diff env/lib/python3.9/site-packages/planemo/commands/cmd_test.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/commands/cmd_test.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,84 @@
+"""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
+
+
[e-mail]('test')
[e-mail]_tools_arg(multiple=True, allow_uris=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]_target_options()
[e-mail]_config_options()
[e-mail]_options()
[e-mail]_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)