Add SynonymReplacement (#73)

src/data/examples/examples.yaml

@@ -59,29 +59,39 @@ Test_6:
   command_with_curie: remove synonym 'foo' for GO:0005634
   command_with_uri: remove synonym 'foo' for http://purl.obolibrary.org/obo/GO_0005634
 Test_7:
+  id: CHANGE:001
+  type: SynonymReplacement
+  old_value: '''cell nucleus'''
+  new_value: '''cell NUCLEUS'''
+  about_node: GO:0005634
+  about_node_representation: curie
+  command_with_curie: change synonym 'cell nucleus' for GO:0005634 to 'cell NUCLEUS'
+  command_with_uri: change synonym 'cell nucleus' for http://purl.obolibrary.org/obo/GO_0005634
+    to 'cell NUCLEUS'
+Test_8:
   id: CHANGE:001
   type: AddNodeToSubset
   about_node: GO:0005634
   about_node_representation: curie
   in_subset: foo
   command_with_curie: add GO:0005634 to subset foo
   command_with_uri: add http://purl.obolibrary.org/obo/GO_0005634 to subset foo
-Test_8:
+Test_9:
   id: CHANGE:001
   type: RemoveNodeFromSubset
   about_node: GO:0005634
   about_node_representation: curie
   in_subset: foo
   command_with_curie: remove GO:0005634 from subset foo
   command_with_uri: remove http://purl.obolibrary.org/obo/GO_0005634 from subset foo
-Test_9:
+Test_10:
   id: CHANGE:001
   type: ClassCreation
   about_node_representation: curie
   node_id: GO:9999999
   command_with_curie: create GO:9999999
   command_with_uri: create http://purl.obolibrary.org/obo/GO_9999999
-Test_10:
+Test_11:
   id: CHANGE:001
   type: NodeCreation
   about_node: GO:9999999
@@ -90,7 +100,7 @@ Test_10:
   name: '''foo'''
   command_with_curie: create node GO:9999999 'foo'
   command_with_uri: TODO
-Test_11:
+Test_12:
   id: CHANGE:001
   type: EdgeCreation
   object_type: curie
@@ -102,7 +112,7 @@ Test_11:
   command_with_curie: create edge GO:0005634 BFO:0000050 GO:0009411
   command_with_uri: create edge http://purl.obolibrary.org/obo/GO_0005634 http://purl.obolibrary.org/obo/BFO_0000050
     http://purl.obolibrary.org/obo/GO_0009411
-Test_12:
+Test_13:
   id: CHANGE:001
   type: PlaceUnder
   object_type: curie
@@ -114,7 +124,7 @@ Test_12:
   command_with_curie: create edge GO:0005634 rdfs:subClassOf GO:0009411
   command_with_uri: create edge http://purl.obolibrary.org/obo/GO_0005634 http://www.w3.org/2000/01/rdf-schema#subClassOf
     http://purl.obolibrary.org/obo/GO_0009411
-Test_13:
+Test_14:
   id: CHANGE:001
   type: PredicateChange
   old_value: BFO:0000050
@@ -130,7 +140,7 @@ Test_13:
     object_representation: curie
   command_with_curie: change relationship between GO:0005635 and GO:0005634 from BFO:0000050
     to rdfs:subClassOf
-Test_14:
+Test_15:
   id: CHANGE:001
   type: PredicateChange
   old_value: rdfs:subClassOf
@@ -149,7 +159,7 @@ Test_14:
   command_with_uri: change relationship between http://purl.obolibrary.org/obo/GO_0005634
     and http://purl.obolibrary.org/obo/GO_0043231 from http://www.w3.org/2000/01/rdf-schema#subClassOf
     to http://purl.obolibrary.org/obo/BFO_0000050
-Test_15:
+Test_16:
   id: CHANGE:001
   type: RemoveUnder
   object_type: curie
@@ -161,7 +171,7 @@ Test_15:
   command_with_curie: delete edge GO:0005634 rdfs:subClassOf GO:0043231
   command_with_uri: delete edge http://purl.obolibrary.org/obo/GO_0005634 http://www.w3.org/2000/01/rdf-schema#subClassOf
     http://purl.obolibrary.org/obo/GO_0043231
-Test_16:
+Test_17:
   id: CHANGE:001
   type: EdgeDeletion
   object_type: curie
@@ -172,7 +182,7 @@ Test_16:
   predicate_type: curie
   command_with_curie: delete edge GO:0005635 BFO:0000050 GO:0005634
   command_with_uri: TODO
-Test_17:
+Test_18:
   id: CHANGE:001
   type: NodeDeepening
   old_value: GO:0043231
@@ -186,15 +196,15 @@ Test_17:
   new_object_type: curie
   command_with_curie: deepen GO:0005739 from GO:0043231 to GO:0005634
   command_with_uri: TODO
-Test_18:
+Test_19:
   id: CHANGE:001
   type: NewTextDefinition
   new_value: '''this is dummy description'''
   about_node: GO:0005635
   about_node_representation: curie
   command_with_curie: add definition 'this is dummy description' to GO:0005635
   command_with_uri: add definition 'this is dummy description' to http://purl.obolibrary.org/obo/GO_0005635
-Test_19:
+Test_20:
   id: CHANGE:001
   type: NodeTextDefinitionChange
   new_value: '''this is dummy description'''
@@ -203,21 +213,21 @@ Test_19:
   command_with_curie: change definition of GO:0005635 to 'this is dummy description'
   command_with_uri: change definition of http://purl.obolibrary.org/obo/GO_0005635
     to 'this is dummy description'
-Test_20:
+Test_21:
   id: CHANGE:001
   type: RemoveTextDefinition
   about_node: GO:0005634
   about_node_representation: curie
   command_with_curie: remove definition for GO:0005634
   command_with_uri: remove definition for http://purl.obolibrary.org/obo/GO_0005634
-Test_21:
+Test_22:
   id: CHANGE:001
   type: NodeObsoletion
   about_node: GO:0005634
   about_node_representation: curie
   command_with_curie: obsolete GO:0005634
   command_with_uri: obsolete http://purl.obolibrary.org/obo/GO_0005634
-Test_22:
+Test_23:
   id: CHANGE:001
   type: NodeObsoletionWithDirectReplacement
   about_node: GO:0005634

