@sjcrh/proteinpaint-server 2.138.3-4 → 2.138.3-7

package/dataset/protected.test.js

@@ -1,10 +1,14 @@
 import termdbTestInit from "./termdb.test.js";
+const minSampleSize = 10;
 function protected_test_default() {
   const ds = termdbTestInit();
   if (!ds.cohort)
     ds.cohort = { termdb: {} };
-  ds.cohort.termdb.hasMinSampleSize = (sampleCount) => {
-    return sampleCount >= 10;
+  ds.cohort.termdb.checkAccessToSampleData = (_, data) => {
+    return {
+      minSampleSize,
+      canAccess: data.sampleCount >= minSampleSize
+    };
   };
   return ds;
 }

package/dataset/termdb.test.js

@@ -114,10 +114,11 @@ function termdb_test_default() {
                   name: "Demographics",
                   plots: [
                     {
-                      chartType: "barchart",
-                      settings: { barchart: { colorBars: true, showPercent: true } },
+                      chartType: "violin",
+                      settings: { violin: { showStats: false } },
                       term: {
-                        id: "agedx"
+                        id: "agedx",
+                        q: { mode: "continuous" }
                       }
                     },
                     {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.138.3-4",
+  "version": "2.138.3-7",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -62,9 +62,9 @@
     "@sjcrh/augen": "2.136.0",
     "@sjcrh/proteinpaint-python": "2.135.2-0",
     "@sjcrh/proteinpaint-r": "2.137.2-0",
-    "@sjcrh/proteinpaint-rust": "2.137.2-0",
-    "@sjcrh/proteinpaint-shared": "2.137.3",
-    "@sjcrh/proteinpaint-types": "2.138.3-4",
+    "@sjcrh/proteinpaint-rust": "2.138.3-7",
+    "@sjcrh/proteinpaint-shared": "2.138.3-7",
+    "@sjcrh/proteinpaint-types": "2.138.3-7",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^9.4.1",

package/routes/termdb.config.js

@@ -265,10 +265,12 @@ function getAllowedTermTypes(ds) {
     for (const t of ds.cohort.termdb.allowedTermTypes)
       typeSet.add(t);
   }
-  if (ds?.queries?.geneExpression)
+  if (ds.queries?.geneExpression)
     typeSet.add(TermTypes.GENE_EXPRESSION);
-  if (ds?.queries?.metaboliteIntensity)
+  if (ds.queries?.metaboliteIntensity)
     typeSet.add(TermTypes.METABOLITE_INTENSITY);
+  if (ds.queries?.ssGSEA)
+    typeSet.add(TermTypes.SSGSEA);
   return [...typeSet];
 }
 function getSelectCohort(ds, req) {

package/routes/termdb.filterTermValues.js

@@ -21,34 +21,30 @@ function init({ genomes }) {
       if (!g)
         throw "invalid genome name";
       const ds = g.datasets?.[req.query.dslabel];
-      getFilters(req.query, ds, res);
+      res.send(await getFilters(req.query, ds));
     } catch (e) {
-      console.log(e);
+      if (e.stack)
+        console.log(e.stack);
       res.send({ status: "error", error: e.message || e });
     }
   };
 }
-async function getFilters(query, ds, res) {
+async function getFilters(query, ds) {
   if (!query.filterByUserSites)
     authApi.mayAdjustFilter(query, ds, query.terms);
-  try {
-    const samplesPerFilter = await getSamplesPerFilter(query, ds);
-    const filtersData = await getData(
-      {
-        terms: query.terms,
-        __protected__: query.__protected__
-      },
-      ds
-    );
-    const tw2List = {};
-    for (const tw of query.terms) {
-      tw2List[tw.term.id] = getList(samplesPerFilter, filtersData, tw, query.showAll);
-    }
-    res.send({ ...tw2List });
-  } catch (e) {
-    console.log(e);
-    res.send({ error: e.message || e });
+  const samplesPerFilter = await getSamplesPerFilter(query, ds);
+  const filtersData = await getData(
+    {
+      terms: query.terms,
+      __protected__: query.__protected__
+    },
+    ds
+  );
+  const tw2List = {};
+  for (const tw of query.terms) {
+    tw2List[tw.term.id] = getList(samplesPerFilter, filtersData, tw, query.showAll);
   }
+  return { ...tw2List };
 }
 function getList(samplesPerFilter, filtersData, tw, showAll) {
   const values = Object.values(tw.term.values);