Mercurial > repos > shellac > sam_consensus_v3

annotate env/lib/python3.9/site-packages/schema_salad/main.py @ 0:4f3585e2f14b draft default tip

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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author shellac
date Mon, 22 Mar 2021 18:12:50 +0000
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 """Command line interface to schema-salad."""
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2
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3 import argparse
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4 import logging
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5 import os
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6 import sys
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7 from typing import Any, Dict, List, Mapping, MutableSequence, Optional, Union, cast
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8 from urllib.parse import urlparse
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9
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10 import pkg_resources # part of setuptools
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11 from rdflib.parser import Parser
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12 from rdflib.plugin import register
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13 from ruamel.yaml.comments import CommentedMap, CommentedSeq
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14
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15 from . import codegen, jsonld_context, schema
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16 from .avro.schema import SchemaParseException
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17 from .exceptions import ValidationException, to_one_line_messages
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18 from .makedoc import makedoc
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19 from .ref_resolver import Loader, file_uri
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20 from .utils import json_dumps
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21
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22 register("json-ld", Parser, "rdflib_jsonld.parser", "JsonLDParser")
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23 _logger = logging.getLogger("salad")
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24
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25
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26 def printrdf(
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27 workflow: str,
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28 wf: Union[CommentedMap, CommentedSeq],
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29 ctx: Dict[str, Any],
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30 sr: str,
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31 ) -> None:
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32 g = jsonld_context.makerdf(workflow, wf, ctx)
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33 print(g.serialize(format=sr, encoding="utf-8").decode("utf-8"))
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34
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35
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36 def main(argsl: Optional[List[str]] = None) -> int:
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37 if argsl is None:
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38 argsl = sys.argv[1:]
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39
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40 parser = argparse.ArgumentParser()
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41 parser.add_argument(
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42 "--rdf-serializer",
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43 help="Output RDF serialization format used by --print-rdf"
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44 "(one of turtle (default), n3, nt, xml)",
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45 default="turtle",
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46 )
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47
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48 parser.add_argument(
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49 "--skip-schemas",
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50 action="store_true",
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51 default=False,
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52 help="If specified, ignore $schemas sections.",
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53 )
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54 parser.add_argument(
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55 "--strict-foreign-properties",
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56 action="store_true",
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57 help="Strict checking of foreign properties",
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58 default=False,
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59 )
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60
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61 exgroup = parser.add_mutually_exclusive_group()
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62 exgroup.add_argument(
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63 "--print-jsonld-context",
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64 action="store_true",
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65 help="Print JSON-LD context for schema",
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66 )
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67 exgroup.add_argument("--print-rdfs", action="store_true", help="Print RDF schema")
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68 exgroup.add_argument("--print-avro", action="store_true", help="Print Avro schema")
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69
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70 exgroup.add_argument(
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71 "--print-rdf",
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72 action="store_true",
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73 help="Print corresponding RDF graph for document",
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74 )
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75 exgroup.add_argument(
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76 "--print-pre", action="store_true", help="Print document after preprocessing"
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77 )
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78 exgroup.add_argument("--print-index", action="store_true", help="Print node index")
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79 exgroup.add_argument(
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80 "--print-metadata", action="store_true", help="Print document metadata"
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81 )
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82 exgroup.add_argument(
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83 "--print-inheritance-dot",
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84 action="store_true",
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85 help="Print graphviz file of inheritance",
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86 )
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87 exgroup.add_argument(
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88 "--print-fieldrefs-dot",
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89 action="store_true",
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90 help="Print graphviz file of field refs",
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91 )
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92
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93 exgroup.add_argument(
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94 "--codegen",
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95 type=str,
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96 metavar="language",
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97 help="Generate classes in target language, currently supported: python, java",
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98 )
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99
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100 parser.add_argument(
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101 "--codegen-target",
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102 type=str,
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103 default=None,
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104 help="Defaults to sys.stdout for python and ./ for Java",
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105 )
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106
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107 parser.add_argument(
