Mercurial > repos > shellac > guppy_basecaller

annotate env/bin/prov-convert @ 3:758bc20232e8 draft

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"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:20:52 -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 convert -- Convert PROV-JSON to RDF, PROV-N, PROV-XML, or graphical formats (SVG, PDF, PNG)
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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 License
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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 from prov import serializers
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25
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26
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27 logger = logging.getLogger(__name__)
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28
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29 __all__ = []
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30 __version__ = 0.1
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31 __date__ = '2014-03-14'
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32 __updated__ = '2016-10-19'
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33
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34 DEBUG = 0
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35 TESTRUN = 0
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36 PROFILE = 0
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37
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38 GRAPHVIZ_SUPPORTED_FORMATS = {
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39 'bmp', 'canon', 'cmap', 'cmapx', 'cmapx_np', 'dot', 'eps', 'fig', 'gtk', 'gv', 'ico', 'imap', 'imap_np', 'ismap',
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40 'jpe', 'jpeg', 'jpg', 'pdf', 'plain', 'plain-ext', 'png', 'ps', 'ps2', 'svg', 'svgz', 'tif', 'tiff', 'tk',
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41 'vml', 'vmlz', 'x11', 'xdot', 'xlib'
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42 }
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43
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44
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45 @six.python_2_unicode_compatible
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46 class CLIError(Exception):
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47 """Generic exception to raise and log different fatal errors."""
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48 def __init__(self, msg):
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49 super(CLIError).__init__(type(self))
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50 self.msg = "E: %s" % msg
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51
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52 def __str__(self):
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53 return self.msg
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54
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55
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56 def convert_file(infile, outfile, output_format):
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57 prov_doc = ProvDocument.deserialize(infile)
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58
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59 # Formats not supported by prov.serializers
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60 if output_format == 'provn':
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61 outfile.write(prov_doc.get_provn().encode())
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62 elif output_format in GRAPHVIZ_SUPPORTED_FORMATS:
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63 from prov.dot import prov_to_dot
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64 dot = prov_to_dot(prov_doc)
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65 content = dot.create(format=output_format)
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66 outfile.write(content)
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67 else:
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68 # Try supported serializers:
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69 try:
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70 prov_doc.serialize(outfile, format=output_format)
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71 except serializers.DoNotExist:
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72 raise CLIError('Output format "%s" is not supported.' % output_format)
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73
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74
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75 def main(argv=None): # IGNORE:C0111
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76 """Command line options."""
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77
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78 if argv is None:
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79 argv = sys.argv
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80 else:
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81 sys.argv.extend(argv)
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82
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83 program_name = os.path.basename(sys.argv[0])
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84 program_version = "v%s" % __version__
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85 program_build_date = str(__updated__)
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86 program_version_message = '%%(prog)s %s (%s)' % (program_version, program_build_date)
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87 program_shortdesc = __import__('__main__').__doc__.split("\n")[1]
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88 program_license = '''%s
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89
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90 Created by Trung Dong Huynh on %s.
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91 Copyright 2016 University of Southampton. All rights reserved.
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92
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93 Licensed under the MIT License
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94 https://github.com/trungdong/prov/blob/master/LICENSE
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95
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96 Distributed on an "AS IS" basis without warranties
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97 or conditions of any kind, either express or implied.
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98
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99 USAGE
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100 ''' % (program_shortdesc, str(__date__))
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101
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102 try:
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103 # Setup argument parser
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104 parser = ArgumentParser(description=program_license, formatter_class=RawDescriptionHelpFormatter)
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105 parser.add_argument('-f', '--format', dest='format', action='store', default='json',
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106 help='output format: json, xml, provn, or one supported by GraphViz (e.g. svg, pdf)')
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107 parser.add_argument('infile', nargs='?', type=FileType('r'), default=sys.stdin)
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108 parser.add_argument('outfile', nargs='?', type=FileType('wb'), default=sys.stdout)
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109 parser.add_argument('-V', '--version', action='version', version=program_version_message)
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110
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111 args = None
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112 try:
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113 # Process arguments
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114 args = parser.parse_args()
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115 convert_file(args.infile, args.outfile, args.format.lower())
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116 finally:
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117 if args:
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118 if args.infile:
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119 args.infile.close()
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120 if args.outfile:
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121 args.outfile.close()
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122
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123 return 0
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124 except KeyboardInterrupt:
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125 # handle keyboard interrupt
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126 return 0
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127 except Exception as e:
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128 if DEBUG or TESTRUN:
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129 traceback.print_exc()
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130 raise e
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131 indent = len(program_name) * " "
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132 sys.stderr.write(program_name + ": " + str(e) + "\n")
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133 sys.stderr.write(indent + " for help use --help")
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134 return 2
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135
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136 if __name__ == "__main__":
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137 logging.basicConfig(level=(logging.DEBUG if DEBUG else logging.INFO))
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138 if TESTRUN:
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139 import doctest
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140 doctest.testmod()
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141 if PROFILE:
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142 import cProfile
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143 import pstats
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144 profile_filename = 'converter_profile.txt'
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145 cProfile.run('main()', profile_filename)
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146 statsfile = open("profile_stats.txt", "wb")
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147 p = pstats.Stats(profile_filename, stream=statsfile)
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148 stats = p.strip_dirs().sort_stats('cumulative')
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149 stats.print_stats()
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150 statsfile.close()
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151 sys.exit(0)
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152 sys.exit(main())