@sjcrh/proteinpaint-server 2.73.0 → 2.74.0

package/dataset/termdb.test.js

@@ -191,7 +191,13 @@ var termdb_test_default = {
       src: "native",
       file: "files/hg38/TermdbTest/TermdbTest.fpkm.matrix.gz"
     },
-    topVariablyExpressedGenes: { src: "native" }
+    topVariablyExpressedGenes: {
+      src: "native"
+    },
+    WSImages: {
+      type: "H&E",
+      imageBySampleFolder: "hg38-test/TermdbTest/wsimages"
+    }
   },
   assayAvailability: {
     // term used below must be annotated on samples rather than patients(root). otherwise matrix will pull wrong samples for geneVariant term

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.73.0",
+  "version": "2.74.0",
   "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": "2.73.0",
+    "@sjcrh/proteinpaint-rust": "2.74.0",
     "better-sqlite3": "^9.4.1",
     "body-parser": "^1.15.2",
     "canvas": "~2.11.2",

package/routes/genesetOverrepresentation.js

@@ -1,4 +1,6 @@
 import { run_rust } from "@sjcrh/proteinpaint-rust";
+import serverconfig from "#src/serverconfig.js";
+import path from "path";
 const api = {
   endpoint: "genesetOverrepresentation",
   methods: {
@@ -31,14 +33,17 @@ function init({ genomes }) {
 async function run_genesetOverrepresentation_analysis(q, genomes) {
   if (!genomes[q.genome].termdbs)
     throw "termdb database is not available for " + q.genome;
-  const gene_overrepresentation_input = {
+  const gene_overrepresentation_input_type = {
     sample_genes: q.sample_genes,
-    background_genes: q.background_genes,
-    db: genomes[q.genome].termdbs.msigdb.cohort.db.connection.name,
-    gene_set_group: q.geneSetGroup
+    msigdb: genomes[q.genome].termdbs.msigdb.cohort.db.connection.name,
+    gene_set_group: q.geneSetGroup,
+    genedb: path.join(serverconfig.tpmasterdir, genomes[q.genome].genedb.dbfile)
   };
+  if (q.background_genes) {
+    gene_overrepresentation_input_type.background_genes = q.background_genes;
+  }
   const time1 = (/* @__PURE__ */ new Date()).valueOf();
-  const rust_output = await run_rust("genesetORA", JSON.stringify(gene_overrepresentation_input));
+  const rust_output = await run_rust("genesetORA", JSON.stringify(gene_overrepresentation_input_type));
   const time2 = (/* @__PURE__ */ new Date()).valueOf();
   console.log("Time taken to run rust gene over representation pipeline:", time2 - time1, "ms");
   let result;

package/routes/genomes.js

@@ -85,7 +85,8 @@ function clientcopy_genome(genomename, genomes) {
     minorchr: g.minorchr,
     tracks: g.tracks,
     hicenzymefragment: g.hicenzymefragment,
-    datasets: {}
+    datasets: {},
+    hideOnClient: g.hideOnClient
   };
   if (g.termdbs) {
     g2.termdbs = {};

package/routes/termdb.config.js

@@ -78,6 +78,8 @@ function make(q, res, ds, genome) {
     c.logscaleBase2 = tdb.logscaleBase2;
   if (tdb.useCasesExcluded)
     c.useCasesExcluded = tdb.useCasesExcluded;
+  if (tdb.excludedTermtypeByTarget)
+    c.excludedTermtypeByTarget = tdb.excludedTermtypeByTarget;
   if (ds.assayAvailability)
     c.assayAvailability = ds.assayAvailability;
   if (ds.customTwQByType)
@@ -171,7 +173,7 @@ function addNonDictionaryQueries(c, ds, genome) {
       delete q2.singleSampleGenomeQuantification[k].folder;
     }
   }
-  if (q.NIdata) {
+  if (q.NIdata && serverconfig.features.showBrainImaging) {
     q2.NIdata = {};
     for (const k in q.NIdata) {
       q2.NIdata[k] = JSON.parse(JSON.stringify(q.NIdata[k]));

package/routes/wsimages.js

@@ -11,10 +11,10 @@ const api = {
     get: {
       init,
       request: {
-        typeId: "any"
+        typeId: "GetWSImagesRequest"
       },
       response: {
-        typeId: "any"
+        typeId: "GetWSImagesResponse"
       }
     },
     post: {
@@ -26,16 +26,17 @@ const api = {
 function init({ genomes }) {
   return async (req, res) => {
     try {
-      const g = genomes[req.query.genome];
+      const query = req.query;
+      const g = genomes[query.genome];
       if (!g)
         throw "invalid genome name";
-      const ds = g.datasets[req.query.dslabel];
+      const ds = g.datasets[query.dslabel];
       if (!ds)
         throw "invalid dataset name";
-      const sampleId = req.query.sampleId;
+      const sampleId = query.sampleId;
       if (!sampleId)
         throw "invalid sampleId";
-      const wsimage = req.query.wsimage;
+      const wsimage = query.wsimage;
       if (!wsimage)
         throw "invalid wsimage";
       const cookieJar = new CookieJar();