def run_test(index, test_id): def register(job_data): tool_test_results.append({ 'id': test_id, 'has_data': True, 'data': job_data, }) try: if log: log.info("Executing test '%s'", test_id) verify_tool( tool_id, galaxy_interactor, test_index=index, tool_version=tool_version, register_job_data=register, quiet=True, test_history=test_history, client_test_config=client_test_config, ) tests_passed.append(test_id) if log: log.info("Test '%s' passed", test_id) except Exception as e: if log: log.warning("Test '%s' failed", test_id, exc_info=True) test_exceptions.append((test_id, e))
def do_it(self, tool_id=None, tool_version=None, test_index=0, resource_parameters={}): """ Run through a tool test case. """ if tool_id is None: tool_id = self.tool_id assert tool_id verify_tool(tool_id, self.galaxy_interactor, resource_parameters=resource_parameters, test_index=test_index, tool_version=tool_version, register_job_data=register_job_data)
def run_tool_test(self, tool_id, index=0, resource_parameters={}): host, port, url = target_url_parts() galaxy_interactor_kwds = { "galaxy_url": url, "master_api_key": get_master_api_key(), "api_key": get_user_api_key(), "keep_outputs_dir": None, } galaxy_interactor = GalaxyInteractorApi(**galaxy_interactor_kwds) verify_tool(tool_id=tool_id, test_index=index, galaxy_interactor=galaxy_interactor, resource_parameters=resource_parameters)
def _run_test_case(self, test_case): if hasattr(test_case, "job_path"): # Simple file-based job path. return super(GalaxyEngine, self)._run_test_case(test_case) else: with self.ensure_runnables_served([test_case.runnable]) as config: galaxy_interactor_kwds = { "galaxy_url": config.galaxy_url, "master_api_key": config.master_api_key, "api_key": config.user_api_key, "keep_outputs_dir": "", # TODO: this... } tool_id = test_case.tool_id test_index = test_case.test_index tool_version = test_case.tool_version galaxy_interactor = interactor.GalaxyInteractorApi( **galaxy_interactor_kwds) test_results = [] def _register_job_data(job_data): test_results.append({ 'id': tool_id + "-" + str(test_index), 'has_data': True, 'data': job_data, }) verbose = self._ctx.verbose try: if verbose: # TODO: this is pretty hacky, it'd be better to send a stream # and capture the output information somehow. interactor.VERBOSE_GALAXY_ERRORS = True interactor.verify_tool( tool_id, galaxy_interactor, test_index=test_index, tool_version=tool_version, register_job_data=_register_job_data, quiet=not verbose, ) except Exception: pass return test_results[0]
def run_test(): run_retries = retries job_data = None job_exception = None def register(job_data_): nonlocal job_data job_data = job_data_ try: while run_retries >= 0: job_exception = None try: if log: log.info("Executing test '%s'", test_id) verify_tool(tool_id, galaxy_interactor, test_index=test_index, tool_version=tool_version, register_job_data=register, publish_history=publish_history, **verify_kwds) if log: log.info("Test '%s' passed", test_id) break except Exception as e: if log: log.warning("Test '%s' failed", test_id, exc_info=True) job_exception = e run_retries -= 1 finally: if job_data is not None: results.register_result({ "id": test_id, "has_data": True, "data": job_data, }) if job_exception is not None: was_recorded = job_data is not None test_exception = TestException(tool_id, job_exception, was_recorded) results.register_exception(test_exception)
def main(argv=None): if argv is None: argv = sys.argv[1:] args = _arg_parser().parse_args(argv) client_test_config_path = args.client_test_config if client_test_config_path is not None: with open(client_test_config_path, "r") as f: client_test_config = yaml.full_load(f) else: client_test_config = {} def get_option(key): arg_val = getattr(args, key, None) if arg_val is None and key in client_test_config: val = client_test_config.get(key) else: val = arg_val return val output_json_path = get_option("output_json") galaxy_interactor_kwds = { "galaxy_url": get_option("galaxy_url"), "master_api_key": get_option("admin_key"), "api_key": get_option("key"), "keep_outputs_dir": args.output, } tool_id = args.tool_id tool_version = args.tool_version tools_client_test_config = DictClientTestConfig( client_test_config.get("tools")) galaxy_interactor = GalaxyInteractorApi(**galaxy_interactor_kwds) raw_test_index = args.test_index if raw_test_index == ALL_TESTS: tool_test_dicts = galaxy_interactor.get_tool_tests( tool_id, tool_version=tool_version) test_indices = list(range(len(tool_test_dicts))) else: test_indices = [int(raw_test_index)] test_results = [] if args.append: assert output_json_path != "-" with open(output_json_path) as f: previous_results = json.load(f) test_results = previous_results["tests"] exceptions = [] verbose = args.verbose for test_index in test_indices: if tool_version: tool_id_and_version = "{}/{}".format(tool_id, tool_version) else: tool_id_and_version = tool_id test_identifier = "tool %s test # %d" % (tool_id_and_version, test_index) def register(job_data): test_results.append({ 'id': tool_id + "-" + str(test_index), 'has_data': True, 'data': job_data, }) try: verify_tool( tool_id, galaxy_interactor, test_index=test_index, tool_version=tool_version, register_job_data=register, quiet=not verbose, force_path_paste=args.force_path_paste, client_test_config=tools_client_test_config, ) if verbose: print("%s passed" % test_identifier) except Exception as e: if verbose: print("{} failed, {}".format(test_identifier, e)) exceptions.append(e) report_obj = { 'version': '0.1', 'tests': test_results, } if output_json_path: if output_json_path == "-": print(json.dumps(report_obj)) else: with open(output_json_path, "w") as f: json.dump(report_obj, f) if exceptions: raise exceptions[0]