Found samples with misaligned ploidy with their provided imputed sex: ['NA20872_1']", + ], + }, + '234_1': { + 'samples': ['NA19678_1'], + 'reasons': [ + "Found samples with misaligned ploidy with their provided imputed sex: ['NA19678_1']", + ], + }, + 'bcd_1': { + 'samples': ['NA20878_1'], + 'reasons': [ + "Found samples with misaligned ploidy with their provided imputed sex: ['NA20878_1']", + ], + }, + 'cde_1': { + 'samples': ['NA20881_1'], + 'reasons': [ + "Found samples with misaligned ploidy with their provided imputed sex: ['NA20881_1']", + ], + }, + }, + }, + }, + ) + + @patch( + 'loading_pipeline.lib.tasks.write_remapped_and_subsetted_callset.FeatureFlag', + ) + def test_write_remapped_and_subsetted_callset_task_combined_validation_errors( + self, + mock_ff: Mock, + ) -> None: + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_3_DIFFERENT_FAMILIES, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0113_test_project', + ) + worker = luigi.worker.Worker() + + wrsc_task_1 = WriteRemappedAndSubsettedCallsetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id=TEST_RUN_ID, + sample_type=SampleType.WGS, + callset_path=TEST_VCF, + project_guids=['R0113_test_project'], + project_i=0, + validations_to_skip=[ALL_VALIDATIONS], + skip_expect_tdr_metrics=True, + ) + worker.add(wrsc_task_1) + worker.run() + + # Second run: load pedigree 7 where all families fail validation checks + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_7, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0114_project4', + ) + worker_2 = luigi.worker.Worker() + + wrsc_task_2 = WriteRemappedAndSubsettedCallsetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id=TEST_RUN_ID, + sample_type=SampleType.WGS, + callset_path=TEST_VCF, + project_guids=['R0114_project4'], + project_i=0, + validations_to_skip=[ALL_VALIDATIONS], + skip_expect_tdr_metrics=True, + ) + worker_2.add(wrsc_task_2) + worker_2.run() + + # Verify second task does not complete (all families failed) + self.assertFalse(wrsc_task_2.complete()) + + # Verify validation errors for second run + updated_validation_errors_task = UpdatedValidationErrorsForRunTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WES, + callset_path=TEST_VCF, + project_guids=['R0113_test_project', 'R0114_project4'], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + self.assertTrue(updated_validation_errors_task.complete()) + with updated_validation_errors_task.output().open('r') as f: + validation_errors = json.load(f) + + # Verify that all families failed in the second run + self.assertIn( + 'All families failed validation checks', + validation_errors['error_messages'], + ) + # Should have missing samples, sex checks, and ploidy checks all failing + failed_samples = validation_errors['failed_family_samples'] + self.assertGreater( + len(failed_samples['missing_samples']), + 0, + 'Expected missing_samples to have failures', + ) + self.assertGreater( + len(failed_samples['sex_check']), + 0, + 'Expected sex_check to have failures', + ) + self.assertGreater( + len(failed_samples['ploidy_check']), + 0, + 'Expected ploidy_check to have failures', + ) + # Verify that both project guids are in the validation errors + self.assertIn('R0113_test_project', validation_errors['project_guids']) + self.assertIn('R0114_project4', validation_errors['project_guids']) diff --git a/loading_pipeline/lib/tasks/write_sample_qc_json.py b/loading_pipeline/lib/tasks/write_sample_qc_json.py new file mode 100644 index 0000000000..e09c93086f --- /dev/null +++ b/loading_pipeline/lib/tasks/write_sample_qc_json.py @@ -0,0 +1,96 @@ +import json +from collections import defaultdict + +import hail as hl +import hailtop.fs as hfs +import luigi +import luigi.util +import onnx + +from loading_pipeline.lib.methods.sample_qc import call_sample_qc +from loading_pipeline.lib.misc.callsets import get_callset_mt +from loading_pipeline.lib.misc.io import checkpoint, import_tdr_qc_metrics +from loading_pipeline.lib.paths import ( + ancestry_model_rf_path, + sample_qc_json_path, + tdr_metrics_dir, +) +from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset +from loading_pipeline.lib.tasks.base.base_loading_run_params import BaseLoadingRunParams +from loading_pipeline.lib.tasks.files import GCSorLocalTarget, RawFileTask +from loading_pipeline.lib.tasks.reference_data.updated_reference_dataset import ( + UpdatedReferenceDatasetTask, +) +from loading_pipeline.lib.tasks.write_remapped_and_subsetted_callset import ( + WriteRemappedAndSubsettedCallsetTask, +) +from loading_pipeline.lib.tasks.write_tdr_metrics_files import WriteTDRMetricsFilesTask + + +@luigi.util.inherits(BaseLoadingRunParams) +class WriteSampleQCJsonTask(luigi.Task): + def output(self) -> luigi.Target: + return GCSorLocalTarget( + sample_qc_json_path( + self.reference_genome, + self.dataset_type, + self.callset_path, + ), + ) + + def requires(self): + remapped_and_subsetted_callsets = [ + self.clone( + WriteRemappedAndSubsettedCallsetTask, + project_i=i, + ) + for i in range(len(self.project_guids)) + ] + return [ + self.clone(WriteTDRMetricsFilesTask), + self.clone( + UpdatedReferenceDatasetTask, + reference_dataset=ReferenceDataset.gnomad_qc, + ), + RawFileTask(ancestry_model_rf_path()), + *remapped_and_subsetted_callsets, + ] + + def run(self): + callset_mt = get_callset_mt( + self.reference_genome, + self.dataset_type, + self.callset_path, + self.project_guids, + ) + callset_mt, _ = checkpoint(callset_mt) + tdr_metrics_ht = None + for tdr_metrics_file in hfs.ls( + tdr_metrics_dir(self.reference_genome, self.dataset_type), + ): + if not tdr_metrics_ht: + tdr_metrics_ht = import_tdr_qc_metrics(tdr_metrics_file.path) + continue + tdr_metrics_ht = tdr_metrics_ht.union( + import_tdr_qc_metrics(tdr_metrics_file.path), + ) + pop_pca_loadings_ht = hl.read_table(self.input()[1].path) + with hfs.open(self.input()[2].path, 'rb') as f: + ancestry_rf_model = onnx.load(f) + callset_mt = call_sample_qc( + callset_mt, + tdr_metrics_ht, + pop_pca_loadings_ht, + ancestry_rf_model, + self.sample_type, + ) + ht = callset_mt.cols() + sample_qc_dict = defaultdict(dict) + for row in ht.flatten().collect(): + r = dict(row) + sample_id = r.pop('s') + for field, value in r.items(): + sample_qc_dict[sample_id][field] = value + + with self.output().open('w') as f: + json.dump(sample_qc_dict, f) diff --git a/loading_pipeline/lib/tasks/write_sample_qc_json_test.py b/loading_pipeline/lib/tasks/write_sample_qc_json_test.py new file mode 100644 index 0000000000..1c2709c9b7 --- /dev/null +++ b/loading_pipeline/lib/tasks/write_sample_qc_json_test.py @@ -0,0 +1,269 @@ +import json +import os +import shutil +from unittest.mock import Mock, patch + +import hail as hl +import hailtop.fs as hfs +import luigi.worker + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS +from loading_pipeline.lib.paths import ancestry_model_rf_path, tdr_metrics_dir +from loading_pipeline.lib.tasks.write_sample_qc_json import WriteSampleQCJsonTask +from loading_pipeline.lib.test.misc import copy_project_pedigree_to_mocked_dir +from loading_pipeline.lib.test.mock_complete_task import MockCompleteTask +from loading_pipeline.lib.test.mocked_reference_datasets_testcase import ( + MockedReferenceDatasetsTestCase, +) + +TEST_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' +TEST_PEDIGREE_3_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_3_remap.tsv' +TEST_TDR_METRICS_FILE = 'loading_pipeline/var/test/tdr_metrics.tsv' +TEST_RUN_ID = 'manual__2024-04-03' + +PCA_SCORES = [0.00212, 0.011, 0.0105, 0.161, 0.026] + [0.1 for _ in range(15)] +EXPECTED_ANC_PROBABILITIES = { + 'prob_afr': 0.02, + 'prob_ami': 0.0, + 'prob_amr': 0.02, + 'prob_asj': 0.9, + 'prob_eas': 0.0, + 'prob_fin': 0.0, + 'prob_mid': 0.0, + 'prob_nfe': 0.05, + 'prob_sas': 0.01, +} +TEST_ANCESTRY_IMPUTATION_MODEL_PATH = ( + 'loading_pipeline/var/test/ancestry_imputation_model.onnx' +) + + +class WriteSampleQCJsonTaskTest(MockedReferenceDatasetsTestCase): + @patch('loading_pipeline.lib.methods.sample_qc.assign_population_pcs') + @patch('loading_pipeline.lib.methods.sample_qc.pc_project') + @patch('loading_pipeline.lib.tasks.write_sample_qc_json.WriteTDRMetricsFilesTask') + def test_call_sample_qc( + self, + mock_tdr_task: Mock, + mock_pc_project: Mock, + mock_assign_population_pcs: Mock, + ) -> None: + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_3_REMAP, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0113_test_project', + ) + os.makedirs( + os.path.dirname(ancestry_model_rf_path()), + exist_ok=True, + ) + shutil.copy2(TEST_ANCESTRY_IMPUTATION_MODEL_PATH, ancestry_model_rf_path()) + os.makedirs( + tdr_metrics_dir(ReferenceGenome.GRCh38, DatasetType.SNV_INDEL), + exist_ok=True, + ) + shutil.copy2( + TEST_TDR_METRICS_FILE, + tdr_metrics_dir(ReferenceGenome.GRCh38, DatasetType.SNV_INDEL), + ) + mock_tdr_task.return_value = MockCompleteTask() + mock_pc_project.return_value = hl.Table.parallelize( + [ + { + 's': sample_id, + 'scores': PCA_SCORES, + } + for sample_id in ('HG00731', 'HG00732', 'HG00733', 'NA19675') + ], + hl.tstruct( + s=hl.tstr, + scores=hl.tarray(hl.tfloat64), + ), + key='s', + ) + mock_assign_population_pcs.return_value = ( + hl.Table.parallelize( + [ + { + 's': sample_id, + 'pca_scores': PCA_SCORES, + 'qc_pop': 'asj', + **EXPECTED_ANC_PROBABILITIES, + } + for sample_id in ('HG00731', 'HG00732', 'HG00733', 'NA19675') + ], + hl.tstruct( + s=hl.tstr, + pca_scores=hl.tarray(hl.tfloat64), + qc_pop=hl.tstr, + prob_afr=hl.tfloat64, + prob_ami=hl.tfloat64, + prob_amr=hl.tfloat64, + prob_asj=hl.tfloat64, + prob_eas=hl.tfloat64, + prob_fin=hl.tfloat64, + prob_mid=hl.tfloat64, + prob_nfe=hl.tfloat64, + prob_sas=hl.tfloat64, + ), + key='s', + ), + None, + ) + worker = luigi.worker.Worker() + task = WriteSampleQCJsonTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id=TEST_RUN_ID, + sample_type=SampleType.WGS, + callset_path=TEST_VCF, + project_guids=['R0113_test_project'], + validations_to_skip=[ALL_VALIDATIONS], + ) + worker.add(task) + worker.run() + self.assertTrue(task) + self.assertTrue(hfs.exists(task.output().path)) + + expected_qc_gen_anc_results = { + 'pca_scores': PCA_SCORES, + **EXPECTED_ANC_PROBABILITIES, + **{f'pop_PC{i + 1}': PCA_SCORES[i] for i in range(20)}, + 'qc_gen_anc': 'oth', + } + with task.output().open('r') as f: + res = json.load(f) + + self.assertCountEqual( + res['HG00731_1'], + { + 'seqr_id': 'HG00731_1', + 'vcf_id': 'HG00731', + 'filtered_callrate': 1.0, + 'contamination_rate': 5.099999904632568, + 'percent_bases_at_20x': 93.69000244140625, + 'mean_coverage': 29.309999465942383, + 'filter_flags': ['contamination', 'coverage'], + **expected_qc_gen_anc_results, + 'sample_qc.call_rate': 0.9666666666666667, + 'sample_qc.n_called': 29, + 'sample_qc.n_not_called': 1, + 'sample_qc.n_filtered': 0, + 'sample_qc.n_hom_ref': 16, + 'sample_qc.n_het': 2, + 'sample_qc.n_hom_var': 11, + 'sample_qc.n_non_ref': 13, + 'sample_qc.n_singleton': 1, + 'sample_qc.n_snp': 24, + 'sample_qc.n_insertion': 0, + 'sample_qc.n_deletion': 0, + 'sample_qc.n_transition': 15, + 'sample_qc.n_transversion': 9, + 'sample_qc.n_star': 0, + 'sample_qc.r_ti_tv': 1.6666666666666667, + 'sample_qc.r_het_hom_var': 0.18181818181818182, + 'sample_qc.r_insertion_deletion': None, + 'sample_qc.f_inbreeding.f_stat': 0.284195245767986, + 'sample_qc.f_inbreeding.n_called': 29, + 'sample_qc.f_inbreeding.expected_homs': 26.20594199999999, + 'sample_qc.f_inbreeding.observed_homs': 27, + 'fail_n_snp': True, + 'fail_r_ti_tv': False, + 'fail_r_insertion_deletion': None, + 'fail_n_insertion': True, + 'fail_n_deletion': True, + 'fail_r_het_hom_var': False, + 'fail_call_rate': False, + 'qc_metrics_filters': ['n_deletion', 'n_insertion', 'n_snp'], + }, + ) + self.assertCountEqual( + res['HG00732_1'], + { + 'seqr_id': 'HG00732_1', + 'vcf_id': 'HG00732', + 'filtered_callrate': 1.0, + 'contamination_rate': 5.0, + 'percent_bases_at_20x': 90.0, + 'mean_coverage': 28.0, + 'filter_flags': ['coverage'], + **expected_qc_gen_anc_results, + 'sample_qc.call_rate': 0.9666666666666667, + 'sample_qc.n_called': 29, + 'sample_qc.n_not_called': 1, + 'sample_qc.n_filtered': 0, + 'sample_qc.n_hom_ref': 16, + 'sample_qc.n_het': 4, + 'sample_qc.n_hom_var': 9, + 'sample_qc.n_non_ref': 13, + 'sample_qc.n_singleton': 2, + 'sample_qc.n_snp': 22, + 'sample_qc.n_insertion': 0, + 'sample_qc.n_deletion': 0, + 'sample_qc.n_transition': 13, + 'sample_qc.n_transversion': 9, + 'sample_qc.n_star': 0, + 'sample_qc.r_ti_tv': 1.4444444444444444, + 'sample_qc.r_het_hom_var': 0.4444444444444444, + 'sample_qc.r_insertion_deletion': None, + 'sample_qc.f_inbreeding.f_stat': -0.431609508464028, + 'sample_qc.f_inbreeding.n_called': 29, + 'sample_qc.f_inbreeding.expected_homs': 26.20594199999999, + 'sample_qc.f_inbreeding.observed_homs': 25, + 'fail_n_snp': True, + 'fail_r_ti_tv': False, + 'fail_r_insertion_deletion': None, + 'fail_n_insertion': True, + 'fail_n_deletion': True, + 'fail_r_het_hom_var': False, + 'fail_call_rate': False, + 'qc_metrics_filters': ['n_deletion', 'n_insertion', 'n_snp'], + }, + ) + self.assertCountEqual( + res['HG00733_1'], + { + 'seqr_id': 'HG00733_1', + 'vcf_id': 'HG00733', + 'filtered_callrate': 1.0, + 'contamination_rate': 6.0, + 'percent_bases_at_20x': 85.0, + 'mean_coverage': 36.400001525878906, + 'filter_flags': ['contamination'], + **expected_qc_gen_anc_results, + 'sample_qc.call_rate': 1.0, + 'sample_qc.n_called': 30, + 'sample_qc.n_not_called': 0, + 'sample_qc.n_filtered': 0, + 'sample_qc.n_hom_ref': 17, + 'sample_qc.n_het': 3, + 'sample_qc.n_hom_var': 10, + 'sample_qc.n_non_ref': 13, + 'sample_qc.n_singleton': 0, + 'sample_qc.n_snp': 23, + 'sample_qc.n_insertion': 0, + 'sample_qc.n_deletion': 0, + 'sample_qc.n_transition': 13, + 'sample_qc.n_transversion': 10, + 'sample_qc.n_star': 0, + 'sample_qc.r_ti_tv': 1.3, + 'sample_qc.r_het_hom_var': 0.3, + 'sample_qc.r_insertion_deletion': None, + 'sample_qc.f_inbreeding.f_stat': -0.038400752079048056, + 'sample_qc.f_inbreeding.n_called': 30, + 'sample_qc.f_inbreeding.expected_homs': 27.11094199999999, + 'sample_qc.f_inbreeding.observed_homs': 27, + 'fail_n_snp': True, + 'fail_r_ti_tv': False, + 'fail_r_insertion_deletion': None, + 'fail_n_insertion': True, + 'fail_n_deletion': True, + 'fail_r_het_hom_var': False, + 'fail_call_rate': False, + 'qc_metrics_filters': ['n_deletion', 'n_insertion', 'n_snp'], + }, + ) + self.assertFalse('NA19675' in res) diff --git a/loading_pipeline/lib/tasks/write_sex_check_table.py b/loading_pipeline/lib/tasks/write_sex_check_table.py new file mode 100644 index 0000000000..38efea1b97 --- /dev/null +++ b/loading_pipeline/lib/tasks/write_sex_check_table.py @@ -0,0 +1,79 @@ +import hail as hl +import hailtop.fs as hfs +import luigi + +from loading_pipeline.lib.core.feature_flag import FeatureFlag +from loading_pipeline.lib.methods.sex_check import compute_sex_check_ht +from loading_pipeline.lib.misc.io import import_imputed_sex +from loading_pipeline.lib.paths import ( + imported_callset_path, + sex_check_table_path, + tdr_metrics_dir, +) +from loading_pipeline.lib.tasks.base.base_loading_run_params import BaseLoadingRunParams +from loading_pipeline.lib.tasks.base.base_write import BaseWriteTask +from loading_pipeline.lib.tasks.files import GCSorLocalTarget +from loading_pipeline.lib.tasks.write_postprocessed_callset import ( + WritePostprocessedCallsetTask, +) +from loading_pipeline.lib.tasks.write_tdr_metrics_files import WriteTDRMetricsFilesTask + + +@luigi.util.inherits(BaseLoadingRunParams) +class WriteSexCheckTableTask(BaseWriteTask): + callset_path = luigi.Parameter() + + @property + def predicted_sex_from_tdr(self): + # complicated enough to need a helper :/ + return ( + FeatureFlag.EXPECT_TDR_METRICS + and not self.skip_expect_tdr_metrics + and self.dataset_type.expect_tdr_metrics( + self.reference_genome, + ) + ) + + def output(self) -> luigi.Target: + return GCSorLocalTarget( + sex_check_table_path( + self.reference_genome, + self.dataset_type, + self.callset_path, + ), + ) + + def requires(self) -> list[luigi.Task]: + requirements = [] + if self.predicted_sex_from_tdr: + requirements = [ + *requirements, + self.clone(WriteTDRMetricsFilesTask), + ] + else: + requirements = [ + *requirements, + self.clone(WritePostprocessedCallsetTask), + ] + return requirements + + def create_table(self) -> hl.Table: + ht = None + if self.predicted_sex_from_tdr: + for tdr_metrics_file in hfs.ls( + tdr_metrics_dir(self.reference_genome, self.dataset_type), + ): + if not ht: + ht = import_imputed_sex(tdr_metrics_file.path) + continue + ht = ht.union(import_imputed_sex(tdr_metrics_file.path)) + else: + mt = hl.read_matrix_table( + imported_callset_path( + self.reference_genome, + self.dataset_type, + self.callset_path, + ), + ) + ht = compute_sex_check_ht(mt) + return ht diff --git a/loading_pipeline/lib/tasks/write_sex_check_table_test.py b/loading_pipeline/lib/tasks/write_sex_check_table_test.py new file mode 100644 index 0000000000..1f83d8c991 --- /dev/null +++ b/loading_pipeline/lib/tasks/write_sex_check_table_test.py @@ -0,0 +1,157 @@ +from decimal import Decimal +from unittest.mock import Mock, patch + +import google.cloud.bigquery +import hail as hl +import luigi.worker + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.paths import sex_check_table_path, tdr_metrics_path +from loading_pipeline.lib.tasks.write_sex_check_table import ( + WriteSexCheckTableTask, +) +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + +TEST_SEX_AND_RELATEDNESS_CALLSET_MT = ( + 'loading_pipeline/var/test/callsets/sex_and_relatedness_1.mt' +) + + +class WriteSexCheckTableTaskTest(MockedDatarootTestCase): + @patch('loading_pipeline.lib.tasks.write_tdr_metrics_files.gen_bq_table_names') + @patch('loading_pipeline.lib.tasks.write_tdr_metrics_file.bq_metrics_query') + @patch( + 'loading_pipeline.lib.tasks.write_sex_check_table.FeatureFlag', + ) + def test_snv_sex_check_table_task( + self, + mock_ff: Mock, + mock_bq_metrics_query: Mock, + mock_gen_bq_table_names: Mock, + ) -> None: + mock_ff.EXPECT_TDR_METRICS = True + mock_gen_bq_table_names.return_value = [ + 'datarepo-7242affb.datarepo_RP_3053', + 'datarepo-5a72e31b.datarepo_RP_3056', + ] + mock_bq_metrics_query.side_effect = [ + iter( + [ + google.cloud.bigquery.table.Row( + ( + 'SM-NJ8MF', + 'Unknown', + Decimal('0'), + Decimal('0'), + Decimal('0'), + ), + { + 'collaborator_sample_id': 0, + 'predicted_sex': 1, + 'contamination_rate': 2, + 'percent_bases_at_20x': 3, + 'mean_coverage': 4, + }, + ), + google.cloud.bigquery.table.Row( + ( + 'SM-MWOGC', + 'Female', + Decimal('0'), + Decimal('0'), + Decimal('0'), + ), + { + 'collaborator_sample_id': 0, + 'predicted_sex': 1, + 'contamination_rate': 2, + 'percent_bases_at_20x': 3, + 'mean_coverage': 4, + }, + ), + google.cloud.bigquery.table.Row( + ('SM-MWKWL', 'Male', Decimal('0'), Decimal('0'), Decimal('0')), + { + 'collaborator_sample_id': 0, + 'predicted_sex': 1, + 'contamination_rate': 2, + 'percent_bases_at_20x': 3, + 'mean_coverage': 4, + }, + ), + ], + ), + iter( + [ + google.cloud.bigquery.table.Row( + ('SM-NGE65', 'Male', Decimal('0'), Decimal('0'), Decimal('0')), + { + 'collaborator_sample_id': 0, + 'predicted_sex': 1, + 'contamination_rate': 2, + 'percent_bases_at_20x': 3, + 'mean_coverage': 4, + }, + ), + google.cloud.bigquery.table.Row( + ('SM-NGE5G', 'Male', Decimal('0'), Decimal('0'), Decimal('0')), + { + 'collaborator_sample_id': 0, + 'predicted_sex': 1, + 'contamination_rate': 2, + 'percent_bases_at_20x': 3, + 'mean_coverage': 4, + }, + ), + google.cloud.bigquery.table.Row( + ('SM-NC6LM', 'Male', Decimal('0'), Decimal('0'), Decimal('0')), + { + 'collaborator_sample_id': 0, + 'predicted_sex': 1, + 'contamination_rate': 2, + 'percent_bases_at_20x': 3, + 'mean_coverage': 4, + }, + ), + ], + ), + ] + worker = luigi.worker.Worker() + write_sex_check_table = WriteSexCheckTableTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path='na', + project_guids=['R0113_test_project'], + run_id='manual__2024-04-03', + ) + worker.add(write_sex_check_table) + worker.run() + self.assertTrue(write_sex_check_table.complete()) + sex_check_ht = hl.read_table( + sex_check_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + 'na', + ), + ) + self.assertEqual( + sex_check_ht.collect(), + [ + hl.Struct(s='SM-MWKWL', predicted_sex='M'), + hl.Struct(s='SM-MWOGC', predicted_sex='F'), + hl.Struct(s='SM-NC6LM', predicted_sex='M'), + hl.Struct(s='SM-NGE5G', predicted_sex='M'), + hl.Struct(s='SM-NGE65', predicted_sex='M'), + hl.Struct(s='SM-NJ8MF', predicted_sex='U'), + ], + ) + # Check underlying tdr metrics file. + with open( + tdr_metrics_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + 'datarepo-5a72e31b.datarepo_RP_3056', + ), + ) as f: + self.assertTrue('collaborator_sample_id' in f.read()) diff --git a/loading_pipeline/lib/tasks/write_success_file.py b/loading_pipeline/lib/tasks/write_success_file.py new file mode 100644 index 0000000000..50d92b7bb4 --- /dev/null +++ b/loading_pipeline/lib/tasks/write_success_file.py @@ -0,0 +1,38 @@ +import luigi +import luigi.util + +from loading_pipeline.lib.core.feature_flag import FeatureFlag +from loading_pipeline.lib.paths import pipeline_run_success_file_path +from loading_pipeline.lib.tasks.base.base_loading_run_params import ( + BaseLoadingRunParams, +) +from loading_pipeline.lib.tasks.dataproc.run_pipeline_on_dataproc import ( + RunPipelineOnDataprocTask, +) +from loading_pipeline.lib.tasks.files import GCSorLocalTarget +from loading_pipeline.lib.tasks.run_pipeline import RunPipelineTask + + +@luigi.util.inherits(BaseLoadingRunParams) +class WriteSuccessFileTask(luigi.Task): + attempt_id = luigi.IntParameter() + + def output(self) -> luigi.Target: + return GCSorLocalTarget( + pipeline_run_success_file_path( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + ) + + def requires(self) -> luigi.Task: + return ( + self.clone(RunPipelineOnDataprocTask, attempt_id=self.attempt_id) + if FeatureFlag.RUN_PIPELINE_ON_DATAPROC + else self.clone(RunPipelineTask, attempt_id=self.attempt_id) + ) + + def run(self): + with self.output().open('w') as f: + f.write('') diff --git a/loading_pipeline/lib/tasks/write_success_file_test.py b/loading_pipeline/lib/tasks/write_success_file_test.py new file mode 100644 index 0000000000..f33a5d337e --- /dev/null +++ b/loading_pipeline/lib/tasks/write_success_file_test.py @@ -0,0 +1,34 @@ +from unittest import mock + +import luigi.worker + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.tasks.write_success_file import WriteSuccessFileTask +from loading_pipeline.lib.test.mock_complete_task import MockCompleteTask +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + + +class WriteSuccessFileTaskTest(MockedDatarootTestCase): + @mock.patch( + 'loading_pipeline.lib.tasks.write_success_file.RunPipelineTask', + ) + def test_write_success_file_task( + self, + mock_run_pipeline_task: mock.Mock, + ) -> None: + mock_run_pipeline_task.return_value = MockCompleteTask() + worker = luigi.worker.Worker() + write_success_file = WriteSuccessFileTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path='test_callset', + project_guids=['R0113_test_project'], + run_id='manual__2024-04-03', + attempt_id=0, + ) + worker.add(write_success_file) + worker.run() + self.assertTrue(write_success_file.complete()) + with open(write_success_file.output().path) as f: + self.assertEqual(f.read(), '') diff --git a/loading_pipeline/lib/tasks/write_tdr_metrics_file.py b/loading_pipeline/lib/tasks/write_tdr_metrics_file.py new file mode 100644 index 0000000000..9beefe4932 --- /dev/null +++ b/loading_pipeline/lib/tasks/write_tdr_metrics_file.py @@ -0,0 +1,42 @@ +import csv + +import google.api_core.exceptions +import luigi +import luigi.util + +from loading_pipeline.lib.logger import get_logger +from loading_pipeline.lib.misc.terra_data_repository import ( + BIGQUERY_METRICS, + bq_metrics_query, +) +from loading_pipeline.lib.paths import tdr_metrics_path +from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( + BaseLoadingPipelineParams, +) +from loading_pipeline.lib.tasks.files import GCSorLocalTarget + +logger = get_logger(__name__) + + +@luigi.util.inherits(BaseLoadingPipelineParams) +class WriteTDRMetricsFileTask(luigi.Task): + bq_table_name = luigi.Parameter() + + def output(self) -> luigi.Target: + return GCSorLocalTarget( + tdr_metrics_path( + self.reference_genome, + self.dataset_type, + self.bq_table_name, + ), + ) + + def run(self): + with self.output().open('w') as f: + writer = csv.DictWriter(f, fieldnames=BIGQUERY_METRICS, delimiter='\t') + writer.writeheader() + try: + for row in bq_metrics_query(self.bq_table_name): + writer.writerow(row) + except google.api_core.exceptions.BadRequest: + logger.exception('Query Failed') diff --git a/loading_pipeline/lib/tasks/write_tdr_metrics_files.py b/loading_pipeline/lib/tasks/write_tdr_metrics_files.py new file mode 100644 index 0000000000..488d466c98 --- /dev/null +++ b/loading_pipeline/lib/tasks/write_tdr_metrics_files.py @@ -0,0 +1,28 @@ +import luigi +import luigi.util + +from loading_pipeline.lib.misc.terra_data_repository import gen_bq_table_names +from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( + BaseLoadingPipelineParams, +) +from loading_pipeline.lib.tasks.write_tdr_metrics_file import WriteTDRMetricsFileTask + + +@luigi.util.inherits(BaseLoadingPipelineParams) +class WriteTDRMetricsFilesTask(luigi.Task): + def __init__(self, *args, **kwargs): + super().__init__(*args, **kwargs) + self.dynamic_write_tdr_metrics_file_task = set() + + def complete(self) -> bool: + return len(self.dynamic_write_tdr_metrics_file_task) >= 1 and all( + write_tdr_metrics_file_task.complete() + for write_tdr_metrics_file_task in self.dynamic_write_tdr_metrics_file_task + ) + + def run(self): + for bq_table_name in gen_bq_table_names(): + self.dynamic_write_tdr_metrics_file_task.add( + self.clone(WriteTDRMetricsFileTask, bq_table_name=bq_table_name), + ) + yield self.dynamic_write_tdr_metrics_file_task diff --git a/loading_pipeline/lib/tasks/write_validation_errors_for_run.py b/loading_pipeline/lib/tasks/write_validation_errors_for_run.py new file mode 100644 index 0000000000..c8d4d2b238 --- /dev/null +++ b/loading_pipeline/lib/tasks/write_validation_errors_for_run.py @@ -0,0 +1,128 @@ +import json +from collections.abc import Callable + +import luigi +import luigi.freezing +import luigi.util + +from loading_pipeline.lib.misc.validation import SeqrValidationError +from loading_pipeline.lib.paths import validation_errors_for_run_path +from loading_pipeline.lib.tasks.base.base_loading_run_params import BaseLoadingRunParams +from loading_pipeline.lib.tasks.files import GCSorLocalTarget + + +def _deep_merge_dicts(existing: dict, new: dict) -> dict: + """Recursively merge new dict into existing dict.""" + result = existing.copy() + for key, new_value in new.items(): + if ( + key in result + and isinstance(result[key], dict) + and isinstance(new_value, dict) + ): + result[key] = _deep_merge_dicts(result[key], new_value) + else: + result[key] = new_value + return result + + +@luigi.util.inherits(BaseLoadingRunParams) +class UpdatedValidationErrorsForRunTask(luigi.Task): + project_guids = luigi.ListParameter() + error_messages = luigi.ListParameter(default=[]) + error_body = luigi.DictParameter(default={}) + + def complete(self) -> bool: + """Check if all input project_guids and error_messages are contained in the output.""" + output_path = self.output() + if not output_path.exists(): + return False + + with output_path.open('r') as f: + data = json.load(f) + + output_project_guids = set(data.get('project_guids', [])) + output_error_messages = set(data.get('error_messages', [])) + + input_project_guids = set(self.project_guids) + input_error_messages = set(self.error_messages) + + # Check if all input items are in output + return input_project_guids.issubset( + output_project_guids, + ) and input_error_messages.issubset(output_error_messages) + + def to_single_error_message(self) -> str: + with self.output().open('r') as f: + error_messages = json.load(f)['error_messages'] + if len(error_messages) == 1: + return error_messages[0] + return f'Multiple validation errors encountered: {error_messages}' + + def output(self) -> luigi.Target: + return GCSorLocalTarget( + validation_errors_for_run_path( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + ) + + def run(self) -> None: + output_path = self.output() + + # Load existing data if file exists + existing_data = {} + if output_path.exists(): + with output_path.open('r') as f: + existing_data = json.load(f) + + # Append new project_guids to existing ones and deduplicate while preserving order + project_guids = list( + dict.fromkeys( + existing_data.get('project_guids', []) + list(self.project_guids), + ), + ) + + # Append new error_messages to existing ones and deduplicate while preserving order + error_messages = list( + dict.fromkeys( + existing_data.get('error_messages', []) + list(self.error_messages), + ), + ) + + # Merge error_body with new data recursively + error_body = _deep_merge_dicts( + { + k: v + for k, v in existing_data.items() + if k not in ('project_guids', 'error_messages') + }, + luigi.freezing.recursively_unfreeze(self.error_body), + ) + + validation_errors_json = { + 'project_guids': project_guids, + 'error_messages': error_messages, + **error_body, + } + with output_path.open('w') as f: + json.dump(validation_errors_json, f) + + +def with_persisted_validation_errors(f: Callable) -> Callable[[Callable], Callable]: + def wrapper(self: luigi.Task): + try: + return f(self) + except SeqrValidationError as e: + updated_validation_errors_for_run_task = self.clone( + UpdatedValidationErrorsForRunTask, + error_messages=[e.msg], + error_body=e.error_body, + ) + updated_validation_errors_for_run_task.run() + raise SeqrValidationError( + updated_validation_errors_for_run_task.to_single_error_message(), + ) from None + + return wrapper diff --git a/loading_pipeline/lib/tasks/write_variant_annotations_vcf.py b/loading_pipeline/lib/tasks/write_variant_annotations_vcf.py new file mode 100644 index 0000000000..bda611824e --- /dev/null +++ b/loading_pipeline/lib/tasks/write_variant_annotations_vcf.py @@ -0,0 +1,49 @@ +import hail as hl +import hailtop.fs as hfs +import luigi + +from loading_pipeline.lib.annotations.fields import get_fields +from loading_pipeline.lib.paths import ( + variant_annotations_table_path, + variant_annotations_vcf_path, +) +from loading_pipeline.lib.tasks.base.base_loading_run_params import BaseLoadingRunParams +from loading_pipeline.lib.tasks.files import GCSorLocalTarget + + +@luigi.util.inherits(BaseLoadingRunParams) +class WriteVariantAnnotationsVCF(luigi.Task): + def output(self) -> luigi.Target: + return GCSorLocalTarget( + variant_annotations_vcf_path( + self.reference_genome, + self.dataset_type, + ), + ) + + def complete(self) -> bool: + return not self.dataset_type.should_export_to_vcf + + def run(self) -> None: + if not hfs.exists( + variant_annotations_table_path( + self.reference_genome, + self.dataset_type, + ), + ): + return + ht = hl.read_table( + variant_annotations_table_path( + self.reference_genome, + self.dataset_type, + ), + ) + ht = ht.annotate( + **get_fields( + ht, + self.dataset_type.export_vcf_annotation_fns, + **self.param_kwargs, + ), + ) + ht = ht.key_by('locus', 'alleles') + hl.export_vcf(ht, self.output().path, tabix=True) diff --git a/loading_pipeline/lib/tasks/write_variant_annotations_vcf_test.py b/loading_pipeline/lib/tasks/write_variant_annotations_vcf_test.py new file mode 100644 index 0000000000..4bad466b67 --- /dev/null +++ b/loading_pipeline/lib/tasks/write_variant_annotations_vcf_test.py @@ -0,0 +1,91 @@ +import gzip +from unittest.mock import Mock, patch + +import hailtop.fs as hfs +import luigi.worker + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS +from loading_pipeline.lib.tasks.update_variant_annotations_table_with_new_variants import ( + UpdateVariantAnnotationsTableWithNewVariantsTask, +) +from loading_pipeline.lib.tasks.write_variant_annotations_vcf import ( + WriteVariantAnnotationsVCF, +) +from loading_pipeline.lib.test.misc import copy_project_pedigree_to_mocked_dir +from loading_pipeline.lib.test.mocked_reference_datasets_testcase import ( + MockedReferenceDatasetsTestCase, +) + +TEST_SV_VCF = 'loading_pipeline/var/test/callsets/sv_1.vcf' +TEST_PEDIGREE_5 = 'loading_pipeline/var/test/pedigrees/test_pedigree_5.tsv' + +GENE_ID_MAPPING = { + 'OR4F5': 'ENSG00000186092', + 'PLEKHG4B': 'ENSG00000153404', + 'OR4F16': 'ENSG00000186192', + 'OR4F29': 'ENSG00000284733', + 'FBXO28': 'ENSG00000143756', + 'SAMD11': 'ENSG00000187634', + 'C1orf174': 'ENSG00000198912', + 'TAS1R1': 'ENSG00000173662', + 'FAM131C': 'ENSG00000185519', + 'RCC2': 'ENSG00000179051', + 'NBPF3': 'ENSG00000142794', + 'AGBL4': 'ENSG00000186094', + 'KIAA1614': 'ENSG00000135835', + 'MR1': 'ENSG00000153029', + 'STX6': 'ENSG00000135823', + 'XPR1': 'ENSG00000143324', +} + + +class WriteVariantAnnotationsVCFTest(MockedReferenceDatasetsTestCase): + @patch( + 'loading_pipeline.lib.tasks.write_new_variants_table.load_gencode_gene_symbol_to_gene_id', + ) + def test_sv_export_vcf( + self, + mock_load_gencode: Mock, + ) -> None: + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_5, + ReferenceGenome.GRCh38, + DatasetType.SV, + SampleType.WGS, + 'R0115_test_project2', + ) + mock_load_gencode.return_value = GENE_ID_MAPPING + worker = luigi.worker.Worker() + update_variant_annotations_task = ( + UpdateVariantAnnotationsTableWithNewVariantsTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SV, + run_id='run_id1', + sample_type=SampleType.WGS, + callset_path=TEST_SV_VCF, + project_guids=['R0115_test_project2'], + validations_to_skip=[ALL_VALIDATIONS], + skip_expect_tdr_metrics=True, + ) + ) + worker.add(update_variant_annotations_task) + worker.run() + self.assertTrue(update_variant_annotations_task.complete()) + write_variant_annotations_vcf_task = WriteVariantAnnotationsVCF( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SV, + run_id='run_id1', + sample_type=SampleType.WGS, + callset_path=TEST_SV_VCF, + ) + worker.add(write_variant_annotations_vcf_task) + worker.run() + self.assertTrue( + hfs.exists( + write_variant_annotations_vcf_task.output().path, + ), + ) + with hfs.open(write_variant_annotations_vcf_task.output().path, 'rb') as f: + buf = f.read() + self.assertTrue(gzip.decompress(buf).startswith(b'##fileformat=VCFv4.2')) diff --git a/loading_pipeline/lib/test/__init__.py b/loading_pipeline/lib/test/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/loading_pipeline/lib/test/clickhouse_schema_testcase.py b/loading_pipeline/lib/test/clickhouse_schema_testcase.py new file mode 100644 index 0000000000..fc26f8cc64 --- /dev/null +++ b/loading_pipeline/lib/test/clickhouse_schema_testcase.py @@ -0,0 +1,127 @@ +import unittest + +from loading_pipeline.lib.core import Env +from loading_pipeline.lib.misc.clickhouse import ( + STAGING_CLICKHOUSE_DATABASE, + get_clickhouse_client, +) + +TEST_SCHEMA = 'loading_pipeline/var/test/test_clickhouse_schema.sql' + + +class ClickhouseSchemaTestCase(unittest.TestCase): + def setUp(self): + super().setUp() + client = get_clickhouse_client() + client.execute( + f""" + DROP DATABASE IF EXISTS {STAGING_CLICKHOUSE_DATABASE}; + """, + ) + client.execute( + f""" + DROP DATABASE IF EXISTS {Env.CLICKHOUSE_DATABASE}; + """, + ) + client.execute( + f""" + CREATE DATABASE {Env.CLICKHOUSE_DATABASE}; + """, + ) + client = get_clickhouse_client(database=Env.CLICKHOUSE_DATABASE) + client.execute( + """ + CREATE DICTIONARY seqrdb_gene_ids + ( + `gene_id` String, + `seqrdb_id` String, + `affected` String + ) + PRIMARY KEY gene_id + SOURCE(NULL()) + LIFETIME(0) + LAYOUT(HASHED()) + """, + ) + client.execute( + """ + CREATE DICTIONARY seqrdb_affected_status_dict + ( + `family_guid` String, + `sampleId` String, + `affected` String + ) + PRIMARY KEY family_guid, sampleId + SOURCE(NULL()) + LIFETIME(0) + LAYOUT(COMPLEX_KEY_HASHED()) + """, + ) + client.execute( + """ + CREATE DICTIONARY `GRCh38/SNV_INDEL/project_partitions_dict` + ( + `project_guid` String, + `n_partitions` UInt32 + ) + PRIMARY KEY project_guid + SOURCE(NULL()) + LIFETIME(0) + LAYOUT(COMPLEX_KEY_HASHED()) + """, + ) + client.execute( + """ + CREATE DICTIONARY `GRCh38/SNV_INDEL/reference_data/gnomad_genomes` + ( + `key` UInt32, + `filter_af` Decimal(9, 8) + ) + PRIMARY KEY key + SOURCE(NULL()) + LIFETIME(0) + LAYOUT(COMPLEX_KEY_HASHED()) + """, + ) + with open(TEST_SCHEMA) as f: + sql = f.read() + commands = [cmd.strip() for cmd in sql.split(';') if cmd.strip()] + for cmd in commands: + client.execute(cmd) + client.execute( + f""" + CREATE DICTIONARY `GRCh38/SNV_INDEL/gt_stats_dict` + ( + `key` UInt32, + `ac_wes` UInt64, + `ac_wgs` UInt64, + `ac_affected` UInt64, + `hom_wes` UInt64, + `hom_wgs` UInt64, + `hom_affected` UInt64 + ) + PRIMARY KEY key + SOURCE( + CLICKHOUSE( + USER {Env.CLICKHOUSE_WRITER_USER} PASSWORD {Env.CLICKHOUSE_WRITER_PASSWORD} + DB {Env.CLICKHOUSE_DATABASE} TABLE `GRCh38/SNV_INDEL/gt_stats` + ) + ) + LIFETIME(0) + LAYOUT(FLAT(MAX_ARRAY_SIZE 1000000000)) + """, + ) + + def tearDown(self): + super().tearDown() + client = get_clickhouse_client() + client.execute( + f""" + DROP DATABASE IF EXISTS {STAGING_CLICKHOUSE_DATABASE}; + """, + ) + client.execute( + f""" + DROP DATABASE IF EXISTS {Env.CLICKHOUSE_DATABASE}; + """, + ) diff --git a/loading_pipeline/lib/test/misc.py b/loading_pipeline/lib/test/misc.py new file mode 100644 index 0000000000..3f21bab165 --- /dev/null +++ b/loading_pipeline/lib/test/misc.py @@ -0,0 +1,46 @@ +import os +import shutil + +import numpy as np + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.paths import project_pedigree_path + + +def convert_ndarray_to_list(obj): + if isinstance(obj, np.ndarray): + return [convert_ndarray_to_list(item) for item in obj.tolist()] + if isinstance(obj, dict): + return {k: convert_ndarray_to_list(v) for k, v in obj.items()} + if isinstance(obj, list): + return [convert_ndarray_to_list(item) for item in obj] + return obj + + +def copy_project_pedigree_to_mocked_dir( + pedigree_path: str, + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + sample_type: SampleType, + project_guid: str, +): + os.makedirs( + os.path.dirname( + project_pedigree_path( + reference_genome, + dataset_type, + sample_type, + project_guid, + ), + ), + exist_ok=True, + ) + shutil.copy2( + pedigree_path, + project_pedigree_path( + reference_genome, + dataset_type, + sample_type, + project_guid, + ), + ) diff --git a/loading_pipeline/lib/test/mock_complete_task.py b/loading_pipeline/lib/test/mock_complete_task.py new file mode 100644 index 0000000000..5740df9678 --- /dev/null +++ b/loading_pipeline/lib/test/mock_complete_task.py @@ -0,0 +1,6 @@ +import luigi + + +class MockCompleteTask(luigi.Task): + def complete(self): + return True diff --git a/loading_pipeline/lib/test/mocked_dataroot_testcase.py b/loading_pipeline/lib/test/mocked_dataroot_testcase.py new file mode 100644 index 0000000000..204b3225a4 --- /dev/null +++ b/loading_pipeline/lib/test/mocked_dataroot_testcase.py @@ -0,0 +1,27 @@ +import os +import shutil +import tempfile +import unittest +from unittest.mock import patch + +from loading_pipeline.lib.core import Env + + +class MockedDatarootTestCase(unittest.TestCase): + def setUp(self) -> None: + super().setUp() + patcher = patch( + 'loading_pipeline.lib.paths.Env', + wraps=Env, + ) # wraps to ensure other attributes behave as they are. + self.mock_env = patcher.start() + self.addCleanup(patcher.stop) # https://stackoverflow.com/a/37534051 + for field_name in Env.__dataclass_fields__: + if field_name.endswith('_DIR'): + setattr(self.mock_env, field_name, tempfile.TemporaryDirectory().name) + + def tearDown(self) -> None: + super().tearDown() + for field_name in Env.__dataclass_fields__: + if os.path.isdir(getattr(self.mock_env, field_name)): + shutil.rmtree(getattr(self.mock_env, field_name)) diff --git a/loading_pipeline/lib/test/mocked_reference_datasets_testcase.py b/loading_pipeline/lib/test/mocked_reference_datasets_testcase.py new file mode 100644 index 0000000000..ee58892be2 --- /dev/null +++ b/loading_pipeline/lib/test/mocked_reference_datasets_testcase.py @@ -0,0 +1,38 @@ +import os +import shutil + +from loading_pipeline.lib.core.definitions import ReferenceGenome +from loading_pipeline.lib.paths import valid_reference_dataset_path +from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + +REFERENCE_DATASETS_PATH = 'loading_pipeline/var/test/reference_datasets' + + +class MockedReferenceDatasetsTestCase(MockedDatarootTestCase): + def setUp(self) -> None: + super().setUp() + for reference_genome in ReferenceGenome: + path = os.path.join( + REFERENCE_DATASETS_PATH, + reference_genome.value, + ) + # Use listdir, allowing for missing datasets + # in the tests. + for dataset_name in os.listdir( + path, + ): + # Copy the entire directory tree under + # the dataset name. + shutil.copytree( + os.path.join(path, dataset_name), + os.path.dirname( + valid_reference_dataset_path( + reference_genome, + ReferenceDataset(dataset_name), + ), + ), + ) + + def tearDown(self): + super().tearDown() diff --git a/loading_pipeline/ops/__init__.py b/loading_pipeline/ops/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel.py b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel.py new file mode 100644 index 0000000000..4636e44ae3 --- /dev/null +++ b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel.py @@ -0,0 +1,114 @@ +#################################################### +# +# This script is provided as means to repartition an existing `GRCh38/SNV_INDEL/entries` table +# from a project-only partitioning strategy to one that includes project subpartitions. +# Very large genome projects with thousands of families will require additional +# splitting to maintain reasonable loading performance and to keep partition size under +# the recommended ClickHouse maximum. Unfortunately, a ClickHouse table partition definition +# is static upon creation, necessitating the expensive table re-write process demonstrated below. +# +# Post seqr-platform version x.x.x, the subpartition-ing strategy is provided by default; +# earlier installations will continue to function as-is. This script is meant to +# be run under human supervision and with caution. +# +# At the end of this script, you should run the following SQL to finalize the migration: +# EXCHANGE TABLES seqr.'GRCh38/SNV_INDEL/entries' AND staging_grch38_snvindel_repartition.'GRCh38/SNV_INDEL/repartitioned_entries' +# DROP DATABASE `staging_grch38_snvindel_repartition`; +# +# Resource Requirements: +# - Free disk space equal to 2.5x the usage of your current `GRCh38/SNV_INDEL/entries` table. +# +#################################################### +import argparse + +from loading_pipeline.lib.core.environment import Env +from loading_pipeline.lib.misc.clickhouse import ( + logged_query, + normalize_partition, +) + +REPARTITION_DATABASE_NAME = 'staging_grch38_snvindel_repartition' + + +def get_partitions_for_project(project_guid: str): + rows = logged_query( + """ + SELECT DISTINCT partition + FROM system.parts + WHERE + database = %(database)s + AND table = %(table)s + AND partition like %(project_guid)s + """, + { + 'database': REPARTITION_DATABASE_NAME, + 'table': 'GRCh38/SNV_INDEL/repartitioned_entries', + 'project_guid': f'%{project_guid}%', + }, + ) + return [normalize_partition(row[0]) for row in rows] + + +def main(max_insert_threads: int, project_guids: list[str]): + logged_query( + f""" + CREATE DATABASE IF NOT EXISTS {REPARTITION_DATABASE_NAME}; + """, + ) + logged_query( + f""" + CREATE TABLE IF NOT EXISTS {REPARTITION_DATABASE_NAME}.`GRCh38/SNV_INDEL/repartitioned_entries` + AS {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` + ENGINE = CollapsingMergeTree(sign) + PARTITION BY (project_guid, partition_id) + SETTINGS deduplicate_merge_projection_mode = 'rebuild' + """, + ) + if not project_guids: + project_guids = [ + x[0] + for x in logged_query( + f""" + SELECT DISTINCT project_guid from {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` + """, + ) + ] + for project_guid in project_guids: + for partition in get_partitions_for_project( + project_guid, + ): + logged_query( + f""" + ALTER TABLE {REPARTITION_DATABASE_NAME}.`GRCh38/SNV_INDEL/repartitioned_entries` + DROP PARTITION %(partition)s + """, + {'partition': partition}, + ) + logged_query( + f""" + INSERT INTO {REPARTITION_DATABASE_NAME}.`GRCh38/SNV_INDEL/repartitioned_entries` + SELECT * FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` + WHERE project_guid=%(project_guid)s + SETTINGS max_insert_threads=%(max_insert_threads)s + """, + {'project_guid': project_guid, 'max_insert_threads': max_insert_threads}, + timeout=99999, + ) + + +if __name__ == '__main__': + parser = argparse.ArgumentParser() + parser.add_argument( + '--max-insert-threads', + type=int, + default=4, + help='Maximum number of insert threads to use (default: 4).', + ) + parser.add_argument( + '--project-guids', + nargs='+', + required=False, + help='Optionally provide an override list of project guids: --project-guids proj1 proj2 proj3', + ) + args = parser.parse_args() + main(args.max_insert_threads, args.project_guids) diff --git a/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py new file mode 100644 index 0000000000..214d35b939 --- /dev/null +++ b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py @@ -0,0 +1,120 @@ +import unittest + +from loading_pipeline.lib.core.environment import Env +from loading_pipeline.lib.misc.clickhouse import get_clickhouse_client +from loading_pipeline.ops.repartition_clickhouse_grch38_snv_indel import ( + REPARTITION_DATABASE_NAME, + main, +) + + +class RepartitionGRCh38SnvIndelTest(unittest.TestCase): + def setUp(self): + client = get_clickhouse_client() + client.execute( + f""" + DROP DATABASE IF EXISTS {Env.CLICKHOUSE_DATABASE} + PARALLEL WITH + DROP DATABASE IF EXISTS {REPARTITION_DATABASE_NAME}; + """, + ) + client.execute( + f""" + CREATE DATABASE {Env.CLICKHOUSE_DATABASE} + PARALLEL WITH + CREATE DATABASE {REPARTITION_DATABASE_NAME}; + """, + ) + client.execute( + f""" + CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` ( + `key` UInt32, + `project_guid` LowCardinality(String), + `family_guid` String, + `is_annotated_in_any_gene` Boolean, + `sign` Int8, + `n_partitions` UInt8 MATERIALIZED 2, + `partition_id` UInt8 MATERIALIZED farmHash64(family_guid) % n_partitions, + PROJECTION xpos_projection + ( + SELECT * + ORDER BY is_annotated_in_any_gene + ) + ) + ENGINE = CollapsingMergeTree(sign) + PARTITION BY project_guid + ORDER BY (project_guid, family_guid, key) + SETTINGS deduplicate_merge_projection_mode = 'rebuild'; + """, + ) + client.execute( + f""" + INSERT INTO {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` + VALUES + (0, 'project_a', 'family_a1', 0, 1), + (1, 'project_a', 'family_a2', 0, 1), + (2, 'project_a', 'family_a3', 0, 1), + (0, 'project_b', 'family_b1', 0, 1), + (1, 'project_b', 'family_b2', 0, 1), + (2, 'project_b', 'family_b2', 0, 1), + (0, 'project_c', 'family_c1', 1, 1), + (3, 'project_c', 'family_c2', 1, 1), + """, + ) + client.execute( + f""" + CREATE DICTIONARY {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_partitions_dict` + ( + `project_guid` String, + `n_partitions` UInt8 + ) + PRIMARY KEY project_guid + SOURCE( + CLICKHOUSE( + USER '{Env.CLICKHOUSE_WRITER_USER}' PASSWORD '{Env.CLICKHOUSE_WRITER_PASSWORD}' + DB {Env.CLICKHOUSE_DATABASE} QUERY 'SELECT project_guid, 3 FROM `GRCh38/SNV_INDEL/entries`' + ) + ) + LIFETIME(0) + LAYOUT(FLAT(MAX_ARRAY_SIZE 10000)) + """, + ) + + def test_main_all_projects(self): + client = get_clickhouse_client() + main(1, []) + res = client.execute( + f""" + SELECT *, n_partitions, partition_id FROM {REPARTITION_DATABASE_NAME}.`GRCh38/SNV_INDEL/repartitioned_entries` + """, + ) + self.assertCountEqual( + res, + [ + (3, 'project_c', 'family_c2', True, 1, 2, 1), + (0, 'project_b', 'family_b1', 0, 1, 2, 1), + (1, 'project_b', 'family_b2', 0, 1, 2, 1), + (2, 'project_b', 'family_b2', 0, 1, 2, 1), + (2, 'project_a', 'family_a3', 0, 1, 2, 0), + (0, 'project_a', 'family_a1', 0, 1, 2, 1), + (1, 'project_a', 'family_a2', 0, 1, 2, 1), + (0, 'project_c', 'family_c1', True, 1, 2, 0), + ], + ) + + def test_main_one_project(self): + client = get_clickhouse_client() + main(1, ['project_a']) + res = client.execute( + f""" + SELECT *, n_partitions, partition_id FROM {REPARTITION_DATABASE_NAME}.`GRCh38/SNV_INDEL/repartitioned_entries` + """, + ) + self.assertCountEqual( + res, + [ + (2, 'project_a', 'family_a3', 0, 1, 2, 0), + (0, 'project_a', 'family_a1', 0, 1, 2, 1), + (1, 'project_a', 'family_a2', 0, 1, 2, 1), + ], + ) diff --git a/loading_pipeline/pyproject.toml b/loading_pipeline/pyproject.toml new file mode 100644 index 0000000000..f06f1fc691 --- /dev/null +++ b/loading_pipeline/pyproject.toml @@ -0,0 +1,115 @@ +[project] +name = "seqr-loading-pipeline" +dynamic = ['version'] +requires-python = ">=3.11" +dependencies = [ + "hail==0.2.138", # NB: when upgrading hail, manually verify the below jupyter pins + "luigi==3.5.2", + "gnomad==0.8.0", + "aiofiles==24.1.0", + "pydantic==2.8.2", + "clickhouse-driver==0.2.9", + "slacker==0.14.0", + "ipykernel==6.29.2", # matches pinned version in hail init_notebook.py + "jupyter-console==6.6.3", # matches pinned version in hail init_notebook.py + "qtconsole==5.6.1", # matches pinned version in hail init_notebook.py + + # Git/URL installs (PEP 508 direct references) + "gnomad-qc @ git+https://github.com/broadinstitute/gnomad_qc.git@v4.1", + "onnxconverter-common @ git+https://github.com/microsoft/onnxconverter-common.git@f7a8eb699caa6f6a78d3bdfbcaf5dfbd43569ebd", + + # Dataproc + "pip==23.2.1", + "google-cloud-dataproc==5.16.0", + "google-cloud-bigquery==3.29.0", + "google-api-python-client==2.159.0", +] + +[dependency-groups] +prod = [ + "sqlalchemy<2.0.0" # This is required for the Luigi UI but nothing else. +] +dev = [ + "coverage>=7.2.2", + "pytest>=7.0.0", + "pytest-cov>=4.0.0", + "responses>=0.23.1", + "ruff==0.11.3", + "shellcheck-py>=0.10.0", + "pysam", + "pyarrow", +] + +[tool.uv] +exclude-dependencies = ["psycopg2-binary", "psycopg2"] + +[tool.setuptools] +include-package-data = true + +[tool.setuptools.package-data] +"loading_pipeline.var" = ["liftover/*.over.chain.gz"] + +[tool.setuptools.packages.find] +include = ["loading_pipeline*"] +exclude = ["loading_pipeline.bin", "loading_pipeline.deploy", "loading_pipeline*test*"] +namespaces = false + +[tool.ruff] +extend-exclude = [ + 'download_and_create_reference_datasets/v02/*', + 'gcloud_dataproc/*', + 'hail_scripts/*', + 'kubernetes/*', + 'luigi_pipeline/lib/*', + 'luigi_pipeline/seqr*.py', + 'luigi_pipeline/tests/data/*', +] +ignore = [ + # Individual Rules + "E501", # Black is less aggressive here when touching comments and strings, we're going to let those through. + "G004", # logging-f-string, these are fine for now + + # Rule Groupings + "D", # pydocstyle is for docs... we have none + "FBT", # flake-boolean-trap... disallows boolean args to functions... fixing this code will require refactors. + "ANN", # flake8-annotations is for typed code + "DJ", # django specific + "PYI", # pyi is typing stub files + "PT", # pytest specific + "PTH", # pathlib is preferred, but we're not using it yet + "PD", # pandas specific + "NPY", # numpy specific + "TD", # todos + "FIX", # fixmes +] +line-length = 88 +select = [ + "ALL" +] +target-version = "py311" + +[tool.ruff.flake8-quotes] +inline-quotes = "single" + +[tool.ruff.per-file-ignores] +'*test*' = [ + 'ARG002', # allow unused method arguments + 'SLF001', # allow private access + 'PLR0913', # allow high arity functions + 'S101', # allow asserts in tests +] +'*migration*' = [ + 'N999', # allow invalid module names +] +'*clickhouse*' = [ + 'S608' # unsafe sql +] +'*pipeline_worker*' = [ + 'S608' # unsafe sql +] + +[tool.ruff.pylint] +max-args = 6 + +[tool.ruff.format] +quote-style = "single" diff --git a/loading_pipeline/uv.lock b/loading_pipeline/uv.lock new file mode 100644 index 0000000000..eba2806f11 --- 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HG00733 NA19675 NA19678 NA19679 NA20870 NA20872 NA20874 NA20875 NA20876 NA20877 NA20878 NA20881 NA20885 NA20888 +1 871269 . A C 368.47 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-1.74060e+01;DP=351;Dels=0.00000e+00;FS=9.28030e+01;HaplotypeScore=5.13800e-01;InbreedingCoeff=-3.32000e-02;MQ=5.93000e+01;MQ0=0;MQRankSum=2.37300e+00;QD=4.80000e-01;ReadPosRankSum=-1.17980e+01;SNPEFF_AMINO_ACID_CHANGE=R141;SNPEFF_CODON_CHANGE=cgA/cgC;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_871152_871276;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=SAMD11;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000342066;VQSLOD=-8.16700e-01;culprit=QD;CSQ=C|ENSG00000187634|ENST00000455979|Transcript|upstream_gene_variant|||||||1|3386|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187634|ENST00000420190|Transcript|synonymous_variant|512|423|141|R|cgA/cgC||1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000411579||Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI000155D47C|||5/7|||ENST00000420190.1:c.423N>C|ENST00000420190.1:c.423N>C(p.%3D)|||||||||||||||POSITION:0.787709497206704||NON_CAN_SPLICE_SURR|||||||,C|ENSG00000268179|ENST00000598827|Transcript|upstream_gene_variant|||||||1|4824|-1|AL645608.1|Clone_based_ensembl_gene||protein_coding|YES|||ENSP00000471152||M0R0C9_HUMAN|UPI0000D61E05||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187634|ENST00000437963|Transcript|downstream_gene_variant|||||||1|96|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000393181||Q5SV95_HUMAN&I7FV93_HUMAN|UPI000155D47B||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187634|ENST00000478729|Transcript|upstream_gene_variant|||||||1|4457|1|SAMD11|HGNC|28706|processed_transcript||||||||||||||||||||||||||||||||||||||,C|ENSG00000187634|ENST00000342066|Transcript|synonymous_variant|506|423|141|R|cgA/cgC||1||1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04|||5/14|||ENST00000342066.3:c.423N>C|ENST00000342066.3:c.423N>C(p.%3D)|||||||||||||||POSITION:0.206744868035191||NON_CAN_SPLICE_SURR|||||||,C|ENSG00000187634|ENST00000341065|Transcript|synonymous_variant|194|195|65|R|cgA/cgC||1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A|||3/12|||ENST00000341065.4:c.194N>C|ENST00000341065.4:c.194N>C(p.%3D)|||||||||||||||POSITION:0.110231769361221||NON_CAN_SPLICE_SURR|||||||,C||ENSR00000528855|RegulatoryFeature|regulatory_region_variant|||||||1||||||regulatory_region|||||||||||||||||||||||||||||||||||||| GT:AD:DP:GQ:PL 0/0:34,0:34:99:0,102,1073 0/0:34,0:34:99:0,102,1064 0/0:37,0:37:99:0,108,1155 0/0:8,3:11:24:0,24,226 0/1:11,4:16:32:32,0,300 0/0:10,0:10:30:0,30,306 0/0:13,0:13:39:0,39,410 0/0:11,0:11:33:0,33,323 0/0:21,3:23:12:0,12,434 0/0:19,0:19:57:0,57,581 0/0:25,4:28:27:0,27,553 0/0:17,1:18:51:0,51,524 0/0:25,0:25:75:0,75,759 0/0:21,0:21:63:0,63,687 0/0:23,4:27:69:0,69,709 0/0:22,2:24:60:0,60,562 +1 874734 rs145967298 C T 2645.29 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-7.95400e+00;DB;DP=484;Dels=0.00000e+00;FS=7.13100e+00;HaplotypeScore=3.21100e-01;InbreedingCoeff=-6.80000e-03;MQ=5.85800e+01;MQ0=1;MQRankSum=7.38500e+00;QD=1.23600e+01;ReadPosRankSum=-7.54000e-01;SNPEFF_AMINO_ACID_CHANGE=S200;SNPEFF_CODON_CHANGE=agC/agT;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_874655_874840;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=SAMD11;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000342066;VQSLOD=5.39000e+00;culprit=InbreedingCoeff;CSQ=T|ENSG00000187634|ENST00000420190|Transcript|downstream_gene_variant||||||rs145967298|1|63|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000411579||Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI000155D47C||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187634|ENST00000342066|Transcript|synonymous_variant|683|600|200|S|agC/agT|rs145967298|1||1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04|||7/14|||ENST00000342066.3:c.600N>T|ENST00000342066.3:c.600N>T(p.%3D)|T:0.0009||T:0.01|||T:0.000227|T:0.001628||||||||POSITION:0.293255131964809||NON_CAN_SPLICE_SURR|||||||,T|ENSG00000188976|ENST00000327044|Transcript|downstream_gene_variant||||||rs145967298|1|4850|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187634|ENST00000464948|Transcript|upstream_gene_variant||||||rs145967298|1|2812|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628|||||||||||||||||,T|ENSG00000187634|ENST00000466827|Transcript|upstream_gene_variant||||||rs145967298|1|2749|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628|||||||||||||||||,T|ENSG00000187634|ENST00000474461|Transcript|upstream_gene_variant||||||rs145967298|1|1722|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628|||||||||||||||||,T|ENSG00000188976|ENST00000483767|Transcript|downstream_gene_variant||||||rs145967298|1|4850|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628|||||||||||||||||,T|ENSG00000187634|ENST00000455979|Transcript|synonymous_variant|80|81|27|S|agC/agT|rs145967298|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479|||1/7|||ENST00000455979.1:c.80N>T|ENST00000455979.1:c.80N>T(p.%3D)|T:0.0009||T:0.01|||T:0.000227|T:0.001628||||||||POSITION:0.0498461538461538||NON_CAN_SPLICE_SURR|||||||,T|ENSG00000187634|ENST00000437963|Transcript|downstream_gene_variant||||||rs145967298|1|3561|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000393181||Q5SV95_HUMAN&I7FV93_HUMAN|UPI000155D47B||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187634|ENST00000478729|Transcript|upstream_gene_variant||||||rs145967298|1|992|1|SAMD11|HGNC|28706|processed_transcript|||||||||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628|||||||||||||||||,T|ENSG00000188976|ENST00000477976|Transcript|downstream_gene_variant||||||rs145967298|1|4851|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628|||||||||||||||||,T|ENSG00000187634|ENST00000341065|Transcript|synonymous_variant|371|372|124|S|agC/agT|rs145967298|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A|||5/12|||ENST00000341065.4:c.371N>T|ENST00000341065.4:c.371N>T(p.%3D)|T:0.0009||T:0.01|||T:0.000227|T:0.001628||||||||POSITION:0.210288298473714||NON_CAN_SPLICE_SURR|||||||,T||ENSR00001516735|RegulatoryFeature|regulatory_region_variant||||||rs145967298|1||||||regulatory_region|||||||||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628||||||||||||||||| GT:AD:DP:GQ:PL 0/0:37,0:37:99:0,111,1368 0/0:24,0:24:66:0,66,870 0/0:32,0:32:96:0,96,1183 0/0:8,0:8:24:0,24,245 0/0:8,0:8:24:0,24,267 0/0:9,0:9:27:0,27,318 0/0:26,0:26:75:0,75,879 0/0:31,0:31:93:0,93,1120 0/0:39,0:39:99:0,117,1375 0/0:56,0:56:99:0,169,2023 0/1:21,22:42:99:519,0,613 0/0:29,0:29:87:0,87,1048 0/0:43,0:43:99:0,129,1556 0/0:20,0:20:60:0,60,741 0/0:45,0:45:99:0,135,1586 0/0:35,0:35:99:0,105,1239 +1 876499 rs4372192 A G 212847.01 PASS AC=31;AF=9.69000e-01;AN=32;BaseQRankSum=2.42570e+01;DB;DP=122;Dels=1.00000e-02;FS=9.96800e+00;HaplotypeScore=2.51500e-01;InbreedingCoeff=4.11000e-02;MQ=5.91300e+01;MQ0=0;MQRankSum=7.64000e-01;QD=3.03200e+01;ReadPosRankSum=2.13900e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=4.70000e+00;culprit=MQ;CSQ=G|ENSG00000187634|ENST00000420190|Transcript|downstream_gene_variant||||||rs4372192|1|1828|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000411579||Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI000155D47C||||||||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676||||||||||EXON_INTRON_UNDEF&ANC_ALLELE|||||||,G|ENSG00000188976|ENST00000496938|Transcript|downstream_gene_variant||||||rs4372192|1|4200|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676|||||||||||||||||,G|ENSG00000187634|ENST00000342066|Transcript|intron_variant||||||rs4372192|1||1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04||||7/13||ENST00000342066.3:c.707-25N>G||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676||||||||INTRON_SIZE:1683||NON_CAN_SPLICE&ANC_ALLELE|||||||,G|ENSG00000188976|ENST00000327044|Transcript|downstream_gene_variant||||||rs4372192|1|3085|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676||||||||||EXON_INTRON_UNDEF&ANC_ALLELE|||||||,G|ENSG00000187634|ENST00000464948|Transcript|upstream_gene_variant||||||rs4372192|1|1047|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676|||||||||||||||||,G|ENSG00000187634|ENST00000466827|Transcript|upstream_gene_variant||||||rs4372192|1|984|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676|||||||||||||||||,G|ENSG00000187634|ENST00000474461|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|44|||||rs4372192|1||1|SAMD11|HGNC|28706|retained_intron||||||||||1/4|||ENST00000474461.1:n.44N>G||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676|||||||||||||||||,G|ENSG00000187634|ENST00000455979|Transcript|intron_variant||||||rs4372192|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479||||1/6||ENST00000455979.1:c.187-25N>G||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676||||||||INTRON_SIZE:1683||NON_CAN_SPLICE&ANC_ALLELE|||||||,G|ENSG00000188976|ENST00000483767|Transcript|downstream_gene_variant||||||rs4372192|1|3085|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676|||||||||||||||||,G|ENSG00000187634|ENST00000478729|Transcript|intron_variant&non_coding_transcript_variant||||||rs4372192|1||1|SAMD11|HGNC|28706|processed_transcript|||||||||||1/2||ENST00000478729.1:n.118-25N>G||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676|||||||||||||||||,G|ENSG00000188976|ENST00000477976|Transcript|downstream_gene_variant||||||rs4372192|1|3086|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676|||||||||||||||||,G|ENSG00000187634|ENST00000341065|Transcript|intron_variant||||||rs4372192|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A||||5/11||ENST00000341065.4:c.430-25N>G||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676||||||||INTRON_SIZE:1731||NON_CAN_SPLICE&ANC_ALLELE|||||||,G||ENSR00000528857|RegulatoryFeature|regulatory_region_variant||||||rs4372192|1||||||regulatory_region|||||||||||||||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676||||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,7:7:21:253,21,0 1/1:0,8:8:24:296,24,0 1/1:0,4:4:12:148,12,0 1/1:0,5:5:15:184,15,0 1/1:0,1:1:3:39,3,0 1/1:0,5:5:15:176,15,0 1/1:0,9:9:27:316,27,0 1/1:0,11:11:33:397,33,0 1/1:0,7:7:18:212,18,0 1/1:0,11:11:27:369,27,0 1/1:0,13:13:39:492,39,0 0/1:7,9:15:99:235,0,158 1/1:0,7:7:18:231,18,0 1/1:0,4:4:12:154,12,0 1/1:0,8:8:24:296,24,0 1/1:0,7:7:21:270,21,0 +1 878314 rs142558220 G C 2808.55 VQSRTrancheSNP99.00to99.90 AC=3;AF=9.40000e-02;AN=32;BaseQRankSum=1.88800e+00;DB;DP=117;Dels=0.00000e+00;FS=1.06220e+01;HaplotypeScore=2.21900e-01;InbreedingCoeff=3.64000e-02;MQ=5.94000e+01;MQ0=1;MQRankSum=1.65200e+00;QD=9.46000e+00;ReadPosRankSum=-3.88300e+00;SNPEFF_AMINO_ACID_CHANGE=G480;SNPEFF_CODON_CHANGE=ggG/ggC;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_877939_878438;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=SAMD11;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000342066;VQSLOD=6.85000e+00;culprit=QD;CSQ=C|ENSG00000187634|ENST00000420190|Transcript|downstream_gene_variant||||||rs142558220&COSM426784|1|3643|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000411579||Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI000155D47C||||||||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000188976|ENST00000496938|Transcript|downstream_gene_variant||||||rs142558220&COSM426784|1|2385|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1|||||||||||||||,C|ENSG00000187634|ENST00000342066|Transcript|synonymous_variant|1523|1440|480|G|ggG/ggC|rs142558220&COSM426784|1||1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04|||11/14|||ENST00000342066.3:c.1440N>C|ENST00000342066.3:c.1440N>C(p.%3D)|C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1||||||POSITION:0.703812316715543||NON_CAN_SPLICE_SURR|||||||,C|ENSG00000188976|ENST00000327044|Transcript|downstream_gene_variant||||||rs142558220&COSM426784|1|1270|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187634|ENST00000464948|Transcript|downstream_gene_variant||||||rs142558220&COSM426784|1|42|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1|||||||||||||||,C|ENSG00000187634|ENST00000466827|Transcript|downstream_gene_variant||||||rs142558220&COSM426784|1|132|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1|||||||||||||||,C|ENSG00000187634|ENST00000474461|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|802|||||rs142558220&COSM426784|1||1|SAMD11|HGNC|28706|retained_intron||||||||||4/4|||ENST00000474461.1:n.802N>C||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1|||||||||||||||,C|ENSG00000187634|ENST00000455979|Transcript|synonymous_variant|920|921|307|G|ggG/ggC|rs142558220&COSM426784|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479|||5/7|||ENST00000455979.1:c.920N>C|ENST00000455979.1:c.920N>C(p.%3D)|C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1||||||POSITION:0.566769230769231||NON_CAN_SPLICE_SURR|||||||,C|ENSG00000188976|ENST00000483767|Transcript|downstream_gene_variant||||||rs142558220&COSM426784|1|1270|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1|||||||||||||||,C|ENSG00000187634|ENST00000478729|Transcript|downstream_gene_variant||||||rs142558220&COSM426784|1|761|1|SAMD11|HGNC|28706|processed_transcript|||||||||||||||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1|||||||||||||||,C|ENSG00000188976|ENST00000477976|Transcript|downstream_gene_variant||||||rs142558220&COSM426784|1|1271|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1|||||||||||||||,C|ENSG00000187634|ENST00000341065|Transcript|synonymous_variant|1163|1164|388|G|ggG/ggC|rs142558220&COSM426784|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A|||9/12|||ENST00000341065.4:c.1163N>C|ENST00000341065.4:c.1163N>C(p.%3D)|C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1||||||POSITION:0.65799886941775||NON_CAN_SPLICE_SURR|||||||,C||ENSR00000528857|RegulatoryFeature|regulatory_region_variant||||||rs142558220&COSM426784|1||||||regulatory_region|||||||||||||||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1||||||||||||||| GT:AD:DP:GQ:PL 0/1:2,1:3:30:30,0,67 0/0:2,0:2:6:0,6,82 0/1:2,3:5:61:93,0,61 0/0:2,0:2:6:0,6,72 0/0:1,0:1:3:0,3,37 0/1:2,3:5:54:93,0,54 0/0:16,0:16:45:0,45,560 0/0:5,0:5:15:0,15,188 0/0:12,0:12:33:0,33,414 0/0:10,0:10:30:0,30,393 0/0:16,0:16:48:0,48,617 0/0:5,0:5:15:0,15,181 0/0:5,0:5:15:0,15,193 0/0:13,0:13:36:0,36,439 0/0:9,0:9:24:0,24,317 0/0:8,0:8:21:0,21,276 +1 878809 rs191952374 C T 1761.84 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-7.95300e+00;DB;DP=453;Dels=0.00000e+00;FS=1.68300e+00;HaplotypeScore=2.28500e-01;InbreedingCoeff=-3.10000e-03;MQ=5.91000e+01;MQ0=0;MQRankSum=1.29700e+00;QD=1.36600e+01;ReadPosRankSum=-8.52000e-01;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=9.25000e+00;culprit=InbreedingCoeff;CSQ=T|ENSG00000187634|ENST00000420190|Transcript|downstream_gene_variant||||||rs191952374|1|4138|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000411579||Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI000155D47C||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000496938|Transcript|downstream_gene_variant||||||rs191952374|1|1890|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636|||||||||||||||||,T|ENSG00000187634|ENST00000342066|Transcript|intron_variant||||||rs191952374|1||1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04||||12/13||ENST00000342066.3:c.1689+52N>T||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636||||||||INTRON_SIZE:320||NON_CAN_SPLICE|||||||,T|ENSG00000188976|ENST00000327044|Transcript|downstream_gene_variant||||||rs191952374|1|775|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187634|ENST00000464948|Transcript|downstream_gene_variant||||||rs191952374|1|537|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636|||||||||||||||||,T|ENSG00000187634|ENST00000466827|Transcript|downstream_gene_variant||||||rs191952374|1|627|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636|||||||||||||||||,T|ENSG00000187634|ENST00000474461|Transcript|downstream_gene_variant||||||rs191952374|1|435|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636|||||||||||||||||,T|ENSG00000187634|ENST00000455979|Transcript|intron_variant||||||rs191952374|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479||||6/6||ENST00000455979.1:c.1169+52N>T||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636||||||||INTRON_SIZE:320||NON_CAN_SPLICE|||||||,T|ENSG00000188976|ENST00000483767|Transcript|downstream_gene_variant||||||rs191952374|1|775|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636|||||||||||||||||,T|ENSG00000187634|ENST00000478729|Transcript|downstream_gene_variant||||||rs191952374|1|1256|1|SAMD11|HGNC|28706|processed_transcript|||||||||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636|||||||||||||||||,T|ENSG00000188976|ENST00000477976|Transcript|downstream_gene_variant||||||rs191952374|1|776|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636|||||||||||||||||,T|ENSG00000187634|ENST00000341065|Transcript|intron_variant||||||rs191952374|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A||||10/11||ENST00000341065.4:c.1412+52N>T||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636||||||||INTRON_SIZE:320||NON_CAN_SPLICE|||||||,T||ENSR00000528858|RegulatoryFeature|regulatory_region_variant||||||rs191952374|1||||||regulatory_region|||||||||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636||||||||||||||||| GT:AD:DP:GQ:PL 0/0:35,0:35:99:0,105,1323 0/0:24,0:24:72:0,72,960 0/0:31,0:31:93:0,93,1172 0/0:10,0:10:30:0,30,376 0/0:10,0:10:30:0,30,370 0/0:12,0:12:36:0,36,453 0/0:35,0:35:99:0,105,1376 0/0:33,0:33:99:0,99,1273 0/0:31,0:31:93:0,93,1240 0/0:33,0:33:96:0,96,1192 0/0:33,0:33:99:0,99,1281 0/0:25,0:25:75:0,75,983 0/1:18,16:33:99:488,0,504 0/0:33,0:33:99:0,99,1273 0/0:44,0:44:99:0,132,1698 0/0:31,0:31:90:0,90,1198 +1 879576 rs115979567 C T 18648.64 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-2.26830e+01;DB;DP=839;Dels=0.00000e+00;FS=2.49350e+01;HaplotypeScore=4.12600e-01;InbreedingCoeff=-2.18000e-02;MQ=5.92100e+01;MQ0=1;MQRankSum=1.02100e+00;QD=1.36100e+01;ReadPosRankSum=7.91400e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=4.39000e+00;culprit=InbreedingCoeff;CSQ=T|ENSG00000187634|ENST00000420190|Transcript|downstream_gene_variant||||||rs115979567|1|4905|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000411579||Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI000155D47C||||||||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000496938|Transcript|downstream_gene_variant||||||rs115979567|1|1123|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120|||||||||||||||||,T|ENSG00000187634|ENST00000342066|Transcript|3_prime_UTR_variant|2172|||||rs115979567|1||1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04|||14/14|||ENST00000342066.3:c.*43N>T||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120||||||||||NON_CAN_SPLICE_SURR|||||||,T|ENSG00000188976|ENST00000327044|Transcript|downstream_gene_variant||||||rs115979567|1|8|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187634|ENST00000464948|Transcript|downstream_gene_variant||||||rs115979567|1|1304|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120|||||||||||||||||,T|ENSG00000187634|ENST00000466827|Transcript|downstream_gene_variant||||||rs115979567|1|1394|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120|||||||||||||||||,T|ENSG00000187634|ENST00000474461|Transcript|downstream_gene_variant||||||rs115979567|1|1202|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120|||||||||||||||||,T|ENSG00000187634|ENST00000455979|Transcript|3_prime_UTR_variant|1668|||||rs115979567|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479|||7/7|||ENST00000455979.1:c.*43N>T||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120||||||||||NON_CAN_SPLICE_SURR|||||||,T|ENSG00000188976|ENST00000483767|Transcript|downstream_gene_variant||||||rs115979567|1|8|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120|||||||||||||||||,T|ENSG00000187634|ENST00000478729|Transcript|downstream_gene_variant||||||rs115979567|1|2023|1|SAMD11|HGNC|28706|processed_transcript|||||||||||||||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120|||||||||||||||||,T|ENSG00000188976|ENST00000477976|Transcript|downstream_gene_variant||||||rs115979567|1|9|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120|||||||||||||||||,T|ENSG00000187634|ENST00000341065|Transcript|3_prime_UTR_variant|1812|||||rs115979567|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A|||12/12|||ENST00000341065.4:c.*43N>T||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120||||||||||NON_CAN_SPLICE_SURR||||||| GT:AD:DP:GQ:PL 0/0:66,0:66:99:0,199,2441 0/1:25,28:51:99:767,0,834 0/0:55,0:55:99:0,166,2079 0/0:11,0:11:33:0,33,392 0/0:15,0:15:45:0,45,554 0/0:17,0:17:51:0,51,622 0/0:50,0:50:99:0,150,1966 0/0:65,0:65:99:0,196,2507 0/0:60,0:60:99:0,181,2268 0/0:70,0:70:99:0,211,2589 0/0:64,0:64:99:0,193,2452 0/0:65,0:65:99:0,196,2507 0/0:56,0:56:99:0,169,2117 0/0:60,0:60:99:0,181,2359 0/0:79,0:79:99:0,238,2986 0/0:55,0:55:99:0,165,2099 +1 881070 rs41285794 G A 20769.13 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-9.52200e+00;DB;DP=1185;Dels=0.00000e+00;FS=1.15500e+01;HaplotypeScore=1.69500e-01;InbreedingCoeff=-1.83000e-02;MQ=5.90700e+01;MQ0=0;MQRankSum=1.85940e+01;QD=1.31500e+01;ReadPosRankSum=-8.90700e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=SAMD11;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000342066;VQSLOD=4.22000e+00;culprit=InbreedingCoeff;CSQ=A|ENSG00000188976|ENST00000496938|Transcript|upstream_gene_variant||||||rs41285794|1|128|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651|||||||||||||||||,A|ENSG00000187634|ENST00000342066|Transcript|downstream_gene_variant||||||rs41285794|1|1115|1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04||||||||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000188976|ENST00000327044|Transcript|intron_variant||||||rs41285794|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||16/18||ENST00000327044.6:c.1918-37N>T||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651||||||||INTRON_SIZE:519||NON_CAN_SPLICE|||||||,A|ENSG00000187634|ENST00000464948|Transcript|downstream_gene_variant||||||rs41285794|1|2798|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651|||||||||||||||||,A|ENSG00000187634|ENST00000466827|Transcript|downstream_gene_variant||||||rs41285794|1|2888|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651|||||||||||||||||,A|ENSG00000187634|ENST00000474461|Transcript|downstream_gene_variant||||||rs41285794|1|2696|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651|||||||||||||||||,A|ENSG00000187634|ENST00000455979|Transcript|downstream_gene_variant||||||rs41285794|1|1431|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479||||||||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000188976|ENST00000483767|Transcript|intron_variant&non_coding_transcript_variant||||||rs41285794|1||-1|NOC2L|HGNC|24517|retained_intron|||||||||||2/4||ENST00000483767.1:n.774-37N>T||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651|||||||||||||||||,A|ENSG00000187634|ENST00000478729|Transcript|downstream_gene_variant||||||rs41285794|1|3517|1|SAMD11|HGNC|28706|processed_transcript|||||||||||||||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651|||||||||||||||||,A|ENSG00000188976|ENST00000477976|Transcript|intron_variant&non_coding_transcript_variant||||||rs41285794|1||-1|NOC2L|HGNC|24517|retained_intron|||||||||||14/16||ENST00000477976.1:n.3365-37N>T||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651|||||||||||||||||,A|ENSG00000187634|ENST00000341065|Transcript|downstream_gene_variant||||||rs41285794|1|1115|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A||||||||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651||||||||||EXON_INTRON_UNDEF||||||| GT:AD:DP:GQ:PL 0/0:78,0:78:99:0,235,2947 0/0:66,0:66:99:0,199,2595 0/0:59,0:59:99:0,178,2182 0/0:37,0:37:99:0,111,1365 0/0:36,0:36:99:0,108,1331 0/0:33,0:33:99:0,99,1192 0/0:69,0:69:99:0,208,2662 0/0:88,0:88:99:0,265,3395 0/0:98,0:98:99:0,295,3781 0/1:36,31:64:99:982,0,1021 0/0:86,0:86:99:0,259,3318 0/0:93,0:93:99:0,280,3588 0/0:92,0:92:99:0,277,3549 0/0:102,0:102:99:0,307,3935 0/0:89,0:89:99:0,268,3433 0/0:95,0:95:99:0,286,3665 +1 881627 rs2272757 G A 411792.28 PASS AC=22;AF=6.88000e-01;AN=32;BaseQRankSum=-3.32930e+01;DB;DP=644;Dels=0.00000e+00;FS=2.51600e+00;HaplotypeScore=5.86200e-01;InbreedingCoeff=3.09600e-01;MQ=5.88200e+01;MQ0=7;MQRankSum=6.81600e+00;QD=2.28900e+01;ReadPosRankSum=1.01500e+00;SNPEFF_AMINO_ACID_CHANGE=L615;SNPEFF_CODON_CHANGE=Ctg/Ttg;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_881553_881666;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=4.35000e+00;culprit=MQ;CSQ=A|ENSG00000188976|ENST00000496938|Transcript|upstream_gene_variant||||||rs2272757&COSM1344685|1|685|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1|||||||||||||||,A|ENSG00000187634|ENST00000342066|Transcript|downstream_gene_variant||||||rs2272757&COSM1344685|1|1672|1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04||||||||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000188976|ENST00000327044|Transcript|synonymous_variant|1893|1843|615|L|Ctg/Ttg|rs2272757&COSM1344685|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C|||16/19||Pfam_domain:PF03715&Superfamily_domains:SSF48371|ENST00000327044.6:c.1843N>T|ENST00000327044.6:c.1843N>T(p.%3D)|A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1||||||POSITION:0.819111111111111||NON_CAN_SPLICE_SURR|||||||,A|ENSG00000187634|ENST00000464948|Transcript|downstream_gene_variant||||||rs2272757&COSM1344685|1|3355|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1|||||||||||||||,A|ENSG00000187634|ENST00000466827|Transcript|downstream_gene_variant||||||rs2272757&COSM1344685|1|3445|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1|||||||||||||||,A|ENSG00000187634|ENST00000474461|Transcript|downstream_gene_variant||||||rs2272757&COSM1344685|1|3253|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1|||||||||||||||,A|ENSG00000187634|ENST00000455979|Transcript|downstream_gene_variant||||||rs2272757&COSM1344685|1|1988|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479||||||||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000188976|ENST00000483767|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|699|||||rs2272757&COSM1344685|1||-1|NOC2L|HGNC|24517|retained_intron||||||||||2/5|||ENST00000483767.1:n.699N>T||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1|||||||||||||||,A|ENSG00000187634|ENST00000478729|Transcript|downstream_gene_variant||||||rs2272757&COSM1344685|1|4074|1|SAMD11|HGNC|28706|processed_transcript|||||||||||||||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1|||||||||||||||,A|ENSG00000188976|ENST00000477976|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|3290|||||rs2272757&COSM1344685|1||-1|NOC2L|HGNC|24517|retained_intron||||||||||14/17|||ENST00000477976.1:n.3290N>T||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1|||||||||||||||,A|ENSG00000187634|ENST00000341065|Transcript|downstream_gene_variant||||||rs2272757&COSM1344685|1|1672|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A||||||||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1||||||||EXON_INTRON_UNDEF||||||| GT:AD:DP:GQ:PL 1/1:0,39:38:99:1384,111,0 0/0:61,0:61:99:0,184,2353 0/1:24,17:38:99:494,0,613 1/1:0,16:16:48:550,48,0 1/1:0,18:18:54:649,54,0 1/1:0,25:25:66:826,66,0 1/1:0,51:51:99:1886,153,0 0/1:25,23:46:99:661,0,639 1/1:0,33:33:99:1220,99,0 1/1:0,52:52:99:1879,156,0 1/1:0,45:45:99:1701,135,0 0/0:58,0:58:99:0,175,2237 0/1:17,18:34:99:523,0,478 1/1:0,44:44:99:1627,132,0 0/1:20,25:41:99:674,0,488 0/0:44,1:44:99:0,120,1521 +1 881918 rs35471880 G A 26418.87 PASS AC=5;AF=1.56000e-01;AN=32;BaseQRankSum=6.25300e+00;DB;DP=1040;Dels=0.00000e+00;FS=2.27620e+01;HaplotypeScore=2.29500e-01;InbreedingCoeff=-2.81000e-02;MQ=5.57400e+01;MQ0=40;MQRankSum=1.69390e+01;QD=1.18200e+01;ReadPosRankSum=-6.75000e-01;SNPEFF_AMINO_ACID_CHANGE=S556L;SNPEFF_CODON_CHANGE=tCg/tTg;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_881782_881925;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=1.82000e+00;culprit=MQ;CSQ=A|ENSG00000188976|ENST00000496938|Transcript|upstream_gene_variant||||||rs35471880|1|976|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628|||||||||||||||||,A|ENSG00000187634|ENST00000342066|Transcript|downstream_gene_variant||||||rs35471880|1|1963|1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04||||||||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000188976|ENST00000327044|Transcript|missense_variant|1717|1667|556|S/L|tCg/tTg|rs35471880|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C|deleterious(0.03)|benign(0.311)|15/19||Pfam_domain:PF03715&Superfamily_domains:SSF48371|ENST00000327044.6:c.1667N>T|ENSP00000317992.6:p.Ser556Leu|A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628||||||||POSITION:0.740888888888889||NON_CAN_SPLICE_SURR||B%3BB%3BB|16.43|D|T|D|T,A|ENSG00000187634|ENST00000464948|Transcript|downstream_gene_variant||||||rs35471880|1|3646|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628|||||||||||||||||,A|ENSG00000187634|ENST00000466827|Transcript|downstream_gene_variant||||||rs35471880|1|3736|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628|||||||||||||||||,A|ENSG00000187634|ENST00000474461|Transcript|downstream_gene_variant||||||rs35471880|1|3544|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628|||||||||||||||||,A|ENSG00000187634|ENST00000455979|Transcript|downstream_gene_variant||||||rs35471880|1|2279|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479||||||||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000188976|ENST00000483767|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|523|||||rs35471880|1||-1|NOC2L|HGNC|24517|retained_intron||||||||||1/5|||ENST00000483767.1:n.523N>T||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628|||||||||||||||||,A|ENSG00000187634|ENST00000478729|Transcript|downstream_gene_variant||||||rs35471880|1|4365|1|SAMD11|HGNC|28706|processed_transcript|||||||||||||||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628|||||||||||||||||,A|ENSG00000188976|ENST00000477976|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|3114|||||rs35471880|1||-1|NOC2L|HGNC|24517|retained_intron||||||||||13/17|||ENST00000477976.1:n.3114N>T||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628|||||||||||||||||,A|ENSG00000187634|ENST00000341065|Transcript|downstream_gene_variant||||||rs35471880|1|1963|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A||||||||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628||||||||||EXON_INTRON_UNDEF||||||| GT:AD:DP:GQ:PL 0/0:73,0:73:99:0,220,2699 0/0:70,0:70:99:0,211,2589 0/0:66,0:66:99:0,199,2385 0/1:12,18:29:99:475,0,278 0/0:28,0:28:78:0,78,843 0/1:18,10:27:99:271,0,511 0/1:34,36:67:99:876,0,921 0/1:37,38:74:99:966,0,944 0/0:69,0:69:99:0,208,2493 0/0:93,0:93:99:0,280,3279 0/1:41,32:70:99:777,0,1118 0/0:76,0:76:99:0,229,2746 0/0:73,0:73:99:0,220,2573 0/0:69,0:69:99:0,208,2493 0/0:82,0:82:99:0,247,2963 0/0:74,0:74:99:0,223,2609 +1 883485 . C T 81.94 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-3.68100e+00;DP=94;Dels=0.00000e+00;FS=0.00000e+00;HaplotypeScore=1.64200e-01;InbreedingCoeff=-2.46000e-02;MQ=5.53400e+01;MQ0=0;MQRankSum=3.55900e+00;QD=3.03000e+00;ReadPosRankSum=-1.07900e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=SAMD11;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000342066;VQSLOD=-3.92700e-01;culprit=MQ;CSQ=T|ENSG00000188976|ENST00000483767|Transcript|upstream_gene_variant||||||rs374301410|1|1045|-1|NOC2L|HGNC|24517|retained_intron||||||||||||||||||||T:0|T:0.000117|||||||||||||||||,T|ENSG00000187634|ENST00000455979|Transcript|downstream_gene_variant||||||rs374301410|1|3846|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479|||||||||||||T:0|T:0.000117||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000496938|Transcript|upstream_gene_variant||||||rs374301410|1|2543|-1|NOC2L|HGNC|24517|processed_transcript||||||||||||||||||||T:0|T:0.000117|||||||||||||||||,T|ENSG00000187634|ENST00000342066|Transcript|downstream_gene_variant||||||rs374301410|1|3530|1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04|||||||||||||T:0|T:0.000117||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000327044|Transcript|intron_variant||||||rs374301410|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||14/18||ENST00000327044.6:c.1659+26N>A|||||||T:0|T:0.000117||||||||INTRON_SIZE:1585||NON_CAN_SPLICE|||||||,T|ENSG00000188976|ENST00000477976|Transcript|intron_variant&non_coding_transcript_variant||||||rs374301410|1||-1|NOC2L|HGNC|24517|retained_intron|||||||||||12/16||ENST00000477976.1:n.3106+26N>A|||||||T:0|T:0.000117|||||||||||||||||,T|ENSG00000187634|ENST00000341065|Transcript|downstream_gene_variant||||||rs374301410|1|3530|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A|||||||||||||T:0|T:0.000117||||||||||EXON_INTRON_UNDEF||||||| GT:AD:DP:GQ:PL 0/0:8,0:8:24:0,24,304 0/0:3,0:3:9:0,9,118 0/0:5,0:5:15:0,15,178 0/0:5,0:5:15:0,15,181 0/0:2,0:2:6:0,6,69 0/0:4,0:5:12:0,12,145 0/0:6,0:6:18:0,18,217 0/0:10,0:10:30:0,30,378 0/0:11,0:11:33:0,33,411 0/1:5,1:6:14:14,0,181 0/0:10,0:10:30:0,30,373 0/0:4,0:4:9:0,9,114 0/0:5,0:5:15:0,15,193 0/0:4,0:4:12:0,12,157 0/0:6,0:6:18:0,18,229 0/0:3,0:4:9:0,9,122 +1 883625 rs4970378 A G 232503.78 PASS AC=30;AF=1.00000e+00;AN=30;DB;DP=117;Dels=0.00000e+00;FS=0.00000e+00;HaplotypeScore=1.37000e-01;InbreedingCoeff=-1.43000e-02;MQ=5.74300e+01;MQ0=0;QD=3.66300e+01;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=SAMD11;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000342066;VQSLOD=-2.60400e-01;culprit=MQ;CSQ=G|ENSG00000188976|ENST00000483767|Transcript|upstream_gene_variant||||||rs4970378|1|1185|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||A:0.0000|||||G:0.999543||||||||||||||||||,G|ENSG00000187634|ENST00000455979|Transcript|downstream_gene_variant||||||rs4970378|1|3986|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479||||||||A:0.0000|||||G:0.999543|||||||||||EXON_INTRON_UNDEF&ANC_ALLELE|||||||,G|ENSG00000188976|ENST00000496938|Transcript|upstream_gene_variant||||||rs4970378|1|2683|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.0000|||||G:0.999543||||||||||||||||||,G|ENSG00000187634|ENST00000342066|Transcript|downstream_gene_variant||||||rs4970378|1|3670|1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04||||||||A:0.0000|||||G:0.999543|||||||||||EXON_INTRON_UNDEF&ANC_ALLELE|||||||,G|ENSG00000188976|ENST00000327044|Transcript|intron_variant||||||rs4970378|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||13/18||ENST00000327044.6:c.1558-13N>C||A:0.0000|||||G:0.999543|||||||||INTRON_SIZE:257||NON_CAN_SPLICE&ANC_ALLELE|||||||,G|ENSG00000188976|ENST00000477976|Transcript|intron_variant&non_coding_transcript_variant||||||rs4970378|1||-1|NOC2L|HGNC|24517|retained_intron|||||||||||11/16||ENST00000477976.1:n.3005-13N>C||A:0.0000|||||G:0.999543||||||||||||||||||,G|ENSG00000187634|ENST00000341065|Transcript|downstream_gene_variant||||||rs4970378|1|3670|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A||||||||A:0.0000|||||G:0.999543|||||||||||EXON_INTRON_UNDEF&ANC_ALLELE||||||| GT:AD:DP:GQ:PL 1/1:0,4:4:12:151,12,0 1/1:0,3:3:9:118,9,0 1/1:0,6:6:18:212,18,0 1/1:0,5:5:15:185,15,0 ./.:.:.:.:. 1/1:0,4:4:12:142,12,0 1/1:0,13:13:39:501,39,0 1/1:0,8:8:21:276,21,0 1/1:0,19:19:57:718,57,0 1/1:0,9:9:27:340,27,0 1/1:0,12:12:36:454,36,0 1/1:0,4:4:12:151,12,0 1/1:0,5:5:15:198,15,0 1/1:0,16:16:48:605,48,0 1/1:0,3:3:9:119,9,0 1/1:0,5:6:15:191,15,0 +1 883918 rs139116730 G A 4594.12 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=6.89000e+00;DB;DP=1146;Dels=0.00000e+00;FS=4.31330e+01;HaplotypeScore=8.65000e-02;InbreedingCoeff=-4.00000e-03;MQ=5.62500e+01;MQ0=14;MQRankSum=1.10440e+01;QD=1.07800e+01;ReadPosRankSum=-1.97100e+00;SNPEFF_AMINO_ACID_CHANGE=S503;SNPEFF_CODON_CHANGE=tcC/tcT;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_883870_883983;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=5.95000e-01;culprit=MQ;CSQ=A|ENSG00000188976|ENST00000483767|Transcript|upstream_gene_variant||||||rs139116730|1|1478|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||A:0.0005||||A:0.0013|A:0.000227|A:0.003488|||||||||||||||||,A|ENSG00000187634|ENST00000455979|Transcript|downstream_gene_variant||||||rs139116730|1|4279|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479||||||||A:0.0005||||A:0.0013|A:0.000227|A:0.003488||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000188976|ENST00000496938|Transcript|upstream_gene_variant||||||rs139116730|1|2976|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.0005||||A:0.0013|A:0.000227|A:0.003488|||||||||||||||||,A|ENSG00000187634|ENST00000342066|Transcript|downstream_gene_variant||||||rs139116730|1|3963|1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04||||||||A:0.0005||||A:0.0013|A:0.000227|A:0.003488||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000188976|ENST00000327044|Transcript|synonymous_variant|1559|1509|503|S|tcC/tcT|rs139116730|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C|||13/19||Pfam_domain:PF03715&Superfamily_domains:SSF48371|ENST00000327044.6:c.1509N>T|ENST00000327044.6:c.1509N>T(p.%3D)|A:0.0005||||A:0.0013|A:0.000227|A:0.003488||||||||POSITION:0.670666666666667||NON_CAN_SPLICE_SURR|||||||,A|ENSG00000188976|ENST00000477976|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2956|||||rs139116730|1||-1|NOC2L|HGNC|24517|retained_intron||||||||||11/17|||ENST00000477976.1:n.2956N>T||A:0.0005||||A:0.0013|A:0.000227|A:0.003488|||||||||||||||||,A|ENSG00000187634|ENST00000341065|Transcript|downstream_gene_variant||||||rs139116730|1|3963|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A||||||||A:0.0005||||A:0.0013|A:0.000227|A:0.003488||||||||||EXON_INTRON_UNDEF||||||| GT:AD:DP:GQ:PL 0/0:76,0:76:99:0,229,2746 0/0:47,0:47:99:0,141,1738 0/0:75,0:75:99:0,226,2710 0/0:36,0:36:99:0,108,1201 0/0:37,0:37:99:0,111,1271 0/0:42,0:42:99:0,126,1443 0/0:74,0:74:99:0,223,2609 0/0:82,0:82:99:0,247,2963 0/0:120,0:120:99:0,361,4336 0/0:96,0:96:99:0,289,3468 0/1:38,33:68:99:823,0,921 0/0:78,0:78:99:0,235,2818 0/0:56,0:56:99:0,169,1974 0/0:92,0:92:99:0,277,3402 0/0:78,0:78:99:0,235,2884 0/0:89,0:89:99:0,268,3216 +1 887560 rs3748595 A C 806833.88 PASS AC=31;AF=9.69000e-01;AN=32;BaseQRankSum=5.43470e+01;DB;DP=472;Dels=0.00000e+00;FS=1.69080e+01;HaplotypeScore=2.91900e-01;InbreedingCoeff=7.38000e-02;MQ=5.93900e+01;MQ0=0;MQRankSum=1.20610e+01;QD=3.46800e+01;ReadPosRankSum=7.92100e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000487214;VQSLOD=6.35000e-01;culprit=FS;CSQ=C|ENSG00000188976|ENST00000327044|Transcript|intron_variant||||||rs3748595|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||10/18||ENST00000327044.6:c.1192-41N>G||A:0.1602|C:0.78|C:0.86|C:0.86|C:0.85|C:0.831139|C:0.932674||||||||INTRON_SIZE:272||NON_CAN_SPLICE&ANC_ALLELE|||||||,C|ENSG00000188976|ENST00000477976|Transcript|intron_variant&non_coding_transcript_variant||||||rs3748595|1||-1|NOC2L|HGNC|24517|retained_intron|||||||||||8/16||ENST00000477976.1:n.2639-41N>G||A:0.1602|C:0.78|C:0.86|C:0.86|C:0.85|C:0.831139|C:0.932674|||||||||||||||||,C|ENSG00000188976|ENST00000487214|Transcript|downstream_gene_variant||||||rs3748595|1|2246|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.1602|C:0.78|C:0.86|C:0.86|C:0.85|C:0.831139|C:0.932674||||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,44:44:99:1706,132,0 1/1:0,43:43:99:1773,129,0 1/1:0,41:41:99:1582,123,0 1/1:0,19:19:54:687,54,0 1/1:0,23:23:69:851,69,0 1/1:0,10:10:30:370,30,0 1/1:0,33:33:99:1320,99,0 1/1:1,25:25:75:1020,75,0 1/1:0,26:26:78:1040,78,0 1/1:0,25:25:75:1000,75,0 1/1:0,36:36:99:1461,108,0 0/1:23,14:36:99:439,0,642 1/1:0,23:23:69:930,69,0 1/1:0,28:28:84:1121,84,0 1/1:0,23:23:69:904,69,0 1/1:0,37:37:99:1420,108,0 +1 887801 rs3828047 A G 1348829.24 PASS AC=31;AF=9.69000e-01;AN=32;BaseQRankSum=4.41560e+01;DB;DP=777;Dels=0.00000e+00;FS=8.43510e+01;HaplotypeScore=3.07000e-01;InbreedingCoeff=-1.77000e-02;MQ=5.58800e+01;MQ0=35;MQRankSum=-2.15910e+01;QD=3.44400e+01;ReadPosRankSum=5.44300e+00;SNPEFF_AMINO_ACID_CHANGE=T394;SNPEFF_CODON_CHANGE=acT/acC;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_887792_887980;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=-6.22100e-01;culprit=MQ;CSQ=G|ENSG00000188976|ENST00000327044|Transcript|synonymous_variant|1232|1182|394|T|acT/acC|rs3828047&COSM426785|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C|||10/19||Pfam_domain:PF03715&Superfamily_domains:SSF48371|ENST00000327044.6:c.1182N>C|ENST00000327044.6:c.1182N>C(p.%3D)|A:0.0716|G:0.90|G:0.92|G:0.92|G:0.95|G:0.906037|G:0.938372||0&1||||||POSITION:0.525333333333333||NON_CAN_SPLICE_SURR&ANC_ALLELE|||||||,G|ENSG00000188976|ENST00000477976|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2629|||||rs3828047&COSM426785|1||-1|NOC2L|HGNC|24517|retained_intron||||||||||8/17|||ENST00000477976.1:n.2629N>C||A:0.0716|G:0.90|G:0.92|G:0.92|G:0.95|G:0.906037|G:0.938372||0&1|||||||||||||||,G|ENSG00000188976|ENST00000487214|Transcript|downstream_gene_variant||||||rs3828047&COSM426785|1|2005|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.0716|G:0.90|G:0.92|G:0.92|G:0.95|G:0.906037|G:0.938372||0&1||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,42:42:99:1553,126,0 1/1:0,48:48:99:1824,138,0 1/1:0,54:54:99:1997,163,0 1/1:0,17:18:48:615,48,0 1/1:0,33:33:99:1220,99,0 1/1:0,30:30:90:1134,90,0 1/1:0,60:60:99:2315,181,0 1/1:0,44:44:99:1526,120,0 1/1:0,71:71:99:2791,214,0 1/1:0,48:48:99:1887,144,0 1/1:0,61:61:99:2398,184,0 0/1:29,33:59:99:915,0,742 1/1:0,30:30:90:1157,90,0 1/1:0,59:59:99:2321,178,0 1/1:0,55:55:99:2137,166,0 1/1:0,65:65:99:2507,196,0 +1 888529 . G A 1833.13 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-9.33700e+00;DP=387;Dels=0.00000e+00;FS=8.33000e-01;HaplotypeScore=1.94900e-01;InbreedingCoeff=-4.20000e-03;MQ=5.60200e+01;MQ0=0;MQRankSum=5.49600e+00;QD=1.10400e+01;ReadPosRankSum=-2.04000e-01;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000487214;VQSLOD=1.38000e+00;culprit=MQ;CSQ=A|ENSG00000188976|ENST00000327044|Transcript|intron_variant||||||rs373469542|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||9/18||ENST00000327044.6:c.1002+26N>T|||||||A:0.000908|A:0||||||||INTRON_SIZE:574||NON_CAN_SPLICE|||||||,A|ENSG00000188976|ENST00000477976|Transcript|intron_variant&non_coding_transcript_variant||||||rs373469542|1||-1|NOC2L|HGNC|24517|retained_intron|||||||||||7/16||ENST00000477976.1:n.2449+26N>T|||||||A:0.000908|A:0|||||||||||||||||,A|ENSG00000188976|ENST00000487214|Transcript|downstream_gene_variant||||||rs373469542|1|1277|-1|NOC2L|HGNC|24517|processed_transcript||||||||||||||||||||A:0.000908|A:0||||||||||||||||| GT:AD:DP:GQ:PL 0/0:19,0:19:57:0,57,703 0/0:26,0:26:78:0,78,1022 0/0:23,0:23:69:0,69,869 0/0:15,0:15:45:0,45,555 0/0:16,0:16:48:0,48,603 0/0:16,0:16:48:0,48,606 0/0:32,0:32:96:0,96,1258 0/0:26,0:26:72:0,72,944 0/0:24,0:24:69:0,69,898 0/1:12,15:26:99:432,0,321 0/0:31,0:31:93:0,93,1240 0/0:24,0:24:72:0,72,944 0/0:20,0:20:60:0,60,756 0/0:27,0:27:78:0,78,1029 0/0:36,0:36:99:0,108,1415 0/0:26,0:26:78:0,78,1022 +1 888659 rs3748597 T C 907727.36 PASS AC=31;AF=9.69000e-01;AN=32;BaseQRankSum=4.09230e+01;DB;DP=542;Dels=0.00000e+00;FS=4.67910e+01;HaplotypeScore=2.81100e-01;InbreedingCoeff=-1.65000e-02;MQ=5.48600e+01;MQ0=44;MQRankSum=-2.23740e+01;QD=3.38200e+01;ReadPosRankSum=8.50400e+00;SNPEFF_AMINO_ACID_CHANGE=I300V;SNPEFF_CODON_CHANGE=Atc/Gtc;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_888555_888668;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=-6.49600e-01;culprit=MQ;CSQ=C|ENSG00000188976|ENST00000469563|Transcript|downstream_gene_variant||||||rs3748597|1|4967|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0716|C:0.90|C:0.92|C:0.92|C:0.95|C:0.905767|C:0.938372|||||||||||||||||,C|ENSG00000188976|ENST00000327044|Transcript|missense_variant|948|898|300|I/V|Atc/Gtc|rs3748597|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C|tolerated(0.98)|benign(0)|9/19||Superfamily_domains:SSF48371|ENST00000327044.6:c.898N>G|ENSP00000317992.6:p.Ile300Val|T:0.0716|C:0.90|C:0.92|C:0.92|C:0.95|C:0.905767|C:0.938372||||||||POSITION:0.399111111111111||NON_CAN_SPLICE_SURR&ANC_ALLELE||B|0.940|P|T|T|T,C|ENSG00000188976|ENST00000477976|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2345|||||rs3748597|1||-1|NOC2L|HGNC|24517|retained_intron||||||||||7/17|||ENST00000477976.1:n.2345N>G||T:0.0716|C:0.90|C:0.92|C:0.92|C:0.95|C:0.905767|C:0.938372|||||||||||||||||,C|ENSG00000188976|ENST00000487214|Transcript|downstream_gene_variant||||||rs3748597|1|1147|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||T:0.0716|C:0.90|C:0.92|C:0.92|C:0.95|C:0.905767|C:0.938372||||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,33:33:96:1198,96,0 1/1:0,29:29:87:1140,87,0 1/1:0,27:27:81:998,81,0 1/1:0,27:27:81:962,81,0 1/1:0,19:19:57:686,57,0 1/1:0,22:22:63:796,63,0 1/1:0,39:39:99:1474,117,0 1/1:0,39:39:99:1504,117,0 1/1:0,32:32:96:1183,96,0 1/1:0,44:44:99:1654,129,0 1/1:0,55:55:99:2079,166,0 0/1:17,21:36:99:502,0,410 1/1:0,37:37:99:1398,111,0 1/1:0,44:44:99:1697,132,0 1/1:0,32:32:96:1209,96,0 1/1:0,27:27:81:1016,81,0 +1 889158 rs56262069 G C 909575.03 PASS AC=31;AF=9.69000e-01;AN=32;BaseQRankSum=3.68810e+01;DB;DP=579;Dels=0.00000e+00;FS=2.80669e+02;HaplotypeScore=5.39300e-01;InbreedingCoeff=7.80000e-02;MQ=5.90100e+01;MQ0=0;MQRankSum=-1.97700e+00;QD=3.19700e+01;ReadPosRankSum=8.43100e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000469563;VQSLOD=9.10000e-02;culprit=MQRankSum;CSQ=C|ENSG00000188976|ENST00000469563|Transcript|downstream_gene_variant||||||rs13303056|1|4468|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||G:0.1529|||||||||||||||||||||||,C|ENSG00000188976|ENST00000327044|Transcript|splice_region_variant&intron_variant||||||rs13303056|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||8/18||ENST00000327044.6:c.888+4N>G||G:0.1529||||||||||||||INTRON_SIZE:493||NON_CAN_SPLICE&ANC_ALLELE|||||||,C|ENSG00000188976|ENST00000477976|Transcript|splice_region_variant&intron_variant&non_coding_transcript_variant||||||rs13303056|1||-1|NOC2L|HGNC|24517|retained_intron|||||||||||6/16||ENST00000477976.1:n.2335+4N>G||G:0.1529|||||||||||||||||||||||,C|ENSG00000188976|ENST00000487214|Transcript|downstream_gene_variant||||||rs13303056|1|648|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||G:0.1529||||||||||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,45:45:99:1664,135,0 1/1:0,21:21:63:810,63,0 1/1:0,27:27:81:975,81,0 1/1:0,19:18:51:638,51,0 1/1:0,20:20:60:700,60,0 1/1:0,18:18:54:635,54,0 1/1:0,40:40:99:1512,120,0 1/1:0,34:34:99:1312,102,0 1/1:0,45:45:99:1615,132,0 1/1:0,40:40:99:1543,120,0 1/1:0,62:62:99:2392,187,0 0/1:23,19:40:99:499,0,598 1/1:0,45:45:99:1664,135,0 1/1:0,48:48:99:1814,144,0 1/1:0,39:39:99:1503,117,0 1/1:0,37:37:99:1398,111,0 +1 889159 rs13302945 A C 937927.21 PASS AC=31;AF=9.69000e-01;AN=32;BaseQRankSum=5.17190e+01;DB;DP=586;Dels=0.00000e+00;FS=2.49622e+02;HaplotypeScore=5.35000e-01;InbreedingCoeff=7.77000e-02;MQ=5.90200e+01;MQ0=0;MQRankSum=1.48040e+01;QD=3.22600e+01;ReadPosRankSum=8.79200e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000469563;VQSLOD=1.40000e-01;culprit=MQ;CSQ=C|ENSG00000188976|ENST00000469563|Transcript|downstream_gene_variant||||||rs13302945|1|4467|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||A:0.1538|C:0.79|C:0.87|C:0.88|C:0.85|C:0.823342|C:0.932294|||||||||||||||||,C|ENSG00000188976|ENST00000327044|Transcript|splice_region_variant&intron_variant||||||rs13302945|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||8/18||ENST00000327044.6:c.888+3N>G||A:0.1538|C:0.79|C:0.87|C:0.88|C:0.85|C:0.823342|C:0.932294||||||||INTRON_SIZE:493||NON_CAN_SPLICE&ANC_ALLELE|||||||,C|ENSG00000188976|ENST00000477976|Transcript|splice_region_variant&intron_variant&non_coding_transcript_variant||||||rs13302945|1||-1|NOC2L|HGNC|24517|retained_intron|||||||||||6/16||ENST00000477976.1:n.2335+3N>G||A:0.1538|C:0.79|C:0.87|C:0.88|C:0.85|C:0.823342|C:0.932294|||||||||||||||||,C|ENSG00000188976|ENST00000487214|Transcript|downstream_gene_variant||||||rs13302945|1|647|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.1538|C:0.79|C:0.87|C:0.88|C:0.85|C:0.823342|C:0.932294||||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,44:44:99:1663,132,0 1/1:0,21:21:63:794,63,0 1/1:0,28:28:84:1058,84,0 1/1:0,19:18:51:634,51,0 1/1:0,21:21:63:782,63,0 1/1:0,18:18:54:650,54,0 1/1:0,42:42:99:1587,126,0 1/1:0,34:34:99:1312,102,0 1/1:0,45:45:99:1657,132,0 1/1:0,41:41:99:1582,123,0 1/1:0,61:61:99:2353,184,0 0/1:24,19:41:99:482,0,633 1/1:0,43:43:99:1625,129,0 1/1:0,52:52:99:1965,156,0 1/1:0,42:42:99:1557,123,0 1/1:0,35:35:99:1323,105,0 +1 889238 rs3828049 G A 52801.55 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-4.91500e+00;DB;DP=911;Dels=0.00000e+00;FS=4.16200e+01;HaplotypeScore=2.87900e-01;InbreedingCoeff=3.34000e-02;MQ=5.93400e+01;MQ0=1;MQRankSum=3.62800e+00;QD=1.41200e+01;ReadPosRankSum=-2.71000e+00;SNPEFF_AMINO_ACID_CHANGE=A271V;SNPEFF_CODON_CHANGE=gCg/gTg;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_889162_889272;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=5.38000e+00;culprit=MQRankSum;CSQ=A|ENSG00000188976|ENST00000469563|Transcript|downstream_gene_variant||||||rs3828049&COSM1602748|1|4388|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||A:0.0537|A:0.02|A:0.08|A:0.08|A:0.05|A:0.021562|A:0.060363||0&1|||||||||||||||,A|ENSG00000188976|ENST00000327044|Transcript|missense_variant|862|812|271|A/V|gCg/gTg|rs3828049&COSM1602748|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C|deleterious(0.04)|benign(0.034)|8/19||Superfamily_domains:SSF48371|ENST00000327044.6:c.812N>T|ENSP00000317992.6:p.Ala271Val|A:0.0537|A:0.02|A:0.08|A:0.08|A:0.05|A:0.021562|A:0.060363||0&1||||||POSITION:0.360888888888889||NON_CAN_SPLICE_SURR||D%3BP%3BP|21.3|N|T|D|T,A|ENSG00000188976|ENST00000477976|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2259|||||rs3828049&COSM1602748|1||-1|NOC2L|HGNC|24517|retained_intron||||||||||6/17|||ENST00000477976.1:n.2259N>T||A:0.0537|A:0.02|A:0.08|A:0.08|A:0.05|A:0.021562|A:0.060363||0&1|||||||||||||||,A|ENSG00000188976|ENST00000487214|Transcript|downstream_gene_variant||||||rs3828049&COSM1602748|1|568|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.0537|A:0.02|A:0.08|A:0.08|A:0.05|A:0.021562|A:0.060363||0&1||||||||||||||| GT:AD:DP:GQ:PL 0/0:53,0:53:99:0,159,1960 0/0:56,0:56:99:0,169,2071 0/0:42,0:42:99:0,126,1517 0/0:23,0:23:69:0,69,763 0/0:31,0:31:93:0,93,1007 0/0:26,0:26:69:0,69,754 0/0:55,0:55:99:0,166,1987 0/0:59,0:59:99:0,178,2132 0/0:67,0:67:99:0,202,2362 0/0:79,0:79:99:0,238,2854 0/0:82,0:82:99:0,247,2963 0/1:32,31:62:99:888,0,808 0/0:75,0:75:99:0,226,2644 0/0:66,0:66:99:0,199,2385 0/0:68,0:68:99:0,205,2397 0/0:67,0:67:99:0,202,2362 +1 894573 rs13303010 G A 310883.38 PASS AC=30;AF=9.38000e-01;AN=32;BaseQRankSum=1.22670e+01;DB;DP=304;Dels=0.00000e+00;FS=2.34720e+01;HaplotypeScore=3.24800e-01;InbreedingCoeff=4.23300e-01;MQ=5.89800e+01;MQ0=0;MQRankSum=1.80380e+01;QD=2.67400e+01;ReadPosRankSum=2.89300e+00;SNPEFF_EFFECT=INTRON;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=1.10000e+00;culprit=MQ;CSQ=A|ENSG00000187961|ENST00000466300|Transcript|upstream_gene_variant||||||rs13303010|1|3534|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||G:0.3480|A:0.18|A:0.71|A:0.69|A:0.90|A:0.284570|A:0.896942|||||||||||||||||,A|ENSG00000188976|ENST00000327044|Transcript|intron_variant||||||rs13303010|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||1/18||ENST00000327044.6:c.26+22N>T||G:0.3480|A:0.18|A:0.71|A:0.69|A:0.90|A:0.284570|A:0.896942||||||||INTRON_SIZE:133||NON_CAN_SPLICE|||||||,A|ENSG00000187961|ENST00000338591|Transcript|upstream_gene_variant||||||rs13303010|1|1394|1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||||||G:0.3480|A:0.18|A:0.71|A:0.69|A:0.90|A:0.284570|A:0.896942||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000187961|ENST00000463212|Transcript|upstream_gene_variant||||||rs13303010|1|2256|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||G:0.3480|A:0.18|A:0.71|A:0.69|A:0.90|A:0.284570|A:0.896942|||||||||||||||||,A|ENSG00000188976|ENST00000469563|Transcript|intron_variant&non_coding_transcript_variant||||||rs13303010|1||-1|NOC2L|HGNC|24517|retained_intron|||||||||||1/1||ENST00000469563.1:n.42+22N>T||G:0.3480|A:0.18|A:0.71|A:0.69|A:0.90|A:0.284570|A:0.896942|||||||||||||||||,A|ENSG00000188976|ENST00000477976|Transcript|upstream_gene_variant||||||rs13303010|1|735|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||G:0.3480|A:0.18|A:0.71|A:0.69|A:0.90|A:0.284570|A:0.896942|||||||||||||||||,A|ENSG00000187961|ENST00000481067|Transcript|upstream_gene_variant||||||rs13303010|1|4359|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||G:0.3480|A:0.18|A:0.71|A:0.69|A:0.90|A:0.284570|A:0.896942|||||||||||||||||,A|ENSG00000188976|ENST00000487214|Transcript|intron_variant&non_coding_transcript_variant||||||rs13303010|1||-1|NOC2L|HGNC|24517|processed_transcript|||||||||||1/6||ENST00000487214.1:n.95+22N>T||G:0.3480|A:0.18|A:0.71|A:0.69|A:0.90|A:0.284570|A:0.896942|||||||||||||||||,A||ENSR00000528861|RegulatoryFeature|regulatory_region_variant||||||rs13303010|1||||||regulatory_region|||||||||||||||G:0.3480|A:0.18|A:0.71|A:0.69|A:0.90|A:0.284570|A:0.896942||||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,24:24:72:898,72,0 0/1:10,8:17:99:196,0,291 1/1:0,13:12:36:454,36,0 1/1:0,7:7:21:254,21,0 1/1:0,5:5:15:181,15,0 1/1:0,13:13:36:428,36,0 1/1:0,31:31:93:1120,93,0 1/1:0,24:24:72:867,72,0 1/1:0,26:26:78:924,78,0 1/1:0,26:26:78:958,78,0 1/1:0,19:19:57:670,57,0 0/1:17,6:22:99:127,0,513 1/1:0,20:20:60:723,60,0 1/1:0,23:23:69:869,69,0 1/1:0,19:19:57:686,57,0 1/1:0,16:16:48:505,48,0 +1 896922 . C T 1253.52 PASS AC=2;AF=6.30000e-02;AN=32;BaseQRankSum=-8.14600e+00;DP=943;Dels=0.00000e+00;FS=5.89500e+00;HaplotypeScore=1.37200e-01;InbreedingCoeff=-1.30000e-03;MQ=5.92800e+01;MQ0=0;MQRankSum=1.05600e+00;QD=1.01100e+01;ReadPosRankSum=-1.19000e+00;SNPEFF_AMINO_ACID_CHANGE=A119;SNPEFF_CODON_CHANGE=gcC/gcT;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_896673_896932;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000338591;VQSLOD=8.89000e+00;culprit=InbreedingCoeff;CSQ=T|ENSG00000187961|ENST00000466300|Transcript|upstream_gene_variant|||||||1|1185|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E|||||||||||||||||||||||||||||||,T|ENSG00000188976|ENST00000327044|Transcript|upstream_gene_variant|||||||1|2252|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187961|ENST00000338591|Transcript|synonymous_variant|464|357|119|A|gcC/gcT||1||1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0|||2/12||Pfam_domain:PF00651&PROSITE_profiles:PS50097&SMART_domains:SM00225&Superfamily_domains:SSF54695&PIRSF_domain:PIRSF037037|ENST00000338591.3:c.357N>T|ENST00000338591.3:c.357N>T(p.%3D)|||||||||||||||POSITION:0.1850699844479||NON_CAN_SPLICE_SURR|||||||,T|ENSG00000187583|ENST00000379409|Transcript|upstream_gene_variant|||||||1|4960|1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187961|ENST00000463212|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|94||||||1||1|KLHL17|HGNC|24023|retained_intron||||||||||1/2|||ENST00000463212.1:n.94N>T|||||||||||||||||||||||||,T|ENSG00000187583|ENST00000379407|Transcript|upstream_gene_variant|||||||1|4960|1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000469563|Transcript|upstream_gene_variant|||||||1|2286|-1|NOC2L|HGNC|24517|retained_intron||||||||||||||||||||||||||||||||||||||,T|ENSG00000187583|ENST00000379410|Transcript|upstream_gene_variant|||||||1|4955|1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000477976|Transcript|upstream_gene_variant|||||||1|3084|-1|NOC2L|HGNC|24517|retained_intron||||||||||||||||||||||||||||||||||||||,T|ENSG00000187961|ENST00000481067|Transcript|upstream_gene_variant|||||||1|2010|1|KLHL17|HGNC|24023|retained_intron||||||||||||||||||||||||||||||||||||||,T|ENSG00000188976|ENST00000487214|Transcript|upstream_gene_variant|||||||1|2233|-1|NOC2L|HGNC|24517|processed_transcript||||||||||||||||||||||||||||||||||||||,T||ENSR00000528861|RegulatoryFeature|regulatory_region_variant|||||||1||||||regulatory_region|||||||||||||||||||||||||||||||||||||| GT:AD:DP:GQ:PL 0/0:71,0:71:99:0,214,2684 0/0:69,0:69:99:0,208,2713 0/0:68,0:68:99:0,205,2515 0/0:20,0:20:57:0,57,722 0/0:29,0:29:87:0,87,1096 0/0:36,0:36:99:0,99,1225 0/0:61,0:61:99:0,184,2353 0/0:58,0:58:99:0,175,2192 0/0:68,0:68:99:0,205,2673 0/1:41,25:63:99:678,0,1190 0/0:87,0:87:99:0,262,3356 0/0:52,0:52:99:0,157,2006 0/1:35,23:55:99:651,0,922 0/0:79,0:79:99:0,238,3048 0/0:73,0:73:99:0,220,2816 0/0:54,0:54:99:0,163,2045 +1 897325 rs4970441 G C 2226684.78 PASS AC=31;AF=9.69000e-01;AN=32;BaseQRankSum=3.69960e+01;DB;DP=1475;Dels=0.00000e+00;FS=1.12830e+01;HaplotypeScore=4.66400e-01;InbreedingCoeff=1.15000e-01;MQ=5.95500e+01;MQ0=1;MQRankSum=2.60000e-02;QD=3.33700e+01;ReadPosRankSum=6.38900e+00;SNPEFF_AMINO_ACID_CHANGE=A203;SNPEFF_CODON_CHANGE=gcG/gcC;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_897206_897427;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000338591;VQSLOD=5.29000e+00;culprit=ReadPosRankSum;CSQ=C|ENSG00000187961|ENST00000466300|Transcript|upstream_gene_variant||||||rs4970441|1|782|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163|||||||||||||||||,C|ENSG00000188976|ENST00000327044|Transcript|upstream_gene_variant||||||rs4970441|1|2655|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000338591|Transcript|synonymous_variant|716|609|203|A|gcG/gcC|rs4970441|1||1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0|||4/12||Pfam_domain:PF07707&SMART_domains:SM00875&PIRSF_domain:PIRSF037037|ENST00000338591.3:c.609N>C|ENST00000338591.3:c.609N>C(p.%3D)|G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163||||||||POSITION:0.315707620528771||NON_CAN_SPLICE_SURR|||||||,C|ENSG00000187583|ENST00000379409|Transcript|upstream_gene_variant||||||rs4970441|1|4557|1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06||||||||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000463212|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|422|||||rs4970441|1||1|KLHL17|HGNC|24023|retained_intron||||||||||2/2|||ENST00000463212.1:n.422N>C||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163|||||||||||||||||,C|ENSG00000187583|ENST00000379407|Transcript|upstream_gene_variant||||||rs4970441|1|4557|1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF||||||||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000188976|ENST00000469563|Transcript|upstream_gene_variant||||||rs4970441|1|2689|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163|||||||||||||||||,C|ENSG00000187583|ENST00000379410|Transcript|upstream_gene_variant||||||rs4970441|1|4552|1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8||||||||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000188976|ENST00000477976|Transcript|upstream_gene_variant||||||rs4970441|1|3487|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163|||||||||||||||||,C|ENSG00000187961|ENST00000481067|Transcript|upstream_gene_variant||||||rs4970441|1|1607|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163|||||||||||||||||,C|ENSG00000188976|ENST00000487214|Transcript|upstream_gene_variant||||||rs4970441|1|2636|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163||||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,94:94:99:3476,283,0 1/1:0,87:87:99:3356,262,0 1/1:0,108:108:99:3994,325,0 1/1:0,56:56:99:2023,169,0 1/1:0,59:59:99:2182,178,0 1/1:0,46:46:99:1701,138,0 1/1:0,100:100:99:3780,301,0 1/1:0,127:127:99:4800,382,0 1/1:0,127:127:99:4899,382,0 1/1:0,127:127:99:4800,382,0 1/1:0,117:117:99:4422,352,0 0/1:42,33:71:99:891,0,1116 1/1:0,78:78:99:2948,235,0 1/1:0,107:107:99:4128,322,0 1/1:0,95:95:99:3665,286,0 1/1:0,76:76:99:2873,229,0 +1 898313 . C T 4423.71 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=1.00100e+01;DP=235;Dels=0.00000e+00;FS=6.83200e+00;HaplotypeScore=5.07500e-01;InbreedingCoeff=9.84000e-02;MQ=5.92600e+01;MQ0=0;MQRankSum=-5.62000e-01;QD=1.22500e+01;ReadPosRankSum=-4.59200e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000463212;VQSLOD=3.67000e+00;culprit=MQRankSum;CSQ=T|ENSG00000187961|ENST00000466300|Transcript|intron_variant&NMD_transcript_variant||||||rs375277853|1||1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||1/5||ENST00000466300.1:c.191+16N>T|||||||||||||||||||||||||,T|ENSG00000188976|ENST00000327044|Transcript|upstream_gene_variant||||||rs375277853|1|3643|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187961|ENST00000338591|Transcript|intron_variant||||||rs375277853|1||1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||6/11||ENST00000338591.3:c.1042+16N>T||||||||||||||||INTRON_SIZE:191||NON_CAN_SPLICE|||||||,T|ENSG00000187583|ENST00000379409|Transcript|upstream_gene_variant||||||rs375277853|1|3569|1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs375277853|1|455|1|KLHL17|HGNC|24023|retained_intron||||||||||||||||||||||||||||||||||||||,T|ENSG00000187583|ENST00000379407|Transcript|upstream_gene_variant||||||rs375277853|1|3569|1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000469563|Transcript|upstream_gene_variant||||||rs375277853|1|3677|-1|NOC2L|HGNC|24517|retained_intron||||||||||||||||||||||||||||||||||||||,T|ENSG00000187583|ENST00000379410|Transcript|upstream_gene_variant||||||rs375277853|1|3564|1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000477976|Transcript|upstream_gene_variant||||||rs375277853|1|4475|-1|NOC2L|HGNC|24517|retained_intron||||||||||||||||||||||||||||||||||||||,T|ENSG00000187961|ENST00000481067|Transcript|upstream_gene_variant||||||rs375277853|1|619|1|KLHL17|HGNC|24023|retained_intron||||||||||||||||||||||||||||||||||||||,T|ENSG00000188976|ENST00000487214|Transcript|upstream_gene_variant||||||rs375277853|1|3624|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||||||||||||||||||||||||| GT:AD:DP:GQ:PL 0/0:19,0:19:57:0,57,653 0/0:12,0:12:36:0,36,423 0/0:21,0:21:63:0,63,740 0/0:6,0:6:15:0,15,157 0/0:2,0:2:6:0,6,63 0/0:6,0:6:15:0,15,159 0/0:14,0:14:42:0,42,455 0/0:18,0:18:54:0,54,624 0/0:14,0:14:39:0,39,447 0/0:25,0:25:72:0,72,805 0/0:16,0:16:48:0,48,564 0/1:13,8:20:99:190,0,314 0/0:21,0:21:63:0,63,702 0/0:17,1:18:18:0,18,560 0/0:11,0:11:30:0,30,342 0/0:12,0:12:36:0,36,393 +1 898323 rs6605071 T C 353673.96 PASS AC=31;AF=9.69000e-01;AN=32;BaseQRankSum=1.91890e+01;DB;DP=221;Dels=0.00000e+00;FS=9.64600e+00;HaplotypeScore=4.04000e-01;InbreedingCoeff=-2.15000e-02;MQ=5.91700e+01;MQ0=0;MQRankSum=-4.60000e-02;QD=3.77900e+01;ReadPosRankSum=3.36900e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000463212;VQSLOD=4.11000e+00;culprit=InbreedingCoeff;CSQ=C|ENSG00000187961|ENST00000466300|Transcript|intron_variant&NMD_transcript_variant||||||rs6605071|1||1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||1/5||ENST00000466300.1:c.191+26N>C||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859|||||||||||||||||,C|ENSG00000188976|ENST00000327044|Transcript|upstream_gene_variant||||||rs6605071|1|3653|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859||||||||||EXON_INTRON_UNDEF&ANC_ALLELE|||||||,C|ENSG00000187961|ENST00000338591|Transcript|intron_variant||||||rs6605071|1||1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||6/11||ENST00000338591.3:c.1042+26N>C||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859||||||||INTRON_SIZE:191||NON_CAN_SPLICE&ANC_ALLELE|||||||,C|ENSG00000187583|ENST00000379409|Transcript|upstream_gene_variant||||||rs6605071|1|3559|1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06||||||||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859||||||||||EXON_INTRON_UNDEF&ANC_ALLELE|||||||,C|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs6605071|1|465|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859|||||||||||||||||,C|ENSG00000187583|ENST00000379407|Transcript|upstream_gene_variant||||||rs6605071|1|3559|1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF||||||||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859||||||||||EXON_INTRON_UNDEF&ANC_ALLELE|||||||,C|ENSG00000188976|ENST00000469563|Transcript|upstream_gene_variant||||||rs6605071|1|3687|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859|||||||||||||||||,C|ENSG00000187583|ENST00000379410|Transcript|upstream_gene_variant||||||rs6605071|1|3554|1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8||||||||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859||||||||||EXON_INTRON_UNDEF&ANC_ALLELE|||||||,C|ENSG00000188976|ENST00000477976|Transcript|upstream_gene_variant||||||rs6605071|1|4485|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859|||||||||||||||||,C|ENSG00000187961|ENST00000481067|Transcript|upstream_gene_variant||||||rs6605071|1|609|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859|||||||||||||||||,C|ENSG00000188976|ENST00000487214|Transcript|upstream_gene_variant||||||rs6605071|1|3634|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859||||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,18:18:54:688,54,0 1/1:0,8:8:24:315,24,0 1/1:0,15:15:45:579,45,0 1/1:0,7:7:21:262,21,0 1/1:0,3:3:9:111,9,0 1/1:0,4:4:9:122,9,0 1/1:0,20:20:60:786,60,0 1/1:0,16:16:48:641,48,0 1/1:0,13:13:36:457,36,0 1/1:0,27:27:78:1030,78,0 1/1:0,18:18:54:720,54,0 0/1:13,4:17:99:112,0,396 1/1:0,18:18:54:708,54,0 1/1:0,13:13:39:525,39,0 1/1:0,10:10:30:393,30,0 1/1:1,13:14:5:460,5,0 +1 898467 rs41285808 C T 14490.29 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-2.26300e+00;DB;DP=270;Dels=0.00000e+00;FS=1.33000e+00;HaplotypeScore=2.81700e-01;InbreedingCoeff=3.75000e-02;MQ=5.93000e+01;MQ0=0;MQRankSum=3.96000e+00;QD=1.37100e+01;ReadPosRankSum=-1.57400e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000463212;VQSLOD=7.17000e+00;culprit=FS;CSQ=T|ENSG00000187961|ENST00000466300|Transcript|synonymous_variant&NMD_transcript_variant|247|249|83|P|ccC/ccT|rs41285808|1||1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E|||2/6|||ENST00000466300.1:c.247N>T|ENST00000466300.1:c.247N>T(p.%3D)|T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672|||||||||||||||||,T|ENSG00000188976|ENST00000327044|Transcript|upstream_gene_variant||||||rs41285808|1|3797|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187961|ENST00000338591|Transcript|intron_variant||||||rs41285808|1||1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||6/11||ENST00000338591.3:c.1043-22N>T||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672||||||||INTRON_SIZE:191||NON_CAN_SPLICE|||||||,T|ENSG00000187583|ENST00000379409|Transcript|upstream_gene_variant||||||rs41285808|1|3415|1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06||||||||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs41285808|1|609|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672|||||||||||||||||,T|ENSG00000187583|ENST00000379407|Transcript|upstream_gene_variant||||||rs41285808|1|3415|1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF||||||||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000469563|Transcript|upstream_gene_variant||||||rs41285808|1|3831|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672|||||||||||||||||,T|ENSG00000187583|ENST00000379410|Transcript|upstream_gene_variant||||||rs41285808|1|3410|1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8||||||||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000477976|Transcript|upstream_gene_variant||||||rs41285808|1|4629|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672|||||||||||||||||,T|ENSG00000187961|ENST00000481067|Transcript|upstream_gene_variant||||||rs41285808|1|465|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672|||||||||||||||||,T|ENSG00000188976|ENST00000487214|Transcript|upstream_gene_variant||||||rs41285808|1|3778|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672||||||||||||||||| GT:AD:DP:GQ:PL 0/0:28,0:28:84:0,84,1030 0/0:15,0:15:45:0,45,579 0/0:25,0:25:75:0,75,916 0/0:6,0:6:18:0,18,197 0/0:5,0:5:15:0,15,172 0/0:3,0:3:9:0,9,100 0/0:14,0:14:42:0,42,480 0/0:22,0:22:66:0,66,817 0/0:23,0:23:69:0,69,831 0/0:12,0:12:36:0,36,431 0/0:18,0:18:51:0,51,646 0/1:17,10:26:99:278,0,440 0/0:21,0:21:51:0,51,644 0/0:13,0:13:39:0,39,481 0/0:18,0:18:54:0,54,666 0/0:21,0:21:60:0,60,723 +1 899959 . G GC 2073.57 PASS AC=1;AF=5.00000e-02;AN=20;BaseQRankSum=8.77000e-01;DP=19;FS=1.24470e+02;HaplotypeScore=1.51273e+01;InbreedingCoeff=6.94000e-02;MQ=4.52200e+01;MQ0=0;MQRankSum=-8.47500e+00;QD=1.40100e+01;ReadPosRankSum=4.26000e-01;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000463212;CSQ=C|ENSG00000187583|ENST00000379409|Transcript|upstream_gene_variant||||||TMP_ESP_1_899960_899959|1|1922|1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06|||||||||||||C:0.152075|C:0.090390||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||TMP_ESP_1_899960_899959|1|2101|1|KLHL17|HGNC|24023|retained_intron||||||||||||||||||||C:0.152075|C:0.090390|||||||||||||||||,C|ENSG00000187583|ENST00000379407|Transcript|upstream_gene_variant||||||TMP_ESP_1_899960_899959|1|1922|1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF|||||||||||||C:0.152075|C:0.090390||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000466300|Transcript|downstream_gene_variant||||||TMP_ESP_1_899960_899959|1|49|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E|||||||||||||C:0.152075|C:0.090390|||||||||||||||||,C|ENSG00000187583|ENST00000379410|Transcript|upstream_gene_variant||||||TMP_ESP_1_899960_899959|1|1917|1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8|||||||||||||C:0.152075|C:0.090390||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000481067|Transcript|downstream_gene_variant||||||TMP_ESP_1_899960_899959|1|415|1|KLHL17|HGNC|24023|retained_intron||||||||||||||||||||C:0.152075|C:0.090390|||||||||||||||||,C|ENSG00000187961|ENST00000338591|Transcript|intron_variant||||||TMP_ESP_1_899960_899959|1||1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||11/11||ENST00000338591.3:c.1700+49_1700+50insC|||||||C:0.152075|C:0.090390||||||||INTRON_SIZE:432||NON_CAN_SPLICE||||||| GT:AD:DP:GQ:PL ./.:.:.:.:. ./.:.:.:.:. 0/0:3,0:3:9:0,9,136 0/0:1,0:1:3:0,3,45 0/0:1,0:1:3:0,3,45 0/0:2,0:2:6:0,6,91 0/1:3,1:4:28:28,0,124 0/0:2,0:2:6:0,6,74 0/0:2,0:2:6:0,6,91 0/0:2,0:2:6:0,6,91 ./.:.:.:.:. ./.:.:.:.:. ./.:.:.:.:. 0/0:1,0:1:3:0,3,45 ./.:.:.:.:. 0/0:1,0:1:3:0,3,45 +1 900505 rs28705211 G C 222602.28 PASS AC=8;AF=2.50000e-01;AN=32;BaseQRankSum=6.97200e+00;DB;DP=885;Dels=0.00000e+00;FS=4.61940e+01;HaplotypeScore=1.18840e+00;InbreedingCoeff=1.98200e-01;MQ=5.92300e+01;MQ0=0;MQRankSum=1.76580e+01;QD=1.80400e+01;ReadPosRankSum=1.01980e+01;SNPEFF_AMINO_ACID_CHANGE=V497;SNPEFF_CODON_CHANGE=gtG/gtC;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_900343_901094;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000455747;VQSLOD=1.37000e+00;culprit=HaplotypeScore;CSQ=C|ENSG00000187583|ENST00000379409|Transcript|upstream_gene_variant||||||rs28705211&COSM426805|1|1377|1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06||||||||C:0.1648|C:0.02|C:0.22|C:0.09|C:0.28||||0&1|20637081|||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs28705211&COSM426805|1|2647|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||C:0.1648|C:0.02|C:0.22|C:0.09|C:0.28||||0&1|20637081||||||||||||||,C|ENSG00000187583|ENST00000379407|Transcript|upstream_gene_variant||||||rs28705211&COSM426805|1|1377|1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF||||||||C:0.1648|C:0.02|C:0.22|C:0.09|C:0.28||||0&1|20637081|||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000466300|Transcript|downstream_gene_variant||||||rs28705211&COSM426805|1|595|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||C:0.1648|C:0.02|C:0.22|C:0.09|C:0.28||||0&1|20637081||||||||||||||,C|ENSG00000187583|ENST00000379410|Transcript|upstream_gene_variant||||||rs28705211&COSM426805|1|1372|1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8||||||||C:0.1648|C:0.02|C:0.22|C:0.09|C:0.28||||0&1|20637081|||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000481067|Transcript|downstream_gene_variant||||||rs28705211&COSM426805|1|961|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||C:0.1648|C:0.02|C:0.22|C:0.09|C:0.28||||0&1|20637081||||||||||||||,C|ENSG00000187961|ENST00000338591|Transcript|synonymous_variant|1970|1863|621|V|gtG/gtC|rs28705211&COSM426805|1||1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0|||12/12||SMART_domains:SM00612&Superfamily_domains:SSF117281&PIRSF_domain:PIRSF037037|ENST00000338591.3:c.1863N>C|ENST00000338591.3:c.1863N>C(p.%3D)|C:0.1648|C:0.02|C:0.22|C:0.09|C:0.28||||0&1|20637081|||||POSITION:0.965785381026439||END_TRUNC&NON_CAN_SPLICE_SURR||||||| GT:AD:DP:GQ:PL 0/0:87,0:87:99:0,262,3217 0/1:43,24:61:99:697,0,1146 0/1:35,29:60:99:812,0,913 0/0:23,0:23:69:0,69,851 0/0:22,0:22:66:0,66,788 0/0:33,1:34:96:0,96,1150 0/0:54,0:54:99:0,162,1973 0/1:32,27:56:99:720,0,880 0/0:79,0:79:99:0,235,2850 0/0:74,0:74:99:0,214,2587 0/0:65,0:65:99:0,196,2354 0/1:24,26:48:99:738,0,687 0/1:27,28:54:99:795,0,709 0/0:58,0:58:99:0,175,2173 0/1:28,27:54:99:805,0,735 1/1:0,56:56:99:2066,169,0 +1 902024 rs181910588 G A 406.47 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-3.35500e+00;DB;DP=225;Dels=0.00000e+00;FS=1.03150e+01;HaplotypeScore=3.56800e-01;InbreedingCoeff=-1.33000e-02;MQ=5.93500e+01;MQ0=0;MQRankSum=1.21200e+00;QD=1.09900e+01;ReadPosRankSum=-1.50700e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000338591;VQSLOD=6.64000e+00;culprit=InbreedingCoeff;CSQ=A|ENSG00000187583|ENST00000480267|Transcript|upstream_gene_variant||||||rs181910588|1|4231|1|PLEKHN1|HGNC|25284|retained_intron|||||||||||||||A:0.0023|A:0.01||||A:0.001842|A:0|||||||||||||||||,A|ENSG00000187961|ENST00000466300|Transcript|downstream_gene_variant||||||rs181910588|1|2114|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||A:0.0023|A:0.01||||A:0.001842|A:0|||||||||||||||||,A|ENSG00000187961|ENST00000338591|Transcript|downstream_gene_variant||||||rs181910588|1|929|1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||||||A:0.0023|A:0.01||||A:0.001842|A:0||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs181910588|1|4166|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0023|A:0.01||||A:0.001842|A:0|||||||||||||||||,A|ENSG00000187583|ENST00000379409|Transcript|intron_variant||||||rs181910588|1||1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06||||1/14||ENST00000379409.2:c.83+30N>A||A:0.0023|A:0.01||||A:0.001842|A:0||||||||INTRON_SIZE:89||NON_CAN_SPLICE|||||||,A|ENSG00000187583|ENST00000379407|Transcript|intron_variant||||||rs181910588|1||1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF||||1/14||ENST00000379407.3:c.83+30N>A||A:0.0023|A:0.01||||A:0.001842|A:0||||||||INTRON_SIZE:89||NON_CAN_SPLICE|||||||,A|ENSG00000187961|ENST00000481067|Transcript|downstream_gene_variant||||||rs181910588|1|2480|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0023|A:0.01||||A:0.001842|A:0|||||||||||||||||,A|ENSG00000187583|ENST00000379410|Transcript|intron_variant||||||rs181910588|1||1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8||||1/15||ENST00000379410.3:c.83+30N>A||A:0.0023|A:0.01||||A:0.001842|A:0||||||||INTRON_SIZE:89||NON_CAN_SPLICE|||||||,A||ENSR00000528862|RegulatoryFeature|regulatory_region_variant||||||rs181910588|1||||||regulatory_region|||||||||||||||A:0.0023|A:0.01||||A:0.001842|A:0||||||||||||||||| GT:AD:DP:GQ:PL 0/0:18,0:18:54:0,54,689 0/0:21,0:21:63:0,63,797 0/0:17,0:17:48:0,48,608 0/0:5,0:5:15:0,15,182 0/0:9,0:9:27:0,27,333 0/0:7,0:7:21:0,21,253 0/0:18,0:18:54:0,54,680 0/0:7,0:7:21:0,21,259 0/0:17,0:17:51:0,51,614 0/0:19,0:19:54:0,54,647 0/0:20,0:20:60:0,60,756 0/0:14,0:14:42:0,42,518 0/0:13,0:13:36:0,36,466 0/0:14,0:14:42:0,42,535 0/1:9,1:11:4:4,0,296 0/0:15,0:15:45:0,45,551 +1 902069 rs116147894 T C 13024.04 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=2.08840e+01;DB;DP=157;Dels=0.00000e+00;FS=3.07700e+00;HaplotypeScore=2.10500e-01;InbreedingCoeff=1.00200e-01;MQ=5.91800e+01;MQ0=0;MQRankSum=7.75000e-01;QD=1.56200e+01;ReadPosRankSum=-5.68400e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000338591;VQSLOD=7.17000e+00;culprit=MQ;CSQ=C|ENSG00000187583|ENST00000480267|Transcript|upstream_gene_variant||||||rs116147894|1|4186|1|PLEKHN1|HGNC|25284|retained_intron|||||||||||||||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163|||||||||||||||||,C|ENSG00000187961|ENST00000466300|Transcript|downstream_gene_variant||||||rs116147894|1|2159|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163|||||||||||||||||,C|ENSG00000187961|ENST00000338591|Transcript|downstream_gene_variant||||||rs116147894|1|974|1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||||||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs116147894|1|4211|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163|||||||||||||||||,C|ENSG00000187583|ENST00000379409|Transcript|intron_variant||||||rs116147894|1||1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06||||1/14||ENST00000379409.2:c.84-15N>C||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163||||||||INTRON_SIZE:89||NON_CAN_SPLICE|||||||,C|ENSG00000187583|ENST00000379407|Transcript|intron_variant||||||rs116147894|1||1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF||||1/14||ENST00000379407.3:c.84-15N>C||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163||||||||INTRON_SIZE:89||NON_CAN_SPLICE|||||||,C|ENSG00000187961|ENST00000481067|Transcript|downstream_gene_variant||||||rs116147894|1|2525|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163|||||||||||||||||,C|ENSG00000187583|ENST00000379410|Transcript|intron_variant||||||rs116147894|1||1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8||||1/15||ENST00000379410.3:c.84-15N>C||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163||||||||INTRON_SIZE:89||NON_CAN_SPLICE|||||||,C||ENSR00000528862|RegulatoryFeature|regulatory_region_variant||||||rs116147894|1||||||regulatory_region|||||||||||||||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163||||||||||||||||| GT:AD:DP:GQ:PL 0/0:10,0:10:30:0,30,367 0/1:12,2:13:3:3,0,418 0/0:14,0:14:42:0,42,514 0/0:4,0:4:12:0,12,144 0/0:5,0:5:15:0,15,176 0/0:4,0:4:12:0,12,145 0/0:17,0:17:48:0,48,603 0/0:6,0:6:18:0,18,227 0/0:10,0:10:30:0,30,361 0/0:10,0:10:30:0,30,372 0/0:12,0:12:36:0,36,434 0/0:7,0:7:21:0,21,259 0/0:7,0:7:21:0,21,255 0/0:11,0:11:30:0,30,375 0/0:12,0:12:36:0,36,426 0/0:15,0:15:45:0,45,530 +1 902088 . G A 324.34 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-5.34900e+00;DP=133;Dels=0.00000e+00;FS=7.94000e-01;HaplotypeScore=1.50400e-01;InbreedingCoeff=3.03000e-02;MQ=5.93200e+01;MQ0=0;MQRankSum=2.32200e+00;QD=7.91000e+00;ReadPosRankSum=-2.12100e+00;SNPEFF_AMINO_ACID_CHANGE=D30N;SNPEFF_CODON_CHANGE=Gac/Aac;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_902084_902183;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=PLEKHN1;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000379407;VQSLOD=5.23000e+00;culprit=QD;CSQ=A|ENSG00000187583|ENST00000480267|Transcript|upstream_gene_variant||||||rs201730138|1|4167|1|PLEKHN1|HGNC|25284|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187961|ENST00000466300|Transcript|downstream_gene_variant||||||rs201730138|1|2178|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187961|ENST00000338591|Transcript|downstream_gene_variant||||||rs201730138|1|993|1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||||||A:0.0005||A:0.0028|||A:0|A:0.000600||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs201730138|1|4230|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187583|ENST00000379409|Transcript|missense_variant|118|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06|tolerated(0.26)|benign(0.034)|2/15|||ENST00000379409.2:c.88N>A|ENSP00000368719.2:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0441767068273092||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A|ENSG00000187583|ENST00000379407|Transcript|missense_variant|118|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF|tolerated(0.25)|benign(0.072)|2/15|||ENST00000379407.3:c.88N>A|ENSP00000368717.2:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0508376660889659||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A|ENSG00000187961|ENST00000481067|Transcript|downstream_gene_variant||||||rs201730138|1|2544|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187583|ENST00000379410|Transcript|missense_variant|123|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8|tolerated(0.25)|benign(0.072)|2/16|||ENST00000379410.3:c.88N>A|ENSP00000368720.3:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0479302832244009||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A||ENSR00000528862|RegulatoryFeature|regulatory_region_variant||||||rs201730138|1||||||regulatory_region|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600||||||||||||||||| GT:AD:DP:GQ:PL 0/1:10,1:11:1:1,0,264 0/0:13,0:13:33:0,33,447 0/0:10,0:10:30:0,30,371 0/0:4,0:4:12:0,12,141 0/0:1,0:1:3:0,3,39 0/0:4,0:4:12:0,12,145 0/0:18,0:18:51:0,51,665 0/0:4,0:4:12:0,12,148 0/0:5,0:5:15:0,15,193 0/0:9,0:9:24:0,24,320 0/0:10,0:10:30:0,30,378 0/0:4,0:4:12:0,12,160 0/0:10,0:10:30:0,30,387 0/0:7,0:7:21:0,21,247 0/0:9,0:9:27:0,27,350 0/0:14,0:14:42:0,42,540 +1 902088 . G ACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACT 324.34 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-5.34900e+00;DP=133;Dels=0.00000e+00;FS=7.94000e-01;HaplotypeScore=1.50400e-01;InbreedingCoeff=3.03000e-02;MQ=5.93200e+01;MQ0=0;MQRankSum=2.32200e+00;QD=7.91000e+00;ReadPosRankSum=-2.12100e+00;SNPEFF_AMINO_ACID_CHANGE=D30N;SNPEFF_CODON_CHANGE=Gac/Aac;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_902084_902183;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=PLEKHN1;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000379407;VQSLOD=5.23000e+00;culprit=QD;CSQ=A|ENSG00000187583|ENST00000480267|Transcript|upstream_gene_variant||||||rs201730138|1|4167|1|PLEKHN1|HGNC|25284|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187961|ENST00000466300|Transcript|downstream_gene_variant||||||rs201730138|1|2178|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187961|ENST00000338591|Transcript|downstream_gene_variant||||||rs201730138|1|993|1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||||||A:0.0005||A:0.0028|||A:0|A:0.000600||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs201730138|1|4230|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187583|ENST00000379409|Transcript|missense_variant|118|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06|tolerated(0.26)|benign(0.034)|2/15|||ENST00000379409.2:c.88N>A|ENSP00000368719.2:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0441767068273092||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A|ENSG00000187583|ENST00000379407|Transcript|missense_variant|118|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF|tolerated(0.25)|benign(0.072)|2/15|||ENST00000379407.3:c.88N>A|ENSP00000368717.2:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0508376660889659||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A|ENSG00000187961|ENST00000481067|Transcript|downstream_gene_variant||||||rs201730138|1|2544|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187583|ENST00000379410|Transcript|missense_variant|123|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8|tolerated(0.25)|benign(0.072)|2/16|||ENST00000379410.3:c.88N>A|ENSP00000368720.3:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0479302832244009||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A||ENSR00000528862|RegulatoryFeature|regulatory_region_variant||||||rs201730138|1||||||regulatory_region|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600||||||||||||||||| GT:AD:DP:GQ:PL 0/1:10,1:11:1:1,0,264 0/0:13,0:13:33:0,33,447 0/0:10,0:10:30:0,30,371 0/0:4,0:4:12:0,12,141 0/0:1,0:1:3:0,3,39 0/0:4,0:4:12:0,12,145 0/0:18,0:18:51:0,51,665 0/0:4,0:4:12:0,12,148 0/0:5,0:5:15:0,15,193 0/0:9,0:9:24:0,24,320 0/0:10,0:10:30:0,30,378 0/0:4,0:4:12:0,12,160 0/0:10,0:10:30:0,30,387 0/0:7,0:7:21:0,21,247 0/0:9,0:9:27:0,27,350 0/0:14,0:14:42:0,42,540 +GL000207.1 1 . G A 324.34 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-5.34900e+00;DP=133;Dels=0.00000e+00;FS=7.94000e-01;HaplotypeScore=1.50400e-01;InbreedingCoeff=3.03000e-02;MQ=5.93200e+01;MQ0=0;MQRankSum=2.32200e+00;QD=7.91000e+00;ReadPosRankSum=-2.12100e+00;SNPEFF_AMINO_ACID_CHANGE=D30N;SNPEFF_CODON_CHANGE=Gac/Aac;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_902084_902183;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=PLEKHN1;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000379407;VQSLOD=5.23000e+00;culprit=QD;CSQ=A|ENSG00000187583|ENST00000480267|Transcript|upstream_gene_variant||||||rs201730138|1|4167|1|PLEKHN1|HGNC|25284|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187961|ENST00000466300|Transcript|downstream_gene_variant||||||rs201730138|1|2178|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187961|ENST00000338591|Transcript|downstream_gene_variant||||||rs201730138|1|993|1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||||||A:0.0005||A:0.0028|||A:0|A:0.000600||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs201730138|1|4230|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187583|ENST00000379409|Transcript|missense_variant|118|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06|tolerated(0.26)|benign(0.034)|2/15|||ENST00000379409.2:c.88N>A|ENSP00000368719.2:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0441767068273092||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A|ENSG00000187583|ENST00000379407|Transcript|missense_variant|118|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF|tolerated(0.25)|benign(0.072)|2/15|||ENST00000379407.3:c.88N>A|ENSP00000368717.2:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0508376660889659||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A|ENSG00000187961|ENST00000481067|Transcript|downstream_gene_variant||||||rs201730138|1|2544|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187583|ENST00000379410|Transcript|missense_variant|123|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8|tolerated(0.25)|benign(0.072)|2/16|||ENST00000379410.3:c.88N>A|ENSP00000368720.3:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0479302832244009||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A||ENSR00000528862|RegulatoryFeature|regulatory_region_variant||||||rs201730138|1||||||regulatory_region|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600||||||||||||||||| GT:AD:DP:GQ:PL 0/1:10,1:11:1:1,0,264 0/0:13,0:13:33:0,33,447 0/0:10,0:10:30:0,30,371 0/0:4,0:4:12:0,12,141 0/0:1,0:1:3:0,3,39 0/0:4,0:4:12:0,12,145 0/0:18,0:18:51:0,51,665 0/0:4,0:4:12:0,12,148 0/0:5,0:5:15:0,15,193 0/0:9,0:9:24:0,24,320 0/0:10,0:10:30:0,30,378 0/0:4,0:4:12:0,12,160 0/0:10,0:10:30:0,30,387 0/0:7,0:7:21:0,21,247 0/0:9,0:9:27:0,27,350 0/0:14,0:14:42:0,42,540 diff --git a/loading_pipeline/var/test/callsets/1kg_corrupt.vcf.gz b/loading_pipeline/var/test/callsets/1kg_corrupt.vcf.gz new file mode 100644 index 0000000000000000000000000000000000000000..c175f00b6ab30fdb0009c51dbcd9d1ead290d550 GIT binary patch literal 14872 zcmV+zI_Je7iwFP^yboyr1MPk5Qye+A=V$JpaVMr@X1ko|=&kb75g0Jdj*T(UeediS z2jgZuj_bBNFnxDBqW<_jM^a`gAF9gCdVn{;n1swyN;-O--+BJ&PyhV*>Gq#r?tZmRTcy)o{V_TQG8e7Tjr>|psa&mq=zGW}3##Zy=&2OK+ z+~Y^D-ha8f9b5YB^FQuxZ-2oFdi3S?pZ^?N{PnAoDbtXOjh>0G+sko42{wKNUQeC5 zZ`;GYvc%=Z;dt6z{xo!dsf*m+{BrT->%@LtonM^1eEIJ1_1XEGcZWx3$M24QJUl-= 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+##contig= +##contig= +##contig= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00731 HG00732 HG00733 NA19675 NA19678 NA19679 NA20870 NA20872 NA20874 NA20875 NA20876 NA20877 NA20878 NA20881 NA20885 NA20888 +1 871269 . A C 368.47 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-1.74060e+01;DP=351;Dels=0.00000e+00;FS=9.28030e+01;HaplotypeScore=5.13800e-01;InbreedingCoeff=-3.32000e-02;MQ=5.93000e+01;MQ0=0;MQRankSum=2.37300e+00;QD=4.80000e-01;ReadPosRankSum=-1.17980e+01;SNPEFF_AMINO_ACID_CHANGE=R141;SNPEFF_CODON_CHANGE=cgA/cgC;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_871152_871276;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=SAMD11;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000342066;VQSLOD=-8.16700e-01;culprit=QD;CSQ=C|ENSG00000187634|ENST00000455979|Transcript|upstream_gene_variant|||||||1|3386|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187634|ENST00000420190|Transcript|synonymous_variant|512|423|141|R|cgA/cgC||1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000411579||Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI000155D47C|||5/7|||ENST00000420190.1:c.423N>C|ENST00000420190.1:c.423N>C(p.%3D)|||||||||||||||POSITION:0.787709497206704||NON_CAN_SPLICE_SURR|||||||,C|ENSG00000268179|ENST00000598827|Transcript|upstream_gene_variant|||||||1|4824|-1|AL645608.1|Clone_based_ensembl_gene||protein_coding|YES|||ENSP00000471152||M0R0C9_HUMAN|UPI0000D61E05||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187634|ENST00000437963|Transcript|downstream_gene_variant|||||||1|96|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000393181||Q5SV95_HUMAN&I7FV93_HUMAN|UPI000155D47B||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187634|ENST00000478729|Transcript|upstream_gene_variant|||||||1|4457|1|SAMD11|HGNC|28706|processed_transcript||||||||||||||||||||||||||||||||||||||,C|ENSG00000187634|ENST00000342066|Transcript|synonymous_variant|506|423|141|R|cgA/cgC||1||1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04|||5/14|||ENST00000342066.3:c.423N>C|ENST00000342066.3:c.423N>C(p.%3D)|||||||||||||||POSITION:0.206744868035191||NON_CAN_SPLICE_SURR|||||||,C|ENSG00000187634|ENST00000341065|Transcript|synonymous_variant|194|195|65|R|cgA/cgC||1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A|||3/12|||ENST00000341065.4:c.194N>C|ENST00000341065.4:c.194N>C(p.%3D)|||||||||||||||POSITION:0.110231769361221||NON_CAN_SPLICE_SURR|||||||,C||ENSR00000528855|RegulatoryFeature|regulatory_region_variant|||||||1||||||regulatory_region|||||||||||||||||||||||||||||||||||||| GT:AD:DP:GQ:PL 0/0:34,0:34:99:0,102,1073 0/0:34,0:34:99:0,102,1064 0/0:37,0:37:99:0,108,1155 0/0:8,3:11:24:0,24,226 0/1:11,4:16:32:32,0,300 0/0:10,0:10:30:0,30,306 0/0:13,0:13:39:0,39,410 0/0:11,0:11:33:0,33,323 0/0:21,3:23:12:0,12,434 0/0:19,0:19:57:0,57,581 0/0:25,4:28:27:0,27,553 0/0:17,1:18:51:0,51,524 0/0:25,0:25:75:0,75,759 0/0:21,0:21:63:0,63,687 0/0:23,4:27:69:0,69,709 0/0:22,2:24:60:0,60,562 +1 874734 rs145967298 C T 2645.29 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-7.95400e+00;DB;DP=484;Dels=0.00000e+00;FS=7.13100e+00;HaplotypeScore=3.21100e-01;InbreedingCoeff=-6.80000e-03;MQ=5.85800e+01;MQ0=1;MQRankSum=7.38500e+00;QD=1.23600e+01;ReadPosRankSum=-7.54000e-01;SNPEFF_AMINO_ACID_CHANGE=S200;SNPEFF_CODON_CHANGE=agC/agT;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_874655_874840;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=SAMD11;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000342066;VQSLOD=5.39000e+00;culprit=InbreedingCoeff;CSQ=T|ENSG00000187634|ENST00000420190|Transcript|downstream_gene_variant||||||rs145967298|1|63|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000411579||Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI000155D47C||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187634|ENST00000342066|Transcript|synonymous_variant|683|600|200|S|agC/agT|rs145967298|1||1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04|||7/14|||ENST00000342066.3:c.600N>T|ENST00000342066.3:c.600N>T(p.%3D)|T:0.0009||T:0.01|||T:0.000227|T:0.001628||||||||POSITION:0.293255131964809||NON_CAN_SPLICE_SURR|||||||,T|ENSG00000188976|ENST00000327044|Transcript|downstream_gene_variant||||||rs145967298|1|4850|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187634|ENST00000464948|Transcript|upstream_gene_variant||||||rs145967298|1|2812|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628|||||||||||||||||,T|ENSG00000187634|ENST00000466827|Transcript|upstream_gene_variant||||||rs145967298|1|2749|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628|||||||||||||||||,T|ENSG00000187634|ENST00000474461|Transcript|upstream_gene_variant||||||rs145967298|1|1722|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628|||||||||||||||||,T|ENSG00000188976|ENST00000483767|Transcript|downstream_gene_variant||||||rs145967298|1|4850|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628|||||||||||||||||,T|ENSG00000187634|ENST00000455979|Transcript|synonymous_variant|80|81|27|S|agC/agT|rs145967298|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479|||1/7|||ENST00000455979.1:c.80N>T|ENST00000455979.1:c.80N>T(p.%3D)|T:0.0009||T:0.01|||T:0.000227|T:0.001628||||||||POSITION:0.0498461538461538||NON_CAN_SPLICE_SURR|||||||,T|ENSG00000187634|ENST00000437963|Transcript|downstream_gene_variant||||||rs145967298|1|3561|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000393181||Q5SV95_HUMAN&I7FV93_HUMAN|UPI000155D47B||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187634|ENST00000478729|Transcript|upstream_gene_variant||||||rs145967298|1|992|1|SAMD11|HGNC|28706|processed_transcript|||||||||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628|||||||||||||||||,T|ENSG00000188976|ENST00000477976|Transcript|downstream_gene_variant||||||rs145967298|1|4851|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628|||||||||||||||||,T|ENSG00000187634|ENST00000341065|Transcript|synonymous_variant|371|372|124|S|agC/agT|rs145967298|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A|||5/12|||ENST00000341065.4:c.371N>T|ENST00000341065.4:c.371N>T(p.%3D)|T:0.0009||T:0.01|||T:0.000227|T:0.001628||||||||POSITION:0.210288298473714||NON_CAN_SPLICE_SURR|||||||,T||ENSR00001516735|RegulatoryFeature|regulatory_region_variant||||||rs145967298|1||||||regulatory_region|||||||||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628||||||||||||||||| GT:AD:DP:GQ:PL 0/0:37,0:37:99:0,111,1368 0/0:24,0:24:66:0,66,870 0/0:32,0:32:96:0,96,1183 0/0:8,0:8:24:0,24,245 0/0:8,0:8:24:0,24,267 0/0:9,0:9:27:0,27,318 0/0:26,0:26:75:0,75,879 0/0:31,0:31:93:0,93,1120 0/0:39,0:39:99:0,117,1375 0/0:56,0:56:99:0,169,2023 0/1:21,22:42:99:519,0,613 0/0:29,0:29:87:0,87,1048 0/0:43,0:43:99:0,129,1556 0/0:20,0:20:60:0,60,741 0/0:45,0:45:99:0,135,1586 0/0:35,0:35:99:0,105,1239 +1 876499 rs4372192 A G 212847.01 PASS AC=31;AF=9.69000e-01;AN=32;BaseQRankSum=2.42570e+01;DB;DP=122;Dels=1.00000e-02;FS=9.96800e+00;HaplotypeScore=2.51500e-01;InbreedingCoeff=4.11000e-02;MQ=5.91300e+01;MQ0=0;MQRankSum=7.64000e-01;QD=3.03200e+01;ReadPosRankSum=2.13900e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=4.70000e+00;culprit=MQ;CSQ=G|ENSG00000187634|ENST00000420190|Transcript|downstream_gene_variant||||||rs4372192|1|1828|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000411579||Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI000155D47C||||||||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676||||||||||EXON_INTRON_UNDEF&ANC_ALLELE|||||||,G|ENSG00000188976|ENST00000496938|Transcript|downstream_gene_variant||||||rs4372192|1|4200|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676|||||||||||||||||,G|ENSG00000187634|ENST00000342066|Transcript|intron_variant||||||rs4372192|1||1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04||||7/13||ENST00000342066.3:c.707-25N>G||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676||||||||INTRON_SIZE:1683||NON_CAN_SPLICE&ANC_ALLELE|||||||,G|ENSG00000188976|ENST00000327044|Transcript|downstream_gene_variant||||||rs4372192|1|3085|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676||||||||||EXON_INTRON_UNDEF&ANC_ALLELE|||||||,G|ENSG00000187634|ENST00000464948|Transcript|upstream_gene_variant||||||rs4372192|1|1047|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676|||||||||||||||||,G|ENSG00000187634|ENST00000466827|Transcript|upstream_gene_variant||||||rs4372192|1|984|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676|||||||||||||||||,G|ENSG00000187634|ENST00000474461|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|44|||||rs4372192|1||1|SAMD11|HGNC|28706|retained_intron||||||||||1/4|||ENST00000474461.1:n.44N>G||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676|||||||||||||||||,G|ENSG00000187634|ENST00000455979|Transcript|intron_variant||||||rs4372192|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479||||1/6||ENST00000455979.1:c.187-25N>G||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676||||||||INTRON_SIZE:1683||NON_CAN_SPLICE&ANC_ALLELE|||||||,G|ENSG00000188976|ENST00000483767|Transcript|downstream_gene_variant||||||rs4372192|1|3085|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676|||||||||||||||||,G|ENSG00000187634|ENST00000478729|Transcript|intron_variant&non_coding_transcript_variant||||||rs4372192|1||1|SAMD11|HGNC|28706|processed_transcript|||||||||||1/2||ENST00000478729.1:n.118-25N>G||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676|||||||||||||||||,G|ENSG00000188976|ENST00000477976|Transcript|downstream_gene_variant||||||rs4372192|1|3086|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676|||||||||||||||||,G|ENSG00000187634|ENST00000341065|Transcript|intron_variant||||||rs4372192|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A||||5/11||ENST00000341065.4:c.430-25N>G||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676||||||||INTRON_SIZE:1731||NON_CAN_SPLICE&ANC_ALLELE|||||||,G||ENSR00000528857|RegulatoryFeature|regulatory_region_variant||||||rs4372192|1||||||regulatory_region|||||||||||||||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676||||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,7:7:21:253,21,0 1/1:0,8:8:24:296,24,0 1/1:0,4:4:12:148,12,0 1/1:0,5:5:15:184,15,0 1/1:0,1:1:3:39,3,0 1/1:0,5:5:15:176,15,0 1/1:0,9:9:27:316,27,0 1/1:0,11:11:33:397,33,0 1/1:0,7:7:18:212,18,0 1/1:0,11:11:27:369,27,0 1/1:0,13:13:39:492,39,0 0/1:7,9:15:99:235,0,158 1/1:0,7:7:18:231,18,0 1/1:0,4:4:12:154,12,0 1/1:0,8:8:24:296,24,0 1/1:0,7:7:21:270,21,0 +1 878314 rs142558220 G C 2808.55 PASS AC=3;AF=9.40000e-02;AN=32;BaseQRankSum=1.88800e+00;DB;DP=117;Dels=0.00000e+00;FS=1.06220e+01;HaplotypeScore=2.21900e-01;InbreedingCoeff=3.64000e-02;MQ=5.94000e+01;MQ0=1;MQRankSum=1.65200e+00;QD=9.46000e+00;ReadPosRankSum=-3.88300e+00;SNPEFF_AMINO_ACID_CHANGE=G480;SNPEFF_CODON_CHANGE=ggG/ggC;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_877939_878438;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=SAMD11;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000342066;VQSLOD=6.85000e+00;culprit=QD;CSQ=C|ENSG00000187634|ENST00000420190|Transcript|downstream_gene_variant||||||rs142558220&COSM426784|1|3643|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000411579||Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI000155D47C||||||||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000188976|ENST00000496938|Transcript|downstream_gene_variant||||||rs142558220&COSM426784|1|2385|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1|||||||||||||||,C|ENSG00000187634|ENST00000342066|Transcript|synonymous_variant|1523|1440|480|G|ggG/ggC|rs142558220&COSM426784|1||1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04|||11/14|||ENST00000342066.3:c.1440N>C|ENST00000342066.3:c.1440N>C(p.%3D)|C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1||||||POSITION:0.703812316715543||NON_CAN_SPLICE_SURR|||||||,C|ENSG00000188976|ENST00000327044|Transcript|downstream_gene_variant||||||rs142558220&COSM426784|1|1270|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187634|ENST00000464948|Transcript|downstream_gene_variant||||||rs142558220&COSM426784|1|42|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1|||||||||||||||,C|ENSG00000187634|ENST00000466827|Transcript|downstream_gene_variant||||||rs142558220&COSM426784|1|132|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1|||||||||||||||,C|ENSG00000187634|ENST00000474461|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|802|||||rs142558220&COSM426784|1||1|SAMD11|HGNC|28706|retained_intron||||||||||4/4|||ENST00000474461.1:n.802N>C||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1|||||||||||||||,C|ENSG00000187634|ENST00000455979|Transcript|synonymous_variant|920|921|307|G|ggG/ggC|rs142558220&COSM426784|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479|||5/7|||ENST00000455979.1:c.920N>C|ENST00000455979.1:c.920N>C(p.%3D)|C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1||||||POSITION:0.566769230769231||NON_CAN_SPLICE_SURR|||||||,C|ENSG00000188976|ENST00000483767|Transcript|downstream_gene_variant||||||rs142558220&COSM426784|1|1270|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1|||||||||||||||,C|ENSG00000187634|ENST00000478729|Transcript|downstream_gene_variant||||||rs142558220&COSM426784|1|761|1|SAMD11|HGNC|28706|processed_transcript|||||||||||||||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1|||||||||||||||,C|ENSG00000188976|ENST00000477976|Transcript|downstream_gene_variant||||||rs142558220&COSM426784|1|1271|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1|||||||||||||||,C|ENSG00000187634|ENST00000341065|Transcript|synonymous_variant|1163|1164|388|G|ggG/ggC|rs142558220&COSM426784|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A|||9/12|||ENST00000341065.4:c.1163N>C|ENST00000341065.4:c.1163N>C(p.%3D)|C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1||||||POSITION:0.65799886941775||NON_CAN_SPLICE_SURR|||||||,C||ENSR00000528857|RegulatoryFeature|regulatory_region_variant||||||rs142558220&COSM426784|1||||||regulatory_region|||||||||||||||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1||||||||||||||| GT:AD:DP:GQ:PL 0/1:2,1:3:30:30,0,67 0/0:2,0:2:6:0,6,82 0/1:2,3:5:61:93,0,61 0/0:2,0:2:6:0,6,72 0/0:1,0:1:3:0,3,37 0/1:2,3:5:54:93,0,54 0/0:16,0:16:45:0,45,560 0/0:5,0:5:15:0,15,188 0/0:12,0:12:33:0,33,414 0/0:10,0:10:30:0,30,393 0/0:16,0:16:48:0,48,617 0/0:5,0:5:15:0,15,181 0/0:5,0:5:15:0,15,193 0/0:13,0:13:36:0,36,439 0/0:9,0:9:24:0,24,317 0/0:8,0:8:21:0,21,276 +1 878809 rs191952374 C T 1761.84 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-7.95300e+00;DB;DP=453;Dels=0.00000e+00;FS=1.68300e+00;HaplotypeScore=2.28500e-01;InbreedingCoeff=-3.10000e-03;MQ=5.91000e+01;MQ0=0;MQRankSum=1.29700e+00;QD=1.36600e+01;ReadPosRankSum=-8.52000e-01;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=9.25000e+00;culprit=InbreedingCoeff;CSQ=T|ENSG00000187634|ENST00000420190|Transcript|downstream_gene_variant||||||rs191952374|1|4138|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000411579||Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI000155D47C||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000496938|Transcript|downstream_gene_variant||||||rs191952374|1|1890|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636|||||||||||||||||,T|ENSG00000187634|ENST00000342066|Transcript|intron_variant||||||rs191952374|1||1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04||||12/13||ENST00000342066.3:c.1689+52N>T||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636||||||||INTRON_SIZE:320||NON_CAN_SPLICE|||||||,T|ENSG00000188976|ENST00000327044|Transcript|downstream_gene_variant||||||rs191952374|1|775|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187634|ENST00000464948|Transcript|downstream_gene_variant||||||rs191952374|1|537|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636|||||||||||||||||,T|ENSG00000187634|ENST00000466827|Transcript|downstream_gene_variant||||||rs191952374|1|627|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636|||||||||||||||||,T|ENSG00000187634|ENST00000474461|Transcript|downstream_gene_variant||||||rs191952374|1|435|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636|||||||||||||||||,T|ENSG00000187634|ENST00000455979|Transcript|intron_variant||||||rs191952374|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479||||6/6||ENST00000455979.1:c.1169+52N>T||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636||||||||INTRON_SIZE:320||NON_CAN_SPLICE|||||||,T|ENSG00000188976|ENST00000483767|Transcript|downstream_gene_variant||||||rs191952374|1|775|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636|||||||||||||||||,T|ENSG00000187634|ENST00000478729|Transcript|downstream_gene_variant||||||rs191952374|1|1256|1|SAMD11|HGNC|28706|processed_transcript|||||||||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636|||||||||||||||||,T|ENSG00000188976|ENST00000477976|Transcript|downstream_gene_variant||||||rs191952374|1|776|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636|||||||||||||||||,T|ENSG00000187634|ENST00000341065|Transcript|intron_variant||||||rs191952374|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A||||10/11||ENST00000341065.4:c.1412+52N>T||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636||||||||INTRON_SIZE:320||NON_CAN_SPLICE|||||||,T||ENSR00000528858|RegulatoryFeature|regulatory_region_variant||||||rs191952374|1||||||regulatory_region|||||||||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636||||||||||||||||| GT:AD:DP:GQ:PL 0/0:35,0:35:99:0,105,1323 0/0:24,0:24:72:0,72,960 0/0:31,0:31:93:0,93,1172 0/0:10,0:10:30:0,30,376 0/0:10,0:10:30:0,30,370 0/0:12,0:12:36:0,36,453 0/0:35,0:35:99:0,105,1376 0/0:33,0:33:99:0,99,1273 0/0:31,0:31:93:0,93,1240 0/0:33,0:33:96:0,96,1192 0/0:33,0:33:99:0,99,1281 0/0:25,0:25:75:0,75,983 0/1:18,16:33:99:488,0,504 0/0:33,0:33:99:0,99,1273 0/0:44,0:44:99:0,132,1698 0/0:31,0:31:90:0,90,1198 +1 879576 rs115979567 C T 18648.64 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-2.26830e+01;DB;DP=839;Dels=0.00000e+00;FS=2.49350e+01;HaplotypeScore=4.12600e-01;InbreedingCoeff=-2.18000e-02;MQ=5.92100e+01;MQ0=1;MQRankSum=1.02100e+00;QD=1.36100e+01;ReadPosRankSum=7.91400e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=4.39000e+00;culprit=InbreedingCoeff;CSQ=T|ENSG00000187634|ENST00000420190|Transcript|downstream_gene_variant||||||rs115979567|1|4905|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000411579||Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI000155D47C||||||||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000496938|Transcript|downstream_gene_variant||||||rs115979567|1|1123|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120|||||||||||||||||,T|ENSG00000187634|ENST00000342066|Transcript|3_prime_UTR_variant|2172|||||rs115979567|1||1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04|||14/14|||ENST00000342066.3:c.*43N>T||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120||||||||||NON_CAN_SPLICE_SURR|||||||,T|ENSG00000188976|ENST00000327044|Transcript|downstream_gene_variant||||||rs115979567|1|8|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187634|ENST00000464948|Transcript|downstream_gene_variant||||||rs115979567|1|1304|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120|||||||||||||||||,T|ENSG00000187634|ENST00000466827|Transcript|downstream_gene_variant||||||rs115979567|1|1394|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120|||||||||||||||||,T|ENSG00000187634|ENST00000474461|Transcript|downstream_gene_variant||||||rs115979567|1|1202|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120|||||||||||||||||,T|ENSG00000187634|ENST00000455979|Transcript|3_prime_UTR_variant|1668|||||rs115979567|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479|||7/7|||ENST00000455979.1:c.*43N>T||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120||||||||||NON_CAN_SPLICE_SURR|||||||,T|ENSG00000188976|ENST00000483767|Transcript|downstream_gene_variant||||||rs115979567|1|8|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120|||||||||||||||||,T|ENSG00000187634|ENST00000478729|Transcript|downstream_gene_variant||||||rs115979567|1|2023|1|SAMD11|HGNC|28706|processed_transcript|||||||||||||||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120|||||||||||||||||,T|ENSG00000188976|ENST00000477976|Transcript|downstream_gene_variant||||||rs115979567|1|9|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120|||||||||||||||||,T|ENSG00000187634|ENST00000341065|Transcript|3_prime_UTR_variant|1812|||||rs115979567|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A|||12/12|||ENST00000341065.4:c.*43N>T||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120||||||||||NON_CAN_SPLICE_SURR||||||| GT:AD:DP:GQ:PL 0/0:66,0:66:99:0,199,2441 0/1:25,28:51:99:767,0,834 0/0:55,0:55:99:0,166,2079 0/0:11,0:11:33:0,33,392 0/0:15,0:15:45:0,45,554 0/0:17,0:17:51:0,51,622 0/0:50,0:50:99:0,150,1966 0/0:65,0:65:99:0,196,2507 0/0:60,0:60:99:0,181,2268 0/0:70,0:70:99:0,211,2589 0/0:64,0:64:99:0,193,2452 0/0:65,0:65:99:0,196,2507 0/0:56,0:56:99:0,169,2117 0/0:60,0:60:99:0,181,2359 0/0:79,0:79:99:0,238,2986 0/0:55,0:55:99:0,165,2099 +1 881070 rs41285794 G A 20769.13 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-9.52200e+00;DB;DP=1185;Dels=0.00000e+00;FS=1.15500e+01;HaplotypeScore=1.69500e-01;InbreedingCoeff=-1.83000e-02;MQ=5.90700e+01;MQ0=0;MQRankSum=1.85940e+01;QD=1.31500e+01;ReadPosRankSum=-8.90700e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=SAMD11;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000342066;VQSLOD=4.22000e+00;culprit=InbreedingCoeff;CSQ=A|ENSG00000188976|ENST00000496938|Transcript|upstream_gene_variant||||||rs41285794|1|128|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651|||||||||||||||||,A|ENSG00000187634|ENST00000342066|Transcript|downstream_gene_variant||||||rs41285794|1|1115|1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04||||||||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000188976|ENST00000327044|Transcript|intron_variant||||||rs41285794|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||16/18||ENST00000327044.6:c.1918-37N>T||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651||||||||INTRON_SIZE:519||NON_CAN_SPLICE|||||||,A|ENSG00000187634|ENST00000464948|Transcript|downstream_gene_variant||||||rs41285794|1|2798|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651|||||||||||||||||,A|ENSG00000187634|ENST00000466827|Transcript|downstream_gene_variant||||||rs41285794|1|2888|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651|||||||||||||||||,A|ENSG00000187634|ENST00000474461|Transcript|downstream_gene_variant||||||rs41285794|1|2696|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651|||||||||||||||||,A|ENSG00000187634|ENST00000455979|Transcript|downstream_gene_variant||||||rs41285794|1|1431|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479||||||||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000188976|ENST00000483767|Transcript|intron_variant&non_coding_transcript_variant||||||rs41285794|1||-1|NOC2L|HGNC|24517|retained_intron|||||||||||2/4||ENST00000483767.1:n.774-37N>T||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651|||||||||||||||||,A|ENSG00000187634|ENST00000478729|Transcript|downstream_gene_variant||||||rs41285794|1|3517|1|SAMD11|HGNC|28706|processed_transcript|||||||||||||||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651|||||||||||||||||,A|ENSG00000188976|ENST00000477976|Transcript|intron_variant&non_coding_transcript_variant||||||rs41285794|1||-1|NOC2L|HGNC|24517|retained_intron|||||||||||14/16||ENST00000477976.1:n.3365-37N>T||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651|||||||||||||||||,A|ENSG00000187634|ENST00000341065|Transcript|downstream_gene_variant||||||rs41285794|1|1115|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A||||||||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651||||||||||EXON_INTRON_UNDEF||||||| GT:AD:DP:GQ:PL 0/0:78,0:78:99:0,235,2947 0/0:66,0:66:99:0,199,2595 0/0:59,0:59:99:0,178,2182 0/0:37,0:37:99:0,111,1365 0/0:36,0:36:99:0,108,1331 0/0:33,0:33:99:0,99,1192 0/0:69,0:69:99:0,208,2662 0/0:88,0:88:99:0,265,3395 0/0:98,0:98:99:0,295,3781 0/1:36,31:64:99:982,0,1021 0/0:86,0:86:99:0,259,3318 0/0:93,0:93:99:0,280,3588 0/0:92,0:92:99:0,277,3549 0/0:102,0:102:99:0,307,3935 0/0:89,0:89:99:0,268,3433 0/0:95,0:95:99:0,286,3665 +1 881627 rs2272757 G A 411792.28 PASS AC=22;AF=6.88000e-01;AN=32;BaseQRankSum=-3.32930e+01;DB;DP=644;Dels=0.00000e+00;FS=2.51600e+00;HaplotypeScore=5.86200e-01;InbreedingCoeff=3.09600e-01;MQ=5.88200e+01;MQ0=7;MQRankSum=6.81600e+00;QD=2.28900e+01;ReadPosRankSum=1.01500e+00;SNPEFF_AMINO_ACID_CHANGE=L615;SNPEFF_CODON_CHANGE=Ctg/Ttg;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_881553_881666;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=4.35000e+00;culprit=MQ;CSQ=A|ENSG00000188976|ENST00000496938|Transcript|upstream_gene_variant||||||rs2272757&COSM1344685|1|685|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1|||||||||||||||,A|ENSG00000187634|ENST00000342066|Transcript|downstream_gene_variant||||||rs2272757&COSM1344685|1|1672|1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04||||||||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000188976|ENST00000327044|Transcript|synonymous_variant|1893|1843|615|L|Ctg/Ttg|rs2272757&COSM1344685|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C|||16/19||Pfam_domain:PF03715&Superfamily_domains:SSF48371|ENST00000327044.6:c.1843N>T|ENST00000327044.6:c.1843N>T(p.%3D)|A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1||||||POSITION:0.819111111111111||NON_CAN_SPLICE_SURR|||||||,A|ENSG00000187634|ENST00000464948|Transcript|downstream_gene_variant||||||rs2272757&COSM1344685|1|3355|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1|||||||||||||||,A|ENSG00000187634|ENST00000466827|Transcript|downstream_gene_variant||||||rs2272757&COSM1344685|1|3445|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1|||||||||||||||,A|ENSG00000187634|ENST00000474461|Transcript|downstream_gene_variant||||||rs2272757&COSM1344685|1|3253|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1|||||||||||||||,A|ENSG00000187634|ENST00000455979|Transcript|downstream_gene_variant||||||rs2272757&COSM1344685|1|1988|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479||||||||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000188976|ENST00000483767|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|699|||||rs2272757&COSM1344685|1||-1|NOC2L|HGNC|24517|retained_intron||||||||||2/5|||ENST00000483767.1:n.699N>T||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1|||||||||||||||,A|ENSG00000187634|ENST00000478729|Transcript|downstream_gene_variant||||||rs2272757&COSM1344685|1|4074|1|SAMD11|HGNC|28706|processed_transcript|||||||||||||||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1|||||||||||||||,A|ENSG00000188976|ENST00000477976|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|3290|||||rs2272757&COSM1344685|1||-1|NOC2L|HGNC|24517|retained_intron||||||||||14/17|||ENST00000477976.1:n.3290N>T||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1|||||||||||||||,A|ENSG00000187634|ENST00000341065|Transcript|downstream_gene_variant||||||rs2272757&COSM1344685|1|1672|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A||||||||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1||||||||EXON_INTRON_UNDEF||||||| GT:AD:DP:GQ:PL 1/1:0,39:38:99:1384,111,0 0/0:61,0:61:99:0,184,2353 0/1:24,17:38:99:494,0,613 1/1:0,16:16:48:550,48,0 1/1:0,18:18:54:649,54,0 1/1:0,25:25:66:826,66,0 1/1:0,51:51:99:1886,153,0 0/1:25,23:46:99:661,0,639 1/1:0,33:33:99:1220,99,0 1/1:0,52:52:99:1879,156,0 1/1:0,45:45:99:1701,135,0 0/0:58,0:58:99:0,175,2237 0/1:17,18:34:99:523,0,478 1/1:0,44:44:99:1627,132,0 0/1:20,25:41:99:674,0,488 0/0:44,1:44:99:0,120,1521 +1 881918 rs35471880 G A 26418.87 PASS AC=5;AF=1.56000e-01;AN=32;BaseQRankSum=6.25300e+00;DB;DP=1040;Dels=0.00000e+00;FS=2.27620e+01;HaplotypeScore=2.29500e-01;InbreedingCoeff=-2.81000e-02;MQ=5.57400e+01;MQ0=40;MQRankSum=1.69390e+01;QD=1.18200e+01;ReadPosRankSum=-6.75000e-01;SNPEFF_AMINO_ACID_CHANGE=S556L;SNPEFF_CODON_CHANGE=tCg/tTg;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_881782_881925;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=1.82000e+00;culprit=MQ;CSQ=A|ENSG00000188976|ENST00000496938|Transcript|upstream_gene_variant||||||rs35471880|1|976|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628|||||||||||||||||,A|ENSG00000187634|ENST00000342066|Transcript|downstream_gene_variant||||||rs35471880|1|1963|1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04||||||||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000188976|ENST00000327044|Transcript|missense_variant|1717|1667|556|S/L|tCg/tTg|rs35471880|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C|deleterious(0.03)|benign(0.311)|15/19||Pfam_domain:PF03715&Superfamily_domains:SSF48371|ENST00000327044.6:c.1667N>T|ENSP00000317992.6:p.Ser556Leu|A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628||||||||POSITION:0.740888888888889||NON_CAN_SPLICE_SURR||B%3BB%3BB|16.43|D|T|D|T,A|ENSG00000187634|ENST00000464948|Transcript|downstream_gene_variant||||||rs35471880|1|3646|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628|||||||||||||||||,A|ENSG00000187634|ENST00000466827|Transcript|downstream_gene_variant||||||rs35471880|1|3736|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628|||||||||||||||||,A|ENSG00000187634|ENST00000474461|Transcript|downstream_gene_variant||||||rs35471880|1|3544|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628|||||||||||||||||,A|ENSG00000187634|ENST00000455979|Transcript|downstream_gene_variant||||||rs35471880|1|2279|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479||||||||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000188976|ENST00000483767|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|523|||||rs35471880|1||-1|NOC2L|HGNC|24517|retained_intron||||||||||1/5|||ENST00000483767.1:n.523N>T||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628|||||||||||||||||,A|ENSG00000187634|ENST00000478729|Transcript|downstream_gene_variant||||||rs35471880|1|4365|1|SAMD11|HGNC|28706|processed_transcript|||||||||||||||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628|||||||||||||||||,A|ENSG00000188976|ENST00000477976|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|3114|||||rs35471880|1||-1|NOC2L|HGNC|24517|retained_intron||||||||||13/17|||ENST00000477976.1:n.3114N>T||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628|||||||||||||||||,A|ENSG00000187634|ENST00000341065|Transcript|downstream_gene_variant||||||rs35471880|1|1963|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A||||||||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628||||||||||EXON_INTRON_UNDEF||||||| GT:AD:DP:GQ:PL 0/0:73,0:73:99:0,220,2699 0/0:70,0:70:99:0,211,2589 0/0:66,0:66:99:0,199,2385 0/1:12,18:29:99:475,0,278 0/0:28,0:28:78:0,78,843 0/1:18,10:27:99:271,0,511 0/1:34,36:67:99:876,0,921 0/1:37,38:74:99:966,0,944 0/0:69,0:69:99:0,208,2493 0/0:93,0:93:99:0,280,3279 0/1:41,32:70:99:777,0,1118 0/0:76,0:76:99:0,229,2746 0/0:73,0:73:99:0,220,2573 0/0:69,0:69:99:0,208,2493 0/0:82,0:82:99:0,247,2963 0/0:74,0:74:99:0,223,2609 +1 883485 . C T 81.94 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-3.68100e+00;DP=94;Dels=0.00000e+00;FS=0.00000e+00;HaplotypeScore=1.64200e-01;InbreedingCoeff=-2.46000e-02;MQ=5.53400e+01;MQ0=0;MQRankSum=3.55900e+00;QD=3.03000e+00;ReadPosRankSum=-1.07900e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=SAMD11;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000342066;VQSLOD=-3.92700e-01;culprit=MQ;CSQ=T|ENSG00000188976|ENST00000483767|Transcript|upstream_gene_variant||||||rs374301410|1|1045|-1|NOC2L|HGNC|24517|retained_intron||||||||||||||||||||T:0|T:0.000117|||||||||||||||||,T|ENSG00000187634|ENST00000455979|Transcript|downstream_gene_variant||||||rs374301410|1|3846|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479|||||||||||||T:0|T:0.000117||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000496938|Transcript|upstream_gene_variant||||||rs374301410|1|2543|-1|NOC2L|HGNC|24517|processed_transcript||||||||||||||||||||T:0|T:0.000117|||||||||||||||||,T|ENSG00000187634|ENST00000342066|Transcript|downstream_gene_variant||||||rs374301410|1|3530|1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04|||||||||||||T:0|T:0.000117||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000327044|Transcript|intron_variant||||||rs374301410|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||14/18||ENST00000327044.6:c.1659+26N>A|||||||T:0|T:0.000117||||||||INTRON_SIZE:1585||NON_CAN_SPLICE|||||||,T|ENSG00000188976|ENST00000477976|Transcript|intron_variant&non_coding_transcript_variant||||||rs374301410|1||-1|NOC2L|HGNC|24517|retained_intron|||||||||||12/16||ENST00000477976.1:n.3106+26N>A|||||||T:0|T:0.000117|||||||||||||||||,T|ENSG00000187634|ENST00000341065|Transcript|downstream_gene_variant||||||rs374301410|1|3530|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A|||||||||||||T:0|T:0.000117||||||||||EXON_INTRON_UNDEF||||||| GT:AD:DP:GQ:PL 0/0:8,0:8:24:0,24,304 0/0:3,0:3:9:0,9,118 0/0:5,0:5:15:0,15,178 0/0:5,0:5:15:0,15,181 0/0:2,0:2:6:0,6,69 0/0:4,0:5:12:0,12,145 0/0:6,0:6:18:0,18,217 0/0:10,0:10:30:0,30,378 0/0:11,0:11:33:0,33,411 0/1:5,1:6:14:14,0,181 0/0:10,0:10:30:0,30,373 0/0:4,0:4:9:0,9,114 0/0:5,0:5:15:0,15,193 0/0:4,0:4:12:0,12,157 0/0:6,0:6:18:0,18,229 0/0:3,0:4:9:0,9,122 +1 883625 rs4970378 A G 232503.78 PASS AC=30;AF=1.00000e+00;AN=30;DB;DP=117;Dels=0.00000e+00;FS=0.00000e+00;HaplotypeScore=1.37000e-01;InbreedingCoeff=-1.43000e-02;MQ=5.74300e+01;MQ0=0;QD=3.66300e+01;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=SAMD11;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000342066;VQSLOD=-2.60400e-01;culprit=MQ;CSQ=G|ENSG00000188976|ENST00000483767|Transcript|upstream_gene_variant||||||rs4970378|1|1185|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||A:0.0000|||||G:0.999543||||||||||||||||||,G|ENSG00000187634|ENST00000455979|Transcript|downstream_gene_variant||||||rs4970378|1|3986|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479||||||||A:0.0000|||||G:0.999543|||||||||||EXON_INTRON_UNDEF&ANC_ALLELE|||||||,G|ENSG00000188976|ENST00000496938|Transcript|upstream_gene_variant||||||rs4970378|1|2683|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.0000|||||G:0.999543||||||||||||||||||,G|ENSG00000187634|ENST00000342066|Transcript|downstream_gene_variant||||||rs4970378|1|3670|1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04||||||||A:0.0000|||||G:0.999543|||||||||||EXON_INTRON_UNDEF&ANC_ALLELE|||||||,G|ENSG00000188976|ENST00000327044|Transcript|intron_variant||||||rs4970378|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||13/18||ENST00000327044.6:c.1558-13N>C||A:0.0000|||||G:0.999543|||||||||INTRON_SIZE:257||NON_CAN_SPLICE&ANC_ALLELE|||||||,G|ENSG00000188976|ENST00000477976|Transcript|intron_variant&non_coding_transcript_variant||||||rs4970378|1||-1|NOC2L|HGNC|24517|retained_intron|||||||||||11/16||ENST00000477976.1:n.3005-13N>C||A:0.0000|||||G:0.999543||||||||||||||||||,G|ENSG00000187634|ENST00000341065|Transcript|downstream_gene_variant||||||rs4970378|1|3670|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A||||||||A:0.0000|||||G:0.999543|||||||||||EXON_INTRON_UNDEF&ANC_ALLELE||||||| GT:AD:DP:GQ:PL 1/1:0,4:4:12:151,12,0 1/1:0,3:3:9:118,9,0 1/1:0,6:6:18:212,18,0 1/1:0,5:5:15:185,15,0 ./.:.:.:.:. 1/1:0,4:4:12:142,12,0 1/1:0,13:13:39:501,39,0 1/1:0,8:8:21:276,21,0 1/1:0,19:19:57:718,57,0 1/1:0,9:9:27:340,27,0 1/1:0,12:12:36:454,36,0 1/1:0,4:4:12:151,12,0 1/1:0,5:5:15:198,15,0 1/1:0,16:16:48:605,48,0 1/1:0,3:3:9:119,9,0 1/1:0,5:6:15:191,15,0 +1 883918 rs139116730 G A 4594.12 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=6.89000e+00;DB;DP=1146;Dels=0.00000e+00;FS=4.31330e+01;HaplotypeScore=8.65000e-02;InbreedingCoeff=-4.00000e-03;MQ=5.62500e+01;MQ0=14;MQRankSum=1.10440e+01;QD=1.07800e+01;ReadPosRankSum=-1.97100e+00;SNPEFF_AMINO_ACID_CHANGE=S503;SNPEFF_CODON_CHANGE=tcC/tcT;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_883870_883983;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=5.95000e-01;culprit=MQ;CSQ=A|ENSG00000188976|ENST00000483767|Transcript|upstream_gene_variant||||||rs139116730|1|1478|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||A:0.0005||||A:0.0013|A:0.000227|A:0.003488|||||||||||||||||,A|ENSG00000187634|ENST00000455979|Transcript|downstream_gene_variant||||||rs139116730|1|4279|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479||||||||A:0.0005||||A:0.0013|A:0.000227|A:0.003488||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000188976|ENST00000496938|Transcript|upstream_gene_variant||||||rs139116730|1|2976|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.0005||||A:0.0013|A:0.000227|A:0.003488|||||||||||||||||,A|ENSG00000187634|ENST00000342066|Transcript|downstream_gene_variant||||||rs139116730|1|3963|1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04||||||||A:0.0005||||A:0.0013|A:0.000227|A:0.003488||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000188976|ENST00000327044|Transcript|synonymous_variant|1559|1509|503|S|tcC/tcT|rs139116730|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C|||13/19||Pfam_domain:PF03715&Superfamily_domains:SSF48371|ENST00000327044.6:c.1509N>T|ENST00000327044.6:c.1509N>T(p.%3D)|A:0.0005||||A:0.0013|A:0.000227|A:0.003488||||||||POSITION:0.670666666666667||NON_CAN_SPLICE_SURR|||||||,A|ENSG00000188976|ENST00000477976|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2956|||||rs139116730|1||-1|NOC2L|HGNC|24517|retained_intron||||||||||11/17|||ENST00000477976.1:n.2956N>T||A:0.0005||||A:0.0013|A:0.000227|A:0.003488|||||||||||||||||,A|ENSG00000187634|ENST00000341065|Transcript|downstream_gene_variant||||||rs139116730|1|3963|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A||||||||A:0.0005||||A:0.0013|A:0.000227|A:0.003488||||||||||EXON_INTRON_UNDEF||||||| GT:AD:DP:GQ:PL 0/0:76,0:76:99:0,229,2746 0/0:47,0:47:99:0,141,1738 0/0:75,0:75:99:0,226,2710 0/0:36,0:36:99:0,108,1201 0/0:37,0:37:99:0,111,1271 0/0:42,0:42:99:0,126,1443 0/0:74,0:74:99:0,223,2609 0/0:82,0:82:99:0,247,2963 0/0:120,0:120:99:0,361,4336 0/0:96,0:96:99:0,289,3468 0/1:38,33:68:99:823,0,921 0/0:78,0:78:99:0,235,2818 0/0:56,0:56:99:0,169,1974 0/0:92,0:92:99:0,277,3402 0/0:78,0:78:99:0,235,2884 0/0:89,0:89:99:0,268,3216 +1 887560 rs3748595 A C 806833.88 PASS AC=31;AF=9.69000e-01;AN=32;BaseQRankSum=5.43470e+01;DB;DP=472;Dels=0.00000e+00;FS=1.69080e+01;HaplotypeScore=2.91900e-01;InbreedingCoeff=7.38000e-02;MQ=5.93900e+01;MQ0=0;MQRankSum=1.20610e+01;QD=3.46800e+01;ReadPosRankSum=7.92100e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000487214;VQSLOD=6.35000e-01;culprit=FS;CSQ=C|ENSG00000188976|ENST00000327044|Transcript|intron_variant||||||rs3748595|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||10/18||ENST00000327044.6:c.1192-41N>G||A:0.1602|C:0.78|C:0.86|C:0.86|C:0.85|C:0.831139|C:0.932674||||||||INTRON_SIZE:272||NON_CAN_SPLICE&ANC_ALLELE|||||||,C|ENSG00000188976|ENST00000477976|Transcript|intron_variant&non_coding_transcript_variant||||||rs3748595|1||-1|NOC2L|HGNC|24517|retained_intron|||||||||||8/16||ENST00000477976.1:n.2639-41N>G||A:0.1602|C:0.78|C:0.86|C:0.86|C:0.85|C:0.831139|C:0.932674|||||||||||||||||,C|ENSG00000188976|ENST00000487214|Transcript|downstream_gene_variant||||||rs3748595|1|2246|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.1602|C:0.78|C:0.86|C:0.86|C:0.85|C:0.831139|C:0.932674||||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,44:44:99:1706,132,0 1/1:0,43:43:99:1773,129,0 1/1:0,41:41:99:1582,123,0 1/1:0,19:19:54:687,54,0 1/1:0,23:23:69:851,69,0 1/1:0,10:10:30:370,30,0 1/1:0,33:33:99:1320,99,0 1/1:1,25:25:75:1020,75,0 1/1:0,26:26:78:1040,78,0 1/1:0,25:25:75:1000,75,0 1/1:0,36:36:99:1461,108,0 0/1:23,14:36:99:439,0,642 1/1:0,23:23:69:930,69,0 1/1:0,28:28:84:1121,84,0 1/1:0,23:23:69:904,69,0 1/1:0,37:37:99:1420,108,0 +1 887801 rs3828047 A G 1348829.24 PASS AC=31;AF=9.69000e-01;AN=32;BaseQRankSum=4.41560e+01;DB;DP=777;Dels=0.00000e+00;FS=8.43510e+01;HaplotypeScore=3.07000e-01;InbreedingCoeff=-1.77000e-02;MQ=5.58800e+01;MQ0=35;MQRankSum=-2.15910e+01;QD=3.44400e+01;ReadPosRankSum=5.44300e+00;SNPEFF_AMINO_ACID_CHANGE=T394;SNPEFF_CODON_CHANGE=acT/acC;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_887792_887980;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=-6.22100e-01;culprit=MQ;CSQ=G|ENSG00000188976|ENST00000327044|Transcript|synonymous_variant|1232|1182|394|T|acT/acC|rs3828047&COSM426785|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C|||10/19||Pfam_domain:PF03715&Superfamily_domains:SSF48371|ENST00000327044.6:c.1182N>C|ENST00000327044.6:c.1182N>C(p.