@sjcrh/proteinpaint-server 2.57.1-1 → 2.58.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.57.1-1",
+  "version": "2.58.0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -61,7 +61,7 @@
   },
   "dependencies": {
     "@sjcrh/augen": "2.46.0",
-    "@sjcrh/proteinpaint-rust": "2.57.1-1",
+    "@sjcrh/proteinpaint-rust": "2.58.0",
     "better-sqlite3": "^9.4.1",
     "body-parser": "^1.15.2",
     "canvas": "~2.11.2",

package/routes/genesetOverrepresentation.js

@@ -46,7 +46,6 @@ async function run_genesetOverrepresentation_analysis(q, genomes) {
     if (line.startsWith("pathway_p_values:")) {
       result = JSON.parse(line.replace("pathway_p_values:", ""));
     } else {
-      console.log(line);
     }
   }
   return result;

package/routes/healthcheck.js

@@ -7,6 +7,19 @@ const api = {
         return async (req, res) => {
           try {
             const health = await getStat(genomes);
+            const q = req.query;
+            if (q.dslabel) {
+              for (const gn in genomes) {
+                const ds = genomes[gn]?.datasets?.[q.dslabel];
+                if (!ds?.getHealth)
+                  continue;
+                if (!health.byDataset)
+                  health.byDataset = {};
+                if (!health.byDataset[q.dslabel])
+                  health.byDataset[q.dslabel] = {};
+                health.byDataset[q.dslabel][gn] = ds.getHealth(ds);
+              }
+            }
             res.send(health);
           } catch (e) {
             res.send({ status: "error", error: e.message || e });

package/routes/hicdata.genome.js

@@ -0,0 +1,93 @@
+import { fileurl } from "#src/utils.js";
+import { spawn } from "child_process";
+import readline from "readline";
+import serverconfig from "#src/serverconfig.js";
+const api = {
+  endpoint: "hicgenome",
+  methods: {
+    get: {
+      init,
+      request: {
+        typeId: "HicdataRequest"
+      },
+      response: {
+        typeId: "HicdataResponse"
+      }
+    },
+    post: {
+      alternativeFor: "get",
+      init
+    }
+  }
+};
+function init() {
+  return async (req, res) => {
+    const data = [];
+    const erroutput = [];
+    const [e, file, isurl] = fileurl({ query: req.query });
+    if (e)
+      res.send({ error: "illegal file name" });
+    const matrixType = req.query.matrixType == "log(oe)" ? "oe" : req.query.matrixType ? req.query.matrixType : "observed";
+    const promises = req.query.chrlst.map((lead, i) => {
+      return req.query.chrlst.slice(0, i + 1).map((follow, j) => {
+        if (j <= i) {
+          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 ps = spawn(serverconfig.hicstraw, par);
+            const rl = readline.createInterface({ input: ps.stdout });
+            const items = [];
+            let linenot3fields = 0;
+            let fieldnotnumerical = 0;
+            rl.on("line", (line) => {
+              const l = line.split("	");
+              if (l.length != 3) {
+                linenot3fields++;
+                return;
+              }
+              const n1 = Number.parseInt(l[0]);
+              const n2 = Number.parseInt(l[1]);
+              const v = req.query.matrixType == "log(oe)" ? Math.log(Number.parseFloat(l[2])) : Number.parseFloat(l[2]);
+              if (Number.isNaN(n1) || Number.isNaN(n2) || Number.isNaN(v)) {
+                fieldnotnumerical++;
+                return;
+              }
+              if (req.query.mincutoff != void 0 && v <= req.query.mincutoff) {
+                return;
+              }
+              items.push([n1, n2, v]);
+            });
+            data.push({ items, lead, follow });
+            ps.stderr.on("data", (i2) => erroutput.push(`${lead} - ${follow}: `, i2));
+            ps.on("close", () => {
+              if (erroutput.length)
+                reject({ error: erroutput.join("") });
+              if (linenot3fields)
+                reject({ error: `${linenot3fields} lines have other than 3 fields` });
+              if (fieldnotnumerical)
+                reject(`${fieldnotnumerical} lines have non-numerical values in any of the 3 fields`);
+              resolve();
+            });
+          });
+        }
+      });
+    }).flat();
+    Promise.allSettled(promises).then(() => res.send({ data, error: erroutput.join("") })).catch((e2) => {
+      res.send({ error: e2?.message || e2 });
+      if (e2 instanceof Error && e2.stack)
+        console.log(e2);
+    });
+  };
+}
+export {
+  api
+};

package/routes/termdb.cluster.js

@@ -32,7 +32,7 @@ function init({ genomes }) {
       if (!ds)
         throw "invalid dataset name";
       if (ds.__gdc && !ds.__gdc.doneCaching)
-        throw "The server has not finished caching the case IDs: try again in ~2 minutes";
+        throw "The server has not finished caching the case IDs: try again in about 2 minutes.";
       if (q.dataType == dtgeneexpression) {
         if (!ds.queries?.geneExpression)
           throw "no geneExpression data on this dataset";

package/routes/termdb.topVariablyExpressedGenes.js

@@ -110,7 +110,7 @@ function gdcValidateQuery(ds, genome) {
       return serverconfig.features.gdcGenes;
     }
     if (!ds.__gdc.doneCaching)
-      throw "The server has not finished caching the case IDs: try again in ~2 minutes";
+      throw "The server has not finished caching the case IDs: try again in about 2 minutes.";
     const caseLst = await gdcGetCasesWithExpressionDataFromCohort(q, ds);
     if (caseLst.length == 0) {
       return [];