Merge pull request #26 from INCATools/add-definition

Add `NewTextDefinition`

src/data/examples/examples.yaml

@@ -170,3 +170,11 @@ Test_15:
   new_object_type: curie
   command_with_curie: deepen GO:0005739 from GO:0043231 to GO:0005634
   command_with_uri: TODO
+Test_16:
+  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

src/docs/examples.md

@@ -144,3 +144,12 @@ old_object_type: curie
 new_object_type: curie
 
 ```
+## Example: New definition of a node.
+Class: [`NewTextDefinition`](https://w3id.org/kgcl/NewTextDefinition) </br></br>Command: `add definition 'this is dummy description' to GO:0005635`</br></br>YAML:
+```
+id: CHANGE:001
+new_value: this is dummy description
+about_node: GO:0005635
+about_node_representation: curie
+
+```

src/kgcl_schema/grammar/kgcl.lark

@@ -15,6 +15,7 @@
            | remove_synonym 
            | remove_from_subset
            | add_to_subset 
+           | add_definition
 
 rename : "rename" _WS [id _WS "from" _WS] old_label ["@" old_language] _WS ("to"|"as"|"->") _WS new_label ["@" new_language]
 
@@ -45,6 +46,7 @@ change_relationship: "change relationship between" _WS entity_subject _WS "and"
 
 change_annotation: "change annotation of" _WS entity_subject _WS "with" _WS entity_predicate _WS "from" _WS old_entity_object _WS "to" _WS new_entity_object
 
+add_definition: "add definition" _WS definition _WS "to" _WS entity
 
 remove_from_subset :  "remove" _WS id _WS "from subset" _WS subset
 add_to_subset :  "add" _WS id _WS "to subset" _WS subset
@@ -64,6 +66,7 @@ filler: _entity
 label : SINGLE_QUOTE_LITERAL
 old_label : SINGLE_QUOTE_LITERAL
 new_label : SINGLE_QUOTE_LITERAL
+definition : SINGLE_QUOTE_LITERAL
 
 language: LANGUAGE_TAG
 old_language : LANGUAGE_TAG

src/kgcl_schema/grammar/parser.py

@@ -13,6 +13,7 @@
     EdgeCreation,
     EdgeDeletion,
     NewSynonym,
+    NewTextDefinition,
     NodeAnnotationChange,
     NodeCreation,
     NodeDeepening,
@@ -119,6 +120,8 @@ def parse_statement(input: str) -> Change:
         return parse_remove_from_subset(tree, id)
     elif command == "remove_synonym":
         return parse_remove_synonym(tree, id)
+    elif command == "add_definition":
+        return parse_add_definition(tree, id)
     else:
         raise NotImplementedError("No implementation for KGCL command: " + command)
 
@@ -208,6 +211,19 @@ def parse_create_class(tree, id):
     )
 
 
+def parse_add_definition(tree, id):
+    """Add definition to class."""
+    entity_token = extract(tree, "entity")
+    new_value = extract(tree, "definition")
+    entity, representation = get_entity_representation(entity_token)
+    return NewTextDefinition(
+        id=id,
+        about_node=entity,
+        about_node_representation=representation,
+        new_value=new_value,
+    )
+
+
 # the KGCL model suggests the command
 # 'create node {id} {label} with {annotation set}'
 # TODO: handling of {annotation set}

src/kgcl_schema/grammar/render_operations.py

@@ -6,6 +6,7 @@
     EdgeCreation,
     EdgeDeletion,
     NewSynonym,
+    NewTextDefinition,
     NodeAnnotationChange,
     NodeCreation,
     NodeDeepening,
@@ -256,3 +257,8 @@ def render(kgcl_instance: Change) -> str:
         old_value = kgcl_instance.old_value
         new_value = kgcl_instance.new_value
         return "deepen " + subject + " from " + old_value + " to " + new_value
+
+    if type(kgcl_instance) is NewTextDefinition:
+        subject = kgcl_instance.about_node
+        definition = kgcl_instance.new_value
+        return "add definition " + definition + " to " + subject

tests/cases.py

@@ -1,6 +1,7 @@
 from typing import Tuple, Optional, List, Union
 
 from kgcl_schema.datamodel.kgcl import (
+    NewTextDefinition,
     NodeObsoletionWithDirectReplacement,
     NodeRename,
     NodeObsoletion,
@@ -293,4 +294,15 @@
         ),
         None,
     ),
+    (
+        f"add definition 'this is dummy description' to {NUCLEAR_ENVELOPE}",
+        f"add definition 'this is dummy description' to {NUCLEAR_ENVELOPE_URI}",
+        NewTextDefinition(
+            id=UID,
+            new_value="'this is dummy description'",
+            about_node="GO:0005635",
+            about_node_representation="curie",
+        ),
+        None,
+    ),
 ]

tests/test_case_dumpers.py

@@ -47,6 +47,7 @@
     "RemoveUnder": "Remove node from under another node.",
     "EdgeDeletion": "Deletion of an edge.",
     "NodeDeepening": "Deepening of a node.",
+    "NewTextDefinition": "New definition of a node.",
 }