fix: add logfire spans to cli

src/basic_memory/cli/commands/db.py

@@ -1,6 +1,8 @@
 """Database management commands."""
 
 import asyncio
+
+import logfire
 import typer
 from loguru import logger
 
@@ -13,13 +15,14 @@ def reset(
     reindex: bool = typer.Option(False, "--reindex", help="Rebuild indices from filesystem"),
 ):  # pragma: no cover
     """Reset database (drop all tables and recreate)."""
-    if typer.confirm("This will delete all data. Are you sure?"):
-        logger.info("Resetting database...")
-        asyncio.run(migrations.reset_database())
+    with logfire.span("reset"):  # pyright: ignore [reportGeneralTypeIssues]
+        if typer.confirm("This will delete all data in your db. Are you sure?"):
+            logger.info("Resetting database...")
+            asyncio.run(migrations.reset_database())
 
-        if reindex:
-            # Import and run sync
-            from basic_memory.cli.commands.sync import sync
+            if reindex:
+                # Import and run sync
+                from basic_memory.cli.commands.sync import sync
 
-            logger.info("Rebuilding search index from filesystem...")
-            sync(watch=False)  # pyright: ignore
+                logger.info("Rebuilding search index from filesystem...")
+                sync(watch=False)  # pyright: ignore

src/basic_memory/cli/commands/import_chatgpt.py

@@ -6,6 +6,7 @@ from datetime import datetime
 from pathlib import Path
 from typing import Dict, Any, List, Annotated, Set, Optional
 
+import logfire
 import typer
 from loguru import logger
 from rich.console import Console
@@ -225,35 +226,38 @@ def import_chatgpt(
     After importing, run 'basic-memory sync' to index the new files.
     """
 
-    try:
-        if conversations_json:
-            if not conversations_json.exists():
-                typer.echo(f"Error: File not found: {conversations_json}", err=True)
-                raise typer.Exit(1)
+    with logfire.span("import chatgpt"):  # pyright: ignore [reportGeneralTypeIssues]
+        try:
+            if conversations_json:
+                if not conversations_json.exists():
+                    typer.echo(f"Error: File not found: {conversations_json}", err=True)
+                    raise typer.Exit(1)
 
-            # Get markdown processor
-            markdown_processor = asyncio.run(get_markdown_processor())
+                # Get markdown processor
+                markdown_processor = asyncio.run(get_markdown_processor())
 
-            # Process the file
-            base_path = config.home / folder
-            console.print(f"\nImporting chats from {conversations_json}...writing to {base_path}")
-            results = asyncio.run(
-                process_chatgpt_json(conversations_json, folder, markdown_processor)
-            )
-
-            # Show results
-            console.print(
-                Panel(
-                    f"[green]Import complete![/green]\n\n"
-                    f"Imported {results['conversations']} conversations\n"
-                    f"Containing {results['messages']} messages",
-                    expand=False,
+                # Process the file
+                base_path = config.home / folder
+                console.print(
+                    f"\nImporting chats from {conversations_json}...writing to {base_path}"
+                )
+                results = asyncio.run(
+                    process_chatgpt_json(conversations_json, folder, markdown_processor)
                 )
-            )
 
-        console.print("\nRun 'basic-memory sync' to index the new files.")
+                # Show results
+                console.print(
+                    Panel(
+                        f"[green]Import complete![/green]\n\n"
+                        f"Imported {results['conversations']} conversations\n"
+                        f"Containing {results['messages']} messages",
+                        expand=False,
+                    )
+                )
 
-    except Exception as e:
-        logger.error("Import failed")
-        typer.echo(f"Error during import: {e}", err=True)
-        raise typer.Exit(1)
+            console.print("\nRun 'basic-memory sync' to index the new files.")
+
+        except Exception as e:
+            logger.error("Import failed")
+            typer.echo(f"Error during import: {e}", err=True)
+            raise typer.Exit(1)

src/basic_memory/cli/commands/import_claude_conversations.py

@@ -6,6 +6,7 @@ from datetime import datetime
 from pathlib import Path
 from typing import Dict, Any, List, Annotated
 
+import logfire
 import typer
 from loguru import logger
 from rich.console import Console
@@ -178,34 +179,35 @@ def import_claude(
     After importing, run 'basic-memory sync' to index the new files.
     """
 
