--- a/env/bin/prov-convert	Thu May 14 16:47:39 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,152 +0,0 @@
-#!/Users/pldms/Development/Projects/2020/david-matthews-galaxy/guppy_basecaller/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:    trungdong@donggiang.com
-@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())
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