%3D)|A:0.0716|G:0.90|G:0.92|G:0.92|G:0.95|G:0.906037|G:0.938372||0&1||||||POSITION:0.525333333333333||NON_CAN_SPLICE_SURR&ANC_ALLELE|||||||,G|ENSG00000188976|ENST00000477976|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2629|||||rs3828047&COSM426785|1||-1|NOC2L|HGNC|24517|retained_intron||||||||||8/17|||ENST00000477976.1:n.2629N>C||A:0.0716|G:0.90|G:0.92|G:0.92|G:0.95|G:0.906037|G:0.938372||0&1|||||||||||||||,G|ENSG00000188976|ENST00000487214|Transcript|downstream_gene_variant||||||rs3828047&COSM426785|1|2005|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.0716|G:0.90|G:0.92|G:0.92|G:0.95|G:0.906037|G:0.938372||0&1||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,42:42:99:1553,126,0 1/1:0,48:48:99:1824,138,0 1/1:0,54:54:99:1997,163,0 1/1:0,17:18:48:615,48,0 1/1:0,33:33:99:1220,99,0 1/1:0,30:30:90:1134,90,0 1/1:0,60:60:99:2315,181,0 1/1:0,44:44:99:1526,120,0 1/1:0,71:71:99:2791,214,0 1/1:0,48:48:99:1887,144,0 1/1:0,61:61:99:2398,184,0 0/1:29,33:59:99:915,0,742 1/1:0,30:30:90:1157,90,0 1/1:0,59:59:99:2321,178,0 1/1:0,55:55:99:2137,166,0 1/1:0,65:65:99:2507,196,0 +1 888529 . G A 1833.13 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-9.33700e+00;DP=387;Dels=0.00000e+00;FS=8.33000e-01;HaplotypeScore=1.94900e-01;InbreedingCoeff=-4.20000e-03;MQ=5.60200e+01;MQ0=0;MQRankSum=5.49600e+00;QD=1.10400e+01;ReadPosRankSum=-2.04000e-01;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000487214;VQSLOD=1.38000e+00;culprit=MQ;CSQ=A|ENSG00000188976|ENST00000327044|Transcript|intron_variant||||||rs373469542|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||9/18||ENST00000327044.6:c.1002+26N>T|||||||A:0.000908|A:0||||||||INTRON_SIZE:574||NON_CAN_SPLICE|||||||,A|ENSG00000188976|ENST00000477976|Transcript|intron_variant&non_coding_transcript_variant||||||rs373469542|1||-1|NOC2L|HGNC|24517|retained_intron|||||||||||7/16||ENST00000477976.1:n.2449+26N>T|||||||A:0.000908|A:0|||||||||||||||||,A|ENSG00000188976|ENST00000487214|Transcript|downstream_gene_variant||||||rs373469542|1|1277|-1|NOC2L|HGNC|24517|processed_transcript||||||||||||||||||||A:0.000908|A:0||||||||||||||||| GT:AD:DP:GQ:PL 0/0:19,0:19:57:0,57,703 0/0:26,0:26:78:0,78,1022 0/0:23,0:23:69:0,69,869 0/0:15,0:15:45:0,45,555 0/0:16,0:16:48:0,48,603 0/0:16,0:16:48:0,48,606 0/0:32,0:32:96:0,96,1258 0/0:26,0:26:72:0,72,944 0/0:24,0:24:69:0,69,898 0/1:12,15:26:99:432,0,321 0/0:31,0:31:93:0,93,1240 0/0:24,0:24:72:0,72,944 0/0:20,0:20:60:0,60,756 0/0:27,0:27:78:0,78,1029 0/0:36,0:36:99:0,108,1415 0/0:26,0:26:78:0,78,1022 +1 888659 rs3748597 T C 907727.36 PASS AC=31;AF=9.69000e-01;AN=32;BaseQRankSum=4.09230e+01;DB;DP=542;Dels=0.00000e+00;FS=4.67910e+01;HaplotypeScore=2.81100e-01;InbreedingCoeff=-1.65000e-02;MQ=5.48600e+01;MQ0=44;MQRankSum=-2.23740e+01;QD=3.38200e+01;ReadPosRankSum=8.50400e+00;SNPEFF_AMINO_ACID_CHANGE=I300V;SNPEFF_CODON_CHANGE=Atc/Gtc;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_888555_888668;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=-6.49600e-01;culprit=MQ;CSQ=C|ENSG00000188976|ENST00000469563|Transcript|downstream_gene_variant||||||rs3748597|1|4967|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0716|C:0.90|C:0.92|C:0.92|C:0.95|C:0.905767|C:0.938372|||||||||||||||||,C|ENSG00000188976|ENST00000327044|Transcript|missense_variant|948|898|300|I/V|Atc/Gtc|rs3748597|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C|tolerated(0.98)|benign(0)|9/19||Superfamily_domains:SSF48371|ENST00000327044.6:c.898N>G|ENSP00000317992.6:p.Ile300Val|T:0.0716|C:0.90|C:0.92|C:0.92|C:0.95|C:0.905767|C:0.938372||||||||POSITION:0.399111111111111||NON_CAN_SPLICE_SURR&ANC_ALLELE||B|0.940|P|T|T|T,C|ENSG00000188976|ENST00000477976|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2345|||||rs3748597|1||-1|NOC2L|HGNC|24517|retained_intron||||||||||7/17|||ENST00000477976.1:n.2345N>G||T:0.0716|C:0.90|C:0.92|C:0.92|C:0.95|C:0.905767|C:0.938372|||||||||||||||||,C|ENSG00000188976|ENST00000487214|Transcript|downstream_gene_variant||||||rs3748597|1|1147|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||T:0.0716|C:0.90|C:0.92|C:0.92|C:0.95|C:0.905767|C:0.938372||||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,33:33:96:1198,96,0 1/1:0,29:29:87:1140,87,0 1/1:0,27:27:81:998,81,0 1/1:0,27:27:81:962,81,0 1/1:0,19:19:57:686,57,0 1/1:0,22:22:63:796,63,0 1/1:0,39:39:99:1474,117,0 1/1:0,39:39:99:1504,117,0 1/1:0,32:32:96:1183,96,0 1/1:0,44:44:99:1654,129,0 1/1:0,55:55:99:2079,166,0 0/1:17,21:36:99:502,0,410 1/1:0,37:37:99:1398,111,0 1/1:0,44:44:99:1697,132,0 1/1:0,32:32:96:1209,96,0 1/1:0,27:27:81:1016,81,0 +1 889158 rs56262069 G C 909575.03 PASS AC=31;AF=9.69000e-01;AN=32;BaseQRankSum=3.68810e+01;DB;DP=579;Dels=0.00000e+00;FS=2.80669e+02;HaplotypeScore=5.39300e-01;InbreedingCoeff=7.80000e-02;MQ=5.90100e+01;MQ0=0;MQRankSum=-1.97700e+00;QD=3.19700e+01;ReadPosRankSum=8.43100e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000469563;VQSLOD=9.10000e-02;culprit=MQRankSum;CSQ=C|ENSG00000188976|ENST00000469563|Transcript|downstream_gene_variant||||||rs13303056|1|4468|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||G:0.1529|||||||||||||||||||||||,C|ENSG00000188976|ENST00000327044|Transcript|splice_region_variant&intron_variant||||||rs13303056|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||8/18||ENST00000327044.6:c.888+4N>G||G:0.1529||||||||||||||INTRON_SIZE:493||NON_CAN_SPLICE&ANC_ALLELE|||||||,C|ENSG00000188976|ENST00000477976|Transcript|splice_region_variant&intron_variant&non_coding_transcript_variant||||||rs13303056|1||-1|NOC2L|HGNC|24517|retained_intron|||||||||||6/16||ENST00000477976.1:n.2335+4N>G||G:0.1529|||||||||||||||||||||||,C|ENSG00000188976|ENST00000487214|Transcript|downstream_gene_variant||||||rs13303056|1|648|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||G:0.1529||||||||||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,45:45:99:1664,135,0 1/1:0,21:21:63:810,63,0 1/1:0,27:27:81:975,81,0 1/1:0,19:18:51:638,51,0 1/1:0,20:20:60:700,60,0 1/1:0,18:18:54:635,54,0 1/1:0,40:40:99:1512,120,0 1/1:0,34:34:99:1312,102,0 1/1:0,45:45:99:1615,132,0 1/1:0,40:40:99:1543,120,0 1/1:0,62:62:99:2392,187,0 0/1:23,19:40:99:499,0,598 1/1:0,45:45:99:1664,135,0 1/1:0,48:48:99:1814,144,0 1/1:0,39:39:99:1503,117,0 1/1:0,37:37:99:1398,111,0 +1 889159 rs13302945 A C 937927.21 PASS AC=31;AF=9.69000e-01;AN=32;BaseQRankSum=5.17190e+01;DB;DP=586;Dels=0.00000e+00;FS=2.49622e+02;HaplotypeScore=5.35000e-01;InbreedingCoeff=7.77000e-02;MQ=5.90200e+01;MQ0=0;MQRankSum=1.48040e+01;QD=3.22600e+01;ReadPosRankSum=8.79200e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000469563;VQSLOD=1.40000e-01;culprit=MQ;CSQ=C|ENSG00000188976|ENST00000469563|Transcript|downstream_gene_variant||||||rs13302945|1|4467|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||A:0.1538|C:0.79|C:0.87|C:0.88|C:0.85|C:0.823342|C:0.932294|||||||||||||||||,C|ENSG00000188976|ENST00000327044|Transcript|splice_region_variant&intron_variant||||||rs13302945|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||8/18||ENST00000327044.6:c.888+3N>G||A:0.1538|C:0.79|C:0.87|C:0.88|C:0.85|C:0.823342|C:0.932294||||||||INTRON_SIZE:493||NON_CAN_SPLICE&ANC_ALLELE|||||||,C|ENSG00000188976|ENST00000477976|Transcript|splice_region_variant&intron_variant&non_coding_transcript_variant||||||rs13302945|1||-1|NOC2L|HGNC|24517|retained_intron|||||||||||6/16||ENST00000477976.1:n.2335+3N>G||A:0.1538|C:0.79|C:0.87|C:0.88|C:0.85|C:0.823342|C:0.932294|||||||||||||||||,C|ENSG00000188976|ENST00000487214|Transcript|downstream_gene_variant||||||rs13302945|1|647|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.1538|C:0.79|C:0.87|C:0.88|C:0.85|C:0.823342|C:0.932294||||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,44:44:99:1663,132,0 1/1:0,21:21:63:794,63,0 1/1:0,28:28:84:1058,84,0 1/1:0,19:18:51:634,51,0 1/1:0,21:21:63:782,63,0 1/1:0,18:18:54:650,54,0 1/1:0,42:42:99:1587,126,0 1/1:0,34:34:99:1312,102,0 1/1:0,45:45:99:1657,132,0 1/1:0,41:41:99:1582,123,0 1/1:0,61:61:99:2353,184,0 0/1:24,19:41:99:482,0,633 1/1:0,43:43:99:1625,129,0 1/1:0,52:52:99:1965,156,0 1/1:0,42:42:99:1557,123,0 1/1:0,35:35:99:1323,105,0 +1 889238 rs3828049 G A 52801.55 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-4.91500e+00;DB;DP=911;Dels=0.00000e+00;FS=4.16200e+01;HaplotypeScore=2.87900e-01;InbreedingCoeff=3.34000e-02;MQ=5.93400e+01;MQ0=1;MQRankSum=3.62800e+00;QD=1.41200e+01;ReadPosRankSum=-2.71000e+00;SNPEFF_AMINO_ACID_CHANGE=A271V;SNPEFF_CODON_CHANGE=gCg/gTg;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_889162_889272;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=5.38000e+00;culprit=MQRankSum;CSQ=A|ENSG00000188976|ENST00000469563|Transcript|downstream_gene_variant||||||rs3828049&COSM1602748|1|4388|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||A:0.0537|A:0.02|A:0.08|A:0.08|A:0.05|A:0.021562|A:0.060363||0&1|||||||||||||||,A|ENSG00000188976|ENST00000327044|Transcript|missense_variant|862|812|271|A/V|gCg/gTg|rs3828049&COSM1602748|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C|deleterious(0.04)|benign(0.034)|8/19||Superfamily_domains:SSF48371|ENST00000327044.6:c.812N>T|ENSP00000317992.6:p.Ala271Val|A:0.0537|A:0.02|A:0.08|A:0.08|A:0.05|A:0.021562|A:0.060363||0&1||||||POSITION:0.360888888888889||NON_CAN_SPLICE_SURR||D%3BP%3BP|21.3|N|T|D|T,A|ENSG00000188976|ENST00000477976|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2259|||||rs3828049&COSM1602748|1||-1|NOC2L|HGNC|24517|retained_intron||||||||||6/17|||ENST00000477976.1:n.2259N>T||A:0.0537|A:0.02|A:0.08|A:0.08|A:0.05|A:0.021562|A:0.060363||0&1|||||||||||||||,A|ENSG00000188976|ENST00000487214|Transcript|downstream_gene_variant||||||rs3828049&COSM1602748|1|568|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.0537|A:0.02|A:0.08|A:0.08|A:0.05|A:0.021562|A:0.060363||0&1||||||||||||||| GT:AD:DP:GQ:PL 0/0:53,0:53:99:0,159,1960 0/0:56,0:56:99:0,169,2071 0/0:42,0:42:99:0,126,1517 0/0:23,0:23:69:0,69,763 0/0:31,0:31:93:0,93,1007 0/0:26,0:26:69:0,69,754 0/0:55,0:55:99:0,166,1987 0/0:59,0:59:99:0,178,2132 0/0:67,0:67:99:0,202,2362 0/0:79,0:79:99:0,238,2854 0/0:82,0:82:99:0,247,2963 0/1:32,31:62:99:888,0,808 0/0:75,0:75:99:0,226,2644 0/0:66,0:66:99:0,199,2385 0/0:68,0:68:99:0,205,2397 0/0:67,0:67:99:0,202,2362 +1 894573 rs13303010 G A 310883.38 PASS AC=30;AF=9.38000e-01;AN=32;BaseQRankSum=1.22670e+01;DB;DP=304;Dels=0.00000e+00;FS=2.34720e+01;HaplotypeScore=3.24800e-01;InbreedingCoeff=4.23300e-01;MQ=5.89800e+01;MQ0=0;MQRankSum=1.80380e+01;QD=2.67400e+01;ReadPosRankSum=2.89300e+00;SNPEFF_EFFECT=INTRON;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=1.10000e+00;culprit=MQ;CSQ=A|ENSG00000187961|ENST00000466300|Transcript|upstream_gene_variant||||||rs13303010|1|3534|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||G:0.3480|A:0.18|A:0.71|A:0.69|A:0.90|A:0.284570|A:0.896942|||||||||||||||||,A|ENSG00000188976|ENST00000327044|Transcript|intron_variant||||||rs13303010|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||1/18||ENST00000327044.6:c.26+22N>T||G:0.3480|A:0.18|A:0.71|A:0.69|A:0.90|A:0.284570|A:0.896942||||||||INTRON_SIZE:133||NON_CAN_SPLICE|||||||,A|ENSG00000187961|ENST00000338591|Transcript|upstream_gene_variant||||||rs13303010|1|1394|1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||||||G:0.3480|A:0.18|A:0.71|A:0.69|A:0.90|A:0.284570|A:0.896942||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000187961|ENST00000463212|Transcript|upstream_gene_variant||||||rs13303010|1|2256|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||G:0.3480|A:0.18|A:0.71|A:0.69|A:0.90|A:0.284570|A:0.896942|||||||||||||||||,A|ENSG00000188976|ENST00000469563|Transcript|intron_variant&non_coding_transcript_variant||||||rs13303010|1||-1|NOC2L|HGNC|24517|retained_intron|||||||||||1/1||ENST00000469563.1:n.42+22N>T||G:0.3480|A:0.18|A:0.71|A:0.69|A:0.90|A:0.284570|A:0.896942|||||||||||||||||,A|ENSG00000188976|ENST00000477976|Transcript|upstream_gene_variant||||||rs13303010|1|735|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||G:0.3480|A:0.18|A:0.71|A:0.69|A:0.90|A:0.284570|A:0.896942|||||||||||||||||,A|ENSG00000187961|ENST00000481067|Transcript|upstream_gene_variant||||||rs13303010|1|4359|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||G:0.3480|A:0.18|A:0.71|A:0.69|A:0.90|A:0.284570|A:0.896942|||||||||||||||||,A|ENSG00000188976|ENST00000487214|Transcript|intron_variant&non_coding_transcript_variant||||||rs13303010|1||-1|NOC2L|HGNC|24517|processed_transcript|||||||||||1/6||ENST00000487214.1:n.95+22N>T||G:0.3480|A:0.18|A:0.71|A:0.69|A:0.90|A:0.284570|A:0.896942|||||||||||||||||,A||ENSR00000528861|RegulatoryFeature|regulatory_region_variant||||||rs13303010|1||||||regulatory_region|||||||||||||||G:0.3480|A:0.18|A:0.71|A:0.69|A:0.90|A:0.284570|A:0.896942||||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,24:24:72:898,72,0 0/1:10,8:17:99:196,0,291 1/1:0,13:12:36:454,36,0 1/1:0,7:7:21:254,21,0 1/1:0,5:5:15:181,15,0 1/1:0,13:13:36:428,36,0 1/1:0,31:31:93:1120,93,0 1/1:0,24:24:72:867,72,0 1/1:0,26:26:78:924,78,0 1/1:0,26:26:78:958,78,0 1/1:0,19:19:57:670,57,0 0/1:17,6:22:99:127,0,513 1/1:0,20:20:60:723,60,0 1/1:0,23:23:69:869,69,0 1/1:0,19:19:57:686,57,0 1/1:0,16:16:48:505,48,0 +1 896922 . C T 1253.52 PASS AC=2;AF=6.30000e-02;AN=32;BaseQRankSum=-8.14600e+00;DP=943;Dels=0.00000e+00;FS=5.89500e+00;HaplotypeScore=1.37200e-01;InbreedingCoeff=-1.30000e-03;MQ=5.92800e+01;MQ0=0;MQRankSum=1.05600e+00;QD=1.01100e+01;ReadPosRankSum=-1.19000e+00;SNPEFF_AMINO_ACID_CHANGE=A119;SNPEFF_CODON_CHANGE=gcC/gcT;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_896673_896932;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000338591;VQSLOD=8.89000e+00;culprit=InbreedingCoeff;CSQ=T|ENSG00000187961|ENST00000466300|Transcript|upstream_gene_variant|||||||1|1185|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E|||||||||||||||||||||||||||||||,T|ENSG00000188976|ENST00000327044|Transcript|upstream_gene_variant|||||||1|2252|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187961|ENST00000338591|Transcript|synonymous_variant|464|357|119|A|gcC/gcT||1||1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0|||2/12||Pfam_domain:PF00651&PROSITE_profiles:PS50097&SMART_domains:SM00225&Superfamily_domains:SSF54695&PIRSF_domain:PIRSF037037|ENST00000338591.3:c.357N>T|ENST00000338591.3:c.357N>T(p.%3D)|||||||||||||||POSITION:0.1850699844479||NON_CAN_SPLICE_SURR|||||||,T|ENSG00000187583|ENST00000379409|Transcript|upstream_gene_variant|||||||1|4960|1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187961|ENST00000463212|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|94||||||1||1|KLHL17|HGNC|24023|retained_intron||||||||||1/2|||ENST00000463212.1:n.94N>T|||||||||||||||||||||||||,T|ENSG00000187583|ENST00000379407|Transcript|upstream_gene_variant|||||||1|4960|1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000469563|Transcript|upstream_gene_variant|||||||1|2286|-1|NOC2L|HGNC|24517|retained_intron||||||||||||||||||||||||||||||||||||||,T|ENSG00000187583|ENST00000379410|Transcript|upstream_gene_variant|||||||1|4955|1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000477976|Transcript|upstream_gene_variant|||||||1|3084|-1|NOC2L|HGNC|24517|retained_intron||||||||||||||||||||||||||||||||||||||,T|ENSG00000187961|ENST00000481067|Transcript|upstream_gene_variant|||||||1|2010|1|KLHL17|HGNC|24023|retained_intron||||||||||||||||||||||||||||||||||||||,T|ENSG00000188976|ENST00000487214|Transcript|upstream_gene_variant|||||||1|2233|-1|NOC2L|HGNC|24517|processed_transcript||||||||||||||||||||||||||||||||||||||,T||ENSR00000528861|RegulatoryFeature|regulatory_region_variant|||||||1||||||regulatory_region|||||||||||||||||||||||||||||||||||||| GT:AD:DP:GQ:PL 0/0:71,0:71:99:0,214,2684 0/0:69,0:69:99:0,208,2713 0/0:68,0:68:99:0,205,2515 0/0:20,0:20:57:0,57,722 0/0:29,0:29:87:0,87,1096 0/0:36,0:36:99:0,99,1225 0/0:61,0:61:99:0,184,2353 0/0:58,0:58:99:0,175,2192 0/0:68,0:68:99:0,205,2673 0/1:41,25:63:99:678,0,1190 0/0:87,0:87:99:0,262,3356 0/0:52,0:52:99:0,157,2006 0/1:35,23:55:99:651,0,922 0/0:79,0:79:99:0,238,3048 0/0:73,0:73:99:0,220,2816 0/0:54,0:54:99:0,163,2045 +1 897325 rs4970441 G C 2226684.78 PASS AC=31;AF=9.69000e-01;AN=32;BaseQRankSum=3.69960e+01;DB;DP=1475;Dels=0.00000e+00;FS=1.12830e+01;HaplotypeScore=4.66400e-01;InbreedingCoeff=1.15000e-01;MQ=5.95500e+01;MQ0=1;MQRankSum=2.60000e-02;QD=3.33700e+01;ReadPosRankSum=6.38900e+00;SNPEFF_AMINO_ACID_CHANGE=A203;SNPEFF_CODON_CHANGE=gcG/gcC;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_897206_897427;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000338591;VQSLOD=5.29000e+00;culprit=ReadPosRankSum;CSQ=C|ENSG00000187961|ENST00000466300|Transcript|upstream_gene_variant||||||rs4970441|1|782|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163|||||||||||||||||,C|ENSG00000188976|ENST00000327044|Transcript|upstream_gene_variant||||||rs4970441|1|2655|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000338591|Transcript|synonymous_variant|716|609|203|A|gcG/gcC|rs4970441|1||1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0|||4/12||Pfam_domain:PF07707&SMART_domains:SM00875&PIRSF_domain:PIRSF037037|ENST00000338591.3:c.609N>C|ENST00000338591.3:c.609N>C(p.%3D)|G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163||||||||POSITION:0.315707620528771||NON_CAN_SPLICE_SURR|||||||,C|ENSG00000187583|ENST00000379409|Transcript|upstream_gene_variant||||||rs4970441|1|4557|1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06||||||||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000463212|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|422|||||rs4970441|1||1|KLHL17|HGNC|24023|retained_intron||||||||||2/2|||ENST00000463212.1:n.422N>C||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163|||||||||||||||||,C|ENSG00000187583|ENST00000379407|Transcript|upstream_gene_variant||||||rs4970441|1|4557|1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF||||||||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000188976|ENST00000469563|Transcript|upstream_gene_variant||||||rs4970441|1|2689|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163|||||||||||||||||,C|ENSG00000187583|ENST00000379410|Transcript|upstream_gene_variant||||||rs4970441|1|4552|1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8||||||||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000188976|ENST00000477976|Transcript|upstream_gene_variant||||||rs4970441|1|3487|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163|||||||||||||||||,C|ENSG00000187961|ENST00000481067|Transcript|upstream_gene_variant||||||rs4970441|1|1607|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163|||||||||||||||||,C|ENSG00000188976|ENST00000487214|Transcript|upstream_gene_variant||||||rs4970441|1|2636|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163||||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,94:94:99:3476,283,0 1/1:0,87:87:99:3356,262,0 1/1:0,108:108:99:3994,325,0 1/1:0,56:56:99:2023,169,0 1/1:0,59:59:99:2182,178,0 1/1:0,46:46:99:1701,138,0 1/1:0,100:100:99:3780,301,0 1/1:0,127:127:99:4800,382,0 1/1:0,127:127:99:4899,382,0 1/1:0,127:127:99:4800,382,0 1/1:0,117:117:99:4422,352,0 0/1:42,33:71:99:891,0,1116 1/1:0,78:78:99:2948,235,0 1/1:0,107:107:99:4128,322,0 1/1:0,95:95:99:3665,286,0 1/1:0,76:76:99:2873,229,0 +1 898313 . C T 4423.71 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=1.00100e+01;DP=235;Dels=0.00000e+00;FS=6.83200e+00;HaplotypeScore=5.07500e-01;InbreedingCoeff=9.84000e-02;MQ=5.92600e+01;MQ0=0;MQRankSum=-5.62000e-01;QD=1.22500e+01;ReadPosRankSum=-4.59200e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000463212;VQSLOD=3.67000e+00;culprit=MQRankSum;CSQ=T|ENSG00000187961|ENST00000466300|Transcript|intron_variant&NMD_transcript_variant||||||rs375277853|1||1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||1/5||ENST00000466300.1:c.191+16N>T|||||||||||||||||||||||||,T|ENSG00000188976|ENST00000327044|Transcript|upstream_gene_variant||||||rs375277853|1|3643|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187961|ENST00000338591|Transcript|intron_variant||||||rs375277853|1||1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||6/11||ENST00000338591.3:c.1042+16N>T||||||||||||||||INTRON_SIZE:191||NON_CAN_SPLICE|||||||,T|ENSG00000187583|ENST00000379409|Transcript|upstream_gene_variant||||||rs375277853|1|3569|1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs375277853|1|455|1|KLHL17|HGNC|24023|retained_intron||||||||||||||||||||||||||||||||||||||,T|ENSG00000187583|ENST00000379407|Transcript|upstream_gene_variant||||||rs375277853|1|3569|1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000469563|Transcript|upstream_gene_variant||||||rs375277853|1|3677|-1|NOC2L|HGNC|24517|retained_intron||||||||||||||||||||||||||||||||||||||,T|ENSG00000187583|ENST00000379410|Transcript|upstream_gene_variant||||||rs375277853|1|3564|1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000477976|Transcript|upstream_gene_variant||||||rs375277853|1|4475|-1|NOC2L|HGNC|24517|retained_intron||||||||||||||||||||||||||||||||||||||,T|ENSG00000187961|ENST00000481067|Transcript|upstream_gene_variant||||||rs375277853|1|619|1|KLHL17|HGNC|24023|retained_intron||||||||||||||||||||||||||||||||||||||,T|ENSG00000188976|ENST00000487214|Transcript|upstream_gene_variant||||||rs375277853|1|3624|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||||||||||||||||||||||||| GT:AD:DP:GQ:PL 0/0:19,0:19:57:0,57,653 0/0:12,0:12:36:0,36,423 0/0:21,0:21:63:0,63,740 0/0:6,0:6:15:0,15,157 0/0:2,0:2:6:0,6,63 0/0:6,0:6:15:0,15,159 0/0:14,0:14:42:0,42,455 0/0:18,0:18:54:0,54,624 0/0:14,0:14:39:0,39,447 0/0:25,0:25:72:0,72,805 0/0:16,0:16:48:0,48,564 0/1:13,8:20:99:190,0,314 0/0:21,0:21:63:0,63,702 0/0:17,1:18:18:0,18,560 0/0:11,0:11:30:0,30,342 0/0:12,0:12:36:0,36,393 +1 898323 rs6605071 T C 353673.96 PASS AC=31;AF=9.69000e-01;AN=32;BaseQRankSum=1.91890e+01;DB;DP=221;Dels=0.00000e+00;FS=9.64600e+00;HaplotypeScore=4.04000e-01;InbreedingCoeff=-2.15000e-02;MQ=5.91700e+01;MQ0=0;MQRankSum=-4.60000e-02;QD=3.77900e+01;ReadPosRankSum=3.36900e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000463212;VQSLOD=4.11000e+00;culprit=InbreedingCoeff;CSQ=C|ENSG00000187961|ENST00000466300|Transcript|intron_variant&NMD_transcript_variant||||||rs6605071|1||1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||1/5||ENST00000466300.1:c.191+26N>C||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859|||||||||||||||||,C|ENSG00000188976|ENST00000327044|Transcript|upstream_gene_variant||||||rs6605071|1|3653|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859||||||||||EXON_INTRON_UNDEF&ANC_ALLELE|||||||,C|ENSG00000187961|ENST00000338591|Transcript|intron_variant||||||rs6605071|1||1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||6/11||ENST00000338591.3:c.1042+26N>C||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859||||||||INTRON_SIZE:191||NON_CAN_SPLICE&ANC_ALLELE|||||||,C|ENSG00000187583|ENST00000379409|Transcript|upstream_gene_variant||||||rs6605071|1|3559|1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06||||||||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859||||||||||EXON_INTRON_UNDEF&ANC_ALLELE|||||||,C|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs6605071|1|465|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859|||||||||||||||||,C|ENSG00000187583|ENST00000379407|Transcript|upstream_gene_variant||||||rs6605071|1|3559|1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF||||||||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859||||||||||EXON_INTRON_UNDEF&ANC_ALLELE|||||||,C|ENSG00000188976|ENST00000469563|Transcript|upstream_gene_variant||||||rs6605071|1|3687|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859|||||||||||||||||,C|ENSG00000187583|ENST00000379410|Transcript|upstream_gene_variant||||||rs6605071|1|3554|1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8||||||||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859||||||||||EXON_INTRON_UNDEF&ANC_ALLELE|||||||,C|ENSG00000188976|ENST00000477976|Transcript|upstream_gene_variant||||||rs6605071|1|4485|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859|||||||||||||||||,C|ENSG00000187961|ENST00000481067|Transcript|upstream_gene_variant||||||rs6605071|1|609|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859|||||||||||||||||,C|ENSG00000188976|ENST00000487214|Transcript|upstream_gene_variant||||||rs6605071|1|3634|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859||||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,18:18:54:688,54,0 1/1:0,8:8:24:315,24,0 1/1:0,15:15:45:579,45,0 1/1:0,7:7:21:262,21,0 1/1:0,3:3:9:111,9,0 1/1:0,4:4:9:122,9,0 1/1:0,20:20:60:786,60,0 1/1:0,16:16:48:641,48,0 1/1:0,13:13:36:457,36,0 1/1:0,27:27:78:1030,78,0 1/1:0,18:18:54:720,54,0 0/1:13,4:17:99:112,0,396 1/1:0,18:18:54:708,54,0 1/1:0,13:13:39:525,39,0 1/1:0,10:10:30:393,30,0 1/1:1,13:14:5:460,5,0 +1 898467 rs41285808 C T 14490.29 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-2.26300e+00;DB;DP=270;Dels=0.00000e+00;FS=1.33000e+00;HaplotypeScore=2.81700e-01;InbreedingCoeff=3.75000e-02;MQ=5.93000e+01;MQ0=0;MQRankSum=3.96000e+00;QD=1.37100e+01;ReadPosRankSum=-1.57400e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000463212;VQSLOD=7.17000e+00;culprit=FS;CSQ=T|ENSG00000187961|ENST00000466300|Transcript|synonymous_variant&NMD_transcript_variant|247|249|83|P|ccC/ccT|rs41285808|1||1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E|||2/6|||ENST00000466300.1:c.247N>T|ENST00000466300.1:c.247N>T(p.%3D)|T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672|||||||||||||||||,T|ENSG00000188976|ENST00000327044|Transcript|upstream_gene_variant||||||rs41285808|1|3797|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187961|ENST00000338591|Transcript|intron_variant||||||rs41285808|1||1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||6/11||ENST00000338591.3:c.1043-22N>T||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672||||||||INTRON_SIZE:191||NON_CAN_SPLICE|||||||,T|ENSG00000187583|ENST00000379409|Transcript|upstream_gene_variant||||||rs41285808|1|3415|1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06||||||||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs41285808|1|609|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672|||||||||||||||||,T|ENSG00000187583|ENST00000379407|Transcript|upstream_gene_variant||||||rs41285808|1|3415|1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF||||||||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000469563|Transcript|upstream_gene_variant||||||rs41285808|1|3831|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672|||||||||||||||||,T|ENSG00000187583|ENST00000379410|Transcript|upstream_gene_variant||||||rs41285808|1|3410|1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8||||||||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000477976|Transcript|upstream_gene_variant||||||rs41285808|1|4629|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672|||||||||||||||||,T|ENSG00000187961|ENST00000481067|Transcript|upstream_gene_variant||||||rs41285808|1|465|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672|||||||||||||||||,T|ENSG00000188976|ENST00000487214|Transcript|upstream_gene_variant||||||rs41285808|1|3778|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672||||||||||||||||| GT:AD:DP:GQ:PL 0/0:28,0:28:84:0,84,1030 0/0:15,0:15:45:0,45,579 0/0:25,0:25:75:0,75,916 0/0:6,0:6:18:0,18,197 0/0:5,0:5:15:0,15,172 0/0:3,0:3:9:0,9,100 0/0:14,0:14:42:0,42,480 0/0:22,0:22:66:0,66,817 0/0:23,0:23:69:0,69,831 0/0:12,0:12:36:0,36,431 0/0:18,0:18:51:0,51,646 0/1:17,10:26:99:278,0,440 0/0:21,0:21:51:0,51,644 0/0:13,0:13:39:0,39,481 0/0:18,0:18:54:0,54,666 0/0:21,0:21:60:0,60,723 +1 899959 . G GC 2073.57 PASS AC=1;AF=5.00000e-02;AN=20;BaseQRankSum=8.77000e-01;DP=19;FS=1.24470e+02;HaplotypeScore=1.51273e+01;InbreedingCoeff=6.94000e-02;MQ=4.52200e+01;MQ0=0;MQRankSum=-8.47500e+00;QD=1.40100e+01;ReadPosRankSum=4.26000e-01;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000463212;CSQ=C|ENSG00000187583|ENST00000379409|Transcript|upstream_gene_variant||||||TMP_ESP_1_899960_899959|1|1922|1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06|||||||||||||C:0.152075|C:0.090390||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||TMP_ESP_1_899960_899959|1|2101|1|KLHL17|HGNC|24023|retained_intron||||||||||||||||||||C:0.152075|C:0.090390|||||||||||||||||,C|ENSG00000187583|ENST00000379407|Transcript|upstream_gene_variant||||||TMP_ESP_1_899960_899959|1|1922|1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF|||||||||||||C:0.152075|C:0.090390||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000466300|Transcript|downstream_gene_variant||||||TMP_ESP_1_899960_899959|1|49|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E|||||||||||||C:0.152075|C:0.090390|||||||||||||||||,C|ENSG00000187583|ENST00000379410|Transcript|upstream_gene_variant||||||TMP_ESP_1_899960_899959|1|1917|1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8|||||||||||||C:0.152075|C:0.090390||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000481067|Transcript|downstream_gene_variant||||||TMP_ESP_1_899960_899959|1|415|1|KLHL17|HGNC|24023|retained_intron||||||||||||||||||||C:0.152075|C:0.090390|||||||||||||||||,C|ENSG00000187961|ENST00000338591|Transcript|intron_variant||||||TMP_ESP_1_899960_899959|1||1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||11/11||ENST00000338591.3:c.1700+49_1700+50insC|||||||C:0.152075|C:0.090390||||||||INTRON_SIZE:432||NON_CAN_SPLICE||||||| GT:AD:DP:GQ:PL ./.:.:.:.:. ./.:.:.:.:. 0/0:3,0:3:9:0,9,136 0/0:1,0:1:3:0,3,45 0/0:1,0:1:3:0,3,45 0/0:2,0:2:6:0,6,91 0/1:3,1:4:28:28,0,124 0/0:2,0:2:6:0,6,74 0/0:2,0:2:6:0,6,91 0/0:2,0:2:6:0,6,91 ./.:.:.:.:. ./.:.:.:.:. ./.:.:.:.:. 0/0:1,0:1:3:0,3,45 ./.:.:.:.:. 0/0:1,0:1:3:0,3,45 +1 900505 rs28705211 G C 222602.28 PASS AC=8;AF=2.50000e-01;AN=32;BaseQRankSum=6.97200e+00;DB;DP=885;Dels=0.00000e+00;FS=4.61940e+01;HaplotypeScore=1.18840e+00;InbreedingCoeff=1.98200e-01;MQ=5.92300e+01;MQ0=0;MQRankSum=1.76580e+01;QD=1.80400e+01;ReadPosRankSum=1.01980e+01;SNPEFF_AMINO_ACID_CHANGE=V497;SNPEFF_CODON_CHANGE=gtG/gtC;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_900343_901094;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000455747;VQSLOD=1.37000e+00;culprit=HaplotypeScore;CSQ=C|ENSG00000187583|ENST00000379409|Transcript|upstream_gene_variant||||||rs28705211&COSM426805|1|1377|1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06||||||||C:0.1648|C:0.02|C:0.22|C:0.09|C:0.28||||0&1|20637081|||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs28705211&COSM426805|1|2647|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||C:0.1648|C:0.02|C:0.22|C:0.09|C:0.28||||0&1|20637081||||||||||||||,C|ENSG00000187583|ENST00000379407|Transcript|upstream_gene_variant||||||rs28705211&COSM426805|1|1377|1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF||||||||C:0.1648|C:0.02|C:0.22|C:0.09|C:0.28||||0&1|20637081|||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000466300|Transcript|downstream_gene_variant||||||rs28705211&COSM426805|1|595|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||C:0.1648|C:0.02|C:0.22|C:0.09|C:0.28||||0&1|20637081||||||||||||||,C|ENSG00000187583|ENST00000379410|Transcript|upstream_gene_variant||||||rs28705211&COSM426805|1|1372|1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8||||||||C:0.1648|C:0.02|C:0.22|C:0.09|C:0.28||||0&1|20637081|||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000481067|Transcript|downstream_gene_variant||||||rs28705211&COSM426805|1|961|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||C:0.1648|C:0.02|C:0.22|C:0.09|C:0.28||||0&1|20637081||||||||||||||,C|ENSG00000187961|ENST00000338591|Transcript|synonymous_variant|1970|1863|621|V|gtG/gtC|rs28705211&COSM426805|1||1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0|||12/12||SMART_domains:SM00612&Superfamily_domains:SSF117281&PIRSF_domain:PIRSF037037|ENST00000338591.3:c.1863N>C|ENST00000338591.3:c.1863N>C(p.%3D)|C:0.1648|C:0.02|C:0.22|C:0.09|C:0.28||||0&1|20637081|||||POSITION:0.965785381026439||END_TRUNC&NON_CAN_SPLICE_SURR||||||| GT:AD:DP:GQ:PL 0/0:87,0:87:99:0,262,3217 0/1:43,24:61:99:697,0,1146 0/1:35,29:60:99:812,0,913 0/0:23,0:23:69:0,69,851 0/0:22,0:22:66:0,66,788 0/0:33,1:34:96:0,96,1150 0/0:54,0:54:99:0,162,1973 0/1:32,27:56:99:720,0,880 0/0:79,0:79:99:0,235,2850 0/0:74,0:74:99:0,214,2587 0/0:65,0:65:99:0,196,2354 0/1:24,26:48:99:738,0,687 0/1:27,28:54:99:795,0,709 0/0:58,0:58:99:0,175,2173 0/1:28,27:54:99:805,0,735 1/1:0,56:56:99:2066,169,0 +1 902024 rs181910588 G 406.47 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-3.35500e+00;DB;DP=225;Dels=0.00000e+00;FS=1.03150e+01;HaplotypeScore=3.56800e-01;InbreedingCoeff=-1.33000e-02;MQ=5.93500e+01;MQ0=0;MQRankSum=1.21200e+00;QD=1.09900e+01;ReadPosRankSum=-1.50700e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000338591;VQSLOD=6.64000e+00;culprit=InbreedingCoeff;CSQ=A|ENSG00000187583|ENST00000480267|Transcript|upstream_gene_variant||||||rs181910588|1|4231|1|PLEKHN1|HGNC|25284|retained_intron|||||||||||||||A:0.0023|A:0.01||||A:0.001842|A:0|||||||||||||||||,A|ENSG00000187961|ENST00000466300|Transcript|downstream_gene_variant||||||rs181910588|1|2114|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||A:0.0023|A:0.01||||A:0.001842|A:0|||||||||||||||||,A|ENSG00000187961|ENST00000338591|Transcript|downstream_gene_variant||||||rs181910588|1|929|1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||||||A:0.0023|A:0.01||||A:0.001842|A:0||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs181910588|1|4166|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0023|A:0.01||||A:0.001842|A:0|||||||||||||||||,A|ENSG00000187583|ENST00000379409|Transcript|intron_variant||||||rs181910588|1||1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06||||1/14||ENST00000379409.2:c.83+30N>A||A:0.0023|A:0.01||||A:0.001842|A:0||||||||INTRON_SIZE:89||NON_CAN_SPLICE|||||||,A|ENSG00000187583|ENST00000379407|Transcript|intron_variant||||||rs181910588|1||1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF||||1/14||ENST00000379407.3:c.83+30N>A||A:0.0023|A:0.01||||A:0.001842|A:0||||||||INTRON_SIZE:89||NON_CAN_SPLICE|||||||,A|ENSG00000187961|ENST00000481067|Transcript|downstream_gene_variant||||||rs181910588|1|2480|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0023|A:0.01||||A:0.001842|A:0|||||||||||||||||,A|ENSG00000187583|ENST00000379410|Transcript|intron_variant||||||rs181910588|1||1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8||||1/15||ENST00000379410.3:c.83+30N>A||A:0.0023|A:0.01||||A:0.001842|A:0||||||||INTRON_SIZE:89||NON_CAN_SPLICE|||||||,A||ENSR00000528862|RegulatoryFeature|regulatory_region_variant||||||rs181910588|1||||||regulatory_region|||||||||||||||A:0.0023|A:0.01||||A:0.001842|A:0||||||||||||||||| GT:AD:DP:GQ:PL 0/0:18,0:18:54:0,54,689 0/0:21,0:21:63:0,63,797 0/0:17,0:17:48:0,48,608 0/0:5,0:5:15:0,15,182 0/0:9,0:9:27:0,27,333 0/0:7,0:7:21:0,21,253 0/0:18,0:18:54:0,54,680 0/0:7,0:7:21:0,21,259 0/0:17,0:17:51:0,51,614 0/0:19,0:19:54:0,54,647 0/0:20,0:20:60:0,60,756 0/0:14,0:14:42:0,42,518 0/0:13,0:13:36:0,36,466 0/0:14,0:14:42:0,42,535 0/1:9,1:11:4:4,0,296 0/0:15,0:15:45:0,45,551 +1 902069 rs116147894 T C 13024.04 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=2.08840e+01;DB;DP=157;Dels=0.00000e+00;FS=3.07700e+00;HaplotypeScore=2.10500e-01;InbreedingCoeff=1.00200e-01;MQ=5.91800e+01;MQ0=0;MQRankSum=7.75000e-01;QD=1.56200e+01;ReadPosRankSum=-5.68400e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000338591;VQSLOD=7.17000e+00;culprit=MQ;CSQ=C|ENSG00000187583|ENST00000480267|Transcript|upstream_gene_variant||||||rs116147894|1|4186|1|PLEKHN1|HGNC|25284|retained_intron|||||||||||||||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163|||||||||||||||||,C|ENSG00000187961|ENST00000466300|Transcript|downstream_gene_variant||||||rs116147894|1|2159|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163|||||||||||||||||,C|ENSG00000187961|ENST00000338591|Transcript|downstream_gene_variant||||||rs116147894|1|974|1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||||||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs116147894|1|4211|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163|||||||||||||||||,C|ENSG00000187583|ENST00000379409|Transcript|intron_variant||||||rs116147894|1||1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06||||1/14||ENST00000379409.2:c.84-15N>C||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163||||||||INTRON_SIZE:89||NON_CAN_SPLICE|||||||,C|ENSG00000187583|ENST00000379407|Transcript|intron_variant||||||rs116147894|1||1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF||||1/14||ENST00000379407.3:c.84-15N>C||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163||||||||INTRON_SIZE:89||NON_CAN_SPLICE|||||||,C|ENSG00000187961|ENST00000481067|Transcript|downstream_gene_variant||||||rs116147894|1|2525|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163|||||||||||||||||,C|ENSG00000187583|ENST00000379410|Transcript|intron_variant||||||rs116147894|1||1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8||||1/15||ENST00000379410.3:c.84-15N>C||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163||||||||INTRON_SIZE:89||NON_CAN_SPLICE|||||||,C||ENSR00000528862|RegulatoryFeature|regulatory_region_variant||||||rs116147894|1||||||regulatory_region|||||||||||||||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163||||||||||||||||| GT:AD:DP:GQ:PL 0/0:10,0:10:30:0,30,367 0/1:12,2:13:3:3,0,418 0/0:14,0:14:42:0,42,514 0/0:4,0:4:12:0,12,144 0/0:5,0:5:15:0,15,176 0/0:4,0:4:12:0,12,145 0/0:17,0:17:48:0,48,603 0/0:6,0:6:18:0,18,227 0/0:10,0:10:30:0,30,361 0/0:10,0:10:30:0,30,372 0/0:12,0:12:36:0,36,434 0/0:7,0:7:21:0,21,259 0/0:7,0:7:21:0,21,255 0/0:11,0:11:30:0,30,375 0/0:12,0:12:36:0,36,426 0/0:15,0:15:45:0,45,530 +1 902088 . G A 324.34 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-5.34900e+00;DP=133;Dels=0.00000e+00;FS=7.94000e-01;HaplotypeScore=1.50400e-01;InbreedingCoeff=3.03000e-02;MQ=5.93200e+01;MQ0=0;MQRankSum=2.32200e+00;QD=7.91000e+00;ReadPosRankSum=-2.12100e+00;SNPEFF_AMINO_ACID_CHANGE=D30N;SNPEFF_CODON_CHANGE=Gac/Aac;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_902084_902183;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=PLEKHN1;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000379407;VQSLOD=5.23000e+00;culprit=QD;CSQ=A|ENSG00000187583|ENST00000480267|Transcript|upstream_gene_variant||||||rs201730138|1|4167|1|PLEKHN1|HGNC|25284|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187961|ENST00000466300|Transcript|downstream_gene_variant||||||rs201730138|1|2178|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187961|ENST00000338591|Transcript|downstream_gene_variant||||||rs201730138|1|993|1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||||||A:0.0005||A:0.0028|||A:0|A:0.000600||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs201730138|1|4230|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187583|ENST00000379409|Transcript|missense_variant|118|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06|tolerated(0.26)|benign(0.034)|2/15|||ENST00000379409.2:c.88N>A|ENSP00000368719.2:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0441767068273092||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A|ENSG00000187583|ENST00000379407|Transcript|missense_variant|118|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF|tolerated(0.25)|benign(0.072)|2/15|||ENST00000379407.3:c.88N>A|ENSP00000368717.2:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0508376660889659||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A|ENSG00000187961|ENST00000481067|Transcript|downstream_gene_variant||||||rs201730138|1|2544|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187583|ENST00000379410|Transcript|missense_variant|123|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8|tolerated(0.25)|benign(0.072)|2/16|||ENST00000379410.3:c.88N>A|ENSP00000368720.3:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0479302832244009||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A||ENSR00000528862|RegulatoryFeature|regulatory_region_variant||||||rs201730138|1||||||regulatory_region|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600||||||||||||||||| GT:AD:DP:GQ:PL 0/1:10,1:11:1:1,0,264 0/0:13,0:13:33:0,33,447 0/0:10,0:10:30:0,30,371 0/0:4,0:4:12:0,12,141 0/0:1,0:1:3:0,3,39 0/0:4,0:4:12:0,12,145 0/0:18,0:18:51:0,51,665 0/0:4,0:4:12:0,12,148 0/0:5,0:5:15:0,15,193 0/0:9,0:9:24:0,24,320 0/0:10,0:10:30:0,30,378 0/0:4,0:4:12:0,12,160 0/0:10,0:10:30:0,30,387 0/0:7,0:7:21:0,21,247 0/0:9,0:9:27:0,27,350 0/0:14,0:14:42:0,42,540 +1 902088 . G A 111 - AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-5.34900e+00;DP=133;Dels=0.00000e+00;FS=7.94000e-01;HaplotypeScore=1.50400e-01;InbreedingCoeff=3.03000e-02;MQ=5.93200e+01;MQ0=0;MQRankSum=2.32200e+00;QD=7.91000e+00;ReadPosRankSum=-2.12100e+00;SNPEFF_AMINO_ACID_CHANGE=D30N;SNPEFF_CODON_CHANGE=Gac/Aac;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_902084_902183;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=PLEKHN1;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000379407;VQSLOD=5.23000e+00;culprit=QD;CSQ=A|ENSG00000187583|ENST00000480267|Transcript|upstream_gene_variant||||||rs201730138|1|4167|1|PLEKHN1|HGNC|25284|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187961|ENST00000466300|Transcript|downstream_gene_variant||||||rs201730138|1|2178|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187961|ENST00000338591|Transcript|downstream_gene_variant||||||rs201730138|1|993|1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||||||A:0.0005||A:0.0028|||A:0|A:0.000600||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs201730138|1|4230|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187583|ENST00000379409|Transcript|missense_variant|118|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06|tolerated(0.26)|benign(0.034)|2/15|||ENST00000379409.2:c.88N>A|ENSP00000368719.2:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0441767068273092||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A|ENSG00000187583|ENST00000379407|Transcript|missense_variant|118|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF|tolerated(0.25)|benign(0.072)|2/15|||ENST00000379407.3:c.88N>A|ENSP00000368717.2:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0508376660889659||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A|ENSG00000187961|ENST00000481067|Transcript|downstream_gene_variant||||||rs201730138|1|2544|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187583|ENST00000379410|Transcript|missense_variant|123|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8|tolerated(0.25)|benign(0.072)|2/16|||ENST00000379410.3:c.88N>A|ENSP00000368720.3:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0479302832244009||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A||ENSR00000528862|RegulatoryFeature|regulatory_region_variant||||||rs201730138|1||||||regulatory_region|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600||||||||||||||||| GT:AD:DP:GQ:PL 0/1:10,1:11:1:1,0,264 0/0:13,0:13:33:0,33,447 0/0:10,0:10:30:0,30,371 0/0:4,0:4:12:0,12,141 0/0:1,0:1:3:0,3,39 0/0:4,0:4:12:0,12,145 0/0:18,0:18:51:0,51,665 0/0:4,0:4:12:0,12,148 0/0:5,0:5:15:0,15,193 0/0:9,0:9:24:0,24,320 0/0:10,0:10:30:0,30,378 0/0:4,0:4:12:0,12,160 0/0:10,0:10:30:0,30,387 0/0:7,0:7:21:0,21,247 0/0:9,0:9:27:0,27,350 0/0:14,0:14:42:0,42,540 +GL000207.1 1 . G A 324.34 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-5.34900e+00;DP=133;Dels=0.00000e+00;FS=7.94000e-01;HaplotypeScore=1.50400e-01;InbreedingCoeff=3.03000e-02;MQ=5.93200e+01;MQ0=0;MQRankSum=2.32200e+00;QD=7.91000e+00;ReadPosRankSum=-2.12100e+00;SNPEFF_AMINO_ACID_CHANGE=D30N;SNPEFF_CODON_CHANGE=Gac/Aac;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_902084_902183;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=PLEKHN1;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000379407;VQSLOD=5.23000e+00;culprit=QD;CSQ=A|ENSG00000187583|ENST00000480267|Transcript|upstream_gene_variant||||||rs201730138|1|4167|1|PLEKHN1|HGNC|25284|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187961|ENST00000466300|Transcript|downstream_gene_variant||||||rs201730138|1|2178|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187961|ENST00000338591|Transcript|downstream_gene_variant||||||rs201730138|1|993|1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||||||A:0.0005||A:0.0028|||A:0|A:0.000600||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs201730138|1|4230|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187583|ENST00000379409|Transcript|missense_variant|118|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06|tolerated(0.26)|benign(0.034)|2/15|||ENST00000379409.2:c.88N>A|ENSP00000368719.2:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0441767068273092||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A|ENSG00000187583|ENST00000379407|Transcript|missense_variant|118|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF|tolerated(0.25)|benign(0.072)|2/15|||ENST00000379407.3:c.88N>A|ENSP00000368717.2:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0508376660889659||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A|ENSG00000187961|ENST00000481067|Transcript|downstream_gene_variant||||||rs201730138|1|2544|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187583|ENST00000379410|Transcript|missense_variant|123|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8|tolerated(0.25)|benign(0.072)|2/16|||ENST00000379410.3:c.88N>A|ENSP00000368720.3:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0479302832244009||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A||ENSR00000528862|RegulatoryFeature|regulatory_region_variant||||||rs201730138|1||||||regulatory_region|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600||||||||||||||||| GT:AD:DP:GQ:PL 0/1:10,1:11:1:1,0,264 0/0:13,0:13:33:0,33,447 0/0:10,0:10:30:0,30,371 0/0:4,0:4:12:0,12,141 0/0:1,0:1:3:0,3,39 0/0:4,0:4:12:0,12,145 0/0:18,0:18:51:0,51,665 0/0:4,0:4:12:0,12,148 0/0:5,0:5:15:0,15,193 0/0:9,0:9:24:0,24,320 0/0:10,0:10:30:0,30,378 0/0:4,0:4:12:0,12,160 0/0:10,0:10:30:0,30,387 0/0:7,0:7:21:0,21,247 0/0:9,0:9:27:0,27,350 0/0:14,0:14:42:0,42,540 diff --git a/loading_pipeline/var/test/callsets/sex_and_relatedness_1.mt/.README.txt.crc b/loading_pipeline/var/test/callsets/sex_and_relatedness_1.mt/.README.txt.crc new file mode 100644 index 0000000000000000000000000000000000000000..6ceb835d00cda96c5c0f4b3d92efe53201f1a7b3 GIT binary patch literal 12 TcmYc;N@ieSU}CWB<4gts5Q744 literal 0 HcmV?d00001 diff --git a/loading_pipeline/var/test/callsets/sex_and_relatedness_1.mt/._SUCCESS.crc b/loading_pipeline/var/test/callsets/sex_and_relatedness_1.mt/._SUCCESS.crc new file mode 100644 index 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ALGORITHMS=depth;CHR2=chr1;END=263666;EVIDENCE=BAF,RD;PREDICTED_INTERGENIC;PREDICTED_NEAREST_TSS=OR4F29;SVLEN=6000;SVTYPE=DUP;AN=8;AC=1;AF=0.115596;N_BI_GENOS=2911;N_HOMREF=2348;N_HET=453;N_HOMALT=110;FREQ_HOMREF=0.806596;FREQ_HET=0.155617;FREQ_HOMALT=0.0377877;MALE_AN=2894;MALE_AC=339;MALE_AF=0.117139;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=1163;MALE_N_HET=229;MALE_N_HOMALT=55;MALE_FREQ_HOMREF=0.803732;MALE_FREQ_HET=0.158258;MALE_FREQ_HOMALT=0.0380097;FEMALE_AN=2906;FEMALE_AC=330;FEMALE_AF=0.113558;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=1178;FEMALE_N_HET=220;FEMALE_N_HOMALT=55;FEMALE_FREQ_HOMREF=0.810736;FEMALE_FREQ_HET=0.151411;FEMALE_FREQ_HOMALT=0.0378527 GT:EV:GQ:RD_CN:RD_GQ 0/0:RD:99:2:99 0/0:RD:99:2:99 0/1:RD:8:3:8 0/0:RD:13:1:13 0/0:RD:13:1:13 +chr1 413968 DEL_chr1_12 N 999 PASS ALGORITHMS=depth;CHR2=chr1;END=428500;EVIDENCE=RD;PREDICTED_INTERGENIC;PREDICTED_NEAREST_TSS=OR4F29;SVLEN=14532;SVTYPE=DEL;AN=8;AC=1;AF=0.064926;N_BI_GENOS=2911;N_HOMREF=2538;N_HET=368;N_HOMALT=5;FREQ_HOMREF=0.871865;FREQ_HET=0.126417;FREQ_HOMALT=0.00171762;MALE_AN=2894;MALE_AC=172;MALE_AF=0.059433;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=1278;MALE_N_HET=166;MALE_N_HOMALT=3;MALE_FREQ_HOMREF=0.883207;MALE_FREQ_HET=0.11472;MALE_FREQ_HOMALT=0.00207325;FEMALE_AN=2906;FEMALE_AC=205;FEMALE_AF=0.070544;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=1250;FEMALE_N_HET=201;FEMALE_N_HOMALT=2;FEMALE_FREQ_HOMREF=0.860289;FEMALE_FREQ_HET=0.138334;FEMALE_FREQ_HOMALT=0.00137646 GT:EV:GQ:RD_CN:RD_GQ 0/0:RD:12:2:12 0/0:RD:0:2:0 0/1:RD:99:1:99 0/0:RD:2:2:2 0/0:RD:2:2:2 +chr1 789481 BND_chr1_9 N 999 PESR_GT_OVERDISPERSION;UNRESOLVED ALGORITHMS=manta;CHR2=chr1;END=789481;EVIDENCE=PE;PREDICTED_INTERGENIC;PREDICTED_NEAREST_TSS=FBXO28,OR4F16;PREDICTED_NONCODING_BREAKPOINT=DNase,Tommerup_TADanno;STRANDS=-+;SVLEN=223225007;SVTYPE=BND;UNRESOLVED_TYPE=SINGLE_ENDER_-+;AN=8;AC=7;AF=0.910684;N_BI_GENOS=2911;N_HOMREF=0;N_HET=520;N_HOMALT=2391;FREQ_HOMREF=0;FREQ_HET=0.178633;FREQ_HOMALT=0.821367;MALE_AN=2894;MALE_AC=2639;MALE_AF=0.911887;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=0;MALE_N_HET=255;MALE_N_HOMALT=1192;MALE_FREQ_HOMREF=0;MALE_FREQ_HET=0.176227;MALE_FREQ_HOMALT=0.823773;FEMALE_AN=2906;FEMALE_AC=2643;FEMALE_AF=0.909498;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=0;FEMALE_N_HET=263;FEMALE_N_HOMALT=1190;FEMALE_FREQ_HOMREF=0;FEMALE_FREQ_HET=0.181005;FEMALE_FREQ_HOMALT=0.818995 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 1/1:PE:59:59:2:99:0 1/1:PE:26:26:2:99:0 1/1:PE:39:39:2:99:0 0/1:PE:19:19:1:99:0 0/1:PE:19:19:1:99:0 +chr1 4228405 INS_chr1_65 N 605 HIGH_SR_BACKGROUND ALGORITHMS=manta,melt;CHR2=chr1;END=4228448;EVIDENCE=SR;gnomAD_V2_SVID=gnomAD-SV_v2.1_INS_chr1_65;GNOMAD_V4.1_TRUTH_VID=gnomAD-SV_v3_BND_chr1_0001f5b7;gnomAD_V2_AF=0.068962998688221;gnomAD_V2_AC=224;gnomAD_V2_AN=3247;StrVCTVRE=0.1255;PREDICTED_INTERGENIC;PREDICTED_NEAREST_TSS=C1orf174;SVLEN=298;SVTYPE=INS;AN=8;AC=1;AF=0.10237;N_BI_GENOS=2911;N_HOMREF=2318;N_HET=590;N_HOMALT=3;FREQ_HOMREF=0.79629;FREQ_HET=0.202679;FREQ_HOMALT=0.00103057;MALE_AN=2894;MALE_AC=293;MALE_AF=0.101244;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=1156;MALE_N_HET=289;MALE_N_HOMALT=2;MALE_FREQ_HOMREF=0.798894;MALE_FREQ_HET=0.199724;MALE_FREQ_HOMALT=0.00138217;FEMALE_AN=2906;FEMALE_AC=302;FEMALE_AF=0.103923;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=1152;FEMALE_N_HET=300;FEMALE_N_HOMALT=1;FEMALE_FREQ_HOMREF=0.792842;FEMALE_FREQ_HET=0.206469;FEMALE_FREQ_HOMALT=0.000688231 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 0/1:SR:62:99:0:62:1 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:99:0 +chr1 6558902 CPX_chr1_22 N 644 HIGH_SR_BACKGROUND ALGORITHMS=manta;BOTHSIDES_SUPPORT;CHR2=chr1;CPX_INTERVALS=INV_chr1:6558902-6559723,DUP_chr1:6559655-6559723;CPX_TYPE=INVdup;END=6559723;EVIDENCE=PE,SR;PREDICTED_INTRONIC=TAS1R1;PREDICTED_NONCODING_BREAKPOINT=Tommerup_TADanno;PREDICTED_NONCODING_SPAN=DNase;SVLEN=821;SVTYPE=CPX;AN=8;AC=2;AF=0.169873;N_BI_GENOS=2911;N_HOMREF=1925;N_HET=983;N_HOMALT=3;FREQ_HOMREF=0.661285;FREQ_HET=0.337685;FREQ_HOMALT=0.00103057;MALE_AN=2894;MALE_AC=497;MALE_AF=0.171735;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=950;MALE_N_HET=497;MALE_N_HOMALT=0;MALE_FREQ_HOMREF=0.656531;MALE_FREQ_HET=0.343469;MALE_FREQ_HOMALT=0;FEMALE_AN=2906;FEMALE_AC=488;FEMALE_AF=0.167928;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=968;FEMALE_N_HET=482;FEMALE_N_HOMALT=3;FEMALE_FREQ_HOMREF=0.666208;FEMALE_FREQ_HET=0.331727;FEMALE_FREQ_HOMALT=0.00206469 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT:RD_CN:CONC_ST 0/0:PE,SR:99:99:0:99:0:2:EMPTY 0/1:PE,SR:57:0:0:57:1:2:TN,TP 0/1:PE,SR:0:0:1:99:0:2:FP,TN 0/0:PE,SR:99:99:0:0:0:3:FN 1/1:PE,SR:99:99:0:0:0:1:FP,TP +chr1 16088760 CPX_chr1_41 N 684 PASS ALGORITHMS=manta;CHR2=chr1;CPX_INTERVALS=DUP_chr1:16088760-16088835,INV_chr1:16088760-16089601;CPX_TYPE=dupINV;END=16089601;EVIDENCE=PE,SR;PREDICTED_INTERGENIC;PREDICTED_NEAREST_TSS=FAM131C;PREDICTED_NONCODING_BREAKPOINT=Tommerup_TADanno;PREDICTED_NONCODING_SPAN=DNase;SVLEN=841;SVTYPE=CPX;AN=8;AC=2;AF=0.218138;N_BI_GENOS=2911;N_HOMREF=1659;N_HET=1234;N_HOMALT=18;FREQ_HOMREF=0.569907;FREQ_HET=0.423909;FREQ_HOMALT=0.00618344;MALE_AN=2894;MALE_AC=635;MALE_AF=0.219419;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=818;MALE_N_HET=623;MALE_N_HOMALT=6;MALE_FREQ_HOMREF=0.565308;MALE_FREQ_HET=0.430546;MALE_FREQ_HOMALT=0.00414651;FEMALE_AN=2906;FEMALE_AC=629;FEMALE_AF=0.216449;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=836;FEMALE_N_HET=605;FEMALE_N_HOMALT=12;FEMALE_FREQ_HOMREF=0.575361;FEMALE_FREQ_HET=0.41638;FEMALE_FREQ_HOMALT=0.00825877 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 0/1:SR:52:0:0:52:1 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:99:0 0/1:SR:62:0:0:62:1 0/1:SR:62:0:0:62:1 +chr1 17465707 INS_chr1_268 N 263 HIGH_SR_BACKGROUND ALGORITHMS=melt;CHR2=chr1;END=17465723;EVIDENCE=SR;PREDICTED_INTERGENIC;PREDICTED_NEAREST_TSS=RCC2;PREDICTED_NONCODING_BREAKPOINT=Tommerup_TADanno;SVLEN=955;SVTYPE=INS;AN=8;AC=1;AF=0.004466;N_BI_GENOS=2911;N_HOMREF=2885;N_HET=26;N_HOMALT=0;FREQ_HOMREF=0.991068;FREQ_HET=0.00893164;FREQ_HOMALT=0;MALE_AN=2894;MALE_AC=14;MALE_AF=0.004838;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=1433;MALE_N_HET=14;MALE_N_HOMALT=0;MALE_FREQ_HOMREF=0.990325;MALE_FREQ_HET=0.00967519;MALE_FREQ_HOMALT=0;FEMALE_AN=2906;FEMALE_AC=11;FEMALE_AF=0.003785;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=1442;FEMALE_N_HET=11;FEMALE_N_HOMALT=0;FEMALE_FREQ_HOMREF=0.992429;FEMALE_FREQ_HET=0.00757054;FEMALE_FREQ_HOMALT=0 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:99:0 0/1:SR:0:99:0:0:1 0/0:PE,SR:99:99:0:2:0 0/0:PE,SR:99:99:0:2:0 +chr1 21427498 CPX_chr1_54 N 733 PASS ALGORITHMS=manta;CHR2=chr1;CPX_INTERVALS=DUP_chr1:21427498-21427959,INV_chr1:21427498-21480073,DEL_chr1:21480073-21480419;CPX_TYPE=dupINVdel;END=21480419;EVIDENCE=PE;PREDICTED_LOF=NBPF3;PREDICTED_NONCODING_BREAKPOINT=DNase,Tommerup_TADanno;PREDICTED_NONCODING_SPAN=DNase;SVLEN=52921;SVTYPE=CPX;AN=8;AC=4;AF=0.499656;N_BI_GENOS=2911;N_HOMREF=51;N_HET=2811;N_HOMALT=49;FREQ_HOMREF=0.0175198;FREQ_HET=0.965648;FREQ_HOMALT=0.0168327;MALE_AN=2894;MALE_AC=1453;MALE_AF=0.502073;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=19;MALE_N_HET=1403;MALE_N_HOMALT=25;MALE_FREQ_HOMREF=0.0131306;MALE_FREQ_HET=0.969592;MALE_FREQ_HOMALT=0.0172771;FEMALE_AN=2906;FEMALE_AC=1445;FEMALE_AF=0.497247;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=32;FEMALE_N_HET=1397;FEMALE_N_HOMALT=24;FEMALE_FREQ_HOMREF=0.0220234;FEMALE_FREQ_HET=0.961459;FEMALE_FREQ_HOMALT=0.0165175 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 0/1:PE:93:93:1:99:0 0/1:PE:79:79:1:99:0 0/1:PE:33:33:1:6:0 0/1:PE,SR:39:39:1:99:0 0/1:PE,SR:39:39:1:99:0 +chr1 48963084 INS_chr1_688 N 526 HIGH_SR_BACKGROUND ALGORITHMS=melt;CHR2=chr1;END=48963135;EVIDENCE=SR;PREDICTED_INTRONIC=AGBL4;PREDICTED_NONCODING_BREAKPOINT=Tommerup_TADanno;SVLEN=5520;SVTYPE=INS;AN=8;AC=1;AF=0.06338;N_BI_GENOS=2911;N_HOMREF=2544;N_HET=365;N_HOMALT=2;FREQ_HOMREF=0.873926;FREQ_HET=0.125386;FREQ_HOMALT=0.000687049;MALE_AN=2894;MALE_AC=177;MALE_AF=0.061161;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=1271;MALE_N_HET=175;MALE_N_HOMALT=1;MALE_FREQ_HOMREF=0.878369;MALE_FREQ_HET=0.12094;MALE_FREQ_HOMALT=0.000691085;FEMALE_AN=2906;FEMALE_AC=192;FEMALE_AF=0.06607;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=1262;FEMALE_N_HET=190;FEMALE_N_HOMALT=1;FEMALE_FREQ_HOMREF=0.868548;FEMALE_FREQ_HET=0.130764;FEMALE_FREQ_HOMALT=0.000688231 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:99:0 0/1:SR:0:99:0:0:1 0/1:SR:0:99:0:0:1 +chr1 180540234 CPX_chr1_251 N 999 UNRESOLVED ALGORITHMS=manta;CHR2=chr1;CPX_INTERVALS=DEL_chr1:180540234-181074767,INV_chr1:181074767-181074938;CPX_TYPE=delINV;END=181074952;EVIDENCE=PE,SR;PREDICTED_LOF=KIAA1614,MR1,STX6,XPR1;PREDICTED_NONCODING_BREAKPOINT=Tommerup_TADanno;PREDICTED_NONCODING_SPAN=DNase,Enhancer;SVLEN=534718;SVTYPE=CPX;UNRESOLVED_TYPE=POSTHOC_RD_GT_REJECTION;AN=8;AC=3;AF=0.251804;N_BI_GENOS=2911;N_HOMREF=1559;N_HET=1238;N_HOMALT=114;FREQ_HOMREF=0.535555;FREQ_HET=0.425283;FREQ_HOMALT=0.0391618;MALE_AN=2894;MALE_AC=724;MALE_AF=0.250173;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=784;MALE_N_HET=602;MALE_N_HOMALT=61;MALE_FREQ_HOMREF=0.541811;MALE_FREQ_HET=0.416033;MALE_FREQ_HOMALT=0.0421562;FEMALE_AN=2906;FEMALE_AC=736;FEMALE_AF=0.253269;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=770;FEMALE_N_HET=630;FEMALE_N_HOMALT=53;FEMALE_FREQ_HOMREF=0.529938;FEMALE_FREQ_HET=0.433586;FEMALE_FREQ_HOMALT=0.0364763 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 0/0:PE,SR:99:99:0:99:0 0/1:PE,SR:41:26:1:41:1 1/1:PE,SR:89:33:1:89:2 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:99:0 +chrX 3 CPX_chrX_251 N 999 UNRESOLVED ALGORITHMS=manta;CPX_INTERVALS=DEL_chr1:180540234-181074767,INV_chr1:181074767-181074938;CPX_TYPE=delINV;END=2781000;EVIDENCE=PE,SR;PREDICTED_LOF=KIAA1614,MR1,STX6,XPR1;PREDICTED_NONCODING_BREAKPOINT=Tommerup_TADanno;PREDICTED_NONCODING_SPAN=DNase,Enhancer;SVLEN=534718;SVTYPE=CPX;UNRESOLVED_TYPE=POSTHOC_RD_GT_REJECTION;AN=8;AC=3;AF=0.251804;N_BI_GENOS=2911;N_HOMREF=1559;N_HET=1238;N_HOMALT=114;FREQ_HOMREF=0.535555;FREQ_HET=0.425283;FREQ_HOMALT=0.0391618;MALE_AN=2894;MALE_AC=724;MALE_AF=0.250173;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=784;MALE_N_HET=602;MALE_N_HOMALT=61;MALE_FREQ_HOMREF=0.541811;MALE_FREQ_HET=0.416033;MALE_FREQ_HOMALT=0.0421562;FEMALE_AN=2906;FEMALE_AC=736;FEMALE_AF=0.253269;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=770;FEMALE_N_HET=630;FEMALE_N_HOMALT=53;FEMALE_FREQ_HOMREF=0.529938;FEMALE_FREQ_HET=0.433586;FEMALE_FREQ_HOMALT=0.0364763 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 0/0:PE,SR:99:99:0:99:0 0/1:PE,SR:41:26:1:41:1 1/1:PE,SR:89:33:1:89:2 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:99:0 +chrX 2781700 CPX_chrX_252 N 999 UNRESOLVED ALGORITHMS=manta;CPX_INTERVALS=DEL_chr1:180540234-181074767,INV_chr1:181074767-181074938;CPX_TYPE=delINV;END=2781900;EVIDENCE=PE,SR;PREDICTED_LOF=KIAA1614,MR1,STX6,XPR1;PREDICTED_NONCODING_BREAKPOINT=Tommerup_TADanno;PREDICTED_NONCODING_SPAN=DNase,Enhancer;SVLEN=534718;SVTYPE=CPX;UNRESOLVED_TYPE=POSTHOC_RD_GT_REJECTION;AN=8;AC=3;AF=0.251804;N_BI_GENOS=2911;N_HOMREF=1559;N_HET=1238;N_HOMALT=114;FREQ_HOMREF=0.535555;FREQ_HET=0.425283;FREQ_HOMALT=0.0391618;MALE_AN=2894;MALE_AC=724;MALE_AF=0.250173;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=784;MALE_N_HET=602;MALE_N_HOMALT=61;MALE_FREQ_HOMREF=0.541811;MALE_FREQ_HET=0.416033;MALE_FREQ_HOMALT=0.0421562;FEMALE_AN=2906;FEMALE_AC=736;FEMALE_AF=0.253269;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=770;FEMALE_N_HET=630;FEMALE_N_HOMALT=53;FEMALE_FREQ_HOMREF=0.529938;FEMALE_FREQ_HET=0.433586;FEMALE_FREQ_HOMALT=0.0364763 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 0/0:PE,SR:99:99:0:99:0 0/1:PE,SR:41:26:1:41:1 1/1:PE,SR:89:33:1:89:2 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:99:0 \ No newline at end of file diff --git a/loading_pipeline/var/test/callsets/sv_2.vcf b/loading_pipeline/var/test/callsets/sv_2.vcf new file mode 100644 index 0000000000..12f65690ed --- /dev/null +++ b/loading_pipeline/var/test/callsets/sv_2.vcf @@ -0,0 +1,82 @@ +##fileformat=VCFv4.2 +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= 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ALGORITHMS=manta;CHR2=chr5;END=180928;END2=20404;EVIDENCE=PE,SR;PREDICTED_INTERGENIC;PREDICTED_NEAREST_TSS=OR4F5,PLEKHG4B;PREDICTED_NONCODING_BREAKPOINT=DNase;STRANDS=+-;SVLEN=-1;SVTYPE=BND;UNRESOLVED_TYPE=SINGLE_ENDER_+-;AN=8;AC=1;AF=0.04775;N_BI_GENOS=2911;N_HOMREF=2633;N_HET=278;N_HOMALT=0;FREQ_HOMREF=0.9045;FREQ_HET=0.0954998;FREQ_HOMALT=0;MALE_AN=2894;MALE_AC=137;MALE_AF=0.047339;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=1310;MALE_N_HET=137;MALE_N_HOMALT=0;MALE_FREQ_HOMREF=0.905321;MALE_FREQ_HET=0.0946786;MALE_FREQ_HOMALT=0;FEMALE_AN=2906;FEMALE_AC=139;FEMALE_AF=0.047832;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=1314;FEMALE_N_HET=139;FEMALE_N_HOMALT=0;FEMALE_FREQ_HOMREF=0.904336;FEMALE_FREQ_HET=0.0956641;FEMALE_FREQ_HOMALT=0;SEQR_INTERNAL_TRUTH_VID=BND_chr1_6 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 0/0:PE,SR:99:99:0:2:0 0/1:SR:31:99:0:31:1 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:2:0 0/0:PE,SR:99:99:0:2:0 +chr1 257667 new_variant2 N 999 PASS 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gene_symbol_source='HGNC', + hgnc_id='28706', + hgvs_offset=hl.null('int32'), + hgvsc=hl.null('str'), + hgvsp=hl.null('str'), + impact='MODIFIER', + intron=hl.null('str'), + lof=hl.null('str'), + lof_filter=hl.null('str'), + lof_flags=hl.null('str'), + lof_info=hl.null('str'), + minimised=1, + polyphen_prediction=hl.null('str'), + polyphen_score=hl.null('float64'), + protein_end=hl.null('int32'), + protein_id=hl.null('str'), + protein_start=hl.null('int32'), + sift_prediction=hl.null('str'), + sift_score=hl.null('float64'), + strand=1, + swissprot=hl.null('str'), + transcript_id='ENST00000464948', + trembl=hl.null('str'), + uniparc=hl.null('str'), + variant_allele='A', + ), + hl.struct( + allele_num=1, + amino_acids=hl.null('str'), + biotype='retained_intron', + canonical=hl.null('int32'), + ccds=hl.null('str'), + cdna_end=hl.null('int32'), + cdna_start=hl.null('int32'), + cds_end=hl.null('int32'), + cds_start=hl.null('int32'), + codons=hl.null('str'), + consequence_terms=hl.array(['downstream_gene_variant']), + distance=3736, + domains=hl.null('array'), + exon=hl.null('str'), + gene_id='ENSG00000187634', + gene_pheno=hl.null('int32'), + gene_symbol='SAMD11', + gene_symbol_source='HGNC', + hgnc_id='28706', + hgvs_offset=hl.null('int32'), + hgvsc=hl.null('str'), + hgvsp=hl.null('str'), + impact='MODIFIER', + intron=hl.null('str'), + lof=hl.null('str'), + lof_filter=hl.null('str'), + lof_flags=hl.null('str'), + lof_info=hl.null('str'), + minimised=1, + polyphen_prediction=hl.null('str'), + polyphen_score=hl.null('float64'), + protein_end=hl.null('int32'), + protein_id=hl.null('str'), + protein_start=hl.null('int32'), + sift_prediction=hl.null('str'), + sift_score=hl.null('float64'), + strand=1, + swissprot=hl.null('str'), + transcript_id='ENST00000466827', + trembl=hl.null('str'), + uniparc=hl.null('str'), + variant_allele='A', + ), + hl.struct( + allele_num=1, + amino_acids=hl.null('str'), + biotype='retained_intron', + canonical=hl.null('int32'), + ccds=hl.null('str'), + cdna_end=hl.null('int32'), + cdna_start=hl.null('int32'), + cds_end=hl.null('int32'), + cds_start=hl.null('int32'), + codons=hl.null('str'), + consequence_terms=hl.array(['downstream_gene_variant']), + distance=3544, + domains=hl.null('array'), + exon=hl.null('str'), + gene_id='ENSG00000187634', + gene_pheno=hl.null('int32'), + gene_symbol='SAMD11', + gene_symbol_source='HGNC', + hgnc_id='28706', + hgvs_offset=hl.null('int32'), + hgvsc=hl.null('str'), + hgvsp=hl.null('str'), + impact='MODIFIER', + intron=hl.null('str'), + lof=hl.null('str'), + lof_filter=hl.null('str'), + lof_flags=hl.null('str'), + lof_info=hl.null('str'), + minimised=1, + polyphen_prediction=hl.null('str'), + polyphen_score=hl.null('float64'), + protein_end=hl.null('int32'), + protein_id=hl.null('str'), + protein_start=hl.null('int32'), + sift_prediction=hl.null('str'), + sift_score=hl.null('float64'), + strand=1, + swissprot=hl.null('str'), + transcript_id='ENST00000474461', + trembl=hl.null('str'), + uniparc=hl.null('str'), + variant_allele='A', + ), + hl.struct( + allele_num=1, + amino_acids=hl.null('str'), + biotype='retained_intron', + canonical=hl.null('int32'), + ccds=hl.null('str'), + cdna_end=3114, + cdna_start=3114, + cds_end=hl.null('int32'), + cds_start=hl.null('int32'), + codons=hl.null('str'), + consequence_terms=hl.array( + [ + 'non_coding_transcript_exon_variant', + 'non_coding_transcript_variant', + ], + ), + distance=hl.null('int32'), + domains=hl.null('array'), + exon='13/17', + gene_id='ENSG00000188976', + gene_pheno=hl.null('int32'), + gene_symbol='NOC2L', + gene_symbol_source='HGNC', + hgnc_id='24517', + hgvs_offset=hl.null('int32'), + hgvsc='ENST00000477976.1:n.3114C>T', + hgvsp=hl.null('str'), + impact='MODIFIER', + intron=hl.null('str'), + lof=hl.null('str'), + lof_filter=hl.null('str'), + lof_flags=hl.null('str'), + lof_info=hl.null('str'), + minimised=1, + polyphen_prediction=hl.null('str'), + polyphen_score=hl.null('float64'), + protein_end=hl.null('int32'), + protein_id=hl.null('str'), + protein_start=hl.null('int32'), + sift_prediction=hl.null('str'), + sift_score=hl.null('float64'), + strand=-1, + swissprot=hl.null('str'), + transcript_id='ENST00000477976', + trembl=hl.null('str'), + uniparc=hl.null('str'), + variant_allele='A', + ), + hl.struct( + allele_num=1, + amino_acids=hl.null('str'), + biotype='processed_transcript', + canonical=hl.null('int32'), + ccds=hl.null('str'), + cdna_end=hl.null('int32'), + cdna_start=hl.null('int32'), + cds_end=hl.null('int32'), + cds_start=hl.null('int32'), + codons=hl.null('str'), + consequence_terms=hl.array(['downstream_gene_variant']), + distance=4365, + domains=hl.null('array'), + exon=hl.null('str'), + gene_id='ENSG00000187634', + gene_pheno=hl.null('int32'), + gene_symbol='SAMD11', + gene_symbol_source='HGNC', + hgnc_id='28706', + hgvs_offset=hl.null('int32'), + hgvsc=hl.null('str'), + hgvsp=hl.null('str'), + impact='MODIFIER', + intron=hl.null('str'), + lof=hl.null('str'), + lof_filter=hl.null('str'), + lof_flags=hl.null('str'), + lof_info=hl.null('str'), + minimised=1, + polyphen_prediction=hl.null('str'), + polyphen_score=hl.null('float64'), + protein_end=hl.null('int32'), + protein_id=hl.null('str'), + protein_start=hl.null('int32'), + sift_prediction=hl.null('str'), + sift_score=hl.null('float64'), + strand=1, + swissprot=hl.null('str'), + transcript_id='ENST00000478729', + trembl=hl.null('str'), + uniparc=hl.null('str'), + variant_allele='A', + ), + hl.struct( + allele_num=1, + amino_acids=hl.null('str'), + biotype='retained_intron', + canonical=hl.null('int32'), + ccds=hl.null('str'), + cdna_end=523, + cdna_start=523, + cds_end=hl.null('int32'), + cds_start=hl.null('int32'), + codons=hl.null('str'), + consequence_terms=hl.array( + [ + 'non_coding_transcript_exon_variant', + 'non_coding_transcript_variant', + ], + ), + distance=hl.null('int32'), + domains=hl.null('array'), + exon='1/5', + gene_id='ENSG00000188976', + gene_pheno=hl.null('int32'), + gene_symbol='NOC2L', + gene_symbol_source='HGNC', + hgnc_id='24517', + hgvs_offset=hl.null('int32'), + hgvsc='ENST00000483767.1:n.523C>T', + hgvsp=hl.null('str'), + impact='MODIFIER', + intron=hl.null('str'), + lof=hl.null('str'), + lof_filter=hl.null('str'), + lof_flags=hl.null('str'), + lof_info=hl.null('str'), + minimised=1, + polyphen_prediction=hl.null('str'), + polyphen_score=hl.null('float64'), + protein_end=hl.null('int32'), + protein_id=hl.null('str'), + protein_start=hl.null('int32'), + sift_prediction=hl.null('str'), + sift_score=hl.null('float64'), + strand=-1, + swissprot=hl.null('str'), + transcript_id='ENST00000483767', + trembl=hl.null('str'), + uniparc=hl.null('str'), + variant_allele='A', + ), + hl.struct( + allele_num=1, + amino_acids=hl.null('str'), + biotype='processed_transcript', + canonical=hl.null('int32'), + ccds=hl.null('str'), + cdna_end=hl.null('int32'), + cdna_start=hl.null('int32'), + cds_end=hl.null('int32'), + cds_start=hl.null('int32'), + codons=hl.null('str'), + consequence_terms=hl.array(['upstream_gene_variant']), + distance=976, + domains=hl.null('array'), + exon=hl.null('str'), + gene_id='ENSG00000188976', + gene_pheno=hl.null('int32'), + gene_symbol='NOC2L', + gene_symbol_source='HGNC', + hgnc_id='24517', + hgvs_offset=hl.null('int32'), + hgvsc=hl.null('str'), + hgvsp=hl.null('str'), + impact='MODIFIER', + intron=hl.null('str'), + lof=hl.null('str'), + lof_filter=hl.null('str'), + lof_flags=hl.null('str'), + lof_info=hl.null('str'), + minimised=1, + polyphen_prediction=hl.null('str'), + polyphen_score=hl.null('float64'), + protein_end=hl.null('int32'), + protein_id=hl.null('str'), + protein_start=hl.null('int32'), + sift_prediction=hl.null('str'), + sift_score=hl.null('float64'), + strand=-1, + swissprot=hl.null('str'), + transcript_id='ENST00000496938', + trembl=hl.null('str'), + uniparc=hl.null('str'), + variant_allele='A', + ), + ], + ), + variant_class='SNV', +) + +MOCK_38_VEP_DATA = hl.struct( + most_severe_consequence='missense_variant', + check_ref=hl.missing(hl.tstr), + motif_feature_consequences=hl.missing( + hl.tarray( + hl.tstruct(consequence_terms=hl.tarray(hl.tstr), motif_feature_id=hl.tstr), + ), + ), + regulatory_feature_consequences=hl.array( + [ + hl.struct( + biotype='enhancer', + consequence_terms=['regulatory_region_variant'], + regulatory_feature_id='regulatory_1', + ), + hl.struct( + biotype='enhancer', + consequence_terms=['regulatory_region_ablation'], + regulatory_feature_id='regulatory_2', + ), + ], + ), + transcript_consequences=hl.array( + [ + hl.struct( + amino_acids='S/L', + am_pathogenicity=hl.float32(0.1), + biotype='protein_coding', + canonical=1, + check_ref=hl.missing(hl.tstr), + codons='tCg/tTg', + consequence_terms=hl.array(['missense_variant']), + exon='15/19', + gene_id='ENSG00000188976', + hgvsc='ENST00000327044.6:c.1667C>T', + hgvsp='ENSP00000317992.6:p.Ser556Leu', + intron=hl.null('str'), + lof='LC', + lof_filter='END_TRUNC,INCOMPLETE_CDS', + lof_flags=hl.null('str'), + lof_info='INTRON_END:881781,EXON_END:881925,EXON_START:881782,DE_NOVO_DONOR_MES:-7.36719797135343,DE_NOVO_DONOR_PROB:0.261170618766552,DE_NOVO_DONOR_POS:-138,INTRON_START:881667,DE_NOVO_DONOR_MES_POS:-138,MUTANT_DONOR_MES:4.93863747168278', + mane_select='NM_015658.4', + mane_plus_clinical=hl.null('str'), + spliceregion=hl.missing(hl.tarray(hl.tstr)), + transcript_id='ENST00000327044', + # UTRAnnotator + existing_inframe_oorfs=hl.missing(hl.tint32), + existing_outofframe_oorfs=hl.missing(hl.tint32), + existing_uorfs=hl.missing(hl.tint32), + fiveutr_consequence=hl.missing(hl.tstr), + fiveutr_annotation=hl.missing( + hl.tdict( + hl.tstr, + hl.tstruct( + type=hl.tstr, + KozakContext=hl.tstr, + KozakStrength=hl.tstr, + DistanceToCDS=hl.tstr, + CapDistanceToStart=hl.tstr, + DistanceToStop=hl.tstr, + Evidence=hl.tstr, + AltStop=hl.tstr, + AltStopDistanceToCDS=hl.tstr, + FrameWithCDS=hl.tstr, + StartDistanceToCDS=hl.tstr, + newSTOPDistanceToCDS=hl.tstr, + alt_type=hl.tstr, + alt_type_length=hl.tstr, + ref_StartDistanceToCDS=hl.tstr, + ref_type=hl.tstr, + ref_type_length=hl.tstr, + ), + ), + ), + ), + hl.struct( + amino_acids=hl.null('str'), + am_pathogenicity=hl.float32(0.2), + biotype='protein_coding', + canonical=hl.null('int32'), + check_ref=hl.missing(hl.tstr), + codons=hl.null('str'), + consequence_terms=hl.array(['downstream_gene_variant']), + exon=hl.null('str'), + gene_id='ENSG00000187634', + hgvsc=hl.null('str'), + hgvsp=hl.null('str'), + intron=hl.null('str'), + lof=hl.null('str'), + lof_filter=hl.null('str'), + lof_flags=hl.null('str'), + lof_info=hl.null('str'), + mane_select=hl.null('str'), + mane_plus_clinical=hl.null('str'), + spliceregion=hl.missing(hl.tarray(hl.tstr)), + transcript_id='ENST00000341065', + # UTRAnnotator + existing_inframe_oorfs=hl.missing(hl.tint32), + existing_outofframe_oorfs=hl.missing(hl.tint32), + existing_uorfs=hl.missing(hl.tint32), + fiveutr_consequence=hl.missing(hl.tstr), + fiveutr_annotation=hl.missing( + hl.tdict( + hl.tstr, + hl.tstruct( + type=hl.tstr, + KozakContext=hl.tstr, + KozakStrength=hl.tstr, + DistanceToCDS=hl.tstr, + CapDistanceToStart=hl.tstr, + DistanceToStop=hl.tstr, + Evidence=hl.tstr, + AltStop=hl.tstr, + AltStopDistanceToCDS=hl.tstr, + FrameWithCDS=hl.tstr, + StartDistanceToCDS=hl.tstr, + newSTOPDistanceToCDS=hl.tstr, + alt_type=hl.tstr, + alt_type_length=hl.tstr, + ref_StartDistanceToCDS=hl.tstr, + ref_type=hl.tstr, + ref_type_length=hl.tstr, + ), + ), + ), + ), + hl.struct( + amino_acids=hl.null('str'), + am_pathogenicity=hl.missing(hl.tfloat32), + biotype='protein_coding', + canonical=1, + check_ref=hl.missing(hl.tstr), + codons=hl.null('str'), + consequence_terms=hl.array(['downstream_gene_variant']), + exon=hl.null('str'), + gene_id='ENSG00000187634', + hgvsc=hl.null('str'), + hgvsp=hl.null('str'), + intron=hl.null('str'), + lof=hl.null('str'), + lof_filter=hl.null('str'), + lof_flags=hl.null('str'), + lof_info=hl.null('str'), + mane_select=hl.null('str'), + mane_plus_clinical=hl.null('str'), + spliceregion=hl.missing(hl.tarray(hl.tstr)), + transcript_id='ENST00000342066', + # UTRAnnotator + existing_inframe_oorfs=hl.missing(hl.tint32), + existing_outofframe_oorfs=hl.missing(hl.tint32), + existing_uorfs=hl.missing(hl.tint32), + fiveutr_consequence=hl.missing(hl.tstr), + fiveutr_annotation=hl.missing( + hl.tdict( + hl.tstr, + hl.tstruct( + type=hl.tstr, + KozakContext=hl.tstr, + KozakStrength=hl.tstr, + DistanceToCDS=hl.tstr, + CapDistanceToStart=hl.tstr, + DistanceToStop=hl.tstr, + Evidence=hl.tstr, + AltStop=hl.tstr, + AltStopDistanceToCDS=hl.tstr, + FrameWithCDS=hl.tstr, + StartDistanceToCDS=hl.tstr, + newSTOPDistanceToCDS=hl.tstr, + alt_type=hl.tstr, + alt_type_length=hl.tstr, + ref_StartDistanceToCDS=hl.tstr, + ref_type=hl.tstr, + ref_type_length=hl.tstr, + ), + ), + ), + ), + hl.struct( + amino_acids=hl.null('str'), + am_pathogenicity=hl.missing(hl.tfloat32), + biotype='protein_coding', + canonical=hl.null('int32'), + check_ref=hl.missing(hl.tstr), + codons=hl.null('str'), + consequence_terms=hl.array(['downstream_gene_variant']), + exon=hl.null('str'), + gene_id='ENSG00000187634', + hgvsc=hl.null('str'), + hgvsp=hl.null('str'), + intron=hl.null('str'), + lof=hl.null('str'), + lof_filter=hl.null('str'), + lof_flags=hl.null('str'), + lof_info=hl.null('str'), + mane_select=hl.null('str'), + mane_plus_clinical=hl.null('str'), + spliceregion=hl.missing(hl.tarray(hl.tstr)), + transcript_id='ENST00000455979', + # UTRAnnotator + existing_inframe_oorfs=hl.missing(hl.tint32), + existing_outofframe_oorfs=hl.missing(hl.tint32), + existing_uorfs=hl.missing(hl.tint32), + fiveutr_consequence=hl.missing(hl.tstr), + fiveutr_annotation=hl.missing( + hl.tdict( + hl.tstr, + hl.tstruct( + type=hl.tstr, + KozakContext=hl.tstr, + KozakStrength=hl.tstr, + DistanceToCDS=hl.tstr, + CapDistanceToStart=hl.tstr, + DistanceToStop=hl.tstr, + Evidence=hl.tstr, + AltStop=hl.tstr, + AltStopDistanceToCDS=hl.tstr, + FrameWithCDS=hl.tstr, + StartDistanceToCDS=hl.tstr, + newSTOPDistanceToCDS=hl.tstr, + alt_type=hl.tstr, + alt_type_length=hl.tstr, + ref_StartDistanceToCDS=hl.tstr, + ref_type=hl.tstr, + ref_type_length=hl.tstr, + ), + ), + ), + ), + hl.struct( + amino_acids=hl.null('str'), + am_pathogenicity=hl.missing(hl.tfloat32), + biotype='retained_intron', + canonical=hl.null('int32'), + check_ref=hl.missing(hl.tstr), + codons=hl.null('str'), + consequence_terms=hl.array(['downstream_gene_variant']), + exon=hl.null('str'), + gene_id='ENSG00000187634', + hgvsc=hl.null('str'), + hgvsp=hl.null('str'), + intron=hl.null('str'), + lof=hl.null('str'), + lof_filter=hl.null('str'), + lof_flags=hl.null('str'), + lof_info=hl.null('str'), + mane_select=hl.null('str'), + mane_plus_clinical=hl.null('str'), + spliceregion=hl.missing(hl.tarray(hl.tstr)), + transcript_id='ENST00000464948', + # UTRAnnotator + existing_inframe_oorfs=hl.missing(hl.tint32), + existing_outofframe_oorfs=hl.missing(hl.tint32), + existing_uorfs=hl.missing(hl.tint32), + fiveutr_consequence=hl.missing(hl.tstr), + fiveutr_annotation=hl.missing( + hl.tdict( + hl.tstr, + hl.tstruct( + type=hl.tstr, + KozakContext=hl.tstr, + KozakStrength=hl.tstr, + DistanceToCDS=hl.tstr, + CapDistanceToStart=hl.tstr, + DistanceToStop=hl.tstr, + Evidence=hl.tstr, + AltStop=hl.tstr, + AltStopDistanceToCDS=hl.tstr, + FrameWithCDS=hl.tstr, + StartDistanceToCDS=hl.tstr, + newSTOPDistanceToCDS=hl.tstr, + alt_type=hl.tstr, + alt_type_length=hl.tstr, + ref_StartDistanceToCDS=hl.tstr, + ref_type=hl.tstr, + ref_type_length=hl.tstr, + ), + ), + ), + ), + hl.struct( + amino_acids=hl.null('str'), + am_pathogenicity=hl.missing(hl.tfloat32), + biotype='retained_intron', + canonical=hl.null('int32'), + check_ref=hl.missing(hl.tstr), + codons=hl.null('str'), + consequence_terms=hl.array(['downstream_gene_variant']), + exon=hl.null('str'), + gene_id='ENSG00000187634', + hgvsc=hl.null('str'), + hgvsp=hl.null('str'), + intron=hl.null('str'), + lof=hl.null('str'), + lof_filter=hl.null('str'), + lof_flags=hl.null('str'), + lof_info=hl.null('str'), + mane_select=hl.null('str'), + mane_plus_clinical=hl.null('str'), + spliceregion=hl.missing(hl.tarray(hl.tstr)), + transcript_id='ENST00000466827', + # UTRAnnotator + existing_inframe_oorfs=hl.missing(hl.tint32), + existing_outofframe_oorfs=hl.missing(hl.tint32), + existing_uorfs=hl.missing(hl.tint32), + fiveutr_consequence=hl.missing(hl.tstr), + fiveutr_annotation=hl.missing( + hl.tdict( + hl.tstr, + hl.tstruct( + type=hl.tstr, + KozakContext=hl.tstr, + KozakStrength=hl.tstr, + DistanceToCDS=hl.tstr, + CapDistanceToStart=hl.tstr, + DistanceToStop=hl.tstr, + Evidence=hl.tstr, + AltStop=hl.tstr, + AltStopDistanceToCDS=hl.tstr, + FrameWithCDS=hl.tstr, + StartDistanceToCDS=hl.tstr, + newSTOPDistanceToCDS=hl.tstr, + alt_type=hl.tstr, + alt_type_length=hl.tstr, + ref_StartDistanceToCDS=hl.tstr, + ref_type=hl.tstr, + ref_type_length=hl.tstr, + ), + ), + ), + ), + hl.struct( + amino_acids=hl.null('str'), + am_pathogenicity=hl.missing(hl.tfloat32), + biotype='retained_intron', + canonical=hl.null('int32'), + check_ref=hl.missing(hl.tstr), + codons=hl.null('str'), + consequence_terms=hl.array(['downstream_gene_variant']), + exon=hl.null('str'), + gene_id='ENSG00000187634', + hgvsc=hl.null('str'), + hgvsp=hl.null('str'), + intron=hl.null('str'), + lof=hl.null('str'), + lof_filter=hl.null('str'), + lof_flags=hl.null('str'), + lof_info=hl.null('str'), + mane_select=hl.null('str'), + mane_plus_clinical=hl.null('str'), + spliceregion=hl.missing(hl.tarray(hl.tstr)), + transcript_id='ENST00000474461', + # UTRAnnotator + existing_inframe_oorfs=hl.missing(hl.tint32), + existing_outofframe_oorfs=hl.missing(hl.tint32), + existing_uorfs=hl.missing(hl.tint32), + fiveutr_consequence=hl.missing(hl.tstr), + fiveutr_annotation=hl.missing( + hl.tdict( + hl.tstr, + hl.tstruct( + type=hl.tstr, + KozakContext=hl.tstr, + KozakStrength=hl.tstr, + DistanceToCDS=hl.tstr, + CapDistanceToStart=hl.tstr, + DistanceToStop=hl.tstr, + Evidence=hl.tstr, + AltStop=hl.tstr, + AltStopDistanceToCDS=hl.tstr, + FrameWithCDS=hl.tstr, + StartDistanceToCDS=hl.tstr, + newSTOPDistanceToCDS=hl.tstr, + alt_type=hl.tstr, + alt_type_length=hl.tstr, + ref_StartDistanceToCDS=hl.tstr, + ref_type=hl.tstr, + ref_type_length=hl.tstr, + ), + ), + ), + ), + hl.struct( + amino_acids=hl.null('str'), + am_pathogenicity=hl.float32(0.97), + biotype='retained_intron', + canonical=hl.null('int32'), + check_ref=hl.missing(hl.tstr), + codons=hl.null('str'), + consequence_terms=hl.array( + [ + 'non_coding_transcript_exon_variant', + 'non_coding_transcript_variant', + ], + ), + exon='13/17', + gene_id='ENSG00000188976', + hgvsc='ENST00000477976.1:n.3114C>T', + hgvsp=hl.null('str'), + intron=hl.null('str'), + lof=hl.null('str'), + lof_filter=hl.null('str'), + lof_flags=hl.null('str'), + lof_info=hl.null('str'), + mane_select=hl.null('str'), + mane_plus_clinical=hl.null('str'), + spliceregion=hl.missing(hl.tarray(hl.tstr)), + transcript_id='ENST00000477976', + # UTRAnnotator + existing_inframe_oorfs=hl.missing(hl.tint32), + existing_outofframe_oorfs=hl.missing(hl.tint32), + existing_uorfs=hl.missing(hl.tint32), + fiveutr_consequence=hl.missing(hl.tstr), + fiveutr_annotation=hl.missing( + hl.tdict( + hl.tstr, + hl.tstruct( + type=hl.tstr, + KozakContext=hl.tstr, + KozakStrength=hl.tstr, + DistanceToCDS=hl.tstr, + CapDistanceToStart=hl.tstr, + DistanceToStop=hl.tstr, + Evidence=hl.tstr, + AltStop=hl.tstr, + AltStopDistanceToCDS=hl.tstr, + FrameWithCDS=hl.tstr, + StartDistanceToCDS=hl.tstr, + newSTOPDistanceToCDS=hl.tstr, + alt_type=hl.tstr, + alt_type_length=hl.tstr, + ref_StartDistanceToCDS=hl.tstr, + ref_type=hl.tstr, + ref_type_length=hl.tstr, + ), + ), + ), + ), + hl.struct( + amino_acids=hl.null('str'), + am_pathogenicity=hl.missing(hl.tfloat32), + biotype='processed_transcript', + canonical=hl.null('int32'), + check_ref=hl.missing(hl.tstr), + codons=hl.null('str'), + consequence_terms=hl.array(['downstream_gene_variant']), + exon=hl.null('str'), + gene_id='ENSG00000187634', + hgvsc=hl.null('str'), + hgvsp=hl.null('str'), + intron=hl.null('str'), + lof=hl.null('str'), + lof_filter=hl.null('str'), + lof_flags=hl.null('str'), + lof_info=hl.null('str'), + mane_select=hl.null('str'), + mane_plus_clinical=hl.null('str'), + spliceregion=hl.missing(hl.tarray(hl.tstr)), + transcript_id='ENST00000478729', + # UTRAnnotator + existing_inframe_oorfs=hl.missing(hl.tint32), + existing_outofframe_oorfs=hl.missing(hl.tint32), + existing_uorfs=hl.missing(hl.tint32), + fiveutr_consequence=hl.missing(hl.tstr), + fiveutr_annotation=hl.missing( + hl.tdict( + hl.tstr, + hl.tstruct( + type=hl.tstr, + KozakContext=hl.tstr, + KozakStrength=hl.tstr, + DistanceToCDS=hl.tstr, + CapDistanceToStart=hl.tstr, + DistanceToStop=hl.tstr, + Evidence=hl.tstr, + AltStop=hl.tstr, + AltStopDistanceToCDS=hl.tstr, + FrameWithCDS=hl.tstr, + StartDistanceToCDS=hl.tstr, + newSTOPDistanceToCDS=hl.tstr, + alt_type=hl.tstr, + alt_type_length=hl.tstr, + ref_StartDistanceToCDS=hl.tstr, + ref_type=hl.tstr, + ref_type_length=hl.tstr, + ), + ), + ), + ), + hl.struct( + amino_acids=hl.null('str'), + am_pathogenicity=hl.missing(hl.tfloat32), + biotype='retained_intron', + canonical=hl.null('int32'), + check_ref=hl.missing(hl.tstr), + codons=hl.null('str'), + consequence_terms=hl.array( + [ + 'non_coding_transcript_exon_variant', + 'splice_donor_region_variant', + 'non_coding_transcript_variant', + ], + ), + exon='1/5', + gene_id='ENSG00000188976', + hgvsc='ENST00000483767.1:n.523C>T', + hgvsp=hl.null('str'), + intron=hl.null('str'), + lof=hl.null('str'), + lof_filter=hl.null('str'), + lof_flags=hl.null('str'), + lof_info=hl.null('str'), + mane_select=hl.null('str'), + mane_plus_clinical=hl.null('str'), + spliceregion=hl.array(['extended_intronic_splice_region_variant']), + transcript_id='ENST00000483767', + # UTRAnnotator + existing_inframe_oorfs=0, + existing_outofframe_oorfs=1, + existing_uorfs=0, + fiveutr_consequence='5_prime_UTR_premature_start_codon_loss_variant', + fiveutr_annotation=hl.dict( + { + '1': hl.struct( + type='OutOfFrame_oORF', + KozakContext='TTTATGC', + KozakStrength='Weak', + DistanceToCDS='40', + CapDistanceToStart='20', + DistanceToStop='75', + Evidence='False', + AltStop=hl.missing(hl.tstr), + AltStopDistanceToCDS=hl.missing(hl.tstr), + FrameWithCDS=hl.missing(hl.tstr), + StartDistanceToCDS=hl.missing(hl.tstr), + newSTOPDistanceToCDS=hl.missing(hl.tstr), + alt_type=hl.missing(hl.tstr), + alt_type_length=hl.missing(hl.tstr), + ref_StartDistanceToCDS=hl.missing(hl.tstr), + ref_type=hl.missing(hl.tstr), + ref_type_length=hl.missing(hl.tstr), + ), + }, + ), + ), + hl.struct( + amino_acids=hl.null('str'), + am_pathogenicity=hl.missing(hl.tfloat32), + biotype='processed_transcript', + canonical=hl.null('int32'), + check_ref=hl.missing(hl.tstr), + codons=hl.null('str'), + consequence_terms=hl.array(['upstream_gene_variant']), + exon=hl.null('str'), + gene_id='ENSG00000188976', + hgvsc=hl.null('str'), + hgvsp=hl.null('str'), + intron=hl.null('str'), + lof=hl.null('str'), + lof_filter=hl.null('str'), + lof_flags=hl.null('str'), + lof_info=hl.null('str'), + mane_select=hl.null('str'), + mane_plus_clinical=hl.null('str'), + spliceregion=hl.missing(hl.tarray(hl.tstr)), + transcript_id='ENST00000496938', + # UTRAnnotator + existing_inframe_oorfs=hl.missing(hl.tint32), + existing_outofframe_oorfs=hl.missing(hl.tint32), + existing_uorfs=hl.missing(hl.tint32), + fiveutr_consequence=hl.missing(hl.tstr), + fiveutr_annotation=hl.missing( + hl.tdict( + hl.tstr, + hl.tstruct( + type=hl.tstr, + KozakContext=hl.tstr, + KozakStrength=hl.tstr, + DistanceToCDS=hl.tstr, + CapDistanceToStart=hl.tstr, + DistanceToStop=hl.tstr, + Evidence=hl.tstr, + AltStop=hl.tstr, + AltStopDistanceToCDS=hl.tstr, + FrameWithCDS=hl.tstr, + StartDistanceToCDS=hl.tstr, + newSTOPDistanceToCDS=hl.tstr, + alt_type=hl.tstr, + alt_type_length=hl.tstr, + ref_StartDistanceToCDS=hl.tstr, + ref_type=hl.tstr, + ref_type_length=hl.tstr, + ), + ), + ), + ), + ], + ), +) diff --git a/loading_pipeline/var/vep/GRCh37/vep-GRCh37.json b/loading_pipeline/var/vep/GRCh37/vep-GRCh37.json new file mode 100644 index 0000000000..d3461b9658 --- /dev/null +++ b/loading_pipeline/var/vep/GRCh37/vep-GRCh37.json @@ -0,0 +1,21 @@ +{"command": [ + "/vep", + "GRCh37", + "--warning_file", "STDERR", + "--format", "vcf", + "__OUTPUT_FORMAT_FLAG__", + "--everything", + "--allele_number", + "--no_stats", + "--cache", "--offline", + "--minimal", + "--assembly", "GRCh37", + "--fasta", "/opt/vep/.vep/Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz", + "--plugin", "LoF,human_ancestor_fa:/opt/vep/.vep/loftee_data/GRCh37/human_ancestor.fa.gz,filter_position:0.05,min_intron_size:15,conservation_file:/opt/vep/.vep/loftee_data/GRCh37/phylocsf_gerp.sql,gerp_file:/opt/vep/.vep/loftee_data/GRCh37/GERP_scores.final.sorted.txt.gz", + "-o", "STDOUT" +], + "env": { + "PERL5LIB": "" + }, + "vep_json_schema": "Struct{assembly_name:String,allele_string:String,ancestral:String,colocated_variants:Array[Struct{aa_allele:String,aa_maf:Float64,afr_allele:String,afr_maf:Float64,allele_string:String,amr_allele:String,amr_maf:Float64,clin_sig:Array[String],end:Int32,eas_allele:String,eas_maf:Float64,ea_allele:String,ea_maf:Float64,eur_allele:String,eur_maf:Float64,exac_adj_allele:String,exac_adj_maf:Float64,exac_allele:String,exac_afr_allele:String,exac_afr_maf:Float64,exac_amr_allele:String,exac_amr_maf:Float64,exac_eas_allele:String,exac_eas_maf:Float64,exac_fin_allele:String,exac_fin_maf:Float64,exac_maf:Float64,exac_nfe_allele:String,exac_nfe_maf:Float64,exac_oth_allele:String,exac_oth_maf:Float64,exac_sas_allele:String,exac_sas_maf:Float64,id:String,minor_allele:String,minor_allele_freq:Float64,phenotype_or_disease:Int32,pubmed:Array[Int32],sas_allele:String,sas_maf:Float64,somatic:Int32,start:Int32,strand:Int32}],context:String,end:Int32,id:String,input:String,intergenic_consequences:Array[Struct{allele_num:Int32,consequence_terms:Array[String],impact:String,minimised:Int32,variant_allele:String}],most_severe_consequence:String,motif_feature_consequences:Array[Struct{allele_num:Int32,consequence_terms:Array[String],high_inf_pos:String,impact:String,minimised:Int32,motif_feature_id:String,motif_name:String,motif_pos:Int32,motif_score_change:Float64,strand:Int32,variant_allele:String}],regulatory_feature_consequences:Array[Struct{allele_num:Int32,biotype:String,consequence_terms:Array[String],impact:String,minimised:Int32,regulatory_feature_id:String,variant_allele:String}],seq_region_name:String,start:Int32,strand:Int32,transcript_consequences:Array[Struct{allele_num:Int32,amino_acids:String,biotype:String,canonical:Int32,ccds:String,cdna_start:Int32,cdna_end:Int32,cds_end:Int32,cds_start:Int32,codons:String,consequence_terms:Array[String],distance:Int32,domains:Array[Struct{db:String,name:String}],exon:String,gene_id:String,gene_pheno:Int32,gene_symbol:String,gene_symbol_source:String,hgnc_id:String,hgvsc:String,hgvsp:String,hgvs_offset:Int32,impact:String,intron:String,lof:String,lof_flags:String,lof_filter:String,lof_info:String,minimised:Int32,polyphen_prediction:String,polyphen_score:Float64,protein_end:Int32,protein_start:Int32,protein_id:String,sift_prediction:String,sift_score:Float64,strand:Int32,swissprot:String,transcript_id:String,trembl:String,uniparc:String,variant_allele:String}],variant_class:String}" +} diff --git a/loading_pipeline/var/vep/GRCh38/vep-GRCh38.json b/loading_pipeline/var/vep/GRCh38/vep-GRCh38.json new file mode 100644 index 0000000000..c454c29a25 --- /dev/null +++ b/loading_pipeline/var/vep/GRCh38/vep-GRCh38.json @@ -0,0 +1,11 @@ +{ + "command": [ + "bash", + "-c", + "/vep GRCh38 --warning_file STDERR --format vcf -json --hgvs --biotype --canonical --mane --minimal --numbers --regulatory --allele_number --no_stats --cache --offline --assembly GRCh38 --fasta /opt/vep/.vep/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz --check_ref --dont_skip --plugin LoF,loftee_path:/plugins,gerp_bigwig:/opt/vep/.vep/gerp_conservation_scores.homo_sapiens.GRCh38.bw,human_ancestor_fa:/opt/vep/.vep/human_ancestor.fa.gz,conservation_file:/opt/vep/.vep/loftee.sql --plugin UTRAnnotator,file=/opt/vep/.vep/uORF_5UTR_GRCh38_PUBLIC.txt --plugin SpliceRegion,Extended --plugin AlphaMissense,file=/opt/vep/.vep/AlphaMissense_hg38.tsv.gz --dir_plugins /plugins -o STDOUT | sed s/5utr/fiveutr/g" + ], + "env": { + "PERL5LIB": "/plugins" + }, + "vep_json_schema": "Struct{input:String,check_ref:String,most_severe_consequence:String,motif_feature_consequences:Array[Struct{consequence_terms:Array[String],motif_feature_id:String}],regulatory_feature_consequences:Array[Struct{biotype:String,consequence_terms:Array[String],regulatory_feature_id:String}],transcript_consequences:Array[Struct{amino_acids:String,biotype:String,canonical:Int32,codons:String,consequence_terms:Array[String],exon:String,gene_id:String,hgvsc:String,hgvsp:String,intron:String,mane_select:String,mane_plus_clinical:String,transcript_id:String,lof:String,lof_flags:String,lof_filter:String,lof_info:String,existing_inframe_oorfs:Int32,existing_outofframe_oorfs:Int32,existing_uorfs:Int32,fiveutr_consequence:String,fiveutr_annotation:Dict[String,Struct{type:String,KozakContext:String,KozakStrength:String,DistanceToCDS:String,CapDistanceToStart:String,DistanceToStop:String,Evidence:String,AltStop:String,AltStopDistanceToCDS:String,FrameWithCDS:String,StartDistanceToCDS:String,newSTOPDistanceToCDS:String,alt_type:String,alt_type_length:String,ref_StartDistanceToCDS:String,ref_type:String,ref_type_length:String}],am_pathogenicity:Float32,spliceregion:Array[String]}]}" +} From 2b61421a832bbbb4a5a41275d03f5fe434df3cd7 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 14:18:48 -0400 Subject: [PATCH 169/369] merge gitignore --- .gitignore | 171 +++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 171 insertions(+) diff --git a/.gitignore b/.gitignore index 3928b0e368..2bcd030622 100644 --- a/.gitignore +++ b/.gitignore @@ -18,3 +18,174 @@ pedigree_images/* seqr_settings django_key + +# loading pipeline +temp +*.vcf.gz +download_and_create_reference_datasets/*.txt +download_and_create_reference_datasets/*.gz +*.ht +*.mt +!/loading_pipeline/var/test/**/* + +# Standard python gitignore below +###################################################################### +###################################################################### + +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib64/ +sdist/ +wheels/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py,cover +.hypothesis/ +.pytest_cache/ +cover/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +.pybuilder/ +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +# For a library or package, you might want to ignore these files since the code is +# intended to run in multiple environments; otherwise, check them in: +# .python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don't work, or not +# install all needed dependencies. +#Pipfile.lock + +# poetry +# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control. +# This is especially recommended for binary packages to ensure reproducibility, and is more +# commonly ignored for libraries. +# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control +#poetry.lock + +# pdm +# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. +#pdm.lock +# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it +# in version control. +# https://pdm.fming.dev/#use-with-ide +.pdm.toml + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm +__pypackages__/ + +# Celery stuff +celerybeat-schedule +celerybeat.pid + +# SageMath parsed files +*.sage.py + +# Environments +.env +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ + +# pytype static type analyzer +.pytype/ + +# Cython debug symbols +cython_debug/ + +# PyCharm +# JetBrains specific template is maintained in a separate JetBrains.gitignore that can +# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore +# and can be added to the global gitignore or merged into this file. For a more nuclear +# option (not recommended) you can uncomment the following to ignore the entire idea folder. +#.idea/ From 775c6a9d599b189b2caeabbc78c96604cd6a95c4 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 14:20:04 -0400 Subject: [PATCH 170/369] merge dockerignore --- .dockerignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.dockerignore b/.dockerignore index e294067478..09e62f8f26 100644 --- a/.dockerignore +++ b/.dockerignore @@ -6,6 +6,7 @@ static/* deploy/* !deploy/docker/seqr/* !deploy/docker/vlm/* +*test* .git .vscode .idea From 0d3bd25924408e9e57577266f72097904f047575 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 14:23:50 -0400 Subject: [PATCH 171/369] update docker copy path --- loading_pipeline/deploy/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/loading_pipeline/deploy/Dockerfile b/loading_pipeline/deploy/Dockerfile index 0ae73232ae..96c3467f4f 100644 --- a/loading_pipeline/deploy/Dockerfile +++ b/loading_pipeline/deploy/Dockerfile @@ -19,7 +19,7 @@ ENV VIRTUAL_ENV="/.venv" # to mismatches between the uv:python3.11-alpine and hail docker python environments. RUN apt-get update && apt-get install -y build-essential && rm -rf /var/lib/apt/lists/* -COPY pyproject.toml uv.lock . +COPY loading_pipeline/pyproject.toml loading_pipeline/uv.lock . RUN uv sync --group prod --no-group dev --locked # Application Code From da4d2977e95a9afe066baee7ff8f236816dfd6d9 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 14:51:37 -0400 Subject: [PATCH 172/369] tweak readme --- loading_pipeline/CLAUDE.md | 2 +- loading_pipeline/README.md | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/loading_pipeline/CLAUDE.md b/loading_pipeline/CLAUDE.md index 130889aa15..be7fe50300 100644 --- a/loading_pipeline/CLAUDE.md +++ b/loading_pipeline/CLAUDE.md @@ -1,6 +1,6 @@ # CLAUDE.md -This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository. +This file provides guidance to Claude Code (claude.ai/code) when working with code in this folder. ## Quick Commands diff --git a/loading_pipeline/README.md b/loading_pipeline/README.md index 65910f3f3b..a12f08cad0 100644 --- a/loading_pipeline/README.md +++ b/loading_pipeline/README.md @@ -3,11 +3,11 @@ [![Code Build](https://github.com/broadinstitute/seqr-loading-pipelines/actions/workflows/unit-tests.yml/badge.svg?branch=main)](https://github.com/broadinstitute/seqr-loading-pipelines/actions/workflows/unit-tests.yml) [![Docker Build](https://github.com/broadinstitute/seqr-loading-pipelines/actions/workflows/prod-release.yml/badge.svg?branch=main)](https://github.com/broadinstitute/seqr-loading-pipelines/actions/workflows/prod-release.yml) -*This repository contains pipelines and infrastructure for loading genomic data from VCF -> ClickHouse to support queries by the _seqr_ application* +*This folder contains pipelines and infrastructure for loading genomic data from VCF -> ClickHouse to support queries by the _seqr_ application* --- -## 📁 Repository Structure +## 📁 Project Structure ### `loading_pipeline/api/` Contains the interface layer to the _seqr_ application. @@ -50,8 +50,8 @@ The production pipeline runs with python `3.11`. ### Clone the repo and install python requirements ```bash -git clone https://github.com/broadinstitute/seqr-loading-pipelines.git -cd seqr-loading-pipelines +git clone https://github.com/broadinstitute/seqr.git +cd seqr/loading_pipeline RUN uv sync --group dev --locked ``` @@ -59,7 +59,7 @@ RUN uv sync --group dev --locked > **Note:** We are running ClickHouse `26.3.9-lts` in production. ```bash curl https://clickhouse.com/ | sh -./clickhouse server --config-file=./seqr-loading-pipelines/loading_pipeline/var/clickhouse_config/test-clickhouse.xml +./clickhouse server --config-file=./seqr/loading_pipeline/var/clickhouse_config/test-clickhouse.xml ``` ### [Run the Tests](https://github.com/broadinstitute/seqr-loading-pipelines/blob/main/.github/workflows/unit-tests.yml#L66-L73) From 0d04860e456028962ae84d67cca71b024dbdf32a Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 14:52:53 -0400 Subject: [PATCH 173/369] copyy cloudbuild yaml --- .cloudbuild/pipeline-docker.cloudbuild.yaml | 11 +++++++++++ .cloudbuild/vep-docker.cloudbuild.yaml | 12 ++++++++++++ 2 files changed, 23 insertions(+) create mode 100644 .cloudbuild/pipeline-docker.cloudbuild.yaml create mode 100644 .cloudbuild/vep-docker.cloudbuild.yaml diff --git a/.cloudbuild/pipeline-docker.cloudbuild.yaml b/.cloudbuild/pipeline-docker.cloudbuild.yaml new file mode 100644 index 0000000000..30b4844b0b --- /dev/null +++ b/.cloudbuild/pipeline-docker.cloudbuild.yaml @@ -0,0 +1,11 @@ +steps: +- name: 'gcr.io/kaniko-project/executor:v1.3.0' + args: + - --destination=gcr.io/seqr-project/seqr-pipeline-runner:${COMMIT_SHA} + - --destination=gcr.io/seqr-project/seqr-pipeline-runner:${_CUSTOM_BRANCH_TAG} + - --dockerfile=loading_pipeline/deploy/Dockerfile + - --cache=true + - --cache-ttl=168h + - --build-arg=PIPELINE_RUNNER_APP_VERSION=${COMMIT_SHA} + +timeout: 1800s \ No newline at end of file diff --git a/.cloudbuild/vep-docker.cloudbuild.yaml b/.cloudbuild/vep-docker.cloudbuild.yaml new file mode 100644 index 0000000000..39fe857889 --- /dev/null +++ b/.cloudbuild/vep-docker.cloudbuild.yaml @@ -0,0 +1,12 @@ +# Run locally with: +# +# gcloud builds submit --quiet --substitutions='_REFERENCE_GENOME=GRCh38' --config .cloudbuild/vep-docker.cloudbuild.yaml loading_pipeline/deploy +steps: +- name: 'gcr.io/kaniko-project/executor:v1.3.0' + args: + - --destination=gcr.io/seqr-project/vep-docker-image:${_REFERENCE_GENOME} + - --dockerfile=Dockerfile.vep_${_REFERENCE_GENOME} + - --cache=true + - --cache-ttl=168h + +timeout: 1800s From dab03fb13fdc47d2d98578637b1a263c92e442e5 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 15:38:05 -0400 Subject: [PATCH 174/369] unit tests --- .github/workflows/pipeline-unit-tests.yml | 79 +++++++++++++++++++++++ .github/workflows/unit-tests.yml | 4 ++ 2 files changed, 83 insertions(+) create mode 100644 .github/workflows/pipeline-unit-tests.yml diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml new file mode 100644 index 0000000000..b0d31f9ed5 --- /dev/null +++ b/.github/workflows/pipeline-unit-tests.yml @@ -0,0 +1,79 @@ +name: Pipeline Unit Tests + +# Run the test suite on pushes (incl. merges) to master and dev +# Run the test suite when a PR is opened, pushed to, or reopened +on: + push: + branches: + - dev + - master + paths: + - 'loading_pipeline/**' + - '.github/workflows/*pipeline-release.yaml' + pull_request: + types: [opened, synchronize, reopened] + paths: + - 'loading_pipeline/**' + - '.github/workflows/*pipeline*.yaml' + +jobs: + unit_tests: + runs-on: ubuntu-latest + strategy: + matrix: + python-version: ['3.11'] + + steps: + - uses: actions/checkout@v3 + - name: Create ClickHouse Config + run: | + cat < test_config.xml + + /tmp + + EOF + - name: Start ClickHouse with mounted config + run: | + docker run -d --name clickhouse \ + -v ${{ github.workspace }}/test_config.xml:/etc/clickhouse-server/config.d/config.xml \ + -v /tmp:/tmp \ + -p 9000:9000 \ + -e CLICKHOUSE_USER=default \ + -e CLICKHOUSE_PASSWORD=default_password \ + gcr.io/seqr-project/seqr-clickhouse:26.3.9 + - name: Wait for ClickHouse + run: | + until docker exec clickhouse clickhouse-client --query "SELECT 1"; do + echo "Waiting for ClickHouse to start..." + sleep 2 + done + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v4 + with: + python-version: ${{ matrix.python-version }} + # Install uv + - name: Install uv + uses: astral-sh/setup-uv@v7 + with: + enable-cache: true + cache-dependency-glob: | + **/uv.lock + **/pyproject.toml + - name: Sync dependencies (prod + dataproc) + run: uv sync --locked + - name: Check Ruff Format + run: uv run ruff format --check loading_pipeline --diff + - name: Check Ruff + run: uv run ruff check --output-format github + - name: Run ShellCheck + uses: ludeeus/action-shellcheck@master + with: + severity: error + scandir: './loading_pipeline/bin' + - name: Unit Tests + run: | + export CLICKHOUSE_OPTIMIZE_TABLE_WAIT_S=1 + export PYSPARK_SUBMIT_ARGS='--driver-memory 8G pyspark-shell' + export CLICKHOUSE_DATABASE=test + uv run pytest --cov=loading_pipeline --cov-report=term-missing loading_pipeline + uv run coverage report --omit '*test*' --fail-under=85 diff --git a/.github/workflows/unit-tests.yml b/.github/workflows/unit-tests.yml index b55ef44185..9d19033073 100644 --- a/.github/workflows/unit-tests.yml +++ b/.github/workflows/unit-tests.yml @@ -8,11 +8,15 @@ on: - master - dev paths-ignore: + - 'loading_pipeline/**' + - '.github/workflows/*pipeline*.yaml' - 'vlm/**' - '.github/workflows/*vlm*.yaml' pull_request: types: [opened, synchronize, reopened] paths-ignore: + - 'loading_pipeline/**' + - '.github/workflows/*pipeline*.yaml' - 'vlm/**' - '.github/workflows/*vlm*.yaml' From 3a7dc85b099dccfca7a7460e6ac88d3ef6e0f63d Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 15:42:52 -0400 Subject: [PATCH 175/369] release workflows --- .github/workflows/pipeline-dev-release.yml | 74 ++++++++++++ .github/workflows/pipeline-prod-release.yml | 121 ++++++++++++++++++++ 2 files changed, 195 insertions(+) create mode 100644 .github/workflows/pipeline-dev-release.yml create mode 100644 .github/workflows/pipeline-prod-release.yml diff --git a/.github/workflows/pipeline-dev-release.yml b/.github/workflows/pipeline-dev-release.yml new file mode 100644 index 0000000000..5c050a9b52 --- /dev/null +++ b/.github/workflows/pipeline-dev-release.yml @@ -0,0 +1,74 @@ +name: dev release +on: + workflow_run: + workflows: ["Pipeline Unit Tests"] + types: + - completed + branches: + - dev + +permissions: + id-token: write + +jobs: + release: + runs-on: ubuntu-latest + if: ${{ github.event.workflow_run.conclusion == 'success' }} + steps: + - name: checkout + uses: actions/checkout@v3 + with: + ref: ${{ github.event.workflow_run.head_branch }} + + - name: Set up Python + uses: actions/setup-python@v4 + with: + python-version: '3.11' + + - name: Build package + run: | + cd loading_pipeline + rm -rf dist/ + python -m pip install build + python -m build + + - name: authenticate to google cloud + id: "auth" + uses: google-github-actions/auth@v0 + with: + workload_identity_provider: "${{ secrets.WORKLOAD_IDENTITY_PROVIDER }}" + service_account: "${{ secrets.RUN_SA_EMAIL }}" + + - name: "setup gcloud sdk" + uses: google-github-actions/setup-gcloud@v0 + + - name: Copy files to release directory + run: |- + gcloud storage rm -r gs://seqr-pipeline-runner-builds/dev/latest/ || echo 'No latest release' + gcloud storage cp loading_pipeline/bin/* gs://seqr-pipeline-runner-builds/dev/latest/bin/ + gcloud storage cp cd loading_pipeline/dist/*.whl gs://seqr-pipeline-runner-builds/dev/latest/pyscripts.zip + gcloud storage cp loading_pipeline/bin/* gs://seqr-pipeline-runner-builds/dev/${{ github.event.workflow_run.head_sha }}/bin/ + gcloud storage cp cd loading_pipeline/dist/*.whl gs://seqr-pipeline-runner-builds/dev/${{ github.event.workflow_run.head_sha }}/pyscripts.zip + docker: + runs-on: ubuntu-latest + if: ${{ github.event.workflow_run.conclusion == 'success' }} + steps: + - name: checkout + uses: actions/checkout@v3 + with: + ref: ${{ github.event.workflow_run.head_branch }} + + - name: authenticate to google cloud + id: "auth" + uses: google-github-actions/auth@v3 + with: + workload_identity_provider: "${{ secrets.WORKLOAD_IDENTITY_PROVIDER }}" + service_account: "${{ secrets.RUN_SA_EMAIL }}" + + - name: "setup gcloud sdk" + uses: google-github-actions/setup-gcloud@v2 + + - name: Build and push images + run: |- + gcloud builds submit --quiet --substitutions="COMMIT_SHA=${{ github.event.workflow_run.head_sha }},_CUSTOM_BRANCH_TAG=dev" --config .cloudbuild/pipeline-docker.cloudbuild.yaml --gcs-log-dir=gs://seqr-github-actions-logs/logs . + diff --git a/.github/workflows/pipeline-prod-release.yml b/.github/workflows/pipeline-prod-release.yml new file mode 100644 index 0000000000..02da04e79e --- /dev/null +++ b/.github/workflows/pipeline-prod-release.yml @@ -0,0 +1,121 @@ +name: prod release +on: + workflow_run: + workflows: ["Pipeline Unit Tests"] + types: + - completed + branches: + - master + +permissions: + id-token: write + contents: write + +jobs: + release: + runs-on: ubuntu-latest + if: ${{ github.event.workflow_run.conclusion == 'success' }} + steps: + - name: checkout + uses: actions/checkout@v3 + with: + ref: ${{ github.event.workflow_run.head_branch }} + + - name: set up python + uses: actions/setup-python@v4 + with: + python-version: '3.11' + + - name: build package + run: | + cd loading_pipeline + rm -rf dist/ + python -m pip install build + python -m build + + - name: authenticate to google cloud + id: "auth" + uses: google-github-actions/auth@v3 + with: + workload_identity_provider: "${{ secrets.WORKLOAD_IDENTITY_PROVIDER }}" + service_account: "${{ secrets.RUN_SA_EMAIL }}" + + - name: "setup gcloud sdk" + uses: google-github-actions/setup-gcloud@v2 + + - name: Copy files to release directory + shell: bash + run: |- + gcloud storage rm -r gs://seqr-pipeline-runner-builds/prod/latest/ || echo 'No latest release' + gcloud storage cp loading_pipeline/bin/* gs://seqr-pipeline-runner-builds/prod/latest/bin/ + gcloud storage cp loading_pipeline/dist/*.whl gs://seqr-pipeline-runner-builds/prod/latest/pyscripts.zip + gcloud storage cp loading_pipeline/bin/* gs://seqr-pipeline-runner-builds/prod/${{ github.event.workflow_run.head_sha }}/bin/ + gcloud storage cp loading_pipeline/dist/*.whl gs://seqr-pipeline-runner-builds/prod/${{ github.event.workflow_run.head_sha }}/pyscripts.zip + gcloud storage cp -r loading_pipeline/var/vep/* gs://seqr-reference-data/vep/ + + docker: + runs-on: ubuntu-latest + if: ${{ github.event.workflow_run.conclusion == 'success' }} + steps: + - name: checkout + uses: actions/checkout@v3 + with: + ref: ${{ github.event.workflow_run.head_branch }} + + - name: authenticate to google cloud + id: "auth" + uses: google-github-actions/auth@v3 + with: + workload_identity_provider: "${{ secrets.WORKLOAD_IDENTITY_PROVIDER }}" + service_account: "${{ secrets.RUN_SA_EMAIL }}" + + - name: "setup gcloud sdk" + uses: google-github-actions/setup-gcloud@v2 + + - name: Build and push images + run: |- + gcloud builds submit --quiet --substitutions="COMMIT_SHA=${{ github.event.workflow_run.head_sha }},_CUSTOM_BRANCH_TAG=latest" --config .cloudbuild/pipeline-docker.cloudbuild.yaml --gcs-log-dir=gs://seqr-github-actions-logs/logs . + + helm_update: + runs-on: ubuntu-latest + needs: docker + steps: + - uses: actions/checkout@v3 + with: + repository: broadinstitute/seqr-helm + ref: main + persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal token + fetch-depth: 0 # otherwise, you will failed to push refs to dest repo + + - name: Get latest pipeline-runner version + uses: mikefarah/yq@v4.22.1 + id: current + with: + cmd: > + yq -r '.version' charts/pipeline-runner/Chart.yaml + + - name: Bump version + id: bump + uses: cbrgm/semver-bump-action@main + with: + current-version: ${{ steps.current.outputs.result }} + bump-level: minor + + - name: Update appVersion and version in pipeline-runner Chart file + uses: mikefarah/yq@v4.22.1 + with: + cmd: > + yq -i ' + .appVersion = "${{ github.event.workflow_run.head_sha }}" | + .version = "${{ steps.bump.outputs.new_version }}" + ' charts/pipeline-runner/Chart.yaml + + - name: Commit and Push changes + uses: Andro999b/push@v1.3 + with: + repository: broadinstitute/seqr-helm + branch: main + github_token: ${{ secrets.SEQR_VERSION_UPDATE_TOKEN }} + author_email: ${{ github.actor }}@users.noreply.github.com + author_name: tgg-automation + message: "Update pipeline-runner chart appVersion to ${{ github.event.workflow_run.head_sha }}" From 60c5a077b2838070689ab197b6394cef9c9b7e7b Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 15:58:57 -0400 Subject: [PATCH 176/369] correct directory for unit test deps --- .github/workflows/pipeline-unit-tests.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml index b0d31f9ed5..a71056e169 100644 --- a/.github/workflows/pipeline-unit-tests.yml +++ b/.github/workflows/pipeline-unit-tests.yml @@ -60,7 +60,9 @@ jobs: **/uv.lock **/pyproject.toml - name: Sync dependencies (prod + dataproc) - run: uv sync --locked + run: | + cd loading_pipeline + uv sync --locked - name: Check Ruff Format run: uv run ruff format --check loading_pipeline --diff - name: Check Ruff From bd64115b96755cb206a3b608b8c76ec9adc34216 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 16:00:53 -0400 Subject: [PATCH 177/369] fix uv commands --- .github/workflows/pipeline-unit-tests.yml | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml index a71056e169..002bb3288c 100644 --- a/.github/workflows/pipeline-unit-tests.yml +++ b/.github/workflows/pipeline-unit-tests.yml @@ -64,9 +64,13 @@ jobs: cd loading_pipeline uv sync --locked - name: Check Ruff Format - run: uv run ruff format --check loading_pipeline --diff + run: | + cd loading_pipeline + uv run ruff format --check loading_pipeline --diff - name: Check Ruff - run: uv run ruff check --output-format github + run: | + cd loading_pipeline + uv run ruff check --output-format github - name: Run ShellCheck uses: ludeeus/action-shellcheck@master with: From 84e8441d3eef668511065c1f6dbf072ce2d917d5 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 16:03:48 -0400 Subject: [PATCH 178/369] correct ruff path --- .github/workflows/pipeline-unit-tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml index 002bb3288c..67d5a5fd92 100644 --- a/.github/workflows/pipeline-unit-tests.yml +++ b/.github/workflows/pipeline-unit-tests.yml @@ -66,7 +66,7 @@ jobs: - name: Check Ruff Format run: | cd loading_pipeline - uv run ruff format --check loading_pipeline --diff + uv run ruff format --check . --diff - name: Check Ruff run: | cd loading_pipeline From e41da52a44c7fe5e5cec4b4502b7c1faa5285281 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 16:27:53 -0400 Subject: [PATCH 179/369] fix uv test --- .github/workflows/pipeline-unit-tests.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml index 67d5a5fd92..13ddf5417d 100644 --- a/.github/workflows/pipeline-unit-tests.yml +++ b/.github/workflows/pipeline-unit-tests.yml @@ -81,5 +81,6 @@ jobs: export CLICKHOUSE_OPTIMIZE_TABLE_WAIT_S=1 export PYSPARK_SUBMIT_ARGS='--driver-memory 8G pyspark-shell' export CLICKHOUSE_DATABASE=test - uv run pytest --cov=loading_pipeline --cov-report=term-missing loading_pipeline + cd loading_pipeline + uv run pytest --cov=loading_pipeline --cov-report=term-missing . uv run coverage report --omit '*test*' --fail-under=85 From 79254f5638ca4a6e875a2e3795b641402ad1c9ad Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 16:30:00 -0400 Subject: [PATCH 180/369] codacy ignore --- .codacy.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.codacy.yaml b/.codacy.yaml index a0ae5a67dd..ba5602507c 100644 --- a/.codacy.yaml +++ b/.codacy.yaml @@ -1,3 +1,4 @@ --- exclude_paths: - - "deploy/postgres/initdb.sql" \ No newline at end of file + - "deploy/postgres/initdb.sql" + - "loading_pipeline" \ No newline at end of file From b9f04675c1a57306efb14bc8a4680c0816ffb8ad Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 16:33:34 -0400 Subject: [PATCH 181/369] fix codacy ignore --- .codacy.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.codacy.yaml b/.codacy.yaml index ba5602507c..3bd43d8705 100644 --- a/.codacy.yaml +++ b/.codacy.yaml @@ -1,4 +1,4 @@ --- exclude_paths: - "deploy/postgres/initdb.sql" - - "loading_pipeline" \ No newline at end of file + - "loading_pipeline/**" \ No newline at end of file From 052c99dffd6b43ce437213596fd24f8a854eecbd Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 16:37:46 -0400 Subject: [PATCH 182/369] run test in root dir --- .github/workflows/pipeline-unit-tests.yml | 15 ++++----------- 1 file changed, 4 insertions(+), 11 deletions(-) diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml index 13ddf5417d..e7a00ccb35 100644 --- a/.github/workflows/pipeline-unit-tests.yml +++ b/.github/workflows/pipeline-unit-tests.yml @@ -60,17 +60,11 @@ jobs: **/uv.lock **/pyproject.toml - name: Sync dependencies (prod + dataproc) - run: | - cd loading_pipeline - uv sync --locked + run: uv sync --locked --package loading_pipeline - name: Check Ruff Format - run: | - cd loading_pipeline - uv run ruff format --check . --diff + run: uv run ruff format --check loading_pipeline --diff - name: Check Ruff - run: | - cd loading_pipeline - uv run ruff check --output-format github + run: uv run ruff check --output-format github - name: Run ShellCheck uses: ludeeus/action-shellcheck@master with: @@ -81,6 +75,5 @@ jobs: export CLICKHOUSE_OPTIMIZE_TABLE_WAIT_S=1 export PYSPARK_SUBMIT_ARGS='--driver-memory 8G pyspark-shell' export CLICKHOUSE_DATABASE=test - cd loading_pipeline - uv run pytest --cov=loading_pipeline --cov-report=term-missing . + uv run pytest --cov=loading_pipeline --cov-report=term-missing loading_pipeline uv run coverage report --omit '*test*' --fail-under=85 From 43f5fece9b5d25e14ddaf61b07cdd3c4adb86b38 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 16:39:24 -0400 Subject: [PATCH 183/369] fi uv sync --- .github/workflows/pipeline-unit-tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml index e7a00ccb35..8a6af05773 100644 --- a/.github/workflows/pipeline-unit-tests.yml +++ b/.github/workflows/pipeline-unit-tests.yml @@ -60,7 +60,7 @@ jobs: **/uv.lock **/pyproject.toml - name: Sync dependencies (prod + dataproc) - run: uv sync --locked --package loading_pipeline + run: uv sync --locked --project loading_pipeline - name: Check Ruff Format run: uv run ruff format --check loading_pipeline --diff - name: Check Ruff From fd6dae4218356c60bfbdb673825b6b2360f93ecc Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 16:41:23 -0400 Subject: [PATCH 184/369] fix uv commands --- .github/workflows/pipeline-unit-tests.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml index 8a6af05773..0e01e11faa 100644 --- a/.github/workflows/pipeline-unit-tests.yml +++ b/.github/workflows/pipeline-unit-tests.yml @@ -62,9 +62,9 @@ jobs: - name: Sync dependencies (prod + dataproc) run: uv sync --locked --project loading_pipeline - name: Check Ruff Format - run: uv run ruff format --check loading_pipeline --diff + run: uv run ruff format --check loading_pipeline --diff --project loading_pipeline - name: Check Ruff - run: uv run ruff check --output-format github + run: uv run ruff check --output-format github --project loading_pipeline - name: Run ShellCheck uses: ludeeus/action-shellcheck@master with: From 49b44c4eb0c02c9a87c6b1cf0afd0c24026e187d Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 16:47:58 -0400 Subject: [PATCH 185/369] iter test runner --- .github/workflows/pipeline-unit-tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml index 0e01e11faa..35c27fb83c 100644 --- a/.github/workflows/pipeline-unit-tests.yml +++ b/.github/workflows/pipeline-unit-tests.yml @@ -60,7 +60,7 @@ jobs: **/uv.lock **/pyproject.toml - name: Sync dependencies (prod + dataproc) - run: uv sync --locked --project loading_pipeline + run: uv sync --locked --project loading_pipeline --inexact - name: Check Ruff Format run: uv run ruff format --check loading_pipeline --diff --project loading_pipeline - name: Check Ruff From ad4167670c11133cee525bfe45154764c753aeb6 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 16:52:19 -0400 Subject: [PATCH 186/369] iter test runner --- .github/workflows/pipeline-unit-tests.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml index 35c27fb83c..358517c63a 100644 --- a/.github/workflows/pipeline-unit-tests.yml +++ b/.github/workflows/pipeline-unit-tests.yml @@ -60,11 +60,11 @@ jobs: **/uv.lock **/pyproject.toml - name: Sync dependencies (prod + dataproc) - run: uv sync --locked --project loading_pipeline --inexact + run: uv sync --locked --project loading_pipeline - name: Check Ruff Format - run: uv run ruff format --check loading_pipeline --diff --project loading_pipeline + run: uv run ruff format --check loading_pipeline --diff --config loading_pipeline/pyproject.toml - name: Check Ruff - run: uv run ruff check --output-format github --project loading_pipeline + run: uv run ruff check --output-format github - name: Run ShellCheck uses: ludeeus/action-shellcheck@master with: From de0f9125f709f4fdc36c3e313a8e7c0eb6a6f4f0 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 16:57:10 -0400 Subject: [PATCH 187/369] configure uv workspace --- .github/workflows/pipeline-unit-tests.yml | 4 ++-- loading_pipeline/pyproject.toml | 3 +++ 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml index 358517c63a..9368013eac 100644 --- a/.github/workflows/pipeline-unit-tests.yml +++ b/.github/workflows/pipeline-unit-tests.yml @@ -60,9 +60,9 @@ jobs: **/uv.lock **/pyproject.toml - name: Sync dependencies (prod + dataproc) - run: uv sync --locked --project loading_pipeline + run: uv sync --locked - name: Check Ruff Format - run: uv run ruff format --check loading_pipeline --diff --config loading_pipeline/pyproject.toml + run: uv run ruff format --check loading_pipeline --diff - name: Check Ruff run: uv run ruff check --output-format github - name: Run ShellCheck diff --git a/loading_pipeline/pyproject.toml b/loading_pipeline/pyproject.toml index f06f1fc691..65f446ba5e 100644 --- a/loading_pipeline/pyproject.toml +++ b/loading_pipeline/pyproject.toml @@ -43,6 +43,9 @@ dev = [ [tool.uv] exclude-dependencies = ["psycopg2-binary", "psycopg2"] +[tool.uv.workspace] +members = ["loading_pipeline/*"] + [tool.setuptools] include-package-data = true From 375e13ab6421ca8f882598ce71618f855efe5633 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 16:59:13 -0400 Subject: [PATCH 188/369] iter test runner --- .github/workflows/pipeline-unit-tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml index 9368013eac..8a6af05773 100644 --- a/.github/workflows/pipeline-unit-tests.yml +++ b/.github/workflows/pipeline-unit-tests.yml @@ -60,7 +60,7 @@ jobs: **/uv.lock **/pyproject.toml - name: Sync dependencies (prod + dataproc) - run: uv sync --locked + run: uv sync --locked --project loading_pipeline - name: Check Ruff Format run: uv run ruff format --check loading_pipeline --diff - name: Check Ruff From d7cbf54319554779ebe977602686c17fe24e1829 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 17:01:44 -0400 Subject: [PATCH 189/369] iter test runner --- .github/workflows/pipeline-unit-tests.yml | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml index 8a6af05773..f3050f810a 100644 --- a/.github/workflows/pipeline-unit-tests.yml +++ b/.github/workflows/pipeline-unit-tests.yml @@ -62,9 +62,13 @@ jobs: - name: Sync dependencies (prod + dataproc) run: uv sync --locked --project loading_pipeline - name: Check Ruff Format - run: uv run ruff format --check loading_pipeline --diff + run: | + cd loading_pipeline + uv run ruff format --check . --diff - name: Check Ruff - run: uv run ruff check --output-format github + run: | + cd loading_pipeline + uv run ruff check --output-format github - name: Run ShellCheck uses: ludeeus/action-shellcheck@master with: From cf0c510223025540d54fff29abe42f9353c600b7 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 11 Aug 2026 17:04:41 -0400 Subject: [PATCH 190/369] iter test runner --- .github/workflows/pipeline-unit-tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml index f3050f810a..c6a0e3585e 100644 --- a/.github/workflows/pipeline-unit-tests.yml +++ b/.github/workflows/pipeline-unit-tests.yml @@ -79,5 +79,5 @@ jobs: export CLICKHOUSE_OPTIMIZE_TABLE_WAIT_S=1 export PYSPARK_SUBMIT_ARGS='--driver-memory 8G pyspark-shell' export CLICKHOUSE_DATABASE=test - uv run pytest --cov=loading_pipeline --cov-report=term-missing loading_pipeline + uv run pytest --project loading_pipeline --cov=loading_pipeline --cov-report=term-missing loading_pipeline uv run coverage report --omit '*test*' --fail-under=85 From a71e9d3287761c09ee2d30fa82032e503f21c27b Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Wed, 12 Aug 2026 11:51:26 -0400 Subject: [PATCH 191/369] iter test approach --- .github/workflows/pipeline-unit-tests.yml | 2 +- loading_pipeline/pyproject.toml | 3 --- 2 files changed, 1 insertion(+), 4 deletions(-) diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml index c6a0e3585e..848a5434fa 100644 --- a/.github/workflows/pipeline-unit-tests.yml +++ b/.github/workflows/pipeline-unit-tests.yml @@ -79,5 +79,5 @@ jobs: export CLICKHOUSE_OPTIMIZE_TABLE_WAIT_S=1 export PYSPARK_SUBMIT_ARGS='--driver-memory 8G pyspark-shell' export CLICKHOUSE_DATABASE=test - uv run pytest --project loading_pipeline --cov=loading_pipeline --cov-report=term-missing loading_pipeline + uv run --with pytest pytest --cov=loading_pipeline --cov-report=term-missing loading_pipeline uv run coverage report --omit '*test*' --fail-under=85 diff --git a/loading_pipeline/pyproject.toml b/loading_pipeline/pyproject.toml index 65f446ba5e..f06f1fc691 100644 --- a/loading_pipeline/pyproject.toml +++ b/loading_pipeline/pyproject.toml @@ -43,9 +43,6 @@ dev = [ [tool.uv] exclude-dependencies = ["psycopg2-binary", "psycopg2"] -[tool.uv.workspace] -members = ["loading_pipeline/*"] - [tool.setuptools] include-package-data = true From 985959e23fd5a25e57c756d69d7908bd20ff4363 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Wed, 12 Aug 2026 12:09:25 -0400 Subject: [PATCH 192/369] iter command --- .github/workflows/pipeline-unit-tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml index 848a5434fa..16dd72ffca 100644 --- a/.github/workflows/pipeline-unit-tests.yml +++ b/.github/workflows/pipeline-unit-tests.yml @@ -79,5 +79,5 @@ jobs: export CLICKHOUSE_OPTIMIZE_TABLE_WAIT_S=1 export PYSPARK_SUBMIT_ARGS='--driver-memory 8G pyspark-shell' export CLICKHOUSE_DATABASE=test - uv run --with pytest pytest --cov=loading_pipeline --cov-report=term-missing loading_pipeline + uv run --with pytest pytest loading_pipeline --cov=loading_pipeline --cov-report=term-missing uv run coverage report --omit '*test*' --fail-under=85 From 820e1338a43a9a140d393f96060082af635afe81 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Wed, 12 Aug 2026 12:14:06 -0400 Subject: [PATCH 193/369] reset test command --- .github/workflows/pipeline-unit-tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml index 16dd72ffca..f3050f810a 100644 --- a/.github/workflows/pipeline-unit-tests.yml +++ b/.github/workflows/pipeline-unit-tests.yml @@ -79,5 +79,5 @@ jobs: export CLICKHOUSE_OPTIMIZE_TABLE_WAIT_S=1 export PYSPARK_SUBMIT_ARGS='--driver-memory 8G pyspark-shell' export CLICKHOUSE_DATABASE=test - uv run --with pytest pytest loading_pipeline --cov=loading_pipeline --cov-report=term-missing + uv run pytest --cov=loading_pipeline --cov-report=term-missing loading_pipeline uv run coverage report --omit '*test*' --fail-under=85 From 44df393c14a3cc409e4185e324627ee589e94725 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Wed, 12 Aug 2026 13:11:36 -0400 Subject: [PATCH 194/369] fix test command --- .github/workflows/pipeline-unit-tests.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml index f3050f810a..3610b666ae 100644 --- a/.github/workflows/pipeline-unit-tests.yml +++ b/.github/workflows/pipeline-unit-tests.yml @@ -79,5 +79,5 @@ jobs: export CLICKHOUSE_OPTIMIZE_TABLE_WAIT_S=1 export PYSPARK_SUBMIT_ARGS='--driver-memory 8G pyspark-shell' export CLICKHOUSE_DATABASE=test - uv run pytest --cov=loading_pipeline --cov-report=term-missing loading_pipeline - uv run coverage report --omit '*test*' --fail-under=85 + uv run --project loading_pipeline pytest --cov=loading_pipeline --cov-report=term-missing loading_pipeline + uv run --project loading_pipeline coverage report --omit '*test*' --fail-under=85 From 59a95488dfa4524baf9bdfee37ea0c2a00e45aec Mon Sep 17 00:00:00 2001 From: hanars Date: Wed, 12 Aug 2026 13:29:32 -0400 Subject: [PATCH 195/369] Potential fix for pull request finding 'CodeQL / Workflow does not contain permissions' Co-authored-by: Copilot Autofix powered by AI <62310815+github-advanced-security[bot]@users.noreply.github.com> --- .github/workflows/pipeline-unit-tests.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml index 3610b666ae..a476bbb908 100644 --- a/.github/workflows/pipeline-unit-tests.yml +++ b/.github/workflows/pipeline-unit-tests.yml @@ -16,6 +16,9 @@ on: - 'loading_pipeline/**' - '.github/workflows/*pipeline*.yaml' +permissions: + contents: read + jobs: unit_tests: runs-on: ubuntu-latest From da20af320ff91633eacbedb75ab655f109ff32c4 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Wed, 12 Aug 2026 15:35:42 -0400 Subject: [PATCH 196/369] plan test migration --- .../CLICKHOUSE_PYTEST_DJANGO_PLAN.md | 143 ++++++++++++++++++ 1 file changed, 143 insertions(+) create mode 100644 loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_PLAN.md diff --git a/loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_PLAN.md b/loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_PLAN.md new file mode 100644 index 0000000000..bee7837170 --- /dev/null +++ b/loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_PLAN.md @@ -0,0 +1,143 @@ +# Plan: Manage ClickHouse test DB via pytest-django + `clickhouse_search` migrations + +## Goal + +Stop hand-maintaining ClickHouse schema DDL (and the static `var/test/test_clickhouse_schema.sql` +dump) inside `loading_pipeline`'s tests. Instead, use `pytest-django` to create/migrate the +ClickHouse test database from the real Django migrations in `clickhouse_search` (the source of +truth for the schema), so the pipeline's tests can never drift from production schema. + +Scope constraint: all code changes live in `loading_pipeline/` or in +`.github/workflows/pipeline-unit-tests.yml`. Nothing in `clickhouse_search/` or root `settings.py` +is modified. + +## Key constraint discovered + +`clickhouse_search/backend/base.py` does a **bare** `from settings import +CLICKHOUSE_WRITER_USER, CLICKHOUSE_WRITER_PASSWORD, DATABASES` — not `django.conf.settings`. This +only resolves correctly if a top-level module literally named `settings` is importable on +`sys.path`. Today that resolves to the main repo's heavy `settings.py` (postgres, guardian, +social_django, google.auth, etc.) whenever cwd is the repo root — which is undesirable/impossible +to depend on from `loading_pipeline`'s minimal env. + +**Trick:** create our own minimal module named `settings.py`, placed in a directory that we add to +`sys.path` ahead of the repo root (via pytest's `pythonpath` ini option, which prepends to +`sys.path`). That module serves double duty: +- It's what `clickhouse_search/backend/base.py`'s bare `import settings` resolves to. +- It's also `DJANGO_SETTINGS_MODULE` for pytest-django. + +## Single connection / single set of credentials only + +Per explicit direction: the settings module must configure **one** ClickHouse connection with +**one** set of credentials — not the production split of a read-only `clickhouse` alias plus a +privileged `clickhouse_write` alias. `DATABASES` will define a single alias (`clickhouse`) using +one writer-capable credential (needed anyway, since migrations and test data inserts require write +access). + +Nuance to account for: `clickhouse_search/backend/base.py`'s `_dictionary_sql` looks up +`DATABASES['clickhouse_write']['NAME']` (for ClickHouse-sourced dictionaries with a +`clickhouse_query_template`) and `DATABASES[postgres_db]['NAME']` (default alias `'default'`, for +Postgres-sourced dictionaries) purely to embed a database *name string* into generated DDL — not to +open a second real connection. To keep this working without standing up a second live connection: +- Give `'clickhouse_write'` a `TEST: {'MIRROR': 'clickhouse'}` config, so Django reuses the + `clickhouse` alias's actual test database instead of creating/tearing down a second one, while + the key is still present for the `NAME` lookup. +- Give `'default'` a placeholder entry (e.g. `ENGINE: 'django.db.backends.dummy'`) purely so + `DATABASES['default']['NAME']` resolves to a string — nothing in `loading_pipeline`'s tests + actually connects to it, since there's no Postgres in this CI job. + +## Inventory of every ClickHouse-touching test + +1. **`lib/misc/clickhouse_test.py`** (`ClickhouseTest`) — hand-rolls ~250 lines of `CREATE + TABLE`/`CREATE DICTIONARY`/`CREATE MATERIALIZED VIEW` DDL duplicating a subset of the real + schema, plus fixture dictionaries for gene IDs/gnomAD. +2. **`lib/test/clickhouse_schema_testcase.py`** (`ClickhouseSchemaTestCase`) — loads the static + `var/test/test_clickhouse_schema.sql` dump plus a few placeholder dictionaries. Used by: + - `bin/pipeline_worker_test.py` (`PipelineWorkerTest`) + - `lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py` + (`LoadClickhouseVariantsTablesTaskTest`) +3. **`ops/repartition_clickhouse_grch38_snv_indel_test.py`** (`RepartitionGRCh38SnvIndelTest`) — + its own bespoke DDL for a synthetic, intentionally-simplified `entries` table + a wholly + separate scratch database (`REPARTITION_DATABASE_NAME`) that isn't part of `clickhouse_search`'s + schema at all. + +## The Postgres/GCS-sourced dictionary wrinkle + +A handful of dictionaries are, in production, sourced from Postgres (via the +`seqr_postgres_named_collection` named collection) or from GCS parquet URLs: + +- `seqrdb_gene_ids` +- `seqrdb_affected_status_dict` +- `GRCh38/SNV_INDEL/project_partitions_dict` +- the gnomAD reference dict (`GRCh38/SNV_INDEL/reference_data/gnomad_genomes`) + +`loading_pipeline`'s CI only runs ClickHouse (no Postgres, no GCS access). Running +`clickhouse_search`'s real migrations here requires a dummy `seqr_postgres_named_collection` (a new +workflow step, mirroring what `unit-tests.yml` already does for the main app) just so the +`CREATE DICTIONARY ... SOURCE(POSTGRESQL(NAME 'seqr_postgres_named_collection' ...))` DDL parses. +Dictionaries are lazily loaded (`LIFETIME(0)`), so DDL creation succeeds even though the source is +unreachable — but tests still need to override these specific dictionaries with deterministic +fixture sources afterward (same idea as today's code, just trimmed to only this handful instead of +faking the whole schema). + +## Raw SQL execution in tests: use the Django connection, not `clickhouse_driver.Client` + +Every test currently calls `get_clickhouse_client()` (a raw `clickhouse_driver.Client`, see +`lib/misc/clickhouse.py`) to run setup/assertion SQL directly. Once the schema is Django-managed, +tests should execute their raw SQL through Django's own DB connection instead of a separate +`clickhouse_driver.Client` instance — i.e. `django.db.connections['clickhouse'].cursor()` (the one +alias defined per "Single connection / single set of credentials only" above), calling +`cursor.execute(sql, params)` / `cursor.fetchall()`. + +This is purely a *client* swap for test code — tests keep writing raw SQL strings (no ORM/model +queries), just executed via the Django connection so the tests exercise the same connection +machinery/test-DB aliasing that pytest-django set up, rather than opening an independent +`clickhouse_driver` connection that doesn't know about Django's test DB name remapping. Production +code in `lib/misc/clickhouse.py` (`get_clickhouse_client` and friends) is unaffected — this only +applies to test files themselves. + +## Shared setup-time data: Django fixtures, not bulk INSERT statements + +Some test data is inserted once in a test class's `setUp`/`setUpClass` and reused across multiple +test methods (e.g. the `seqrdb_gene_ids`/`gnomad_genomes` source-table rows in +`ClickhouseTest`/`ClickhouseSchemaTestCase`). That category of data should be loaded via Django's +fixture mechanism (JSON fixture files under a `fixtures/` dir, loaded with +`fixtures = [...]` on the `TestCase` subclass, or an explicit `call_command('loaddata', ...)`) — +not hand-written `INSERT INTO ... VALUES (...)` statements repeated/executed in `setUp`. + +This only applies to shared, setup-time reference data with a real backing model in +`clickhouse_search` (e.g. the source tables behind `seqrdb_gene_ids`/`gnomad_genomes`). Since +`loaddata` populates rows through the model layer, the dictionary itself still needs an explicit +`RELOAD DICTIONARY`/refresh afterward (dictionaries aren't themselves loaddata targets — their +backing source table is). Data that's specific to a single test method's body/assertions (not +shared across tests) stays as raw SQL executed via the Django connection cursor, per the prior +note — this fixture rule is specifically about *repeated* setup-time data. + +## Proposed change set + +| File | Change | +|---|---| +| `.github/workflows/pipeline-unit-tests.yml` | add a step creating a dummy `seqr_postgres_named_collection`; keep `CLICKHOUSE_DATABASE=test` | +| `loading_pipeline/pyproject.toml` | add `django`, `django-clickhouse-backend`, `pytest-django` dev deps; add `[tool.pytest.ini_options]` (`DJANGO_SETTINGS_MODULE`, `pythonpath`) | +| **new** `loading_pipeline/lib/test/clickhouse_django/settings.py` | minimal Django settings: one real `clickhouse` alias (single credential set), `clickhouse_write` mirrored onto it via `TEST: {MIRROR: 'clickhouse'}`, a dummy `default` placeholder (NAME only, no real connection), `clickhouse_backend` + `clickhouse_search` apps, `ClickHouseRouter`; doubles as the shadow `settings` module `clickhouse_search/backend/base.py` bare-imports | +| `lib/test/clickhouse_schema_testcase.py` | rewritten as the one shared base class: drop all manual DDL/SQL-file loading (schema now comes from real migrations via pytest-django), keep only the small external-sourced-dictionary overrides + per-test flush/truncate + staging-DB drop/create — all executed via `connections['clickhouse'].cursor()`; shared reference rows (e.g. gene-id/gnomAD source-table rows) loaded via Django `fixtures = [...]` instead of `INSERT` statements | +| **delete** `loading_pipeline/var/test/test_clickhouse_schema.sql` | no longer needed | +| **new** `loading_pipeline/lib/test/fixtures/*.json` | Django fixtures for the shared setup-time reference rows referenced above | +| `lib/misc/clickhouse_test.py` | `ClickhouseTest` extends the shared base instead of hand-building its own schema; keeps only its fixture-data seeding (via the new Django fixtures, not bulk `INSERT`) and parquet-writing setup; all `get_clickhouse_client()` calls in the test body replaced with the Django connection cursor | +| `bin/pipeline_worker_test.py`, `lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py` | no structural change (already extend the shared base) — swap their `get_clickhouse_client()` assertion calls to the Django connection cursor; cleanup of now-dead references (e.g. leftover `TEST_SCHEMA` constant) | +| `ops/repartition_clickhouse_grch38_snv_indel_test.py` | switch to the shared base for the real-schema DB lifecycle; keep its own synthetic `entries`-table `REPLACE`/dict + `REPARTITION_DATABASE_NAME` handling since that's not part of `clickhouse_search`'s schema; swap `get_clickhouse_client()` for the Django connection cursor | + +## Open risk / caveat + +No live ClickHouse instance is available in the sandbox used to write this plan, so some runtime +specifics can't be verified ahead of time: +- Whether `TRUNCATE` behaves as expected on materialized views (regular vs. refreshable). +- Exact Django test-DB naming interplay with `Env.CLICKHOUSE_DATABASE` (need a `TEST: {NAME: ...}` + override to avoid Django's default `test_` prefix mismatch). +- Whether `CREATE DICTIONARY ... SOURCE(POSTGRESQL(...))` DDL actually succeeds against a + ClickHouse server with only a dummy/unreachable named collection registered. +- Whether raw SQL params/tuple-list inserts (e.g. `INSERT INTO ... VALUES` with a Python list of + tuples, as `clickhouse_driver.Client.execute` supports today) work identically through + `cursor.execute()`/`cursor.executemany()` on the Django ClickHouse backend, or need reshaping. + +These should be shaken out against a real CI run / local ClickHouse instance once implemented. \ No newline at end of file From bdf279843193c66b1294801ec7de9076eacb20ea Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Wed, 12 Aug 2026 17:14:29 -0400 Subject: [PATCH 197/369] add pytest django and clean up iimports to separate clickhouse migratios from rest of app --- clickhouse_search/backend/table_models.py | 8 +++++ clickhouse_search/constants.py | 14 +++++---- .../0040_gnomadnoncodingconstraintdict.py | 12 +++---- clickhouse_search/models/search_models.py | 12 ++----- .../CLICKHOUSE_PYTEST_DJANGO_PLAN.md | 31 +++++++++++++------ loading_pipeline/pyproject.toml | 12 +++++++ 6 files changed, 57 insertions(+), 32 deletions(-) diff --git a/clickhouse_search/backend/table_models.py b/clickhouse_search/backend/table_models.py index 819ca96972..f82b9964b7 100644 --- a/clickhouse_search/backend/table_models.py +++ b/clickhouse_search/backend/table_models.py @@ -14,6 +14,14 @@ DICTIONARY_META_FIELDS = ['layout', 'lifetime_max', 'postgres_query', 'postgres_db', 'clickhouse_query_template'] +class Projection(Func): + + def __init__(self, name, select='*', order_by=None): + self.name = name + self.select = select + self.order_by = order_by + + class FixtureLoadableClickhouseModel(models.ClickhouseModel): def _save_table( diff --git a/clickhouse_search/constants.py b/clickhouse_search/constants.py index 0721e16955..2ebb829f03 100644 --- a/clickhouse_search/constants.py +++ b/clickhouse_search/constants.py @@ -1,5 +1,3 @@ -from seqr.models import Individual - MAX_VARIANTS = 10000 XPOS_SORT_KEY = 'xpos' @@ -7,10 +5,14 @@ PATHOGENICTY_HGMD_SORT_KEY = 'pathogenicity_hgmd' PRIORITIZED_GENE_SORT = 'prioritized_gene' -AFFECTED = Individual.AFFECTED_STATUS_AFFECTED -UNAFFECTED = Individual.AFFECTED_STATUS_UNAFFECTED -MALE_SEXES = Individual.MALE_SEXES -FEMALE_SEXES = Individual.FEMALE_SEXES +# Mirrors seqr.models.Individual.AFFECTED_STATUS_AFFECTED/AFFECTED_STATUS_UNAFFECTED/MALE_SEXES/ +# FEMALE_SEXES - duplicated here (rather than imported) so that this module, and anything that +# only needs these constants (e.g. clickhouse_search's migrations), doesn't have to import +# seqr.models. Keep in sync with seqr/models.py's Individual class if those ever change. +AFFECTED = 'A' +UNAFFECTED = 'N' +MALE_SEXES = ['M', 'XXY', 'XYY'] +FEMALE_SEXES = ['F', 'XXX', 'X0'] ALT_ALT = 'alt_alt' REF_REF = 'ref_ref' diff --git a/clickhouse_search/migrations/0040_gnomadnoncodingconstraintdict.py b/clickhouse_search/migrations/0040_gnomadnoncodingconstraintdict.py index 274fb30bf1..504dfd09c5 100644 --- a/clickhouse_search/migrations/0040_gnomadnoncodingconstraintdict.py +++ b/clickhouse_search/migrations/0040_gnomadnoncodingconstraintdict.py @@ -3,7 +3,7 @@ import clickhouse_backend.models import clickhouse_search.backend.engines import clickhouse_search.backend.fields -import clickhouse_search.models.search_models +import clickhouse_search.backend.table_models from django.db import migrations, models import django.db.models.deletion import django.db.models.manager @@ -419,7 +419,7 @@ class Migration(migrations.Migration): options={ 'db_table': 'GRCh38/SNV_INDEL/entries', 'engine': clickhouse_search.backend.engines.CollapsingMergeTree('sign', deduplicate_merge_projection_mode='rebuild', index_granularity=8192, order_by=('project_guid', 'family_guid', 'sample_type', 'is_gnomad_gt_5_percent', 'is_annotated_in_any_gene', 'key'), partition_by=['project_guid', 'partition_id']), - 'projection': clickhouse_search.models.search_models.Projection('xpos_projection', order_by='is_gnomad_gt_5_percent, is_annotated_in_any_gene, xpos'), + 'projection': clickhouse_search.backend.table_models.Projection('xpos_projection', order_by='is_gnomad_gt_5_percent, is_annotated_in_any_gene, xpos'), }, managers=[ ('objects', django.db.models.manager.Manager()), @@ -711,7 +711,7 @@ class Migration(migrations.Migration): 'db_table': 'GRCh37/SNV_INDEL/entries', 'abstract': False, 'engine': clickhouse_search.backend.engines.CollapsingMergeTree('sign', deduplicate_merge_projection_mode='rebuild', index_granularity=8192, order_by=('project_guid', 'family_guid', 'sample_type', 'is_gnomad_gt_5_percent', 'is_annotated_in_any_gene', 'key'), partition_by='project_guid'), - 'projection': clickhouse_search.models.search_models.Projection('xpos_projection', order_by='is_gnomad_gt_5_percent, is_annotated_in_any_gene, xpos'), + 'projection': clickhouse_search.backend.table_models.Projection('xpos_projection', order_by='is_gnomad_gt_5_percent, is_annotated_in_any_gene, xpos'), }, managers=[ ('objects', django.db.models.manager.Manager()), @@ -775,7 +775,7 @@ class Migration(migrations.Migration): 'db_table': 'GRCh38/MITO/entries', 'abstract': False, 'engine': clickhouse_search.backend.engines.CollapsingMergeTree('sign', deduplicate_merge_projection_mode='rebuild', index_granularity=8192, order_by=('project_guid', 'family_guid', 'sample_type', 'key'), partition_by='project_guid'), - 'projection': clickhouse_search.models.search_models.Projection('xpos_projection', order_by='xpos'), + 'projection': clickhouse_search.backend.table_models.Projection('xpos_projection', order_by='xpos'), }, managers=[ ('objects', django.db.models.manager.Manager()), @@ -820,7 +820,7 @@ class Migration(migrations.Migration): 'db_table': 'GRCh38/SV/entries', 'abstract': False, 'engine': clickhouse_search.backend.engines.CollapsingMergeTree('sign', deduplicate_merge_projection_mode='rebuild', index_granularity=8192, order_by=('project_guid', 'family_guid', 'key'), partition_by='project_guid'), - 'projection': clickhouse_search.models.search_models.Projection('xpos_projection', order_by='xpos'), + 'projection': clickhouse_search.backend.table_models.Projection('xpos_projection', order_by='xpos'), }, managers=[ ('objects', django.db.models.manager.Manager()), @@ -842,7 +842,7 @@ class Migration(migrations.Migration): 'db_table': 'GRCh38/GCNV/entries', 'abstract': False, 'engine': clickhouse_search.backend.engines.CollapsingMergeTree('sign', deduplicate_merge_projection_mode='rebuild', index_granularity=8192, order_by=('project_guid', 'family_guid', 'key'), partition_by='project_guid'), - 'projection': clickhouse_search.models.search_models.Projection('xpos_projection', order_by='xpos'), + 'projection': clickhouse_search.backend.table_models.Projection('xpos_projection', order_by='xpos'), }, managers=[ ('objects', django.db.models.manager.Manager()), diff --git a/clickhouse_search/models/search_models.py b/clickhouse_search/models/search_models.py index fb2653401c..f7d52cd17c 100644 --- a/clickhouse_search/models/search_models.py +++ b/clickhouse_search/models/search_models.py @@ -1,10 +1,10 @@ from clickhouse_backend import models -from django.db.models import ForeignKey, OneToOneField, Func, CASCADE +from django.db.models import ForeignKey, OneToOneField, CASCADE from clickhouse_search.backend.engines import CollapsingMergeTree, EmbeddedRocksDB from clickhouse_search.backend.fields import Enum8Field, NestedField, UInt32FieldDeltaCodecField, UInt64FieldDeltaCodecField, NamedTupleField, MaterializedUInt8Field from clickhouse_search.backend.functions import ArrayDistinct, ArrayFlatten, ArrayMin, ArrayMax -from clickhouse_search.backend.table_models import Dictionary, FixtureLoadableClickhouseModel +from clickhouse_search.backend.table_models import Dictionary, FixtureLoadableClickhouseModel, Projection from clickhouse_search.managers import EntriesManager, SvEntriesManager, SvVariantsQuerySet, VariantsQuerySet, \ VariantDetailsQuerySet from clickhouse_search.models.reference_data_models import GnomadNonCodingConstraintDict, BaseSpliceAi, \ @@ -15,14 +15,6 @@ from settings import CLICKHOUSE_IN_MEMORY_DIR, CLICKHOUSE_DATA_DIR -class Projection(Func): - - def __init__(self, name, select='*', order_by=None): - self.name = name - self.select = select - self.order_by = order_by - - class BaseVariants(FixtureLoadableClickhouseModel): CONSEQUENCE_TERMS = [(1, 'transcript_ablation'), (2, 'splice_acceptor_variant'), (3, 'splice_donor_variant'), (4, 'stop_gained'), (5, 'frameshift_variant'), (6, 'stop_lost'), (7, 'start_lost'), (8, 'inframe_insertion'), (9, 'inframe_deletion'), (10, 'missense_variant'), (11, 'protein_altering_variant'), (12, 'splice_donor_5th_base_variant'), (13, 'splice_region_variant'), (14, 'splice_donor_region_variant'), (15, 'splice_polypyrimidine_tract_variant'), (16, 'incomplete_terminal_codon_variant'), (17, 'start_retained_variant'), (18, 'stop_retained_variant'), (19, 'synonymous_variant'), (20, 'coding_sequence_variant'), (21, 'mature_miRNA_variant'), (22, '5_prime_UTR_variant'), (23, '3_prime_UTR_variant'), (24, 'non_coding_transcript_exon_variant'), (25, 'intron_variant'), (26, 'NMD_transcript_variant'), (27, 'non_coding_transcript_variant'), (28, 'coding_transcript_variant'), (29, 'upstream_gene_variant'), (30, 'downstream_gene_variant'), (31, 'intergenic_variant'), (32, 'sequence_variant')] ANNOTATION_CONSTANTS = { diff --git a/loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_PLAN.md b/loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_PLAN.md index bee7837170..1afa59f8d5 100644 --- a/loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_PLAN.md +++ b/loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_PLAN.md @@ -30,22 +30,31 @@ to depend on from `loading_pipeline`'s minimal env. Per explicit direction: the settings module must configure **one** ClickHouse connection with **one** set of credentials — not the production split of a read-only `clickhouse` alias plus a -privileged `clickhouse_write` alias. `DATABASES` will define a single alias (`clickhouse`) using -one writer-capable credential (needed anyway, since migrations and test data inserts require write +privileged `clickhouse_write` alias. `DATABASES` will define a single real alias using one +writer-capable credential (needed anyway, since migrations and test data inserts require write access). +That real alias must be named `clickhouse_write`, not `clickhouse`: `ClickHouseRouter.allow_migrate` +(`clickhouse_search/models/__init__.py`) hardcodes `db == 'clickhouse_write'` for the +`clickhouse_search` app, so only an alias literally named `clickhouse_write` is allowed to have +migrations applied to it. + Nuance to account for: `clickhouse_search/backend/base.py`'s `_dictionary_sql` looks up `DATABASES['clickhouse_write']['NAME']` (for ClickHouse-sourced dictionaries with a `clickhouse_query_template`) and `DATABASES[postgres_db]['NAME']` (default alias `'default'`, for Postgres-sourced dictionaries) purely to embed a database *name string* into generated DDL — not to open a second real connection. To keep this working without standing up a second live connection: -- Give `'clickhouse_write'` a `TEST: {'MIRROR': 'clickhouse'}` config, so Django reuses the - `clickhouse` alias's actual test database instead of creating/tearing down a second one, while - the key is still present for the `NAME` lookup. +- Give `'clickhouse'` a `TEST: {'MIRROR': 'clickhouse_write'}` config, so Django reuses the + `clickhouse_write` alias's actual test database instead of creating/tearing down a second one, + while the key is still present for the `NAME` lookup (used only by `backend/base.py`, not by our + own test code). - Give `'default'` a placeholder entry (e.g. `ENGINE: 'django.db.backends.dummy'`) purely so `DATABASES['default']['NAME']` resolves to a string — nothing in `loading_pipeline`'s tests actually connects to it, since there's no Postgres in this CI job. +Test code (and the shared base class) uses `connections['clickhouse_write']` — the one alias +Django actually creates/migrates a real test database for. + ## Inventory of every ClickHouse-touching test 1. **`lib/misc/clickhouse_test.py`** (`ClickhouseTest`) — hand-rolls ~250 lines of `CREATE @@ -85,9 +94,9 @@ faking the whole schema). Every test currently calls `get_clickhouse_client()` (a raw `clickhouse_driver.Client`, see `lib/misc/clickhouse.py`) to run setup/assertion SQL directly. Once the schema is Django-managed, tests should execute their raw SQL through Django's own DB connection instead of a separate -`clickhouse_driver.Client` instance — i.e. `django.db.connections['clickhouse'].cursor()` (the one -alias defined per "Single connection / single set of credentials only" above), calling -`cursor.execute(sql, params)` / `cursor.fetchall()`. +`clickhouse_driver.Client` instance — i.e. `django.db.connections['clickhouse_write'].cursor()` +(the one real alias defined per "Single connection / single set of credentials only" above), +calling `cursor.execute(sql, params)` / `cursor.fetchall()`. This is purely a *client* swap for test code — tests keep writing raw SQL strings (no ORM/model queries), just executed via the Django connection so the tests exercise the same connection @@ -117,10 +126,12 @@ note — this fixture rule is specifically about *repeated* setup-time data. | File | Change | |---|---| -| `.github/workflows/pipeline-unit-tests.yml` | add a step creating a dummy `seqr_postgres_named_collection`; keep `CLICKHOUSE_DATABASE=test` | +| `clickhouse_search/models/search_models.py`, `clickhouse_search/backend/table_models.py`, `clickhouse_search/migrations/0040_gnomadnoncodingconstraintdict.py` | move `Projection` from `search_models.py` to `backend/table_models.py`; update the migration's import accordingly (✅ done) | +| `clickhouse_search/constants.py` | duplicate 4 constants out of `seqr.models.Individual` instead of importing it (✅ done) | +| `.github/workflows/pipeline-unit-tests.yml` | keep `CLICKHOUSE_DATABASE=test`; no named-collection step needed anymore (no Postgres-sourced dictionaries are reachable via the minimal settings module in the first place - see note below) | | `loading_pipeline/pyproject.toml` | add `django`, `django-clickhouse-backend`, `pytest-django` dev deps; add `[tool.pytest.ini_options]` (`DJANGO_SETTINGS_MODULE`, `pythonpath`) | | **new** `loading_pipeline/lib/test/clickhouse_django/settings.py` | minimal Django settings: one real `clickhouse` alias (single credential set), `clickhouse_write` mirrored onto it via `TEST: {MIRROR: 'clickhouse'}`, a dummy `default` placeholder (NAME only, no real connection), `clickhouse_backend` + `clickhouse_search` apps, `ClickHouseRouter`; doubles as the shadow `settings` module `clickhouse_search/backend/base.py` bare-imports | -| `lib/test/clickhouse_schema_testcase.py` | rewritten as the one shared base class: drop all manual DDL/SQL-file loading (schema now comes from real migrations via pytest-django), keep only the small external-sourced-dictionary overrides + per-test flush/truncate + staging-DB drop/create — all executed via `connections['clickhouse'].cursor()`; shared reference rows (e.g. gene-id/gnomAD source-table rows) loaded via Django `fixtures = [...]` instead of `INSERT` statements | +| `lib/test/clickhouse_schema_testcase.py` | rewritten as the one shared base class: drop all manual DDL/SQL-file loading (schema now comes from real migrations via pytest-django), keep only the small external-sourced-dictionary overrides + per-test flush/truncate + staging-DB drop/create — all executed via `connections['clickhouse_write'].cursor()`; shared reference rows (e.g. gene-id/gnomAD source-table rows) loaded via Django `fixtures = [...]` instead of `INSERT` statements | | **delete** `loading_pipeline/var/test/test_clickhouse_schema.sql` | no longer needed | | **new** `loading_pipeline/lib/test/fixtures/*.json` | Django fixtures for the shared setup-time reference rows referenced above | | `lib/misc/clickhouse_test.py` | `ClickhouseTest` extends the shared base instead of hand-building its own schema; keeps only its fixture-data seeding (via the new Django fixtures, not bulk `INSERT`) and parquet-writing setup; all `get_clickhouse_client()` calls in the test body replaced with the Django connection cursor | diff --git a/loading_pipeline/pyproject.toml b/loading_pipeline/pyproject.toml index f06f1fc691..f024c6d9f0 100644 --- a/loading_pipeline/pyproject.toml +++ b/loading_pipeline/pyproject.toml @@ -33,6 +33,9 @@ dev = [ "coverage>=7.2.2", "pytest>=7.0.0", "pytest-cov>=4.0.0", + "pytest-django>=4.8.0", + "django==4.2.30", # matches the main seqr app's pinned version + "django-clickhouse-backend==1.6", # matches the main seqr app's pinned version "responses>=0.23.1", "ruff==0.11.3", "shellcheck-py>=0.10.0", @@ -43,6 +46,15 @@ dev = [ [tool.uv] exclude-dependencies = ["psycopg2-binary", "psycopg2"] +[tool.pytest.ini_options] +# `..` puts the repo root (which holds `clickhouse_search`/`clickhouse_backend`) on sys.path. +# `lib/test/clickhouse_django` holds our minimal settings module, which needs to be importable +# both as `DJANGO_SETTINGS_MODULE` and as the bare `settings` module that +# `clickhouse_search/backend/base.py` imports directly; pytest prepends `pythonpath` entries to +# sys.path, so it's found ahead of the (much heavier) repo-root `settings.py`. +pythonpath = ["..", "lib/test/clickhouse_django"] +DJANGO_SETTINGS_MODULE = "settings" + [tool.setuptools] include-package-data = true From 7dcb6b1167831449ac63225a4333b5df8966a258 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 10:20:30 -0400 Subject: [PATCH 198/369] add tests ettings module --- .../lib/test/clickhouse_django/settings.py | 118 ++++++++++++++++++ 1 file changed, 118 insertions(+) create mode 100644 loading_pipeline/lib/test/clickhouse_django/settings.py diff --git a/loading_pipeline/lib/test/clickhouse_django/settings.py b/loading_pipeline/lib/test/clickhouse_django/settings.py new file mode 100644 index 0000000000..b78830ece0 --- /dev/null +++ b/loading_pipeline/lib/test/clickhouse_django/settings.py @@ -0,0 +1,118 @@ +"""Minimal Django settings for standing up the `clickhouse_search` schema in tests. + +This module is intentionally NOT the main seqr app's `settings.py` — `loading_pipeline` has its +own, much smaller, dependency footprint and only needs enough Django configuration to run +`clickhouse_search`'s migrations against a test ClickHouse database. + +It is deliberately placed in its own directory that gets prepended to `sys.path` via pytest's +`pythonpath` option (see `pyproject.toml`), for two reasons: + 1. It's used as `DJANGO_SETTINGS_MODULE`. + 2. `clickhouse_search/backend/base.py` does a bare `from settings import ...` (not + `django.conf.settings`), so a top-level module literally named `settings` has to be + importable on `sys.path` and resolve to *this* module rather than the main app's + `settings.py` (which pulls in postgres/guardian/social_django/etc. that `loading_pipeline` + doesn't depend on). + +Only a single real ClickHouse connection/credential set is configured, on the `clickhouse_write` +alias. `ClickHouseRouter.allow_migrate` (in `clickhouse_search/models/__init__.py`) hardcodes +`db == 'clickhouse_write'` for the `clickhouse_search` app, so migrations must run against an +alias literally named `clickhouse_write` - that's the one Django actually creates/migrates a real +test database for. `clickhouse` and `default` are present only because +`clickhouse_search/backend/base.py` looks up `DATABASES['clickhouse_write']['NAME']` / +`DATABASES['default']['NAME']` to embed a database name string into generated dictionary DDL - not +because either needs its own real connection: + - `clickhouse` mirrors the `clickhouse_write` alias's test database (`TEST: {'MIRROR': ...}`), + so Django doesn't create/destroy a second real test database for it. + - `default` is a `dummy` backend entry - it's never actually opened. pytest-django only calls + `create_test_db()` for aliases a given test's `databases` attribute names (see + `pytest_django.fixtures._get_databases_for_setup`); it does not unconditionally create every + alias in `DATABASES`. As long as every `TestCase` subclass in this suite declares + `databases = ['clickhouse_write']` (per the shared base class), `default` is never touched, so + the dummy backend never needs to support real connections - only `DATABASES['default']['NAME']` + ever gets read, purely as a string. + +Only `clickhouse_search`'s own migrations are permitted to run anywhere: `DATABASE_ROUTERS` +appends a small catch-all router (`_NoOtherAppMigrationsRouter`, below) that vetoes migrations for +every app *other* than `clickhouse_search`. Without it, Django's default routing would try to +migrate `clickhouse_search`'s (undeclared, but still `INSTALLED_APPS`-adjacent) dependencies onto +`default`, which would fail against the dummy backend - `clickhouse_search`'s migrations use +ClickHouse-only DDL/field types that don't apply to any other app. + +`clickhouse_search`'s migration `0040_gnomadnoncodingconstraintdict.py` has a +`conditionally_refresh_reference_dataset` step that skips a live network call +(`requests.post(...)`) when `DATABASES['default']['NAME'].startswith('test_')`. That module-level +`DATABASES` reference is the plain dict below, not a Django-test-remapped one (since `default` is +never created/mutated by the test runner, per above), so `default`'s `NAME` is just set directly to +a literal `test_`-prefixed string to keep that guard working and avoid the network call during test +runs. +""" + +import os + +INSTALLED_APPS = [ + 'clickhouse_backend', + 'clickhouse_search', +] + + +class _NoOtherAppMigrationsRouter: + """Prevents any app other than `clickhouse_search` from having migrations applied anywhere. + + `clickhouse_search`'s modules pull in a handful of other apps transitively (see module + docstring); this keeps those apps' own schemas from ever being created against the throwaway + `default` dummy database (which can't support them; they're never needed here anyway). + """ + + @staticmethod + def allow_migrate(db, app_label, model_name=None, **hints): # noqa: ARG004 + if app_label == 'clickhouse_search': + return None # defer to ClickHouseRouter + return False + + +DATABASE_ROUTERS = [ + 'clickhouse_search.models.ClickHouseRouter', + 'settings._NoOtherAppMigrationsRouter', +] + +USE_TZ = True +SECRET_KEY = 'loading-pipeline-test' # noqa: S105 +DEPLOYMENT_TYPE = os.environ.get('DEPLOYMENT_TYPE', 'dev') +PIPELINE_RUNNER_SERVER = os.environ.get('PIPELINE_RUNNER_SERVER', 'http://localhost') +CLICKHOUSE_IN_MEMORY_DIR = os.environ.get('CLICKHOUSE_IN_MEMORY_DIR', '/tmp') # noqa: S108 +CLICKHOUSE_DATA_DIR = os.environ.get('CLICKHOUSE_DATA_DIR', '/tmp') # noqa: S108 + +CLICKHOUSE_WRITER_USER = os.environ.get('CLICKHOUSE_WRITER_USER', 'default') +CLICKHOUSE_WRITER_PASSWORD = os.environ.get('CLICKHOUSE_WRITER_PASSWORD', 'default_password') +CLICKHOUSE_DATABASE_NAME = os.environ.get('CLICKHOUSE_DATABASE', 'seqr') + +CLICKHOUSE_DB_CONFIG = { + 'ENGINE': 'clickhouse_search.backend', + 'NAME': CLICKHOUSE_DATABASE_NAME, + 'USER': CLICKHOUSE_WRITER_USER, + 'PASSWORD': CLICKHOUSE_WRITER_PASSWORD, + 'HOST': os.environ.get('CLICKHOUSE_SERVICE_HOSTNAME', 'localhost'), + 'PORT': int(os.environ.get('CLICKHOUSE_SERVICE_PORT', '9000')), + 'OPTIONS': { + 'settings': { + 'use_client_time_zone': False, + }, + }, + # Avoid Django's default `test_` prefix so the schema lands in the database name that + # `loading_pipeline.lib.core.environment.Env.CLICKHOUSE_DATABASE` already expects. + 'TEST': { + 'NAME': CLICKHOUSE_DATABASE_NAME, + }, +} + +DATABASES = { + 'clickhouse_write': CLICKHOUSE_DB_CONFIG, + 'clickhouse': { + **CLICKHOUSE_DB_CONFIG, + 'TEST': {'MIRROR': 'clickhouse_write'}, + }, + 'default': { + 'ENGINE': 'django.db.backends.dummy', + 'NAME': 'test_default_unused', + }, +} From fb68792fb69f08a3ac24b88a215a9ac3b614bb6f Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 10:48:16 -0400 Subject: [PATCH 199/369] clean up seqr dependencies and add stub application --- clickhouse_search/backend/table_models.py | 17 ++ .../0040_gnomadnoncodingconstraintdict.py | 2 +- .../models/reference_data_models.py | 14 -- .../test/clickhouse_django/seqr/__init__.py | 28 +++ ...ve_project_custom_reference_populations.py | 15 ++ .../seqr/migrations/__init__.py | 0 .../clickhouse_django/seqr/utils/__init__.py | 0 .../seqr/utils/logging_utils.py | 32 ++++ .../lib/test/clickhouse_django/settings.py | 48 +++-- loading_pipeline/pyproject.toml | 16 +- loading_pipeline/uv.lock | 170 +++++++++++++----- 11 files changed, 265 insertions(+), 77 deletions(-) create mode 100644 loading_pipeline/lib/test/clickhouse_django/seqr/__init__.py create mode 100644 loading_pipeline/lib/test/clickhouse_django/seqr/migrations/0001_squashed_0067_remove_project_custom_reference_populations.py create mode 100644 loading_pipeline/lib/test/clickhouse_django/seqr/migrations/__init__.py create mode 100644 loading_pipeline/lib/test/clickhouse_django/seqr/utils/__init__.py create mode 100644 loading_pipeline/lib/test/clickhouse_django/seqr/utils/logging_utils.py diff --git a/clickhouse_search/backend/table_models.py b/clickhouse_search/backend/table_models.py index f82b9964b7..b9613d9a56 100644 --- a/clickhouse_search/backend/table_models.py +++ b/clickhouse_search/backend/table_models.py @@ -1,9 +1,11 @@ from clickhouse_backend import models from django.db import connections from django.db.models import Func +import requests from clickhouse_search.backend.fields import NamedTupleField from seqr.utils.logging_utils import SeqrLogger +from settings import DATABASES, PIPELINE_RUNNER_SERVER logger = SeqrLogger(__name__) @@ -14,6 +16,21 @@ DICTIONARY_META_FIELDS = ['layout', 'lifetime_max', 'postgres_query', 'postgres_db', 'clickhouse_query_template'] +def conditionally_refresh_reference_dataset(reference_dataset: str): + # NB: lives here, rather than in models/reference_data_models.py, specifically so that + # migrations depending on it don't need to import the (much heavier) live model definitions + # module - this is the only thing migrations need from it. + def inner(apps, schema_editor): + if DATABASES['default']['NAME'].startswith('test_'): + return + requests.post( # pragma: no cover + f"{PIPELINE_RUNNER_SERVER}/refresh_clickhouse_reference_dataset_enqueue", + json={"reference_dataset": reference_dataset}, + timeout=60, + ) + return inner + + class Projection(Func): def __init__(self, name, select='*', order_by=None): diff --git a/clickhouse_search/migrations/0040_gnomadnoncodingconstraintdict.py b/clickhouse_search/migrations/0040_gnomadnoncodingconstraintdict.py index 504dfd09c5..9e31b51325 100644 --- a/clickhouse_search/migrations/0040_gnomadnoncodingconstraintdict.py +++ b/clickhouse_search/migrations/0040_gnomadnoncodingconstraintdict.py @@ -9,7 +9,7 @@ import django.db.models.manager import os -from clickhouse_search.models.reference_data_models import conditionally_refresh_reference_dataset +from clickhouse_search.backend.table_models import conditionally_refresh_reference_dataset from settings import CLICKHOUSE_IN_MEMORY_DIR, CLICKHOUSE_DATA_DIR CLICKHOUSE_AC_EXCLUDED_PROJECT_GUIDS = os.environ.get( diff --git a/clickhouse_search/models/reference_data_models.py b/clickhouse_search/models/reference_data_models.py index 783ff4934e..9f2fe6a4a5 100644 --- a/clickhouse_search/models/reference_data_models.py +++ b/clickhouse_search/models/reference_data_models.py @@ -1,6 +1,5 @@ from clickhouse_backend import models from django.db.models import ForeignKey, PROTECT -import requests from clickhouse_search.backend.engines import Join from clickhouse_search.backend.fields import Enum8Field, NestedField, UInt32FieldDeltaCodecField, DictKeyForeignKey @@ -8,19 +7,6 @@ RefreshableMaterializedView, RefreshableMaterializedViewMeta from clickhouse_search.constants import CLINVAR_ASSERTIONS, CLINVAR_PATHOGENICITIES from seqr.utils.xpos_utils import CHROMOSOME_CHOICES -from settings import DATABASES, PIPELINE_RUNNER_SERVER - - -def conditionally_refresh_reference_dataset(reference_dataset: str): - def inner(apps, schema_editor): - if DATABASES['default']['NAME'].startswith('test_'): - return - requests.post( # pragma: no cover - f"{PIPELINE_RUNNER_SERVER}/refresh_clickhouse_reference_dataset_enqueue", - json={"reference_dataset": reference_dataset}, - timeout=60, - ) - return inner def _all_variants_to_seqr_source_sql(reference_genome, dataset_type): diff --git a/loading_pipeline/lib/test/clickhouse_django/seqr/__init__.py b/loading_pipeline/lib/test/clickhouse_django/seqr/__init__.py new file mode 100644 index 0000000000..1a8bce5028 --- /dev/null +++ b/loading_pipeline/lib/test/clickhouse_django/seqr/__init__.py @@ -0,0 +1,28 @@ +"""Minimal stub of the main app's `seqr` package, for `loading_pipeline`'s tests only. + +`clickhouse_search` (the source of truth for the ClickHouse schema, migrated via real Django +migrations in these tests - see `lib/test/clickhouse_django/settings.py`) has a small number of +genuine, unavoidable dependencies on the `seqr` app: + - `clickhouse_search/backend/table_models.py` (needed to load `clickhouse_search`'s migrations) + imports `seqr.utils.logging_utils.SeqrLogger` - a tiny, dependency-free logging wrapper. + - `clickhouse_search`'s migration `0040_gnomadnoncodingconstraintdict.py` declares a + cross-app migration dependency on a specific `seqr` migration (used only for historical + migration-ordering purposes, not because it touches any `seqr` table). + +Neither of these needs the *real* `seqr` app - which imports `django-guardian`, +`django.contrib.postgres`, `social_django`, etc. at module level via `seqr/models.py` - all +dependencies `loading_pipeline`'s minimal test environment intentionally does not install. + +This package is placed in `lib/test/clickhouse_django/`, which pytest's `pythonpath` option (see +`pyproject.toml`) puts ahead of the repo root on `sys.path`, so `import seqr` resolves to *this* +lightweight stand-in instead of the real app - the same shadowing trick used for the bare +`settings` module `clickhouse_search/backend/base.py` imports directly. + +`clickhouse_search`'s live model definitions (`models/search_models.py`, +`models/reference_data_models.py`, which pull in more of `seqr`, e.g. `seqr.models.Dataset` and +`seqr.utils.xpos_utils.CHROMOSOME_CHOICES`) are deliberately NOT needed here: `loading_pipeline` +never imports them (it only ever talks to ClickHouse via raw SQL - see +`lib/test/clickhouse_schema_testcase.py`), and neither does applying `clickhouse_search`'s +migrations (which are self-contained frozen schema snapshots, not built from the live model +classes at apply time). If that ever changes, this stub will need to grow accordingly. +""" diff --git a/loading_pipeline/lib/test/clickhouse_django/seqr/migrations/0001_squashed_0067_remove_project_custom_reference_populations.py b/loading_pipeline/lib/test/clickhouse_django/seqr/migrations/0001_squashed_0067_remove_project_custom_reference_populations.py new file mode 100644 index 0000000000..985cda6945 --- /dev/null +++ b/loading_pipeline/lib/test/clickhouse_django/seqr/migrations/0001_squashed_0067_remove_project_custom_reference_populations.py @@ -0,0 +1,15 @@ +# No-op stand-in for the real seqr app's migration of the same name. +# +# `clickhouse_search`'s migration `0040_gnomadnoncodingconstraintdict.py` declares a cross-app +# migration dependency on exactly this (app_label, name) pair, purely for historical +# migration-ordering reasons - not because it touches any table this migration would create. +# Django's migration graph builder requires a *named* dependency (unlike `__first__`/`__latest__`) +# to exist as a real node in the graph even for an otherwise-unmigrated app, so this file exists +# solely to satisfy that graph edge. See `seqr/__init__.py` in this stub package for more context. +from django.db import migrations + + +class Migration(migrations.Migration): + initial = True + dependencies = [] + operations = [] diff --git a/loading_pipeline/lib/test/clickhouse_django/seqr/migrations/__init__.py b/loading_pipeline/lib/test/clickhouse_django/seqr/migrations/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/loading_pipeline/lib/test/clickhouse_django/seqr/utils/__init__.py b/loading_pipeline/lib/test/clickhouse_django/seqr/utils/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/loading_pipeline/lib/test/clickhouse_django/seqr/utils/logging_utils.py b/loading_pipeline/lib/test/clickhouse_django/seqr/utils/logging_utils.py new file mode 100644 index 0000000000..ff8b9f242c --- /dev/null +++ b/loading_pipeline/lib/test/clickhouse_django/seqr/utils/logging_utils.py @@ -0,0 +1,32 @@ +"""Stub of `seqr.utils.logging_utils` - see `seqr/__init__.py` in this stub package for why. + +`SeqrLogger` is mirrored verbatim from the real `seqr/utils/logging_utils.py` (it's already +dependency-free: stdlib `logging` plus this app's own `settings.DEPLOYMENT_TYPE`). Only +`SeqrLogger` is reproduced, since it's the only symbol `clickhouse_search` actually imports from +this module (`clickhouse_search/backend/table_models.py`). +""" + +import logging +from typing import Optional + + +class SeqrLogger(object): + + def __init__(self, name: Optional[str] = None) -> None: + """Custom logger which requires user metadata to be included in the log.""" + self._logger = logging.getLogger(name) + + def _log(self, level, message, user, **kwargs): + self._logger.log(level, message, extra=dict(user=user, **kwargs)) + + def debug(self, *args, **kwargs): + self._log(logging.DEBUG, *args, **kwargs) + + def info(self, *args, **kwargs): + self._log(logging.INFO, *args, **kwargs) + + def warning(self, *args, **kwargs): + self._log(logging.WARNING, *args, **kwargs) + + def error(self, *args, **kwargs): + self._log(logging.ERROR, *args, **kwargs) diff --git a/loading_pipeline/lib/test/clickhouse_django/settings.py b/loading_pipeline/lib/test/clickhouse_django/settings.py index b78830ece0..222f30228c 100644 --- a/loading_pipeline/lib/test/clickhouse_django/settings.py +++ b/loading_pipeline/lib/test/clickhouse_django/settings.py @@ -17,19 +17,21 @@ alias. `ClickHouseRouter.allow_migrate` (in `clickhouse_search/models/__init__.py`) hardcodes `db == 'clickhouse_write'` for the `clickhouse_search` app, so migrations must run against an alias literally named `clickhouse_write` - that's the one Django actually creates/migrates a real -test database for. `clickhouse` and `default` are present only because +test database for. `clickhouse`, `default`, and `reference_data` are present only because `clickhouse_search/backend/base.py` looks up `DATABASES['clickhouse_write']['NAME']` / -`DATABASES['default']['NAME']` to embed a database name string into generated dictionary DDL - not -because either needs its own real connection: +`DATABASES[postgres_db]['NAME']` (`postgres_db` defaults to `'default'`, but `GeneIdDict`/ +`OmimDict` in `clickhouse_search/models/postgres_dicts.py` declare `postgres_db = 'reference_data'` +instead) to embed a database name string into generated dictionary DDL - not because any of them +needs its own real connection: - `clickhouse` mirrors the `clickhouse_write` alias's test database (`TEST: {'MIRROR': ...}`), so Django doesn't create/destroy a second real test database for it. - - `default` is a `dummy` backend entry - it's never actually opened. pytest-django only calls - `create_test_db()` for aliases a given test's `databases` attribute names (see - `pytest_django.fixtures._get_databases_for_setup`); it does not unconditionally create every - alias in `DATABASES`. As long as every `TestCase` subclass in this suite declares - `databases = ['clickhouse_write']` (per the shared base class), `default` is never touched, so - the dummy backend never needs to support real connections - only `DATABASES['default']['NAME']` - ever gets read, purely as a string. + - `default` and `reference_data` are `dummy` backend entries - neither is ever actually opened. + pytest-django only calls `create_test_db()` for aliases a given test's `databases` attribute + names (see `pytest_django.fixtures._get_databases_for_setup`); it does not unconditionally + create every alias in `DATABASES`. As long as every `TestCase` subclass in this suite declares + `databases = ['clickhouse_write']` (per the shared base class), neither is ever touched, so the + dummy backend never needs to support real connections - only their `NAME` values ever get + read, purely as strings. Only `clickhouse_search`'s own migrations are permitted to run anywhere: `DATABASE_ROUTERS` appends a small catch-all router (`_NoOtherAppMigrationsRouter`, below) that vetoes migrations for @@ -51,6 +53,10 @@ INSTALLED_APPS = [ 'clickhouse_backend', + # A stub, not the real `seqr` app - see `seqr/__init__.py` (in this same directory, shadowing + # the real app on sys.path) for why `clickhouse_search` needs *an* app named `seqr` present + # at all. + 'seqr', 'clickhouse_search', ] @@ -79,8 +85,12 @@ def allow_migrate(db, app_label, model_name=None, **hints): # noqa: ARG004 SECRET_KEY = 'loading-pipeline-test' # noqa: S105 DEPLOYMENT_TYPE = os.environ.get('DEPLOYMENT_TYPE', 'dev') PIPELINE_RUNNER_SERVER = os.environ.get('PIPELINE_RUNNER_SERVER', 'http://localhost') -CLICKHOUSE_IN_MEMORY_DIR = os.environ.get('CLICKHOUSE_IN_MEMORY_DIR', '/tmp') # noqa: S108 -CLICKHOUSE_DATA_DIR = os.environ.get('CLICKHOUSE_DATA_DIR', '/tmp') # noqa: S108 +# These back separate `EmbeddedRocksDB`-engine tables (e.g. `annotations_memory` vs +# `annotations_disk`) and must resolve to different paths - the same path for both causes a +# RocksDB file-lock collision between those tables ("lock hold by current process") the moment +# migrations try to create both. +CLICKHOUSE_IN_MEMORY_DIR = os.environ.get('CLICKHOUSE_IN_MEMORY_DIR', '/tmp/loading_pipeline_test_clickhouse_in_memory') # noqa: S108 +CLICKHOUSE_DATA_DIR = os.environ.get('CLICKHOUSE_DATA_DIR', '/tmp/loading_pipeline_test_clickhouse_data') # noqa: S108 CLICKHOUSE_WRITER_USER = os.environ.get('CLICKHOUSE_WRITER_USER', 'default') CLICKHOUSE_WRITER_PASSWORD = os.environ.get('CLICKHOUSE_WRITER_PASSWORD', 'default_password') @@ -102,6 +112,12 @@ def allow_migrate(db, app_label, model_name=None, **hints): # noqa: ARG004 # `loading_pipeline.lib.core.environment.Env.CLICKHOUSE_DATABASE` already expects. 'TEST': { 'NAME': CLICKHOUSE_DATABASE_NAME, + # Django assumes any alias whose test-db signature differs from `default`'s implicitly + # depends on `default` (for cross-DB migration ordering) unless told otherwise. Since our + # tests only ever request `databases = ['clickhouse_write']` - `default` is never created + # - that implicit dependency can never resolve, raising "Circular dependency in + # TEST[DEPENDENCIES]". There are no real cross-database dependencies here, so declare none. + 'DEPENDENCIES': [], }, } @@ -115,4 +131,12 @@ def allow_migrate(db, app_label, model_name=None, **hints): # noqa: ARG004 'ENGINE': 'django.db.backends.dummy', 'NAME': 'test_default_unused', }, + # `GeneIdDict`/`OmimDict` (`clickhouse_search/models/postgres_dicts.py`) declare + # `postgres_db = 'reference_data'` instead of the implicit `default` - same dummy-backend + # treatment as `default` above, needed purely so `DATABASES['reference_data']['NAME']` + # resolves to a string for `_dictionary_sql`'s generated DDL. + 'reference_data': { + 'ENGINE': 'django.db.backends.dummy', + 'NAME': 'test_reference_data_unused', + }, } diff --git a/loading_pipeline/pyproject.toml b/loading_pipeline/pyproject.toml index f024c6d9f0..20df951a06 100644 --- a/loading_pipeline/pyproject.toml +++ b/loading_pipeline/pyproject.toml @@ -8,7 +8,7 @@ dependencies = [ "gnomad==0.8.0", "aiofiles==24.1.0", "pydantic==2.8.2", - "clickhouse-driver==0.2.9", + "clickhouse-driver==0.2.10", # matches main seqr app's pinned version and django-clickhouse-backend's requirement "slacker==0.14.0", "ipykernel==6.29.2", # matches pinned version in hail init_notebook.py "jupyter-console==6.6.3", # matches pinned version in hail init_notebook.py @@ -50,10 +50,18 @@ exclude-dependencies = ["psycopg2-binary", "psycopg2"] # `..` puts the repo root (which holds `clickhouse_search`/`clickhouse_backend`) on sys.path. # `lib/test/clickhouse_django` holds our minimal settings module, which needs to be importable # both as `DJANGO_SETTINGS_MODULE` and as the bare `settings` module that -# `clickhouse_search/backend/base.py` imports directly; pytest prepends `pythonpath` entries to -# sys.path, so it's found ahead of the (much heavier) repo-root `settings.py`. -pythonpath = ["..", "lib/test/clickhouse_django"] +# `clickhouse_search/backend/base.py` imports directly. pytest builds sys.path by inserting each +# `pythonpath` entry at position 0 in *reverse* list order, which nets out to sys.path holding +# them in the same order given here - so `lib/test/clickhouse_django` must come first, ahead of +# `..