Merge pull request #303 from umccr/build/deps-update

build: deps update

htsget-actix/Cargo.toml

@@ -28,11 +28,8 @@ rustls = "0.23"
 actix-cors = "0.7"
 http_1 = { package = "http", version = "1" }
 http = "0.2"
-rustls-pemfile = "2"
 serde = { version = "1", features = ["derive"] }
 serde_json = "1"
-futures-util = { version = "0.3" }
-futures = { version = "0.3" }
 tokio = { version = "1", features = ["macros", "rt-multi-thread"] }
 
 tracing-actix-web = "0.7"
@@ -41,10 +38,11 @@ tracing = "0.1"
 htsget-http = { version = "0.5.2", path = "../htsget-http", default-features = false }
 htsget-search = { version = "0.10.0", path = "../htsget-search", default-features = false }
 htsget-config = { version = "0.13.0", path = "../htsget-config", default-features = false }
-htsget-test = { version = "0.7.2", path = "../htsget-test", features = ["http"], default-features = false }
 htsget-axum = { version = "0.3.0", path = "../htsget-axum", default-features = false }
 
 [dev-dependencies]
+htsget-test = { path = "../htsget-test", features = ["http"], default-features = false }
+
 async-trait = "0.1"
 
 criterion = { version = "0.5", features = ["async_tokio"] }

htsget-axum/Cargo.toml

@@ -39,27 +39,25 @@ rustls = "0.23"
 hyper-util = "0.1"
 tower-http = { version = "0.6", features = ["trace", "cors", "fs"] }
 http = "1"
-axum = { version = "0.7", features = ["http2"] }
-axum-extra = { version = "0.9", features = ["erased-json"] }
+axum = { version = "0.8", features = ["http2"] }
+axum-extra = { version = "0.10", features = ["erased-json"] }
 tower = { version = "0.5", features = ["make", "util"] }
 
 # Async
 tokio-rustls = "0.26"
 tokio = { version = "1", features = ["macros", "rt-multi-thread"] }
-futures = { version = "0.3" }
 async-trait = "0.1"
 
 # Tracing and error
-thiserror = "1"
+thiserror = "2"
 tracing = "0.1"
 
 htsget-config = { version = "0.13.0", path = "../htsget-config", default-features = false }
-htsget-test = { version = "0.7.2", path = "../htsget-test", features = ["http"], default-features = false }
 htsget-search = { version = "0.10.0", path = "../htsget-search", default-features = false }
 htsget-http = { version = "0.5.2", path = "../htsget-http", default-features = false }
 
 [dev-dependencies]
-tempfile = "3"
-data-url = "0.3"
+htsget-test = { path = "../htsget-test", features = ["http"], default-features = false }
 
+tempfile = "3"
 reqwest = { version = "0.12", default-features = false, features = ["json", "blocking", "rustls-tls"] }

htsget-axum/src/server/data.rs

@@ -34,7 +34,7 @@ impl DataServer {
   /// Create the router for the data server.
   pub fn router<P: AsRef<Path>>(cors: CorsConfig, path: P) -> Router {
     Router::new()
-      .nest_service("/", ServeDir::new(path))
+      .fallback_service(ServeDir::new(path))
       .layer(configure_cors(cors))
       .layer(TraceLayer::new_for_http())
   }

htsget-axum/src/server/ticket.rs

@@ -11,6 +11,7 @@ use htsget_config::config::service_info::ServiceInfo;
 use htsget_config::config::ticket_server::TicketServerConfig;
 use htsget_config::config::Config;
 use htsget_search::HtsGet;
+use http::{StatusCode, Uri};
 use std::net::SocketAddr;
 use tokio::task::JoinHandle;
 use tower::ServiceBuilder;
@@ -69,12 +70,13 @@ where
         "/reads/service-info",
         get(reads_service_info::<H>).post(reads_service_info::<H>),
       )
-      .route("/reads/*id", get(get::reads).post(post::reads))
+      .route("/reads/{*id}", get(get::reads).post(post::reads))
       .route(
         "/variants/service-info",
         get(variants_service_info::<H>).post(variants_service_info::<H>),
       )
-      .route("/variants/*id", get(get::variants).post(post::variants))
+      .route("/variants/{*id}", get(get::variants).post(post::variants))
+      .fallback(Self::fallback)
       .layer(
         ServiceBuilder::new()
           .layer(TraceLayer::new_for_http())
@@ -87,6 +89,11 @@ where
   pub fn local_addr(&self) -> Result<SocketAddr> {
     self.server.local_addr()
   }
+
+  /// A handler for when a route is not found.
+  async fn fallback(uri: Uri) -> (StatusCode, String) {
+    (StatusCode::NOT_FOUND, format!("No route for {uri}"))
+  }
 }
 
