nexus.py

from llama_index.indices.managed.vectara import VectaraIndex
from dotenv import load_dotenv
import os
from docx import Document
from llama_index.llms.together import TogetherLLM
from llama_index.core.llms import ChatMessage, MessageRole
from Bio import Entrez 
import ssl
from transformers import AutoModelForSequenceClassification, AutoTokenizer
import streamlit as st
from googleapiclient.discovery import build
from typing import List, Optional

load_dotenv()

os.environ["VECTARA_INDEX_API_KEY"] = os.getenv("VECTARA_INDEX_API_KEY", "zwt_Vo9cpGzm6QVtABcdnzVq6QXLdGIP4YAcvcyEAA")
os.environ["VECTARA_QUERY_API_KEY"] = os.getenv("VECTARA_QUERY_API_KEY", "zqt_Vo9cpBoyEjUQdcTVo2W5hmMKPueBUroBLoGwNQ")
os.environ["VECTARA_API_KEY"] = os.getenv("VECTARA_API_KEY", "zut_Vo9cpHni2hWF_DPJAXmRFKkWzRTWbi-8JwnSxA")
os.environ["VECTARA_CORPUS_ID"] = os.getenv("VECTARA_CORPUS_ID", "2")
os.environ["VECTARA_CUSTOMER_ID"] = os.getenv("VECTARA_CUSTOMER_ID", "1452235940")
os.environ["TOGETHER_API"] = os.getenv("TOGETHER_API", "7e6c200b7b36924bc1b4a5973859a20d2efa7180e9b5c977301173a6c099136b")
os.environ["GOOGLE_SEARCH_API_KEY"] = os.getenv("GOOGLE_SEARCH_API_KEY", "AIzaSyALmmMjvmrmHGtjjuPLEMy6Bp2qgMQJ3Ck")

index = VectaraIndex()
endpoint = 'https://api.together.xyz/inference'

def search_pubmed(query: str) -> Optional[List[str]]:
    Entrez.email = "[email protected]"  
    try:
        ssl._create_default_https_context = ssl._create_unverified_context
        handle = Entrez.esearch(db="pubmed", term=query, retmax=3)
        record = Entrez.read(handle)
        id_list = record["IdList"]
        if not id_list:
            return None
        handle = Entrez.efetch(db="pubmed", id=id_list, retmode="xml")
        articles = Entrez.read(handle)
        results = []
        for article in articles['PubmedArticle']:
            try:
                medline_citation = article['MedlineCitation']
                article_data = medline_citation['Article']
                title = article_data['ArticleTitle']
                abstract = article_data.get('Abstract', {}).get('AbstractText', [""])[0]
                result = f"**Title:** {title}\n**Abstract:** {abstract}\n"
                result += f"**Link:** https://pubmed.ncbi.nlm.nih.gov/{medline_citation['PMID']}\n\n"
                results.append(result)
            except KeyError as e:
                print(f"Error parsing article: {article}, Error: {e}")
        return results
    except Exception as e:
        print(f"Error accessing PubMed: {e}")
        return None

def chat_with_pubmed(article_text, article_link):
    try:
        llm = TogetherLLM(model="QWEN/QWEN1.5-14B-CHAT", api_key=os.environ['TOGETHER_API'])
        messages = [
            ChatMessage(role=MessageRole.SYSTEM, content="You are a helpful AI assistant summarizing and answering questions about the following medical research article: " + article_link),
            ChatMessage(role=MessageRole.USER, content=article_text)
        ]
        response = llm.chat(messages)
        return str(response) if response else "I'm sorry, I couldn't generate a summary for this article."
    except Exception as e:
        print(f"Error in chat_with_pubmed: {e}")
        return "An error occurred while generating a summary."

def search_web(query: str, num_results: int = 3) -> Optional[List[str]]:
    try:
        service = build("customsearch", "v1", developerKey=os.environ["GOOGLE_SEARCH_API_KEY"])
        res = service.cse().list(q=query, cx="6128965e5bcae442b", num=num_results).execute()
        if "items" not in res:
            return None
        results = []
        for item in res["items"]:
            title = item["title"]
            link = item["link"]
            snippet = item["snippet"]
            result = f"**Title:** {title}\n**Link:** {link}\n**Snippet:** {snippet}\n\n"
            results.append(result)
        return results
    except Exception as e:
        print(f"Error performing web search: {e}")
        return None

def NEXUS_chatbot(user_input, chat_history=None):
    if chat_history is None:
        chat_history = []
    response_parts = []
    try:
        try:
            query_str = user_input
            response = index.as_query_engine().query(query_str)
            response_parts.append(f"**NEXUS Vectara Knowledge Base Response:**\n{response.response}")
        except Exception as e:
            print(f"Error in Vectara search: {e}")
            response_parts.append("Vectara knowledge base is currently unavailable.")

