Source code for galaxy.webapps.tool_shed.app

import logging
import sys
import time

import galaxy.datatypes.registry
import galaxy.quota
import galaxy.tools.data
import galaxy.webapps.tool_shed.model
import tool_shed.repository_registry
import tool_shed.repository_types.registry
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
from tool_shed.grids.repository_grid_filter_manager import RepositoryGridFilterManager
from . import config

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