Mercurial > repos > shellac > sam_consensus_v3
view env/lib/python3.9/site-packages/planemo/commands/cmd_test.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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"""Module describing the planemo ``test`` command.""" import click from planemo import options from planemo.cli import command_function from planemo.engine.test import ( test_runnables, ) from planemo.io import temp_directory from planemo.runnable import ( RunnableType, ) from planemo.runnable_resolve import for_runnable_identifiers @click.command('test') @options.optional_tools_arg(multiple=True, allow_uris=True) @click.option( "--failed", is_flag=True, help="Re-run only failed tests. This command will read " "tool_test_output.json to determine which tests failed so this " "file must have been produced with the same set of tool ids " "previously.", default=False, ) @click.option( "--polling_backoff", type=int, help="Poll resources with an increasing interval between requests. " "Useful when testing against remote and/or production " "instances to limit generated traffic.", default="0", ) @options.galaxy_target_options() @options.galaxy_config_options() @options.test_options() @options.engine_options() @command_function def cli(ctx, uris, **kwds): """Run specified tool's tests within Galaxy. 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 addition 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 configured 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. """ with temp_directory(dir=ctx.planemo_directory) as temp_path: # Create temp dir(s) outside of temp, docker can't mount $TEMPDIR on OSX runnables = for_runnable_identifiers(ctx, uris, kwds, temp_path=temp_path) # pick a default engine type if needed is_cwl = all(r.type in {RunnableType.cwl_tool, RunnableType.cwl_workflow} for r in runnables) if kwds.get("engine", None) is None: if is_cwl: kwds["engine"] = "cwltool" elif kwds.get('galaxy_url', None): kwds["engine"] = "external_galaxy" else: kwds["engine"] = "galaxy" return_value = test_runnables(ctx, runnables, original_paths=uris, **kwds) ctx.exit(return_value)