Merge pull request #265 from umccr/feat/c4gh-misc

refactor: C4GH and storage changes

htsget-actix/Cargo.toml

@@ -13,12 +13,12 @@ repository = "https://github.com/umccr/htsget-rs"
 [features]
 s3-storage = ["htsget-config/s3-storage", "htsget-search/s3-storage", "htsget-http/s3-storage", "htsget-axum/s3-storage", "htsget-test/s3-storage"]
 url-storage = ["htsget-config/url-storage", "htsget-search/url-storage", "htsget-http/url-storage", "htsget-axum/url-storage", "htsget-test/url-storage"]
-c4gh-experimental = [
-    "htsget-config/c4gh-experimental",
-    "htsget-search/c4gh-experimental",
-    "htsget-http/c4gh-experimental",
-    "htsget-axum/c4gh-experimental",
-    "htsget-test/c4gh-experimental"
+experimental = [
+    "htsget-config/experimental",
+    "htsget-search/experimental",
+    "htsget-http/experimental",
+    "htsget-axum/experimental",
+    "htsget-test/experimental"
 ]
 default = []
 

htsget-actix/README.md

@@ -31,7 +31,7 @@ This crate is used for running a local instance of htsget-rs. It is based on:
 
 ## Usage
 
-This application has the same functionality as [htsget-axum]. To use it, following the [htsget-axum][htsget-axum-usage] instructions, and
+This application has the same functionality as [htsget-axum]. To use it, following the [htsget-axum][htsget-axum] instructions, and
 replace any calls to `htsget-axum` with `htsget-actix`.
 
 It is recommended to use [htsget-axum] because it better fits with the rest of [htsget-rs]. For example [htsget-actix]
@@ -50,7 +50,7 @@ are exposed in the public API.
 This crate has the following features:
 * `s3-storage`: used to enable `S3Storage` functionality.
 * `url-storage`: used to enable `UrlStorage` functionality.
-* `c4gh-experimental`: used to enable `C4GHStorage` functionality.
+* `experimental`: used to enable `C4GHStorage` functionality.
 
 ## Benchmarks
 Benchmarks for this crate written using [Criterion.rs][criterion-rs], and aim to compare the performance of this crate with the
@@ -76,6 +76,7 @@ cargo bench -p htsget-axum -- HEAVY
 [criterion-rs]: https://github.com/bheisler/criterion.rs
 [htsget-refserver]: https://github.com/ga4gh/htsget-refserver
 [data-vcf]: ../data/vcf
+[htsget-axum]: ../htsget-axum/README.md#usage
 
 ## License
 

htsget-actix/src/handlers/get.rs

@@ -17,7 +17,7 @@ use super::handle_response;
 
 /// GET request reads endpoint
 #[instrument(skip(app_state))]
-pub async fn reads<H: HtsGet + Send + Sync + 'static>(
+pub async fn reads<H: HtsGet + Clone + Send + Sync + 'static>(
   request: Query<HashMap<String, String>>,
   path: Path<String>,
   http_request: HttpRequest,
@@ -32,7 +32,7 @@ pub async fn reads<H: HtsGet + Send + Sync + 'static>(
 
 /// GET request variants endpoint
 #[instrument(skip(app_state))]
-pub async fn variants<H: HtsGet + Send + Sync + 'static>(
+pub async fn variants<H: HtsGet + Clone + Send + Sync + 'static>(
   request: Query<HashMap<String, String>>,
   path: Path<String>,
   http_request: HttpRequest,

htsget-actix/src/handlers/post.rs

@@ -18,7 +18,7 @@ use super::handle_response;
 
 /// POST request reads endpoint
 #[instrument(skip(app_state))]
-pub async fn reads<H: HtsGet + Send + Sync + 'static>(
+pub async fn reads<H: HtsGet + Clone + Send + Sync + 'static>(
   request: Query<HashMap<String, String>>,
   body: Json<PostRequest>,
   path: Path<String>,
@@ -42,7 +42,7 @@ pub async fn reads<H: HtsGet + Send + Sync + 'static>(
 
 /// POST request variants endpoint
 #[instrument(skip(app_state))]
-pub async fn variants<H: HtsGet + Send + Sync + 'static>(
+pub async fn variants<H: HtsGet + Clone + Send + Sync + 'static>(
   request: Query<HashMap<String, String>>,
   body: Json<PostRequest>,
   path: Path<String>,

htsget-actix/src/handlers/service_info.rs

@@ -12,7 +12,7 @@ use crate::AppState;
 
