LiftoverError - null value in column "conversion_tool"

[davmlaw]

View details in Rollbar: https://app.rollbar.com/a/jimmy.andrews/fix/item/VariantGrid/5459

  File "/opt/variantgrid/classification/tasks/classification_import_process_variants_task.py", line 114, in liftover_classification_import
    create_liftover_pipelines(classification_import.user, allele_qs, import_source, genome_build)
  File "/opt/variantgrid/snpdb/liftover.py", line 48, in create_liftover_pipelines
    liftover = LiftoverRun.objects.create(user=user,

NotNullViolation: null value in column "conversion_tool" of relation "snpdb_liftoverrun" violates not-null constraint
DETAIL:  Failing row contains (4823, 2024-10-23 03:11:08.790847+00, 2024-10-23 03:11:08.791004+00, null, null, GRCh38, 2, null, null).

[davmlaw]

I think I went back and forth making a method a return vs yield and ended up yielding None rather than nothing

liftover._liftover_using_source_variant_coordinate starts with setting conversion_tool = None

Then we loop through and try and find way to liftover (just BCFTools)

If nothing found, then conversion_tool left as None

This eventually causes trouble as build_liftover_allele_variant_coordinate_error in create_liftover_pipelines has entry where convert_tool is None, then dies when trying to create LiftoverRun.conversion_tool = None

Solution is to just not yield anything from _liftover_using_source_variant_coordinate