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annotate planemo/lib/python3.7/site-packages/schema_salad/schema.py @ 1:56ad4e20f292 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:32:28 -0400
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1
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1 """Functions to process Schema Salad schemas."""
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2 from __future__ import absolute_import
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3
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4 import copy
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5 import hashlib
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6 from typing import (
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7 IO,
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8 Any,
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9 Dict,
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10 List,
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11 Mapping,
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12 MutableMapping,
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13 MutableSequence,
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14 Optional,
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15 Set,
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16 Tuple,
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17 TypeVar,
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18 Union,
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19 cast,
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20 )
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21
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22 from future.utils import raise_from
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23 from pkg_resources import resource_stream
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24 from six import iteritems, string_types
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25 from six.moves import urllib
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26 from typing_extensions import Text # pylint: disable=unused-import
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27
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28 from ruamel import yaml
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29 from ruamel.yaml.comments import CommentedMap, CommentedSeq
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30 from schema_salad.utils import (
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31 add_dictlist,
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32 aslist,
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33 convert_to_dict,
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34 flatten,
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35 json_dumps,
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36 )
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37
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38 from . import _logger, jsonld_context, ref_resolver, validate
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39 from .exceptions import (
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40 ClassValidationException,
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41 ValidationException,
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42 SchemaSaladException,
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43 )
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44 from .avro.schema import Names, SchemaParseException, make_avsc_object
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45 from .ref_resolver import Loader
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46 from .sourceline import SourceLine, add_lc_filename, relname
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47
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48 SALAD_FILES = (
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49 "metaschema.yml",
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50 "metaschema_base.yml",
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51 "salad.md",
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52 "field_name.yml",
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53 "import_include.md",
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54 "link_res.yml",
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55 "ident_res.yml",
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56 "vocab_res.yml",
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57 "vocab_res.yml",
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58 "field_name_schema.yml",
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59 "field_name_src.yml",
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60 "field_name_proc.yml",
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61 "ident_res_schema.yml",
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62 "ident_res_src.yml",
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63 "ident_res_proc.yml",
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64 "link_res_schema.yml",
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65 "link_res_src.yml",
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66 "link_res_proc.yml",
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67 "vocab_res_schema.yml",
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68 "vocab_res_src.yml",
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69 "vocab_res_proc.yml",
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70 "map_res.yml",
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71 "map_res_schema.yml",
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72 "map_res_src.yml",
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73 "map_res_proc.yml",
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74 "typedsl_res.yml",
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75 "typedsl_res_schema.yml",
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76 "typedsl_res_src.yml",
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77 "typedsl_res_proc.yml",
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78 "sfdsl_res.yml",
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79 "sfdsl_res_schema.yml",
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80 "sfdsl_res_src.yml",
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81 "sfdsl_res_proc.yml",
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82 )
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83
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84 saladp = "https://w3id.org/cwl/salad#"
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85
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86
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87 def get_metaschema(): # type: () -> Tuple[Names, List[Dict[Text, Any]], Loader]
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88 """Instantiate the metaschema."""