-    try:
-        if not conversations_json.exists():
-            typer.echo(f"Error: File not found: {conversations_json}", err=True)
-            raise typer.Exit(1)
+    with logfire.span("import claude conversations"):  # pyright: ignore [reportGeneralTypeIssues]
+        try:
+            if not conversations_json.exists():
+                typer.echo(f"Error: File not found: {conversations_json}", err=True)
+                raise typer.Exit(1)
 
-        # Get markdown processor
-        markdown_processor = asyncio.run(get_markdown_processor())
+            # Get markdown processor
+            markdown_processor = asyncio.run(get_markdown_processor())
 
-        # Process the file
-        base_path = config.home / folder
-        console.print(f"\nImporting chats from {conversations_json}...writing to {base_path}")
-        results = asyncio.run(
-            process_conversations_json(conversations_json, base_path, markdown_processor)
-        )
-
-        # Show results
-        console.print(
-            Panel(
-                f"[green]Import complete![/green]\n\n"
-                f"Imported {results['conversations']} conversations\n"
-                f"Containing {results['messages']} messages",
-                expand=False,
+            # Process the file
+            base_path = config.home / folder
+            console.print(f"\nImporting chats from {conversations_json}...writing to {base_path}")
+            results = asyncio.run(
+                process_conversations_json(conversations_json, base_path, markdown_processor)
             )
-        )
 
-        console.print("\nRun 'basic-memory sync' to index the new files.")
+            # Show results
+            console.print(
+                Panel(
+                    f"[green]Import complete![/green]\n\n"
+                    f"Imported {results['conversations']} conversations\n"
+                    f"Containing {results['messages']} messages",
+                    expand=False,
+                )
+            )
 
-    except Exception as e:
-        logger.error("Import failed")
-        typer.echo(f"Error during import: {e}", err=True)
-        raise typer.Exit(1)
+            console.print("\nRun 'basic-memory sync' to index the new files.")
+
+        except Exception as e:
+            logger.error("Import failed")
+            typer.echo(f"Error during import: {e}", err=True)
+            raise typer.Exit(1)

src/basic_memory/cli/commands/import_claude_projects.py

@@ -5,6 +5,7 @@ import json
 from pathlib import Path
 from typing import Dict, Any, Annotated, Optional
 
+import logfire
 import typer
 from loguru import logger
 from rich.console import Console
@@ -160,36 +161,36 @@ def import_projects(
 
     After importing, run 'basic-memory sync' to index the new files.
     """
+    with logfire.span("import claude projects"):  # pyright: ignore [reportGeneralTypeIssues]
+        try:
+            if projects_json:
+                if not projects_json.exists():
+                    typer.echo(f"Error: File not found: {projects_json}", err=True)
+                    raise typer.Exit(1)
 
-    try:
-        if projects_json:
-            if not projects_json.exists():
-                typer.echo(f"Error: File not found: {projects_json}", err=True)
-                raise typer.Exit(1)
+                # Get markdown processor
+                markdown_processor = asyncio.run(get_markdown_processor())
 
-            # Get markdown processor
-            markdown_processor = asyncio.run(get_markdown_processor())
-
-            # Process the file
-            base_path = config.home / base_folder if base_folder else config.home
-            console.print(f"\nImporting projects from {projects_json}...writing to {base_path}")
-            results = asyncio.run(
-                process_projects_json(projects_json, base_path, markdown_processor)
-            )
-
-            # Show results
-            console.print(
-                Panel(
-                    f"[green]Import complete![/green]\n\n"
-                    f"Imported {results['documents']} project documents\n"
-                    f"Imported {results['prompts']} prompt templates",
-                    expand=False,
+                # Process the file
+                base_path = config.home / base_folder if base_folder else config.home
+                console.print(f"\nImporting projects from {projects_json}...writing to {base_path}")
+                results = asyncio.run(
+                    process_projects_json(projects_json, base_path, markdown_processor)
                 )
-            )
 
-        console.print("\nRun 'basic-memory sync' to index the new files.")
+                # Show results
+                console.print(
+                    Panel(
+                        f"[green]Import complete![/green]\n\n"
+                        f"Imported {results['documents']} project documents\n"
+                        f"Imported {results['prompts']} prompt templates",
+                        expand=False,
+                    )
+                )
 
