@sjcrh/proteinpaint-rust 2.84.0 → 2.110.0

package/index.js

@@ -43,16 +43,22 @@ exports.run_rust = function (binfile, input_data) {
 	})
 }
 
-exports.run_rust_stream = 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: ${stderr.join('').trim()}`
-		reject(errmsg)
+		//if (stderr.length) errmsg += `killed run_rust('${binfile}'), stderr: ${stderr.join('').trim()}`
+		//reject(errmsg)
+		console.log(59, error)
 	}
 
 	const childStream = new Transform({
@@ -62,11 +68,23 @@ exports.run_rust_stream = function (binfile, input_data) {
 		}
 	})
 	ps.stdout.pipe(childStream)
-	childStream.on('error', err => {
-		reject(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 err = stderr.join('').trim()
+			const errmsg = `!!! stream_rust('${binfile}') stderr: !!!\n${err}`
+			console.log(errmsg)
+			emitJson(err)
+		} else {
+			emitJson({ ok: true, status: 'ok', message: 'Processing complete' })
+		}
 	})
-	childStream.on('close', code => {
-		childStream.end()
+	ps.on('error', err => {
+		console.log(74, `stream_rust().on('error')`, err)
+		emitJson(stderr.join('').trim())
 	})
+	// below will duplicate ps.on('close') event above
+	// childStream.on('end', () => console.log(`-- childStream done --`))
 	return childStream
 }

package/package.json

@@ -1,5 +1,5 @@
 {
-	"version": "2.84.0",
+	"version": "2.110.0",
 	"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": "v2.84.0"
+	"pp_release_tag": "v2.110.0"
 }

package/src/DEanalysis.rs

@@ -11,7 +11,7 @@ use nalgebra::base::Matrix;
 use nalgebra::base::VecStorage;
 use nalgebra::DMatrix;
 use nalgebra::ViewStorage;
-use ndarray::Array1;
+//use ndarray::Array1;
 use ndarray::Array2;
 use ndarray::Dim;
 use serde::{Deserialize, Serialize};
@@ -25,7 +25,7 @@ use std::io::Read;
 use std::str::FromStr;
 use std::sync::{Arc, Mutex}; // Multithreading library
 use std::thread;
-use std::time::Instant;
+//use std::time::Instant;
 //use std::cmp::Ordering;
 //use std::env;
 use std::io;
@@ -73,43 +73,45 @@ fn input_data_from_HDF5(
     Vec<String>,
 ) {
     let file = HDF5File::open(&hdf5_filename).unwrap(); // open for reading
-    let ds_dim = file.dataset("dims").unwrap(); // open the dataset
+
+    //let ds_dim = file.dataset("dims").unwrap(); // open the dataset
     let mut input_vector: Vec<f64> = Vec::with_capacity(500 * 65000);
     let mut case_indexes: Vec<usize> = Vec::with_capacity(case_list.len());
     let mut control_indexes: Vec<usize> = Vec::with_capacity(control_list.len());
     // Check the data type and read the dataset accordingly
-    let data_dim: Array1<_> = ds_dim.read::<usize, Dim<[usize; 1]>>().unwrap();
-    let num_samples = data_dim[0]; // Number of total columns in the dataset
-    let num_genes = data_dim[1]; // Number of total rows in the dataset
-    println!("num_samples bulk:{}", num_samples);
-    println!("num_genes bulk:{}", num_genes);
+    //let data_dim: Array1<_> = ds_dim.read::<usize, Dim<[usize; 1]>>().unwrap();
+    //let num_samples = data_dim[0]; // Number of total columns in the dataset
+    //let num_genes = data_dim[1]; // Number of total rows in the dataset
+
+    //println!("num_samples bulk:{}", num_samples);
+    //println!("num_genes bulk:{}", num_genes);
 
