feat: add remap and family loading failures as validation exceptions … #1005
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bpblanken
commented
Jan 2, 2025
| self.missing_samples = missing_samples | ||
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| def vcf_remap(mt: hl.MatrixTable) -> hl.MatrixTable: |
| CallsetTask(self.callset_path), | ||
| ] | ||
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| @with_persisted_validation_errors |
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this decorator manages the try/except/write validation errors patterns more DRYly
| 'error_messages': [ | ||
| 'All families failed validation checks', | ||
| ], | ||
| 'failed_family_samples': { |
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Preserves the structure of the failed_family_samples that exists in the metadata.json.
hanars
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Jan 2, 2025
bpblanken
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Jan 7, 2025
* Add service account credentialing (#997) * Add service account credentialing * ruff * feat: Handle parsing empty predicted sex into Unknown (#1000) * Add helper functions for querying `Terra Data Repository` (#998) * Add service account credentialing * ruff * First pass * tests passing * add coverage of bigquery test * change function names * use generators everywhere * bq requirement * resolver * Update sample id name * Build Sex Check Table from TDR Metrics (#999) * refactor: Move feature flags to FeatureFlag enum. (#1002) * refactor: Move feature flags out of environment to their own dataclass * lint: ruff * ruff * bugfix: exclude samples from relationship checking that are not present in the expected loadable samples (#1003) * bugfix: exclude samples from relationship checking that are not present in the expected loadable samples * cleanup * feat: add remap and family loading failures as validation exceptions … (#1005) * feat: add remap and family loading failures as validation exceptions rather than runtime errors * move on * Update write_remapped_and_subsetted_callset_test.py * ruff * feat: Add ability to run tasks dataproc. (#948) * Support gcs dirs in rsync * ws * Add create dataproc cluster task * add dataproc * ruff * requirements * still struggling * Gencode refactor to remove gcs * bump reqs * Run dataproc job * lib * running * merge requirements * Flip'em * Better exception handling * Cleaner approach if less generalizable * write a test * Fix tests * lint * Add test for success * refactor to use a base class... better for adding support for multiple jobs * cleanup * ruff * Fix missing mock * Fix flapping test * pr comments
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…rather than runtime errors
#1004