Mercurial > repos > shellac > sam_consensus_v3

annotate env/lib/python3.9/site-packages/schema_salad/schema.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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1 """Functions to process Schema Salad schemas."""
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2
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3 import copy
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4 import hashlib
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5 from typing import (
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6 IO,
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7 Any,
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8 Dict,
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9 List,
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10 Mapping,
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11 MutableMapping,
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12 MutableSequence,
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13 Optional,
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14 Set,
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15 Tuple,
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16 TypeVar,
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17 Union,
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18 cast,
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19 )
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20 from urllib.parse import urldefrag, urlparse
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21
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22 from pkg_resources import resource_stream
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23 from ruamel import yaml
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24 from ruamel.yaml.comments import CommentedMap, CommentedSeq
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25
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26 from schema_salad.utils import (
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27 CacheType,
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28 ResolveType,
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29 add_dictlist,
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30 aslist,
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31 convert_to_dict,
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32 flatten,
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33 json_dumps,
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34 )
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35
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36 from . import _logger, jsonld_context, ref_resolver, validate
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37 from .avro.schema import Names, SchemaParseException, make_avsc_object
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38 from .exceptions import (
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39 ClassValidationException,
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40 SchemaSaladException,
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41 ValidationException,
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42 )
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43 from .ref_resolver import Loader
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44 from .sourceline import SourceLine, add_lc_filename, relname
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45
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46 SALAD_FILES = (
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47 "metaschema.yml",
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48 "metaschema_base.yml",
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49 "salad.md",
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50 "field_name.yml",
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51 "import_include.md",
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52 "link_res.yml",
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53 "ident_res.yml",
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54 "vocab_res.yml",
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55 "vocab_res.yml",
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56 "field_name_schema.yml",
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57 "field_name_src.yml",
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58 "field_name_proc.yml",
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59 "ident_res_schema.yml",
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60 "ident_res_src.yml",
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61 "ident_res_proc.yml",
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62 "link_res_schema.yml",
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63 "link_res_src.yml",
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64 "link_res_proc.yml",
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65 "vocab_res_schema.yml",
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66 "vocab_res_src.yml",
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67 "vocab_res_proc.yml",
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68 "map_res.yml",
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69 "map_res_schema.yml",
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70 "map_res_src.yml",
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71 "map_res_proc.yml",
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72 "typedsl_res.yml",
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73 "typedsl_res_schema.yml",
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74 "typedsl_res_src.yml",
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75 "typedsl_res_proc.yml",
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76 "sfdsl_res.yml",
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77 "sfdsl_res_schema.yml",
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78 "sfdsl_res_src.yml",
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79 "sfdsl_res_proc.yml",
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80 )
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81
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82 saladp = "https://w3id.org/cwl/salad#"
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83
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84
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85 def get_metaschema() -> Tuple[Names, List[Dict[str, str]], Loader]:
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86 """Instantiate the metaschema."""