src/docs/examples.md

@@ -50,6 +50,17 @@ old_value: foo
 about_node: GO:0005634
 about_node_representation: curie
 
+```
+## Example: Replace synonym of a node.
+Class: [`SynonymReplacement`](https://w3id.org/kgcl/SynonymReplacement) </br></br>Command: `change synonym 'cell nucleus' for GO:0005634 to 'cell NUCLEUS'`</br></br>YAML:
+```
+id: CHANGE:001
+type: SynonymReplacement
+old_value: cell nucleus
+new_value: cell NUCLEUS
+about_node: GO:0005634
+about_node_representation: curie
+
 ```
 ## Example: Addition of a node to a subset.
 Class: [`AddNodeToSubset`](https://w3id.org/kgcl/AddNodeToSubset) </br></br>Command: `add GO:0005634 to subset foo`</br></br>YAML:

src/kgcl_schema/datamodel/kgcl.py

@@ -1,5 +1,5 @@
 # Auto generated from kgcl.yaml by pythongen.py version: 0.0.1
-# Generation date: 2024-03-08T08:41:57
+# Generation date: 2024-03-29T11:44:23
 # Schema: kgcl_schema
 #
 # id: https://w3id.org/kgcl
@@ -1573,6 +1573,7 @@ class SynonymReplacement(NodeSynonymChange):
     id: Union[str, SynonymReplacementId] = None
     old_value: Optional[str] = None
     new_value: Optional[str] = None
+    qualifier: Optional[str] = None
     has_textual_diff: Optional[Union[dict, "TextualDiff"]] = None
 
     def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
@@ -1587,6 +1588,9 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         if self.new_value is not None and not isinstance(self.new_value, str):
             self.new_value = str(self.new_value)
 
+        if self.qualifier is not None and not isinstance(self.qualifier, str):
+            self.qualifier = str(self.qualifier)
+
         if self.has_textual_diff is not None and not isinstance(self.has_textual_diff, TextualDiff):
             self.has_textual_diff = TextualDiff()
 

src/kgcl_schema/grammar/kgcl.lark

@@ -18,6 +18,7 @@
            | add_definition
            | change_definition
            | remove_definition
+           | change_synonym
 
 rename : "rename" _WS [id _WS "from" _WS] old_label ["@" old_language] _WS ("to"|"as"|"->") _WS new_label ["@" new_language]
 
@@ -29,6 +30,8 @@ synonym_qualifier : /exact|narrow|broad|related/
 
 remove_synonym: "remove" _WS "synonym" _WS synonym ["@" language] _WS "for" _WS entity
 
+change_synonym: "change" _WS [synonym_qualifier _WS] "synonym" _WS synonym ["@" language] _WS "for" _WS entity _WS ("to"|"->") _WS new_synonym
+
 delete : "delete" _WS entity
 
 obsolete : "obsolete" _WS entity
@@ -62,6 +65,8 @@ id : ID
 
 subset: ID
 synonym : LABEL
+old_synonym: LABEL
+new_synonym: LABEL
 
 subclass: _entity
 superclass: _entity

src/kgcl_schema/grammar/parser.py

@@ -35,6 +35,7 @@
     RemoveUnder,
     Session,
     RemoveTextDefinition,
+    SynonymReplacement,
 )
 from kgcl_schema.datamodel.ontology_model import Edge
 from kgcl_schema.utils import to_json, to_rdf, to_yaml
@@ -138,6 +139,8 @@ def parse_statement(input: str) -> Change:
         return parse_change_definition(tree, id)
     elif command == "remove_definition":
         return parse_remove_definition(tree, id)
+    elif command == "change_synonym":
+        return parse_change_synonym(tree, id)
     else:
         raise NotImplementedError("No implementation for KGCL command: " + command)
 
@@ -223,6 +226,20 @@ def parse_remove_synonym(tree, id):
         language=language_token,
