feat: add lightrag support (#474) bump:patch

* feat: add lightrag support

* docs: update README

README.md

@@ -187,6 +187,18 @@ documents and developers who want to build their own RAG pipeline.
 
 <details>
 
+<summary>Setup LIGHTRAG</summary>
+
+- Install LightRAG: `pip install git+https://github.com/HKUDS/LightRAG.git`
+- `LightRAG` install might introduce version conflicts, see [this issue](https://github.com/Cinnamon/kotaemon/issues/440)
+  - To quickly fix: `pip uninstall hnswlib chroma-hnswlib && pip install chroma-hnswlib`
+- Launch Kotaemon with `USE_LIGHTRAG=true` environment variable.
+- Set your default LLM & Embedding models in Resources setting and it will be recognized automatically from LightRAG.
+
+</details>
+
+<details>
+
 <summary>Setup MS GRAPHRAG</summary>
 
 - **Non-Docker Installation**: If you are not using Docker, install GraphRAG with the following command:

flowsettings.py

@@ -287,41 +287,31 @@ SETTINGS_REASONING = {
 }
 
 USE_NANO_GRAPHRAG = config("USE_NANO_GRAPHRAG", default=False, cast=bool)
-GRAPHRAG_INDEX_TYPE = (
+USE_LIGHTRAG = config("USE_LIGHTRAG", default=False, cast=bool)
-    "ktem.index.file.graph.GraphRAGIndex"
+
-    if not USE_NANO_GRAPHRAG
+if USE_NANO_GRAPHRAG:
-    else "ktem.index.file.graph.NanoGraphRAGIndex"
+    GRAPHRAG_INDEX_TYPE = "ktem.index.file.graph.NanoGraphRAGIndex"
-)
+elif USE_LIGHTRAG:
+    GRAPHRAG_INDEX_TYPE = "ktem.index.file.graph.LightRAGIndex"
+else:
+    GRAPHRAG_INDEX_TYPE = "ktem.index.file.graph.GraphRAGIndex"
+
 KH_INDEX_TYPES = [
     "ktem.index.file.FileIndex",
     GRAPHRAG_INDEX_TYPE,
 ]
 
-GRAPHRAG_INDEX = (
+GRAPHRAG_INDEX = {
-    {
+    "name": GRAPHRAG_INDEX_TYPE.split(".")[-1].replace("Index", ""),  # get last name
-        "name": "GraphRAG",
+    "config": {
-        "config": {
+        "supported_file_types": (
-            "supported_file_types": (
+            ".png, .jpeg, .jpg, .tiff, .tif, .pdf, .xls, .xlsx, .doc, .docx, "
-                ".png, .jpeg, .jpg, .tiff, .tif, .pdf, .xls, .xlsx, .doc, .docx, "
+            ".pptx, .csv, .html, .mhtml, .txt, .md, .zip"
-                ".pptx, .csv, .html, .mhtml, .txt, .md, .zip"
+        ),
-            ),
+        "private": False,
-            "private": False,
+    },
-        },
+    "index_type": GRAPHRAG_INDEX_TYPE,
-        "index_type": "ktem.index.file.graph.GraphRAGIndex",
+}
-    }
-    if not USE_NANO_GRAPHRAG
-    else {
-        "name": "NanoGraphRAG",
-        "config": {
-            "supported_file_types": (
-                ".png, .jpeg, .jpg, .tiff, .tif, .pdf, .xls, .xlsx, .doc, .docx, "
-                ".pptx, .csv, .html, .mhtml, .txt, .md, .zip"
-            ),
-            "private": False,
-        },
-        "index_type": "ktem.index.file.graph.NanoGraphRAGIndex",
-    }
-)
 
 KH_INDICES = [
     {

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

@@ -1,4 +1,5 @@
 from .graph_index import GraphRAGIndex
+from .light_graph_index import LightRAGIndex
 from .nano_graph_index import NanoGraphRAGIndex
 
-__all__ = ["GraphRAGIndex", "NanoGraphRAGIndex"]
+__all__ = ["GraphRAGIndex", "NanoGraphRAGIndex", "LightRAGIndex"]

