Merge branch 'main' of https://github.com/umccr/htsget-rs into feature/aws-vpc-lattice-support

# Conflicts:
#	Cargo.lock
#	htsget-lambda/src/main.rs

Author: mmalenic

Cargo.lock

@@ -7,6 +7,30 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [0.11.2](https://github.com/umccr/htsget-rs/compare/htsget-actix-v0.11.1...htsget-actix-v0.11.2) - 2025-09-03
+
+### Added
+
+- add auth logic to post requests and always allow headers to succeed
+- add suppressed errors options to axum and actix ticket servers
+
+## [0.11.1](https://github.com/umccr/htsget-rs/compare/htsget-actix-v0.11.0...htsget-actix-v0.11.1) - 2025-08-21
+
+### Other
+
+- update Cargo.lock dependencies
+
+## [0.11.0](https://github.com/umccr/htsget-rs/compare/htsget-actix-v0.10.0...htsget-actix-v0.11.0) - 2025-08-15
+
+### Fixed
+
+- [**breaking**] add restrictions to file locations and ensure that the data server local path lines up as expected
+
+### Other
+
+- remove duplicate changelog section
+- Merge pull request #320 from umccr/feat/auth
+
 ## [0.10.0](https://github.com/umccr/htsget-rs/compare/htsget-actix-v0.9.0...htsget-actix-v0.10.0) - 2025-08-11
 
 ### Added

htsget-actix/CHANGELOG.md

@@ -1,6 +1,6 @@
 [package]
 name = "htsget-actix"
-version = "0.10.0"
+version = "0.11.2"
 rust-version = "1.86"
 authors = ["Daniel del Castillo de la Rosa <[email protected]>", "Marko Malenic <[email protected]>", "Roman Valls Guimera <[email protected]>"]
 edition = "2024"
@@ -26,6 +26,7 @@ default = []
 actix-web = { version = "4", features = ["rustls-0_23"] }
 rustls = "0.23"
 actix-cors = "0.7"
+actix-utils = "3"
 http_1 = { package = "http", version = "1" }
 http = "0.2"
 serde = { version = "1", features = ["derive"] }
@@ -39,10 +40,10 @@ axum = { version = "0.8", features = ["http2"] }
 tracing-actix-web = "0.7"
 tracing = "0.1"
 
-htsget-http = { version = "0.7.0", path = "../htsget-http", default-features = false }
-htsget-search = { version = "0.11.1", path = "../htsget-search", default-features = false }
-htsget-config = { version = "0.15.1", path = "../htsget-config", default-features = false }
-htsget-axum = { version = "0.5.0", path = "../htsget-axum", default-features = false }
+htsget-http = { version = "0.7.3", path = "../htsget-http", default-features = false }
+htsget-search = { version = "0.11.4", path = "../htsget-search", default-features = false }
+htsget-config = { version = "0.17.0", path = "../htsget-config", default-features = false }
+htsget-axum = { version = "0.6.2", path = "../htsget-axum", default-features = false }
 
 [dev-dependencies]
 htsget-test = { path = "../htsget-test", features = ["http"], default-features = false }

htsget-actix/Cargo.toml

@@ -230,6 +230,7 @@ fn criterion_benchmark(c: &mut Criterion) {
     tags: None,
     notags: None,
     regions: None,
+    encryption_scheme: None,
   };
   bench_pair(
     &mut group,
@@ -250,6 +251,7 @@ fn criterion_benchmark(c: &mut Criterion) {
       start: None,
       end: None,
     }]),
+    encryption_scheme: None,
   };
   bench_pair(
     &mut group,
@@ -277,6 +279,7 @@ fn criterion_benchmark(c: &mut Criterion) {
         end: Some(5008321),
       },
     ]),
+    encryption_scheme: None,
   };
   bench_pair(
     &mut group,
@@ -297,6 +300,7 @@ fn criterion_benchmark(c: &mut Criterion) {
       start: Some(1),
       end: Some(153),
     }]),
+    encryption_scheme: None,
   };
   bench_pair(
     &mut group,
@@ -317,6 +321,7 @@ fn criterion_benchmark(c: &mut Criterion) {
       start: None,
       end: None,
     }]),
+    encryption_scheme: None,
   };
   bench_pair(
     &mut group,

htsget-actix/benches/request_benchmarks.rs

@@ -1,33 +1,43 @@
 use std::collections::HashMap;
 
+use actix_web::web::ReqData;
 use actix_web::{
   HttpRequest, Responder,
   web::{Data, Path, Query},
 };
-use tracing::info;
-use tracing::instrument;
-
 use htsget_http::{Endpoint, get};
 use htsget_search::HtsGet;
+use serde_json::Value;
+use tracing::info;
+use tracing::instrument;
 
+use super::handle_response;
 use crate::AppState;
 use crate::handlers::extract_request;
 
-use super::handle_response;
-
 /// GET request reads endpoint
 #[instrument(skip(app_state))]
 pub async fn reads<H: HtsGet + Clone + Send + Sync + 'static>(
   request: Query<HashMap<String, String>>,
   path: Path<String>,
   http_request: HttpRequest,
+  extension: Option<ReqData<Value>>,
   app_state: Data<AppState<H>>,
 ) -> impl Responder {
   let request = extract_request(request, path, http_request);
 
   info!(request = ?request, "reads endpoint GET request");
 
