From a405c92e0e779cda5b6918a619e2a000de8ebca2 Mon Sep 17 00:00:00 2001
From: Trish Whetzel <plwhetzel@gmail.com>
Date: Mon, 3 Jun 2024 15:51:12 -0700
Subject: [PATCH 1/9] rename edge to mapping

---
 src/oaklib/interfaces/differ_interface.py | 20 +++++++++++---------
 1 file changed, 11 insertions(+), 9 deletions(-)

diff --git a/src/oaklib/interfaces/differ_interface.py b/src/oaklib/interfaces/differ_interface.py
index 36e939922..ffde29ccf 100644
--- a/src/oaklib/interfaces/differ_interface.py
+++ b/src/oaklib/interfaces/differ_interface.py
@@ -11,9 +11,11 @@
     Change,
     ClassCreation,
     Edge,
-    EdgeChange,
-    EdgeCreation,
     EdgeDeletion,
+    Mapping,
+    MappingChange,
+    MappingCreation,
+    MappingDeletion,
     NewSynonym,
     NewTextDefinition,
     NodeCreation,
@@ -275,34 +277,34 @@ def diff(
             if mappings_added_set:
                 for mapping in mappings_added_set:
                     predicate, xref = mapping
-                    edge_created = EdgeCreation(
+                    mapping_created = MappingCreation(
                         id=_gen_id(),
                         subject=entity,
                         predicate=predicate,
                         object=xref,
                     )
-                    yield edge_created
+                    yield mapping_created
             if mappings_removed_set:
                 for mapping in mappings_removed_set:
                     predicate, xref = mapping
-                    deleted_edge = EdgeDeletion(
+                    deleted_mapping = MappingDeletion(
                         id=_gen_id(),
                         subject=entity,
                         predicate=predicate,
                         object=xref,
                     )
-                    yield deleted_edge
+                    yield deleted_mapping
             if mapping_changed_set:
                 for changes in mapping_changed_set:
                     object, new_predicate, old_predicate = changes
-                    edge_change = EdgeChange(
+                    mapping_change = MappingChange(
                         id=_gen_id(),
-                        about_edge=Edge(subject=entity, predicate=old_predicate, object=object),
+                        about_mapping=Mapping(subject=entity, predicate=old_predicate, object=object),
                         old_value=old_predicate,
                         new_value=new_predicate,
                     )
 
-                    yield edge_change
+                    yield mapping_change
 
             # ! Subset changes
             self_subsets = set(self.terms_subsets([entity]))

From cd55742f5c0567e5ffd16b88cfc62cb50957f04e Mon Sep 17 00:00:00 2001
From: Chris Mungall <cjm@berkeleybop.org>
Date: Tue, 4 Jun 2024 08:49:18 -0700
Subject: [PATCH 2/9] Update differ_interface.py

---
 src/oaklib/interfaces/differ_interface.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/oaklib/interfaces/differ_interface.py b/src/oaklib/interfaces/differ_interface.py
index ffde29ccf..d64824a38 100644
--- a/src/oaklib/interfaces/differ_interface.py
+++ b/src/oaklib/interfaces/differ_interface.py
@@ -12,7 +12,6 @@
     ClassCreation,
     Edge,
     EdgeDeletion,
-    Mapping,
     MappingChange,
     MappingCreation,
     MappingDeletion,

From e6c326aed21a5e4324e9f9c9bff41c39b6312f1b Mon Sep 17 00:00:00 2001
From: Harshad Hegde <hegdehb@gmail.com>
Date: Mon, 17 Jun 2024 10:36:53 -0500
Subject: [PATCH 3/9] Added MappingReplacement and RemoveMapping

---
 src/oaklib/interfaces/differ_interface.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/oaklib/interfaces/differ_interface.py b/src/oaklib/interfaces/differ_interface.py
index d64824a38..5fd796080 100644
--- a/src/oaklib/interfaces/differ_interface.py
+++ b/src/oaklib/interfaces/differ_interface.py
@@ -12,9 +12,8 @@
     ClassCreation,
     Edge,
     EdgeDeletion,
-    MappingChange,
     MappingCreation,
-    MappingDeletion,
+    MappingReplacement,
     NewSynonym,
     NewTextDefinition,
     NodeCreation,
@@ -27,6 +26,7 @@
     NodeTextDefinitionChange,
     NodeUnobsoletion,
     PredicateChange,
+    RemoveMapping,
     RemoveNodeFromSubset,
     RemoveSynonym,
     RemoveTextDefinition,
@@ -286,7 +286,7 @@ def diff(
             if mappings_removed_set:
                 for mapping in mappings_removed_set:
                     predicate, xref = mapping
-                    deleted_mapping = MappingDeletion(
+                    deleted_mapping = RemoveMapping(
                         id=_gen_id(),
                         subject=entity,
                         predicate=predicate,
@@ -296,9 +296,9 @@ def diff(
             if mapping_changed_set:
                 for changes in mapping_changed_set:
                     object, new_predicate, old_predicate = changes
-                    mapping_change = MappingChange(
+                    mapping_change = MappingReplacement(
                         id=_gen_id(),
-                        about_mapping=Mapping(subject=entity, predicate=old_predicate, object=object),
+                        about_mapping=Edge(subject=entity, predicate=old_predicate, object=object),
                         old_value=old_predicate,
                         new_value=new_predicate,
                     )

