Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/schema_salad/metaschema/metaschema.yml @ 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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0
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1 $base: "https://w3id.org/cwl/salad#"
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2
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3 $namespaces:
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4 sld: "https://w3id.org/cwl/salad#"
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5 dct: "http://purl.org/dc/terms/"
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6 rdf: "http://www.w3.org/1999/02/22-rdf-syntax-ns#"
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7 rdfs: "http://www.w3.org/2000/01/rdf-schema#"
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8 xsd: "http://www.w3.org/2001/XMLSchema#"
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9
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10 $graph:
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11
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12 - name: "Semantic_Annotations_for_Linked_Avro_Data"
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13 type: documentation
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14 doc:
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15 - $include: salad.md
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16 - $import: field_name.yml
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17 - $import: ident_res.yml
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18 - $import: link_res.yml
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19 - $import: vocab_res.yml
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20 - $include: import_include.md
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21 - $import: map_res.yml
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22 - $import: typedsl_res.yml
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23 - $import: sfdsl_res.yml
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24
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25 - name: "Link_Validation"
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26 type: documentation
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27 doc: |
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28 # Link validation
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29
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30 Once a document has been preprocessed, an implementation may validate
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31 links. The link validation traversal may visit fields which the schema
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32 designates as link fields and check that each URI references an existing
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33 object in the current document, an imported document, file system, or
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34 network resource. Failure to validate links may be a fatal error. Link
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35 validation behavior for individual fields may be modified by `identity` and
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36 `noLinkCheck` in the `jsonldPredicate` section of the field schema.
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37
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38
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39 - name: "Schema_Validation"
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40 type: documentation
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41 doc: |
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42 # Validating a document against a schema
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43
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44 To validate a document against the schema, first [apply
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45 preprocessing](#Document_preprocessing), then, use the following
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46 algorithm.
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47
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48 1. The document root must be an object or a list. If the document root is an
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49 object containing the field `$graph` (which must be a list of
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50 objects), then validation applies to each object in the list.
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51 2. For each object, attempt to validate as one of the record types
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52 flagged with `documentRoot: true`.
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53 3. To validate a record, go through `fields` and recursively
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54 validate each field of the object.
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55 4. For fields with a list of types (type union), go through each
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56 type in the list and recursively validate the type. For the
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57 field to be valid, at least one type in the union must be valid.
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58 5. Missing fields are considered `null`. To validate, the allowed types
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59 for the field must include `null`
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60 6. Primitive types are null, boolean, int, long, float, double,
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61 string. To validate, the value in the document must have one
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62 of these type. For numerics, the value appearing in the
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63 document must fit into the specified type.
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64 7. To validate an array, the value in the document must be a list,
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65 and each item in the list must recursively validate as a type
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66 in `items`.
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67 8. To validate an enum, the value in the document be a string, and
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68 the value must be equal to the short name of one of the values
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69 listed in `symbols`.
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70 9. As a special case, a field with the `Expression` type validates string values
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71 which contain a CWL parameter reference or expression in the form
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72 `$(...)` or `${...}`
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73
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74 # - name: "JSON_LD_Context"
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75 # type: documentation
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76 # doc: |
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77 # # Generating JSON-LD Context
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78
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79 # How to generate the json-ld context...
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80
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81
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82 - $import: metaschema_base.yml
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83
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84 - name: JsonldPredicate
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85 type: record
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86 doc: |
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87 Attached to a record field to define how the parent record field is handled for
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88 URI resolution and JSON-LD context generation.
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89 fields:
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90 - name: _id
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91 type: string?
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92 jsonldPredicate:
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93 _id: sld:_id
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94 _type: "@id"
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95 identity: true
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96 doc: |
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97 The predicate URI that this field corresponds to.
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98 Corresponds to JSON-LD `@id` directive.
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99 - name: _type
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100 type: string?
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101 doc: |
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102 The context type hint, corresponds to JSON-LD `@type` directive.
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103
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104 * If the value of this field is `@id` and `identity` is false or
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105 unspecified, the parent field must be resolved using the link
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106 resolution rules. If `identity` is true, the parent field must be
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107 resolved using the identifier expansion rules.
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108
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109 * If the value of this field is `@vocab`, the parent field must be
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110 resolved using the vocabulary resolution rules.
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111
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112 - name: _container
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113 type: string?
