@sjcrh/proteinpaint-server 2.137.1 → 2.137.2-1

package/dataset/termdb.test.js

@@ -264,14 +264,43 @@ function termdb_test_default() {
       },
       geneExpression: {
         src: "native",
-        file: "files/hg38/TermdbTest/TermdbTest.fpkm.matrix.h5"
+        file: "files/hg38/TermdbTest/rnaseq/TermdbTest.fpkm.matrix.h5"
       },
       topVariablyExpressedGenes: {
         src: "native"
       },
       rnaseqGeneCount: {
         storage_type: "HDF5",
-        file: "files/hg38/TermdbTest/TermdbTest.geneCounts.h5"
+        file: "files/hg38/TermdbTest/rnaseq/TermdbTest.geneCounts.h5"
+      },
+      singleCell: {
+        samples: {
+          sampleColumns: [{ termid: "sex" }],
+          extraSampleTabLabel: "sex"
+        },
+        data: {
+          sameLegend: true,
+          src: "native",
+          plots: [
+            {
+              name: "scRNA",
+              folder: "files/hg38/TermdbTest/scrna/umap",
+              fileSuffix: "_umap.txt",
+              colorColumns: [
+                {
+                  index: 3,
+                  name: "CellType"
+                }
+              ],
+              coordsColumns: { x: 1, y: 2 },
+              selected: true
+            }
+          ]
+        },
+        geneExpression: {
+          src: "native",
+          folder: "files/hg38/TermdbTest/scrna/geneExpHdf5"
+        }
       },
       WSImages: {
         type: "H&E",

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.137.1",
+  "version": "2.137.2-1",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -61,10 +61,10 @@
   "dependencies": {
     "@sjcrh/augen": "2.136.0",
     "@sjcrh/proteinpaint-python": "2.135.2-0",
-    "@sjcrh/proteinpaint-r": "2.130.0",
-    "@sjcrh/proteinpaint-rust": "2.136.0",
-    "@sjcrh/proteinpaint-shared": "2.137.1",
-    "@sjcrh/proteinpaint-types": "2.137.1",
+    "@sjcrh/proteinpaint-r": "2.137.2-0",
+    "@sjcrh/proteinpaint-rust": "2.137.2-0",
+    "@sjcrh/proteinpaint-shared": "2.137.2-1",
+    "@sjcrh/proteinpaint-types": "2.137.2-1",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^9.4.1",

package/routes/filterTermValues.js

@@ -37,14 +37,15 @@ function getList(samplesPerFilter, filtersData, tw) {
   }
   const annotations = data.filter((s) => s != void 0).map((sample) => sample[tw.$id]?.value);
   const sampleValues = Array.from(new Set(annotations));
+  const filteredValues = [];
   for (const value of values) {
-    value.value = value.label;
-    const label = value.label;
-    value.disabled = !sampleValues.includes(label);
+    const label = value.label.replace(/["']/g, "");
+    const disabled = !sampleValues.includes(value.key || value.label);
+    filteredValues.push({ value: value.key || value.label, label, disabled });
   }
-  values.unshift({ label: "", value: "" });
-  values.sort((a, b) => a.label.localeCompare(b.label));
-  return values;
+  filteredValues.unshift({ label: "", value: "" });
+  filteredValues.sort((a, b) => a.label.localeCompare(b.label));
+  return filteredValues;
 }
 async function getFilters(query, ds, genome, res) {
   try {

package/routes/profileFormScores.js

@@ -29,7 +29,7 @@ function init({ genomes }) {
   };
 }
 async function getScoresDict(query, ds, genome) {
-  const terms = [...query.scoreTerms];
+  const terms = [...query.scoreTerms, query.facilityTW];
   if (query.scScoreTerms)
     terms.push(...query.scScoreTerms);
   const data = await getData(
@@ -70,7 +70,9 @@ async function getScoresDict(query, ds, genome) {
       const percents = getSCPercentsDict(d, samples2);
       term2Score[d.term.id] = percents;
     }
-  const hospital = sampleData?.[query.facilityTW.$id]?.value;
+  const facilityValue = sampleData?.[query.facilityTW.$id];
+  const termValue = query.facilityTW.term.values[facilityValue?.value];
+  const hospital = termValue?.label || termValue?.key;
   return { term2Score, sites, hospital, n: sampleData ? 1 : samples.length };
 }
 function getDict(key, sample) {

