fix: batch fix 3 bugs - exclude filter, progress feedback, KuzuDB cleanup

src/codegraphcontext/cli/cli_helpers.py

@@ -235,7 +235,7 @@ async def _run_index_with_progress(graph_builder: GraphBuilder, path_obj: Path,
                     progress.update(task_id, total=job.total_files, completed=job.processed_files)
 
                 # Update the current filename in the UI
-                current_file = job.current_file or ""
+                current_file = job.current_file or job.status_message or ""
                 if len(current_file) > 40:
                     current_file = "..." + current_file[-37:]
                 progress.update(task_id, filename=current_file)

src/codegraphcontext/core/database_kuzu.py

@@ -298,16 +298,26 @@ def _run_schema_migrations(self):
                 raise RuntimeError("Kuzu Schema Migration Failed") from e
 
     def close_driver(self):
-        """Closes the connection pool."""
+        """Closes the connection pool and releases database resources."""
         if self._db is not None:
-            info_logger("Closing KùzuDB connection pool")
-            # Clear the pool
-            while not self._pool.empty():
-                try:
-                    self._pool.get_nowait()
-                except:
-                    break
-            self._db = None
+            with self._lock:
+                if self._db is None:
+                    return
+                info_logger("Closing KùzuDB connection pool")
+                # Clear and close all connections in the pool
+                while self._pool is not None and not self._pool.empty():
+                    try:
+                        conn = self._pool.get_nowait()
+                        try:
+                            conn.close()
+                        except Exception:
+                            pass
+                    except:
+                        break
+                self._pool = None
+                # Drop database reference to trigger KuzuDB cleanup
+                self._db = None
+                import gc; gc.collect()
 
     def is_connected(self) -> bool:
         """Checks if the database connection is currently active."""

src/codegraphcontext/core/jobs.py

@@ -33,6 +33,7 @@ class JobInfo:
     total_files: int = 0
     processed_files: int = 0
     current_file: Optional[str] = None
+    status_message: Optional[str] = None
     estimated_duration: Optional[float] = None
     actual_duration: Optional[float] = None
     errors: List[str] = None

src/codegraphcontext/tools/code_finder.py

@@ -780,7 +780,13 @@ def find_dead_code(self, exclude_decorated_with: Optional[List[str]] = None, rep
 
         with self.driver.session() as session:
             repo_filter = "AND func.path STARTS WITH $repo_path" if repo_path else ""
-            decorator_filter = "AND ALL(decorator_name IN $exclude_decorated_with WHERE NOT decorator_name IN func.decorators)" if exclude_decorated_with else ""
+            decorator_filter = ""
+            if exclude_decorated_with:
+                any_conditions = " AND ".join(
+                    f"NOT ANY(d IN func.decorators WHERE d CONTAINS '{p.replace(chr(39), chr(39)+chr(39))}')"
+                    for p in exclude_decorated_with
+                )
+                decorator_filter = f"AND {any_conditions}"
             func_ignore = cypher_path_not_under_ignore_dirs("func.path")
             caller_ignore = cypher_path_not_under_ignore_dirs("caller.path")
 
@@ -816,9 +822,7 @@ def find_dead_code(self, exclude_decorated_with: Optional[List[str]] = None, rep
             params = {}
             if repo_path:
                 params["repo_path"] = repo_path
-            if exclude_decorated_with:
-                params["exclude_decorated_with"] = exclude_decorated_with
-
+
             result = session.run(query, **params)
 
             return {

src/codegraphcontext/tools/indexing/pipeline.py

@@ -105,6 +105,8 @@ async def process_file(file: Path) -> Optional[Dict[str, Any]]:
     )
 