-    except Exception as e:
-        logger.error("Import failed")
-        typer.echo(f"Error during import: {e}", err=True)
-        raise typer.Exit(1)
+            console.print("\nRun 'basic-memory sync' to index the new files.")
+
+        except Exception as e:
+            logger.error("Import failed")
+            typer.echo(f"Error during import: {e}", err=True)
+            raise typer.Exit(1)

src/basic_memory/cli/commands/import_memory_json.py

@@ -5,6 +5,7 @@ import json
 from pathlib import Path
 from typing import Dict, Any, List, Annotated
 
+import logfire
 import typer
 from loguru import logger
 from rich.console import Console
@@ -113,32 +114,33 @@ def memory_json(
     After importing, run 'basic-memory sync' to index the new files.
     """
 
-    if not json_path.exists():
-        typer.echo(f"Error: File not found: {json_path}", err=True)
-        raise typer.Exit(1)
+    with logfire.span("import memory_json"):  # pyright: ignore [reportGeneralTypeIssues]
+        if not json_path.exists():
+            typer.echo(f"Error: File not found: {json_path}", err=True)
+            raise typer.Exit(1)
 
-    try:
-        # Get markdown processor
-        markdown_processor = asyncio.run(get_markdown_processor())
+        try:
+            # Get markdown processor
+            markdown_processor = asyncio.run(get_markdown_processor())
 
-        # Process the file
-        base_path = config.home
-        console.print(f"\nImporting from {json_path}...writing to {base_path}")
-        results = asyncio.run(process_memory_json(json_path, base_path, markdown_processor))
+            # Process the file
+            base_path = config.home
+            console.print(f"\nImporting from {json_path}...writing to {base_path}")
+            results = asyncio.run(process_memory_json(json_path, base_path, markdown_processor))
 
-        # Show results
-        console.print(
-            Panel(
-                f"[green]Import complete![/green]\n\n"
-                f"Created {results['entities']} entities\n"
-                f"Added {results['relations']} relations",
-                expand=False,
+            # Show results
+            console.print(
+                Panel(
+                    f"[green]Import complete![/green]\n\n"
+                    f"Created {results['entities']} entities\n"
+                    f"Added {results['relations']} relations",
+                    expand=False,
+                )
             )
-        )
 
-        console.print("\nRun 'basic-memory sync' to index the new files.")
+            console.print("\nRun 'basic-memory sync' to index the new files.")
 
-    except Exception as e:
-        logger.error("Import failed")
-        typer.echo(f"Error during import: {e}", err=True)
-        raise typer.Exit(1)
+        except Exception as e:
+            logger.error("Import failed")
+            typer.echo(f"Error during import: {e}", err=True)
+            raise typer.Exit(1)

src/basic_memory/cli/commands/mcp.py

@@ -17,4 +17,4 @@ def mcp():  # pragma: no cover
     home_dir = config.home
     logger.info(f"Starting Basic Memory MCP server {basic_memory.__version__}")
     logger.info(f"Home directory: {home_dir}")
-    mcp_server.run()
+    mcp_server.run()

src/basic_memory/cli/commands/status.py

@@ -3,6 +3,7 @@
 import asyncio
 from typing import Set, Dict
 
+import logfire
 import typer
 from loguru import logger
 from rich.console import Console
@@ -146,9 +147,10 @@ def status(
     verbose: bool = typer.Option(False, "--verbose", "-v", help="Show detailed file information"),
 ):
     """Show sync status between files and database."""
-    try:
-        sync_service = asyncio.run(get_file_change_scanner())
-        asyncio.run(run_status(sync_service, verbose))  # pragma: no cover
-    except Exception as e:
-        logger.exception(f"Error checking status: {e}")
-        raise typer.Exit(code=1)  # pragma: no cover
+    with logfire.span("status"):  # pyright: ignore [reportGeneralTypeIssues]
+        try:
+            sync_service = asyncio.run(get_file_change_scanner())
+            asyncio.run(run_status(sync_service, verbose))  # pragma: no cover
+        except Exception as e:
+            logger.exception(f"Error checking status: {e}")
+            raise typer.Exit(code=1)  # pragma: no cover

src/basic_memory/db.py

@@ -4,7 +4,6 @@ from enum import Enum, auto
 from pathlib import Path
 from typing import AsyncGenerator, Optional
 