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89 loader = ref_resolver.Loader(
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90 {
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91 "Any": saladp + "Any",
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92 "ArraySchema": saladp + "ArraySchema",
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93 "Array_symbol": saladp + "ArraySchema/type/Array_symbol",
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94 "DocType": saladp + "DocType",
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95 "Documentation": saladp + "Documentation",
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96 "Documentation_symbol": saladp + "Documentation/type/Documentation_symbol",
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97 "Documented": saladp + "Documented",
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98 "EnumSchema": saladp + "EnumSchema",
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99 "Enum_symbol": saladp + "EnumSchema/type/Enum_symbol",
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100 "JsonldPredicate": saladp + "JsonldPredicate",
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101 "NamedType": saladp + "NamedType",
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102 "PrimitiveType": saladp + "PrimitiveType",
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103 "RecordField": saladp + "RecordField",
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104 "RecordSchema": saladp + "RecordSchema",
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105 "Record_symbol": saladp + "RecordSchema/type/Record_symbol",
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106 "SaladEnumSchema": saladp + "SaladEnumSchema",
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107 "SaladRecordField": saladp + "SaladRecordField",
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108 "SaladRecordSchema": saladp + "SaladRecordSchema",
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109 "SchemaDefinedType": saladp + "SchemaDefinedType",
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110 "SpecializeDef": saladp + "SpecializeDef",
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111 "_container": saladp + "JsonldPredicate/_container",
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112 "_id": {"@id": saladp + "_id", "@type": "@id", "identity": True},
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113 "_type": saladp + "JsonldPredicate/_type",
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114 "abstract": saladp + "SaladRecordSchema/abstract",
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115 "array": saladp + "array",
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116 "boolean": "http://www.w3.org/2001/XMLSchema#boolean",
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117 "dct": "http://purl.org/dc/terms/",
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118 "default": {"@id": saladp + "default", "noLinkCheck": True},
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119 "doc": "rdfs:comment",
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120 "docAfter": {"@id": saladp + "docAfter", "@type": "@id"},
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121 "docChild": {"@id": saladp + "docChild", "@type": "@id"},
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122 "docParent": {"@id": saladp + "docParent", "@type": "@id"},
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123 "documentRoot": saladp + "SchemaDefinedType/documentRoot",
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124 "documentation": saladp + "documentation",
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125 "double": "http://www.w3.org/2001/XMLSchema#double",
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parents:
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126 "enum": saladp + "enum",
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127 "extends": {"@id": saladp + "extends", "@type": "@id", "refScope": 1},
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128 "fields": {
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129 "@id": saladp + "fields",
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parents:
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130 "mapPredicate": "type",
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parents:
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131 "mapSubject": "name",
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132 },
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133 "float": "http://www.w3.org/2001/XMLSchema#float",
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134 "identity": saladp + "JsonldPredicate/identity",
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135 "inVocab": saladp + "NamedType/inVocab",
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136 "int": "http://www.w3.org/2001/XMLSchema#int",
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137 "items": {"@id": saladp + "items", "@type": "@vocab", "refScope": 2},
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138 "jsonldPredicate": "sld:jsonldPredicate",
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139 "long": "http://www.w3.org/2001/XMLSchema#long",
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140 "mapPredicate": saladp + "JsonldPredicate/mapPredicate",
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141 "mapSubject": saladp + "JsonldPredicate/mapSubject",
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142 "name": "@id",
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143 "noLinkCheck": saladp + "JsonldPredicate/noLinkCheck",
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144 "null": saladp + "null",
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145 "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
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146 "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
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147 "record": saladp + "record",
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148 "refScope": saladp + "JsonldPredicate/refScope",
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149 "sld": saladp,
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150 "specialize": {
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151 "@id": saladp + "specialize",
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152 "mapPredicate": "specializeTo",
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153 "mapSubject": "specializeFrom",
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154 },
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155 "specializeFrom": {
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156 "@id": saladp + "specializeFrom",
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157 "@type": "@id",
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158 "refScope": 1,
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159 },
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160 "specializeTo": {
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161 "@id": saladp + "specializeTo",
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162 "@type": "@id",
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163 "refScope": 1,
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164 },
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165 "string": "http://www.w3.org/2001/XMLSchema#string",
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166 "subscope": saladp + "JsonldPredicate/subscope",
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167 "symbols": {"@id": saladp + "symbols", "@type": "@id", "identity": True},
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168 "type": {
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169 "@id": saladp + "type",
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170 "@type": "@vocab",
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171 "refScope": 2,
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172 "typeDSL": True,
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173 },
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174 "typeDSL": saladp + "JsonldPredicate/typeDSL",
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175 "xsd": "http://www.w3.org/2001/XMLSchema#",
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176 }
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177 )
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178
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179 for salad in SALAD_FILES:
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180 with resource_stream(__name__, "metaschema/" + salad) as stream:
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181 loader.cache["https://w3id.org/cwl/" + salad] = stream.read()
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182
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183 with resource_stream(__name__, "metaschema/metaschema.yml") as stream:
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184 loader.cache["https://w3id.org/cwl/salad"] = stream.read()
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185
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186 j = yaml.round_trip_load(loader.cache["https://w3id.org/cwl/salad"])
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187 add_lc_filename(j, "metaschema.yml")
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188 j, _ = loader.resolve_all(j, saladp)
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189
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190 sch_obj = make_avro(j, loader)
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191 try:
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192 sch_names = make_avro_schema_from_avro(sch_obj)
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193 except SchemaParseException:
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194 _logger.error("Metaschema error, avro was:\n%s", json_dumps(sch_obj, indent=4))
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195 raise
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196 validate_doc(sch_names, j, loader, strict=True)
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197 return (sch_names, j, loader)
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198
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199
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200 def add_namespaces(metadata, namespaces):
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201 # type: (Mapping[Text, Any], MutableMapping[Text, Text]) -> None
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202 """Collect the provided namespaces, checking for conflicts."""
