import json from profile import Profile from tests.base_test import BaseTest from crc.services.ldap_service import LdapService from datetime import datetime, timezone from unittest.mock import patch from crc.models.email import EmailModel from crc import session, app from crc.models.protocol_builder import ProtocolBuilderStatus, \ ProtocolBuilderStudySchema from crc.models.file import FileModel from crc.models.task_event import TaskEventModel from crc.models.study import StudyEvent, StudyModel, StudySchema, StudyStatus, StudyEventType, StudyAssociated from crc.models.workflow import WorkflowSpecModel, WorkflowModel from crc.services.file_service import FileService from crc.services.workflow_processor import WorkflowProcessor class TestStudyApi(BaseTest): TEST_STUDY = { "title": "Phase III Trial of Genuine People Personalities (GPP) Autonomous Intelligent Emotional Agents " "for Interstellar Spacecraft", "last_updated": datetime.utcnow(), "primary_investigator_id": "tmm2x", "user_uid": "dhf8r", } def add_test_study(self): study_schema = StudySchema().dump(self.TEST_STUDY) study_schema['status'] = StudyStatus.in_progress.value rv = self.app.post('/v1.0/study', content_type="application/json", headers=self.logged_in_headers(), data=json.dumps(study_schema)) self.assert_success(rv) return json.loads(rv.get_data(as_text=True)) def test_study_basics(self): self.load_example_data() study = session.query(StudyModel).first() self.assertIsNotNone(study) def test_get_study(self): """Generic test, but pretty detailed, in that the study should return a categorized list of workflows This starts with out loading the example data, to show that all the bases are covered from ground 0.""" """NOTE: The protocol builder is not enabled or mocked out. As the master workflow (which is empty), and the test workflow do not need it, and it is disabled in the configuration.""" self.load_example_data() new_study = self.add_test_study() new_study = session.query(StudyModel).filter_by(id=new_study["id"]).first() api_response = self.app.get('/v1.0/study/%i' % new_study.id, headers=self.logged_in_headers(), content_type="application/json") self.assert_success(api_response) study = StudySchema().loads(api_response.get_data(as_text=True)) self.assertEqual(study.title, self.TEST_STUDY['title']) self.assertEqual(study.primary_investigator_id, self.TEST_STUDY['primary_investigator_id']) self.assertEqual(study.user_uid, self.TEST_STUDY['user_uid']) # Categories are read only, so switching to sub-scripting here. # This assumes there is one test category set up in the example data. category = study.categories[0] self.assertEqual("Test Category", category['display_name']) self.assertEqual(False, category['admin']) self.assertEqual(1, len(category["workflows"])) workflow = category["workflows"][0] self.assertEqual("Random Fact", workflow["display_name"]) self.assertEqual("optional", workflow["state"]) self.assertEqual("not_started", workflow["status"]) self.assertEqual(0, workflow["total_tasks"]) self.assertEqual(0, workflow["completed_tasks"]) def test_get_study_has_details_about_files(self): # Set up the study and attach a file to it. self.load_example_data() self.create_reference_document() workflow = self.create_workflow('file_upload_form') processor = WorkflowProcessor(workflow) task = processor.next_task() irb_code = "UVACompl_PRCAppr" # The first file referenced in pb required docs. FileService.add_workflow_file(workflow_id=workflow.id, task_spec_name=task.get_name(), name="anything.png", content_type="png", binary_data=b'1234', irb_doc_code=irb_code) api_response = self.app.get('/v1.0/study/%i' % workflow.study_id, headers=self.logged_in_headers(), content_type="application/json") self.assert_success(api_response) study = StudySchema().loads(api_response.get_data(as_text=True)) self.assertEqual(1, len(study.files)) self.assertEqual("UVA Compliance", study.files[0]["document"]["category1"]) self.assertEqual("Cancer Center's PRC Approval Form", study.files[0]["document"]["description"]) # TODO: WRITE A TEST FOR STUDY FILES def test_add_study(self): self.load_example_data() study = self.add_test_study() db_study = session.query(StudyModel).filter_by(id=study['id']).first() self.assertIsNotNone(db_study) self.assertEqual(study["title"], db_study.title) self.assertEqual(study["primary_investigator_id"], db_study.primary_investigator_id) self.assertEqual(study["sponsor"], db_study.sponsor) self.assertEqual(study["ind_number"], db_study.ind_number) self.assertEqual(study["user_uid"], db_study.user_uid) workflow_spec_count = session.query(WorkflowSpecModel).filter(WorkflowSpecModel.is_master_spec == False).count() workflow_count = session.query(WorkflowModel).filter(WorkflowModel.study_id == study['id']).count() self.assertEqual(workflow_spec_count, workflow_count) study_event = session.query(StudyEvent).first() self.assertIsNotNone(study_event) self.assertEqual(study_event.status, StudyStatus.in_progress) self.assertEqual(study_event.event_type, StudyEventType.user) self.assertFalse(study_event.comment) self.assertEqual(study_event.user_uid, self.test_uid) def test_update_study(self): self.load_example_data() update_comment = 'Updating the study' study: StudyModel = session.query(StudyModel).first() study.title = "Pilot Study of Fjord Placement for Single Fraction Outcomes to Cortisol Susceptibility" study_schema = StudySchema().dump(study) study_schema['status'] = StudyStatus.hold.value study_schema['comment'] = update_comment rv = self.app.put('/v1.0/study/%i' % study.id, content_type="application/json", headers=self.logged_in_headers(), data=json.dumps(study_schema)) self.assert_success(rv) json_data = json.loads(rv.get_data(as_text=True)) self.assertEqual(study.title, json_data['title']) self.assertEqual(study.status.value, json_data['status']) # Making sure events history is being properly recorded study_event = session.query(StudyEvent).first() self.assertIsNotNone(study_event) self.assertEqual(study_event.status, StudyStatus.hold) self.assertEqual(study_event.event_type, StudyEventType.user) self.assertEqual(study_event.comment, update_comment) self.assertEqual(study_event.user_uid, self.test_uid) @patch('crc.services.protocol_builder.ProtocolBuilderService.get_investigators') # mock_investigators @patch('crc.services.protocol_builder.ProtocolBuilderService.get_required_docs') # mock_docs @patch('crc.services.protocol_builder.ProtocolBuilderService.get_study_details') # mock_details @patch('crc.services.protocol_builder.ProtocolBuilderService.get_studies') # mock_studies def test_get_all_studies(self, mock_studies, mock_details, mock_docs, mock_investigators): # Enable the protocol builder for these tests, as the master_workflow and other workflows # depend on using the PB for data. app.config['PB_ENABLED'] = True self.load_example_data() s = StudyModel( id=54321, # This matches one of the ids from the study_details_json data. title='The impact of pandemics on dog owner sanity after 12 days', user_uid='dhf8r', ) session.add(s) session.commit() num_db_studies_before = session.query(StudyModel).count() # Mock Protocol Builder responses studies_response = self.protocol_builder_response('user_studies.json') mock_studies.return_value = ProtocolBuilderStudySchema(many=True).loads(studies_response) details_response = self.protocol_builder_response('study_details.json') mock_details.return_value = json.loads(details_response) docs_response = self.protocol_builder_response('required_docs.json') mock_docs.return_value = json.loads(docs_response) investigators_response = self.protocol_builder_response('investigators.json') mock_investigators.return_value = json.loads(investigators_response) # Make the api call to get all studies api_response = self.app.get('/v1.0/study', headers=self.logged_in_headers(), content_type="application/json") self.assert_success(api_response) json_data = json.loads(api_response.get_data(as_text=True)) num_abandoned = 0 num_in_progress = 0 num_open = 0 for study in json_data: if study['status'] == 'abandoned': # One study does not exist in user_studies.json num_abandoned += 1 if study['status'] == 'in_progress': # One study is marked complete without HSR Number num_in_progress += 1 if study['status'] == 'open_for_enrollment': # Currently, we don't automatically set studies to open for enrollment num_open += 1 db_studies_after = session.query(StudyModel).all() num_db_studies_after = len(db_studies_after) self.assertGreater(num_db_studies_after, num_db_studies_before) self.assertEqual(num_abandoned, 1) self.assertEqual(num_open, 0) # Currently, we don't automatically set studies to open for enrollment self.assertEqual(num_in_progress, 2) self.assertEqual(len(json_data), num_db_studies_after) # The sum below is off, since we don't automatically set studies to Open for Enrollment # Leaving the test here because we will need it again # when we implement a new way to set Open for Enrollment # self.assertEqual(num_open + num_in_progress + num_abandoned, num_db_studies_after) # Automatic events check in_progress_events = session.query(StudyEvent).filter_by(status=StudyStatus.in_progress) self.assertEqual(in_progress_events.count(), 1) # 1 study is in progress abandoned_events = session.query(StudyEvent).filter_by(status=StudyStatus.abandoned) self.assertEqual(abandoned_events.count(), 1) # 1 study has been abandoned # We don't currently set any studies to Open for Enrollment automatically # Leaving the test here because we will need it again # when we implement a new way to set Open for Enrollment # open_for_enrollment_events = session.query(StudyEvent).filter_by(status=StudyStatus.open_for_enrollment) # self.assertEqual(open_for_enrollment_events.count(), 1) # 1 study was moved to open for enrollment @patch('crc.services.protocol_builder.ProtocolBuilderService.get_investigators') # mock_studies @patch('crc.services.protocol_builder.ProtocolBuilderService.get_required_docs') # mock_docs @patch('crc.services.protocol_builder.ProtocolBuilderService.get_study_details') # mock_details @patch('crc.services.protocol_builder.ProtocolBuilderService.get_studies') # mock_studies def test_get_single_study(self, mock_studies, mock_details, mock_docs, mock_investigators): # Mock Protocol Builder responses studies_response = self.protocol_builder_response('user_studies.json') mock_studies.return_value = ProtocolBuilderStudySchema(many=True).loads(studies_response) details_response = self.protocol_builder_response('study_details.json') mock_details.return_value = json.loads(details_response) docs_response = self.protocol_builder_response('required_docs.json') mock_docs.return_value = json.loads(docs_response) investigators_response = self.protocol_builder_response('investigators.json') mock_investigators.return_value = json.loads(investigators_response) self.load_example_data() study = session.query(StudyModel).first() rv = self.app.get('/v1.0/study/%i' % study.id, follow_redirects=True, headers=self.logged_in_headers(), content_type="application/json") self.assert_success(rv) json_data = json.loads(rv.get_data(as_text=True)) self.assertEqual(study.id, json_data['id']) self.assertEqual(study.title, json_data['title']) self.assertEqual(study.status.value, json_data['status']) self.assertEqual(study.primary_investigator_id, json_data['primary_investigator_id']) self.assertEqual(study.sponsor, json_data['sponsor']) self.assertEqual(study.ind_number, json_data['ind_number']) def test_delete_study(self): self.load_example_data() study = session.query(StudyModel).first() rv = self.app.delete('/v1.0/study/%i' % study.id, headers=self.logged_in_headers()) self.assert_success(rv) def test_delete_workflow(self): self.load_example_data() workflow = session.query(WorkflowModel).first() FileService.add_workflow_file(workflow_id=workflow.id, task_spec_name='TaskSpec01', name="anything.png", content_type="text", binary_data=b'5678', irb_doc_code="UVACompl_PRCAppr" ) workflow_files = session.query(FileModel).filter_by(workflow_id=workflow.id) self.assertEqual(workflow_files.count(), 1) workflow_files_ids = [file.id for file in workflow_files] rv = self.app.delete(f'/v1.0/workflow/{workflow.id}', headers=self.logged_in_headers()) self.assert_success(rv) # No files should have the deleted workflow id anymore workflow_files = session.query(FileModel).filter_by(workflow_id=workflow.id) self.assertEqual(workflow_files.count(), 0) # Finally, let's confirm the file was archived workflow_files = session.query(FileModel).filter(FileModel.id.in_(workflow_files_ids)) for file in workflow_files: self.assertTrue(file.archived) self.assertIsNone(file.workflow_id) def