#!/usr/bin/env python
# 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
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# 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 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):
fastr.log.info('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 re.search(r'^\[INFO\] *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.utils.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()