@sjcrh/proteinpaint-server 2.63.4 → 2.63.6

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": "2.63.4",
+  "version": "2.63.6",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",

package/routes/termdb.config.js

@@ -84,8 +84,7 @@ function make(q, res, ds, genome) {
   addRestrictAncestries(c, tdb);
   addScatterplots(c, ds);
   addMatrixplots(c, ds);
-  addGenomicQueries(c, ds, genome);
-  addImageQueries(c, ds);
+  addNonDictionaryQueries(c, ds, genome);
   res.send({ termdbConfig: c });
 }
 function addRestrictAncestries(c, tdb) {
@@ -95,13 +94,6 @@ function addRestrictAncestries(c, tdb) {
     return { name: i.name, tvs: i.tvs, PCcount: i.PCcount };
   });
 }
-function addImageQueries(c, ds) {
-  const q = ds.queries;
-  const q2 = c.queries;
-  if (q.images) {
-    q2.images = {};
-  }
-}
 function addScatterplots(c, ds) {
   if (!ds.cohort.scatterplots)
     return;
@@ -126,7 +118,7 @@ function addMatrixplots(c, ds) {
     return { name: p.name };
   });
 }
-function addGenomicQueries(c, ds, genome) {
+function addNonDictionaryQueries(c, ds, genome) {
   const q = ds.queries;
   if (!q)
     return;
@@ -210,6 +202,12 @@ function addGenomicQueries(c, ds, genome) {
         refName: q.singleCell.data.refName
       }
     };
+    if (q.singleCell.geneExpression) {
+      q2.singleCell.geneExpression = {};
+    }
+  }
+  if (q.images) {
+    q2.images = {};
   }
 }
 function getAllowedTermTypes(ds) {

package/routes/termdb.singlecellSamples.js

@@ -1,6 +1,7 @@
 import fs from "fs";
 import path from "path";
-import { read_file } from "#src/utils.js";
+import { spawn } from "child_process";
+import { read_file, get_header_txt } from "#src/utils.js";
 import serverconfig from "#src/serverconfig.js";
 import { gdc_validate_query_singleCell_samples, gdc_validate_query_singleCell_data } from "#src/mds3.gdc.js";
 const api = {
@@ -53,19 +54,27 @@ async function validate_query_singleCell(ds, genome) {
   if (q.samples.src == "gdcapi") {
     gdc_validate_query_singleCell_samples(ds, genome);
   } else if (q.samples.src == "native") {
-    getSamplesNative(q.samples, ds);
+    validateSamplesNative(q.samples, ds);
   } else {
     throw "unknown singleCell.samples.src";
   }
   if (q.data.src == "gdcapi") {
     gdc_validate_query_singleCell_data(ds, genome);
   } else if (q.data.src == "native") {
-    getDataNative(q.data, ds);
+    validateDataNative(q.data);
   } else {
     throw "unknown singleCell.data.src";
   }
+  if (q.geneExpression) {
+    if (q.geneExpression.src == "native") {
+      validateGeneExpressionNative(q.geneExpression);
+    } else if (q.geneExpression.src == "gdcapi") {
+    } else {
+      throw "unknown singleCell.geneExpression.src";
+    }
+  }
 }
-async function getSamplesNative(S, ds) {
+async function validateSamplesNative(S, ds) {
   const samples = {};
   if (S.sampleColumns) {
     for (const term of S.sampleColumns) {
@@ -81,7 +90,7 @@ async function getSamplesNative(S, ds) {
     return { samples: Object.values(samples) };
   };
 }
-function getDataNative(D, ds) {
+function validateDataNative(D) {
   const nameSet = /* @__PURE__ */ new Set();
   for (const plot of D.plots) {
     if (nameSet.has(plot.name))
@@ -128,6 +137,42 @@ function getDataNative(D, ds) {
     }
   };
 }
+function validateGeneExpressionNative(G) {
+  G.get = async (q) => {
+    const tsvfile = path.join(serverconfig.tpmasterdir, G.folder, q.sample);
+    try {
+      await fs.promises.stat(tsvfile);
+    } catch (e) {
+      throw "geneExp matrix file not found or readable for this sample";
+    }
+    const header = await get_header_txt(tsvfile);
+    return await grepMatrix4geneExpression(tsvfile, q.gene, header);
+  };
+}
+function grepMatrix4geneExpression(tsvfile, gene, header) {
+  return new Promise((resolve, reject) => {
+    const cp = spawn("grep", ["-m", "1", gene + "	", tsvfile]);
+    const out = [], err = [];
+    cp.stdout.on("data", (d) => out.push(d));
+    cp.stderr.on("data", (d) => err.push(d));
+    cp.on("close", () => {
+      const e = err.join("");
+      if (e)
+        reject(e);
+      const l = out.join("").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))
+          continue;
+        cell2value[header[i]] = v;
+      }
+      resolve(cell2value);
+    });
+  });
+}
 export {
   api,
   validate_query_singleCell