Add test configuration and files for CWL extension mode

tests/conf/run_cwl_test.conf

@@ -0,0 +1,2 @@
+order:
+- ./cwl/python.cwl

tests/cwl/python.cwl

@@ -0,0 +1,25 @@
+cwlVersion: v1.2
+class: CommandLineTool
+
+requirements:
+  DockerRequirement:
+    dockerPull: python:3.11.8-alpine3.19
+  InlineJavascriptRequirement: {}
+
+baseCommand: ["python"]
+
+successCodes: [0, 139]
+
+inputs:
+  input_file:
+    type: File
+    inputBinding:
+      position: 1
+
+outputs: {}
+
+$namespaces:
+  tataki: https://github.com/sapporo-wes/tataki
+
+tataki:edam_id: http://edamontology.org/format_3996
+tataki:label: Python script

tests/inputs/toy.py

@@ -0,0 +1,7 @@
+def create_list_w_list_comprehension(start, end):
+    return [x for x in range(start, end + 1)]
+
+if __name__ == "__main__":
+    start, end = 1, 10
+    result = create_list_w_list_comprehension(start, end)
+    print(f"{result}")

tests/integration_tests.rs

@@ -16,8 +16,6 @@ test cases:
 - --quiet
 - --verbose
 - -c cwl.conf
-
-
 */
 
 #[test]
@@ -196,13 +194,11 @@ fn can_be_verbose() {
     assert!(stderr.contains("DEBUG"));
 }
 
-// TODO
-/*
 #[test]
 fn can_run_cwl() {
     let out = tataki(
-        &["./inputs/toy.bam", "./inputs/toy.fa"],
-        &["-c", "./inputs/cwl.conf"],
+        &["./inputs/toy.py", "./inputs/toy.fa"],
+        &["-c", "./conf/run_cwl_test.conf"],
     );
 
     let stdout = out.stdout;
@@ -214,7 +210,7 @@ fn can_run_cwl() {
         .expect("Failed to parse the output as CSV");
 
     let mut expected_output_rdr =
-        csv::Reader::from_path(Path::new("tests/outputs/expected_output_cwl.csv"))
+        csv::Reader::from_path(Path::new("tests/outputs/expected_output_run_cwl.csv"))
             .expect("Failed to read the expected output file");
     let expected_output_records = expected_output_rdr
         .records()
@@ -223,4 +219,3 @@ fn can_run_cwl() {
 
     assert_eq!(output_records, expected_output_records);
 }
-*/

tests/outputs/expected_output_run_cwl.csv

@@ -0,0 +1,3 @@
+File Path,Edam ID,Label
+./inputs/toy.py,http://edamontology.org/format_3996,Python script
+./inputs/toy.fa,,