Merge branch 'master' into feature/protocol_status

crc/api.yml

@@ -608,7 +608,7 @@ paths:
               schema:
                 $ref: "#/components/schemas/Workflow"
     delete:
-      operationId: crc.api.workflow.delete
+      operationId: crc.api.workflow.delete_workflow
       summary: Removes an existing workflow
       tags:
         - Workflows and Tasks

crc/api/workflow.py

@@ -9,6 +9,7 @@ from crc.models.stats import WorkflowStatsModel, TaskEventModel
 from crc.models.workflow import WorkflowModel, WorkflowSpecModelSchema, WorkflowSpecModel, WorkflowSpecCategoryModel, \
     WorkflowSpecCategoryModelSchema
 from crc.services.file_service import FileService
+from crc.services.study_service import StudyService
 from crc.services.workflow_processor import WorkflowProcessor
 from crc.services.workflow_service import WorkflowService
 
@@ -78,8 +79,8 @@ def delete_workflow_specification(spec_id):
         FileService.delete_file(file.id)
 
     # Delete all stats and workflow models related to this specification
-    session.query(WorkflowStatsModel).filter_by(workflow_spec_id=spec_id).delete()
+    for workflow in session.query(WorkflowModel).filter_by(workflow_spec_id=spec_id):
-    session.query(WorkflowModel).filter_by(workflow_spec_id=spec_id).delete()
+        StudyService.delete_workflow(workflow)
     session.query(WorkflowSpecModel).filter_by(id=spec_id).delete()
     session.commit()
 
@@ -115,11 +116,8 @@ def get_workflow(workflow_id, soft_reset=False, hard_reset=False):
     return WorkflowApiSchema().dump(workflow_api_model)
 
 
-def delete(workflow_id):
+def delete_workflow(workflow_id):
-    session.query(TaskEventModel).filter_by(workflow_id=workflow_id).delete()
+    StudyService.delete_workflow(workflow_id)
-    session.query(WorkflowStatsModel).filter_by(workflow_id=workflow_id).delete()
-    session.query(WorkflowModel).filter_by(id=workflow_id).delete()
-    session.commit()
 
 def set_current_task(workflow_id, task_id):
     workflow_model = session.query(WorkflowModel).filter_by(id=workflow_id).first()

crc/services/study_service.py

@@ -52,12 +52,21 @@ class StudyService(object):
 
     @staticmethod
     def delete_study(study_id):
-        session.query(WorkflowStatsModel).filter_by(study_id=study_id).delete()
         session.query(TaskEventModel).filter_by(study_id=study_id).delete()
-        session.query(WorkflowModel).filter_by(study_id=study_id).delete()
+        session.query(WorkflowStatsModel).filter_by(study_id=study_id).delete()
+        for workflow in session.query(WorkflowModel).filter_by(study_id=study_id):
+            StudyService.delete_workflow(workflow.id)
         session.query(StudyModel).filter_by(id=study_id).delete()
         session.commit()
 
+    @staticmethod
+    def delete_workflow(workflow_id):
+        for file in session.query(FileModel).filter_by(workflow_id=workflow_id).all():
+            FileService.delete_file(file.id)
+        session.query(TaskEventModel).filter_by(workflow_id=workflow_id).delete()
+        session.query(WorkflowStatsModel).filter_by(workflow_id=workflow_id).delete()
+        session.query(WorkflowModel).filter_by(id=workflow_id).delete()
+
     @staticmethod
     def get_categories():
         """Returns a list of category objects, in the correct order."""

tests/test_tasks_api.py

@@ -164,6 +164,11 @@ class TestTasksApi(BaseTest):
         json_data = json.loads(rv.get_data(as_text=True))
         files = FileModelSchema(many=True).load(json_data, session=session)
         self.assertTrue(len(files) == 1)
+        # Assure we can still delete the study even when there is a file attached to a workflow.
+        rv = self.app.delete('/v1.0/study/%i' % workflow.study_id, headers=self.logged_in_headers())
+        self.assert_success(rv)
+
+
 
     def test_get_documentation_populated_in_end(self):
         self.load_example_data()

tests/test_workflow_processor_multi_instance.py

@@ -1,22 +1,13 @@
-import logging
-import os
-import string
-import random
 from unittest.mock import patch
 
