tool_factory_docker: toolfactory/galaxy-tool-test comparison

comparison toolfactory/galaxy-tool-test @ 0:83f8bb78781e draft

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author	fubar
date	Fri, 11 Dec 2020 02:51:15 +0000
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--1:000000000000
+:83f8bb78781e
+#!/usr/bin/env python
+import argparse
+import datetime as dt
+import json
+import logging
+import os
+import sys
+import tempfile
+from collections import namedtuple
+from concurrent.futures import thread, ThreadPoolExecutor
+import yaml
+from galaxy.tool_util.verify.interactor import (
+DictClientTestConfig,
+GalaxyInteractorApi,
+verify_tool,
+)
+DESCRIPTION = """Script to quickly run a tool test against a running Galaxy instance."""
+DEFAULT_SUITE_NAME = "Galaxy Tool Tests"
+ALL_TESTS = -1
+ALL_TOOLS = "*"
+ALL_VERSION = "*"
+LATEST_VERSION = None
+TestReference = namedtuple("TestReference", ["tool_id", "tool_version", "test_index"])
+TestException = namedtuple("TestException", ["tool_id", "exception", "was_recorded"])
+class Results:
+def __init__(self, default_suitename, test_json, append=False):
+self.test_json = test_json or "-"
+test_results = []
+test_exceptions = []
+suitename = default_suitename
+if append:
+assert test_json != "-"
+with open(test_json) as f:
+previous_results = json.load(f)
+test_results = previous_results["tests"]
+if "suitename" in previous_results:
+suitename = previous_results["suitename"]
+self.test_results = test_results
+self.test_exceptions = test_exceptions
+self.suitename = suitename
+def register_result(self, result):
+self.test_results.append(result)
+def register_exception(self, test_exception):
+self.test_exceptions.append(test_exception)
+def already_successful(self, test_reference):
+test_id = _test_id_for_reference(test_reference)
+for test_result in self.test_results:
+if test_result.get('id') != test_id:
+continue
+has_data = test_result.get('has_data', False)
+if has_data:
+test_data = test_result.get("data", {})
+if 'status' in test_data and test_data['status'] == 'success':
+return True
+return False
+def write(self):
+tests = sorted(self.test_results, key=lambda el: el['id'])
+n_passed, n_failures, n_skips = 0, 0, 0
+n_errors = len([e for e in self.test_exceptions if not e.was_recorded])
+for test in tests:
+has_data = test.get('has_data', False)
+if has_data:
+test_data = test.get("data", {})
+if 'status' not in test_data:
+raise Exception(f"Test result data {test_data} doesn't contain a status key.")
+status = test_data['status']
+if status == "success":
+n_passed += 1
+elif status == "error":
+n_errors += 1
+elif status == "skip":
+n_skips += 1
+elif status == "failure":
+n_failures += 1
+report_obj = {
+'version': '0.1',
+'suitename': self.suitename,
+'results': {
+'total': n_passed + n_failures + n_skips + n_errors,
+'errors': n_errors,
+'failures': n_failures,
+'skips': n_skips,
+},
+'tests': tests,
+}
+if self.test_json == "-":
+print(json.dumps(report_obj))
+else:
+with open(self.test_json, "w") as f:
+json.dump(report_obj, f)
+def info_message(self):
+messages = []
+passed_tests = self._tests_with_status('success')
+messages.append("Passed tool tests ({}): {}".format(
+len(passed_tests),
+[t["id"] for t in passed_tests]
+))
+failed_tests = self._tests_with_status('failure')
+messages.append("Failed tool tests ({}): {}".format(
+len(failed_tests),
+[t["id"] for t in failed_tests]
+))
+skiped_tests = self._tests_with_status('skip')
+messages.append("Skipped tool tests ({}): {}".format(
+len(skiped_tests),
+[t["id"] for t in skiped_tests]
+))
+errored_tests = self._tests_with_status('error')
+messages.append("Errored tool tests ({}): {}".format(
+len(errored_tests),
+[t["id"] for t in errored_tests]
+))
+return "\n".join(messages)
+@property
+def success_count(self):
+self._tests_with_status('success')
+@property
+def skip_count(self):
+self._tests_with_status('skip')
+@property
+def error_count(self):
+return self._tests_with_status('error') + len(self.test_exceptions)
+@property
+def failure_count(self):
+return self._tests_with_status('failure')
+def _tests_with_status(self, status):
+return [t for t in self.test_results if t.get("data", {}).get("status") == status]
+def test_tools(
+galaxy_interactor,
+test_references,
+results,
+log=None,
+parallel_tests=1,
+history_per_test_case=False,
+no_history_cleanup=False,
+retries=0,
+verify_kwds=None,
+):
+"""Run through tool tests and write report.
+Refactor this into Galaxy in 21.01.
