Source code for

# 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
from fastr.helpers.iohelpers import load_gpickle, load_json
from fastr.utils.cmd import add_parser_doc_link
FASTR_LOG_TYPE = 'none'  # Do not get info about fastr

[docs]def get_parser(): parser = argparse.ArgumentParser( description="Extract selected information from the extra job info. The path" " is the selection of the data to retrieve. Every parts of the" " path (separated by a /) is seen as the index for the previous" " object. So for example to get the stdout of a job, you could use" " 'fastr cat __fastr_extra_job_info__.json process/stdout'." ) 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, list(data.keys()))) if isinstance(data, str): 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 = add_parser_doc_link(get_parser(), __file__) args = parser.parse_args() fastr_cat(args.infile, args.path)
if __name__ == '__main__': main()