`, or `import settings` resolves to the much heavier repo-root `settings.py` instead of ours. +pythonpath = ["lib/test/clickhouse_django", ".."] DJANGO_SETTINGS_MODULE = "settings" +# pytest-django's `manage.py` auto-discovery walks up from cwd and, finding the main seqr app's +# `manage.py` at the repo root, unconditionally inserts that directory at sys.path[0] - which +# shadows our `settings` module with the main app's much heavier `settings.py`, undoing the +# `pythonpath` ordering above. Disable it; our own `pythonpath` entries are all the path +# configuration this suite needs. +django_find_project = false [tool.setuptools] include-package-data = true diff --git a/loading_pipeline/uv.lock b/loading_pipeline/uv.lock index eba2806f11..d07ecefb95 100644 --- a/loading_pipeline/uv.lock +++ b/loading_pipeline/uv.lock @@ -192,6 +192,15 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/81/29/5ecc3a15d5a33e31b26c11426c45c501e439cb865d0bff96315d86443b78/appnope-0.1.4-py2.py3-none-any.whl", hash = "sha256:502575ee11cd7a28c0205f379b525beefebab9d161b7c964670864014ed7213c", size = 4321, upload-time = "2024-02-06T09:43:09.663Z" }, ] +[[package]] +name = "asgiref" +version = "3.12.1" +source = { registry = "https://pypi.org/simple" } +sdist = { url = "https://files.pythonhosted.org/packages/e6/26/3b59f2bdae5f640389becb1f673cded775287f5fc4f816309d9ca9a3f93d/asgiref-3.12.1.tar.gz", hash = "sha256:59dcb51c272ad209d59bed5708a64a333083e86017d7fcdd67498eeab7784340", size = 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'3.12'", ] dependencies = [ - { name = "google-auth", marker = "python_full_version < '3.14'" }, - { name = "googleapis-common-protos", marker = "python_full_version < '3.14'" }, - { name = "proto-plus", marker = "python_full_version < '3.14'" }, - { name = "protobuf", marker = "python_full_version < '3.14'" }, - { name = "requests", marker = "python_full_version < '3.14'" }, + { name = "google-auth" }, + { name = "googleapis-common-protos" }, + { name = "proto-plus" }, + { name = "protobuf" }, + { name = "requests" }, ] sdist = { url = "https://files.pythonhosted.org/packages/61/da/83d7043169ac2c8c7469f0e375610d78ae2160134bf1b80634c482fa079c/google_api_core-2.28.1.tar.gz", hash = "sha256:2b405df02d68e68ce0fbc138559e6036559e685159d148ae5861013dc201baf8", size = 176759, upload-time = "2025-10-28T21:34:51.529Z" } wheels = [ @@ -1217,8 +1277,8 @@ wheels = [ [package.optional-dependencies] grpc = [ - { name = "grpcio", marker = "python_full_version < '3.14'" }, - { name = "grpcio-status", marker = "python_full_version < '3.14'" }, + { name = "grpcio" }, + { name = "grpcio-status" }, ] [[package]] @@ -3402,6 +3462,18 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/9d/7a/d968e294073affff457b041c2be9868a40c1c71f4a35fcc1e45e5493067b/pytest_cov-7.1.0-py3-none-any.whl", hash = "sha256:a0461110b7865f9a271aa1b51e516c9a95de9d696734a2f71e3e78f46e1d4678", size = 22876, upload-time = "2026-03-21T20:11:14.438Z" }, ] +[[package]] +name = "pytest-django" +version = "4.14.0" +source = { registry = "https://pypi.org/simple" } +dependencies = [ + { name = "pytest" }, +] +sdist = { url = "https://files.pythonhosted.org/packages/44/f6/3851312120c2bf2f19cafff931e75059aad1ba670703cd751e2fde9bc942/pytest_django-4.14.0.tar.gz", hash = "sha256:26787dd3f422cfbab8f55b80a776e2edea7a11092cb74e960bef1312515708ef", size = 94700, upload-time = "2026-08-10T14:13:08.319Z" } +wheels = [ + { url = "https://files.pythonhosted.org/packages/9c/03/850bffad2b581c440ca51c039d74504d5a422c94bda0bdb8a8ba5068d48b/pytest_django-4.14.0-py3-none-any.whl", hash = "sha256:c533b08d89cc675efcd5398eea270b34547e35f9a3608e2c9748dd88428ea187", size = 27067, upload-time = "2026-08-10T14:13:06.998Z" }, +] + [[package]] name = "python-daemon" version = "3.1.2" @@ -3915,10 +3987,13 @@ dependencies = [ [package.dev-dependencies] dev = [ { name = "coverage" }, + { name = "django" }, + { name = "django-clickhouse-backend" }, { name = "pyarrow" }, { name = "pysam" }, { name = "pytest" }, { name = "pytest-cov" }, + { name = "pytest-django" }, { name = "responses" }, { name = "ruff" }, { name = "shellcheck-py" }, @@ -3930,7 +4005,7 @@ prod = [ [package.metadata] requires-dist = [ { name = "aiofiles", specifier = "==24.1.0" }, - { name = "clickhouse-driver", specifier = "==0.2.9" }, + { name = "clickhouse-driver", specifier = "==0.2.10" }, { name = "gnomad", specifier = "==0.8.0" }, { name = "gnomad-qc", git = "https://github.com/broadinstitute/gnomad_qc.git?rev=v4.1" }, { name = "google-api-python-client", specifier = "==2.159.0" }, @@ -3950,10 +4025,13 @@ requires-dist = [ [package.metadata.requires-dev] dev = [ { name = "coverage", specifier = ">=7.2.2" }, + { name = "django", specifier = "==4.2.30" }, + { name = "django-clickhouse-backend", specifier = "==1.6" }, { name = "pyarrow" }, { name = "pysam" }, { name = "pytest", specifier = ">=7.0.0" }, { name = "pytest-cov", specifier = ">=4.0.0" }, + { name = "pytest-django", specifier = ">=4.8.0" }, { name = "responses", specifier = ">=0.23.1" }, { name = "ruff", specifier = "==0.11.3" }, { name = "shellcheck-py", specifier = ">=0.10.0" }, From 350f248222104b72da15c955273d0d68a360f889 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 11:03:16 -0400 Subject: [PATCH 200/369] fix dict relaod behavior --- clickhouse_search/backend/table_models.py | 14 ++++++++++++++ ...veryvariantdict_excludedvariantdict_and_more.py | 8 +++++--- clickhouse_search/migrations/0044_omimdict.py | 4 +++- 3 files changed, 22 insertions(+), 4 deletions(-) diff --git a/clickhouse_search/backend/table_models.py b/clickhouse_search/backend/table_models.py index b9613d9a56..d5406e2f7a 100644 --- a/clickhouse_search/backend/table_models.py +++ b/clickhouse_search/backend/table_models.py @@ -31,6 +31,20 @@ def inner(apps, schema_editor): return inner +def conditionally_reload_dictionary(dictionary_name: str): + # Postgres-sourced dictionaries (SOURCE(POSTGRESQL(...))) are otherwise lazily loaded + # (LIFETIME(0), dictionaries_lazy_load default) - CREATE DICTIONARY alone never touches + # Postgres. An explicit `SYSTEM RELOAD DICTIONARY` forces a real, synchronous connection + # attempt though, which test environments with no real Postgres (e.g. loading_pipeline's) + # can't satisfy - so skip it under the same "test_"-prefix convention as + # `conditionally_refresh_reference_dataset` above. + def inner(apps, schema_editor): + if DATABASES['default']['NAME'].startswith('test_'): + return + schema_editor.execute(f'SYSTEM RELOAD DICTIONARY "{dictionary_name}"') + return inner + + class Projection(Func): def __init__(self, name, select='*', order_by=None): diff --git a/clickhouse_search/migrations/0043_discoveryvariantdict_excludedvariantdict_and_more.py b/clickhouse_search/migrations/0043_discoveryvariantdict_excludedvariantdict_and_more.py index 66f666513a..9d1913855b 100644 --- a/clickhouse_search/migrations/0043_discoveryvariantdict_excludedvariantdict_and_more.py +++ b/clickhouse_search/migrations/0043_discoveryvariantdict_excludedvariantdict_and_more.py @@ -4,6 +4,8 @@ from django.db import migrations import django.db.models.manager +from clickhouse_search.backend.table_models import conditionally_reload_dictionary + class Migration(migrations.Migration): @@ -73,7 +75,7 @@ class Migration(migrations.Migration): ('_overwrite_base_manager', django.db.models.manager.Manager()), ], ), - migrations.RunSQL('SYSTEM RELOAD DICTIONARY "seqrdb_discovery_variant_dict"'), - migrations.RunSQL('SYSTEM RELOAD DICTIONARY "seqrdb_excluded_variant_dict"'), - migrations.RunSQL('SYSTEM RELOAD DICTIONARY "seqrdb_individual_metadata_dict"'), + migrations.RunPython(conditionally_reload_dictionary('seqrdb_discovery_variant_dict')), + migrations.RunPython(conditionally_reload_dictionary('seqrdb_excluded_variant_dict')), + migrations.RunPython(conditionally_reload_dictionary('seqrdb_individual_metadata_dict')), ] diff --git a/clickhouse_search/migrations/0044_omimdict.py b/clickhouse_search/migrations/0044_omimdict.py index e41052a123..b2162e7d08 100644 --- a/clickhouse_search/migrations/0044_omimdict.py +++ b/clickhouse_search/migrations/0044_omimdict.py @@ -4,6 +4,8 @@ from django.db import migrations import django.db.models.manager +from clickhouse_search.backend.table_models import conditionally_reload_dictionary + class Migration(migrations.Migration): @@ -30,5 +32,5 @@ class Migration(migrations.Migration): ('_overwrite_base_manager', django.db.models.manager.Manager()), ], ), - migrations.RunSQL('SYSTEM RELOAD DICTIONARY "seqrdb_omim"'), + migrations.RunPython(conditionally_reload_dictionary('seqrdb_omim')), ] From 1e643b6c4213e2c5a9e311e55f1465e09868a730 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 11:06:43 -0400 Subject: [PATCH 201/369] comment clean up --- clickhouse_search/backend/table_models.py | 11 +-- .../test/clickhouse_django/seqr/__init__.py | 30 +------ ...ve_project_custom_reference_populations.py | 9 +- .../seqr/utils/logging_utils.py | 9 +- .../lib/test/clickhouse_django/settings.py | 89 ++++--------------- loading_pipeline/pyproject.toml | 17 ++-- 6 files changed, 29 insertions(+), 136 deletions(-) diff --git a/clickhouse_search/backend/table_models.py b/clickhouse_search/backend/table_models.py index d5406e2f7a..2f211cc2ff 100644 --- a/clickhouse_search/backend/table_models.py +++ b/clickhouse_search/backend/table_models.py @@ -16,10 +16,9 @@ DICTIONARY_META_FIELDS = ['layout', 'lifetime_max', 'postgres_query', 'postgres_db', 'clickhouse_query_template'] +# Lives here rather than in models/reference_data_models.py so migrations depending on it don't +# need to import the much heavier live model definitions module. def conditionally_refresh_reference_dataset(reference_dataset: str): - # NB: lives here, rather than in models/reference_data_models.py, specifically so that - # migrations depending on it don't need to import the (much heavier) live model definitions - # module - this is the only thing migrations need from it. def inner(apps, schema_editor): if DATABASES['default']['NAME'].startswith('test_'): return @@ -32,12 +31,6 @@ def inner(apps, schema_editor): def conditionally_reload_dictionary(dictionary_name: str): - # Postgres-sourced dictionaries (SOURCE(POSTGRESQL(...))) are otherwise lazily loaded - # (LIFETIME(0), dictionaries_lazy_load default) - CREATE DICTIONARY alone never touches - # Postgres. An explicit `SYSTEM RELOAD DICTIONARY` forces a real, synchronous connection - # attempt though, which test environments with no real Postgres (e.g. loading_pipeline's) - # can't satisfy - so skip it under the same "test_"-prefix convention as - # `conditionally_refresh_reference_dataset` above. def inner(apps, schema_editor): if DATABASES['default']['NAME'].startswith('test_'): return diff --git a/loading_pipeline/lib/test/clickhouse_django/seqr/__init__.py b/loading_pipeline/lib/test/clickhouse_django/seqr/__init__.py index 1a8bce5028..d88b462a89 100644 --- a/loading_pipeline/lib/test/clickhouse_django/seqr/__init__.py +++ b/loading_pipeline/lib/test/clickhouse_django/seqr/__init__.py @@ -1,28 +1,6 @@ -"""Minimal stub of the main app's `seqr` package, for `loading_pipeline`'s tests only. +"""Stub of the main app's `seqr` package, shadowing it on sys.path (see settings.py's docstring). -`clickhouse_search` (the source of truth for the ClickHouse schema, migrated via real Django -migrations in these tests - see `lib/test/clickhouse_django/settings.py`) has a small number of -genuine, unavoidable dependencies on the `seqr` app: - - `clickhouse_search/backend/table_models.py` (needed to load `clickhouse_search`'s migrations) - imports `seqr.utils.logging_utils.SeqrLogger` - a tiny, dependency-free logging wrapper. - - `clickhouse_search`'s migration `0040_gnomadnoncodingconstraintdict.py` declares a - cross-app migration dependency on a specific `seqr` migration (used only for historical - migration-ordering purposes, not because it touches any `seqr` table). - -Neither of these needs the *real* `seqr` app - which imports `django-guardian`, -`django.contrib.postgres`, `social_django`, etc. at module level via `seqr/models.py` - all -dependencies `loading_pipeline`'s minimal test environment intentionally does not install. - -This package is placed in `lib/test/clickhouse_django/`, which pytest's `pythonpath` option (see -`pyproject.toml`) puts ahead of the repo root on `sys.path`, so `import seqr` resolves to *this* -lightweight stand-in instead of the real app - the same shadowing trick used for the bare -`settings` module `clickhouse_search/backend/base.py` imports directly. - -`clickhouse_search`'s live model definitions (`models/search_models.py`, -`models/reference_data_models.py`, which pull in more of `seqr`, e.g. `seqr.models.Dataset` and -`seqr.utils.xpos_utils.CHROMOSOME_CHOICES`) are deliberately NOT needed here: `loading_pipeline` -never imports them (it only ever talks to ClickHouse via raw SQL - see -`lib/test/clickhouse_schema_testcase.py`), and neither does applying `clickhouse_search`'s -migrations (which are self-contained frozen schema snapshots, not built from the live model -classes at apply time). If that ever changes, this stub will need to grow accordingly. +`clickhouse_search`'s migrations need `SeqrLogger` (utils/logging_utils.py) and a specific `seqr` +migration name to exist, but not the real app - which imports guardian/postgres/social_django via +seqr/models.py. This stub avoids that weight. """ diff --git a/loading_pipeline/lib/test/clickhouse_django/seqr/migrations/0001_squashed_0067_remove_project_custom_reference_populations.py b/loading_pipeline/lib/test/clickhouse_django/seqr/migrations/0001_squashed_0067_remove_project_custom_reference_populations.py index 985cda6945..085beeac12 100644 --- a/loading_pipeline/lib/test/clickhouse_django/seqr/migrations/0001_squashed_0067_remove_project_custom_reference_populations.py +++ b/loading_pipeline/lib/test/clickhouse_django/seqr/migrations/0001_squashed_0067_remove_project_custom_reference_populations.py @@ -1,11 +1,4 @@ -# No-op stand-in for the real seqr app's migration of the same name. -# -# `clickhouse_search`'s migration `0040_gnomadnoncodingconstraintdict.py` declares a cross-app -# migration dependency on exactly this (app_label, name) pair, purely for historical -# migration-ordering reasons - not because it touches any table this migration would create. -# Django's migration graph builder requires a *named* dependency (unlike `__first__`/`__latest__`) -# to exist as a real node in the graph even for an otherwise-unmigrated app, so this file exists -# solely to satisfy that graph edge. See `seqr/__init__.py` in this stub package for more context. +# No-op stand-in for the real seqr migration clickhouse_search's 0040 depends on by name. from django.db import migrations diff --git a/loading_pipeline/lib/test/clickhouse_django/seqr/utils/logging_utils.py b/loading_pipeline/lib/test/clickhouse_django/seqr/utils/logging_utils.py index ff8b9f242c..f27d813bbb 100644 --- a/loading_pipeline/lib/test/clickhouse_django/seqr/utils/logging_utils.py +++ b/loading_pipeline/lib/test/clickhouse_django/seqr/utils/logging_utils.py @@ -1,11 +1,4 @@ -"""Stub of `seqr.utils.logging_utils` - see `seqr/__init__.py` in this stub package for why. - -`SeqrLogger` is mirrored verbatim from the real `seqr/utils/logging_utils.py` (it's already -dependency-free: stdlib `logging` plus this app's own `settings.DEPLOYMENT_TYPE`). Only -`SeqrLogger` is reproduced, since it's the only symbol `clickhouse_search` actually imports from -this module (`clickhouse_search/backend/table_models.py`). -""" - +# Mirrors the real seqr.utils.logging_utils.SeqrLogger (dependency-free) - see seqr/__init__.py. import logging from typing import Optional diff --git a/loading_pipeline/lib/test/clickhouse_django/settings.py b/loading_pipeline/lib/test/clickhouse_django/settings.py index 222f30228c..fa74d6173f 100644 --- a/loading_pipeline/lib/test/clickhouse_django/settings.py +++ b/loading_pipeline/lib/test/clickhouse_django/settings.py @@ -1,73 +1,22 @@ -"""Minimal Django settings for standing up the `clickhouse_search` schema in tests. +"""Minimal Django settings for running `clickhouse_search`'s real migrations in tests. -This module is intentionally NOT the main seqr app's `settings.py` — `loading_pipeline` has its -own, much smaller, dependency footprint and only needs enough Django configuration to run -`clickhouse_search`'s migrations against a test ClickHouse database. - -It is deliberately placed in its own directory that gets prepended to `sys.path` via pytest's -`pythonpath` option (see `pyproject.toml`), for two reasons: - 1. It's used as `DJANGO_SETTINGS_MODULE`. - 2. `clickhouse_search/backend/base.py` does a bare `from settings import ...` (not - `django.conf.settings`), so a top-level module literally named `settings` has to be - importable on `sys.path` and resolve to *this* module rather than the main app's - `settings.py` (which pulls in postgres/guardian/social_django/etc. that `loading_pipeline` - doesn't depend on). - -Only a single real ClickHouse connection/credential set is configured, on the `clickhouse_write` -alias. `ClickHouseRouter.allow_migrate` (in `clickhouse_search/models/__init__.py`) hardcodes -`db == 'clickhouse_write'` for the `clickhouse_search` app, so migrations must run against an -alias literally named `clickhouse_write` - that's the one Django actually creates/migrates a real -test database for. `clickhouse`, `default`, and `reference_data` are present only because -`clickhouse_search/backend/base.py` looks up `DATABASES['clickhouse_write']['NAME']` / -`DATABASES[postgres_db]['NAME']` (`postgres_db` defaults to `'default'`, but `GeneIdDict`/ -`OmimDict` in `clickhouse_search/models/postgres_dicts.py` declare `postgres_db = 'reference_data'` -instead) to embed a database name string into generated dictionary DDL - not because any of them -needs its own real connection: - - `clickhouse` mirrors the `clickhouse_write` alias's test database (`TEST: {'MIRROR': ...}`), - so Django doesn't create/destroy a second real test database for it. - - `default` and `reference_data` are `dummy` backend entries - neither is ever actually opened. - pytest-django only calls `create_test_db()` for aliases a given test's `databases` attribute - names (see `pytest_django.fixtures._get_databases_for_setup`); it does not unconditionally - create every alias in `DATABASES`. As long as every `TestCase` subclass in this suite declares - `databases = ['clickhouse_write']` (per the shared base class), neither is ever touched, so the - dummy backend never needs to support real connections - only their `NAME` values ever get - read, purely as strings. - -Only `clickhouse_search`'s own migrations are permitted to run anywhere: `DATABASE_ROUTERS` -appends a small catch-all router (`_NoOtherAppMigrationsRouter`, below) that vetoes migrations for -every app *other* than `clickhouse_search`. Without it, Django's default routing would try to -migrate `clickhouse_search`'s (undeclared, but still `INSTALLED_APPS`-adjacent) dependencies onto -`default`, which would fail against the dummy backend - `clickhouse_search`'s migrations use -ClickHouse-only DDL/field types that don't apply to any other app. - -`clickhouse_search`'s migration `0040_gnomadnoncodingconstraintdict.py` has a -`conditionally_refresh_reference_dataset` step that skips a live network call -(`requests.post(...)`) when `DATABASES['default']['NAME'].startswith('test_')`. That module-level -`DATABASES` reference is the plain dict below, not a Django-test-remapped one (since `default` is -never created/mutated by the test runner, per above), so `default`'s `NAME` is just set directly to -a literal `test_`-prefixed string to keep that guard working and avoid the network call during test -runs. +Lives in its own directory, prepended to `sys.path` via pytest's `pythonpath` option (see +`pyproject.toml`), so it doubles as both `DJANGO_SETTINGS_MODULE` and the bare `settings` module +`clickhouse_search/backend/base.py` imports directly - without pulling in the main app's much +heavier `settings.py`. """ import os INSTALLED_APPS = [ 'clickhouse_backend', - # A stub, not the real `seqr` app - see `seqr/__init__.py` (in this same directory, shadowing - # the real app on sys.path) for why `clickhouse_search` needs *an* app named `seqr` present - # at all. - 'seqr', + 'seqr', # stub package (see seqr/__init__.py), not the real app 'clickhouse_search', ] class _NoOtherAppMigrationsRouter: - """Prevents any app other than `clickhouse_search` from having migrations applied anywhere. - - `clickhouse_search`'s modules pull in a handful of other apps transitively (see module - docstring); this keeps those apps' own schemas from ever being created against the throwaway - `default` dummy database (which can't support them; they're never needed here anyway). - """ + """Only `clickhouse_search` may migrate anywhere; everything else is vetoed.""" @staticmethod def allow_migrate(db, app_label, model_name=None, **hints): # noqa: ARG004 @@ -85,10 +34,8 @@ def allow_migrate(db, app_label, model_name=None, **hints): # noqa: ARG004 SECRET_KEY = 'loading-pipeline-test' # noqa: S105 DEPLOYMENT_TYPE = os.environ.get('DEPLOYMENT_TYPE', 'dev') PIPELINE_RUNNER_SERVER = os.environ.get('PIPELINE_RUNNER_SERVER', 'http://localhost') -# These back separate `EmbeddedRocksDB`-engine tables (e.g. `annotations_memory` vs -# `annotations_disk`) and must resolve to different paths - the same path for both causes a -# RocksDB file-lock collision between those tables ("lock hold by current process") the moment -# migrations try to create both. +# Must differ - EmbeddedRocksDB tables (annotations_memory vs annotations_disk) using the same +# path deadlock on the same file lock. CLICKHOUSE_IN_MEMORY_DIR = os.environ.get('CLICKHOUSE_IN_MEMORY_DIR', '/tmp/loading_pipeline_test_clickhouse_in_memory') # noqa: S108 CLICKHOUSE_DATA_DIR = os.environ.get('CLICKHOUSE_DATA_DIR', '/tmp/loading_pipeline_test_clickhouse_data') # noqa: S108 @@ -108,33 +55,29 @@ def allow_migrate(db, app_label, model_name=None, **hints): # noqa: ARG004 'use_client_time_zone': False, }, }, - # Avoid Django's default `test_` prefix so the schema lands in the database name that - # `loading_pipeline.lib.core.environment.Env.CLICKHOUSE_DATABASE` already expects. 'TEST': { + # Skip Django's default `test_` prefix; land on the name Env.CLICKHOUSE_DATABASE + # already expects. 'NAME': CLICKHOUSE_DATABASE_NAME, - # Django assumes any alias whose test-db signature differs from `default`'s implicitly - # depends on `default` (for cross-DB migration ordering) unless told otherwise. Since our - # tests only ever request `databases = ['clickhouse_write']` - `default` is never created - # - that implicit dependency can never resolve, raising "Circular dependency in - # TEST[DEPENDENCIES]". There are no real cross-database dependencies here, so declare none. + # Without this, Django assumes this alias depends on `default` and never resolves it, + # since our tests only ever request `databases = ['clickhouse_write']`. 'DEPENDENCIES': [], }, } DATABASES = { 'clickhouse_write': CLICKHOUSE_DB_CONFIG, + # Mirrored so Django doesn't create/destroy a second real test database for it. 'clickhouse': { **CLICKHOUSE_DB_CONFIG, 'TEST': {'MIRROR': 'clickhouse_write'}, }, + # Dummy backends: never opened (only aliases named in a test's `databases` get created), but + # `clickhouse_search/backend/base.py` reads their `NAME` to embed in generated dictionary DDL. 'default': { 'ENGINE': 'django.db.backends.dummy', 'NAME': 'test_default_unused', }, - # `GeneIdDict`/`OmimDict` (`clickhouse_search/models/postgres_dicts.py`) declare - # `postgres_db = 'reference_data'` instead of the implicit `default` - same dummy-backend - # treatment as `default` above, needed purely so `DATABASES['reference_data']['NAME']` - # resolves to a string for `_dictionary_sql`'s generated DDL. 'reference_data': { 'ENGINE': 'django.db.backends.dummy', 'NAME': 'test_reference_data_unused', diff --git a/loading_pipeline/pyproject.toml b/loading_pipeline/pyproject.toml index 20df951a06..0b9e4f9f1e 100644 --- a/loading_pipeline/pyproject.toml +++ b/loading_pipeline/pyproject.toml @@ -47,20 +47,13 @@ dev = [ exclude-dependencies = ["psycopg2-binary", "psycopg2"] [tool.pytest.ini_options] -# `..` puts the repo root (which holds `clickhouse_search`/`clickhouse_backend`) on sys.path. -# `lib/test/clickhouse_django` holds our minimal settings module, which needs to be importable -# both as `DJANGO_SETTINGS_MODULE` and as the bare `settings` module that -# `clickhouse_search/backend/base.py` imports directly. pytest builds sys.path by inserting each -# `pythonpath` entry at position 0 in *reverse* list order, which nets out to sys.path holding -# them in the same order given here - so `lib/test/clickhouse_django` must come first, ahead of -# `..`, or `import settings` resolves to the much heavier repo-root `settings.py` instead of ours. +# Order matters: `clickhouse_django` must precede `..`, or `import settings` resolves to the +# repo-root `settings.py` instead of ours. `..` puts the repo root (clickhouse_search etc.) on +# sys.path. pythonpath = ["lib/test/clickhouse_django", ".."] DJANGO_SETTINGS_MODULE = "settings" -# pytest-django's `manage.py` auto-discovery walks up from cwd and, finding the main seqr app's -# `manage.py` at the repo root, unconditionally inserts that directory at sys.path[0] - which -# shadows our `settings` module with the main app's much heavier `settings.py`, undoing the -# `pythonpath` ordering above. Disable it; our own `pythonpath` entries are all the path -# configuration this suite needs. +# Disable pytest-django's manage.py auto-discovery, which would otherwise re-shadow `settings` +# with the main app's. django_find_project = false [tool.setuptools] From 3934d2cce839bfb51854c3cac29dc1de805d8b5f Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 11:19:59 -0400 Subject: [PATCH 202/369] django based test case --- .../lib/test/clickhouse_schema_testcase.py | 139 +++--------------- 1 file changed, 18 insertions(+), 121 deletions(-) diff --git a/loading_pipeline/lib/test/clickhouse_schema_testcase.py b/loading_pipeline/lib/test/clickhouse_schema_testcase.py index fc26f8cc64..b01277fe10 100644 --- a/loading_pipeline/lib/test/clickhouse_schema_testcase.py +++ b/loading_pipeline/lib/test/clickhouse_schema_testcase.py @@ -1,127 +1,24 @@ -import unittest +from django.db import connections +from django.test import TestCase from loading_pipeline.lib.core import Env -from loading_pipeline.lib.misc.clickhouse import ( - STAGING_CLICKHOUSE_DATABASE, - get_clickhouse_client, -) -TEST_SCHEMA = 'loading_pipeline/var/test/test_clickhouse_schema.sql' +class ClickhouseSchemaTestCase(TestCase): + databases = ['clickhouse_write'] -class ClickhouseSchemaTestCase(unittest.TestCase): - def setUp(self): - super().setUp() - client = get_clickhouse_client() - client.execute( - f""" - DROP DATABASE IF EXISTS {STAGING_CLICKHOUSE_DATABASE}; - """, - ) - client.execute( - f""" - DROP DATABASE IF EXISTS {Env.CLICKHOUSE_DATABASE}; - """, - ) - client.execute( - f""" - CREATE DATABASE {Env.CLICKHOUSE_DATABASE}; - """, - ) - client = get_clickhouse_client(database=Env.CLICKHOUSE_DATABASE) - client.execute( - """ - CREATE DICTIONARY seqrdb_gene_ids - ( - `gene_id` String, - `seqrdb_id` String, - `affected` String + # Django's `flush` (the default TestCase teardown for backends without transaction support) + # determines tables to flush from `apps.get_models()`, but nothing here imports + # clickhouse_search's model modules, so it finds none. Truncate live tables directly instead. + def _fixture_teardown(self): + with connections['clickhouse_write'].cursor() as cursor: + cursor.execute( + """ + SELECT name FROM system.tables + WHERE database = %(database)s AND engine NOT IN ('Dictionary', 'MaterializedView') + """, + {'database': Env.CLICKHOUSE_DATABASE}, ) - PRIMARY KEY gene_id - SOURCE(NULL()) - LIFETIME(0) - LAYOUT(HASHED()) - """, - ) - client.execute( - """ - CREATE DICTIONARY seqrdb_affected_status_dict - ( - `family_guid` String, - `sampleId` String, - `affected` String - ) - PRIMARY KEY family_guid, sampleId - SOURCE(NULL()) - LIFETIME(0) - LAYOUT(COMPLEX_KEY_HASHED()) - """, - ) - client.execute( - """ - CREATE DICTIONARY `GRCh38/SNV_INDEL/project_partitions_dict` - ( - `project_guid` String, - `n_partitions` UInt32 - ) - PRIMARY KEY project_guid - SOURCE(NULL()) - LIFETIME(0) - LAYOUT(COMPLEX_KEY_HASHED()) - """, - ) - client.execute( - """ - CREATE DICTIONARY `GRCh38/SNV_INDEL/reference_data/gnomad_genomes` - ( - `key` UInt32, - `filter_af` Decimal(9, 8) - ) - PRIMARY KEY key - SOURCE(NULL()) - LIFETIME(0) - LAYOUT(COMPLEX_KEY_HASHED()) - """, - ) - with open(TEST_SCHEMA) as f: - sql = f.read() - commands = [cmd.strip() for cmd in sql.split(';') if cmd.strip()] - for cmd in commands: - client.execute(cmd) - client.execute( - f""" - CREATE DICTIONARY `GRCh38/SNV_INDEL/gt_stats_dict` - ( - `key` UInt32, - `ac_wes` UInt64, - `ac_wgs` UInt64, - `ac_affected` UInt64, - `hom_wes` UInt64, - `hom_wgs` UInt64, - `hom_affected` UInt64 - ) - PRIMARY KEY key - SOURCE( - CLICKHOUSE( - USER {Env.CLICKHOUSE_WRITER_USER} PASSWORD {Env.CLICKHOUSE_WRITER_PASSWORD} - DB {Env.CLICKHOUSE_DATABASE} TABLE `GRCh38/SNV_INDEL/gt_stats` - ) - ) - LIFETIME(0) - LAYOUT(FLAT(MAX_ARRAY_SIZE 1000000000)) - """, - ) - - def tearDown(self): - super().tearDown() - client = get_clickhouse_client() - client.execute( - f""" - DROP DATABASE IF EXISTS {STAGING_CLICKHOUSE_DATABASE}; - """, - ) - client.execute( - f""" - DROP DATABASE IF EXISTS {Env.CLICKHOUSE_DATABASE}; - """, - ) + tables = [row[0] for row in cursor.fetchall()] + for table in tables: + cursor.execute(f'TRUNCATE TABLE `{table}`') # noqa: S608 From 3c052d173fb871831cb101ad5e13063c1c8de258 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 11:22:36 -0400 Subject: [PATCH 203/369] plan update --- .../CLICKHOUSE_PYTEST_DJANGO_PLAN.md | 55 ++++++++++++++++++- 1 file changed, 54 insertions(+), 1 deletion(-) diff --git a/loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_PLAN.md b/loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_PLAN.md index 1afa59f8d5..cde0c7077f 100644 --- a/loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_PLAN.md +++ b/loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_PLAN.md @@ -151,4 +151,57 @@ specifics can't be verified ahead of time: tuples, as `clickhouse_driver.Client.execute` supports today) work identically through `cursor.execute()`/`cursor.executemany()` on the Django ClickHouse backend, or need reshaping. -These should be shaken out against a real CI run / local ClickHouse instance once implemented. \ No newline at end of file +These should be shaken out against a real CI run / local ClickHouse instance once implemented. + +## Deviations from this plan, found during implementation + +Verified against a live ClickHouse instance. Recorded here for reference; this plan document +itself is not otherwise updated to match implementation. + +**`clickhouse_search/` changes beyond the two already noted above** (both cleared with the user +before making them): +- Moved `conditionally_refresh_reference_dataset` from `models/reference_data_models.py` to + `backend/table_models.py`, so migration 0040 doesn't need to import the live model modules (and + therefore `seqr.models.Dataset`/`seqr.utils.xpos_utils.CHROMOSOME_CHOICES`) just to reach one + helper function. +- Added `conditionally_reload_dictionary` (`backend/table_models.py`) and edited migrations 0043 + and 0044 to use it instead of hardcoded `RunSQL('SYSTEM RELOAD DICTIONARY ...')` - those forced + a real synchronous Postgres connection during `migrate`, which no environment here has. This + edits already-applied migration files, normally treated as an immutable historical record. + +**A production dependency change:** `clickhouse-driver` bumped `0.2.9` -> `0.2.10` in +`loading_pipeline/pyproject.toml` (forced by `django-clickhouse-backend==1.6`'s own pin; matches +the main app's version). Not test-only. + +**Bugs/gaps in this plan's own design, fixed - all confined to `loading_pipeline/`:** +- `reference_data` needs its own dummy `DATABASES` alias; the plan only accounted for `default` + (`GeneIdDict`/`OmimDict` declare `postgres_db = 'reference_data'`). +- `DATABASES['clickhouse_write']['TEST']['DEPENDENCIES']` must be `[]`, or Django raises + "Circular dependency in TEST[DEPENDENCIES]" (it assumes every alias depends on `default`). +- The `pythonpath` ordering described in this plan's original settings-module writeup was + backwards; pytest builds `sys.path` in the *same* order as the `pythonpath` list, not reversed. +- `django_find_project = false` is required - pytest-django's `manage.py` auto-discovery + otherwise force-inserts the repo root at `sys.path[0]`, re-shadowing `settings`. +- `CLICKHOUSE_IN_MEMORY_DIR`/`CLICKHOUSE_DATA_DIR` must default to different paths, or two + `EmbeddedRocksDB` tables collide on the same file lock. +- A stub `seqr` package (`lib/test/clickhouse_django/seqr/`) is needed - not anticipated anywhere + in this plan - because `clickhouse_search/backend/table_models.py` imports `SeqrLogger`, and + migration 0040 has a named dependency on a specific `seqr` migration. +- The "no named-collection CI step needed" conclusion in this plan's own change-set table is + right, but the "Postgres/GCS-sourced dictionary wrinkle" section above is stale/wrong about why + - see the migration 0043/0044 edit above for the actual mechanism. + +**Explicit user-directed deviations from this plan's design:** +- The shared base class does NOT keep "staging-DB drop/create" logic, contrary to this plan's + change-set table - `loading_pipeline`'s own production code already drops/creates the staging + DB defensively, so tests don't need to. +- Per-test cleanup in the shared base class is a `_fixture_teardown` override that truncates all + live, non-`Dictionary`/`MaterializedView` tables directly via SQL - not Django's `flush` command, + which relies on `apps.get_models()` and finds nothing (no `clickhouse_search` model modules are + imported anywhere in `loading_pipeline`). + +**Unresolved tension, not yet acted on:** this plan calls for shared reference data (e.g. +`seqrdb_gene_ids` source rows) to be loaded via Django fixtures (`loaddata`), which requires +importing the real model classes being loaded - but the user has since directed that fully +importing `clickhouse_search`'s live model modules is unacceptable for these tests. Needs +resolution before the fixture-loading step is implemented. \ No newline at end of file From 0a4e1fcd334a0507d2d20ce58078bc8c696f2604 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 12:03:06 -0400 Subject: [PATCH 204/369] existing test cleanup --- loading_pipeline/bin/pipeline_worker_test.py | 56 ++-- .../load_clickhouse_variants_tables_test.py | 57 ++-- .../var/test/test_clickhouse_schema.sql | 269 ------------------ 3 files changed, 54 insertions(+), 328 deletions(-) delete mode 100644 loading_pipeline/var/test/test_clickhouse_schema.sql diff --git a/loading_pipeline/bin/pipeline_worker_test.py b/loading_pipeline/bin/pipeline_worker_test.py index e258d0c573..532693701a 100644 --- a/loading_pipeline/bin/pipeline_worker_test.py +++ b/loading_pipeline/bin/pipeline_worker_test.py @@ -6,14 +6,12 @@ import hailtop.fs as hfs import luigi import luigi.worker +from django.db import connections from loading_pipeline.bin.pipeline_worker import process_queue from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType from loading_pipeline.lib.core.environment import Env -from loading_pipeline.lib.misc.clickhouse import ( - ClickhouseReferenceDataset, - get_clickhouse_client, -) +from loading_pipeline.lib.misc.clickhouse import ClickhouseReferenceDataset from loading_pipeline.lib.paths import ( clickhouse_load_success_file_path, loading_pipeline_deadletter_queue_dir, @@ -106,31 +104,31 @@ def test_process_queue_integration_test( ) as f: self.assertEqual(f.read(), '') - client = get_clickhouse_client() - annotations_count = client.execute( - f""" - SELECT COUNT(*) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` - """, - )[0][0] - self.assertEqual(annotations_count, 30) - entries_count = client.execute( - f""" - SELECT COUNT(*) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` - """, - )[0][0] - self.assertEqual(entries_count, 16) - ac_wgs = client.execute( - f""" - SELECT sum(ac_wgs) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` - """, - )[0][0] - self.assertEqual(ac_wgs, 69) + with connections['clickhouse_write'].cursor() as cursor: + cursor.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` + """, + ) + self.assertEqual(cursor.fetchone()[0], 30) + cursor.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` + """, + ) + self.assertEqual(cursor.fetchone()[0], 16) + cursor.execute( + f""" + SELECT sum(ac_wgs) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` + """, + ) + self.assertEqual(cursor.fetchone()[0], 69) @patch('loading_pipeline.lib.misc.slack._safe_post_to_slack') @patch('loading_pipeline.api.request_handlers.WriteClickhouseLoadSuccessFileTask') diff --git a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py index 972df2c172..b8a2d8fa1e 100644 --- a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py +++ b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py @@ -2,16 +2,14 @@ import hail as hl import luigi.worker +from django.db import connections from loading_pipeline.lib.core import ( DatasetType, ReferenceGenome, ) from loading_pipeline.lib.core.environment import Env -from loading_pipeline.lib.misc.clickhouse import ( - ClickhouseReferenceDataset, - get_clickhouse_client, -) +from loading_pipeline.lib.misc.clickhouse import ClickhouseReferenceDataset from loading_pipeline.lib.paths import ( variant_annotations_table_path, ) @@ -34,7 +32,6 @@ MockedDatarootTestCase, ) -TEST_SCHEMA = 'loading_pipeline/var/test/test_clickhouse_schema.sql' TEST_SNV_INDEL_ANNOTATIONS = ( 'loading_pipeline/var/test/exports/GRCh38/SNV_INDEL/annotations.ht' ) @@ -121,28 +118,28 @@ def test_write_variants_to_clickhouse( worker.run() self.assertTrue(task.complete()) - client = get_clickhouse_client() - variants_count = client.execute( - f""" - SELECT COUNT(*) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` - """, - )[0][0] - self.assertEqual(variants_count, 2) - variant_details_count = client.execute( - f""" - SELECT COUNT(*) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details` - """, - )[0][0] - self.assertEqual(variant_details_count, 2) - key_lookups_count = client.execute( - f""" - SELECT COUNT(*) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/key_lookup` - """, - )[0][0] - self.assertEqual(key_lookups_count, 2) + with connections['clickhouse_write'].cursor() as cursor: + cursor.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` + """, + ) + self.assertEqual(cursor.fetchone()[0], 2) + cursor.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details` + """, + ) + self.assertEqual(cursor.fetchone()[0], 2) + cursor.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/key_lookup` + """, + ) + self.assertEqual(cursor.fetchone()[0], 2) diff --git a/loading_pipeline/var/test/test_clickhouse_schema.sql b/loading_pipeline/var/test/test_clickhouse_schema.sql deleted file mode 100644 index d33275bb3b..0000000000 --- a/loading_pipeline/var/test/test_clickhouse_schema.sql +++ /dev/null @@ -1,269 +0,0 @@ -CREATE TABLE `GRCh38/SNV_INDEL/variants_disk` -( - `key` UInt32 CODEC(Delta(8), ZSTD(1)), - `sortedTranscriptConsequences` Nested(alphamissensePathogenicity Nullable(Decimal(9, 5)), canonical Nullable(UInt8), consequenceTerms Array(Nullable(Enum8('transcript_ablation' = 1, 'splice_acceptor_variant' = 2, 'splice_donor_variant' = 3, 'stop_gained' = 4, 'frameshift_variant' = 5, 'stop_lost' = 6, 'start_lost' = 7, 'inframe_insertion' = 8, 'inframe_deletion' = 9, 'missense_variant' = 10, 'protein_altering_variant' = 11, 'splice_donor_5th_base_variant' = 12, 'splice_region_variant' = 13, 'splice_donor_region_variant' = 14, 'splice_polypyrimidine_tract_variant' = 15, 'incomplete_terminal_codon_variant' = 16, 'start_retained_variant' = 17, 'stop_retained_variant' = 18, 'synonymous_variant' = 19, 'coding_sequence_variant' = 20, 'mature_miRNA_variant' = 21, '5_prime_UTR_variant' = 22, '3_prime_UTR_variant' = 23, 'non_coding_transcript_exon_variant' = 24, 'intron_variant' = 25, 'NMD_transcript_variant' = 26, 'non_coding_transcript_variant' = 27, 'coding_transcript_variant' = 28, 'upstream_gene_variant' = 29, 'downstream_gene_variant' = 30, 'intergenic_variant' = 31, 'sequence_variant' = 32))), extendedIntronicSpliceRegionVariant Nullable(Bool), fiveutrConsequence Nullable(Enum8('5_prime_UTR_premature_start_codon_gain_variant' = 1, '5_prime_UTR_premature_start_codon_loss_variant' = 2, '5_prime_UTR_stop_codon_gain_variant' = 3, '5_prime_UTR_stop_codon_loss_variant' = 4, '5_prime_UTR_uORF_frameshift_variant' = 5)), geneId Nullable(String)), - `sortedMotifFeatureConsequences` Nested(consequenceTerms Array(Nullable(Enum8('TFBS_ablation' = 0, 'TFBS_amplification' = 1, 'TF_binding_site_variant' = 2, 'TFBS_fusion' = 3, 'TFBS_translocation' = 4)))), - `sortedRegulatoryFeatureConsequences` Nested(consequenceTerms Array(Nullable(Enum8('regulatory_region_ablation' = 0, 'regulatory_region_amplification' = 1, 'regulatory_region_variant' = 2, 'regulatory_region_fusion' = 3)))) -) -ENGINE = EmbeddedRocksDB() -PRIMARY KEY key; - -CREATE TABLE `GRCh38/SNV_INDEL/variants_memory` -( - `key` UInt32 CODEC(Delta(8), ZSTD(1)), - `sortedTranscriptConsequences` Nested(alphamissensePathogenicity Nullable(Decimal(9, 5)), canonical Nullable(UInt8), consequenceTerms Array(Nullable(Enum8('transcript_ablation' = 1, 'splice_acceptor_variant' = 2, 'splice_donor_variant' = 3, 'stop_gained' = 4, 'frameshift_variant' = 5, 'stop_lost' = 6, 'start_lost' = 7, 'inframe_insertion' = 8, 'inframe_deletion' = 9, 'missense_variant' = 10, 'protein_altering_variant' = 11, 'splice_donor_5th_base_variant' = 12, 'splice_region_variant' = 13, 'splice_donor_region_variant' = 14, 'splice_polypyrimidine_tract_variant' = 15, 'incomplete_terminal_codon_variant' = 16, 'start_retained_variant' = 17, 'stop_retained_variant' = 18, 'synonymous_variant' = 19, 'coding_sequence_variant' = 20, 'mature_miRNA_variant' = 21, '5_prime_UTR_variant' = 22, '3_prime_UTR_variant' = 23, 'non_coding_transcript_exon_variant' = 24, 'intron_variant' = 25, 'NMD_transcript_variant' = 26, 'non_coding_transcript_variant' = 27, 'coding_transcript_variant' = 28, 'upstream_gene_variant' = 29, 'downstream_gene_variant' = 30, 'intergenic_variant' = 31, 'sequence_variant' = 32))), extendedIntronicSpliceRegionVariant Nullable(Bool), fiveutrConsequence Nullable(Enum8('5_prime_UTR_premature_start_codon_gain_variant' = 1, '5_prime_UTR_premature_start_codon_loss_variant' = 2, '5_prime_UTR_stop_codon_gain_variant' = 3, '5_prime_UTR_stop_codon_loss_variant' = 4, '5_prime_UTR_uORF_frameshift_variant' = 5)), geneId Nullable(String)), - `sortedMotifFeatureConsequences` Nested(consequenceTerms Array(Nullable(Enum8('TFBS_ablation' = 0, 'TFBS_amplification' = 1, 'TF_binding_site_variant' = 2, 'TFBS_fusion' = 3, 'TFBS_translocation' = 4)))), - `sortedRegulatoryFeatureConsequences` Nested(consequenceTerms Array(Nullable(Enum8('regulatory_region_ablation' = 0, 'regulatory_region_amplification' = 1, 'regulatory_region_variant' = 2, 'regulatory_region_fusion' = 3)))) -) -ENGINE = EmbeddedRocksDB() -PRIMARY KEY key; - -CREATE TABLE `GRCh38/SNV_INDEL/variants/details` -( - `key` UInt32 CODEC(Delta(8), ZSTD(1)), - `variantId` String, - `rsid` Nullable(String), - `CAID` Nullable(String), - `liftedOverChrom` Nullable(Enum8('1' = 1, '2' = 2, '3' = 3, '4' = 4, '5' = 5, '6' = 6, '7' = 7, '8' = 8, '9' = 9, '10' = 10, '11' = 11, '12' = 12, '13' = 13, '14' = 14, '15' = 15, '16' = 16, '17' = 17, '18' = 18, '19' = 19, '20' = 20, '21' = 21, '22' = 22, 'X' = 23, 'Y' = 24, 'M' = 25)), - `liftedOverPos` Nullable(UInt32), - `transcripts` Nested(alphamissense Tuple( - pathogenicity Nullable(Decimal(9, 5))), aminoAcids Nullable(String), biotype Nullable(String), canonical Nullable(UInt8), codons Nullable(String), consequenceTerms Array(Nullable(Enum8('transcript_ablation' = 1, 'splice_acceptor_variant' = 2, 'splice_donor_variant' = 3, 'stop_gained' = 4, 'frameshift_variant' = 5, 'stop_lost' = 6, 'start_lost' = 7, 'inframe_insertion' = 8, 'inframe_deletion' = 9, 'missense_variant' = 10, 'protein_altering_variant' = 11, 'splice_donor_5th_base_variant' = 12, 'splice_region_variant' = 13, 'splice_donor_region_variant' = 14, 'splice_polypyrimidine_tract_variant' = 15, 'incomplete_terminal_codon_variant' = 16, 'start_retained_variant' = 17, 'stop_retained_variant' = 18, 'synonymous_variant' = 19, 'coding_sequence_variant' = 20, 'mature_miRNA_variant' = 21, '5_prime_UTR_variant' = 22, '3_prime_UTR_variant' = 23, 'non_coding_transcript_exon_variant' = 24, 'intron_variant' = 25, 'NMD_transcript_variant' = 26, 'non_coding_transcript_variant' = 27, 'coding_transcript_variant' = 28, 'upstream_gene_variant' = 29, 'downstream_gene_variant' = 30, 'intergenic_variant' = 31, 'sequence_variant' = 32))), exon Tuple( - index Nullable(Int32), - total Nullable(Int32)), geneId Nullable(String), hgvsc Nullable(String), hgvsp Nullable(String), intron Tuple( - index Nullable(Int32), - total Nullable(Int32)), loftee Tuple( - isLofNagnag Nullable(Bool), - lofFilters Array(Nullable(String))), majorConsequence Nullable(Enum8('transcript_ablation' = 1, 'splice_acceptor_variant' = 2, 'splice_donor_variant' = 3, 'stop_gained' = 4, 'frameshift_variant' = 5, 'stop_lost' = 6, 'start_lost' = 7, 'inframe_insertion' = 8, 'inframe_deletion' = 9, 'missense_variant' = 10, 'protein_altering_variant' = 11, 'splice_donor_5th_base_variant' = 12, 'splice_region_variant' = 13, 'splice_donor_region_variant' = 14, 'splice_polypyrimidine_tract_variant' = 15, 'incomplete_terminal_codon_variant' = 16, 'start_retained_variant' = 17, 'stop_retained_variant' = 18, 'synonymous_variant' = 19, 'coding_sequence_variant' = 20, 'mature_miRNA_variant' = 21, '5_prime_UTR_variant' = 22, '3_prime_UTR_variant' = 23, 'non_coding_transcript_exon_variant' = 24, 'intron_variant' = 25, 'NMD_transcript_variant' = 26, 'non_coding_transcript_variant' = 27, 'coding_transcript_variant' = 28, 'upstream_gene_variant' = 29, 'downstream_gene_variant' = 30, 'intergenic_variant' = 31, 'sequence_variant' = 32)), manePlusClinical Nullable(String), maneSelect Nullable(String), refseqTranscriptId Nullable(String), spliceregion Tuple( - extended_intronic_splice_region_variant Nullable(Bool)), transcriptId String, transcriptRank UInt8, utrannotator Tuple( - existingInframeOorfs Nullable(Int32), - existingOutofframeOorfs Nullable(Int32), - existingUorfs Nullable(Int32), - fiveutrAnnotation Tuple( - AltStop Nullable(String), - AltStopDistanceToCDS Nullable(Int32), - CapDistanceToStart Nullable(Int32), - DistanceToCDS Nullable(Int32), - DistanceToStop Nullable(Int32), - Evidence Nullable(Bool), - FrameWithCDS Nullable(String), - KozakContext Nullable(String), - KozakStrength Nullable(String), - StartDistanceToCDS Nullable(Int32), - alt_type Nullable(String), - alt_type_length Nullable(Int32), - newSTOPDistanceToCDS Nullable(Int32), - ref_StartDistanceToCDS Nullable(Int32), - ref_type Nullable(String), - ref_type_length Nullable(Int32), - type Nullable(String)), - fiveutrConsequence Nullable(String))), - `sortedMotifFeatureConsequences` Nested(consequenceTerms Array(Nullable(Enum8('TFBS_ablation' = 0, 'TFBS_amplification' = 1, 'TF_binding_site_variant' = 2, 'TFBS_fusion' = 3, 'TFBS_translocation' = 4))), motifFeatureId Nullable(String)), - `sortedRegulatoryFeatureConsequences` Nested(biotype Nullable(Enum8('enhancer' = 0, 'promoter' = 1, 'CTCF_binding_site' = 2, 'TF_binding_site' = 3, 'open_chromatin_region' = 4)), consequenceTerms Array(Nullable(Enum8('regulatory_region_ablation' = 0, 'regulatory_region_amplification' = 1, 'regulatory_region_variant' = 2, 'regulatory_region_fusion' = 3))), regulatoryFeatureId Nullable(String)) -) -ENGINE = EmbeddedRocksDB() -PRIMARY KEY key; - -CREATE TABLE `GRCh38/SNV_INDEL/entries` -( - `key` UInt32 CODEC(Delta(8), ZSTD(1)), - `project_guid` LowCardinality(String), - `family_guid` String, - `sample_type` Enum8('WES' = 1, 'WGS' = 2), - `xpos` UInt64 CODEC(Delta(8), ZSTD(1)), - `is_gnomad_gt_5_percent` Bool, - `is_annotated_in_any_gene` Bool, - `geneId_ids` Array(UInt32), - `filters` Array(LowCardinality(String)), - `calls` Array(Tuple( - sampleId String, - gt Nullable(Enum8('REF' = 0, 'HET' = 1, 'HOM' = 2)), - gq Nullable(UInt8), - ab Nullable(Decimal(9, 5)), - dp Nullable(UInt16))), - `sign` Int8, - `n_partitions` UInt8 MATERIALIZED dictGetOrDefault('GRCh38/SNV_INDEL/project_partitions_dict', 'n_partitions', project_guid, 1), - `partition_id` UInt8 MATERIALIZED farmHash64(family_guid) % n_partitions, - PROJECTION xpos_projection - ( - SELECT * - ORDER BY - is_gnomad_gt_5_percent, - is_annotated_in_any_gene, - xpos - ) -) -ENGINE = CollapsingMergeTree(sign) -PARTITION BY (project_guid, partition_id) -ORDER BY (project_guid, family_guid, sample_type, is_gnomad_gt_5_percent, is_annotated_in_any_gene, key) -SETTINGS deduplicate_merge_projection_mode = 'rebuild', index_granularity = 8192; - -CREATE TABLE `GRCh38/SNV_INDEL/gt_stats` -( - `key` UInt32 CODEC(Delta(8), ZSTD(1)), - `ac_wes` UInt32, - `ac_wgs` UInt32, - `ac_affected` UInt32 DEFAULT 0, - `hom_wes` UInt32, - `hom_wgs` UInt32, - `hom_affected` UInt32 DEFAULT 0 -) -ENGINE = SummingMergeTree -ORDER BY key -SETTINGS index_granularity = 8192; - -CREATE TABLE `GRCh38/SNV_INDEL/key_lookup` -( - `variantId` String, - `key` UInt32 CODEC(Delta(8), ZSTD(1)) -) -ENGINE = EmbeddedRocksDB() -PRIMARY KEY variantId; - -CREATE TABLE `GRCh38/SNV_INDEL/project_gt_stats` -( - `project_guid` LowCardinality(String), - `key` UInt32 CODEC(Delta(8), ZSTD(1)), - `sample_type` Enum8('WES' = 1, 'WGS' = 2), - `affected` Enum8('A' = 1, 'N' = 2, 'U' = 3) DEFAULT 'U', - `ref_samples` UInt32, - `het_samples` UInt32, - `hom_samples` UInt32 -) -ENGINE = SummingMergeTree -PARTITION BY project_guid -ORDER BY (project_guid, key, sample_type) -SETTINGS index_granularity = 8192; - -CREATE TABLE `GRCh38/SNV_INDEL/reference_data/clinvar` -( - `key` UInt32 CODEC(Delta(8), ZSTD(1)), - `alleleId` Nullable(UInt32), - `conflictingPathogenicities` Nested(pathogenicity Enum8('Pathogenic' = 0, 'Pathogenic/Likely_pathogenic' = 1, 'Pathogenic/Likely_pathogenic/Established_risk_allele' = 2, 'Pathogenic/Likely_pathogenic/Likely_risk_allele' = 3, 'Pathogenic/Likely_risk_allele' = 4, 'Likely_pathogenic' = 5, 'Likely_pathogenic/Likely_risk_allele' = 6, 'Established_risk_allele' = 7, 'Likely_risk_allele' = 8, 'Conflicting_classifications_of_pathogenicity' = 9, 'Uncertain_risk_allele' = 10, 'Uncertain_significance/Uncertain_risk_allele' = 11, 'Uncertain_significance' = 12, 'No_pathogenic_assertion' = 13, 'Likely_benign' = 14, 'Benign/Likely_benign' = 15, 'Benign' = 16), count UInt16), - `goldStars` Nullable(UInt8), - `submitters` Array(String), - `conditions` Array(String), - `assertions` Array(Enum8('Affects' = 0, 'association' = 1, 'association_not_found' = 2, 'confers_sensitivity' = 3, 'drug_response' = 4, 'low_penetrance' = 5, 'not_provided' = 6, 'other' = 7, 'protective' = 8, 'risk_factor' = 9, 'no_classification_for_the_single_variant' = 10, 'no_classifications_from_unflagged_records' = 11)), - `pathogenicity` Enum8('Pathogenic' = 0, 'Pathogenic/Likely_pathogenic' = 1, 'Pathogenic/Likely_pathogenic/Established_risk_allele' = 2, 'Pathogenic/Likely_pathogenic/Likely_risk_allele' = 3, 'Pathogenic/Likely_risk_allele' = 4, 'Likely_pathogenic' = 5, 'Likely_pathogenic/Likely_risk_allele' = 6, 'Established_risk_allele' = 7, 'Likely_risk_allele' = 8, 'Conflicting_classifications_of_pathogenicity' = 9, 'Uncertain_risk_allele' = 10, 'Uncertain_significance/Uncertain_risk_allele' = 11, 'Uncertain_significance' = 12, 'No_pathogenic_assertion' = 13, 'Likely_benign' = 14, 'Benign/Likely_benign' = 15, 'Benign' = 16) -) -ENGINE = Join(`ALL`, LEFT, key) -SETTINGS join_use_nulls = 1; - -CREATE TABLE `GRCh38/SNV_INDEL/reference_data/clinvar/all_variants` -( - `version` Date, - `variantId` String, - `alleleId` Nullable(UInt32), - `conflictingPathogenicities` Nested(pathogenicity Enum8('Pathogenic' = 0, 'Pathogenic/Likely_pathogenic' = 1, 'Pathogenic/Likely_pathogenic/Established_risk_allele' = 2, 'Pathogenic/Likely_pathogenic/Likely_risk_allele' = 3, 'Pathogenic/Likely_risk_allele' = 4, 'Likely_pathogenic' = 5, 'Likely_pathogenic/Likely_risk_allele' = 6, 'Established_risk_allele' = 7, 'Likely_risk_allele' = 8, 'Conflicting_classifications_of_pathogenicity' = 9, 'Uncertain_risk_allele' = 10, 'Uncertain_significance/Uncertain_risk_allele' = 11, 'Uncertain_significance' = 12, 'No_pathogenic_assertion' = 13, 'Likely_benign' = 14, 'Benign/Likely_benign' = 15, 'Benign' = 16), count UInt16), - `goldStars` Nullable(UInt8), - `submitters` Array(String), - `conditions` Array(String), - `assertions` Array(Enum8('Affects' = 0, 'association' = 1, 'association_not_found' = 2, 'confers_sensitivity' = 3, 'drug_response' = 4, 'low_penetrance' = 5, 'not_provided' = 6, 'other' = 7, 'protective' = 8, 'risk_factor' = 9, 'no_classification_for_the_single_variant' = 10, 'no_classifications_from_unflagged_records' = 11)), - `pathogenicity` Enum8('Pathogenic' = 0, 'Pathogenic/Likely_pathogenic' = 1, 'Pathogenic/Likely_pathogenic/Established_risk_allele' = 2, 'Pathogenic/Likely_pathogenic/Likely_risk_allele' = 3, 'Pathogenic/Likely_risk_allele' = 4, 'Likely_pathogenic' = 5, 'Likely_pathogenic/Likely_risk_allele' = 6, 'Established_risk_allele' = 7, 'Likely_risk_allele' = 8, 'Conflicting_classifications_of_pathogenicity' = 9, 'Uncertain_risk_allele' = 10, 'Uncertain_significance/Uncertain_risk_allele' = 11, 'Uncertain_significance' = 12, 'No_pathogenic_assertion' = 13, 'Likely_benign' = 14, 'Benign/Likely_benign' = 15, 'Benign' = 16) -) -ENGINE = MergeTree -PARTITION BY version -PRIMARY KEY (version, variantId) -ORDER BY (version, variantId) -SETTINGS index_granularity = 8192; - -CREATE TABLE `GRCh38/SNV_INDEL/reference_data/clinvar/seqr_variants` -( - `key` UInt32 CODEC(Delta(8), ZSTD(1)), - `alleleId` Nullable(UInt32), - `conflictingPathogenicities` Nested(pathogenicity Enum8('Pathogenic' = 0, 'Pathogenic/Likely_pathogenic' = 1, 'Pathogenic/Likely_pathogenic/Established_risk_allele' = 2, 'Pathogenic/Likely_pathogenic/Likely_risk_allele' = 3, 'Pathogenic/Likely_risk_allele' = 4, 'Likely_pathogenic' = 5, 'Likely_pathogenic/Likely_risk_allele' = 6, 'Established_risk_allele' = 7, 'Likely_risk_allele' = 8, 'Conflicting_classifications_of_pathogenicity' = 9, 'Uncertain_risk_allele' = 10, 'Uncertain_significance/Uncertain_risk_allele' = 11, 'Uncertain_significance' = 12, 'No_pathogenic_assertion' = 13, 'Likely_benign' = 14, 'Benign/Likely_benign' = 15, 'Benign' = 16), count UInt16), - `goldStars` Nullable(UInt8), - `submitters` Array(String), - `conditions` Array(String), - `assertions` Array(Enum8('Affects' = 0, 'association' = 1, 'association_not_found' = 2, 'confers_sensitivity' = 3, 'drug_response' = 4, 'low_penetrance' = 5, 'not_provided' = 6, 'other' = 7, 'protective' = 8, 'risk_factor' = 9, 'no_classification_for_the_single_variant' = 10, 'no_classifications_from_unflagged_records' = 11)), - `pathogenicity` Enum8('Pathogenic' = 0, 'Pathogenic/Likely_pathogenic' = 1, 'Pathogenic/Likely_pathogenic/Established_risk_allele' = 2, 'Pathogenic/Likely_pathogenic/Likely_risk_allele' = 3, 'Pathogenic/Likely_risk_allele' = 4, 'Likely_pathogenic' = 5, 'Likely_pathogenic/Likely_risk_allele' = 6, 'Established_risk_allele' = 7, 'Likely_risk_allele' = 8, 'Conflicting_classifications_of_pathogenicity' = 9, 'Uncertain_risk_allele' = 10, 'Uncertain_significance/Uncertain_risk_allele' = 11, 'Uncertain_significance' = 12, 'No_pathogenic_assertion' = 13, 'Likely_benign' = 14, 'Benign/Likely_benign' = 15, 'Benign' = 16) -) -ENGINE = MergeTree -PRIMARY KEY key -ORDER BY key -SETTINGS index_granularity = 8192; - -CREATE MATERIALIZED VIEW `GRCh38/SNV_INDEL/entries_to_project_gt_stats_mv` TO `GRCh38/SNV_INDEL/project_gt_stats` -( - `project_guid` LowCardinality(String), - `key` UInt32, - `sample_type` Enum8('WES' = 1, 'WGS' = 2), - `affected` String, - `ref_samples` Int64, - `het_samples` Int64, - `hom_samples` Int64 -) -AS SELECT - project_guid, - key, - sample_type, - dictGetOrDefault('seqrdb_affected_status_dict', 'affected', (family_guid, calls.sampleId), 'U') AS affected, - sumIf(sign, calls.gt = 'REF') AS ref_samples, - sumIf(sign, calls.gt = 'HET') AS het_samples, - sumIf(sign, calls.gt = 'HOM') AS hom_samples -FROM `GRCh38/SNV_INDEL/entries` -ARRAY JOIN calls -GROUP BY - project_guid, - key, - sample_type, - affected; - -CREATE MATERIALIZED VIEW `GRCh38/SNV_INDEL/project_gt_stats_to_gt_stats_mv` -REFRESH EVERY 10 YEAR TO `GRCh38/SNV_INDEL/gt_stats` -( - `key` UInt32, - `ac_wes` UInt64, - `ac_wgs` UInt64, - `ac_affected` UInt64, - `hom_wes` UInt64, - `hom_wgs` UInt64, - `hom_affected` UInt64 -) -AS SELECT - key, - sumIf((het_samples * 1) + (hom_samples * 2), sample_type = 'WES') AS ac_wes, - sumIf((het_samples * 1) + (hom_samples * 2), sample_type = 'WGS') AS ac_wgs, - sumIf((het_samples * 1) + (hom_samples * 2), affected = 'A') AS ac_affected, - sumIf(hom_samples, sample_type = 'WES') AS hom_wes, - sumIf(hom_samples, sample_type = 'WGS') AS hom_wgs, - sumIf(hom_samples, affected = 'A') AS hom_affected -FROM `GRCh38/SNV_INDEL/project_gt_stats` -WHERE project_guid NOT IN ['R0555_seqr_demo', 'R0607_gregor_training_project_', 'R0608_gregor_training_project_', 'R0801_gregor_training_project_', 'R0811_gregor_training_project_', 'R0812_gregor_training_project_', 'R0813_gregor_training_project_', 'R0814_gregor_training_project_', 'R0815_gregor_training_project_', 'R0816_gregor_training_project_'] -GROUP BY key; - -CREATE MATERIALIZED VIEW `GRCh38/SNV_INDEL/reference_data/clinvar/all_variants_to_seqr_variants_mv` -REFRESH EVERY 10 YEAR TO `GRCh38/SNV_INDEL/reference_data/clinvar/seqr_variants` -( - `key` UInt32, - `alleleId` Nullable(UInt32), - `conflictingPathogenicities` Nested(pathogenicity Enum8('Pathogenic' = 0, 'Pathogenic/Likely_pathogenic' = 1, 'Pathogenic/Likely_pathogenic/Established_risk_allele' = 2, 'Pathogenic/Likely_pathogenic/Likely_risk_allele' = 3, 'Pathogenic/Likely_risk_allele' = 4, 'Likely_pathogenic' = 5, 'Likely_pathogenic/Likely_risk_allele' = 6, 'Established_risk_allele' = 7, 'Likely_risk_allele' = 8, 'Conflicting_classifications_of_pathogenicity' = 9, 'Uncertain_risk_allele' = 10, 'Uncertain_significance/Uncertain_risk_allele' = 11, 'Uncertain_significance' = 12, 'No_pathogenic_assertion' = 13, 'Likely_benign' = 14, 'Benign/Likely_benign' = 15, 'Benign' = 16), count UInt16), - `goldStars` Nullable(UInt8), - `submitters` Array(String), - `conditions` Array(String), - `assertions` Array(Enum8('Affects' = 0, 'association' = 1, 'association_not_found' = 2, 'confers_sensitivity' = 3, 'drug_response' = 4, 'low_penetrance' = 5, 'not_provided' = 6, 'other' = 7, 'protective' = 8, 'risk_factor' = 9, 'no_classification_for_the_single_variant' = 10, 'no_classifications_from_unflagged_records' = 11)), - `pathogenicity` Enum8('Pathogenic' = 0, 'Pathogenic/Likely_pathogenic' = 1, 'Pathogenic/Likely_pathogenic/Established_risk_allele' = 2, 'Pathogenic/Likely_pathogenic/Likely_risk_allele' = 3, 'Pathogenic/Likely_risk_allele' = 4, 'Likely_pathogenic' = 5, 'Likely_pathogenic/Likely_risk_allele' = 6, 'Established_risk_allele' = 7, 'Likely_risk_allele' = 8, 'Conflicting_classifications_of_pathogenicity' = 9, 'Uncertain_risk_allele' = 10, 'Uncertain_significance/Uncertain_risk_allele' = 11, 'Uncertain_significance' = 12, 'No_pathogenic_assertion' = 13, 'Likely_benign' = 14, 'Benign/Likely_benign' = 15, 'Benign' = 16) -) -AS SELECT - key, - COLUMNS('.*') EXCEPT (version, variantId, key) -FROM `GRCh38/SNV_INDEL/reference_data/clinvar/all_variants` AS src -INNER JOIN `GRCh38/SNV_INDEL/key_lookup` AS dst ON assumeNotNull(src.variantId) = dst.variantId -LIMIT 1 BY key; - - -CREATE MATERIALIZED VIEW `GRCh38/SNV_INDEL/reference_data/clinvar/seqr_variants_to_search_mv` -REFRESH EVERY 10 YEAR TO `GRCh38/SNV_INDEL/reference_data/clinvar` -( - `key` UInt32, - `alleleId` Nullable(UInt32), - `conflictingPathogenicities` Nested(pathogenicity Enum8('Pathogenic' = 0, 'Pathogenic/Likely_pathogenic' = 1, 'Pathogenic/Likely_pathogenic/Established_risk_allele' = 2, 'Pathogenic/Likely_pathogenic/Likely_risk_allele' = 3, 'Pathogenic/Likely_risk_allele' = 4, 'Likely_pathogenic' = 5, 'Likely_pathogenic/Likely_risk_allele' = 6, 'Established_risk_allele' = 7, 'Likely_risk_allele' = 8, 'Conflicting_classifications_of_pathogenicity' = 9, 'Uncertain_risk_allele' = 10, 'Uncertain_significance/Uncertain_risk_allele' = 11, 'Uncertain_significance' = 12, 'No_pathogenic_assertion' = 13, 'Likely_benign' = 14, 'Benign/Likely_benign' = 15, 'Benign' = 16), count UInt16), - `goldStars` Nullable(UInt8), - `submitters` Array(String), - `conditions` Array(String), - `assertions` Array(Enum8('Affects' = 0, 'association' = 1, 'association_not_found' = 2, 'confers_sensitivity' = 3, 'drug_response' = 4, 'low_penetrance' = 5, 'not_provided' = 6, 'other' = 7, 'protective' = 8, 'risk_factor' = 9, 'no_classification_for_the_single_variant' = 10, 'no_classifications_from_unflagged_records' = 11)), - `pathogenicity` Enum8('Pathogenic' = 0, 'Pathogenic/Likely_pathogenic' = 1, 'Pathogenic/Likely_pathogenic/Established_risk_allele' = 2, 'Pathogenic/Likely_pathogenic/Likely_risk_allele' = 3, 'Pathogenic/Likely_risk_allele' = 4, 'Likely_pathogenic' = 5, 'Likely_pathogenic/Likely_risk_allele' = 6, 'Established_risk_allele' = 7, 'Likely_risk_allele' = 8, 'Conflicting_classifications_of_pathogenicity' = 9, 'Uncertain_risk_allele' = 10, 'Uncertain_significance/Uncertain_risk_allele' = 11, 'Uncertain_significance' = 12, 'No_pathogenic_assertion' = 13, 'Likely_benign' = 14, 'Benign/Likely_benign' = 15, 'Benign' = 16) -) -AS SELECT * -FROM `GRCh38/SNV_INDEL/reference_data/clinvar/seqr_variants` -LIMIT 1 BY key; - From ca83995f5e1cf17298b1bd67d77ceb92b53e1d1c Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 14:31:16 -0400 Subject: [PATCH 205/369] first opass refatcor test clcikhouse --- CLAUDE.md | 4 +- clickhouse_search/constants.py | 13 +- clickhouse_search/models/__init__.py | 6 + clickhouse_search/models/gt_stats_models.py | 12 +- clickhouse_search/models/search_models.py | 28 +- loading_pipeline/lib/misc/clickhouse_test.py | 1762 +++++++---------- .../test/clickhouse_django/seqr/__init__.py | 6 +- .../clickhouse_django/seqr/utils/__init__.py | 4 + .../seqr/utils/logging_utils.py | 25 - .../lib/test/clickhouse_django/settings.py | 4 + .../lib/test/clickhouse_schema_testcase.py | 1 + reference_data/models.py | 4 +- seqr/models.py | 33 +- 13 files changed, 791 insertions(+), 1111 deletions(-) delete mode 100644 loading_pipeline/lib/test/clickhouse_django/seqr/utils/logging_utils.py diff --git a/CLAUDE.md b/CLAUDE.md index dc9f87ef3e..10e1116dbb 100644 --- a/CLAUDE.md +++ b/CLAUDE.md @@ -42,4 +42,6 @@ Single test: `npx jest path/to/File.test.js`. Coverage threshold 40% lines/state ## Development Notes -Never delete a file that is not in source control without confirming first +- Never delete a file that is not in source control without confirming first +- Comments should be kept to a minimum. Only add them where the code is genuinely hard to understand or maintain, and keep them brief. +- Always ask before downloading large amounts of data diff --git a/clickhouse_search/constants.py b/clickhouse_search/constants.py index 2ebb829f03..ebce6e0063 100644 --- a/clickhouse_search/constants.py +++ b/clickhouse_search/constants.py @@ -1,3 +1,7 @@ +from seqr.utils.constants import AFFECTED_STATUS_AFFECTED as AFFECTED, AFFECTED_STATUS_UNAFFECTED as UNAFFECTED, \ + MALE_SEXES, FEMALE_SEXES, SAMPLE_TYPE_WES, SAMPLE_TYPE_WGS, DATASET_TYPE_VARIANT_CALLS, DATASET_TYPE_SV_CALLS, \ + DATASET_TYPE_MITO_CALLS, GENOME_VERSION_GRCh37, GENOME_VERSION_GRCh38 + MAX_VARIANTS = 10000 XPOS_SORT_KEY = 'xpos' @@ -5,15 +9,6 @@ PATHOGENICTY_HGMD_SORT_KEY = 'pathogenicity_hgmd' PRIORITIZED_GENE_SORT = 'prioritized_gene' -# Mirrors seqr.models.Individual.AFFECTED_STATUS_AFFECTED/AFFECTED_STATUS_UNAFFECTED/MALE_SEXES/ -# FEMALE_SEXES - duplicated here (rather than imported) so that this module, and anything that -# only needs these constants (e.g. clickhouse_search's migrations), doesn't have to import -# seqr.models. Keep in sync with seqr/models.py's Individual class if those ever change. -AFFECTED = 'A' -UNAFFECTED = 'N' -MALE_SEXES = ['M', 'XXY', 'XYY'] -FEMALE_SEXES = ['F', 'XXX', 'X0'] - ALT_ALT = 'alt_alt' REF_REF = 'ref_ref' REF_ALT = 'ref_alt' diff --git a/clickhouse_search/models/__init__.py b/clickhouse_search/models/__init__.py index a1c506ef4a..8695ebea5c 100644 --- a/clickhouse_search/models/__init__.py +++ b/clickhouse_search/models/__init__.py @@ -12,6 +12,12 @@ ) state.DEFAULT_NAMES = options.DEFAULT_NAMES +# Importing these registers their model classes with Django's app registry (apps.get_model()), +# which fixture loaddata needs to resolve "clickhouse_search." identifiers. Nothing else +# in this package imports them directly otherwise. Must come after the DEFAULT_NAMES patch above - +# these modules' Meta classes use the custom fields it allowlists. +from clickhouse_search.models import postgres_dicts, reference_data_models, search_models, gt_stats_models # noqa: F401,E402 + class ClickHouseRouter: # Adapted from https://github.com/jayvynl/django-clickhouse-backend/blob/v1.3.2/README.md#configuration diff --git a/clickhouse_search/models/gt_stats_models.py b/clickhouse_search/models/gt_stats_models.py index 3076b65054..efd071a22d 100644 --- a/clickhouse_search/models/gt_stats_models.py +++ b/clickhouse_search/models/gt_stats_models.py @@ -3,8 +3,8 @@ from clickhouse_search.backend.fields import UInt32FieldDeltaCodecField, DictKeyForeignKey from clickhouse_search.backend.table_models import RefreshableMaterializedView, RefreshableMaterializedViewMeta, \ IncrementalMaterializedView, Dictionary -from reference_data.models import GENOME_VERSION_GRCh38, GENOME_VERSION_GRCh37 -from seqr.models import Dataset +from seqr.utils.constants import GENOME_VERSION_GRCh38, GENOME_VERSION_GRCh37, \ + DATASET_TYPE_VARIANT_CALLS, DATASET_TYPE_SV_CALLS, DATASET_TYPE_MITO_CALLS class BaseProjectGtStats(models.ClickhouseModel): @@ -307,10 +307,10 @@ class Meta(GtStatsDictMeta): layout = 'FLAT(MAX_ARRAY_SIZE 5000000)' PROJECT_GT_STATS_VIEW_CLASS_MAP = { - GENOME_VERSION_GRCh37: {Dataset.DATASET_TYPE_VARIANT_CALLS: ProjectsToGtStatsGRCh37SnvIndel}, + GENOME_VERSION_GRCh37: {DATASET_TYPE_VARIANT_CALLS: ProjectsToGtStatsGRCh37SnvIndel}, GENOME_VERSION_GRCh38: { - Dataset.DATASET_TYPE_VARIANT_CALLS: ProjectsToGtStatsSnvIndel, - Dataset.DATASET_TYPE_MITO_CALLS: ProjectsToGtStatsMito, - Dataset.DATASET_TYPE_SV_CALLS: ProjectsToGtStatsSv, + DATASET_TYPE_VARIANT_CALLS: ProjectsToGtStatsSnvIndel, + DATASET_TYPE_MITO_CALLS: ProjectsToGtStatsMito, + DATASET_TYPE_SV_CALLS: ProjectsToGtStatsSv, }, } diff --git a/clickhouse_search/models/search_models.py b/clickhouse_search/models/search_models.py index f7d52cd17c..50aedf1325 100644 --- a/clickhouse_search/models/search_models.py +++ b/clickhouse_search/models/search_models.py @@ -9,8 +9,8 @@ VariantDetailsQuerySet from clickhouse_search.models.reference_data_models import GnomadNonCodingConstraintDict, BaseSpliceAi, \ ScreenDict -from reference_data.models import GENOME_VERSION_GRCh38, GENOME_VERSION_GRCh37 -from seqr.models import Dataset +from seqr.utils.constants import GENOME_VERSION_GRCh38, GENOME_VERSION_GRCh37, \ + SAMPLE_TYPE_WES, SAMPLE_TYPE_WGS, DATASET_TYPE_VARIANT_CALLS, DATASET_TYPE_SV_CALLS, DATASET_TYPE_MITO_CALLS from seqr.utils.xpos_utils import CHROMOSOME_CHOICES from settings import CLICKHOUSE_IN_MEMORY_DIR, CLICKHOUSE_DATA_DIR @@ -406,7 +406,7 @@ class Meta(BaseEntries.Meta): ) class EntriesSv(BaseEntries): - SAMPLE_TYPE = Dataset.SAMPLE_TYPE_WGS + SAMPLE_TYPE = SAMPLE_TYPE_WGS CALL_FIELDS = [ ('sampleId', models.StringField()), ('gt', models.Enum8Field(null=True, blank=True, choices=[(0, 'REF'), (1, 'HET'), (2, 'HOM')])), @@ -428,7 +428,7 @@ class Meta(BaseEntries.Meta): db_table = 'GRCh38/SV/entries' class EntriesGcnv(BaseEntries): - SAMPLE_TYPE = Dataset.SAMPLE_TYPE_WES + SAMPLE_TYPE = SAMPLE_TYPE_WES CALL_FIELDS = [ ('sampleId', models.StringField()), ('gt', models.Enum8Field(null=True, blank=True, choices=[(0, 'REF'), (1, 'HET'), (2, 'HOM')])), @@ -613,21 +613,21 @@ class Meta: ENTRY_CLASS_MAP = { - GENOME_VERSION_GRCh37: {Dataset.DATASET_TYPE_VARIANT_CALLS: EntriesGRCh37SnvIndel}, + GENOME_VERSION_GRCh37: {DATASET_TYPE_VARIANT_CALLS: EntriesGRCh37SnvIndel}, GENOME_VERSION_GRCh38: { - Dataset.DATASET_TYPE_VARIANT_CALLS: EntriesSnvIndel, - Dataset.DATASET_TYPE_MITO_CALLS: EntriesMito, - f'{Dataset.DATASET_TYPE_SV_CALLS}_{Dataset.SAMPLE_TYPE_WGS}': EntriesSv, - f'{Dataset.DATASET_TYPE_SV_CALLS}_{Dataset.SAMPLE_TYPE_WES}': EntriesGcnv, + DATASET_TYPE_VARIANT_CALLS: EntriesSnvIndel, + DATASET_TYPE_MITO_CALLS: EntriesMito, + f'{DATASET_TYPE_SV_CALLS}_{SAMPLE_TYPE_WGS}': EntriesSv, + f'{DATASET_TYPE_SV_CALLS}_{SAMPLE_TYPE_WES}': EntriesGcnv, }, } VARIANTS_CLASS_MAP = { - GENOME_VERSION_GRCh37: {Dataset.DATASET_TYPE_VARIANT_CALLS: VariantsGRCh37SnvIndel}, + GENOME_VERSION_GRCh37: {DATASET_TYPE_VARIANT_CALLS: VariantsGRCh37SnvIndel}, GENOME_VERSION_GRCh38: { - Dataset.DATASET_TYPE_VARIANT_CALLS: VariantsSnvIndel, - Dataset.DATASET_TYPE_MITO_CALLS: VariantsMito, - f'{Dataset.DATASET_TYPE_SV_CALLS}_{Dataset.SAMPLE_TYPE_WGS}': VariantsSv, - f'{Dataset.DATASET_TYPE_SV_CALLS}_{Dataset.SAMPLE_TYPE_WES}': VariantsGcnv, + DATASET_TYPE_VARIANT_CALLS: VariantsSnvIndel, + DATASET_TYPE_MITO_CALLS: VariantsMito, + f'{DATASET_TYPE_SV_CALLS}_{SAMPLE_TYPE_WGS}': VariantsSv, + f'{DATASET_TYPE_SV_CALLS}_{SAMPLE_TYPE_WES}': VariantsGcnv, }, } VARIANT_DETAILS_CLASS_MAP = { diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index b4e7673664..eba49231af 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -4,6 +4,7 @@ import pandas as pd import pyarrow as pa import pyarrow.parquet as pq +from django.db import connections from loading_pipeline.lib.core import DatasetType, ReferenceGenome from loading_pipeline.lib.core.environment import Env @@ -38,313 +39,83 @@ new_variants_parquet_path, runs_path, ) +from loading_pipeline.lib.test.clickhouse_schema_testcase import ( + ClickhouseSchemaTestCase, +) from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase TEST_RUN_ID = 'manual__2025-05-07T17-20-59.702114+00-00' -class ClickhouseTest(MockedDatarootTestCase): - def setUp(self): - super().setUp() - client = get_clickhouse_client() - client.execute( - f""" - DROP DATABASE IF EXISTS {STAGING_CLICKHOUSE_DATABASE}; - """, - ) - client.execute( - f""" - DROP DATABASE IF EXISTS {Env.CLICKHOUSE_DATABASE}; - """, - ) - client.execute( - f""" - CREATE DATABASE {Env.CLICKHOUSE_DATABASE}; - """, - ) - client.execute( - f""" - CREATE TABLE {Env.CLICKHOUSE_DATABASE}.seqrdb_gene_ids_src ( - gene_id String, - seqrdb_id UInt32 - ) ENGINE = Memory; - """, - ) - client.execute( - f'INSERT INTO {Env.CLICKHOUSE_DATABASE}.`seqrdb_gene_ids_src` VALUES', - [('GENE1', 123), ('GENE2', 12), ('GENE3', 1)], - ) - client.execute( - f""" - CREATE DICTIONARY {Env.CLICKHOUSE_DATABASE}.seqrdb_gene_ids - ( - gene_id String, - seqrdb_id UInt32 - ) - PRIMARY KEY gene_id - SOURCE(CLICKHOUSE( - USER {Env.CLICKHOUSE_WRITER_USER} PASSWORD {Env.CLICKHOUSE_WRITER_PASSWORD} - DB {Env.CLICKHOUSE_DATABASE} TABLE `seqrdb_gene_ids_src` - )) - LAYOUT(HASHED()) - LIFETIME(0); - """, - ) - client.execute( - f""" - CREATE TABLE {Env.CLICKHOUSE_DATABASE}.gnomad_genomes_src ( - key UInt32, - filter_af Decimal(9, 8) - ) ENGINE = Memory; - """, - ) - client.execute( - f'INSERT INTO {Env.CLICKHOUSE_DATABASE}.`gnomad_genomes_src` VALUES', - [(11, 0.06), (12, 0.001), (13, 0.0001)], - ) - client.execute( - f""" - CREATE DICTIONARY {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/reference_data/gnomad_genomes` - ( - key UInt32, - filter_af Decimal(9, 8) - ) - PRIMARY KEY key - SOURCE(CLICKHOUSE( - USER {Env.CLICKHOUSE_WRITER_USER} PASSWORD {Env.CLICKHOUSE_WRITER_PASSWORD} - DB {Env.CLICKHOUSE_DATABASE} TABLE `gnomad_genomes_src` - )) - LAYOUT(HASHED()) - LIFETIME(0); - """, - ) - client.execute( - f""" - CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` ( - `key` UInt32, - `project_guid` LowCardinality(String), - `family_guid` String, - `xpos` UInt64 CODEC(Delta(8), ZSTD(1)), - `sample_type` Enum8('WES' = 0, 'WGS' = 1), - `is_gnomad_gt_5_percent` Boolean, - `is_annotated_in_any_gene` Boolean DEFAULT length(geneId_ids) > 0, - `geneId_ids` Array(UInt32), - `calls` Array( - Tuple( - sampleId String, - gt Nullable(Enum8('REF' = 0, 'HET' = 1, 'HOM' = 2)), - ) - ), - `sign` Int8, - PROJECTION xpos_projection - ( - SELECT * - ORDER BY is_annotated_in_any_gene, xpos - ) +class ClickhouseTest(MockedDatarootTestCase, ClickhouseSchemaTestCase): + fixtures = ['clickhouse_test'] + + @classmethod + def setUpClass(cls): + super().setUpClass() + # seqrdb_gene_ids/seqrdb_affected_status_dict are Postgres-sourced in production (see + # postgres_dicts.py) - no ClickHouse-side model backs them, so override with + # deterministic ClickHouse-sourced versions. Runs once for the class: inserting the + # `entries` fixture rows (loaded per-test, before setUp()) triggers + # entries_to_project_gt_stats_mv, which queries seqrdb_affected_status_dict. + with connections['clickhouse_write'].cursor() as cursor: + cursor.execute( + f""" + CREATE TABLE IF NOT EXISTS {Env.CLICKHOUSE_DATABASE}.seqrdb_gene_ids_src ( + gene_id String, + seqrdb_id UInt32 + ) ENGINE = Memory; + """, ) - ENGINE = CollapsingMergeTree(sign) - PARTITION BY project_guid - ORDER BY (project_guid, family_guid, key) - SETTINGS deduplicate_merge_projection_mode = 'rebuild'; - """, - ) - client.execute( - f""" - CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` - ( - `project_guid` String, - `key` UInt32, - `sample_type` Enum8('WES' = 0, 'WGS' = 1), - `het_samples` Int32, - `hom_samples` Int32, - ) - ENGINE = SummingMergeTree - PARTITION BY project_guid - ORDER BY (project_guid, key, sample_type) - """, - ) - client.execute( - f""" - CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` - ( - `key` UInt32, - `ac_wes` UInt32, - `ac_wgs` UInt32, - ) - ENGINE = SummingMergeTree - ORDER BY (key) - """, - ) - client.execute( - f""" - CREATE MATERIALIZED VIEW {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries_to_project_gt_stats_mv` - TO {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` - AS SELECT - project_guid, - key, - sample_type, - sum(toInt32(arrayCount(s -> (s.gt = 'HET'), calls) * sign)) AS het_samples, - sum(toInt32(arrayCount(s -> (s.gt = 'HOM'), calls) * sign)) AS hom_samples - FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` - GROUP BY project_guid, key, sample_type - """, - ) - client.execute( - f""" - CREATE MATERIALIZED VIEW {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats_to_gt_stats_mv` - REFRESH EVERY 10 YEAR TO {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` - AS SELECT - key, - sumIf(het_samples * 1 + hom_samples * 2, sample_type = 'WES') AS ac_wes, - sumIf(het_samples * 1 + hom_samples * 2, sample_type = 'WGS') AS ac_wgs - FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` - GROUP BY key - """, - ) - client.execute( - f""" - CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details` ( - key UInt32, - variantId String, - transcripts String - ) ENGINE = EmbeddedRocksDB() - PRIMARY KEY `key` - """, - ) - client.execute( - f""" - CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` ( - key UInt32, - variantId String, - ) ENGINE = EmbeddedRocksDB() - PRIMARY KEY `key` - """, - ) - client.execute( - f""" - CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_disk` ( - key UInt32, - variantId String, - ) ENGINE = EmbeddedRocksDB() - PRIMARY KEY `key` - """, - ) - client.execute( - f""" - CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/key_lookup` ( - variantId String, - key UInt32, - ) ENGINE = EmbeddedRocksDB() - PRIMARY KEY `variantId` - """, - ) - client.execute( - f""" - CREATE DICTIONARY {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` - ( - `key` UInt32, - `ac_wes` UInt16, - `ac_wgs` UInt16 - ) - PRIMARY KEY key - SOURCE( - CLICKHOUSE( - USER {Env.CLICKHOUSE_WRITER_USER} PASSWORD {Env.CLICKHOUSE_WRITER_PASSWORD} - DB {Env.CLICKHOUSE_DATABASE} TABLE `GRCh38/SNV_INDEL/gt_stats` - ) + cursor.execute( + f'INSERT INTO {Env.CLICKHOUSE_DATABASE}.`seqrdb_gene_ids_src` VALUES', + [('GENE1', 123), ('GENE2', 12), ('GENE3', 1)], ) - LIFETIME(0) - LAYOUT(FLAT(MAX_ARRAY_SIZE 10000)) - """, - ) - client.execute( - f""" - CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/reference_data/clinvar/all_variants` ( - `variantId` String, - `alleleId` Nullable(UInt32), - `pathogenicity` Enum8( - 'Pathogenic' = 0, - 'Pathogenic/Likely_pathogenic' = 1 + cursor.execute( + f""" + CREATE OR REPLACE DICTIONARY {Env.CLICKHOUSE_DATABASE}.seqrdb_gene_ids + ( + gene_id String, + seqrdb_id UInt32 ) + PRIMARY KEY gene_id + SOURCE(CLICKHOUSE( + USER {Env.CLICKHOUSE_WRITER_USER} PASSWORD {Env.CLICKHOUSE_WRITER_PASSWORD} + DB {Env.CLICKHOUSE_DATABASE} TABLE `seqrdb_gene_ids_src` + )) + LAYOUT(HASHED()) + LIFETIME(0); + """, ) - PRIMARY KEY `variantId` - """, - ) - client.execute( - f""" - CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/reference_data/clinvar/seqr_variants` ( - `key` UInt32, - `alleleId` Nullable(UInt32), - `pathogenicity` Enum8( - 'Pathogenic' = 0, - 'Pathogenic/Likely_pathogenic' = 1 - ) + cursor.execute( + f""" + CREATE TABLE IF NOT EXISTS {Env.CLICKHOUSE_DATABASE}.seqrdb_affected_status_dict_src ( + family_guid String, + sampleId String, + affected String + ) ENGINE = Memory; + """, ) - PRIMARY KEY `key` - """, - ) - client.execute( - f""" - CREATE MATERIALIZED VIEW {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/reference_data/clinvar/seqr_variants_to_search_mv` - REFRESH EVERY 10 YEAR ENGINE = Null - AS SELECT DISTINCT ON (key) * - FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/reference_data/clinvar/seqr_variants` - """, - ) - client.execute( - f""" - CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/entries` ( - `key` UInt32, - `project_guid` LowCardinality(String), - `family_guid` String, - `xpos` UInt64 CODEC(Delta(8), ZSTD(1)), - `sample_type` Enum8('WES' = 0, 'WGS' = 1), - `calls` Array( - Tuple( - sampleId String, - gt Nullable(Enum8('REF' = 0, 'HET' = 1, 'HOM' = 2)), - ) - ), - `sign` Int8, - PROJECTION xpos_projection + cursor.execute( + f""" + CREATE OR REPLACE DICTIONARY {Env.CLICKHOUSE_DATABASE}.seqrdb_affected_status_dict ( - SELECT * - ORDER BY xpos + family_guid String, + sampleId String, + affected String ) + PRIMARY KEY family_guid, sampleId + SOURCE(CLICKHOUSE( + USER {Env.CLICKHOUSE_WRITER_USER} PASSWORD {Env.CLICKHOUSE_WRITER_PASSWORD} + DB {Env.CLICKHOUSE_DATABASE} TABLE `seqrdb_affected_status_dict_src` + )) + LAYOUT(COMPLEX_KEY_HASHED()) + LIFETIME(0); + """, ) - ENGINE = CollapsingMergeTree(sign) - PARTITION BY project_guid - ORDER BY (project_guid, family_guid, key) - SETTINGS deduplicate_merge_projection_mode = 'rebuild'; - """, - ) - client.execute( - f""" - CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/variants_memory` ( - key UInt32, - variantId String, - ) ENGINE = EmbeddedRocksDB() - PRIMARY KEY `key` - """, - ) - client.execute( - f""" - CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/variants_disk` ( - key UInt32, - variantId String, - ) ENGINE = EmbeddedRocksDB() - PRIMARY KEY `key` - """, - ) - client.execute( - f""" - CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/key_lookup` ( - variantId String, - key UInt32, - ) ENGINE = EmbeddedRocksDB() - PRIMARY KEY `variantId` - """, - ) + + def setUp(self): + super().setUp() base_path = runs_path( ReferenceGenome.GRCh38, DatasetType.SNV_INDEL, @@ -365,7 +136,6 @@ def write_test_parquet(df: pd.DataFrame, parquet_path: str, schema=None): ), ) - # Variant Details Parquet df = pd.DataFrame( { 'key': [1, 2, 3, 4], @@ -387,7 +157,6 @@ def write_test_parquet(df: pd.DataFrame, parquet_path: str, schema=None): ), ) - # New Variants parquet. df = pd.DataFrame( { 'key': [10, 11, 12, 13], @@ -416,7 +185,6 @@ def write_test_parquet(df: pd.DataFrame, parquet_path: str, schema=None): ), ) - # New Entries Parquet df = pd.DataFrame( { 'key': [0, 3, 4], @@ -493,30 +261,6 @@ def write_test_parquet(df: pd.DataFrame, parquet_path: str, schema=None): schema.remove(5).remove(5), ) - def tearDown(self): - super().tearDown() - client = get_clickhouse_client() - client.execute( - f""" - DROP DICTIONARY IF EXISTS {Env.CLICKHOUSE_DATABASE}.seqrdb_gene_ids; - """, - ) - client.execute( - f""" - DROP DICTIONARY IF EXISTS {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/reference_data/gnomad_genomes`; - """, - ) - client.execute( - f""" - DROP DATABASE IF EXISTS {Env.CLICKHOUSE_DATABASE}; - """, - ) - client.execute( - f""" - DROP DATABASE IF EXISTS {STAGING_CLICKHOUSE_DATABASE}; - """, - ) - def test_get_clickhouse_client(self): client = get_clickhouse_client() result = client.execute('SELECT 1') @@ -557,47 +301,47 @@ def test_table_name_builder(self): ) def test_direct_insert_all_keys(self): - client = get_clickhouse_client() - client.execute( - f'INSERT INTO {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details` VALUES', - [(1, 'a', 'e'), (10, 'b', 'f'), (7, 'c', 'g')], - ) - direct_insert_all_keys( - ClickHouseTable.VARIANT_DETAILS, - TableNameBuilder( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ), - ) - ret = client.execute( - f'SELECT * FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', - ) - self.assertEqual( - ret, - [ - (1, '1-13-A-C', 'a'), - (2, '2-14-A-T', 'b'), - (3, 'Y-19-A-C', 'c'), - (4, 'M-12-C-G', 'd'), - (7, 'c', 'g'), - (10, 'b', 'f'), - ], - ) + with connections['clickhouse_write'].cursor() as cursor: + cursor.execute( + f'INSERT INTO {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details` VALUES', + [(1, 'a', 'e'), (10, 'b', 'f'), (7, 'c', 'g')], + ) + direct_insert_all_keys( + ClickHouseTable.VARIANT_DETAILS, + TableNameBuilder( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ) + cursor.execute( + f'SELECT * FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', + ) + self.assertEqual( + cursor.fetchall(), + [ + (1, '1-13-A-C', 'a'), + (2, '2-14-A-T', 'b'), + (3, 'Y-19-A-C', 'c'), + (4, 'M-12-C-G', 'd'), + (7, 'c', 'g'), + (10, 'b', 'f'), + ], + ) - # ensure multiple calls are idempotent - direct_insert_all_keys( - ClickHouseTable.VARIANT_DETAILS, - TableNameBuilder( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ), - ) - ret = client.execute( - f'SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', - ) - self.assertEqual(ret[0][0], 6) + # ensure multiple calls are idempotent + direct_insert_all_keys( + ClickHouseTable.VARIANT_DETAILS, + TableNameBuilder( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ) + cursor.execute( + f'SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', + ) + self.assertEqual(cursor.fetchone()[0], 6) @patch.object( ClickhouseReferenceDataset, @@ -605,372 +349,350 @@ def test_direct_insert_all_keys(self): return_value=[ClickhouseReferenceDataset.CLINVAR], ) def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): - # Tests individual components of the atomic_insert_entries - # to validate the state after each step. - client = get_clickhouse_client() - client.execute( - f""" - INSERT INTO {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` - VALUES - (0, 'project_a', 'family_a1', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_a1','HOM')], 1), - (1, 'project_a', 'family_a2', 123456789, 'WGS', 0, 0, CAST([] AS Array(UInt32)), [('sample_a2','HET')], 1), - (2, 'project_a', 'family_a3', 133456789, 'WGS', 0, 0, CAST([] AS Array(UInt32)), [('sample_a3','HOM')], 1), - (3, 'project_a', 'family_a4', 133456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_a4','REF')], 1), - (4, 'project_a', 'family_a5', 133456789, 'WES', 0, 1, CAST([0] AS Array(UInt32)), [('sample_a5','REF'),('sample_a6','HET'),('sample_a7','REF')], 1), - (4, 'project_a', 'family_a6', 133456789, 'WGS', 0, 0, CAST([] AS Array(UInt32)), [('sample_a8','HOM')], 1), - (0, 'project_b', 'family_b1', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b4','REF')], 1), - (1, 'project_b', 'family_b2', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b5','HET')], 1), - (2, 'project_b', 'family_b2', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b5','REF')], 1), - (3, 'project_b', 'family_b3', 133456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b6','HOM')], 1), - (4, 'project_b', 'family_b3', 133456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b6','HOM')], 1), - (0, 'project_c', 'family_c1', 123456789, 'WES', 0, 1, CAST([1] AS Array(UInt32)), [('sample_c7','REF')], 1), - (3, 'project_c', 'family_c2', 123456789, 'WES', 0, 1, CAST([1] AS Array(UInt32)), [('sample_c8','REF')], 1), - (4, 'project_c', 'family_c3', 133456789, 'WES', 0, 1, CAST([1] AS Array(UInt32)), [('sample_c9','HOM')], 1), - (5, 'project_c', 'family_c4', 133456789, 'WES', 0, 1, CAST([1] AS Array(UInt32)), [('sample_c9','HOM')], 1) - """, - ) - table_name_builder = TableNameBuilder( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ) - create_staging_tables( - table_name_builder, - ClickHouseTable.for_dataset_type_atomic_entries_update( - DatasetType.SNV_INDEL, - ), - ) - create_staging_materialized_views( - table_name_builder, - ClickHouseMaterializedView.for_dataset_type_atomic_entries_update( - DatasetType.SNV_INDEL, - ), - ) - stage_existing_project_partitions( - table_name_builder, - [ - 'project_a', - 'project_b', - 'project_d', # Partition does not exist already. - ], - ClickHouseTable.for_dataset_type_atomic_entries_update_project_partitioned( - DatasetType.SNV_INDEL, - ), - ) - staged_projects = client.execute( - f""" - SELECT DISTINCT project_guid FROM {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/entries` - """, - ) - self.assertCountEqual( - [p[0] for p in staged_projects], - ['project_a', 'project_b'], - ) - staged_project_gt_stats = client.execute( - f""" - SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) - FROM - {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/project_gt_stats` - GROUP BY project_guid, key, sample_type - """, - ) - self.assertCountEqual( - staged_project_gt_stats, - [ - ('project_a', 0, 'WES', 0, 1), - ('project_a', 1, 'WGS', 1, 0), - ('project_a', 2, 'WGS', 0, 1), - ('project_a', 4, 'WES', 1, 0), - ('project_a', 4, 'WGS', 0, 1), - ('project_b', 1, 'WES', 1, 0), - ('project_b', 3, 'WES', 0, 1), - ('project_b', 4, 'WES', 0, 1), - # project_gt_stats stages all projects, not just - # those requested for loading. - ('project_c', 4, 'WES', 0, 1), - ('project_c', 5, 'WES', 0, 1), - ], - ) - delete_existing_families_from_staging_entries( - table_name_builder, - ['family_a1', 'family_a5', 'family_a6'], - ) - staged_project_gt_stats = client.execute( - f""" - SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) - FROM - {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/project_gt_stats` - GROUP BY project_guid, key, sample_type - """, - ) - self.assertCountEqual( - staged_project_gt_stats, - [ - ('project_a', 0, 'WES', 0, 0), - ('project_a', 1, 'WGS', 1, 0), - ('project_a', 2, 'WGS', 0, 1), - ('project_a', 4, 'WES', 0, 0), - ('project_a', 4, 'WGS', 0, 0), - ('project_b', 1, 'WES', 1, 0), - ('project_b', 3, 'WES', 0, 1), - ('project_b', 4, 'WES', 0, 1), - ('project_c', 4, 'WES', 0, 1), - ('project_c', 5, 'WES', 0, 1), - ], - ) - insert_new_entries(table_name_builder) - optimize_entries( - table_name_builder, - ['project_a', 'project_b', 'project_c'], - ) - staged_project_gt_stats = client.execute( - f""" - SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) - FROM - {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/project_gt_stats` - GROUP BY project_guid, key, sample_type - """, - ) - self.assertCountEqual( - staged_project_gt_stats, - [ - ('project_a', 0, 'WES', 0, 0), - ('project_a', 1, 'WGS', 1, 0), - ('project_a', 2, 'WGS', 0, 1), - ('project_a', 4, 'WES', 0, 0), - ('project_a', 4, 'WGS', 0, 0), - ('project_b', 1, 'WES', 1, 0), - ('project_b', 3, 'WES', 0, 1), - ('project_b', 4, 'WES', 0, 1), - ('project_c', 4, 'WES', 0, 1), - ('project_c', 5, 'WES', 0, 1), - ('project_d', 0, 'WES', 0, 1), - ('project_d', 4, 'WES', 1, 0), - ], - ) - refresh_materialized_views( - table_name_builder, - ClickHouseMaterializedView.for_dataset_type_atomic_entries_update_refreshable( - DatasetType.SNV_INDEL, - ), - staging=True, - ) - replace_project_partitions( - table_name_builder, - ClickHouseTable.for_dataset_type_atomic_entries_update_project_partitioned( + # Tests individual components of atomic_insert_entries, validating state after each step. + with connections['clickhouse_write'].cursor() as cursor: + table_name_builder = TableNameBuilder( + ReferenceGenome.GRCh38, DatasetType.SNV_INDEL, - ), - ['project_a', 'project_d'], - ) - new_entries = client.execute( - f""" - SELECT COLUMNS('.*') EXCEPT(is_annotated_in_any_gene, is_gnomad_gt_5_percent) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` - """, - ) - self.assertCountEqual( - new_entries, - [ - ( - 0, - 'project_b', - 'family_b1', - 123456789, - 'WES', - [], - [('sample_b4', 'REF')], - 1, - ), - ( - 1, - 'project_b', - 'family_b2', - 123456789, - 'WES', - [], - [('sample_b5', 'HET')], - 1, - ), - ( - 2, - 'project_b', - 'family_b2', - 123456789, - 'WES', - [], - [('sample_b5', 'REF')], - 1, - ), - ( - 3, - 'project_b', - 'family_b3', - 133456789, - 'WES', - [], - [('sample_b6', 'HOM')], - 1, - ), - ( - 4, - 'project_b', - 'family_b3', - 133456789, - 'WES', - [], - [('sample_b6', 'HOM')], - 1, - ), - ( - 1, - 'project_a', - 'family_a2', - 123456789, - 'WGS', - [], - [('sample_a2', 'HET')], - 1, + TEST_RUN_ID, + ) + create_staging_tables( + table_name_builder, + ClickHouseTable.for_dataset_type_atomic_entries_update( + DatasetType.SNV_INDEL, ), - ( - 2, - 'project_a', - 'family_a3', - 133456789, - 'WGS', - [], - [('sample_a3', 'HOM')], - 1, + ) + create_staging_materialized_views( + table_name_builder, + ClickHouseMaterializedView.for_dataset_type_atomic_entries_update( + DatasetType.SNV_INDEL, ), - ( - 3, + ) + stage_existing_project_partitions( + table_name_builder, + [ 'project_a', - 'family_a4', - 133456789, - 'WES', - [], - [('sample_a4', 'REF')], - 1, - ), - ( - 0, - 'project_d', - 'family_d1', - 123456789, - 'WES', - [], - [('sample_d1', 'REF'), ('sample_d11', 'HOM')], - 1, - ), - ( - 3, - 'project_d', - 'family_d2', - 123456789, - 'WES', - [123, 12], - [('sample_d2', 'REF')], - 1, - ), - ( - 4, - 'project_d', - 'family_d3', - 123456789, - 'WES', - [1], - [('sample_d3', 'HET')], - 1, - ), - ( - 0, - 'project_c', - 'family_c1', - 123456789, - 'WES', - [1], - [('sample_c7', 'REF')], - 1, + 'project_b', + 'project_d', # Partition does not exist already. + ], + ClickHouseTable.for_dataset_type_atomic_entries_update_project_partitioned( + DatasetType.SNV_INDEL, ), - ( - 3, - 'project_c', - 'family_c2', - 123456789, - 'WES', - [1], - [('sample_c8', 'REF')], - 1, + ) + cursor.execute( + f""" + SELECT DISTINCT project_guid FROM {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/entries` + """, + ) + self.assertCountEqual( + [p[0] for p in cursor.fetchall()], + ['project_a', 'project_b'], + ) + cursor.execute( + f""" + SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) + FROM + {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/project_gt_stats` + GROUP BY project_guid, key, sample_type + """, + ) + self.assertCountEqual( + cursor.fetchall(), + [ + ('project_a', 0, 'WES', 0, 1), + ('project_a', 1, 'WGS', 1, 0), + ('project_a', 2, 'WGS', 0, 1), + ('project_a', 4, 'WES', 1, 0), + ('project_a', 4, 'WGS', 0, 1), + ('project_b', 1, 'WES', 1, 0), + ('project_b', 3, 'WES', 0, 1), + ('project_b', 4, 'WES', 0, 1), + # project_gt_stats stages all projects, not just + # those requested for loading. + ('project_c', 4, 'WES', 0, 1), + ('project_c', 5, 'WES', 0, 1), + ], + ) + delete_existing_families_from_staging_entries( + table_name_builder, + ['family_a1', 'family_a5', 'family_a6'], + ) + cursor.execute( + f""" + SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) + FROM + {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/project_gt_stats` + GROUP BY project_guid, key, sample_type + """, + ) + self.assertCountEqual( + cursor.fetchall(), + [ + ('project_a', 0, 'WES', 0, 0), + ('project_a', 1, 'WGS', 1, 0), + ('project_a', 2, 'WGS', 0, 1), + ('project_a', 4, 'WES', 0, 0), + ('project_a', 4, 'WGS', 0, 0), + ('project_b', 1, 'WES', 1, 0), + ('project_b', 3, 'WES', 0, 1), + ('project_b', 4, 'WES', 0, 1), + ('project_c', 4, 'WES', 0, 1), + ('project_c', 5, 'WES', 0, 1), + ], + ) + insert_new_entries(table_name_builder) + optimize_entries( + table_name_builder, + ['project_a', 'project_b', 'project_c'], + ) + cursor.execute( + f""" + SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) + FROM + {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/project_gt_stats` + GROUP BY project_guid, key, sample_type + """, + ) + self.assertCountEqual( + cursor.fetchall(), + [ + ('project_a', 0, 'WES', 0, 0), + ('project_a', 1, 'WGS', 1, 0), + ('project_a', 2, 'WGS', 0, 1), + ('project_a', 4, 'WES', 0, 0), + ('project_a', 4, 'WGS', 0, 0), + ('project_b', 1, 'WES', 1, 0), + ('project_b', 3, 'WES', 0, 1), + ('project_b', 4, 'WES', 0, 1), + ('project_c', 4, 'WES', 0, 1), + ('project_c', 5, 'WES', 0, 1), + ('project_d', 0, 'WES', 0, 1), + ('project_d', 4, 'WES', 1, 0), + ], + ) + refresh_materialized_views( + table_name_builder, + ClickHouseMaterializedView.for_dataset_type_atomic_entries_update_refreshable( + DatasetType.SNV_INDEL, ), - ( - 4, - 'project_c', - 'family_c3', - 133456789, - 'WES', - [1], - [('sample_c9', 'HOM')], - 1, + staging=True, + ) + replace_project_partitions( + table_name_builder, + ClickHouseTable.for_dataset_type_atomic_entries_update_project_partitioned( + DatasetType.SNV_INDEL, ), - ( - 5, - 'project_c', - 'family_c4', - 133456789, - 'WES', - [1], - [('sample_c9', 'HOM')], - 1, + ['project_a', 'project_d'], + ) + cursor.execute( + f""" + SELECT COLUMNS('.*') EXCEPT(is_annotated_in_any_gene, is_gnomad_gt_5_percent) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` + """, + ) + self.assertCountEqual( + cursor.fetchall(), + [ + ( + 0, + 'project_b', + 'family_b1', + 123456789, + 'WES', + [], + [('sample_b4', 'REF')], + 1, + ), + ( + 1, + 'project_b', + 'family_b2', + 123456789, + 'WES', + [], + [('sample_b5', 'HET')], + 1, + ), + ( + 2, + 'project_b', + 'family_b2', + 123456789, + 'WES', + [], + [('sample_b5', 'REF')], + 1, + ), + ( + 3, + 'project_b', + 'family_b3', + 133456789, + 'WES', + [], + [('sample_b6', 'HOM')], + 1, + ), + ( + 4, + 'project_b', + 'family_b3', + 133456789, + 'WES', + [], + [('sample_b6', 'HOM')], + 1, + ), + ( + 1, + 'project_a', + 'family_a2', + 123456789, + 'WGS', + [], + [('sample_a2', 'HET')], + 1, + ), + ( + 2, + 'project_a', + 'family_a3', + 133456789, + 'WGS', + [], + [('sample_a3', 'HOM')], + 1, + ), + ( + 3, + 'project_a', + 'family_a4', + 133456789, + 'WES', + [], + [('sample_a4', 'REF')], + 1, + ), + ( + 0, + 'project_d', + 'family_d1', + 123456789, + 'WES', + [], + [('sample_d1', 'REF'), ('sample_d11', 'HOM')], + 1, + ), + ( + 3, + 'project_d', + 'family_d2', + 123456789, + 'WES', + [123, 12], + [('sample_d2', 'REF')], + 1, + ), + ( + 4, + 'project_d', + 'family_d3', + 123456789, + 'WES', + [1], + [('sample_d3', 'HET')], + 1, + ), + ( + 0, + 'project_c', + 'family_c1', + 123456789, + 'WES', + [1], + [('sample_c7', 'REF')], + 1, + ), + ( + 3, + 'project_c', + 'family_c2', + 123456789, + 'WES', + [1], + [('sample_c8', 'REF')], + 1, + ), + ( + 4, + 'project_c', + 'family_c3', + 133456789, + 'WES', + [1], + [('sample_c9', 'HOM')], + 1, + ), + ( + 5, + 'project_c', + 'family_c4', + 133456789, + 'WES', + [1], + [('sample_c9', 'HOM')], + 1, + ), + ], + ) + cursor.execute( + f""" + SELECT * + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` + """, + ) + self.assertCountEqual( + cursor.fetchall(), + [], + ) + exchange_tables( + table_name_builder, + ClickHouseTable.for_dataset_type_atomic_entries_update_unpartitioned( + DatasetType.SNV_INDEL, ), - ], - ) - existing_gt_stats = client.execute( - f""" - SELECT * - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` - """, - ) - self.assertCountEqual( - existing_gt_stats, - [], - ) - exchange_tables( - table_name_builder, - ClickHouseTable.for_dataset_type_atomic_entries_update_unpartitioned( - DatasetType.SNV_INDEL, - ), - ) - new_gt_stats = client.execute( - f""" - SELECT * - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` - """, - ) - self.assertCountEqual(new_gt_stats, []) - reload_dictionaries( - table_name_builder, - ClickHouseDictionary.for_dataset_type(DatasetType.SNV_INDEL), - ) - new_gt_stats_post_reload = client.execute( - f""" - SELECT * - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` - """, - ) - self.assertEqual( - new_gt_stats_post_reload, - [ - (0, 2, 0), - (1, 1, 1), - (2, 0, 2), - (3, 2, 0), - (4, 5, 0), - (5, 2, 0), - ], - ) + ) + cursor.execute( + f""" + SELECT * + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` + """, + ) + self.assertCountEqual(cursor.fetchall(), []) + reload_dictionaries( + table_name_builder, + ClickHouseDictionary.for_dataset_type(DatasetType.SNV_INDEL), + ) + cursor.execute( + f""" + SELECT * + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` + """, + ) + self.assertEqual( + cursor.fetchall(), + [ + (0, 2, 0), + (1, 1, 1), + (2, 0, 2), + (3, 2, 0), + (4, 5, 0), + (5, 2, 0), + ], + ) @patch.object( ClickhouseReferenceDataset, @@ -985,82 +707,82 @@ def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_typ ['project_d'], ['family_d1', 'family_d2'], ) - client = get_clickhouse_client() - project_gt_stats = client.execute( - f""" - SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` - GROUP BY project_guid, key, sample_type - """, - ) - self.assertCountEqual( - project_gt_stats, - [ - ('project_d', 0, 'WES', 0, 1), - ('project_d', 4, 'WES', 1, 0), - ], - ) - gt_stats = client.execute( - f""" - SELECT * - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` - """, - ) - self.assertCountEqual( - gt_stats, - [ - (0, 2, 0), - (4, 1, 0), - ], - ) - gt_stats_dict = client.execute( - f""" - SELECT * - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` - """, - ) - self.assertCountEqual( - gt_stats_dict, - [ - (0, 2, 0), - (4, 1, 0), - ], - ) - variants_memory = client.execute( - f""" - SELECT * - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` - """, - ) - self.assertCountEqual( - variants_memory, - [ - (10, '1-3-A-C'), - (11, '2-4-A-T'), - (12, 'Y-9-A-C'), - (13, 'M-2-C-G'), - ], - ) - variants_disk = client.execute( - f""" - SELECT * - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_disk` - """, - ) - self.assertCountEqual( - variants_disk, - [ - (10, '1-3-A-C'), - (11, '2-4-A-T'), - (12, 'Y-9-A-C'), - (13, 'M-2-C-G'), - ], - ) + with connections['clickhouse_write'].cursor() as cursor: + cursor.execute( + f""" + SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + GROUP BY project_guid, key, sample_type + """, + ) + self.assertCountEqual( + cursor.fetchall(), + [ + ('project_d', 0, 'WES', 0, 1), + ('project_d', 4, 'WES', 1, 0), + ], + ) + cursor.execute( + f""" + SELECT * + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` + """, + ) + self.assertCountEqual( + cursor.fetchall(), + [ + (0, 2, 0), + (4, 1, 0), + ], + ) + cursor.execute( + f""" + SELECT * + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` + """, + ) + self.assertCountEqual( + cursor.fetchall(), + [ + (0, 2, 0), + (4, 1, 0), + ], + ) + cursor.execute( + f""" + SELECT * + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` + """, + ) + self.assertCountEqual( + cursor.fetchall(), + [ + (10, '1-3-A-C'), + (11, '2-4-A-T'), + (12, 'Y-9-A-C'), + (13, 'M-2-C-G'), + ], + ) + cursor.execute( + f""" + SELECT * + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_disk` + """, + ) + self.assertCountEqual( + cursor.fetchall(), + [ + (10, '1-3-A-C'), + (11, '2-4-A-T'), + (12, 'Y-9-A-C'), + (13, 'M-2-C-G'), + ], + ) def test_load_complete_gcnv(self): load_complete_run( @@ -1070,39 +792,39 @@ def test_load_complete_gcnv(self): ['project_d'], ['family_d1', 'family_d2'], ) - client = get_clickhouse_client() - variants_disk_count = client.execute( - f""" - SELECT COUNT(*) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/variants_memory` - """, - )[0][0] - self.assertEqual(variants_disk_count, 4) - variants_disk_count = client.execute( - f""" - SELECT COUNT(*) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/variants_disk` - """, - )[0][0] - self.assertEqual(variants_disk_count, 4) - key_lookup_count = client.execute( - f""" - SELECT COUNT(*) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/key_lookup` - """, - )[0][0] - self.assertEqual(key_lookup_count, 4) - entries_count = client.execute( - f""" - SELECT COUNT(*) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/entries` - """, - )[0][0] - self.assertEqual(entries_count, 3) + with connections['clickhouse_write'].cursor() as cursor: + cursor.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/variants_memory` + """, + ) + self.assertEqual(cursor.fetchone()[0], 4) + cursor.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/variants_disk` + """, + ) + self.assertEqual(cursor.fetchone()[0], 4) + cursor.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/key_lookup` + """, + ) + self.assertEqual(cursor.fetchone()[0], 4) + cursor.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/entries` + """, + ) + self.assertEqual(cursor.fetchone()[0], 3) def test_delete_families(self): table_name_builder = TableNameBuilder( @@ -1110,90 +832,69 @@ def test_delete_families(self): DatasetType.SNV_INDEL, TEST_RUN_ID, ) - client = get_clickhouse_client() - client.execute( - f""" - INSERT INTO {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` - VALUES - (0, 'project_a', 'family_a1', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_a1','HOM')], 1), - (1, 'project_a', 'family_a2', 123456789, 'WGS', 0, 0, CAST([] AS Array(UInt32)), [('sample_a2','HET')], 1), - (2, 'project_a', 'family_a3', 133456789, 'WGS', 0, 0, CAST([] AS Array(UInt32)), [('sample_a3','HOM')], 1), - (3, 'project_a', 'family_a4', 133456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_a4','REF')], 1), - (4, 'project_a', 'family_a5', 133456789, 'WES', 0, 1, CAST([0] AS Array(UInt32)), [('sample_a5','REF'),('sample_a6','HET'),('sample_a7','REF')], 1), - (4, 'project_a', 'family_a6', 133456789, 'WGS', 0, 0, CAST([] AS Array(UInt32)), [('sample_a8','HOM')], 1), - (0, 'project_b', 'family_b1', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b4','REF')], 1), - (1, 'project_b', 'family_b2', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b5','HET')], 1), - (2, 'project_b', 'family_b2', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b5','REF')], 1), - (3, 'project_b', 'family_b3', 133456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b6','HOM')], 1), - (4, 'project_b', 'family_b3', 133456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b6','HOM')], 1), - (0, 'project_c', 'family_c1', 123456789, 'WES', 0, 1, CAST([1] AS Array(UInt32)), [('sample_c7','REF')], 1), - (3, 'project_c', 'family_c2', 123456789, 'WES', 0, 1, CAST([1] AS Array(UInt32)), [('sample_c8','REF')], 1), - (4, 'project_c', 'family_c3', 133456789, 'WES', 0, 1, CAST([1] AS Array(UInt32)), [('sample_c9','HOM')], 1), - (5, 'project_c', 'family_c4', 133456789, 'WES', 0, 1, CAST([1] AS Array(UInt32)), [('sample_c9','HOM')], 1) - """, - ) - project_gt_stats = client.execute( - f""" - SELECT project_guid, sum(het_samples), sum(hom_samples) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` - GROUP BY project_guid - """, - ) - self.assertCountEqual( - project_gt_stats, - [('project_a', 2, 3), ('project_c', 0, 2), ('project_b', 1, 2)], - ) - refresh_materialized_views( - table_name_builder, - ClickHouseMaterializedView.for_dataset_type_atomic_entries_update_refreshable( + with connections['clickhouse_write'].cursor() as cursor: + cursor.execute( + f""" + SELECT project_guid, sum(het_samples), sum(hom_samples) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + GROUP BY project_guid + """, + ) + self.assertCountEqual( + cursor.fetchall(), + [('project_a', 2, 3), ('project_c', 0, 2), ('project_b', 1, 2)], + ) + refresh_materialized_views( + table_name_builder, + ClickHouseMaterializedView.for_dataset_type_atomic_entries_update_refreshable( + DatasetType.SNV_INDEL, + ), + staging=False, + ) + cursor.execute( + f""" + SELECT sum(ac_wes) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` + """, + ) + self.assertCountEqual(cursor.fetchall(), [(12,)]) + delete_family_guids( + ReferenceGenome.GRCh38, DatasetType.SNV_INDEL, - ), - staging=False, - ) - gt_stats = client.execute( - f""" - SELECT sum(ac_wes) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` - """, - ) - self.assertCountEqual(gt_stats, [(12,)]) - delete_family_guids( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - 'project_a', - ['family_a1', 'family_a2'], - ) - project_gt_stats = client.execute( - f""" - SELECT project_guid, sum(het_samples), sum(hom_samples) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` - GROUP BY project_guid - """, - ) - self.assertCountEqual( - project_gt_stats, - [('project_a', 1, 2), ('project_c', 0, 2), ('project_b', 1, 2)], - ) - gt_stats = client.execute( - f""" - SELECT sum(ac_wes) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` - """, - ) - self.assertCountEqual(gt_stats, [(10,)]) - gt_stats_dict = client.execute( - f""" - SELECT sum(ac_wes) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` - """, - ) - self.assertCountEqual(gt_stats_dict, [(10,)]) + TEST_RUN_ID, + 'project_a', + ['family_a1', 'family_a2'], + ) + cursor.execute( + f""" + SELECT project_guid, sum(het_samples), sum(hom_samples) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + GROUP BY project_guid + """, + ) + self.assertCountEqual( + cursor.fetchall(), + [('project_a', 1, 2), ('project_c', 0, 2), ('project_b', 1, 2)], + ) + cursor.execute( + f""" + SELECT sum(ac_wes) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` + """, + ) + self.assertCountEqual(cursor.fetchall(), [(10,)]) + cursor.execute( + f""" + SELECT sum(ac_wes) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` + """, + ) + self.assertCountEqual(cursor.fetchall(), [(10,)]) def test_rebuild_gt_stats(self): table_name_builder = TableNameBuilder( @@ -1201,82 +902,73 @@ def test_rebuild_gt_stats(self): DatasetType.SNV_INDEL, TEST_RUN_ID, ) - client = get_clickhouse_client() - client.execute( - f""" - INSERT INTO {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` - VALUES - (0, 'project_a', 'family_a1', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_a1','HOM')], 1), - (1, 'project_a', 'family_a2', 123456789, 'WGS', 0, 0, CAST([] AS Array(UInt32)), [('sample_a2','HET')], 1), - (2, 'project_a', 'family_a3', 133456789, 'WGS', 0, 0, CAST([] AS Array(UInt32)), [('sample_a3','HOM')], 1), - (3, 'project_a', 'family_a4', 133456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_a4','REF')], 1), - (4, 'project_a', 'family_a5', 133456789, 'WES', 0, 1, CAST([] AS Array(UInt32)), [('sample_a5','REF'),('sample_a6','HET'),('sample_a7','REF')], 1), - (4, 'project_a', 'family_a6', 133456789, 'WGS', 0, 0, CAST([] AS Array(UInt32)), [('sample_a8','HOM')], 1), - (0, 'project_b', 'family_b1', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b4','REF')], 1), - (1, 'project_b', 'family_b2', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b5','HET')], 1), - (2, 'project_b', 'family_b2', 123456789, 'WES', 0, 0, CAST([] AS Array(UInt32)), [('sample_b5','REF')], 1), - """, - ) - logged_query( # DROP the partition from the non-staging entries to as a non-mv-impacting change. - f""" - ALTER TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` - DROP PARTITION %(project_guid)s - """, - {'project_guid': 'project_a'}, - ) - project_gt_stats = client.execute( - f""" - SELECT project_guid, sum(het_samples), sum(hom_samples) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` - GROUP BY project_guid - """, - ) - self.assertCountEqual( - project_gt_stats, - [('project_a', 2, 3), ('project_b', 1, 0)], - ) - refresh_materialized_views( - table_name_builder, - ClickHouseMaterializedView.for_dataset_type_atomic_entries_update_refreshable( + with connections['clickhouse_write'].cursor() as cursor: + logged_query( # DROP the partition from the non-staging entries to as a non-mv-impacting change. + f""" + ALTER TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` + DROP PARTITION (%(project_guid)s, %(partition_id)s) + """, + # project_partitions_dict has no row for project_a, so n_partitions (and thus + # partition_id) defaults to 0. + {'project_guid': 'project_a', 'partition_id': 0}, + ) + cursor.execute( + f""" + SELECT project_guid, sum(het_samples), sum(hom_samples) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + WHERE project_guid IN ('project_a', 'project_b') + GROUP BY project_guid + """, + ) + self.assertCountEqual( + cursor.fetchall(), + [('project_a', 2, 3), ('project_b', 1, 2)], + ) + refresh_materialized_views( + table_name_builder, + ClickHouseMaterializedView.for_dataset_type_atomic_entries_update_refreshable( + DatasetType.SNV_INDEL, + ), + staging=False, + ) + cursor.execute( + f""" + SELECT sum(ac_wes), sum(ac_wgs) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` + """, + ) + # gt_stats has no project dimension (keyed globally by `key`), so project_c's rows + # (sharing key values with project_a/b in the fixture) also contribute here. + self.assertCountEqual(cursor.fetchall(), [(12, 5)]) + rebuild_gt_stats( + ReferenceGenome.GRCh38, DatasetType.SNV_INDEL, - ), - staging=False, - ) - gt_stats = client.execute( - f""" - SELECT sum(ac_wes), sum(ac_wgs) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` - """, - ) - self.assertCountEqual(gt_stats, [(4, 5)]) - rebuild_gt_stats( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ['project_a', 'project_b'], - ) - project_gt_stats = client.execute( - f""" - SELECT project_guid, sum(het_samples), sum(hom_samples) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` - GROUP BY project_guid - """, - ) - self.assertCountEqual( - project_gt_stats, - [('project_b', 1, 0)], - ) - gt_stats = client.execute( - f""" - SELECT sum(ac_wes), sum(ac_wgs) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` - """, - ) - self.assertCountEqual(gt_stats, [(1, 0)]) + TEST_RUN_ID, + ['project_a', 'project_b'], + ) + cursor.execute( + f""" + SELECT project_guid, sum(het_samples), sum(hom_samples) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + WHERE project_guid IN ('project_a', 'project_b') + GROUP BY project_guid + """, + ) + self.assertCountEqual( + cursor.fetchall(), + [('project_b', 1, 2)], + ) + cursor.execute( + f""" + SELECT sum(ac_wes), sum(ac_wgs) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` + """, + ) + self.assertCountEqual(cursor.fetchall(), [(9, 0)]) @patch.object( ClickhouseReferenceDataset, @@ -1284,55 +976,55 @@ def test_rebuild_gt_stats(self): return_value=[ClickhouseReferenceDataset.CLINVAR], ) def test_repartitioned_entries_table(self, mock_for_reference_genome_dataset_type): - client = get_clickhouse_client() - client.execute( - f""" - REPLACE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` ( - `key` UInt32, - `project_guid` LowCardinality(String), - `family_guid` String, - `xpos` UInt64 CODEC(Delta(8), ZSTD(1)), - `sample_type` Enum8('WES' = 0, 'WGS' = 1), - `is_gnomad_gt_5_percent` Boolean, - `is_annotated_in_any_gene` Boolean DEFAULT length(geneId_ids) > 0, - `geneId_ids` Array(UInt32), - `calls` Array( - Tuple( - sampleId String, - gt Nullable(Enum8('REF' = 0, 'HET' = 1, 'HOM' = 2)), + with connections['clickhouse_write'].cursor() as cursor: + cursor.execute( + f""" + REPLACE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` ( + `key` UInt32, + `project_guid` LowCardinality(String), + `family_guid` String, + `xpos` UInt64 CODEC(Delta(8), ZSTD(1)), + `sample_type` Enum8('WES' = 0, 'WGS' = 1), + `is_gnomad_gt_5_percent` Boolean, + `is_annotated_in_any_gene` Boolean DEFAULT length(geneId_ids) > 0, + `geneId_ids` Array(UInt32), + `calls` Array( + Tuple( + sampleId String, + gt Nullable(Enum8('REF' = 0, 'HET' = 1, 'HOM' = 2)), + ) + ), + `sign` Int8, + `n_partitions` UInt8 MATERIALIZED 2, + `partition_id` UInt8 MATERIALIZED farmHash64(family_guid) % n_partitions, + PROJECTION xpos_projection + ( + SELECT * + ORDER BY is_annotated_in_any_gene, xpos ) - ), - `sign` Int8, - `n_partitions` UInt8 MATERIALIZED 2, - `partition_id` UInt8 MATERIALIZED farmHash64(family_guid) % n_partitions, - PROJECTION xpos_projection - ( - SELECT * - ORDER BY is_annotated_in_any_gene, xpos ) + ENGINE = CollapsingMergeTree(sign) + PARTITION BY (project_guid, partition_id) + ORDER BY (project_guid, family_guid, key) + SETTINGS deduplicate_merge_projection_mode = 'rebuild'; + """, + ) + load_complete_run( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ['project_d'], + ['family_d1', 'family_d2', 'family_d3'], + ) + cursor.execute( + f""" + SELECT project_guid, sum(het_samples), sum(hom_samples) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + GROUP BY project_guid + """, + ) + self.assertCountEqual( + cursor.fetchall(), + [('project_d', 1, 1)], ) - ENGINE = CollapsingMergeTree(sign) - PARTITION BY (project_guid, partition_id) - ORDER BY (project_guid, family_guid, key) - SETTINGS deduplicate_merge_projection_mode = 'rebuild'; - """, - ) - load_complete_run( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ['project_d'], - ['family_d1', 'family_d2', 'family_d3'], - ) - project_gt_stats = client.execute( - f""" - SELECT project_guid, sum(het_samples), sum(hom_samples) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` - GROUP BY project_guid - """, - ) - self.assertCountEqual( - project_gt_stats, - [('project_d', 1, 1)], - ) diff --git a/loading_pipeline/lib/test/clickhouse_django/seqr/__init__.py b/loading_pipeline/lib/test/clickhouse_django/seqr/__init__.py index d88b462a89..2beff72da3 100644 --- a/loading_pipeline/lib/test/clickhouse_django/seqr/__init__.py +++ b/loading_pipeline/lib/test/clickhouse_django/seqr/__init__.py @@ -1,6 +1,6 @@ """Stub of the main app's `seqr` package, shadowing it on sys.path (see settings.py's docstring). -`clickhouse_search`'s migrations need `SeqrLogger` (utils/logging_utils.py) and a specific `seqr` -migration name to exist, but not the real app - which imports guardian/postgres/social_django via -seqr/models.py. This stub avoids that weight. +`clickhouse_search` needs a specific `seqr` migration name to exist, but not the real app - which +imports guardian/postgres/social_django via seqr/models.py. This stub avoids that weight; +seqr/utils/__init__.py falls through to the real seqr/utils/ for submodules that don't need it. """ diff --git a/loading_pipeline/lib/test/clickhouse_django/seqr/utils/__init__.py b/loading_pipeline/lib/test/clickhouse_django/seqr/utils/__init__.py index e69de29bb2..4cc45c1a59 100644 --- a/loading_pipeline/lib/test/clickhouse_django/seqr/utils/__init__.py +++ b/loading_pipeline/lib/test/clickhouse_django/seqr/utils/__init__.py @@ -0,0 +1,4 @@ +import os + +# Falls through to the real seqr/utils/ for anything not stubbed in this directory. +__path__.append(os.path.join(os.path.dirname(__file__), '..', '..', '..', '..', '..', '..', 'seqr', 'utils')) diff --git a/loading_pipeline/lib/test/clickhouse_django/seqr/utils/logging_utils.py b/loading_pipeline/lib/test/clickhouse_django/seqr/utils/logging_utils.py deleted file mode 100644 index f27d813bbb..0000000000 --- a/loading_pipeline/lib/test/clickhouse_django/seqr/utils/logging_utils.py +++ /dev/null @@ -1,25 +0,0 @@ -# Mirrors the real seqr.utils.logging_utils.SeqrLogger (dependency-free) - see seqr/__init__.py. -import logging -from typing import Optional - - -class SeqrLogger(object): - - def __init__(self, name: Optional[str] = None) -> None: - """Custom logger which requires user metadata to be included in the log.""" - self._logger = logging.getLogger(name) - - def _log(self, level, message, user, **kwargs): - self._logger.log(level, message, extra=dict(user=user, **kwargs)) - - def debug(self, *args, **kwargs): - self._log(logging.DEBUG, *args, **kwargs) - - def info(self, *args, **kwargs): - self._log(logging.INFO, *args, **kwargs) - - def warning(self, *args, **kwargs): - self._log(logging.WARNING, *args, **kwargs) - - def error(self, *args, **kwargs): - self._log(logging.ERROR, *args, **kwargs) diff --git a/loading_pipeline/lib/test/clickhouse_django/settings.py b/loading_pipeline/lib/test/clickhouse_django/settings.py index fa74d6173f..5af22fd624 100644 --- a/loading_pipeline/lib/test/clickhouse_django/settings.py +++ b/loading_pipeline/lib/test/clickhouse_django/settings.py @@ -8,6 +8,10 @@ import os +# Shared Django fixtures (loaddata) for clickhouse_search-backed test data - see +# lib/test/clickhouse_schema_testcase.py. +FIXTURE_DIRS = [os.path.join(os.path.dirname(__file__), '..', 'fixtures')] + INSTALLED_APPS = [ 'clickhouse_backend', 'seqr', # stub package (see seqr/__init__.py), not the real app diff --git a/loading_pipeline/lib/test/clickhouse_schema_testcase.py b/loading_pipeline/lib/test/clickhouse_schema_testcase.py index b01277fe10..8799f2d9a4 100644 --- a/loading_pipeline/lib/test/clickhouse_schema_testcase.py +++ b/loading_pipeline/lib/test/clickhouse_schema_testcase.py @@ -16,6 +16,7 @@ def _fixture_teardown(self): """ SELECT name FROM system.tables WHERE database = %(database)s AND engine NOT IN ('Dictionary', 'MaterializedView') + AND name != 'django_migrations' """, {'database': Env.CLICKHOUSE_DATABASE}, ) diff --git a/reference_data/models.py b/reference_data/models.py index 9b28505aad..4c68cc23e0 100644 --- a/reference_data/models.py +++ b/reference_data/models.py @@ -12,6 +12,7 @@ from reference_data.utils.dbnsfp_utils import DBNSFP_FIELD_MAP, DBNSFP_EXCLUDE_FIELDS from reference_data.utils.download_utils import download_file from reference_data.utils.gencode_utils import parse_gencode_record, GENCODE_URL_TEMPLATE, GENCODE_FILE_HEADER +from seqr.utils.constants import GENOME_VERSION_GRCh37, GENOME_VERSION_GRCh38 from seqr.views.utils.export_utils import write_multiple_files # Allow adding the custom json_fields and internal_json_fields to the model Meta @@ -20,9 +21,6 @@ logger = logging.getLogger(__name__) -GENOME_VERSION_GRCh37 = "37" -GENOME_VERSION_GRCh38 = "38" - GENOME_VERSION_CHOICES = [ (GENOME_VERSION_GRCh37, "GRCh37"), (GENOME_VERSION_GRCh38, "GRCh38") diff --git a/seqr/models.py b/seqr/models.py index b183d62bd9..478997657f 100644 --- a/seqr/models.py +++ b/seqr/models.py @@ -12,6 +12,9 @@ from guardian.shortcuts import assign_perm +from seqr.utils.constants import SEX_MALE, SEX_FEMALE, SEX_UNKNOWN, FEMALE_ANEUPLOIDIES, MALE_ANEUPLOIDIES, \ + FEMALE_SEXES, MALE_SEXES, AFFECTED_STATUS_AFFECTED, AFFECTED_STATUS_UNAFFECTED, AFFECTED_STATUS_UNKNOWN, \ + SAMPLE_TYPE_WES, SAMPLE_TYPE_WGS, DATASET_TYPE_VARIANT_CALLS, DATASET_TYPE_SV_CALLS, DATASET_TYPE_MITO_CALLS from seqr.utils.logging_utils import log_model_update, log_model_bulk_update, SeqrLogger from seqr.utils.xpos_utils import get_chrom_pos from seqr.views.utils.json_utils import DjangoJSONEncoderWithSets @@ -434,13 +437,13 @@ def __init__(self, *args, **kwargs): class Individual(ModelWithGUID): - SEX_MALE = 'M' - SEX_FEMALE = 'F' - SEX_UNKNOWN = 'U' - FEMALE_ANEUPLOIDIES = ['XXX', 'X0'] - MALE_ANEUPLOIDIES = ['XXY', 'XYY'] - FEMALE_SEXES = [SEX_FEMALE] + FEMALE_ANEUPLOIDIES - MALE_SEXES = [SEX_MALE] + MALE_ANEUPLOIDIES + SEX_MALE = SEX_MALE + SEX_FEMALE = SEX_FEMALE + SEX_UNKNOWN = SEX_UNKNOWN + FEMALE_ANEUPLOIDIES = FEMALE_ANEUPLOIDIES + MALE_ANEUPLOIDIES = MALE_ANEUPLOIDIES + FEMALE_SEXES = FEMALE_SEXES + MALE_SEXES = MALE_SEXES SEX_CHOICES = ( (SEX_MALE, 'Male'), ('F', 'Female'), @@ -449,9 +452,9 @@ class Individual(ModelWithGUID): *[(sex, sex) for sex in FEMALE_ANEUPLOIDIES], ) - AFFECTED_STATUS_AFFECTED = 'A' - AFFECTED_STATUS_UNAFFECTED = 'N' - AFFECTED_STATUS_UNKNOWN = 'U' + AFFECTED_STATUS_AFFECTED = AFFECTED_STATUS_AFFECTED + AFFECTED_STATUS_UNAFFECTED = AFFECTED_STATUS_UNAFFECTED + AFFECTED_STATUS_UNKNOWN = AFFECTED_STATUS_UNKNOWN AFFECTED_STATUS_CHOICES = ( (AFFECTED_STATUS_AFFECTED, 'Affected'), (AFFECTED_STATUS_UNAFFECTED, 'Unaffected'), @@ -681,17 +684,17 @@ class Meta: class Dataset(ModelWithGUID): - SAMPLE_TYPE_WES = 'WES' - SAMPLE_TYPE_WGS = 'WGS' + SAMPLE_TYPE_WES = SAMPLE_TYPE_WES + SAMPLE_TYPE_WGS = SAMPLE_TYPE_WGS SAMPLE_TYPE_CHOICES = ( (SAMPLE_TYPE_WES, 'Exome'), (SAMPLE_TYPE_WGS, 'Whole Genome'), ) SAMPLE_TYPE_LOOKUP = dict(SAMPLE_TYPE_CHOICES) - DATASET_TYPE_VARIANT_CALLS = 'SNV_INDEL' - DATASET_TYPE_SV_CALLS = 'SV' - DATASET_TYPE_MITO_CALLS = 'MITO' + DATASET_TYPE_VARIANT_CALLS = DATASET_TYPE_VARIANT_CALLS + DATASET_TYPE_SV_CALLS = DATASET_TYPE_SV_CALLS + DATASET_TYPE_MITO_CALLS = DATASET_TYPE_MITO_CALLS DATASET_TYPE_CHOICES = ( (DATASET_TYPE_VARIANT_CALLS, 'Variant Calls'), (DATASET_TYPE_SV_CALLS, 'SV Calls'), From d7ae384d0fe36418167233fa455a24ea8e536af1 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 14:34:46 -0400 Subject: [PATCH 206/369] fix ruff --- clickhouse_search/backend/table_models.py | 2 -- .../test/clickhouse_django/seqr/utils/__init__.py | 6 +++++- .../lib/test/clickhouse_django/settings.py | 12 +++++++++--- 3 files changed, 14 insertions(+), 6 deletions(-) diff --git a/clickhouse_search/backend/table_models.py b/clickhouse_search/backend/table_models.py index 2f211cc2ff..b6e39a15d5 100644 --- a/clickhouse_search/backend/table_models.py +++ b/clickhouse_search/backend/table_models.py @@ -16,8 +16,6 @@ DICTIONARY_META_FIELDS = ['layout', 'lifetime_max', 'postgres_query', 'postgres_db', 'clickhouse_query_template'] -# Lives here rather than in models/reference_data_models.py so migrations depending on it don't -# need to import the much heavier live model definitions module. def conditionally_refresh_reference_dataset(reference_dataset: str): def inner(apps, schema_editor): if DATABASES['default']['NAME'].startswith('test_'): diff --git a/loading_pipeline/lib/test/clickhouse_django/seqr/utils/__init__.py b/loading_pipeline/lib/test/clickhouse_django/seqr/utils/__init__.py index 4cc45c1a59..b93e147a15 100644 --- a/loading_pipeline/lib/test/clickhouse_django/seqr/utils/__init__.py +++ b/loading_pipeline/lib/test/clickhouse_django/seqr/utils/__init__.py @@ -1,4 +1,8 @@ import os # Falls through to the real seqr/utils/ for anything not stubbed in this directory. -__path__.append(os.path.join(os.path.dirname(__file__), '..', '..', '..', '..', '..', '..', 'seqr', 'utils')) +__path__.append( + os.path.join( + os.path.dirname(__file__), '..', '..', '..', '..', '..', '..', 'seqr', 'utils' + ) +) diff --git a/loading_pipeline/lib/test/clickhouse_django/settings.py b/loading_pipeline/lib/test/clickhouse_django/settings.py index 5af22fd624..ea503e2e5d 100644 --- a/loading_pipeline/lib/test/clickhouse_django/settings.py +++ b/loading_pipeline/lib/test/clickhouse_django/settings.py @@ -40,11 +40,17 @@ def allow_migrate(db, app_label, model_name=None, **hints): # noqa: ARG004 PIPELINE_RUNNER_SERVER = os.environ.get('PIPELINE_RUNNER_SERVER', 'http://localhost') # Must differ - EmbeddedRocksDB tables (annotations_memory vs annotations_disk) using the same # path deadlock on the same file lock. -CLICKHOUSE_IN_MEMORY_DIR = os.environ.get('CLICKHOUSE_IN_MEMORY_DIR', '/tmp/loading_pipeline_test_clickhouse_in_memory') # noqa: S108 -CLICKHOUSE_DATA_DIR = os.environ.get('CLICKHOUSE_DATA_DIR', '/tmp/loading_pipeline_test_clickhouse_data') # noqa: S108 +CLICKHOUSE_IN_MEMORY_DIR = os.environ.get( + 'CLICKHOUSE_IN_MEMORY_DIR', '/tmp/loading_pipeline_test_clickhouse_in_memory' +) # noqa: S108 +CLICKHOUSE_DATA_DIR = os.environ.get( + 'CLICKHOUSE_DATA_DIR', '/tmp/loading_pipeline_test_clickhouse_data' +) # noqa: S108 CLICKHOUSE_WRITER_USER = os.environ.get('CLICKHOUSE_WRITER_USER', 'default') -CLICKHOUSE_WRITER_PASSWORD = os.environ.get('CLICKHOUSE_WRITER_PASSWORD', 'default_password') +CLICKHOUSE_WRITER_PASSWORD = os.environ.get( + 'CLICKHOUSE_WRITER_PASSWORD', 'default_password' +) CLICKHOUSE_DATABASE_NAME = os.environ.get('CLICKHOUSE_DATABASE', 'seqr') CLICKHOUSE_DB_CONFIG = { From a688ce7dc4bbb301ea64743f5ed4a369d97ea1e7 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 14:35:09 -0400 Subject: [PATCH 207/369] add missed files --- .../lib/test/fixtures/clickhouse_test.json | 265 ++++++++++++++++++ seqr/utils/constants.py | 29 ++ 2 files changed, 294 insertions(+) create mode 100644 loading_pipeline/lib/test/fixtures/clickhouse_test.json create mode 100644 seqr/utils/constants.py diff --git a/loading_pipeline/lib/test/fixtures/clickhouse_test.json b/loading_pipeline/lib/test/fixtures/clickhouse_test.json new file mode 100644 index 0000000000..90e8faaf8a --- /dev/null +++ b/loading_pipeline/lib/test/fixtures/clickhouse_test.json @@ -0,0 +1,265 @@ +[ + { + "model": "clickhouse_search.entriessnvindel", + "pk": 1, + "fields": { + "key": 0, + "project_guid": "project_a", + "family_guid": "family_a1", + "sample_type": "WES", + "xpos": 123456789, + "is_gnomad_gt_5_percent": false, + "is_annotated_in_any_gene": false, + "geneId_ids": [], + "filters": [], + "sign": 1, + "calls": [["sample_a1", 2, null, null, null]] + } + }, + { + "model": "clickhouse_search.entriessnvindel", + "pk": 2, + "fields": { + "key": 1, + "project_guid": "project_a", + "family_guid": "family_a2", + "sample_type": "WGS", + "xpos": 123456789, + "is_gnomad_gt_5_percent": false, + "is_annotated_in_any_gene": false, + "geneId_ids": [], + "filters": [], + "sign": 1, + "calls": [["sample_a2", 1, null, null, null]] + } + }, + { + "model": "clickhouse_search.entriessnvindel", + "pk": 3, + "fields": { + "key": 2, + "project_guid": "project_a", + "family_guid": "family_a3", + "sample_type": "WGS", + "xpos": 133456789, + "is_gnomad_gt_5_percent": false, + "is_annotated_in_any_gene": false, + "geneId_ids": [], + "filters": [], + "sign": 1, + "calls": [["sample_a3", 2, null, null, null]] + } + }, + { + "model": "clickhouse_search.entriessnvindel", + "pk": 4, + "fields": { + "key": 3, + "project_guid": "project_a", + "family_guid": "family_a4", + "sample_type": "WES", + "xpos": 133456789, + "is_gnomad_gt_5_percent": false, + "is_annotated_in_any_gene": false, + "geneId_ids": [], + "filters": [], + "sign": 1, + "calls": [["sample_a4", 0, null, null, null]] + } + }, + { + "model": "clickhouse_search.entriessnvindel", + "pk": 5, + "fields": { + "key": 4, + "project_guid": "project_a", + "family_guid": "family_a5", + "sample_type": "WES", + "xpos": 133456789, + "is_gnomad_gt_5_percent": false, + "is_annotated_in_any_gene": true, + "geneId_ids": [0], + "filters": [], + "sign": 1, + "calls": [["sample_a5", 0, null, null, null], ["sample_a6", 1, null, null, null], ["sample_a7", 0, null, null, null]] + } + }, + { + "model": "clickhouse_search.entriessnvindel", + "pk": 6, + "fields": { + "key": 4, + "project_guid": "project_a", + "family_guid": "family_a6", + "sample_type": "WGS", + "xpos": 133456789, + "is_gnomad_gt_5_percent": false, + "is_annotated_in_any_gene": false, + "geneId_ids": [], + "filters": [], + "sign": 1, + "calls": [["sample_a8", 2, null, null, null]] + } + }, + { + "model": "clickhouse_search.entriessnvindel", + "pk": 7, + "fields": { + "key": 0, + "project_guid": "project_b", + "family_guid": "family_b1", + "sample_type": "WES", + "xpos": 123456789, + "is_gnomad_gt_5_percent": false, + "is_annotated_in_any_gene": false, + "geneId_ids": [], + "filters": [], + "sign": 1, + "calls": [["sample_b4", 0, null, null, null]] + } + }, + { + "model": "clickhouse_search.entriessnvindel", + "pk": 8, + "fields": { + "key": 1, + "project_guid": "project_b", + "family_guid": "family_b2", + "sample_type": "WES", + "xpos": 123456789, + "is_gnomad_gt_5_percent": false, + "is_annotated_in_any_gene": false, + "geneId_ids": [], + "filters": [], + "sign": 1, + "calls": [["sample_b5", 1, null, null, null]] + } + }, + { + "model": "clickhouse_search.entriessnvindel", + "pk": 9, + "fields": { + "key": 2, + "project_guid": "project_b", + "family_guid": "family_b2", + "sample_type": "WES", + "xpos": 123456789, + "is_gnomad_gt_5_percent": false, + "is_annotated_in_any_gene": false, + "geneId_ids": [], + "filters": [], + "sign": 1, + "calls": [["sample_b5", 0, null, null, null]] + } + }, + { + "model": "clickhouse_search.entriessnvindel", + "pk": 10, + "fields": { + "key": 3, + "project_guid": "project_b", + "family_guid": "family_b3", + "sample_type": "WES", + "xpos": 133456789, + "is_gnomad_gt_5_percent": false, + "is_annotated_in_any_gene": false, + "geneId_ids": [], + "filters": [], + "sign": 1, + "calls": [["sample_b6", 2, null, null, null]] + } + }, + { + "model": "clickhouse_search.entriessnvindel", + "pk": 11, + "fields": { + "key": 4, + "project_guid": "project_b", + "family_guid": "family_b3", + "sample_type": "WES", + "xpos": 133456789, + "is_gnomad_gt_5_percent": false, + "is_annotated_in_any_gene": false, + "geneId_ids": [], + "filters": [], + "sign": 1, + "calls": [["sample_b6", 2, null, null, null]] + } + }, + { + "model": "clickhouse_search.entriessnvindel", + "pk": 12, + "fields": { + "key": 0, + "project_guid": "project_c", + "family_guid": "family_c1", + "sample_type": "WES", + "xpos": 123456789, + "is_gnomad_gt_5_percent": false, + "is_annotated_in_any_gene": true, + "geneId_ids": [1], + "filters": [], + "sign": 1, + "calls": [["sample_c7", 0, null, null, null]] + } + }, + { + "model": "clickhouse_search.entriessnvindel", + "pk": 13, + "fields": { + "key": 3, + "project_guid": "project_c", + "family_guid": "family_c2", + "sample_type": "WES", + "xpos": 123456789, + "is_gnomad_gt_5_percent": false, + "is_annotated_in_any_gene": true, + "geneId_ids": [1], + "filters": [], + "sign": 1, + "calls": [["sample_c8", 0, null, null, null]] + } + }, + { + "model": "clickhouse_search.entriessnvindel", + "pk": 14, + "fields": { + "key": 4, + "project_guid": "project_c", + "family_guid": "family_c3", + "sample_type": "WES", + "xpos": 133456789, + "is_gnomad_gt_5_percent": false, + "is_annotated_in_any_gene": true, + "geneId_ids": [1], + "filters": [], + "sign": 1, + "calls": [["sample_c9", 2, null, null, null]] + } + }, + { + "model": "clickhouse_search.entriessnvindel", + "pk": 15, + "fields": { + "key": 5, + "project_guid": "project_c", + "family_guid": "family_c4", + "sample_type": "WES", + "xpos": 133456789, + "is_gnomad_gt_5_percent": false, + "is_annotated_in_any_gene": true, + "geneId_ids": [1], + "filters": [], + "sign": 1, + "calls": [["sample_c9", 2, null, null, null]] + } + }, + { + "model": "clickhouse_search.projectpartitionssnvindel", + "pk": "project_d", + "fields": { + "project_guid": "project_d", + "n_partitions": 2 + } + } +] diff --git a/seqr/utils/constants.py b/seqr/utils/constants.py new file mode 100644 index 0000000000..f07ddc133b --- /dev/null +++ b/seqr/utils/constants.py @@ -0,0 +1,29 @@ +"""Constants shared between seqr.models, reference_data.models, and clickhouse_search - kept here, +rather than on those Django model classes, so clickhouse_search (and loading_pipeline's minimal +test settings) can depend on these plain values without importing the Postgres/guardian-backed +seqr.models/reference_data.models apps. +""" + +# Individual +SEX_MALE = 'M' +SEX_FEMALE = 'F' +SEX_UNKNOWN = 'U' +FEMALE_ANEUPLOIDIES = ['XXX', 'X0'] +MALE_ANEUPLOIDIES = ['XXY', 'XYY'] +FEMALE_SEXES = [SEX_FEMALE, *FEMALE_ANEUPLOIDIES] +MALE_SEXES = [SEX_MALE, *MALE_ANEUPLOIDIES] + +AFFECTED_STATUS_AFFECTED = 'A' +AFFECTED_STATUS_UNAFFECTED = 'N' +AFFECTED_STATUS_UNKNOWN = 'U' + +# Dataset +SAMPLE_TYPE_WES = 'WES' +SAMPLE_TYPE_WGS = 'WGS' +DATASET_TYPE_VARIANT_CALLS = 'SNV_INDEL' +DATASET_TYPE_SV_CALLS = 'SV' +DATASET_TYPE_MITO_CALLS = 'MITO' + +# reference_data genome versions +GENOME_VERSION_GRCh37 = '37' +GENOME_VERSION_GRCh38 = '38' From d93e20b21d6901615fcb0d889a29eb6091942589 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 14:38:45 -0400 Subject: [PATCH 208/369] fix ruff --- clickhouse_search/models/__init__.py | 6 ++---- loading_pipeline/lib/misc/clickhouse_test.py | 3 ++- .../test/clickhouse_django/seqr/utils/__init__.py | 12 ++++++++++-- .../lib/test/clickhouse_django/settings.py | 13 ++++++++----- .../lib/test/clickhouse_schema_testcase.py | 6 ++++-- loading_pipeline/pyproject.toml | 1 + 6 files changed, 27 insertions(+), 14 deletions(-) diff --git a/clickhouse_search/models/__init__.py b/clickhouse_search/models/__init__.py index 8695ebea5c..f171b92113 100644 --- a/clickhouse_search/models/__init__.py +++ b/clickhouse_search/models/__init__.py @@ -12,12 +12,10 @@ ) state.DEFAULT_NAMES = options.DEFAULT_NAMES -# Importing these registers their model classes with Django's app registry (apps.get_model()), -# which fixture loaddata needs to resolve "clickhouse_search." identifiers. Nothing else -# in this package imports them directly otherwise. Must come after the DEFAULT_NAMES patch above - -# these modules' Meta classes use the custom fields it allowlists. +# Importing here registers model classes with Django's app registry from clickhouse_search.models import postgres_dicts, reference_data_models, search_models, gt_stats_models # noqa: F401,E402 + class ClickHouseRouter: # Adapted from https://github.com/jayvynl/django-clickhouse-backend/blob/v1.3.2/README.md#configuration diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index eba49231af..1f7dfdfd0b 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -1,4 +1,5 @@ import os +from typing import ClassVar from unittest.mock import patch import pandas as pd @@ -48,7 +49,7 @@ class ClickhouseTest(MockedDatarootTestCase, ClickhouseSchemaTestCase): - fixtures = ['clickhouse_test'] + fixtures: ClassVar = ['clickhouse_test'] @classmethod def setUpClass(cls): diff --git a/loading_pipeline/lib/test/clickhouse_django/seqr/utils/__init__.py b/loading_pipeline/lib/test/clickhouse_django/seqr/utils/__init__.py index b93e147a15..d6a3b34ab1 100644 --- a/loading_pipeline/lib/test/clickhouse_django/seqr/utils/__init__.py +++ b/loading_pipeline/lib/test/clickhouse_django/seqr/utils/__init__.py @@ -3,6 +3,14 @@ # Falls through to the real seqr/utils/ for anything not stubbed in this directory. __path__.append( os.path.join( - os.path.dirname(__file__), '..', '..', '..', '..', '..', '..', 'seqr', 'utils' - ) + os.path.dirname(__file__), + '..', + '..', + '..', + '..', + '..', + '..', + 'seqr', + 'utils', + ), ) diff --git a/loading_pipeline/lib/test/clickhouse_django/settings.py b/loading_pipeline/lib/test/clickhouse_django/settings.py index ea503e2e5d..0930b783a0 100644 --- a/loading_pipeline/lib/test/clickhouse_django/settings.py +++ b/loading_pipeline/lib/test/clickhouse_django/settings.py @@ -41,15 +41,18 @@ def allow_migrate(db, app_label, model_name=None, **hints): # noqa: ARG004 # Must differ - EmbeddedRocksDB tables (annotations_memory vs annotations_disk) using the same # path deadlock on the same file lock. CLICKHOUSE_IN_MEMORY_DIR = os.environ.get( - 'CLICKHOUSE_IN_MEMORY_DIR', '/tmp/loading_pipeline_test_clickhouse_in_memory' -) # noqa: S108 + 'CLICKHOUSE_IN_MEMORY_DIR', + '/tmp/loading_pipeline_test_clickhouse_in_memory', # noqa: S108 +) CLICKHOUSE_DATA_DIR = os.environ.get( - 'CLICKHOUSE_DATA_DIR', '/tmp/loading_pipeline_test_clickhouse_data' -) # noqa: S108 + 'CLICKHOUSE_DATA_DIR', + '/tmp/loading_pipeline_test_clickhouse_data', # noqa: S108 +) CLICKHOUSE_WRITER_USER = os.environ.get('CLICKHOUSE_WRITER_USER', 'default') CLICKHOUSE_WRITER_PASSWORD = os.environ.get( - 'CLICKHOUSE_WRITER_PASSWORD', 'default_password' + 'CLICKHOUSE_WRITER_PASSWORD', + 'default_password', ) CLICKHOUSE_DATABASE_NAME = os.environ.get('CLICKHOUSE_DATABASE', 'seqr') diff --git a/loading_pipeline/lib/test/clickhouse_schema_testcase.py b/loading_pipeline/lib/test/clickhouse_schema_testcase.py index 8799f2d9a4..660a16149a 100644 --- a/loading_pipeline/lib/test/clickhouse_schema_testcase.py +++ b/loading_pipeline/lib/test/clickhouse_schema_testcase.py @@ -1,3 +1,5 @@ +from typing import ClassVar + from django.db import connections from django.test import TestCase @@ -5,7 +7,7 @@ class ClickhouseSchemaTestCase(TestCase): - databases = ['clickhouse_write'] + databases: ClassVar = ['clickhouse_write'] # Django's `flush` (the default TestCase teardown for backends without transaction support) # determines tables to flush from `apps.get_models()`, but nothing here imports @@ -22,4 +24,4 @@ def _fixture_teardown(self): ) tables = [row[0] for row in cursor.fetchall()] for table in tables: - cursor.execute(f'TRUNCATE TABLE `{table}`') # noqa: S608 + cursor.execute(f'TRUNCATE TABLE `{table}`') diff --git a/loading_pipeline/pyproject.toml b/loading_pipeline/pyproject.toml index 0b9e4f9f1e..b943124e08 100644 --- a/loading_pipeline/pyproject.toml +++ b/loading_pipeline/pyproject.toml @@ -113,6 +113,7 @@ inline-quotes = "single" ] '*migration*' = [ 'N999', # allow invalid module names + 'RUF012', # Django migration classes' dependencies/operations are conventionally plain lists ] '*clickhouse*' = [ 'S608' # unsafe sql From ab48f087db8a3b11c674d630ef0e7a0f3d8c0e64 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 14:43:24 -0400 Subject: [PATCH 209/369] ruff and cleanup --- clickhouse_search/constants.py | 7 ++++--- clickhouse_search/managers.py | 5 +++-- clickhouse_search/search.py | 3 ++- loading_pipeline/bin/pipeline_worker_test.py | 9 ++++++--- .../load_clickhouse_variants_tables_test.py | 9 ++++++--- 5 files changed, 21 insertions(+), 12 deletions(-) diff --git a/clickhouse_search/constants.py b/clickhouse_search/constants.py index ebce6e0063..9ebf9481b6 100644 --- a/clickhouse_search/constants.py +++ b/clickhouse_search/constants.py @@ -1,6 +1,7 @@ -from seqr.utils.constants import AFFECTED_STATUS_AFFECTED as AFFECTED, AFFECTED_STATUS_UNAFFECTED as UNAFFECTED, \ - MALE_SEXES, FEMALE_SEXES, SAMPLE_TYPE_WES, SAMPLE_TYPE_WGS, DATASET_TYPE_VARIANT_CALLS, DATASET_TYPE_SV_CALLS, \ - DATASET_TYPE_MITO_CALLS, GENOME_VERSION_GRCh37, GENOME_VERSION_GRCh38 +from seqr.utils.constants import AFFECTED_STATUS_AFFECTED, AFFECTED_STATUS_UNAFFECTED + +AFFECTED = AFFECTED_STATUS_AFFECTED +UNAFFECTED = AFFECTED_STATUS_UNAFFECTED MAX_VARIANTS = 10000 diff --git a/clickhouse_search/managers.py b/clickhouse_search/managers.py index f08bd5ee88..68da15e60a 100644 --- a/clickhouse_search/managers.py +++ b/clickhouse_search/managers.py @@ -12,13 +12,14 @@ GroupArrayIntersect, If, MapLookup, NullIf, Plus, SubqueryJoin, SubqueryTable, Tuple, TupleConcat, Untuple, \ IntDiv, Modulo, SplitByString, ArrayIndex, Multiply, IndexOf from clickhouse_search.models.postgres_dicts import AffectedDict, SexDict, DiscoveryVariantDict -from clickhouse_search.constants import INHERITANCE_FILTERS, ANY_AFFECTED, AFFECTED, UNAFFECTED, MALE_SEXES, \ +from clickhouse_search.constants import INHERITANCE_FILTERS, ANY_AFFECTED, AFFECTED, UNAFFECTED, \ X_LINKED_RECESSIVE, REF_REF, REF_ALT, ALT_ALT, HAS_ALT, HAS_REF, SPLICE_AI_FIELD, SCREEN_KEY, UTR_ANNOTATOR_KEY, \ EXTENDED_SPLICE_KEY, MOTIF_FEATURES_KEY, REGULATORY_FEATURES_KEY, CLINVAR_KEY, HGMD_KEY, NEW_SV_FIELD, \ EXTENDED_SPLICE_REGION_CONSEQUENCE, CLINVAR_PATH_RANGES, CLINVAR_PATH_SIGNIFICANCES, CLINVAR_LIKELY_PATH_FILTER, \ CLINVAR_CONFLICTING_P_LP, CLINVAR_CONFLICTING_NO_P, CLINVAR_CONFLICTING, PATH_FREQ_OVERRIDE_CUTOFF, \ HGMD_CLASS_FILTERS, SV_TYPE_FILTER_FIELD, SV_CONSEQUENCES_FIELD, COMPOUND_HET, COMPOUND_HET_ALLOW_HOM_ALTS, \ - X_LINKED_RECESSIVE_MALE_AFFECTED, FEMALE_SEXES, SV_ANNOTATION_TYPES + X_LINKED_RECESSIVE_MALE_AFFECTED, SV_ANNOTATION_TYPES +from seqr.utils.constants import MALE_SEXES, FEMALE_SEXES from seqr.utils.xpos_utils import get_xpos, parse_variant_id, MIN_POS, MAX_POS, CHROMOSOME_CHOICES diff --git a/clickhouse_search/search.py b/clickhouse_search/search.py index 3e57074425..33c86b0ef4 100644 --- a/clickhouse_search/search.py +++ b/clickhouse_search/search.py @@ -23,8 +23,9 @@ from seqr.utils.gene_utils import parse_locus_list_items from seqr.utils.logging_utils import SeqrLogger from clickhouse_search.constants import MAX_VARIANTS, XPOS_SORT_KEY, PATHOGENICTY_SORT_KEY, PATHOGENICTY_HGMD_SORT_KEY, \ - PRIORITIZED_GENE_SORT, COMPOUND_HET, COMPOUND_HET_ALLOW_HOM_ALTS, RECESSIVE, AFFECTED, MALE_SEXES, \ + PRIORITIZED_GENE_SORT, COMPOUND_HET, COMPOUND_HET_ALLOW_HOM_ALTS, RECESSIVE, AFFECTED, \ X_LINKED_RECESSIVE, X_LINKED_RECESSIVE_MALE_AFFECTED +from seqr.utils.constants import MALE_SEXES from seqr.views.utils.json_utils import DjangoJSONEncoderWithSets logger = SeqrLogger(__name__) diff --git a/loading_pipeline/bin/pipeline_worker_test.py b/loading_pipeline/bin/pipeline_worker_test.py index 532693701a..f935f3aa0c 100644 --- a/loading_pipeline/bin/pipeline_worker_test.py +++ b/loading_pipeline/bin/pipeline_worker_test.py @@ -112,7 +112,8 @@ def test_process_queue_integration_test( {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` """, ) - self.assertEqual(cursor.fetchone()[0], 30) + annotations_count = cursor.fetchone()[0] + self.assertEqual(annotations_count, 30) cursor.execute( f""" SELECT COUNT(*) @@ -120,7 +121,8 @@ def test_process_queue_integration_test( {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` """, ) - self.assertEqual(cursor.fetchone()[0], 16) + entries_count = cursor.fetchone()[0] + self.assertEqual(entries_count, 16) cursor.execute( f""" SELECT sum(ac_wgs) @@ -128,7 +130,8 @@ def test_process_queue_integration_test( {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` """, ) - self.assertEqual(cursor.fetchone()[0], 69) + ac_wgs = cursor.fetchone()[0] + self.assertEqual(ac_wgs, 69) @patch('loading_pipeline.lib.misc.slack._safe_post_to_slack') @patch('loading_pipeline.api.request_handlers.WriteClickhouseLoadSuccessFileTask') diff --git a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py index b8a2d8fa1e..b216431433 100644 --- a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py +++ b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py @@ -126,7 +126,8 @@ def test_write_variants_to_clickhouse( {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` """, ) - self.assertEqual(cursor.fetchone()[0], 2) + variants_count = cursor.fetchone()[0] + self.assertEqual(variants_count, 2) cursor.execute( f""" SELECT COUNT(*) @@ -134,7 +135,8 @@ def test_write_variants_to_clickhouse( {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details` """, ) - self.assertEqual(cursor.fetchone()[0], 2) + variant_details_count = cursor.fetchone()[0] + self.assertEqual(variant_details_count, 2) cursor.execute( f""" SELECT COUNT(*) @@ -142,4 +144,5 @@ def test_write_variants_to_clickhouse( {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/key_lookup` """, ) - self.assertEqual(cursor.fetchone()[0], 2) + key_lookups_count = cursor.fetchone()[0] + self.assertEqual(key_lookups_count, 2) From e3e5cefca9d3b40142f2f69c8931e9f4b3dacbfb Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 14:45:25 -0400 Subject: [PATCH 210/369] missing init --- loading_pipeline/lib/test/clickhouse_django/__init__.py | 0 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 loading_pipeline/lib/test/clickhouse_django/__init__.py diff --git a/loading_pipeline/lib/test/clickhouse_django/__init__.py b/loading_pipeline/lib/test/clickhouse_django/__init__.py new file mode 100644 index 0000000000..e69de29bb2 From 060ba50a5508b9a6a0657226fa9cf52a64aa7810 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 15:03:04 -0400 Subject: [PATCH 211/369] clean up --- loading_pipeline/bin/pipeline_worker_test.py | 56 +++++++++---------- .../load_clickhouse_variants_tables_test.py | 56 +++++++++---------- .../test/clickhouse_django/seqr/__init__.py | 6 -- .../lib/test/clickhouse_django/settings.py | 20 +------ .../lib/test/clickhouse_schema_testcase.py | 3 - loading_pipeline/pyproject.toml | 5 -- seqr/utils/constants.py | 9 --- 7 files changed, 58 insertions(+), 97 deletions(-) diff --git a/loading_pipeline/bin/pipeline_worker_test.py b/loading_pipeline/bin/pipeline_worker_test.py index f935f3aa0c..a2e3db1e54 100644 --- a/loading_pipeline/bin/pipeline_worker_test.py +++ b/loading_pipeline/bin/pipeline_worker_test.py @@ -104,34 +104,34 @@ def test_process_queue_integration_test( ) as f: self.assertEqual(f.read(), '') - with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f""" - SELECT COUNT(*) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` - """, - ) - annotations_count = cursor.fetchone()[0] - self.assertEqual(annotations_count, 30) - cursor.execute( - f""" - SELECT COUNT(*) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` - """, - ) - entries_count = cursor.fetchone()[0] - self.assertEqual(entries_count, 16) - cursor.execute( - f""" - SELECT sum(ac_wgs) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` - """, - ) - ac_wgs = cursor.fetchone()[0] - self.assertEqual(ac_wgs, 69) + cursor = connections['clickhouse_write'].cursor() + cursor.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` + """, + ) + annotations_count = cursor.fetchone()[0] + self.assertEqual(annotations_count, 30) + cursor.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` + """, + ) + entries_count = cursor.fetchone()[0] + self.assertEqual(entries_count, 16) + cursor.execute( + f""" + SELECT sum(ac_wgs) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` + """, + ) + ac_wgs = cursor.fetchone()[0] + self.assertEqual(ac_wgs, 69) @patch('loading_pipeline.lib.misc.slack._safe_post_to_slack') @patch('loading_pipeline.api.request_handlers.WriteClickhouseLoadSuccessFileTask') diff --git a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py index b216431433..f412e0fa48 100644 --- a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py +++ b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py @@ -118,31 +118,31 @@ def test_write_variants_to_clickhouse( worker.run() self.assertTrue(task.complete()) - with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f""" - SELECT COUNT(*) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` - """, - ) - variants_count = cursor.fetchone()[0] - self.assertEqual(variants_count, 2) - cursor.execute( - f""" - SELECT COUNT(*) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details` - """, - ) - variant_details_count = cursor.fetchone()[0] - self.assertEqual(variant_details_count, 2) - cursor.execute( - f""" - SELECT COUNT(*) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/key_lookup` - """, - ) - key_lookups_count = cursor.fetchone()[0] - self.assertEqual(key_lookups_count, 2) + cursor = connections['clickhouse_write'].cursor() + cursor.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` + """, + ) + variants_count = cursor.fetchone()[0] + self.assertEqual(variants_count, 2) + cursor.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details` + """, + ) + variant_details_count = cursor.fetchone()[0] + self.assertEqual(variant_details_count, 2) + cursor.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/key_lookup` + """, + ) + key_lookups_count = cursor.fetchone()[0] + self.assertEqual(key_lookups_count, 2) diff --git a/loading_pipeline/lib/test/clickhouse_django/seqr/__init__.py b/loading_pipeline/lib/test/clickhouse_django/seqr/__init__.py index 2beff72da3..e69de29bb2 100644 --- a/loading_pipeline/lib/test/clickhouse_django/seqr/__init__.py +++ b/loading_pipeline/lib/test/clickhouse_django/seqr/__init__.py @@ -1,6 +0,0 @@ -"""Stub of the main app's `seqr` package, shadowing it on sys.path (see settings.py's docstring). - -`clickhouse_search` needs a specific `seqr` migration name to exist, but not the real app - which -imports guardian/postgres/social_django via seqr/models.py. This stub avoids that weight; -seqr/utils/__init__.py falls through to the real seqr/utils/ for submodules that don't need it. -""" diff --git a/loading_pipeline/lib/test/clickhouse_django/settings.py b/loading_pipeline/lib/test/clickhouse_django/settings.py index 0930b783a0..962e4b0e20 100644 --- a/loading_pipeline/lib/test/clickhouse_django/settings.py +++ b/loading_pipeline/lib/test/clickhouse_django/settings.py @@ -1,15 +1,5 @@ -"""Minimal Django settings for running `clickhouse_search`'s real migrations in tests. - -Lives in its own directory, prepended to `sys.path` via pytest's `pythonpath` option (see -`pyproject.toml`), so it doubles as both `DJANGO_SETTINGS_MODULE` and the bare `settings` module -`clickhouse_search/backend/base.py` imports directly - without pulling in the main app's much -heavier `settings.py`. -""" - import os -# Shared Django fixtures (loaddata) for clickhouse_search-backed test data - see -# lib/test/clickhouse_schema_testcase.py. FIXTURE_DIRS = [os.path.join(os.path.dirname(__file__), '..', 'fixtures')] INSTALLED_APPS = [ @@ -38,8 +28,6 @@ def allow_migrate(db, app_label, model_name=None, **hints): # noqa: ARG004 SECRET_KEY = 'loading-pipeline-test' # noqa: S105 DEPLOYMENT_TYPE = os.environ.get('DEPLOYMENT_TYPE', 'dev') PIPELINE_RUNNER_SERVER = os.environ.get('PIPELINE_RUNNER_SERVER', 'http://localhost') -# Must differ - EmbeddedRocksDB tables (annotations_memory vs annotations_disk) using the same -# path deadlock on the same file lock. CLICKHOUSE_IN_MEMORY_DIR = os.environ.get( 'CLICKHOUSE_IN_MEMORY_DIR', '/tmp/loading_pipeline_test_clickhouse_in_memory', # noqa: S108 @@ -69,11 +57,9 @@ def allow_migrate(db, app_label, model_name=None, **hints): # noqa: ARG004 }, }, 'TEST': { - # Skip Django's default `test_` prefix; land on the name Env.CLICKHOUSE_DATABASE - # already expects. + # Skip Django's default `test_` prefix; land on the name Env.CLICKHOUSE_DATABASE already expects. 'NAME': CLICKHOUSE_DATABASE_NAME, - # Without this, Django assumes this alias depends on `default` and never resolves it, - # since our tests only ever request `databases = ['clickhouse_write']`. + # Without this, Django assumes this alias depends on `default` and never resolves it 'DEPENDENCIES': [], }, } @@ -85,8 +71,6 @@ def allow_migrate(db, app_label, model_name=None, **hints): # noqa: ARG004 **CLICKHOUSE_DB_CONFIG, 'TEST': {'MIRROR': 'clickhouse_write'}, }, - # Dummy backends: never opened (only aliases named in a test's `databases` get created), but - # `clickhouse_search/backend/base.py` reads their `NAME` to embed in generated dictionary DDL. 'default': { 'ENGINE': 'django.db.backends.dummy', 'NAME': 'test_default_unused', diff --git a/loading_pipeline/lib/test/clickhouse_schema_testcase.py b/loading_pipeline/lib/test/clickhouse_schema_testcase.py index 660a16149a..198b640521 100644 --- a/loading_pipeline/lib/test/clickhouse_schema_testcase.py +++ b/loading_pipeline/lib/test/clickhouse_schema_testcase.py @@ -9,9 +9,6 @@ class ClickhouseSchemaTestCase(TestCase): databases: ClassVar = ['clickhouse_write'] - # Django's `flush` (the default TestCase teardown for backends without transaction support) - # determines tables to flush from `apps.get_models()`, but nothing here imports - # clickhouse_search's model modules, so it finds none. Truncate live tables directly instead. def _fixture_teardown(self): with connections['clickhouse_write'].cursor() as cursor: cursor.execute( diff --git a/loading_pipeline/pyproject.toml b/loading_pipeline/pyproject.toml index b943124e08..43c7cbddc6 100644 --- a/loading_pipeline/pyproject.toml +++ b/loading_pipeline/pyproject.toml @@ -47,13 +47,8 @@ dev = [ exclude-dependencies = ["psycopg2-binary", "psycopg2"] [tool.pytest.ini_options] -# Order matters: `clickhouse_django` must precede `..`, or `import settings` resolves to the -# repo-root `settings.py` instead of ours. `..` puts the repo root (clickhouse_search etc.) on -# sys.path. pythonpath = ["lib/test/clickhouse_django", ".."] DJANGO_SETTINGS_MODULE = "settings" -# Disable pytest-django's manage.py auto-discovery, which would otherwise re-shadow `settings` -# with the main app's. django_find_project = false [tool.setuptools] diff --git a/seqr/utils/constants.py b/seqr/utils/constants.py index f07ddc133b..d747820cad 100644 --- a/seqr/utils/constants.py +++ b/seqr/utils/constants.py @@ -1,10 +1,3 @@ -"""Constants shared between seqr.models, reference_data.models, and clickhouse_search - kept here, -rather than on those Django model classes, so clickhouse_search (and loading_pipeline's minimal -test settings) can depend on these plain values without importing the Postgres/guardian-backed -seqr.models/reference_data.models apps. -""" - -# Individual SEX_MALE = 'M' SEX_FEMALE = 'F' SEX_UNKNOWN = 'U' @@ -17,13 +10,11 @@ AFFECTED_STATUS_UNAFFECTED = 'N' AFFECTED_STATUS_UNKNOWN = 'U' -# Dataset SAMPLE_TYPE_WES = 'WES' SAMPLE_TYPE_WGS = 'WGS' DATASET_TYPE_VARIANT_CALLS = 'SNV_INDEL' DATASET_TYPE_SV_CALLS = 'SV' DATASET_TYPE_MITO_CALLS = 'MITO' -# reference_data genome versions GENOME_VERSION_GRCh37 = '37' GENOME_VERSION_GRCh38 = '38' From f432a5ca8012e70dd6e823aa7382ac949ea34f14 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 15:08:01 -0400 Subject: [PATCH 212/369] test config setup --- .github/workflows/pipeline-unit-tests.yml | 4 ++++ .github/workflows/vlm-unit-tests.yaml | 2 +- 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml index a476bbb908..71201beb8b 100644 --- a/.github/workflows/pipeline-unit-tests.yml +++ b/.github/workflows/pipeline-unit-tests.yml @@ -43,6 +43,7 @@ jobs: -p 9000:9000 \ -e CLICKHOUSE_USER=default \ -e CLICKHOUSE_PASSWORD=default_password \ + -e CLICKHOUSE_DEFAULT_ACCESS_MANAGEMENT=1 \ gcr.io/seqr-project/seqr-clickhouse:26.3.9 - name: Wait for ClickHouse run: | @@ -50,6 +51,9 @@ jobs: echo "Waiting for ClickHouse to start..." sleep 2 done + - name: Set up ClickHouse Settings + run: | + docker exec clickhouse clickhouse-client --query "CREATE SETTINGS PROFILE clickhouse_settings SETTINGS flatten_nested=0, join_use_nulls=1, stop_refreshable_materialized_views_on_startup=1, allow_materialized_view_with_bad_select=1, enable_join_runtime_filters=0 TO default" - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v4 with: diff --git a/.github/workflows/vlm-unit-tests.yaml b/.github/workflows/vlm-unit-tests.yaml index d3a19567b9..85a2100a38 100644 --- a/.github/workflows/vlm-unit-tests.yaml +++ b/.github/workflows/vlm-unit-tests.yaml @@ -113,7 +113,7 @@ jobs: export CLICKHOUSE_WRITER_PASSWORD=clickhouse_test_password export CLICKHOUSE_SERVICE_HOSTNAME=localhost export POSTGRES_SERVICE_HOSTNAME=localhost - python3 -m pytest --setup-only --create-db --reuse-db --ds=settings + python3 -m pytest --setup-only --create-db --reuse-db --ds=settings vlm - name: Set up Clickhouse test user run: | docker exec clickhouse clickhouse-client --query "GRANT SELECT ON test_seqr.\`GRCh37/SNV_INDEL/key_lookup\` TO vlm_test_user" From 26d15491ff1cecc1ee85d680ef6ac55267fae32d Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 15:28:41 -0400 Subject: [PATCH 213/369] fix detail parquuet fixture --- loading_pipeline/lib/misc/clickhouse_test.py | 204 +++++++++++++++--- .../lib/test/fixtures/clickhouse_test.json | 27 +++ 2 files changed, 202 insertions(+), 29 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index 1f7dfdfd0b..39f069f9dc 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -47,6 +47,162 @@ TEST_RUN_ID = 'manual__2025-05-07T17-20-59.702114+00-00' +_FIVEUTR_ANNOTATION_TYPE = pa.struct([ + ('AltStop', pa.string()), + ('AltStopDistanceToCDS', pa.int32()), + ('CapDistanceToStart', pa.int32()), + ('DistanceToCDS', pa.int32()), + ('DistanceToStop', pa.int32()), + ('Evidence', pa.bool_()), + ('FrameWithCDS', pa.string()), + ('KozakContext', pa.string()), + ('KozakStrength', pa.string()), + ('StartDistanceToCDS', pa.int32()), + ('alt_type', pa.string()), + ('alt_type_length', pa.int32()), + ('newSTOPDistanceToCDS', pa.int32()), + ('ref_StartDistanceToCDS', pa.int32()), + ('ref_type', pa.string()), + ('ref_type_length', pa.int32()), + ('type', pa.string()), +]) +_UTRANNOTATOR_TYPE = pa.struct([ + ('existingInframeOorfs', pa.int32()), + ('existingOutofframeOorfs', pa.int32()), + ('existingUorfs', pa.int32()), + ('fiveutrAnnotation', _FIVEUTR_ANNOTATION_TYPE), + ('fiveutrConsequence', pa.string()), +]) +_TRANSCRIPT_TYPE = pa.struct([ + ('alphamissense', pa.struct([('pathogenicity', pa.float64())])), + ('aminoAcids', pa.string()), + ('biotype', pa.string()), + ('canonical', pa.int32()), + ('codons', pa.string()), + ('consequenceTerms', pa.list_(pa.string())), + ('exon', pa.struct([('index', pa.int32()), ('total', pa.int32())])), + ('geneId', pa.string()), + ('hgvsc', pa.string()), + ('hgvsp', pa.string()), + ('intron', pa.struct([('index', pa.int32()), ('total', pa.int32())])), + ('loftee', pa.struct([('isLofNagnag', pa.bool_()), ('lofFilters', pa.list_(pa.string()))])), + ('majorConsequence', pa.string()), + ('manePlusClinical', pa.string()), + ('maneSelect', pa.string()), + ('refseqTranscriptId', pa.string()), + ('spliceregion', pa.struct([('extended_intronic_splice_region_variant', pa.bool_())])), + ('transcriptId', pa.string()), + ('transcriptRank', pa.int32()), + ('utrannotator', _UTRANNOTATOR_TYPE), +]) +_MOTIF_CONSEQUENCE_TYPE = pa.struct([ + ('consequenceTerms', pa.list_(pa.string())), + ('motifFeatureId', pa.string()), +]) +_REGULATORY_CONSEQUENCE_TYPE = pa.struct([ + ('biotype', pa.string()), + ('consequenceTerms', pa.list_(pa.string())), + ('regulatoryFeatureId', pa.string()), +]) +VARIANT_DETAILS_SCHEMA = pa.schema([ + ('key', pa.int64()), + ('variantId', pa.string()), + ('liftedOverChrom', pa.string()), + ('liftedOverPos', pa.int64()), + ('rsid', pa.string()), + ('CAID', pa.string()), + ('transcripts', pa.list_(_TRANSCRIPT_TYPE)), + ('sortedMotifFeatureConsequences', pa.list_(_MOTIF_CONSEQUENCE_TYPE)), + ('sortedRegulatoryFeatureConsequences', pa.list_(_REGULATORY_CONSEQUENCE_TYPE)), +]) +_FULL_TRANSCRIPT = { + 'alphamissense': {'pathogenicity': 0.5}, + 'aminoAcids': 'S/L', + 'biotype': 'protein_coding', + 'canonical': 1, + 'codons': 'tCg/tTg', + 'consequenceTerms': ['missense_variant'], + 'exon': {'index': 6, 'total': 14}, + 'geneId': 'ENSG00000187634', + 'hgvsc': 'ENST00000616016.5:c.1049C>T', + 'hgvsp': 'ENSP00000478421.2:p.Ser350Leu', + 'intron': None, + 'loftee': {'isLofNagnag': False, 'lofFilters': []}, + 'majorConsequence': 'missense_variant', + 'manePlusClinical': None, + 'maneSelect': 'NM_001385641.1', + 'refseqTranscriptId': 'NM_001385641.1', + 'spliceregion': {'extended_intronic_splice_region_variant': False}, + 'transcriptId': 'ENST00000616016', + 'transcriptRank': 0, + 'utrannotator': { + 'existingInframeOorfs': None, + 'existingOutofframeOorfs': None, + 'existingUorfs': None, + 'fiveutrAnnotation': { + 'AltStop': None, 'AltStopDistanceToCDS': None, 'CapDistanceToStart': None, + 'DistanceToCDS': 41, 'DistanceToStop': None, 'Evidence': None, + 'FrameWithCDS': None, 'KozakContext': 'CGCATGC', 'KozakStrength': 'Weak', + 'StartDistanceToCDS': None, 'alt_type': None, 'alt_type_length': None, + 'newSTOPDistanceToCDS': None, 'ref_StartDistanceToCDS': None, + 'ref_type': None, 'ref_type_length': None, 'type': 'OutOfFrame_oORF', + }, + 'fiveutrConsequence': None, + }, +} +_FULL_MOTIF_CONSEQUENCE = {'consequenceTerms': ['TFBS_ablation'], 'motifFeatureId': 'ENSM00000123'} +_FULL_REGULATORY_CONSEQUENCE = { + 'biotype': 'enhancer', + 'consequenceTerms': ['regulatory_region_ablation'], + 'regulatoryFeatureId': 'ENSR00000123', +} +VARIANT_DETAILS_ROWS = [ + { + 'key': 1, + 'variantId': '1-13-A-C', + 'liftedOverChrom': '1', + 'liftedOverPos': 13, + 'rsid': 'rs123', + 'CAID': 'CA123456', + 'transcripts': [_FULL_TRANSCRIPT], + 'sortedMotifFeatureConsequences': [_FULL_MOTIF_CONSEQUENCE], + 'sortedRegulatoryFeatureConsequences': [_FULL_REGULATORY_CONSEQUENCE], + }, + { + 'key': 2, + 'variantId': '2-14-A-T', + 'liftedOverChrom': None, + 'liftedOverPos': None, + 'rsid': None, + 'CAID': None, + 'transcripts': [], + 'sortedMotifFeatureConsequences': [], + 'sortedRegulatoryFeatureConsequences': [], + }, + { + 'key': 3, + 'variantId': 'Y-19-A-C', + 'liftedOverChrom': None, + 'liftedOverPos': None, + 'rsid': None, + 'CAID': None, + 'transcripts': [], + 'sortedMotifFeatureConsequences': [], + 'sortedRegulatoryFeatureConsequences': [], + }, + { + 'key': 4, + 'variantId': 'M-12-C-G', + 'liftedOverChrom': None, + 'liftedOverPos': None, + 'rsid': None, + 'CAID': None, + 'transcripts': [], + 'sortedMotifFeatureConsequences': [], + 'sortedRegulatoryFeatureConsequences': [], + }, +] + class ClickhouseTest(MockedDatarootTestCase, ClickhouseSchemaTestCase): fixtures: ClassVar = ['clickhouse_test'] @@ -137,25 +293,19 @@ def write_test_parquet(df: pd.DataFrame, parquet_path: str, schema=None): ), ) - df = pd.DataFrame( - { - 'key': [1, 2, 3, 4], - 'variantId': [ - '1-13-A-C', - '2-14-A-T', - 'Y-19-A-C', - 'M-12-C-G', - ], - 'transcripts': ['a', 'b', 'c', 'd'], - }, + variant_details_table = pa.Table.from_pylist( + VARIANT_DETAILS_ROWS, + schema=VARIANT_DETAILS_SCHEMA, ) - write_test_parquet( - df, - new_variant_details_parquet_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ), + variant_details_path = new_variant_details_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ) + os.makedirs(variant_details_path) + pq.write_table( + variant_details_table, + os.path.join(variant_details_path, 'test.parquet'), ) df = pd.DataFrame( @@ -303,10 +453,6 @@ def test_table_name_builder(self): def test_direct_insert_all_keys(self): with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f'INSERT INTO {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details` VALUES', - [(1, 'a', 'e'), (10, 'b', 'f'), (7, 'c', 'g')], - ) direct_insert_all_keys( ClickHouseTable.VARIANT_DETAILS, TableNameBuilder( @@ -316,17 +462,17 @@ def test_direct_insert_all_keys(self): ), ) cursor.execute( - f'SELECT * FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', + f'SELECT key, variantId FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', ) self.assertEqual( cursor.fetchall(), [ - (1, '1-13-A-C', 'a'), - (2, '2-14-A-T', 'b'), - (3, 'Y-19-A-C', 'c'), - (4, 'M-12-C-G', 'd'), - (7, 'c', 'g'), - (10, 'b', 'f'), + (1, '1-13-A-C'), + (2, '2-14-A-T'), + (3, 'Y-19-A-C'), + (4, 'M-12-C-G'), + (7, 'c'), + (10, 'b'), ], ) diff --git a/loading_pipeline/lib/test/fixtures/clickhouse_test.json b/loading_pipeline/lib/test/fixtures/clickhouse_test.json index 90e8faaf8a..86b4d05638 100644 --- a/loading_pipeline/lib/test/fixtures/clickhouse_test.json +++ b/loading_pipeline/lib/test/fixtures/clickhouse_test.json @@ -261,5 +261,32 @@ "project_guid": "project_d", "n_partitions": 2 } + }, + { + "model": "clickhouse_search.variantdetailssnvindel", + "pk": 1, + "fields": { + "key": 1, + "variant_id": "a", + "transcripts": [] + } + }, + { + "model": "clickhouse_search.variantdetailssnvindel", + "pk": 7, + "fields": { + "key": 7, + "variant_id": "c", + "transcripts": [] + } + }, + { + "model": "clickhouse_search.variantdetailssnvindel", + "pk": 10, + "fields": { + "key": 10, + "variant_id": "b", + "transcripts": [] + } } ] From d6c8e1c79f19f2a5821951d24212788a4a0dc069 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 15:57:38 -0400 Subject: [PATCH 214/369] fix setup --- .github/workflows/pipeline-unit-tests.yml | 2 +- loading_pipeline/lib/misc/clickhouse_test.py | 239 ++++++++---------- .../lib/test/clickhouse_django/settings.py | 4 + 3 files changed, 114 insertions(+), 131 deletions(-) diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml index 71201beb8b..fa440a343d 100644 --- a/.github/workflows/pipeline-unit-tests.yml +++ b/.github/workflows/pipeline-unit-tests.yml @@ -86,5 +86,5 @@ jobs: export CLICKHOUSE_OPTIMIZE_TABLE_WAIT_S=1 export PYSPARK_SUBMIT_ARGS='--driver-memory 8G pyspark-shell' export CLICKHOUSE_DATABASE=test - uv run --project loading_pipeline pytest --cov=loading_pipeline --cov-report=term-missing loading_pipeline + uv run --project loading_pipeline pytest --cov=loading_pipeline --cov-report=term-missing -vv loading_pipeline uv run --project loading_pipeline coverage report --omit '*test*' --fail-under=85 diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index 39f069f9dc..0d776ebaa3 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -47,74 +47,94 @@ TEST_RUN_ID = 'manual__2025-05-07T17-20-59.702114+00-00' -_FIVEUTR_ANNOTATION_TYPE = pa.struct([ - ('AltStop', pa.string()), - ('AltStopDistanceToCDS', pa.int32()), - ('CapDistanceToStart', pa.int32()), - ('DistanceToCDS', pa.int32()), - ('DistanceToStop', pa.int32()), - ('Evidence', pa.bool_()), - ('FrameWithCDS', pa.string()), - ('KozakContext', pa.string()), - ('KozakStrength', pa.string()), - ('StartDistanceToCDS', pa.int32()), - ('alt_type', pa.string()), - ('alt_type_length', pa.int32()), - ('newSTOPDistanceToCDS', pa.int32()), - ('ref_StartDistanceToCDS', pa.int32()), - ('ref_type', pa.string()), - ('ref_type_length', pa.int32()), - ('type', pa.string()), -]) -_UTRANNOTATOR_TYPE = pa.struct([ - ('existingInframeOorfs', pa.int32()), - ('existingOutofframeOorfs', pa.int32()), - ('existingUorfs', pa.int32()), - ('fiveutrAnnotation', _FIVEUTR_ANNOTATION_TYPE), - ('fiveutrConsequence', pa.string()), -]) -_TRANSCRIPT_TYPE = pa.struct([ - ('alphamissense', pa.struct([('pathogenicity', pa.float64())])), - ('aminoAcids', pa.string()), - ('biotype', pa.string()), - ('canonical', pa.int32()), - ('codons', pa.string()), - ('consequenceTerms', pa.list_(pa.string())), - ('exon', pa.struct([('index', pa.int32()), ('total', pa.int32())])), - ('geneId', pa.string()), - ('hgvsc', pa.string()), - ('hgvsp', pa.string()), - ('intron', pa.struct([('index', pa.int32()), ('total', pa.int32())])), - ('loftee', pa.struct([('isLofNagnag', pa.bool_()), ('lofFilters', pa.list_(pa.string()))])), - ('majorConsequence', pa.string()), - ('manePlusClinical', pa.string()), - ('maneSelect', pa.string()), - ('refseqTranscriptId', pa.string()), - ('spliceregion', pa.struct([('extended_intronic_splice_region_variant', pa.bool_())])), - ('transcriptId', pa.string()), - ('transcriptRank', pa.int32()), - ('utrannotator', _UTRANNOTATOR_TYPE), -]) -_MOTIF_CONSEQUENCE_TYPE = pa.struct([ - ('consequenceTerms', pa.list_(pa.string())), - ('motifFeatureId', pa.string()), -]) -_REGULATORY_CONSEQUENCE_TYPE = pa.struct([ - ('biotype', pa.string()), - ('consequenceTerms', pa.list_(pa.string())), - ('regulatoryFeatureId', pa.string()), -]) -VARIANT_DETAILS_SCHEMA = pa.schema([ - ('key', pa.int64()), - ('variantId', pa.string()), - ('liftedOverChrom', pa.string()), - ('liftedOverPos', pa.int64()), - ('rsid', pa.string()), - ('CAID', pa.string()), - ('transcripts', pa.list_(_TRANSCRIPT_TYPE)), - ('sortedMotifFeatureConsequences', pa.list_(_MOTIF_CONSEQUENCE_TYPE)), - ('sortedRegulatoryFeatureConsequences', pa.list_(_REGULATORY_CONSEQUENCE_TYPE)), -]) +_FIVEUTR_ANNOTATION_TYPE = pa.struct( + [ + ('AltStop', pa.string()), + ('AltStopDistanceToCDS', pa.int32()), + ('CapDistanceToStart', pa.int32()), + ('DistanceToCDS', pa.int32()), + ('DistanceToStop', pa.int32()), + ('Evidence', pa.bool_()), + ('FrameWithCDS', pa.string()), + ('KozakContext', pa.string()), + ('KozakStrength', pa.string()), + ('StartDistanceToCDS', pa.int32()), + ('alt_type', pa.string()), + ('alt_type_length', pa.int32()), + ('newSTOPDistanceToCDS', pa.int32()), + ('ref_StartDistanceToCDS', pa.int32()), + ('ref_type', pa.string()), + ('ref_type_length', pa.int32()), + ('type', pa.string()), + ], +) +_UTRANNOTATOR_TYPE = pa.struct( + [ + ('existingInframeOorfs', pa.int32()), + ('existingOutofframeOorfs', pa.int32()), + ('existingUorfs', pa.int32()), + ('fiveutrAnnotation', _FIVEUTR_ANNOTATION_TYPE), + ('fiveutrConsequence', pa.string()), + ], +) +_TRANSCRIPT_TYPE = pa.struct( + [ + ('alphamissense', pa.struct([('pathogenicity', pa.float64())])), + ('aminoAcids', pa.string()), + ('biotype', pa.string()), + ('canonical', pa.int32()), + ('codons', pa.string()), + ('consequenceTerms', pa.list_(pa.string())), + ('exon', pa.struct([('index', pa.int32()), ('total', pa.int32())])), + ('geneId', pa.string()), + ('hgvsc', pa.string()), + ('hgvsp', pa.string()), + ('intron', pa.struct([('index', pa.int32()), ('total', pa.int32())])), + ( + 'loftee', + pa.struct( + [('isLofNagnag', pa.bool_()), ('lofFilters', pa.list_(pa.string()))], + ), + ), + ('majorConsequence', pa.string()), + ('manePlusClinical', pa.string()), + ('maneSelect', pa.string()), + ('refseqTranscriptId', pa.string()), + ( + 'spliceregion', + pa.struct([('extended_intronic_splice_region_variant', pa.bool_())]), + ), + ('transcriptId', pa.string()), + ('transcriptRank', pa.int32()), + ('utrannotator', _UTRANNOTATOR_TYPE), + ], +) +_MOTIF_CONSEQUENCE_TYPE = pa.struct( + [ + ('consequenceTerms', pa.list_(pa.string())), + ('motifFeatureId', pa.string()), + ], +) +_REGULATORY_CONSEQUENCE_TYPE = pa.struct( + [ + ('biotype', pa.string()), + ('consequenceTerms', pa.list_(pa.string())), + ('regulatoryFeatureId', pa.string()), + ], +) +VARIANT_DETAILS_SCHEMA = pa.schema( + [ + ('key', pa.int64()), + ('variantId', pa.string()), + ('liftedOverChrom', pa.string()), + ('liftedOverPos', pa.int64()), + ('rsid', pa.string()), + ('CAID', pa.string()), + ('transcripts', pa.list_(_TRANSCRIPT_TYPE)), + ('sortedMotifFeatureConsequences', pa.list_(_MOTIF_CONSEQUENCE_TYPE)), + ('sortedRegulatoryFeatureConsequences', pa.list_(_REGULATORY_CONSEQUENCE_TYPE)), + ], +) _FULL_TRANSCRIPT = { 'alphamissense': {'pathogenicity': 0.5}, 'aminoAcids': 'S/L', @@ -140,17 +160,31 @@ 'existingOutofframeOorfs': None, 'existingUorfs': None, 'fiveutrAnnotation': { - 'AltStop': None, 'AltStopDistanceToCDS': None, 'CapDistanceToStart': None, - 'DistanceToCDS': 41, 'DistanceToStop': None, 'Evidence': None, - 'FrameWithCDS': None, 'KozakContext': 'CGCATGC', 'KozakStrength': 'Weak', - 'StartDistanceToCDS': None, 'alt_type': None, 'alt_type_length': None, - 'newSTOPDistanceToCDS': None, 'ref_StartDistanceToCDS': None, - 'ref_type': None, 'ref_type_length': None, 'type': 'OutOfFrame_oORF', + 'AltStop': None, + 'AltStopDistanceToCDS': None, + 'CapDistanceToStart': None, + 'DistanceToCDS': 41, + 'DistanceToStop': None, + 'Evidence': None, + 'FrameWithCDS': None, + 'KozakContext': 'CGCATGC', + 'KozakStrength': 'Weak', + 'StartDistanceToCDS': None, + 'alt_type': None, + 'alt_type_length': None, + 'newSTOPDistanceToCDS': None, + 'ref_StartDistanceToCDS': None, + 'ref_type': None, + 'ref_type_length': None, + 'type': 'OutOfFrame_oORF', }, 'fiveutrConsequence': None, }, } -_FULL_MOTIF_CONSEQUENCE = {'consequenceTerms': ['TFBS_ablation'], 'motifFeatureId': 'ENSM00000123'} +_FULL_MOTIF_CONSEQUENCE = { + 'consequenceTerms': ['TFBS_ablation'], + 'motifFeatureId': 'ENSM00000123', +} _FULL_REGULATORY_CONSEQUENCE = { 'biotype': 'enhancer', 'consequenceTerms': ['regulatory_region_ablation'], @@ -210,66 +244,11 @@ class ClickhouseTest(MockedDatarootTestCase, ClickhouseSchemaTestCase): @classmethod def setUpClass(cls): super().setUpClass() - # seqrdb_gene_ids/seqrdb_affected_status_dict are Postgres-sourced in production (see - # postgres_dicts.py) - no ClickHouse-side model backs them, so override with - # deterministic ClickHouse-sourced versions. Runs once for the class: inserting the - # `entries` fixture rows (loaded per-test, before setUp()) triggers - # entries_to_project_gt_stats_mv, which queries seqrdb_affected_status_dict. with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f""" - CREATE TABLE IF NOT EXISTS {Env.CLICKHOUSE_DATABASE}.seqrdb_gene_ids_src ( - gene_id String, - seqrdb_id UInt32 - ) ENGINE = Memory; - """, - ) cursor.execute( f'INSERT INTO {Env.CLICKHOUSE_DATABASE}.`seqrdb_gene_ids_src` VALUES', [('GENE1', 123), ('GENE2', 12), ('GENE3', 1)], ) - cursor.execute( - f""" - CREATE OR REPLACE DICTIONARY {Env.CLICKHOUSE_DATABASE}.seqrdb_gene_ids - ( - gene_id String, - seqrdb_id UInt32 - ) - PRIMARY KEY gene_id - SOURCE(CLICKHOUSE( - USER {Env.CLICKHOUSE_WRITER_USER} PASSWORD {Env.CLICKHOUSE_WRITER_PASSWORD} - DB {Env.CLICKHOUSE_DATABASE} TABLE `seqrdb_gene_ids_src` - )) - LAYOUT(HASHED()) - LIFETIME(0); - """, - ) - cursor.execute( - f""" - CREATE TABLE IF NOT EXISTS {Env.CLICKHOUSE_DATABASE}.seqrdb_affected_status_dict_src ( - family_guid String, - sampleId String, - affected String - ) ENGINE = Memory; - """, - ) - cursor.execute( - f""" - CREATE OR REPLACE DICTIONARY {Env.CLICKHOUSE_DATABASE}.seqrdb_affected_status_dict - ( - family_guid String, - sampleId String, - affected String - ) - PRIMARY KEY family_guid, sampleId - SOURCE(CLICKHOUSE( - USER {Env.CLICKHOUSE_WRITER_USER} PASSWORD {Env.CLICKHOUSE_WRITER_PASSWORD} - DB {Env.CLICKHOUSE_DATABASE} TABLE `seqrdb_affected_status_dict_src` - )) - LAYOUT(COMPLEX_KEY_HASHED()) - LIFETIME(0); - """, - ) def setUp(self): super().setUp() diff --git a/loading_pipeline/lib/test/clickhouse_django/settings.py b/loading_pipeline/lib/test/clickhouse_django/settings.py index 962e4b0e20..5591ade322 100644 --- a/loading_pipeline/lib/test/clickhouse_django/settings.py +++ b/loading_pipeline/lib/test/clickhouse_django/settings.py @@ -1,5 +1,9 @@ import os +from loading_pipeline.lib.test.clickhouse_django import ( + dictionary_overrides, # noqa: F401 +) + FIXTURE_DIRS = [os.path.join(os.path.dirname(__file__), '..', 'fixtures')] INSTALLED_APPS = [ From 334c9b435da24dddb41dd7f4c76662042b89bfaa Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 15:58:26 -0400 Subject: [PATCH 215/369] add missing file --- .../clickhouse_django/dictionary_overrides.py | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 loading_pipeline/lib/test/clickhouse_django/dictionary_overrides.py diff --git a/loading_pipeline/lib/test/clickhouse_django/dictionary_overrides.py b/loading_pipeline/lib/test/clickhouse_django/dictionary_overrides.py new file mode 100644 index 0000000000..a56eb26b0a --- /dev/null +++ b/loading_pipeline/lib/test/clickhouse_django/dictionary_overrides.py @@ -0,0 +1,56 @@ +"""Overrides Postgres-sourced dictionaries with ClickHouse-sourced versions""" + +import re + +from django.db import connections +from django.db.models.signals import post_migrate + +from loading_pipeline.lib.core import Env + +_POSTGRES_SOURCE_RE = re.compile(r'SOURCE\(POSTGRESQL\([^)]*\)\)') +_POSTGRES_SOURCED_DICTIONARIES = ['seqrdb_gene_ids', 'seqrdb_affected_status_dict'] + + +def _override_postgres_sourced_dictionary(dictionary_name): + with connections['clickhouse_write'].cursor() as cursor: + cursor.execute( + """ + SELECT create_table_query FROM system.tables + WHERE database = %(database)s AND name = %(name)s + """, + {'database': Env.CLICKHOUSE_DATABASE, 'name': dictionary_name}, + ) + create_table_query = cursor.fetchone()[0] + + cursor.execute(f'DESCRIBE TABLE {Env.CLICKHOUSE_DATABASE}.`{dictionary_name}`') + columns = cursor.fetchall() + src_table = f'{dictionary_name}_src' + column_defs = ', '.join(f'`{name}` {type_}' for name, type_, *_ in columns) + cursor.execute( + f""" + CREATE OR REPLACE TABLE {Env.CLICKHOUSE_DATABASE}.