@sjcrh/proteinpaint-rust 2.177.0 → 2.178.0

package/index.js

@@ -26,13 +26,30 @@ const binaryDir = path.join(__dirname, '/target/release/')
 if (!fs.existsSync(binaryDir)) throw `missing rust binary directory='${binaryDir}'`
 if (!fs.readdirSync(binaryDir).length) throw `empty rust binary directory='${binaryDir}'`
 
-export function run_rust(binfile, input_data, args = []) {
+export function run_rust(binfile, input_data, args = [], { signal } = {}) {
 	return new Promise((resolve, reject) => {
 		const binpath = path.join(__dirname, '/target/release/', binfile)
+
+		if (signal?.aborted) {
+			reject(new Error(`run_rust('${binfile}'): aborted before start`))
+			return
+		}
+
 		const ps = spawn(binpath, args)
 		const stdout = []
 		const stderr = []
 
+		if (signal) {
+			const onAbort = () => {
+				if (!ps.killed) {
+					ps.kill()
+					reject(new Error(`run_rust('${binfile}'): aborted`))
+				}
+			}
+			signal.addEventListener('abort', onAbort, { once: true })
+			ps.on('close', () => signal.removeEventListener('abort', onAbort))
+		}
+
 		try {
 			Readable.from(input_data).pipe(ps.stdin)
 		} catch (error) {

package/package.json

@@ -1,5 +1,5 @@
 {
-	"version": "2.177.0",
+	"version": "2.178.0",
 	"name": "@sjcrh/proteinpaint-rust",
 	"type": "module",
 	"description": "Rust-based utilities for proteinpaint",

package/src/validateHDF5.rs

@@ -1,7 +1,7 @@
 // syntax:
 // echo '{"hdf5_file":"/path/to/my/local/file.h5"}' | ./target/release/validateHDF5
 
-use hdf5::types::VarLenAscii;
+use hdf5::types::{VarLenAscii, VarLenUnicode};
 use hdf5::{File, Result};
 use ndarray::Array1;
 use ndarray::Dim;
@@ -20,12 +20,17 @@ pub fn detect_hdf5_format(hdf5_filename: &str) -> Result<&'static str> {
     let has_data_group = file.group("data").is_ok();
     let has_sample_names = file.dataset("sample_names").is_ok();
 
+    // Check for promoter DNA methylation format (has meta/samples/names)
+    let has_meta_sample_names = file.dataset("meta/samples/names").is_ok();
+
     if has_counts && has_gene_names && has_samples {
         // eprintln!("Dense format detected");
         Ok("dense")
     } else if has_data_group && has_sample_names {
         // eprintln!("Sparse format detected");
         Ok("sparse")
+    } else if has_meta_sample_names {
+        Ok("dna_meth_promoter")
     } else {
         // eprintln!("Unknown format detected");
         Ok("unknown")
@@ -132,6 +137,27 @@ pub fn validate_hdf5_file(hdf5_filename: String) -> Result<()> {
                 }
             })
         }
+        "dna_meth_promoter" => {
+            // For promoter DNA methylation format - only read sample names
+            let mut sample_names: Vec<String> = Vec::new();
+            if let Ok(ds_samples) = file.dataset("meta/samples/names") {
+                if let Ok(samples) = ds_samples.read_1d::<VarLenUnicode>() {
+                    for sample in samples.iter() {
+                        sample_names.push(sample.to_string());
+                    }
+                } else {
+                    eprintln!("Error reading meta/samples/names as VarLenUnicode");
+                }
+            }
+
+            serde_json::json!({
+                "status": "success",
+                "message": "HDF5 promoter DNA methylation file loaded successfully",
+                "file_path": hdf5_filename,
+                "format": "dna_meth_promoter",
+                "sampleNames": sample_names
+            })
+        }
         _ => {
             // For unknown format
             serde_json::json!({