Kyle Ferriter

GA4GH GKS API review

7

Some schema notes I took while testing the `va` API: (1) Numeric type mismatch means graphql cannot map `value` fields to the same query field. - SequenceLocation.start is a -...

Create hashable BaseModel subclass in order to enforce uniqueItems with Set annotation

3

We just need to define what to use as the hash value that will work across all the models. https://github.com/pydantic/pydantic/issues/1303#issuecomment-599712964 @ahwagner if are going to go ahead with making every...

pre-commit hook causes unexpected problems on existing codebase

1

**Describe the bug** When I take existing code in `main` and run the pre-commit checks installed by `make devready`, it fails, which means contributors cannot commit code to many existing...

Change IndefiniteRange.value to be an integer

4

See https://github.com/ga4gh/va-spec/issues/129

This will help ensure that changes made to schemas or directories are reflected in the references made from the docs files

Change seqrepo dataproxy env vars to all use SEQREPO_DATAPROXY_URI

5

biocommons.seqrepo uses `SEQREPO_DATAPROXY_URI` to point to a filesystem or HTTP endpoint for a seqrepo instance. * Change SEQREPO_REST_URL in vrs-python `conftest.py` to use SEQREPO_DATAPROXY_URI * Change SEQREPO_URI in vrs-python `hgvs_tools.py`...

VCF Annotator CLI support for reading/writing stdin/stdout

6

Closes #529 Tested with stdin/out and this vcf file: ``` $ curl -O https://raw.githubusercontent.com/c-BIG/NPM-sample-qc/refs/heads/master/tests/NA12878-chr14-AKT1_1000genomes-dragen-3.7.6/NA12878-chr14-AKT1.vcf.gz $ export GA4GH_VRS_DATAPROXY_URI=seqrepo+file://$HOME/dev/data/seqrepo/2024-12-20 # existing functionality (file in, file out) $ vrs-annotate vcf NA12878-chr14-AKT1.vcf.gz --vcf-out NA12878-chr14-AKT1.VRS-ANNOTATED.vcf.gz...

compose docs and volume mount examples

3

Closes #526