def cli(ctx, paths, **kwds):
"""Run the tests in the specified tool tests in a Galaxy instance.
All referenced tools (by default all the tools in the current working
directory) will be tested and the results quickly summarized.
To run these tests planemo needs a Galaxy instance to utilize, planemo
will search parent directories to see if any is a Galaxy instance
- but one can pick the Galaxy instance to use with the --galaxy_root
option or force planemo to download a disposable instance with the
``--install_galaxy`` flag.
In additon to to quick summary printed to the console - various detailed
output summaries can be configured. ``tool_test_output.html`` (settable
via ``--test_output``) will contain a human consumable HTML report
describing the test run. A JSON file (settable via ``--test_output_json``
and defaulting to ``tool_test_output.json``) will also be created. These
files can can be disabled by passing in empty arguments or globally by
setting the values ``default_test_output`` and/or
``default_test_output_json`` in ``~/.planemo.yml`` to ``null``. For
continuous integration testing a xUnit-style report can be confiured using
the ``--test_output_xunit``.
planemo uses temporarily generated config files and environment variables
to attempt to shield this execution of Galaxy from manually launched runs
against that same Galaxy root - but this may not be bullet proof yet so
please careful and do not try this against production Galaxy instances.
"""
process_defaults(ctx, kwds)
kwds["for_tests"] = True
with galaxy_config.galaxy_config(ctx, paths, **kwds) as config:
return_value = run_in_config(ctx, config, **kwds)
if return_value:
sys.exit(return_value)
def cli(ctx, paths, **kwds):
"""Run the tests in the specified tool tests in a Galaxy instance.
All referenced tools (by default all the tools in the current working
directory) will be tested and the results quickly summarized.
To run these tests planemo needs a Galaxy instance to utilize, planemo
will search parent directories to see if any is a Galaxy instance
- but one can pick the Galaxy instance to use with the --galaxy_root
option or force planemo to download a disposable instance with the
``--install_galaxy`` flag.
In additon to to quick summary printed to the console - various detailed
output summaries can be configured. ``tool_test_output.html`` (settable
via ``--test_output``) will contain a human consumable HTML report
describing the test run. A JSON file (settable via ``--test_output_json``
and defaulting to ``tool_test_output.json``) will also be created. These
files can can be disabled by passing in empty arguments or globally by
setting the values ``default_test_output`` and/or
``default_test_output_json`` in ``~/.planemo.yml`` to ``null``. For
continuous integration testing a xUnit-style report can be confiured using
the ``--test_output_xunit``.
planemo uses temporarily generated config files and environment variables
to attempt to shield this execution of Galaxy from manually launched runs
against that same Galaxy root - but this may not be bullet proof yet so
please careful and do not try this against production Galaxy instances.
"""
kwds["for_tests"] = True
with galaxy_config.galaxy_config(ctx, paths, **kwds) as config:
return_value = run_in_config(ctx, config, **kwds)
if return_value:
sys.exit(return_value)
def cli(ctx, paths, **kwds):
""" Run tests of published shed artifacts.
This command will start a Galaxy instance configured to target the
specified shed, find published artifacts (tools and dependencies)
corresponding to command-line arguments and ``.shed.yml`` file(s),
install these artifacts, and run the tool tests for these commands.
This command requires the target to be version 15.07 or newer.
"""
galaxy_test.process_defaults(ctx, kwds)
install_args_list = shed.install_arg_lists(ctx, paths, **kwds)
port = get_free_port()
kwds["port"] = port
return_code = 1
with galaxy_serve.shed_serve(ctx, install_args_list, **kwds) as config:
config.kill()
return_code = galaxy_test.run_in_config(
ctx,
config,
installed=True,
**kwds
)
if return_code:
sys.exit(return_code)
def cli(ctx, paths, **kwds):
""" Run tests of published shed artifacts.
This command will start a Galaxy instance configured to target the
specified shed, find published artifacts (tools and dependencies)
corresponding to command-line arguments and ``.shed.yml`` file(s),
install these artifacts, and run the tool tests for these commands.
This command requires the target to be version 15.07 or newer.
"""
install_args_list = shed.install_arg_lists(ctx, paths, **kwds)
port = get_free_port()
kwds["port"] = port
return_code = 1
with galaxy_serve.shed_serve(ctx, install_args_list, **kwds) as config:
config.kill()
return_code = galaxy_test.run_in_config(ctx,
config,
installed=True,
**kwds)
if return_code:
sys.exit(return_code)