Merge pull request #192 from linkml/model-1.3rc

Prepare model files for release 1.3
linkml · Jul 14, 2022 · dd2378e · dd2378e
2 parents 885e95a + 2a46c65
commit dd2378e
Show file tree

Hide file tree

Showing 60 changed files with 11,025 additions and 3,083 deletions.
diff --git a/linkml_runtime/linkml_model/annotations.py b/linkml_runtime/linkml_model/annotations.py
@@ -1,5 +1,5 @@
 # Auto generated from annotations.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-04-30T01:16:43
+# Generation date: 2022-07-13T02:59:53
 # Schema: annotations
 #
 # id: https://w3id.org/linkml/annotations

diff --git a/linkml_runtime/linkml_model/extensions.py b/linkml_runtime/linkml_model/extensions.py
@@ -1,5 +1,5 @@
 # Auto generated from extensions.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-04-30T01:16:50
+# Generation date: 2022-07-13T02:59:55
 # Schema: extensions
 #
 # id: https://w3id.org/linkml/extensions

diff --git a/linkml_runtime/linkml_model/graphql/meta.graphql b/linkml_runtime/linkml_model/graphql/meta.graphql
@@ -56,6 +56,21 @@ type AnonymousClassExpression implements ClassExpression
     slotConditions: [SlotDefinition]
   }
 
+type AnonymousEnumExpression implements EnumExpression
+  {
+    codeSet: Uriorcurie
+    codeSetTag: String
+    codeSetVersion: String
+    pvFormula: PvFormulaOptions
+    permissibleValues: [PermissibleValue]
+    include: [AnonymousEnumExpression]
+    minus: [AnonymousEnumExpression]
+    inherits: [EnumDefinition]
+    reachableFrom: ReachabilityQuery
+    matches: MatchQuery
+    concepts: [Uriorcurie]
+  }
+
 type AnonymousExpression implements Expression, Extensible, Annotatable, CommonMetadata
   {
     extensions: [Extension]
@@ -118,6 +133,7 @@ type AnonymousSlotExpression implements SlotExpression
     rank: Integer
     range: Element
     rangeExpression: AnonymousClassExpression
+    enumRange: EnumExpression
     required: Boolean
     recommended: Boolean
     inlined: Boolean
@@ -126,6 +142,8 @@ type AnonymousSlotExpression implements SlotExpression
     maximumValue: Integer
     pattern: String
     structuredPattern: PatternExpression
+    unit: UnitOfMeasure
+    implicitPrefix: String
     equalsString: String
     equalsStringIn: [String]
     equalsNumber: Integer
@@ -144,6 +162,8 @@ type AnonymousTypeExpression implements TypeExpression
   {
     pattern: String
     structuredPattern: PatternExpression
+    unit: UnitOfMeasure
+    implicitPrefix: String
     equalsString: String
     equalsStringIn: [String]
     equalsNumber: Integer
@@ -386,7 +406,7 @@ type Element implements Extensible, Annotatable, CommonMetadata
     rank: Integer
   }
 
-type EnumDefinition
+type EnumDefinition implements EnumExpression
   {
     name: String!
     idPrefixes: [Ncname]
@@ -420,11 +440,45 @@ type EnumDefinition
     narrowMappings: [Uriorcurie]
     broadMappings: [Uriorcurie]
     rank: Integer
+    isA: Definition
+    abstract: Boolean
+    mixin: Boolean
+    mixins: [Definition]
+    applyTo: [Definition]
+    valuesFrom: [Uriorcurie]
+    createdBy: Uriorcurie
+    createdOn: Datetime
+    lastUpdatedOn: Datetime
+    modifiedBy: Uriorcurie
+    status: Uriorcurie
+    stringSerialization: String
+    enumUri: Uriorcurie
+    codeSet: Uriorcurie
+    codeSetTag: String
+    codeSetVersion: String
+    pvFormula: PvFormulaOptions
+    permissibleValues: [PermissibleValue]
+    include: [AnonymousEnumExpression]
+    minus: [AnonymousEnumExpression]
+    inherits: [EnumDefinition]
+    reachableFrom: ReachabilityQuery
+    matches: MatchQuery
+    concepts: [Uriorcurie]
+  }
+
+type EnumExpression
+  {
     codeSet: Uriorcurie
     codeSetTag: String
     codeSetVersion: String
     pvFormula: PvFormulaOptions
     permissibleValues: [PermissibleValue]
+    include: [AnonymousEnumExpression]
+    minus: [AnonymousEnumExpression]
+    inherits: [EnumDefinition]
+    reachableFrom: ReachabilityQuery
+    matches: MatchQuery
+    concepts: [Uriorcurie]
   }
 
