Add unit test for ensembl.io.genomio.genome_metadata.prepare module #312
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also update NCBI's provider URLS
…and add unit tests
Dishalodha
reviewed
Mar 7, 2024
| assembly["version"] = int(values[1]) | ||
| version = accession.partition(".")[2] | ||
| if version: | ||
| assembly["version"] = int(version) | ||
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| def add_genebuild_metadata(genome_data: Dict) -> None: |
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Perhaps use a bit more descriptive function name here. Perhaps: add_genebuild_version_metadata
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This function is adding both version and start_date, so I think in this case the function name is appropriate. That being said, maybe referring to annotation rather than genebuild would be more accurate, but that can be discussed separaterly.
ens-LCampbell
approved these changes
Mar 8, 2024
MatBarba
approved these changes
Mar 19, 2024
| if (not "provider_name" in assembly) and (not "provider_url" in assembly): | ||
| assembly["provider_name"] = provider["assembly"]["provider_name"] | ||
| assembly["provider_url"] = provider["assembly"]["provider_url"] | ||
| assembly["provider_url"] = f'{provider["assembly"]["provider_url"]}/{accession}' |
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Not sure we want the accession here: It's the URL for the provider, not for the data (and there is no guarantee the provider_url can have /accession be valid outside of Refseq)
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Updated all methods (review docstrings, improve readability and reduce code complexity) and added unit tests for all of them.