@sjcrh/proteinpaint-server 2.87.1 → 2.88.1

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.87.1",
+  "version": "2.88.1",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -61,7 +61,7 @@
     "@sjcrh/augen": "2.87.0",
     "@sjcrh/proteinpaint-rust": "2.84.0",
     "@sjcrh/proteinpaint-shared": "2.87.1",
-    "@sjcrh/proteinpaint-types": "2.87.1",
+    "@sjcrh/proteinpaint-types": "2.88.0",
     "better-sqlite3": "^9.4.1",
     "body-parser": "^1.15.2",
     "canvas": "~2.11.2",

package/routes/termdb.config.js

@@ -44,7 +44,6 @@ function make(q, res, ds, genome) {
     selectCohort: tdb.selectCohort,
     // optional
     supportedChartTypes: tdb.q?.getSupportedChartTypes(auth),
-    hiddenChartTypes: ds.cohort.hiddenChartTypes,
     renamedChartTypes: ds.cohort.renamedChartTypes,
     allowedTermTypes: getAllowedTermTypes(ds),
     termMatch2geneSet: tdb.termMatch2geneSet,

package/routes/termdb.singlecellSamples.js

@@ -2,6 +2,7 @@ import fs from "fs";
 import path from "path";
 import { read_file } from "#src/utils.js";
 import run_R from "#src/run_R.js";
+import { joinUrl, mayLog } from "#src/helpers.ts";
 import { run_rust } from "@sjcrh/proteinpaint-rust";
 import serverconfig from "#src/serverconfig.js";
 import { termdbSingleCellSamplesPayload } from "#types/checkers";
@@ -226,17 +227,25 @@ function gdc_validateGeneExpression(G, ds, genome) {
   G.sample2gene2expressionBins = {};
   G.get = async (q) => {
     try {
-      const uuid = ds.__gdc.map2caseid.get(q.sample.sID);
       const fileid = q.sample.eID;
+      const hdf5id = ds.__gdc.scrnaAnalysis2hdf5.get(fileid);
+      if (!hdf5id)
+        throw "cannot map eID to hdf5 id";
       const aliasLst = genome.genedb.getAliasByName.all(q.gene);
       const gencodeId = aliasLst.find((a) => a?.alias.toUpperCase().startsWith("ENSG"))?.alias;
+      if (!gencodeId)
+        throw "cannot map gene symbol to GENCODE";
       const body = {
-        case_id: uuid,
         gene_ids: [gencodeId],
-        file_id: fileid
+        file_id: hdf5id
       };
       const { host } = ds.getHostHeaders(q);
-      const out = await ky.post(path.join(host.rest, "scrna_seq/gene_expression"), { timeout: false, json: body }).json();
+      const t = Date.now();
+      const response = await ky.post(joinUrl(host.rest, "scrna_seq/gene_expression"), { timeout: false, json: body });
+      if (!response.ok)
+        throw `HTTP Error: ${response.status} ${response.statusText}`;
+      const out = await response.json();
+      mayLog("gdc scrna gene exp", q.gene, Date.now() - t);
       const result = out.data[0].cells;
       const data = {};
       for (const r of result) {