@sjcrh/proteinpaint-server 2.82.0 → 2.83.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.82.0",
+  "version": "2.83.0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -43,7 +43,7 @@
     "@babel/preset-env": "^7.9.6",
     "@babel/preset-typescript": "^7.21.4",
     "@babel/register": "^7.14.5",
-    "@sjcrh/proteinpaint-types": "2.82.0",
+    "@sjcrh/proteinpaint-types": "2.83.0",
     "@types/node": "^20.11.24",
     "@types/tough-cookie": "^4.0.5",
     "@typescript-eslint/eslint-plugin": "^5.60.0",
@@ -64,7 +64,7 @@
   "dependencies": {
     "@sjcrh/augen": "2.46.0",
     "@sjcrh/proteinpaint-rust": "2.81.5",
-    "@sjcrh/proteinpaint-shared": "2.79.4",
+    "@sjcrh/proteinpaint-shared": "2.83.0",
     "better-sqlite3": "^9.4.1",
     "body-parser": "^1.15.2",
     "canvas": "~2.11.2",

package/routes/termdb.cluster.js

@@ -6,7 +6,8 @@ import { gdc_validate_query_geneExpression } from "#src/mds3.gdc.js";
 import { mayLimitSamples } from "#src/mds3.filter.js";
 import { clusterMethodLst, distanceMethodLst } from "#shared/clustering.js";
 import { getResult as getResultGene } from "#src/gene.js";
-import { TermTypes } from "#shared/terms.js";
+import { TermTypes, NUMERIC_DICTIONARY_TERM } from "#shared/terms.js";
+import { getData } from "#src/termdb.matrix.js";
 const api = {
   endpoint: "termdb/cluster",
   methods: {
@@ -34,8 +35,8 @@ function init({ genomes }) {
         throw "invalid dataset name";
       if (ds.__gdc && !ds.__gdc.doneCaching)
         throw "The server has not finished caching the case IDs: try again in about 2 minutes.";
-      if (q.dataType == TermTypes.GENE_EXPRESSION || q.dataType == TermTypes.METABOLITE_INTENSITY) {
-        if (!ds.queries?.[q.dataType])
+      if ([TermTypes.GENE_EXPRESSION, TermTypes.METABOLITE_INTENSITY, NUMERIC_DICTIONARY_TERM].includes(q.dataType)) {
+        if (!ds.queries?.[q.dataType] && q.dataType !== NUMERIC_DICTIONARY_TERM)
           throw `no ${q.dataType} data on this dataset`;
         if (!q.terms)
           throw `missing gene list`;
@@ -43,7 +44,7 @@ function init({ genomes }) {
           throw `gene list is not an array`;
         if (q.terms.length < 3)
           throw `A minimum of three genes is required for clustering. Please refresh this page to clear this error.`;
-        result = await getResult(q, ds);
+        result = await getResult(q, ds, g);
       } else {
         throw "unknown q.dataType " + q.dataType;
       }
@@ -58,13 +59,20 @@ function init({ genomes }) {
     res.send(result);
   };
 }
-async function getResult(q, ds) {
+async function getResult(q, ds, genome) {
   let _q = q;
   if (q.dataType == TermTypes.GENE_EXPRESSION) {
     _q = JSON.parse(JSON.stringify(q));
     _q.forClusteringAnalysis = true;
   }
-  const { term2sample2value, byTermId, bySampleId } = await ds.queries[q.dataType].get(_q);
+  let term2sample2value, byTermId, bySampleId;
+  if (q.dataType == NUMERIC_DICTIONARY_TERM) {
+    ;
+    ({ term2sample2value, byTermId, bySampleId } = await getNumericDictTermAnnotation(q, ds, genome));
+  } else {
+    ;
+    ({ term2sample2value, byTermId, bySampleId } = await ds.queries[q.dataType].get(_q));
+  }
   if (term2sample2value.size == 0)
     throw "no data";
   if (term2sample2value.size == 1) {
@@ -77,6 +85,25 @@ async function getResult(q, ds) {
     console.log("clustering done:", Date.now() - t, "ms");
   return { clustering, byTermId, bySampleId };
 }
+async function getNumericDictTermAnnotation(q, ds, genome) {
+  const getDataArgs = {
+    filter: q.filter,
+    terms: q.terms.map((term) => ({ term, q: { mode: "continuous" } }))
+  };
+  const data = await getData(getDataArgs, ds, genome);
+  const term2sample2value = /* @__PURE__ */ new Map();
+  for (const [key, sampleData] of Object.entries(data.samples)) {
+    for (const [term, value] of Object.entries(sampleData)) {
+      if (term !== "sample") {
+        if (!term2sample2value.has(term)) {
+          term2sample2value.set(term, {});
+        }
+        term2sample2value.get(term)[key] = value.value;
+      }
+    }
+  }
+  return { term2sample2value, byTermId: data.refs.byTermId, bySampleId: data.refs.bySampleId };
+}
 async function doClustering(data, q, numCases = 1e3) {
   const sampleSet = /* @__PURE__ */ new Set();
   for (const o of data.values()) {

package/routes/termdb.config.js

@@ -52,6 +52,7 @@ function make(q, res, ds, genome) {
     dataDownloadCatch: tdb.dataDownloadCatch,
     matrix: tdb.matrix,
     hierCluster: tdb.hierCluster,
+    numericDictTermCluster: tdb.numericDictTermCluster,
     mclass: tdb.mclass,
     alwaysRefillCategoricalTermValues: tdb.alwaysRefillCategoricalTermValues,
     isGeneSetTermdb: tdb.isGeneSetTermdb,