Mercurial > repos > bcclaywell > argo_navis

annotate venv/lib/python2.7/site-packages/planemo/cli.py @ 0:d67268158946 draft

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planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
author bcclaywell
date Mon, 12 Oct 2015 17:43:33 -0400
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1 import os
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2 import sys
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3
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4 import click
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5
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6 # Hack to place Galaxy modules on PYTHONPATH - without
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7 # actually having them on the real external PYTHONPATH.
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8 import planemo_ext
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9 planemo_ext_path = planemo_ext.__path__[0]
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10 sys.path.append(os.path.join(planemo_ext_path))
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11
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12 from .io import error # noqa, import must happen after Galaxy hack
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13 from .config import read_global_config # noqa, ditto
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14 from planemo import __version__ # noqa, ditto
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15
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16
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17 CONTEXT_SETTINGS = dict(auto_envvar_prefix='PLANEMO')
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18 COMMAND_ALIASES = {
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19 "l": "lint",
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20 "t": "test",
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21 "s": "serve",
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22 }
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23
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24
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25 class Context(object):
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26
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27 def __init__(self):
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28 self.home = os.getcwd()
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29 self._global_config = None
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30 # Will be set by planemo CLI driver
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31 self.verbose = False
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32 self.planemo_config = None
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33 self.planemo_directory = None
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34
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35 @property
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36 def global_config(self):
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37 if self._global_config is None:
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38 self._global_config = read_global_config(self.planemo_config)
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39 return self._global_config
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40
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41 def log(self, msg, *args):
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42 """Logs a message to stderr."""
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43 if args:
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44 msg %= args
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45 click.echo(msg, file=sys.stderr)
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46
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47 def vlog(self, msg, *args):
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48 """Logs a message to stderr only if verbose is enabled."""
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49 if self.verbose:
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50 self.log(msg, *args)
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51
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52 @property
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53 def workspace(self):
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54 if not self.planemo_directory:
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55 raise Exception("No planemo workspace defined.")
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56 workspace = self.planemo_directory
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57 if not os.path.exists(workspace):
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58 os.makedirs(workspace)
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59 if not os.path.isdir(workspace):
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60 template = "Planemo workspace directory [%s] unavailable."
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61 message = template % workspace
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62 raise Exception(message)
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63 return workspace
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64
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65
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66 pass_context = click.make_pass_decorator(Context, ensure=True)
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67 cmd_folder = os.path.abspath(os.path.join(os.path.dirname(__file__),
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68 'commands'))
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69
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70
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71 def list_cmds():
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72 rv = []
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73 for filename in os.listdir(cmd_folder):
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74 if filename.endswith('.py') and \
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75 filename.startswith('cmd_'):
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76 rv.append(filename[len("cmd_"):-len(".py")])
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77 rv.sort()
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78 return rv
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79
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80
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81 def name_to_command(name):
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82 try:
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83 if sys.version_info[0] == 2:
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84 name = name.encode('ascii', 'replace')
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85 mod_name = 'planemo.commands.cmd_' + name
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86 mod = __import__(mod_name, None, None, ['cli'])
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87 except ImportError as e:
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88 error("Problem loading command %s, exception %s" % (name, e))
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89 return
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90 return mod.cli
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91
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92
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93 class PlanemoCLI(click.MultiCommand):
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94
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95 def list_commands(self, ctx):
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96 return list_cmds()
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97
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98 def get_command(self, ctx, name):
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99 if name in COMMAND_ALIASES:
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100 name = COMMAND_ALIASES[name]
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101 return name_to_command(name)
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102
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103
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104 @click.command(cls=PlanemoCLI, context_settings=CONTEXT_SETTINGS)
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105 @click.version_option(__version__)
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106 @click.option('-v', '--verbose', is_flag=True,
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107 help='Enables verbose mode.')
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108 @click.option('--config',
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109 default="~/.planemo.yml",
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110 envvar="PLANEMO_GLOBAL_CONFIG_PATH",
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111 help="Planemo configuration YAML file.")
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112 @click.option('--directory',
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113 default="~/.planemo",
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114 envvar="PLANEMO_GLOBAL_WORKSPACE",
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115 help="Workspace for planemo.")
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116 @pass_context
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117 def planemo(ctx, config, directory, verbose):
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118 """Utilities to assist with the development of Galaxy tools."""
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119 ctx.verbose = verbose
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120 ctx.planemo_config = os.path.expanduser(config)
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121 ctx.planemo_directory = os.path.expanduser(directory)