WDL test.

Author: DailyDreaming

test/test_integration.py

@@ -26,8 +26,8 @@ def tearDown(self):
                     time.sleep(3)
                 except OSError as e:
                     print(e)
-
-        shutil.rmtree('workflows')
+        if os.path.exists('workflows'):
+            shutil.rmtree('workflows')
         unittest.TestCase.tearDown(self)
 
     def test_dockstore_md5sum(self):
@@ -72,6 +72,19 @@ def run_cwl_md5sum(cwl_input):
     return os.path.join(output_dir, 'md5sum.txt'), response['workflow_id']
 
 
+def run_wdl_md5sum(cwl_input):
+    """Pass a local md5sum wdl to the wes-service server, and return the path of the output file that was created."""
+    endpoint = 'http://localhost:8080/ga4gh/wes/v1/workflows'
+    params = '{"ga4ghMd5.inputFile": "' + os.path.abspath('testdata/md5sum.input') + '"}'
+    parts = [("workflow_params", params),
+             ("workflow_type", "WDL"),
+             ("workflow_type_version", "v1.0"),
+             ("workflow_url", cwl_input)]
+    response = requests.post(endpoint, files=parts).json()
+    output_dir = os.path.abspath(os.path.join('workflows', response['workflow_id'], 'outdir'))
+    return os.path.join(output_dir, 'md5sum.txt'), response['workflow_id']
+
+
 def get_log_request(run_id):
     endpoint = 'http://localhost:8080/ga4gh/wes/v1/workflows/{}'.format(run_id)
     return requests.get(endpoint).json()
@@ -124,6 +137,13 @@ def setUp(self):
                                                    shell=True)
         time.sleep(5)
 
+    def test_wdl_md5sum(self):
+        """Pass a local md5sum cwl to the wes-service server, and check for the correct output."""
+        cwl_local_path = os.path.abspath('testdata/md5sum.wdl')
+        output_filepath, _ = run_wdl_md5sum(cwl_input=cwl_local_path)
+
+        self.assertTrue(check_for_file(output_filepath), 'Output file was not found: ' + str(output_filepath))
+
 
 # Prevent pytest/unittest's discovery from attempting to discover the base test class.
 del IntegrationTest

testdata/md5sum.wdl

@@ -0,0 +1,22 @@
+task md5 {
+  File inputFile
+
+  command {
+    /bin/my_md5sum ${inputFile}
+  }
+
+ output {
+    File value = "md5sum.txt"
+ }
+
+ runtime {
+   docker: "quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4"
+   cpu: 1
+   memory: "512 MB"
+ }
+}
+
+workflow ga4ghMd5 {
+ File inputFile
+ call md5 { input: inputFile=inputFile }
+}

testdata/md5sum.wdl.json

@@ -0,0 +1 @@
+{"ga4ghMd5.inputFile": "md5sum.input"}

wes_service/toil_wes.py

@@ -55,7 +55,7 @@ def write_workflow(self, request, opts, wftype='cwl'):
         elif wftype == 'wdl':
             command_args = ['toil-wdl-runner'] + extra + [workflow_url, self.input_json]
         elif wftype == 'py':
-            command_args = ['python'] + extra + [workflow_url]
+            command_args = ['python'] + extra + [self.input_wf_filename]
         else:
             raise RuntimeError('workflow_type is not "cwl", "wdl", or "py": ' + str(wftype))
 
@@ -261,14 +261,14 @@ def RunWorkflow(self):
         for k, ls in connexion.request.files.iterlists():
             for v in ls:
                 if k == "workflow_descriptor":
-                    filename = secure_filename(v.filename)
+                    filename = secure_filename(os.path.basename(v.filename))
                     v.save(os.path.join(tempdir, filename))
+                    body["workflow_url"] = "file:///%s/%s" % (tempdir, filename)
                 elif k in ("workflow_params", "tags", "workflow_engine_parameters"):
                     body[k] = json.loads(v.read())
                 else:
                     body[k] = v.read()
 
-        body["workflow_url"] = "file:///%s/%s" % (tempdir, body["workflow_url"])
         index = body["workflow_url"].find("http")
         if index > 0:
             body["workflow_url"] = body["workflow_url"][index:]