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203 for key, value in metadata.items():
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204 if key not in namespaces:
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205 namespaces[key] = value
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206 elif namespaces[key] != value:
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207 raise ValidationException(
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208 "Namespace prefix '{}' has conflicting definitions '{}'"
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209 " and '{}'.".format(key, namespaces[key], value)
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210 )
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211
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212
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213 def collect_namespaces(metadata):
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214 # type: (Mapping[Text, Any]) -> Dict[Text, Text]
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215 """Walk through the metadata object, collecting namespace declarations."""
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216 namespaces = {} # type: Dict[Text, Text]
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217 if "$import_metadata" in metadata:
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218 for value in metadata["$import_metadata"].values():
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219 add_namespaces(collect_namespaces(value), namespaces)
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220 if "$namespaces" in metadata:
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221 add_namespaces(metadata["$namespaces"], namespaces)
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222 return namespaces
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223
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224
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225 schema_type = Tuple[Loader, Union[Names, SchemaParseException], Dict[Text, Any], Loader]
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226
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227
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228 def load_schema(
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229 schema_ref, # type: Union[CommentedMap, CommentedSeq, Text]
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230 cache=None, # type: Optional[Dict[Text, Text]]
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231 ):
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232 # type: (...) -> schema_type
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233 """
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234 Load a schema that can be used to validate documents using load_and_validate.
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235
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236 return: document_loader, avsc_names, schema_metadata, metaschema_loader
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237 """
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238
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239 metaschema_names, _metaschema_doc, metaschema_loader = get_metaschema()
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240 if cache is not None:
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241 metaschema_loader.cache.update(cache)
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242 schema_doc, schema_metadata = metaschema_loader.resolve_ref(schema_ref, "")
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243
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244 if not isinstance(schema_doc, MutableSequence):
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245 raise ValidationException("Schema reference must resolve to a list.")
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246
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247 validate_doc(metaschema_names, schema_doc, metaschema_loader, True)
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248 metactx = schema_metadata.get("@context", {})
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249 metactx.update(collect_namespaces(schema_metadata))
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250 schema_ctx = jsonld_context.salad_to_jsonld_context(schema_doc, metactx)[0]
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251
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252 # Create the loader that will be used to load the target document.
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253 document_loader = Loader(schema_ctx, cache=cache)
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254
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255 # Make the Avro validation that will be used to validate the target
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256 # document
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257 avsc_names = make_avro_schema(schema_doc, document_loader)
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258
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259 return document_loader, avsc_names, schema_metadata, metaschema_loader
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260
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261
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262 def load_and_validate(
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263 document_loader, # type: Loader
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264 avsc_names, # type: Names
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265 document, # type: Union[CommentedMap, Text]
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266 strict, # type: bool
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267 strict_foreign_properties=False, # type: bool
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268 ):
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269 # type: (...) -> Tuple[Any, Dict[Text, Any]]
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270 """Load a document and validate it with the provided schema.