 type Example
@@ -489,6 +543,12 @@ type LocalName
     localNameValue: String!
   }
 
+type MatchQuery
+  {
+    identifierPattern: String
+    sourceOntology: Uriorcurie
+  }
+
 type PathExpression implements Expression, Extensible, Annotatable, CommonMetadata
   {
     followedBy: PathExpression
@@ -567,6 +627,7 @@ type PermissibleValue implements Extensible, Annotatable, CommonMetadata
     text: String!
     description: String
     meaning: Uriorcurie
+    unit: UnitOfMeasure
     isA: PermissibleValue
     mixins: [PermissibleValue]
     extensions: [Extension]
@@ -603,6 +664,16 @@ type Prefix
     prefixReference: Uri!
   }
 
+type ReachabilityQuery
+  {
+    sourceOntology: Uriorcurie
+    sourceNodes: [Uriorcurie]
+    relationshipTypes: [Uriorcurie]
+    isDirect: Boolean
+    includeSelf: Boolean
+    traverseUp: Boolean
+  }
+
 type SchemaDefinition
   {
     idPrefixes: [Ncname]
@@ -747,11 +818,13 @@ type SlotDefinition implements SlotExpression
     pathRule: PathExpression
     disjointWith: [SlotDefinition]
     childrenAreMutuallyDisjoint: Boolean
+    unionOf: [TypeDefinition]
     isA: SlotDefinition
     mixins: [SlotDefinition]
     applyTo: [SlotDefinition]
     range: Element
     rangeExpression: AnonymousClassExpression
+    enumRange: EnumExpression
     required: Boolean
     recommended: Boolean
     inlined: Boolean
@@ -760,6 +833,8 @@ type SlotDefinition implements SlotExpression
     maximumValue: Integer
     pattern: String
     structuredPattern: PatternExpression
+    unit: UnitOfMeasure
+    implicitPrefix: String
     equalsString: String
     equalsStringIn: [String]
     equalsNumber: Integer
@@ -778,6 +853,7 @@ interface SlotExpression
   {
     range: Element
     rangeExpression: AnonymousClassExpression
+    enumRange: EnumExpression
     required: Boolean
     recommended: Boolean
     inlined: Boolean
@@ -786,6 +862,8 @@ interface SlotExpression
     maximumValue: Integer
     pattern: String
     structuredPattern: PatternExpression
+    unit: UnitOfMeasure
+    implicitPrefix: String
     equalsString: String
     equalsStringIn: [String]
     equalsNumber: Integer
@@ -908,8 +986,11 @@ type TypeDefinition implements TypeExpression
     base: String
     uri: Uriorcurie
     repr: String
+    unionOf: [TypeDefinition]
     pattern: String
     structuredPattern: PatternExpression
+    unit: UnitOfMeasure
+    implicitPrefix: String
     equalsString: String
     equalsStringIn: [String]
     equalsNumber: Integer
@@ -925,6 +1006,8 @@ interface TypeExpression
   {
     pattern: String
     structuredPattern: PatternExpression
+    unit: UnitOfMeasure
+    implicitPrefix: String
     equalsString: String
     equalsStringIn: [String]
     equalsNumber: Integer
@@ -969,4 +1052,32 @@ type UniqueKey implements Extensible, Annotatable, CommonMetadata
     rank: Integer
   }
 