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87 loader = ref_resolver.Loader(
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88 {
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89 "Any": saladp + "Any",
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90 "ArraySchema": saladp + "ArraySchema",
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91 "Array_symbol": saladp + "ArraySchema/type/Array_symbol",
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92 "DocType": saladp + "DocType",
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93 "Documentation": saladp + "Documentation",
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94 "Documentation_symbol": saladp + "Documentation/type/Documentation_symbol",
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95 "Documented": saladp + "Documented",
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96 "EnumSchema": saladp + "EnumSchema",
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97 "Enum_symbol": saladp + "EnumSchema/type/Enum_symbol",
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98 "JsonldPredicate": saladp + "JsonldPredicate",
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99 "NamedType": saladp + "NamedType",
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100 "PrimitiveType": saladp + "PrimitiveType",
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101 "RecordField": saladp + "RecordField",
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102 "RecordSchema": saladp + "RecordSchema",
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103 "Record_symbol": saladp + "RecordSchema/type/Record_symbol",
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104 "SaladEnumSchema": saladp + "SaladEnumSchema",
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105 "SaladRecordField": saladp + "SaladRecordField",
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106 "SaladRecordSchema": saladp + "SaladRecordSchema",
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107 "SchemaDefinedType": saladp + "SchemaDefinedType",
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108 "SpecializeDef": saladp + "SpecializeDef",
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109 "_container": saladp + "JsonldPredicate/_container",
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110 "_id": {"@id": saladp + "_id", "@type": "@id", "identity": True},
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111 "_type": saladp + "JsonldPredicate/_type",
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112 "abstract": saladp + "SaladRecordSchema/abstract",
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113 "array": saladp + "array",
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114 "boolean": "http://www.w3.org/2001/XMLSchema#boolean",
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115 "dct": "http://purl.org/dc/terms/",
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116 "default": {"@id": saladp + "default", "noLinkCheck": True},
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117 "doc": "rdfs:comment",
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118 "docAfter": {"@id": saladp + "docAfter", "@type": "@id"},
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119 "docChild": {"@id": saladp + "docChild", "@type": "@id"},
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120 "docParent": {"@id": saladp + "docParent", "@type": "@id"},
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121 "documentRoot": saladp + "SchemaDefinedType/documentRoot",
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122 "documentation": saladp + "documentation",
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123 "double": "http://www.w3.org/2001/XMLSchema#double",
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124 "enum": saladp + "enum",
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125 "extends": {"@id": saladp + "extends", "@type": "@id", "refScope": 1},
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126 "fields": {
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127 "@id": saladp + "fields",
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128 "mapPredicate": "type",
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129 "mapSubject": "name",
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130 },
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131 "float": "http://www.w3.org/2001/XMLSchema#float",
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132 "identity": saladp + "JsonldPredicate/identity",
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133 "inVocab": saladp + "NamedType/inVocab",
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134 "int": "http://www.w3.org/2001/XMLSchema#int",
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135 "items": {"@id": saladp + "items", "@type": "@vocab", "refScope": 2},
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136 "jsonldPredicate": "sld:jsonldPredicate",
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137 "long": "http://www.w3.org/2001/XMLSchema#long",
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138 "mapPredicate": saladp + "JsonldPredicate/mapPredicate",
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139 "mapSubject": saladp + "JsonldPredicate/mapSubject",
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140 "name": "@id",
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141 "noLinkCheck": saladp + "JsonldPredicate/noLinkCheck",
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142 "null": saladp + "null",
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143 "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
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144 "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
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145 "record": saladp + "record",
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146 "refScope": saladp + "JsonldPredicate/refScope",
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147 "sld": saladp,
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148 "specialize": {
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149 "@id": saladp + "specialize",
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150 "mapPredicate": "specializeTo",
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151 "mapSubject": "specializeFrom",
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152 },
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153 "specializeFrom": {
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154 "@id": saladp + "specializeFrom",
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155 "@type": "@id",
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156 "refScope": 1,
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157 },
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158 "specializeTo": {
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159 "@id": saladp + "specializeTo",
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160 "@type": "@id",
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161 "refScope": 1,
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162 },
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163 "string": "http://www.w3.org/2001/XMLSchema#string",
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164 "subscope": saladp + "JsonldPredicate/subscope",
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165 "symbols": {"@id": saladp + "symbols", "@type": "@id", "identity": True},
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166 "type": {
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167 "@id": saladp + "type",
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168 "@type": "@vocab",
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169 "refScope": 2,
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170 "typeDSL": True,
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171 },
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172 "typeDSL": saladp + "JsonldPredicate/typeDSL",
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173 "xsd": "http://www.w3.org/2001/XMLSchema#",
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174 }
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175 )
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176
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177 for salad in SALAD_FILES:
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178 with resource_stream("schema_salad", "metaschema/" + salad) as stream:
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179 loader.cache["https://w3id.org/cwl/" + salad] = stream.read().decode(
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180 "UTF-8"
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181 )
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182
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183 with resource_stream("schema_salad", "metaschema/metaschema.yml") as stream:
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184 loader.cache["https://w3id.org/cwl/salad"] = stream.read().decode("UTF-8")
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185
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186 j = yaml.main.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 j2 = loader.resolve_all(j, saladp)[0]
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189
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190 if not isinstance(j2, list):
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191 _logger.error("%s", j2)
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192 raise SchemaParseException(f"Not a list: {j2}")
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193 else:
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194 sch_obj = make_avro(j2, loader)
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195 try:
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196 sch_names = make_avro_schema_from_avro(sch_obj)
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197 except SchemaParseException:
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198 _logger.error("Metaschema error, avro was:\n%s", json_dumps(sch_obj, indent=4))
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199 raise
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200 validate_doc(sch_names, j2, loader, strict=True)
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201 return (sch_names, j2, loader)
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202
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203
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204 def add_namespaces(
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205 metadata: Mapping[str, Any], namespaces: MutableMapping[str, str]
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206 ) -> None:
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207 """Collect the provided namespaces, checking for conflicts."""
