@sjcrh/proteinpaint-server 2.59.0 → 2.60.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.59.0",
+  "version": "2.60.0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -61,7 +61,7 @@
   },
   "dependencies": {
     "@sjcrh/augen": "2.46.0",
-    "@sjcrh/proteinpaint-rust": "2.59.0",
+    "@sjcrh/proteinpaint-rust": "2.60.0",
     "better-sqlite3": "^9.4.1",
     "body-parser": "^1.15.2",
     "canvas": "~2.11.2",

package/routes/termdb.cluster.js

@@ -137,7 +137,7 @@ async function validate_query_geneExpression(ds, genome) {
   const q = ds.queries.geneExpression;
   if (!q)
     return;
-  q.gene2bins = {};
+  q.geneExpression2bins = {};
   if (q.src == "gdcapi") {
     gdc_validate_query_geneExpression(ds, genome);
     return;
@@ -169,7 +169,6 @@ async function validateNative(q, ds, genome) {
         throw "queries.geneExpression: unknown sample from header: " + l[i];
       q.samples.push(id);
     }
-    console.log(q.samples.length, "samples from geneExpression of", ds.label);
   }
   q.get = async (param) => {
     const limitSamples = await mayLimitSamples(param, q.samples, ds);
@@ -193,8 +192,10 @@ async function validateNative(q, ds, genome) {
         continue;
       if (!g.chr) {
         const re = getResultGene(genome, { input: g.gene, deep: 1 });
-        if (!re.gmlst || re.gmlst.length == 0)
-          throw "unknown gene";
+        if (!re.gmlst || re.gmlst.length == 0) {
+          console.warn("unknown gene:" + g.gene);
+          continue;
+        }
         const i = re.gmlst.find((i2) => i2.isdefault) || re.gmlst[0];
         g.start = i.start;
         g.stop = i.stop;
@@ -225,6 +226,8 @@ async function validateNative(q, ds, genome) {
         gene2sample2value.set(g.gene, s2v);
     }
     const byTermId = {};
+    if (gene2sample2value.size == 0)
+      throw "no data available for the input " + param.genes?.map((g) => g.gene).join(", ");
     return { gene2sample2value, byTermId, bySampleId };
   };
 }

package/routes/termdb.config.js

@@ -3,6 +3,7 @@ import { authApi } from "#src/auth.js";
 import { get_ds_tdb } from "#src/termdb.js";
 import { mayCopyFromCookie } from "#src/utils.js";
 import { mayComputeTermtypeByCohort } from "#src/termdb.server.init.js";
+import { TermTypes } from "#shared/terms.js";
 const api = {
   endpoint: "termdb/config",
   methods: {
@@ -168,6 +169,12 @@ function addGenomicQueries(c, ds, genome) {
       delete q2.singleSampleGenomeQuantification[k].folder;
     }
   }
+  if (q.NIdata) {
+    q2.NIdata = {};
+    for (const k in q.NIdata) {
+      q2.NIdata[k] = JSON.parse(JSON.stringify(q.NIdata[k]));
+    }
+  }
   if (q.singleSampleGbtk) {
     q2.singleSampleGbtk = {};
     for (const k in q.singleSampleGbtk) {
@@ -207,7 +214,9 @@ function getAllowedTermTypes(ds) {
     typeSet.add("geneVariant");
   }
   if (ds?.queries?.geneExpression)
-    typeSet.add("geneExpression");
+    typeSet.add(TermTypes.GENE_EXPRESSION);
+  if (ds?.queries?.metaboliteIntensity)
+    typeSet.add(TermTypes.METABOLITE_INTENSITY);
   return [...typeSet];
 }
 export {

package/routes/termdb.getdescrstats.js

@@ -81,7 +81,7 @@ async function trigger_getdescrstats(q, res, ds, genome) {
   for (const key in data.samples) {
     const sample = data.samples[key];
     const value = sample[q.tw.$id].value;
-    if (q.tw.values?.[value]?.uncomputable) {
+    if (q.tw.q.hiddenValues?.[value]) {
       continue;
     }
     if (q.settings?.violin?.unit === "log") {