Merge pull request #28 from linkml/model_update_3

Model update 3
linkml · Aug 19, 2021 · 9c502ad · 9c502ad
2 parents 7533c13 + 92cae47
commit 9c502ad
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diff --git a/AUTHORS b/AUTHORS
@@ -1,3 +1,6 @@
 Chris Mungall <[email protected]>
+Gaurav Vaidya <[email protected]>
 GitHub Action <[email protected]>
 Harold Solbrig <[email protected]>
+cmungall <[email protected]>
+hsolbrig <[email protected]>
diff --git a/ChangeLog b/ChangeLog
@@ -1,6 +1,27 @@
 CHANGES
 =======
 
+* Update to latest model
+
+v1.0.12
+-------
+
+* Added leaf/root methods
+* Added additional methods
+* Adding more examples
+* Adding a new library schemaview
+* replace hyphen with underscore when underscoring names
+* Add the actual test to the pull request action
+
+v1.0.11
+-------
+
+* Update test\_issue\_368\_enums.py
+* Try relative paths on linkml\_runtime/linkml\_model/\_\_init\_\_.py
+* Add publish step to update AUTHORS and ChangeLog
+* Test change on AUTHORS
+* Update to copy of linkml-model 1.0.1
+* Replaced \_\_str\_\_() repr of EnumDefinitionImpl
 * Fix syntax for pr-test version in github actions
 * Add a couple more unit tests
 * Further fixes for issue #12.  Introduce \`remove\_empty\_items\` into all dumpers

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: 2021-06-30 17:04
+# Generation date: 2021-08-19 17:51
 # Schema: annotations
 #
 # id: https://w3id.org/linkml/annotations
@@ -9,7 +9,7 @@
 import dataclasses
 import sys
 import re
-from jsonasobj2 import JsonObj
+from jsonasobj2 import JsonObj, as_dict
 from typing import Optional, List, Union, Dict, ClassVar, Any
 from dataclasses import dataclass
 

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: 2021-06-30 17:04
+# Generation date: 2021-08-19 17:51
 # Schema: extensions
 #
 # id: https://w3id.org/linkml/extensions
@@ -9,7 +9,7 @@
 import dataclasses
 import sys
 import re
-from jsonasobj2 import JsonObj
+from jsonasobj2 import JsonObj, as_dict
 from typing import Optional, List, Union, Dict, ClassVar, Any
 from dataclasses import dataclass
 

diff --git a/linkml_runtime/linkml_model/graphql/meta.graphql b/linkml_runtime/linkml_model/graphql/meta.graphql
@@ -345,6 +345,7 @@ type SlotDefinition
     inlinedAsList: Boolean
     key: Boolean
     identifier: Boolean
+    designatesType: Boolean
     alias: String
     owner: Definition
     domainOf: [ClassDefinition]

diff --git a/linkml_runtime/linkml_model/json/annotations.json b/linkml_runtime/linkml_model/json/annotations.json
@@ -316,9 +316,9 @@
   ],
   "metamodel_version": "1.7.0",
   "source_file": "annotations.yaml",
-  "source_file_date": "Wed Jun 30 17:02:39 2021",
+  "source_file_date": "Thu Aug 19 17:49:00 2021",
   "source_file_size": 833,
-  "generation_date": "2021-06-30 17:04",
+  "generation_date": "2021-08-19 17:50",
   "@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
@@ -260,9 +260,9 @@
   ],
   "metamodel_version": "1.7.0",
   "source_file": "extensions.yaml",
-  "source_file_date": "Wed Jun 30 17:02:39 2021",
+  "source_file_date": "Thu Aug 19 17:49:00 2021",
   "source_file_size": 1043,
-  "generation_date": "2021-06-30 17:04",
+  "generation_date": "2021-08-19 17:50",
   "@type": "SchemaDefinition",
   "@context": [
     "https://w3id.org/linkml/types.context.jsonld",

diff --git a/linkml_runtime/linkml_model/json/mappings.json b/linkml_runtime/linkml_model/json/mappings.json
@@ -311,9 +311,9 @@
   ],
   "metamodel_version": "1.7.0",
   "source_file": "mappings.yaml",
-  "source_file_date": "Wed Jun 30 17:02:39 2021",
+  "source_file_date": "Thu Aug 19 17:49:00 2021",
   "source_file_size": 2656,
-  "generation_date": "2021-06-30 17:04",
+  "generation_date": "2021-08-19 17:50",
   "@type": "SchemaDefinition",
   "@context": [
     "https://w3id.org/linkml/types.context.jsonld",

