app.py

"""
Streamlit application for the Pharmaceutical R&D Knowledge Ecosystem.
"""

import streamlit as st
import os
import pandas as pd
import json
import tempfile
import time
from datetime import datetime

from pdf_processor import PDFProcessor
from knowledge_store import KnowledgeStore
from llm_interface import LLMInterface
from graph_builder import (
    init_handlers,
    build_document_extraction_graph,
    build_protocol_coach_graph,
    build_content_authoring_graph,
    build_traceability_graph
)

# =========================================================================
# App Setup and Configuration
# =========================================================================

# Page configuration
st.set_page_config(
    page_title="Pharma R&D Knowledge Ecosystem",
    page_icon="💊",
    layout="wide",
    initial_sidebar_state="expanded"
)

# Initialize session state variables if they don't exist
if "chat_history" not in st.session_state:
    st.session_state.chat_history = []
    
if "documents" not in st.session_state:
    st.session_state.documents = []
    
if "knowledge_base_stats" not in st.session_state:
    st.session_state.knowledge_base_stats = {
        "documents": 0,
        "studies": 0,
        "endpoints": 0,
        "objectives": 0,
        "vectors": 0
    }

# Initialize our handlers and graphs
@st.cache_resource
def initialize_app():
    """Initialize app resources and LangGraph workflows."""
    # Get API key from environment or secrets
    api_key = os.environ.get("ANTHROPIC_API_KEY")
    if not api_key and hasattr(st, "secrets") and "ANTHROPIC_API_KEY" in st.secrets:
        api_key = st.secrets["ANTHROPIC_API_KEY"]
    
    # Initialize handlers
    pdf_processor, knowledge_store, llm_interface = init_handlers(api_key)
    
    # Build LangGraph workflows
    extraction_graph = build_document_extraction_graph()
    coach_graph = build_protocol_coach_graph()
    authoring_graph = build_content_authoring_graph()
    traceability_graph = build_traceability_graph()
    
    return {
        "pdf_processor": pdf_processor,
        "knowledge_store": knowledge_store,
        "llm_interface": llm_interface,
        "extraction_graph": extraction_graph,
        "coach_graph": coach_graph,
        "authoring_graph": authoring_graph,
        "traceability_graph": traceability_graph
    }

# Initialize app resources
app_resources = initialize_app()
pdf_processor = app_resources["pdf_processor"]
knowledge_store = app_resources["knowledge_store"]
llm_interface = app_resources["llm_interface"]
extraction_graph = app_resources["extraction_graph"]
coach_graph = app_resources["coach_graph"]
authoring_graph = app_resources["authoring_graph"]
traceability_graph = app_resources["traceability_graph"]

# =========================================================================
# Helper Functions
# =========================================================================

def update_knowledge_base_stats():
    """Update the knowledge base statistics in session state."""
    try:
        # Get counts of different entity types
        documents = knowledge_store.get_all_documents()
        document_count = len(documents)
        
        # Get unique protocol IDs
        protocol_ids = set()
        for doc in documents:
            if "protocol_id" in doc and doc["protocol_id"]:
                protocol_ids.add(doc["protocol_id"])
        
        # Get vector store stats
        vector_stats = knowledge_store.get_vector_store_stats()
        vector_count = vector_stats.get("document_count", 0)
        
        # Count objectives and endpoints across all protocols
        objective_count = 0
        endpoint_count = 0
        for protocol_id in protocol_ids:
            objectives = knowledge_store.get_objectives_by_protocol_id(protocol_id)
            endpoints = knowledge_store.get_endpoints_by_protocol_id(protocol_id)
            objective_count += len(objectives)
            endpoint_count += len(endpoints)
        
        # Update session state
        st.session_state.knowledge_base_stats = {
            "documents": document_count,
            "studies": len(protocol_ids),
            "objectives": objective_count,
            "endpoints": endpoint_count,
            "vectors": vector_count
        }
    except Exception as e:
        st.error(f"Error updating knowledge base stats: {e}")

def process_document(uploaded_file):
    """Process an uploaded document and store in knowledge base."""
    try:
        # Create a progress bar
        progress_bar = st.progress(0)
        status_text = st.empty()
        
        # Step 1: Save the uploaded file
        status_text.text("Saving uploaded file...")
        progress_bar.progress(10)
        
        # Save uploaded file temporarily
        with tempfile.NamedTemporaryFile(delete=False, suffix=".pdf") as tmp_file:
            tmp_file.write(uploaded_file.getbuffer())
            file_path = tmp_file.name
        