-    let now_gene_names = Instant::now();
+    //let now_gene_names = Instant::now();
     let ds_gene_names = file.dataset("gene_names").unwrap();
-    println!("ds_gene_names:{:?}", ds_gene_names);
+    //println!("ds_gene_names:{:?}", ds_gene_names);
     let gene_names = ds_gene_names
         .read::<VarLenAscii, Dim<[usize; 1]>>()
         .unwrap();
-    println!("\tgene_names = {:?}", gene_names);
-    println!("\tgene_names.shape() = {:?}", gene_names.shape());
-    println!("\tgene_names.strides() = {:?}", gene_names.strides());
-    println!("\tgene_names.ndim() = {:?}", gene_names.ndim());
-    println!("Time for parsing gene names:{:?}", now_gene_names.elapsed());
+    //println!("\tgene_names = {:?}", gene_names);
+    //println!("\tgene_names.shape() = {:?}", gene_names.shape());
+    //println!("\tgene_names.strides() = {:?}", gene_names.strides());
+    //println!("\tgene_names.ndim() = {:?}", gene_names.ndim());
+    //println!("Time for parsing gene names:{:?}", now_gene_names.elapsed());
 
-    let now_gene_symbols = Instant::now();
+    //let now_gene_symbols = Instant::now();
     let ds_gene_symbols = file.dataset("gene_symbols").unwrap();
-    println!("ds_gene_symbols:{:?}", ds_gene_symbols);
+    //println!("ds_gene_symbols:{:?}", ds_gene_symbols);
     let gene_symbols = ds_gene_symbols
         .read::<VarLenAscii, Dim<[usize; 1]>>()
         .unwrap();
-    println!("\tgene_symbols = {:?}", gene_symbols);
-    println!("\tgene_symbols.shape() = {:?}", gene_symbols.shape());
-    println!("\tgene_symbols.strides() = {:?}", gene_symbols.strides());
-    println!("\tgene_symbols.ndim() = {:?}", gene_symbols.ndim());
-    println!(
-        "Time for parsing gene symbols:{:?}",
-        now_gene_symbols.elapsed()
-    );
+    //println!("\tgene_symbols = {:?}", gene_symbols);
+    //println!("\tgene_symbols.shape() = {:?}", gene_symbols.shape());
+    //println!("\tgene_symbols.strides() = {:?}", gene_symbols.strides());
+    //println!("\tgene_symbols.ndim() = {:?}", gene_symbols.ndim());
+    //println!(
+    //    "Time for parsing gene symbols:{:?}",
+    //    now_gene_symbols.elapsed()
+    //);
 
     let mut gene_names_string: Vec<String> = Vec::with_capacity(gene_names.len());
     let mut gene_symbols_string: Vec<String> = Vec::with_capacity(gene_symbols.len());
@@ -118,17 +120,17 @@ fn input_data_from_HDF5(
         gene_symbols_string.push(gene_symbols[i].to_string());
     }
 
-    let now_samples = Instant::now();
+    //let now_samples = Instant::now();
     let ds_samples = file.dataset("samples").unwrap();
     let samples = ds_samples.read::<VarLenAscii, Dim<[usize; 1]>>().unwrap();
-    println!("\tsamples = {:?}", samples);
-    println!("\tsamples.shape() = {:?}", samples.shape());
-    println!("\tsamples.strides() = {:?}", samples.strides());
-    println!("\tsamples.ndim() = {:?}", samples.ndim());
-    println!("Time for parsing samples:{:?}", now_samples.elapsed());
+    //println!("\tsamples = {:?}", samples);
+    //println!("\tsamples.shape() = {:?}", samples.shape());
+    //println!("\tsamples.strides() = {:?}", samples.strides());
+    //println!("\tsamples.ndim() = {:?}", samples.ndim());
+    //println!("Time for parsing samples:{:?}", now_samples.elapsed());
 
     //Find all columns values that are populated for the given gene
-    let now_counts = Instant::now();
+    //let now_counts = Instant::now();
     let ds_counts = file.dataset("counts").unwrap(); // open the dataset
 
     let mut global_sample_index = 0;
@@ -189,7 +191,7 @@ fn input_data_from_HDF5(
         global_sample_index += 1;
     }
 