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

@@ -0,0 +1,26 @@
+from typing import Any
+
+from ..base import BaseFileIndexRetriever
+from .graph_index import GraphRAGIndex
+from .lightrag_pipelines import LightRAGIndexingPipeline, LightRAGRetrieverPipeline
+
+
+class LightRAGIndex(GraphRAGIndex):
+    def _setup_indexing_cls(self):
+        self._indexing_pipeline_cls = LightRAGIndexingPipeline
+
+    def _setup_retriever_cls(self):
+        self._retriever_pipeline_cls = [LightRAGRetrieverPipeline]
+
+    def get_retriever_pipelines(
+        self, settings: dict, user_id: int, selected: Any = None
+    ) -> list["BaseFileIndexRetriever"]:
+        _, file_ids, _ = selected
+        retrievers = [
+            LightRAGRetrieverPipeline(
+                file_ids=file_ids,
+                Index=self._resources["Index"],
+            )
+        ]
+
+        return retrievers

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

@@ -0,0 +1,386 @@
+import asyncio
+import glob
+import logging
+import os
+import re
+from pathlib import Path
+from typing import Generator
+
+import numpy as np
+import pandas as pd
+from ktem.db.models import engine
+from ktem.embeddings.manager import embedding_models_manager as embeddings
+from ktem.llms.manager import llms
+from sqlalchemy.orm import Session
+from theflow.settings import settings
+
+from kotaemon.base import Document, Param, RetrievedDocument
+from kotaemon.base.schema import AIMessage, HumanMessage, SystemMessage
+
+from ..pipelines import BaseFileIndexRetriever
+from .pipelines import GraphRAGIndexingPipeline
+from .visualize import create_knowledge_graph, visualize_graph
+
+try:
+    from lightrag import LightRAG, QueryParam
+    from lightrag.operate import (
+        _find_most_related_edges_from_entities,
+        _find_most_related_text_unit_from_entities,
+    )
+    from lightrag.utils import EmbeddingFunc, compute_args_hash
+
+except ImportError:
+    print(
+        (
+            "LightRAG dependencies not installed. "
+            "Try `pip install git+https://github.com/HKUDS/LightRAG.git` to install. "
+            "LighthRAG retriever pipeline will not work properly."
+        )
+    )
+
+
+logging.getLogger("lightrag").setLevel(logging.INFO)
+
+
+filestorage_path = Path(settings.KH_FILESTORAGE_PATH) / "lightrag"
+filestorage_path.mkdir(parents=True, exist_ok=True)
+
+INDEX_BATCHSIZE = 2
+
+
+def get_llm_func(model):
+    async def llm_func(
+        prompt, system_prompt=None, history_messages=[], **kwargs
+    ) -> str:
+        input_messages = [SystemMessage(text=system_prompt)] if system_prompt else []
+
+        hashing_kv = kwargs.pop("hashing_kv", None)
+        if history_messages:
+            for msg in history_messages:
+                if msg.get("role") == "user":
+                    input_messages.append(HumanMessage(text=msg["content"]))
+                else:
+                    input_messages.append(AIMessage(text=msg["content"]))
+
+        input_messages.append(HumanMessage(text=prompt))
+
+        if hashing_kv is not None:
+            args_hash = compute_args_hash("model", input_messages)
+            if_cache_return = await hashing_kv.get_by_id(args_hash)
+            if if_cache_return is not None:
+                return if_cache_return["return"]
+
+        output = model(input_messages).text
+
+        print("-" * 50)
+        print(output, "\n", "-" * 50)
+
+        if hashing_kv is not None:
+            await hashing_kv.upsert({args_hash: {"return": output, "model": "model"}})
+
+        return output
+
+    return llm_func
+
+
+def get_embedding_func(model):
+    async def embedding_func(texts: list[str]) -> np.ndarray:
+        outputs = model(texts)
+        embedding_outputs = np.array([doc.embedding for doc in outputs])
+
+        return embedding_outputs
+
+    return embedding_func
+
+
+def get_default_models_wrapper():
+    # setup model functions
+    default_embedding = embeddings.get_default()
+    default_embedding_dim = len(default_embedding(["Hi"])[0].embedding)
+    embedding_func = EmbeddingFunc(
+        embedding_dim=default_embedding_dim,
+        max_token_size=8192,
+        func=get_embedding_func(default_embedding),
+    )
+    print("GraphRAG embedding dim", default_embedding_dim)
+
+    default_llm = llms.get_default()
+    llm_func = get_llm_func(default_llm)
+
