Source code for fastr.utils.cmd.prov

#!/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
# 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 fastr
import gzip
import cPickle as pickle

[docs]def get_parser(): parser = argparse.ArgumentParser(description="Get PROV information from the result pickle. When no options are given, the provenance syntax is printed to stdout in PROV-JSON format.") parser.add_argument('result', metavar='RESULTFILE', nargs='?', type=str, help='File of the job to execute (default ./__fastr_result__.pickle.gz)') parser.add_argument('-so', '--syntax-out-file', type=str, help="Write the syntax to file.") parser.add_argument('-sf', '--syntax-format', default='json', type=str, help="Choices are: [json], provn or xml") parser.add_argument('-i', '--indent', type=int, default=2, help="Indent size of the serialized documents.") parser.add_argument('-vo', '--visualize-out-file', type=str, help="Visualize the provenance. The most preferred format is svg. You can specify any format pydot supports. Specify the format by postfixing the filename with an extension.") return parser
[docs]def get_prov_document(result): with, 'rb') as fh: data = pickle.load(fh) return data.provenance.document
[docs]def main(args=None, unknown_args=None): """ Get PROV information from the result pickle. """ if args is None and unknown_args is None: # No arguments were parsed yet, parse them now parser = get_parser() args, unknown_args = parser.parse_known_args() if args.result is not None: result = args.result else: curdir_contents = os.listdir('.') if '__fastr_result__.pickle.gz' in curdir_contents: result = '__fastr_result__.pickle.gz' else: fastr.log.critical('No result given and cannot find __fastr_result__.pickle.gz in current directory!') exit() # Get the prov document. provenance = get_prov_document(result) syntax_format = args.syntax_format if args.syntax_out_file: provenance.serialize(destination=args.syntax_out_file, format=syntax_format)"Written the provenance syntax in {} format to: {}".format(syntax_format, args.syntax_out_file)) if args.visualize_out_file: provenance.plot(args.visualize_out_file, show_element_attributes=False, show_relation_attributes=False)"Vizualized the provenance in: {}".format(args.visualize_out_file)) if not args.visualize_out_file and not args.syntax_out_file: # There is no output file give so let the serializer print to stdout. print(provenance.serialize(format=syntax_format, indent=2))
if __name__ == '__main__': main()