def _init_client(spec, require_token=False):
if 'api_url' in spec:
client = girder_client.GirderClient(
apiUrl=spec['api_url'],
cacheSettings=_get_cache_settings(spec))
elif 'host' in spec:
scheme = spec.get('scheme', 'http')
port = spec.get('port', {
'http': 80,
'https': 443
}[scheme])
api_root = spec.get('api_root', '/api/v1')
client = girder_client.GirderClient(
host=spec['host'], scheme=scheme, apiRoot=api_root, port=port,
cacheSettings=_get_cache_settings(spec))
else:
raise Exception('You must pass either an api_url or host key for '
'Girder input and output bindings.')
if 'token' in spec:
client.setToken(spec['token'])
elif require_token:
raise Exception('You must pass a token for Girder authentication.')
return client
def _gc(self):
gc = girder_client.GirderClient(apiUrl=self.api_url)
if self.api_key is not None:
gc = girder_client.GirderClient(apiUrl=self.api_url)
gc.authenticate(apiKey=self.api_key)
elif self.token is not None:
gc.token = self.token
return gc
def get_gc(self):
connection_info = 'https://data.kitware.com/api/v1'
try:
gc = girder_client.GirderClient(apiUrl=connection_info)
gc.authenticate(**self.credentials)
return gc
except:
try:
gc = girder_client.GirderClient(apiUrl=connection_info)
except:
raise ValueError("Cannot connect to the Girder.")
return gc
def connect_to_api(apiurl, apikey=None, interactive=True):
"""Connect to a specific girder API.
Parameters
----------
apiurl : str
URL to the AP to connect to.
apikey : str
API authentication token key
interactive : bool
Whether to use interactive mode instead.
Returns
-------
girder_client.GirderClient
Authenticated girder client.
"""
assert interactive or (apikey is not None)
gc = girder_client.GirderClient(apiUrl=apiurl)
if apikey is not None:
interactive = False
if interactive:
gc.authenticate(interactive=True)
else:
gc.authenticate(apiKey=apikey)
return gc
def authenticate_me(self, **kwargs):
connection_info = 'https://data.kitware.com/api/v1'
username = kwargs['username']
password = kwargs['password']
try:
gc = girder_client.GirderClient(apiUrl=connection_info)
gc.authenticate(username, password)
db = get_db()
with db_session:
p = db.Providers.select().filter(provider=self.name).first()
provider_metadata = {
'provider': self.name,
'username': username,
'password': password,
}
if p is None:
db.Providers(**provider_metadata)
else:
p.set(**provider_metadata)
return True
except:
log.error(
"Either credentials invalid or unable to connect to the Girder live server."
)
return False
def __init__(self,
item_id=None,
token=None,
name='gaia_result.json',
uri='',
**kwargs):
"""
Read and write GeoJSON data to/from Girder
:param item_id: Item id to read/write from/to
:param uri: location of temporary file
:param kwargs: Other keyword arguments
"""
self.id = item_id
self.token = token
if uri:
self.uri = uri
else:
tmpdir = tempfile.mkdtemp()
self.uri = tempfile.mkstemp(suffix='.json', dir=tmpdir)[1]
self.filename = name
girderPort = config.getConfig()['server.socket_port']
client = girder_client.GirderClient(port=girderPort)
client.token = token
self.client = client
self.meta = self.client.getItem(item_id)
super(MinervaVectorIO, self).__init__(uri=self.uri, **kwargs)
def setUp(self):
base.TestCase.setUp(self)
admin = {
'email': '*****@*****.**',
'login': '******',
'firstName': 'Admin',
'lastName': 'Last',
'password': '******',
'admin': True
}
self.admin = User().createUser(**admin)
self.gc = girder_client.GirderClient(
apiUrl='http://127.0.0.1:%d/api/v1' %
(int(os.environ['GIRDER_PORT'])))
self.gc.authenticate(username='******', password='******')
self.publicFolder = self.gc.get(
'resource/lookup',
parameters={'path': 'user/%s/Public' % self.admin['login']})
wsi_path = os.path.join(
TEST_DATA_DIR,
'TCGA-A2-A0YE-01Z-00-DX1.8A2E3094-5755-42BC-969D-7F0A2ECA0F39.svs')
self.wsiFile = self.gc.uploadFile(self.publicFolder['_id'],
stream=open(wsi_path, 'rb'),
name=os.path.basename(wsi_path),
size=os.stat(wsi_path).st_size,
parentType='folder')
annotations_path = wsi_path + '_annotations.json'
self.gc.post('annotation/item/%s' % self.wsiFile['itemId'],
data=open(annotations_path, 'rb').read(),
headers={'Content-Type': 'application/json'})
def get_test_data(client, opts):
"""
Make sure we have a test collection with a folder with test data.
