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annotate env/lib/python3.9/site-packages/galaxy/util/script.py @ 0:4f3585e2f14b draft default tip

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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author shellac
date Mon, 22 Mar 2021 18:12:50 +0000
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1 """Utilities for Galaxy scripts
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2 """
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3 import argparse
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4 import logging
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5 import os
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6 import sys
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7
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8 from galaxy.util.properties import find_config_file, load_app_properties
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9
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10 DESCRIPTION = None
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11 ACTIONS = None
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12 ARGUMENTS = None
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13 DEFAULT_ACTION = None
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14
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15 ARG_HELP_CONFIG_FILE = """
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16 Galaxy config file (defaults to $GALAXY_ROOT/config/galaxy.yml if that file exists
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17 or else to ./config/galaxy.ini if that exists). If this isn't set on the
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18 command line it can be set with the environment variable GALAXY_CONFIG_FILE.
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19 """
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20
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21 # ARG_HELP_CONFIG_SECTION = """
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22 # Section containing application configuration in the target config file specified with
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23 # -c/--config-file. This defaults to 'galaxy' for YAML/JSON configuration files and 'main'
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24 # with 'app:' prepended for INI. If this isn't set on the command line it can be set with
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25 # the environment variable GALAXY_CONFIG_SECTION.
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26 # """
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27
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28
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29 def main_factory(description=None, actions=None, arguments=None, default_action=None):
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30 global DESCRIPTION, ACTIONS, ARGUMENTS, DEFAULT_ACTION
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31 DESCRIPTION = description
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32 ACTIONS = actions or {}
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33 ARGUMENTS = arguments or []
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34 DEFAULT_ACTION = default_action
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35 return main
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36
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37
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38 def main(argv=None):
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39 """Entry point for conversion process."""
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40 if argv is None:
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41 argv = sys.argv[1:]
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42 args = _arg_parser().parse_args(argv)
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43 kwargs = app_properties_from_args(args)
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44 action = args.action
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45 action_func = ACTIONS[action]
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46 action_func(args, kwargs)
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47
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48
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49 def app_properties_from_args(args, legacy_config_override=None, app=None):
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50 config_file = config_file_from_args(args, legacy_config_override=legacy_config_override, app=app)
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51 config_section = getattr(args, "config_section", None)
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52 app_properties = load_app_properties(config_file=config_file, config_section=config_section)
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53 return app_properties
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54
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55
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56 def config_file_from_args(args, legacy_config_override=None, app=None):
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57 app = app or getattr(args, "app", "galaxy")
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58 config_file = legacy_config_override or args.config_file or find_config_file(app)
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59 return config_file
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60
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61
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62 def populate_config_args(parser):
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63 # config and config-file respected because we have used different arguments at different
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64 # time for scripts.
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65
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66 # Options (e.g. option_name) not found in this file can have their defaults overridden
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67 # set setting GALAXY_CONFIG_OPTION_NAME where OPTION_NAME is option_name converted to upper case.
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68 # Options specified in that file can be overridden for this program set setting
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69 # GALAXY_CONFIG_OVERRIDE_OPTION_NAME to a new value.
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70 parser.add_argument("-c", "--config-file", "--config",
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71 default=os.environ.get('GALAXY_CONFIG_FILE', None),
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72 help=ARG_HELP_CONFIG_FILE)
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73 parser.add_argument("--config-section",
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74 default=os.environ.get('GALAXY_CONFIG_SECTION', None),
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75 help=argparse.SUPPRESS) # See ARG_HELP_CONFIG_SECTION comment above for unsuppressed details.
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76
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77
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78 def _arg_parser():
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79 parser = argparse.ArgumentParser(description=DESCRIPTION)
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80 parser.add_argument('action', metavar='ACTION', type=str,
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81 choices=list(ACTIONS.keys()),
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82 default=DEFAULT_ACTION,
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83 nargs='?' if DEFAULT_ACTION is not None else None,
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84 help='action to perform')
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85 populate_config_args(parser)
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86 parser.add_argument("--app",
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87 default=os.environ.get('GALAXY_APP', 'galaxy'))
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88 for argument in ARGUMENTS:
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89 parser.add_argument(*argument[0], **argument[1])
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90 return parser
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91
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92
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93 def set_log_handler(filename=None, stream=None):
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94 if filename:
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95 handler = logging.FileHandler(filename)
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96 else:
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97 handler = logging.StreamHandler(stream=stream)
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98 return handler