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TASK-7205 - Variant Browser infinite loop when using Cellbase v4 #1005

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merged 2 commits into from
Dec 17, 2024
Merged

TASK-7205 - Variant Browser infinite loop when using Cellbase v4 #1005

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e435d27
wc: Remove workaround for compatibility with old cellbase versions #T…
jmjuanes Dec 4, 2024
bc09bb7
Merge branch 'release-2.12.x' into TASK-7205
jmjuanes Dec 17, 2024
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56 changes: 1 addition & 55 deletions src/webcomponents/variant/variant-browser-grid.js
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Original file line number Diff line number Diff line change
Expand Up @@ -238,61 +238,7 @@ export default class VariantBrowserGrid extends LitElement {

this.opencgaSession.opencgaClient.variants()
.query(this.filters)
.then(res => {
// FIXME A quick temporary fix -> TASK-947
if (this.opencgaSession?.project?.cellbase?.version === "v4" || this.opencgaSession?.project?.internal?.cellbase?.version === "v4") {
let found = false;
const variants = res.responses[0].results;
for (const variant of variants) {
for (const ct of variant.annotation.consequenceTypes) {
if (ct.transcriptFlags || ct.transcriptAnnotationFlags) {
found = true;
break;
}
}
}

if (!found) {
this.cellbaseClient = new CellBaseClient({
host: this.opencgaSession?.project?.cellbase?.url || this.opencgaSession?.project?.internal?.cellbase?.url,
// host: "https://ws.opencb.org/cellbase-4.8.2",
version: "v4",
species: "hsapiens",
});
const variantIds = variants.map(v => v.id);
this.cellbaseClient.get("genomic", "variant", variantIds.join(","), "annotation", {
assembly: this.opencgaSession.project.organism.assembly,
exclude: "populationFrequencies,conservation,expression,geneDisease,drugInteraction"
}).then(response => {
const annotatedVariants = response.responses;
for (let i = 0; i < variants.length; i++) {
// Store annotatedVariant in a Map, so we can search later and we do not need them to have the same order
const annotatedVariantsMap = new Map();
for (const av of annotatedVariants[i].results[0].consequenceTypes) {
// We can ignore the CTs without ensemblTranscriptId since they do not have flags.
if (av.ensemblTranscriptId) {
annotatedVariantsMap.set(av.ensemblTranscriptId, av);
}
}

for (let j = 0; j < variants[i].annotation.consequenceTypes.length; j++) {
if (variants[i].annotation.consequenceTypes[j].ensemblTranscriptId) {
// We can ignore the CTs without ensemblTranscriptId since they do not have flags.
const annotatedVariant = annotatedVariantsMap.get(variants[i].annotation.consequenceTypes[j].ensemblTranscriptId).transcriptAnnotationFlags;
if (annotatedVariant) {
variants[i].annotation.consequenceTypes[j].transcriptFlags = annotatedVariant;
variants[i].annotation.consequenceTypes[j].transcriptAnnotationFlags = annotatedVariant;
}
}
}
}
}).catch(error => {
console.log(error);
});
}
}
params.success(res);
})
.then(response => params.success(response))
.catch(error => {
console.error(error);
params.error(error);
Expand Down