@sjcrh/proteinpaint-server 2.69.0 → 2.69.1-0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.69.0",
+  "version": "2.69.1-0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",

package/routes/genesetEnrichment.js

@@ -1,4 +1,5 @@
 import fs from "fs";
+import path from "path";
 import { spawn } from "child_process";
 import { Readable } from "stream";
 import serverconfig from "../src/serverconfig.js";
@@ -22,7 +23,20 @@ function init({ genomes }) {
   return async (req, res) => {
     try {
       const results = await run_genesetEnrichment_analysis(req.query, genomes);
-      res.send(results);
+      if (!req.query.geneset_name) {
+        res.send(results);
+      } else {
+        res.sendFile(results, (err) => {
+          fs.unlink(results, (del_err) => {
+            if (del_err) {
+              console.error("Error deleting file " + results + ":", del_err);
+            }
+          });
+          if (err) {
+            res.status(404).send("Image not found");
+          }
+        });
+      }
     } catch (e) {
       res.send({ status: "error", error: e.message || e });
     }
@@ -36,7 +50,10 @@ async function run_genesetEnrichment_analysis(q, genomes) {
     fold_change: q.fold_change,
     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
-    gene_set_group: q.geneSetGroup
+    geneset_group: q.geneSetGroup,
+    cachedir: serverconfig.cachedir,
+    geneset_name: q.geneset_name,
+    pickle_file: q.pickle_file
   };
   const gsea_output = await run_gsea(
     `${serverconfig.binpath}/utils/gsea.py`,
@@ -44,14 +61,25 @@ async function run_genesetEnrichment_analysis(q, genomes) {
     // "/" is needed for python to accept the bracket "{" as a bracket
   );
   let result;
+  let data_found = false;
+  let image_found = false;
   for (const line of gsea_output.split("\n")) {
     if (line.startsWith("result: ")) {
       result = JSON.parse(line.replace("result: ", ""));
+      data_found = true;
+    } else if (line.startsWith("image: ")) {
+      result = JSON.parse(line.replace("image: ", ""));
+      image_found = true;
     } else {
       console.log(line);
     }
   }
-  return result;
+  if (data_found) {
+    return result;
+  } else if (image_found) {
+    const imagePath = path.join(serverconfig.cachedir, result.image_file);
+    return imagePath;
+  }
 }
 async function run_gsea(path2, data) {
   try {