src/document_retrieval.py

import os
import shutil
import sys
from typing import Any, Dict, List, Optional

import torch
import yaml
from dotenv import load_dotenv
from langchain.chains.base import Chain
from langchain.docstore.document import Document
from langchain.prompts import BasePromptTemplate, load_prompt
from langchain_core.callbacks import CallbackManagerForChainRun
from langchain_core.language_models import BaseLanguageModel
from langchain_core.output_parsers import StrOutputParser
from langchain_core.retrievers import BaseRetriever
from transformers import AutoModelForSequenceClassification, AutoTokenizer

current_dir = os.path.dirname(os.path.abspath(__file__)) # src/ directory
kit_dir = os.path.abspath(os.path.join(current_dir, '..')) # EKR/ directory 
repo_dir = os.path.abspath(os.path.join(kit_dir, '..'))
sys.path.append(kit_dir)
sys.path.append(repo_dir)

#import streamlit as st

from utils.model_wrappers.api_gateway import APIGateway
from utils.vectordb.vector_db import VectorDb
from utils.visual.env_utils import get_wandb_key

CONFIG_PATH = os.path.join(kit_dir, 'config.yaml')
PERSIST_DIRECTORY = os.path.join(kit_dir, 'data/my-vector-db')

#load_dotenv(os.path.join(kit_dir, '.env'))


from utils.parsing.sambaparse import parse_doc_universal

# Handle the WANDB_API_KEY resolution before importing weave
#wandb_api_key = get_wandb_key()

# If WANDB_API_KEY is set, proceed with weave initialization
#if wandb_api_key:
#    import weave

    # Initialize Weave with your project name
#    weave.init('sambanova_ekr')
#else:
#    print('WANDB_API_KEY is not set. Weave initialization skipped.')


class RetrievalQAChain(Chain):
    """class for question-answering."""

    retriever: BaseRetriever
    rerank: bool = True
    llm: BaseLanguageModel
    qa_prompt: BasePromptTemplate
    final_k_retrieved_documents: int = 3

    @property
    def input_keys(self) -> List[str]:
        """Input keys.
        :meta private:
        """
        return ['question']

    @property
    def output_keys(self) -> List[str]:
        """Output keys.
        :meta private:
        """
        return ['answer', 'source_documents']

    def _format_docs(self, docs):
        return '\n\n'.join(doc.page_content for doc in docs)

    def rerank_docs(self, query, docs, final_k):
        # Lazy hardcoding for now
        tokenizer = AutoTokenizer.from_pretrained('BAAI/bge-reranker-large')
        reranker = AutoModelForSequenceClassification.from_pretrained('BAAI/bge-reranker-large')
        pairs = []
        for d in docs:
            pairs.append([query, d.page_content])

        with torch.no_grad():
            inputs = tokenizer(
                pairs,
                padding=True,
                truncation=True,
                return_tensors='pt',
                max_length=512,
            )
            scores = (
                reranker(**inputs, return_dict=True)
                .logits.view(
                    -1,
                )
                .float()
            )

        scores_list = scores.tolist()
        scores_sorted_idx = sorted(range(len(scores_list)), key=lambda k: scores_list[k], reverse=True)

        docs_sorted = [docs[k] for k in scores_sorted_idx]
        # docs_sorted = [docs[k] for k in scores_sorted_idx if scores_list[k]>0]
        docs_sorted = docs_sorted[:final_k]

        return docs_sorted

    def _call(
        self,
        inputs: Dict[str, Any],
        run_manager: Optional[CallbackManagerForChainRun] = None,
    ) -> Dict[str, Any]:
        qa_chain = self.qa_prompt | self.llm | StrOutputParser()
        response = {}
        documents = self.retriever.invoke(inputs['question'])
        if self.rerank:
            documents = self.rerank_docs(inputs['question'], documents, self.final_k_retrieved_documents)
        docs = self._format_docs(documents)
        response['answer'] = qa_chain.invoke({'question': inputs['question'], 'context': docs})
        response['source_documents'] = documents
        return response


class DocumentRetrieval:
    def __init__(self, sambanova_api_key):
        self.vectordb = VectorDb()
        config_info = self.get_config_info()
        self.api_info = config_info[0]
        self.llm_info = config_info[1]
        self.embedding_model_info = config_info[2]
        self.retrieval_info = config_info[3]
        self.prompts = config_info[4]
        self.prod_mode = config_info[5]
        self.retriever = None
        self.llm = self.set_llm(sambanova_api_key)

    def get_config_info(self):
        """
        Loads json config file
        """
        # Read config file
        with open(CONFIG_PATH, 'r') as yaml_file:
            config = yaml.safe_load(yaml_file)
        api_info = config['api']
        llm_info = config['llm']
        embedding_model_info = config['embedding_model']
        retrieval_info = config['retrieval']
        prompts = config['prompts']
        prod_mode = config['prod_mode']

        return api_info, llm_info, embedding_model_info, retrieval_info, prompts, prod_mode

    def set_llm(self, sambanova_api_key):
        #if self.prod_mode:
        #    sambanova_api_key = st.session_state.SAMBANOVA_API_KEY
        #else:
        #    if 'SAMBANOVA_API_KEY' in st.session_state:
        #        sambanova_api_key = os.environ.get('SAMBANOVA_API_KEY') or st.session_state.SAMBANOVA_API_KEY
        #    else:
        #        sambanova_api_key = os.environ.get('SAMBANOVA_API_KEY')
        
        #sambanova_api_key = os.environ.get('SAMBANOVA_API_KEY')

        llm = APIGateway.load_llm(
            type=self.api_info,
            streaming=True,
            coe=self.llm_info['coe'],
            do_sample=self.llm_info['do_sample'],
            max_tokens_to_generate=self.llm_info['max_tokens_to_generate'],
            temperature=self.llm_info['temperature'],
            select_expert=self.llm_info['select_expert'],
            process_prompt=False,
            sambanova_api_key=sambanova_api_key,
        )
        return llm

    def parse_doc(self, docs: List, additional_metadata: Optional[Dict] = None) -> List[Document]:
        """
        Parse the uploaded documents and return a list of LangChain documents.