        # Step 2: Process through LangGraph extraction workflow
        status_text.text("Parsing document...")
        progress_bar.progress(20)
        
        # Initialize state for extraction
        initial_state = {
            "document_path": file_path,
            "status": "initialized"
        }
        
        # Run extraction workflow
        result_state = extraction_graph.invoke(initial_state)
        
        # Update progress based on status
        if result_state.get("status") == "error":
            status_text.text(f"Error: {result_state.get('error', 'Unknown error')}")
            progress_bar.progress(100)
            return {
                "status": "error",
                "error": result_state.get("error", "Unknown error"),
                "filename": uploaded_file.name
            }
        
        # Update progress
        status_text.text("Processing completed successfully!")
        progress_bar.progress(100)
        
        # Update knowledge base stats
        update_knowledge_base_stats()
        
        # Return result
        return {
            "status": "success",
            "filename": uploaded_file.name,
            "document_id": result_state.get("document_id"),
            "protocol_id": result_state.get("extracted_study", {}).get("protocol_id")
        }
    except Exception as e:
        st.error(f"Error processing document: {e}")
        return {
            "status": "error",
            "error": str(e),
            "filename": uploaded_file.name
        }
    finally:
        # Clean up temporary file
        if 'file_path' in locals():
            try:
                os.unlink(file_path)
            except:
                pass

def chat_with_protocol_coach(query):
    """Process a query through the Protocol Coach."""
    try:
        # Initialize state for Protocol Coach
        initial_state = {
            "query": query,
            "chat_history": st.session_state.chat_history
        }
        
        # Run Protocol Coach workflow
        result_state = coach_graph.invoke(initial_state)
        
        return {
            "status": "success",
            "response": result_state.get("response", "I couldn't generate a response."),
            "context": result_state.get("retrieved_context", [])
        }
    except Exception as e:
        return {
            "status": "error",
            "error": str(e)
        }

def generate_document_section(section_type, protocol_id=None, style_guide=None):
    """Generate a document section using the content authoring workflow."""
    try:
        # Initialize state for Content Authoring
        initial_state = {
            "section_type": section_type,
            "target_protocol_id": protocol_id,
            "style_guide": style_guide
        }
        
        # Run Content Authoring workflow
        result_state = authoring_graph.invoke(initial_state)
        
        return {
            "status": "success",
            "content": result_state.get("generated_content", "I couldn't generate the content."),
            "context": result_state.get("retrieved_context", [])
        }
    except Exception as e:
        return {
            "status": "error",
            "error": str(e)
        }

def analyze_document_traceability(source_id, target_id, entity_type):
    """Analyze traceability between two documents."""
    try:
        # Initialize state for Traceability Analysis
        initial_state = {
            "source_document_id": source_id,
            "target_document_id": target_id,
            "entity_type": entity_type
        }
        
        # Run Traceability Analysis workflow
        result_state = traceability_graph.invoke(initial_state)
        
        return {
            "status": "success",
            "analysis": result_state.get("analysis", "I couldn't perform the analysis."),
            "matched_pairs": result_state.get("matched_pairs", [])
        }
    except Exception as e:
        return {
            "status": "error",
            "error": str(e)
        }

# =========================================================================
# Sidebar: Document Upload and Management
# =========================================================================

def render_sidebar():
    """Render the sidebar for document management."""
    st.sidebar.title("Document Management")
    
    # Knowledge Base Stats
    st.sidebar.subheader("Knowledge Base Stats")
    stats = st.session_state.knowledge_base_stats
    col1, col2 = st.sidebar.columns(2)
    col1.metric("Documents", stats["documents"])
    col2.metric("Studies", stats["studies"])
    col1.metric("Objectives", stats["objectives"])
    col2.metric("Endpoints", stats["endpoints"])
    st.sidebar.metric("Vector Chunks", stats["vectors"])
    
    # Document Upload
    st.sidebar.subheader("Upload Documents")
    uploaded_files = st.sidebar.file_uploader(
        "Upload Protocol/SAP PDFs", 
        type="pdf", 
        accept_multiple_files=True,
        help="Upload clinical documents (Protocol, SAP, etc.) to add to the knowledge base."
    )
    
