1.7.0 release candidate

linkml · Jan 30, 2024 · 57224a7 · 57224a7
1 parent aab9842
commit 57224a7
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Showing 23 changed files with 7,619 additions and 7,266 deletions.
diff --git a/linkml_model/annotations.py b/linkml_model/annotations.py
@@ -1,5 +1,5 @@
-# Auto generated from annotations.yaml by pythongen.py version: 0.9.0
-# Generation date: 2023-09-01T13:21:10
+# Auto generated from annotations.yaml by pythongen.py version: 0.0.1
+# Generation date: 2024-01-29T16:05:46
 # Schema: annotations
 #
 # id: https://w3id.org/linkml/annotations
@@ -49,7 +49,7 @@ class Annotatable(YAMLRoot):
     """
     _inherited_slots: ClassVar[List[str]] = []
 
-    class_class_uri: ClassVar[URIRef] = LINKML.Annotatable
+    class_class_uri: ClassVar[URIRef] = LINKML["Annotatable"]
     class_class_curie: ClassVar[str] = "linkml:Annotatable"
     class_name: ClassVar[str] = "annotatable"
     class_model_uri: ClassVar[URIRef] = LINKML.Annotatable
@@ -69,7 +69,7 @@ class Annotation(Extension):
     """
     _inherited_slots: ClassVar[List[str]] = []
 
-    class_class_uri: ClassVar[URIRef] = LINKML.Annotation
+    class_class_uri: ClassVar[URIRef] = LINKML["Annotation"]
     class_class_curie: ClassVar[str] = "linkml:Annotation"
     class_name: ClassVar[str] = "annotation"
     class_model_uri: ClassVar[URIRef] = LINKML.Annotation

diff --git a/linkml_model/array.py b/linkml_model/array.py
diff --git a/linkml_model/datasets.py b/linkml_model/datasets.py
@@ -1,5 +1,5 @@
-# Auto generated from datasets.yaml by pythongen.py version: 0.9.0
-# Generation date: 2023-09-01T13:21:13
+# Auto generated from datasets.yaml by pythongen.py version: 0.0.1
+# Generation date: 2024-01-29T16:05:52
 # Schema: datasets
 #
 # id: https://w3id.org/linkml/datasets
@@ -30,7 +30,7 @@
 dataclasses._init_fn = dataclasses_init_fn_with_kwargs
 
 # Namespaces
-BIBO = CurieNamespace('bibo', 'http://example.org/UNKNOWN/bibo/')
+BIBO = CurieNamespace('bibo', 'http://purl.org/ontology/bibo/')
 CSVW = CurieNamespace('csvw', 'http://www.w3.org/ns/csvw#')
 DATASETS = CurieNamespace('datasets', 'https://w3id.org/linkml/report')
 DCAT = CurieNamespace('dcat', 'http://www.w3.org/ns/dcat#')
@@ -39,7 +39,7 @@
 FRICTIONLESS = CurieNamespace('frictionless', 'https://specs.frictionlessdata.io/')
 LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/')
 MEDIATYPES = CurieNamespace('mediatypes', 'https://www.iana.org/assignments/media-types/')
-OSLC = CurieNamespace('oslc', 'http://example.org/UNKNOWN/oslc/')
+OSLC = CurieNamespace('oslc', 'http://open-services.net/ns/core#')
 OWL = CurieNamespace('owl', 'http://www.w3.org/2002/07/owl#')
 PAV = CurieNamespace('pav', 'http://purl.org/pav/')
 PROV = CurieNamespace('prov', 'http://www.w3.org/ns/prov#')
@@ -75,7 +75,7 @@ class Information(YAMLRoot):
     """
     _inherited_slots: ClassVar[List[str]] = []
 
-    class_class_uri: ClassVar[URIRef] = DATASETS.Information
+    class_class_uri: ClassVar[URIRef] = DATASETS["Information"]
     class_class_curie: ClassVar[str] = "datasets:Information"
     class_name: ClassVar[str] = "Information"
     class_model_uri: ClassVar[URIRef] = DATASETS.Information
@@ -172,7 +172,7 @@ class DataPackage(Information):
     """
     _inherited_slots: ClassVar[List[str]] = []
 
