Mercurial > repos > shellac > guppy_basecaller

comparison env/bin/prov-convert @ 5:9b1c78e6ba9c draft default tip

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"planemo upload commit 6c0a8142489327ece472c84e558c47da711a9142"
author shellac
date Mon, 01 Jun 2020 08:59:25 -0400
parents 79f47841a781
children
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4:79f47841a781 5:9b1c78e6ba9c
1 #!/Users/pldms/Development/Projects/2020/david-matthews-galaxy/guppy_basecaller/env/bin/python3
2 # encoding: utf-8
3 """
4 convert -- Convert PROV-JSON to RDF, PROV-N, PROV-XML, or graphical formats (SVG, PDF, PNG)
5
6 @author: Trung Dong Huynh
7
8 @copyright: 2016 University of Southampton, United Kingdom. All rights reserved.
9
10 @license: MIT License
11
12 @contact: trungdong@donggiang.com
13 @deffield updated: 2016-10-19
14 """
15
16 from argparse import ArgumentParser, RawDescriptionHelpFormatter, FileType
17 import os
18 import sys
19 import logging
20 import traceback
21 import six
22
23 from prov.model import ProvDocument
24 from prov import serializers
25
26
27 logger = logging.getLogger(__name__)
28
29 __all__ = []
30 __version__ = 0.1
31 __date__ = '2014-03-14'
32 __updated__ = '2016-10-19'
33
34 DEBUG = 0
35 TESTRUN = 0
36 PROFILE = 0
37
38 GRAPHVIZ_SUPPORTED_FORMATS = {
39 'bmp', 'canon', 'cmap', 'cmapx', 'cmapx_np', 'dot', 'eps', 'fig', 'gtk', 'gv', 'ico', 'imap', 'imap_np', 'ismap',
40 'jpe', 'jpeg', 'jpg', 'pdf', 'plain', 'plain-ext', 'png', 'ps', 'ps2', 'svg', 'svgz', 'tif', 'tiff', 'tk',
41 'vml', 'vmlz', 'x11', 'xdot', 'xlib'
42 }
43
44
45 @six.python_2_unicode_compatible
46 class CLIError(Exception):
47 """Generic exception to raise and log different fatal errors."""
48 def __init__(self, msg):
49 super(CLIError).__init__(type(self))
50 self.msg = "E: %s" % msg
51
52 def __str__(self):
53 return self.msg
54
55
56 def convert_file(infile, outfile, output_format):
57 prov_doc = ProvDocument.deserialize(infile)
58
59 # Formats not supported by prov.serializers
60 if output_format == 'provn':
61 outfile.write(prov_doc.get_provn().encode())
62 elif output_format in GRAPHVIZ_SUPPORTED_FORMATS:
63 from prov.dot import prov_to_dot
64 dot = prov_to_dot(prov_doc)
65 content = dot.create(format=output_format)
66 outfile.write(content)
67 else:
68 # Try supported serializers:
69 try:
70 prov_doc.serialize(outfile, format=output_format)
71 except serializers.DoNotExist:
72 raise CLIError('Output format "%s" is not supported.' % output_format)
73
74
75 def main(argv=None): # IGNORE:C0111
76 """Command line options."""
77
78 if argv is None:
79 argv = sys.argv
80 else:
81 sys.argv.extend(argv)
82
83 program_name = os.path.basename(sys.argv[0])
84 program_version = "v%s" % __version__
85 program_build_date = str(__updated__)
86 program_version_message = '%%(prog)s %s (%s)' % (program_version, program_build_date)
87 program_shortdesc = __import__('__main__').__doc__.split("\n")[1]
88 program_license = '''%s
89
90 Created by Trung Dong Huynh on %s.
91 Copyright 2016 University of Southampton. All rights reserved.
92
93 Licensed under the MIT License
94 https://github.com/trungdong/prov/blob/master/LICENSE
95
96 Distributed on an "AS IS" basis without warranties
97 or conditions of any kind, either express or implied.
98
99 USAGE
100 ''' % (program_shortdesc, str(__date__))
101
102 try:
103 # Setup argument parser
104 parser = ArgumentParser(description=program_license, formatter_class=RawDescriptionHelpFormatter)
105 parser.add_argument('-f', '--format', dest='format', action='store', default='json',
106 help='output format: json, xml, provn, or one supported by GraphViz (e.g. svg, pdf)')
107 parser.add_argument('infile', nargs='?', type=FileType('r'), default=sys.stdin)
108 parser.add_argument('outfile', nargs='?', type=FileType('wb'), default=sys.stdout)
109 parser.add_argument('-V', '--version', action='version', version=program_version_message)
110
111 args = None
112 try:
113 # Process arguments
114 args = parser.parse_args()
115 convert_file(args.infile, args.outfile, args.format.lower())
116 finally:
117 if args:
118 if args.infile:
119 args.infile.close()
120 if args.outfile:
121 args.outfile.close()
122
123 return 0
124 except KeyboardInterrupt:
125 # handle keyboard interrupt
126 return 0
127 except Exception as e:
128 if DEBUG or TESTRUN:
129 traceback.print_exc()
130 raise e
131 indent = len(program_name) * " "
132 sys.stderr.write(program_name + ": " + str(e) + "\n")
133 sys.stderr.write(indent + " for help use --help")
134 return 2
135
136 if __name__ == "__main__":
137 logging.basicConfig(level=(logging.DEBUG if DEBUG else logging.INFO))
138 if TESTRUN:
139 import doctest
140 doctest.testmod()
141 if PROFILE:
142 import cProfile
143 import pstats
144 profile_filename = 'converter_profile.txt'
145 cProfile.run('main()', profile_filename)
146 statsfile = open("profile_stats.txt", "wb")
147 p = pstats.Stats(profile_filename, stream=statsfile)
148 stats = p.strip_dirs().sort_stats('cumulative')
149 stats.print_stats()
150 statsfile.close()
151 sys.exit(0)
152 sys.exit(main())