@sjcrh/proteinpaint-server 2.98.0 → 2.98.1-0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.98.0",
+  "version": "2.98.1-0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -61,7 +61,7 @@
     "@sjcrh/augen": "2.87.0",
     "@sjcrh/proteinpaint-rust": "2.84.0",
     "@sjcrh/proteinpaint-shared": "2.98.0",
-    "@sjcrh/proteinpaint-types": "2.98.0",
+    "@sjcrh/proteinpaint-types": "2.98.1-0",
     "better-sqlite3": "^9.4.1",
     "body-parser": "^1.15.2",
     "canvas": "~2.11.2",

package/routes/termdb.config.js

@@ -27,7 +27,7 @@ function init({ genomes }) {
       if (!genome)
         throw "invalid genome";
       const [ds] = get_ds_tdb(genome, q);
-      return make(q, res, ds, genome);
+      return make(q, req, res, ds, genome);
     } catch (e) {
       res.send({ error: e.message || e });
       if (e.stack)
@@ -37,13 +37,12 @@ function init({ genomes }) {
     }
   };
 }
-function make(q, res, ds, genome) {
+function make(q, req, res, ds, genome) {
   const tdb = ds.cohort.termdb;
-  const auth = { embedder: q.embedder };
   const c = {
     selectCohort: tdb.selectCohort,
     // optional
-    supportedChartTypes: tdb.q?.getSupportedChartTypes(auth),
+    supportedChartTypes: tdb.q?.getSupportedChartTypes(req),
     renamedChartTypes: ds.cohort.renamedChartTypes,
     allowedTermTypes: getAllowedTermTypes(ds),
     termMatch2geneSet: tdb.termMatch2geneSet,
@@ -68,8 +67,6 @@ function make(q, res, ds, genome) {
     c.plotConfigByCohort = tdb.plotConfigByCohort;
   if (tdb.multipleTestingCorrection)
     c.multipleTestingCorrection = tdb.multipleTestingCorrection;
-  if (tdb.neuroOncRegression)
-    c.neuroOncRegression = tdb.neuroOncRegression;
   if (tdb.helpPages)
     c.helpPages = tdb.helpPages;
   if (tdb.minTimeSinceDx)
@@ -90,15 +87,19 @@ function make(q, res, ds, genome) {
     c.excludedTermtypeByTarget = tdb.excludedTermtypeByTarget;
   if (tdb.survival)
     c.survival = tdb.survival;
+  if (tdb.regression)
+    c.regression = tdb.regression;
   if (ds.assayAvailability)
     c.assayAvailability = ds.assayAvailability;
   if (ds.customTwQByType)
     c.customTwQByType = ds.customTwQByType;
-  c.requiredAuth = authApi.getRequiredCredForDsEmbedder(q.dslabel, q.embedder);
   addRestrictAncestries(c, tdb);
   addScatterplots(c, ds);
   addMatrixplots(c, ds);
   addNonDictionaryQueries(c, ds, genome);
+  c.requiredAuth = authApi.getRequiredCredForDsEmbedder(q.dslabel, q.embedder);
+  const info = authApi.getNonsensitiveInfo(req);
+  c.clientAuthResult = info.clientAuthResult || {};
   res.send({ termdbConfig: c });
 }
 function addRestrictAncestries(c, tdb) {

package/routes/termdb.violin.js

@@ -122,7 +122,7 @@ function divideValues(q, data, sampleType) {
     key2values,
     min: absMin,
     max: absMax,
-    uncomputableValueObj: sortObj(uncomputableValues)
+    uncomputableValues: sortObj(uncomputableValues)
   };
 }
 function sortObj(object) {
@@ -148,16 +148,14 @@ function setResponse(valuesObject, data, q, sampleType) {
         seriesId: key,
         plotValueCount: values?.length,
         color: overlayTerm?.term?.values?.[key]?.color || null,
-        divideTwBins: isNumericTerm(overlayTerm.term) ? numericBins(overlayTerm, data) : null,
-        uncomputableValueObj: Object.keys(valuesObject.uncomputableValueObj).length > 0 ? valuesObject.uncomputableValueObj : null
+        divideTwBins: isNumericTerm(overlayTerm.term) ? numericBins(overlayTerm, data) : null
       });
     } else {
-      const plot = {
+      plots.push({
         label: sampleType,
         values,
         plotValueCount: values.length
-      };
-      plots.push(plot);
+      });
     }
   }
   const result = {
@@ -165,7 +163,7 @@ function setResponse(valuesObject, data, q, sampleType) {
     max: valuesObject.max,
     plots,
     pvalues: [],
-    uncomputableValueObj: Object.keys(valuesObject.uncomputableValueObj).length > 0 ? valuesObject.uncomputableValueObj : null
+    uncomputableValues: Object.keys(valuesObject.uncomputableValues).length > 0 ? valuesObject.uncomputableValues : null
   };
   return result;
 }
@@ -222,9 +220,8 @@ function createCanvasImg(q, result, ds) {
         ctx.stroke();
       });
     plot.src = canvas.toDataURL();
-    const isKDE = q.isKDE;
-    plot.density = getBinsDensity(axisScale, plot, isKDE, q.ticks);
-    plot.summaryStats = summaryStats(plot.values);
+    plot.density = getBinsDensity(axisScale, plot, q.isKDE, q.ticks);
+    plot.summaryStats = summaryStats(plot.values).values;
     delete plot.values;
   }
 }