def process_resources(xnat, ident, xnat_experiment):
"""Export any non-dicom resources from the XNAT archive"""
logger.info("Extracting {} resources from {}".format(
len(xnat_experiment.resource_files), xnat_experiment.name))
base_path = os.path.join(cfg.get_path('resources'), str(ident))
if not os.path.isdir(base_path):
logger.info("Creating resources dir {}".format(base_path))
try:
os.makedirs(base_path)
except OSError:
logger.error("Failed creating resources dir {}".format(base_path))
return
for label in xnat_experiment.resource_IDs:
if label == 'No Label':
target_path = os.path.join(base_path, 'MISC')
else:
target_path = os.path.join(base_path, label)
try:
target_path = datman.utils.define_folder(target_path)
except OSError:
logger.error("Failed creating target folder: {}"
.format(target_path))
continue
xnat_resource_id = xnat_experiment.resource_IDs[label]
try:
resources = xnat.get_resource_list(xnat_experiment.project,
xnat_experiment.subject,
xnat_experiment.name,
xnat_resource_id)
except Exception as e:
logger.error("Failed getting resource {} for experiment {}. "
"Reason - {}".format(xnat_resource_id,
xnat_experiment.name,
e))
continue
if not resources:
continue
for resource in resources:
resource_path = os.path.join(target_path, resource['URI'])
if os.path.isfile(resource_path):
logger.debug("Resource {} from experiment {} already exists"
.format(resource['name'], xnat_experiment.name))
else:
logger.info("Downloading {} from experiment {}"
.format(resource['name'], xnat_experiment.name))
download_resource(xnat,
xnat_experiment,
xnat_resource_id,
resource['URI'],
resource_path)
def process_resources(xnat_project, session_label, experiment_label, data):
"""Export any non-dicom resources from the xnat archive"""
global cfg
logger.info('Extracting {} resources from {}'.format(
len(data), session_label))
base_path = os.path.join(cfg.get_path('resources'), session_label)
if not os.path.isdir(base_path):
logger.info('Creating dir:{}'.format(base_path))
try:
os.makedirs(base_path)
except OSError:
logger.error('Failed creating resources dir:{}.'.format(base_path))
return
for item in data['items']:
try:
data_type = item['data_fields']['label']
except KeyError:
data_type = 'misc'
target_path = os.path.join(base_path, data_type)
try:
target_path = datman.utils.define_folder(target_path)
except OSError:
logger.error(
'Failed creating target folder:{}'.format(target_path))
continue
xnat_resource_id = item['data_fields']['xnat_abstractresource_id']
try:
resources = xnat.get_resource_list(xnat_project, session_label,
experiment_label,
xnat_resource_id)
if not resources:
continue
except Exception as e:
logger.error('Failed getting resource:{} '
'for session:{} in project:{}'.format(
xnat_resource_id, session_label, e))
continue
for resource in resources:
resource_path = os.path.join(target_path, resource['URI'])
if os.path.isfile(resource_path):
logger.debug('Resource:{} found for session:{}'.format(
resource['name'], session_label))
else:
logger.info('Resource:{} not found for session:{}'.format(
resource['name'], session_label))
_ = get_resource(xnat_project, session_label, experiment_label,
xnat_resource_id, resource['URI'],
resource_path)
check_duplicates(resource, base_path, target_path)