From 7f8d81fbb6c2b720e3349597f8762598b8ae8f37 Mon Sep 17 00:00:00 2001
From: Harshad Hegde <hegdehb@gmail.com>
Date: Tue, 18 Jun 2024 15:30:18 -0500
Subject: [PATCH 4/9] MappingPredicateChange

---
 src/oaklib/interfaces/differ_interface.py     |  10 +-
 .../utilities/writers/change_handler.py       | 109 ++++++++++++------
 2 files changed, 78 insertions(+), 41 deletions(-)

diff --git a/src/oaklib/interfaces/differ_interface.py b/src/oaklib/interfaces/differ_interface.py
index 5fd796080..27ce52a3e 100644
--- a/src/oaklib/interfaces/differ_interface.py
+++ b/src/oaklib/interfaces/differ_interface.py
@@ -13,7 +13,8 @@
     Edge,
     EdgeDeletion,
     MappingCreation,
-    MappingReplacement,
+    # MappingReplacement,
+    MappingPredicateChange,
     NewSynonym,
     NewTextDefinition,
     NodeCreation,
@@ -288,7 +289,7 @@ def diff(
                     predicate, xref = mapping
                     deleted_mapping = RemoveMapping(
                         id=_gen_id(),
-                        subject=entity,
+                        about_node=entity,
                         predicate=predicate,
                         object=xref,
                     )
@@ -296,9 +297,10 @@ def diff(
             if mapping_changed_set:
                 for changes in mapping_changed_set:
                     object, new_predicate, old_predicate = changes
-                    mapping_change = MappingReplacement(
+                    mapping_change = MappingPredicateChange(
                         id=_gen_id(),
-                        about_mapping=Edge(subject=entity, predicate=old_predicate, object=object),
+                        about_node = entity,
+                        object=object,
                         old_value=old_predicate,
                         new_value=new_predicate,
                     )
diff --git a/src/oaklib/utilities/writers/change_handler.py b/src/oaklib/utilities/writers/change_handler.py
index e959c2867..0e11aa4ac 100644
--- a/src/oaklib/utilities/writers/change_handler.py
+++ b/src/oaklib/utilities/writers/change_handler.py
@@ -25,15 +25,15 @@ def write_markdown_table(self, title: str, header: str, rows: List[str]) -> None
     def handle_generic_change(
         self, value: List[object], title: str, header: str, row_format: str
     ) -> None:
-        rows = [row_format.format(change=change) for change in value]
+        rows = list({row_format.format(change=change) for change in value})
         self.write_markdown_table(f"{title}: {len(rows)}", header, rows)
 
     def handle_new_synonym(self, value):
         # Create rows for the table
-        rows = [
+        rows = list({
             f"| {self._format_entity_labels(obj.about_node)} | {obj.new_value} | {obj.predicate} |"
             for obj in value
-        ]
+        })
 
         # Define the header for the table
         header = "| Term | New Synonym | Predicate |"
@@ -43,11 +43,11 @@ def handle_new_synonym(self, value):
 
     def handle_edge_deletion(self, value):
         # Create rows for the table
-        rows = [
+        rows = list({
             f"| {self._format_entity_labels(change.subject)} | {self._format_entity_labels(change.predicate)} |\
                 {self._format_entity_labels(change.object)} |"
             for change in value
-        ]
+        })
 
         # Define the header for the table
         header = "| Subject| Predicate| Object|"
@@ -57,11 +57,11 @@ def handle_edge_deletion(self, value):
 
     def handle_edge_creation(self, value):
         # Create rows for the table
-        rows = [
+        rows = list({
             f"| {self._format_entity_labels(change.subject)} | {self._format_entity_labels(change.predicate)} |\
                 {self._format_entity_labels(change.object)} |"
             for change in value
-        ]
+        })
 
         # Define the header for the table
         header = "| Subject | Predicate | Object|"
@@ -71,12 +71,12 @@ def handle_edge_creation(self, value):
 
     def handle_edge_change(self, value):
         # Create rows for the table
-        rows = [
+        rows = list({
             f"| {self._format_entity_labels(change.about_edge.subject)} | \
                 {self._format_entity_labels(change.about_edge.predicate)} | \
                 {self._format_entity_labels(change.old_value)} | {self._format_entity_labels(change.new_value)} |"
             for change in value
-        ]
+        })
 
         # Define the header for the table
         header = "| Subject | Predicate | Old Object | New Object |"
@@ -86,12 +86,12 @@ def handle_edge_change(self, value):
 
     def handle_node_move(self, value):
         # Create rows for the table
-        rows = [
+        rows = list({
             f"| {self._format_entity_labels(change.about_edge.subject)} | \
                 {self._format_entity_labels(change.about_edge.predicate)} |\
                 {self._format_entity_labels(change.about_edge.object)} |"
             for change in value
-        ]
+        })
 
         # Define the header for the table
         header = "| Subject | Predicate | Object |"
@@ -101,13 +101,13 @@ def handle_node_move(self, value):
 
     def handle_predicate_change(self, value):
         # Create rows for the table
-        rows = [
+        rows = list({
             f"| {self._format_entity_labels(change.about_edge.subject)} | \
                 {self._format_entity_labels(change.old_value)} |\
                 {self._format_entity_labels(change.new_value)} | \
                 {self._format_entity_labels(change.about_edge.object)} |"
             for change in value
-        ]
+        })
 