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208 for key, value in metadata.items():
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209 if key not in namespaces:
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210 namespaces[key] = value
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211 elif namespaces[key] != value:
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212 raise ValidationException(
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213 "Namespace prefix '{}' has conflicting definitions '{}'"
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214 " and '{}'.".format(key, namespaces[key], value)
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215 )
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216
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217
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218 def collect_namespaces(metadata: Mapping[str, Any]) -> Dict[str, str]:
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219 """Walk through the metadata object, collecting namespace declarations."""
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220 namespaces = {} # type: Dict[str, str]
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221 if "$import_metadata" in metadata:
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222 for value in metadata["$import_metadata"].values():
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223 add_namespaces(collect_namespaces(value), namespaces)
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224 if "$namespaces" in metadata:
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225 add_namespaces(metadata["$namespaces"], namespaces)
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226 return namespaces
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227
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228
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229 schema_type = Tuple[Loader, Union[Names, SchemaParseException], Dict[str, Any], Loader]
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230
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231
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232 def load_schema(
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233 schema_ref: ResolveType,
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234 cache: Optional[CacheType] = None,
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235 ) -> schema_type:
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236 """
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237 Load a schema that can be used to validate documents using load_and_validate.
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238
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239 return: document_loader, avsc_names, schema_metadata, metaschema_loader
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240 """
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241
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242 metaschema_names, _metaschema_doc, metaschema_loader = get_metaschema()
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243 if cache is not None:
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244 metaschema_loader.cache.update(cache)
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245 schema_doc, schema_metadata = metaschema_loader.resolve_ref(schema_ref, "")
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246
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247 if not isinstance(schema_doc, MutableSequence):
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248 raise ValidationException("Schema reference must resolve to a list.")
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249
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250 validate_doc(metaschema_names, schema_doc, metaschema_loader, True)
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251 metactx = schema_metadata.get("@context", {})
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252 metactx.update(collect_namespaces(schema_metadata))
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253 schema_ctx = jsonld_context.salad_to_jsonld_context(schema_doc, metactx)[0]
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254
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255 # Create the loader that will be used to load the target document.
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256 document_loader = Loader(schema_ctx, cache=cache)
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257
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258 # Make the Avro validation that will be used to validate the target
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259 # document
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260 avsc_names = make_avro_schema(schema_doc, document_loader)
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261
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262 return document_loader, avsc_names, schema_metadata, metaschema_loader
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263
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264
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265 def load_and_validate(
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266 document_loader: Loader,
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267 avsc_names: Names,
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268 document: Union[CommentedMap, str],
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269 strict: bool,
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270 strict_foreign_properties: bool = False,
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271 ) -> Tuple[Any, Dict[str, Any]]:
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272 """Load a document and validate it with the provided schema.