-    println!("Time for parsing HDF5 data:{:?}", now_counts.elapsed());
+    //println!("Time for parsing HDF5 data:{:?}", now_counts.elapsed());
     //println!(
     //    "case + control length:{}",
     //    case_list.len() + control_list.len()
@@ -221,7 +223,7 @@ fn input_data_from_text(
     Vec<String>,
     Vec<String>,
 ) {
-    let input_time = Instant::now();
+    //let input_time = Instant::now();
     let mut file = File::open(filename).unwrap();
     let mut num_lines: usize = 0;
     let mut input_vector: Vec<f64> = Vec::with_capacity(500 * 65000);
@@ -350,7 +352,7 @@ fn input_data_from_text(
         let genes_symbols_temp = Arc::new(Mutex::new(Vec::<String>::new()));
         let input_vector_temp = Arc::new(Mutex::new(Vec::<f64>::new()));
         let mut handles = vec![]; // Vector to store handle which is used to prevent one thread going ahead of another
-        println!("Number of threads used:{}", max_threads);
+                                  //println!("Number of threads used:{}", max_threads);
         for thread_num in 0..max_threads {
             let case_indexes_original = Arc::clone(&case_indexes_original);
             let control_indexes_original = Arc::clone(&control_indexes_original);
@@ -485,7 +487,7 @@ fn input_data_from_text(
     //println!("num_columns:{}", num_columns);
     //println!("num_lines * num_columns:{}", num_lines * num_columns);
     //println!("input_vector:{:?}", input_vector.len());
-    println!("Time for inputting data:{:?}", input_time.elapsed());
+    //println!("Time for inputting data:{:?}", input_time.elapsed());
     let dm = DMatrix::from_row_slice(num_lines, num_columns, &input_vector);
     //println!("dm:{:?}", dm);
     (dm, case_indexes, control_indexes, gene_names, gene_symbols)
@@ -513,14 +515,15 @@ struct PValueIndexes {
 // Used to get the sample names from HDF5 file at PP server startup
 fn get_DE_samples(hdf5_filename: &String) {
     let file = HDF5File::open(&hdf5_filename).unwrap(); // open for reading
-    let now_samples = Instant::now();
+
+    //let now_samples = Instant::now();
     let ds_samples = file.dataset("samples").unwrap();
     let samples = ds_samples.read::<VarLenAscii, Dim<[usize; 1]>>().unwrap();
-    println!("\tsamples = {:?}", samples);
-    println!("\tsamples.shape() = {:?}", samples.shape());
-    println!("\tsamples.strides() = {:?}", samples.strides());
-    println!("\tsamples.ndim() = {:?}", samples.ndim());
-    println!("Time for parsing samples:{:?}", now_samples.elapsed());
+    //println!("\tsamples = {:?}", samples);
+    //println!("\tsamples.shape() = {:?}", samples.shape());
+    //println!("\tsamples.strides() = {:?}", samples.strides());
+    //println!("\tsamples.ndim() = {:?}", samples.ndim());
+    //println!("Time for parsing samples:{:?}", now_samples.elapsed());
 
     let mut output_string = "".to_string();
     for i in 0..samples.len() {
@@ -544,7 +547,7 @@ fn get_DE_samples(hdf5_filename: &String) {
             output_string += &",";
         }
     }
-    println!("output_string:{}", output_string);
+    println!("{}", output_string);
 }
 
