app.py

#!/usr/bin/env python3
# -*- coding: utf-8 -*-

"""
Patient Matching Pipeline - Gradio Web Interface

This interface allows users to:
1. Configure models (embedder, trial_checker, boilerplate_checker)
2. Upload patient database OR load pre-embedded patients
3. Enter set of clinical criteria (trial eligibility criteria)
4. Get ranked patient recommendations with eligibility predictions
"""

import gradio as gr
import pandas as pd
import numpy as np
import torch
import os
import json
import pickle
import html
from typing import List, Tuple
from pathlib import Path
import pyarrow.parquet as pq

# HuggingFace imports
from transformers import (
    AutoTokenizer, 
    AutoModelForSequenceClassification,
)
from sentence_transformers import SentenceTransformer

# Try to import configuration
try:
    import config
    HAS_CONFIG = True
    print("✓ Found config.py - will auto-load models on startup")
except ImportError:
    HAS_CONFIG = False
    print("○ No config.py found - using manual model loading")

# ============================================================================
# GLOBAL STATE
# ============================================================================

class AppState:
    def __init__(self):
        self.embedder_model = None
        self.embedder_tokenizer = None
        self.trial_checker_model = None
        self.trial_checker_tokenizer = None
        self.boilerplate_checker_model = None
        self.boilerplate_checker_tokenizer = None
        
        self.patient_df = None
        self.patient_embeddings = None
        self.patient_preview_df = None
        
        # Store last results for export
        self.last_results_df = None
        
        self.device = "cuda" if torch.cuda.is_available() else "cpu"
        
        self.auto_load_status = {
            "embedder": "",
            "trial_checker": "",
            "boilerplate_checker": "",
            "patients": ""
        }
    
    def reset_patients(self):
        self.patient_df = None
        self.patient_embeddings = None
        self.patient_preview_df = None

state = AppState()

# ============================================================================
# CONSTANTS
# ============================================================================

MAX_EMBEDDER_SEQ_LEN = 2500
MAX_TRIAL_CHECKER_LENGTH = 4096
MAX_BOILERPLATE_CHECKER_LENGTH = 3192
CLASSIFIER_BATCH_SIZE = 32  # Batch size for trial_checker and boilerplate_checker inference

# Default templates
DEFAULT_CLINICAL_SPACE_TEMPLATE = """Age range allowed: 
Sex allowed: 
Cancer type allowed: 
Histology allowed: 
Cancer burden allowed: 
Prior treatment required: 
Prior treatment excluded: 
Biomarkers required: 
Biomarkers excluded: """

DEFAULT_BOILERPLATE_TEMPLATE = """History of pneumonitis: 
Heart failure or cardiac dysfunction: 
Renal dysfunction: 
Liver dysfunction: 
Uncontrolled brain metastases: 
HIV or hepatitis infection: 
Poor performance status (ECOG >= 2): 
Other relevant exclusions: """

# ============================================================================
# UTILITY FUNCTIONS
# ============================================================================

def truncate_text(text: str, tokenizer, max_tokens: int = 1500) -> str:
    """Truncate text to a maximum number of tokens."""
    return tokenizer.decode(
        tokenizer.encode(text, add_special_tokens=True, truncation=True, max_length=max_tokens),
        skip_special_tokens=True
    )


def format_probability_visual(val, is_exclusion=False):
    """Format probabilities with visual indicators."""
    try:
        val_float = float(val)
    except:
        return val

    if not is_exclusion:
        # High eligibility is good
        if val_float >= 0.8:
            return f"🟢 **{val_float:.2f}**"
        elif val_float >= 0.5:
            return f"🟡 {val_float:.2f}"
        else:
            return f"🔴 {val_float:.2f}"
    else:
        # High exclusion is bad
        if val_float >= 0.5:
            return f"🔴 **{val_float:.2f}**"
        elif val_float >= 0.2:
            return f"🟡 {val_float:.2f}"
        else:
            return f"🟢 {val_float:.2f}"


# ============================================================================
# AUTO-LOADING FROM CONFIG
# ============================================================================

def auto_load_models_from_config():
    """Auto-load models specified in config.py"""
    if not HAS_CONFIG:
        return
    
    print("\n" + "="*70)
    print("AUTO-LOADING MODELS FROM CONFIG")
    print("="*70)
    
