@sjcrh/proteinpaint-server 2.132.1-4 → 2.133.1

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.132.1-4",
+  "version": "2.133.1",
   "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": "2.121.0",
-    "@sjcrh/proteinpaint-python": "2.132.1-4",
+    "@sjcrh/proteinpaint-python": "2.133.0",
     "@sjcrh/proteinpaint-r": "2.130.0",
-    "@sjcrh/proteinpaint-rust": "2.132.1-0",
+    "@sjcrh/proteinpaint-rust": "2.133.0",
     "@sjcrh/proteinpaint-shared": "2.132.1-2",
-    "@sjcrh/proteinpaint-types": "2.132.1-1",
+    "@sjcrh/proteinpaint-types": "2.133.0",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^9.4.1",

package/routes/gdc.grin2.run.js

@@ -2,7 +2,6 @@ import { runGRIN2Payload } from "#types/checkers";
 import { stream_rust } from "@sjcrh/proteinpaint-rust";
 import serverconfig from "#src/serverconfig.js";
 import path from "path";
-import { formatElapsedTime } from "@sjcrh/proteinpaint-shared/time.js";
 import { run_python } from "@sjcrh/proteinpaint-python";
 const api = {
   endpoint: "gdc/runGRIN2",
@@ -154,8 +153,9 @@ function init({ genomes }) {
         }
       }
       console.log("[GRIN2] Rust execution completed");
-      const downloadTime = formatElapsedTime(Date.now() - downloadStartTime);
-      console.log(`[GRIN2] Rust processing took ${downloadTime}`);
+      const downloadTime = Date.now() - downloadStartTime;
+      const downloadTimeToPrint = Math.round(downloadTime / 1e3);
+      console.log(`[GRIN2] Rust processing took ${downloadTimeToPrint}`);
       const rustResult = parseJsonlOutput(rustOutput);
       if (!rustResult) {
         throw new Error("Failed to process MAF files: No result from Rust");
@@ -199,8 +199,9 @@ function init({ genomes }) {
       }
       console.log("[GRIN2] python execution completed");
       console.log(`[GRIN2] Python stderr: ${pyResult.stderr}`);
-      const grin2AnalysisTime = formatElapsedTime(Date.now() - grin2AnalysisStart);
-      console.log(`[GRIN2] Rust processing took ${grin2AnalysisTime}`);
+      const grin2AnalysisTime = Date.now() - grin2AnalysisStart;
+      const grin2AnalysisTimeToPrint = Math.round(grin2AnalysisTime / 1e3);
+      console.log(`[GRIN2] Python processing took ${grin2AnalysisTimeToPrint}`);
       let resultData;
       try {
         resultData = JSON.parse(pyResult);
@@ -208,7 +209,7 @@ function init({ genomes }) {
         const pngImg = resultData.png[0];
         const topGeneTable = resultData.topGeneTable || null;
         const analysisStats = parsedRustResult.summary || {};
-        const totalProcessTime = formatElapsedTime(Date.now() - downloadStartTime);
+        const totalProcessTime = Math.round((downloadTime + grin2AnalysisTime) / 1e3);
         console.log("[GRIN2] Total GRIN2 processing time:", totalProcessTime);
         return res.json({
           pngImg,
@@ -216,8 +217,8 @@ function init({ genomes }) {
           rustResult: parsedRustResult,
           analysisStats,
           timing: {
-            rustProcessingTime: downloadTime,
-            grin2ProcessingTime: grin2AnalysisTime,
+            rustProcessingTime: downloadTimeToPrint,
+            grin2ProcessingTime: grin2AnalysisTimeToPrint,
             totalTime: totalProcessTime
           },
           status: "success"