:param client: girder client.
:param opts: command line options.
"""
collName = 'HistomicsTK Tests'
collection = client.resourceLookup('/collection/' + collName, True)
if not collection:
collection = client.createCollection(collName, public=True)
folderName = 'Images'
folder = client.resourceLookup(
'/collection/%s/%s' % (collName, folderName), True)
if not folder:
folder = client.createFolder(collection['_id'],
folderName,
parentType='collection')
if opts.get('test') != 'local':
remote = girder_client.GirderClient(
apiUrl='https://data.kitware.com/api/v1')
remoteFolder = remote.resourceLookup(
'/collection/HistomicsTK/Deployment test images')
for item in remote.listItem(remoteFolder['_id']):
localPath = '/collection/%s/%s/%s' % (collName, folderName,
item['name'])
localItem = client.resourceLookup(localPath, True)
if localItem:
client.delete('item/%s' % localItem['_id'])
localItem = client.createItem(folder['_id'], item['name'])
for remoteFile in remote.listFile(item['_id']):
with tempfile.NamedTemporaryFile() as tf:
fileName = tf.name
tf.close()
sys.stdout.write('Downloading %s' % remoteFile['name'])
sys.stdout.flush()
remote.downloadFile(remoteFile['_id'], fileName)
sys.stdout.write(' .')
sys.stdout.flush()
client.uploadFileToItem(localItem['_id'],
fileName,
filename=remoteFile['name'],
mimeType=remoteFile['mimeType'])
sys.stdout.write('.\n')
sys.stdout.flush()
for item in list(client.listItem(folder['_id'])):
if item['name'].endswith('.anot'):
sys.stdout.write('Deleting %s\n' % item['name'])
sys.stdout.flush()
client.delete('item/%s' % item['_id'])
continue
if 'largeImage' not in item:
sys.stdout.write('Making large_item %s ' % item['name'])
sys.stdout.flush()
job = client.post('item/%s/tiles' % item['_id'])
if job is not None:
job = wait_for_job(client, job)
else:
print('done')
return folder
def saveAndUploadScene(self, username, api_key, api_url):
sceneName = "Scene-" + strftime("%Y%m%d-%H%M%S") + ".mrb"
from os.path import expanduser
home = expanduser("~")
sceneSaveFilename = os.path.join(home, sceneName)
print 'saving scene to file: ' + sceneSaveFilename
slicer.util.saveScene(sceneSaveFilename)
print 'saving file done'
print 'saving to Girder'
patient_folder = '5a54e3b6210e501a6c95f73b'
import girder_client
gc = girder_client.GirderClient(apiUrl=api_url)
gc.authenticate(username=username, apiKey=api_key)
# create an item
item = gc.createItem(parentFolderId=patient_folder, name=sceneName)
# set some metadata on the item
metadata = {
'patient_id': '0',
'acquisition_date': '2018-01-12'
}
gc.addMetadataToItem(item['_id'], metadata)
# upload the file itself
# 'example.zip' is a local file
gc.uploadFileToItem(itemId=item['_id'], filepath=sceneSaveFilename)
def argvToList(x=sys.argv):
""" Return a Full List of Items """
# Get commandLine to get full annotation list
commandLen = len(x)
if commandLen > 4:
sys.exit('Command Line Argvs Error: { Url, User, Password }')
else:
url = x[1]
user = x[2]
password = x[3]
url = url + '/api/v1'
# Initialize Girder CLient instance
gc = girder_client.GirderClient(apiUrl=url)
# Authentication
try:
gc.authenticate(user, password)
except requests.ConnectionError:
sys.exit(
'Authentication Failed! Your url, username, and password might be wrong.'
