def __init__(self, default_base_path, conf_file=None, app_config={}):
"""
Create a new dependency manager looking for packages under the paths listed
in `base_paths`. The default base path is app.config.tool_dependency_dir.
"""
if not os.path.exists(default_base_path):
log.warning("Path '%s' does not exist, ignoring",
default_base_path)
if not os.path.isdir(default_base_path):
log.warning("Path '%s' is not directory, ignoring",
default_base_path)
self.__app_config = app_config
self.default_base_path = os.path.abspath(default_base_path)
self.resolver_classes = self.__resolvers_dict()
plugin_source = None
dependency_resolver_dicts = app_config.get("dependency_resolvers")
if dependency_resolver_dicts is not None:
plugin_source = plugin_config.PluginConfigSource(
'dict', dependency_resolver_dicts)
else:
plugin_source = self.__build_dependency_resolvers_plugin_source(
conf_file)
self.dependency_resolvers = self.__parse_resolver_conf_plugins(
plugin_source)
self._enabled_container_types = []
self._destination_for_container_type = {}
def __default_dependency_resolvers_source(self):
return plugin_config.PluginConfigSource('dict', [
{
"type": "tool_shed_packages"
},
{
"type": "galaxy_packages"
},
{
"type": "conda"
},
{
"type": "galaxy_packages",
"versionless": True
},
{
"type": "conda",
"versionless": True
},
])
def set_destination_conf_dicts(self, destination_id, conf_dicts):
plugin_source = plugin_config.PluginConfigSource('dict', conf_dicts)
instrumenter = JobInstrumenter(self.plugin_classes, plugin_source)
self.set_destination_instrumenter(destination_id, instrumenter)
from galaxy.util import plugin_config
log = logging.getLogger(__name__)
DEFAULT_CONFIG = [
{
'type': 'email',
'verbose': True,
'user_submission': True,
},
{
'type': 'sentry',
'user_submission': False,
},
]
DEFAULT_PLUGINS_SOURCE = plugin_config.PluginConfigSource(
'dict', DEFAULT_CONFIG)
class ErrorReports:
"""Load and store a collection of :class:`ErrorPlugin` objects."""
def __init__(self, conf_file=None, **kwargs):
"""Load :class:`ErrorPlugin` objects from specified configuration file."""
self.plugin_classes = self.__plugins_dict()
self.default_error_plugin = ErrorPlugin.from_file(
self.plugin_classes, conf_file, **kwargs)
self.error_plugin = collections.defaultdict(
lambda: self.default_error_plugin)
def __plugins_dict(self):
import galaxy.tools.error_reports.plugins
return plugin_config.plugins_dict(galaxy.tools.error_reports.plugins,
def set_destination_conf_element(self, destination_id, element):
plugin_source = plugin_config.PluginConfigSource('xml', element)
instrumenter = JobInstrumenter(self.plugin_classes, plugin_source)
self.set_destination_instrumenter(destination_id, instrumenter)
