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 from_file(plugin_classes, conf_file, **kwargs):
plugins_source = DEFAULT_PLUGINS_SOURCE
if conf_file and os.path.exists(conf_file):
plugins_source = plugin_config.plugin_source_from_path(conf_file)
if not plugins_source.source:
return NULL_ERROR_PLUGIN
return ErrorPlugin(plugin_classes, plugins_source, **kwargs)
def __build_dependency_resolvers_plugin_source(self, conf_file):
if not conf_file:
return self.__default_dependency_resolvers_source()
if not os.path.exists(conf_file):
log.debug("Unable to find config file '%s'", conf_file)
return self.__default_dependency_resolvers_source()
plugin_source = plugin_config.plugin_source_from_path(conf_file)
return plugin_source
def __build_dependency_resolvers( self, conf_file ):
if not conf_file:
return self.__default_dependency_resolvers()
if not os.path.exists( conf_file ):
log.debug( "Unable to find config file '%s'", conf_file)
return self.__default_dependency_resolvers()
plugin_source = plugin_config.plugin_source_from_path( conf_file )
return self.__parse_resolver_conf_xml( plugin_source )
def __build_container_resolvers( self, app_info ):
conf_file = getattr(app_info, 'containers_resolvers_config_file', None)
if not conf_file:
return self.__default_containers_resolvers()
if not os.path.exists( conf_file ):
log.debug( "Unable to find config file '%s'", conf_file)
return self.__default_containers_resolvers()
plugin_source = plugin_config.plugin_source_from_path( conf_file )
return self.__parse_resolver_conf_xml( plugin_source )
def _load_plugins_from_file(self, conf_file):
plugin_source = plugin_config.plugin_source_from_path(conf_file)
return self._parse_plugin_source(plugin_source)
def from_file(plugin_classes, conf_file, **kwargs):
if not conf_file or not os.path.exists(conf_file):
return NULL_JOB_INSTRUMENTER
plugins_source = plugin_config.plugin_source_from_path(conf_file)
return JobInstrumenter(plugin_classes, plugins_source, **kwargs)
def from_file(plugin_classes, conf_file, **kwargs):
if not conf_file or not os.path.exists(conf_file):
return NULL_JOB_INSTRUMENTER
plugins_source = plugin_config.plugin_source_from_path(conf_file)
return JobInstrumenter(plugin_classes, plugins_source, **kwargs)
def __build_dependency_resolvers( self, conf_file ):
if not conf_file or not os.path.exists( conf_file ):
return self.__default_dependency_resolvers()
plugin_source = plugin_config.plugin_source_from_path( conf_file )
return self.__parse_resolver_conf_xml( plugin_source )
def __build_dependency_resolvers(self, conf_file):
if not conf_file or not os.path.exists(conf_file):
return self.__default_dependency_resolvers()
plugin_source = plugin_config.plugin_source_from_path(conf_file)
return self.__parse_resolver_conf_xml(plugin_source)
def from_file(plugin_classes, conf_file, **kwargs):
if not conf_file or not os.path.exists(conf_file):
return NULL_ERROR_PLUGIN
plugins_source = plugin_config.plugin_source_from_path(conf_file)
return ErrorPlugin(plugin_classes, plugins_source, **kwargs)
