fix: selecting search all does not work on LightRAG / NanoGraphRAG (#627) #none

* fix: base path

* fix: select all doesn't work

* fix: adding new documents should update the existing index within the file collection instead of creating new one #561

* fix linter issues

* feat: update NanoGraphRAG with global collection search

---------

Co-authored-by: Tadashi <tadashi@cinnamon.is>

flowsettings.py

@@ -317,6 +317,7 @@ SETTINGS_REASONING = {
     },
 }
 
+USE_GLOBAL_GRAPHRAG = config("USE_GLOBAL_GRAPHRAG", default=True, cast=bool)
 USE_NANO_GRAPHRAG = config("USE_NANO_GRAPHRAG", default=False, cast=bool)
 USE_LIGHTRAG = config("USE_LIGHTRAG", default=True, cast=bool)
 USE_MS_GRAPHRAG = config("USE_MS_GRAPHRAG", default=True, cast=bool)

libs/ktem/ktem/index/file/graph/graph_index.py

@@ -25,7 +25,7 @@ class GraphRAGIndex(FileIndex):
     def get_retriever_pipelines(
         self, settings: dict, user_id: int, selected: Any = None
     ) -> list["BaseFileIndexRetriever"]:
-        _, file_ids, _ = selected
+        file_ids = self._selector_ui.get_selected_ids(selected)
         retrievers = [
             GraphRAGRetrieverPipeline(
                 file_ids=file_ids,

libs/ktem/ktem/index/file/graph/light_graph_index.py

@@ -1,4 +1,8 @@
-from typing import Any
+from typing import Any, Optional
+from uuid import uuid4
+
+from ktem.db.engine import engine
+from sqlalchemy.orm import Session
 
 from ..base import BaseFileIndexIndexing, BaseFileIndexRetriever
 from .graph_index import GraphRAGIndex
@@ -6,12 +10,35 @@ from .lightrag_pipelines import LightRAGIndexingPipeline, LightRAGRetrieverPipel
 
 
 class LightRAGIndex(GraphRAGIndex):
+    def __init__(self, app, id: int, name: str, config: dict):
+        super().__init__(app, id, name, config)
+        self._collection_graph_id: Optional[str] = None
+
     def _setup_indexing_cls(self):
         self._indexing_pipeline_cls = LightRAGIndexingPipeline
 
     def _setup_retriever_cls(self):
         self._retriever_pipeline_cls = [LightRAGRetrieverPipeline]
 
+    def _get_or_create_collection_graph_id(self):
+        if self._collection_graph_id:
+            return self._collection_graph_id
+
+        # Try to find existing graph ID for this collection
+        with Session(engine) as session:
+            result = (
+                session.query(self._resources["Index"].target_id)  # type: ignore
+                .filter(
+                    self._resources["Index"].relation_type == "graph"  # type: ignore
+                )
+                .first()
+            )
+            if result:
+                self._collection_graph_id = result[0]
+            else:
+                self._collection_graph_id = str(uuid4())
+        return self._collection_graph_id
+
     def get_indexing_pipeline(self, settings, user_id) -> BaseFileIndexIndexing:
         pipeline = super().get_indexing_pipeline(settings, user_id)
         # indexing settings
@@ -23,12 +50,14 @@ class LightRAGIndex(GraphRAGIndex):
         }
         # set the prompts
         pipeline.prompts = striped_settings
+        # set collection graph id
+        pipeline.collection_graph_id = self._get_or_create_collection_graph_id()
         return pipeline
 
     def get_retriever_pipelines(
         self, settings: dict, user_id: int, selected: Any = None
     ) -> list["BaseFileIndexRetriever"]:
-        _, file_ids, _ = selected
+        file_ids = self._selector_ui.get_selected_ids(selected)
         # retrieval settings
         prefix = f"index.options.{self.id}."
         search_type = settings.get(prefix + "search_type", "local")

libs/ktem/ktem/index/file/graph/lightrag_pipelines.py

@@ -242,6 +242,40 @@ class LightRAGIndexingPipeline(GraphRAGIndexingPipeline):
     """GraphRAG specific indexing pipeline"""
 
     prompts: dict[str, str] = {}
+    collection_graph_id: str
+
+    def store_file_id_with_graph_id(self, file_ids: list[str | None]):
+        if not settings.USE_GLOBAL_GRAPHRAG:
+            return super().store_file_id_with_graph_id(file_ids)
+
+        # Use the collection-wide graph ID for LightRAG
+        graph_id = self.collection_graph_id
+
+        # Record all files under this graph_id
+        with Session(engine) as session:
+            for file_id in file_ids:
+                if not file_id:
+                    continue
+                # Check if mapping already exists
+                existing = (
+                    session.query(self.Index)
+                    .filter(
+                        self.Index.source_id == file_id,
+                        self.Index.target_id == graph_id,
+                        self.Index.relation_type == "graph",
+                    )
+                    .first()
+                )
+                if not existing:
+                    node = self.Index(
+                        source_id=file_id,
+                        target_id=graph_id,
+                        relation_type="graph",
+                    )
+                    session.add(node)
+            session.commit()
+
+        return graph_id
 
