def __init__(self, **kwargs): print >> sys.stderr, "python path is: " + ", ".join(sys.path) self.name = "community" # Read config file and check for errors self.config = config.Configuration(**kwargs) self.config.check() config.configure_logging(self.config) # Set up datatypes registry self.datatypes_registry = galaxy.datatypes.registry.Registry() self.datatypes_registry.load_datatypes(self.config.root, self.config.datatypes_config) # Determine the database url if self.config.database_connection: db_url = self.config.database_connection else: db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % self.config.database # Initialize database / check for appropriate schema version from galaxy.webapps.community.model.migrate.check import create_or_verify_database create_or_verify_database(db_url, self.config.database_engine_options) # Setup the database engine and ORM from galaxy.webapps.community.model import mapping self.model = mapping.init(self.config.file_path, db_url, self.config.database_engine_options) # Security helper self.security = security.SecurityHelper( id_secret=self.config.id_secret) # Tag handler self.tag_handler = CommunityTagHandler() # Tool data tables - never pass a config file here because the tool shed should always have an empty dictionary! self.tool_data_tables = galaxy.tools.data.ToolDataTableManager( self.config.tool_data_path) # The tool shed has no toolbox, but this attribute is still required. self.toolbox = tools.ToolBox([], self.config.tool_path, self) # Load security policy self.security_agent = self.model.security_agent self.quota_agent = galaxy.quota.NoQuotaAgent(self.model) # TODO: Add OpenID support self.openid_providers = OpenIDProviders() self.shed_counter = self.model.shed_counter # Let the HgwebConfigManager know where the hgweb.config file is located. self.hgweb_config_manager = self.model.hgweb_config_manager self.hgweb_config_manager.hgweb_config_dir = self.config.hgweb_config_dir print >> sys.stderr, "Tool shed hgweb.config file is: ", self.hgweb_config_manager.hgweb_config
def __init__( self, **kwargs ): print >> sys.stderr, "python path is: " + ", ".join( sys.path ) self.name = "community" # Read config file and check for errors self.config = config.Configuration( **kwargs ) self.config.check() config.configure_logging( self.config ) # Set up datatypes registry self.datatypes_registry = galaxy.datatypes.registry.Registry() self.datatypes_registry.load_datatypes( self.config.root, self.config.datatypes_config ) # Determine the database url if self.config.database_connection: db_url = self.config.database_connection else: db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % self.config.database # Initialize database / check for appropriate schema version from galaxy.webapps.community.model.migrate.check import create_or_verify_database create_or_verify_database( db_url, self.config.database_engine_options ) # Setup the database engine and ORM from galaxy.webapps.community.model import mapping self.model = mapping.init( self.config.file_path, db_url, self.config.database_engine_options ) # Security helper self.security = security.SecurityHelper( id_secret=self.config.id_secret ) # Tag handler self.tag_handler = CommunityTagHandler() # Tool data tables - never pass a config file here because the tool shed should always have an empty dictionary! self.tool_data_tables = galaxy.tools.data.ToolDataTableManager( self.config.tool_data_path ) # The tool shed has no toolbox, but this attribute is still required. self.toolbox = tools.ToolBox( [], self.config.tool_path, self ) # Load security policy self.security_agent = self.model.security_agent self.quota_agent = galaxy.quota.NoQuotaAgent( self.model ) # TODO: Add OpenID support self.openid_providers = OpenIDProviders() self.shed_counter = self.model.shed_counter # Let the HgwebConfigManager know where the hgweb.config file is located. self.hgweb_config_manager = self.model.hgweb_config_manager self.hgweb_config_manager.hgweb_config_dir = self.config.hgweb_config_dir print >> sys.stderr, "Tool shed hgweb.config file is: ", self.hgweb_config_manager.hgweb_config
def __init__( self, **kwargs ): print >> sys.stderr, "python path is: " + ", ".join( sys.path ) # Read config file and check for errors self.config = config.Configuration( **kwargs ) self.config.check() config.configure_logging( self.config ) # Set up datatypes registry self.datatypes_registry = galaxy.datatypes.registry.Registry() # TODO: Handle datatypes included in repositories - the following will only load datatypes_conf.xml. self.datatypes_registry.load_datatypes( self.config.root, self.config.datatypes_config ) # Determine the database url if self.config.database_connection: db_url = self.config.database_connection else: db_url = "sqlite://%s?isolation_level=IMMEDIATE" % self.config.database # Initialize database / check for appropriate schema version from galaxy.webapps.community.model.migrate.check import create_or_verify_database create_or_verify_database( db_url, self.config.database_engine_options ) # Setup the database engine and ORM from galaxy.webapps.community.model import mapping self.model = mapping.init( self.config.file_path, db_url, self.config.database_engine_options ) # Security helper self.security = security.SecurityHelper( id_secret=self.config.id_secret ) # Tag handler self.tag_handler = CommunityTagHandler() # Tool data tables self.tool_data_tables = galaxy.tools.data.ToolDataTableManager( self.config.tool_data_table_config_path ) # The tool shed has no toolbox, but this attribute is still required. self.toolbox = None # Load security policy self.security_agent = self.model.security_agent self.quota_agent = galaxy.quota.NoQuotaAgent( self.model ) # TODO: Add OpenID support self.openid_providers = OpenIDProviders() self.shed_counter = self.model.shed_counter