diff env/lib/python3.7/site-packages/planemo/commands/cmd_test.py @ 5:9b1c78e6ba9c draft default tip

"planemo upload commit 6c0a8142489327ece472c84e558c47da711a9142"

--- a/env/lib/python3.7/site-packages/planemo/commands/cmd_test.py	Thu May 14 16:47:39 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,103 +0,0 @@
-"""Module describing the planemo ``test`` command."""
-import click
-
-from planemo import options
-from planemo.cli import command_function
-from planemo.engine import (
-    engine_context,
-)
-from planemo.galaxy import galaxy_config
-from planemo.galaxy.config import _find_test_data
-from planemo.galaxy.test import (
-    handle_reports_and_summary,
-    run_in_config,
-)
-from planemo.io import temp_directory
-from planemo.runnable import (
-    for_paths,
-    RunnableType,
-)
-
-
[e-mail]('test')
[e-mail]_tools_arg(multiple=True)
[e-mail](
-    "--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,
-)
[e-mail](
-    "--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",
-)
[e-mail](
-    "--history_name",
-    help="Name for history (if a history is generated as part of testing.)"
-)
[e-mail]_target_options()
[e-mail]_config_options()
[e-mail]_options()
[e-mail]_options()
-@command_function
-def cli(ctx, paths, **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 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.
-    """
-    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_paths(paths, temp_path=temp_path)
-        is_cwl = all(r.type in {RunnableType.cwl_tool, RunnableType.cwl_workflow} for r in runnables)
-        if kwds.get("engine") is None:
-            kwds["engine"] = "galaxy" if not is_cwl else "cwltool"
-
-        engine_type = kwds["engine"]
-        test_engine_testable = {RunnableType.galaxy_tool, RunnableType.galaxy_datamanager, RunnableType.directory}
-        enable_test_engines = any(r.type not in test_engine_testable for r in runnables)
-        enable_test_engines = enable_test_engines or engine_type != "galaxy"
-        if enable_test_engines:
-            ctx.vlog("Using test engine type %s" % engine_type)
-            with engine_context(ctx, **kwds) as engine:
-                test_data = engine.test(runnables)
-                return_value = handle_reports_and_summary(ctx, test_data.structured_data, kwds=kwds)
-        else:
-            ctx.vlog("Running traditional Galaxy tool tests using run_tests.sh in Galaxy root %s" % engine_type)
-            kwds["for_tests"] = True
-            if kwds.get('update_test_data'):
-                non_copied_runnables = for_paths(paths)
-                kwds['test_data_target_dir'] = _find_test_data(non_copied_runnables, **kwds)
-            with galaxy_config(ctx, runnables, **kwds) as config:
-                return_value = run_in_config(ctx, config, **kwds)
-
-    ctx.exit(return_value)