+    return llm_func, embedding_func, default_llm, default_embedding
+
+
+def prepare_graph_index_path(graph_id: str):
+    root_path = Path(filestorage_path) / graph_id
+    input_path = root_path / "input"
+
+    return root_path, input_path
+
+
+def list_of_list_to_df(data: list[list]) -> pd.DataFrame:
+    df = pd.DataFrame(data[1:], columns=data[0])
+    return df
+
+
+def clean_quote(input: str) -> str:
+    return re.sub(r"[\"']", "", input)
+
+
+async def lightrag_build_local_query_context(
+    graph_func,
+    query,
+    query_param,
+):
+    knowledge_graph_inst = graph_func.chunk_entity_relation_graph
+    entities_vdb = graph_func.entities_vdb
+    text_chunks_db = graph_func.text_chunks
+
+    results = await entities_vdb.query(query, top_k=query_param.top_k)
+    if not len(results):
+        raise ValueError("No results found")
+
+    node_datas = await asyncio.gather(
+        *[knowledge_graph_inst.get_node(r["entity_name"]) for r in results]
+    )
+    node_degrees = await asyncio.gather(
+        *[knowledge_graph_inst.node_degree(r["entity_name"]) for r in results]
+    )
+    node_datas = [
+        {**n, "entity_name": k["entity_name"], "rank": d}
+        for k, n, d in zip(results, node_datas, node_degrees)
+        if n is not None
+    ]
+    use_text_units = await _find_most_related_text_unit_from_entities(
+        node_datas, query_param, text_chunks_db, knowledge_graph_inst
+    )
+    use_relations = await _find_most_related_edges_from_entities(
+        node_datas, query_param, knowledge_graph_inst
+    )
+    logging.info(
+        f"Local query uses {len(node_datas)} entities, "
+        f"{len(use_relations)} relations, {len(use_text_units)} text units"
+    )
+    entites_section_list = [["id", "entity", "type", "description", "rank"]]
+    for i, n in enumerate(node_datas):
+        entites_section_list.append(
+            [
+                str(i),
+                clean_quote(n["entity_name"]),
+                n.get("entity_type", "UNKNOWN"),
+                clean_quote(n.get("description", "UNKNOWN")),
+                n["rank"],
+            ]
+        )
+    entities_df = list_of_list_to_df(entites_section_list)
+
+    relations_section_list = [
+        ["id", "source", "target", "description", "keywords", "weight", "rank"]
+    ]
+    for i, e in enumerate(use_relations):
+        relations_section_list.append(
+            [
+                str(i),
+                clean_quote(e["src_tgt"][0]),
+                clean_quote(e["src_tgt"][1]),
+                clean_quote(e["description"]),
+                e["keywords"],
+                e["weight"],
+                e["rank"],
+            ]
+        )
+    relations_df = list_of_list_to_df(relations_section_list)
+
+    text_units_section_list = [["id", "content"]]
+    for i, t in enumerate(use_text_units):
+        text_units_section_list.append([str(i), t["content"]])
+    sources_df = list_of_list_to_df(text_units_section_list)
+
+    return entities_df, relations_df, sources_df
+
+
+def build_graphrag(working_dir, llm_func, embedding_func):
+    graphrag_func = LightRAG(
+        working_dir=working_dir,
+        llm_model_func=llm_func,
+        embedding_func=embedding_func,
+    )
+    return graphrag_func
+
+
+class LightRAGIndexingPipeline(GraphRAGIndexingPipeline):
+    """GraphRAG specific indexing pipeline"""
+
+    def call_graphrag_index(self, graph_id: str, docs: list[Document]):
+        _, input_path = prepare_graph_index_path(graph_id)
+        input_path.mkdir(parents=True, exist_ok=True)
+
+        (
+            llm_func,
+            embedding_func,
+            default_llm,
+            default_embedding,
+        ) = get_default_models_wrapper()
+        print(
+            f"Indexing GraphRAG with LLM {default_llm} "
+            f"and Embedding {default_embedding}..."
+        )
+
+        all_docs = [
+            doc.text for doc in docs if doc.metadata.get("type", "text") == "text"
+        ]
+
+        yield Document(
+            channel="debug",
+            text="[GraphRAG] Creating index... This can take a long time.",
+        )
+
+        # remove all .json files in the input_path directory (previous cache)
+        json_files = glob.glob(f"{input_path}/*.json")
+        for json_file in json_files:
+            os.remove(json_file)
+
+        # indexing
+        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.",
