@sjcrh/proteinpaint-rust 2.111.0 → 2.112.0

package/index.js

@@ -1,7 +1,10 @@
 const path = require('path'),
-	spawn = require('child_process').spawn,
+	{ spawn, exec } = require('child_process'),
 	Readable = require('stream').Readable,
-	Transform = require('stream').Transform
+	Transform = require('stream').Transform,
+	{ promisify } = require('util')
+
+const execPromise = promisify(exec)
 
 exports.run_rust = function (binfile, input_data) {
 	return new Promise((resolve, reject) => {
@@ -45,47 +48,154 @@ exports.run_rust = function (binfile, input_data) {
 
 exports.stream_rust = function (binfile, input_data, emitJson) {
 	const binpath = path.join(__dirname, '/target/release/', binfile)
-	const ps = spawn(binpath)
-	const stderr = []
-	try {
-		// from GDC API -> ps.stdin -> ps.stdout -> transformed stream
-		Readable.from(input_data).pipe(ps.stdin)
-		//reader.on('data', ps.stdout.pipe)
-		//reader.on('error', ps.stderr.pipe)
-		//return reader
-	} catch (error) {
-		ps.kill()
-		let errmsg = error
-		//if (stderr.length) errmsg += `killed run_rust('${binfile}'), stderr: ${stderr.join('').trim()}`
-		//reject(errmsg)
-		console.log(59, error)
-	}
 
