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fix: stores/sevarInfo can limit csq to HGNC ID #154

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merged 1 commit into from
Mar 1, 2024
Merged

fix: stores/sevarInfo can limit csq to HGNC ID #154

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28 changes: 19 additions & 9 deletions src/stores/seqvarInfo/store.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,9 @@ export const useSeqvarInfoStore = defineStore('seqvarInfo', () => {
/** The Seqvar that the previous record has been retrieved for. */
const seqvar = ref<Seqvar | undefined>(undefined)

/** The optional HGNC ID to limit the query to. */
const hgncId = ref<string | undefined>(undefined)

/** Variant-related information from annonars. */
const varAnnos = ref<SeqvarInfoResult | undefined>(undefined)

Expand All @@ -44,6 +47,7 @@ export const useSeqvarInfoStore = defineStore('seqvarInfo', () => {
const clearData = () => {
storeState.value = StoreState.Initial
seqvar.value = undefined
hgncId.value = undefined
varAnnos.value = undefined
txCsq.value = undefined
geneInfo.value = undefined
Expand All @@ -54,12 +58,18 @@ export const useSeqvarInfoStore = defineStore('seqvarInfo', () => {
* Initialize and oad data from the server.
*
* @param seqvar$ The sequence variant to use for the query.
* @param hgncId$ Optional HGNC ID to limit the query to.
* @param forceReload Whether to force-reload in case the variant is the same.
* @returns
*/
const initialize = async (seqvar$: Seqvar, forceReload: boolean = false) => {
const initialize = async (seqvar$: Seqvar, hgncId$?: string, forceReload: boolean = false) => {
// Protect against loading multiple times.
if (!forceReload && storeState.value !== StoreState.Initial && equal(seqvar$, seqvar.value)) {
if (
!forceReload &&
storeState.value !== StoreState.Initial &&
equal(seqvar$, seqvar.value) &&
hgncId$ === hgncId.value
) {
return initializeRes.value
}

Expand All @@ -71,32 +81,31 @@ export const useSeqvarInfoStore = defineStore('seqvarInfo', () => {
const annonarsClient = new AnnonarsClient()
const mehariClient = new MehariClient()
const vigunoClient = new VigunoClient()
let hgncId = ''

// Retrieve variant information from annonars and mehari.
initializeRes.value = Promise.all([
annonarsClient.fetchVariantInfo(seqvar$).then((data) => {
varAnnos.value = data.result
}),
mehariClient.retrieveSeqvarsCsq(seqvar$).then((data) => {
mehariClient.retrieveSeqvarsCsq(seqvar$, hgncId$).then((data) => {
txCsq.value = data.result ?? []
})
])
.then((): Promise<any> => {
if (txCsq.value !== undefined && txCsq.value.length !== 0) {
hgncId = txCsq.value[0].geneId
const localHgncId = txCsq.value[0].geneId
return Promise.all([
annonarsClient.fetchGeneInfo(hgncId).then((data) => {
annonarsClient.fetchGeneInfo(localHgncId).then((data) => {
for (const gene of data.genes) {
if (gene.hgnc!.hgncId === hgncId) {
if (gene.hgnc!.hgncId === localHgncId) {
geneInfo.value = gene
}
}
}),
annonarsClient.fetchGeneClinvarInfo(hgncId).then((data) => {
annonarsClient.fetchGeneClinvarInfo(localHgncId).then((data) => {
geneClinvar.value = data
}),
vigunoClient.fetchHpoTermsForHgncId(hgncId).then((data) => {
vigunoClient.fetchHpoTermsForHgncId(localHgncId).then((data) => {
hpoTerms.value = data.result
})
])
Expand All @@ -105,6 +114,7 @@ export const useSeqvarInfoStore = defineStore('seqvarInfo', () => {
}
})
.then(() => {
hgncId.value = hgncId$
seqvar.value = seqvar$
storeState.value = StoreState.Active
})
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