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273
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274 return data, metadata
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275 """
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276 try:
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277 if isinstance(document, CommentedMap):
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278 data, metadata = document_loader.resolve_all(
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279 document,
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280 document["id"],
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281 checklinks=True,
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282 strict_foreign_properties=strict_foreign_properties,
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283 )
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284 else:
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285 data, metadata = document_loader.resolve_ref(
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286 document,
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287 checklinks=True,
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288 strict_foreign_properties=strict_foreign_properties,
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289 )
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290
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291 validate_doc(
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292 avsc_names,
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293 data,
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294 document_loader,
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295 strict,
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296 strict_foreign_properties=strict_foreign_properties,
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297 )
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298 except ValidationException as exc:
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299 raise ValidationException("", None, [exc]) from exc
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300 return data, metadata
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301
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302
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303 def validate_doc(
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304 schema_names: Names,
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305 doc: ResolveType,
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306 loader: Loader,
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307 strict: bool,
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308 strict_foreign_properties: bool = False,
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309 ) -> None:
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310 """Validate a document using the provided schema."""
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311 has_root = False
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312 for root in schema_names.names.values():
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313 if (hasattr(root, "get_prop") and root.get_prop("documentRoot")) or (
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314 "documentRoot" in root.props
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315 ):
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316 has_root = True
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317 break
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318
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319 if not has_root:
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320 raise ValidationException("No document roots defined in the schema")
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321
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322 if isinstance(doc, MutableSequence):
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323 vdoc = doc
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324 elif isinstance(doc, CommentedMap):
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325 vdoc = CommentedSeq([doc])
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326 vdoc.lc.add_kv_line_col(0, [doc.lc.line, doc.lc.col])
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327 vdoc.lc.filename = doc.lc.filename
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328 else:
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329 raise ValidationException("Document must be dict or list")
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330
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331 roots = []
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332 for root in schema_names.names.values():
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333 if (hasattr(root, "get_prop") and root.get_prop("documentRoot")) or (
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334 root.props.get("documentRoot")
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335 ):
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336 roots.append(root)
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337
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338 anyerrors = []
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339 for pos, item in enumerate(vdoc):
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340 sourceline = SourceLine(vdoc, pos, str)
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341 success = False
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342 for root in roots:
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343 success = validate.validate_ex(
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344 root,
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345 item,
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346 loader.identifiers,
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347 strict,
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348 foreign_properties=loader.foreign_properties,
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349 raise_ex=False,
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350 skip_foreign_properties=loader.skip_schemas,
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351 strict_foreign_properties=strict_foreign_properties,
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352 )
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353 if success:
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354 break
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355
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356 if not success:
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357 errors = [] # type: List[SchemaSaladException]
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358 for root in roots:
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359 if hasattr(root, "get_prop"):
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360 name = root.get_prop("name")
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361 elif hasattr(root, "name"):
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362 name = root.name
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363
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364 try:
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365 validate.validate_ex(
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366 root,
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367 item,
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368 loader.identifiers,
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369 strict,
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370 foreign_properties=loader.foreign_properties,
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371 raise_ex=True,
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372 skip_foreign_properties=loader.skip_schemas,
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373 strict_foreign_properties=strict_foreign_properties,
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374 )
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375 except ClassValidationException as exc1:
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376 errors = [
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shellac
parents:
diff changeset
377 ClassValidationException(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
378 f"tried `{name}` but", sourceline, [exc1]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
379 )
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shellac
parents:
diff changeset
380 ]
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shellac
parents:
diff changeset
381 break
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shellac
parents:
diff changeset
382 except ValidationException as exc2:
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shellac
parents:
diff changeset
383 errors.append(
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parents:
diff changeset
384 ValidationException(f"tried `{name}` but", sourceline, [exc2])
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shellac
parents:
diff changeset
385 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
386
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parents:
diff changeset
387 objerr = "Invalid"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
388 for ident in loader.identifiers:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
389 if ident in item:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
390 objerr = "Object `{}` is not valid because".format(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
391 relname(item[ident])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
392 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
393 break
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parents:
diff changeset
394 anyerrors.append(ValidationException(objerr, sourceline, errors, "-"))
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shellac
parents:
diff changeset
395 if anyerrors:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
396 raise ValidationException("", None, anyerrors, "*")
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shellac
parents:
diff changeset
397
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shellac
parents:
diff changeset
398
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shellac
parents:
diff changeset
399 def get_anon_name(
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parents:
diff changeset
400 rec: MutableMapping[str, Union[str, Dict[str, str], List[str]]]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
401 ) -> str:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
402 """Calculate a reproducible name for anonymous types."""
