def get_resource(xnat_project, xnat_session, xnat_experiment,
xnat_resource_group, xnat_resource_id, target_path):
"""Download a single resource file from xnat. Target path should be
full path to store the file, including filename"""
try:
archive = xnat.get_resource(xnat_project,
xnat_session,
xnat_experiment,
xnat_resource_group,
xnat_resource_id,
zipped=False)
except Exception as e:
logger.error(
'Failed downloading resource archive from:{} with reason:{}'.
format(xnat_session, e))
return
# check that the target path exists
target_dir = os.path.split(target_path)[0]
if not os.path.exists(target_dir):
try:
os.makedirs(target_dir)
except OSError:
logger.error('Failed to create directory:{}'.format(target_dir))
return
# copy the downloaded file to the target location
try:
source = archive[1]
if not DRYRUN:
shutil.copyfile(source, target_path)
except:
logger.error('Failed copying resource:{} to target:{}.'.format(
source, target_path))
# # extract the files from the archive, ignoring the filestructure
# try:
# with zipfile.ZipFile(archive[1]) as zip_file:
# member = zip_file.namelist()[0]
# source = zip_file.open(member)
# if not DRYRUN:
# with open(target_path, 'wb') as target:
# shutil.copyfileobj(source, target)
# target.close()
# except:
# logger.error('Failed extracting resources archive:{}'
# .format(xnat_session), exc_info=True)
# finally delete the temporary archive
try:
os.remove(archive[1])
except OSError:
logger.error(
'Failed to remove temporary archive:{} on system:{}'.format(
archive, platform.node()))
return (target_path)
def get_resource_archive_from_xnat(xnat_project, session, resourceid):
"""Downloads and extracts a resource archive from xnat
to a local temp file
Returns the path to the tempfile (for later cleanup)"""
logger.debug('Downloadind resources for:{}, series:{}.'.format(
session, resourceid))
try:
resource_archive = xnat.get_resource(xnat_project, session, session,
resourceid)
except Exception as e:
return None
return (resource_archive)
def download_resource(xnat, xnat_experiment, xnat_resource_id,
xnat_resource_uri, target_path):
"""
Download a single resource file from XNAT. Target path should be
full path to store the file, including filename
"""
try:
source = xnat.get_resource(xnat_experiment.project,
xnat_experiment.subject,
xnat_experiment.name,
xnat_resource_id,
xnat_resource_uri,
zipped=False)
except Exception as e:
logger.error("Failed downloading resource archive from {} with "
"reason: {}".format(xnat_experiment.name, e))
return
# check that the target path exists
target_dir = os.path.split(target_path)[0]
if not os.path.exists(target_dir):
try:
os.makedirs(target_dir)
except OSError:
logger.error("Failed to create directory: {}".format(target_dir))
return
# copy the downloaded file to the target location
try:
if not DRYRUN:
shutil.copyfile(source, target_path)
except (IOError, OSError):
logger.error("Failed copying resource {} to target {}".format(
source, target_path))
# finally delete the temporary archive
try:
os.remove(source)
except OSError:
logger.error(
"Failed to remove temporary archive {} on system {}".format(
source, platform.node()))
return target_path
def get_resource(xnat_project, xnat_session, xnat_experiment,
xnat_resource_group, xnat_resource_id, target_path):
"""Download a single resource file from xnat. Target path should be
full path to store the file, including filename"""
try:
archive = xnat.get_resource(xnat_project,
xnat_session,
xnat_experiment,
xnat_resource_group,
xnat_resource_id,
zipped=False)
except Exception as e:
logger.error(
'Failed downloading resource archive from:{} with reason:{}'.
format(xnat_session, e))
return
# check that the target path exists
target_dir = os.path.split(target_path)[0]
if not os.path.exists(target_dir):
try:
os.makedirs(target_dir)
except OSError:
logger.error('Failed to create directory:{}'.format(target_dir))
return
# copy the downloaded file to the target location
try:
source = archive[1]
if not DRYRUN:
shutil.copyfile(source, target_path)
except:
logger.error('Failed copying resource:{} to target:{}.'.format(
source, target_path))
# finally delete the temporary archive
try:
os.remove(archive[1])
except OSError:
logger.error(
'Failed to remove temporary archive:{} on system:{}'.format(
archive, platform.node()))
return (target_path)