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271
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272 return data, metadata
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273 """
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274 try:
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275 if isinstance(document, CommentedMap):
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276 data, metadata = document_loader.resolve_all(
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277 document,
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278 document["id"],
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279 checklinks=True,
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280 strict_foreign_properties=strict_foreign_properties,
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281 )
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282 else:
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283 data, metadata = document_loader.resolve_ref(
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284 document,
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285 checklinks=True,
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286 strict_foreign_properties=strict_foreign_properties,
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287 )
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288
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289 validate_doc(
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290 avsc_names,
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291 data,
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292 document_loader,
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293 strict,
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294 strict_foreign_properties=strict_foreign_properties,
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295 )
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296 except ValidationException as exc:
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297 raise_from(ValidationException("", None, [exc]), exc)
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298 return data, metadata
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299
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300
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301 def validate_doc(
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302 schema_names, # type: Names
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303 doc, # type: Union[Dict[Text, Any], List[Dict[Text, Any]], Text, None]
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304 loader, # type: Loader
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305 strict, # type: bool
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306 strict_foreign_properties=False, # type: bool
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307 ):
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308 # type: (...) -> None
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309 """Validate a document using the provided schema."""
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310 has_root = False
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311 for root in schema_names.names.values():
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312 if (hasattr(root, "get_prop") and root.get_prop(u"documentRoot")) or (
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313 u"documentRoot" in root.props
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314 ):
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315 has_root = True
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316 break
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317
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318 if not has_root:
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319 raise ValidationException("No document roots defined in the schema")
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320
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321 if isinstance(doc, MutableSequence):
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322 vdoc = doc
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323 elif isinstance(doc, CommentedMap):
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324 vdoc = CommentedSeq([doc])
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325 vdoc.lc.add_kv_line_col(0, [doc.lc.line, doc.lc.col])
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326 vdoc.lc.filename = doc.lc.filename
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327 else:
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328 raise ValidationException("Document must be dict or list")
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329
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330 roots = []
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331 for root in schema_names.names.values():
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332 if (hasattr(root, "get_prop") and root.get_prop(u"documentRoot")) or (
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333 root.props.get(u"documentRoot")
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334 ):
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335 roots.append(root)
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336
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337 anyerrors = []
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338 for pos, item in enumerate(vdoc):
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339 sourceline = SourceLine(vdoc, pos, Text)
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340 success = False
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341 for root in roots:
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342 success = validate.validate_ex(
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343 root,
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344 item,
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345 loader.identifiers,
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346 strict,
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347 foreign_properties=loader.foreign_properties,
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348 raise_ex=False,
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349 skip_foreign_properties=loader.skip_schemas,
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350 strict_foreign_properties=strict_foreign_properties,
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351 )
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352 if success:
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353 break
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354
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355 if not success:
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356 errors = [] # type: List[SchemaSaladException]
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357 for root in roots:
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358 if hasattr(root, "get_prop"):
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359 name = root.get_prop(u"name")
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360 elif hasattr(root, "name"):
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361 name = root.name
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362
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363 try:
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364 validate.validate_ex(
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365 root,
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366 item,
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367 loader.identifiers,
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368 strict,
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369 foreign_properties=loader.foreign_properties,
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370 raise_ex=True,
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371 skip_foreign_properties=loader.skip_schemas,
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372 strict_foreign_properties=strict_foreign_properties,
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373 )
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374 except ClassValidationException as exc:
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375 errors = [
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376 ClassValidationException(
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377 "tried `{}` but".format(name), sourceline, [exc]
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378 )
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379 ]
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380 break
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381 except ValidationException as exc:
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diff changeset
382 errors.append(
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diff changeset
383 ValidationException(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
384 "tried `{}` but".format(name), sourceline, [exc]
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diff changeset
385 )
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parents:
diff changeset
386 )
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387
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388 objerr = u"Invalid"
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parents:
diff changeset
389 for ident in loader.identifiers:
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parents:
diff changeset
390 if ident in item:
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391 objerr = u"Object `{}` is not valid because".format(
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392 relname(item[ident])
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393 )
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394 break
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395 anyerrors.append(ValidationException(objerr, sourceline, errors, "-"))
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396 if anyerrors:
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397 raise ValidationException("", None, anyerrors, "*")
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398
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399
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400 def get_anon_name(rec):
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401 # type: (MutableMapping[Text, Union[Text, Dict[Text, Text]]]) -> Text
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402 """Calculate a reproducible name for anonymous types."""
