issue #1103 - Create ClinGen liftover failure record

snpdb/liftover.py

@@ -222,12 +222,22 @@ def _liftover_using_dest_variant_coordinate(allele, dest_genome_build: GenomeBui
 
     conversion_tool = None
     g_hgvs = None
+    clingen_failure_message = None
     if allele.clingen_allele:
         try:
             g_hgvs = allele.clingen_allele.get_g_hgvs(dest_genome_build)
             conversion_tool = AlleleConversionTool.CLINGEN_ALLELE_REGISTRY
         except ValueError:  # Various contig errors all subclass from this
-            pass
+            clingen_failure_message = f"{allele.clingen_allele} did not contain g.HGVS for {dest_genome_build}"
+    else:
+        clingen_failure_message = f"No ClinGenAllele for variant"
+
+    # Store the fact that we couldn't use ClinGen
+    if clingen_failure_message:
+        lr = LiftoverRun.get_clingen_auto_fail_liftover_run(dest_genome_build)
+        AlleleLiftover.objects.create(liftover=lr, allele=allele, status=ProcessingStatus.ERROR,
+                                      error={"message": clingen_failure_message})
+
     if g_hgvs is None:
         if settings.LIFTOVER_DBSNP_ENABLED:
             va = allele.variantallele_set.all().first()

snpdb/models/models_variant.py

@@ -26,6 +26,7 @@
 from library.django_utils.django_partition import RelatedModelsPartitionModel
 from library.genomics import format_chrom
 from library.genomics.vcf_enums import VCFSymbolicAllele
+from library.guardian_utils import admin_bot
 from library.preview_request import PreviewModelMixin, PreviewKeyValue
 from library.utils import FormerTuple, sha256sum_str
 from snpdb.models import Wiki
@@ -909,6 +910,24 @@ class LiftoverRun(TimeStampedModel):
                                             related_name="liftover_source_genome_build")
     genome_build = models.ForeignKey(GenomeBuild, on_delete=CASCADE)  # destination
 
+    @staticmethod
+    def get_clingen_auto_fail_liftover_run(genome_build: GenomeBuild) -> 'LiftoverRun':
+        """ We can know straight away we're going to fail a ClinGen run (missing ClinGenAllele, no data for the build)
+            but would still like to record the failure - so put them all in 1 LiftoverRun per build """
+        kwargs = {
+            "user": admin_bot(),
+            "genome_build": genome_build,
+            "conversion_tool": AlleleConversionTool.CLINGEN_ALLELE_REGISTRY,
+        }
+        # There should have been 1 created in 'one_off_legacy_populate_allele_liftover'
+        lr = LiftoverRun.objects.filter(**kwargs).order_by("pk").first()
+        if not lr:
+            # Otherwise create it
+            lr = LiftoverRun.objects.create(**kwargs)
+        return lr
+
+
+
     def get_absolute_url(self):
         return reverse("view_liftover_run", kwargs={"liftover_run_id": self.pk})