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.gz
Update docs to reflect optional fields.
Remove reference set from RNA paths in build test data
Allow nullity for referencesetid field in models
Safely access the referenceset name in a few places
Make repo manager safely access referenceset for featuresets, RNA, annotations
We should strongly consider a PR at the schemas that removes the referenceId as 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.
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.