 /// Gets the JSON to return for a service-info endpoint
 #[instrument(skip(app_state))]
-pub fn get_service_info_json<H: HtsGet + Send + Sync + 'static>(
+pub fn get_service_info_json<H: HtsGet + Clone + Send + Sync + 'static>(
   app_state: &AppState<H>,
   endpoint: Endpoint,
 ) -> impl Responder {
@@ -26,14 +26,14 @@ pub fn get_service_info_json<H: HtsGet + Send + Sync + 'static>(
 }
 
 /// Gets the JSON to return for the reads service-info endpoint
-pub async fn reads_service_info<H: HtsGet + Send + Sync + 'static>(
+pub async fn reads_service_info<H: HtsGet + Clone + Send + Sync + 'static>(
   app_state: Data<AppState<H>>,
 ) -> impl Responder {
   get_service_info_json(app_state.get_ref(), Endpoint::Reads)
 }
 
 /// Gets the JSON to return for the variants service-info endpoint
-pub async fn variants_service_info<H: HtsGet + Send + Sync + 'static>(
+pub async fn variants_service_info<H: HtsGet + Clone + Send + Sync + 'static>(
   app_state: Data<AppState<H>>,
 ) -> impl Responder {
   get_service_info_json(app_state.get_ref(), Endpoint::Variants)

htsget-actix/src/lib.rs

@@ -1,5 +1,3 @@
-use std::sync::Arc;
-
 use actix_cors::Cors;
 use actix_web::dev::Server;
 use actix_web::{web, App, HttpServer};
@@ -18,19 +16,19 @@ pub mod handlers;
 
 /// Represents the actix app state.
 pub struct AppState<H: HtsGet> {
-  pub htsget: Arc<H>,
+  pub htsget: H,
   pub config_service_info: ServiceInfo,
 }
 
 /// Configure the query server.
-pub fn configure_server<H: HtsGet + Send + Sync + 'static>(
+pub fn configure_server<H: HtsGet + Clone + Send + Sync + 'static>(
   service_config: &mut web::ServiceConfig,
   htsget: H,
   config_service_info: ServiceInfo,
 ) {
   service_config
     .app_data(web::Data::new(AppState {
-      htsget: Arc::new(htsget),
+      htsget,
       config_service_info,
     }))
     .service(

htsget-axum/Cargo.toml

@@ -24,11 +24,11 @@ url-storage = [
     "htsget-test/url-storage",
     "htsget-http/url-storage"
 ]
-c4gh-experimental = [
-    "htsget-config/c4gh-experimental",
-    "htsget-search/c4gh-experimental",
-    "htsget-test/c4gh-experimental",
-    "htsget-http/c4gh-experimental"
+experimental = [
+    "htsget-config/experimental",
+    "htsget-search/experimental",
+    "htsget-test/experimental",
+    "htsget-http/experimental"
 ]
 default = []
 
@@ -40,7 +40,7 @@ tower-http = { version = "0.5", features = ["trace", "cors", "fs"] }
 http = "1"
 axum = { version = "0.7", features = ["http2"] }
 axum-extra = { version = "0.9", features = ["erased-json"] }
-tower = { version = "0.4", features = ["make"] }
+tower = { version = "0.5", features = ["make", "util"] }
 
 # Async
 tokio-rustls = "0.26"

htsget-axum/README.md

@@ -108,7 +108,7 @@ for more details on how to configure this.
 Run the server with the following to enable Crypt4GH support using the [example config][example-config]:
 
 ```sh
-cargo run -p htsget-axum --features c4gh-experimental -- --config htsget-config/examples/config-files/c4gh.toml
+cargo run -p htsget-axum --features experimental -- --config htsget-config/examples/config-files/c4gh.toml
 ```
 
 Crypt4GH encrypted byte ranges can be queried:
@@ -171,7 +171,7 @@ htsget-rs. It also contains the data block server which fetches data from a `Loc
 This crate has the following features:
 * `s3-storage`: used to enable `S3Storage` functionality.
 * `url-storage`: used to enable `UrlStorage` functionality.
-* `c4gh-experimental`: used to enable `C4GHStorage` functionality.
+* `experimental`: used to enable `C4GHStorage` functionality.
 
 ## License
 

htsget-axum/src/handlers/post.rs

@@ -14,7 +14,7 @@ use crate::server::AppState;
 use super::handle_response;
 
 /// POST request reads endpoint.
-pub async fn reads<H: HtsGet + Send + Sync + 'static>(
+pub async fn reads<H: HtsGet + Clone + Send + Sync + 'static>(
   request: Query<HashMap<String, String>>,
   path: Path<String>,
   headers: HeaderMap,
@@ -27,7 +27,7 @@ pub async fn reads<H: HtsGet + Send + Sync + 'static>(
 }
 