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shellac
parents:
diff changeset
403 if "name" in rec:
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shellac
parents:
diff changeset
404 name = rec["name"]
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shellac
parents:
diff changeset
405 if isinstance(name, str):
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parents:
diff changeset
406 return name
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
407 raise ValidationException(f"Expected name field to be a string, was {name}")
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shellac
parents:
diff changeset
408 anon_name = ""
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shellac
parents:
diff changeset
409 if rec["type"] in ("enum", saladp + "enum"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
410 for sym in rec["symbols"]:
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parents:
diff changeset
411 anon_name += sym
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shellac
parents:
diff changeset
412 return "enum_" + hashlib.sha1(anon_name.encode("UTF-8")).hexdigest() # nosec
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
413 if rec["type"] in ("record", saladp + "record"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
414 for field in rec["fields"]:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
415 if isinstance(field, Mapping):
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parents:
diff changeset
416 anon_name += field["name"]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
417 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
418 raise ValidationException(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
419 "Expected entries in 'fields' to also be maps, was {}.".format(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
420 field
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
421 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
422 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
423 return "record_" + hashlib.sha1(anon_name.encode("UTF-8")).hexdigest() # nosec
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
424 if rec["type"] in ("array", saladp + "array"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
425 return ""
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
426 raise ValidationException("Expected enum or record, was {}".format(rec["type"]))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
427
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
428
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
429 def replace_type(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
430 items: Any,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
431 spec: Dict[str, Any],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
432 loader: Loader,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
433 found: Set[str],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
434 find_embeds: bool = True,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
435 deepen: bool = True,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
436 ) -> Any:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
437 """ Go through and replace types in the 'spec' mapping"""
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
438
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
439 if isinstance(items, MutableMapping):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
440 # recursively check these fields for types to replace
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
441 if items.get("type") in ("record", "enum") and items.get("name"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
442 if items["name"] in found:
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shellac
parents:
diff changeset
443 return items["name"]
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shellac
parents:
diff changeset
444 found.add(items["name"])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
445
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
446 if not deepen:
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shellac
parents:
diff changeset
447 return items
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
448
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
449 items = copy.copy(items)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
450 if not items.get("name"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
451 items["name"] = get_anon_name(items)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
452 for name in ("type", "items", "fields"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
453 if name in items:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
454 items[name] = replace_type(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
455 items[name],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
456 spec,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
457 loader,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
458 found,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
459 find_embeds=find_embeds,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
460 deepen=find_embeds,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
461 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
462 if isinstance(items[name], MutableSequence):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
463 items[name] = flatten(items[name])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
464
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
465 return items
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
466 if isinstance(items, MutableSequence):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
467 # recursively transform list
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
468 return [
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
469 replace_type(i, spec, loader, found, find_embeds=find_embeds, deepen=deepen)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
470 for i in items
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
471 ]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
472 if isinstance(items, str):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
473 # found a string which is a symbol corresponding to a type.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
474 replace_with = None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
475 if items in loader.vocab:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
476 # If it's a vocabulary term, first expand it to its fully qualified
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
477 # URI
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
478 items = loader.vocab[items]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
479
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
480 if items in spec:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
481 # Look up in specialization map
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
482 replace_with = spec[items]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
483
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
484 if replace_with:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
485 return replace_type(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
486 replace_with, spec, loader, found, find_embeds=find_embeds
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
487 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
488 found.add(items)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
489 return items
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
490
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
491
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
492 def avro_name(url: str) -> str:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
493 """
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
494 Turn a URL into an Avro-safe name.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
495
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
