@sjcrh/proteinpaint-server 2.77.1 → 2.79.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.77.1",
+  "version": "2.79.0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -62,7 +62,7 @@
   },
   "dependencies": {
     "@sjcrh/augen": "2.46.0",
-    "@sjcrh/proteinpaint-rust": "2.75.0",
+    "@sjcrh/proteinpaint-rust": "2.78.0",
     "better-sqlite3": "^9.4.1",
     "body-parser": "^1.15.2",
     "canvas": "~2.11.2",

package/routes/termdb.config.js

@@ -58,7 +58,8 @@ function make(q, res, ds, genome) {
     lollipop: tdb.lollipop,
     urlTemplates: tdb.urlTemplates,
     title: "title" in ds.cohort ? ds.cohort.title : { text: ds.label },
-    hideGroupsTab: ds.cohort.hideGroupsTab
+    hideGroupsTab: ds.cohort.hideGroupsTab,
+    tracks: tdb.tracks
   };
   if (tdb.chartConfigByType)
     c.chartConfigByType = tdb.chartConfigByType;
@@ -86,6 +87,8 @@ function make(q, res, ds, genome) {
     c.excludedTermtypeByTarget = tdb.excludedTermtypeByTarget;
   if (tdb.about)
     c.about = tdb.about;
+  if (tdb.survival)
+    c.survival = tdb.survival;
   if (ds.assayAvailability)
     c.assayAvailability = ds.assayAvailability;
   if (ds.customTwQByType)

package/routes/termdb.singlecellSamples.js

@@ -2,9 +2,11 @@ import fs from "fs";
 import path from "path";
 import { read_file } from "#src/utils.js";
 import run_R from "#src/run_R.js";
+import { run_rust } from "@sjcrh/proteinpaint-rust";
 import serverconfig from "#src/serverconfig.js";
 import { validate_query_singleCell_DEgenes } from "./termdb.singlecellDEgenes.ts";
 import { gdc_validate_query_singleCell_samples, gdc_validate_query_singleCell_data } from "#src/mds3.gdc.js";
+import ky from "ky";
 const api = {
   endpoint: "termdb/singlecellSamples",
   methods: {
@@ -66,6 +68,7 @@ async function validate_query_singleCell(ds, genome) {
     if (q.geneExpression.src == "native") {
       validateGeneExpressionNative(q.geneExpression);
     } else if (q.geneExpression.src == "gdcapi") {
+      gdc_validateGeneExpression(q.geneExpression, ds, genome);
     } else {
       throw "unknown singleCell.geneExpression.src";
     }
@@ -108,7 +111,11 @@ function validateDataNative(D, ds) {
       for (const plot of D.plots) {
         if (!q.plots.includes(plot.name))
           continue;
-        const tsvfile = path.join(serverconfig.tpmasterdir, plot.folder, q.sample + plot.fileSuffix);
+        const tsvfile = path.join(
+          serverconfig.tpmasterdir,
+          plot.folder,
+          (q.sample.eID || q.sample.sID) + plot.fileSuffix
+        );
         if (!file2Lines[tsvfile]) {
           try {
             await fs.promises.stat(tsvfile);
@@ -154,23 +161,81 @@ function validateDataNative(D, ds) {
   };
 }
 function validateGeneExpressionNative(G) {
+  G.sample2gene2expressionBins = {};
+  if (G.storage_type == "RDS" || !G.storage_type) {
+    G.get = async (q) => {
+      const rdsfile = path.join(serverconfig.tpmasterdir, G.folder, (q.sample.eID || q.sample.sID) + ".rds");
+      try {
+        await fs.promises.stat(rdsfile);
+      } catch (e) {
+        return {};
+      }
+      let out;
+      try {
+        out = JSON.parse(
+          await run_R(path.join(serverconfig.binpath, "utils", "getGeneFromMatrix.R"), null, [rdsfile, q.gene])
+        );
+      } catch (e) {
+        return {};
+      }
+      console.log("out:", out);
+      return out;
+    };
+  } else if (G.storage_type == "HDF5") {
+    G.get = async (q) => {
+      const rdsfile = path.join(serverconfig.tpmasterdir, G.folder, (q.sample.eID || q.sample.sID) + ".h5");
+      try {
+        await fs.promises.stat(rdsfile);
+      } catch (e) {
+        return {};
+      }
+      const read_hdf5_input_type = { gene: q.gene, hdf5_file: rdsfile };
+      let out;
+      try {
+        const time1 = (/* @__PURE__ */ new Date()).valueOf();
+        const rust_output = await run_rust("readHDF5", JSON.stringify(read_hdf5_input_type));
+        const time2 = (/* @__PURE__ */ new Date()).valueOf();
+        console.log("Time taken to query HDF5 file:", time2 - time1, "ms");
+        for (const line of rust_output.split("\n")) {
+          if (line.startsWith("output_string:")) {
+            out = JSON.parse(line.replace("output_string:", ""));
+          } else {
+            console.log(line);
+          }
+        }
+      } catch (e) {
+        return {};
+      }
+      return out;
+    };
+  }
+}
+function gdc_validateGeneExpression(G, ds, genome) {
   G.sample2gene2expressionBins = {};
   G.get = async (q) => {
-    const rdsfile = path.join(serverconfig.tpmasterdir, G.folder, q.sample + ".rds");
     try {
-      await fs.promises.stat(rdsfile);
-    } catch (e) {
-      return {};
-    }
-    let out;
-    try {
-      out = JSON.parse(
-        await run_R(path.join(serverconfig.binpath, "utils", "getGeneFromMatrix.R"), null, [rdsfile, q.gene])
-      );
+      const uuid = ds.__gdc.map2caseid.get(q.sample.sID);
+      const fileid = q.sample.eID;
+      const aliasLst = genome.genedb.getAliasByName.all(q.gene);
+      const gencodeId = aliasLst.find((a) => a?.alias.toUpperCase().startsWith("ENSG"))?.alias;
+      const body = {
+        case_id: uuid,
+        gene_ids: [gencodeId],
+        file_id: fileid
+      };
+      const { host } = ds.getHostHeaders(q);
+      const out = await ky.post(path.join(host.rest, "scrna_seq/gene_expression"), { timeout: false, json: body }).json();
+      const result = out.data[0].cells;
+      const data = {};
+      for (const r of result) {
+        data[r.cell_id] = r.value;
+      }
+      return data;
     } catch (e) {
-      return {};
+      if (e.stack)
+        console.log(e.stack);
+      return { error: e.message || e };
     }
-    return out;
   };
 }
 export {