-from SpiffWorkflow.bpmn.specs.EndEvent import EndEvent
+from crc import session
-
-from crc import session, db, app
-from crc.api.common import ApiError
 from crc.models.api_models import MultiInstanceType
-from crc.models.file import FileModel, FileDataModel, CONTENT_TYPES
 from crc.models.study import StudyModel
-from crc.models.workflow import WorkflowSpecModel, WorkflowStatus, WorkflowModel
+from crc.models.workflow import WorkflowStatus
-from crc.services.file_service import FileService
 from crc.services.study_service import StudyService
+from crc.services.workflow_processor import WorkflowProcessor
 from crc.services.workflow_service import WorkflowService
 from tests.base_test import BaseTest
-from crc.services.workflow_processor import WorkflowProcessor
 
 
 class TestWorkflowProcessorMultiInstance(BaseTest):
@@ -96,3 +87,66 @@ class TestWorkflowProcessorMultiInstance(BaseTest):
             task.data['StudyInfo']['investigators'])
 
         self.assertEqual(WorkflowStatus.complete, processor.get_status())
+
+
+    @patch('crc.services.protocol_builder.requests.get')
+    def test_create_and_complete_workflow_parallel(self, mock_get):
+        """Unlike the test above, the parallel task allows us to complete the items in any order."""
+
+        mock_get.return_value.ok = True
+        mock_get.return_value.text = self.protocol_builder_response('investigators.json')
+
+        self.load_example_data()
+        workflow_spec_model = self.load_test_spec("multi_instance_parallel")
+        study = session.query(StudyModel).first()
+        processor = self.get_processor(study, workflow_spec_model)
+        processor.bpmn_workflow.do_engine_steps()
+
+        # In the Parallel instance, there should be three tasks, all of them in the ready state.
+        next_user_tasks = processor.next_user_tasks()
+        self.assertEqual(3, len(next_user_tasks))
+
+        # We can complete the tasks out of order.
+        task = next_user_tasks[2]
+
+        self.assertEquals(
+            {
+                'DC': {'user_id': 'asd3v', 'type_full': 'Department Contact'},
+                'IRBC': {'user_id': 'asdf32', 'type_full': 'IRB Coordinator'},
+                'PI': {'user_id': 'dhf8r', 'type_full': 'Primary Investigator'}
+            },
+            task.data['StudyInfo']['investigators'])
+
+        self.assertEqual(WorkflowStatus.user_input_required, processor.get_status())
+        self.assertEquals("dhf8r", task.data["investigator"]["user_id"])  # The last of the tasks
+
+        api_task = WorkflowService.spiff_task_to_api_task(task)
+        self.assertEquals(MultiInstanceType.parallel, api_task.mi_type)
+        task.update_data({"email":"dhf8r@virginia.edu"})
+        processor.complete_task(task)
+        processor.do_engine_steps()
+
+        task = next_user_tasks[0]
+        api_task = WorkflowService.spiff_task_to_api_task(task)
+        self.assertEqual("MutiInstanceTask", api_task.name)
+        task.update_data({"email":"asd3v@virginia.edu"})
+        processor.complete_task(task)
+        processor.do_engine_steps()
+
+        task = next_user_tasks[1]
+        api_task = WorkflowService.spiff_task_to_api_task(task)
+        self.assertEqual("MutiInstanceTask", task.get_name())
+        task.update_data({"email":"asdf32@virginia.edu"})
+        processor.complete_task(task)
+        processor.do_engine_steps()
+
+        # Completing the tasks out of order, still provides the correct information.
+        self.assertEquals(
+            {
+                'DC': {'user_id': 'asd3v', 'type_full': 'Department Contact', 'email': 'asd3v@virginia.edu'},
+                'IRBC': {'user_id': 'asdf32', 'type_full': 'IRB Coordinator', "email": "asdf32@virginia.edu"},
+                'PI': {'user_id': 'dhf8r', 'type_full': 'Primary Investigator', "email": "dhf8r@virginia.edu"}
+            },
+            task.data['StudyInfo']['investigators'])
+
+        self.assertEqual(WorkflowStatus.complete, processor.get_status())