Merge pull request #25 from INCATools/remove-synonym

Remove synonym

src/data/examples/examples.yaml

@@ -51,13 +51,21 @@ Test_5:
   command_with_curie: create broad synonym 'foo'@en for GO:0005634
   command_with_uri: create broad synonym 'foo'@en for http://purl.obolibrary.org/obo/GO_0005634
 Test_6:
+  id: CHANGE:001
+  type: RemoveSynonym
+  old_value: foo
+  about_node: GO:0005634
+  about_node_representation: curie
+  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: 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_7:
+Test_8:
   id: CHANGE:001
   type: NodeCreation
   about_node: GO:9999999
@@ -66,7 +74,7 @@ Test_7:
   name: '''foo'''
   command_with_curie: create node GO:9999999 'foo'
   command_with_uri: TODO
-Test_8:
+Test_9:
   id: CHANGE:001
   type: EdgeCreation
   object_type: curie
@@ -78,7 +86,7 @@ Test_8:
   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_9:
+Test_10:
   id: CHANGE:001
   type: PlaceUnder
   object_type: curie
@@ -90,7 +98,7 @@ Test_9:
   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_10:
+Test_11:
   id: CHANGE:001
   type: PredicateChange
   old_value: BFO:0000050
@@ -106,7 +114,7 @@ Test_10:
     object_representation: curie
   command_with_curie: change relationship between GO:0005635 and GO:0005634 from BFO:0000050
     to rdfs:subClassOf
-Test_11:
+Test_12:
   id: CHANGE:001
   type: PredicateChange
   old_value: rdfs:subClassOf
@@ -125,7 +133,7 @@ Test_11:
   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_12:
+Test_13:
   id: CHANGE:001
   type: RemoveUnder
   object_type: curie
@@ -137,7 +145,7 @@ Test_12:
   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_13:
+Test_14:
   id: CHANGE:001
   type: EdgeDeletion
   object_type: curie
@@ -148,7 +156,7 @@ Test_13:
   predicate_type: curie
   command_with_curie: delete edge GO:0005635 BFO:0000050 GO:0005634
   command_with_uri: TODO
-Test_14:
+Test_15:
   id: CHANGE:001
   type: NodeDeepening
   old_value: GO:0043231

src/docs/examples.md

@@ -36,6 +36,15 @@ about_node: GO:0005634
 about_node_representation: curie
 qualifier: exact
 
+```
+## Example: Removal of a synonym.
+Class: [`RemoveSynonym`](https://w3id.org/kgcl/RemoveSynonym) </br></br>Command: `remove synonym 'foo' for GO:0005634`</br></br>YAML:
+```
+id: CHANGE:001
+old_value: foo
+about_node: GO:0005634
+about_node_representation: curie
+
 ```
 ## Example: Creation of new class.
 Class: [`ClassCreation`](https://w3id.org/kgcl/ClassCreation) </br></br>Command: `create GO:9999999`</br></br>YAML:

src/kgcl_schema/grammar/kgcl.lark

@@ -12,6 +12,7 @@
            | create_edge
            | delete_edge 
            | create_synonym 
+           | remove_synonym 
            | remove_from_subset
            | add_to_subset 
 
@@ -23,6 +24,8 @@ create_class: "create" _WS id
 create_synonym: "create" _WS [synonym_qualifier _WS] "synonym" _WS synonym ["@" language] _WS "for" _WS entity
 synonym_qualifier : /exact|narrow|broad|related/
 
+remove_synonym: "remove" _WS "synonym" _WS synonym ["@" language] _WS "for" _WS entity
+
 delete : "delete" _WS entity
 
 obsolete : "obsolete" _WS entity

src/kgcl_schema/grammar/parser.py

@@ -25,6 +25,7 @@
     NodeUnobsoletion,
     PlaceUnder,
     PredicateChange,
+    RemoveSynonym,
     RemovedNodeFromSubset,
     RemoveUnder,
     Session,
@@ -116,6 +117,8 @@ def parse_statement(input: str) -> Change:
         return parse_create_synonym(tree, id)
     elif command == "remove_from_subset":
         return parse_remove_from_subset(tree, id)
+    elif command == "remove_synonym":
+        return parse_remove_synonym(tree, id)
     else:
         raise NotImplementedError("No implementation for KGCL command: " + command)
 
@@ -174,6 +177,27 @@ def parse_create_synonym(tree, id):
     )
 
 
+def parse_remove_synonym(tree, id):
+    """Remove a synonym."""
+    entity_token = extract(tree, "entity")
+    entity, representation = get_entity_representation(entity_token)
+
+    synonym_string_token = extract(tree, "synonym")
+    synonym, _ = get_entity_representation(synonym_string_token)
+
+    language_token = extract(tree, "language")
+    # qualifier_token = extract(tree, "synonym_qualifier")
+
+    return RemoveSynonym(
+        id=id,
+        old_value=synonym,
+        about_node=entity,
+        about_node_representation=representation,
+        # qualifier=qualifier_token,
+        language=language_token,
+    )
+
+
 def parse_create_class(tree, id):
     """Create new class."""
     term_id_token = extract(tree, "id")

src/kgcl_schema/grammar/render_operations.py

@@ -17,6 +17,7 @@
     NodeUnobsoletion,
     PlaceUnder,
     PredicateChange,
+    RemoveSynonym,
     RemoveUnder,
     Change,
 )
@@ -209,6 +210,22 @@ def render(kgcl_instance: Change) -> str:
         else:
             return "create synonym " + synonym + " for " + subject
 
+    if type(kgcl_instance) is RemoveSynonym:
+        subject = render_entity(kgcl_instance.about_node, "uri")
+        synonym = render_entity(kgcl_instance.old_value, "label")
+        # qualifier = kgcl_instance.qualifier
+        language = kgcl_instance.language
+
+        if language is not None:
+            synonym = synonym + "@" + language
+
+        # if qualifier is not None:
+        #     return (
+        #         "remove " + qualifier + " synonym" + " " + synonym + " for " + subject
+        #     )
+        # else:
+        return "remove synonym " + synonym + " for " + subject
+
     if type(kgcl_instance) is PlaceUnder:
         subclass = render_entity(kgcl_instance.subject, "uri")
         superclass = render_entity(kgcl_instance.object, "uri")

tests/cases.py

@@ -11,6 +11,7 @@
     NodeCreation,
     EdgeCreation,
     PlaceUnder,
+    RemoveSynonym,
     RemoveUnder,
     EdgeDeletion,
     NodeDeepening,
@@ -131,6 +132,17 @@
         ),
         None,
     ),
+    (
+        f"remove synonym 'foo' for {NUCLEUS}",
+        f"remove synonym 'foo' for {NUCLEUS_URI}",
+        RemoveSynonym(
+            id=UID,
+            about_node=NUCLEUS,
+            about_node_representation="curie",
+            old_value="foo",
+        ),
+        None,
+    ),
     (
         f"create {NEW_TERM}",
         f"create {NEW_TERM_URI}",

tests/test_case_dumpers.py

@@ -37,6 +37,7 @@
     "NodeRename": "Rename node.",
     "NodeObsoletion": "Obsolete node.",
     "NewSynonym": "Addition of a new synonym.",
+    "RemoveSynonym": "Removal of a synonym.",
     "ClassCreation": "Creation of new class.",
     "PredicateChange": "Change predicate.",
     "Change": "Change node.",