Merge branch 'master' into parser

INCATools · Mar 1, 2022 · d5c31ee · d5c31ee
2 parents 1a30267 + cf8d73b
commit d5c31ee
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Showing 17 changed files with 1,047 additions and 353 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -14,5 +14,5 @@ install:
 
 # command to run tests
 script: 
-  - touch src/schema/ocl.yaml && make test
+  - touch src/schema/kgcl.yaml && make test
 
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/examples/de-novo.yaml b/examples/de-novo.yaml
@@ -11,6 +11,8 @@ change_set:
 - {type: NewSynonym, about_node: ANAT:Forelimb, new_value: "upper limb"}
 - {type: ClassCreation, node_id: ANAT:Hindlimb, name: "hindlimb", superclass: ANAT:Limb}
 - {type: NewSynonym, about_node: ANAT:Hindlimb, new_value: "lower limb"}
+- {type: SetLanguageForName, about_node: ANAT:Hindlimb, new_value: "en"}
+- {type: NewSynonym, about_node: ANAT:Mouse, new_value: "bouche", language: "fr"}
 #- {type: ClassCreation, node_id: ANAT:Foot, name: "foot", superclass: ANAT:BodyPart, relationship: {predicate: ANAT:part-of, filler: ANAT:Hindlimb}}
 #- {type: ClassCreation, node_id: ANAT:Hand, name: "hand", superclass: ANAT:BodyPart, relationship: {predicate: ANAT:part-of, filler: ANAT:Hindlimb}, was_generated_by: uuid:e887d3aac33f} ## deliberate mistake
 #- {type: NodeMove, about_node: ANAT:Hand, old_predicate: ANAT:part-of, new_predicate: ANAT:Hindlimb, new_parent: ANAT:Forelimb}

diff --git a/graphql/kgcl.graphql b/graphql/kgcl.graphql
@@ -22,6 +22,7 @@ type AddNodeToSubset implements AddToSubset
     oldValue: String
     newValue: String
     aboutNode: Node
+    language: LanguageTag
     inSubset: OntologySubset
   }
 
@@ -86,6 +87,7 @@ type ClassCreation
     oldValue: String
     newValue: String
     aboutNode: Node
+    language: LanguageTag
     nodeId: Node
     name: String
     owlType: OwlTypeEnum
@@ -134,16 +136,10 @@ interface Creation
 
 type DatatypeChange
   {
-    id: String!
-    wasGeneratedBy: Activity
-    seeAlso: String
-    pullRequest: String
-    creator: String
-    changeDate: String
-    contributor: String
-    hasUndo: Change
-    oldValue: String
-    newValue: String
+  }
+
+interface DatatypeOrLanguageTagChange
+  {
   }
 
 interface Deletion
@@ -275,6 +271,12 @@ type InstanceNode
     owlType: OwlTypeEnum
   }
 
+type LanguageTagChange
+  {
+    oldValue: LanguageTag
+    newValue: LanguageTag
+  }
+
 type LogicalAxiomChange
   {
     id: String!
@@ -293,6 +295,26 @@ 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!
@@ -321,6 +343,7 @@ type NameBecomesSynonym
     oldValue: String
     newValue: String
     aboutNode: Node
+    language: LanguageTag
     change1: NodeRename
     change2: NewSynonym
     changeDescription: String
@@ -338,6 +361,7 @@ type NewSynonym
     hasUndo: Change
     oldValue: String
     aboutNode: Node
+    language: LanguageTag
     newValue: String
   }
 
@@ -353,6 +377,7 @@ type NewTextDefinition
     hasUndo: Change
     oldValue: String
     aboutNode: Node
+    language: LanguageTag
     newValue: String
   }
 
@@ -377,6 +402,7 @@ type NodeAnnotationChange
     oldValue: String
     newValue: String
     aboutNode: Node
+    language: LanguageTag
   }
 
 type NodeAnnotationReplacement
@@ -392,6 +418,7 @@ type NodeAnnotationReplacement
     oldValue: String
     newValue: String
     aboutNode: Node
+    language: LanguageTag
   }
 
 interface NodeChange
@@ -407,6 +434,7 @@ interface NodeChange
     oldValue: String
     newValue: String
     aboutNode: Node
+    language: LanguageTag
   }
 
 type NodeCreation implements Creation
@@ -422,6 +450,7 @@ type NodeCreation implements Creation
     oldValue: String
     newValue: String
     aboutNode: Node
+    language: LanguageTag
     nodeId: Node
     name: String
     owlType: OwlTypeEnum
@@ -459,6 +488,7 @@ type NodeDeletion implements Deletion
     oldValue: String
     newValue: String
     aboutNode: Node
+    language: LanguageTag
     changeDescription: String
   }
 
