Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/salad.md @ 0:4f3585e2f14b draft default tip
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author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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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 <peter.amstutz@curii.com>, Arvados Project, Curii Corporation |
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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. |