        Args:
            docs (List[UploadFile]): A list of uploaded files.
            additional_metadata (Optional[Dict], optional): Additional metadata to include in the processed documents.
                Defaults to an empty dictionary.

        Returns:
            List[Document]: A list of LangChain documents.
        """
        if additional_metadata is None:
            additional_metadata = {}

        # Create the data/tmp folder if it doesn't exist
        temp_folder = os.path.join(kit_dir, 'data/tmp')
        if not os.path.exists(temp_folder):
            os.makedirs(temp_folder)
        else:
            # If there are already files there, delete them
            for filename in os.listdir(temp_folder):
                file_path = os.path.join(temp_folder, filename)
                try:
                    if os.path.isfile(file_path) or os.path.islink(file_path):
                        os.unlink(file_path)
                    elif os.path.isdir(file_path):
                        shutil.rmtree(file_path)
                except Exception as e:
                    print(f'Failed to delete {file_path}. Reason: {e}')

        # Save all selected files to the tmp dir with their file names
        #for doc in docs:
        #    temp_file = os.path.join(temp_folder, doc.name)
        #    with open(temp_file, 'wb') as f:
        #        f.write(doc.getvalue())

        for doc_info in docs:
            file_name, file_obj = doc_info
            temp_file = os.path.join(temp_folder, file_name)
            with open(temp_file, 'wb') as f:
                f.write(file_obj.read())

        # Pass in the temp folder for processing into the parse_doc_universal function
        _, _, langchain_docs = parse_doc_universal(doc=temp_folder, additional_metadata=additional_metadata)
        return langchain_docs

    def load_embedding_model(self):
        embeddings = APIGateway.load_embedding_model(
            type=self.embedding_model_info['type'],
            batch_size=self.embedding_model_info['batch_size'],
            coe=self.embedding_model_info['coe'],
            select_expert=self.embedding_model_info['select_expert'],
        )
        return embeddings

    def create_vector_store(self, text_chunks, embeddings, output_db=None, collection_name=None):
        print(f'Collection name is {collection_name}')
        vectorstore = self.vectordb.create_vector_store(
            text_chunks, embeddings, output_db=output_db, collection_name=collection_name, db_type='chroma'
        )
        return vectorstore

    def load_vdb(self, db_path, embeddings, collection_name=None):
        print(f'Loading collection name is {collection_name}')
        vectorstore = self.vectordb.load_vdb(db_path, embeddings, db_type='chroma', collection_name=collection_name)
        return vectorstore

    def init_retriever(self, vectorstore):
        if self.retrieval_info['rerank']:
            self.retriever = vectorstore.as_retriever(
                search_type='similarity_score_threshold',
                search_kwargs={
                    'score_threshold': self.retrieval_info['score_threshold'],
                    'k': self.retrieval_info['k_retrieved_documents'],
                },
            )
        else:
            self.retriever = vectorstore.as_retriever(
                search_type='similarity_score_threshold',
                search_kwargs={
                    'score_threshold': self.retrieval_info['score_threshold'],
                    'k': self.retrieval_info['final_k_retrieved_documents'],
                },
            )

    def get_qa_retrieval_chain(self):
        """
        Generate a qa_retrieval chain using a language model.

        This function uses a language model, specifically a SambaNova LLM, to generate a qa_retrieval chain
        based on the input vector store of text chunks.

        Parameters:
        vectorstore (Chroma): A Vector Store containing embeddings of text chunks used as context
                            for generating the conversation chain.

        Returns:
        RetrievalQA: A chain ready for QA without memory
        """
        # customprompt = load_prompt(os.path.join(kit_dir, self.prompts["qa_prompt"]))
        # qa_chain = customprompt | self.llm | StrOutputParser()

        # response = {}
        # documents = self.retriever.invoke(question)
        # if self.retrieval_info["rerank"]:
        #     documents = self.rerank_docs(question, documents, self.retrieval_info["final_k_retrieved_documents"])
        # docs = self._format_docs(documents)

        # response["answer"] = qa_chain.invoke({"question": question, "context": docs})
        # response["source_documents"] = documents

        retrievalQAChain = RetrievalQAChain(
            retriever=self.retriever,
            llm=self.llm,
            qa_prompt=load_prompt(os.path.join(kit_dir, self.prompts['qa_prompt'])),
            rerank=self.retrieval_info['rerank'],
            final_k_retrieved_documents=self.retrieval_info['final_k_retrieved_documents'],
        )
        return retrievalQAChain

    def get_conversational_qa_retrieval_chain(self):
        """
        Generate a conversational retrieval qa chain using a language model.

        This function uses a language model, specifically a SambaNova LLM, to generate a conversational_qa_retrieval chain
        based on the chat history and the relevant retrieved content from the input vector store of text chunks.

        Parameters:
        vectorstore (Chroma): A Vector Store containing embeddings of text chunks used as context
                                        for generating the conversation chain.

        Returns:
        RetrievalQA: A chain ready for QA with memory
        """