@sjcrh/proteinpaint-rust 2.178.0 → 2.180.0

package/index.js

@@ -83,6 +83,11 @@ export function run_rust(binfile, input_data, args = [], { signal } = {}) {
 	})
 }
 
+// May need to add an abort signal as argument like in run_rust above.
+// Or it's likely not needed since a closed stream connection from a web browser
+// will already trigger an error. `stream_rust()` was heavily tested manually
+// while troubleshooting and fixing the idle rust processes the led to memory leacks
+// as part of `/gdc/mafBuild` handler code, leave this code as-is for now.
 export function stream_rust(binfile, input_data, emitJson) {
 	const binpath = path.join(__dirname, '/target/release/', binfile)
 

package/package.json

@@ -1,5 +1,5 @@
 {
-	"version": "2.178.0",
+	"version": "2.180.0",
 	"name": "@sjcrh/proteinpaint-rust",
 	"type": "module",
 	"description": "Rust-based utilities for proteinpaint",

package/src/gdcmaf.rs

@@ -4,10 +4,12 @@
   Input JSON:
     host: GDC host
     fileIdLst: An array of uuid
+    headers: required headers for GDC API
   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
+      headers='{"X-Forwarded-Agent": "Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.…ML, like Gecko) Chrome/142.0.0.0 Safari/537.36 Edg/142.0.0.0", "X-Forwarded-For": "127.0.0.1"}'
+    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"], "headers": '$headers'}'|./target/release/gdcmaf
 */
 
 use flate2::Compression;
@@ -139,6 +141,31 @@ async fn main() -> Result<(), Box<dyn std::error::Error>> {
         //url.push(Path::new(&host).join(&v.as_str().unwrap()).display().to_string());
         url.push(format!("{}/{}", host.trim_end_matches('/'), v.as_str().unwrap()));
     }
+    let mut req_headers = reqwest::header::HeaderMap::new();
+    if let Some(headers_val) = file_id_lst_js.get("headers") {
+        let headers_obj = match headers_val.as_object() {
+            Some(obj) => obj,
+            None => {
+                let header_error = ErrorEntry {
+                    url: String::new(),
+                    error: "headers is not an object".to_string(),
+                };
+                let header_error_js = serde_json::to_string(&header_error).unwrap();
+                writeln!(io::stderr(), "{}", header_error_js).expect("Failed to output stderr!");
+                return Err(Box::new(std::io::Error::new(
+                    std::io::ErrorKind::InvalidInput,
+                    "headers is not an object",
+                )) as Box<dyn std::error::Error>);
+            }
+        };
+        for (key, value) in headers_obj {
+            req_headers.insert(
+                reqwest::header::HeaderName::from_bytes(key.as_bytes()).expect("Invalid header key"),
+                reqwest::header::HeaderValue::from_str(value.as_str().expect("Invalid string value"))
+                    .expect("Invalid header value"),
+            );
+        }
+    }
 
     // read columns as array from input json and convert data type from Vec<Value> to Vec<String>
     let maf_col: Vec<String>;
@@ -176,10 +203,12 @@ async fn main() -> Result<(), Box<dyn std::error::Error>> {
 
     //downloading maf files parallelly and merge them into single maf file
     let download_futures = futures::stream::iter(url.into_iter().map(|url| {
+        let req_headers_clone = req_headers.clone();
         async move {
             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 {