Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/schema_salad/main.py @ 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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
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1 """Command line interface to schema-salad."""
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2 from __future__ import absolute_import, print_function
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3
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4 import argparse
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5 import logging
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6 import os
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7 import sys
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8 from typing import Any, Dict, List, Mapping, MutableSequence, Optional, Union, cast
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9
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10 import pkg_resources # part of setuptools
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11 import six
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12 from rdflib.parser import Parser
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13 from rdflib.plugin import register
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14 from six.moves import urllib
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15 from typing_extensions import Text # pylint: disable=unused-import
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16
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17 from ruamel.yaml.comments import CommentedSeq
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18
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19 from . import codegen, jsonld_context, schema
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20 from .avro.schema import SchemaParseException
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21 from .exceptions import ValidationException, to_one_line_messages
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22 from .makedoc import makedoc
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23 from .ref_resolver import Loader, file_uri
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24 from .utils import json_dumps
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25
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26 # move to a regular typing import when Python 3.3-3.6 is no longer supported
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27
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28
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29 register("json-ld", Parser, "rdflib_jsonld.parser", "JsonLDParser")
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30 _logger = logging.getLogger("salad")
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31
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32
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33 def printrdf(
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34 workflow, # type: str
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35 wf, # type: Union[List[Dict[Text, Any]], Dict[Text, Any]]
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36 ctx, # type: Dict[Text, Any]
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37 sr, # type: str
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38 ):
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39 # type: (...) -> None
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40 g = jsonld_context.makerdf(workflow, wf, ctx)
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41 print(g.serialize(format=sr, encoding="utf-8").decode("utf-8"))
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42
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43
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44 def main(argsl=None): # type: (Optional[List[str]]) -> int
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45 if argsl is None:
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46 argsl = sys.argv[1:]
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47
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48 parser = argparse.ArgumentParser()
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49 parser.add_argument(
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50 "--rdf-serializer",
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51 help="Output RDF serialization format used by --print-rdf"
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52 "(one of turtle (default), n3, nt, xml)",
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53 default="turtle",
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54 )
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55
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56 parser.add_argument(
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57 "--skip-schemas",
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58 action="store_true",
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59 default=False,
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60 help="If specified, ignore $schemas sections.",
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61 )
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62 parser.add_argument(
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63 "--strict-foreign-properties",
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64 action="store_true",
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65 help="Strict checking of foreign properties",
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66 default=False,
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67 )
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68
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69 exgroup = parser.add_mutually_exclusive_group()
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70 exgroup.add_argument(
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71 "--print-jsonld-context",
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72 action="store_true",
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73 help="Print JSON-LD context for schema",
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74 )
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75 exgroup.add_argument("--print-rdfs", action="store_true", help="Print RDF schema")
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76 exgroup.add_argument("--print-avro", action="store_true", help="Print Avro schema")
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77
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78 exgroup.add_argument(
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79 "--print-rdf",
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80 action="store_true",
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81 help="Print corresponding RDF graph for document",
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82 )
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83 exgroup.add_argument(
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84 "--print-pre", action="store_true", help="Print document after preprocessing"
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85 )
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86 exgroup.add_argument("--print-index", action="store_true", help="Print node index")
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87 exgroup.add_argument(
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88 "--print-metadata", action="store_true", help="Print document metadata"
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89 )
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90 exgroup.add_argument(
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91 "--print-inheritance-dot",
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92 action="store_true",
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93 help="Print graphviz file of inheritance",
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94 )
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95 exgroup.add_argument(
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96 "--print-fieldrefs-dot",
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97 action="store_true",
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98 help="Print graphviz file of field refs",
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99 )
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100
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101 exgroup.add_argument(
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102 "--codegen",
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103 type=str,