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114 doc: |
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115 Structure hint, corresponds to JSON-LD `@container` directive.
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116 - name: identity
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117 type: boolean?
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118 doc: |
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119 If true and `_type` is `@id` this indicates that the parent field must
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120 be resolved according to identity resolution rules instead of link
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121 resolution rules. In addition, the field value is considered an
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122 assertion that the linked value exists; absence of an object in the loaded document
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123 with the URI is not an error.
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124 - name: noLinkCheck
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125 type: boolean?
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126 doc: |
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127 If true, this indicates that link validation traversal must stop at
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128 this field. This field (it is is a URI) or any fields under it (if it
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129 is an object or array) are not subject to link checking.
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130 - name: mapSubject
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131 type: string?
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132 doc: |
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133 If the value of the field is a JSON object, it must be transformed
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134 into an array of JSON objects, where each key-value pair from the
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135 source JSON object is a list item, the list items must be JSON objects,
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136 and the key is assigned to the field specified by `mapSubject`.
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137 - name: mapPredicate
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138 type: string?
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139 doc: |
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140 Only applies if `mapSubject` is also provided. If the value of the
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141 field is a JSON object, it is transformed as described in `mapSubject`,
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142 with the addition that when the value of a map item is not an object,
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143 the item is transformed to a JSON object with the key assigned to the
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144 field specified by `mapSubject` and the value assigned to the field
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145 specified by `mapPredicate`.
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146 - name: refScope
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147 type: int?
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148 doc: |
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149 If the field contains a relative reference, it must be resolved by
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150 searching for valid document references in each successive parent scope
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151 in the document fragment. For example, a reference of `foo` in the
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152 context `#foo/bar/baz` will first check for the existence of
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153 `#foo/bar/baz/foo`, followed by `#foo/bar/foo`, then `#foo/foo` and
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154 then finally `#foo`. The first valid URI in the search order shall be
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155 used as the fully resolved value of the identifier. The value of the
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156 refScope field is the specified number of levels from the containing
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157 identifer scope before starting the search, so if `refScope: 2` then
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158 "baz" and "bar" must be stripped to get the base `#foo` and search
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159 `#foo/foo` and the `#foo`. The last scope searched must be the top
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160 level scope before determining if the identifier cannot be resolved.
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161 - name: typeDSL
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162 type: boolean?
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163 doc: |
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164 Field must be expanded based on the the Schema Salad type DSL.
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165 - name: secondaryFilesDSL
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166 type: boolean?
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167 doc: |
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168 Field must be expanded based on the the Schema Salad secondary file DSL.
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169 - name: subscope
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170 type: string?
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171 doc: |
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172 Append the subscope to the current scope when performing
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173 identifier resolution to objects under this field.
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174
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175 - name: SpecializeDef
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176 type: record
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177 fields:
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178 - name: specializeFrom
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179 type: string
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180 doc: "The data type to be replaced"
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181 jsonldPredicate:
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182 _id: "sld:specializeFrom"
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183 _type: "@id"
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184 refScope: 1
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185
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186 - name: specializeTo
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187 type: string
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188 doc: "The new data type to replace with"
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189 jsonldPredicate:
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190 _id: "sld:specializeTo"
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191 _type: "@id"
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192 refScope: 1
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193
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194
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195 - name: NamedType
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196 type: record
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197 abstract: true
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198 docParent: "#Schema"
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199 fields:
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200 - name: name
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201 type: string
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202 jsonldPredicate: "@id"
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203 doc: "The identifier for this type"
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204 - name: inVocab
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205 type: boolean?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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206 default: true
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207 doc: |
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208 If "true" (the default), include the short name of this type
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209 in the vocabulary. The vocabulary are all the symbols (field
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210 names and other identifiers, such as classes and enum values)
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211 which can be used in the document without a namespace prefix.
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212 These are the keys of the JSON-LD context. If false, do not
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213 include the short name in the vocabulary.
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214
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215 This is useful for specifying schema extensions that will be
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216 included in validation without introducing ambiguity by
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217 introducing non-standard terms into the vocabulary.
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218
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219
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220 - name: DocType
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221 type: record
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222 extends: Documented
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223 abstract: true
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224 docParent: "#Schema"
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225 fields:
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226 - name: docParent
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227 type: string?
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228 doc: |
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229 Hint to indicate that during documentation generation, documentation
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230 for this type should appear in a subsection under `docParent`.