)
fullList = getFullList(gc)
return gc, fullList
def testPatch(self):
patchUrl = 'patch'
patchRequest = {
'valid': False
}
# Test json request
jsonBody = {
'foo': 'bar'
}
def _patchJson(url, request):
body = request.body
if isinstance(body, bytes):
body = body.decode('utf8')
patchRequest['valid'] = json.loads(body) == jsonBody
return httmock.response(200, {}, {}, request=request)
patch = httmock.urlmatch(
path=r'^.*%s$' % patchUrl, method='PUT')(_patchJson)
with httmock.HTTMock(patch):
client = girder_client.GirderClient()
client.put(patchUrl, json=jsonBody)
# Check we got the right request
self.assertTrue(patchRequest['valid'])
# Now try raw message body
patchRequest['valid'] = False
rawBody = 'raw'
def _patchRaw(url, request):
patchRequest['valid'] = request.body == rawBody
return httmock.response(200, {}, {}, request=request)
patch = httmock.urlmatch(
path=r'^.*%s$' % patchUrl, method='PUT')(_patchRaw)
with httmock.HTTMock(patch):
client = girder_client.GirderClient()
client.put(patchUrl, data=rawBody)
# Check we got the right request
self.assertTrue(patchRequest['valid'])
def run_girder_init(apiUrl):
createInitialUser(apiUrl)
gc = girder_client.GirderClient(apiUrl=apiUrl)
gc.authenticate("admin", "letmein")
setGirderSetting("core.cors.allow_origin",
"http://localhost:8080, http://localhost:9001", gc)
createAssetstore(gc)
createIngestFolders(gc)
def uploadToGirder(folderPath, girder_api_key, girder_parent_id):
gc = girder_client.GirderClient(apiUrl=config.GIRDER_API)
gc.authenticate(apiKey=girder_api_key)
gc.upload(folderPath, girder_parent_id)
ls = gc.listFolder(girder_parent_id, name=folderPath.split("/")[-1])
return list(ls)[0]
def login():
global token, mc, gc # TODO - not global
token = pydas.login(email=MIDAS_LOGIN,
api_key=MIDAS_API_KEY,
url=MIDAS_URL)
mc = pydas.session.communicator
gc = girder_client.GirderClient(apiUrl=GIRDER_URL)
gc.authenticate(username=GIRDER_LOGIN, apiKey=GIRDER_API_KEY)
def get_sample_data(adminUser, collName='Sample Images', folderName='Images'):
"""
As needed, download sample data.
:param adminUser: a user to create and modify collections and folders.
:param collName: the collection name where the data will be added.
:param folderName: the folder name where the data will bed aded.
:returns: the folder where the sample data is located.
"""
try:
import girder_client
except ImportError:
logger.error('girder_client is unavailable. Cannot get sample data.')
return
from girder.models.item import Item
from girder.models.upload import Upload
from girder_large_image.models.image_item import ImageItem
folder = get_collection_folder(adminUser, collName, folderName)
remote = girder_client.GirderClient(
apiUrl='https://data.kitware.com/api/v1')
remoteFolder = remote.resourceLookup(
'/collection/HistomicsTK/Deployment test images')
sampleItems = []
for remoteItem in remote.listItem(remoteFolder['_id']):
item = Item().findOne({
'folderId': folder['_id'],
'name': remoteItem['name']
})
if item and len(list(Item().childFiles(item, limit=1))):
sampleItems.append(item)
continue
if not item:
item = Item().createItem(remoteItem['name'],
creator=adminUser,
folder=folder)
for remoteFile in remote.listFile(remoteItem['_id']):
with tempfile.NamedTemporaryFile() as tf:
fileName = tf.name
tf.close()
logger.info('Downloading %s', remoteFile['name'])
remote.downloadFile(remoteFile['_id'], fileName)
Upload().uploadFromFile(open(fileName, 'rb'),
os.path.getsize(fileName),
name=remoteItem['name'],
parentType='item',
parent=item,
user=adminUser)
sampleItems.append(item)
for item in sampleItems:
if 'largeImage' not in item:
logger.info('Making large_item %s', item['name'])
try:
ImageItem().createImageItem(item, createJob=False)
except Exception:
pass
logger.info('done')
return folder
def createGirderClient(api_url, api_key=None, username=None, password=None):
gc = girder_client.GirderClient(apiUrl=api_url)
if username and password:
gc.authenticate(username=username, password=password)
elif api_key:
gc.authenticate(apiKey=api_key)
return gc
def check_admin_login(apiUrl):
gc = girder_client.GirderClient(apiUrl=apiUrl)
try:
gc.authenticate(ADMIN_USER, ADMIN_PASS)
except girder_client.AuthenticationError:
