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Hot Fix: Guard clinical & genomic search against nodes missing discovery counts #273

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Hot Fix: Guard clinical & genomic search against nodes missing discovery counts #273

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28 changes: 22 additions & 6 deletions src/views/clinicalGenomic/widgets/dataVisualization.jsx
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Original file line number Diff line number Diff line change
Expand Up @@ -93,22 +93,38 @@ function DataVisualization() {

// Check the clinical results to see if we can fill in any censored data with real ones
Object.entries(clinical).forEach(([siteName, site]) => {
Object.keys(site.summary?.[dataKey]).forEach((key) => {
// A clinical node can return results without a summary for this category;
// Object.keys(undefined) would throw, so skip such nodes.
const clinicalSummary = site.summary?.[dataKey];
if (!clinicalSummary) {
return;
}
Object.keys(clinicalSummary).forEach((key) => {
if (isObject) {
Object.keys(site.summary[dataKey]).forEach((innerKey) => {
if (isCensored(dataObj[transformer(siteName, key)][innerKey])) {
const siteValue = site.summary[dataKey][innerKey];
// Discovery may not have returned counts for this node (offline, timed
// out, a 403 from federation, or a name mismatch between the discovery
// and clinical responses). Without a matching per-site bucket there is
// nothing to fill in, and indexing it by program id would throw
// "Cannot read properties of undefined (reading '<program>')".
const discoveryBucket = dataObj[transformer(siteName, key)];
const targetBucket = newDataObj[transformer(siteName, key)];
if (!discoveryBucket || !targetBucket) {
return;
}
Object.keys(clinicalSummary).forEach((innerKey) => {
if (isCensored(discoveryBucket[innerKey])) {
const siteValue = clinicalSummary[innerKey];
// Same guard as the numeric path below: only substitute a real
// numeric per-site count. A censored per-site value (e.g. "<5")
// assigned here would put a string into the stacked-chart series
// and trigger Highcharts #14 (string sent to numeric series).
if (typeof siteValue === 'number') {
newDataObj[transformer(siteName, key)][innerKey] = siteValue;
targetBucket[innerKey] = siteValue;
}
}
});
} else if (isCensored(dataObj[transformer(siteName, key)])) {
const siteValue = site.summary[dataKey][key];
const siteValue = clinicalSummary[key];
// Only fold in real numeric per-site counts. If the per-site value is
// itself censored (e.g. "<5"), we can't recover the real number, so skip
// it — otherwise `0 + "<5"` would produce the string "0<5" and Highcharts
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