fix integrity error handling when setting forward relation refs

Signed-off-by: phernandez <paul@basicmachines.co>

src/basic_memory/sync/sync_service.py

@@ -1026,16 +1026,27 @@ class SyncService:
                             "to_name": resolved_entity.title,
                         },
                     )
-                except IntegrityError:  # pragma: no cover
+                    # update search index only on successful resolution
+                    await self.search_service.index_entity(resolved_entity)
+                except IntegrityError:
+                    # IntegrityError means a relation with this (from_id, to_id, relation_type)
+                    # already exists. The UPDATE was rolled back, so our unresolved relation
+                    # (to_id=NULL) still exists in the database. We delete it because:
+                    # 1. It's redundant - a resolved relation already captures this relationship
+                    # 2. If we don't delete it, future syncs will try to resolve it again
+                    #    and get the same IntegrityError
                     logger.debug(
-                        "Ignoring duplicate relation "
+                        "Deleting duplicate unresolved relation "
                         f"relation_id={relation.id} "
                         f"from_id={relation.from_id} "
-                        f"to_name={relation.to_name}"
+                        f"to_name={relation.to_name} "
+                        f"resolved_to_id={resolved_entity.id}"
                     )
-
-                # update search index
-                await self.search_service.index_entity(resolved_entity)
+                    try:
+                        await self.relation_repository.delete(relation.id)
+                    except Exception as e:
+                        # Log but don't fail - the relation may have been deleted already
+                        logger.debug(f"Could not delete duplicate relation {relation.id}: {e}")
 
     async def _quick_count_files(self, directory: Path) -> int:
         """Fast file count using find command.

tests/sync/test_sync_service.py

@@ -106,6 +106,89 @@ Target content
     assert source.relations[0].to_name == target.title
 
 
+@pytest.mark.asyncio
+async def test_resolve_relations_deletes_duplicate_unresolved_relation(
+    sync_service: SyncService,
+    project_config: ProjectConfig,
+    entity_service: EntityService,
+):
+    """Test that resolve_relations deletes duplicate unresolved relations on IntegrityError.
+
+    When resolving a forward reference would create a duplicate (from_id, to_id, relation_type),
+    the unresolved relation should be deleted since a resolved version already exists.
+    """
+    from unittest.mock import patch
+    from sqlalchemy.exc import IntegrityError
+    from basic_memory.models import Relation
+
+    project_dir = project_config.home
+
+    # Create source entity
+    source_content = """
+---
+type: knowledge
+---
+# Source Entity
+Content
+"""
+    await create_test_file(project_dir / "source.md", source_content)
+
+    # Create target entity
+    target_content = """
+---
+type: knowledge
+---
+# Target Entity
+Content
+"""
+    await create_test_file(project_dir / "target.md", target_content)
+
+    # Sync to create both entities
+    await sync_service.sync(project_config.home)
+
+    source = await entity_service.get_by_permalink("source")
+    await entity_service.get_by_permalink("target")
+
+    # Create an unresolved relation that will resolve to target
+    unresolved_relation = Relation(
+        from_id=source.id,
+        to_id=None,  # Unresolved
+        to_name="target",  # Will resolve to target entity
+        relation_type="relates_to",
+    )
+    await sync_service.relation_repository.add(unresolved_relation)
+    unresolved_id = unresolved_relation.id
+
+    # Verify we have the unresolved relation
+    source = await entity_service.get_by_permalink("source")
+    assert len(source.outgoing_relations) == 1
+    assert source.outgoing_relations[0].to_id is None
+
+    # Mock the repository update to raise IntegrityError (simulating existing duplicate)
+
+    async def mock_update_raises_integrity_error(entity_id, data):
+        # Simulate: a resolved relation with same (from_id, to_id, relation_type) already exists
+        raise IntegrityError(
+            "UNIQUE constraint failed: relation.from_id, relation.to_id, relation.relation_type",
+            None,
+            None,
+        )
+
+    with patch.object(
+        sync_service.relation_repository, "update", side_effect=mock_update_raises_integrity_error
+    ):
+        # Call resolve_relations - should hit IntegrityError and delete the duplicate
+        await sync_service.resolve_relations()
+
+    # Verify the unresolved relation was deleted
+    deleted = await sync_service.relation_repository.find_by_id(unresolved_id)
+    assert deleted is None
+
+    # Verify no unresolved relations remain
+    unresolved = await sync_service.relation_repository.find_unresolved_relations()
+    assert len(unresolved) == 0
+
+
 @pytest.mark.asyncio
 async def test_sync(
     sync_service: SyncService, project_config: ProjectConfig, entity_service: EntityService