         # Define the header for the table
         header = "| Subject | Old Predicate | New Predicate | Object |"
@@ -117,9 +117,9 @@ def handle_predicate_change(self, value):
 
     def handle_node_rename(self, value):
         # Create rows for the table
-        rows = [
+        rows = list({
             f"| {change.about_node} | {change.old_value} | {change.new_value} |" for change in value
-        ]
+        })
 
         # Define the header for the table
         header = "| ID | Old Label | New Label |"
@@ -129,10 +129,10 @@ def handle_node_rename(self, value):
 
     def handle_remove_synonym(self, value):
         # Create rows for the table
-        rows = [
+        rows = list({
             f"| {self._format_entity_labels(change.about_node)} | {change.old_value} |"
             for change in value
-        ]
+        })
 
         # Define the header for the table
         header = "| Term | Removed Synonym |"
@@ -142,11 +142,11 @@ def handle_remove_synonym(self, value):
 
     def hand_synonym_predicate_change(self, value):
         # Create rows for the table
-        rows = [
+        rows = list({
             f"| {self._format_entity_labels(change.about_node)} | {change.old_value} |\
                   {change.new_value} | {change.target} |"
             for change in value
-        ]
+        })
 
         # Define the header for the table
         header = "| Term | Old Predicate | New Predicate | Synonym |"
@@ -156,11 +156,11 @@ def hand_synonym_predicate_change(self, value):
 
     def handle_node_text_definition_change(self, value):
         # Create rows for the table
-        rows = [
+        rows = list({
             f"| {self._format_entity_labels(change.about_node)} | {change.old_value} |\
                   {change.new_value} |"
             for change in value
-        ]
+        })
 
         # Define the header for the table
         header = "| Term | Old Text Definition | New Text Definition |"
@@ -170,11 +170,11 @@ def handle_node_text_definition_change(self, value):
 
     def handle_node_text_definition(self, value):
         # Create rows for the table
-        rows = [
+        rows = list({
             f"| {self._format_entity_labels(change.about_node)} | {change.old_value} |\
                   {change.new_value} |"
             for change in value
-        ]
+        })
 
         # Define the header for the table
         header = "| Term | Old Text Definition | New Text Definition |"
@@ -184,7 +184,7 @@ def handle_node_text_definition(self, value):
 
     def handle_node_unobsoletion(self, value):
         # Create rows for the table
-        rows = [f"| {self._format_entity_labels(change.about_node)} |" for change in value]
+        rows = list({f"| {self._format_entity_labels(change.about_node)} |" for change in value})
 
         # Define the header for the table
         header = "| Term |"
@@ -194,7 +194,7 @@ def handle_node_unobsoletion(self, value):
 
     def handle_node_creation(self, value):
         # Create rows for the table
-        rows = [f"| {self._format_entity_labels(change.about_node)} |" for change in value]
+        rows = list({f"| {self._format_entity_labels(change.about_node)} |" for change in value})
 
         # Define the header for the table
         header = "| Term |"
@@ -204,7 +204,7 @@ def handle_node_creation(self, value):
 
     def handle_class_creation(self, value):
         # Create rows for the table
-        rows = [f"| {self._format_entity_labels(change.about_node)} |" for change in value]
+        rows = list({f"| {self._format_entity_labels(change.about_node)} |" for change in value})
 
         # Define the header for the table
         header = "| Term |"
@@ -214,7 +214,7 @@ def handle_class_creation(self, value):
 
     def handle_node_deletion(self, value):
         # Create rows for the table
-        rows = [f"| {self._format_entity_labels(change.about_node)} |" for change in value]
+        rows = list({f"| {self._format_entity_labels(change.about_node)} |" for change in value})
 
         # Define the header for the table
         header = "| Term |"
@@ -224,28 +224,28 @@ def handle_node_deletion(self, value):
 
     def handle_new_text_definition(self, value):
         # Create rows for the table
-        rows = [
+        rows = list({
             f"| {self._format_entity_labels(change.about_node)} | {change.new_value} |"
             for change in value
-        ]
+        })
         header = "| Term | New Text Definition |"
         self.write_markdown_table(f"Text definitions added: {len(rows)}", header, rows)
 
     def handle_remove_text_definition(self, value):
         # Create rows for the table
-        rows = [
+        rows = list({
             f"| {self._format_entity_labels(change.about_node)} | {change.old_value} |"
             for change in value
-        ]
+        })
         header = "| Term | Removed Text Definition |"
         self.write_markdown_table(f"Text definitions removed: {len(rows)}", header, rows)
 
     def handle_node_obsoletion_with_direct_replacement(self, value):
-        rows = [
+        rows = list({
             f"| {self._format_entity_labels(change.about_node)} |\
                   {self._format_entity_labels(change.has_direct_replacement)} |"
             for change in value
-        ]
+        })
         header = "| Term | Replacement |"
         self.write_markdown_table(f"Nodes obsoleted with replacement: {len(rows)}", header, rows)
 
