Go mapping #25
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Go mapping #25
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- Create ontology_mapping agent directory structure - Add unit tests for data models (OntologyMapping, OntologyMappingResponse) - Tests currently failing (RED) - models not yet implemented - Following TDD workflow 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
- Add OntologyMapping and OntologyMappingResponse Pydantic models - All unit tests now passing (GREEN) - Models include comprehensive Google-style docstrings with RST syntax - Support for optional fields and metadata 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
- Test configuration loading from environment variables - Test default values for target ontologies - Test custom ontology list parsing - Test workdir creation - Tests currently failing - config not yet implemented 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
- Add OntologyMappingDependencies dataclass - Support environment-based configuration (WORKDIR, TARGET_ONTOLOGIES) - Auto-create workdir if it doesn't exist - All configuration tests passing (GREEN) - Comprehensive Google-style docstrings with RST syntax 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
- Add search functions for GO, CL, UBERON, ChEBI ontologies - Use OAKlib to query Ontology Lookup Service (OLS) - Include error handling and logging - Limit results to top 10 matches per search - Google-style docstrings with RST syntax 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
- Test agent building and configuration - Test mapping biological processes to GO - Test mapping cellular components to GO - Test handling of unmapped terms - Test custom model configuration - Tests currently failing - agent not yet implemented 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
- Add oaklib>=0.6.21 to dependencies - Sync dependencies with uv - Required for OLS (Ontology Lookup Service) integration 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
- Add main agent with factory function build_ontology_mapping_agent() - Add helper function map_terms_to_go() for convenient usage - Register OAKlib search tools (GO, CL, UBERON, ChEBI) - Implement GO-focused system prompt - Fix Unicode encoding issues in system prompt - Update __init__.py to export agent functions - Fix integration tests for agent building - Agent building tests passing 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
- Change result.data to result.output (correct pydantic-ai API) - Fix Unicode arrow characters in docstrings - Integration tests should now pass 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
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