climateqa/engine/chains/retrieve_documents.py

import sys
import os
from contextlib import contextmanager

from langchain_core.tools import tool
from langchain_core.runnables import chain
from langchain_core.runnables import RunnableParallel, RunnablePassthrough
from langchain_core.runnables import RunnableLambda

from ..reranker import rerank_docs, rerank_and_sort_docs
# from ...knowledge.retriever import ClimateQARetriever
from ...knowledge.openalex import OpenAlexRetriever
from .keywords_extraction import make_keywords_extraction_chain
from ..utils import log_event
from langchain_core.vectorstores import VectorStore
from typing import List
from langchain_core.documents.base import Document
from ..llm import get_llm
from .prompts import retrieve_chapter_prompt_template
from langchain_core.prompts import ChatPromptTemplate
from langchain_core.output_parsers import StrOutputParser
from ..vectorstore import get_pinecone_vectorstore
from ..embeddings import get_embeddings_function


import asyncio

from typing import Any, Dict, List, Tuple


def divide_into_parts(target, parts):
    # Base value for each part
    base = target // parts
    # Remainder to distribute
    remainder = target % parts
    # List to hold the result
    result = []
    
    for i in range(parts):
        if i < remainder:
            # These parts get base value + 1
            result.append(base + 1)
        else:
            # The rest get the base value
            result.append(base)
    
    return result


@contextmanager
def suppress_output():
    # Open a null device
    with open(os.devnull, 'w') as devnull:
        # Store the original stdout and stderr
        old_stdout = sys.stdout
        old_stderr = sys.stderr
        # Redirect stdout and stderr to the null device
        sys.stdout = devnull
        sys.stderr = devnull
        try:
            yield
        finally:
            # Restore stdout and stderr
            sys.stdout = old_stdout
            sys.stderr = old_stderr


@tool
def query_retriever(question):
    """Just a dummy tool to simulate the retriever query"""
    return question

def _add_sources_used_in_metadata(docs,sources,question,index):
    for doc in docs:
        doc.metadata["sources_used"] = sources
        doc.metadata["question_used"] = question
        doc.metadata["index_used"] = index
    return docs

def _get_k_summary_by_question(n_questions):
    if n_questions == 0:
        return 0
    elif n_questions == 1:
        return 5
    elif n_questions == 2:
        return 3
    elif n_questions == 3:
        return 2
    else:
        return 1
    
def _get_k_images_by_question(n_questions):
    if n_questions == 0:
        return 0
    elif n_questions == 1:
        return 7
    elif n_questions == 2:
        return 5
    elif n_questions == 3:
        return 3
    else:
        return 1
    
def _add_metadata_and_score(docs: List) -> Document:
    # Add score to metadata
    docs_with_metadata = []
    for i,(doc,score) in enumerate(docs):
        doc.page_content = doc.page_content.replace("\r\n"," ")
        doc.metadata["similarity_score"] = score
        doc.metadata["content"] = doc.page_content
        if doc.metadata["page_number"] != "N/A":
            doc.metadata["page_number"] = int(doc.metadata["page_number"]) + 1
        else:
            doc.metadata["page_number"] = 1
        # doc.page_content = f"""Doc {i+1} - {doc.metadata['short_name']}: {doc.page_content}"""
        docs_with_metadata.append(doc)
    return docs_with_metadata

def remove_duplicates_chunks(docs):
    # Remove duplicates or almost duplicates
    docs = sorted(docs,key=lambda x: x[1],reverse=True)
    seen = set()
    result = []
    for doc in docs:
        if doc[0].page_content not in seen:
            seen.add(doc[0].page_content)
            result.append(doc)
    return result

def get_ToCs(version: str) :

    filters_text = {
        "chunk_type":"toc",
        "version": version
    }
    embeddings_function = get_embeddings_function()
    vectorstore = get_pinecone_vectorstore(embeddings_function, index_name="climateqa-v2")
    tocs = vectorstore.similarity_search_with_score(query="",filter = filters_text)

    # remove duplicates or almost duplicates
    tocs = remove_duplicates_chunks(tocs)
    
    return tocs

async def get_POC_relevant_documents(
    query: str,
    vectorstore:VectorStore,
    sources:list = ["Acclimaterra","PCAET","Plan Biodiversite"],
    search_figures:bool = False,
    search_only:bool = False,
    k_documents:int = 10,
    threshold:float = 0.6,
    k_images: int = 5,
    reports:list = [],
    min_size:int = 200,
) :
    # Prepare base search kwargs
    filters = {}
    docs_question = []
    docs_images = []