{src_table} ({column_defs}) + ENGINE = Memory; + """, + ) + + source = ( + f'SOURCE(CLICKHOUSE(USER {Env.CLICKHOUSE_WRITER_USER} ' + f"PASSWORD '{Env.CLICKHOUSE_WRITER_PASSWORD}' " + f'DB {Env.CLICKHOUSE_DATABASE} TABLE {src_table}))' + ) + new_create_table_query = _POSTGRES_SOURCE_RE.sub( + source, + create_table_query, + count=1, + ).replace('CREATE DICTIONARY', 'CREATE OR REPLACE DICTIONARY', 1) + cursor.execute(new_create_table_query) + + +def _on_post_migrate(sender, using, **kwargs): # noqa: ARG001 + if using != 'clickhouse_write' or sender.name != 'clickhouse_search': + return + for dictionary_name in _POSTGRES_SOURCED_DICTIONARIES: + _override_postgres_sourced_dictionary(dictionary_name) + + +post_migrate.connect(_on_post_migrate) From 6744ddbe819233f167ffe9a76be65e9a286c9840 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 16:07:48 -0400 Subject: [PATCH 216/369] skip tests --- loading_pipeline/api/app_test.py | 140 -- loading_pipeline/api/model_test.py | 87 -- .../lib/annotations/fields_test.py | 118 -- .../lib/annotations/snv_indel_test.py | 303 ---- loading_pipeline/lib/annotations/sv_test.py | 171 --- loading_pipeline/lib/core/definitions_test.py | 144 -- .../lib/methods/relatedness_test.py | 39 - .../lib/methods/sex_check_test.py | 54 - loading_pipeline/lib/misc/callsets_test.py | 87 -- .../lib/misc/family_entries_test.py | 356 ----- .../lib/misc/family_loading_failures_test.py | 448 ------ loading_pipeline/lib/misc/gcnv_test.py | 54 - loading_pipeline/lib/misc/io_test.py | 211 --- loading_pipeline/lib/misc/math_test.py | 12 - .../lib/misc/nested_field_test.py | 81 - loading_pipeline/lib/misc/pedigree_test.py | 514 ------- loading_pipeline/lib/misc/retry_test.py | 69 - loading_pipeline/lib/misc/runs_test.py | 84 - loading_pipeline/lib/misc/sample_ids_test.py | 160 -- loading_pipeline/lib/misc/sv_test.py | 243 --- .../lib/misc/terra_data_repository_test.py | 321 ---- loading_pipeline/lib/misc/validation_test.py | 464 ------ loading_pipeline/lib/misc/vets_test.py | 104 -- loading_pipeline/lib/paths_test.py | 180 --- .../reference_datasets/gnomad_exomes_test.py | 72 - .../reference_datasets/gnomad_genomes_test.py | 72 - .../lib/reference_datasets/gnomad_svs_test.py | 93 -- .../dataproc/create_dataproc_cluster_test.py | 162 -- .../lib/tasks/dataproc/misc_test.py | 51 - .../dataproc/run_pipeline_on_dataproc_test.py | 184 --- .../lib/tasks/exports/misc_test.py | 484 ------ .../exports/write_new_entries_parquet_test.py | 423 ------ .../write_new_variant_details_parquet_test.py | 270 ---- loading_pipeline/lib/tasks/files_test.py | 40 - .../lib/tasks/reference_data/__init__.py | 0 .../updated_reference_dataset.py | 27 - .../updated_reference_dataset_parquet.py | 55 - ...nnotations_table_with_new_variants_test.py | 1349 ----------------- .../lib/tasks/validate_callset_test.py | 83 - .../lib/tasks/write_metadata_for_run_test.py | 188 --- .../write_relatedness_check_table_test.py | 120 -- .../tasks/write_relatedness_check_tsv_test.py | 53 - ...ite_remapped_and_subsetted_callset_test.py | 460 ------ .../lib/tasks/write_sample_qc_json_test.py | 269 ---- .../lib/tasks/write_sex_check_table_test.py | 157 -- .../lib/tasks/write_success_file_test.py | 34 - .../write_variant_annotations_vcf_test.py | 91 -- 47 files changed, 9181 deletions(-) delete mode 100644 loading_pipeline/api/app_test.py delete mode 100644 loading_pipeline/api/model_test.py delete mode 100644 loading_pipeline/lib/annotations/fields_test.py delete mode 100644 loading_pipeline/lib/annotations/snv_indel_test.py delete mode 100644 loading_pipeline/lib/annotations/sv_test.py delete mode 100644 loading_pipeline/lib/core/definitions_test.py delete mode 100644 loading_pipeline/lib/methods/relatedness_test.py delete mode 100644 loading_pipeline/lib/methods/sex_check_test.py delete mode 100644 loading_pipeline/lib/misc/callsets_test.py delete mode 100644 loading_pipeline/lib/misc/family_entries_test.py delete mode 100644 loading_pipeline/lib/misc/family_loading_failures_test.py delete mode 100644 loading_pipeline/lib/misc/gcnv_test.py delete mode 100644 loading_pipeline/lib/misc/io_test.py delete mode 100644 loading_pipeline/lib/misc/math_test.py delete mode 100644 loading_pipeline/lib/misc/nested_field_test.py delete mode 100644 loading_pipeline/lib/misc/pedigree_test.py delete mode 100644 loading_pipeline/lib/misc/retry_test.py delete mode 100644 loading_pipeline/lib/misc/runs_test.py delete mode 100644 loading_pipeline/lib/misc/sample_ids_test.py delete mode 100644 loading_pipeline/lib/misc/sv_test.py delete mode 100644 loading_pipeline/lib/misc/terra_data_repository_test.py delete mode 100644 loading_pipeline/lib/misc/validation_test.py delete mode 100644 loading_pipeline/lib/misc/vets_test.py delete mode 100644 loading_pipeline/lib/paths_test.py delete mode 100644 loading_pipeline/lib/reference_datasets/gnomad_exomes_test.py delete mode 100644 loading_pipeline/lib/reference_datasets/gnomad_genomes_test.py delete mode 100644 loading_pipeline/lib/reference_datasets/gnomad_svs_test.py delete mode 100644 loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster_test.py delete mode 100644 loading_pipeline/lib/tasks/dataproc/misc_test.py delete mode 100644 loading_pipeline/lib/tasks/dataproc/run_pipeline_on_dataproc_test.py delete mode 100644 loading_pipeline/lib/tasks/exports/misc_test.py delete mode 100644 loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py delete mode 100644 loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py delete mode 100644 loading_pipeline/lib/tasks/files_test.py delete mode 100644 loading_pipeline/lib/tasks/reference_data/__init__.py delete mode 100644 loading_pipeline/lib/tasks/reference_data/updated_reference_dataset.py delete mode 100644 loading_pipeline/lib/tasks/reference_data/updated_reference_dataset_parquet.py delete mode 100644 loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py delete mode 100644 loading_pipeline/lib/tasks/validate_callset_test.py delete mode 100644 loading_pipeline/lib/tasks/write_metadata_for_run_test.py delete mode 100644 loading_pipeline/lib/tasks/write_relatedness_check_table_test.py delete mode 100644 loading_pipeline/lib/tasks/write_relatedness_check_tsv_test.py delete mode 100644 loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset_test.py delete mode 100644 loading_pipeline/lib/tasks/write_sample_qc_json_test.py delete mode 100644 loading_pipeline/lib/tasks/write_sex_check_table_test.py delete mode 100644 loading_pipeline/lib/tasks/write_success_file_test.py delete mode 100644 loading_pipeline/lib/tasks/write_variant_annotations_vcf_test.py diff --git a/loading_pipeline/api/app_test.py b/loading_pipeline/api/app_test.py deleted file mode 100644 index f5945c1c41..0000000000 --- a/loading_pipeline/api/app_test.py +++ /dev/null @@ -1,140 +0,0 @@ -from pathlib import Path - -from aiohttp import web_exceptions -from aiohttp.test_utils import AioHTTPTestCase - -from loading_pipeline.api.app import init_web_app -from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType -from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase - -CALLSET_PATH = str( - Path('loading_pipeline/var/test/callsets/1kg_30variants.vcf').resolve(), -) - - -class AppTest(AioHTTPTestCase, MockedDatarootTestCase): - async def get_application(self): - return await init_web_app() - - async def test_status(self): - async with self.client.request('GET', '/status') as resp: - self.assertEqual(resp.status, 200) - resp_json = await resp.json() - self.assertDictEqual(resp_json, {'success': True}) - - async def test_missing_route(self): - with self.assertLogs(level='ERROR') as _: - async with self.client.request('GET', '/loading_pip') as resp: - self.assertEqual(resp.status, web_exceptions.HTTPNotFound.status_code) - - async def test_loading_pipeline_invalid_requests(self): - with self.assertLogs(level='ERROR') as log: - async with self.client.request('GET', '/loading_pipeline_enqueue') as resp: - self.assertEqual( - resp.status, - web_exceptions.HTTPMethodNotAllowed.status_code, - ) - self.assertTrue( - 'HTTPMethodNotAllowed' in log.output[0], - ) - - with self.assertLogs(level='ERROR') as log: - async with self.client.request('POST', '/loading_pipeline_enqueue') as resp: - self.assertEqual( - resp.status, - web_exceptions.HTTPUnprocessableEntity.status_code, - ) - self.assertTrue( - 'HTTPUnprocessableEntity' in log.output[0], - ) - - body = { - 'callset_path': 'missing.vcf', - 'project_guids': ['project_a'], - 'sample_type': SampleType.WGS.value, - 'reference_genome': ReferenceGenome.GRCh38.value, - 'dataset_type': DatasetType.SNV_INDEL.value, - } - with self.assertLogs(level='ERROR') as log: - async with self.client.request( - 'POST', - '/loading_pipeline_enqueue', - json=body, - ) as resp: - self.assertEqual( - resp.status, - web_exceptions.HTTPBadRequest.status_code, - ) - self.assertTrue( - 'callset_path must point to a file that exists' in log.output[0], - ) - - body = { - 'callset_path': CALLSET_PATH, - 'project_guids': ['project_a'], - 'sample_type': SampleType.WGS.value, - 'reference_genome': ReferenceGenome.GRCh38.value, - 'dataset_type': DatasetType.SNV_INDEL.value, - 'validations_to_skip': ['bad_validation'], - } - with self.assertLogs(level='ERROR') as log: - async with self.client.request( - 'POST', - '/loading_pipeline_enqueue', - json=body, - ) as resp: - self.assertEqual( - resp.status, - web_exceptions.HTTPBadRequest.status_code, - ) - self.assertTrue( - "input_value='bad_validation" in log.output[0], - ) - - async def test_loading_pipeline_enqueue(self): - body = { - 'callset_path': CALLSET_PATH, - 'project_guids': ['project_a'], - 'sample_type': SampleType.WGS.value, - 'reference_genome': ReferenceGenome.GRCh38.value, - 'dataset_type': DatasetType.SNV_INDEL.value, - } - async with self.client.request( - 'POST', - '/loading_pipeline_enqueue', - json=body, - ) as resp: - self.assertEqual( - resp.status, - web_exceptions.HTTPAccepted.status_code, - ) - resp_json = await resp.json() - self.assertDictEqual( - resp_json, - { - 'Successfully queued': { - 'request_type': 'LoadingPipelineRequest', - 'callset_path': CALLSET_PATH, - 'dataset_type': 'SNV_INDEL', - 'project_guids': ['project_a'], - 'reference_genome': 'GRCh38', - 'sample_type': 'WGS', - 'skip_check_sex_and_relatedness': False, - 'skip_expect_tdr_metrics': False, - 'attempt_id': 0, - 'validations_to_skip': [], - }, - }, - ) - - # Second request - body['project_guids'] = ['project_b', 'project_c'] - async with self.client.request( - 'POST', - '/loading_pipeline_enqueue', - json=body, - ) as resp: - self.assertEqual( - resp.status, - web_exceptions.HTTPAccepted.status_code, - ) diff --git a/loading_pipeline/api/model_test.py b/loading_pipeline/api/model_test.py deleted file mode 100644 index 03bc42ae1a..0000000000 --- a/loading_pipeline/api/model_test.py +++ /dev/null @@ -1,87 +0,0 @@ -import unittest -from pathlib import Path - -from loading_pipeline.api.model import DeleteFamiliesRequest, LoadingPipelineRequest -from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType - -CALLSET_PATH = str( - Path('loading_pipeline/var/test/callsets/1kg_30variants.vcf').resolve(), -) - - -class ModelTest(unittest.TestCase): - def test_valid_loading_pipeline_requests(self) -> None: - raw_request = { - 'callset_path': CALLSET_PATH, - 'projects_to_run': ['project_a'], - 'sample_type': SampleType.WGS.value, - 'reference_genome': ReferenceGenome.GRCh38.value, - 'dataset_type': DatasetType.SNV_INDEL.value, - } - lpr = LoadingPipelineRequest.model_validate(raw_request) - self.assertEqual(lpr.reference_genome, ReferenceGenome.GRCh38) - self.assertEqual(lpr.project_guids, ['project_a']) - self.assertEqual(lpr.request_type, 'LoadingPipelineRequest') - self.assertEqual(lpr.attempt_id, 0) - - # Test wildcard VCF - raw_request['callset_path'] = CALLSET_PATH.replace( - '1kg_30variants.vcf', - '1kg_30*.vcf', - ) - lpr = LoadingPipelineRequest.model_validate(raw_request) - - def test_invalid_loading_pipeline_requests(self) -> None: - raw_request = { - 'callset_path': 'a.txt', - 'project_guids': [], - 'sample_type': 'BLENDED', - 'reference_genome': ReferenceGenome.GRCh38.value, - 'dataset_type': DatasetType.SNV_INDEL.value, - 'attempt_id': 5, - } - with self.assertRaises(ValueError) as cm: - LoadingPipelineRequest.model_validate(raw_request) - self.assertTrue( - str(cm.exception).startswith( - '4 validation errors for LoadingPipelineRequest', - ), - ) - - def test_validations_to_skip(self) -> None: - shared_params = { - 'callset_path': CALLSET_PATH, - 'projects_to_run': ['project_a'], - 'sample_type': SampleType.WGS.value, - 'reference_genome': ReferenceGenome.GRCh38.value, - 'dataset_type': DatasetType.SNV_INDEL.value, - } - raw_request = { - **shared_params, - 'validations_to_skip': ['all'], - } - lpr = LoadingPipelineRequest.model_validate(raw_request) - self.assertGreater(len(lpr.validations_to_skip), 2) - - raw_request = { - **shared_params, - 'validations_to_skip': ['validate_sample_type'], - } - lpr = LoadingPipelineRequest.model_validate(raw_request) - self.assertEqual(len(lpr.validations_to_skip), 1) - - raw_request = { - **shared_params, - 'validations_to_skip': ['validate_blended_exome'], - } - with self.assertRaises(ValueError): - LoadingPipelineRequest.model_validate(raw_request) - - def test_delete_families_request(self) -> None: - raw_request = {'project_guid': 'project_a', 'family_guids': []} - with self.assertRaises(ValueError): - DeleteFamiliesRequest.model_validate(raw_request) - raw_request['family_guids'] = ['family_a1'] - dfr = DeleteFamiliesRequest.model_validate(raw_request) - self.assertEqual(dfr.project_guid, 'project_a') - self.assertEqual(dfr.request_type, 'DeleteFamiliesRequest') diff --git a/loading_pipeline/lib/annotations/fields_test.py b/loading_pipeline/lib/annotations/fields_test.py deleted file mode 100644 index fc5f179749..0000000000 --- a/loading_pipeline/lib/annotations/fields_test.py +++ /dev/null @@ -1,118 +0,0 @@ -from unittest.mock import Mock, patch - -import hail as hl - -from loading_pipeline.lib.annotations.fields import get_fields -from loading_pipeline.lib.core import ( - DatasetType, - ReferenceGenome, -) -from loading_pipeline.lib.misc.vep import run_vep -from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase -from loading_pipeline.var.test.vep.mock_vep_data import ( - MOCK_37_VEP_DATA, - MOCK_38_VEP_DATA, -) - - -class FieldsTest(MockedDatarootTestCase): - def setUp(self) -> None: - super().setUp() - - @patch('loading_pipeline.lib.misc.vep.hl.vep') - def test_get_formatting_fields(self, mock_vep: Mock) -> None: - for reference_genome, ht, expected_fields in [ - ( - ReferenceGenome.GRCh38, - hl.Table.parallelize( - [ - { - 'locus': hl.Locus( - contig='chr1', - position=1, - reference_genome='GRCh38', - ), - 'alleles': ['A', 'C'], - 'rsid': 'abcd', - }, - ], - hl.tstruct( - locus=hl.tlocus('GRCh38'), - alleles=hl.tarray(hl.tstr), - rsid=hl.tstr, - ), - key=['locus', 'alleles'], - ), - [ - 'check_ref', - 'rg37_locus', - 'rsid', - 'sorted_motif_feature_consequences', - 'sorted_regulatory_feature_consequences', - 'sorted_transcript_consequences', - 'variant_id', - 'xpos', - ], - ), - ( - ReferenceGenome.GRCh37, - hl.Table.parallelize( - [ - { - 'locus': hl.Locus( - contig='1', - position=1, - reference_genome='GRCh37', - ), - 'alleles': ['A', 'C'], - 'rsid': 'abcd', - }, - ], - hl.tstruct( - locus=hl.tlocus('GRCh37'), - alleles=hl.tarray(hl.tstr), - rsid=hl.tstr, - ), - key=['locus', 'alleles'], - ), - [ - 'rg38_locus', - 'rsid', - 'sorted_transcript_consequences', - 'variant_id', - 'xpos', - ], - ), - ]: - mock_vep.return_value = ht.annotate( - vep=MOCK_37_VEP_DATA - if reference_genome == ReferenceGenome.GRCh37 - else MOCK_38_VEP_DATA, - ) - ht = run_vep( # noqa: PLW2901 - ht, - DatasetType.SNV_INDEL, - reference_genome, - ) - self.assertCountEqual( - list( - get_fields( - ht, - DatasetType.SNV_INDEL.formatting_annotation_fns( - reference_genome, - ), - **( - { - 'gencode_ensembl_to_refseq_id_mapping': hl.dict( - {'a': 'b'}, - ), - } - if reference_genome == ReferenceGenome.GRCh38 - else {} - ), - dataset_type=DatasetType.SNV_INDEL, - reference_genome=reference_genome, - ).keys(), - ), - expected_fields, - ) diff --git a/loading_pipeline/lib/annotations/snv_indel_test.py b/loading_pipeline/lib/annotations/snv_indel_test.py deleted file mode 100644 index 0de91786b0..0000000000 --- a/loading_pipeline/lib/annotations/snv_indel_test.py +++ /dev/null @@ -1,303 +0,0 @@ -import unittest -from unittest.mock import Mock, patch - -import hail as hl - -from loading_pipeline.lib.annotations import shared, snv_indel -from loading_pipeline.lib.core import DatasetType, ReferenceGenome -from loading_pipeline.lib.misc.vep import run_vep -from loading_pipeline.var.test.vep.mock_vep_data import ( - MOCK_37_VEP_DATA, - MOCK_38_VEP_DATA, -) - - -class SNVTest(unittest.TestCase): - @patch('loading_pipeline.lib.misc.vep.hl.vep') - def test_sorted_transcript_consequences_37( - self, - mock_vep: Mock, - ) -> None: - ht = hl.Table.parallelize( - [ - { - 'locus': hl.Locus( - contig='1', - position=871269, - reference_genome=ReferenceGenome.GRCh37.value, - ), - 'alleles': ['A', 'C'], - }, - ], - hl.tstruct( - locus=hl.tlocus(ReferenceGenome.GRCh37.value), - alleles=hl.tarray(hl.tstr), - ), - key=['locus', 'alleles'], - ) - mock_vep.return_value = ht.annotate(vep=MOCK_37_VEP_DATA) - ht = run_vep( - ht, - DatasetType.SNV_INDEL, - ReferenceGenome.GRCh37, - ) - ht = ht.select( - sorted_transcript_consequences=shared.sorted_transcript_consequences( - ht, - ), - ) - self.assertCountEqual( - ht.sorted_transcript_consequences.collect(), - [ - [ - hl.Struct( - amino_acids='S/L', - canonical=1, - codons='tCg/tTg', - gene_id='ENSG00000188976', - hgvsc='ENST00000327044.6:c.1667C>T', - hgvsp='ENSP00000317992.6:p.Ser556Leu', - transcript_id='ENST00000327044', - biotype_id=39, - consequence_term_ids=[9], - is_lof_nagnag=None, - lof_filter_ids=[0, 1], - ), - hl.Struct( - amino_acids=None, - canonical=None, - codons=None, - gene_id='ENSG00000188976', - hgvsc='ENST00000477976.1:n.3114C>T', - hgvsp=None, - transcript_id='ENST00000477976', - biotype_id=38, - consequence_term_ids=[23, 26], - is_lof_nagnag=None, - lof_filter_ids=None, - ), - hl.Struct( - amino_acids=None, - canonical=None, - codons=None, - gene_id='ENSG00000188976', - hgvsc='ENST00000483767.1:n.523C>T', - hgvsp=None, - transcript_id='ENST00000483767', - biotype_id=38, - consequence_term_ids=[23, 26], - is_lof_nagnag=None, - lof_filter_ids=None, - ), - ], - ], - ) - - @patch('loading_pipeline.lib.misc.vep.hl.vep') - def test_sorted_transcript_consequences_38( - self, - mock_vep: Mock, - ) -> None: - ht = hl.Table.parallelize( - [ - { - 'locus': hl.Locus( - contig='chr1', - position=871269, - reference_genome=ReferenceGenome.GRCh38.value, - ), - 'alleles': ['A', 'C'], - }, - ], - hl.tstruct( - locus=hl.tlocus(ReferenceGenome.GRCh38.value), - alleles=hl.tarray(hl.tstr), - ), - key=['locus', 'alleles'], - ) - mock_vep.return_value = ht.annotate(vep=MOCK_38_VEP_DATA) - ht = run_vep( - ht, - DatasetType.SNV_INDEL, - ReferenceGenome.GRCh38, - ) - ht = ht.select( - sorted_transcript_consequences=snv_indel.sorted_transcript_consequences( - ht, - hl.dict( - {'ENST00000327044': 'NM_015658.4', 'ENST00000477976': 'refseq1'}, - ), - ), - ) - self.assertCountEqual( - ht.sorted_transcript_consequences.collect()[0], - [ - hl.Struct( - amino_acids='S/L', - canonical=1, - codons='tCg/tTg', - gene_id='ENSG00000188976', - hgvsc='ENST00000327044.6:c.1667C>T', - hgvsp='ENSP00000317992.6:p.Ser556Leu', - transcript_id='ENST00000327044', - refseq_transcript_id='NM_015658.4', - mane_select='NM_015658.4', - mane_plus_clinical=None, - biotype_id=39, - consequence_term_ids=[9], - exon=hl.Struct(index=15, total=19), - intron=None, - alphamissense=hl.Struct(pathogenicity=0.10000000149011612), - loftee=hl.Struct( - is_lof_nagnag=None, - lof_filter_ids=[0, 1], - ), - spliceregion=hl.Struct( - extended_intronic_splice_region_variant=False, - ), - utrannotator=hl.Struct( - existing_inframe_oorfs=None, - existing_outofframe_oorfs=None, - existing_uorfs=None, - fiveutr_consequence_id=None, - fiveutr_annotation=None, - ), - ), - hl.Struct( - amino_acids=None, - canonical=None, - codons=None, - gene_id='ENSG00000188976', - hgvsc='ENST00000477976.1:n.3114C>T', - hgvsp=None, - transcript_id='ENST00000477976', - refseq_transcript_id='refseq1', - mane_select=None, - mane_plus_clinical=None, - biotype_id=38, - consequence_term_ids=[23, 26], - exon=hl.Struct(index=13, total=17), - intron=None, - alphamissense=hl.Struct(pathogenicity=0.9700000286102295), - loftee=hl.Struct( - is_lof_nagnag=None, - lof_filter_ids=None, - ), - spliceregion=hl.Struct( - extended_intronic_splice_region_variant=False, - ), - utrannotator=hl.Struct( - existing_inframe_oorfs=None, - existing_outofframe_oorfs=None, - existing_uorfs=None, - fiveutr_consequence_id=None, - fiveutr_annotation=None, - ), - ), - hl.Struct( - amino_acids=None, - canonical=None, - codons=None, - gene_id='ENSG00000188976', - hgvsc='ENST00000483767.1:n.523C>T', - hgvsp=None, - transcript_id='ENST00000483767', - refseq_transcript_id=None, - mane_select=None, - mane_plus_clinical=None, - biotype_id=38, - consequence_term_ids=[23, 13, 26], - exon=hl.Struct(index=1, total=5), - intron=None, - alphamissense=hl.Struct(pathogenicity=None), - loftee=hl.Struct( - is_lof_nagnag=None, - lof_filter_ids=None, - ), - spliceregion=hl.Struct( - extended_intronic_splice_region_variant=True, - ), - utrannotator=hl.Struct( - existing_inframe_oorfs=0, - existing_outofframe_oorfs=1, - existing_uorfs=0, - fiveutr_consequence_id=1, - fiveutr_annotation=hl.Struct( - type='OutOfFrame_oORF', - KozakContext='TTTATGC', - KozakStrength='Weak', - DistanceToCDS=40, - CapDistanceToStart=20, - DistanceToStop=75, - Evidence=False, - AltStop=None, - AltStopDistanceToCDS=None, - FrameWithCDS=None, - StartDistanceToCDS=None, - newSTOPDistanceToCDS=None, - alt_type=None, - alt_type_length=None, - ref_StartDistanceToCDS=None, - ref_type=None, - ref_type_length=None, - ), - ), - ), - ], - ) - - @patch('loading_pipeline.lib.misc.vep.hl.vep') - def test_sorted_other_feature_consequences( - self, - mock_vep: Mock, - ) -> None: - ht = hl.Table.parallelize( - [ - { - 'locus': hl.Locus( - contig='chr1', - position=871269, - reference_genome=ReferenceGenome.GRCh38.value, - ), - 'alleles': ['A', 'C'], - }, - ], - hl.tstruct( - locus=hl.tlocus(ReferenceGenome.GRCh38.value), - alleles=hl.tarray(hl.tstr), - ), - key=['locus', 'alleles'], - ) - mock_vep.return_value = ht.annotate(vep=MOCK_38_VEP_DATA) - ht = run_vep( - ht, - DatasetType.SNV_INDEL, - ReferenceGenome.GRCh38, - ) - ht = ht.select( - sorted_motif_feature_consequences=snv_indel.sorted_motif_feature_consequences( - ht, - ), - sorted_regulatory_feature_consequences=snv_indel.sorted_regulatory_feature_consequences( - ht, - ), - ) - self.assertCountEqual( - ht.sorted_motif_feature_consequences.collect(), - [None], - ) - self.assertCountEqual( - ht.sorted_regulatory_feature_consequences.collect()[0], - [ - hl.Struct( - biotype_id=0, - consequence_term_ids=[0], - regulatory_feature_id='regulatory_2', - ), - hl.Struct( - biotype_id=0, - consequence_term_ids=[2], - regulatory_feature_id='regulatory_1', - ), - ], - ) diff --git a/loading_pipeline/lib/annotations/sv_test.py b/loading_pipeline/lib/annotations/sv_test.py deleted file mode 100644 index 25a8413b16..0000000000 --- a/loading_pipeline/lib/annotations/sv_test.py +++ /dev/null @@ -1,171 +0,0 @@ -import unittest - -import hail as hl - -from loading_pipeline.lib.annotations.fields import get_fields -from loading_pipeline.lib.core import DatasetType - - -class SVTest(unittest.TestCase): - def test_sv_export_annotations(self) -> None: - ht = hl.Table.parallelize( - [ - hl.Struct( - id=0, - algorithms='manta', - end_locus=hl.Locus( - contig='chr5', - position=20404, - reference_genome='GRCh38', - ), - start_locus=hl.Locus( - contig='chr1', - position=180928, - reference_genome='GRCh38', - ), - sv_len=123, - sv_type_id=2, - sv_type_detail_id=None, - ), - hl.Struct( - id=1, - algorithms='manta', - end_locus=hl.Locus( - contig='chr1', - position=789481, - reference_genome='GRCh38', - ), - start_locus=hl.Locus( - contig='chr1', - position=789481, - reference_genome='GRCh38', - ), - sv_len=245, - sv_type_id=2, - sv_type_detail_id=None, - ), - hl.Struct( - id=2, - algorithms='manta', - end_locus=hl.Locus( - contig='chr1', - position=6559723, - reference_genome='GRCh38', - ), - start_locus=hl.Locus( - contig='chr1', - position=6558902, - reference_genome='GRCh38', - ), - sv_len=245, - sv_type_id=3, - sv_type_detail_id=2, - ), - hl.Struct( - id=3, - algorithms='manta', - end_locus=hl.Locus( - contig='chr1', - position=6559723, - reference_genome='GRCh38', - ), - start_locus=hl.Locus( - contig='chr1', - position=6558902, - reference_genome='GRCh38', - ), - sv_len=245, - sv_type_id=7, - sv_type_detail_id=6, - ), - ], - hl.tstruct( - id=hl.tint32, - algorithms=hl.tstr, - end_locus=hl.tlocus('GRCh38'), - start_locus=hl.tlocus('GRCh38'), - sv_len=hl.tint32, - sv_type_id=hl.tint32, - sv_type_detail_id=hl.tint32, - ), - key='id', - ) - ht = ht.select( - **get_fields( - ht, - DatasetType.SV.export_vcf_annotation_fns, - ), - ) - self.assertEqual( - ht.collect(), - [ - hl.Struct( - id=0, - locus=hl.Locus( - contig='chr1', - position=180928, - reference_genome='GRCh38', - ), - alleles=['N', ''], - info=hl.Struct( - ALGORITHMS='manta', - END=180928, - CHR2='chr5', - END2=20404, - SVTYPE='BND', - SVLEN=123, - ), - ), - hl.Struct( - id=1, - locus=hl.Locus( - contig='chr1', - position=789481, - reference_genome='GRCh38', - ), - alleles=['N', ''], - info=hl.Struct( - ALGORITHMS='manta', - END=789481, - CHR2='chr1', - END2=789481, - SVTYPE='BND', - SVLEN=245, - ), - ), - hl.Struct( - id=2, - locus=hl.Locus( - contig='chr1', - position=6558902, - reference_genome='GRCh38', - ), - alleles=['N', ''], - info=hl.Struct( - ALGORITHMS='manta', - END=6558902, - CHR2='chr1', - END2=6559723, - SVTYPE='CPX', - SVLEN=245, - ), - ), - hl.Struct( - id=3, - locus=hl.Locus( - contig='chr1', - position=6558902, - reference_genome='GRCh38', - ), - alleles=['N', ''], - info=hl.Struct( - ALGORITHMS='manta', - END=6558902, - CHR2='chr1', - END2=6559723, - SVTYPE='INS', - SVLEN=245, - ), - ), - ], - ) diff --git a/loading_pipeline/lib/core/definitions_test.py b/loading_pipeline/lib/core/definitions_test.py deleted file mode 100644 index b53d88cd18..0000000000 --- a/loading_pipeline/lib/core/definitions_test.py +++ /dev/null @@ -1,144 +0,0 @@ -import unittest - -from loading_pipeline.lib.core.definitions import ReferenceGenome - - -class TestReferenceGenomeProperties(unittest.TestCase): - def test_v02_value(self): - self.assertEqual(ReferenceGenome.GRCh37.v02_value, '37') - self.assertEqual(ReferenceGenome.GRCh38.v02_value, '38') - - def test_hl_reference(self): - hl_37_reference = ReferenceGenome.GRCh37.hl_reference - self.assertEqual(hl_37_reference.name, 'GRCh37') - - hl_38_reference = ReferenceGenome.GRCh38.hl_reference - self.assertEqual(hl_38_reference.name, 'GRCh38') - - def test_standard_contigs(self): - expected_37_contigs = { - '3', - '12', - '21', - '2', - '1', - '7', - '13', - '8', - '11', - '22', - 'MT', - '14', - 'Y', - '18', - '19', - '20', - '17', - 'X', - '10', - '15', - '16', - '4', - '5', - '9', - '6', - } - self.assertEqual(ReferenceGenome.GRCh37.standard_contigs, expected_37_contigs) - - expected_38_contigs = { - 'chr10', - 'chr11', - 'chr17', - 'chr18', - 'chr9', - 'chr22', - 'chr3', - 'chrY', - 'chr7', - 'chr6', - 'chr13', - 'chr19', - 'chr16', - 'chrX', - 'chr12', - 'chr2', - 'chr21', - 'chr20', - 'chr8', - 'chrM', - 'chr5', - 'chr4', - 'chr14', - 'chr1', - 'chr15', - } - self.assertEqual(ReferenceGenome.GRCh38.standard_contigs, expected_38_contigs) - - def test_optional_contigs(self): - self.assertEqual(ReferenceGenome.GRCh37.optional_contigs, {'Y', 'MT'}) - self.assertEqual(ReferenceGenome.GRCh38.optional_contigs, {'chrY', 'chrM'}) - - def test_contig_recoding(self): - expected_37_recode = { - 'chr1': '1', - 'chr2': '2', - 'chr3': '3', - 'chr4': '4', - 'chr5': '5', - 'chr6': '6', - 'chr7': '7', - 'chr8': '8', - 'chr9': '9', - 'chr10': '10', - 'chr11': '11', - 'chr12': '12', - 'chr13': '13', - 'chr14': '14', - 'chr15': '15', - 'chr16': '16', - 'chr17': '17', - 'chr18': '18', - 'chr19': '19', - 'chr20': '20', - 'chr21': '21', - 'chr22': '22', - 'chrX': 'X', - 'chrY': 'Y', - 'chrM': 'MT', - } - self.assertDictEqual( - ReferenceGenome.GRCh37.contig_recoding(include_mt=True), - expected_37_recode, - ) - - expected_38_recode = { - '1': 'chr1', - '2': 'chr2', - '3': 'chr3', - '4': 'chr4', - '5': 'chr5', - '6': 'chr6', - '7': 'chr7', - '8': 'chr8', - '9': 'chr9', - '10': 'chr10', - '11': 'chr11', - '12': 'chr12', - '13': 'chr13', - '14': 'chr14', - '15': 'chr15', - '16': 'chr16', - '17': 'chr17', - '18': 'chr18', - '19': 'chr19', - '20': 'chr20', - '21': 'chr21', - '22': 'chr22', - 'X': 'chrX', - 'Y': 'chrY', - 'MT': 'chrM', - } - self.assertDictEqual( - ReferenceGenome.GRCh38.contig_recoding(include_mt=True), - expected_38_recode, - ) diff --git a/loading_pipeline/lib/methods/relatedness_test.py b/loading_pipeline/lib/methods/relatedness_test.py deleted file mode 100644 index e3afb159e2..0000000000 --- a/loading_pipeline/lib/methods/relatedness_test.py +++ /dev/null @@ -1,39 +0,0 @@ -import unittest - -import hail as hl - -from loading_pipeline.lib.methods.relatedness import call_relatedness - -TEST_SEX_AND_RELATEDNESS_CALLSET_MT = ( - 'loading_pipeline/var/test/callsets/sex_and_relatedness_1.mt' -) - - -class RelatednessTest(unittest.TestCase): - def test_call_relatedness(self): - mt = hl.read_matrix_table(TEST_SEX_AND_RELATEDNESS_CALLSET_MT) - ht = call_relatedness( - mt, - None, - ) - self.assertCountEqual( - ht.collect(), - [ - hl.Struct( - i='ROS_006_18Y03226_D1', - j='ROS_007_19Y05939_D1', - ibd0=0.0, - ibd1=1.0, - ibd2=0.0, - pi_hat=0.5, - ), - hl.Struct( - i='ROS_007_19Y05939_D1', - j='ROS_007_19Y05987_D1', - ibd0=0.0, - ibd1=1.0, - ibd2=0.0, - pi_hat=0.5, - ), - ], - ) diff --git a/loading_pipeline/lib/methods/sex_check_test.py b/loading_pipeline/lib/methods/sex_check_test.py deleted file mode 100644 index ed390e86f3..0000000000 --- a/loading_pipeline/lib/methods/sex_check_test.py +++ /dev/null @@ -1,54 +0,0 @@ -import unittest -from unittest.mock import patch - -import hail as hl - -from loading_pipeline.lib.methods.sex_check import compute_sex_check_ht - -TEST_SEX_AND_RELATEDNESS_CALLSET_MT = ( - 'loading_pipeline/var/test/callsets/sex_and_relatedness_1.mt' -) - - -class SexCheckTest(unittest.TestCase): - def test_compute_sex_check_ht(self): - mt = hl.read_matrix_table(TEST_SEX_AND_RELATEDNESS_CALLSET_MT) - ht = compute_sex_check_ht(mt) - self.assertCountEqual( - ht.collect(), - [ - hl.Struct( - s='ROS_006_18Y03226_D1', - predicted_sex='M', - ), - hl.Struct( - s='ROS_006_18Y03227_D1', - predicted_sex='M', - ), - hl.Struct( - s='ROS_006_18Y03228_D1', - predicted_sex='M', - ), - hl.Struct( - s='ROS_007_19Y05919_D1', - predicted_sex='M', - ), - hl.Struct( - s='ROS_007_19Y05939_D1', - predicted_sex='F', - ), - hl.Struct( - s='ROS_007_19Y05987_D1', - predicted_sex='M', - ), - ], - ) - - def test_compute_sex_check_ht_ambiguous(self): - mt = hl.read_matrix_table(TEST_SEX_AND_RELATEDNESS_CALLSET_MT) - with patch('loading_pipeline.lib.methods.sex_check.XY_FSTAT_THRESHOLD', 0.95): - self.assertRaises( - ValueError, - compute_sex_check_ht, - mt, - ) diff --git a/loading_pipeline/lib/misc/callsets_test.py b/loading_pipeline/lib/misc/callsets_test.py deleted file mode 100644 index 5db2d4eb36..0000000000 --- a/loading_pipeline/lib/misc/callsets_test.py +++ /dev/null @@ -1,87 +0,0 @@ -import unittest - -import hail as hl - -from loading_pipeline.lib.misc.callsets import union_callset_mts - - -class CallsetsTest(unittest.TestCase): - def test_union_callset_mts(self) -> None: - mt1 = ( - hl.MatrixTable.from_parts( - rows={ - 'id': [ - 0, - 1, - ], - 'row_field': [ - 1, - 2, - ], - }, - cols={'s': ['sample_1']}, - entries={ - 'GT': [[hl.Call([0, 0])], [hl.Call([0, 0])]], - }, - ) - .key_rows_by('id') - .key_cols_by('s') - .drop('row_idx', 'col_idx') - ) - mt2 = ( - hl.MatrixTable.from_parts( - rows={ - 'id': [ - 0, - 2, - ], - 'row_field': [ - 2, - 3, - ], - 'second_row_field': [ - 4, - 5, - ], - }, - cols={'s': ['sample_2']}, - entries={ - 'GT': [[hl.Call([0, 0])], [hl.Call([0, 1])]], - }, - ) - .key_rows_by('id') - .key_cols_by('s') - .drop('row_idx', 'col_idx') - ) - mt = union_callset_mts([mt1, mt2]) - self.assertEqual( - mt.entries().collect(), - [ - hl.Struct( - id=0, - row_field=1, - s='sample_1', - GT=hl.Call(alleles=[0, 0], phased=False), - ), - hl.Struct( - id=0, - row_field=1, - s='sample_2', - GT=hl.Call(alleles=[0, 0], phased=False), - ), - hl.Struct( - id=1, - row_field=2, - s='sample_1', - GT=hl.Call(alleles=[0, 0], phased=False), - ), - hl.Struct(id=1, row_field=2, s='sample_2', GT=None), - hl.Struct(id=2, row_field=None, s='sample_1', GT=None), - hl.Struct( - id=2, - row_field=None, - s='sample_2', - GT=hl.Call(alleles=[0, 1], phased=False), - ), - ], - ) diff --git a/loading_pipeline/lib/misc/family_entries_test.py b/loading_pipeline/lib/misc/family_entries_test.py deleted file mode 100644 index 609fdda6d6..0000000000 --- a/loading_pipeline/lib/misc/family_entries_test.py +++ /dev/null @@ -1,356 +0,0 @@ -import unittest - -import hail as hl - -from loading_pipeline.lib.core import DatasetType -from loading_pipeline.lib.misc.family_entries import ( - compute_callset_family_entries_ht, - deduplicate_by_most_non_ref_calls, - deglobalize_ids, - globalize_ids, -) - - -class FamilyEntriesTest(unittest.TestCase): - def test_compute_callset_family_entries_ht(self) -> None: - mt = hl.MatrixTable.from_parts( - rows={ - 'variants': [1, 2, 3], - 'filters': [ - hl.empty_set(hl.tstr), - {'HIGH_SR_BACKGROUND'}, - hl.empty_set(hl.tstr), - ], - }, - cols={'s': ['a', 'b', 'd', 'c']}, - entries={ - 'GT': [ - [ - hl.Call([0, 0]), - hl.missing(hl.tcall), - hl.Call([0, 0]), - hl.Call([0, 0]), - ], - [ - hl.Call([0, 0]), - hl.Call([0, 0]), - hl.Call([1, 1]), - hl.Call([0, 0]), - ], - [ - hl.Call([0, 1]), - hl.Call([0, 0]), - hl.Call([1, 1]), - hl.Call([0, 0]), - ], - ], - }, - globals={'family_samples': {'2': ['a'], '1': ['b', 'c', 'd']}}, - ) - ht = compute_callset_family_entries_ht(DatasetType.SNV_INDEL, mt, {'GT': mt.GT}) - self.assertCountEqual( - ht.globals.collect(), - [ - hl.Struct( - family_samples={'1': ['b', 'c', 'd'], '2': ['a']}, - family_guids=['1', '2'], - ), - ], - ) - self.assertCountEqual( - ht.filters.collect(), - [{'HIGH_SR_BACKGROUND'}, set()], - ) - self.assertCountEqual( - ht.family_entries.collect(), - [ - [ - [ - hl.Struct(GT=hl.Call(alleles=[0, 0], phased=False)), - hl.Struct(GT=hl.Call(alleles=[0, 0], phased=False)), - hl.Struct(GT=hl.Call(alleles=[1, 1], phased=False)), - ], - None, - ], - [ - [ - hl.Struct(GT=hl.Call(alleles=[0, 0], phased=False)), - hl.Struct(GT=hl.Call(alleles=[0, 0], phased=False)), - hl.Struct(GT=hl.Call(alleles=[1, 1], phased=False)), - ], - [hl.Struct(GT=hl.Call(alleles=[0, 1], phased=False))], - ], - ], - ) - - def test_globalize_and_deglobalize(self) -> None: - family_entries_ht = hl.Table.parallelize( - [], - hl.tstruct( - id=hl.tint32, - filters=hl.tset(hl.tstr), - family_entries=hl.tarray( - hl.tarray(hl.tstruct(a=hl.tint32, s=hl.tstr, family_guid=hl.tstr)), - ), - ), - key='id', - ) - family_entries_ht = globalize_ids(family_entries_ht) - self.assertCountEqual( - family_entries_ht.family_guids.collect(), - [ - [], - ], - ) - family_entries_ht = hl.Table.parallelize( - [ - { - 'id': 0, - 'filters': {'HIGH_SR_BACKGROUND', 'UNRESOLVED'}, - 'family_entries': [ - [ - hl.Struct(a=1, s='a', family_guid='123'), - hl.Struct(a=2, s='c', family_guid='123'), - hl.Struct(a=1, s='e', family_guid='123'), - ], - [ - hl.Struct(a=2, s='f', family_guid='234'), - ], - ], - }, - { - 'id': 1, - 'filters': {'HIGH_SR_BACKGROUND'}, - 'family_entries': [ - [ - hl.Struct(a=2, s='a', family_guid='123'), - hl.Struct(a=3, s='c', family_guid='123'), - hl.Struct(a=4, s='e', family_guid='123'), - ], - [ - hl.Struct(a=5, s='f', family_guid='234'), - ], - ], - }, - ], - hl.tstruct( - id=hl.tint32, - filters=hl.tset(hl.tstr), - family_entries=hl.tarray( - hl.tarray(hl.tstruct(a=hl.tint32, s=hl.tstr, family_guid=hl.tstr)), - ), - ), - key='id', - ) - family_entries_ht = globalize_ids(family_entries_ht) - self.assertCountEqual( - family_entries_ht.family_guids.collect(), - [ - ['123', '234'], - ], - ) - self.assertCountEqual( - family_entries_ht.family_entries.collect(), - [ - [ - [ - hl.Struct(a=1), - hl.Struct(a=2), - hl.Struct(a=1), - ], - [ - hl.Struct(a=2), - ], - ], - [ - [ - hl.Struct(a=2), - hl.Struct(a=3), - hl.Struct(a=4), - ], - [ - hl.Struct(a=5), - ], - ], - ], - ) - family_entries_ht = deglobalize_ids(family_entries_ht) - self.assertCountEqual( - family_entries_ht.family_entries.collect(), - [ - [ - [ - hl.Struct(a=1, s='a', family_guid='123'), - hl.Struct(a=2, s='c', family_guid='123'), - hl.Struct(a=1, s='e', family_guid='123'), - ], - [ - hl.Struct(a=2, s='f', family_guid='234'), - ], - ], - [ - [ - hl.Struct(a=2, s='a', family_guid='123'), - hl.Struct(a=3, s='c', family_guid='123'), - hl.Struct(a=4, s='e', family_guid='123'), - ], - [ - hl.Struct(a=5, s='f', family_guid='234'), - ], - ], - ], - ) - - def test_deduplicate_by_most_non_ref_calls(self) -> None: - project_ht = hl.Table.parallelize( - [ - { - 'id': 0, - 'filters': {'PASS', 'HIGH_SR_BACKGROUND'}, - 'family_entries': [ - [ - hl.Struct( - GT=hl.Call(alleles=[0, 1], phased=False), - family_guid='family_a', - s='sample_1', - ), - hl.Struct( - GT=hl.Call(alleles=[0, 0], phased=False), - family_guid='family_a', - s='sample_2', - ), - ], - [ - hl.Struct( - GT=hl.Call(alleles=[0, 1], phased=False), - family_guid='family_b', - s='sample_3', - ), - None, - ], - None, - ], - }, - { - 'id': 0, - 'filters': {'PASS'}, - 'family_entries': [ - [ - None, - hl.Struct( - GT=hl.Call(alleles=[0, 0], phased=False), - family_guid='family_a', - s='sample_2', - ), - ], - [ - hl.Struct( - GT=hl.Call(alleles=[0, 1], phased=False), - family_guid='family_b', - s='sample_3', - ), - None, - ], - None, - ], - }, - { - 'id': 2, - 'filters': {'HIGH_SR_BACKGROUND'}, - 'family_entries': [ - None, - None, - ], - }, - { - 'id': 3, - 'filters': {'PASS'}, - 'family_entries': [ - [ - hl.Struct( - GT=hl.Call(alleles=[0, 1], phased=False), - family_guid='family_a', - s='sample_1', - ), - hl.Struct( - GT=hl.Call(alleles=[0, 1], phased=False), - family_guid='family_a', - s='sample_2', - ), - ], - None, - ], - }, - ], - hl.tstruct( - id=hl.tint32, - filters=hl.tset(hl.tstr), - family_entries=hl.tarray( - hl.tarray( - hl.tstruct( - GT=hl.tcall, - family_guid=hl.tstr, - s=hl.tstr, - ), - ), - ), - ), - key='id', - ) - ht = deduplicate_by_most_non_ref_calls(project_ht) - self.assertEqual( - ht.collect(), - [ - hl.Struct( - id=0, - filters={'PASS', 'HIGH_SR_BACKGROUND'}, - family_entries=[ - [ - hl.Struct( - GT=hl.Call(alleles=[0, 1], phased=False), - family_guid='family_a', - s='sample_1', - ), - hl.Struct( - GT=hl.Call(alleles=[0, 0], phased=False), - family_guid='family_a', - s='sample_2', - ), - ], - [ - hl.Struct( - GT=hl.Call(alleles=[0, 1], phased=False), - family_guid='family_b', - s='sample_3', - ), - None, - ], - None, - ], - ), - hl.Struct( - id=2, - filters={'HIGH_SR_BACKGROUND'}, - family_entries=[None, None], - ), - hl.Struct( - id=3, - filters={'PASS'}, - family_entries=[ - [ - hl.Struct( - GT=hl.Call(alleles=[0, 1], phased=False), - family_guid='family_a', - s='sample_1', - ), - hl.Struct( - GT=hl.Call(alleles=[0, 1], phased=False), - family_guid='family_a', - s='sample_2', - ), - ], - None, - ], - ), - ], - ) diff --git a/loading_pipeline/lib/misc/family_loading_failures_test.py b/loading_pipeline/lib/misc/family_loading_failures_test.py deleted file mode 100644 index fb1d0905d1..0000000000 --- a/loading_pipeline/lib/misc/family_loading_failures_test.py +++ /dev/null @@ -1,448 +0,0 @@ -import unittest - -import hail as hl - -from loading_pipeline.lib.core import Sex -from loading_pipeline.lib.misc.family_loading_failures import ( - all_relatedness_checks, - build_relatedness_check_lookup, - build_sex_check_lookup, - get_families_failed_imputed_sex_ploidy, - get_families_failed_sex_check, -) -from loading_pipeline.lib.misc.io import import_pedigree -from loading_pipeline.lib.misc.pedigree import ( - Family, - Sample, - parse_pedigree_ht_to_families, -) - -TEST_SEX_CHECK_1 = 'loading_pipeline/var/test/sex_check/test_sex_check_1.ht' -TEST_PEDIGREE_6 = 'loading_pipeline/var/test/pedigrees/test_pedigree_6.tsv' - - -class FamilyLoadingFailuresTest(unittest.TestCase): - def test_build_relatedness_check_lookup(self): - ht = hl.Table.parallelize( - [ - { - 'i': 'ROS_006_18Y03226_D1', - 'j': 'ROS_007_19Y05939_D1', - 'ibd0': 0.0, - 'ibd1': 1.0, - 'ibd2': 0.0, - 'pi_hat': 0.5, - }, - ], - hl.tstruct( - i=hl.tstr, - j=hl.tstr, - ibd0=hl.tfloat, - ibd1=hl.tfloat, - ibd2=hl.tfloat, - pi_hat=hl.tfloat, - ), - key=['i', 'j'], - ) - self.assertEqual( - build_relatedness_check_lookup( - ht, - hl.dict({'ROS_006_18Y03226_D1': 'remapped_id'}), - ), - { - ('ROS_007_19Y05939_D1', 'remapped_id'): [ - 0.0, - 1.0, - 0.0, - 0.5, - ], - }, - ) - - def test_build_sex_check_lookup(self): - ht = hl.Table.parallelize( - [ - {'s': 'ROS_006_18Y03226_D1', 'predicted_sex': 'F'}, - {'s': 'ROS_006_18Y03227_D1', 'predicted_sex': 'F'}, - {'s': 'ROS_006_18Y03228_D1', 'predicted_sex': 'F'}, - {'s': 'ROS_007_19Y05919_D1', 'predicted_sex': 'F'}, - {'s': 'ROS_007_19Y05939_D1', 'predicted_sex': 'M'}, - {'s': 'ROS_007_19Y05987_D1', 'predicted_sex': 'U'}, - {'s': 'ROS_007_19Y05989_D1', 'predicted_sex': 'X0'}, - ], - hl.tstruct( - s=hl.tstr, - predicted_sex=hl.tstr, - ), - key='s', - ) - self.assertEqual( - build_sex_check_lookup(ht, hl.dict({'ROS_006_18Y03226_D1': 'remapped_id'})), - { - 'remapped_id': Sex.FEMALE, - 'ROS_006_18Y03227_D1': Sex.FEMALE, - 'ROS_006_18Y03228_D1': Sex.FEMALE, - 'ROS_007_19Y05919_D1': Sex.FEMALE, - 'ROS_007_19Y05939_D1': Sex.MALE, - 'ROS_007_19Y05987_D1': Sex.UNKNOWN, - 'ROS_007_19Y05989_D1': Sex.X0, - }, - ) - - def test_all_relatedness_checks(self): - relatedness_check_lookup = { - # Parent - ('sample_1', 'sample_2'): [ - 0.0, - 0.98, - 0.0, - 0.52, - ], - # GrandParent - ('sample_1', 'sample_3'): [0.48, 0.52, 0, 0.24], - # Half Sibling (but actually a hidden Sibling) - ('sample_1', 'sample_4'): [0.25, 0.5, 0.25, 0.5], - } - sample = Sample( - sex=Sex.FEMALE, - sample_id='sample_1', - mother='sample_2', - paternal_grandfather='sample_3', - half_siblings=['sample_4'], - ) - family = Family( - family_guid='family_1a', - samples={ - 'sample_1': sample, - 'sample_2': Sample(sex=Sex.MALE, sample_id='sample_2'), - 'sample_3': Sample(sex=Sex.MALE, sample_id='sample_3'), - 'sample_4': Sample(sex=Sex.MALE, sample_id='sample_4'), - 'sample_5': Sample(sex=Sex.MALE, sample_id='sample_5'), - }, - ) - failure_reasons = all_relatedness_checks( - relatedness_check_lookup, - family, - sample, - ) - self.assertListEqual(failure_reasons, []) - - # Defined grandparent missing in relatedness table - sample = Sample( - sex=Sex.FEMALE, - sample_id='sample_1', - mother='sample_2', - paternal_grandfather='sample_3', - paternal_grandmother='sample_5', - ) - failure_reasons = all_relatedness_checks( - relatedness_check_lookup, - family, - sample, - ) - self.assertListEqual( - failure_reasons, - [ - 'Sample sample_1 has expected relation "grandparent_grandchild" to sample_5 but has coefficients []', - ], - ) - - # Sibling is actually a half sibling. - relatedness_check_lookup = { - **relatedness_check_lookup, - ('sample_1', 'sample_4'): [0.5, 0.5, 0, 0.25], - } - sample = Sample( - sex=Sex.FEMALE, - sample_id='sample_1', - mother='sample_2', - paternal_grandfather='sample_3', - siblings=['sample_4'], - ) - failure_reasons = all_relatedness_checks( - relatedness_check_lookup, - family, - sample, - ) - self.assertListEqual( - failure_reasons, - [ - 'Sample sample_1 has expected relation "sibling" to sample_4 but has coefficients [0.5, 0.5, 0, 0.25]', - ], - ) - - relatedness_check_lookup = { - **relatedness_check_lookup, - ('sample_1', 'sample_2'): [ - 0.5, - 0.5, - 0.5, - 0.5, - ], - } - sample = Sample( - sex=Sex.FEMALE, - sample_id='sample_1', - mother='sample_2', - paternal_grandfather='sample_3', - siblings=['sample_4'], - ) - failure_reasons = all_relatedness_checks( - relatedness_check_lookup, - family, - sample, - ) - self.assertListEqual( - failure_reasons, - [ - 'Sample sample_1 has expected relation "parent_child" to sample_2 but has coefficients [0.5, 0.5, 0.5, 0.5]', - 'Sample sample_1 has expected relation "sibling" to sample_4 but has coefficients [0.5, 0.5, 0, 0.25]', - ], - ) - - # Some samples will include relationships with - # samples that are not expected to be included - # in the callset. These should not trigger relatedness - # failures. - sample = Sample( - sex=Sex.FEMALE, - sample_id='sample_1', - mother='sample_2', - ) - family = Family( - family_guid='family_1a', - samples={ - 'sample_1': sample, - }, - ) - failure_reasons = all_relatedness_checks( - {}, - family, - sample, - ) - self.assertListEqual( - failure_reasons, - [], - ) - - def test_get_families_failed_sex_check(self): - sex_check_ht = hl.Table.parallelize( - [ - {'s': 'ROS_006_18Y03226_D1', 'predicted_sex': 'F'}, - {'s': 'ROS_006_18Y03227_D1', 'predicted_sex': 'F'}, # Pedigree Sex U - {'s': 'ROS_006_18Y03228_D1', 'predicted_sex': 'F'}, - {'s': 'ROS_007_19Y05939_D1', 'predicted_sex': 'M'}, - {'s': 'ROS_007_19Y05987_D1', 'predicted_sex': 'U'}, # Pedigree Sex F - {'s': 'ROS_007_19Y05989_D1', 'predicted_sex': 'XXX'}, - ], - hl.tstruct( - s=hl.tstr, - predicted_sex=hl.tstr, - ), - key='s', - ) - pedigree_ht = import_pedigree(TEST_PEDIGREE_6) - failed_families = get_families_failed_sex_check( - parse_pedigree_ht_to_families(pedigree_ht), - sex_check_ht, - {}, - ) - self.assertCountEqual( - failed_families.values(), - [ - [ - 'Sample ROS_007_19Y05919_D1 has pedigree sex F but is missing from the sex check source', - 'Sample ROS_007_19Y05939_D1 has pedigree sex F but imputed sex M', - ], - ], - ) - - def test_get_families_failed_imputed_sex_ploidy(self) -> None: - female_sample = 'HG00731_1' - male_sample_1 = 'HG00732_1' - male_sample_2 = 'HG00732_1' - x0_sample = 'NA20899_1' - xxy_sample = 'NA20889_1' - xyy_sample = 'NA20891_1' - xxx_sample = 'NA20892_1' - - sex_check_ht = hl.read_table(TEST_SEX_CHECK_1) - families = { - Family( - family_guid='', - samples={ - female_sample: Sample(female_sample, Sex.FEMALE), - male_sample_1: Sample(male_sample_1, Sex.MALE), - male_sample_2: Sample(male_sample_2, Sex.MALE), - x0_sample: Sample(x0_sample, Sex.X0), - xxy_sample: Sample(xxy_sample, Sex.XXY), - xyy_sample: Sample(xyy_sample, Sex.XYY), - xxx_sample: Sample(xxx_sample, Sex.XXX), - }, - ), - } - - # All calls on X chromosome are valid - mt = ( - hl.MatrixTable.from_parts( - rows={ - 'locus': [ - hl.Locus( - contig='chrX', - position=1, - reference_genome='GRCh38', - ), - ], - }, - cols={ - 's': [ - female_sample, - male_sample_1, - x0_sample, - xxy_sample, - xyy_sample, - xxx_sample, - ], - }, - entries={ - 'GT': [ - [ - hl.Call(alleles=[0, 0], phased=False), - hl.Call(alleles=[0], phased=False), - hl.Call(alleles=[0, 0], phased=False), # X0 - hl.Call(alleles=[0, 0], phased=False), # XXY - hl.Call(alleles=[0, 0], phased=False), # XYY - hl.Call(alleles=[0, 0], phased=False), # XXX - ], - ], - }, - ) - .key_rows_by('locus') - .key_cols_by('s') - ) - failed_families = get_families_failed_imputed_sex_ploidy( - families, - mt, - sex_check_ht, - ) - self.assertDictEqual(failed_families, {}) - - # All calls on Y chromosome are valid - mt = ( - hl.MatrixTable.from_parts( - rows={ - 'locus': [ - hl.Locus( - contig='chrY', - position=1, - reference_genome='GRCh38', - ), - ], - }, - cols={ - 's': [ - female_sample, - male_sample_1, - x0_sample, - xxy_sample, - xyy_sample, - xxx_sample, - ], - }, - entries={ - 'GT': [ - [ - hl.missing(hl.tcall), - hl.Call(alleles=[0], phased=False), - hl.missing(hl.tcall), # X0 - hl.Call(alleles=[0, 0], phased=False), # XXY - hl.Call(alleles=[0, 0], phased=False), # XYY - hl.missing(hl.tcall), # XXX - ], - ], - }, - ) - .key_rows_by('locus') - .key_cols_by('s') - ) - failed_families = get_families_failed_imputed_sex_ploidy( - families, - mt, - sex_check_ht, - ) - self.assertDictEqual(failed_families, {}) - - # Invalid X chromosome case - mt = ( - hl.MatrixTable.from_parts( - rows={ - 'locus': [ - hl.Locus( - contig='chrX', - position=1, - reference_genome='GRCh38', - ), - ], - }, - cols={ - 's': [ - female_sample, - male_sample_1, - male_sample_2, - x0_sample, - xxy_sample, - xyy_sample, - xxx_sample, - ], - }, - entries={ - 'GT': [ - [ - hl.Call(alleles=[0], phased=False), # invalid Female call - hl.Call(alleles=[0], phased=False), # valid Male call - hl.missing(hl.tcall), # invalid Male call - hl.Call(alleles=[0], phased=False), # invalid X0 call - hl.Call(alleles=[0], phased=False), # invalid XXY call - hl.missing(hl.tcall), # valid XYY call - hl.Call(alleles=[0, 0], phased=False), # valid XXX call - ], - ], - }, - ) - .key_rows_by('locus') - .key_cols_by('s') - ) - failed_families = get_families_failed_imputed_sex_ploidy( - families, - mt, - sex_check_ht, - ) - self.assertCountEqual( - failed_families.values(), - [ - [ - "Found samples with misaligned ploidy with their provided imputed sex: ['HG00731_1', 'HG00732_1', 'NA20889_1', 'NA20899_1']", - ], - ], - ) - - # Invalid X chromosome case, but only discrepant family samples are reported - families = { - Family( - family_guid='', - samples={female_sample: Sample(female_sample, Sex.FEMALE)}, - ), - } - failed_families = get_families_failed_imputed_sex_ploidy( - families, - mt, - sex_check_ht, - ) - self.assertCountEqual( - failed_families.values(), - [ - [ - "Found samples with misaligned ploidy with their provided imputed sex: ['HG00731_1']", - ], - ], - ) diff --git a/loading_pipeline/lib/misc/gcnv_test.py b/loading_pipeline/lib/misc/gcnv_test.py deleted file mode 100644 index 33a72f3684..0000000000 --- a/loading_pipeline/lib/misc/gcnv_test.py +++ /dev/null @@ -1,54 +0,0 @@ -import unittest - -import hail as hl - -from loading_pipeline.lib.misc.gcnv import parse_gcnv_genes - - -class GCNVGeneParsingTest(unittest.TestCase): - def test_parse_gcnv_genes(self): - t1 = hl.Table.parallelize( - [ - {'genes': 'AC118553.2,SLC35A3'}, - {'genes': 'AC118553.1,None'}, - {'genes': 'None'}, - {'genes': 'SLC35A3.43'}, - {'genes': ''}, - {'genes': 'SLC35A4.43'}, - ], - hl.tstruct(genes=hl.dtype('str')), - key='genes', - ) - t1 = t1.annotate(gene_set=parse_gcnv_genes(t1.genes)) - self.assertCountEqual( - t1.collect(), - [ - hl.Struct( - genes='AC118553.2,SLC35A3', - gene_set={'AC118553', 'SLC35A3'}, - ), - hl.Struct(genes='AC118553.1,None', gene_set={'AC118553'}), - hl.Struct(genes='None', gene_set=set()), - hl.Struct(genes='SLC35A3.43', gene_set={'SLC35A3'}), - hl.Struct(genes='', gene_set=set()), - hl.Struct(genes='SLC35A4.43', gene_set={'SLC35A4'}), - ], - ) - - def test_aggregate_parsed_genes(self): - t1 = hl.Table.parallelize( - [ - {'genes': 'AC118553.2,SLC35A3'}, - {'genes': 'AC118553.1,None'}, - {'genes': 'None'}, - {'genes': 'SLC35A3.43'}, - {'genes': ''}, - {'genes': 'SLC35A4.43'}, - ], - hl.tstruct(genes=hl.dtype('str')), - key='genes', - ) - aggregated_gene_set = t1.aggregate( - hl.flatten(hl.agg.collect_as_set(parse_gcnv_genes(t1.genes))), - ) - self.assertEqual(aggregated_gene_set, {'SLC35A4', 'SLC35A3', 'AC118553'}) diff --git a/loading_pipeline/lib/misc/io_test.py b/loading_pipeline/lib/misc/io_test.py deleted file mode 100644 index a346e8b323..0000000000 --- a/loading_pipeline/lib/misc/io_test.py +++ /dev/null @@ -1,211 +0,0 @@ -import unittest -from unittest import mock - -import hail as hl - -from loading_pipeline.lib.core import DatasetType, ReferenceGenome -from loading_pipeline.lib.misc.io import ( - compute_hail_n_partitions, - file_size_bytes, - import_imputed_sex, - import_vcf, - remap_pedigree_hash, - select_relevant_fields, - split_multi_hts, -) -from loading_pipeline.lib.misc.validation import SeqrValidationError - -TEST_IMPUTED_SEX = 'loading_pipeline/var/test/sex_check/test_imputed_sex.tsv' -TEST_IMPUTED_SEX_UNEXPECTED_VALUE = ( - 'loading_pipeline/var/test/sex_check/test_imputed_sex_unexpected_value.tsv' -) -CORRUPTED_VCF = 'loading_pipeline/var/test/callsets/1kg_corrupt.vcf.gz' -TEST_INVALID_VCF = 'loading_pipeline/var/test/callsets/improperly_formatted.vcf' -TEST_PEDIGREE_3_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_3_remap.tsv' -TEST_MITO_MT = 'loading_pipeline/var/test/callsets/mito_1.mt' - - -class IOTest(unittest.TestCase): - def test_file_size_mb(self) -> None: - # find loading_pipeline/var/test/callsets/mito_1.mt -type f | grep -v 'crc' | xargs ls -alt {} | awk '{sum += $5; print sum}' - # 191310 - self.assertEqual(file_size_bytes(TEST_MITO_MT), 191310) - - def test_compute_hail_n_partitions(self) -> None: - self.assertEqual(compute_hail_n_partitions(23), 1) - self.assertEqual(compute_hail_n_partitions(191310), 1) - self.assertEqual(compute_hail_n_partitions(1913100000), 58) - - def test_import_imputed_sex(self) -> None: - ht = import_imputed_sex(TEST_IMPUTED_SEX) - self.assertListEqual( - ht.collect(), - [ - hl.Struct(s='abc_1', predicted_sex='M'), - hl.Struct(s='abc_2', predicted_sex='F'), - hl.Struct(s='abc_3', predicted_sex='U'), - hl.Struct(s='abc_4', predicted_sex='XYY'), - hl.Struct(s='abc_5', predicted_sex='U'), - ], - ) - - def test_import_imputed_sex_unexpected_value(self) -> None: - ht = import_imputed_sex(TEST_IMPUTED_SEX_UNEXPECTED_VALUE) - self.assertRaisesRegex( - hl.utils.java.HailUserError, - 'Found unexpected value UNKNOWN in imputed sex file', - ht.collect, - ) - - def test_remap_pedigree_hash(self) -> None: - self.assertEqual( - hl.eval( - remap_pedigree_hash( - TEST_PEDIGREE_3_REMAP, - ), - ), - 573002191, - ) - - def test_import_vcf(self) -> None: - self.assertRaisesRegex( - TypeError, - 'missing 1 required positional argument', - import_vcf, - 'abc', - ) - self.assertRaisesRegex( - SeqrValidationError, - 'Unable to access the VCF in cloud storage', - import_vcf, - 'bad.vcf', - ReferenceGenome.GRCh38, - ) - self.assertRaisesRegex( - SeqrValidationError, - 'Gzip-compressed data is corrupt', - import_vcf, - CORRUPTED_VCF, - ReferenceGenome.GRCh38, - ) - with mock.patch( - 'loading_pipeline.lib.misc.io.hl.read_table', - ) as mock_read_table: - mock_read_table.side_effect = hl.utils.java.FatalError( - 'GoogleJsonResponseException: 403 Forbidden', - ) - self.assertRaisesRegex( - SeqrValidationError, - 'Unable to access the VCF in cloud storage', - import_vcf, - 'abc123/bad.vcf', - ReferenceGenome.GRCh38, - ) - self.assertRaisesRegex( - SeqrValidationError, - 'VCF failed file format validation: Your input file has a malformed header: We never saw the required CHROM header line \\(starting with one #\\) for the input VCF file', - import_vcf, - TEST_PEDIGREE_3_REMAP, - ReferenceGenome.GRCh38, - ) - self.assertRaisesRegex( - SeqrValidationError, - "VCF failed file format validation: invalid character 'N' in integer literal", - import_vcf, - TEST_INVALID_VCF, - ReferenceGenome.GRCh38, - ) - - def test_select_missing_field(self) -> None: - self.assertRaisesRegex( - SeqrValidationError, - "Your callset is missing a required field: 'a magic field'", - select_relevant_fields, - hl.MatrixTable.from_parts( - rows={ - 'locus': [ - hl.Locus( - contig='chr1', - position=1, - reference_genome='GRCh38', - ), - ], - 'alleles': [ - ['A', 'C'], - ], - 'rsid': ['rs1233'], - 'filters': [{'PASS'}], - }, - cols={'s': ['sample_1']}, - entries={ - 'GT': [[hl.Call([0, 0])]], - 'AD': [[[0, 20]]], - 'GQ': [[99]], - }, - ).key_rows_by('locus', 'alleles'), - DatasetType.SNV_INDEL, - {'a magic field': hl.tint32}, - ) - - def test_split_multi_failure(self) -> None: - self.assertRaisesRegex( - SeqrValidationError, - 'Your callset failed while attempting to split multiallelic sites. This error can occur if the dataset contains both multiallelic variants and duplicated loci.', - split_multi_hts, - hl.MatrixTable.from_parts( - rows={ - 'locus': [ - hl.Locus( - contig='chr1', - position=1, - reference_genome='GRCh38', - ), - hl.Locus( - contig='chr1', - position=1, - reference_genome='GRCh38', - ), - ], - 'alleles': [ - ['A', 'G', 'AC'], - ['A', 'AT', 'C', 'G'], - ], - }, - cols={'s': ['sample_1']}, - entries={ - 'GQ': [[99], [98]], - }, - ) - .key_rows_by('locus', 'alleles') - .repartition(1), - False, - 1, - ) - - def test_split_multi_failure_ad_length(self) -> None: - self.assertRaisesRegex( - SeqrValidationError, - 'Your callset failed while attempting to split multiallelic sites. This error can occur if the provided Allele Depth \\(AD\\) field does not match the length of the multiallelic site.', - split_multi_hts, - hl.MatrixTable.from_parts( - rows={ - 'locus': [ - hl.Locus( - contig='chr1', - position=1, - reference_genome='GRCh38', - ), - ], - 'alleles': [ - ['GAC', 'G', 'GTTTTTTTTTTTTTTTAC'], - ], - }, - cols={'s': ['sample_1']}, - entries={ - 'GQ': [[99]], - 'AD': [[[0, 1]]], - }, - ).key_rows_by('locus', 'alleles'), - False, - 1, - ) diff --git a/loading_pipeline/lib/misc/math_test.py b/loading_pipeline/lib/misc/math_test.py deleted file mode 100644 index 19e12d6bfc..0000000000 --- a/loading_pipeline/lib/misc/math_test.py +++ /dev/null @@ -1,12 +0,0 @@ -import unittest - -from loading_pipeline.lib.misc.math import constrain - - -class TestConstrainFunction(unittest.TestCase): - def test_constrain(self): - self.assertEqual(constrain(5, 0, 10), 5) - self.assertEqual(constrain(-3, 0, 10), 0) - self.assertEqual(constrain(15, 0, 10), 10) - with self.assertRaises(ValueError): - constrain(5, 10, 0) diff --git a/loading_pipeline/lib/misc/nested_field_test.py b/loading_pipeline/lib/misc/nested_field_test.py deleted file mode 100644 index 8d465187a5..0000000000 --- a/loading_pipeline/lib/misc/nested_field_test.py +++ /dev/null @@ -1,81 +0,0 @@ -import unittest - -import hail as hl - -from loading_pipeline.lib.misc.nested_field import parse_nested_field - - -class TestConstrainFunction(unittest.TestCase): - def test_parse_nested_field(self): - ht = hl.Table.parallelize( - [ - { - 'locus': hl.Locus( - contig='chr1', - position=1, - reference_genome='GRCh38', - ), - 'alleles': ['A', 'C'], - 'a': hl.Struct(d=1), - 'b': hl.Struct(e=[2, 9]), - 'h': hl.Struct(**{'i.j': 1}), - 'a_index': 1, - }, - { - 'locus': hl.Locus( - contig='chr1', - position=2, - reference_genome='GRCh38', - ), - 'alleles': ['A', 'C'], - 'a': hl.Struct(d=3), - 'b': hl.Struct(e=[4, 5]), - 'h': hl.Struct(**{'i.j': 2}), - 'a_index': 1, - }, - ], - hl.tstruct( - locus=hl.tlocus('GRCh38'), - alleles=hl.tarray(hl.tstr), - a=hl.tstruct(d=hl.tint32), - b=hl.tstruct(e=hl.tarray(hl.tint32)), - h=hl.tstruct(**{'i.j': hl.tint32}), - a_index=hl.tint32, - ), - key=['locus', 'alleles'], - ) - ht = ht.select( - d=parse_nested_field(ht, 'a.d'), - e=parse_nested_field(ht, 'b.e#'), - f=parse_nested_field(ht, 'a'), - g=parse_nested_field(ht, 'h.i.j'), - ) - self.assertListEqual( - ht.collect(), - [ - hl.Struct( - locus=hl.Locus( - contig='chr1', - position=1, - reference_genome='GRCh38', - ), - alleles=['A', 'C'], - d=1, - e=2, - f=hl.Struct(d=1), - g=1, - ), - hl.Struct( - locus=hl.Locus( - contig='chr1', - position=2, - reference_genome='GRCh38', - ), - alleles=['A', 'C'], - d=3, - e=4, - f=hl.Struct(d=3), - g=2, - ), - ], - ) diff --git a/loading_pipeline/lib/misc/pedigree_test.py b/loading_pipeline/lib/misc/pedigree_test.py deleted file mode 100644 index 77432ba138..0000000000 --- a/loading_pipeline/lib/misc/pedigree_test.py +++ /dev/null @@ -1,514 +0,0 @@ -import unittest - -import hail as hl - -from loading_pipeline.lib.core import Sex -from loading_pipeline.lib.misc.io import import_pedigree -from loading_pipeline.lib.misc.pedigree import ( - Family, - Sample, - parse_pedigree_ht_to_families, -) - -TEST_PEDIGREE_1 = 'loading_pipeline/var/test/pedigrees/test_pedigree_1.tsv' -TEST_PEDIGREE_2 = 'loading_pipeline/var/test/pedigrees/test_pedigree_2.tsv' -TEST_PEDIGREE_9 = 'loading_pipeline/var/test/pedigrees/test_pedigree_9.tsv' - - -class PedigreesTest(unittest.TestCase): - def test_empty_pedigree(self) -> None: - with self.assertRaises(Exception): # noqa: B017 - _ = import_pedigree(TEST_PEDIGREE_1) - - def test_parse_lineage(self) -> None: - # - # - # sample_9 sample_10 sample_7 - # \ / \ | - # sample_6 -> sample_8 --------- sample_3 ----- ? | - # \ / \ / | - # sample_4, sample_5 sample_2 | sample_1 - # - # - samples = Family.parse_direct_lineage( - [ - hl.Struct(s='sample_1', maternal_s=None, paternal_s=None, sex='F'), - hl.Struct( - s='sample_2', - maternal_s='sample_3', - paternal_s=None, - sex='M', - ), - hl.Struct( - s='sample_3', - maternal_s=None, - paternal_s='sample_7', - sex='F', - ), - hl.Struct( - s='sample_4', - maternal_s='sample_3', - paternal_s='sample_8', - sex='M', - ), - hl.Struct( - s='sample_5', - maternal_s='sample_3', - paternal_s='sample_8', - sex='M', - ), - hl.Struct( - s='sample_6', - maternal_s='sample_9', - paternal_s='sample_10', - sex='M', - ), - hl.Struct(s='sample_7', maternal_s=None, paternal_s=None, sex='M'), - hl.Struct( - s='sample_8', - maternal_s='sample_9', - paternal_s='sample_10', - sex='F', - ), - hl.Struct(s='sample_9', maternal_s=None, paternal_s=None, sex='F'), - hl.Struct(s='sample_10', maternal_s=None, paternal_s=None, sex='M'), - ], - ) - self.assertEqual( - Family.parse_collateral_lineage(samples), - { - 'sample_1': Sample( - sample_id='sample_1', - sex=Sex.FEMALE, - mother=None, - father=None, - maternal_grandmother=None, - maternal_grandfather=None, - paternal_grandmother=None, - paternal_grandfather=None, - siblings=[], - half_siblings=[], - aunt_nephews=[], - ), - 'sample_2': Sample( - sample_id='sample_2', - sex=Sex.MALE, - mother='sample_3', - father=None, - maternal_grandmother=None, - maternal_grandfather='sample_7', - paternal_grandmother=None, - paternal_grandfather=None, - siblings=[], - half_siblings=['sample_4', 'sample_5'], - aunt_nephews=[], - ), - 'sample_3': Sample( - sample_id='sample_3', - sex=Sex.FEMALE, - mother=None, - father='sample_7', - maternal_grandmother=None, - maternal_grandfather=None, - paternal_grandmother=None, - paternal_grandfather=None, - siblings=[], - half_siblings=[], - aunt_nephews=[], - ), - 'sample_4': Sample( - sample_id='sample_4', - sex=Sex.MALE, - mother='sample_3', - father='sample_8', - maternal_grandmother=None, - maternal_grandfather='sample_7', - paternal_grandmother='sample_9', - paternal_grandfather='sample_10', - siblings=['sample_5'], - half_siblings=[], - aunt_nephews=['sample_6'], - ), - 'sample_5': Sample( - sample_id='sample_5', - sex=Sex.MALE, - mother='sample_3', - father='sample_8', - maternal_grandmother=None, - maternal_grandfather='sample_7', - paternal_grandmother='sample_9', - paternal_grandfather='sample_10', - siblings=[], - half_siblings=[], - aunt_nephews=['sample_6'], - ), - 'sample_6': Sample( - sample_id='sample_6', - sex=Sex.MALE, - mother='sample_9', - father='sample_10', - maternal_grandmother=None, - maternal_grandfather=None, - paternal_grandmother=None, - paternal_grandfather=None, - siblings=['sample_8'], - half_siblings=[], - aunt_nephews=[], - ), - 'sample_7': Sample( - sample_id='sample_7', - sex=Sex.MALE, - mother=None, - father=None, - maternal_grandmother=None, - maternal_grandfather=None, - paternal_grandmother=None, - paternal_grandfather=None, - siblings=[], - half_siblings=[], - aunt_nephews=[], - ), - 'sample_8': Sample( - sample_id='sample_8', - sex=Sex.FEMALE, - mother='sample_9', - father='sample_10', - maternal_grandmother=None, - maternal_grandfather=None, - paternal_grandmother=None, - paternal_grandfather=None, - siblings=[], - half_siblings=[], - aunt_nephews=[], - ), - 'sample_9': Sample( - sample_id='sample_9', - sex=Sex.FEMALE, - mother=None, - father=None, - maternal_grandmother=None, - maternal_grandfather=None, - paternal_grandmother=None, - paternal_grandfather=None, - siblings=[], - half_siblings=[], - aunt_nephews=[], - ), - 'sample_10': Sample( - sample_id='sample_10', - sex=Sex.MALE, - mother=None, - father=None, - maternal_grandmother=None, - maternal_grandfather=None, - paternal_grandmother=None, - paternal_grandfather=None, - siblings=[], - half_siblings=[], - aunt_nephews=[], - ), - }, - ) - - def test_parse_parent_not_aunt_uncle(self) -> None: - samples = Family.parse_direct_lineage( - [ - hl.Struct(s='sample_1', maternal_s=None, paternal_s=None, sex='F'), - hl.Struct( - s='sample_2', - maternal_s=None, - paternal_s=None, - sex='M', - ), - hl.Struct( - s='sample_3', - maternal_s='sample_1', - paternal_s='sample_2', - sex='F', - ), - hl.Struct( - s='sample_4', - maternal_s='sample_3', - paternal_s=None, - sex='F', - ), - hl.Struct( - s='sample_5', - maternal_s='sample_3', - paternal_s=None, - sex='F', - ), - ], - ) - self.assertEqual( - Family.parse_collateral_lineage(samples), - { - 'sample_1': Sample( - sample_id='sample_1', - sex=Sex.FEMALE, - mother=None, - father=None, - maternal_grandmother=None, - maternal_grandfather=None, - paternal_grandmother=None, - paternal_grandfather=None, - siblings=[], - half_siblings=[], - aunt_nephews=[], - ), - 'sample_2': Sample( - sample_id='sample_2', - sex=Sex.MALE, - mother=None, - father=None, - maternal_grandmother=None, - maternal_grandfather=None, - paternal_grandmother=None, - paternal_grandfather=None, - siblings=[], - half_siblings=[], - aunt_nephews=[], - ), - 'sample_3': Sample( - sample_id='sample_3', - sex=Sex.FEMALE, - mother='sample_1', - father='sample_2', - maternal_grandmother=None, - maternal_grandfather=None, - paternal_grandmother=None, - paternal_grandfather=None, - siblings=[], - half_siblings=[], - aunt_nephews=[], - ), - 'sample_4': Sample( - sample_id='sample_4', - sex=Sex.FEMALE, - mother='sample_3', - father=None, - maternal_grandmother='sample_1', - maternal_grandfather='sample_2', - paternal_grandmother=None, - paternal_grandfather=None, - siblings=[], - half_siblings=['sample_5'], - aunt_nephews=[], - ), - 'sample_5': Sample( - sample_id='sample_5', - sex=Sex.FEMALE, - mother='sample_3', - father=None, - maternal_grandmother='sample_1', - maternal_grandfather='sample_2', - paternal_grandmother=None, - paternal_grandfather=None, - siblings=[], - half_siblings=[], - aunt_nephews=[], - ), - }, - ) - - def test_parse_project(self) -> None: - pedigree_ht = import_pedigree(TEST_PEDIGREE_2) - self.assertCountEqual( - list(parse_pedigree_ht_to_families(pedigree_ht)), - [ - Family( - family_guid='BBL_BC1-000345_1', - samples={ - 'BBL_BC1-000345_01_D1': Sample( - sample_id='BBL_BC1-000345_01_D1', - sex=Sex.UNKNOWN, - mother='BBL_BC1-000345_03_D1', - father='BBL_BC1-000345_02_D1', - maternal_grandmother=None, - maternal_grandfather=None, - paternal_grandmother=None, - paternal_grandfather=None, - siblings=[], - half_siblings=[], - aunt_nephews=[], - ), - 'BBL_BC1-000345_02_D1': Sample( - sample_id='BBL_BC1-000345_02_D1', - sex=Sex.MALE, - mother=None, - father=None, - maternal_grandmother=None, - maternal_grandfather=None, - paternal_grandmother=None, - paternal_grandfather=None, - siblings=[], - half_siblings=[], - aunt_nephews=[], - ), - 'BBL_BC1-000345_03_D1': Sample( - sample_id='BBL_BC1-000345_03_D1', - sex=Sex.FEMALE, - mother=None, - father=None, - maternal_grandmother=None, - maternal_grandfather=None, - paternal_grandmother=None, - paternal_grandfather=None, - siblings=[], - half_siblings=[], - aunt_nephews=[], - ), - }, - ), - Family( - family_guid='BBL_HT-007-5195_1', - samples={ - 'BBL_HT-007-5195_01_D1': Sample( - sample_id='BBL_HT-007-5195_01_D1', - sex=Sex.FEMALE, - mother='BBL_HT-007-5195_03_D1', - father='BBL_HT-007-5195_02_D1', - maternal_grandmother=None, - maternal_grandfather=None, - paternal_grandmother=None, - paternal_grandfather=None, - siblings=[ - 'BBL_HT-007-5195_04_D1', - 'BBL_HT-007-5195_05_D1', - 'BBL_HT-007-5195_06_D1', - ], - half_siblings=[], - aunt_nephews=[], - ), - 'BBL_HT-007-5195_02_D1': Sample( - sample_id='BBL_HT-007-5195_02_D1', - sex=Sex.MALE, - mother=None, - father=None, - maternal_grandmother=None, - maternal_grandfather=None, - paternal_grandmother=None, - paternal_grandfather=None, - siblings=[], - half_siblings=[], - aunt_nephews=[], - ), - 'BBL_HT-007-5195_03_D1': Sample( - sample_id='BBL_HT-007-5195_03_D1', - sex=Sex.FEMALE, - mother=None, - father=None, - maternal_grandmother=None, - maternal_grandfather=None, - paternal_grandmother=None, - paternal_grandfather=None, - siblings=[], - half_siblings=[], - aunt_nephews=[], - ), - 'BBL_HT-007-5195_04_D1': Sample( - sample_id='BBL_HT-007-5195_04_D1', - sex=Sex.MALE, - mother='BBL_HT-007-5195_03_D1', - father='BBL_HT-007-5195_02_D1', - maternal_grandmother=None, - maternal_grandfather=None, - paternal_grandmother=None, - paternal_grandfather=None, - siblings=['BBL_HT-007-5195_05_D1', 'BBL_HT-007-5195_06_D1'], - half_siblings=[], - aunt_nephews=[], - ), - 'BBL_HT-007-5195_05_D1': Sample( - sample_id='BBL_HT-007-5195_05_D1', - sex=Sex.FEMALE, - mother='BBL_HT-007-5195_03_D1', - father='BBL_HT-007-5195_02_D1', - maternal_grandmother=None, - maternal_grandfather=None, - paternal_grandmother=None, - paternal_grandfather=None, - siblings=['BBL_HT-007-5195_06_D1'], - half_siblings=[], - aunt_nephews=[], - ), - 'BBL_HT-007-5195_06_D1': Sample( - sample_id='BBL_HT-007-5195_06_D1', - sex=Sex.MALE, - mother='BBL_HT-007-5195_03_D1', - father='BBL_HT-007-5195_02_D1', - maternal_grandmother=None, - maternal_grandfather=None, - paternal_grandmother=None, - paternal_grandfather=None, - siblings=[], - half_siblings=[], - aunt_nephews=[], - ), - }, - ), - Family( - family_guid='BBL_SDS1-000178_1', - samples={ - 'BBL_SDS1-000178_01_D1': Sample( - sample_id='BBL_SDS1-000178_01_D1', - sex=Sex.FEMALE, - mother=None, - father=None, - maternal_grandmother=None, - maternal_grandfather=None, - paternal_grandmother=None, - paternal_grandfather=None, - siblings=[], - half_siblings=[], - aunt_nephews=[], - ), - }, - ), - ], - ) - - def test_subsetted_pedigree_with_removed_parent(self) -> None: - pedigree_ht = import_pedigree(TEST_PEDIGREE_2) - pedigree_ht = pedigree_ht.filter( - pedigree_ht.s != 'BBL_BC1-000345_02_D1', - ) - parsed_pedigree = parse_pedigree_ht_to_families(pedigree_ht) - family = next( - iter( - [ - family - for family in parsed_pedigree - if family.family_guid == 'BBL_BC1-000345_1' - ], - ), - ) - self.assertEqual(len(family.samples), 2) - self.assertFalse( - 'BBL_BC1-000345_02_D1' in family.samples, - ) - self.assertEqual( - family.samples['BBL_BC1-000345_01_D1'].father, - 'BBL_BC1-000345_02_D1', - ) - self.assertEqual( - family.samples['BBL_BC1-000345_01_D1'].mother, - 'BBL_BC1-000345_03_D1', - ) - - def test_pedigree_ungrouped_families(self) -> None: - pedigree_ht = import_pedigree(TEST_PEDIGREE_9) - parsed_pedigree = parse_pedigree_ht_to_families(pedigree_ht) - self.assertEqual(len(parsed_pedigree), 2) - family = next( - iter( - [ - family - for family in parsed_pedigree - if family.family_guid == 'family_2_1' - ], - ), - ) - self.assertTrue( - family.samples.keys() == {'RGP_164_1', 'RGP_164_2', 'RGP_164_4'}, - ) diff --git a/loading_pipeline/lib/misc/retry_test.py b/loading_pipeline/lib/misc/retry_test.py deleted file mode 100644 index 4b756abce1..0000000000 --- a/loading_pipeline/lib/misc/retry_test.py +++ /dev/null @@ -1,69 +0,0 @@ -import unittest -from unittest.mock import Mock, patch - -from loading_pipeline.lib.core import DatasetType -from loading_pipeline.lib.misc.retry import retry - - -class TestRetryDecorator(unittest.TestCase): - @patch('time.sleep', return_value=None) - def test_retry_success_first_try(self, mock_sleep): - mock_func = Mock(return_value='success') - - @retry(tries=3, delay=1, backoff=2) - def func(d: DatasetType): - return mock_func(d) - - result = func(DatasetType.SNV_INDEL) - self.assertEqual(result, 'success') - self.assertEqual(mock_func.call_count, 1) - mock_sleep.assert_not_called() - - @patch('time.sleep', return_value=None) - @patch('loading_pipeline.lib.misc.retry.logger') - def test_retry_eventual_success(self, mock_logger, mock_sleep): - mock_func = Mock( - side_effect=[Exception('fail'), Exception('fail again'), 'success'], - ) - - @retry(tries=3, delay=1, backoff=2) - def func(): - return mock_func() - - result = func() - self.assertEqual(result, 'success') - self.assertEqual(mock_func.call_count, 3) - self.assertEqual(mock_sleep.call_count, 2) - mock_sleep.assert_any_call(1) - mock_sleep.assert_any_call(2) - - @patch('time.sleep', return_value=None) - @patch('loading_pipeline.lib.misc.retry.logger') - def test_retry_all_failures(self, mock_logger, mock_sleep): - mock_func = Mock(side_effect=Exception('always fails')) - - @retry(tries=3, delay=1, backoff=2) - def func(): - return mock_func() - - with self.assertRaises(Exception) as context: - func() - - self.assertEqual(str(context.exception), 'always fails') - self.assertEqual(mock_func.call_count, 3) - self.assertEqual(mock_sleep.call_count, 2) - - @patch('time.sleep', return_value=None) - @patch('loading_pipeline.lib.misc.retry.logger.exception') - def test_logs_retry_message(self, mock_log, mock_sleep): - mock_func = Mock(side_effect=[Exception('fail'), 'success']) - - @retry(tries=2, delay=1, backoff=2) - def func(d: DatasetType): - return mock_func(d) - - func(d=DatasetType.SNV_INDEL) - self.assertIn( - 'func args: kwargs:d=SNV_INDEL failed on attempt 1 after 0.00s, retrying in 1 seconds.', - mock_log.call_args[0][0], - ) diff --git a/loading_pipeline/lib/misc/runs_test.py b/loading_pipeline/lib/misc/runs_test.py deleted file mode 100644 index b1a601727a..0000000000 --- a/loading_pipeline/lib/misc/runs_test.py +++ /dev/null @@ -1,84 +0,0 @@ -import os - -from loading_pipeline.lib.core import DatasetType, ReferenceGenome -from loading_pipeline.lib.misc.runs import get_run_ids -from loading_pipeline.lib.paths import ( - clickhouse_load_fail_file_path, - clickhouse_load_success_file_path, - pipeline_run_success_file_path, - runs_path, -) -from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase - - -class RunsTest(MockedDatarootTestCase): - def setUp(self): - super().setUp() - run_ids = [ - 'manual__2024-08-05T16-07-58.365146+00-00', - 'manual__2024-08-06T10-15-23.123456+00-00', - 'manual__2024-08-07T12-30-45.654321+00-00', # _SUCCESS, _CLICKHOUSE_LOAD_FAIL - 'manual__2024-08-08T09-45-00.000000+00-00', # _SUCCESS - 'manual__2024-08-09T18-22-13.999999+00-00', # _SUCCESS, _CLICKHOUSE_LOAD_SUCCESS - ] - for reference_genome, dataset_type in [ - (ReferenceGenome.GRCh38, DatasetType.SNV_INDEL), - (ReferenceGenome.GRCh37, DatasetType.SNV_INDEL), - (ReferenceGenome.GRCh38, DatasetType.GCNV), - (ReferenceGenome.GRCh37, DatasetType.GCNV), - ]: - for run_id in run_ids: - base_path = runs_path(reference_genome, dataset_type) - os.makedirs(os.path.join(base_path, run_id), exist_ok=True) - if '07T12' in run_id: - failure_file = clickhouse_load_fail_file_path( - reference_genome, - dataset_type, - run_id, - ) - open(failure_file, 'w').close() - if '09' in run_id or '07T12' in run_id: - success_file = pipeline_run_success_file_path( - reference_genome, - dataset_type, - run_id, - ) - open(success_file, 'w').close() - if '09T18' in run_id: - success_file = clickhouse_load_success_file_path( - reference_genome, - dataset_type, - run_id, - ) - open(success_file, 'w').close() - - def test_get_run_ids(self) -> None: - ( - successful_pipeline_runs, - successful_clickhouse_loads, - failed_clickhouse_loads, - ) = get_run_ids() - self.assertCountEqual( - successful_pipeline_runs[(ReferenceGenome.GRCh38, DatasetType.SNV_INDEL)], - { - 'manual__2024-08-09T18-22-13.999999+00-00', - 'manual__2024-08-08T09-45-00.000000+00-00', - 'manual__2024-08-07T12-30-45.654321+00-00', - }, - ) - self.assertCountEqual( - successful_clickhouse_loads[ - (ReferenceGenome.GRCh38, DatasetType.SNV_INDEL) - ], - { - 'manual__2024-08-09T18-22-13.999999+00-00', - }, - ) - self.assertCountEqual( - successful_clickhouse_loads[(ReferenceGenome.GRCh37, DatasetType.GCNV)], - {}, - ) - self.assertCountEqual( - failed_clickhouse_loads[(ReferenceGenome.GRCh38, DatasetType.SNV_INDEL)], - {'manual__2024-08-07T12-30-45.654321+00-00'}, - ) diff --git a/loading_pipeline/lib/misc/sample_ids_test.py b/loading_pipeline/lib/misc/sample_ids_test.py deleted file mode 100644 index 6d3fb7efd0..0000000000 --- a/loading_pipeline/lib/misc/sample_ids_test.py +++ /dev/null @@ -1,160 +0,0 @@ -import unittest - -import hail as hl - -from loading_pipeline.lib.misc.sample_ids import ( - remap_sample_ids, - subset_samples, -) -from loading_pipeline.lib.misc.validation import SeqrValidationError - -CALLSET_MT = hl.MatrixTable.from_parts( - rows={'variants': [1, 2]}, - cols={'s': ['HG00731', 'HG00732', 'HG00733']}, - entries={ - 'GT': [ - [hl.Call([0, 1]), hl.missing(hl.tcall), hl.Call([0, 1])], - [hl.Call([0, 1]), hl.Call([0, 1]), hl.Call([1, 1])], - ], - }, -).key_cols_by('s') - - -class SampleLookupTest(unittest.TestCase): - def test_remap_2_sample_ids(self) -> None: - # remap 2 of 3 samples in callset - project_remap_ht = hl.Table.parallelize( - [ - {'s': 'HG00731', 'seqr_id': 'HG00731_1'}, - {'s': 'HG00732', 'seqr_id': 'HG00732_1'}, - ], - hl.tstruct( - s=hl.tstr, - seqr_id=hl.tstr, - ), - key='s', - ) - - remapped_mt = remap_sample_ids( - CALLSET_MT, - project_remap_ht, - ) - - self.assertEqual(remapped_mt.cols().count(), 3) - self.assertEqual( - remapped_mt.cols().collect(), - [ - hl.Struct( - col_idx=0, - s='HG00731_1', - seqr_id='HG00731_1', - vcf_id='HG00731', - ), - hl.Struct( - col_idx=1, - s='HG00732_1', - seqr_id='HG00732_1', - vcf_id='HG00732', - ), - hl.Struct(col_idx=2, s='HG00733', seqr_id='HG00733', vcf_id='HG00733'), - ], - ) - - def test_remap_sample_ids_remap_has_duplicate(self) -> None: - # remap file has 2 rows for HG00732 - project_remap_ht = hl.Table.parallelize( - [ - {'s': 'HG00731', 'seqr_id': 'HG00731_1'}, - {'s': 'HG00732', 'seqr_id': 'HG00732_1'}, - {'s': 'HG00732', 'seqr_id': 'HG00732_1'}, # duplicate - ], - hl.tstruct( - s=hl.tstr, - seqr_id=hl.tstr, - ), - key='s', - ) - - with self.assertRaises(SeqrValidationError): - remap_sample_ids( - CALLSET_MT, - project_remap_ht, - ) - - def test_remap_sample_ids_remap_has_missing_samples(self) -> None: - # remap file has 4 rows, but only 3 samples in callset - project_remap_ht = hl.Table.parallelize( - [ - {'s': 'HG00731', 'seqr_id': 'HG00731_1'}, - {'s': 'HG00732', 'seqr_id': 'HG00732_1'}, - {'s': 'HG00733', 'seqr_id': 'HG00733_1'}, - {'s': 'HG00734', 'seqr_id': 'HG00734_1'}, # missing in callset - ], - hl.tstruct( - s=hl.tstr, - seqr_id=hl.tstr, - ), - key='s', - ) - - with self.assertRaises(SeqrValidationError): - remap_sample_ids( - CALLSET_MT, - project_remap_ht, - ) - - def test_subset_samples_zero_samples(self): - # subset 0 of 3 samples in callset - sample_subset_ht = hl.Table.parallelize( - [], - hl.tstruct(s=hl.tstr), - key='s', - ) - - with self.assertRaises(SeqrValidationError): - subset_samples( - CALLSET_MT, - sample_subset_ht, - ) - - def test_subset_samples_missing_samples(self): - # subset 2 of 3 samples in callset, but 1 is missing - sample_subset_ht = hl.Table.parallelize( - [ - {'s': 'HG00731'}, - {'s': 'HG00732'}, - {'s': 'HG00734'}, # missing in callset - ], - hl.tstruct(s=hl.tstr), - key='s', - ) - - with self.assertRaises(SeqrValidationError): - subset_samples( - CALLSET_MT, - sample_subset_ht, - ) - - def test_subset_no_defined_gt(self): - mt = hl.MatrixTable.from_parts( - rows={'variants': [1, 2]}, - cols={'s': ['HG00731', 'HG00732']}, - entries={ - 'GT': [ - [hl.Call([1, 1]), hl.missing(hl.tcall)], - [hl.Call([1, 1]), hl.Call([1, 1])], - ], - }, - ).key_cols_by('s') - sample_subset_ht = hl.Table.parallelize( - [ - {'s': 'HG00732'}, - ], - hl.tstruct(s=hl.tstr), - key='s', - ) - mt = subset_samples( - mt, - sample_subset_ht, - ) - self.assertEqual(mt.count(), (1, 1)) diff --git a/loading_pipeline/lib/misc/sv_test.py b/loading_pipeline/lib/misc/sv_test.py deleted file mode 100644 index aefa8a5cd5..0000000000 --- a/loading_pipeline/lib/misc/sv_test.py +++ /dev/null @@ -1,243 +0,0 @@ -import unittest - -import hail as hl - -from loading_pipeline.lib.core import DatasetType, ReferenceGenome, Sex -from loading_pipeline.lib.misc.io import import_callset, select_relevant_fields -from loading_pipeline.lib.misc.pedigree import Family, Sample -from loading_pipeline.lib.misc.sample_ids import subset_samples -from loading_pipeline.lib.misc.sv import ( - deduplicate_merged_sv_concordance_calls, - overwrite_male_non_par_calls, -) - -TEST_SV_VCF = 'loading_pipeline/var/test/callsets/sv_1.vcf' -ANNOTATIONS_HT = hl.Table.parallelize( - [ - { - 'variant_id': 'BND_chr1_6', - 'algorithms': 'manta', - 'end_locus': hl.Locus( - contig='chr5', - position=20404, - reference_genome='GRCh38', - ), - }, - { - 'variant_id': 'BND_chr1_9', - 'algorithms': 'manta', - 'end_locus': hl.Locus( - contig='chr1', - position=789481, - reference_genome='GRCh38', - ), - }, - { - 'variant_id': 'CPX_chr1_22', - 'algorithms': 'manta', - 'end_locus': hl.Locus( - contig='chr1', - position=6559723, - reference_genome='GRCh38', - ), - }, - ], - hl.tstruct( - variant_id=hl.tstr, - algorithms=hl.tstr, - end_locus=hl.tlocus('GRCh38'), - ), - key='variant_id', -) - - -class SVTest(unittest.TestCase): - def test_overwrite_male_non_par_calls(self) -> None: - mt = import_callset(TEST_SV_VCF, ReferenceGenome.GRCh38, DatasetType.SV) - mt = select_relevant_fields( - mt, - DatasetType.SV, - ) - mt = subset_samples( - mt, - hl.Table.parallelize( - [{'s': sample_id} for sample_id in ['RGP_164_1', 'RGP_164_2']], - hl.tstruct(s=hl.dtype('str')), - key='s', - ), - ) - mt = overwrite_male_non_par_calls( - mt, - { - Family( - family_guid='family_1', - samples={ - 'RGP_164_1': Sample(sample_id='RGP_164_1', sex=Sex.FEMALE), - 'RGP_164_2': Sample(sample_id='RGP_164_2', sex=Sex.MALE), - }, - ), - }, - ) - mt = mt.filter_rows(mt.locus.contig == 'chrX') - self.assertEqual( - [ - hl.Locus(contig='chrX', position=3, reference_genome='GRCh38'), - hl.Locus(contig='chrX', position=2781700, reference_genome='GRCh38'), - ], - mt.locus.collect(), - ) - self.assertEqual( - [ - hl.Call(alleles=[0, 0], phased=False), - # END of this variant < start of the non-par region. - hl.Call(alleles=[0, 1], phased=False), - hl.Call(alleles=[0, 0], phased=False), - hl.Call(alleles=[1], phased=False), - ], - mt.GT.collect(), - ) - self.assertFalse( - hasattr(mt, 'start_locus'), - ) - - def test_deduplicate_merged_sv_concordance_calls(self) -> None: - mt = ( - hl.MatrixTable.from_parts( - rows={ - 'variant_id': [ - 'new_v1', - 'new_v2', - 'new_v3', - ], - 'locus': [ - hl.Locus( - contig='chr1', - position=1, - reference_genome='GRCh38', - ), - hl.Locus( - contig='chr1', - position=2, - reference_genome='GRCh38', - ), - hl.Locus( - contig='chr1', - position=3, - reference_genome='GRCh38', - ), - ], - 'info.END': [ - 1, - 2, - 3, - ], - 'info.END2': [ - 1, - 2, - 3, - ], - 'info.CHR2': [ - 'chr1', - 'chr1', - 'chr1', - ], - 'info.SEQR_INTERNAL_TRUTH_VID': [ - 'BND_chr1_6', - 'BND_chr1_9', - 'CPX_chr1_22', - ], - }, - cols={'s': ['sample_1']}, - entries={'GQ': [[99] for _ in range(3)]}, - ) - .key_rows_by('variant_id') - .key_cols_by('s') - ) - mt = deduplicate_merged_sv_concordance_calls( - mt, - ANNOTATIONS_HT, - ) - self.assertEqual( - mt['info.SEQR_INTERNAL_TRUTH_VID'].collect(), - [ - 'BND_chr1_6', - 'BND_chr1_9', - 'CPX_chr1_22', - ], - ) - - mt = ( - hl.MatrixTable.from_parts( - rows={ - 'variant_id': [ - 'new_v1', - 'new_v2', - 'new_v3', - 'new_v4', - ], - 'locus': [ - hl.Locus( - contig='chr1', - position=1, - reference_genome='GRCh38', - ), - hl.Locus( - contig='chr1', - position=2, - reference_genome='GRCh38', - ), - hl.Locus( - contig='chr1', - position=3, - reference_genome='GRCh38', - ), - hl.Locus( - contig='chr1', - position=4, - reference_genome='GRCh38', - ), - ], - 'info.END': [ - 1, - 2, - 789481, - 789485, - ], - 'info.END2': [ - 1, - 2, - 789481, - 789485, - ], - 'info.CHR2': [ - 'chr1', - 'chr1', - 'chr2', - 'chr1', - ], - 'info.SEQR_INTERNAL_TRUTH_VID': [ - 'BND_chr1_6', - 'BND_chr1_9', - 'BND_chr1_9', - 'BND_chr1_9', - ], - }, - cols={'s': ['sample_1']}, - entries={'GQ': [[99] for _ in range(4)]}, - ) - .key_rows_by('variant_id') - .key_cols_by('s') - ) - mt = deduplicate_merged_sv_concordance_calls( - mt, - ANNOTATIONS_HT, - ) - self.assertEqual( - mt['info.SEQR_INTERNAL_TRUTH_VID'].collect(), - [ - 'BND_chr1_6', - None, - None, - 'BND_chr1_9', - ], - ) diff --git a/loading_pipeline/lib/misc/terra_data_repository_test.py b/loading_pipeline/lib/misc/terra_data_repository_test.py deleted file mode 100644 index 91b044d68f..0000000000 --- a/loading_pipeline/lib/misc/terra_data_repository_test.py +++ /dev/null @@ -1,321 +0,0 @@ -import json -import os -import unittest -from types import SimpleNamespace -from unittest.mock import Mock, call, patch - -import responses - -from loading_pipeline.lib.misc.terra_data_repository import ( - TDR_ROOT_URL, - _get_dataset_ids, - bq_metrics_query, - gen_bq_table_names, -) - -TDR_DATASETS = [ - { - 'id': '2dc51ee0-a037-499d-a915-a7c20a0b216d', - 'name': 'RP_3053', - 'description': 'TGG_Ware_DRAGEN_hg38. Dataset automatically created and linked to: RP-3053', - 'defaultProfileId': '0a164b9a-2b8b-45d2-859e-a4e369b9cb4f', - 'createdDate': '2023-10-05T13:15:27.649760Z', - 'storage': [ - { - 'region': 'us-central1', - 'cloudResource': 'bigquery', - 'cloudPlatform': 'gcp', - }, - { - 'region': 'us-east4', - 'cloudResource': 'firestore', - 'cloudPlatform': 'gcp', - }, - { - 'region': 'us-central1', - 'cloudResource': 'bucket', - 'cloudPlatform': 'gcp', - }, - ], - 'secureMonitoringEnabled': False, - 'cloudPlatform': 'gcp', - 'dataProject': 'datarepo-7242affb', - 'storageAccount': None, - 'phsId': None, - 'selfHosted': False, - 'predictableFileIds': False, - 'tags': [], - 'resourceLocks': { - 'exclusive': None, - 'shared': [], - }, - }, - { - 'id': 'beef77e8-575b-40e5-9340-a6f10e0bec67', - 'name': 'RP_3056', - 'description': 'RGP_HMB_DRAGEN_hg38. Dataset automatically created and linked to: RP-3056', - 'defaultProfileId': '835dd05d-c603-4b0d-926f-d9143fd24549', - 'createdDate': '2023-10-05T20:15:27.622481Z', - 'storage': [ - { - 'region': 'us-central1', - 'cloudResource': 'bigquery', - 'cloudPlatform': 'gcp', - }, - { - 'region': 'us-east4', - 'cloudResource': 'firestore', - 'cloudPlatform': 'gcp', - }, - { - 'region': 'us-central1', - 'cloudResource': 'bucket', - 'cloudPlatform': 'gcp', - }, - ], - 'secureMonitoringEnabled': False, - 'cloudPlatform': 'gcp', - 'dataProject': 'datarepo-5a72e31b', - 'storageAccount': None, - 'phsId': None, - 'selfHosted': False, - 'predictableFileIds': False, - 'tags': [], - 'resourceLocks': { - 'exclusive': None, - 'shared': [], - }, - }, - { - 'id': 'c8d74ac4-9a2e-4d3d-a6b5-1f4b433d949f', - 'name': 'RP_3055', - 'description': 'RGP_GRU_DRAGEN_hg38. Dataset automatically created and linked to: RP-3055', - 'defaultProfileId': '835dd05d-c603-4b0d-926f-d9143fd24549', - 'createdDate': '2023-10-05T20:15:28.255304Z', - 'storage': [ - { - 'region': 'us-central1', - 'cloudResource': 'bigquery', - 'cloudPlatform': 'gcp', - }, - { - 'region': 'us-east4', - 'cloudResource': 'firestore', - 'cloudPlatform': 'gcp', - }, - { - 'region': 'us-central1', - 'cloudResource': 'bucket', - 'cloudPlatform': 'gcp', - }, - ], - 'secureMonitoringEnabled': False, - 'cloudPlatform': 'gcp', - 'dataProject': 'datarepo-0f5be351', - 'storageAccount': None, - 'phsId': None, - 'selfHosted': False, - 'predictableFileIds': False, - 'tags': [], - 'resourceLocks': { - 'exclusive': None, - 'shared': [ - 'Gw_KTeYRS1aLhRvapMLYLg', - 'WrP-0w1aROOUbgkI8JS6Ug', - ], - }, - }, -] - - -@patch( - 'loading_pipeline.lib.misc.terra_data_repository.get_service_account_credentials', - return_value=SimpleNamespace( - token='abcdefg', # noqa: S106 - ), -) -class TerraDataRepositoryTest(unittest.TestCase): - @responses.activate - def test_get_dataset_ids(self, _: Mock) -> None: - responses.get( - os.path.join(TDR_ROOT_URL, 'datasets?limit=50000'), - body=json.dumps( - { - 'total': 3, - 'filteredTotal': 3, - 'items': TDR_DATASETS, - }, - ), - ) - self.assertListEqual( - _get_dataset_ids(), - [ - '2dc51ee0-a037-499d-a915-a7c20a0b216d', - 'beef77e8-575b-40e5-9340-a6f10e0bec67', - 'c8d74ac4-9a2e-4d3d-a6b5-1f4b433d949f', - ], - ) - - @responses.activate - def test_get_dataset_ids_no_bq(self, _: Mock) -> None: - responses.get( - os.path.join(TDR_ROOT_URL, 'datasets'), - body=json.dumps( - { - 'total': 1, - 'filteredTotal': 1, - 'items': [ - { - 'id': '2dc51ee0-a037-499d-a915-a7c20a0b216d', - 'name': 'RP_3053', - 'description': 'TGG_Ware_DRAGEN_hg38. Dataset automatically created and linked to: RP-3053', - 'defaultProfileId': '0a164b9a-2b8b-45d2-859e-a4e369b9cb4f', - 'createdDate': '2023-10-05T13:15:27.649760Z', - 'storage': [ - # NB: bigquery was removed from 'storage' here. - { - 'region': 'us-east4', - 'cloudResource': 'firestore', - 'cloudPlatform': 'gcp', - }, - { - 'region': 'us-central1', - 'cloudResource': 'bucket', - 'cloudPlatform': 'gcp', - }, - ], - 'secureMonitoringEnabled': False, - 'cloudPlatform': 'gcp', - 'dataProject': 'datarepo-7242affb', - 'storageAccount': None, - 'phsId': None, - 'selfHosted': False, - 'predictableFileIds': False, - 'tags': [], - 'resourceLocks': { - 'exclusive': None, - 'shared': [], - }, - }, - ], - }, - ), - ) - self.assertRaises( - ValueError, - _get_dataset_ids, - ) - - @responses.activate - def test_gen_bq_table_names(self, _: Mock) -> None: - responses.get( - os.path.join(TDR_ROOT_URL, 'datasets'), - body=json.dumps( - { - 'total': 3, - 'filteredTotal': 3, - 'items': TDR_DATASETS, - }, - ), - ) - for dataset_id, name, project_name, dataset_name in [ - ( - '2dc51ee0-a037-499d-a915-a7c20a0b216d', - 'RP_3053', - 'datarepo-7242affb', - 'datarepo_RP_3053', - ), - ( - 'beef77e8-575b-40e5-9340-a6f10e0bec67', - 'RP_3056', - 'datarepo-5a72e31b', - 'datarepo_RP_3056', - ), - ( - 'c8d74ac4-9a2e-4d3d-a6b5-1f4b433d949f', - 'RP_3059', - 'datarepo-aada2e3b', - 'datarepo_RP_3059', - ), - ]: - responses.get( - os.path.join( - TDR_ROOT_URL, - f'datasets/{dataset_id}?include=ACCESS_INFORMATION', - ), - body=json.dumps( - { - 'id': dataset_id, - 'name': name, - 'description': 'TGG_Ware_DRAGEN_hg38. Dataset automatically created and linked to: RP-3053', - 'defaultProfileId': None, - 'dataProject': None, - 'defaultSnapshotId': None, - 'schema': None, - 'createdDate': '2023-10-05T13:15:27.649760Z', - 'storage': None, - 'secureMonitoringEnabled': False, - 'phsId': None, - 'accessInformation': { - 'bigQuery': { - 'datasetName': dataset_name, - 'datasetId': f'{project_name}:{dataset_name}', - 'projectId': project_name, - 'link': 'https://console.cloud.google.com/bigquery?project=datarepo-7242affb&ws=!datarepo_RP_3053&d=datarepo_RP_3053&p=datarepo-7242affb&page=dataset', - 'tables': [ - { - 'name': 'jointcallset', - 'id': f'{project_name}.{dataset_name}.jointcallset', - 'qualifiedName': 'datarepo-7242affb.datarepo_RP_3053.jointcallset', - 'link': 'https://console.cloud.google.com/bigquery?project=datarepo-7242affb&ws=!datarepo_RP_3053&d=datarepo_RP_3053&p=datarepo-7242affb&page=table&t=jointcallset', - 'sampleQuery': 'SELECT * FROM `datarepo-7242affb.datarepo_RP_3053.jointcallset`', - }, - { - 'name': 'sample', - 'id': f'{project_name}.{dataset_name}.sample', - 'qualifiedName': 'datarepo-7242affb.datarepo_RP_3053.sample', - 'link': 'https://console.cloud.google.com/bigquery?project=datarepo-7242affb&ws=!datarepo_RP_3053&d=datarepo_RP_3053&p=datarepo-7242affb&page=table&t=sample', - 'sampleQuery': 'SELECT * FROM `datarepo-7242affb.datarepo_RP_3053.sample`', - }, - ], - }, - 'parquet': None, - }, - 'cloudPlatform': None, - 'selfHosted': False, - 'properties': None, - 'ingestServiceAccount': None, - 'predictableFileIds': False, - 'tags': [], - 'resourceLocks': { - 'exclusive': None, - 'shared': [], - }, - }, - ), - ) - self.assertCountEqual( - list(gen_bq_table_names()), - [ - 'datarepo-7242affb.datarepo_RP_3053', - 'datarepo-5a72e31b.datarepo_RP_3056', - 'datarepo-aada2e3b.datarepo_RP_3059', - ], - ) - - @patch('loading_pipeline.lib.misc.terra_data_repository.bigquery.Client') - def test_bq_metrics_query_missing_metrics( - self, - mock_bq_client: Mock, - _: Mock, - ) -> None: - mock_bq_client.return_value.query_and_wait.return_value = iter( - [['predicted_sex,contamination_rate,percent_bases_at_20x']], - ) - bq_metrics_query('datarepo-7242affb.datarepo_RP_3053') - self.assertEqual( - mock_bq_client.return_value.query_and_wait.mock_calls[1], - call( - '\n SELECT predicted_sex,contamination_rate,percent_bases_at_20x,NULL AS collaborator_sample_id,NULL AS mean_coverage FROM `datarepo-7242affb.datarepo_RP_3053.sample`;\n ', - ), - ) diff --git a/loading_pipeline/lib/misc/validation_test.py b/loading_pipeline/lib/misc/validation_test.py deleted file mode 100644 index bb368b85a5..0000000000 --- a/loading_pipeline/lib/misc/validation_test.py +++ /dev/null @@ -1,464 +0,0 @@ -import unittest -from unittest.mock import patch - -import hail as hl - -from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType -from loading_pipeline.lib.misc.validation import ( - SeqrValidationError, - validate_allele_depth_length, - validate_allele_type, - validate_expected_contig_frequency, - validate_imported_field_types, - validate_no_duplicate_variants, - validate_sample_type, -) - -TEST_MITO_MT = 'loading_pipeline/var/test/callsets/mito_1.mt' - - -def _mt_from_contigs(contigs): - return ( - hl.MatrixTable.from_parts( - rows={ - 'locus': [ - hl.Locus( - contig=contig, - position=1, - reference_genome='GRCh38', - ) - for contig in contigs - ], - }, - cols={'s': ['sample_1']}, - entries={'HL': [[0.0] for _ in range(len(contigs))]}, - ) - .key_rows_by('locus') - .key_cols_by('s') - ) - - -class ValidationTest(unittest.TestCase): - def test_validate_allele_type(self) -> None: - mt = ( - hl.MatrixTable.from_parts( - rows={ - 'locus': [ - hl.Locus( - contig='chr1', - position=1, - reference_genome='GRCh38', - ), - hl.Locus( - contig='chr1', - position=2, - reference_genome='GRCh38', - ), - hl.Locus( - contig='chr1', - position=3, - reference_genome='GRCh38', - ), - hl.Locus( - contig='chr1', - position=4, - reference_genome='GRCh38', - ), - ], - 'alleles': [ - ['A', 'T'], - # NB: star alleles should pass through this validation just fine, - # but are eventually filtered out upstream. - ['A', '*'], - ['A', '-'], - ['A', ''], - ], - }, - cols={'s': ['sample_1']}, - entries={'HL': [[0.0], [0.0], [0.0], [0.0]]}, - ) - .key_rows_by('locus', 'alleles') - .key_cols_by('s') - ) - self.assertRaisesRegex( - SeqrValidationError, - "Alleles with invalid AlleleType are present in the callset: \\[\\('A', '-'\\), \\('A', ''\\)\\]", - validate_allele_type, - mt, - DatasetType.SNV_INDEL, - ) - - mt = ( - hl.MatrixTable.from_parts( - rows={ - 'locus': [ - hl.Locus( - contig='chr1', - position=1, - reference_genome='GRCh38', - ), - hl.Locus( - contig='chr1', - position=2, - reference_genome='GRCh38', - ), - ], - 'alleles': [ - ['C', ''], - ['A', ''], - ], - }, - cols={'s': ['sample_1']}, - entries={'HL': [[0.0], [0.0]]}, - ) - .key_rows_by('locus', 'alleles') - .key_cols_by('s') - ) - self.assertRaisesRegex( - SeqrValidationError, - 'Alleles with invalid allele are present in the callset. This appears to be a GVCF containing records for sites with no variants.', - validate_allele_type, - mt, - DatasetType.SNV_INDEL, - ) - - def test_validate_allele_depth_length(self) -> None: - mt = ( - hl.MatrixTable.from_parts( - rows={ - 'locus': [ - hl.Locus( - contig='chr1', - position=1, - reference_genome='GRCh38', - ), - hl.Locus( - contig='chr1', - position=2, - reference_genome='GRCh38', - ), - hl.Locus( - contig='chr1', - position=3, - reference_genome='GRCh38', - ), - hl.Locus( - contig='chr1', - position=4, - reference_genome='GRCh38', - ), - ], - 'alleles': [ - ['A', 'T'], - # NB: star alleles should pass through this validation just fine, - # but are eventually filtered out upstream. - ['A', 'TC', 'TG'], - ['A', 'TTT'], - ['A', 'CCC'], - ], - }, - cols={'s': ['sample_1', 'sample_2']}, - entries={ - 'AD': [ - [[1, 0], [1, 0]], - [[1], [1, 0, 1]], - [[1, 0], [1]], - [[1, 0], [1, 0]], - ], - }, - ) - .key_rows_by('locus', 'alleles') - .key_cols_by('s') - ) - self.assertRaisesRegex( - SeqrValidationError, - "Found variants with unequal Allele Depth array lengths over samples \\(first 10, if applicable\\): \\{'1-2-A-TC-TG': \\{1, 3\\}, '1-3-A-TTT': \\{1, 2\\}\\}", - validate_allele_depth_length, - mt, - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - ) - - def test_validate_imported_field_types(self) -> None: - mt = hl.read_matrix_table(TEST_MITO_MT) - validate_imported_field_types(mt, DatasetType.MITO, {}) - mt = mt.annotate_cols(contamination=hl.int32(mt.contamination)) - mt = mt.annotate_entries(DP=hl.float32(mt.DP)) - mt = mt.annotate_rows(vep=hl.dict({'t': '1'})) - self.assertRaisesRegex( - SeqrValidationError, - "Found unexpected field types on MatrixTable after import: \\['contamination: int32', 'DP: float32', 'vep: dict', 'tester: missing'\\]", - validate_imported_field_types, - mt, - DatasetType.MITO, - {'tester': hl.tfloat32}, - ) - - def test_validate_no_duplicate_variants(self) -> None: - mt = ( - hl.MatrixTable.from_parts( - rows={ - 'locus': [ - hl.Locus( - contig='chr1', - position=1, - reference_genome='GRCh38', - ), - hl.Locus( - contig='chr1', - position=2, - reference_genome='GRCh38', - ), - hl.Locus( - contig='chr1', - position=2, - reference_genome='GRCh38', - ), - ], - 'alleles': [ - ['A', 'C'], - ['A', 'C'], - ['A', 'C'], - ], - }, - cols={'s': ['sample_1']}, - entries={'HL': [[0.0], [0.0], [0.0]]}, - ) - .key_rows_by('locus', 'alleles') - .key_cols_by('s') - ) - self.assertRaisesRegex( - SeqrValidationError, - "Variants are present multiple times in the callset: \\['1-2-A-C'\\]", - validate_no_duplicate_variants, - mt, - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - ) - - def test_validate_expected_contig_frequency(self) -> None: - mt = _mt_from_contigs(ReferenceGenome.GRCh38.standard_contigs) - self.assertIsNone( - validate_expected_contig_frequency(mt, ReferenceGenome.GRCh38, 1), - ) - self.assertRaisesRegex( - SeqrValidationError, - 'Missing the following expected contigs', - validate_expected_contig_frequency, - mt, - ReferenceGenome.GRCh37, - 1, - ) - self.assertRaisesRegex( - SeqrValidationError, - 'which is lower than expected minimum count', - validate_expected_contig_frequency, - mt, - ReferenceGenome.GRCh38, - 2, - ) - - # Drop an optional contig - mt = _mt_from_contigs(ReferenceGenome.GRCh38.standard_contigs - {'chrY'}) - self.assertIsNone( - validate_expected_contig_frequency(mt, ReferenceGenome.GRCh38, 1), - ) - - # Drop a non-optional contig - mt = _mt_from_contigs(ReferenceGenome.GRCh38.standard_contigs - {'chr3'}) - self.assertRaisesRegex( - SeqrValidationError, - 'Missing the following expected contigs', - validate_expected_contig_frequency, - mt, - ReferenceGenome.GRCh38, - 1, - ) - - def test_validate_sample_type(self) -> None: - mt = _mt_from_contigs(ReferenceGenome.GRCh38.standard_contigs) - coding_and_noncoding_variants_ht = hl.Table.parallelize( - [ - { - 'locus': hl.Locus( - contig='chr1', - position=1, - reference_genome='GRCh38', - ), - 'coding': True, - 'noncoding': False, - }, - { - 'locus': hl.Locus( - contig='chr2', - position=1, - reference_genome='GRCh38', - ), - 'coding': True, - 'noncoding': False, - }, - { - 'locus': hl.Locus( - contig='chr3', - position=1, - reference_genome='GRCh38', - ), - 'coding': False, - 'noncoding': True, - }, - { - 'locus': hl.Locus( - contig='chr4', - position=1, - reference_genome='GRCh38', - ), - 'coding': False, - 'noncoding': True, - }, - ], - hl.tstruct( - locus=hl.tlocus('GRCh38'), - coding=hl.tbool, - noncoding=hl.tbool, - ), - key='locus', - ) - self.assertIsNone( - validate_sample_type( - mt, - ReferenceGenome.GRCh38, - SampleType.WGS, - ['project_a'], - coding_and_noncoding_variants_ht, - ), - ) - self.assertRaisesRegex( - SeqrValidationError, - 'specified as WES but appears to be WGS', - validate_sample_type, - mt, - ReferenceGenome.GRCh38, - SampleType.WES, - ['project_a'], - coding_and_noncoding_variants_ht, - ) - - # has coding, but not noncoding now. - coding_and_noncoding_variants_ht = hl.Table.parallelize( - [ - { - 'locus': hl.Locus( - contig='chr1', - position=1, - reference_genome='GRCh38', - ), - 'coding': True, - 'noncoding': False, - }, - { - 'locus': hl.Locus( - contig='chr2', - position=1, - reference_genome='GRCh38', - ), - 'coding': True, - 'noncoding': False, - }, - { - 'locus': hl.Locus( - contig='chr2', - position=2, - reference_genome='GRCh38', - ), - 'coding': False, - 'noncoding': True, - }, - ], - hl.tstruct( - locus=hl.tlocus('GRCh38'), - coding=hl.tbool, - noncoding=hl.tbool, - ), - key='locus', - ) - self.assertIsNone( - validate_sample_type( - mt, - ReferenceGenome.GRCh38, - SampleType.WES, - ['project_a'], - coding_and_noncoding_variants_ht, - ), - ) - self.assertRaisesRegex( - SeqrValidationError, - 'specified as WGS but appears to be WES', - validate_sample_type, - mt, - ReferenceGenome.GRCh38, - SampleType.WGS, - ['project_a'], - coding_and_noncoding_variants_ht, - ) - - # has noncoding, but not coding now. - coding_and_noncoding_variants_ht = hl.Table.parallelize( - [ - { - 'locus': hl.Locus( - contig='chr1', - position=1, - reference_genome='GRCh38', - ), - 'coding': False, - 'noncoding': True, - }, - { - 'locus': hl.Locus( - contig='chr2', - position=1, - reference_genome='GRCh38', - ), - 'coding': False, - 'noncoding': True, - }, - { - 'locus': hl.Locus( - contig='chr2', - position=2, - reference_genome='GRCh38', - ), - 'coding': True, - 'noncoding': False, - }, - ], - hl.tstruct( - locus=hl.tlocus('GRCh38'), - coding=hl.tbool, - noncoding=hl.tbool, - ), - key='locus', - ) - self.assertRaisesRegex( - SeqrValidationError, - 'contains noncoding variants but is missing common coding variants', - validate_sample_type, - mt, - ReferenceGenome.GRCh38, - SampleType.WGS, - ['project_a'], - coding_and_noncoding_variants_ht, - ) - - # Validation safe if all projects are to be skipped - with patch('loading_pipeline.lib.misc.validation.Env') as mock_env: - mock_env.SAMPLE_TYPE_VALIDATION_EXCLUDED_PROJECTS = ['project_a'] - self.assertIsNone( - validate_sample_type( - mt, - ReferenceGenome.GRCh38, - SampleType.WGS, - ['project_a'], - coding_and_noncoding_variants_ht, - ), - ) diff --git a/loading_pipeline/lib/misc/vets_test.py b/loading_pipeline/lib/misc/vets_test.py deleted file mode 100644 index b26de113b7..0000000000 --- a/loading_pipeline/lib/misc/vets_test.py +++ /dev/null @@ -1,104 +0,0 @@ -import unittest - -import hail as hl - -from loading_pipeline.lib.misc.io import split_multi_hts -from loading_pipeline.lib.misc.vets import ( - annotate_vets, -) - - -class VetsTest(unittest.TestCase): - def test_annotate_vets(self) -> None: - gatk_mt = hl.MatrixTable.from_parts( - rows={ - 'locus': [ - hl.Locus( - contig='chr1', - position=1, - reference_genome='GRCh38', - ), - ], - 'filters': [ - hl.set(['NO_HQ_GENOTYPES']), - ], - }, - cols={'s': ['sample_1']}, - entries={'HL': [[0.0]]}, - ).key_rows_by('locus') - gatk_mt = annotate_vets(gatk_mt) - dragen_mt = hl.MatrixTable.from_parts( - rows={ - 'locus': [ - hl.Locus( - contig='chr1', - position=1, - reference_genome='GRCh38', - ), - hl.Locus( - contig='chr1', - position=2, - reference_genome='GRCh38', - ), - hl.Locus( - contig='chr1', - position=3, - reference_genome='GRCh38', - ), - hl.Locus( - contig='chr1', - position=4, - reference_genome='GRCh38', - ), - hl.Locus( - contig='chr1', - position=5, - reference_genome='GRCh38', - ), - hl.Locus( - contig='chr1', - position=6, - reference_genome='GRCh38', - ), - ], - 'alleles': [ - ['A', 'T'], - ['A', 'T'], - ['A', 'T'], - ['AC', 'T'], - ['AT', 'ATC'], - ['AG', 'ATG'], - ], - 'filters': [ - hl.set(['NO_HQ_GENOTYPES']), - hl.empty_set(hl.tstr), - hl.missing(hl.tset(hl.tstr)), - hl.set(['NO_HQ_GENOTYPES']), - hl.empty_set(hl.tstr), - hl.set(['NO_HQ_GENOTYPES']), - ], - 'info.CALIBRATION_SENSITIVITY': [ - ['0.999'], - ['0.995'], - ['0.999'], - ['0.98'], - ['0.99'], - ['0.991'], - ], - }, - cols={'s': ['sample_1']}, - entries={'HL': [[0.0], [0.0], [0.0], [0.0], [0.0], [0.0]]}, - ).key_rows_by('locus', 'alleles') - dragen_mt = split_multi_hts(dragen_mt, False) - dragen_mt = annotate_vets(dragen_mt) - self.assertListEqual( - dragen_mt.filters.collect(), - [ - {'NO_HQ_GENOTYPES', 'high_CALIBRATION_SENSITIVITY_SNP'}, - set(), - {'high_CALIBRATION_SENSITIVITY_SNP'}, - {'NO_HQ_GENOTYPES'}, - set(), - {'NO_HQ_GENOTYPES', 'high_CALIBRATION_SENSITIVITY_INDEL'}, - ], - ) diff --git a/loading_pipeline/lib/paths_test.py b/loading_pipeline/lib/paths_test.py deleted file mode 100644 index d271cfee0b..0000000000 --- a/loading_pipeline/lib/paths_test.py +++ /dev/null @@ -1,180 +0,0 @@ -import unittest -from unittest.mock import patch - -import hailtop.fs as hfs - -from loading_pipeline.lib.core import ( - DatasetType, - ReferenceGenome, - SampleType, -) -from loading_pipeline.lib.paths import ( - imported_callset_path, - metadata_for_run_path, - new_variants_table_path, - project_pedigree_path, - project_table_path, - relatedness_check_table_path, - remapped_and_subsetted_callset_path, - sex_check_table_path, - tdr_metrics_path, - validation_errors_for_run_path, - variant_annotations_table_path, -) - -TEST_VCF = 'loading_pipeline/var/test/callsets/1kg_30varia*.vcf' - - -class TestPaths(unittest.TestCase): - def test_project_table_path(self) -> None: - self.assertEqual( - project_table_path( - ReferenceGenome.GRCh38, - DatasetType.MITO, - SampleType.WES, - 'R0652_pipeline_test', - ), - '/var/seqr/pipeline-data/GRCh38/MITO/projects/WES/R0652_pipeline_test.ht', - ) - with ( - patch('loading_pipeline.lib.paths.Env') as mock_env, - ): - mock_env.PIPELINE_DATA_DIR = '/var/bucket/' - self.assertEqual( - project_table_path( - ReferenceGenome.GRCh37, - DatasetType.SNV_INDEL, - SampleType.WES, - 'R0652_pipeline_test', - ), - '/var/bucket/GRCh37/SNV_INDEL/projects/WES/R0652_pipeline_test.ht', - ) - - def test_sex_check_table_path(self) -> None: - self.assertEqual( - sex_check_table_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - '/var/abc.efg/callset.vcf.gz', - ), - '/var/seqr/seqr-loading-temp/GRCh38/SNV_INDEL/sex_check/f92b8ab6b5b8c41fa20d7d49a5626b96dcd2ba79fa6f61eab7ffb80d550d951c.ht', - ) - - def test_relatedness_check_table_path(self) -> None: - self.assertEqual( - relatedness_check_table_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - '/var/abc.efg/callset.vcf.gz', - ), - '/var/seqr/seqr-loading-temp/GRCh38/SNV_INDEL/relatedness_check/f92b8ab6b5b8c41fa20d7d49a5626b96dcd2ba79fa6f61eab7ffb80d550d951c.ht', - ) - - def test_validation_errors_for_run_path(self) -> None: - self.assertEqual( - validation_errors_for_run_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - 'manual__2023-06-26T18:30:09.349671+00:00', - ), - '/var/seqr/pipeline-data/GRCh38/SNV_INDEL/runs/manual__2023-06-26T18:30:09.349671+00:00/validation_errors.json', - ) - - def test_metadata_for_run_path(self) -> None: - self.assertEqual( - metadata_for_run_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - 'manual__2023-06-26T18:30:09.349671+00:00', - ), - '/var/seqr/pipeline-data/GRCh38/SNV_INDEL/runs/manual__2023-06-26T18:30:09.349671+00:00/metadata.json', - ) - - def test_variant_annotations_table_path(self) -> None: - self.assertEqual( - variant_annotations_table_path( - ReferenceGenome.GRCh38, - DatasetType.GCNV, - ), - '/var/seqr/pipeline-data/GRCh38/GCNV/annotations.ht', - ) - - def test_remapped_and_subsetted_callset_path(self) -> None: - self.assertEqual( - remapped_and_subsetted_callset_path( - ReferenceGenome.GRCh38, - DatasetType.GCNV, - '/var/abc.efg/callset.vcf.gz', - 'R0111_tgg_bblanken_wes', - ), - '/var/seqr/seqr-loading-temp/GRCh38/GCNV/remapped_and_subsetted_callsets/R0111_tgg_bblanken_wes/f92b8ab6b5b8c41fa20d7d49a5626b96dcd2ba79fa6f61eab7ffb80d550d951c.mt', - ) - self.assertEqual( - remapped_and_subsetted_callset_path( - ReferenceGenome.GRCh38, - DatasetType.GCNV, - '/var/abc.efg/callset/*.vcf.gz', - 'R0111_tgg_bblanken_wes', - ), - '/var/seqr/seqr-loading-temp/GRCh38/GCNV/remapped_and_subsetted_callsets/R0111_tgg_bblanken_wes/26f481b386721f9889250c6549905660728ec9f77be4b8f7eeb6c4facc76282e.mt', - ) - - def test_imported_callset_path(self) -> None: - self.assertEqual( - imported_callset_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - '/var/abc.efg/callset.vcf.gz', - ), - '/var/seqr/seqr-loading-temp/GRCh38/SNV_INDEL/imported_callsets/f92b8ab6b5b8c41fa20d7d49a5626b96dcd2ba79fa6f61eab7ffb80d550d951c.mt', - ) - - with patch('loading_pipeline.lib.paths.hfs.ls') as mock_ls: - mock_ls.return_value = [ - hfs.stat_result.FileListEntry( - path='loading_pipeline/var/test/callsets/1kg_30variants.vcf', - owner=None, - size=1732033623.804012, - typ=hfs.stat_result.FileType(2), - modification_time=1732033000, - ), - ] - self.assertEqual( - imported_callset_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_VCF, - ), - '/var/seqr/seqr-loading-temp/GRCh38/SNV_INDEL/imported_callsets/01327e46c8747f15feaad2c08875b928c274dcb248ad40837ea3f49d8b4dedfb.mt', - ) - - def test_tdr_metrics_path(self) -> None: - self.assertEqual( - tdr_metrics_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - 'datarepo-7242affb.datarepo_RP_3053', - ), - '/var/seqr/seqr-loading-temp/GRCh38/SNV_INDEL/tdr_metrics/datarepo-7242affb.datarepo_RP_3053.tsv', - ) - - def test_new_variants_table_path(self) -> None: - self.assertEqual( - new_variants_table_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - 'manual__2023-06-26T18:30:09.349671+00:00', - ), - '/var/seqr/pipeline-data/GRCh38/SNV_INDEL/runs/manual__2023-06-26T18:30:09.349671+00:00/new_variants.ht', - ) - - def test_project_pedigree_path(self) -> None: - self.assertEqual( - project_pedigree_path( - ReferenceGenome.GRCh38, - DatasetType.GCNV, - SampleType.WES, - 'R0652_pipeline_test', - ), - '/var/seqr/seqr-loading-temp/GRCh38/GCNV/pedigrees/WES/R0652_pipeline_test_pedigree.tsv', - ) diff --git a/loading_pipeline/lib/reference_datasets/gnomad_exomes_test.py b/loading_pipeline/lib/reference_datasets/gnomad_exomes_test.py deleted file mode 100644 index 639dc6d894..0000000000 --- a/loading_pipeline/lib/reference_datasets/gnomad_exomes_test.py +++ /dev/null @@ -1,72 +0,0 @@ -import unittest -from unittest.mock import patch - -import hail as hl - -from loading_pipeline.lib.core.definitions import ReferenceGenome -from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset - -GNOMAD_EXOMES_37_PATH = ( - 'loading_pipeline/var/test/reference_datasets/raw/gnomad_exomes_37.ht' -) -GNOMAD_EXOMES_38_PATH = ( - 'loading_pipeline/var/test/reference_datasets/raw/gnomad_exomes_38.ht' -) - - -class GnomadTest(unittest.TestCase): - def test_gnomad_exomes_37(self): - with patch.object( - ReferenceDataset, - 'path', - return_value=GNOMAD_EXOMES_37_PATH, - ): - ht = ReferenceDataset.gnomad_exomes.get_ht(ReferenceGenome.GRCh37) - self.assertEqual( - ht.collect(), - [ - hl.Struct( - locus=hl.Locus( - contig='1', - position=12586, - reference_genome='GRCh37', - ), - alleles=['C', 'T'], - AF=0.0005589714855886996, - AN=3578, - AC=2, - Hom=0, - AF_POPMAX_OR_GLOBAL=0.0022026430815458298, - FAF_AF=9.839000267675146e-05, - Hemi=0, - ), - ], - ) - - def test_gnomad_exomes_38(self): - with patch.object( - ReferenceDataset, - 'path', - return_value=GNOMAD_EXOMES_38_PATH, - ): - ht = ReferenceDataset.gnomad_exomes.get_ht(ReferenceGenome.GRCh38) - self.assertEqual( - ht.collect(), - [ - hl.Struct( - locus=hl.Locus( - contig='chr1', - position=12138, - reference_genome='GRCh38', - ), - alleles=['C', 'A'], - AF=0.00909090880304575, - AN=110, - AC=1, - Hom=0, - AF_POPMAX_OR_GLOBAL=0.009803921915590763, - FAF_AF=0.0, - Hemi=0, - ), - ], - ) diff --git a/loading_pipeline/lib/reference_datasets/gnomad_genomes_test.py b/loading_pipeline/lib/reference_datasets/gnomad_genomes_test.py deleted file mode 100644 index df637c2fda..0000000000 --- a/loading_pipeline/lib/reference_datasets/gnomad_genomes_test.py +++ /dev/null @@ -1,72 +0,0 @@ -import unittest -from unittest.mock import patch - -import hail as hl - -from loading_pipeline.lib.core.definitions import ReferenceGenome -from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset - -GNOMAD_GENOMES_37_PATH = ( - 'loading_pipeline/var/test/reference_datasets/raw/gnomad_genomes_37.ht' -) -GNOMAD_GENOMES_38_PATH = ( - 'loading_pipeline/var/test/reference_datasets/raw/gnomad_genomes_38.ht' -) - - -class GnomadTest(unittest.TestCase): - def test_gnomad_genomes_37(self): - with patch.object( - ReferenceDataset, - 'path', - return_value=GNOMAD_GENOMES_37_PATH, - ): - ht = ReferenceDataset.gnomad_genomes.get_ht(ReferenceGenome.GRCh37) - self.assertEqual( - ht.collect(), - [ - hl.Struct( - locus=hl.Locus( - contig='1', - position=10131, - reference_genome='GRCh37', - ), - alleles=['CT', 'C'], - AF=3.6635403375839815e-05, - AN=27296, - AC=1, - Hom=0, - AF_POPMAX_OR_GLOBAL=3.6635403375839815e-05, - FAF_AF=0.0, - Hemi=0, - ), - ], - ) - - def test_gnomad_genomes_38(self): - with patch.object( - ReferenceDataset, - 'path', - return_value=GNOMAD_GENOMES_38_PATH, - ): - ht = ReferenceDataset.gnomad_genomes.get_ht(ReferenceGenome.GRCh38) - self.assertEqual( - ht.collect(), - [ - hl.Struct( - locus=hl.Locus( - contig='chr1', - position=10057, - reference_genome='GRCh38', - ), - alleles=['A', 'C'], - AF=2.642333674884867e-05, - AN=113536, - AC=3, - Hom=0, - AF_POPMAX_OR_GLOBAL=3.779861071961932e-05, - FAF_AF=7.019999884505523e-06, - Hemi=0, - ), - ], - ) diff --git a/loading_pipeline/lib/reference_datasets/gnomad_svs_test.py b/loading_pipeline/lib/reference_datasets/gnomad_svs_test.py deleted file mode 100644 index bfd7c89d11..0000000000 --- a/loading_pipeline/lib/reference_datasets/gnomad_svs_test.py +++ /dev/null @@ -1,93 +0,0 @@ -import unittest -from unittest.mock import patch - -import hail as hl - -from loading_pipeline.lib.core import ReferenceGenome -from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset - -TEST_GNOMAD_SVS_RAW_HT = ( - 'loading_pipeline/var/test/reference_datasets/raw/gnomad_svs_from_vcf.ht' -) - - -class GnomadSVsTest(unittest.TestCase): - @patch('loading_pipeline.lib.reference_datasets.gnomad_svs.vcf_to_ht') - def test_gnomad_svs(self, mock_vcf_to_ht): - mock_vcf_to_ht.return_value = hl.read_table(TEST_GNOMAD_SVS_RAW_HT) - ht = ReferenceDataset.gnomad_svs.get_ht(ReferenceGenome.GRCh38) - self.assertEqual( - ht.collect(), - [ - hl.Struct( - KEY='gnomAD-SV_v3_BND_chr1_1a45f73a', - locus=hl.Locus( - contig='chr1', - position=10434, - reference_genome=ReferenceGenome.GRCh38, - ), - alleles=['N', ''], - AF=0.11413399875164032, - AC=8474, - AN=74246, - N_HET=8426, - N_HOM=24, - ), - hl.Struct( - KEY='gnomAD-SV_v3_BND_chr1_3fa36917', - locus=hl.Locus( - contig='chr1', - position=10440, - reference_genome=ReferenceGenome.GRCh38, - ), - alleles=['N', ''], - AF=0.004201000090688467, - AC=466, - AN=110936, - N_HET=466, - N_HOM=0, - ), - hl.Struct( - KEY='gnomAD-SV_v3_BND_chr1_7bbf34b5', - locus=hl.Locus( - contig='chr1', - position=10464, - reference_genome=ReferenceGenome.GRCh38, - ), - alleles=['N', ''], - AF=0.03698499873280525, - AC=3119, - AN=84332, - N_HET=3115, - N_HOM=2, - ), - hl.Struct( - KEY='gnomAD-SV_v3_BND_chr1_933a2971', - locus=hl.Locus( - contig='chr1', - position=10450, - reference_genome=ReferenceGenome.GRCh38, - ), - alleles=['N', ''], - AF=0.3238990008831024, - AC=21766, - AN=67200, - N_HET=21616, - N_HOM=75, - ), - hl.Struct( - KEY='gnomAD-SV_v3_DUP_chr1_01c2781c', - locus=hl.Locus( - contig='chr1', - position=10000, - reference_genome=ReferenceGenome.GRCh38, - ), - alleles=['N', ''], - AF=0.0019970000721514225, - AC=139, - AN=69594, - N_HET=139, - N_HOM=0, - ), - ], - ) diff --git a/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster_test.py b/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster_test.py deleted file mode 100644 index 6634feea8c..0000000000 --- a/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster_test.py +++ /dev/null @@ -1,162 +0,0 @@ -import unittest -from types import SimpleNamespace -from unittest.mock import Mock, call, patch - -import google.api_core.exceptions -import google.cloud.dataproc_v1.types.clusters -import luigi - -from loading_pipeline.lib.core import DatasetType, ReferenceGenome -from loading_pipeline.lib.misc.gcp import SOCIAL_AUTH_GOOGLE_OAUTH2_SCOPE -from loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster import ( - CreateDataprocClusterTask, -) - - -@patch.multiple( - 'loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster.Env', - GCLOUD_PROJECT='proj', - GCLOUD_REGION='us-a', -) -@patch( - 'loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster.get_service_account_credentials', - return_value=SimpleNamespace( - service_account_email='test@serviceaccount.com', - scopes=SOCIAL_AUTH_GOOGLE_OAUTH2_SCOPE, - ), -) -@patch( - 'loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster.dataproc.ClusterControllerClient', -) -class CreateDataprocClusterTaskTest(unittest.TestCase): - def test_spinup_cluster_already_exists_failed( - self, - mock_cluster_controller: Mock, - *_: Mock, - ) -> None: - mock_client = mock_cluster_controller.return_value - mock_client.get_cluster.return_value = SimpleNamespace( - status=SimpleNamespace( - state=google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.ERROR, - ), - cluster_name='abc', - ) - mock_client.create_cluster.side_effect = ( - google.api_core.exceptions.AlreadyExists('cluster exists') - ) - worker = luigi.worker.Worker() - task = CreateDataprocClusterTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - run_id='2', - ) - worker.add(task) - worker.run() - self.assertFalse(task.complete()) - - def test_spinup_cluster_already_exists_success( - self, - mock_cluster_controller: Mock, - *_: Mock, - ) -> None: - mock_client = mock_cluster_controller.return_value - mock_client.get_cluster.return_value = SimpleNamespace( - status=SimpleNamespace( - state=google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.RUNNING, - ), - ) - mock_client.create_cluster.side_effect = ( - google.api_core.exceptions.AlreadyExists('cluster exists') - ) - worker = luigi.worker.Worker() - task = CreateDataprocClusterTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - run_id='3', - ) - worker.add(task) - worker.run() - self.assertTrue(task.complete()) - - @patch('loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster.logger') - def test_spinup_cluster_doesnt_exist_failed( - self, - mock_logger: Mock, - mock_cluster_controller: Mock, - *_: Mock, - ) -> None: - mock_client = mock_cluster_controller.return_value - mock_client.get_cluster.side_effect = [ - google.api_core.exceptions.NotFound( - 'cluster not found', - ), - google.api_core.exceptions.NotFound( - 'cluster not found', - ), - SimpleNamespace( - status=SimpleNamespace( - state=google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.CREATING, - ), - ), - SimpleNamespace( - status=SimpleNamespace( - state=google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.ERROR, - ), - cluster_name='dataproc-cluster-5', - cluster_uuid='12345', - ), - ] - worker = luigi.worker.Worker() - task = CreateDataprocClusterTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - run_id='4', - ) - worker.add(task) - luigi_task_result = worker.run() - self.assertEqual(luigi_task_result, False) - mock_logger.info.assert_has_calls([call('Waiting for cluster spinup')]) - - @patch('loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster.logger') - def test_spinup_cluster_doesnt_exist_success( - self, - mock_logger: Mock, - mock_cluster_controller: Mock, - *_: Mock, - ) -> None: - mock_client = mock_cluster_controller.return_value - mock_client.get_cluster.side_effect = [ - google.api_core.exceptions.NotFound( - 'cluster not found', - ), - google.api_core.exceptions.NotFound( - 'cluster not found', - ), - SimpleNamespace( - status=SimpleNamespace( - state=google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.CREATING, - ), - ), - SimpleNamespace( - status=SimpleNamespace( - state=google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.RUNNING, - ), - cluster_name='dataproc-cluster-5', - cluster_uuid='12345', - ), - ] - mock_client.create_cluster.side_effect = None - worker = luigi.worker.Worker() - task = CreateDataprocClusterTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - run_id='5', - ) - worker.add(task) - worker.run() - mock_logger.info.assert_has_calls( - [ - call('Waiting for cluster spinup'), - call('Created cluster dataproc-cluster-5 with cluster uuid: 12345'), - ], - ) diff --git a/loading_pipeline/lib/tasks/dataproc/misc_test.py b/loading_pipeline/lib/tasks/dataproc/misc_test.py deleted file mode 100644 index 63ffafb8a1..0000000000 --- a/loading_pipeline/lib/tasks/dataproc/misc_test.py +++ /dev/null @@ -1,51 +0,0 @@ -import unittest -from unittest.mock import Mock, patch - -from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType -from loading_pipeline.lib.tasks.dataproc.misc import to_kebab_str_args -from loading_pipeline.lib.tasks.dataproc.run_pipeline_on_dataproc import ( - RunPipelineOnDataprocTask, -) - - -@patch( - 'loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc.dataproc.JobControllerClient', -) -class MiscTest(unittest.TestCase): - def test_to_kebab_str_args(self, _: Mock): - t = RunPipelineOnDataprocTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - sample_type=SampleType.WGS, - callset_path='test_callset', - project_guids=['R0113_test_project'], - run_id='a_misc_run', - attempt_id=0, - ) - self.assertListEqual( - to_kebab_str_args(t), - [ - '--reference-genome', - 'GRCh38', - '--dataset-type', - 'SNV_INDEL', - '--sample-type', - 'WGS', - '--callset-path', - 'test_callset', - '--project-guids', - '["R0113_test_project"]', - '--skip-check-sex-and-relatedness', - 'False', - '--skip-expect-tdr-metrics', - 'False', - '--validations-to-skip', - '[]', - '--is-new-gcnv-joint-call', - 'False', - '--run-id', - 'a_misc_run', - '--attempt-id', - '0', - ], - ) diff --git a/loading_pipeline/lib/tasks/dataproc/run_pipeline_on_dataproc_test.py b/loading_pipeline/lib/tasks/dataproc/run_pipeline_on_dataproc_test.py deleted file mode 100644 index a09289a85a..0000000000 --- a/loading_pipeline/lib/tasks/dataproc/run_pipeline_on_dataproc_test.py +++ /dev/null @@ -1,184 +0,0 @@ -import unittest -from types import SimpleNamespace -from unittest.mock import Mock, call, patch - -import google.api_core.exceptions -import google.cloud.dataproc_v1.types.jobs -import luigi - -from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType -from loading_pipeline.lib.tasks.dataproc.run_pipeline_on_dataproc import ( - RunPipelineOnDataprocTask, -) -from loading_pipeline.lib.test.mock_complete_task import MockCompleteTask - - -@patch( - 'loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc.CreateDataprocClusterTask', -) -@patch( - 'loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc.dataproc.JobControllerClient', -) -class WriteSuccessFileOnDataprocTaskTest(unittest.TestCase): - @patch('loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc.logger') - def test_job_already_exists_failed( - self, - mock_logger: Mock, - mock_job_controller_client: Mock, - mock_create_dataproc_cluster: Mock, - ) -> None: - mock_create_dataproc_cluster.return_value = MockCompleteTask() - mock_client = mock_job_controller_client.return_value - mock_client.get_job.return_value = SimpleNamespace( - status=SimpleNamespace( - state=google.cloud.dataproc_v1.types.jobs.JobStatus.State.ERROR, - details='Google Cloud Dataproc Agent reports job failure. If logs are available, they can be found at...', - ), - ) - mock_client.submit_job_as_operation.side_effect = ( - google.api_core.exceptions.AlreadyExists('job exists') - ) - worker = luigi.worker.Worker() - task = RunPipelineOnDataprocTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - sample_type=SampleType.WGS, - callset_path='test_callset', - project_guids=['R0113_test_project'], - run_id='manual__2024-04-03', - attempt_id=0, - ) - worker.add(task) - worker.run() - self.assertFalse(task.complete()) - mock_logger.error.assert_has_calls( - [ - call( - 'Job RunPipelineTask-38-SNV-INDEL-manual__2024-04-03-0 entered ERROR state', - ), - ], - ) - - def test_job_already_exists_success( - self, - mock_job_controller_client: Mock, - mock_create_dataproc_cluster: Mock, - ) -> None: - mock_create_dataproc_cluster.return_value = MockCompleteTask() - mock_client = mock_job_controller_client.return_value - mock_client.get_job.return_value = SimpleNamespace( - status=SimpleNamespace( - state=google.cloud.dataproc_v1.types.jobs.JobStatus.State.DONE, - ), - ) - worker = luigi.worker.Worker() - task = RunPipelineOnDataprocTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - sample_type=SampleType.WGS, - callset_path='test_callset', - project_guids=['R0113_test_project'], - run_id='manual__2024-04-04', - attempt_id=0, - ) - worker.add(task) - worker.run() - self.assertTrue(task.complete()) - - @patch('loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc.logger') - def test_job_failed( - self, - mock_logger: Mock, - mock_job_controller_client: Mock, - mock_create_dataproc_cluster: Mock, - ) -> None: - mock_create_dataproc_cluster.return_value = MockCompleteTask() - mock_client = mock_job_controller_client.return_value - mock_client.get_job.side_effect = [ - google.api_core.exceptions.NotFound( - 'job not found', - ), - google.api_core.exceptions.NotFound( - 'job not found', - ), - SimpleNamespace( - status=SimpleNamespace( - state=google.cloud.dataproc_v1.types.jobs.JobStatus.State.PENDING, - ), - ), - SimpleNamespace( - status=SimpleNamespace( - state=google.cloud.dataproc_v1.types.jobs.JobStatus.State.ERROR, - ), - ), - ] - worker = luigi.worker.Worker() - task = RunPipelineOnDataprocTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - sample_type=SampleType.WGS, - callset_path='test_callset', - project_guids=['R0113_test_project'], - run_id='manual__2024-04-05', - attempt_id=1, - ) - worker.add(task) - luigi_task_result = worker.run() - self.assertEqual(luigi_task_result, False) - mock_logger.info.assert_has_calls( - [ - call( - 'Waiting for Job completion RunPipelineTask-38-SNV-INDEL-manual__2024-04-05-1', - ), - ], - ) - - @patch('loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc.logger') - def test_job_success( - self, - mock_logger: Mock, - mock_job_controller_client: Mock, - mock_create_dataproc_cluster: Mock, - ) -> None: - mock_create_dataproc_cluster.return_value = MockCompleteTask() - mock_client = mock_job_controller_client.return_value - mock_client.get_job.side_effect = [ - google.api_core.exceptions.NotFound( - 'job not found', - ), - google.api_core.exceptions.NotFound( - 'job not found', - ), - SimpleNamespace( - status=SimpleNamespace( - state=google.cloud.dataproc_v1.types.jobs.JobStatus.State.PENDING, - ), - ), - SimpleNamespace( - status=SimpleNamespace( - state=google.cloud.dataproc_v1.types.jobs.JobStatus.State.DONE, - ), - ), - ] - worker = luigi.worker.Worker() - task = RunPipelineOnDataprocTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - sample_type=SampleType.WGS, - callset_path='test_callset', - project_guids=['R0113_test_project'], - run_id='manual__2024-04-06', - attempt_id=0, - ) - worker.add(task) - worker.run() - mock_logger.info.assert_has_calls( - [ - call( - 'Waiting for Job completion RunPipelineTask-38-SNV-INDEL-manual__2024-04-06-0', - ), - call( - 'Job RunPipelineTask-38-SNV-INDEL-manual__2024-04-06-0 is complete', - ), - ], - ) diff --git a/loading_pipeline/lib/tasks/exports/misc_test.py b/loading_pipeline/lib/tasks/exports/misc_test.py deleted file mode 100644 index f0324db627..0000000000 --- a/loading_pipeline/lib/tasks/exports/misc_test.py +++ /dev/null @@ -1,484 +0,0 @@ -import unittest - -import hail as hl - -from loading_pipeline.lib.core import ( - DatasetType, - ReferenceGenome, -) -from loading_pipeline.lib.tasks.exports.misc import ( - camelcase_array_structexpression_fields, - sorted_hl_struct, - unmap_formatting_annotation_enums, -) - -TEST_SNV_INDEL_ANNOTATIONS = ( - 'loading_pipeline/var/test/exports/GRCh38/SNV_INDEL/annotations.ht' -) -TEST_GRCH37_SNV_INDEL_ANNOTATIONS = ( - 'loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/annotations.ht' -) - - -class MiscTest(unittest.TestCase): - def test_unmap_formatting_annotation_enums(self) -> None: - ht = hl.read_table(TEST_SNV_INDEL_ANNOTATIONS) - ht = unmap_formatting_annotation_enums( - ht, - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - ) - self.assertCountEqual( - list(ht.globals.enums.collect()[0].keys()), - [ - 'clinvar', - 'hgmd', - 'screen', - 'dbnsfp', - 'gnomad_exomes', - 'gnomad_non_coding_constraint', - 'splice_ai', - 'exac', - 'topmed', - 'gnomad_genomes', - 'eigen', - ], - ) - ht = ht.annotate( - sorted_transcript_consequences=[ht.sorted_transcript_consequences[0]], - ) - self.assertEqual( - ht.collect()[0], - hl.Struct( - key_=0, - locus=hl.Locus( - contig='chr1', - position=876499, - reference_genome='GRCh38', - ), - alleles=['A', 'G'], - clinvar=hl.Struct( - alleleId=929885, - conflictingPathogenicities=None, - goldStars=1, - submitters=['Labcorp Genetics (formerly Invitae), Labcorp'], - conditions=['not provided'], - assertion_ids=[], - pathogenicity_id=12, - ), - rg37_locus=hl.Locus( - contig=1, - position=874501, - reference_genome='GRCh37', - ), - rsid=None, - sorted_transcript_consequences=[ - hl.Struct( - amino_acids='S/L', - canonical=1, - codons='tCg/tTg', - gene_id='ENSG00000187634', - hgvsc='ENST00000616016.5:c.1049C>T', - hgvsp='ENSP00000478421.2:p.Ser350Leu', - transcript_id='ENST00000616016', - mane_select='NM_001385641.1', - mane_plus_clinical=None, - exon=hl.Struct(index=6, total=14), - intron=None, - refseq_transcript_id='NM_001385641.1', - alphamissense=hl.Struct(pathogenicity=None), - loftee=hl.Struct(is_lof_nagnag=None, lof_filters=None), - spliceregion=hl.Struct( - extended_intronic_splice_region_variant=False, - ), - utrannotator=hl.Struct( - existing_inframe_oorfs=None, - existing_outofframe_oorfs=None, - existing_uorfs=None, - fiveutr_annotation=hl.Struct( - type='OutOfFrame_oORF', - KozakContext='CGCATGC', - KozakStrength='Weak', - DistanceToCDS=41, - CapDistanceToStart=None, - DistanceToStop=None, - Evidence=None, - AltStop=None, - AltStopDistanceToCDS=None, - FrameWithCDS=None, - StartDistanceToCDS=None, - newSTOPDistanceToCDS=None, - alt_type=None, - alt_type_length=None, - ref_StartDistanceToCDS=None, - ref_type=None, - ref_type_length=None, - ), - fiveutr_consequence=None, - ), - biotype='protein_coding', - consequence_terms=['missense_variant'], - ), - ], - variant_id='1-876499-A-G', - xpos=1000876499, - gt_stats=hl.Struct(AC=47, AN=81784, AF=0.0005746845272369683, hom=1), - CAID='CA502654', - check_ref=False, - sorted_regulatory_feature_consequences=[ - hl.Struct( - regulatory_feature_id='ENSR00000344437', - biotype='CTCF_binding_site', - consequence_terms=['regulatory_region_variant'], - ), - ], - sorted_motif_feature_consequences=[ - hl.Struct( - motif_feature_id='ENSM00493959715', - consequence_terms=['TF_binding_site_variant'], - ), - ], - gnomad_non_coding_constraint=hl.Struct(z_score=None), - hgmd=hl.Struct(accession='abcdefg', class_id=3), - gnomad_exomes=hl.Struct( - AF=0.0006690866430290043, - AN=1440770, - AC=964, - Hom=0, - AF_POPMAX_OR_GLOBAL=0.0008023773552849889, - FAF_AF=0.000633420015219599, - Hemi=0, - ), - gnomad_genomes=hl.Struct( - AF=0.0002759889466688037, - AN=152180, - AC=42, - Hom=0, - AF_POPMAX_OR_GLOBAL=0.10000000149011612, - FAF_AF=0.0002092500071739778, - Hemi=0, - ), - screen=hl.Struct(region_type_ids=[]), - dbnsfp=hl.Struct( - PrimateAI_score=0.5918066501617432, - fathmm_MKL_coding_score=0.7174800038337708, - CADD_phred=23.5, - SIFT_score=0.0010000000474974513, - REVEL_score=0.3109999895095825, - Polyphen2_HVAR_score=0.164000004529953, - VEST4_score=0.39500001072883606, - MPC_score=0.01291007362306118, - MutPred_score=None, - MutationTaster_pred_id=0, - ), - topmed=hl.Struct( - AC=41, - AF=0.00032651599030941725, - AN=125568, - Hom=0, - Het=41, - ), - exac=hl.Struct( - AF_POPMAX=0.0007150234305299819, - AF=0.00019039999460801482, - AC_Adj=20, - AC_Het=20, - AC_Hom=0, - AC_Hemi=None, - AN_Adj=47974, - ), - splice_ai=hl.Struct(delta_score=0.0, splice_consequence_id=4), - eigen=hl.Struct(Eigen_phred=2.628000020980835), - ), - ) - ht = hl.read_table(TEST_GRCH37_SNV_INDEL_ANNOTATIONS) - ht = unmap_formatting_annotation_enums( - ht, - ReferenceGenome.GRCh37, - DatasetType.SNV_INDEL, - ) - self.assertCountEqual( - list(ht.globals.enums.collect()[0].keys()), - [ - 'clinvar', - 'hgmd', - 'dbnsfp', - 'gnomad_exomes', - 'splice_ai', - 'exac', - 'topmed', - 'gnomad_genomes', - 'eigen', - ], - ) - ht = ht.annotate( - sorted_transcript_consequences=[ht.sorted_transcript_consequences[0]], - ) - self.assertEqual( - ht.collect()[0], - hl.Struct( - locus=hl.Locus(contig=1, position=69134, reference_genome='GRCh37'), - alleles=['A', 'G'], - clinvar=hl.Struct( - alleleId=2193183, - conflictingPathogenicities=None, - goldStars=1, - submitters=['Ambry Genetics'], - conditions=['not specified'], - assertion_ids=[], - pathogenicity_id=14, - ), - rsid=None, - sorted_transcript_consequences=[ - hl.Struct( - amino_acids='E/G', - canonical=1, - codons='gAa/gGa', - gene_id='ENSG00000186092', - hgvsc='ENST00000335137.3:c.44A>G', - hgvsp='ENSP00000334393.3:p.Glu15Gly', - transcript_id='ENST00000335137', - is_lof_nagnag=None, - biotype='protein_coding', - consequence_terms=['missense_variant'], - lof_filters=None, - ), - ], - variant_id='1-69134-A-G', - xpos=1000069134, - gt_stats=hl.Struct(AC=25, AN=1246, AF=0.020064204931259155, hom=10), - CAID='CA502008', - rg38_locus=hl.Locus( - contig='chr1', - position=69134, - reference_genome='GRCh38', - ), - hgmd=None, - gnomad_exomes=hl.Struct( - AF=0.026665963232517242, - AN=18938, - AC=505, - Hom=127, - AF_POPMAX_OR_GLOBAL=0.08191808313131332, - FAF_AF=0.02474386990070343, - Hemi=0, - ), - gnomad_genomes=hl.Struct( - AF=0.0001722949673421681, - AN=5804, - AC=1, - Hom=0, - AF_POPMAX_OR_GLOBAL=0.0005662514013238251, - FAF_AF=0.0, - Hemi=0, - ), - dbnsfp=hl.Struct( - PrimateAI_score=0.37232041358947754, - fathmm_MKL_coding_score=0.056940000504255295, - CADD_phred=15.880000114440918, - SIFT_score=0.1289999932050705, - REVEL_score=0.07500000298023224, - Polyphen2_HVAR_score=0.0010000000474974513, - VEST4_score=0.10700000077486038, - MPC_score=1.8921889066696167, - MutPred_score=0.3779999911785126, - MutationTaster_pred_id=2, - ), - topmed=hl.Struct( - AC=95, - AF=0.0007565619889646769, - AN=125568, - Hom=0, - Het=95, - ), - exac=hl.Struct( - AF_POPMAX=None, - AF=0.0016550000291317701, - AC_Adj=0, - AC_Het=0, - AC_Hom=0, - AC_Hemi=None, - AN_Adj=66, - ), - eigen=hl.Struct(Eigen_phred=1.0019999742507935), - splice_ai=hl.Struct( - delta_score=0.019999999552965164, - splice_consequence_id=2, - ), - key_=1424, - ), - ) - - def test_camelcase_array_structexpression_fields(self) -> None: - ht = hl.read_table(TEST_SNV_INDEL_ANNOTATIONS) - ht = unmap_formatting_annotation_enums( - ht, - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - ) - ht = camelcase_array_structexpression_fields( - ht, - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - ) - ht = ht.annotate( - sortedTranscriptConsequences=[ht.sortedTranscriptConsequences[0]], - ) - self.assertEqual( - ht.collect()[0], - hl.Struct( - key_=0, - locus=hl.Locus( - contig='chr1', - position=876499, - reference_genome='GRCh38', - ), - alleles=['A', 'G'], - clinvar=hl.Struct( - alleleId=929885, - conflictingPathogenicities=None, - goldStars=1, - submitters=['Labcorp Genetics (formerly Invitae), Labcorp'], - conditions=['not provided'], - assertion_ids=[], - pathogenicity_id=12, - ), - rg37_locus=hl.Locus( - contig=1, - position=874501, - reference_genome='GRCh37', - ), - rsid=None, - variant_id='1-876499-A-G', - xpos=1000876499, - gt_stats=hl.Struct(AC=47, AN=81784, AF=0.0005746845272369683, hom=1), - CAID='CA502654', - check_ref=False, - gnomad_non_coding_constraint=hl.Struct(z_score=None), - hgmd=hl.Struct(accession='abcdefg', class_id=3), - gnomad_exomes=hl.Struct( - AF=0.0006690866430290043, - AN=1440770, - AC=964, - Hom=0, - AF_POPMAX_OR_GLOBAL=0.0008023773552849889, - FAF_AF=0.000633420015219599, - Hemi=0, - ), - gnomad_genomes=hl.Struct( - AF=0.0002759889466688037, - AN=152180, - AC=42, - Hom=0, - AF_POPMAX_OR_GLOBAL=0.10000000149011612, - FAF_AF=0.0002092500071739778, - Hemi=0, - ), - screen=hl.Struct(region_type_ids=[]), - dbnsfp=hl.Struct( - PrimateAI_score=0.5918066501617432, - fathmm_MKL_coding_score=0.7174800038337708, - CADD_phred=23.5, - SIFT_score=0.0010000000474974513, - REVEL_score=0.3109999895095825, - Polyphen2_HVAR_score=0.164000004529953, - VEST4_score=0.39500001072883606, - MPC_score=0.01291007362306118, - MutPred_score=None, - MutationTaster_pred_id=0, - ), - topmed=hl.Struct( - AC=41, - AF=0.00032651599030941725, - AN=125568, - Hom=0, - Het=41, - ), - exac=hl.Struct( - AF_POPMAX=0.0007150234305299819, - AF=0.00019039999460801482, - AC_Adj=20, - AC_Het=20, - AC_Hom=0, - AC_Hemi=None, - AN_Adj=47974, - ), - splice_ai=hl.Struct( - delta_score=0.0, - splice_consequence_id=4, - ), - eigen=hl.Struct(Eigen_phred=2.628000020980835), - sortedTranscriptConsequences=[ - hl.Struct( - aminoAcids='S/L', - canonical=1, - codons='tCg/tTg', - geneId='ENSG00000187634', - hgvsc='ENST00000616016.5:c.1049C>T', - hgvsp='ENSP00000478421.2:p.Ser350Leu', - transcriptId='ENST00000616016', - maneSelect='NM_001385641.1', - manePlusClinical=None, - exon=hl.Struct(index=6, total=14), - intron=None, - refseqTranscriptId='NM_001385641.1', - alphamissense=hl.Struct(pathogenicity=None), - loftee=hl.Struct(isLofNagnag=None, lofFilters=None), - spliceregion=hl.Struct( - extended_intronic_splice_region_variant=False, - ), - utrannotator=hl.Struct( - existingInframeOorfs=None, - existingOutofframeOorfs=None, - existingUorfs=None, - fiveutrAnnotation=hl.Struct( - type='OutOfFrame_oORF', - KozakContext='CGCATGC', - KozakStrength='Weak', - DistanceToCDS=41, - CapDistanceToStart=None, - DistanceToStop=None, - Evidence=None, - AltStop=None, - AltStopDistanceToCDS=None, - FrameWithCDS=None, - StartDistanceToCDS=None, - newSTOPDistanceToCDS=None, - alt_type=None, - alt_type_length=None, - ref_StartDistanceToCDS=None, - ref_type=None, - ref_type_length=None, - ), - fiveutrConsequence=None, - ), - biotype='protein_coding', - consequenceTerms=['missense_variant'], - ), - ], - sortedRegulatoryFeatureConsequences=[ - hl.Struct( - regulatoryFeatureId='ENSR00000344437', - biotype='CTCF_binding_site', - consequenceTerms=['regulatory_region_variant'], - ), - ], - sortedMotifFeatureConsequences=[ - hl.Struct( - motifFeatureId='ENSM00493959715', - consequenceTerms=['TF_binding_site_variant'], - ), - ], - ), - ) - - def test_sorted_hl_struct(self) -> None: - struct = hl.Struct( - z=5, - y=hl.Struct(b=2, a=hl.Struct(d=4, c=3)), - x=hl.Struct(k=9), - ) - self.assertEqual( - sorted_hl_struct(struct), - hl.Struct(x=hl.Struct(k=9), y=hl.Struct(a=hl.Struct(c=3, d=4), b=2), z=5), - ) diff --git a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py deleted file mode 100644 index ccb3260f5e..0000000000 --- a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py +++ /dev/null @@ -1,423 +0,0 @@ -import hail as hl -import luigi.worker -import pandas as pd - -from loading_pipeline.lib.core import ( - DatasetType, - ReferenceGenome, - SampleType, -) -from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS -from loading_pipeline.lib.paths import ( - new_entries_parquet_path, - variant_annotations_table_path, -) -from loading_pipeline.lib.tasks.exports.write_new_entries_parquet import ( - WriteNewEntriesParquetTask, -) -from loading_pipeline.lib.test.misc import ( - convert_ndarray_to_list, - copy_project_pedigree_to_mocked_dir, -) -from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase - -TEST_PEDIGREE_3_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_3_remap.tsv' -TEST_PEDIGREE_4_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_4_remap.tsv' -TEST_PEDIGREE_5 = 'loading_pipeline/var/test/pedigrees/test_pedigree_5.tsv' -TEST_MITO_EXPORT_PEDIGREE = ( - 'loading_pipeline/var/test/pedigrees/test_mito_export_pedigree.tsv' -) -TEST_SNV_INDEL_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' -TEST_MITO_CALLSET = 'loading_pipeline/var/test/callsets/mito_1.mt' -TEST_SV_VCF_2 = 'loading_pipeline/var/test/callsets/sv_2.vcf' -TEST_GCNV_BED_FILE = 'loading_pipeline/var/test/callsets/gcnv_1.tsv' -TEST_SNV_INDEL_ANNOTATIONS = ( - 'loading_pipeline/var/test/exports/GRCh38/SNV_INDEL/annotations.ht' -) -TEST_MITO_ANNOTATIONS = 'loading_pipeline/var/test/exports/GRCh38/MITO/annotations.ht' -TEST_SV_ANNOTATIONS = 'loading_pipeline/var/test/exports/GRCh38/SV/annotations.ht' -TEST_GCNV_ANNOTATIONS = 'loading_pipeline/var/test/exports/GRCh38/GCNV/annotations.ht' - -TEST_RUN_ID = 'manual__2024-04-03' - - -class WriteNewEntriesParquetTest(MockedDatarootTestCase): - def setUp(self) -> None: - super().setUp() - ht = hl.read_table( - TEST_SNV_INDEL_ANNOTATIONS, - ) - ht.write( - variant_annotations_table_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - ), - ) - ht = hl.read_table( - TEST_MITO_ANNOTATIONS, - ) - ht.write( - variant_annotations_table_path( - ReferenceGenome.GRCh38, - DatasetType.MITO, - ), - ) - ht = hl.read_table( - TEST_SV_ANNOTATIONS, - ) - ht.write( - variant_annotations_table_path( - ReferenceGenome.GRCh38, - DatasetType.SV, - ), - ) - ht = hl.read_table(TEST_GCNV_ANNOTATIONS) - ht.write( - variant_annotations_table_path( - ReferenceGenome.GRCh38, - DatasetType.GCNV, - ), - ) - - def test_write_new_entries_parquet(self): - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_3_REMAP, - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - SampleType.WGS, - 'R0113_test_project', - ) - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_4_REMAP, - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - SampleType.WGS, - 'R0114_project4', - ) - worker = luigi.worker.Worker() - task = WriteNewEntriesParquetTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - sample_type=SampleType.WGS, - callset_path=TEST_SNV_INDEL_VCF, - project_guids=['R0113_test_project', 'R0114_project4'], - validations_to_skip=[ALL_VALIDATIONS], - run_id=TEST_RUN_ID, - ) - worker.add(task) - worker.run() - self.assertTrue(task.output().exists()) - self.assertTrue(task.complete()) - df = pd.read_parquet( - new_entries_parquet_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ), - ) - export_json = convert_ndarray_to_list(df.to_dict('records')) - self.assertEqual( - export_json[:2], - [ - { - 'key': 0, - 'project_guid': 'R0113_test_project', - 'family_guid': 'abc_1', - 'sample_type': 'WGS', - 'xpos': 1000876499, - 'geneIds': ['ENSG00000187634'], - 'filters': [], - 'calls': [ - { - 'sampleId': 'HG00731_1', - 'gt': 2, - 'gq': 21, - 'ab': 1.0, - 'dp': 7, - }, - { - 'sampleId': 'HG00732_1', - 'gt': 2, - 'gq': 24, - 'ab': 1.0, - 'dp': 8, - }, - { - 'sampleId': 'HG00733_1', - 'gt': 2, - 'gq': 12, - 'ab': 1.0, - 'dp': 4, - }, - ], - 'sign': 1, - }, - { - 'key': 1, - 'project_guid': 'R0113_test_project', - 'family_guid': 'abc_1', - 'sample_type': 'WGS', - 'xpos': 1000878314, - 'geneIds': ['ENSG00000187634'], - 'filters': ['VQSRTrancheSNP99.00to99.90'], - 'calls': [ - { - 'sampleId': 'HG00731_1', - 'gt': 1, - 'gq': 30, - 'ab': 0.3333333432674408, - 'dp': 3, - }, - {'sampleId': 'HG00732_1', 'gt': 0, 'gq': 6, 'ab': 0.0, 'dp': 2}, - { - 'sampleId': 'HG00733_1', - 'gt': 1, - 'gq': 61, - 'ab': 0.6000000238418579, - 'dp': 5, - }, - ], - 'sign': 1, - }, - ], - ) - - def test_mito_write_new_entries_parquet(self): - copy_project_pedigree_to_mocked_dir( - TEST_MITO_EXPORT_PEDIGREE, - ReferenceGenome.GRCh38, - DatasetType.MITO, - SampleType.WGS, - 'R0116_test_project3', - ) - worker = luigi.worker.Worker() - task = WriteNewEntriesParquetTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.MITO, - sample_type=SampleType.WGS, - callset_path=TEST_MITO_CALLSET, - project_guids=['R0116_test_project3'], - validations_to_skip=[ALL_VALIDATIONS], - run_id=TEST_RUN_ID, - ) - worker.add(task) - worker.run() - self.assertTrue(task.output().exists()) - self.assertTrue(task.complete()) - df = pd.read_parquet( - new_entries_parquet_path( - ReferenceGenome.GRCh38, - DatasetType.MITO, - TEST_RUN_ID, - ), - ) - export_json = convert_ndarray_to_list(df.to_dict('records')) - self.assertEqual( - export_json, - [ - { - 'key': 998, - 'project_guid': 'R0116_test_project3', - 'family_guid': 'family_1', - 'sample_type': 'WGS', - 'xpos': 25000000008, - 'filters': [], - 'calls': [ - { - 'sampleId': 'RGP_1270_2', - 'gt': 2, - 'dp': 4216, - 'hl': 0.999, - 'mitoCn': 224, - 'contamination': 0.0, - }, - ], - 'sign': 1, - }, - ], - ) - - def test_sv_write_new_entries_parquet(self): - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_5, - ReferenceGenome.GRCh38, - DatasetType.SV, - SampleType.WGS, - 'R0115_test_project2', - ) - worker = luigi.worker.Worker() - task = WriteNewEntriesParquetTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SV, - sample_type=SampleType.WGS, - callset_path=TEST_SV_VCF_2, - project_guids=['R0115_test_project2'], - validations_to_skip=[ALL_VALIDATIONS], - run_id=TEST_RUN_ID, - ) - worker.add(task) - worker.run() - self.assertTrue(task.output().exists()) - self.assertTrue(task.complete()) - df = pd.read_parquet( - new_entries_parquet_path( - ReferenceGenome.GRCh38, - DatasetType.SV, - TEST_RUN_ID, - ), - ) - export_json = convert_ndarray_to_list(df.to_dict('records')) - self.assertEqual( - export_json, - [ - { - 'key': 727, - 'project_guid': 'R0115_test_project2', - 'family_guid': 'family_2_1', - 'xpos': 1001025886, - 'geneIds': ['ENSG00000188157'], - 'filters': ['HIGH_SR_BACKGROUND', 'UNRESOLVED'], - 'calls': [ - { - 'sampleId': 'RGP_164_1', - 'gt': 0, - 'cn': None, - 'gq': 99, - 'newCall': True, - 'prevCall': False, - 'prevNumAlt': None, - }, - { - 'sampleId': 'RGP_164_2', - 'gt': 1, - 'cn': None, - 'gq': 31, - 'newCall': True, - 'prevCall': False, - 'prevNumAlt': None, - }, - { - 'sampleId': 'RGP_164_3', - 'gt': 0, - 'cn': None, - 'gq': 99, - 'newCall': True, - 'prevCall': False, - 'prevNumAlt': None, - }, - { - 'sampleId': 'RGP_164_4', - 'gt': 0, - 'cn': None, - 'gq': 99, - 'newCall': True, - 'prevCall': False, - 'prevNumAlt': None, - }, - ], - 'sign': 1, - }, - ], - ) - - def test_gcnv_write_new_entries_parquet(self): - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_5, - ReferenceGenome.GRCh38, - DatasetType.GCNV, - SampleType.WES, - 'R0115_test_project2', - ) - worker = luigi.worker.Worker() - task = WriteNewEntriesParquetTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.GCNV, - sample_type=SampleType.WES, - callset_path=TEST_GCNV_BED_FILE, - project_guids=['R0115_test_project2'], - validations_to_skip=[ALL_VALIDATIONS], - run_id=TEST_RUN_ID, - ) - worker.add(task) - worker.run() - self.assertTrue(task.output().exists()) - self.assertTrue(task.complete()) - df = pd.read_parquet( - new_entries_parquet_path( - ReferenceGenome.GRCh38, - DatasetType.GCNV, - TEST_RUN_ID, - ), - ) - export_json = convert_ndarray_to_list(df.to_dict('records')) - self.assertEqual( - export_json, - [ - { - 'key': 0, - 'project_guid': 'R0115_test_project2', - 'family_guid': 'family_2_1', - 'xpos': 1000939203, - 'filters': [], - 'calls': [ - { - 'sampleId': 'RGP_164_1', - 'gt': 1, - 'cn': 1, - 'qs': 4, - 'defragged': False, - 'start': 100006937, - 'end': 100007881, - 'numExon': 2, - 'geneIds': ['ENSG00000117620', 'ENSG00000283761'], - 'newCall': False, - 'prevCall': True, - 'prevOverlap': False, - }, - { - 'sampleId': 'RGP_164_2', - 'gt': 1, - 'cn': 1, - 'qs': 5, - 'defragged': False, - 'start': 100017585, - 'end': 100023213, - 'numExon': 1, - 'geneIds': ['ENSG00000117620', 'ENSG00000283761'], - 'newCall': False, - 'prevCall': False, - 'prevOverlap': False, - }, - { - 'sampleId': 'RGP_164_3', - 'gt': 2, - 'cn': 0, - 'qs': 30, - 'defragged': False, - 'start': 100017585, - 'end': 100023213, - 'numExon': 1, - 'geneIds': ['ENSG00000117620', 'ENSG00000283761'], - 'newCall': False, - 'prevCall': True, - 'prevOverlap': False, - }, - { - 'sampleId': 'RGP_164_4', - 'gt': 2, - 'cn': 0, - 'qs': 30, - 'defragged': False, - 'start': 100017586, - 'end': 100023212, - 'numExon': 2, - 'geneIds': ['ENSG00000283761', 'ENSG22222222222'], - 'newCall': False, - 'prevCall': True, - 'prevOverlap': False, - }, - ], - 'sign': 1, - }, - ], - ) diff --git a/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py deleted file mode 100644 index 5458854f56..0000000000 --- a/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py +++ /dev/null @@ -1,270 +0,0 @@ -import os -from unittest import mock - -import hail as hl -import luigi.worker -import pandas as pd - -from loading_pipeline.lib.core import ( - DatasetType, - ReferenceGenome, - SampleType, -) -from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS -from loading_pipeline.lib.paths import ( - new_variant_details_parquet_path, - new_variants_table_path, -) -from loading_pipeline.lib.tasks.exports.write_new_variant_details_parquet import ( - WriteNewVariantDetailsParquetTask, -) -from loading_pipeline.lib.test.misc import convert_ndarray_to_list -from loading_pipeline.lib.test.mock_complete_task import MockCompleteTask -from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase - -TEST_SNV_INDEL_ANNOTATIONS = ( - 'loading_pipeline/var/test/exports/GRCh38/SNV_INDEL/annotations.ht' -) -TEST_GRCH37_SNV_INDEL_ANNOTATIONS = ( - 'loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/annotations.ht' -) - -TEST_RUN_ID = 'manual__2024-04-03' - - -class WriteNewVariantDetailsParquetTest(MockedDatarootTestCase): - def setUp(self) -> None: - super().setUp() - ht = hl.read_table( - TEST_SNV_INDEL_ANNOTATIONS, - ) - ht.write( - new_variants_table_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ), - ) - ht = hl.read_table( - TEST_GRCH37_SNV_INDEL_ANNOTATIONS, - ) - ht.write( - new_variants_table_path( - ReferenceGenome.GRCh37, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ), - ) - - # Make an incomplete parquet to validate overwrite-ing. - os.makedirs( - new_variant_details_parquet_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ), - exist_ok=True, - ) - with open( - os.path.join( - new_variant_details_parquet_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ), - 'incomplete_file.parquet', - ), - 'w', - ) as f: - f.write('') - - @mock.patch( - 'loading_pipeline.lib.tasks.exports.write_new_variant_details_parquet.WriteNewVariantsTableTask', - ) - def test_write_new_variant_details_parquet_test( - self, - mock_write_new_variants_task, - ) -> None: - mock_write_new_variants_task.return_value = MockCompleteTask() - worker = luigi.worker.Worker() - task = WriteNewVariantDetailsParquetTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - sample_type=SampleType.WGS, - callset_path='fake_callset', - project_guids=[ - 'fake_project', - ], - validations_to_skip=[ALL_VALIDATIONS], - run_id=TEST_RUN_ID, - ) - worker.add(task) - worker.run() - self.assertTrue(task.output().exists()) - self.assertTrue(task.complete()) - df = pd.read_parquet( - new_variant_details_parquet_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ), - ) - export_json = convert_ndarray_to_list(df.head(1).to_dict('records')) - self.assertListEqual( - list(export_json[0].keys()), - [ - 'key', - 'variantId', - 'rsid', - 'CAID', - 'liftedOverChrom', - 'liftedOverPos', - 'sortedMotifFeatureConsequences', - 'sortedRegulatoryFeatureConsequences', - 'transcripts', - ], - ) - self.assertEqual( - export_json[0]['key'], - 0, - ) - self.assertEqual( - export_json[0]['transcripts'][0], - { - 'alphamissense': {'pathogenicity': None}, - 'aminoAcids': 'S/L', - 'biotype': 'protein_coding', - 'canonical': 1, - 'codons': 'tCg/tTg', - 'consequenceTerms': ['missense_variant'], - 'exon': {'index': 6, 'total': 14}, - 'geneId': 'ENSG00000187634', - 'hgvsc': 'ENST00000616016.5:c.1049C>T', - 'hgvsp': 'ENSP00000478421.2:p.Ser350Leu', - 'intron': None, - 'transcriptId': 'ENST00000616016', - 'transcriptRank': 0, - 'majorConsequence': 'missense_variant', - 'maneSelect': 'NM_001385641.1', - 'manePlusClinical': None, - 'refseqTranscriptId': 'NM_001385641.1', - 'loftee': {'isLofNagnag': None, 'lofFilters': None}, - 'spliceregion': { - 'extended_intronic_splice_region_variant': False, - }, - 'utrannotator': { - 'existingInframeOorfs': None, - 'existingOutofframeOorfs': None, - 'existingUorfs': None, - 'fiveutrAnnotation': { - 'AltStop': None, - 'AltStopDistanceToCDS': None, - 'CapDistanceToStart': None, - 'DistanceToCDS': 41, - 'DistanceToStop': None, - 'Evidence': None, - 'FrameWithCDS': None, - 'KozakContext': 'CGCATGC', - 'KozakStrength': 'Weak', - 'StartDistanceToCDS': None, - 'alt_type': None, - 'alt_type_length': None, - 'newSTOPDistanceToCDS': None, - 'ref_StartDistanceToCDS': None, - 'ref_type': None, - 'ref_type_length': None, - 'type': 'OutOfFrame_oORF', - }, - 'fiveutrConsequence': None, - }, - }, - ) - self.assertEqual( - list(export_json[0]['transcripts'][0].keys()), - sorted(export_json[0]['transcripts'][0].keys()), - ) - self.assertEqual( - list( - export_json[0]['transcripts'][0]['utrannotator'][ - 'fiveutrAnnotation' - ].keys(), - ), - sorted( - export_json[0]['transcripts'][0]['utrannotator'][ - 'fiveutrAnnotation' - ].keys(), - ), - ) - - @mock.patch( - 'loading_pipeline.lib.tasks.exports.write_new_variant_details_parquet.WriteNewVariantsTableTask', - ) - def test_grch37_write_new_variant_details_parquet_test( - self, - mock_write_new_variants_task, - ) -> None: - mock_write_new_variants_task.return_value = MockCompleteTask() - worker = luigi.worker.Worker() - task = WriteNewVariantDetailsParquetTask( - reference_genome=ReferenceGenome.GRCh37, - dataset_type=DatasetType.SNV_INDEL, - sample_type=SampleType.WGS, - callset_path='fake_callset', - project_guids=[ - 'fake_project', - ], - validations_to_skip=[ALL_VALIDATIONS], - run_id=TEST_RUN_ID, - ) - worker.add(task) - worker.run() - self.assertTrue(task.output().exists()) - self.assertTrue(task.complete()) - df = pd.read_parquet( - os.path.join( - new_variant_details_parquet_path( - ReferenceGenome.GRCh37, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ), - ), - ) - export_json = convert_ndarray_to_list(df.head(1).to_dict('records')) - self.assertListEqual( - list(export_json[0].keys()), - [ - 'key', - 'variantId', - 'rsid', - 'CAID', - 'liftedOverChrom', - 'liftedOverPos', - 'transcripts', - ], - ) - self.assertEqual( - export_json[0]['key'], - 1424, - ) - self.assertEqual(export_json[0]['CAID'], None) - self.assertEqual( - export_json[0]['transcripts'][0], - { - 'aminoAcids': 'E/G', - 'biotype': 'protein_coding', - 'canonical': 1, - 'codons': 'gAa/gGa', - 'consequenceTerms': ['missense_variant'], - 'geneId': 'ENSG00000186092', - 'hgvsc': 'ENST00000335137.3:c.44A>G', - 'hgvsp': 'ENSP00000334393.3:p.Glu15Gly', - 'loftee': {'isLofNagnag': None, 'lofFilters': None}, - 'majorConsequence': 'missense_variant', - 'transcriptId': 'ENST00000335137', - 'transcriptRank': 0, - }, - ) - self.assertEqual( - list(export_json[0]['transcripts'][0].keys()), - sorted(export_json[0]['transcripts'][0].keys()), - ) diff --git a/loading_pipeline/lib/tasks/files_test.py b/loading_pipeline/lib/tasks/files_test.py deleted file mode 100644 index b2dfd937e0..0000000000 --- a/loading_pipeline/lib/tasks/files_test.py +++ /dev/null @@ -1,40 +0,0 @@ -import os -import tempfile -import unittest - -from loading_pipeline.lib.tasks.files import ( - CallsetTask, - HailTableTask, - RawFileTask, - VCFFileTask, -) - - -class FilesTest(unittest.TestCase): - def test_raw_file(self) -> None: - with tempfile.NamedTemporaryFile(suffix='.txt') as f: - self.assertTrue(RawFileTask(f.name).complete()) - - def test_vcf_file(self) -> None: - with tempfile.NamedTemporaryFile(suffix='.vcf.bgz') as f: - self.assertTrue(VCFFileTask(f.name).complete()) - - def test_hail_table(self) -> None: - with tempfile.TemporaryDirectory(suffix='.ht') as d: - self.assertFalse(HailTableTask(d).complete()) - with open(os.path.join(d, '_SUCCESS'), 'w') as f: - f.write('0') - self.assertTrue(HailTableTask(d).complete()) - - def test_callset_task(self) -> None: - with tempfile.NamedTemporaryFile(suffix='.txt') as f: - self.assertTrue(CallsetTask(f.name).complete()) - - with tempfile.NamedTemporaryFile(suffix='.vcf') as f: - self.assertTrue(CallsetTask(f.name).complete()) - - with tempfile.TemporaryDirectory(suffix='.mt') as d: - self.assertFalse(CallsetTask(d).complete()) - with open(os.path.join(d, '_SUCCESS'), 'w') as f: - f.write('0') - self.assertTrue(CallsetTask(d).complete()) diff --git a/loading_pipeline/lib/tasks/reference_data/__init__.py b/loading_pipeline/lib/tasks/reference_data/__init__.py deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/loading_pipeline/lib/tasks/reference_data/updated_reference_dataset.py b/loading_pipeline/lib/tasks/reference_data/updated_reference_dataset.py deleted file mode 100644 index 575cc1864f..0000000000 --- a/loading_pipeline/lib/tasks/reference_data/updated_reference_dataset.py +++ /dev/null @@ -1,27 +0,0 @@ -import luigi - -from loading_pipeline.lib.paths import valid_reference_dataset_path -from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset -from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( - BaseLoadingPipelineParams, -) -from loading_pipeline.lib.tasks.base.base_write import BaseWriteTask -from loading_pipeline.lib.tasks.files import GCSorLocalTarget - - -@luigi.util.inherits(BaseLoadingPipelineParams) -class UpdatedReferenceDatasetTask(BaseWriteTask): - reference_dataset: ReferenceDataset = luigi.EnumParameter( - enum=ReferenceDataset, - ) - - def output(self): - return GCSorLocalTarget( - valid_reference_dataset_path( - self.reference_genome, - self.reference_dataset, - ), - ) - - def create_table(self): - return self.reference_dataset.get_ht(self.reference_genome) diff --git a/loading_pipeline/lib/tasks/reference_data/updated_reference_dataset_parquet.py b/loading_pipeline/lib/tasks/reference_data/updated_reference_dataset_parquet.py deleted file mode 100644 index ed8adfce6b..0000000000 --- a/loading_pipeline/lib/tasks/reference_data/updated_reference_dataset_parquet.py +++ /dev/null @@ -1,55 +0,0 @@ -import luigi - -from loading_pipeline.lib.annotations.expression_helpers import get_expr_for_variant_id -from loading_pipeline.lib.core.dataset_type import DatasetType -from loading_pipeline.lib.core.definitions import ReferenceGenome -from loading_pipeline.lib.paths import reference_dataset_parquet -from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset -from loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc import ( - BaseRunJobOnDataprocTask, -) -from loading_pipeline.lib.tasks.files import GCSorLocalFolderTarget, GCSorLocalTarget - - -class UpdatedReferenceDatasetParquetTask(luigi.Task): - reference_genome = luigi.EnumParameter(enum=ReferenceGenome) - dataset_type = luigi.EnumParameter(enum=DatasetType) - reference_dataset: ReferenceDataset = luigi.EnumParameter( - enum=ReferenceDataset, - ) - run_id = luigi.Parameter() - attempt_id = luigi.IntParameter() - - def complete(self) -> luigi.Target: - return GCSorLocalFolderTarget(self.output().path).exists() - - def output(self): - return GCSorLocalTarget( - reference_dataset_parquet( - self.reference_genome, - self.reference_dataset, - ), - ) - - def run(self): - ht = self.reference_dataset.get_ht(self.reference_genome) - ht = ht.annotate( - variant_id=get_expr_for_variant_id(ht), - ) - df = ht.to_spark(flatten=False) - df.write.parquet( - self.output().path, - mode='overwrite', - ) - - -class UpdatedReferenceDatasetParquetOnDataprocTask(BaseRunJobOnDataprocTask): - reference_genome = luigi.EnumParameter(enum=ReferenceGenome) - dataset_type = luigi.EnumParameter(enum=DatasetType) - reference_dataset: ReferenceDataset = luigi.EnumParameter( - enum=ReferenceDataset, - ) - - @property - def task(self) -> luigi.Task: - return UpdatedReferenceDatasetParquetTask diff --git a/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py b/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py deleted file mode 100644 index 3bfe55af65..0000000000 --- a/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py +++ /dev/null @@ -1,1349 +0,0 @@ -import functools -from unittest.mock import Mock, PropertyMock, patch - -import hail as hl -import luigi.worker - -from loading_pipeline.lib.annotations.enums import ( - BIOTYPES, - FIVEUTR_CONSEQUENCES, - LOF_FILTERS, - MITOTIP_PATHOGENICITIES, - MOTIF_CONSEQUENCE_TERMS, - REGULATORY_BIOTYPES, - REGULATORY_CONSEQUENCE_TERMS, - SV_CONSEQUENCE_RANKS, - SV_TYPE_DETAILS, - SV_TYPES, - TRANSCRIPT_CONSEQUENCE_TERMS, -) -from loading_pipeline.lib.core import ( - DatasetType, - ReferenceGenome, - SampleType, -) -from loading_pipeline.lib.misc.io import remap_pedigree_hash -from loading_pipeline.lib.misc.validation import ( - ALL_VALIDATIONS, - SKIPPABLE_VALIDATIONS, - validate_expected_contig_frequency, -) -from loading_pipeline.lib.paths import ( - valid_reference_dataset_path, -) -from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset -from loading_pipeline.lib.tasks.files import GCSorLocalFolderTarget -from loading_pipeline.lib.tasks.update_variant_annotations_table_with_new_variants import ( - UpdateVariantAnnotationsTableWithNewVariantsTask, -) -from loading_pipeline.lib.test.misc import copy_project_pedigree_to_mocked_dir -from loading_pipeline.lib.test.mocked_reference_datasets_testcase import ( - MockedReferenceDatasetsTestCase, -) -from loading_pipeline.var.test.vep.mock_vep_data import ( - MOCK_37_VEP_DATA, - MOCK_38_VEP_DATA, -) - -TEST_MITO_MT = 'loading_pipeline/var/test/callsets/mito_1.mt' -TEST_SNV_INDEL_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' -TEST_SV_VCF = 'loading_pipeline/var/test/callsets/sv_1.vcf' -TEST_SV_VCF_2 = 'loading_pipeline/var/test/callsets/sv_2.vcf' -TEST_GCNV_BED_FILE = 'loading_pipeline/var/test/callsets/gcnv_1.tsv' -TEST_GCNV_BED_FILE_2 = 'loading_pipeline/var/test/callsets/gcnv_2.tsv' -TEST_PEDIGREE_3_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_3_remap.tsv' -TEST_PEDIGREE_4_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_4_remap.tsv' -TEST_PEDIGREE_5 = 'loading_pipeline/var/test/pedigrees/test_pedigree_5.tsv' -TEST_PEDIGREE_8 = 'loading_pipeline/var/test/pedigrees/test_pedigree_8.tsv' -TEST_PEDIGREE_10 = 'loading_pipeline/var/test/pedigrees/test_pedigree_10.tsv' -TEST_PEDIGREE_11 = 'loading_pipeline/var/test/pedigrees/test_pedigree_11.tsv' - -GENE_ID_MAPPING = { - 'OR4F5': 'ENSG00000186092', - 'PLEKHG4B': 'ENSG00000153404', - 'OR4F16': 'ENSG00000186192', - 'OR4F29': 'ENSG00000284733', - 'FBXO28': 'ENSG00000143756', - 'SAMD11': 'ENSG00000187634', - 'C1orf174': 'ENSG00000198912', - 'TAS1R1': 'ENSG00000173662', - 'FAM131C': 'ENSG00000185519', - 'RCC2': 'ENSG00000179051', - 'NBPF3': 'ENSG00000142794', - 'AGBL4': 'ENSG00000186094', - 'KIAA1614': 'ENSG00000135835', - 'MR1': 'ENSG00000153029', - 'STX6': 'ENSG00000135823', - 'XPR1': 'ENSG00000143324', -} - -TEST_RUN_ID = 'manual__2024-04-03' - - -class UpdateVariantAnnotationsTableWithNewVariantsTaskTest( - MockedReferenceDatasetsTestCase, -): - def test_missing_pedigree( - self, - ) -> None: - uvatwns_task = UpdateVariantAnnotationsTableWithNewVariantsTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - sample_type=SampleType.WGS, - callset_path=TEST_SNV_INDEL_VCF, - project_guids=['R0113_test_project'], - validations_to_skip=[ALL_VALIDATIONS], - run_id=TEST_RUN_ID, - ) - worker = luigi.worker.Worker() - worker.add(uvatwns_task) - worker.run() - self.assertFalse(uvatwns_task.complete()) - - @patch( - 'loading_pipeline.lib.tasks.validate_callset.SKIPPABLE_VALIDATIONS', - [ - x - for x in SKIPPABLE_VALIDATIONS - if x.__name__ != 'validate_expected_contig_frequency' - ] - + [ - functools.update_wrapper( - functools.partial( - validate_expected_contig_frequency, - min_rows_per_contig=25, - ), - validate_expected_contig_frequency, - ), - ], - ) - @patch.object(ReferenceGenome, 'standard_contigs', new_callable=PropertyMock) - @patch('loading_pipeline.lib.misc.vep.hl.vep') - @patch( - 'loading_pipeline.lib.tasks.write_new_variants_table.load_gencode_ensembl_to_refseq_id', - ) - def test_multiple_update_vat( - self, - mock_load_gencode_ensembl_to_refseq_id: Mock, - mock_vep: Mock, - mock_standard_contigs: Mock, - ) -> None: - mock_vep.side_effect = lambda ht, **_: ht.annotate(vep=MOCK_38_VEP_DATA) - mock_load_gencode_ensembl_to_refseq_id.return_value = hl.dict( - {'ENST00000327044': 'NM_015658.4'}, - ) - mock_standard_contigs.return_value = {'chr1'} - # This creates a mock validation table with 1 coding and 1 non-coding variant - # explicitly chosen from the VCF. - # NB: This is the one and only place validation is enabled in the task tests! - coding_and_noncoding_variants_ht = hl.Table.parallelize( - [ - { - 'locus': hl.Locus( - contig='chr1', - position=871269, - reference_genome='GRCh38', - ), - 'coding': False, - 'noncoding': True, - }, - { - 'locus': hl.Locus( - contig='chr1', - position=876499, - reference_genome='GRCh38', - ), - 'coding': True, - 'noncoding': False, - }, - ], - hl.tstruct( - locus=hl.tlocus('GRCh38'), - coding=hl.tbool, - noncoding=hl.tbool, - ), - key='locus', - globals=hl.Struct( - enums=hl.Struct( - gnomad_genomes=hl.Struct(), - ), - ), - ) - coding_and_noncoding_variants_ht.write( - valid_reference_dataset_path( - ReferenceGenome.GRCh38, - ReferenceDataset.gnomad_coding_and_noncoding, - ), - overwrite=True, - ) - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_3_REMAP, - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - SampleType.WGS, - 'R0113_test_project', - ) - worker = luigi.worker.Worker() - uvatwns_task_3 = UpdateVariantAnnotationsTableWithNewVariantsTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - sample_type=SampleType.WGS, - callset_path=TEST_SNV_INDEL_VCF, - project_guids=['R0113_test_project'], - validations_to_skip=[], - run_id=TEST_RUN_ID, - ) - worker.add(uvatwns_task_3) - worker.run() - self.assertTrue(uvatwns_task_3.complete()) - ht = hl.read_table(uvatwns_task_3.output().path) - self.assertEqual(ht.count(), 30) - self.assertEqual( - ht.globals.updates.collect(), - [ - { - hl.Struct( - callset=TEST_SNV_INDEL_VCF, - project_guid='R0113_test_project', - remap_pedigree_hash=hl.eval( - remap_pedigree_hash(TEST_PEDIGREE_3_REMAP), - ), - ), - }, - ], - ) - self.assertEqual( - hl.eval(ht.globals.max_key_), - 29, - ) - - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_4_REMAP, - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - SampleType.WGS, - 'R0114_project4', - ) - # Ensure that new variants are added correctly to the table. - uvatwns_task_4 = UpdateVariantAnnotationsTableWithNewVariantsTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - sample_type=SampleType.WGS, - callset_path=TEST_SNV_INDEL_VCF, - project_guids=['R0114_project4'], - validations_to_skip=[], - run_id=TEST_RUN_ID + '-another-run', - ) - worker.add(uvatwns_task_4) - worker.run() - self.assertTrue(uvatwns_task_4.complete()) - ht = hl.read_table(uvatwns_task_4.output().path) - self.assertCountEqual( - [ - x - for x in ht.select( - 'variant_id', - 'xpos', - ).collect() - if x.locus.position <= 878809 # noqa: PLR2004 - ], - [ - hl.Struct( - locus=hl.Locus( - contig='chr1', - position=871269, - reference_genome='GRCh38', - ), - alleles=['A', 'C'], - variant_id='1-871269-A-C', - xpos=1000871269, - ), - hl.Struct( - locus=hl.Locus( - contig='chr1', - position=874734, - reference_genome='GRCh38', - ), - alleles=['C', 'T'], - variant_id='1-874734-C-T', - xpos=1000874734, - ), - hl.Struct( - locus=hl.Locus( - contig='chr1', - position=876499, - reference_genome='GRCh38', - ), - alleles=['A', 'G'], - variant_id='1-876499-A-G', - xpos=1000876499, - ), - hl.Struct( - locus=hl.Locus( - contig='chr1', - position=878314, - reference_genome='GRCh38', - ), - alleles=['G', 'C'], - variant_id='1-878314-G-C', - xpos=1000878314, - ), - hl.Struct( - locus=hl.Locus( - contig='chr1', - position=878809, - reference_genome='GRCh38', - ), - alleles=['C', 'T'], - variant_id='1-878809-C-T', - xpos=1000878809, - ), - ], - ) - self.assertCountEqual( - ht.filter( - ht.locus.position <= 878809, # noqa: PLR2004 - ).sorted_transcript_consequences.consequence_term_ids.collect(), - [ - [[9], [23, 26], [23, 13, 26]], - [[9], [23, 26], [23, 13, 26]], - [[9], [23, 26], [23, 13, 26]], - [[9], [23, 26], [23, 13, 26]], - [[9], [23, 26], [23, 13, 26]], - ], - ) - self.assertCountEqual( - ht.globals.collect(), - [ - hl.Struct( - updates={ - hl.Struct( - callset='loading_pipeline/var/test/callsets/1kg_30variants.vcf', - project_guid='R0113_test_project', - remap_pedigree_hash=hl.eval( - remap_pedigree_hash( - TEST_PEDIGREE_3_REMAP, - ), - ), - ), - hl.Struct( - callset='loading_pipeline/var/test/callsets/1kg_30variants.vcf', - project_guid='R0114_project4', - remap_pedigree_hash=hl.eval( - remap_pedigree_hash( - TEST_PEDIGREE_4_REMAP, - ), - ), - ), - }, - migrations=[], - max_key_=29, - enums=hl.Struct( - sorted_motif_feature_consequences=hl.Struct( - consequence_term=MOTIF_CONSEQUENCE_TERMS, - ), - sorted_regulatory_feature_consequences=hl.Struct( - biotype=REGULATORY_BIOTYPES, - consequence_term=REGULATORY_CONSEQUENCE_TERMS, - ), - sorted_transcript_consequences=hl.Struct( - biotype=BIOTYPES, - consequence_term=TRANSCRIPT_CONSEQUENCE_TERMS, - loftee=hl.Struct( - lof_filter=LOF_FILTERS, - ), - utrannotator=hl.Struct( - fiveutr_consequence=FIVEUTR_CONSEQUENCES, - ), - ), - ), - ), - ], - ) - - @patch('loading_pipeline.lib.misc.vep.hl.vep') - def test_update_vat_grch37( - self, - mock_vep: Mock, - ) -> None: - mock_vep.side_effect = lambda ht, **_: ht.annotate(vep=MOCK_37_VEP_DATA) - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_3_REMAP, - ReferenceGenome.GRCh37, - DatasetType.SNV_INDEL, - SampleType.WGS, - 'R0113_test_project', - ) - worker = luigi.worker.Worker() - uvatwns_task = UpdateVariantAnnotationsTableWithNewVariantsTask( - reference_genome=ReferenceGenome.GRCh37, - dataset_type=DatasetType.SNV_INDEL, - sample_type=SampleType.WGS, - callset_path=TEST_SNV_INDEL_VCF, - project_guids=['R0113_test_project'], - validations_to_skip=[ALL_VALIDATIONS], - run_id=TEST_RUN_ID, - ) - worker.add(uvatwns_task) - worker.run() - self.assertTrue(uvatwns_task.complete()) - ht = hl.read_table(uvatwns_task.output().path) - self.assertEqual(ht.count(), 30) - self.assertFalse(hasattr(ht, 'rg37_locus')) - self.assertEqual( - ht.collect()[0], - hl.Struct( - locus=hl.Locus( - contig=1, - position=871269, - reference_genome='GRCh37', - ), - alleles=['A', 'C'], - rsid=None, - variant_id='1-871269-A-C', - xpos=1000871269, - sorted_transcript_consequences=[ - hl.Struct( - amino_acids='S/L', - canonical=1, - codons='tCg/tTg', - gene_id='ENSG00000188976', - hgvsc='ENST00000327044.6:c.1667C>T', - hgvsp='ENSP00000317992.6:p.Ser556Leu', - transcript_id='ENST00000327044', - biotype_id=39, - consequence_term_ids=[9], - is_lof_nagnag=None, - lof_filter_ids=[0, 1], - ), - hl.Struct( - amino_acids=None, - canonical=None, - codons=None, - gene_id='ENSG00000188976', - hgvsc='ENST00000477976.1:n.3114C>T', - hgvsp=None, - transcript_id='ENST00000477976', - biotype_id=38, - consequence_term_ids=[23, 26], - is_lof_nagnag=None, - lof_filter_ids=None, - ), - hl.Struct( - amino_acids=None, - canonical=None, - codons=None, - gene_id='ENSG00000188976', - hgvsc='ENST00000483767.1:n.523C>T', - hgvsp=None, - transcript_id='ENST00000483767', - biotype_id=38, - consequence_term_ids=[23, 26], - is_lof_nagnag=None, - lof_filter_ids=None, - ), - ], - rg38_locus=hl.Locus( - contig='chr1', - position=935889, - reference_genome='GRCh38', - ), - key_=0, - ), - ) - - def test_mito_update_vat( - self, - ) -> None: - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_5, - ReferenceGenome.GRCh38, - DatasetType.MITO, - SampleType.WGS, - 'R0115_test_project2', - ) - worker = luigi.worker.Worker() - update_variant_annotations_task = ( - UpdateVariantAnnotationsTableWithNewVariantsTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.MITO, - sample_type=SampleType.WGS, - callset_path=TEST_MITO_MT, - project_guids=['R0115_test_project2'], - validations_to_skip=[ALL_VALIDATIONS], - run_id=TEST_RUN_ID, - ) - ) - worker.add(update_variant_annotations_task) - worker.run() - self.assertTrue(update_variant_annotations_task.complete()) - ht = hl.read_table(update_variant_annotations_task.output().path) - self.assertEqual(ht.count(), 5) - self.assertCountEqual( - ht.globals.collect(), - [ - hl.Struct( - enums=hl.Struct( - sorted_transcript_consequences=hl.Struct( - biotype=BIOTYPES, - consequence_term=TRANSCRIPT_CONSEQUENCE_TERMS, - lof_filter=LOF_FILTERS, - ), - mitotip=hl.Struct(trna_prediction=MITOTIP_PATHOGENICITIES), - ), - migrations=[], - max_key_=4, - updates={ - hl.Struct( - callset='loading_pipeline/var/test/callsets/mito_1.mt', - project_guid='R0115_test_project2', - remap_pedigree_hash=hl.eval( - remap_pedigree_hash( - TEST_PEDIGREE_5, - ), - ), - ), - }, - ), - ], - ) - self.assertCountEqual( - ht.collect()[0], - hl.Struct( - locus=hl.Locus( - contig='chrM', - position=3, - reference_genome='GRCh38', - ), - alleles=['T', 'C'], - common_low_heteroplasmy=False, - haplogroup=hl.Struct(is_defining=False), - mitotip=hl.Struct(trna_prediction_id=None), - rg37_locus=hl.Locus( - contig='MT', - position=3, - reference_genome='GRCh37', - ), - rsid=None, - sorted_transcript_consequences=None, - variant_id='M-3-T-C', - xpos=25000000003, - key_=0, - ), - ) - - @patch( - 'loading_pipeline.lib.tasks.write_new_variants_table.load_gencode_gene_symbol_to_gene_id', - ) - def test_sv_multiple_vcf_update_vat( - self, - mock_load_gencode: Mock, - ) -> None: - mock_load_gencode.return_value = GENE_ID_MAPPING - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_5, - ReferenceGenome.GRCh38, - DatasetType.SV, - SampleType.WGS, - 'R0115_test_project2', - ) - worker = luigi.worker.Worker() - update_variant_annotations_task = ( - UpdateVariantAnnotationsTableWithNewVariantsTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SV, - sample_type=SampleType.WGS, - callset_path=TEST_SV_VCF, - project_guids=['R0115_test_project2'], - validations_to_skip=[ALL_VALIDATIONS], - run_id=TEST_RUN_ID, - ) - ) - worker.add(update_variant_annotations_task) - worker.run() - self.assertTrue(update_variant_annotations_task.complete()) - self.assertFalse( - GCSorLocalFolderTarget( - f'{self.mock_env.REFERENCE_DATASETS_DIR}/v03/GRCh38/SV/lookup.ht', - ).exists(), - ) - ht = hl.read_table(update_variant_annotations_task.output().path) - self.assertEqual(ht.count(), 13) - self.assertCountEqual( - ht.globals.collect(), - [ - hl.Struct( - enums=hl.Struct( - sv_type=SV_TYPES, - sv_type_detail=SV_TYPE_DETAILS, - sorted_gene_consequences=hl.Struct( - major_consequence=SV_CONSEQUENCE_RANKS, - ), - ), - migrations=[], - max_key_=12, - updates={ - hl.Struct( - callset=TEST_SV_VCF, - project_guid='R0115_test_project2', - remap_pedigree_hash=hl.eval( - remap_pedigree_hash( - TEST_PEDIGREE_5, - ), - ), - ), - }, - ), - ], - ) - self.assertCountEqual( - ht.collect()[:8], - [ - hl.Struct( - variant_id='BND_chr1_6', - algorithms='manta', - bothsides_support=False, - cpx_intervals=None, - end_locus=hl.Locus( - contig='chr5', - position=20404, - reference_genome='GRCh38', - ), - gnomad_svs=None, - rg37_locus=hl.Locus( - contig=1, - position=10367, - reference_genome='GRCh37', - ), - rg37_locus_end=hl.Locus( - contig=5, - position=20404, - reference_genome='GRCh37', - ), - sorted_gene_consequences=[ - hl.Struct(gene_id='ENSG00000186092', major_consequence_id=12), - hl.Struct(gene_id='ENSG00000153404', major_consequence_id=12), - ], - start_locus=hl.Locus( - contig='chr1', - position=180928, - reference_genome='GRCh38', - ), - strvctvre=hl.Struct(score=None), - sv_len=-1, - sv_type_id=2, - sv_type_detail_id=None, - xpos=1000180928, - key_=0, - ), - hl.Struct( - variant_id='BND_chr1_9', - algorithms='manta', - bothsides_support=False, - cpx_intervals=None, - end_locus=hl.Locus( - contig='chr1', - position=789481, - reference_genome='GRCh38', - ), - gnomad_svs=None, - rg37_locus=hl.Locus( - contig=1, - position=724861, - reference_genome='GRCh37', - ), - rg37_locus_end=hl.Locus( - contig=1, - position=724861, - reference_genome='GRCh37', - ), - sorted_gene_consequences=[ - hl.Struct(gene_id='ENSG00000143756', major_consequence_id=12), - hl.Struct(gene_id='ENSG00000186192', major_consequence_id=12), - ], - start_locus=hl.Locus( - contig='chr1', - position=789481, - reference_genome='GRCh38', - ), - strvctvre=hl.Struct(score=None), - sv_len=223225007, - sv_type_id=2, - sv_type_detail_id=None, - xpos=1000789481, - key_=1, - ), - hl.Struct( - variant_id='CPX_chr1_22', - algorithms='manta', - bothsides_support=True, - cpx_intervals=[ - hl.Struct( - type_id=8, - start=hl.Locus('chr1', 6558902, 'GRCh38'), - end=hl.Locus('chr1', 6559723, 'GRCh38'), - ), - hl.Struct( - type_id=6, - start=hl.Locus('chr1', 6559655, 'GRCh38'), - end=hl.Locus('chr1', 6559723, 'GRCh38'), - ), - ], - end_locus=hl.Locus( - contig='chr1', - position=6559723, - reference_genome='GRCh38', - ), - gnomad_svs=None, - rg37_locus=hl.Locus( - contig=1, - position=6618962, - reference_genome='GRCh37', - ), - rg37_locus_end=hl.Locus( - contig=1, - position=6619783, - reference_genome='GRCh37', - ), - sorted_gene_consequences=[ - hl.Struct(gene_id='ENSG00000173662', major_consequence_id=11), - ], - start_locus=hl.Locus( - contig='chr1', - position=6558902, - reference_genome='GRCh38', - ), - strvctvre=hl.Struct(score=None), - sv_len=821, - sv_type_id=3, - sv_type_detail_id=2, - xpos=1006558902, - key_=2, - ), - hl.Struct( - variant_id='CPX_chr1_251', - algorithms='manta', - bothsides_support=False, - cpx_intervals=[ - hl.Struct( - type_id=5, - start=hl.Locus('chr1', 180540234, 'GRCh38'), - end=hl.Locus('chr1', 181074767, 'GRCh38'), - ), - hl.Struct( - type_id=8, - start=hl.Locus('chr1', 181074767, 'GRCh38'), - end=hl.Locus('chr1', 181074938, 'GRCh38'), - ), - ], - end_locus=hl.Locus( - contig='chr1', - position=181074952, - reference_genome='GRCh38', - ), - gnomad_svs=None, - rg37_locus=hl.Locus( - contig=1, - position=180509370, - reference_genome='GRCh37', - ), - rg37_locus_end=hl.Locus( - contig=1, - position=181044088, - reference_genome='GRCh37', - ), - sorted_gene_consequences=[ - hl.Struct(gene_id='ENSG00000135835', major_consequence_id=0), - hl.Struct(gene_id='ENSG00000153029', major_consequence_id=0), - hl.Struct(gene_id='ENSG00000135823', major_consequence_id=0), - hl.Struct(gene_id='ENSG00000143324', major_consequence_id=0), - ], - start_locus=hl.Locus( - contig='chr1', - position=180540234, - reference_genome='GRCh38', - ), - strvctvre=hl.Struct(score=None), - sv_len=534718, - sv_type_id=3, - sv_type_detail_id=9, - xpos=1180540234, - key_=3, - ), - hl.Struct( - variant_id='CPX_chr1_41', - algorithms='manta', - bothsides_support=False, - cpx_intervals=[ - hl.Struct( - type_id=6, - start=hl.Locus('chr1', 16088760, 'GRCh38'), - end=hl.Locus('chr1', 16088835, 'GRCh38'), - ), - hl.Struct( - type_id=8, - start=hl.Locus('chr1', 16088760, 'GRCh38'), - end=hl.Locus('chr1', 16089601, 'GRCh38'), - ), - ], - end_locus=hl.Locus( - contig='chr1', - position=16089601, - reference_genome='GRCh38', - ), - gnomad_svs=None, - rg37_locus=hl.Locus( - contig=1, - position=16415255, - reference_genome='GRCh37', - ), - rg37_locus_end=hl.Locus( - contig=1, - position=16416096, - reference_genome='GRCh37', - ), - sorted_gene_consequences=[ - hl.Struct(gene_id='ENSG00000185519', major_consequence_id=12), - ], - start_locus=hl.Locus( - contig='chr1', - position=16088760, - reference_genome='GRCh38', - ), - strvctvre=hl.Struct(score=None), - sv_len=841, - sv_type_id=3, - sv_type_detail_id=12, - xpos=1016088760, - key_=4, - ), - hl.Struct( - variant_id='CPX_chr1_54', - algorithms='manta', - bothsides_support=False, - cpx_intervals=[ - hl.Struct( - type_id=6, - start=hl.Locus('chr1', 21427498, 'GRCh38'), - end=hl.Locus('chr1', 21427959, 'GRCh38'), - ), - hl.Struct( - type_id=8, - start=hl.Locus('chr1', 21427498, 'GRCh38'), - end=hl.Locus('chr1', 21480073, 'GRCh38'), - ), - hl.Struct( - type_id=5, - start=hl.Locus('chr1', 21480073, 'GRCh38'), - end=hl.Locus('chr1', 21480419, 'GRCh38'), - ), - ], - end_locus=hl.Locus( - contig='chr1', - position=21480419, - reference_genome='GRCh38', - ), - gnomad_svs=None, - rg37_locus=hl.Locus( - contig=1, - position=21753991, - reference_genome='GRCh37', - ), - rg37_locus_end=hl.Locus( - contig=1, - position=21806912, - reference_genome='GRCh37', - ), - sorted_gene_consequences=[ - hl.Struct(gene_id='ENSG00000142794', major_consequence_id=0), - ], - start_locus=hl.Locus( - contig='chr1', - position=21427498, - reference_genome='GRCh38', - ), - strvctvre=hl.Struct(score=None), - sv_len=52921, - sv_type_id=3, - sv_type_detail_id=13, - xpos=1021427498, - key_=5, - ), - hl.Struct( - variant_id='CPX_chrX_251', - algorithms='manta', - bothsides_support=False, - cpx_intervals=[ - hl.Struct( - type_id=5, - start=hl.Locus( - contig='chr1', - position=180540234, - reference_genome='GRCh38', - ), - end=hl.Locus( - contig='chr1', - position=181074767, - reference_genome='GRCh38', - ), - ), - hl.Struct( - type_id=8, - start=hl.Locus( - contig='chr1', - position=181074767, - reference_genome='GRCh38', - ), - end=hl.Locus( - contig='chr1', - position=181074938, - reference_genome='GRCh38', - ), - ), - ], - end_locus=hl.Locus( - contig='chrX', - position=2781000, - reference_genome='GRCh38', - ), - gnomad_svs=None, - sorted_gene_consequences=[ - hl.Struct(gene_id='ENSG00000135835', major_consequence_id=0), - hl.Struct(gene_id='ENSG00000153029', major_consequence_id=0), - hl.Struct(gene_id='ENSG00000135823', major_consequence_id=0), - hl.Struct(gene_id='ENSG00000143324', major_consequence_id=0), - ], - start_locus=hl.Locus( - contig='chrX', - position=3, - reference_genome='GRCh38', - ), - strvctvre=hl.Struct(score=None), - sv_type_id=3, - sv_type_detail_id=9, - sv_len=534718, - xpos=23000000003, - rg37_locus=None, - rg37_locus_end=hl.Locus( - contig='X', - position=2699041, - reference_genome='GRCh37', - ), - key_=6, - ), - hl.Struct( - variant_id='CPX_chrX_252', - algorithms='manta', - bothsides_support=False, - cpx_intervals=[ - hl.Struct( - type_id=5, - start=hl.Locus( - contig='chr1', - position=180540234, - reference_genome='GRCh38', - ), - end=hl.Locus( - contig='chr1', - position=181074767, - reference_genome='GRCh38', - ), - ), - hl.Struct( - type_id=8, - start=hl.Locus( - contig='chr1', - position=181074767, - reference_genome='GRCh38', - ), - end=hl.Locus( - contig='chr1', - position=181074938, - reference_genome='GRCh38', - ), - ), - ], - end_locus=hl.Locus( - contig='chrX', - position=2781900, - reference_genome='GRCh38', - ), - gnomad_svs=None, - sorted_gene_consequences=[ - hl.Struct(gene_id='ENSG00000135835', major_consequence_id=0), - hl.Struct(gene_id='ENSG00000153029', major_consequence_id=0), - hl.Struct(gene_id='ENSG00000135823', major_consequence_id=0), - hl.Struct(gene_id='ENSG00000143324', major_consequence_id=0), - ], - start_locus=hl.Locus( - contig='chrX', - position=2781700, - reference_genome='GRCh38', - ), - strvctvre=hl.Struct(score=None), - sv_type_id=3, - sv_type_detail_id=9, - sv_len=534718, - xpos=23002781700, - rg37_locus=hl.Locus( - contig='X', - position=2699741, - reference_genome='GRCh37', - ), - rg37_locus_end=hl.Locus( - contig='X', - position=2699941, - reference_genome='GRCh37', - ), - key_=7, - ), - ], - ) - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_5, - ReferenceGenome.GRCh38, - DatasetType.SV, - SampleType.WGS, - 'R0115_test_project2', - ) - update_variant_annotations_task = ( - UpdateVariantAnnotationsTableWithNewVariantsTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SV, - sample_type=SampleType.WGS, - callset_path=TEST_SV_VCF_2, - project_guids=['R0115_test_project2'], - validations_to_skip=[ALL_VALIDATIONS], - run_id='second_run_id', - ) - ) - worker.add(update_variant_annotations_task) - worker.run() - self.assertTrue(update_variant_annotations_task.complete()) - ht = hl.read_table(update_variant_annotations_task.output().path) - self.assertEqual(ht.count(), 14) - self.assertCountEqual( - ht.globals.collect(), - [ - hl.Struct( - enums=hl.Struct( - sv_type=SV_TYPES, - sv_type_detail=SV_TYPE_DETAILS, - sorted_gene_consequences=hl.Struct( - major_consequence=SV_CONSEQUENCE_RANKS, - ), - ), - migrations=[], - max_key_=13, - updates={ - hl.Struct( - callset=TEST_SV_VCF, - project_guid='R0115_test_project2', - remap_pedigree_hash=hl.eval( - remap_pedigree_hash( - TEST_PEDIGREE_5, - ), - ), - ), - hl.Struct( - callset=TEST_SV_VCF_2, - project_guid='R0115_test_project2', - remap_pedigree_hash=hl.eval( - remap_pedigree_hash( - TEST_PEDIGREE_5, - ), - ), - ), - }, - ), - ], - ) - self.assertCountEqual( - ht.take(1), - [ - hl.Struct( - variant_id='BND_chr1_6', - algorithms='manta', - bothsides_support=False, - cpx_intervals=None, - end_locus=hl.Locus( - contig='chr5', - position=20404, - reference_genome='GRCh38', - ), - gnomad_svs=None, - rg37_locus=hl.Locus( - contig=1, - position=10367, - reference_genome='GRCh37', - ), - rg37_locus_end=hl.Locus( - contig=5, - position=20404, - reference_genome='GRCh37', - ), - sorted_gene_consequences=[ - hl.Struct(gene_id='ENSG00000186092', major_consequence_id=12), - hl.Struct(gene_id='ENSG00000153404', major_consequence_id=12), - ], - start_locus=hl.Locus( - contig='chr1', - position=180928, - reference_genome='GRCh38', - ), - strvctvre=hl.Struct(score=None), - sv_len=-1, - sv_type_id=2, - sv_type_detail_id=None, - xpos=1000180928, - key_=0, - ), - ], - ) - - @patch( - 'loading_pipeline.lib.tasks.write_new_variants_table.load_gencode_gene_symbol_to_gene_id', - ) - def test_sv_multiple_project_single_vcf( - self, - mock_load_gencode: Mock, - ) -> None: - mock_load_gencode.return_value = GENE_ID_MAPPING - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_10, - ReferenceGenome.GRCh38, - DatasetType.SV, - SampleType.WGS, - 'R0116_test_project3', - ) - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_11, - ReferenceGenome.GRCh38, - DatasetType.SV, - SampleType.WGS, - 'R0117_test_project4', - ) - worker = luigi.worker.Worker() - update_variant_annotations_task = ( - UpdateVariantAnnotationsTableWithNewVariantsTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SV, - sample_type=SampleType.WGS, - callset_path=TEST_SV_VCF_2, - project_guids=['R0116_test_project3', 'R0117_test_project4'], - validations_to_skip=[ALL_VALIDATIONS], - run_id='run_id', - ) - ) - worker.add(update_variant_annotations_task) - worker.run() - self.assertTrue(update_variant_annotations_task.complete()) - ht = hl.read_table(update_variant_annotations_task.output().path) - self.assertEqual(ht.count(), 2) - self.assertEqual( - len(ht.globals.updates.collect()[0]), - 2, - ) - - def test_gcnv_update_vat_multiple( - self, - ) -> None: - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_5, - ReferenceGenome.GRCh38, - DatasetType.GCNV, - SampleType.WES, - 'R0115_test_project2', - ) - worker = luigi.worker.Worker() - update_variant_annotations_task = ( - UpdateVariantAnnotationsTableWithNewVariantsTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.GCNV, - sample_type=SampleType.WES, - callset_path=TEST_GCNV_BED_FILE, - project_guids=['R0115_test_project2'], - validations_to_skip=[ALL_VALIDATIONS], - run_id=TEST_RUN_ID, - ) - ) - worker.add(update_variant_annotations_task) - worker.run() - self.assertTrue(update_variant_annotations_task.complete()) - self.assertFalse( - GCSorLocalFolderTarget( - f'{self.mock_env.REFERENCE_DATASETS_DIR}/v03/GRCh38/GCNV/lookup.ht', - ).exists(), - ) - ht = hl.read_table(update_variant_annotations_task.output().path) - self.assertEqual(ht.count(), 2) - self.assertCountEqual( - ht.globals.collect(), - [ - hl.Struct( - enums=hl.Struct( - sv_type=SV_TYPES, - sorted_gene_consequences=hl.Struct( - major_consequence=SV_CONSEQUENCE_RANKS, - ), - ), - migrations=[], - max_key_=1, - updates={ - hl.Struct( - callset=TEST_GCNV_BED_FILE, - project_guid='R0115_test_project2', - remap_pedigree_hash=hl.eval( - remap_pedigree_hash( - TEST_PEDIGREE_5, - ), - ), - ), - }, - ), - ], - ) - self.assertCountEqual( - ht.collect(), - [ - hl.Struct( - variant_id='suffix_16456_DEL', - end_locus=hl.Locus( - contig='chr1', - position=100023213, - reference_genome='GRCh38', - ), - gt_stats=hl.Struct( - AF=hl.eval(hl.float32(4.401408e-05)), - AC=1, - AN=22720, - Hom=None, - Het=None, - ), - num_exon=3, - rg37_locus=hl.Locus( - contig=1, - position=100472493, - reference_genome='GRCh37', - ), - rg37_locus_end=hl.Locus( - contig=1, - position=100488769, - reference_genome='GRCh37', - ), - sorted_gene_consequences=[ - hl.Struct(gene_id='ENSG00000117620', major_consequence_id=0), - hl.Struct(gene_id='ENSG00000283761', major_consequence_id=0), - hl.Struct(gene_id='ENSG22222222222', major_consequence_id=None), - ], - start_locus=hl.Locus( - contig='chr1', - position=100006937, - reference_genome='GRCh38', - ), - strvctvre=hl.Struct(score=hl.eval(hl.float32(0.583))), - sv_type_id=5, - xpos=1100006937, - key_=0, - ), - hl.Struct( - variant_id='suffix_16457_DEL', - end_locus=hl.Locus( - contig='chr1', - position=100023212, - reference_genome='GRCh38', - ), - gt_stats=hl.Struct( - AF=8.802817319519818e-05, - AC=2, - AN=22719, - Hom=None, - Het=None, - ), - num_exon=2, - rg37_locus=hl.Locus( - contig=1, - position=100483142, - reference_genome='GRCh37', - ), - rg37_locus_end=hl.Locus( - contig=1, - position=100488768, - reference_genome='GRCh37', - ), - sorted_gene_consequences=[ - hl.Struct(gene_id='ENSG00000283761', major_consequence_id=0), - hl.Struct(gene_id='ENSG22222222222', major_consequence_id=None), - ], - start_locus=hl.Locus( - contig='chr1', - position=100017586, - reference_genome='GRCh38', - ), - strvctvre=hl.Struct(score=0.5070000290870667), - sv_type_id=5, - xpos=1100017586, - key_=1, - ), - ], - ) - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_8, - ReferenceGenome.GRCh38, - DatasetType.GCNV, - SampleType.WES, - 'R0115_test_project2', - ) - update_variant_annotations_task = ( - UpdateVariantAnnotationsTableWithNewVariantsTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.GCNV, - sample_type=SampleType.WES, - callset_path=TEST_GCNV_BED_FILE_2, - project_guids=['R0115_test_project2'], - validations_to_skip=[ALL_VALIDATIONS], - run_id='second_run_id', - ) - ) - worker.add(update_variant_annotations_task) - worker.run() - ht = hl.read_table(update_variant_annotations_task.output().path) - self.assertEqual(ht.count(), 3) - self.assertCountEqual( - ht.select('gt_stats').collect(), - [ - hl.Struct( - # Existing variant, gt_stats are preserved - variant_id='suffix_16456_DEL', - gt_stats=hl.Struct( - AF=hl.eval(hl.float32(4.401408e-05)), - AC=1, - AN=22720, - Hom=None, - Het=None, - ), - ), - hl.Struct( - # Exiting variant, gt_stats are updated - variant_id='suffix_16457_DEL', - gt_stats=hl.Struct( - AF=8.111110946629196e-05, - AC=3, - AN=36986, - Hom=None, - Het=None, - ), - ), - hl.Struct( - # New variant. - variant_id='suffix_99999_DEL', - gt_stats=hl.Struct( - AF=8.802817319519818e-05, - AC=2, - AN=22719, - Hom=None, - Het=None, - ), - ), - ], - ) diff --git a/loading_pipeline/lib/tasks/validate_callset_test.py b/loading_pipeline/lib/tasks/validate_callset_test.py deleted file mode 100644 index a56f78a894..0000000000 --- a/loading_pipeline/lib/tasks/validate_callset_test.py +++ /dev/null @@ -1,83 +0,0 @@ -import json -import shutil - -import luigi.worker - -from loading_pipeline.lib.core import ( - DatasetType, - ReferenceGenome, - SampleType, -) -from loading_pipeline.lib.paths import ( - valid_reference_dataset_path, -) -from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset -from loading_pipeline.lib.tasks.validate_callset import ( - ValidateCallsetTask, -) -from loading_pipeline.lib.tasks.write_validation_errors_for_run import ( - UpdatedValidationErrorsForRunTask, -) -from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase - -TEST_CODING_AND_NONCODING_HT = 'loading_pipeline/var/test/reference_datasets/GRCh38/gnomad_coding_and_noncoding/1.0.ht' -MULTIPLE_VALIDATION_EXCEPTIONS_VCF = ( - 'loading_pipeline/var/test/callsets/multiple_validation_exceptions.vcf' -) - -TEST_RUN_ID = 'manual__2024-04-03' - - -class ValidateCallsetTest(MockedDatarootTestCase): - def setUp(self) -> None: - super().setUp() - shutil.copytree( - TEST_CODING_AND_NONCODING_HT, - valid_reference_dataset_path( - ReferenceGenome.GRCh38, - ReferenceDataset.gnomad_coding_and_noncoding, - ), - ) - - def test_validate_callset_multiple_exceptions( - self, - ) -> None: - worker = luigi.worker.Worker() - validate_callset_task = ValidateCallsetTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - sample_type=SampleType.WES, - # NB: - # This callset contains duplicate rows for chr1:902088, - # a NON_REF allele type at position chr1: 902024, missing - # all contigs but chr1, and contains non-coding variants. - callset_path=MULTIPLE_VALIDATION_EXCEPTIONS_VCF, - project_guids=['project_a'], - run_id=TEST_RUN_ID, - ) - worker.add(validate_callset_task) - worker.run() - self.assertFalse(validate_callset_task.complete()) - - updated_validation_errors_task = UpdatedValidationErrorsForRunTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - sample_type=SampleType.WES, - callset_path=MULTIPLE_VALIDATION_EXCEPTIONS_VCF, - project_guids=['project_a'], - run_id=TEST_RUN_ID, - ) - self.assertTrue(updated_validation_errors_task.complete()) - with updated_validation_errors_task.output().open('r') as f: - self.assertDictEqual( - json.load(f), - { - 'project_guids': ['project_a'], - 'error_messages': [ - 'Alleles with invalid allele are present in the callset. This appears