cr-connect-workflow/tests/test_study_api.py

210 lines
9.9 KiB
Python

import json
from datetime import datetime, timezone
from unittest.mock import patch, Mock
from crc import session
from crc.models.api_models import WorkflowApiSchema
from crc.models.study import StudyModel, StudyModelSchema
from crc.models.protocol_builder import ProtocolBuilderStatus, ProtocolBuilderStudyDetailsSchema, \
ProtocolBuilderStudySchema
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()
db_studies_before = session.query(StudyModel).all()
num_db_studies_before = len(db_studies_before)
# Mock Protocol Builder response
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)
self.load_example_data()
api_response = self.app.get('/v1.0/study',
follow_redirects=True,
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)
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)
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)
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))