@sjcrh/proteinpaint-server 2.109.0 → 2.109.1

package/dataset/termdb.test.js

@@ -7,18 +7,13 @@ var termdb_test_default = {
   cohort: {
     massNav: {
       tabs: {
-        // about: {
-        // 	hide: true,
-        // 	order: 4,
-        // 	top: 'test',
-        // 	mid: 'test about',
-        // 	btm: 'test',
-        // 	html: 'Test'
-        // },
-        // charts: {
-        // 	top: 'test charts',
-        // 	mid: 'mid test'
-        // }
+        about: {
+          dataRelease: {
+            version: "?",
+            link: "testLink"
+          },
+          additionalInfo: "<a href=testLink>Tutorial</a> <a href=testLink>Get help</a>"
+        }
       }
     },
     db: {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.109.0",
+  "version": "2.109.1",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -17,7 +17,7 @@
     "dev": "npm run start",
     "prestart": "tsx emitImports.js dev > server.js",
     "start": "tsx watch . /start.js",
-    "test:unit": "tsx emitImports.js unit > serverTests.js && tsx serverTests.js && rm -rf ./cache",
+    "test:unit": "tsx emitImports.js unit > serverTests.js && c8 tsx serverTests.js && rm -rf ./cache",
     "getconf": "../build/getConfigProp.js",
     "doc": "../augen/build.sh routes shared/types/routes shared/checkers ../public/docs/server",
     "mjs": "esbuild \"$DIR/*.ts\" --platform=node --outdir=\"$DIR\" --format=esm",
@@ -46,6 +46,7 @@
     "@types/tough-cookie": "^4.0.5",
     "@typescript-eslint/eslint-plugin": "^8.13.0",
     "babel-loader": "^8.2.2",
+    "c8": "^10.1.3",
     "esbuild": "^0.19.12",
     "glob": "^10.4.5",
     "node-watch": "^0.7.1",
@@ -58,10 +59,10 @@
     "typescript": "^5.6.3"
   },
   "dependencies": {
-    "@sjcrh/augen": "2.87.0",
+    "@sjcrh/augen": "2.109.1-0",
     "@sjcrh/proteinpaint-rust": "2.99.0",
-    "@sjcrh/proteinpaint-shared": "2.109.0",
-    "@sjcrh/proteinpaint-types": "2.109.0",
+    "@sjcrh/proteinpaint-shared": "2.109.1",
+    "@sjcrh/proteinpaint-types": "2.109.1",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^9.4.1",
@@ -82,7 +83,7 @@
     "ky": "^1.2.1",
     "lazy": "^1.0.11",
     "micromatch": "^4.0.5",
-    "minimatch": "^3.1.2",
+    "minimatch": "^10.0.1",
     "node-fetch": "^2.6.1",
     "partjson": "^0.58.2",
     "redis": "^4.7.0",

package/routes/termdb.cluster.js

@@ -10,6 +10,7 @@ import { getResult as getResultGene } from "#src/gene.js";
 import { TermTypes, NUMERIC_DICTIONARY_TERM } from "#shared/terms.js";
 import { getData } from "#src/termdb.matrix.js";
 import { termType2label } from "#shared/terms.js";
+import { mayLog } from "#src/helpers.ts";
 const api = {
   endpoint: "termdb/cluster",
   methods: {
@@ -74,8 +75,10 @@ async function getResult(q, ds, genome) {
     ;
     ({ term2sample2value, byTermId, bySampleId } = await ds.queries[q.dataType].get(_q));
   }
+  const removedHierClusterTerms = [];
   for (const [term, obj] of term2sample2value) {
     if (Object.keys(obj).length === 0) {
+      removedHierClusterTerms.push(term);
       term2sample2value.delete(term);
       delete byTermId[term];
     }
@@ -88,9 +91,11 @@ async function getResult(q, ds, genome) {
   }
   const t = Date.now();
   const clustering = await doClustering(term2sample2value, q, Object.keys(bySampleId).length);
-  if (serverconfig.debugmode)
-    console.log("clustering done:", Date.now() - t, "ms");
-  return { clustering, byTermId, bySampleId };
+  mayLog("clustering done:", Date.now() - t, "ms");
+  const result = { clustering, byTermId, bySampleId };
+  if (removedHierClusterTerms.length)
+    result.removedHierClusterTerms = removedHierClusterTerms;
+  return result;
 }
 async function getNumericDictTermAnnotation(q, ds, genome) {
   const getDataArgs = {

package/routes/termdb.singleSampleMutation.js

@@ -46,14 +46,7 @@ async function validate_query_singleSampleMutation(ds, genome) {
     gdcValidate_query_singleSampleMutation(ds, genome);
   } else if (_q.src == "native") {
     _q.get = async (q) => {
-      let fileName = q.sample;
-      if (ds.cohort?.termdb?.q?.sampleName2id) {
-        fileName = ds.cohort.termdb.q.sampleName2id(q.sample);
-        if (fileName == void 0) {
-          return [];
-        }
-      }
-      const file = path.join(serverconfig.tpmasterdir, _q.folder, fileName.toString());
+      const file = path.join(serverconfig.tpmasterdir, _q.folder, q.sample);
       try {
         await fs.promises.stat(file);
       } catch (e) {

package/routes/termdb.violin.js

@@ -220,7 +220,7 @@ function createCanvasImg(q, result, ds) {
         ctx.stroke();
       });
     plot.src = canvas.toDataURL();
-    plot.density = getBinsDensity(axisScale, plot, q.isKDE, q.ticks);
+    plot.density = getBinsDensity(plot, q.isKDE, q.ticks);
     plot.summaryStats = summaryStats(plot.values).values;
     delete plot.values;
   }