     @classmethod
     def get_user_settings(cls) -> dict:
@@ -295,46 +329,54 @@ class LightRAGIndexingPipeline(GraphRAGIndexingPipeline):
 
         yield Document(
             channel="debug",
-            text="[GraphRAG] Creating index... This can take a long time.",
+            text="[GraphRAG] Creating/Updating index... This can take a long time.",
         )
 
-        # remove all .json files in the input_path directory (previous cache)
+        # Check if graph already exists
+        graph_file = input_path / "graph_chunk_entity_relation.graphml"
+        is_incremental = graph_file.exists()
+
+        # Only clear cache if it's a new graph
+        if not is_incremental:
             json_files = glob.glob(f"{input_path}/*.json")
             for json_file in json_files:
                 os.remove(json_file)
 
-        # indexing
+        # Initialize or load existing GraphRAG
         graphrag_func = build_graphrag(
             input_path,
             llm_func=llm_func,
             embedding_func=embedding_func,
         )
-        # output must be contain: Loaded graph from
+
-        # ..input/graph_chunk_entity_relation.graphml with xxx nodes, xxx edges
         total_docs = len(all_docs)
         process_doc_count = 0
         yield Document(
             channel="debug",
-            text=f"[GraphRAG] Indexed {process_doc_count} / {total_docs} documents.",
+            text=(
+                f"[GraphRAG] {'Updating' if is_incremental else 'Creating'} index: "
+                f"{process_doc_count} / {total_docs} documents."
+            ),
         )
 
         for doc_id in range(0, len(all_docs), INDEX_BATCHSIZE):
             cur_docs = all_docs[doc_id : doc_id + INDEX_BATCHSIZE]
             combined_doc = "\n".join(cur_docs)
 
+            # Use insert for incremental updates
             graphrag_func.insert(combined_doc)
             process_doc_count += len(cur_docs)
             yield Document(
                 channel="debug",
                 text=(
-                    f"[GraphRAG] Indexed {process_doc_count} "
+                    f"[GraphRAG] {'Updated' if is_incremental else 'Indexed'} "
-                    f"/ {total_docs} documents."
+                    f"{process_doc_count} / {total_docs} documents."
                 ),
             )
 
         yield Document(
             channel="debug",
-            text="[GraphRAG] Indexing finished.",
+            text=f"[GraphRAG] {'Update' if is_incremental else 'Indexing'} finished.",
         )
 
     def stream(

libs/ktem/ktem/index/file/graph/nano_graph_index.py

@@ -1,4 +1,8 @@
-from typing import Any
+from typing import Any, Optional
+from uuid import uuid4
+
+from ktem.db.engine import engine
+from sqlalchemy.orm import Session
 
 from ..base import BaseFileIndexIndexing, BaseFileIndexRetriever
 from .graph_index import GraphRAGIndex
@@ -6,12 +10,35 @@ from .nano_pipelines import NanoGraphRAGIndexingPipeline, NanoGraphRAGRetrieverP
 
 
 class NanoGraphRAGIndex(GraphRAGIndex):
+    def __init__(self, app, id: int, name: str, config: dict):
+        super().__init__(app, id, name, config)
+        self._collection_graph_id: Optional[str] = None
+
     def _setup_indexing_cls(self):
         self._indexing_pipeline_cls = NanoGraphRAGIndexingPipeline
 
     def _setup_retriever_cls(self):
         self._retriever_pipeline_cls = [NanoGraphRAGRetrieverPipeline]
 
