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Make referencesets optional when possible#1596
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david4096 wants to merge 3 commits intoga4gh:masterfrom
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Make referencesets optional when possible#1596david4096 wants to merge 3 commits intoga4gh:masterfrom
david4096 wants to merge 3 commits intoga4gh:masterfrom
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david4096
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Mar 2, 2017
| sep="\t") | ||
| print("\tVariantSets:") | ||
| for variantSet in dataset.getVariantSets(): | ||
| referenceSetName = "" |
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These should be refactored into one method, safeGetReferenceSetName.
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Allow nullity for referencesetid field in models Safely access the referenceset name in a few places
Remove reference set from RNA (it's not in the schemas) Adding functions to safely get reference set name and ID
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david4096
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Mar 4, 2017
| def safeGetReferenceSetByName(self, referenceSetName): | ||
| """ | ||
| Gets a reference set by name from the repository throwing a useful | ||
| exception if it is not found. |
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The repo manager requires that a reference set is provided when it is really only a metadata item from the perspective of the variants, features, and RNA. For this reason, we can make it an optional flag at the repo manager.
I am able to add a variant set using just:
python repo_dev.py add-variantset ga4gh-example-data/registry.db brca1 ga4gh-example-data/brca1_1kgPhase3_variants.vcf.gzAllow nullity for referencesetid field in modelsSafely access the referenceset name in a few placesWe should strongly consider a PR at the schemas that removes the
referenceIdas a required field of a reads search, as that is the only endpoint that can't implement this feature.Works to close #1528, thanks @ejacox for helping us keep focus on usability features.