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104 metavar="language",
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105 help="Generate classes in target language, currently supported: python, java",
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106 )
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107
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108 parser.add_argument(
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109 "--codegen-target",
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110 type=str,
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111 default=None,
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112 help="Defaults to sys.stdout for python and ./ for Java",
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113 )
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114
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115 parser.add_argument(
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116 "--codegen-examples",
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117 type=str,
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118 metavar="directory",
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119 default=None,
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120 help="Directory of example documents for test case generation (Java only).",
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121 )
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122
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123 exgroup.add_argument(
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124 "--print-oneline",
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125 action="store_true",
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126 help="Print each error message in oneline",
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127 )
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128
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129 exgroup.add_argument(
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130 "--print-doc", action="store_true", help="Print HTML schema documentation page"
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131 )
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132
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133 exgroup = parser.add_mutually_exclusive_group()
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134 exgroup.add_argument(
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135 "--strict",
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136 action="store_true",
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137 help="Strict validation (unrecognized or out of place fields are error)",
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138 default=True,
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139 dest="strict",
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140 )
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141 exgroup.add_argument(
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142 "--non-strict",
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143 action="store_false",
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144 help="Lenient validation (ignore unrecognized fields)",
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145 default=True,
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146 dest="strict",
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147 )
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148
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149 exgroup = parser.add_mutually_exclusive_group()
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150 exgroup.add_argument("--verbose", action="store_true", help="Default logging")
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151 exgroup.add_argument(
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152 "--quiet", action="store_true", help="Only print warnings and errors."
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153 )
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154 exgroup.add_argument("--debug", action="store_true", help="Print even more logging")
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155
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156 parser.add_argument(
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157 "--only",
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158 action="append",
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159 help="Use with --print-doc, document only listed types",
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160 )
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161 parser.add_argument(
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162 "--redirect",
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163 action="append",
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164 help="Use with --print-doc, override default link for type",
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165 )
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166 parser.add_argument(
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167 "--brand", help="Use with --print-doc, set the 'brand' text in nav bar"
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168 )
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169 parser.add_argument(
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170 "--brandlink", help="Use with --print-doc, set the link for 'brand' in nav bar"
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171 )
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172 parser.add_argument(
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173 "--primtype",
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174 default="#PrimitiveType",
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175 help="Use with --print-doc, link to use for primitive types (string, int etc)",
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176 )
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177
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178 parser.add_argument("schema", type=str, nargs="?", default=None)
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179 parser.add_argument("document", type=str, nargs="?", default=None)
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180 parser.add_argument(
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181 "--version", "-v", action="store_true", help="Print version", default=None
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182 )
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183
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184 args = parser.parse_args(argsl)
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185
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186 if args.version is None and args.schema is None:
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parents:
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187 print("{}: error: too few arguments".format(sys.argv[0]))
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188 return 1
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189
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parents:
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190 if args.quiet:
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191 _logger.setLevel(logging.WARN)
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parents:
diff changeset
192 if args.debug:
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193 _logger.setLevel(logging.DEBUG)
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194
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195 pkg = pkg_resources.require("schema_salad")
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parents:
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196 if pkg:
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parents:
diff changeset
197 if args.version:
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198 print("{} Current version: {}".format(sys.argv[0], pkg[0].version))
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199 return 0
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parents:
diff changeset
200 else:
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diff changeset
201 _logger.info("%s Current version: %s", sys.argv[0], pkg[0].version)
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parents:
diff changeset
202
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diff changeset
203 # Get the metaschema to validate the schema
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204 metaschema_names, metaschema_doc, metaschema_loader = schema.get_metaschema()
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diff changeset
