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annotate env/lib/python3.7/site-packages/schema_salad/metaschema/salad.md @ 0:26e78fe6e8c4 draft

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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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1 # Semantic Annotations for Linked Avro Data (SALAD)
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2
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3 Author:
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4
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5 * Peter Amstutz <pamstutz@veritasgenetics.com>, Veritas Genetics
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6
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7 Contributors:
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8
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9 * The developers of Apache Avro
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10 * The developers of JSON-LD
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11 * Nebojša Tijanić <nebojsa.tijanic@sbgenomics.com>, Seven Bridges Genomics
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12
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13 # Abstract
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14
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15 Salad is a schema language for describing structured linked data documents
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16 in JSON or YAML documents. A Salad schema provides rules for
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17 preprocessing, structural validation, and link checking for documents
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18 described by a Salad schema. Salad builds on JSON-LD and the Apache Avro
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19 data serialization system, and extends Avro with features for rich data
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20 modeling such as inheritance, template specialization, object identifiers,
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21 and object references. Salad was developed to provide a bridge between the
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22 record oriented data modeling supported by Apache Avro and the Semantic
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23 Web.
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24
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25 # Status of This Document
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26
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27 This document is the product of the [Common Workflow Language working
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28 group](https://groups.google.com/forum/#!forum/common-workflow-language). The
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29 latest version of this document is available in the "schema_salad" repository at
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30
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31 https://github.com/common-workflow-language/schema_salad
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32
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33 The products of the CWL working group (including this document) are made available
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34 under the terms of the Apache License, version 2.0.
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35
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36 <!--ToC-->
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37
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38 # Introduction
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39
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40 The JSON data model is an extremely popular way to represent structured
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41 data. It is attractive because of its relative simplicity and is a
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42 natural fit with the standard types of many programming languages.
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43 However, this simplicity means that basic JSON lacks expressive features
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44 useful for working with complex data structures and document formats, such
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45 as schemas, object references, and namespaces.
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46
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47 JSON-LD is a W3C standard providing a way to describe how to interpret a
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48 JSON document as Linked Data by means of a "context". JSON-LD provides a
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49 powerful solution for representing object references and namespaces in JSON
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50 based on standard web URIs, but is not itself a schema language. Without a
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51 schema providing a well defined structure, it is difficult to process an
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52 arbitrary JSON-LD document as idiomatic JSON because there are many ways to
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53 express the same data that are logically equivalent but structurally
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54 distinct.
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55
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56 Several schema languages exist for describing and validating JSON data,
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57 such as the Apache Avro data serialization system, however none understand
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58 linked data. As a result, to fully take advantage of JSON-LD to build the
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59 next generation of linked data applications, one must maintain separate
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60 JSON schema, JSON-LD context, RDF schema, and human documentation, despite
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61 significant overlap of content and obvious need for these documents to stay
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62 synchronized.
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63
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64 Schema Salad is designed to address this gap. It provides a schema
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65 language and processing rules for describing structured JSON content
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66 permitting URI resolution and strict document validation. The schema
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67 language supports linked data through annotations that describe the linked
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68 data interpretation of the content, enables generation of JSON-LD context
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69 and RDF schema, and production of RDF triples by applying the JSON-LD
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70 context. The schema language also provides for robust support of inline
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71 documentation.
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72
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73 ## Introduction to v1.1
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74
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75 This is the third version of of the Schema Salad specification. It is
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76 developed concurrently with v1.1 of the Common Workflow Language for use in
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77 specifying the Common Workflow Language, however Schema Salad is intended to be
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78 useful to a broader audience. Compared to the v1.0 schema salad
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79 specification, the following changes have been made:
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80
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81 * Support for `default` values on record fields to specify default values
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82 * Add subscoped fields (fields which introduce a new inner scope for identifiers)
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83 * Add the *inVocab* flag (default true) to indicate if a type is added to the vocabulary of well known terms or must be prefixed
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84 * Add *secondaryFilesDSL* micro DSL (domain specific language) to convert text strings to a secondaryFiles record type used in CWL
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85 * The `$mixin` feature has been removed from the specification, as it
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86 is poorly documented, not included in conformance testing,
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87 and not widely supported.