@@ -255,22 +255,54 @@ def handle_node_obsoletion(self, value):
         self.write_markdown_table(f"Nodes obsoleted without replacement: {len(rows)}", header, rows)
 
     def handle_node_direct_merge(self, value):
-        rows = [
+        rows = list({
             f"| {self._format_entity_labels(change.about_node)} |\
                   {self._format_entity_labels(change.has_direct_replacement)} |"
             for change in value
-        ]
+        })
         header = "| Term | Replacement |"
         self.write_markdown_table(f"Nodes merged: {len(rows)}", header, rows)
 
     def handle_add_node_to_subset(self, value):
-        rows = [
+        rows = list({
             f"| {self._format_entity_labels(change.about_node)} | {change.in_subset} |"
             for change in value
-        ]
+        })
         header = "| Term | Subset |"
         self.write_markdown_table(f"Nodes added to subset: {len(rows)}", header, rows)
 
+    def handle_mapping_creation(self, value):
+        rows = list({
+            f"| {self._format_entity_labels(change.subject)} | {change.predicate} | {self._format_entity_labels(change.object)} |"
+            for change in value
+        })
+        header = "| Subject | Predicate | Object |"
+        self.write_markdown_table(f"Mappings added: {len(rows)}", header, rows)
+    
+    def handle_mapping_predicate_change(self, value):
+        # Create rows for the table
+        rows = list({
+            f"| {self._format_entity_labels(change.about_node)} | \
+                {self._format_entity_labels(change.old_value)} |\
+                {self._format_entity_labels(change.new_value)} | \
+                {self._format_entity_labels(change.object)} |"
+            for change in value
+        })
+
+        # Define the header for the table
+        header = "| Subject | Old Mapping Predicate | New Mapping Predicate | Object |"
+
+        # Write the "Predicate Changed" section as a collapsible markdown table
+        self.write_markdown_table(f"Mappings changed: {len(rows)}", header, rows)
+
+    def handle_remove_mapping(self, value):
+        rows = list({
+            f"| {self._format_entity_labels(change.about_node)} | {change.predicate} | {self._format_entity_labels(change.object)} |"
+            for change in value
+        })
+        header = "| Subject | Predicate | Object |"
+        self.write_markdown_table(f"Mappings removed: {len(rows)}", header, rows)
+
     # def handle_datatype_or_language_tag_change(self, value):
     #     # Implement datatype or language tag change handling logic here
     #     logging.info("Datatype or language tag change handling not yet implemented.")
@@ -340,6 +372,9 @@ def process_changes(self, curie_or_change: Dict[str, Change]):
             "EdgeCreation": self.handle_edge_creation,
             "EdgeChange": self.handle_edge_change,
             "AddNodeToSubset": self.handle_add_node_to_subset,
+            "MappingPredicateChange": self.handle_mapping_predicate_change,
+            "MappingCreation": self.handle_mapping_creation,
+            "RemoveMapping": self.handle_remove_mapping,
             # "DatatypeOrLanguageTagChange": self.handle_datatype_or_language_tag_change,
             # "LanguageTagChange": self.handle_language_tag_change,
             # "DatatypeChange": self.handle_datatype_change,

From e76839dd83eda1c3fe973c1e662d958c7a9cbb52 Mon Sep 17 00:00:00 2001
From: Harshad Hegde <hegdehb@gmail.com>
Date: Tue, 18 Jun 2024 15:38:18 -0500
Subject: [PATCH 5/9] formatted

---
 src/oaklib/interfaces/differ_interface.py     |   2 +-
 .../utilities/writers/change_handler.py       | 193 +++++++++++-------
 2 files changed, 118 insertions(+), 77 deletions(-)

diff --git a/src/oaklib/interfaces/differ_interface.py b/src/oaklib/interfaces/differ_interface.py
index 27ce52a3e..31665f02b 100644
--- a/src/oaklib/interfaces/differ_interface.py
+++ b/src/oaklib/interfaces/differ_interface.py
@@ -299,7 +299,7 @@ def diff(
                     object, new_predicate, old_predicate = changes
                     mapping_change = MappingPredicateChange(
                         id=_gen_id(),
-                        about_node = entity,
+                        about_node=entity,
                         object=object,
                         old_value=old_predicate,
                         new_value=new_predicate,
diff --git a/src/oaklib/utilities/writers/change_handler.py b/src/oaklib/utilities/writers/change_handler.py
index 0e11aa4ac..3d49ecc38 100644
--- a/src/oaklib/utilities/writers/change_handler.py
+++ b/src/oaklib/utilities/writers/change_handler.py
@@ -30,10 +30,12 @@ def handle_generic_change(
 
     def handle_new_synonym(self, value):
         # Create rows for the table
-        rows = list({
-            f"| {self._format_entity_labels(obj.about_node)} | {obj.new_value} | {obj.predicate} |"
-            for obj in value
-        })
+        rows = list(
+            {
+                f"| {self._format_entity_labels(obj.about_node)} | {obj.new_value} | {obj.predicate} |"
+                for obj in value
+            }
+        )
 
         # Define the header for the table
         header = "| Term | New Synonym | Predicate |"
@@ -43,11 +45,13 @@ def handle_new_synonym(self, value):
 
     def handle_edge_deletion(self, value):
         # Create rows for the table
-        rows = list({
-            f"| {self._format_entity_labels(change.subject)} | {self._format_entity_labels(change.predicate)} |\
+        rows = list(
+            {
+                f"| {self._format_entity_labels(change.subject)} | {self._format_entity_labels(change.predicate)} |\
                 {self._format_entity_labels(change.object)} |"
-            for change in value
-        })
+                for change in value
+            }
+        )
 
