@sjcrh/proteinpaint-server 2.126.0 → 2.126.2

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.126.0",
+  "version": "2.126.2",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -62,10 +62,10 @@
   "dependencies": {
     "@sjcrh/augen": "2.121.0",
     "@sjcrh/proteinpaint-python": "2.118.0",
-    "@sjcrh/proteinpaint-r": "2.126.0",
-    "@sjcrh/proteinpaint-rust": "2.126.0",
+    "@sjcrh/proteinpaint-r": "2.126.2",
+    "@sjcrh/proteinpaint-rust": "2.126.2",
     "@sjcrh/proteinpaint-shared": "2.126.0",
-    "@sjcrh/proteinpaint-types": "2.126.0",
+    "@sjcrh/proteinpaint-types": "2.126.1",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^9.4.1",

package/routes/genesetEnrichment.js

@@ -3,7 +3,6 @@ import fs from "fs";
 import path from "path";
 import serverconfig from "#src/serverconfig.js";
 import { run_python } from "@sjcrh/proteinpaint-python";
-import { run_rust } from "@sjcrh/proteinpaint-rust";
 import { mayLog } from "#src/helpers.ts";
 const api = {
   endpoint: "genesetEnrichment",
@@ -55,21 +54,14 @@ async function run_genesetEnrichment_analysis(q, genomes) {
     db: genomes[q.genome].termdbs.msigdb.cohort.db.connection.name,
     // For now msigdb has been added, but later databases other than msigdb may be used
     geneset_group: q.geneSetGroup,
+    cachedir: cachedir_gsea,
+    geneset_name: q.geneset_name,
+    pickle_file: q.pickle_file,
+    num_permutations: q.num_permutations,
     genedb: path.join(serverconfig.tpmasterdir, genomes[q.genome].genedb.dbfile),
     filter_non_coding_genes: q.filter_non_coding_genes
   };
-  let gsea_output;
-  if (q.method == "blitzgsea") {
-    genesetenrichment_input.cachedir = cachedir_gsea;
-    genesetenrichment_input.pickle_file = q.pickle_file;
-    genesetenrichment_input.geneset_name = q.geneset_name;
-    genesetenrichment_input.num_permutations = q.num_permutations;
-    gsea_output = await run_python("gsea.py", "/" + JSON.stringify(genesetenrichment_input));
-  } else if (q.method == "cerno") {
-    gsea_output = await run_rust("cerno", JSON.stringify(genesetenrichment_input));
-  } else {
-    throw "Unknown method:" + q.method;
-  }
+  const gsea_output = await run_python("gsea.py", "/" + JSON.stringify(genesetenrichment_input));
   let result;
   let data_found = false;
   let image_found = false;

package/routes/termdb.cluster.js

@@ -36,7 +36,7 @@ function init({ genomes }) {
       const ds = g.datasets[q.dslabel];
       if (!ds)
         throw "invalid dataset name";
-      if (!ds.__gdc?.doneCaching)
+      if (ds.label === "GDC" && !ds.__gdc?.doneCaching)
         throw "The server has not finished caching the case IDs: try again in about 2 minutes.";
       if ([TermTypes.GENE_EXPRESSION, TermTypes.METABOLITE_INTENSITY, NUMERIC_DICTIONARY_TERM].includes(q.dataType)) {
         if (!ds.queries?.[q.dataType] && q.dataType !== NUMERIC_DICTIONARY_TERM)

package/routes/termdb.topVariablyExpressedGenes.js

@@ -179,7 +179,7 @@ function gdcValidateQuery(ds, genome) {
       );
       return serverconfig.features.gdcGenes;
     }
-    if (!ds.__gdc?.doneCaching) {
+    if (ds.label === "GDC" && !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);