    # Load embedder
    if config.MODEL_CONFIG.get("embedder"):
        print(f"\n[1/3] Loading embedder: {config.MODEL_CONFIG['embedder']}")
        status, _, _ = load_embedder_model(config.MODEL_CONFIG["embedder"])
        state.auto_load_status["embedder"] = status
        print(status)
    
    # Load trial checker
    if config.MODEL_CONFIG.get("trial_checker"):
        print(f"\n[2/3] Loading trial checker: {config.MODEL_CONFIG['trial_checker']}")
        status, _ = load_trial_checker(config.MODEL_CONFIG["trial_checker"])
        state.auto_load_status["trial_checker"] = status
        print(status)
    
    # Load boilerplate checker
    if config.MODEL_CONFIG.get("boilerplate_checker"):
        print(f"\n[3/3] Loading boilerplate checker: {config.MODEL_CONFIG['boilerplate_checker']}")
        status, _ = load_boilerplate_checker(config.MODEL_CONFIG["boilerplate_checker"])
        state.auto_load_status["boilerplate_checker"] = status
        print(status)
    
    print("\n" + "="*70)
    print("MODEL AUTO-LOADING COMPLETE")
    print("="*70 + "\n")


def auto_load_patients_from_config():
    """Auto-load patient database from config.py - prefers pre-embedded over fresh embedding."""
    if not HAS_CONFIG:
        return
    
    # Check for pre-embedded patients first (much faster)
    if hasattr(config, 'PREEMBEDDED_PATIENTS') and config.PREEMBEDDED_PATIENTS:
        preembed_path = config.PREEMBEDDED_PATIENTS
        
        # Handle URL paths for Hugging Face datasets
        if preembed_path.startswith("http://") or preembed_path.startswith("https://"):
            print("\n" + "="*70)
            print(f"AUTO-LOADING PRE-EMBEDDED PATIENTS (URL): {preembed_path}")
            print("="*70)
            
            status, preview = load_preembedded_patients(preembed_path)
            state.auto_load_status["patients"] = status
            state.patient_preview_df = preview
            
            print("="*70)
            print("PRE-EMBEDDED PATIENTS AUTO-LOADING COMPLETE")
            print("="*70 + "\n")
            return

        # Check for new parquet format first, then fall back to old format
        parquet_path = preembed_path if preembed_path.endswith('.parquet') else f"{preembed_path}.parquet"
        old_format_data = f"{preembed_path}_data.pkl"
        
        if os.path.exists(parquet_path):
            # New parquet format
            print("\n" + "="*70)
            print(f"AUTO-LOADING PRE-EMBEDDED PATIENTS (parquet): {parquet_path}")
            print("="*70)
            
            status, preview = load_preembedded_patients(parquet_path)
            state.auto_load_status["patients"] = status
            state.patient_preview_df = preview
            
            print("="*70)
            print("PRE-EMBEDDED PATIENTS AUTO-LOADING COMPLETE")
            print("="*70 + "\n")
            return
        elif os.path.exists(old_format_data):
            # Old format (pkl + npy + json)
            print("\n" + "="*70)
            print(f"AUTO-LOADING PRE-EMBEDDED PATIENTS (legacy): {preembed_path}")
            print("="*70)
            
            status, preview = load_preembedded_patients(preembed_path)
            state.auto_load_status["patients"] = status
            state.patient_preview_df = preview
            
            print("="*70)
            print("PRE-EMBEDDED PATIENTS AUTO-LOADING COMPLETE")
            print("="*70 + "\n")
            return
        else:
            print(f"✗ Pre-embedded patient files not found: {preembed_path}")
            state.auto_load_status["patients"] = f"✗ Pre-embedded files not found: {preembed_path}"
        return
    