diff --git a/linkml_runtime/linkml_model/json/meta.json b/linkml_runtime/linkml_model/json/meta.json
@@ -878,6 +878,9 @@
         "schema:schemaVersion"
       ],
       "description": "particular version of schema",
+      "in_subset": [
+        "owl"
+      ],
       "from_schema": "https://w3id.org/linkml/meta",
       "domain": "SchemaDefinition",
       "range": "string",
@@ -1564,6 +1567,21 @@
       ],
       "@type": "SlotDefinition"
     },
+    {
+      "name": "designates_type",
+      "definition_uri": "https://w3id.org/linkml/designates_type",
+      "description": "True means that the key slot(s) is used to determine the instantiation (types) relation between objects and a ClassDefinition",
+      "from_schema": "https://w3id.org/linkml/meta",
+      "domain": "SlotDefinition",
+      "range": "boolean",
+      "slot_uri": "https://w3id.org/linkml/designates_type",
+      "inherited": true,
+      "owner": "SlotDefinition",
+      "domain_of": [
+        "SlotDefinition"
+      ],
+      "@type": "SlotDefinition"
+    },
     {
       "name": "alias",
       "definition_uri": "https://w3id.org/linkml/alias",
@@ -2742,11 +2760,11 @@
         "column",
         "variable"
       ],
-      "description": "the definition of a property or a slot",
-      "from_schema": "https://w3id.org/linkml/meta",
       "close_mappings": [
         "rdf:Property"
       ],
+      "description": "the definition of a property or a slot",
+      "from_schema": "https://w3id.org/linkml/meta",
       "is_a": "Definition",
       "slots": [
         "name",
@@ -2798,6 +2816,7 @@
         "inlined_as_list",
         "key",
         "identifier",
+        "designates_type",
         "alias",
         "owner",
         "domain_of",
@@ -2829,11 +2848,11 @@
         "message",
         "observation"
       ],
-      "description": "the definition of a class or interface",
-      "from_schema": "https://w3id.org/linkml/meta",
       "close_mappings": [
         "owl:Class"
       ],
+      "description": "the definition of a class or interface",
+      "from_schema": "https://w3id.org/linkml/meta",
       "is_a": "Definition",
       "slots": [
         "name",
@@ -3058,9 +3077,9 @@
   ],
   "metamodel_version": "1.7.0",
   "source_file": "meta.yaml",
-  "source_file_date": "Wed Jun 30 17:02:39 2021",
-  "source_file_size": 34275,
-  "generation_date": "2021-06-30 17:04",
+  "source_file_date": "Thu Aug 19 17:49:00 2021",
+  "source_file_size": 34566,
+  "generation_date": "2021-08-19 17:50",
   "@type": "SchemaDefinition",
   "@context": [
     "https://w3id.org/linkml/types.context.jsonld",

diff --git a/linkml_runtime/linkml_model/json/types.json b/linkml_runtime/linkml_model/json/types.json
@@ -169,9 +169,9 @@
   ],
   "metamodel_version": "1.7.0",
   "source_file": "types.yaml",
-  "source_file_date": "Wed Jun 30 17:02:39 2021",
+  "source_file_date": "Thu Aug 19 17:49:00 2021",
   "source_file_size": 2676,
-  "generation_date": "2021-06-30 17:04",
+  "generation_date": "2021-08-19 17:50",
   "@type": "SchemaDefinition",
   "@context": [
     {

diff --git a/linkml_runtime/linkml_model/jsonld/annotations.context.jsonld b/linkml_runtime/linkml_model/jsonld/annotations.context.jsonld
@@ -1,5 +1,5 @@
 {
-   "_comments": "Auto generated from annotations.yaml by jsonldcontextgen.py version: 0.1.1\n    Generation date: 2021-06-30 17:04\n    Schema: annotations\n    \n    id: https://w3id.org/linkml/annotations\n    description: Annotations mixin\n    license: https://creativecommons.org/publicdomain/zero/1.0/\n    ",
+   "_comments": "Auto generated from annotations.yaml by jsonldcontextgen.py version: 0.1.1\n    Generation date: 2021-08-19 17:50\n    Schema: annotations\n    \n    id: https://w3id.org/linkml/annotations\n    description: Annotations mixin\n    license: https://creativecommons.org/publicdomain/zero/1.0/\n    ",
    "@context": {
       "linkml": "https://w3id.org/linkml/",
       "@vocab": "https://w3id.org/linkml/",

