def test_get_predefined_brush_label_elements(prepare_environment: Any) -> None:
"""Test for fetching Predefined Brush Label Elements."""
# Step 1. Prepare a structure for the test
dataset = DatasetsRepository.add_new_dataset('KIDNEYS', 'Kidneys')
task = TasksRepository.add_task('MARK_KIDNEYS', 'Mark Kidneys',
'path/to/image', ['KIDNEYS'], [])
label_tag = LabelTagsRepository.add_new_tag('EXAMPLE_TAG', 'Example Tag',
[LabelTool.RECTANGLE], task.id)
scan = ScansRepository.add_new_scan(dataset, 3)
user_id = UsersRepository.add_new_user(
User('user@medtagger', 'HASH', 'Admin', 'Admin'))
user = UsersRepository.get_user_by_id(user_id)
# Step 2. Add Label with Brush Elements
label = LabelsRepository.add_new_label(scan.id,
task.key,
user,
LabelingTime(0),
is_predefined=True)
LabelsRepository.add_new_brush_label_element(label.id, 0, 0, 0, b'',
label_tag)
LabelsRepository.add_new_brush_label_element(label.id, 1, 0, 0, b'',
label_tag)
LabelsRepository.add_new_brush_label_element(label.id, 2, 0, 0, b'',
label_tag)
# Step 3. Check if there is is Predefined Label
brush_label_elements = LabelsRepository.get_predefined_brush_label_elements(
scan.id, task.id, 0, 3)
assert len(brush_label_elements) == 3
brush_label_elements = LabelsRepository.get_predefined_brush_label_elements(
scan.id, task.id, 0, 1)
assert len(brush_label_elements) == 1
def test_get_predefined_label_for_scan_in_task__predefined_label(
prepare_environment: Any) -> None:
"""Test for fetching Predefined Label that exists."""
# Step 1. Prepare a structure for the test
dataset = DatasetsRepository.add_new_dataset('KIDNEYS', 'Kidneys')
task = TasksRepository.add_task('MARK_KIDNEYS', 'Mark Kidneys',
'path/to/image', ['KIDNEYS'], [])
LabelTagsRepository.add_new_tag('EXAMPLE_TAG', 'Example Tag',
[LabelTool.RECTANGLE], task.id)
scan = ScansRepository.add_new_scan(dataset, 0)
user_id = UsersRepository.add_new_user(
User('user@medtagger', 'HASH', 'Admin', 'Admin'))
user = UsersRepository.get_user_by_id(user_id)
# Step 2. Add Label which is predefined
label = LabelsRepository.add_new_label(scan.id,
task.key,
user,
LabelingTime(0),
is_predefined=True)
# Step 3. Check if there is is Predefined Label
predefined_label = LabelsRepository.get_predefined_label_for_scan_in_task(
scan, task)
assert predefined_label
assert predefined_label.id == label.id
def get_user_by_email_success_fixture(mocker: Any) -> None:
"""Return fixture for get user by email method used in create user business method."""
mocked_user_repository = mocker.patch.object(UsersRepository,
'get_user_by_email')
mocked_user_repository.return_value = User('*****@*****.**', 'medtagger',
'First', 'Last')
return mocked_user_repository
def insert_admin_account() -> None:
"""Insert default admin account."""
user_email = '*****@*****.**'
password = '******'
password_hash = hash_password(password)
with db_session() as session:
user_exists = session.query(
exists().where(User.email == user_email)).scalar()
if user_exists:
logger.warning('Admin user already exists with email "%s"',
user_email)
return
role = Role.query.filter_by(name='admin').first()
if not role:
logger.error(
'Role not found! You have probably forgot to apply fixtures.')
return
user = User(user_email, password_hash, 'Admin', 'Medtagger')
user.roles.append(role)
session.add(user)
logger.info('User added with email "%s" and password "%s"', user_email,
password)
def create_user(email: str, password: str, first_name: str,
last_name: str) -> int:
"""Create user with the given user information. Password is being hashed.
:param email: user email in string format
:param password: user password in string format
:param first_name: user first name in string format
:param last_name: user last name in string format
:return: id of the new user
"""
user = UsersRepository.get_user_by_email(email)
if user:
raise InvalidArgumentsException('User with this email already exist')
password_hash = hash_password(password)
new_user = User(email, password_hash, first_name, last_name)
role = RolesRepository.get_role_with_name('volunteer')
if not role:
raise InvalidArgumentsException('Role does not exist.')
new_user.roles.append(role)
return UsersRepository.add_new_user(new_user)
def test_get_predefined_label_for_scan_in_task__predefined_label_for_given_task(
prepare_environment: Any) -> None:
"""Test for fetching Predefined Label only for specific Task."""
# Step 1. Prepare a structure for the test
dataset = DatasetsRepository.add_new_dataset('KIDNEYS', 'Kidneys')
task_left = TasksRepository.add_task('MARK_LEFT', 'Mark Left',
'path/to/image', ['KIDNEYS'], '', [],
[])
task_right = TasksRepository.add_task('MARK_RIGHT', 'Mark Right',
'path/to/image', ['KIDNEYS'], '', [],
[])
LabelTagsRepository.add_new_tag('EXAMPLE_TAG', 'Example Tag',
[LabelTool.RECTANGLE], task_left.id)
scan = ScansRepository.add_new_scan(dataset, 0)
user_id = UsersRepository.add_new_user(
User('user@medtagger', 'HASH', 'Admin', 'Admin'))
user = UsersRepository.get_user_by_id(user_id)
# Step 2. Add Labels for each Task
label_left = LabelsRepository.add_new_label(scan.id,
task_left.key,
user,
LabelingTime(0),
is_predefined=True)
label_right = LabelsRepository.add_new_label(scan.id,
task_right.key,
user,
LabelingTime(0),
is_predefined=True)
# Step 3. Check if there are these Predefined Labels
predefined_label = LabelsRepository.get_predefined_label_for_scan_in_task(
scan, task_left)
assert predefined_label
assert predefined_label.id == label_left.id
predefined_label = LabelsRepository.get_predefined_label_for_scan_in_task(
scan, task_right)
assert predefined_label
assert predefined_label.id == label_right.id
def create_user(email: str, password: str, first_name: str,
last_name: str) -> Tuple[int, str]:
"""Create user with the given user information. Password is being hashed.
:param email: user email in string format
:param password: user password in string format
:param first_name: user first name in string format
:param last_name: user last name in string format
:return: tuple with user id and authentication token
"""
user = UsersRepository.get_user_by_email(email)
if user:
raise InvalidArgumentsException('User with this email already exists')
password_hash = hash_password(password)
new_user = User(email, password_hash, first_name, last_name)
role = RolesRepository.get_role_with_name('volunteer')
if not role:
raise InvalidArgumentsException('Role does not exist.')
new_user.roles.append(role)
user_id = UsersRepository.add_new_user(new_user)
user_token = generate_auth_token(new_user)
return user_id, user_token
def set_user_info(user: User, first_name: str, last_name: str) -> None:
"""Set user's info."""
with db_transaction_session() as session:
user.first_name = first_name
user.last_name = last_name
session.add(user)