def test_create_update_and_delete_user():
response = requests.post(uri('auth', '/tokens'), headers=login_header('ralph', 'secret'))
assert response.status_code == 201
token = response.json()['token']
data = {
'username': generate_string(),
'password': '******',
'email': '{}@yoda.com'.format(generate_string()),
}
# Create user
response = requests.post(uri('auth', '/users'), json=data, headers=token_header(token))
assert response.status_code == 201
user_id = response.json()['id']
# Update user and check update was successful
data['first_name'] = 'John'
response = requests.put(uri('auth', '/users/{}'.format(user_id)), json=data, headers=token_header(token))
assert response.status_code == 200
response = requests.get(uri('auth', '/users/{}'.format(user_id)), headers=token_header(token))
assert response.status_code == 200
assert response.json()['first_name'] == 'John'
# Delete user and check it no longer exists
response = requests.delete(uri('auth', '/users/{}'.format(user_id)), headers=token_header(token))
assert response.status_code == 204
response = requests.get(uri('auth', '/users/{}'.format(user_id)), headers=token_header(token))
assert response.status_code == 404
def upload_model_archive(file_path, repository_id, token):
response = requests.get(uri('storage', '/file-types?name=binary'), headers=token_header(token))
file_type_id = response.json()[0]['id']
response = requests.get(uri('storage', '/scan-types?name=none'), headers=token_header(token))
scan_type_id = response.json()[0]['id']
try:
_, storage_id = upload_file(file_path, file_type_id, scan_type_id, repository_id, token)
return storage_id
except RuntimeError as e:
print('Failed to upload model ({})'.format(e.message))
def test_upload_and_download():
if os.getenv('DATA_DIR', None) is None:
return
response = requests.post(uri('auth', '/tokens'),
headers=login_header('ralph', 'secret'))
assert response.status_code == 201
token = response.json()['token']
response = requests.get(uri('storage', '/file-types?names=txt'),
headers=token_header(token))
assert response.status_code == 200
file_type_id = response.json()[0]['id']
response = requests.get(uri('storage', '/scan-types?name=none'),
headers=token_header(token))
assert response.status_code == 200
scan_type_id = response.json()[0]['id']
name = 'repository-{}'.format(generate_string(8))
response = requests.post(uri('storage', '/repositories'),
json={'name': name},
headers=token_header(token))
assert response.status_code == 201
repository_id = response.json()['id']
file_name = os.path.join(os.getenv('DATA_DIR'), 'data.nii.gz')
file_id, _ = upload_file(file_name, file_type_id, scan_type_id,
repository_id, token)
response = requests.get(uri(
'storage', '/repositories/{}/files/{}'.format(repository_id, file_id)),
headers=token_header(token))
assert response.status_code == 200
storage_id = response.json()['storage_id']
response = requests.get(uri('storage', '/downloads/{}'.format(storage_id)),
headers=token_header(token))
assert response.status_code == 200
assert response.content
with open('tmp.nii.gz', 'wb') as f:
for chunk in response.iter_content(1024 * 1024):
f.write(chunk)
n = os.path.getsize('tmp.nii.gz')
m = os.path.getsize(file_name)
assert n == m
os.system('rm -f tmp.nii.gz')
def test_users():
response = requests.post(uri('auth', '/tokens'), headers=login_header('ralph', 'secret'))
assert response.status_code == 201
token = response.json()['token']
response = requests.get(uri('auth', '/users'), headers=token_header(token))
assert response.status_code == 200
assert len(response.json()) >= 4
def test_create_update_and_delete_group():
response = requests.post(uri('auth', '/tokens'), headers=login_header('ralph', 'secret'))
assert response.status_code == 201
token = response.json()['token']
data = {'name': generate_string()}
# Create group
response = requests.post(uri('auth', '/user-groups'), json=data, headers=token_header(token))
assert response.status_code == 201
user_group_id = response.json()['id']
