def test_list_reference_files(self):
ExampleDataLoader.clean_db()
file_name = DocumentService.DOCUMENT_LIST
filepath = os.path.join(app.root_path, 'static', 'reference',
'irb_documents.xlsx')
with open(filepath, 'rb') as myfile:
file_data = myfile.read()
data = {'file': (io.BytesIO(file_data), file_name)}
rv = self.app.post('/v1.0/reference_file',
data=data,
follow_redirects=True,
content_type='multipart/form-data',
headers=self.logged_in_headers())
self.assert_success(rv)
rv = self.app.get('/v1.0/reference_file',
follow_redirects=True,
content_type="application/json",
headers=self.logged_in_headers())
self.assert_success(rv)
json_data = json.loads(rv.get_data(as_text=True))
self.assertEqual(1, len(json_data))
file = FileModelSchema(many=True).load(json_data, session=session)
self.assertEqual(file_name, file[0].name)
self.assertTrue(file[0].is_reference)
def load_example_data(self, use_crc_data=False, use_rrt_data=False):
"""use_crc_data will cause this to load the mammoth collection of documents
we built up developing crc, use_rrt_data will do the same for hte rrt project,
otherwise it depends on a small setup for running tests."""
from example_data import ExampleDataLoader
ExampleDataLoader.clean_db()
# If in production mode, only add the first user.
if app.config['PRODUCTION']:
ldap_info = LdapService.user_info(self.users[0]['uid'])
session.add(
UserModel(uid=self.users[0]['uid'], ldap_info=ldap_info))
else:
for user_json in self.users:
ldap_info = LdapService.user_info(user_json['uid'])
session.add(
UserModel(uid=user_json['uid'], ldap_info=ldap_info))
if use_crc_data:
ExampleDataLoader().load_all()
elif use_rrt_data:
ExampleDataLoader().load_rrt()
else:
ExampleDataLoader().load_test_data()
session.commit()
for study_json in self.studies:
study_model = StudyModel(**study_json)
session.add(study_model)
StudyService._add_all_workflow_specs_to_study(study_model)
session.commit()
update_seq = f"ALTER SEQUENCE %s RESTART WITH %s" % (
StudyModel.__tablename__ + '_id_seq', study_model.id + 1)
print("Update Sequence." + update_seq)
session.execute(update_seq)
session.flush()
specs = session.query(WorkflowSpecModel).all()
self.assertIsNotNone(specs)
for spec in specs:
files = session.query(FileModel).filter_by(
workflow_spec_id=spec.id).all()
self.assertIsNotNone(files)
self.assertGreater(len(files), 0)
for file in files:
# file_data = session.query(FileDataModel).filter_by(file_model_id=file.id).all()
file_data = SpecFileService().get_spec_file_data(file.id).data
self.assertIsNotNone(file_data)
self.assertGreater(len(file_data), 0)
def create_user_with_study_and_workflow(self):
# clear it all out.
from example_data import ExampleDataLoader
ExampleDataLoader.clean_db()
# Assure some basic models are in place, This is a damn mess. Our database models need an overhaul to make
# this easier - better relationship modeling is now critical.
self.load_test_spec("top_level_workflow", master_spec=True)
user = db.session.query(UserModel).filter(
UserModel.uid == "dhf8r").first()
if not user:
user = UserModel(uid="dhf8r",
email_address="*****@*****.**",
display_name="Stayathome Smellalots")
db.session.add(user)
db.session.commit()
else:
for study in db.session.query(StudyModel).all():
StudyService().delete_study(study.id)
study = StudyModel(
title="My title",
protocol_builder_status=ProtocolBuilderStatus.ACTIVE,
user_uid=user.uid)
db.session.add(study)
cat = WorkflowSpecCategoryModel(name="approvals",
display_name="Approvals",
display_order=0)
db.session.add(cat)
db.session.commit()
self.assertIsNotNone(cat.id)
self.load_test_spec("random_fact", category_id=cat.id)
self.assertIsNotNone(study.id)
workflow = WorkflowModel(workflow_spec_id="random_fact",
study_id=study.id,
status=WorkflowStatus.not_started,
last_updated=datetime.now())
db.session.add(workflow)
db.session.commit()
# Assure there is a master specification, one standard spec, and lookup tables.
ExampleDataLoader().load_reference_documents()
return user
def load_example_data(self, use_crc_data=False, use_rrt_data=False):
"""use_crc_data will cause this to load the mammoth collection of documents
we built up developing crc, use_rrt_data will do the same for hte rrt project,
otherwise it depends on a small setup for running tests."""
from example_data import ExampleDataLoader
ExampleDataLoader.clean_db()
if use_crc_data:
ExampleDataLoader().load_all()
elif use_rrt_data:
ExampleDataLoader().load_rrt()
else:
ExampleDataLoader().load_test_data()
for user_json in self.users:
db.session.add(UserModel(**user_json))
db.session.commit()
for study_json in self.studies:
study_model = StudyModel(**study_json)
db.session.add(study_model)
StudyService._add_all_workflow_specs_to_study(study_model)
db.session.execute(Sequence(StudyModel.__tablename__ + '_id_seq'))
db.session.commit()
db.session.flush()
specs = session.query(WorkflowSpecModel).all()
self.assertIsNotNone(specs)
for spec in specs:
files = session.query(FileModel).filter_by(
workflow_spec_id=spec.id).all()
self.assertIsNotNone(files)
self.assertGreater(len(files), 0)
for spec in specs:
files = session.query(FileModel).filter_by(
workflow_spec_id=spec.id).all()
self.assertIsNotNone(files)
self.assertGreater(len(files), 0)
for file in files:
file_data = session.query(FileDataModel).filter_by(
file_model_id=file.id).all()
self.assertIsNotNone(file_data)
self.assertGreater(len(file_data), 0)
def test_list_reference_files(self):
ExampleDataLoader.clean_db()
file_name = FileService.DOCUMENT_LIST
data = {'file': (io.BytesIO(b"abcdef"), file_name)}
rv = self.app.put('/v1.0/reference_file/%s' % file_name,
data=data,
follow_redirects=True,
content_type='multipart/form-data',
headers=self.logged_in_headers())
rv = self.app.get('/v1.0/reference_file',
follow_redirects=True,
content_type="application/json",
headers=self.logged_in_headers())
self.assert_success(rv)
json_data = json.loads(rv.get_data(as_text=True))
self.assertEqual(1, len(json_data))
file = FileModelSchema(many=True).load(json_data, session=session)
self.assertEqual(file_name, file[0].name)
self.assertTrue(file[0].is_reference)
def tearDown(self):
ExampleDataLoader.clean_db()
g.user = None
self.auths = {}
def tearDown(self):
ExampleDataLoader.clean_db()
self.logout()
self.auths = {}
self.clear_test_sync_files()
def delete_example_data(self, use_crc_data=False, use_rrt_data=False):
"""
delete everything that matters in the local database - this is used to
test ground zero copy of workflow specs.
"""
ExampleDataLoader.clean_db()
def clear_db():
"""Load example data into the database."""
from example_data import ExampleDataLoader
ExampleDataLoader.clean_db()
def load_example_rrt_data():
"""Load example data into the database."""
from example_data import ExampleDataLoader
ExampleDataLoader.clean_db()
ExampleDataLoader().load_rrt()
def load_example_data():
"""Load example data into the database."""
from example_data import ExampleDataLoader
ExampleDataLoader.clean_db()
ExampleDataLoader().load_all()
ExampleDataLoader().load_default_user()