 /// Spawn a task to run the ticket server.

htsget-config/Cargo.toml

@@ -17,11 +17,10 @@ experimental = ["dep:crypt4gh", "dep:tokio", "dep:futures-util"]
 default = []
 
 [dependencies]
-thiserror = "1"
+thiserror = "2"
 async-trait = "0.1"
-noodles = { version = "0.83", features = ["core"] }
+noodles = { version = "0.87", features = ["core"] }
 serde = { version = "1", features = ["derive"] }
-serde_with = "3"
 serde_json = "1"
 serde_regex = "1"
 regex = "1"

htsget-http/Cargo.toml

@@ -17,14 +17,16 @@ experimental = ["htsget-config/experimental", "htsget-search/experimental", "hts
 default = []
 
 [dependencies]
-thiserror = "1"
+thiserror = "2"
 serde = { version = "1", features = ["derive"] }
 serde_json = "1"
 http = "1"
 htsget-search = { version = "0.10.0", path = "../htsget-search", default-features = false }
 htsget-config = { version = "0.13.0", path = "../htsget-config", default-features = false }
-htsget-test = { version = "0.7.2", path = "../htsget-test", default-features = false }
 futures = { version = "0.3" }
 tokio = { version = "1", features = ["macros", "rt-multi-thread"] }
 tracing = "0.1"
 cfg-if = "1"
+
+[dev-dependencies]
+htsget-test = { path = "../htsget-test", default-features = false }

htsget-lambda/Cargo.toml

@@ -11,38 +11,21 @@ homepage = "https://github.com/umccr/htsget-rs/blob/main/htsget-lambda/README.md
 repository = "https://github.com/umccr/htsget-rs"
 
 [features]
-aws = ["htsget-axum/aws", "htsget-config/aws", "htsget-search/aws", "htsget-http/aws", "htsget-test/aws"]
-url = ["htsget-axum/url", "htsget-config/url", "htsget-search/url", "htsget-http/url", "htsget-test/url"]
+aws = ["htsget-axum/aws", "htsget-config/aws", "htsget-http/aws"]
+url = ["htsget-axum/url", "htsget-config/url", "htsget-http/url"]
 experimental = [
     "htsget-axum/experimental",
     "htsget-config/experimental",
-    "htsget-search/experimental",
-    "htsget-http/experimental",
-    "htsget-test/experimental"
+    "htsget-http/experimental"
 ]
 default = []
 
 [dependencies]
 tokio = { version = "1", features = ["macros", "rt-multi-thread"] }
-tower-http = { version = "0.6", features = ["cors"] }
 rustls = "0.23"
-lambda_http = { version = "0.13" }
-lambda_runtime = { version = "0.13" }
-serde = { version = "1" }
-serde_json = "1"
-mime = "0.3"
-regex = "1"
+lambda_http = { version = "0.14" }
 tracing = "0.1"
-tracing-subscriber = "0.3"
-bytes = "1"
 
 htsget-config = { version = "0.13.0", path = "../htsget-config", default-features = false }
-htsget-search = { version = "0.10.0", path = "../htsget-search", default-features = false }
 htsget-http = { version = "0.5.2", path = "../htsget-http", default-features = false }
-htsget-test = { version = "0.7.2", path = "../htsget-test", features = ["http"], default-features = false }
 htsget-axum = { version = "0.3.0", path = "../htsget-axum", default-features = false }
-
-[dev-dependencies]
-async-trait = "0.1"
-query_map = { version = "0.7", features = ["url-query"] }
-tempfile = "3"

htsget-search/Cargo.toml

@@ -37,21 +37,20 @@ futures-util = "0.3"
 async-trait = "0.1"
 
 # Noodles
-noodles = { version = "0.83", features = ["async", "core", "bgzf", "bam", "bcf", "cram", "csi", "sam", "tabix", "vcf"] }
+noodles = { version = "0.87", features = ["async", "core", "bgzf", "bam", "bcf", "cram", "csi", "sam", "tabix", "vcf"] }
 
 # Error control, tracing, config
-thiserror = "1"
+http = "1"
 tracing = "0.1"
 
 htsget-config = { version = "0.13.0", path = "../htsget-config", default-features = false }
 htsget-storage = { version = "0.3.0", path = "../htsget-storage", default-features = false }
-htsget-test = { version = "0.7.2", path = "../htsget-test", features = ["http"], default-features = false }
 
 [dev-dependencies]
 tempfile = "3"
-http = "1"
 
 criterion = { version = "0.5", features = ["async_tokio"] }
+htsget-test = { path = "../htsget-test", features = ["http"], default-features = false }
 