-    class_class_uri: ClassVar[URIRef] = VOID.Dataset
+    class_class_uri: ClassVar[URIRef] = VOID["Dataset"]
     class_class_curie: ClassVar[str] = "void:Dataset"
     class_name: ClassVar[str] = "DataPackage"
     class_model_uri: ClassVar[URIRef] = DATASETS.DataPackage
@@ -200,7 +200,7 @@ class DataResource(Information):
     """
     _inherited_slots: ClassVar[List[str]] = []
 
-    class_class_uri: ClassVar[URIRef] = DCAT.Distribution
+    class_class_uri: ClassVar[URIRef] = DCAT["Distribution"]
     class_class_curie: ClassVar[str] = "dcat:Distribution"
     class_name: ClassVar[str] = "DataResource"
     class_model_uri: ClassVar[URIRef] = DATASETS.DataResource
@@ -267,7 +267,7 @@ class FormatDialect(YAMLRoot):
     """
     _inherited_slots: ClassVar[List[str]] = []
 
-    class_class_uri: ClassVar[URIRef] = DATASETS.FormatDialect
+    class_class_uri: ClassVar[URIRef] = DATASETS["FormatDialect"]
     class_class_curie: ClassVar[str] = "datasets:FormatDialect"
     class_name: ClassVar[str] = "FormatDialect"
     class_model_uri: ClassVar[URIRef] = DATASETS.FormatDialect
@@ -328,22 +328,22 @@ class FormatEnum(EnumDefinitionImpl):
 
     N3 = PermissibleValue(
         text="N3",
-        meaning=FORMATS.N3)
+        meaning=FORMATS["N3"])
     Microdata = PermissibleValue(
         text="Microdata",
-        meaning=FORMATS.microdata)
+        meaning=FORMATS["microdata"])
     POWDER = PermissibleValue(
         text="POWDER",
-        meaning=FORMATS.POWDER)
+        meaning=FORMATS["POWDER"])
     RDFa = PermissibleValue(
         text="RDFa",
-        meaning=FORMATS.RDFa)
+        meaning=FORMATS["RDFa"])
     Turtle = PermissibleValue(
         text="Turtle",
-        meaning=FORMATS.Turtle)
+        meaning=FORMATS["Turtle"])
     TriG = PermissibleValue(
         text="TriG",
-        meaning=FORMATS.TriG)
+        meaning=FORMATS["TriG"])
     YAML = PermissibleValue(text="YAML")
     JSON = PermissibleValue(text="JSON")
 
@@ -368,19 +368,19 @@ def _addvals(cls):
         setattr(cls, "LD Patch",
             PermissibleValue(
                 text="LD Patch",
-                meaning=FORMATS.LD_Patch))
+                meaning=FORMATS["LD_Patch"]))
         setattr(cls, "OWL XML Serialization",
             PermissibleValue(
                 text="OWL XML Serialization",
-                meaning=FORMATS.OWL_XML))
+                meaning=FORMATS["OWL_XML"]))
         setattr(cls, "OWL Functional Syntax",
             PermissibleValue(
                 text="OWL Functional Syntax",
-                meaning=FORMATS.OWL_Functional))
+                meaning=FORMATS["OWL_Functional"]))
         setattr(cls, "OWL Manchester Syntax",
             PermissibleValue(
                 text="OWL Manchester Syntax",
-                meaning=FORMATS.OWL_Manchester))
+                meaning=FORMATS["OWL_Manchester"]))
         setattr(cls, "POWDER-S",
             PermissibleValue(
                 text="POWDER-S",
@@ -396,31 +396,31 @@ def _addvals(cls):
         setattr(cls, "RDF/JSON",
             PermissibleValue(
                 text="RDF/JSON",
-                meaning=FORMATS.RDF_JSON))
+                meaning=FORMATS["RDF_JSON"]))
         setattr(cls, "RDF/XML",
             PermissibleValue(
                 text="RDF/XML",
-                meaning=FORMATS.RDF_XML))
+                meaning=FORMATS["RDF_XML"]))
         setattr(cls, "RIF XML Syntax",
             PermissibleValue(
                 text="RIF XML Syntax",
-                meaning=FORMATS.RIF_XML))
+                meaning=FORMATS["RIF_XML"]))
         setattr(cls, "SPARQL Results in XML",
             PermissibleValue(
                 text="SPARQL Results in XML",
-                meaning=FORMATS.SPARQL_Results_XML))
+                meaning=FORMATS["SPARQL_Results_XML"]))
         setattr(cls, "SPARQL Results in JSON",
             PermissibleValue(
                 text="SPARQL Results in JSON",
-                meaning=FORMATS.SPARQL_Results_JSON))
+                meaning=FORMATS["SPARQL_Results_JSON"]))
         setattr(cls, "SPARQL Results in CSV",
             PermissibleValue(
                 text="SPARQL Results in CSV",
-                meaning=FORMATS.SPARQL_Results_CSV))
+                meaning=FORMATS["SPARQL_Results_CSV"]))
         setattr(cls, "SPARQL Results in TSV",
             PermissibleValue(
                 text="SPARQL Results in TSV",
-                meaning=FORMATS.SPARQL_Results_TSV))
+                meaning=FORMATS["SPARQL_Results_TSV"]))
 
