@sjcrh/proteinpaint-server 2.116.1-1 → 2.117.0

package/dataset/termdb.test.js

@@ -194,7 +194,8 @@ var termdb_test_default = {
     },
     geneExpression: {
       src: "native",
-      file: "files/hg38/TermdbTest/TermdbTest.fpkm.matrix.gz"
+      hdf5File: true,
+      file: "files/hg38/TermdbTest/TermdbTest.fpkm.matrix.h5"
     },
     topVariablyExpressedGenes: {
       src: "native"

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.116.1-1",
+  "version": "2.117.0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -66,9 +66,9 @@
   },
   "dependencies": {
     "@sjcrh/augen": "2.116.0",
-    "@sjcrh/proteinpaint-rust": "2.116.0",
-    "@sjcrh/proteinpaint-shared": "2.116.1-1",
-    "@sjcrh/proteinpaint-types": "2.116.1-1",
+    "@sjcrh/proteinpaint-rust": "2.117.0",
+    "@sjcrh/proteinpaint-shared": "2.117.0",
+    "@sjcrh/proteinpaint-types": "2.117.0",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^9.4.1",

package/routes/termdb.cluster.js

@@ -12,6 +12,7 @@ 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";
+import { formatElapsedTime } from "#shared/time.js";
 const api = {
   endpoint: "termdb/cluster",
   methods: {
@@ -102,7 +103,7 @@ async function getResult(q, ds, genome) {
   }
   const t = Date.now();
   const clustering = await doClustering(term2sample2value, q, Object.keys(bySampleId).length);
-  mayLog("clustering done:", Date.now() - t, "ms");
+  mayLog("clustering done:", formatElapsedTime(Date.now() - t));
   const result = { clustering, byTermId, bySampleId };
   if (removedHierClusterTerms.length)
     result.removedHierClusterTerms = removedHierClusterTerms;
@@ -239,19 +240,19 @@ async function validateHDF5File(filePath) {
     };
   }
 }
-async function queryGeneExpression(hdf5_file, geneName) {
+async function queryGeneExpression(hdf5_file, geneNames) {
   const jsonInput = JSON.stringify({
     hdf5_file,
-    gene: geneName
+    gene: geneNames
   });
   try {
     const result = await run_rust("readHDF5", jsonInput);
-    if (!result || Object.keys(result).length === 0) {
+    if (!result || result.length === 0) {
       throw new Error("Failed to retrieve expression data: Empty or missing response");
     }
     return result;
   } catch (error) {
-    console.error(`Error querying gene expression for ${geneName}`);
+    console.error(`Error querying gene expression for ${geneNames}`);
     throw error;
   }
 }
@@ -294,13 +295,30 @@ async function validateNative(q, ds, genome) {
       }
       const term2sample2value = /* @__PURE__ */ new Map();
       const byTermId = {};
+      const geneNames = [];
       for (const geneTerm of param.terms) {
-        if (!geneTerm.gene)
-          continue;
-        try {
-          const geneQuery = await queryGeneExpression(q.file, geneTerm.gene);
-          const geneData = JSON.parse(geneQuery);
-          const samplesData = geneData.samples || {};
+        if (geneTerm.gene) {
+          geneNames.push(geneTerm.gene);
+        }
+      }
+      if (geneNames.length === 0) {
+        console.log("No genes to query");
+        return { term2sample2value, byTermId };
+      }
+      const time1 = Date.now();
+      try {
+        const geneData = JSON.parse(await queryGeneExpression(q.file, geneNames));
+        mayLog("Time taken to run gene query:", formatElapsedTime(Date.now() - time1));
+        const genesData = geneData.genes || { [geneNames[0]]: geneData };
+        for (const geneTerm of param.terms) {
+          if (!geneTerm.gene)
+            continue;
+          const geneResult = genesData[geneTerm.gene];
+          if (!geneResult) {
+            console.warn(`No data found for gene ${geneTerm.gene} in the response`);
+            continue;
+          }
+          const samplesData = geneResult.samples || {};
           const s2v = {};
           for (const [sampleName, value] of Object.entries(samplesData)) {
             const sampleId = ds.cohort.termdb.q.sampleName2id(sampleName);
@@ -308,16 +326,14 @@ async function validateNative(q, ds, genome) {
               continue;
             if (limitSamples && !limitSamples.has(sampleId))
               continue;
-            s2v[sampleId] = Number(value);
+            s2v[sampleId] = value;
           }
-          console.log(`Gene ${geneTerm.gene} has ${Object.keys(s2v).length} samples with data`);
           if (Object.keys(s2v).length) {
             term2sample2value.set(geneTerm.gene, s2v);
           }
-        } catch (error) {
-          console.warn(`Error processing gene ${geneTerm.gene}:`, error);
-          continue;
         }
+      } catch (error) {
+        console.error(`Error processing batch gene query:`, error);
       }
       if (term2sample2value.size == 0) {
         throw "No data available for the input " + param.terms?.map((g) => g.gene).join(", ");

package/routes/termdb.config.js

@@ -41,6 +41,7 @@ function make(q, req, res, ds, genome) {
   const c = {
     selectCohort: getSelectCohort(ds, req),
     supportedChartTypes: tdb.q?.getSupportedChartTypes(req),
+    hiddenTermIds: tdb.hiddenTermIds,
     renamedChartTypes: ds.cohort.renamedChartTypes,
     allowedTermTypes: getAllowedTermTypes(ds),
     termMatch2geneSet: tdb.termMatch2geneSet,
@@ -60,7 +61,8 @@ function make(q, req, res, ds, genome) {
     sampleTypes: ds.cohort.termdb.sampleTypes,
     hasSampleAncestry: ds.cohort.termdb.hasSampleAncestry,
     defaultChartType: ds.cohort.defaultChartType,
-    invalidTokenErrorHandling: tdb.invalidTokenErrorHandling
+    invalidTokenErrorHandling: tdb.invalidTokenErrorHandling,
+    colorMap: tdb.colorMap
   };
   if (tdb.plotConfigByCohort)
     c.plotConfigByCohort = tdb.plotConfigByCohort;

package/routes/termdb.topVariablyExpressedGenes.js

@@ -5,6 +5,8 @@ import { get_samples } from "#src/termdb.sql.js";
 import { makeFilter } from "#src/mds3.gdc.js";
 import { cachedFetch } from "#src/utils.js";
 import { joinUrl } from "#shared/joinUrl.js";
+import { formatElapsedTime } from "#shared/time.js";
+import { mayLog } from "#src/helpers.ts";
 const api = {
   endpoint: "termdb/topVariablyExpressedGenes",
   methods: {
@@ -35,8 +37,7 @@ function init({ genomes }) {
       result = {
         genes: await ds.queries.topVariablyExpressedGenes.getGenes(q)
       };
-      if (serverconfig.debugmode)
-        console.log("topVariablyExpressedGenes", Date.now() - t, "ms");
+      mayLog("topVariablyExpressedGenes", formatElapsedTime(Date.now() - t));
     } catch (e) {
       result = { status: e.status || 400, error: e.message || e };
     }