Mercurial > repos > shellac > guppy_basecaller

annotate env/bin/prov-compare @ 4:79f47841a781 draft

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"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:47:39 -0400
parents 26e78fe6e8c4
children
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1 #!/Users/pldms/Development/Projects/2020/david-matthews-galaxy/guppy_basecaller/env/bin/python3
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2 # encoding: utf-8
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3 """
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4 prov-compare -- Compare two PROV-JSON, PROV-XML, or RDF (PROV-O) files for equivalence
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5
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6 @author: Trung Dong Huynh
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7
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8 @copyright: 2016 University of Southampton, United Kingdom. All rights reserved.
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9
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10 @license: MIT Licence
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11
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12 @contact: trungdong@donggiang.com
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13 @deffield updated: 2016-10-19
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14 """
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15
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16 from argparse import ArgumentParser, RawDescriptionHelpFormatter, FileType
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17 import os
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18 import sys
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19 import logging
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20 import traceback
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21 import six
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22
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23 from prov.model import ProvDocument
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24
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25
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26 logger = logging.getLogger(__name__)
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27
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28 __all__ = []
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29 __version__ = 0.1
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30 __date__ = '2015-06-16'
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31 __updated__ = '2016-10-19'
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32
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33 DEBUG = 0
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34 TESTRUN = 0
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35 PROFILE = 0
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36
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37
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38 @six.python_2_unicode_compatible
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39 class CLIError(Exception):
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40 """Generic exception to raise and log different fatal errors."""
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41 def __init__(self, msg):
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42 super(CLIError).__init__(type(self))
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43 self.msg = "E: %s" % msg
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44
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45 def __str__(self):
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46 return self.msg
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47
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48
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49 def main(argv=None): # IGNORE:C0111
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50 """Command line options."""
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51
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52 if argv is None:
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53 argv = sys.argv
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54 else:
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55 sys.argv.extend(argv)
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56
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57 program_name = os.path.basename(sys.argv[0])
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58 program_version = "v%s" % __version__
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59 program_build_date = str(__updated__)
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60 program_version_message = '%%(prog)s %s (%s)' % (program_version, program_build_date)
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61 program_shortdesc = __import__('__main__').__doc__.split("\n")[1]
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62 program_license = '''%s
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63
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64 Created by Trung Dong Huynh on %s.
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65 Copyright 2016 University of Southampton. All rights reserved.
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66
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67 Licensed under the MIT License
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68 https://github.com/trungdong/prov/blob/master/LICENSE
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69
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70 Distributed on an "AS IS" basis without warranties
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71 or conditions of any kind, either express or implied.
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72
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73 USAGE
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74 ''' % (program_shortdesc, str(__date__))
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75
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76 try:
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77 # Setup argument parser
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78 parser = ArgumentParser(description=program_license, formatter_class=RawDescriptionHelpFormatter)
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79 parser.add_argument('file1', nargs='?', type=FileType('r'))
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80 parser.add_argument('file2', nargs='?', type=FileType('r'))
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81 parser.add_argument('-f', '--format1', dest='format1', action='store', default='json',
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82 help='File 1\'s format: json or xml')
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83 parser.add_argument('-F', '--format2', dest='format2', action='store', default='json',
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84 help='File 2\'s format: json or xml')
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85 parser.add_argument('-V', '--version', action='version', version=program_version_message)
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86
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87 args = None
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88 try:
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89 # Process arguments
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90 args = parser.parse_args()
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91 doc1 = ProvDocument.deserialize(args.file1, format=args.format1.lower())
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92 doc2 = ProvDocument.deserialize(args.file2, format=args.format2.lower())
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93 return doc1 != doc2
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94
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95 finally:
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96 if args:
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97 if args.file1:
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98 args.file1.close()
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99 if args.file2:
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100 args.file2.close()
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101
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102 except Exception as e:
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103 if DEBUG or TESTRUN:
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104 traceback.print_exc()
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105 raise e
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106 indent = len(program_name) * " "
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107 sys.stderr.write(program_name + ": " + str(e) + "\n")
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108 sys.stderr.write(indent + " for help use --help")
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109 return 2
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110
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111 if __name__ == "__main__":
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112 logging.basicConfig(level=(logging.DEBUG if DEBUG else logging.INFO))
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113 if TESTRUN:
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114 import doctest
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115 doctest.testmod()
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116 if PROFILE:
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117 import cProfile
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118 import pstats
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119 profile_filename = 'prov_compare_profile.txt'
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120 cProfile.run('main()', profile_filename)
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121 statsfile = open("profile_stats.txt", "wb")
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122 p = pstats.Stats(profile_filename, stream=statsfile)
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123 stats = p.strip_dirs().sort_stats('cumulative')
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124 stats.print_stats()
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125 statsfile.close()
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126 sys.exit(0)
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127 sys.exit(main())