    # TODO add source selection
    # if len(reports) > 0:
    #     filters["short_name"] = {"$in":reports}
    # else:
    #     filters["source"] = { "$in": sources}
        
    filters_text = {
        **filters,
        "chunk_type":"text",
        # "report_type": {}, # TODO  to be completed to choose the right documents / chapters according to the analysis of the question
    }
    
    docs_question = vectorstore.similarity_search_with_score(query=query,filter = filters_text,k = k_documents)
    # remove duplicates or almost duplicates
    docs_question = remove_duplicates_chunks(docs_question)
    docs_question = [x for x in docs_question if x[1] > threshold]
    
    if search_figures:
        # Images
        filters_image = {
            **filters,
            "chunk_type":"image"
        }
        docs_images = vectorstore.similarity_search_with_score(query=query,filter = filters_image,k = k_images)
        
    docs_question, docs_images = _add_metadata_and_score(docs_question), _add_metadata_and_score(docs_images)
    
    docs_question = [x for x in docs_question if len(x.page_content) > min_size]
    
    return {
        "docs_question" : docs_question,
        "docs_images" : docs_images
    }

async def get_POC_documents_by_ToC_relevant_documents(
    query: str,
    tocs: list,
    vectorstore:VectorStore,
    version: str,
    sources:list = ["Acclimaterra","PCAET","Plan Biodiversite"],
    search_figures:bool = False,
    search_only:bool = False,
    k_documents:int = 10,
    threshold:float = 0.6,
    k_images: int = 5,
    reports:list = [],
    min_size:int = 200,
    proportion: float = 0.5,
) :
    """
        Args:
            - tocs : list with the table of contents of each document
            - version : version of the parsed documents (e.g. "v4")
            - proportion : share of documents retrieved using ToCs
    """
    # Prepare base search kwargs
    filters = {}
    docs_question = []
    docs_images = []

    # TODO add source selection
    # if len(reports) > 0:
    #     filters["short_name"] = {"$in":reports}
    # else:
    #     filters["source"] = { "$in": sources}
    
    k_documents_toc = round(k_documents * proportion)
    
    relevant_tocs = await get_relevant_toc_level_for_query(query, tocs)
    
    print(f"Relevant ToCs : {relevant_tocs}")
    # Transform the ToC dict {"document": str, "chapter": str} into a list of string 
    toc_filters = [toc['chapter'] for toc in relevant_tocs]

    filters_text_toc = {
        **filters,
        "chunk_type":"text",
        "toc_level0": {"$in": toc_filters},
        "version": version
        # "report_type": {}, # TODO  to be completed to choose the right documents / chapters according to the analysis of the question
    }
    
    docs_question = vectorstore.similarity_search_with_score(query=query,filter = filters_text_toc,k = k_documents_toc)

    filters_text = {
        **filters,
        "chunk_type":"text",
        "version": version
        # "report_type": {}, # TODO  to be completed to choose the right documents / chapters according to the analysis of the question
    }

    docs_question += vectorstore.similarity_search_with_score(query=query,filter = filters_text,k = k_documents - k_documents_toc)

    # remove duplicates or almost duplicates
    docs_question = remove_duplicates_chunks(docs_question)
    docs_question = [x for x in docs_question if x[1] > threshold]
    
    if search_figures:
        # Images
        filters_image = {
            **filters,
            "chunk_type":"image"
        }
        docs_images = vectorstore.similarity_search_with_score(query=query,filter = filters_image,k = k_images)
        
    docs_question, docs_images = _add_metadata_and_score(docs_question), _add_metadata_and_score(docs_images)
    
    docs_question = [x for x in docs_question if len(x.page_content) > min_size]
    
    return {
        "docs_question" : docs_question,
        "docs_images" : docs_images
    }
    

async def get_IPCC_relevant_documents(
    query: str,
    vectorstore:VectorStore,
    sources:list = ["IPCC","IPBES","IPOS"],
    search_figures:bool = False,
    reports:list = [],
    threshold:float = 0.6,
    k_summary:int = 3,
    k_total:int = 10,
    k_images: int = 5,
    namespace:str = "vectors",
    min_size:int = 200,
    search_only:bool = False,
) :

    # Check if all elements in the list are either IPCC or IPBES
    assert isinstance(sources,list)
    assert sources
    assert all([x in ["IPCC","IPBES","IPOS"] for x in sources])
    assert k_total > k_summary, "k_total should be greater than k_summary"