package/routes/profileScores.js

@@ -49,9 +49,6 @@ async function getScores(query, ds, genome) {
   let sites = lst.map((s) => {
     return { label: data.refs.bySampleId[s.sample].label, value: s.sample };
   });
-  sites = lst.map((s) => {
-    return { label: data.refs.bySampleId[s.sample].label, value: s.sample };
-  });
   if (query.userSites) {
     sites = sites.filter((s) => query.userSites.includes(s.label));
   }
@@ -70,7 +67,9 @@ async function getScores(query, ds, genome) {
   for (const d of query.scoreTerms) {
     term2Score[d.score.term.id] = getPercentage(d, samples, sampleData);
   }
-  const hospital = sampleData?.[query.facilityTW.$id]?.value;
+  const facilityValue = sampleData?.[query.facilityTW.$id];
+  const termValue = query.facilityTW.term.values[facilityValue?.value];
+  const hospital = termValue?.label || termValue?.key;
   return { term2Score, sites, hospital, n: sampleData ? 1 : samples.length };
 }
 function getPercentage(d, samples, sampleData) {

package/routes/termdb.singlecellSamples.js

@@ -55,7 +55,7 @@ async function validate_query_singleCell(ds, genome) {
     throw "singleCell.samples{} not object";
   if (typeof q.samples.get == "function") {
   } else {
-    validateSamplesNative(q.samples, q.data, ds);
+    await validateSamplesNative(q.samples, q.data, ds);
   }
   if (typeof q.data != "object")
     throw "singleCell.data{} not object";
@@ -99,32 +99,31 @@ function validateImages(images) {
 async function validateSamplesNative(S, D, ds) {
   const samples = /* @__PURE__ */ new Map();
   for (const plot of D.plots) {
-    try {
-      for (const fn of await fs.promises.readdir(path.join(serverconfig.tpmasterdir, plot.folder))) {
-        let sampleName = fn;
-        if (plot.fileSuffix) {
-          if (!fn.endsWith(plot.fileSuffix))
-            continue;
-          sampleName = fn.split(plot.fileSuffix)[0];
-        }
-        if (!sampleName)
-          continue;
-        const sid = ds.cohort.termdb.q.sampleName2id(sampleName);
-        if (sid == void 0)
-          continue;
-        samples.set(sid, { sample: sampleName });
+    for (const fn of await fs.promises.readdir(path.join(serverconfig.tpmasterdir, plot.folder))) {
+      let sampleName = fn;
+      if (plot.fileSuffix) {
+        if (!fn.endsWith(plot.fileSuffix))
+          throw `singlecell.sample file name ${fn} does not end with required suffix ${plot.fileSuffix}`;
+        sampleName = fn.split(plot.fileSuffix)[0];
       }
-    } catch (e) {
-      console.log("cannot readdir on singleCell.data.plot[].folder", e);
+      if (!sampleName)
+        throw `singlecell.sample: cannot derive sample name from file name ${fn}`;
+      const sid = ds.cohort.termdb.q.sampleName2id(sampleName);
+      if (sid == void 0)
+        throw `singlecell.sample: unknown sample name ${sampleName}`;
+      samples.set(sid, { sample: sampleName });
     }
   }
   if (S.sampleColumns) {
-    for (const term of S.sampleColumns) {
-      const s2v = ds.cohort.termdb.q.getAllValues4term(term.termid);
+    for (const { termid } of S.sampleColumns) {
+      const term = ds.cohort.termdb.q.termjsonByOneid(termid);
+      if (!term)
+        throw "unknown termid from singlecell.samples.sampleColumns[]";
+      const s2v = ds.cohort.termdb.q.getAllValues4term(termid);
       for (const [sid, v] of s2v.entries()) {
         if (!samples.has(sid))
           continue;
-        samples.get(sid)[term.termid] = v;
+        samples.get(sid)[termid] = term.values?.[v]?.label || v;
       }
     }
   }