def process_archive(file_name, dicom_dir):
"""Upload data from a zip archive to the xnat server"""
try:
scanid = get_scanid(file_name)
except datman.scanid.ParseException as e:
logger.error("Failed to find valid identifier for {}. Reason: {}"
"".format(file_name, e))
return
# Make full path after ID conversion, in case user gave different naming
# convention than file system uses.
archive_file = os.path.join(dicom_dir, str(scanid) + ".zip")
xnat = datman.xnat.get_connection(CFG,
site=scanid.site,
url=SERVER_OVERRIDE,
auth=AUTH,
server_cache=SERVERS)
xnat_subject = get_xnat_subject(scanid, xnat)
if not xnat_subject:
# failed to get xnat info
return
exper_id = scanid.get_xnat_experiment_id()
try:
xnat_experiment = xnat_subject.experiments[exper_id]
except KeyError:
data_exists = False
resource_exists = False
else:
try:
data_exists, resource_exists = check_files_exist(archive_file,
xnat_experiment,
xnat)
except Exception:
logger.error("Failed checking xnat for experiment {}".format(
exper_id))
return
if not data_exists:
logger.info("Uploading dicoms from {}".format(archive_file))
try:
upload_dicom_data(archive_file, xnat_subject.project, scanid, xnat)
except Exception as e:
logger.error("Failed uploading archive {} to xnat project {} "
"for subject {}. Check Prearchive. Reason - {}"
.format(archive_file, xnat_subject.project,
xnat_subject.name, e))
if not resource_exists:
logger.debug("Uploading resource from: {}".format(archive_file))
try:
upload_non_dicom_data(archive_file, xnat_subject.project, scanid,
xnat)
except Exception as e:
logger.debug("An exception occurred: {}".format(e))
pass
def upload_dicom_data(archive, xnat_project, scanid, xnat):
# XNAT API for upload fails if the zip contains a mix of dicom and nifti.
# OPT CU definitely contains a mix and others may later on. Soooo
# here's an ugly but effective fix! The niftis will get uploaded with
# upload_non_dicom_data and added to resources - Dawn
if not contains_niftis(archive):
xnat.put_dicoms(xnat_project, scanid.get_xnat_subject_id(),
scanid.get_xnat_experiment_id(), archive)
return
# Need to account for when only niftis are available
with datman.utils.make_temp_directory() as temp:
new_archive = strip_niftis(archive, temp)
if new_archive:
xnat.put_dicoms(xnat_project, scanid.get_xnat_subject_id(),
scanid.get_xnat_experiment_id(), new_archive)
else:
logger.info("No dicoms exist within archive {}, skipping dicom "
"upload!".format(archive))
def upload_non_dicom_data(archive, xnat_project, scanid, xnat):
with zipfile.ZipFile(archive) as zf:
resource_files = datman.utils.get_resources(zf)
logger.info("Uploading {} files of non-dicom data...".format(
len(resource_files)))
uploaded_files = []
for item in resource_files:
# convert to HTTP language
try:
contents = zf.read(item)
# By default files are placed in a MISC subfolder
# if this is changed it may require changes to
# check_duplicate_resources()
xnat.put_resource(xnat_project, scanid.get_xnat_subject_id(),
scanid.get_xnat_experiment_id(), item,
contents, "MISC")
uploaded_files.append(item)
except Exception as e:
logger.error("Failed uploading file {} with error:{}".format(
item, str(e)))
return uploaded_files