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108 "--codegen-examples",
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109 type=str,
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110 metavar="directory",
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111 default=None,
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112 help="Directory of example documents for test case generation (Java only).",
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113 )
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114
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115 parser.add_argument(
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116 "--codegen-package",
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117 type=str,
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118 metavar="dotted.package",
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119 default=None,
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120 help="Optional override of the package name which is other derived "
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121 "from the base URL (Java only).",
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122 ),
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123
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124 parser.add_argument(
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125 "--codegen-copyright",
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126 type=str,
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127 metavar="copyright_string",
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128 default=None,
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129 help="Optional copyright of the input schema.",
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130 ),
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131
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132 exgroup.add_argument(
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133 "--print-oneline",
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134 action="store_true",
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135 help="Print each error message in oneline",
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136 )
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137
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138 exgroup.add_argument(
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139 "--print-doc", action="store_true", help="Print HTML schema documentation page"
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140 )
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141
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142 exgroup_strict = parser.add_mutually_exclusive_group()
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143 exgroup_strict.add_argument(
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144 "--strict",
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145 action="store_true",
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146 help="Strict validation (unrecognized or out of place fields are error)",
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147 default=True,
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148 dest="strict",
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149 )
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150 exgroup_strict.add_argument(
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151 "--non-strict",
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152 action="store_false",
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153 help="Lenient validation (ignore unrecognized fields)",
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154 default=True,
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155 dest="strict",
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156 )
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157
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158 exgroup_volume = parser.add_mutually_exclusive_group()
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159 exgroup_volume.add_argument(
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160 "--verbose", action="store_true", help="Default logging"
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161 )
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162 exgroup_volume.add_argument(
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163 "--quiet", action="store_true", help="Only print warnings and errors."
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164 )
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165 exgroup_volume.add_argument(
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166 "--debug", action="store_true", help="Print even more logging"
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167 )
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168
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169 parser.add_argument(
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170 "--only",
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171 action="append",
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172 help="Use with --print-doc, document only listed types",
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173 )
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174 parser.add_argument(
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175 "--redirect",
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176 action="append",
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177 help="Use with --print-doc, override default link for type",
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178 )
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179 parser.add_argument(
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180 "--brand", help="Use with --print-doc, set the 'brand' text in nav bar"
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181 )
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182 parser.add_argument(
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183 "--brandlink", help="Use with --print-doc, set the link for 'brand' in nav bar"
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184 )
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185 parser.add_argument(
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186 "--primtype",
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187 default="#PrimitiveType",
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188 help="Use with --print-doc, link to use for primitive types (string, int etc)",
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189 )
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190
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191 parser.add_argument("schema", type=str, nargs="?", default=None)
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192 parser.add_argument("document", type=str, nargs="?", default=None)
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193 parser.add_argument(
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194 "--version", "-v", action="store_true", help="Print version", default=None
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195 )
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196
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197 args = parser.parse_args(argsl)
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198
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199 if args.version is None and args.schema is None:
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200 print("{}: error: too few arguments".format(sys.argv[0]))
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201 return 1
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202
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203 if args.quiet:
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204 _logger.setLevel(logging.WARN)
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205 if args.debug:
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206 _logger.setLevel(logging.DEBUG)
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207
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208 pkg = pkg_resources.require("schema_salad")
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209 if pkg:
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210 if args.version:
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211 print("{} Current version: {}".format(sys.argv[0], pkg[0].version))
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212 return 0
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213 else:
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214 _logger.info("%s Current version: %s", sys.argv[0], pkg[0].version)
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215
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216 # Get the metaschema to validate the schema
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217 metaschema_names, metaschema_doc, metaschema_loader = schema.get_metaschema()