-  handle_response(get(app_state.get_ref().htsget.clone(), request, Endpoint::Reads).await)
+  handle_response(
+    get(
+      app_state.get_ref().htsget.clone(),
+      request,
+      Endpoint::Reads,
+      app_state.auth.clone(),
+      extension.map(|extension| extension.into_inner()),
+    )
+    .await,
+  )
 }
 
 /// GET request variants endpoint
@@ -36,6 +46,7 @@ pub async fn variants<H: HtsGet + Clone + Send + Sync + 'static>(
   request: Query<HashMap<String, String>>,
   path: Path<String>,
   http_request: HttpRequest,
+  extension: Option<ReqData<Value>>,
   app_state: Data<AppState<H>>,
 ) -> impl Responder {
   let request = extract_request(request, path, http_request);
@@ -47,6 +58,8 @@ pub async fn variants<H: HtsGet + Clone + Send + Sync + 'static>(
       app_state.get_ref().htsget.clone(),
       request,
       Endpoint::Variants,
+      app_state.auth.clone(),
+      extension.map(|extension| extension.into_inner()),
     )
     .await,
   )

htsget-actix/src/handlers/get.rs

@@ -2,10 +2,9 @@ use std::collections::HashMap;
 
 use actix_web::web::{Path, Query};
 use actix_web::{Either, HttpRequest, Responder, http::StatusCode};
-use http::{HeaderMap as HttpHeaderMap, HeaderName, Method};
-
 use htsget_config::types::{JsonResponse, Request};
 use htsget_http::Result;
+use http::{HeaderMap as HttpHeaderMap, HeaderName, Method};
 use pretty_json::PrettyJson;
 
 pub use crate::handlers::service_info::{
@@ -16,7 +15,7 @@ pub mod get;
 pub mod post;
 pub mod service_info;
 
-mod pretty_json;
+pub(crate) mod pretty_json;
 
 pub(crate) struct HeaderMap(HttpHeaderMap);
 

htsget-actix/src/handlers/mod.rs

@@ -1,28 +1,27 @@
 use std::collections::HashMap;
 
-use actix_web::web::Query;
+use actix_web::web::{Query, ReqData};
 use actix_web::{
   HttpRequest, Responder,
   web::{Data, Json, Path},
 };
-use tracing::info;
-use tracing::instrument;
-
 use htsget_http::{Endpoint, PostRequest, post};
 use htsget_search::HtsGet;
+use serde_json::Value;
+use tracing::info;
+use tracing::instrument;
 
+use super::{extract_request, handle_response};
 use crate::AppState;
-use crate::handlers::extract_request;
-
-use super::handle_response;
 
 /// POST request reads endpoint
 #[instrument(skip(app_state))]
 pub async fn reads<H: HtsGet + Clone + Send + Sync + 'static>(
   request: Query<HashMap<String, String>>,
-  body: Json<PostRequest>,
   path: Path<String>,
   http_request: HttpRequest,
+  extension: Option<ReqData<Value>>,
+  body: Json<PostRequest>,
   app_state: Data<AppState<H>>,
 ) -> impl Responder {
   let request = extract_request(request, path, http_request);
@@ -35,6 +34,8 @@ pub async fn reads<H: HtsGet + Clone + Send + Sync + 'static>(
       body.into_inner(),
       request,
       Endpoint::Reads,
+      app_state.auth.clone(),
+      extension.map(|extension| extension.into_inner()),
     )
     .await,
   )
@@ -44,9 +45,10 @@ pub async fn reads<H: HtsGet + Clone + Send + Sync + 'static>(
 #[instrument(skip(app_state))]
 pub async fn variants<H: HtsGet + Clone + Send + Sync + 'static>(
   request: Query<HashMap<String, String>>,
-  body: Json<PostRequest>,
   path: Path<String>,
   http_request: HttpRequest,
+  extension: Option<ReqData<Value>>,
+  body: Json<PostRequest>,
   app_state: Data<AppState<H>>,
 ) -> impl Responder {
   let request = extract_request(request, path, http_request);
@@ -59,6 +61,8 @@ pub async fn variants<H: HtsGet + Clone + Send + Sync + 'static>(
       body.into_inner(),
       request,
       Endpoint::Variants,
+      app_state.auth.clone(),
+      extension.map(|extension| extension.into_inner()),
     )
     .await,
   )

htsget-actix/src/handlers/post.rs

@@ -4,15 +4,28 @@ use serde::Serialize;
 
 pub struct PrettyJson<T>(pub T);
 
+impl<T> TryFrom<PrettyJson<T>> for String
+where
+  T: Serialize,
+{
+  type Error = serde_json::Error;
+
+  fn try_from(json: PrettyJson<T>) -> Result<Self, Self::Error> {
+    let mut body = serde_json::to_string_pretty(&json.0)?;
+    body.push('\n');
+
+    Ok(body)
+  }
+}
+
 impl<T: Serialize> Responder for PrettyJson<T> {
   type Body = BoxBody;
 
   fn respond_to(self, _: &HttpRequest) -> HttpResponse {
-    let mut body = match serde_json::to_string_pretty(&self.0) {
+    let body = match String::try_from(self) {
       Ok(body) => body,
-      Err(e) => return HttpResponse::from_error(e),
+      Err(err) => return HttpResponse::from_error(err),
     };
-    body.push('\n');
 
     HttpResponse::build(StatusCode::OK)
       .content_type("application/json")