     t0 = time.time()
+    if job_id:
+        job_manager.update_job(job_id, status_message="Resolving inheritance links...")
     info_logger(f"[INHERITS] Resolving inheritance links across {len(all_file_data)} files...")
     inheritance_batch, csharp_files = build_inheritance_and_csharp_files(all_file_data, imports_map)
     writer.write_inheritance_links(inheritance_batch, csharp_files, imports_map)
@@ -117,6 +119,8 @@ async def process_file(file: Path) -> Optional[Dict[str, Any]]:
         None,
         diagnostics=call_resolution_diagnostics,
     )
+    if job_id:
+        job_manager.update_job(job_id, status_message="Writing function CALLS edges...")
     writer.write_function_call_groups(*resolved_calls)
     t2 = time.time()
     info_logger(f"Function calls created in {t2 - t1:.1f}s. Total post-processing: {t2 - t0:.1f}s")
@@ -125,10 +129,14 @@ async def process_file(file: Path) -> Optional[Dict[str, Any]]:
     # C++ method definitions live in .cpp while the Class node lives in .h.
     # The per-file write cannot create these edges reliably due to ordering;
     # this single repo-scoped pass runs after every node is in the graph.
+    if job_id:
+        job_manager.update_job(job_id, status_message="Linking C++ class-function edges...")
     info_logger("[CPP] Linking C++ out-of-line method definitions to their classes...")
     writer.write_cpp_class_function_links(resolved_repo_path_str)
 
     # ── Spring injection edges (#887) ─────────────────────────────────────────
+    if job_id:
+        job_manager.update_job(job_id, status_message="Processing Spring injection edges...")
     spring_inject_batch = []
     for fd in all_file_data:
         injections = fd.get("spring_injections")
@@ -155,6 +163,8 @@ async def process_file(file: Path) -> Optional[Dict[str, Any]]:
 
     # ── Maven / Gradle build graph (#888) ────────────────────────────────────
     if not is_dependency and path.is_dir():
+        if job_id:
+            job_manager.update_job(job_id, status_message="Processing Maven build graph...")
         try:
             from ...tools.languages.maven import parse_repo_maven
             maven_data = parse_repo_maven(path.resolve())
@@ -163,6 +173,8 @@ async def process_file(file: Path) -> Optional[Dict[str, Any]]:
         except Exception as _me:
             info_logger(f"[MAVEN] Build graph failed (skipping): {_me}")
 
+        if job_id:
+            job_manager.update_job(job_id, status_message="Processing Gradle build graph...")
         try:
             from ...tools.languages.gradle import parse_repo_gradle
             gradle_data = parse_repo_gradle(path.resolve())
@@ -172,6 +184,8 @@ async def process_file(file: Path) -> Optional[Dict[str, Any]]:
             info_logger(f"[GRADLE] Build graph failed (skipping): {_ge}")
 
     # ── ORM / datasource code linkage (#843) ─────────────────────────────────
+    if job_id:
+        job_manager.update_job(job_id, status_message="Processing ORM mappings...")
     orm_batch = []
     for fd in all_file_data:
         orm_mappings = fd.get("orm_mappings")
@@ -189,6 +203,8 @@ async def process_file(file: Path) -> Optional[Dict[str, Any]]:
 
     # ── MyBatis XML mapper READS / WRITES edges ───────────────────────────────
     if not is_dependency and path.is_dir():
+        if job_id:
+            job_manager.update_job(job_id, status_message="Processing MyBatis XML mappers...")
         try:
             from ...tools.languages.mybatis import find_and_parse_mybatis_mappers
             mybatis_batch = find_and_parse_mybatis_mappers(path.resolve())
@@ -200,6 +216,8 @@ async def process_file(file: Path) -> Optional[Dict[str, Any]]:
     # ── Phase 4: embedding generation (optional, config-gated) ────────────────
     from ...cli.config_manager import get_config_value as _gcv
     if (_gcv("ENABLE_VECTOR_RESOLVE") or "false").lower() == "true":
+        if job_id:
+            job_manager.update_job(job_id, status_message="Generating embeddings...")
         try:
             from .embeddings import EmbeddingPipeline
             repo_path_str = str(path.resolve())
@@ -211,6 +229,8 @@ async def process_file(file: Path) -> Optional[Dict[str, Any]]:
 
     # ── Phase 5: inheritance-aware re-resolution (optional, config-gated) ─────
     if (_gcv("ENABLE_INHERIT_RESOLVE") or "false").lower() == "true":
+        if job_id:
+            job_manager.update_job(job_id, status_message="Running inheritance re-resolution...")
         try:
             from .resolution.post_resolution import run_inheritance_reresolve
             vector_resolver = None