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88
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89 ## References to Other Specifications
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90
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91 **Javascript Object Notation (JSON)**: http://json.org
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92
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93 **JSON Linked Data (JSON-LD)**: http://json-ld.org
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94
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95 **YAML**: https://yaml.org/spec/1.2/spec.html
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96
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97 **Avro**: https://avro.apache.org/docs/current/spec.html
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98
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99 **Uniform Resource Identifier (URI) Generic Syntax**: https://tools.ietf.org/html/rfc3986)
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100
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101 **Resource Description Framework (RDF)**: http://www.w3.org/RDF/
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102
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103 **UTF-8**: https://www.ietf.org/rfc/rfc2279.txt)
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104
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105 ## Scope
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106
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107 This document describes the syntax, data model, algorithms, and schema
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108 language for working with Salad documents. It is not intended to document
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109 a specific implementation of Salad, however it may serve as a reference for
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110 the behavior of conforming implementations.
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111
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112 ## Terminology
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113
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114 The terminology used to describe Salad documents is defined in the Concepts
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115 section of the specification. The terms defined in the following list are
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116 used in building those definitions and in describing the actions of an
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117 Salad implementation:
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118
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119 **may**: Conforming Salad documents and Salad implementations are permitted but
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120 not required to be interpreted as described.
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121
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122 **must**: Conforming Salad documents and Salad implementations are required
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123 to be interpreted as described; otherwise they are in error.
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124
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125 **error**: A violation of the rules of this specification; results are
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126 undefined. Conforming implementations may detect and report an error and may
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127 recover from it.
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128
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129 **fatal error**: A violation of the rules of this specification; results
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130 are undefined. Conforming implementations must not continue to process the
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131 document and may report an error.
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132
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133 **at user option**: Conforming software may or must (depending on the modal verb in
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134 the sentence) behave as described; if it does, it must provide users a means to
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135 enable or disable the behavior described.
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136
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137 # Document model
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138
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139 ## Data concepts
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140
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141 An **object** is a data structure equivalent to the "object" type in JSON,
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142 consisting of a unordered set of name/value pairs (referred to here as
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143 **fields**) and where the name is a string and the value is a string, number,
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144 boolean, array, or object.
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145
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146 A **document** is a file containing a serialized object, or an array of
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147 objects.
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148
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149 A **document type** is a class of files that share a common structure and
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150 semantics.
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151
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152 A **document schema** is a formal description of the grammar of a document type.
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153
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154 A **base URI** is a context-dependent URI used to resolve relative references.
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155
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156 An **identifier** is a URI that designates a single document or single
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157 object within a document.
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158
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159 A **vocabulary** is the set of symbolic field names and enumerated symbols defined
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160 by a document schema, where each term maps to absolute URI.
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161
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162 ## Syntax
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163
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164 Conforming Salad v1.1 documents are serialized and loaded using a
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165 subset of YAML 1.2 syntax and UTF-8 text encoding. Salad documents
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166 are written using the [JSON-compatible subset of YAML described in
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167 section 10.2](https://yaml.org/spec/1.2/spec.html#id2803231). The
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168 following features of YAML must not be used in conforming Salad
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169 documents:
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170
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171 * Use of explicit node tags with leading `!` or `!!`
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172 * Use of anchors with leading `&` and aliases with leading `*`
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173 * %YAML directives
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174 * %TAG directives
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175
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176 It is a fatal error if the document is not valid YAML.
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177
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178 A Salad document must consist only of either a single root object or an
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179 array of objects.
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180
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181 ## Document context
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182
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183 ### Implied context
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184
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185 The implicit context consists of the vocabulary defined by the schema and
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186 the base URI. By default, the base URI must be the URI that was used to
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187 load the document. It may be overridden by an explicit context.
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188
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189 ### Explicit context
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190
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191 If a document consists of a root object, this object may contain the
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192 fields `$base`, `$namespaces`, `$schemas`, and `$graph`:
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193
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194 * `$base`: Must be a string. Set the base URI for the document used to
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195 resolve relative references.
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196
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197 * `$namespaces`: Must be an object with strings as values. The keys of
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198 the object are namespace prefixes used in the document; the values of
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199 the object are the prefix expansions.
