This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Source code for galaxy.tools.verify.script

#!/usr/bin/env python
from __future__ import print_function

import argparse
import json
import sys

from galaxy.tools.verify.interactor import GalaxyInteractorApi, verify_tool

DESCRIPTION = """Script to quickly run a tool test against a running Galaxy instance."""
ALL_TESTS = "*all_tests*"

[docs]def main(argv=None): if argv is None: argv = sys.argv[1:] args = _arg_parser().parse_args(argv) galaxy_interactor_kwds = { "galaxy_url": args.galaxy_url, "master_api_key": args.admin_key, "api_key": args.key, "keep_outputs_dir": args.output, } tool_id = args.tool_id tool_version = args.tool_version 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: with open(args.output_json, "r") 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 = "%s/%s" % (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 ) if verbose: print("%s passed" % test_identifier) except Exception as e: if verbose: print("%s failed, %s" % (test_identifier, e)) exceptions.append(e) report_obj = { 'version': '0.1', 'tests': test_results, } output_json = args.output_json if output_json: if args.output_json == "-": assert not args.append print(json.dumps(report_obj)) else: with open(args.output_json, "w") as f: json.dump(report_obj, f) if exceptions: raise exceptions[0]
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=None, help='Tool ID') parser.add_argument('--tool-version', default=None, help='Tool Version') parser.add_argument('-i', '--test-index', default=ALL_TESTS, 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('-j', '--output-json', default=None, help='output metadata json') parser.add_argument('--verbose', default=False, action="store_true", help="Verbose logging.") return parser if __name__ == "__main__": main()