diff env/lib/python3.9/site-packages/planemo/cli.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.9/site-packages/planemo/cli.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,152 @@
+"""The module describes a CLI framework extending ``click``."""
+import functools
+import os
+import sys
+
+import click
+
+from planemo import __version__
+from planemo.context import configure_standard_planemo_logging, PlanemoContext
+from planemo.exit_codes import ExitCodeException
+from planemo.galaxy import profiles
+from .config import OptionSource
+from .io import error
+
+
+CONTEXT_SETTINGS = dict(auto_envvar_prefix='PLANEMO')
+COMMAND_ALIASES = {
+    "l": "lint",
+    "o": "open",
+    "t": "test",
+    "s": "serve",
+}
+
+
+class PlanemoCliContext(PlanemoContext):
+    """Describe context of Planemo CLI computation.
+
+    Extend PlanemoContext with operations for CLI concerns (exit code) and
+    for interacting with the click library.
+    """
+
+    def _log_message(self, message):
+        click.echo(message, file=sys.stderr)
+
+    def exit(self, exit_code):
+        """Exit planemo with the supplied exit code."""
+        self.vlog("Exiting planemo with exit code [%d]" % exit_code)
+        raise ExitCodeException(exit_code)
+
+
+pass_context = click.make_pass_decorator(PlanemoCliContext, ensure=True)
+cmd_folder = os.path.abspath(os.path.join(os.path.dirname(__file__),
+                                          'commands'))
+
+
+def list_cmds():
+    """List planemo commands from commands folder."""
+    rv = []
+    for filename in os.listdir(cmd_folder):
+        if filename.endswith('.py') and \
+           filename.startswith('cmd_'):
+            rv.append(filename[len("cmd_"):-len(".py")])
+    rv.sort()
+    return rv
+
+
+def name_to_command(name):
+    """Convert a subcommand name to the cli function for that command.
+
+    Command <X> is defined by the method 'planemo.commands.cmd_<x>:cli',
+    this method uses `__import__` to load and return that method.
+    """
+    try:
+        if sys.version_info[0] == 2:
+            name = name.encode('ascii', 'replace')
+        mod_name = 'planemo.commands.cmd_' + name
+        mod = __import__(mod_name, None, None, ['cli'])
+    except ImportError as e:
+        error("Problem loading command %s, exception %s" % (name, e))
+        return
+    return mod.cli
+
+
+class PlanemoCLI(click.MultiCommand):
+
+    def list_commands(self, ctx):
+        return list_cmds()
+
+    def get_command(self, ctx, name):
+        if name in COMMAND_ALIASES:
+            name = COMMAND_ALIASES[name]
+        return name_to_command(name)
+
+
+def command_function(f):
+    """Extension point for processing kwds after click callbacks."""
+    @functools.wraps(f)
+    def handle_blended_options(*args, **kwds):
+        profile = kwds.get("profile", None)
+        if profile:
+            ctx = args[0]
+            profile_defaults = profiles.ensure_profile(
+                ctx, profile, **kwds
+            )
+            _setup_profile_options(ctx, profile_defaults, kwds)
+
+        try:
+            return f(*args, **kwds)
+        except ExitCodeException as e:
+            sys.exit(e.exit_code)
+
+    return pass_context(handle_blended_options)
+
+
+def _setup_profile_options(ctx, profile_defaults, kwds):
+    for key, value in profile_defaults.items():
+        option_present = key in kwds
+        option_cli_specified = option_present and (ctx.get_option_source(key) == OptionSource.cli)
+        use_profile_option = not option_present or not option_cli_specified
+        if use_profile_option:
+            kwds[key] = value
+            ctx.set_option_source(
+                key, OptionSource.profile, force=True
+            )
+
+
[e-mail](cls=PlanemoCLI, context_settings=CONTEXT_SETTINGS)
[e-mail]_option(__version__)
[e-mail]('-v', '--verbose', is_flag=True,
+              help='Enables verbose mode.')
[e-mail]('--config',
+              default="~/.planemo.yml",
+              envvar="PLANEMO_GLOBAL_CONFIG_PATH",
+              help="Planemo configuration YAML file.")
[e-mail]('--directory',
+              default="~/.planemo",
+              envvar="PLANEMO_GLOBAL_WORKSPACE",
+              help="Workspace for planemo.")
+@pass_context
+def planemo(ctx, config, directory, verbose, configure_logging=True):
+    """A command-line toolkit for building tools and workflows for Galaxy.
+
+    Check out the full documentation for Planemo online
+    http://planemo.readthedocs.org or open with ``planemo docs``.
+
+    All the individual planemo commands support the ``--help`` option, for
+    example use ``planemo lint --help`` for more details on checking tools.
+    """
+    ctx.verbose = verbose
+    if configure_logging:
+        configure_standard_planemo_logging(verbose)
+    ctx.planemo_config = os.path.expanduser(config)
+    ctx.planemo_directory = os.path.expanduser(directory)
+
+
+__all__ = (
+    "command_function",
+    "list_cmds",
+    "name_to_command",
+    "planemo",
+    "PlanemoCliContext",
+)