Warning

This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Source code for tool_shed.tool_shed_registry

import logging

from six.moves.urllib import request as urlrequest

from galaxy.util.odict import odict
from tool_shed.util import common_util, xml_util

log = logging.getLogger( __name__ )


[docs]class Registry( object ):
[docs] def __init__( self, root_dir=None, config=None ): self.tool_sheds = odict() self.tool_sheds_auth = odict() if root_dir and config: # Parse tool_sheds_conf.xml tree, error_message = xml_util.parse_xml( config ) if tree is None: log.warning( "Unable to load references to tool sheds defined in file %s" % str( config ) ) else: root = tree.getroot() log.debug( 'Loading references to tool sheds from %s' % config ) for elem in root.findall( 'tool_shed' ): try: name = elem.get( 'name', None ) url = elem.get( 'url', None ) username = elem.get( 'user', None ) password = elem.get( 'pass', None ) if name and url: self.tool_sheds[ name ] = url self.tool_sheds_auth[ name ] = None log.debug( 'Loaded reference to tool shed: %s' % name ) if name and url and username and password: pass_mgr = urlrequest.HTTPPasswordMgrWithDefaultRealm() pass_mgr.add_password( None, url, username, password ) self.tool_sheds_auth[ name ] = pass_mgr except Exception as e: log.warning( 'Error loading reference to tool shed "%s", problem: %s' % ( name, str( e ) ) )
[docs] def password_manager_for_url( self, url ): """ If the tool shed is using external auth, the client to the tool shed must authenticate to that as well. This provides access to the six.moves.urllib.request.HTTPPasswordMgrWithdefaultRealm() object for the url passed in. Following more what galaxy.demo_sequencer.controllers.common does might be more appropriate at some stage... """ url_sans_protocol = common_util.remove_protocol_from_tool_shed_url( url ) for shed_name, shed_url in self.tool_sheds.items(): shed_url_sans_protocol = common_util.remove_protocol_from_tool_shed_url( shed_url ) if url_sans_protocol.startswith( shed_url_sans_protocol ): return self.tool_sheds_auth[ shed_name ] log.debug( "Invalid url '%s' received by tool shed registry's password_manager_for_url method." % str( url ) ) return None
[docs] def url_auth( self, url ): password_manager = self.password_manager_for_url( url ) if password_manager is not None: return urlrequest.HTTPBasicAuthHandler( password_manager )