    # Process uploaded files if any
    if uploaded_files:
        if st.sidebar.button("Process Documents"):
            with st.sidebar.expander("Processing Results", expanded=True):
                for uploaded_file in uploaded_files:
                    st.write(f"Processing: {uploaded_file.name}")
                    result = process_document(uploaded_file)
                    
                    if result["status"] == "success":
                        st.success(f"Successfully processed {result['filename']}")
                        
                        # Add to documents list if not already there
                        doc_exists = False
                        for doc in st.session_state.documents:
                            if doc.get("filename") == result["filename"]:
                                doc_exists = True
                                break
                        
                        if not doc_exists:
                            st.session_state.documents.append({
                                "filename": result["filename"],
                                "document_id": result.get("document_id"),
                                "protocol_id": result.get("protocol_id"),
                                "processed_date": datetime.now().strftime("%Y-%m-%d %H:%M")
                            })
                    else:
                        st.error(f"Error processing {result['filename']}: {result.get('error', 'Unknown error')}")
    
    # Document list
    st.sidebar.subheader("Processed Documents")
    if not st.session_state.documents:
        st.sidebar.info("No documents processed yet.")
    else:
        for i, doc in enumerate(st.session_state.documents):
            with st.sidebar.expander(f"{doc['filename']}"):
                st.write(f"**Protocol ID:** {doc.get('protocol_id', 'Unknown')}")
                st.write(f"**Processed:** {doc.get('processed_date', 'Unknown')}")
    
    # Refresh Stats Button
    if st.sidebar.button("Refresh Stats"):
        update_knowledge_base_stats()
        st.sidebar.success("Stats refreshed!")

# =========================================================================
# Main Content Tabs
# =========================================================================

def render_protocol_coach_tab():
    """Render the Protocol Coach chatbot tab."""
    st.header("Protocol Coach Chatbot")
    st.info("Ask questions about the protocol documents in the knowledge base. The Protocol Coach will retrieve relevant information to answer your questions.")
    
    # Initialize or display chat history
    for message in st.session_state.chat_history:
        with st.chat_message(message["role"]):
            st.markdown(message["content"])
    
    # Chat input
    if query := st.chat_input("Ask about protocols..."):
        # Add user message to chat history and display
        st.session_state.chat_history.append({"role": "user", "content": query})
        with st.chat_message("user"):
            st.markdown(query)
        
        # Process query
        with st.chat_message("assistant"):
            with st.spinner("Thinking..."):
                result = chat_with_protocol_coach(query)
                if result["status"] == "success":
                    st.markdown(result["response"])
                    
                    # Show context sources if debug mode enabled
                    if st.session_state.get("debug_mode", False):
                        with st.expander("Context Sources"):
                            for i, ctx in enumerate(result.get("context", [])):
                                st.write(f"**Source {i+1}:** {ctx.get('metadata', {}).get('source', 'Unknown')}")
                                st.write(f"**Section:** {ctx.get('metadata', {}).get('section', 'Unknown')}")
                                st.write("---")
                    
                    # Add assistant response to chat history
                    st.session_state.chat_history.append({"role": "assistant", "content": result["response"]})
                else:
                    st.error(f"Error: {result.get('error', 'Unknown error')}")
                    st.session_state.chat_history.append({"role": "assistant", "content": f"Error: {result.get('error', 'Unknown error')}"})

def render_content_authoring_tab():
    """Render the Content Authoring tab."""
    st.header("Content Authoring Assistant")
    st.info("Generate document sections based on knowledge extracted from similar documents.")
    
    col1, col2 = st.columns([1, 1])
    
    with col1:
        st.subheader("Content Generation Settings")
        
        # Section Type Selection
        section_types = [
            "Introduction",
            "Objectives and Endpoints",
            "Study Design",
            "Study Population",
            "Statistical Considerations",
            "Inclusion Criteria",
            "Exclusion Criteria",
            "Safety Assessments",
            "Pharmacokinetic Assessments"
        ]
        section_type = st.selectbox("Select Section Type", section_types)
        
        # Protocol Selection for Context (Optional)
        protocol_options = ["--None--"]
        for doc in st.session_state.documents:
            if doc.get("protocol_id"):
                protocol_options.append(doc.get("protocol_id"))
        
        target_protocol = st.selectbox(
            "Target Protocol ID (Optional)",
            protocol_options
        )
        target_protocol = None if target_protocol == "--None--" else target_protocol
        
        # Style Guide (Optional)
        style_guide = st.text_area(
            "Style Guide (Optional)",
            placeholder="Enter any specific style guidelines or content requirements..."
        )
        