diff --git a/linkml_runtime/linkml_model/jsonld/annotations.model.context.jsonld b/linkml_runtime/linkml_model/jsonld/annotations.model.context.jsonld
@@ -1,5 +1,5 @@
 {
-   "_comments": "Auto generated from annotations.yaml by jsonldcontextgen.py version: 0.1.1\n    Generation date: 2021-06-30 17:04\n    Schema: annotations\n    \n    id: https://w3id.org/linkml/annotations\n    description: Annotations mixin\n    license: https://creativecommons.org/publicdomain/zero/1.0/\n    ",
+   "_comments": "Auto generated from annotations.yaml by jsonldcontextgen.py version: 0.1.1\n    Generation date: 2021-08-19 17:50\n    Schema: annotations\n    \n    id: https://w3id.org/linkml/annotations\n    description: Annotations mixin\n    license: https://creativecommons.org/publicdomain/zero/1.0/\n    ",
    "@context": {
       "linkml": "https://w3id.org/linkml/",
       "@vocab": "https://w3id.org/linkml/",

diff --git a/linkml_runtime/linkml_model/jsonld/context.jsonld b/linkml_runtime/linkml_model/jsonld/context.jsonld
@@ -1,5 +1,5 @@
 {
-   "_comments": "Auto generated from meta.yaml by jsonldcontextgen.py version: 0.1.1\n    Generation date: 2021-06-30 17:04\n    Schema: meta\n    \n    id: https://w3id.org/linkml/meta\n    description: A metamodel for defining linked open data schemas\n    license: https://creativecommons.org/publicdomain/zero/1.0/\n    ",
+   "_comments": "Auto generated from meta.yaml by jsonldcontextgen.py version: 0.1.1\n    Generation date: 2021-08-17 19:04\n    Schema: meta\n    \n    id: https://w3id.org/linkml/meta\n    description: A metamodel for defining linked open data schemas\n    license: https://creativecommons.org/publicdomain/zero/1.0/\n    ",
    "@context": {
       "IAO": {
          "@id": "http://purl.obolibrary.org/obo/IAO_",
@@ -82,6 +82,9 @@
       "description": {
          "@id": "skos:definition"
       },
+      "designates_type": {
+         "@type": "xsd:boolean"
+      },
       "domain": {
          "@type": "@id"
       },

diff --git a/linkml_runtime/linkml_model/jsonld/extensions.context.jsonld b/linkml_runtime/linkml_model/jsonld/extensions.context.jsonld
@@ -1,5 +1,5 @@
 {
-   "_comments": "Auto generated from extensions.yaml by jsonldcontextgen.py version: 0.1.1\n    Generation date: 2021-06-30 17:04\n    Schema: extensions\n    \n    id: https://w3id.org/linkml/extensions\n    description: Extension mixin\n    license: https://creativecommons.org/publicdomain/zero/1.0/\n    ",
+   "_comments": "Auto generated from extensions.yaml by jsonldcontextgen.py version: 0.1.1\n    Generation date: 2021-08-19 17:50\n    Schema: extensions\n    \n    id: https://w3id.org/linkml/extensions\n    description: Extension mixin\n    license: https://creativecommons.org/publicdomain/zero/1.0/\n    ",
    "@context": {
       "linkml": "https://w3id.org/linkml/",
       "@vocab": "https://w3id.org/linkml/",

diff --git a/linkml_runtime/linkml_model/jsonld/extensions.model.context.jsonld b/linkml_runtime/linkml_model/jsonld/extensions.model.context.jsonld
@@ -1,5 +1,5 @@
 {
-   "_comments": "Auto generated from extensions.yaml by jsonldcontextgen.py version: 0.1.1\n    Generation date: 2021-06-30 17:04\n    Schema: extensions\n    \n    id: https://w3id.org/linkml/extensions\n    description: Extension mixin\n    license: https://creativecommons.org/publicdomain/zero/1.0/\n    ",
+   "_comments": "Auto generated from extensions.yaml by jsonldcontextgen.py version: 0.1.1\n    Generation date: 2021-08-19 17:50\n    Schema: extensions\n    \n    id: https://w3id.org/linkml/extensions\n    description: Extension mixin\n    license: https://creativecommons.org/publicdomain/zero/1.0/\n    ",
    "@context": {
       "linkml": "https://w3id.org/linkml/",
       "@vocab": "https://w3id.org/linkml/",

