@sjcrh/proteinpaint-server 2.135.1 → 2.135.2

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.135.1",
+  "version": "2.135.2",
   "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": "2.135.0",
+    "@sjcrh/proteinpaint-python": "2.135.2-0",
     "@sjcrh/proteinpaint-r": "2.130.0",
-    "@sjcrh/proteinpaint-rust": "2.135.0",
-    "@sjcrh/proteinpaint-shared": "2.135.1",
-    "@sjcrh/proteinpaint-types": "2.135.0",
+    "@sjcrh/proteinpaint-rust": "2.135.2-0",
+    "@sjcrh/proteinpaint-shared": "2.135.2-0",
+    "@sjcrh/proteinpaint-types": "2.135.2-0",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^9.4.1",

package/routes/gdc.grin2.run.js

@@ -1,9 +1,10 @@
 import { runGRIN2Payload } from "#types/checkers";
-import { stream_rust } from "@sjcrh/proteinpaint-rust";
+import { run_rust } from "@sjcrh/proteinpaint-rust";
 import serverconfig from "#src/serverconfig.js";
 import path from "path";
 import { run_python } from "@sjcrh/proteinpaint-python";
 import { mayLog } from "#src/helpers.ts";
+const MAX_RECORD = 1e5;
 const api = {
   endpoint: "gdc/runGRIN2",
   methods: {
@@ -43,12 +44,13 @@ async function runGrin2(genomes, req, res) {
     caseFiles: parsedRequest.caseFiles,
     mafOptions: parsedRequest.mafOptions,
     cnvOptions: parsedRequest.cnvOptions,
-    chromosomes: []
+    chromosomes: [],
+    max_record: MAX_RECORD
   };
   const pyInput = {
     genedb: path.join(serverconfig.tpmasterdir, g.genedb.dbfile),
     chromosomelist: {},
-    lesion: []
+    lesion: ""
   };
   for (const c in g.majorchr) {
     if (ds.queries.singleSampleMutation?.discoPlot?.skipChrM) {
@@ -58,63 +60,33 @@ async function runGrin2(genomes, req, res) {
     rustInput.chromosomes.push(c);
     pyInput.chromosomelist[c] = g.majorchr[c];
   }
-  let rustOutput = "";
-  let buffer = "";
   const downloadStartTime = Date.now();
-  const streamResult = stream_rust("gdcGRIN2", JSON.stringify(rustInput), (errors) => {
-    if (errors) {
-      throw new Error(`Rust process failed: ${errors}`);
-    }
-  });
-  if (!streamResult) {
-    throw new Error("Failed to start Rust streaming process");
-  }
-  for await (const chunk of streamResult.rustStream) {
-    const chunkStr = chunk.toString();
-    rustOutput += chunkStr;
-    buffer += chunkStr;
-    const lines = buffer.split("\n");
-    buffer = lines.pop() || "";
-    for (const line of lines) {
-      const trimmedLine = line.trim();
-      if (trimmedLine) {
-        try {
-          const data = JSON.parse(trimmedLine);
-          if (data.type === "summary") {
-            mayLog(`[GRIN2] Download complete: ${data.successful_files}/${data.total_files} files successful`);
-            if (data.failed_files > 0) {
-              mayLog(`[GRIN2] ${data.failed_files} files failed`);
-            }
-          }
-        } catch (_parseError) {
-        }
-      }
-    }
-  }
+  const rustOutput = await run_rust("gdcGRIN2", JSON.stringify(rustInput));
   mayLog("[GRIN2] Rust execution completed");
   const downloadTime = Date.now() - downloadStartTime;
   const downloadTimeToPrint = Math.round(downloadTime / 1e3);
-  mayLog(`[GRIN2] Rust processing took ${downloadTimeToPrint}`);
-  const rustResult = parseJsonlOutput(rustOutput);
-  if (!rustResult) {
-    throw new Error("Failed to process MAF files: No result from Rust");
+  mayLog(`[GRIN2] Rust processing took ${downloadTimeToPrint} seconds`);
+  const parsedRustResult = parseRustOutput(rustOutput);
+  if (!parsedRustResult) {
+    throw new Error("Failed to process files: No result from Rust");
   }
-  const parsedRustResult = rustResult;
