--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/venv/lib/python2.7/site-packages/planemo/galaxy_test/actions.py	Mon Oct 12 17:43:33 2015 -0400
@@ -0,0 +1,214 @@
+import os
+
+import click
+
+from . import structures as test_structures
+from planemo.io import info, warn
+from planemo import galaxy_run
+from planemo.reports import build_report
+
+
+from galaxy.tools.deps.commands import shell
+
+XUNIT_UPGRADE_MESSAGE = ("This version of Galaxy does not support xUnit - "
+                         "please update to newest development brach.")
+NO_XUNIT_MESSAGE = ("Cannot locate xUnit report option for tests - update "
+                    "Galaxy for more detailed breakdown.")
+NO_JSON_MESSAGE = ("Cannot locate json report option for tests - update "
+                   "Galaxy for more detailed breakdown.")
+NO_TESTS_MESSAGE = "No tests were executed - see Galaxy output for details."
+ALL_TESTS_PASSED_MESSAGE = "All %d test(s) executed passed."
+PROBLEM_COUNT_MESSAGE = ("There were problems with %d test(s) - out of %d "
+                         "test(s) executed. See %s for detailed breakdown.")
+GENERIC_PROBLEMS_MESSAGE = ("One or more tests failed. See %s for detailed "
+                            "breakdown.")
+GENERIC_TESTS_PASSED_MESSAGE = "No failing tests encountered."
+
+
+def run_in_config(ctx, config, **kwds):
+    config_directory = config.config_directory
+    html_report_file = kwds["test_output"]
+
+    job_output_files = kwds.get("job_output_files", None)
+    if job_output_files is None:
+        job_output_files = os.path.join(config_directory, "jobfiles")
+
+    xunit_supported, xunit_report_file = __xunit_state(kwds, config)
+    structured_report_file = __structured_report_file(kwds, config)
+
+    info("Testing using galaxy_root %s", config.galaxy_root)
+    # TODO: Allow running dockerized Galaxy here instead.
+    server_ini = os.path.join(config_directory, "galaxy.ini")
+    config.env["GALAXY_CONFIG_FILE"] = server_ini
+    config.env["GALAXY_TEST_VERBOSE_ERRORS"] = "true"
+    config.env["GALAXY_TEST_SAVE"] = job_output_files
+
+    cd_to_galaxy_command = "cd %s" % config.galaxy_root
+    test_cmd = test_structures.GalaxyTestCommand(
+        html_report_file,
+        xunit_report_file,
+        structured_report_file,
+        failed=kwds.get("failed", False),
+        installed=kwds.get("installed", False),
+    ).build()
+    cmd = "; ".join([
+        cd_to_galaxy_command,
+        galaxy_run.ACTIVATE_COMMAND,  # TODO: this should be moved to
+                                      # run_tests.sh to match run.sh.
