@sjcrh/proteinpaint-rust 2.34.0 → 2.38.0

package/Cargo.toml

@@ -26,7 +26,7 @@ serde = {version = "^1.0.147", features = ["derive"]}
 serde_json="^1.0.88"
 num = "^0.4.1"
 csv = "^1.2.2"
-#r_mathlib="^0.2.0" # Uncomment this line to activate DE expression app for high sample sizes
+r_mathlib="^0.2.0" # Uncomment this line to activate DE expression app for high sample sizes
 tokio = { version="1", features = ["full"] }
 reqwest = "0.11"
 flate2 = "1"
@@ -81,6 +81,6 @@ path="src/gene_variance.rs"
 #path="src/wilcoxon.rs"
 
 # Uncomment the lines below to use DE app for higher sample sizes
-#[[bin]]
-#name="DEanalysis"
-#path="src/DEanalysis.rs"
+[[bin]]
+name="DEanalysis"
+path="src/DEanalysis.rs"

package/package.json

@@ -1,5 +1,5 @@
 {
-  "version": "2.34.0",
+  "version": "2.38.0",
   "name": "@sjcrh/proteinpaint-rust",
   "description": "Rust-based utilities for proteinpaint",
   "main": "index.js",

package/src/gdcmaf.rs

@@ -1,3 +1,15 @@
+/*
+	This script download cohort maf files from GDC, combine them into a single file, and output the sorted file based on chromsome and Start_Position.
+
+	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/", "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;
@@ -85,14 +97,14 @@ const MAF_COL: [&str;96] = ["Hugo_Symbol", "Entrez_Gene_Id", "Center", "NCBI_Bui
 async fn main() -> Result<(),Box<dyn std::error::Error>> {
     // Accepting the piped input json from jodejs and assign to the variable
     // host: GDC host
-    // save output into json string
     // url: urls to download single maf files
     let mut buffer = String::new();
     io::stdin().read_line(&mut buffer)?;
     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["host"].as_str().unwrap();
+    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();
-    for v in file_id_lst_js["fileIdLst"].as_array().unwrap() {
+    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());
     };