def rename_xnat_session(xnat, orig_name, new_name, project=None):
"""Rename a session on XNAT.
Args:
xnat (:obj:`datman.xnat.xnat`): A connection to the XNAT server.
orig_name (:obj:`str`): The current session name on XNAT.
new_name (:obj:`str`): The new name to apply to the session.
project (:obj:`str`, optional): The XNAT project the session belongs
to. If not given, it will be guessed based on orig_name. Defaults
to None.
Raises:
XnatException: If problems internal to
:obj:`datman.xnat.xnat.rename_session` occur.
requests.HTTPError: If XNAT's API reports issues.
Returns:
bool: True if rename succeeded, False otherwise
"""
if not project:
project = get_project(orig_name)
try:
ident = datman.scanid.parse(new_name)
except ParseException:
raise ParseException("New ID {} for experiment {} doesnt match a "
"supported naming convention.".format(
new_name, orig_name))
logger.info("Renaming {} to {} in project {}".format(
orig_name, new_name, project))
orig_subject = xnat.find_subject(project, orig_name)
try:
xnat.rename_subject(project, orig_subject, ident.get_xnat_subject_id())
except HTTPError as e:
if e.response.status_code == 500:
# This happens on success sometimes (usually when experiment
# is empty). Check if the rename succeeded.
try:
xnat.get_subject(project, ident.get_xnat_subject_id())
except XnatException:
raise e
xnat.rename_experiment(project, ident.get_xnat_subject_id(), orig_name,
ident.get_xnat_experiment_id())
def download_subjects(xnat, xnat_project, destination):
try:
current_zips = os.listdir(destination)
except FileNotFoundError:
if DRYRUN:
logger.info(f"DRYRUN - Skipping creation of {destination}")
else:
os.mkdir(destination)
for subject_id in xnat.get_subject_ids(xnat_project):
try:
subject = xnat.get_subject(xnat_project, subject_id)
except Exception as e:
logger.error("Failed to get subject {} from xnat. "
"Reason: {}".format(subject_id, e))
continue
exp_names = [item for item in subject.experiments.keys()]
if not exp_names:
logger.error("Subject {} has no experiments.".format(subject.name))
continue
if len(exp_names) > 1:
logger.error(
f"Found {len(exp_names)} experiments for subject "
f"{subject.name}. Only one was expected. Skipping subject.")
continue
experiment = subject.experiments[exp_names[0]]
zip_name = subject.name.upper() + ".zip"
zip_path = os.path.join(destination, zip_name)
if zip_name in current_zips and not update_needed(
zip_path, experiment, xnat):
logger.debug("All data downloaded for {}. Passing.".format(
experiment.name))
continue
if DRYRUN:
logger.info("Would have downloaded experiment {} from project "
"{} to {}".format(experiment.name, xnat_project,
zip_path))
continue
with datman.utils.make_temp_directory() as temp:
try:
temp_zip = experiment.download(xnat, temp, zip_name=zip_name)
except Exception as e:
logger.error("Cant download experiment {}. Reason: {}"
"".format(experiment, e))
continue
restructure_zip(temp_zip, zip_path)
def get_xnat_subject(ident, xnat):
"""Get an XNAT subject from the server.
Args:
ident (:obj:`datman.scanid.Identifier`): A datman identifier instance
for a supported naming convention.
xnat (:obj:`datman.xnat.xnat`): An XNAT connection to the server
to upload to.
Raises:
XnatException: If the server or project is not accessible.
Returns:
:obj:`datman.xnat.XNATSubject` or None
"""
# get the expected xnat project name from the config filename
try:
xnat_project = CFG.get_key("XnatArchive",
site=ident.site)
except datman.config.UndefinedSetting:
logger.warning("Study {}, Site {}, xnat archive not defined in config"
.format(ident.study, ident.site))
return None
# check we can get the archive from xnat
try:
found = xnat.get_projects(xnat_project)
except datman.exceptions.XnatException as e:
logger.error("Failed to get XNAT project {} for study {} and site "
"{}. Reason - {}".format(xnat_project, ident.study,
ident.site, e))
return None
if not found:
logger.error("No match found for XNAT project {} on server {}".format(
xnat_project, xnat.server))
return None
# check we can get or create the session in xnat
try:
xnat_subject = xnat.get_subject(xnat_project,
ident.get_xnat_subject_id(),
create=True)
except datman.exceptions.XnatException as e:
logger.error("Study {}, site {}, archive {} Failed getting session {}"
" from xnat with reason {}"
.format(ident.study, ident.site,
xnat_project, ident.get_xnat_subject_id(), e))
return None
return xnat_subject