205
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diff changeset
206 # Load schema document and resolve refs
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diff changeset
207
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diff changeset
208 schema_uri = args.schema
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parents:
diff changeset
209 if not (
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diff changeset
210 urllib.parse.urlparse(schema_uri)[0]
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parents:
diff changeset
211 and urllib.parse.urlparse(schema_uri)[0] in [u"http", u"https", u"file"]
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parents:
diff changeset
212 ):
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diff changeset
213 schema_uri = file_uri(os.path.abspath(schema_uri))
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parents:
diff changeset
214 schema_raw_doc = metaschema_loader.fetch(schema_uri)
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parents:
diff changeset
215
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parents:
diff changeset
216 try:
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diff changeset
217 schema_doc, schema_metadata = metaschema_loader.resolve_all(
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parents:
diff changeset
218 schema_raw_doc, schema_uri
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parents:
diff changeset
219 )
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shellac
parents:
diff changeset
220 except ValidationException as e:
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parents:
diff changeset
221 _logger.error(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
222 "Schema `%s` failed link checking:\n%s",
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parents:
diff changeset
223 args.schema,
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parents:
diff changeset
224 Text(e),
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parents:
diff changeset
225 exc_info=(True if args.debug else False),
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parents:
diff changeset
226 )
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parents:
diff changeset
227 _logger.debug("Index is %s", list(metaschema_loader.idx.keys()))
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parents:
diff changeset
228 _logger.debug("Vocabulary is %s", list(metaschema_loader.vocab.keys()))
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diff changeset
229 return 1
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parents:
diff changeset
230 except (RuntimeError) as e:
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parents:
diff changeset
231 _logger.error(
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parents:
diff changeset
232 "Schema `%s` read error:\n%s",
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parents:
diff changeset
233 args.schema,
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parents:
diff changeset
234 Text(e),
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parents:
diff changeset
235 exc_info=(True if args.debug else False),
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parents:
diff changeset
236 )
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shellac
parents:
diff changeset
237 return 1
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shellac
parents:
diff changeset
238
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shellac
parents:
diff changeset
239 if args.print_doc:
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shellac
parents:
diff changeset
240 makedoc(args)
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shellac
parents:
diff changeset
241 return 0
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shellac
parents:
diff changeset
242
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
243 # Optionally print the schema after ref resolution
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parents:
diff changeset
244 if not args.document and args.print_pre:
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shellac
parents:
diff changeset
245 print(json_dumps(schema_doc, indent=4))
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shellac
parents:
diff changeset
246 return 0
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shellac
parents:
diff changeset
247
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parents:
diff changeset
248 if not args.document and args.print_index:
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shellac
parents:
diff changeset
249 print(json_dumps(list(metaschema_loader.idx.keys()), indent=4))
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shellac
parents:
diff changeset
250 return 0
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shellac
parents:
diff changeset
251
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parents:
diff changeset
252 # Validate the schema document against the metaschema
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parents:
diff changeset
253 try:
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shellac
parents:
diff changeset
254 schema.validate_doc(
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parents:
diff changeset
255 metaschema_names, schema_doc, metaschema_loader, args.strict
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shellac
parents:
diff changeset
256 )
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shellac
parents:
diff changeset
257 except ValidationException as e:
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parents:
diff changeset
258 _logger.error("While validating schema `%s`:\n%s", args.schema, Text(e))
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shellac
parents:
diff changeset
259 return 1
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shellac
parents:
diff changeset
260
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
261 # Get the json-ld context and RDFS representation from the schema
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shellac
parents:
diff changeset
262 metactx = schema.collect_namespaces(schema_metadata)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
263 if "$base" in schema_metadata:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
264 metactx["@base"] = schema_metadata["$base"]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
265 if isinstance(schema_doc, CommentedSeq):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
266 (schema_ctx, rdfs) = jsonld_context.salad_to_jsonld_context(schema_doc, metactx)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
267 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
268 raise ValidationException(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
269 "Expected a CommentedSeq, got {}: {}.".format(type(schema_doc), schema_doc)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
270 )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
271
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
272 # Create the loader that will be used to load the target document.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
273 document_loader = Loader(schema_ctx, skip_schemas=args.skip_schemas)
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parents:
diff changeset
274
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
275 if args.codegen:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
276 codegen.codegen(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
277 args.codegen,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
278 cast(List[Dict[Text, Any]], schema_doc),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
279 schema_metadata,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
280 document_loader,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
281 target=args.codegen_target,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
282 examples=args.codegen_examples,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
283 )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
284 return 0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
285
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shellac
parents:
diff changeset
286 # Make the Avro validation that will be used to validate the target
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shellac
parents:
diff changeset
287 # document
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parents:
diff changeset
288 if isinstance(schema_doc, MutableSequence):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
289 avsc_obj = schema.make_avro(schema_doc, document_loader)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
290 try:
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shellac
