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