        # Generate Button
        generate_button = st.button("Generate Content")
        
        # Debug toggle
        st.session_state.debug_mode = st.checkbox("Show Context Sources", value=st.session_state.get("debug_mode", False))
    
    with col2:
        st.subheader("Generated Content")
        
        if generate_button:
            with st.spinner("Generating content..."):
                result = generate_document_section(
                    section_type=section_type,
                    protocol_id=target_protocol,
                    style_guide=style_guide if style_guide else None
                )
                
                if result["status"] == "success":
                    st.markdown(result["content"])
                    
                    # Show context sources if debug mode enabled
                    if st.session_state.get("debug_mode", False):
                        with st.expander("Context Sources"):
                            for i, ctx in enumerate(result.get("context", [])):
                                st.write(f"**Source {i+1}:** {ctx.get('metadata', {}).get('source', 'Unknown')}")
                                st.write(f"**Section:** {ctx.get('metadata', {}).get('section', 'Unknown')}")
                                st.write("---")
                else:
                    st.error(f"Error: {result.get('error', 'Unknown error')}")

def render_traceability_tab():
    """Render the Document Traceability tab."""
    st.header("Cross-Document Traceability")
    st.info("Analyze relationships between related documents (e.g., Protocol and SAP).")
    
    col1, col2 = st.columns([1, 1])
    
    with col1:
        st.subheader("Traceability Analysis Settings")
        
        # Document Selection
        document_options = []
        for doc in st.session_state.documents:
            document_options.append({
                "id": doc.get("document_id", ""),
                "label": f"{doc['filename']} ({doc.get('protocol_id', 'Unknown')})"
            })
        
        # Source Document
        source_options = [{"id": "", "label": "--Select Source Document--"}] + document_options
        source_doc = st.selectbox(
            "Source Document",
            options=source_options,
            format_func=lambda x: x["label"]
        )
        
        # Target Document 
        target_options = [{"id": "", "label": "--Select Target Document--"}] + document_options
        target_doc = st.selectbox(
            "Target Document",
            options=target_options,
            format_func=lambda x: x["label"]
        )
        
        # Entity Type
        entity_types = [
            {"id": "objectives", "label": "Study Objectives"},
            {"id": "endpoints", "label": "Endpoints"},
            {"id": "population", "label": "Population Criteria"}
        ]
        entity_type = st.selectbox(
            "Entity Type to Compare",
            options=entity_types,
            format_func=lambda x: x["label"]
        )
        
        # Analyze Button
        analyze_button = st.button("Analyze Traceability")
    
    with col2:
        st.subheader("Analysis Results")
        
        if analyze_button:
            if not source_doc["id"] or not target_doc["id"]:
                st.error("Please select both source and target documents.")
            else:
                with st.spinner("Analyzing traceability..."):
                    result = analyze_document_traceability(
                        source_id=source_doc["id"],
                        target_id=target_doc["id"],
                        entity_type=entity_type["id"]
                    )
                    
                    if result["status"] == "success":
                        st.markdown(result["analysis"])
                        
                        # Show matched pairs if debug mode enabled
                        if st.session_state.get("debug_mode", False) and result.get("matched_pairs"):
                            with st.expander("Matched Entity Pairs"):
                                for i, pair in enumerate(result["matched_pairs"]):
                                    st.write(f"**Pair {i+1}**")
                                    st.write(f"**Source:** {pair.get('source_text', 'Unknown')}")
                                    st.write(f"**Target:** {pair.get('target_text', 'Unknown')}")
                                    st.write("---")
                    else:
                        st.error(f"Error: {result.get('error', 'Unknown error')}")

def render_knowledge_explorer_tab():
    """Render the Knowledge Base Explorer tab."""
    st.header("Knowledge Base Explorer")
    st.info("Explore the structured data extracted from documents in the knowledge base.")
    