         # Define the header for the table
         header = "| Subject| Predicate| Object|"
@@ -57,11 +61,13 @@ def handle_edge_deletion(self, value):
 
     def handle_edge_creation(self, value):
         # Create rows for the table
-        rows = list({
-            f"| {self._format_entity_labels(change.subject)} | {self._format_entity_labels(change.predicate)} |\
+        rows = list(
+            {
+                f"| {self._format_entity_labels(change.subject)} | {self._format_entity_labels(change.predicate)} |\
                 {self._format_entity_labels(change.object)} |"
-            for change in value
-        })
+                for change in value
+            }
+        )
 
         # Define the header for the table
         header = "| Subject | Predicate | Object|"
@@ -71,12 +77,14 @@ def handle_edge_creation(self, value):
 
     def handle_edge_change(self, value):
         # Create rows for the table
-        rows = list({
-            f"| {self._format_entity_labels(change.about_edge.subject)} | \
+        rows = list(
+            {
+                f"| {self._format_entity_labels(change.about_edge.subject)} | \
                 {self._format_entity_labels(change.about_edge.predicate)} | \
                 {self._format_entity_labels(change.old_value)} | {self._format_entity_labels(change.new_value)} |"
-            for change in value
-        })
+                for change in value
+            }
+        )
 
         # Define the header for the table
         header = "| Subject | Predicate | Old Object | New Object |"
@@ -86,12 +94,14 @@ def handle_edge_change(self, value):
 
     def handle_node_move(self, value):
         # Create rows for the table
-        rows = list({
-            f"| {self._format_entity_labels(change.about_edge.subject)} | \
+        rows = list(
+            {
+                f"| {self._format_entity_labels(change.about_edge.subject)} | \
                 {self._format_entity_labels(change.about_edge.predicate)} |\
                 {self._format_entity_labels(change.about_edge.object)} |"
-            for change in value
-        })
+                for change in value
+            }
+        )
 
         # Define the header for the table
         header = "| Subject | Predicate | Object |"
@@ -101,13 +111,15 @@ def handle_node_move(self, value):
 
     def handle_predicate_change(self, value):
         # Create rows for the table
-        rows = list({
-            f"| {self._format_entity_labels(change.about_edge.subject)} | \
+        rows = list(
+            {
+                f"| {self._format_entity_labels(change.about_edge.subject)} | \
                 {self._format_entity_labels(change.old_value)} |\
                 {self._format_entity_labels(change.new_value)} | \
                 {self._format_entity_labels(change.about_edge.object)} |"
-            for change in value
-        })
+                for change in value
+            }
+        )
 
         # Define the header for the table
         header = "| Subject | Old Predicate | New Predicate | Object |"
@@ -117,9 +129,12 @@ def handle_predicate_change(self, value):
 
     def handle_node_rename(self, value):
         # Create rows for the table
-        rows = list({
-            f"| {change.about_node} | {change.old_value} | {change.new_value} |" for change in value
-        })
+        rows = list(
+            {
+                f"| {change.about_node} | {change.old_value} | {change.new_value} |"
+                for change in value
+            }
+        )
 
         # Define the header for the table
         header = "| ID | Old Label | New Label |"
@@ -129,10 +144,12 @@ def handle_node_rename(self, value):
 
     def handle_remove_synonym(self, value):
         # Create rows for the table
-        rows = list({
-            f"| {self._format_entity_labels(change.about_node)} | {change.old_value} |"
-            for change in value
-        })
+        rows = list(
+            {
+                f"| {self._format_entity_labels(change.about_node)} | {change.old_value} |"
+                for change in value
+            }
+        )
 
         # Define the header for the table
         header = "| Term | Removed Synonym |"
@@ -142,11 +159,13 @@ def handle_remove_synonym(self, value):
 
     def hand_synonym_predicate_change(self, value):
         # Create rows for the table
-        rows = list({
-            f"| {self._format_entity_labels(change.about_node)} | {change.old_value} |\
+        rows = list(
+            {
+                f"| {self._format_entity_labels(change.about_node)} | {change.old_value} |\
                   {change.new_value} | {change.target} |"
-            for change in value
-        })
+                for change in value
+            }
+        )
 
         # Define the header for the table
         header = "| Term | Old Predicate | New Predicate | Synonym |"
@@ -156,11 +175,13 @@ def hand_synonym_predicate_change(self, value):
 
     def handle_node_text_definition_change(self, value):
         # Create rows for the table
-        rows = list({
-            f"| {self._format_entity_labels(change.about_node)} | {change.old_value} |\
+        rows = list(
+            {
+                f"| {self._format_entity_labels(change.about_node)} | {change.old_value} |\
                   {change.new_value} |"
-            for change in value
-        })
+                for change in value
+            }
+        )
 
         # Define the header for the table
         header = "| Term | Old Text Definition | New Text Definition |"
@@ -170,11 +191,13 @@ def handle_node_text_definition_change(self, value):
 
     def handle_node_text_definition(self, value):
         # Create rows for the table
-        rows = list({
-            f"| {self._format_entity_labels(change.about_node)} | {change.old_value} |\
+        rows = list(
+            {
+                f"| {self._format_entity_labels(change.about_node)} | {change.old_value} |\
                   {change.new_value} |"
-            for change in value
-        })
+                for change in value
+            }
+        )
 