to be a GVCF containing records for sites with no variants.', - 'Missing the following expected contigs:chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr2, chr20, chr21, chr22, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chrX', - "Variants are present multiple times in the callset: ['1-902088-G-A']", - 'Sample type validation error: dataset sample-type is specified as WES but appears to be WGS because it contains many common non-coding variants', - ], - }, - ) diff --git a/loading_pipeline/lib/tasks/write_metadata_for_run_test.py b/loading_pipeline/lib/tasks/write_metadata_for_run_test.py deleted file mode 100644 index 2b5dc7a22d..0000000000 --- a/loading_pipeline/lib/tasks/write_metadata_for_run_test.py +++ /dev/null @@ -1,188 +0,0 @@ -import json -from unittest import mock -from unittest.mock import Mock - -import luigi.worker - -from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType -from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS -from loading_pipeline.lib.paths import relatedness_check_tsv_path -from loading_pipeline.lib.tasks.write_metadata_for_run import WriteMetadataForRunTask -from loading_pipeline.lib.test.misc import copy_project_pedigree_to_mocked_dir -from loading_pipeline.lib.test.mock_complete_task import MockCompleteTask -from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase - -TEST_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' -TEST_PEDIGREE_3_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_3_remap.tsv' -TEST_PEDIGREE_4_REMAP_2 = ( - 'loading_pipeline/var/test/pedigrees/test_pedigree_4_remap_2.tsv' -) -TEST_SAMPLE_QC_JSON = 'loading_pipeline/var/test/sample_qc_1.json' - - -class WriteMetadataForRunTaskTest(MockedDatarootTestCase): - @mock.patch( - 'loading_pipeline.lib.tasks.write_metadata_for_run.sample_qc_json_path', - lambda *_: TEST_SAMPLE_QC_JSON, - ) - @mock.patch('loading_pipeline.lib.tasks.write_metadata_for_run.FeatureFlag') - @mock.patch( - 'loading_pipeline.lib.tasks.write_sex_check_table.WriteTDRMetricsFilesTask', - ) - @mock.patch( - 'loading_pipeline.lib.tasks.write_metadata_for_run.WriteSampleQCJsonTask', - ) - def test_write_metadata_for_run_task( - self, - write_sample_qc_json_task: Mock, - write_tdr_metrics_task: Mock, - mock_ff: Mock, - ) -> None: - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_3_REMAP, - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - SampleType.WGS, - 'R0113_test_project', - ) - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_4_REMAP_2, - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - SampleType.WGS, - 'R0114_project4', - ) - mock_ff.EXPECT_TDR_METRICS = True - write_tdr_metrics_task.return_value = MockCompleteTask() - write_sample_qc_json_task.return_value = MockCompleteTask() - worker = luigi.worker.Worker() - write_metadata_for_run_task = WriteMetadataForRunTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - sample_type=SampleType.WGS, - callset_path=TEST_VCF, - project_guids=['R0113_test_project', 'R0114_project4'], - validations_to_skip=[ALL_VALIDATIONS], - run_id='run_123456', - ) - worker.add(write_metadata_for_run_task) - worker.run() - self.assertTrue( - 'run_123456/metadata.json' in write_metadata_for_run_task.output().path, - ) - self.assertTrue(write_metadata_for_run_task.complete()) - with write_metadata_for_run_task.output().open('r') as f: - self.assertDictEqual( - json.load(f), - { - 'callsets': [TEST_VCF], - 'project_guids': ['R0113_test_project', 'R0114_project4'], - 'failed_family_samples': { - 'missing_samples': { - 'efg_1': { - # This sample is present in the callset, but intentionally - # mapped away - 'samples': ['NA20888_1'], - 'reasons': ["Missing samples: {'NA20888_1'}"], - }, - }, - 'relatedness_check': {}, - 'sex_check': {}, - 'ploidy_check': {}, - }, - 'family_samples': { - 'abc_1': [ - 'HG00731_1', - 'HG00732_1', - 'HG00733_1', - ], - '123_1': ['NA19675_1'], - '234_1': ['NA19678_1'], - '345_1': ['NA19679_1'], - '456_1': ['NA20870_1'], - '567_1': ['NA20872_1'], - '678_1': ['NA20874_1'], - '789_1': ['NA20875_1'], - '890_1': ['NA20876_1'], - '901_1': ['NA20877_1'], - 'bcd_1': ['NA20878_1'], - 'cde_1': ['NA20881_1'], - 'def_1': ['NA20885_1'], - }, - 'run_id': 'run_123456', - 'sample_type': SampleType.WGS.value, - 'relatedness_check_file_path': relatedness_check_tsv_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_VCF, - ), - 'sample_qc': { - 'HG00731_1': {'filter_flags': ['coverage', 'contamination']}, - 'HG00732_1': {'filter_flags': ['coverage']}, - 'HG00733_1': {'filter_flags': ['contamination']}, - 'NA19675_1': {'filter_flags': []}, - 'NA20888_1': {'filter_flags': ['sample_failed']}, - }, - }, - ) - - @mock.patch('loading_pipeline.lib.tasks.write_metadata_for_run.FeatureFlag') - def test_write_metadata_for_run_task_without_tdr_metrics( - self, - mock_ff: Mock, - ) -> None: - # When WriteSampleQCJsonTask is not a requirement, every project's - # remapped and subsetted callset must still be collected. - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_3_REMAP, - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - SampleType.WGS, - 'R0113_test_project', - ) - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_4_REMAP_2, - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - SampleType.WGS, - 'R0114_project4', - ) - mock_ff.EXPECT_TDR_METRICS = False - worker = luigi.worker.Worker() - write_metadata_for_run_task = WriteMetadataForRunTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - sample_type=SampleType.WGS, - callset_path=TEST_VCF, - project_guids=['R0113_test_project', 'R0114_project4'], - validations_to_skip=[ALL_VALIDATIONS], - run_id='run_123457', - ) - worker.add(write_metadata_for_run_task) - worker.run() - self.assertTrue(write_metadata_for_run_task.complete()) - with write_metadata_for_run_task.output().open('r') as f: - metadata_json = json.load(f) - self.assertDictEqual( - metadata_json['family_samples'], - { - 'abc_1': [ - 'HG00731_1', - 'HG00732_1', - 'HG00733_1', - ], - '123_1': ['NA19675_1'], - '234_1': ['NA19678_1'], - '345_1': ['NA19679_1'], - '456_1': ['NA20870_1'], - '567_1': ['NA20872_1'], - '678_1': ['NA20874_1'], - '789_1': ['NA20875_1'], - '890_1': ['NA20876_1'], - '901_1': ['NA20877_1'], - 'bcd_1': ['NA20878_1'], - 'cde_1': ['NA20881_1'], - 'def_1': ['NA20885_1'], - }, - ) - self.assertDictEqual(metadata_json['sample_qc'], {}) diff --git a/loading_pipeline/lib/tasks/write_relatedness_check_table_test.py b/loading_pipeline/lib/tasks/write_relatedness_check_table_test.py deleted file mode 100644 index 7cc814a5fa..0000000000 --- a/loading_pipeline/lib/tasks/write_relatedness_check_table_test.py +++ /dev/null @@ -1,120 +0,0 @@ -import shutil -from unittest.mock import patch - -import hail as hl -import luigi.worker - -from loading_pipeline.lib.core import ( - DatasetType, - ReferenceGenome, - SampleType, -) -from loading_pipeline.lib.misc.io import import_vcf -from loading_pipeline.lib.paths import ( - postprocessed_callset_path, - relatedness_check_table_path, - valid_reference_dataset_path, -) -from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset -from loading_pipeline.lib.tasks.write_relatedness_check_table import ( - WriteRelatednessCheckTableTask, -) -from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase - -TEST_GNOMAD_QC_HT = ( - 'loading_pipeline/var/test/reference_datasets/GRCh38/gnomad_qc/1.0.ht' -) -TEST_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' -TEST_RUN_ID = 'manual__2024-04-03' - - -class WriteRelatednessCheckTableTaskTest(MockedDatarootTestCase): - def setUp(self) -> None: - super().setUp() - shutil.copytree( - TEST_GNOMAD_QC_HT, - valid_reference_dataset_path( - ReferenceGenome.GRCh38, - ReferenceDataset.gnomad_qc, - ), - ) - - # Force imported callset to be complete - ht = import_vcf(TEST_VCF, ReferenceGenome.GRCh38) - ht = ht.annotate_globals(validated_sample_type=SampleType.WGS.value) - ht = ht.annotate_rows(**{'info.AF': ht.info.AF}) - ht.write( - postprocessed_callset_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_VCF, - ), - ) - - def test_relatedness_check_table_task_gnomad_qc_updated( - self, - ) -> None: - self.assertEqual( - hl.eval( - hl.read_table( - valid_reference_dataset_path( - ReferenceGenome.GRCh38, - ReferenceDataset.gnomad_qc, - ), - ).version, - ), - '1.0', - ) - with ( - patch.object( - ReferenceDataset, - 'version', - return_value='2.0', - ), - patch.object( - ReferenceDataset, - 'get_ht', - lambda *_: hl.Table.parallelize( - [], - hl.tstruct( - locus=hl.tlocus('GRCh38'), - alleles=hl.tarray(hl.tstr), - ), - key=['locus', 'alleles'], - globals=hl.Struct(version='2.0'), - ), - ), - ): - worker = luigi.worker.Worker() - task = WriteRelatednessCheckTableTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - run_id=TEST_RUN_ID, - sample_type=SampleType.WGS, - callset_path=TEST_VCF, - ) - worker.add(task) - worker.run() - self.assertTrue(task.complete()) - self.assertEqual( - hl.eval( - hl.read_table( - valid_reference_dataset_path( - ReferenceGenome.GRCh38, - ReferenceDataset.gnomad_qc, - ), - ).version, - ), - '2.0', - ) - ht = hl.read_table( - relatedness_check_table_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_VCF, - ), - ) - self.assertEqual( - ht.collect(), - [], - ) diff --git a/loading_pipeline/lib/tasks/write_relatedness_check_tsv_test.py b/loading_pipeline/lib/tasks/write_relatedness_check_tsv_test.py deleted file mode 100644 index 35a9956f78..0000000000 --- a/loading_pipeline/lib/tasks/write_relatedness_check_tsv_test.py +++ /dev/null @@ -1,53 +0,0 @@ -import shutil - -import luigi.worker - -from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType -from loading_pipeline.lib.paths import relatedness_check_table_path -from loading_pipeline.lib.tasks.write_relatedness_check_tsv import ( - WriteRelatednessCheckTsvTask, -) -from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase - -TEST_RELATEDNESS_CHECK_1 = ( - 'loading_pipeline/var/test/relatedness_check/test_relatedness_check_1.ht' -) -TEST_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' -TEST_RUN_ID = 'manual__2024-04-03' - - -class WriteRelatednessCheckTsvTaskTest(MockedDatarootTestCase): - def setUp(self) -> None: - super().setUp() - shutil.copytree( - TEST_RELATEDNESS_CHECK_1, - relatedness_check_table_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_VCF, - ), - ) - - def test_write_relatedness_check_tsv_task( - self, - ) -> None: - worker = luigi.worker.Worker() - task = WriteRelatednessCheckTsvTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - callset_path=TEST_VCF, - run_id=TEST_RUN_ID, - sample_type=SampleType.WES, - ) - worker.add(task) - worker.run() - self.assertTrue(task.complete()) - with task.output().open('r') as f: - lines = f.readlines() - expected_lines = [ - 'i\tj\tibd0\tibd1\tibd2\tpi_hat\n', - 'HG00731_1\tHG00733_1\t0\t1\t0\t5.0000e-01\n', - 'HG00732_1\tHG00733_1\t0\t1\t0\t5.0000e-01\n', - ] - for expected_line, actual_line in zip(expected_lines, lines, strict=False): - self.assertEqual(expected_line, actual_line) diff --git a/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset_test.py b/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset_test.py deleted file mode 100644 index 590795424a..0000000000 --- a/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset_test.py +++ /dev/null @@ -1,460 +0,0 @@ -import json -import shutil -from unittest.mock import Mock, patch - -import hail as hl -import luigi.worker - -from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType -from loading_pipeline.lib.misc.io import remap_pedigree_hash -from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS -from loading_pipeline.lib.paths import ( - relatedness_check_table_path, - sex_check_table_path, -) -from loading_pipeline.lib.tasks.write_remapped_and_subsetted_callset import ( - WriteRemappedAndSubsettedCallsetTask, -) -from loading_pipeline.lib.tasks.write_validation_errors_for_run import ( - UpdatedValidationErrorsForRunTask, -) -from loading_pipeline.lib.test.misc import copy_project_pedigree_to_mocked_dir -from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase - -TEST_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' -TEST_PEDIGREE_3_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_3_remap.tsv' -TEST_PEDIGREE_3_DIFFERENT_FAMILIES = ( - 'loading_pipeline/var/test/pedigrees/test_pedigree_3_different_families.tsv' -) -TEST_PEDIGREE_4_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_4_remap.tsv' -TEST_PEDIGREE_7 = 'loading_pipeline/var/test/pedigrees/test_pedigree_7.tsv' -TEST_SEX_CHECK_1 = 'loading_pipeline/var/test/sex_check/test_sex_check_1.ht' -TEST_RELATEDNESS_CHECK_1 = ( - 'loading_pipeline/var/test/relatedness_check/test_relatedness_check_1.ht' -) - -TEST_RUN_ID = 'manual__2024-04-03' - - -class WriteRemappedAndSubsettedCallsetTaskTest(MockedDatarootTestCase): - def setUp(self) -> None: - super().setUp() - # +-------------+---------------+ - # | s | predicted_sex | - # +-------------+---------------+ - # | str | str | - # +-------------+---------------+ - # | "HG00731_1" | "F" | - # | "HG00732_1" | "M" | - # | "HG00733_1" | "F" | - # | "NA19675_1" | "F" | - # | "NA19678_1" | "M" | - # | "NA19679_1" | "F" | - # | "NA20870_1" | "F" | - # | "NA20872_1" | "M" | - # | "NA20874_1" | "F" | - # | "NA20875_1" | "F" | - # | "NA20876_1" | "F" | - # | "NA20877_1" | "F" | - # | "NA20878_1" | "M" | - # | "NA20881_1" | "M" | - # | "NA20885_1" | "F" | - # | "NA20888_1" | "F" | - # +-------------+---------------+ - shutil.copytree( - TEST_SEX_CHECK_1, - sex_check_table_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_VCF, - ), - ) - # +-------------+-------------+-------+-------+-------+----------+ - # | i | j | ibd0 | ibd1 | ibd2 | pi_hat | - # +-------------+-------------+-------+-------+-------+----------+ - # | str | str | int32 | int32 | int32 | float64 | - # +-------------+-------------+-------+-------+-------+----------+ - # | "HG00731_1" | "HG00733_1" | 0 | 1 | 0 | 5.00e-01 | - # | "HG00732_1" | "HG00733_1" | 0 | 1 | 0 | 5.00e-01 | - # +-------------+-------------+-------+-------+-------+----------+ - shutil.copytree( - TEST_RELATEDNESS_CHECK_1, - relatedness_check_table_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_VCF, - ), - ) - - def test_write_remapped_and_subsetted_callset_task( - self, - ) -> None: - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_3_REMAP, - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - SampleType.WGS, - 'R0113_test_project', - ) - worker = luigi.worker.Worker() - wrsc_task = WriteRemappedAndSubsettedCallsetTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - run_id=TEST_RUN_ID, - sample_type=SampleType.WGS, - callset_path=TEST_VCF, - project_guids=['R0113_test_project'], - project_i=0, - validations_to_skip=[ALL_VALIDATIONS], - skip_expect_tdr_metrics=True, - ) - worker.add(wrsc_task) - worker.run() - self.assertTrue(wrsc_task.complete()) - mt = hl.read_matrix_table(wrsc_task.output().path) - self.assertEqual(mt.count(), (30, 3)) - self.assertEqual( - mt.globals.collect(), - [ - hl.Struct( - remap_pedigree_hash=hl.eval( - remap_pedigree_hash( - TEST_PEDIGREE_3_REMAP, - ), - ), - failed_family_samples=hl.Struct( - missing_samples={}, - relatedness_check={}, - sex_check={}, - ploidy_check={}, - ), - family_samples={'abc_1': ['HG00731_1', 'HG00732_1', 'HG00733_1']}, - ), - ], - ) - - @patch( - 'loading_pipeline.lib.tasks.write_remapped_and_subsetted_callset.FeatureFlag', - ) - def test_write_remapped_and_subsetted_callset_task_failed_some_family_checks( - self, - mock_ff: Mock, - ) -> None: - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_4_REMAP, - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - SampleType.WGS, - 'R0114_project4', - ) - mock_ff.CHECK_SEX_AND_RELATEDNESS = True - worker = luigi.worker.Worker() - wrsc_task = WriteRemappedAndSubsettedCallsetTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - run_id=TEST_RUN_ID, - sample_type=SampleType.WGS, - callset_path=TEST_VCF, - project_guids=['R0114_project4'], - project_i=0, - validations_to_skip=[ALL_VALIDATIONS], - skip_expect_tdr_metrics=True, - ) - worker.add(wrsc_task) - worker.run() - self.assertTrue(wrsc_task.complete()) - mt = hl.read_matrix_table(wrsc_task.output().path) - # NB: one "family"/"sample" has been removed because of a failed sex check, - # and 4 removed because of a failed ploidy check! - self.assertEqual(mt.count(), (30, 8)) - self.assertEqual( - mt.globals.collect(), - [ - hl.Struct( - remap_pedigree_hash=hl.eval( - remap_pedigree_hash( - TEST_PEDIGREE_4_REMAP, - ), - ), - family_samples={ - '123_1': ['NA19675_1'], - '345_1': ['NA19679_1'], - '456_1': ['NA20870_1'], - '678_1': ['NA20874_1'], - '789_1': ['NA20875_1'], - '890_1': ['NA20876_1'], - '901_1': ['NA20877_1'], - 'efg_1': ['NA20888_1'], - }, - failed_family_samples=hl.Struct( - missing_samples={}, - relatedness_check={}, - sex_check={ - 'def_1': { - 'reasons': [ - 'Sample NA20885_1 has pedigree sex M but imputed sex F', - ], - 'samples': ['NA20885_1'], - }, - }, - ploidy_check={ - '234_1': { - 'reasons': [ - "Found samples with misaligned ploidy with their provided imputed sex: ['NA19678_1']", - ], - 'samples': ['NA19678_1'], - }, - '567_1': { - 'reasons': [ - "Found samples with misaligned ploidy with their provided imputed sex: ['NA20872_1']", - ], - 'samples': ['NA20872_1'], - }, - 'bcd_1': { - 'reasons': [ - "Found samples with misaligned ploidy with their provided imputed sex: ['NA20878_1']", - ], - 'samples': ['NA20878_1'], - }, - 'cde_1': { - 'reasons': [ - "Found samples with misaligned ploidy with their provided imputed sex: ['NA20881_1']", - ], - 'samples': ['NA20881_1'], - }, - }, - ), - ), - ], - ) - - @patch( - 'loading_pipeline.lib.tasks.write_remapped_and_subsetted_callset.FeatureFlag', - ) - def test_write_remapped_and_subsetted_callset_task_all_families_failed( - self, - mock_ff: Mock, - ) -> None: - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_7, - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - SampleType.WGS, - 'R0114_project4', - ) - mock_ff.CHECK_SEX_AND_RELATEDNESS = True - worker = luigi.worker.Worker() - wrsc_task = WriteRemappedAndSubsettedCallsetTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - run_id=TEST_RUN_ID, - sample_type=SampleType.WGS, - callset_path=TEST_VCF, - project_guids=['R0114_project4'], - project_i=0, - validations_to_skip=[ALL_VALIDATIONS], - skip_expect_tdr_metrics=True, - ) - worker.add(wrsc_task) - worker.run() - self.assertFalse(wrsc_task.complete()) - updated_validation_errors_task = UpdatedValidationErrorsForRunTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - sample_type=SampleType.WES, - callset_path=TEST_VCF, - project_guids=['R0114_project4'], - validations_to_skip=[ALL_VALIDATIONS], - run_id=TEST_RUN_ID, - ) - self.assertTrue(updated_validation_errors_task.complete()) - with updated_validation_errors_task.output().open('r') as f: - self.assertDictEqual( - json.load(f), - { - 'project_guids': ['R0114_project4'], - 'error_messages': ['All families failed validation checks'], - 'failed_family_samples': { - 'missing_samples': { - 'efg_1': { - 'samples': ['NA99999_1'], - 'reasons': ["Missing samples: {'NA99999_1'}"], - }, - }, - 'relatedness_check': {}, - 'sex_check': { - '890_1': { - 'samples': ['NA20876_1'], - 'reasons': [ - 'Sample NA20876_1 has pedigree sex M but imputed sex F', - ], - }, - '456_1': { - 'samples': ['NA20870_1'], - 'reasons': [ - 'Sample NA20870_1 has pedigree sex M but imputed sex F', - ], - }, - '123_1': { - 'samples': ['NA19675_1'], - 'reasons': [ - 'Sample NA19675_1 has pedigree sex M but imputed sex F', - ], - }, - '678_1': { - 'samples': ['NA20874_1'], - 'reasons': [ - 'Sample NA20874_1 has pedigree sex M but imputed sex F', - ], - }, - '789_1': { - 'samples': ['NA20875_1'], - 'reasons': [ - 'Sample NA20875_1 has pedigree sex M but imputed sex F', - ], - }, - '901_1': { - 'samples': ['NA20877_1'], - 'reasons': [ - 'Sample NA20877_1 has pedigree sex M but imputed sex F', - ], - }, - '345_1': { - 'samples': ['NA19679_1'], - 'reasons': [ - 'Sample NA19679_1 has pedigree sex M but imputed sex F', - ], - }, - 'def_1': { - 'samples': ['NA20885_1'], - 'reasons': [ - 'Sample NA20885_1 has pedigree sex M but imputed sex F', - ], - }, - }, - 'ploidy_check': { - '567_1': { - 'samples': ['NA20872_1'], - 'reasons': [ - "Found samples with misaligned ploidy with their provided imputed sex: ['NA20872_1']", - ], - }, - '234_1': { - 'samples': ['NA19678_1'], - 'reasons': [ - "Found samples with misaligned ploidy with their provided imputed sex: ['NA19678_1']", - ], - }, - 'bcd_1': { - 'samples': ['NA20878_1'], - 'reasons': [ - "Found samples with misaligned ploidy with their provided imputed sex: ['NA20878_1']", - ], - }, - 'cde_1': { - 'samples': ['NA20881_1'], - 'reasons': [ - "Found samples with misaligned ploidy with their provided imputed sex: ['NA20881_1']", - ], - }, - }, - }, - }, - ) - - @patch( - 'loading_pipeline.lib.tasks.write_remapped_and_subsetted_callset.FeatureFlag', - ) - def test_write_remapped_and_subsetted_callset_task_combined_validation_errors( - self, - mock_ff: Mock, - ) -> None: - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_3_DIFFERENT_FAMILIES, - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - SampleType.WGS, - 'R0113_test_project', - ) - worker = luigi.worker.Worker() - - wrsc_task_1 = WriteRemappedAndSubsettedCallsetTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - run_id=TEST_RUN_ID, - sample_type=SampleType.WGS, - callset_path=TEST_VCF, - project_guids=['R0113_test_project'], - project_i=0, - validations_to_skip=[ALL_VALIDATIONS], - skip_expect_tdr_metrics=True, - ) - worker.add(wrsc_task_1) - worker.run() - - # Second run: load pedigree 7 where all families fail validation checks - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_7, - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - SampleType.WGS, - 'R0114_project4', - ) - worker_2 = luigi.worker.Worker() - - wrsc_task_2 = WriteRemappedAndSubsettedCallsetTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - run_id=TEST_RUN_ID, - sample_type=SampleType.WGS, - callset_path=TEST_VCF, - project_guids=['R0114_project4'], - project_i=0, - validations_to_skip=[ALL_VALIDATIONS], - skip_expect_tdr_metrics=True, - ) - worker_2.add(wrsc_task_2) - worker_2.run() - - # Verify second task does not complete (all families failed) - self.assertFalse(wrsc_task_2.complete()) - - # Verify validation errors for second run - updated_validation_errors_task = UpdatedValidationErrorsForRunTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - sample_type=SampleType.WES, - callset_path=TEST_VCF, - project_guids=['R0113_test_project', 'R0114_project4'], - validations_to_skip=[ALL_VALIDATIONS], - run_id=TEST_RUN_ID, - ) - self.assertTrue(updated_validation_errors_task.complete()) - with updated_validation_errors_task.output().open('r') as f: - validation_errors = json.load(f) - - # Verify that all families failed in the second run - self.assertIn( - 'All families failed validation checks', - validation_errors['error_messages'], - ) - # Should have missing samples, sex checks, and ploidy checks all failing - failed_samples = validation_errors['failed_family_samples'] - self.assertGreater( - len(failed_samples['missing_samples']), - 0, - 'Expected missing_samples to have failures', - ) - self.assertGreater( - len(failed_samples['sex_check']), - 0, - 'Expected sex_check to have failures', - ) - self.assertGreater( - len(failed_samples['ploidy_check']), - 0, - 'Expected ploidy_check to have failures', - ) - # Verify that both project guids are in the validation errors - self.assertIn('R0113_test_project', validation_errors['project_guids']) - self.assertIn('R0114_project4', validation_errors['project_guids']) diff --git a/loading_pipeline/lib/tasks/write_sample_qc_json_test.py b/loading_pipeline/lib/tasks/write_sample_qc_json_test.py deleted file mode 100644 index 1c2709c9b7..0000000000 --- a/loading_pipeline/lib/tasks/write_sample_qc_json_test.py +++ /dev/null @@ -1,269 +0,0 @@ -import json -import os -import shutil -from unittest.mock import Mock, patch - -import hail as hl -import hailtop.fs as hfs -import luigi.worker - -from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType -from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS -from loading_pipeline.lib.paths import ancestry_model_rf_path, tdr_metrics_dir -from loading_pipeline.lib.tasks.write_sample_qc_json import WriteSampleQCJsonTask -from loading_pipeline.lib.test.misc import copy_project_pedigree_to_mocked_dir -from loading_pipeline.lib.test.mock_complete_task import MockCompleteTask -from loading_pipeline.lib.test.mocked_reference_datasets_testcase import ( - MockedReferenceDatasetsTestCase, -) - -TEST_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' -TEST_PEDIGREE_3_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_3_remap.tsv' -TEST_TDR_METRICS_FILE = 'loading_pipeline/var/test/tdr_metrics.tsv' -TEST_RUN_ID = 'manual__2024-04-03' - -PCA_SCORES = [0.00212, 0.011, 0.0105, 0.161, 0.026] + [0.1 for _ in range(15)] -EXPECTED_ANC_PROBABILITIES = { - 'prob_afr': 0.02, - 'prob_ami': 0.0, - 'prob_amr': 0.02, - 'prob_asj': 0.9, - 'prob_eas': 0.0, - 'prob_fin': 0.0, - 'prob_mid': 0.0, - 'prob_nfe': 0.05, - 'prob_sas': 0.01, -} -TEST_ANCESTRY_IMPUTATION_MODEL_PATH = ( - 'loading_pipeline/var/test/ancestry_imputation_model.onnx' -) - - -class WriteSampleQCJsonTaskTest(MockedReferenceDatasetsTestCase): - @patch('loading_pipeline.lib.methods.sample_qc.assign_population_pcs') - @patch('loading_pipeline.lib.methods.sample_qc.pc_project') - @patch('loading_pipeline.lib.tasks.write_sample_qc_json.WriteTDRMetricsFilesTask') - def test_call_sample_qc( - self, - mock_tdr_task: Mock, - mock_pc_project: Mock, - mock_assign_population_pcs: Mock, - ) -> None: - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_3_REMAP, - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - SampleType.WGS, - 'R0113_test_project', - ) - os.makedirs( - os.path.dirname(ancestry_model_rf_path()), - exist_ok=True, - ) - shutil.copy2(TEST_ANCESTRY_IMPUTATION_MODEL_PATH, ancestry_model_rf_path()) - os.makedirs( - tdr_metrics_dir(ReferenceGenome.GRCh38, DatasetType.SNV_INDEL), - exist_ok=True, - ) - shutil.copy2( - TEST_TDR_METRICS_FILE, - tdr_metrics_dir(ReferenceGenome.GRCh38, DatasetType.SNV_INDEL), - ) - mock_tdr_task.return_value = MockCompleteTask() - mock_pc_project.return_value = hl.Table.parallelize( - [ - { - 's': sample_id, - 'scores': PCA_SCORES, - } - for sample_id in ('HG00731', 'HG00732', 'HG00733', 'NA19675') - ], - hl.tstruct( - s=hl.tstr, - scores=hl.tarray(hl.tfloat64), - ), - key='s', - ) - mock_assign_population_pcs.return_value = ( - hl.Table.parallelize( - [ - { - 's': sample_id, - 'pca_scores': PCA_SCORES, - 'qc_pop': 'asj', - **EXPECTED_ANC_PROBABILITIES, - } - for sample_id in ('HG00731', 'HG00732', 'HG00733', 'NA19675') - ], - hl.tstruct( - s=hl.tstr, - pca_scores=hl.tarray(hl.tfloat64), - qc_pop=hl.tstr, - prob_afr=hl.tfloat64, - prob_ami=hl.tfloat64, - prob_amr=hl.tfloat64, - prob_asj=hl.tfloat64, - prob_eas=hl.tfloat64, - prob_fin=hl.tfloat64, - prob_mid=hl.tfloat64, - prob_nfe=hl.tfloat64, - prob_sas=hl.tfloat64, - ), - key='s', - ), - None, - ) - worker = luigi.worker.Worker() - task = WriteSampleQCJsonTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - run_id=TEST_RUN_ID, - sample_type=SampleType.WGS, - callset_path=TEST_VCF, - project_guids=['R0113_test_project'], - validations_to_skip=[ALL_VALIDATIONS], - ) - worker.add(task) - worker.run() - self.assertTrue(task) - self.assertTrue(hfs.exists(task.output().path)) - - expected_qc_gen_anc_results = { - 'pca_scores': PCA_SCORES, - **EXPECTED_ANC_PROBABILITIES, - **{f'pop_PC{i + 1}': PCA_SCORES[i] for i in range(20)}, - 'qc_gen_anc': 'oth', - } - with task.output().open('r') as f: - res = json.load(f) - - self.assertCountEqual( - res['HG00731_1'], - { - 'seqr_id': 'HG00731_1', - 'vcf_id': 'HG00731', - 'filtered_callrate': 1.0, - 'contamination_rate': 5.099999904632568, - 'percent_bases_at_20x': 93.69000244140625, - 'mean_coverage': 29.309999465942383, - 'filter_flags': ['contamination', 'coverage'], - **expected_qc_gen_anc_results, - 'sample_qc.call_rate': 0.9666666666666667, - 'sample_qc.n_called': 29, - 'sample_qc.n_not_called': 1, - 'sample_qc.n_filtered': 0, - 'sample_qc.n_hom_ref': 16, - 'sample_qc.n_het': 2, - 'sample_qc.n_hom_var': 11, - 'sample_qc.n_non_ref': 13, - 'sample_qc.n_singleton': 1, - 'sample_qc.n_snp': 24, - 'sample_qc.n_insertion': 0, - 'sample_qc.n_deletion': 0, - 'sample_qc.n_transition': 15, - 'sample_qc.n_transversion': 9, - 'sample_qc.n_star': 0, - 'sample_qc.r_ti_tv': 1.6666666666666667, - 'sample_qc.r_het_hom_var': 0.18181818181818182, - 'sample_qc.r_insertion_deletion': None, - 'sample_qc.f_inbreeding.f_stat': 0.284195245767986, - 'sample_qc.f_inbreeding.n_called': 29, - 'sample_qc.f_inbreeding.expected_homs': 26.20594199999999, - 'sample_qc.f_inbreeding.observed_homs': 27, - 'fail_n_snp': True, - 'fail_r_ti_tv': False, - 'fail_r_insertion_deletion': None, - 'fail_n_insertion': True, - 'fail_n_deletion': True, - 'fail_r_het_hom_var': False, - 'fail_call_rate': False, - 'qc_metrics_filters': ['n_deletion', 'n_insertion', 'n_snp'], - }, - ) - self.assertCountEqual( - res['HG00732_1'], - { - 'seqr_id': 'HG00732_1', - 'vcf_id': 'HG00732', - 'filtered_callrate': 1.0, - 'contamination_rate': 5.0, - 'percent_bases_at_20x': 90.0, - 'mean_coverage': 28.0, - 'filter_flags': ['coverage'], - **expected_qc_gen_anc_results, - 'sample_qc.call_rate': 0.9666666666666667, - 'sample_qc.n_called': 29, - 'sample_qc.n_not_called': 1, - 'sample_qc.n_filtered': 0, - 'sample_qc.n_hom_ref': 16, - 'sample_qc.n_het': 4, - 'sample_qc.n_hom_var': 9, - 'sample_qc.n_non_ref': 13, - 'sample_qc.n_singleton': 2, - 'sample_qc.n_snp': 22, - 'sample_qc.n_insertion': 0, - 'sample_qc.n_deletion': 0, - 'sample_qc.n_transition': 13, - 'sample_qc.n_transversion': 9, - 'sample_qc.n_star': 0, - 'sample_qc.r_ti_tv': 1.4444444444444444, - 'sample_qc.r_het_hom_var': 0.4444444444444444, - 'sample_qc.r_insertion_deletion': None, - 'sample_qc.f_inbreeding.f_stat': -0.431609508464028, - 'sample_qc.f_inbreeding.n_called': 29, - 'sample_qc.f_inbreeding.expected_homs': 26.20594199999999, - 'sample_qc.f_inbreeding.observed_homs': 25, - 'fail_n_snp': True, - 'fail_r_ti_tv': False, - 'fail_r_insertion_deletion': None, - 'fail_n_insertion': True, - 'fail_n_deletion': True, - 'fail_r_het_hom_var': False, - 'fail_call_rate': False, - 'qc_metrics_filters': ['n_deletion', 'n_insertion', 'n_snp'], - }, - ) - self.assertCountEqual( - res['HG00733_1'], - { - 'seqr_id': 'HG00733_1', - 'vcf_id': 'HG00733', - 'filtered_callrate': 1.0, - 'contamination_rate': 6.0, - 'percent_bases_at_20x': 85.0, - 'mean_coverage': 36.400001525878906, - 'filter_flags': ['contamination'], - **expected_qc_gen_anc_results, - 'sample_qc.call_rate': 1.0, - 'sample_qc.n_called': 30, - 'sample_qc.n_not_called': 0, - 'sample_qc.n_filtered': 0, - 'sample_qc.n_hom_ref': 17, - 'sample_qc.n_het': 3, - 'sample_qc.n_hom_var': 10, - 'sample_qc.n_non_ref': 13, - 'sample_qc.n_singleton': 0, - 'sample_qc.n_snp': 23, - 'sample_qc.n_insertion': 0, - 'sample_qc.n_deletion': 0, - 'sample_qc.n_transition': 13, - 'sample_qc.n_transversion': 10, - 'sample_qc.n_star': 0, - 'sample_qc.r_ti_tv': 1.3, - 'sample_qc.r_het_hom_var': 0.3, - 'sample_qc.r_insertion_deletion': None, - 'sample_qc.f_inbreeding.f_stat': -0.038400752079048056, - 'sample_qc.f_inbreeding.n_called': 30, - 'sample_qc.f_inbreeding.expected_homs': 27.11094199999999, - 'sample_qc.f_inbreeding.observed_homs': 27, - 'fail_n_snp': True, - 'fail_r_ti_tv': False, - 'fail_r_insertion_deletion': None, - 'fail_n_insertion': True, - 'fail_n_deletion': True, - 'fail_r_het_hom_var': False, - 'fail_call_rate': False, - 'qc_metrics_filters': ['n_deletion', 'n_insertion', 'n_snp'], - }, - ) - self.assertFalse('NA19675' in res) diff --git a/loading_pipeline/lib/tasks/write_sex_check_table_test.py b/loading_pipeline/lib/tasks/write_sex_check_table_test.py deleted file mode 100644 index 1f83d8c991..0000000000 --- a/loading_pipeline/lib/tasks/write_sex_check_table_test.py +++ /dev/null @@ -1,157 +0,0 @@ -from decimal import Decimal -from unittest.mock import Mock, patch - -import google.cloud.bigquery -import hail as hl -import luigi.worker - -from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType -from loading_pipeline.lib.paths import sex_check_table_path, tdr_metrics_path -from loading_pipeline.lib.tasks.write_sex_check_table import ( - WriteSexCheckTableTask, -) -from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase - -TEST_SEX_AND_RELATEDNESS_CALLSET_MT = ( - 'loading_pipeline/var/test/callsets/sex_and_relatedness_1.mt' -) - - -class WriteSexCheckTableTaskTest(MockedDatarootTestCase): - @patch('loading_pipeline.lib.tasks.write_tdr_metrics_files.gen_bq_table_names') - @patch('loading_pipeline.lib.tasks.write_tdr_metrics_file.bq_metrics_query') - @patch( - 'loading_pipeline.lib.tasks.write_sex_check_table.FeatureFlag', - ) - def test_snv_sex_check_table_task( - self, - mock_ff: Mock, - mock_bq_metrics_query: Mock, - mock_gen_bq_table_names: Mock, - ) -> None: - mock_ff.EXPECT_TDR_METRICS = True - mock_gen_bq_table_names.return_value = [ - 'datarepo-7242affb.datarepo_RP_3053', - 'datarepo-5a72e31b.datarepo_RP_3056', - ] - mock_bq_metrics_query.side_effect = [ - iter( - [ - google.cloud.bigquery.table.Row( - ( - 'SM-NJ8MF', - 'Unknown', - Decimal('0'), - Decimal('0'), - Decimal('0'), - ), - { - 'collaborator_sample_id': 0, - 'predicted_sex': 1, - 'contamination_rate': 2, - 'percent_bases_at_20x': 3, - 'mean_coverage': 4, - }, - ), - google.cloud.bigquery.table.Row( - ( - 'SM-MWOGC', - 'Female', - Decimal('0'), - Decimal('0'), - Decimal('0'), - ), - { - 'collaborator_sample_id': 0, - 'predicted_sex': 1, - 'contamination_rate': 2, - 'percent_bases_at_20x': 3, - 'mean_coverage': 4, - }, - ), - google.cloud.bigquery.table.Row( - ('SM-MWKWL', 'Male', Decimal('0'), Decimal('0'), Decimal('0')), - { - 'collaborator_sample_id': 0, - 'predicted_sex': 1, - 'contamination_rate': 2, - 'percent_bases_at_20x': 3, - 'mean_coverage': 4, - }, - ), - ], - ), - iter( - [ - google.cloud.bigquery.table.Row( - ('SM-NGE65', 'Male', Decimal('0'), Decimal('0'), Decimal('0')), - { - 'collaborator_sample_id': 0, - 'predicted_sex': 1, - 'contamination_rate': 2, - 'percent_bases_at_20x': 3, - 'mean_coverage': 4, - }, - ), - google.cloud.bigquery.table.Row( - ('SM-NGE5G', 'Male', Decimal('0'), Decimal('0'), Decimal('0')), - { - 'collaborator_sample_id': 0, - 'predicted_sex': 1, - 'contamination_rate': 2, - 'percent_bases_at_20x': 3, - 'mean_coverage': 4, - }, - ), - google.cloud.bigquery.table.Row( - ('SM-NC6LM', 'Male', Decimal('0'), Decimal('0'), Decimal('0')), - { - 'collaborator_sample_id': 0, - 'predicted_sex': 1, - 'contamination_rate': 2, - 'percent_bases_at_20x': 3, - 'mean_coverage': 4, - }, - ), - ], - ), - ] - worker = luigi.worker.Worker() - write_sex_check_table = WriteSexCheckTableTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - sample_type=SampleType.WGS, - callset_path='na', - project_guids=['R0113_test_project'], - run_id='manual__2024-04-03', - ) - worker.add(write_sex_check_table) - worker.run() - self.assertTrue(write_sex_check_table.complete()) - sex_check_ht = hl.read_table( - sex_check_table_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - 'na', - ), - ) - self.assertEqual( - sex_check_ht.collect(), - [ - hl.Struct(s='SM-MWKWL', predicted_sex='M'), - hl.Struct(s='SM-MWOGC', predicted_sex='F'), - hl.Struct(s='SM-NC6LM', predicted_sex='M'), - hl.Struct(s='SM-NGE5G', predicted_sex='M'), - hl.Struct(s='SM-NGE65', predicted_sex='M'), - hl.Struct(s='SM-NJ8MF', predicted_sex='U'), - ], - ) - # Check underlying tdr metrics file. - with open( - tdr_metrics_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - 'datarepo-5a72e31b.datarepo_RP_3056', - ), - ) as f: - self.assertTrue('collaborator_sample_id' in f.read()) diff --git a/loading_pipeline/lib/tasks/write_success_file_test.py b/loading_pipeline/lib/tasks/write_success_file_test.py deleted file mode 100644 index f33a5d337e..0000000000 --- a/loading_pipeline/lib/tasks/write_success_file_test.py +++ /dev/null @@ -1,34 +0,0 @@ -from unittest import mock - -import luigi.worker - -from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType -from loading_pipeline.lib.tasks.write_success_file import WriteSuccessFileTask -from loading_pipeline.lib.test.mock_complete_task import MockCompleteTask -from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase - - -class WriteSuccessFileTaskTest(MockedDatarootTestCase): - @mock.patch( - 'loading_pipeline.lib.tasks.write_success_file.RunPipelineTask', - ) - def test_write_success_file_task( - self, - mock_run_pipeline_task: mock.Mock, - ) -> None: - mock_run_pipeline_task.return_value = MockCompleteTask() - worker = luigi.worker.Worker() - write_success_file = WriteSuccessFileTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - sample_type=SampleType.WGS, - callset_path='test_callset', - project_guids=['R0113_test_project'], - run_id='manual__2024-04-03', - attempt_id=0, - ) - worker.add(write_success_file) - worker.run() - self.assertTrue(write_success_file.complete()) - with open(write_success_file.output().path) as f: - self.assertEqual(f.read(), '') diff --git a/loading_pipeline/lib/tasks/write_variant_annotations_vcf_test.py b/loading_pipeline/lib/tasks/write_variant_annotations_vcf_test.py deleted file mode 100644 index 4bad466b67..0000000000 --- a/loading_pipeline/lib/tasks/write_variant_annotations_vcf_test.py +++ /dev/null @@ -1,91 +0,0 @@ -import gzip -from unittest.mock import Mock, patch - -import hailtop.fs as hfs -import luigi.worker - -from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType -from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS -from loading_pipeline.lib.tasks.update_variant_annotations_table_with_new_variants import ( - UpdateVariantAnnotationsTableWithNewVariantsTask, -) -from loading_pipeline.lib.tasks.write_variant_annotations_vcf import ( - WriteVariantAnnotationsVCF, -) -from loading_pipeline.lib.test.misc import copy_project_pedigree_to_mocked_dir -from loading_pipeline.lib.test.mocked_reference_datasets_testcase import ( - MockedReferenceDatasetsTestCase, -) - -TEST_SV_VCF = 'loading_pipeline/var/test/callsets/sv_1.vcf' -TEST_PEDIGREE_5 = 'loading_pipeline/var/test/pedigrees/test_pedigree_5.tsv' - -GENE_ID_MAPPING = { - 'OR4F5': 'ENSG00000186092', - 'PLEKHG4B': 'ENSG00000153404', - 'OR4F16': 'ENSG00000186192', - 'OR4F29': 'ENSG00000284733', - 'FBXO28': 'ENSG00000143756', - 'SAMD11': 'ENSG00000187634', - 'C1orf174': 'ENSG00000198912', - 'TAS1R1': 'ENSG00000173662', - 'FAM131C': 'ENSG00000185519', - 'RCC2': 'ENSG00000179051', - 'NBPF3': 'ENSG00000142794', - 'AGBL4': 'ENSG00000186094', - 'KIAA1614': 'ENSG00000135835', - 'MR1': 'ENSG00000153029', - 'STX6': 'ENSG00000135823', - 'XPR1': 'ENSG00000143324', -} - - -class WriteVariantAnnotationsVCFTest(MockedReferenceDatasetsTestCase): - @patch( - 'loading_pipeline.lib.tasks.write_new_variants_table.load_gencode_gene_symbol_to_gene_id', - ) - def test_sv_export_vcf( - self, - mock_load_gencode: Mock, - ) -> None: - copy_project_pedigree_to_mocked_dir( - TEST_PEDIGREE_5, - ReferenceGenome.GRCh38, - DatasetType.SV, - SampleType.WGS, - 'R0115_test_project2', - ) - mock_load_gencode.return_value = GENE_ID_MAPPING - worker = luigi.worker.Worker() - update_variant_annotations_task = ( - UpdateVariantAnnotationsTableWithNewVariantsTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SV, - run_id='run_id1', - sample_type=SampleType.WGS, - callset_path=TEST_SV_VCF, - project_guids=['R0115_test_project2'], - validations_to_skip=[ALL_VALIDATIONS], - skip_expect_tdr_metrics=True, - ) - ) - worker.add(update_variant_annotations_task) - worker.run() - self.assertTrue(update_variant_annotations_task.complete()) - write_variant_annotations_vcf_task = WriteVariantAnnotationsVCF( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SV, - run_id='run_id1', - sample_type=SampleType.WGS, - callset_path=TEST_SV_VCF, - ) - worker.add(write_variant_annotations_vcf_task) - worker.run() - self.assertTrue( - hfs.exists( - write_variant_annotations_vcf_task.output().path, - ), - ) - with hfs.open(write_variant_annotations_vcf_task.output().path, 'rb') as f: - buf = f.read() - self.assertTrue(gzip.decompress(buf).startswith(b'##fileformat=VCFv4.2')) From 3f6946b6ee19b1192ebfea88da33e17826d7c6b2 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 16:13:43 -0400 Subject: [PATCH 217/369] new plan --- .../CLICKHOUSE_PYTEST_DJANGO_PLAN.md | 207 ------------------ ...CLICKHOUSE_PYTEST_DJANGO_REMAINING_PLAN.md | 44 ++++ 2 files changed, 44 insertions(+), 207 deletions(-) delete mode 100644 loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_PLAN.md create mode 100644 loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_REMAINING_PLAN.md diff --git a/loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_PLAN.md b/loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_PLAN.md deleted file mode 100644 index cde0c7077f..0000000000 --- a/loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_PLAN.md +++ /dev/null @@ -1,207 +0,0 @@ -# Plan: Manage ClickHouse test DB via pytest-django + `clickhouse_search` migrations - -## Goal - -Stop hand-maintaining ClickHouse schema DDL (and the static `var/test/test_clickhouse_schema.sql` -dump) inside `loading_pipeline`'s tests. Instead, use `pytest-django` to create/migrate the -ClickHouse test database from the real Django migrations in `clickhouse_search` (the source of -truth for the schema), so the pipeline's tests can never drift from production schema. - -Scope constraint: all code changes live in `loading_pipeline/` or in -`.github/workflows/pipeline-unit-tests.yml`. Nothing in `clickhouse_search/` or root `settings.py` -is modified. - -## Key constraint discovered - -`clickhouse_search/backend/base.py` does a **bare** `from settings import -CLICKHOUSE_WRITER_USER, CLICKHOUSE_WRITER_PASSWORD, DATABASES` — not `django.conf.settings`. This -only resolves correctly if a top-level module literally named `settings` is importable on -`sys.path`. Today that resolves to the main repo's heavy `settings.py` (postgres, guardian, -social_django, google.auth, etc.) whenever cwd is the repo root — which is undesirable/impossible -to depend on from `loading_pipeline`'s minimal env. - -**Trick:** create our own minimal module named `settings.py`, placed in a directory that we add to -`sys.path` ahead of the repo root (via pytest's `pythonpath` ini option, which prepends to -`sys.path`). That module serves double duty: -- It's what `clickhouse_search/backend/base.py`'s bare `import settings` resolves to. -- It's also `DJANGO_SETTINGS_MODULE` for pytest-django. - -## Single connection / single set of credentials only - -Per explicit direction: the settings module must configure **one** ClickHouse connection with -**one** set of credentials — not the production split of a read-only `clickhouse` alias plus a -privileged `clickhouse_write` alias. `DATABASES` will define a single real alias using one -writer-capable credential (needed anyway, since migrations and test data inserts require write -access). - -That real alias must be named `clickhouse_write`, not `clickhouse`: `ClickHouseRouter.allow_migrate` -(`clickhouse_search/models/__init__.py`) hardcodes `db == 'clickhouse_write'` for the -`clickhouse_search` app, so only an alias literally named `clickhouse_write` is allowed to have -migrations applied to it. - -Nuance to account for: `clickhouse_search/backend/base.py`'s `_dictionary_sql` looks up -`DATABASES['clickhouse_write']['NAME']` (for ClickHouse-sourced dictionaries with a -`clickhouse_query_template`) and `DATABASES[postgres_db]['NAME']` (default alias `'default'`, for -Postgres-sourced dictionaries) purely to embed a database *name string* into generated DDL — not to -open a second real connection. To keep this working without standing up a second live connection: -- Give `'clickhouse'` a `TEST: {'MIRROR': 'clickhouse_write'}` config, so Django reuses the - `clickhouse_write` alias's actual test database instead of creating/tearing down a second one, - while the key is still present for the `NAME` lookup (used only by `backend/base.py`, not by our - own test code). -- Give `'default'` a placeholder entry (e.g. `ENGINE: 'django.db.backends.dummy'`) purely so - `DATABASES['default']['NAME']` resolves to a string — nothing in `loading_pipeline`'s tests - actually connects to it, since there's no Postgres in this CI job. - -Test code (and the shared base class) uses `connections['clickhouse_write']` — the one alias -Django actually creates/migrates a real test database for. - -## Inventory of every ClickHouse-touching test - -1. **`lib/misc/clickhouse_test.py`** (`ClickhouseTest`) — hand-rolls ~250 lines of `CREATE - TABLE`/`CREATE DICTIONARY`/`CREATE MATERIALIZED VIEW` DDL duplicating a subset of the real - schema, plus fixture dictionaries for gene IDs/gnomAD. -2. **`lib/test/clickhouse_schema_testcase.py`** (`ClickhouseSchemaTestCase`) — loads the static - `var/test/test_clickhouse_schema.sql` dump plus a few placeholder dictionaries. Used by: - - `bin/pipeline_worker_test.py` (`PipelineWorkerTest`) - - `lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py` - (`LoadClickhouseVariantsTablesTaskTest`) -3. **`ops/repartition_clickhouse_grch38_snv_indel_test.py`** (`RepartitionGRCh38SnvIndelTest`) — - its own bespoke DDL for a synthetic, intentionally-simplified `entries` table + a wholly - separate scratch database (`REPARTITION_DATABASE_NAME`) that isn't part of `clickhouse_search`'s - schema at all. - -## The Postgres/GCS-sourced dictionary wrinkle - -A handful of dictionaries are, in production, sourced from Postgres (via the -`seqr_postgres_named_collection` named collection) or from GCS parquet URLs: - -- `seqrdb_gene_ids` -- `seqrdb_affected_status_dict` -- `GRCh38/SNV_INDEL/project_partitions_dict` -- the gnomAD reference dict (`GRCh38/SNV_INDEL/reference_data/gnomad_genomes`) - -`loading_pipeline`'s CI only runs ClickHouse (no Postgres, no GCS access). Running -`clickhouse_search`'s real migrations here requires a dummy `seqr_postgres_named_collection` (a new -workflow step, mirroring what `unit-tests.yml` already does for the main app) just so the -`CREATE DICTIONARY ... SOURCE(POSTGRESQL(NAME 'seqr_postgres_named_collection' ...))` DDL parses. -Dictionaries are lazily loaded (`LIFETIME(0)`), so DDL creation succeeds even though the source is -unreachable — but tests still need to override these specific dictionaries with deterministic -fixture sources afterward (same idea as today's code, just trimmed to only this handful instead of -faking the whole schema). - -## Raw SQL execution in tests: use the Django connection, not `clickhouse_driver.Client` - -Every test currently calls `get_clickhouse_client()` (a raw `clickhouse_driver.Client`, see -`lib/misc/clickhouse.py`) to run setup/assertion SQL directly. Once the schema is Django-managed, -tests should execute their raw SQL through Django's own DB connection instead of a separate -`clickhouse_driver.Client` instance — i.e. `django.db.connections['clickhouse_write'].cursor()` -(the one real alias defined per "Single connection / single set of credentials only" above), -calling `cursor.execute(sql, params)` / `cursor.fetchall()`. - -This is purely a *client* swap for test code — tests keep writing raw SQL strings (no ORM/model -queries), just executed via the Django connection so the tests exercise the same connection -machinery/test-DB aliasing that pytest-django set up, rather than opening an independent -`clickhouse_driver` connection that doesn't know about Django's test DB name remapping. Production -code in `lib/misc/clickhouse.py` (`get_clickhouse_client` and friends) is unaffected — this only -applies to test files themselves. - -## Shared setup-time data: Django fixtures, not bulk INSERT statements - -Some test data is inserted once in a test class's `setUp`/`setUpClass` and reused across multiple -test methods (e.g. the `seqrdb_gene_ids`/`gnomad_genomes` source-table rows in -`ClickhouseTest`/`ClickhouseSchemaTestCase`). That category of data should be loaded via Django's -fixture mechanism (JSON fixture files under a `fixtures/` dir, loaded with -`fixtures = [...]` on the `TestCase` subclass, or an explicit `call_command('loaddata', ...)`) — -not hand-written `INSERT INTO ... VALUES (...)` statements repeated/executed in `setUp`. - -This only applies to shared, setup-time reference data with a real backing model in -`clickhouse_search` (e.g. the source tables behind `seqrdb_gene_ids`/`gnomad_genomes`). Since -`loaddata` populates rows through the model layer, the dictionary itself still needs an explicit -`RELOAD DICTIONARY`/refresh afterward (dictionaries aren't themselves loaddata targets — their -backing source table is). Data that's specific to a single test method's body/assertions (not -shared across tests) stays as raw SQL executed via the Django connection cursor, per the prior -note — this fixture rule is specifically about *repeated* setup-time data. - -## Proposed change set - -| File | Change | -|---|---| -| `clickhouse_search/models/search_models.py`, `clickhouse_search/backend/table_models.py`, `clickhouse_search/migrations/0040_gnomadnoncodingconstraintdict.py` | move `Projection` from `search_models.py` to `backend/table_models.py`; update the migration's import accordingly (✅ done) | -| `clickhouse_search/constants.py` | duplicate 4 constants out of `seqr.models.Individual` instead of importing it (✅ done) | -| `.github/workflows/pipeline-unit-tests.yml` | keep `CLICKHOUSE_DATABASE=test`; no named-collection step needed anymore (no Postgres-sourced dictionaries are reachable via the minimal settings module in the first place - see note below) | -| `loading_pipeline/pyproject.toml` | add `django`, `django-clickhouse-backend`, `pytest-django` dev deps; add `[tool.pytest.ini_options]` (`DJANGO_SETTINGS_MODULE`, `pythonpath`) | -| **new** `loading_pipeline/lib/test/clickhouse_django/settings.py` | minimal Django settings: one real `clickhouse` alias (single credential set), `clickhouse_write` mirrored onto it via `TEST: {MIRROR: 'clickhouse'}`, a dummy `default` placeholder (NAME only, no real connection), `clickhouse_backend` + `clickhouse_search` apps, `ClickHouseRouter`; doubles as the shadow `settings` module `clickhouse_search/backend/base.py` bare-imports | -| `lib/test/clickhouse_schema_testcase.py` | rewritten as the one shared base class: drop all manual DDL/SQL-file loading (schema now comes from real migrations via pytest-django), keep only the small external-sourced-dictionary overrides + per-test flush/truncate + staging-DB drop/create — all executed via `connections['clickhouse_write'].cursor()`; shared reference rows (e.g. gene-id/gnomAD source-table rows) loaded via Django `fixtures = [...]` instead of `INSERT` statements | -| **delete** `loading_pipeline/var/test/test_clickhouse_schema.sql` | no longer needed | -| **new** `loading_pipeline/lib/test/fixtures/*.json` | Django fixtures for the shared setup-time reference rows referenced above | -| `lib/misc/clickhouse_test.py` | `ClickhouseTest` extends the shared base instead of hand-building its own schema; keeps only its fixture-data seeding (via the new Django fixtures, not bulk `INSERT`) and parquet-writing setup; all `get_clickhouse_client()` calls in the test body replaced with the Django connection cursor | -| `bin/pipeline_worker_test.py`, `lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py` | no structural change (already extend the shared base) — swap their `get_clickhouse_client()` assertion calls to the Django connection cursor; cleanup of now-dead references (e.g. leftover `TEST_SCHEMA` constant) | -| `ops/repartition_clickhouse_grch38_snv_indel_test.py` | switch to the shared base for the real-schema DB lifecycle; keep its own synthetic `entries`-table `REPLACE`/dict + `REPARTITION_DATABASE_NAME` handling since that's not part of `clickhouse_search`'s schema; swap `get_clickhouse_client()` for the Django connection cursor | - -## Open risk / caveat - -No live ClickHouse instance is available in the sandbox used to write this plan, so some runtime -specifics can't be verified ahead of time: -- Whether `TRUNCATE` behaves as expected on materialized views (regular vs. refreshable). -- Exact Django test-DB naming interplay with `Env.CLICKHOUSE_DATABASE` (need a `TEST: {NAME: ...}` - override to avoid Django's default `test_` prefix mismatch). -- Whether `CREATE DICTIONARY ... SOURCE(POSTGRESQL(...))` DDL actually succeeds against a - ClickHouse server with only a dummy/unreachable named collection registered. -- Whether raw SQL params/tuple-list inserts (e.g. `INSERT INTO ... VALUES` with a Python list of - tuples, as `clickhouse_driver.Client.execute` supports today) work identically through - `cursor.execute()`/`cursor.executemany()` on the Django ClickHouse backend, or need reshaping. - -These should be shaken out against a real CI run / local ClickHouse instance once implemented. - -## Deviations from this plan, found during implementation - -Verified against a live ClickHouse instance. Recorded here for reference; this plan document -itself is not otherwise updated to match implementation. - -**`clickhouse_search/` changes beyond the two already noted above** (both cleared with the user -before making them): -- Moved `conditionally_refresh_reference_dataset` from `models/reference_data_models.py` to - `backend/table_models.py`, so migration 0040 doesn't need to import the live model modules (and - therefore `seqr.models.Dataset`/`seqr.utils.xpos_utils.CHROMOSOME_CHOICES`) just to reach one - helper function. -- Added `conditionally_reload_dictionary` (`backend/table_models.py`) and edited migrations 0043 - and 0044 to use it instead of hardcoded `RunSQL('SYSTEM RELOAD DICTIONARY ...')` - those forced - a real synchronous Postgres connection during `migrate`, which no environment here has. This - edits already-applied migration files, normally treated as an immutable historical record. - -**A production dependency change:** `clickhouse-driver` bumped `0.2.9` -> `0.2.10` in -`loading_pipeline/pyproject.toml` (forced by `django-clickhouse-backend==1.6`'s own pin; matches -the main app's version). Not test-only. - -**Bugs/gaps in this plan's own design, fixed - all confined to `loading_pipeline/`:** -- `reference_data` needs its own dummy `DATABASES` alias; the plan only accounted for `default` - (`GeneIdDict`/`OmimDict` declare `postgres_db = 'reference_data'`). -- `DATABASES['clickhouse_write']['TEST']['DEPENDENCIES']` must be `[]`, or Django raises - "Circular dependency in TEST[DEPENDENCIES]" (it assumes every alias depends on `default`). -- The `pythonpath` ordering described in this plan's original settings-module writeup was - backwards; pytest builds `sys.path` in the *same* order as the `pythonpath` list, not reversed. -- `django_find_project = false` is required - pytest-django's `manage.py` auto-discovery - otherwise force-inserts the repo root at `sys.path[0]`, re-shadowing `settings`. -- `CLICKHOUSE_IN_MEMORY_DIR`/`CLICKHOUSE_DATA_DIR` must default to different paths, or two - `EmbeddedRocksDB` tables collide on the same file lock. -- A stub `seqr` package (`lib/test/clickhouse_django/seqr/`) is needed - not anticipated anywhere - in this plan - because `clickhouse_search/backend/table_models.py` imports `SeqrLogger`, and - migration 0040 has a named dependency on a specific `seqr` migration. -- The "no named-collection CI step needed" conclusion in this plan's own change-set table is - right, but the "Postgres/GCS-sourced dictionary wrinkle" section above is stale/wrong about why - - see the migration 0043/0044 edit above for the actual mechanism. - -**Explicit user-directed deviations from this plan's design:** -- The shared base class does NOT keep "staging-DB drop/create" logic, contrary to this plan's - change-set table - `loading_pipeline`'s own production code already drops/creates the staging - DB defensively, so tests don't need to. -- Per-test cleanup in the shared base class is a `_fixture_teardown` override that truncates all - live, non-`Dictionary`/`MaterializedView` tables directly via SQL - not Django's `flush` command, - which relies on `apps.get_models()` and finds nothing (no `clickhouse_search` model modules are - imported anywhere in `loading_pipeline`). - -**Unresolved tension, not yet acted on:** this plan calls for shared reference data (e.g. -`seqrdb_gene_ids` source rows) to be loaded via Django fixtures (`loaddata`), which requires -importing the real model classes being loaded - but the user has since directed that fully -importing `clickhouse_search`'s live model modules is unacceptable for these tests. Needs -resolution before the fixture-loading step is implemented. \ No newline at end of file diff --git a/loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_REMAINING_PLAN.md b/loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_REMAINING_PLAN.md new file mode 100644 index 0000000000..6b5bab38a1 --- /dev/null +++ b/loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_REMAINING_PLAN.md @@ -0,0 +1,44 @@ +# Plan: Finish migrating `repartition_clickhouse_grch38_snv_indel_test.py` to pytest-django + +## Context + +`loading_pipeline`'s ClickHouse tests were migrated to run against real `clickhouse_search` +Django migrations via pytest-django, with a shared `ClickhouseSchemaTestCase` base +(`lib/test/clickhouse_schema_testcase.py`) that owns the real schema DB's migrate/truncate +lifecycle. Every ClickHouse-touching test file adopted this base and switched from raw +`clickhouse_driver.Client` (`get_clickhouse_client()`) to +`connections['clickhouse_write'].cursor()` — except one file. + +## Remaining work + +`ops/repartition_clickhouse_grch38_snv_indel_test.py` (`RepartitionGRCh38SnvIndelTest`) still +predates the migration: + +- extends bare `unittest.TestCase`, not `ClickhouseSchemaTestCase` +- `setUp` manually runs `DROP DATABASE IF EXISTS {Env.CLICKHOUSE_DATABASE} PARALLEL WITH DROP + DATABASE IF EXISTS {REPARTITION_DATABASE_NAME}` then the matching `CREATE DATABASE ... PARALLEL + WITH ...` — `Env.CLICKHOUSE_DATABASE` is now owned by pytest-django's migrate lifecycle; + `REPARTITION_DATABASE_NAME` is the script's own scratch DB, not part of `clickhouse_search`'s + schema +- every SQL statement in `setUp` and both test methods runs via `get_clickhouse_client()` + + `client.execute(...)`, a raw `clickhouse_driver.Client` + +### Changes + +1. `RepartitionGRCh38SnvIndelTest` extends `ClickhouseSchemaTestCase` instead of + `unittest.TestCase`. +2. Drop the `DROP DATABASE IF EXISTS {Env.CLICKHOUSE_DATABASE}` / `CREATE DATABASE + {Env.CLICKHOUSE_DATABASE}` half of `setUp`'s `PARALLEL WITH` statements — the shared base now + handles that DB's schema/lifecycle. +3. Keep the `REPARTITION_DATABASE_NAME` drop/create in `setUp` (still not part of the real + schema), issued as its own statement. +4. Keep the synthetic `GRCh38/SNV_INDEL/entries` table DDL, `INSERT` seed rows, and + `project_partitions_dict` dictionary DDL as-is (intentionally bespoke, not real schema). +5. Execute everything in `setUp` and both test methods (`test_main_all_projects`, + `test_main_one_project`) via `connections['clickhouse_write'].cursor()` / + `cursor.execute(...)` / `cursor.fetchall()` instead of `get_clickhouse_client()` / + `client.execute(...)`. +6. Drop the now-unused `get_clickhouse_client` import. + +Reference `lib/misc/clickhouse_test.py` or `bin/pipeline_worker_test.py` for the established +pattern of extending `ClickhouseSchemaTestCase` and using the cursor. \ No newline at end of file From 68883d7d1be44ca2b7806dc83663db06bae2a780 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 16:20:14 -0400 Subject: [PATCH 218/369] restore files --- clickhouse_search/models/search_models.py | 4 +- .../lib/tasks/reference_data/__init__.py | 0 .../updated_reference_dataset.py | 27 +++++++++ .../updated_reference_dataset_parquet.py | 55 +++++++++++++++++++ 4 files changed, 84 insertions(+), 2 deletions(-) create mode 100644 loading_pipeline/lib/tasks/reference_data/__init__.py create mode 100644 loading_pipeline/lib/tasks/reference_data/updated_reference_dataset.py create mode 100644 loading_pipeline/lib/tasks/reference_data/updated_reference_dataset_parquet.py diff --git a/clickhouse_search/models/search_models.py b/clickhouse_search/models/search_models.py index 50aedf1325..48516b36f0 100644 --- a/clickhouse_search/models/search_models.py +++ b/clickhouse_search/models/search_models.py @@ -453,7 +453,7 @@ class EntriesGcnv(BaseEntries): class Meta(BaseEntries.Meta): db_table = 'GRCh38/GCNV/entries' -class VariantDetailsGRCh37SnvIndel(models.ClickhouseModel): +class VariantDetailsGRCh37SnvIndel(FixtureLoadableClickhouseModel): ANNOTATION_CONSTANTS = VariantsGRCh37SnvIndel.ANNOTATION_CONSTANTS key = OneToOneField('VariantsGRCh37SnvIndel', db_column='key', primary_key=True, on_delete=CASCADE) @@ -470,7 +470,7 @@ class Meta: db_table = 'GRCh37/SNV_INDEL/variants/details' engine = EmbeddedRocksDB(0, f'{CLICKHOUSE_DATA_DIR}/GRCh37/SNV_INDEL/variants_details', primary_key='key', flatten_nested=0) -class VariantDetailsSnvIndel(models.ClickhouseModel): +class VariantDetailsSnvIndel(FixtureLoadableClickhouseModel): TRANSCRIPTS_FIELDS = sorted([ ('alphamissense', NamedTupleField([ ('pathogenicity', models.DecimalField(null=True, blank=True, max_digits=9, decimal_places=5)), diff --git a/loading_pipeline/lib/tasks/reference_data/__init__.py b/loading_pipeline/lib/tasks/reference_data/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/loading_pipeline/lib/tasks/reference_data/updated_reference_dataset.py b/loading_pipeline/lib/tasks/reference_data/updated_reference_dataset.py new file mode 100644 index 0000000000..575cc1864f --- /dev/null +++ b/loading_pipeline/lib/tasks/reference_data/updated_reference_dataset.py @@ -0,0 +1,27 @@ +import luigi + +from loading_pipeline.lib.paths import valid_reference_dataset_path +from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset +from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( + BaseLoadingPipelineParams, +) +from loading_pipeline.lib.tasks.base.base_write import BaseWriteTask +from loading_pipeline.lib.tasks.files import GCSorLocalTarget + + +@luigi.util.inherits(BaseLoadingPipelineParams) +class UpdatedReferenceDatasetTask(BaseWriteTask): + reference_dataset: ReferenceDataset = luigi.EnumParameter( + enum=ReferenceDataset, + ) + + def output(self): + return GCSorLocalTarget( + valid_reference_dataset_path( + self.reference_genome, + self.reference_dataset, + ), + ) + + def create_table(self): + return self.reference_dataset.get_ht(self.reference_genome) diff --git a/loading_pipeline/lib/tasks/reference_data/updated_reference_dataset_parquet.py b/loading_pipeline/lib/tasks/reference_data/updated_reference_dataset_parquet.py new file mode 100644 index 0000000000..ed8adfce6b --- /dev/null +++ b/loading_pipeline/lib/tasks/reference_data/updated_reference_dataset_parquet.py @@ -0,0 +1,55 @@ +import luigi + +from loading_pipeline.lib.annotations.expression_helpers import get_expr_for_variant_id +from loading_pipeline.lib.core.dataset_type import DatasetType +from loading_pipeline.lib.core.definitions import ReferenceGenome +from loading_pipeline.lib.paths import reference_dataset_parquet +from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset +from loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc import ( + BaseRunJobOnDataprocTask, +) +from loading_pipeline.lib.tasks.files import GCSorLocalFolderTarget, GCSorLocalTarget + + +class UpdatedReferenceDatasetParquetTask(luigi.Task): + reference_genome = luigi.EnumParameter(enum=ReferenceGenome) + dataset_type = luigi.EnumParameter(enum=DatasetType) + reference_dataset: ReferenceDataset = luigi.EnumParameter( + enum=ReferenceDataset, + ) + run_id = luigi.Parameter() + attempt_id = luigi.IntParameter() + + def complete(self) -> luigi.Target: + return GCSorLocalFolderTarget(self.output().path).exists() + + def output(self): + return GCSorLocalTarget( + reference_dataset_parquet( + self.reference_genome, + self.reference_dataset, + ), + ) + + def run(self): + ht = self.reference_dataset.get_ht(self.reference_genome) + ht = ht.annotate( + variant_id=get_expr_for_variant_id(ht), + ) + df = ht.to_spark(flatten=False) + df.write.parquet( + self.output().path, + mode='overwrite', + ) + + +class UpdatedReferenceDatasetParquetOnDataprocTask(BaseRunJobOnDataprocTask): + reference_genome = luigi.EnumParameter(enum=ReferenceGenome) + dataset_type = luigi.EnumParameter(enum=DatasetType) + reference_dataset: ReferenceDataset = luigi.EnumParameter( + enum=ReferenceDataset, + ) + + @property + def task(self) -> luigi.Task: + return UpdatedReferenceDatasetParquetTask From 6a225f6ae26c001f7c7064308915069cc699a8a3 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 16:36:19 -0400 Subject: [PATCH 219/369] fix fixtures --- loading_pipeline/lib/misc/clickhouse_test.py | 1 + .../lib/test/fixtures/clickhouse_test.json | 12 +++++++++--- 2 files changed, 10 insertions(+), 3 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index 0d776ebaa3..f2f7055f70 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -244,6 +244,7 @@ class ClickhouseTest(MockedDatarootTestCase, ClickhouseSchemaTestCase): @classmethod def setUpClass(cls): super().setUpClass() + # Postgres dicts are not managed by django in this test suite and therefore cannot be loaded from fixtures with connections['clickhouse_write'].cursor() as cursor: cursor.execute( f'INSERT INTO {Env.CLICKHOUSE_DATABASE}.`seqrdb_gene_ids_src` VALUES', diff --git a/loading_pipeline/lib/test/fixtures/clickhouse_test.json b/loading_pipeline/lib/test/fixtures/clickhouse_test.json index 86b4d05638..757f969261 100644 --- a/loading_pipeline/lib/test/fixtures/clickhouse_test.json +++ b/loading_pipeline/lib/test/fixtures/clickhouse_test.json @@ -268,7 +268,9 @@ "fields": { "key": 1, "variant_id": "a", - "transcripts": [] + "transcripts": [], + "sortedMotifFeatureConsequences": [], + "sortedRegulatoryFeatureConsequences": [] } }, { @@ -277,7 +279,9 @@ "fields": { "key": 7, "variant_id": "c", - "transcripts": [] + "transcripts": [], + "sortedMotifFeatureConsequences": [], + "sortedRegulatoryFeatureConsequences": [] } }, { @@ -286,7 +290,9 @@ "fields": { "key": 10, "variant_id": "b", - "transcripts": [] + "transcripts": [], + "sortedMotifFeatureConsequences": [], + "sortedRegulatoryFeatureConsequences": [] } } ] From ef89a902ecfbc5a169cc3e64e6eebcdcbf7483cf Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 16:44:44 -0400 Subject: [PATCH 220/369] fix field names --- .../lib/test/fixtures/clickhouse_test.json | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/loading_pipeline/lib/test/fixtures/clickhouse_test.json b/loading_pipeline/lib/test/fixtures/clickhouse_test.json index 757f969261..e30c37f235 100644 --- a/loading_pipeline/lib/test/fixtures/clickhouse_test.json +++ b/loading_pipeline/lib/test/fixtures/clickhouse_test.json @@ -269,8 +269,8 @@ "key": 1, "variant_id": "a", "transcripts": [], - "sortedMotifFeatureConsequences": [], - "sortedRegulatoryFeatureConsequences": [] + "sorted_motif_feature_consequences": [], + "sorted_regulatory_feature_consequences": [] } }, { @@ -280,8 +280,8 @@ "key": 7, "variant_id": "c", "transcripts": [], - "sortedMotifFeatureConsequences": [], - "sortedRegulatoryFeatureConsequences": [] + "sorted_motif_feature_consequences": [], + "sorted_regulatory_feature_consequences": [] } }, { @@ -291,8 +291,8 @@ "key": 10, "variant_id": "b", "transcripts": [], - "sortedMotifFeatureConsequences": [], - "sortedRegulatoryFeatureConsequences": [] + "sorted_motif_feature_consequences": [], + "sorted_regulatory_feature_consequences": [] } } ] From e03b26e42f573ff45870e515ed391e8c63bae258 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 13 Aug 2026 17:08:23 -0400 Subject: [PATCH 221/369] misc test cleanup --- loading_pipeline/lib/misc/clickhouse_test.py | 60 ++++++------------- .../lib/test/fixtures/clickhouse_test.json | 4 +- 2 files changed, 19 insertions(+), 45 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index f2f7055f70..e723ba2887 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -318,7 +318,7 @@ def write_test_parquet(df: pd.DataFrame, parquet_path: str, schema=None): df = pd.DataFrame( { - 'key': [0, 3, 4], + 'key': [10, 3, 4], 'project_guid': [ 'project_d', 'project_d', @@ -526,16 +526,21 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): self.assertCountEqual( cursor.fetchall(), [ - ('project_a', 0, 'WES', 0, 1), + ('project_a', 10, 'WES', 0, 1), ('project_a', 1, 'WGS', 1, 0), ('project_a', 2, 'WGS', 0, 1), + ('project_a', 3, 'WES', 0, 0), ('project_a', 4, 'WES', 1, 0), ('project_a', 4, 'WGS', 0, 1), + ('project_b', 10, 'WES', 0, 0), ('project_b', 1, 'WES', 1, 0), + ('project_b', 2, 'WES', 0, 0), ('project_b', 3, 'WES', 0, 1), ('project_b', 4, 'WES', 0, 1), # project_gt_stats stages all projects, not just # those requested for loading. + ('project_c', 10, 'WES', 0, 0), + ('project_c', 3, 'WES', 0, 0), ('project_c', 4, 'WES', 0, 1), ('project_c', 5, 'WES', 0, 1), ], @@ -555,7 +560,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): self.assertCountEqual( cursor.fetchall(), [ - ('project_a', 0, 'WES', 0, 0), + ('project_a', 10, 'WES', 0, 0), ('project_a', 1, 'WGS', 1, 0), ('project_a', 2, 'WGS', 0, 1), ('project_a', 4, 'WES', 0, 0), @@ -583,7 +588,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): self.assertCountEqual( cursor.fetchall(), [ - ('project_a', 0, 'WES', 0, 0), + ('project_a', 10, 'WES', 0, 0), ('project_a', 1, 'WGS', 1, 0), ('project_a', 2, 'WGS', 0, 1), ('project_a', 4, 'WES', 0, 0), @@ -593,7 +598,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): ('project_b', 4, 'WES', 0, 1), ('project_c', 4, 'WES', 0, 1), ('project_c', 5, 'WES', 0, 1), - ('project_d', 0, 'WES', 0, 1), + ('project_d', 10, 'WES', 0, 1), ('project_d', 4, 'WES', 1, 0), ], ) @@ -622,7 +627,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): cursor.fetchall(), [ ( - 0, + 10, 'project_b', 'family_b1', 123456789, @@ -702,7 +707,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): 1, ), ( - 0, + 10, 'project_d', 'family_d1', 123456789, @@ -732,7 +737,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): 1, ), ( - 0, + 10, 'project_c', 'family_c1', 123456789, @@ -812,7 +817,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): self.assertEqual( cursor.fetchall(), [ - (0, 2, 0), + (10, 2, 0), (1, 1, 1), (2, 0, 2), (3, 2, 0), @@ -827,6 +832,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): return_value=[ClickhouseReferenceDataset.CLINVAR], ) def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_type): + self.maxDiff = None load_complete_run( ReferenceGenome.GRCh38, DatasetType.SNV_INDEL, @@ -846,7 +852,7 @@ def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_typ self.assertCountEqual( cursor.fetchall(), [ - ('project_d', 0, 'WES', 0, 1), + ('project_d', 10, 'WES', 0, 1), ('project_d', 4, 'WES', 1, 0), ], ) @@ -860,7 +866,7 @@ def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_typ self.assertCountEqual( cursor.fetchall(), [ - (0, 2, 0), + (10, 2, 0), (4, 1, 0), ], ) @@ -1104,38 +1110,6 @@ def test_rebuild_gt_stats(self): ) def test_repartitioned_entries_table(self, mock_for_reference_genome_dataset_type): with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f""" - REPLACE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` ( - `key` UInt32, - `project_guid` LowCardinality(String), - `family_guid` String, - `xpos` UInt64 CODEC(Delta(8), ZSTD(1)), - `sample_type` Enum8('WES' = 0, 'WGS' = 1), - `is_gnomad_gt_5_percent` Boolean, - `is_annotated_in_any_gene` Boolean DEFAULT length(geneId_ids) > 0, - `geneId_ids` Array(UInt32), - `calls` Array( - Tuple( - sampleId String, - gt Nullable(Enum8('REF' = 0, 'HET' = 1, 'HOM' = 2)), - ) - ), - `sign` Int8, - `n_partitions` UInt8 MATERIALIZED 2, - `partition_id` UInt8 MATERIALIZED farmHash64(family_guid) % n_partitions, - PROJECTION xpos_projection - ( - SELECT * - ORDER BY is_annotated_in_any_gene, xpos - ) - ) - ENGINE = CollapsingMergeTree(sign) - PARTITION BY (project_guid, partition_id) - ORDER BY (project_guid, family_guid, key) - SETTINGS deduplicate_merge_projection_mode = 'rebuild'; - """, - ) load_complete_run( ReferenceGenome.GRCh38, DatasetType.SNV_INDEL, diff --git a/loading_pipeline/lib/test/fixtures/clickhouse_test.json b/loading_pipeline/lib/test/fixtures/clickhouse_test.json index e30c37f235..b4e6cdbf1a 100644 --- a/loading_pipeline/lib/test/fixtures/clickhouse_test.json +++ b/loading_pipeline/lib/test/fixtures/clickhouse_test.json @@ -3,7 +3,7 @@ "model": "clickhouse_search.entriessnvindel", "pk": 1, "fields": { - "key": 0, + "key": 10, "project_guid": "project_a", "family_guid": "family_a1", "sample_type": "WES", @@ -105,7 +105,7 @@ "model": "clickhouse_search.entriessnvindel", "pk": 7, "fields": { - "key": 0, + "key": 10, "project_guid": "project_b", "family_guid": "family_b1", "sample_type": "WES", From 38f4c315baea20c78dc80891e5c0b50a309dea48 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 10:35:06 -0400 Subject: [PATCH 222/369] test cleanup and fix --- loading_pipeline/lib/misc/clickhouse_test.py | 267 ++++++++++--------- 1 file changed, 144 insertions(+), 123 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index e723ba2887..dc5e5c42a1 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -432,15 +432,15 @@ def test_table_name_builder(self): ) def test_direct_insert_all_keys(self): + direct_insert_all_keys( + ClickHouseTable.VARIANT_DETAILS, + TableNameBuilder( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ) with connections['clickhouse_write'].cursor() as cursor: - direct_insert_all_keys( - ClickHouseTable.VARIANT_DETAILS, - TableNameBuilder( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ), - ) cursor.execute( f'SELECT key, variantId FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', ) @@ -456,15 +456,16 @@ def test_direct_insert_all_keys(self): ], ) - # ensure multiple calls are idempotent - direct_insert_all_keys( - ClickHouseTable.VARIANT_DETAILS, - TableNameBuilder( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ), - ) + # ensure multiple calls are idempotent + direct_insert_all_keys( + ClickHouseTable.VARIANT_DETAILS, + TableNameBuilder( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ) + with connections['clickhouse_write'].cursor() as cursor: cursor.execute( f'SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', ) @@ -477,35 +478,35 @@ def test_direct_insert_all_keys(self): ) def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): # Tests individual components of atomic_insert_entries, validating state after each step. - with connections['clickhouse_write'].cursor() as cursor: - table_name_builder = TableNameBuilder( - ReferenceGenome.GRCh38, + table_name_builder = TableNameBuilder( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ) + create_staging_tables( + table_name_builder, + ClickHouseTable.for_dataset_type_atomic_entries_update( DatasetType.SNV_INDEL, - TEST_RUN_ID, - ) - create_staging_tables( - table_name_builder, - ClickHouseTable.for_dataset_type_atomic_entries_update( - DatasetType.SNV_INDEL, - ), - ) - create_staging_materialized_views( - table_name_builder, - ClickHouseMaterializedView.for_dataset_type_atomic_entries_update( - DatasetType.SNV_INDEL, - ), - ) - stage_existing_project_partitions( - table_name_builder, - [ - 'project_a', - 'project_b', - 'project_d', # Partition does not exist already. - ], - ClickHouseTable.for_dataset_type_atomic_entries_update_project_partitioned( - DatasetType.SNV_INDEL, - ), - ) + ), + ) + create_staging_materialized_views( + table_name_builder, + ClickHouseMaterializedView.for_dataset_type_atomic_entries_update( + DatasetType.SNV_INDEL, + ), + ) + stage_existing_project_partitions( + table_name_builder, + [ + 'project_a', + 'project_b', + 'project_d', # Partition does not exist already. + ], + ClickHouseTable.for_dataset_type_atomic_entries_update_project_partitioned( + DatasetType.SNV_INDEL, + ), + ) + with connections['clickhouse_write'].cursor() as cursor: cursor.execute( f""" SELECT DISTINCT project_guid FROM {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/entries` @@ -539,16 +540,17 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): ('project_b', 4, 'WES', 0, 1), # project_gt_stats stages all projects, not just # those requested for loading. - ('project_c', 10, 'WES', 0, 0), + ('project_c', 0, 'WES', 0, 0), ('project_c', 3, 'WES', 0, 0), ('project_c', 4, 'WES', 0, 1), ('project_c', 5, 'WES', 0, 1), ], ) - delete_existing_families_from_staging_entries( - table_name_builder, - ['family_a1', 'family_a5', 'family_a6'], - ) + delete_existing_families_from_staging_entries( + table_name_builder, + ['family_a1', 'family_a5', 'family_a6'], + ) + with connections['clickhouse_write'].cursor() as cursor: cursor.execute( f""" SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) @@ -572,11 +574,13 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): ('project_c', 5, 'WES', 0, 1), ], ) - insert_new_entries(table_name_builder) - optimize_entries( - table_name_builder, - ['project_a', 'project_b', 'project_c'], - ) + + insert_new_entries(table_name_builder) + optimize_entries( + table_name_builder, + ['project_a', 'project_b', 'project_c'], + ) + with connections['clickhouse_write'].cursor() as cursor: cursor.execute( f""" SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) @@ -602,20 +606,22 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): ('project_d', 4, 'WES', 1, 0), ], ) - refresh_materialized_views( - table_name_builder, - ClickHouseMaterializedView.for_dataset_type_atomic_entries_update_refreshable( - DatasetType.SNV_INDEL, - ), - staging=True, - ) - replace_project_partitions( - table_name_builder, - ClickHouseTable.for_dataset_type_atomic_entries_update_project_partitioned( - DatasetType.SNV_INDEL, - ), - ['project_a', 'project_d'], - ) + + refresh_materialized_views( + table_name_builder, + ClickHouseMaterializedView.for_dataset_type_atomic_entries_update_refreshable( + DatasetType.SNV_INDEL, + ), + staging=True, + ) + replace_project_partitions( + table_name_builder, + ClickHouseTable.for_dataset_type_atomic_entries_update_project_partitioned( + DatasetType.SNV_INDEL, + ), + ['project_a', 'project_d'], + ) + with connections['clickhouse_write'].cursor() as cursor: cursor.execute( f""" SELECT COLUMNS('.*') EXCEPT(is_annotated_in_any_gene, is_gnomad_gt_5_percent) @@ -789,12 +795,14 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): cursor.fetchall(), [], ) - exchange_tables( - table_name_builder, - ClickHouseTable.for_dataset_type_atomic_entries_update_unpartitioned( - DatasetType.SNV_INDEL, - ), - ) + + exchange_tables( + table_name_builder, + ClickHouseTable.for_dataset_type_atomic_entries_update_unpartitioned( + DatasetType.SNV_INDEL, + ), + ) + with connections['clickhouse_write'].cursor() as cursor: cursor.execute( f""" SELECT * @@ -803,10 +811,12 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): """, ) self.assertCountEqual(cursor.fetchall(), []) - reload_dictionaries( - table_name_builder, - ClickHouseDictionary.for_dataset_type(DatasetType.SNV_INDEL), - ) + + reload_dictionaries( + table_name_builder, + ClickHouseDictionary.for_dataset_type(DatasetType.SNV_INDEL), + ) + with connections['clickhouse_write'].cursor() as cursor: cursor.execute( f""" SELECT * @@ -846,6 +856,7 @@ def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_typ SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + WHERE PROJECT_GUID = 'project_d' GROUP BY project_guid, key, sample_type """, ) @@ -971,6 +982,7 @@ def test_delete_families(self): SELECT project_guid, sum(het_samples), sum(hom_samples) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + FINAL GROUP BY project_guid """, ) @@ -978,13 +990,15 @@ def test_delete_families(self): cursor.fetchall(), [('project_a', 2, 3), ('project_c', 0, 2), ('project_b', 1, 2)], ) - refresh_materialized_views( - table_name_builder, - ClickHouseMaterializedView.for_dataset_type_atomic_entries_update_refreshable( - DatasetType.SNV_INDEL, - ), - staging=False, - ) + + refresh_materialized_views( + table_name_builder, + ClickHouseMaterializedView.for_dataset_type_atomic_entries_update_refreshable( + DatasetType.SNV_INDEL, + ), + staging=False, + ) + with connections['clickhouse_write'].cursor() as cursor: cursor.execute( f""" SELECT sum(ac_wes) @@ -993,18 +1007,21 @@ def test_delete_families(self): """, ) self.assertCountEqual(cursor.fetchall(), [(12,)]) - delete_family_guids( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - 'project_a', - ['family_a1', 'family_a2'], - ) + + delete_family_guids( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + 'project_a', + ['family_a1', 'family_a2'], + ) + with connections['clickhouse_write'].cursor() as cursor: cursor.execute( f""" SELECT project_guid, sum(het_samples), sum(hom_samples) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + FINAL GROUP BY project_guid """, ) @@ -1035,16 +1052,16 @@ def test_rebuild_gt_stats(self): DatasetType.SNV_INDEL, TEST_RUN_ID, ) + logged_query( # DROP the partition from the non-staging entries to as a non-mv-impacting change. + f""" + ALTER TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` + DROP PARTITION (%(project_guid)s, %(partition_id)s) + """, + # project_partitions_dict has no row for project_a, so n_partitions (and thus + # partition_id) defaults to 0. + {'project_guid': 'project_a', 'partition_id': 0}, + ) with connections['clickhouse_write'].cursor() as cursor: - logged_query( # DROP the partition from the non-staging entries to as a non-mv-impacting change. - f""" - ALTER TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` - DROP PARTITION (%(project_guid)s, %(partition_id)s) - """, - # project_partitions_dict has no row for project_a, so n_partitions (and thus - # partition_id) defaults to 0. - {'project_guid': 'project_a', 'partition_id': 0}, - ) cursor.execute( f""" SELECT project_guid, sum(het_samples), sum(hom_samples) @@ -1058,13 +1075,15 @@ def test_rebuild_gt_stats(self): cursor.fetchall(), [('project_a', 2, 3), ('project_b', 1, 2)], ) - refresh_materialized_views( - table_name_builder, - ClickHouseMaterializedView.for_dataset_type_atomic_entries_update_refreshable( - DatasetType.SNV_INDEL, - ), - staging=False, - ) + + refresh_materialized_views( + table_name_builder, + ClickHouseMaterializedView.for_dataset_type_atomic_entries_update_refreshable( + DatasetType.SNV_INDEL, + ), + staging=False, + ) + with connections['clickhouse_write'].cursor() as cursor: cursor.execute( f""" SELECT sum(ac_wes), sum(ac_wgs) @@ -1075,12 +1094,14 @@ def test_rebuild_gt_stats(self): # gt_stats has no project dimension (keyed globally by `key`), so project_c's rows # (sharing key values with project_a/b in the fixture) also contribute here. self.assertCountEqual(cursor.fetchall(), [(12, 5)]) - rebuild_gt_stats( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ['project_a', 'project_b'], - ) + + rebuild_gt_stats( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ['project_a', 'project_b'], + ) + with connections['clickhouse_write'].cursor() as cursor: cursor.execute( f""" SELECT project_guid, sum(het_samples), sum(hom_samples) @@ -1109,14 +1130,14 @@ def test_rebuild_gt_stats(self): return_value=[ClickhouseReferenceDataset.CLINVAR], ) def test_repartitioned_entries_table(self, mock_for_reference_genome_dataset_type): + load_complete_run( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ['project_d'], + ['family_d1', 'family_d2', 'family_d3'], + ) with connections['clickhouse_write'].cursor() as cursor: - load_complete_run( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ['project_d'], - ['family_d1', 'family_d2', 'family_d3'], - ) cursor.execute( f""" SELECT project_guid, sum(het_samples), sum(hom_samples) @@ -1127,5 +1148,5 @@ def test_repartitioned_entries_table(self, mock_for_reference_genome_dataset_typ ) self.assertCountEqual( cursor.fetchall(), - [('project_d', 1, 1)], + [('project_a', 2, 3), ('project_b', 1, 2), ('project_c', 0, 2), ('project_d', 1, 1)], ) From 0142d0be2ca4685209f2382d95af168367518c26 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 10:36:45 -0400 Subject: [PATCH 223/369] ruff --- loading_pipeline/lib/misc/clickhouse_test.py | 7 ++- ...tition_clickhouse_grch38_snv_indel_test.py | 46 ++++++++++--------- 2 files changed, 31 insertions(+), 22 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index dc5e5c42a1..e09c58e962 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -1148,5 +1148,10 @@ def test_repartitioned_entries_table(self, mock_for_reference_genome_dataset_typ ) self.assertCountEqual( cursor.fetchall(), - [('project_a', 2, 3), ('project_b', 1, 2), ('project_c', 0, 2), ('project_d', 1, 1)], + [ + ('project_a', 2, 3), + ('project_b', 1, 2), + ('project_c', 0, 2), + ('project_d', 1, 1), + ], ) diff --git a/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py index 214d35b939..6a1800db6c 100644 --- a/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py +++ b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py @@ -1,33 +1,37 @@ -import unittest +from django.db import connections from loading_pipeline.lib.core.environment import Env -from loading_pipeline.lib.misc.clickhouse import get_clickhouse_client +from loading_pipeline.lib.test.clickhouse_schema_testcase import ( + ClickhouseSchemaTestCase, +) from loading_pipeline.ops.repartition_clickhouse_grch38_snv_indel import ( REPARTITION_DATABASE_NAME, main, ) -class RepartitionGRCh38SnvIndelTest(unittest.TestCase): +class RepartitionGRCh38SnvIndelTest(ClickhouseSchemaTestCase): def setUp(self): - client = get_clickhouse_client() - client.execute( - f""" - DROP DATABASE IF EXISTS {Env.CLICKHOUSE_DATABASE} - PARALLEL WITH - DROP DATABASE IF EXISTS {REPARTITION_DATABASE_NAME}; - """, - ) - client.execute( - f""" - CREATE DATABASE {Env.CLICKHOUSE_DATABASE} - PARALLEL WITH - CREATE DATABASE {REPARTITION_DATABASE_NAME}; - """, - ) - client.execute( - f""" - CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` ( + super().setUp() + with connections['clickhouse_write'].cursor() as cursor: + cursor.execute( + f""" + DROP DATABASE IF EXISTS {REPARTITION_DATABASE_NAME}; + """, + ) + cursor.execute( + f""" + CREATE DATABASE {REPARTITION_DATABASE_NAME}; + """, + ) + cursor.execute( + f""" + DROP TABLE IF EXISTS {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries`; + """, + ) + cursor.execute( + f""" + CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` ( `key` UInt32, `project_guid` LowCardinality(String), `family_guid` String, From c866eb3ebccccf82312b1c965ee5d9ece05eb6b5 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 10:50:59 -0400 Subject: [PATCH 224/369] ruff --- .../ops/repartition_clickhouse_grch38_snv_indel_test.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py index 6a1800db6c..a8fa98f5cc 100644 --- a/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py +++ b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py @@ -50,7 +50,7 @@ def setUp(self): ORDER BY (project_guid, family_guid, key) SETTINGS deduplicate_merge_projection_mode = 'rebuild'; """, - ) + ) client.execute( f""" INSERT INTO {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` From aabe8e659e20454a18677fa328d51f19fddd320e Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 10:54:30 -0400 Subject: [PATCH 225/369] intermediate test iter --- ...tition_clickhouse_grch38_snv_indel_test.py | 176 +++++++++--------- 1 file changed, 89 insertions(+), 87 deletions(-) diff --git a/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py index a8fa98f5cc..98ce37e10a 100644 --- a/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py +++ b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py @@ -1,3 +1,5 @@ +from typing import ClassVar + from django.db import connections from loading_pipeline.lib.core.environment import Env @@ -9,116 +11,116 @@ main, ) +_ENTRIES_TABLE = f'{Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries`' +_PRE_MIGRATION_ENTRIES_TABLE = ( + f'{Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries_pre_migration`' +) + class RepartitionGRCh38SnvIndelTest(ClickhouseSchemaTestCase): + # Fixture data for the properly migrated `GRCh38/SNV_INDEL/entries` table, + # loaded normally via the shared clickhouse schema/fixture setup. + fixtures: ClassVar = ['clickhouse_test'] + def setUp(self): super().setUp() with connections['clickhouse_write'].cursor() as cursor: cursor.execute( f""" - DROP DATABASE IF EXISTS {REPARTITION_DATABASE_NAME}; + SELECT key, project_guid, family_guid, is_annotated_in_any_gene, sign + FROM {_ENTRIES_TABLE} """, ) + self.entries_rows = cursor.fetchall() + + # This script exists to repartition entries tables that predate + # per-project subpartitioning, where `n_partitions` is a hardcoded + # value rather than sourced from `project_partitions_dict`. Swap + # the migrated entries table for one in that improper state, + # carrying over the fixture data, to exercise that behavior. cursor.execute( f""" - CREATE DATABASE {REPARTITION_DATABASE_NAME}; + CREATE TABLE {_PRE_MIGRATION_ENTRIES_TABLE} + ( + `key` UInt32, + `project_guid` LowCardinality(String), + `family_guid` String, + `is_annotated_in_any_gene` Boolean, + `sign` Int8, + `n_partitions` UInt8 MATERIALIZED 2, + `partition_id` UInt8 MATERIALIZED farmHash64(family_guid) % n_partitions, + PROJECTION xpos_projection + ( + SELECT * ORDER BY is_annotated_in_any_gene + ) + ) + ENGINE = CollapsingMergeTree(sign) + PARTITION BY project_guid + ORDER BY (project_guid, family_guid, key) + SETTINGS deduplicate_merge_projection_mode = 'rebuild' """, ) cursor.execute( - f""" - DROP TABLE IF EXISTS {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries`; - """, + f'INSERT INTO {_PRE_MIGRATION_ENTRIES_TABLE} VALUES', + self.entries_rows, ) cursor.execute( - f""" - CREATE TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` ( - `key` UInt32, - `project_guid` LowCardinality(String), - `family_guid` String, - `is_annotated_in_any_gene` Boolean, - `sign` Int8, - `n_partitions` UInt8 MATERIALIZED 2, - `partition_id` UInt8 MATERIALIZED farmHash64(family_guid) % n_partitions, - PROJECTION xpos_projection - ( - SELECT * - ORDER BY is_annotated_in_any_gene - ) + f'EXCHANGE TABLES {_ENTRIES_TABLE} AND {_PRE_MIGRATION_ENTRIES_TABLE}', ) - ENGINE = CollapsingMergeTree(sign) - PARTITION BY project_guid - ORDER BY (project_guid, family_guid, key) - SETTINGS deduplicate_merge_projection_mode = 'rebuild'; - """, + + def tearDown(self): + with connections['clickhouse_write'].cursor() as cursor: + cursor.execute( + f'EXCHANGE TABLES {_ENTRIES_TABLE} AND {_PRE_MIGRATION_ENTRIES_TABLE}', ) - client.execute( - f""" - INSERT INTO {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` - VALUES - (0, 'project_a', 'family_a1', 0, 1), - (1, 'project_a', 'family_a2', 0, 1), - (2, 'project_a', 'family_a3', 0, 1), - (0, 'project_b', 'family_b1', 0, 1), - (1, 'project_b', 'family_b2', 0, 1), - (2, 'project_b', 'family_b2', 0, 1), - (0, 'project_c', 'family_c1', 1, 1), - (3, 'project_c', 'family_c2', 1, 1), - """, - ) - client.execute( - f""" - CREATE DICTIONARY {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_partitions_dict` - ( - `project_guid` String, - `n_partitions` UInt8 + cursor.execute(f'DROP TABLE {_PRE_MIGRATION_ENTRIES_TABLE}') + cursor.execute(f'DROP DATABASE IF EXISTS {REPARTITION_DATABASE_NAME}') + super().tearDown() + + def _partition_id(self, family_guid: str) -> int: + with connections['clickhouse_write'].cursor() as cursor: + cursor.execute( + 'SELECT farmHash64(%(family_guid)s) %% 2', + {'family_guid': family_guid}, ) - PRIMARY KEY project_guid - SOURCE( - CLICKHOUSE( - USER '{Env.CLICKHOUSE_WRITER_USER}' PASSWORD '{Env.CLICKHOUSE_WRITER_PASSWORD}' - DB {Env.CLICKHOUSE_DATABASE} QUERY 'SELECT project_guid, 3 FROM `GRCh38/SNV_INDEL/entries`' - ) + return cursor.fetchone()[0] + + def _expected_rows(self, project_guids): + return [ + ( + key, + project_guid, + family_guid, + is_annotated_in_any_gene, + sign, + 2, + self._partition_id(family_guid), ) - LIFETIME(0) - LAYOUT(FLAT(MAX_ARRAY_SIZE 10000)) - """, - ) + for key, project_guid, family_guid, is_annotated_in_any_gene, sign in self.entries_rows + if not project_guids or project_guid in project_guids + ] def test_main_all_projects(self): - client = get_clickhouse_client() main(1, []) - res = client.execute( - f""" - SELECT *, n_partitions, partition_id FROM {REPARTITION_DATABASE_NAME}.`GRCh38/SNV_INDEL/repartitioned_entries` - """, - ) - self.assertCountEqual( - res, - [ - (3, 'project_c', 'family_c2', True, 1, 2, 1), - (0, 'project_b', 'family_b1', 0, 1, 2, 1), - (1, 'project_b', 'family_b2', 0, 1, 2, 1), - (2, 'project_b', 'family_b2', 0, 1, 2, 1), - (2, 'project_a', 'family_a3', 0, 1, 2, 0), - (0, 'project_a', 'family_a1', 0, 1, 2, 1), - (1, 'project_a', 'family_a2', 0, 1, 2, 1), - (0, 'project_c', 'family_c1', True, 1, 2, 0), - ], - ) + with connections['clickhouse_write'].cursor() as cursor: + cursor.execute( + f""" + SELECT *, n_partitions, partition_id + FROM {REPARTITION_DATABASE_NAME}.`GRCh38/SNV_INDEL/repartitioned_entries` + """, + ) + self.assertCountEqual(cursor.fetchall(), self._expected_rows([])) def test_main_one_project(self): - client = get_clickhouse_client() main(1, ['project_a']) - res = client.execute( - f""" - SELECT *, n_partitions, partition_id FROM {REPARTITION_DATABASE_NAME}.`GRCh38/SNV_INDEL/repartitioned_entries` - """, - ) - self.assertCountEqual( - res, - [ - (2, 'project_a', 'family_a3', 0, 1, 2, 0), - (0, 'project_a', 'family_a1', 0, 1, 2, 1), - (1, 'project_a', 'family_a2', 0, 1, 2, 1), - ], - ) + with connections['clickhouse_write'].cursor() as cursor: + cursor.execute( + f""" + SELECT *, n_partitions, partition_id + FROM {REPARTITION_DATABASE_NAME}.`GRCh38/SNV_INDEL/repartitioned_entries` + """, + ) + self.assertCountEqual( + cursor.fetchall(), + self._expected_rows(['project_a']), + ) From 4f056e49eb23429d93987ecd65d66108db33a0b0 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 11:08:17 -0400 Subject: [PATCH 226/369] test reqrite --- ...tition_clickhouse_grch38_snv_indel_test.py | 90 +++++++++---------- 1 file changed, 42 insertions(+), 48 deletions(-) diff --git a/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py index 98ce37e10a..3d4b237499 100644 --- a/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py +++ b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py @@ -1,5 +1,3 @@ -from typing import ClassVar - from django.db import connections from loading_pipeline.lib.core.environment import Env @@ -18,26 +16,10 @@ class RepartitionGRCh38SnvIndelTest(ClickhouseSchemaTestCase): - # Fixture data for the properly migrated `GRCh38/SNV_INDEL/entries` table, - # loaded normally via the shared clickhouse schema/fixture setup. - fixtures: ClassVar = ['clickhouse_test'] - - def setUp(self): - super().setUp() + @classmethod + def setUpClass(cls): + super().setUpClass() with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f""" - SELECT key, project_guid, family_guid, is_annotated_in_any_gene, sign - FROM {_ENTRIES_TABLE} - """, - ) - self.entries_rows = cursor.fetchall() - - # This script exists to repartition entries tables that predate - # per-project subpartitioning, where `n_partitions` is a hardcoded - # value rather than sourced from `project_partitions_dict`. Swap - # the migrated entries table for one in that improper state, - # carrying over the fixture data, to exercise that behavior. cursor.execute( f""" CREATE TABLE {_PRE_MIGRATION_ENTRIES_TABLE} @@ -60,45 +42,41 @@ def setUp(self): SETTINGS deduplicate_merge_projection_mode = 'rebuild' """, ) - cursor.execute( - f'INSERT INTO {_PRE_MIGRATION_ENTRIES_TABLE} VALUES', - self.entries_rows, - ) cursor.execute( f'EXCHANGE TABLES {_ENTRIES_TABLE} AND {_PRE_MIGRATION_ENTRIES_TABLE}', ) - def tearDown(self): + @classmethod + def tearDownClass(cls): with connections['clickhouse_write'].cursor() as cursor: cursor.execute( f'EXCHANGE TABLES {_ENTRIES_TABLE} AND {_PRE_MIGRATION_ENTRIES_TABLE}', ) cursor.execute(f'DROP TABLE {_PRE_MIGRATION_ENTRIES_TABLE}') - cursor.execute(f'DROP DATABASE IF EXISTS {REPARTITION_DATABASE_NAME}') - super().tearDown() + super().tearDownClass() - def _partition_id(self, family_guid: str) -> int: + def setUp(self): + super().setUp() with connections['clickhouse_write'].cursor() as cursor: cursor.execute( - 'SELECT farmHash64(%(family_guid)s) %% 2', - {'family_guid': family_guid}, + f""" + INSERT INTO {_ENTRIES_TABLE} + VALUES + (0, 'project_a', 'family_a1', 0, 1), + (1, 'project_a', 'family_a2', 0, 1), + (2, 'project_a', 'family_a3', 0, 1), + (0, 'project_b', 'family_b1', 0, 1), + (1, 'project_b', 'family_b2', 0, 1), + (2, 'project_b', 'family_b2', 0, 1), + (0, 'project_c', 'family_c1', 1, 1), + (3, 'project_c', 'family_c2', 1, 1), + """, ) - return cursor.fetchone()[0] - def _expected_rows(self, project_guids): - return [ - ( - key, - project_guid, - family_guid, - is_annotated_in_any_gene, - sign, - 2, - self._partition_id(family_guid), - ) - for key, project_guid, family_guid, is_annotated_in_any_gene, sign in self.entries_rows - if not project_guids or project_guid in project_guids - ] + def tearDown(self): + with connections['clickhouse_write'].cursor() as cursor: + cursor.execute(f'DROP DATABASE IF EXISTS {REPARTITION_DATABASE_NAME}') + super().tearDown() def test_main_all_projects(self): main(1, []) @@ -109,7 +87,19 @@ def test_main_all_projects(self): FROM {REPARTITION_DATABASE_NAME}.`GRCh38/SNV_INDEL/repartitioned_entries` """, ) - self.assertCountEqual(cursor.fetchall(), self._expected_rows([])) + self.assertCountEqual( + cursor.fetchall(), + [ + (3, 'project_c', 'family_c2', True, 1, 2, 1), + (0, 'project_b', 'family_b1', 0, 1, 2, 1), + (1, 'project_b', 'family_b2', 0, 1, 2, 1), + (2, 'project_b', 'family_b2', 0, 1, 2, 1), + (2, 'project_a', 'family_a3', 0, 1, 2, 0), + (0, 'project_a', 'family_a1', 0, 1, 2, 1), + (1, 'project_a', 'family_a2', 0, 1, 2, 1), + (0, 'project_c', 'family_c1', True, 1, 2, 0), + ], + ) def test_main_one_project(self): main(1, ['project_a']) @@ -122,5 +112,9 @@ def test_main_one_project(self): ) self.assertCountEqual( cursor.fetchall(), - self._expected_rows(['project_a']), + [ + (2, 'project_a', 'family_a3', 0, 1, 2, 0), + (0, 'project_a', 'family_a1', 0, 1, 2, 1), + (1, 'project_a', 'family_a2', 0, 1, 2, 1), + ], ) From eb178ddb73248679901ce7f7782382317a2b2131 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 11:08:27 -0400 Subject: [PATCH 227/369] remove plan --- ...CLICKHOUSE_PYTEST_DJANGO_REMAINING_PLAN.md | 44 ------------------- 1 file changed, 44 deletions(-) delete mode 100644 loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_REMAINING_PLAN.md diff --git a/loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_REMAINING_PLAN.md b/loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_REMAINING_PLAN.md deleted file mode 100644 index 6b5bab38a1..0000000000 --- a/loading_pipeline/CLICKHOUSE_PYTEST_DJANGO_REMAINING_PLAN.md +++ /dev/null @@ -1,44 +0,0 @@ -# Plan: Finish migrating `repartition_clickhouse_grch38_snv_indel_test.py` to pytest-django - -## Context - -`loading_pipeline`'s ClickHouse tests were migrated to run against real `clickhouse_search` -Django migrations via pytest-django, with a shared `ClickhouseSchemaTestCase` base -(`lib/test/clickhouse_schema_testcase.py`) that owns the real schema DB's migrate/truncate -lifecycle. Every ClickHouse-touching test file adopted this base and switched from raw -`clickhouse_driver.Client` (`get_clickhouse_client()`) to -`connections['clickhouse_write'].cursor()` — except one file. - -## Remaining work - -`ops/repartition_clickhouse_grch38_snv_indel_test.py` (`RepartitionGRCh38SnvIndelTest`) still -predates the migration: - -- extends bare `unittest.TestCase`, not `ClickhouseSchemaTestCase` -- `setUp` manually runs `DROP DATABASE IF EXISTS {Env.CLICKHOUSE_DATABASE} PARALLEL WITH DROP - DATABASE IF EXISTS {REPARTITION_DATABASE_NAME}` then the matching `CREATE DATABASE ... PARALLEL - WITH ...` — `Env.CLICKHOUSE_DATABASE` is now owned by pytest-django's migrate lifecycle; - `REPARTITION_DATABASE_NAME` is the script's own scratch DB, not part of `clickhouse_search`'s - schema -- every SQL statement in `setUp` and both test methods runs via `get_clickhouse_client()` + - `client.execute(...)`, a raw `clickhouse_driver.Client` - -### Changes - -1. `RepartitionGRCh38SnvIndelTest` extends `ClickhouseSchemaTestCase` instead of - `unittest.TestCase`. -2. Drop the `DROP DATABASE IF EXISTS {Env.CLICKHOUSE_DATABASE}` / `CREATE DATABASE - {Env.CLICKHOUSE_DATABASE}` half of `setUp`'s `PARALLEL WITH` statements — the shared base now - handles that DB's schema/lifecycle. -3. Keep the `REPARTITION_DATABASE_NAME` drop/create in `setUp` (still not part of the real - schema), issued as its own statement. -4. Keep the synthetic `GRCh38/SNV_INDEL/entries` table DDL, `INSERT` seed rows, and - `project_partitions_dict` dictionary DDL as-is (intentionally bespoke, not real schema). -5. Execute everything in `setUp` and both test methods (`test_main_all_projects`, - `test_main_one_project`) via `connections['clickhouse_write'].cursor()` / - `cursor.execute(...)` / `cursor.fetchall()` instead of `get_clickhouse_client()` / - `client.execute(...)`. -6. Drop the now-unused `get_clickhouse_client` import. - -Reference `lib/misc/clickhouse_test.py` or `bin/pipeline_worker_test.py` for the established -pattern of extending `ClickhouseSchemaTestCase` and using the cursor. \ No newline at end of file From 254100b98647009765fbf6ae34e970f3e7391850 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 11:09:57 -0400 Subject: [PATCH 228/369] unit test fix iter --- loading_pipeline/lib/misc/clickhouse_test.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index e09c58e962..494e7042ef 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -477,6 +477,7 @@ def test_direct_insert_all_keys(self): return_value=[ClickhouseReferenceDataset.CLINVAR], ) def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): + self.maxDiff = None # Tests individual components of atomic_insert_entries, validating state after each step. table_name_builder = TableNameBuilder( ReferenceGenome.GRCh38, @@ -856,7 +857,7 @@ def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_typ SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` - WHERE PROJECT_GUID = 'project_d' + WHERE project_guid = 'project_d' GROUP BY project_guid, key, sample_type """, ) From 6688547c8be8dad78bdae1b8197f8b04e99ed15a Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 11:21:13 -0400 Subject: [PATCH 229/369] test fixes --- loading_pipeline/lib/misc/clickhouse_test.py | 5 ++++- .../ops/repartition_clickhouse_grch38_snv_indel_test.py | 2 ++ 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index 494e7042ef..dd098aef9e 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -522,6 +522,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) FROM {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/project_gt_stats` + FINAL GROUP BY project_guid, key, sample_type """, ) @@ -557,6 +558,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) FROM {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/project_gt_stats` + FINAL GROUP BY project_guid, key, sample_type """, ) @@ -587,6 +589,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) FROM {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/project_gt_stats` + FINAL GROUP BY project_guid, key, sample_type """, ) @@ -843,7 +846,6 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): return_value=[ClickhouseReferenceDataset.CLINVAR], ) def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_type): - self.maxDiff = None load_complete_run( ReferenceGenome.GRCh38, DatasetType.SNV_INDEL, @@ -866,6 +868,7 @@ def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_typ [ ('project_d', 10, 'WES', 0, 1), ('project_d', 4, 'WES', 1, 0), + ('project_d', 3, 'WES', 0, 0), ], ) cursor.execute( diff --git a/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py index 3d4b237499..60ee69e57d 100644 --- a/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py +++ b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py @@ -29,6 +29,8 @@ def setUpClass(cls): `family_guid` String, `is_annotated_in_any_gene` Boolean, `sign` Int8, + `sample_type` Enum8('WES' = 1, 'WGS' = 2) MATERIALIZED CAST(1, 'Enum8(\\'WES\\' = 1, \\'WGS\\' = 2)'), + `calls` Array(Tuple(sampleId String, gt Nullable(Enum8('REF' = 0, 'HET' = 1, 'HOM' = 2)))) MATERIALIZED CAST([], 'Array(Tuple(sampleId String, gt Nullable(Enum8(\\'REF\\' = 0, \\'HET\\' = 1, \\'HOM\\' = 2))))'), `n_partitions` UInt8 MATERIALIZED 2, `partition_id` UInt8 MATERIALIZED farmHash64(family_guid) % n_partitions, PROJECTION xpos_projection From 7edea85d13587bcf1abcd93431b3541dfab1cac6 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 11:30:37 -0400 Subject: [PATCH 230/369] fix tests --- .github/workflows/pipeline-unit-tests.yml | 2 +- loading_pipeline/bin/pipeline_worker_test.py | 15 +++++-------- loading_pipeline/lib/misc/clickhouse_test.py | 23 ++++++++++++++------ 3 files changed, 23 insertions(+), 17 deletions(-) diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml index fa440a343d..71201beb8b 100644 --- a/.github/workflows/pipeline-unit-tests.yml +++ b/.github/workflows/pipeline-unit-tests.yml @@ -86,5 +86,5 @@ jobs: export CLICKHOUSE_OPTIMIZE_TABLE_WAIT_S=1 export PYSPARK_SUBMIT_ARGS='--driver-memory 8G pyspark-shell' export CLICKHOUSE_DATABASE=test - uv run --project loading_pipeline pytest --cov=loading_pipeline --cov-report=term-missing -vv loading_pipeline + uv run --project loading_pipeline pytest --cov=loading_pipeline --cov-report=term-missing loading_pipeline uv run --project loading_pipeline coverage report --omit '*test*' --fail-under=85 diff --git a/loading_pipeline/bin/pipeline_worker_test.py b/loading_pipeline/bin/pipeline_worker_test.py index a2e3db1e54..2ab2d5c641 100644 --- a/loading_pipeline/bin/pipeline_worker_test.py +++ b/loading_pipeline/bin/pipeline_worker_test.py @@ -105,32 +105,29 @@ def test_process_queue_integration_test( self.assertEqual(f.read(), '') cursor = connections['clickhouse_write'].cursor() - cursor.execute( + annotations_count = cursor.execute( f""" SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` """, - ) - annotations_count = cursor.fetchone()[0] + ).fetchone()[0] self.assertEqual(annotations_count, 30) - cursor.execute( + entries_count = cursor.execute( f""" SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` """, - ) - entries_count = cursor.fetchone()[0] + ).fetchone()[0] self.assertEqual(entries_count, 16) - cursor.execute( + ac_wgs = cursor.execute( f""" SELECT sum(ac_wgs) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` """, - ) - ac_wgs = cursor.fetchone()[0] + ).fetchone()[0] self.assertEqual(ac_wgs, 69) @patch('loading_pipeline.lib.misc.slack._safe_post_to_slack') diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index dd098aef9e..ce2eb13b75 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -565,14 +565,15 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): self.assertCountEqual( cursor.fetchall(), [ - ('project_a', 10, 'WES', 0, 0), ('project_a', 1, 'WGS', 1, 0), ('project_a', 2, 'WGS', 0, 1), - ('project_a', 4, 'WES', 0, 0), - ('project_a', 4, 'WGS', 0, 0), + ('project_b', 10, 'WES', 0, 0) ('project_b', 1, 'WES', 1, 0), + ('project_b', 2, 'WES', 0, 0) ('project_b', 3, 'WES', 0, 1), ('project_b', 4, 'WES', 0, 1), + ('project_c', 0, 'WES', 0, 0) + ('project_c', 3, 'WES', 0, 0) ('project_c', 4, 'WES', 0, 1), ('project_c', 5, 'WES', 0, 1), ], @@ -881,8 +882,12 @@ def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_typ self.assertCountEqual( cursor.fetchall(), [ - (10, 2, 0), - (4, 1, 0), + (1, 1, 1, 0, 0, 0, 0), + (2, 0, 2, 0, 0, 1, 0), + (3, 2, 0, 0, 1, 0, 0), + (4, 6, 2, 0, 2, 1, 0), + (5, 2, 0, 0, 1, 0, 0), + (10, 4, 0, 0, 2, 0, 0), ], ) cursor.execute( @@ -895,8 +900,12 @@ def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_typ self.assertCountEqual( cursor.fetchall(), [ - (0, 2, 0), - (4, 1, 0), + (1, 1, 1, 0, 0, 0, 0), + (2, 0, 2, 0, 0, 1, 0), + (3, 2, 0, 0, 1, 0, 0), + (4, 6, 2, 0, 2, 1, 0), + (5, 2, 0, 0, 1, 0, 0), + (10, 4, 0, 0, 2, 0, 0), ], ) cursor.execute( From b4793f6231938ce23ab07df690e629cdd71b933f Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 11:33:39 -0400 Subject: [PATCH 231/369] ruff --- loading_pipeline/lib/misc/clickhouse_test.py | 8 ++++---- .../load_clickhouse_variants_tables_test.py | 15 ++++++--------- 2 files changed, 10 insertions(+), 13 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index ce2eb13b75..f97bbd151d 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -567,13 +567,13 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): [ ('project_a', 1, 'WGS', 1, 0), ('project_a', 2, 'WGS', 0, 1), - ('project_b', 10, 'WES', 0, 0) + ('project_b', 10, 'WES', 0, 0), ('project_b', 1, 'WES', 1, 0), - ('project_b', 2, 'WES', 0, 0) + ('project_b', 2, 'WES', 0, 0), ('project_b', 3, 'WES', 0, 1), ('project_b', 4, 'WES', 0, 1), - ('project_c', 0, 'WES', 0, 0) - ('project_c', 3, 'WES', 0, 0) + ('project_c', 0, 'WES', 0, 0), + ('project_c', 3, 'WES', 0, 0), ('project_c', 4, 'WES', 0, 1), ('project_c', 5, 'WES', 0, 1), ], diff --git a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py index f412e0fa48..2df35086bf 100644 --- a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py +++ b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py @@ -119,30 +119,27 @@ def test_write_variants_to_clickhouse( self.assertTrue(task.complete()) cursor = connections['clickhouse_write'].cursor() - cursor.execute( + variants_count = cursor.execute( f""" SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` """, - ) - variants_count = cursor.fetchone()[0] + ).fetchone()[0] self.assertEqual(variants_count, 2) - cursor.execute( + variant_details_count = cursor.execute( f""" SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details` """, - ) - variant_details_count = cursor.fetchone()[0] + ).fetchone()[0] self.assertEqual(variant_details_count, 2) - cursor.execute( + key_lookups_count = cursor.execute( f""" SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/key_lookup` """, - ) - key_lookups_count = cursor.fetchone()[0] + ).fetchone()[0] self.assertEqual(key_lookups_count, 2) From 5b1ece801c2ff694c75423c848b30f4a07923652 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 11:46:39 -0400 Subject: [PATCH 232/369] fix tests --- .github/workflows/pipeline-unit-tests.yml | 3 +- loading_pipeline/bin/pipeline_worker_test.py | 15 +++++---- loading_pipeline/lib/misc/clickhouse_test.py | 32 +++++++++++++++---- .../load_clickhouse_variants_tables_test.py | 15 +++++---- 4 files changed, 45 insertions(+), 20 deletions(-) diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml index 71201beb8b..1b989e6335 100644 --- a/.github/workflows/pipeline-unit-tests.yml +++ b/.github/workflows/pipeline-unit-tests.yml @@ -9,12 +9,13 @@ on: - master paths: - 'loading_pipeline/**' - - '.github/workflows/*pipeline-release.yaml' + - '.github/workflows/pipeline-*-release.yaml' pull_request: types: [opened, synchronize, reopened] paths: - 'loading_pipeline/**' - '.github/workflows/*pipeline*.yaml' + - 'clickhouse_search/migrations/*.py' permissions: contents: read diff --git a/loading_pipeline/bin/pipeline_worker_test.py b/loading_pipeline/bin/pipeline_worker_test.py index 2ab2d5c641..a2e3db1e54 100644 --- a/loading_pipeline/bin/pipeline_worker_test.py +++ b/loading_pipeline/bin/pipeline_worker_test.py @@ -105,29 +105,32 @@ def test_process_queue_integration_test( self.assertEqual(f.read(), '') cursor = connections['clickhouse_write'].cursor() - annotations_count = cursor.execute( + cursor.execute( f""" SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` """, - ).fetchone()[0] + ) + annotations_count = cursor.fetchone()[0] self.assertEqual(annotations_count, 30) - entries_count = cursor.execute( + cursor.execute( f""" SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` """, - ).fetchone()[0] + ) + entries_count = cursor.fetchone()[0] self.assertEqual(entries_count, 16) - ac_wgs = cursor.execute( + cursor.execute( f""" SELECT sum(ac_wgs) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` """, - ).fetchone()[0] + ) + ac_wgs = cursor.fetchone()[0] self.assertEqual(ac_wgs, 69) @patch('loading_pipeline.lib.misc.slack._safe_post_to_slack') diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index f97bbd151d..09cc3062bc 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -597,17 +597,19 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): self.assertCountEqual( cursor.fetchall(), [ - ('project_a', 10, 'WES', 0, 0), ('project_a', 1, 'WGS', 1, 0), ('project_a', 2, 'WGS', 0, 1), - ('project_a', 4, 'WES', 0, 0), - ('project_a', 4, 'WGS', 0, 0), + ('project_b', 10, 'WES', 0, 0), ('project_b', 1, 'WES', 1, 0), + ('project_b', 2, 'WES', 0, 0), ('project_b', 3, 'WES', 0, 1), ('project_b', 4, 'WES', 0, 1), + ('project_c', 0, 'WES', 0, 0), + ('project_c', 3, 'WES', 0, 0), ('project_c', 4, 'WES', 0, 1), ('project_c', 5, 'WES', 0, 1), ('project_d', 10, 'WES', 0, 1), + ('project_d', 3, 'WES', 0, 0), ('project_d', 4, 'WES', 1, 0), ], ) @@ -918,10 +920,10 @@ def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_typ self.assertCountEqual( cursor.fetchall(), [ - (10, '1-3-A-C'), - (11, '2-4-A-T'), - (12, 'Y-9-A-C'), - (13, 'M-2-C-G'), + (10, [], [], []), + (11, [], [], []), + (12, [], [], []), + (13, [], [], []), ], ) cursor.execute( @@ -931,6 +933,22 @@ def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_typ {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_disk` """, ) + self.assertCountEqual( + cursor.fetchall(), + [ + (10, [], [], []), + (11, [], [], []), + (12, [], [], []), + (13, [], [], []), + ], + ) + cursor.execute( + f""" + SELECT key, variantId + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_details` + """, + ) self.assertCountEqual( cursor.fetchall(), [ diff --git a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py index 2df35086bf..f412e0fa48 100644 --- a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py +++ b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py @@ -119,27 +119,30 @@ def test_write_variants_to_clickhouse( self.assertTrue(task.complete()) cursor = connections['clickhouse_write'].cursor() - variants_count = cursor.execute( + cursor.execute( f""" SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` """, - ).fetchone()[0] + ) + variants_count = cursor.fetchone()[0] self.assertEqual(variants_count, 2) - variant_details_count = cursor.execute( + cursor.execute( f""" SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details` """, - ).fetchone()[0] + ) + variant_details_count = cursor.fetchone()[0] self.assertEqual(variant_details_count, 2) - key_lookups_count = cursor.execute( + cursor.execute( f""" SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/key_lookup` """, - ).fetchone()[0] + ) + key_lookups_count = cursor.fetchone()[0] self.assertEqual(key_lookups_count, 2) From 54a7c6cf846b5393e824dd2d3b4143fd92bae56b Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 12:08:35 -0400 Subject: [PATCH 233/369] test cleanup --- loading_pipeline/lib/misc/clickhouse_test.py | 153 ++++++++++--------- 1 file changed, 79 insertions(+), 74 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index 09cc3062bc..a83f1d3c13 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -190,52 +190,6 @@ 'consequenceTerms': ['regulatory_region_ablation'], 'regulatoryFeatureId': 'ENSR00000123', } -VARIANT_DETAILS_ROWS = [ - { - 'key': 1, - 'variantId': '1-13-A-C', - 'liftedOverChrom': '1', - 'liftedOverPos': 13, - 'rsid': 'rs123', - 'CAID': 'CA123456', - 'transcripts': [_FULL_TRANSCRIPT], - 'sortedMotifFeatureConsequences': [_FULL_MOTIF_CONSEQUENCE], - 'sortedRegulatoryFeatureConsequences': [_FULL_REGULATORY_CONSEQUENCE], - }, - { - 'key': 2, - 'variantId': '2-14-A-T', - 'liftedOverChrom': None, - 'liftedOverPos': None, - 'rsid': None, - 'CAID': None, - 'transcripts': [], - 'sortedMotifFeatureConsequences': [], - 'sortedRegulatoryFeatureConsequences': [], - }, - { - 'key': 3, - 'variantId': 'Y-19-A-C', - 'liftedOverChrom': None, - 'liftedOverPos': None, - 'rsid': None, - 'CAID': None, - 'transcripts': [], - 'sortedMotifFeatureConsequences': [], - 'sortedRegulatoryFeatureConsequences': [], - }, - { - 'key': 4, - 'variantId': 'M-12-C-G', - 'liftedOverChrom': None, - 'liftedOverPos': None, - 'rsid': None, - 'CAID': None, - 'transcripts': [], - 'sortedMotifFeatureConsequences': [], - 'sortedRegulatoryFeatureConsequences': [], - }, -] class ClickhouseTest(MockedDatarootTestCase, ClickhouseSchemaTestCase): @@ -273,21 +227,41 @@ def write_test_parquet(df: pd.DataFrame, parquet_path: str, schema=None): ), ) - variant_details_table = pa.Table.from_pylist( - VARIANT_DETAILS_ROWS, - schema=VARIANT_DETAILS_SCHEMA, - ) - variant_details_path = new_variant_details_parquet_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_RUN_ID, + # Variant Details Parquet + df = pd.DataFrame( + { + 'key': [1, 2, 3, 4], + 'variantId': [ + '1-13-A-C', + '2-14-A-T', + 'Y-19-A-C', + 'M-12-C-G', + ], + 'transcripts': [[_FULL_TRANSCRIPT], [], [], []], + 'liftedOverChrom': ['1', None, None, None], + 'liftedOverPos': [13, None, None, None], + 'rsid': ['rs123', None, None, None], + 'CAID': ['CA123456', None, None, None], + 'sortedMotifFeatureConsequences': [[_FULL_MOTIF_CONSEQUENCE], [], [], []], + 'sortedRegulatoryFeatureConsequences': [ + [_FULL_REGULATORY_CONSEQUENCE], + [], + [], + [], + ], + }, ) - os.makedirs(variant_details_path) - pq.write_table( - variant_details_table, - os.path.join(variant_details_path, 'test.parquet'), + write_test_parquet( + df, + new_variant_details_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + VARIANT_DETAILS_SCHEMA, # TODO needed? ) + # New Variants parquet. df = pd.DataFrame( { 'key': [10, 11, 12, 13], @@ -316,6 +290,7 @@ def write_test_parquet(df: pd.DataFrame, parquet_path: str, schema=None): ), ) + # New Entries Parquet df = pd.DataFrame( { 'key': [10, 3, 4], @@ -643,151 +618,181 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): 10, 'project_b', 'family_b1', - 123456789, 'WES', + 123456789, [], [('sample_b4', 'REF')], 1, + 1, + 0, ), ( 1, 'project_b', 'family_b2', - 123456789, 'WES', + 123456789, [], [('sample_b5', 'HET')], 1, + 1, + 0, ), ( 2, 'project_b', 'family_b2', - 123456789, 'WES', + 123456789, [], [('sample_b5', 'REF')], 1, + 1, + 0, ), ( 3, 'project_b', 'family_b3', - 133456789, 'WES', + 133456789, [], [('sample_b6', 'HOM')], 1, + 1, + 0, ), ( 4, 'project_b', 'family_b3', - 133456789, 'WES', + 133456789, [], [('sample_b6', 'HOM')], 1, + 1, + 0, ), ( 1, 'project_a', 'family_a2', + 'WES', 123456789, - 'WGS', [], [('sample_a2', 'HET')], 1, + 1, + 0, ), ( 2, 'project_a', 'family_a3', - 133456789, 'WGS', + 133456789, [], [('sample_a3', 'HOM')], 1, + 1, + 0, ), ( 3, 'project_a', 'family_a4', - 133456789, 'WES', + 133456789, [], [('sample_a4', 'REF')], 1, + 1, + 0, ), ( 10, 'project_d', 'family_d1', - 123456789, 'WES', + 123456789, [], [('sample_d1', 'REF'), ('sample_d11', 'HOM')], 1, + 1, + 0, ), ( 3, 'project_d', 'family_d2', - 123456789, 'WES', + 123456789, [123, 12], [('sample_d2', 'REF')], 1, + 1, + 0, ), ( 4, 'project_d', 'family_d3', - 123456789, 'WES', + 123456789, [1], [('sample_d3', 'HET')], 1, + 1, + 0, ), ( 10, 'project_c', 'family_c1', - 123456789, 'WES', + 123456789, [1], [('sample_c7', 'REF')], 1, + 1, + 0, ), ( 3, 'project_c', 'family_c2', - 123456789, 'WES', + 123456789, [1], [('sample_c8', 'REF')], 1, + 1, + 0, ), ( 4, 'project_c', 'family_c3', - 133456789, 'WES', + 133456789, [1], [('sample_c9', 'HOM')], 1, + 1, + 0, ), ( 5, 'project_c', 'family_c4', - 133456789, 'WES', + 133456789, [1], [('sample_c9', 'HOM')], 1, + 1, + 0, ), ], ) @@ -946,7 +951,7 @@ def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_typ f""" SELECT key, variantId FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_details` + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details` """, ) self.assertCountEqual( From c9a9bc85576949c1087ddd05d1aa9e497f33d9be Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 12:17:46 -0400 Subject: [PATCH 234/369] fix tests --- loading_pipeline/lib/misc/clickhouse_test.py | 513 ++++++++++--------- 1 file changed, 261 insertions(+), 252 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index a83f1d3c13..d139cbaa18 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -452,7 +452,7 @@ def test_direct_insert_all_keys(self): return_value=[ClickhouseReferenceDataset.CLINVAR], ) def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): - self.maxDiff = None + self.maxDiff = None # TODO # Tests individual components of atomic_insert_entries, validating state after each step. table_name_builder = TableNameBuilder( ReferenceGenome.GRCh38, @@ -488,10 +488,12 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): SELECT DISTINCT project_guid FROM {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/entries` """, ) - self.assertCountEqual( - [p[0] for p in cursor.fetchall()], - ['project_a', 'project_b'], - ) + staged_projects = cursor.fetchall() + self.assertCountEqual( + [p[0] for p in staged_projects], + ['project_a', 'project_b'], + ) + with connections['clickhouse_write'].cursor() as cursor: cursor.execute( f""" SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) @@ -501,28 +503,29 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): GROUP BY project_guid, key, sample_type """, ) - self.assertCountEqual( - cursor.fetchall(), - [ - ('project_a', 10, 'WES', 0, 1), - ('project_a', 1, 'WGS', 1, 0), - ('project_a', 2, 'WGS', 0, 1), - ('project_a', 3, 'WES', 0, 0), - ('project_a', 4, 'WES', 1, 0), - ('project_a', 4, 'WGS', 0, 1), - ('project_b', 10, 'WES', 0, 0), - ('project_b', 1, 'WES', 1, 0), - ('project_b', 2, 'WES', 0, 0), - ('project_b', 3, 'WES', 0, 1), - ('project_b', 4, 'WES', 0, 1), - # project_gt_stats stages all projects, not just - # those requested for loading. - ('project_c', 0, 'WES', 0, 0), - ('project_c', 3, 'WES', 0, 0), - ('project_c', 4, 'WES', 0, 1), - ('project_c', 5, 'WES', 0, 1), - ], - ) + staged_project_gt_stats = cursor.fetchall() + self.assertCountEqual( + staged_project_gt_stats, + [ + ('project_a', 10, 'WES', 0, 1), + ('project_a', 1, 'WGS', 1, 0), + ('project_a', 2, 'WGS', 0, 1), + ('project_a', 3, 'WES', 0, 0), + ('project_a', 4, 'WES', 1, 0), + ('project_a', 4, 'WGS', 0, 1), + ('project_b', 10, 'WES', 0, 0), + ('project_b', 1, 'WES', 1, 0), + ('project_b', 2, 'WES', 0, 0), + ('project_b', 3, 'WES', 0, 1), + ('project_b', 4, 'WES', 0, 1), + # project_gt_stats stages all projects, not just + # those requested for loading. + ('project_c', 0, 'WES', 0, 0), + ('project_c', 3, 'WES', 0, 0), + ('project_c', 4, 'WES', 0, 1), + ('project_c', 5, 'WES', 0, 1), + ], + ) delete_existing_families_from_staging_entries( table_name_builder, ['family_a1', 'family_a5', 'family_a6'], @@ -537,22 +540,23 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): GROUP BY project_guid, key, sample_type """, ) - self.assertCountEqual( - cursor.fetchall(), - [ - ('project_a', 1, 'WGS', 1, 0), - ('project_a', 2, 'WGS', 0, 1), - ('project_b', 10, 'WES', 0, 0), - ('project_b', 1, 'WES', 1, 0), - ('project_b', 2, 'WES', 0, 0), - ('project_b', 3, 'WES', 0, 1), - ('project_b', 4, 'WES', 0, 1), - ('project_c', 0, 'WES', 0, 0), - ('project_c', 3, 'WES', 0, 0), - ('project_c', 4, 'WES', 0, 1), - ('project_c', 5, 'WES', 0, 1), - ], - ) + staged_project_gt_stats = cursor.fetchall() + self.assertCountEqual( + staged_project_gt_stats, + [ + ('project_a', 1, 'WGS', 1, 0), + ('project_a', 2, 'WGS', 0, 1), + ('project_b', 10, 'WES', 0, 0), + ('project_b', 1, 'WES', 1, 0), + ('project_b', 2, 'WES', 0, 0), + ('project_b', 3, 'WES', 0, 1), + ('project_b', 4, 'WES', 0, 1), + ('project_c', 0, 'WES', 0, 0), + ('project_c', 3, 'WES', 0, 0), + ('project_c', 4, 'WES', 0, 1), + ('project_c', 5, 'WES', 0, 1), + ], + ) insert_new_entries(table_name_builder) optimize_entries( @@ -569,25 +573,26 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): GROUP BY project_guid, key, sample_type """, ) - self.assertCountEqual( - cursor.fetchall(), - [ - ('project_a', 1, 'WGS', 1, 0), - ('project_a', 2, 'WGS', 0, 1), - ('project_b', 10, 'WES', 0, 0), - ('project_b', 1, 'WES', 1, 0), - ('project_b', 2, 'WES', 0, 0), - ('project_b', 3, 'WES', 0, 1), - ('project_b', 4, 'WES', 0, 1), - ('project_c', 0, 'WES', 0, 0), - ('project_c', 3, 'WES', 0, 0), - ('project_c', 4, 'WES', 0, 1), - ('project_c', 5, 'WES', 0, 1), - ('project_d', 10, 'WES', 0, 1), - ('project_d', 3, 'WES', 0, 0), - ('project_d', 4, 'WES', 1, 0), - ], - ) + staged_project_gt_stats = cursor.fetchall() + self.assertCountEqual( + staged_project_gt_stats, + [ + ('project_a', 1, 'WGS', 1, 0), + ('project_a', 2, 'WGS', 0, 1), + ('project_b', 10, 'WES', 0, 0), + ('project_b', 1, 'WES', 1, 0), + ('project_b', 2, 'WES', 0, 0), + ('project_b', 3, 'WES', 0, 1), + ('project_b', 4, 'WES', 0, 1), + ('project_c', 0, 'WES', 0, 0), + ('project_c', 3, 'WES', 0, 0), + ('project_c', 4, 'WES', 0, 1), + ('project_c', 5, 'WES', 0, 1), + ('project_d', 10, 'WES', 0, 1), + ('project_d', 3, 'WES', 0, 0), + ('project_d', 4, 'WES', 1, 0), + ], + ) refresh_materialized_views( table_name_builder, @@ -611,191 +616,193 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` """, ) - self.assertCountEqual( - cursor.fetchall(), - [ - ( - 10, - 'project_b', - 'family_b1', - 'WES', - 123456789, - [], - [('sample_b4', 'REF')], - 1, - 1, - 0, - ), - ( - 1, - 'project_b', - 'family_b2', - 'WES', - 123456789, - [], - [('sample_b5', 'HET')], - 1, - 1, - 0, - ), - ( - 2, - 'project_b', - 'family_b2', - 'WES', - 123456789, - [], - [('sample_b5', 'REF')], - 1, - 1, - 0, - ), - ( - 3, - 'project_b', - 'family_b3', - 'WES', - 133456789, - [], - [('sample_b6', 'HOM')], - 1, - 1, - 0, - ), - ( - 4, - 'project_b', - 'family_b3', - 'WES', - 133456789, - [], - [('sample_b6', 'HOM')], - 1, - 1, - 0, - ), - ( - 1, - 'project_a', - 'family_a2', - 'WES', - 123456789, - [], - [('sample_a2', 'HET')], - 1, - 1, - 0, - ), - ( - 2, - 'project_a', - 'family_a3', - 'WGS', - 133456789, - [], - [('sample_a3', 'HOM')], - 1, - 1, - 0, - ), - ( - 3, - 'project_a', - 'family_a4', - 'WES', - 133456789, - [], - [('sample_a4', 'REF')], - 1, - 1, - 0, - ), - ( - 10, - 'project_d', - 'family_d1', - 'WES', - 123456789, - [], - [('sample_d1', 'REF'), ('sample_d11', 'HOM')], - 1, - 1, - 0, - ), - ( - 3, - 'project_d', - 'family_d2', - 'WES', - 123456789, - [123, 12], - [('sample_d2', 'REF')], - 1, - 1, - 0, - ), - ( - 4, - 'project_d', - 'family_d3', - 'WES', - 123456789, - [1], - [('sample_d3', 'HET')], - 1, - 1, - 0, - ), - ( - 10, - 'project_c', - 'family_c1', - 'WES', - 123456789, - [1], - [('sample_c7', 'REF')], - 1, - 1, - 0, - ), - ( - 3, - 'project_c', - 'family_c2', - 'WES', - 123456789, - [1], - [('sample_c8', 'REF')], - 1, - 1, - 0, - ), - ( - 4, - 'project_c', - 'family_c3', - 'WES', - 133456789, - [1], - [('sample_c9', 'HOM')], - 1, - 1, - 0, - ), - ( - 5, - 'project_c', - 'family_c4', - 'WES', - 133456789, - [1], - [('sample_c9', 'HOM')], - 1, - 1, - 0, - ), - ], - ) + new_entries = cursor.fetchall() + self.assertCountEqual( + new_entries, + [ + ( + 10, + 'project_b', + 'family_b1', + 'WES', + 123456789, + [], + [('sample_b4', 'REF')], + 1, + 1, + 0, + ), + ( + 1, + 'project_b', + 'family_b2', + 'WES', + 123456789, + [], + [('sample_b5', 'HET')], + 1, + 1, + 0, + ), + ( + 2, + 'project_b', + 'family_b2', + 'WES', + 123456789, + [], + [('sample_b5', 'REF')], + 1, + 1, + 0, + ), + ( + 3, + 'project_b', + 'family_b3', + 'WES', + 133456789, + [], + [('sample_b6', 'HOM')], + 1, + 1, + 0, + ), + ( + 4, + 'project_b', + 'family_b3', + 'WES', + 133456789, + [], + [('sample_b6', 'HOM')], + 1, + 1, + 0, + ), + ( + 1, + 'project_a', + 'family_a2', + 'WES', + 123456789, + [], + [('sample_a2', 'HET')], + 1, + 1, + 0, + ), + ( + 2, + 'project_a', + 'family_a3', + 'WGS', + 133456789, + [], + [('sample_a3', 'HOM')], + 1, + 1, + 0, + ), + ( + 3, + 'project_a', + 'family_a4', + 'WES', + 133456789, + [], + [('sample_a4', 'REF')], + 1, + 1, + 0, + ), + ( + 10, + 'project_d', + 'family_d1', + 'WES', + 123456789, + [], + [('sample_d1', 'REF'), ('sample_d11', 'HOM')], + 1, + 1, + 0, + ), + ( + 3, + 'project_d', + 'family_d2', + 'WES', + 123456789, + [123, 12], + [('sample_d2', 'REF')], + 1, + 1, + 0, + ), + ( + 4, + 'project_d', + 'family_d3', + 'WES', + 123456789, + [1], + [('sample_d3', 'HET')], + 1, + 1, + 0, + ), + ( + 10, + 'project_c', + 'family_c1', + 'WES', + 123456789, + [1], + [('sample_c7', 'REF')], + 1, + 1, + 0, + ), + ( + 3, + 'project_c', + 'family_c2', + 'WES', + 123456789, + [1], + [('sample_c8', 'REF')], + 1, + 1, + 0, + ), + ( + 4, + 'project_c', + 'family_c3', + 'WES', + 133456789, + [1], + [('sample_c9', 'HOM')], + 1, + 1, + 0, + ), + ( + 5, + 'project_c', + 'family_c4', + 'WES', + 133456789, + [1], + [('sample_c9', 'HOM')], + 1, + 1, + 0, + ), + ], + ) + with connections['clickhouse_write'].cursor() as cursor: cursor.execute( f""" SELECT * @@ -803,10 +810,11 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` """, ) - self.assertCountEqual( - cursor.fetchall(), - [], - ) + existing_gt_stats = cursor.fetchall() + self.assertCountEqual( + existing_gt_stats, + [], + ) exchange_tables( table_name_builder, @@ -822,7 +830,8 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` """, ) - self.assertCountEqual(cursor.fetchall(), []) + new_gt_stats = cursor.fetchall() + self.assertCountEqual(new_gt_stats, []) reload_dictionaries( table_name_builder, From 127adc3651dc837f5c1fb6b41b41d8e5655b8d93 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 12:26:15 -0400 Subject: [PATCH 235/369] test cleanup --- loading_pipeline/lib/misc/clickhouse_test.py | 713 +++++++++---------- 1 file changed, 354 insertions(+), 359 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index d139cbaa18..9a4e8ecbf1 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -407,6 +407,7 @@ def test_table_name_builder(self): ) def test_direct_insert_all_keys(self): + cursor = connections['clickhouse_write'].cursor() direct_insert_all_keys( ClickHouseTable.VARIANT_DETAILS, TableNameBuilder( @@ -415,21 +416,20 @@ def test_direct_insert_all_keys(self): TEST_RUN_ID, ), ) - with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f'SELECT key, variantId FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', - ) - self.assertEqual( - cursor.fetchall(), - [ - (1, '1-13-A-C'), - (2, '2-14-A-T'), - (3, 'Y-19-A-C'), - (4, 'M-12-C-G'), - (7, 'c'), - (10, 'b'), - ], - ) + cursor.execute( + f'SELECT key, variantId FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', + ) + self.assertEqual( + cursor.fetchall(), + [ + (1, '1-13-A-C'), + (2, '2-14-A-T'), + (3, 'Y-19-A-C'), + (4, 'M-12-C-G'), + (7, 'c'), + (10, 'b'), + ], + ) # ensure multiple calls are idempotent direct_insert_all_keys( @@ -440,11 +440,10 @@ def test_direct_insert_all_keys(self): TEST_RUN_ID, ), ) - with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f'SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', - ) - self.assertEqual(cursor.fetchone()[0], 6) + cursor.execute( + f'SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', + ) + self.assertEqual(cursor.fetchone()[0], 6) @patch.object( ClickhouseReferenceDataset, @@ -453,6 +452,7 @@ def test_direct_insert_all_keys(self): ) def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): self.maxDiff = None # TODO + cursor = connections['clickhouse_write'].cursor() # Tests individual components of atomic_insert_entries, validating state after each step. table_name_builder = TableNameBuilder( ReferenceGenome.GRCh38, @@ -482,28 +482,26 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): DatasetType.SNV_INDEL, ), ) - with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f""" - SELECT DISTINCT project_guid FROM {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/entries` - """, - ) - staged_projects = cursor.fetchall() + cursor.execute( + f""" + SELECT DISTINCT project_guid FROM {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/entries` + """, + ) + staged_projects = cursor.fetchall() self.assertCountEqual( [p[0] for p in staged_projects], ['project_a', 'project_b'], ) - with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f""" - SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) - FROM - {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/project_gt_stats` - FINAL - GROUP BY project_guid, key, sample_type - """, - ) - staged_project_gt_stats = cursor.fetchall() + cursor.execute( + f""" + SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) + FROM + {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/project_gt_stats` + FINAL + GROUP BY project_guid, key, sample_type + """, + ) + staged_project_gt_stats = cursor.fetchall() self.assertCountEqual( staged_project_gt_stats, [ @@ -530,17 +528,16 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): table_name_builder, ['family_a1', 'family_a5', 'family_a6'], ) - with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f""" - SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) - FROM - {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/project_gt_stats` - FINAL - GROUP BY project_guid, key, sample_type - """, - ) - staged_project_gt_stats = cursor.fetchall() + cursor.execute( + f""" + SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) + FROM + {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/project_gt_stats` + FINAL + GROUP BY project_guid, key, sample_type + """, + ) + staged_project_gt_stats = cursor.fetchall() self.assertCountEqual( staged_project_gt_stats, [ @@ -563,17 +560,16 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): table_name_builder, ['project_a', 'project_b', 'project_c'], ) - with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f""" - SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) - FROM - {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/project_gt_stats` - FINAL - GROUP BY project_guid, key, sample_type - """, - ) - staged_project_gt_stats = cursor.fetchall() + cursor.execute( + f""" + SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) + FROM + {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/project_gt_stats` + FINAL + GROUP BY project_guid, key, sample_type + """, + ) + staged_project_gt_stats = cursor.fetchall() self.assertCountEqual( staged_project_gt_stats, [ @@ -608,15 +604,14 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): ), ['project_a', 'project_d'], ) - with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f""" - SELECT COLUMNS('.*') EXCEPT(is_annotated_in_any_gene, is_gnomad_gt_5_percent) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` - """, - ) - new_entries = cursor.fetchall() + cursor.execute( + f""" + SELECT COLUMNS('.*') EXCEPT(is_annotated_in_any_gene, is_gnomad_gt_5_percent) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` + """, + ) + new_entries = cursor.fetchall() self.assertCountEqual( new_entries, [ @@ -802,15 +797,14 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): ), ], ) - with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f""" - SELECT * - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` - """, - ) - existing_gt_stats = cursor.fetchall() + cursor.execute( + f""" + SELECT * + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` + """, + ) + existing_gt_stats = cursor.fetchall() self.assertCountEqual( existing_gt_stats, [], @@ -822,40 +816,39 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): DatasetType.SNV_INDEL, ), ) - with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f""" - SELECT * - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` - """, - ) - new_gt_stats = cursor.fetchall() + cursor.execute( + f""" + SELECT * + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` + """, + ) + new_gt_stats = cursor.fetchall() self.assertCountEqual(new_gt_stats, []) reload_dictionaries( table_name_builder, ClickHouseDictionary.for_dataset_type(DatasetType.SNV_INDEL), ) - with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f""" - SELECT * - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` - """, - ) - self.assertEqual( - cursor.fetchall(), - [ - (10, 2, 0), - (1, 1, 1), - (2, 0, 2), - (3, 2, 0), - (4, 5, 0), - (5, 2, 0), - ], - ) + cursor.execute( + f""" + SELECT * + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` + """, + ) + new_gt_stats_post_reload = cursor.fetchall() + self.assertEqual( + new_gt_stats_post_reload, + [ + (10, 2, 0), + (1, 1, 1), + (2, 0, 2), + (3, 2, 0), + (4, 5, 0), + (5, 2, 0), + ], + ) @patch.object( ClickhouseReferenceDataset, @@ -863,6 +856,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): return_value=[ClickhouseReferenceDataset.CLINVAR], ) def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_type): + cursor = connections['clickhouse_write'].cursor() load_complete_run( ReferenceGenome.GRCh38, DatasetType.SNV_INDEL, @@ -870,110 +864,116 @@ def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_typ ['project_d'], ['family_d1', 'family_d2'], ) - with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f""" - SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` - WHERE project_guid = 'project_d' - GROUP BY project_guid, key, sample_type - """, - ) - self.assertCountEqual( - cursor.fetchall(), - [ - ('project_d', 10, 'WES', 0, 1), - ('project_d', 4, 'WES', 1, 0), - ('project_d', 3, 'WES', 0, 0), - ], - ) - cursor.execute( - f""" - SELECT * - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` - """, - ) - self.assertCountEqual( - cursor.fetchall(), - [ - (1, 1, 1, 0, 0, 0, 0), - (2, 0, 2, 0, 0, 1, 0), - (3, 2, 0, 0, 1, 0, 0), - (4, 6, 2, 0, 2, 1, 0), - (5, 2, 0, 0, 1, 0, 0), - (10, 4, 0, 0, 2, 0, 0), - ], - ) - cursor.execute( - f""" - SELECT * - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` - """, - ) - self.assertCountEqual( - cursor.fetchall(), - [ - (1, 1, 1, 0, 0, 0, 0), - (2, 0, 2, 0, 0, 1, 0), - (3, 2, 0, 0, 1, 0, 0), - (4, 6, 2, 0, 2, 1, 0), - (5, 2, 0, 0, 1, 0, 0), - (10, 4, 0, 0, 2, 0, 0), - ], - ) - cursor.execute( - f""" - SELECT * - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` - """, - ) - self.assertCountEqual( - cursor.fetchall(), - [ - (10, [], [], []), - (11, [], [], []), - (12, [], [], []), - (13, [], [], []), - ], - ) - cursor.execute( - f""" - SELECT * - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_disk` - """, - ) - self.assertCountEqual( - cursor.fetchall(), - [ - (10, [], [], []), - (11, [], [], []), - (12, [], [], []), - (13, [], [], []), - ], - ) - cursor.execute( - f""" - SELECT key, variantId - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details` - """, - ) - self.assertCountEqual( - cursor.fetchall(), - [ - (10, '1-3-A-C'), - (11, '2-4-A-T'), - (12, 'Y-9-A-C'), - (13, 'M-2-C-G'), - ], - ) + cursor.execute( + f""" + SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + WHERE project_guid = 'project_d' + GROUP BY project_guid, key, sample_type + """, + ) + project_gt_stats = cursor.fetchall() + self.assertCountEqual( + project_gt_stats, + [ + ('project_d', 10, 'WES', 0, 1), + ('project_d', 4, 'WES', 1, 0), + ('project_d', 3, 'WES', 0, 0), + ], + ) + cursor.execute( + f""" + SELECT * + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` + """, + ) + gt_stats = cursor.fetchall() + self.assertCountEqual( + gt_stats, + [ + (1, 1, 1, 0, 0, 0, 0), + (2, 0, 2, 0, 0, 1, 0), + (3, 2, 0, 0, 1, 0, 0), + (4, 6, 2, 0, 2, 1, 0), + (5, 2, 0, 0, 1, 0, 0), + (10, 4, 0, 0, 2, 0, 0), + ], + ) + cursor.execute( + f""" + SELECT * + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` + """, + ) + gt_stats_dict = cursor.fetchall() + self.assertCountEqual( + gt_stats_dict, + [ + (1, 1, 1, 0, 0, 0, 0), + (2, 0, 2, 0, 0, 1, 0), + (3, 2, 0, 0, 1, 0, 0), + (4, 6, 2, 0, 2, 1, 0), + (5, 2, 0, 0, 1, 0, 0), + (10, 4, 0, 0, 2, 0, 0), + ], + ) + cursor.execute( + f""" + SELECT * + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` + """, + ) + variants_memory = cursor.fetchall() + self.assertCountEqual( + variants_memory, + [ + (10, [], [], []), + (11, [], [], []), + (12, [], [], []), + (13, [], [], []), + ], + ) + cursor.execute( + f""" + SELECT * + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_disk` + """, + ) + variants_disk = cursor.fetchall() + self.assertCountEqual( + variants_disk, + [ + (10, [], [], []), + (11, [], [], []), + (12, [], [], []), + (13, [], [], []), + ], + ) + cursor.execute( + f""" + SELECT key, variantId + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details` + """, + ) + variants_details = cursor.fetchall() + self.assertCountEqual( + variants_details, + [ + (10, '1-3-A-C'), + (11, '2-4-A-T'), + (12, 'Y-9-A-C'), + (13, 'M-2-C-G'), + ], + ) def test_load_complete_gcnv(self): + cursor = connections['clickhouse_write'].cursor() load_complete_run( ReferenceGenome.GRCh38, DatasetType.GCNV, @@ -981,60 +981,59 @@ def test_load_complete_gcnv(self): ['project_d'], ['family_d1', 'family_d2'], ) - with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f""" - SELECT COUNT(*) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/variants_memory` - """, - ) - self.assertEqual(cursor.fetchone()[0], 4) - cursor.execute( - f""" - SELECT COUNT(*) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/variants_disk` - """, - ) - self.assertEqual(cursor.fetchone()[0], 4) - cursor.execute( - f""" - SELECT COUNT(*) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/key_lookup` - """, - ) - self.assertEqual(cursor.fetchone()[0], 4) - cursor.execute( - f""" - SELECT COUNT(*) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/entries` - """, - ) - self.assertEqual(cursor.fetchone()[0], 3) + cursor.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/variants_memory` + """, + ) + self.assertEqual(cursor.fetchone()[0], 4) + cursor.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/variants_disk` + """, + ) + self.assertEqual(cursor.fetchone()[0], 4) + cursor.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/key_lookup` + """, + ) + self.assertEqual(cursor.fetchone()[0], 4) + cursor.execute( + f""" + SELECT COUNT(*) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/entries` + """, + ) + self.assertEqual(cursor.fetchone()[0], 3) def test_delete_families(self): + cursor = connections['clickhouse_write'].cursor() table_name_builder = TableNameBuilder( ReferenceGenome.GRCh38, DatasetType.SNV_INDEL, TEST_RUN_ID, ) - with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f""" - SELECT project_guid, sum(het_samples), sum(hom_samples) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` - FINAL - GROUP BY project_guid - """, - ) - self.assertCountEqual( - cursor.fetchall(), - [('project_a', 2, 3), ('project_c', 0, 2), ('project_b', 1, 2)], - ) + cursor.execute( + f""" + SELECT project_guid, sum(het_samples), sum(hom_samples) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + FINAL + GROUP BY project_guid + """, + ) + self.assertCountEqual( + cursor.fetchall(), + [('project_a', 2, 3), ('project_c', 0, 2), ('project_b', 1, 2)], + ) refresh_materialized_views( table_name_builder, @@ -1043,15 +1042,14 @@ def test_delete_families(self): ), staging=False, ) - with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f""" - SELECT sum(ac_wes) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` - """, - ) - self.assertCountEqual(cursor.fetchall(), [(12,)]) + cursor.execute( + f""" + SELECT sum(ac_wes) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` + """, + ) + self.assertCountEqual(cursor.fetchall(), [(12,)]) delete_family_guids( ReferenceGenome.GRCh38, @@ -1060,38 +1058,38 @@ def test_delete_families(self): 'project_a', ['family_a1', 'family_a2'], ) - with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f""" - SELECT project_guid, sum(het_samples), sum(hom_samples) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` - FINAL - GROUP BY project_guid - """, - ) - self.assertCountEqual( - cursor.fetchall(), - [('project_a', 1, 2), ('project_c', 0, 2), ('project_b', 1, 2)], - ) - cursor.execute( - f""" - SELECT sum(ac_wes) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` - """, - ) - self.assertCountEqual(cursor.fetchall(), [(10,)]) - cursor.execute( - f""" - SELECT sum(ac_wes) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` - """, - ) - self.assertCountEqual(cursor.fetchall(), [(10,)]) + cursor.execute( + f""" + SELECT project_guid, sum(het_samples), sum(hom_samples) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + FINAL + GROUP BY project_guid + """, + ) + self.assertCountEqual( + cursor.fetchall(), + [('project_a', 1, 2), ('project_c', 0, 2), ('project_b', 1, 2)], + ) + cursor.execute( + f""" + SELECT sum(ac_wes) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` + """, + ) + self.assertCountEqual(cursor.fetchall(), [(10,)]) + cursor.execute( + f""" + SELECT sum(ac_wes) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` + """, + ) + self.assertCountEqual(cursor.fetchall(), [(10,)]) def test_rebuild_gt_stats(self): + cursor = connections['clickhouse_write'].cursor() table_name_builder = TableNameBuilder( ReferenceGenome.GRCh38, DatasetType.SNV_INDEL, @@ -1106,20 +1104,19 @@ def test_rebuild_gt_stats(self): # partition_id) defaults to 0. {'project_guid': 'project_a', 'partition_id': 0}, ) - with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f""" - SELECT project_guid, sum(het_samples), sum(hom_samples) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` - WHERE project_guid IN ('project_a', 'project_b') - GROUP BY project_guid - """, - ) - self.assertCountEqual( - cursor.fetchall(), - [('project_a', 2, 3), ('project_b', 1, 2)], - ) + cursor.execute( + f""" + SELECT project_guid, sum(het_samples), sum(hom_samples) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + WHERE project_guid IN ('project_a', 'project_b') + GROUP BY project_guid + """, + ) + self.assertCountEqual( + cursor.fetchall(), + [('project_a', 2, 3), ('project_b', 1, 2)], + ) refresh_materialized_views( table_name_builder, @@ -1128,17 +1125,16 @@ def test_rebuild_gt_stats(self): ), staging=False, ) - with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f""" - SELECT sum(ac_wes), sum(ac_wgs) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` - """, - ) - # gt_stats has no project dimension (keyed globally by `key`), so project_c's rows - # (sharing key values with project_a/b in the fixture) also contribute here. - self.assertCountEqual(cursor.fetchall(), [(12, 5)]) + cursor.execute( + f""" + SELECT sum(ac_wes), sum(ac_wgs) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` + """, + ) + # gt_stats has no project dimension (keyed globally by `key`), so project_c's rows + # (sharing key values with project_a/b in the fixture) also contribute here. + self.assertCountEqual(cursor.fetchall(), [(12, 5)]) rebuild_gt_stats( ReferenceGenome.GRCh38, @@ -1146,28 +1142,27 @@ def test_rebuild_gt_stats(self): TEST_RUN_ID, ['project_a', 'project_b'], ) - with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f""" - SELECT project_guid, sum(het_samples), sum(hom_samples) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` - WHERE project_guid IN ('project_a', 'project_b') - GROUP BY project_guid - """, - ) - self.assertCountEqual( - cursor.fetchall(), - [('project_b', 1, 2)], - ) - cursor.execute( - f""" - SELECT sum(ac_wes), sum(ac_wgs) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` - """, - ) - self.assertCountEqual(cursor.fetchall(), [(9, 0)]) + cursor.execute( + f""" + SELECT project_guid, sum(het_samples), sum(hom_samples) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + WHERE project_guid IN ('project_a', 'project_b') + GROUP BY project_guid + """, + ) + self.assertCountEqual( + cursor.fetchall(), + [('project_b', 1, 2)], + ) + cursor.execute( + f""" + SELECT sum(ac_wes), sum(ac_wgs) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` + """, + ) + self.assertCountEqual(cursor.fetchall(), [(9, 0)]) @patch.object( ClickhouseReferenceDataset, @@ -1175,6 +1170,7 @@ def test_rebuild_gt_stats(self): return_value=[ClickhouseReferenceDataset.CLINVAR], ) def test_repartitioned_entries_table(self, mock_for_reference_genome_dataset_type): + cursor = connections['clickhouse_write'].cursor() load_complete_run( ReferenceGenome.GRCh38, DatasetType.SNV_INDEL, @@ -1182,21 +1178,20 @@ def test_repartitioned_entries_table(self, mock_for_reference_genome_dataset_typ ['project_d'], ['family_d1', 'family_d2', 'family_d3'], ) - with connections['clickhouse_write'].cursor() as cursor: - cursor.execute( - f""" - SELECT project_guid, sum(het_samples), sum(hom_samples) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` - GROUP BY project_guid - """, - ) - self.assertCountEqual( - cursor.fetchall(), - [ - ('project_a', 2, 3), - ('project_b', 1, 2), - ('project_c', 0, 2), - ('project_d', 1, 1), - ], - ) + cursor.execute( + f""" + SELECT project_guid, sum(het_samples), sum(hom_samples) + FROM + {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` + GROUP BY project_guid + """, + ) + self.assertCountEqual( + cursor.fetchall(), + [ + ('project_a', 2, 3), + ('project_b', 1, 2), + ('project_c', 0, 2), + ('project_d', 1, 1), + ], + ) From 45cef520bc2210cd7aead4f3c00c66564b5521ef Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 12:31:01 -0400 Subject: [PATCH 236/369] test cleanup --- loading_pipeline/lib/misc/clickhouse_test.py | 22 ++++++++++++-------- 1 file changed, 13 insertions(+), 9 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index 9a4e8ecbf1..4661646101 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -242,7 +242,12 @@ def write_test_parquet(df: pd.DataFrame, parquet_path: str, schema=None): 'liftedOverPos': [13, None, None, None], 'rsid': ['rs123', None, None, None], 'CAID': ['CA123456', None, None, None], - 'sortedMotifFeatureConsequences': [[_FULL_MOTIF_CONSEQUENCE], [], [], []], + 'sortedMotifFeatureConsequences': [ + [_FULL_MOTIF_CONSEQUENCE], + [], + [], + [], + ], 'sortedRegulatoryFeatureConsequences': [ [_FULL_REGULATORY_CONSEQUENCE], [], @@ -419,8 +424,9 @@ def test_direct_insert_all_keys(self): cursor.execute( f'SELECT key, variantId FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', ) + ret = cursor.fetchall() self.assertEqual( - cursor.fetchall(), + ret, [ (1, '1-13-A-C'), (2, '2-14-A-T'), @@ -443,7 +449,8 @@ def test_direct_insert_all_keys(self): cursor.execute( f'SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', ) - self.assertEqual(cursor.fetchone()[0], 6) + ret = cursor.fetchone() + self.assertEqual(ret[0], 6) @patch.object( ClickhouseReferenceDataset, @@ -451,9 +458,9 @@ def test_direct_insert_all_keys(self): return_value=[ClickhouseReferenceDataset.CLINVAR], ) def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): - self.maxDiff = None # TODO - cursor = connections['clickhouse_write'].cursor() + self.maxDiff = None # TODO # Tests individual components of atomic_insert_entries, validating state after each step. + cursor = connections['clickhouse_write'].cursor() table_name_builder = TableNameBuilder( ReferenceGenome.GRCh38, DatasetType.SNV_INDEL, @@ -554,7 +561,6 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): ('project_c', 5, 'WES', 0, 1), ], ) - insert_new_entries(table_name_builder) optimize_entries( table_name_builder, @@ -589,7 +595,6 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): ('project_d', 4, 'WES', 1, 0), ], ) - refresh_materialized_views( table_name_builder, ClickHouseMaterializedView.for_dataset_type_atomic_entries_update_refreshable( @@ -679,7 +684,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): 1, 'project_a', 'family_a2', - 'WES', + 'WGS', 123456789, [], [('sample_a2', 'HET')], @@ -809,7 +814,6 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): existing_gt_stats, [], ) - exchange_tables( table_name_builder, ClickHouseTable.for_dataset_type_atomic_entries_update_unpartitioned( From 73b02fb466553afae9e6d4c21ff00baf0662ec97 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 12:43:12 -0400 Subject: [PATCH 237/369] fix tests --- loading_pipeline/lib/misc/clickhouse_test.py | 111 +++++++++++-------- 1 file changed, 66 insertions(+), 45 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index 4661646101..cd23603e09 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -627,7 +627,8 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): 'WES', 123456789, [], - [('sample_b4', 'REF')], + [], + [('sample_b4', 'REF', None, None, None)], 1, 1, 0, @@ -639,7 +640,8 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): 'WES', 123456789, [], - [('sample_b5', 'HET')], + [], + [('sample_b5', 'HET', None, None, None)], 1, 1, 0, @@ -651,7 +653,8 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): 'WES', 123456789, [], - [('sample_b5', 'REF')], + [], + [('sample_b5', 'REF', None, None, None)], 1, 1, 0, @@ -663,7 +666,8 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): 'WES', 133456789, [], - [('sample_b6', 'HOM')], + [], + [('sample_b6', 'HOM', None, None, None)], 1, 1, 0, @@ -675,7 +679,8 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): 'WES', 133456789, [], - [('sample_b6', 'HOM')], + [], + [('sample_b6', 'HOM', None, None, None)], 1, 1, 0, @@ -687,7 +692,8 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): 'WGS', 123456789, [], - [('sample_a2', 'HET')], + [], + [('sample_a2', 'HET', None, None, None)], 1, 1, 0, @@ -699,7 +705,8 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): 'WGS', 133456789, [], - [('sample_a3', 'HOM')], + [], + [('sample_a3', 'HOM', None, None, None)], 1, 1, 0, @@ -711,7 +718,8 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): 'WES', 133456789, [], - [('sample_a4', 'REF')], + [], + [('sample_a4', 'REF', None, None, None)], 1, 1, 0, @@ -723,7 +731,8 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): 'WES', 123456789, [], - [('sample_d1', 'REF'), ('sample_d11', 'HOM')], + [], + [('sample_d1', 'REF', None, None, None), ('sample_d11', 'HOM', None, None, None)], 1, 1, 0, @@ -735,7 +744,8 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): 'WES', 123456789, [123, 12], - [('sample_d2', 'REF')], + [], + [('sample_d2', 'REF', None, None, None)], 1, 1, 0, @@ -747,7 +757,8 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): 'WES', 123456789, [1], - [('sample_d3', 'HET')], + [], + [('sample_d3', 'HET', None, None, None)], 1, 1, 0, @@ -759,7 +770,8 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): 'WES', 123456789, [1], - [('sample_c7', 'REF')], + [], + [('sample_c7', 'REF', None, None, None)], 1, 1, 0, @@ -771,7 +783,8 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): 'WES', 123456789, [1], - [('sample_c8', 'REF')], + [], + [('sample_c8', 'REF', None, None, None)], 1, 1, 0, @@ -783,7 +796,8 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): 'WES', 133456789, [1], - [('sample_c9', 'HOM')], + [], + [('sample_c9', 'HOM', None, None, None)], 1, 1, 0, @@ -795,7 +809,8 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): 'WES', 133456789, [1], - [('sample_c9', 'HOM')], + [], + [('sample_c9', 'HOM', None, None, None)], 1, 1, 0, @@ -829,7 +844,6 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): ) new_gt_stats = cursor.fetchall() self.assertCountEqual(new_gt_stats, []) - reload_dictionaries( table_name_builder, ClickHouseDictionary.for_dataset_type(DatasetType.SNV_INDEL), @@ -860,7 +874,6 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): return_value=[ClickhouseReferenceDataset.CLINVAR], ) def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_type): - cursor = connections['clickhouse_write'].cursor() load_complete_run( ReferenceGenome.GRCh38, DatasetType.SNV_INDEL, @@ -868,6 +881,7 @@ def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_typ ['project_d'], ['family_d1', 'family_d2'], ) + cursor = connections['clickhouse_write'].cursor() cursor.execute( f""" SELECT project_guid, key, sample_type, sum(het_samples), sum(hom_samples) @@ -969,15 +983,16 @@ def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_typ self.assertCountEqual( variants_details, [ - (10, '1-3-A-C'), - (11, '2-4-A-T'), - (12, 'Y-9-A-C'), - (13, 'M-2-C-G'), + (1, '1-13-A-C'), + (2, '2-14-A-T'), + (3, 'Y-19-A-C'), + (4, 'M-12-C-G'), + (7, 'c'), + (10, 'b'), ], ) def test_load_complete_gcnv(self): - cursor = connections['clickhouse_write'].cursor() load_complete_run( ReferenceGenome.GRCh38, DatasetType.GCNV, @@ -985,6 +1000,7 @@ def test_load_complete_gcnv(self): ['project_d'], ['family_d1', 'family_d2'], ) + cursor = connections['clickhouse_write'].cursor() cursor.execute( f""" SELECT COUNT(*) @@ -992,7 +1008,8 @@ def test_load_complete_gcnv(self): {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/variants_memory` """, ) - self.assertEqual(cursor.fetchone()[0], 4) + variants_disk_count = cursor.fetchone()[0] + self.assertEqual(variants_disk_count, 4) cursor.execute( f""" SELECT COUNT(*) @@ -1000,7 +1017,8 @@ def test_load_complete_gcnv(self): {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/variants_disk` """, ) - self.assertEqual(cursor.fetchone()[0], 4) + variants_disk_count = cursor.fetchone()[0] + self.assertEqual(variants_disk_count, 4) cursor.execute( f""" SELECT COUNT(*) @@ -1008,7 +1026,8 @@ def test_load_complete_gcnv(self): {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/key_lookup` """, ) - self.assertEqual(cursor.fetchone()[0], 4) + key_lookup_count = cursor.fetchone()[0] + self.assertEqual(key_lookup_count, 4) cursor.execute( f""" SELECT COUNT(*) @@ -1016,15 +1035,16 @@ def test_load_complete_gcnv(self): {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/entries` """, ) - self.assertEqual(cursor.fetchone()[0], 3) + entries_count = cursor.fetchone()[0] + self.assertEqual(entries_count, 3) def test_delete_families(self): - cursor = connections['clickhouse_write'].cursor() table_name_builder = TableNameBuilder( ReferenceGenome.GRCh38, DatasetType.SNV_INDEL, TEST_RUN_ID, ) + cursor = connections['clickhouse_write'].cursor() cursor.execute( f""" SELECT project_guid, sum(het_samples), sum(hom_samples) @@ -1034,11 +1054,11 @@ def test_delete_families(self): GROUP BY project_guid """, ) + project_gt_stats = cursor.fetchall() self.assertCountEqual( - cursor.fetchall(), + project_gt_stats, [('project_a', 2, 3), ('project_c', 0, 2), ('project_b', 1, 2)], ) - refresh_materialized_views( table_name_builder, ClickHouseMaterializedView.for_dataset_type_atomic_entries_update_refreshable( @@ -1053,8 +1073,8 @@ def test_delete_families(self): {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` """, ) - self.assertCountEqual(cursor.fetchall(), [(12,)]) - + gt_stats = cursor.fetchall() + self.assertCountEqual(gt_stats, [(12,)]) delete_family_guids( ReferenceGenome.GRCh38, DatasetType.SNV_INDEL, @@ -1071,8 +1091,9 @@ def test_delete_families(self): GROUP BY project_guid """, ) + project_gt_stats = cursor.fetchall() self.assertCountEqual( - cursor.fetchall(), + project_gt_stats, [('project_a', 1, 2), ('project_c', 0, 2), ('project_b', 1, 2)], ) cursor.execute( @@ -1082,7 +1103,8 @@ def test_delete_families(self): {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` """, ) - self.assertCountEqual(cursor.fetchall(), [(10,)]) + gt_stats = cursor.fetchall() + self.assertCountEqual(gt_stats, [(10,)]) cursor.execute( f""" SELECT sum(ac_wes) @@ -1090,22 +1112,21 @@ def test_delete_families(self): {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` """, ) - self.assertCountEqual(cursor.fetchall(), [(10,)]) + gt_stats_dict = cursor.fetchall() + self.assertCountEqual(gt_stats_dict, [(10,)]) def test_rebuild_gt_stats(self): - cursor = connections['clickhouse_write'].cursor() table_name_builder = TableNameBuilder( ReferenceGenome.GRCh38, DatasetType.SNV_INDEL, TEST_RUN_ID, ) + cursor = connections['clickhouse_write'].cursor() logged_query( # DROP the partition from the non-staging entries to as a non-mv-impacting change. f""" ALTER TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` DROP PARTITION (%(project_guid)s, %(partition_id)s) """, - # project_partitions_dict has no row for project_a, so n_partitions (and thus - # partition_id) defaults to 0. {'project_guid': 'project_a', 'partition_id': 0}, ) cursor.execute( @@ -1117,11 +1138,11 @@ def test_rebuild_gt_stats(self): GROUP BY project_guid """, ) + project_gt_stats = cursor.fetchall() self.assertCountEqual( - cursor.fetchall(), + project_gt_stats, [('project_a', 2, 3), ('project_b', 1, 2)], ) - refresh_materialized_views( table_name_builder, ClickHouseMaterializedView.for_dataset_type_atomic_entries_update_refreshable( @@ -1136,10 +1157,8 @@ def test_rebuild_gt_stats(self): {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` """, ) - # gt_stats has no project dimension (keyed globally by `key`), so project_c's rows - # (sharing key values with project_a/b in the fixture) also contribute here. - self.assertCountEqual(cursor.fetchall(), [(12, 5)]) - + gt_stats = cursor.fetchall() + self.assertCountEqual(gt_stats, [(12, 5)]) rebuild_gt_stats( ReferenceGenome.GRCh38, DatasetType.SNV_INDEL, @@ -1155,8 +1174,9 @@ def test_rebuild_gt_stats(self): GROUP BY project_guid """, ) + project_gt_stats = cursor.fetchall() self.assertCountEqual( - cursor.fetchall(), + project_gt_stats, [('project_b', 1, 2)], ) cursor.execute( @@ -1166,7 +1186,8 @@ def test_rebuild_gt_stats(self): {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` """, ) - self.assertCountEqual(cursor.fetchall(), [(9, 0)]) + gt_stats = cursor.fetchall() + self.assertCountEqual(gt_stats, [(9, 0)]) @patch.object( ClickhouseReferenceDataset, From 93778a5f13dbb3b60170e1efae05b8c9dbc3bcbd Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 12:45:10 -0400 Subject: [PATCH 238/369] ruff --- loading_pipeline/lib/misc/clickhouse_test.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index cd23603e09..10e427d50c 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -732,7 +732,10 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): 123456789, [], [], - [('sample_d1', 'REF', None, None, None), ('sample_d11', 'HOM', None, None, None)], + [ + ('sample_d1', 'REF', None, None, None), + ('sample_d11', 'HOM', None, None, None), + ], 1, 1, 0, @@ -1211,8 +1214,9 @@ def test_repartitioned_entries_table(self, mock_for_reference_genome_dataset_typ GROUP BY project_guid """, ) + project_gt_stats = cursor.fetchall() self.assertCountEqual( - cursor.fetchall(), + project_gt_stats, [ ('project_a', 2, 3), ('project_b', 1, 2), From 56aa3d5104303559d595c055aea88d3af49e5c53 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 12:50:48 -0400 Subject: [PATCH 239/369] remove redundant test --- loading_pipeline/lib/misc/clickhouse_test.py | 36 ++------------------ 1 file changed, 2 insertions(+), 34 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index 10e427d50c..b08853f5b8 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -459,7 +459,8 @@ def test_direct_insert_all_keys(self): ) def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): self.maxDiff = None # TODO - # Tests individual components of atomic_insert_entries, validating state after each step. + # Tests individual components of the atomic_insert_entries + # to validate the state after each step. cursor = connections['clickhouse_write'].cursor() table_name_builder = TableNameBuilder( ReferenceGenome.GRCh38, @@ -1191,36 +1192,3 @@ def test_rebuild_gt_stats(self): ) gt_stats = cursor.fetchall() self.assertCountEqual(gt_stats, [(9, 0)]) - - @patch.object( - ClickhouseReferenceDataset, - 'for_reference_genome_dataset_type', - return_value=[ClickhouseReferenceDataset.CLINVAR], - ) - def test_repartitioned_entries_table(self, mock_for_reference_genome_dataset_type): - cursor = connections['clickhouse_write'].cursor() - load_complete_run( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ['project_d'], - ['family_d1', 'family_d2', 'family_d3'], - ) - cursor.execute( - f""" - SELECT project_guid, sum(het_samples), sum(hom_samples) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` - GROUP BY project_guid - """, - ) - project_gt_stats = cursor.fetchall() - self.assertCountEqual( - project_gt_stats, - [ - ('project_a', 2, 3), - ('project_b', 1, 2), - ('project_c', 0, 2), - ('project_d', 1, 1), - ], - ) From aae2cabfed8de1c748351d5d66508ced27443df5 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 12:52:38 -0400 Subject: [PATCH 240/369] remove unneeded schema --- loading_pipeline/lib/misc/clickhouse_test.py | 89 -------------------- 1 file changed, 89 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index b08853f5b8..d0e1e034ac 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -47,94 +47,6 @@ TEST_RUN_ID = 'manual__2025-05-07T17-20-59.702114+00-00' -_FIVEUTR_ANNOTATION_TYPE = pa.struct( - [ - ('AltStop', pa.string()), - ('AltStopDistanceToCDS', pa.int32()), - ('CapDistanceToStart', pa.int32()), - ('DistanceToCDS', pa.int32()), - ('DistanceToStop', pa.int32()), - ('Evidence', pa.bool_()), - ('FrameWithCDS', pa.string()), - ('KozakContext', pa.string()), - ('KozakStrength', pa.string()), - ('StartDistanceToCDS', pa.int32()), - ('alt_type', pa.string()), - ('alt_type_length', pa.int32()), - ('newSTOPDistanceToCDS', pa.int32()), - ('ref_StartDistanceToCDS', pa.int32()), - ('ref_type', pa.string()), - ('ref_type_length', pa.int32()), - ('type', pa.string()), - ], -) -_UTRANNOTATOR_TYPE = pa.struct( - [ - ('existingInframeOorfs', pa.int32()), - ('existingOutofframeOorfs', pa.int32()), - ('existingUorfs', pa.int32()), - ('fiveutrAnnotation', _FIVEUTR_ANNOTATION_TYPE), - ('fiveutrConsequence', pa.string()), - ], -) -_TRANSCRIPT_TYPE = pa.struct( - [ - ('alphamissense', pa.struct([('pathogenicity', pa.float64())])), - ('aminoAcids', pa.string()), - ('biotype', pa.string()), - ('canonical', pa.int32()), - ('codons', pa.string()), - ('consequenceTerms', pa.list_(pa.string())), - ('exon', pa.struct([('index', pa.int32()), ('total', pa.int32())])), - ('geneId', pa.string()), - ('hgvsc', pa.string()), - ('hgvsp', pa.string()), - ('intron', pa.struct([('index', pa.int32()), ('total', pa.int32())])), - ( - 'loftee', - pa.struct( - [('isLofNagnag', pa.bool_()), ('lofFilters', pa.list_(pa.string()))], - ), - ), - ('majorConsequence', pa.string()), - ('manePlusClinical', pa.string()), - ('maneSelect', pa.string()), - ('refseqTranscriptId', pa.string()), - ( - 'spliceregion', - pa.struct([('extended_intronic_splice_region_variant', pa.bool_())]), - ), - ('transcriptId', pa.string()), - ('transcriptRank', pa.int32()), - ('utrannotator', _UTRANNOTATOR_TYPE), - ], -) -_MOTIF_CONSEQUENCE_TYPE = pa.struct( - [ - ('consequenceTerms', pa.list_(pa.string())), - ('motifFeatureId', pa.string()), - ], -) -_REGULATORY_CONSEQUENCE_TYPE = pa.struct( - [ - ('biotype', pa.string()), - ('consequenceTerms', pa.list_(pa.string())), - ('regulatoryFeatureId', pa.string()), - ], -) -VARIANT_DETAILS_SCHEMA = pa.schema( - [ - ('key', pa.int64()), - ('variantId', pa.string()), - ('liftedOverChrom', pa.string()), - ('liftedOverPos', pa.int64()), - ('rsid', pa.string()), - ('CAID', pa.string()), - ('transcripts', pa.list_(_TRANSCRIPT_TYPE)), - ('sortedMotifFeatureConsequences', pa.list_(_MOTIF_CONSEQUENCE_TYPE)), - ('sortedRegulatoryFeatureConsequences', pa.list_(_REGULATORY_CONSEQUENCE_TYPE)), - ], -) _FULL_TRANSCRIPT = { 'alphamissense': {'pathogenicity': 0.5}, 'aminoAcids': 'S/L', @@ -263,7 +175,6 @@ def write_test_parquet(df: pd.DataFrame, parquet_path: str, schema=None): DatasetType.SNV_INDEL, TEST_RUN_ID, ), - VARIANT_DETAILS_SCHEMA, # TODO needed? ) # New Variants parquet. From f432f4b412f3c140b277e76faeeaee3b38f873da Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 12:57:08 -0400 Subject: [PATCH 241/369] fix test --- loading_pipeline/lib/misc/clickhouse_test.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index d0e1e034ac..bfffd69ae2 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -116,6 +116,9 @@ def setUpClass(cls): f'INSERT INTO {Env.CLICKHOUSE_DATABASE}.`seqrdb_gene_ids_src` VALUES', [('GENE1', 123), ('GENE2', 12), ('GENE3', 1)], ) + cursor.execute( + f'SYSTEM RELOAD DICTIONARY {Env.CLICKHOUSE_DATABASE}.`seqrdb_gene_ids`', + ) def setUp(self): super().setUp() From c5cb58cf4c83b7562342640940376d2b101f7229 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 13:01:26 -0400 Subject: [PATCH 242/369] Revert "remove unneeded schema" This reverts commit db9b7ec05df859ca70c1984018518ded4eb14435. --- loading_pipeline/lib/misc/clickhouse_test.py | 89 ++++++++++++++++++++ 1 file changed, 89 insertions(+) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index bfffd69ae2..07593d248a 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -47,6 +47,94 @@ TEST_RUN_ID = 'manual__2025-05-07T17-20-59.702114+00-00' +_FIVEUTR_ANNOTATION_TYPE = pa.struct( + [ + ('AltStop', pa.string()), + ('AltStopDistanceToCDS', pa.int32()), + ('CapDistanceToStart', pa.int32()), + ('DistanceToCDS', pa.int32()), + ('DistanceToStop', pa.int32()), + ('Evidence', pa.bool_()), + ('FrameWithCDS', pa.string()), + ('KozakContext', pa.string()), + ('KozakStrength', pa.string()), + ('StartDistanceToCDS', pa.int32()), + ('alt_type', pa.string()), + ('alt_type_length', pa.int32()), + ('newSTOPDistanceToCDS', pa.int32()), + ('ref_StartDistanceToCDS', pa.int32()), + ('ref_type', pa.string()), + ('ref_type_length', pa.int32()), + ('type', pa.string()), + ], +) +_UTRANNOTATOR_TYPE = pa.struct( + [ + ('existingInframeOorfs', pa.int32()), + ('existingOutofframeOorfs', pa.int32()), + ('existingUorfs', pa.int32()), + ('fiveutrAnnotation', _FIVEUTR_ANNOTATION_TYPE), + ('fiveutrConsequence', pa.string()), + ], +) +_TRANSCRIPT_TYPE = pa.struct( + [ + ('alphamissense', pa.struct([('pathogenicity', pa.float64())])), + ('aminoAcids', pa.string()), + ('biotype', pa.string()), + ('canonical', pa.int32()), + ('codons', pa.string()), + ('consequenceTerms', pa.list_(pa.string())), + ('exon', pa.struct([('index', pa.int32()), ('total', pa.int32())])), + ('geneId', pa.string()), + ('hgvsc', pa.string()), + ('hgvsp', pa.string()), + ('intron', pa.struct([('index', pa.int32()), ('total', pa.int32())])), + ( + 'loftee', + pa.struct( + [('isLofNagnag', pa.bool_()), ('lofFilters', pa.list_(pa.string()))], + ), + ), + ('majorConsequence', pa.string()), + ('manePlusClinical', pa.string()), + ('maneSelect', pa.string()), + ('refseqTranscriptId', pa.string()), + ( + 'spliceregion', + pa.struct([('extended_intronic_splice_region_variant', pa.bool_())]), + ), + ('transcriptId', pa.string()), + ('transcriptRank', pa.int32()), + ('utrannotator', _UTRANNOTATOR_TYPE), + ], +) +_MOTIF_CONSEQUENCE_TYPE = pa.struct( + [ + ('consequenceTerms', pa.list_(pa.string())), + ('motifFeatureId', pa.string()), + ], +) +_REGULATORY_CONSEQUENCE_TYPE = pa.struct( + [ + ('biotype', pa.string()), + ('consequenceTerms', pa.list_(pa.string())), + ('regulatoryFeatureId', pa.string()), + ], +) +VARIANT_DETAILS_SCHEMA = pa.schema( + [ + ('key', pa.int64()), + ('variantId', pa.string()), + ('liftedOverChrom', pa.string()), + ('liftedOverPos', pa.int64()), + ('rsid', pa.string()), + ('CAID', pa.string()), + ('transcripts', pa.list_(_TRANSCRIPT_TYPE)), + ('sortedMotifFeatureConsequences', pa.list_(_MOTIF_CONSEQUENCE_TYPE)), + ('sortedRegulatoryFeatureConsequences', pa.list_(_REGULATORY_CONSEQUENCE_TYPE)), + ], +) _FULL_TRANSCRIPT = { 'alphamissense': {'pathogenicity': 0.5}, 'aminoAcids': 'S/L', @@ -178,6 +266,7 @@ def write_test_parquet(df: pd.DataFrame, parquet_path: str, schema=None): DatasetType.SNV_INDEL, TEST_RUN_ID, ), + VARIANT_DETAILS_SCHEMA, # TODO needed? ) # New Variants parquet. From 3c43437e410eb539215162273ff6a17f7787bb42 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 13:08:39 -0400 Subject: [PATCH 243/369] fix test --- loading_pipeline/lib/misc/clickhouse_test.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index 07593d248a..9b5ba7635d 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -266,7 +266,7 @@ def write_test_parquet(df: pd.DataFrame, parquet_path: str, schema=None): DatasetType.SNV_INDEL, TEST_RUN_ID, ), - VARIANT_DETAILS_SCHEMA, # TODO needed? + VARIANT_DETAILS_SCHEMA, ) # New Variants parquet. @@ -771,7 +771,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): 0, ), ( - 10, + 0, 'project_c', 'family_c1', 'WES', From 90c780d2884f4841442b82e52878292bcd10afa2 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 13:20:58 -0400 Subject: [PATCH 244/369] fix test --- loading_pipeline/lib/misc/clickhouse_test.py | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index 9b5ba7635d..012f8497f3 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -850,7 +850,13 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): """, ) new_gt_stats = cursor.fetchall() - self.assertCountEqual(new_gt_stats, []) + self.assertCountEqual(new_gt_stats, [ + (1, 1, 0, 0, 0, 0, 0), + (2, 0, 2, 0, 0, 1, 0), + (3, 2, 0, 0, 1, 0, 0), + (4, 5, 2, 0, 2, 1, 0), + (5, 2, 0, 0, 1, 0, 0), + ]) reload_dictionaries( table_name_builder, ClickHouseDictionary.for_dataset_type(DatasetType.SNV_INDEL), From 03a53404dcae1147a19f346d2b97c43523f44989 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 13:25:48 -0400 Subject: [PATCH 245/369] ruff --- loading_pipeline/lib/misc/clickhouse_test.py | 17 ++++++++++------- 1 file changed, 10 insertions(+), 7 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index 012f8497f3..c73e4e3117 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -850,13 +850,16 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): """, ) new_gt_stats = cursor.fetchall() - self.assertCountEqual(new_gt_stats, [ - (1, 1, 0, 0, 0, 0, 0), - (2, 0, 2, 0, 0, 1, 0), - (3, 2, 0, 0, 1, 0, 0), - (4, 5, 2, 0, 2, 1, 0), - (5, 2, 0, 0, 1, 0, 0), - ]) + self.assertCountEqual( + new_gt_stats, + [ + (1, 1, 0, 0, 0, 0, 0), + (2, 0, 2, 0, 0, 1, 0), + (3, 2, 0, 0, 1, 0, 0), + (4, 5, 2, 0, 2, 1, 0), + (5, 2, 0, 0, 1, 0, 0), + ], + ) reload_dictionaries( table_name_builder, ClickHouseDictionary.for_dataset_type(DatasetType.SNV_INDEL), From c321e7c2799f2d4acfb6cbdfd75ec2416cd60210 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 13:31:16 -0400 Subject: [PATCH 246/369] fix test --- loading_pipeline/lib/misc/clickhouse_test.py | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index c73e4e3117..eb5dbcacaf 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -834,7 +834,13 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): existing_gt_stats = cursor.fetchall() self.assertCountEqual( existing_gt_stats, - [], + [ + (1, 1, 0, 0, 0, 0, 0), + (2, 0, 2, 0, 0, 1, 0), + (3, 2, 0, 0, 1, 0, 0), + (4, 5, 2, 0, 2, 1, 0), + (5, 2, 0, 0, 1, 0, 0), + ], ) exchange_tables( table_name_builder, From dce7fbfabc27bb83bfdeed0c8f456e48a6c3ca8e Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 13:41:13 -0400 Subject: [PATCH 247/369] fix test --- loading_pipeline/lib/misc/clickhouse_test.py | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index eb5dbcacaf..7aa6fd34fb 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -881,12 +881,12 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): self.assertEqual( new_gt_stats_post_reload, [ - (10, 2, 0), - (1, 1, 1), - (2, 0, 2), - (3, 2, 0), - (4, 5, 0), - (5, 2, 0), + (10, 2, 0, 0, 1, 0, 0), + (1, 1, 1, 0, 0, 0, 0), + (2, 0, 2, 0, 0, 1, 0), + (3, 2, 0, 0, 1, 0, 0), + (4, 5, 0, 0, 2, 0, 0), + (5, 2, 0, 0, 1, 0, 0), ], ) From c1556ba55d2c9d03a2e4494ef19f633cef287048 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 13:46:29 -0400 Subject: [PATCH 248/369] fix test --- loading_pipeline/lib/misc/clickhouse_test.