496 If the URL has no fragment, return this plain URL.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
497
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
498 Extract either the last part of the URL fragment past the slash, otherwise
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
499 the whole fragment.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
500 """
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
501 frg = urldefrag(url)[1]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
502 if frg != "":
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
503 if "/" in frg:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
504 return frg[frg.rindex("/") + 1 :]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
505 return frg
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shellac
parents:
diff changeset
506 return url
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shellac
parents:
diff changeset
507
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shellac
parents:
diff changeset
508
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
509 Avro = TypeVar("Avro", MutableMapping[str, Any], MutableSequence[Any], str)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
510
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shellac
parents:
diff changeset
511
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shellac
parents:
diff changeset
512 def make_valid_avro(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
513 items: Avro,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
514 alltypes: Dict[str, Dict[str, Any]],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
515 found: Set[str],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
516 union: bool = False,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
517 ) -> Union[
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
518 Avro, MutableMapping[str, str], str, List[Union[Any, MutableMapping[str, str], str]]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
519 ]:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
520 """Convert our schema to be more avro like."""
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
521 # Possibly could be integrated into our fork of avro/schema.py?
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
522 if isinstance(items, MutableMapping):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
523 avro = copy.copy(items)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
524 if avro.get("name") and avro.get("inVocab", True):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
525 avro["name"] = avro_name(avro["name"])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
526
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
527 if "type" in avro and avro["type"] in (
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
528 saladp + "record",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
529 saladp + "enum",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
530 "record",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
531 "enum",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
532 ):
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parents:
diff changeset
533 if (hasattr(avro, "get") and avro.get("abstract")) or ("abstract" in avro):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
534 return avro
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
535 if avro["name"] in found:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
536 return cast(str, avro["name"])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
537 found.add(avro["name"])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
538 for field in ("type", "items", "values", "fields"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
539 if field in avro:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
540 avro[field] = make_valid_avro(avro[field], alltypes, found, union=True)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
541 if "symbols" in avro:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
542 avro["symbols"] = [avro_name(sym) for sym in avro["symbols"]]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
543 return avro
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
544 if isinstance(items, MutableSequence):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
545 ret = []
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
546 for i in items:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
547 ret.append(make_valid_avro(i, alltypes, found, union=union))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
548 return ret
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
549 if union and isinstance(items, str):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
550 if items in alltypes and avro_name(items) not in found:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
551 return make_valid_avro(alltypes[items], alltypes, found, union=union)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
552 return avro_name(items)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
553 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
554 return items
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
555
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shellac
parents:
diff changeset
556
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
557 def deepcopy_strip(item: Any) -> Any:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
558 """
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
559 Make a deep copy of list and dict objects.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
560
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
561 Intentionally do not copy attributes. This is to discard CommentedMap and
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
562 CommentedSeq metadata which is very expensive with regular copy.deepcopy.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
563 """
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
564
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
565 if isinstance(item, MutableMapping):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
566 return {k: deepcopy_strip(v) for k, v in item.items()}
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
567 if isinstance(item, MutableSequence):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
568 return [deepcopy_strip(k) for k in item]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
569 return item
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shellac
parents:
diff changeset
570
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shellac
parents:
diff changeset
571
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shellac
parents:
diff changeset
572 def extend_and_specialize(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
573 items: List[Dict[str, Any]], loader: Loader
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
574 ) -> List[Dict[str, Any]]:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
575 """
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
576 Apply 'extend' and 'specialize' to fully materialize derived record types.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
577 """
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shellac
parents:
diff changeset
578
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shellac
parents:
diff changeset
579 items2 = deepcopy_strip(items)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
580 types = {i["name"]: i for i in items2} # type: Dict[str, Any]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
581 results = []
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
582
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
583 for stype in items2:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
584 if "extends" in stype:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
585 specs = {} # type: Dict[str, str]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
