app.py

# ------------------------------
# Imports & Initial Configuration
# ------------------------------
import streamlit as st
# Set the page configuration immediately—this must be the first Streamlit command.
st.set_page_config(page_title="NeuroResearch AI", layout="wide", initial_sidebar_state="expanded")

from langchain_openai import OpenAIEmbeddings
from langchain_community.vectorstores import Chroma
from langchain_core.messages import HumanMessage, AIMessage, ToolMessage
from langchain.text_splitter import RecursiveCharacterTextSplitter
from langgraph.graph import END, StateGraph
from langgraph.prebuilt import ToolNode
from langgraph.graph.message import add_messages
from typing_extensions import TypedDict, Annotated
from typing import Sequence, Dict, List, Optional, Any
import chromadb
import re
import os
import requests
import hashlib
import json
import time
from langchain.tools.retriever import create_retriever_tool
from concurrent.futures import ThreadPoolExecutor, as_completed
from datetime import datetime

# ------------------------------
# State Schema Definition
# ------------------------------
class AgentState(TypedDict):
    messages: Annotated[Sequence[AIMessage | HumanMessage | ToolMessage], add_messages]
    context: Dict[str, Any]
    metadata: Dict[str, Any]

# ------------------------------
# Configuration
# ------------------------------
class ResearchConfig:
    DEEPSEEK_API_KEY = os.environ.get("DEEPSEEK_API_KEY")
    CHROMA_PATH = "chroma_db"
    CHUNK_SIZE = 512
    CHUNK_OVERLAP = 64
    MAX_CONCURRENT_REQUESTS = 5
    EMBEDDING_DIMENSIONS = 1536
    DOCUMENT_MAP = {
        "Research Report: Results of a New AI Model Improving Image Recognition Accuracy to 98%": 
            "CV-Transformer Hybrid Architecture",
        "Academic Paper Summary: Why Transformers Became the Mainstream Architecture in Natural Language Processing": 
            "Transformer Architecture Analysis",
        "Latest Trends in Machine Learning Methods Using Quantum Computing": 
            "Quantum ML Frontiers"
    }
    ANALYSIS_TEMPLATE = """Analyze these technical documents with scientific rigor:
{context}

Respond with:
1. Key Technical Contributions (bullet points)
2. Novel Methodologies
3. Empirical Results (with metrics)
4. Potential Applications
5. Limitations & Future Directions

Format: Markdown with LaTeX mathematical notation where applicable
"""

# Validate API key configuration
if not ResearchConfig.DEEPSEEK_API_KEY:
    st.error("""**Research Portal Configuration Required**  
1. Obtain DeepSeek API key: [platform.deepseek.com](https://platform.deepseek.com/)  
2. Configure secret: `DEEPSEEK_API_KEY` in Space settings  
3. Rebuild deployment""")
    st.stop()

# ------------------------------
# Quantum Document Processing
# ------------------------------
class QuantumDocumentManager:
    def __init__(self):
        self.client = chromadb.PersistentClient(path=ResearchConfig.CHROMA_PATH)
        self.embeddings = OpenAIEmbeddings(
            model="text-embedding-3-large",
            dimensions=ResearchConfig.EMBEDDING_DIMENSIONS
        )
        
    def create_collection(self, documents: List[str], collection_name: str) -> Chroma:
        splitter = RecursiveCharacterTextSplitter(
            chunk_size=ResearchConfig.CHUNK_SIZE,
            chunk_overlap=ResearchConfig.CHUNK_OVERLAP,
            separators=["\n\n", "\n", "|||"]
        )
        docs = splitter.create_documents(documents)
        # Debug: log the number of chunks created for the collection.
        st.write(f"Created {len(docs)} chunks for collection '{collection_name}'")
        return Chroma.from_documents(
            documents=docs,
            embedding=self.embeddings,
            client=self.client,
            collection_name=collection_name,
            ids=[self._document_id(doc.page_content) for doc in docs]
        )
    
    def _document_id(self, content: str) -> str:
        return f"{hashlib.sha256(content.encode()).hexdigest()[:16]}-{int(time.time())}"