    # Fall back to fresh embedding if no pre-embedded patients specified
    if not hasattr(config, 'DEFAULT_PATIENT_DB') or not config.DEFAULT_PATIENT_DB:
        print("○ No patient database specified in config")
        return
    
    if not os.path.exists(config.DEFAULT_PATIENT_DB):
        print(f"✗ Default patient database not found: {config.DEFAULT_PATIENT_DB}")
        state.auto_load_status["patients"] = f"✗ Patient database file not found: {config.DEFAULT_PATIENT_DB}"
        return
    
    if state.embedder_model is None:
        print("○ Embedder not loaded yet - skipping patient database auto-load")
        state.auto_load_status["patients"] = "○ Waiting for embedder model to be loaded..."
        return
    
    print("\n" + "="*70)
    print(f"AUTO-LOADING PATIENT DATABASE: {config.DEFAULT_PATIENT_DB}")
    print("="*70)
    
    class FilePath:
        def __init__(self, path):
            self.name = path
    
    status, preview = load_and_embed_patients(FilePath(config.DEFAULT_PATIENT_DB), show_progress=True)
    state.auto_load_status["patients"] = status
    state.patient_preview_df = preview
    
    print("="*70)
    print("PATIENT DATABASE AUTO-LOADING COMPLETE")
    print("="*70 + "\n")


# ============================================================================
# MODEL LOADING FUNCTIONS
# ============================================================================

def load_embedder_model(model_path: str) -> Tuple[str, str, str]:
    """Load sentence transformer embedder model."""
    try:
        will_need_reembed = state.patient_df is not None and len(state.patient_df) > 0
        
        if will_need_reembed:
            warning_msg = f"\n⚠️  Warning: {len(state.patient_df)} patients are currently loaded. They will need to be re-embedded with the new model."
        else:
            warning_msg = ""
        
        state.embedder_model = SentenceTransformer(model_path, device=state.device, trust_remote_code=True)
        state.embedder_tokenizer = AutoTokenizer.from_pretrained(model_path, trust_remote_code=True)
        
        # Set the instruction prompt
        try:
            state.embedder_model.prompts['query'] = (
                "Instruct: Given a cancer patient summary, retrieve clinical trial options "
                "that are reasonable for that patient; or, given a clinical trial option, "
                "retrieve cancer patients who are reasonable candidates for that trial."
            )
        except:
            pass
        
        try:
            state.embedder_model.max_seq_length = MAX_EMBEDDER_SEQ_LEN
        except:
            pass
        
        success_msg = f"✓ Embedder model loaded from {model_path}{warning_msg}"
        
        if will_need_reembed:
            state.patient_embeddings = None
            success_msg += "\n→ Patient embeddings cleared. Please reload patient database to re-embed."
        
        return success_msg, "", warning_msg
    except Exception as e:
        return f"✗ Error loading embedder model: {str(e)}", str(e), ""


def load_trial_checker(model_path: str) -> Tuple[str, str]:
    """Load ModernBERT trial checker."""
    try:
        state.trial_checker_tokenizer = AutoTokenizer.from_pretrained(model_path)
        state.trial_checker_model = AutoModelForSequenceClassification.from_pretrained(
            model_path,
            torch_dtype=torch.float16 if state.device == "cuda" else torch.float32
        ).to(state.device)
        state.trial_checker_model.eval()
        return f"✓ Trial checker loaded from {model_path}", ""
    except Exception as e:
        return f"✗ Error loading trial checker: {str(e)}", str(e)


def load_boilerplate_checker(model_path: str) -> Tuple[str, str]:
    """Load ModernBERT boilerplate checker."""
    try:
        state.boilerplate_checker_tokenizer = AutoTokenizer.from_pretrained(model_path)
        state.boilerplate_checker_model = AutoModelForSequenceClassification.from_pretrained(
            model_path,
            torch_dtype=torch.float16 if state.device == "cuda" else torch.float32
        ).to(state.device)
        state.boilerplate_checker_model.eval()
        return f"✓ Boilerplate checker loaded from {model_path}", ""
    except Exception as e:
        return f"✗ Error loading boilerplate checker: {str(e)}", str(e)


# ============================================================================
# PATIENT DATA LOADING
# ============================================================================

def load_preembedded_patients(preembedded_path: str) -> Tuple[str, pd.DataFrame]:
    """Load pre-embedded patient database from disk.
    