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200
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201 * `$schemas`: Must be an array of strings. This field may list URI
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202 references to documents in RDF-XML format which will be queried for RDF
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203 schema data. The subjects and predicates described by the RDF schema
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204 may provide additional semantic context for the document, and may be
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205 used for validation of prefixed extension fields found in the document.
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206
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207 Other directives beginning with `$` must be ignored.
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208
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209 ## Document graph
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210
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211 If a document consists of a single root object, this object may contain the
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212 field `$graph`. This field must be an array of objects. If present, this
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213 field holds the primary content of the document. A document that consists
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214 of array of objects at the root is an implicit graph.
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215
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216 ## Document metadata
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217
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218 If a document consists of a single root object, metadata about the
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219 document, such as authorship, may be declared in the root object.
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220
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221 ## Document schema
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222
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223 Document preprocessing, link validation and schema validation require a
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224 document schema. A schema may consist of:
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225
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226 * At least one record definition object which defines valid fields that
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227 make up a record type. Record field definitions include the valid types
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228 that may be assigned to each field and annotations to indicate fields
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229 that represent identifiers and links, described below in "Semantic
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230 Annotations".
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231
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232 * Any number of enumerated type objects which define a set of finite set of symbols that are
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233 valid value of the type.
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234
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235 * Any number of documentation objects which allow in-line documentation of the schema.
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236
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237 The schema for defining a salad schema (the metaschema) is described in
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238 detail in the [Schema](#Schema) section.
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239
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240 ## Record field annotations
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241
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242 In a document schema, record field definitions may include the field
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243 `jsonldPredicate`, which may be either a string or object. Implementations
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244 must use the following document preprocessing of fields by the following
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245 rules:
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246
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247 * If the value of `jsonldPredicate` is `@id`, the field is an identifier
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248 field.
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249
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250 * If the value of `jsonldPredicate` is an object, and contains that
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251 object contains the field `_type` with the value `@id`, the field is a
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252 link field subject to [link validation](#Link_validation).
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253
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254 * If the value of `jsonldPredicate` is an object which contains the
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255 field `_type` with the value `@vocab`, the field value is subject to
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256 [vocabulary resolution](#Vocabulary_resolution).
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257
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258 ## Document traversal
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259
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260 To perform document document preprocessing, link validation and schema
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261 validation, the document must be traversed starting from the fields or
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262 array items of the root object or array and recursively visiting each child
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263 item which contains an object or arrays.
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264
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265 ## Short names
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266
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267 The "short name" of an fully qualified identifier is the portion of
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268 the identifier following the final slash `/` of either the fragment
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269 identifier following `#` or the path portion, if there is no fragment.
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270 Some examples:
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271
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272 * the short name of `http://example.com/foo` is `foo`
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273 * the short name of `http://example.com/#bar` is `bar`
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274 * the short name of `http://example.com/foo/bar` is `bar`
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275 * the short name of `http://example.com/foo#bar` is `bar`
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276 * the short name of `http://example.com/#foo/bar` is `bar`
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277 * the short name of `http://example.com/foo#bar/baz` is `baz`
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278
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279 ## Inheritance and specialization
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280
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281 A record definition may inherit from one or more record definitions
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282 with the `extends` field. This copies the fields defined in the
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283 parent record(s) as the base for the new record. A record definition
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284 may `specialize` type declarations of the fields inherited from the
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285 base record. For each field inherited from the base record, any
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286 instance of the type in `specializeFrom` is replaced with the type in
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287 `specializeTo`. The type in `specializeTo` should extend from the
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288 type in `specializeFrom`.
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289
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290 A record definition may be `abstract`. This means the record
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291 definition is not used for validation on its own, but may be extended
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292 by other definitions. If an abstract type appears in a field
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293 definition, it is logically replaced with a union of all concrete
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294 subtypes of the abstract type. In other words, the field value does
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295 not validate as the abstract type, but must validate as some concrete
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296 type that inherits from the abstract type.
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297
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298 # Document preprocessing
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299
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300 After processing the explicit context (if any), document preprocessing
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301 begins. Starting from the document root, object fields values or array
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302 items which contain objects or arrays are recursively traversed
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303 depth-first. For each visited object, field names, identifier fields, link
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304 fields, vocabulary fields, and `$import` and `$include` directives must be
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305 processed as described in this section. The order of traversal of child
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306 nodes within a parent node is undefined.