fix(server): harden liftOver/TransVar subprocesses and auto-restart t…

docker-compose.yml

@@ -7,6 +7,7 @@ services:
 
   server:
     image: zhandongliulab/marrvel-server
+    restart: unless-stopped
     working_dir: /MARRVEL/server
     volumes:
       - "${LOCAL_BASE}/.env:/MARRVEL/server/.env"

server/utils/liftover.js

@@ -1,85 +1,97 @@
 const fs = require('fs');
 const config = require('../config');
 
+const cleanupTempFile = (filePath) => {
+  try {
+    fs.unlinkSync(filePath);
+  } catch (error) {
+    if (error.code !== 'ENOENT') {
+      console.error(`Error cleaning up temp file ${filePath}: ${error.message}`);
+    }
+  }
+};
+
 exports.liftover = async (chr, pos, fromOrg, fromDb, toOrg, toDb,
   minMatch, isMultiRegionAllowed, minQuery, minChain, minBlocks, isThickFudgeSet) => {
-  // generate input BED file with random name
-  const inputBed = `/tmp/${Math.random().toString(36).substring(2, 15)}.bed`;
-  fs.writeFileSync(inputBed, `chr${chr}\t${pos}\t${pos}\n`);
-  // generate output BED file with random name
-  const outputBed = `/tmp/${Math.random().toString(36).substring(2, 15)}.bed`;
-  // generate unlifted BED file with random name
-  const unliftedBed = `/tmp/${Math.random().toString(36).substring(2, 15)}.bed`;
-
   if (!config.liftoverCmdTool[fromOrg][fromDb][toOrg][toDb]) {
     throw new Error('liftOver chain file is not configured properly');
   }
-  const cmdArgs = [
-    inputBed,
-    config.liftoverCmdTool[fromOrg][fromDb][toOrg][toDb],
-    outputBed,
-    unliftedBed
-  ];
-  if (minBlocks) {
-    cmdArgs.push(`-minBlocks=${minBlocks}`);
-  }
-  if (isThickFudgeSet) {
-    cmdArgs.push('-fudgeThick');
-  }
-  if (minMatch) {
-    cmdArgs.push(`-minMatch=${minMatch}`);
-  }
-  if (isMultiRegionAllowed) {
-    cmdArgs.push('-multiple');
-  }
-  if (minQuery) {
-    cmdArgs.push(`-minSizeQ=${minQuery}`);
-  }
-  if (minChain) {
-    cmdArgs.push(`-minChainT=${minChain}`);
-  }
 
-  // run liftOver command line tool
-  try {
-    await runLiftover(cmdArgs);
-  } catch (error) {
-    console.error(`Error occurred while running liftOver: ${error.message}`);
-    return {
-      message: 'Error occurred while running liftOver'
-    };
-  }
-  // read output BED file
-  let lifted = null;
+  // generate input/output/unlifted BED files with random names
+  const inputBed = `/tmp/${Math.random().toString(36).substring(2, 15)}.bed`;
+  const outputBed = `/tmp/${Math.random().toString(36).substring(2, 15)}.bed`;
+  const unliftedBed = `/tmp/${Math.random().toString(36).substring(2, 15)}.bed`;
+
   try {
-    const output = fs.readFileSync(outputBed, 'utf8');
-    lifted = (output.split('\n')[0] || '').split('\t');
-  } catch (error) {
-    console.error(`Error reading output BED file: ${error.message}`);
-    return {
-      message: 'Error reading output BED file'
-    };
-  }
-  if (!lifted || lifted.length < 2) {
+    fs.writeFileSync(inputBed, `chr${chr}\t${pos}\t${pos}\n`);
+
+    const cmdArgs = [
+      inputBed,
+      config.liftoverCmdTool[fromOrg][fromDb][toOrg][toDb],
+      outputBed,
+      unliftedBed
+    ];
+    if (minBlocks) {
+      cmdArgs.push(`-minBlocks=${minBlocks}`);
+    }
+    if (isThickFudgeSet) {
+      cmdArgs.push('-fudgeThick');
+    }
+    if (minMatch) {
+      cmdArgs.push(`-minMatch=${minMatch}`);
+    }
+    if (isMultiRegionAllowed) {
+      cmdArgs.push('-multiple');
+    }
+    if (minQuery) {
+      cmdArgs.push(`-minSizeQ=${minQuery}`);
+    }
+    if (minChain) {
+      cmdArgs.push(`-minChainT=${minChain}`);
+    }
+
+    // run liftOver command line tool
+    try {
+      await runLiftover(cmdArgs);
+    } catch (error) {
+      console.error(`Error occurred while running liftOver: ${error.message}`);
+      return {
+        message: 'Error occurred while running liftOver'
+      };
+    }
+    // read output BED file
+    let lifted = null;
+    try {
+      const output = fs.readFileSync(outputBed, 'utf8');
+      lifted = (output.split('\n')[0] || '').split('\t');
+    } catch (error) {
+      console.error(`Error reading output BED file: ${error.message}`);
+      return {
+        message: 'Error reading output BED file'
+      };
+    }
+    if (!lifted || lifted.length < 2) {
+      return {
+        message: 'No lifted position found'
+      };
+    }
     return {
-      message: 'No lifted position found'
+      inputChr: chr,
+      inputPos: pos,
+      chr: lifted[0].replace('chr', ''),
+      pos: parseInt(lifted[1])
     };
+  } finally {
+    cleanupTempFile(inputBed);
+    cleanupTempFile(outputBed);
+    cleanupTempFile(unliftedBed);
   }
-  // clean up temporary files
-  fs.unlinkSync(inputBed);
-  fs.unlinkSync(outputBed);
-  fs.unlinkSync(unliftedBed);
-  return {
-    inputChr: chr,
-    inputPos: pos,
-    chr: lifted[0].replace('chr', ''),
-    pos: parseInt(lifted[1])
-  };
 };
 
 const runLiftover = (args) => {
   return new Promise((resolve, reject) => {
     const spawn = require('child_process').spawn;
-    const child = spawn(config.liftoverCmdTool.path, args);
+    const child = spawn(config.liftoverCmdTool.path, args, { timeout: 15000, killSignal: 'SIGKILL' });
     let stdout = '';
     let stderr = '';
     child.stdout.on('data', (data) => {
@@ -88,7 +100,10 @@ const runLiftover = (args) => {
     child.stderr.on('data', (data) => {
       stderr += data.toString();
     });
-    child.on('close', (code) => {
+    child.on('close', (code, signal) => {
+      if (signal) {
+        return reject(new Error(`liftOver process was killed (signal: ${signal})`));
+      }
       if (code !== 0) {
         return reject(new Error(`liftOver process exited with code ${code}: ${stderr}`));
       }

server/utils/transvar.js

@@ -24,7 +24,7 @@ const appendGene = (data) => {
 const executeTransvar = (option) => {
   return new Promise((resolve, reject) => {
     const { spawn } = require('child_process');
-    const proc = spawn(transvarPath, option);
+    const proc = spawn(transvarPath, option, { timeout: 30000, killSignal: 'SIGKILL' });
 
     let stdout = '';
     const stderr = [];
@@ -37,7 +37,11 @@ const executeTransvar = (option) => {
       stderr.push(err);
     });
 
-    proc.on('close', (code) => {
+    proc.on('close', (code, signal) => {
+      if (signal) {
+        reject(new Error(`transvar process was killed (signal: ${signal})`));
+        return;
+      }
       resolve({
         code,
         stdout,