    # Prepare base search kwargs
    filters = {}

    if len(reports) > 0:
        filters["short_name"] = {"$in":reports}
    else:
        filters["source"] = { "$in": sources}

    # INIT 
    docs_summaries = []
    docs_full = []
    docs_images = []

    if search_only:
        # Only search for images if search_only is True
        if search_figures:
            filters_image = {
                **filters,
                "chunk_type":"image"
            }
            docs_images = vectorstore.similarity_search_with_score(query=query,filter = filters_image,k = k_images)
            docs_images = _add_metadata_and_score(docs_images)
    else:
        # Regular search flow for text and optionally images
        # Search for k_summary documents in the summaries dataset
        filters_summaries = {
            **filters,
            "chunk_type":"text",
            "report_type": { "$in":["SPM"]},
        }

        docs_summaries = vectorstore.similarity_search_with_score(query=query,filter = filters_summaries,k = k_summary)
        docs_summaries = [x for x in docs_summaries if x[1] > threshold]

        # Search for k_total - k_summary documents in the full reports dataset
        filters_full = {
            **filters,
            "chunk_type":"text",
            "report_type": { "$nin":["SPM"]},
        }
        docs_full = vectorstore.similarity_search_with_score(query=query,filter = filters_full,k = k_total)
        
        if search_figures:
            # Images
            filters_image = {
                **filters,
                "chunk_type":"image"
            }
            docs_images = vectorstore.similarity_search_with_score(query=query,filter = filters_image,k = k_images)

        docs_summaries, docs_full, docs_images = _add_metadata_and_score(docs_summaries), _add_metadata_and_score(docs_full), _add_metadata_and_score(docs_images)
        
        # Filter if length are below threshold
        docs_summaries = [x for x in docs_summaries if len(x.page_content) > min_size]
        docs_full = [x for x in docs_full if len(x.page_content) > min_size]
    
    return {
        "docs_summaries" : docs_summaries,
        "docs_full" : docs_full,
        "docs_images" : docs_images,
    }


    
def concatenate_documents(index, source_type, docs_question_dict, k_by_question, k_summary_by_question, k_images_by_question):
    # Keep the right number of documents - The k_summary documents from SPM are placed in front
    if source_type == "IPx": 
        docs_question = docs_question_dict["docs_summaries"][:k_summary_by_question] + docs_question_dict["docs_full"][:(k_by_question - k_summary_by_question)]
    elif source_type == "POC" :
        docs_question = docs_question_dict["docs_question"][:k_by_question]
    else :
        raise ValueError("source_type should be either Vector or POC")
        # docs_question = [doc for key in docs_question_dict.keys() for doc in docs_question_dict[key]][:(k_by_question)]
    
    images_question = docs_question_dict["docs_images"][:k_images_by_question]
    
    return docs_question, images_question



# The chain callback is not necessary, but it propagates the langchain callbacks to the astream_events logger to display intermediate results
# @chain
async def retrieve_documents( 
    current_question: Dict[str, Any], 
    config: Dict[str, Any], 
    source_type: str, 
    vectorstore: VectorStore,
    reranker: Any,
    version: str = "",
    search_figures: bool = False,
    search_only: bool = False,
    reports: list = [],
    rerank_by_question: bool = True,
    k_images_by_question: int = 5,
    k_before_reranking: int = 100,
    k_by_question: int = 5,
    k_summary_by_question: int = 3,
    tocs: list = [],
    by_toc=False
) -> Tuple[List[Document], List[Document]]:
    """
    Unpack the first question of the remaining questions, and retrieve and rerank corresponding documents, based on the question and selected_sources 
    
    Args:
        state (dict): The current state containing documents, related content, relevant content sources, remaining questions and n_questions.
        current_question (dict): The current question being processed.
        config (dict): Configuration settings for logging and other purposes.
        vectorstore (object): The vector store used to retrieve relevant documents.
        reranker (object): The reranker used to rerank the retrieved documents.
        llm (object): The language model used for processing.
        rerank_by_question (bool, optional): Whether to rerank documents by question. Defaults to True.
        k_final (int, optional): The final number of documents to retrieve. Defaults to 15.
        k_before_reranking (int, optional): The number of documents to retrieve before reranking. Defaults to 100.
        k_summary (int, optional): The number of summary documents to retrieve. Defaults to 5.
        k_images (int, optional): The number of image documents to retrieve. Defaults to 5.
    Returns:
        dict: The updated state containing the retrieved and reranked documents, related content, and remaining questions.
    """
    sources = current_question["sources"]
    question = current_question["question"]
    index = current_question["index"]
    source_type = current_question["source_type"]
    