 /// POST request variants endpoint.
-pub async fn variants<H: HtsGet + Send + Sync + 'static>(
+pub async fn variants<H: HtsGet + Clone + Send + Sync + 'static>(
   request: Query<HashMap<String, String>>,
   path: Path<String>,
   headers: HeaderMap,

htsget-axum/src/server/mod.rs

@@ -36,13 +36,13 @@ use crate::server::ticket::TicketServer;
 /// Represents the axum app state.
 #[derive(Debug, Clone)]
 pub struct AppState<H: HtsGet> {
-  pub(crate) htsget: Arc<H>,
+  pub(crate) htsget: H,
   pub(crate) service_info: ServiceInfo,
 }
 
 impl<H: HtsGet> AppState<H> {
   /// Create a new app state.
-  pub fn new(htsget: Arc<H>, service_info: ServiceInfo) -> Self {
+  pub fn new(htsget: H, service_info: ServiceInfo) -> Self {
     Self {
       htsget,
       service_info,

htsget-axum/src/server/ticket.rs

@@ -10,7 +10,6 @@ use htsget_config::config::cors::CorsConfig;
 use htsget_config::config::{Config, ServiceInfo, TicketServerConfig};
 use htsget_search::HtsGet;
 use std::net::SocketAddr;
-use std::sync::Arc;
 use tokio::task::JoinHandle;
 use tower::ServiceBuilder;
 use tower_http::trace::TraceLayer;
@@ -79,7 +78,7 @@ where
           .layer(TraceLayer::new_for_http())
           .layer(configure_cors(cors)),
       )
-      .with_state(AppState::new(Arc::new(htsget), service_info))
+      .with_state(AppState::new(htsget, service_info))
   }
 
   /// Get the local address the server has bound to.

htsget-config/Cargo.toml

@@ -13,13 +13,13 @@ repository = "https://github.com/umccr/htsget-rs"
 [features]
 s3-storage = []
 url-storage = ["dep:reqwest"]
-c4gh-experimental = ["dep:crypt4gh"]
+experimental = ["dep:crypt4gh"]
 default = []
 
 [dependencies]
 thiserror = "1"
 async-trait = "0.1"
-noodles = { version = "0.80", features = ["core"] }
+noodles = { version = "0.82", features = ["core"] }
 serde = { version = "1", features = ["derive"] }
 serde_with = "3"
 serde_regex = "1"

htsget-config/README.md

@@ -491,7 +491,7 @@ See the MinIO deployment [example][minio-deployment] for more information on how
 ### Crypt4GH
 
 There is experimental support for serving [Crypt4GH][c4gh] encrypted files. This can be enabled by compiling with the 
-`c4gh-experimental` feature flag.
+`experimental` feature flag.
 
 This allows htsget-rs to read Crypt4GH files and serve them encrypted, directly to the client. In the process of
 serving the data, htsget-rs will decrypt the headers of the Crypt4GH files and reencrypt them so that the client can read
@@ -535,7 +535,7 @@ regex, and changing it by using a substitution string.
 This crate has the following features:
 * `s3-storage`: used to enable `S3Storage` functionality.
 * `url-storage`: used to enable `UrlStorage` functionality.
-* `c4gh-experimental`: used to enable `C4GHStorage` functionality.
+* `experimental`: used to enable `C4GHStorage` functionality.
 
 ## License
 

htsget-config/examples/config-files/c4gh.toml

@@ -1,5 +1,5 @@
 # An example of running htsget-rs with Crypt4GH enabled.
-# Run with `cargo run -p htsget-axum --features c4gh-experimental -- --config htsget-config/examples/config-files/c4gh.toml`
+# Run with `cargo run -p htsget-axum --features experimental -- --config htsget-config/examples/config-files/c4gh.toml`
 
 ticket_server_addr = "127.0.0.1:8080"
 data_server_addr = "127.0.0.1:8081"

htsget-config/src/storage/object/mod.rs

@@ -1,10 +1,10 @@
 //! Defines the type of object used by storage.
 //!
 
-#[cfg(feature = "c4gh-experimental")]
+#[cfg(feature = "experimental")]
 pub mod c4gh;
 
-#[cfg(feature = "c4gh-experimental")]
+#[cfg(feature = "experimental")]
 use crate::storage::object::c4gh::C4GHKeys;
 use serde::{Deserialize, Serialize};
 
@@ -15,7 +15,7 @@ use serde::{Deserialize, Serialize};
 pub enum ObjectType {
   #[default]
   Regular,
-  #[cfg(feature = "c4gh-experimental")]
+  #[cfg(feature = "experimental")]
   C4GH {
     #[serde(flatten, skip_serializing)]
     keys: C4GHKeys,

htsget-http/Cargo.toml

@@ -13,7 +13,7 @@ repository = "https://github.com/umccr/htsget-rs"
 [features]
 s3-storage = ["htsget-config/s3-storage", "htsget-search/s3-storage", "htsget-test/s3-storage"]
 url-storage = ["htsget-config/url-storage", "htsget-search/url-storage", "htsget-test/url-storage"]
-c4gh-experimental = ["htsget-config/c4gh-experimental", "htsget-search/c4gh-experimental", "htsget-test/c4gh-experimental"]
+experimental = ["htsget-config/experimental", "htsget-search/experimental", "htsget-test/experimental"]
 default = []
 
