aivanov_database/omop/CHANGELOG.md

Changelog

All notable changes to the OMOP Data Pipeline project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[0.1.0] - 2024-01-XX

Added

• Initial release of OMOP CDM 5.4 Data Pipeline
• Complete OMOP CDM 5.4 schema implementation (30+ tables)
• Staging schema for raw data ingestion
• Audit schema for ETL tracking and data quality metrics
• Extractor component for batch and incremental extraction
• Concept Mapper with LRU caching and multi-level mapping strategy
• Transformer for all major OMOP tables (PERSON, VISIT_OCCURRENCE, CONDITION_OCCURRENCE, etc.)
• Validator with comprehensive data quality checks
• Loader with bulk insert and UPSERT capabilities
• Orchestrator for coordinating complete ETL flow
• Parallel processing with ThreadPoolExecutor
• Error Handler with retry logic, circuit breaker, and checkpoint/resume
• CLI interface with comprehensive commands
• Vocabulary Loader for OMOP vocabularies
• Configuration management with YAML and environment variables
• Comprehensive logging with file rotation
• Database connection pooling with retry logic
• Pydantic models for all OMOP tables
• PostgreSQL sequences for ID generation

Features

• Automated concept mapping with fallback strategies
• Batch processing with configurable batch sizes
• Multi-threaded parallel processing
• Transaction management with automatic rollback
• Foreign key validation before loading
• Date validation and parsing
• Referential integrity checks
• OMOP compliance validation
• Unmapped code tracking
• Execution statistics and audit trail
• Progress bars for long-running operations
• Verbose logging mode

Documentation

• README with quick start guide
• User guide with detailed instructions
• Architecture documentation
• Transformation rules documentation
• API documentation in code
• Configuration examples

Requirements

• Python 3.12+
• PostgreSQL 16.11+
• SQLAlchemy 2.0+
• Pydantic 2.5+
• Click 8.1+
• Other dependencies in requirements.txt

[Unreleased]

Planned

• Property-based tests with Hypothesis
• Integration tests for complete ETL flow
• Performance benchmarking suite
• Docker containerization
• CI/CD pipeline
• Data Quality Dashboard integration
• Additional source data formats (HL7, FHIR)
• Incremental ETL mode
• Data lineage tracking
• Web-based monitoring dashboard
• REST API for programmatic access