def update_study(study_id, config, skip_delete=False, delete_all=False):
"""Update all settings stored in the database for the given study.
Args:
study_id (str): The ID of the study to update.
config (:obj:`datman.config.config`): a Datman config object.
skip_delete (bool, optional): Don't prompt the user and skip deletion
of any records no longer defined in the config files.
delete_all (bool, optional): Don't prompt the user and delete any
records no longer defined in the config files.
"""
try:
config.set_study(study_id)
except Exception as e:
logger.error(f"Can't access config for {study_id}. Reason - {e}")
return
try:
ignore = config.get_key("DbIgnore")
except UndefinedSetting:
ignore = False
if ignore:
return
study = dashboard.queries.get_studies(study_id, create=True)[0]
update_setting(study, "description", config, "Description")
update_setting(study, "name", config, "FullName")
update_setting(study, "is_open", config, "IsOpen")
update_redcap(config)
try:
sites = config.get_sites()
except UndefinedSetting:
logger.error(f"No sites defined for {study_id}")
return
undefined = [site_id for site_id in study.sites if site_id not in sites]
delete_records(
undefined,
prompt=("Site {} will be deleted from study "
f"{study.id}. Any records referencing this study/site pair "
"will be removed."),
delete_func=lambda x: study.delete_site(x),
skip_delete=skip_delete,
delete_all=delete_all)
for site_id in sites:
update_site(study,
site_id,
config,
skip_delete=skip_delete,
delete_all=delete_all)
def get_projects(config):
"""Find all XNAT projects and the list of scan sites uploaded to each one.
Args:
config (:obj:`datman.config.config`): The config for a study
Returns:
dict: A map of XNAT project names to the URL(s) of the server holding
that project.
"""
projects = {}
for site in config.get_sites():
xnat_project = config.get_key("XNAT_Archive", site=site)
projects.setdefault(xnat_project, set()).add(site)
return projects
def main():
global DRYRUN
arguments = docopt(__doc__)
xnat_project = arguments['<project>']
xnat_server = arguments['<server>']
username = arguments['<username>']
password = arguments['<password>']
destination = arguments['<destination>']
study = arguments['<study>']
given_site = arguments['--site']
use_server = arguments['--log-to-server']
DRYRUN = arguments['--dry-run']
if arguments['--debug']:
logger.setLevel(logging.DEBUG)
elif arguments['--verbose']:
logger.setLevel(logging.INFO)
elif arguments['--quiet']:
logger.setLevel(logging.ERROR)
if not study:
with datman.xnat.xnat(xnat_server, username, password) as xnat:
download_subjects(xnat, xnat_project, destination)
return
config = datman.config.config(study=study)
if use_server:
add_server_handler(config)
sites = [given_site] if given_site else config.get_sites()
for site in sites:
try:
credentials_file, server, project, destination = get_xnat_config(
config, site)
except KeyError as e:
logger.error("{}".format(e))
continue
username, password = get_credentials(credentials_file)
with datman.xnat.xnat(server, username, password) as xnat:
download_subjects(xnat, project, destination)
def main():
global DRYRUN
arguments = docopt(__doc__)
xnat_project = arguments['<project>']
xnat_server = arguments['<server>']
username = arguments['<username>']
password = arguments['<password>']
destination = arguments['<destination>']
study = arguments['<study>']
given_site = arguments['--site']
use_server = arguments['--log-to-server']
DRYRUN = arguments['--dry-run']
if arguments['--debug']:
logger.setLevel(logging.DEBUG)
elif arguments['--verbose']:
logger.setLevel(logging.INFO)
elif arguments['--quiet']:
logger.setLevel(logging.ERROR)
if not study:
with datman.xnat.xnat(xnat_server, username, password) as xnat:
get_sessions(xnat, xnat_project, destination)
return
config = datman.config.config(study=study)
if use_server:
add_server_handler(config)
sites = [given_site] if given_site else config.get_sites()
for site in sites:
try:
credentials_file, server, project, destination = get_xnat_config(
config, site)
except KeyError as e:
logger.error("{}".format(e.message))
continue
username, password = get_credentials(credentials_file)
with datman.xnat.xnat(server, username, password) as xnat:
get_sessions(xnat, project, destination)
def test_updating_study_calls_update_site_for_configured_sites(
self, mock_update, config, db_study):
pc.update_study("SPINS", config, skip_delete=True)
assert mock_update.call_count == len(config.get_sites())