 [dependencies]

htsget-http/README.md

@@ -38,7 +38,7 @@ These functions take query and endpoint information, and process it using [htsge
 This crate has the following features:
 * `s3-storage`: used to enable `S3Storage` functionality.
 * `url-storage`: used to enable `UrlStorage` functionality.
-* `c4gh-experimental`: used to enable `C4GHStorage` functionality.
+* `experimental`: used to enable `C4GHStorage` functionality.
 
 [warp]: https://github.com/seanmonstar/warp
 [htsget-search]: ../htsget-search

htsget-http/src/http_core.rs

@@ -1,5 +1,3 @@
-use std::sync::Arc;
-
 use futures::stream::FuturesOrdered;
 use futures::StreamExt;
 use tokio::select;
@@ -19,7 +17,7 @@ use crate::{
 /// consulted [here](https://samtools.github.io/hts-specs/htsget.html)
 #[instrument(level = "debug", skip_all, ret)]
 pub async fn get(
-  searcher: Arc<impl HtsGet + Send + Sync + 'static>,
+  searcher: impl HtsGet + Send + Sync + 'static,
   request: Request,
   endpoint: Endpoint,
 ) -> Result<JsonResponse> {
@@ -39,7 +37,7 @@ pub async fn get(
 /// The parameters can be consulted [here](https://samtools.github.io/hts-specs/htsget.html)
 #[instrument(level = "debug", skip_all, ret)]
 pub async fn post(
-  searcher: Arc<impl HtsGet + Send + Sync + 'static>,
+  searcher: impl HtsGet + Clone + Send + Sync + 'static,
   body: PostRequest,
   request: Request,
   endpoint: Endpoint,

htsget-http/src/lib.rs

@@ -83,7 +83,6 @@ fn merge_responses(responses: Vec<Response>) -> Option<Response> {
 mod tests {
   use std::collections::HashMap;
   use std::path::PathBuf;
-  use std::sync::Arc;
 
   use http::uri::Authority;
 
@@ -270,8 +269,8 @@ mod tests {
       .join("data")
   }
 
-  fn get_searcher() -> Arc<impl HtsGet> {
-    Arc::new(HtsGetFromStorage::new(Storage::new(
+  fn get_searcher() -> impl HtsGet + Clone {
+    HtsGetFromStorage::new(Storage::new(
       LocalStorage::new(
         get_base_path(),
         ConfigLocalStorage::new(
@@ -283,6 +282,6 @@ mod tests {
         ),
       )
       .unwrap(),
-    )))
+    ))
   }
 }

htsget-http/src/service_info.rs

@@ -1,5 +1,3 @@
-use std::sync::Arc;
-
 use serde::{Deserialize, Serialize};
 use tracing::debug;
 use tracing::instrument;
@@ -97,7 +95,7 @@ pub fn get_service_info_with(
 #[instrument(level = "debug", skip_all)]
 pub fn get_service_info_json(
   endpoint: Endpoint,
-  searcher: Arc<impl HtsGet + Send + Sync + 'static>,
+  searcher: impl HtsGet + Send + Sync + 'static,
   config: &ConfigServiceInfo,
 ) -> ServiceInfo {
   debug!(endpoint = ?endpoint,"getting service-info response for endpoint");

htsget-lambda/Cargo.toml

@@ -13,12 +13,12 @@ repository = "https://github.com/umccr/htsget-rs"
 [features]
 s3-storage = ["htsget-axum/s3-storage", "htsget-config/s3-storage", "htsget-search/s3-storage", "htsget-http/s3-storage", "htsget-test/s3-storage"]
 url-storage = ["htsget-axum/url-storage", "htsget-config/url-storage", "htsget-search/url-storage", "htsget-http/url-storage", "htsget-test/url-storage"]
-c4gh-experimental = [
-    "htsget-axum/c4gh-experimental",
-    "htsget-config/c4gh-experimental",
-    "htsget-search/c4gh-experimental",
-    "htsget-http/c4gh-experimental",
-    "htsget-test/c4gh-experimental"
+experimental = [
+    "htsget-axum/experimental",
+    "htsget-config/experimental",
+    "htsget-search/experimental",
+    "htsget-http/experimental",
+    "htsget-test/experimental"
 ]
 default = []