Minor change to replace reqwest by ureq

Makefile

@@ -1,5 +1,5 @@
 wasm:
-	wasm-pack build --target bundler --release gtars-wasm
+	wasm-pack build --target web --release gtars-wasm
 	jq '.name = "@databio/gtars" | .repository = {"type": "git", "url": "https://github.com/databio/gtars"}' gtars-wasm/pkg/package.json > tmp.json && mv tmp.json gtars-wasm/pkg/package.json
 
 test:

gtars-bbcache/Cargo.toml

@@ -1,14 +1,14 @@
 [package]
 name = "gtars-bbcache"
-version = "0.5.1"
+version = "0.5.2"
 edition = "2024"
 description = "Rust implementation of bbcache: a caching system for BED files on bedbase.org"
 license = "MIT"
 repository = "https://github.com/databio/gtars"
 
 [dependencies]
 biocrs = "0.1.0"
-reqwest = { version = "0.12.15", features = ["blocking"] }
+ureq = "3.1.4"
 shellexpand = "3"
 tabled = "0.20.0"
 dirs = "6.0.0"
@@ -18,7 +18,7 @@ anyhow = { workspace = true }
 serde_json = { workspace = true }
 
 # our code
-gtars-core = { path = "../gtars-core", version="0.5.1" }
+gtars-core = { path = "../gtars-core", version="0.5.3" }
 
 [dev-dependencies]
 rstest = "0.26.1"

gtars-bbcache/src/client.rs

@@ -7,7 +7,7 @@ use anyhow::{Context, Ok, Result, anyhow};
 use biocrs::biocache::BioCache;
 use biocrs::models::{NewResource, Resource};
 
-use reqwest::blocking::get;
+use ureq::get;
 use std::fs::{File, create_dir_all, read_dir, remove_dir, remove_file};
 use std::io::{BufRead, BufReader, Error, ErrorKind, Write};
 use std::path::{Path, PathBuf};
@@ -367,7 +367,12 @@ impl BBClient {
     fn download_bedset_data(&self, bedset_id: &str) -> Result<Vec<String>> {
         let bedset_url = format!("{}/v1/bedset/{}/bedfiles", self.bedbase_api, bedset_id);
 
-        let response = get(&bedset_url)?.text()?;
+        let response = get(&bedset_url)
+            .call()
+            .map_err(|e| anyhow!("Failed to GET {}: {}", bedset_url, e))?
+            .body_mut()
+            .read_to_string()
+            .map_err(|e| anyhow!("Failed to read response body for {}: {}", bedset_url, e))?;
 
         let json: serde_json::Value = serde_json::from_str(&response)?;
 

gtars-core/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "gtars-core"
-version = "0.5.2"
+version = "0.5.3"
 edition = "2021"
 description = "Core library for gtars: tools for high performance genomic interval analysis"
 license = "MIT"
@@ -9,7 +9,7 @@ repository = "https://github.com/databio/gtars"
 [dependencies]
 md-5 = "0.10.6"
 num-traits = "0.2.19"
-reqwest = { version = "0.12.23", features = ["blocking"], optional=true }
+ureq = {version = "3.1.4", optional=true}
 tokio = "1.47.1"
 bigtools = { version = "0.5.6", optional = true }
 
@@ -24,4 +24,4 @@ tempfile = "3.21.0"
 [features]
 default = []
 bigbed = ["dep:bigtools"]
-http = ["dep:reqwest"]
+http = ["dep:ureq"]

gtars-core/src/models/region_set.rs

@@ -183,7 +183,7 @@ impl TryFrom<String> for RegionSet {
     type Error = anyhow::Error;
 
     fn try_from(value: String) -> Result<Self> {
-        println!("Converting String to Path: {}", value);
+        // println!("Converting String to Path: {}", value);
         RegionSet::try_from(Path::new(&value))
     }
 }
@@ -567,14 +567,13 @@ mod tests {
     }
 
     #[rstest]
-    #[ignore = "Failing but low priority for now"]
     fn test_open_from_url() {
-        let file_path = String::from("https://github.com/databio/gtars/raw/refs/heads/master/gtars/tests/data/regionset/dummy.narrowPeak.bed.gz");
+        let file_path = String::from("https://www.encodeproject.org/files/ENCFF321QPN/@@download/ENCFF321QPN.bed.gz");
         assert!(RegionSet::try_from(file_path).is_ok());
     }
 