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218
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219 # Load schema document and resolve refs
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220
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221 schema_uri = args.schema
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222 if not (
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223 urlparse(schema_uri)[0] and urlparse(schema_uri)[0] in ["http", "https", "file"]
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224 ):
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225 schema_uri = file_uri(os.path.abspath(schema_uri))
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226 schema_raw_doc = metaschema_loader.fetch(schema_uri)
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227
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228 try:
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229 schema_doc, schema_metadata = metaschema_loader.resolve_all(
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230 schema_raw_doc, schema_uri
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231 )
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232 except ValidationException as e:
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233 _logger.error(
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234 "Schema `%s` failed link checking:\n%s",
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235 args.schema,
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236 str(e),
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237 exc_info=(True if args.debug else False),
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238 )
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239 _logger.debug("Index is %s", list(metaschema_loader.idx.keys()))
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240 _logger.debug("Vocabulary is %s", list(metaschema_loader.vocab.keys()))
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241 return 1
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242 except (RuntimeError) as e:
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243 _logger.error(
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244 "Schema `%s` read error:\n%s",
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245 args.schema,
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246 str(e),
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247 exc_info=(True if args.debug else False),
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248 )
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249 return 1
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250
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251 if args.print_doc:
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252 makedoc(args)
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253 return 0
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254
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255 # Optionally print the schema after ref resolution
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parents:
diff changeset
256 if not args.document and args.print_pre:
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parents:
diff changeset
257 print(json_dumps(schema_doc, indent=4))
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parents:
diff changeset
258 return 0
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parents:
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259
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parents:
diff changeset
260 if not args.document and args.print_index:
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parents:
diff changeset
261 print(json_dumps(list(metaschema_loader.idx.keys()), indent=4))
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parents:
diff changeset
262 return 0
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parents:
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263
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264 # Validate the schema document against the metaschema
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parents:
diff changeset
265 try:
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parents:
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266 schema.validate_doc(
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parents:
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267 metaschema_names, schema_doc, metaschema_loader, args.strict
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268 )
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parents:
diff changeset
269 except ValidationException as e:
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270 _logger.error("While validating schema `%s`:\n%s", args.schema, str(e))
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271 return 1
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parents:
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272
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273 # Get the json-ld context and RDFS representation from the schema
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parents:
diff changeset
274 metactx = schema.collect_namespaces(schema_metadata)
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parents:
diff changeset
275 if "$base" in schema_metadata:
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276 metactx["@base"] = schema_metadata["$base"]
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parents:
diff changeset
277 if isinstance(schema_doc, CommentedSeq):
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parents:
diff changeset
278 (schema_ctx, rdfs) = jsonld_context.salad_to_jsonld_context(schema_doc, metactx)
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279 else:
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280 raise ValidationException(
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281 "Expected a CommentedSeq, got {}: {}.".format(type(schema_doc), schema_doc)
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parents:
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282 )
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parents:
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283
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parents:
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284 # Create the loader that will be used to load the target document.
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285 document_loader = Loader(schema_ctx, skip_schemas=args.skip_schemas)
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286
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parents:
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287 if args.codegen:
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parents:
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288 codegen.codegen(
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diff changeset
289 args.codegen,
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290 cast(List[Dict[str, Any]], schema_doc),
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parents:
diff changeset
291 schema_metadata,
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parents:
diff changeset
292 document_loader,
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diff changeset
293 target=args.codegen_target,
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parents:
diff changeset
294 examples=args.codegen_examples,
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diff changeset
295 package=args.codegen_package,
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parents:
diff changeset
296 copyright=args.codegen_copyright,
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parents:
diff changeset
297 )
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shellac
parents:
diff changeset
298 return 0
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parents:
diff changeset
299
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parents:
diff changeset
300 # Make the Avro validation that will be used to validate the target
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parents:
diff changeset
301 # document
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parents:
diff changeset
302 if isinstance(schema_doc, MutableSequence):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
303 avsc_obj = schema.make_avro(schema_doc, document_loader)
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shellac
parents:
diff changeset
304 try:
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parents:
diff changeset
305 avsc_names = schema.make_avro_schema_from_avro(avsc_obj)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
306 except SchemaParseException as err:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
307 _logger.error(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
308 "Schema `%s` error:\n%s",
