Merge pull request #69 from rust-bio/fix_tests

Change test for annotate_dgidb

Author: FelixMoelder

.github/workflows/rust.yml

@@ -52,10 +52,10 @@ jobs:
         run: |
           sudo apt-get install --yes libgsl0-dev
 
-      - name: Install starcode
+      - name: Install test dependencies
         run: |
           export PATH="/usr/share/miniconda/bin:$PATH"
-          conda create -c bioconda -c conda-forge -n starcode starcode
+          conda create -c bioconda -c conda-forge -n dependencies starcode bcftools
 
       - name: Install stable toolchain
         uses: actions-rs/toolchain@v1
@@ -66,6 +66,6 @@ jobs:
       - name: Run cargo test
         run: |
           export PATH="/usr/share/miniconda/bin:$PATH"
-          source activate starcode
+          source activate dependencies
           cargo test -- --test-threads=1
 

tests/expected/annotate_dgidb_drugbank_test.bcf

@@ -291,28 +291,12 @@ fn test_collapse_reads_to_fragments_from_bam() {
 
 #[test]
 fn test_vcf_annotate_dgidb() {
-    assert!(
-        Command::new("bash")
-            .arg("-c")
-            .arg("target/debug/rbt vcf-annotate-dgidb tests/annotate_dgidb_test.vcf > /tmp/annotate_dgidb_test.bcf")
-            .spawn().unwrap().wait().unwrap().success());
-    test_output(
-        "/tmp/annotate_dgidb_test.bcf",
-        "tests/expected/annotate_dgidb_test.bcf",
-    );
-}
-
-#[test]
-fn test_vcf_annotate_dgidb_drugbank() {
-    assert!(
-        Command::new("bash")
+    let exec_test = Command::new("bash")
             .arg("-c")
-            .arg("target/debug/rbt vcf-annotate-dgidb tests/annotate_dgidb_test.vcf -s DrugBank > /tmp/annotate_dgidb_drugbank_test.bcf")
-            .spawn().unwrap().wait().unwrap().success());
-    test_output(
-        "/tmp/annotate_dgidb_drugbank_test.bcf",
-        "tests/expected/annotate_dgidb_drugbank_test.bcf",
-    );
+            .arg("target/debug/rbt vcf-annotate-dgidb tests/annotate_dgidb_test.vcf | bcftools view - | wc -l").output()
+            .expect("failed to execute process");
+    assert!(exec_test.status.success());
+    assert_eq!(String::from_utf8(exec_test.stdout).unwrap().trim(), "65");
 }
 
 #[test]