parents:
diff changeset
291 avsc_names = schema.make_avro_schema_from_avro(avsc_obj)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
292 except SchemaParseException as err:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
293 _logger.error(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
294 "Schema `%s` error:\n%s",
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
295 args.schema,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
296 Text(err),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
297 exc_info=((type(err), err, None) if args.debug else None),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
298 )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
299 if args.print_avro:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
300 print(json_dumps(avsc_obj, indent=4))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
301 return 1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
302 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
303 _logger.error("Schema `%s` must be a list.", args.schema)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
304 return 1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
305
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
306 # Optionally print Avro-compatible schema from schema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
307 if args.print_avro:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
308 print(json_dumps(avsc_obj, indent=4))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
309 return 0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
310
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
311 # Optionally print the json-ld context from the schema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
312 if args.print_jsonld_context:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
313 j = {"@context": schema_ctx}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
314 print(json_dumps(j, indent=4, sort_keys=True))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
315 return 0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
316
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
317 # Optionally print the RDFS graph from the schema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
318 if args.print_rdfs:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
319 print(rdfs.serialize(format=args.rdf_serializer).decode("utf-8"))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
320 return 0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
321
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
322 if args.print_metadata and not args.document:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
323 print(json_dumps(schema_metadata, indent=4))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
324 return 0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
325
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
326 if args.print_inheritance_dot:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
327 schema.print_inheritance(schema_doc, sys.stdout)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
328 return 0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
329
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
330 if args.print_fieldrefs_dot:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
331 schema.print_fieldrefs(schema_doc, document_loader, sys.stdout)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
332 return 0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
333
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
334 # If no document specified, all done.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
335 if not args.document:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
336 print("Schema `{}` is valid".format(args.schema))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
337 return 0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
338
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
339 # Load target document and resolve refs
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
340 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
341 uri = args.document
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
342 document, doc_metadata = document_loader.resolve_ref(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
343 uri, strict_foreign_properties=args.strict_foreign_properties
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
344 )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
345 except ValidationException as e:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
346 msg = to_one_line_messages(e) if args.print_oneline else six.text_type(e)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
347 _logger.error(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
348 "Document `%s` failed validation:\n%s",
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
349 args.document,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
350 msg,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
351 exc_info=args.debug,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
352 )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
353 return 1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
354
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
355 # Optionally print the document after ref resolution
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
356 if args.print_pre:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
357 print(json_dumps(document, indent=4))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
358 return 0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
359
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
360 if args.print_index:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
361 print(json_dumps(list(document_loader.idx.keys()), indent=4))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
362 return 0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
363
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
364 # Validate the user document against the schema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
365 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
366 schema.validate_doc(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
367 avsc_names,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
368 document,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
369 document_loader,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
370 args.strict,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
371 strict_foreign_properties=args.strict_foreign_properties,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
372 )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
373 except ValidationException as e:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
374 msg = to_one_line_messages(e) if args.print_oneline else six.text_type(e)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
375 _logger.error("While validating document `%s`:\n%s" % (args.document, msg))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
376 return 1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
377
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
378 # Optionally convert the document to RDF
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
379 if args.print_rdf:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
380 if isinstance(document, (Mapping, MutableSequence)):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
381 printrdf(args.document, document, schema_ctx, args.rdf_serializer)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
382 return 0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
383 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
384 print("Document must be a dictionary or list.")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
385 return 1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
386
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
387 if args.print_metadata:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
388 print(json_dumps(doc_metadata, indent=4))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
389 return 0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
390
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
391 print("Document `{}` is valid".format(args.document))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
392
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
393 return 0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
394
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
395
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
396 if __name__ == "__main__":
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
397 sys.exit(main(sys.argv[1:]))