@sjcrh/proteinpaint-server 2.58.0-0 → 2.58.0

package/package.json

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

package/routes/genesetOverrepresentation.js

@@ -46,7 +46,6 @@ async function run_genesetOverrepresentation_analysis(q, genomes) {
     if (line.startsWith("pathway_p_values:")) {
       result = JSON.parse(line.replace("pathway_p_values:", ""));
     } else {
-      console.log(line);
     }
   }
   return result;

package/routes/healthcheck.js

@@ -7,6 +7,19 @@ const api = {
         return async (req, res) => {
           try {
             const health = await getStat(genomes);
+            const q = req.query;
+            if (q.dslabel) {
+              for (const gn in genomes) {
+                const ds = genomes[gn]?.datasets?.[q.dslabel];
+                if (!ds?.getHealth)
+                  continue;
+                if (!health.byDataset)
+                  health.byDataset = {};
+                if (!health.byDataset[q.dslabel])
+                  health.byDataset[q.dslabel] = {};
+                health.byDataset[q.dslabel][gn] = ds.getHealth(ds);
+              }
+            }
             res.send(health);
           } catch (e) {
             res.send({ status: "error", error: e.message || e });

package/routes/termdb.cluster.js

@@ -32,7 +32,7 @@ function init({ genomes }) {
       if (!ds)
         throw "invalid dataset name";
       if (ds.__gdc && !ds.__gdc.doneCaching)
-        throw "The server has not finished caching the case IDs: try again in ~2 minutes";
+        throw "The server has not finished caching the case IDs: try again in about 2 minutes.";
       if (q.dataType == dtgeneexpression) {
         if (!ds.queries?.geneExpression)
           throw "no geneExpression data on this dataset";

package/routes/termdb.topVariablyExpressedGenes.js

@@ -110,7 +110,7 @@ function gdcValidateQuery(ds, genome) {
       return serverconfig.features.gdcGenes;
     }
     if (!ds.__gdc.doneCaching)
-      throw "The server has not finished caching the case IDs: try again in ~2 minutes";
+      throw "The server has not finished caching the case IDs: try again in about 2 minutes.";
     const caseLst = await gdcGetCasesWithExpressionDataFromCohort(q, ds);
     if (caseLst.length == 0) {
       return [];