+        )
+
+        for doc_id in range(0, len(all_docs), INDEX_BATCHSIZE):
+            cur_docs = all_docs[doc_id : doc_id + INDEX_BATCHSIZE]
+            graphrag_func.insert(cur_docs)
+            process_doc_count += len(cur_docs)
+            yield Document(
+                channel="debug",
+                text=(
+                    f"[GraphRAG] Indexed {process_doc_count} "
+                    f"/ {total_docs} documents."
+                ),
+            )
+
+        yield Document(
+            channel="debug",
+            text="[GraphRAG] Indexing finished.",
+        )
+
+    def stream(
+        self, file_paths: str | Path | list[str | Path], reindex: bool = False, **kwargs
+    ) -> Generator[
+        Document, None, tuple[list[str | None], list[str | None], list[Document]]
+    ]:
+        file_ids, errors, all_docs = yield from super().stream(
+            file_paths, reindex=reindex, **kwargs
+        )
+
+        return file_ids, errors, all_docs
+
+
+class LightRAGRetrieverPipeline(BaseFileIndexRetriever):
+    """GraphRAG specific retriever pipeline"""
+
+    Index = Param(help="The SQLAlchemy Index table")
+    file_ids: list[str] = []
+
+    def _build_graph_search(self):
+        file_id = self.file_ids[0]
+
+        # retrieve the graph_id from the index
+        with Session(engine) as session:
+            graph_id = (
+                session.query(self.Index.target_id)
+                .filter(self.Index.source_id == file_id)
+                .filter(self.Index.relation_type == "graph")
+                .first()
+            )
+            graph_id = graph_id[0] if graph_id else None
+            assert graph_id, f"GraphRAG index not found for file_id: {file_id}"
+
+        _, input_path = prepare_graph_index_path(graph_id)
+        input_path.mkdir(parents=True, exist_ok=True)
+
+        llm_func, embedding_func, _, _ = get_default_models_wrapper()
+        graphrag_func = build_graphrag(
+            input_path,
+            llm_func=llm_func,
+            embedding_func=embedding_func,
+        )
+        query_params = QueryParam(mode="local", only_need_context=True)
+
+        return graphrag_func, query_params
+
+    def _to_document(self, header: str, context_text: str) -> RetrievedDocument:
+        return RetrievedDocument(
+            text=context_text,
+            metadata={
+                "file_name": header,
+                "type": "table",
+                "llm_trulens_score": 1.0,
+            },
+            score=1.0,
+        )
+
+    def format_context_records(
+        self, entities, relationships, sources
+    ) -> list[RetrievedDocument]:
+        docs = []
+        context: str = ""
+
+        # entities current parsing error
+        header = "<b>Entities</b>\n"
+        context = entities[["entity", "description"]].to_markdown(index=False)
+        docs.append(self._to_document(header, context))
+
+        header = "\n<b>Relationships</b>\n"
+        context = relationships[["source", "target", "description"]].to_markdown(
+            index=False
+        )
+        docs.append(self._to_document(header, context))
+
+        header = "\n<b>Sources</b>\n"
+        context = ""
+        for _, row in sources.iterrows():
+            title, content = row["id"], row["content"]
+            context += f"\n\n<h5>Source <b>#{title}</b></h5>\n"
+            context += content
+        docs.append(self._to_document(header, context))
+
+        return docs
+
+    def plot_graph(self, relationships):
+        G = create_knowledge_graph(relationships)
+        plot = visualize_graph(G)
+        return plot
+
+    def run(
+        self,
+        text: str,
+    ) -> list[RetrievedDocument]:
+        if not self.file_ids:
+            return []
+
+        graphrag_func, query_params = self._build_graph_search()
+        entities, relationships, sources = asyncio.run(
+            lightrag_build_local_query_context(graphrag_func, text, query_params)
+        )
+
+        documents = self.format_context_records(entities, relationships, sources)
+        plot = self.plot_graph(relationships)
+
+        return documents + [
+            RetrievedDocument(
+                text="",
+                metadata={
+                    "file_name": "GraphRAG",
+                    "type": "plot",
+                    "data": plot,
+                },
+            ),
+        ]

