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Update DatasetResultBox.js
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fixing counts and exception for no variant search
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@mbaudis
mbaudis committed Jun 7, 2024
1 parent 13f9daf commit bcccc8d
Showing 1 changed file with 33 additions and 46 deletions.
79 changes: 33 additions & 46 deletions src/components/searchResults/DatasetResultBox.js
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Original file line number Diff line number Diff line change
Expand Up @@ -55,13 +55,9 @@ export function DatasetResultBox({ data: responseSet, responseMeta, query }) {
resultsHandovers.find(({ info: { contentId } }) => contentId === givenId)

// obviously should be looped somehow...

const biosamplesHandover = handoverById(HANDOVER_IDS.biosamples)
const biocount = biosamplesHandover.info.count
const biosamplesReply = useProgenetixApi(
biosamplesHandover && replaceWithProxy(biosamplesHandover.url)
)
const biosamplesTableHandover = handoverById(HANDOVER_IDS.biosamplestable)
const biocount = biosamplesHandover.info.count
biosamplesHandover.pages = []
biosamplesTableHandover.pages = []
var cntr = 0
Expand All @@ -70,61 +66,49 @@ export function DatasetResultBox({ data: responseSet, responseMeta, query }) {
const pagu = "&skip=" + skpr + "&limit=" + limit
cntr += limit
skpr += 1
biosamplesTableHandover.pages.push({"url": biosamplesTableHandover.url + pagu, "label": "Part" + skpr})
biosamplesHandover.pages.push({"url": biosamplesHandover.url + pagu, "label": "Part" + skpr})
biosamplesHandover.pages.push({"url": replaceWithProxy(biosamplesHandover.url + pagu), "label": "Part" + skpr})
biosamplesTableHandover.pages.push({"url": replaceWithProxy(biosamplesTableHandover.url + pagu), "label": "Part" + skpr})
}

const variantsHandover = handoverById(HANDOVER_IDS.variants)
const varcount = variantsHandover.info.count
const variantsReply = useProgenetixApi(
variantsHandover && replaceWithProxy(variantsHandover.url)
)
const vcfHandover = handoverById(HANDOVER_IDS.vcf)
const pgxsegHandover = handoverById(HANDOVER_IDS.pgxseg)
variantsHandover.pages = []
vcfHandover.pages = []
pgxsegHandover.pages = []
cntr = 0
skpr = 0
while (cntr < varcount) {
const pagu = "&skip=" + skpr + "&limit=" + limit
cntr += limit
skpr += 1
variantsHandover.pages.push({"url": variantsHandover.url + pagu, "label": "Part" + skpr})
vcfHandover.pages.push({"url": vcfHandover.url + pagu, "label": "Part" + skpr})
pgxsegHandover.pages.push({"url": pgxsegHandover.url + pagu, "label": "Part" + skpr})
const varcount = variantsHandover?.info.count ? variantsHandover?.info.count : 0
// variants are optional and existence has to be checked at several places
if (varcount > 0) {
variantsHandover.pages = []
vcfHandover.pages = []
pgxsegHandover.pages = []
cntr = 0
skpr = 0
while (cntr < varcount) {
const pagu = "&skip=" + skpr + "&limit=" + limit
cntr += limit
skpr += 1
variantsHandover.pages.push({"url": replaceWithProxy(variantsHandover.url + pagu), "label": "Part" + skpr})
vcfHandover.pages.push({"url": replaceWithProxy(vcfHandover.url + pagu), "label": "Part" + skpr})
pgxsegHandover.pages.push({"url": replaceWithProxy(pgxsegHandover.url + pagu), "label": "Part" + skpr})
}
}


// const phenopacketsHandover = handoverById(HANDOVER_IDS.phenopackets)
const UCSCbedHandoverURL = handoverById(HANDOVER_IDS.UCSClink) === undefined ? false : handoverById(HANDOVER_IDS.UCSClink).url


const biosamplesmapURL = handoverById(HANDOVER_IDS.biosamplesmap) === undefined ? false : handoverById(HANDOVER_IDS.biosamplesmap).url

// Data retrieval; variants are optional and existence has to be checked at several places
const variantsReply = useProgenetixApi(varcount > 0 ? variantsHandover.pages[0].url : "")
const biosamplesReply = useProgenetixApi(biosamplesHandover.pages[0].url)
const retrievedSampleCount = biosamplesReply?.data?.response?.resultSets[0]?.results.length

// the histogram is only rendered but correct handover is needed, obviously
let histoplotUrl
let visualizationLink
if (handoverById(HANDOVER_IDS.histoplot)) {
histoplotUrl = handoverById(HANDOVER_IDS.histoplot).url
histoplotUrl = handoverById(HANDOVER_IDS.histoplot).url + "&limit=" + limit
let visualizationAccessId = new URLSearchParams(
new URL(histoplotUrl).search
).get("accessid")
// let visualizationFileId = new URLSearchParams(
// new URL(histoplotUrl).search
// ).get("fileId")
// let visualizationSkip = new URLSearchParams(
// new URL(histoplotUrl).search
// ).get("skip")
// let visualizationLimit = new URLSearchParams(
// new URL(histoplotUrl).search
// ).get("limit")
visualizationLink = getVisualizationLink(id, visualizationAccessId, "", 0, 0, paginatedResultsCount)
}

var retrievedCount = resultsCount
if (biosamplesReply?.data?.response?.resultSets[0].results) {
retrievedCount = biosamplesReply?.data?.response?.resultSets[0].results.length
visualizationLink = getVisualizationLink(id, visualizationAccessId, "", 0, limit, paginatedResultsCount)
}

// main / samples / variants
Expand All @@ -136,7 +120,7 @@ export function DatasetResultBox({ data: responseSet, responseMeta, query }) {
// (biosample) => !!biosample.provenance?.geoLocation
// ) && tabNames.push(TABS.samplesMap)

if (handoverById(HANDOVER_IDS.variants)) tabNames.push(TABS.variants)
if (varcount > 0) tabNames.push(TABS.variants)

const [selectedTab, setSelectedTab] = useState(tabNames[0])

Expand Down Expand Up @@ -191,7 +175,7 @@ export function DatasetResultBox({ data: responseSet, responseMeta, query }) {
</div>
<div>
<b>Retrieved Samples: </b>
{retrievedCount}
{retrievedSampleCount}
</div>
{info.counts.variants > 0 ? (
<div>
Expand Down Expand Up @@ -261,9 +245,12 @@ export function DatasetResultBox({ data: responseSet, responseMeta, query }) {
</div>
) : null}
{tabComponent ? <div>{tabComponent}</div> : null}
<hr/>

{biosamplesTableHandover?.pages && (
<br/>
<hr/>
<h2 className="subtitle has-text-dark">{id} Data Downloads</h2>

{biosamplesTableHandover?.pages && (
<div className="tabs">
<div>
<b>Download Sample Data (TSV)</b>
Expand Down

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