     )
 
+def parse_change_synonym(tree, id):
+    """Change the synonym of a class."""
+    entity_token = extract(tree, "entity")
+    old_value = extract(tree, "synonym")
+    new_value = extract(tree, "new_synonym")
+    entity, representation = get_entity_representation(entity_token)
+    return SynonymReplacement(
+        id=id,
+        about_node=entity,
+        about_node_representation=representation,
+        new_value=new_value,
+        old_value=old_value,
+    )
+
 
 def parse_create_class(tree, id):
     """Create new class."""

src/kgcl_schema/grammar/render_operations.py

@@ -25,6 +25,7 @@
     RemoveTextDefinition,
     RemoveUnder,
     Change,
+    SynonymReplacement,
 )
 from lark.lexer import Token
 
@@ -231,6 +232,38 @@ def render(kgcl_instance: Change) -> str:
         # else:
         return "remove synonym " + synonym + " for " + subject
 
+    if type(kgcl_instance) is SynonymReplacement:
+        subject = render_entity(kgcl_instance.about_node, "uri")
+        old_synonym = render_entity(kgcl_instance.old_value, "label")
+        new_synonym = render_entity(kgcl_instance.new_value, "label")
+        qualifier = kgcl_instance.qualifier
+        language = kgcl_instance.language
+
+        if language is not None:
+            old_synonym = old_synonym + "@" + language
+            new_synonym = new_synonym + "@" + language
+
+        if qualifier is not None:
+            return (
+                "change "
+                + qualifier
+                + " synonym "
+                + old_synonym
+                + " for "
+                + subject
+                + " to "
+                + new_synonym
+            )
+        else:
+            return (
+                "change synonym "
+                + old_synonym
+                + " for "
+                + subject
+                + " to "
+                + new_synonym
+            )
+
     if type(kgcl_instance) is PlaceUnder:
         subclass = render_entity(kgcl_instance.subject, "uri")
         superclass = render_entity(kgcl_instance.object, "uri")

src/kgcl_schema/schema/kgcl.yaml

@@ -479,6 +479,7 @@ classes:
     slots:
     - old_value
     - new_value
+    - qualifier
     - has_textual_diff
   SynonymPredicateChange:
     aliases:

tests/cases.py

@@ -20,6 +20,7 @@
     NodeDeepening,
     AddNodeToSubset,
     RemoveNodeFromSubset,
+    SynonymReplacement,
 )
 from kgcl_schema.datamodel.ontology_model import Edge
 
@@ -148,6 +149,18 @@
         ),
         None,
     ),
+    (
+        f"change synonym 'cell nucleus' for {NUCLEUS} to 'cell NUCLEUS'",
+        f"change synonym 'cell nucleus' for {NUCLEUS_URI} to 'cell NUCLEUS'",
+        SynonymReplacement(
+            id=UID,
+            about_node=NUCLEUS,
+            about_node_representation="curie",
+            old_value="'cell nucleus'",
+            new_value="'cell NUCLEUS'",
+        ),
+        None,
+    ),
     (
         f"add {NUCLEUS} to subset foo",
         f"add {NUCLEUS_URI} to subset foo",

tests/test_case_dumpers.py

@@ -52,6 +52,7 @@
     "NewTextDefinition": "New definition of a node.",
     "NodeTextDefinitionChange": "Update defintion of a node.",
     "RemoveTextDefinition": "Remove definition of a node.",
+    "SynonymReplacement": "Replace synonym of a node.",
 }