import json from datetime import datetime, timezone from unittest.mock import patch from crc import session from crc.models.api_models import WorkflowApiSchema, WorkflowApi from crc.models.protocol_builder import ProtocolBuilderStatus, ProtocolBuilderStudyDetailsSchema, \ ProtocolBuilderStudySchema from crc.models.study import StudyModel, StudyModelSchema from crc.models.workflow import WorkflowSpecModel, WorkflowSpecModelSchema, WorkflowModel, WorkflowStatus from tests.base_test import BaseTest class TestStudyApi(BaseTest): def test_study_basics(self): self.load_example_data() study = session.query(StudyModel).first() self.assertIsNotNone(study) def test_add_study(self): self.load_example_data() study = { "id": 12345, "title": "Phase III Trial of Genuine People Personalities (GPP) Autonomous Intelligent Emotional Agents " "for Interstellar Spacecraft", "last_updated": datetime.now(tz=timezone.utc), "protocol_builder_status": ProtocolBuilderStatus.IN_PROCESS, "primary_investigator_id": "tricia.marie.mcmillan@heartofgold.edu", "sponsor": "Sirius Cybernetics Corporation", "ind_number": "567890", "user_uid": "dhf8r", } rv = self.app.post('/v1.0/study', content_type="application/json", headers=self.logged_in_headers(), data=json.dumps(StudyModelSchema().dump(study))) self.assert_success(rv) db_study = session.query(StudyModel).filter_by(id=12345).first() self.assertIsNotNone(db_study) self.assertEqual(study["title"], db_study.title) self.assertAlmostEqual(study["last_updated"], db_study.last_updated) self.assertEqual(study["protocol_builder_status"], db_study.protocol_builder_status) 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) def test_update_study(self): self.load_example_data() study: StudyModel = session.query(StudyModel).first() study.title = "Pilot Study of Fjord Placement for Single Fraction Outcomes to Cortisol Susceptibility" study.protocol_builder_status = ProtocolBuilderStatus.REVIEW_COMPLETE rv = self.app.put('/v1.0/study/%i' % study.id, content_type="application/json", headers=self.logged_in_headers(), data=json.dumps(StudyModelSchema().dump(study))) self.assert_success(rv) 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.protocol_builder_status, db_study.protocol_builder_status) @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): 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 = ProtocolBuilderStudyDetailsSchema().loads(details_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)) api_studies = StudyModelSchema(many=True).load(json_data, session=session) num_inactive = 0 num_active = 0 for study in api_studies: if study.inactive: num_inactive += 1 else: num_active += 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.assertGreater(num_inactive, 0) self.assertGreater(num_active, 0) self.assertEqual(len(api_studies), num_db_studies_after) self.assertEqual(num_active + num_inactive, num_db_studies_after) # Assure that the existing study is properly updated. test_study = session.query(StudyModel).filter_by(id=54321).first() self.assertFalse(test_study.inactive) def test_study_api_get_single_study(self): 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)) study2 = StudyModelSchema().load(json_data, session=session) self.assertEqual(study, study2) self.assertEqual(study.id, study2.id) self.assertEqual(study.title, study2.title) self.assertEqual(study.last_updated, study2.last_updated) self.assertEqual(study.protocol_builder_status, study2.protocol_builder_status) self.assertEqual(study.primary_investigator_id, study2.primary_investigator_id) self.assertEqual(study.sponsor, study2.sponsor) self.assertEqual(study.ind_number, study2.ind_number) def test_add_workflow_to_study(self): self.load_example_data() study = session.query(StudyModel).first() self.assertEqual(0, session.query(WorkflowModel).count()) spec = session.query(WorkflowSpecModel).first() rv = self.app.post('/v1.0/study/%i/workflows' % study.id, content_type="application/json", headers=self.logged_in_headers(), data=json.dumps(WorkflowSpecModelSchema().dump(spec))) self.assert_success(rv) self.assertEqual(1, session.query(WorkflowModel).count()) workflow_model = session.query(WorkflowModel).first() self.assertEqual(study.id, workflow_model.study_id) self.assertEqual(WorkflowStatus.user_input_required, workflow_model.status) self.assertIsNotNone(workflow_model.bpmn_workflow_json) self.assertEqual(spec.id, workflow_model.workflow_spec_id) json_data = json.loads(rv.get_data(as_text=True)) workflow2 = WorkflowApiSchema().load(json_data) self.assertEqual(workflow_model.id, workflow2.id) 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_study_with_workflow(self): self.load_example_data() study = session.query(StudyModel).first() spec = session.query(WorkflowSpecModel).first() rv = self.app.post('/v1.0/study/%i/workflows' % study.id, content_type="application/json", headers=self.logged_in_headers(), data=json.dumps(WorkflowSpecModelSchema().dump(spec))) rv = self.app.delete('/v1.0/study/%i' % study.id, headers=self.logged_in_headers()) self.assert_failure(rv, error_code="study_integrity_error") def test_delete_workflow(self): self.load_example_data() study = session.query(StudyModel).first() spec = session.query(WorkflowSpecModel).first() rv = self.app.post('/v1.0/study/%i/workflows' % study.id, content_type="application/json", headers=self.logged_in_headers(), data=json.dumps(WorkflowSpecModelSchema().dump(spec))) self.assertEqual(1, session.query(WorkflowModel).count()) json_data = json.loads(rv.get_data(as_text=True)) workflow = WorkflowApiSchema().load(json_data) rv = self.app.delete('/v1.0/workflow/%i' % workflow.id, headers=self.logged_in_headers()) self.assert_success(rv) self.assertEqual(0, session.query(WorkflowModel).count()) def test_get_study_workflows(self): self.load_example_data() # Should have no workflows to start study = session.query(StudyModel).first() response_before = self.app.get('/v1.0/study/%i/workflows' % study.id, content_type="application/json", headers=self.logged_in_headers()) self.assert_success(response_before) json_data_before = json.loads(response_before.get_data(as_text=True)) workflows_before = WorkflowApiSchema(many=True).load(json_data_before) self.assertEqual(0, len(workflows_before)) # Add a workflow spec = session.query(WorkflowSpecModel).first() add_response = self.app.post('/v1.0/study/%i/workflows' % study.id, content_type="application/json", headers=self.logged_in_headers(), data=json.dumps(WorkflowSpecModelSchema().dump(spec))) self.assert_success(add_response) # Should have one workflow now 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(1, len(workflows_after)) # """ # Assure that when we create a new study, the status of the workflows in that study # reflects information we have read in from the protocol builder. # """ # def test_top_level_workflow(self): # # # Set up the status workflow # self.load_test_spec('top_level_workflow', master_spec=True) # # # Create a new study. # self. # # # Add all available non-status workflows to the study # specs = session.query(WorkflowSpecModel).filter_by(is_status=False).all() # for spec in specs: # add_response = self.app.post('/v1.0/study/%i/workflows' % study.id, # content_type="application/json", # headers=self.logged_in_headers(), # data=json.dumps(WorkflowSpecModelSchema().dump(spec))) # self.assert_success(add_response) # # 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)