@sjcrh/proteinpaint-server 2.58.1-0 → 2.60.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.58.1-0",
+  "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": "2.58.0",
+    "@sjcrh/proteinpaint-rust": "2.60.0",
     "better-sqlite3": "^9.4.1",
     "body-parser": "^1.15.2",
     "canvas": "~2.11.2",

package/routes/termdb.categories.js

@@ -19,14 +19,7 @@ const api = {
               dslabel: "TermdbTest",
               embedder: "localhost",
               getcategories: 1,
-              tid: "diaggrp",
-              term1_q: {
-                isAtomic: true,
-                hiddenValues: {},
-                type: "values",
-                groupsetting: { disabled: true },
-                mode: "discrete"
-              },
+              term: { id: "diaggrp" },
               filter: {
                 type: "tvslst",
                 in: true,
@@ -85,22 +78,8 @@ function init({ genomes }) {
   };
 }
 async function trigger_getcategories(q, res, tdb, ds, genome) {
-  if (!q.tid)
-    throw ".tid missing";
-  let term;
-  if (q.type == "geneVariant") {
-    term = { id: q.name, name: q.name, type: "geneVariant", isleaf: true };
-    if (q.gene) {
-      term.gene = q.gene;
-    } else {
-      term.chr = q.chr;
-      term.start = q.start;
-      term.stop = q.stop;
-    }
-  } else {
-    term = tdb.q.termjsonByOneid(q.tid);
-  }
-  const tw = q.type == "geneVariant" ? { $id: q.gene || q.name || q.tid, term, q: { isAtomic: true } } : { $id: q.tid, id: q.tid, term, q: q.term1_q || getDefaultQ(term, q) };
+  const $id = Math.random().toString();
+  const tw = { $id, term: q.term, q: q.term1_q || getDefaultQ(q.term, q) };
   const arg = {
     filter: q.filter,
     terms: [tw],
@@ -113,7 +92,7 @@ async function trigger_getcategories(q, res, tdb, ds, genome) {
   if (data.error)
     throw data.error;
   const lst = [];
-  if (q.type == "geneVariant") {
+  if (q.term.type == "geneVariant") {
     const samples = data.samples;
     const dtClassMap = /* @__PURE__ */ new Map();
     if (ds.assayAvailability?.byDt) {
@@ -125,7 +104,7 @@ async function trigger_getcategories(q, res, tdb, ds, genome) {
     }
     const sampleCountedFor = /* @__PURE__ */ new Set();
     for (const [sampleId, sampleData] of Object.entries(samples)) {
-      const key = tw.$id;
+      const key = $id;
       const values = sampleData[key].values;
       sampleCountedFor.clear();
       for (const value of values) {
@@ -163,7 +142,7 @@ async function trigger_getcategories(q, res, tdb, ds, genome) {
   } else {
     const key2count = /* @__PURE__ */ new Map();
     for (const sid in data.samples) {
-      const v = data.samples[sid][q.tid];
+      const v = data.samples[sid][$id];
       if (!v)
         continue;
       if (!("key" in v))
@@ -174,14 +153,14 @@ async function trigger_getcategories(q, res, tdb, ds, genome) {
       lst.push({
         samplecount: count,
         key,
-        label: data.refs?.byTermId?.[q.tid]?.events?.find((e) => e.event === key).label || term?.values?.[key]?.label || key
+        label: data.refs?.byTermId?.[$id]?.events?.find((e) => e.event === key).label || q.term?.values?.[key]?.label || key
       });
     }
   }
   const orderedLabels = getOrderedLabels(
-    term,
-    data.refs?.byTermId?.[q.tid]?.bins || [],
-    data.refs?.byTermId?.[q.tid]?.events,
+    q.term,
+    data.refs?.byTermId?.[$id]?.bins || [],
+    data.refs?.byTermId?.[$id]?.events,
     q.term1_q
   );
   if (orderedLabels.length) {

package/routes/termdb.cluster.js

@@ -6,6 +6,7 @@ import { gdc_validate_query_geneExpression } from "#src/mds3.gdc.js";
 import { mayLimitSamples } from "#src/mds3.filter.js";
 import { dtgeneexpression } from "#shared/common.js";
 import { clusterMethodLst, distanceMethodLst } from "#shared/clustering.js";
+import { getResult as getResultGene } from "#src/gene.js";
 const api = {
   endpoint: "termdb/cluster",
   methods: {
@@ -136,7 +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;
@@ -168,7 +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);
@@ -191,13 +191,15 @@ async function validateNative(q, ds, genome) {
       if (!g.gene)
         continue;
       if (!g.chr) {
-        const lst = genome.genedb.getjsonbyname.all(g.gene);
-        if (lst.length == 0)
+        const re = getResultGene(genome, { input: g.gene, deep: 1 });
+        if (!re.gmlst || re.gmlst.length == 0) {
+          console.warn("unknown gene:" + g.gene);
           continue;
-        const j = JSON.parse(lst.find((i) => i.isdefault).genemodel || lst[0].genemodel);
-        g.start = j.start;
-        g.stop = j.stop;
-        g.chr = j.chr;
+        }
+        const i = re.gmlst.find((i2) => i2.isdefault) || re.gmlst[0];
+        g.start = i.start;
+        g.stop = i.stop;
+        g.chr = i.chr;
       }
       const s2v = {};
       await utils.get_lines_bigfile({
@@ -224,6 +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

@@ -75,11 +75,13 @@ function init({ genomes }) {
 async function trigger_getdescrstats(q, res, ds, genome) {
   const terms = [q.tw];
   const data = await getData({ filter: q.filter, terms }, ds, genome);
+  if (data.error)
+    throw data.error;
   const values = [];
   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") {