@sjcrh/proteinpaint-server 2.120.2-0 → 2.121.1-0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.120.2-0",
+  "version": "2.121.1-0",
   "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": "2.120.2-0",
+    "@sjcrh/augen": "2.121.0",
     "@sjcrh/proteinpaint-python": "2.118.0",
-    "@sjcrh/proteinpaint-rust": "2.120.2-0",
-    "@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/genesetEnrichment.js

@@ -4,6 +4,7 @@ import path from "path";
 import serverconfig from "#src/serverconfig.js";
 import { run_python } from "@sjcrh/proteinpaint-python";
 import { mayLog } from "#src/helpers.ts";
+import { DeleteCacheFiles } from "#src/DeleteCacheFiles.ts";
 const api = {
   endpoint: "genesetEnrichment",
   methods: {
@@ -47,13 +48,19 @@ function init({ genomes }) {
 async function run_genesetEnrichment_analysis(q, genomes) {
   if (!genomes[q.genome].termdbs)
     throw "termdb database is not available for " + q.genome;
+  const cache = new DeleteCacheFiles({
+    cachedir: serverconfig.cachedir_gsea,
+    fileExtensions: [".pkl"],
+    maxSize: 1e6
+  });
+  await cache.mayResetCacheCheckTimeout(cache.checkWait);
   const genesetenrichment_input = {
     genes: q.genes,
     fold_change: q.fold_change,
     db: genomes[q.genome].termdbs.msigdb.cohort.db.connection.name,
     // For now msigdb has been added, but later databases other than msigdb may be used
     geneset_group: q.geneSetGroup,
-    cachedir: serverconfig.cachedir,
+    cachedir: serverconfig.cachedir_gsea,
     geneset_name: q.geneset_name,
     pickle_file: q.pickle_file,
     num_permutations: q.num_permutations,
@@ -78,7 +85,7 @@ async function run_genesetEnrichment_analysis(q, genomes) {
   if (data_found)
     return result;
   if (image_found)
-    return path.join(serverconfig.cachedir, result.image_file);
+    return path.join(serverconfig.cachedir_gsea, result.image_file);
   throw "data or image not found in gsea output; this should not happen";
 }
 export {

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: {