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Pull request overview
This PR introduces USDM JSON generation for activities and study cells, along with supporting database migrations and UI enhancements.
- Adds scripts to export USDM-compliant JSON for activities and study cells
- Implements database migrations for epoch_uid and activity label/description fields
- Enhances UI to support activity editing with label and description
Reviewed changes
Copilot reviewed 12 out of 14 changed files in this pull request and generated 2 comments.
Show a summary per file
| File | Description |
|---|---|
| src/usdm/generate_activities.py | Generates USDM Activity-Output JSON with biomedical concept references |
| src/usdm/generate_study_cells.py | Generates USDM StudyCells-Output JSON with arm/epoch/element relationships |
| src/soa_builder/web/utils.py | Adds concept_uid generation and table column checking utilities |
| src/soa_builder/web/routers/activities.py | Extends activity CRUD with label/description, adds UI form handlers |
| src/soa_builder/web/routers/epochs.py | Adds epoch_uid generation and backfills for USDM compliance |
| src/soa_builder/web/migrate_database.py | Adds epoch_uid migration with unique indexing |
| src/soa_builder/web/initialize_database.py | Updates schema to include activity label/description and concept_uid columns |
| src/soa_builder/web/app.py | Integrates migrations, updates freeze/rollback logic for new schema fields |
| src/soa_builder/web/templates/edit.html | Adds inline editing forms for activity properties |
| src/soa_builder/web/schemas.py | Adds optional label/description fields to ActivityCreate/Update |
| tests/test_study_cell_uid_reuse.py | Tests that study_cell_uid is reused for same arm/epoch combinations |
| tests/test_study_cell_uid_reuse_later.py | Tests that study_cell_uid is reused when elements are added later |
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src/usdm/generate_activities.py
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| rows = cur.fetchall() | ||
| conn.close() | ||
| bc_uids = [r[0] for r in rows] or [] | ||
| print(bc_uids) |
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Debug print statement should be removed from production code. This will output to stdout during normal execution, potentially interfering with the JSON output when using stdout mode.
Suggested change
| print(bc_uids) |
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Added scripts to generate the 'activities' and 'studyCells' entities in the USDM JSON format.