issue #1060 - variant details page, create allele for all variants no…

…t just shorty clingen ones
SACGF · May 22, 2024 · fca2f1b · fca2f1b
1 parent ba183cc
commit fca2f1b
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Showing 2 changed files with 17 additions and 16 deletions.
diff --git a/snpdb/clingen_allele.py b/snpdb/clingen_allele.py
@@ -282,10 +282,6 @@ def get_variant_allele_for_variant(genome_build: GenomeBuild, variant: Variant,
         Successful calls link variants in all builds (that exist)
         errors are only stored on the requesting build """
 
-    if not variant.can_have_clingen_allele:
-        msg = f"No ClinGenAllele for variant: {variant}"
-        raise ClinGenAlleleAPIException(msg)
-
     # In a very rare race condition, we may have 2 VariantAlleles created, in which case just use 1st
     if va := VariantAllele.objects.filter(variant=variant, genome_build=genome_build).order_by("pk").first():
         if va.needs_clingen_call():
@@ -295,10 +291,11 @@ def get_variant_allele_for_variant(genome_build: GenomeBuild, variant: Variant,
                 pass  # Got the allele, have to accept can't get ClinGen
     else:
         if settings.CLINGEN_ALLELE_REGISTRY_LOGIN:
-            try:
-                va = variant_allele_clingen(genome_build, variant, clingen_api=clingen_api)
-            except ClinGenAlleleTooLargeException:
-                pass  # only recoverable exception
+            if variant.can_have_clingen_allele:
+                try:
+                    va = variant_allele_clingen(genome_build, variant, clingen_api=clingen_api)
+                except ClinGenAlleleTooLargeException:
+                    pass  # only recoverable exception
 
         if va is None:
             logging.debug("Not using ClinGen")
@@ -397,6 +394,10 @@ def get_clingen_allele_for_variant(genome_build: GenomeBuild, variant: Variant,
     if clingen_api is None:
         clingen_api = ClinGenAlleleRegistryAPI()
 
+    if not variant.can_have_clingen_allele:
+        msg = f"No ClinGenAllele possible for variant: {variant}"
+        raise ClinGenAlleleAPIException(msg)
+
     va = get_variant_allele_for_variant(genome_build, variant, clingen_api=clingen_api)
     if va.allele.clingen_allele is None:
         logging.error("ClinGen Allele failed!")

diff --git a/variantopedia/templates/variantopedia/variant_details.html b/variantopedia/templates/variantopedia/variant_details.html
@@ -399,19 +399,19 @@
     if (variantAllele) {
         populateVariantAllele(variantAllele);
     } else {
-    {% if variant.can_have_clingen_allele %}
         // Use Ajax to create + retrieve ClinGenAllele
         let variantAlleleForVariantUrl = "{% url 'variant_allele_for_variant' variant.pk genome_build.pk %}";
         $.ajax(variantAlleleForVariantUrl, {
             suppressErrors: true,
-            success: populateVariantAllele
+            success: populateVariantAllele,
+            error: function() {
+                console.log("Error retrieving allele");
+                // Can't retrieve, just show basics
+                let variantString = "{{ variant|safe }}";
+                let linkData = {variant_string: variantString, variant_coordinate: variantString};
+                populateVariantAllele({link_data: linkData});
+            }
         });
-    {% else %}
-        // Can't retrieve, just show basics
-        let variantString = "{{ variant|safe }}";
-        let linkData = {variant_string: variantString, variant_coordinate: variantString};
-        populateVariantAllele({link_data: linkData});
-    {% endif %}
     }
 
     handlePubMedLinks("{{ variant_annotation.pubmed|default_if_none:''|safe }}");