@@ -474,6 +504,7 @@ type NodeDirectMerge implements AllowsAutomaticReplacementOfEdges
     hasUndo: Change
     oldValue: String
     newValue: String
+    language: LanguageTag
     hasNondirectReplacement: [Node]
     associatedChangeSet: [Change]
     about: OntologyElement
@@ -512,6 +543,7 @@ type NodeObsoletion implements Obsoletion
     oldValue: String
     newValue: String
     aboutNode: Node
+    language: LanguageTag
     hasDirectReplacement: Node
     hasNondirectReplacement: [Node]
     changeDescription: String
@@ -532,6 +564,7 @@ type NodeObsoletionWithDirectReplacement implements AllowsAutomaticReplacementOf
     oldValue: String
     newValue: String
     aboutNode: Node
+    language: LanguageTag
     hasNondirectReplacement: [Node]
     associatedChangeSet: [Change]
     about: OntologyElement
@@ -552,6 +585,7 @@ type NodeObsoletionWithNoDirectReplacement
     oldValue: String
     newValue: String
     aboutNode: Node
+    language: LanguageTag
     hasDirectReplacement: Node
     associatedChangeSet: [Change]
     about: OntologyElement
@@ -570,6 +604,7 @@ type NodeRename
     contributor: String
     hasUndo: Change
     aboutNode: Node
+    language: LanguageTag
     oldValue: String
     newValue: String
     hasTextualDiff: TextualDiff
@@ -606,6 +641,7 @@ type NodeSynonymChange
     oldValue: String
     newValue: String
     aboutNode: Node
+    language: LanguageTag
   }
 
 interface NodeTextDefinitionChange
@@ -621,6 +657,7 @@ interface NodeTextDefinitionChange
     oldValue: String
     newValue: String
     aboutNode: Node
+    language: LanguageTag
   }
 
 type NodeUnobsoletion implements Unobsoletion
@@ -636,6 +673,7 @@ type NodeUnobsoletion implements Unobsoletion
     oldValue: String
     newValue: String
     aboutNode: Node
+    language: LanguageTag
     changeDescription: String
     replacedBy: Node
     consider: Node
@@ -716,6 +754,7 @@ type RemoveSynonym
     hasUndo: Change
     newValue: String
     aboutNode: Node
+    language: LanguageTag
     oldValue: String
   }
 
@@ -731,6 +770,7 @@ type RemoveTextDefinition
     hasUndo: Change
     newValue: String
     aboutNode: Node
+    language: LanguageTag
     oldValue: String
   }
 
@@ -746,6 +786,7 @@ type RemovedNodeFromSubset implements RemoveFromSubset
     hasUndo: Change
     oldValue: String
     newValue: String
+    language: LanguageTag
     changeDescription: String
     aboutNode: Node
     subset: String
@@ -758,6 +799,23 @@ type Session
     activitySet: [Activity]
   }
 
+type SetLanguageForName implements LanguageTagChange
+  {
+    id: String!
+    wasGeneratedBy: Activity
+    seeAlso: String
+    pullRequest: String
+    creator: String
+    changeDate: String
+    contributor: String
+    hasUndo: Change
+    aboutNode: Node
+    language: LanguageTag
+    oldValue: String
+    newValue: String
+    changeDescription: String
+  }
+
 interface SimpleChange
   {
     id: String!
@@ -788,6 +846,7 @@ type SynonymPredicateChange
     contributor: String
     hasUndo: Change
     aboutNode: Node
+    language: LanguageTag
     oldValue: String
     newValue: String
     hasTextualDiff: TextualDiff
@@ -804,6 +863,7 @@ type SynonymReplacement
     contributor: String
     hasUndo: Change
     aboutNode: Node
+    language: LanguageTag
     oldValue: String
     newValue: String
     hasTextualDiff: TextualDiff
@@ -820,6 +880,7 @@ type TextDefinitionReplacement
     contributor: String
     hasUndo: Change
     aboutNode: Node
+    language: LanguageTag
     oldValue: String
     newValue: String
     hasTextualDiff: TextualDiff