@sjcrh/proteinpaint-server 2.131.0 → 2.132.1-0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.131.0",
+  "version": "2.132.1-0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -63,9 +63,9 @@
     "@sjcrh/augen": "2.121.0",
     "@sjcrh/proteinpaint-python": "2.118.0",
     "@sjcrh/proteinpaint-r": "2.130.0",
-    "@sjcrh/proteinpaint-rust": "2.130.0",
-    "@sjcrh/proteinpaint-shared": "2.129.6",
-    "@sjcrh/proteinpaint-types": "2.131.0",
+    "@sjcrh/proteinpaint-rust": "2.132.1-0",
+    "@sjcrh/proteinpaint-shared": "2.132.0",
+    "@sjcrh/proteinpaint-types": "2.132.1-0",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^9.4.1",

package/routes/gdc.grin2.list.js

@@ -29,14 +29,24 @@ function init({ genomes }) {
       const ds = g.datasets?.GDC;
       if (!ds)
         throw "hg38 GDC missing";
-      const result = {
-        files: [],
-        filesTotal: 0,
-        maxTotalSizeCompressed: 0,
-        fileCounts: { maf: 0 }
-      };
-      await mayListMafFiles(req.query, result, ds);
-      await mayListCnvFiles(req.query, result, ds);
+      console.log("GRIN2 List Route Received:", JSON.stringify(req.query, null, 2));
+      const result = {};
+      if (req.query.mafOptions) {
+        result.mafFiles = {
+          files: [],
+          filesTotal: 0,
+          maxTotalSizeCompressed: 0,
+          fileCounts: { maf: 0 }
+        };
+        await listMafFiles(req.query, result, ds);
+      }
+      if (req.query.cnvOptions) {
+        result.cnvFiles = {
+          files: [],
+          maxTotalSizeCompressed
+        };
+        await listCnvFiles(req.query, result, ds);
+      }
       res.send(result);
     } catch (e) {
       if (e.stack)
@@ -45,9 +55,12 @@ function init({ genomes }) {
     }
   };
 }
-async function mayListMafFiles(q, result, ds) {
+async function listMafFiles(q, result, ds) {
   if (!q.mafOptions)
     return;
+  if (!result.mafFiles) {
+    throw new Error("result.mafFiles must be initialized before calling listMafFiles");
+  }
   const filters = {
     op: "and",
     content: [
@@ -158,12 +171,12 @@ If you want to include it, please increase the maxFileSizeAllowed in the code.`
     );
   }
   deduplicatedFiles.sort((a, b) => b.file_size - a.file_size);
-  result.files.push(...deduplicatedFiles);
-  result.filesTotal = re.data.pagination.total;
-  if (result.fileCounts) {
-    result.fileCounts.maf = files.length;
+  result.mafFiles.files.push(...deduplicatedFiles);
+  result.mafFiles.filesTotal = re.data.pagination.total;
+  if (result.mafFiles.fileCounts) {
+    result.mafFiles.fileCounts.maf = files.length;
   }
-  result.deduplicationStats = {
+  result.mafFiles.deduplicationStats = {
     originalFileCount: files.length,
     deduplicatedFileCount: deduplicatedFiles.length,
     duplicatesRemoved,
@@ -171,8 +184,7 @@ If you want to include it, please increase the maxFileSizeAllowed in the code.`
     filteredFiles
   };
 }
-async function mayListCnvFiles(q, result, ds) {
-  result.cnvFiles = { files: [] };
+async function listCnvFiles(q, result, ds) {
   if (!q.cnvOptions) {
     console.log("No cnvOptions provided, returning empty cnvFiles");
     return;
@@ -240,11 +252,11 @@ async function mayListCnvFiles(q, result, ds) {
         cnvFiles.push(file);
       }
     }
-    result.cnvFiles = { files: cnvFiles };
+    result.cnvFiles = { files: cnvFiles, maxTotalSizeCompressed };
     console.log(`Successfully processed ${cnvFiles.length} CNV files`);
   } catch (error) {
     console.error("Error fetching CNV files:", error);
-    result.cnvFiles = { files: [] };
+    result.cnvFiles = { files: [], maxTotalSizeCompressed };
   }
 }
 export {