# Update group and check update successful
data['name'] = generate_string()
response = requests.put(uri('auth', '/user-groups/{}'.format(user_group_id)), json=data, headers=token_header(token))
assert response.status_code == 200
response = requests.get(uri('auth', '/user-groups/{}'.format(user_group_id)), headers=token_header(token))
assert response.status_code == 200
assert response.json()['name'] == data['name']
# Add user to group and check it was added
response = requests.get(uri('auth', '/users?username=ralph'), headers=token_header(token))
assert response.status_code == 200
user_id = response.json()[0]['id']
response = requests.put(uri('auth', '/user-groups/{}/users/{}'.format(user_group_id, user_id)), headers=token_header(token))
assert response.status_code == 200
response = requests.get(uri('auth', '/user-groups/{}/users'.format(user_group_id)), headers=token_header(token))
assert response.status_code == 200
assert len(response.json()) == 1
assert response.json()[0]['username'] == 'ralph'
# Remove user from group and check it was successfully removed
response = requests.delete(uri('auth', '/user-groups/{}/users/{}'.format(user_group_id, user_id)), headers=token_header(token))
assert response.status_code == 200
response = requests.get(uri('auth', '/user-groups/{}/users'.format(user_group_id)), headers=token_header(token))
assert response.status_code == 200
assert len(response.json()) == 0
# Delete group and check it no longer exists
response = requests.delete(uri('auth', '/user-groups/{}'.format(user_group_id)), headers=token_header(token))
assert response.status_code == 204
response = requests.get(uri('auth', '/user-groups/{}'.format(user_group_id)), headers=token_header(token))
assert response.status_code == 404
def download_file(storage_id, target_dir, token, extension=None):
response = requests.get(uri('storage', '/downloads/{}'.format(storage_id)),
headers=token_header(token))
file_path = os.path.join(target_dir, storage_id)
if extension:
if not extension.startswith('.'):
extension = '.{}'.format(extension)
file_path = '{}{}'.format(file_path, extension)
with open(file_path, 'wb') as f:
for chunk in response.iter_content(1024 * 1024):
f.write(chunk)
return file_path
def test_check_token():
response = requests.post(uri('auth', '/tokens'), headers=login_header('ralph', 'secret'))
assert response.status_code == 201
token1 = response.json()['token']
response = requests.post(uri('auth', '/tokens'), headers=login_header('quentin', 'secret'))
assert response.status_code == 201
token2 = response.json()['token']
assert token1 != token2
response = requests.post(uri('auth', '/token-checks'), json={'token': token2}, headers=token_header(token1))
assert response.status_code == 201
response = requests.post(uri('auth', '/token-checks'), headers=token_header('1234'))
assert response.status_code == 403
def upload_file(file_name, file_type_id, scan_type_id, repository_id, token):
session_id = None
file_id = None
storage_id = None
with open(file_name, 'rb') as f:
i = 0
n = os.path.getsize(file_name)
chunk_size = int(n / 10)
for chunk in read_chunks(f, chunk_size):
content_length = len(chunk)
content_range = 'bytes {}-{}/{}'.format(i, i + len(chunk) - 1, n)
headers = token_header(token)
headers.update({
'Content-Length':
'{}'.format(content_length),
'Content-Type':
'application/octet-stream',
'Content-Disposition':
'attachment; filename={}'.format(file_name),
'X-Content-Range':
content_range,
'X-Session-ID':
session_id,
'X-File-Type':
'{}'.format(file_type_id),
'X-Scan-Type':
'{}'.format(scan_type_id),
'X-Repository-ID':
'{}'.format(repository_id)
})
response = requests.post(uri('storage', '/uploads'),
headers=headers,
data=chunk)
if response.status_code == 201:
file_id = response.json()['id']
storage_id = response.json()['storage_id']
break
if response.status_code != 202:
raise RuntimeError('Response not 202 ({})'.format(
response.status_code))
session_id = response.headers['X-Session-ID']