# Initialize document collections
qdm = QuantumDocumentManager()
research_docs = qdm.create_collection([
    "Research Report: Results of a New AI Model Improving Image Recognition Accuracy to 98%",
    "Academic Paper Summary: Why Transformers Became the Mainstream Architecture in Natural Language Processing",
    "Latest Trends in Machine Learning Methods Using Quantum Computing"
], "research")

development_docs = qdm.create_collection([
    "Project A: UI Design Completed, API Integration in Progress",
    "Project B: Testing New Feature X, Bug Fixes Needed",
    "Product Y: In the Performance Optimization Stage Before Release"
], "development")

# ------------------------------
# Advanced Retrieval System
# ------------------------------
class ResearchRetriever:
    def __init__(self):
        self.retrievers = {
            "research": research_docs.as_retriever(
                search_type="mmr",
                search_kwargs={
                    'k': 4,
                    'fetch_k': 20,
                    'lambda_mult': 0.85
                }
            ),
            "development": development_docs.as_retriever(
                search_type="similarity",
                search_kwargs={'k': 3}
            )
        }
    
    def retrieve(self, query: str, domain: str) -> List[Any]:
        try:
            results = self.retrievers[domain].invoke(query)
            st.write(f"[DEBUG] Retrieved {len(results)} documents for query: '{query}' in domain '{domain}'")
            return results
        except KeyError:
            st.error(f"[ERROR] Retrieval domain '{domain}' not found.")
            return []

retriever = ResearchRetriever()

# ------------------------------
# Cognitive Processing Unit
# ------------------------------
class CognitiveProcessor:
    def __init__(self):
        self.executor = ThreadPoolExecutor(max_workers=ResearchConfig.MAX_CONCURRENT_REQUESTS)
        self.session_id = hashlib.sha256(datetime.now().isoformat().encode()).hexdigest()[:12]
    
    def process_query(self, prompt: str) -> Dict:
        futures = []
        for _ in range(3):  # Triple redundancy for robustness
            futures.append(self.executor.submit(
                self._execute_api_request,
                prompt
            ))
        
        results = []
        for future in as_completed(futures):
            try:
                results.append(future.result())
            except Exception as e:
                st.error(f"Processing Error: {str(e)}")
        
        return self._consensus_check(results)
    
    def _execute_api_request(self, prompt: str) -> Dict:
        headers = {
            "Authorization": f"Bearer {ResearchConfig.DEEPSEEK_API_KEY}",
            "Content-Type": "application/json",
            "X-Research-Session": self.session_id
        }
        
        try:
            response = requests.post(
                "https://api.deepseek.com/v1/chat/completions",
                headers=headers,
                json={
                    "model": "deepseek-chat",
                    "messages": [{
                        "role": "user",
                        "content": f"Respond as Senior AI Researcher:\n{prompt}"
                    }],
                    "temperature": 0.7,
                    "max_tokens": 1500,
                    "top_p": 0.9
                },
                timeout=45
            )
            response.raise_for_status()
            return response.json()
        except requests.exceptions.RequestException as e:
            return {"error": str(e)}
    
    def _consensus_check(self, results: List[Dict]) -> Dict:
        valid = [r for r in results if "error" not in r]
        if not valid:
            return {"error": "All API requests failed"}
        # Choose the result with the longest content for robustness.
        return max(valid, key=lambda x: len(x.get('choices', [{}])[0].get('message', {}).get('content', '')))

