Source code for galaxy.tool_shed.galaxy_install.migrate.common

import configparser
import os
import sys

import galaxy.config
from galaxy.tool_shed.galaxy_install import (
    installed_repository_manager,
    tool_migration_manager
)


[docs]class MigrateToolsApplication(galaxy.config.ConfiguresGalaxyMixin):
    """Encapsulates the state of a basic Galaxy Universe application in order to initiate the Install Manager"""

[docs]    def __init__(self, tools_migration_config):
        install_dependencies = 'install_dependencies' in sys.argv
        galaxy_config_file = 'galaxy.ini'
        self.name = 'galaxy'
        if '-c' in sys.argv:
            pos = sys.argv.index('-c')
            sys.argv.pop(pos)
            galaxy_config_file = sys.argv.pop(pos)
        if not os.path.exists(galaxy_config_file):
            print(f"Galaxy config file does not exist (hint: use '-c config.ini' for non-standard locations): {galaxy_config_file}")
            sys.exit(1)
        config_parser = configparser.ConfigParser({'here': os.getcwd()})
        config_parser.read(galaxy_config_file)
        galaxy_config_dict = {}
        for key, value in config_parser.items("app:main"):
            galaxy_config_dict[key] = value
        self.config = galaxy.config.Configuration(**galaxy_config_dict)

        self.config.update_integrated_tool_panel = True

        self._configure_object_store()

        self._configure_security()

        self._configure_models()

        self._configure_datatypes_registry()

        self._configure_tool_data_tables(from_shed_config=True)

        self._configure_toolbox()

        self._configure_tool_shed_registry()

        self.installed_repository_manager = installed_repository_manager.InstalledRepositoryManager(self)

        # Get the latest tool migration script number to send to the Install manager.
        latest_migration_script_number = int(tools_migration_config.split('_')[0])
        # The value of migrated_tools_config is migrated_tools_conf.xml, and is reserved for
        # containing only those tools that have been eliminated from the distribution and moved
        # to the tool shed.  A side-effect of instantiating the ToolMigrationManager is the automatic
        # installation of all appropriate tool shed repositories.
        self.tool_migration_manager = \
            tool_migration_manager.ToolMigrationManager(app=self,
                                                        latest_migration_script_number=latest_migration_script_number,
                                                        tool_shed_install_config=os.path.join(self.config.root,
                                                                                              'scripts',
                                                                                              'migrate_tools',
                                                                                              tools_migration_config),
                                                        migrated_tools_config=self.config.migrated_tools_config,
                                                        install_dependencies=install_dependencies)

    @property
    def sa_session(self):
        return self.model.session

[docs]    def shutdown(self):
        self.object_store.shutdown()