 fn main() {
@@ -559,7 +562,7 @@ fn main() {
             let input_json = json::parse(&input);
             match input_json {
                 Ok(json_string) => {
-                    let now = Instant::now();
+                    //let now = Instant::now();
                     let file_name = &json_string["input_file"]
                         .to_owned()
                         .as_str()
@@ -567,7 +570,7 @@ fn main() {
                         .to_string()
                         .split(",")
                         .collect();
-                    println!("file_name:{}", file_name);
+                    //println!("file_name:{}", file_name);
                     let data_type_option = json_string["data_type"].as_str().to_owned();
                     match data_type_option {
                         Some(x) => {
@@ -643,7 +646,7 @@ fn main() {
                                         gene_symbols,
                                     ) = input_data_from_HDF5(file_name, &case_list, &control_list);
                                 }
-                                let filtering_time = Instant::now();
+                                //let filtering_time = Instant::now();
                                 let (
                                     filtered_matrix,
                                     lib_sizes,
@@ -658,21 +661,21 @@ fn main() {
                                     gene_names,
                                     gene_symbols,
                                 );
-                                println!("filtering time:{:?}", filtering_time.elapsed());
+                                //println!("filtering time:{:?}", filtering_time.elapsed());
                                 //println!("filtered_matrix_rows:{:?}", filtered_matrix.nrows());
                                 //println!("filtered_matrix_cols:{:?}", filtered_matrix.ncols());
-                                let cpm_normalization_time = Instant::now();
+                                //let cpm_normalization_time = Instant::now();
                                 let mut normalized_matrix = cpm(&filtered_matrix);
-                                println!(
-                                    "cpm normalization time:{:?}",
-                                    cpm_normalization_time.elapsed()
-                                );
-                                let tmm_normalization_time = Instant::now();
+                                //println!(
+                                //    "cpm normalization time:{:?}",
+                                //    cpm_normalization_time.elapsed()
+                                //);
+                                //let tmm_normalization_time = Instant::now();
                                 let norm_factors = tmm_normalization(filtered_matrix, &lib_sizes);
-                                println!(
-                                    "tmm normalization time:{:?}",
-                                    tmm_normalization_time.elapsed()
-                                );
+                                //println!(
+                                //    "tmm normalization time:{:?}",
+                                //    tmm_normalization_time.elapsed()
+                                //);
                                 //println!("norm_factors:{:?}", norm_factors);
 
                                 for col in 0..normalized_matrix.ncols() {
@@ -683,19 +686,19 @@ fn main() {
                                     }
                                 }
                                 //println!("normalized_matrix:{:?}", normalized_matrix);
-                                println!("Number of cases:{}", case_list.len());
-                                println!("Number of controls:{}", control_list.len());
-                                println!("Time for pre-processing:{:?}", now.elapsed());
+                                //println!("Number of cases:{}", case_list.len());
+                                //println!("Number of controls:{}", control_list.len());
+                                //println!("Time for pre-processing:{:?}", now.elapsed());
                                 // Using Wilcoxon test for differential gene expression
 
-                                let now2 = Instant::now();
+                                //let now2 = Instant::now();
                                 let mut p_values: Vec<PValueIndexes> =
                                     Vec::with_capacity(normalized_matrix.nrows());
                                 const THRESHOLD: usize = 50; // This determines whether the Wilcoxon exact test or the normal test will be used based on sample size.
 
                                 //println!("case_indexes:{:?}", case_indexes);
                                 //println!("control_indexes:{:?}", control_indexes);
-                                let num_normalized_rows = normalized_matrix.nrows();
+                                //let num_normalized_rows = normalized_matrix.nrows();
                                 if normalized_matrix.nrows() * normalized_matrix.ncols()
                                     < PAR_CUTOFF
                                 {
@@ -857,13 +860,13 @@ fn main() {
                                     p_values.append(&mut *p_values_temp.lock().unwrap());
                                 }
                                 //println!("p_values:{:?}", p_values);
-                                println!(
-                                    "Time for running {} wilcoxon tests:{:?}",
-                                    num_normalized_rows,
-                                    now2.elapsed()
-                                );
+                                //println!(
+                                //    "Time for running {} wilcoxon tests:{:?}",
+                                //    num_normalized_rows,
+                                //    now2.elapsed()
+                                //);
                                 let adjusted_p_values = adjust_p_values(p_values);
-                                println!("adjusted_p_values:{}", adjusted_p_values);
+                                println!("{}", adjusted_p_values);
                                 //let fold_changes =
                                 //    calculate_fold_change(normalized_matrix, case_indexes, control_indexes);
                             }
@@ -873,10 +876,10 @@ fn main() {
                         }
                     }
                 }
-                Err(error) => println!("Incorrect json: {}", error),
+                Err(error) => panic!("Incorrect json: {}", error),
             }
         }
-        Err(error) => println!("Piping error: {}", error),
+        Err(error) => panic!("Piping error: {}", error),
     }
 }
 
