test: add more server tests and fix Dockerfile.dockerignore

Author: mmalenic

Cargo.lock

@@ -1,10 +1,12 @@
 *
 
 !/htsget-actix
+!/htsget-axum
 !/htsget-config
 !/htsget-http
 !/htsget-lambda
 !/htsget-search
+!/htsget-storage
 !/htsget-test
 !/Cargo.toml
 !/Cargo.lock

deploy/Dockerfile.dockerignore

@@ -306,7 +306,7 @@ mod tests {
   }
 
   #[tokio::test]
-  async fn get_route_invalid_method() {
+  async fn test_errors() {
     server::test_errors(&AxumTestServer::default()).await;
   }
 }

htsget-axum/src/server/ticket.rs

@@ -18,7 +18,7 @@ default = []
 [dependencies]
 thiserror = "1"
 async-trait = "0.1"
-noodles = { version = "0.78", features = ["core"] }
+noodles = { version = "0.80", features = ["core"] }
 serde = { version = "1", features = ["derive"] }
 serde_with = "3"
 serde_regex = "1"

htsget-config/Cargo.toml

@@ -38,8 +38,8 @@ See [htsget-search] for details on how to structure files.
 
 ### As a library
 
-There shouldn't be any need to interact with this crate as a library, however some functions which deal with
-routing queries are exposed in the public API.
+There is no need to interact with this crate as a library. Note that the Lambda function itself doesn't have any
+library code, and it instead uses `htsget-axum`. Please use that crate for functionality related to routing.
 
 #### Feature flags
 

htsget-lambda/README.md

@@ -0,0 +1,3 @@
+//! htsget-lambda no longer has any library functions. Please use `htsget-axum` for similar
+//! functionality on routers and logic.
+//!

htsget-lambda/src/lib.rs

@@ -32,7 +32,7 @@ futures-util = "0.3"
 async-trait = "0.1"
 
 # Noodles
-noodles = { version = "0.78", features = ["async", "core", "bgzf", "bam", "bcf", "cram", "csi", "sam", "tabix", "vcf"] }
+noodles = { version = "0.80", features = ["async", "core", "bgzf", "bam", "bcf", "cram", "csi", "sam", "tabix", "vcf"] }
 
 # Error control, tracing, config
 thiserror = "1"

htsget-search/Cargo.toml

@@ -42,7 +42,7 @@ default = []
 # Server tests dependencies
 htsget-config = { version = "0.10.1", path = "../htsget-config", default-features = false, optional = true }
 
-noodles = { version = "0.78", optional = true, features = ["async", "bgzf", "vcf", "cram", "bcf", "bam", "fasta"] }
+noodles = { version = "0.80", 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 }

htsget-test/Cargo.toml

@@ -6,7 +6,7 @@ use futures::future::join_all;
 use futures::{Stream, TryStreamExt};
 use htsget_config::types::{Class, Format, Response, Url};
 use http::{HeaderMap, HeaderName, HeaderValue};
-use noodles::{bam, bcf, bgzf, cram, fasta, vcf};
+use noodles::{bam, bcf, bgzf, cram, vcf};
 use reqwest::Client;
 use std::future::Future;
 use std::io;
@@ -199,7 +199,6 @@ impl ReadRecords {
           .read_file_definition()
           .await
           .map_err(TestError::read_record)?;
-        let repository = fasta::Repository::default();
         let header = reader
           .read_file_header()
           .await
@@ -208,9 +207,7 @@ impl ReadRecords {
           .map_err(TestError::read_record)?;
         println!("{:#?}", header);
 
-        self
-          .iterate_records(reader.records(&repository, &header))
-          .await
+        self.iterate_records(reader.records(&header)).await
       }
       Format::Vcf => {
         let mut reader =

htsget-test/src/http/concat.rs

@@ -290,6 +290,52 @@ where
     StatusCode::NOT_FOUND,
   )
   .await;
+
+  test_error_response(
+    tester,
+    tester
+      .request()
+      .method(Method::GET)
+      .uri("/variants/1-vcf/sample1-bcbio-cancer?format=BED"),
+    StatusCode::BAD_REQUEST,
+  )
+  .await;
+  test_error_response(
+    tester,
+    tester
+      .request()
+      .method(Method::GET)
+      .uri("/variants/1-vcf/sample1-bcbio-cancer?class=header&start=1"),
+    StatusCode::BAD_REQUEST,
+  )
+  .await;
+  test_error_response(
+    tester,
+    tester
+      .request()
+      .method(Method::GET)
+      .uri("/variants/1-vcf/sample1-bcbio-cancer?referenceName=*&start=1"),
+    StatusCode::BAD_REQUEST,
+  )
+  .await;
+  test_error_response(
+    tester,
+    tester
+      .request()
+      .method(Method::GET)
+      .uri("/variants/1-vcf/sample1-bcbio-cancer?referenceName=chr1&start=2&end=1"),
+    StatusCode::BAD_REQUEST,
+  )
+  .await;
+  test_error_response(
+    tester,
+    tester
+      .request()
+      .method(Method::GET)
+      .uri("/variants/1-vcf/sample1-bcbio-cancer?referenceName=*&end=1"),
+    StatusCode::BAD_REQUEST,
+  )
+  .await;
 }
 
 /// An example VCF search response.