586 if "specialize" in stype:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
587 for spec in aslist(stype["specialize"]):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
588 specs[spec["specializeFrom"]] = spec["specializeTo"]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
589
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
590 exfields = [] # type: List[str]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
591 exsym = [] # type: List[str]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
592 for ex in aslist(stype["extends"]):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
593 if ex not in types:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
594 raise ValidationException(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
595 "Extends {} in {} refers to invalid base type.".format(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
596 stype["extends"], stype["name"]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
597 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
598 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
599
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
600 basetype = copy.copy(types[ex])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
601
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
602 if stype["type"] == "record":
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
603 if specs:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
604 basetype["fields"] = replace_type(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
605 basetype.get("fields", []), specs, loader, set()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
606 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
607
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
608 for field in basetype.get("fields", []):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
609 if "inherited_from" not in field:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
610 field["inherited_from"] = ex
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
611
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
612 exfields.extend(basetype.get("fields", []))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
613 elif stype["type"] == "enum":
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
614 exsym.extend(basetype.get("symbols", []))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
615
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
616 if stype["type"] == "record":
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
617 stype = copy.copy(stype)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
618 exfields.extend(stype.get("fields", []))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
619 stype["fields"] = exfields
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
620
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
621 fieldnames = set() # type: Set[str]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
622 for field in stype["fields"]:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
623 if field["name"] in fieldnames:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
624 raise ValidationException(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
625 "Field name {} appears twice in {}".format(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
626 field["name"], stype["name"]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
627 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
628 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
629 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
630 fieldnames.add(field["name"])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
631 elif stype["type"] == "enum":
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
632 stype = copy.copy(stype)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
633 exsym.extend(stype.get("symbols", []))
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shellac
parents:
diff changeset
634 stype["symbol"] = exsym
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shellac
parents:
diff changeset
635
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
636 types[stype["name"]] = stype
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shellac
parents:
diff changeset
637
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
638 results.append(stype)
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parents:
diff changeset
639
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
640 ex_types = {}
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shellac
parents:
diff changeset
641 for result in results:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
642 ex_types[result["name"]] = result
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shellac
parents:
diff changeset
643
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
644 extended_by = {} # type: Dict[str, str]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
645 for result in results:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
646 if "extends" in result:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
647 for ex in aslist(result["extends"]):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
648 if ex_types[ex].get("abstract"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
649 add_dictlist(extended_by, ex, ex_types[result["name"]])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
650 add_dictlist(extended_by, avro_name(ex), ex_types[ex])
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shellac
parents:
diff changeset
651
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shellac
parents:
diff changeset
652 for result in results:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
653 if result.get("abstract") and result["name"] not in extended_by:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
654 raise ValidationException(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
655 "{} is abstract but missing a concrete subtype".format(result["name"])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
656 )
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shellac
parents:
diff changeset
657
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shellac
parents:
diff changeset
658 for result in results:
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shellac
parents:
diff changeset
659 if "fields" in result:
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shellac
parents:
diff changeset
660 result["fields"] = replace_type(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
661 result["fields"], extended_by, loader, set()
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shellac
parents:
diff changeset
662 )
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shellac
parents:
diff changeset
663
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shellac
parents:
diff changeset
664 return results
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shellac
parents:
diff changeset
665
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shellac
parents:
diff changeset
666
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shellac
parents:
diff changeset
667 def make_avro(
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shellac
parents:
diff changeset
668 i: List[Dict[str, Any]],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
669 loader: Loader,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
670 ) -> List[Any]:
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shellac
parents:
diff changeset
671
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shellac
parents:
diff changeset
672 j = extend_and_specialize(i, loader)
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shellac
parents:
diff changeset
673
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shellac
parents:
diff changeset
674 name_dict = {} # type: Dict[str, Dict[str, Any]]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
675 for entry in j:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
676 name_dict[entry["name"]] = entry