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231 jsonldPredicate:
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232 _id: "sld:docParent"
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233 _type: "@id"
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234
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235 - name: docChild
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236 type:
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237 - string?
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238 - string[]?
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239 doc: |
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240 Hint to indicate that during documentation generation, documentation
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241 for `docChild` should appear in a subsection under this type.
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242 jsonldPredicate:
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243 _id: "sld:docChild"
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244 _type: "@id"
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245
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246 - name: docAfter
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247 type: string?
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248 doc: |
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249 Hint to indicate that during documentation generation, documentation
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250 for this type should appear after the `docAfter` section at the same
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251 level.
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252 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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253 _id: "sld:docAfter"
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254 _type: "@id"
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255
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256
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257 - name: SchemaDefinedType
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258 type: record
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259 extends: DocType
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260 doc: |
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261 Abstract base for schema-defined types.
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262 abstract: true
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263 fields:
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264 - name: jsonldPredicate
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265 type:
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266 - string?
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267 - JsonldPredicate?
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268 doc: |
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269 Annotate this type with linked data context.
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270 jsonldPredicate: sld:jsonldPredicate
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271
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272 - name: documentRoot
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273 type: boolean?
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274 doc: |
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275 If true, indicates that the type is a valid at the document root. At
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276 least one type in a schema must be tagged with `documentRoot: true`.
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277
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278
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279 - name: SaladRecordField
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280 type: record
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281 extends: RecordField
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282 doc: "A field of a record."
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283 fields:
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284 - name: jsonldPredicate
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285 type:
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286 - string?
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287 - JsonldPredicate?
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288 doc: |
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289 Annotate this type with linked data context.
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290 jsonldPredicate: "sld:jsonldPredicate"
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291 - name: default
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292 type: Any?
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293 jsonldPredicate:
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294 _id: sld:default
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295 noLinkCheck: true
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296 doc: |
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297 The default value to use for this field if the field is missing or "null".
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298
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299
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300 - name: SaladRecordSchema
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301 docParent: "#Schema"
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302 type: record
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303 extends: [NamedType, RecordSchema, SchemaDefinedType]
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304 documentRoot: true
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305 specialize:
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306 RecordField: SaladRecordField
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307 fields:
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308 - name: abstract
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309 type: boolean?
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310 doc: |
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311 If true, this record is abstract and may be used as a base for other
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312 records, but is not valid on its own.
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313
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314 - name: extends
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315 type:
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316 - string?
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317 - string[]?
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318 jsonldPredicate:
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319 _id: "sld:extends"
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320 _type: "@id"
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321 refScope: 1
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322 doc: |
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323 Indicates that this record inherits fields from one or more base records.
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324
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325 - name: specialize
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326 type:
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327 - SpecializeDef[]?
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328 doc: |
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329 Only applies if `extends` is declared. Apply type specialization using the
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330 base record as a template. For each field inherited from the base
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331 record, replace any instance of the type `specializeFrom` with
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332 `specializeTo`.
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333 jsonldPredicate:
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334 _id: "sld:specialize"
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335 mapSubject: specializeFrom
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336 mapPredicate: specializeTo
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337
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338 - name: SaladEnumSchema
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339 docParent: "#Schema"
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340 type: record
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341 extends: [NamedType, EnumSchema, SchemaDefinedType]
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342 documentRoot: true
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343 doc: |
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344 Define an enumerated type.
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345 fields:
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346 - name: extends
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347 type:
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348 - string?
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349 - string[]?
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350 jsonldPredicate:
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351 _id: "sld:extends"
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352 _type: "@id"
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353 refScope: 1
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354 doc: |
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355 Indicates that this enum inherits symbols from a base enum.
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356
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357
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358 - name: Documentation
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359 type: record
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360 docParent: "#Schema"
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361 extends: [NamedType, DocType]
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362 documentRoot: true
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363 doc: |
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364 A documentation section. This type exists to facilitate self-documenting
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365 schemas but has no role in formal validation.
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366 fields:
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367 - name: type
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368 doc: "Must be `documentation`"
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369 type:
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370 type: enum
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371 symbols:
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372 - "sld:documentation"
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373 jsonldPredicate:
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374 _id: "sld:type"
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375 _type: "@vocab"
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376 typeDSL: true
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377 refScope: 2