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403 if "name" in rec:
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404 name = rec["name"]
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parents:
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405 if isinstance(name, Text):
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406 return name
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407 raise ValidationException(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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408 "Expected name field to be a string, was {}".format(name)
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409 )
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410 anon_name = u""
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411 if rec["type"] in ("enum", saladp + "enum"):
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412 for sym in rec["symbols"]:
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413 anon_name += sym
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414 return "enum_" + hashlib.sha1(anon_name.encode("UTF-8")).hexdigest()
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415 if rec["type"] in ("record", saladp + "record"):
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416 for field in rec["fields"]:
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417 if isinstance(field, Mapping):
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418 anon_name += field[u"name"]
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419 else:
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420 raise ValidationException(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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421 "Expected entries in 'fields' to also be maps, was {}.".format(
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diff changeset
422 field
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423 )
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424 )
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diff changeset
425 return u"record_" + hashlib.sha1(anon_name.encode("UTF-8")).hexdigest()
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426 if rec["type"] in ("array", saladp + "array"):
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427 return u""
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428 raise ValidationException("Expected enum or record, was {}".format(rec["type"]))
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429
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430
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431 def replace_type(items, spec, loader, found, find_embeds=True, deepen=True):
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432 # type: (Any, Dict[Text, Any], Loader, Set[Text], bool, bool) -> Any
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433 """ Go through and replace types in the 'spec' mapping"""
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434
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diff changeset
435 if isinstance(items, MutableMapping):
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436 # recursively check these fields for types to replace
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437 if items.get("type") in ("record", "enum") and items.get("name"):
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diff changeset
438 if items["name"] in found:
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439 return items["name"]
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440 found.add(items["name"])
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441
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442 if not deepen:
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443 return items
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444
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445 items = copy.copy(items)
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446 if not items.get("name"):
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447 items["name"] = get_anon_name(items)
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448 for name in ("type", "items", "fields"):
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449 if name in items:
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450 items[name] = replace_type(
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451 items[name],
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diff changeset
452 spec,
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453 loader,
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454 found,
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455 find_embeds=find_embeds,
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456 deepen=find_embeds,
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457 )
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458 if isinstance(items[name], MutableSequence):
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459 items[name] = flatten(items[name])
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460
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461 return items
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diff changeset
462 if isinstance(items, MutableSequence):
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463 # recursively transform list
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464 return [
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465 replace_type(i, spec, loader, found, find_embeds=find_embeds, deepen=deepen)
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466 for i in items
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467 ]
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468 if isinstance(items, string_types):
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diff changeset
469 # found a string which is a symbol corresponding to a type.
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470 replace_with = None
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471 if items in loader.vocab:
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diff changeset
472 # If it's a vocabulary term, first expand it to its fully qualified
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473 # URI
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474 items = loader.vocab[items]
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475
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476 if items in spec:
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477 # Look up in specialization map
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478 replace_with = spec[items]
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479
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480 if replace_with:
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481 return replace_type(
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diff changeset
482 replace_with, spec, loader, found, find_embeds=find_embeds
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diff changeset
483 )
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484 found.add(items)
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diff changeset
485 return items
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486
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487
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488 def avro_name(url): # type: (Text) -> Text
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489 """
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490 Turn a URL into an Avro-safe name.
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491
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492 If the URL has no fragment, return this plain URL.
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493
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494 Extract either the last part of the URL fragment past the slash, otherwise
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495 the whole fragment.
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496 """
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497 frg = urllib.parse.urldefrag(url)[1]
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diff changeset
498 if frg != "":
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499 if "/" in frg:
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500 return frg[frg.rindex("/") + 1 :]
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501 return frg
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diff changeset
502 return url
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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503
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504
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505 Avro = TypeVar("Avro", Dict[Text, Any], List[Any], Text)
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guerler
parents:
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506
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507
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508 def make_valid_avro(
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509 items, # type: Avro
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diff changeset
510 alltypes, # type: Dict[Text, Dict[Text, Any]]
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511 found, # type: Set[Text]
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diff changeset
512 union=False, # type: bool
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
513 ): # type: (...) -> Union[Avro, Dict[Text, Text], Text]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
514 """Convert our schema to be more avro like."""