 # Slots
 class slots:

diff --git a/linkml_model/excel/meta.xlsx b/linkml_model/excel/meta.xlsx
diff --git a/linkml_model/extensions.py b/linkml_model/extensions.py
@@ -1,5 +1,5 @@
-# Auto generated from extensions.yaml by pythongen.py version: 0.9.0
-# Generation date: 2023-09-01T13:21:14
+# Auto generated from extensions.yaml by pythongen.py version: 0.0.1
+# Generation date: 2024-01-29T16:05:53
 # Schema: extensions
 #
 # id: https://w3id.org/linkml/extensions
@@ -50,7 +50,7 @@ class Extension(YAMLRoot):
     """
     _inherited_slots: ClassVar[List[str]] = []
 
-    class_class_uri: ClassVar[URIRef] = LINKML.Extension
+    class_class_uri: ClassVar[URIRef] = LINKML["Extension"]
     class_class_curie: ClassVar[str] = "linkml:Extension"
     class_name: ClassVar[str] = "extension"
     class_model_uri: ClassVar[URIRef] = LINKML.Extension
@@ -77,7 +77,7 @@ class Extensible(YAMLRoot):
     """
     _inherited_slots: ClassVar[List[str]] = []
 
-    class_class_uri: ClassVar[URIRef] = LINKML.Extensible
+    class_class_uri: ClassVar[URIRef] = LINKML["Extensible"]
     class_class_curie: ClassVar[str] = "linkml:Extensible"
     class_name: ClassVar[str] = "extensible"
     class_model_uri: ClassVar[URIRef] = LINKML.Extensible

