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Minor change to replace reqwest by ureq #218

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Merged
khoroshevskyi merged 10 commits into from
Dec 10, 2025
Merged

Minor change to replace reqwest by ureq #218

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e2c535a
save draft before test
ClaudeHu Dec 8, 2025
4261b5f
adjustmenet for different version
ClaudeHu Dec 8, 2025
81d528d
remove comments
ClaudeHu Dec 8, 2025
9766858
save draft
ClaudeHu Dec 9, 2025
00e3e95
pass test
ClaudeHu Dec 10, 2025
6560677
avoid url within this repo
ClaudeHu Dec 10, 2025
d227eb0
avoid BEDbase usage in test
ClaudeHu Dec 10, 2025
8923084
Update gtars-core/src/utils.rs
ClaudeHu Dec 10, 2025
d193cb9
Updated rust and python versions
khoroshevskyi Dec 10, 2025
5c1cb78
adjustment for more Rust-like code
ClaudeHu Dec 10, 2025
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2 changes: 1 addition & 1 deletion gtars-bbcache/Cargo.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ 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"
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9 changes: 7 additions & 2 deletions gtars-bbcache/src/client.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -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};
Expand Down Expand Up @@ -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()
Comment on lines +373 to +374
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Copilot AI Dec 8, 2025

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The .body_mut().read_to_string() pattern is incorrect for ureq. The read_to_string() method from std::io::Read requires a mutable String buffer as an argument (e.g., read_to_string(&mut buffer)), but this code doesn't provide one.

For ureq 3.x, the correct pattern is to use .into_string() which consumes the response and returns Result<String, Error>:

let response = get(&bedset_url)
    .call()
    .map_err(|e| anyhow!("Failed to GET {}: {}", bedset_url, e))?
    .into_string()
    .map_err(|e| anyhow!("Failed to read response body for {}: {}", bedset_url, e))?;

This is more idiomatic, handles errors properly, and avoids the need for the intermediate .body_mut() call.

Suggested change
.body_mut()
.read_to_string()
.into_string()

Copilot uses AI. Check for mistakes.
.map_err(|e| anyhow!("Failed to read response body for {}: {}", bedset_url, e))?;

let json: serde_json::Value = serde_json::from_str(&response)?;

Expand Down