UniProt Parser Refactor – Improved Modularity, Identifier Extraction, and Test Coverage #45
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| if os.path.exists(tmp_path): | ||
| try: | ||
| os.remove(tmp_path) | ||
| except Exception: |
Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
## develop #45 +/- ##
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+ Coverage 51.18% 51.75% +0.57%
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Files 59 61 +2
Lines 3048 3223 +175
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+ Hits 1560 1668 +108
- Misses 1488 1555 +67
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Remove .DS_Store from tests directory Fixing path problems that were preventing module import Removing `tests/` directory from under `tests` UniRef updates lint First steps towards using external IDs for CDM entities organize uniprot.py revise uniprot.py and test_uniprot.py format: apply ruff formatting to uniprot parser change the format format Regenerate uv.lock Uniprot branch file movements Fix formatting / tests / docs update uniref and test uniref reformat uniprot and uniref update uniprot.py and test any data files used by the test should go in test/data formatting uniprot.py Fix UniRef parsing tests and stabilize timestamp handling Remove large uniprot archaea test data directory style: apply Ruff formatting to uniprot-refactor-v2
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This refactor introduces a cleaner, modular, and more maintainable architecture for UniProt data parsing within the cdm_data_loader_utils package. The new design separates concerns across multiple parser components, centralizes shared identifier extraction, enhances XML utilities, and adds a comprehensive test suite to ensure long-term stability.
Key improvements include:
• Modular parser structure under cdm_data_loader_utils/parsers/
• Unified shared identifier extraction (shared_identifiers.py)
• Robust XML parsing utilities (xml_utils.py)
• Refactored UniProt parser (uniprot.py) with clearer logic paths
• Complete tests for UniProt refactor, including:
• shared identifiers
• XML utilities
• UniProt entry parsing
• Cleaner directory layout aligned with CDM conventions
This refactor provides a foundation for future expansion (features, evidence, associations, and publications) while improving maintainability and reducing duplicated logic.