-  if (parsedRustResult.successful_data && Array.isArray(parsedRustResult.successful_data)) {
-    pyInput.lesion = parsedRustResult.successful_data.flat();
-    mayLog(`[GRIN2] Extracted ${pyInput.lesion.length} records for python script`);
+  if (parsedRustResult.successful_data !== void 0 && parsedRustResult.successful_data !== null) {
+    pyInput.lesion = parsedRustResult.successful_data;
+    mayLog(`[GRIN2] Extracted ${parsedRustResult.successful_data.length.toLocaleString()} characters for python script`);
     mayLog(
-      `[GRIN2] Success: ${parsedRustResult.summary.successful_files}, Failed: ${parsedRustResult.summary.failed_files}`
+      `[GRIN2] Success: ${parsedRustResult.summary.successful_files.toLocaleString()}, Failed: ${parsedRustResult.summary.failed_files.toLocaleString()}`
     );
   } else {
-    throw "Unexpected Rust result format";
+    throw "No successful data returned from Rust processing";
   }
   const grin2AnalysisStart = Date.now();
-  const pyResult = await run_python("gdcGRIN2.py", JSON.stringify(pyInput));
-  mayLog(`[GRIN2] Python stderr: ${pyResult.stderr}`);
+  const pyResult = await run_python("grin2PpWrapper.py", JSON.stringify(pyInput));
+  if (pyResult.stderr?.trim()) {
+    mayLog(`[GRIN2] Python stderr: ${pyResult.stderr}`);
+  }
   const grin2AnalysisTime = Date.now() - grin2AnalysisStart;
   const grin2AnalysisTimeToPrint = Math.round(grin2AnalysisTime / 1e3);
-  mayLog(`[GRIN2] Python processing took ${grin2AnalysisTimeToPrint}`);
+  mayLog(`[GRIN2] Python processing took ${grin2AnalysisTimeToPrint} seconds`);
   const resultData = JSON.parse(pyResult);
   const pngImg = resultData.png[0];
   const topGeneTable = resultData.topGeneTable || null;
@@ -131,88 +103,36 @@ async function runGrin2(genomes, req, res) {
     status: "success"
   });
 }
-function parseJsonlOutput(rustOutput) {
-  const lines = rustOutput.trim().split("\n");
-  const allSuccessfulData = [];
-  let finalSummary = null;
-  let processedFiles = 0;
-  const MAX_RECORDS = 1e5;
-  let totalRecordsProcessed = 0;
-  let isCapReached = false;
-  for (const line of lines) {
-    const trimmedLine = line.trim();
-    if (trimmedLine) {
-      try {
-        const data = JSON.parse(trimmedLine);
-        if (data.type === "data") {
-          if (isCapReached) {
-            mayLog(`[GRIN2] Skipping file ${data.case_id} - record cap of ${MAX_RECORDS} already reached`);
-            continue;
-          }
-          const remainingCapacity = MAX_RECORDS - totalRecordsProcessed;
-          const incomingRecords = data.data.length;
-          let recordsToProcess;
-          let recordsProcessedThisFile;
-          if (incomingRecords <= remainingCapacity) {
-            recordsToProcess = data.data;
-            recordsProcessedThisFile = incomingRecords;
-          } else {
-            recordsToProcess = data.data.slice(0, remainingCapacity);
-            recordsProcessedThisFile = remainingCapacity;
-            isCapReached = true;
-            mayLog(
-              `[GRIN2] Record cap reached! Processing only ${recordsProcessedThisFile} of ${incomingRecords} records from file ${data.case_id}`
-            );
-          }
-          processedFiles++;
-          allSuccessfulData.push(recordsToProcess);
-          totalRecordsProcessed += recordsProcessedThisFile;
-          mayLog(
-            `[GRIN2] Processed file ${processedFiles}: ${data.case_id} (${data.data_type}) - ${recordsProcessedThisFile} records`
-          );
-          mayLog(`[GRIN2] Total records processed: ${totalRecordsProcessed}/${MAX_RECORDS}`);
-          if (isCapReached) {
