comparison env/bin/prov-convert @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

0:4f3585e2f14b

#!/Users/cmdms/OneDrive-UOB/Development/Projects/2021/sam-consensus-v3/env/bin/python3
# encoding: utf-8
"""
convert -- Convert PROV-JSON to RDF, PROV-N, PROV-XML, or graphical formats (SVG, PDF, PNG)

@author:     Trung Dong Huynh

@copyright:  2016 University of Southampton, United Kingdom. All rights reserved.

@license:    MIT License

@contact:    [e-mail]
@deffield    updated: 2016-10-19
"""

from argparse import ArgumentParser, RawDescriptionHelpFormatter, FileType
import os
import sys
import logging
import traceback
import six

from prov.model import ProvDocument
from prov import serializers


logger = logging.getLogger(__name__)

__all__ = []
__version__ = 0.1
__date__ = '2014-03-14'
__updated__ = '2016-10-19'

DEBUG = 0
TESTRUN = 0
PROFILE = 0

GRAPHVIZ_SUPPORTED_FORMATS = {
    'bmp', 'canon', 'cmap', 'cmapx', 'cmapx_np', 'dot', 'eps', 'fig', 'gtk', 'gv', 'ico', 'imap', 'imap_np', 'ismap',
    'jpe', 'jpeg', 'jpg', 'pdf', 'plain', 'plain-ext', 'png', 'ps', 'ps2', 'svg', 'svgz', 'tif', 'tiff', 'tk',
    'vml', 'vmlz', 'x11', 'xdot', 'xlib'
}


@six.python_2_unicode_compatible
class CLIError(Exception):
    """Generic exception to raise and log different fatal errors."""
    def __init__(self, msg):
        super(CLIError).__init__(type(self))
        self.msg = "E: %s" % msg

    def __str__(self):
        return self.msg


def convert_file(infile, outfile, output_format):
    prov_doc = ProvDocument.deserialize(infile)

    # Formats not supported by prov.serializers
    if output_format == 'provn':
        outfile.write(prov_doc.get_provn().encode())
    elif output_format in GRAPHVIZ_SUPPORTED_FORMATS:
        from prov.dot import prov_to_dot
        dot = prov_to_dot(prov_doc)
        content = dot.create(format=output_format)
        outfile.write(content)
    else:
        # Try supported serializers:
        try:
            prov_doc.serialize(outfile, format=output_format)
        except serializers.DoNotExist:
            raise CLIError('Output format "%s" is not supported.' % output_format)


def main(argv=None):  # IGNORE:C0111
    """Command line options."""

    if argv is None:
        argv = sys.argv
    else:
        sys.argv.extend(argv)

    program_name = os.path.basename(sys.argv[0])
    program_version = "v%s" % __version__
    program_build_date = str(__updated__)
    program_version_message = '%%(prog)s %s (%s)' % (program_version, program_build_date)
    program_shortdesc = __import__('__main__').__doc__.split("\n")[1]
    program_license = '''%s

  Created by Trung Dong Huynh on %s.
  Copyright 2016 University of Southampton. All rights reserved.

  Licensed under the MIT License
  https://github.com/trungdong/prov/blob/master/LICENSE

  Distributed on an "AS IS" basis without warranties
  or conditions of any kind, either express or implied.

USAGE
''' % (program_shortdesc, str(__date__))

    try:
        # Setup argument parser
        parser = ArgumentParser(description=program_license, formatter_class=RawDescriptionHelpFormatter)
        parser.add_argument('-f', '--format', dest='format', action='store', default='json',
                            help='output format: json, xml, provn, or one supported by GraphViz (e.g. svg, pdf)')
        parser.add_argument('infile', nargs='?', type=FileType('r'), default=sys.stdin)
        parser.add_argument('outfile', nargs='?', type=FileType('wb'), default=sys.stdout)
        parser.add_argument('-V', '--version', action='version', version=program_version_message)

        args = None
        try:
            # Process arguments
            args = parser.parse_args()
            convert_file(args.infile, args.outfile, args.format.lower())
        finally:
            if args:
                if args.infile:
                    args.infile.close()
                if args.outfile:
                    args.outfile.close()

        return 0
    except KeyboardInterrupt:
        # handle keyboard interrupt
        return 0
    except Exception as e:
        if DEBUG or TESTRUN:
            traceback.print_exc()
            raise e
        indent = len(program_name) * " "
        sys.stderr.write(program_name + ": " + str(e) + "\n")
        sys.stderr.write(indent + "  for help use --help")
        return 2

if __name__ == "__main__":
    logging.basicConfig(level=(logging.DEBUG if DEBUG else logging.INFO))
    if TESTRUN:
        import doctest
        doctest.testmod()
    if PROFILE:
        import cProfile
        import pstats
        profile_filename = 'converter_profile.txt'
        cProfile.run('main()', profile_filename)
        statsfile = open("profile_stats.txt", "wb")
        p = pstats.Stats(profile_filename, stream=statsfile)
        stats = p.strip_dirs().sort_stats('cumulative')
        stats.print_stats()
        statsfile.close()
        sys.exit(0)
    sys.exit(main())