mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Nicola Soranzo
21b44bf348
using the following command: ``` autopep8 -i -r --exclude $(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -sd,) --select E201,E202 . ```
88 lines
2.8 KiB
Python
88 lines
2.8 KiB
Python
import argparse
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import os.path
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import sys
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sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib')))
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from galaxy.util.properties import find_config_file, load_app_properties
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from galaxy.config import (
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configure_logging,
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find_path,
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find_root,
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parse_dependency_options,
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)
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from galaxy.tools.deps import CachedDependencyManager, DependencyManager, NullDependencyManager
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DESCRIPTION = "Script to manage tool dependencies (with focus on a Conda environments)."
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def main(argv=None):
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"""Entry point for conversion process."""
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if argv is None:
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argv = sys.argv[1:]
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args = _arg_parser().parse_args(argv)
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action = args.action
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action_func = ACTIONS[action]
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action_func(args)
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def _init_if_needed(args):
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kwargs = _app_properties(args)
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# If conda_auto_init is set, simply building the Conda resolver will call handle installation.
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_build_dependency_manager_no_config(kwargs)
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def _app_properties(args):
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config_file = find_config_file("config/galaxy.ini", "universe_wsgi.ini", args.config_file)
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app_properties = load_app_properties(ini_file=config_file)
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return app_properties
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def _arg_parser():
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parser = argparse.ArgumentParser(description=DESCRIPTION)
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parser.add_argument('action', metavar='ACTION', type=str,
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choices=ACTIONS.keys(),
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help='action to perform')
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parser.add_argument("-c", "--config-file", default=None)
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return parser
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def _build_dependency_manager_no_config(kwargs):
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"""Simplified variant of build_dependency_manager from galaxy.tools.deps.
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The canonical factory method requires a full Galaxy configuration object
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which we do not have available in this script (an optimization).
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"""
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configure_logging(kwargs)
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root = find_root(kwargs)
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dependency_resolvers_config_file = find_path(kwargs, "dependency_resolvers_config_file", root)
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use_dependencies, tool_dependency_dir, use_cached_dependency_manager, tool_dependency_cache_dir, precache_dependencies = \
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parse_dependency_options(kwargs, root, dependency_resolvers_config_file)
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if not use_dependencies:
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dependency_manager = NullDependencyManager()
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else:
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dependency_manager_kwds = {
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'default_base_path': tool_dependency_dir,
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'conf_file': dependency_resolvers_config_file,
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'app_config': kwargs,
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}
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if use_cached_dependency_manager:
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dependency_manager_kwds['tool_dependency_cache_dir'] = tool_dependency_cache_dir
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dependency_manager = CachedDependencyManager(**dependency_manager_kwds)
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else:
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dependency_manager = DependencyManager(**dependency_manager_kwds)
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return dependency_manager
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ACTIONS = {
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"init_if_needed": _init_if_needed,
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}
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if __name__ == '__main__':
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main()
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