@sjcrh/proteinpaint-server 2.81.2-2 → 2.81.2

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.81.2-2",
+  "version": "2.81.2",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",

package/routes/termdb.topVariablyExpressedGenes.js

@@ -1,9 +1,9 @@
-import path from "path";
 import { run_rust } from "@sjcrh/proteinpaint-rust";
 import serverconfig from "#src/serverconfig.js";
 import { get_samples } from "#src/termdb.sql.js";
 import { makeFilter } from "#src/mds3.gdc.js";
 import { cachedFetch } from "#src/utils.js";
+import { resolve } from "url";
 const api = {
   endpoint: "termdb/topVariablyExpressedGenes",
   methods: {
@@ -178,21 +178,32 @@ function gdcValidateQuery(ds, genome) {
       );
       return serverconfig.features.gdcGenes;
     }
-    if (!ds.__gdc.doneCaching) {
+    if (!ds.__gdc?.doneCaching) {
       throw "The server has not finished caching the case IDs: try again in about 2 minutes.";
     }
     const { host, headers } = ds.getHostHeaders(q);
-    const url = path.join(host.geneExp, "/gene_expression/gene_selection");
+    const url = resolve(host.geneExp, "/gene_expression/gene_selection");
     try {
-      const response = await cachedFetch(url, {
-        method: "POST",
-        headers,
-        body: getGeneSelectionArg(q)
-      });
+      const response = await cachedFetch(
+        url,
+        {
+          method: "POST",
+          headers,
+          body: getGeneSelectionArg(q)
+        },
+        {
+          // noCache: true, // !!! for testing only !!!
+          getErrMessage: (response2) => {
+            const body = response2?.body || response2;
+            return Array.isArray(body?.gene_selection) ? "" : body?.message || body?.error || JSON.stringify(body);
+          }
+        }
+      );
       const re = response.body;
       const genes = [];
-      if (!Array.isArray(re.gene_selection))
-        throw "re.gene_selection[] is not array";
+      if (!Array.isArray(re.gene_selection)) {
+        throw "re.gene_selection[] is not array: " + JSON.stringify(re);
+      }
       for (const i of re.gene_selection) {
         if (i.gene_id && typeof i.gene_id == "string") {
           const t = genome.genedb.getNameByAlias.get(i.gene_id);