app.py

import streamlit as st # for web UI creation 
from sentence_transformers import SentenceTransformer # this is for embedding queries into dense vectors 
from pinecone import Pinecone, ServerlessSpec # for accessing pinecone vector DB 
import os # for readhing environment variable 
from langchain_huggingface import HuggingFaceEndpoint # for accessing HuggingFace inference endpoint 
from langchain.prompts import PromptTemplate
import firebase_admin  # for access to firebase 
from firebase_admin import credentials, firestore
from dotenv import load_dotenv

# === Load environment variables ===
load_dotenv(".env.local")

# === CONFIG ===
PINECONE_API_KEY = os.getenv("PINECONE_API_KEY")
PINECONE_ENV = os.getenv("PINECONE_ENV")
HF_TOKEN = os.getenv("HUGGINGFACEHUB_API_TOKEN")
USER_ID = "demo_user" # static user for testing 

# === Require Authentication ===
if "user" not in st.session_state or "email" not in st.session_state["user"]:
    st.error("Please sign in with your Google account to access the Clinical Trial Discovery tool.")
    st.stop()

USER_ID = st.session_state["user"]["email"]  # use email as unique user ID

# === Firebase Setup ===
if not firebase_admin._apps:
    cred = credentials.Certificate("service-account-key.json")
    firebase_admin.initialize_app(cred)
db = firestore.client()

# === Pinecone Setup ===
pc = Pinecone(api_key=PINECONE_API_KEY)
INDEX_NAME = "clinical-trials-rag"
index = pc.Index(INDEX_NAME)

# === Embedding Model ===
embed_model = SentenceTransformer("pritamdeka/BioBERT-mnli-snli-scinli-scitail-mednli-stsb") # BioBERT sentence transformer model

# === LLM Setup ===
llm = HuggingFaceEndpoint(
    endpoint_url="https://f9eftfrz5qna6j32.us-east-1.aws.endpoints.huggingface.cloud", # Inference Endpoint Built from Hugging Face. Pay per hour. 
    huggingfacehub_api_token=HF_TOKEN,
    temperature=0.7,
    max_new_tokens=256
)

# === Prompt Template ===
prompt_template = PromptTemplate.from_template(
    """
Context:
{context}

Conversation so far:
{history}

User: {question}
Bot:"""
)

# === Session State Setup ===
if "chat_history" not in st.session_state:
    st.session_state.chat_history = []

# === Tabs ===
tab1, tab2 = st.tabs(["🔍 Ask a Question", "⭐ Bookmarked Trials"])

# === TAB 1: Conversational Chatbot ===
with tab1:
    st.title("🔎 Clinical Trial Discovery Chatbot")

    st.markdown("""
    💡 **Example question formats:**
    - What clinical trials are available for non-small cell lung cancer in California?
    - List phase 3 trials for Type 1 Diabetes recruiting in 2025.
    - What studies on immunotherapy for melanoma are active in Europe?
    - Are there trials targeting heart disease patients over 65?
    """)
    
    for q, a in st.session_state.chat_history:
        st.markdown(f"**User:** {q}")
        st.markdown(f"**Bot:** {a}")

    user_query = st.text_input("🔍 Enter your clinical trial question below:") # actual query input part 

    if user_query: # triggers query upon user type action 
        with st.spinner("Retrieving relevant trials..."): # display spinner while pinecone DB being searched 
            vec = embed_model.encode(user_query).tolist() # embed query using the BioBERT sentence transforme
            results = index.query(vector=vec, top_k=5, include_metadata=True) # search pinecone vector DB. Look for 5 most similar vectors
            contexts = [r["metadata"]["text"] for r in results["matches"]]
            nct_ids = [r["metadata"].get("nct_id", "") for r in results["matches"]] 
        # Prep the prompt for the LLM
        joined_context = "\n".join(contexts) # joins the retrieved trial summary into one contextual block
        chat_history_text = "\n".join(f"User: {q}\nBot: {a}" for q, a in st.session_state.chat_history) # records chat session history 
        prompt = prompt_template.format(context=joined_context, question=user_query, history=chat_history_text) # fills prompt template

        # this part calls the LLM endpoint to generate the answer
        with st.spinner("Generating answer..."):
            answer = llm(prompt)
        st.session_state.chat_history.append((user_query, answer))

        st.subheader("🧠 Answer:") # display answer in UI 
        st.write(answer)

        st.markdown("---")
        st.subheader("📋 Related Clinical Trials") # display the related trials under the answer 

        for i, match in enumerate(results["matches"]): # loop through pinecone search results and display them
            meta = match["metadata"]
            nct_id = meta.get("nct_id", f"chunk_{i}") # assigns fallback chuck ID if 'nct_id' is missing 
            chunk_text = meta.get("text", "")[:400] # shows the first 400 characters of the trial chunk
            with st.expander(f"Trial: {nct_id}"): # create an expandable block for each trial 
                # Fetch full trial details from Firestore
                trial_doc = db.collection("ClinicalTrials").document(nct_id).get()
                if trial_doc.exists:
                    trial_data = trial_doc.to_dict()
                    for k, v in trial_data.items():
                        st.markdown(f"**{k.replace('_', ' ').title()}:** {v}")
                else:
                    st.warning("⚠️ Full trial details not found in Firestore. Showing partial match.")
                    st.write(meta.get("text", "")[:400] + "...")
                # add bookmark button instead each expander. Book marks are saved to /users/demo_user/Bookmarks/{nct_id} 
                if st.button(f"⭐ Bookmark {nct_id}", key=f"bookmark_{i}"):
                    db.collection("Users").document(USER_ID).collection("Bookmarks").document(nct_id).set({
                        "nct_id": nct_id,
                        "text": meta.get("text", "")[:400]
                    })
                    st.success(f"Bookmarked {nct_id} to Firestore.")

# === TAB 2: Bookmarked Trials ===
with tab2:
    st.title("⭐ Your Bookmarked Trials")
    # retrieve bookmarks from firestore 
    docs = db.collection("Users").document(USER_ID).collection("Bookmarks").stream()
    bookmarks = [doc.to_dict() for doc in docs]

    # if no bookmarks, show message. 
    if not bookmarks:
        st.info("You haven't bookmarked any trials yet.")
    else: # otherwise display bookmarked trials in expanders 
        for b in bookmarks:
            with st.expander(f"{b['nct_id']}"):
                st.write(b["text"])