Dev - #5477

Merged

hanars merged 187 commits into

Jun 10, 2026

Commits on May 20, 2026

update test requirements
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use django for db setup
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update requiremnts
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use seqr requiremnts
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use venv
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no seqr app migrations
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fix venv
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split setup steps
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remove venv for now
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add postgres
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Merge branch 'vlm-no-hail' of https://github.com/broadinstitute/seqr into vlm-shared-test-db
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Commits on May 21, 2026

depndency install order
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psycopg setup
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add clickhous eports
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env reset
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fix clcikhouse host
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explicitly create database
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use default github actions docker
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fix clickhouse hostname
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remove extra psycopg
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test setup order
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add clikhouse data dirs
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use venv
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reload users
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setup order
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run all db migrations
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install postrgres db too
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postgres db setup
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use pytest for test db creation
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depndency install
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use setup_databases explicitly
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pytest django
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clean up
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pytest setup runner
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debug
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undo debug
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do not actually run tests
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Commits on May 26, 2026

restart venv
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no venv debug
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correct db name
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Revert "no venv debug"
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install soiurce
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use explicit venv python for pytest
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explicitly skip pytest ui
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delete old jsx python test
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clean up
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clean up
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missing dependencies
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9591a59
more requirements
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install order
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DJANGO_SETTINGS_MODULE
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use migrate directly
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create db
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back to pytets
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rename test db
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aa9b3ec
fix syntax
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verbosity
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actually keep db
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more verbose
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actually run test
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skip tests
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run tests
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run single test
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do not recreate db
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try setup only
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unblock django db access
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enable databases for vlm tests
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better fixture
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custom db setup
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clean up
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cleaner args
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fix typing
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run vlm tests on fixture update
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no custom django settings
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set up default db
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clickhouse settings move up
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settings profile
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clickhouse grant permissions
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users config
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Commits on May 27, 2026

use config
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clean up
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clean up
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remove user grants for now
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reload users again
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readd user rants
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remove unused file
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clickhouse official docker for tests
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test user access managemnt
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add settings
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vlm test access maagement
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reload config
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restart clickhouse after confi update
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wait for restart
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explicit sleep for restart
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change order
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test with service wait loop
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use correct port ofr curl
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correct endpoint
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seqr hosted clickhouse image
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health check clean up
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debug test failure
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debug test failure
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debug test failure
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debug test failure
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try cache settings
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settings iter
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settings iter
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settings iter
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Commits on May 28, 2026

settings iter
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settings iter
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settings iter
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settings iter
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settings iter
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settings iter
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settings iter
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clean up
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Merge branch 'clickhouse-bump-unit-test-version' of https://github.com/broadinstitute/seqr into vlm-shared-test-db
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setup for bumped version
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adjust settings profile
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run without pytest setup
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add dbs
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initialize reference data db
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skip postgres setup
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reference data db
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postgres iage name
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fix reference data db reate
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create clickhouse db
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back to pytest
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Commits on May 29, 2026

create dbs
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fix loaddata
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debug clickhouse users
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remove debug
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escape chars
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fix user creation
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remove invalid arg
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lower verbosity
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Revert "setup for bumped version"
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Revert "Merge branch 'clickhouse-bump-unit-test-version' of https://github.com/broadinstitute/seqr into vlm-shared-test-db"
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settings cleanup
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Merge branch 'dev' of https://github.com/broadinstitute/seqr into vlm-shared-test-db
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restore merge issues
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pip cache
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pip cache order
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remove unneeded fixture
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verride method
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override method
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update test
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reload gt stats
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correct counts
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correct counts
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update total counts
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fix counts
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update coverage
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Merge branch 'dev' of https://github.com/broadinstitute/seqr into vlm-shared-test-db
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e65db74
Merge branch 'dev' of https://github.com/broadinstitute/seqr into vlm-shared-test-db
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29a3ec7
fix vlm requirements install
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disable rna reference tracks for grach37
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Merge pull request #5468 from broadinstitute/rna-seq-hg37-references
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Merge pull request #5467 from broadinstitute/vlm-docker-reequirents
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update gnomad constartint citation
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fix linting
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Commits on Jun 1, 2026

Merge pull request #5469 from broadinstitute/gnomad-constraint-citation
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2e5be0c

Commits on Jun 3, 2026

sync tag updates to postgres dicts
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reload metadata on project update
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family update reload
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Commits on Jun 4, 2026

individual update reloads
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log user with relaods
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fix tests
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fix saved variant data tests
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test family updte metadata
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individual tests
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test project updates
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test saved variant relaod
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fix tests
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pr feedback
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Commits on Jun 8, 2026

Merge pull request #5456 from broadinstitute/clickhouse-bump-unit-test-version
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Merge branch 'dev' of https://github.com/broadinstitute/seqr into vlm-shared-test-db
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actually merge dev
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update for newwer verrsion
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clean up db config for clickhouse
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fix settings vars
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Commits on Jun 9, 2026

Commits on Jun 10, 2026