test_delete_study_with_workflow_and_status_etc(self): self.load_example_data() workflow = session.query(WorkflowModel).first() stats1 = StudyEvent( study_id=workflow.study_id, status=StudyStatus.in_progress, comment='Some study status change event', event_type=StudyEventType.user, user_uid=self.users[0]['uid'], ) LdapService.user_info('dhf8r') # Assure that there is a dhf8r in ldap for StudyAssociated. email = EmailModel(subject="x", study_id=workflow.study_id) associate = StudyAssociated(study_id=workflow.study_id, uid=self.users[0]['uid']) event = StudyEvent(study_id=workflow.study_id) session.add_all([email, associate, event]) stats2 = TaskEventModel(study_id=workflow.study_id, workflow_id=workflow.id, user_uid=self.users[0]['uid']) session.add_all([stats1, stats2]) session.commit() rv = self.app.delete('/v1.0/study/%i' % workflow.study_id, headers=self.logged_in_headers()) self.assert_success(rv) del_study = session.query(StudyModel).filter(StudyModel.id == workflow.study_id).first() self.assertIsNone(del_study) # """ # Workflow Specs that have been made available (or not) to a particular study via the status.bpmn should be flagged # as available (or not) when the list of a study's workflows is retrieved. # """ # @patch('crc.services.protocol_builder.ProtocolBuilderService.get_studies') # @patch('crc.services.protocol_builder.ProtocolBuilderService.get_investigators') # @patch('crc.services.protocol_builder.ProtocolBuilderService.get_required_docs') # @patch('crc.services.protocol_builder.ProtocolBuilderService.get_study_details') # def test_workflow_spec_status(self, # mock_details, # mock_required_docs, # mock_investigators, # mock_studies): # # # Mock Protocol Builder response # studies_response = self.protocol_builder_response('user_studies.json') # mock_studies.return_value = ProtocolBuilderStudySchema(many=True).loads(studies_response) # # investigators_response = self.protocol_builder_response('investigators.json') # mock_investigators.return_value = ProtocolBuilderInvestigatorSchema(many=True).loads(investigators_response) # # required_docs_response = self.protocol_builder_response('required_docs.json') # mock_required_docs.return_value = ProtocolBuilderRequiredDocumentSchema(many=True).loads(required_docs_response) # # details_response = self.protocol_builder_response('study_details.json') # mock_details.return_value = ProtocolBuilderStudyDetailsSchema().loads(details_response) # # self.load_example_data() # study = session.query(StudyModel).first() # study_id = study.id # # # Add status workflow # self.load_test_spec('top_level_workflow') # # # Assure the top_level_workflow is added to the study # top_level_spec = session.query(WorkflowSpecModel).filter_by(is_master_spec=True).first() # self.assertIsNotNone(top_level_spec) # # # # for is_active in [False, True]: # # Set all workflow specs to inactive|active # update_status_response = self.app.put('/v1.0/workflow/%i/task/%s/data' % (status_workflow.id, status_task_id), # headers=self.logged_in_headers(), # content_type="application/json", # data=json.dumps({'some_input': is_active})) # self.assert_success(update_status_response) # json_workflow_api = json.loads(update_status_response.get_data(as_text=True)) # updated_workflow_api: WorkflowApi = WorkflowApiSchema().load(json_workflow_api) # self.assertIsNotNone(updated_workflow_api) # self.assertEqual(updated_workflow_api.status, WorkflowStatus.complete) # self.assertIsNotNone(updated_workflow_api.last_task) # self.assertIsNotNone(updated_workflow_api.last_task['data']) # self.assertIsNotNone(updated_workflow_api.last_task['data']['some_input']) # self.assertEqual(updated_workflow_api.last_task['data']['some_input'], is_active) # # # List workflows for study # response_after = self.app.get('/v1.0/study/%i/workflows' % study.id, # content_type="application/json", # headers=self.logged_in_headers()) # self.assert_success(response_after) # # json_data_after = json.loads(response_after.get_data(as_text=True)) # workflows_after = WorkflowApiSchema(many=True).load(json_data_after) # self.assertEqual(len(specs), len(workflows_after)) # # # All workflows should be inactive|active # for workflow in workflows_after: # self.assertEqual(workflow.is_active, is_active)