@@ -1321,7 +1324,7 @@ fn filter_by_expr(
             positives.push(row);
         }
     }
-    println!("positives length:{}", positives.len());
+    //println!("positives length:{}", positives.len());
     //println!("row_sums:{:?}", row_sums);
     //println!("keep_cpm:{:?}", keep_cpm);
     //println!("positive_cpm:{}", positive_cpm);
@@ -1337,8 +1340,8 @@ fn filter_by_expr(
     let mut filtered_genes: Vec<String> = Vec::with_capacity(positives.len());
     let mut filtered_gene_symbols: Vec<String> = Vec::with_capacity(positives.len());
     let mut i = 0;
-    println!("filtered_matrix rows:{}", filtered_matrix.nrows());
-    println!("filtered_matrix cols:{}", filtered_matrix.ncols());
+    //println!("filtered_matrix rows:{}", filtered_matrix.nrows());
+    //println!("filtered_matrix cols:{}", filtered_matrix.ncols());
     for index in positives {
         let row = raw_data.row(index);
         filtered_genes.push(gene_names[index].to_owned());

package/src/gdcmaf.rs

@@ -13,17 +13,25 @@
 use flate2::read::GzDecoder;
 use flate2::write::GzEncoder;
 use flate2::Compression;
-use serde_json::Value;
+use serde_json::{Value,json};
 use std::path::Path;
 use futures::StreamExt;
 use std::io::{self,Read,Write};
+use std::sync::Mutex;
 
 
+// Struct to hold error information
+#[derive(serde::Serialize)]
+struct ErrorEntry {
+    url: String,
+    error: String,
+}
 
-fn select_maf_col(d:String,columns:&Vec<String>) -> Vec<u8> {
+fn select_maf_col(d:String,columns:&Vec<String>,url:&str,errors: &Mutex<Vec<ErrorEntry>>) -> (Vec<u8>,i32) {
     let mut maf_str: String = String::new();
     let mut header_indices: Vec<usize> = Vec::new();
     let lines = d.trim_end().split("\n");
+    let mut mafrows = 0;
     for line in lines {
         if line.starts_with("#") {
             continue
@@ -33,6 +41,11 @@ fn select_maf_col(d:String,columns:&Vec<String>) -> Vec<u8> {
                 if let Some(index) = header.iter().position(|x| x == col) {
                     header_indices.push(index);
                 } else {
+                    let error_msg = format!("Column {} was not found", col);
+                    errors.lock().unwrap().push(ErrorEntry {
+                        url: url.to_string().clone(),
+                        error: error_msg.clone(),
+                    });
                     panic!("{} was not found!",col);
                 }
             }
@@ -44,14 +57,17 @@ fn select_maf_col(d:String,columns:&Vec<String>) -> Vec<u8> {
             };
             maf_str.push_str(maf_out_lst.join("\t").as_str());
             maf_str.push_str("\n");
+            mafrows += 1;
         }
     };
-    maf_str.as_bytes().to_vec()
+    (maf_str.as_bytes().to_vec(),mafrows)
 }
 
 
 #[tokio::main]
 async fn main() -> Result<(),Box<dyn std::error::Error>> {
+    // Create a thread-container for errors
+    let errors = Mutex::new(Vec::<ErrorEntry>::new());
     // Accepting the piped input json from jodejs and assign to the variable
     // host: GDC host
     // url: urls to download single maf files
@@ -75,9 +91,17 @@ async fn main() -> Result<(),Box<dyn std::error::Error>> {
                 .map(|v| v.to_string().replace("\"",""))
                 .collect::<Vec<String>>();
         } else {
+            errors.lock().unwrap().push(ErrorEntry {
+                url: String::new(),
+                error: "The columns of arg is not an array".to_string(),
+            });
             panic!("Columns is not an array");
         }
     } else {
+        errors.lock().unwrap().push(ErrorEntry {
+            url: String::new(),
+            error: "The key columns is missed from arg".to_string(),
+        });
         panic!("Columns was not selected");
     };
     
