Merge pull request #34 from broadinstitute/se-add-workflow-hold-param

Add on_hold param to start_workflow

cromwell_tools/cromwell_tools.py

@@ -134,7 +134,7 @@ def wait_until_workflow_completes(
 @retry(reraise=True, wait=wait_exponential(multiplier=1, max=10), stop=stop_after_delay(20))
 def start_workflow(
         wdl_file, inputs_file, url, options_file=None, inputs_file2=None, zip_file=None, user=None,
-        password=None, caas_key=None, collection_name=None, label=None, validate_labels=True):
+        password=None, caas_key=None, collection_name=None, label=None, validate_labels=True, on_hold=False):
     """
     Use HTTP POST to start workflow in Cromwell and retry with exponentially increasing wait times between requests
     if there are any failures. View statistics about the retries with `start_workflow.retry.statistics`.
@@ -156,7 +156,8 @@ def start_workflow(
     :param str collection_name: (optional) collection in SAM that the workflow should belong to.
     :param str|_io.BytesIO label: (optional) JSON file containing a collection of key/value pairs for workflow labels.
     :param bool validate_labels: (optional) Whether to validate labels or not, using cromwell-tools' built-in
-     validators. It is set to True by default.
+                validators. It is set to True by default.
+    :param bool on_hold: (optional) Whether to submit the workflow in "On Hold" status.
 
     :return requests.Response response: HTTP response from cromwell.
     """
@@ -166,6 +167,7 @@ def start_workflow(
     files = {
         'workflowSource': wdl_file,
         'workflowInputs': inputs_file,
+        'workflowOnHold': json.dumps(on_hold)
     }
 
     if inputs_file2 is not None:

cromwell_tools/scripts/cromwell-tools

@@ -36,6 +36,7 @@ def _start_workflow(arguments):
         url=arguments.cromwell_url + '/api/workflows/v1',
         user=user,
         password=password,
+        on_hold=arguments.on_hold
     )
     response.raise_for_status()  # determine if workflow succeeded
     print(response.json()['id'])
@@ -111,6 +112,7 @@ if __name__ == '__main__':
     run.add_argument('--inputs-json', type=str, required=True)
     run.add_argument('--inputs2-json', type=str)
     run.add_argument('--options-file', type=str)
+    run.add_argument('--on-hold', type=str)
 
     # wait arguments
     wait.add_argument('--workflow-ids', nargs='+', required=True)

cromwell_tools/tests/test_cromwell_tools.py

@@ -47,6 +47,7 @@ def setUp(self):
         self.inputs_file2 = io.BytesIO(b"inputs_file2_content")
         self.options_file = io.BytesIO(b"options_file_content")
         self.label = io.BytesIO(b'{"test-label-key": "test-label-value"}')
+        self.on_hold = False
         self.url = "https://fake_url"
         self.user = "fake_user"
         self.password = "fake_password"
@@ -65,7 +66,7 @@ def _request_callback(request, context):
         mock_request.post(self.url, json=_request_callback)
         result = cromwell_tools.start_workflow(
             self.wdl_file, self.inputs_file, self.url, self.options_file, self.inputs_file2, self.zip_file, self.user,
-            self.password, label=self.label)
+            self.password, label=self.label, on_hold=self.on_hold)
         self.assertEqual(result.status_code, 200)
         self.assertEqual(result.headers.get('test'), 'header')
 
@@ -84,7 +85,7 @@ def _request_callback(request, context):
         with self.assertRaises(requests.HTTPError):
             result = cromwell_tools.start_workflow(
                 self.wdl_file, self.inputs_file, self.url, self.options_file, self.inputs_file2, self.zip_file,
-                self.user, self.password, label=self.label)
+                self.user, self.password, label=self.label, on_hold=self.on_hold)
             self.assertNotEqual(mock_request.call_count, 1)
 
         # Reset default retry value
@@ -103,7 +104,7 @@ def _request_callback(request, context):
         mock_request.post(self.url, json=_request_callback)
         result = cromwell_tools.start_workflow(
             self.wdl_file, self.inputs_file, self.url, self.options_file, self.inputs_file2, self.zip_file,
-            caas_key=self.caas_key, label=self.label)
+            caas_key=self.caas_key, label=self.label, on_hold=self.on_hold)
         self.assertEqual(result.status_code, 200)
         self.assertEqual(result.headers.get('test'), 'header')