 [[bench]]
 name = "search-benchmarks"

htsget-search/src/cram_search.rs

@@ -21,7 +21,7 @@ use htsget_config::types::Interval;
 
 use crate::search::{Search, SearchAll, SearchReads};
 use crate::Class::Body;
-use crate::{ConcurrencyError, ParsedHeader};
+use crate::ConcurrencyError;
 use crate::{Format, HtsGetError, Query, Result};
 use htsget_storage::types::{BytesPosition, DataBlock};
 use htsget_storage::{Storage, Streamable};
@@ -137,15 +137,7 @@ impl Search<PhantomData<Self>, Index, AsyncReader, Header> for CramSearch {
   }
 
   async fn read_header(reader: &mut AsyncReader) -> io::Result<Header> {
-    reader.read_file_definition().await?;
-
-    Ok(
-      reader
-        .read_file_header()
-        .await?
-        .parse::<ParsedHeader<Header>>()?
-        .into_inner(),
-    )
+    reader.read_header().await
   }
 
   async fn read_index_inner<T: AsyncRead + Send + Unpin>(inner: T) -> io::Result<Index> {

htsget-search/src/lib.rs

@@ -12,9 +12,6 @@ pub use htsget_storage::Storage;
 
 pub use htsget_storage::local::FileStorage;
 
-use std::fmt::Display;
-use std::str::FromStr;
-
 use async_trait::async_trait;
 use tokio::task::JoinError;
 
@@ -43,30 +40,6 @@ pub trait HtsGet {
   }
 }
 
-/// A struct to represent a parsed header
-pub struct ParsedHeader<T>(T);
-
-impl<T> ParsedHeader<T> {
-  /// Get the inner header value.
-  pub fn into_inner(self) -> T {
-    self.0
-  }
-}
-
-impl<T> FromStr for ParsedHeader<T>
-where
-  T: FromStr,
-  <T as FromStr>::Err: Display,
-{
-  type Err = HtsGetError;
-
-  fn from_str(header: &str) -> Result<Self> {
-    Ok(ParsedHeader(header.parse::<T>().map_err(|err| {
-      HtsGetError::parse_error(format!("parsing header: {}", err))
-    })?))
-  }
-}
-
 pub(crate) struct ConcurrencyError(JoinError);
 
 impl ConcurrencyError {

htsget-storage/Cargo.toml

@@ -34,7 +34,7 @@ http = "1"
 cfg-if = "1"
 
 # Async
-tokio = { version = "1", features = ["macros", "rt-multi-thread", "io-util"] }
+tokio = { version = "1", features = ["macros", "rt-multi-thread", "io-util", "fs"] }
 tokio-util = { version = "0.7", features = ["io", "compat"] }
 futures = { version = "0.3" }
 futures-util = "0.3"
@@ -54,20 +54,18 @@ crypt4gh = { version = "0.4", git = "https://github.com/EGA-archive/crypt4gh-rus
 bincode = { version = "1", optional = true }
 
 # Error control, tracing, config
-thiserror = "1"
+thiserror = "2"
 tracing = "0.1"
 base64 = "0.22"
 
 htsget-config = { version = "0.13.0", path = "../htsget-config", default-features = false }
-htsget-test = { version = "0.7.2", path = "../htsget-test", features = ["http"], default-features = false }
 
 [dev-dependencies]
 tower-http = { version = "0.6", features = ["fs"] }
-axum = "0.7"
+axum = "0.8"
 tempfile = "3"
 data-url = "0.3"
 
 # Axum server
 reqwest = { version = "0.12", default-features = false, features = ["rustls-tls"] }
-
-criterion = { version = "0.5", features = ["async_tokio"] }
+htsget-test = { path = "../htsget-test", features = ["http"], default-features = false }

htsget-test/Cargo.toml

@@ -42,7 +42,7 @@ default = []
 # Server tests dependencies
 htsget-config = { version = "0.13.0", path = "../htsget-config", default-features = false, optional = true }
 
-noodles = { version = "0.83", optional = true, features = ["async", "bgzf", "vcf", "cram", "bcf", "bam", "fasta"] }
+noodles = { version = "0.87", optional = true, features = ["async", "bgzf", "vcf", "cram", "bcf", "bam", "fasta"] }
 
 reqwest = { version = "0.12", default-features = false, features = ["json", "rustls-tls"], optional = true }
 tokio = { version = "1", features = ["rt-multi-thread", "fs"], optional = true }
@@ -67,4 +67,4 @@ crypt4gh = { version = "0.4", git = "https://github.com/EGA-archive/crypt4gh-rus
 
 # Default dependencies
 rcgen = "0.13"
-thiserror = "1"
+thiserror = "2"

release-plz.toml

@@ -0,0 +1,3 @@
+[[package]]
+name = "htsget-test"
+release = false