         # Define the header for the table
         header = "| Term | Old Text Definition | New Text Definition |"
@@ -224,28 +247,34 @@ def handle_node_deletion(self, value):
 
     def handle_new_text_definition(self, value):
         # Create rows for the table
-        rows = list({
-            f"| {self._format_entity_labels(change.about_node)} | {change.new_value} |"
-            for change in value
-        })
+        rows = list(
+            {
+                f"| {self._format_entity_labels(change.about_node)} | {change.new_value} |"
+                for change in value
+            }
+        )
         header = "| Term | New Text Definition |"
         self.write_markdown_table(f"Text definitions added: {len(rows)}", header, rows)
 
     def handle_remove_text_definition(self, value):
         # Create rows for the table
-        rows = list({
-            f"| {self._format_entity_labels(change.about_node)} | {change.old_value} |"
-            for change in value
-        })
+        rows = list(
+            {
+                f"| {self._format_entity_labels(change.about_node)} | {change.old_value} |"
+                for change in value
+            }
+        )
         header = "| Term | Removed Text Definition |"
         self.write_markdown_table(f"Text definitions removed: {len(rows)}", header, rows)
 
     def handle_node_obsoletion_with_direct_replacement(self, value):
-        rows = list({
-            f"| {self._format_entity_labels(change.about_node)} |\
+        rows = list(
+            {
+                f"| {self._format_entity_labels(change.about_node)} |\
                   {self._format_entity_labels(change.has_direct_replacement)} |"
-            for change in value
-        })
+                for change in value
+            }
+        )
         header = "| Term | Replacement |"
         self.write_markdown_table(f"Nodes obsoleted with replacement: {len(rows)}", header, rows)
 
@@ -255,39 +284,48 @@ def handle_node_obsoletion(self, value):
         self.write_markdown_table(f"Nodes obsoleted without replacement: {len(rows)}", header, rows)
 
     def handle_node_direct_merge(self, value):
-        rows = list({
-            f"| {self._format_entity_labels(change.about_node)} |\
+        rows = list(
+            {
+                f"| {self._format_entity_labels(change.about_node)} |\
                   {self._format_entity_labels(change.has_direct_replacement)} |"
-            for change in value
-        })
+                for change in value
+            }
+        )
         header = "| Term | Replacement |"
         self.write_markdown_table(f"Nodes merged: {len(rows)}", header, rows)
 
     def handle_add_node_to_subset(self, value):
-        rows = list({
-            f"| {self._format_entity_labels(change.about_node)} | {change.in_subset} |"
-            for change in value
-        })
+        rows = list(
+            {
+                f"| {self._format_entity_labels(change.about_node)} | {change.in_subset} |"
+                for change in value
+            }
+        )
         header = "| Term | Subset |"
         self.write_markdown_table(f"Nodes added to subset: {len(rows)}", header, rows)
 
     def handle_mapping_creation(self, value):
-        rows = list({
-            f"| {self._format_entity_labels(change.subject)} | {change.predicate} | {self._format_entity_labels(change.object)} |"
-            for change in value
-        })
+        rows = list(
+            {
+                f"""| {self._format_entity_labels(change.subject)}
+                | {change.predicate} | {self._format_entity_labels(change.object)} |"""
+                for change in value
+            }
+        )
         header = "| Subject | Predicate | Object |"
         self.write_markdown_table(f"Mappings added: {len(rows)}", header, rows)
-    
+
     def handle_mapping_predicate_change(self, value):
         # Create rows for the table
-        rows = list({
-            f"| {self._format_entity_labels(change.about_node)} | \
+        rows = list(
+            {
+                f"| {self._format_entity_labels(change.about_node)} | \
                 {self._format_entity_labels(change.old_value)} |\
                 {self._format_entity_labels(change.new_value)} | \
                 {self._format_entity_labels(change.object)} |"
-            for change in value
-        })
+                for change in value
+            }
+        )
 
         # Define the header for the table
         header = "| Subject | Old Mapping Predicate | New Mapping Predicate | Object |"
@@ -296,10 +334,13 @@ def handle_mapping_predicate_change(self, value):
         self.write_markdown_table(f"Mappings changed: {len(rows)}", header, rows)
 
     def handle_remove_mapping(self, value):
-        rows = list({
-            f"| {self._format_entity_labels(change.about_node)} | {change.predicate} | {self._format_entity_labels(change.object)} |"
-            for change in value
-        })
+        rows = list(
+            {
+                f"""| {self._format_entity_labels(change.about_node)}
+                | {change.predicate} | {self._format_entity_labels(change.object)} |"""
+                for change in value
+            }
+        )
         header = "| Subject | Predicate | Object |"
         self.write_markdown_table(f"Mappings removed: {len(rows)}", header, rows)
 

From 26da7777c91a3d73709986ef6a231a57365d42f1 Mon Sep 17 00:00:00 2001
From: Harshad Hegde <hegdehb@gmail.com>
Date: Tue, 18 Jun 2024 16:39:50 -0500
Subject: [PATCH 6/9] Added mapping change