+type UnitOfMeasure
+  {
+    symbol: String
+    exactMappings: [Uriorcurie]
+    ucumCode: String
+    derivation: String
+    hasQuantityKind: Uriorcurie
+    iec61360code: String
+  }
+
+type ValidationReport
+  {
+    results: [ValidationResult]
+  }
+
+type ValidationResult
+  {
+    type: Nodeidentifier
+    severity: SeverityOptions
+    subject: Nodeidentifier
+    instantiates: Nodeidentifier
+    predicate: Nodeidentifier
+    object: Nodeidentifier
+    objectStr: String
+    nodeSource: Nodeidentifier
+    info: String
+  }
+
 
diff --git a/linkml_runtime/linkml_model/json/annotations.json b/linkml_runtime/linkml_model/json/annotations.json
@@ -120,6 +120,17 @@
       "repr": "str",
       "@type": "TypeDefinition"
     },
+    {
+      "name": "date_or_datetime",
+      "definition_uri": "https://w3id.org/linkml/DateOrDatetime",
+      "description": "Either a date or a datetime",
+      "from_schema": "https://w3id.org/linkml/types",
+      "imported_from": "linkml:types",
+      "base": "str",
+      "uri": "https://w3id.org/linkml/DateOrDatetime",
+      "repr": "str",
+      "@type": "TypeDefinition"
+    },
     {
       "name": "uriorcurie",
       "definition_uri": "https://w3id.org/linkml/Uriorcurie",
@@ -189,13 +200,13 @@
       "domain": "Annotatable",
       "slot_uri": "https://w3id.org/linkml/annotations",
       "multivalued": true,
-      "inlined": true,
       "owner": "Annotation",
       "domain_of": [
         "Annotatable",
         "Annotation"
       ],
       "range": "Annotation",
+      "inlined": true,
       "@type": "SlotDefinition"
     },
     {
@@ -207,13 +218,13 @@
       "domain": "Extensible",
       "slot_uri": "https://w3id.org/linkml/extensions",
       "multivalued": true,
-      "inlined": true,
       "owner": "Extensible",
       "domain_of": [
         "Extension",
         "Extensible"
       ],
       "range": "Extension",
+      "inlined": true,
       "@type": "SlotDefinition"
     },
     {
@@ -317,9 +328,9 @@
   ],
   "metamodel_version": "1.7.0",
   "source_file": "annotations.yaml",
-  "source_file_date": "2022-04-30T01:12:23",
+  "source_file_date": "2022-07-13T02:58:15",
   "source_file_size": 833,
-  "generation_date": "2022-04-30T01:14:31",
+  "generation_date": "2022-07-13T02:59:19",
   "@type": "SchemaDefinition",
   "@context": [
     "https://w3id.org/linkml/types.context.jsonld",

diff --git a/linkml_runtime/linkml_model/json/extensions.json b/linkml_runtime/linkml_model/json/extensions.json
@@ -119,6 +119,17 @@
       "repr": "str",
       "@type": "TypeDefinition"
     },
+    {
+      "name": "date_or_datetime",
+      "definition_uri": "https://w3id.org/linkml/DateOrDatetime",
+      "description": "Either a date or a datetime",
+      "from_schema": "https://w3id.org/linkml/types",
+      "imported_from": "linkml:types",
+      "base": "str",
+      "uri": "https://w3id.org/linkml/DateOrDatetime",
+      "repr": "str",
+      "@type": "TypeDefinition"
+    },
     {
       "name": "uriorcurie",
       "definition_uri": "https://w3id.org/linkml/Uriorcurie",
@@ -187,13 +198,13 @@
       "domain": "Extensible",
       "slot_uri": "https://w3id.org/linkml/extensions",
       "multivalued": true,
-      "inlined": true,
       "owner": "Extensible",
       "domain_of": [
         "Extension",
         "Extensible"
       ],
       "range": "Extension",
+      "inlined": true,
       "@type": "SlotDefinition"
     },
     {
@@ -261,9 +272,9 @@
   ],
   "metamodel_version": "1.7.0",
   "source_file": "extensions.yaml",
-  "source_file_date": "2022-04-30T01:12:23",
+  "source_file_date": "2022-07-13T02:58:15",
   "source_file_size": 1057,
-  "generation_date": "2022-04-30T01:14:40",
+  "generation_date": "2022-07-13T02:59:23",
   "@type": "SchemaDefinition",
   "@context": [
     "https://w3id.org/linkml/types.context.jsonld",