@sjcrh/proteinpaint-rust 2.191.6 → 2.193.0

package/Cargo.toml

@@ -25,7 +25,6 @@ statrs = "^0.16.0"
 libc = "0.2"
 fishers_exact="^1.0.1"
 bio = "1.5.0"
-bigtools = "^0.1.11"
 libmath = "^0.2.1"
 json = "^0.12.4"
 serde = {version = "^1.0.147", features = ["derive"]}
@@ -67,9 +66,6 @@ path="src/indel.rs"
 name="fisher"
 path="src/fisher.rs"
 
-[[bin]]
-name="bigwig"
-path="src/bigwig.rs"
 
 [[bin]]
 name="sv"
@@ -107,10 +103,6 @@ path="src/readHDF5.rs"
 name="validateHDF5"
 path="src/validateHDF5.rs"
 
-[[bin]]
-name="gdcGRIN2"
-path="src/gdcGRIN2.rs"
-
 [[bin]]
 name="cerno"
 path="src/cerno.rs"

package/package.json

@@ -1,5 +1,5 @@
 {
-	"version": "2.191.6",
+	"version": "2.193.0",
 	"name": "@sjcrh/proteinpaint-rust",
 	"type": "module",
 	"description": "Rust-based utilities for proteinpaint",

package/src/gdcmaf.rs

@@ -201,46 +201,24 @@ async fn main() -> Result<(), Box<dyn std::error::Error>> {
         )) as Box<dyn std::error::Error>);
     };
 
-    let client = reqwest::Client::builder()
-        .timeout(Duration::from_secs(30)) // 30-second timeout per request
-        .connect_timeout(Duration::from_secs(15))
-        .pool_max_idle_per_host(0) // avoid "connection closed before message completed" race
-        .build()
-        .map_err(|e| {
-            let client_error = ErrorEntry {
-                url: String::new(),
-                error: format!("Client build error: {}", e),
-            };
-            let client_error_js = serde_json::to_string(&client_error)
-                .unwrap_or_else(|_| "{\"url\":\"\",\"error\":\"Failed to serialize client build error\"}".to_string());
-            writeln!(io::stderr(), "{}", client_error_js).expect("Failed to write client build error to stderr");
-            e
-        })?;
-
     //downloading maf files parallelly and merge them into single maf file
     let download_futures = futures::stream::iter(url.into_iter().map(|url| {
-        let client = client.clone();
-        let req_headers = req_headers.clone();
+        let req_headers_clone = req_headers.clone();
         async move {
-            // bounded retry for transient transport failures
-            // (IncompleteMessage / TimedOut / connect), up to 3 attempts with backoff
-            let mut attempt: u32 = 0;
-            let send_result = loop {
-                attempt += 1;
-                let mut request = client.get(&url);
-                for (name, value) in req_headers.iter() {
-                    request = request.header(name.clone(), value.clone()); // == .header("X-Forwarded-Agent", …) etc.
-                }
-                match request.send().await {
-                    Ok(resp) => break Ok(resp),
-                    Err(e) if attempt < 3 && (e.is_request() || e.is_timeout() || e.is_connect()) => {
-                        tokio::time::sleep(Duration::from_millis(500 * attempt as u64)).await;
-                        continue;
-                    }
-                    Err(e) => break Err(e),
-                }
-            };
-            match send_result {
+            let client = reqwest::Client::builder()
+                .timeout(Duration::from_secs(60)) // 60-second timeout per request
+                .connect_timeout(Duration::from_secs(15))
+                .default_headers(req_headers_clone.clone())
+                .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) => {
                         let mut decoder = GzDecoder::new(&content[..]);
@@ -262,11 +240,11 @@ async fn main() -> Result<(), Box<dyn std::error::Error>> {
                     }
                 },
                 Ok(resp) => {
-                    let error_msg = format!("HTTP error: {:?}", resp.status());
+                    let error_msg = format!("HTTP error: {}", resp.status());
                     Err((url.clone(), error_msg))
                 }
                 Err(e) => {
-                    let error_msg = format!("Server request failed: {:?}", e);
+                    let error_msg = format!("Server request failed: {}", e);
                     Err((url.clone(), error_msg))
                 }
             }
@@ -286,7 +264,7 @@ async fn main() -> Result<(), Box<dyn std::error::Error>> {
     }
 
     download_futures
-        .buffer_unordered(10)
+        .buffer_unordered(20)
         .for_each(|result| {
             let encoder = Arc::clone(&encoder); // Clone the Arc for each task
             let maf_col_cp = maf_col.clone();