@sjcrh/proteinpaint-server 2.137.2-0 → 2.137.2-2

package/dataset/termdb.test.js

@@ -141,7 +141,7 @@ function termdb_test_default() {
                     {
                       chartType: "barchart",
                       term: { id: "diaggrp" },
-                      settings: { barchart: { colorBars: true, showPercent: true } }
+                      settings: { barchart: { colorBars: true, showPercent: true, colorUsing: "generated" } }
                     }
                   ]
                 },

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.137.2-0",
+  "version": "2.137.2-2",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -63,8 +63,8 @@
     "@sjcrh/proteinpaint-python": "2.135.2-0",
     "@sjcrh/proteinpaint-r": "2.137.2-0",
     "@sjcrh/proteinpaint-rust": "2.137.2-0",
-    "@sjcrh/proteinpaint-shared": "2.137.1",
-    "@sjcrh/proteinpaint-types": "2.137.2-0",
+    "@sjcrh/proteinpaint-shared": "2.137.2-2",
+    "@sjcrh/proteinpaint-types": "2.137.2-2",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^9.4.1",

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.config.js

@@ -61,7 +61,8 @@ function make(q, req, res, ds, genome) {
     hasSampleAncestry: ds.cohort.termdb.hasSampleAncestry,
     defaultChartType: ds.cohort.defaultChartType,
     invalidTokenErrorHandling: tdb.invalidTokenErrorHandling,
-    colorMap: tdb.colorMap
+    colorMap: tdb.colorMap,
+    defaultTw4correlationPlot: tdb.defaultTw4correlationPlot
   };
   if (tdb.plotConfigByCohort)
     c.plotConfigByCohort = tdb.plotConfigByCohort;