Update ClinVar pipeline for new XML format

.tool-versions

@@ -1,2 +1,3 @@
 nodejs 18.17.1
 pnpm 8.14.3
+python 3.9.17

browser/src/ClinvarVariantsTrack/ClinvarVariantDetails.tsx

@@ -137,7 +137,7 @@ const ClinvarVariantDetails = ({
               []
             )}
         </AttributeListItem>
-        <AttributeListItem label="Clinical significance">
+        <AttributeListItem label="Germline classification">
           {clinvarVariant.clinical_significance}
         </AttributeListItem>
         <AttributeListItem label="Review status">

browser/src/ClinvarVariantsTrack/ClinvarVariantTooltip.tsx

@@ -72,7 +72,7 @@ const ClinvarVariantTooltip = ({ variant }: ClinvarVariantTooltipProps) => (
     <strong>{variant.variant_id}</strong>
     <ClinvarVariantAttributeList>
       <div>
-        <dt>Clinical significance</dt>
+        <dt>Germline classification</dt>
         <dd>{variant.clinical_significance}</dd>
       </div>
       <div>

browser/src/ClinvarVariantsTrack/clinvarVariantCategories.ts

@@ -13,6 +13,7 @@ const CLINICAL_SIGNIFICANCE_GROUPS = {
   uncertain: new Set([
     'Uncertain significance',
     'Conflicting interpretations of pathogenicity',
+    'Conflicting classifications of pathogenicity',
     'conflicting data from submitters',
   ]),
   benign: new Set(['Benign', 'Likely benign', 'Benign/Likely benign']),
@@ -22,6 +23,7 @@ const CLINICAL_SIGNIFICANCE_GROUPS = {
     'Affects',
     'protective',
     'no interpretation for the single variant',
+    'no classification for the single variant',
     'not provided',
     'association not found',
   ]),

browser/src/SubmissionsList.tsx

@@ -45,7 +45,7 @@ const SubmissionsList = ({ submissions }: SubmissionsListProps) => (
               // @ts-expect-error TS(2769) FIXME: No overload matches this call.
               .reduce((acc, el, i) => (i === 0 ? [...acc, el] : [...acc, ', ', el]), [])}
           </AttributeListItem>
-          <AttributeListItem label="Clinical significance">
+          <AttributeListItem label="Germline classification">
             {submission.clinical_significance || '–'}
           </AttributeListItem>
           <AttributeListItem label="Review status">{submission.review_status}</AttributeListItem>

browser/src/VariantPage/VariantClinvarInfo.tsx

@@ -50,7 +50,7 @@ const VariantClinvarInfo = ({ clinvar }: VariantClinvarInfoProps) => {
               []
             )}
         </AttributeListItem>
-        <AttributeListItem label="Clinical significance">
+        <AttributeListItem label="Germline classification">
           {clinvar.clinical_significance}
         </AttributeListItem>
         <AttributeListItem label="Review status">

browser/src/__snapshots__/SubmissionsList.spec.tsx.snap

@@ -19,7 +19,7 @@ exports[`SubmissionsList has no unexpected changes 1`] = `
         </Link__ExternalLink>
       </AttributeListItem>
       <AttributeListItem
-        label="Clinical significance"
+        label="Germline classification"
       >
         Benign
       </AttributeListItem>
@@ -52,7 +52,7 @@ exports[`SubmissionsList has no unexpected changes 1`] = `
         </Link__ExternalLink>
       </AttributeListItem>
       <AttributeListItem
-        label="Clinical significance"
+        label="Germline classification"
       >
         Benign
       </AttributeListItem>

data-pipeline/requirements.txt

@@ -1,5 +1,5 @@
 elasticsearch~=7.17
-hail==0.2.127
+hail==0.2.128
 tqdm
 loguru
 attrs