diff --git a/linkml_runtime/linkml_model/jsonld/mappings.context.jsonld b/linkml_runtime/linkml_model/jsonld/mappings.context.jsonld
@@ -1,5 +1,5 @@
 {
-   "_comments": "Auto generated from mappings.yaml by jsonldcontextgen.py version: 0.1.1\n    Generation date: 2021-06-30 17:04\n    Schema: mappings\n    \n    id: https://w3id.org/linkml/mappings\n    description: LinkML model for mappings\n    license: https://creativecommons.org/publicdomain/zero/1.0/\n    ",
+   "_comments": "Auto generated from mappings.yaml by jsonldcontextgen.py version: 0.1.1\n    Generation date: 2021-08-19 17:50\n    Schema: mappings\n    \n    id: https://w3id.org/linkml/mappings\n    description: LinkML model for mappings\n    license: https://creativecommons.org/publicdomain/zero/1.0/\n    ",
    "@context": {
       "IAO": {
          "@id": "http://purl.obolibrary.org/obo/IAO_",

diff --git a/linkml_runtime/linkml_model/jsonld/mappings.model.context.jsonld b/linkml_runtime/linkml_model/jsonld/mappings.model.context.jsonld
@@ -1,5 +1,5 @@
 {
-   "_comments": "Auto generated from mappings.yaml by jsonldcontextgen.py version: 0.1.1\n    Generation date: 2021-06-30 17:04\n    Schema: mappings\n    \n    id: https://w3id.org/linkml/mappings\n    description: LinkML model for mappings\n    license: https://creativecommons.org/publicdomain/zero/1.0/\n    ",
+   "_comments": "Auto generated from mappings.yaml by jsonldcontextgen.py version: 0.1.1\n    Generation date: 2021-08-19 17:50\n    Schema: mappings\n    \n    id: https://w3id.org/linkml/mappings\n    description: LinkML model for mappings\n    license: https://creativecommons.org/publicdomain/zero/1.0/\n    ",
    "@context": {
       "IAO": {
          "@id": "http://purl.obolibrary.org/obo/IAO_",

diff --git a/linkml_runtime/linkml_model/jsonld/meta.context.jsonld b/linkml_runtime/linkml_model/jsonld/meta.context.jsonld
@@ -1,5 +1,5 @@
 {
-   "_comments": "Auto generated from meta.yaml by jsonldcontextgen.py version: 0.1.1\n    Generation date: 2021-06-30 17:04\n    Schema: meta\n    \n    id: https://w3id.org/linkml/meta\n    description: A metamodel for defining linked open data schemas\n    license: https://creativecommons.org/publicdomain/zero/1.0/\n    ",
+   "_comments": "Auto generated from meta.yaml by jsonldcontextgen.py version: 0.1.1\n    Generation date: 2021-08-19 17:50\n    Schema: meta\n    \n    id: https://w3id.org/linkml/meta\n    description: A metamodel for defining linked open data schemas\n    license: https://creativecommons.org/publicdomain/zero/1.0/\n    ",
    "@context": {
       "IAO": {
          "@id": "http://purl.obolibrary.org/obo/IAO_",
@@ -82,6 +82,9 @@
       "description": {
          "@id": "skos:definition"
       },
+      "designates_type": {
+         "@type": "xsd:boolean"
+      },
       "domain": {
          "@type": "@id"
       },