print('Cannot login admin, it probably does not exist')
return False
return True
def loadData(self, fold, set):
entries = self.dataCSVFile.loc[(self.dataCSVFile["Fold"] == fold)
& (self.dataCSVFile["Set"] == set)]
images = []
imageLabels = []
numFilesWritten = 0
if "GirderID" in self.dataCSVFile.columns:
LabelNames = self.dataCSVFile.columns[8:]
for labelName in LabelNames:
imageLabels[labelName] = []
if self.gClient == None:
self.gClient = girder_client.GirderClient(
apiUrl=entries["Girder_URL"][0])
userName = input("Username: "******"Password: "******"GirderID"][i]
fileName = entries["FileName"][i]
if not os.path.isfile(os.path.join(tempFileDir, fileName)):
self.gClient.downloadItem(fileID, tempFileDir)
numFilesWritten += 1
print(numFilesWritten)
image = cv2.imread(os.path.join(tempFileDir, fileName), 0)
resized = cv2.resize(image, (224, 224))
images.append(numpy.array(resized))
for labelName in LabelNames:
imageLabels[labelName].append(entries[labelName][i])
else:
for i in entries.index:
#Read in the ultrasound image
filePath = entries["Folder"][i]
fileName = entries["FileName"][i]
image = cv2.imread(os.path.join(filePath, fileName), 0)
# print(os.path.join(filePath,fileName))
processed = self.process_ultrasound(image)
images.append(numpy.array(processed))
#Read in the segmentation image
fileName_seg = entries["VesselsCombined"][i]
segmentation = cv2.imread(os.path.join(filePath, fileName_seg),
0)
processed_seg = self.process_seg(segmentation)
imageLabels.append(numpy.array(processed_seg))
return numpy.array(images), numpy.array(imageLabels)
def main():
# Use the API key to authenticate.
key = os.environ.get('GIRDER_API_KEY')
if key is None:
print(
'Environment variable GIRDER_API_KEY is blank. Cannot upload files.',
file=sys.stderr)
return 1
gc = girder_client.GirderClient(host='data.kitware.com', scheme='https')
# The api key needs scopes of at least
# ["core.data.write","core.data.read","core.user_info.read"]
gc.authenticate(apiKey=key)
# Retrieve the target folder, which should be at ~/Public/Travis\ GeoJS
user = gc.get('user/me')
if user is None:
print('No user logged in; API key may be bad.', file=sys.stderr)
return 1
folder = gc.get('resource/lookup',
parameters={'path': 'collection/GeoJS/Public'})
folder = gc.loadOrCreateFolder('Travis GeoJS', folder['_id'], 'folder')
travis_build_number = os.environ.get('TRAVIS_BUILD_NUMBER')
folderName = travis_build_number
if os.environ.get('TRAVIS_EVENT_TYPE') == 'pull_request':
folderName += ' PR #%s %s' % (
os.environ.get('TRAVIS_PULL_REQUEST'),
os.environ.get('TRAVIS_PULL_REQUEST_BRANCH'))
elif os.environ.get('TRAVIS_BRANCH'):
folderName += ' ' + os.environ.get('TRAVIS_BRANCH')
# folder = gc.loadOrCreateFolder(folderName, folder['_id'], 'folder')
try:
folder = six.next(
gc.listFolder(folder['_id'], 'folder', name=folderName))
except StopIteration:
folder = gc.createFolder(folder['_id'], folderName,
os.environ.get('TRAVIS_COMMIT_MESSAGE', ''))
# If we have a build matrix, this could be of use
# travis_job_number = os.environ.get('TRAVIS_JOB_NUMBER')
# folder = gc.loadOrCreateFolder(travis_job_number, folder['_id'], 'folder')
# Upload the files specified on the command line, creating an item for each
for fileName in sys.argv[1:]:
(dirname, filename) = os.path.split(fileName)
size = os.stat(fileName).st_size
print(dirname, filename)
with open(fileName, 'rb') as fd:
gc.uploadFile(parentId=folder['_id'],
stream=fd,
name=filename,
size=size,
parentType='folder')
print('uploaded')
def submit_results(user, csv_results, description=None):
client = girder_client.GirderClient(apiUrl=GIRDER_URL)
upload_challenge_data(client,
user,
'prostatex',
csv_results,
metadata=description)
print(
"Done. The results of your submission will appear shortly on the leaderboard at http://ismi17.diagnijmegen.nl/"
)
def __init__(self, config, aws_section='aws', girder_section='girder'):
self.verbose = 0
self.config = config
self.aws_section = aws_section
self.girder_section = girder_section
self.client = girder_client.GirderClient(apiUrl=self.girder_api_url)
self.client.authenticate(self.girder_user, self.girder_password)
def _get_girder_client(self):