        pubmed_results = search_pubmed(user_input)
        if pubmed_results:
            response_parts.append("**PubMed Articles (Chat & Summarize):**")
            for article_text in pubmed_results:
                title, abstract, link = article_text.split("\n")[:3]
                chat_summary = chat_with_pubmed(abstract, link)
                response_parts.append(f"{title}\n{chat_summary}\n{link}\n")
        else:
            response_parts.append("No relevant PubMed articles found.")

        web_results = search_web(user_input)
        if web_results:
            response_parts.append("**Web Search Results:**")
            response_parts.extend(web_results)
        else:
            response_parts.append("No relevant web search results found.")

        response_text = "\n\n".join(response_parts)
    except Exception as e:
        print(f"Error in chatbot: {e}")
        response_text = f"An error occurred: {str(e)}. Please try again later or rephrase your question."

    chat_history.append((user_input, response_text))
    return response_text, chat_history

def show_info_popup():
    with st.expander("How to use NEXUS"):
        st.write("""
        **NEXUS is an AI-powered chatbot designed to assist with medical information.**
        **Capabilities:**
        *   **Answers general medical questions:** NEXUS utilizes a curated medical knowledge base to provide answers to a wide range of health-related inquiries.
        *   **Summarizes relevant research articles from PubMed:** The chatbot can retrieve and summarize research articles from the PubMed database, making complex scientific information more accessible.
        *   **Provides insights from a curated medical knowledge base:** Beyond simple answers, NEXUS offers additional insights and context from its knowledge base to enhance understanding. 
        *   **Perform safe web searches related to your query:** The chatbot can perform web searches using the Google Search API, ensuring the safety and relevance of the results.
        **Limitations:**
        *   **Not a substitute for professional medical advice:** NEXUS is not intended to replace professional medical diagnosis and treatment. Always consult a qualified healthcare provider for personalized medical advice.
        *   **General knowledge and educational purposes:** The information provided by NEXUS is for general knowledge and educational purposes only and may not be exhaustive or specific to individual situations.
        *   **Under development:** NEXUS is still under development and may occasionally provide inaccurate or incomplete information. It's important to critically evaluate responses and cross-reference with reliable sources.
        **How to use:**
        1.  **Type your medical question in the text box.**
        2.  **NEXUS will provide a comprehensive response combining information from various sources.** This may include insights from its knowledge base, summaries of relevant research articles, and safe web search results.
        3.  **You can continue the conversation by asking follow-up questions or providing additional context.** This helps NEXUS refine its search and offer more tailored information.
        4.  **In case NEXUS doesn't show the output, please check your internet connection or rerun the same command.**
        """)

if 'chat_history' not in st.session_state:
    st.session_state.chat_history = []

def display_chat_history():
    for user_msg, bot_msg in st.session_state.chat_history:
        st.info(f"**You:** {user_msg}")
        st.success(f"**NEXUS:** {bot_msg}")

def clear_chat():
    st.session_state.chat_history = []

def main():
    st.set_page_config(page_title="NEXUS Chatbot", layout="wide")
    st.markdown(
        """
        <style>
        .css-18e3th9 {
            padding-top: 2rem;
            padding-right: 1rem;
            padding-bottom: 2rem;
            padding-left: 1rem;
        }
        .stButton>button {
            background-color: #4CAF50;
            color: white;
        }
        body {
            background-color: #F0FDF4;
            color: #333333;
        }
        .stMarkdown h1, .stMarkdown h2, .stMarkdown h3, .stMarkdown h4, .stMarkdown h5, .stMarkdown h6 {
            color: #388E3C;
        }
        </style>
        """,
        unsafe_allow_html=True,
    )
    st.title("NEXUS Chatbot")
    st.write("Ask your medical questions and get reliable information!")
    example_questions = [
        "What are the symptoms of COVID-19?",
        "How can I manage my diabetes?",
        "What are the potential side effects of ibuprofen?",
        "What lifestyle changes can help prevent heart disease?"
    ]
    st.sidebar.header("Example Questions")
    for question in example_questions:
        st.sidebar.write(question)
    output_container = st.container()
    input_container = st.container()
    with input_container:
        user_input = st.text_input("You: ", key="input_placeholder", placeholder="Type your medical question here...")
        new_chat_button = st.button("Start New Chat")
        if new_chat_button:
            st.session_state.chat_history = []
    if user_input:
        response, st.session_state.chat_history = NEXUS_chatbot(user_input, st.session_state.chat_history)
        with output_container:
            display_chat_history()
    show_info_popup()

if __name__ == "__main__":
    main()