#!/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 fastr.execution.executionscript
from fastr.utils.cmd import add_parser_doc_link
[docs]def get_parser():
parser = argparse.ArgumentParser(description="Execute a job or network from commandline.")
parser.add_argument('network', metavar='NETWORKFILE', type=str, help='File of the network to execute')
return parser
[docs]def create_network_parser(network):
parser = argparse.ArgumentParser(description="Execute the {} Network".format(network.id))
for source in network.sourcelist:
parser.add_argument('--{}'.format(source),
metavar=source.upper(),
required=True,
nargs='*',
help='Source data for {}'.format(source))
for sink in network.sinklist:
parser.add_argument('--{}'.format(sink),
metavar=sink.upper(),
required=True,
help='The Sink output specification for {}'.format(sink))
return parser
[docs]def main():
"""
Run a Network from the commandline
"""
# No arguments were parsed yet, parse them now
parser = add_parser_doc_link(get_parser(), __file__)
args, unknown_args = parser.parse_known_args()
network = fastr.Network.loadf(args.network)
network_parser = create_network_parser(network)
network_args = vars(network_parser.parse_args(unknown_args))
# Split data in Source and Sink data
source_data = {}
for source in network.sourcelist:
source_data[source] = network_args[source]
sink_data = {}
for sink in network.sinklist:
sink_data[sink] = network_args[sink]
fastr.log.info('Source data: {}'.format(source_data))
fastr.log.info('Sink data: {}'.format(sink_data))
network.execute(source_data, sink_data)
if __name__ == '__main__':
main()