-import logfire
 
 from basic_memory.config import ProjectConfig
 from alembic import command

src/basic_memory/mcp/tools/knowledge.py

@@ -4,7 +4,6 @@ import logfire
 
 from basic_memory.mcp.server import mcp
 from basic_memory.mcp.tools.utils import call_get, call_post
-from basic_memory.schemas.base import Permalink
 from basic_memory.schemas.memory import memory_url_path
 from basic_memory.schemas.request import (
     GetEntitiesRequest,
@@ -25,7 +24,7 @@ async def get_entity(identifier: str) -> EntityResponse:
     Args:
         identifier: Path identifier for the entity
     """
-    with logfire.span("Getting entity", permalink=identifier) as s:
+    with logfire.span("Getting entity", permalink=identifier):  # pyright: ignore [reportGeneralTypeIssues]
         permalink = memory_url_path(identifier)
         url = f"/knowledge/entities/{permalink}"
         response = await call_get(client, url)
@@ -44,10 +43,14 @@ async def get_entities(request: GetEntitiesRequest) -> EntityListResponse:
     Returns:
         EntityListResponse containing complete details for each requested entity
     """
-    with logfire.span("Getting multiple entities", permalink_count=len(request.permalinks)) as s:
+    with logfire.span("Getting multiple entities", permalink_count=len(request.permalinks)):  # pyright: ignore [reportGeneralTypeIssues]
         url = "/knowledge/entities"
         response = await call_get(
-            client, url, params=[("permalink", memory_url_path(identifier)) for identifier in request.permalinks]
+            client,
+            url,
+            params=[
+                ("permalink", memory_url_path(identifier)) for identifier in request.permalinks
+            ],
         )
         return EntityListResponse.model_validate(response.json())
 
@@ -57,9 +60,9 @@ async def get_entities(request: GetEntitiesRequest) -> EntityListResponse:
 )
 async def delete_entities(request: DeleteEntitiesRequest) -> DeleteEntitiesResponse:
     """Delete entities from the knowledge graph."""
-    with logfire.span("Deleting entities", permalink_count=len(request.permalinks)) as s:
+    with logfire.span("Deleting entities", permalink_count=len(request.permalinks)):  # pyright: ignore [reportGeneralTypeIssues]
         url = "/knowledge/entities/delete"
-        
+
         request.permalinks = [memory_url_path(permlink) for permlink in request.permalinks]
         response = await call_post(client, url, json=request.model_dump())
-        return DeleteEntitiesResponse.model_validate(response.json())
+        return DeleteEntitiesResponse.model_validate(response.json())

src/basic_memory/mcp/tools/memory.py

@@ -66,7 +66,7 @@ async def build_context(
         # Research the history of a feature
         build_context("memory://features/knowledge-graph", timeframe="3 months ago")
     """
-    with logfire.span("Building context", url=url, depth=depth, timeframe=timeframe) as s:
+    with logfire.span("Building context", url=url, depth=depth, timeframe=timeframe):  # pyright: ignore [reportGeneralTypeIssues]
         logger.info(f"Building context from {url}")
         url = normalize_memory_url(url)
         response = await call_get(
@@ -134,7 +134,7 @@ async def recent_activity(
         - For focused queries, consider using build_context with a specific URI
         - Max timeframe is 1 year in the past
     """
-    with logfire.span("Getting recent activity", type=type, depth=depth, timeframe=timeframe) as s:
+    with logfire.span("Getting recent activity", type=type, depth=depth, timeframe=timeframe):  # pyright: ignore [reportGeneralTypeIssues]
         logger.info(
             f"Getting recent activity from {type}, depth={depth}, timeframe={timeframe}, max_results={max_results}"
         )
@@ -151,4 +151,4 @@ async def recent_activity(
             "/memory/recent",
             params=params,
         )
-        return GraphContext.model_validate(response.json())
+        return GraphContext.model_validate(response.json())

src/basic_memory/mcp/tools/notes.py

@@ -62,7 +62,7 @@ async def write_note(
         - Relation counts (resolved/unresolved)
         - Tags if present
     """
-    with logfire.span("Writing note", title=title, folder=folder) as s:
+    with logfire.span("Writing note", title=title, folder=folder):  # pyright: ignore [reportGeneralTypeIssues]
         logger.info(f"Writing note folder:'{folder}' title: '{title}'")
 
