fix: adjust to annonars clinvar_public cardinality changes (#209) (#210)

Release-As: 0.7.0
bihealth · Jun 9, 2024 · 18df4a5 · 18df4a5
1 parent 8ad0981
commit 18df4a5
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Showing 8 changed files with 121 additions and 267 deletions.
diff --git a/protos/annonars/clinvar_data/clinvar_public.proto b/protos/annonars/clinvar_data/clinvar_public.proto
@@ -731,28 +731,21 @@ message Trait {
 
     /* nested elements */
 
-    // names
-    //
-    // NB: in XSD this is explictely given as unbounded but XML always has
-    // one element
+    // Name(s) of the trait.
     repeated GenericSetElement names = 1;
-    // symbols (NB: never occur in the XML)
-    repeated GenericSetElement symbols = 2;
-    // attributes (NB: never occur in the XML)
-    repeated AttributeSetElement attributes = 3;
     // Citation list.
-    repeated Citation citations = 4;
+    repeated Citation citations = 2;
     // Xref list.
-    repeated Xref xrefs = 5;
+    repeated Xref xrefs = 3;
     // Comment list.
-    repeated Comment comments = 6;
+    repeated Comment comments = 4;
     // Sources
-    repeated string sources = 7;
+    repeated string sources = 5;
 
     /* attributes */
 
     // Trait type.
-    Type type = 8;
+    Type type = 6;
   }
 
   // names
@@ -985,7 +978,7 @@ message AggregateClassificationSet {
   // The aggregate germline classification.
   optional AggregatedGermlineClassification germline_classification = 1;
   // The aggregate somatic clinical impact.
-  repeated AggregatedSomaticClinicalImpact somatic_clinical_impacts = 2;
+  optional AggregatedSomaticClinicalImpact somatic_clinical_impact = 2;
   // The aggregate oncogenicity classification.
   optional AggregatedOncogenicityClassification oncogenicity_classification = 3;
 }
@@ -1116,7 +1109,7 @@ message ClassificationScv {
   optional string germline_classification = 2;
   // Information on the clinical impact; mutually exlusive with `germline_classification`
   // and `oncogenicity_classification`.
-  optional SomaticClinicalImpact somatic_clinical_impacts = 3;
+  optional SomaticClinicalImpact somatic_clinical_impact = 3;
   // The oncogenicity classification; mutually exlusive with `germline_classification`
   // and `oncogenicity_classification`.
   optional string oncogenicity_classification = 4;
@@ -1770,7 +1763,7 @@ message AlleleScv {
   // being reported.
   repeated Gene genes = 1;
   // Name provided by the submitter.
-  repeated OtherName names = 2;
+  OtherName name = 2;
   // Variant type.
   optional string variant_type = 3;
   // Location.
@@ -1811,7 +1804,7 @@ message HaplotypeScv {
   // Names other than 'preferred' used for the haplotype.
   repeated OtherName other_names = 3;
   // Classification of the variant.
-  optional AggregateClassificationSet classification = 4;
+  optional AggregateClassificationSet classifications = 4;
   // Functional consequences of the variant.
   repeated FunctionalConsequence functional_consequences = 5;
   // List of attributes.
@@ -2129,8 +2122,8 @@ message ClinicalAssertion {
   // Replaced list; mutually exclusive with replaces
   repeated ClinicalAssertionRecordHistory replaceds = 6;
 
-  // SCV classifications.
-  repeated ClassificationScv classifications = 7;
+  // SCV classification.
+  ClassificationScv classifications = 7;
   // The assertion.
   Assertion assertion = 8;
   // Attributes.

diff --git a/protos/annonars/clinvar_data/gene_impact.proto b/protos/annonars/clinvar_data/gene_impact.proto
@@ -4,6 +4,8 @@ syntax = "proto3";
 
 package annonars.clinvar_data.gene_impact;
 
+import "annonars/clinvar_data/clinvar_public.proto";
+
 // Enumeration with the variant consequence.
 enum GeneImpact {
   // unspecified impact

diff --git a/src/api/annonars/__snapshots__/client.spec.ts.snap b/src/api/annonars/__snapshots__/client.spec.ts.snap
diff --git a/src/components/SeqvarClinvarCard/SeqvarClinvarCard.vue b/src/components/SeqvarClinvarCard/SeqvarClinvarCard.vue
@@ -1,8 +1,7 @@
 <script setup lang="ts">
-import { computed, ref } from 'vue'
+import { ref } from 'vue'
 
 import { ExtractedVcvRecordList } from '../../pbs/annonars/clinvar/minimal'
-import { AggregatedSomaticClinicalImpact } from '../../pbs/annonars/clinvar_data/clinvar_public'
 import DocsLink from '../DocsLink/DocsLink.vue'
 import GermlineClassification from './GermlineClassification.vue'
 import RcvRow from './RcvRow.vue'
@@ -16,17 +15,6 @@ const props = defineProps<{
   clinvarRecords?: ExtractedVcvRecordList
 }>()
 