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
677 avro = make_valid_avro(j, name_dict, set())
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
678
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
679 return [
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
680 t
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
681 for t in avro
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
682 if isinstance(t, MutableMapping)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
683 and not t.get("abstract")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
684 and t.get("type") != "documentation"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
685 ]
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shellac
parents:
diff changeset
686
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shellac
parents:
diff changeset
687
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shellac
parents:
diff changeset
688 def make_avro_schema(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
689 i: List[Any],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
690 loader: Loader,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
691 ) -> Names:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
692 """
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
693 All in one convenience function.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
694
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
695 Call make_avro() and make_avro_schema_from_avro() separately if you need
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
696 the intermediate result for diagnostic output.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
697 """
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shellac
parents:
diff changeset
698 names = Names()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
699 avro = make_avro(i, loader)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
700 make_avsc_object(convert_to_dict(avro), names)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
701 return names
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
702
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
703
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
704 def make_avro_schema_from_avro(avro: List[Union[Avro, Dict[str, str], str]]) -> Names:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
705 names = Names()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
706 make_avsc_object(convert_to_dict(avro), names)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
707 return names
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
708
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
709
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
710 def shortname(inputid: str) -> str:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
711 """Returns the last segment of the provided fragment or path."""
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
712 parsed_id = urlparse(inputid)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
713 if parsed_id.fragment:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
714 return parsed_id.fragment.split("/")[-1]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
715 return parsed_id.path.split("/")[-1]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
716
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
717
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
718 def print_inheritance(doc: List[Dict[str, Any]], stream: IO[Any]) -> None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
719 """Write a Grapviz inheritance graph for the supplied document."""
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
720 stream.write("digraph {\n")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
721 for entry in doc:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
722 if entry["type"] == "record":
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
723 label = name = shortname(entry["name"])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
724 fields = entry.get("fields", [])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
725 if fields:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
726 label += "\\n* {}\\l".format(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
727 "\\l* ".join(shortname(field["name"]) for field in fields)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
728 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
729 shape = "ellipse" if entry.get("abstract") else "box"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
730 stream.write(f'"{name}" [shape={shape} label="{label}"];\n')
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
731 if "extends" in entry:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
732 for target in aslist(entry["extends"]):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
733 stream.write('"{}" -> "{}";\n'.format(shortname(target), name))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
734 stream.write("}\n")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
735
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
736
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
737 def print_fieldrefs(doc: List[Dict[str, Any]], loader: Loader, stream: IO[Any]) -> None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
738 """Write a GraphViz graph of the relationships between the fields."""
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
739 obj = extend_and_specialize(doc, loader)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
740
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
741 primitives = {
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
742 "http://www.w3.org/2001/XMLSchema#string",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
743 "http://www.w3.org/2001/XMLSchema#boolean",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
744 "http://www.w3.org/2001/XMLSchema#int",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
745 "http://www.w3.org/2001/XMLSchema#long",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
746 saladp + "null",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
747 saladp + "enum",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
748 saladp + "array",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
749 saladp + "record",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
750 saladp + "Any",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
751 }
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
752
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
753 stream.write("digraph {\n")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
754 for entry in obj:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
755 if entry.get("abstract"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
756 continue
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
757 if entry["type"] == "record":
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
758 label = shortname(entry["name"])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
759 for field in entry.get("fields", []):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
760 found = set() # type: Set[str]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
761 field_name = shortname(field["name"])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
762 replace_type(field["type"], {}, loader, found, find_embeds=False)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
763 for each_type in found:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
764 if each_type not in primitives:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
765 stream.write(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
766 '"{}" -> "{}" [label="{}"];\n'.format(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
767 label, shortname(each_type), field_name
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
768 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
769 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
770 stream.write("}\n")