         # Create the entity request
@@ -81,25 +81,29 @@ async def write_note(
         url = f"/knowledge/entities/{entity.permalink}"
         response = await call_put(client, url, json=entity.model_dump())
         result = EntityResponse.model_validate(response.json())
-        
+
         # Format semantic summary based on status code
         action = "Created" if response.status_code == 201 else "Updated"
-        summary = [f"# {action} {result.file_path} ({result.checksum[:8]})", f"permalink: {result.permalink}"]
+        assert result.checksum is not None
+        summary = [
+            f"# {action} {result.file_path} ({result.checksum[:8]})",
+            f"permalink: {result.permalink}",
+        ]
 
         if result.observations:
             categories = {}
             for obs in result.observations:
                 categories[obs.category] = categories.get(obs.category, 0) + 1
-            
+
             summary.append("\n## Observations")
             for category, count in sorted(categories.items()):
                 summary.append(f"- {category}: {count}")
-                
+
         if result.relations:
             unresolved = sum(1 for r in result.relations if not r.to_id)
             resolved = len(result.relations) - unresolved
-            
-            summary.append("\n## Relations") 
+
+            summary.append("\n## Relations")
             summary.append(f"- Resolved: {resolved}")
             if unresolved:
                 summary.append(f"- Unresolved: {unresolved}")
@@ -164,7 +168,7 @@ async def read_note(identifier: str) -> str:
     - Last modified timestamp
     - Content checksum
     """
-    with logfire.span("Reading note", identifier=identifier) as s:
+    with logfire.span("Reading note", identifier=identifier):  # pyright: ignore [reportGeneralTypeIssues]
         logger.info(f"Reading note {identifier}")
         url = memory_url_path(identifier)
         response = await call_get(client, f"/resource/{url}")
@@ -188,7 +192,7 @@ async def delete_note(identifier: str) -> bool:
         # Delete by permalink
         delete_note("notes/project-planning")
     """
-    with logfire.span("Deleting note", identifier=identifier) as s:
+    with logfire.span("Deleting note", identifier=identifier):  # pyright: ignore [reportGeneralTypeIssues]
         response = await call_delete(client, f"/knowledge/entities/{identifier}")
         result = DeleteEntitiesResponse.model_validate(response.json())
-        return result.deleted
+        return result.deleted

src/basic_memory/mcp/tools/search.py

@@ -1,4 +1,5 @@
 """Search tools for Basic Memory MCP server."""
+
 import logfire
 from loguru import logger
 
@@ -24,7 +25,7 @@ async def search(query: SearchQuery) -> SearchResponse:
     Returns:
         SearchResponse with search results and metadata
     """
-    with logfire.span("Searching for {query}", qurey=query):
+    with logfire.span("Searching for {query}", qurey=query):  # pyright: ignore [reportGeneralTypeIssues]
         logger.info(f"Searching for {query}")
         response = await call_post(client, "/search/", json=query.model_dump())
         return SearchResponse.model_validate(response.json())

src/basic_memory/schemas/delete.py

@@ -34,4 +34,4 @@ class DeleteEntitiesRequest(BaseModel):
     4. Deletes the corresponding markdown file
     """
 
-    permalinks: Annotated[List[Permalink], MinLen(1)]
+    permalinks: Annotated[List[Permalink], MinLen(1)]

src/basic_memory/schemas/request.py

@@ -55,4 +55,4 @@ class GetEntitiesRequest(BaseModel):
 
 
 class CreateRelationsRequest(BaseModel):
-    relations: List[Relation]
+    relations: List[Relation]

src/basic_memory/sync/sync_service.py

@@ -3,6 +3,7 @@
 from pathlib import Path
 from typing import Dict
 
+import logfire
 from loguru import logger
 from sqlalchemy.exc import IntegrityError
 
@@ -61,105 +62,113 @@ class SyncService:
 
     async def sync(self, directory: Path) -> SyncReport:
         """Sync knowledge files with database."""
-        changes = await self.scanner.find_knowledge_changes(directory)
-        logger.info(f"Found {changes.total_changes} knowledge changes")
 
