@sjcrh/proteinpaint-server 2.63.5 → 2.64.0

package/genome/hg38.test.js

@@ -4,6 +4,18 @@ const genome = {
   genedb: {
     dbfile: "anno/genes.hg38.test.db"
   },
+  termdbs: {
+    msigdb: {
+      label: "MSigDB",
+      cohort: {
+        db: { file: "files/hg38/TermdbTest/msigdb/db" },
+        // nest file under TermdbTest since the folder is auto symlinked
+        termdb: {
+          isGeneSetTermdb: true
+        }
+      }
+    }
+  },
   tracks: [
     {
       __isgene: true,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.63.5",
+  "version": "2.64.0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",

package/routes/genesetEnrichment.js

@@ -0,0 +1,107 @@
+import fs from "fs";
+import { spawn } from "child_process";
+import { Readable } from "stream";
+import serverconfig from "../src/serverconfig.js";
+const api = {
+  endpoint: "genesetEnrichment",
+  methods: {
+    all: {
+      init,
+      request: {
+        typeId: "genesetEnrichmentRequest"
+      },
+      response: {
+        typeId: "genesetEnrichmentResponse"
+        // will combine this with type checker
+        //valid: (t) => {}
+      }
+    }
+  }
+};
+function init({ genomes }) {
+  return async (req, res) => {
+    try {
+      const results = await run_genesetEnrichment_analysis(req.query, genomes);
+      res.send(results);
+    } catch (e) {
+      res.send({ status: "error", error: e.message || e });
+    }
+  };
+}
+async function run_genesetEnrichment_analysis(q, genomes) {
+  if (!genomes[q.genome].termdbs)
+    throw "termdb database is not available for " + q.genome;
+  const genesetenrichment_input = {
+    genes: q.genes,
+    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
+  };
+  const gsea_output = await run_gsea(
+    `${serverconfig.binpath}/utils/gsea.py`,
+    "/" + JSON.stringify(genesetenrichment_input)
+    // "/" is needed for python to accept the bracket "{" as a bracket
+  );
+  let result;
+  for (const line of gsea_output.split("\n")) {
+    if (line.startsWith("result: ")) {
+      result = JSON.parse(line.replace("result: ", ""));
+    } else {
+      console.log(line);
+    }
+  }
+  return result;
+}
+async function run_gsea(path2, data) {
+  try {
+    await fs.promises.stat(path2);
+  } catch (e) {
+    throw `${path2} does not exist`;
+  }
+  return new Promise((resolve, reject) => {
+    const _stdout = [];
+    const _stderr = [];
+    const sp = spawn(serverconfig.python, [path2]);
+    if (data) {
+      try {
+        const input = data.endsWith("\n") ? data : data + "\n";
+        Readable.from(input).pipe(sp.stdin);
+      } catch (e) {
+        sp.kill();
+        let errmsg = e;
+        const stderr = _stderr.join("").trim();
+        if (stderr)
+          errmsg += `
+python stderr: ${stderr}`;
+        reject(errmsg);
+      }
+    }
+    sp.stdout.on("data", (data2) => _stdout.push(data2));
+    sp.stderr.on("data", (data2) => _stderr.push(data2));
+    sp.on("error", (err) => reject(err));
+    sp.on("close", (code) => {
+      const stdout = _stdout.join("").trim();
+      const stderr = _stderr.join("").trim();
+      if (code !== 0) {
+        let errmsg = `python process exited with non-zero status code=${code}`;
+        if (stdout)
+          errmsg += `
+python stdout: ${stdout}`;
+        if (stderr)
+          errmsg += `
+python stderr: ${stderr}`;
+        reject(errmsg);
+      }
+      if (stderr) {
+        const errmsg = `python process emitted standard error
+python stderr: ${stderr}`;
+        reject(errmsg);
+      }
+      resolve(stdout);
+    });
+  });
+}
+export {
+  api
+};

package/routes/termdb.config.js

@@ -42,7 +42,7 @@ function make(q, res, ds, genome) {
   const c = {
     selectCohort: tdb.selectCohort,
     // optional
-    supportedChartTypes: tdb.q.getSupportedChartTypes(q.embedder),
+    supportedChartTypes: tdb.q?.getSupportedChartTypes(q.embedder),
     hiddenChartTypes: ds.cohort.hiddenChartTypes,
     renamedChartTypes: ds.cohort.renamedChartTypes,
     allowedTermTypes: getAllowedTermTypes(ds),