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-Updated get_paths to new path structure -Defaults to is_current but accepts version (integrated or partial) -Added input validation -VEP code was simplified to call on the get_paths -tests were updated and new tests created -test data: ensembl_release.label was made to look like real data and associated tests were updated
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Will need updates to this PR following schema updates in PR #169 |
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This pull request refactors the way assembly accession-based paths are generated and used within the ensembl-metadata-api codebase.
Key Changes:
Introduced format_accession_path Utility:
Added a new function, format_accession_path, in src/ensembl/production/metadata/api/factories/utils.py.
This function takes an assembly accession (e.g., GCF_043381705.1) and converts it to a standardized path format (e.g., GCF/043/381/705/1).
It validates the accession format and raises errors for invalid formats.
Refactored Path Construction in Adaptors:
Updated genome.py and vep.py adaptors to use format_accession_path for path handling.
Replaced previous logic that constructed paths using the scientific name and accession, resulting in more consistent and structured paths.
Paths that previously looked like Saccharomyces_cerevisiae_S288c/GCA_000146045.2/... now look like GCA/000/146/045/2/....
Updated Tests:
Introduced new tests for the path generation to cover previous releases.
Updated existing tests to work with the change in expected data.
Updated ensembl_release.label data to match current standard and all associated tests
Adjusted tests in test_utils.py to match the new path format.
Added unit tests to validate the new format_accession_path utility, including tests for valid, invalid, and edge case inputs.