-        # Handle moves first
-        for old_path, new_path in changes.moves.items():
-            logger.debug(f"Moving entity: {old_path} -> {new_path}")
-            entity = await self.entity_repository.get_by_file_path(old_path)
-            if entity:
-                # Update file_path but keep the same permalink for link stability
-                updated = await self.entity_repository.update(
-                    entity.id, {"file_path": new_path, "checksum": changes.checksums[new_path]}
-                )
-                # update search index
-                if updated:
-                    await self.search_service.index_entity(updated)
+        with logfire.span("sync", directory=directory):  # pyright: ignore [reportGeneralTypeIssues]
+            changes = await self.scanner.find_knowledge_changes(directory)
+            logger.info(f"Found {changes.total_changes} knowledge changes")
 
-        # Handle deletions next
-        # remove rows from db for files no longer present
-        for path in changes.deleted:
-            await self.handle_entity_deletion(path)
+            # Handle moves first
+            for old_path, new_path in changes.moves.items():
+                logger.debug(f"Moving entity: {old_path} -> {new_path}")
+                entity = await self.entity_repository.get_by_file_path(old_path)
+                if entity:
+                    # Update file_path but keep the same permalink for link stability
+                    updated = await self.entity_repository.update(
+                        entity.id, {"file_path": new_path, "checksum": changes.checksums[new_path]}
+                    )
+                    # update search index
+                    if updated:
+                        await self.search_service.index_entity(updated)
 
-        # Parse files that need updating
-        parsed_entities: Dict[str, EntityMarkdown] = {}
+            # Handle deletions next
+            # remove rows from db for files no longer present
+            for path in changes.deleted:
+                await self.handle_entity_deletion(path)
 
-        for path in [*changes.new, *changes.modified]:
-            entity_markdown = await self.entity_parser.parse_file(directory / path)
-            parsed_entities[path] = entity_markdown
+            # Parse files that need updating
+            parsed_entities: Dict[str, EntityMarkdown] = {}
 
-        # First pass: Create/update entities
-        # entities will have a null checksum to indicate they are not complete
-        for path, entity_markdown in parsed_entities.items():
-            # Get unique permalink and update markdown if needed
-            permalink = await self.entity_service.resolve_permalink(
-                Path(path), markdown=entity_markdown
-            )
+            for path in [*changes.new, *changes.modified]:
+                entity_markdown = await self.entity_parser.parse_file(directory / path)
+                parsed_entities[path] = entity_markdown
 
-            if permalink != entity_markdown.frontmatter.permalink:
-                # Add/update permalink in frontmatter
-                logger.info(f"Adding permalink '{permalink}' to file: {path}")
-
-                # update markdown
-                entity_markdown.frontmatter.metadata["permalink"] = permalink
-
-                # update file frontmatter
-                updated_checksum = await file_utils.update_frontmatter(
-                    directory / path, {"permalink": permalink}
+            # First pass: Create/update entities
+            # entities will have a null checksum to indicate they are not complete
+            for path, entity_markdown in parsed_entities.items():
+                # Get unique permalink and update markdown if needed
+                permalink = await self.entity_service.resolve_permalink(
+                    Path(path), markdown=entity_markdown
                 )
 
-                # Update checksum in changes report since file was modified
-                changes.checksums[path] = updated_checksum
+                if permalink != entity_markdown.frontmatter.permalink:
+                    # Add/update permalink in frontmatter
+                    logger.info(f"Adding permalink '{permalink}' to file: {path}")
 
-            # if the file is new, create an entity
-            if path in changes.new:
-                # Create entity with final permalink
-                logger.debug(f"Creating new entity_markdown: {path}")
-                await self.entity_service.create_entity_from_markdown(Path(path), entity_markdown)
-            # otherwise we need to update the entity and observations
-            else:
-                logger.debug(f"Updating entity_markdown: {path}")
-                await self.entity_service.update_entity_and_observations(
+                    # update markdown
+                    entity_markdown.frontmatter.metadata["permalink"] = permalink
+
+                    # update file frontmatter
+                    updated_checksum = await file_utils.update_frontmatter(
+                        directory / path, {"permalink": permalink}
+                    )
+
+                    # Update checksum in changes report since file was modified
+                    changes.checksums[path] = updated_checksum
+
+                # if the file is new, create an entity
+                if path in changes.new:
+                    # Create entity with final permalink
+                    logger.debug(f"Creating new entity_markdown: {path}")
+                    await self.entity_service.create_entity_from_markdown(
+                        Path(path), entity_markdown
+                    )
+                # otherwise we need to update the entity and observations
+                else:
+                    logger.debug(f"Updating entity_markdown: {path}")
+                    await self.entity_service.update_entity_and_observations(
+                        Path(path), entity_markdown
+                    )
+
+            # Second pass
+            for path, entity_markdown in parsed_entities.items():
+                logger.debug(f"Updating relations for: {path}")
+
+                # Process relations
+                checksum = changes.checksums[path]
+                entity = await self.entity_service.update_entity_relations(
                     Path(path), entity_markdown
                 )
 