+	const ps = spawn(binpath)
 	const childStream = new Transform({
 		transform(chunk, encoding, callback) {
 			this.push(chunk)
 			callback()
 		}
 	})
-	ps.stdout.pipe(childStream)
+	// we only want to run this interval loop inside a container, not in dev/test CI
+	if (binfile == 'gdcmaf') trackByPid(ps.pid, binfile)
+	const stderr = []
+	try {
+		// from route handler -> input_data -> ps.stdin -> ps.stdout -> transformed stream -> express response.pipe()
+		Readable.from(input_data)
+			.pipe(ps.stdin)
+			.on('error', err => {
+				emitErrors({ error: `error piping input data to spawned ${binfile} process` })
+			})
+	} catch (error) {
+		console.log(`Error piping input_data into ${binfile}`, error)
+		return
+	}
+
+	// uncomment to trigger childStream.destroy()
+	// setTimeout(() => { console.log(74, 'childStream.destroy()'); childStream.destroy();}, 1000)
+	// childStream.destroy() does not seem to trigger ps.stdout.pipe('...').on('error') callback,
+	// which is okay as long as the server doesn't crash and ps get's killed eventually
+	ps.stdout.pipe(childStream).on('error', err => console.log('ps.stdout.pipe(childStream) error', err))
+
 	ps.stderr.on('data', data => stderr.push(data))
-	ps.on('close', code => { //console.log(72, stderr.length)
-		if (stderr.length) {
-			// handle rust stderr
-			const errors = stderr.join('').trim().split('\n').map(JSON.parse)
-			//const errmsg = `!!! stream_rust('${binfile}') stderr: !!!`
-			//console.log(errmsg, errors)
-			emitJson({errors})
+
+	ps.on('close', code => {
+		if (trackedPids.has(ps.pid)) trackedPids.delete(ps.pid)
+		if (stderr.length || killedPids.has(ps.pid) || code !== 0) {
+			emitErrors(null, ps.pid, code)
 		} else {
-			emitJson({ ok: true, status: 'ok', message: 'Processing complete' })
+			emitJson()
 		}
 	})
 	ps.on('error', err => {
-		//console.log(74, `stream_rust().on('error')`, err)
-		const errors = stderr.join('').trim().split('\n').map(JSON.parse)
-		emitJson({errors})
+		if (trackedPids.has(ps.pid)) trackedPids.delete(ps.pid)
+		// console.log(74, `stream_rust().on('error')`, err)
+		emitErrors(null, ps.pid)
+	})
+	ps.on('SIGTERM', err => {
+		console.log(err)
+	})
+
+	function emitErrors(error, pid, code = 0) {
+		// concatenate stderr uint8arr into a string
+		let errors = stderr.join('').trim()
+		if (error) errors += `\n` + error
+		if (pid && killedPids.has(ps.pid) && !trackedPids.has(ps.pid)) {
+			errors += '\n' + JSON.stringify({ error: `server error: MAF file processing terminated (expired process)` })
+			killedPids.delete(pid)
+		} else if (pid && code !== 0) {
+			// may result from errors in spawned process code, or external signal (like `kill -9` in terminal)
+			errors += '\n' + JSON.stringify({ error: `server error: MAF file processing terminated (code=${code})` })
+		}
+		emitJson(errors)
+	}
+
+	// on('end') will duplicate ps.on('close') event above
+	// childStream.on('end', () => console.log(`childStream.on(end)`))
+
+	// this may duplicate ps.on('error'), unless the error happened within the transform
+	childStream.on('error', err => {
+		console.log('stream_rust childStream.on(error)', err)
+		try {
+			childStream.destroy(err)
+		} catch (e) {
+			console.log(e)
+		}
 	})
-	// below will duplicate ps.on('close') event above
-	// childStream.on('end', () => console.log(`-- childStream done --`))
-	return childStream
+
+	function endStream() {
+		try {
+			if (!childStream.writableEnded) {
+				console.log('trigger childStream.destroy() in endStream()')
+				childStream.destroy()
+			}
+		} catch (e) {
+			console.log('error triggering childStream.destroy()', e)
+		}
+		try {
+			if (!ps.killed) {
+				console.log('trigger ps.kill() in endStream()')
+				ps.kill()
+			}
+			if (trackedPids.has(ps.pid)) trackedPids.delete(ps.pid)
+		} catch (e) {
+			console.log('error triggering ps.kill()', e)
+		}
+	}
+
+	return { rustStream: childStream, endStream }
+}
+
+const trackedPids = new Map() // will be used to monitor expired processes
+const killedPids = new Set() // will be used to detect killed processes, to help with error detection
+const PSKILL_INTERVAL_MS = 30000 // every 30 seconds
+let psKillInterval
+
+// default maxElapsed = 5 * 60 * 1000 millisecond = 300000 or 5 minutes, change to 0 to test
+// may allow configuration of maxElapsed by dataset/argument
+function trackByPid(pid, name, maxElapsed = 300000) {
+	if (!pid) return
+	// only track by value (integer, string), not reference object
+	// NOTE: a reused/reassigned process.pid will be replaced by the most recent process
+	trackedPids.set(pid, { name, expires: Date.now() + maxElapsed })
+	if (!psKillInterval) psKillInterval = setInterval(killExpiredProcesses, PSKILL_INTERVAL_MS)
+	// uncomment below to test
+	// console.log([...trackedPids.entries()])
+	// if (maxElapsed < 10000) setTimeout(killExpiredProcesses, 1000) // uncomment for testing only
+}
+
+//
+// Use one setInterval() to monitor >= 1 process,
+// instead of a separate setTimeout() for each process.
+// This is more reliable as setTimeout would use spawned ps.kill(),
+// which may not exist when the timeout callback is executed and
+// thus would require clearTimeout(closured_variable). Tracking by
+// pid does not rely on a usable 'ps' variable to kill itself.
+//
+function killExpiredProcesses() {
+	//console.log(149, 'killExpiredProcesses()')
+	killedPids.clear()
+	const time = Date.now()
+	for (const [pid, info] of trackedPids.entries()) {
+		if (info.expires > time) continue
+		try {
+			// true if process exists
+			process.kill(pid, 0)
+		} catch (_) {
+			// no need to kill, but remove from tracking
+			trackedPids.delete(pid)
+			// prevent misleading logs of 'unable to kill ...'
+			continue
+		}
+		const label = `rust process ${info.name} (pid=${pid})`
+		try {
+			// detect if process exists before killing it
+			process.kill(pid, 'SIGTERM')
+			trackedPids.delete(pid)
+			killedPids.add(pid)
+			console.log(`killed ${label}`)
+		} catch (err) {
+			console.log(`unable to kill ${label}`, err)
+		}
+	}
 }

