Mercurial > repos > bcclaywell > argo_navis
view venv/lib/python2.7/site-packages/planemo/galaxy_test/actions.py @ 0:d67268158946 draft
planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
author | bcclaywell |
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date | Mon, 12 Oct 2015 17:43:33 -0400 |
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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