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Fix issue with sv tab sending large list of mutations for annotation #4885

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merged 1 commit into from
Apr 5, 2024
Merged

Fix issue with sv tab sending large list of mutations for annotation #4885

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7 changes: 2 additions & 5 deletions src/pages/patientView/structuralVariant/column/AnnotationColumnFormatter.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -154,17 +154,14 @@ export default class AnnotationColumnFormatter {
uniqueSampleKeyToTumorType?: { [sampleId: string]: string },
studyIdToStudy?: { [studyId: string]: CancerStudy }
): IndicatorQueryResp | undefined {
if (
uniqueSampleKeyToTumorType === null ||
oncoKbData.indicatorMap === null
) {
if (!uniqueSampleKeyToTumorType || !oncoKbData.indicatorMap) {
return undefined;
}

const id = generateQueryStructuralVariantId(
structuralVariantData[0].site1EntrezGeneId,
structuralVariantData[0].site2EntrezGeneId,
uniqueSampleKeyToTumorType![
uniqueSampleKeyToTumorType[
structuralVariantData[0].uniqueSampleKey
],
deriveStructuralVariantType(structuralVariantData[0])
Expand Down
57 changes: 38 additions & 19 deletions src/pages/resultsView/ResultsViewPageStore.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -3440,25 +3440,25 @@ export class ResultsViewPageStore extends AnalysisStore
},
});

readonly structuralVariantsByGene = remoteData({
readonly structuralVariantsByEntrezGeneId = remoteData({
await: () => [this.structuralVariants],
invoke: async () => {
const svByGene: Record<string, StructuralVariant[]> = {};
const svByGene: Record<number, StructuralVariant[]> = {};
this.structuralVariants.result!.forEach(sv => {
if (sv.site1HugoSymbol) {
svByGene[sv.site1HugoSymbol] =
svByGene[sv.site1HugoSymbol] || [];
svByGene[sv.site1HugoSymbol].push(sv);
if (sv.site1EntrezGeneId) {
svByGene[sv.site1EntrezGeneId] =
svByGene[sv.site1EntrezGeneId] || [];
svByGene[sv.site1EntrezGeneId].push(sv);
}

if (sv.site2HugoSymbol) {
if (sv.site2EntrezGeneId) {
if (
!sv.site1HugoSymbol ||
sv.site2HugoSymbol !== sv.site1HugoSymbol
!sv.site1EntrezGeneId ||
sv.site2EntrezGeneId !== sv.site1EntrezGeneId
) {
svByGene[sv.site2HugoSymbol] =
svByGene[sv.site2HugoSymbol] || [];
svByGene[sv.site2HugoSymbol].push(sv);
svByGene[sv.site2EntrezGeneId] =
svByGene[sv.site2EntrezGeneId] || [];
svByGene[sv.site2EntrezGeneId].push(sv);
}
}
});
Expand Down Expand Up @@ -5021,13 +5021,17 @@ export class ResultsViewPageStore extends AnalysisStore
{
await: () => [
this.genes,
this.structuralVariantsByGene,
this.structuralVariantsByEntrezGeneId,
this.studyIdToStudy,
this.molecularProfileIdToMolecularProfile,
this.samples,
this.uniqueSampleKeyToTumorType,
],
invoke: () => {
if (this.genes.result && this.structuralVariantsByGene.result) {
if (
this.genes.result &&
this.structuralVariantsByEntrezGeneId.result
) {
return Promise.resolve(
this.genes.result.reduce(
(
Expand All @@ -5042,9 +5046,8 @@ export class ResultsViewPageStore extends AnalysisStore
gene,
this.studyIdToStudy,
this.molecularProfileIdToMolecularProfile,
this.structuralVariantsByGene.result![
gene.hugoGeneSymbol
] || [],
this.structuralVariantsByEntrezGeneId
.result![gene.entrezGeneId] || [],
this.uniqueSampleKeyToTumorType.result!,
this.structuralVariantOncoKbData,
this.oncoKbCancerGenes,
Expand Down Expand Up @@ -5840,10 +5843,25 @@ export class ResultsViewPageStore extends AnalysisStore
default: [],
});

readonly oncoKbAnnotatedGenesForStructuralVariants = remoteData<{
[entrezGeneId: number]: boolean;
}>({
await: () => [
this.oncoKbAnnotatedGenes,
this.structuralVariantsByEntrezGeneId,
],
invoke: async () => {
const entrezGeneIds = Object.keys(
this.structuralVariantsByEntrezGeneId.result!
).map(Number);
return _.pick(this.oncoKbAnnotatedGenes.result, entrezGeneIds);
},
});

readonly structuralVariantOncoKbData = remoteData<IOncoKbData>(
{
await: () => [
this.oncoKbAnnotatedGenes,
this.oncoKbAnnotatedGenesForStructuralVariants,
this.structuralVariantData,
this.clinicalDataForSamples,
this.studies,
Expand All @@ -5853,7 +5871,8 @@ export class ResultsViewPageStore extends AnalysisStore
if (getServerConfig().show_oncokb) {
return fetchStructuralVariantOncoKbData(
this.uniqueSampleKeyToTumorType.result!,
this.oncoKbAnnotatedGenes.result || {},
this.oncoKbAnnotatedGenesForStructuralVariants.result ||
{},
this.structuralVariantData
);
} else {
Expand Down
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