@sjcrh/proteinpaint-server 2.63.3-3 → 2.63.5

package/utils/burden.R

@@ -40,7 +40,7 @@ load(survData)
 ############################ These are the input values in APP that users can change. Edgar, these should be the same as the APP before, variable names and units. #############
 ### Input the primary DX. 
 # pr=5
-agecut=40   ##### Edgar, This is not an user input paramter, but we input this. This depends on the DX. For example, here for CNS we use 40. For HL DX, it is 55. I will give this value for each DX.
+# agecut=40   ##### Edgar, This is not an user input paramter, but we input this. This depends on the DX. For example, here for CNS we use 40. For HL DX, it is 55. I will give this value for each DX.
 
 # # # Input person's values, 18 input X's , plus the input primary DX
 # 	sexval=1  #sex, take value 1 for male and 0 for female
@@ -88,6 +88,8 @@ newdata_chc_sampled=newdata_chc_sampled[newdata_chc_sampled$t.endage<=60,]
 
 # paste(names(input), input, sep = ":", collapse = ",")
 pr=input$diaggrp
+# agecut was previously hardcoded to 40 above
+agecut=c('1'=50, '2'=45, '3'=55, '4'=50, '5'=40, '6'=60, '7'=50, '8'=45, '9'=45, '10'=45, '11'=50 )[pr]
 sexval=input$sex
 newdata_chc_sampled$sex=input$sex # sexval
 newdata_chc_sampled$white=input$white # whiteval

package/routes/genesetEnrichment.js

@@ -1,110 +0,0 @@
-import fs from "fs";
-import { spawn } from "child_process";
-import { Readable } from "stream";
-import path from "path";
-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,
-    gene_set_group: q.geneSetGroup
-  };
-  const gsea_output = await run_gsea(
-    path.join(serverconfig.binpath, "../python/src", "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 = [];
-    let python_path = "python3";
-    if (serverconfig.py_path)
-      python_path = serverconfig.py_path;
-    const sp = spawn(python_path, [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
-};