diff --git a/linkml_runtime/linkml_model/jsonld/meta.model.context.jsonld b/linkml_runtime/linkml_model/jsonld/meta.model.context.jsonld
@@ -1,5 +1,5 @@
 {
-   "_comments": "Auto generated from meta.yaml by jsonldcontextgen.py version: 0.1.1\n    Generation date: 2021-06-30 17:04\n    Schema: meta\n    \n    id: https://w3id.org/linkml/meta\n    description: A metamodel for defining linked open data schemas\n    license: https://creativecommons.org/publicdomain/zero/1.0/\n    ",
+   "_comments": "Auto generated from meta.yaml by jsonldcontextgen.py version: 0.1.1\n    Generation date: 2021-08-19 17:50\n    Schema: meta\n    \n    id: https://w3id.org/linkml/meta\n    description: A metamodel for defining linked open data schemas\n    license: https://creativecommons.org/publicdomain/zero/1.0/\n    ",
    "@context": {
       "IAO": {
          "@id": "http://purl.obolibrary.org/obo/IAO_",
@@ -82,6 +82,9 @@
       "description": {
          "@id": "skos:definition"
       },
+      "designates_type": {
+         "@type": "xsd:boolean"
+      },
       "domain": {
          "@type": "@id"
       },

diff --git a/linkml_runtime/linkml_model/jsonld/types.context.jsonld b/linkml_runtime/linkml_model/jsonld/types.context.jsonld
@@ -1,5 +1,5 @@
 {
-   "_comments": "Auto generated from types.yaml by jsonldcontextgen.py version: 0.1.1\n    Generation date: 2021-06-30 17:04\n    Schema: types\n    \n    id: https://w3id.org/linkml/types\n    description: Shared type definitions for the core LinkML mode and metamodel\n    license: https://creativecommons.org/publicdomain/zero/1.0/\n    ",
+   "_comments": "Auto generated from types.yaml by jsonldcontextgen.py version: 0.1.1\n    Generation date: 2021-08-19 17:50\n    Schema: types\n    \n    id: https://w3id.org/linkml/types\n    description: Shared type definitions for the core LinkML mode and metamodel\n    license: https://creativecommons.org/publicdomain/zero/1.0/\n    ",
    "@context": {
       "linkml": "https://w3id.org/linkml/",
       "shex": "http://www.w3.org/ns/shex#",

diff --git a/linkml_runtime/linkml_model/jsonld/types.model.context.jsonld b/linkml_runtime/linkml_model/jsonld/types.model.context.jsonld
@@ -1,5 +1,5 @@
 {
-   "_comments": "Auto generated from types.yaml by jsonldcontextgen.py version: 0.1.1\n    Generation date: 2021-06-30 17:04\n    Schema: types\n    \n    id: https://w3id.org/linkml/types\n    description: Shared type definitions for the core LinkML mode and metamodel\n    license: https://creativecommons.org/publicdomain/zero/1.0/\n    ",
+   "_comments": "Auto generated from types.yaml by jsonldcontextgen.py version: 0.1.1\n    Generation date: 2021-08-19 17:50\n    Schema: types\n    \n    id: https://w3id.org/linkml/types\n    description: Shared type definitions for the core LinkML mode and metamodel\n    license: https://creativecommons.org/publicdomain/zero/1.0/\n    ",
    "@context": {
       "linkml": "https://w3id.org/linkml/",
       "shex": "http://www.w3.org/ns/shex#",

diff --git a/linkml_runtime/linkml_model/jsonschema/annotations.schema.json b/linkml_runtime/linkml_model/jsonschema/annotations.schema.json
@@ -1,6 +1,7 @@
 {
    "$id": "https://w3id.org/linkml/annotations",
    "$schema": "http://json-schema.org/draft-07/schema#",
+   "additionalProperties": true,
    "definitions": {
       "Annotation": {
          "additionalProperties": false,

diff --git a/linkml_runtime/linkml_model/jsonschema/extensions.schema.json b/linkml_runtime/linkml_model/jsonschema/extensions.schema.json
@@ -1,6 +1,7 @@
 {
    "$id": "https://w3id.org/linkml/extensions",
    "$schema": "http://json-schema.org/draft-07/schema#",
+   "additionalProperties": true,
    "definitions": {
       "Extension": {
          "additionalProperties": false,

diff --git a/linkml_runtime/linkml_model/jsonschema/mappings.schema.json b/linkml_runtime/linkml_model/jsonschema/mappings.schema.json
@@ -1,6 +1,7 @@
 {
    "$id": "https://w3id.org/linkml/mappings",
    "$schema": "http://json-schema.org/draft-07/schema#",
+   "additionalProperties": true,
    "definitions": {},
    "properties": {},
    "title": "mappings",