def get_tags(self, site=None, study=None):
"""
Returns a TagInfo instance.
If you get the tags without a study set or without specifying a site
you get the configuration of all defined tags from 'ExportSettings' in
the system config file.
If you specify a site, you get the configuration for that site merged
with the configuration of 'ExportSettings' for the tags matching that
site. If there's a key conflict between 'ExportInfo' (study config) and
'ExportSettings' (system config) the values in 'ExportInfo' will
override the values in 'ExportSettings'.
"""
if site:
export_info = self.get_key("ExportInfo", site=site)
else:
export_info = {}
try:
export_settings = self.get_key("ExportSettings")
except UndefinedSetting:
raise UndefinedSetting("Tag dictionary 'ExportSettings' not "
"defined in main configuration file.")
return TagInfo(export_settings, export_info)
def set_study(self, study_name):
"""
This function can take just the study ID for every study except DTI. So
where possible, please give it an exact match to a project name or a
full session ID.
"""
# make the supplied project_name case insensitive
valid_projects = {k.lower(): k for k in self.get_key("Projects")}
if study_name.lower() in valid_projects:
study_name = study_name.upper()
else:
# This will raise an exception if given only the 'DTI' id because
# two studies are mapped to this ID. Give set_study() a full
# session ID to avoid this
study_name = self.map_xnat_archive_to_project(study_name)
self.study_name = study_name
config_path = self.get_key("ConfigDir")
projects = self.get_key("Projects")
try:
study_yaml = projects[study_name]
except KeyError:
raise UndefinedSetting(f"Study {study_name} not configured.")
project_settings_file = os.path.join(config_path, study_yaml)
self.study_config = self.load_yaml(project_settings_file)
self.study_config_path = project_settings_file
def get_path(self, path_type, study=None):
"""returns the absolute path to a folder type"""
paths = self.get_key("Paths")
try:
sub_dir = paths[path_type]
except KeyError:
raise UndefinedSetting(f"Path {path_type} not defined")
return os.path.join(self.get_study_base(), sub_dir)
def _search_system_conf(self, key):
"""
Searches the global system-wide settings for 'key'. Will not search
recursively (i.e. will not check within studies or sites)
Raises UndefinedSetting if key is not found.
"""
try:
value = self.system_config[key]
except KeyError:
raise UndefinedSetting(f"'{key}' not set")
return value
def _search_study_conf(self, key):
"""
Search the current study's config for 'key'. Does not search
recursively i.e. will not check all sites.
Raises UndefinedSetting if key is not found
"""
if not self.study_config:
raise ConfigException("Study not set.")
try:
value = self.study_config[key]
except KeyError:
raise UndefinedSetting(
f"'{key}' not defined for study {self.study_name}")
return value
def _search_site_conf(self, site, key):
"""
Search a specific study's site for 'key'.
Raises 'UndefinedSetting' if the key does not exist
"""
try:
site_conf = self._search_study_conf("Sites")
except UndefinedSetting:
raise ConfigException(
f"'Sites' not defined for study {self.study_name}")
try:
site_conf = site_conf[site]
except KeyError:
raise ConfigException(
f"Site '{site}' not found for study {self.study_name}")
try:
value = site_conf[key]
except KeyError:
raise UndefinedSetting(f"'{key}' not set for site {site}")
return value
def _search_local_conf(self, key):
"""
Searches the currently configured system (i.e. the system found in
'SystemSettings' for 'key')
Raises UndefinedSetting if key is not found
"""
try:
system_settings = self._search_system_conf("SystemSettings")
except UndefinedSetting:
raise ConfigException("'SystemSettings' not defined")
try:
local_system = system_settings[self.system]
except KeyError:
raise ConfigException(
f"System '{key}' not defined in SystemSettings")
try:
value = local_system[key]
except KeyError:
raise UndefinedSetting(
f"'{key}' not defined for system {self.system}")
return value