# ------------------------------
# Research Workflow Engine
# ------------------------------
class ResearchWorkflow:
    def __init__(self):
        self.processor = CognitiveProcessor()
        self.workflow = StateGraph(AgentState)
        self._build_workflow()

    def _build_workflow(self):
        # Register nodes in the state graph
        self.workflow.add_node("ingest", self.ingest_query)
        self.workflow.add_node("retrieve", self.retrieve_documents)
        self.workflow.add_node("analyze", self.analyze_content)
        self.workflow.add_node("validate", self.validate_output)
        self.workflow.add_node("refine", self.refine_results)

        self.workflow.set_entry_point("ingest")
        self.workflow.add_edge("ingest", "retrieve")
        self.workflow.add_edge("retrieve", "analyze")
        self.workflow.add_conditional_edges(
            "analyze",
            self._quality_check,
            {"valid": "validate", "invalid": "refine"}
        )
        self.workflow.add_edge("validate", END)
        self.workflow.add_edge("refine", "retrieve")

        self.app = self.workflow.compile()

    def ingest_query(self, state: AgentState) -> Dict:
        try:
            query = state["messages"][-1].content
            st.write(f"[DEBUG] Ingesting query: {query}")
            return {
                "messages": [AIMessage(content="Query ingested successfully")],
                "context": {"raw_query": query},
                "metadata": {"timestamp": datetime.now().isoformat()}
            }
        except Exception as e:
            return self._error_state(f"Ingestion Error: {str(e)}")

    def retrieve_documents(self, state: AgentState) -> Dict:
        try:
            query = state["context"]["raw_query"]
            docs = retriever.retrieve(query, "research")
            st.write(f"[DEBUG] Retrieved {len(docs)} documents from retrieval node.")
            return {
                "messages": [AIMessage(content=f"Retrieved {len(docs)} documents")],
                "context": {
                    "documents": docs,
                    "retrieval_time": time.time()
                }
            }
        except Exception as e:
            return self._error_state(f"Retrieval Error: {str(e)}")

    def analyze_content(self, state: AgentState) -> Dict:
        try:
            # Ensure documents are present before proceeding.
            if "documents" not in state["context"] or not state["context"]["documents"]:
                return self._error_state("No documents retrieved; please check your query or retrieval process.")
            
            # Concatenate all document content for analysis.
            docs = "\n\n".join([d.page_content for d in state["context"]["documents"] if hasattr(d, "page_content")])
            st.write(f"[DEBUG] Analyzing content from {len(state['context']['documents'])} documents.")
            prompt = ResearchConfig.ANALYSIS_TEMPLATE.format(context=docs)
            response = self.processor.process_query(prompt)
            
            if "error" in response:
                return self._error_state(response["error"])
            
            return {
                "messages": [AIMessage(content=response['choices'][0]['message']['content'])],
                "context": {"analysis": response}
            }
        except Exception as e:
            return self._error_state(f"Analysis Error: {str(e)}")

    def validate_output(self, state: AgentState) -> Dict:
        analysis = state["messages"][-1].content
        validation_prompt = f"""Validate research analysis:
{analysis}

Check for:
1. Technical accuracy
2. Citation support
3. Logical consistency
4. Methodological soundness

Respond with 'VALID' or 'INVALID'"""
        
        response = self.processor.process_query(validation_prompt)
        return {
            "messages": [AIMessage(content=analysis + f"\n\nValidation: {response.get('choices', [{}])[0].get('message', {}).get('content', '')}")]
        }

    def refine_results(self, state: AgentState) -> Dict:
        refinement_prompt = f"""Refine this analysis:
{state["messages"][-1].content}

Improve:
1. Technical precision
2. Empirical grounding
3. Theoretical coherence"""
        
        response = self.processor.process_query(refinement_prompt)
        return {
            "messages": [AIMessage(content=response.get('choices', [{}])[0].get('message', {}).get('content', ''))],
            "context": state["context"]
        }

    def _quality_check(self, state: AgentState) -> str:
        content = state["messages"][-1].content
        return "valid" if "VALID" in content else "invalid"

    def _error_state(self, message: str) -> Dict:
        st.write(f"[ERROR] {message}")
        return {
            "messages": [AIMessage(content=f"❌ {message}")],
            "context": {"error": True},
            "metadata": {"status": "error"}
        }