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index 7aa6fd34fb..b7a46695d5 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -881,12 +881,12 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): self.assertEqual( new_gt_stats_post_reload, [ - (10, 2, 0, 0, 1, 0, 0), (1, 1, 1, 0, 0, 0, 0), (2, 0, 2, 0, 0, 1, 0), (3, 2, 0, 0, 1, 0, 0), (4, 5, 0, 0, 2, 0, 0), (5, 2, 0, 0, 1, 0, 0), + (10, 2, 0, 0, 1, 0, 0), ], ) From 18c7feba0d0815c17ddd670987554e902b071338 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 13:54:05 -0400 Subject: [PATCH 249/369] Revert "skip tests" This reverts commit 32c4dbecb82a8ca1a0f4e3baeee6d1ab1743638d. --- loading_pipeline/api/app_test.py | 140 ++ loading_pipeline/api/model_test.py | 87 ++ .../lib/annotations/fields_test.py | 118 ++ .../lib/annotations/snv_indel_test.py | 303 ++++ loading_pipeline/lib/annotations/sv_test.py | 171 +++ loading_pipeline/lib/core/definitions_test.py | 144 ++ .../lib/methods/relatedness_test.py | 39 + .../lib/methods/sex_check_test.py | 54 + loading_pipeline/lib/misc/callsets_test.py | 87 ++ .../lib/misc/family_entries_test.py | 356 +++++ .../lib/misc/family_loading_failures_test.py | 448 ++++++ loading_pipeline/lib/misc/gcnv_test.py | 54 + loading_pipeline/lib/misc/io_test.py | 211 +++ loading_pipeline/lib/misc/math_test.py | 12 + .../lib/misc/nested_field_test.py | 81 + loading_pipeline/lib/misc/pedigree_test.py | 514 +++++++ loading_pipeline/lib/misc/retry_test.py | 69 + loading_pipeline/lib/misc/runs_test.py | 84 + loading_pipeline/lib/misc/sample_ids_test.py | 160 ++ loading_pipeline/lib/misc/sv_test.py | 243 +++ .../lib/misc/terra_data_repository_test.py | 321 ++++ loading_pipeline/lib/misc/validation_test.py | 464 ++++++ loading_pipeline/lib/misc/vets_test.py | 104 ++ loading_pipeline/lib/paths_test.py | 180 +++ .../reference_datasets/gnomad_exomes_test.py | 72 + .../reference_datasets/gnomad_genomes_test.py | 72 + .../lib/reference_datasets/gnomad_svs_test.py | 93 ++ .../dataproc/create_dataproc_cluster_test.py | 162 ++ .../lib/tasks/dataproc/misc_test.py | 51 + .../dataproc/run_pipeline_on_dataproc_test.py | 184 +++ .../lib/tasks/exports/misc_test.py | 484 ++++++ .../exports/write_new_entries_parquet_test.py | 423 ++++++ .../write_new_variant_details_parquet_test.py | 270 ++++ loading_pipeline/lib/tasks/files_test.py | 40 + ...nnotations_table_with_new_variants_test.py | 1349 +++++++++++++++++ .../lib/tasks/validate_callset_test.py | 83 + .../lib/tasks/write_metadata_for_run_test.py | 188 +++ .../write_relatedness_check_table_test.py | 120 ++ .../tasks/write_relatedness_check_tsv_test.py | 53 + ...ite_remapped_and_subsetted_callset_test.py | 460 ++++++ .../lib/tasks/write_sample_qc_json_test.py | 269 ++++ .../lib/tasks/write_sex_check_table_test.py | 157 ++ .../lib/tasks/write_success_file_test.py | 34 + .../write_variant_annotations_vcf_test.py | 91 ++ 44 files changed, 9099 insertions(+) create mode 100644 loading_pipeline/api/app_test.py create mode 100644 loading_pipeline/api/model_test.py create mode 100644 loading_pipeline/lib/annotations/fields_test.py create mode 100644 loading_pipeline/lib/annotations/snv_indel_test.py create mode 100644 loading_pipeline/lib/annotations/sv_test.py create mode 100644 loading_pipeline/lib/core/definitions_test.py create mode 100644 loading_pipeline/lib/methods/relatedness_test.py create mode 100644 loading_pipeline/lib/methods/sex_check_test.py create mode 100644 loading_pipeline/lib/misc/callsets_test.py create mode 100644 loading_pipeline/lib/misc/family_entries_test.py create mode 100644 loading_pipeline/lib/misc/family_loading_failures_test.py create mode 100644 loading_pipeline/lib/misc/gcnv_test.py create mode 100644 loading_pipeline/lib/misc/io_test.py create mode 100644 loading_pipeline/lib/misc/math_test.py create mode 100644 loading_pipeline/lib/misc/nested_field_test.py create mode 100644 loading_pipeline/lib/misc/pedigree_test.py create mode 100644 loading_pipeline/lib/misc/retry_test.py create mode 100644 loading_pipeline/lib/misc/runs_test.py create mode 100644 loading_pipeline/lib/misc/sample_ids_test.py create mode 100644 loading_pipeline/lib/misc/sv_test.py create mode 100644 loading_pipeline/lib/misc/terra_data_repository_test.py create mode 100644 loading_pipeline/lib/misc/validation_test.py create mode 100644 loading_pipeline/lib/misc/vets_test.py create mode 100644 loading_pipeline/lib/paths_test.py create mode 100644 loading_pipeline/lib/reference_datasets/gnomad_exomes_test.py create mode 100644 loading_pipeline/lib/reference_datasets/gnomad_genomes_test.py create mode 100644 loading_pipeline/lib/reference_datasets/gnomad_svs_test.py create mode 100644 loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster_test.py create mode 100644 loading_pipeline/lib/tasks/dataproc/misc_test.py create mode 100644 loading_pipeline/lib/tasks/dataproc/run_pipeline_on_dataproc_test.py create mode 100644 loading_pipeline/lib/tasks/exports/misc_test.py create mode 100644 loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py create mode 100644 loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py create mode 100644 loading_pipeline/lib/tasks/files_test.py create mode 100644 loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py create mode 100644 loading_pipeline/lib/tasks/validate_callset_test.py create mode 100644 loading_pipeline/lib/tasks/write_metadata_for_run_test.py create mode 100644 loading_pipeline/lib/tasks/write_relatedness_check_table_test.py create mode 100644 loading_pipeline/lib/tasks/write_relatedness_check_tsv_test.py create mode 100644 loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset_test.py create mode 100644 loading_pipeline/lib/tasks/write_sample_qc_json_test.py create mode 100644 loading_pipeline/lib/tasks/write_sex_check_table_test.py create mode 100644 loading_pipeline/lib/tasks/write_success_file_test.py create mode 100644 loading_pipeline/lib/tasks/write_variant_annotations_vcf_test.py diff --git a/loading_pipeline/api/app_test.py b/loading_pipeline/api/app_test.py new file mode 100644 index 0000000000..f5945c1c41 --- /dev/null +++ b/loading_pipeline/api/app_test.py @@ -0,0 +1,140 @@ +from pathlib import Path + +from aiohttp import web_exceptions +from aiohttp.test_utils import AioHTTPTestCase + +from loading_pipeline.api.app import init_web_app +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + +CALLSET_PATH = str( + Path('loading_pipeline/var/test/callsets/1kg_30variants.vcf').resolve(), +) + + +class AppTest(AioHTTPTestCase, MockedDatarootTestCase): + async def get_application(self): + return await init_web_app() + + async def test_status(self): + async with self.client.request('GET', '/status') as resp: + self.assertEqual(resp.status, 200) + resp_json = await resp.json() + self.assertDictEqual(resp_json, {'success': True}) + + async def test_missing_route(self): + with self.assertLogs(level='ERROR') as _: + async with self.client.request('GET', '/loading_pip') as resp: + self.assertEqual(resp.status, web_exceptions.HTTPNotFound.status_code) + + async def test_loading_pipeline_invalid_requests(self): + with self.assertLogs(level='ERROR') as log: + async with self.client.request('GET', '/loading_pipeline_enqueue') as resp: + self.assertEqual( + resp.status, + web_exceptions.HTTPMethodNotAllowed.status_code, + ) + self.assertTrue( + 'HTTPMethodNotAllowed' in log.output[0], + ) + + with self.assertLogs(level='ERROR') as log: + async with self.client.request('POST', '/loading_pipeline_enqueue') as resp: + self.assertEqual( + resp.status, + web_exceptions.HTTPUnprocessableEntity.status_code, + ) + self.assertTrue( + 'HTTPUnprocessableEntity' in log.output[0], + ) + + body = { + 'callset_path': 'missing.vcf', + 'project_guids': ['project_a'], + 'sample_type': SampleType.WGS.value, + 'reference_genome': ReferenceGenome.GRCh38.value, + 'dataset_type': DatasetType.SNV_INDEL.value, + } + with self.assertLogs(level='ERROR') as log: + async with self.client.request( + 'POST', + '/loading_pipeline_enqueue', + json=body, + ) as resp: + self.assertEqual( + resp.status, + web_exceptions.HTTPBadRequest.status_code, + ) + self.assertTrue( + 'callset_path must point to a file that exists' in log.output[0], + ) + + body = { + 'callset_path': CALLSET_PATH, + 'project_guids': ['project_a'], + 'sample_type': SampleType.WGS.value, + 'reference_genome': ReferenceGenome.GRCh38.value, + 'dataset_type': DatasetType.SNV_INDEL.value, + 'validations_to_skip': ['bad_validation'], + } + with self.assertLogs(level='ERROR') as log: + async with self.client.request( + 'POST', + '/loading_pipeline_enqueue', + json=body, + ) as resp: + self.assertEqual( + resp.status, + web_exceptions.HTTPBadRequest.status_code, + ) + self.assertTrue( + "input_value='bad_validation" in log.output[0], + ) + + async def test_loading_pipeline_enqueue(self): + body = { + 'callset_path': CALLSET_PATH, + 'project_guids': ['project_a'], + 'sample_type': SampleType.WGS.value, + 'reference_genome': ReferenceGenome.GRCh38.value, + 'dataset_type': DatasetType.SNV_INDEL.value, + } + async with self.client.request( + 'POST', + '/loading_pipeline_enqueue', + json=body, + ) as resp: + self.assertEqual( + resp.status, + web_exceptions.HTTPAccepted.status_code, + ) + resp_json = await resp.json() + self.assertDictEqual( + resp_json, + { + 'Successfully queued': { + 'request_type': 'LoadingPipelineRequest', + 'callset_path': CALLSET_PATH, + 'dataset_type': 'SNV_INDEL', + 'project_guids': ['project_a'], + 'reference_genome': 'GRCh38', + 'sample_type': 'WGS', + 'skip_check_sex_and_relatedness': False, + 'skip_expect_tdr_metrics': False, + 'attempt_id': 0, + 'validations_to_skip': [], + }, + }, + ) + + # Second request + body['project_guids'] = ['project_b', 'project_c'] + async with self.client.request( + 'POST', + '/loading_pipeline_enqueue', + json=body, + ) as resp: + self.assertEqual( + resp.status, + web_exceptions.HTTPAccepted.status_code, + ) diff --git a/loading_pipeline/api/model_test.py b/loading_pipeline/api/model_test.py new file mode 100644 index 0000000000..03bc42ae1a --- /dev/null +++ b/loading_pipeline/api/model_test.py @@ -0,0 +1,87 @@ +import unittest +from pathlib import Path + +from loading_pipeline.api.model import DeleteFamiliesRequest, LoadingPipelineRequest +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType + +CALLSET_PATH = str( + Path('loading_pipeline/var/test/callsets/1kg_30variants.vcf').resolve(), +) + + +class ModelTest(unittest.TestCase): + def test_valid_loading_pipeline_requests(self) -> None: + raw_request = { + 'callset_path': CALLSET_PATH, + 'projects_to_run': ['project_a'], + 'sample_type': SampleType.WGS.value, + 'reference_genome': ReferenceGenome.GRCh38.value, + 'dataset_type': DatasetType.SNV_INDEL.value, + } + lpr = LoadingPipelineRequest.model_validate(raw_request) + self.assertEqual(lpr.reference_genome, ReferenceGenome.GRCh38) + self.assertEqual(lpr.project_guids, ['project_a']) + self.assertEqual(lpr.request_type, 'LoadingPipelineRequest') + self.assertEqual(lpr.attempt_id, 0) + + # Test wildcard VCF + raw_request['callset_path'] = CALLSET_PATH.replace( + '1kg_30variants.vcf', + '1kg_30*.vcf', + ) + lpr = LoadingPipelineRequest.model_validate(raw_request) + + def test_invalid_loading_pipeline_requests(self) -> None: + raw_request = { + 'callset_path': 'a.txt', + 'project_guids': [], + 'sample_type': 'BLENDED', + 'reference_genome': ReferenceGenome.GRCh38.value, + 'dataset_type': DatasetType.SNV_INDEL.value, + 'attempt_id': 5, + } + with self.assertRaises(ValueError) as cm: + LoadingPipelineRequest.model_validate(raw_request) + self.assertTrue( + str(cm.exception).startswith( + '4 validation errors for LoadingPipelineRequest', + ), + ) + + def test_validations_to_skip(self) -> None: + shared_params = { + 'callset_path': CALLSET_PATH, + 'projects_to_run': ['project_a'], + 'sample_type': SampleType.WGS.value, + 'reference_genome': ReferenceGenome.GRCh38.value, + 'dataset_type': DatasetType.SNV_INDEL.value, + } + raw_request = { + **shared_params, + 'validations_to_skip': ['all'], + } + lpr = LoadingPipelineRequest.model_validate(raw_request) + self.assertGreater(len(lpr.validations_to_skip), 2) + + raw_request = { + **shared_params, + 'validations_to_skip': ['validate_sample_type'], + } + lpr = LoadingPipelineRequest.model_validate(raw_request) + self.assertEqual(len(lpr.validations_to_skip), 1) + + raw_request = { + **shared_params, + 'validations_to_skip': ['validate_blended_exome'], + } + with self.assertRaises(ValueError): + LoadingPipelineRequest.model_validate(raw_request) + + def test_delete_families_request(self) -> None: + raw_request = {'project_guid': 'project_a', 'family_guids': []} + with self.assertRaises(ValueError): + DeleteFamiliesRequest.model_validate(raw_request) + raw_request['family_guids'] = ['family_a1'] + dfr = DeleteFamiliesRequest.model_validate(raw_request) + self.assertEqual(dfr.project_guid, 'project_a') + self.assertEqual(dfr.request_type, 'DeleteFamiliesRequest') diff --git a/loading_pipeline/lib/annotations/fields_test.py b/loading_pipeline/lib/annotations/fields_test.py new file mode 100644 index 0000000000..fc5f179749 --- /dev/null +++ b/loading_pipeline/lib/annotations/fields_test.py @@ -0,0 +1,118 @@ +from unittest.mock import Mock, patch + +import hail as hl + +from loading_pipeline.lib.annotations.fields import get_fields +from loading_pipeline.lib.core import ( + DatasetType, + ReferenceGenome, +) +from loading_pipeline.lib.misc.vep import run_vep +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase +from loading_pipeline.var.test.vep.mock_vep_data import ( + MOCK_37_VEP_DATA, + MOCK_38_VEP_DATA, +) + + +class FieldsTest(MockedDatarootTestCase): + def setUp(self) -> None: + super().setUp() + + @patch('loading_pipeline.lib.misc.vep.hl.vep') + def test_get_formatting_fields(self, mock_vep: Mock) -> None: + for reference_genome, ht, expected_fields in [ + ( + ReferenceGenome.GRCh38, + hl.Table.parallelize( + [ + { + 'locus': hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + 'alleles': ['A', 'C'], + 'rsid': 'abcd', + }, + ], + hl.tstruct( + locus=hl.tlocus('GRCh38'), + alleles=hl.tarray(hl.tstr), + rsid=hl.tstr, + ), + key=['locus', 'alleles'], + ), + [ + 'check_ref', + 'rg37_locus', + 'rsid', + 'sorted_motif_feature_consequences', + 'sorted_regulatory_feature_consequences', + 'sorted_transcript_consequences', + 'variant_id', + 'xpos', + ], + ), + ( + ReferenceGenome.GRCh37, + hl.Table.parallelize( + [ + { + 'locus': hl.Locus( + contig='1', + position=1, + reference_genome='GRCh37', + ), + 'alleles': ['A', 'C'], + 'rsid': 'abcd', + }, + ], + hl.tstruct( + locus=hl.tlocus('GRCh37'), + alleles=hl.tarray(hl.tstr), + rsid=hl.tstr, + ), + key=['locus', 'alleles'], + ), + [ + 'rg38_locus', + 'rsid', + 'sorted_transcript_consequences', + 'variant_id', + 'xpos', + ], + ), + ]: + mock_vep.return_value = ht.annotate( + vep=MOCK_37_VEP_DATA + if reference_genome == ReferenceGenome.GRCh37 + else MOCK_38_VEP_DATA, + ) + ht = run_vep( # noqa: PLW2901 + ht, + DatasetType.SNV_INDEL, + reference_genome, + ) + self.assertCountEqual( + list( + get_fields( + ht, + DatasetType.SNV_INDEL.formatting_annotation_fns( + reference_genome, + ), + **( + { + 'gencode_ensembl_to_refseq_id_mapping': hl.dict( + {'a': 'b'}, + ), + } + if reference_genome == ReferenceGenome.GRCh38 + else {} + ), + dataset_type=DatasetType.SNV_INDEL, + reference_genome=reference_genome, + ).keys(), + ), + expected_fields, + ) diff --git a/loading_pipeline/lib/annotations/snv_indel_test.py b/loading_pipeline/lib/annotations/snv_indel_test.py new file mode 100644 index 0000000000..0de91786b0 --- /dev/null +++ b/loading_pipeline/lib/annotations/snv_indel_test.py @@ -0,0 +1,303 @@ +import unittest +from unittest.mock import Mock, patch + +import hail as hl + +from loading_pipeline.lib.annotations import shared, snv_indel +from loading_pipeline.lib.core import DatasetType, ReferenceGenome +from loading_pipeline.lib.misc.vep import run_vep +from loading_pipeline.var.test.vep.mock_vep_data import ( + MOCK_37_VEP_DATA, + MOCK_38_VEP_DATA, +) + + +class SNVTest(unittest.TestCase): + @patch('loading_pipeline.lib.misc.vep.hl.vep') + def test_sorted_transcript_consequences_37( + self, + mock_vep: Mock, + ) -> None: + ht = hl.Table.parallelize( + [ + { + 'locus': hl.Locus( + contig='1', + position=871269, + reference_genome=ReferenceGenome.GRCh37.value, + ), + 'alleles': ['A', 'C'], + }, + ], + hl.tstruct( + locus=hl.tlocus(ReferenceGenome.GRCh37.value), + alleles=hl.tarray(hl.tstr), + ), + key=['locus', 'alleles'], + ) + mock_vep.return_value = ht.annotate(vep=MOCK_37_VEP_DATA) + ht = run_vep( + ht, + DatasetType.SNV_INDEL, + ReferenceGenome.GRCh37, + ) + ht = ht.select( + sorted_transcript_consequences=shared.sorted_transcript_consequences( + ht, + ), + ) + self.assertCountEqual( + ht.sorted_transcript_consequences.collect(), + [ + [ + hl.Struct( + amino_acids='S/L', + canonical=1, + codons='tCg/tTg', + gene_id='ENSG00000188976', + hgvsc='ENST00000327044.6:c.1667C>T', + hgvsp='ENSP00000317992.6:p.Ser556Leu', + transcript_id='ENST00000327044', + biotype_id=39, + consequence_term_ids=[9], + is_lof_nagnag=None, + lof_filter_ids=[0, 1], + ), + hl.Struct( + amino_acids=None, + canonical=None, + codons=None, + gene_id='ENSG00000188976', + hgvsc='ENST00000477976.1:n.3114C>T', + hgvsp=None, + transcript_id='ENST00000477976', + biotype_id=38, + consequence_term_ids=[23, 26], + is_lof_nagnag=None, + lof_filter_ids=None, + ), + hl.Struct( + amino_acids=None, + canonical=None, + codons=None, + gene_id='ENSG00000188976', + hgvsc='ENST00000483767.1:n.523C>T', + hgvsp=None, + transcript_id='ENST00000483767', + biotype_id=38, + consequence_term_ids=[23, 26], + is_lof_nagnag=None, + lof_filter_ids=None, + ), + ], + ], + ) + + @patch('loading_pipeline.lib.misc.vep.hl.vep') + def test_sorted_transcript_consequences_38( + self, + mock_vep: Mock, + ) -> None: + ht = hl.Table.parallelize( + [ + { + 'locus': hl.Locus( + contig='chr1', + position=871269, + reference_genome=ReferenceGenome.GRCh38.value, + ), + 'alleles': ['A', 'C'], + }, + ], + hl.tstruct( + locus=hl.tlocus(ReferenceGenome.GRCh38.value), + alleles=hl.tarray(hl.tstr), + ), + key=['locus', 'alleles'], + ) + mock_vep.return_value = ht.annotate(vep=MOCK_38_VEP_DATA) + ht = run_vep( + ht, + DatasetType.SNV_INDEL, + ReferenceGenome.GRCh38, + ) + ht = ht.select( + sorted_transcript_consequences=snv_indel.sorted_transcript_consequences( + ht, + hl.dict( + {'ENST00000327044': 'NM_015658.4', 'ENST00000477976': 'refseq1'}, + ), + ), + ) + self.assertCountEqual( + ht.sorted_transcript_consequences.collect()[0], + [ + hl.Struct( + amino_acids='S/L', + canonical=1, + codons='tCg/tTg', + gene_id='ENSG00000188976', + hgvsc='ENST00000327044.6:c.1667C>T', + hgvsp='ENSP00000317992.6:p.Ser556Leu', + transcript_id='ENST00000327044', + refseq_transcript_id='NM_015658.4', + mane_select='NM_015658.4', + mane_plus_clinical=None, + biotype_id=39, + consequence_term_ids=[9], + exon=hl.Struct(index=15, total=19), + intron=None, + alphamissense=hl.Struct(pathogenicity=0.10000000149011612), + loftee=hl.Struct( + is_lof_nagnag=None, + lof_filter_ids=[0, 1], + ), + spliceregion=hl.Struct( + extended_intronic_splice_region_variant=False, + ), + utrannotator=hl.Struct( + existing_inframe_oorfs=None, + existing_outofframe_oorfs=None, + existing_uorfs=None, + fiveutr_consequence_id=None, + fiveutr_annotation=None, + ), + ), + hl.Struct( + amino_acids=None, + canonical=None, + codons=None, + gene_id='ENSG00000188976', + hgvsc='ENST00000477976.1:n.3114C>T', + hgvsp=None, + transcript_id='ENST00000477976', + refseq_transcript_id='refseq1', + mane_select=None, + mane_plus_clinical=None, + biotype_id=38, + consequence_term_ids=[23, 26], + exon=hl.Struct(index=13, total=17), + intron=None, + alphamissense=hl.Struct(pathogenicity=0.9700000286102295), + loftee=hl.Struct( + is_lof_nagnag=None, + lof_filter_ids=None, + ), + spliceregion=hl.Struct( + extended_intronic_splice_region_variant=False, + ), + utrannotator=hl.Struct( + existing_inframe_oorfs=None, + existing_outofframe_oorfs=None, + existing_uorfs=None, + fiveutr_consequence_id=None, + fiveutr_annotation=None, + ), + ), + hl.Struct( + amino_acids=None, + canonical=None, + codons=None, + gene_id='ENSG00000188976', + hgvsc='ENST00000483767.1:n.523C>T', + hgvsp=None, + transcript_id='ENST00000483767', + refseq_transcript_id=None, + mane_select=None, + mane_plus_clinical=None, + biotype_id=38, + consequence_term_ids=[23, 13, 26], + exon=hl.Struct(index=1, total=5), + intron=None, + alphamissense=hl.Struct(pathogenicity=None), + loftee=hl.Struct( + is_lof_nagnag=None, + lof_filter_ids=None, + ), + spliceregion=hl.Struct( + extended_intronic_splice_region_variant=True, + ), + utrannotator=hl.Struct( + existing_inframe_oorfs=0, + existing_outofframe_oorfs=1, + existing_uorfs=0, + fiveutr_consequence_id=1, + fiveutr_annotation=hl.Struct( + type='OutOfFrame_oORF', + KozakContext='TTTATGC', + KozakStrength='Weak', + DistanceToCDS=40, + CapDistanceToStart=20, + DistanceToStop=75, + Evidence=False, + AltStop=None, + AltStopDistanceToCDS=None, + FrameWithCDS=None, + StartDistanceToCDS=None, + newSTOPDistanceToCDS=None, + alt_type=None, + alt_type_length=None, + ref_StartDistanceToCDS=None, + ref_type=None, + ref_type_length=None, + ), + ), + ), + ], + ) + + @patch('loading_pipeline.lib.misc.vep.hl.vep') + def test_sorted_other_feature_consequences( + self, + mock_vep: Mock, + ) -> None: + ht = hl.Table.parallelize( + [ + { + 'locus': hl.Locus( + contig='chr1', + position=871269, + reference_genome=ReferenceGenome.GRCh38.value, + ), + 'alleles': ['A', 'C'], + }, + ], + hl.tstruct( + locus=hl.tlocus(ReferenceGenome.GRCh38.value), + alleles=hl.tarray(hl.tstr), + ), + key=['locus', 'alleles'], + ) + mock_vep.return_value = ht.annotate(vep=MOCK_38_VEP_DATA) + ht = run_vep( + ht, + DatasetType.SNV_INDEL, + ReferenceGenome.GRCh38, + ) + ht = ht.select( + sorted_motif_feature_consequences=snv_indel.sorted_motif_feature_consequences( + ht, + ), + sorted_regulatory_feature_consequences=snv_indel.sorted_regulatory_feature_consequences( + ht, + ), + ) + self.assertCountEqual( + ht.sorted_motif_feature_consequences.collect(), + [None], + ) + self.assertCountEqual( + ht.sorted_regulatory_feature_consequences.collect()[0], + [ + hl.Struct( + biotype_id=0, + consequence_term_ids=[0], + regulatory_feature_id='regulatory_2', + ), + hl.Struct( + biotype_id=0, + consequence_term_ids=[2], + regulatory_feature_id='regulatory_1', + ), + ], + ) diff --git a/loading_pipeline/lib/annotations/sv_test.py b/loading_pipeline/lib/annotations/sv_test.py new file mode 100644 index 0000000000..25a8413b16 --- /dev/null +++ b/loading_pipeline/lib/annotations/sv_test.py @@ -0,0 +1,171 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.annotations.fields import get_fields +from loading_pipeline.lib.core import DatasetType + + +class SVTest(unittest.TestCase): + def test_sv_export_annotations(self) -> None: + ht = hl.Table.parallelize( + [ + hl.Struct( + id=0, + algorithms='manta', + end_locus=hl.Locus( + contig='chr5', + position=20404, + reference_genome='GRCh38', + ), + start_locus=hl.Locus( + contig='chr1', + position=180928, + reference_genome='GRCh38', + ), + sv_len=123, + sv_type_id=2, + sv_type_detail_id=None, + ), + hl.Struct( + id=1, + algorithms='manta', + end_locus=hl.Locus( + contig='chr1', + position=789481, + reference_genome='GRCh38', + ), + start_locus=hl.Locus( + contig='chr1', + position=789481, + reference_genome='GRCh38', + ), + sv_len=245, + sv_type_id=2, + sv_type_detail_id=None, + ), + hl.Struct( + id=2, + algorithms='manta', + end_locus=hl.Locus( + contig='chr1', + position=6559723, + reference_genome='GRCh38', + ), + start_locus=hl.Locus( + contig='chr1', + position=6558902, + reference_genome='GRCh38', + ), + sv_len=245, + sv_type_id=3, + sv_type_detail_id=2, + ), + hl.Struct( + id=3, + algorithms='manta', + end_locus=hl.Locus( + contig='chr1', + position=6559723, + reference_genome='GRCh38', + ), + start_locus=hl.Locus( + contig='chr1', + position=6558902, + reference_genome='GRCh38', + ), + sv_len=245, + sv_type_id=7, + sv_type_detail_id=6, + ), + ], + hl.tstruct( + id=hl.tint32, + algorithms=hl.tstr, + end_locus=hl.tlocus('GRCh38'), + start_locus=hl.tlocus('GRCh38'), + sv_len=hl.tint32, + sv_type_id=hl.tint32, + sv_type_detail_id=hl.tint32, + ), + key='id', + ) + ht = ht.select( + **get_fields( + ht, + DatasetType.SV.export_vcf_annotation_fns, + ), + ) + self.assertEqual( + ht.collect(), + [ + hl.Struct( + id=0, + locus=hl.Locus( + contig='chr1', + position=180928, + reference_genome='GRCh38', + ), + alleles=['N', ''], + info=hl.Struct( + ALGORITHMS='manta', + END=180928, + CHR2='chr5', + END2=20404, + SVTYPE='BND', + SVLEN=123, + ), + ), + hl.Struct( + id=1, + locus=hl.Locus( + contig='chr1', + position=789481, + reference_genome='GRCh38', + ), + alleles=['N', ''], + info=hl.Struct( + ALGORITHMS='manta', + END=789481, + CHR2='chr1', + END2=789481, + SVTYPE='BND', + SVLEN=245, + ), + ), + hl.Struct( + id=2, + locus=hl.Locus( + contig='chr1', + position=6558902, + reference_genome='GRCh38', + ), + alleles=['N', ''], + info=hl.Struct( + ALGORITHMS='manta', + END=6558902, + CHR2='chr1', + END2=6559723, + SVTYPE='CPX', + SVLEN=245, + ), + ), + hl.Struct( + id=3, + locus=hl.Locus( + contig='chr1', + position=6558902, + reference_genome='GRCh38', + ), + alleles=['N', ''], + info=hl.Struct( + ALGORITHMS='manta', + END=6558902, + CHR2='chr1', + END2=6559723, + SVTYPE='INS', + SVLEN=245, + ), + ), + ], + ) diff --git a/loading_pipeline/lib/core/definitions_test.py b/loading_pipeline/lib/core/definitions_test.py new file mode 100644 index 0000000000..b53d88cd18 --- /dev/null +++ b/loading_pipeline/lib/core/definitions_test.py @@ -0,0 +1,144 @@ +import unittest + +from loading_pipeline.lib.core.definitions import ReferenceGenome + + +class TestReferenceGenomeProperties(unittest.TestCase): + def test_v02_value(self): + self.assertEqual(ReferenceGenome.GRCh37.v02_value, '37') + self.assertEqual(ReferenceGenome.GRCh38.v02_value, '38') + + def test_hl_reference(self): + hl_37_reference = ReferenceGenome.GRCh37.hl_reference + self.assertEqual(hl_37_reference.name, 'GRCh37') + + hl_38_reference = ReferenceGenome.GRCh38.hl_reference + self.assertEqual(hl_38_reference.name, 'GRCh38') + + def test_standard_contigs(self): + expected_37_contigs = { + '3', + '12', + '21', + '2', + '1', + '7', + '13', + '8', + '11', + '22', + 'MT', + '14', + 'Y', + '18', + '19', + '20', + '17', + 'X', + '10', + '15', + '16', + '4', + '5', + '9', + '6', + } + self.assertEqual(ReferenceGenome.GRCh37.standard_contigs, expected_37_contigs) + + expected_38_contigs = { + 'chr10', + 'chr11', + 'chr17', + 'chr18', + 'chr9', + 'chr22', + 'chr3', + 'chrY', + 'chr7', + 'chr6', + 'chr13', + 'chr19', + 'chr16', + 'chrX', + 'chr12', + 'chr2', + 'chr21', + 'chr20', + 'chr8', + 'chrM', + 'chr5', + 'chr4', + 'chr14', + 'chr1', + 'chr15', + } + self.assertEqual(ReferenceGenome.GRCh38.standard_contigs, expected_38_contigs) + + def test_optional_contigs(self): + self.assertEqual(ReferenceGenome.GRCh37.optional_contigs, {'Y', 'MT'}) + self.assertEqual(ReferenceGenome.GRCh38.optional_contigs, {'chrY', 'chrM'}) + + def test_contig_recoding(self): + expected_37_recode = { + 'chr1': '1', + 'chr2': '2', + 'chr3': '3', + 'chr4': '4', + 'chr5': '5', + 'chr6': '6', + 'chr7': '7', + 'chr8': '8', + 'chr9': '9', + 'chr10': '10', + 'chr11': '11', + 'chr12': '12', + 'chr13': '13', + 'chr14': '14', + 'chr15': '15', + 'chr16': '16', + 'chr17': '17', + 'chr18': '18', + 'chr19': '19', + 'chr20': '20', + 'chr21': '21', + 'chr22': '22', + 'chrX': 'X', + 'chrY': 'Y', + 'chrM': 'MT', + } + self.assertDictEqual( + ReferenceGenome.GRCh37.contig_recoding(include_mt=True), + expected_37_recode, + ) + + expected_38_recode = { + '1': 'chr1', + '2': 'chr2', + '3': 'chr3', + '4': 'chr4', + '5': 'chr5', + '6': 'chr6', + '7': 'chr7', + '8': 'chr8', + '9': 'chr9', + '10': 'chr10', + '11': 'chr11', + '12': 'chr12', + '13': 'chr13', + '14': 'chr14', + '15': 'chr15', + '16': 'chr16', + '17': 'chr17', + '18': 'chr18', + '19': 'chr19', + '20': 'chr20', + '21': 'chr21', + '22': 'chr22', + 'X': 'chrX', + 'Y': 'chrY', + 'MT': 'chrM', + } + self.assertDictEqual( + ReferenceGenome.GRCh38.contig_recoding(include_mt=True), + expected_38_recode, + ) diff --git a/loading_pipeline/lib/methods/relatedness_test.py b/loading_pipeline/lib/methods/relatedness_test.py new file mode 100644 index 0000000000..e3afb159e2 --- /dev/null +++ b/loading_pipeline/lib/methods/relatedness_test.py @@ -0,0 +1,39 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.methods.relatedness import call_relatedness + +TEST_SEX_AND_RELATEDNESS_CALLSET_MT = ( + 'loading_pipeline/var/test/callsets/sex_and_relatedness_1.mt' +) + + +class RelatednessTest(unittest.TestCase): + def test_call_relatedness(self): + mt = hl.read_matrix_table(TEST_SEX_AND_RELATEDNESS_CALLSET_MT) + ht = call_relatedness( + mt, + None, + ) + self.assertCountEqual( + ht.collect(), + [ + hl.Struct( + i='ROS_006_18Y03226_D1', + j='ROS_007_19Y05939_D1', + ibd0=0.0, + ibd1=1.0, + ibd2=0.0, + pi_hat=0.5, + ), + hl.Struct( + i='ROS_007_19Y05939_D1', + j='ROS_007_19Y05987_D1', + ibd0=0.0, + ibd1=1.0, + ibd2=0.0, + pi_hat=0.5, + ), + ], + ) diff --git a/loading_pipeline/lib/methods/sex_check_test.py b/loading_pipeline/lib/methods/sex_check_test.py new file mode 100644 index 0000000000..ed390e86f3 --- /dev/null +++ b/loading_pipeline/lib/methods/sex_check_test.py @@ -0,0 +1,54 @@ +import unittest +from unittest.mock import patch + +import hail as hl + +from loading_pipeline.lib.methods.sex_check import compute_sex_check_ht + +TEST_SEX_AND_RELATEDNESS_CALLSET_MT = ( + 'loading_pipeline/var/test/callsets/sex_and_relatedness_1.mt' +) + + +class SexCheckTest(unittest.TestCase): + def test_compute_sex_check_ht(self): + mt = hl.read_matrix_table(TEST_SEX_AND_RELATEDNESS_CALLSET_MT) + ht = compute_sex_check_ht(mt) + self.assertCountEqual( + ht.collect(), + [ + hl.Struct( + s='ROS_006_18Y03226_D1', + predicted_sex='M', + ), + hl.Struct( + s='ROS_006_18Y03227_D1', + predicted_sex='M', + ), + hl.Struct( + s='ROS_006_18Y03228_D1', + predicted_sex='M', + ), + hl.Struct( + s='ROS_007_19Y05919_D1', + predicted_sex='M', + ), + hl.Struct( + s='ROS_007_19Y05939_D1', + predicted_sex='F', + ), + hl.Struct( + s='ROS_007_19Y05987_D1', + predicted_sex='M', + ), + ], + ) + + def test_compute_sex_check_ht_ambiguous(self): + mt = hl.read_matrix_table(TEST_SEX_AND_RELATEDNESS_CALLSET_MT) + with patch('loading_pipeline.lib.methods.sex_check.XY_FSTAT_THRESHOLD', 0.95): + self.assertRaises( + ValueError, + compute_sex_check_ht, + mt, + ) diff --git a/loading_pipeline/lib/misc/callsets_test.py b/loading_pipeline/lib/misc/callsets_test.py new file mode 100644 index 0000000000..5db2d4eb36 --- /dev/null +++ b/loading_pipeline/lib/misc/callsets_test.py @@ -0,0 +1,87 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.misc.callsets import union_callset_mts + + +class CallsetsTest(unittest.TestCase): + def test_union_callset_mts(self) -> None: + mt1 = ( + hl.MatrixTable.from_parts( + rows={ + 'id': [ + 0, + 1, + ], + 'row_field': [ + 1, + 2, + ], + }, + cols={'s': ['sample_1']}, + entries={ + 'GT': [[hl.Call([0, 0])], [hl.Call([0, 0])]], + }, + ) + .key_rows_by('id') + .key_cols_by('s') + .drop('row_idx', 'col_idx') + ) + mt2 = ( + hl.MatrixTable.from_parts( + rows={ + 'id': [ + 0, + 2, + ], + 'row_field': [ + 2, + 3, + ], + 'second_row_field': [ + 4, + 5, + ], + }, + cols={'s': ['sample_2']}, + entries={ + 'GT': [[hl.Call([0, 0])], [hl.Call([0, 1])]], + }, + ) + .key_rows_by('id') + .key_cols_by('s') + .drop('row_idx', 'col_idx') + ) + mt = union_callset_mts([mt1, mt2]) + self.assertEqual( + mt.entries().collect(), + [ + hl.Struct( + id=0, + row_field=1, + s='sample_1', + GT=hl.Call(alleles=[0, 0], phased=False), + ), + hl.Struct( + id=0, + row_field=1, + s='sample_2', + GT=hl.Call(alleles=[0, 0], phased=False), + ), + hl.Struct( + id=1, + row_field=2, + s='sample_1', + GT=hl.Call(alleles=[0, 0], phased=False), + ), + hl.Struct(id=1, row_field=2, s='sample_2', GT=None), + hl.Struct(id=2, row_field=None, s='sample_1', GT=None), + hl.Struct( + id=2, + row_field=None, + s='sample_2', + GT=hl.Call(alleles=[0, 1], phased=False), + ), + ], + ) diff --git a/loading_pipeline/lib/misc/family_entries_test.py b/loading_pipeline/lib/misc/family_entries_test.py new file mode 100644 index 0000000000..609fdda6d6 --- /dev/null +++ b/loading_pipeline/lib/misc/family_entries_test.py @@ -0,0 +1,356 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.core import DatasetType +from loading_pipeline.lib.misc.family_entries import ( + compute_callset_family_entries_ht, + deduplicate_by_most_non_ref_calls, + deglobalize_ids, + globalize_ids, +) + + +class FamilyEntriesTest(unittest.TestCase): + def test_compute_callset_family_entries_ht(self) -> None: + mt = hl.MatrixTable.from_parts( + rows={ + 'variants': [1, 2, 3], + 'filters': [ + hl.empty_set(hl.tstr), + {'HIGH_SR_BACKGROUND'}, + hl.empty_set(hl.tstr), + ], + }, + cols={'s': ['a', 'b', 'd', 'c']}, + entries={ + 'GT': [ + [ + hl.Call([0, 0]), + hl.missing(hl.tcall), + hl.Call([0, 0]), + hl.Call([0, 0]), + ], + [ + hl.Call([0, 0]), + hl.Call([0, 0]), + hl.Call([1, 1]), + hl.Call([0, 0]), + ], + [ + hl.Call([0, 1]), + hl.Call([0, 0]), + hl.Call([1, 1]), + hl.Call([0, 0]), + ], + ], + }, + globals={'family_samples': {'2': ['a'], '1': ['b', 'c', 'd']}}, + ) + ht = compute_callset_family_entries_ht(DatasetType.SNV_INDEL, mt, {'GT': mt.GT}) + self.assertCountEqual( + ht.globals.collect(), + [ + hl.Struct( + family_samples={'1': ['b', 'c', 'd'], '2': ['a']}, + family_guids=['1', '2'], + ), + ], + ) + self.assertCountEqual( + ht.filters.collect(), + [{'HIGH_SR_BACKGROUND'}, set()], + ) + self.assertCountEqual( + ht.family_entries.collect(), + [ + [ + [ + hl.Struct(GT=hl.Call(alleles=[0, 0], phased=False)), + hl.Struct(GT=hl.Call(alleles=[0, 0], phased=False)), + hl.Struct(GT=hl.Call(alleles=[1, 1], phased=False)), + ], + None, + ], + [ + [ + hl.Struct(GT=hl.Call(alleles=[0, 0], phased=False)), + hl.Struct(GT=hl.Call(alleles=[0, 0], phased=False)), + hl.Struct(GT=hl.Call(alleles=[1, 1], phased=False)), + ], + [hl.Struct(GT=hl.Call(alleles=[0, 1], phased=False))], + ], + ], + ) + + def test_globalize_and_deglobalize(self) -> None: + family_entries_ht = hl.Table.parallelize( + [], + hl.tstruct( + id=hl.tint32, + filters=hl.tset(hl.tstr), + family_entries=hl.tarray( + hl.tarray(hl.tstruct(a=hl.tint32, s=hl.tstr, family_guid=hl.tstr)), + ), + ), + key='id', + ) + family_entries_ht = globalize_ids(family_entries_ht) + self.assertCountEqual( + family_entries_ht.family_guids.collect(), + [ + [], + ], + ) + family_entries_ht = hl.Table.parallelize( + [ + { + 'id': 0, + 'filters': {'HIGH_SR_BACKGROUND', 'UNRESOLVED'}, + 'family_entries': [ + [ + hl.Struct(a=1, s='a', family_guid='123'), + hl.Struct(a=2, s='c', family_guid='123'), + hl.Struct(a=1, s='e', family_guid='123'), + ], + [ + hl.Struct(a=2, s='f', family_guid='234'), + ], + ], + }, + { + 'id': 1, + 'filters': {'HIGH_SR_BACKGROUND'}, + 'family_entries': [ + [ + hl.Struct(a=2, s='a', family_guid='123'), + hl.Struct(a=3, s='c', family_guid='123'), + hl.Struct(a=4, s='e', family_guid='123'), + ], + [ + hl.Struct(a=5, s='f', family_guid='234'), + ], + ], + }, + ], + hl.tstruct( + id=hl.tint32, + filters=hl.tset(hl.tstr), + family_entries=hl.tarray( + hl.tarray(hl.tstruct(a=hl.tint32, s=hl.tstr, family_guid=hl.tstr)), + ), + ), + key='id', + ) + family_entries_ht = globalize_ids(family_entries_ht) + self.assertCountEqual( + family_entries_ht.family_guids.collect(), + [ + ['123', '234'], + ], + ) + self.assertCountEqual( + family_entries_ht.family_entries.collect(), + [ + [ + [ + hl.Struct(a=1), + hl.Struct(a=2), + hl.Struct(a=1), + ], + [ + hl.Struct(a=2), + ], + ], + [ + [ + hl.Struct(a=2), + hl.Struct(a=3), + hl.Struct(a=4), + ], + [ + hl.Struct(a=5), + ], + ], + ], + ) + family_entries_ht = deglobalize_ids(family_entries_ht) + self.assertCountEqual( + family_entries_ht.family_entries.collect(), + [ + [ + [ + hl.Struct(a=1, s='a', family_guid='123'), + hl.Struct(a=2, s='c', family_guid='123'), + hl.Struct(a=1, s='e', family_guid='123'), + ], + [ + hl.Struct(a=2, s='f', family_guid='234'), + ], + ], + [ + [ + hl.Struct(a=2, s='a', family_guid='123'), + hl.Struct(a=3, s='c', family_guid='123'), + hl.Struct(a=4, s='e', family_guid='123'), + ], + [ + hl.Struct(a=5, s='f', family_guid='234'), + ], + ], + ], + ) + + def test_deduplicate_by_most_non_ref_calls(self) -> None: + project_ht = hl.Table.parallelize( + [ + { + 'id': 0, + 'filters': {'PASS', 'HIGH_SR_BACKGROUND'}, + 'family_entries': [ + [ + hl.Struct( + GT=hl.Call(alleles=[0, 1], phased=False), + family_guid='family_a', + s='sample_1', + ), + hl.Struct( + GT=hl.Call(alleles=[0, 0], phased=False), + family_guid='family_a', + s='sample_2', + ), + ], + [ + hl.Struct( + GT=hl.Call(alleles=[0, 1], phased=False), + family_guid='family_b', + s='sample_3', + ), + None, + ], + None, + ], + }, + { + 'id': 0, + 'filters': {'PASS'}, + 'family_entries': [ + [ + None, + hl.Struct( + GT=hl.Call(alleles=[0, 0], phased=False), + family_guid='family_a', + s='sample_2', + ), + ], + [ + hl.Struct( + GT=hl.Call(alleles=[0, 1], phased=False), + family_guid='family_b', + s='sample_3', + ), + None, + ], + None, + ], + }, + { + 'id': 2, + 'filters': {'HIGH_SR_BACKGROUND'}, + 'family_entries': [ + None, + None, + ], + }, + { + 'id': 3, + 'filters': {'PASS'}, + 'family_entries': [ + [ + hl.Struct( + GT=hl.Call(alleles=[0, 1], phased=False), + family_guid='family_a', + s='sample_1', + ), + hl.Struct( + GT=hl.Call(alleles=[0, 1], phased=False), + family_guid='family_a', + s='sample_2', + ), + ], + None, + ], + }, + ], + hl.tstruct( + id=hl.tint32, + filters=hl.tset(hl.tstr), + family_entries=hl.tarray( + hl.tarray( + hl.tstruct( + GT=hl.tcall, + family_guid=hl.tstr, + s=hl.tstr, + ), + ), + ), + ), + key='id', + ) + ht = deduplicate_by_most_non_ref_calls(project_ht) + self.assertEqual( + ht.collect(), + [ + hl.Struct( + id=0, + filters={'PASS', 'HIGH_SR_BACKGROUND'}, + family_entries=[ + [ + hl.Struct( + GT=hl.Call(alleles=[0, 1], phased=False), + family_guid='family_a', + s='sample_1', + ), + hl.Struct( + GT=hl.Call(alleles=[0, 0], phased=False), + family_guid='family_a', + s='sample_2', + ), + ], + [ + hl.Struct( + GT=hl.Call(alleles=[0, 1], phased=False), + family_guid='family_b', + s='sample_3', + ), + None, + ], + None, + ], + ), + hl.Struct( + id=2, + filters={'HIGH_SR_BACKGROUND'}, + family_entries=[None, None], + ), + hl.Struct( + id=3, + filters={'PASS'}, + family_entries=[ + [ + hl.Struct( + GT=hl.Call(alleles=[0, 1], phased=False), + family_guid='family_a', + s='sample_1', + ), + hl.Struct( + GT=hl.Call(alleles=[0, 1], phased=False), + family_guid='family_a', + s='sample_2', + ), + ], + None, + ], + ), + ], + ) diff --git a/loading_pipeline/lib/misc/family_loading_failures_test.py b/loading_pipeline/lib/misc/family_loading_failures_test.py new file mode 100644 index 0000000000..fb1d0905d1 --- /dev/null +++ b/loading_pipeline/lib/misc/family_loading_failures_test.py @@ -0,0 +1,448 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.core import Sex +from loading_pipeline.lib.misc.family_loading_failures import ( + all_relatedness_checks, + build_relatedness_check_lookup, + build_sex_check_lookup, + get_families_failed_imputed_sex_ploidy, + get_families_failed_sex_check, +) +from loading_pipeline.lib.misc.io import import_pedigree +from loading_pipeline.lib.misc.pedigree import ( + Family, + Sample, + parse_pedigree_ht_to_families, +) + +TEST_SEX_CHECK_1 = 'loading_pipeline/var/test/sex_check/test_sex_check_1.ht' +TEST_PEDIGREE_6 = 'loading_pipeline/var/test/pedigrees/test_pedigree_6.tsv' + + +class FamilyLoadingFailuresTest(unittest.TestCase): + def test_build_relatedness_check_lookup(self): + ht = hl.Table.parallelize( + [ + { + 'i': 'ROS_006_18Y03226_D1', + 'j': 'ROS_007_19Y05939_D1', + 'ibd0': 0.0, + 'ibd1': 1.0, + 'ibd2': 0.0, + 'pi_hat': 0.5, + }, + ], + hl.tstruct( + i=hl.tstr, + j=hl.tstr, + ibd0=hl.tfloat, + ibd1=hl.tfloat, + ibd2=hl.tfloat, + pi_hat=hl.tfloat, + ), + key=['i', 'j'], + ) + self.assertEqual( + build_relatedness_check_lookup( + ht, + hl.dict({'ROS_006_18Y03226_D1': 'remapped_id'}), + ), + { + ('ROS_007_19Y05939_D1', 'remapped_id'): [ + 0.0, + 1.0, + 0.0, + 0.5, + ], + }, + ) + + def test_build_sex_check_lookup(self): + ht = hl.Table.parallelize( + [ + {'s': 'ROS_006_18Y03226_D1', 'predicted_sex': 'F'}, + {'s': 'ROS_006_18Y03227_D1', 'predicted_sex': 'F'}, + {'s': 'ROS_006_18Y03228_D1', 'predicted_sex': 'F'}, + {'s': 'ROS_007_19Y05919_D1', 'predicted_sex': 'F'}, + {'s': 'ROS_007_19Y05939_D1', 'predicted_sex': 'M'}, + {'s': 'ROS_007_19Y05987_D1', 'predicted_sex': 'U'}, + {'s': 'ROS_007_19Y05989_D1', 'predicted_sex': 'X0'}, + ], + hl.tstruct( + s=hl.tstr, + predicted_sex=hl.tstr, + ), + key='s', + ) + self.assertEqual( + build_sex_check_lookup(ht, hl.dict({'ROS_006_18Y03226_D1': 'remapped_id'})), + { + 'remapped_id': Sex.FEMALE, + 'ROS_006_18Y03227_D1': Sex.FEMALE, + 'ROS_006_18Y03228_D1': Sex.FEMALE, + 'ROS_007_19Y05919_D1': Sex.FEMALE, + 'ROS_007_19Y05939_D1': Sex.MALE, + 'ROS_007_19Y05987_D1': Sex.UNKNOWN, + 'ROS_007_19Y05989_D1': Sex.X0, + }, + ) + + def test_all_relatedness_checks(self): + relatedness_check_lookup = { + # Parent + ('sample_1', 'sample_2'): [ + 0.0, + 0.98, + 0.0, + 0.52, + ], + # GrandParent + ('sample_1', 'sample_3'): [0.48, 0.52, 0, 0.24], + # Half Sibling (but actually a hidden Sibling) + ('sample_1', 'sample_4'): [0.25, 0.5, 0.25, 0.5], + } + sample = Sample( + sex=Sex.FEMALE, + sample_id='sample_1', + mother='sample_2', + paternal_grandfather='sample_3', + half_siblings=['sample_4'], + ) + family = Family( + family_guid='family_1a', + samples={ + 'sample_1': sample, + 'sample_2': Sample(sex=Sex.MALE, sample_id='sample_2'), + 'sample_3': Sample(sex=Sex.MALE, sample_id='sample_3'), + 'sample_4': Sample(sex=Sex.MALE, sample_id='sample_4'), + 'sample_5': Sample(sex=Sex.MALE, sample_id='sample_5'), + }, + ) + failure_reasons = all_relatedness_checks( + relatedness_check_lookup, + family, + sample, + ) + self.assertListEqual(failure_reasons, []) + + # Defined grandparent missing in relatedness table + sample = Sample( + sex=Sex.FEMALE, + sample_id='sample_1', + mother='sample_2', + paternal_grandfather='sample_3', + paternal_grandmother='sample_5', + ) + failure_reasons = all_relatedness_checks( + relatedness_check_lookup, + family, + sample, + ) + self.assertListEqual( + failure_reasons, + [ + 'Sample sample_1 has expected relation "grandparent_grandchild" to sample_5 but has coefficients []', + ], + ) + + # Sibling is actually a half sibling. + relatedness_check_lookup = { + **relatedness_check_lookup, + ('sample_1', 'sample_4'): [0.5, 0.5, 0, 0.25], + } + sample = Sample( + sex=Sex.FEMALE, + sample_id='sample_1', + mother='sample_2', + paternal_grandfather='sample_3', + siblings=['sample_4'], + ) + failure_reasons = all_relatedness_checks( + relatedness_check_lookup, + family, + sample, + ) + self.assertListEqual( + failure_reasons, + [ + 'Sample sample_1 has expected relation "sibling" to sample_4 but has coefficients [0.5, 0.5, 0, 0.25]', + ], + ) + + relatedness_check_lookup = { + **relatedness_check_lookup, + ('sample_1', 'sample_2'): [ + 0.5, + 0.5, + 0.5, + 0.5, + ], + } + sample = Sample( + sex=Sex.FEMALE, + sample_id='sample_1', + mother='sample_2', + paternal_grandfather='sample_3', + siblings=['sample_4'], + ) + failure_reasons = all_relatedness_checks( + relatedness_check_lookup, + family, + sample, + ) + self.assertListEqual( + failure_reasons, + [ + 'Sample sample_1 has expected relation "parent_child" to sample_2 but has coefficients [0.5, 0.5, 0.5, 0.5]', + 'Sample sample_1 has expected relation "sibling" to sample_4 but has coefficients [0.5, 0.5, 0, 0.25]', + ], + ) + + # Some samples will include relationships with + # samples that are not expected to be included + # in the callset. These should not trigger relatedness + # failures. + sample = Sample( + sex=Sex.FEMALE, + sample_id='sample_1', + mother='sample_2', + ) + family = Family( + family_guid='family_1a', + samples={ + 'sample_1': sample, + }, + ) + failure_reasons = all_relatedness_checks( + {}, + family, + sample, + ) + self.assertListEqual( + failure_reasons, + [], + ) + + def test_get_families_failed_sex_check(self): + sex_check_ht = hl.Table.parallelize( + [ + {'s': 'ROS_006_18Y03226_D1', 'predicted_sex': 'F'}, + {'s': 'ROS_006_18Y03227_D1', 'predicted_sex': 'F'}, # Pedigree Sex U + {'s': 'ROS_006_18Y03228_D1', 'predicted_sex': 'F'}, + {'s': 'ROS_007_19Y05939_D1', 'predicted_sex': 'M'}, + {'s': 'ROS_007_19Y05987_D1', 'predicted_sex': 'U'}, # Pedigree Sex F + {'s': 'ROS_007_19Y05989_D1', 'predicted_sex': 'XXX'}, + ], + hl.tstruct( + s=hl.tstr, + predicted_sex=hl.tstr, + ), + key='s', + ) + pedigree_ht = import_pedigree(TEST_PEDIGREE_6) + failed_families = get_families_failed_sex_check( + parse_pedigree_ht_to_families(pedigree_ht), + sex_check_ht, + {}, + ) + self.assertCountEqual( + failed_families.values(), + [ + [ + 'Sample ROS_007_19Y05919_D1 has pedigree sex F but is missing from the sex check source', + 'Sample ROS_007_19Y05939_D1 has pedigree sex F but imputed sex M', + ], + ], + ) + + def test_get_families_failed_imputed_sex_ploidy(self) -> None: + female_sample = 'HG00731_1' + male_sample_1 = 'HG00732_1' + male_sample_2 = 'HG00732_1' + x0_sample = 'NA20899_1' + xxy_sample = 'NA20889_1' + xyy_sample = 'NA20891_1' + xxx_sample = 'NA20892_1' + + sex_check_ht = hl.read_table(TEST_SEX_CHECK_1) + families = { + Family( + family_guid='', + samples={ + female_sample: Sample(female_sample, Sex.FEMALE), + male_sample_1: Sample(male_sample_1, Sex.MALE), + male_sample_2: Sample(male_sample_2, Sex.MALE), + x0_sample: Sample(x0_sample, Sex.X0), + xxy_sample: Sample(xxy_sample, Sex.XXY), + xyy_sample: Sample(xyy_sample, Sex.XYY), + xxx_sample: Sample(xxx_sample, Sex.XXX), + }, + ), + } + + # All calls on X chromosome are valid + mt = ( + hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chrX', + position=1, + reference_genome='GRCh38', + ), + ], + }, + cols={ + 's': [ + female_sample, + male_sample_1, + x0_sample, + xxy_sample, + xyy_sample, + xxx_sample, + ], + }, + entries={ + 'GT': [ + [ + hl.Call(alleles=[0, 0], phased=False), + hl.Call(alleles=[0], phased=False), + hl.Call(alleles=[0, 0], phased=False), # X0 + hl.Call(alleles=[0, 0], phased=False), # XXY + hl.Call(alleles=[0, 0], phased=False), # XYY + hl.Call(alleles=[0, 0], phased=False), # XXX + ], + ], + }, + ) + .key_rows_by('locus') + .key_cols_by('s') + ) + failed_families = get_families_failed_imputed_sex_ploidy( + families, + mt, + sex_check_ht, + ) + self.assertDictEqual(failed_families, {}) + + # All calls on Y chromosome are valid + mt = ( + hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chrY', + position=1, + reference_genome='GRCh38', + ), + ], + }, + cols={ + 's': [ + female_sample, + male_sample_1, + x0_sample, + xxy_sample, + xyy_sample, + xxx_sample, + ], + }, + entries={ + 'GT': [ + [ + hl.missing(hl.tcall), + hl.Call(alleles=[0], phased=False), + hl.missing(hl.tcall), # X0 + hl.Call(alleles=[0, 0], phased=False), # XXY + hl.Call(alleles=[0, 0], phased=False), # XYY + hl.missing(hl.tcall), # XXX + ], + ], + }, + ) + .key_rows_by('locus') + .key_cols_by('s') + ) + failed_families = get_families_failed_imputed_sex_ploidy( + families, + mt, + sex_check_ht, + ) + self.assertDictEqual(failed_families, {}) + + # Invalid X chromosome case + mt = ( + hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chrX', + position=1, + reference_genome='GRCh38', + ), + ], + }, + cols={ + 's': [ + female_sample, + male_sample_1, + male_sample_2, + x0_sample, + xxy_sample, + xyy_sample, + xxx_sample, + ], + }, + entries={ + 'GT': [ + [ + hl.Call(alleles=[0], phased=False), # invalid Female call + hl.Call(alleles=[0], phased=False), # valid Male call + hl.missing(hl.tcall), # invalid Male call + hl.Call(alleles=[0], phased=False), # invalid X0 call + hl.Call(alleles=[0], phased=False), # invalid XXY call + hl.missing(hl.tcall), # valid XYY call + hl.Call(alleles=[0, 0], phased=False), # valid XXX call + ], + ], + }, + ) + .key_rows_by('locus') + .key_cols_by('s') + ) + failed_families = get_families_failed_imputed_sex_ploidy( + families, + mt, + sex_check_ht, + ) + self.assertCountEqual( + failed_families.values(), + [ + [ + "Found samples with misaligned ploidy with their provided imputed sex: ['HG00731_1', 'HG00732_1', 'NA20889_1', 'NA20899_1']", + ], + ], + ) + + # Invalid X chromosome case, but only discrepant family samples are reported + families = { + Family( + family_guid='', + samples={female_sample: Sample(female_sample, Sex.FEMALE)}, + ), + } + failed_families = get_families_failed_imputed_sex_ploidy( + families, + mt, + sex_check_ht, + ) + self.assertCountEqual( + failed_families.values(), + [ + [ + "Found samples with misaligned ploidy with their provided imputed sex: ['HG00731_1']", + ], + ], + ) diff --git a/loading_pipeline/lib/misc/gcnv_test.py b/loading_pipeline/lib/misc/gcnv_test.py new file mode 100644 index 0000000000..33a72f3684 --- /dev/null +++ b/loading_pipeline/lib/misc/gcnv_test.py @@ -0,0 +1,54 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.misc.gcnv import parse_gcnv_genes + + +class GCNVGeneParsingTest(unittest.TestCase): + def test_parse_gcnv_genes(self): + t1 = hl.Table.parallelize( + [ + {'genes': 'AC118553.2,SLC35A3'}, + {'genes': 'AC118553.1,None'}, + {'genes': 'None'}, + {'genes': 'SLC35A3.43'}, + {'genes': ''}, + {'genes': 'SLC35A4.43'}, + ], + hl.tstruct(genes=hl.dtype('str')), + key='genes', + ) + t1 = t1.annotate(gene_set=parse_gcnv_genes(t1.genes)) + self.assertCountEqual( + t1.collect(), + [ + hl.Struct( + genes='AC118553.2,SLC35A3', + gene_set={'AC118553', 'SLC35A3'}, + ), + hl.Struct(genes='AC118553.1,None', gene_set={'AC118553'}), + hl.Struct(genes='None', gene_set=set()), + hl.Struct(genes='SLC35A3.43', gene_set={'SLC35A3'}), + hl.Struct(genes='', gene_set=set()), + hl.Struct(genes='SLC35A4.43', gene_set={'SLC35A4'}), + ], + ) + + def test_aggregate_parsed_genes(self): + t1 = hl.Table.parallelize( + [ + {'genes': 'AC118553.2,SLC35A3'}, + {'genes': 'AC118553.1,None'}, + {'genes': 'None'}, + {'genes': 'SLC35A3.43'}, + {'genes': ''}, + {'genes': 'SLC35A4.43'}, + ], + hl.tstruct(genes=hl.dtype('str')), + key='genes', + ) + aggregated_gene_set = t1.aggregate( + hl.flatten(hl.agg.collect_as_set(parse_gcnv_genes(t1.genes))), + ) + self.assertEqual(aggregated_gene_set, {'SLC35A4', 'SLC35A3', 'AC118553'}) diff --git a/loading_pipeline/lib/misc/io_test.py b/loading_pipeline/lib/misc/io_test.py new file mode 100644 index 0000000000..a346e8b323 --- /dev/null +++ b/loading_pipeline/lib/misc/io_test.py @@ -0,0 +1,211 @@ +import unittest +from unittest import mock + +import hail as hl + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome +from loading_pipeline.lib.misc.io import ( + compute_hail_n_partitions, + file_size_bytes, + import_imputed_sex, + import_vcf, + remap_pedigree_hash, + select_relevant_fields, + split_multi_hts, +) +from loading_pipeline.lib.misc.validation import SeqrValidationError + +TEST_IMPUTED_SEX = 'loading_pipeline/var/test/sex_check/test_imputed_sex.tsv' +TEST_IMPUTED_SEX_UNEXPECTED_VALUE = ( + 'loading_pipeline/var/test/sex_check/test_imputed_sex_unexpected_value.tsv' +) +CORRUPTED_VCF = 'loading_pipeline/var/test/callsets/1kg_corrupt.vcf.gz' +TEST_INVALID_VCF = 'loading_pipeline/var/test/callsets/improperly_formatted.vcf' +TEST_PEDIGREE_3_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_3_remap.tsv' +TEST_MITO_MT = 'loading_pipeline/var/test/callsets/mito_1.mt' + + +class IOTest(unittest.TestCase): + def test_file_size_mb(self) -> None: + # find loading_pipeline/var/test/callsets/mito_1.mt -type f | grep -v 'crc' | xargs ls -alt {} | awk '{sum += $5; print sum}' + # 191310 + self.assertEqual(file_size_bytes(TEST_MITO_MT), 191310) + + def test_compute_hail_n_partitions(self) -> None: + self.assertEqual(compute_hail_n_partitions(23), 1) + self.assertEqual(compute_hail_n_partitions(191310), 1) + self.assertEqual(compute_hail_n_partitions(1913100000), 58) + + def test_import_imputed_sex(self) -> None: + ht = import_imputed_sex(TEST_IMPUTED_SEX) + self.assertListEqual( + ht.collect(), + [ + hl.Struct(s='abc_1', predicted_sex='M'), + hl.Struct(s='abc_2', predicted_sex='F'), + hl.Struct(s='abc_3', predicted_sex='U'), + hl.Struct(s='abc_4', predicted_sex='XYY'), + hl.Struct(s='abc_5', predicted_sex='U'), + ], + ) + + def test_import_imputed_sex_unexpected_value(self) -> None: + ht = import_imputed_sex(TEST_IMPUTED_SEX_UNEXPECTED_VALUE) + self.assertRaisesRegex( + hl.utils.java.HailUserError, + 'Found unexpected value UNKNOWN in imputed sex file', + ht.collect, + ) + + def test_remap_pedigree_hash(self) -> None: + self.assertEqual( + hl.eval( + remap_pedigree_hash( + TEST_PEDIGREE_3_REMAP, + ), + ), + 573002191, + ) + + def test_import_vcf(self) -> None: + self.assertRaisesRegex( + TypeError, + 'missing 1 required positional argument', + import_vcf, + 'abc', + ) + self.assertRaisesRegex( + SeqrValidationError, + 'Unable to access the VCF in cloud storage', + import_vcf, + 'bad.vcf', + ReferenceGenome.GRCh38, + ) + self.assertRaisesRegex( + SeqrValidationError, + 'Gzip-compressed data is corrupt', + import_vcf, + CORRUPTED_VCF, + ReferenceGenome.GRCh38, + ) + with mock.patch( + 'loading_pipeline.lib.misc.io.hl.read_table', + ) as mock_read_table: + mock_read_table.side_effect = hl.utils.java.FatalError( + 'GoogleJsonResponseException: 403 Forbidden', + ) + self.assertRaisesRegex( + SeqrValidationError, + 'Unable to access the VCF in cloud storage', + import_vcf, + 'abc123/bad.vcf', + ReferenceGenome.GRCh38, + ) + self.assertRaisesRegex( + SeqrValidationError, + 'VCF failed file format validation: Your input file has a malformed header: We never saw the required CHROM header line \\(starting with one #\\) for the input VCF file', + import_vcf, + TEST_PEDIGREE_3_REMAP, + ReferenceGenome.GRCh38, + ) + self.assertRaisesRegex( + SeqrValidationError, + "VCF failed file format validation: invalid character 'N' in integer literal", + import_vcf, + TEST_INVALID_VCF, + ReferenceGenome.GRCh38, + ) + + def test_select_missing_field(self) -> None: + self.assertRaisesRegex( + SeqrValidationError, + "Your callset is missing a required field: 'a magic field'", + select_relevant_fields, + hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + ], + 'alleles': [ + ['A', 'C'], + ], + 'rsid': ['rs1233'], + 'filters': [{'PASS'}], + }, + cols={'s': ['sample_1']}, + entries={ + 'GT': [[hl.Call([0, 0])]], + 'AD': [[[0, 20]]], + 'GQ': [[99]], + }, + ).key_rows_by('locus', 'alleles'), + DatasetType.SNV_INDEL, + {'a magic field': hl.tint32}, + ) + + def test_split_multi_failure(self) -> None: + self.assertRaisesRegex( + SeqrValidationError, + 'Your callset failed while attempting to split multiallelic sites. This error can occur if the dataset contains both multiallelic variants and duplicated loci.', + split_multi_hts, + hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + ], + 'alleles': [ + ['A', 'G', 'AC'], + ['A', 'AT', 'C', 'G'], + ], + }, + cols={'s': ['sample_1']}, + entries={ + 'GQ': [[99], [98]], + }, + ) + .key_rows_by('locus', 'alleles') + .repartition(1), + False, + 1, + ) + + def test_split_multi_failure_ad_length(self) -> None: + self.assertRaisesRegex( + SeqrValidationError, + 'Your callset failed while attempting to split multiallelic sites. This error can occur if the provided Allele Depth \\(AD\\) field does not match the length of the multiallelic site.', + split_multi_hts, + hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + ], + 'alleles': [ + ['GAC', 'G', 'GTTTTTTTTTTTTTTTAC'], + ], + }, + cols={'s': ['sample_1']}, + entries={ + 'GQ': [[99]], + 'AD': [[[0, 1]]], + }, + ).key_rows_by('locus', 'alleles'), + False, + 1, + ) diff --git a/loading_pipeline/lib/misc/math_test.py b/loading_pipeline/lib/misc/math_test.py new file mode 100644 index 0000000000..19e12d6bfc --- /dev/null +++ b/loading_pipeline/lib/misc/math_test.py @@ -0,0 +1,12 @@ +import unittest + +from loading_pipeline.lib.misc.math import constrain + + +class TestConstrainFunction(unittest.TestCase): + def test_constrain(self): + self.assertEqual(constrain(5, 0, 10), 5) + self.assertEqual(constrain(-3, 0, 10), 0) + self.assertEqual(constrain(15, 0, 10), 10) + with self.assertRaises(ValueError): + constrain(5, 10, 0) diff --git a/loading_pipeline/lib/misc/nested_field_test.py b/loading_pipeline/lib/misc/nested_field_test.py new file mode 100644 index 0000000000..8d465187a5 --- /dev/null +++ b/loading_pipeline/lib/misc/nested_field_test.py @@ -0,0 +1,81 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.misc.nested_field import parse_nested_field + + +class TestConstrainFunction(unittest.TestCase): + def test_parse_nested_field(self): + ht = hl.Table.parallelize( + [ + { + 'locus': hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + 'alleles': ['A', 'C'], + 'a': hl.Struct(d=1), + 'b': hl.Struct(e=[2, 9]), + 'h': hl.Struct(**{'i.j': 1}), + 'a_index': 1, + }, + { + 'locus': hl.Locus( + contig='chr1', + position=2, + reference_genome='GRCh38', + ), + 'alleles': ['A', 'C'], + 'a': hl.Struct(d=3), + 'b': hl.Struct(e=[4, 5]), + 'h': hl.Struct(**{'i.j': 2}), + 'a_index': 1, + }, + ], + hl.tstruct( + locus=hl.tlocus('GRCh38'), + alleles=hl.tarray(hl.tstr), + a=hl.tstruct(d=hl.tint32), + b=hl.tstruct(e=hl.tarray(hl.tint32)), + h=hl.tstruct(**{'i.j': hl.tint32}), + a_index=hl.tint32, + ), + key=['locus', 'alleles'], + ) + ht = ht.select( + d=parse_nested_field(ht, 'a.d'), + e=parse_nested_field(ht, 'b.e#'), + f=parse_nested_field(ht, 'a'), + g=parse_nested_field(ht, 'h.i.j'), + ) + self.assertListEqual( + ht.collect(), + [ + hl.Struct( + locus=hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + alleles=['A', 'C'], + d=1, + e=2, + f=hl.Struct(d=1), + g=1, + ), + hl.Struct( + locus=hl.Locus( + contig='chr1', + position=2, + reference_genome='GRCh38', + ), + alleles=['A', 'C'], + d=3, + e=4, + f=hl.Struct(d=3), + g=2, + ), + ], + ) diff --git a/loading_pipeline/lib/misc/pedigree_test.py b/loading_pipeline/lib/misc/pedigree_test.py new file mode 100644 index 0000000000..77432ba138 --- /dev/null +++ b/loading_pipeline/lib/misc/pedigree_test.py @@ -0,0 +1,514 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.core import Sex +from loading_pipeline.lib.misc.io import import_pedigree +from loading_pipeline.lib.misc.pedigree import ( + Family, + Sample, + parse_pedigree_ht_to_families, +) + +TEST_PEDIGREE_1 = 'loading_pipeline/var/test/pedigrees/test_pedigree_1.tsv' +TEST_PEDIGREE_2 = 'loading_pipeline/var/test/pedigrees/test_pedigree_2.tsv' +TEST_PEDIGREE_9 = 'loading_pipeline/var/test/pedigrees/test_pedigree_9.tsv' + + +class PedigreesTest(unittest.TestCase): + def test_empty_pedigree(self) -> None: + with self.assertRaises(Exception): # noqa: B017 + _ = import_pedigree(TEST_PEDIGREE_1) + + def test_parse_lineage(self) -> None: + # + # + # sample_9 sample_10 sample_7 + # \ / \ | + # sample_6 -> sample_8 --------- sample_3 ----- ? | + # \ / \ / | + # sample_4, sample_5 sample_2 | sample_1 + # + # + samples = Family.parse_direct_lineage( + [ + hl.Struct(s='sample_1', maternal_s=None, paternal_s=None, sex='F'), + hl.Struct( + s='sample_2', + maternal_s='sample_3', + paternal_s=None, + sex='M', + ), + hl.Struct( + s='sample_3', + maternal_s=None, + paternal_s='sample_7', + sex='F', + ), + hl.Struct( + s='sample_4', + maternal_s='sample_3', + paternal_s='sample_8', + sex='M', + ), + hl.Struct( + s='sample_5', + maternal_s='sample_3', + paternal_s='sample_8', + sex='M', + ), + hl.Struct( + s='sample_6', + maternal_s='sample_9', + paternal_s='sample_10', + sex='M', + ), + hl.Struct(s='sample_7', maternal_s=None, paternal_s=None, sex='M'), + hl.Struct( + s='sample_8', + maternal_s='sample_9', + paternal_s='sample_10', + sex='F', + ), + hl.Struct(s='sample_9', maternal_s=None, paternal_s=None, sex='F'), + hl.Struct(s='sample_10', maternal_s=None, paternal_s=None, sex='M'), + ], + ) + self.assertEqual( + Family.parse_collateral_lineage(samples), + { + 'sample_1': Sample( + sample_id='sample_1', + sex=Sex.FEMALE, + mother=None, + father=None, + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'sample_2': Sample( + sample_id='sample_2', + sex=Sex.MALE, + mother='sample_3', + father=None, + maternal_grandmother=None, + maternal_grandfather='sample_7', + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=['sample_4', 'sample_5'], + aunt_nephews=[], + ), + 'sample_3': Sample( + sample_id='sample_3', + sex=Sex.FEMALE, + mother=None, + father='sample_7', + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'sample_4': Sample( + sample_id='sample_4', + sex=Sex.MALE, + mother='sample_3', + father='sample_8', + maternal_grandmother=None, + maternal_grandfather='sample_7', + paternal_grandmother='sample_9', + paternal_grandfather='sample_10', + siblings=['sample_5'], + half_siblings=[], + aunt_nephews=['sample_6'], + ), + 'sample_5': Sample( + sample_id='sample_5', + sex=Sex.MALE, + mother='sample_3', + father='sample_8', + maternal_grandmother=None, + maternal_grandfather='sample_7', + paternal_grandmother='sample_9', + paternal_grandfather='sample_10', + siblings=[], + half_siblings=[], + aunt_nephews=['sample_6'], + ), + 'sample_6': Sample( + sample_id='sample_6', + sex=Sex.MALE, + mother='sample_9', + father='sample_10', + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=['sample_8'], + half_siblings=[], + aunt_nephews=[], + ), + 'sample_7': Sample( + sample_id='sample_7', + sex=Sex.MALE, + mother=None, + father=None, + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'sample_8': Sample( + sample_id='sample_8', + sex=Sex.FEMALE, + mother='sample_9', + father='sample_10', + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'sample_9': Sample( + sample_id='sample_9', + sex=Sex.FEMALE, + mother=None, + father=None, + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'sample_10': Sample( + sample_id='sample_10', + sex=Sex.MALE, + mother=None, + father=None, + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + }, + ) + + def test_parse_parent_not_aunt_uncle(self) -> None: + samples = Family.parse_direct_lineage( + [ + hl.Struct(s='sample_1', maternal_s=None, paternal_s=None, sex='F'), + hl.Struct( + s='sample_2', + maternal_s=None, + paternal_s=None, + sex='M', + ), + hl.Struct( + s='sample_3', + maternal_s='sample_1', + paternal_s='sample_2', + sex='F', + ), + hl.Struct( + s='sample_4', + maternal_s='sample_3', + paternal_s=None, + sex='F', + ), + hl.Struct( + s='sample_5', + maternal_s='sample_3', + paternal_s=None, + sex='F', + ), + ], + ) + self.assertEqual( + Family.parse_collateral_lineage(samples), + { + 'sample_1': Sample( + sample_id='sample_1', + sex=Sex.FEMALE, + mother=None, + father=None, + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'sample_2': Sample( + sample_id='sample_2', + sex=Sex.MALE, + mother=None, + father=None, + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'sample_3': Sample( + sample_id='sample_3', + sex=Sex.FEMALE, + mother='sample_1', + father='sample_2', + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'sample_4': Sample( + sample_id='sample_4', + sex=Sex.FEMALE, + mother='sample_3', + father=None, + maternal_grandmother='sample_1', + maternal_grandfather='sample_2', + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=['sample_5'], + aunt_nephews=[], + ), + 'sample_5': Sample( + sample_id='sample_5', + sex=Sex.FEMALE, + mother='sample_3', + father=None, + maternal_grandmother='sample_1', + maternal_grandfather='sample_2', + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + }, + ) + + def test_parse_project(self) -> None: + pedigree_ht = import_pedigree(TEST_PEDIGREE_2) + self.assertCountEqual( + list(parse_pedigree_ht_to_families(pedigree_ht)), + [ + Family( + family_guid='BBL_BC1-000345_1', + samples={ + 'BBL_BC1-000345_01_D1': Sample( + sample_id='BBL_BC1-000345_01_D1', + sex=Sex.UNKNOWN, + mother='BBL_BC1-000345_03_D1', + father='BBL_BC1-000345_02_D1', + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'BBL_BC1-000345_02_D1': Sample( + sample_id='BBL_BC1-000345_02_D1', + sex=Sex.MALE, + mother=None, + father=None, + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'BBL_BC1-000345_03_D1': Sample( + sample_id='BBL_BC1-000345_03_D1', + sex=Sex.FEMALE, + mother=None, + father=None, + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + }, + ), + Family( + family_guid='BBL_HT-007-5195_1', + samples={ + 'BBL_HT-007-5195_01_D1': Sample( + sample_id='BBL_HT-007-5195_01_D1', + sex=Sex.FEMALE, + mother='BBL_HT-007-5195_03_D1', + father='BBL_HT-007-5195_02_D1', + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[ + 'BBL_HT-007-5195_04_D1', + 'BBL_HT-007-5195_05_D1', + 'BBL_HT-007-5195_06_D1', + ], + half_siblings=[], + aunt_nephews=[], + ), + 'BBL_HT-007-5195_02_D1': Sample( + sample_id='BBL_HT-007-5195_02_D1', + sex=Sex.MALE, + mother=None, + father=None, + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'BBL_HT-007-5195_03_D1': Sample( + sample_id='BBL_HT-007-5195_03_D1', + sex=Sex.FEMALE, + mother=None, + father=None, + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + 'BBL_HT-007-5195_04_D1': Sample( + sample_id='BBL_HT-007-5195_04_D1', + sex=Sex.MALE, + mother='BBL_HT-007-5195_03_D1', + father='BBL_HT-007-5195_02_D1', + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=['BBL_HT-007-5195_05_D1', 'BBL_HT-007-5195_06_D1'], + half_siblings=[], + aunt_nephews=[], + ), + 'BBL_HT-007-5195_05_D1': Sample( + sample_id='BBL_HT-007-5195_05_D1', + sex=Sex.FEMALE, + mother='BBL_HT-007-5195_03_D1', + father='BBL_HT-007-5195_02_D1', + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=['BBL_HT-007-5195_06_D1'], + half_siblings=[], + aunt_nephews=[], + ), + 'BBL_HT-007-5195_06_D1': Sample( + sample_id='BBL_HT-007-5195_06_D1', + sex=Sex.MALE, + mother='BBL_HT-007-5195_03_D1', + father='BBL_HT-007-5195_02_D1', + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + }, + ), + Family( + family_guid='BBL_SDS1-000178_1', + samples={ + 'BBL_SDS1-000178_01_D1': Sample( + sample_id='BBL_SDS1-000178_01_D1', + sex=Sex.FEMALE, + mother=None, + father=None, + maternal_grandmother=None, + maternal_grandfather=None, + paternal_grandmother=None, + paternal_grandfather=None, + siblings=[], + half_siblings=[], + aunt_nephews=[], + ), + }, + ), + ], + ) + + def test_subsetted_pedigree_with_removed_parent(self) -> None: + pedigree_ht = import_pedigree(TEST_PEDIGREE_2) + pedigree_ht = pedigree_ht.filter( + pedigree_ht.s != 'BBL_BC1-000345_02_D1', + ) + parsed_pedigree = parse_pedigree_ht_to_families(pedigree_ht) + family = next( + iter( + [ + family + for family in parsed_pedigree + if family.family_guid == 'BBL_BC1-000345_1' + ], + ), + ) + self.assertEqual(len(family.samples), 2) + self.assertFalse( + 'BBL_BC1-000345_02_D1' in family.samples, + ) + self.assertEqual( + family.samples['BBL_BC1-000345_01_D1'].father, + 'BBL_BC1-000345_02_D1', + ) + self.assertEqual( + family.samples['BBL_BC1-000345_01_D1'].mother, + 'BBL_BC1-000345_03_D1', + ) + + def test_pedigree_ungrouped_families(self) -> None: + pedigree_ht = import_pedigree(TEST_PEDIGREE_9) + parsed_pedigree = parse_pedigree_ht_to_families(pedigree_ht) + self.assertEqual(len(parsed_pedigree), 2) + family = next( + iter( + [ + family + for family in parsed_pedigree + if family.family_guid == 'family_2_1' + ], + ), + ) + self.assertTrue( + family.samples.keys() == {'RGP_164_1', 'RGP_164_2', 'RGP_164_4'}, + ) diff --git a/loading_pipeline/lib/misc/retry_test.py b/loading_pipeline/lib/misc/retry_test.py new file mode 100644 index 0000000000..4b756abce1 --- /dev/null +++ b/loading_pipeline/lib/misc/retry_test.py @@ -0,0 +1,69 @@ +import unittest +from unittest.mock import Mock, patch + +from loading_pipeline.lib.core import DatasetType +from loading_pipeline.lib.misc.retry import retry + + +class TestRetryDecorator(unittest.TestCase): + @patch('time.sleep', return_value=None) + def test_retry_success_first_try(self, mock_sleep): + mock_func = Mock(return_value='success') + + @retry(tries=3, delay=1, backoff=2) + def func(d: DatasetType): + return mock_func(d) + + result = func(DatasetType.SNV_INDEL) + self.assertEqual(result, 'success') + self.assertEqual(mock_func.call_count, 1) + mock_sleep.assert_not_called() + + @patch('time.sleep', return_value=None) + @patch('loading_pipeline.lib.misc.retry.logger') + def test_retry_eventual_success(self, mock_logger, mock_sleep): + mock_func = Mock( + side_effect=[Exception('fail'), Exception('fail again'), 'success'], + ) + + @retry(tries=3, delay=1, backoff=2) + def func(): + return mock_func() + + result = func() + self.assertEqual(result, 'success') + self.assertEqual(mock_func.call_count, 3) + self.assertEqual(mock_sleep.call_count, 2) + mock_sleep.assert_any_call(1) + mock_sleep.assert_any_call(2) + + @patch('time.sleep', return_value=None) + @patch('loading_pipeline.lib.misc.retry.logger') + def test_retry_all_failures(self, mock_logger, mock_sleep): + mock_func = Mock(side_effect=Exception('always fails')) + + @retry(tries=3, delay=1, backoff=2) + def func(): + return mock_func() + + with self.assertRaises(Exception) as context: + func() + + self.assertEqual(str(context.exception), 'always fails') + self.assertEqual(mock_func.call_count, 3) + self.assertEqual(mock_sleep.call_count, 2) + + @patch('time.sleep', return_value=None) + @patch('loading_pipeline.lib.misc.retry.logger.exception') + def test_logs_retry_message(self, mock_log, mock_sleep): + mock_func = Mock(side_effect=[Exception('fail'), 'success']) + + @retry(tries=2, delay=1, backoff=2) + def func(d: DatasetType): + return mock_func(d) + + func(d=DatasetType.SNV_INDEL) + self.assertIn( + 'func args: kwargs:d=SNV_INDEL failed on attempt 1 after 0.00s, retrying in 1 seconds.', + mock_log.call_args[0][0], + ) diff --git a/loading_pipeline/lib/misc/runs_test.py b/loading_pipeline/lib/misc/runs_test.py new file mode 100644 index 0000000000..b1a601727a --- /dev/null +++ b/loading_pipeline/lib/misc/runs_test.py @@ -0,0 +1,84 @@ +import os + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome +from loading_pipeline.lib.misc.runs import get_run_ids +from loading_pipeline.lib.paths import ( + clickhouse_load_fail_file_path, + clickhouse_load_success_file_path, + pipeline_run_success_file_path, + runs_path, +) +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + + +class RunsTest(MockedDatarootTestCase): + def setUp(self): + super().setUp() + run_ids = [ + 'manual__2024-08-05T16-07-58.365146+00-00', + 'manual__2024-08-06T10-15-23.123456+00-00', + 'manual__2024-08-07T12-30-45.654321+00-00', # _SUCCESS, _CLICKHOUSE_LOAD_FAIL + 'manual__2024-08-08T09-45-00.000000+00-00', # _SUCCESS + 'manual__2024-08-09T18-22-13.999999+00-00', # _SUCCESS, _CLICKHOUSE_LOAD_SUCCESS + ] + for reference_genome, dataset_type in [ + (ReferenceGenome.GRCh38, DatasetType.SNV_INDEL), + (ReferenceGenome.GRCh37, DatasetType.SNV_INDEL), + (ReferenceGenome.GRCh38, DatasetType.GCNV), + (ReferenceGenome.GRCh37, DatasetType.GCNV), + ]: + for run_id in run_ids: + base_path = runs_path(reference_genome, dataset_type) + os.makedirs(os.path.join(base_path, run_id), exist_ok=True) + if '07T12' in run_id: + failure_file = clickhouse_load_fail_file_path( + reference_genome, + dataset_type, + run_id, + ) + open(failure_file, 'w').close() + if '09' in run_id or '07T12' in run_id: + success_file = pipeline_run_success_file_path( + reference_genome, + dataset_type, + run_id, + ) + open(success_file, 'w').close() + if '09T18' in run_id: + success_file = clickhouse_load_success_file_path( + reference_genome, + dataset_type, + run_id, + ) + open(success_file, 'w').close() + + def test_get_run_ids(self) -> None: + ( + successful_pipeline_runs, + successful_clickhouse_loads, + failed_clickhouse_loads, + ) = get_run_ids() + self.assertCountEqual( + successful_pipeline_runs[(ReferenceGenome.GRCh38, DatasetType.SNV_INDEL)], + { + 'manual__2024-08-09T18-22-13.999999+00-00', + 'manual__2024-08-08T09-45-00.000000+00-00', + 'manual__2024-08-07T12-30-45.654321+00-00', + }, + ) + self.assertCountEqual( + successful_clickhouse_loads[ + (ReferenceGenome.GRCh38, DatasetType.SNV_INDEL) + ], + { + 'manual__2024-08-09T18-22-13.999999+00-00', + }, + ) + self.assertCountEqual( + successful_clickhouse_loads[(ReferenceGenome.GRCh37, DatasetType.GCNV)], + {}, + ) + self.assertCountEqual( + failed_clickhouse_loads[(ReferenceGenome.GRCh38, DatasetType.SNV_INDEL)], + {'manual__2024-08-07T12-30-45.654321+00-00'}, + ) diff --git a/loading_pipeline/lib/misc/sample_ids_test.py b/loading_pipeline/lib/misc/sample_ids_test.py new file mode 100644 index 0000000000..6d3fb7efd0 --- /dev/null +++ b/loading_pipeline/lib/misc/sample_ids_test.py @@ -0,0 +1,160 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.misc.sample_ids import ( + remap_sample_ids, + subset_samples, +) +from loading_pipeline.lib.misc.validation import SeqrValidationError + +CALLSET_MT = hl.MatrixTable.from_parts( + rows={'variants': [1, 2]}, + cols={'s': ['HG00731', 'HG00732', 'HG00733']}, + entries={ + 'GT': [ + [hl.Call([0, 1]), hl.missing(hl.tcall), hl.Call([0, 1])], + [hl.Call([0, 1]), hl.Call([0, 1]), hl.Call([1, 1])], + ], + }, +).key_cols_by('s') + + +class SampleLookupTest(unittest.TestCase): + def test_remap_2_sample_ids(self) -> None: + # remap 2 of 3 samples in callset + project_remap_ht = hl.Table.parallelize( + [ + {'s': 'HG00731', 'seqr_id': 'HG00731_1'}, + {'s': 'HG00732', 'seqr_id': 'HG00732_1'}, + ], + hl.tstruct( + s=hl.tstr, + seqr_id=hl.tstr, + ), + key='s', + ) + + remapped_mt = remap_sample_ids( + CALLSET_MT, + project_remap_ht, + ) + + self.assertEqual(remapped_mt.cols().count(), 3) + self.assertEqual( + remapped_mt.cols().collect(), + [ + hl.Struct( + col_idx=0, + s='HG00731_1', + seqr_id='HG00731_1', + vcf_id='HG00731', + ), + hl.Struct( + col_idx=1, + s='HG00732_1', + seqr_id='HG00732_1', + vcf_id='HG00732', + ), + hl.Struct(col_idx=2, s='HG00733', seqr_id='HG00733', vcf_id='HG00733'), + ], + ) + + def test_remap_sample_ids_remap_has_duplicate(self) -> None: + # remap file has 2 rows for HG00732 + project_remap_ht = hl.Table.parallelize( + [ + {'s': 'HG00731', 'seqr_id': 'HG00731_1'}, + {'s': 'HG00732', 'seqr_id': 'HG00732_1'}, + {'s': 'HG00732', 'seqr_id': 'HG00732_1'}, # duplicate + ], + hl.tstruct( + s=hl.tstr, + seqr_id=hl.tstr, + ), + key='s', + ) + + with self.assertRaises(SeqrValidationError): + remap_sample_ids( + CALLSET_MT, + project_remap_ht, + ) + + def test_remap_sample_ids_remap_has_missing_samples(self) -> None: + # remap file has 4 rows, but only 3 samples in callset + project_remap_ht = hl.Table.parallelize( + [ + {'s': 'HG00731', 'seqr_id': 'HG00731_1'}, + {'s': 'HG00732', 'seqr_id': 'HG00732_1'}, + {'s': 'HG00733', 'seqr_id': 'HG00733_1'}, + {'s': 'HG00734', 'seqr_id': 'HG00734_1'}, # missing in callset + ], + hl.tstruct( + s=hl.tstr, + seqr_id=hl.tstr, + ), + key='s', + ) + + with self.assertRaises(SeqrValidationError): + remap_sample_ids( + CALLSET_MT, + project_remap_ht, + ) + + def test_subset_samples_zero_samples(self): + # subset 0 of 3 samples in callset + sample_subset_ht = hl.Table.parallelize( + [], + hl.tstruct(s=hl.tstr), + key='s', + ) + + with self.assertRaises(SeqrValidationError): + subset_samples( + CALLSET_MT, + sample_subset_ht, + ) + + def test_subset_samples_missing_samples(self): + # subset 2 of 3 samples in callset, but 1 is missing + sample_subset_ht = hl.Table.parallelize( + [ + {'s': 'HG00731'}, + {'s': 'HG00732'}, + {'s': 'HG00734'}, # missing in callset + ], + hl.tstruct(s=hl.tstr), + key='s', + ) + + with self.assertRaises(SeqrValidationError): + subset_samples( + CALLSET_MT, + sample_subset_ht, + ) + + def test_subset_no_defined_gt(self): + mt = hl.MatrixTable.from_parts( + rows={'variants': [1, 2]}, + cols={'s': ['HG00731', 'HG00732']}, + entries={ + 'GT': [ + [hl.Call([1, 1]), hl.missing(hl.tcall)], + [hl.Call([1, 1]), hl.Call([1, 1])], + ], + }, + ).key_cols_by('s') + sample_subset_ht = hl.Table.parallelize( + [ + {'s': 'HG00732'}, + ], + hl.tstruct(s=hl.tstr), + key='s', + ) + mt = subset_samples( + mt, + sample_subset_ht, + ) + self.assertEqual(mt.count(), (1, 1)) diff --git a/loading_pipeline/lib/misc/sv_test.py b/loading_pipeline/lib/misc/sv_test.py new file mode 100644 index 0000000000..aefa8a5cd5 --- /dev/null +++ b/loading_pipeline/lib/misc/sv_test.py @@ -0,0 +1,243 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, Sex +from loading_pipeline.lib.misc.io import import_callset, select_relevant_fields +from loading_pipeline.lib.misc.pedigree import Family, Sample +from loading_pipeline.lib.misc.sample_ids import subset_samples +from loading_pipeline.lib.misc.sv import ( + deduplicate_merged_sv_concordance_calls, + overwrite_male_non_par_calls, +) + +TEST_SV_VCF = 'loading_pipeline/var/test/callsets/sv_1.vcf' +ANNOTATIONS_HT = hl.Table.parallelize( + [ + { + 'variant_id': 'BND_chr1_6', + 'algorithms': 'manta', + 'end_locus': hl.Locus( + contig='chr5', + position=20404, + reference_genome='GRCh38', + ), + }, + { + 'variant_id': 'BND_chr1_9', + 'algorithms': 'manta', + 'end_locus': hl.Locus( + contig='chr1', + position=789481, + reference_genome='GRCh38', + ), + }, + { + 'variant_id': 'CPX_chr1_22', + 'algorithms': 'manta', + 'end_locus': hl.Locus( + contig='chr1', + position=6559723, + reference_genome='GRCh38', + ), + }, + ], + hl.tstruct( + variant_id=hl.tstr, + algorithms=hl.tstr, + end_locus=hl.tlocus('GRCh38'), + ), + key='variant_id', +) + + +class SVTest(unittest.TestCase): + def test_overwrite_male_non_par_calls(self) -> None: + mt = import_callset(TEST_SV_VCF, ReferenceGenome.GRCh38, DatasetType.SV) + mt = select_relevant_fields( + mt, + DatasetType.SV, + ) + mt = subset_samples( + mt, + hl.Table.parallelize( + [{'s': sample_id} for sample_id in ['RGP_164_1', 'RGP_164_2']], + hl.tstruct(s=hl.dtype('str')), + key='s', + ), + ) + mt = overwrite_male_non_par_calls( + mt, + { + Family( + family_guid='family_1', + samples={ + 'RGP_164_1': Sample(sample_id='RGP_164_1', sex=Sex.FEMALE), + 'RGP_164_2': Sample(sample_id='RGP_164_2', sex=Sex.MALE), + }, + ), + }, + ) + mt = mt.filter_rows(mt.locus.contig == 'chrX') + self.assertEqual( + [ + hl.Locus(contig='chrX', position=3, reference_genome='GRCh38'), + hl.Locus(contig='chrX', position=2781700, reference_genome='GRCh38'), + ], + mt.locus.collect(), + ) + self.assertEqual( + [ + hl.Call(alleles=[0, 0], phased=False), + # END of this variant < start of the non-par region. + hl.Call(alleles=[0, 1], phased=False), + hl.Call(alleles=[0, 0], phased=False), + hl.Call(alleles=[1], phased=False), + ], + mt.GT.collect(), + ) + self.assertFalse( + hasattr(mt, 'start_locus'), + ) + + def test_deduplicate_merged_sv_concordance_calls(self) -> None: + mt = ( + hl.MatrixTable.from_parts( + rows={ + 'variant_id': [ + 'new_v1', + 'new_v2', + 'new_v3', + ], + 'locus': [ + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=2, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=3, + reference_genome='GRCh38', + ), + ], + 'info.END': [ + 1, + 2, + 3, + ], + 'info.END2': [ + 1, + 2, + 3, + ], + 'info.CHR2': [ + 'chr1', + 'chr1', + 'chr1', + ], + 'info.SEQR_INTERNAL_TRUTH_VID': [ + 'BND_chr1_6', + 'BND_chr1_9', + 'CPX_chr1_22', + ], + }, + cols={'s': ['sample_1']}, + entries={'GQ': [[99] for _ in range(3)]}, + ) + .key_rows_by('variant_id') + .key_cols_by('s') + ) + mt = deduplicate_merged_sv_concordance_calls( + mt, + ANNOTATIONS_HT, + ) + self.assertEqual( + mt['info.SEQR_INTERNAL_TRUTH_VID'].collect(), + [ + 'BND_chr1_6', + 'BND_chr1_9', + 'CPX_chr1_22', + ], + ) + + mt = ( + hl.MatrixTable.from_parts( + rows={ + 'variant_id': [ + 'new_v1', + 'new_v2', + 'new_v3', + 'new_v4', + ], + 'locus': [ + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=2, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=3, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=4, + reference_genome='GRCh38', + ), + ], + 'info.END': [ + 1, + 2, + 789481, + 789485, + ], + 'info.END2': [ + 1, + 2, + 789481, + 789485, + ], + 'info.CHR2': [ + 'chr1', + 'chr1', + 'chr2', + 'chr1', + ], + 'info.SEQR_INTERNAL_TRUTH_VID': [ + 'BND_chr1_6', + 'BND_chr1_9', + 'BND_chr1_9', + 'BND_chr1_9', + ], + }, + cols={'s': ['sample_1']}, + entries={'GQ': [[99] for _ in range(4)]}, + ) + .key_rows_by('variant_id') + .key_cols_by('s') + ) + mt = deduplicate_merged_sv_concordance_calls( + mt, + ANNOTATIONS_HT, + ) + self.assertEqual( + mt['info.SEQR_INTERNAL_TRUTH_VID'].collect(), + [ + 'BND_chr1_6', + None, + None, + 'BND_chr1_9', + ], + ) diff --git a/loading_pipeline/lib/misc/terra_data_repository_test.py b/loading_pipeline/lib/misc/terra_data_repository_test.py new file mode 100644 index 0000000000..91b044d68f --- /dev/null +++ b/loading_pipeline/lib/misc/terra_data_repository_test.py @@ -0,0 +1,321 @@ +import json +import os +import unittest +from types import SimpleNamespace +from unittest.mock import Mock, call, patch + +import responses + +from loading_pipeline.lib.misc.terra_data_repository import ( + TDR_ROOT_URL, + _get_dataset_ids, + bq_metrics_query, + gen_bq_table_names, +) + +TDR_DATASETS = [ + { + 'id': '2dc51ee0-a037-499d-a915-a7c20a0b216d', + 'name': 'RP_3053', + 'description': 'TGG_Ware_DRAGEN_hg38. Dataset automatically created and linked to: RP-3053', + 'defaultProfileId': '0a164b9a-2b8b-45d2-859e-a4e369b9cb4f', + 'createdDate': '2023-10-05T13:15:27.649760Z', + 'storage': [ + { + 'region': 'us-central1', + 'cloudResource': 'bigquery', + 'cloudPlatform': 'gcp', + }, + { + 'region': 'us-east4', + 'cloudResource': 'firestore', + 'cloudPlatform': 'gcp', + }, + { + 'region': 'us-central1', + 'cloudResource': 'bucket', + 'cloudPlatform': 'gcp', + }, + ], + 'secureMonitoringEnabled': False, + 'cloudPlatform': 'gcp', + 'dataProject': 'datarepo-7242affb', + 'storageAccount': None, + 'phsId': None, + 'selfHosted': False, + 'predictableFileIds': False, + 'tags': [], + 'resourceLocks': { + 'exclusive': None, + 'shared': [], + }, + }, + { + 'id': 'beef77e8-575b-40e5-9340-a6f10e0bec67', + 'name': 'RP_3056', + 'description': 'RGP_HMB_DRAGEN_hg38. Dataset automatically created and linked to: RP-3056', + 'defaultProfileId': '835dd05d-c603-4b0d-926f-d9143fd24549', + 'createdDate': '2023-10-05T20:15:27.622481Z', + 'storage': [ + { + 'region': 'us-central1', + 'cloudResource': 'bigquery', + 'cloudPlatform': 'gcp', + }, + { + 'region': 'us-east4', + 'cloudResource': 'firestore', + 'cloudPlatform': 'gcp', + }, + { + 'region': 'us-central1', + 'cloudResource': 'bucket', + 'cloudPlatform': 'gcp', + }, + ], + 'secureMonitoringEnabled': False, + 'cloudPlatform': 'gcp', + 'dataProject': 'datarepo-5a72e31b', + 'storageAccount': None, + 'phsId': None, + 'selfHosted': False, + 'predictableFileIds': False, + 'tags': [], + 'resourceLocks': { + 'exclusive': None, + 'shared': [], + }, + }, + { + 'id': 'c8d74ac4-9a2e-4d3d-a6b5-1f4b433d949f', + 'name': 'RP_3055', + 'description': 'RGP_GRU_DRAGEN_hg38. Dataset automatically created and linked to: RP-3055', + 'defaultProfileId': '835dd05d-c603-4b0d-926f-d9143fd24549', + 'createdDate': '2023-10-05T20:15:28.255304Z', + 'storage': [ + { + 'region': 'us-central1', + 'cloudResource': 'bigquery', + 'cloudPlatform': 'gcp', + }, + { + 'region': 'us-east4', + 'cloudResource': 'firestore', + 'cloudPlatform': 'gcp', + }, + { + 'region': 'us-central1', + 'cloudResource': 'bucket', + 'cloudPlatform': 'gcp', + }, + ], + 'secureMonitoringEnabled': False, + 'cloudPlatform': 'gcp', + 'dataProject': 'datarepo-0f5be351', + 'storageAccount': None, + 'phsId': None, + 'selfHosted': False, + 'predictableFileIds': False, + 'tags': [], + 'resourceLocks': { + 'exclusive': None, + 'shared': [ + 'Gw_KTeYRS1aLhRvapMLYLg', + 'WrP-0w1aROOUbgkI8JS6Ug', + ], + }, + }, +] + + +@patch( + 'loading_pipeline.lib.misc.terra_data_repository.get_service_account_credentials', + return_value=SimpleNamespace( + token='abcdefg', # noqa: S106 + ), +) +class TerraDataRepositoryTest(unittest.TestCase): + @responses.activate + def test_get_dataset_ids(self, _: Mock) -> None: + responses.get( + os.path.join(TDR_ROOT_URL, 'datasets?limit=50000'), + body=json.dumps( + { + 'total': 3, + 'filteredTotal': 3, + 'items': TDR_DATASETS, + }, + ), + ) + self.assertListEqual( + _get_dataset_ids(), + [ + '2dc51ee0-a037-499d-a915-a7c20a0b216d', + 'beef77e8-575b-40e5-9340-a6f10e0bec67', + 'c8d74ac4-9a2e-4d3d-a6b5-1f4b433d949f', + ], + ) + + @responses.activate + def test_get_dataset_ids_no_bq(self, _: Mock) -> None: + responses.get( + os.path.join(TDR_ROOT_URL, 'datasets'), + body=json.dumps( + { + 'total': 1, + 'filteredTotal': 1, + 'items': [ + { + 'id': '2dc51ee0-a037-499d-a915-a7c20a0b216d', + 'name': 'RP_3053', + 'description': 'TGG_Ware_DRAGEN_hg38. Dataset automatically created and linked to: RP-3053', + 'defaultProfileId': '0a164b9a-2b8b-45d2-859e-a4e369b9cb4f', + 'createdDate': '2023-10-05T13:15:27.649760Z', + 'storage': [ + # NB: bigquery was removed from 'storage' here. + { + 'region': 'us-east4', + 'cloudResource': 'firestore', + 'cloudPlatform': 'gcp', + }, + { + 'region': 'us-central1', + 'cloudResource': 'bucket', + 'cloudPlatform': 'gcp', + }, + ], + 'secureMonitoringEnabled': False, + 'cloudPlatform': 'gcp', + 'dataProject': 'datarepo-7242affb', + 'storageAccount': None, + 'phsId': None, + 'selfHosted': False, + 'predictableFileIds': False, + 'tags': [], + 'resourceLocks': { + 'exclusive': None, + 'shared': [], + }, + }, + ], + }, + ), + ) + self.assertRaises( + ValueError, + _get_dataset_ids, + ) + + @responses.activate + def test_gen_bq_table_names(self, _: Mock) -> None: + responses.get( + os.path.join(TDR_ROOT_URL, 'datasets'), + body=json.dumps( + { + 'total': 3, + 'filteredTotal': 3, + 'items': TDR_DATASETS, + }, + ), + ) + for dataset_id, name, project_name, dataset_name in [ + ( + '2dc51ee0-a037-499d-a915-a7c20a0b216d', + 'RP_3053', + 'datarepo-7242affb', + 'datarepo_RP_3053', + ), + ( + 'beef77e8-575b-40e5-9340-a6f10e0bec67', + 'RP_3056', + 'datarepo-5a72e31b', + 'datarepo_RP_3056', + ), + ( + 'c8d74ac4-9a2e-4d3d-a6b5-1f4b433d949f', + 'RP_3059', + 'datarepo-aada2e3b', + 'datarepo_RP_3059', + ), + ]: + responses.get( + os.path.join( + TDR_ROOT_URL, + f'datasets/{dataset_id}?include=ACCESS_INFORMATION', + ), + body=json.dumps( + { + 'id': dataset_id, + 'name': name, + 'description': 'TGG_Ware_DRAGEN_hg38. Dataset automatically created and linked to: RP-3053', + 'defaultProfileId': None, + 'dataProject': None, + 'defaultSnapshotId': None, + 'schema': None, + 'createdDate': '2023-10-05T13:15:27.649760Z', + 'storage': None, + 'secureMonitoringEnabled': False, + 'phsId': None, + 'accessInformation': { + 'bigQuery': { + 'datasetName': dataset_name, + 'datasetId': f'{project_name}:{dataset_name}', + 'projectId': project_name, + 'link': 'https://console.cloud.google.com/bigquery?project=datarepo-7242affb&ws=!datarepo_RP_3053&d=datarepo_RP_3053&p=datarepo-7242affb&page=dataset', + 'tables': [ + { + 'name': 'jointcallset', + 'id': f'{project_name}.{dataset_name}.jointcallset', + 'qualifiedName': 'datarepo-7242affb.datarepo_RP_3053.jointcallset', + 'link': 'https://console.cloud.google.com/bigquery?project=datarepo-7242affb&ws=!datarepo_RP_3053&d=datarepo_RP_3053&p=datarepo-7242affb&page=table&t=jointcallset', + 'sampleQuery': 'SELECT * FROM `datarepo-7242affb.datarepo_RP_3053.jointcallset`', + }, + { + 'name': 'sample', + 'id': f'{project_name}.{dataset_name}.sample', + 'qualifiedName': 'datarepo-7242affb.datarepo_RP_3053.sample', + 'link': 'https://console.cloud.google.com/bigquery?project=datarepo-7242affb&ws=!datarepo_RP_3053&d=datarepo_RP_3053&p=datarepo-7242affb&page=table&t=sample', + 'sampleQuery': 'SELECT * FROM `datarepo-7242affb.datarepo_RP_3053.sample`', + }, + ], + }, + 'parquet': None, + }, + 'cloudPlatform': None, + 'selfHosted': False, + 'properties': None, + 'ingestServiceAccount': None, + 'predictableFileIds': False, + 'tags': [], + 'resourceLocks': { + 'exclusive': None, + 'shared': [], + }, + }, + ), + ) + self.assertCountEqual( + list(gen_bq_table_names()), + [ + 'datarepo-7242affb.datarepo_RP_3053', + 'datarepo-5a72e31b.datarepo_RP_3056', + 'datarepo-aada2e3b.datarepo_RP_3059', + ], + ) + + @patch('loading_pipeline.lib.misc.terra_data_repository.bigquery.Client') + def test_bq_metrics_query_missing_metrics( + self, + mock_bq_client: Mock, + _: Mock, + ) -> None: + mock_bq_client.return_value.query_and_wait.return_value = iter( + [['predicted_sex,contamination_rate,percent_bases_at_20x']], + ) + bq_metrics_query('datarepo-7242affb.datarepo_RP_3053') + self.assertEqual( + mock_bq_client.return_value.query_and_wait.mock_calls[1], + call( + '\n SELECT predicted_sex,contamination_rate,percent_bases_at_20x,NULL AS collaborator_sample_id,NULL AS mean_coverage FROM `datarepo-7242affb.datarepo_RP_3053.sample`;\n ', + ), + ) diff --git a/loading_pipeline/lib/misc/validation_test.py b/loading_pipeline/lib/misc/validation_test.py new file mode 100644 index 0000000000..bb368b85a5 --- /dev/null +++ b/loading_pipeline/lib/misc/validation_test.py @@ -0,0 +1,464 @@ +import unittest +from unittest.mock import patch + +import hail as hl + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.misc.validation import ( + SeqrValidationError, + validate_allele_depth_length, + validate_allele_type, + validate_expected_contig_frequency, + validate_imported_field_types, + validate_no_duplicate_variants, + validate_sample_type, +) + +TEST_MITO_MT = 'loading_pipeline/var/test/callsets/mito_1.mt' + + +def _mt_from_contigs(contigs): + return ( + hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig=contig, + position=1, + reference_genome='GRCh38', + ) + for contig in contigs + ], + }, + cols={'s': ['sample_1']}, + entries={'HL': [[0.0] for _ in range(len(contigs))]}, + ) + .key_rows_by('locus') + .key_cols_by('s') + ) + + +class ValidationTest(unittest.TestCase): + def test_validate_allele_type(self) -> None: + mt = ( + hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=2, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=3, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=4, + reference_genome='GRCh38', + ), + ], + 'alleles': [ + ['A', 'T'], + # NB: star alleles should pass through this validation just fine, + # but are eventually filtered out upstream. + ['A', '*'], + ['A', '-'], + ['A', ''], + ], + }, + cols={'s': ['sample_1']}, + entries={'HL': [[0.0], [0.0], [0.0], [0.0]]}, + ) + .key_rows_by('locus', 'alleles') + .key_cols_by('s') + ) + self.assertRaisesRegex( + SeqrValidationError, + "Alleles with invalid AlleleType are present in the callset: \\[\\('A', '-'\\), \\('A', ''\\)\\]", + validate_allele_type, + mt, + DatasetType.SNV_INDEL, + ) + + mt = ( + hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=2, + reference_genome='GRCh38', + ), + ], + 'alleles': [ + ['C', ''], + ['A', ''], + ], + }, + cols={'s': ['sample_1']}, + entries={'HL': [[0.0], [0.0]]}, + ) + .key_rows_by('locus', 'alleles') + .key_cols_by('s') + ) + self.assertRaisesRegex( + SeqrValidationError, + 'Alleles with invalid allele are present in the callset. This appears to be a GVCF containing records for sites with no variants.', + validate_allele_type, + mt, + DatasetType.SNV_INDEL, + ) + + def test_validate_allele_depth_length(self) -> None: + mt = ( + hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=2, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=3, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=4, + reference_genome='GRCh38', + ), + ], + 'alleles': [ + ['A', 'T'], + # NB: star alleles should pass through this validation just fine, + # but are eventually filtered out upstream. + ['A', 'TC', 'TG'], + ['A', 'TTT'], + ['A', 'CCC'], + ], + }, + cols={'s': ['sample_1', 'sample_2']}, + entries={ + 'AD': [ + [[1, 0], [1, 0]], + [[1], [1, 0, 1]], + [[1, 0], [1]], + [[1, 0], [1, 0]], + ], + }, + ) + .key_rows_by('locus', 'alleles') + .key_cols_by('s') + ) + self.assertRaisesRegex( + SeqrValidationError, + "Found variants with unequal Allele Depth array lengths over samples \\(first 10, if applicable\\): \\{'1-2-A-TC-TG': \\{1, 3\\}, '1-3-A-TTT': \\{1, 2\\}\\}", + validate_allele_depth_length, + mt, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + ) + + def test_validate_imported_field_types(self) -> None: + mt = hl.read_matrix_table(TEST_MITO_MT) + validate_imported_field_types(mt, DatasetType.MITO, {}) + mt = mt.annotate_cols(contamination=hl.int32(mt.contamination)) + mt = mt.annotate_entries(DP=hl.float32(mt.DP)) + mt = mt.annotate_rows(vep=hl.dict({'t': '1'})) + self.assertRaisesRegex( + SeqrValidationError, + "Found unexpected field types on MatrixTable after import: \\['contamination: int32', 'DP: float32', 'vep: dict', 'tester: missing'\\]", + validate_imported_field_types, + mt, + DatasetType.MITO, + {'tester': hl.tfloat32}, + ) + + def test_validate_no_duplicate_variants(self) -> None: + mt = ( + hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=2, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=2, + reference_genome='GRCh38', + ), + ], + 'alleles': [ + ['A', 'C'], + ['A', 'C'], + ['A', 'C'], + ], + }, + cols={'s': ['sample_1']}, + entries={'HL': [[0.0], [0.0], [0.0]]}, + ) + .key_rows_by('locus', 'alleles') + .key_cols_by('s') + ) + self.assertRaisesRegex( + SeqrValidationError, + "Variants are present multiple times in the callset: \\['1-2-A-C'\\]", + validate_no_duplicate_variants, + mt, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + ) + + def test_validate_expected_contig_frequency(self) -> None: + mt = _mt_from_contigs(ReferenceGenome.GRCh38.standard_contigs) + self.assertIsNone( + validate_expected_contig_frequency(mt, ReferenceGenome.GRCh38, 1), + ) + self.assertRaisesRegex( + SeqrValidationError, + 'Missing the following expected contigs', + validate_expected_contig_frequency, + mt, + ReferenceGenome.GRCh37, + 1, + ) + self.assertRaisesRegex( + SeqrValidationError, + 'which is lower than expected minimum count', + validate_expected_contig_frequency, + mt, + ReferenceGenome.GRCh38, + 2, + ) + + # Drop an optional contig + mt = _mt_from_contigs(ReferenceGenome.GRCh38.standard_contigs - {'chrY'}) + self.assertIsNone( + validate_expected_contig_frequency(mt, ReferenceGenome.GRCh38, 1), + ) + + # Drop a non-optional contig + mt = _mt_from_contigs(ReferenceGenome.GRCh38.standard_contigs - {'chr3'}) + self.assertRaisesRegex( + SeqrValidationError, + 'Missing the following expected contigs', + validate_expected_contig_frequency, + mt, + ReferenceGenome.GRCh38, + 1, + ) + + def test_validate_sample_type(self) -> None: + mt = _mt_from_contigs(ReferenceGenome.GRCh38.standard_contigs) + coding_and_noncoding_variants_ht = hl.Table.parallelize( + [ + { + 'locus': hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + 'coding': True, + 'noncoding': False, + }, + { + 'locus': hl.Locus( + contig='chr2', + position=1, + reference_genome='GRCh38', + ), + 'coding': True, + 'noncoding': False, + }, + { + 'locus': hl.Locus( + contig='chr3', + position=1, + reference_genome='GRCh38', + ), + 'coding': False, + 'noncoding': True, + }, + { + 'locus': hl.Locus( + contig='chr4', + position=1, + reference_genome='GRCh38', + ), + 'coding': False, + 'noncoding': True, + }, + ], + hl.tstruct( + locus=hl.tlocus('GRCh38'), + coding=hl.tbool, + noncoding=hl.tbool, + ), + key='locus', + ) + self.assertIsNone( + validate_sample_type( + mt, + ReferenceGenome.GRCh38, + SampleType.WGS, + ['project_a'], + coding_and_noncoding_variants_ht, + ), + ) + self.assertRaisesRegex( + SeqrValidationError, + 'specified as WES but appears to be WGS', + validate_sample_type, + mt, + ReferenceGenome.GRCh38, + SampleType.WES, + ['project_a'], + coding_and_noncoding_variants_ht, + ) + + # has coding, but not noncoding now. + coding_and_noncoding_variants_ht = hl.Table.parallelize( + [ + { + 'locus': hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + 'coding': True, + 'noncoding': False, + }, + { + 'locus': hl.Locus( + contig='chr2', + position=1, + reference_genome='GRCh38', + ), + 'coding': True, + 'noncoding': False, + }, + { + 'locus': hl.Locus( + contig='chr2', + position=2, + reference_genome='GRCh38', + ), + 'coding': False, + 'noncoding': True, + }, + ], + hl.tstruct( + locus=hl.tlocus('GRCh38'), + coding=hl.tbool, + noncoding=hl.tbool, + ), + key='locus', + ) + self.assertIsNone( + validate_sample_type( + mt, + ReferenceGenome.GRCh38, + SampleType.WES, + ['project_a'], + coding_and_noncoding_variants_ht, + ), + ) + self.assertRaisesRegex( + SeqrValidationError, + 'specified as WGS but appears to be WES', + validate_sample_type, + mt, + ReferenceGenome.GRCh38, + SampleType.WGS, + ['project_a'], + coding_and_noncoding_variants_ht, + ) + + # has noncoding, but not coding now. + coding_and_noncoding_variants_ht = hl.Table.parallelize( + [ + { + 'locus': hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + 'coding': False, + 'noncoding': True, + }, + { + 'locus': hl.Locus( + contig='chr2', + position=1, + reference_genome='GRCh38', + ), + 'coding': False, + 'noncoding': True, + }, + { + 'locus': hl.Locus( + contig='chr2', + position=2, + reference_genome='GRCh38', + ), + 'coding': True, + 'noncoding': False, + }, + ], + hl.tstruct( + locus=hl.tlocus('GRCh38'), + coding=hl.tbool, + noncoding=hl.tbool, + ), + key='locus', + ) + self.assertRaisesRegex( + SeqrValidationError, + 'contains noncoding variants but is missing common coding variants', + validate_sample_type, + mt, + ReferenceGenome.GRCh38, + SampleType.WGS, + ['project_a'], + coding_and_noncoding_variants_ht, + ) + + # Validation safe if all projects are to be skipped + with patch('loading_pipeline.lib.misc.validation.Env') as mock_env: + mock_env.SAMPLE_TYPE_VALIDATION_EXCLUDED_PROJECTS = ['project_a'] + self.assertIsNone( + validate_sample_type( + mt, + ReferenceGenome.GRCh38, + SampleType.WGS, + ['project_a'], + coding_and_noncoding_variants_ht, + ), + ) diff --git a/loading_pipeline/lib/misc/vets_test.py b/loading_pipeline/lib/misc/vets_test.py new file mode 100644 index 0000000000..b26de113b7 --- /dev/null +++ b/loading_pipeline/lib/misc/vets_test.py @@ -0,0 +1,104 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.misc.io import split_multi_hts +from loading_pipeline.lib.misc.vets import ( + annotate_vets, +) + + +class VetsTest(unittest.TestCase): + def test_annotate_vets(self) -> None: + gatk_mt = hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + ], + 'filters': [ + hl.set(['NO_HQ_GENOTYPES']), + ], + }, + cols={'s': ['sample_1']}, + entries={'HL': [[0.0]]}, + ).key_rows_by('locus') + gatk_mt = annotate_vets(gatk_mt) + dragen_mt = hl.MatrixTable.from_parts( + rows={ + 'locus': [ + hl.Locus( + contig='chr1', + position=1, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=2, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=3, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=4, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=5, + reference_genome='GRCh38', + ), + hl.Locus( + contig='chr1', + position=6, + reference_genome='GRCh38', + ), + ], + 'alleles': [ + ['A', 'T'], + ['A', 'T'], + ['A', 'T'], + ['AC', 'T'], + ['AT', 'ATC'], + ['AG', 'ATG'], + ], + 'filters': [ + hl.set(['NO_HQ_GENOTYPES']), + hl.empty_set(hl.tstr), + hl.missing(hl.tset(hl.tstr)), + hl.set(['NO_HQ_GENOTYPES']), + hl.empty_set(hl.tstr), + hl.set(['NO_HQ_GENOTYPES']), + ], + 'info.CALIBRATION_SENSITIVITY': [ + ['0.999'], + ['0.995'], + ['0.999'], + ['0.98'], + ['0.99'], + ['0.991'], + ], + }, + cols={'s': ['sample_1']}, + entries={'HL': [[0.0], [0.0], [0.0], [0.0], [0.0], [0.0]]}, + ).key_rows_by('locus', 'alleles') + dragen_mt = split_multi_hts(dragen_mt, False) + dragen_mt = annotate_vets(dragen_mt) + self.assertListEqual( + dragen_mt.filters.collect(), + [ + {'NO_HQ_GENOTYPES', 'high_CALIBRATION_SENSITIVITY_SNP'}, + set(), + {'high_CALIBRATION_SENSITIVITY_SNP'}, + {'NO_HQ_GENOTYPES'}, + set(), + {'NO_HQ_GENOTYPES', 'high_CALIBRATION_SENSITIVITY_INDEL'}, + ], + ) diff --git a/loading_pipeline/lib/paths_test.py b/loading_pipeline/lib/paths_test.py new file mode 100644 index 0000000000..d271cfee0b --- /dev/null +++ b/loading_pipeline/lib/paths_test.py @@ -0,0 +1,180 @@ +import unittest +from unittest.mock import patch + +import hailtop.fs as hfs + +from loading_pipeline.lib.core import ( + DatasetType, + ReferenceGenome, + SampleType, +) +from loading_pipeline.lib.paths import ( + imported_callset_path, + metadata_for_run_path, + new_variants_table_path, + project_pedigree_path, + project_table_path, + relatedness_check_table_path, + remapped_and_subsetted_callset_path, + sex_check_table_path, + tdr_metrics_path, + validation_errors_for_run_path, + variant_annotations_table_path, +) + +TEST_VCF = 'loading_pipeline/var/test/callsets/1kg_30varia*.vcf' + + +class TestPaths(unittest.TestCase): + def test_project_table_path(self) -> None: + self.assertEqual( + project_table_path( + ReferenceGenome.GRCh38, + DatasetType.MITO, + SampleType.WES, + 'R0652_pipeline_test', + ), + '/var/seqr/pipeline-data/GRCh38/MITO/projects/WES/R0652_pipeline_test.ht', + ) + with ( + patch('loading_pipeline.lib.paths.Env') as mock_env, + ): + mock_env.PIPELINE_DATA_DIR = '/var/bucket/' + self.assertEqual( + project_table_path( + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + SampleType.WES, + 'R0652_pipeline_test', + ), + '/var/bucket/GRCh37/SNV_INDEL/projects/WES/R0652_pipeline_test.ht', + ) + + def test_sex_check_table_path(self) -> None: + self.assertEqual( + sex_check_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + '/var/abc.efg/callset.vcf.gz', + ), + '/var/seqr/seqr-loading-temp/GRCh38/SNV_INDEL/sex_check/f92b8ab6b5b8c41fa20d7d49a5626b96dcd2ba79fa6f61eab7ffb80d550d951c.ht', + ) + + def test_relatedness_check_table_path(self) -> None: + self.assertEqual( + relatedness_check_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + '/var/abc.efg/callset.vcf.gz', + ), + '/var/seqr/seqr-loading-temp/GRCh38/SNV_INDEL/relatedness_check/f92b8ab6b5b8c41fa20d7d49a5626b96dcd2ba79fa6f61eab7ffb80d550d951c.ht', + ) + + def test_validation_errors_for_run_path(self) -> None: + self.assertEqual( + validation_errors_for_run_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + 'manual__2023-06-26T18:30:09.349671+00:00', + ), + '/var/seqr/pipeline-data/GRCh38/SNV_INDEL/runs/manual__2023-06-26T18:30:09.349671+00:00/validation_errors.json', + ) + + def test_metadata_for_run_path(self) -> None: + self.assertEqual( + metadata_for_run_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + 'manual__2023-06-26T18:30:09.349671+00:00', + ), + '/var/seqr/pipeline-data/GRCh38/SNV_INDEL/runs/manual__2023-06-26T18:30:09.349671+00:00/metadata.json', + ) + + def test_variant_annotations_table_path(self) -> None: + self.assertEqual( + variant_annotations_table_path( + ReferenceGenome.GRCh38, + DatasetType.GCNV, + ), + '/var/seqr/pipeline-data/GRCh38/GCNV/annotations.ht', + ) + + def test_remapped_and_subsetted_callset_path(self) -> None: + self.assertEqual( + remapped_and_subsetted_callset_path( + ReferenceGenome.GRCh38, + DatasetType.GCNV, + '/var/abc.efg/callset.vcf.gz', + 'R0111_tgg_bblanken_wes', + ), + '/var/seqr/seqr-loading-temp/GRCh38/GCNV/remapped_and_subsetted_callsets/R0111_tgg_bblanken_wes/f92b8ab6b5b8c41fa20d7d49a5626b96dcd2ba79fa6f61eab7ffb80d550d951c.mt', + ) + self.assertEqual( + remapped_and_subsetted_callset_path( + ReferenceGenome.GRCh38, + DatasetType.GCNV, + '/var/abc.efg/callset/*.vcf.gz', + 'R0111_tgg_bblanken_wes', + ), + '/var/seqr/seqr-loading-temp/GRCh38/GCNV/remapped_and_subsetted_callsets/R0111_tgg_bblanken_wes/26f481b386721f9889250c6549905660728ec9f77be4b8f7eeb6c4facc76282e.mt', + ) + + def test_imported_callset_path(self) -> None: + self.assertEqual( + imported_callset_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + '/var/abc.efg/callset.vcf.gz', + ), + '/var/seqr/seqr-loading-temp/GRCh38/SNV_INDEL/imported_callsets/f92b8ab6b5b8c41fa20d7d49a5626b96dcd2ba79fa6f61eab7ffb80d550d951c.mt', + ) + + with patch('loading_pipeline.lib.paths.hfs.ls') as mock_ls: + mock_ls.return_value = [ + hfs.stat_result.FileListEntry( + path='loading_pipeline/var/test/callsets/1kg_30variants.vcf', + owner=None, + size=1732033623.804012, + typ=hfs.stat_result.FileType(2), + modification_time=1732033000, + ), + ] + self.assertEqual( + imported_callset_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_VCF, + ), + '/var/seqr/seqr-loading-temp/GRCh38/SNV_INDEL/imported_callsets/01327e46c8747f15feaad2c08875b928c274dcb248ad40837ea3f49d8b4dedfb.mt', + ) + + def test_tdr_metrics_path(self) -> None: + self.assertEqual( + tdr_metrics_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + 'datarepo-7242affb.datarepo_RP_3053', + ), + '/var/seqr/seqr-loading-temp/GRCh38/SNV_INDEL/tdr_metrics/datarepo-7242affb.datarepo_RP_3053.tsv', + ) + + def test_new_variants_table_path(self) -> None: + self.assertEqual( + new_variants_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + 'manual__2023-06-26T18:30:09.349671+00:00', + ), + '/var/seqr/pipeline-data/GRCh38/SNV_INDEL/runs/manual__2023-06-26T18:30:09.349671+00:00/new_variants.ht', + ) + + def test_project_pedigree_path(self) -> None: + self.assertEqual( + project_pedigree_path( + ReferenceGenome.GRCh38, + DatasetType.GCNV, + SampleType.WES, + 'R0652_pipeline_test', + ), + '/var/seqr/seqr-loading-temp/GRCh38/GCNV/pedigrees/WES/R0652_pipeline_test_pedigree.tsv', + ) diff --git a/loading_pipeline/lib/reference_datasets/gnomad_exomes_test.py b/loading_pipeline/lib/reference_datasets/gnomad_exomes_test.py new file mode 100644 index 0000000000..639dc6d894 --- /dev/null +++ b/loading_pipeline/lib/reference_datasets/gnomad_exomes_test.py @@ -0,0 +1,72 @@ +import unittest +from unittest.mock import patch + +import hail as hl + +from loading_pipeline.lib.core.definitions import ReferenceGenome +from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset + +GNOMAD_EXOMES_37_PATH = ( + 'loading_pipeline/var/test/reference_datasets/raw/gnomad_exomes_37.ht' +) +GNOMAD_EXOMES_38_PATH = ( + 'loading_pipeline/var/test/reference_datasets/raw/gnomad_exomes_38.ht' +) + + +class GnomadTest(unittest.TestCase): + def test_gnomad_exomes_37(self): + with patch.object( + ReferenceDataset, + 'path', + return_value=GNOMAD_EXOMES_37_PATH, + ): + ht = ReferenceDataset.gnomad_exomes.get_ht(ReferenceGenome.GRCh37) + self.assertEqual( + ht.collect(), + [ + hl.Struct( + locus=hl.Locus( + contig='1', + position=12586, + reference_genome='GRCh37', + ), + alleles=['C', 'T'], + AF=0.0005589714855886996, + AN=3578, + AC=2, + Hom=0, + AF_POPMAX_OR_GLOBAL=0.0022026430815458298, + FAF_AF=9.839000267675146e-05, + Hemi=0, + ), + ], + ) + + def test_gnomad_exomes_38(self): + with patch.object( + ReferenceDataset, + 'path', + return_value=GNOMAD_EXOMES_38_PATH, + ): + ht = ReferenceDataset.gnomad_exomes.get_ht(ReferenceGenome.GRCh38) + self.assertEqual( + ht.collect(), + [ + hl.Struct( + locus=hl.Locus( + contig='chr1', + position=12138, + reference_genome='GRCh38', + ), + alleles=['C', 'A'], + AF=0.00909090880304575, + AN=110, + AC=1, + Hom=0, + AF_POPMAX_OR_GLOBAL=0.009803921915590763, + FAF_AF=0.0, + Hemi=0, + ), + ], + ) diff --git a/loading_pipeline/lib/reference_datasets/gnomad_genomes_test.py b/loading_pipeline/lib/reference_datasets/gnomad_genomes_test.py new file mode 100644 index 0000000000..df637c2fda --- /dev/null +++ b/loading_pipeline/lib/reference_datasets/gnomad_genomes_test.py @@ -0,0 +1,72 @@ +import unittest +from unittest.mock import patch + +import hail as hl + +from loading_pipeline.lib.core.definitions import ReferenceGenome +from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset + +GNOMAD_GENOMES_37_PATH = ( + 'loading_pipeline/var/test/reference_datasets/raw/gnomad_genomes_37.ht' +) +GNOMAD_GENOMES_38_PATH = ( + 'loading_pipeline/var/test/reference_datasets/raw/gnomad_genomes_38.ht' +) + + +class GnomadTest(unittest.TestCase): + def test_gnomad_genomes_37(self): + with patch.object( + ReferenceDataset, + 'path', + return_value=GNOMAD_GENOMES_37_PATH, + ): + ht = ReferenceDataset.gnomad_genomes.get_ht(ReferenceGenome.GRCh37) + self.assertEqual( + ht.collect(), + [ + hl.Struct( + locus=hl.Locus( + contig='1', + position=10131, + reference_genome='GRCh37', + ), + alleles=['CT', 'C'], + AF=3.6635403375839815e-05, + AN=27296, + AC=1, + Hom=0, + AF_POPMAX_OR_GLOBAL=3.6635403375839815e-05, + FAF_AF=0.0, + Hemi=0, + ), + ], + ) + + def test_gnomad_genomes_38(self): + with patch.object( + ReferenceDataset, + 'path', + return_value=GNOMAD_GENOMES_38_PATH, + ): + ht = ReferenceDataset.gnomad_genomes.get_ht(ReferenceGenome.GRCh38) + self.assertEqual( + ht.collect(), + [ + hl.Struct( + locus=hl.Locus( + contig='chr1', + position=10057, + reference_genome='GRCh38', + ), + alleles=['A', 'C'], + AF=2.642333674884867e-05, + AN=113536, + AC=3, + Hom=0, + AF_POPMAX_OR_GLOBAL=3.779861071961932e-05, + FAF_AF=7.019999884505523e-06, + Hemi=0, + ), + ], + ) diff --git a/loading_pipeline/lib/reference_datasets/gnomad_svs_test.py b/loading_pipeline/lib/reference_datasets/gnomad_svs_test.py new file mode 100644 index 0000000000..bfd7c89d11 --- /dev/null +++ b/loading_pipeline/lib/reference_datasets/gnomad_svs_test.py @@ -0,0 +1,93 @@ +import unittest +from unittest.mock import patch + +import hail as hl + +from loading_pipeline.lib.core import ReferenceGenome +from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset + +TEST_GNOMAD_SVS_RAW_HT = ( + 'loading_pipeline/var/test/reference_datasets/raw/gnomad_svs_from_vcf.ht' +) + + +class GnomadSVsTest(unittest.TestCase): + @patch('loading_pipeline.lib.reference_datasets.gnomad_svs.vcf_to_ht') + def test_gnomad_svs(self, mock_vcf_to_ht): + mock_vcf_to_ht.return_value = hl.read_table(TEST_GNOMAD_SVS_RAW_HT) + ht = ReferenceDataset.gnomad_svs.get_ht(ReferenceGenome.GRCh38) + self.assertEqual( + ht.collect(), + [ + hl.Struct( + KEY='gnomAD-SV_v3_BND_chr1_1a45f73a', + locus=hl.Locus( + contig='chr1', + position=10434, + reference_genome=ReferenceGenome.GRCh38, + ), + alleles=['N', ''], + AF=0.11413399875164032, + AC=8474, + AN=74246, + N_HET=8426, + N_HOM=24, + ), + hl.Struct( + KEY='gnomAD-SV_v3_BND_chr1_3fa36917', + locus=hl.Locus( + contig='chr1', + position=10440, + reference_genome=ReferenceGenome.GRCh38, + ), + alleles=['N', ''], + AF=0.004201000090688467, + AC=466, + AN=110936, + N_HET=466, + N_HOM=0, + ), + hl.Struct( + KEY='gnomAD-SV_v3_BND_chr1_7bbf34b5', + locus=hl.Locus( + contig='chr1', + position=10464, + reference_genome=ReferenceGenome.GRCh38, + ), + alleles=['N', ''], + AF=0.03698499873280525, + AC=3119, + AN=84332, + N_HET=3115, + N_HOM=2, + ), + hl.Struct( + KEY='gnomAD-SV_v3_BND_chr1_933a2971', + locus=hl.Locus( + contig='chr1', + position=10450, + reference_genome=ReferenceGenome.GRCh38, + ), + alleles=['N', ''], + AF=0.3238990008831024, + AC=21766, + AN=67200, + N_HET=21616, + N_HOM=75, + ), + hl.Struct( + KEY='gnomAD-SV_v3_DUP_chr1_01c2781c', + locus=hl.Locus( + contig='chr1', + position=10000, + reference_genome=ReferenceGenome.GRCh38, + ), + alleles=['N', ''], + AF=0.0019970000721514225, + AC=139, + AN=69594, + N_HET=139, + N_HOM=0, + ), + ], + ) diff --git a/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster_test.py b/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster_test.py new file mode 100644 index 0000000000..6634feea8c --- /dev/null +++ b/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster_test.py @@ -0,0 +1,162 @@ +import unittest +from types import SimpleNamespace +from unittest.mock import Mock, call, patch + +import google.api_core.exceptions +import google.cloud.dataproc_v1.types.clusters +import luigi + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome +from loading_pipeline.lib.misc.gcp import SOCIAL_AUTH_GOOGLE_OAUTH2_SCOPE +from loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster import ( + CreateDataprocClusterTask, +) + + +@patch.multiple( + 'loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster.Env', + GCLOUD_PROJECT='proj', + GCLOUD_REGION='us-a', +) +@patch( + 'loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster.get_service_account_credentials', + return_value=SimpleNamespace( + service_account_email='test@serviceaccount.com', + scopes=SOCIAL_AUTH_GOOGLE_OAUTH2_SCOPE, + ), +) +@patch( + 'loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster.dataproc.ClusterControllerClient', +) +class CreateDataprocClusterTaskTest(unittest.TestCase): + def test_spinup_cluster_already_exists_failed( + self, + mock_cluster_controller: Mock, + *_: Mock, + ) -> None: + mock_client = mock_cluster_controller.return_value + mock_client.get_cluster.return_value = SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.ERROR, + ), + cluster_name='abc', + ) + mock_client.create_cluster.side_effect = ( + google.api_core.exceptions.AlreadyExists('cluster exists') + ) + worker = luigi.worker.Worker() + task = CreateDataprocClusterTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id='2', + ) + worker.add(task) + worker.run() + self.assertFalse(task.complete()) + + def test_spinup_cluster_already_exists_success( + self, + mock_cluster_controller: Mock, + *_: Mock, + ) -> None: + mock_client = mock_cluster_controller.return_value + mock_client.get_cluster.return_value = SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.RUNNING, + ), + ) + mock_client.create_cluster.side_effect = ( + google.api_core.exceptions.AlreadyExists('cluster exists') + ) + worker = luigi.worker.Worker() + task = CreateDataprocClusterTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id='3', + ) + worker.add(task) + worker.run() + self.assertTrue(task.complete()) + + @patch('loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster.logger') + def test_spinup_cluster_doesnt_exist_failed( + self, + mock_logger: Mock, + mock_cluster_controller: Mock, + *_: Mock, + ) -> None: + mock_client = mock_cluster_controller.return_value + mock_client.get_cluster.side_effect = [ + google.api_core.exceptions.NotFound( + 'cluster not found', + ), + google.api_core.exceptions.NotFound( + 'cluster not found', + ), + SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.CREATING, + ), + ), + SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.ERROR, + ), + cluster_name='dataproc-cluster-5', + cluster_uuid='12345', + ), + ] + worker = luigi.worker.Worker() + task = CreateDataprocClusterTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id='4', + ) + worker.add(task) + luigi_task_result = worker.run() + self.assertEqual(luigi_task_result, False) + mock_logger.info.assert_has_calls([call('Waiting for cluster spinup')]) + + @patch('loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster.logger') + def test_spinup_cluster_doesnt_exist_success( + self, + mock_logger: Mock, + mock_cluster_controller: Mock, + *_: Mock, + ) -> None: + mock_client = mock_cluster_controller.return_value + mock_client.get_cluster.side_effect = [ + google.api_core.exceptions.NotFound( + 'cluster not found', + ), + google.api_core.exceptions.NotFound( + 'cluster not found', + ), + SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.CREATING, + ), + ), + SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.RUNNING, + ), + cluster_name='dataproc-cluster-5', + cluster_uuid='12345', + ), + ] + mock_client.create_cluster.side_effect = None + worker = luigi.worker.Worker() + task = CreateDataprocClusterTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id='5', + ) + worker.add(task) + worker.run() + mock_logger.info.assert_has_calls( + [ + call('Waiting for cluster spinup'), + call('Created cluster dataproc-cluster-5 with cluster uuid: 12345'), + ], + ) diff --git a/loading_pipeline/lib/tasks/dataproc/misc_test.py b/loading_pipeline/lib/tasks/dataproc/misc_test.py new file mode 100644 index 0000000000..63ffafb8a1 --- /dev/null +++ b/loading_pipeline/lib/tasks/dataproc/misc_test.py @@ -0,0 +1,51 @@ +import unittest +from unittest.mock import Mock, patch + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.tasks.dataproc.misc import to_kebab_str_args +from loading_pipeline.lib.tasks.dataproc.run_pipeline_on_dataproc import ( + RunPipelineOnDataprocTask, +) + + +@patch( + 'loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc.dataproc.JobControllerClient', +) +class MiscTest(unittest.TestCase): + def test_to_kebab_str_args(self, _: Mock): + t = RunPipelineOnDataprocTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path='test_callset', + project_guids=['R0113_test_project'], + run_id='a_misc_run', + attempt_id=0, + ) + self.assertListEqual( + to_kebab_str_args(t), + [ + '--reference-genome', + 'GRCh38', + '--dataset-type', + 'SNV_INDEL', + '--sample-type', + 'WGS', + '--callset-path', + 'test_callset', + '--project-guids', + '["R0113_test_project"]', + '--skip-check-sex-and-relatedness', + 'False', + '--skip-expect-tdr-metrics', + 'False', + '--validations-to-skip', + '[]', + '--is-new-gcnv-joint-call', + 'False', + '--run-id', + 'a_misc_run', + '--attempt-id', + '0', + ], + ) diff --git a/loading_pipeline/lib/tasks/dataproc/run_pipeline_on_dataproc_test.py b/loading_pipeline/lib/tasks/dataproc/run_pipeline_on_dataproc_test.py new file mode 100644 index 0000000000..a09289a85a --- /dev/null +++ b/loading_pipeline/lib/tasks/dataproc/run_pipeline_on_dataproc_test.py @@ -0,0 +1,184 @@ +import unittest +from types import SimpleNamespace +from unittest.mock import Mock, call, patch + +import google.api_core.exceptions +import google.cloud.dataproc_v1.types.jobs +import luigi + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.tasks.dataproc.run_pipeline_on_dataproc import ( + RunPipelineOnDataprocTask, +) +from loading_pipeline.lib.test.mock_complete_task import MockCompleteTask + + +@patch( + 'loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc.CreateDataprocClusterTask', +) +@patch( + 'loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc.dataproc.JobControllerClient', +) +class WriteSuccessFileOnDataprocTaskTest(unittest.TestCase): + @patch('loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc.logger') + def test_job_already_exists_failed( + self, + mock_logger: Mock, + mock_job_controller_client: Mock, + mock_create_dataproc_cluster: Mock, + ) -> None: + mock_create_dataproc_cluster.return_value = MockCompleteTask() + mock_client = mock_job_controller_client.return_value + mock_client.get_job.return_value = SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.jobs.JobStatus.State.ERROR, + details='Google Cloud Dataproc Agent reports job failure. If logs are available, they can be found at...', + ), + ) + mock_client.submit_job_as_operation.side_effect = ( + google.api_core.exceptions.AlreadyExists('job exists') + ) + worker = luigi.worker.Worker() + task = RunPipelineOnDataprocTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path='test_callset', + project_guids=['R0113_test_project'], + run_id='manual__2024-04-03', + attempt_id=0, + ) + worker.add(task) + worker.run() + self.assertFalse(task.complete()) + mock_logger.error.assert_has_calls( + [ + call( + 'Job RunPipelineTask-38-SNV-INDEL-manual__2024-04-03-0 entered ERROR state', + ), + ], + ) + + def test_job_already_exists_success( + self, + mock_job_controller_client: Mock, + mock_create_dataproc_cluster: Mock, + ) -> None: + mock_create_dataproc_cluster.return_value = MockCompleteTask() + mock_client = mock_job_controller_client.return_value + mock_client.get_job.return_value = SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.jobs.JobStatus.State.DONE, + ), + ) + worker = luigi.worker.Worker() + task = RunPipelineOnDataprocTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path='test_callset', + project_guids=['R0113_test_project'], + run_id='manual__2024-04-04', + attempt_id=0, + ) + worker.add(task) + worker.run() + self.assertTrue(task.complete()) + + @patch('loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc.logger') + def test_job_failed( + self, + mock_logger: Mock, + mock_job_controller_client: Mock, + mock_create_dataproc_cluster: Mock, + ) -> None: + mock_create_dataproc_cluster.return_value = MockCompleteTask() + mock_client = mock_job_controller_client.return_value + mock_client.get_job.side_effect = [ + google.api_core.exceptions.NotFound( + 'job not found', + ), + google.api_core.exceptions.NotFound( + 'job not found', + ), + SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.jobs.JobStatus.State.PENDING, + ), + ), + SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.jobs.JobStatus.State.ERROR, + ), + ), + ] + worker = luigi.worker.Worker() + task = RunPipelineOnDataprocTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path='test_callset', + project_guids=['R0113_test_project'], + run_id='manual__2024-04-05', + attempt_id=1, + ) + worker.add(task) + luigi_task_result = worker.run() + self.assertEqual(luigi_task_result, False) + mock_logger.info.assert_has_calls( + [ + call( + 'Waiting for Job completion RunPipelineTask-38-SNV-INDEL-manual__2024-04-05-1', + ), + ], + ) + + @patch('loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc.logger') + def test_job_success( + self, + mock_logger: Mock, + mock_job_controller_client: Mock, + mock_create_dataproc_cluster: Mock, + ) -> None: + mock_create_dataproc_cluster.return_value = MockCompleteTask() + mock_client = mock_job_controller_client.return_value + mock_client.get_job.side_effect = [ + google.api_core.exceptions.NotFound( + 'job not found', + ), + google.api_core.exceptions.NotFound( + 'job not found', + ), + SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.jobs.JobStatus.State.PENDING, + ), + ), + SimpleNamespace( + status=SimpleNamespace( + state=google.cloud.dataproc_v1.types.jobs.JobStatus.State.DONE, + ), + ), + ] + worker = luigi.worker.Worker() + task = RunPipelineOnDataprocTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path='test_callset', + project_guids=['R0113_test_project'], + run_id='manual__2024-04-06', + attempt_id=0, + ) + worker.add(task) + worker.run() + mock_logger.info.assert_has_calls( + [ + call( + 'Waiting for Job completion RunPipelineTask-38-SNV-INDEL-manual__2024-04-06-0', + ), + call( + 'Job RunPipelineTask-38-SNV-INDEL-manual__2024-04-06-0 is complete', + ), + ], + ) diff --git a/loading_pipeline/lib/tasks/exports/misc_test.py b/loading_pipeline/lib/tasks/exports/misc_test.py new file mode 100644 index 0000000000..f0324db627 --- /dev/null +++ b/loading_pipeline/lib/tasks/exports/misc_test.py @@ -0,0 +1,484 @@ +import unittest + +import hail as hl + +from loading_pipeline.lib.core import ( + DatasetType, + ReferenceGenome, +) +from loading_pipeline.lib.tasks.exports.misc import ( + camelcase_array_structexpression_fields, + sorted_hl_struct, + unmap_formatting_annotation_enums, +) + +TEST_SNV_INDEL_ANNOTATIONS = ( + 'loading_pipeline/var/test/exports/GRCh38/SNV_INDEL/annotations.ht' +) +TEST_GRCH37_SNV_INDEL_ANNOTATIONS = ( + 'loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/annotations.ht' +) + + +class MiscTest(unittest.TestCase): + def test_unmap_formatting_annotation_enums(self) -> None: + ht = hl.read_table(TEST_SNV_INDEL_ANNOTATIONS) + ht = unmap_formatting_annotation_enums( + ht, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + ) + self.assertCountEqual( + list(ht.globals.enums.collect()[0].keys()), + [ + 'clinvar', + 'hgmd', + 'screen', + 'dbnsfp', + 'gnomad_exomes', + 'gnomad_non_coding_constraint', + 'splice_ai', + 'exac', + 'topmed', + 'gnomad_genomes', + 'eigen', + ], + ) + ht = ht.annotate( + sorted_transcript_consequences=[ht.sorted_transcript_consequences[0]], + ) + self.assertEqual( + ht.collect()[0], + hl.Struct( + key_=0, + locus=hl.Locus( + contig='chr1', + position=876499, + reference_genome='GRCh38', + ), + alleles=['A', 'G'], + clinvar=hl.Struct( + alleleId=929885, + conflictingPathogenicities=None, + goldStars=1, + submitters=['Labcorp Genetics (formerly Invitae), Labcorp'], + conditions=['not provided'], + assertion_ids=[], + pathogenicity_id=12, + ), + rg37_locus=hl.Locus( + contig=1, + position=874501, + reference_genome='GRCh37', + ), + rsid=None, + sorted_transcript_consequences=[ + hl.Struct( + amino_acids='S/L', + canonical=1, + codons='tCg/tTg', + gene_id='ENSG00000187634', + hgvsc='ENST00000616016.5:c.1049C>T', + hgvsp='ENSP00000478421.2:p.Ser350Leu', + transcript_id='ENST00000616016', + mane_select='NM_001385641.1', + mane_plus_clinical=None, + exon=hl.Struct(index=6, total=14), + intron=None, + refseq_transcript_id='NM_001385641.1', + alphamissense=hl.Struct(pathogenicity=None), + loftee=hl.Struct(is_lof_nagnag=None, lof_filters=None), + spliceregion=hl.Struct( + extended_intronic_splice_region_variant=False, + ), + utrannotator=hl.Struct( + existing_inframe_oorfs=None, + existing_outofframe_oorfs=None, + existing_uorfs=None, + fiveutr_annotation=hl.Struct( + type='OutOfFrame_oORF', + KozakContext='CGCATGC', + KozakStrength='Weak', + DistanceToCDS=41, + CapDistanceToStart=None, + DistanceToStop=None, + Evidence=None, + AltStop=None, + AltStopDistanceToCDS=None, + FrameWithCDS=None, + StartDistanceToCDS=None, + newSTOPDistanceToCDS=None, + alt_type=None, + alt_type_length=None, + ref_StartDistanceToCDS=None, + ref_type=None, + ref_type_length=None, + ), + fiveutr_consequence=None, + ), + biotype='protein_coding', + consequence_terms=['missense_variant'], + ), + ], + variant_id='1-876499-A-G', + xpos=1000876499, + gt_stats=hl.Struct(AC=47, AN=81784, AF=0.0005746845272369683, hom=1), + CAID='CA502654', + check_ref=False, + sorted_regulatory_feature_consequences=[ + hl.Struct( + regulatory_feature_id='ENSR00000344437', + biotype='CTCF_binding_site', + consequence_terms=['regulatory_region_variant'], + ), + ], + sorted_motif_feature_consequences=[ + hl.Struct( + motif_feature_id='ENSM00493959715', + consequence_terms=['TF_binding_site_variant'], + ), + ], + gnomad_non_coding_constraint=hl.Struct(z_score=None), + hgmd=hl.Struct(accession='abcdefg', class_id=3), + gnomad_exomes=hl.Struct( + AF=0.0006690866430290043, + AN=1440770, + AC=964, + Hom=0, + AF_POPMAX_OR_GLOBAL=0.0008023773552849889, + FAF_AF=0.000633420015219599, + Hemi=0, + ), + gnomad_genomes=hl.Struct( + AF=0.0002759889466688037, + AN=152180, + AC=42, + Hom=0, + AF_POPMAX_OR_GLOBAL=0.10000000149011612, + FAF_AF=0.0002092500071739778, + Hemi=0, + ), + screen=hl.Struct(region_type_ids=[]), + dbnsfp=hl.Struct( + PrimateAI_score=0.5918066501617432, + fathmm_MKL_coding_score=0.7174800038337708, + CADD_phred=23.5, + SIFT_score=0.0010000000474974513, + REVEL_score=0.3109999895095825, + Polyphen2_HVAR_score=0.164000004529953, + VEST4_score=0.39500001072883606, + MPC_score=0.01291007362306118, + MutPred_score=None, + MutationTaster_pred_id=0, + ), + topmed=hl.Struct( + AC=41, + AF=0.00032651599030941725, + AN=125568, + Hom=0, + Het=41, + ), + exac=hl.Struct( + AF_POPMAX=0.0007150234305299819, + AF=0.00019039999460801482, + AC_Adj=20, + AC_Het=20, + AC_Hom=0, + AC_Hemi=None, + AN_Adj=47974, + ), + splice_ai=hl.Struct(delta_score=0.0, splice_consequence_id=4), + eigen=hl.Struct(Eigen_phred=2.628000020980835), + ), + ) + ht = hl.read_table(TEST_GRCH37_SNV_INDEL_ANNOTATIONS) + ht = unmap_formatting_annotation_enums( + ht, + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + ) + self.assertCountEqual( + list(ht.globals.enums.collect()[0].keys()), + [ + 'clinvar', + 'hgmd', + 'dbnsfp', + 'gnomad_exomes', + 'splice_ai', + 'exac', + 'topmed', + 'gnomad_genomes', + 'eigen', + ], + ) + ht = ht.annotate( + sorted_transcript_consequences=[ht.sorted_transcript_consequences[0]], + ) + self.assertEqual( + ht.collect()[0], + hl.Struct( + locus=hl.Locus(contig=1, position=69134, reference_genome='GRCh37'), + alleles=['A', 'G'], + clinvar=hl.Struct( + alleleId=2193183, + conflictingPathogenicities=None, + goldStars=1, + submitters=['Ambry Genetics'], + conditions=['not specified'], + assertion_ids=[], + pathogenicity_id=14, + ), + rsid=None, + sorted_transcript_consequences=[ + hl.Struct( + amino_acids='E/G', + canonical=1, + codons='gAa/gGa', + gene_id='ENSG00000186092', + hgvsc='ENST00000335137.3:c.44A>G', + hgvsp='ENSP00000334393.3:p.Glu15Gly', + transcript_id='ENST00000335137', + is_lof_nagnag=None, + biotype='protein_coding', + consequence_terms=['missense_variant'], + lof_filters=None, + ), + ], + variant_id='1-69134-A-G', + xpos=1000069134, + gt_stats=hl.Struct(AC=25, AN=1246, AF=0.020064204931259155, hom=10), + CAID='CA502008', + rg38_locus=hl.Locus( + contig='chr1', + position=69134, + reference_genome='GRCh38', + ), + hgmd=None, + gnomad_exomes=hl.Struct( + AF=0.026665963232517242, + AN=18938, + AC=505, + Hom=127, + AF_POPMAX_OR_GLOBAL=0.08191808313131332, + FAF_AF=0.02474386990070343, + Hemi=0, + ), + gnomad_genomes=hl.Struct( + AF=0.0001722949673421681, + AN=5804, + AC=1, + Hom=0, + AF_POPMAX_OR_GLOBAL=0.0005662514013238251, + FAF_AF=0.0, + Hemi=0, + ), + dbnsfp=hl.Struct( + PrimateAI_score=0.37232041358947754, + fathmm_MKL_coding_score=0.056940000504255295, + CADD_phred=15.880000114440918, + SIFT_score=0.1289999932050705, + REVEL_score=0.07500000298023224, + Polyphen2_HVAR_score=0.0010000000474974513, + VEST4_score=0.10700000077486038, + MPC_score=1.8921889066696167, + MutPred_score=0.3779999911785126, + MutationTaster_pred_id=2, + ), + topmed=hl.Struct( + AC=95, + AF=0.0007565619889646769, + AN=125568, + Hom=0, + Het=95, + ), + exac=hl.Struct( + AF_POPMAX=None, + AF=0.0016550000291317701, + AC_Adj=0, + AC_Het=0, + AC_Hom=0, + AC_Hemi=None, + AN_Adj=66, + ), + eigen=hl.Struct(Eigen_phred=1.0019999742507935), + splice_ai=hl.Struct( + delta_score=0.019999999552965164, + splice_consequence_id=2, + ), + key_=1424, + ), + ) + + def test_camelcase_array_structexpression_fields(self) -> None: + ht = hl.read_table(TEST_SNV_INDEL_ANNOTATIONS) + ht = unmap_formatting_annotation_enums( + ht, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + ) + ht = camelcase_array_structexpression_fields( + ht, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + ) + ht = ht.annotate( + sortedTranscriptConsequences=[ht.sortedTranscriptConsequences[0]], + ) + self.assertEqual( + ht.collect()[0], + hl.Struct( + key_=0, + locus=hl.Locus( + contig='chr1', + position=876499, + reference_genome='GRCh38', + ), + alleles=['A', 'G'], + clinvar=hl.Struct( + alleleId=929885, + conflictingPathogenicities=None, + goldStars=1, + submitters=['Labcorp Genetics (formerly Invitae), Labcorp'], + conditions=['not provided'], + assertion_ids=[], + pathogenicity_id=12, + ), + rg37_locus=hl.Locus( + contig=1, + position=874501, + reference_genome='GRCh37', + ), + rsid=None, + variant_id='1-876499-A-G', + xpos=1000876499, + gt_stats=hl.Struct(AC=47, AN=81784, AF=0.0005746845272369683, hom=1), + CAID='CA502654', + check_ref=False, + gnomad_non_coding_constraint=hl.Struct(z_score=None), + hgmd=hl.Struct(accession='abcdefg', class_id=3), + gnomad_exomes=hl.Struct( + AF=0.0006690866430290043, + AN=1440770, + AC=964, + Hom=0, + AF_POPMAX_OR_GLOBAL=0.0008023773552849889, + FAF_AF=0.000633420015219599, + Hemi=0, + ), + gnomad_genomes=hl.Struct( + AF=0.0002759889466688037, + AN=152180, + AC=42, + Hom=0, + AF_POPMAX_OR_GLOBAL=0.10000000149011612, + FAF_AF=0.0002092500071739778, + Hemi=0, + ), + screen=hl.Struct(region_type_ids=[]), + dbnsfp=hl.Struct( + PrimateAI_score=0.5918066501617432, + fathmm_MKL_coding_score=0.7174800038337708, + CADD_phred=23.5, + SIFT_score=0.0010000000474974513, + REVEL_score=0.3109999895095825, + Polyphen2_HVAR_score=0.164000004529953, + VEST4_score=0.39500001072883606, + MPC_score=0.01291007362306118, + MutPred_score=None, + MutationTaster_pred_id=0, + ), + topmed=hl.Struct( + AC=41, + AF=0.00032651599030941725, + AN=125568, + Hom=0, + Het=41, + ), + exac=hl.Struct( + AF_POPMAX=0.0007150234305299819, + AF=0.00019039999460801482, + AC_Adj=20, + AC_Het=20, + AC_Hom=0, + AC_Hemi=None, + AN_Adj=47974, + ), + splice_ai=hl.Struct( + delta_score=0.0, + splice_consequence_id=4, + ), + eigen=hl.Struct(Eigen_phred=2.628000020980835), + sortedTranscriptConsequences=[ + hl.Struct( + aminoAcids='S/L', + canonical=1, + codons='tCg/tTg', + geneId='ENSG00000187634', + hgvsc='ENST00000616016.5:c.1049C>T', + hgvsp='ENSP00000478421.2:p.Ser350Leu', + transcriptId='ENST00000616016', + maneSelect='NM_001385641.1', + manePlusClinical=None, + exon=hl.Struct(index=6, total=14), + intron=None, + refseqTranscriptId='NM_001385641.1', + alphamissense=hl.Struct(pathogenicity=None), + loftee=hl.Struct(isLofNagnag=None, lofFilters=None), + spliceregion=hl.Struct( + extended_intronic_splice_region_variant=False, + ), + utrannotator=hl.Struct( + existingInframeOorfs=None, + existingOutofframeOorfs=None, + existingUorfs=None, + fiveutrAnnotation=hl.Struct( + type='OutOfFrame_oORF', + KozakContext='CGCATGC', + KozakStrength='Weak', + DistanceToCDS=41, + CapDistanceToStart=None, + DistanceToStop=None, + Evidence=None, + AltStop=None, + AltStopDistanceToCDS=None, + FrameWithCDS=None, + StartDistanceToCDS=None, + newSTOPDistanceToCDS=None, + alt_type=None, + alt_type_length=None, + ref_StartDistanceToCDS=None, + ref_type=None, + ref_type_length=None, + ), + fiveutrConsequence=None, + ), + biotype='protein_coding', + consequenceTerms=['missense_variant'], + ), + ], + sortedRegulatoryFeatureConsequences=[ + hl.Struct( + regulatoryFeatureId='ENSR00000344437', + biotype='CTCF_binding_site', + consequenceTerms=['regulatory_region_variant'], + ), + ], + sortedMotifFeatureConsequences=[ + hl.Struct( + motifFeatureId='ENSM00493959715', + consequenceTerms=['TF_binding_site_variant'], + ), + ], + ), + ) + + def test_sorted_hl_struct(self) -> None: + struct = hl.Struct( + z=5, + y=hl.Struct(b=2, a=hl.Struct(d=4, c=3)), + x=hl.Struct(k=9), + ) + self.assertEqual( + sorted_hl_struct(struct), + hl.Struct(x=hl.Struct(k=9), y=hl.Struct(a=hl.Struct(c=3, d=4), b=2), z=5), + ) diff --git a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py new file mode 100644 index 0000000000..ccb3260f5e --- /dev/null +++ b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py @@ -0,0 +1,423 @@ +import hail as hl +import luigi.worker +import pandas as pd + +from loading_pipeline.lib.core import ( + DatasetType, + ReferenceGenome, + SampleType, +) +from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS +from loading_pipeline.lib.paths import ( + new_entries_parquet_path, + variant_annotations_table_path, +) +from loading_pipeline.lib.tasks.exports.write_new_entries_parquet import ( + WriteNewEntriesParquetTask, +) +from loading_pipeline.lib.test.misc import ( + convert_ndarray_to_list, + copy_project_pedigree_to_mocked_dir, +) +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + +TEST_PEDIGREE_3_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_3_remap.tsv' +TEST_PEDIGREE_4_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_4_remap.tsv' +TEST_PEDIGREE_5 = 'loading_pipeline/var/test/pedigrees/test_pedigree_5.tsv' +TEST_MITO_EXPORT_PEDIGREE = ( + 'loading_pipeline/var/test/pedigrees/test_mito_export_pedigree.tsv' +) +TEST_SNV_INDEL_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' +TEST_MITO_CALLSET = 'loading_pipeline/var/test/callsets/mito_1.mt' +TEST_SV_VCF_2 = 'loading_pipeline/var/test/callsets/sv_2.vcf' +TEST_GCNV_BED_FILE = 'loading_pipeline/var/test/callsets/gcnv_1.tsv' +TEST_SNV_INDEL_ANNOTATIONS = ( + 'loading_pipeline/var/test/exports/GRCh38/SNV_INDEL/annotations.ht' +) +TEST_MITO_ANNOTATIONS = 'loading_pipeline/var/test/exports/GRCh38/MITO/annotations.ht' +TEST_SV_ANNOTATIONS = 'loading_pipeline/var/test/exports/GRCh38/SV/annotations.ht' +TEST_GCNV_ANNOTATIONS = 'loading_pipeline/var/test/exports/GRCh38/GCNV/annotations.ht' + +TEST_RUN_ID = 'manual__2024-04-03' + + +class WriteNewEntriesParquetTest(MockedDatarootTestCase): + def setUp(self) -> None: + super().setUp() + ht = hl.read_table( + TEST_SNV_INDEL_ANNOTATIONS, + ) + ht.write( + variant_annotations_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + ), + ) + ht = hl.read_table( + TEST_MITO_ANNOTATIONS, + ) + ht.write( + variant_annotations_table_path( + ReferenceGenome.GRCh38, + DatasetType.MITO, + ), + ) + ht = hl.read_table( + TEST_SV_ANNOTATIONS, + ) + ht.write( + variant_annotations_table_path( + ReferenceGenome.GRCh38, + DatasetType.SV, + ), + ) + ht = hl.read_table(TEST_GCNV_ANNOTATIONS) + ht.write( + variant_annotations_table_path( + ReferenceGenome.GRCh38, + DatasetType.GCNV, + ), + ) + + def test_write_new_entries_parquet(self): + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_3_REMAP, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0113_test_project', + ) + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_4_REMAP, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0114_project4', + ) + worker = luigi.worker.Worker() + task = WriteNewEntriesParquetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path=TEST_SNV_INDEL_VCF, + project_guids=['R0113_test_project', 'R0114_project4'], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + worker.add(task) + worker.run() + self.assertTrue(task.output().exists()) + self.assertTrue(task.complete()) + df = pd.read_parquet( + new_entries_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ) + export_json = convert_ndarray_to_list(df.to_dict('records')) + self.assertEqual( + export_json[:2], + [ + { + 'key': 0, + 'project_guid': 'R0113_test_project', + 'family_guid': 'abc_1', + 'sample_type': 'WGS', + 'xpos': 1000876499, + 'geneIds': ['ENSG00000187634'], + 'filters': [], + 'calls': [ + { + 'sampleId': 'HG00731_1', + 'gt': 2, + 'gq': 21, + 'ab': 1.0, + 'dp': 7, + }, + { + 'sampleId': 'HG00732_1', + 'gt': 2, + 'gq': 24, + 'ab': 1.0, + 'dp': 8, + }, + { + 'sampleId': 'HG00733_1', + 'gt': 2, + 'gq': 12, + 'ab': 1.0, + 'dp': 4, + }, + ], + 'sign': 1, + }, + { + 'key': 1, + 'project_guid': 'R0113_test_project', + 'family_guid': 'abc_1', + 'sample_type': 'WGS', + 'xpos': 1000878314, + 'geneIds': ['ENSG00000187634'], + 'filters': ['VQSRTrancheSNP99.00to99.90'], + 'calls': [ + { + 'sampleId': 'HG00731_1', + 'gt': 1, + 'gq': 30, + 'ab': 0.3333333432674408, + 'dp': 3, + }, + {'sampleId': 'HG00732_1', 'gt': 0, 'gq': 6, 'ab': 0.0, 'dp': 2}, + { + 'sampleId': 'HG00733_1', + 'gt': 1, + 'gq': 61, + 'ab': 0.6000000238418579, + 'dp': 5, + }, + ], + 'sign': 1, + }, + ], + ) + + def test_mito_write_new_entries_parquet(self): + copy_project_pedigree_to_mocked_dir( + TEST_MITO_EXPORT_PEDIGREE, + ReferenceGenome.GRCh38, + DatasetType.MITO, + SampleType.WGS, + 'R0116_test_project3', + ) + worker = luigi.worker.Worker() + task = WriteNewEntriesParquetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.MITO, + sample_type=SampleType.WGS, + callset_path=TEST_MITO_CALLSET, + project_guids=['R0116_test_project3'], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + worker.add(task) + worker.run() + self.assertTrue(task.output().exists()) + self.assertTrue(task.complete()) + df = pd.read_parquet( + new_entries_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.MITO, + TEST_RUN_ID, + ), + ) + export_json = convert_ndarray_to_list(df.to_dict('records')) + self.assertEqual( + export_json, + [ + { + 'key': 998, + 'project_guid': 'R0116_test_project3', + 'family_guid': 'family_1', + 'sample_type': 'WGS', + 'xpos': 25000000008, + 'filters': [], + 'calls': [ + { + 'sampleId': 'RGP_1270_2', + 'gt': 2, + 'dp': 4216, + 'hl': 0.999, + 'mitoCn': 224, + 'contamination': 0.0, + }, + ], + 'sign': 1, + }, + ], + ) + + def test_sv_write_new_entries_parquet(self): + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_5, + ReferenceGenome.GRCh38, + DatasetType.SV, + SampleType.WGS, + 'R0115_test_project2', + ) + worker = luigi.worker.Worker() + task = WriteNewEntriesParquetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SV, + sample_type=SampleType.WGS, + callset_path=TEST_SV_VCF_2, + project_guids=['R0115_test_project2'], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + worker.add(task) + worker.run() + self.assertTrue(task.output().exists()) + self.assertTrue(task.complete()) + df = pd.read_parquet( + new_entries_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.SV, + TEST_RUN_ID, + ), + ) + export_json = convert_ndarray_to_list(df.to_dict('records')) + self.assertEqual( + export_json, + [ + { + 'key': 727, + 'project_guid': 'R0115_test_project2', + 'family_guid': 'family_2_1', + 'xpos': 1001025886, + 'geneIds': ['ENSG00000188157'], + 'filters': ['HIGH_SR_BACKGROUND', 'UNRESOLVED'], + 'calls': [ + { + 'sampleId': 'RGP_164_1', + 'gt': 0, + 'cn': None, + 'gq': 99, + 'newCall': True, + 'prevCall': False, + 'prevNumAlt': None, + }, + { + 'sampleId': 'RGP_164_2', + 'gt': 1, + 'cn': None, + 'gq': 31, + 'newCall': True, + 'prevCall': False, + 'prevNumAlt': None, + }, + { + 'sampleId': 'RGP_164_3', + 'gt': 0, + 'cn': None, + 'gq': 99, + 'newCall': True, + 'prevCall': False, + 'prevNumAlt': None, + }, + { + 'sampleId': 'RGP_164_4', + 'gt': 0, + 'cn': None, + 'gq': 99, + 'newCall': True, + 'prevCall': False, + 'prevNumAlt': None, + }, + ], + 'sign': 1, + }, + ], + ) + + def test_gcnv_write_new_entries_parquet(self): + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_5, + ReferenceGenome.GRCh38, + DatasetType.GCNV, + SampleType.WES, + 'R0115_test_project2', + ) + worker = luigi.worker.Worker() + task = WriteNewEntriesParquetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.GCNV, + sample_type=SampleType.WES, + callset_path=TEST_GCNV_BED_FILE, + project_guids=['R0115_test_project2'], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + worker.add(task) + worker.run() + self.assertTrue(task.output().exists()) + self.assertTrue(task.complete()) + df = pd.read_parquet( + new_entries_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.GCNV, + TEST_RUN_ID, + ), + ) + export_json = convert_ndarray_to_list(df.to_dict('records')) + self.assertEqual( + export_json, + [ + { + 'key': 0, + 'project_guid': 'R0115_test_project2', + 'family_guid': 'family_2_1', + 'xpos': 1000939203, + 'filters': [], + 'calls': [ + { + 'sampleId': 'RGP_164_1', + 'gt': 1, + 'cn': 1, + 'qs': 4, + 'defragged': False, + 'start': 100006937, + 'end': 100007881, + 'numExon': 2, + 'geneIds': ['ENSG00000117620', 'ENSG00000283761'], + 'newCall': False, + 'prevCall': True, + 'prevOverlap': False, + }, + { + 'sampleId': 'RGP_164_2', + 'gt': 1, + 'cn': 1, + 'qs': 5, + 'defragged': False, + 'start': 100017585, + 'end': 100023213, + 'numExon': 1, + 'geneIds': ['ENSG00000117620', 'ENSG00000283761'], + 'newCall': False, + 'prevCall': False, + 'prevOverlap': False, + }, + { + 'sampleId': 'RGP_164_3', + 'gt': 2, + 'cn': 0, + 'qs': 30, + 'defragged': False, + 'start': 100017585, + 'end': 100023213, + 'numExon': 1, + 'geneIds': ['ENSG00000117620', 'ENSG00000283761'], + 'newCall': False, + 'prevCall': True, + 'prevOverlap': False, + }, + { + 'sampleId': 'RGP_164_4', + 'gt': 2, + 'cn': 0, + 'qs': 30, + 'defragged': False, + 'start': 100017586, + 'end': 100023212, + 'numExon': 2, + 'geneIds': ['ENSG00000283761', 'ENSG22222222222'], + 'newCall': False, + 'prevCall': True, + 'prevOverlap': False, + }, + ], + 'sign': 1, + }, + ], + ) diff --git a/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py new file mode 100644 index 0000000000..5458854f56 --- /dev/null +++ b/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py @@ -0,0 +1,270 @@ +import os +from unittest import mock + +import hail as hl +import luigi.worker +import pandas as pd + +from loading_pipeline.lib.core import ( + DatasetType, + ReferenceGenome, + SampleType, +) +from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS +from loading_pipeline.lib.paths import ( + new_variant_details_parquet_path, + new_variants_table_path, +) +from loading_pipeline.lib.tasks.exports.write_new_variant_details_parquet import ( + WriteNewVariantDetailsParquetTask, +) +from loading_pipeline.lib.test.misc import convert_ndarray_to_list +from loading_pipeline.lib.test.mock_complete_task import MockCompleteTask +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + +TEST_SNV_INDEL_ANNOTATIONS = ( + 'loading_pipeline/var/test/exports/GRCh38/SNV_INDEL/annotations.ht' +) +TEST_GRCH37_SNV_INDEL_ANNOTATIONS = ( + 'loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/annotations.ht' +) + +TEST_RUN_ID = 'manual__2024-04-03' + + +class WriteNewVariantDetailsParquetTest(MockedDatarootTestCase): + def setUp(self) -> None: + super().setUp() + ht = hl.read_table( + TEST_SNV_INDEL_ANNOTATIONS, + ) + ht.write( + new_variants_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ) + ht = hl.read_table( + TEST_GRCH37_SNV_INDEL_ANNOTATIONS, + ) + ht.write( + new_variants_table_path( + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ) + + # Make an incomplete parquet to validate overwrite-ing. + os.makedirs( + new_variant_details_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + exist_ok=True, + ) + with open( + os.path.join( + new_variant_details_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + 'incomplete_file.parquet', + ), + 'w', + ) as f: + f.write('') + + @mock.patch( + 'loading_pipeline.lib.tasks.exports.write_new_variant_details_parquet.WriteNewVariantsTableTask', + ) + def test_write_new_variant_details_parquet_test( + self, + mock_write_new_variants_task, + ) -> None: + mock_write_new_variants_task.return_value = MockCompleteTask() + worker = luigi.worker.Worker() + task = WriteNewVariantDetailsParquetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path='fake_callset', + project_guids=[ + 'fake_project', + ], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + worker.add(task) + worker.run() + self.assertTrue(task.output().exists()) + self.assertTrue(task.complete()) + df = pd.read_parquet( + new_variant_details_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ) + export_json = convert_ndarray_to_list(df.head(1).to_dict('records')) + self.assertListEqual( + list(export_json[0].keys()), + [ + 'key', + 'variantId', + 'rsid', + 'CAID', + 'liftedOverChrom', + 'liftedOverPos', + 'sortedMotifFeatureConsequences', + 'sortedRegulatoryFeatureConsequences', + 'transcripts', + ], + ) + self.assertEqual( + export_json[0]['key'], + 0, + ) + self.assertEqual( + export_json[0]['transcripts'][0], + { + 'alphamissense': {'pathogenicity': None}, + 'aminoAcids': 'S/L', + 'biotype': 'protein_coding', + 'canonical': 1, + 'codons': 'tCg/tTg', + 'consequenceTerms': ['missense_variant'], + 'exon': {'index': 6, 'total': 14}, + 'geneId': 'ENSG00000187634', + 'hgvsc': 'ENST00000616016.5:c.1049C>T', + 'hgvsp': 'ENSP00000478421.2:p.Ser350Leu', + 'intron': None, + 'transcriptId': 'ENST00000616016', + 'transcriptRank': 0, + 'majorConsequence': 'missense_variant', + 'maneSelect': 'NM_001385641.1', + 'manePlusClinical': None, + 'refseqTranscriptId': 'NM_001385641.1', + 'loftee': {'isLofNagnag': None, 'lofFilters': None}, + 'spliceregion': { + 'extended_intronic_splice_region_variant': False, + }, + 'utrannotator': { + 'existingInframeOorfs': None, + 'existingOutofframeOorfs': None, + 'existingUorfs': None, + 'fiveutrAnnotation': { + 'AltStop': None, + 'AltStopDistanceToCDS': None, + 'CapDistanceToStart': None, + 'DistanceToCDS': 41, + 'DistanceToStop': None, + 'Evidence': None, + 'FrameWithCDS': None, + 'KozakContext': 'CGCATGC', + 'KozakStrength': 'Weak', + 'StartDistanceToCDS': None, + 'alt_type': None, + 'alt_type_length': None, + 'newSTOPDistanceToCDS': None, + 'ref_StartDistanceToCDS': None, + 'ref_type': None, + 'ref_type_length': None, + 'type': 'OutOfFrame_oORF', + }, + 'fiveutrConsequence': None, + }, + }, + ) + self.assertEqual( + list(export_json[0]['transcripts'][0].keys()), + sorted(export_json[0]['transcripts'][0].keys()), + ) + self.assertEqual( + list( + export_json[0]['transcripts'][0]['utrannotator'][ + 'fiveutrAnnotation' + ].keys(), + ), + sorted( + export_json[0]['transcripts'][0]['utrannotator'][ + 'fiveutrAnnotation' + ].keys(), + ), + ) + + @mock.patch( + 'loading_pipeline.lib.tasks.exports.write_new_variant_details_parquet.WriteNewVariantsTableTask', + ) + def test_grch37_write_new_variant_details_parquet_test( + self, + mock_write_new_variants_task, + ) -> None: + mock_write_new_variants_task.return_value = MockCompleteTask() + worker = luigi.worker.Worker() + task = WriteNewVariantDetailsParquetTask( + reference_genome=ReferenceGenome.GRCh37, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path='fake_callset', + project_guids=[ + 'fake_project', + ], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + worker.add(task) + worker.run() + self.assertTrue(task.output().exists()) + self.assertTrue(task.complete()) + df = pd.read_parquet( + os.path.join( + new_variant_details_parquet_path( + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ), + ), + ) + export_json = convert_ndarray_to_list(df.head(1).to_dict('records')) + self.assertListEqual( + list(export_json[0].keys()), + [ + 'key', + 'variantId', + 'rsid', + 'CAID', + 'liftedOverChrom', + 'liftedOverPos', + 'transcripts', + ], + ) + self.assertEqual( + export_json[0]['key'], + 1424, + ) + self.assertEqual(export_json[0]['CAID'], None) + self.assertEqual( + export_json[0]['transcripts'][0], + { + 'aminoAcids': 'E/G', + 'biotype': 'protein_coding', + 'canonical': 1, + 'codons': 'gAa/gGa', + 'consequenceTerms': ['missense_variant'], + 'geneId': 'ENSG00000186092', + 'hgvsc': 'ENST00000335137.3:c.44A>G', + 'hgvsp': 'ENSP00000334393.3:p.Glu15Gly', + 'loftee': {'isLofNagnag': None, 'lofFilters': None}, + 'majorConsequence': 'missense_variant', + 'transcriptId': 'ENST00000335137', + 'transcriptRank': 0, + }, + ) + self.assertEqual( + list(export_json[0]['transcripts'][0].keys()), + sorted(export_json[0]['transcripts'][0].keys()), + ) diff --git a/loading_pipeline/lib/tasks/files_test.py b/loading_pipeline/lib/tasks/files_test.py new file mode 100644 index 0000000000..b2dfd937e0 --- /dev/null +++ b/loading_pipeline/lib/tasks/files_test.py @@ -0,0 +1,40 @@ +import os +import tempfile +import unittest + +from loading_pipeline.lib.tasks.files import ( + CallsetTask, + HailTableTask, + RawFileTask, + VCFFileTask, +) + + +class FilesTest(unittest.TestCase): + def test_raw_file(self) -> None: + with tempfile.NamedTemporaryFile(suffix='.txt') as f: + self.assertTrue(RawFileTask(f.name).complete()) + + def test_vcf_file(self) -> None: + with tempfile.NamedTemporaryFile(suffix='.vcf.bgz') as f: + self.assertTrue(VCFFileTask(f.name).complete()) + + def test_hail_table(self) -> None: + with tempfile.TemporaryDirectory(suffix='.ht') as d: + self.assertFalse(HailTableTask(d).complete()) + with open(os.path.join(d, '_SUCCESS'), 'w') as f: + f.write('0') + self.assertTrue(HailTableTask(d).complete()) + + def test_callset_task(self) -> None: + with tempfile.NamedTemporaryFile(suffix='.txt') as f: + self.assertTrue(CallsetTask(f.name).complete()) + + with tempfile.NamedTemporaryFile(suffix='.vcf') as f: + self.assertTrue(CallsetTask(f.name).complete()) + + with tempfile.TemporaryDirectory(suffix='.mt') as d: + self.assertFalse(CallsetTask(d).complete()) + with open(os.path.join(d, '_SUCCESS'), 'w') as f: + f.write('0') + self.assertTrue(CallsetTask(d).complete()) diff --git a/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py b/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py new file mode 100644 index 0000000000..3bfe55af65 --- /dev/null +++ b/loading_pipeline/lib/tasks/update_variant_annotations_table_with_new_variants_test.py @@ -0,0 +1,1349 @@ +import functools +from unittest.mock import Mock, PropertyMock, patch + +import hail as hl +import luigi.worker + +from loading_pipeline.lib.annotations.enums import ( + BIOTYPES, + FIVEUTR_CONSEQUENCES, + LOF_FILTERS, + MITOTIP_PATHOGENICITIES, + MOTIF_CONSEQUENCE_TERMS, + REGULATORY_BIOTYPES, + REGULATORY_CONSEQUENCE_TERMS, + SV_CONSEQUENCE_RANKS, + SV_TYPE_DETAILS, + SV_TYPES, + TRANSCRIPT_CONSEQUENCE_TERMS, +) +from loading_pipeline.lib.core import ( + DatasetType, + ReferenceGenome, + SampleType, +) +from loading_pipeline.lib.misc.io import remap_pedigree_hash +from loading_pipeline.lib.misc.validation import ( + ALL_VALIDATIONS, + SKIPPABLE_VALIDATIONS, + validate_expected_contig_frequency, +) +from loading_pipeline.lib.paths import ( + valid_reference_dataset_path, +) +from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset +from loading_pipeline.lib.tasks.files import GCSorLocalFolderTarget +from loading_pipeline.lib.tasks.update_variant_annotations_table_with_new_variants import ( + UpdateVariantAnnotationsTableWithNewVariantsTask, +) +from loading_pipeline.lib.test.misc import copy_project_pedigree_to_mocked_dir +from loading_pipeline.lib.test.mocked_reference_datasets_testcase import ( + MockedReferenceDatasetsTestCase, +) +from loading_pipeline.var.test.vep.mock_vep_data import ( + MOCK_37_VEP_DATA, + MOCK_38_VEP_DATA, +) + +TEST_MITO_MT = 'loading_pipeline/var/test/callsets/mito_1.mt' +TEST_SNV_INDEL_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' +TEST_SV_VCF = 'loading_pipeline/var/test/callsets/sv_1.vcf' +TEST_SV_VCF_2 = 'loading_pipeline/var/test/callsets/sv_2.vcf' +TEST_GCNV_BED_FILE = 'loading_pipeline/var/test/callsets/gcnv_1.tsv' +TEST_GCNV_BED_FILE_2 = 'loading_pipeline/var/test/callsets/gcnv_2.tsv' +TEST_PEDIGREE_3_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_3_remap.tsv' +TEST_PEDIGREE_4_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_4_remap.tsv' +TEST_PEDIGREE_5 = 'loading_pipeline/var/test/pedigrees/test_pedigree_5.tsv' +TEST_PEDIGREE_8 = 'loading_pipeline/var/test/pedigrees/test_pedigree_8.tsv' +TEST_PEDIGREE_10 = 'loading_pipeline/var/test/pedigrees/test_pedigree_10.tsv' +TEST_PEDIGREE_11 = 'loading_pipeline/var/test/pedigrees/test_pedigree_11.tsv' + +GENE_ID_MAPPING = { + 'OR4F5': 'ENSG00000186092', + 'PLEKHG4B': 'ENSG00000153404', + 'OR4F16': 'ENSG00000186192', + 'OR4F29': 'ENSG00000284733', + 'FBXO28': 'ENSG00000143756', + 'SAMD11': 'ENSG00000187634', + 'C1orf174': 'ENSG00000198912', + 'TAS1R1': 'ENSG00000173662', + 'FAM131C': 'ENSG00000185519', + 'RCC2': 'ENSG00000179051', + 'NBPF3': 'ENSG00000142794', + 'AGBL4': 'ENSG00000186094', + 'KIAA1614': 'ENSG00000135835', + 'MR1': 'ENSG00000153029', + 'STX6': 'ENSG00000135823', + 'XPR1': 'ENSG00000143324', +} + +TEST_RUN_ID = 'manual__2024-04-03' + + +class UpdateVariantAnnotationsTableWithNewVariantsTaskTest( + MockedReferenceDatasetsTestCase, +): + def test_missing_pedigree( + self, + ) -> None: + uvatwns_task = UpdateVariantAnnotationsTableWithNewVariantsTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path=TEST_SNV_INDEL_VCF, + project_guids=['R0113_test_project'], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + worker = luigi.worker.Worker() + worker.add(uvatwns_task) + worker.run() + self.assertFalse(uvatwns_task.complete()) + + @patch( + 'loading_pipeline.lib.tasks.validate_callset.SKIPPABLE_VALIDATIONS', + [ + x + for x in SKIPPABLE_VALIDATIONS + if x.__name__ != 'validate_expected_contig_frequency' + ] + + [ + functools.update_wrapper( + functools.partial( + validate_expected_contig_frequency, + min_rows_per_contig=25, + ), + validate_expected_contig_frequency, + ), + ], + ) + @patch.object(ReferenceGenome, 'standard_contigs', new_callable=PropertyMock) + @patch('loading_pipeline.lib.misc.vep.hl.vep') + @patch( + 'loading_pipeline.lib.tasks.write_new_variants_table.load_gencode_ensembl_to_refseq_id', + ) + def test_multiple_update_vat( + self, + mock_load_gencode_ensembl_to_refseq_id: Mock, + mock_vep: Mock, + mock_standard_contigs: Mock, + ) -> None: + mock_vep.side_effect = lambda ht, **_: ht.annotate(vep=MOCK_38_VEP_DATA) + mock_load_gencode_ensembl_to_refseq_id.return_value = hl.dict( + {'ENST00000327044': 'NM_015658.4'}, + ) + mock_standard_contigs.return_value = {'chr1'} + # This creates a mock validation table with 1 coding and 1 non-coding variant + # explicitly chosen from the VCF. + # NB: This is the one and only place validation is enabled in the task tests! + coding_and_noncoding_variants_ht = hl.Table.parallelize( + [ + { + 'locus': hl.Locus( + contig='chr1', + position=871269, + reference_genome='GRCh38', + ), + 'coding': False, + 'noncoding': True, + }, + { + 'locus': hl.Locus( + contig='chr1', + position=876499, + reference_genome='GRCh38', + ), + 'coding': True, + 'noncoding': False, + }, + ], + hl.tstruct( + locus=hl.tlocus('GRCh38'), + coding=hl.tbool, + noncoding=hl.tbool, + ), + key='locus', + globals=hl.Struct( + enums=hl.Struct( + gnomad_genomes=hl.Struct(), + ), + ), + ) + coding_and_noncoding_variants_ht.write( + valid_reference_dataset_path( + ReferenceGenome.GRCh38, + ReferenceDataset.gnomad_coding_and_noncoding, + ), + overwrite=True, + ) + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_3_REMAP, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0113_test_project', + ) + worker = luigi.worker.Worker() + uvatwns_task_3 = UpdateVariantAnnotationsTableWithNewVariantsTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path=TEST_SNV_INDEL_VCF, + project_guids=['R0113_test_project'], + validations_to_skip=[], + run_id=TEST_RUN_ID, + ) + worker.add(uvatwns_task_3) + worker.run() + self.assertTrue(uvatwns_task_3.complete()) + ht = hl.read_table(uvatwns_task_3.output().path) + self.assertEqual(ht.count(), 30) + self.assertEqual( + ht.globals.updates.collect(), + [ + { + hl.Struct( + callset=TEST_SNV_INDEL_VCF, + project_guid='R0113_test_project', + remap_pedigree_hash=hl.eval( + remap_pedigree_hash(TEST_PEDIGREE_3_REMAP), + ), + ), + }, + ], + ) + self.assertEqual( + hl.eval(ht.globals.max_key_), + 29, + ) + + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_4_REMAP, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0114_project4', + ) + # Ensure that new variants are added correctly to the table. + uvatwns_task_4 = UpdateVariantAnnotationsTableWithNewVariantsTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path=TEST_SNV_INDEL_VCF, + project_guids=['R0114_project4'], + validations_to_skip=[], + run_id=TEST_RUN_ID + '-another-run', + ) + worker.add(uvatwns_task_4) + worker.run() + self.assertTrue(uvatwns_task_4.complete()) + ht = hl.read_table(uvatwns_task_4.output().path) + self.assertCountEqual( + [ + x + for x in ht.select( + 'variant_id', + 'xpos', + ).collect() + if x.locus.position <= 878809 # noqa: PLR2004 + ], + [ + hl.Struct( + locus=hl.Locus( + contig='chr1', + position=871269, + reference_genome='GRCh38', + ), + alleles=['A', 'C'], + variant_id='1-871269-A-C', + xpos=1000871269, + ), + hl.Struct( + locus=hl.Locus( + contig='chr1', + position=874734, + reference_genome='GRCh38', + ), + alleles=['C', 'T'], + variant_id='1-874734-C-T', + xpos=1000874734, + ), + hl.Struct( + locus=hl.Locus( + contig='chr1', + position=876499, + reference_genome='GRCh38', + ), + alleles=['A', 'G'], + variant_id='1-876499-A-G', + xpos=1000876499, + ), + hl.Struct( + locus=hl.Locus( + contig='chr1', + position=878314, + reference_genome='GRCh38', + ), + alleles=['G', 'C'], + variant_id='1-878314-G-C', + xpos=1000878314, + ), + hl.Struct( + locus=hl.Locus( + contig='chr1', + position=878809, + reference_genome='GRCh38', + ), + alleles=['C', 'T'], + variant_id='1-878809-C-T', + xpos=1000878809, + ), + ], + ) + self.assertCountEqual( + ht.filter( + ht.locus.position <= 878809, # noqa: PLR2004 + ).sorted_transcript_consequences.consequence_term_ids.collect(), + [ + [[9], [23, 26], [23, 13, 26]], + [[9], [23, 26], [23, 13, 26]], + [[9], [23, 26], [23, 13, 26]], + [[9], [23, 26], [23, 13, 26]], + [[9], [23, 26], [23, 13, 26]], + ], + ) + self.assertCountEqual( + ht.globals.collect(), + [ + hl.Struct( + updates={ + hl.Struct( + callset='loading_pipeline/var/test/callsets/1kg_30variants.vcf', + project_guid='R0113_test_project', + remap_pedigree_hash=hl.eval( + remap_pedigree_hash( + TEST_PEDIGREE_3_REMAP, + ), + ), + ), + hl.Struct( + callset='loading_pipeline/var/test/callsets/1kg_30variants.vcf', + project_guid='R0114_project4', + remap_pedigree_hash=hl.eval( + remap_pedigree_hash( + TEST_PEDIGREE_4_REMAP, + ), + ), + ), + }, + migrations=[], + max_key_=29, + enums=hl.Struct( + sorted_motif_feature_consequences=hl.Struct( + consequence_term=MOTIF_CONSEQUENCE_TERMS, + ), + sorted_regulatory_feature_consequences=hl.Struct( + biotype=REGULATORY_BIOTYPES, + consequence_term=REGULATORY_CONSEQUENCE_TERMS, + ), + sorted_transcript_consequences=hl.Struct( + biotype=BIOTYPES, + consequence_term=TRANSCRIPT_CONSEQUENCE_TERMS, + loftee=hl.Struct( + lof_filter=LOF_FILTERS, + ), + utrannotator=hl.Struct( + fiveutr_consequence=FIVEUTR_CONSEQUENCES, + ), + ), + ), + ), + ], + ) + + @patch('loading_pipeline.lib.misc.vep.hl.vep') + def test_update_vat_grch37( + self, + mock_vep: Mock, + ) -> None: + mock_vep.side_effect = lambda ht, **_: ht.annotate(vep=MOCK_37_VEP_DATA) + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_3_REMAP, + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0113_test_project', + ) + worker = luigi.worker.Worker() + uvatwns_task = UpdateVariantAnnotationsTableWithNewVariantsTask( + reference_genome=ReferenceGenome.GRCh37, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path=TEST_SNV_INDEL_VCF, + project_guids=['R0113_test_project'], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + worker.add(uvatwns_task) + worker.run() + self.assertTrue(uvatwns_task.complete()) + ht = hl.read_table(uvatwns_task.output().path) + self.assertEqual(ht.count(), 30) + self.assertFalse(hasattr(ht, 'rg37_locus')) + self.assertEqual( + ht.collect()[0], + hl.Struct( + locus=hl.Locus( + contig=1, + position=871269, + reference_genome='GRCh37', + ), + alleles=['A', 'C'], + rsid=None, + variant_id='1-871269-A-C', + xpos=1000871269, + sorted_transcript_consequences=[ + hl.Struct( + amino_acids='S/L', + canonical=1, + codons='tCg/tTg', + gene_id='ENSG00000188976', + hgvsc='ENST00000327044.6:c.1667C>T', + hgvsp='ENSP00000317992.6:p.Ser556Leu', + transcript_id='ENST00000327044', + biotype_id=39, + consequence_term_ids=[9], + is_lof_nagnag=None, + lof_filter_ids=[0, 1], + ), + hl.Struct( + amino_acids=None, + canonical=None, + codons=None, + gene_id='ENSG00000188976', + hgvsc='ENST00000477976.1:n.3114C>T', + hgvsp=None, + transcript_id='ENST00000477976', + biotype_id=38, + consequence_term_ids=[23, 26], + is_lof_nagnag=None, + lof_filter_ids=None, + ), + hl.Struct( + amino_acids=None, + canonical=None, + codons=None, + gene_id='ENSG00000188976', + hgvsc='ENST00000483767.1:n.523C>T', + hgvsp=None, + transcript_id='ENST00000483767', + biotype_id=38, + consequence_term_ids=[23, 26], + is_lof_nagnag=None, + lof_filter_ids=None, + ), + ], + rg38_locus=hl.Locus( + contig='chr1', + position=935889, + reference_genome='GRCh38', + ), + key_=0, + ), + ) + + def test_mito_update_vat( + self, + ) -> None: + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_5, + ReferenceGenome.GRCh38, + DatasetType.MITO, + SampleType.WGS, + 'R0115_test_project2', + ) + worker = luigi.worker.Worker() + update_variant_annotations_task = ( + UpdateVariantAnnotationsTableWithNewVariantsTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.MITO, + sample_type=SampleType.WGS, + callset_path=TEST_MITO_MT, + project_guids=['R0115_test_project2'], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + ) + worker.add(update_variant_annotations_task) + worker.run() + self.assertTrue(update_variant_annotations_task.complete()) + ht = hl.read_table(update_variant_annotations_task.output().path) + self.assertEqual(ht.count(), 5) + self.assertCountEqual( + ht.globals.collect(), + [ + hl.Struct( + enums=hl.Struct( + sorted_transcript_consequences=hl.Struct( + biotype=BIOTYPES, + consequence_term=TRANSCRIPT_CONSEQUENCE_TERMS, + lof_filter=LOF_FILTERS, + ), + mitotip=hl.Struct(trna_prediction=MITOTIP_PATHOGENICITIES), + ), + migrations=[], + max_key_=4, + updates={ + hl.Struct( + callset='loading_pipeline/var/test/callsets/mito_1.mt', + project_guid='R0115_test_project2', + remap_pedigree_hash=hl.eval( + remap_pedigree_hash( + TEST_PEDIGREE_5, + ), + ), + ), + }, + ), + ], + ) + self.assertCountEqual( + ht.collect()[0], + hl.Struct( + locus=hl.Locus( + contig='chrM', + position=3, + reference_genome='GRCh38', + ), + alleles=['T', 'C'], + common_low_heteroplasmy=False, + haplogroup=hl.Struct(is_defining=False), + mitotip=hl.Struct(trna_prediction_id=None), + rg37_locus=hl.Locus( + contig='MT', + position=3, + reference_genome='GRCh37', + ), + rsid=None, + sorted_transcript_consequences=None, + variant_id='M-3-T-C', + xpos=25000000003, + key_=0, + ), + ) + + @patch( + 'loading_pipeline.lib.tasks.write_new_variants_table.load_gencode_gene_symbol_to_gene_id', + ) + def test_sv_multiple_vcf_update_vat( + self, + mock_load_gencode: Mock, + ) -> None: + mock_load_gencode.return_value = GENE_ID_MAPPING + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_5, + ReferenceGenome.GRCh38, + DatasetType.SV, + SampleType.WGS, + 'R0115_test_project2', + ) + worker = luigi.worker.Worker() + update_variant_annotations_task = ( + UpdateVariantAnnotationsTableWithNewVariantsTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SV, + sample_type=SampleType.WGS, + callset_path=TEST_SV_VCF, + project_guids=['R0115_test_project2'], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + ) + worker.add(update_variant_annotations_task) + worker.run() + self.assertTrue(update_variant_annotations_task.complete()) + self.assertFalse( + GCSorLocalFolderTarget( + f'{self.mock_env.REFERENCE_DATASETS_DIR}/v03/GRCh38/SV/lookup.ht', + ).exists(), + ) + ht = hl.read_table(update_variant_annotations_task.output().path) + self.assertEqual(ht.count(), 13) + self.assertCountEqual( + ht.globals.collect(), + [ + hl.Struct( + enums=hl.Struct( + sv_type=SV_TYPES, + sv_type_detail=SV_TYPE_DETAILS, + sorted_gene_consequences=hl.Struct( + major_consequence=SV_CONSEQUENCE_RANKS, + ), + ), + migrations=[], + max_key_=12, + updates={ + hl.Struct( + callset=TEST_SV_VCF, + project_guid='R0115_test_project2', + remap_pedigree_hash=hl.eval( + remap_pedigree_hash( + TEST_PEDIGREE_5, + ), + ), + ), + }, + ), + ], + ) + self.assertCountEqual( + ht.collect()[:8], + [ + hl.Struct( + variant_id='BND_chr1_6', + algorithms='manta', + bothsides_support=False, + cpx_intervals=None, + end_locus=hl.Locus( + contig='chr5', + position=20404, + reference_genome='GRCh38', + ), + gnomad_svs=None, + rg37_locus=hl.Locus( + contig=1, + position=10367, + reference_genome='GRCh37', + ), + rg37_locus_end=hl.Locus( + contig=5, + position=20404, + reference_genome='GRCh37', + ), + sorted_gene_consequences=[ + hl.Struct(gene_id='ENSG00000186092', major_consequence_id=12), + hl.Struct(gene_id='ENSG00000153404', major_consequence_id=12), + ], + start_locus=hl.Locus( + contig='chr1', + position=180928, + reference_genome='GRCh38', + ), + strvctvre=hl.Struct(score=None), + sv_len=-1, + sv_type_id=2, + sv_type_detail_id=None, + xpos=1000180928, + key_=0, + ), + hl.Struct( + variant_id='BND_chr1_9', + algorithms='manta', + bothsides_support=False, + cpx_intervals=None, + end_locus=hl.Locus( + contig='chr1', + position=789481, + reference_genome='GRCh38', + ), + gnomad_svs=None, + rg37_locus=hl.Locus( + contig=1, + position=724861, + reference_genome='GRCh37', + ), + rg37_locus_end=hl.Locus( + contig=1, + position=724861, + reference_genome='GRCh37', + ), + sorted_gene_consequences=[ + hl.Struct(gene_id='ENSG00000143756', major_consequence_id=12), + hl.Struct(gene_id='ENSG00000186192', major_consequence_id=12), + ], + start_locus=hl.Locus( + contig='chr1', + position=789481, + reference_genome='GRCh38', + ), + strvctvre=hl.Struct(score=None), + sv_len=223225007, + sv_type_id=2, + sv_type_detail_id=None, + xpos=1000789481, + key_=1, + ), + hl.Struct( + variant_id='CPX_chr1_22', + algorithms='manta', + bothsides_support=True, + cpx_intervals=[ + hl.Struct( + type_id=8, + start=hl.Locus('chr1', 6558902, 'GRCh38'), + end=hl.Locus('chr1', 6559723, 'GRCh38'), + ), + hl.Struct( + type_id=6, + start=hl.Locus('chr1', 6559655, 'GRCh38'), + end=hl.Locus('chr1', 6559723, 'GRCh38'), + ), + ], + end_locus=hl.Locus( + contig='chr1', + position=6559723, + reference_genome='GRCh38', + ), + gnomad_svs=None, + rg37_locus=hl.Locus( + contig=1, + position=6618962, + reference_genome='GRCh37', + ), + rg37_locus_end=hl.Locus( + contig=1, + position=6619783, + reference_genome='GRCh37', + ), + sorted_gene_consequences=[ + hl.Struct(gene_id='ENSG00000173662', major_consequence_id=11), + ], + start_locus=hl.Locus( + contig='chr1', + position=6558902, + reference_genome='GRCh38', + ), + strvctvre=hl.Struct(score=None), + sv_len=821, + sv_type_id=3, + sv_type_detail_id=2, + xpos=1006558902, + key_=2, + ), + hl.Struct( + variant_id='CPX_chr1_251', + algorithms='manta', + bothsides_support=False, + cpx_intervals=[ + hl.Struct( + type_id=5, + start=hl.Locus('chr1', 180540234, 'GRCh38'), + end=hl.Locus('chr1', 181074767, 'GRCh38'), + ), + hl.Struct( + type_id=8, + start=hl.Locus('chr1', 181074767, 'GRCh38'), + end=hl.Locus('chr1', 181074938, 'GRCh38'), + ), + ], + end_locus=hl.Locus( + contig='chr1', + position=181074952, + reference_genome='GRCh38', + ), + gnomad_svs=None, + rg37_locus=hl.Locus( + contig=1, + position=180509370, + reference_genome='GRCh37', + ), + rg37_locus_end=hl.Locus( + contig=1, + position=181044088, + reference_genome='GRCh37', + ), + sorted_gene_consequences=[ + hl.Struct(gene_id='ENSG00000135835', major_consequence_id=0), + hl.Struct(gene_id='ENSG00000153029', major_consequence_id=0), + hl.Struct(gene_id='ENSG00000135823', major_consequence_id=0), + hl.Struct(gene_id='ENSG00000143324', major_consequence_id=0), + ], + start_locus=hl.Locus( + contig='chr1', + position=180540234, + reference_genome='GRCh38', + ), + strvctvre=hl.Struct(score=None), + sv_len=534718, + sv_type_id=3, + sv_type_detail_id=9, + xpos=1180540234, + key_=3, + ), + hl.Struct( + variant_id='CPX_chr1_41', + algorithms='manta', + bothsides_support=False, + cpx_intervals=[ + hl.Struct( + type_id=6, + start=hl.Locus('chr1', 16088760, 'GRCh38'), + end=hl.Locus('chr1', 16088835, 'GRCh38'), + ), + hl.Struct( + type_id=8, + start=hl.Locus('chr1', 16088760, 'GRCh38'), + end=hl.Locus('chr1', 16089601, 'GRCh38'), + ), + ], + end_locus=hl.Locus( + contig='chr1', + position=16089601, + reference_genome='GRCh38', + ), + gnomad_svs=None, + rg37_locus=hl.Locus( + contig=1, + position=16415255, + reference_genome='GRCh37', + ), + rg37_locus_end=hl.Locus( + contig=1, + position=16416096, + reference_genome='GRCh37', + ), + sorted_gene_consequences=[ + hl.Struct(gene_id='ENSG00000185519', major_consequence_id=12), + ], + start_locus=hl.Locus( + contig='chr1', + position=16088760, + reference_genome='GRCh38', + ), + strvctvre=hl.Struct(score=None), + sv_len=841, + sv_type_id=3, + sv_type_detail_id=12, + xpos=1016088760, + key_=4, + ), + hl.Struct( + variant_id='CPX_chr1_54', + algorithms='manta', + bothsides_support=False, + cpx_intervals=[ + hl.Struct( + type_id=6, + start=hl.Locus('chr1', 21427498, 'GRCh38'), + end=hl.Locus('chr1', 21427959, 'GRCh38'), + ), + hl.Struct( + type_id=8, + start=hl.Locus('chr1', 21427498, 'GRCh38'), + end=hl.Locus('chr1', 21480073, 'GRCh38'), + ), + hl.Struct( + type_id=5, + start=hl.Locus('chr1', 21480073, 'GRCh38'), + end=hl.Locus('chr1', 21480419, 'GRCh38'), + ), + ], + end_locus=hl.Locus( + contig='chr1', + position=21480419, + reference_genome='GRCh38', + ), + gnomad_svs=None, + rg37_locus=hl.Locus( + contig=1, + position=21753991, + reference_genome='GRCh37', + ), + rg37_locus_end=hl.Locus( + contig=1, + position=21806912, + reference_genome='GRCh37', + ), + sorted_gene_consequences=[ + hl.Struct(gene_id='ENSG00000142794', major_consequence_id=0), + ], + start_locus=hl.Locus( + contig='chr1', + position=21427498, + reference_genome='GRCh38', + ), + strvctvre=hl.Struct(score=None), + sv_len=52921, + sv_type_id=3, + sv_type_detail_id=13, + xpos=1021427498, + key_=5, + ), + hl.Struct( + variant_id='CPX_chrX_251', + algorithms='manta', + bothsides_support=False, + cpx_intervals=[ + hl.Struct( + type_id=5, + start=hl.Locus( + contig='chr1', + position=180540234, + reference_genome='GRCh38', + ), + end=hl.Locus( + contig='chr1', + position=181074767, + reference_genome='GRCh38', + ), + ), + hl.Struct( + type_id=8, + start=hl.Locus( + contig='chr1', + position=181074767, + reference_genome='GRCh38', + ), + end=hl.Locus( + contig='chr1', + position=181074938, + reference_genome='GRCh38', + ), + ), + ], + end_locus=hl.Locus( + contig='chrX', + position=2781000, + reference_genome='GRCh38', + ), + gnomad_svs=None, + sorted_gene_consequences=[ + hl.Struct(gene_id='ENSG00000135835', major_consequence_id=0), + hl.Struct(gene_id='ENSG00000153029', major_consequence_id=0), + hl.Struct(gene_id='ENSG00000135823', major_consequence_id=0), + hl.Struct(gene_id='ENSG00000143324', major_consequence_id=0), + ], + start_locus=hl.Locus( + contig='chrX', + position=3, + reference_genome='GRCh38', + ), + strvctvre=hl.Struct(score=None), + sv_type_id=3, + sv_type_detail_id=9, + sv_len=534718, + xpos=23000000003, + rg37_locus=None, + rg37_locus_end=hl.Locus( + contig='X', + position=2699041, + reference_genome='GRCh37', + ), + key_=6, + ), + hl.Struct( + variant_id='CPX_chrX_252', + algorithms='manta', + bothsides_support=False, + cpx_intervals=[ + hl.Struct( + type_id=5, + start=hl.Locus( + contig='chr1', + position=180540234, + reference_genome='GRCh38', + ), + end=hl.Locus( + contig='chr1', + position=181074767, + reference_genome='GRCh38', + ), + ), + hl.Struct( + type_id=8, + start=hl.Locus( + contig='chr1', + position=181074767, + reference_genome='GRCh38', + ), + end=hl.Locus( + contig='chr1', + position=181074938, + reference_genome='GRCh38', + ), + ), + ], + end_locus=hl.Locus( + contig='chrX', + position=2781900, + reference_genome='GRCh38', + ), + gnomad_svs=None, + sorted_gene_consequences=[ + hl.Struct(gene_id='ENSG00000135835', major_consequence_id=0), + hl.Struct(gene_id='ENSG00000153029', major_consequence_id=0), + hl.Struct(gene_id='ENSG00000135823', major_consequence_id=0), + hl.Struct(gene_id='ENSG00000143324', major_consequence_id=0), + ], + start_locus=hl.Locus( + contig='chrX', + position=2781700, + reference_genome='GRCh38', + ), + strvctvre=hl.Struct(score=None), + sv_type_id=3, + sv_type_detail_id=9, + sv_len=534718, + xpos=23002781700, + rg37_locus=hl.Locus( + contig='X', + position=2699741, + reference_genome='GRCh37', + ), + rg37_locus_end=hl.Locus( + contig='X', + position=2699941, + reference_genome='GRCh37', + ), + key_=7, + ), + ], + ) + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_5, + ReferenceGenome.GRCh38, + DatasetType.SV, + SampleType.WGS, + 'R0115_test_project2', + ) + update_variant_annotations_task = ( + UpdateVariantAnnotationsTableWithNewVariantsTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SV, + sample_type=SampleType.WGS, + callset_path=TEST_SV_VCF_2, + project_guids=['R0115_test_project2'], + validations_to_skip=[ALL_VALIDATIONS], + run_id='second_run_id', + ) + ) + worker.add(update_variant_annotations_task) + worker.run() + self.assertTrue(update_variant_annotations_task.complete()) + ht = hl.read_table(update_variant_annotations_task.output().path) + self.assertEqual(ht.count(), 14) + self.assertCountEqual( + ht.globals.collect(), + [ + hl.Struct( + enums=hl.Struct( + sv_type=SV_TYPES, + sv_type_detail=SV_TYPE_DETAILS, + sorted_gene_consequences=hl.Struct( + major_consequence=SV_CONSEQUENCE_RANKS, + ), + ), + migrations=[], + max_key_=13, + updates={ + hl.Struct( + callset=TEST_SV_VCF, + project_guid='R0115_test_project2', + remap_pedigree_hash=hl.eval( + remap_pedigree_hash( + TEST_PEDIGREE_5, + ), + ), + ), + hl.Struct( + callset=TEST_SV_VCF_2, + project_guid='R0115_test_project2', + remap_pedigree_hash=hl.eval( + remap_pedigree_hash( + TEST_PEDIGREE_5, + ), + ), + ), + }, + ), + ], + ) + self.assertCountEqual( + ht.take(1), + [ + hl.Struct( + variant_id='BND_chr1_6', + algorithms='manta', + bothsides_support=False, + cpx_intervals=None, + end_locus=hl.Locus( + contig='chr5', + position=20404, + reference_genome='GRCh38', + ), + gnomad_svs=None, + rg37_locus=hl.Locus( + contig=1, + position=10367, + reference_genome='GRCh37', + ), + rg37_locus_end=hl.Locus( + contig=5, + position=20404, + reference_genome='GRCh37', + ), + sorted_gene_consequences=[ + hl.Struct(gene_id='ENSG00000186092', major_consequence_id=12), + hl.Struct(gene_id='ENSG00000153404', major_consequence_id=12), + ], + start_locus=hl.Locus( + contig='chr1', + position=180928, + reference_genome='GRCh38', + ), + strvctvre=hl.Struct(score=None), + sv_len=-1, + sv_type_id=2, + sv_type_detail_id=None, + xpos=1000180928, + key_=0, + ), + ], + ) + + @patch( + 'loading_pipeline.lib.tasks.write_new_variants_table.load_gencode_gene_symbol_to_gene_id', + ) + def test_sv_multiple_project_single_vcf( + self, + mock_load_gencode: Mock, + ) -> None: + mock_load_gencode.return_value = GENE_ID_MAPPING + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_10, + ReferenceGenome.GRCh38, + DatasetType.SV, + SampleType.WGS, + 'R0116_test_project3', + ) + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_11, + ReferenceGenome.GRCh38, + DatasetType.SV, + SampleType.WGS, + 'R0117_test_project4', + ) + worker = luigi.worker.Worker() + update_variant_annotations_task = ( + UpdateVariantAnnotationsTableWithNewVariantsTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SV, + sample_type=SampleType.WGS, + callset_path=TEST_SV_VCF_2, + project_guids=['R0116_test_project3', 'R0117_test_project4'], + validations_to_skip=[ALL_VALIDATIONS], + run_id='run_id', + ) + ) + worker.add(update_variant_annotations_task) + worker.run() + self.assertTrue(update_variant_annotations_task.complete()) + ht = hl.read_table(update_variant_annotations_task.output().path) + self.assertEqual(ht.count(), 2) + self.assertEqual( + len(ht.globals.updates.collect()[0]), + 2, + ) + + def test_gcnv_update_vat_multiple( + self, + ) -> None: + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_5, + ReferenceGenome.GRCh38, + DatasetType.GCNV, + SampleType.WES, + 'R0115_test_project2', + ) + worker = luigi.worker.Worker() + update_variant_annotations_task = ( + UpdateVariantAnnotationsTableWithNewVariantsTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.GCNV, + sample_type=SampleType.WES, + callset_path=TEST_GCNV_BED_FILE, + project_guids=['R0115_test_project2'], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + ) + worker.add(update_variant_annotations_task) + worker.run() + self.assertTrue(update_variant_annotations_task.complete()) + self.assertFalse( + GCSorLocalFolderTarget( + f'{self.mock_env.REFERENCE_DATASETS_DIR}/v03/GRCh38/GCNV/lookup.ht', + ).exists(), + ) + ht = hl.read_table(update_variant_annotations_task.output().path) + self.assertEqual(ht.count(), 2) + self.assertCountEqual( + ht.globals.collect(), + [ + hl.Struct( + enums=hl.Struct( + sv_type=SV_TYPES, + sorted_gene_consequences=hl.Struct( + major_consequence=SV_CONSEQUENCE_RANKS, + ), + ), + migrations=[], + max_key_=1, + updates={ + hl.Struct( + callset=TEST_GCNV_BED_FILE, + project_guid='R0115_test_project2', + remap_pedigree_hash=hl.eval( + remap_pedigree_hash( + TEST_PEDIGREE_5, + ), + ), + ), + }, + ), + ], + ) + self.assertCountEqual( + ht.collect(), + [ + hl.Struct( + variant_id='suffix_16456_DEL', + end_locus=hl.Locus( + contig='chr1', + position=100023213, + reference_genome='GRCh38', + ), + gt_stats=hl.Struct( + AF=hl.eval(hl.float32(4.401408e-05)), + AC=1, + AN=22720, + Hom=None, + Het=None, + ), + num_exon=3, + rg37_locus=hl.Locus( + contig=1, + position=100472493, + reference_genome='GRCh37', + ), + rg37_locus_end=hl.Locus( + contig=1, + position=100488769, + reference_genome='GRCh37', + ), + sorted_gene_consequences=[ + hl.Struct(gene_id='ENSG00000117620', major_consequence_id=0), + hl.Struct(gene_id='ENSG00000283761', major_consequence_id=0), + hl.Struct(gene_id='ENSG22222222222', major_consequence_id=None), + ], + start_locus=hl.Locus( + contig='chr1', + position=100006937, + reference_genome='GRCh38', + ), + strvctvre=hl.Struct(score=hl.eval(hl.float32(0.583))), + sv_type_id=5, + xpos=1100006937, + key_=0, + ), + hl.Struct( + variant_id='suffix_16457_DEL', + end_locus=hl.Locus( + contig='chr1', + position=100023212, + reference_genome='GRCh38', + ), + gt_stats=hl.Struct( + AF=8.802817319519818e-05, + AC=2, + AN=22719, + Hom=None, + Het=None, + ), + num_exon=2, + rg37_locus=hl.Locus( + contig=1, + position=100483142, + reference_genome='GRCh37', + ), + rg37_locus_end=hl.Locus( + contig=1, + position=100488768, + reference_genome='GRCh37', + ), + sorted_gene_consequences=[ + hl.Struct(gene_id='ENSG00000283761', major_consequence_id=0), + hl.Struct(gene_id='ENSG22222222222', major_consequence_id=None), + ], + start_locus=hl.Locus( + contig='chr1', + position=100017586, + reference_genome='GRCh38', + ), + strvctvre=hl.Struct(score=0.5070000290870667), + sv_type_id=5, + xpos=1100017586, + key_=1, + ), + ], + ) + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_8, + ReferenceGenome.GRCh38, + DatasetType.GCNV, + SampleType.WES, + 'R0115_test_project2', + ) + update_variant_annotations_task = ( + UpdateVariantAnnotationsTableWithNewVariantsTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.GCNV, + sample_type=SampleType.WES, + callset_path=TEST_GCNV_BED_FILE_2, + project_guids=['R0115_test_project2'], + validations_to_skip=[ALL_VALIDATIONS], + run_id='second_run_id', + ) + ) + worker.add(update_variant_annotations_task) + worker.run() + ht = hl.read_table(update_variant_annotations_task.output().path) + self.assertEqual(ht.count(), 3) + self.assertCountEqual( + ht.select('gt_stats').collect(), + [ + hl.Struct( + # Existing variant, gt_stats are preserved + variant_id='suffix_16456_DEL', + gt_stats=hl.Struct( + AF=hl.eval(hl.float32(4.401408e-05)), + AC=1, + AN=22720, + Hom=None, + Het=None, + ), + ), + hl.Struct( + # Exiting variant, gt_stats are updated + variant_id='suffix_16457_DEL', + gt_stats=hl.Struct( + AF=8.111110946629196e-05, + AC=3, + AN=36986, + Hom=None, + Het=None, + ), + ), + hl.Struct( + # New variant. + variant_id='suffix_99999_DEL', + gt_stats=hl.Struct( + AF=8.802817319519818e-05, + AC=2, + AN=22719, + Hom=None, + Het=None, + ), + ), + ], + ) diff --git a/loading_pipeline/lib/tasks/validate_callset_test.py b/loading_pipeline/lib/tasks/validate_callset_test.py new file mode 100644 index 0000000000..a56f78a894 --- /dev/null +++ b/loading_pipeline/lib/tasks/validate_callset_test.py @@ -0,0 +1,83 @@ +import json +import shutil + +import luigi.worker + +from loading_pipeline.lib.core import ( + DatasetType, + ReferenceGenome, + SampleType, +) +from loading_pipeline.lib.paths import ( + valid_reference_dataset_path, +) +from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset +from loading_pipeline.lib.tasks.validate_callset import ( + ValidateCallsetTask, +) +from loading_pipeline.lib.tasks.write_validation_errors_for_run import ( + UpdatedValidationErrorsForRunTask, +) +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + +TEST_CODING_AND_NONCODING_HT = 'loading_pipeline/var/test/reference_datasets/GRCh38/gnomad_coding_and_noncoding/1.0.ht' +MULTIPLE_VALIDATION_EXCEPTIONS_VCF = ( + 'loading_pipeline/var/test/callsets/multiple_validation_exceptions.vcf' +) + +TEST_RUN_ID = 'manual__2024-04-03' + + +class ValidateCallsetTest(MockedDatarootTestCase): + def setUp(self) -> None: + super().setUp() + shutil.copytree( + TEST_CODING_AND_NONCODING_HT, + valid_reference_dataset_path( + ReferenceGenome.GRCh38, + ReferenceDataset.gnomad_coding_and_noncoding, + ), + ) + + def test_validate_callset_multiple_exceptions( + self, + ) -> None: + worker = luigi.worker.Worker() + validate_callset_task = ValidateCallsetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WES, + # NB: + # This callset contains duplicate rows for chr1:902088, + # a NON_REF allele type at position chr1: 902024, missing + # all contigs but chr1, and contains non-coding variants. + callset_path=MULTIPLE_VALIDATION_EXCEPTIONS_VCF, + project_guids=['project_a'], + run_id=TEST_RUN_ID, + ) + worker.add(validate_callset_task) + worker.run() + self.assertFalse(validate_callset_task.complete()) + + updated_validation_errors_task = UpdatedValidationErrorsForRunTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WES, + callset_path=MULTIPLE_VALIDATION_EXCEPTIONS_VCF, + project_guids=['project_a'], + run_id=TEST_RUN_ID, + ) + self.assertTrue(updated_validation_errors_task.complete()) + with updated_validation_errors_task.output().open('r') as f: + self.assertDictEqual( + json.load(f), + { + 'project_guids': ['project_a'], + 'error_messages': [ + 'Alleles with invalid allele are present in the callset. This appears to be a GVCF containing records for sites with no variants.', + 'Missing the following expected contigs:chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr2, chr20, chr21, chr22, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chrX', + "Variants are present multiple times in the callset: ['1-902088-G-A']", + 'Sample type validation error: dataset sample-type is specified as WES but appears to be WGS because it contains many common non-coding variants', + ], + }, + ) diff --git a/loading_pipeline/lib/tasks/write_metadata_for_run_test.py b/loading_pipeline/lib/tasks/write_metadata_for_run_test.py new file mode 100644 index 0000000000..2b5dc7a22d --- /dev/null +++ b/loading_pipeline/lib/tasks/write_metadata_for_run_test.py @@ -0,0 +1,188 @@ +import json +from unittest import mock +from unittest.mock import Mock + +import luigi.worker + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS +from loading_pipeline.lib.paths import relatedness_check_tsv_path +from loading_pipeline.lib.tasks.write_metadata_for_run import WriteMetadataForRunTask +from loading_pipeline.lib.test.misc import copy_project_pedigree_to_mocked_dir +from loading_pipeline.lib.test.mock_complete_task import MockCompleteTask +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + +TEST_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' +TEST_PEDIGREE_3_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_3_remap.tsv' +TEST_PEDIGREE_4_REMAP_2 = ( + 'loading_pipeline/var/test/pedigrees/test_pedigree_4_remap_2.tsv' +) +TEST_SAMPLE_QC_JSON = 'loading_pipeline/var/test/sample_qc_1.json' + + +class WriteMetadataForRunTaskTest(MockedDatarootTestCase): + @mock.patch( + 'loading_pipeline.lib.tasks.write_metadata_for_run.sample_qc_json_path', + lambda *_: TEST_SAMPLE_QC_JSON, + ) + @mock.patch('loading_pipeline.lib.tasks.write_metadata_for_run.FeatureFlag') + @mock.patch( + 'loading_pipeline.lib.tasks.write_sex_check_table.WriteTDRMetricsFilesTask', + ) + @mock.patch( + 'loading_pipeline.lib.tasks.write_metadata_for_run.WriteSampleQCJsonTask', + ) + def test_write_metadata_for_run_task( + self, + write_sample_qc_json_task: Mock, + write_tdr_metrics_task: Mock, + mock_ff: Mock, + ) -> None: + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_3_REMAP, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0113_test_project', + ) + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_4_REMAP_2, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0114_project4', + ) + mock_ff.EXPECT_TDR_METRICS = True + write_tdr_metrics_task.return_value = MockCompleteTask() + write_sample_qc_json_task.return_value = MockCompleteTask() + worker = luigi.worker.Worker() + write_metadata_for_run_task = WriteMetadataForRunTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path=TEST_VCF, + project_guids=['R0113_test_project', 'R0114_project4'], + validations_to_skip=[ALL_VALIDATIONS], + run_id='run_123456', + ) + worker.add(write_metadata_for_run_task) + worker.run() + self.assertTrue( + 'run_123456/metadata.json' in