@sjcrh/proteinpaint-server 2.53.0 → 2.55.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.53.0",
+  "version": "2.55.0",
   "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": "2.49.0",
+    "@sjcrh/proteinpaint-rust": "2.55.0",
     "better-sqlite3": "^9.4.1",
     "body-parser": "^1.15.2",
     "canvas": "~2.11.2",

package/routes/gdc.maf.js

@@ -73,6 +73,8 @@ async function listMafFiles(q, ds) {
       "file_size",
       "cases.project.project_id",
       // for display only
+      "cases.case_id",
+      // case uuid for making case url link to portal
       "cases.submitter_id",
       // used when listing all cases & files
       "cases.samples.sample_type"
@@ -100,9 +102,10 @@ async function listMafFiles(q, ds) {
     const file = {
       id: h.id,
       project_id: c.project.project_id,
-      file_size: h.file_size
+      file_size: h.file_size,
+      case_submitter_id: c.submitter_id,
+      case_uuid: c.case_id
     };
-    file.case_submitter_id = c.submitter_id;
     if (c.samples) {
       file.sample_types = c.samples.map((i) => i.sample_type).sort();
     }

package/routes/gdc.topMutatedGenes.js

@@ -1,5 +1,5 @@
 import { mclasscnvgain, mclasscnvloss, dtsnvindel } from "#shared/common.js";
-import got from "got";
+import ky from "ky";
 const api = {
   endpoint: "gdc/topMutatedGenes",
   methods: {
@@ -29,6 +29,10 @@ function init({ genomes }) {
       res.send(payload);
     } catch (e) {
       res.send({ status: "error", error: e.message || e });
+      if (e.stack)
+        console.log(e.stack);
+      else
+        console.trace(e);
     }
   };
 }
@@ -232,11 +236,12 @@ async function getGenesGraphql(q, ds) {
   const { host, headers } = ds.getHostHeaders(q);
   const query = queryV2.query;
   const variables = queryV2.getVariables(q);
-  const response = await got.post(host.graphql, {
+  const re = await ky.post(host.graphql, {
+    timeout: false,
+    // do not let ky timeout
     headers,
-    body: JSON.stringify({ query, variables })
-  });
-  const re = JSON.parse(response.body);
+    json: { query, variables }
+  }).json();
   const genes = [];
   for (const g of re.data.genesTableViewer.explore.genes.hits.edges) {
     if (typeof g.node != "object")

package/routes/termdb.cluster.js

@@ -5,6 +5,7 @@ import serverconfig from "#src/serverconfig.js";
 import { gdc_validate_query_geneExpression } from "#src/mds3.gdc.js";
 import { mayLimitSamples } from "#src/mds3.filter.js";
 import { dtgeneexpression } from "#shared/common.js";
+import { clusterMethodLst, distanceMethodLst } from "#shared/clustering.js";
 const api = {
   endpoint: "termdb/cluster",
   methods: {
@@ -71,6 +72,10 @@ async function doClustering(data, q) {
       sampleSet.add(s);
     break;
   }
+  if (!clusterMethodLst.find((i) => i.value == q.clusterMethod))
+    throw "Invalid cluster method";
+  if (!distanceMethodLst.find((i) => i.value == q.distanceMethod))
+    throw "Invalid distance method";
   const inputData = {
     matrix: [],
     row_names: [],
@@ -78,6 +83,7 @@ async function doClustering(data, q) {
     col_names: [...sampleSet],
     // samples
     cluster_method: q.clusterMethod,
+    distance_method: q.distanceMethod,
     plot_image: false
     // When true causes cluster.rs to plot the image into a png file (EXPERIMENTAL)
   };

package/routes/termdb.config.js

@@ -25,7 +25,7 @@ function init({ genomes }) {
       const genome = genomes[q.genome];
       if (!genome)
         throw "invalid genome";
-      const [ds, tdb] = get_ds_tdb(genome, q);
+      const [ds] = get_ds_tdb(genome, q);
       return make(q, res, ds, genome);
     } catch (e) {
       res.send({ error: e.message || e });
@@ -105,7 +105,8 @@ function addScatterplots(c, ds) {
       colorColumn: p.colorColumn,
       sampleType: p.sampleType,
       coordsColumns: p.coordsColumns,
-      settings: p.settings
+      settings: p.settings,
+      sampleCategory: p.sampleCategory
     };
   });
 }
@@ -131,6 +132,9 @@ function addGenomicQueries(c, ds, genome) {
       allowSNPs: q.snvindel.allowSNPs
     };
   }
+  if (q.svfusion) {
+    q2.svfusion = {};
+  }
   if (q.cnv) {
     q2.cnv = {};
     for (const k of [
@@ -145,6 +149,11 @@ function addGenomicQueries(c, ds, genome) {
         q2.cnv[k] = q.cnv[k];
     }
   }
+  if (q.geneCnv) {
+    if (!q2.cnv) {
+      q2.cnv = {};
+    }
+  }
   if (q.topMutatedGenes)
     q2.topMutatedGenes = q.topMutatedGenes;
   if (q.topVariablyExpressedGenes)