Added replacement to parse while node obsoletion. (#15)

* Added replacement to parse while node obsoletion. * corrected tests * test install again due to Windows error on gh
INCATools · Oct 27, 2022 · 13cf4a5 · 13cf4a5
1 parent ab3d997
commit 13cf4a5
Show file tree

Hide file tree

Showing 4 changed files with 22 additions and 14 deletions.
diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml
@@ -33,7 +33,9 @@ jobs:
     #    install your root project, if required 
     #----------------------------------------------      
     - name: Install library
-      run: poetry install --no-interaction
+      run: |
+        pip install -U poetry
+        poetry install --no-interaction
 
     #----------------------------------------------
     #              run pytest

diff --git a/src/kgcl_schema/grammar/parser.py b/src/kgcl_schema/grammar/parser.py
@@ -11,8 +11,8 @@
                                         EdgeDeletion, NewSynonym,
                                         NodeAnnotationChange, NodeCreation,
                                         NodeDeepening, NodeDeletion, NodeMove,
-                                        NodeObsoletion, NodeRename,
-                                        NodeShallowing, NodeUnobsoletion,
+                                        NodeObsoletion, NodeObsoletionWithDirectReplacement,
+                                        NodeRename, NodeShallowing, NodeUnobsoletion,
                                         PlaceUnder, PredicateChange,
                                         RemovedNodeFromSubset, RemoveUnder,
                                         Session)
@@ -452,13 +452,19 @@ def parse_obsolete(tree, id):
     entity, representation = get_entity_representation(entity_token)
 
     replacement_token = extract(tree, "replacement")
-
-    return NodeObsoletion(
-        id=id,
-        about_node=entity,
-        about_node_representation=representation,
-        has_direct_replacement=replacement_token,
-    )
+    if replacement_token:
+        return NodeObsoletionWithDirectReplacement(
+            id=id,
+            about_node=entity,
+            about_node_representation=representation,
+            has_direct_replacement=replacement_token,
+        )
+    else:
+        return NodeObsoletion(
+            id=id,
+            about_node=entity,
+            about_node_representation=representation
+        )
 
 
 def parse_rename(tree, id):

diff --git a/src/kgcl_schema/grammar/render_operations.py b/src/kgcl_schema/grammar/render_operations.py
@@ -3,7 +3,7 @@
 
 from kgcl_schema.datamodel.kgcl import (ClassCreation, EdgeCreation, EdgeDeletion,
                                         NewSynonym, NodeAnnotationChange, NodeCreation, NodeDeepening,
-                                        NodeDeletion, NodeMove, NodeObsoletion,
+                                        NodeDeletion, NodeMove, NodeObsoletion, NodeObsoletionWithDirectReplacement,
                                         NodeRename, NodeUnobsoletion, PlaceUnder,
                                         PredicateChange, RemoveUnder, Change)
 from lark.lexer import Token
@@ -102,7 +102,7 @@ def render(kgcl_instance: Change) -> str:
             + new_object
         )
 
-    if type(kgcl_instance) is NodeObsoletion:
+    if type(kgcl_instance) is NodeObsoletion or type(kgcl_instance) is NodeObsoletionWithDirectReplacement:
         subject = render_entity(kgcl_instance.about_node, "uri")
         # TODO: type this correctly
         replacement = render_entity(kgcl_instance.has_direct_replacement, "uri")

diff --git a/tests/cases.py b/tests/cases.py
@@ -1,6 +1,6 @@
 from typing import Tuple, Optional, List, Union
 
-from kgcl_schema.datamodel.kgcl import NodeRename, NodeObsoletion, NewSynonym, ClassCreation, PredicateChange, Change, \
+from kgcl_schema.datamodel.kgcl import NodeObsoletionWithDirectReplacement, NodeRename, NodeObsoletion, NewSynonym, ClassCreation, PredicateChange, Change, \
     NodeCreation, EdgeCreation, PlaceUnder, RemoveUnder, EdgeDeletion, NodeDeepening
 from kgcl_schema.datamodel.ontology_model import Edge
 
@@ -85,7 +85,7 @@
     (
         f"obsolete {NUCLEUS} with replacement {TERM2}",
         None,
-        NodeObsoletion(id=UID,
+        NodeObsoletionWithDirectReplacement(id=UID,
                        about_node=NUCLEUS,
                        about_node_representation='curie',
                        has_direct_replacement=TERM2),