# ------------------------------
# Research Interface
# ------------------------------
class ResearchInterface:
    def __init__(self):
        self.workflow = ResearchWorkflow()
        # Do not call st.set_page_config here because it has already been called at the top.
        self._inject_styles()
        self._build_sidebar()
        self._build_main_interface()

    def _inject_styles(self):
        st.markdown("""
        <style>
        :root {
            --primary: #2ecc71;
            --secondary: #3498db;
            --background: #0a0a0a;
            --text: #ecf0f1;
        }
        
        .stApp {
            background: var(--background);
            color: var(--text);
            font-family: 'Roboto', sans-serif;
        }
        
        .stTextArea textarea {
            background: #1a1a1a !important;
            color: var(--text) !important;
            border: 2px solid var(--secondary);
            border-radius: 8px;
            padding: 1rem;
        }
        
        .stButton>button {
            background: linear-gradient(135deg, var(--primary), var(--secondary));
            border: none;
            border-radius: 8px;
            padding: 1rem 2rem;
            transition: all 0.3s;
        }
        
        .stButton>button:hover {
            transform: translateY(-2px);
            box-shadow: 0 4px 12px rgba(46, 204, 113, 0.3);
        }
        
        .stExpander {
            background: #1a1a1a;
            border: 1px solid #2a2a2a;
            border-radius: 8px;
            margin: 1rem 0;
        }
        </style>
        """, unsafe_allow_html=True)

    def _build_sidebar(self):
        with st.sidebar:
            st.title("🔍 Research Database")
            st.subheader("Technical Papers")
            for title, short in ResearchConfig.DOCUMENT_MAP.items():
                with st.expander(short):
                    st.markdown(f"```\n{title}\n```")
            
            st.subheader("Analysis Metrics")
            st.metric("Vector Collections", 2)
            st.metric("Embedding Dimensions", ResearchConfig.EMBEDDING_DIMENSIONS)

    def _build_main_interface(self):
        st.title("🧠 NeuroResearch AI")
        query = st.text_area("Research Query:", height=200,
                             placeholder="Enter technical research question...")
        
        if st.button("Execute Analysis", type="primary"):
            self._execute_analysis(query)

    def _execute_analysis(self, query: str):
        try:
            with st.spinner("Initializing Quantum Analysis..."):
                results = self.workflow.app.stream(
                    {"messages": [HumanMessage(content=query)], "context": {}, "metadata": {}}
                )
                for event in results:
                    self._render_event(event)
                st.success("✅ Analysis Completed Successfully")
        except Exception as e:
            st.error(f"""**Analysis Failed**
{str(e)}
Potential issues:
- Complex query structure
- Document correlation failure
- Temporal processing constraints""")

    def _render_event(self, event: Dict):
        if 'ingest' in event:
            with st.container():
                st.success("✅ Query Ingested")
        elif 'retrieve' in event:
            with st.container():
                docs = event['retrieve']['context']['documents']
                st.info(f"📚 Retrieved {len(docs)} documents")
                with st.expander("View Retrieved Documents", expanded=False):
                    for i, doc in enumerate(docs, 1):
                        st.markdown(f"**Document {i}**")
                        st.code(doc.page_content, language='text')
        elif 'analyze' in event:
            with st.container():
                content = event['analyze']['messages'][0].content
                with st.expander("Technical Analysis Report", expanded=True):
                    st.markdown(content)
        elif 'validate' in event:
            with st.container():
                content = event['validate']['messages'][0].content
                if "VALID" in content:
                    st.success("✅ Validation Passed")
                    with st.expander("View Validated Analysis", expanded=True):
                        st.markdown(content.split("Validation:")[0])
                else:
                    st.warning("⚠️ Validation Issues Detected")
                    with st.expander("View Validation Details", expanded=True):
                        st.markdown(content)

if __name__ == "__main__":
    ResearchInterface()