-        # Second pass
-        for path, entity_markdown in parsed_entities.items():
-            logger.debug(f"Updating relations for: {path}")
+                # add to search index
+                await self.search_service.index_entity(entity)
 
-            # Process relations
-            checksum = changes.checksums[path]
-            entity = await self.entity_service.update_entity_relations(Path(path), entity_markdown)
+                # Set final checksum to mark sync complete
+                await self.entity_repository.update(entity.id, {"checksum": checksum})
 
-            # add to search index
-            await self.search_service.index_entity(entity)
-
-            # Set final checksum to mark sync complete
-            await self.entity_repository.update(entity.id, {"checksum": checksum})
-
-        # Third pass: Try to resolve any forward references
-        logger.debug("Attempting to resolve forward references")
-        for relation in await self.relation_repository.find_unresolved_relations():
-            target_entity = await self.entity_service.link_resolver.resolve_link(relation.to_name)
-            # check we found a link that is not the source
-            if target_entity and target_entity.id != relation.from_id:
-                logger.debug(
-                    f"Resolved forward reference: {relation.to_name} -> {target_entity.permalink}"
+            # Third pass: Try to resolve any forward references
+            logger.debug("Attempting to resolve forward references")
+            for relation in await self.relation_repository.find_unresolved_relations():
+                target_entity = await self.entity_service.link_resolver.resolve_link(
+                    relation.to_name
                 )
-
-                try:
-                    await self.relation_repository.update(
-                        relation.id,
-                        {
-                            "to_id": target_entity.id,
-                            "to_name": target_entity.title,  # Update to actual title
-                        },
+                # check we found a link that is not the source
+                if target_entity and target_entity.id != relation.from_id:
+                    logger.debug(
+                        f"Resolved forward reference: {relation.to_name} -> {target_entity.permalink}"
                     )
-                except IntegrityError:
-                    logger.debug(f"Ignoring duplicate relation {relation}")
 
-                # update search index
-                await self.search_service.index_entity(target_entity)
+                    try:
+                        await self.relation_repository.update(
+                            relation.id,
+                            {
+                                "to_id": target_entity.id,
+                                "to_name": target_entity.title,  # Update to actual title
+                            },
+                        )
+                    except IntegrityError:
+                        logger.debug(f"Ignoring duplicate relation {relation}")
 
-        return changes
+                    # update search index
+                    await self.search_service.index_entity(target_entity)
+
+            return changes

tests/mcp/test_tool_knowledge.py

@@ -32,6 +32,7 @@ async def test_get_single_entity(client):
     assert entity.permalink == "test/test-note"
     assert len(entity.observations) == 1
 
+
 @pytest.mark.asyncio
 async def test_get_single_entity_memory_url(client):
     """Test retrieving a single entity."""
@@ -81,6 +82,7 @@ async def test_get_multiple_entities(client):
     assert "test/test-note-1" in permalinks
     assert "test/test-note-2" in permalinks
 
+
 @pytest.mark.asyncio
 async def test_get_multiple_entities_memory_ur(client):
     """Test retrieving multiple entities."""
@@ -97,7 +99,9 @@ async def test_get_multiple_entities_memory_ur(client):
     )
 
     # Get both entities
-    request = GetEntitiesRequest(permalinks=["memory://test/test-note-1", "memory://test/test-note-2"])
+    request = GetEntitiesRequest(
+        permalinks=["memory://test/test-note-1", "memory://test/test-note-2"]
+    )
     response = await get_entities(request)
 
     # Verify we got both entities
@@ -128,6 +132,7 @@ async def test_delete_entities(client):
     with pytest.raises(ToolError):
         await get_entity("test/test-note")
 
+
 @pytest.mark.asyncio
 async def test_delete_entities_memory_url(client):
     """Test deleting entities."""