@@ -85,39 +109,89 @@ async fn main() -> Result<(),Box<dyn std::error::Error>> {
     let download_futures = futures::stream::iter(
         url.into_iter().map(|url|{
             async move {
-                let result = reqwest::get(&url).await;
-                if let Ok(resp) = result {
-                    let content = resp.bytes().await.unwrap();
-                    let mut decoder = GzDecoder::new(&content[..]);
-                    let mut decompressed_content = Vec::new();
-                    let read_content = decoder.read_to_end(&mut decompressed_content);
-                    if let Ok(_) = read_content {
-                        let text = String::from_utf8_lossy(&decompressed_content).to_string();
-                        text
-                    } else {
-                        let error_msg = "Failed to read content downloaded from: ".to_string() + &url;
-                        error_msg
+                match reqwest::get(&url).await {
+                    Ok(resp) if resp.status().is_success() => {
+                        match resp.bytes().await {
+                            Ok(content) => {
+                                let mut decoder = GzDecoder::new(&content[..]);
+                                let mut decompressed_content = Vec::new();
+                                match decoder.read_to_end(&mut decompressed_content) {
+                                    Ok(_) => {
+                                        let text = String::from_utf8_lossy(&decompressed_content).to_string();
+                                        return Ok((url.clone(),text))
+                                    }
+                                    Err(e) => {
+                                        let error_msg = format!("Decompression failed: {}", e);
+                                        Err((url.clone(), error_msg))
+                                    }
+                                }
+                            }
+                            Err(e) => {
+                                let error_msg = format!("Decompression failed: {}", e);
+                                Err((url.clone(), error_msg))
+                            }
+                        }
+                    }
+                    Ok(resp) => {
+                        let error_msg = format!("HTTP error: {}", resp.status());
+                        Err((url.clone(), error_msg))
+                    }
+                    Err(e) => {
+                        let error_msg = format!("Server request failed: {}", e);
+                        Err((url.clone(), error_msg))
                     }
-                } else {
-                    let error_msg = "Failed to download: ".to_string() + &url;
-                    error_msg
                 }
             }
         })
     );
 
-    // output
+    // 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");
-    download_futures.buffer_unordered(20).for_each(|item| {
-        if item.starts_with("Failed") {
-            eprintln!("{}",item);
-        } else {
-            let maf_bit = select_maf_col(item,&maf_col);
-            let _ = encoder.write_all(&maf_bit).expect("Failed to write file");
-        };
-        async {}
-    }).await;
+
+    // Collect all results before processing
+    let results = download_futures.buffer_unordered(50).collect::<Vec<_>>().await;
+
+    // Process results after all downloads are complete
+    for result in results {
+        match result {
+            Ok((url, content)) => {
+                let (maf_bit,mafrows) = select_maf_col(content, &maf_col, &url, &errors);
+                if mafrows > 0 {
+                    let _  = encoder.write_all(&maf_bit).expect("Failed to write file");
+                } else {
+                    errors.lock().unwrap().push(ErrorEntry {
+                        url: url.clone(),
+                        error: "Empty maf file".to_string(),
+                    });
+                }
+            }
+            Err((url, error)) => {
+                errors.lock().unwrap().push(ErrorEntry {
+                    url,
+                    error,
+                })
+            }
+        }
+    };
+
+    // Finalize output and printing errors
+    encoder.finish().expect("Maf file output error!");
+
+    // Manually flush stdout
+    io::stdout().flush().expect("Failed to flush stdout");
+    
+    // After processing all downloads, output the errors as JSON to stderr
+    let errors = errors.lock().unwrap();
+    if !errors.is_empty() {
+        let error_json = json!({
+            "errors": errors.iter().collect::<Vec<&ErrorEntry>>()
+        });
+        let mut stderr = io::stderr();
+        writeln!(stderr, "{}", error_json).expect("Failed to output stderr!");
+        io::stderr().flush().expect("Failed to flush stderr");
+    };
+
     Ok(())
 }