import streamlit as st from langchain.text_splitter import RecursiveCharacterTextSplitter from langchain_community.document_loaders import DirectoryLoader, UnstructuredFileLoader, PDFMinerLoader from langchain_community.vectorstores import Qdrant from langchain_community.embeddings import SentenceTransformerEmbeddings from langchain_community.retrievers import BM25Retriever from qdrant_client import QdrantClient from qdrant_client.http.exceptions import ResponseHandlingException from glob import glob from llama_index.vector_stores.qdrant import QdrantVectorStore from langchain.chains import RetrievalQA from transformers import AutoTokenizer, AutoModel from sentence_transformers import models, SentenceTransformer from langchain.embeddings.base import Embeddings from qdrant_client.models import VectorParams import torch import base64 from langchain_community.llms import LlamaCpp from langchain_core.prompts import PromptTemplate from huggingface_hub import hf_hub_download from tempfile import NamedTemporaryFile from langchain.retrievers import EnsembleRetriever # Set page configuration st.set_page_config(layout="wide") st.markdown(""" """, unsafe_allow_html=True) # Streamlit secrets qdrant_url = st.secrets["QDRANT_URL"] qdrant_api_key = st.secrets["QDRANT_API_KEY"] # For debugging only - remove or comment out these lines after verification #st.write(f"QDRANT_URL: {qdrant_url}") #st.write(f"QDRANT_API_KEY: {qdrant_api_key}") class ClinicalBertEmbeddings(Embeddings): def __init__(self, model_name: str = "medicalai/ClinicalBERT"): self.tokenizer = AutoTokenizer.from_pretrained(model_name) self.model = AutoModel.from_pretrained(model_name) self.model.eval() def embed(self, text: str): inputs = self.tokenizer(text, return_tensors="pt", padding=True, truncation=True, max_length=512) with torch.no_grad(): outputs = self.model(**inputs) embeddings = self.mean_pooling(outputs, inputs['attention_mask']) return embeddings.squeeze().numpy() def mean_pooling(self, model_output, attention_mask): token_embeddings = model_output[0] # First element of model_output contains all token embeddings input_mask_expanded = attention_mask.unsqueeze(-1).expand(token_embeddings.size()).float() return torch.sum(token_embeddings * input_mask_expanded, 1) / torch.clamp(input_mask_expanded.sum(1), min=1e-9) def embed_documents(self, texts): return [self.embed(text) for text in texts] def embed_query(self, text): return self.embed(text) @st.cache_resource def load_model(): model_name = "aaditya/OpenBioLLM-Llama3-8B-GGUF" model_file = "openbiollm-llama3-8b.Q5_K_M.gguf" model_path = hf_hub_download(model_name, filename=model_file, local_dir='./') return LlamaCpp( model_path=model_path, temperature=0.3, n_ctx=2048, top_p=1 ) # Initialize embeddings @st.cache_resource def load_embeddings(): return ClinicalBertEmbeddings(model_name="medicalai/ClinicalBERT") # Initialize database @st.cache_resource def setup_qdrant(): try: if not qdrant_url or not qdrant_api_key: raise ValueError("QDRANT_URL or QDRANT_API_KEY not set in environment variables.") # Initialize Qdrant client client = QdrantClient( url=qdrant_url, api_key=qdrant_api_key, port=443, # Assuming HTTPS should use port 443 ) st.write("Qdrant client initialized successfully.") # Create or recreate collection collection_name = "vector_db" try: collection_info = client.get_collection(collection_name=collection_name) st.write(f"Collection '{collection_name}' already exists.") except ResponseHandlingException: st.write(f"Collection '{collection_name}' does not exist. Creating a new one.") client.recreate_collection( collection_name=collection_name, vectors_config=VectorParams(size=768, distance="Cosine") ) st.write(f"Collection '{collection_name}' created successfully.") embeddings = load_embeddings() st.write("Embeddings model loaded successfully.") return Qdrant(client=client, embeddings=embeddings, collection_name=collection_name) except Exception as e: st.error(f"Failed to initialize Qdrant: {e}") return None # Initialize database db = setup_qdrant() if db is None: st.error("Qdrant setup failed, exiting.") else: st.success("Qdrant setup successful.") # Load models llm = load_model() embeddings = load_embeddings() # Define prompt template prompt_template = """Use the following pieces of information to answer the user's question. If you don't know the answer, just say that you don't know, don't try to make up an answer. Context: {context} Question: {question} Only return the helpful answer. Answer must be detailed and well explained. Helpful answer: """ prompt = PromptTemplate(template=prompt_template, input_variables=['context', 'question']) # Define retriever # Define Streamlit app def process_answer(query): chain_type_kwargs = {"prompt": prompt} global ensemble_retriever qa = RetrievalQA.from_chain_type( llm=llm, chain_type="stuff", retriever=ensemble_retriever, return_source_documents=True, chain_type_kwargs=chain_type_kwargs, verbose=True ) response = qa(query) answer = response['result'] source_document = response['source_documents'][0].page_content doc = response['source_documents'][0].metadata['source'] return answer, source_document, doc def display_pdf(file): with open(file, "rb") as f: base64_pdf = base64.b64encode(f.read()).decode('utf-8') pdf_display = f'' st.markdown(pdf_display, unsafe_allow_html=True) def main(): st.title("PDF Question Answering System") uploaded_file = st.file_uploader("Upload your PDF", type=["pdf"]) if uploaded_file is not None: # Save uploaded PDF with NamedTemporaryFile(delete=False, suffix=".pdf") as temp_file: temp_file.write(uploaded_file.read()) temp_file_path = temp_file.name # Display PDF st.subheader("PDF Preview") display_pdf(temp_file_path) # Load and process PDF loader = PDFMinerLoader(temp_file_path) documents = loader.load() text_splitter = RecursiveCharacterTextSplitter(chunk_size=500, chunk_overlap=50) texts = text_splitter.split_documents(documents) # Update the Qdrant database with the new PDF content try: db.add_documents(texts) st.success("PDF processed and vector database updated!") global ensemble_retriever # Initialize retriever after documents are added bm25_retriever = BM25Retriever.from_documents(documents=texts) bm25_retriever.k = 3 qdrant_retriever = db.as_retriever(search_kwargs={"k":1}) # Combine both retrievers using EnsembleRetriever ensemble_retriever = EnsembleRetriever( retrievers=[qdrant_retriever, bm25_retriever], weights=[0.5, 0.5] # Adjust weights based on desired contribution ) except Exception as e: st.error(f"Error updating database: {e}") st.subheader("Ask a question about the PDF") user_input = st.text_input("Your question:") if st.button('Get Response'): if user_input: try: answer, source_document, doc = process_answer(user_input) st.write("*Answer:*", answer) st.write("*Source Document:*", source_document) st.write("*Document Source:*", doc) except Exception as e: st.error(f"Error processing query: {e}") else: st.warning("Please enter a query.") if __name__ == "__main__": main()