Add gene ID utils and refactor eFP expression endpoint#305
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rmobmina wants to merge 37 commits intoBioAnalyticResource:devfrom
Open
Add gene ID utils and refactor eFP expression endpoint#305rmobmina wants to merge 37 commits intoBioAnalyticResource:devfrom
rmobmina wants to merge 37 commits intoBioAnalyticResource:devfrom
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- Replace manual REGEX with BARUtils validators for all species - Add descriptive error messages for each species (e.g., "Invalid Cannabis gene ID") - Add comprehensive Sphinx/reST docstrings to all ORM files - Improve validation logic to handle both AGI and probeset IDs correctly - Fix SQL injection vulnerability by validating schema identifiers - Add identifier validation (alphanumeric + underscore only) before SQL construction Security: Addresses CodeQL high-severity SQL injection alert by validating all database/table/column identifiers match safe pattern before use in queries
- Fix trailing whitespace and blank line issues in efp_proxy.py - Fix missing blank lines in microarray_gene_expression.py - Add noqa comments for E402 in test_efp_data.py (imports after sys.path modification) - Remove unused variable retry_url - Fix spacing after commas in long list - Fix indentation issues
- Fix syntax error in efp_data.py (incomplete regex pattern) - Refactor efp_data.py to use class-based static methods (EFPDataService) following the BARUtils pattern for consistency - Add backward compatibility wrappers for existing function imports - Simplify efp_schemas.py by grouping similar schemas: * Created _simple_schema() helper for 5-column schemas * Created _schema_with_qa_columns() helper for QA column schemas * Reduced code duplication while maintaining same functionality - All changes tested with Docker build and Python syntax checks
- Updated _schema_with_qa_columns to properly handle length for string types - Added file_name_len and call_len parameters with defaults - Fixed shoot_apex schema to specify lengths for string columns (16, 2) - Fixes KeyError: 'length' in efp_dynamic.py model generation
- Fixes bootstrap script MySQL connection in Docker - Bootstrap script now connects to BAR_mysqldb instead of localhost socket - API starts successfully and serves on port 5000
- Check HTTP status code before parsing JSON response - Return 502 Bad Gateway when external API fails or returns non-200 - Catch JSONDecodeError when external API returns invalid response - Fixes test failure when atted.jp API is down or returns 403
MySQL doesn't allow TEXT/BLOB columns in primary keys without a key length. When bot_id_type='text' or probeset_type='text' is specified, the column type changes to TEXT but was still marked as primary_key=True, causing: OperationalError: (1170, "BLOB/TEXT column 'data_bot_id' used in key specification without a key length") Changes: - In _simple_schema(), when probeset_type='text', set primary_key=False - In _simple_schema(), when bot_id_type='text', set primary_key=False - Ensures data_signal remains a primary key for all databases Affected databases (11 total): - affydb, canola, canola_original, canola_seed - hnahal, human, humandb - meristemdb, rohan, rpatel, tomato_atlas All 58 tests pass with 5,643 subtests.
These scripts are called by config/init.sh to create simple eFP MySQL databases from schema definitions in CI, where SQLite mirrors are not available.
VinLau
reviewed
Mar 23, 2026
| OsAffx.1.1.S1_at (Rice chip) | ||
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| Conversion pipeline used by the gene expression endpoint: | ||
| 1. is_probeset_id(gene_id) → skip conversion if already a probeset |
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Documentation or logic is wrong - you need to convert a probeset ID to a gene identifier.
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Adds api/utils/gene_id_utils.py
Refactors api/resources/gene_expression.py
Adds constants for special database behavior
Updates .flake8