+"""
+verify_kwds = (verify_kwds or {}).copy()
+tool_test_start = dt.datetime.now()
+history_created = False
+if history_per_test_case:
+test_history = None
+else:
+history_created = True
+test_history = galaxy_interactor.new_history(history_name=f"History for {results.suitename}")
+verify_kwds.update({
+"no_history_cleanup": no_history_cleanup,
+"test_history": test_history,
+})
+with ThreadPoolExecutor(max_workers=parallel_tests) as executor:
+try:
+for test_reference in test_references:
+_test_tool(
+executor=executor,
+test_reference=test_reference,
+results=results,
+galaxy_interactor=galaxy_interactor,
+log=log,
+retries=retries,
+verify_kwds=verify_kwds,
+)
+finally:
+# Always write report, even if test was cancelled.
+try:
+executor.shutdown(wait=True)
+except KeyboardInterrupt:
+executor._threads.clear()
+thread._threads_queues.clear()
+results.write()
+if log:
+log.info("Report written to '%s'", os.path.abspath(results.test_json))
+log.info(results.info_message())
+log.info("Total tool test time: {}".format(dt.datetime.now() - tool_test_start))
+if history_created and not no_history_cleanup:
+galaxy_interactor.delete_history(test_history)
+def _test_id_for_reference(test_reference):
+tool_id = test_reference.tool_id
+tool_version = test_reference.tool_version
+test_index = test_reference.test_index
+if tool_version and tool_id.endswith("/" + tool_version):
+tool_id = tool_id[:-len("/" + tool_version)]
+label_base = tool_id
+if tool_version:
+label_base += "/" + str(tool_version)
+test_id = label_base + "-" + str(test_index)
+return test_id
+def _test_tool(
+executor,
+test_reference,
+results,
+galaxy_interactor,
+log,
+retries,
+verify_kwds,
+):
+tool_id = test_reference.tool_id
+tool_version = test_reference.tool_version
+test_index = test_reference.test_index
+# If given a tool_id with a version suffix, strip it off so we can treat tool_version
+# correctly at least in client_test_config.
+if tool_version and tool_id.endswith("/" + tool_version):
+tool_id = tool_id[:-len("/" + tool_version)]
+test_id = _test_id_for_reference(test_reference)
+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, **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)
+executor.submit(run_test)
+def build_case_references(
+galaxy_interactor,
+tool_id=ALL_TOOLS,
+tool_version=LATEST_VERSION,
+test_index=ALL_TESTS,
+page_size=0,
+page_number=0,
+check_against=None,
+log=None,
+):
+test_references = []
+if tool_id == ALL_TOOLS:
+tests_summary = galaxy_interactor.get_tests_summary()
+for tool_id, tool_versions_dict in tests_summary.items():
+for tool_version, summary in tool_versions_dict.items():
+for test_index in range(summary["count"]):
+test_reference = TestReference(tool_id, tool_version, test_index)
+test_references.append(test_reference)
+else:
+assert tool_id
+tool_test_dicts = galaxy_interactor.get_tool_tests(tool_id, tool_version=tool_version) or {}
+for i, tool_test_dict in enumerate(tool_test_dicts):
+this_tool_version = tool_test_dict.get("tool_version", tool_version)
+this_test_index = i
+if test_index == ALL_TESTS or i == test_index:
+test_reference = TestReference(tool_id, this_tool_version, this_test_index)
+test_references.append(test_reference)
+if check_against:
+filtered_test_references = []
+for test_reference in test_references:
+if check_against.already_successful(test_reference):
+if log is not None:
+log.debug(f"Found successful test for {test_reference}, skipping")
+continue
+filtered_test_references.append(test_reference)
+log.info(f"Skipping {len(test_references)-len(filtered_test_references)} out of {len(test_references)} tests.")
+test_references = filtered_test_references
+if page_size > 0:
+slice_start = page_size * page_number
+slice_end = page_size * (page_number + 1)
+test_references = test_references[slice_start:slice_end]
+return test_references
+def main(argv=None):
+if argv is None:
+argv = sys.argv[1:]
+args = _arg_parser().parse_args(argv)
+log = setup_global_logger(__name__, verbose=args.verbose)
+client_test_config_path = args.client_test_config
+if client_test_config_path is not None:
+log.debug(f"Reading client config path {client_test_config_path}")
+with open(client_test_config_path) 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,
+"download_attempts": get_option("download_attempts"),
+"download_sleep": get_option("download_sleep"),
+}
+tool_id = args.tool_id
+tool_version = args.tool_version
+tools_client_test_config = DictClientTestConfig(client_test_config.get("tools"))
+verbose = args.verbose
+galaxy_interactor = GalaxyInteractorApi(**galaxy_interactor_kwds)
+results = Results(args.suite_name, output_json_path, append=args.append)
+check_against = None if not args.skip_successful else results
+test_references = build_case_references(
+galaxy_interactor,
+tool_id=tool_id,
+tool_version=tool_version,
+test_index=args.test_index,
+page_size=args.page_size,
+page_number=args.page_number,
+check_against=check_against,
+log=log,
+)
+log.debug(f"Built {len(test_references)} test references to executed.")