package/package.json

@@ -1,5 +1,5 @@
 {
-	"version": "2.111.0",
+	"version": "2.112.0",
 	"name": "@sjcrh/proteinpaint-rust",
 	"description": "Rust-based utilities for proteinpaint",
 	"main": "index.js",
@@ -38,5 +38,5 @@
 	"devDependencies": {
 		"tape": "^5.2.2"
 	},
-	"pp_release_tag": "v2.111.0"
+	"pp_release_tag": "v2.112.0"
 }

package/src/gdcmaf.rs

@@ -1,22 +1,25 @@
 /*
-	This script download cohort maf files from GDC, concatenate them into a single file that includes user specified columns.
+  This script download cohort maf files from GDC, concatenate them into a single file that includes user specified columns.
 
-	Input JSON:
-		host: GDC host
-		fileIdLst: An array of uuid
-	Output gzip compressed maf file to stdout.
+  Input JSON:
+    host: GDC host
+    fileIdLst: An array of uuid
+  Output gzip compressed maf file to stdout.
 
-	Example of usage:
-		echo '{"host": "https://api.gdc.cancer.gov/data/","columns": ["Hugo_Symbol", "Entrez_Gene_Id", "Center", "NCBI_Build", "Chromosome", "Start_Position"], "fileIdLst": ["8b31d6d1-56f7-4aa8-b026-c64bafd531e7", "b429fcc1-2b59-4b4c-a472-fb27758f6249"]}'|./target/release/gdcmaf
+  Example of usage:
+    echo '{"host": "https://api.gdc.cancer.gov/data/","columns": ["Hugo_Symbol", "Entrez_Gene_Id", "Center", "NCBI_Build", "Chromosome", "Start_Position"], "fileIdLst": ["8b31d6d1-56f7-4aa8-b026-c64bafd531e7", "b429fcc1-2b59-4b4c-a472-fb27758f6249"]}'|./target/release/gdcmaf
 */
 
 use flate2::read::GzDecoder;
 use flate2::write::GzEncoder;
 use flate2::Compression;
 use serde_json::{Value};
-use std::path::Path;
 use futures::StreamExt;
 use std::io::{self,Read,Write};
+use std::time::Duration;
+use tokio::io::{AsyncReadExt, BufReader};
+use tokio::time::timeout;
+use std::sync::{Arc, Mutex};
 
