linkml-1.0.4

INCATools · Aug 19, 2021 · 7c711a3 · 7c711a3
1 parent 7c63429
commit 7c711a3
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Showing 10 changed files with 502 additions and 206 deletions.
diff --git a/Makefile b/Makefile
@@ -5,7 +5,7 @@ SCHEMA_NAMES = $(patsubst $(SCHEMA_DIR)/%.yaml, %, $(SOURCE_FILES))
 
 SCHEMA_NAME = kgcl
 SCHEMA_SRC = $(SCHEMA_DIR)/$(SCHEMA_NAME).yaml
-TGTS = graphql jsonschema ldcontext docs  owl csv graphql python shex
+TGTS = graphql jsonschema ldcontext docs  owl csv graphql python shex sql
 
 #GEN_OPTS = --no-mergeimports
 GEN_OPTS = 
@@ -22,10 +22,10 @@ t:
 echo:
 	echo $(patsubst %,gen-%,$(TGTS))
 
-test: all pytest
+test: all test_framework
 
-pytest:
-	pytest
+test_framework:
+	pipenv run python -m unittest discover -p 'test_*.py'
 
 install:
 	. environment.sh
@@ -80,7 +80,7 @@ target/ldcontext/%.context.jsonld: $(SCHEMA_DIR)/%.yaml tdir-ldcontext
 
 ###  -- SQL schema --
 # TODO: modularize imports. For now imports are merged.
-gen-sqlddl: target/sql/$(SCHEMA_NAME).schema.sql
+gen-sql: target/sql/$(SCHEMA_NAME).schema.sql
 target/sql/%.schema.sql: $(SCHEMA_DIR)/%.yaml tdir-sql
 	gen-sqlddl $(GEN_OPTS) --dialect sqlite $< > $@
 

diff --git a/graphql/kgcl.graphql b/graphql/kgcl.graphql
@@ -293,6 +293,26 @@ type LogicalDefinition
   {
   }
 
+type MappingCreation implements Creation
+  {
+    id: String!
+    wasGeneratedBy: Activity
+    seeAlso: String
+    pullRequest: String
+    creator: String
+    changeDate: String
+    contributor: String
+    hasUndo: Change
+    oldValue: String
+    newValue: String
+    aboutEdge: Edge
+    subject: Node
+    predicate: Node
+    object: Node
+    annotationSet: Annotation
+    changeDescription: String
+  }
+
 type MultiNodeObsoletion
   {
     id: String!

diff --git a/jsonschema/kgcl.schema.json b/jsonschema/kgcl.schema.json
@@ -1,6 +1,7 @@
 {
    "$id": "https://w3id.org/kgcl",
    "$schema": "http://json-schema.org/draft-07/schema#",
+   "additionalProperties": true,
    "definitions": {
       "Activity": {
          "additionalProperties": false,
@@ -190,7 +191,7 @@
                "type": "string"
             },
             "owl_type": {
-               "type": "string"
+               "$ref": "#/definitions/OwlTypeEnum"
             },
             "pull_request": {
                "type": "string"
@@ -225,7 +226,7 @@
                "type": "string"
             },
             "owl_type": {
-               "type": "string"
+               "$ref": "#/definitions/OwlTypeEnum"
             }
          },
          "required": [
@@ -260,7 +261,7 @@
                "type": "string"
             },
             "synonym_predicates": {
-               "$ref": "string"
+               "$ref": null
             }
          },
          "required": [],
@@ -636,7 +637,7 @@
                "type": "string"
             },
             "owl_type": {
-               "type": "string"
+               "$ref": "#/definitions/OwlTypeEnum"
             }
          },
          "required": [
@@ -697,6 +698,71 @@
          "title": "LogicalDefinition",
          "type": "object"
       },
+      "MappingCreation": {
+         "additionalProperties": false,
+         "description": "A specific kind of edge creation in which the created edge is a mapping.",
+         "properties": {
+            "about_edge": {
+               "$ref": "#/definitions/Edge"
+            },
+            "annotation_set": {
+               "$ref": "#/definitions/Annotation"
+            },
+            "change_date": {
+               "type": "string"
+            },
+            "change_description": {
+               "type": "string"
+            },
+            "contributor": {
+               "type": "string"
+            },
+            "creator": {
+               "type": "string"
+            },
+            "has_undo": {
+               "description": "A change that reverses this change",
+               "type": "string"
+            },
+            "id": {
+               "type": "string"
+            },
+            "new_value": {
+               "description": "The value of a property held in the new instance of the ontology",
+               "type": "string"
+            },
+            "object": {
+               "description": "This corresponds to object_id in SSSOM",
+               "type": "string"
+            },
+            "old_value": {
+               "description": "The value of a property held in the old instance of the ontology",
+               "type": "string"
+            },
+            "predicate": {
+               "description": "This corresponds to predicate_id in SSSOM. The value of this is typically a predicate from SKOS",
+               "type": "string"
+            },
+            "pull_request": {
+               "type": "string"
+            },
+            "see_also": {
+               "type": "string"
+            },
+            "subject": {
+               "description": "This corresponds to subject_id in SSSOM",
+               "type": "string"
+            },
+            "was_generated_by": {
+               "type": "string"
+            }
+         },
+         "required": [
+            "id"
+         ],
+         "title": "MappingCreation",
+         "type": "object"
+      },
       "MultiNodeObsoletion": {
          "additionalProperties": false,
          "description": "A complex change consisting of multiple obsoletions.",
@@ -913,7 +979,7 @@
                "type": "string"
             },
             "owl_type": {
-               "type": "string"
+               "$ref": "#/definitions/OwlTypeEnum"
             }
          },
          "required": [
@@ -1061,7 +1127,7 @@
                "type": "string"
             },
             "owl_type": {
-               "type": "string"
+               "$ref": "#/definitions/OwlTypeEnum"
             },
             "pull_request": {
                "type": "string"
@@ -1747,6 +1813,16 @@
          "title": "OntologySubset",
          "type": "object"
       },
+      "OwlTypeEnum": {
+         "description": "",
+         "enum": [
+            "CLASS",
+            "OBJECT_PROPERTY",
+            "NAMED_INDIVIDUAL"
+         ],
+         "title": "OwlTypeEnum",
+         "type": "string"
+      },
       "PlaceUnder": {
          "additionalProperties": false,
          "description": "An edge creation where the predicate is owl:subClassOf",
@@ -2154,6 +2230,17 @@
          "title": "SynonymReplacement",
          "type": "object"
       },
+      "SynonymScopeEnum": {
+         "description": "",
+         "enum": [
+            "related",
+            "broad",
+            "narrow",
+            "exact"
+         ],
+         "title": "SynonymScopeEnum",
+         "type": "string"
+      },
       "TextDefinitionReplacement": {
          "additionalProperties": false,
          "description": "A node change where a text definition is modified",