Fix Docker runtime issues, add CI checks, and refactor eFP schemas #296
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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
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