 // Struct to hold error information
 #[derive(serde::Serialize)]
@@ -45,6 +48,9 @@ fn select_maf_col(d:String,columns:&Vec<String>,url:&str) -> Result<(Vec<u8>,i32
                         return Err((url.to_string(), error_msg));
                     }
                 }
+            };
+            if header_indices.is_empty() {
+                return Err((url.to_string(), "No matching columns found".to_string()));
             }
         } else {
             let maf_cont_lst: Vec<String> = line.split("\t").map(|s| s.to_string()).collect();
@@ -67,16 +73,67 @@ async fn main() -> Result<(),Box<dyn std::error::Error>> {
     // Accepting the piped input json from jodejs and assign to the variable
     // host: GDC host
     // url: urls to download single maf files
-    let mut buffer = String::new();
-    io::stdin().read_line(&mut buffer)?;
+    let timeout_duration = Duration::from_secs(5); // Set a 10-second timeout
+
+    // Wrap the read operation in a timeout
+    let result = timeout(timeout_duration, async {
+        let mut buffer = String::new(); // Initialize an empty string to store input
+        let mut reader = BufReader::new(tokio::io::stdin()); // Create a buffered reader for stdin 
+        reader.read_to_string(&mut buffer).await?; // Read a line asynchronously
+        Ok::<String, io::Error>(buffer) // Return the input as a Result
+    })
+    .await;
+    // Handle the result of the timeout operation
+    let  file_id_lst_js: Value = match result {
+        Ok(Ok(buffer)) => {
+            match serde_json::from_str(&buffer) {
+                Ok(js) => js,
+                Err(e) => {
+                    let stdin_error = ErrorEntry {
+                        url: String::new(),
+                        error: format!("JSON parsing error: {}", e),
+                    };
+                    writeln!(io::stderr(), "{}", serde_json::to_string(&stdin_error).unwrap()).unwrap();
+                    return Err(Box::new(std::io::Error::new(
+                        std::io::ErrorKind::InvalidInput,
+                        "JSON parsing error!",
+                    )) as Box<dyn std::error::Error>);
+                }
+            }
+        }
+        Ok(Err(_e)) => {
+            let stdin_error = ErrorEntry {
+                url: String::new(),
+                error: "Error reading from stdin.".to_string(),
+            };
+            let stdin_error_js = serde_json::to_string(&stdin_error).unwrap();
+            writeln!(io::stderr(), "{}", stdin_error_js).expect("Failed to output stderr!");
+            return Err(Box::new(std::io::Error::new(
+                std::io::ErrorKind::InvalidInput,
+                "Failed to output stderr!",
+            )) as Box<dyn std::error::Error>);
+        }
+        Err(_) => {
+            let stdin_error = ErrorEntry {
+                url: String::new(),
+                error: "Timeout while reading from stdin.".to_string(),
+            };
+            let stdin_error_js = serde_json::to_string(&stdin_error).unwrap();
+            writeln!(io::stderr(), "{}", stdin_error_js).expect("Failed to output stderr!");
+            return Err(Box::new(std::io::Error::new(
+                std::io::ErrorKind::InvalidInput,
+                "The columns in arg is not an array",
+            )) as Box<dyn std::error::Error>);
+        }
+    };
 
     // reading the input from PP
-    let file_id_lst_js = serde_json::from_str::<Value>(&buffer).expect("Error reading input and serializing to JSON");
     let host = file_id_lst_js.get("host").expect("Host was not provided").as_str().expect("Host is not a string");
     let mut url: Vec<String> = Vec::new();
     let file_id_lst = file_id_lst_js.get("fileIdLst").expect("File ID list is missed!").as_array().expect("File ID list is not an array");
     for v in file_id_lst {
-        url.push(Path::new(&host).join(&v.as_str().unwrap()).display().to_string());
+        //url.push(Path::new(&host).join(&v.as_str().unwrap()).display().to_string());
+        url.push(format!("{}/{}",host.trim_end_matches('/'), v.as_str().unwrap()));
     };
 
     // read columns as array from input json and convert data type from Vec<Value> to Vec<String>
@@ -117,7 +174,19 @@ async fn main() -> Result<(),Box<dyn std::error::Error>> {
     let download_futures = futures::stream::iter(
         url.into_iter().map(|url|{
             async move {
-                match reqwest::get(&url).await {
+                let client = reqwest::Client::builder()
+                    .timeout(Duration::from_secs(60)) // 60-second timeout per request
+                    .connect_timeout(Duration::from_secs(15))
+                    .build()
+                    .map_err(|_e| {
+                        let client_error = ErrorEntry{
+                            url: url.clone(),
+                            error: "Client build error".to_string(),
+                        };
+                        let client_error_js = serde_json::to_string(&client_error).unwrap();
+                        writeln!(io::stderr(), "{}", client_error_js).expect("Failed to build reqwest client!");
+                    });
+                match client.unwrap().get(&url).send().await {
                     Ok(resp) if resp.status().is_success() => {
                         match resp.bytes().await {
                             Ok(content) => {
@@ -154,50 +223,65 @@ async fn main() -> Result<(),Box<dyn std::error::Error>> {
     );
 