+    def _get_or_create_collection_graph_id(self):
+        if self._collection_graph_id:
+            return self._collection_graph_id
+
+        # Try to find existing graph ID for this collection
+        with Session(engine) as session:
+            result = (
+                session.query(self._resources["Index"].target_id)  # type: ignore
+                .filter(
+                    self._resources["Index"].relation_type == "graph"  # type: ignore
+                )
+                .first()
+            )
+            if result:
+                self._collection_graph_id = result[0]
+            else:
+                self._collection_graph_id = str(uuid4())
+        return self._collection_graph_id
+
     def get_indexing_pipeline(self, settings, user_id) -> BaseFileIndexIndexing:
         pipeline = super().get_indexing_pipeline(settings, user_id)
         # indexing settings
@@ -23,12 +50,14 @@ class NanoGraphRAGIndex(GraphRAGIndex):
         }
         # set the prompts
         pipeline.prompts = striped_settings
+        # set collection graph id
+        pipeline.collection_graph_id = self._get_or_create_collection_graph_id()
         return pipeline
 
     def get_retriever_pipelines(
         self, settings: dict, user_id: int, selected: Any = None
     ) -> list["BaseFileIndexRetriever"]:
-        _, file_ids, _ = selected
+        file_ids = self._selector_ui.get_selected_ids(selected)
         # retrieval settings
         prefix = f"index.options.{self.id}."
         search_type = settings.get(prefix + "search_type", "local")

libs/ktem/ktem/index/file/graph/nano_pipelines.py

@@ -238,6 +238,40 @@ class NanoGraphRAGIndexingPipeline(GraphRAGIndexingPipeline):
     """GraphRAG specific indexing pipeline"""
 
     prompts: dict[str, str] = {}
+    collection_graph_id: str
+
+    def store_file_id_with_graph_id(self, file_ids: list[str | None]):
+        if not settings.USE_GLOBAL_GRAPHRAG:
+            return super().store_file_id_with_graph_id(file_ids)
+
+        # Use the collection-wide graph ID for LightRAG
+        graph_id = self.collection_graph_id
+
+        # Record all files under this graph_id
+        with Session(engine) as session:
+            for file_id in file_ids:
+                if not file_id:
+                    continue
+                # Check if mapping already exists
+                existing = (
+                    session.query(self.Index)
+                    .filter(
+                        self.Index.source_id == file_id,
+                        self.Index.target_id == graph_id,
+                        self.Index.relation_type == "graph",
+                    )
+                    .first()
+                )
+                if not existing:
+                    node = self.Index(
+                        source_id=file_id,
+                        target_id=graph_id,
+                        relation_type="graph",
+                    )
+                    session.add(node)
+            session.commit()
+
+        return graph_id
 
     @classmethod
     def get_user_settings(cls) -> dict:
@@ -291,45 +325,54 @@ class NanoGraphRAGIndexingPipeline(GraphRAGIndexingPipeline):
 
         yield Document(
             channel="debug",
-            text="[GraphRAG] Creating index... This can take a long time.",
+            text="[GraphRAG] Creating/Updating index... This can take a long time.",
         )
 
-        # remove all .json files in the input_path directory (previous cache)
+        # Check if graph already exists
+        graph_file = input_path / "graph_chunk_entity_relation.graphml"
+        is_incremental = graph_file.exists()
+
+        # Only clear cache if it's a new graph
+        if not is_incremental:
             json_files = glob.glob(f"{input_path}/*.json")
             for json_file in json_files:
                 os.remove(json_file)
 
-        # indexing
+        # Initialize or load existing GraphRAG
         graphrag_func = build_graphrag(
             input_path,
             llm_func=llm_func,
             embedding_func=embedding_func,
         )
-        # output must be contain: Loaded graph from
+
-        # ..input/graph_chunk_entity_relation.graphml with xxx nodes, xxx edges
         total_docs = len(all_docs)
         process_doc_count = 0
         yield Document(
             channel="debug",
-            text=f"[GraphRAG] Indexed {process_doc_count} / {total_docs} documents.",
+            text=(
+                f"[GraphRAG] {'Updating' if is_incremental else 'Creating'} index: "
+                f"{process_doc_count} / {total_docs} documents."
+            ),
         )
+
         for doc_id in range(0, len(all_docs), INDEX_BATCHSIZE):
             cur_docs = all_docs[doc_id : doc_id + INDEX_BATCHSIZE]
             combined_doc = "\n".join(cur_docs)
 
+            # Use insert for incremental updates
             graphrag_func.insert(combined_doc)
             process_doc_count += len(cur_docs)
             yield Document(
                 channel="debug",
                 text=(
-                    f"[GraphRAG] Indexed {process_doc_count} "
+                    f"[GraphRAG] {'Updated' if is_incremental else 'Indexed'} "
-                    f"/ {total_docs} documents."
+                    f"{process_doc_count} / {total_docs} documents."
                 ),
             )
 
         yield Document(
             channel="debug",
-            text="[GraphRAG] Indexing finished.",
+            text=f"[GraphRAG] {'Update' if is_incremental else 'Indexing'} finished.",
         )
 
     def stream(