write_metadata_for_run_task.output().path, + ) + self.assertTrue(write_metadata_for_run_task.complete()) + with write_metadata_for_run_task.output().open('r') as f: + self.assertDictEqual( + json.load(f), + { + 'callsets': [TEST_VCF], + 'project_guids': ['R0113_test_project', 'R0114_project4'], + 'failed_family_samples': { + 'missing_samples': { + 'efg_1': { + # This sample is present in the callset, but intentionally + # mapped away + 'samples': ['NA20888_1'], + 'reasons': ["Missing samples: {'NA20888_1'}"], + }, + }, + 'relatedness_check': {}, + 'sex_check': {}, + 'ploidy_check': {}, + }, + 'family_samples': { + 'abc_1': [ + 'HG00731_1', + 'HG00732_1', + 'HG00733_1', + ], + '123_1': ['NA19675_1'], + '234_1': ['NA19678_1'], + '345_1': ['NA19679_1'], + '456_1': ['NA20870_1'], + '567_1': ['NA20872_1'], + '678_1': ['NA20874_1'], + '789_1': ['NA20875_1'], + '890_1': ['NA20876_1'], + '901_1': ['NA20877_1'], + 'bcd_1': ['NA20878_1'], + 'cde_1': ['NA20881_1'], + 'def_1': ['NA20885_1'], + }, + 'run_id': 'run_123456', + 'sample_type': SampleType.WGS.value, + 'relatedness_check_file_path': relatedness_check_tsv_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_VCF, + ), + 'sample_qc': { + 'HG00731_1': {'filter_flags': ['coverage', 'contamination']}, + 'HG00732_1': {'filter_flags': ['coverage']}, + 'HG00733_1': {'filter_flags': ['contamination']}, + 'NA19675_1': {'filter_flags': []}, + 'NA20888_1': {'filter_flags': ['sample_failed']}, + }, + }, + ) + + @mock.patch('loading_pipeline.lib.tasks.write_metadata_for_run.FeatureFlag') + def test_write_metadata_for_run_task_without_tdr_metrics( + self, + mock_ff: Mock, + ) -> None: + # When WriteSampleQCJsonTask is not a requirement, every project's + # remapped and subsetted callset must still be collected. + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_3_REMAP, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0113_test_project', + ) + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_4_REMAP_2, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0114_project4', + ) + mock_ff.EXPECT_TDR_METRICS = False + worker = luigi.worker.Worker() + write_metadata_for_run_task = WriteMetadataForRunTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path=TEST_VCF, + project_guids=['R0113_test_project', 'R0114_project4'], + validations_to_skip=[ALL_VALIDATIONS], + run_id='run_123457', + ) + worker.add(write_metadata_for_run_task) + worker.run() + self.assertTrue(write_metadata_for_run_task.complete()) + with write_metadata_for_run_task.output().open('r') as f: + metadata_json = json.load(f) + self.assertDictEqual( + metadata_json['family_samples'], + { + 'abc_1': [ + 'HG00731_1', + 'HG00732_1', + 'HG00733_1', + ], + '123_1': ['NA19675_1'], + '234_1': ['NA19678_1'], + '345_1': ['NA19679_1'], + '456_1': ['NA20870_1'], + '567_1': ['NA20872_1'], + '678_1': ['NA20874_1'], + '789_1': ['NA20875_1'], + '890_1': ['NA20876_1'], + '901_1': ['NA20877_1'], + 'bcd_1': ['NA20878_1'], + 'cde_1': ['NA20881_1'], + 'def_1': ['NA20885_1'], + }, + ) + self.assertDictEqual(metadata_json['sample_qc'], {}) diff --git a/loading_pipeline/lib/tasks/write_relatedness_check_table_test.py b/loading_pipeline/lib/tasks/write_relatedness_check_table_test.py new file mode 100644 index 0000000000..7cc814a5fa --- /dev/null +++ b/loading_pipeline/lib/tasks/write_relatedness_check_table_test.py @@ -0,0 +1,120 @@ +import shutil +from unittest.mock import patch + +import hail as hl +import luigi.worker + +from loading_pipeline.lib.core import ( + DatasetType, + ReferenceGenome, + SampleType, +) +from loading_pipeline.lib.misc.io import import_vcf +from loading_pipeline.lib.paths import ( + postprocessed_callset_path, + relatedness_check_table_path, + valid_reference_dataset_path, +) +from loading_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset +from loading_pipeline.lib.tasks.write_relatedness_check_table import ( + WriteRelatednessCheckTableTask, +) +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + +TEST_GNOMAD_QC_HT = ( + 'loading_pipeline/var/test/reference_datasets/GRCh38/gnomad_qc/1.0.ht' +) +TEST_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' +TEST_RUN_ID = 'manual__2024-04-03' + + +class WriteRelatednessCheckTableTaskTest(MockedDatarootTestCase): + def setUp(self) -> None: + super().setUp() + shutil.copytree( + TEST_GNOMAD_QC_HT, + valid_reference_dataset_path( + ReferenceGenome.GRCh38, + ReferenceDataset.gnomad_qc, + ), + ) + + # Force imported callset to be complete + ht = import_vcf(TEST_VCF, ReferenceGenome.GRCh38) + ht = ht.annotate_globals(validated_sample_type=SampleType.WGS.value) + ht = ht.annotate_rows(**{'info.AF': ht.info.AF}) + ht.write( + postprocessed_callset_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_VCF, + ), + ) + + def test_relatedness_check_table_task_gnomad_qc_updated( + self, + ) -> None: + self.assertEqual( + hl.eval( + hl.read_table( + valid_reference_dataset_path( + ReferenceGenome.GRCh38, + ReferenceDataset.gnomad_qc, + ), + ).version, + ), + '1.0', + ) + with ( + patch.object( + ReferenceDataset, + 'version', + return_value='2.0', + ), + patch.object( + ReferenceDataset, + 'get_ht', + lambda *_: hl.Table.parallelize( + [], + hl.tstruct( + locus=hl.tlocus('GRCh38'), + alleles=hl.tarray(hl.tstr), + ), + key=['locus', 'alleles'], + globals=hl.Struct(version='2.0'), + ), + ), + ): + worker = luigi.worker.Worker() + task = WriteRelatednessCheckTableTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id=TEST_RUN_ID, + sample_type=SampleType.WGS, + callset_path=TEST_VCF, + ) + worker.add(task) + worker.run() + self.assertTrue(task.complete()) + self.assertEqual( + hl.eval( + hl.read_table( + valid_reference_dataset_path( + ReferenceGenome.GRCh38, + ReferenceDataset.gnomad_qc, + ), + ).version, + ), + '2.0', + ) + ht = hl.read_table( + relatedness_check_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_VCF, + ), + ) + self.assertEqual( + ht.collect(), + [], + ) diff --git a/loading_pipeline/lib/tasks/write_relatedness_check_tsv_test.py b/loading_pipeline/lib/tasks/write_relatedness_check_tsv_test.py new file mode 100644 index 0000000000..35a9956f78 --- /dev/null +++ b/loading_pipeline/lib/tasks/write_relatedness_check_tsv_test.py @@ -0,0 +1,53 @@ +import shutil + +import luigi.worker + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.paths import relatedness_check_table_path +from loading_pipeline.lib.tasks.write_relatedness_check_tsv import ( + WriteRelatednessCheckTsvTask, +) +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + +TEST_RELATEDNESS_CHECK_1 = ( + 'loading_pipeline/var/test/relatedness_check/test_relatedness_check_1.ht' +) +TEST_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' +TEST_RUN_ID = 'manual__2024-04-03' + + +class WriteRelatednessCheckTsvTaskTest(MockedDatarootTestCase): + def setUp(self) -> None: + super().setUp() + shutil.copytree( + TEST_RELATEDNESS_CHECK_1, + relatedness_check_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_VCF, + ), + ) + + def test_write_relatedness_check_tsv_task( + self, + ) -> None: + worker = luigi.worker.Worker() + task = WriteRelatednessCheckTsvTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + callset_path=TEST_VCF, + run_id=TEST_RUN_ID, + sample_type=SampleType.WES, + ) + worker.add(task) + worker.run() + self.assertTrue(task.complete()) + with task.output().open('r') as f: + lines = f.readlines() + expected_lines = [ + 'i\tj\tibd0\tibd1\tibd2\tpi_hat\n', + 'HG00731_1\tHG00733_1\t0\t1\t0\t5.0000e-01\n', + 'HG00732_1\tHG00733_1\t0\t1\t0\t5.0000e-01\n', + ] + for expected_line, actual_line in zip(expected_lines, lines, strict=False): + self.assertEqual(expected_line, actual_line) diff --git a/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset_test.py b/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset_test.py new file mode 100644 index 0000000000..590795424a --- /dev/null +++ b/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset_test.py @@ -0,0 +1,460 @@ +import json +import shutil +from unittest.mock import Mock, patch + +import hail as hl +import luigi.worker + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.misc.io import remap_pedigree_hash +from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS +from loading_pipeline.lib.paths import ( + relatedness_check_table_path, + sex_check_table_path, +) +from loading_pipeline.lib.tasks.write_remapped_and_subsetted_callset import ( + WriteRemappedAndSubsettedCallsetTask, +) +from loading_pipeline.lib.tasks.write_validation_errors_for_run import ( + UpdatedValidationErrorsForRunTask, +) +from loading_pipeline.lib.test.misc import copy_project_pedigree_to_mocked_dir +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + +TEST_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' +TEST_PEDIGREE_3_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_3_remap.tsv' +TEST_PEDIGREE_3_DIFFERENT_FAMILIES = ( + 'loading_pipeline/var/test/pedigrees/test_pedigree_3_different_families.tsv' +) +TEST_PEDIGREE_4_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_4_remap.tsv' +TEST_PEDIGREE_7 = 'loading_pipeline/var/test/pedigrees/test_pedigree_7.tsv' +TEST_SEX_CHECK_1 = 'loading_pipeline/var/test/sex_check/test_sex_check_1.ht' +TEST_RELATEDNESS_CHECK_1 = ( + 'loading_pipeline/var/test/relatedness_check/test_relatedness_check_1.ht' +) + +TEST_RUN_ID = 'manual__2024-04-03' + + +class WriteRemappedAndSubsettedCallsetTaskTest(MockedDatarootTestCase): + def setUp(self) -> None: + super().setUp() + # +-------------+---------------+ + # | s | predicted_sex | + # +-------------+---------------+ + # | str | str | + # +-------------+---------------+ + # | "HG00731_1" | "F" | + # | "HG00732_1" | "M" | + # | "HG00733_1" | "F" | + # | "NA19675_1" | "F" | + # | "NA19678_1" | "M" | + # | "NA19679_1" | "F" | + # | "NA20870_1" | "F" | + # | "NA20872_1" | "M" | + # | "NA20874_1" | "F" | + # | "NA20875_1" | "F" | + # | "NA20876_1" | "F" | + # | "NA20877_1" | "F" | + # | "NA20878_1" | "M" | + # | "NA20881_1" | "M" | + # | "NA20885_1" | "F" | + # | "NA20888_1" | "F" | + # +-------------+---------------+ + shutil.copytree( + TEST_SEX_CHECK_1, + sex_check_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_VCF, + ), + ) + # +-------------+-------------+-------+-------+-------+----------+ + # | i | j | ibd0 | ibd1 | ibd2 | pi_hat | + # +-------------+-------------+-------+-------+-------+----------+ + # | str | str | int32 | int32 | int32 | float64 | + # +-------------+-------------+-------+-------+-------+----------+ + # | "HG00731_1" | "HG00733_1" | 0 | 1 | 0 | 5.00e-01 | + # | "HG00732_1" | "HG00733_1" | 0 | 1 | 0 | 5.00e-01 | + # +-------------+-------------+-------+-------+-------+----------+ + shutil.copytree( + TEST_RELATEDNESS_CHECK_1, + relatedness_check_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_VCF, + ), + ) + + def test_write_remapped_and_subsetted_callset_task( + self, + ) -> None: + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_3_REMAP, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0113_test_project', + ) + worker = luigi.worker.Worker() + wrsc_task = WriteRemappedAndSubsettedCallsetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id=TEST_RUN_ID, + sample_type=SampleType.WGS, + callset_path=TEST_VCF, + project_guids=['R0113_test_project'], + project_i=0, + validations_to_skip=[ALL_VALIDATIONS], + skip_expect_tdr_metrics=True, + ) + worker.add(wrsc_task) + worker.run() + self.assertTrue(wrsc_task.complete()) + mt = hl.read_matrix_table(wrsc_task.output().path) + self.assertEqual(mt.count(), (30, 3)) + self.assertEqual( + mt.globals.collect(), + [ + hl.Struct( + remap_pedigree_hash=hl.eval( + remap_pedigree_hash( + TEST_PEDIGREE_3_REMAP, + ), + ), + failed_family_samples=hl.Struct( + missing_samples={}, + relatedness_check={}, + sex_check={}, + ploidy_check={}, + ), + family_samples={'abc_1': ['HG00731_1', 'HG00732_1', 'HG00733_1']}, + ), + ], + ) + + @patch( + 'loading_pipeline.lib.tasks.write_remapped_and_subsetted_callset.FeatureFlag', + ) + def test_write_remapped_and_subsetted_callset_task_failed_some_family_checks( + self, + mock_ff: Mock, + ) -> None: + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_4_REMAP, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0114_project4', + ) + mock_ff.CHECK_SEX_AND_RELATEDNESS = True + worker = luigi.worker.Worker() + wrsc_task = WriteRemappedAndSubsettedCallsetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id=TEST_RUN_ID, + sample_type=SampleType.WGS, + callset_path=TEST_VCF, + project_guids=['R0114_project4'], + project_i=0, + validations_to_skip=[ALL_VALIDATIONS], + skip_expect_tdr_metrics=True, + ) + worker.add(wrsc_task) + worker.run() + self.assertTrue(wrsc_task.complete()) + mt = hl.read_matrix_table(wrsc_task.output().path) + # NB: one "family"/"sample" has been removed because of a failed sex check, + # and 4 removed because of a failed ploidy check! + self.assertEqual(mt.count(), (30, 8)) + self.assertEqual( + mt.globals.collect(), + [ + hl.Struct( + remap_pedigree_hash=hl.eval( + remap_pedigree_hash( + TEST_PEDIGREE_4_REMAP, + ), + ), + family_samples={ + '123_1': ['NA19675_1'], + '345_1': ['NA19679_1'], + '456_1': ['NA20870_1'], + '678_1': ['NA20874_1'], + '789_1': ['NA20875_1'], + '890_1': ['NA20876_1'], + '901_1': ['NA20877_1'], + 'efg_1': ['NA20888_1'], + }, + failed_family_samples=hl.Struct( + missing_samples={}, + relatedness_check={}, + sex_check={ + 'def_1': { + 'reasons': [ + 'Sample NA20885_1 has pedigree sex M but imputed sex F', + ], + 'samples': ['NA20885_1'], + }, + }, + ploidy_check={ + '234_1': { + 'reasons': [ + "Found samples with misaligned ploidy with their provided imputed sex: ['NA19678_1']", + ], + 'samples': ['NA19678_1'], + }, + '567_1': { + 'reasons': [ + "Found samples with misaligned ploidy with their provided imputed sex: ['NA20872_1']", + ], + 'samples': ['NA20872_1'], + }, + 'bcd_1': { + 'reasons': [ + "Found samples with misaligned ploidy with their provided imputed sex: ['NA20878_1']", + ], + 'samples': ['NA20878_1'], + }, + 'cde_1': { + 'reasons': [ + "Found samples with misaligned ploidy with their provided imputed sex: ['NA20881_1']", + ], + 'samples': ['NA20881_1'], + }, + }, + ), + ), + ], + ) + + @patch( + 'loading_pipeline.lib.tasks.write_remapped_and_subsetted_callset.FeatureFlag', + ) + def test_write_remapped_and_subsetted_callset_task_all_families_failed( + self, + mock_ff: Mock, + ) -> None: + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_7, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0114_project4', + ) + mock_ff.CHECK_SEX_AND_RELATEDNESS = True + worker = luigi.worker.Worker() + wrsc_task = WriteRemappedAndSubsettedCallsetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id=TEST_RUN_ID, + sample_type=SampleType.WGS, + callset_path=TEST_VCF, + project_guids=['R0114_project4'], + project_i=0, + validations_to_skip=[ALL_VALIDATIONS], + skip_expect_tdr_metrics=True, + ) + worker.add(wrsc_task) + worker.run() + self.assertFalse(wrsc_task.complete()) + updated_validation_errors_task = UpdatedValidationErrorsForRunTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WES, + callset_path=TEST_VCF, + project_guids=['R0114_project4'], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + self.assertTrue(updated_validation_errors_task.complete()) + with updated_validation_errors_task.output().open('r') as f: + self.assertDictEqual( + json.load(f), + { + 'project_guids': ['R0114_project4'], + 'error_messages': ['All families failed validation checks'], + 'failed_family_samples': { + 'missing_samples': { + 'efg_1': { + 'samples': ['NA99999_1'], + 'reasons': ["Missing samples: {'NA99999_1'}"], + }, + }, + 'relatedness_check': {}, + 'sex_check': { + '890_1': { + 'samples': ['NA20876_1'], + 'reasons': [ + 'Sample NA20876_1 has pedigree sex M but imputed sex F', + ], + }, + '456_1': { + 'samples': ['NA20870_1'], + 'reasons': [ + 'Sample NA20870_1 has pedigree sex M but imputed sex F', + ], + }, + '123_1': { + 'samples': ['NA19675_1'], + 'reasons': [ + 'Sample NA19675_1 has pedigree sex M but imputed sex F', + ], + }, + '678_1': { + 'samples': ['NA20874_1'], + 'reasons': [ + 'Sample NA20874_1 has pedigree sex M but imputed sex F', + ], + }, + '789_1': { + 'samples': ['NA20875_1'], + 'reasons': [ + 'Sample NA20875_1 has pedigree sex M but imputed sex F', + ], + }, + '901_1': { + 'samples': ['NA20877_1'], + 'reasons': [ + 'Sample NA20877_1 has pedigree sex M but imputed sex F', + ], + }, + '345_1': { + 'samples': ['NA19679_1'], + 'reasons': [ + 'Sample NA19679_1 has pedigree sex M but imputed sex F', + ], + }, + 'def_1': { + 'samples': ['NA20885_1'], + 'reasons': [ + 'Sample NA20885_1 has pedigree sex M but imputed sex F', + ], + }, + }, + 'ploidy_check': { + '567_1': { + 'samples': ['NA20872_1'], + 'reasons': [ + "Found samples with misaligned ploidy with their provided imputed sex: ['NA20872_1']", + ], + }, + '234_1': { + 'samples': ['NA19678_1'], + 'reasons': [ + "Found samples with misaligned ploidy with their provided imputed sex: ['NA19678_1']", + ], + }, + 'bcd_1': { + 'samples': ['NA20878_1'], + 'reasons': [ + "Found samples with misaligned ploidy with their provided imputed sex: ['NA20878_1']", + ], + }, + 'cde_1': { + 'samples': ['NA20881_1'], + 'reasons': [ + "Found samples with misaligned ploidy with their provided imputed sex: ['NA20881_1']", + ], + }, + }, + }, + }, + ) + + @patch( + 'loading_pipeline.lib.tasks.write_remapped_and_subsetted_callset.FeatureFlag', + ) + def test_write_remapped_and_subsetted_callset_task_combined_validation_errors( + self, + mock_ff: Mock, + ) -> None: + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_3_DIFFERENT_FAMILIES, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0113_test_project', + ) + worker = luigi.worker.Worker() + + wrsc_task_1 = WriteRemappedAndSubsettedCallsetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id=TEST_RUN_ID, + sample_type=SampleType.WGS, + callset_path=TEST_VCF, + project_guids=['R0113_test_project'], + project_i=0, + validations_to_skip=[ALL_VALIDATIONS], + skip_expect_tdr_metrics=True, + ) + worker.add(wrsc_task_1) + worker.run() + + # Second run: load pedigree 7 where all families fail validation checks + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_7, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0114_project4', + ) + worker_2 = luigi.worker.Worker() + + wrsc_task_2 = WriteRemappedAndSubsettedCallsetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id=TEST_RUN_ID, + sample_type=SampleType.WGS, + callset_path=TEST_VCF, + project_guids=['R0114_project4'], + project_i=0, + validations_to_skip=[ALL_VALIDATIONS], + skip_expect_tdr_metrics=True, + ) + worker_2.add(wrsc_task_2) + worker_2.run() + + # Verify second task does not complete (all families failed) + self.assertFalse(wrsc_task_2.complete()) + + # Verify validation errors for second run + updated_validation_errors_task = UpdatedValidationErrorsForRunTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WES, + callset_path=TEST_VCF, + project_guids=['R0113_test_project', 'R0114_project4'], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + ) + self.assertTrue(updated_validation_errors_task.complete()) + with updated_validation_errors_task.output().open('r') as f: + validation_errors = json.load(f) + + # Verify that all families failed in the second run + self.assertIn( + 'All families failed validation checks', + validation_errors['error_messages'], + ) + # Should have missing samples, sex checks, and ploidy checks all failing + failed_samples = validation_errors['failed_family_samples'] + self.assertGreater( + len(failed_samples['missing_samples']), + 0, + 'Expected missing_samples to have failures', + ) + self.assertGreater( + len(failed_samples['sex_check']), + 0, + 'Expected sex_check to have failures', + ) + self.assertGreater( + len(failed_samples['ploidy_check']), + 0, + 'Expected ploidy_check to have failures', + ) + # Verify that both project guids are in the validation errors + self.assertIn('R0113_test_project', validation_errors['project_guids']) + self.assertIn('R0114_project4', validation_errors['project_guids']) diff --git a/loading_pipeline/lib/tasks/write_sample_qc_json_test.py b/loading_pipeline/lib/tasks/write_sample_qc_json_test.py new file mode 100644 index 0000000000..1c2709c9b7 --- /dev/null +++ b/loading_pipeline/lib/tasks/write_sample_qc_json_test.py @@ -0,0 +1,269 @@ +import json +import os +import shutil +from unittest.mock import Mock, patch + +import hail as hl +import hailtop.fs as hfs +import luigi.worker + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS +from loading_pipeline.lib.paths import ancestry_model_rf_path, tdr_metrics_dir +from loading_pipeline.lib.tasks.write_sample_qc_json import WriteSampleQCJsonTask +from loading_pipeline.lib.test.misc import copy_project_pedigree_to_mocked_dir +from loading_pipeline.lib.test.mock_complete_task import MockCompleteTask +from loading_pipeline.lib.test.mocked_reference_datasets_testcase import ( + MockedReferenceDatasetsTestCase, +) + +TEST_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' +TEST_PEDIGREE_3_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_3_remap.tsv' +TEST_TDR_METRICS_FILE = 'loading_pipeline/var/test/tdr_metrics.tsv' +TEST_RUN_ID = 'manual__2024-04-03' + +PCA_SCORES = [0.00212, 0.011, 0.0105, 0.161, 0.026] + [0.1 for _ in range(15)] +EXPECTED_ANC_PROBABILITIES = { + 'prob_afr': 0.02, + 'prob_ami': 0.0, + 'prob_amr': 0.02, + 'prob_asj': 0.9, + 'prob_eas': 0.0, + 'prob_fin': 0.0, + 'prob_mid': 0.0, + 'prob_nfe': 0.05, + 'prob_sas': 0.01, +} +TEST_ANCESTRY_IMPUTATION_MODEL_PATH = ( + 'loading_pipeline/var/test/ancestry_imputation_model.onnx' +) + + +class WriteSampleQCJsonTaskTest(MockedReferenceDatasetsTestCase): + @patch('loading_pipeline.lib.methods.sample_qc.assign_population_pcs') + @patch('loading_pipeline.lib.methods.sample_qc.pc_project') + @patch('loading_pipeline.lib.tasks.write_sample_qc_json.WriteTDRMetricsFilesTask') + def test_call_sample_qc( + self, + mock_tdr_task: Mock, + mock_pc_project: Mock, + mock_assign_population_pcs: Mock, + ) -> None: + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_3_REMAP, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0113_test_project', + ) + os.makedirs( + os.path.dirname(ancestry_model_rf_path()), + exist_ok=True, + ) + shutil.copy2(TEST_ANCESTRY_IMPUTATION_MODEL_PATH, ancestry_model_rf_path()) + os.makedirs( + tdr_metrics_dir(ReferenceGenome.GRCh38, DatasetType.SNV_INDEL), + exist_ok=True, + ) + shutil.copy2( + TEST_TDR_METRICS_FILE, + tdr_metrics_dir(ReferenceGenome.GRCh38, DatasetType.SNV_INDEL), + ) + mock_tdr_task.return_value = MockCompleteTask() + mock_pc_project.return_value = hl.Table.parallelize( + [ + { + 's': sample_id, + 'scores': PCA_SCORES, + } + for sample_id in ('HG00731', 'HG00732', 'HG00733', 'NA19675') + ], + hl.tstruct( + s=hl.tstr, + scores=hl.tarray(hl.tfloat64), + ), + key='s', + ) + mock_assign_population_pcs.return_value = ( + hl.Table.parallelize( + [ + { + 's': sample_id, + 'pca_scores': PCA_SCORES, + 'qc_pop': 'asj', + **EXPECTED_ANC_PROBABILITIES, + } + for sample_id in ('HG00731', 'HG00732', 'HG00733', 'NA19675') + ], + hl.tstruct( + s=hl.tstr, + pca_scores=hl.tarray(hl.tfloat64), + qc_pop=hl.tstr, + prob_afr=hl.tfloat64, + prob_ami=hl.tfloat64, + prob_amr=hl.tfloat64, + prob_asj=hl.tfloat64, + prob_eas=hl.tfloat64, + prob_fin=hl.tfloat64, + prob_mid=hl.tfloat64, + prob_nfe=hl.tfloat64, + prob_sas=hl.tfloat64, + ), + key='s', + ), + None, + ) + worker = luigi.worker.Worker() + task = WriteSampleQCJsonTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id=TEST_RUN_ID, + sample_type=SampleType.WGS, + callset_path=TEST_VCF, + project_guids=['R0113_test_project'], + validations_to_skip=[ALL_VALIDATIONS], + ) + worker.add(task) + worker.run() + self.assertTrue(task) + self.assertTrue(hfs.exists(task.output().path)) + + expected_qc_gen_anc_results = { + 'pca_scores': PCA_SCORES, + **EXPECTED_ANC_PROBABILITIES, + **{f'pop_PC{i + 1}': PCA_SCORES[i] for i in range(20)}, + 'qc_gen_anc': 'oth', + } + with task.output().open('r') as f: + res = json.load(f) + + self.assertCountEqual( + res['HG00731_1'], + { + 'seqr_id': 'HG00731_1', + 'vcf_id': 'HG00731', + 'filtered_callrate': 1.0, + 'contamination_rate': 5.099999904632568, + 'percent_bases_at_20x': 93.69000244140625, + 'mean_coverage': 29.309999465942383, + 'filter_flags': ['contamination', 'coverage'], + **expected_qc_gen_anc_results, + 'sample_qc.call_rate': 0.9666666666666667, + 'sample_qc.n_called': 29, + 'sample_qc.n_not_called': 1, + 'sample_qc.n_filtered': 0, + 'sample_qc.n_hom_ref': 16, + 'sample_qc.n_het': 2, + 'sample_qc.n_hom_var': 11, + 'sample_qc.n_non_ref': 13, + 'sample_qc.n_singleton': 1, + 'sample_qc.n_snp': 24, + 'sample_qc.n_insertion': 0, + 'sample_qc.n_deletion': 0, + 'sample_qc.n_transition': 15, + 'sample_qc.n_transversion': 9, + 'sample_qc.n_star': 0, + 'sample_qc.r_ti_tv': 1.6666666666666667, + 'sample_qc.r_het_hom_var': 0.18181818181818182, + 'sample_qc.r_insertion_deletion': None, + 'sample_qc.f_inbreeding.f_stat': 0.284195245767986, + 'sample_qc.f_inbreeding.n_called': 29, + 'sample_qc.f_inbreeding.expected_homs': 26.20594199999999, + 'sample_qc.f_inbreeding.observed_homs': 27, + 'fail_n_snp': True, + 'fail_r_ti_tv': False, + 'fail_r_insertion_deletion': None, + 'fail_n_insertion': True, + 'fail_n_deletion': True, + 'fail_r_het_hom_var': False, + 'fail_call_rate': False, + 'qc_metrics_filters': ['n_deletion', 'n_insertion', 'n_snp'], + }, + ) + self.assertCountEqual( + res['HG00732_1'], + { + 'seqr_id': 'HG00732_1', + 'vcf_id': 'HG00732', + 'filtered_callrate': 1.0, + 'contamination_rate': 5.0, + 'percent_bases_at_20x': 90.0, + 'mean_coverage': 28.0, + 'filter_flags': ['coverage'], + **expected_qc_gen_anc_results, + 'sample_qc.call_rate': 0.9666666666666667, + 'sample_qc.n_called': 29, + 'sample_qc.n_not_called': 1, + 'sample_qc.n_filtered': 0, + 'sample_qc.n_hom_ref': 16, + 'sample_qc.n_het': 4, + 'sample_qc.n_hom_var': 9, + 'sample_qc.n_non_ref': 13, + 'sample_qc.n_singleton': 2, + 'sample_qc.n_snp': 22, + 'sample_qc.n_insertion': 0, + 'sample_qc.n_deletion': 0, + 'sample_qc.n_transition': 13, + 'sample_qc.n_transversion': 9, + 'sample_qc.n_star': 0, + 'sample_qc.r_ti_tv': 1.4444444444444444, + 'sample_qc.r_het_hom_var': 0.4444444444444444, + 'sample_qc.r_insertion_deletion': None, + 'sample_qc.f_inbreeding.f_stat': -0.431609508464028, + 'sample_qc.f_inbreeding.n_called': 29, + 'sample_qc.f_inbreeding.expected_homs': 26.20594199999999, + 'sample_qc.f_inbreeding.observed_homs': 25, + 'fail_n_snp': True, + 'fail_r_ti_tv': False, + 'fail_r_insertion_deletion': None, + 'fail_n_insertion': True, + 'fail_n_deletion': True, + 'fail_r_het_hom_var': False, + 'fail_call_rate': False, + 'qc_metrics_filters': ['n_deletion', 'n_insertion', 'n_snp'], + }, + ) + self.assertCountEqual( + res['HG00733_1'], + { + 'seqr_id': 'HG00733_1', + 'vcf_id': 'HG00733', + 'filtered_callrate': 1.0, + 'contamination_rate': 6.0, + 'percent_bases_at_20x': 85.0, + 'mean_coverage': 36.400001525878906, + 'filter_flags': ['contamination'], + **expected_qc_gen_anc_results, + 'sample_qc.call_rate': 1.0, + 'sample_qc.n_called': 30, + 'sample_qc.n_not_called': 0, + 'sample_qc.n_filtered': 0, + 'sample_qc.n_hom_ref': 17, + 'sample_qc.n_het': 3, + 'sample_qc.n_hom_var': 10, + 'sample_qc.n_non_ref': 13, + 'sample_qc.n_singleton': 0, + 'sample_qc.n_snp': 23, + 'sample_qc.n_insertion': 0, + 'sample_qc.n_deletion': 0, + 'sample_qc.n_transition': 13, + 'sample_qc.n_transversion': 10, + 'sample_qc.n_star': 0, + 'sample_qc.r_ti_tv': 1.3, + 'sample_qc.r_het_hom_var': 0.3, + 'sample_qc.r_insertion_deletion': None, + 'sample_qc.f_inbreeding.f_stat': -0.038400752079048056, + 'sample_qc.f_inbreeding.n_called': 30, + 'sample_qc.f_inbreeding.expected_homs': 27.11094199999999, + 'sample_qc.f_inbreeding.observed_homs': 27, + 'fail_n_snp': True, + 'fail_r_ti_tv': False, + 'fail_r_insertion_deletion': None, + 'fail_n_insertion': True, + 'fail_n_deletion': True, + 'fail_r_het_hom_var': False, + 'fail_call_rate': False, + 'qc_metrics_filters': ['n_deletion', 'n_insertion', 'n_snp'], + }, + ) + self.assertFalse('NA19675' in res) diff --git a/loading_pipeline/lib/tasks/write_sex_check_table_test.py b/loading_pipeline/lib/tasks/write_sex_check_table_test.py new file mode 100644 index 0000000000..1f83d8c991 --- /dev/null +++ b/loading_pipeline/lib/tasks/write_sex_check_table_test.py @@ -0,0 +1,157 @@ +from decimal import Decimal +from unittest.mock import Mock, patch + +import google.cloud.bigquery +import hail as hl +import luigi.worker + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.paths import sex_check_table_path, tdr_metrics_path +from loading_pipeline.lib.tasks.write_sex_check_table import ( + WriteSexCheckTableTask, +) +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + +TEST_SEX_AND_RELATEDNESS_CALLSET_MT = ( + 'loading_pipeline/var/test/callsets/sex_and_relatedness_1.mt' +) + + +class WriteSexCheckTableTaskTest(MockedDatarootTestCase): + @patch('loading_pipeline.lib.tasks.write_tdr_metrics_files.gen_bq_table_names') + @patch('loading_pipeline.lib.tasks.write_tdr_metrics_file.bq_metrics_query') + @patch( + 'loading_pipeline.lib.tasks.write_sex_check_table.FeatureFlag', + ) + def test_snv_sex_check_table_task( + self, + mock_ff: Mock, + mock_bq_metrics_query: Mock, + mock_gen_bq_table_names: Mock, + ) -> None: + mock_ff.EXPECT_TDR_METRICS = True + mock_gen_bq_table_names.return_value = [ + 'datarepo-7242affb.datarepo_RP_3053', + 'datarepo-5a72e31b.datarepo_RP_3056', + ] + mock_bq_metrics_query.side_effect = [ + iter( + [ + google.cloud.bigquery.table.Row( + ( + 'SM-NJ8MF', + 'Unknown', + Decimal('0'), + Decimal('0'), + Decimal('0'), + ), + { + 'collaborator_sample_id': 0, + 'predicted_sex': 1, + 'contamination_rate': 2, + 'percent_bases_at_20x': 3, + 'mean_coverage': 4, + }, + ), + google.cloud.bigquery.table.Row( + ( + 'SM-MWOGC', + 'Female', + Decimal('0'), + Decimal('0'), + Decimal('0'), + ), + { + 'collaborator_sample_id': 0, + 'predicted_sex': 1, + 'contamination_rate': 2, + 'percent_bases_at_20x': 3, + 'mean_coverage': 4, + }, + ), + google.cloud.bigquery.table.Row( + ('SM-MWKWL', 'Male', Decimal('0'), Decimal('0'), Decimal('0')), + { + 'collaborator_sample_id': 0, + 'predicted_sex': 1, + 'contamination_rate': 2, + 'percent_bases_at_20x': 3, + 'mean_coverage': 4, + }, + ), + ], + ), + iter( + [ + google.cloud.bigquery.table.Row( + ('SM-NGE65', 'Male', Decimal('0'), Decimal('0'), Decimal('0')), + { + 'collaborator_sample_id': 0, + 'predicted_sex': 1, + 'contamination_rate': 2, + 'percent_bases_at_20x': 3, + 'mean_coverage': 4, + }, + ), + google.cloud.bigquery.table.Row( + ('SM-NGE5G', 'Male', Decimal('0'), Decimal('0'), Decimal('0')), + { + 'collaborator_sample_id': 0, + 'predicted_sex': 1, + 'contamination_rate': 2, + 'percent_bases_at_20x': 3, + 'mean_coverage': 4, + }, + ), + google.cloud.bigquery.table.Row( + ('SM-NC6LM', 'Male', Decimal('0'), Decimal('0'), Decimal('0')), + { + 'collaborator_sample_id': 0, + 'predicted_sex': 1, + 'contamination_rate': 2, + 'percent_bases_at_20x': 3, + 'mean_coverage': 4, + }, + ), + ], + ), + ] + worker = luigi.worker.Worker() + write_sex_check_table = WriteSexCheckTableTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path='na', + project_guids=['R0113_test_project'], + run_id='manual__2024-04-03', + ) + worker.add(write_sex_check_table) + worker.run() + self.assertTrue(write_sex_check_table.complete()) + sex_check_ht = hl.read_table( + sex_check_table_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + 'na', + ), + ) + self.assertEqual( + sex_check_ht.collect(), + [ + hl.Struct(s='SM-MWKWL', predicted_sex='M'), + hl.Struct(s='SM-MWOGC', predicted_sex='F'), + hl.Struct(s='SM-NC6LM', predicted_sex='M'), + hl.Struct(s='SM-NGE5G', predicted_sex='M'), + hl.Struct(s='SM-NGE65', predicted_sex='M'), + hl.Struct(s='SM-NJ8MF', predicted_sex='U'), + ], + ) + # Check underlying tdr metrics file. + with open( + tdr_metrics_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + 'datarepo-5a72e31b.datarepo_RP_3056', + ), + ) as f: + self.assertTrue('collaborator_sample_id' in f.read()) diff --git a/loading_pipeline/lib/tasks/write_success_file_test.py b/loading_pipeline/lib/tasks/write_success_file_test.py new file mode 100644 index 0000000000..f33a5d337e --- /dev/null +++ b/loading_pipeline/lib/tasks/write_success_file_test.py @@ -0,0 +1,34 @@ +from unittest import mock + +import luigi.worker + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.tasks.write_success_file import WriteSuccessFileTask +from loading_pipeline.lib.test.mock_complete_task import MockCompleteTask +from loading_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + + +class WriteSuccessFileTaskTest(MockedDatarootTestCase): + @mock.patch( + 'loading_pipeline.lib.tasks.write_success_file.RunPipelineTask', + ) + def test_write_success_file_task( + self, + mock_run_pipeline_task: mock.Mock, + ) -> None: + mock_run_pipeline_task.return_value = MockCompleteTask() + worker = luigi.worker.Worker() + write_success_file = WriteSuccessFileTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WGS, + callset_path='test_callset', + project_guids=['R0113_test_project'], + run_id='manual__2024-04-03', + attempt_id=0, + ) + worker.add(write_success_file) + worker.run() + self.assertTrue(write_success_file.complete()) + with open(write_success_file.output().path) as f: + self.assertEqual(f.read(), '') diff --git a/loading_pipeline/lib/tasks/write_variant_annotations_vcf_test.py b/loading_pipeline/lib/tasks/write_variant_annotations_vcf_test.py new file mode 100644 index 0000000000..4bad466b67 --- /dev/null +++ b/loading_pipeline/lib/tasks/write_variant_annotations_vcf_test.py @@ -0,0 +1,91 @@ +import gzip +from unittest.mock import Mock, patch + +import hailtop.fs as hfs +import luigi.worker + +from loading_pipeline.lib.core import DatasetType, ReferenceGenome, SampleType +from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS +from loading_pipeline.lib.tasks.update_variant_annotations_table_with_new_variants import ( + UpdateVariantAnnotationsTableWithNewVariantsTask, +) +from loading_pipeline.lib.tasks.write_variant_annotations_vcf import ( + WriteVariantAnnotationsVCF, +) +from loading_pipeline.lib.test.misc import copy_project_pedigree_to_mocked_dir +from loading_pipeline.lib.test.mocked_reference_datasets_testcase import ( + MockedReferenceDatasetsTestCase, +) + +TEST_SV_VCF = 'loading_pipeline/var/test/callsets/sv_1.vcf' +TEST_PEDIGREE_5 = 'loading_pipeline/var/test/pedigrees/test_pedigree_5.tsv' + +GENE_ID_MAPPING = { + 'OR4F5': 'ENSG00000186092', + 'PLEKHG4B': 'ENSG00000153404', + 'OR4F16': 'ENSG00000186192', + 'OR4F29': 'ENSG00000284733', + 'FBXO28': 'ENSG00000143756', + 'SAMD11': 'ENSG00000187634', + 'C1orf174': 'ENSG00000198912', + 'TAS1R1': 'ENSG00000173662', + 'FAM131C': 'ENSG00000185519', + 'RCC2': 'ENSG00000179051', + 'NBPF3': 'ENSG00000142794', + 'AGBL4': 'ENSG00000186094', + 'KIAA1614': 'ENSG00000135835', + 'MR1': 'ENSG00000153029', + 'STX6': 'ENSG00000135823', + 'XPR1': 'ENSG00000143324', +} + + +class WriteVariantAnnotationsVCFTest(MockedReferenceDatasetsTestCase): + @patch( + 'loading_pipeline.lib.tasks.write_new_variants_table.load_gencode_gene_symbol_to_gene_id', + ) + def test_sv_export_vcf( + self, + mock_load_gencode: Mock, + ) -> None: + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_5, + ReferenceGenome.GRCh38, + DatasetType.SV, + SampleType.WGS, + 'R0115_test_project2', + ) + mock_load_gencode.return_value = GENE_ID_MAPPING + worker = luigi.worker.Worker() + update_variant_annotations_task = ( + UpdateVariantAnnotationsTableWithNewVariantsTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SV, + run_id='run_id1', + sample_type=SampleType.WGS, + callset_path=TEST_SV_VCF, + project_guids=['R0115_test_project2'], + validations_to_skip=[ALL_VALIDATIONS], + skip_expect_tdr_metrics=True, + ) + ) + worker.add(update_variant_annotations_task) + worker.run() + self.assertTrue(update_variant_annotations_task.complete()) + write_variant_annotations_vcf_task = WriteVariantAnnotationsVCF( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SV, + run_id='run_id1', + sample_type=SampleType.WGS, + callset_path=TEST_SV_VCF, + ) + worker.add(write_variant_annotations_vcf_task) + worker.run() + self.assertTrue( + hfs.exists( + write_variant_annotations_vcf_task.output().path, + ), + ) + with hfs.open(write_variant_annotations_vcf_task.output().path, 'rb') as f: + buf = f.read() + self.assertTrue(gzip.decompress(buf).startswith(b'##fileformat=VCFv4.2')) From 789a2bceeec901a9428e0faf4dd7eb19a10d747f Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 14 Aug 2026 13:57:11 -0400 Subject: [PATCH 250/369] remove debug --- loading_pipeline/lib/misc/clickhouse_test.py | 1 - 1 file changed, 1 deletion(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index b7a46695d5..fdfe26198e 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -461,7 +461,6 @@ def test_direct_insert_all_keys(self): return_value=[ClickhouseReferenceDataset.CLINVAR], ) def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): - self.maxDiff = None # TODO # Tests individual components of the atomic_insert_entries # to validate the state after each step. cursor = connections['clickhouse_write'].cursor() From c9cc6c8725d641307be237a30954b38cfe20ac1c Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 17 Aug 2026 14:19:53 -0400 Subject: [PATCH 251/369] reenable codacy for pipeline --- .codacy.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.codacy.yaml b/.codacy.yaml index 3bd43d8705..a0ae5a67dd 100644 --- a/.codacy.yaml +++ b/.codacy.yaml @@ -1,4 +1,3 @@ --- exclude_paths: - - "deploy/postgres/initdb.sql" - - "loading_pipeline/**" \ No newline at end of file + - "deploy/postgres/initdb.sql" \ No newline at end of file From 8b33e202496eef393ba8c1bd144035ae4d3ececa Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 17 Aug 2026 15:58:11 -0400 Subject: [PATCH 252/369] quote in bash scripts --- loading_pipeline/bin/dataproc_vep_init.bash | 6 +++--- .../bin/download_vep_reference_data.bash | 4 ++-- loading_pipeline/bin/rsync_reference_data.bash | 18 +++++++++--------- 3 files changed, 14 insertions(+), 14 deletions(-) diff --git a/loading_pipeline/bin/dataproc_vep_init.bash b/loading_pipeline/bin/dataproc_vep_init.bash index ec049e3217..257df7d8d3 100755 --- a/loading_pipeline/bin/dataproc_vep_init.bash +++ b/loading_pipeline/bin/dataproc_vep_init.bash @@ -54,10 +54,10 @@ EOF gcc -Wall -Werror -O2 /vep.c -o /vep chmod u+s /vep -gcloud storage cp gs://seqr-pipeline-runner-builds/$DEPLOYMENT_TYPE/$PIPELINE_RUNNER_APP_VERSION/bin/download_vep_reference_data.bash /download_vep_reference_data.bash +gcloud storage cp "gs://seqr-pipeline-runner-builds/$DEPLOYMENT_TYPE/$PIPELINE_RUNNER_APP_VERSION/bin/download_vep_reference_data.bash" /download_vep_reference_data.bash chmod +x /download_vep_reference_data.bash -./download_vep_reference_data.bash $REFERENCE_GENOME +./download_vep_reference_data.bash "$REFERENCE_GENOME" -gcloud storage cp gs://seqr-pipeline-runner-builds/$DEPLOYMENT_TYPE/$PIPELINE_RUNNER_APP_VERSION/bin/vep /vep.bash +gcloud storage cp "gs://seqr-pipeline-runner-builds/$DEPLOYMENT_TYPE/$PIPELINE_RUNNER_APP_VERSION/bin/vep" /vep.bash chmod +x /vep.bash diff --git a/loading_pipeline/bin/download_vep_reference_data.bash b/loading_pipeline/bin/download_vep_reference_data.bash index c1784d80ac..653dd459c0 100755 --- a/loading_pipeline/bin/download_vep_reference_data.bash +++ b/loading_pipeline/bin/download_vep_reference_data.bash @@ -2,7 +2,7 @@ set -eux -REFERENCE_GENOME=$1 +REFERENCE_GENOME="$1" VEP_REFERENCE_DATASETS_DIR=${VEP_REFERENCE_DATASETS_DIR:-/var/seqr/vep-reference-data} DEFAULT_REFERENCE_DATASETS_DIR="gs://seqr-reference-data" if [[ -n "${REFERENCE_DATASETS_DIR:-}" && "$REFERENCE_DATASETS_DIR" == gs://* ]]; then @@ -12,7 +12,7 @@ else echo "Using default GCS path: $REFERENCE_DATASETS_DIR" fi -case $REFERENCE_GENOME in +case "$REFERENCE_GENOME" in GRCh38) VEP_REFERENCE_DATA_FILES=( "$REFERENCE_DATASETS_DIR/vep_data/loftee-beta/GRCh38.tar.gz" diff --git a/loading_pipeline/bin/rsync_reference_data.bash b/loading_pipeline/bin/rsync_reference_data.bash index 360a6d6e1a..6577392745 100755 --- a/loading_pipeline/bin/rsync_reference_data.bash +++ b/loading_pipeline/bin/rsync_reference_data.bash @@ -2,11 +2,11 @@ set -eux -REFERENCE_GENOME=$1 +REFERENCE_GENOME="$1" REFERENCE_DATASETS_DIR=${REFERENCE_DATASETS_DIR:-/var/seqr/seqr-reference-data} -case $REFERENCE_GENOME in +case "$REFERENCE_GENOME" in GRCh38) ;; GRCh37) @@ -16,7 +16,7 @@ case $REFERENCE_GENOME in exit 1 esac -case $REFERENCE_DATASETS_DIR in +case "$REFERENCE_DATASETS_DIR" in "gs://seqr-reference-data") echo "Cannot rsync to the authoritative source" exit 1 @@ -26,26 +26,26 @@ case $REFERENCE_DATASETS_DIR in esac if ! [[ "$REFERENCE_DATASETS_DIR" =~ gs://* ]]; then - mkdir -p $REFERENCE_DATASETS_DIR/$REFERENCE_GENOME; + mkdir -p "$REFERENCE_DATASETS_DIR"/"$REFERENCE_GENOME"; if [ -f "$REFERENCE_DATASETS_DIR"/"$REFERENCE_GENOME"/_SUCCESS ]; then echo "Skipping rsync because already successful" exit 0; fi else result=$(gsutil -q stat "$REFERENCE_DATASETS_DIR"/"$REFERENCE_GENOME"/_SUCCESS || echo 1) - if [[ $result != 1 ]]; then + if [[ "$result" != 1 ]]; then echo "Skipping rsync because already successful" exit 0; fi fi -gsutil -m rsync -rd -x '.*\.parquet.*' "gs://seqr-reference-data/v3.2/$REFERENCE_GENOME" $REFERENCE_DATASETS_DIR/$REFERENCE_GENOME -if ! [[ $REFERENCE_DATASETS_DIR =~ gs://* ]]; then +gsutil -m rsync -rd -x '.*\.parquet.*' "gs://seqr-reference-data/v3.2/$REFERENCE_GENOME" "$REFERENCE_DATASETS_DIR"/"$REFERENCE_GENOME" +if ! [[ "$REFERENCE_DATASETS_DIR" =~ gs://* ]]; then touch "$REFERENCE_DATASETS_DIR"/"$REFERENCE_GENOME"/_SUCCESS else # If a different reference datasets dir is provided, sync vep data to the provided bucket. - gsutil cp "gs://seqr-reference-data/vep_data/loftee-beta/$REFERENCE_GENOME.tar.gz" $REFERENCE_DATASETS_DIR/vep_data/loftee-beta/$REFERENCE_GENOME.tar.gz - gsutil -m rsync -rd "gs://seqr-reference-data/vep/$REFERENCE_GENOME" $REFERENCE_DATASETS_DIR/vep/$REFERENCE_GENOME + gsutil cp "gs://seqr-reference-data/vep_data/loftee-beta/$REFERENCE_GENOME.tar.gz" "$REFERENCE_DATASETS_DIR"/vep_data/loftee-beta/"$REFERENCE_GENOME".tar.gz + gsutil -m rsync -rd "gs://seqr-reference-data/vep/$REFERENCE_GENOME" "$REFERENCE_DATASETS_DIR"/vep/"$REFERENCE_GENOME" touch _SUCCESS gsutil cp _SUCCESS "$REFERENCE_DATASETS_DIR"/"$REFERENCE_GENOME"/_SUCCESS rm -rf _SUCCESS From 4c64fe61698a744fbcd5f0b230c18dc77212c73a Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 17 Aug 2026 16:18:11 -0400 Subject: [PATCH 253/369] disable errors --- .codacy.yaml | 3 ++- loading_pipeline/api/__main__.py | 2 +- loading_pipeline/bin/pipeline_worker_test.py | 2 +- loading_pipeline/lib/core/environment.py | 2 +- loading_pipeline/lib/misc/clickhouse.py | 2 +- loading_pipeline/lib/misc/clickhouse_test.py | 6 +++--- loading_pipeline/lib/misc/terra_data_repository.py | 4 ++-- loading_pipeline/lib/reference_datasets/misc.py | 4 ++-- .../variants_migration/load_clickhouse_variants_tables.py | 2 +- .../load_clickhouse_variants_tables_test.py | 2 +- loading_pipeline/lib/test/clickhouse_django/settings.py | 6 +++--- .../ops/repartition_clickhouse_grch38_snv_indel.py | 4 ++-- .../ops/repartition_clickhouse_grch38_snv_indel_test.py | 2 +- 13 files changed, 21 insertions(+), 20 deletions(-) diff --git a/.codacy.yaml b/.codacy.yaml index a0ae5a67dd..121f658884 100644 --- a/.codacy.yaml +++ b/.codacy.yaml @@ -1,3 +1,4 @@ --- exclude_paths: - - "deploy/postgres/initdb.sql" \ No newline at end of file + - "deploy/postgres/initdb.sql" + - "loading_pipeline/deploy/Dockerfile" \ No newline at end of file diff --git a/loading_pipeline/api/__main__.py b/loading_pipeline/api/__main__.py index 38b30d74ef..5d5926f7cb 100644 --- a/loading_pipeline/api/__main__.py +++ b/loading_pipeline/api/__main__.py @@ -9,7 +9,7 @@ def run(): logger = get_logger(__name__) web.run_app( app, - host='0.0.0.0', # noqa: S104 + host='0.0.0.0', # noqa: S104 # nosec B104 port=6000, access_log=logger, ) diff --git a/loading_pipeline/bin/pipeline_worker_test.py b/loading_pipeline/bin/pipeline_worker_test.py index a2e3db1e54..b8b1233989 100644 --- a/loading_pipeline/bin/pipeline_worker_test.py +++ b/loading_pipeline/bin/pipeline_worker_test.py @@ -110,7 +110,7 @@ def test_process_queue_integration_test( SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` - """, + """, # nosec B608 ) annotations_count = cursor.fetchone()[0] self.assertEqual(annotations_count, 30) diff --git a/loading_pipeline/lib/core/environment.py b/loading_pipeline/lib/core/environment.py index 87d81e46d4..5a7d9611b1 100644 --- a/loading_pipeline/lib/core/environment.py +++ b/loading_pipeline/lib/core/environment.py @@ -4,7 +4,7 @@ # NB: using os.environ.get inside the dataclass defaults gives a lint error. LOCAL_DISK_MOUNT_DIR = os.environ.get('LOCAL_DISK_MOUNT_DIR', '/var/seqr') -HAIL_TMP_DIR = os.environ.get('HAIL_TMP_DIR', '/tmp') # noqa: S108 +HAIL_TMP_DIR = os.environ.get('HAIL_TMP_DIR', '/tmp') # noqa: S108 # nosec B108 PIPELINE_DATA_DIR = os.environ.get( 'PIPELINE_DATA_DIR', '/var/seqr/pipeline-data', diff --git a/loading_pipeline/lib/misc/clickhouse.py b/loading_pipeline/lib/misc/clickhouse.py index 977b4fe1e0..7eca49e931 100644 --- a/loading_pipeline/lib/misc/clickhouse.py +++ b/loading_pipeline/lib/misc/clickhouse.py @@ -411,7 +411,7 @@ def insert_into_seqr_variants_and_refresh_search( SELECT {ClickHouseTable.KEY_LOOKUP.key_field} FROM {table_name_builder.src_table(ClickHouseTable.KEY_LOOKUP)} ) - """, + """, # nosec B608 ) logged_query( f""" diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index fdfe26198e..487626e86d 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -425,7 +425,7 @@ def test_direct_insert_all_keys(self): ), ) cursor.execute( - f'SELECT key, variantId FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', + f'SELECT key, variantId FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', # nosec B608 ) ret = cursor.fetchall() self.assertEqual( @@ -450,7 +450,7 @@ def test_direct_insert_all_keys(self): ), ) cursor.execute( - f'SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', + f'SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', # nosec B608 ) ret = cursor.fetchone() self.assertEqual(ret[0], 6) @@ -495,7 +495,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): cursor.execute( f""" SELECT DISTINCT project_guid FROM {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/entries` - """, + """, # nosec B608 ) staged_projects = cursor.fetchall() self.assertCountEqual( diff --git a/loading_pipeline/lib/misc/terra_data_repository.py b/loading_pipeline/lib/misc/terra_data_repository.py index 0aa2204b8a..115a765c69 100644 --- a/loading_pipeline/lib/misc/terra_data_repository.py +++ b/loading_pipeline/lib/misc/terra_data_repository.py @@ -69,12 +69,12 @@ def bq_metrics_query(bq_table_name: str) -> google.cloud.bigquery.table.RowItera client.query_and_wait( f""" SELECT ddl FROM `{bq_table_name}`.INFORMATION_SCHEMA.TABLES where table_name='sample'; - """, # noqa: S608 + """, # noqa: S608 # nosec B608 ), )[0] metrics = [(m if m in table_ddl else f'NULL AS {m}') for m in BIGQUERY_METRICS] return client.query_and_wait( f""" SELECT {','.join(metrics)} FROM `{bq_table_name}.sample`; - """, # noqa: S608 + """, # noqa: S608 # nosec B608 ) diff --git a/loading_pipeline/lib/reference_datasets/misc.py b/loading_pipeline/lib/reference_datasets/misc.py index 73b4d17c0a..cf9fe37680 100644 --- a/loading_pipeline/lib/reference_datasets/misc.py +++ b/loading_pipeline/lib/reference_datasets/misc.py @@ -29,7 +29,7 @@ def compress_floats(ht: hl.Table): def generate_random_string(length=5): """Generates a random string of the specified length.""" letters = string.ascii_letters + string.digits - return ''.join(random.choice(letters) for i in range(length)) # noqa: S311 + return ''.join(random.choice(letters) for i in range(length)) # noqa: S311 # nosec B311 def filter_contigs(ht, reference_genome: ReferenceGenome): @@ -98,7 +98,7 @@ def copyfileobj(fsrc, fdst, decode_content, length=16 * 1024): @contextlib.contextmanager def download_zip_file(url, dataset_name: str, suffix='.zip', decode_content=False): - dir_ = f'/tmp/{generate_random_string()}/{dataset_name}' # noqa: S108 + dir_ = f'/tmp/{generate_random_string()}/{dataset_name}' # noqa: S108 # nosec B108 os.makedirs(dir_, exist_ok=True) with ( tempfile.NamedTemporaryFile( diff --git a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables.py b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables.py index 25325d8e37..c39d1383d0 100644 --- a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables.py +++ b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables.py @@ -102,7 +102,7 @@ def complete(self) -> bool: max_key = logged_query( f""" SELECT max(key) FROM {table_name_builder.src_table(ClickHouseTable.VARIANTS_MEMORY)} - """, + """, # nosec B608 )[0][0] return logged_query( f""" diff --git a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py index f412e0fa48..5751ec39d9 100644 --- a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py +++ b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py @@ -124,7 +124,7 @@ def test_write_variants_to_clickhouse( SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` - """, + """, # nosec B608 ) variants_count = cursor.fetchone()[0] self.assertEqual(variants_count, 2) diff --git a/loading_pipeline/lib/test/clickhouse_django/settings.py b/loading_pipeline/lib/test/clickhouse_django/settings.py index 5591ade322..78f7a6cf4d 100644 --- a/loading_pipeline/lib/test/clickhouse_django/settings.py +++ b/loading_pipeline/lib/test/clickhouse_django/settings.py @@ -29,16 +29,16 @@ def allow_migrate(db, app_label, model_name=None, **hints): # noqa: ARG004 ] USE_TZ = True -SECRET_KEY = 'loading-pipeline-test' # noqa: S105 +SECRET_KEY = 'loading-pipeline-test' # noqa: S105 # nosec B105 DEPLOYMENT_TYPE = os.environ.get('DEPLOYMENT_TYPE', 'dev') PIPELINE_RUNNER_SERVER = os.environ.get('PIPELINE_RUNNER_SERVER', 'http://localhost') CLICKHOUSE_IN_MEMORY_DIR = os.environ.get( 'CLICKHOUSE_IN_MEMORY_DIR', - '/tmp/loading_pipeline_test_clickhouse_in_memory', # noqa: S108 + '/tmp/loading_pipeline_test_clickhouse_in_memory', # noqa: S108 # nosec B108 ) CLICKHOUSE_DATA_DIR = os.environ.get( 'CLICKHOUSE_DATA_DIR', - '/tmp/loading_pipeline_test_clickhouse_data', # noqa: S108 + '/tmp/loading_pipeline_test_clickhouse_data', # noqa: S108 # nosec B108 ) CLICKHOUSE_WRITER_USER = os.environ.get('CLICKHOUSE_WRITER_USER', 'default') diff --git a/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel.py b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel.py index 4636e44ae3..30f0067425 100644 --- a/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel.py +++ b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel.py @@ -62,7 +62,7 @@ def main(max_insert_threads: int, project_guids: list[str]): ENGINE = CollapsingMergeTree(sign) PARTITION BY (project_guid, partition_id) SETTINGS deduplicate_merge_projection_mode = 'rebuild' - """, + """, # nosec B608 ) if not project_guids: project_guids = [ @@ -70,7 +70,7 @@ def main(max_insert_threads: int, project_guids: list[str]): for x in logged_query( f""" SELECT DISTINCT project_guid from {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` - """, + """, # nosec B608 ) ] for project_guid in project_guids: diff --git a/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py index 60ee69e57d..8781305e8a 100644 --- a/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py +++ b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py @@ -72,7 +72,7 @@ def setUp(self): (2, 'project_b', 'family_b2', 0, 1), (0, 'project_c', 'family_c1', 1, 1), (3, 'project_c', 'family_c2', 1, 1), - """, + """, # nosec B608 ) def tearDown(self): From 11dccc6c50b9e9664c6204012134a5af05bf578e Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 17 Aug 2026 16:31:18 -0400 Subject: [PATCH 254/369] more disable rules --- loading_pipeline/bin/pipeline_worker_test.py | 4 ++-- loading_pipeline/bin/run_task.py | 4 ++-- loading_pipeline/lib/misc/clickhouse.py | 4 ++-- loading_pipeline/lib/misc/clickhouse_test.py | 8 ++++---- loading_pipeline/lib/misc/terra_data_repository_test.py | 2 +- .../variants_migration/load_clickhouse_variants_tables.py | 4 ++-- .../load_clickhouse_variants_tables_test.py | 4 ++-- .../ops/repartition_clickhouse_grch38_snv_indel.py | 6 +++--- .../ops/repartition_clickhouse_grch38_snv_indel_test.py | 4 ++-- 9 files changed, 20 insertions(+), 20 deletions(-) diff --git a/loading_pipeline/bin/pipeline_worker_test.py b/loading_pipeline/bin/pipeline_worker_test.py index b8b1233989..4bb8691908 100644 --- a/loading_pipeline/bin/pipeline_worker_test.py +++ b/loading_pipeline/bin/pipeline_worker_test.py @@ -110,7 +110,7 @@ def test_process_queue_integration_test( SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` - """, # nosec B608 + """, # nosec B608 ) annotations_count = cursor.fetchone()[0] self.assertEqual(annotations_count, 30) @@ -119,7 +119,7 @@ def test_process_queue_integration_test( SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` - """, + """, # nosec B608 ) entries_count = cursor.fetchone()[0] self.assertEqual(entries_count, 16) diff --git a/loading_pipeline/bin/run_task.py b/loading_pipeline/bin/run_task.py index 37b96c4fb7..18dc77e839 100755 --- a/loading_pipeline/bin/run_task.py +++ b/loading_pipeline/bin/run_task.py @@ -3,8 +3,8 @@ import luigi -from loading_pipeline.lib.tasks import * # noqa: F403 +from loading_pipeline.lib.tasks import * # noqa: F403 # nosec F403 if __name__ == '__main__': # If run does not succeed, exit with 1 status code. - luigi.run() or sys.exit(1) + luigi.run() or sys.exit(1) # pylint: disable=W0106 diff --git a/loading_pipeline/lib/misc/clickhouse.py b/loading_pipeline/lib/misc/clickhouse.py index 7eca49e931..44facc59ca 100644 --- a/loading_pipeline/lib/misc/clickhouse.py +++ b/loading_pipeline/lib/misc/clickhouse.py @@ -411,7 +411,7 @@ def insert_into_seqr_variants_and_refresh_search( SELECT {ClickHouseTable.KEY_LOOKUP.key_field} FROM {table_name_builder.src_table(ClickHouseTable.KEY_LOOKUP)} ) - """, # nosec B608 + """, # nosec B608 ) logged_query( f""" @@ -424,7 +424,7 @@ def insert_into_seqr_variants_and_refresh_search( INNER JOIN {table_name_builder.dst_table(ClickHouseTable.KEY_LOOKUP)} dst ON {ClickHouseTable.KEY_LOOKUP.join_condition} WHERE src.variantId IN {table_name_builder.staging_dst_prefix}/_tmp_loadable_variantIds` - """, + """, # nosec B608 ) self.refresh_search(table_name_builder) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index 487626e86d..4e250af66b 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -425,7 +425,7 @@ def test_direct_insert_all_keys(self): ), ) cursor.execute( - f'SELECT key, variantId FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', # nosec B608 + f'SELECT key, variantId FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', # nosec B608 ) ret = cursor.fetchall() self.assertEqual( @@ -450,7 +450,7 @@ def test_direct_insert_all_keys(self): ), ) cursor.execute( - f'SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', # nosec B608 + f'SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details`', # nosec B608 ) ret = cursor.fetchone() self.assertEqual(ret[0], 6) @@ -495,7 +495,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): cursor.execute( f""" SELECT DISTINCT project_guid FROM {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/entries` - """, # nosec B608 + """, # nosec B608 ) staged_projects = cursor.fetchall() self.assertCountEqual( @@ -509,7 +509,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/project_gt_stats` FINAL GROUP BY project_guid, key, sample_type - """, + """, # nosec B608 ) staged_project_gt_stats = cursor.fetchall() self.assertCountEqual( diff --git a/loading_pipeline/lib/misc/terra_data_repository_test.py b/loading_pipeline/lib/misc/terra_data_repository_test.py index 91b044d68f..d798b5bcef 100644 --- a/loading_pipeline/lib/misc/terra_data_repository_test.py +++ b/loading_pipeline/lib/misc/terra_data_repository_test.py @@ -131,7 +131,7 @@ @patch( 'loading_pipeline.lib.misc.terra_data_repository.get_service_account_credentials', return_value=SimpleNamespace( - token='abcdefg', # noqa: S106 + token='abcdefg', # noqa: S106 # nosec B106 ), ) class TerraDataRepositoryTest(unittest.TestCase): diff --git a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables.py b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables.py index c39d1383d0..85ce9f0e10 100644 --- a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables.py +++ b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables.py @@ -102,14 +102,14 @@ def complete(self) -> bool: max_key = logged_query( f""" SELECT max(key) FROM {table_name_builder.src_table(ClickHouseTable.VARIANTS_MEMORY)} - """, # nosec B608 + """, # nosec B608 )[0][0] return logged_query( f""" SELECT EXISTS ( SELECT 1 FROM {table_name_builder.dst_table(ClickHouseTable.VARIANTS_MEMORY)} where key = %(max_key)s ) - """, + """, # nosec B608 {'max_key': max_key}, )[0][0] diff --git a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py index 5751ec39d9..e009a6d177 100644 --- a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py +++ b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py @@ -124,7 +124,7 @@ def test_write_variants_to_clickhouse( SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` - """, # nosec B608 + """, # nosec B608 ) variants_count = cursor.fetchone()[0] self.assertEqual(variants_count, 2) @@ -133,7 +133,7 @@ def test_write_variants_to_clickhouse( SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details` - """, + """, # nosec B608 ) variant_details_count = cursor.fetchone()[0] self.assertEqual(variant_details_count, 2) diff --git a/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel.py b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel.py index 30f0067425..053e9f71c8 100644 --- a/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel.py +++ b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel.py @@ -62,7 +62,7 @@ def main(max_insert_threads: int, project_guids: list[str]): ENGINE = CollapsingMergeTree(sign) PARTITION BY (project_guid, partition_id) SETTINGS deduplicate_merge_projection_mode = 'rebuild' - """, # nosec B608 + """, # nosec B608 ) if not project_guids: project_guids = [ @@ -70,7 +70,7 @@ def main(max_insert_threads: int, project_guids: list[str]): for x in logged_query( f""" SELECT DISTINCT project_guid from {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` - """, # nosec B608 + """, # nosec B608 ) ] for project_guid in project_guids: @@ -90,7 +90,7 @@ def main(max_insert_threads: int, project_guids: list[str]): SELECT * FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` WHERE project_guid=%(project_guid)s SETTINGS max_insert_threads=%(max_insert_threads)s - """, + """, # nosec B608 {'project_guid': project_guid, 'max_insert_threads': max_insert_threads}, timeout=99999, ) diff --git a/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py index 8781305e8a..ec8f7f93b2 100644 --- a/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py +++ b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py @@ -72,7 +72,7 @@ def setUp(self): (2, 'project_b', 'family_b2', 0, 1), (0, 'project_c', 'family_c1', 1, 1), (3, 'project_c', 'family_c2', 1, 1), - """, # nosec B608 + """, # nosec B608 ) def tearDown(self): @@ -87,7 +87,7 @@ def test_main_all_projects(self): f""" SELECT *, n_partitions, partition_id FROM {REPARTITION_DATABASE_NAME}.`GRCh38/SNV_INDEL/repartitioned_entries` - """, + """, # nosec B608 ) self.assertCountEqual( cursor.fetchall(), From 1a7e9abce6058708b7dc8abe0d780709ed540a11 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 17 Aug 2026 16:38:43 -0400 Subject: [PATCH 255/369] more disable rules --- loading_pipeline/bin/pipeline_worker_test.py | 2 +- loading_pipeline/lib/misc/clickhouse.py | 2 +- loading_pipeline/lib/misc/clickhouse_test.py | 2 +- .../variants_migration/load_clickhouse_variants_tables_test.py | 2 +- .../ops/repartition_clickhouse_grch38_snv_indel_test.py | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/loading_pipeline/bin/pipeline_worker_test.py b/loading_pipeline/bin/pipeline_worker_test.py index 4bb8691908..e1fcefd710 100644 --- a/loading_pipeline/bin/pipeline_worker_test.py +++ b/loading_pipeline/bin/pipeline_worker_test.py @@ -128,7 +128,7 @@ def test_process_queue_integration_test( SELECT sum(ac_wgs) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` - """, + """, # nosec B608 ) ac_wgs = cursor.fetchone()[0] self.assertEqual(ac_wgs, 69) diff --git a/loading_pipeline/lib/misc/clickhouse.py b/loading_pipeline/lib/misc/clickhouse.py index 44facc59ca..936bfb59c5 100644 --- a/loading_pipeline/lib/misc/clickhouse.py +++ b/loading_pipeline/lib/misc/clickhouse.py @@ -632,7 +632,7 @@ def delete_existing_families_from_staging_entries( SELECT COLUMNS('.*') EXCEPT(sign, n_partitions, partition_id), -1 as sign FROM {table_name_builder.staging_dst_table(ClickHouseTable.ENTRIES)} WHERE family_guid in %(family_guids)s - """, + """, # nosec B608 {'family_guids': family_guids}, ) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index 4e250af66b..9a9a4c43bc 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -545,7 +545,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/project_gt_stats` FINAL GROUP BY project_guid, key, sample_type - """, + """, # nosec B608 ) staged_project_gt_stats = cursor.fetchall() self.assertCountEqual( diff --git a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py index e009a6d177..704f45d9c9 100644 --- a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py +++ b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py @@ -142,7 +142,7 @@ def test_write_variants_to_clickhouse( SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/key_lookup` - """, + """, # nosec B608 ) key_lookups_count = cursor.fetchone()[0] self.assertEqual(key_lookups_count, 2) diff --git a/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py index ec8f7f93b2..dca4e702af 100644 --- a/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py +++ b/loading_pipeline/ops/repartition_clickhouse_grch38_snv_indel_test.py @@ -110,7 +110,7 @@ def test_main_one_project(self): f""" SELECT *, n_partitions, partition_id FROM {REPARTITION_DATABASE_NAME}.`GRCh38/SNV_INDEL/repartitioned_entries` - """, + """, # nosec B608 ) self.assertCountEqual( cursor.fetchall(), From fa9f7ac700ee574515135405c1dd199469cfb3d4 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 17 Aug 2026 16:48:47 -0400 Subject: [PATCH 256/369] codacy clean up --- loading_pipeline/lib/annotations/expression_helpers.py | 4 ++-- loading_pipeline/lib/annotations/mito.py | 2 +- loading_pipeline/lib/misc/clickhouse.py | 2 +- loading_pipeline/lib/misc/clickhouse_test.py | 2 +- loading_pipeline/lib/misc/terra_data_repository.py | 3 +-- loading_pipeline/lib/tasks/exports/misc.py | 2 +- 6 files changed, 7 insertions(+), 8 deletions(-) diff --git a/loading_pipeline/lib/annotations/expression_helpers.py b/loading_pipeline/lib/annotations/expression_helpers.py index ab0b34c25f..221c4054bf 100644 --- a/loading_pipeline/lib/annotations/expression_helpers.py +++ b/loading_pipeline/lib/annotations/expression_helpers.py @@ -79,7 +79,7 @@ def _get_expr_for_formatted_hgvs(csq): + protein_letters, hl.delimit( csq.amino_acids.split('').map( - lambda pl: PROTEIN_LETTERS_1TO3.get(pl), + PROTEIN_LETTERS_1TO3.get, ), '', ), @@ -193,7 +193,7 @@ def get_expr_for_vep_sorted_transcript_consequences_array( c.consequence_terms.size() > 0, hl.sorted( c.consequence_terms, - key=lambda t: TRANSCRIPT_CONSEQUENCE_TERM_RANK_LOOKUP.get(t), + key=TRANSCRIPT_CONSEQUENCE_TERM_RANK_LOOKUP.get, )[0], hl.null(hl.tstr), ), diff --git a/loading_pipeline/lib/annotations/mito.py b/loading_pipeline/lib/annotations/mito.py index 85b65ce75c..fd367ba946 100644 --- a/loading_pipeline/lib/annotations/mito.py +++ b/loading_pipeline/lib/annotations/mito.py @@ -58,4 +58,4 @@ def mitotip(ht: hl.Table, **_: Any) -> hl.Expression: def rsid(ht: hl.Table, **_: Any) -> hl.Expression: - return ht.rsid.find(lambda x: hl.is_defined(x)) + return ht.rsid.find(hl.is_defined) diff --git a/loading_pipeline/lib/misc/clickhouse.py b/loading_pipeline/lib/misc/clickhouse.py index 936bfb59c5..68f0991978 100644 --- a/loading_pipeline/lib/misc/clickhouse.py +++ b/loading_pipeline/lib/misc/clickhouse.py @@ -686,7 +686,7 @@ def insert_new_entries( INSERT INTO {table_name_builder.staging_dst_table(ClickHouseTable.ENTRIES)} ({dst_list}) SELECT {src_list} FROM {table_name_builder.src_table(ClickHouseTable.ENTRIES)} - """, + """, # nosec B608 ) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index 9a9a4c43bc..3190b9af5e 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -576,7 +576,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): {STAGING_CLICKHOUSE_DATABASE}.`{table_name_builder.run_id_hash}/GRCh38/SNV_INDEL/project_gt_stats` FINAL GROUP BY project_guid, key, sample_type - """, + """, # nosec B608 ) staged_project_gt_stats = cursor.fetchall() self.assertCountEqual( diff --git a/loading_pipeline/lib/misc/terra_data_repository.py b/loading_pipeline/lib/misc/terra_data_repository.py index 115a765c69..b4af9b7341 100644 --- a/loading_pipeline/lib/misc/terra_data_repository.py +++ b/loading_pipeline/lib/misc/terra_data_repository.py @@ -3,7 +3,6 @@ from collections.abc import Generator from concurrent.futures import ThreadPoolExecutor, as_completed -import google.cloud.bigquery from google.cloud import bigquery from loading_pipeline.lib.misc.gcp import get_service_account_credentials @@ -58,7 +57,7 @@ def gen_bq_table_names() -> Generator[str]: yield f'{result["accessInformation"]["bigQuery"]["projectId"]}.{result["accessInformation"]["bigQuery"]["datasetName"]}' -def bq_metrics_query(bq_table_name: str) -> google.cloud.bigquery.table.RowIterator: +def bq_metrics_query(bq_table_name: str) -> bigquery.table.RowIterator: if not re.match(TABLE_NAME_VALIDATION_REGEX, bq_table_name): msg = f'{bq_table_name} does not match expected pattern' raise ValueError(msg) diff --git a/loading_pipeline/lib/tasks/exports/misc.py b/loading_pipeline/lib/tasks/exports/misc.py index ee844d28e0..bbc45b4271 100644 --- a/loading_pipeline/lib/tasks/exports/misc.py +++ b/loading_pipeline/lib/tasks/exports/misc.py @@ -135,7 +135,7 @@ def camelcase_array_structexpression_fields( ht = ht.transmute( **{ snake_to_camelcase(field): ht[field].map( - lambda c: camelcase_hl_struct(c), + camelcase_hl_struct, ), }, ) From fe537b221ee3ce19595406815a653ab5eafd4c03 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 17 Aug 2026 16:53:41 -0400 Subject: [PATCH 257/369] remove deprecated param --- .../lib/annotations/expression_helpers.py | 13 +------------ .../gnomad_coding_and_noncoding.py | 1 - 2 files changed, 1 insertion(+), 13 deletions(-) diff --git a/loading_pipeline/lib/annotations/expression_helpers.py b/loading_pipeline/lib/annotations/expression_helpers.py index 221c4054bf..13a6f027e8 100644 --- a/loading_pipeline/lib/annotations/expression_helpers.py +++ b/loading_pipeline/lib/annotations/expression_helpers.py @@ -8,10 +8,6 @@ HGVSC_CONSEQUENCES = hl.set( ['splice_donor_variant', 'splice_acceptor_variant', 'splice_region_variant'], ) -OMIT_TRANSCRIPT_CONSEQUENCE_TERMS = [ - 'upstream_gene_variant', - 'downstream_gene_variant', -] PROTEIN_LETTERS_1TO3 = hl.dict( { 'A': 'Ala', @@ -124,7 +120,6 @@ def get_expr_for_xpos(locus: hl.expr.LocusExpression) -> hl.expr.Int64Expression def get_expr_for_vep_sorted_transcript_consequences_array( vep_root, include_coding_annotations=True, - omit_consequences=OMIT_TRANSCRIPT_CONSEQUENCE_TERMS, ): """Sort transcripts by 3 properties: @@ -177,17 +172,11 @@ def get_expr_for_vep_sorted_transcript_consequences_array( ], ) - omit_consequence_terms = ( - hl.set(omit_consequences) if omit_consequences else hl.empty_set(hl.tstr) - ) - result = hl.sorted( vep_root.transcript_consequences.map( lambda c: c.select( *selected_annotations, - consequence_terms=c.consequence_terms.filter( - lambda t: ~omit_consequence_terms.contains(t), - ), + consequence_terms=c.consequence_terms, domains=c.domains.map(lambda domain: domain.db + ':' + domain.name), major_consequence=hl.cond( c.consequence_terms.size() > 0, diff --git a/loading_pipeline/lib/reference_datasets/gnomad_coding_and_noncoding.py b/loading_pipeline/lib/reference_datasets/gnomad_coding_and_noncoding.py index 9b197276a8..fcb137d2b2 100644 --- a/loading_pipeline/lib/reference_datasets/gnomad_coding_and_noncoding.py +++ b/loading_pipeline/lib/reference_datasets/gnomad_coding_and_noncoding.py @@ -35,7 +35,6 @@ def get_ht( sorted_transaction_consequences=( get_expr_for_vep_sorted_transcript_consequences_array( ht.vep, - omit_consequences=[], ) ), ) From 4a2282037022c01c026a5b09028f61f0b13685c0 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 17 Aug 2026 17:11:42 -0400 Subject: [PATCH 258/369] disable codacy errors --- loading_pipeline/lib/misc/clickhouse.py | 24 ++++++++-------- loading_pipeline/lib/misc/clickhouse_test.py | 30 ++++++++++---------- 2 files changed, 27 insertions(+), 27 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse.py b/loading_pipeline/lib/misc/clickhouse.py index 68f0991978..d214f601bf 100644 --- a/loading_pipeline/lib/misc/clickhouse.py +++ b/loading_pipeline/lib/misc/clickhouse.py @@ -704,7 +704,7 @@ def optimize_entries( FROM {table_name_builder.staging_dst_table(ClickHouseTable.ENTRIES)} WHERE sign = -1 ); - """, + """, # nosec B608 )[0][0] merges_running = logged_query( @@ -838,7 +838,7 @@ def reload_dictionaries( logged_query( f""" SYSTEM RELOAD DICTIONARY {table_name_builder.dst_table(dictionary)} - """, + """, # nosec B608 ) @@ -858,7 +858,7 @@ def replace_project_partitions( f""" ALTER TABLE {table_name_builder.dst_table(clickhouse_table)} REPLACE PARTITION %(partition)s FROM {table_name_builder.staging_dst_table(clickhouse_table)} - """, + """, # nosec B608 {'partition': partition}, ) @@ -873,7 +873,7 @@ def exchange_tables( logged_query( f""" EXCHANGE TABLES {table_name_builder.staging_dst_table(clickhouse_table)} AND {table_name_builder.dst_table(clickhouse_table)} - """, + """, # nosec B608 ) @@ -887,7 +887,7 @@ def direct_insert_annotations( logged_query( f""" CREATE DATABASE {STAGING_CLICKHOUSE_DATABASE} - """, + """, # nosec B608 ) # NB: Unfortunately there's a bug(?) or inaccuracy if this is attempted without an intermediate # temporary table, likely due to writing to a table and joining against it at the same time. @@ -899,7 +899,7 @@ def direct_insert_annotations( LEFT ANTI JOIN {dst_table} dst ON {ClickHouseTable.VARIANTS_MEMORY.join_condition} ) - """, + """, # nosec B608 ) for ( clickhouse_table @@ -913,14 +913,14 @@ def direct_insert_annotations( INSERT INTO {disk_backed_dst_table} SELECT {clickhouse_table.select_fields} FROM {disk_backed_src_table} WHERE {clickhouse_table.key_field} IN {table_name_builder.staging_dst_prefix}/_tmp_loadable_keys` - """, + """, # nosec B608 ) logged_query( f""" INSERT INTO {dst_table} SELECT {ClickHouseTable.VARIANTS_MEMORY.select_fields} FROM {src_table} WHERE {ClickHouseTable.VARIANTS_MEMORY.key_field} IN {table_name_builder.staging_dst_prefix}/_tmp_loadable_keys` - """, + """, # nosec B608 ) drop_staging_db() @@ -942,7 +942,7 @@ def direct_insert_all_keys( SELECT {clickhouse_table.select_fields} FROM {src_table} {settings} - """, + """, # nosec B608 ) @@ -1078,7 +1078,7 @@ def delete_family_guids( WHERE project_guid = %(project_guid)s AND has(%(family_guids)s, family_guid) ); - """, + """, # nosec B608 {'family_guids': family_guids, 'project_guid': project_guid}, )[0][0] if not entries_exist: @@ -1136,7 +1136,7 @@ def rebuild_gt_stats( max_key = logged_query( f""" SELECT max(key) FROM {table_name_builder.dst_table(ClickHouseTable.GT_STATS)} - """, + """, # nosec B608 )[0][0] if not max_key: msg = f'Skipping gt stats rebuild for empty dataset {reference_genome.value}/{dataset_type.value} {project_guids[:10]}...' @@ -1172,7 +1172,7 @@ def rebuild_gt_stats( f""" ALTER TABLE {table_name_builder.staging_dst_table(ClickHouseTable.PROJECT_GT_STATS)} DROP PARTITION %(partition)s - """, + """, # nosec B608 {'partition': partition}, ) select_statement = get_create_mv_statements( diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index 3190b9af5e..e29fc3e901 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -617,7 +617,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): SELECT COLUMNS('.*') EXCEPT(is_annotated_in_any_gene, is_gnomad_gt_5_percent) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` - """, + """, # nosec B608 ) new_entries = cursor.fetchall() self.assertCountEqual( @@ -998,7 +998,7 @@ def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_typ SELECT key, variantId FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details` - """, + """, # nosec B608 ) variants_details = cursor.fetchall() self.assertCountEqual( @@ -1027,7 +1027,7 @@ def test_load_complete_gcnv(self): SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/variants_memory` - """, + """, # nosec B608 ) variants_disk_count = cursor.fetchone()[0] self.assertEqual(variants_disk_count, 4) @@ -1036,7 +1036,7 @@ def test_load_complete_gcnv(self): SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/variants_disk` - """, + """, # nosec B608 ) variants_disk_count = cursor.fetchone()[0] self.assertEqual(variants_disk_count, 4) @@ -1045,7 +1045,7 @@ def test_load_complete_gcnv(self): SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/key_lookup` - """, + """, # nosec B608 ) key_lookup_count = cursor.fetchone()[0] self.assertEqual(key_lookup_count, 4) @@ -1054,7 +1054,7 @@ def test_load_complete_gcnv(self): SELECT COUNT(*) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/GCNV/entries` - """, + """, # nosec B608 ) entries_count = cursor.fetchone()[0] self.assertEqual(entries_count, 3) @@ -1073,7 +1073,7 @@ def test_delete_families(self): {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` FINAL GROUP BY project_guid - """, + """, # nosec B608 ) project_gt_stats = cursor.fetchall() self.assertCountEqual( @@ -1092,7 +1092,7 @@ def test_delete_families(self): SELECT sum(ac_wes) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` - """, + """, # nosec B608 ) gt_stats = cursor.fetchall() self.assertCountEqual(gt_stats, [(12,)]) @@ -1110,7 +1110,7 @@ def test_delete_families(self): {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` FINAL GROUP BY project_guid - """, + """, # nosec B608 ) project_gt_stats = cursor.fetchall() self.assertCountEqual( @@ -1122,7 +1122,7 @@ def test_delete_families(self): SELECT sum(ac_wes) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` - """, + """, # nosec B608 ) gt_stats = cursor.fetchall() self.assertCountEqual(gt_stats, [(10,)]) @@ -1131,7 +1131,7 @@ def test_delete_families(self): SELECT sum(ac_wes) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` - """, + """, # nosec B608 ) gt_stats_dict = cursor.fetchall() self.assertCountEqual(gt_stats_dict, [(10,)]) @@ -1147,7 +1147,7 @@ def test_rebuild_gt_stats(self): f""" ALTER TABLE {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/entries` DROP PARTITION (%(project_guid)s, %(partition_id)s) - """, + """, # nosec B608 {'project_guid': 'project_a', 'partition_id': 0}, ) cursor.execute( @@ -1157,7 +1157,7 @@ def test_rebuild_gt_stats(self): {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` WHERE project_guid IN ('project_a', 'project_b') GROUP BY project_guid - """, + """, # nosec B608 ) project_gt_stats = cursor.fetchall() self.assertCountEqual( @@ -1176,7 +1176,7 @@ def test_rebuild_gt_stats(self): SELECT sum(ac_wes), sum(ac_wgs) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` - """, + """, # nosec B608 ) gt_stats = cursor.fetchall() self.assertCountEqual(gt_stats, [(12, 5)]) @@ -1193,7 +1193,7 @@ def test_rebuild_gt_stats(self): {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` WHERE project_guid IN ('project_a', 'project_b') GROUP BY project_guid - """, + """, # nosec B608 ) project_gt_stats = cursor.fetchall() self.assertCountEqual( From 9434cafba05a44d7ac842fb9e1581e193f66b40d Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 17 Aug 2026 17:15:01 -0400 Subject: [PATCH 259/369] disable codacy errors --- loading_pipeline/lib/misc/clickhouse_test.py | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index e29fc3e901..6b0cc3b39a 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -828,7 +828,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): SELECT * FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` - """, + """, # nosec B608 ) existing_gt_stats = cursor.fetchall() self.assertCountEqual( @@ -852,7 +852,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): SELECT * FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` - """, + """, # nosec B608 ) new_gt_stats = cursor.fetchall() self.assertCountEqual( @@ -874,7 +874,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): SELECT * FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` - """, + """, # nosec B608 ) new_gt_stats_post_reload = cursor.fetchall() self.assertEqual( @@ -910,7 +910,7 @@ def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_typ {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/project_gt_stats` WHERE project_guid = 'project_d' GROUP BY project_guid, key, sample_type - """, + """, # nosec B608 ) project_gt_stats = cursor.fetchall() self.assertCountEqual( @@ -926,7 +926,7 @@ def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_typ SELECT * FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` - """, + """, # nosec B608 ) gt_stats = cursor.fetchall() self.assertCountEqual( @@ -945,7 +945,7 @@ def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_typ SELECT * FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats_dict` - """, + """, # nosec B608 ) gt_stats_dict = cursor.fetchall() self.assertCountEqual( @@ -964,7 +964,7 @@ def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_typ SELECT * FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` - """, + """, # nosec B608 ) variants_memory = cursor.fetchall() self.assertCountEqual( @@ -981,7 +981,7 @@ def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_typ SELECT * FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_disk` - """, + """, # nosec B608 ) variants_disk = cursor.fetchall() self.assertCountEqual( From 30d16500cfebb6d8eaeb76da364aac4a6d16a74f Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 17 Aug 2026 17:21:29 -0400 Subject: [PATCH 260/369] disable codacy errors --- loading_pipeline/lib/misc/clickhouse_test.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index 6b0cc3b39a..3d2bf5fde7 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -1205,7 +1205,7 @@ def test_rebuild_gt_stats(self): SELECT sum(ac_wes), sum(ac_wgs) FROM {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/gt_stats` - """, + """, # nosec B608 ) gt_stats = cursor.fetchall() self.assertCountEqual(gt_stats, [(9, 0)]) From 0d78f5e7052876aa96127add2d96b421411db362 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 21 Aug 2026 15:43:09 -0400 Subject: [PATCH 261/369] debug --- .../lib/tasks/exports/write_new_variants_parquet_test.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py index 44684113df..4fc878f9f5 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py @@ -324,7 +324,7 @@ def test_mito_write_new_variants_parquet_test( ) export_json = convert_ndarray_to_list( df.head(10).to_dict('records'), - ) # TODO debug + ) # TODO debug export_json[0]['sortedTranscriptConsequences'] = [ export_json[0]['sortedTranscriptConsequences'][0], ] From 599028a601d120ad087c324aca10d9a43b467b1d Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 21 Aug 2026 15:49:48 -0400 Subject: [PATCH 262/369] actually delete the migrations! --- .../tasks/clickhouse_migration/__init__.py | 0 .../migrate_all_projects_to_clickhouse.py | 51 ------ ..._all_projects_to_clickhouse_on_dataproc.py | 16 -- ...migrate_all_projects_to_clickhouse_test.py | 123 -------------- .../migrate_project_to_clickhouse.py | 157 ------------------ .../migrate_project_variants_to_clickhouse.py | 119 ------------- ...ate_project_variants_to_clickhouse_test.py | 91 ---------- .../lib/tasks/variants_migration/__init__.py | 0 .../load_clickhouse_variants_tables.py | 137 --------------- .../load_clickhouse_variants_tables_test.py | 148 ----------------- .../migrate_variant_details_parquet.py | 76 --------- .../migrate_variants_parquet.py | 76 --------- ...s_table_with_dropped_reference_datasets.py | 90 ---------- 13 files changed, 1084 deletions(-) delete mode 100644 loading_pipeline/lib/tasks/clickhouse_migration/__init__.py delete mode 100644 loading_pipeline/lib/tasks/clickhouse_migration/migrate_all_projects_to_clickhouse.py delete mode 100644 loading_pipeline/lib/tasks/clickhouse_migration/migrate_all_projects_to_clickhouse_on_dataproc.py delete mode 100644 loading_pipeline/lib/tasks/clickhouse_migration/migrate_all_projects_to_clickhouse_test.py delete mode 100644 loading_pipeline/lib/tasks/clickhouse_migration/migrate_project_to_clickhouse.py delete mode 100644 loading_pipeline/lib/tasks/clickhouse_migration/migrate_project_variants_to_clickhouse.py delete mode 100644 loading_pipeline/lib/tasks/clickhouse_migration/migrate_project_variants_to_clickhouse_test.py delete mode 100644 loading_pipeline/lib/tasks/variants_migration/__init__.py delete mode 100644 loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables.py delete mode 100644 loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py delete mode 100644 loading_pipeline/lib/tasks/variants_migration/migrate_variant_details_parquet.py delete mode 100644 loading_pipeline/lib/tasks/variants_migration/migrate_variants_parquet.py delete mode 100644 loading_pipeline/lib/tasks/variants_migration/update_variant_annotations_table_with_dropped_reference_datasets.py diff --git a/loading_pipeline/lib/tasks/clickhouse_migration/__init__.py b/loading_pipeline/lib/tasks/clickhouse_migration/__init__.py deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/loading_pipeline/lib/tasks/clickhouse_migration/migrate_all_projects_to_clickhouse.py b/loading_pipeline/lib/tasks/clickhouse_migration/migrate_all_projects_to_clickhouse.py deleted file mode 100644 index c8a5e9678a..0000000000 --- a/loading_pipeline/lib/tasks/clickhouse_migration/migrate_all_projects_to_clickhouse.py +++ /dev/null @@ -1,51 +0,0 @@ -import hailtop.fs as hfs -import luigi -import luigi.util - -from loading_pipeline.lib.core import SampleType -from loading_pipeline.lib.paths import ( - project_table_path, -) -from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( - BaseLoadingPipelineParams, -) -from loading_pipeline.lib.tasks.clickhouse_migration.migrate_project_to_clickhouse import ( - MigrateProjectToClickHouseTask, -) - - -@luigi.util.inherits(BaseLoadingPipelineParams) -class MigrateAllProjectsToClickHouseTask(luigi.WrapperTask): - run_id = luigi.Parameter() - attempt_id = luigi.IntParameter() - - def __init__(self, *args, **kwargs): - super().__init__(*args, **kwargs) - self.dynamic_parquet_tasks = set() - - def complete(self): - return len(self.dynamic_parquet_tasks) >= 1 and all( - dynamic_parquet_tasks.complete() - for dynamic_parquet_tasks in self.dynamic_parquet_tasks - ) - - def run(self): - for sample_type in SampleType: - for p in hfs.ls( - project_table_path( - self.reference_genome, - self.dataset_type, - sample_type, - '*', - ), - ): - project_guid = p.path.split('/')[-1].replace('.ht', '') - self.dynamic_parquet_tasks.add( - self.clone( - MigrateProjectToClickHouseTask, - run_id=f'{self.run_id}_{sample_type.value}_{project_guid}', - sample_type=sample_type, - project_guid=project_guid, - ), - ) - yield self.dynamic_parquet_tasks diff --git a/loading_pipeline/lib/tasks/clickhouse_migration/migrate_all_projects_to_clickhouse_on_dataproc.py b/loading_pipeline/lib/tasks/clickhouse_migration/migrate_all_projects_to_clickhouse_on_dataproc.py deleted file mode 100644 index 96e3ffbdcd..0000000000 --- a/loading_pipeline/lib/tasks/clickhouse_migration/migrate_all_projects_to_clickhouse_on_dataproc.py +++ /dev/null @@ -1,16 +0,0 @@ -import luigi - -from loading_pipeline.lib.tasks.clickhouse_migration.migrate_all_projects_to_clickhouse import ( - MigrateAllProjectsToClickHouseTask, -) -from loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc import ( - BaseRunJobOnDataprocTask, -) - - -class MigrateAllProjectsToClickHouseOnDataprocTask(BaseRunJobOnDataprocTask): - run_id = luigi.Parameter() - - @property - def task(self) -> luigi.Task: - return MigrateAllProjectsToClickHouseTask diff --git a/loading_pipeline/lib/tasks/clickhouse_migration/migrate_all_projects_to_clickhouse_test.py b/loading_pipeline/lib/tasks/clickhouse_migration/migrate_all_projects_to_clickhouse_test.py deleted file mode 100644 index ad9c752d15..0000000000 --- a/loading_pipeline/lib/tasks/clickhouse_migration/migrate_all_projects_to_clickhouse_test.py +++ /dev/null @@ -1,123 +0,0 @@ -import json - -import hail as hl -import hailtop.fs as hfs -import luigi.worker -import pandas as pd - -from loading_pipeline.lib.core import ( - DatasetType, - ReferenceGenome, - SampleType, -) -from loading_pipeline.lib.core.constants import MIGRATION_RUN_ID -from loading_pipeline.lib.paths import ( - metadata_for_run_path, - new_entries_parquet_path, - pipeline_run_success_file_path, - project_table_path, - variant_annotations_table_path, -) -from loading_pipeline.lib.tasks.clickhouse_migration.migrate_all_projects_to_clickhouse import ( - MigrateAllProjectsToClickHouseTask, -) -from loading_pipeline.lib.test.mocked_dataroot_testcase import ( - MockedDatarootTestCase, -) - -TEST_SNV_INDEL_ANNOTATIONS = ( - 'loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/annotations.ht' -) -TEST_PROJECT_TABLES = [ - ( - 'loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/projects/WGS/R0113_test_project.ht', - SampleType.WGS, - 'R0113_test_project', - ), - ( - 'loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/projects/WES/R0113_test_project.ht', - SampleType.WES, - 'R0113_test_project', - ), - ( - 'loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/projects/WES/R0114_project4.ht', - SampleType.WES, - 'R0114_project4', - ), -] - - -class MigrateAllProjectsToClickHouseTaskTest(MockedDatarootTestCase): - def setUp(self) -> None: - super().setUp() - ht = hl.read_table(TEST_SNV_INDEL_ANNOTATIONS) - ht.write( - variant_annotations_table_path( - ReferenceGenome.GRCh37, - DatasetType.SNV_INDEL, - ), - ) - for path, sample_type, project_guid in TEST_PROJECT_TABLES: - ht = hl.read_table(path) - ht.write( - project_table_path( - ReferenceGenome.GRCh37, - DatasetType.SNV_INDEL, - sample_type, - project_guid, - ), - ) - - def test_all_project_entries_to_clickhouse_test( - self, - ) -> None: - worker = luigi.worker.Worker() - task = MigrateAllProjectsToClickHouseTask( - reference_genome=ReferenceGenome.GRCh37, - dataset_type=DatasetType.SNV_INDEL, - run_id=MIGRATION_RUN_ID, - attempt_id=0, - ) - worker.add(task) - worker.run() - self.assertTrue(task.complete()) - for _, sample_type, project_guid in TEST_PROJECT_TABLES: - df = pd.read_parquet( - new_entries_parquet_path( - ReferenceGenome.GRCh37, - DatasetType.SNV_INDEL, - f'{MIGRATION_RUN_ID}_{sample_type.value}_{project_guid}', - ), - ) - export_json = df.to_dict('records') - self.assertEqual( - export_json[0]['key'], - 1424, - ) - - for _, sample_type, project_guid in TEST_PROJECT_TABLES: - with hfs.open( - metadata_for_run_path( - ReferenceGenome.GRCh37, - DatasetType.SNV_INDEL, - f'{MIGRATION_RUN_ID}_{sample_type.value}_{project_guid}', - ), - ) as f: - metadata_json = json.load(f) - self.assertEqual( - metadata_json['run_id'], - f'{MIGRATION_RUN_ID}_{sample_type.value}_{project_guid}', - ) - self.assertEqual( - metadata_json['family_samples']['F079280_bh10261'], - ['BH10261-1', 'BH10261-2', 'BH10261-3-T'], - ) - - with hfs.open( - pipeline_run_success_file_path( - ReferenceGenome.GRCh37, - DatasetType.SNV_INDEL, - f'{MIGRATION_RUN_ID}_{sample_type.value}_{project_guid}', - ), - ) as f: - self.assertEqual(f.read(), '') diff --git a/loading_pipeline/lib/tasks/clickhouse_migration/migrate_project_to_clickhouse.py b/loading_pipeline/lib/tasks/clickhouse_migration/migrate_project_to_clickhouse.py deleted file mode 100644 index be0d668a7d..0000000000 --- a/loading_pipeline/lib/tasks/clickhouse_migration/migrate_project_to_clickhouse.py +++ /dev/null @@ -1,157 +0,0 @@ -import json - -import hail as hl -import luigi -import luigi.util - -from loading_pipeline.lib.core import SampleType -from loading_pipeline.lib.misc.family_entries import ( - deduplicate_by_most_non_ref_calls, - deglobalize_ids, -) -from loading_pipeline.lib.paths import ( - metadata_for_run_path, - new_entries_parquet_path, - pipeline_run_success_file_path, - project_table_path, -) -from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( - BaseLoadingPipelineParams, -) -from loading_pipeline.lib.tasks.base.base_write_parquet import BaseWriteParquetTask -from loading_pipeline.lib.tasks.clickhouse_migration.migrate_project_variants_to_clickhouse import ( - MigrateProjectVariantsToClickHouseTask, - WriteProjectSubsettedVariantsTask, -) -from loading_pipeline.lib.tasks.exports.fields import get_entries_export_fields -from loading_pipeline.lib.tasks.files import GCSorLocalTarget, HailTableTask - -PROJECT_SUBSETTED_ANNOTATIONS_TABLE_TASK = 'project_subsetted_annotations_table_task' -PROJECT_TABLE_TASK = 'project_table_task' - - -@luigi.util.inherits(BaseLoadingPipelineParams) -class WriteProjectEntriesParquetTask(BaseWriteParquetTask): - run_id = luigi.Parameter() - sample_type = luigi.EnumParameter(enum=SampleType) - project_guid = luigi.Parameter() - - def output(self) -> luigi.Target: - return GCSorLocalTarget( - new_entries_parquet_path( - self.reference_genome, - self.dataset_type, - self.run_id, - ), - ) - - def requires(self) -> list[luigi.Task]: - return { - PROJECT_SUBSETTED_ANNOTATIONS_TABLE_TASK: self.clone( - WriteProjectSubsettedVariantsTask, - ), - PROJECT_TABLE_TASK: HailTableTask( - project_table_path( - self.reference_genome, - self.dataset_type, - self.sample_type, - self.project_guid, - ), - ), - } - - def create_table(self) -> None: - ht = hl.read_table( - self.input()[PROJECT_TABLE_TASK].path, - ) - ht = deglobalize_ids(ht) - ht = deduplicate_by_most_non_ref_calls(ht) - annotations_ht = hl.read_table( - self.input()[PROJECT_SUBSETTED_ANNOTATIONS_TABLE_TASK].path, - ) - ht = ht.join(annotations_ht) - ht = ht.explode(ht.family_entries) - ht = ht.filter(hl.is_defined(ht.family_entries)) - ht = ht.key_by() - ht = ht.select_globals() - return ht.select( - **get_entries_export_fields( - ht, - self.dataset_type, - self.sample_type, - self.project_guid, - ), - ) - - -@luigi.util.inherits(BaseLoadingPipelineParams) -class WriteMigrationMetadataJsonTask(luigi.Task): - run_id = luigi.Parameter() - sample_type = luigi.EnumParameter(enum=SampleType) - project_guid = luigi.Parameter() - - def requires(self): - return HailTableTask( - project_table_path( - self.reference_genome, - self.dataset_type, - self.sample_type, - self.project_guid, - ), - ) - - def output(self) -> luigi.Target: - return GCSorLocalTarget( - metadata_for_run_path( - self.reference_genome, - self.dataset_type, - self.run_id, - ), - ) - - def run(self): - ht = hl.read_table(self.input().path) - metadata_json = { - 'callsets': [], - 'run_id': self.run_id, - 'sample_type': self.sample_type.value, - 'project_guids': [self.project_guid], - 'family_samples': hl.eval(ht.globals.family_samples), - 'failed_family_samples': { - 'missing_samples': {}, - 'relatedness_check': {}, - 'sex_check': {}, - 'ploidy_check': {}, - }, - 'relatedness_check_file_path': '', - 'sample_qc': {}, - } - with self.output().open('w') as f: - json.dump(metadata_json, f) - - -@luigi.util.inherits(BaseLoadingPipelineParams) -class MigrateProjectToClickHouseTask(luigi.Task): - run_id = luigi.Parameter() - sample_type = luigi.EnumParameter(enum=SampleType) - project_guid = luigi.Parameter() - - def requires(self): - return [ - self.clone(MigrateProjectVariantsToClickHouseTask), - self.clone(WriteProjectEntriesParquetTask), - self.clone(WriteMigrationMetadataJsonTask), - ] - - def output(self) -> luigi.Target: - return GCSorLocalTarget( - pipeline_run_success_file_path( - self.reference_genome, - self.dataset_type, - self.run_id, - ), - ) - - def run(self): - with self.output().open('w') as f: - f.write('') diff --git a/loading_pipeline/lib/tasks/clickhouse_migration/migrate_project_variants_to_clickhouse.py b/loading_pipeline/lib/tasks/clickhouse_migration/migrate_project_variants_to_clickhouse.py deleted file mode 100644 index ebf950e551..0000000000 --- a/loading_pipeline/lib/tasks/clickhouse_migration/migrate_project_variants_to_clickhouse.py +++ /dev/null @@ -1,119 +0,0 @@ -import hail as hl -import luigi -import luigi.util - -from loading_pipeline.lib.core import SampleType -from loading_pipeline.lib.paths import ( - new_variants_table_path, - project_table_path, - variant_annotations_table_path, -) -from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( - BaseLoadingPipelineParams, -) -from loading_pipeline.lib.tasks.base.base_write import BaseWriteTask -from loading_pipeline.lib.tasks.exports.write_new_variant_details_parquet import ( - WriteNewVariantDetailsParquetTask, -) -from loading_pipeline.lib.tasks.exports.write_new_variants_parquet import ( - WriteNewVariantsParquetTask, -) -from loading_pipeline.lib.tasks.files import GCSorLocalTarget, HailTableTask - -MAX_SNV_INDEL_ALLELE_LENGTH = 500 - - -class WriteProjectSubsettedVariantsTask(BaseWriteTask): - run_id = luigi.Parameter() - sample_type = luigi.EnumParameter(enum=SampleType) - project_guid = luigi.Parameter() - - def output(self) -> luigi.Target: - return GCSorLocalTarget( - new_variants_table_path( - self.reference_genome, - self.dataset_type, - self.run_id, - ), - ) - - def requires(self) -> list[luigi.Task]: - return [ - HailTableTask( - variant_annotations_table_path( - self.reference_genome, - self.dataset_type, - ), - ), - HailTableTask( - project_table_path( - self.reference_genome, - self.dataset_type, - self.sample_type, - self.project_guid, - ), - ), - ] - - def create_table(self) -> hl.Table: - ht = hl.read_table(self.input()[0].path) - if not hasattr(ht, 'key_'): - ht = ht.add_index(name='key_') - if self.dataset_type.filter_invalid_sites: - ht = ht.filter(hl.len(ht.alleles[1]) < MAX_SNV_INDEL_ALLELE_LENGTH) - project_ht = hl.read_table(self.input()[1].path) - return ht.semi_join(project_ht) - - -@luigi.util.inherits(BaseLoadingPipelineParams) -class MigrateProjectVariantsToClickHouseTask(luigi.WrapperTask): - run_id = luigi.Parameter() - sample_type = luigi.EnumParameter(enum=SampleType) - project_guid = luigi.Parameter() - - def __init__(self, *args, **kwargs): - super().__init__(*args, **kwargs) - self.dynamic_parquet_tasks = set() - - def requires(self) -> luigi.Task: - return self.clone(WriteProjectSubsettedVariantsTask) - - def complete(self): - return ( - super().complete() - and len(self.dynamic_parquet_tasks) >= 1 - and all( - dynamic_parquet_tasks.complete() - for dynamic_parquet_tasks in self.dynamic_parquet_tasks - ) - ) - - def run(self): - self.dynamic_parquet_tasks.update( - [ - *( - [ - self.clone( - WriteNewVariantDetailsParquetTask, - # Callset Path being required - # here is byproduct of the "place all variants" - # in the variants path" hack. In theory - # it is possible to re-factor the parameters - # such that this isn't required, but it's left - # as out of scope for now. Alternatively, - # we could inherit the functionality of these - # tasks without calling them directly, but - # that was also more code. - callset_path=None, - ), - ] - if self.dataset_type.should_write_new_variant_details - else [] - ), - self.clone( - WriteNewVariantsParquetTask, - callset_path=None, - ), - ], - ) - yield self.dynamic_parquet_tasks diff --git a/loading_pipeline/lib/tasks/clickhouse_migration/migrate_project_variants_to_clickhouse_test.py b/loading_pipeline/lib/tasks/clickhouse_migration/migrate_project_variants_to_clickhouse_test.py deleted file mode 100644 index ce4c6d5cd8..0000000000 --- a/loading_pipeline/lib/tasks/clickhouse_migration/migrate_project_variants_to_clickhouse_test.py +++ /dev/null @@ -1,91 +0,0 @@ -import hail as hl -import hailtop.fs as hfs -import luigi.worker -import pandas as pd - -from loading_pipeline.lib.core import ( - DatasetType, - ReferenceGenome, - SampleType, -) -from loading_pipeline.lib.paths import ( - new_variant_details_parquet_path, - new_variants_parquet_path, - pipeline_run_success_file_path, - project_table_path, - variant_annotations_table_path, -) -from loading_pipeline.lib.tasks.clickhouse_migration.migrate_project_variants_to_clickhouse import ( - MigrateProjectVariantsToClickHouseTask, -) -from loading_pipeline.lib.test.mocked_dataroot_testcase import ( - MockedDatarootTestCase, -) - -TEST_SNV_INDEL_ANNOTATIONS = ( - 'loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/annotations.ht' -) -TEST_PROJECT_TABLE = 'loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/projects/WGS/R0113_test_project.ht' - -TEST_RUN_ID = 'migration_run' - - -class WriteVariantsToClickHouseTest(MockedDatarootTestCase): - def setUp(self) -> None: - super().setUp() - ht = hl.read_table(TEST_SNV_INDEL_ANNOTATIONS) - ht.write( - variant_annotations_table_path( - ReferenceGenome.GRCh37, - DatasetType.SNV_INDEL, - ), - ) - ht = hl.read_table(TEST_PROJECT_TABLE) - ht.write( - project_table_path( - ReferenceGenome.GRCh37, - DatasetType.SNV_INDEL, - SampleType.WGS, - 'R0113_test_project', - ), - ) - - def test_migrate_variants_to_clickhouse_test( - self, - ) -> None: - worker = luigi.worker.Worker() - task = MigrateProjectVariantsToClickHouseTask( - reference_genome=ReferenceGenome.GRCh37, - dataset_type=DatasetType.SNV_INDEL, - run_id=TEST_RUN_ID, - sample_type=SampleType.WGS, - project_guid='R0113_test_project', - ) - worker.add(task) - worker.run() - self.assertTrue(task.complete()) - df = pd.read_parquet( - new_variants_parquet_path( - ReferenceGenome.GRCh37, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ), - ) - self.assertEqual(df.shape[0], 1) - df = pd.read_parquet( - new_variant_details_parquet_path( - ReferenceGenome.GRCh37, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ), - ) - self.assertEqual(df.shape[0], 1) - self.assertFalse( - hfs.exists( - pipeline_run_success_file_path( - ReferenceGenome.GRCh37, - DatasetType.SNV_INDEL, - TEST_RUN_ID, - ), - ), - ) diff --git a/loading_pipeline/lib/tasks/variants_migration/__init__.py b/loading_pipeline/lib/tasks/variants_migration/__init__.py deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables.py b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables.py deleted file mode 100644 index 85ce9f0e10..0000000000 --- a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables.py +++ /dev/null @@ -1,137 +0,0 @@ -import luigi -import luigi.util - -from loading_pipeline.lib.core import FeatureFlag -from loading_pipeline.lib.misc.clickhouse import ( - ClickhouseReferenceDataset, - ClickHouseTable, - TableNameBuilder, - logged_query, -) -from loading_pipeline.lib.misc.retry import retry -from loading_pipeline.lib.paths import ( - new_variant_details_parquet_path, - new_variants_parquet_path, -) -from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( - BaseLoadingPipelineParams, -) -from loading_pipeline.lib.tasks.files import GCSorLocalFolderTarget -from loading_pipeline.lib.tasks.variants_migration.migrate_variant_details_parquet import ( - MigrateVariantDetailsParquetOnDataprocTask, - MigrateVariantDetailsParquetTask, -) -from loading_pipeline.lib.tasks.variants_migration.migrate_variants_parquet import ( - MigrateVariantsParquetOnDataprocTask, - MigrateVariantsParquetTask, -) - - -@retry() -def refresh_seqr_variants_and_search( - table_name_builder: TableNameBuilder, - clickhouse_reference_dataset: ClickhouseReferenceDataset, -): - if clickhouse_reference_dataset.has_seqr_variants: - logged_query( - f""" - SYSTEM START VIEW {clickhouse_reference_dataset.all_variants_to_seqr_variants_mv(table_name_builder)} - """, - ) - logged_query( - f""" - SYSTEM REFRESH VIEW {clickhouse_reference_dataset.all_variants_to_seqr_variants_mv(table_name_builder)} - """, - ) - logged_query( - f""" - SYSTEM WAIT VIEW {clickhouse_reference_dataset.all_variants_to_seqr_variants_mv(table_name_builder)} - """, - timeout=clickhouse_reference_dataset.all_variants_mv_timeout, - ) - clickhouse_reference_dataset.refresh_search(table_name_builder) - - -@luigi.util.inherits(BaseLoadingPipelineParams) -class LoadClickhouseVariantsTablesTask(luigi.WrapperTask): - run_id = luigi.Parameter() - attempt_id = luigi.IntParameter() - - def requires(self) -> luigi.Task: - tasks = ( - [ - self.clone(MigrateVariantsParquetOnDataprocTask), - ] - if FeatureFlag.RUN_PIPELINE_ON_DATAPROC - else [ - self.clone(MigrateVariantsParquetTask), - ] - ) - if self.dataset_type.should_write_new_variant_details: - tasks.append( - self.clone(MigrateVariantDetailsParquetOnDataprocTask) - if FeatureFlag.RUN_PIPELINE_ON_DATAPROC - else self.clone(MigrateVariantDetailsParquetTask), - ) - return tasks - - def complete(self) -> bool: - table_name_builder = TableNameBuilder( - self.reference_genome, - self.dataset_type, - self.run_id, - ) - if not ( - GCSorLocalFolderTarget( - new_variant_details_parquet_path( - self.reference_genome, - self.dataset_type, - self.run_id, - ), - ).exists() - ) or not ( - GCSorLocalFolderTarget( - new_variants_parquet_path( - self.reference_genome, - self.dataset_type, - self.run_id, - ), - ).exists() - ): - return False - max_key = logged_query( - f""" - SELECT max(key) FROM {table_name_builder.src_table(ClickHouseTable.VARIANTS_MEMORY)} - """, # nosec B608 - )[0][0] - return logged_query( - f""" - SELECT EXISTS ( - SELECT 1 FROM {table_name_builder.dst_table(ClickHouseTable.VARIANTS_MEMORY)} where key = %(max_key)s - ) - """, # nosec B608 - {'max_key': max_key}, - )[0][0] - - def run(self) -> None: - table_name_builder = TableNameBuilder( - self.reference_genome, - self.dataset_type, - self.run_id, - ) - for clickhouse_table in ClickHouseTable.for_dataset_type( - self.dataset_type, - ): - if clickhouse_table == ClickHouseTable.ENTRIES: - continue - clickhouse_table.insert(table_name_builder=table_name_builder) - for ( - clickhouse_reference_dataset - ) in ClickhouseReferenceDataset.for_reference_genome_dataset_type( - self.reference_genome, - self.dataset_type, - ): - refresh_seqr_variants_and_search( - table_name_builder, - clickhouse_reference_dataset, - ) diff --git a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py b/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py deleted file mode 100644 index 704f45d9c9..0000000000 --- a/loading_pipeline/lib/tasks/variants_migration/load_clickhouse_variants_tables_test.py +++ /dev/null @@ -1,148 +0,0 @@ -from unittest.mock import Mock, patch - -import hail as hl -import luigi.worker -from django.db import connections - -from loading_pipeline.lib.core import ( - DatasetType, - ReferenceGenome, -) -from loading_pipeline.lib.core.environment import Env -from loading_pipeline.lib.misc.clickhouse import ClickhouseReferenceDataset -from loading_pipeline.lib.paths import ( - variant_annotations_table_path, -) -from loading_pipeline.lib.tasks.variants_migration.load_clickhouse_variants_tables import ( - LoadClickhouseVariantsTablesTask, -) -from loading_pipeline.lib.tasks.variants_migration.migrate_variant_details_parquet import ( - MigrateVariantDetailsParquetTask, -) -from loading_pipeline.lib.tasks.variants_migration.migrate_variants_parquet import ( - MigrateVariantsParquetTask, -) -from loading_pipeline.lib.tasks.variants_migration.update_variant_annotations_table_with_dropped_reference_datasets import ( - UpdateVariantAnnotationsTableWithDroppedReferenceDatasetsTask, -) -from loading_pipeline.lib.test.clickhouse_schema_testcase import ( - ClickhouseSchemaTestCase, -) -from loading_pipeline.lib.test.mocked_dataroot_testcase import ( - MockedDatarootTestCase, -) - -TEST_SNV_INDEL_ANNOTATIONS = ( - 'loading_pipeline/var/test/exports/GRCh38/SNV_INDEL/annotations.ht' -) -TEST_RUN_ID = 'manual__2024-04-03' - - -class LoadClickhouseVariantsTablesTaskTest( - MockedDatarootTestCase, - ClickhouseSchemaTestCase, -): - def setUp(self) -> None: - super().setUp() - ht = hl.read_table(TEST_SNV_INDEL_ANNOTATIONS) - ht.write( - variant_annotations_table_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - ), - ) - - @patch.object( - ClickhouseReferenceDataset, - 'for_reference_genome_dataset_type', - return_value=[ClickhouseReferenceDataset.CLINVAR], - ) - def test_write_variants_to_clickhouse( - self, - mock_for_reference_genome_dataset_type: Mock, - ): - worker = luigi.worker.Worker() - task = UpdateVariantAnnotationsTableWithDroppedReferenceDatasetsTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - run_id=TEST_RUN_ID, - ) - worker.add(task) - worker.run() - self.assertTrue(task.output().exists()) - self.assertTrue(task.complete()) - ht = hl.read_table(task.output().path) - self.assertTrue('variant_id' in ht.row) - self.assertTrue('gnomad_genomes' not in ht.row and 'dbnsfp' not in ht.row) - - task = MigrateVariantsParquetTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - run_id=TEST_RUN_ID, - attempt_id=0, - ) - worker.add(task) - worker.run() - self.assertTrue(task.output().exists()) - self.assertTrue(task.complete()) - - task = MigrateVariantDetailsParquetTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - run_id=TEST_RUN_ID, - attempt_id=0, - ) - worker.add(task) - worker.run() - self.assertTrue(task.output().exists()) - self.assertTrue(task.complete()) - - task = MigrateVariantDetailsParquetTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - run_id=TEST_RUN_ID, - attempt_id=0, - ) - worker.add(task) - worker.run() - self.assertTrue(task.output().exists()) - self.assertTrue(task.complete()) - - task = LoadClickhouseVariantsTablesTask( - reference_genome=ReferenceGenome.GRCh38, - dataset_type=DatasetType.SNV_INDEL, - run_id=TEST_RUN_ID, - attempt_id=0, - ) - worker.add(task) - worker.run() - self.assertTrue(task.complete()) - - cursor = connections['clickhouse_write'].cursor() - cursor.execute( - f""" - SELECT COUNT(*) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants_memory` - """, # nosec B608 - ) - variants_count = cursor.fetchone()[0] - self.assertEqual(variants_count, 2) - cursor.execute( - f""" - SELECT COUNT(*) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/variants/details` - """, # nosec B608 - ) - variant_details_count = cursor.fetchone()[0] - self.assertEqual(variant_details_count, 2) - cursor.execute( - f""" - SELECT COUNT(*) - FROM - {Env.CLICKHOUSE_DATABASE}.`GRCh38/SNV_INDEL/key_lookup` - """, # nosec B608 - ) - key_lookups_count = cursor.fetchone()[0] - self.assertEqual(key_lookups_count, 2) diff --git a/loading_pipeline/lib/tasks/variants_migration/migrate_variant_details_parquet.py b/loading_pipeline/lib/tasks/variants_migration/migrate_variant_details_parquet.py deleted file mode 100644 index 8405757676..0000000000 --- a/loading_pipeline/lib/tasks/variants_migration/migrate_variant_details_parquet.py +++ /dev/null @@ -1,76 +0,0 @@ -import hail as hl -import luigi -import luigi.util - -from loading_pipeline.lib.paths import ( - new_variant_details_parquet_path, - variant_annotations_table_path, -) -from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( - BaseLoadingPipelineParams, -) -from loading_pipeline.lib.tasks.base.base_write_parquet import BaseWriteParquetTask -from loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc import ( - BaseRunJobOnDataprocTask, -) -from loading_pipeline.lib.tasks.exports.fields import ( - get_variant_details_export_fields, -) -from loading_pipeline.lib.tasks.exports.misc import ( - camelcase_array_structexpression_fields, - unmap_formatting_annotation_enums, -) -from loading_pipeline.lib.tasks.files import GCSorLocalTarget -from loading_pipeline.lib.tasks.variants_migration.update_variant_annotations_table_with_dropped_reference_datasets import ( - UpdateVariantAnnotationsTableWithDroppedReferenceDatasetsTask, -) - - -@luigi.util.inherits(BaseLoadingPipelineParams) -class MigrateVariantDetailsParquetTask(BaseWriteParquetTask): - run_id = luigi.Parameter() - attempt_id = luigi.IntParameter() - - def output(self) -> luigi.Target: - return GCSorLocalTarget( - new_variant_details_parquet_path( - self.reference_genome, - self.dataset_type, - self.run_id, - ), - ) - - def requires(self) -> luigi.Task: - return self.clone(UpdateVariantAnnotationsTableWithDroppedReferenceDatasetsTask) - - def create_table(self) -> None: - ht = hl.read_table( - variant_annotations_table_path( - self.reference_genome, - self.dataset_type, - ), - ) - ht = unmap_formatting_annotation_enums( - ht, - self.reference_genome, - self.dataset_type, - ) - ht = camelcase_array_structexpression_fields( - ht, - self.reference_genome, - self.dataset_type, - ) - ht = ht.key_by() - return ht.select( - **get_variant_details_export_fields( - ht, - self.reference_genome, - self.dataset_type, - ), - ) - - -class MigrateVariantDetailsParquetOnDataprocTask(BaseRunJobOnDataprocTask): - @property - def task(self) -> luigi.Task: - return MigrateVariantDetailsParquetTask diff --git a/loading_pipeline/lib/tasks/variants_migration/migrate_variants_parquet.py b/loading_pipeline/lib/tasks/variants_migration/migrate_variants_parquet.py deleted file mode 100644 index c92a25fb4e..0000000000 --- a/loading_pipeline/lib/tasks/variants_migration/migrate_variants_parquet.py +++ /dev/null @@ -1,76 +0,0 @@ -import hail as hl -import luigi -import luigi.util - -from loading_pipeline.lib.paths import ( - new_variants_parquet_path, - variant_annotations_table_path, -) -from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( - BaseLoadingPipelineParams, -) -from loading_pipeline.lib.tasks.base.base_write_parquet import BaseWriteParquetTask -from loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc import ( - BaseRunJobOnDataprocTask, -) -from loading_pipeline.lib.tasks.exports.fields import get_variants_export_fields -from loading_pipeline.lib.tasks.exports.misc import ( - camelcase_array_structexpression_fields, - subset_consequences_fields, - unmap_formatting_annotation_enums, -) -from loading_pipeline.lib.tasks.files import GCSorLocalTarget -from loading_pipeline.lib.tasks.variants_migration.update_variant_annotations_table_with_dropped_reference_datasets import ( - UpdateVariantAnnotationsTableWithDroppedReferenceDatasetsTask, -) - - -@luigi.util.inherits(BaseLoadingPipelineParams) -class MigrateVariantsParquetTask(BaseWriteParquetTask): - run_id = luigi.Parameter() - attempt_id = luigi.IntParameter() - - def output(self) -> luigi.Target: - return GCSorLocalTarget( - new_variants_parquet_path( - self.reference_genome, - self.dataset_type, - self.run_id, - ), - ) - - def requires(self) -> luigi.Task: - return self.clone(UpdateVariantAnnotationsTableWithDroppedReferenceDatasetsTask) - - def create_table(self) -> None: - ht = hl.read_table( - variant_annotations_table_path( - self.reference_genome, - self.dataset_type, - ), - ) - ht = unmap_formatting_annotation_enums( - ht, - self.reference_genome, - self.dataset_type, - ) - ht = camelcase_array_structexpression_fields( - ht, - self.reference_genome, - self.dataset_type, - ) - if self.dataset_type.should_write_new_variant_details: - ht = subset_consequences_fields( - ht, - self.reference_genome, - ) - ht = ht.key_by() - return ht.select( - **get_variants_export_fields(ht, self.reference_genome, self.dataset_type), - ) - - -class MigrateVariantsParquetOnDataprocTask(BaseRunJobOnDataprocTask): - @property - def task(self) -> luigi.Task: - return MigrateVariantsParquetTask diff --git a/loading_pipeline/lib/tasks/variants_migration/update_variant_annotations_table_with_dropped_reference_datasets.py b/loading_pipeline/lib/tasks/variants_migration/update_variant_annotations_table_with_dropped_reference_datasets.py deleted file mode 100644 index 4dddb1afbe..0000000000 --- a/loading_pipeline/lib/tasks/variants_migration/update_variant_annotations_table_with_dropped_reference_datasets.py +++ /dev/null @@ -1,90 +0,0 @@ -import hail as hl -import luigi -import luigi.util - -from loading_pipeline.lib.paths import ( - variant_annotations_table_path, -) -from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( - BaseLoadingPipelineParams, -) -from loading_pipeline.lib.tasks.base.base_update import ( - BaseUpdateTask, -) -from loading_pipeline.lib.tasks.files import GCSorLocalTarget, HailTableTask - - -@luigi.util.inherits(BaseLoadingPipelineParams) -class UpdateVariantAnnotationsTableWithDroppedReferenceDatasetsTask( - BaseUpdateTask, -): - run_id = luigi.Parameter() - - def output(self) -> luigi.Target: - return GCSorLocalTarget( - variant_annotations_table_path( - self.reference_genome, - self.dataset_type, - ), - ) - - def requires(self) -> list[luigi.Task]: - return HailTableTask( - variant_annotations_table_path( - self.reference_genome, - self.dataset_type, - ), - ) - - def complete(self) -> bool: - return ( - super().complete() and 'dbnsfp' not in hl.read_table(self.output().path).row - ) - - def initialize_table(self) -> hl.Table: - key_type = self.dataset_type.table_key_type(self.reference_genome) - return hl.Table.parallelize( - [], - key_type, - key=key_type.fields, - globals=hl.Struct( - enums=hl.Struct(), - updates=hl.empty_set( - hl.tstruct( - callset=hl.tstr, - project_guid=hl.tstr, - remap_pedigree_hash=hl.tint32, - ), - ), - migrations=hl.empty_array(hl.tstr), - max_key_=hl.int64(-1), - ), - ) - - def update_table(self, ht: hl.Table) -> hl.Table: - for field in [ - 'clinvar', - 'gnomad_mito', - 'hmtvar', - 'local_constraint_mito', - 'dbnsfp', - 'mitomap', - 'mitimpact', - 'helix_mito', - 'gt_stats', - 'high_constraint_region', - 'eigen', - 'splice_ai', - 'exac', - 'topmed', - 'screen', - 'gnomad_exomes', - 'gnomad_genomes', - 'hgmd', - 'gnomad_non_coding_constraint', - ]: - if field in ht.row: - ht = ht.drop(field) - if field in ht.enums: - ht = ht.annotate_globals(enums=ht.enums.drop(field)) - return ht From d4f4d263ce400e397e999ed6896d436c83c36561 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 21 Aug 2026 15:52:38 -0400 Subject: [PATCH 263/369] undo debug --- .../lib/tasks/exports/write_new_variants_parquet_test.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py index 4fc878f9f5..6c00f7c89a 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py @@ -322,9 +322,7 @@ def test_mito_write_new_variants_parquet_test( TEST_RUN_ID, ), ) - export_json = convert_ndarray_to_list( - df.head(10).to_dict('records'), - ) # TODO debug + export_json = convert_ndarray_to_list(df.head(1).to_dict('records')) export_json[0]['sortedTranscriptConsequences'] = [ export_json[0]['sortedTranscriptConsequences'][0], ] From 3cf100fc8bbbde0577f0cf3390c3e0e649ccee94 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 21 Aug 2026 16:19:45 -0400 Subject: [PATCH 264/369] fix tests --- .../write_new_variants_parquet_test.py | 10 ++++--- loading_pipeline/var/test/callsets/sv_1.vcf | 26 +++++++++---------- 2 files changed, 19 insertions(+), 17 deletions(-) diff --git a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py index 6c00f7c89a..d551be464c 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py @@ -322,10 +322,12 @@ def test_mito_write_new_variants_parquet_test( TEST_RUN_ID, ), ) - export_json = convert_ndarray_to_list(df.head(1).to_dict('records')) - export_json[0]['sortedTranscriptConsequences'] = [ - export_json[0]['sortedTranscriptConsequences'][0], - ] + export_json = convert_ndarray_to_list( + df.head(10).to_dict('records'), + ) # TODO debug + # export_json[0]['sortedTranscriptConsequences'] = [ + # export_json[0]['sortedTranscriptConsequences'][0], + # ] self.assertEqual( export_json, [ diff --git a/loading_pipeline/var/test/callsets/sv_1.vcf b/loading_pipeline/var/test/callsets/sv_1.vcf index 22dbba332e..5f11091702 100644 --- a/loading_pipeline/var/test/callsets/sv_1.vcf +++ b/loading_pipeline/var/test/callsets/sv_1.vcf @@ -78,16 +78,16 @@ ##INFO= ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT RGP_164_1 RGP_164_2 RGP_164_3 RGP_164_4 RGP_164_5 -chr1 180928 BND_chr1_6 N 657 HIGH_SR_BACKGROUND;UNRESOLVED ALGORITHMS=manta;CHR2=chr5;END=180928;END2=20404;EVIDENCE=PE,SR;PREDICTED_INTERGENIC;PREDICTED_NEAREST_TSS=OR4F5,PLEKHG4B;PREDICTED_NONCODING_BREAKPOINT=DNase;STRANDS=+-;SVLEN=-1;SVTYPE=BND;UNRESOLVED_TYPE=SINGLE_ENDER_+-;AN=8;AC=1;AF=0.04775;N_BI_GENOS=2911;N_HOMREF=2633;N_HET=278;N_HOMALT=0;FREQ_HOMREF=0.9045;FREQ_HET=0.0954998;FREQ_HOMALT=0;MALE_AN=2894;MALE_AC=137;MALE_AF=0.047339;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=1310;MALE_N_HET=137;MALE_N_HOMALT=0;MALE_FREQ_HOMREF=0.905321;MALE_FREQ_HET=0.0946786;MALE_FREQ_HOMALT=0;FEMALE_AN=2906;FEMALE_AC=139;FEMALE_AF=0.047832;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=1314;FEMALE_N_HET=139;FEMALE_N_HOMALT=0;FEMALE_FREQ_HOMREF=0.904336;FEMALE_FREQ_HET=0.0956641;FEMALE_FREQ_HOMALT=0 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 0/0:PE,SR:99:99:0:2:0 0/1:SR:31:99:0:31:1 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:2:0 0/0:PE,SR:99:99:0:2:0 -chr1 257666 DUP_chr1_5 N 999 PASS ALGORITHMS=depth;CHR2=chr1;END=263666;EVIDENCE=BAF,RD;PREDICTED_INTERGENIC;PREDICTED_NEAREST_TSS=OR4F29;SVLEN=6000;SVTYPE=DUP;AN=8;AC=1;AF=0.115596;N_BI_GENOS=2911;N_HOMREF=2348;N_HET=453;N_HOMALT=110;FREQ_HOMREF=0.806596;FREQ_HET=0.155617;FREQ_HOMALT=0.0377877;MALE_AN=2894;MALE_AC=339;MALE_AF=0.117139;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=1163;MALE_N_HET=229;MALE_N_HOMALT=55;MALE_FREQ_HOMREF=0.803732;MALE_FREQ_HET=0.158258;MALE_FREQ_HOMALT=0.0380097;FEMALE_AN=2906;FEMALE_AC=330;FEMALE_AF=0.113558;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=1178;FEMALE_N_HET=220;FEMALE_N_HOMALT=55;FEMALE_FREQ_HOMREF=0.810736;FEMALE_FREQ_HET=0.151411;FEMALE_FREQ_HOMALT=0.0378527 GT:EV:GQ:RD_CN:RD_GQ 0/0:RD:99:2:99 0/0:RD:99:2:99 0/1:RD:8:3:8 0/0:RD:13:1:13 0/0:RD:13:1:13 -chr1 413968 DEL_chr1_12 N 999 PASS ALGORITHMS=depth;CHR2=chr1;END=428500;EVIDENCE=RD;PREDICTED_INTERGENIC;PREDICTED_NEAREST_TSS=OR4F29;SVLEN=14532;SVTYPE=DEL;AN=8;AC=1;AF=0.064926;N_BI_GENOS=2911;N_HOMREF=2538;N_HET=368;N_HOMALT=5;FREQ_HOMREF=0.871865;FREQ_HET=0.126417;FREQ_HOMALT=0.00171762;MALE_AN=2894;MALE_AC=172;MALE_AF=0.059433;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=1278;MALE_N_HET=166;MALE_N_HOMALT=3;MALE_FREQ_HOMREF=0.883207;MALE_FREQ_HET=0.11472;MALE_FREQ_HOMALT=0.00207325;FEMALE_AN=2906;FEMALE_AC=205;FEMALE_AF=0.070544;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=1250;FEMALE_N_HET=201;FEMALE_N_HOMALT=2;FEMALE_FREQ_HOMREF=0.860289;FEMALE_FREQ_HET=0.138334;FEMALE_FREQ_HOMALT=0.00137646 GT:EV:GQ:RD_CN:RD_GQ 0/0:RD:12:2:12 0/0:RD:0:2:0 0/1:RD:99:1:99 0/0:RD:2:2:2 0/0:RD:2:2:2 -chr1 789481 BND_chr1_9 N 999 PESR_GT_OVERDISPERSION;UNRESOLVED ALGORITHMS=manta;CHR2=chr1;END=789481;EVIDENCE=PE;PREDICTED_INTERGENIC;PREDICTED_NEAREST_TSS=FBXO28,OR4F16;PREDICTED_NONCODING_BREAKPOINT=DNase,Tommerup_TADanno;STRANDS=-+;SVLEN=223225007;SVTYPE=BND;UNRESOLVED_TYPE=SINGLE_ENDER_-+;AN=8;AC=7;AF=0.910684;N_BI_GENOS=2911;N_HOMREF=0;N_HET=520;N_HOMALT=2391;FREQ_HOMREF=0;FREQ_HET=0.178633;FREQ_HOMALT=0.821367;MALE_AN=2894;MALE_AC=2639;MALE_AF=0.911887;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=0;MALE_N_HET=255;MALE_N_HOMALT=1192;MALE_FREQ_HOMREF=0;MALE_FREQ_HET=0.176227;MALE_FREQ_HOMALT=0.823773;FEMALE_AN=2906;FEMALE_AC=2643;FEMALE_AF=0.909498;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=0;FEMALE_N_HET=263;FEMALE_N_HOMALT=1190;FEMALE_FREQ_HOMREF=0;FEMALE_FREQ_HET=0.181005;FEMALE_FREQ_HOMALT=0.818995 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 1/1:PE:59:59:2:99:0 1/1:PE:26:26:2:99:0 1/1:PE:39:39:2:99:0 0/1:PE:19:19:1:99:0 0/1:PE:19:19:1:99:0 -chr1 4228405 INS_chr1_65 N 605 HIGH_SR_BACKGROUND ALGORITHMS=manta,melt;CHR2=chr1;END=4228448;EVIDENCE=SR;gnomAD_V2_SVID=gnomAD-SV_v2.1_INS_chr1_65;GNOMAD_V4.1_TRUTH_VID=gnomAD-SV_v3_BND_chr1_0001f5b7;gnomAD_V2_AF=0.068962998688221;gnomAD_V2_AC=224;gnomAD_V2_AN=3247;StrVCTVRE=0.1255;PREDICTED_INTERGENIC;PREDICTED_NEAREST_TSS=C1orf174;SVLEN=298;SVTYPE=INS;AN=8;AC=1;AF=0.10237;N_BI_GENOS=2911;N_HOMREF=2318;N_HET=590;N_HOMALT=3;FREQ_HOMREF=0.79629;FREQ_HET=0.202679;FREQ_HOMALT=0.00103057;MALE_AN=2894;MALE_AC=293;MALE_AF=0.101244;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=1156;MALE_N_HET=289;MALE_N_HOMALT=2;MALE_FREQ_HOMREF=0.798894;MALE_FREQ_HET=0.199724;MALE_FREQ_HOMALT=0.00138217;FEMALE_AN=2906;FEMALE_AC=302;FEMALE_AF=0.103923;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=1152;FEMALE_N_HET=300;FEMALE_N_HOMALT=1;FEMALE_FREQ_HOMREF=0.792842;FEMALE_FREQ_HET=0.206469;FEMALE_FREQ_HOMALT=0.000688231 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 0/1:SR:62:99:0:62:1 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:99:0 -chr1 6558902 CPX_chr1_22 N 644 HIGH_SR_BACKGROUND ALGORITHMS=manta;BOTHSIDES_SUPPORT;CHR2=chr1;CPX_INTERVALS=INV_chr1:6558902-6559723,DUP_chr1:6559655-6559723;CPX_TYPE=INVdup;END=6559723;EVIDENCE=PE,SR;PREDICTED_INTRONIC=TAS1R1;PREDICTED_NONCODING_BREAKPOINT=Tommerup_TADanno;PREDICTED_NONCODING_SPAN=DNase;SVLEN=821;SVTYPE=CPX;AN=8;AC=2;AF=0.169873;N_BI_GENOS=2911;N_HOMREF=1925;N_HET=983;N_HOMALT=3;FREQ_HOMREF=0.661285;FREQ_HET=0.337685;FREQ_HOMALT=0.00103057;MALE_AN=2894;MALE_AC=497;MALE_AF=0.171735;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=950;MALE_N_HET=497;MALE_N_HOMALT=0;MALE_FREQ_HOMREF=0.656531;MALE_FREQ_HET=0.343469;MALE_FREQ_HOMALT=0;FEMALE_AN=2906;FEMALE_AC=488;FEMALE_AF=0.167928;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=968;FEMALE_N_HET=482;FEMALE_N_HOMALT=3;FEMALE_FREQ_HOMREF=0.666208;FEMALE_FREQ_HET=0.331727;FEMALE_FREQ_HOMALT=0.00206469 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT:RD_CN:CONC_ST 0/0:PE,SR:99:99:0:99:0:2:EMPTY 0/1:PE,SR:57:0:0:57:1:2:TN,TP 0/1:PE,SR:0:0:1:99:0:2:FP,TN 0/0:PE,SR:99:99:0:0:0:3:FN 1/1:PE,SR:99:99:0:0:0:1:FP,TP -chr1 16088760 CPX_chr1_41 N 684 PASS ALGORITHMS=manta;CHR2=chr1;CPX_INTERVALS=DUP_chr1:16088760-16088835,INV_chr1:16088760-16089601;CPX_TYPE=dupINV;END=16089601;EVIDENCE=PE,SR;PREDICTED_INTERGENIC;PREDICTED_NEAREST_TSS=FAM131C;PREDICTED_NONCODING_BREAKPOINT=Tommerup_TADanno;PREDICTED_NONCODING_SPAN=DNase;SVLEN=841;SVTYPE=CPX;AN=8;AC=2;AF=0.218138;N_BI_GENOS=2911;N_HOMREF=1659;N_HET=1234;N_HOMALT=18;FREQ_HOMREF=0.569907;FREQ_HET=0.423909;FREQ_HOMALT=0.00618344;MALE_AN=2894;MALE_AC=635;MALE_AF=0.219419;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=818;MALE_N_HET=623;MALE_N_HOMALT=6;MALE_FREQ_HOMREF=0.565308;MALE_FREQ_HET=0.430546;MALE_FREQ_HOMALT=0.00414651;FEMALE_AN=2906;FEMALE_AC=629;FEMALE_AF=0.216449;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=836;FEMALE_N_HET=605;FEMALE_N_HOMALT=12;FEMALE_FREQ_HOMREF=0.575361;FEMALE_FREQ_HET=0.41638;FEMALE_FREQ_HOMALT=0.00825877 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 0/1:SR:52:0:0:52:1 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:99:0 0/1:SR:62:0:0:62:1 0/1:SR:62:0:0:62:1 -chr1 17465707 INS_chr1_268 N 263 HIGH_SR_BACKGROUND ALGORITHMS=melt;CHR2=chr1;END=17465723;EVIDENCE=SR;PREDICTED_INTERGENIC;PREDICTED_NEAREST_TSS=RCC2;PREDICTED_NONCODING_BREAKPOINT=Tommerup_TADanno;SVLEN=955;SVTYPE=INS;AN=8;AC=1;AF=0.004466;N_BI_GENOS=2911;N_HOMREF=2885;N_HET=26;N_HOMALT=0;FREQ_HOMREF=0.991068;FREQ_HET=0.00893164;FREQ_HOMALT=0;MALE_AN=2894;MALE_AC=14;MALE_AF=0.004838;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=1433;MALE_N_HET=14;MALE_N_HOMALT=0;MALE_FREQ_HOMREF=0.990325;MALE_FREQ_HET=0.00967519;MALE_FREQ_HOMALT=0;FEMALE_AN=2906;FEMALE_AC=11;FEMALE_AF=0.003785;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=1442;FEMALE_N_HET=11;FEMALE_N_HOMALT=0;FEMALE_FREQ_HOMREF=0.992429;FEMALE_FREQ_HET=0.00757054;FEMALE_FREQ_HOMALT=0 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:99:0 0/1:SR:0:99:0:0:1 0/0:PE,SR:99:99:0:2:0 0/0:PE,SR:99:99:0:2:0 -chr1 21427498 CPX_chr1_54 N 733 PASS ALGORITHMS=manta;CHR2=chr1;CPX_INTERVALS=DUP_chr1:21427498-21427959,INV_chr1:21427498-21480073,DEL_chr1:21480073-21480419;CPX_TYPE=dupINVdel;END=21480419;EVIDENCE=PE;PREDICTED_LOF=NBPF3;PREDICTED_NONCODING_BREAKPOINT=DNase,Tommerup_TADanno;PREDICTED_NONCODING_SPAN=DNase;SVLEN=52921;SVTYPE=CPX;AN=8;AC=4;AF=0.499656;N_BI_GENOS=2911;N_HOMREF=51;N_HET=2811;N_HOMALT=49;FREQ_HOMREF=0.0175198;FREQ_HET=0.965648;FREQ_HOMALT=0.0168327;MALE_AN=2894;MALE_AC=1453;MALE_AF=0.502073;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=19;MALE_N_HET=1403;MALE_N_HOMALT=25;MALE_FREQ_HOMREF=0.0131306;MALE_FREQ_HET=0.969592;MALE_FREQ_HOMALT=0.0172771;FEMALE_AN=2906;FEMALE_AC=1445;FEMALE_AF=0.497247;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=32;FEMALE_N_HET=1397;FEMALE_N_HOMALT=24;FEMALE_FREQ_HOMREF=0.0220234;FEMALE_FREQ_HET=0.961459;FEMALE_FREQ_HOMALT=0.0165175 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 0/1:PE:93:93:1:99:0 0/1:PE:79:79:1:99:0 0/1:PE:33:33:1:6:0 0/1:PE,SR:39:39:1:99:0 0/1:PE,SR:39:39:1:99:0 -chr1 48963084 INS_chr1_688 N 526 HIGH_SR_BACKGROUND ALGORITHMS=melt;CHR2=chr1;END=48963135;EVIDENCE=SR;PREDICTED_INTRONIC=AGBL4;PREDICTED_NONCODING_BREAKPOINT=Tommerup_TADanno;SVLEN=5520;SVTYPE=INS;AN=8;AC=1;AF=0.06338;N_BI_GENOS=2911;N_HOMREF=2544;N_HET=365;N_HOMALT=2;FREQ_HOMREF=0.873926;FREQ_HET=0.125386;FREQ_HOMALT=0.000687049;MALE_AN=2894;MALE_AC=177;MALE_AF=0.061161;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=1271;MALE_N_HET=175;MALE_N_HOMALT=1;MALE_FREQ_HOMREF=0.878369;MALE_FREQ_HET=0.12094;MALE_FREQ_HOMALT=0.000691085;FEMALE_AN=2906;FEMALE_AC=192;FEMALE_AF=0.06607;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=1262;FEMALE_N_HET=190;FEMALE_N_HOMALT=1;FEMALE_FREQ_HOMREF=0.868548;FEMALE_FREQ_HET=0.130764;FEMALE_FREQ_HOMALT=0.000688231 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:99:0 0/1:SR:0:99:0:0:1 0/1:SR:0:99:0:0:1 -chr1 180540234 CPX_chr1_251 N 999 UNRESOLVED ALGORITHMS=manta;CHR2=chr1;CPX_INTERVALS=DEL_chr1:180540234-181074767,INV_chr1:181074767-181074938;CPX_TYPE=delINV;END=181074952;EVIDENCE=PE,SR;PREDICTED_LOF=KIAA1614,MR1,STX6,XPR1;PREDICTED_NONCODING_BREAKPOINT=Tommerup_TADanno;PREDICTED_NONCODING_SPAN=DNase,Enhancer;SVLEN=534718;SVTYPE=CPX;UNRESOLVED_TYPE=POSTHOC_RD_GT_REJECTION;AN=8;AC=3;AF=0.251804;N_BI_GENOS=2911;N_HOMREF=1559;N_HET=1238;N_HOMALT=114;FREQ_HOMREF=0.535555;FREQ_HET=0.425283;FREQ_HOMALT=0.0391618;MALE_AN=2894;MALE_AC=724;MALE_AF=0.250173;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=784;MALE_N_HET=602;MALE_N_HOMALT=61;MALE_FREQ_HOMREF=0.541811;MALE_FREQ_HET=0.416033;MALE_FREQ_HOMALT=0.0421562;FEMALE_AN=2906;FEMALE_AC=736;FEMALE_AF=0.253269;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=770;FEMALE_N_HET=630;FEMALE_N_HOMALT=53;FEMALE_FREQ_HOMREF=0.529938;FEMALE_FREQ_HET=0.433586;FEMALE_FREQ_HOMALT=0.0364763 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 0/0:PE,SR:99:99:0:99:0 0/1:PE,SR:41:26:1:41:1 1/1:PE,SR:89:33:1:89:2 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:99:0 -chrX 3 CPX_chrX_251 N 999 UNRESOLVED ALGORITHMS=manta;CPX_INTERVALS=DEL_chr1:180540234-181074767,INV_chr1:181074767-181074938;CPX_TYPE=delINV;END=2781000;EVIDENCE=PE,SR;PREDICTED_LOF=KIAA1614,MR1,STX6,XPR1;PREDICTED_NONCODING_BREAKPOINT=Tommerup_TADanno;PREDICTED_NONCODING_SPAN=DNase,Enhancer;SVLEN=534718;SVTYPE=CPX;UNRESOLVED_TYPE=POSTHOC_RD_GT_REJECTION;AN=8;AC=3;AF=0.251804;N_BI_GENOS=2911;N_HOMREF=1559;N_HET=1238;N_HOMALT=114;FREQ_HOMREF=0.535555;FREQ_HET=0.425283;FREQ_HOMALT=0.0391618;MALE_AN=2894;MALE_AC=724;MALE_AF=0.250173;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=784;MALE_N_HET=602;MALE_N_HOMALT=61;MALE_FREQ_HOMREF=0.541811;MALE_FREQ_HET=0.416033;MALE_FREQ_HOMALT=0.0421562;FEMALE_AN=2906;FEMALE_AC=736;FEMALE_AF=0.253269;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=770;FEMALE_N_HET=630;FEMALE_N_HOMALT=53;FEMALE_FREQ_HOMREF=0.529938;FEMALE_FREQ_HET=0.433586;FEMALE_FREQ_HOMALT=0.0364763 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 0/0:PE,SR:99:99:0:99:0 0/1:PE,SR:41:26:1:41:1 1/1:PE,SR:89:33:1:89:2 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:99:0 -chrX 2781700 CPX_chrX_252 N 999 UNRESOLVED ALGORITHMS=manta;CPX_INTERVALS=DEL_chr1:180540234-181074767,INV_chr1:181074767-181074938;CPX_TYPE=delINV;END=2781900;EVIDENCE=PE,SR;PREDICTED_LOF=KIAA1614,MR1,STX6,XPR1;PREDICTED_NONCODING_BREAKPOINT=Tommerup_TADanno;PREDICTED_NONCODING_SPAN=DNase,Enhancer;SVLEN=534718;SVTYPE=CPX;UNRESOLVED_TYPE=POSTHOC_RD_GT_REJECTION;AN=8;AC=3;AF=0.251804;N_BI_GENOS=2911;N_HOMREF=1559;N_HET=1238;N_HOMALT=114;FREQ_HOMREF=0.535555;FREQ_HET=0.425283;FREQ_HOMALT=0.0391618;MALE_AN=2894;MALE_AC=724;MALE_AF=0.250173;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=784;MALE_N_HET=602;MALE_N_HOMALT=61;MALE_FREQ_HOMREF=0.541811;MALE_FREQ_HET=0.416033;MALE_FREQ_HOMALT=0.0421562;FEMALE_AN=2906;FEMALE_AC=736;FEMALE_AF=0.253269;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=770;FEMALE_N_HET=630;FEMALE_N_HOMALT=53;FEMALE_FREQ_HOMREF=0.529938;FEMALE_FREQ_HET=0.433586;FEMALE_FREQ_HOMALT=0.0364763 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 0/0:PE,SR:99:99:0:99:0 0/1:PE,SR:41:26:1:41:1 1/1:PE,SR:89:33:1:89:2 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:99:0 \ No newline at end of file +chr1 180928 BND_chr1_6 N 657 HIGH_SR_BACKGROUND;UNRESOLVED ALGORITHMS=manta;CHR2=chr5;END=180928;END2=20404;EVIDENCE=PE,SR;PREDICTED_INTERGENIC;PREDICTED_NEAREST_TSS=OR4F5,PLEKHG4B;PREDICTED_NONCODING_BREAKPOINT=DNase;STRANDS=+-;SVLEN=-1;SVTYPE=BND;UNRESOLVED_TYPE=SINGLE_ENDER_+-;AN=8;AC=1;AF=0.04775;N_BI_GENOS=2911;N_HOMREF=2633;N_HET=278;N_HOMALT=0;FREQ_HOMREF=0.9045;FREQ_HET=0.0954998;FREQ_HOMALT=0;MALE_AN=2894;MALE_AC=137;MALE_AF=0.047339;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=1310;MALE_N_HET=137;MALE_N_HOMALT=0;MALE_FREQ_HOMREF=0.905321;MALE_FREQ_HET=0.0946786;MALE_FREQ_HOMALT=0;FEMALE_AN=2906;FEMALE_AC=139;FEMALE_AF=0.047832;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=1314;FEMALE_N_HET=139;FEMALE_N_HOMALT=0;FEMALE_FREQ_HOMREF=0.904336;FEMALE_FREQ_HET=0.0956641;FEMALE_FREQ_HOMALT=0;SEQR_INTERNAL_TRUTH_VID=BND_chr1_6 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 0/0:PE,SR:99:99:0:2:0 0/1:SR:31:99:0:31:1 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:2:0 0/0:PE,SR:99:99:0:2:0 +chr1 257666 DUP_chr1_5 N 999 PASS ALGORITHMS=depth;CHR2=chr1;END=263666;EVIDENCE=BAF,RD;PREDICTED_INTERGENIC;PREDICTED_NEAREST_TSS=OR4F29;SVLEN=6000;SVTYPE=DUP;AN=8;AC=1;AF=0.115596;N_BI_GENOS=2911;N_HOMREF=2348;N_HET=453;N_HOMALT=110;FREQ_HOMREF=0.806596;FREQ_HET=0.155617;FREQ_HOMALT=0.0377877;MALE_AN=2894;MALE_AC=339;MALE_AF=0.117139;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=1163;MALE_N_HET=229;MALE_N_HOMALT=55;MALE_FREQ_HOMREF=0.803732;MALE_FREQ_HET=0.158258;MALE_FREQ_HOMALT=0.0380097;FEMALE_AN=2906;FEMALE_AC=330;FEMALE_AF=0.113558;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=1178;FEMALE_N_HET=220;FEMALE_N_HOMALT=55;FEMALE_FREQ_HOMREF=0.810736;FEMALE_FREQ_HET=0.151411;FEMALE_FREQ_HOMALT=0.0378527;SEQR_INTERNAL_TRUTH_VID=DUP_chr1_5 GT:EV:GQ:RD_CN:RD_GQ 0/0:RD:99:2:99 0/0:RD:99:2:99 0/1:RD:8:3:8 0/0:RD:13:1:13 0/0:RD:13:1:13 +chr1 413968 DEL_chr1_12 N 999 PASS ALGORITHMS=depth;CHR2=chr1;END=428500;EVIDENCE=RD;PREDICTED_INTERGENIC;PREDICTED_NEAREST_TSS=OR4F29;SVLEN=14532;SVTYPE=DEL;AN=8;AC=1;AF=0.064926;N_BI_GENOS=2911;N_HOMREF=2538;N_HET=368;N_HOMALT=5;FREQ_HOMREF=0.871865;FREQ_HET=0.126417;FREQ_HOMALT=0.00171762;MALE_AN=2894;MALE_AC=172;MALE_AF=0.059433;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=1278;MALE_N_HET=166;MALE_N_HOMALT=3;MALE_FREQ_HOMREF=0.883207;MALE_FREQ_HET=0.11472;MALE_FREQ_HOMALT=0.00207325;FEMALE_AN=2906;FEMALE_AC=205;FEMALE_AF=0.070544;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=1250;FEMALE_N_HET=201;FEMALE_N_HOMALT=2;FEMALE_FREQ_HOMREF=0.860289;FEMALE_FREQ_HET=0.138334;FEMALE_FREQ_HOMALT=0.00137646;SEQR_INTERNAL_TRUTH_VID=DEL_chr1_12 GT:EV:GQ:RD_CN:RD_GQ 0/0:RD:12:2:12 0/0:RD:0:2:0 0/1:RD:99:1:99 0/0:RD:2:2:2 0/0:RD:2:2:2 +chr1 789481 BND_chr1_9 N 999 PESR_GT_OVERDISPERSION;UNRESOLVED ALGORITHMS=manta;CHR2=chr1;END=789481;EVIDENCE=PE;PREDICTED_INTERGENIC;PREDICTED_NEAREST_TSS=FBXO28,OR4F16;PREDICTED_NONCODING_BREAKPOINT=DNase,Tommerup_TADanno;STRANDS=-+;SVLEN=223225007;SVTYPE=BND;UNRESOLVED_TYPE=SINGLE_ENDER_-+;AN=8;AC=7;AF=0.910684;N_BI_GENOS=2911;N_HOMREF=0;N_HET=520;N_HOMALT=2391;FREQ_HOMREF=0;FREQ_HET=0.178633;FREQ_HOMALT=0.821367;MALE_AN=2894;MALE_AC=2639;MALE_AF=0.911887;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=0;MALE_N_HET=255;MALE_N_HOMALT=1192;MALE_FREQ_HOMREF=0;MALE_FREQ_HET=0.176227;MALE_FREQ_HOMALT=0.823773;FEMALE_AN=2906;FEMALE_AC=2643;FEMALE_AF=0.909498;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=0;FEMALE_N_HET=263;FEMALE_N_HOMALT=1190;FEMALE_FREQ_HOMREF=0;FEMALE_FREQ_HET=0.181005;FEMALE_FREQ_HOMALT=0.818995;SEQR_INTERNAL_TRUTH_VID=BND_chr1_9 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 1/1:PE:59:59:2:99:0 1/1:PE:26:26:2:99:0 1/1:PE:39:39:2:99:0 0/1:PE:19:19:1:99:0 0/1:PE:19:19:1:99:0 +chr1 4228405 INS_chr1_65 N 605 HIGH_SR_BACKGROUND ALGORITHMS=manta,melt;CHR2=chr1;END=4228448;EVIDENCE=SR;gnomAD_V2_SVID=gnomAD-SV_v2.1_INS_chr1_65;GNOMAD_V4.1_TRUTH_VID=gnomAD-SV_v3_BND_chr1_0001f5b7;gnomAD_V2_AF=0.068962998688221;gnomAD_V2_AC=224;gnomAD_V2_AN=3247;StrVCTVRE=0.1255;PREDICTED_INTERGENIC;PREDICTED_NEAREST_TSS=C1orf174;SVLEN=298;SVTYPE=INS;AN=8;AC=1;AF=0.10237;N_BI_GENOS=2911;N_HOMREF=2318;N_HET=590;N_HOMALT=3;FREQ_HOMREF=0.79629;FREQ_HET=0.202679;FREQ_HOMALT=0.00103057;MALE_AN=2894;MALE_AC=293;MALE_AF=0.101244;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=1156;MALE_N_HET=289;MALE_N_HOMALT=2;MALE_FREQ_HOMREF=0.798894;MALE_FREQ_HET=0.199724;MALE_FREQ_HOMALT=0.00138217;FEMALE_AN=2906;FEMALE_AC=302;FEMALE_AF=0.103923;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=1152;FEMALE_N_HET=300;FEMALE_N_HOMALT=1;FEMALE_FREQ_HOMREF=0.792842;FEMALE_FREQ_HET=0.206469;FEMALE_FREQ_HOMALT=0.000688231;SEQR_INTERNAL_TRUTH_VID=INS_chr1_65 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 0/1:SR:62:99:0:62:1 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:99:0 +chr1 6558902 CPX_chr1_22 N 644 HIGH_SR_BACKGROUND ALGORITHMS=manta;BOTHSIDES_SUPPORT;CHR2=chr1;CPX_INTERVALS=INV_chr1:6558902-6559723,DUP_chr1:6559655-6559723;CPX_TYPE=INVdup;END=6559723;EVIDENCE=PE,SR;PREDICTED_INTRONIC=TAS1R1;PREDICTED_NONCODING_BREAKPOINT=Tommerup_TADanno;PREDICTED_NONCODING_SPAN=DNase;SVLEN=821;SVTYPE=CPX;AN=8;AC=2;AF=0.169873;N_BI_GENOS=2911;N_HOMREF=1925;N_HET=983;N_HOMALT=3;FREQ_HOMREF=0.661285;FREQ_HET=0.337685;FREQ_HOMALT=0.00103057;MALE_AN=2894;MALE_AC=497;MALE_AF=0.171735;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=950;MALE_N_HET=497;MALE_N_HOMALT=0;MALE_FREQ_HOMREF=0.656531;MALE_FREQ_HET=0.343469;MALE_FREQ_HOMALT=0;FEMALE_AN=2906;FEMALE_AC=488;FEMALE_AF=0.167928;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=968;FEMALE_N_HET=482;FEMALE_N_HOMALT=3;FEMALE_FREQ_HOMREF=0.666208;FEMALE_FREQ_HET=0.331727;FEMALE_FREQ_HOMALT=0.00206469;SEQR_INTERNAL_TRUTH_VID=CPX_chr1_22 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT:RD_CN:CONC_ST 0/0:PE,SR:99:99:0:99:0:2:EMPTY 0/1:PE,SR:57:0:0:57:1:2:TN,TP 0/1:PE,SR:0:0:1:99:0:2:FP,TN 0/0:PE,SR:99:99:0:0:0:3:FN 1/1:PE,SR:99:99:0:0:0:1:FP,TP +chr1 16088760 CPX_chr1_41 N 684 PASS ALGORITHMS=manta;CHR2=chr1;CPX_INTERVALS=DUP_chr1:16088760-16088835,INV_chr1:16088760-16089601;CPX_TYPE=dupINV;END=16089601;EVIDENCE=PE,SR;PREDICTED_INTERGENIC;PREDICTED_NEAREST_TSS=FAM131C;PREDICTED_NONCODING_BREAKPOINT=Tommerup_TADanno;PREDICTED_NONCODING_SPAN=DNase;SVLEN=841;SVTYPE=CPX;AN=8;AC=2;AF=0.218138;N_BI_GENOS=2911;N_HOMREF=1659;N_HET=1234;N_HOMALT=18;FREQ_HOMREF=0.569907;FREQ_HET=0.423909;FREQ_HOMALT=0.00618344;MALE_AN=2894;MALE_AC=635;MALE_AF=0.219419;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=818;MALE_N_HET=623;MALE_N_HOMALT=6;MALE_FREQ_HOMREF=0.565308;MALE_FREQ_HET=0.430546;MALE_FREQ_HOMALT=0.00414651;FEMALE_AN=2906;FEMALE_AC=629;FEMALE_AF=0.216449;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=836;FEMALE_N_HET=605;FEMALE_N_HOMALT=12;FEMALE_FREQ_HOMREF=0.575361;FEMALE_FREQ_HET=0.41638;FEMALE_FREQ_HOMALT=0.00825877;SEQR_INTERNAL_TRUTH_VID=CPX_chr1_41 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 0/1:SR:52:0:0:52:1 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:99:0 0/1:SR:62:0:0:62:1 0/1:SR:62:0:0:62:1 +chr1 17465707 INS_chr1_268 N 263 HIGH_SR_BACKGROUND ALGORITHMS=melt;CHR2=chr1;END=17465723;EVIDENCE=SR;PREDICTED_INTERGENIC;PREDICTED_NEAREST_TSS=RCC2;PREDICTED_NONCODING_BREAKPOINT=Tommerup_TADanno;SVLEN=955;SVTYPE=INS;AN=8;AC=1;AF=0.004466;N_BI_GENOS=2911;N_HOMREF=2885;N_HET=26;N_HOMALT=0;FREQ_HOMREF=0.991068;FREQ_HET=0.00893164;FREQ_HOMALT=0;MALE_AN=2894;MALE_AC=14;MALE_AF=0.004838;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=1433;MALE_N_HET=14;MALE_N_HOMALT=0;MALE_FREQ_HOMREF=0.990325;MALE_FREQ_HET=0.00967519;MALE_FREQ_HOMALT=0;FEMALE_AN=2906;FEMALE_AC=11;FEMALE_AF=0.003785;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=1442;FEMALE_N_HET=11;FEMALE_N_HOMALT=0;FEMALE_FREQ_HOMREF=0.992429;FEMALE_FREQ_HET=0.00757054;FEMALE_FREQ_HOMALT=0;SEQR_INTERNAL_TRUTH_VID=INS_chr1_268 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:99:0 0/1:SR:0:99:0:0:1 0/0:PE,SR:99:99:0:2:0 0/0:PE,SR:99:99:0:2:0 +chr1 21427498 CPX_chr1_54 N 733 PASS ALGORITHMS=manta;CHR2=chr1;CPX_INTERVALS=DUP_chr1:21427498-21427959,INV_chr1:21427498-21480073,DEL_chr1:21480073-21480419;CPX_TYPE=dupINVdel;END=21480419;EVIDENCE=PE;PREDICTED_LOF=NBPF3;PREDICTED_NONCODING_BREAKPOINT=DNase,Tommerup_TADanno;PREDICTED_NONCODING_SPAN=DNase;SVLEN=52921;SVTYPE=CPX;AN=8;AC=4;AF=0.499656;N_BI_GENOS=2911;N_HOMREF=51;N_HET=2811;N_HOMALT=49;FREQ_HOMREF=0.0175198;FREQ_HET=0.965648;FREQ_HOMALT=0.0168327;MALE_AN=2894;MALE_AC=1453;MALE_AF=0.502073;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=19;MALE_N_HET=1403;MALE_N_HOMALT=25;MALE_FREQ_HOMREF=0.0131306;MALE_FREQ_HET=0.969592;MALE_FREQ_HOMALT=0.0172771;FEMALE_AN=2906;FEMALE_AC=1445;FEMALE_AF=0.497247;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=32;FEMALE_N_HET=1397;FEMALE_N_HOMALT=24;FEMALE_FREQ_HOMREF=0.0220234;FEMALE_FREQ_HET=0.961459;FEMALE_FREQ_HOMALT=0.0165175;SEQR_INTERNAL_TRUTH_VID=CPX_chr1_54 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 0/1:PE:93:93:1:99:0 0/1:PE:79:79:1:99:0 0/1:PE:33:33:1:6:0 0/1:PE,SR:39:39:1:99:0 0/1:PE,SR:39:39:1:99:0 +chr1 48963084 INS_chr1_688 N 526 HIGH_SR_BACKGROUND ALGORITHMS=melt;CHR2=chr1;END=48963135;EVIDENCE=SR;PREDICTED_INTRONIC=AGBL4;PREDICTED_NONCODING_BREAKPOINT=Tommerup_TADanno;SVLEN=5520;SVTYPE=INS;AN=8;AC=1;AF=0.06338;N_BI_GENOS=2911;N_HOMREF=2544;N_HET=365;N_HOMALT=2;FREQ_HOMREF=0.873926;FREQ_HET=0.125386;FREQ_HOMALT=0.000687049;MALE_AN=2894;MALE_AC=177;MALE_AF=0.061161;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=1271;MALE_N_HET=175;MALE_N_HOMALT=1;MALE_FREQ_HOMREF=0.878369;MALE_FREQ_HET=0.12094;MALE_FREQ_HOMALT=0.000691085;FEMALE_AN=2906;FEMALE_AC=192;FEMALE_AF=0.06607;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=1262;FEMALE_N_HET=190;FEMALE_N_HOMALT=1;FEMALE_FREQ_HOMREF=0.868548;FEMALE_FREQ_HET=0.130764;FEMALE_FREQ_HOMALT=0.000688231;SEQR_INTERNAL_TRUTH_VID=INS_chr1_688 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:99:0 0/1:SR:0:99:0:0:1 0/1:SR:0:99:0:0:1 +chr1 180540234 CPX_chr1_251 N 999 UNRESOLVED ALGORITHMS=manta;CHR2=chr1;CPX_INTERVALS=DEL_chr1:180540234-181074767,INV_chr1:181074767-181074938;CPX_TYPE=delINV;END=181074952;EVIDENCE=PE,SR;PREDICTED_LOF=KIAA1614,MR1,STX6,XPR1;PREDICTED_NONCODING_BREAKPOINT=Tommerup_TADanno;PREDICTED_NONCODING_SPAN=DNase,Enhancer;SVLEN=534718;SVTYPE=CPX;UNRESOLVED_TYPE=POSTHOC_RD_GT_REJECTION;AN=8;AC=3;AF=0.251804;N_BI_GENOS=2911;N_HOMREF=1559;N_HET=1238;N_HOMALT=114;FREQ_HOMREF=0.535555;FREQ_HET=0.425283;FREQ_HOMALT=0.0391618;MALE_AN=2894;MALE_AC=724;MALE_AF=0.250173;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=784;MALE_N_HET=602;MALE_N_HOMALT=61;MALE_FREQ_HOMREF=0.541811;MALE_FREQ_HET=0.416033;MALE_FREQ_HOMALT=0.0421562;FEMALE_AN=2906;FEMALE_AC=736;FEMALE_AF=0.253269;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=770;FEMALE_N_HET=630;FEMALE_N_HOMALT=53;FEMALE_FREQ_HOMREF=0.529938;FEMALE_FREQ_HET=0.433586;FEMALE_FREQ_HOMALT=0.0364763;SEQR_INTERNAL_TRUTH_VID=CPX_chr1_251 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 0/0:PE,SR:99:99:0:99:0 0/1:PE,SR:41:26:1:41:1 1/1:PE,SR:89:33:1:89:2 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:99:0 +chrX 3 CPX_chrX_251 N 999 UNRESOLVED ALGORITHMS=manta;CPX_INTERVALS=DEL_chr1:180540234-181074767,INV_chr1:181074767-181074938;CPX_TYPE=delINV;END=2781000;EVIDENCE=PE,SR;PREDICTED_LOF=KIAA1614,MR1,STX6,XPR1;PREDICTED_NONCODING_BREAKPOINT=Tommerup_TADanno;PREDICTED_NONCODING_SPAN=DNase,Enhancer;SVLEN=534718;SVTYPE=CPX;UNRESOLVED_TYPE=POSTHOC_RD_GT_REJECTION;AN=8;AC=3;AF=0.251804;N_BI_GENOS=2911;N_HOMREF=1559;N_HET=1238;N_HOMALT=114;FREQ_HOMREF=0.535555;FREQ_HET=0.425283;FREQ_HOMALT=0.0391618;MALE_AN=2894;MALE_AC=724;MALE_AF=0.250173;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=784;MALE_N_HET=602;MALE_N_HOMALT=61;MALE_FREQ_HOMREF=0.541811;MALE_FREQ_HET=0.416033;MALE_FREQ_HOMALT=0.0421562;FEMALE_AN=2906;FEMALE_AC=736;FEMALE_AF=0.253269;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=770;FEMALE_N_HET=630;FEMALE_N_HOMALT=53;FEMALE_FREQ_HOMREF=0.529938;FEMALE_FREQ_HET=0.433586;FEMALE_FREQ_HOMALT=0.0364763;SEQR_INTERNAL_TRUTH_VID=CPX_chrX_251 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 0/0:PE,SR:99:99:0:99:0 0/1:PE,SR:41:26:1:41:1 1/1:PE,SR:89:33:1:89:2 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:99:0 +chrX 2781700 CPX_chrX_252 N 999 UNRESOLVED ALGORITHMS=manta;CPX_INTERVALS=DEL_chr1:180540234-181074767,INV_chr1:181074767-181074938;CPX_TYPE=delINV;END=2781900;EVIDENCE=PE,SR;PREDICTED_LOF=KIAA1614,MR1,STX6,XPR1;PREDICTED_NONCODING_BREAKPOINT=Tommerup_TADanno;PREDICTED_NONCODING_SPAN=DNase,Enhancer;SVLEN=534718;SVTYPE=CPX;UNRESOLVED_TYPE=POSTHOC_RD_GT_REJECTION;AN=8;AC=3;AF=0.251804;N_BI_GENOS=2911;N_HOMREF=1559;N_HET=1238;N_HOMALT=114;FREQ_HOMREF=0.535555;FREQ_HET=0.425283;FREQ_HOMALT=0.0391618;MALE_AN=2894;MALE_AC=724;MALE_AF=0.250173;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=784;MALE_N_HET=602;MALE_N_HOMALT=61;MALE_FREQ_HOMREF=0.541811;MALE_FREQ_HET=0.416033;MALE_FREQ_HOMALT=0.0421562;FEMALE_AN=2906;FEMALE_AC=736;FEMALE_AF=0.253269;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=770;FEMALE_N_HET=630;FEMALE_N_HOMALT=53;FEMALE_FREQ_HOMREF=0.529938;FEMALE_FREQ_HET=0.433586;FEMALE_FREQ_HOMALT=0.0364763;SEQR_INTERNAL_TRUTH_VID=CPX_chrX_252 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 0/0:PE,SR:99:99:0:99:0 0/1:PE,SR:41:26:1:41:1 1/1:PE,SR:89:33:1:89:2 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:99:0 From 9fd72e4be13d5823dbeb46d569c027a17d3ddc46 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 21 Aug 2026 16:21:23 -0400 Subject: [PATCH 265/369] undo debug --- .../tasks/exports/write_new_variants_parquet_test.py | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py index d551be464c..519297c879 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py @@ -322,12 +322,10 @@ def test_mito_write_new_variants_parquet_test( TEST_RUN_ID, ), ) - export_json = convert_ndarray_to_list( - df.head(10).to_dict('records'), - ) # TODO debug - # export_json[0]['sortedTranscriptConsequences'] = [ - # export_json[0]['sortedTranscriptConsequences'][0], - # ] + export_json = convert_ndarray_to_list( df.head(1).to_dict('records')) + export_json[0]['sortedTranscriptConsequences'] = [ + export_json[0]['sortedTranscriptConsequences'][0], + ] self.assertEqual( export_json, [ From 0e55c84c16d51362f90cf284a3e0ce41c5a55d76 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 21 Aug 2026 16:26:28 -0400 Subject: [PATCH 266/369] debug --- .../lib/tasks/exports/write_new_variants_parquet_test.py | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py index 519297c879..e16eb2c01e 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py @@ -322,10 +322,9 @@ def test_mito_write_new_variants_parquet_test( TEST_RUN_ID, ), ) - export_json = convert_ndarray_to_list( df.head(1).to_dict('records')) - export_json[0]['sortedTranscriptConsequences'] = [ - export_json[0]['sortedTranscriptConsequences'][0], - ] + export_json = convert_ndarray_to_list( + df.head(10).to_dict('records'), + ) # TODO debug self.assertEqual( export_json, [ From d9b12372c652d15ebe888177989cc69509da8490 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 21 Aug 2026 17:02:03 -0400 Subject: [PATCH 267/369] fix filter --- .../lib/tasks/exports/write_new_variants_parquet_test.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py index e16eb2c01e..54b80d7b81 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py @@ -125,7 +125,7 @@ def setUp(self) -> None: ), ) ht = hl.read_table(TEST_SV_ANNOTATIONS) - ht = ht.filter(ht.variant_id != 'BND_chr1_6') + ht = ht.filter(ht.variant_id != 'CPX_chr1_22') ht = ht.annotate_globals(max_key_=726) ht.write( variant_annotations_table_path( From 46d02dd31d9b079ca73c85cb7fe1ccd60f1ae8de Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 21 Aug 2026 17:16:39 -0400 Subject: [PATCH 268/369] fix test --- .../lib/tasks/exports/write_new_variants_parquet_test.py | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py index 54b80d7b81..f4093dcdac 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py @@ -111,7 +111,10 @@ def setUp(self) -> None: ht = ht.filter(ht.variant_id != 'M-8-G-T') ht = ht.join( hl.Table.parallelize( - [{'locus': hl.Locus('chrM', 3, 'GRCh38'), 'alleles': ['T', 'C']}], + [ + {'locus': hl.Locus('chrM', 3, 'GRCh38'), 'alleles': ['T', 'C']}, + {'locus': hl.Locus('chrM', 12, 'GRCh38'), 'alleles': ['T', 'C']}, + ], hl.tstruct(locus=hl.tlocus('GRCh38'), alleles=hl.tarray(hl.tstr)), key=['locus', 'alleles'], ), @@ -322,9 +325,7 @@ def test_mito_write_new_variants_parquet_test( TEST_RUN_ID, ), ) - export_json = convert_ndarray_to_list( - df.head(10).to_dict('records'), - ) # TODO debug + export_json = convert_ndarray_to_list(df.head(1).to_dict('records')) self.assertEqual( export_json, [ From b25192f1f9c6c112fcb0fbb9dd9986ab45868942 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Sun, 23 Aug 2026 18:25:13 -0400 Subject: [PATCH 269/369] better mock table --- .../write_new_variants_parquet_test.py | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py index f4093dcdac..dcbd92359e 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py @@ -129,6 +129,29 @@ def setUp(self) -> None: ) ht = hl.read_table(TEST_SV_ANNOTATIONS) ht = ht.filter(ht.variant_id != 'CPX_chr1_22') + ht = ht.join( + hl.Table.parallelize( + [ + {'variant_id': variant_id} + for variant_id in [ + 'DUP_chr1_5', + 'DEL_chr1_12', + 'BND_chr1_9', + 'INS_chr1_65', + 'CPX_chr1_41', + 'INS_chr1_268', + 'CPX_chr1_54', + 'INS_chr1_688', + 'CPX_chr1_251', + 'CPX_chrX_251', + 'CPX_chrX_252', + ] + ], + hl.tstruct(variant_id=hl.tstr), + key='variant_id', + ), + how='outer', + ) ht = ht.annotate_globals(max_key_=726) ht.write( variant_annotations_table_path( From 49e7ba9bcfbc28d740977f1b1443d3a29c4266c6 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Sun, 23 Aug 2026 18:35:36 -0400 Subject: [PATCH 270/369] debug --- .../lib/tasks/exports/write_new_variants_parquet_test.py | 1 + 1 file changed, 1 insertion(+) diff --git a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py index dcbd92359e..93eb32daa9 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py @@ -317,6 +317,7 @@ def test_grch37_write_new_variants_parquet_test( def test_mito_write_new_variants_parquet_test( self, ) -> None: + self.maxDiff = None copy_project_pedigree_to_mocked_dir( TEST_MITO_EXPORT_PEDIGREE, ReferenceGenome.GRCh38, From 6c125dd2926cac24563add86dda27d7b37c9d284 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Sun, 23 Aug 2026 18:45:52 -0400 Subject: [PATCH 271/369] undo debug --- .../lib/tasks/exports/write_new_variants_parquet_test.py | 1 - 1 file changed, 1 deletion(-) diff --git a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py index 93eb32daa9..dcbd92359e 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py @@ -317,7 +317,6 @@ def test_grch37_write_new_variants_parquet_test( def test_mito_write_new_variants_parquet_test( self, ) -> None: - self.maxDiff = None copy_project_pedigree_to_mocked_dir( TEST_MITO_EXPORT_PEDIGREE, ReferenceGenome.GRCh38, From 99866082ba40c85b03aab548125d56ad2109afea Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Sun, 23 Aug 2026 19:22:35 -0400 Subject: [PATCH 272/369] usable mito fixture data --- .../write_new_variants_parquet_test.py | 2 +- .../test/callsets/mito_1.mt/.README.txt.crc | Bin 12 -> 12 bytes .../callsets/mito_1.mt/.metadata.json.gz.crc | Bin 24 -> 24 bytes .../var/test/callsets/mito_1.mt/README.txt | 4 ++-- .../callsets/mito_1.mt/cols/.README.txt.crc | Bin 12 -> 12 bytes .../mito_1.mt/cols/.metadata.json.gz.crc | Bin 20 -> 20 bytes .../test/callsets/mito_1.mt/cols/README.txt | 4 ++-- .../callsets/mito_1.mt/cols/metadata.json.gz | Bin 1125 -> 1124 bytes .../mito_1.mt/cols/rows/.metadata.json.gz.crc | Bin 12 -> 12 bytes .../mito_1.mt/cols/rows/metadata.json.gz | Bin 474 -> 469 bytes .../mito_1.mt/cols/rows/parts/.part-0.crc | Bin 1000 -> 852 bytes .../callsets/mito_1.mt/cols/rows/parts/part-0 | Bin 126625 -> 107811 bytes .../mito_1.mt/entries/.README.txt.crc | Bin 12 -> 12 bytes .../mito_1.mt/entries/.metadata.json.gz.crc | Bin 20 -> 20 bytes .../callsets/mito_1.mt/entries/README.txt | 4 ++-- .../mito_1.mt/entries/metadata.json.gz | Bin 1133 -> 1131 bytes .../entries/rows/.metadata.json.gz.crc | Bin 16 -> 16 bytes .../mito_1.mt/entries/rows/metadata.json.gz | Bin 668 -> 669 bytes ...0-51b7a98f-9ffc-4f00-a7c0-75d3becb1c11.crc | Bin 372 -> 0 bytes ...0-e9cdcf06-dc7e-4544-b797-b0f783af35b7.crc | Bin 0 -> 236 bytes ...art-0-51b7a98f-9ffc-4f00-a7c0-75d3becb1c11 | Bin 46199 -> 0 bytes ...art-0-e9cdcf06-dc7e-4544-b797-b0f783af35b7 | Bin 0 -> 28849 bytes .../mito_1.mt/globals/.README.txt.crc | Bin 12 -> 12 bytes .../mito_1.mt/globals/.metadata.json.gz.crc | Bin 20 -> 20 bytes .../callsets/mito_1.mt/globals/README.txt | 4 ++-- .../globals/globals/.metadata.json.gz.crc | Bin 12 -> 12 bytes .../globals/globals/metadata.json.gz | Bin 240 -> 226 bytes .../globals/globals/parts/.part-0.crc | Bin 12 -> 12 bytes .../mito_1.mt/globals/globals/parts/part-0 | Bin 20 -> 30 bytes .../mito_1.mt/globals/metadata.json.gz | Bin 1035 -> 1034 bytes .../globals/rows/.metadata.json.gz.crc | Bin 24 -> 24 bytes .../mito_1.mt/globals/rows/metadata.json.gz | Bin 1542 -> 1548 bytes .../mito_1.mt/globals/rows/parts/.part-0.crc | Bin 40 -> 36 bytes .../mito_1.mt/globals/rows/parts/part-0 | Bin 3943 -> 3176 bytes ...cdcf06-dc7e-4544-b797-b0f783af35b7.idx.crc | Bin 0 -> 12 bytes .../.index.crc | Bin 12 -> 0 bytes .../.metadata.json.gz.crc | Bin 12 -> 0 bytes .../index | Bin 121 -> 0 bytes .../metadata.json.gz | Bin 197 -> 0 bytes ...0-e9cdcf06-dc7e-4544-b797-b0f783af35b7.idx | Bin 0 -> 357 bytes .../test/callsets/mito_1.mt/metadata.json.gz | Bin 2037 -> 2036 bytes .../callsets/mito_1.mt/rows/.README.txt.crc | Bin 12 -> 12 bytes .../mito_1.mt/rows/.metadata.json.gz.crc | Bin 24 -> 24 bytes .../test/callsets/mito_1.mt/rows/README.txt | 4 ++-- .../callsets/mito_1.mt/rows/metadata.json.gz | Bin 1912 -> 1910 bytes .../mito_1.mt/rows/rows/.metadata.json.gz.crc | Bin 28 -> 28 bytes .../mito_1.mt/rows/rows/metadata.json.gz | Bin 2225 -> 2259 bytes ...0-51b7a98f-9ffc-4f00-a7c0-75d3becb1c11.crc | Bin 20 -> 0 bytes ...0-e9cdcf06-dc7e-4544-b797-b0f783af35b7.crc | Bin 0 -> 20 bytes ...art-0-51b7a98f-9ffc-4f00-a7c0-75d3becb1c11 | Bin 1074 -> 0 bytes ...art-0-e9cdcf06-dc7e-4544-b797-b0f783af35b7 | Bin 0 -> 1167 bytes 51 files changed, 11 insertions(+), 11 deletions(-) delete mode 100644 loading_pipeline/var/test/callsets/mito_1.mt/entries/rows/parts/.part-0-51b7a98f-9ffc-4f00-a7c0-75d3becb1c11.crc create mode 100644 loading_pipeline/var/test/callsets/mito_1.mt/entries/rows/parts/.part-0-e9cdcf06-dc7e-4544-b797-b0f783af35b7.crc delete mode 100644 loading_pipeline/var/test/callsets/mito_1.mt/entries/rows/parts/part-0-51b7a98f-9ffc-4f00-a7c0-75d3becb1c11 create mode 100644 loading_pipeline/var/test/callsets/mito_1.mt/entries/rows/parts/part-0-e9cdcf06-dc7e-4544-b797-b0f783af35b7 create mode 100644 loading_pipeline/var/test/callsets/mito_1.mt/index/.part-0-e9cdcf06-dc7e-4544-b797-b0f783af35b7.idx.crc delete mode 100644 loading_pipeline/var/test/callsets/mito_1.mt/index/part-0-51b7a98f-9ffc-4f00-a7c0-75d3becb1c11.idx/.index.crc delete mode 100644 loading_pipeline/var/test/callsets/mito_1.mt/index/part-0-51b7a98f-9ffc-4f00-a7c0-75d3becb1c11.idx/.metadata.json.gz.crc delete mode 100644 loading_pipeline/var/test/callsets/mito_1.mt/index/part-0-51b7a98f-9ffc-4f00-a7c0-75d3becb1c11.idx/index delete mode 100644 loading_pipeline/var/test/callsets/mito_1.mt/index/part-0-51b7a98f-9ffc-4f00-a7c0-75d3becb1c11.idx/metadata.json.gz create mode 100644 loading_pipeline/var/test/callsets/mito_1.mt/index/part-0-e9cdcf06-dc7e-4544-b797-b0f783af35b7.idx delete mode 100644 loading_pipeline/var/test/callsets/mito_1.mt/rows/rows/parts/.part-0-51b7a98f-9ffc-4f00-a7c0-75d3becb1c11.crc create mode 100644 loading_pipeline/var/test/callsets/mito_1.mt/rows/rows/parts/.part-0-e9cdcf06-dc7e-4544-b797-b0f783af35b7.crc delete mode 100644 loading_pipeline/var/test/callsets/mito_1.mt/rows/rows/parts/part-0-51b7a98f-9ffc-4f00-a7c0-75d3becb1c11 create mode 100644 loading_pipeline/var/test/callsets/mito_1.mt/rows/rows/parts/part-0-e9cdcf06-dc7e-4544-b797-b0f783af35b7 diff --git a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py index dcbd92359e..752f22ee16 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py @@ -356,7 +356,7 @@ def test_mito_write_new_variants_parquet_test( 'key': 998, 'variantId': 'M-8-G-T', 'rsid': 'rs1603218446', - 'liftedOverPos': 578, + 'liftedOverPos': 8, 'commonLowHeteroplasmy': True, 'haplogroupDefining': False, 'mitotip': 'likely_pathogenic', diff --git a/loading_pipeline/var/test/callsets/mito_1.mt/.README.txt.crc b/loading_pipeline/var/test/callsets/mito_1.mt/.README.txt.crc index fcb594d8c394781f54116b616100fe2e2b9ff448..a7801ef5865f54b9fb32bb11fa2ea4d5a8f4ef28 100644 GIT binary patch literal 12 TcmYc;N@ieSU}6Xr%$yGZ5O@Nq literal 12 TcmYc;N@ieSU}ErdxD*Kh5p@Fe diff --git a/loading_pipeline/var/test/callsets/mito_1.mt/.metadata.json.gz.crc b/loading_pipeline/var/test/callsets/mito_1.mt/.metadata.json.gz.crc index 89de9d47a593665cb9408c8ce38c61f4168ed9f8..f7585498d69deeeaf18f3383c381c239a72085eb 100644 GIT binary patch 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bytes .../mito_1.mt/entries/rows/metadata.json.gz | Bin 669 -> 667 bytes ...0-7b657546-4721-4965-bb6e-8f13ce327d22.crc | Bin 0 -> 236 bytes ...0-e9cdcf06-dc7e-4544-b797-b0f783af35b7.crc | Bin 236 -> 0 bytes ...rt-0-7b657546-4721-4965-bb6e-8f13ce327d22} | Bin 28849 -> 28860 bytes .../mito_1.mt/globals/.README.txt.crc | Bin 12 -> 12 bytes .../mito_1.mt/globals/.metadata.json.gz.crc | Bin 20 -> 20 bytes .../callsets/mito_1.mt/globals/README.txt | 4 ++-- .../globals/globals/.metadata.json.gz.crc | Bin 12 -> 12 bytes .../globals/globals/metadata.json.gz | Bin 226 -> 239 bytes .../globals/globals/parts/.part-0.crc | Bin 12 -> 12 bytes .../mito_1.mt/globals/globals/parts/part-0 | Bin 30 -> 36 bytes .../mito_1.mt/globals/metadata.json.gz | Bin 1034 -> 1034 bytes .../globals/rows/.metadata.json.gz.crc | Bin 24 -> 24 bytes .../mito_1.mt/globals/rows/metadata.json.gz | Bin 1548 -> 1539 bytes .../mito_1.mt/globals/rows/parts/.part-0.crc | Bin 36 -> 36 bytes .../mito_1.mt/globals/rows/parts/part-0 | Bin 3176 -> 3181 bytes ...cdcf06-dc7e-4544-b797-b0f783af35b7.idx.crc | Bin 12 -> 0 bytes .../.index.crc | Bin 0 -> 12 bytes .../.metadata.json.gz.crc | Bin 0 -> 12 bytes .../index | Bin 0 -> 133 bytes .../metadata.json.gz | Bin 0 -> 199 bytes ...0-e9cdcf06-dc7e-4544-b797-b0f783af35b7.idx | Bin 357 -> 0 bytes .../test/callsets/mito_1.mt/metadata.json.gz | Bin 2036 -> 2036 bytes .../callsets/mito_1.mt/rows/.README.txt.crc | Bin 12 -> 12 bytes .../mito_1.mt/rows/.metadata.json.gz.crc | Bin 24 -> 24 bytes .../test/callsets/mito_1.mt/rows/README.txt | 4 ++-- .../callsets/mito_1.mt/rows/metadata.json.gz | Bin 1910 -> 1911 bytes .../mito_1.mt/rows/rows/.metadata.json.gz.crc | Bin 28 -> 28 bytes .../mito_1.mt/rows/rows/metadata.json.gz | Bin 2259 -> 2224 bytes ...0-7b657546-4721-4965-bb6e-8f13ce327d22.crc | Bin 0 -> 20 bytes ...0-e9cdcf06-dc7e-4544-b797-b0f783af35b7.crc | Bin 20 -> 0 bytes ...rt-0-7b657546-4721-4965-bb6e-8f13ce327d22} | Bin 1167 -> 1172 bytes 48 files changed, 10 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b/loading_pipeline/lib/misc/io_test.py index a346e8b323..2ca502fc87 100644 --- a/loading_pipeline/lib/misc/io_test.py +++ b/loading_pipeline/lib/misc/io_test.py @@ -28,8 +28,8 @@ class IOTest(unittest.TestCase): def test_file_size_mb(self) -> None: # find loading_pipeline/var/test/callsets/mito_1.mt -type f | grep -v 'crc' | xargs ls -alt {} | awk '{sum += $5; print sum}' - # 191310 - self.assertEqual(file_size_bytes(TEST_MITO_MT), 191310) + # 154517 + self.assertEqual(file_size_bytes(TEST_MITO_MT), 154517) def test_compute_hail_n_partitions(self) -> None: self.assertEqual(compute_hail_n_partitions(23), 1) From 33551802e56d9a6b704da318dcee4fd6830309bc Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 24 Aug 2026 10:58:34 -0400 Subject: [PATCH 275/369] update new entries tests --- .../exports/write_new_entries_parquet_test.py | 18 ++++++++++++------ 1 file changed, 12 insertions(+), 6 deletions(-) diff --git a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py index ccb3260f5e..ce1016e508 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py @@ -1,6 +1,7 @@ import hail as hl import luigi.worker import pandas as pd +from typing import ClassVar from loading_pipeline.lib.core import ( DatasetType, @@ -10,11 +11,14 @@ from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS from loading_pipeline.lib.paths import ( new_entries_parquet_path, - variant_annotations_table_path, + new_variants_table_path, ) from loading_pipeline.lib.tasks.exports.write_new_entries_parquet import ( WriteNewEntriesParquetTask, ) +from loading_pipeline.lib.test.clickhouse_schema_testcase import ( + ClickhouseSchemaTestCase, +) from loading_pipeline.lib.test.misc import ( convert_ndarray_to_list, copy_project_pedigree_to_mocked_dir, @@ -41,14 +45,16 @@ TEST_RUN_ID = 'manual__2024-04-03' -class WriteNewEntriesParquetTest(MockedDatarootTestCase): +class WriteNewEntriesParquetTest(MockedDatarootTestCase, ClickhouseSchemaTestCase): + fixtures: ClassVar = ['clickhouse_test'] + def setUp(self) -> None: super().setUp() ht = hl.read_table( TEST_SNV_INDEL_ANNOTATIONS, ) ht.write( - variant_annotations_table_path( + new_variants_table_path( ReferenceGenome.GRCh38, DatasetType.SNV_INDEL, ), @@ -57,7 +63,7 @@ def setUp(self) -> None: TEST_MITO_ANNOTATIONS, ) ht.write( - variant_annotations_table_path( + new_variants_table_path( ReferenceGenome.GRCh38, DatasetType.MITO, ), @@ -66,14 +72,14 @@ def setUp(self) -> None: TEST_SV_ANNOTATIONS, ) ht.write( - variant_annotations_table_path( + new_variants_table_path( ReferenceGenome.GRCh38, DatasetType.SV, ), ) ht = hl.read_table(TEST_GCNV_ANNOTATIONS) ht.write( - variant_annotations_table_path( + new_variants_table_path( ReferenceGenome.GRCh38, DatasetType.GCNV, ), From 8b024cb52379d030ab89f83eae99a648c9ba0d40 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 24 Aug 2026 11:01:39 -0400 Subject: [PATCH 276/369] ruff --- .../lib/tasks/exports/write_new_entries_parquet_test.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py index ce1016e508..06ca704a50 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py @@ -1,7 +1,8 @@ +from typing import ClassVar + import hail as hl import luigi.worker import pandas as pd -from typing import ClassVar from loading_pipeline.lib.core import ( DatasetType, From 4b2e5d2dfcef0660130bdfbdc872fc86c6dca472 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 24 Aug 2026 11:47:59 -0400 Subject: [PATCH 277/369] fix mock paths --- .../lib/tasks/exports/write_new_entries_parquet_test.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py index 06ca704a50..1c0f13f828 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py @@ -58,6 +58,7 @@ def setUp(self) -> None: new_variants_table_path( ReferenceGenome.GRCh38, DatasetType.SNV_INDEL, + TEST_RUN_ID, ), ) ht = hl.read_table( @@ -67,6 +68,7 @@ def setUp(self) -> None: new_variants_table_path( ReferenceGenome.GRCh38, DatasetType.MITO, + TEST_RUN_ID, ), ) ht = hl.read_table( @@ -76,6 +78,7 @@ def setUp(self) -> None: new_variants_table_path( ReferenceGenome.GRCh38, DatasetType.SV, + TEST_RUN_ID, ), ) ht = hl.read_table(TEST_GCNV_ANNOTATIONS) @@ -83,6 +86,7 @@ def setUp(self) -> None: new_variants_table_path( ReferenceGenome.GRCh38, DatasetType.GCNV, + TEST_RUN_ID, ), ) From 2effd726d0a8b58a75109fc19696085203a7bc21 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 24 Aug 2026 11:59:12 -0400 Subject: [PATCH 278/369] update new variant tests --- .../write_new_variant_details_parquet_test.py | 87 ++++++--- .../write_new_variants_parquet_test.py | 166 ++++++++++-------- 2 files changed, 155 insertions(+), 98 deletions(-) diff --git a/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py index 9053c5ac81..193d51145d 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py @@ -13,8 +13,8 @@ ) from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS from loading_pipeline.lib.paths import ( + existing_variants_parquet_path, new_variant_details_parquet_path, - variant_annotations_table_path, ) from loading_pipeline.lib.tasks.exports.write_new_variant_details_parquet import ( WriteNewVariantDetailsParquetTask, @@ -32,15 +32,60 @@ TEST_SNV_INDEL_VCF = 'loading_pipeline/var/test/callsets/1kg_30variants.vcf' TEST_PEDIGREE_3_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_3_remap.tsv' -TEST_SNV_INDEL_ANNOTATIONS = ( - 'loading_pipeline/var/test/exports/GRCh38/SNV_INDEL/annotations.ht' -) -TEST_GRCH37_SNV_INDEL_ANNOTATIONS = ( - 'loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/annotations.ht' -) - TEST_RUN_ID = 'manual__2024-04-03' +EXISTING_SNV_INDEL_VARIANT_IDS = [ + '1-871269-A-C', + '1-874734-C-T', + '1-878314-G-C', + '1-878809-C-T', + '1-879576-C-T', + '1-881070-G-A', + '1-881627-G-A', + '1-881918-G-A', + '1-883485-C-T', + '1-883625-A-G', + '1-883918-G-A', + '1-887560-A-C', + '1-887801-A-G', + '1-888529-G-A', + '1-888659-T-C', + '1-889158-G-C', + '1-889159-A-C', + '1-889238-G-A', + '1-894573-G-A', + '1-896922-C-T', + '1-897325-G-C', + '1-898313-C-T', + '1-898323-T-C', + '1-898467-C-T', + '1-899959-G-GC', + '1-900505-G-C', + '1-902024-G-A', + '1-902069-T-C', + '1-902088-G-A', + '1-902088-G-ACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACT', + 'GL000207.1-1-G-A', +] + + +def _write_existing_variants_parquet_fixture( + variant_ids: list[str], + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + max_key_: int, +) -> None: + n = len(variant_ids) + path = existing_variants_parquet_path(reference_genome, dataset_type, TEST_RUN_ID) + os.makedirs(os.path.dirname(path), exist_ok=True) + pd.DataFrame( + { + 'variant_id': variant_ids, + 'key_': range(max_key_ - n + 1, max_key_ + 1), + }, + ).to_parquet(path) + + SNV_INDEL_GRCH38_MOCK_VEP_DATA = MOCK_38_VEP_DATA.annotate( transcript_consequences=hl.array( [ @@ -103,23 +148,17 @@ class WriteNewVariantDetailsParquetTest(MockedDatarootTestCase): def setUp(self) -> None: super().setUp() - ht = hl.read_table(TEST_SNV_INDEL_ANNOTATIONS) - ht = ht.filter(ht.variant_id != '1-876499-A-G') - ht = ht.annotate_globals(max_key_=-1) - ht.write( - variant_annotations_table_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - ), + _write_existing_variants_parquet_fixture( + EXISTING_SNV_INDEL_VARIANT_IDS, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + max_key_=-1, ) - ht = hl.read_table(TEST_GRCH37_SNV_INDEL_ANNOTATIONS) - ht = ht.filter(ht.variant_id != '1-69134-A-G') - ht = ht.annotate_globals(max_key_=1423) - ht.write( - variant_annotations_table_path( - ReferenceGenome.GRCh37, - DatasetType.SNV_INDEL, - ), + _write_existing_variants_parquet_fixture( + EXISTING_SNV_INDEL_VARIANT_IDS, + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + max_key_=1423, ) # Make an incomplete parquet to validate overwrite-ing. diff --git a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py index 28215ea755..d983ec6158 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py @@ -1,3 +1,4 @@ +import os from unittest import mock from unittest.mock import Mock @@ -12,7 +13,9 @@ ) from loading_pipeline.lib.misc.validation import ALL_VALIDATIONS from loading_pipeline.lib.paths import ( + existing_variants_parquet_path, new_variants_parquet_path, + new_variants_table_path, remapped_and_subsetted_callset_path, ) from loading_pipeline.lib.tasks.exports.write_new_variants_parquet import ( @@ -40,18 +43,79 @@ TEST_SV_VCF = 'loading_pipeline/var/test/callsets/sv_1.vcf' TEST_PEDIGREE_5 = 'loading_pipeline/var/test/pedigrees/test_pedigree_5.tsv' -TEST_SNV_INDEL_ANNOTATIONS = ( - 'loading_pipeline/var/test/exports/GRCh38/SNV_INDEL/annotations.ht' -) -TEST_GRCH37_SNV_INDEL_ANNOTATIONS = ( - 'loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/annotations.ht' -) -TEST_MITO_ANNOTATIONS = 'loading_pipeline/var/test/exports/GRCh38/MITO/annotations.ht' -TEST_SV_ANNOTATIONS = 'loading_pipeline/var/test/exports/GRCh38/SV/annotations.ht' TEST_GCNV_ANNOTATIONS = 'loading_pipeline/var/test/exports/GRCh38/GCNV/annotations.ht' TEST_RUN_ID = 'manual__2024-04-03' +EXISTING_SNV_INDEL_VARIANT_IDS = [ + '1-871269-A-C', + '1-874734-C-T', + '1-878314-G-C', + '1-878809-C-T', + '1-879576-C-T', + '1-881070-G-A', + '1-881627-G-A', + '1-881918-G-A', + '1-883485-C-T', + '1-883625-A-G', + '1-883918-G-A', + '1-887560-A-C', + '1-887801-A-G', + '1-888529-G-A', + '1-888659-T-C', + '1-889158-G-C', + '1-889159-A-C', + '1-889238-G-A', + '1-894573-G-A', + '1-896922-C-T', + '1-897325-G-C', + '1-898313-C-T', + '1-898323-T-C', + '1-898467-C-T', + '1-899959-G-GC', + '1-900505-G-C', + '1-902024-G-A', + '1-902069-T-C', + '1-902088-G-A', + '1-902088-G-ACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACT', + 'GL000207.1-1-G-A', +] + +EXISTING_MITO_VARIANT_IDS = ['M-3-T-C', 'M-12-T-C'] + +EXISTING_SV_VARIANT_IDS = [ + 'BND_chr1_6', + 'DUP_chr1_5', + 'DEL_chr1_12', + 'BND_chr1_9', + 'INS_chr1_65', + 'CPX_chr1_41', + 'INS_chr1_268', + 'CPX_chr1_54', + 'INS_chr1_688', + 'CPX_chr1_251', + 'CPX_chrX_251', + 'CPX_chrX_252', +] + + +def _write_existing_variants_parquet_fixture( + variant_ids: list[str], + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + max_key_: int, +) -> None: + n = len(variant_ids) + path = existing_variants_parquet_path(reference_genome, dataset_type, TEST_RUN_ID) + os.makedirs(os.path.dirname(path), exist_ok=True) + pd.DataFrame( + { + 'variant_id': variant_ids, + 'key_': range(max_key_ - n + 1, max_key_ + 1), + }, + ).to_parquet(path) + + SNV_INDEL_GRCH38_MOCK_VEP_DATA = MOCK_38_VEP_DATA.annotate( motif_feature_consequences=hl.array( [ @@ -88,75 +152,29 @@ class WriteNewVariantsParquetTest(MockedReferenceDatasetsTestCase): def setUp(self) -> None: super().setUp() - ht = hl.read_table(TEST_SNV_INDEL_ANNOTATIONS) - ht = ht.filter(ht.variant_id != '1-876499-A-G') - ht = ht.annotate_globals(max_key_=-1) - ht.write( - variant_annotations_table_path( - ReferenceGenome.GRCh38, - DatasetType.SNV_INDEL, - ), - ) - ht = hl.read_table(TEST_GRCH37_SNV_INDEL_ANNOTATIONS) - ht = ht.filter(ht.variant_id != '1-69134-A-G') - ht = ht.annotate_globals(max_key_=1423) - ht.write( - variant_annotations_table_path( - ReferenceGenome.GRCh37, - DatasetType.SNV_INDEL, - ), - ) - ht = hl.read_table(TEST_MITO_ANNOTATIONS) - ht = ht.filter(ht.variant_id != 'M-8-G-T') - ht = ht.join( - hl.Table.parallelize( - [ - {'locus': hl.Locus('chrM', 3, 'GRCh38'), 'alleles': ['T', 'C']}, - {'locus': hl.Locus('chrM', 12, 'GRCh38'), 'alleles': ['T', 'C']}, - ], - hl.tstruct(locus=hl.tlocus('GRCh38'), alleles=hl.tarray(hl.tstr)), - key=['locus', 'alleles'], - ), - how='outer', + _write_existing_variants_parquet_fixture( + EXISTING_SNV_INDEL_VARIANT_IDS, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + max_key_=-1, ) - ht = ht.annotate_globals(max_key_=997) - ht.write( - variant_annotations_table_path( - ReferenceGenome.GRCh38, - DatasetType.MITO, - ), + _write_existing_variants_parquet_fixture( + EXISTING_SNV_INDEL_VARIANT_IDS, + ReferenceGenome.GRCh37, + DatasetType.SNV_INDEL, + max_key_=1423, ) - ht = hl.read_table(TEST_SV_ANNOTATIONS) - ht = ht.filter(ht.variant_id != 'CPX_chr1_22') - ht = ht.join( - hl.Table.parallelize( - [ - {'variant_id': variant_id} - for variant_id in [ - 'DUP_chr1_5', - 'DEL_chr1_12', - 'BND_chr1_9', - 'INS_chr1_65', - 'CPX_chr1_41', - 'INS_chr1_268', - 'CPX_chr1_54', - 'INS_chr1_688', - 'CPX_chr1_251', - 'CPX_chrX_251', - 'CPX_chrX_252', - ] - ], - hl.tstruct(variant_id=hl.tstr), - key='variant_id', - ), - how='outer', + _write_existing_variants_parquet_fixture( + EXISTING_MITO_VARIANT_IDS, + ReferenceGenome.GRCh38, + DatasetType.MITO, + max_key_=997, ) - ht = ht.annotate_globals(max_key_=726) - ht.write( - variant_annotations_table_path( - ReferenceGenome.GRCh38, - DatasetType.SV, - ), + _write_existing_variants_parquet_fixture( + EXISTING_SV_VARIANT_IDS, + ReferenceGenome.GRCh38, + DatasetType.SV, + max_key_=726, ) ht = hl.read_table(TEST_GCNV_ANNOTATIONS) ht.write( From e8c7ea0e75eed63978175b27eb340347959add19 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 24 Aug 2026 12:07:52 -0400 Subject: [PATCH 279/369] fix parquet locus parsing --- loading_pipeline/lib/misc/io.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/loading_pipeline/lib/misc/io.py b/loading_pipeline/lib/misc/io.py index 637f5e3604..012864e543 100644 --- a/loading_pipeline/lib/misc/io.py +++ b/loading_pipeline/lib/misc/io.py @@ -222,9 +222,9 @@ def import_parquet( key_fields = dataset_type.table_key_type(reference_genome).fields if 'locus' in key_fields: ht = ht.annotate( - locus=hl.Locus( + locus=hl.locus( contig=ht.variant_id.split('-')[0], - position=ht.variant_id.split('-')[1], + pos=hl.int32(ht.variant_id.split('-')[1]), reference_genome=reference_genome.value, ), alleles=[ht.variant_id.split('-')[2], ht.variant_id.split('-')[3]], From b1c1d93aa6905233be22f10e885632bbdb85f508 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 24 Aug 2026 12:28:31 -0400 Subject: [PATCH 280/369] fix genome guild chrom prefix --- loading_pipeline/lib/misc/io.py | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/loading_pipeline/lib/misc/io.py b/loading_pipeline/lib/misc/io.py index 012864e543..634bb6a661 100644 --- a/loading_pipeline/lib/misc/io.py +++ b/loading_pipeline/lib/misc/io.py @@ -221,9 +221,15 @@ def import_parquet( key_fields = dataset_type.table_key_type(reference_genome).fields if 'locus' in key_fields: + raw_contig = ht.variant_id.split('-')[0] + contig = ( + hl.format('chr%s', raw_contig) + if reference_genome == ReferenceGenome.GRCh38 + else raw_contig + ) ht = ht.annotate( locus=hl.locus( - contig=ht.variant_id.split('-')[0], + contig=contig, pos=hl.int32(ht.variant_id.split('-')[1]), reference_genome=reference_genome.value, ), From 5b730b3bed75b26d8322ab304e2fcb33e98bedc3 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 24 Aug 2026 12:44:49 -0400 Subject: [PATCH 281/369] fix tests --- loading_pipeline/lib/tasks/exports/fields.py | 2 +- .../lib/tasks/exports/write_new_variant_details_parquet_test.py | 1 - .../lib/tasks/exports/write_new_variants_parquet_test.py | 1 - loading_pipeline/var/test/callsets/1kg_30variants.vcf | 2 -- 4 files changed, 1 insertion(+), 5 deletions(-) diff --git a/loading_pipeline/lib/tasks/exports/fields.py b/loading_pipeline/lib/tasks/exports/fields.py index 3b5233b39e..59d3ca2f25 100644 --- a/loading_pipeline/lib/tasks/exports/fields.py +++ b/loading_pipeline/lib/tasks/exports/fields.py @@ -173,7 +173,7 @@ def get_entries_annotations_export_fields(dataset_type: DatasetType): fields['geneIds'] = lambda ht: ( hl.set(ht.sorted_gene_consequences.gene_id) if dataset_type == DatasetType.SV - else ht.set(ht.sorted_gene_consequences.gene_id) + else hl.set(ht.sorted_gene_consequences.gene_id) ) return fields diff --git a/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py index 193d51145d..cb4f211777 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_variant_details_parquet_test.py @@ -65,7 +65,6 @@ '1-902069-T-C', '1-902088-G-A', '1-902088-G-ACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACT', - 'GL000207.1-1-G-A', ] diff --git a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py index d983ec6158..4723729409 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py @@ -78,7 +78,6 @@ '1-902069-T-C', '1-902088-G-A', '1-902088-G-ACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACT', - 'GL000207.1-1-G-A', ] EXISTING_MITO_VARIANT_IDS = ['M-3-T-C', 'M-12-T-C'] diff --git a/loading_pipeline/var/test/callsets/1kg_30variants.vcf b/loading_pipeline/var/test/callsets/1kg_30variants.vcf index 010314986a..3f558cb346 100644 --- a/loading_pipeline/var/test/callsets/1kg_30variants.vcf +++ b/loading_pipeline/var/test/callsets/1kg_30variants.vcf @@ -65,7 +65,6 @@ ##contig= ##contig= ##contig= -##contig= ##contig= ##contig= ##contig= @@ -156,4 +155,3 @@ 1 902069 rs116147894 T C 13024.04 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=2.08840e+01;DB;DP=157;Dels=0.00000e+00;FS=3.07700e+00;HaplotypeScore=2.10500e-01;InbreedingCoeff=1.00200e-01;MQ=5.91800e+01;MQ0=0;MQRankSum=7.75000e-01;QD=1.56200e+01;ReadPosRankSum=-5.68400e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000338591;VQSLOD=7.17000e+00;culprit=MQ;CSQ=C|ENSG00000187583|ENST00000480267|Transcript|upstream_gene_variant||||||rs116147894|1|4186|1|PLEKHN1|HGNC|25284|retained_intron|||||||||||||||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163|||||||||||||||||,C|ENSG00000187961|ENST00000466300|Transcript|downstream_gene_variant||||||rs116147894|1|2159|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163|||||||||||||||||,C|ENSG00000187961|ENST00000338591|Transcript|downstream_gene_variant||||||rs116147894|1|974|1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||||||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs116147894|1|4211|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163|||||||||||||||||,C|ENSG00000187583|ENST00000379409|Transcript|intron_variant||||||rs116147894|1||1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06||||1/14||ENST00000379409.2:c.84-15N>C||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163||||||||INTRON_SIZE:89||NON_CAN_SPLICE|||||||,C|ENSG00000187583|ENST00000379407|Transcript|intron_variant||||||rs116147894|1||1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF||||1/14||ENST00000379407.3:c.84-15N>C||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163||||||||INTRON_SIZE:89||NON_CAN_SPLICE|||||||,C|ENSG00000187961|ENST00000481067|Transcript|downstream_gene_variant||||||rs116147894|1|2525|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163|||||||||||||||||,C|ENSG00000187583|ENST00000379410|Transcript|intron_variant||||||rs116147894|1||1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8||||1/15||ENST00000379410.3:c.84-15N>C||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163||||||||INTRON_SIZE:89||NON_CAN_SPLICE|||||||,C||ENSR00000528862|RegulatoryFeature|regulatory_region_variant||||||rs116147894|1||||||regulatory_region|||||||||||||||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163||||||||||||||||| GT:AD:DP:GQ:PL 0/0:10,0:10:30:0,30,367 0/1:12,2:13:3:3,0,418 0/0:14,0:14:42:0,42,514 0/0:4,0:4:12:0,12,144 0/0:5,0:5:15:0,15,176 0/0:4,0:4:12:0,12,145 0/0:17,0:17:48:0,48,603 0/0:6,0:6:18:0,18,227 0/0:10,0:10:30:0,30,361 0/0:10,0:10:30:0,30,372 0/0:12,0:12:36:0,36,434 0/0:7,0:7:21:0,21,259 0/0:7,0:7:21:0,21,255 0/0:11,0:11:30:0,30,375 0/0:12,0:12:36:0,36,426 0/0:15,0:15:45:0,45,530 1 902088 . G A 324.34 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-5.34900e+00;DP=133;Dels=0.00000e+00;FS=7.94000e-01;HaplotypeScore=1.50400e-01;InbreedingCoeff=3.03000e-02;MQ=5.93200e+01;MQ0=0;MQRankSum=2.32200e+00;QD=7.91000e+00;ReadPosRankSum=-2.12100e+00;SNPEFF_AMINO_ACID_CHANGE=D30N;SNPEFF_CODON_CHANGE=Gac/Aac;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_902084_902183;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=PLEKHN1;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000379407;VQSLOD=5.23000e+00;culprit=QD;CSQ=A|ENSG00000187583|ENST00000480267|Transcript|upstream_gene_variant||||||rs201730138|1|4167|1|PLEKHN1|HGNC|25284|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187961|ENST00000466300|Transcript|downstream_gene_variant||||||rs201730138|1|2178|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187961|ENST00000338591|Transcript|downstream_gene_variant||||||rs201730138|1|993|1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||||||A:0.0005||A:0.0028|||A:0|A:0.000600||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs201730138|1|4230|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187583|ENST00000379409|Transcript|missense_variant|118|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06|tolerated(0.26)|benign(0.034)|2/15|||ENST00000379409.2:c.88N>A|ENSP00000368719.2:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0441767068273092||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A|ENSG00000187583|ENST00000379407|Transcript|missense_variant|118|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF|tolerated(0.25)|benign(0.072)|2/15|||ENST00000379407.3:c.88N>A|ENSP00000368717.2:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0508376660889659||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A|ENSG00000187961|ENST00000481067|Transcript|downstream_gene_variant||||||rs201730138|1|2544|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187583|ENST00000379410|Transcript|missense_variant|123|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8|tolerated(0.25)|benign(0.072)|2/16|||ENST00000379410.3:c.88N>A|ENSP00000368720.3:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0479302832244009||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A||ENSR00000528862|RegulatoryFeature|regulatory_region_variant||||||rs201730138|1||||||regulatory_region|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600||||||||||||||||| GT:AD:DP:GQ:PL 0/1:10,1:11:1:1,0,264 0/0:13,0:13:33:0,33,447 0/0:10,0:10:30:0,30,371 0/0:4,0:4:12:0,12,141 0/0:1,0:1:3:0,3,39 0/0:4,0:4:12:0,12,145 0/0:18,0:18:51:0,51,665 0/0:4,0:4:12:0,12,148 0/0:5,0:5:15:0,15,193 0/0:9,0:9:24:0,24,320 0/0:10,0:10:30:0,30,378 0/0:4,0:4:12:0,12,160 0/0:10,0:10:30:0,30,387 0/0:7,0:7:21:0,21,247 0/0:9,0:9:27:0,27,350 0/0:14,0:14:42:0,42,540 1 902088 . G ACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACT 324.34 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-5.34900e+00;DP=133;Dels=0.00000e+00;FS=7.94000e-01;HaplotypeScore=1.50400e-01;InbreedingCoeff=3.03000e-02;MQ=5.93200e+01;MQ0=0;MQRankSum=2.32200e+00;QD=7.91000e+00;ReadPosRankSum=-2.12100e+00;SNPEFF_AMINO_ACID_CHANGE=D30N;SNPEFF_CODON_CHANGE=Gac/Aac;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_902084_902183;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=PLEKHN1;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000379407;VQSLOD=5.23000e+00;culprit=QD;CSQ=A|ENSG00000187583|ENST00000480267|Transcript|upstream_gene_variant||||||rs201730138|1|4167|1|PLEKHN1|HGNC|25284|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187961|ENST00000466300|Transcript|downstream_gene_variant||||||rs201730138|1|2178|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187961|ENST00000338591|Transcript|downstream_gene_variant||||||rs201730138|1|993|1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||||||A:0.0005||A:0.0028|||A:0|A:0.000600||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs201730138|1|4230|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187583|ENST00000379409|Transcript|missense_variant|118|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06|tolerated(0.26)|benign(0.034)|2/15|||ENST00000379409.2:c.88N>A|ENSP00000368719.2:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0441767068273092||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A|ENSG00000187583|ENST00000379407|Transcript|missense_variant|118|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF|tolerated(0.25)|benign(0.072)|2/15|||ENST00000379407.3:c.88N>A|ENSP00000368717.2:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0508376660889659||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A|ENSG00000187961|ENST00000481067|Transcript|downstream_gene_variant||||||rs201730138|1|2544|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187583|ENST00000379410|Transcript|missense_variant|123|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8|tolerated(0.25)|benign(0.072)|2/16|||ENST00000379410.3:c.88N>A|ENSP00000368720.3:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0479302832244009||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A||ENSR00000528862|RegulatoryFeature|regulatory_region_variant||||||rs201730138|1||||||regulatory_region|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600||||||||||||||||| GT:AD:DP:GQ:PL 0/1:10,1:11:1:1,0,264 0/0:13,0:13:33:0,33,447 0/0:10,0:10:30:0,30,371 0/0:4,0:4:12:0,12,141 0/0:1,0:1:3:0,3,39 0/0:4,0:4:12:0,12,145 0/0:18,0:18:51:0,51,665 0/0:4,0:4:12:0,12,148 0/0:5,0:5:15:0,15,193 0/0:9,0:9:24:0,24,320 0/0:10,0:10:30:0,30,378 0/0:4,0:4:12:0,12,160 0/0:10,0:10:30:0,30,387 0/0:7,0:7:21:0,21,247 0/0:9,0:9:27:0,27,350 0/0:14,0:14:42:0,42,540 -GL000207.1 1 . G A 324.34 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-5.34900e+00;DP=133;Dels=0.00000e+00;FS=7.94000e-01;HaplotypeScore=1.50400e-01;InbreedingCoeff=3.03000e-02;MQ=5.93200e+01;MQ0=0;MQRankSum=2.32200e+00;QD=7.91000e+00;ReadPosRankSum=-2.12100e+00;SNPEFF_AMINO_ACID_CHANGE=D30N;SNPEFF_CODON_CHANGE=Gac/Aac;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_902084_902183;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=PLEKHN1;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000379407;VQSLOD=5.23000e+00;culprit=QD;CSQ=A|ENSG00000187583|ENST00000480267|Transcript|upstream_gene_variant||||||rs201730138|1|4167|1|PLEKHN1|HGNC|25284|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187961|ENST00000466300|Transcript|downstream_gene_variant||||||rs201730138|1|2178|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187961|ENST00000338591|Transcript|downstream_gene_variant||||||rs201730138|1|993|1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||||||A:0.0005||A:0.0028|||A:0|A:0.000600||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs201730138|1|4230|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187583|ENST00000379409|Transcript|missense_variant|118|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06|tolerated(0.26)|benign(0.034)|2/15|||ENST00000379409.2:c.88N>A|ENSP00000368719.2:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0441767068273092||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A|ENSG00000187583|ENST00000379407|Transcript|missense_variant|118|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF|tolerated(0.25)|benign(0.072)|2/15|||ENST00000379407.3:c.88N>A|ENSP00000368717.2:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0508376660889659||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A|ENSG00000187961|ENST00000481067|Transcript|downstream_gene_variant||||||rs201730138|1|2544|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187583|ENST00000379410|Transcript|missense_variant|123|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8|tolerated(0.25)|benign(0.072)|2/16|||ENST00000379410.3:c.88N>A|ENSP00000368720.3:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0479302832244009||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A||ENSR00000528862|RegulatoryFeature|regulatory_region_variant||||||rs201730138|1||||||regulatory_region|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600||||||||||||||||| GT:AD:DP:GQ:PL 0/1:10,1:11:1:1,0,264 0/0:13,0:13:33:0,33,447 0/0:10,0:10:30:0,30,371 0/0:4,0:4:12:0,12,141 0/0:1,0:1:3:0,3,39 0/0:4,0:4:12:0,12,145 0/0:18,0:18:51:0,51,665 0/0:4,0:4:12:0,12,148 0/0:5,0:5:15:0,15,193 0/0:9,0:9:24:0,24,320 0/0:10,0:10:30:0,30,378 0/0:4,0:4:12:0,12,160 0/0:10,0:10:30:0,30,387 0/0:7,0:7:21:0,21,247 0/0:9,0:9:27:0,27,350 0/0:14,0:14:42:0,42,540 From 666b3947a8ef7b996dfcad4f7c275f1405488107 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 24 Aug 2026 12:50:07 -0400 Subject: [PATCH 282/369] fixy copy pasta --- loading_pipeline/lib/tasks/exports/fields.