@sjcrh/proteinpaint-server 2.120.1 → 2.121.0

package/dataset/termdb.test.js

@@ -154,12 +154,6 @@ function termdb_test_default() {
       cnv: {
         file: "files/hg38/TermdbTest/TermdbTest_CNV_gene.gz"
       },
-      /*
-      on the fly cnv calls from gene body probe signals are no longer used
-      probe2cnv:{
-      	file: 'files/hg19/pnet/PNET.probesignals.gz'
-      }
-      */
       singleSampleMutation: {
         src: "native",
         sample_id_key: "sample_id",
@@ -197,6 +191,10 @@ function termdb_test_default() {
       topVariablyExpressedGenes: {
         src: "native"
       },
+      rnaseqGeneCount: {
+        storage_type: "HDF5",
+        file: "files/hg38/TermdbTest/TermdbTest.geneCounts.h5"
+      },
       WSImages: {
         type: "H&E",
         imageBySampleFolder: "files/hg38/TermdbTest/wsimages"

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.120.1",
+  "version": "2.121.0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -65,11 +65,11 @@
     "typescript": "^5.6.3"
   },
   "dependencies": {
-    "@sjcrh/augen": "2.120.1",
+    "@sjcrh/augen": "2.121.0",
     "@sjcrh/proteinpaint-python": "2.118.0",
-    "@sjcrh/proteinpaint-rust": "2.120.1",
-    "@sjcrh/proteinpaint-shared": "2.120.1",
-    "@sjcrh/proteinpaint-types": "2.119.0",
+    "@sjcrh/proteinpaint-rust": "2.121.0",
+    "@sjcrh/proteinpaint-shared": "2.121.0",
+    "@sjcrh/proteinpaint-types": "2.121.0",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^9.4.1",

package/routes/burden.js

@@ -15,7 +15,6 @@ const api = {
     }
   }
 };
-const MAXBOOTNUM = 20;
 function init({ genomes }) {
   return async function handler(req, res) {
     try {
@@ -124,9 +123,6 @@ async function compute95ci(result, cumburden) {
   }
   await cumburden.db.connection.prepare(`UPDATE estimates SET ci95=? WHERE id=?`).run(JSON.stringify(result.ci95), result.id);
 }
-function sortNumericValue(a, b) {
-  return a < b ? -1 : 1;
-}
 function formatPayload(estimates) {
   const rawKeys = Object.keys(estimates["1"]).filter((k) => k.startsWith("["));
   const renamedKeys = rawKeys.map((k) => `burden${k.split(",")[0].slice(1)}`);

package/routes/termdb.topMutatedGenes.js

@@ -38,7 +38,7 @@ function init({ genomes }) {
     }
   };
 }
-function validate_query_getTopMutatedGenes(ds, genome) {
+function validate_query_getTopMutatedGenes(ds) {
   const q = ds.queries?.topMutatedGenes;
   if (!q)
     return;

package/routes/termdb.violin.js

@@ -10,7 +10,6 @@ import { numericBins, parseValues } from "./termdb.boxplot.ts";
 import serverconfig from "../src/serverconfig.js";
 import run_R from "../src/run_R.js";
 import path from "path";
-const minSampleSize = 5;
 const api = {
   endpoint: "termdb/violin",
   methods: {