    Supports two formats:
    1. New format: Single parquet file with patient_embedding column
       - Path should end with .parquet
       - Embeddings stored as lists in patient_embedding column
       - Metadata stored in parquet file metadata
       
    2. Legacy format: Separate pkl/npy/json files
       - Path is a prefix (e.g., "patient_embeddings")
       - Creates patient_embeddings_data.pkl, _vectors.npy, _metadata.json
    """
    try:
        # Determine format based on path
        is_parquet = preembedded_path.endswith('.parquet') or os.path.exists(f"{preembedded_path}.parquet") if not preembedded_path.endswith('.parquet') else True
        
        if is_parquet:
            return _load_preembedded_parquet(preembedded_path)
        else:
            return _load_preembedded_legacy(preembedded_path)
        
    except Exception as e:
        import traceback
        traceback.print_exc()
        return f"✗ Error loading pre-embedded patients: {str(e)}", None


def _load_preembedded_parquet(parquet_path: str) -> Tuple[str, pd.DataFrame]:
    """Load pre-embedded patients from new single parquet format."""
    is_url = parquet_path.startswith("http://") or parquet_path.startswith("https://")

    # Ensure .parquet extension for local files
    if not is_url and not parquet_path.endswith('.parquet'):
        parquet_path = f"{parquet_path}.parquet"
    
    if not is_url and not os.path.exists(parquet_path):
        return f"✗ Pre-embedded parquet file not found: {parquet_path}", None
    
    print(f"\n{'='*70}")
    print(f"LOADING PRE-EMBEDDED PATIENTS (Parquet Format)")
    print(f"{'='*70}")
    print(f"Loading from: {parquet_path}")
    
    try:
        # Read parquet file - from URL or local path
        if is_url:
            df = pd.read_parquet(parquet_path)
            # For remote files, we can't easily read pyarrow metadata without downloading
            # the file first, so we'll just load the dataframe directly.
            print(f"Metadata: (Skipped for URL)")
        else:
            # Read local parquet file with pyarrow to access metadata
            parquet_file = pq.read_table(parquet_path)
            
            # Extract metadata if available
            if parquet_file.schema.metadata and b'patient_embedding_metadata' in parquet_file.schema.metadata:
                metadata = json.loads(parquet_file.schema.metadata[b'patient_embedding_metadata'].decode('utf-8'))
                print(f"Metadata:")
                print(f"  Created: {metadata.get('created_at', 'unknown')}")
                print(f"  Embedder: {metadata.get('embedder_model', 'unknown')}")
                print(f"  Patients: {metadata.get('num_patients', 'unknown')}")
                print(f"  Embedding dim: {metadata.get('embedding_dim', 'unknown')}")
            
            # Convert to pandas
            df = parquet_file.to_pandas()

    except Exception as e:
        error_msg = f"✗ Failed to read parquet file from {parquet_path}: {str(e)}"
        print(error_msg)
        return error_msg, None

    print(f"✓ Loaded {len(df)} patients")
    print(f"  Columns: {', '.join(df.columns.tolist())}")
    
    # Check for required columns
    if 'patient_embedding' not in df.columns:
        return f"✗ Parquet file missing 'patient_embedding' column: {parquet_path}", None
    
    if 'patient_id' not in df.columns:
        return f"✗ Parquet file missing 'patient_id' column: {parquet_path}", None
    
    if 'patient_summary' not in df.columns:
        return f"✗ Parquet file missing 'patient_summary' column: {parquet_path}", None
    
    # Check boilerplate column
    if 'patient_boilerplate' in df.columns:
        non_empty_bp = (df['patient_boilerplate'].astype(str).str.strip().str.len() > 0).sum()
        print(f"  ✓ patient_boilerplate column: {non_empty_bp}/{len(df)} patients have boilerplate text")
    else:
        print(f"  ⚠ No patient_boilerplate column found")
        df['patient_boilerplate'] = ''
    
    # Extract embeddings from column and convert to numpy array
    print(f"Converting embeddings to numpy array...")
    embeddings = np.array(df['patient_embedding'].tolist(), dtype=np.float32)
    print(f"✓ Loaded embeddings: {embeddings.shape}")
    