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
515 # Possibly could be integrated into our fork of avro/schema.py?
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parents:
diff changeset
516 if isinstance(items, MutableMapping):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
517 items = copy.copy(items)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
518 if items.get("name") and items.get("inVocab", True):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
519 items["name"] = avro_name(items["name"])
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
520
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
521 if "type" in items and items["type"] in (
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
522 saladp + "record",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
523 saladp + "enum",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
524 "record",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
525 "enum",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
526 ):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
527 if (hasattr(items, "get") and items.get("abstract")) or (
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
528 "abstract" in items
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
529 ):
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guerler
parents:
diff changeset
530 return items
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
531 if items["name"] in found:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
532 return cast(Text, items["name"])
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
533 found.add(items["name"])
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
534 for field in ("type", "items", "values", "fields"):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
535 if field in items:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
536 items[field] = make_valid_avro(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
537 items[field], alltypes, found, union=True
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
538 )
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
539 if "symbols" in items:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
540 items["symbols"] = [avro_name(sym) for sym in items["symbols"]]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
541 return items
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
542 if isinstance(items, MutableSequence):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
543 ret = []
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
544 for i in items:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
545 ret.append(make_valid_avro(i, alltypes, found, union=union))
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
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diff changeset
546 return ret
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
547 if union and isinstance(items, string_types):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
548 if items in alltypes and avro_name(items) not in found:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
549 return cast(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
550 Dict[Text, Text],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
551 make_valid_avro(alltypes[items], alltypes, found, union=union),
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
552 )
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
553 items = avro_name(items)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
554 return items
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
555
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
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diff changeset
556
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
557 def deepcopy_strip(item): # type: (Any) -> Any
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
558 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
559 Make a deep copy of list and dict objects.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
560
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
561 Intentionally do not copy attributes. This is to discard CommentedMap and
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
562 CommentedSeq metadata which is very expensive with regular copy.deepcopy.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
563 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
564
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
565 if isinstance(item, MutableMapping):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
566 return {k: deepcopy_strip(v) for k, v in iteritems(item)}
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
567 if isinstance(item, MutableSequence):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
568 return [deepcopy_strip(k) for k in item]
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guerler
parents:
diff changeset
569 return item
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
570
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
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diff changeset
571
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
572 def extend_and_specialize(items, loader):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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573 # type: (List[Dict[Text, Any]], Loader) -> List[Dict[Text, Any]]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
574 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
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diff changeset
575 Apply 'extend' and 'specialize' to fully materialize derived record types.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
576 """
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diff changeset
577
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diff changeset
578 items = deepcopy_strip(items)
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diff changeset
579 types = {i["name"]: i for i in items} # type: Dict[Text, Any]
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580 results = []
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guerler
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diff changeset
581
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
582 for stype in items:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
583 if "extends" in stype:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
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diff changeset
584 specs = {} # type: Dict[Text, Text]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
585 if "specialize" in stype:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
586 for spec in aslist(stype["specialize"]):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
587 specs[spec["specializeFrom"]] = spec["specializeTo"]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
588
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guerler
parents:
diff changeset
589 exfields = [] # type: List[Text]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
590 exsym = [] # type: List[Text]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
591 for ex in aslist(stype["extends"]):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
592 if ex not in types:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
593 raise ValidationException(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
594 "Extends {} in {} refers to invalid base type.".format(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
595 stype["extends"], stype["name"]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
596 )
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
597 )
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
598
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
599 basetype = copy.copy(types[ex])
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
600
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
601 if stype["type"] == "record":
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
602 if specs:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
603 basetype["fields"] = replace_type(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
604 basetype.get("fields", []), specs, loader, set()
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
605 )
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
606
