diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml new file mode 100644 index 0000000..4bc49bd --- /dev/null +++ b/.github/workflows/tests.yml @@ -0,0 +1,35 @@ +name: Tests + +on: + push: + branches: [ main, master, dev/v2026.01 ] + pull_request: + branches: [ main, master, dev/v2026.01 ] + +jobs: + test: + runs-on: ubuntu-latest + env: + FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true + strategy: + fail-fast: false + matrix: + python-version: ["3.9", "3.10", "3.11", "3.12", "3.13", "3.14"] + + steps: + - uses: actions/checkout@v4 + + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python-version }} + allow-prereleases: true + + - name: Install dependencies + run: | + python -m pip install --upgrade pip + python -m pip install .[dev] + + - name: Run tests + run: | + python -m pytest diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..a3b9125 --- /dev/null +++ b/.gitignore @@ -0,0 +1,45 @@ +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# Distribution / packaging +build/ +dist/ +*.egg-info/ +*.egg + +# Virtual environments +.venv/ +venv/ +ENV/ +env/ + +# IDEs +.idea/ +*.swp +*.swo +*~ + +# Jupyter Notebook +.ipynb_checkpoints/ + +# Pytest +.pytest_cache/ + +# Operating System +.DS_Store +Thumbs.db +Desktop.ini + +# Logs and temporary files +*.log +*.tmp + +AI agents +.junie/memory + +# EM-DAT files for testing +data/260311_emdat_new.xlsx +test_emdat.py + diff --git a/.junie/instructions/data.md b/.junie/instructions/data.md new file mode 100644 index 0000000..c7898b5 --- /dev/null +++ b/.junie/instructions/data.md @@ -0,0 +1,19 @@ +# Reference Data & Metadata Management + +EM-TEST relies on reference data to validate EM-DAT content. + +## 1. Reference Files +Reference data is stored in `emtest\validation_data\`. +- **`classification_tree.toml`**: The source of truth for disaster types and subgroups. +- **`UNSD_M49_standards.csv`**: Reference for country and region names. +- **`gaul_adm1_code.txt`**: GAUL administrative level 1 codes. + +## 2. Loading Data +Reference data is loaded by `emtest\validation_data\data_loader.py`. +When adding new reference files, update the `data_loader.py` and ensure they are included in `pyproject.toml` under `tool.setuptools.package-data`. + +## 3. Metadata and Citations +- **`CITATION.cff`**: Project citation info for scientific researchers. +- **`LICENSE`**: MIT License. +- **Versioning**: Follow semantic versioning, which is reflected in `pyproject.toml`. +- **README Updates**: If you add new validation checks, update the corresponding tables in `README.md`. diff --git a/.junie/instructions/domain.md b/.junie/instructions/domain.md new file mode 100644 index 0000000..999bacc --- /dev/null +++ b/.junie/instructions/domain.md @@ -0,0 +1,22 @@ +# EM-DAT Domain Knowledge + +EM-TEST validates data related to international disasters. + +## 1. Geospatial Consistency +- **ISO3 Codes**: Country codes should be valid ISO-3166-1 alpha-3 codes. +- **Geography**: Valid latitude (-90 to 90) and longitude (-180 to 180). +- **Standards**: The project follows UNSD M49 standards for country and area codes. + +## 2. Temporal Logic +Disaster numbers (`DisNo.`) contain the year the disaster was recorded. +- **Consistency**: `Start Year` should generally match the year in `DisNo.`. +- **Duration**: `Start Year/Month/Day` must be before or equal to `End Year/Month/Day`. + +## 3. Classification +Disasters are categorized hierarchically: +- **Disaster Group** (e.g., Natural) +- **Disaster Subgroup** (e.g., Meteorological) +- **Disaster Type** (e.g., Storm) +- **Disaster Subtype** (e.g., Tropical cyclone) + +Validation must ensure that combinations of these fields follow the official `classification_tree.toml`. diff --git a/.junie/instructions/validation.md b/.junie/instructions/validation.md new file mode 100644 index 0000000..f45e0f2 --- /dev/null +++ b/.junie/instructions/validation.md @@ -0,0 +1,23 @@ +# Data Validation with Pandera and Pandas + +The core of EM-TEST is built on `pandera` and `pandas`. + +## 1. Schema Definition +Schemas are defined in `emtest\validation_schemas.py`. +- **`DataFrameSchema`**: Use this to define per-column constraints. +- **Nullability**: In Pandas, the standard `int` type is not nullable. Use `float` for columns that contain integers but may have null values (e.g., `Start Month`, `Start Day`). + +## 2. Custom Checks +Complex validation logic should be implemented in `emtest\custom_checks.py`. +- **Single-Column Checks**: Implement logic for a specific field (e.g., `check_disno`, `check_month`). +- **Multi-Column ("Wide") Checks**: Use these for consistency between fields (e.g., `check_start_end_year_consistency`). + +## 3. Regular Expression Engineering +Identifiers are often validated via Regex: +- **DisNo format**: `^\d{4}-\d{4}-[A-Z]{3}$` (Year-Sequence-CountryISO). +- **External IDs**: GLIDE numbers and other identifiers rely on specific patterns. + +## 4. Testing Pattern +Since there are no traditional automated tests, verify changes using the example script: +- `python examples\validation_script.py` +This script uses the schema to validate a sample dataset. diff --git a/AGENT.md b/AGENT.md new file mode 100644 index 0000000..cbfa344 --- /dev/null +++ b/AGENT.md @@ -0,0 +1,21 @@ +# EM-TEST Agent Instructions + +EM-TEST is a Python-based testing framework for [EM-DAT](https://www.emdat.be/) disaster datasets using `pandas` and `pandera`. + +## Quick Start +- **Environment**: Python 3.11+, managed with `uv`. +- **Install**: `uv sync` +- **Core Logic**: `emtest/` module. +- **Validation**: `emtest/validation_schemas.py` and `emtest/custom_checks.py`. + +## Progressive Disclosure Instructions +For specific tasks, refer to the following guides: + +- [**Data Validation**](.junie/instructions/validation.md): Writing schemas, custom checks, and handling nullable types. +- [**EM-DAT Domain**](.junie/instructions/domain.md): Geospatial, temporal, and classification logic for disaster data. +- [**Reference Data & Metadata**](.junie/instructions/data.md): Managing reference files and project metadata (`CITATION.cff`). + +## General Principles +- **Transparency**: Every check must be well-documented. +- **Reproducibility**: Use `uv` for consistent environments. +- **Consistency**: Maintain the existing `pandera` schema structure. diff --git a/CITATION.cff b/CITATION.cff index ad69044..703d191 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -19,6 +19,6 @@ keywords: - testing-framework - python license: MIT -version: 2024.12.0 -date-released: '2024-12-04' +version: 2026.04.0 +date-released: '2026-04-08' diff --git a/LICENSE b/LICENSE index 0164d12..ef3a329 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) 2024 EM-DAT +Copyright (c) 2026 EM-DAT Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/README.md b/README.md index 417c2c1..418babe 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,8 @@ # EM-TEST +[![Tests](https://github.com/em-dat/em-test/actions/workflows/tests.yml/badge.svg)](https://github.com/em-dat/em-test/actions/workflows/tests.yml) +![Python Versions](https://img.shields.io/badge/python-3.9%20%7C%203.10%20%7C%203.11%20%7C%203.12%20%7C%203.13%20%7C%203.14-blue) +[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14275790.svg)](https://doi.org/10.5281/zenodo.14275790) EM-TEST is a testing framework for [EM-DAT](https://www.emdat.be/) public @@ -7,14 +10,14 @@ data, built on the [`pandas`](https://pandas.pydata.org/) and [`pandera`](https://pandera.readthedocs.io/en/stable/) Python packages. > [!IMPORTANT] -> This version of EM-TEST has been built for EM-DAT public data on 2024/08/26. +> This version of EM-TEST has been built for EM-DAT public data on 2026/04/08. > Some tests might fail for versions prior to this date. EM-TEST is not > suitable for EM-DAT versions prior to September 26, 2023. ## Why using EM-TEST? The EM-DAT database is a long-lasting project that has started in 1988. In the -past, data was encoded manually sometimes using free text fields without +past, data was encoded manually, sometimes using free text fields without constraints. The EM-TEST framework was initially developed to identify issues in the data, prior to the redesign of the database. EM-TEST is to some extent redundant with many existing constraints in the EM-DAT database. @@ -39,48 +42,32 @@ So, why use EM-TEST? Here are five reasons: ### Prerequisites -EM-TEST was developed using **Python 3.11** with the following dependencies: +EM-TEST targets **Python 3.9+** and is known to work on Python 3.9–3.14. -``` -openpyxl~=3.1 -pandas~=2.2 -pandera~=0.20 -toml~=0.10 -``` +Refer to the `pyproject.toml` file for the list of required dependencies. ### Installation -1. Download the project or clone the repository to your local machine using Git +1. Clone the repository: ```bash git clone https://github.com/em-dat/EM-TEST.git +cd EM-TEST ``` -2. Navigate to the project's directory -3. Create a Python virtual environment (or alternatives) - -On macOS and Linux: - -```bash -python3 -m venv env # Create virtual environment -source env/bin/activate # Activate virtual environment -``` - -On Windows: +2. Set up the environment: -```bash -python -m venv env # Create virtual environment -.