diff --git a/linkml_model/graphql/meta.graphql b/linkml_model/graphql/meta.graphql
@@ -160,8 +160,8 @@ type AnonymousSlotExpression implements SlotExpression
     recommended: Boolean
     inlined: Boolean
     inlinedAsList: Boolean
-    minimumValue: Integer
-    maximumValue: Integer
+    minimumValue: Anything
+    maximumValue: Anything
     pattern: String
     structuredPattern: PatternExpression
     unit: UnitOfMeasure
@@ -190,8 +190,8 @@ type AnonymousTypeExpression implements TypeExpression
     equalsString: String
     equalsStringIn: [String]
     equalsNumber: Integer
-    minimumValue: Integer
-    maximumValue: Integer
+    minimumValue: Anything
+    maximumValue: Anything
     noneOf: [AnonymousTypeExpression]
     exactlyOneOf: [AnonymousTypeExpression]
     anyOf: [AnonymousTypeExpression]
@@ -210,6 +210,7 @@ type ClassDefinition implements ClassExpression
   {
     name: String!
     idPrefixes: [Ncname]
+    idPrefixesAreClosed: Boolean
     definitionUri: Uriorcurie
     localNames: [LocalName]
     conformsTo: String
@@ -378,6 +379,7 @@ interface Definition
   {
     name: String!
     idPrefixes: [Ncname]
+    idPrefixesAreClosed: Boolean
     definitionUri: Uriorcurie
     localNames: [LocalName]
     conformsTo: String
@@ -431,6 +433,7 @@ type Element implements Extensible, Annotatable, CommonMetadata
   {
     name: String!
     idPrefixes: [Ncname]
+    idPrefixesAreClosed: Boolean
     definitionUri: Uriorcurie
     localNames: [LocalName]
     conformsTo: String
@@ -477,6 +480,7 @@ type EnumDefinition implements EnumExpression
   {
     name: String!
     idPrefixes: [Ncname]
+    idPrefixesAreClosed: Boolean
     definitionUri: Uriorcurie
     localNames: [LocalName]
     conformsTo: String
@@ -782,6 +786,7 @@ type ReachabilityQuery
 type SchemaDefinition
   {
     idPrefixes: [Ncname]
+    idPrefixesAreClosed: Boolean
     definitionUri: Uriorcurie
     localNames: [LocalName]
     conformsTo: String
@@ -856,6 +861,7 @@ type SlotDefinition implements SlotExpression
   {
     name: String!
     idPrefixes: [Ncname]
+    idPrefixesAreClosed: Boolean
     definitionUri: Uriorcurie
     localNames: [LocalName]
     conformsTo: String
@@ -947,8 +953,8 @@ type SlotDefinition implements SlotExpression
     recommended: Boolean
     inlined: Boolean
     inlinedAsList: Boolean
-    minimumValue: Integer
-    maximumValue: Integer
+    minimumValue: Anything
+    maximumValue: Anything
     pattern: String
     structuredPattern: PatternExpression
     unit: UnitOfMeasure
@@ -977,8 +983,8 @@ interface SlotExpression
     recommended: Boolean
     inlined: Boolean
     inlinedAsList: Boolean
-    minimumValue: Integer
-    maximumValue: Integer
+    minimumValue: Anything
+    maximumValue: Anything
     pattern: String
     structuredPattern: PatternExpression
     unit: UnitOfMeasure
@@ -1043,6 +1049,7 @@ type SubsetDefinition
   {
     name: String!
     idPrefixes: [Ncname]
+    idPrefixesAreClosed: Boolean
     definitionUri: Uriorcurie
     localNames: [LocalName]
     conformsTo: String
@@ -1089,6 +1096,7 @@ type TypeDefinition implements TypeExpression
   {
     name: String!
     idPrefixes: [Ncname]
+    idPrefixesAreClosed: Boolean
     definitionUri: Uriorcurie
     localNames: [LocalName]
     conformsTo: String
@@ -1141,8 +1149,8 @@ type TypeDefinition implements TypeExpression
     equalsString: String
     equalsStringIn: [String]
     equalsNumber: Integer
-    minimumValue: Integer
-    maximumValue: Integer
+    minimumValue: Anything
+    maximumValue: Anything
     noneOf: [AnonymousTypeExpression]
     exactlyOneOf: [AnonymousTypeExpression]
     anyOf: [AnonymousTypeExpression]
@@ -1158,8 +1166,8 @@ interface TypeExpression
     equalsString: String
     equalsStringIn: [String]
     equalsNumber: Integer
-    minimumValue: Integer
-    maximumValue: Integer
+    minimumValue: Anything
+    maximumValue: Anything
     noneOf: [AnonymousTypeExpression]
     exactlyOneOf: [AnonymousTypeExpression]
     anyOf: [AnonymousTypeExpression]

diff --git a/linkml_model/jsonld/meta.context.jsonld b/linkml_model/jsonld/meta.context.jsonld
@@ -1,7 +1,7 @@
 {
    "comments": {
       "description": "Auto generated by LinkML jsonld context generator",
-      "generation_date": "2023-09-01T13:19:55",
+      "generation_date": "2024-01-29T16:06:12",
       "source": "meta.yaml"
    },
    "@context": {
@@ -11,6 +11,10 @@
       },
       "NCIT": "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#",
       "OIO": "http://www.geneontology.org/formats/oboInOwl#",
+      "SIO": {
+         "@id": "http://semanticscience.org/resource/SIO_",
+         "@prefix": true
+      },
       "bibo": "http://purl.org/ontology/bibo/",
       "cdisc": "http://rdf.cdisc.org/mms#",
       "dcterms": "http://purl.org/dc/terms/",
@@ -227,6 +231,9 @@
       "id": {
          "@type": "@id"
       },
+      "id_prefixes_are_closed": {
+         "@type": "xsd:boolean"
+      },
       "identifier": {
          "@type": "xsd:boolean"
       },
@@ -346,7 +353,7 @@
          "@type": "xsd:integer"
       },
       "maximum_value": {
-         "@type": "xsd:integer"
+         "@type": "@id"
       },
       "meaning": {
          "@type": "@id"
@@ -355,7 +362,7 @@
          "@type": "xsd:integer"
       },
       "minimum_value": {
-         "@type": "xsd:integer"
+         "@type": "@id"
       },
       "minus": {
          "@type": "@id"