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

@@ -28,7 +28,7 @@ try:
         _find_most_related_edges_from_entities,
         _find_most_related_text_unit_from_entities,
     )
-    from nano_graphrag._utils import EmbeddingFunc
+    from nano_graphrag._utils import EmbeddingFunc, compute_args_hash
 
 except ImportError:
     print(
@@ -46,6 +46,8 @@ logging.getLogger("nano-graphrag").setLevel(logging.INFO)
 filestorage_path = Path(settings.KH_FILESTORAGE_PATH) / "nano_graphrag"
 filestorage_path.mkdir(parents=True, exist_ok=True)
 
+INDEX_BATCHSIZE = 4
+
 
 def get_llm_func(model):
     async def llm_func(
@@ -53,6 +55,7 @@ def get_llm_func(model):
     ) -> str:
         input_messages = [SystemMessage(text=system_prompt)] if system_prompt else []
 
+        hashing_kv = kwargs.pop("hashing_kv", None)
         if history_messages:
             for msg in history_messages:
                 if msg.get("role") == "user":
@@ -61,11 +64,21 @@ def get_llm_func(model):
                     input_messages.append(AIMessage(text=msg["content"]))
 
         input_messages.append(HumanMessage(text=prompt))
+
+        if hashing_kv is not None:
+            args_hash = compute_args_hash("model", input_messages)
+            if_cache_return = await hashing_kv.get_by_id(args_hash)
+            if if_cache_return is not None:
+                return if_cache_return["return"]
+
         output = model(input_messages).text
 
         print("-" * 50)
         print(output, "\n", "-" * 50)
 
+        if hashing_kv is not None:
+            await hashing_kv.upsert({args_hash: {"return": output, "model": "model"}})
+
         return output
 
     return llm_func
@@ -196,7 +209,6 @@ def build_graphrag(working_dir, llm_func, embedding_func):
         best_model_func=llm_func,
         cheap_model_func=llm_func,
         embedding_func=embedding_func,
-        embedding_func_max_async=4,
     )
     return graphrag_func
 
@@ -241,7 +253,23 @@ class NanoGraphRAGIndexingPipeline(GraphRAGIndexingPipeline):
         )
         # output must be contain: Loaded graph from
         # ..input/graph_chunk_entity_relation.graphml with xxx nodes, xxx edges
-        graphrag_func.insert(all_docs)
+        total_docs = len(all_docs)
+        process_doc_count = 0
+        yield Document(
+            channel="debug",
+            text=f"[GraphRAG] Indexed {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]
+            graphrag_func.insert(cur_docs)
+            process_doc_count += len(cur_docs)
+            yield Document(
+                channel="debug",
+                text=(
+                    f"[GraphRAG] Indexed {process_doc_count} "
+                    f"/ {total_docs} documents."
+                ),
+            )
 
         yield Document(
             channel="debug",