package/routes/gdc.grin2.run.js

@@ -21,13 +21,18 @@ function parseJsonlOutput(rustOutput) {
   const lines = rustOutput.trim().split("\n");
   const allSuccessfulData = [];
   let finalSummary = null;
+  let processedFiles = 0;
   for (const line of lines) {
     const trimmedLine = line.trim();
     if (trimmedLine) {
       try {
         const data = JSON.parse(trimmedLine);
         if (data.type === "data") {
+          processedFiles++;
           allSuccessfulData.push(data.data);
+          console.log(
+            `[GRIN2] Processed file ${processedFiles}: ${data.case_id} (${data.data_type}) - ${data.data.length} records`
+          );
         } else if (data.type === "summary") {
           finalSummary = data;
           console.log(`[GRIN2] Download complete: ${data.successful_files}/${data.total_files} files successful`);
@@ -55,7 +60,9 @@ function parseJsonlOutput(rustOutput) {
       filtered_records: finalSummary.filtered_records || 0,
       filtered_maf_records: finalSummary.filtered_maf_records || 0,
       filtered_cnv_records: finalSummary.filtered_cnv_records || 0,
-      filtered_records_by_case: finalSummary.filtered_records_by_case || {}
+      filtered_records_by_case: finalSummary.filtered_records_by_case || {},
+      included_maf_records: finalSummary.included_maf_records || 0,
+      included_cnv_records: finalSummary.included_cnv_records || 0
     }
   };
 }
@@ -74,8 +81,10 @@ function init({ genomes }) {
       console.log(`[GRIN2] Parsed request: ${JSON.stringify(parsedRequest)}`);
       const rustInput = JSON.stringify({
         caseFiles: parsedRequest.caseFiles,
-        mafOptions: parsedRequest.mafOptions
+        mafOptions: parsedRequest.mafOptions,
+        cnvOptions: parsedRequest.cnvOptions
       });
+      console.log(`[GRIN2] Rust input: ${rustInput}`);
       console.log("[GRIN2] Executing Rust function with streaming...");
       let rustOutput = "";
       let buffer = "";
@@ -144,10 +153,11 @@ function init({ genomes }) {
         // The mutation string from Rust
       });
       console.log("[GRIN2] Executing R script...");
-      const rAnalysisTime = Date.now();
+      const grin2AnalysisStart = Date.now();
       const rResult = await run_R("gdcGRIN2.R", rInput, []);
       console.log("[GRIN2] R execution completed");
-      console.log(`[GRIN2] R analysis took ${formatElapsedTime(Date.now() - rAnalysisTime)}`);
+      const grin2AnalysisTime = formatElapsedTime(Date.now() - grin2AnalysisStart);
+      console.log(`[GRIN2] Rust processing took ${grin2AnalysisTime}`);
       let resultData;
       try {
         resultData = JSON.parse(rResult);
@@ -155,12 +165,18 @@ function init({ genomes }) {
         const pngImg = resultData.png[0];
         const topGeneTable = resultData.topGeneTable || null;
         const analysisStats = parsedRustResult.summary || {};
-        console.log("[GRIN2] Total GRIN2 processing time:", formatElapsedTime(Date.now() - downloadStartTime));
+        const totalProcessTime = formatElapsedTime(Date.now() - downloadStartTime);
+        console.log("[GRIN2] Total GRIN2 processing time:", totalProcessTime);
         return res.json({
           pngImg,
           topGeneTable,
           rustResult: parsedRustResult,
           analysisStats,
+          timing: {
+            rustProcessingTime: downloadTime,
+            grin2ProcessingTime: grin2AnalysisTime,
+            totalTime: totalProcessTime
+          },
           status: "success"
         });
       } catch (parseError) {

package/routes/termdb.categories.js

@@ -41,6 +41,7 @@ async function trigger_getcategories(q, res, tdb, ds, genome) {
   const $id = q.tw.$id;
   const arg = {
     filter: q.filter,
+    filter0: q.filter0,
     terms: [q.tw],
     currentGeneNames: q.currentGeneNames,
     // optional, from mds3 mayAddGetCategoryArgs()