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

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Jun 9, 2024
Merged

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

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31 changes: 12 additions & 19 deletions protos/annonars/clinvar_data/clinvar_public.proto
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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;
}
Expand Down Expand Up @@ -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;
Expand Down Expand Up @@ -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.
Expand Down Expand Up @@ -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.
Expand Down Expand Up @@ -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.
Expand Down
2 changes: 2 additions & 0 deletions protos/annonars/clinvar_data/gene_impact.proto
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Expand Up @@ -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
Expand Down
18 changes: 3 additions & 15 deletions src/api/annonars/__snapshots__/client.spec.ts.snap
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23 changes: 4 additions & 19 deletions src/components/SeqvarClinvarCard/SeqvarClinvarCard.vue
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Original file line number Diff line number Diff line change
@@ -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'
Expand All @@ -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>
Expand Down Expand Up @@ -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
Expand Down
32 changes: 10 additions & 22 deletions src/components/StrucvarClinvarCard/StrucvarClinvarCard.vue
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Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down Expand Up @@ -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)
}

Expand Down Expand Up @@ -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"
Expand All @@ -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">
Expand Down Expand Up @@ -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"
Expand All @@ -232,7 +220,7 @@ const expanded = ref<string[]>([])
<span
:title="
AGGREGATE_SOMATIC_CLINICAL_IMPACT_REVIEW_STATUS_LABEL[
somaticClinicalImpact.reviewStatus
record!.classifications?.somaticClinicalImpact.reviewStatus
]
"
>
Expand All @@ -241,7 +229,7 @@ const expanded = ref<string[]>([])
v-if="
i <=
AGGREGATE_SOMATIC_CLINICAL_IMPACT_REVIEW_STATUS_STARS[
somaticClinicalImpact.reviewStatus
record!.classifications?.somaticClinicalImpact.reviewStatus
]
"
>
Expand Down
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