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 galaxy.webapps.tool_shed.app

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.config import configure_logging
from galaxy.managers.tags import CommunityTagManager
from galaxy.openid.providers import OpenIDProviders
from galaxy.util.dbkeys import GenomeBuilds
from galaxy.web import security
from galaxy.web.stack import application_stack_instance
import tool_shed.repository_registry
import tool_shed.repository_types.registry
from tool_shed.grids.repository_grid_filter_manager import RepositoryGridFilterManager

import logging
log = logging.getLogger(__name__)


[docs]class UniverseApplication(object): """Encapsulates the state of a Universe application"""
[docs] def __init__(self, **kwd): log.debug("python path is: %s", ", ".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() configure_logging(self.config) self.application_stack = application_stack_instance() # 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()) log.debug("Tool shed hgweb.config file is: %s", self.hgweb_config_manager.hgweb_config)
[docs] def shutdown(self): pass