Source code for fastr.utils.cmd.test

# Copyright 2011-2014 Biomedical Imaging Group Rotterdam, Departments of
# Medical Informatics and Radiology, Erasmus MC, Rotterdam, The Netherlands
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# See the License for the specific language governing permissions and
# limitations under the License.

import argparse
import os
import re
import subprocess
import sys
from fastr.utils.cmd import add_parser_doc_link

[docs]def directory(path): """ Make sure the path is a valid directory for argparse """ path = os.path.abspath(os.path.expanduser(path)) if not os.path.isdir(path): raise ValueError('Reference should be a valid directory') return path
[docs]def tool(value): """ Make sure the value is a correct tool for argparse or reference directory """ import fastr try: return[value] except fastr.exceptions.FastrError: return directory(value)
[docs]def check_tool(args): import fastr if isinstance(args.tool, str): tool_ref_file = os.path.join(args.tool, fastr.core.tool.Tool.TOOL_REFERENCE_FILE_NAME) if os.path.isfile(tool_ref_file): fastr.core.tool.Tool.test_tool(args.tool) else: fastr.log.warning('Could not find valid reference data in {}'.format(args.tool)) else: try:'Testing Tool {} {}'.format(args.tool.ns_id, args.tool.command_version)) args.tool.test() except fastr.exceptions.FastrValueError as e: fastr.log.error('Tool is not valid: {}'.format(e))
[docs]def check_tools(args): import fastr for (_, _, _), tool in sorted( if tool.tests is not None and len(tool.tests) > 0: # Suppress logging during test old_level = fastr.config.loglevel fastr.config.loglevel = 50 result = tool.test() fastr.config.loglevel = old_level if len(result) > 0:'{}/{}: FAILED'.format(tool.ns_id, tool.command_version)) else:'{}/{}: PASSED'.format(tool.ns_id, tool.command_version))
[docs]def check_network(args): import fastr # Test if it is a Network or Tool reference directory network_file = os.path.join(args.reference, fastr.Network.NETWORK_DUMP_FILE_NAME) if os.path.isfile(network_file):'Found Network reference data, testing network') fastr.Network.test(args.reference) else: fastr.log.warning('Could not find valid network reference data in {}'.format(args.reference))
[docs]def check_networks(args): import fastr # Try to test all subdirectories (use them as reference dir) subdirs = sorted(x for x in os.listdir(args.reference) if os.path.isdir(os.path.join(args.reference, x))) results = [] for subdir in sorted(subdirs): network_dir = os.path.join(args.reference, subdir) print('Testing {}... '.format(network_dir)), sys.stdout.flush() # Make sure the directory is a valid test directory if not os.path.exists(os.path.join(network_dir, fastr.Network.NETWORK_DUMP_FILE_NAME)): print('SKIPPED') continue # Create a result entry result = { 'name': subdir, 'reference': network_dir, } results.append(result) # Run the test in a subprocess (to isolate tests and # avoid resource hogging between tests) command = ['fastr', 'test', 'network', network_dir] process = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE) stdout, stderr = process.communicate() # Save results result['stdout'] = stdout result['stderr'] = stderr result['return_code'] = process.returncode # Check if result is valid passed = len(stderr) == process.returncode == 0 passed = passed and'^\[INFO\] *network:\d\d\d\d >> Run and reference were equal! Test passed!$', stdout, re.MULTILINE) is not None result['passed'] = passed if len(stderr) == 0: print('PASSED' if passed else 'FAILED') else: print('ERROR') if args.result: from fastr.helpers.iohelpers import save_json save_json(args.result, results) if all(x['passed'] for x in results): print('ALL TEST PASSED') else: print('ENCOUNTERED FAILURES') return results
[docs]def get_parser(): parser = argparse.ArgumentParser(description="Run a tests for a fastr resource.") subparsers = parser.add_subparsers(help='There are different resources that can be tested') tool_parser = subparsers.add_parser('tool', help='Test a single tool') tool_parser.add_argument('tool', metavar='TOOL', type=tool, help='Tool to test or directory with tool reference data') tool_parser.set_defaults(func=check_tool) tools_parser = subparsers.add_parser('tools', help='Test all tools known to fastr') tools_parser.set_defaults(func=check_tools) network_parser = subparsers.add_parser('network', help='Test a single network') network_parser.add_argument('reference', metavar='NETWORK', type=directory, help='The reference data to test the Network') network_parser.set_defaults(func=check_network) networks_parser = subparsers.add_parser('networks', help='Test all network references inside subdirectories') networks_parser.add_argument('reference', metavar='REFERENCE', type=directory, help='path of the directory containing subdirectories with reference data') networks_parser.add_argument('--result', metavar='RESULT.json', type=str, required=False, help='Write the results of the test to a JSON file') networks_parser.set_defaults(func=check_networks) return parser
[docs]def main(): """ Run the tests of a tool to verify the proper function """ # No arguments were parsed yet, parse them now parser = add_parser_doc_link(get_parser(), __file__) args, unknown_args = parser.parse_known_args() # Ship off subparser to correct function args.func(args)
if __name__ == '__main__': main()