---
 .../simpleobo/simple_obo_implementation.py    | 27 +++++++++++++------
 1 file changed, 19 insertions(+), 8 deletions(-)

diff --git a/src/oaklib/implementations/simpleobo/simple_obo_implementation.py b/src/oaklib/implementations/simpleobo/simple_obo_implementation.py
index 3e0d05d1f..4720c4d7f 100644
--- a/src/oaklib/implementations/simpleobo/simple_obo_implementation.py
+++ b/src/oaklib/implementations/simpleobo/simple_obo_implementation.py
@@ -907,14 +907,14 @@ def _tv_dict(stanza: Stanza) -> Dict[str, List[str]]:
             elif tag == TAG_SUBSET:
                 if node_is_deleted:
                     continue
-                subsets1 = stanza1.simple_values(TAG_SUBSET)
-                subsets2 = stanza2.simple_values(TAG_SUBSET)
-                for subset in subsets1:
-                    if subset not in subsets2:
-                        yield kgcl.RemoveNodeFromSubset(id=_id(), about_node=t1id, in_subset=subset)
-                for subset in subsets2:
-                    if subset not in subsets1:
-                        yield kgcl.AddNodeToSubset(id=_id(), about_node=t2id, in_subset=subset)
+                xrefs1 = stanza1.simple_values(TAG_SUBSET)
+                xrefs2 = stanza2.simple_values(TAG_SUBSET)
+                for xref in xrefs1:
+                    if xref not in xrefs2:
+                        yield kgcl.RemoveNodeFromSubset(id=_id(), about_node=t1id, in_subset=xref)
+                for xref in xrefs2:
+                    if xref not in xrefs1:
+                        yield kgcl.AddNodeToSubset(id=_id(), about_node=t2id, in_subset=xref)
             elif tag == TAG_IS_A:
                 isas1 = stanza1.simple_values(TAG_IS_A)
                 isas2 = stanza2.simple_values(TAG_IS_A)
@@ -950,6 +950,17 @@ def _tv_dict(stanza: Stanza) -> Dict[str, List[str]]:
                         yield kgcl.NewSynonym(
                             id=_id(), about_node=t2id, new_value=syn[0], predicate=pred
                         )
+            elif tag == TAG_XREF:
+                if node_is_deleted:
+                    continue
+                xrefs1 = stanza1.simple_values(TAG_XREF)
+                xrefs2 = stanza2.simple_values(TAG_XREF)
+                for xref in xrefs1:
+                    if xref not in xrefs2:
+                        yield kgcl.RemoveMapping(id=_id(), about_node=t1id, object=xref, predicate=HAS_DBXREF)
+                for xref in xrefs2:
+                    if xref not in xrefs1:
+                        yield kgcl.MappingCreation(id=_id(), subject=t2id, object=xref, predicate=HAS_DBXREF)
 
     def different_from(self, entity: CURIE, other_ontology: DifferInterface) -> bool:
         t1 = self._stanza(entity, strict=False)

From 57fff8cfca6f2d4b38dd4a0c8f8a3664c05da9ac Mon Sep 17 00:00:00 2001
From: Harshad Hegde <hegdehb@gmail.com>
Date: Tue, 18 Jun 2024 16:53:05 -0500
Subject: [PATCH 7/9] simpleobo + mapping change implemented

---
 .../simpleobo/simple_obo_implementation.py           |  8 ++++++--
 tests/input/go-nucleus-modified.obo                  |  2 +-
 tests/test_cli.py                                    | 12 +++++++++++-
 3 files changed, 18 insertions(+), 4 deletions(-)

diff --git a/src/oaklib/implementations/simpleobo/simple_obo_implementation.py b/src/oaklib/implementations/simpleobo/simple_obo_implementation.py
index 4720c4d7f..bcee7b2be 100644
--- a/src/oaklib/implementations/simpleobo/simple_obo_implementation.py
+++ b/src/oaklib/implementations/simpleobo/simple_obo_implementation.py
@@ -957,10 +957,14 @@ def _tv_dict(stanza: Stanza) -> Dict[str, List[str]]:
                 xrefs2 = stanza2.simple_values(TAG_XREF)
                 for xref in xrefs1:
                     if xref not in xrefs2:
-                        yield kgcl.RemoveMapping(id=_id(), about_node=t1id, object=xref, predicate=HAS_DBXREF)
+                        yield kgcl.RemoveMapping(
+                            id=_id(), about_node=t1id, object=xref, predicate=HAS_DBXREF
+                        )
                 for xref in xrefs2:
                     if xref not in xrefs1:
-                        yield kgcl.MappingCreation(id=_id(), subject=t2id, object=xref, predicate=HAS_DBXREF)
+                        yield kgcl.MappingCreation(
+                            id=_id(), subject=t2id, object=xref, predicate=HAS_DBXREF
+                        )
 
     def different_from(self, entity: CURIE, other_ontology: DifferInterface) -> bool:
         t1 = self._stanza(entity, strict=False)
diff --git a/tests/input/go-nucleus-modified.obo b/tests/input/go-nucleus-modified.obo
index 7df9d994d..155604b12 100644
--- a/tests/input/go-nucleus-modified.obo
+++ b/tests/input/go-nucleus-modified.obo
@@ -377,7 +377,6 @@ subset: goslim_yeast
 synonym: "cell or subcellular entity" EXACT []
 synonym: "cellular component" EXACT []
 synonym: "subcellular entity" RELATED [NIF_Subcellular:nlx_subcell_100315]
-xref: NIF_Subcellular:sao1337158144
 is_a: BFO:0000040 ! material entity
 disjoint_from: GO:0008150 ! biological_process
 
