@sjcrh/proteinpaint-server 2.58.0-0 → 2.58.1-0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.58.0-0",
+  "version": "2.58.1-0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -61,7 +61,7 @@
   },
   "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";
@@ -136,7 +136,7 @@ async function validate_query_geneExpression(ds, genome) {
   const q = ds.queries.geneExpression;
   if (!q)
     return;
-  q.gene2density = {};
+  q.gene2bins = {};
   if (q.src == "gdcapi") {
     gdc_validate_query_geneExpression(ds, genome);
     return;

package/routes/termdb.getdescrstats.js

@@ -1,5 +1,5 @@
-import { get_rows_by_one_key } from "../src/termdb.sql.js";
 import Summarystats from "../shared/descriptive.stats.js";
+import { getData } from "#src/termdb.matrix.js";
 const api = {
   endpoint: "termdb/descrstats",
   methods: {
@@ -64,7 +64,7 @@ function init({ genomes }) {
       const tdb = ds.cohort.termdb;
       if (!tdb)
         throw "invalid termdb object";
-      await trigger_getdescrstats(q, res, ds);
+      await trigger_getdescrstats(q, res, ds, g);
     } catch (e) {
       res.send({ error: e?.message || e });
       if (e instanceof Error && e.stack)
@@ -72,20 +72,14 @@ function init({ genomes }) {
     }
   };
 }
-async function trigger_getdescrstats(q, res, ds) {
-  const term = ds.cohort.termdb.q.termjsonByOneid(q.tid);
-  if (!term)
-    throw "invalid termid";
-  if (term.type != "float" && term.type != "integer")
-    throw "not numerical term";
-  const rows = await get_rows_by_one_key({
-    ds,
-    key: q.tid,
-    filter: q.filter
-  });
+async function trigger_getdescrstats(q, res, ds, genome) {
+  const terms = [q.tw];
+  const data = await getData({ filter: q.filter, terms }, ds, genome);
   const values = [];
-  for (const { value } of rows) {
-    if (term.values?.[value]?.uncomputable) {
+  for (const key in data.samples) {
+    const sample = data.samples[key];
+    const value = sample[q.tw.$id].value;
+    if (q.tw.values?.[value]?.uncomputable) {
       continue;
     }
     if (q.settings?.violin?.unit === "log") {
@@ -93,7 +87,7 @@ async function trigger_getdescrstats(q, res, ds) {
         continue;
       }
     }
-    values.push(value);
+    values.push(parseFloat(value));
   }
   res.send(Summarystats(values));
 }

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 [];