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comparison env/lib/python3.7/site-packages/galaxy/util/script.py @ 5:9b1c78e6ba9c draft default tip

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"planemo upload commit 6c0a8142489327ece472c84e558c47da711a9142"
author shellac
date Mon, 01 Jun 2020 08:59:25 -0400
parents 79f47841a781
children
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4:79f47841a781 5:9b1c78e6ba9c
1 """Utilities for Galaxy scripts
2 """
3 import argparse
4 import os
5 import sys
6
7 from galaxy.util.properties import find_config_file, load_app_properties
8
9 DESCRIPTION = None
10 ACTIONS = None
11 ARGUMENTS = None
12 DEFAULT_ACTION = None
13
14 ARG_HELP_CONFIG_FILE = """
15 Galaxy config file (defaults to $GALAXY_ROOT/config/galaxy.yml if that file exists
16 or else to ./config/galaxy.ini if that exists). If this isn't set on the
17 command line it can be set with the environment variable GALAXY_CONFIG_FILE.
18 """
19
20 # ARG_HELP_CONFIG_SECTION = """
21 # Section containing application configuration in the target config file specified with
22 # -c/--config-file. This defaults to 'galaxy' for YAML/JSON configuration files and 'main'
23 # with 'app:' prepended for INI. If this isn't set on the command line it can be set with
24 # the environment variable GALAXY_CONFIG_SECTION.
25 # """
26
27
28 def main_factory(description=None, actions=None, arguments=None, default_action=None):
29 global DESCRIPTION, ACTIONS, ARGUMENTS, DEFAULT_ACTION
30 DESCRIPTION = description
31 ACTIONS = actions or {}
32 ARGUMENTS = arguments or []
33 DEFAULT_ACTION = default_action
34 return main
35
36
37 def main(argv=None):
38 """Entry point for conversion process."""
39 if argv is None:
40 argv = sys.argv[1:]
41 args = _arg_parser().parse_args(argv)
42 kwargs = app_properties_from_args(args)
43 action = args.action
44 action_func = ACTIONS[action]
45 action_func(args, kwargs)
46
47
48 def app_properties_from_args(args, legacy_config_override=None, app=None):
49 config_file = config_file_from_args(args, legacy_config_override=legacy_config_override, app=app)
50 config_section = getattr(args, "config_section", None)
51 app_properties = load_app_properties(config_file=config_file, config_section=config_section)
52 return app_properties
53
54
55 def config_file_from_args(args, legacy_config_override=None, app=None):
56 app = app or getattr(args, "app", "galaxy")
57 config_file = legacy_config_override or args.config_file or find_config_file(app)
58 return config_file
59
60
61 def populate_config_args(parser):
62 # config and config-file respected because we have used different arguments at different
63 # time for scripts.
64
65 # Options (e.g. option_name) not found in this file can have their defaults overridden
66 # set setting GALAXY_CONFIG_OPTION_NAME where OPTION_NAME is option_name converted to upper case.
67 # Options specified in that file can be overridden for this program set setting
68 # GALAXY_CONFIG_OVERRIDE_OPTION_NAME to a new value.
69 parser.add_argument("-c", "--config-file", "--config",
70 default=os.environ.get('GALAXY_CONFIG_FILE', None),
71 help=ARG_HELP_CONFIG_FILE)
72 parser.add_argument("--config-section",
73 default=os.environ.get('GALAXY_CONFIG_SECTION', None),
74 help=argparse.SUPPRESS) # See ARG_HELP_CONFIG_SECTION comment above for unsuppressed details.
75
76
77 def _arg_parser():
78 parser = argparse.ArgumentParser(description=DESCRIPTION)
79 parser.add_argument('action', metavar='ACTION', type=str,
80 choices=list(ACTIONS.keys()),
81 default=DEFAULT_ACTION,
82 nargs='?' if DEFAULT_ACTION is not None else None,
83 help='action to perform')
84 populate_config_args(parser)
85 parser.add_argument("--app",
86 default=os.environ.get('GALAXY_APP', 'galaxy'))
87 for argument in ARGUMENTS:
88 parser.add_argument(*argument[0], **argument[1])
89 return parser