    # Remove embedding column from dataframe (we store it separately in memory)
    df_without_embeddings = df.drop(columns=['patient_embedding'])
    
    state.patient_df = df_without_embeddings
    state.patient_embeddings = embeddings
    
    print(f"{'='*70}")
    print(f"PRE-EMBEDDED PATIENTS LOADED SUCCESSFULLY")
    print(f"{'='*70}\n")
    
    preview = df_without_embeddings[['patient_id', 'patient_summary']].head(10)
    return f"✓ Loaded {len(df)} pre-embedded patients from {os.path.basename(parquet_path)}", preview


def _load_preembedded_legacy(preembedded_prefix: str) -> Tuple[str, pd.DataFrame]:
    """Load pre-embedded patients from legacy format (pkl + npy + json files)."""
    data_file = f"{preembedded_prefix}_data.pkl"
    vectors_file = f"{preembedded_prefix}_vectors.npy"
    metadata_file = f"{preembedded_prefix}_metadata.json"
    
    if not os.path.exists(data_file):
        return f"✗ Pre-embedded data file not found: {data_file}", None
    if not os.path.exists(vectors_file):
        return f"✗ Pre-embedded vectors file not found: {vectors_file}", None
    
    print(f"\n{'='*70}")
    print(f"LOADING PRE-EMBEDDED PATIENTS (Legacy Format)")
    print(f"{'='*70}")
    print(f"Loading from: {preembedded_prefix}_*")
    
    if os.path.exists(metadata_file):
        with open(metadata_file, 'r') as f:
            metadata = json.load(f)
        print(f"Metadata:")
        print(f"  Created: {metadata.get('created_at', 'unknown')}")
        print(f"  Embedder: {metadata.get('embedder_model', 'unknown')}")
        print(f"  Patients: {metadata.get('num_patients', 'unknown')}")
        print(f"  Embedding dim: {metadata.get('embedding_dim', 'unknown')}")
    
    print(f"Loading patient dataframe...")
    with open(data_file, 'rb') as f:
        df = pickle.load(f)
    print(f"✓ Loaded {len(df)} patients")
    print(f"  Columns: {', '.join(df.columns.tolist())}")
    
    # Check boilerplate column
    if 'patient_boilerplate' in df.columns:
        non_empty_bp = (df['patient_boilerplate'].astype(str).str.strip().str.len() > 0).sum()
        print(f"  ✓ patient_boilerplate column: {non_empty_bp}/{len(df)} patients have boilerplate text")
    else:
        print(f"  ⚠ No patient_boilerplate column found")
        df['patient_boilerplate'] = ''
    
    print(f"Loading embeddings...")
    embeddings = np.load(vectors_file)
    print(f"✓ Loaded embeddings: {embeddings.shape}")
    
    if len(df) != embeddings.shape[0]:
        return (
            f"✗ Mismatch: {len(df)} patients but {embeddings.shape[0]} embeddings",
            None
        )
    
    state.patient_df = df
    state.patient_embeddings = embeddings
    
    print(f"{'='*70}")
    print(f"PRE-EMBEDDED PATIENTS LOADED SUCCESSFULLY")
    print(f"{'='*70}\n")
    
    preview = df[['patient_id', 'patient_summary']].head(10)
    return f"✓ Loaded {len(df)} pre-embedded patients from {preembedded_prefix}_*", preview


def load_and_embed_patients(file, show_progress: bool = False) -> Tuple[str, pd.DataFrame]:
    """Load patient database and embed summaries."""
    try:
        if state.embedder_model is None:
            return "✗ Please load the embedder model first!", None
        
        # Read file
        if file.name.endswith('.parquet'):
            df = pd.read_parquet(file.name)
        elif file.name.endswith('.csv'):
            df = pd.read_csv(file.name)
        elif file.name.endswith(('.xlsx', '.xls')):
            df = pd.read_excel(file.name)
        else:
            return "✗ Unsupported format. Use Parquet, CSV, or Excel.", None
        
        # Check required columns
        required_cols = ['patient_id', 'patient_summary']
        missing = [col for col in required_cols if col not in df.columns]
        if missing:
            return f"✗ Missing columns: {', '.join(missing)}", None
        