\env\Scripts\activate # Activate virtual environment -``` +- **Using uv (recommended):** + ```bash + uv sync --all-extras --dev + ``` -4. Install the project and its dependencies - -```bash -pip install -r requirements.txt # Install the dependencies -python setup.py install # Install the project -``` - -Check out the subsequent sections to understand how to use the project. +- **Using pip:** + ```bash + python -m venv .venv + source .venv/bin/activate # Or .\.venv\Scripts\Activate on Windows + python -m pip install -e ".[dev]" + ``` ### Validate EM-DAT Content @@ -102,6 +89,17 @@ emdat_schema.validate(emdat) See the "examples" folder of this repository. +### Running Tests + +If you have installed the development dependencies, you can run the test suite +using `pytest`: + +```bash +uv run pytest +``` + +This will execute all validation tests and unit tests for custom checks. + ## EM-DAT Validation Schema ### Data Type Validation @@ -155,6 +153,7 @@ schema. | Total Damage, Adjusted ('000 US$) | float | True | False | | CPI | float | True | False | | Admin Units | str | True | False | +| GADM Admin Units | str | True | False | | Entry Date | Timestamp | False | False | | Last Update | Timestamp | False | False | @@ -179,16 +178,16 @@ that are not listed in the currently used reference See [EM-DAT Documentation](https://doc.emdat.be/docs/data-structure-and-content/spatial-information/#united-nations-m49-standard-country-or-area-codes)). EM-DAT has a few exceptions for oversea territories and historical countries not included in the current reference. -This is somewhat normal given polical changes throughout History, yet, -EM-TEST allows to explicitly flag which cases are in EM-DAT thanks to the +This is somewhat normal given political changes throughout History, yet, +EM-TEST allows explicitly flaging which cases are in EM-DAT thanks to the implemented warning. Regarding the warning comparing the Start Year to the year included in the -DisNo., `check_disno_vs_start_year `, both year should be identical. However, +DisNo., `check_disno_vs_start_year `, both years should be identical. However, it may happen that in the final reference used to describe the disaster event, -the official start date has been updated. Such a change is more likely for slow -onset disasters like droughts. For this reason, the test is implemented as a -warning that will retrieve these cases, as well as potential errors in the +the official start date has been updated. Such a change is more likely for +slow-onset disasters like droughts. For this reason, the test is implemented as +a warning that will retrieve these cases, as well as potential errors in the year definition. Finally, we test the 'CPI' value to be in the range 0-110. Technically, @@ -246,6 +245,7 @@ See [EM-DAT Documentation](https://doc.emdat.be/docs/protocols/economic-adjustme | Total Damage, Adjusted ('000 US$) | greater_than(0.) | Test whether value is greater than 0 | Error | | CPI | in_range(0., 110.) | Test whether value is within range 0-110. | Warning | | Admin Units | is_valid_json | Test whether value is a json string | Error | +| GADM Admin Units | is_valid_json | Test whether value is a json string | Error | | Entry Date | in_range(1988/1/1, CURRENT_DATE) | Test whether value is within valid date range | Error | | Last Update | in_range(1988/1/1, CURRENT_DATE) | Test whether value is within valid date range | Error | @@ -276,7 +276,7 @@ multi-column checks are listed below. ## How to Contribute? If you notice an anomaly in the EM-DAT public data that could be prevented using -the EM-TEST framework, we encourage you to submit an issue, using the [GitHub +the EM-TEST framework, we encourage you to submit an issue using the [GitHub issue tracker](https://github.com/em-dat/em-test/issues). We will consider the addition of new tests to update the framework. @@ -291,17 +291,17 @@ citation below or the citation metadata file `CITATION.cff`. Wathelet, Valentin}, title = {EM-TEST: A Testing Framework for the EM-DAT Data}, month = dec, - year = 2024, + year = 2026, publisher = {Zenodo}, - version = {2024.12.0}, + version = {2026.04.0}, doi = {10.5281/zenodo.14275790}, url = {https://doi.org/10.5281/zenodo.14275790} } ``` Or ->Delforge, D., & Wathelet, V. (2024). EM-TEST: A Testing Framework for the -> EM-DAT Data (2024.12.0). Zenodo. https://doi.org/10.5281/zenodo.14275790 +>Delforge, D., & Wathelet, V. (2026). EM-TEST: A Testing Framework for the +> EM-DAT Data (2026.04.0). Zenodo. https://doi.org/10.5281/zenodo.14275790 ## Useful Links diff --git a/checklist.md b/checklist.md new file mode 100644 index 0000000..c5ad397 --- /dev/null +++ b/checklist.md @@ -0,0 +1,37 @@ +# Release Checklist + +This checklist outlines the items to check, modify, and do before finalizing the release of EM-TEST. + +## 1. Versioning and Metadata +- [ ] Synchronize version number in `pyproject.toml`. +- [ ] Synchronize version number in `emtest/__init__.py`. +- [ ] Update version and release date in `CITATION.cff` and within the How to Cite section of `README.md`. +- [ ] Check if `README.md` requires any version-specific updates (e.g., supported Python versions, installation steps). +- [ ] Ensure the license year is up to date if necessary. + +## 2. Code and Logic +- [ ] Review all `TODO` and `FIXME` comments in the codebase. +- [ ] Verify that all custom checks in `emtest/custom_checks.py` are properly tested. +- [ ] Ensure `emtest/validation_schemas.py` reflects the latest EM-DAT public data structure. +- [ ] Check for any hardcoded paths in scripts and examples (e.g., `examples/validation_script.py`). + +## 3. Data Files +- [ ] Update `emtest/validation_data/UNSD_M49_standards.csv` if new standards are available. +- [ ] Verify GAUL codes in `gaul_adm1_code.txt` and `gaul_adm2_code.txt`. +- [ ] Review classification lists in `classification_tree.toml` and associated Python files. + +## 4. Documentation and Examples +- [ ] Verify that `examples/example_notebook.ipynb` runs without errors. +- [ ] Ensure `examples/validation_script.py` and other example scripts work with the provided test data. +- [ ] Update `README.md` with any new features or changes in usage. +- [ ] Check that links in documentation are not broken. + +## 5. Testing and CI/CD +- [ ] Run the full test suite using `pytest`. +- [ ] Ensure all GitHub Actions workflows are passing. +- [ ] Add regression tests for any bugs fixed in this release cycle. +- [ ] Verify that the package can be built successfully (`python -m build`). + +## 6. Final Steps +- [ ] Create a git tag for the version (e.g., `v2026.03.0`). +- [ ] Draft release notes summarizing key changes, bug fixes, and improvements. diff --git a/data/fake_emdat_test.xlsx b/data/fake_emdat_test.xlsx index bebf3f6..f0e707d 100644 Binary files a/data/fake_emdat_test.xlsx and b/data/fake_emdat_test.xlsx differ diff --git a/emtest/__init__.py b/emtest/__init__.py index 7ccc364..88fbadb 100644 --- a/emtest/__init__.py +++ b/emtest/__init__.py @@ -1,4 +1,4 @@ -__version__ = '2024.12.0' +__version__ = '2026.04.0' __author__ = 'Damien Delforge, Valentin Wathelet' from emtest.validation_schemas import ( diff --git a/emtest/custom_checks.py b/emtest/custom_checks.py index 112c83d..3c55197 100644 --- a/emtest/custom_checks.py +++ b/emtest/custom_checks.py @@ -3,17 +3,51 @@ import json import re -from typing import Any, Literal +from typing import Any, Literal, Optional, Union import pandas as pd from pandera.typing import Series -from .validation_data.areas import ADM1_GAUL_LIST, ADM2_GAUL_LIST +from .validation_data.areas import ADM1_GAUL_LIST, ADM2_GAUL_LIST, \ + SUBREGION_LIST, REGION_LIST, COUNTRY_LIST, ISO3_LIST +from .validation_data.classification import KEY_LIST, GROUP_LIST, TYPE_LIST, \ + SUBTYPE_LIST, SUBGROUP_LIST +from .validation_data.magnitude import