test(search): integration tests for crypt4gh and fix CRAM eof range

umccr · Apr 18, 2024 · 7e5ee23 · 7e5ee23
1 parent 31c72e2
commit 7e5ee23
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Showing 12 changed files with 1,397 additions and 294 deletions.
diff --git a/Cargo.lock b/Cargo.lock
diff --git a/data/crypt4gh/htsnexus_test_NA12878.cram.c4gh b/data/crypt4gh/htsnexus_test_NA12878.cram.c4gh
diff --git a/data/crypt4gh/sample1-bcbio-cancer.bcf.c4gh b/data/crypt4gh/sample1-bcbio-cancer.bcf.c4gh
diff --git a/data/crypt4gh/spec-v4.3.vcf.gz.c4gh b/data/crypt4gh/spec-v4.3.vcf.gz.c4gh
diff --git a/htsget-config/src/types.rs b/htsget-config/src/types.rs
@@ -43,7 +43,7 @@ impl KeyType {
   /// Get the key type from an ending.
   pub fn from_ending<K: AsRef<str>>(key: K) -> KeyType {
     if key.as_ref().ends_with(Format::Bam.index_file_ending())
-      || key.as_ref().ends_with(Format::Vcf.index_file_ending())
+      || key.as_ref().ends_with(Format::Bcf.index_file_ending())
       || key.as_ref().ends_with(Format::Cram.index_file_ending())
       || key.as_ref().ends_with(Format::Vcf.index_file_ending())
       || key.as_ref().ends_with(".bam.gzi")

diff --git a/htsget-search/Cargo.toml b/htsget-search/Cargo.toml
@@ -82,6 +82,7 @@ serde = "1.0"
 [dev-dependencies]
 tempfile = "3.6"
 data-url = "0.3"
+walkdir = "2.5"
 
 # Axum server
 reqwest = { version = "0.11", default-features = false, features = ["rustls-tls"] }