Refactor Score Ranges to Score Calibrations and Strengthen Their Data Model #545
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…single primary definition
For use with urn:mavedb:00000097-0-2
Adds a standalone score calibration model to replace the `score_ranges` property of score sets. This model better supports generically typed score ranges, publication identifiers directly associated with score ranges and odds paths provided independently of functional classes.
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DB Migration steps for this branch Checkout the commit git checkout 129d7daefb0c18d0f70f20ee633cb17a02a3cc37
DB_PORT=5434 DB_DATABASE_NAME=mavedb DB_USERNAME=postgres DB_PASSWORD=XXX poetry run alembic upgrade headRun the manual migration DB_PORT=5434 DB_DATABASE_NAME=mavedb DB_USERNAME=postgres DB_PASSWORD=XXX poetry run python3 alembic/manual_migrations/migrate_score_ranges_to_calibrations.pyCheckout the commit git checkout 3da28919a6f6173ad0d65c768b172dfffbf730fc
DB_PORT=5434 DB_DATABASE_NAME=mavedb DB_USERNAME=postgres DB_PASSWORD=XXX poetry run alembic upgrade headCheckout the head commit at main and upgrade to the alembic head git checkout main
DB_PORT=5434 DB_DATABASE_NAME=mavedb DB_USERNAME=postgres DB_PASSWORD=XXX poetry run alembic upgrade head |
… strengths, and reworked score calibrations
- Refactored score range jsonb in score sets into a separate data model with db tables and publication associations - Removed tests related to score ranges and replaced them with tests for score calibrations. - Updated test cases to validate the creation of score sets with investigator-provided calibrations. - Ensured that score set creation fails when non-investigator provided calibrations are included. - Adjusted error assertions to reflect changes in validation logic for score calibrations.
- Removed the `investigator_provided` field from `ScoreCalibrationBase` and adjusted related validation logic. - Updated `SavedScoreCalibration` to include `investigator_provided` as a boolean field. - Modified validation error messages to include specific locations in the request body. - Changed references from `InvestigatorProvidedScoreCalibrationCreate` to `ScoreCalibrationCreate` in `ScoreSetCreate`. - Updated test constants and removed unnecessary test cases related to `investigator_provided`. - Enhanced tests for creating score calibrations to ensure correct behavior for investigator-provided settings. - Adjusted tests to reflect changes in the model structure and validation logic.
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This pull request introduces a major refactor of how score calibrations and functional ranges are handled in the database and application logic. The changes migrate from storing score ranges directly on
ScoreSetobjects to a new, dedicatedscore_calibrationstable, update related migration scripts, and improve the logic for variant classification using these calibrations. Additionally, new ACMG classification utilities are introduced.Database schema migrations and refactoring:
score_calibrationsandscore_calibration_publication_identifierstables, and migrated existing score range data fromScoreSetto this new structure. (alembic/versions/002f6f9ec7ac_add_score_calibration_table.py)score_rangesproperty from thescoresetstable and provided a downgrade path to restore it if needed. (alembic/versions/f5a72192fafd_remove_score_range_property_from_score_.py)score_calibrationstable to remove thenamecolumn and add anotescolumn, updating the schema for future flexibility. (alembic/versions/8886f0453125_remove_name_add_notes_to_calibrations.py)Application logic and classification improvements:
score_calibrationsstructure and itsfunctional_ranges, replacing prior logic that relied onscore_rangesonScoreSet. This includes renaming and updating the main classification functions and ensuring robust error handling when calibrations are missing. (src/mavedb/lib/annotation/classification.py) [1] [2] [3]New utilities for ACMG classification:
src/mavedb/lib/acmg.py)