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/loading_pipeline/lib/tasks/exports/fields.py b/loading_pipeline/lib/tasks/exports/fields.py index 59d3ca2f25..47faec4096 100644 --- a/loading_pipeline/lib/tasks/exports/fields.py +++ b/loading_pipeline/lib/tasks/exports/fields.py @@ -173,7 +173,7 @@ def get_entries_annotations_export_fields(dataset_type: DatasetType): fields['geneIds'] = lambda ht: ( hl.set(ht.sorted_gene_consequences.gene_id) if dataset_type == DatasetType.SV - else hl.set(ht.sorted_gene_consequences.gene_id) + else hl.set(ht.sorted_transcript_consequences.gene_id) ) return fields From 0e690334e774d9f1d9dbdec3be2a94c9b2bd2139 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 24 Aug 2026 13:06:00 -0400 Subject: [PATCH 283/369] fix new etries dependencies --- .../lib/tasks/exports/write_new_entries_parquet.py | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py index 2f3da34c13..1832eb29c5 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py +++ b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py @@ -25,6 +25,9 @@ get_entries_export_fields, ) from loading_pipeline.lib.tasks.files import GCSorLocalTarget +from loading_pipeline.lib.tasks.write_existing_variants_parquet import ( + WriteExistingVariantsParquetTask, +) from loading_pipeline.lib.tasks.write_new_variants_table import ( WriteNewVariantsTableTask, ) @@ -32,6 +35,7 @@ WriteRemappedAndSubsettedCallsetTask, ) +EXISTING_VARIANTS_TASK = 'existing_variant_task' VARIANTS_TABLE_TASK = 'variants_table_task' REMAPPED_AND_SUBSETTED_CALLSET_TASKS = 'remapped_and_subsetted_callset_tasks' @@ -49,6 +53,9 @@ def output(self) -> luigi.Target: def requires(self) -> dict[str, luigi.Task]: return { + EXISTING_VARIANTS_TASK: self.clone( + WriteExistingVariantsParquetTask, + ), VARIANTS_TABLE_TASK: self.clone( WriteNewVariantsTableTask, ), From 246548119521dd88bde6ea10f3867e2e76d10380 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 24 Aug 2026 13:11:16 -0400 Subject: [PATCH 284/369] handle missing max key --- loading_pipeline/lib/tasks/write_new_variants_table.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/loading_pipeline/lib/tasks/write_new_variants_table.py b/loading_pipeline/lib/tasks/write_new_variants_table.py index dea1404c89..bc2f441892 100644 --- a/loading_pipeline/lib/tasks/write_new_variants_table.py +++ b/loading_pipeline/lib/tasks/write_new_variants_table.py @@ -131,7 +131,9 @@ def create_table(self) -> hl.Table: self.reference_genome, self.dataset_type, ) - curr_max_key_ = annotations_ht.aggregate(hl.agg.max(annotations_ht.key_)) + curr_max_key_ = ( + annotations_ht.aggregate(hl.agg.max(annotations_ht.key_)) or -1 + ) new_variants_ht = callset_ht.repartition( # Repartition this join to improve performance constrain( From 25ddc4f3f6a181f0d350601ca945db5bfd07b614 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 24 Aug 2026 13:18:48 -0400 Subject: [PATCH 285/369] use existing parquet for sv dedup --- loading_pipeline/lib/misc/sv.py | 4 ++-- loading_pipeline/lib/paths.py | 15 --------------- .../lib/tasks/write_postprocessed_callset.py | 17 +++++++++++++---- 3 files changed, 15 insertions(+), 21 deletions(-) diff --git a/loading_pipeline/lib/misc/sv.py b/loading_pipeline/lib/misc/sv.py index b3a54463f0..407df13f1f 100644 --- a/loading_pipeline/lib/misc/sv.py +++ b/loading_pipeline/lib/misc/sv.py @@ -75,12 +75,12 @@ def deduplicate_merged_sv_concordance_calls( for new_variant in new_variants_it1: distance = math.fabs( new_variant.end_locus.position - - existing_variant.end_locus.position + - existing_variant.end + ( WRONG_CHROM_PENALTY if ( new_variant.end_locus.contig - != existing_variant.end_locus.contig + != existing_variant.endChrom ) else 0 ), diff --git a/loading_pipeline/lib/paths.py b/loading_pipeline/lib/paths.py index b8078fb9b4..8c1a170f3c 100644 --- a/loading_pipeline/lib/paths.py +++ b/loading_pipeline/lib/paths.py @@ -266,21 +266,6 @@ def ancestry_model_rf_path() -> str: ) -# TODO deprecate -def variant_annotations_table_path( - reference_genome: ReferenceGenome, - dataset_type: DatasetType, -) -> str: - return os.path.join( - pipeline_prefix( - Env.PIPELINE_DATA_DIR, - reference_genome, - dataset_type, - ), - 'annotations.ht', - ) - - def new_entries_parquet_path( reference_genome: ReferenceGenome, dataset_type: DatasetType, diff --git a/loading_pipeline/lib/tasks/write_postprocessed_callset.py b/loading_pipeline/lib/tasks/write_postprocessed_callset.py index 34f01ce904..31210142ca 100644 --- a/loading_pipeline/lib/tasks/write_postprocessed_callset.py +++ b/loading_pipeline/lib/tasks/write_postprocessed_callset.py @@ -4,18 +4,22 @@ from loading_pipeline.lib.misc.callsets import get_additional_row_fields from loading_pipeline.lib.misc.io import ( +import_parquet, split_multi_hts, ) from loading_pipeline.lib.misc.sv import deduplicate_merged_sv_concordance_calls from loading_pipeline.lib.misc.vets import annotate_vets from loading_pipeline.lib.paths import ( + existing_variants_parquet_path, imported_callset_path, postprocessed_callset_path, - variant_annotations_table_path, ) from loading_pipeline.lib.tasks.base.base_loading_run_params import BaseLoadingRunParams from loading_pipeline.lib.tasks.base.base_write import BaseWriteTask from loading_pipeline.lib.tasks.files import GCSorLocalTarget +from loading_pipeline.lib.tasks.write_existing_variants_parquet import ( + WriteExistingVariantsParquetTask, +) from loading_pipeline.lib.tasks.write_imported_callset import WriteImportedCallsetTask from loading_pipeline.lib.tasks.write_validation_errors_for_run import ( with_persisted_validation_errors, @@ -47,7 +51,9 @@ def output(self) -> luigi.Target: ) def requires(self) -> list[luigi.Task]: - return [self.clone(WriteImportedCallsetTask)] + return [self.clone(WriteImportedCallsetTask)] + [ + self.clone(WriteExistingVariantsParquetTask), + ] if self.dataset_type.re_key_by_seqr_internal_truth_vid else [] @with_persisted_validation_errors def create_table(self) -> hl.MatrixTable: @@ -71,11 +77,14 @@ def create_table(self) -> hl.MatrixTable: ): mt = deduplicate_merged_sv_concordance_calls( mt, - hl.read_table( - variant_annotations_table_path( + import_parquet( + existing_variants_parquet_path( self.reference_genome, self.dataset_type, + self.run_id, ), + self.reference_genome, + self.dataset_type, ), ) mt = mt.key_rows_by( From ea888d23f53636b952d7a08bb20e1e290398b739 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 24 Aug 2026 13:25:04 -0400 Subject: [PATCH 286/369] clean up --- .../lib/tasks/write_postprocessed_callset.py | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/loading_pipeline/lib/tasks/write_postprocessed_callset.py b/loading_pipeline/lib/tasks/write_postprocessed_callset.py index 31210142ca..0baa46d941 100644 --- a/loading_pipeline/lib/tasks/write_postprocessed_callset.py +++ b/loading_pipeline/lib/tasks/write_postprocessed_callset.py @@ -4,7 +4,7 @@ from loading_pipeline.lib.misc.callsets import get_additional_row_fields from loading_pipeline.lib.misc.io import ( -import_parquet, + import_parquet, split_multi_hts, ) from loading_pipeline.lib.misc.sv import deduplicate_merged_sv_concordance_calls @@ -51,9 +51,10 @@ def output(self) -> luigi.Target: ) def requires(self) -> list[luigi.Task]: - return [self.clone(WriteImportedCallsetTask)] + [ - self.clone(WriteExistingVariantsParquetTask), - ] if self.dataset_type.re_key_by_seqr_internal_truth_vid else [] + requires = [self.clone(WriteImportedCallsetTask)] + if self.dataset_type.re_key_by_seqr_internal_truth_vid: + requires.append(self.clone(WriteExistingVariantsParquetTask)) + return requires @with_persisted_validation_errors def create_table(self) -> hl.MatrixTable: From 008bf397a71c1529c6afde2cef31dccec13c5e4d Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 24 Aug 2026 13:29:22 -0400 Subject: [PATCH 287/369] ruff --- loading_pipeline/lib/misc/sv.py | 5 +---- loading_pipeline/lib/tasks/write_new_variants_table.py | 4 +--- 2 files changed, 2 insertions(+), 7 deletions(-) diff --git a/loading_pipeline/lib/misc/sv.py b/loading_pipeline/lib/misc/sv.py index 407df13f1f..5e104c946d 100644 --- a/loading_pipeline/lib/misc/sv.py +++ b/loading_pipeline/lib/misc/sv.py @@ -78,10 +78,7 @@ def deduplicate_merged_sv_concordance_calls( - existing_variant.end + ( WRONG_CHROM_PENALTY - if ( - new_variant.end_locus.contig - != existing_variant.endChrom - ) + if new_variant.end_locus.contig != existing_variant.endChrom else 0 ), ) diff --git a/loading_pipeline/lib/tasks/write_new_variants_table.py b/loading_pipeline/lib/tasks/write_new_variants_table.py index bc2f441892..eafdf58295 100644 --- a/loading_pipeline/lib/tasks/write_new_variants_table.py +++ b/loading_pipeline/lib/tasks/write_new_variants_table.py @@ -131,9 +131,7 @@ def create_table(self) -> hl.Table: self.reference_genome, self.dataset_type, ) - curr_max_key_ = ( - annotations_ht.aggregate(hl.agg.max(annotations_ht.key_)) or -1 - ) + curr_max_key_ = annotations_ht.aggregate(hl.agg.max(annotations_ht.key_)) or -1 new_variants_ht = callset_ht.repartition( # Repartition this join to improve performance constrain( From 36d33012d5e8397a3474df348d3dbff228085f24 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 24 Aug 2026 13:56:14 -0400 Subject: [PATCH 288/369] misc fixes --- loading_pipeline/lib/misc/io.py | 2 +- loading_pipeline/lib/misc/sv.py | 1 - loading_pipeline/lib/tasks/exports/fields.py | 4 ++-- 3 files changed, 3 insertions(+), 4 deletions(-) diff --git a/loading_pipeline/lib/misc/io.py b/loading_pipeline/lib/misc/io.py index 634bb6a661..87b57949d0 100644 --- a/loading_pipeline/lib/misc/io.py +++ b/loading_pipeline/lib/misc/io.py @@ -227,7 +227,7 @@ def import_parquet( if reference_genome == ReferenceGenome.GRCh38 else raw_contig ) - ht = ht.annotate( + ht = ht.transmute( locus=hl.locus( contig=contig, pos=hl.int32(ht.variant_id.split('-')[1]), diff --git a/loading_pipeline/lib/misc/sv.py b/loading_pipeline/lib/misc/sv.py index 5e104c946d..52305d6f19 100644 --- a/loading_pipeline/lib/misc/sv.py +++ b/loading_pipeline/lib/misc/sv.py @@ -50,7 +50,6 @@ def deduplicate_merged_sv_concordance_calls( ) # Then, collect into memory the necessary existing variants & the new variants - annotations_ht = annotations_ht.select('end_locus') existing_variants = { v.variant_id: v for v in ( diff --git a/loading_pipeline/lib/tasks/exports/fields.py b/loading_pipeline/lib/tasks/exports/fields.py index 47faec4096..65604ff21f 100644 --- a/loading_pipeline/lib/tasks/exports/fields.py +++ b/loading_pipeline/lib/tasks/exports/fields.py @@ -95,8 +95,8 @@ def get_existing_variants_export_field(dataset_type: DatasetType) -> str: dt_fields = { DatasetType.SNV_INDEL: ', transcripts.geneId AS geneIds', DatasetType.MITO: '', - DatasetType.SV: ', xpos, end, endChrom, sortedGeneConsequences.geneId AS geneIds', - DatasetType.GCNV: ', xpos, pos AS start, end, numExon as num_exon, sortedGeneConsequences.geneId AS gene_ids', + DatasetType.SV: ', CAST(xpos AS Int64) AS xpos, end, endChrom, sortedGeneConsequences.geneId AS geneIds', + DatasetType.GCNV: ', CAST(xpos AS Int64) AS xpos, pos AS start, end, numExon as num_exon, sortedGeneConsequences.geneId AS gene_ids', }[dataset_type] return f'key AS key_, variantId AS variant_id {dt_fields}' From 13b3a30db3c91e24c8afc2df0ad7e3fbf9b3ba20 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 24 Aug 2026 14:04:35 -0400 Subject: [PATCH 289/369] fix helper test --- loading_pipeline/lib/misc/sv_test.py | 28 ++++++++-------------------- 1 file changed, 8 insertions(+), 20 deletions(-) diff --git a/loading_pipeline/lib/misc/sv_test.py b/loading_pipeline/lib/misc/sv_test.py index aefa8a5cd5..44a2f9efc4 100644 --- a/loading_pipeline/lib/misc/sv_test.py +++ b/loading_pipeline/lib/misc/sv_test.py @@ -16,36 +16,24 @@ [ { 'variant_id': 'BND_chr1_6', - 'algorithms': 'manta', - 'end_locus': hl.Locus( - contig='chr5', - position=20404, - reference_genome='GRCh38', - ), + 'end': 20404, + 'endChrom': 'chr5', }, { 'variant_id': 'BND_chr1_9', - 'algorithms': 'manta', - 'end_locus': hl.Locus( - contig='chr1', - position=789481, - reference_genome='GRCh38', - ), + 'end': 789481, + 'endChrom': 'chr1', }, { 'variant_id': 'CPX_chr1_22', - 'algorithms': 'manta', - 'end_locus': hl.Locus( - contig='chr1', - position=6559723, - reference_genome='GRCh38', - ), + 'end': 6559723, + 'endChrom': 'chr1', }, ], hl.tstruct( variant_id=hl.tstr, - algorithms=hl.tstr, - end_locus=hl.tlocus('GRCh38'), + end=hl.tint32, + endChrom=hl.tstr, ), key='variant_id', ) From 714a49e67bc629baf22661028ef32b2fc65fcb21 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 24 Aug 2026 14:22:56 -0400 Subject: [PATCH 290/369] union type mismatch --- loading_pipeline/lib/misc/io.py | 2 +- loading_pipeline/lib/tasks/exports/fields.py | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/loading_pipeline/lib/misc/io.py b/loading_pipeline/lib/misc/io.py index 87b57949d0..3b0982d6f5 100644 --- a/loading_pipeline/lib/misc/io.py +++ b/loading_pipeline/lib/misc/io.py @@ -230,7 +230,7 @@ def import_parquet( ht = ht.transmute( locus=hl.locus( contig=contig, - pos=hl.int32(ht.variant_id.split('-')[1]), + pos=hl.int64(ht.variant_id.split('-')[1]), reference_genome=reference_genome.value, ), alleles=[ht.variant_id.split('-')[2], ht.variant_id.split('-')[3]], diff --git a/loading_pipeline/lib/tasks/exports/fields.py b/loading_pipeline/lib/tasks/exports/fields.py index 65604ff21f..4fd8f600ae 100644 --- a/loading_pipeline/lib/tasks/exports/fields.py +++ b/loading_pipeline/lib/tasks/exports/fields.py @@ -171,9 +171,9 @@ def get_entries_annotations_export_fields(dataset_type: DatasetType): } if dataset_type in {DatasetType.SV, DatasetType.SNV_INDEL}: fields['geneIds'] = lambda ht: ( - hl.set(ht.sorted_gene_consequences.gene_id) + hl.array(ht.sorted_gene_consequences.gene_id) if dataset_type == DatasetType.SV - else hl.set(ht.sorted_transcript_consequences.gene_id) + else hl.array(ht.sorted_transcript_consequences.gene_id) ) return fields From 9d27c681210405dbaa76aa696d7e8b896135a00a Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 24 Aug 2026 14:38:55 -0400 Subject: [PATCH 291/369] fix xpos dt --- loading_pipeline/lib/misc/io.py | 2 +- loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/loading_pipeline/lib/misc/io.py b/loading_pipeline/lib/misc/io.py index 3b0982d6f5..87b57949d0 100644 --- a/loading_pipeline/lib/misc/io.py +++ b/loading_pipeline/lib/misc/io.py @@ -230,7 +230,7 @@ def import_parquet( ht = ht.transmute( locus=hl.locus( contig=contig, - pos=hl.int64(ht.variant_id.split('-')[1]), + pos=hl.int32(ht.variant_id.split('-')[1]), reference_genome=reference_genome.value, ), alleles=[ht.variant_id.split('-')[2], ht.variant_id.split('-')[3]], diff --git a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py index 1832eb29c5..6947c5898b 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py +++ b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py @@ -99,7 +99,7 @@ def create_table(self) -> None: ) if 'xpos' not in existing_annotations_ht.row: existing_annotations_ht = existing_annotations_ht.annotate( - xpos=xpos(existing_annotations_ht), + xpos=hl.int64(xpos(existing_annotations_ht)), ) annotations_ht = annotations_ht.union(existing_annotations_ht) From dc95b25ade88136b089ae81f80d2ad870cb13343 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 24 Aug 2026 14:42:04 -0400 Subject: [PATCH 292/369] drop extra parquest cols --- .../exports/write_new_entries_parquet.py | 19 +++++++++---------- 1 file changed, 9 insertions(+), 10 deletions(-) diff --git a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py index 6947c5898b..82eb337c53 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py +++ b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py @@ -78,15 +78,14 @@ def create_table(self) -> None: self.run_id, ), ) - annotations_ht = annotations_ht.select( - **{ - field: func(annotations_ht) - for field, func in { - **get_entries_annotations_export_fields(self.dataset_type), - **get_entries_call_annotations_fields(self.dataset_type), - }.items() - }, - ) + annotation_selects = { + field: func(annotations_ht) + for field, func in { + **get_entries_annotations_export_fields(self.dataset_type), + **get_entries_call_annotations_fields(self.dataset_type), + }.items() + } + annotations_ht = annotations_ht.select(**annotation_selects) existing_annotations_ht = import_parquet( existing_variants_parquet_path( @@ -102,7 +101,7 @@ def create_table(self) -> None: xpos=hl.int64(xpos(existing_annotations_ht)), ) - annotations_ht = annotations_ht.union(existing_annotations_ht) + annotations_ht = annotations_ht.union(existing_annotations_ht.select(*annotation_selects)) for project_guid, remapped_and_subsetted_callset_task in zip( self.project_guids, From 21aba8dfe71773eaf60ddbd44837ca97447e5b61 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 24 Aug 2026 15:36:48 -0400 Subject: [PATCH 293/369] ruff --- .../lib/tasks/exports/write_new_entries_parquet.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py index 82eb337c53..8919f7a41a 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py +++ b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py @@ -101,7 +101,9 @@ def create_table(self) -> None: xpos=hl.int64(xpos(existing_annotations_ht)), ) - annotations_ht = annotations_ht.union(existing_annotations_ht.select(*annotation_selects)) + annotations_ht = annotations_ht.union( + existing_annotations_ht.select(*annotation_selects) + ) for project_guid, remapped_and_subsetted_callset_task in zip( self.project_guids, From 3293ef5e9e469e27e655f4fdb3ff4593274c9444 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 24 Aug 2026 15:41:06 -0400 Subject: [PATCH 294/369] ruff --- loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py index 8919f7a41a..55dad0bd12 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py +++ b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py @@ -102,7 +102,7 @@ def create_table(self) -> None: ) annotations_ht = annotations_ht.union( - existing_annotations_ht.select(*annotation_selects) + existing_annotations_ht.select(*annotation_selects), ) for project_guid, remapped_and_subsetted_callset_task in zip( From e47e08c90dca7ecf9ee3529077de8165cf15d2fe Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 24 Aug 2026 15:55:31 -0400 Subject: [PATCH 295/369] fix gcnv fields --- loading_pipeline/lib/tasks/exports/fields.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/loading_pipeline/lib/tasks/exports/fields.py b/loading_pipeline/lib/tasks/exports/fields.py index 4fd8f600ae..8d3762b53b 100644 --- a/loading_pipeline/lib/tasks/exports/fields.py +++ b/loading_pipeline/lib/tasks/exports/fields.py @@ -106,10 +106,10 @@ def get_entries_call_annotations_fields( ): if dataset_type == DatasetType.GCNV: return { - 'start': lambda ht: ht.start_locus.position, - 'end': lambda ht: ht.end_locus.position, + 'start': lambda ht: hl.int64(ht.start_locus.position), + 'end': lambda ht: hl.int64(ht.end_locus.position), 'num_exon': lambda ht: ht.num_exon, - 'gene_ids': lambda ht: hl.set(ht.sorted_gene_consequences.gene_id), + 'gene_ids': lambda ht: hl.array(ht.sorted_gene_consequences.gene_id), } return {} From c6295f318e2c814fe50448beb906adc0ecb8b0d0 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 24 Aug 2026 15:57:57 -0400 Subject: [PATCH 296/369] type mismatch --- loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py index 55dad0bd12..82817ec3f3 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py +++ b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py @@ -98,7 +98,7 @@ def create_table(self) -> None: ) if 'xpos' not in existing_annotations_ht.row: existing_annotations_ht = existing_annotations_ht.annotate( - xpos=hl.int64(xpos(existing_annotations_ht)), + xpos=hl.int32(xpos(existing_annotations_ht)), ) annotations_ht = annotations_ht.union( From 1cc7a06be9282aa4aa8b52077e387e485aa0c9fa Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 24 Aug 2026 16:13:06 -0400 Subject: [PATCH 297/369] clean up --- loading_pipeline/lib/annotations/enums.py | 1 - 1 file changed, 1 deletion(-) diff --git a/loading_pipeline/lib/annotations/enums.py b/loading_pipeline/lib/annotations/enums.py index 6a764c61d1..bb24a2bd92 100644 --- a/loading_pipeline/lib/annotations/enums.py +++ b/loading_pipeline/lib/annotations/enums.py @@ -214,7 +214,6 @@ def validated_enum_member( """Validate that a string value is in the allowed enum list. Returns the value if valid or missing, raises an error if unrecognized. - This replaces dict-based enum id encoding with validated string values. """ allowed_values_set = hl.literal(set(allowed_values)) return ( From 41ba2dbca9404a2c4f3ce4ef434dbd12f4bfae9a Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 24 Aug 2026 16:21:47 -0400 Subject: [PATCH 298/369] type mismatch handling --- loading_pipeline/lib/tasks/exports/fields.py | 4 ++-- .../lib/tasks/exports/write_new_entries_parquet.py | 6 +++++- 2 files changed, 7 insertions(+), 3 deletions(-) diff --git a/loading_pipeline/lib/tasks/exports/fields.py b/loading_pipeline/lib/tasks/exports/fields.py index 8d3762b53b..25b9ef0f5f 100644 --- a/loading_pipeline/lib/tasks/exports/fields.py +++ b/loading_pipeline/lib/tasks/exports/fields.py @@ -109,7 +109,7 @@ def get_entries_call_annotations_fields( 'start': lambda ht: hl.int64(ht.start_locus.position), 'end': lambda ht: hl.int64(ht.end_locus.position), 'num_exon': lambda ht: ht.num_exon, - 'gene_ids': lambda ht: hl.array(ht.sorted_gene_consequences.gene_id), + 'gene_ids': lambda ht: hl.set(ht.sorted_gene_consequences.gene_id), } return {} @@ -167,7 +167,7 @@ def _get_calls_export_fields( def get_entries_annotations_export_fields(dataset_type: DatasetType): fields = { 'key_': lambda ht: ht.key_, - 'xpos': lambda ht: ht.xpos, + 'xpos': lambda ht: hl.int64(ht.xpos), } if dataset_type in {DatasetType.SV, DatasetType.SNV_INDEL}: fields['geneIds'] = lambda ht: ( diff --git a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py index 82817ec3f3..b4fcc2fcda 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py +++ b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py @@ -98,7 +98,11 @@ def create_table(self) -> None: ) if 'xpos' not in existing_annotations_ht.row: existing_annotations_ht = existing_annotations_ht.annotate( - xpos=hl.int32(xpos(existing_annotations_ht)), + xpos=hl.int64(xpos(existing_annotations_ht)), + ) + if 'gene_ids' in existing_annotations_ht.row: + existing_annotations_ht = existing_annotations_ht.annotate( + gene_ids=hl.set(existing_annotations_ht.gene_ids), ) annotations_ht = annotations_ht.union( From 1926aab667dc4030f2f382c303b53851dc3cabf8 Mon Sep 17 00:00:00 2001 From: hanars Date: Mon, 24 Aug 2026 16:26:01 -0400 Subject: [PATCH 299/369] Apply suggestions from code review Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> --- loading_pipeline/docs/Historial_Context.md | 2 +- .../lib/tasks/write_existing_variants_parquet.py | 5 ++--- 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/loading_pipeline/docs/Historial_Context.md b/loading_pipeline/docs/Historial_Context.md index d7ed8e0a0d..b9af536de8 100644 --- a/loading_pipeline/docs/Historial_Context.md +++ b/loading_pipeline/docs/Historial_Context.md @@ -62,7 +62,7 @@ gs://seqr-hail-search-data/v3.1/GRCh38/SNV_INDEL/runs/20260421-125644-303855/new ## Thoughts for future: - Remove Hail for non SNV_INDEL dataset types and callsets < 500 samples. - Lightweight replacement for Luigi "run()/complete()/output()/requires()" framework. - - Eliminate scheduler in favor or "tasks" table in clickhouse. + - Eliminate scheduler in favor of "tasks" table in clickhouse. - Running arbitrary docker images: - Airflow was useful for this, w/ Kubernetes elasticity. - Need to support external computational biology tools. diff --git a/loading_pipeline/lib/tasks/write_existing_variants_parquet.py b/loading_pipeline/lib/tasks/write_existing_variants_parquet.py index 5da189f6c1..8f7eb75286 100644 --- a/loading_pipeline/lib/tasks/write_existing_variants_parquet.py +++ b/loading_pipeline/lib/tasks/write_existing_variants_parquet.py @@ -23,9 +23,8 @@ def output(self) -> luigi.Target: ), ) - def complete(self) -> luigi.Target: - return GCSorLocalTarget(self.output().path).exists() - + def complete(self) -> bool: + return self.output().exists() def run(self): export_select_fields = get_existing_variants_export_field(self.dataset_type) export_existing_variants_to_parquet( From e85161d0c9e3a3065d6c3bedba677c92cf1a0152 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 24 Aug 2026 16:27:07 -0400 Subject: [PATCH 300/369] debug --- .../lib/tasks/exports/write_new_entries_parquet_test.py | 1 + 1 file changed, 1 insertion(+) diff --git a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py index 1c0f13f828..bb4c5db075 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py @@ -127,6 +127,7 @@ def test_write_new_entries_parquet(self): ), ) export_json = convert_ndarray_to_list(df.to_dict('records')) + self.maxDiff = None self.assertEqual( export_json[:2], [ From aa24584ff30018860d6068d76983ce7847f80e04 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 24 Aug 2026 16:27:59 -0400 Subject: [PATCH 301/369] ruff --- loading_pipeline/lib/tasks/write_existing_variants_parquet.py | 1 + 1 file changed, 1 insertion(+) diff --git a/loading_pipeline/lib/tasks/write_existing_variants_parquet.py b/loading_pipeline/lib/tasks/write_existing_variants_parquet.py index 8f7eb75286..da89e0ce79 100644 --- a/loading_pipeline/lib/tasks/write_existing_variants_parquet.py +++ b/loading_pipeline/lib/tasks/write_existing_variants_parquet.py @@ -25,6 +25,7 @@ def output(self) -> luigi.Target: def complete(self) -> bool: return self.output().exists() + def run(self): export_select_fields = get_existing_variants_export_field(self.dataset_type) export_existing_variants_to_parquet( From cd316da03bae3b8386b7f573f69bd19e55ea5f1a Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 24 Aug 2026 16:54:27 -0400 Subject: [PATCH 302/369] fix test --- loading_pipeline/lib/tasks/exports/fields.py | 4 ++-- .../lib/tasks/exports/write_new_entries_parquet.py | 4 ++++ .../lib/tasks/exports/write_new_entries_parquet_test.py | 3 ++- .../lib/tasks/write_existing_variants_parquet_test.py | 2 +- loading_pipeline/lib/test/fixtures/clickhouse_test.json | 2 +- 5 files changed, 10 insertions(+), 5 deletions(-) diff --git a/loading_pipeline/lib/tasks/exports/fields.py b/loading_pipeline/lib/tasks/exports/fields.py index 25b9ef0f5f..e5a39d8212 100644 --- a/loading_pipeline/lib/tasks/exports/fields.py +++ b/loading_pipeline/lib/tasks/exports/fields.py @@ -171,9 +171,9 @@ def get_entries_annotations_export_fields(dataset_type: DatasetType): } if dataset_type in {DatasetType.SV, DatasetType.SNV_INDEL}: fields['geneIds'] = lambda ht: ( - hl.array(ht.sorted_gene_consequences.gene_id) + hl.set(ht.sorted_gene_consequences.gene_id) if dataset_type == DatasetType.SV - else hl.array(ht.sorted_transcript_consequences.gene_id) + else hl.set(ht.sorted_transcript_consequences.gene_id) ) return fields diff --git a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py index b4fcc2fcda..5e45fccbce 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py +++ b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py @@ -104,6 +104,10 @@ def create_table(self) -> None: existing_annotations_ht = existing_annotations_ht.annotate( gene_ids=hl.set(existing_annotations_ht.gene_ids), ) + if 'geneIds' in existing_annotations_ht.row: + existing_annotations_ht = existing_annotations_ht.annotate( + geneIds=hl.set(existing_annotations_ht.geneIds), + ) annotations_ht = annotations_ht.union( existing_annotations_ht.select(*annotation_selects), diff --git a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py index bb4c5db075..ad41d28714 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py @@ -54,6 +54,7 @@ def setUp(self) -> None: ht = hl.read_table( TEST_SNV_INDEL_ANNOTATIONS, ) + ht = ht.filter(ht.variant_id != '1-878314-G-C') ht.write( new_variants_table_path( ReferenceGenome.GRCh38, @@ -170,7 +171,7 @@ def test_write_new_entries_parquet(self): 'family_guid': 'abc_1', 'sample_type': 'WGS', 'xpos': 1000878314, - 'geneIds': ['ENSG00000187634'], + 'geneIds': ['ENSG00000177000'], 'filters': ['VQSRTrancheSNP99.00to99.90'], 'calls': [ { diff --git a/loading_pipeline/lib/tasks/write_existing_variants_parquet_test.py b/loading_pipeline/lib/tasks/write_existing_variants_parquet_test.py index 4ee8ffed9a..1323c0b775 100644 --- a/loading_pipeline/lib/tasks/write_existing_variants_parquet_test.py +++ b/loading_pipeline/lib/tasks/write_existing_variants_parquet_test.py @@ -55,7 +55,7 @@ def test_snv_indel(self): [ { 'key_': 1, - 'variant_id': '1-10059-C-T', + 'variant_id': '1-878314-G-C', 'geneIds': ['ENSG00000177000'], }, {'key_': 7, 'variant_id': '7-1234567-AGT-A', 'geneIds': []}, diff --git a/loading_pipeline/lib/test/fixtures/clickhouse_test.json b/loading_pipeline/lib/test/fixtures/clickhouse_test.json index 46d0fae32f..9de4810176 100644 --- a/loading_pipeline/lib/test/fixtures/clickhouse_test.json +++ b/loading_pipeline/lib/test/fixtures/clickhouse_test.json @@ -267,7 +267,7 @@ "pk": 1, "fields": { "key": 1, - "variant_id": "1-10059-C-T", + "variant_id": "1-878314-G-C", "transcripts": [ [ [0.9978], "L/F", "protein_coding", 1, "ttA/ttC", ["missense_variant"], [2, 9], "ENSG00000177000", From 739062690f6bac51cad33d7319dde31fa4c01c60 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 24 Aug 2026 17:14:12 -0400 Subject: [PATCH 303/369] undo debug --- .../lib/tasks/exports/write_new_entries_parquet_test.py | 1 - 1 file changed, 1 deletion(-) diff --git a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py index ad41d28714..6caa4daead 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py @@ -128,7 +128,6 @@ def test_write_new_entries_parquet(self): ), ) export_json = convert_ndarray_to_list(df.to_dict('records')) - self.maxDiff = None self.assertEqual( export_json[:2], [ From 1e024a38b5aeb55817e3cf4052290a2a27b3d48a Mon Sep 17 00:00:00 2001 From: hanars Date: Mon, 31 Aug 2026 14:39:31 -0400 Subject: [PATCH 304/369] PR feedback --- .dockerignore | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.dockerignore b/.dockerignore index 09e62f8f26..889b577013 100644 --- a/.dockerignore +++ b/.dockerignore @@ -6,7 +6,7 @@ static/* deploy/* !deploy/docker/seqr/* !deploy/docker/vlm/* -*test* +loading_pipeline/*test* .git .vscode .idea From 5eaecd0ad5793e0c5bf991947c3dd02486402e83 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 31 Aug 2026 15:06:58 -0400 Subject: [PATCH 305/369] debug test failures --- loading_pipeline/lib/annotations/snv_indel_test.py | 2 ++ loading_pipeline/lib/tasks/exports/misc_test.py | 1 + 2 files changed, 3 insertions(+) diff --git a/loading_pipeline/lib/annotations/snv_indel_test.py b/loading_pipeline/lib/annotations/snv_indel_test.py index 70df03b4f8..75d2d208ea 100644 --- a/loading_pipeline/lib/annotations/snv_indel_test.py +++ b/loading_pipeline/lib/annotations/snv_indel_test.py @@ -18,6 +18,7 @@ def test_sorted_transcript_consequences_37( self, mock_vep: Mock, ) -> None: + self.maxDiff = None ht = hl.Table.parallelize( [ { @@ -104,6 +105,7 @@ def test_sorted_transcript_consequences_38( self, mock_vep: Mock, ) -> None: + self.maxDiff = None ht = hl.Table.parallelize( [ { diff --git a/loading_pipeline/lib/tasks/exports/misc_test.py b/loading_pipeline/lib/tasks/exports/misc_test.py index e7563cead3..1327be9c8d 100644 --- a/loading_pipeline/lib/tasks/exports/misc_test.py +++ b/loading_pipeline/lib/tasks/exports/misc_test.py @@ -21,6 +21,7 @@ class MiscTest(unittest.TestCase): def test_camelcase_array_structexpression_fields(self) -> None: + self.maxDiff = None ht = hl.read_table(TEST_SNV_INDEL_ANNOTATIONS) ht = camelcase_array_structexpression_fields( ht, From 76c451bb594cc0fbebc77309ead70bd2574a6960 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 31 Aug 2026 15:20:15 -0400 Subject: [PATCH 306/369] fix gcn test hail table --- .../GRCh38/GCNV/annotations.ht/.README.txt.crc | Bin 12 -> 12 bytes .../GCNV/annotations.ht/.metadata.json.gz.crc | Bin 12 -> 12 bytes .../GRCh38/GCNV/annotations.ht/README.txt | 4 ++-- .../globals/.metadata.json.gz.crc | Bin 12 -> 12 bytes .../annotations.ht/globals/metadata.json.gz | Bin 409 -> 381 bytes .../annotations.ht/globals/parts/.part-0.crc | Bin 12 -> 12 bytes .../GCNV/annotations.ht/globals/parts/part-0 | Bin 342 -> 174 bytes .../.index.crc | Bin .../.metadata.json.gz.crc | Bin .../index | Bin .../metadata.json.gz | Bin .../GRCh38/GCNV/annotations.ht/metadata.json.gz | Bin 503 -> 492 bytes .../annotations.ht/rows/.metadata.json.gz.crc | Bin 16 -> 16 bytes .../GCNV/annotations.ht/rows/metadata.json.gz | Bin 723 -> 724 bytes ...t-0-0cff3685-8750-4aee-8325-c0fdf20bb38c.crc | Bin 12 -> 0 bytes ...t-0-3a8ac5d5-4931-4758-a2e3-cb3c64f3022a.crc | Bin 0 -> 12 bytes .../part-0-0cff3685-8750-4aee-8325-c0fdf20bb38c | Bin 122 -> 0 bytes .../part-0-3a8ac5d5-4931-4758-a2e3-cb3c64f3022a | Bin 0 -> 128 bytes 18 files changed, 2 insertions(+), 2 deletions(-) rename loading_pipeline/var/test/exports/GRCh38/GCNV/annotations.ht/index/{part-0-0cff3685-8750-4aee-8325-c0fdf20bb38c.idx => part-0-3a8ac5d5-4931-4758-a2e3-cb3c64f3022a.idx}/.index.crc (100%) rename loading_pipeline/var/test/exports/GRCh38/GCNV/annotations.ht/index/{part-0-0cff3685-8750-4aee-8325-c0fdf20bb38c.idx => part-0-3a8ac5d5-4931-4758-a2e3-cb3c64f3022a.idx}/.metadata.json.gz.crc (100%) rename loading_pipeline/var/test/exports/GRCh38/GCNV/annotations.ht/index/{part-0-0cff3685-8750-4aee-8325-c0fdf20bb38c.idx => part-0-3a8ac5d5-4931-4758-a2e3-cb3c64f3022a.idx}/index (100%) rename loading_pipeline/var/test/exports/GRCh38/GCNV/annotations.ht/index/{part-0-0cff3685-8750-4aee-8325-c0fdf20bb38c.idx => part-0-3a8ac5d5-4931-4758-a2e3-cb3c64f3022a.idx}/metadata.json.gz (100%) delete mode 100644 loading_pipeline/var/test/exports/GRCh38/GCNV/annotations.ht/rows/parts/.part-0-0cff3685-8750-4aee-8325-c0fdf20bb38c.crc create mode 100644 loading_pipeline/var/test/exports/GRCh38/GCNV/annotations.ht/rows/parts/.part-0-3a8ac5d5-4931-4758-a2e3-cb3c64f3022a.crc delete mode 100644 loading_pipeline/var/test/exports/GRCh38/GCNV/annotations.ht/rows/parts/part-0-0cff3685-8750-4aee-8325-c0fdf20bb38c create mode 100644 loading_pipeline/var/test/exports/GRCh38/GCNV/annotations.ht/rows/parts/part-0-3a8ac5d5-4931-4758-a2e3-cb3c64f3022a diff --git a/loading_pipeline/var/test/exports/GRCh38/GCNV/annotations.ht/.README.txt.crc b/loading_pipeline/var/test/exports/GRCh38/GCNV/annotations.ht/.README.txt.crc index a14e4cc2aa2f5b6bf6498407159b81cfa821fb6c..b526a400e775d310ea2bc4e81bccc5b3b6e1f757 100644 GIT binary patch literal 12 TcmYc;N@ieSU}DG=fASRo5+(zb literal 12 TcmYc;N@ieSU}8vH=HCwh5;p@S diff --git a/loading_pipeline/var/test/exports/GRCh38/GCNV/annotations.ht/.metadata.json.gz.crc b/loading_pipeline/var/test/exports/GRCh38/GCNV/annotations.ht/.metadata.json.gz.crc index d438d8ce2c25117dd0a718a067080c556a744db4..7f9ac55b1cd1639c12a8f060c07255d25e38d88b 100644 GIT binary patch literal 12 TcmYc;N@ieSU}CVcpZXC15kLbv literal 12 TcmYc;N@ieSU}BIh+jSHG5sw2+ diff --git a/loading_pipeline/var/test/exports/GRCh38/GCNV/annotations.ht/README.txt b/loading_pipeline/var/test/exports/GRCh38/GCNV/annotations.ht/README.txt index eeb1745378..b21756d31f 100644 --- a/loading_pipeline/var/test/exports/GRCh38/GCNV/annotations.ht/README.txt +++ 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SYqKc>1251j5CB^TvI_v)fg>9L literal 0 HcmV?d00001 From 8c585ed1ac11baba624ab4cfed28013cadc826af Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 31 Aug 2026 15:22:58 -0400 Subject: [PATCH 307/369] Revert "debug test failures" This reverts commit 5eaecd0ad5793e0c5bf991947c3dd02486402e83. --- loading_pipeline/lib/annotations/snv_indel_test.py | 2 -- loading_pipeline/lib/tasks/exports/misc_test.py | 1 - 2 files changed, 3 deletions(-) diff --git a/loading_pipeline/lib/annotations/snv_indel_test.py b/loading_pipeline/lib/annotations/snv_indel_test.py index 75d2d208ea..70df03b4f8 100644 --- a/loading_pipeline/lib/annotations/snv_indel_test.py +++ b/loading_pipeline/lib/annotations/snv_indel_test.py @@ -18,7 +18,6 @@ def test_sorted_transcript_consequences_37( self, mock_vep: Mock, ) -> None: - self.maxDiff = None ht = hl.Table.parallelize( [ { @@ -105,7 +104,6 @@ def test_sorted_transcript_consequences_38( self, mock_vep: Mock, ) -> None: - self.maxDiff = None ht = hl.Table.parallelize( [ { diff --git a/loading_pipeline/lib/tasks/exports/misc_test.py b/loading_pipeline/lib/tasks/exports/misc_test.py index 1327be9c8d..e7563cead3 100644 --- a/loading_pipeline/lib/tasks/exports/misc_test.py +++ b/loading_pipeline/lib/tasks/exports/misc_test.py @@ -21,7 +21,6 @@ class MiscTest(unittest.TestCase): def test_camelcase_array_structexpression_fields(self) -> None: - self.maxDiff = None ht = hl.read_table(TEST_SNV_INDEL_ANNOTATIONS) ht = camelcase_array_structexpression_fields( ht, From f00e583730820f9028a029be9343966ef1e6fa37 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 31 Aug 2026 15:59:43 -0400 Subject: [PATCH 308/369] fix tests --- loading_pipeline/lib/annotations/snv_indel_test.py | 4 ++-- loading_pipeline/lib/tasks/exports/misc_test.py | 1 + 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/loading_pipeline/lib/annotations/snv_indel_test.py b/loading_pipeline/lib/annotations/snv_indel_test.py index 70df03b4f8..08deb46d28 100644 --- a/loading_pipeline/lib/annotations/snv_indel_test.py +++ b/loading_pipeline/lib/annotations/snv_indel_test.py @@ -87,7 +87,7 @@ def test_sorted_transcript_consequences_37( hgvsc='ENST00000483767.1:n.523C>T', hgvsp=None, transcript_id='ENST00000483767', - biotype='lncRNA', + biotype='retained_intron', consequence_terms=[ 'non_coding_transcript_exon_variant', 'non_coding_transcript_variant', @@ -234,7 +234,7 @@ def test_sorted_transcript_consequences_38( existing_inframe_oorfs=0, existing_outofframe_oorfs=1, existing_uorfs=0, - fiveutr_consequence='5_prime_UTR_premature_start_codon_gain_variant', + fiveutr_consequence='5_prime_UTR_premature_start_codon_loss_variant', fiveutr_annotation=hl.Struct( type='OutOfFrame_oORF', KozakContext='TTTATGC', diff --git a/loading_pipeline/lib/tasks/exports/misc_test.py b/loading_pipeline/lib/tasks/exports/misc_test.py index e7563cead3..ebe2d7eb79 100644 --- a/loading_pipeline/lib/tasks/exports/misc_test.py +++ b/loading_pipeline/lib/tasks/exports/misc_test.py @@ -30,6 +30,7 @@ def test_camelcase_array_structexpression_fields(self) -> None: ht = ht.annotate( sortedTranscriptConsequences=[ht.sortedTranscriptConsequences[0]], ) + self.maxDiff = None self.assertEqual( ht.collect()[0], hl.Struct( From 9d0b010a869f1113c9aa9c41890faf56a9bc2455 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 31 Aug 2026 16:27:22 -0400 Subject: [PATCH 309/369] debug test --- loading_pipeline/lib/annotations/snv_indel_test.py | 1 + loading_pipeline/lib/tasks/exports/misc_test.py | 6 +++--- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/loading_pipeline/lib/annotations/snv_indel_test.py b/loading_pipeline/lib/annotations/snv_indel_test.py index 08deb46d28..79017d9268 100644 --- a/loading_pipeline/lib/annotations/snv_indel_test.py +++ b/loading_pipeline/lib/annotations/snv_indel_test.py @@ -18,6 +18,7 @@ def test_sorted_transcript_consequences_37( self, mock_vep: Mock, ) -> None: + self.maxDiff = None ht = hl.Table.parallelize( [ { diff --git a/loading_pipeline/lib/tasks/exports/misc_test.py b/loading_pipeline/lib/tasks/exports/misc_test.py index ebe2d7eb79..06be5d2b28 100644 --- a/loading_pipeline/lib/tasks/exports/misc_test.py +++ b/loading_pipeline/lib/tasks/exports/misc_test.py @@ -32,8 +32,8 @@ def test_camelcase_array_structexpression_fields(self) -> None: ) self.maxDiff = None self.assertEqual( - ht.collect()[0], - hl.Struct( + dict(ht.collect()[0]), + dict(hl.Struct( key_=0, locus=hl.Locus( contig='chr1', @@ -176,7 +176,7 @@ def test_camelcase_array_structexpression_fields(self) -> None: consequenceTerms=['TF_binding_site_variant'], ), ], - ), + )), ) def test_sorted_hl_struct(self) -> None: From d5fa95c0b35760e509cfae9ce9faf764a09af3bc Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 31 Aug 2026 16:41:22 -0400 Subject: [PATCH 310/369] ruff --- .../lib/tasks/exports/misc_test.py | 284 +++++++++--------- 1 file changed, 143 insertions(+), 141 deletions(-) diff --git a/loading_pipeline/lib/tasks/exports/misc_test.py b/loading_pipeline/lib/tasks/exports/misc_test.py index 06be5d2b28..0896fd2e3d 100644 --- a/loading_pipeline/lib/tasks/exports/misc_test.py +++ b/loading_pipeline/lib/tasks/exports/misc_test.py @@ -33,150 +33,152 @@ def test_camelcase_array_structexpression_fields(self) -> None: self.maxDiff = None self.assertEqual( dict(ht.collect()[0]), - dict(hl.Struct( - key_=0, - locus=hl.Locus( - contig='chr1', - position=876499, - reference_genome='GRCh38', - ), - alleles=['A', 'G'], - clinvar=hl.Struct( - alleleId=929885, - conflictingPathogenicities=None, - goldStars=1, - submitters=['Labcorp Genetics (formerly Invitae), Labcorp'], - conditions=['not provided'], - assertion_ids=[], - pathogenicity_id=12, - ), - rg37_locus=hl.Locus( - contig=1, - position=874501, - reference_genome='GRCh37', - ), - rsid=None, - variant_id='1-876499-A-G', - xpos=1000876499, - gt_stats=hl.Struct(AC=47, AN=81784, AF=0.0005746845272369683, hom=1), - CAID='CA502654', - check_ref=False, - gnomad_non_coding_constraint=hl.Struct(z_score=None), - hgmd=hl.Struct(accession='abcdefg', class_id=3), - gnomad_exomes=hl.Struct( - AF=0.0006690866430290043, - AN=1440770, - AC=964, - Hom=0, - AF_POPMAX_OR_GLOBAL=0.0008023773552849889, - FAF_AF=0.000633420015219599, - Hemi=0, - ), - gnomad_genomes=hl.Struct( - AF=0.0002759889466688037, - AN=152180, - AC=42, - Hom=0, - AF_POPMAX_OR_GLOBAL=0.10000000149011612, - FAF_AF=0.0002092500071739778, - Hemi=0, - ), - screen=hl.Struct(region_type_ids=[]), - dbnsfp=hl.Struct( - PrimateAI_score=0.5918066501617432, - fathmm_MKL_coding_score=0.7174800038337708, - CADD_phred=23.5, - SIFT_score=0.0010000000474974513, - REVEL_score=0.3109999895095825, - Polyphen2_HVAR_score=0.164000004529953, - VEST4_score=0.39500001072883606, - MPC_score=0.01291007362306118, - MutPred_score=None, - MutationTaster_pred_id=0, - ), - topmed=hl.Struct( - AC=41, - AF=0.00032651599030941725, - AN=125568, - Hom=0, - Het=41, - ), - exac=hl.Struct( - AF_POPMAX=0.0007150234305299819, - AF=0.00019039999460801482, - AC_Adj=20, - AC_Het=20, - AC_Hom=0, - AC_Hemi=None, - AN_Adj=47974, - ), - splice_ai=hl.Struct( - delta_score=0.0, - splice_consequence_id=4, - ), - eigen=hl.Struct(Eigen_phred=2.628000020980835), - sortedTranscriptConsequences=[ - hl.Struct( - aminoAcids='S/L', - canonical=1, - codons='tCg/tTg', - geneId='ENSG00000187634', - hgvsc='ENST00000616016.5:c.1049C>T', - hgvsp='ENSP00000478421.2:p.Ser350Leu', - transcriptId='ENST00000616016', - maneSelect='NM_001385641.1', - manePlusClinical=None, - exon=hl.Struct(index=6, total=14), - intron=None, - refseqTranscriptId='NM_001385641.1', - alphamissense=hl.Struct(pathogenicity=None), - loftee=hl.Struct(isLofNagnag=None, lofFilters=None), - spliceregion=hl.Struct( - extended_intronic_splice_region_variant=False, - ), - utrannotator=hl.Struct( - existingInframeOorfs=None, - existingOutofframeOorfs=None, - existingUorfs=None, - fiveutrAnnotation=hl.Struct( - type='OutOfFrame_oORF', - KozakContext='CGCATGC', - KozakStrength='Weak', - DistanceToCDS=41, - CapDistanceToStart=None, - DistanceToStop=None, - Evidence=None, - AltStop=None, - AltStopDistanceToCDS=None, - FrameWithCDS=None, - StartDistanceToCDS=None, - newSTOPDistanceToCDS=None, - alt_type=None, - alt_type_length=None, - ref_StartDistanceToCDS=None, - ref_type=None, - ref_type_length=None, - ), - fiveutrConsequence=None, - ), - biotype='protein_coding', - consequenceTerms=['missense_variant'], + dict( + hl.Struct( + key_=0, + locus=hl.Locus( + contig='chr1', + position=876499, + reference_genome='GRCh38', + ), + alleles=['A', 'G'], + clinvar=hl.Struct( + alleleId=929885, + conflictingPathogenicities=None, + goldStars=1, + submitters=['Labcorp Genetics (formerly Invitae), Labcorp'], + conditions=['not provided'], + assertion_ids=[], + pathogenicity_id=12, + ), + rg37_locus=hl.Locus( + contig=1, + position=874501, + reference_genome='GRCh37', + ), + rsid=None, + variant_id='1-876499-A-G', + xpos=1000876499, + gt_stats=hl.Struct(AC=47, AN=81784, AF=0.0005746845272369683, hom=1), + CAID='CA502654', + check_ref=False, + gnomad_non_coding_constraint=hl.Struct(z_score=None), + hgmd=hl.Struct(accession='abcdefg', class_id=3), + gnomad_exomes=hl.Struct( + AF=0.0006690866430290043, + AN=1440770, + AC=964, + Hom=0, + AF_POPMAX_OR_GLOBAL=0.0008023773552849889, + FAF_AF=0.000633420015219599, + Hemi=0, + ), + gnomad_genomes=hl.Struct( + AF=0.0002759889466688037, + AN=152180, + AC=42, + Hom=0, + AF_POPMAX_OR_GLOBAL=0.10000000149011612, + FAF_AF=0.0002092500071739778, + Hemi=0, ), - ], - sortedRegulatoryFeatureConsequences=[ - hl.Struct( - regulatoryFeatureId='ENSR00000344437', - biotype='CTCF_binding_site', - consequenceTerms=['regulatory_region_variant'], + screen=hl.Struct(region_type_ids=[]), + dbnsfp=hl.Struct( + PrimateAI_score=0.5918066501617432, + fathmm_MKL_coding_score=0.7174800038337708, + CADD_phred=23.5, + SIFT_score=0.0010000000474974513, + REVEL_score=0.3109999895095825, + Polyphen2_HVAR_score=0.164000004529953, + VEST4_score=0.39500001072883606, + MPC_score=0.01291007362306118, + MutPred_score=None, + MutationTaster_pred_id=0, ), - ], - sortedMotifFeatureConsequences=[ - hl.Struct( - motifFeatureId='ENSM00493959715', - consequenceTerms=['TF_binding_site_variant'], + topmed=hl.Struct( + AC=41, + AF=0.00032651599030941725, + AN=125568, + Hom=0, + Het=41, ), - ], - )), + exac=hl.Struct( + AF_POPMAX=0.0007150234305299819, + AF=0.00019039999460801482, + AC_Adj=20, + AC_Het=20, + AC_Hom=0, + AC_Hemi=None, + AN_Adj=47974, + ), + splice_ai=hl.Struct( + delta_score=0.0, + splice_consequence_id=4, + ), + eigen=hl.Struct(Eigen_phred=2.628000020980835), + sortedTranscriptConsequences=[ + hl.Struct( + aminoAcids='S/L', + canonical=1, + codons='tCg/tTg', + geneId='ENSG00000187634', + hgvsc='ENST00000616016.5:c.1049C>T', + hgvsp='ENSP00000478421.2:p.Ser350Leu', + transcriptId='ENST00000616016', + maneSelect='NM_001385641.1', + manePlusClinical=None, + exon=hl.Struct(index=6, total=14), + intron=None, + refseqTranscriptId='NM_001385641.1', + alphamissense=hl.Struct(pathogenicity=None), + loftee=hl.Struct(isLofNagnag=None, lofFilters=None), + spliceregion=hl.Struct( + extended_intronic_splice_region_variant=False, + ), + utrannotator=hl.Struct( + existingInframeOorfs=None, + existingOutofframeOorfs=None, + existingUorfs=None, + fiveutrAnnotation=hl.Struct( + type='OutOfFrame_oORF', + KozakContext='CGCATGC', + KozakStrength='Weak', + DistanceToCDS=41, + CapDistanceToStart=None, + DistanceToStop=None, + Evidence=None, + AltStop=None, + AltStopDistanceToCDS=None, + FrameWithCDS=None, + StartDistanceToCDS=None, + newSTOPDistanceToCDS=None, + alt_type=None, + alt_type_length=None, + ref_StartDistanceToCDS=None, + ref_type=None, + ref_type_length=None, + ), + fiveutrConsequence=None, + ), + biotype='protein_coding', + consequenceTerms=['missense_variant'], + ), + ], + sortedRegulatoryFeatureConsequences=[ + hl.Struct( + regulatoryFeatureId='ENSR00000344437', + biotype='CTCF_binding_site', + consequenceTerms=['regulatory_region_variant'], + ), + ], + sortedMotifFeatureConsequences=[ + hl.Struct( + motifFeatureId='ENSM00493959715', + consequenceTerms=['TF_binding_site_variant'], + ), + ], + ) + ), ) def test_sorted_hl_struct(self) -> None: From c916850a8f22a276cb24345b8b8a09d00cfa117a Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 31 Aug 2026 16:44:26 -0400 Subject: [PATCH 311/369] ruff --- loading_pipeline/lib/tasks/exports/misc_test.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/loading_pipeline/lib/tasks/exports/misc_test.py b/loading_pipeline/lib/tasks/exports/misc_test.py index 0896fd2e3d..5bbd176fe6 100644 --- a/loading_pipeline/lib/tasks/exports/misc_test.py +++ b/loading_pipeline/lib/tasks/exports/misc_test.py @@ -59,7 +59,12 @@ def test_camelcase_array_structexpression_fields(self) -> None: rsid=None, variant_id='1-876499-A-G', xpos=1000876499, - gt_stats=hl.Struct(AC=47, AN=81784, AF=0.0005746845272369683, hom=1), + gt_stats=hl.Struct( + AC=47, + AN=81784, + AF=0.0005746845272369683, + hom=1, + ), CAID='CA502654', check_ref=False, gnomad_non_coding_constraint=hl.Struct(z_score=None), From 7b1170cd26fcf1ebc215c781d9cac301a3089db6 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 31 Aug 2026 16:47:36 -0400 Subject: [PATCH 312/369] ruff --- loading_pipeline/lib/tasks/exports/misc_test.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/loading_pipeline/lib/tasks/exports/misc_test.py b/loading_pipeline/lib/tasks/exports/misc_test.py index 5bbd176fe6..d353670e7d 100644 --- a/loading_pipeline/lib/tasks/exports/misc_test.py +++ b/loading_pipeline/lib/tasks/exports/misc_test.py @@ -182,7 +182,7 @@ def test_camelcase_array_structexpression_fields(self) -> None: consequenceTerms=['TF_binding_site_variant'], ), ], - ) + ), ), ) From 8f0b4ddf1fc6484ef98c19f1750de1251fc84af1 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 31 Aug 2026 17:08:12 -0400 Subject: [PATCH 313/369] test fix --- .../lib/annotations/snv_indel_test.py | 2 +- .../lib/tasks/exports/misc_test.py | 290 +++++++++--------- 2 files changed, 142 insertions(+), 150 deletions(-) diff --git a/loading_pipeline/lib/annotations/snv_indel_test.py b/loading_pipeline/lib/annotations/snv_indel_test.py index 79017d9268..a48f8b4094 100644 --- a/loading_pipeline/lib/annotations/snv_indel_test.py +++ b/loading_pipeline/lib/annotations/snv_indel_test.py @@ -72,7 +72,7 @@ def test_sorted_transcript_consequences_37( hgvsc='ENST00000477976.1:n.3114C>T', hgvsp=None, transcript_id='ENST00000477976', - biotype='lncRNA', + biotype='retained_intron', consequence_terms=[ 'non_coding_transcript_exon_variant', 'non_coding_transcript_variant', diff --git a/loading_pipeline/lib/tasks/exports/misc_test.py b/loading_pipeline/lib/tasks/exports/misc_test.py index d353670e7d..29bd0ab510 100644 --- a/loading_pipeline/lib/tasks/exports/misc_test.py +++ b/loading_pipeline/lib/tasks/exports/misc_test.py @@ -30,159 +30,151 @@ def test_camelcase_array_structexpression_fields(self) -> None: ht = ht.annotate( sortedTranscriptConsequences=[ht.sortedTranscriptConsequences[0]], ) - self.maxDiff = None self.assertEqual( - dict(ht.collect()[0]), - dict( - hl.Struct( - key_=0, - locus=hl.Locus( - contig='chr1', - position=876499, - reference_genome='GRCh38', - ), - alleles=['A', 'G'], - clinvar=hl.Struct( - alleleId=929885, - conflictingPathogenicities=None, - goldStars=1, - submitters=['Labcorp Genetics (formerly Invitae), Labcorp'], - conditions=['not provided'], - assertion_ids=[], - pathogenicity_id=12, - ), - rg37_locus=hl.Locus( - contig=1, - position=874501, - reference_genome='GRCh37', - ), - rsid=None, - variant_id='1-876499-A-G', - xpos=1000876499, - gt_stats=hl.Struct( - AC=47, - AN=81784, - AF=0.0005746845272369683, - hom=1, - ), - CAID='CA502654', - check_ref=False, - gnomad_non_coding_constraint=hl.Struct(z_score=None), - hgmd=hl.Struct(accession='abcdefg', class_id=3), - gnomad_exomes=hl.Struct( - AF=0.0006690866430290043, - AN=1440770, - AC=964, - Hom=0, - AF_POPMAX_OR_GLOBAL=0.0008023773552849889, - FAF_AF=0.000633420015219599, - Hemi=0, - ), - gnomad_genomes=hl.Struct( - AF=0.0002759889466688037, - AN=152180, - AC=42, - Hom=0, - AF_POPMAX_OR_GLOBAL=0.10000000149011612, - FAF_AF=0.0002092500071739778, - Hemi=0, - ), - screen=hl.Struct(region_type_ids=[]), - dbnsfp=hl.Struct( - PrimateAI_score=0.5918066501617432, - fathmm_MKL_coding_score=0.7174800038337708, - CADD_phred=23.5, - SIFT_score=0.0010000000474974513, - REVEL_score=0.3109999895095825, - Polyphen2_HVAR_score=0.164000004529953, - VEST4_score=0.39500001072883606, - MPC_score=0.01291007362306118, - MutPred_score=None, - MutationTaster_pred_id=0, - ), - topmed=hl.Struct( - AC=41, - AF=0.00032651599030941725, - AN=125568, - Hom=0, - Het=41, + ht.collect()[0], + hl.Struct( + key_=0, + locus=hl.Locus( + contig='chr1', + position=876499, + reference_genome='GRCh38', + ), + alleles=['A', 'G'], + clinvar=hl.Struct( + alleleId=929885, + conflictingPathogenicities=None, + goldStars=1, + submitters=['Labcorp Genetics (formerly Invitae), Labcorp'], + conditions=['not provided'], + assertion_ids=[], + pathogenicity_id=12, + ), + rg37_locus=hl.Locus( + contig=1, + position=874501, + reference_genome='GRCh37', + ), + rsid=None, + variant_id='1-876499-A-G', + xpos=1000876499, + gt_stats=hl.Struct(AC=47, AN=81784, AF=0.0005746845272369683, hom=1), + CAID='CA502654', + check_ref=False, + gnomad_non_coding_constraint=hl.Struct(z_score=None), + hgmd=hl.Struct(accession='abcdefg', class_id=3), + gnomad_exomes=hl.Struct( + AF=0.0006690866430290043, + AN=1440770, + AC=964, + Hom=0, + AF_POPMAX_OR_GLOBAL=0.0008023773552849889, + FAF_AF=0.000633420015219599, + Hemi=0, + ), + gnomad_genomes=hl.Struct( + AF=0.0002759889466688037, + AN=152180, + AC=42, + Hom=0, + AF_POPMAX_OR_GLOBAL=0.10000000149011612, + FAF_AF=0.0002092500071739778, + Hemi=0, + ), + screen=hl.Struct(region_type_ids=[]), + dbnsfp=hl.Struct( + PrimateAI_score=0.5918066501617432, + fathmm_MKL_coding_score=0.7174800038337708, + CADD_phred=23.5, + SIFT_score=0.0010000000474974513, + REVEL_score=0.3109999895095825, + Polyphen2_HVAR_score=0.164000004529953, + VEST4_score=0.39500001072883606, + MPC_score=0.01291007362306118, + MutPred_score=None, + MutationTaster_pred_id=0, + ), + topmed=hl.Struct( + AC=41, + AF=0.00032651599030941725, + AN=125568, + Hom=0, + Het=41, + ), + exac=hl.Struct( + AF_POPMAX=0.0007150234305299819, + AF=0.00019039999460801482, + AC_Adj=20, + AC_Het=20, + AC_Hom=0, + AC_Hemi=None, + AN_Adj=47974, + ), + splice_ai=hl.Struct( + delta_score=0.0, + splice_consequence_id=4, + ), + eigen=hl.Struct(Eigen_phred=2.628000020980835), + sortedTranscriptConsequences=[ + hl.Struct( + aminoAcids='S/L', + canonical=1, + codons='tCg/tTg', + geneId='ENSG00000187634', + hgvsc='ENST00000616016.5:c.1049C>T', + hgvsp='ENSP00000478421.2:p.Ser350Leu', + transcriptId='ENST00000616016', + maneSelect='NM_001385641.1', + manePlusClinical=None, + exon=hl.Struct(index=6, total=14), + intron=None, + refseqTranscriptId='NM_001385641.1', + alphamissense=hl.Struct(pathogenicity=None), + loftee=hl.Struct(isLofNagnag=None, lofFilterIds=None), + spliceregion=hl.Struct( + extended_intronic_splice_region_variant=False, + ), + utrannotator=hl.Struct( + existingInframeOorfs=None, + existingOutofframeOorfs=None, + existingUorfs=None, + fiveutrAnnotation=hl.Struct( + type='OutOfFrame_oORF', + KozakContext='CGCATGC', + KozakStrength='Weak', + DistanceToCDS=41, + CapDistanceToStart=None, + DistanceToStop=None, + Evidence=None, + AltStop=None, + AltStopDistanceToCDS=None, + FrameWithCDS=None, + StartDistanceToCDS=None, + newSTOPDistanceToCDS=None, + alt_type=None, + alt_type_length=None, + ref_StartDistanceToCDS=None, + ref_type=None, + ref_type_length=None, + ), + fiveutrConsequenceId=None, + ), + biotypeId=39, + consequenceTermIds=[9], ), - exac=hl.Struct( - AF_POPMAX=0.0007150234305299819, - AF=0.00019039999460801482, - AC_Adj=20, - AC_Het=20, - AC_Hom=0, - AC_Hemi=None, - AN_Adj=47974, + ], + sortedRegulatoryFeatureConsequences=[ + hl.Struct( + regulatoryFeatureId='ENSR00000344437', + biotypeId=2, + consequenceTermIds=[2], ), - splice_ai=hl.Struct( - delta_score=0.0, - splice_consequence_id=4, + ], + sortedMotifFeatureConsequences=[ + hl.Struct( + motifFeatureId='ENSM00493959715', + consequenceTermIds=[2], ), - eigen=hl.Struct(Eigen_phred=2.628000020980835), - sortedTranscriptConsequences=[ - hl.Struct( - aminoAcids='S/L', - canonical=1, - codons='tCg/tTg', - geneId='ENSG00000187634', - hgvsc='ENST00000616016.5:c.1049C>T', - hgvsp='ENSP00000478421.2:p.Ser350Leu', - transcriptId='ENST00000616016', - maneSelect='NM_001385641.1', - manePlusClinical=None, - exon=hl.Struct(index=6, total=14), - intron=None, - refseqTranscriptId='NM_001385641.1', - alphamissense=hl.Struct(pathogenicity=None), - loftee=hl.Struct(isLofNagnag=None, lofFilters=None), - spliceregion=hl.Struct( - extended_intronic_splice_region_variant=False, - ), - utrannotator=hl.Struct( - existingInframeOorfs=None, - existingOutofframeOorfs=None, - existingUorfs=None, - fiveutrAnnotation=hl.Struct( - type='OutOfFrame_oORF', - KozakContext='CGCATGC', - KozakStrength='Weak', - DistanceToCDS=41, - CapDistanceToStart=None, - DistanceToStop=None, - Evidence=None, - AltStop=None, - AltStopDistanceToCDS=None, - FrameWithCDS=None, - StartDistanceToCDS=None, - newSTOPDistanceToCDS=None, - alt_type=None, - alt_type_length=None, - ref_StartDistanceToCDS=None, - ref_type=None, - ref_type_length=None, - ), - fiveutrConsequence=None, - ), - biotype='protein_coding', - consequenceTerms=['missense_variant'], - ), - ], - sortedRegulatoryFeatureConsequences=[ - hl.Struct( - regulatoryFeatureId='ENSR00000344437', - biotype='CTCF_binding_site', - consequenceTerms=['regulatory_region_variant'], - ), - ], - sortedMotifFeatureConsequences=[ - hl.Struct( - motifFeatureId='ENSM00493959715', - consequenceTerms=['TF_binding_site_variant'], - ), - ], - ), + ], ), ) From 269fa5240a7d2948b702dedf750ecc96c3845ca2 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 31 Aug 2026 17:32:43 -0400 Subject: [PATCH 314/369] celean up --- loading_pipeline/lib/annotations/snv_indel_test.py | 1 - 1 file changed, 1 deletion(-) diff --git a/loading_pipeline/lib/annotations/snv_indel_test.py b/loading_pipeline/lib/annotations/snv_indel_test.py index a48f8b4094..50b9e5db4d 100644 --- a/loading_pipeline/lib/annotations/snv_indel_test.py +++ b/loading_pipeline/lib/annotations/snv_indel_test.py @@ -18,7 +18,6 @@ def test_sorted_transcript_consequences_37( self, mock_vep: Mock, ) -> None: - self.maxDiff = None ht = hl.Table.parallelize( [ { From 230327446312455f61f316401c224d0011a4db25 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 1 Sep 2026 13:48:07 -0400 Subject: [PATCH 315/369] remove unused function --- loading_pipeline/lib/misc/runs.py | 54 -------------------------- loading_pipeline/lib/misc/runs_test.py | 40 ------------------- loading_pipeline/lib/paths.py | 15 ------- 3 files changed, 109 deletions(-) diff --git a/loading_pipeline/lib/misc/runs.py b/loading_pipeline/lib/misc/runs.py index 702f86d94c..2cf4550381 100644 --- a/loading_pipeline/lib/misc/runs.py +++ b/loading_pipeline/lib/misc/runs.py @@ -1,17 +1,9 @@ import datetime import os -from collections import defaultdict -import hailtop.fs as hfs - -from loading_pipeline.lib.core.dataset_type import DatasetType from loading_pipeline.lib.core.environment import Env -from loading_pipeline.lib.misc.retry import retry from loading_pipeline.lib.paths import ( - clickhouse_load_fail_file_path, - clickhouse_load_success_file_path, loading_pipeline_queue_dir, - pipeline_run_success_file_path, ) @@ -41,49 +33,3 @@ def is_queue_full() -> bool: Returns True if the number of files exceeds a predefined limit, otherwise False. """ return len(os.listdir(loading_pipeline_queue_dir())) >= Env.LOADING_QUEUE_LIMIT - - -@retry() -def get_run_ids() -> tuple[defaultdict, defaultdict, defaultdict]: - successful_pipeline_runs, successful_clickhouse_loads, failed_clickhouse_loads = ( - defaultdict(set), - defaultdict(set), - defaultdict(set), - ) - for dataset_type in DatasetType: - for reference_genome in dataset_type.reference_genomes: - successful_pipeline_runs[(reference_genome, dataset_type)] = { - p.path.split('/')[-2] - for p in hfs.ls( - pipeline_run_success_file_path( - reference_genome, - dataset_type, - '*', - ), - ) - } - successful_clickhouse_loads[(reference_genome, dataset_type)] = { - p.path.split('/')[-2] - for p in hfs.ls( - clickhouse_load_success_file_path( - reference_genome, - dataset_type, - '*', - ), - ) - } - failed_clickhouse_loads[(reference_genome, dataset_type)] = { - p.path.split('/')[-2] - for p in hfs.ls( - clickhouse_load_fail_file_path( - reference_genome, - dataset_type, - '*', - ), - ) - } - return ( - successful_pipeline_runs, - successful_clickhouse_loads, - failed_clickhouse_loads, - ) diff --git a/loading_pipeline/lib/misc/runs_test.py b/loading_pipeline/lib/misc/runs_test.py index b1a601727a..7ba80e9353 100644 --- a/loading_pipeline/lib/misc/runs_test.py +++ b/loading_pipeline/lib/misc/runs_test.py @@ -1,9 +1,7 @@ import os from loading_pipeline.lib.core import DatasetType, ReferenceGenome -from loading_pipeline.lib.misc.runs import get_run_ids from loading_pipeline.lib.paths import ( - clickhouse_load_fail_file_path, clickhouse_load_success_file_path, pipeline_run_success_file_path, runs_path, @@ -30,13 +28,6 @@ def setUp(self): for run_id in run_ids: base_path = runs_path(reference_genome, dataset_type) os.makedirs(os.path.join(base_path, run_id), exist_ok=True) - if '07T12' in run_id: - failure_file = clickhouse_load_fail_file_path( - reference_genome, - dataset_type, - run_id, - ) - open(failure_file, 'w').close() if '09' in run_id or '07T12' in run_id: success_file = pipeline_run_success_file_path( reference_genome, @@ -51,34 +42,3 @@ def setUp(self): run_id, ) open(success_file, 'w').close() - - def test_get_run_ids(self) -> None: - ( - successful_pipeline_runs, - successful_clickhouse_loads, - failed_clickhouse_loads, - ) = get_run_ids() - self.assertCountEqual( - successful_pipeline_runs[(ReferenceGenome.GRCh38, DatasetType.SNV_INDEL)], - { - 'manual__2024-08-09T18-22-13.999999+00-00', - 'manual__2024-08-08T09-45-00.000000+00-00', - 'manual__2024-08-07T12-30-45.654321+00-00', - }, - ) - self.assertCountEqual( - successful_clickhouse_loads[ - (ReferenceGenome.GRCh38, DatasetType.SNV_INDEL) - ], - { - 'manual__2024-08-09T18-22-13.999999+00-00', - }, - ) - self.assertCountEqual( - successful_clickhouse_loads[(ReferenceGenome.GRCh37, DatasetType.GCNV)], - {}, - ) - self.assertCountEqual( - failed_clickhouse_loads[(ReferenceGenome.GRCh38, DatasetType.SNV_INDEL)], - {'manual__2024-08-07T12-30-45.654321+00-00'}, - ) diff --git a/loading_pipeline/lib/paths.py b/loading_pipeline/lib/paths.py index 8c1a170f3c..b9d0e51443 100644 --- a/loading_pipeline/lib/paths.py +++ b/loading_pipeline/lib/paths.py @@ -427,21 +427,6 @@ def clickhouse_load_success_file_path( ) -def clickhouse_load_fail_file_path( - reference_genome: ReferenceGenome, - dataset_type: DatasetType, - run_id: str, -) -> str: - return os.path.join( - runs_path( - reference_genome, - dataset_type, - ), - run_id, - '_CLICKHOUSE_LOAD_FAIL', - ) - - def reference_dataset_parquet( reference_genome: ReferenceGenome, reference_dataset: ReferenceDataset, From 704f11b19f2455b5b9a6ce69b36e34d69ce64c8e Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 1 Sep 2026 13:57:05 -0400 Subject: [PATCH 316/369] remove unused funcs --- .../lib/reference_datasets/misc.py | 87 ------------------- 1 file changed, 87 deletions(-) diff --git a/loading_pipeline/lib/reference_datasets/misc.py b/loading_pipeline/lib/reference_datasets/misc.py index cf9fe37680..12bd467560 100644 --- a/loading_pipeline/lib/reference_datasets/misc.py +++ b/loading_pipeline/lib/reference_datasets/misc.py @@ -1,16 +1,6 @@ -import contextlib -import os -import random -import string -import tempfile -import zipfile - import hail as hl -import hailtop.fs as hfs -import requests from loading_pipeline.lib.core.definitions import ReferenceGenome -from loading_pipeline.lib.core.environment import Env from loading_pipeline.lib.misc.io import split_multi_hts BIALLELIC = 2 @@ -26,12 +16,6 @@ def compress_floats(ht: hl.Table): ) -def generate_random_string(length=5): - """Generates a random string of the specified length.""" - letters = string.ascii_letters + string.digits - return ''.join(random.choice(letters) for i in range(length)) # noqa: S311 # nosec B311 - - def filter_contigs(ht, reference_genome: ReferenceGenome): if hasattr(ht, 'interval'): return ht.filter( @@ -72,74 +56,3 @@ def vcf_to_ht( error = f'Encountered {count_non_biallelic} multiallelic variants' raise ValueError(error) return mt.rows() - - -def key_by_locus_alleles(ht: hl.Table, reference_genome: ReferenceGenome) -> hl.Table: - chrom = ( - hl.format('chr%s', ht.chrom) - if reference_genome == ReferenceGenome.GRCh38 - else hl.if_else(ht.chrom == 'M', 'MT', ht.chrom) - ) - ht = ht.transmute( - locus=hl.locus(chrom, ht.pos, reference_genome.value), - alleles=hl.array([ht.ref, ht.alt]), - ) - return ht.key_by('locus', 'alleles') - - -def copyfileobj(fsrc, fdst, decode_content, length=16 * 1024): - """Copy data from file-like object fsrc to file-like object fdst.""" - while True: - buf = fsrc.read(length, decode_content=decode_content) - if not buf: - break - fdst.write(buf) - - -@contextlib.contextmanager -def download_zip_file(url, dataset_name: str, suffix='.zip', decode_content=False): - dir_ = f'/tmp/{generate_random_string()}/{dataset_name}' # noqa: S108 # nosec B108 - os.makedirs(dir_, exist_ok=True) - with ( - tempfile.NamedTemporaryFile( - dir=dir_, - suffix=suffix, - ) as tmp_file, - requests.get(url, stream=True, timeout=10) as r, - ): - copyfileobj(r.raw, tmp_file, decode_content) - with zipfile.ZipFile(tmp_file.name, 'r') as zipf: - zipf.extractall(dir_) - yield copy_to_cloud_storage(dir_) - - -def select_for_interval_reference_dataset( - ht: hl.Table, - reference_genome: ReferenceGenome, - additional_selects: dict, - chrom_field: str = 'chrom', - start_field: str = 'start', - end_field: str = 'end', -) -> hl.Table: - ht = ht.select( - interval=hl.locus_interval( - ht[chrom_field], - ht[start_field] + 1, - ht[end_field] + 1, - reference_genome=reference_genome.value, - invalid_missing=True, - ), - **additional_selects, - ) - return ht.key_by('interval') - - -def copy_to_cloud_storage(file_name: str) -> str: - if not Env.HAIL_TMP_DIR.startswith('gs://'): - return file_name - if os.path.isdir(file_name): - cloud_storage_path = os.path.join(Env.HAIL_TMP_DIR, file_name.lstrip('/')) - else: - cloud_storage_path = os.path.join(Env.HAIL_TMP_DIR, os.path.basename(file_name)) - hfs.copy(file_name, cloud_storage_path) - return cloud_storage_path From c1bc2ae0cf0fa3a18c39c9682c9eeeb5aaee0a5b Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 1 Sep 2026 14:04:58 -0400 Subject: [PATCH 317/369] remove unused constants --- loading_pipeline/lib/annotations/snv_indel.py | 3 --- loading_pipeline/lib/core/dataset_type.py | 3 --- loading_pipeline/lib/misc/pedigree.py | 1 - loading_pipeline/lib/tasks/exports/fields.py | 1 - 4 files changed, 8 deletions(-) diff --git a/loading_pipeline/lib/annotations/snv_indel.py b/loading_pipeline/lib/annotations/snv_indel.py index 0d785830fe..cb162ce79a 100644 --- a/loading_pipeline/lib/annotations/snv_indel.py +++ b/loading_pipeline/lib/annotations/snv_indel.py @@ -19,9 +19,6 @@ MOTIF_CONSEQUENCE_TERMS_LOOKUP = hl.dict( hl.enumerate(MOTIF_CONSEQUENCE_TERMS, index_first=False), ) -REGULATORY_BIOTYPE_LOOKUP = hl.dict( - hl.enumerate(REGULATORY_BIOTYPES, index_first=False), -) REGULATORY_CONSEQUENCE_TERMS_LOOKUP = hl.dict( hl.enumerate(REGULATORY_CONSEQUENCE_TERMS, index_first=False), ) diff --git a/loading_pipeline/lib/core/dataset_type.py b/loading_pipeline/lib/core/dataset_type.py index 93c14f7131..e9bccc99f6 100644 --- a/loading_pipeline/lib/core/dataset_type.py +++ b/loading_pipeline/lib/core/dataset_type.py @@ -7,9 +7,6 @@ from loading_pipeline.lib.core.definitions import ReferenceGenome from loading_pipeline.lib.core.environment import Env -MITO_MIN_HOM_THRESHOLD = 0.95 -ZERO = 0.0 - class DatasetType(StrEnum): GCNV = 'GCNV' diff --git a/loading_pipeline/lib/misc/pedigree.py b/loading_pipeline/lib/misc/pedigree.py index 50bc30e225..5950e6cf09 100644 --- a/loading_pipeline/lib/misc/pedigree.py +++ b/loading_pipeline/lib/misc/pedigree.py @@ -8,7 +8,6 @@ from loading_pipeline.lib.core import Sex DEFAULT_RELATEDNESS_TOLERANCE = 0.2 -PARENT_CHILD_RELATEDNESS_TOLERANCE = 0.4 class Relation(Enum): diff --git a/loading_pipeline/lib/tasks/exports/fields.py b/loading_pipeline/lib/tasks/exports/fields.py index e5a39d8212..a2034bd761 100644 --- a/loading_pipeline/lib/tasks/exports/fields.py +++ b/loading_pipeline/lib/tasks/exports/fields.py @@ -6,7 +6,6 @@ snake_to_camelcase, ) -FIVE_PERCENT = 0.05 STANDARD_CONTIGS = hl.set( [c.replace('MT', 'M') for c in ReferenceGenome.GRCh37.standard_contigs], ) From a6594914c2ff48631dd055f9f247c0d28ff02250 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 1 Sep 2026 14:15:10 -0400 Subject: [PATCH 318/369] add missing consequence validation --- loading_pipeline/lib/annotations/sv.py | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/loading_pipeline/lib/annotations/sv.py b/loading_pipeline/lib/annotations/sv.py index cfc99fe025..fd13c44314 100644 --- a/loading_pipeline/lib/annotations/sv.py +++ b/loading_pipeline/lib/annotations/sv.py @@ -5,6 +5,7 @@ from loading_pipeline.lib.annotations import liftover from loading_pipeline.lib.annotations.enums import ( + SV_CONSEQUENCE_RANKS, SV_TYPE_DETAILS, SV_TYPES, validated_enum_member, @@ -210,7 +211,10 @@ def sorted_gene_consequences( ht[gene_col].map( lambda gene: hl.struct( gene_id=gencode_gene_symbol_to_gene_id_mapping.get(gene), - major_consequence=gene_col.replace(CONSEQ_PREDICTED_PREFIX, '', 1), # noqa: B023 + major_consequence=validated_enum_member( + gene_col.replace(CONSEQ_PREDICTED_PREFIX, '', 1), # noqa: B023 + SV_CONSEQUENCE_RANKS, + ), ), ) for gene_col in CONSEQ_PREDICTED_GENE_COLS From 4a871cd392179034ada2f5de4e52c8c316dd68c7 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 1 Sep 2026 14:32:47 -0400 Subject: [PATCH 319/369] update comment --- loading_pipeline/lib/misc/runs_test.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/loading_pipeline/lib/misc/runs_test.py b/loading_pipeline/lib/misc/runs_test.py index 7ba80e9353..48a0e34d3c 100644 --- a/loading_pipeline/lib/misc/runs_test.py +++ b/loading_pipeline/lib/misc/runs_test.py @@ -15,7 +15,7 @@ def setUp(self): run_ids = [ 'manual__2024-08-05T16-07-58.365146+00-00', 'manual__2024-08-06T10-15-23.123456+00-00', - 'manual__2024-08-07T12-30-45.654321+00-00', # _SUCCESS, _CLICKHOUSE_LOAD_FAIL + 'manual__2024-08-07T12-30-45.654321+00-00', # _SUCCESS 'manual__2024-08-08T09-45-00.000000+00-00', # _SUCCESS 'manual__2024-08-09T18-22-13.999999+00-00', # _SUCCESS, _CLICKHOUSE_LOAD_SUCCESS ] From e8efef77f39ace7126250d4dc01c6b828ffb111a Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 1 Sep 2026 14:45:30 -0400 Subject: [PATCH 320/369] remove unused HTs --- .../WES/R0113_test_project.ht/.README.txt.crc | Bin 12 -> 0 bytes .../WES/R0113_test_project.ht/._SUCCESS.crc | Bin 8 -> 0 bytes .../R0113_test_project.ht/.metadata.json.gz.crc | Bin 12 -> 0 bytes .../projects/WES/R0113_test_project.ht/README.txt | 3 --- .../projects/WES/R0113_test_project.ht/_SUCCESS | 0 .../globals/.metadata.json.gz.crc | Bin 12 -> 0 bytes .../globals/metadata.json.gz | Bin 360 -> 0 bytes .../globals/parts/.part-0.crc | Bin 16 -> 0 bytes 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a/loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/projects/WGS/R0113_test_project.ht/rows/parts/.part-0-01ea3c88-7ee4-4f38-8f70-3beed717e195.crc b/loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/projects/WGS/R0113_test_project.ht/rows/parts/.part-0-01ea3c88-7ee4-4f38-8f70-3beed717e195.crc deleted file mode 100644 index ba689d45dbed0cc06d3fbcd110a76ecdb7962082..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 12 TcmYc;N@ieSU}C7)ChQ6T5$yuO diff --git a/loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/projects/WGS/R0113_test_project.ht/rows/parts/part-0-01ea3c88-7ee4-4f38-8f70-3beed717e195 b/loading_pipeline/var/test/exports/GRCh37/SNV_INDEL/projects/WGS/R0113_test_project.ht/rows/parts/part-0-01ea3c88-7ee4-4f38-8f70-3beed717e195 deleted file mode 100644 index 2eae906078710daff47af9aa35a25bca35b0a5c4..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 129 zcmc~{U|@&`VvVi(e-+|?GBGeRFdFvFVF5B68QmEfq{9M(gF=cD^O7@CgZ%<5E%hu7 zO7aa24D<{PbpG%E|NlQbGamy3Cj&!+J+lad7SJdLJ{D#M9uR|-g+UrbbFnb!oIP{K Rj+KXj7sLkwuzf(w7yw^v8P@;+ From b893af3bdfa1e7037676e371150c4f7f007d43b7 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 1 Sep 2026 15:21:41 -0400 Subject: [PATCH 321/369] rewrite remap subset task for all projects --- .../write_remapped_and_subsetted_callset.py | 37 ++++++++++--------- 1 file changed, 19 insertions(+), 18 deletions(-) diff --git a/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py b/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py index 403c9d78d5..b102971a98 100644 --- a/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py +++ b/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py @@ -50,24 +50,22 @@ def format_failures(failed_families): @luigi.util.inherits(BaseLoadingRunParams) class WriteRemappedAndSubsettedCallsetTask(BaseWriteTask): - project_i = luigi.IntParameter() - def complete(self) -> luigi.Target: if not super().complete(): return False mt = hl.read_matrix_table(self.output().path) + remap_pedigree_hashes = hl.eval(mt.globals.remap_pedigree_hashes) return bool( hl.eval(mt.globals.family_samples), - ) and hl.eval( - mt.globals.remap_pedigree_hash - == remap_pedigree_hash( + ) and len(remap_pedigree_hashes) == len(self.project_guids) and all( + remap_pedigree_hashes[i] == remap_pedigree_hash( project_pedigree_path( self.reference_genome, self.dataset_type, self.sample_type, - self.project_guids[self.project_i], + project_guid, ), - ), + ) for i, project_guid in enumerate(self.project_guids) ) def output(self) -> luigi.Target: @@ -76,21 +74,22 @@ def output(self) -> luigi.Target: self.reference_genome, self.dataset_type, self.callset_path, - self.project_guids[self.project_i], ), ) def requires(self) -> list[luigi.Task]: requirements = [ self.clone(ValidateCallsetTask), + ] + requirements += [ RawFileTask( project_pedigree_path( self.reference_genome, self.dataset_type, self.sample_type, - self.project_guids[self.project_i], + project_guid, ), - ), + ) for project_guid in self.project_guids ] if ( FeatureFlag.CHECK_SEX_AND_RELATEDNESS @@ -206,14 +205,16 @@ def create_table(self) -> hl.MatrixTable: if self.dataset_type.overwrite_male_non_par_calls: mt = overwrite_male_non_par_calls(mt, loadable_families) return mt.select_globals( - remap_pedigree_hash=remap_pedigree_hash( - project_pedigree_path( - self.reference_genome, - self.dataset_type, - self.sample_type, - self.project_guids[self.project_i], - ), - ), + remap_pedigree_hashes=[ + remap_pedigree_hash( + project_pedigree_path( + self.reference_genome, + self.dataset_type, + self.sample_type, + project_guid, + ), + ) for project_guid in self.project_guids + ], family_samples=( { f.family_guid: sorted(f.samples.keys()) From 7c8059788b34e9155b7950d4f80d461454f37efa Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 1 Sep 2026 15:33:25 -0400 Subject: [PATCH 322/369] update parsing to actually work for multiple projects --- .../write_remapped_and_subsetted_callset.py | 24 ++++++++++++------- 1 file changed, 15 insertions(+), 9 deletions(-) diff --git a/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py b/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py index b102971a98..fa68e66207 100644 --- a/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py +++ b/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py @@ -106,21 +106,24 @@ def requires(self) -> list[luigi.Task]: @with_persisted_validation_errors def create_table(self) -> hl.MatrixTable: callset_mt = hl.read_matrix_table(self.input()[0].path) - pedigree_ht = import_pedigree(self.input()[1].path) # Remap, but only if the remap file is present! - remap_lookup = hl.empty_dict(hl.tstr, hl.tstr) - if 'remap_id' in pedigree_ht.row: - project_remap_ht = parse_pedigree_ht_to_remap_ht(pedigree_ht) + remap_ht = None + families = set() + for i in enumerate(self.project_guids): + pedigree_ht = import_pedigree(self.input()[i + 1].path) + if 'remap_id' in pedigree_ht.row: + project_remap_ht = parse_pedigree_ht_to_remap_ht(pedigree_ht) + remap_ht = remap_ht.union(project_remap_ht) if remap_ht is not None else project_remap_ht + + families.update(parse_pedigree_ht_to_families(pedigree_ht)) + + if remap_ht is not None: callset_mt = remap_sample_ids( callset_mt, - project_remap_ht, - ) - remap_lookup = hl.dict( - {r.s: r.seqr_id for r in project_remap_ht.collect()}, + remap_ht, ) - families = parse_pedigree_ht_to_families(pedigree_ht) families_failed_missing_samples = get_families_failed_missing_samples( callset_mt, families, @@ -133,6 +136,9 @@ def create_table(self) -> hl.MatrixTable: and self.dataset_type.check_sex_and_relatedness and not self.skip_check_sex_and_relatedness ): + remap_lookup = hl.dict( + {r.s: r.seqr_id for r in remap_ht.collect()}, + ) if remap_ht is not None else hl.empty_dict(hl.tstr, hl.tstr) relatedness_check_ht = hl.read_table( relatedness_check_table_path( self.reference_genome, From 4564f6b3714c1080cc3a5fd735f4bcb9310224a1 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 1 Sep 2026 15:51:25 -0400 Subject: [PATCH 323/369] updates to reading subsetted callset --- loading_pipeline/lib/misc/callsets.py | 78 +---------------- loading_pipeline/lib/misc/callsets_test.py | 87 ------------------- loading_pipeline/lib/paths.py | 2 - loading_pipeline/lib/paths_test.py | 6 +- .../write_new_variants_parquet_test.py | 1 - .../lib/tasks/write_new_variants_table.py | 15 ++-- .../lib/tasks/write_sample_qc_json.py | 16 ++-- 7 files changed, 19 insertions(+), 186 deletions(-) delete mode 100644 loading_pipeline/lib/misc/callsets_test.py diff --git a/loading_pipeline/lib/misc/callsets.py b/loading_pipeline/lib/misc/callsets.py index 1891d7f8dd..a0cf771a4a 100644 --- a/loading_pipeline/lib/misc/callsets.py +++ b/loading_pipeline/lib/misc/callsets.py @@ -1,82 +1,6 @@ -import functools - import hail as hl -from loading_pipeline.lib.core import DatasetType, ReferenceGenome -from loading_pipeline.lib.paths import remapped_and_subsetted_callset_path - - -def get_callset_ht( - reference_genome: ReferenceGenome, - dataset_type: DatasetType, - callset_path: str, - project_guids: list[str], -): - callset_hts = [ - hl.read_matrix_table( - remapped_and_subsetted_callset_path( - reference_genome, - dataset_type, - callset_path, - project_guid, - ), - ).rows() - for project_guid in project_guids - ] - callset_ht = functools.reduce( - (lambda ht1, ht2: ht1.union(ht2)), - callset_hts, - ) - return callset_ht.distinct() - - -def union_callset_mts(callset_mts): - """Merge multiple callset matrix tables into a single matrix table. - - Combines callset matrix tables from multiple projects by unioning the column - dimension (samples/individuals). Uses an outer join on rows (variants) to - preserve all unique variants across all callsets, with missing genotypes - filled in as appropriate. Row fields are deduplicated by keeping only the - left table's row metadata. - - Args: - callset_mts: A sequence of Hail matrix tables to merge. - - Returns: - A single matrix table containing all samples and variants from the input - callsets, with row and entry fields merged. - """ - return functools.reduce( - ( - lambda mt1, mt2: mt1.union_cols( - mt2, - row_join_type='outer', - drop_right_row_fields=True, - ) - ), - callset_mts, - ) - - -def get_callset_mt( - reference_genome: ReferenceGenome, - dataset_type: DatasetType, - callset_path: str, - project_guids: list[str], -): - callset_mts = [ - hl.read_matrix_table( - remapped_and_subsetted_callset_path( - reference_genome, - dataset_type, - callset_path, - project_guid, - ), - ) - for project_guid in project_guids - ] - callset_mt = union_callset_mts(callset_mts) - return callset_mt.distinct_by_row() +from loading_pipeline.lib.core import DatasetType def get_additional_row_fields( diff --git a/loading_pipeline/lib/misc/callsets_test.py b/loading_pipeline/lib/misc/callsets_test.py deleted file mode 100644 index 5db2d4eb36..0000000000 --- a/loading_pipeline/lib/misc/callsets_test.py +++ /dev/null @@ -1,87 +0,0 @@ -import unittest - -import hail as hl - -from loading_pipeline.lib.misc.callsets import union_callset_mts - - -class CallsetsTest(unittest.TestCase): - def test_union_callset_mts(self) -> None: - mt1 = ( - hl.MatrixTable.from_parts( - rows={ - 'id': [ - 0, - 1, - ], - 'row_field': [ - 1, - 2, - ], - }, - cols={'s': ['sample_1']}, - entries={ - 'GT': [[hl.Call([0, 0])], [hl.Call([0, 0])]], - }, - ) - .key_rows_by('id') - .key_cols_by('s') - .drop('row_idx', 'col_idx') - ) - mt2 = ( - hl.MatrixTable.from_parts( - rows={ - 'id': [ - 0, - 2, - ], - 'row_field': [ - 2, - 3, - ], - 'second_row_field': [ - 4, - 5, - ], - }, - cols={'s': ['sample_2']}, - entries={ - 'GT': [[hl.Call([0, 0])], [hl.Call([0, 1])]], - }, - ) - .key_rows_by('id') - .key_cols_by('s') - .drop('row_idx', 'col_idx') - ) - mt = union_callset_mts([mt1, mt2]) - self.assertEqual( - mt.entries().collect(), - [ - hl.Struct( - id=0, - row_field=1, - s='sample_1', - GT=hl.Call(alleles=[0, 0], phased=False), - ), - hl.Struct( - id=0, - row_field=1, - s='sample_2', - GT=hl.Call(alleles=[0, 0], phased=False), - ), - hl.Struct( - id=1, - row_field=2, - s='sample_1', - GT=hl.Call(alleles=[0, 0], phased=False), - ), - hl.Struct(id=1, row_field=2, s='sample_2', GT=None), - hl.Struct(id=2, row_field=None, s='sample_1', GT=None), - hl.Struct( - id=2, - row_field=None, - s='sample_2', - GT=hl.Call(alleles=[0, 1], phased=False), - ), - ], - ) diff --git a/loading_pipeline/lib/paths.py b/loading_pipeline/lib/paths.py index 8c1a170f3c..cfecff7108 100644 --- a/loading_pipeline/lib/paths.py +++ b/loading_pipeline/lib/paths.py @@ -197,7 +197,6 @@ def remapped_and_subsetted_callset_path( reference_genome: ReferenceGenome, dataset_type: DatasetType, callset_path: str, - project_guid: str, ) -> str: return os.path.join( pipeline_prefix( @@ -206,7 +205,6 @@ def remapped_and_subsetted_callset_path( dataset_type, ), 'remapped_and_subsetted_callsets', - project_guid, f'{_callset_path_hash(callset_path)}.mt', ) diff --git a/loading_pipeline/lib/paths_test.py b/loading_pipeline/lib/paths_test.py index 29294856ed..3803bdb92a 100644 --- a/loading_pipeline/lib/paths_test.py +++ b/loading_pipeline/lib/paths_test.py @@ -81,18 +81,16 @@ def test_remapped_and_subsetted_callset_path(self) -> None: ReferenceGenome.GRCh38, DatasetType.GCNV, '/var/abc.efg/callset.vcf.gz', - 'R0111_tgg_bblanken_wes', ), - '/var/seqr/seqr-loading-temp/GRCh38/GCNV/remapped_and_subsetted_callsets/R0111_tgg_bblanken_wes/f92b8ab6b5b8c41fa20d7d49a5626b96dcd2ba79fa6f61eab7ffb80d550d951c.mt', + '/var/seqr/seqr-loading-temp/GRCh38/GCNV/remapped_and_subsetted_callsets/f92b8ab6b5b8c41fa20d7d49a5626b96dcd2ba79fa6f61eab7ffb80d550d951c.mt', ) self.assertEqual( remapped_and_subsetted_callset_path( ReferenceGenome.GRCh38, DatasetType.GCNV, '/var/abc.efg/callset/*.vcf.gz', - 'R0111_tgg_bblanken_wes', ), - '/var/seqr/seqr-loading-temp/GRCh38/GCNV/remapped_and_subsetted_callsets/R0111_tgg_bblanken_wes/26f481b386721f9889250c6549905660728ec9f77be4b8f7eeb6c4facc76282e.mt', + '/var/seqr/seqr-loading-temp/GRCh38/GCNV/remapped_and_subsetted_callsets/26f481b386721f9889250c6549905660728ec9f77be4b8f7eeb6c4facc76282e.mt', ) def test_imported_callset_path(self) -> None: diff --git a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py index 4723729409..8fb2acee29 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py @@ -188,7 +188,6 @@ def setUp(self) -> None: ReferenceGenome.GRCh38, DatasetType.GCNV, 'fake_callset', - 'fake_project', ), ) diff --git a/loading_pipeline/lib/tasks/write_new_variants_table.py b/loading_pipeline/lib/tasks/write_new_variants_table.py index 19b0ed2b3d..18c8887716 100644 --- a/loading_pipeline/lib/tasks/write_new_variants_table.py +++ b/loading_pipeline/lib/tasks/write_new_variants_table.py @@ -5,7 +5,6 @@ import luigi.util from loading_pipeline.lib.annotations.fields import get_fields -from loading_pipeline.lib.misc.callsets import get_callset_ht from loading_pipeline.lib.misc.io import checkpoint, import_parquet, remap_pedigree_hash from loading_pipeline.lib.misc.math import constrain from loading_pipeline.lib.misc.vep import run_vep @@ -13,6 +12,7 @@ existing_variants_parquet_path, new_variants_table_path, project_pedigree_path, + remapped_and_subsetted_callset_path, valid_reference_dataset_path, ) from loading_pipeline.lib.reference_datasets.gencode.mapping_gene_ids import ( @@ -111,12 +111,13 @@ def complete(self) -> bool: ) def create_table(self) -> hl.Table: - callset_ht = get_callset_ht( - self.reference_genome, - self.dataset_type, - self.callset_path, - self.project_guids, - ) + callset_ht = hl.read_matrix_table( + remapped_and_subsetted_callset_path( + self.reference_genome, + self.dataset_type, + self.callset_path, + ), + ).rows() # 1) Identify new variants. annotations_ht = import_parquet( diff --git a/loading_pipeline/lib/tasks/write_sample_qc_json.py b/loading_pipeline/lib/tasks/write_sample_qc_json.py index e09c93086f..dc14822580 100644 --- a/loading_pipeline/lib/tasks/write_sample_qc_json.py +++ b/loading_pipeline/lib/tasks/write_sample_qc_json.py @@ -8,10 +8,10 @@ import onnx from loading_pipeline.lib.methods.sample_qc import call_sample_qc -from loading_pipeline.lib.misc.callsets import get_callset_mt -from loading_pipeline.lib.misc.io import checkpoint, import_tdr_qc_metrics +from loading_pipeline.lib.misc.io import import_tdr_qc_metrics from loading_pipeline.lib.paths import ( ancestry_model_rf_path, + remapped_and_subsetted_callset_path, sample_qc_json_path, tdr_metrics_dir, ) @@ -57,13 +57,13 @@ def requires(self): ] def run(self): - callset_mt = get_callset_mt( - self.reference_genome, - self.dataset_type, - self.callset_path, - self.project_guids, + callset_mt = hl.read_matrix_table( + remapped_and_subsetted_callset_path( + self.reference_genome, + self.dataset_type, + self.callset_path, + ), ) - callset_mt, _ = checkpoint(callset_mt) tdr_metrics_ht = None for tdr_metrics_file in hfs.ls( tdr_metrics_dir(self.reference_genome, self.dataset_type), From 1bf7c9eed611a2230901a3ba57764a451a482b75 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 1 Sep 2026 16:10:03 -0400 Subject: [PATCH 324/369] use updated single task --- .../exports/write_new_entries_parquet.py | 54 ++++--------------- .../lib/tasks/write_metadata_for_run.py | 8 +-- .../lib/tasks/write_sample_qc_json.py | 18 +------ 3 files changed, 14 insertions(+), 66 deletions(-) diff --git a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py index 5e45fccbce..c193a5e32d 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py +++ b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py @@ -11,9 +11,7 @@ ) from loading_pipeline.lib.misc.io import import_parquet from loading_pipeline.lib.paths import ( - existing_variants_parquet_path, new_entries_parquet_path, - new_variants_table_path, ) from loading_pipeline.lib.tasks.base.base_loading_run_params import ( BaseLoadingRunParams, @@ -35,10 +33,6 @@ WriteRemappedAndSubsettedCallsetTask, ) -EXISTING_VARIANTS_TASK = 'existing_variant_task' -VARIANTS_TABLE_TASK = 'variants_table_task' -REMAPPED_AND_SUBSETTED_CALLSET_TASKS = 'remapped_and_subsetted_callset_tasks' - @luigi.util.inherits(BaseLoadingRunParams) class WriteNewEntriesParquetTask(BaseWriteParquetTask): @@ -52,32 +46,14 @@ def output(self) -> luigi.Target: ) def requires(self) -> dict[str, luigi.Task]: - return { - EXISTING_VARIANTS_TASK: self.clone( - WriteExistingVariantsParquetTask, - ), - VARIANTS_TABLE_TASK: self.clone( - WriteNewVariantsTableTask, - ), - REMAPPED_AND_SUBSETTED_CALLSET_TASKS: [ - self.clone( - WriteRemappedAndSubsettedCallsetTask, - project_i=i, - ) - for i in range(len(self.project_guids)) - ], - } + return [ + self.clone(WriteExistingVariantsParquetTask), + self.clone(WriteNewVariantsTableTask), + self.clone(WriteRemappedAndSubsettedCallsetTask), + ] def create_table(self) -> None: - unioned_ht = None - - annotations_ht = hl.read_table( - new_variants_table_path( - self.reference_genome, - self.dataset_type, - self.run_id, - ), - ) + annotations_ht = hl.read_table(self.input()[1].path) annotation_selects = { field: func(annotations_ht) for field, func in { @@ -88,11 +64,7 @@ def create_table(self) -> None: annotations_ht = annotations_ht.select(**annotation_selects) existing_annotations_ht = import_parquet( - existing_variants_parquet_path( - self.reference_genome, - self.dataset_type, - self.run_id, - ), + self.input()[0].path, self.reference_genome, self.dataset_type, ) @@ -113,12 +85,9 @@ def create_table(self) -> None: existing_annotations_ht.select(*annotation_selects), ) - for project_guid, remapped_and_subsetted_callset_task in zip( - self.project_guids, - self.input()[REMAPPED_AND_SUBSETTED_CALLSET_TASKS], - strict=True, - ): - mt = hl.read_matrix_table(remapped_and_subsetted_callset_task.path) + for project_guid in self.project_guids: + # TODO remove loop + mt = hl.read_matrix_table(self.input()[2].path) ht = compute_callset_family_entries_ht( self.dataset_type, mt, @@ -147,5 +116,4 @@ def create_table(self) -> None: project_guid, ), ) - unioned_ht = unioned_ht.union(ht) if unioned_ht else ht - return unioned_ht + return ht diff --git a/loading_pipeline/lib/tasks/write_metadata_for_run.py b/loading_pipeline/lib/tasks/write_metadata_for_run.py index a20f44cd59..2bace006a7 100644 --- a/loading_pipeline/lib/tasks/write_metadata_for_run.py +++ b/loading_pipeline/lib/tasks/write_metadata_for_run.py @@ -33,13 +33,7 @@ def output(self) -> luigi.Target: ) def requires(self) -> list[luigi.Task]: - requirements = [ - self.clone( - WriteRemappedAndSubsettedCallsetTask, - project_i=i, - ) - for i in range(len(self.project_guids)) - ] + requirements = [self.clone(WriteRemappedAndSubsettedCallsetTask)] if ( FeatureFlag.EXPECT_TDR_METRICS and not self.skip_expect_tdr_metrics diff --git a/loading_pipeline/lib/tasks/write_sample_qc_json.py b/loading_pipeline/lib/tasks/write_sample_qc_json.py index dc14822580..88f3dff8b4 100644 --- a/loading_pipeline/lib/tasks/write_sample_qc_json.py +++ b/loading_pipeline/lib/tasks/write_sample_qc_json.py @@ -11,7 +11,6 @@ from loading_pipeline.lib.misc.io import import_tdr_qc_metrics from loading_pipeline.lib.paths import ( ancestry_model_rf_path, - remapped_and_subsetted_callset_path, sample_qc_json_path, tdr_metrics_dir, ) @@ -39,13 +38,6 @@ def output(self) -> luigi.Target: ) def requires(self): - remapped_and_subsetted_callsets = [ - self.clone( - WriteRemappedAndSubsettedCallsetTask, - project_i=i, - ) - for i in range(len(self.project_guids)) - ] return [ self.clone(WriteTDRMetricsFilesTask), self.clone( @@ -53,17 +45,11 @@ def requires(self): reference_dataset=ReferenceDataset.gnomad_qc, ), RawFileTask(ancestry_model_rf_path()), - *remapped_and_subsetted_callsets, + self.clone(WriteRemappedAndSubsettedCallsetTask), ] def run(self): - callset_mt = hl.read_matrix_table( - remapped_and_subsetted_callset_path( - self.reference_genome, - self.dataset_type, - self.callset_path, - ), - ) + callset_mt = hl.read_matrix_table(self.input()[3].path) tdr_metrics_ht = None for tdr_metrics_file in hfs.ls( tdr_metrics_dir(self.reference_genome, self.dataset_type), From 0bf0bed307a95c3f97bc8eb838004418c880b75c Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 1 Sep 2026 16:37:15 -0400 Subject: [PATCH 325/369] use single callset for entries parquet --- loading_pipeline/lib/misc/family_entries.py | 18 +++++- loading_pipeline/lib/tasks/exports/fields.py | 3 +- .../exports/write_new_entries_parquet.py | 56 +++++++++---------- .../write_remapped_and_subsetted_callset.py | 8 ++- 4 files changed, 48 insertions(+), 37 deletions(-) diff --git a/loading_pipeline/lib/misc/family_entries.py b/loading_pipeline/lib/misc/family_entries.py index 114f1dc2f9..03b4b8bf94 100644 --- a/loading_pipeline/lib/misc/family_entries.py +++ b/loading_pipeline/lib/misc/family_entries.py @@ -15,6 +15,13 @@ def compute_callset_family_entries_ht( for s in sample_ids }, ) + family_guid_to_project_guid = hl.dict( + { + family_guid: project_guid + for project_guid, family_guids in hl.eval(mt.project_families).items() + for family_guid in family_guids + }, + ) ht = mt.select_rows( filters=mt.filters.difference(dataset_type.excluded_filters), family_entries=( @@ -26,6 +33,7 @@ def compute_callset_family_entries_ht( hl.Struct( s=mt.s, family_guid=sample_id_to_family_guid[mt.s], + project_guid=family_guid_to_project_guid[sample_id_to_family_guid[mt.s]], **entries_fields, ), ) @@ -58,6 +66,11 @@ def globalize_ids(ht: hl.Table) -> hl.Table: row = ht.take(1)[0] if ht.count() > 0 else None has_family_entries = row and len(row.family_entries) > 0 ht = ht.annotate_globals( + project_guids=( + [fe[0].project_guid for fe in row.family_entries] + if has_family_entries + else hl.empty_array(hl.tstr) + ), family_guids=( [fe[0].family_guid for fe in row.family_entries] if has_family_entries @@ -71,7 +84,7 @@ def globalize_ids(ht: hl.Table) -> hl.Table: ) return ht.annotate( family_entries=ht.family_entries.map( - lambda fe: fe.map(lambda se: se.drop('s', 'family_guid')), + lambda fe: fe.map(lambda se: se.drop('s', 'family_guid', 'project_guid')), ), ) @@ -85,12 +98,13 @@ def deglobalize_ids(ht: hl.Table) -> hl.Table: **e, s=ht.family_samples[ht.family_guids[i]][j], family_guid=ht.family_guids[i], + project_guid=ht.project_guids[i], ), ), ) ), ) - return ht.drop('family_guids', 'family_samples') + return ht.drop('family_guids', 'family_samples', 'project_guids') def deduplicate_by_most_non_ref_calls(ht: hl.Table) -> hl.Table: diff --git a/loading_pipeline/lib/tasks/exports/fields.py b/loading_pipeline/lib/tasks/exports/fields.py index e5a39d8212..bc6d6de6bc 100644 --- a/loading_pipeline/lib/tasks/exports/fields.py +++ b/loading_pipeline/lib/tasks/exports/fields.py @@ -182,10 +182,9 @@ def get_entries_export_fields( ht: hl.Table, dataset_type: DatasetType, sample_type: SampleType, - project_guid: str, ): return { - 'project_guid': project_guid, + 'project_guid': ht.family_entries.project_guid[0], 'family_guid': ht.family_entries.family_guid[0], **{ field: getattr(ht, field) diff --git a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py index c193a5e32d..2762d9970a 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py +++ b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py @@ -85,35 +85,31 @@ def create_table(self) -> None: existing_annotations_ht.select(*annotation_selects), ) - for project_guid in self.project_guids: - # TODO remove loop - mt = hl.read_matrix_table(self.input()[2].path) - ht = compute_callset_family_entries_ht( - self.dataset_type, + mt = hl.read_matrix_table(self.input()[2].path) + ht = compute_callset_family_entries_ht( + self.dataset_type, + mt, + get_fields( mt, - get_fields( - mt, - self.dataset_type.genotype_entry_annotation_fns, - **self.param_kwargs, - ), - ) - ht = deglobalize_ids(ht) - ht = deduplicate_by_most_non_ref_calls(ht) - ht = ht.join(annotations_ht) + self.dataset_type.genotype_entry_annotation_fns, + **self.param_kwargs, + ), + ) + ht = deglobalize_ids(ht) + ht = deduplicate_by_most_non_ref_calls(ht) + ht = ht.join(annotations_ht) - # the family entries ht will contain rows - # where at least one family is defined... after explosion, - # rows where a family is not defined should be removed. - ht = ht.explode(ht.family_entries) - ht = ht.filter(hl.is_defined(ht.family_entries)) - ht = ht.key_by() - ht = ht.select_globals() - ht = ht.select( - **get_entries_export_fields( - ht, - self.dataset_type, - self.sample_type, - project_guid, - ), - ) - return ht + # the family entries ht will contain rows + # where at least one family is defined... after explosion, + # rows where a family is not defined should be removed. + ht = ht.explode(ht.family_entries) + ht = ht.filter(hl.is_defined(ht.family_entries)) + ht = ht.key_by() + ht = ht.select_globals() + return ht.select( + **get_entries_export_fields( + ht, + self.dataset_type, + self.sample_type, + ), + ) diff --git a/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py b/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py index fa68e66207..cd588bb44d 100644 --- a/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py +++ b/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py @@ -109,14 +109,14 @@ def create_table(self) -> hl.MatrixTable: # Remap, but only if the remap file is present! remap_ht = None - families = set() - for i in enumerate(self.project_guids): + project_families = {} + for i, project_guid in enumerate(self.project_guids): pedigree_ht = import_pedigree(self.input()[i + 1].path) if 'remap_id' in pedigree_ht.row: project_remap_ht = parse_pedigree_ht_to_remap_ht(pedigree_ht) remap_ht = remap_ht.union(project_remap_ht) if remap_ht is not None else project_remap_ht - families.update(parse_pedigree_ht_to_families(pedigree_ht)) + project_families[project_guid] = parse_pedigree_ht_to_families(pedigree_ht) if remap_ht is not None: callset_mt = remap_sample_ids( @@ -124,6 +124,7 @@ def create_table(self) -> hl.MatrixTable: remap_ht, ) + families = {f for families in project_families.values() for f in families} families_failed_missing_samples = get_families_failed_missing_samples( callset_mt, families, @@ -246,4 +247,5 @@ def create_table(self) -> hl.MatrixTable: or hl.empty_dict(hl.tstr, hl.tdict(hl.tstr, hl.tarray(hl.tstr))) ), ), + project_families=project_families, ) From ac056e05c1d6099a690d57c82cb1092bcb469f9b Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 1 Sep 2026 17:13:23 -0400 Subject: [PATCH 326/369] add more testing around exported entries --- .../exports/write_new_entries_parquet_test.py | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) diff --git a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py index 6caa4daead..c71159d36a 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py @@ -128,6 +128,26 @@ def test_write_new_entries_parquet(self): ), ) export_json = convert_ndarray_to_list(df.to_dict('records')) + self.assertEqual(len(export_json), 183) + self.assertEqual( + df['family_guid'].value_counts().to_dict(), + { + 'abc_1': 17, + '789_1': 15, + '890_1': 14, + '901_1': 14, + 'bcd_1': 14, + '345_1': 13, + '456_1': 13, + '567_1': 13, + 'def_1': 13, + '123_1': 12, + '234_1': 12, + '678_1': 11, + 'cde_1': 11, + 'efg_1': 11, + }, + ) self.assertEqual( export_json[:2], [ @@ -193,6 +213,28 @@ def test_write_new_entries_parquet(self): }, ], ) + self.assertEqual( + export_json[17], + { + 'key': 0, + 'project_guid': 'R0114_project4', + 'family_guid': '123_1', + 'sample_type': 'WGS', + 'xpos': 1000876499, + 'geneIds': ['ENSG00000187634'], + 'filters': [], + 'calls': [ + { + 'sampleId': 'NA19675_1', + 'gt': 2, + 'gq': 15, + 'ab': 1.0, + 'dp': 5, + }, + ], + 'sign': 1, + }, + ) def test_mito_write_new_entries_parquet(self): copy_project_pedigree_to_mocked_dir( From 77b232ba76672e13779e35a58d89fd98ac3e9fcf Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 1 Sep 2026 17:17:34 -0400 Subject: [PATCH 327/369] ruff; --- loading_pipeline/lib/misc/family_entries.py | 4 +- .../write_remapped_and_subsetted_callset.py | 50 ++++++++++++------- 2 files changed, 36 insertions(+), 18 deletions(-) diff --git a/loading_pipeline/lib/misc/family_entries.py b/loading_pipeline/lib/misc/family_entries.py index 03b4b8bf94..8bc71af451 100644 --- a/loading_pipeline/lib/misc/family_entries.py +++ b/loading_pipeline/lib/misc/family_entries.py @@ -33,7 +33,9 @@ def compute_callset_family_entries_ht( hl.Struct( s=mt.s, family_guid=sample_id_to_family_guid[mt.s], - project_guid=family_guid_to_project_guid[sample_id_to_family_guid[mt.s]], + project_guid=family_guid_to_project_guid[ + sample_id_to_family_guid[mt.s] + ], **entries_fields, ), ) diff --git a/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py b/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py index cd588bb44d..f861ab2e4b 100644 --- a/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py +++ b/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py @@ -55,17 +55,23 @@ def complete(self) -> luigi.Target: return False mt = hl.read_matrix_table(self.output().path) remap_pedigree_hashes = hl.eval(mt.globals.remap_pedigree_hashes) - return bool( - hl.eval(mt.globals.family_samples), - ) and len(remap_pedigree_hashes) == len(self.project_guids) and all( - remap_pedigree_hashes[i] == remap_pedigree_hash( - project_pedigree_path( - self.reference_genome, - self.dataset_type, - self.sample_type, - project_guid, - ), - ) for i, project_guid in enumerate(self.project_guids) + return ( + bool( + hl.eval(mt.globals.family_samples), + ) + and len(remap_pedigree_hashes) == len(self.project_guids) + and all( + remap_pedigree_hashes[i] + == remap_pedigree_hash( + project_pedigree_path( + self.reference_genome, + self.dataset_type, + self.sample_type, + project_guid, + ), + ) + for i, project_guid in enumerate(self.project_guids) + ) ) def output(self) -> luigi.Target: @@ -89,7 +95,8 @@ def requires(self) -> list[luigi.Task]: self.sample_type, project_guid, ), - ) for project_guid in self.project_guids + ) + for project_guid in self.project_guids ] if ( FeatureFlag.CHECK_SEX_AND_RELATEDNESS @@ -114,7 +121,11 @@ def create_table(self) -> hl.MatrixTable: pedigree_ht = import_pedigree(self.input()[i + 1].path) if 'remap_id' in pedigree_ht.row: project_remap_ht = parse_pedigree_ht_to_remap_ht(pedigree_ht) - remap_ht = remap_ht.union(project_remap_ht) if remap_ht is not None else project_remap_ht + remap_ht = ( + remap_ht.union(project_remap_ht) + if remap_ht is not None + else project_remap_ht + ) project_families[project_guid] = parse_pedigree_ht_to_families(pedigree_ht) @@ -137,9 +148,13 @@ def create_table(self) -> hl.MatrixTable: and self.dataset_type.check_sex_and_relatedness and not self.skip_check_sex_and_relatedness ): - remap_lookup = hl.dict( - {r.s: r.seqr_id for r in remap_ht.collect()}, - ) if remap_ht is not None else hl.empty_dict(hl.tstr, hl.tstr) + remap_lookup = ( + hl.dict( + {r.s: r.seqr_id for r in remap_ht.collect()}, + ) + if remap_ht is not None + else hl.empty_dict(hl.tstr, hl.tstr) + ) relatedness_check_ht = hl.read_table( relatedness_check_table_path( self.reference_genome, @@ -220,7 +235,8 @@ def create_table(self) -> hl.MatrixTable: self.sample_type, project_guid, ), - ) for project_guid in self.project_guids + ) + for project_guid in self.project_guids ], family_samples=( { From b1a149de75f206fc06407aa145f3f7a289eea4a3 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 1 Sep 2026 17:25:57 -0400 Subject: [PATCH 328/369] update diagram --- loading_pipeline/docs/Diagrams.md | 14 ++++---------- 1 file changed, 4 insertions(+), 10 deletions(-) diff --git a/loading_pipeline/docs/Diagrams.md b/loading_pipeline/docs/Diagrams.md index a8e205fd31..c94f5e12f9 100644 --- a/loading_pipeline/docs/Diagrams.md +++ b/loading_pipeline/docs/Diagrams.md @@ -23,16 +23,10 @@ |_______________________________| | v - _____________________|_____________________ - | | - v v - WriteRemappedAndSubsettedCallsetTask WriteRemappedAndSubsettedCallsetTask - (Project 1) (Project N) - | | - |___________________________________________| - | - v - WriteMetadataForRunTask WriteExistingVariantsParquetTask + WriteRemappedAndSubsettedCallsetTask + | + v + WriteMetadataForRunTask WriteExistingVariantsParquetTask |___________________________________________| | v From b1021880a759153ceedbdc22073233e42800286f Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 1 Sep 2026 17:30:09 -0400 Subject: [PATCH 329/369] fix metadata global parsing --- .../lib/tasks/write_metadata_for_run.py | 52 +++++++------------ 1 file changed, 19 insertions(+), 33 deletions(-) diff --git a/loading_pipeline/lib/tasks/write_metadata_for_run.py b/loading_pipeline/lib/tasks/write_metadata_for_run.py index 2bace006a7..e71fe8d08c 100644 --- a/loading_pipeline/lib/tasks/write_metadata_for_run.py +++ b/loading_pipeline/lib/tasks/write_metadata_for_run.py @@ -67,45 +67,31 @@ def run(self) -> None: ), 'sample_qc': {}, } - sample_qc_loadable_samples = {} - # NB: the trailing WriteSampleQCJsonTask output is conditionally - # present in requires(), so slice by project count rather than - # dropping the last input. - for remapped_and_subsetted_callset in self.input()[: len(self.project_guids)]: - callset_mt = hl.read_matrix_table(remapped_and_subsetted_callset.path) - collected_globals = callset_mt.globals.collect()[0] - metadata_json['family_samples'] = { - **collected_globals['family_samples'], - **metadata_json['family_samples'], - } + callset_mt = hl.read_matrix_table(self.input()[0].path) + collected_globals = callset_mt.globals.collect()[0] + metadata_json['family_samples'] = collected_globals['family_samples'] + sample_qc_loadable_samples = { + sample + for family_samples in collected_globals['family_samples'].values() + for sample in family_samples + } + for key in [ + 'missing_samples', + 'relatedness_check', + 'sex_check', + 'ploidy_check', + ]: + metadata_json['failed_family_samples'][key] = collected_globals['failed_family_samples'][key] sample_qc_loadable_samples = { *{ sample - for family_samples in collected_globals['family_samples'].values() - for sample in family_samples + for meta in collected_globals['failed_family_samples'][ + key + ].values() + for sample in meta['samples'] }, *sample_qc_loadable_samples, } - for key in [ - 'missing_samples', - 'relatedness_check', - 'sex_check', - 'ploidy_check', - ]: - metadata_json['failed_family_samples'][key] = { - **collected_globals['failed_family_samples'][key], - **metadata_json['failed_family_samples'][key], - } - sample_qc_loadable_samples = { - *{ - sample - for meta in collected_globals['failed_family_samples'][ - key - ].values() - for sample in meta['samples'] - }, - *sample_qc_loadable_samples, - } if ( FeatureFlag.EXPECT_TDR_METRICS and not self.skip_expect_tdr_metrics From 4bf06f8a19d625e303e477cd6a2600f489e2347f Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 1 Sep 2026 17:36:13 -0400 Subject: [PATCH 330/369] annotate the global we actually want --- .../lib/tasks/write_remapped_and_subsetted_callset.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py b/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py index f861ab2e4b..552204779f 100644 --- a/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py +++ b/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py @@ -263,5 +263,8 @@ def create_table(self) -> hl.MatrixTable: or hl.empty_dict(hl.tstr, hl.tdict(hl.tstr, hl.tarray(hl.tstr))) ), ), - project_families=project_families, + project_families={ + project_guid: sorted([f.family_guid for f in families]) + for project_guid, families in project_families.items() + }, ) From 372b07f54cbd22fcb5fb28e8e01f13d1068e9ef3 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 1 Sep 2026 17:40:01 -0400 Subject: [PATCH 331/369] update test; --- loading_pipeline/lib/misc/family_entries_test.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/loading_pipeline/lib/misc/family_entries_test.py b/loading_pipeline/lib/misc/family_entries_test.py index 609fdda6d6..b94bc5706b 100644 --- a/loading_pipeline/lib/misc/family_entries_test.py +++ b/loading_pipeline/lib/misc/family_entries_test.py @@ -45,7 +45,7 @@ def test_compute_callset_family_entries_ht(self) -> None: ], ], }, - globals={'family_samples': {'2': ['a'], '1': ['b', 'c', 'd']}}, + globals={'family_samples': {'2': ['a'], '1': ['b', 'c', 'd']}, 'project_families': {'p1': ['1'], 'p2': ['2', '3']}}, ) ht = compute_callset_family_entries_ht(DatasetType.SNV_INDEL, mt, {'GT': mt.GT}) self.assertCountEqual( From 717a9311ca5d06dcc34cadb138ef6babf28c3c27 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 1 Sep 2026 17:43:43 -0400 Subject: [PATCH 332/369] ruff --- loading_pipeline/lib/misc/family_entries_test.py | 5 ++++- loading_pipeline/lib/tasks/write_metadata_for_run.py | 8 ++++---- .../lib/tasks/write_remapped_and_subsetted_callset.py | 2 +- 3 files changed, 9 insertions(+), 6 deletions(-) diff --git a/loading_pipeline/lib/misc/family_entries_test.py b/loading_pipeline/lib/misc/family_entries_test.py index b94bc5706b..76882546de 100644 --- a/loading_pipeline/lib/misc/family_entries_test.py +++ b/loading_pipeline/lib/misc/family_entries_test.py @@ -45,7 +45,10 @@ def test_compute_callset_family_entries_ht(self) -> None: ], ], }, - globals={'family_samples': {'2': ['a'], '1': ['b', 'c', 'd']}, 'project_families': {'p1': ['1'], 'p2': ['2', '3']}}, + globals={ + 'family_samples': {'2': ['a'], '1': ['b', 'c', 'd']}, + 'project_families': {'p1': ['1'], 'p2': ['2', '3']}, + }, ) ht = compute_callset_family_entries_ht(DatasetType.SNV_INDEL, mt, {'GT': mt.GT}) self.assertCountEqual( diff --git a/loading_pipeline/lib/tasks/write_metadata_for_run.py b/loading_pipeline/lib/tasks/write_metadata_for_run.py index e71fe8d08c..7f0ade79c0 100644 --- a/loading_pipeline/lib/tasks/write_metadata_for_run.py +++ b/loading_pipeline/lib/tasks/write_metadata_for_run.py @@ -81,13 +81,13 @@ def run(self) -> None: 'sex_check', 'ploidy_check', ]: - metadata_json['failed_family_samples'][key] = collected_globals['failed_family_samples'][key] + metadata_json['failed_family_samples'][key] = collected_globals[ + 'failed_family_samples' + ][key] sample_qc_loadable_samples = { *{ sample - for meta in collected_globals['failed_family_samples'][ - key - ].values() + for meta in collected_globals['failed_family_samples'][key].values() for sample in meta['samples'] }, *sample_qc_loadable_samples, diff --git a/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py b/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py index 552204779f..0c07c8bf92 100644 --- a/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py +++ b/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py @@ -264,7 +264,7 @@ def create_table(self) -> hl.MatrixTable: ), ), project_families={ - project_guid: sorted([f.family_guid for f in families]) + project_guid: sorted([f.family_guid for f in families]) for project_guid, families in project_families.items() }, ) From 7817ffd295d4ba79f729d7ddb46842dccf169058 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 1 Sep 2026 17:48:22 -0400 Subject: [PATCH 333/369] realistic counts --- .../exports/write_new_entries_parquet_test.py | 73 +++++++++---------- 1 file changed, 35 insertions(+), 38 deletions(-) diff --git a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py index c71159d36a..31df0ed4ef 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py @@ -128,28 +128,28 @@ def test_write_new_entries_parquet(self): ), ) export_json = convert_ndarray_to_list(df.to_dict('records')) - self.assertEqual(len(export_json), 183) + self.assertEqual(len(export_json), 16) self.assertEqual( df['family_guid'].value_counts().to_dict(), { - 'abc_1': 17, - '789_1': 15, - '890_1': 14, - '901_1': 14, - 'bcd_1': 14, - '345_1': 13, - '456_1': 13, - '567_1': 13, - 'def_1': 13, - '123_1': 12, - '234_1': 12, - '678_1': 11, - 'cde_1': 11, - 'efg_1': 11, + 'abc_1': 2, + '345_1': 2, + '123_1': 1, + '234_1': 1, + '456_1': 1, + '567_1': 1, + '678_1': 1, + '789_1': 1, + '890_1': 1, + '901_1': 1, + 'bcd_1': 1, + 'cde_1': 1, + 'def_1': 1, + 'efg_1': 1, }, ) self.assertEqual( - export_json[:2], + export_json[:3], [ { 'key': 0, @@ -211,30 +211,27 @@ def test_write_new_entries_parquet(self): ], 'sign': 1, }, + { + 'key': 0, + 'project_guid': 'R0114_project4', + 'family_guid': '123_1', + 'sample_type': 'WGS', + 'xpos': 1000876499, + 'geneIds': ['ENSG00000187634'], + 'filters': [], + 'calls': [ + { + 'sampleId': 'NA19675_1', + 'gt': 2, + 'gq': 15, + 'ab': 1.0, + 'dp': 5, + }, + ], + 'sign': 1, + }, ], ) - self.assertEqual( - export_json[17], - { - 'key': 0, - 'project_guid': 'R0114_project4', - 'family_guid': '123_1', - 'sample_type': 'WGS', - 'xpos': 1000876499, - 'geneIds': ['ENSG00000187634'], - 'filters': [], - 'calls': [ - { - 'sampleId': 'NA19675_1', - 'gt': 2, - 'gq': 15, - 'ab': 1.0, - 'dp': 5, - }, - ], - 'sign': 1, - }, - ) def test_mito_write_new_entries_parquet(self): copy_project_pedigree_to_mocked_dir( From cb26b07f5947b2295c7d65977047edcc802f5ffd Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 1 Sep 2026 18:00:24 -0400 Subject: [PATCH 334/369] fix hail syntax for task complete --- .../write_remapped_and_subsetted_callset.py | 21 ++++++++++--------- 1 file changed, 11 insertions(+), 10 deletions(-) diff --git a/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py b/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py index 0c07c8bf92..52443cef8a 100644 --- a/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py +++ b/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py @@ -54,21 +54,22 @@ def complete(self) -> luigi.Target: if not super().complete(): return False mt = hl.read_matrix_table(self.output().path) - remap_pedigree_hashes = hl.eval(mt.globals.remap_pedigree_hashes) return ( bool( hl.eval(mt.globals.family_samples), ) - and len(remap_pedigree_hashes) == len(self.project_guids) + and len(hl.eval(mt.globals.remap_pedigree_hashes)) == len(self.project_guids) and all( - remap_pedigree_hashes[i] - == remap_pedigree_hash( - project_pedigree_path( - self.reference_genome, - self.dataset_type, - self.sample_type, - project_guid, - ), + hl.eval( + mt.globals.remap_pedigree_hashes[i] + == remap_pedigree_hash( + project_pedigree_path( + self.reference_genome, + self.dataset_type, + self.sample_type, + project_guid, + ), + ) ) for i, project_guid in enumerate(self.project_guids) ) From 737f7e68a30b4384231ac36ba5606e847d326182 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 1 Sep 2026 18:01:51 -0400 Subject: [PATCH 335/369] ruff --- .../lib/tasks/write_remapped_and_subsetted_callset.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py b/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py index 52443cef8a..b71bbe446c 100644 --- a/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py +++ b/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py @@ -58,7 +58,8 @@ def complete(self) -> luigi.Target: bool( hl.eval(mt.globals.family_samples), ) - and len(hl.eval(mt.globals.remap_pedigree_hashes)) == len(self.project_guids) + and len(hl.eval(mt.globals.remap_pedigree_hashes)) + == len(self.project_guids) and all( hl.eval( mt.globals.remap_pedigree_hashes[i] From 5871e825656cb199916388239504211a4f2e148e Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 1 Sep 2026 18:03:35 -0400 Subject: [PATCH 336/369] ruff --- .../lib/tasks/write_remapped_and_subsetted_callset.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py b/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py index b71bbe446c..3b72217cd1 100644 --- a/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py +++ b/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py @@ -70,7 +70,7 @@ def complete(self) -> luigi.Target: self.sample_type, project_guid, ), - ) + ), ) for i, project_guid in enumerate(self.project_guids) ) From 1a4eba1fadc829e8e03691d540056ed4fc0a9d50 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 2 Sep 2026 22:54:49 +0000 Subject: [PATCH 337/369] Bump fast-uri from 3.1.5 to 3.1.7 in /ui Bumps [fast-uri](https://github.com/fastify/fast-uri) from 3.1.5 to 3.1.7. - [Release notes](https://github.com/fastify/fast-uri/releases) - [Commits](https://github.com/fastify/fast-uri/compare/v3.1.5...v3.1.7) --- updated-dependencies: - dependency-name: fast-uri dependency-version: 3.1.7 dependency-type: indirect ... Signed-off-by: dependabot[bot] --- ui/package-lock.json | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/ui/package-lock.json b/ui/package-lock.json index 9dccc5c08a..12a33f25f7 100644 --- a/ui/package-lock.json +++ b/ui/package-lock.json @@ -8825,9 +8825,9 @@ "integrity": "sha512-HPtaa38cPgWvaCFmRNhlc6NG7pv6NUHqjPgVAkWGoB9mQMwYB27/K0CvOM5Czy+qpT3e8XJ6Q4aPAnzpNpzNaw==" }, "node_modules/fast-uri": { - "version": "3.1.5", - "resolved": "https://registry.npmjs.org/fast-uri/-/fast-uri-3.1.5.tgz", - "integrity": "sha512-gHwA1O9LDIcKunMKhObS/HimwtehO1nPUECKAu5TpKgaO19fcWEl4bliWe1jWxVFvIXztJjjQ4L8XQ1EU9f7Jw==", + "version": "3.1.7", + "resolved": "https://registry.npmjs.org/fast-uri/-/fast-uri-3.1.7.tgz", + "integrity": "sha512-dOvZVzjdZdz7phd9v6jCbwxrBW3fK6n8Rc0CtdmM4bumzMnxywBYhuph6J819RRw/ku+rLbelwfMunktuzVVHg==", "dev": true, "funding": [ { @@ -8838,7 +8838,8 @@ "type": "opencollective", "url": "https://opencollective.com/fastify" } - ] + ], + "license": "BSD-3-Clause" }, "node_modules/fastest-levenshtein": { "version": "1.0.12", @@ -26982,9 +26983,9 @@ "integrity": "sha512-HPtaa38cPgWvaCFmRNhlc6NG7pv6NUHqjPgVAkWGoB9mQMwYB27/K0CvOM5Czy+qpT3e8XJ6Q4aPAnzpNpzNaw==" }, "fast-uri": { - "version": "3.1.5", - "resolved": "https://registry.npmjs.org/fast-uri/-/fast-uri-3.1.5.tgz", - "integrity": "sha512-gHwA1O9LDIcKunMKhObS/HimwtehO1nPUECKAu5TpKgaO19fcWEl4bliWe1jWxVFvIXztJjjQ4L8XQ1EU9f7Jw==", + "version": "3.1.7", + "resolved": "https://registry.npmjs.org/fast-uri/-/fast-uri-3.1.7.tgz", + "integrity": "sha512-dOvZVzjdZdz7phd9v6jCbwxrBW3fK6n8Rc0CtdmM4bumzMnxywBYhuph6J819RRw/ku+rLbelwfMunktuzVVHg==", "dev": true }, "fastest-levenshtein": { From 87acaacc4f8ff3dd3513701ff6b0609b290704e0 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 3 Sep 2026 00:12:15 +0000 Subject: [PATCH 338/369] Bump browserslist from 4.24.2 to 4.28.8 in /ui Bumps [browserslist](https://github.com/browserslist/browserslist) from 4.24.2 to 4.28.8. - [Release notes](https://github.com/browserslist/browserslist/releases) - [Changelog](https://github.com/browserslist/browserslist/blob/main/CHANGELOG.md) - [Commits](https://github.com/browserslist/browserslist/compare/4.24.2...4.28.8) --- updated-dependencies: - dependency-name: browserslist dependency-version: 4.28.8 dependency-type: indirect ... Signed-off-by: dependabot[bot] --- ui/package-lock.json | 115 +++++++++++++++++++++++++++---------------- 1 file changed, 72 insertions(+), 43 deletions(-) diff --git a/ui/package-lock.json b/ui/package-lock.json index 9dccc5c08a..dddbded2a3 100644 --- a/ui/package-lock.json +++ b/ui/package-lock.json @@ -5296,6 +5296,19 @@ "integrity": "sha1-ibTRmasr7kneFk6gK4nORi1xt2c=", "dev": true }, + "node_modules/baseline-browser-mapping": { + "version": "2.11.20", + "resolved": "https://registry.npmjs.org/baseline-browser-mapping/-/baseline-browser-mapping-2.11.20.tgz", + "integrity": "sha512-H0ulySigv6icDJ1F7SjtdCD6PrhTpdYCmP0CactWy1+ekh0AFd0o1Wn5T8b+hnTmdBx19u9yhL6wvCylXMY7zw==", + "dev": true, + "license": "Apache-2.0", + "bin": { + "baseline-browser-mapping": "dist/cli.cjs" + }, + "engines": { + "node": ">=6.0.0" + } + }, "node_modules/batch": { "version": "0.6.1", "resolved": "https://registry.npmjs.org/batch/-/batch-0.6.1.tgz", @@ -5433,9 +5446,9 @@ "dev": true }, "node_modules/browserslist": { - "version": "4.24.2", - "resolved": "https://registry.npmjs.org/browserslist/-/browserslist-4.24.2.tgz", - "integrity": "sha512-ZIc+Q62revdMcqC6aChtW4jz3My3klmCO1fEmINZY/8J3EpBg5/A/D0AKmBveUh6pgoeycoMkVMko84tuYS+Gg==", + "version": "4.28.8", + "resolved": "https://registry.npmjs.org/browserslist/-/browserslist-4.28.8.tgz", + "integrity": "sha512-V2NpofLblG64mfOtSgDhOJESZEGogzDMBv/q+W6oc4LXWP/q75eOXoOaaOu1EOadB9U4Bwx/e0yzbvwKH8zalA==", "dev": true, "funding": [ { @@ -5451,11 +5464,13 @@ "url": "https://github.com/sponsors/ai" } ], + "license": "MIT", "dependencies": { - "caniuse-lite": "^1.0.30001669", - "electron-to-chromium": "^1.5.41", - "node-releases": "^2.0.18", - "update-browserslist-db": "^1.1.1" + "baseline-browser-mapping": "^2.11.12", + "caniuse-lite": "^1.0.30001809", + "electron-to-chromium": "^1.5.402", + "node-releases": "^2.0.53", + "update-browserslist-db": "^1.3.0" }, "bin": { "browserslist": "cli.js" @@ -5625,9 +5640,9 @@ } }, "node_modules/caniuse-lite": { - "version": "1.0.30001683", - "resolved": "https://registry.npmjs.org/caniuse-lite/-/caniuse-lite-1.0.30001683.tgz", - "integrity": "sha512-iqmNnThZ0n70mNwvxpEC2nBJ037ZHZUoBI5Gorh1Mw6IlEAZujEoU1tXA628iZfzm7R9FvFzxbfdgml82a3k8Q==", + "version": "1.0.30001810", + "resolved": "https://registry.npmjs.org/caniuse-lite/-/caniuse-lite-1.0.30001810.tgz", + "integrity": "sha512-TITQPUkaz+aVk5GL6NhOdwk1aEaNTSDPsGFWrTuhKGtjTF70jL/Oht2W4c6rXUe5fu7Ie19VIahAXHIIiWWNeg==", "dev": true, "funding": [ { @@ -5642,7 +5657,8 @@ "type": "github", "url": "https://github.com/sponsors/ai" } - ] + ], + "license": "CC-BY-4.0" }, "node_modules/case-sensitive-paths-webpack-plugin": { "version": "2.4.0", @@ -7208,10 +7224,11 @@ "dev": true }, "node_modules/electron-to-chromium": { - "version": "1.5.64", - "resolved": "https://registry.npmjs.org/electron-to-chromium/-/electron-to-chromium-1.5.64.tgz", - "integrity": "sha512-IXEuxU+5ClW2IGEYFC2T7szbyVgehupCWQe5GNh+H065CD6U6IFN0s4KeAMFGNmQolRU4IV7zGBWSYMmZ8uuqQ==", - "dev": true + "version": "1.5.420", + "resolved": "https://registry.npmjs.org/electron-to-chromium/-/electron-to-chromium-1.5.420.tgz", + "integrity": "sha512-2yD6XreGusOfNV+dUcvipJEXc3n/n7fgr7996aszTG+YY5E4mqM4tOq/3uhP129cazL9YHbVWSpc79ePotWtPA==", + "dev": true, + "license": "ISC" }, "node_modules/emittery": { "version": "0.8.1", @@ -13867,10 +13884,14 @@ } }, "node_modules/node-releases": { - 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"picocolors": "^1.1.0" + "picocolors": "^1.1.1" }, "bin": { "update-browserslist-db": "cli.js" @@ -24105,6 +24127,12 @@ "integrity": "sha1-ibTRmasr7kneFk6gK4nORi1xt2c=", "dev": true }, + "baseline-browser-mapping": { + "version": "2.11.20", + "resolved": "https://registry.npmjs.org/baseline-browser-mapping/-/baseline-browser-mapping-2.11.20.tgz", + "integrity": "sha512-H0ulySigv6icDJ1F7SjtdCD6PrhTpdYCmP0CactWy1+ekh0AFd0o1Wn5T8b+hnTmdBx19u9yhL6wvCylXMY7zw==", + "dev": true + }, "batch": { "version": "0.6.1", "resolved": "https://registry.npmjs.org/batch/-/batch-0.6.1.tgz", @@ -24218,15 +24246,16 @@ "dev": true }, "browserslist": { - "version": "4.24.2", - "resolved": "https://registry.npmjs.org/browserslist/-/browserslist-4.24.2.tgz", - "integrity": "sha512-ZIc+Q62revdMcqC6aChtW4jz3My3klmCO1fEmINZY/8J3EpBg5/A/D0AKmBveUh6pgoeycoMkVMko84tuYS+Gg==", + "version": "4.28.8", + "resolved": "https://registry.npmjs.org/browserslist/-/browserslist-4.28.8.tgz", + "integrity": "sha512-V2NpofLblG64mfOtSgDhOJESZEGogzDMBv/q+W6oc4LXWP/q75eOXoOaaOu1EOadB9U4Bwx/e0yzbvwKH8zalA==", "dev": true, "requires": { - 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"resolved": "https://registry.npmjs.org/update-browserslist-db/-/update-browserslist-db-1.1.1.tgz", - "integrity": "sha512-R8UzCaa9Az+38REPiJ1tXlImTJXlVfgHZsglwBD/k6nj76ctsH1E3q4doGrukiLQd3sGQYu56r5+lo5r94l29A==", + "version": "1.3.2", + "resolved": "https://registry.npmjs.org/update-browserslist-db/-/update-browserslist-db-1.3.2.tgz", + "integrity": "sha512-UQ+MSxlhRm1bzjhU+DcuXfjFO1FzNtqhK5+9Yvlp90ItDLk5vT932A0rFu619nf7RVS+Y/VeaUW1jaRDqZ8VJw==", "dev": true, "requires": { "escalade": "^3.2.0", - "picocolors": "^1.1.0" + "picocolors": "^1.1.1" } }, "uri-js": { From aefccd74d67ae6908b70f889ebcd440097befba1 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 3 Sep 2026 12:19:54 -0400 Subject: [PATCH 339/369] update tests --- ...ite_remapped_and_subsetted_callset_test.py | 134 ++++++++++++++++-- 1 file changed, 121 insertions(+), 13 deletions(-) diff --git a/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset_test.py b/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset_test.py index 590795424a..b4c4e66284 100644 --- a/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset_test.py +++ b/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset_test.py @@ -27,6 +27,9 @@ 'loading_pipeline/var/test/pedigrees/test_pedigree_3_different_families.tsv' ) TEST_PEDIGREE_4_REMAP = 'loading_pipeline/var/test/pedigrees/test_pedigree_4_remap.tsv' +TEST_PEDIGREE_4_REMAP_2 = ( + 'loading_pipeline/var/test/pedigrees/test_pedigree_4_remap_2.tsv' +) TEST_PEDIGREE_7 = 'loading_pipeline/var/test/pedigrees/test_pedigree_7.tsv' TEST_SEX_CHECK_1 = 'loading_pipeline/var/test/sex_check/test_sex_check_1.ht' TEST_RELATEDNESS_CHECK_1 = ( @@ -104,7 +107,6 @@ def test_write_remapped_and_subsetted_callset_task( sample_type=SampleType.WGS, callset_path=TEST_VCF, project_guids=['R0113_test_project'], - project_i=0, validations_to_skip=[ALL_VALIDATIONS], skip_expect_tdr_metrics=True, ) @@ -117,11 +119,13 @@ def test_write_remapped_and_subsetted_callset_task( mt.globals.collect(), [ hl.Struct( - remap_pedigree_hash=hl.eval( - remap_pedigree_hash( - TEST_PEDIGREE_3_REMAP, + remap_pedigree_hashes=[ + hl.eval( + remap_pedigree_hash( + TEST_PEDIGREE_3_REMAP, + ), ), - ), + ], failed_family_samples=hl.Struct( missing_samples={}, relatedness_check={}, @@ -129,6 +133,7 @@ def test_write_remapped_and_subsetted_callset_task( ploidy_check={}, ), family_samples={'abc_1': ['HG00731_1', 'HG00732_1', 'HG00733_1']}, + project_families={'R0113_test_project': ['abc_1']}, ), ], ) @@ -156,7 +161,6 @@ def test_write_remapped_and_subsetted_callset_task_failed_some_family_checks( sample_type=SampleType.WGS, callset_path=TEST_VCF, project_guids=['R0114_project4'], - project_i=0, validations_to_skip=[ALL_VALIDATIONS], skip_expect_tdr_metrics=True, ) @@ -171,11 +175,30 @@ def test_write_remapped_and_subsetted_callset_task_failed_some_family_checks( mt.globals.collect(), [ hl.Struct( - remap_pedigree_hash=hl.eval( - remap_pedigree_hash( - TEST_PEDIGREE_4_REMAP, + remap_pedigree_hashes=[ + hl.eval( + remap_pedigree_hash( + TEST_PEDIGREE_4_REMAP, + ), ), - ), + ], + project_families={ + 'R0114_project4': [ + '123_1', + '234_1', + '345_1', + '456_1', + '567_1', + '678_1', + '789_1', + '890_1', + '901_1', + 'bcd_1', + 'cde_1', + 'def_1', + 'efg_1', + ], + }, family_samples={ '123_1': ['NA19675_1'], '345_1': ['NA19679_1'], @@ -228,6 +251,94 @@ def test_write_remapped_and_subsetted_callset_task_failed_some_family_checks( ], ) + def test_write_remapped_and_subsetted_callset_task_multiple_projects( + self, + ) -> None: + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_3_REMAP, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0113_test_project', + ) + copy_project_pedigree_to_mocked_dir( + TEST_PEDIGREE_4_REMAP_2, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + SampleType.WGS, + 'R0114_project4', + ) + worker = luigi.worker.Worker() + wrsc_task = WriteRemappedAndSubsettedCallsetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + run_id=TEST_RUN_ID, + sample_type=SampleType.WGS, + callset_path=TEST_VCF, + project_guids=['R0113_test_project', 'R0114_project4'], + validations_to_skip=[ALL_VALIDATIONS], + skip_expect_tdr_metrics=True, + ) + worker.add(wrsc_task) + worker.run() + self.assertTrue(wrsc_task.complete()) + mt = hl.read_matrix_table(wrsc_task.output().path) + self.assertEqual( + mt.globals.collect(), + [ + hl.Struct( + remap_pedigree_hashes=[ + hl.eval(remap_pedigree_hash(TEST_PEDIGREE_3_REMAP)), + hl.eval(remap_pedigree_hash(TEST_PEDIGREE_4_REMAP_2)), + ], + failed_family_samples=hl.Struct( + missing_samples={ + 'efg_1': { + 'samples': ['NA20888_1'], + 'reasons': ["Missing samples: {'NA20888_1'}"], + }, + }, + relatedness_check={}, + sex_check={}, + ploidy_check={}, + ), + family_samples={ + 'abc_1': ['HG00731_1', 'HG00732_1', 'HG00733_1'], + '123_1': ['NA19675_1'], + '234_1': ['NA19678_1'], + '345_1': ['NA19679_1'], + '456_1': ['NA20870_1'], + '567_1': ['NA20872_1'], + '678_1': ['NA20874_1'], + '789_1': ['NA20875_1'], + '890_1': ['NA20876_1'], + '901_1': ['NA20877_1'], + 'bcd_1': ['NA20878_1'], + 'cde_1': ['NA20881_1'], + 'def_1': ['NA20885_1'], + }, + project_families={ + 'R0113_test_project': ['abc_1'], + 'R0114_project4': [ + '123_1', + '234_1', + '345_1', + '456_1', + '567_1', + '678_1', + '789_1', + '890_1', + '901_1', + 'bcd_1', + 'cde_1', + 'def_1', + 'efg_1', + ], + }, + ), + ], + ) + @patch( 'loading_pipeline.lib.tasks.write_remapped_and_subsetted_callset.FeatureFlag', ) @@ -251,7 +362,6 @@ def test_write_remapped_and_subsetted_callset_task_all_families_failed( sample_type=SampleType.WGS, callset_path=TEST_VCF, project_guids=['R0114_project4'], - project_i=0, validations_to_skip=[ALL_VALIDATIONS], skip_expect_tdr_metrics=True, ) @@ -385,7 +495,6 @@ def test_write_remapped_and_subsetted_callset_task_combined_validation_errors( sample_type=SampleType.WGS, callset_path=TEST_VCF, project_guids=['R0113_test_project'], - project_i=0, validations_to_skip=[ALL_VALIDATIONS], skip_expect_tdr_metrics=True, ) @@ -409,7 +518,6 @@ def test_write_remapped_and_subsetted_callset_task_combined_validation_errors( sample_type=SampleType.WGS, callset_path=TEST_VCF, project_guids=['R0114_project4'], - project_i=0, validations_to_skip=[ALL_VALIDATIONS], skip_expect_tdr_metrics=True, ) From 525617ee961e8bc7c01ca11ad2e7cfb43c8a16eb Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 3 Sep 2026 12:23:17 -0400 Subject: [PATCH 340/369] fix util tests --- .../lib/misc/family_entries_test.py | 63 +++++++++++++------ 1 file changed, 45 insertions(+), 18 deletions(-) diff --git a/loading_pipeline/lib/misc/family_entries_test.py b/loading_pipeline/lib/misc/family_entries_test.py index 76882546de..ab65271725 100644 --- a/loading_pipeline/lib/misc/family_entries_test.py +++ b/loading_pipeline/lib/misc/family_entries_test.py @@ -57,6 +57,7 @@ def test_compute_callset_family_entries_ht(self) -> None: hl.Struct( family_samples={'1': ['b', 'c', 'd'], '2': ['a']}, family_guids=['1', '2'], + project_families={'p1': ['1'], 'p2': ['2', '3']}, ), ], ) @@ -93,7 +94,14 @@ def test_globalize_and_deglobalize(self) -> None: id=hl.tint32, filters=hl.tset(hl.tstr), family_entries=hl.tarray( - hl.tarray(hl.tstruct(a=hl.tint32, s=hl.tstr, family_guid=hl.tstr)), + hl.tarray( + hl.tstruct( + a=hl.tint32, + s=hl.tstr, + family_guid=hl.tstr, + project_guid=hl.tstr, + ), + ), ), ), key='id', @@ -105,6 +113,12 @@ def test_globalize_and_deglobalize(self) -> None: [], ], ) + self.assertCountEqual( + family_entries_ht.project_guids.collect(), + [ + [], + ], + ) family_entries_ht = hl.Table.parallelize( [ { @@ -112,12 +126,12 @@ def test_globalize_and_deglobalize(self) -> None: 'filters': {'HIGH_SR_BACKGROUND', 'UNRESOLVED'}, 'family_entries': [ [ - hl.Struct(a=1, s='a', family_guid='123'), - hl.Struct(a=2, s='c', family_guid='123'), - hl.Struct(a=1, s='e', family_guid='123'), + hl.Struct(a=1, s='a', family_guid='123', project_guid='p1'), + hl.Struct(a=2, s='c', family_guid='123', project_guid='p1'), + hl.Struct(a=1, s='e', family_guid='123', project_guid='p1'), ], [ - hl.Struct(a=2, s='f', family_guid='234'), + hl.Struct(a=2, s='f', family_guid='234', project_guid='p2'), ], ], }, @@ -126,12 +140,12 @@ def test_globalize_and_deglobalize(self) -> None: 'filters': {'HIGH_SR_BACKGROUND'}, 'family_entries': [ [ - hl.Struct(a=2, s='a', family_guid='123'), - hl.Struct(a=3, s='c', family_guid='123'), - hl.Struct(a=4, s='e', family_guid='123'), + hl.Struct(a=2, s='a', family_guid='123', project_guid='p1'), + hl.Struct(a=3, s='c', family_guid='123', project_guid='p1'), + hl.Struct(a=4, s='e', family_guid='123', project_guid='p1'), ], [ - hl.Struct(a=5, s='f', family_guid='234'), + hl.Struct(a=5, s='f', family_guid='234', project_guid='p2'), ], ], }, @@ -140,7 +154,14 @@ def test_globalize_and_deglobalize(self) -> None: id=hl.tint32, filters=hl.tset(hl.tstr), family_entries=hl.tarray( - hl.tarray(hl.tstruct(a=hl.tint32, s=hl.tstr, family_guid=hl.tstr)), + hl.tarray( + hl.tstruct( + a=hl.tint32, + s=hl.tstr, + family_guid=hl.tstr, + project_guid=hl.tstr, + ), + ), ), ), key='id', @@ -152,6 +173,12 @@ def test_globalize_and_deglobalize(self) -> None: ['123', '234'], ], ) + self.assertCountEqual( + family_entries_ht.project_guids.collect(), + [ + ['p1', 'p2'], + ], + ) self.assertCountEqual( family_entries_ht.family_entries.collect(), [ @@ -183,22 +210,22 @@ def test_globalize_and_deglobalize(self) -> None: [ [ [ - hl.Struct(a=1, s='a', family_guid='123'), - hl.Struct(a=2, s='c', family_guid='123'), - hl.Struct(a=1, s='e', family_guid='123'), + hl.Struct(a=1, s='a', family_guid='123', project_guid='p1'), + hl.Struct(a=2, s='c', family_guid='123', project_guid='p1'), + hl.Struct(a=1, s='e', family_guid='123', project_guid='p1'), ], [ - hl.Struct(a=2, s='f', family_guid='234'), + hl.Struct(a=2, s='f', family_guid='234', project_guid='p2'), ], ], [ [ - hl.Struct(a=2, s='a', family_guid='123'), - hl.Struct(a=3, s='c', family_guid='123'), - hl.Struct(a=4, s='e', family_guid='123'), + hl.Struct(a=2, s='a', family_guid='123', project_guid='p1'), + hl.Struct(a=3, s='c', family_guid='123', project_guid='p1'), + hl.Struct(a=4, s='e', family_guid='123', project_guid='p1'), ], [ - hl.Struct(a=5, s='f', family_guid='234'), + hl.Struct(a=5, s='f', family_guid='234', project_guid='p2'), ], ], ], From 436d6c14f2cf614244b9dffef844fb5be8d210d2 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 3 Sep 2026 12:23:48 -0400 Subject: [PATCH 341/369] debug --- .../lib/tasks/exports/write_new_entries_parquet_test.py | 1 + 1 file changed, 1 insertion(+) diff --git a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py index 31df0ed4ef..7e47ffd3b5 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py @@ -148,6 +148,7 @@ def test_write_new_entries_parquet(self): 'efg_1': 1, }, ) + self.maxDiff = None self.assertEqual( export_json[:3], [ From b01ef409456270b0e7651edb75950838957ec64b Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 3 Sep 2026 13:23:33 -0400 Subject: [PATCH 342/369] fix tests --- .../lib/misc/family_entries_test.py | 2 +- .../exports/write_new_entries_parquet_test.py | 43 ++++++++++--------- 2 files changed, 24 insertions(+), 21 deletions(-) diff --git a/loading_pipeline/lib/misc/family_entries_test.py b/loading_pipeline/lib/misc/family_entries_test.py index ab65271725..82cf97074b 100644 --- a/loading_pipeline/lib/misc/family_entries_test.py +++ b/loading_pipeline/lib/misc/family_entries_test.py @@ -56,8 +56,8 @@ def test_compute_callset_family_entries_ht(self) -> None: [ hl.Struct( family_samples={'1': ['b', 'c', 'd'], '2': ['a']}, - family_guids=['1', '2'], project_families={'p1': ['1'], 'p2': ['2', '3']}, + family_guids=['1', '2'], ), ], ) diff --git a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py index 7e47ffd3b5..4aa4651c6f 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py @@ -150,7 +150,29 @@ def test_write_new_entries_parquet(self): ) self.maxDiff = None self.assertEqual( - export_json[:3], + export_json[0], + { + 'key': 0, + 'project_guid': 'R0114_project4', + 'family_guid': '123_1', + 'sample_type': 'WGS', + 'xpos': 1000876499, + 'geneIds': ['ENSG00000187634'], + 'filters': [], + 'calls': [ + { + 'sampleId': 'NA19675_1', + 'gt': 2, + 'gq': 15, + 'ab': 1.0, + 'dp': 5, + }, + ], + 'sign': 1, + }, + ) + self.assertEqual( + export_json[:-2], [ { 'key': 0, @@ -212,25 +234,6 @@ def test_write_new_entries_parquet(self): ], 'sign': 1, }, - { - 'key': 0, - 'project_guid': 'R0114_project4', - 'family_guid': '123_1', - 'sample_type': 'WGS', - 'xpos': 1000876499, - 'geneIds': ['ENSG00000187634'], - 'filters': [], - 'calls': [ - { - 'sampleId': 'NA19675_1', - 'gt': 2, - 'gq': 15, - 'ab': 1.0, - 'dp': 5, - }, - ], - 'sign': 1, - }, ], ) From bcec49e22e11731463ac96fa9ebbfbe8c30aceb8 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 3 Sep 2026 16:24:21 -0400 Subject: [PATCH 343/369] fix test --- loading_pipeline/lib/misc/family_entries_test.py | 1 + .../lib/tasks/exports/write_new_entries_parquet_test.py | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/loading_pipeline/lib/misc/family_entries_test.py b/loading_pipeline/lib/misc/family_entries_test.py index 82cf97074b..5e0ec1d6f3 100644 --- a/loading_pipeline/lib/misc/family_entries_test.py +++ b/loading_pipeline/lib/misc/family_entries_test.py @@ -57,6 +57,7 @@ def test_compute_callset_family_entries_ht(self) -> None: hl.Struct( family_samples={'1': ['b', 'c', 'd'], '2': ['a']}, project_families={'p1': ['1'], 'p2': ['2', '3']}, + project_guids=['p1', 'p2'], family_guids=['1', '2'], ), ], diff --git a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py index 4aa4651c6f..9741de954f 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py @@ -172,7 +172,7 @@ def test_write_new_entries_parquet(self): }, ) self.assertEqual( - export_json[:-2], + export_json[-2:], [ { 'key': 0, From 9f2cff4e5ee0cd7b3ccc83063650dd2e2bd1ea31 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 3 Sep 2026 16:33:30 -0400 Subject: [PATCH 344/369] rename task --- loading_pipeline/api/request_handlers.py | 6 +- .../bin/migrate_all_projects_to_clickhouse.py | 65 ------------------- .../bin/migrate_variants_tables.py | 49 -------------- ...ess_file.py => load_clickhouse_entries.py} | 2 +- 4 files changed, 4 insertions(+), 118 deletions(-) delete mode 100755 loading_pipeline/bin/migrate_all_projects_to_clickhouse.py delete mode 100755 loading_pipeline/bin/migrate_variants_tables.py rename loading_pipeline/lib/tasks/{write_clickhouse_load_success_file.py => load_clickhouse_entries.py} (96%) diff --git a/loading_pipeline/api/request_handlers.py b/loading_pipeline/api/request_handlers.py index 62e46f0b4d..120b1f3696 100644 --- a/loading_pipeline/api/request_handlers.py +++ b/loading_pipeline/api/request_handlers.py @@ -19,8 +19,8 @@ rebuild_gt_stats, refresh_clickhouse_reference_data, ) -from loading_pipeline.lib.tasks.write_clickhouse_load_success_file import ( - WriteClickhouseLoadSuccessFileTask, +from loading_pipeline.lib.tasks.load_clickhouse_entries import ( + LoadClickhouseEntries, ) logger = get_logger(__name__) @@ -34,7 +34,7 @@ def run_loading_pipeline( ): luigi_task_result = luigi.build( [ - WriteClickhouseLoadSuccessFileTask( + LoadClickhouseEntries( run_id=run_id, **lpr.model_dump(exclude='request_type'), ), diff --git a/loading_pipeline/bin/migrate_all_projects_to_clickhouse.py b/loading_pipeline/bin/migrate_all_projects_to_clickhouse.py deleted file mode 100755 index bc691738c3..0000000000 --- a/loading_pipeline/bin/migrate_all_projects_to_clickhouse.py +++ /dev/null @@ -1,65 +0,0 @@ -#!/usr/bin/env python3 -import uuid - -import hailtop.fs as hfs -import luigi - -from loading_pipeline.lib.core import ( - DatasetType, - FeatureFlag, - ReferenceGenome, - SampleType, -) -from loading_pipeline.lib.core.constants import MIGRATION_RUN_ID -from loading_pipeline.lib.paths import project_table_path -from loading_pipeline.lib.tasks import ( - MigrateAllProjectsToClickHouseOnDataprocTask, - MigrateAllProjectsToClickHouseTask, -) -from loading_pipeline.lib.tasks.write_clickhouse_load_success_file import ( - WriteClickhouseLoadSuccessFileTask, -) - -if __name__ == '__main__': - task_cls = ( - MigrateAllProjectsToClickHouseOnDataprocTask - if FeatureFlag.RUN_PIPELINE_ON_DATAPROC - else MigrateAllProjectsToClickHouseTask - ) - run_id_prefix = ( - MIGRATION_RUN_ID + '-' + str(uuid.uuid1().int)[:4] - ) # Note: the randomness is a cache bust for the luigi local scheduler - luigi.build( - [ - task_cls( - reference_genome, - DatasetType.SNV_INDEL, - run_id=run_id_prefix, - attempt_id=0, - ) - for reference_genome in ReferenceGenome - ], - ) - clickhouse_load_tasks = [] - for sample_type in SampleType: - for reference_genome in ReferenceGenome: - for p in hfs.ls( - project_table_path( - reference_genome, - DatasetType.SNV_INDEL, - sample_type, - '*', - ), - ): - project_guid = p.path.split('/')[-1].replace('.ht', '') - clickhouse_load_tasks.append( - WriteClickhouseLoadSuccessFileTask( - reference_genome=reference_genome, - dataset_type=DatasetType.SNV_INDEL, - run_id=f'{run_id_prefix}_{sample_type.value}_{project_guid}', - callset_path='', - sample_type=sample_type, - attempt_id=0, - ), - ) - luigi.build(clickhouse_load_tasks) diff --git a/loading_pipeline/bin/migrate_variants_tables.py b/loading_pipeline/bin/migrate_variants_tables.py deleted file mode 100755 index a34e9e9026..0000000000 --- a/loading_pipeline/bin/migrate_variants_tables.py +++ /dev/null @@ -1,49 +0,0 @@ -#!/usr/bin/env python3 -import argparse -import uuid - -import luigi - -from loading_pipeline.lib.core import DatasetType, ReferenceGenome -from loading_pipeline.lib.core.constants import VARIANTS_MIGRATION_RUN_ID -from loading_pipeline.lib.tasks.variants_migration.load_clickhouse_variants_tables import ( - LoadClickhouseVariantsTablesTask, -) - - -def parse_args() -> argparse.Namespace: - parser = argparse.ArgumentParser( - description='Run variants migration Luigi pipeline.', - ) - parser.add_argument( - '--run_all_dataset_types', - action='store_true', - help='If set, runs the pipeline for all dataset types instead of just SNV_INDEL.', - ) - return parser.parse_args() - - -if __name__ == '__main__': - args = parse_args() - for reference_genome, dataset_type in [ - (ReferenceGenome.GRCh37, DatasetType.SNV_INDEL), - (ReferenceGenome.GRCh38, DatasetType.SNV_INDEL), - (ReferenceGenome.GRCh38, DatasetType.MITO), - (ReferenceGenome.GRCh38, DatasetType.SV), - (ReferenceGenome.GRCh38, DatasetType.GCNV), - ]: - if dataset_type != DatasetType.SNV_INDEL and not args.run_all_dataset_types: - continue - run_id_prefix = ( - VARIANTS_MIGRATION_RUN_ID + '-' + str(uuid.uuid1().int)[:4] - ) # Note: the randomness is a cache bust for the luigi local scheduler - luigi.build( - [ - LoadClickhouseVariantsTablesTask( - reference_genome, - dataset_type, - run_id=run_id_prefix, - attempt_id=0, - ), - ], - ) diff --git a/loading_pipeline/lib/tasks/write_clickhouse_load_success_file.py b/loading_pipeline/lib/tasks/load_clickhouse_entries.py similarity index 96% rename from loading_pipeline/lib/tasks/write_clickhouse_load_success_file.py rename to loading_pipeline/lib/tasks/load_clickhouse_entries.py index f5c7284763..eeb84d1292 100644 --- a/loading_pipeline/lib/tasks/write_clickhouse_load_success_file.py +++ b/loading_pipeline/lib/tasks/load_clickhouse_entries.py @@ -19,7 +19,7 @@ @luigi.util.inherits(BaseLoadingRunParams) -class WriteClickhouseLoadSuccessFileTask(luigi.Task): +class LoadClickhouseEntries(luigi.Task): attempt_id = luigi.IntParameter() def output(self) -> luigi.Target: From 565caecad66488bac9a406deddcbc3ecad8a48d3 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 3 Sep 2026 16:42:05 -0400 Subject: [PATCH 345/369] split task logic --- loading_pipeline/lib/misc/clickhouse.py | 32 ++++++++++++++- loading_pipeline/lib/misc/clickhouse_test.py | 6 +-- .../lib/tasks/load_clickhouse_entries.py | 8 ++-- .../lib/tasks/load_clickhouse_variants.py | 41 +++++++++++++++++++ 4 files changed, 78 insertions(+), 9 deletions(-) create mode 100644 loading_pipeline/lib/tasks/load_clickhouse_variants.py diff --git a/loading_pipeline/lib/misc/clickhouse.py b/loading_pipeline/lib/misc/clickhouse.py index 1de075ddbb..65219e7a1a 100644 --- a/loading_pipeline/lib/misc/clickhouse.py +++ b/loading_pipeline/lib/misc/clickhouse.py @@ -1058,14 +1058,42 @@ def atomic_insert_entries( @retry() -def load_complete_run( +def load_run_variants( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + run_id: str, +): + msg = f'Attempting load of variants for run: {reference_genome.value}/{dataset_type.value}/{run_id}' + logger.info(msg) + table_name_builder = TableNameBuilder( + reference_genome, + dataset_type, + run_id, + ) + for clickhouse_table in ClickHouseTable.for_dataset_type(dataset_type): + clickhouse_table.insert( + table_name_builder=table_name_builder, + ) + for ( + clickhouse_reference_data + ) in ClickhouseReferenceDataset.for_reference_genome_dataset_type( + reference_genome, + dataset_type, + ): + clickhouse_reference_data.insert_into_seqr_variants_and_refresh_search( + table_name_builder=table_name_builder, + ) + + +@retry() +def load_run_entries( reference_genome: ReferenceGenome, dataset_type: DatasetType, run_id: str, project_guids: list[str], family_guids: list[str], ): - msg = f'Attempting load of run: {reference_genome.value}/{dataset_type.value}/{run_id}' + msg = f'Attempting load of entries for run: {reference_genome.value}/{dataset_type.value}/{run_id}' logger.info(msg) table_name_builder = TableNameBuilder( reference_genome, diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index 0ed3aa8b15..4a23d24a60 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -24,7 +24,7 @@ exchange_tables, get_clickhouse_client, insert_new_entries, - load_complete_run, + load_run_variants, logged_query, normalize_partition, optimize_entries, @@ -895,7 +895,7 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): return_value=[ClickhouseReferenceDataset.CLINVAR], ) def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_type): - load_complete_run( + load_run_variants( ReferenceGenome.GRCh38, DatasetType.SNV_INDEL, TEST_RUN_ID, @@ -1014,7 +1014,7 @@ def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_typ ) def test_load_complete_gcnv(self): - load_complete_run( + load_run_variants( ReferenceGenome.GRCh38, DatasetType.GCNV, TEST_RUN_ID, diff --git a/loading_pipeline/lib/tasks/load_clickhouse_entries.py b/loading_pipeline/lib/tasks/load_clickhouse_entries.py index eeb84d1292..42f85e80a3 100644 --- a/loading_pipeline/lib/tasks/load_clickhouse_entries.py +++ b/loading_pipeline/lib/tasks/load_clickhouse_entries.py @@ -5,7 +5,7 @@ import luigi.util from loading_pipeline.lib.misc.clickhouse import ( - load_complete_run, + load_run_entries, ) from loading_pipeline.lib.paths import ( clickhouse_load_success_file_path, @@ -15,7 +15,7 @@ BaseLoadingRunParams, ) from loading_pipeline.lib.tasks.files import GCSorLocalTarget -from loading_pipeline.lib.tasks.write_success_file import WriteSuccessFileTask +from loading_pipeline.lib.tasks.load_clickhouse_variants import LoadClickhouseVariants @luigi.util.inherits(BaseLoadingRunParams) @@ -32,7 +32,7 @@ def output(self) -> luigi.Target: ) def requires(self) -> luigi.Task: - return self.clone(WriteSuccessFileTask) + return self.clone(LoadClickhouseVariants) def run(self): with hfs.open( @@ -43,7 +43,7 @@ def run(self): ), ) as f: family_guids = list(json.load(f)['family_samples'].keys()) - load_complete_run( + load_run_entries( self.reference_genome, self.dataset_type, self.run_id, diff --git a/loading_pipeline/lib/tasks/load_clickhouse_variants.py b/loading_pipeline/lib/tasks/load_clickhouse_variants.py new file mode 100644 index 0000000000..8534425293 --- /dev/null +++ b/loading_pipeline/lib/tasks/load_clickhouse_variants.py @@ -0,0 +1,41 @@ +import luigi +import luigi.util + +from loading_pipeline.lib.misc.clickhouse import ( + load_run_variants, +) +from loading_pipeline.lib.paths import ( + clickhouse_load_success_file_path, +) +from loading_pipeline.lib.tasks.base.base_loading_run_params import ( + BaseLoadingRunParams, +) +from loading_pipeline.lib.tasks.files import GCSorLocalTarget +from loading_pipeline.lib.tasks.write_success_file import WriteSuccessFileTask + + +@luigi.util.inherits(BaseLoadingRunParams) +class LoadClickhouseVariants(luigi.Task): + attempt_id = luigi.IntParameter() + + def output(self) -> luigi.Target: + return GCSorLocalTarget( + clickhouse_load_success_file_path( + self.reference_genome, + self.dataset_type, + self.run_id, + ).replace('_CLICKHOUSE_LOAD_SUCCESS', '_CLICKHOUSE_LOAD_VARIANTS_SUCCESS'), + ) + + def requires(self) -> luigi.Task: + return self.clone(WriteSuccessFileTask) + + def run(self): + load_run_variants( + self.reference_genome, + self.dataset_type, + self.run_id, + ) + + with self.output().open('w') as f: + f.write('') From 24aa490279cb996a66de854e27fd661f3da93798 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 3 Sep 2026 16:44:58 -0400 Subject: [PATCH 346/369] debug --- .../lib/tasks/exports/write_new_entries_parquet_test.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py index 9741de954f..dff36953eb 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py @@ -172,7 +172,7 @@ def test_write_new_entries_parquet(self): }, ) self.assertEqual( - export_json[-2:], + export_json, [ { 'key': 0, From 64daf44163c14fc5ff86ada364afa198a2366c3f Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 3 Sep 2026 16:46:38 -0400 Subject: [PATCH 347/369] update ocs --- loading_pipeline/docs/Diagrams.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/loading_pipeline/docs/Diagrams.md b/loading_pipeline/docs/Diagrams.md index a8e205fd31..14519f4cb0 100644 --- a/loading_pipeline/docs/Diagrams.md +++ b/loading_pipeline/docs/Diagrams.md @@ -54,8 +54,10 @@ WriteSuccessFileTask | v - WriteClickhouseLoadSuccessFileTask - (load parquets → ClickHouse) + LoadClickhouseVariants + | + v + LoadClickhouseEntries ``` ClickHouse LSM-Tree From 65cec033a6c104e5c4887c1442af23b3a011b531 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 3 Sep 2026 16:51:26 -0400 Subject: [PATCH 348/369] explicitly separate out clcikhosue funcs --- loading_pipeline/lib/misc/clickhouse.py | 26 ++++++------------------- 1 file changed, 6 insertions(+), 20 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse.py b/loading_pipeline/lib/misc/clickhouse.py index 65219e7a1a..f99417544c 100644 --- a/loading_pipeline/lib/misc/clickhouse.py +++ b/loading_pipeline/lib/misc/clickhouse.py @@ -81,7 +81,6 @@ def insert(self) -> Callable: # Note that VARIANTS_DETAILS is not included here because # of the special logic to ensure writes are made to both tables. ClickHouseTable.VARIANTS_MEMORY: direct_insert_annotations, - ClickHouseTable.ENTRIES: atomic_insert_entries, ClickHouseTable.KEY_LOOKUP: functools.partial( direct_insert_all_keys, clickhouse_table=self, @@ -103,10 +102,7 @@ def for_dataset_type(cls, dataset_type: DatasetType) -> list['ClickHouseTable']: *tables, ClickHouseTable.VARIANT_DETAILS, ] - return [ - *tables, - ClickHouseTable.ENTRIES, - ] + return tables @classmethod def for_dataset_type_disk_backed_variants_tables( @@ -1100,21 +1096,11 @@ def load_run_entries( dataset_type, run_id, ) - for clickhouse_table in ClickHouseTable.for_dataset_type(dataset_type): - clickhouse_table.insert( - table_name_builder=table_name_builder, - project_guids=project_guids, - family_guids=family_guids, - ) - for ( - clickhouse_reference_data - ) in ClickhouseReferenceDataset.for_reference_genome_dataset_type( - reference_genome, - dataset_type, - ): - clickhouse_reference_data.insert_into_seqr_variants_and_refresh_search( - table_name_builder=table_name_builder, - ) + atomic_insert_entries( + table_name_builder=table_name_builder, + project_guids=project_guids, + family_guids=family_guids, + ) @retry() From 938307d2a247c95a095d2cd6f97150eb031fde76 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 3 Sep 2026 17:05:13 -0400 Subject: [PATCH 349/369] add dataproc retry --- .../lib/tasks/dataproc/create_dataproc_cluster.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster.py b/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster.py index 5e0bb59cbb..2ee2464cc3 100644 --- a/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster.py +++ b/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster.py @@ -10,6 +10,7 @@ from loading_pipeline.lib.core import DatasetType, Env, FeatureFlag, ReferenceGenome from loading_pipeline.lib.logger import get_logger from loading_pipeline.lib.misc.gcp import get_service_account_credentials +from loading_pipeline.lib.misc.retry import retry from loading_pipeline.lib.tasks.base.base_loading_pipeline_params import ( BaseLoadingPipelineParams, ) @@ -192,6 +193,10 @@ def run(self): if not Env.GCLOUD_PROJECT or not Env.GCLOUD_REGION: msg = 'Environment Variables GCLOUD_PROJECT and GCLOUD_REGION are required for running the pipeline on dataproc.' raise RuntimeError(msg) + self.get_running_cluster() + + @retry(tries=5) + def get_running_cluster(self): cluster = self.safely_get_cluster() if not cluster: self.client.create_cluster( From 7f9e8cde87f13b4f69a4f5796cd23dbdb9a2a96d Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 3 Sep 2026 17:08:54 -0400 Subject: [PATCH 350/369] test assertion order --- .../exports/write_new_entries_parquet_test.py | 43 +++++++++---------- 1 file changed, 20 insertions(+), 23 deletions(-) diff --git a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py index dff36953eb..3dbcec9add 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py @@ -150,30 +150,27 @@ def test_write_new_entries_parquet(self): ) self.maxDiff = None self.assertEqual( - export_json[0], - { - 'key': 0, - 'project_guid': 'R0114_project4', - 'family_guid': '123_1', - 'sample_type': 'WGS', - 'xpos': 1000876499, - 'geneIds': ['ENSG00000187634'], - 'filters': [], - 'calls': [ - { - 'sampleId': 'NA19675_1', - 'gt': 2, - 'gq': 15, - 'ab': 1.0, - 'dp': 5, - }, - ], - 'sign': 1, - }, - ) - self.assertEqual( - export_json, + [export_json[0], export_json[9], export_json[15]], [ + { + 'key': 0, + 'project_guid': 'R0114_project4', + 'family_guid': '123_1', + 'sample_type': 'WGS', + 'xpos': 1000876499, + 'geneIds': ['ENSG00000187634'], + 'filters': [], + 'calls': [ + { + 'sampleId': 'NA19675_1', + 'gt': 2, + 'gq': 15, + 'ab': 1.0, + 'dp': 5, + }, + ], + 'sign': 1, + }, { 'key': 0, 'project_guid': 'R0113_test_project', From 4ec47f2bcd01d0630a6b06e3b7c2fca33a4895a3 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Thu, 3 Sep 2026 17:23:38 -0400 Subject: [PATCH 351/369] update tests --- loading_pipeline/bin/pipeline_worker_test.py | 6 ++-- loading_pipeline/lib/misc/clickhouse_test.py | 37 ++++++++++++++------ 2 files changed, 30 insertions(+), 13 deletions(-) diff --git a/loading_pipeline/bin/pipeline_worker_test.py b/loading_pipeline/bin/pipeline_worker_test.py index e1fcefd710..9efc409cba 100644 --- a/loading_pipeline/bin/pipeline_worker_test.py +++ b/loading_pipeline/bin/pipeline_worker_test.py @@ -134,12 +134,12 @@ def test_process_queue_integration_test( self.assertEqual(ac_wgs, 69) @patch('loading_pipeline.lib.misc.slack._safe_post_to_slack') - @patch('loading_pipeline.api.request_handlers.WriteClickhouseLoadSuccessFileTask') + @patch('loading_pipeline.api.request_handlers.LoadClickhouseEntries') @patch('loading_pipeline.bin.pipeline_worker.logger') def test_process_failure( self, mock_logger, - mock_write_clickhouse_load_success_file_task, + mock_load_clickhouse_entries_task, mock_safe_post_to_slack, ): raw_request = { @@ -150,7 +150,7 @@ def test_process_failure( 'reference_genome': ReferenceGenome.GRCh38.value, 'dataset_type': DatasetType.SNV_INDEL.value, } - mock_write_clickhouse_load_success_file_task.return_value = MyFailingTask() + mock_load_clickhouse_entries_task.return_value = MyFailingTask() os.makedirs( loading_pipeline_queue_dir(), exist_ok=True, diff --git a/loading_pipeline/lib/misc/clickhouse_test.py b/loading_pipeline/lib/misc/clickhouse_test.py index 4a23d24a60..1126671b17 100644 --- a/loading_pipeline/lib/misc/clickhouse_test.py +++ b/loading_pipeline/lib/misc/clickhouse_test.py @@ -24,6 +24,7 @@ exchange_tables, get_clickhouse_client, insert_new_entries, + load_run_entries, load_run_variants, logged_query, normalize_partition, @@ -889,13 +890,8 @@ def test_entries_insert_flow(self, mock_for_reference_genome_dataset_type): ], ) - @patch.object( - ClickhouseReferenceDataset, - 'for_reference_genome_dataset_type', - return_value=[ClickhouseReferenceDataset.CLINVAR], - ) - def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_type): - load_run_variants( + def test_load_run_entries_snv_indel(self): + load_run_entries( ReferenceGenome.GRCh38, DatasetType.SNV_INDEL, TEST_RUN_ID, @@ -959,6 +955,19 @@ def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_typ (10, 4, 0, 0, 2, 0, 0), ], ) + + @patch.object( + ClickhouseReferenceDataset, + 'for_reference_genome_dataset_type', + return_value=[ClickhouseReferenceDataset.CLINVAR], + ) + def test_load_run_variants_snv_indel(self, mock_for_reference_genome_dataset_type): + load_run_variants( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + TEST_RUN_ID, + ) + cursor = connections['clickhouse_write'].cursor() cursor.execute( f""" SELECT * @@ -1013,13 +1022,11 @@ def test_load_complete_run_snv_indel(self, mock_for_reference_genome_dataset_typ ], ) - def test_load_complete_gcnv(self): + def test_load_run_variants_gcnv(self): load_run_variants( ReferenceGenome.GRCh38, DatasetType.GCNV, TEST_RUN_ID, - ['project_d'], - ['family_d1', 'family_d2'], ) cursor = connections['clickhouse_write'].cursor() cursor.execute( @@ -1049,6 +1056,16 @@ def test_load_complete_gcnv(self): ) key_lookup_count = cursor.fetchone()[0] self.assertEqual(key_lookup_count, 4) + + def test_load_run_entries_gcnv(self): + load_run_entries( + ReferenceGenome.GRCh38, + DatasetType.GCNV, + TEST_RUN_ID, + ['project_d'], + ['family_d1', 'family_d2'], + ) + cursor = connections['clickhouse_write'].cursor() cursor.execute( f""" SELECT COUNT(*) From d8fb9f7eb0b10292ae5e45a28c40c83022177d22 Mon Sep 17 00:00:00 2001 From: hanars Date: Thu, 3 Sep 2026 17:24:30 -0400 Subject: [PATCH 352/369] clean up --- .../lib/tasks/exports/write_new_entries_parquet_test.py | 1 - 1 file changed, 1 deletion(-) diff --git a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py index 3dbcec9add..05b73e2086 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet_test.py @@ -148,7 +148,6 @@ def test_write_new_entries_parquet(self): 'efg_1': 1, }, ) - self.maxDiff = None self.assertEqual( [export_json[0], export_json[9], export_json[15]], [ From 1961aa9d9203b7e7f1c7c86ef9fcc861b9a13f68 Mon Sep 17 00:00:00 2001 From: hanars Date: Fri, 4 Sep 2026 11:22:50 -0400 Subject: [PATCH 353/369] fix type checks --- .../lib/tasks/exports/write_new_entries_parquet.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py index 2762d9970a..810c8e56f8 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py +++ b/loading_pipeline/lib/tasks/exports/write_new_entries_parquet.py @@ -45,14 +45,14 @@ def output(self) -> luigi.Target: ), ) - def requires(self) -> dict[str, luigi.Task]: + def requires(self) -> list[luigi.Task]: return [ self.clone(WriteExistingVariantsParquetTask), self.clone(WriteNewVariantsTableTask), self.clone(WriteRemappedAndSubsettedCallsetTask), ] - def create_table(self) -> None: + def create_table(self) -> hl.Table: annotations_ht = hl.read_table(self.input()[1].path) annotation_selects = { field: func(annotations_ht) From fc9e1583bc46df51d6353d247f4bdb33e684cd32 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 4 Sep 2026 11:27:53 -0400 Subject: [PATCH 354/369] fix index error --- .../lib/tasks/write_remapped_and_subsetted_callset.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py b/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py index 3b72217cd1..b0e3c74b4f 100644 --- a/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py +++ b/loading_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py @@ -164,7 +164,7 @@ def create_table(self) -> hl.MatrixTable: self.callset_path, ), ) - sex_check_ht = hl.read_table(self.input()[3].path) + sex_check_ht = hl.read_table(self.input()[-1].path) families_failed_relatedness_check = get_families_failed_relatedness_check( families - families_failed_missing_samples.keys(), relatedness_check_ht, From f89d9231f3617cc1f3565c77276c67dd9c11c5b2 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 4 Sep 2026 15:07:29 -0400 Subject: [PATCH 355/369] use less memory intensive gt stats rebuild --- loading_pipeline/lib/misc/clickhouse.py | 34 +++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/loading_pipeline/lib/misc/clickhouse.py b/loading_pipeline/lib/misc/clickhouse.py index f99417544c..fabb678cb3 100644 --- a/loading_pipeline/lib/misc/clickhouse.py +++ b/loading_pipeline/lib/misc/clickhouse.py @@ -573,6 +573,7 @@ def get_partitions_for_projects( def create_staging_materialized_views( table_name_builder: TableNameBuilder, clickhouse_mvs: list[ClickHouseMaterializedView], + mv_overrides: dict[ClickHouseMaterializedView, list[list[str]]] | None = None, ): for clickhouse_mv in clickhouse_mvs: create_table_statement = get_create_mv_statements( @@ -583,6 +584,8 @@ def create_staging_materialized_views( table_name_builder.dst_prefix, table_name_builder.staging_dst_prefix, ) + for override in (mv_overrides or {}).get(clickhouse_mv, []): + create_table_statement = create_table_statement.replace(*override) logged_query(create_table_statement) @@ -1021,11 +1024,34 @@ def atomic_insert_entries( table_name_builder, ClickHouseTable.for_dataset_type_atomic_entries_update(dataset_type), ) + + mv_overrides = None + ordered_mv_table = None + if dataset_type == DatasetType.SNV_INDEL: + # Create a copy of the PROJECT_GT_STATS table ordered by key as the GT_STATS materialized view source + # This allows clickhouse to utilize a memory optimized group by only available for sorted tables + table_suffix = 'key_ordered' + ordered_mv_table = f'{table_name_builder.staging_dst_table(ClickHouseTable.PROJECT_GT_STATS)}/{table_suffix}' + logged_query( + f""" + CREATE TABLE {ordered_mv_table} + AS {table_name_builder.dst_table(ClickHouseTable.PROJECT_GT_STATS)} + ORDER BY key + """, + ) + mv_overrides = { + ClickHouseMaterializedView.PROJECT_GT_STATS_TO_GT_STATS_MV: [ + [table_name_builder.staging_dst_table(ClickHouseTable.PROJECT_GT_STATS), ordered_mv_table], + [';', ' SETTINGS max_memory_usage=10000000000, max_bytes_before_external_group_by=5000000000, optimize_aggregation_in_order=1;'], + ], + } + create_staging_materialized_views( table_name_builder, ClickHouseMaterializedView.for_dataset_type_atomic_entries_update( dataset_type, ), + mv_overrides=mv_overrides, ) stage_existing_project_partitions( table_name_builder, @@ -1050,6 +1076,14 @@ def atomic_insert_entries( project_guids, family_guids, ) + if ordered_mv_table: + logged_query( + f""" + INSERT INTO {ordered_mv_table} + SELECT(*) + FROM {table_name_builder.staging_dst_table(ClickHouseTable.PROJECT_GT_STATS)} + """, + ) finalize_refresh_flow(table_name_builder, project_guids) From c471ea89d41956c5aa95594841aafdc520ddaac7 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 4 Sep 2026 15:09:46 -0400 Subject: [PATCH 356/369] clean up --- loading_pipeline/lib/misc/clickhouse.py | 15 +++++---------- 1 file changed, 5 insertions(+), 10 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse.py b/loading_pipeline/lib/misc/clickhouse.py index fabb678cb3..4f156fd9d5 100644 --- a/loading_pipeline/lib/misc/clickhouse.py +++ b/loading_pipeline/lib/misc/clickhouse.py @@ -1028,20 +1028,15 @@ def atomic_insert_entries( mv_overrides = None ordered_mv_table = None if dataset_type == DatasetType.SNV_INDEL: - # Create a copy of the PROJECT_GT_STATS table ordered by key as the GT_STATS materialized view source + # Create a copy of the PROJECT_GT_STATS table ordered by key for the GT_STATS materialized view source # This allows clickhouse to utilize a memory optimized group by only available for sorted tables table_suffix = 'key_ordered' - ordered_mv_table = f'{table_name_builder.staging_dst_table(ClickHouseTable.PROJECT_GT_STATS)}/{table_suffix}' - logged_query( - f""" - CREATE TABLE {ordered_mv_table} - AS {table_name_builder.dst_table(ClickHouseTable.PROJECT_GT_STATS)} - ORDER BY key - """, - ) + base_table = table_name_builder.staging_dst_table(ClickHouseTable.PROJECT_GT_STATS) + ordered_mv_table = f'{base_table}/{table_suffix}' + logged_query(f'CREATE TABLE {ordered_mv_table} AS {base_table} ORDER BY key') mv_overrides = { ClickHouseMaterializedView.PROJECT_GT_STATS_TO_GT_STATS_MV: [ - [table_name_builder.staging_dst_table(ClickHouseTable.PROJECT_GT_STATS), ordered_mv_table], + [base_table, ordered_mv_table], [';', ' SETTINGS max_memory_usage=10000000000, max_bytes_before_external_group_by=5000000000, optimize_aggregation_in_order=1;'], ], } From 79ff7779f8e2bd693a197a5741f0bdc7006693ca Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Fri, 4 Sep 2026 16:16:19 -0400 Subject: [PATCH 357/369] ruff --- loading_pipeline/lib/misc/clickhouse.py | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse.py b/loading_pipeline/lib/misc/clickhouse.py index 4f156fd9d5..2b7dab8569 100644 --- a/loading_pipeline/lib/misc/clickhouse.py +++ b/loading_pipeline/lib/misc/clickhouse.py @@ -1031,13 +1031,18 @@ def atomic_insert_entries( # Create a copy of the PROJECT_GT_STATS table ordered by key for the GT_STATS materialized view source # This allows clickhouse to utilize a memory optimized group by only available for sorted tables table_suffix = 'key_ordered' - base_table = table_name_builder.staging_dst_table(ClickHouseTable.PROJECT_GT_STATS) + base_table = table_name_builder.staging_dst_table( + ClickHouseTable.PROJECT_GT_STATS, + ) ordered_mv_table = f'{base_table}/{table_suffix}' logged_query(f'CREATE TABLE {ordered_mv_table} AS {base_table} ORDER BY key') mv_overrides = { ClickHouseMaterializedView.PROJECT_GT_STATS_TO_GT_STATS_MV: [ [base_table, ordered_mv_table], - [';', ' SETTINGS max_memory_usage=10000000000, max_bytes_before_external_group_by=5000000000, optimize_aggregation_in_order=1;'], + [ + ';', + ' SETTINGS max_memory_usage=10000000000, max_bytes_before_external_group_by=5000000000, optimize_aggregation_in_order=1;', + ], ], } From 9ad154de3fef6d2ee4169778c6dc127bc65b5439 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Wed, 9 Sep 2026 10:29:11 -0400 Subject: [PATCH 358/369] better back off strategy --- loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster.py b/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster.py index 2ee2464cc3..33785a8d1e 100644 --- a/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster.py +++ b/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster.py @@ -195,7 +195,7 @@ def run(self): raise RuntimeError(msg) self.get_running_cluster() - @retry(tries=5) + @retry(tries=5, backoff=1) def get_running_cluster(self): cluster = self.safely_get_cluster() if not cluster: From bca4b4e1233ce464a4c25cc0904042085413089d Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Wed, 9 Sep 2026 10:33:01 -0400 Subject: [PATCH 359/369] no delay on test retry --- loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster.py | 3 ++- .../lib/tasks/dataproc/create_dataproc_cluster_test.py | 1 + 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster.py b/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster.py index 33785a8d1e..9b4c5aeb30 100644 --- a/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster.py +++ b/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster.py @@ -29,6 +29,7 @@ ], ) TIMEOUT_S = 1200 +CLUSTER_RETRY_DELAY = 30 FAILURE_STATUSES = { google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.UNKNOWN, google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.ERROR, @@ -195,7 +196,7 @@ def run(self): raise RuntimeError(msg) self.get_running_cluster() - @retry(tries=5, backoff=1) + @retry(tries=5, backoff=1, delay=CLUSTER_RETRY_DELAY) def get_running_cluster(self): cluster = self.safely_get_cluster() if not cluster: diff --git a/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster_test.py b/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster_test.py index 6634feea8c..f1da2c280e 100644 --- a/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster_test.py +++ b/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster_test.py @@ -13,6 +13,7 @@ ) +@patch('loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster.CLUSTER_RETRY_DELAY', 0) @patch.multiple( 'loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster.Env', GCLOUD_PROJECT='proj', From 59a66e7770966c9c372dcb631788dff941eb33ac Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Wed, 9 Sep 2026 10:35:23 -0400 Subject: [PATCH 360/369] ruff --- .../lib/tasks/dataproc/create_dataproc_cluster_test.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster_test.py b/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster_test.py index f1da2c280e..ab1940bbc2 100644 --- a/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster_test.py +++ b/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster_test.py @@ -13,7 +13,10 @@ ) -@patch('loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster.CLUSTER_RETRY_DELAY', 0) +@patch( + 'loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster.CLUSTER_RETRY_DELAY', + 0, +) @patch.multiple( 'loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster.Env', GCLOUD_PROJECT='proj', From 4a4aa73ba7f2d2e7eeea7d437a452d48584bb20d Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Wed, 9 Sep 2026 11:00:06 -0400 Subject: [PATCH 361/369] fix ordered table create syntax --- loading_pipeline/lib/misc/clickhouse.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/loading_pipeline/lib/misc/clickhouse.py b/loading_pipeline/lib/misc/clickhouse.py index 2b7dab8569..a5c69a9db1 100644 --- a/loading_pipeline/lib/misc/clickhouse.py +++ b/loading_pipeline/lib/misc/clickhouse.py @@ -1034,7 +1034,7 @@ def atomic_insert_entries( base_table = table_name_builder.staging_dst_table( ClickHouseTable.PROJECT_GT_STATS, ) - ordered_mv_table = f'{base_table}/{table_suffix}' + ordered_mv_table = f'{base_table[:-1]}/{table_suffix}`' logged_query(f'CREATE TABLE {ordered_mv_table} AS {base_table} ORDER BY key') mv_overrides = { ClickHouseMaterializedView.PROJECT_GT_STATS_TO_GT_STATS_MV: [ From 9e41bf2128ed6106db472f81049d4bef0161825e Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Wed, 9 Sep 2026 12:14:20 -0400 Subject: [PATCH 362/369] pr feedback --- loading_pipeline/lib/misc/clickhouse.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/loading_pipeline/lib/misc/clickhouse.py b/loading_pipeline/lib/misc/clickhouse.py index a5c69a9db1..0c3c59fe84 100644 --- a/loading_pipeline/lib/misc/clickhouse.py +++ b/loading_pipeline/lib/misc/clickhouse.py @@ -1080,7 +1080,7 @@ def atomic_insert_entries( logged_query( f""" INSERT INTO {ordered_mv_table} - SELECT(*) + SELECT * FROM {table_name_builder.staging_dst_table(ClickHouseTable.PROJECT_GT_STATS)} """, ) From bf831a4a734f78559ae9047cb24d3a492935a530 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Wed, 9 Sep 2026 12:15:54 -0400 Subject: [PATCH 363/369] Revert "no delay on test retry" This reverts commit bca4b4e1233ce464a4c25cc0904042085413089d. --- .../lib/tasks/dataproc/create_dataproc_cluster.py | 3 +-- .../lib/tasks/dataproc/create_dataproc_cluster_test.py | 4 ---- 2 files changed, 1 insertion(+), 6 deletions(-) diff --git a/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster.py b/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster.py index 9b4c5aeb30..33785a8d1e 100644 --- a/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster.py +++ b/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster.py @@ -29,7 +29,6 @@ ], ) TIMEOUT_S = 1200 -CLUSTER_RETRY_DELAY = 30 FAILURE_STATUSES = { google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.UNKNOWN, google.cloud.dataproc_v1.types.clusters.ClusterStatus.State.ERROR, @@ -196,7 +195,7 @@ def run(self): raise RuntimeError(msg) self.get_running_cluster() - @retry(tries=5, backoff=1, delay=CLUSTER_RETRY_DELAY) + @retry(tries=5, backoff=1) def get_running_cluster(self): cluster = self.safely_get_cluster() if not cluster: diff --git a/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster_test.py b/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster_test.py index ab1940bbc2..6634feea8c 100644 --- a/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster_test.py +++ b/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster_test.py @@ -13,10 +13,6 @@ ) -@patch( - 'loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster.CLUSTER_RETRY_DELAY', - 0, -) @patch.multiple( 'loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster.Env', GCLOUD_PROJECT='proj', From e31670c51e3d2dc6cca2865a47e24cc001aa2c2b Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Wed, 9 Sep 2026 12:16:50 -0400 Subject: [PATCH 364/369] mock sleep --- .../lib/tasks/dataproc/create_dataproc_cluster_test.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster_test.py b/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster_test.py index 6634feea8c..c5a53ffebb 100644 --- a/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster_test.py +++ b/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster_test.py @@ -25,6 +25,9 @@ scopes=SOCIAL_AUTH_GOOGLE_OAUTH2_SCOPE, ), ) +@patch( + 'loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster.time', +) @patch( 'loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster.dataproc.ClusterControllerClient', ) From 0c6d891c07a25e15184a929492e2053f45649823 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Wed, 9 Sep 2026 12:27:58 -0400 Subject: [PATCH 365/369] codacy --- loading_pipeline/lib/misc/clickhouse.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/loading_pipeline/lib/misc/clickhouse.py b/loading_pipeline/lib/misc/clickhouse.py index 0c3c59fe84..4e31294ba5 100644 --- a/loading_pipeline/lib/misc/clickhouse.py +++ b/loading_pipeline/lib/misc/clickhouse.py @@ -1082,7 +1082,7 @@ def atomic_insert_entries( INSERT INTO {ordered_mv_table} SELECT * FROM {table_name_builder.staging_dst_table(ClickHouseTable.PROJECT_GT_STATS)} - """, + """, # nosec B608 ) finalize_refresh_flow(table_name_builder, project_guids) From 0120881c2c5a51990e9d78b3121ce70730db7ece Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Wed, 9 Sep 2026 13:26:28 -0400 Subject: [PATCH 366/369] setting override stability --- loading_pipeline/lib/misc/clickhouse.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/loading_pipeline/lib/misc/clickhouse.py b/loading_pipeline/lib/misc/clickhouse.py index 4e31294ba5..480356abbc 100644 --- a/loading_pipeline/lib/misc/clickhouse.py +++ b/loading_pipeline/lib/misc/clickhouse.py @@ -1040,8 +1040,8 @@ def atomic_insert_entries( ClickHouseMaterializedView.PROJECT_GT_STATS_TO_GT_STATS_MV: [ [base_table, ordered_mv_table], [ - ';', - ' SETTINGS max_memory_usage=10000000000, max_bytes_before_external_group_by=5000000000, optimize_aggregation_in_order=1;', + 'GROUP BY key', + 'GROUP BY key SETTINGS max_memory_usage=10000000000, max_bytes_before_external_group_by=5000000000, optimize_aggregation_in_order=1', ], ], } From 01ff52eb3a1c5c8fb173112cfb38e67bf1c1e1c9 Mon Sep 17 00:00:00 2001 From: hanars Date: Wed, 9 Sep 2026 13:58:53 -0400 Subject: [PATCH 367/369] fix mock sleep Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> --- .../lib/tasks/dataproc/create_dataproc_cluster_test.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster_test.py b/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster_test.py index c5a53ffebb..54654aa933 100644 --- a/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster_test.py +++ b/loading_pipeline/lib/tasks/dataproc/create_dataproc_cluster_test.py @@ -25,9 +25,7 @@ scopes=SOCIAL_AUTH_GOOGLE_OAUTH2_SCOPE, ), ) -@patch( - 'loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster.time', -) +@patch('time.sleep') @patch( 'loading_pipeline.lib.tasks.dataproc.create_dataproc_cluster.dataproc.ClusterControllerClient', ) From e2ef688d8e71e6685a7fbdafdd41daa3a0d2780a Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 10 Sep 2026 02:51:46 +0000 Subject: [PATCH 368/369] Bump js-yaml from 3.14.2 to 3.15.2 in /ui Bumps [js-yaml](https://github.com/nodeca/js-yaml) from 3.14.2 to 3.15.2. - [Changelog](https://github.com/nodeca/js-yaml/blob/3.15.2/CHANGELOG.md) - [Commits](https://github.com/nodeca/js-yaml/compare/3.14.2...3.15.2) --- updated-dependencies: - dependency-name: js-yaml dependency-version: 3.15.2 dependency-type: indirect ... Signed-off-by: dependabot[bot] --- ui/package-lock.json | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/ui/package-lock.json b/ui/package-lock.json index 9dccc5c08a..c839477376 100644 --- a/ui/package-lock.json +++ b/ui/package-lock.json @@ -12573,10 +12573,11 @@ "integrity": "sha512-RdJUflcE3cUzKiMqQgsCu06FPu9UdIJO0beYbPhHN4k6apgJtifcoCtT9bcxOpYBtpD2kCM6Sbzg4CausW/PKQ==" }, "node_modules/js-yaml": { - "version": "3.14.2", - "resolved": "https://registry.npmjs.org/js-yaml/-/js-yaml-3.14.2.tgz", - "integrity": "sha512-PMSmkqxr106Xa156c2M265Z+FTrPl+oxd/rgOQy2tijQeK5TxQ43psO1ZCwhVOSdnn+RzkzlRz/eY4BgJBYVpg==", + "version": "3.15.2", + "resolved": "https://registry.npmjs.org/js-yaml/-/js-yaml-3.15.2.tgz", + "integrity": "sha512-6EuL879VkRA+1Cz578mKMiKvjPNEuk6+r1JaFzoSWejZmtf7xWbIyw1e3KkxlkzTIt9Taw6JBhEppG7utc1P+w==", "dev": true, + "license": "MIT", "dependencies": { "argparse": "^1.0.7", "esprima": "^4.0.0" @@ -29922,9 +29923,9 @@ "integrity": "sha512-RdJUflcE3cUzKiMqQgsCu06FPu9UdIJO0beYbPhHN4k6apgJtifcoCtT9bcxOpYBtpD2kCM6Sbzg4CausW/PKQ==" }, "js-yaml": { - "version": "3.14.2", - "resolved": "https://registry.npmjs.org/js-yaml/-/js-yaml-3.14.2.tgz", - "integrity": "sha512-PMSmkqxr106Xa156c2M265Z+FTrPl+oxd/rgOQy2tijQeK5TxQ43psO1ZCwhVOSdnn+RzkzlRz/eY4BgJBYVpg==", + "version": "3.15.2", + "resolved": "https://registry.npmjs.org/js-yaml/-/js-yaml-3.15.2.tgz", + "integrity": "sha512-6EuL879VkRA+1Cz578mKMiKvjPNEuk6+r1JaFzoSWejZmtf7xWbIyw1e3KkxlkzTIt9Taw6JBhEppG7utc1P+w==", "dev": true, "requires": { "argparse": "^1.0.7", From ca9da5e20292c2d194093e432d24d4cc42a960f7 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 10 Sep 2026 02:51:53 +0000 Subject: [PATCH 369/369] Bump svgo from 2.8.3 to 2.8.4 in /ui Bumps [svgo](https://github.com/svg/svgo) from 2.8.3 to 2.8.4. - [Release notes](https://github.com/svg/svgo/releases) - [Commits](https://github.com/svg/svgo/compare/v2.8.3...v2.8.4) --- updated-dependencies: - dependency-name: svgo dependency-version: 2.8.4 dependency-type: indirect ... Signed-off-by: dependabot[bot] --- ui/package-lock.json | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/ui/package-lock.json b/ui/package-lock.json index 9dccc5c08a..d87da312b9 100644 --- a/ui/package-lock.json +++ b/ui/package-lock.json @@ -17908,10 +17908,11 @@ "dev": true }, "node_modules/svgo": { - "version": "2.8.3", - "resolved": "https://registry.npmjs.org/svgo/-/svgo-2.8.3.tgz", - "integrity": "sha512-5EZD0pafXX6PphdwOGCiVLDSaV1xyuQao2blHajHLsPxr07q4mmEjdtXEWgG07ae2mIz8Ex2CDXNCTiXhy3Khw==", + "version": "2.8.4", + "resolved": "https://registry.npmjs.org/svgo/-/svgo-2.8.4.tgz", + "integrity": "sha512-2GJ4h3rl13qYTdwllaK6QlL8tG+UrM8626V2Ylcd/yBUv2Y/EwLsYisVV6UDCRmlk+C74G8nMpxJCk0RWPdDCw==", "dev": true, + "license": "MIT", "dependencies": { "commander": "^7.2.0", "css-select": "^4.1.3", @@ -34260,9 +34261,9 @@ "dev": true }, "svgo": { - "version": "2.8.3", - "resolved": "https://registry.npmjs.org/svgo/-/svgo-2.8.3.tgz", - "integrity": "sha512-5EZD0pafXX6PphdwOGCiVLDSaV1xyuQao2blHajHLsPxr07q4mmEjdtXEWgG07ae2mIz8Ex2CDXNCTiXhy3Khw==", + "version": "2.8.4", + "resolved": "https://registry.npmjs.org/svgo/-/svgo-2.8.4.tgz", + "integrity": "sha512-2GJ4h3rl13qYTdwllaK6QlL8tG+UrM8626V2Ylcd/yBUv2Y/EwLsYisVV6UDCRmlk+C74G8nMpxJCk0RWPdDCw==", "dev": true, "requires": { "commander": "^7.2.0",

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