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()