@sjcrh/proteinpaint-server 2.81.3 → 2.81.5-0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.81.3",
+  "version": "2.81.5-0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",

package/routes/termdb.cluster.js

@@ -37,6 +37,12 @@ function init({ genomes }) {
       if (q.dataType == TermTypes.GENE_EXPRESSION || q.dataType == TermTypes.METABOLITE_INTENSITY) {
         if (!ds.queries?.[q.dataType])
           throw `no ${q.dataType} data on this dataset`;
+        if (!q.terms)
+          throw `missing gene list`;
+        if (!Array.isArray(q.terms))
+          throw `gene list is not an array`;
+        if (q.terms.length < 3)
+          throw `A minimum of three genes is required for clustering. Please refresh this page to clear this error.`;
         result = await getResult(q, ds);
       } else {
         throw "unknown q.dataType " + q.dataType;
@@ -66,18 +72,21 @@ async function getResult(q, ds) {
     return { term: { gene: g, type: TermTypes.GENE_EXPRESSION }, data: term2sample2value.get(g) };
   }
   const t = Date.now();
-  const clustering = await doClustering(term2sample2value, q);
+  const clustering = await doClustering(term2sample2value, q, Object.keys(bySampleId).length);
   if (serverconfig.debugmode)
     console.log("clustering done:", Date.now() - t, "ms");
   return { clustering, byTermId, bySampleId };
 }
-async function doClustering(data, q) {
+async function doClustering(data, q, numCases = 1e3) {
   const sampleSet = /* @__PURE__ */ new Set();
   for (const o of data.values()) {
     for (const s in o)
       sampleSet.add(s);
-    break;
+    if (sampleSet.size >= numCases)
+      break;
   }
+  if (sampleSet.size == 0)
+    throw "termdb.cluster: no samples";
   if (!clusterMethodLst.find((i) => i.value == q.clusterMethod))
     throw "Invalid cluster method";
   if (!distanceMethodLst.find((i) => i.value == q.distanceMethod))
@@ -101,6 +110,8 @@ async function doClustering(data, q) {
     }
     inputData.matrix.push(getZscore(row));
   }
+  if (inputData.matrix.length == 0)
+    throw "Clustering matrix is empty";
   const Routput = JSON.parse(
     await run_R(path.join(serverconfig.binpath, "utils", "hclust.R"), JSON.stringify(inputData))
   );