Benb/split import and validate #829
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…es into benb/split_import_and_validate
| pos = allele_info['coordinates'][0]['end'] | ||
| ref = allele_info['coordinates'][0]['referenceAllele'] | ||
| alt = allele_info['coordinates'][0]['allele'] | ||
| except (KeyError, StopIteration): |
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oof so referenceGenome was missing from the response?
Looking back to https://reg.clinicalgenome.org/doc/AlleleRegistry_1.01.xx_api_v1.pdf, looks like referenceGenome in alleleDefinition is populated conditionally.
We could handle it more explicitly but I think a simply try/except is the better option.
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🤷 yes! I think this is the laziest answer... if any keys are missing just let it be unmappable. manual intervention on this is expensive (I think?)
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| @luigi.util.inherits(BaseLoadingRunParams) | ||
| class ValidateCallsetTask(BaseUpdateTask): |
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is there anything in here that wasn't pulled from WriteImportedCallsetTask?
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lifted line by line.
| mt, | ||
| self.dataset_type, | ||
| self.additional_row_fields(mt), | ||
| additional_row_fields( |
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Can you delete additional_row_fields in this file since you moved it?
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yes! that snuck through good catch!
| @@ -57,7 +57,7 @@ def setUp(self) -> None: | |||
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| # Force imported callset to be complete | |||
| ht = import_vcf(TEST_VCF, ReferenceGenome.GRCh38) | |||
| ht = ht.annotate_globals(sample_type=SampleType.WGS.value) | |||
| ht = ht.annotate_globals(validated_sample_type=SampleType.WGS.value) | |||
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is validated_sample_type used anywhere?
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yes! we check it in the complete method of ValidateCallset.
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The change to this block was necessary because we're "mocking" the upstream task completion.
Benb/split import and validate (#829)
Splits the Import and Validate steps into two disjoint tasks.