@sjcrh/proteinpaint-server 2.123.0 → 2.124.0

package/dataset/termdb.test.js

@@ -5,6 +5,9 @@ copyDataFilesFromRepo2Tp();
 function termdb_test_default() {
   return {
     isMds3: true,
+    isSupportedChartOverride: {
+      runChart: () => true
+    },
     cohort: {
       massNav: {
         tabs: {
@@ -123,16 +126,6 @@ function termdb_test_default() {
         ]
       }
     },
-    customTwQByType: {
-      // dataset-specific termsetting configs on certain term types
-      geneVariant: {
-        default: { cnvGainCutoff: 0.1, cnvLossCutoff: -0.1, cnvMaxLength: 0 },
-        byGene: {
-          // key is term.name, thus possible to use non-gene names e.g. C19MC
-          MYCN: { cnvGainCutoff: 0.5, cnvLossCutoff: -0.1, cnvMaxLength: 0 }
-        }
-      }
-    },
     variant2samples: {
       variantkey: "ssm_id",
       // required, tells client to return ssm_id for identifying variants

package/genome/hg38.js

@@ -14,6 +14,19 @@ var hg38_default = {
         termdb: {
           isGeneSetTermdb: true
         }
+      },
+      analysisGenesetGroups: [
+        { label: "-", value: "-" },
+        { label: "BP: subset of GO", value: "BP: subset of GO" },
+        { label: "MF: subset of GO", value: "MF: subset of GO" },
+        { label: "CC: subset of GO", value: "CC: subset of GO" },
+        { label: "WikiPathways subset of CP", value: "WikiPathways subset of CP" },
+        { label: "REACTOME subset of CP", value: "REACTOME subset of CP" },
+        { label: "H: hallmark gene sets", value: "H: hallmark gene sets" }
+      ],
+      geneORAparam: {
+        minCutoff: 15,
+        maxCutoff: 500
       }
     }
   },

package/genome/hg38.test.js

@@ -13,6 +13,14 @@ const genome = {
         termdb: {
           isGeneSetTermdb: true
         }
+      },
+      analysisGenesetGroups: [
+        { label: "-", value: "-" },
+        { label: "H: hallmark gene sets", value: "H: hallmark gene sets" }
+      ],
+      geneORAparam: {
+        minCutoff: 0,
+        maxCutoff: 500
       }
     }
   },

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.123.0",
+  "version": "2.124.0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -68,9 +68,9 @@
     "@sjcrh/augen": "2.121.0",
     "@sjcrh/proteinpaint-python": "2.118.0",
     "@sjcrh/proteinpaint-r": "2.123.0",
-    "@sjcrh/proteinpaint-rust": "2.123.0",
-    "@sjcrh/proteinpaint-shared": "2.121.0",
-    "@sjcrh/proteinpaint-types": "2.123.0",
+    "@sjcrh/proteinpaint-rust": "2.124.0",
+    "@sjcrh/proteinpaint-shared": "2.124.0",
+    "@sjcrh/proteinpaint-types": "2.124.0",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^9.4.1",

package/routes/genesetOverrepresentation.js

@@ -42,13 +42,7 @@ async function run_genesetOverrepresentation_analysis(q, genomes) {
   const rust_output = await run_rust("genesetORA", JSON.stringify(gene_overrepresentation_input_type));
   const time2 = (/* @__PURE__ */ new Date()).valueOf();
   console.log("Time taken to run rust gene over representation pipeline:", time2 - time1, "ms");
-  let result;
-  for (const line of rust_output.split("\n")) {
-    if (line.startsWith("pathway_p_values:")) {
-      result = JSON.parse(line.replace("pathway_p_values:", ""));
-    } else {
-    }
-  }
+  const result = JSON.parse(rust_output);
   return result;
 }
 export {

package/routes/genomes.js

@@ -93,7 +93,11 @@ function clientcopy_genome(genomename, genomes) {
   if (g.termdbs) {
     g2.termdbs = {};
     for (const k in g.termdbs) {
-      g2.termdbs[k] = { label: g.termdbs[k].label };
+      g2.termdbs[k] = {
+        label: g.termdbs[k].label,
+        analysisGenesetGroups: g.termdbs[k].analysisGenesetGroups,
+        geneORAparam: g.termdbs[k].geneORAparam
+      };
     }
   }
   for (const dsname in g.datasets) {

package/routes/termdb.config.js

@@ -89,8 +89,6 @@ function make(q, req, res, ds, genome) {
     c.regression = tdb.regression;
   if (ds.assayAvailability)
     c.assayAvailability = ds.assayAvailability;
-  if (ds.customTwQByType)
-    c.customTwQByType = ds.customTwQByType;
   if (ds.cohort.correlationVolcano)
     c.correlationVolcano = ds.cohort.correlationVolcano;
   c.requiredAuth = authApi.getRequiredCredForDsEmbedder(q.dslabel, q.embedder);