diff env/bin/prov-compare @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/bin/prov-compare	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,127 @@
+#!/Users/cmdms/OneDrive-UOB/Development/Projects/2021/sam-consensus-v3/env/bin/python3
+# encoding: utf-8
+"""
+prov-compare -- Compare two PROV-JSON, PROV-XML, or RDF (PROV-O) files for equivalence
+
+@author:     Trung Dong Huynh
+
+@copyright:  2016 University of Southampton, United Kingdom. All rights reserved.
+
+@license:    MIT Licence
+
+@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
+
+
+logger = logging.getLogger(__name__)
+
+__all__ = []
+__version__ = 0.1
+__date__ = '2015-06-16'
+__updated__ = '2016-10-19'
+
+DEBUG = 0
+TESTRUN = 0
+PROFILE = 0
+
+
[e-mail]_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 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('file1', nargs='?', type=FileType('r'))
+        parser.add_argument('file2', nargs='?', type=FileType('r'))
+        parser.add_argument('-f', '--format1', dest='format1', action='store', default='json',
+                            help='File 1\'s format: json or xml')
+        parser.add_argument('-F', '--format2', dest='format2', action='store', default='json',
+                            help='File 2\'s format: json or xml')
+        parser.add_argument('-V', '--version', action='version', version=program_version_message)
+
+        args = None
+        try:
+            # Process arguments
+            args = parser.parse_args()
+            doc1 = ProvDocument.deserialize(args.file1, format=args.format1.lower())
+            doc2 = ProvDocument.deserialize(args.file2, format=args.format2.lower())
+            return doc1 != doc2
+
+        finally:
+            if args:
+                if args.file1:
+                    args.file1.close()
+                if args.file2:
+                    args.file2.close()
+
+    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 = 'prov_compare_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())