        # Clean data
        df = df[~df['patient_summary'].isnull()].copy()
        df = df[df['patient_summary'].astype(str).str.strip().str.len() > 0].copy()
        
        if 'patient_boilerplate' not in df.columns:
            df['patient_boilerplate'] = ''
        else:
            df['patient_boilerplate'] = df['patient_boilerplate'].fillna('')
        
        # Prepare texts for embedding
        df['patient_summary_trunc'] = df['patient_summary'].apply(
            lambda x: truncate_text(str(x), state.embedder_tokenizer, max_tokens=1500)
        )
        
        prefix = (
            "Instruct: Given a cancer patient summary, retrieve clinical trial options "
            "that are reasonable for that patient; or, given a clinical trial option, "
            "retrieve cancer patients who are reasonable candidates for that trial. "
        )
        texts_to_embed = [prefix + txt for txt in df['patient_summary_trunc'].tolist()]
        
        if not show_progress:
            gr.Info(f"Embedding {len(df)} patient summaries...")
        else:
            print(f"Embedding {len(df)} patient summaries...")
        
        with torch.no_grad():
            embeddings = state.embedder_model.encode(
                texts_to_embed,
                batch_size=64,
                convert_to_tensor=True,
                normalize_embeddings=True,
                show_progress_bar=show_progress,
                prompt='query'
            )
        
        state.patient_df = df
        state.patient_embeddings = embeddings.cpu().numpy()
        
        preview = df[['patient_id', 'patient_summary']].head(10)
        
        success_msg = f"✓ Loaded and embedded {len(df)} patients"
        if show_progress:
            print(success_msg)
        
        return success_msg, preview
        
    except Exception as e:
        return f"✗ Error processing patients: {str(e)}", None


# ============================================================================
# PATIENT MATCHING
# ============================================================================

def match_patients(
    clinical_space: str, 
    boilerplate_criteria: str,
    top_k_check: int = 1000,
    eligibility_threshold: float = 0.5
) -> Tuple[pd.DataFrame, str]:
    """Match clinical query to patients and run eligibility checks."""
    try:
        if state.embedder_model is None:
            raise ValueError("Embedder model not loaded")
        if state.patient_embeddings is None:
            raise ValueError("Patient database not loaded")
        if state.trial_checker_model is None:
            raise ValueError("Trial checker model not loaded")
        if state.boilerplate_checker_model is None:
            raise ValueError("Boilerplate checker model not loaded")
        
        if not clinical_space or not clinical_space.strip():
            raise ValueError("Please enter clinical criteria")
        
        # Embed clinical query
        prefix = (
            "Instruct: Given a cancer patient summary, retrieve clinical trial options "
            "that are reasonable for that patient; or, given a clinical trial option, "
            "retrieve cancer patients who are reasonable candidates for that trial. "
        )
        
        query_text = truncate_text(clinical_space, state.embedder_tokenizer, max_tokens=MAX_EMBEDDER_SEQ_LEN)
        query_text_with_prefix = prefix + query_text
        
        gr.Info("Ranking all patients by similarity...")
        
        with torch.no_grad():
            query_emb = state.embedder_model.encode(
                [query_text_with_prefix],
                convert_to_tensor=True,
                normalize_embeddings=True,
                prompt='query'
            )
        
        # Calculate similarities for all patients
        query_emb_np = query_emb.cpu().numpy()
        similarities = np.dot(state.patient_embeddings, query_emb_np.T).squeeze()
        
        # Rank all patients by similarity
        sorted_indices = np.argsort(similarities)[::-1]
        
        # Get all patients ranked
        all_patients_ranked = state.patient_df.iloc[sorted_indices].copy()
        all_patients_ranked['similarity_score'] = similarities[sorted_indices]
        
        # Limit to top_k_check for classifier models
        top_k_check = min(top_k_check, len(all_patients_ranked))
        patients_to_check = all_patients_ranked.head(top_k_check).copy()
        
        gr.Info(f"Running eligibility checks on top {len(patients_to_check)} patients...")
        