MAG_UNIT_LIST # Single Checks # ------------- +def check_disno(disno: Series[str]) -> Series[bool]: + """Check that disno is in the correct format.""" + return disno.str.match( + r"^\d{4}-\d{4}-[A-Z]{3}$", na=False + ) + +def check_yes_no(yes_no: Series[str]) -> Series[bool]: + """Check that yes_no is in the correct format.""" + return yes_no.isin(['Yes', 'No']) + +def check_classification_key(classification_key: Series[str]) -> Series[bool]: + """Check that classification key is in the correct format.""" + return classification_key.isin(KEY_LIST) + +def check_group(group: Series[str]) -> Series[bool]: + """Check that group is in the correct format.""" + return group.isin(GROUP_LIST) + +def check_subgroup(subgroup: Series[str]) -> Series[bool]: + """Check that subgroup is in the correct format.""" + return subgroup.isin(SUBGROUP_LIST) + +def check_type(dis_type: Series[str]) -> Series[bool]: + """Check that dis_type is in the correct format.""" + return dis_type.isin(TYPE_LIST) + +def check_subtype(subtype: Series[str]) -> Series[bool]: + """Check that subtype is in the correct format.""" + return subtype.isin(SUBTYPE_LIST) + def check_disno_vs_start_year(start_year: Series[int]) -> Series[bool]: """Check that disno year is the same as start year.""" @@ -30,12 +64,13 @@ def disno_to_year(disno: str) -> int: return disno_year == start_year -def validate_external_id(external_id: str | None) -> bool: +def validate_external_id(external_id: Optional[str]) -> bool: """Validates external ID regex patterns. """ glide_pattern = r"GLIDE:[A-Z]{2}-\d{4}-\d{6}" usgs_pattern = r"USGS:[0-9a-zA-Z]{10}" dfo_pattern = r"DFO:\d{4}" + hanze_pattern = r"HANZE:\d{1,5}" if external_id != external_id: # Skip NaN return True ids = external_id.split("|") @@ -44,12 +79,14 @@ def validate_external_id(external_id: str | None) -> bool: if ( re.match(glide_pattern, id_) or re.match(usgs_pattern, id_) or - re.match(dfo_pattern, id_) + re.match(dfo_pattern, id_) or + re.match(hanze_pattern, id_) ): valid |= bool( re.match(glide_pattern, id_) or re.match(usgs_pattern, id_) or - re.match(dfo_pattern, id_) + re.match(dfo_pattern, id_) or + re.match(hanze_pattern, id_) ) return valid @@ -102,6 +139,37 @@ def validate_iso3_code(iso3_country_code: Series[str]) -> Series[bool]: """ return iso3_country_code.str.match(r'^[A-Z]{3}$') +def check_iso3_code(iso3_country_code: Series[str]) -> Series[bool]: + """Check that country is in the correct format.""" + return iso3_country_code.isin(ISO3_LIST) + + +def check_country(country: Series[str]) -> Series[bool]: + """Check that country is in the correct format.""" + return country.isin(COUNTRY_LIST) + + +def check_subregion(subregion: Series[str]) -> Series[bool]: + """Check that subregion is in the correct format.""" + return subregion.isin(SUBREGION_LIST) + + +def check_region(region: Series[str]) -> Series[bool]: + """Check that region is in the correct format.""" + return region.isin(REGION_LIST) + +def check_magnitude_unit(magnitude_unit: Series[str]) -> Series[bool]: + """Check that magnitude unit is in the correct format.""" + return magnitude_unit.isin(MAG_UNIT_LIST) + +def check_day(day: Series[int]) -> Series[bool]: + """Check that day is in the correct range (1-31).""" + return day.between(1, 31) + +def check_month(month: Series[int]) -> Series[bool]: + """Check that month is in the correct range (1-12).""" + return month.between(1, 12) + # Wide Checks # ----------- @@ -137,7 +205,7 @@ def check_heatwave_magnitude(df: pd.DataFrame) -> Series[bool]: def check_other_magnitude(df: pd.DataFrame) -> Series[bool]: """Check that heat wave is in realistic range""" is_other = ~((df['Classification Key'].str.startswith('nat-geo-ear')) | - (df['Classification Key'].str.startswith('nat-met-ext'))) + (df['Classification Key'].str.startswith('nat-met-ext'))) return ~is_other | df['Magnitude'] > 0 diff --git a/emtest/utils.py b/emtest/utils.py index c309f26..c52311a 100644 --- a/emtest/utils.py +++ b/emtest/utils.py @@ -1,4 +1,5 @@ import copy +from typing import Optional import pandas as pd from pandera import DataFrameSchema, Check @@ -25,7 +26,7 @@ def get_validation_report( schema: DataFrameSchema, add_warnings: bool = False, deduplicate_wide: bool = True, -) -> pd.DataFrame | None: +) -> Optional[pd.DataFrame]: """Return schema errors as a dataframe report""" if add_warnings: schema = set_warnings_to_errors(schema) diff --git a/emtest/validation_data/areas.py b/emtest/validation_data/areas.py index 904a337..fdeff64 100644 --- a/emtest/validation_data/areas.py +++ b/emtest/validation_data/areas.py @@ -2,9 +2,9 @@ areas = load_UNSD_areas() -ISO3_LIST = areas['ISO-alpha3 Code'] -COUNTRY_LIST = areas['Country or Area'] -REGION_LIST = areas['Region Name'] -SUBREGION_LIST = areas['Sub-region Name'] +ISO3_LIST = areas['ISO-alpha3 Code'].tolist() +COUNTRY_LIST = areas['Country or Area'].tolist() +REGION_LIST = areas['Region Name'].tolist() +SUBREGION_LIST = areas['Sub-region Name'].tolist() ADM1_GAUL_LIST = load_GAUL_code(1) ADM2_GAUL_LIST = load_GAUL_code(2) \ No newline at end of file diff --git a/emtest/validation_schemas.py b/emtest/validation_schemas.py index e610696..1564a51 100644 --- a/emtest/validation_schemas.py +++ b/emtest/validation_schemas.py @@ -9,7 +9,8 @@ from datetime import datetime from functools import partial -from pandera import Check, Column, DataFrameSchema, Index, Timestamp +from pandera.pandas import Check, Column, DataFrameSchema, Index, Timestamp +from pandera.typing import Series from .custom_checks import ( is_valid_json, @@ -17,13 +18,17 @@ validate_external_id, validate_iso3_code, check_both_lat_lon_coordinates, + check_disno, check_disno_vs_start_year, check_start_end_consistency, check_coldwave_magnitude, check_earthquake_magnitude, check_heatwave_magnitude, check_other_magnitude, - check_no_day_if_no_month + check_no_day_if_no_month, check_subregion, check_country, check_yes_no, + check_classification_key, check_group, check_subgroup, check_type, + check_subtype, check_iso3_code, check_magnitude_unit, check_region, + check_day, check_month ) from .validation_data.areas import ( COUNTRY_LIST, @@ -50,8 +55,8 @@ str, checks=[ # Should be either "Yes" or "No" - Check.isin( - allowed_values=["Yes", "No"], + Check( + check_yes_no, name='check_yes_no', description="Test whether value is either 'Yes' or 'No'", error="Invalid Historic value" @@ -62,8 +67,8 @@ str, checks=[ # Should belong to KEY_LIST - Check.isin( - KEY_LIST, + Check( + check_classification_key, name='check_classification_key', description="Test whether value is in the reference list", error="Invalid classification key" @@ -74,8 +79,8 @@ str, checks=[ # Should belong to GROUP_LIST - Check.isin( - GROUP_LIST, + Check( + check_group, name='check_goup', description="Test whether value is in the reference list", error="Invalid group name" @@ -86,8 +91,8 @@ str, checks=[ # Should belong to SUBGROUP_LIST - Check.isin( - SUBGROUP_LIST, + Check( + check_subgroup, name='check_subgroup', description="Test whether value is in the reference list", error="Invalid subgroup name" @@ -98,8 +103,8 @@ str, checks=[ # Should belong to TYPE_LIST - Check.isin( - TYPE_LIST, + Check( + check_type, name='check_type', description="Test whether value is in the reference list", error="Invalid type name" @@ -110,8 +115,8 @@ str, checks=[ # Should belong to SUBTYPE_LIST - Check.isin( - SUBTYPE_LIST, + Check( + check_subtype, name='check_subtype', description="Test whether value is in the reference list", error="Invalid subtype name" @@ -141,8 +146,8 @@ error="Invalid ISO3 code", description="Validate values using regular expressions" ), - Check.isin( - ISO3_LIST, + Check( + check_iso3_code, raise_warning=True, name="check_iso3_code", description="Test whether value is in the reference list", @@ -154,8 +159,8 @@ str, checks=[ # Should belong to COUNTRY_LIST - Check.isin( - COUNTRY_LIST, + Check( + check_country, raise_warning=True, name="check_country", description="Test whether value is in the reference list", @@ -167,8 +172,8 @@ str, checks=[ # Should belong to SUBREGION_LIST - Check.isin( - SUBREGION_LIST, + Check( + check_subregion, name="check_subregion", description="Test whether value is in the reference list", error="Subregions not in reference list" @@ -179,8 +184,8 @@ str, checks=[ # Should belong to REGION_LIST - Check.isin( - REGION_LIST, + Check( + check_region, name="check_region", description="Test whether value is in the reference list", error="Regions not in reference list" @@ -194,8 +199,8 @@ str, checks=[ # Should be either "Yes" or "No" - Check.isin( - ["Yes", "No"], + Check( + check_yes_no, name="check_yes_no", description="Test whether value is either 'Yes' or 'No'", error="Invalid OFDA/BHA Response value" @@ -206,8 +211,8 @@ str, checks=[ # Should be either "Yes" or "No" - Check.isin( - ["Yes", "No"], + Check( + check_yes_no, name="check_yes_no", description="Test whether value is either 'Yes' or 'No'", error="Invalid Appeal value" @@ -218,8 +223,8 @@ str, checks=[ # Should be either "Yes" or "No" - Check.isin( - ["Yes", "No"], + Check( + check_yes_no, name="check_yes_no", description="Test whether value is either 'Yes' or 'No'", error="Invalid Declaration value" @@ -244,8 +249,8 @@ "Magnitude Scale": Column( str, checks=[ - Check.isin( - MAG_UNIT_LIST, + Check( + check_magnitude_unit, name="check_magnitude_unit", description="Test whether value is in the reference list", error="Magnitude unit not in reference list" @@ -302,8 +307,8 @@ float, # int is not a nullable type nullable=True, checks=[ - Check.isin( - range(1, 13), + Check( + check_month, name="check_month", description="Test whether value is a valid month number " "(1-12).", @@ -314,8 +319,8 @@ "Start Day": Column( float, # int is not a nullable type checks=[ - Check.isin( - range(1, 32), + Check( + check_day, name="check_day", description="Test whether value is a valid day number " "(1-31).", @@ -339,8 +344,8 @@ "End Month": Column( float, # int is not a nullable type checks=[ - Check.isin( - range(1, 13), + Check( + check_month, name="check_month", description="Test whether value is a valid month number " "(1-31).", @@ -352,8 +357,8 @@ "End Day": Column( float, # int is not a nullable type checks=[ - Check.isin( - range(1, 32), + Check( + check_day, name="check_day", description="Test whether value is a valid day number " "(1-31)." @@ -516,6 +521,19 @@ ], nullable=True ), + "GADM Admin Units": Column( + str, + checks=[ + # See custom_checks.py + Check( + is_valid_json, + description="Test whether value is a json string", + error="Invalid JSON string", + element_wise=True + ), + ], + nullable=True + ), "Entry Date": Column( Timestamp, checks=[ @@ -611,15 +629,14 @@ str, name="DisNo.", checks=[ - # Check DisNo. pattern, e.g., "2004-0659-USA" - Check.str_matches( - r"^\d{4}-\d{4}-[A-Z]{3}$", + Check( + check_disno, name="check_disno", description="Validate value using regular expression.", error="Invalid DisNo. Pattern" ) ], - unique=True + unique=True, ), coerce=True, ordered=True, diff --git a/examples/example_notebook.ipynb b/examples/example_notebook.ipynb index 9a150d3..8cef31e 100644 --- a/examples/example_notebook.ipynb +++ b/examples/example_notebook.ipynb @@ -31,8 +31,8 @@ { "metadata": { "ExecuteTime": { - "end_time": "2024-09-13T12:12:30.202738Z", - "start_time": "2024-09-13T12:12:29.374916Z" + "end_time": "2026-04-08T13:40:47.210380100Z", + "start_time": "2026-04-08T13:40:47.118760800Z" } }, "cell_type": "code", @@ -57,7 +57,7 @@ ] } ], - "execution_count": 1 + "execution_count": 3 }, { "metadata": {}, @@ -72,8 +72,8 @@ { "metadata": { "ExecuteTime": { - "end_time": "2024-09-13T12:12:30.559997Z", - "start_time": "2024-09-13T12:12:30.204294Z" + "end_time": "2026-04-08T13:40:47.351459400Z", + "start_time": "2026-04-08T13:40:47.213638200Z" } }, "cell_type": "code", @@ -87,11 +87,11 @@ "name": "stderr", "output_type": "stream", "text": [ - "C:\\Users\\dadelforge\\Anaconda3\\envs\\emtest\\Lib\\site-packages\\pandera\\backends\\pandas\\base.py:140: SchemaWarning: Column 'ISO' failed element-wise validator number 1: ISO3 code not in reference list failure cases: wrong_iso, SUN, TWN\n", + "C:\\Users\\dadelforge\\Documents\\coding\\em-test\\.venv\\Lib\\site-packages\\pandera\\backends\\pandas\\base.py:145: SchemaWarning: Column 'ISO' failed element-wise validator number 1: ISO3 code not in reference list failure cases: wrong_iso, SUN, TWN\n", " warnings.warn(\n", - "C:\\Users\\dadelforge\\Anaconda3\\envs\\emtest\\Lib\\site-packages\\pandera\\backends\\pandas\\base.py:140: SchemaWarning: Column 'Country' failed element-wise validator number 0: Countries not in reference list failure cases: wrong_country, Soviet Union, Taiwan (Province of China)\n", + "C:\\Users\\dadelforge\\Documents\\coding\\em-test\\.venv\\Lib\\site-packages\\pandera\\backends\\pandas\\base.py:145: SchemaWarning: Column 'Country' failed element-wise validator number 0: Countries not in reference list failure cases: wrong_country, Soviet Union, Taiwan (Province of China)\n", " warnings.warn(\n", - "C:\\Users\\dadelforge\\Anaconda3\\envs\\emtest\\Lib\\site-packages\\pandera\\backends\\pandas\\base.py:140: SchemaWarning: Column 'Start Year' failed element-wise validator number 1: Start year differs from DisNo year failure cases: 1997, 1899, 1975\n", + "C:\\Users\\dadelforge\\Documents\\coding\\em-test\\.venv\\Lib\\site-packages\\pandera\\backends\\pandas\\base.py:145: SchemaWarning: Column 'Start Year' failed element-wise validator number 1: Start year differs from DisNo year failure cases: 1997, 1899, 1975\n", " warnings.warn(\n" ] }, @@ -100,11 +100,11 @@ "evalue": "Column 'Historic' failed element-wise validator number 0: Invalid Historic value failure cases: wrong_historic", "output_type": "error", "traceback": [ - "\u001B[1;31mSchemaError\u001B[0m\u001B[1;31m:\u001B[0m Column 'Historic' failed element-wise validator number 0: Invalid Historic value failure cases: wrong_historic\n" + "\u001B[31mSchemaError\u001B[39m\u001B[31m:\u001B[39m Column 'Historic' failed element-wise validator number 0: Invalid Historic value failure cases: wrong_historic\n" ] } ], - "execution_count": 2 + "execution_count": 4 }, { "metadata": {}, @@ -136,8 +136,8 @@ { "metadata": { "ExecuteTime": { - "end_time": "2024-09-13T12:12:37.923831Z", - "start_time": "2024-09-13T12:12:37.596767Z" + "end_time": "2026-04-08T13:41:03.990637700Z", + "start_time": "2026-04-08T13:41:03.705659500Z" } }, "cell_type": "code", @@ -152,53 +152,53 @@ "id": "19e88b7babd2af5b", "outputs": [ { - "name": "stderr", + "name": "stdout", "output_type": "stream", "text": [ - "C:\\Users\\dadelforge\\Anaconda3\\envs\\emtest\\Lib\\site-packages\\pandera\\backends\\pandas\\base.py:140: SchemaWarning: Column 'ISO' failed element-wise validator number 1: ISO3 code not in reference list failure cases: wrong_iso, SUN, TWN\n", - " warnings.warn(\n", - "C:\\Users\\dadelforge\\Anaconda3\\envs\\emtest\\Lib\\site-packages\\pandera\\backends\\pandas\\base.py:140: SchemaWarning: Column 'Country' failed element-wise validator number 0: Countries not in reference list failure cases: wrong_country, Soviet Union, Taiwan (Province of China)\n", - " warnings.warn(\n", - "C:\\Users\\dadelforge\\Anaconda3\\envs\\emtest\\Lib\\site-packages\\pandera\\backends\\pandas\\base.py:140: SchemaWarning: Column 'Start Year' failed element-wise validator number 1: Start year differs from DisNo year failure cases: 1997, 1899, 1975\n", - " warnings.warn(\n" + "2664 failure cases:\n", + " schema_context column check \\\n", + "39 Index DisNo. Invalid DisNo. Pattern \n", + "1332 DataFrameSchema Location Invalid magnitude \n", + "1780 DataFrameSchema Start Year Invalid magnitude \n", + "1772 DataFrameSchema Start Year Invalid magnitude \n", + "1773 DataFrameSchema Start Year Invalid magnitude \n", + "... ... ... ... \n", + "26 Column Total Affected Invalid Total Affected value \n", + "25 Column No. Homeless Invalid No. Homeless value \n", + "24 Column No. Affected Invalid No. Affected value \n", + "23 Column No. Injured Invalid No. Injured value \n", + "0 Column Historic Invalid Historic value \n", + "\n", + " check_number failure_case index \n", + "39 0 wrong_disno wrong_disno \n", + "1332 9 Volgogradskaya Oblast region 2010-0466-RUS \n", + "1780 9 1980 1980-0156-PHL \n", + "1772 9 2007 2007-0221-SLE \n", + "1773 9 2010 2010-0454-GMB \n", + "... ... ... ... \n", + "26 0 -10.0 2013-0565-CHN \n", + "25 0 -10.0 2011-0368-IRN \n", + "24 0 -10.0 1983-0440-PAK \n", + "23 0 -10.0 2004-0294-FJI \n", + "0 0 wrong_historic 1993-0096-DEU \n", + "\n", + "[2664 rows x 6 columns]\n" ] }, { - "name": "stdout", + "name": "stderr", "output_type": "stream", "text": [ - "2665 failure cases:\n", - " schema_context column check check_number \\\n", - "40 Index DisNo. Invalid DisNo. Pattern 0 \n", - "1332 DataFrameSchema Location Invalid magnitude 9 \n", - "1780 DataFrameSchema Start Year Invalid magnitude 9 \n", - "1772 DataFrameSchema Start Year Invalid magnitude 9 \n", - "1773 DataFrameSchema Start Year Invalid magnitude 9 \n", - "... ... ... ... ... \n", - "26 Column No. Homeless Invalid No. Homeless value 0 \n", - "25 Column No. Affected Invalid No. Affected value 0 \n", - "24 Column No. Injured Invalid No. Injured value 0 \n", - "23 Column Total Deaths Invalid Total Deaths value 0 \n", - "0 Column Historic Invalid Historic value 0 \n", - "\n", - " failure_case index \n", - "40 wrong_disno 0 \n", - "1332 Bihar 1999-0673-IND \n", - "1780 2021 2021-0006-PHL \n", - "1772 2001 2001-0353-CHN \n", - "1773 2007 2007-0221-SLE \n", - "... ... ... \n", - "26 -10.0 2011-0368-IRN \n", - "25 -10.0 1983-0440-PAK \n", - "24 -10.0 2004-0294-FJI \n", - "23 -10.0 2013-0259-CHN \n", - "0 wrong_historic 1993-0096-DEU \n", - "\n", - "[2665 rows x 6 columns]\n" + "C:\\Users\\dadelforge\\Documents\\coding\\em-test\\.venv\\Lib\\site-packages\\pandera\\backends\\pandas\\base.py:145: SchemaWarning: Column 'ISO' failed element-wise validator number 1: ISO3 code not in reference list failure cases: wrong_iso, SUN, TWN\n", + " warnings.warn(\n", + "C:\\Users\\dadelforge\\Documents\\coding\\em-test\\.venv\\Lib\\site-packages\\pandera\\backends\\pandas\\base.py:145: SchemaWarning: Column 'Country' failed element-wise validator number 0: Countries not in reference list failure cases: wrong_country, Soviet Union, Taiwan (Province of China)\n", + " warnings.warn(\n", + "C:\\Users\\dadelforge\\Documents\\coding\\em-test\\.venv\\Lib\\site-packages\\pandera\\backends\\pandas\\base.py:145: SchemaWarning: Column 'Start Year' failed element-wise validator number 1: Start year differs from DisNo year failure cases: 1997, 1899, 1975\n", + " warnings.warn(\n" ] } ], - "execution_count": 3 + "execution_count": 5 }, { "metadata": {}, @@ -209,8 +209,8 @@ { "metadata": { "ExecuteTime": { - "end_time": "2024-09-13T12:12:40.715481Z", - "start_time": "2024-09-13T12:12:40.418985Z" + "end_time": "2026-04-08T13:41:15.466729400Z", + "start_time": "2026-04-08T13:41:15.162582800Z" } }, "cell_type": "code", @@ -224,11 +224,11 @@ "name": "stderr", "output_type": "stream", "text": [ - "C:\\Users\\dadelforge\\Anaconda3\\envs\\emtest\\Lib\\site-packages\\pandera\\backends\\pandas\\base.py:140: SchemaWarning: Column 'ISO' failed element-wise validator number 1: ISO3 code not in reference list failure cases: wrong_iso, SUN, TWN\n", + "C:\\Users\\dadelforge\\Documents\\coding\\em-test\\.venv\\Lib\\site-packages\\pandera\\backends\\pandas\\base.py:145: SchemaWarning: Column 'ISO' failed element-wise validator number 1: ISO3 code not in reference list failure cases: wrong_iso, SUN, TWN\n", " warnings.warn(\n", - "C:\\Users\\dadelforge\\Anaconda3\\envs\\emtest\\Lib\\site-packages\\pandera\\backends\\pandas\\base.py:140: SchemaWarning: Column 'Country' failed element-wise validator number 0: Countries not in reference list failure cases: wrong_country, Soviet Union, Taiwan (Province of China)\n", + "C:\\Users\\dadelforge\\Documents\\coding\\em-test\\.venv\\Lib\\site-packages\\pandera\\backends\\pandas\\base.py:145: SchemaWarning: Column 'Country' failed element-wise validator number 0: Countries not in reference list failure cases: wrong_country, Soviet Union, Taiwan (Province of China)\n", " warnings.warn(\n", - "C:\\Users\\dadelforge\\Anaconda3\\envs\\emtest\\Lib\\site-packages\\pandera\\backends\\pandas\\base.py:140: SchemaWarning: Column 'Start Year' failed element-wise validator number 1: Start year differs from DisNo year failure cases: 1997, 1899, 1975\n", + "C:\\Users\\dadelforge\\Documents\\coding\\em-test\\.venv\\Lib\\site-packages\\pandera\\backends\\pandas\\base.py:145: SchemaWarning: Column 'Start Year' failed element-wise validator number 1: Start year differs from DisNo year failure cases: 1997, 1899, 1975\n", " warnings.warn(\n" ] }, @@ -236,22 +236,22 @@ "data": { "text/plain": [ " schema_context column \\\n", - "40 Index DisNo. \n", - "1652 DataFrameSchema Magnitude \n", - "369 DataFrameSchema Magnitude \n", + "39 Index DisNo. \n", + "1651 DataFrameSchema Magnitude \n", + "368 DataFrameSchema Magnitude \n", + "406 DataFrameSchema Magnitude \n", "407 DataFrameSchema Magnitude \n", - "408 DataFrameSchema Magnitude \n", - "120 DataFrameSchema Start Day \n", - "154 DataFrameSchema End Day \n", - "178 DataFrameSchema Start Year \n", - "73 DataFrameSchema Latitude \n", - "74 DataFrameSchema Longitude \n", + "119 DataFrameSchema Start Day \n", + "153 DataFrameSchema End Day \n", + "177 DataFrameSchema Start Year \n", + "72 DataFrameSchema Latitude \n", + "73 DataFrameSchema Longitude \n", + "326 DataFrameSchema Start Day \n", "327 DataFrameSchema Start Day \n", "328 DataFrameSchema Start Day \n", - "329 DataFrameSchema Start Day \n", - "240 DataFrameSchema Start Month \n", "239 DataFrameSchema Start Month \n", - "241 DataFrameSchema Start Month \n", + "238 DataFrameSchema Start Month \n", + "240 DataFrameSchema Start Month \n", "10 Column OFDA/BHA Response \n", "17 Column Start Year \n", "16 Column Longitude \n", @@ -273,43 +273,42 @@ "19 Column Start Day \n", "1 Column Classification Key \n", "21 Column End Month \n", - "22 Column End Day \n", - "39 Column Last Update \n", - "38 Column Entry Date \n", - "37 Column Admin Units \n", + "31 Column Total Damage ('000 US$) \n", + "38 Column Last Update \n", + "37 Column Entry Date \n", "36 Column Admin Units \n", "35 Column Admin Units \n", "34 Column Admin Units \n", - "33 Column Total Damage, Adjusted ('000 US$) \n", - "32 Column Total Damage ('000 US$) \n", - "31 Column Insured Damage, Adjusted ('000 US$) \n", - "30 Column Insured Damage ('000 US$) \n", - "29 Column Reconstruction Costs, Adjusted ('000 US$) \n", - "28 Column Reconstruction Costs ('000 US$) \n", - "27 Column Total Affected \n", - "26 Column No. Homeless \n", - "25 Column No. Affected \n", - "24 Column No. Injured \n", - "23 Column Total Deaths \n", + "33 Column Admin Units \n", + "32 Column Total Damage, Adjusted ('000 US$) \n", + "30 Column Insured Damage, Adjusted ('000 US$) \n", + "22 Column Total Deaths \n", + "29 Column Insured Damage ('000 US$) \n", + "28 Column Reconstruction Costs, Adjusted ('000 US$) \n", + "27 Column Reconstruction Costs ('000 US$) \n", + "26 Column Total Affected \n", + "25 Column No. Homeless \n", + "24 Column No. Affected \n", + "23 Column No. Injured \n", "0 Column Historic \n", "\n", " check check_number \\\n", - "40 Invalid DisNo. Pattern 0 \n", - "1652 Invalid magnitude 9 \n", - "369 Invalid coldwave magnitude 6 \n", + "39 Invalid DisNo. Pattern 0 \n", + "1651 Invalid magnitude 9 \n", + "368 Invalid coldwave magnitude 6 \n", + "406 Invalid earthquake magnitude 7 \n", "407 Invalid earthquake magnitude 7 \n", - "408 Invalid earthquake magnitude 7 \n", - "120 Missing start month value 1 \n", - "154 Missing end month value 2 \n", - "178 Start date inconsistency at the year resolution 3 \n", + "119 Missing start month value 1 \n", + "153 Missing end month value 2 \n", + "177 Start date inconsistency at the year resolution 3 \n", + "72 Missing latitude or longitude coordinates 0 \n", "73 Missing latitude or longitude coordinates 0 \n", - "74 Missing latitude or longitude coordinates 0 \n", + "326 Start date inconsistency at the day resolution 5 \n", "327 Start date inconsistency at the day resolution 5 \n", "328 Start date inconsistency at the day resolution 5 \n", - "329 Start date inconsistency at the day resolution 5 \n", - "240 Start date inconsistency at the month resolution 4 \n", "239 Start date inconsistency at the month resolution 4 \n", - "241 Start date inconsistency at the month resolution 4 \n", + "238 Start date inconsistency at the month resolution 4 \n", + "240 Start date inconsistency at the month resolution 4 \n", "10 Invalid OFDA/BHA Response value 0 \n", "17 Invalid Start Year value 0 \n", "16 Invalid Longitude value 0 \n", @@ -331,43 +330,42 @@ "19 Invalid Start Day value 0 \n", "1 Invalid classification key 0 \n", "21 Invalid End Month value 0 \n", - "22 isin(range(1, 32)) 0 \n", - "39 Invalid Last Update value 0 \n", - "38 Invalid Entry Date value 0 \n", - "37 Invalid GAUL codes 1 \n", + "31 Invalid Total Damage value 0 \n", + "38 Invalid Last Update value 0 \n", + "37 Invalid Entry Date value 0 \n", "36 Invalid GAUL codes 1 \n", "35 Invalid GAUL codes 1 \n", - "34 Invalid JSON string 0 \n", - "33 Invalid Total Damage, Adjusted value 0 \n", - "32 Invalid Total Damage value 0 \n", - "31 Invalid Insured Damage, Adjusted value 0 \n", - "30 Invalid Insured Damage value 0 \n", - "29 Invalid Reconstruction Costs, Adjusted value 0 \n", - "28 Invalid Reconstruction Costs value 0 \n", - "27 