update cwl/updateCaseList.cwl to fix issues with empty string sample …

…ids when no extra ids are passed in
mskcc · Apr 18, 2022 · d66a777 · d66a777
1 parent b397b7e
commit d66a777
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Showing 2 changed files with 43 additions and 8 deletions.
diff --git a/cwl/updateCaseList.cwl b/cwl/updateCaseList.cwl
@@ -6,13 +6,13 @@ baseCommand: ['bash', 'run.sh']
 requirements:
   InlineJavascriptRequirement: {}
   DockerRequirement:
-    dockerPull: mskcc/helix:21.5.0
+    dockerPull: mskcc/helix:21.5.1
   InitialWorkDirRequirement:
     listing:
       - entryname: run.sh
         entry: |-
           set -eu
-          # get a comma-delim string of the sample names
+          # get a comma-delim string of the sample names ; returns an empty string if there are no sample id's ; updateCaseList ignores empty strings
           samples_arg="${ return inputs.sample_ids.join(',') ; }"
           input_file="${ return inputs.case_list.path ; }"
           output_file="${ return inputs.output_filename }"

diff --git a/tests/test_updateCaseList_cwl.py b/tests/test_updateCaseList_cwl.py
@@ -17,21 +17,24 @@
 class TestUpdateCaseList(PlutoTestCase):
     cwl_file = 'updateCaseList.cwl'
 
-    def test_update_caselist_1(self):
-        """
-        """
+    def setUp(self):
+        super().setUp()
         case_list_str = """case_list_category: all_cases_in_study
 stable_id: pi_123_all
 case_list_name: All Tumors
 case_list_description: All tumor samples
 cancer_study_identifier: pi_123
 case_list_ids: Sample1\tSample2"""
-        input_file = os.path.join(self.tmpdir, "cases.txt")
-        with open(input_file, "w") as fout:
+        self.input_file = os.path.join(self.tmpdir, "cases.txt")
+        with open(self.input_file, "w") as fout:
             fout.write(case_list_str)
 
+    def test_update_caselist_1(self):
+        """
+        Test simple case list update
+        """
         self.input = {
-            "case_list": {"class": "File", "path": input_file},
+            "case_list": {"class": "File", "path": self.input_file},
             "sample_ids": ["Sample3", "Sample4"],
             "output_filename": "cases_all.txt"
         }
@@ -58,6 +61,38 @@ def test_update_caselist_1(self):
         self.assertEqual(text, expected_text)
 
 
+    def test_update_caselist_2(self):
+        """
+        Test update with no files passed
+        """
+        self.input = {
+            "case_list": {"class": "File", "path": self.input_file},
+            "sample_ids": [],
+            "output_filename": "cases_all.txt"
+        }
+        output_json, output_dir = self.run_cwl()
+
+        output_file = os.path.join(output_dir, 'cases_all.txt')
+
+        expected_output = {
+            "output_file": OFile(name = 'cases_all.txt', size = 192, hash = 'f1ad64f51beac01759ae690b2f787fe3978e8882', dir = output_dir)
+        }
+
+        self.assertCWLDictEqual(output_json, expected_output)
+
+        with open(output_file) as fin:
+            text = fin.read()
+
+        expected_text = """case_list_category: all_cases_in_study
+stable_id: pi_123_all
+case_list_name: All Tumors
+case_list_description: All tumor samples
+cancer_study_identifier: pi_123
+case_list_ids: Sample1\tSample2
+"""
+        self.assertEqual(text, expected_text)
+
+
 
 
 if __name__ == "__main__":