155 lines
7.2 KiB
Python
155 lines
7.2 KiB
Python
import json
|
|
from datetime import datetime, timezone
|
|
from unittest.mock import patch
|
|
|
|
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
|
|
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.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.requests.get')
|
|
def test_get_all_studies(self, mock_get):
|
|
self.load_example_data()
|
|
db_studies_before = session.query(StudyModel).all()
|
|
num_db_studies_before = len(db_studies_before)
|
|
|
|
mock_get.return_value.ok = True
|
|
mock_get.return_value.text = self.protocol_builder_response('user_studies.json')
|
|
# pb_response = ProtocolBuilderService.get_studies(self.test_uid)
|
|
# self.assertIsNotNone(pb_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)
|
|
|
|
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)
|
|
|
|
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
|
|
|
|
self.assertEqual(num_inactive, num_db_studies_before)
|
|
self.assertEqual(num_active, num_db_studies_after - num_db_studies_before)
|
|
|
|
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_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)
|
|
self.assert_success(rv)
|
|
self.assertEqual(0, session.query(WorkflowModel).count())
|