i += len(chunk)
return file_id, storage_id
def get_storage_id_for_file(repository_id, file_id, token):
response = requests.get(
uri('storage', '/repositories/{}/files/{}'.format(repository_id, file_id)), headers=token_header(token))
storage_id = response.json()['storage_id']
return storage_id
def test_train_classifier():
if os.getenv('DATA_DIR', None) is None:
return
# Get access token
response = requests.post(uri('auth', '/tokens'),
headers=login_header('ralph', 'secret'))
assert response.status_code == 201
token = response.json()['token']
# Create storage repository
name = 'repository-{}'.format(generate_string(8))
response = requests.post(uri('storage', '/repositories'),
headers=token_header(token),
json={'name': name})
assert response.status_code == 201
repository_id = response.json()['id']
# Get CSV file type ID
response = requests.get(uri('storage', '/file-types?name=csv'),
headers=token_header(token))
assert response.status_code == 200
file_type_id = response.json()[0]['id']
# Get scan type ID
response = requests.get(uri('storage', '/scan-types?name=none'),
headers=token_header(token))
assert response.status_code == 200
scan_type_id = response.json()[0]['id']
# Load features, extract HC and SZ subjects, remove categorical columns and
# save the feature file back to disk
file_path = os.path.join(os.getenv('DATA_DIR'), 'data.csv')
features = pd.read_csv(file_path, index_col='MRid')
subject_labels = list(features['Diagnosis'])
# Upload CSV file with brain features
file_id, _ = upload_file(file_path, file_type_id, scan_type_id,
repository_id, token)
assert file_id
# Train classifier using the uploaded CSV file. As parameters we specify the
# pipeline ID (which in this case is a classifier training pipeline). The 'file_id'
# refers to the CSV file. The parameter 'subject_labels' contains a list of diagnostic
# labels. This list is used to pre-calculate training and testing indices which can be
# passed to the different workers handling the cross-validation folds in parallel.
response = requests.post(uri('compute', '/tasks'),
headers=token_header(token),
json={
'pipeline_name': 'svm_train',
'params': {
'repository_id': repository_id,
'file_id': file_id,
'subject_labels': subject_labels,
'nr_folds': 2,
'index_column': 'MRid',
'target_column': 'Diagnosis',
'kernel': 'rbf',
}
})
assert response.status_code == 201
task_id = response.json()['id']
# Retrieve task status periodically until it finishes successfully. In practice,
# this means the task status == SUCCESS and result != None
classifier_id = 0
while True:
response = requests.get(uri('compute', '/tasks/{}'.format(task_id)),
headers=token_header(token))
assert response.status_code == 200
status = response.json()['status']
assert status == 'PENDING' or status == 'SUCCESS'
result = response.json()['result']
sys.stdout.write('.')
sys.stdout.flush()
if status == 'SUCCESS' and result is not None:
classifier_id = result['classifier_id']
break
time.sleep(2)
# Remove diagnosis column from the feature data. Then select the first subject
# so we can send it to the classifier for prediction.
features.drop('Diagnosis', axis=1, inplace=True)
subject_data = list(features.iloc[0])
subject_label = subject_labels[0]
# Send some data to the trained classifier for prediction
response = requests.post(uri('compute', '/tasks'),
headers=token_header(token),
json={
'pipeline_name': 'svm_predict',
'params': {
'classifier_id': classifier_id,
'subjects': [
subject_data,
],
}
})
assert response.status_code == 201
task_id = response.json()['id']
while True:
response = requests.get(uri('compute', '/tasks/{}'.format(task_id)),
headers=token_header(token))
assert response.status_code == 200
status = response.json()['status']
assert status == 'PENDING' or status == 'SUCCESS'
result = response.json()['result']
sys.stdout.write('.')
sys.stdout.flush()
if status == 'SUCCESS' and result is not None:
assert subject_label == result['predicted_labels'][0]
break
time.sleep(2)
