#!/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
from fastr.utils.iohelpers import load_gpickle, load_json
FASTR_LOG_TYPE = 'none' # Do not get info about fastr
[docs]def get_parser():
parser = argparse.ArgumentParser()
parser.add_argument('infile', metavar='__fastr_extra_job_info__.json', help='result file to cat')
parser.add_argument('path', help='path of the data to print')
return parser
[docs]def fastr_cat(infile, path):
import os
from pprint import pprint
path = path.strip('/').split('/')
if os.path.isdir(infile):
infile = os.path.join(infile, '__fastr_result__.pickle.gz')
if not os.path.isfile(infile):
print('ERROR: Input file does not exist!')
return
if infile.endswith('.pickle.gz'):
try:
job = load_gpickle(infile)
infile = job.extrainfofile
except IOError:
print('ERROR: Could not open {} for reading'.format(infile))
data = load_json(infile)
for part in path:
try:
data = data[part]
except KeyError:
raise KeyError('{} not found in {}'.format(part, data.keys()))
if isinstance(data, basestring):
for line in data.split('\n'):
print line
else:
pprint(data)
[docs]def main():
"""
Print information from a job file
"""
# No arguments were parsed yet, parse them now
parser = get_parser()
args = parser.parse_args()
fastr_cat(args.infile, args.path)
if __name__ == '__main__':
main()