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parents:
diff changeset
309 args.schema,
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parents:
diff changeset
310 str(err),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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diff changeset
311 exc_info=((type(err), err, None) if args.debug else None),
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parents:
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312 )
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parents:
diff changeset
313 if args.print_avro:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
314 print(json_dumps(avsc_obj, indent=4))
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parents:
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315 return 1
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parents:
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316 else:
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diff changeset
317 _logger.error("Schema `%s` must be a list.", args.schema)
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parents:
diff changeset
318 return 1
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shellac
parents:
diff changeset
319
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parents:
diff changeset
320 # Optionally print Avro-compatible schema from schema
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
321 if args.print_avro:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
322 print(json_dumps(avsc_obj, indent=4))
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shellac
parents:
diff changeset
323 return 0
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shellac
parents:
diff changeset
324
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parents:
diff changeset
325 # Optionally print the json-ld context from the schema
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
326 if args.print_jsonld_context:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
327 j = {"@context": schema_ctx}
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
328 print(json_dumps(j, indent=4, sort_keys=True))
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shellac
parents:
diff changeset
329 return 0
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shellac
parents:
diff changeset
330
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shellac
parents:
diff changeset
331 # Optionally print the RDFS graph from the schema
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
332 if args.print_rdfs:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
333 print(rdfs.serialize(format=args.rdf_serializer).decode("utf-8"))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
334 return 0
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
335
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
336 if args.print_metadata and not args.document:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
337 print(json_dumps(schema_metadata, indent=4))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
338 return 0
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
339
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
340 if args.print_inheritance_dot:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
341 schema.print_inheritance(schema_doc, sys.stdout)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
342 return 0
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
343
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
344 if args.print_fieldrefs_dot:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
345 schema.print_fieldrefs(schema_doc, document_loader, sys.stdout)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
346 return 0
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
347
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
348 # If no document specified, all done.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
349 if not args.document:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
350 print(f"Schema `{args.schema}` is valid")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
351 return 0
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
352
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
353 # Load target document and resolve refs
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
354 try:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
355 uri = args.document
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
356 document, doc_metadata = document_loader.resolve_ref(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
357 uri, strict_foreign_properties=args.strict_foreign_properties
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
358 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
359 except ValidationException as e:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
360 msg = to_one_line_messages(e) if args.print_oneline else str(e)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
361 _logger.error(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
362 "Document `%s` failed validation:\n%s",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
363 args.document,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
364 msg,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
365 exc_info=args.debug,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
366 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
367 return 1
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
368
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shellac
parents:
diff changeset
369 # Optionally print the document after ref resolution
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
370 if args.print_pre:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
371 print(json_dumps(document, indent=4))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
372 return 0
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
373
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
374 if args.print_index:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
375 print(json_dumps(list(document_loader.idx.keys()), indent=4))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
376 return 0
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
377
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
378 # Validate the user document against the schema
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
379 try:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
380 schema.validate_doc(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
381 avsc_names,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
382 document,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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383 document_loader,
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384 args.strict,
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385 strict_foreign_properties=args.strict_foreign_properties,
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386 )
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387 except ValidationException as e:
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388 msg2 = to_one_line_messages(e) if args.print_oneline else str(e)
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389 _logger.error(f"While validating document `{args.document}`:\n{msg2}")
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390 return 1
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391
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392 # Optionally convert the document to RDF
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393 if args.print_rdf:
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394 if isinstance(document, (Mapping, MutableSequence)):
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395 printrdf(args.document, document, schema_ctx, args.rdf_serializer)
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396 return 0
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397 else:
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398 print("Document must be a dictionary or list.")
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399 return 1
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400
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401 if args.print_metadata:
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402 print(json_dumps(doc_metadata, indent=4))
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403 return 0
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404
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405 print(f"Document `{args.document}` is valid")
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406
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407 return 0
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408
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409
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410 if __name__ == "__main__":
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411 sys.exit(main(sys.argv[1:]))