        # Run trial checker in batches
        trial_check_inputs = [
            f"{clinical_space}\nNow here is the patient summary:{row['patient_summary']}"
            for _, row in patients_to_check.iterrows()
        ]
        
        trial_probs_list = []
        for i in range(0, len(trial_check_inputs), CLASSIFIER_BATCH_SIZE):
            batch_inputs = trial_check_inputs[i:i + CLASSIFIER_BATCH_SIZE]
            
            batch_encodings = state.trial_checker_tokenizer(
                batch_inputs,
                truncation=True,
                max_length=MAX_TRIAL_CHECKER_LENGTH,
                padding=True,
                return_tensors='pt'
            ).to(state.device)
            
            with torch.no_grad():
                batch_outputs = state.trial_checker_model(**batch_encodings)
                batch_probs = torch.softmax(batch_outputs.logits, dim=1)[:, 1].cpu().numpy()
                trial_probs_list.append(batch_probs)
        
        trial_probs = np.concatenate(trial_probs_list)
        patients_to_check['eligibility_probability'] = trial_probs
        
        # Run boilerplate checker in batches
        # Use patient_boilerplate if available, otherwise fall back to patient_summary
        def get_boilerplate_text(row):
            bp = row.get('patient_boilerplate', '')
            if bp and isinstance(bp, str) and bp.strip():
                return bp
            return row['patient_summary']
        
        boilerplate_check_inputs = [
            f"Patient history: {get_boilerplate_text(row)}\nTrial exclusions:{boilerplate_criteria}"
            for _, row in patients_to_check.iterrows()
        ]
        
        boilerplate_probs_list = []
        for i in range(0, len(boilerplate_check_inputs), CLASSIFIER_BATCH_SIZE):
            batch_inputs = boilerplate_check_inputs[i:i + CLASSIFIER_BATCH_SIZE]
            
            batch_encodings = state.boilerplate_checker_tokenizer(
                batch_inputs,
                truncation=True,
                max_length=MAX_BOILERPLATE_CHECKER_LENGTH,
                padding=True,
                return_tensors='pt'
            ).to(state.device)
            
            with torch.no_grad():
                batch_outputs = state.boilerplate_checker_model(**batch_encodings)
                batch_probs = torch.softmax(batch_outputs.logits, dim=1)[:, 1].cpu().numpy()
                boilerplate_probs_list.append(batch_probs)
        
        boilerplate_probs = np.concatenate(boilerplate_probs_list)
        patients_to_check['exclusion_probability'] = boilerplate_probs
        
        # Sort by eligibility probability
        patients_to_check = patients_to_check.sort_values('eligibility_probability', ascending=False)
        
        # Store full results for export
        state.last_results_df = patients_to_check.copy()
        
        # Calculate bottom line stats
        num_eligible = (patients_to_check['eligibility_probability'] >= eligibility_threshold).sum()
        num_no_exclusion = (patients_to_check['exclusion_probability'] < 0.5).sum()
        num_both = ((patients_to_check['eligibility_probability'] >= eligibility_threshold) & 
                   (patients_to_check['exclusion_probability'] < 0.5)).sum()
        
        bottom_line = f"""
### 📊 Summary: Patients Meeting Your Criteria
| Metric | Count |
|--------|-------|
| Total patients in database | **{len(state.patient_df)}** |
| Top patients checked with classifiers | **{len(patients_to_check)}** |
| Meeting eligibility criteria (≥{eligibility_threshold}) | **{num_eligible}** |
| Without boilerplate exclusions (<0.5) | **{num_no_exclusion}** |
| **Meeting BOTH criteria** | **{num_both}** |
"""
        
        # Format for display
        patients_to_check['eligibility_display'] = patients_to_check['eligibility_probability'].apply(
            lambda x: format_probability_visual(x, is_exclusion=False)
        )
        patients_to_check['exclusion_display'] = patients_to_check['exclusion_probability'].apply(
            lambda x: format_probability_visual(x, is_exclusion=True)
        )
        patients_to_check['similarity_display'] = patients_to_check['similarity_score'].apply(
            lambda x: f"{x:.3f}"
        )
        
        # Truncate summary for display
        patients_to_check['summary_preview'] = patients_to_check['patient_summary'].apply(
            lambda x: str(x)[:300] + "..." if len(str(x)) > 300 else str(x)
        )
        