-            mayLog(`[GRIN2] RECORD CAP REACHED: ${MAX_RECORDS} records processed. Subsequent files will be skipped.`);
-          }
-        } else if (data.type === "summary") {
-          finalSummary = data;
-          mayLog(`[GRIN2] Download complete: ${data.successful_files}/${data.total_files} files successful`);
-          if (isCapReached) {
-            mayLog(`[GRIN2] Processing stopped due to record cap of ${MAX_RECORDS}`);
-            mayLog(`[GRIN2] Total records collected: ${totalRecordsProcessed}`);
-          }
-          if (data.failed_files > 0) {
-            mayLog(`[GRIN2] ${data.failed_files} files failed`);
-          }
-        }
-      } catch (parseError) {
-        console.error("[GRIN2] JSONL parse error:", parseError);
-        console.error("[GRIN2] Problematic line:", trimmedLine);
-      }
+function parseRustOutput(rustOutput) {
+  try {
+    const rustResult = JSON.parse(rustOutput);
+    if (!rustResult.grin2lesion || !rustResult.summary) {
+      throw new Error("Invalid Rust output: missing lesion data or summary");
     }
+    mayLog(`[GRIN2] Parsed Rust output successfully`);
+    return {
+      successful_data: rustResult.grin2lesion,
+      failed_files: rustResult.summary.errors || [],
+      summary: {
+        type: "summary",
+        total_files: rustResult.summary.total_files,
+        successful_files: rustResult.summary.successful_files,
+        failed_files: rustResult.summary.failed_files,
+        errors: rustResult.summary.errors || [],
+        filtered_records: rustResult.summary.filtered_records || 0,
+        filtered_maf_records: rustResult.summary.filtered_maf_records || 0,
+        filtered_cnv_records: rustResult.summary.filtered_cnv_records || 0,
+        included_maf_records: rustResult.summary.included_maf_records || 0,
+        included_cnv_records: rustResult.summary.included_cnv_records || 0,
+        filtered_records_by_case: rustResult.summary.filtered_records_by_case || {},
+        hyper_mutator_records: rustResult.summary.hyper_mutator_records || {},
+        excluded_by_max_record: rustResult.summary.excluded_by_max_record || {},
+        skippedChromosomes: rustResult.summary.skipped_chromosomes || {}
+      }
+    };
+  } catch (error) {
+    throw new Error(`Failed to parse Rust output: ${error instanceof Error ? error.message : "Unknown error"}`);
   }
-  if (!finalSummary) {
-    throw new Error("No summary found in Rust output");
-  }
-  return {
-    successful_data: allSuccessfulData,
-    failed_files: finalSummary.errors || [],
-    summary: {
-      type: "summary",
-      total_files: finalSummary.total_files,
-      successful_files: finalSummary.successful_files,
-      failed_files: finalSummary.failed_files,
-      errors: finalSummary.errors || [],
-      filtered_records: finalSummary.filtered_records || 0,
-      filtered_maf_records: finalSummary.filtered_maf_records || 0,
-      filtered_cnv_records: finalSummary.filtered_cnv_records || 0,
-      included_maf_records: finalSummary.included_maf_records || 0,
-      included_cnv_records: finalSummary.included_cnv_records || 0,
-      filtered_records_by_case: finalSummary.filtered_records_by_case || {},
-      hyper_mutator_records: finalSummary.hyper_mutator_records || {},
-      skippedChromosomes: finalSummary.skipped_chromosomes || {}
-    }
-  };
 }
 export {
   api

package/routes/profileScores.js

@@ -32,7 +32,7 @@ async function getScores(query, ds, genome) {
   const terms = [query.facilityTW];
   for (const term of query.scoreTerms) {
     terms.push(term.score);
-    if (term.maxScore) {
+    if (term.maxScore?.term) {
       terms.push(term.maxScore);
     }
   }