@@ -422,6 +421,7 @@ synonym: "cell nucleus" EXACT []
 synonym: "horsetail nucleus" NARROW [GOC:al, GOC:mah, GOC:vw, PMID:15030757]
 xref: NIF_Subcellular:sao1702920020
 xref: Wikipedia:Cell_nucleus
+xref: foo:test
 is_a: GO:0043231 ! intracellular membrane-bounded organelle
 disjoint_from: GO:0005737 ! cytoplasm
 relationship: in_taxon NCBITaxon:2759 ! Eukaryota
diff --git a/tests/test_cli.py b/tests/test_cli.py
index fc55d3914..399424c10 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -10,7 +10,7 @@
 import rdflib
 import yaml
 from click.testing import CliRunner
-from kgcl_schema.datamodel.kgcl import NodeChange
+from kgcl_schema.datamodel.kgcl import MappingCreation, NodeChange, RemoveMapping
 from linkml_runtime.loaders import json_loader, yaml_loader
 from oaklib import get_adapter
 from oaklib.cli import clear_cli_settings, main
@@ -1266,6 +1266,16 @@ def test_diffs(self):
             self.assertTrue(
                 any(c.about_node == "GO:0033673" for c in changes if isinstance(c, NodeChange))
             )
+            self.assertTrue(
+                any(c.subject == NUCLEUS for c in changes if isinstance(c, MappingCreation))
+            )
+            self.assertTrue(
+                any(
+                    c.about_node == CELLULAR_COMPONENT
+                    for c in changes
+                    if isinstance(c, RemoveMapping)
+                )
+            )
             catalytic_activity_changed = any(
                 c.about_node == CATALYTIC_ACTIVITY for c in changes if isinstance(c, NodeChange)
             )

From cf3bb007388135e3ba8326489990e2e02d2d21bd Mon Sep 17 00:00:00 2001
From: Harshad Hegde <hegdehb@gmail.com>
Date: Thu, 20 Jun 2024 10:41:14 -0500
Subject: [PATCH 8/9] Edited expected changes

---
 tests/test_implementations/__init__.py | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/tests/test_implementations/__init__.py b/tests/test_implementations/__init__.py
index 3446c914b..60beb99a2 100644
--- a/tests/test_implementations/__init__.py
+++ b/tests/test_implementations/__init__.py
@@ -1035,6 +1035,18 @@ def test_diff(self, oi: DifferInterface, oi_modified: DifferInterface):
                 predicate="RO:0002212",
                 object="GO:0016301",
             ),
+            kgcl.RemoveMapping(
+                id=FIXED_ID,
+                about_node="GO:0005575",
+                predicate="oio:hasDbXref",
+                object="NIF_Subcellular:sao1337158144",
+            ),
+            kgcl.MappingCreation(
+                id=FIXED_ID,
+                subject="GO:0005634",
+                predicate="oio:hasDbXref",
+                object="foo:test",
+            ),
         ]
         for ch in diff:
             if isinstance(ch, list):
@@ -1070,6 +1082,18 @@ def test_diff(self, oi: DifferInterface, oi_modified: DifferInterface):
                 new_value="catalytic activity",
             ),
             kgcl.ClassCreation(id=FIXED_ID, about_node="GO:0033673"),
+            kgcl.MappingCreation(
+                id=FIXED_ID,
+                subject="GO:0005575",
+                predicate="oio:hasDbXref",
+                object="NIF_Subcellular:sao1337158144",
+            ),
+            kgcl.RemoveMapping(
+                id=FIXED_ID,
+                about_node="GO:0005634",
+                predicate="oio:hasDbXref",
+                object="foo:test",
+            ),
         ]
         rdiff = list(oi_modified.diff(oi))
         for ch in rdiff:

From 31020761a582708b48856dc014b975f2a419fb52 Mon Sep 17 00:00:00 2001
From: Harshad Hegde <hegdehb@gmail.com>
Date: Thu, 20 Jun 2024 10:42:42 -0500
Subject: [PATCH 9/9] replace hard-coding to vars

---
 tests/test_implementations/__init__.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/test_implementations/__init__.py b/tests/test_implementations/__init__.py
index 60beb99a2..96dadce99 100644
--- a/tests/test_implementations/__init__.py
+++ b/tests/test_implementations/__init__.py
@@ -1037,13 +1037,13 @@ def test_diff(self, oi: DifferInterface, oi_modified: DifferInterface):
             ),
             kgcl.RemoveMapping(
                 id=FIXED_ID,
-                about_node="GO:0005575",
+                about_node=CELLULAR_COMPONENT,
                 predicate="oio:hasDbXref",
                 object="NIF_Subcellular:sao1337158144",
             ),
             kgcl.MappingCreation(
                 id=FIXED_ID,
-                subject="GO:0005634",
+                subject=NUCLEUS,
                 predicate="oio:hasDbXref",
                 object="foo:test",
             ),
@@ -1084,13 +1084,13 @@ def test_diff(self, oi: DifferInterface, oi_modified: DifferInterface):
             kgcl.ClassCreation(id=FIXED_ID, about_node="GO:0033673"),
             kgcl.MappingCreation(
                 id=FIXED_ID,
-                subject="GO:0005575",
+                subject=CELLULAR_COMPONENT,
                 predicate="oio:hasDbXref",
                 object="NIF_Subcellular:sao1337158144",
             ),
             kgcl.RemoveMapping(
                 id=FIXED_ID,
-                about_node="GO:0005634",
+                about_node=NUCLEUS,
                 predicate="oio:hasDbXref",
                 object="foo:test",
             ),