def test_get_paginated_scans_with_invalid_arguments(
prepare_environment: Any) -> None:
"""Test for fetching Scans in the paginated way with invalid arguments."""
api_client = get_api_client()
user_token = get_token_for_logged_in_user('admin')
# Step 1. Prepare a structure for the test
dataset = DatasetsRepository.add_new_dataset('KIDNEYS', 'Kidneys')
# Step 2. Add example Scans to the system
for _ in range(50):
ScansRepository.add_new_scan(dataset, number_of_slices=3)
# Step 3. Fetch them with MedTagger REST API in the wrong way
response = api_client.get('/api/v1/scans?dataset_key=KIDNEYS&page=-1',
headers=get_headers(token=user_token))
assert response.status_code == 400
json_response = json.loads(response.data)
assert json_response['message'] == 'Invalid arguments.'
assert json_response['details'] == 'Page cannot be smaller than 1.'
# Step 4. Make a mistake again
response = api_client.get(
'/api/v1/scans?dataset_key=KIDNEYS&per_page=5000',
headers=get_headers(token=user_token))
assert response.status_code == 400
json_response = json.loads(response.data)
assert json_response['message'] == 'Invalid arguments.'
assert json_response[
'details'] == 'Cannot fetch more than 100 entries at once.'
def test_get_paginated_scans(prepare_environment: Any) -> None:
"""Test for fetching Scans in the paginated way."""
api_client = get_api_client()
user_token = get_token_for_logged_in_user('admin')
# Step 1. Prepare a structure for the test
dataset = DatasetsRepository.add_new_dataset('KIDNEYS', 'Kidneys')
# Step 2. Add example Scans to the system
for _ in range(50):
ScansRepository.add_new_scan(dataset, number_of_slices=3)
# Step 3. Fetch them with MedTagger REST API
response = api_client.get('/api/v1/scans?dataset_key=KIDNEYS',
headers=get_headers(token=user_token))
assert response.status_code == 200
json_response = json.loads(response.data)
assert json_response['pagination']['page'] == 1
assert json_response['pagination']['per_page'] == 25
assert json_response['pagination']['total'] == 50
assert len(json_response['scans']) == 25
# Step 4. Fetch the next page with different size
response = api_client.get(
'/api/v1/scans?dataset_key=KIDNEYS&page=2&per_page=10',
headers=get_headers(token=user_token))
assert response.status_code == 200
json_response = json.loads(response.data)
assert json_response['pagination']['page'] == 2
assert json_response['pagination']['per_page'] == 10
assert json_response['pagination']['total'] == 50
assert len(json_response['scans']) == 10
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 create_empty_scan(dataset_key: str, declared_number_of_slices: int) -> Scan:
"""Create new empty scan.
:param dataset_key: string with dataset key
:param declared_number_of_slices: number of Slices that will be uploaded
:return: Newly created Scan object
"""
user = get_current_user()
dataset = DatasetsRepository.get_dataset_by_key(dataset_key)
return ScansRepository.add_new_scan(dataset, declared_number_of_slices, user)
def test_get_paginated_scans_by_volunteer(prepare_environment: Any) -> None:
"""Test for fetching Scans in the paginated way by volunteers."""
api_client = get_api_client()
user_token = get_token_for_logged_in_user('volunteer')
# Step 1. Prepare a structure for the test
dataset = DatasetsRepository.add_new_dataset('KIDNEYS', 'Kidneys')
# Step 2. Add example Scans to the system
for _ in range(50):
ScansRepository.add_new_scan(dataset, number_of_slices=3)
# Step 3. Fetch them with MedTagger REST API
response = api_client.get('/api/v1/scans?dataset_key=KIDNEYS',
headers=get_headers(token=user_token))
assert response.status_code == 403
json_response = json.loads(response.data)
assert json_response['message'] == 'Access forbidden'
assert json_response[
'details'] == 'You don\'t have required roles to access this method.'
def prepare_scan_and_tag_for_labeling() -> Tuple[models.Scan, models.LabelTag]:
"""Create needed Scan and Label Tag for labeling purpose."""
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',
[definitions.LabelTool.POINT],
task.id)
scan = ScansRepository.add_new_scan(dataset, number_of_slices=3)
for _ in range(3):
scan.add_slice()
return scan, label_tag
def test_get_predefined_label_for_scan_in_task__no_predefined_label(
prepare_environment: Any) -> None:
"""Test for fetching Predefined Label that does not exist."""
# 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)
# Step 2. Check if there is no Predefined Label
predefined_label = LabelsRepository.get_predefined_label_for_scan_in_task(
scan, task)
assert not predefined_label
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
logging.config.fileConfig('logging.conf')
logger = logging.getLogger(__name__)
parser = argparse.ArgumentParser(description='Import data to the MedTagger.')
parser.add_argument('--source', type=str, required=True, help='Source directory')
parser.add_argument('--dataset', type=str, required=True, help='Dataset key for these scans')
args = parser.parse_args()
if __name__ == '__main__':
logger.info('Checking Dataset...')
dataset = DatasetsRepository.get_dataset_by_key(args.dataset)
source = args.source.rstrip('/')
for scan_directory in glob.iglob(source + '/*'):
if not os.path.isdir(scan_directory):
logger.warning('"%s" is not a directory. Skipping...', scan_directory)
continue
logger.info('Adding new Scan from "%s".', scan_directory)
slice_names = glob.glob(scan_directory + '/*.dcm')
number_of_slices = len(slice_names)
scan = ScansRepository.add_new_scan(dataset, number_of_slices, None)
for slice_name in slice_names:
logger.info('Adding new Slice to Scan "%s" based on "%s".', scan.id, slice_name)
with open(slice_name, 'rb') as slice_dicom_file:
_slice = scan.add_slice()
image = slice_dicom_file.read()
parse_dicom_and_update_slice.delay(_slice.id, image)