     // binary output
-    let mut encoder = GzEncoder::new(io::stdout(), Compression::default());
-    let _ = encoder.write_all(&maf_col.join("\t").as_bytes().to_vec()).expect("Failed to write header");
-    let _ = encoder.write_all(b"\n").expect("Failed to write newline");
+    let encoder = Arc::new(Mutex::new(GzEncoder::new(io::stdout(), Compression::default())));
 
-    download_futures.buffer_unordered(20).for_each(|result| {
-        match result {
-            Ok((url, content)) => {
-                match select_maf_col(content, &maf_col, &url) {
-                    Ok((maf_bit,mafrows)) => {
-                        if mafrows > 0 {
-                            encoder.write_all(&maf_bit).expect("Failed to write file");
-                        } else {
+    // Write the header
+    {
+        let mut encoder_guard = encoder.lock().unwrap(); // Lock the Mutex to get access to the inner GzEncoder
+        encoder_guard.write_all(&maf_col.join("\t").as_bytes().to_vec()).expect("Failed to write header");
+        encoder_guard.write_all(b"\n").expect("Failed to write newline");
+    }
+    
+    download_futures.buffer_unordered(20).for_each( |result| {
+        let encoder = Arc::clone(&encoder); // Clone the Arc for each task
+        let maf_col_cp = maf_col.clone();
+        async move {
+            match result {
+                Ok((url, content)) => {
+                    match select_maf_col(content, &maf_col_cp, &url) {
+                        Ok((maf_bit,mafrows)) => {
+                            if mafrows > 0 {
+                                let mut encoder_guard = encoder.lock().unwrap();
+                                encoder_guard.write_all(&maf_bit).expect("Failed to write file");
+                            } else {
+                                let error = ErrorEntry {
+                                    url: url.clone(),
+                                    error: "Empty maf file".to_string(),
+                                };
+                                let error_js = serde_json::to_string(&error).unwrap();
+                                writeln!(io::stderr(), "{}", error_js).expect("Failed to output stderr!");
+                            }
+                        }
+                        Err((url,error)) => {
                             let error = ErrorEntry {
-                                url: url.clone(),
-                                error: "Empty maf file".to_string(),
+                                url,
+                                error,
                             };
                             let error_js = serde_json::to_string(&error).unwrap();
                             writeln!(io::stderr(), "{}", error_js).expect("Failed to output stderr!");
                         }
                     }
-                    Err((url,error)) => {
-                        let error = ErrorEntry {
-                            url,
-                            error,
-                        };
-                        let error_js = serde_json::to_string(&error).unwrap();
-                        writeln!(io::stderr(), "{}", error_js).expect("Failed to output stderr!");
-                    }
                 }
-            }
-            Err((url, error)) => {
-                let error = ErrorEntry {
-                    url,
-                    error,
-                };
-                let error_js = serde_json::to_string(&error).unwrap();
-                writeln!(io::stderr(), "{}", error_js).expect("Failed to output stderr!");
-            }
-        };
-        async {}
+                Err((url, error)) => {
+                    let error = ErrorEntry {
+                        url,
+                        error,
+                    };
+                    let error_js = serde_json::to_string(&error).unwrap();
+                    writeln!(io::stderr(), "{}", error_js).expect("Failed to output stderr!");
+                }
+            };
+        }
     }).await;
     
-    // Finalize output and printing errors
+    // Finalize output
+
+    // Replace the value inside the Mutex with a dummy value (e.g., None)
+    let mut encoder_guard = encoder.lock().unwrap();
+    let encoder = std::mem::replace(&mut *encoder_guard, GzEncoder::new(io::stdout(), Compression::default()));
+    // Finalize the encoder
     encoder.finish().expect("Maf file output error!");
+
     // Manually flush stdout and stderr
     io::stdout().flush().expect("Failed to flush stdout");
     io::stderr().flush().expect("Failed to flush stderr");