test: add tests for orchestrator module

Add initial unit tests for orchestrator module functions
and update orchestrator code to reflect latest wes module
refactoring.

synorchestrator/orchestrator.py

@@ -11,12 +11,13 @@
 import time
 import os
 import datetime as dt
+
 from requests.exceptions import ConnectionError
 from IPython.display import display, clear_output
+
 from synorchestrator.config import wes_config, eval_config, trs_config
 from synorchestrator.util import get_json, ctime2datetime, convert_timedelta
-from synorchestrator.wes.client import WESClient
-from wes_client.util import get_status
+from synorchestrator.wes.wrapper import WES
 from synorchestrator.eval import create_submission
 from synorchestrator.eval import get_submission_bundle
 from synorchestrator.eval import get_submissions
@@ -60,10 +61,10 @@ def run_submission(wes_id, submission_id):
                 " \n - submission ID: {}"
                 .format(wes_id, submission_id))
 
-    client = WESClient(wes_config()[wes_id])
-    run_data = client.run_workflow(submission['data']['wf'],
-                                   submission['data']['jsonyaml'],
-                                   submission['data']['attachments'])
+    wes_instance = WES(wes_config()[wes_id])
+    run_data = wes_instance.run_workflow(submission['data']['wf'],
+                                         submission['data']['jsonyaml'],
+                                         submission['data']['attachments'])
     run_data['start_time'] = dt.datetime.now().ctime()
     update_submission(wes_id, submission_id, 'run', run_data)
     update_submission(wes_id, submission_id, 'status', 'SUBMITTED')

tests/test_orchestrator.py

@@ -0,0 +1,68 @@
+import mock
+import pytest
+
+from bravado.requests_client import RequestsClient
+from bravado.client import SwaggerClient, ResourceDecorator
+from bravado.testing.response_mocks import BravadoResponseMock
+
+from synorchestrator.wes.wrapper import WES
+from synorchestrator.orchestrator import run_submission
+
+
+@pytest.fixture()
+def mock_wes_config():
+    mock_wes_config = {
+        'mock_wes': {
+            'auth': 'auth_token',
+            'auth_type': 'token',
+            'host': '0.0.0.0:8080',
+            'proto': 'https'
+        }
+    }
+    yield mock_wes_config
+
+@pytest.fixture()
+def mock_submission(request):
+    mock_submission = {
+        'mock_sub': {
+            'status': '',
+            'data': {'wf': '',
+                     'jsonyaml': '',
+                     'attachments': []},
+            'wes_id': 'mock_wes',
+            'run': {}
+        }
+    }
+    yield mock_submission
+
+@pytest.fixture()
+def mock_wes(request):
+    mock_wes = mock.Mock(name='mock WES')
+    with mock.patch('synorchestrator.wes.wrapper.WES', 
+                    autospec=True, spec_set=True):
+        yield mock_wes
+
+
+def test_run_submission(mock_submission, 
+                        mock_wes, 
+                        mock_wes_config, 
+                        monkeypatch):
+    monkeypatch.setattr('synorchestrator.orchestrator.get_submission_bundle', 
+                        lambda x,y: mock_submission['mock_sub'])
+    monkeypatch.setattr('synorchestrator.orchestrator.wes_config', 
+                        lambda: mock_wes_config)
+    monkeypatch.setattr('synorchestrator.orchestrator.WES', 
+                        lambda x: mock_wes)
+    monkeypatch.setattr('synorchestrator.orchestrator.update_submission', 
+                        lambda w,x,y,z: None)
+
+    mock_request = mock_submission['mock_sub']['data']
+    mock_wes.run_workflow.return_value = {}
+
+    test_run_data = run_submission(wes_id='mock_wes',
+                                   submission_id='mock_sub')
+
+    mock_wes.run_workflow.assert_called_once_with(mock_request['wf'],
+                                                  mock_request['jsonyaml'],
+                                                  mock_request['attachments'])
+    assert 'start_time' in test_run_data