-type AggregatedSomaticClinicalImpactU = AggregatedSomaticClinicalImpact | undefined
-const clinicalImpacts = computed<AggregatedSomaticClinicalImpactU[]>(() => {
-  if (!props.clinvarRecords?.records?.length) {
-    return [undefined]
-  } else if (props.clinvarRecords?.records[0].classifications?.somaticClinicalImpacts?.length) {
-    return props.clinvarRecords?.records[0].classifications?.somaticClinicalImpacts
-  } else {
-    return [undefined]
-  }
-})
-
 /** Whether the card is expanded; component state. */
 const expand = ref<boolean>(false)
 </script>
@@ -66,12 +54,9 @@ const expand = ref<boolean>(false)
       </v-row>
       <v-row no-gutters class="ml-4 mb-2">
         <v-col cols="6">
-          <template
-            v-for="somaticClinicalImpact in clinicalImpacts"
-            :key="somaticClinicalImpact?.description"
-          >
-            <SomaticClinicalImpact :clinical-impact="somaticClinicalImpact" />
-          </template>
+          <SomaticClinicalImpact
+            :clinical-impact="clinvarRecord?.classifications?.somaticClinicalImpact"
+          />
         </v-col>
         <v-col cols="6">
           <SomaticOncongenicity

diff --git a/src/components/StrucvarClinvarCard/StrucvarClinvarCard.vue b/src/components/StrucvarClinvarCard/StrucvarClinvarCard.vue
@@ -7,10 +7,7 @@ import { computed, ref } from 'vue'
 import { type Strucvar } from '../../lib/genomicVars'
 import { roundIt } from '../../lib/utils'
 import { ResponseRecord as ClinvarSvRecord } from '../../pbs/annonars/clinvar/sv'
-import {
-  AggregateClassificationSet,
-  AggregatedSomaticClinicalImpact
-} from '../../pbs/annonars/clinvar_data/clinvar_public'
+import { AggregateClassificationSet } from '../../pbs/annonars/clinvar_data/clinvar_public'
 import DocsLink from '../DocsLink/DocsLink.vue'
 import {
   AGGREGATE_GERMLINE_REVIEW_STATUS_LABEL,
@@ -64,12 +61,9 @@ const maxStars = (acs: AggregateClassificationSet) => {
   const starsOncogenicity = acs.oncogenicityClassification?.reviewStatus
     ? AGGREGATE_ONCOGENICITY_REVIEW_STATUS_STARS[acs.oncogenicityClassification?.reviewStatus]
     : 0
-  const starsClinicalImpacts = acs.somaticClinicalImpacts.map(
-    (asci: AggregatedSomaticClinicalImpact): number => {
-      return AGGREGATE_SOMATIC_CLINICAL_IMPACT_REVIEW_STATUS_STARS[asci.reviewStatus]
-    }
-  )
-  const starsClinicalImpact = Math.max(...starsClinicalImpacts)
+  const starsClinicalImpact = acs.somaticClinicalImpact?.reviewStatus
+    ? AGGREGATE_SOMATIC_CLINICAL_IMPACT_REVIEW_STATUS_STARS[acs.somaticClinicalImpact?.reviewStatus]
+    : 0
   return Math.max(starsGermline, starsOncogenicity, starsClinicalImpact)
 }
 
@@ -139,10 +133,7 @@ const expanded = ref<string[]>([])
               {{ record!.classifications!.germlineClassification!.description }}
             </v-chip>
           </div>
-          <div
-            v-for="(somaticClinicalImpact, idx) in record!.classifications?.somaticClinicalImpacts"
-            :key="idx"
-          >
+          <div v-if="record!.classifications?.somaticClinicalImpact">
             <v-chip
               bg-color="grey-darken-4"
               title="somatic clinical impact"
@@ -154,9 +145,9 @@ const expanded = ref<string[]>([])
             </v-chip>
             <v-chip
               density="compact"
-              :class="`bg-${clinsigColor(somaticClinicalImpact.description)}`"
+              :class="`bg-${clinsigColor(record!.classifications?.somaticClinicalImpact.description)}`"
             >
-              {{ somaticClinicalImpact.description }}
+              {{ record!.classifications?.somaticClinicalImpact.description }}
             </v-chip>
           </div>
           <div v-if="record!.classifications?.oncogenicityClassification">
@@ -215,10 +206,7 @@ const expanded = ref<string[]>([])
               </span>
             </span>
           </div>
-          <div
-            v-for="(somaticClinicalImpact, idx) in record!.classifications?.somaticClinicalImpacts"
-            :key="idx"
-          >
+          <div v-if="record!.classifications?.somaticClinicalImpact">
             <v-chip
               bg-color="grey-darken-4"
               title="somatic clinical impact"
@@ -232,7 +220,7 @@ const expanded = ref<string[]>([])
             <span
               :title="
                 AGGREGATE_SOMATIC_CLINICAL_IMPACT_REVIEW_STATUS_LABEL[
-                  somaticClinicalImpact.reviewStatus
+                  record!.classifications?.somaticClinicalImpact.reviewStatus
                 ]
               "
             >
@@ -241,7 +229,7 @@ const expanded = ref<string[]>([])
                   v-if="
                     i <=
                     AGGREGATE_SOMATIC_CLINICAL_IMPACT_REVIEW_STATUS_STARS[
-                      somaticClinicalImpact.reviewStatus
+                      record!.classifications?.somaticClinicalImpact.reviewStatus
                     ]
                   "
                 >