issue #1227 - skip empty annotation runs

SACGF · Jan 15, 2025 · e3f4c03 · e3f4c03
1 parent c562336
commit e3f4c03
Showing 1 changed file with 5 additions and 1 deletion.
diff --git a/annotation/management/commands/fix_annotation_sv_c_hgvs.py b/annotation/management/commands/fix_annotation_sv_c_hgvs.py
@@ -18,12 +18,16 @@ class Command(BaseCommand):
 
     def handle(self, *args, **options):
         for genome_build in GenomeBuild.builds_with_annotation():
+            logging.info("Fixing annotation for genome build: %s", genome_build)
             # We should have all the transcripts locally, don't fall back on ClinGen if we error as it'll
             # probably just error there too
             hgvs_matcher = HGVSMatcher(genome_build, clingen_resolution=False, allow_alternative_transcript_version=False)
 
+            # In latest systems, we'll set run to 'skipped' if it didn't dump anything
+            # But historical ones will be finished with annotated count = 0 - so skip those
             run_qs = AnnotationRun.objects.filter(pipeline_type=VariantAnnotationPipelineType.STRUCTURAL_VARIANT,
-                                                  status=AnnotationStatus.FINISHED)
+                                                  status=AnnotationStatus.FINISHED,
+                                                  annotated_count__gt=0)
             total = run_qs.count()
             # Pull down the
             for i, ar in enumerate(run_qs):