Source code for galaxy.util.script

"""Utilities for Galaxy scripts
import argparse
import logging
import os
import sys

from import (


Galaxy config file (defaults to $GALAXY_ROOT/config/galaxy.yml if that file exists
or else to ./config/galaxy.ini if that exists). If this isn't set on the
command line it can be set with the environment variable GALAXY_CONFIG_FILE.

# Section containing application configuration in the target config file specified with
# -c/--config-file. This defaults to 'galaxy' for YAML/JSON configuration files and 'main'
# with 'app:' prepended for INI. If this isn't set on the command line it can be set with
# the environment variable GALAXY_CONFIG_SECTION.
# """

[docs]def main_factory(description=None, actions=None, arguments=None, default_action=None): global DESCRIPTION, ACTIONS, ARGUMENTS, DEFAULT_ACTION DESCRIPTION = description ACTIONS = actions or {} ARGUMENTS = arguments or [] DEFAULT_ACTION = default_action return main
[docs]def main(argv=None): """Entry point for conversion process.""" if argv is None: argv = sys.argv[1:] args = _arg_parser().parse_args(argv) kwargs = app_properties_from_args(args) action = args.action action_func = ACTIONS[action] action_func(args, kwargs)
[docs]def app_properties_from_args(args, legacy_config_override=None, app=None): config_file = config_file_from_args(args, legacy_config_override=legacy_config_override, app=app) config_section = getattr(args, "config_section", None) app_properties = load_app_properties(config_file=config_file, config_section=config_section) return app_properties
[docs]def config_file_from_args(args, legacy_config_override=None, app=None): app = app or getattr(args, "app", "galaxy") config_file = legacy_config_override or args.config_file or find_config_file(app) return config_file
[docs]def populate_config_args(parser): # config and config-file respected because we have used different arguments at different # time for scripts. # Options (e.g. option_name) not found in this file can have their defaults overridden # set setting GALAXY_CONFIG_OPTION_NAME where OPTION_NAME is option_name converted to upper case. # Options specified in that file can be overridden for this program set setting # GALAXY_CONFIG_OVERRIDE_OPTION_NAME to a new value. parser.add_argument( "-c", "--config-file", "--config", default=os.environ.get("GALAXY_CONFIG_FILE", None), help=ARG_HELP_CONFIG_FILE ) parser.add_argument( "--config-section", default=os.environ.get("GALAXY_CONFIG_SECTION", None), help=argparse.SUPPRESS ) # See ARG_HELP_CONFIG_SECTION comment above for unsuppressed details.
def _arg_parser(): parser = argparse.ArgumentParser(description=DESCRIPTION) parser.add_argument( "action", metavar="ACTION", type=str, choices=list(ACTIONS.keys()), default=DEFAULT_ACTION, nargs="?" if DEFAULT_ACTION is not None else None, help="action to perform", ) populate_config_args(parser) parser.add_argument("--app", default=os.environ.get("GALAXY_APP", "galaxy")) for argument in ARGUMENTS: parser.add_argument(*argument[0], **argument[1]) return parser
[docs]def set_log_handler(filename=None, stream=None): if filename: handler = logging.FileHandler(filename) else: handler = logging.StreamHandler(stream=stream) return handler