     #[rstest]
-    #[ignore = "Failing but low priority"]
+    #[ignore = "Avoid BEDbase dependency in CI"]
     fn test_open_from_bedbase() {
         let bbid = String::from("6b2e163a1d4319d99bd465c6c78a9741");
         let region_set = RegionSet::try_from(bbid);

gtars-core/src/utils.rs

@@ -8,9 +8,9 @@ use std::str::FromStr;
 
 use anyhow::{Context, Result};
 use flate2::read::{GzDecoder, MultiGzDecoder};
-#[cfg(feature = "http")]
-use reqwest::blocking::Client;
 use std::error::Error;
+#[cfg(feature = "http")]
+use ureq::{get, Error as UreqError};
 
 use crate::models::region::Region;
 
@@ -133,31 +133,42 @@ pub fn get_dynamic_reader(path: &Path) -> Result<BufReader<Box<dyn Read>>> {
 pub fn get_dynamic_reader_from_url(
     url: &Path,
 ) -> Result<BufReader<Box<dyn std::io::Read>>, Box<dyn Error>> {
-    // Create an HTTP client and fetch the content
-    let mut url: String = url.to_str().unwrap().to_string();
-
-    let is_ftp: bool = url.starts_with("ftp");
+    let mut url_str = url
+        .to_str()
+        .ok_or_else(|| "URL path is not valid UTF-8")?
+        .to_string();
 
+    let is_ftp = url_str.starts_with("ftp://");
     if is_ftp {
         println!("ftp is not fully implemented. Bugs could appear");
-        url = url.replacen("ftp://", "http://", 1);
+        url_str = url_str.replacen("ftp://", "http://", 1);
     }
 
-    let response = Client::new()
-        .get(&url)
-        .send()
-        .with_context(|| format!("Failed to fetch content from URL: {}", &url))?
-        .error_for_status()?
-        .bytes()?;
+    let is_gzipped = url_str.ends_with(".gz");
 
-    // Convert the response into a cursor for reading
-    let cursor = Cursor::new(response);
+    // Perform request
+    let response = match get(&url_str).call() {
+        Ok(resp) => resp,
+        Err(UreqError::StatusCode(code)) => {
+            return Err(format!("HTTP status {} when fetching {}", code, url_str).into())
+        }
+        Err(e) => return Err(format!("Request error when fetching {}: {}", url_str, e).into()),
+    };
+
+    // Read the entire HTTP response body into memory as a Vec<u8>
+    let mut bytes = Vec::new();
+    response
+        .into_body()
+        .into_reader()
+        .read_to_end(&mut bytes)
+        .map_err(|e| format!("Failed reading response body from {}: {}", url_str, e))?;
 
-    let is_gzipped = url.ends_with(".gz");
+    let cursor = Cursor::new(bytes);
 
-    let reader: Box<dyn std::io::Read> = match is_gzipped {
-        true => Box::new(GzDecoder::new(cursor)),
-        false => Box::new(cursor),
+    let reader: Box<dyn std::io::Read> = if is_gzipped {
+        Box::new(GzDecoder::new(cursor))
+    } else {
+        Box::new(cursor)
     };
 
     Ok(BufReader::new(reader))

gtars-python/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "gtars-py"
-version = "0.5.2"
+version = "0.5.3"
 edition = "2021"
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html

gtars/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "gtars"
-version = "0.5.1"
+version = "0.5.2"
 edition = "2024"
 description = "Performance critical tools for genomic interval analysis."
 homepage = "https://github.com/databio/gtars"
@@ -12,7 +12,7 @@ categories = ["science::bioinformatics::genomics", "science::bioinformatics"]
 
 
 [dependencies]
-gtars-core = { path = "../gtars-core", optional = true, version="0.5.1", features = ["bigbed", "http"] }
+gtars-core = { path = "../gtars-core", optional = true, version="0.5.3", features = ["bigbed"] }
 gtars-tokenizers = { path = "../gtars-tokenizers", features = ["huggingface"], optional = true, version="0.5.1" }
 gtars-io = { path = "../gtars-io", optional = true, version="0.5.0" }
 gtars-refget = { path = "../gtars-refget", optional = true, version="0.5.0" }