Invalid Total Affected value 0 \n", - "26 Invalid No. Homeless value 0 \n", - "25 Invalid No. Affected value 0 \n", - "24 Invalid No. Injured value 0 \n", - "23 Invalid Total Deaths value 0 \n", + "34 Invalid GAUL codes 1 \n", + "33 Invalid JSON string 0 \n", + "32 Invalid Total Damage, Adjusted value 0 \n", + "30 Invalid Insured Damage, Adjusted value 0 \n", + "22 Invalid Total Deaths value 0 \n", + "29 Invalid Insured Damage value 0 \n", + "28 Invalid Reconstruction Costs, Adjusted value 0 \n", + "27 Invalid Reconstruction Costs value 0 \n", + "26 Invalid Total Affected value 0 \n", + "25 Invalid No. Homeless value 0 \n", + "24 Invalid No. Affected value 0 \n", + "23 Invalid No. Injured value 0 \n", "0 Invalid Historic value 0 \n", "\n", " failure_case index \n", - "40 wrong_disno 0 \n", - "1652 0.0 2007-0092-LTU \n", - "369 25.0 1986-0015-CHN \n", - "407 2.0 2022-0231-BIH \n", - "408 17.1 1976-0071-IDN \n", - "120 14.0 2015-0465-ITA \n", - "154 22.0 2013-0306-CHN \n", - "178 1975 1974-0088-USA \n", - "73 60.0 2022-0698-MEX \n", - "74 60.0 2009-0033-AFG \n", - "327 20.0 1990-0630-IND \n", - "328 17.0 2021-0165-IDN \n", - "329 16.0 1979-0039-ALB \n", - "240 7.0 2010-0454-GMB \n", - "239 3.0 2021-0165-IDN \n", - "241 8.0 2011-0287-UKR \n", + "39 wrong_disno wrong_disno \n", + "1651 0.0 2007-0092-LTU \n", + "368 25.0 1986-0015-CHN \n", + "406 2.0 2022-0231-BIH \n", + "407 17.1 1976-0071-IDN \n", + "119 14.0 2015-0465-ITA \n", + "153 22.0 2013-0306-CHN \n", + "177 1975 1974-0088-USA \n", + "72 60.0 2022-0698-MEX \n", + "73 60.0 2009-0033-AFG \n", + "326 20.0 1990-0630-IND \n", + "327 17.0 2021-0165-IDN \n", + "328 16.0 1979-0039-ALB \n", + "239 7.0 2010-0454-GMB \n", + "238 3.0 2021-0165-IDN \n", + "240 8.0 2011-0287-UKR \n", "10 wrong_response 2019-0008-BRA \n", "17 1899 2019-0523-IDN \n", "16 181.0 2018-0091-MOZ \n", @@ -389,24 +387,23 @@ "19 32.0 2002-0492-PNG \n", "1 wrong_classif_key 1927-0012-DZA \n", "21 -2.0 1998-0261-AUS \n", - "22 12.5 1990-0630-IND \n", - "39 2100-01-01 00:00:00 1993-0500-CMR \n", - "38 1987-01-01 00:00:00 2010-0466-RUS \n", - "37 [{\"adm1_code\":19888,\"adm1_name\":\"Taiwan Sheng\"}] 2002-0415-TWN \n", - "36 [{\"adm2_code\":198888,\"adm2_name\":\"Honolulu\"}] 2004-0572-USA \n", - "35 wrong_json 1999-0673-IND \n", + "31 -10.0 2005-0639-CHN \n", + "38 2100-01-01 00:00:00 1993-0500-CMR \n", + "37 1987-01-01 00:00:00 2010-0466-RUS \n", + "36 [{\"adm1_code\":19888,\"adm1_name\":\"Taiwan Sheng\"}] 2002-0415-TWN \n", + "35 [{\"adm2_code\":198888,\"adm2_name\":\"Honolulu\"}] 2004-0572-USA \n", "34 wrong_json 1999-0673-IND \n", - "33 -10.0 2009-0186-COD \n", - "32 -10.0 2005-0639-CHN \n", - "31 -10.0 1991-0646-PAK \n", - "30 -10.0 1978-0057-ITA \n", - "29 -10.0 2009-0122-CHN \n", - "28 -10.0 1990-0508-MEX \n", - "27 -10.0 2013-0565-CHN \n", - "26 -10.0 2011-0368-IRN \n", - "25 -10.0 1983-0440-PAK \n", - "24 -10.0 2004-0294-FJI \n", - "23 -10.0 2013-0259-CHN \n", + "33 wrong_json 1999-0673-IND \n", + "32 -10.0 2009-0186-COD \n", + "30 -10.0 1991-0646-PAK \n", + "22 -10.0 2013-0259-CHN \n", + "29 -10.0 1978-0057-ITA \n", + "28 -10.0 2009-0122-CHN \n", + "27 -10.0 1990-0508-MEX \n", + "26 -10.0 2013-0565-CHN \n", + "25 -10.0 2011-0368-IRN \n", + "24 -10.0 1983-0440-PAK \n", + "23 -10.0 2004-0294-FJI \n", "0 wrong_historic 1993-0096-DEU " ], "text/html": [ @@ -438,16 +435,16 @@ " \n", " \n", " \n", - " 40\n", + " 39\n", " Index\n", " DisNo.\n", " Invalid DisNo. Pattern\n", " 0\n", " wrong_disno\n", - " 0\n", + " wrong_disno\n", " \n", " \n", - " 1652\n", + " 1651\n", " DataFrameSchema\n", " Magnitude\n", " Invalid magnitude\n", @@ -456,7 +453,7 @@ " 2007-0092-LTU\n", " \n", " \n", - " 369\n", + " 368\n", " DataFrameSchema\n", " Magnitude\n", " Invalid coldwave magnitude\n", @@ -465,7 +462,7 @@ " 1986-0015-CHN\n", " \n", " \n", - " 407\n", + " 406\n", " DataFrameSchema\n", " Magnitude\n", " Invalid earthquake magnitude\n", @@ -474,7 +471,7 @@ " 2022-0231-BIH\n", " \n", " \n", - " 408\n", + " 407\n", " DataFrameSchema\n", " Magnitude\n", " Invalid earthquake magnitude\n", @@ -483,7 +480,7 @@ " 1976-0071-IDN\n", " \n", " \n", - " 120\n", + " 119\n", " DataFrameSchema\n", " Start Day\n", " Missing start month value\n", @@ -492,7 +489,7 @@ " 2015-0465-ITA\n", " \n", " \n", - " 154\n", + " 153\n", " DataFrameSchema\n", " End Day\n", " Missing end month value\n", @@ -501,7 +498,7 @@ " 2013-0306-CHN\n", " \n", " \n", - " 178\n", + " 177\n", " DataFrameSchema\n", " Start Year\n", " Start date inconsistency at the year resolution\n", @@ -510,7 +507,7 @@ " 1974-0088-USA\n", " \n", " \n", - " 73\n", + " 72\n", " DataFrameSchema\n", " Latitude\n", " Missing latitude or longitude coordinates\n", @@ -519,7 +516,7 @@ " 2022-0698-MEX\n", " \n", " \n", - " 74\n", + " 73\n", " DataFrameSchema\n", " Longitude\n", " Missing latitude or longitude coordinates\n", @@ -528,7 +525,7 @@ " 2009-0033-AFG\n", " \n", " \n", - " 327\n", + " 326\n", " DataFrameSchema\n", " Start Day\n", " Start date inconsistency at the day resolution\n", @@ -537,7 +534,7 @@ " 1990-0630-IND\n", " \n", " \n", - " 328\n", + " 327\n", " DataFrameSchema\n", " Start Day\n", " Start date inconsistency at the day resolution\n", @@ -546,7 +543,7 @@ " 2021-0165-IDN\n", " \n", " \n", - " 329\n", + " 328\n", " DataFrameSchema\n", " Start Day\n", " Start date inconsistency at the day resolution\n", @@ -555,7 +552,7 @@ " 1979-0039-ALB\n", " \n", " \n", - " 240\n", + " 239\n", " DataFrameSchema\n", " Start Month\n", " Start date inconsistency at the month resolution\n", @@ -564,7 +561,7 @@ " 2010-0454-GMB\n", " \n", " \n", - " 239\n", + " 238\n", " DataFrameSchema\n", " Start Month\n", " Start date inconsistency at the month resolution\n", @@ -573,7 +570,7 @@ " 2021-0165-IDN\n", " \n", " \n", - " 241\n", + " 240\n", " DataFrameSchema\n", " Start Month\n", " Start date inconsistency at the month resolution\n", @@ -771,16 +768,16 @@ " 1998-0261-AUS\n", " \n", " \n", - " 22\n", + " 31\n", " Column\n", - " End Day\n", - " isin(range(1, 32))\n", + " Total Damage ('000 US$)\n", + " Invalid Total Damage value\n", " 0\n", - " 12.5\n", - " 1990-0630-IND\n", + " -10.0\n", + " 2005-0639-CHN\n", " \n", " \n", - " 39\n", + " 38\n", " Column\n", " Last Update\n", " Invalid Last Update value\n", @@ -789,7 +786,7 @@ " 1993-0500-CMR\n", " \n", " \n", - " 38\n", + " 37\n", " Column\n", " Entry Date\n", " Invalid Entry Date value\n", @@ -798,7 +795,7 @@ " 2010-0466-RUS\n", " \n", " \n", - " 37\n", + " 36\n", " Column\n", " Admin Units\n", " Invalid GAUL codes\n", @@ -807,7 +804,7 @@ " 2002-0415-TWN\n", " \n", " \n", - " 36\n", + " 35\n", " Column\n", " Admin Units\n", " Invalid GAUL codes\n", @@ -816,7 +813,7 @@ " 2004-0572-USA\n", " \n", " \n", - " 35\n", + " 34\n", " Column\n", " Admin Units\n", " Invalid GAUL codes\n", @@ -825,7 +822,7 @@ " 1999-0673-IND\n", " \n", " \n", - " 34\n", + " 33\n", " Column\n", " Admin Units\n", " Invalid JSON string\n", @@ -834,7 +831,7 @@ " 1999-0673-IND\n", " \n", " \n", - " 33\n", + " 32\n", " Column\n", " Total Damage, Adjusted ('000 US$)\n", " Invalid Total Damage, Adjusted value\n", @@ -843,25 +840,25 @@ " 2009-0186-COD\n", " \n", " \n", - " 32\n", + " 30\n", " Column\n", - " Total Damage ('000 US$)\n", - " Invalid Total Damage value\n", + " Insured Damage, Adjusted ('000 US$)\n", + " Invalid Insured Damage, Adjusted value\n", " 0\n", " -10.0\n", - " 2005-0639-CHN\n", + " 1991-0646-PAK\n", " \n", " \n", - " 31\n", + " 22\n", " Column\n", - " Insured Damage, Adjusted ('000 US$)\n", - " Invalid Insured Damage, Adjusted value\n", + " Total Deaths\n", + " Invalid Total Deaths value\n", " 0\n", " -10.0\n", - " 1991-0646-PAK\n", + " 2013-0259-CHN\n", " \n", " \n", - " 30\n", + " 29\n", " Column\n", " Insured Damage ('000 US$)\n", " Invalid Insured Damage value\n", @@ -870,7 +867,7 @@ " 1978-0057-ITA\n", " \n", " \n", - " 29\n", + " 28\n", " Column\n", " Reconstruction Costs, Adjusted ('000 US$)\n", " Invalid Reconstruction Costs, Adjusted value\n", @@ -879,7 +876,7 @@ " 2009-0122-CHN\n", " \n", " \n", - " 28\n", + " 27\n", " Column\n", " Reconstruction Costs ('000 US$)\n", " Invalid Reconstruction Costs value\n", @@ -888,7 +885,7 @@ " 1990-0508-MEX\n", " \n", " \n", - " 27\n", + " 26\n", " Column\n", " Total Affected\n", " Invalid Total Affected value\n", @@ -897,7 +894,7 @@ " 2013-0565-CHN\n", " \n", " \n", - " 26\n", + " 25\n", " Column\n", " No. Homeless\n", " Invalid No. Homeless value\n", @@ -906,7 +903,7 @@ " 2011-0368-IRN\n", " \n", " \n", - " 25\n", + " 24\n", " Column\n", " No. Affected\n", " Invalid