    print(f"Retrieve documents for question: {question}")
    await log_event({"question":question,"sources":sources,"index":index},"log_retriever",config)

    print(f"""---- Retrieve documents from {current_question["source_type"]}----""")

    
    if source_type == "IPx":
        docs_question_dict = await get_IPCC_relevant_documents(
            query  = question,
            vectorstore=vectorstore,
            search_figures = search_figures,
            sources = sources,
            min_size = 200,
            k_summary = k_before_reranking-1,
            k_total = k_before_reranking,
            k_images = k_images_by_question,
            threshold = 0.5,
            search_only = search_only,
            reports = reports,
        )
    
    if source_type == 'POC':
        if by_toc == True:
            print("---- Retrieve documents by ToC----")
            docs_question_dict = await get_POC_documents_by_ToC_relevant_documents(
                query=question,
                tocs = tocs,
                vectorstore=vectorstore,
                version=version,
                search_figures = search_figures,
                sources = sources,
                threshold = 0.5,
                search_only = search_only,
                reports = reports,
                min_size= 200,
                k_documents= k_before_reranking,
                k_images= k_by_question
            )
        else : 
            docs_question_dict = await get_POC_relevant_documents(
                query = question,
                vectorstore=vectorstore,
                search_figures = search_figures,
                sources = sources,
                threshold = 0.5,
                search_only = search_only,
                reports = reports,
                min_size= 200,
                k_documents= k_before_reranking,
                k_images= k_by_question
            )

    # Rerank
    if reranker is not None and rerank_by_question:
        with suppress_output():
            for key in docs_question_dict.keys():
                docs_question_dict[key] = rerank_and_sort_docs(reranker,docs_question_dict[key],question)
    else:
        # Add a default reranking score
        for doc in docs_question:
            doc.metadata["reranking_score"] = doc.metadata["similarity_score"]
    
    # Keep the right number of documents    
    docs_question, images_question = concatenate_documents(index, source_type, docs_question_dict, k_by_question, k_summary_by_question, k_images_by_question)
        
    # Rerank the documents to put the most relevant in front
    if reranker is not None and rerank_by_question:
        docs_question = rerank_and_sort_docs(reranker, docs_question, question)

    # Add sources used in the metadata
    docs_question = _add_sources_used_in_metadata(docs_question,sources,question,index)
    images_question = _add_sources_used_in_metadata(images_question,sources,question,index)
    
    return docs_question, images_question
    

async def retrieve_documents_for_all_questions(
    search_figures,
    search_only,
    reports,
    questions_list,
    n_questions,
    config, 
    source_type, 
    to_handle_questions_index,
    vectorstore, 
    reranker, 
    rerank_by_question=True, 
    k_final=15, 
    k_before_reranking=100,
    version: str = "",
    tocs: list[dict] = [],
    by_toc: bool = False
):
    """
    Retrieve documents in parallel for all questions.
    """
    # to_handle_questions_index = [x for x in state["questions_list"] if x["source_type"] == "IPx"]
    
    # TODO split les questions selon le type de sources dans le state question + conditions sur le nombre de questions traités par type de source 
    # search_figures = "Figures (IPCC/IPBES)" in state["relevant_content_sources_selection"]
    # search_only = state["search_only"]
    # reports = state["reports"]
    # questions_list = state["questions_list"]
    
    # k_by_question = k_final // state["n_questions"]["total"]
    # k_summary_by_question = _get_k_summary_by_question(state["n_questions"]["total"])
    # k_images_by_question = _get_k_images_by_question(state["n_questions"]["total"])
    k_by_question = k_final // n_questions
    k_summary_by_question = _get_k_summary_by_question(n_questions)
    k_images_by_question = _get_k_images_by_question(n_questions)
    k_before_reranking=100
    
    print(f"Source type here is {source_type}")
    tasks = [
        retrieve_documents(
            current_question=question,
            config=config,
            source_type=source_type,
            vectorstore=vectorstore,
            reranker=reranker,
            search_figures=search_figures,
            search_only=search_only,
            reports=reports,
            rerank_by_question=rerank_by_question,
            k_images_by_question=k_images_by_question,
            k_before_reranking=k_before_reranking,
            k_by_question=k_by_question,
            k_summary_by_question=k_summary_by_question,
            tocs=tocs,
            version=version,
            by_toc=by_toc
        )
        for i, question in enumerate(questions_list) if i in to_handle_questions_index
    ]
    results = await asyncio.gather(*tasks)
    # Combine results
    new_state = {"documents": [], "related_contents": [], "handled_questions_index": to_handle_questions_index}
    for docs_question, images_question in results:
        new_state["documents"].extend(docs_question)
        new_state["related_contents"].extend(images_question)
    return new_state