+verify_kwds = dict(
+client_test_config=tools_client_test_config,
+force_path_paste=args.force_path_paste,
+skip_with_reference_data=not args.with_reference_data,
+quiet=not verbose,
+)
+test_tools(
+galaxy_interactor,
+test_references,
+results,
+log=log,
+parallel_tests=args.parallel_tests,
+history_per_test_case=args.history_per_test_case,
+no_history_cleanup=args.no_history_cleanup,
+verify_kwds=verify_kwds,
+)
+exceptions = results.test_exceptions
+if exceptions:
+exception = exceptions[0]
+if hasattr(exception, "exception"):
+exception = exception.exception
+raise exception
+def setup_global_logger(name, log_file=None, verbose=False):
+formatter = logging.Formatter('%(asctime)s %(levelname)-5s - %(message)s')
+console = logging.StreamHandler()
+console.setFormatter(formatter)
+logger = logging.getLogger(name)
+logger.setLevel(logging.DEBUG if verbose else logging.INFO)
+logger.addHandler(console)
+if not log_file:
+# delete = false is chosen here because it is always nice to have a log file
+# ready if you need to debug. Not having the "if only I had set a log file"
+# moment after the fact.
+temp = tempfile.NamedTemporaryFile(prefix="ephemeris_", delete=False)
+log_file = temp.name
+file_handler = logging.FileHandler(log_file)
+logger.addHandler(file_handler)
+logger.info(f"Storing log file in: {log_file}")
+return logger
+def _arg_parser():
+parser = argparse.ArgumentParser(description=DESCRIPTION)
+parser.add_argument('-u', '--galaxy-url', default="http://localhost:8080", help='Galaxy URL')
+parser.add_argument('-k', '--key', default=None, help='Galaxy User API Key')
+parser.add_argument('-a', '--admin-key', default=None, help='Galaxy Admin API Key')
+parser.add_argument('--force_path_paste', default=False, action="store_true", help='This requires Galaxy-side config option "allow_path_paste" enabled. Allows for fetching test data locally. Only for admins.')
+parser.add_argument('-t', '--tool-id', default=ALL_TOOLS, help='Tool ID')
+parser.add_argument('--tool-version', default=None, help='Tool Version (if tool id supplied). Defaults to just latest version, use * to test all versions')
+parser.add_argument('-i', '--test-index', default=ALL_TESTS, type=int, help='Tool Test Index (starting at 0) - by default all tests will run.')
+parser.add_argument('-o', '--output', default=None, help='directory to dump outputs to')
+parser.add_argument('--append', default=False, action="store_true", help="Extend a test record json (created with --output-json) with additional tests.")
+parser.add_argument('--skip-successful', default=False, action="store_true", help="When used with --append, skip previously run successful tests.")
+parser.add_argument('-j', '--output-json', default=None, help='output metadata json')
+parser.add_argument('--verbose', default=False, action="store_true", help="Verbose logging.")
+parser.add_argument('-c', '--client-test-config', default=None, help="Test config YAML to help with client testing")
+parser.add_argument('--suite-name', default=DEFAULT_SUITE_NAME, help="Suite name for tool test output")
+parser.add_argument('--with-reference-data', dest="with_reference_data", default=False, action="store_true")
+parser.add_argument('--skip-with-reference-data', dest="with_reference_data", action="store_false", help="Skip tests the Galaxy server believes use data tables or loc files.")
+parser.add_argument('--history-per-suite', dest="history_per_test_case", default=False, action="store_false", help="Create new history per test suite (all tests in same history).")
+parser.add_argument('--history-per-test-case', dest="history_per_test_case", action="store_true", help="Create new history per test case.")
+parser.add_argument('--no-history-cleanup', default=False, action="store_true", help="Perserve histories created for testing.")
+parser.add_argument('--parallel-tests', default=1, type=int, help="Parallel tests.")
+parser.add_argument('--retries', default=0, type=int, help="Retry failed tests.")
+parser.add_argument('--page-size', default=0, type=int, help="If positive, use pagination and just run one 'page' to tool tests.")
+parser.add_argument('--page-number', default=0, type=int, help="If page size is used, run this 'page' of tests - starts with 0.")
+parser.add_argument('--download-attempts', default=1, type=int, help="Galaxy may return a transient 500 status code for download if test results are written but not yet accessible.")
+parser.add_argument('--download-sleep', default=1, type=int, help="If download attempts is greater than 1, the amount to sleep between download attempts.")
+return parser
+if __name__ == "__main__":
+main()

Mercurial > repos > fubar > tool_factory_docker

comparison toolfactory/galaxy-tool-test @ 0:83f8bb78781e draft