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
607 for field in basetype.get("fields", []):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
608 if "inherited_from" not in field:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
609 field["inherited_from"] = ex
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
610
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
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diff changeset
611 exfields.extend(basetype.get("fields", []))
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
612 elif stype["type"] == "enum":
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
613 exsym.extend(basetype.get("symbols", []))
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
614
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
615 if stype["type"] == "record":
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
616 stype = copy.copy(stype)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
617 exfields.extend(stype.get("fields", []))
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
618 stype["fields"] = exfields
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
619
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
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diff changeset
620 fieldnames = set() # type: Set[Text]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
621 for field in stype["fields"]:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
622 if field["name"] in fieldnames:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
623 raise ValidationException(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
624 "Field name {} appears twice in {}".format(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
625 field["name"], stype["name"]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
626 )
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
627 )
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
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diff changeset
628 else:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
629 fieldnames.add(field["name"])
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
630 elif stype["type"] == "enum":
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
631 stype = copy.copy(stype)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
632 exsym.extend(stype.get("symbols", []))
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
633 stype["symbol"] = exsym
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guerler
parents:
diff changeset
634
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
635 types[stype["name"]] = stype
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
636
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
637 results.append(stype)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
638
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
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diff changeset
639 ex_types = {}
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
640 for result in results:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
641 ex_types[result["name"]] = result
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diff changeset
642
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diff changeset
643 extended_by = {} # type: Dict[Text, Text]
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parents:
diff changeset
644 for result in results:
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parents:
diff changeset
645 if "extends" in result:
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parents:
diff changeset
646 for ex in aslist(result["extends"]):
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parents:
diff changeset
647 if ex_types[ex].get("abstract"):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
648 add_dictlist(extended_by, ex, ex_types[result["name"]])
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
649 add_dictlist(extended_by, avro_name(ex), ex_types[ex])
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guerler
parents:
diff changeset
650
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parents:
diff changeset
651 for result in results:
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parents:
diff changeset
652 if result.get("abstract") and result["name"] not in extended_by:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
653 raise ValidationException(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
654 "{} is abstract but missing a concrete subtype".format(result["name"])
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parents:
diff changeset
655 )
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diff changeset
656
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parents:
diff changeset
657 for result in results:
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parents:
diff changeset
658 if "fields" in result:
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parents:
diff changeset
659 result["fields"] = replace_type(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
660 result["fields"], extended_by, loader, set()
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diff changeset
661 )
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diff changeset
662
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diff changeset
663 return results
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diff changeset
664
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665
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diff changeset
666 def make_avro(
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diff changeset
667 i, # type: List[Dict[Text, Any]]
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diff changeset
668 loader, # type: Loader
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parents:
diff changeset
669 ): # type: (...) -> List[Any]
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diff changeset
670
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diff changeset
671 j = extend_and_specialize(i, loader)
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diff changeset
672
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diff changeset
673 name_dict = {} # type: Dict[Text, Dict[Text, Any]]
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diff changeset
674 for entry in j:
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parents:
diff changeset
675 name_dict[entry["name"]] = entry
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diff changeset
676 avro = make_valid_avro(j, name_dict, set())
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parents:
diff changeset
677
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diff changeset
678 return [
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diff changeset
679 t
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parents:
diff changeset
680 for t in avro
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parents:
diff changeset
681 if isinstance(t, MutableMapping)
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parents:
diff changeset
682 and not t.get("abstract")
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parents:
diff changeset
683 and t.get("type") != "documentation"
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diff changeset
684 ]
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diff changeset
685
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diff changeset
686
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diff changeset
687 def make_avro_schema(
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688 i, # type: List[Any]
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diff changeset
689 loader, # type: Loader
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diff changeset
690 ): # type: (...) -> Names
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diff changeset
691 """
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parents:
diff changeset
692 All in one convenience function.
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diff changeset
693
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diff changeset
694 Call make_avro() and make_avro_schema_from_avro() separately if you need
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
695 the intermediate result for diagnostic output.
