import config
import sys
import time
import galaxy.datatypes.registry
import galaxy.quota
import galaxy.tools.data
import galaxy.webapps.tool_shed.model
from galaxy import tools
from galaxy.managers.tags import CommunityTagManager
from galaxy.openid.providers import OpenIDProviders
from galaxy.util.dbkeys import GenomeBuilds
from galaxy.web import security
import tool_shed.repository_registry
import tool_shed.repository_types.registry
from tool_shed.grids.repository_grid_filter_manager import RepositoryGridFilterManager
[docs]class UniverseApplication( object ):
"""Encapsulates the state of a Universe application"""
def __init__( self, **kwd ):
print >> sys.stderr, "python path is: " + ", ".join( sys.path )
self.name = "tool_shed"
# Read the tool_shed.ini configuration file and check for errors.
self.config = config.Configuration( **kwd )
self.config.check()
config.configure_logging( self.config )
# Initialize the Galaxy datatypes registry.
self.datatypes_registry = galaxy.datatypes.registry.Registry()
self.datatypes_registry.load_datatypes( self.config.root, self.config.datatypes_config )
# Initialize the Tool Shed repository_types registry.
self.repository_types_registry = tool_shed.repository_types.registry.Registry()
# Initialize the RepositoryGridFilterManager.
self.repository_grid_filter_manager = RepositoryGridFilterManager()
# Determine the Tool Shed database connection string.
if self.config.database_connection:
db_url = self.config.database_connection
else:
db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % self.config.database
# Initialize the Tool Shed database and check for appropriate schema version.
from galaxy.webapps.tool_shed.model.migrate.check import create_or_verify_database
create_or_verify_database( db_url, self.config.database_engine_options )
# Set up the Tool Shed database engine and ORM.
from galaxy.webapps.tool_shed.model import mapping
self.model = mapping.init( self.config.file_path,
db_url,
self.config.database_engine_options )
# Initialize the Tool Shed security helper.
self.security = security.SecurityHelper( id_secret=self.config.id_secret )
# initialize the Tool Shed tag handler.
self.tag_handler = CommunityTagManager( self )
# Initialize the Tool Shed tool data tables. Never pass a configuration 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 )
self.genome_builds = GenomeBuilds( self )
from galaxy import auth
self.auth_manager = auth.AuthManager( self )
# Citation manager needed to load tools.
from galaxy.managers.citations import CitationsManager
self.citations_manager = CitationsManager( self )
# The Tool Shed makes no use of a Galaxy toolbox, but this attribute is still required.
self.toolbox = tools.ToolBox( [], self.config.tool_path, self )
# Initialize the Tool Shed security agent.
self.security_agent = self.model.security_agent
# The Tool Shed makes no use of a quota, but this attribute is still required.
self.quota_agent = galaxy.quota.NoQuotaAgent( self.model )
# TODO: Add OpenID support
self.openid_providers = OpenIDProviders()
# Initialize the baseline Tool Shed statistics component.
self.shed_counter = self.model.shed_counter
# Let the Tool Shed's 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
# Initialize the repository registry.
self.repository_registry = tool_shed.repository_registry.Registry( self )
# used for cachebusting -- refactor this into a *SINGLE* UniverseApplication base.
self.server_starttime = int(time.time())
print >> sys.stderr, "Tool shed hgweb.config file is: ", self.hgweb_config_manager.hgweb_config
[docs] def shutdown( self ):
pass