def __init__(self, file_sources_config, conf_file=None, conf_dict=None, load_stock_plugins=False):
self._file_sources_config = file_sources_config
self._plugin_classes = self._file_source_plugins_dict()
file_sources = []
if conf_file is not None:
file_sources = self._load_plugins_from_file(conf_file)
elif conf_dict is not None:
plugin_source = plugin_config.plugin_source_from_dict(conf_dict)
file_sources = self._parse_plugin_source(plugin_source)
else:
file_sources = []
custom_sources_configured = len(file_sources) > 0
if load_stock_plugins:
stock_file_source_conf_dict = []
def _ensure_loaded(plugin_type):
for file_source in file_sources:
if file_source.plugin_type == plugin_type:
return
stock_file_source_conf_dict.append({'type': plugin_type})
if file_sources_config.library_import_dir is not None:
_ensure_loaded('gximport')
if file_sources_config.user_library_import_dir is not None:
_ensure_loaded('gxuserimport')
if file_sources_config.ftp_upload_dir is not None:
_ensure_loaded('gxftp')
if stock_file_source_conf_dict:
stock_plugin_source = plugin_config.plugin_source_from_dict(stock_file_source_conf_dict)
file_sources.extend(self._parse_plugin_source(stock_plugin_source))
self._file_sources = file_sources
self.custom_sources_configured = custom_sources_configured
def __build_container_resolvers(self, app_info, destination_info):
app_conf_file = getattr(app_info, 'container_resolvers_config_file',
None)
app_conf_dict = getattr(app_info, 'container_resolvers_config_dict',
None)
if destination_info is not None:
conf_file = destination_info.get('container_resolvers_config_file',
app_conf_file)
conf_dict = destination_info.get('container_resolvers',
app_conf_dict)
else:
conf_file = app_conf_file
conf_dict = app_conf_dict
plugin_source = None
if conf_dict:
log.debug(
"Loading container resolution config inline from Galaxy or job configuration file"
)
plugin_source = plugin_config.plugin_source_from_dict(conf_dict)
elif conf_file and not os.path.exists(conf_file):
log.warning(f"Unable to find config file '{conf_file}'")
elif conf_file:
log.debug(
"Loading container resolution config from file '{conf_file}'")
plugin_source = plugin_config.plugin_source_from_path(conf_file)
if plugin_source:
return self._parse_resolver_conf(plugin_source)
return self.__default_container_resolvers()
def __init__(self,
file_sources_config: 'ConfiguredFileSourcesConfig',
conf_file=None,
conf_dict=None,
load_stock_plugins=False):
self._file_sources_config = file_sources_config
self._plugin_classes = self._file_source_plugins_dict()
file_sources = []
if conf_file is not None:
file_sources = self._load_plugins_from_file(conf_file)
elif conf_dict is not None:
plugin_source = plugin_config.plugin_source_from_dict(conf_dict)
file_sources = self._parse_plugin_source(plugin_source)
else:
file_sources = []
custom_sources_configured = len(file_sources) > 0
if load_stock_plugins:
stock_file_source_conf_dict = []
def _ensure_loaded(plugin_type):
for file_source in file_sources:
if file_source.plugin_type == plugin_type:
return
stock_file_source_conf_dict.append({'type': plugin_type})
if file_sources_config.ftp_upload_dir is not None:
_ensure_loaded('gxftp')
if file_sources_config.library_import_dir is not None:
_ensure_loaded('gximport')
if file_sources_config.user_library_import_dir is not None:
_ensure_loaded('gxuserimport')
if stock_file_source_conf_dict:
stock_plugin_source = plugin_config.plugin_source_from_dict(
stock_file_source_conf_dict)
# insert at begining instead of append so FTP and library import appear
# at the top of the list (presumably the most common options). Admins can insert
# these explicitly for greater control.
file_sources = self._parse_plugin_source(
stock_plugin_source) + file_sources
self._file_sources = file_sources
self.custom_sources_configured = custom_sources_configured