@sjcrh/proteinpaint-server 2.143.0 → 2.145.0

package/dataset/termdb.test.js

@@ -213,6 +213,42 @@ function termdb_test_default() {
       // small list of terms for sunburst rings
       sunburst_twLst: [{ id: "sex", q: {} }]
     },
+    assayAvailability: {
+      // term used below must be annotated on samples rather than patients(root). otherwise matrix will pull wrong samples for geneVariant term
+      byDt: {
+        // snvindel, differentiating sample origin
+        1: {
+          byOrigin: {
+            germline: {
+              term_id: "assayavailability_germline",
+              label: "Germline",
+              // human readable label of this origin
+              yes: { value: ["1"] },
+              no: { value: ["2"] }
+            },
+            somatic: {
+              term_id: "wgs_curated",
+              label: "Somatic",
+              yes: { value: ["1"] },
+              no: { value: ["0"] }
+              // the category doesn't exist in termdb but is still supplied since somatic.no{} is required
+            }
+          }
+        },
+        // fusion
+        2: {
+          term_id: "assayavailability_fusion",
+          yes: { value: ["1"] },
+          no: { value: ["2"] }
+        },
+        // cnv
+        4: {
+          term_id: "assayavailability_cnv",
+          yes: { value: ["1"] },
+          no: { value: ["2"] }
+        }
+      }
+    },
     queries: {
       snvindel: {
         forTrack: true,
@@ -312,42 +348,10 @@ function termdb_test_default() {
       WSImages: {
         type: "H&E",
         imageBySampleFolder: "files/hg38/TermdbTest/wsimages"
-      }
-    },
-    assayAvailability: {
-      // term used below must be annotated on samples rather than patients(root). otherwise matrix will pull wrong samples for geneVariant term
-      byDt: {
-        // snvindel, differentiating sample origin
-        1: {
-          byOrigin: {
-            germline: {
-              term_id: "assayavailability_germline",
-              label: "Germline",
-              // human readable label of this origin
-              yes: { value: ["1"] },
-              no: { value: ["2"] }
-            },
-            somatic: {
-              term_id: "wgs_curated",
-              label: "Somatic",
-              yes: { value: ["1"] },
-              no: { value: ["0"] }
-              // the category doesn't exist in termdb but is still supplied since somatic.no{} is required
-            }
-          }
-        },
-        // fusion
-        2: {
-          term_id: "assayavailability_fusion",
-          yes: { value: ["1"] },
-          no: { value: ["2"] }
-        },
-        // cnv
-        4: {
-          term_id: "assayavailability_cnv",
-          yes: { value: ["1"] },
-          no: { value: ["2"] }
-        }
+      },
+      trackLst: {
+        jsonFile: "files/hg38/TermdbTest/trackLst/facet.json",
+        activeTracks: ["bw 1", "bed 1"]
       }
     }
   };

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.143.0",
+  "version": "2.145.0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -61,11 +61,11 @@
   },
   "dependencies": {
     "@sjcrh/augen": "2.143.0",
-    "@sjcrh/proteinpaint-python": "2.143.0",
+    "@sjcrh/proteinpaint-python": "2.144.0",
     "@sjcrh/proteinpaint-r": "2.137.2-0",
-    "@sjcrh/proteinpaint-rust": "2.143.0",
+    "@sjcrh/proteinpaint-rust": "2.145.0",
     "@sjcrh/proteinpaint-shared": "2.143.0",
-    "@sjcrh/proteinpaint-types": "2.143.0",
+    "@sjcrh/proteinpaint-types": "2.145.0",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^9.4.1",

package/routes/gdc.grin2.run.js

@@ -48,7 +48,11 @@ async function runGrin2(genomes, req, res) {
   const pyInput = {
     genedb: path.join(serverconfig.tpmasterdir, g.genedb.dbfile),
     chromosomelist: {},
-    lesion: ""
+    lesion: "",
+    devicePixelRatio: parsedRequest.devicePixelRatio || 2,
+    plot_width: parsedRequest.plot_width || 1e3,
+    plot_height: parsedRequest.plot_height || 400,
+    pngDotRadius: parsedRequest.pngDotRadius || 2
   };
   for (const c in g.majorchr) {
     if (ds.queries.singleSampleMutation?.discoPlot?.skipChrM) {
@@ -89,6 +93,7 @@ async function runGrin2(genomes, req, res) {
   const topGeneTable = resultData.topGeneTable || null;
   const totalProcessTime = downloadTimeToPrint + grin2AnalysisTimeToPrint;
   return res.json({
+    resultData,
     pngImg,
     topGeneTable,
     rustResult: parsedRustResult,

package/routes/grin2.js

@@ -75,9 +75,11 @@ async function runGrin2(g, ds, request) {
     chromosomelist: {},
     lesion: JSON.stringify(lesions),
     devicePixelRatio: request.devicePixelRatio,
-    plot_width: request.plot_width,
-    plot_height: request.plot_height
+    pngDotRadius: request.pngDotRadius,
+    width: request.width,
+    height: request.height
   };
+  mayLog("[GRIN2] Prepared input for Python script:", { ...pyInput });
   for (const c in g.majorchr) {
     if (ds.queries.singleSampleMutation.discoPlot?.skipChrM) {
       if (c.toLowerCase() == "chrm") continue;