# @note We import girder_client here, as only uploading requires it at present.
# If `girder_client` can be imported via Bazel with minimal pain, then we can bubble
# this up to the top-level.
import girder_client
if self._girder_client is None:
self._girder_client = girder_client.GirderClient(
apiUrl=self._api_url)
self._girder_client.authenticate(apiKey=self._api_key)
return self._girder_client
def connect_to_api(apiurl, apikey=None, interactive=True):
"""Connect to a specific girder API"""
assert interactive or (apikey is not None)
gc = girder_client.GirderClient(apiUrl=apiurl)
if apikey is not None:
interactive = False
if interactive:
gc.authenticate(interactive=True)
else:
gc.authenticate(apiKey=apikey)
return gc
def __init__(
self,
api_key,
root_id,
root_type='collection',
host='0.0.0.0',
port=8080,
client=None,
):
# type: (str, str, str, str, int, Any) -> None
'''
Constructs a GirderExporter instances and creates a Girder client.
Args:
api_key (str): Girder API key.
root_id (str): ID of folder or collection under which all data will
be exported.
root_type (str, optional): Root entity type. Default: collection.
Options: folder, collection
host (str, optional): Docker host IP address. Default: 0.0.0.0.
port (int, optional): Docker host port. Default: 8080.
client (object, optional): Client instance, for testing.
Default: None.
Raises:
DataError: If config is invalid.
'''
# sudo ip addr show docker0 | grep inet | grep docker0 | awk '{print $2}' | sed 's/\/.*//'
# will give you the ip address of the docker network which binds to
# localhost
config = dict(
api_key=api_key,
root_id=root_id,
root_type=root_type,
host=host,
port=port,
)
GirderConfig(config).validate()
self._url = f'http://{host}:{port}/api/v1' # type: str
if client is None:
client = girder_client.GirderClient(
apiUrl=self._url) # pragma: no cover
client.authenticate(apiKey=api_key) # pragma: no cover
self._client = client # type: Any
self._root_id = root_id # type: str
self._root_type = root_type # type: str
def testUploadCallbacks(self):
callbackUser = self.model('user').createUser(
firstName='Callback',
lastName='Last',
login='******',
password='******',
email='*****@*****.**')
callbackPublicFolder = six.next(
self.model('folder').childFolders(parentType='user',
parent=callbackUser,
user=None,
limit=1))
callback_counts = {'folder': 0, 'item': 0}
folders = {}
items = {}
folders[self.libTestDir] = False
folder_count = 1 # 1 for self.libTestDir
item_count = 0
for root, dirs, files in os.walk(self.libTestDir):
for name in files:
items[os.path.join(root, name)] = False
item_count += 1
for name in dirs:
folders[os.path.join(root, name)] = False
folder_count += 1
def folder_callback(folder, filepath):
self.assertIn(filepath, folders.keys())
folders[filepath] = True
callback_counts['folder'] += 1
def item_callback(item, filepath):
self.assertIn(filepath, items.keys())
items[filepath] = True
callback_counts['item'] += 1
client = girder_client.GirderClient(port=os.environ['GIRDER_PORT'])
client.authenticate('callback', 'password')
client.add_folder_upload_callback(folder_callback)
client.add_item_upload_callback(item_callback)
client.upload(self.libTestDir, callbackPublicFolder['_id'])
# make sure counts are the same (callbacks not called more than once)
# and that all folders and files have callbacks called on them
self.assertEqual(folder_count, callback_counts['folder'])
self.assertEqual(item_count, callback_counts['item'])
self.assertTrue(all(items.values()))
self.assertTrue(all(folders.values()))
def parse_request_body(data):
gc = girder_client.GirderClient(apiUrl=GIRDER_API_URL)
gc.token = data['girder_token']
user = gc.get("/user/me")
