Merge pull request #356 from sartography/bug/missing_pi_name_246

Bug/missing pi name 246

.gitignore

@@ -14,7 +14,7 @@ local.properties
 .settings/
 .loadpath
 .recommenders
-
+.vscode/
 # External tool builders
 .externalToolBuilders/
 

Pipfile.lock

@@ -979,7 +979,7 @@
         },
         "spiffworkflow": {
             "git": "https://github.com/sartography/SpiffWorkflow.git",
-            "ref": "0b4a878f9b6d4f7fc320c26f59ca5e458a6130e8"
+            "ref": "1df28b940ec0d32b672e59e3d17e7a804cb2b186"
         },
         "sqlalchemy": {
             "hashes": [

crc/api/study.py

@@ -99,6 +99,12 @@ def user_studies():
     user = UserService.current_user(allow_admin_impersonate=True)
     StudyService.synch_with_protocol_builder_if_enabled(user)
     studies = StudyService().get_studies_for_user(user)
+    if len(studies) == 0:
+        studies = StudyService().get_studies_for_user(user, include_invalid=True)
+        if len(studies) > 0:
+            message = f"All studies associated with User: {user.display_name} failed study validation"
+            raise ApiError(code="study_integrity_error", message=message)
+
     results = StudySchema(many=True).dump(studies)
     return results
 

crc/services/study_service.py

@@ -42,7 +42,7 @@ class StudyService(object):
             return True
         return False
 
-    def get_studies_for_user(self, user):
+    def get_studies_for_user(self, user, include_invalid=False):
         """Returns a list of all studies for the given user."""
         associated = session.query(StudyAssociated).filter_by(uid=user.uid, access=True).all()
         associated_studies = [x.study_id for x in associated]
@@ -51,7 +51,7 @@ class StudyService(object):
 
         studies = []
         for study_model in db_studies:
-            if self._is_valid_study(study_model.id):
+            if include_invalid or self._is_valid_study(study_model.id):
                 studies.append(StudyService.get_study(study_model.id, study_model, do_status=False))
         return studies
 

crc/services/workflow_service.py

@@ -781,6 +781,7 @@ class WorkflowService(object):
             if not hasattr(spiff_task.task_spec, 'lane') or spiff_task.task_spec.lane is None:
                 associated = StudyService.get_study_associates(processor.workflow_model.study.id)
                 return [user.uid for user in associated if user.access]
+
             if spiff_task.task_spec.lane not in spiff_task.data:
                 return []  # No users are assignable to the task at this moment
             lane_users = spiff_task.data[spiff_task.task_spec.lane]
@@ -790,7 +791,7 @@ class WorkflowService(object):
             lane_uids = []
             for user in lane_users:
                 if isinstance(user, dict):
-                    if 'value' in user and user['value'] is not None:
+                    if user.get("value"):
                         lane_uids.append(user['value'])
                     else:
                         raise ApiError.from_task(code="task_lane_user_error", message="Spiff Task %s lane user dict must have a key called 'value' with the user's uid in it." %

tests/study/test_study_details_documents.py

@@ -56,7 +56,6 @@ class TestStudyDetailsDocumentsScript(BaseTest):
 
     @patch('crc.services.protocol_builder.requests.get')
     def test_no_validation_error_when_correct_file_exists(self, mock_get):
-
         mock_get.return_value.ok = True
         mock_get.return_value.text = self.protocol_builder_response('required_docs.json')
 

tests/test_wait_event.py

@@ -40,7 +40,7 @@ class TestTimerEvent(BaseTest):
         with self.assertLogs('crc', level='ERROR') as cm:
             WorkflowService.do_waiting()
             self.assertEqual(1, len(cm.output))
-            self.assertRegexpMatches(cm.output[0], f"workflow #%i" % workflow.id)
+            self.assertRegex(cm.output[0], f"workflow #%i" % workflow.id)
-            self.assertRegexpMatches(cm.output[0], f"study #%i" % workflow.study_id)
+            self.assertRegex(cm.output[0], f"study #%i" % workflow.study_id)
 
         self.assertTrue(wf.status == WorkflowStatus.waiting)