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Pull Request Overview
This PR removes support for Azure Open Datasets-based gnomAD public resources as access to gnomAD data in Azure Open Datasets will be deprecated in August. The changes involve removing Azure-specific constants, configuration mappings, path generation logic, and associated tests.
- Removed
AZURE_OPEN_DATASETSconstant and hdinsight provider mapping from configuration - Eliminated Azure-specific path generation logic in resource utilities
- Updated tests to remove Azure-related test cases and parameters
Reviewed Changes
Copilot reviewed 4 out of 4 changed files in this pull request and generated no comments.
| File | Description |
|---|---|
| gnomad/resources/config.py | Removes Azure Open Datasets enum value and hdinsight provider mapping |
| gnomad/resources/resource_utils.py | Removes Azure path generation logic for wasbs:// URLs |
| tests/resources/test_resource_utils.py | Removes Azure-related test cases and updates test parameters |
| docs/resource_sources.rst | Removes documentation reference to Azure HDInsight cluster usage |
Comments suppressed due to low confidence (1)
tests/resources/test_resource_utils.py:194
- This test was previously verifying that environment variables override cloud spark provider detection when hdinsight was detected. Now that hdinsight support is removed, the test should verify this behavior with a different provider or the test case should be updated to reflect the new expected behavior more clearly.
return_value="dataproc",
| ("dataproc", GnomadPublicResourceSource.GOOGLE_CLOUD_PUBLIC_DATASETS), | ||
| ("hdinsight", GnomadPublicResourceSource.AZURE_OPEN_DATASETS), | ||
| ("unknown", GnomadPublicResourceSource.GOOGLE_CLOUD_PUBLIC_DATASETS), | ||
| (None, GnomadPublicResourceSource.GOOGLE_CLOUD_PUBLIC_DATASETS), |
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Just curious why the None is being dropped too since it looks like we would default to google in this case?
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oops, I thought this was something Cursor added -- will add back
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This PR removes support for Azure Open Datasets-based gnomAD public resources. Access to gnomAD data in Azure Open Datasets will be deprecated in August.
Breaking changes in
gnomad/resources/config.py:AZURE_OPEN_DATASETSconstantdefault_resource_sources_by_providerwithinget_default_public_resource_sourcefunction