if user is None:
logging.warn("Bad gider token")
raise tornado.web.HTTPError(401, 'Failed to authenticate with girder')
if data.get('taleId'):
obj = gc.get('/tale/%s' % data['taleId'])
elif data.get('instanceId'):
obj = gc.get('/instance/%s' % data['instanceId'])
else:
obj = None
# TODO: catch possible errors
return gc, user, obj
def get_gc(gc=None, server="lemon"):
global GIRDER_CLIENT
global GIRDER_URL
global GIRDER_KEY
if server == "images":
GIRDER_URL = 'https://images.slide-atlas.org'
GIRDER_KEY = 'MJyaKIJxIkAb8l7OS7mffPE7QvB8H1WxDpyllzcG'
if gc is None:
if GIRDER_CLIENT is None:
GIRDER_CLIENT = girder_client.GirderClient(apiUrl=GIRDER_URL +
'/api/v1')
GIRDER_CLIENT.authenticate(GIRDER_USERNAME, apiKey=GIRDER_KEY)
gc = GIRDER_CLIENT
return gc
def syncPatient(apiKey, destinationLocalFolder):
# api Rest url of the warehouse
url = 'http://humanheart-project.creatis.insa-lyon.fr/database/api/v1'
# Generate the warehouse client
gc = girder_client.GirderClient(apiUrl=url)
# Authentication to the warehouse
gc.authenticate(apiKey=apiKey)
# download the delpel collection in local
gc.downloadResource('5ef3090773e9f0055751d55d',
destinationLocalFolder,
resourceType='collection',
sync=True)
def __init__(self, girder_api_url, username, password):
"""Autheticate with girder instance, prepare for interaction.
param: girder_api_url: the url to the girder instance.
param: username: the user name of the owner of the specific instance
param: password: the password for the user name.
"""
self._client = girder_client.GirderClient(apiUrl=girder_api_url)
self._client.authenticate(username, password)
self._metadata = dict()
self._local_path = None
self._isfolder = False
self._girder_dest_path = None
self._client.addFolderUploadCallback(self.__upload_folder_callback)
self._client.addItemUploadCallback(self.__upload_item_callback)
def upload_baselines(args):
"""
Upload the baseline image tarball to a girder instance.
:param args: a dictionary of arguments, including:
build: the build directory where the tarball is located.
dest: the root url of the Girder instance.
folder: the Girder folder ID to upload to.
apikey: a Girder authentication token. Optional.
username: a Girder username. Optional.
password: a Girder username. Optional.
verbose: the verbosity level.
"""
buildPath = os.path.abspath(os.path.expanduser(args.get('build')))
tarPath = os.path.join(buildPath, 'base-images.tgz')
tarSize = os.path.getsize(tarPath)
# Get the folder we want to upload to to ensure it exists
apiRoot = args['dest'].rstrip('/') + '/api/v1/'
gc = girder_client.GirderClient(apiUrl=apiRoot)
if args.get('apikey'):
gc.authenticate(apiKey=args.get('apikey'))
elif args.get('username') and args.get('password'):
gc.authenticate(username=args.get('username'),
password=args.get('password'))
else:
gc.authenticate(username=args.get('username'), interactive=True)
name = 'Baseline Images %s.tgz' % time.strftime(
'%Y-%m-%d %H:%M:%S', time.localtime(os.path.getmtime(tarPath)))
uploadedFile = gc.uploadFile(parentId=args['folder'],
parentType='folder',
name=name,
stream=open(tarPath, 'rb'),
size=tarSize,
mimeType='application/tar+gzip')
if args['verbose'] >= 1:
print('Upload to file %s' % uploadedFile['_id'])
testDataPath = os.path.abspath('scripts/datastore.js')
if not os.path.isfile(testDataPath):
raise Exception('Cannot update test-data information.')
sha512 = gc.getFile(uploadedFile['_id'])['sha512']
ds = open(testDataPath).read()
start, rest = ds.split("'base-images.tgz': ", 1)
rest, end = rest.split(',', 1)
ds = start + ("'base-images.tgz': '%s'," % sha512) + end
open(testDataPath, 'w').write(ds)
if args['verbose'] >= 1:
print('test-data references updated')
