@sjcrh/proteinpaint-server 2.63.6 → 2.65.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.63.6",
+  "version": "2.65.0",
   "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/hicdata.js

@@ -12,24 +12,25 @@ const api = {
       },
       response: {
         typeId: "HicdataResponse"
-      }
-      /*
+      },
       examples: [
-      	{
-      		request: {
-      			body: {
-      				genome: 'hg38-test',
-      				dslabel: 'TermdbTest',
-      				embedder: 'localhost',
-      				gettermbyid: 'subcohort'
-      			}
-      		},
-      		response: {
-      			header: { status: 200 }
-      		}
-      	}
+        {
+          request: {
+            body: {
+              embedder: "localhost",
+              url: "https://proteinpaint.stjude.org/ppdemo/hg19/hic/hic_demo.hic",
+              matrixType: "observed",
+              nmeth: "NONE",
+              pos1: "3",
+              pos2: "2",
+              resolution: 1e6
+            }
+          },
+          response: {
+            header: { status: 200 }
+          }
+        }
       ]
-      */
     },
     post: {
       alternativeFor: "get",

package/routes/{hicdata.genome.js → hicgenome.js}

@@ -8,11 +8,29 @@ const api = {
     get: {
       init,
       request: {
-        typeId: "HicdataRequest"
+        typeId: "HicGenomeRequest"
       },
       response: {
-        typeId: "HicdataResponse"
-      }
+        typeId: "HicGenomeResponse"
+      },
+      examples: [
+        {
+          request: {
+            body: {
+              chrlst: ["chr1", "chr2"],
+              embedder: "localhost",
+              url: "https://proteinpaint.stjude.org/ppdemo/hg19/hic/hic_demo.hic",
+              matrixType: "observed",
+              nmeth: "NONE",
+              nochr: true,
+              resolution: 25e5
+            }
+          },
+          response: {
+            header: { status: 200 }
+          }
+        }
+      ]
     },
     post: {
       alternativeFor: "get",
@@ -34,15 +52,7 @@ function init() {
           return new Promise((resolve, reject) => {
             const pos1 = req.query.nochr ? lead.replace("chr", "") : lead;
             const pos2 = req.query.nochr ? follow.replace("chr", "") : follow;
-            const par = [
-              matrixType,
-              req.query.nmeth || "NONE",
-              file,
-              pos1,
-              pos2,
-              req.query.isfrag ? "FRAG" : "BP",
-              req.query.resolution
-            ];
+            const par = [matrixType, req.query.nmeth || "NONE", file, pos1, pos2, "BP", req.query.resolution];
             const ps = spawn(serverconfig.hicstraw, par);
             const rl = readline.createInterface({ input: ps.stdout });
             const items = [];
@@ -61,9 +71,6 @@ function init() {
                 fieldnotnumerical++;
                 return;
               }
-              if (req.query.mincutoff != void 0 && v <= req.query.mincutoff) {
-                return;
-              }
               items.push([n1, n2, v]);
             });
             data.push({ items, lead, follow });

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),

package/routes/termdb.singlecellSamples.js

@@ -61,7 +61,7 @@ async function validate_query_singleCell(ds, genome) {
   if (q.data.src == "gdcapi") {
     gdc_validate_query_singleCell_data(ds, genome);
   } else if (q.data.src == "native") {
-    validateDataNative(q.data);
+    validateDataNative(q.data, ds);
   } else {
     throw "unknown singleCell.data.src";
   }
@@ -90,7 +90,7 @@ async function validateSamplesNative(S, ds) {
     return { samples: Object.values(samples) };
   };
 }
-function validateDataNative(D) {
+function validateDataNative(D, ds) {
   const nameSet = /* @__PURE__ */ new Set();
   for (const plot of D.plots) {
     if (nameSet.has(plot.name))
@@ -100,6 +100,10 @@ function validateDataNative(D) {
   D.get = async (q) => {
     try {
       const plots = [];
+      let geneExpMap;
+      if (ds.queries.singleCell.geneExpression && q.gene) {
+        geneExpMap = await ds.queries.singleCell.geneExpression.get({ sample: q.sample, gene: q.gene });
+      }
       for (const plot of D.plots) {
         const tsvfile = path.join(serverconfig.tpmasterdir, plot.folder, q.sample + plot.fileSuffix);
         try {
@@ -116,13 +120,19 @@ function validateDataNative(D) {
         const cells = [];
         for (let i = 1; i < lines.length; i++) {
           const l = lines[i].split("	");
-          const cellId = l[0], x = Number(l[plot.coordsColumns.x]), y = Number(l[plot.coordsColumns.y]);
+          const cellId = lines.length > 3 ? l[0] : void 0, x = Number(l[plot.coordsColumns.x]), y = Number(l[plot.coordsColumns.y]);
           const category = l[plot.colorColumn?.index] || "";
           if (!cellId)
             throw "cell id missing";
           if (!Number.isFinite(x) || !Number.isFinite(y))
             throw "x/y not number";
-          cells.push({ cellId, x, y, category });
+          const cell = { cellId, x, y, category };
+          if (geneExpMap) {
+            if (geneExpMap[cellId] !== void 0) {
+              cell.geneExp = geneExpMap[cellId];
+            }
+          }
+          cells.push(cell);
         }
         plots.push({ name: plot.name, cells, colorBy: plot.colorColumn?.name, colorMap: plot.colorColumn?.colorMap });
       }
@@ -145,7 +155,9 @@ function validateGeneExpressionNative(G) {
     } catch (e) {
       throw "geneExp matrix file not found or readable for this sample";
     }
-    const header = await get_header_txt(tsvfile);
+    const header = (await get_header_txt(tsvfile)).split("	");
+    if (header.length == 0)
+      throw "blank header line";
     return await grepMatrix4geneExpression(tsvfile, q.gene, header);
   };
 }
@@ -159,10 +171,14 @@ function grepMatrix4geneExpression(tsvfile, gene, header) {
       const e = err.join("");
       if (e)
         reject(e);
-      const l = out.join("").split("	");
+      const cell2value = {};
+      const line = out.join("").trim();
+      if (!line) {
+        resolve(cell2value);
+      }
+      const l = line.split("	");
       if (l.length != header.length)
         reject(`number of fields differ between data line and header: ${l.length} ${header.length}`);
-      const cell2value = {};
       for (let i = 1; i < l.length; i++) {
         const v = Number(l[i]);
         if (Number.isNaN(v))