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diff changeset
696 """
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diff changeset
697 names = Names()
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diff changeset
698 avro = make_avro(i, loader)
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guerler
parents:
diff changeset
699 make_avsc_object(convert_to_dict(avro), names)
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diff changeset
700 return names
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diff changeset
701
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diff changeset
702
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diff changeset
703 def make_avro_schema_from_avro(avro):
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parents:
diff changeset
704 # type: (List[Union[Avro, Dict[Text, Text], Text]]) -> Names
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parents:
diff changeset
705 names = Names()
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parents:
diff changeset
706 make_avsc_object(convert_to_dict(avro), names)
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diff changeset
707 return names
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diff changeset
708
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diff changeset
709
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diff changeset
710 def shortname(inputid): # type: (Text) -> Text
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guerler
parents:
diff changeset
711 """Returns the last segment of the provided fragment or path."""
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parents:
diff changeset
712 parsed_id = urllib.parse.urlparse(inputid)
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parents:
diff changeset
713 if parsed_id.fragment:
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parents:
diff changeset
714 return parsed_id.fragment.split(u"/")[-1]
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guerler
parents:
diff changeset
715 return parsed_id.path.split(u"/")[-1]
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guerler
parents:
diff changeset
716
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diff changeset
717
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parents:
diff changeset
718 def print_inheritance(doc, stream):
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guerler
parents:
diff changeset
719 # type: (List[Dict[Text, Any]], IO[Any]) -> None
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guerler
parents:
diff changeset
720 """Write a Grapviz inheritance graph for the supplied document."""
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guerler
parents:
diff changeset
721 stream.write("digraph {\n")
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parents:
diff changeset
722 for entry in doc:
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guerler
parents:
diff changeset
723 if entry["type"] == "record":
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
724 label = name = shortname(entry["name"])
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
725 fields = entry.get("fields", [])
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guerler
parents:
diff changeset
726 if fields:
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guerler
parents:
diff changeset
727 label += "\\n* {}\\l".format(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
728 "\\l* ".join(shortname(field["name"]) for field in fields)
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guerler
parents:
diff changeset
729 )
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guerler
parents:
diff changeset
730 shape = "ellipse" if entry.get("abstract") else "box"
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guerler
parents:
diff changeset
731 stream.write('"{}" [shape={} label="{}"];\n'.format(name, shape, label))
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
732 if "extends" in entry:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
733 for target in aslist(entry["extends"]):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
734 stream.write('"{}" -> "{}";\n'.format(shortname(target), name))
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
735 stream.write("}\n")
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parents:
diff changeset
736
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diff changeset
737
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diff changeset
738 def print_fieldrefs(doc, loader, stream):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
739 # type: (List[Dict[Text, Any]], Loader, IO[Any]) -> None
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
740 """Write a GraphViz graph of the relationships between the fields."""
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
741 obj = extend_and_specialize(doc, loader)
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guerler
parents:
diff changeset
742
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parents:
diff changeset
743 primitives = set(
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guerler
parents:
diff changeset
744 (
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
745 "http://www.w3.org/2001/XMLSchema#string",
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guerler
parents:
diff changeset
746 "http://www.w3.org/2001/XMLSchema#boolean",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
747 "http://www.w3.org/2001/XMLSchema#int",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
748 "http://www.w3.org/2001/XMLSchema#long",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
749 saladp + "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
750 saladp + "enum",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
751 saladp + "array",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
752 saladp + "record",
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guerler
parents:
diff changeset
753 saladp + "Any",
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guerler
parents:
diff changeset
754 )
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
755 )
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guerler
parents:
diff changeset
756
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
757 stream.write("digraph {\n")
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
758 for entry in obj:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
759 if entry.get("abstract"):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
760 continue
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
761 if entry["type"] == "record":
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
762 label = shortname(entry["name"])
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
763 for field in entry.get("fields", []):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
764 found = set() # type: Set[Text]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
765 field_name = shortname(field["name"])
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
766 replace_type(field["type"], {}, loader, found, find_embeds=False)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
767 for each_type in found:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
768 if each_type not in primitives:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
769 stream.write(
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guerler
parents:
diff changeset
770 '"{}" -> "{}" [label="{}"];\n'.format(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
771 label, shortname(each_type), field_name
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
772 )
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
773 )
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
774 stream.write("}\n")