No. Affected value\n", @@ -915,7 +912,7 @@ " 1983-0440-PAK\n", " \n", " \n", - " 24\n", + " 23\n", " Column\n", " No. Injured\n", " Invalid No. Injured value\n", @@ -924,15 +921,6 @@ " 2004-0294-FJI\n", " \n", " \n", - " 23\n", - " Column\n", - " Total Deaths\n", - " Invalid Total Deaths value\n", - " 0\n", - " -10.0\n", - " 2013-0259-CHN\n", - " \n", - " \n", " 0\n", " Column\n", " Historic\n", @@ -946,12 +934,12 @@ "" ] }, - "execution_count": 4, + "execution_count": 6, "metadata": {}, "output_type": "execute_result" } ], - "execution_count": 4 + "execution_count": 6 }, { "metadata": {}, @@ -973,8 +961,8 @@ { "metadata": { "ExecuteTime": { - "end_time": "2024-09-13T12:12:45.018583Z", - "start_time": "2024-09-13T12:12:44.689713Z" + "end_time": "2026-04-08T13:41:33.659199700Z", + "start_time": "2026-04-08T13:41:33.392417900Z" } }, "cell_type": "code", @@ -993,38 +981,38 @@ "name": "stdout", "output_type": "stream", "text": [ - "2674 failure cases:\n", - " schema_context column check check_number \\\n", - "49 Index DisNo. Invalid DisNo. Pattern 0 \n", - "1337 DataFrameSchema Location Invalid magnitude 9 \n", - "1787 DataFrameSchema Start Year Invalid magnitude 9 \n", - "1779 DataFrameSchema Start Year Invalid magnitude 9 \n", - "1780 DataFrameSchema Start Year Invalid magnitude 9 \n", - "... ... ... ... ... \n", - "31 Column End Day isin(range(1, 32)) 0 \n", - "30 Column End Month Invalid End Month value 0 \n", - "29 Column End Year Invalid End Year value 0 \n", - "28 Column Start Day Invalid Start Day value 0 \n", - "0 Column Historic Invalid Historic value 0 \n", + "2673 failure cases:\n", + " schema_context column check check_number \\\n", + "48 Index DisNo. Invalid DisNo. Pattern 0 \n", + "1336 DataFrameSchema Location Invalid magnitude 9 \n", + "1786 DataFrameSchema Start Year Invalid magnitude 9 \n", + "1778 DataFrameSchema Start Year Invalid magnitude 9 \n", + "1779 DataFrameSchema Start Year Invalid magnitude 9 \n", + "... ... ... ... ... \n", + "30 Column End Month Invalid End Month value 0 \n", + "29 Column End Year Invalid End Year value 0 \n", + "28 Column Start Day Invalid Start Day value 0 \n", + "27 Column Start Month Invalid Start Month value 0 \n", + "0 Column Historic Invalid Historic value 0 \n", "\n", " failure_case index \n", - "49 wrong_disno 0 \n", - "1337 Fengcheng (Jiangxi province) 2009-0122-CHN \n", - "1787 2018 2018-0397-ITA \n", - "1779 2021 2021-0052-CMR \n", - "1780 2000 2000-0260-AGO \n", + "48 wrong_disno wrong_disno \n", + "1336 Fengcheng (Jiangxi province) 2009-0122-CHN \n", + "1786 2018 2018-0397-ITA \n", + "1778 2021 2021-0052-CMR \n", + "1779 2000 2000-0260-AGO \n", "... ... ... \n", - "31 12.5 1990-0630-IND \n", "30 -2.0 1998-0261-AUS \n", "29 2100 1981-0106-LKA \n", "28 32.0 2002-0492-PNG \n", + "27 13.0 1983-0084-SUN \n", "0 wrong_historic 1993-0096-DEU \n", "\n", - "[2674 rows x 6 columns]\n" + "[2673 rows x 6 columns]\n" ] } ], - "execution_count": 5 + "execution_count": 7 }, { "metadata": {}, @@ -1033,186 +1021,12 @@ "id": "8f1fe0d62530b2ba" }, { - "metadata": { - "ExecuteTime": { - "end_time": "2024-09-13T12:12:47.801206Z", - "start_time": "2024-09-13T12:12:47.492675Z" - } - }, + "metadata": {}, "cell_type": "code", "source": "get_validation_report(emdat, emdat_schema, add_warnings=True)", "id": "fd16b61f263f5199", - "outputs": [ - { - "data": { - "text/plain": [ - " schema_context column check check_number \\\n", - "49 Index DisNo. Invalid DisNo. Pattern 0 \n", - "1661 DataFrameSchema Magnitude Invalid magnitude 9 \n", - "378 DataFrameSchema Magnitude Invalid coldwave magnitude 6 \n", - "416 DataFrameSchema Magnitude Invalid earthquake magnitude 7 \n", - "417 DataFrameSchema Magnitude Invalid earthquake magnitude 7 \n", - "... ... ... ... ... \n", - "31 Column End Day isin(range(1, 32)) 0 \n", - "30 Column End Month Invalid End Month value 0 \n", - "29 Column End Year Invalid End Year value 0 \n", - "28 Column Start Day Invalid Start Day value 0 \n", - "0 Column Historic Invalid Historic value 0 \n", - "\n", - " failure_case index \n", - "49 wrong_disno 0 \n", - "1661 0.0 2007-0092-LTU \n", - "378 25.0 1986-0015-CHN \n", - "416 2.0 2022-0231-BIH \n", - "417 17.1 1976-0071-IDN \n", - "... ... ... \n", - "31 12.5 1990-0630-IND \n", - "30 -2.0 1998-0261-AUS \n", - "29 2100 1981-0106-LKA \n", - "28 32.0 2002-0492-PNG \n", - "0 wrong_historic 1993-0096-DEU \n", - "\n", - "[65 rows x 6 columns]" - ], - "text/html": [ - "
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schema_contextcolumncheckcheck_numberfailure_caseindex
49IndexDisNo.Invalid DisNo. Pattern0wrong_disno0
1661DataFrameSchemaMagnitudeInvalid magnitude90.02007-0092-LTU
378DataFrameSchemaMagnitudeInvalid coldwave magnitude625.01986-0015-CHN
416DataFrameSchemaMagnitudeInvalid earthquake magnitude72.02022-0231-BIH
417DataFrameSchemaMagnitudeInvalid earthquake magnitude717.11976-0071-IDN
.....................
31ColumnEnd Dayisin(range(1, 32))012.51990-0630-IND
30ColumnEnd MonthInvalid End Month value0-2.01998-0261-AUS
29ColumnEnd YearInvalid End Year value021001981-0106-LKA
28ColumnStart DayInvalid Start Day value032.02002-0492-PNG
0ColumnHistoricInvalid Historic value0wrong_historic1993-0096-DEU
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65 rows × 6 columns

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" - ] - }, - "execution_count": 6, - "metadata": {}, - "output_type": "execute_result" - } - ], - "execution_count": 6 + "outputs": [], + "execution_count": null }, { "metadata": {}, @@ -1229,8 +1043,8 @@ { "metadata": { "ExecuteTime": { - "end_time": "2024-09-13T12:12:51.331600Z", - "start_time": "2024-09-13T12:12:51.312634Z" + "end_time": "2026-04-08T13:41:36.731976100Z", + "start_time": "2026-04-08T13:41:36.701171400Z" } }, "cell_type": "code", @@ -1251,7 +1065,7 @@ ], "id": "6dbfe6036efa61", "outputs": [], - "execution_count": 7 + "execution_count": 8 }, { "metadata": {}, @@ -1262,8 +1076,8 @@ { "metadata": { "ExecuteTime": { - "end_time": "2024-09-13T12:12:54.069479Z", - "start_time": "2024-09-13T12:12:53.956429Z" + "end_time": "2026-04-08T13:41:51.006297800Z", + "start_time": "2026-04-08T13:41:50.909465900Z" } }, "cell_type": "code", @@ -1332,12 +1146,12 @@ "" ] }, - "execution_count": 8, + "execution_count": 9, "metadata": {}, "output_type": "execute_result" } ], - "execution_count": 8 + "execution_count": 9 } ], "metadata": { diff --git a/examples/validation_script.py b/examples/validation_script.py index f14a701..4caa805 100644 --- a/examples/validation_script.py +++ b/examples/validation_script.py @@ -13,7 +13,7 @@ import pandas as pd -EMDAT_PATH: str = 'data/fake_emdat_test.xlsx' +EMDAT_PATH: str = '../data/fake_emdat_test.xlsx' CSV_OUTPUT_NAME: str = 'emdat_test_failure.csv' diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..3186466 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,61 @@ +[build-system] +requires = [ + "setuptools>=68", + "wheel" +] +build-backend = "setuptools.build_meta" + +[project] +name = "emtest" +version = "2026.04.0" +description = "Data validation for EM-DAT datasets." +readme = { file = "README.md", content-type = "text/markdown" } +requires-python = ">=3.9,<4" +license = { file = "LICENSE" } +authors = [ + { name = "Damien Delforge", email = "damien.delforge@uclouvain.be" }, + { name = "Valentin Wathelet" } +] +keywords = ["EM-DAT", "data validation", "disaster database"] +classifiers = [ + "Development Status :: 4 - Beta", + "Intended Audience :: Science/Research", + "License :: OSI Approved :: MIT License", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3 :: Only", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.13", + "Programming Language :: Python :: 3.14", +] +dependencies = [ + "pandera>=0.21", + "pandas>=2.2", + "numpy>=1.26", + "openpyxl>=3.1", + "toml>=0.10", +] + +[project.optional-dependencies] +dev = [ + "ipykernel", + "ipython", + "pandas-stubs", + "pytest", +] + +[project.urls] +Homepage = "https://github.com/em-dat/em-test" +Repository = "https://github.com/em-dat/em-test" + +[tool.setuptools.packages.find] +exclude = ["tests", "examples"] + +[tool.setuptools.package-data] +emtest = [ + "validation_data/*.csv", + "validation_data/*.toml", + "validation_data/*.txt", +] diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index ee3d44c..0000000 --- a/requirements.txt +++ /dev/null @@ -1,4 +0,0 @@ -openpyxl~=3.1 -pandas~=2.2 -pandera~=0.20 -toml~=0.10 diff --git a/setup.py b/setup.py deleted file mode 100644 index 5ad011b..0000000 --- a/setup.py +++ /dev/null @@ -1,39 +0,0 @@ -from setuptools import setup, find_packages - -with open("README.md", "r", encoding="utf-8") as fh: - long_description = fh.read() - -setup( - name='emtest', - version='2024.12.0', - description='Data validation for EM-DAT datasets.', - long_description=long_description, - long_description_content_type="text/markdown", - url='https://github.com/em-dat/em-test', - author='Damien Delforge, Valentin Wathelet', - author_email='damien.delforge@uclouvain.be', - classifiers=[ # Optional, refer to: https://pypi.org/classifiers/ - 'Development Status :: 4 - Beta', - 'Intended Audience :: Science/Research', - 'License :: OSI Approved :: MIT License', - 'Programming Language :: Python :: 3.11', - ], - keywords='EM-DAT, data validation, disaster database', - packages=find_packages(exclude=['tests', 'examples']), - include_package_data=True, - python_requires='>=3.11, <4', - install_requires=[ - 'openpyxl~=3.1', - 'pandas~=2.2', - 'pandera~=0.20', - 'toml~=0.10', - ], - package_data={ - 'emtest': [ - 'validation_data/*.csv', - 'validation_data/*.toml', - 'validation_data/*.txt', - 'validation_data/*.py' - ], - }, -) diff --git a/tests/conftest.py b/tests/conftest.py new file mode 100644 index 0000000..7fc0d9b --- /dev/null +++ b/tests/conftest.py @@ -0,0 +1,62 @@ +import pytest +import pandas as pd + +@pytest.fixture +def valid_emdat_row(): + """Provides a single valid EM-DAT row as a dictionary.""" + return { + "Historic": "No", + "Classification Key": "nat-bio-epi-vir", + "Disaster Group": "Natural", + "Disaster Subgroup": "Biological", + "Disaster Type": "Epidemic", + "Disaster Subtype": "Viral disease", + "External IDs": None, + "Event Name": "Test Event", + "ISO": "BEL", + "Country": "Belgium", + "Subregion": "Western Europe", + "Region": "Europe", + "Location": "Brussels", + "Origin": None, + "Associated Types": None, + "OFDA/BHA Response": "No", + "Appeal": "No", + "Declaration": "No", + "AID Contribution ('000 US$)": None, + "Magnitude": 7.0, + "Magnitude Scale": "Moment Magnitude", + "Latitude": 50.85, + "Longitude": 4.35, + "River Basin": None, + "Start Year": 2024, + "Start Month": 1.0, + "Start Day": 1.0, + "End Year": 2024, + "End Month": 1.0, + "End Day": 2.0, + "Total Deaths": 1.0, + "No. Injured": None, + "No. Affected": None, + "No. Homeless": None, + "Total Affected": 1.0, + "Reconstruction Costs ('000 US$)": None, + "Reconstruction Costs, Adjusted ('000 US$)": None, + "Insured Damage ('000 US$)": None, + "Insured Damage, Adjusted ('000 US$)": None, + "Total Damage ('000 US$)": None, + "Total Damage, Adjusted ('000 US$)": None, + "CPI": 100.0, + "Admin Units": None, + "GADM Admin Units": None, + "Entry Date": pd.Timestamp("2024-01-01"), + "Last Update": pd.Timestamp("2024-01-01") + } + +@pytest.fixture +def valid_df(valid_emdat_row): + """Provides a valid EM-DAT DataFrame.""" + df = pd.DataFrame([valid_emdat_row]) + df.index = ["2024-0001-BEL"] + df.index.name = "DisNo." + return df diff --git a/tests/test_custom_checks.py b/tests/test_custom_checks.py new file mode 100644 index 0000000..1f33a55 --- /dev/null +++ b/tests/test_custom_checks.py @@ -0,0 +1,44 @@ +import pytest +import pandas as pd +from emtest.custom_checks import ( + is_valid_json, + _is_valid_GAUL_code, + check_disno, + check_yes_no, + check_disno_vs_start_year +) + +def test_is_valid_json(): + assert is_valid_json('{"key": "value"}') is True + assert is_valid_json('[1, 2, 3]') is True + assert is_valid_json('invalid json') is False + assert is_valid_json(None) is False + +def test_is_valid_gaul_code(): + # We know from load_GAUL_code example it returns some codes + # Let's assume some codes exist or just test the logic if we can + assert _is_valid_GAUL_code(1232, level=1) is True # Based on example in data_loader + assert _is_valid_GAUL_code(999999, level=1) is False + +def test_check_disno(): + s = pd.Series(["2024-0001-BEL", "1900-9999-USA"]) + assert check_disno(s).all() == True + + s_invalid = pd.Series(["2024-001-BEL"]) # Missing one digit in sequential + assert check_disno(s_invalid).all() == False + +def test_check_yes_no(): + assert check_yes_no(pd.Series(["Yes", "No"])).all() == True + assert check_yes_no(pd.Series(["Yes", "Maybe"])).all() == False + +def test_check_disno_vs_start_year(): + df = pd.DataFrame({ + "Start Year": [2024, 2023] + }, index=["2024-0001-BEL", "2024-0002-BEL"]) + df.index.name = "DisNo." + + # The check_disno_vs_start_year in custom_checks.py takes start_year Series + # and accesses its index. + result = check_disno_vs_start_year(df["Start Year"]) + assert result.iloc[0] == True + assert result.iloc[1] == False diff --git a/tests/test_validation.py b/tests/test_validation.py new file mode 100644 index 0000000..388c199 --- /dev/null +++ b/tests/test_validation.py @@ -0,0 +1,70 @@ +import pytest +import pandas as pd +import pandera as pa +from emtest.validation_schemas import emdat_schema + +def test_valid_df_passes(valid_df): + """Test that the default valid fixture passes the schema.""" + emdat_schema.validate(valid_df) + +def test_invalid_historic(valid_df): + """Test that an invalid 'Historic' value fails.""" + valid_df.loc[valid_df.index[0], "Historic"] = "Maybe" + with pytest.raises(pa.errors.SchemaError, match="Invalid Historic value"): + emdat_schema.validate(valid_df) + +def test_invalid_classification_key(valid_df): + """Test that an invalid 'Classification Key' value fails.""" + valid_df.loc[valid_df.index[0], "Classification Key"] = "InvalidKey" + with pytest.raises(pa.errors.SchemaError, match="Invalid classification key"): + emdat_schema.validate(valid_df) + +def test_invalid_iso_code(valid_df): + """Test that an invalid 'ISO' code fails (regex check).""" + valid_df.loc[valid_df.index[0], "ISO"] = "BXX" # Invalid 3-letter code if we strictly check against reference, but let's see if regex fails it first + # The schema has two checks on ISO: validate_iso3_code (regex) and check_iso3_code (list check, warning only) + # Let's try one that fails regex: + valid_df.loc[valid_df.index[0], "ISO"] = "123" + # We expect a SchemaError for regex AND a SchemaWarning for the list check + with pytest.warns(pa.errors.SchemaWarning, match="ISO3 code not in reference list"): + with pytest.raises(pa.errors.SchemaError, match="Invalid ISO3 code"): + emdat_schema.validate(valid_df) + +def test_invalid_disno_index(valid_df): + """Test that an invalid 'DisNo.' index pattern fails.""" + valid_df.index = ["INVALID-DISNO"] + valid_df.index.name = "DisNo." + # We expect a SchemaError for the index pattern AND a SchemaWarning for the Start Year vs DisNo. check + with pytest.warns(pa.errors.SchemaWarning, match="Start year differs from DisNo year"): + with pytest.raises(pa.errors.SchemaError, match="Invalid DisNo. Pattern"): + emdat_schema.validate(valid_df) + +def test_magnitude_range_checks(valid_df): + """Test magnitude range checks for specific disaster types.""" + # Earthquake magnitude should be between 3 and 10 + valid_df.loc[valid_df.index[0], "Disaster Type"] = "Earthquake" + valid_df.loc[valid_df.index[0], "Magnitude"] = 1.0 + with pytest.raises(pa.errors.SchemaError, match="Invalid earthquake magnitude"): + emdat_schema.validate(valid_df) + +def test_date_consistency(valid_df): + """Test that start date after end date fails.""" + valid_df.loc[valid_df.index[0], "Start Year"] = 2024 + valid_df.loc[valid_df.index[0], "Start Month"] = 12 + valid_df.loc[valid_df.index[0], "End Year"] = 2024 + valid_df.loc[valid_df.index[0], "End Month"] = 1 + with pytest.raises(pa.errors.SchemaError, match="Start date inconsistency at the month resolution"): + emdat_schema.validate(valid_df) + +def test_lat_lon_consistency(valid_df): + """Test that having only one of Latitude/Longitude fails.""" + valid_df.loc[valid_df.index[0], "Latitude"] = 50.0 + valid_df.loc[valid_df.index[0], "Longitude"] = None + with pytest.raises(pa.errors.SchemaError, match="Missing latitude or longitude coordinates"): + emdat_schema.validate(valid_df) + +def test_json_admin_units(valid_df): + """Test that invalid JSON in Admin Units fails.""" + valid_df.loc[valid_df.index[0], "Admin Units"] = "Not a JSON" + with pytest.raises(pa.errors.SchemaError, match="Invalid JSON string"): + emdat_schema.validate(valid_df) diff --git a/uv.lock b/uv.lock new file mode 100644 index 0000000..485e6d4 --- /dev/null +++ b/uv.lock @@ -0,0 +1,1814 @@ +version = 1 +revision = 3 +requires-python = ">=3.9, <4" +resolution-markers = [ + "python_full_version >= '3.14' and 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