+        test_cmd,
+    ])
+    action = "Testing tools"
+    return_code = galaxy_run.run_galaxy_command(
+        ctx,
+        cmd,
+        config.env,
+        action
+    )
+    if kwds.get('update_test_data', False):
+        update_cp_args = (job_output_files, config.test_data_dir)
+        shell('cp -r "%s"/* "%s"' % update_cp_args)
+
+    if xunit_report_file and (not os.path.exists(xunit_report_file)):
+        warn(NO_XUNIT_MESSAGE)
+        xunit_report_file = None
+
+    test_results = test_structures.GalaxyTestResults(
+        structured_report_file,
+        xunit_report_file,
+        html_report_file,
+        return_code,
+    )
+
+    try:
+        test_data = test_results.structured_data
+
+        if 'test_output' in kwds:
+            with open(kwds['test_output'], 'w') as handle:
+                handle.write(build_report.build_report(test_data))
+
+        for kw_name in ('markdown', 'text'):
+            if 'test_output_%s' % kw_name in kwds:
+                with open(kwds['test_output_%s' % kw_name], 'w') as handle:
+                    handle.write(build_report.build_report(test_data, report_type=kw_name))
+
+    except Exception:
+        pass
+
+    __handle_summary(
+        test_results,
+        **kwds
+    )
+
+    return return_code
+
+
+def __handle_summary(
+    test_results,
+    **kwds
+):
+    summary_style = kwds.get("summary")
+    if summary_style == "none":
+        return
+
+    if test_results.has_details:
+        __summarize_tests_full(
+            test_results,
+            **kwds
+        )
+    else:
+        if test_results.exit_code:
+            warn(GENERIC_PROBLEMS_MESSAGE % test_results.output_html_path)
+        else:
+            info(GENERIC_TESTS_PASSED_MESSAGE)
+
+
+def __summarize_tests_full(
+    test_results,
+    **kwds
+):
+    num_tests = test_results.num_tests
+    num_problems = test_results.num_problems
+
+    if num_tests == 0:
+        warn(NO_TESTS_MESSAGE)
+        return
+
+    if num_problems == 0:
+        info(ALL_TESTS_PASSED_MESSAGE % num_tests)
+
+    if num_problems:
+        html_report_file = test_results.output_html_path
+        message_args = (num_problems, num_tests, html_report_file)
+        message = PROBLEM_COUNT_MESSAGE % message_args
+        warn(message)
+
+    for testcase_el in test_results.xunit_testcase_elements:
+        structured_data_tests = test_results.structured_data_tests
+        __summarize_test_case(structured_data_tests, testcase_el, **kwds)
+
+
+def __summarize_test_case(structured_data, testcase_el, **kwds):
+    summary_style = kwds.get("summary")
+    test_id = test_structures.case_id(testcase_el)
+    passed = len(list(testcase_el)) == 0
+    if not passed:
+        state = click.style("failed", bold=True, fg='red')
+    else:
+        state = click.style("passed", bold=True, fg='green')
+    click.echo(test_id.label + ": " + state)
+    if summary_style != "minimal":
+        __print_command_line(structured_data, test_id)
+
+
+def __print_command_line(structured_data, test_id):
+    try:
+        test = [d for d in structured_data if d["id"] == test_id.id][0]["data"]
+    except (KeyError, IndexError):
+        # Failed to find structured data for this test - likely targetting
+        # and older Galaxy version.
+        return
+
+    execution_problem = test.get("execution_problem", None)
+    if execution_problem:
+        click.echo("| command: *could not execute job, no command generated* ")
+        return
+
+    try:
+        command = test["job"]["command_line"]
+    except (KeyError, IndexError):
+        click.echo("| command: *failed to determine command for job* ")
+        return
+
+    click.echo("| command: %s" % command)
+
+
+def __xunit_state(kwds, config):
+    xunit_supported = True
+    if shell("grep -q xunit '%s'/run_tests.sh" % config.galaxy_root):
+        xunit_supported = False
+
+    xunit_report_file = kwds.get("test_output_xunit", None)
+    if xunit_report_file is None and xunit_supported:
+        xunit_report_file = os.path.join(config.config_directory, "xunit.xml")
+    elif xunit_report_file is not None and not xunit_supported:
+        warn(XUNIT_UPGRADE_MESSAGE)
+        xunit_report_file = None
+
+    return xunit_supported, xunit_report_file
+
+
+def __structured_report_file(kwds, config):
+    structured_data_supported = True
+    if shell("grep -q structured_data '%s'/run_tests.sh" % config.galaxy_root):
+        structured_data_supported = False
+
+    structured_report_file = None
+    structured_report_file = kwds.get("test_output_json", None)
+    if structured_report_file is None and structured_data_supported:
+        conf_dir = config.config_directory
+        structured_report_file = os.path.join(conf_dir, "structured_data.json")
+    elif structured_report_file is not None and not structured_data_supported:
+        warn(NO_JSON_MESSAGE)
+        structured_report_file = None
+
+    return structured_report_file