# ToC Retriever
async def get_relevant_toc_level_for_query(
    query: str,
    tocs: list[Document],
) -> list[dict] : 

    doc_list = []
    for doc in tocs:
        doc_name = doc[0].metadata['name']
        toc = doc[0].page_content
        doc_list.append({'document': doc_name, 'toc': toc})

    llm = get_llm(provider="openai",max_tokens = 1024,temperature = 0.0)

    prompt = ChatPromptTemplate.from_template(retrieve_chapter_prompt_template)
    chain = prompt | llm | StrOutputParser()
    response = chain.invoke({"query": query, "doc_list": doc_list})

    try: 
        relevant_tocs = eval(response)
    except Exception as e:
        print(f" Failed to parse the result because of : {e}")

    return relevant_tocs


def make_IPx_retriever_node(vectorstore,reranker,llm,rerank_by_question=True, k_final=15, k_before_reranking=100, k_summary=5):
    
    async def retrieve_IPx_docs(state, config):
        source_type = "IPx"
        IPx_questions_index = [i for i, x in enumerate(state["questions_list"]) if x["source_type"] == "IPx"]

        search_figures = "Figures (IPCC/IPBES)" in state["relevant_content_sources_selection"]
        search_only = state["search_only"]
        reports = state["reports"]
        questions_list = state["questions_list"]
        n_questions=state["n_questions"]["total"]
        
        state = await retrieve_documents_for_all_questions(
            search_figures=search_figures,
            search_only=search_only,
            reports=reports,
            questions_list=questions_list,
            n_questions=n_questions,
            config=config,
            source_type=source_type,
            to_handle_questions_index=IPx_questions_index,
            vectorstore=vectorstore,
            reranker=reranker,
            rerank_by_question=rerank_by_question,
            k_final=k_final,
            k_before_reranking=k_before_reranking,
        )
        return state
    
    return retrieve_IPx_docs


def make_POC_retriever_node(vectorstore,reranker,llm,rerank_by_question=True, k_final=15, k_before_reranking=100, k_summary=5):
    
    async def retrieve_POC_docs_node(state, config):        
        source_type = "POC"
        POC_questions_index = [i for i, x in enumerate(state["questions_list"]) if x["source_type"] == "POC"]
        
        search_figures = "Figures (IPCC/IPBES)" in state["relevant_content_sources_selection"]
        search_only = state["search_only"]
        reports = state["reports"]
        questions_list = state["questions_list"]
        n_questions=state["n_questions"]["total"]
        
        state = await retrieve_documents_for_all_questions(
            search_figures=search_figures,
            search_only=search_only,
            reports=reports,
            questions_list=questions_list,
            n_questions=n_questions,
            config=config,
            source_type=source_type,
            to_handle_questions_index=POC_questions_index,
            vectorstore=vectorstore,
            reranker=reranker,
            rerank_by_question=rerank_by_question,
            k_final=k_final,
            k_before_reranking=k_before_reranking,
        )
        return state
    
    return retrieve_POC_docs_node


def make_POC_by_ToC_retriever_node(
        vectorstore: VectorStore, 
        reranker,
        llm, 
        version: str = "", 
        rerank_by_question=True, 
        k_final=15, 
        k_before_reranking=100, 
        k_summary=5,
    ):
    
    async def retrieve_POC_docs_node(state, config):     
        search_figures = "Figures (IPCC/IPBES)" in state["relevant_content_sources_selection"]
        search_only = state["search_only"]
        search_only = state["search_only"]
        reports = state["reports"]
        questions_list = state["questions_list"]
        n_questions=state["n_questions"]["total"]

        tocs = get_ToCs(version=version)

        source_type = "POC"
        POC_questions_index = [i for i, x in enumerate(state["questions_list"]) if x["source_type"] == "POC"]
        
        state = await retrieve_documents_for_all_questions(
            search_figures=search_figures,
            search_only=search_only,
            config=config,
            reports=reports,
            questions_list=questions_list,
            n_questions=n_questions,
            source_type=source_type,
            to_handle_questions_index=POC_questions_index,
            vectorstore=vectorstore,
            reranker=reranker,
            rerank_by_question=rerank_by_question,
            k_final=k_final,
            k_before_reranking=k_before_reranking,
            tocs=tocs,
            version=version,
            by_toc=True
        )
        return state
    
    return retrieve_POC_docs_node