    # Entity Type Selection
    entity_types = [
        {"id": "studies", "label": "Studies"},
        {"id": "objectives", "label": "Study Objectives"},
        {"id": "endpoints", "label": "Endpoints"},
        {"id": "population", "label": "Population Criteria"},
        {"id": "documents", "label": "Documents"}
    ]
    entity_type = st.selectbox(
        "Select Entity Type",
        options=entity_types,
        format_func=lambda x: x["label"]
    )
    
    # Filter by Protocol ID (Optional)
    protocol_options = ["--All Protocols--"]
    for doc in st.session_state.documents:
        if doc.get("protocol_id") and doc.get("protocol_id") not in protocol_options:
            protocol_options.append(doc.get("protocol_id"))
    
    filter_protocol = st.selectbox(
        "Filter by Protocol ID",
        protocol_options
    )
    filter_protocol = None if filter_protocol == "--All Protocols--" else filter_protocol
    
    # Search Query (Optional)
    search_query = st.text_input(
        "Search Query (Optional)",
        placeholder="Enter text to search for..."
    )
    
    # Display Results
    st.subheader("Results")
    
    try:
        # Retrieve data based on entity type
        if entity_type["id"] == "studies":
            if filter_protocol:
                data = [knowledge_store.get_study_by_protocol_id(filter_protocol)]
            else:
                data = knowledge_store.get_all_studies()
        elif entity_type["id"] == "objectives":
            if filter_protocol:
                data = knowledge_store.get_objectives_by_protocol_id(filter_protocol)
            else:
                # Get all objectives across protocols
                data = []
                documents = knowledge_store.get_all_documents()
                protocol_ids = set()
                for doc in documents:
                    if "protocol_id" in doc and doc["protocol_id"]:
                        protocol_ids.add(doc["protocol_id"])
                
                for pid in protocol_ids:
                    data.extend(knowledge_store.get_objectives_by_protocol_id(pid))
        elif entity_type["id"] == "endpoints":
            if filter_protocol:
                data = knowledge_store.get_endpoints_by_protocol_id(filter_protocol)
            else:
                # Get all endpoints across protocols
                data = []
                documents = knowledge_store.get_all_documents()
                protocol_ids = set()
                for doc in documents:
                    if "protocol_id" in doc and doc["protocol_id"]:
                        protocol_ids.add(doc["protocol_id"])
                
                for pid in protocol_ids:
                    data.extend(knowledge_store.get_endpoints_by_protocol_id(pid))
        elif entity_type["id"] == "population":
            if filter_protocol:
                data = knowledge_store.get_population_criteria_by_protocol_id(filter_protocol)
            else:
                # Get all population criteria across protocols
                data = []
                documents = knowledge_store.get_all_documents()
                protocol_ids = set()
                for doc in documents:
                    if "protocol_id" in doc and doc["protocol_id"]:
                        protocol_ids.add(doc["protocol_id"])
                
                for pid in protocol_ids:
                    data.extend(knowledge_store.get_population_criteria_by_protocol_id(pid))
        elif entity_type["id"] == "documents":
            if filter_protocol:
                data = knowledge_store.get_documents_by_protocol_id(filter_protocol)
            else:
                data = knowledge_store.get_all_documents()
        else:
            data = []
        
        # Filter by search query if provided
        if search_query:
            filtered_data = []
            search_lower = search_query.lower()
            for item in data:
                # Convert item to string for searching
                item_str = json.dumps(item).lower()
                if search_lower in item_str:
                    filtered_data.append(item)
            data = filtered_data
        
        # Display results
        if not data:
            st.info("No data found.")
        else:
            st.write(f"{len(data)} items found")
            
            # Display as table if possible, otherwise as JSON
            try:
                df = pd.DataFrame(data)
                st.dataframe(df, use_container_width=True)
            except Exception as e:
                st.json(data)
    except Exception as e:
        st.error(f"Error retrieving data: {e}")

# =========================================================================
# Main App
# =========================================================================

def main():
    """Main application function."""
    st.title("🧠 Pharmaceutical R&D Knowledge Ecosystem")
    
    # Render the sidebar for document management
    render_sidebar()
    
    # Initialize knowledge base stats on first load
    if st.session_state.knowledge_base_stats["documents"] == 0:
        update_knowledge_base_stats()
    
    # Main content tabs
    tab1, tab2, tab3, tab4 = st.tabs([
        "📝 Content Authoring",
        "🤖 Protocol Coach", 
        "🔍 Knowledge Explorer",
        "🔄 Cross-Document Traceability"
    ])
    
    with tab1:
        render_content_authoring_tab()
    
    with tab2:
        render_protocol_coach_tab()
    
    with tab3:
        render_knowledge_explorer_tab()
    
    with tab4:
        render_traceability_tab()
        
    # Footer
    st.markdown("---")
    st.caption("Pharmaceutical R&D Knowledge Ecosystem | A demonstration of AI-assisted document processing and knowledge management")

if __name__ == "__main__":
    main()