        # Select columns for display
        display_cols = [
            'patient_id', 
            'eligibility_display', 
            'exclusion_display',
            'similarity_display',
            'summary_preview'
        ]
        
        result_df = patients_to_check[display_cols].reset_index(drop=True)
        result_df.columns = [
            'Patient ID', 
            'Eligibility', 
            'Exclusion',
            'Similarity',
            'Summary Preview'
        ]
        
        return result_df, bottom_line
        
    except Exception as e:
        gr.Error(f"Error matching patients: {str(e)}")
        return pd.DataFrame(), f"**Error:** {str(e)}"


def get_patient_details(df: pd.DataFrame, evt: gr.SelectData) -> str:
    """Get full patient details when user clicks on a row."""
    try:
        if df is None or len(df) == 0:
            return "No patient selected"
        
        row_idx = evt.index[0]
        patient_id = df.iloc[row_idx]['Patient ID']
        
        # Find in full results
        if state.last_results_df is None:
            return "No results available"
        
        matching_rows = state.last_results_df[
            state.last_results_df['patient_id'] == patient_id
        ]
        
        if len(matching_rows) == 0:
            return f"Error: Could not find patient {patient_id}"
        
        patient_row = matching_rows.iloc[0]
        
        # Get boilerplate text - use same fallback logic as the checker
        raw_boilerplate = patient_row.get('patient_boilerplate', '')
        has_separate_boilerplate = raw_boilerplate and isinstance(raw_boilerplate, str) and raw_boilerplate.strip()
        
        if has_separate_boilerplate:
            boilerplate_text = raw_boilerplate
        else:
            boilerplate_text = "(No separate boilerplate column - patient summary was used for boilerplate exclusion check)"
        
        # Escape any HTML characters in the text
        summary_escaped = html.escape(str(patient_row['patient_summary']))
        boilerplate_escaped = html.escape(str(boilerplate_text))
        
        details = f"""
# Patient Details: {patient_id}

---

## Scores
- **Eligibility Probability:** {patient_row['eligibility_probability']:.3f}
- **Exclusion Probability:** {patient_row['exclusion_probability']:.3f}
- **Similarity Score:** {patient_row['similarity_score']:.3f}

---

## Full Patient Summary
<pre style="white-space: pre-wrap; word-wrap: break-word; background-color: #1a1a1a; color: #ffffff; padding: 10px; border-radius: 5px; font-family: monospace; font-size: 0.9em;">{summary_escaped}</pre>

---

## Boilerplate Exclusion Check Input
<pre style="white-space: pre-wrap; word-wrap: break-word; background-color: #1a1a1a; color: #ffffff; padding: 10px; border-radius: 5px; font-family: monospace; font-size: 0.9em;">{boilerplate_escaped}</pre>
"""
        return details
        
    except Exception as e:
        return f"Error retrieving patient details: {str(e)}"


def request_identified_patients():
    """Placeholder for requesting identified patient list."""
    if state.last_results_df is None or len(state.last_results_df) == 0:
        gr.Warning("No results to request - run a search first")
        return
    
    # TODO: Implement actual request functionality
    gr.Info("Request functionality not yet implemented")


# ============================================================================
# GRADIO INTERFACE
# ============================================================================

def create_interface():
    
    theme = gr.themes.Soft(
        primary_hue="teal",
        secondary_hue="slate",
    ).set(
        body_background_fill="*neutral_50",
        block_background_fill="white",
        block_border_width="1px",
        block_label_background_fill="*primary_50",
    )

    custom_css = """
    .gradio-container { font-family: 'Inter', Arial, sans-serif !important; }
    .model-status { min-height: 80px !important; font-size: 0.9em; }
    .status-box { background: #f9fafb; border: 1px solid #e5e7eb; border-radius: 8px; padding: 10px; }
    h1 { color: #0d9488; }
    """
    
    # Get templates from config or use defaults
    clinical_space_template = getattr(config, 'CLINICAL_SPACE_TEMPLATE', DEFAULT_CLINICAL_SPACE_TEMPLATE) if HAS_CONFIG else DEFAULT_CLINICAL_SPACE_TEMPLATE
    boilerplate_template = getattr(config, 'BOILERPLATE_TEMPLATE', DEFAULT_BOILERPLATE_TEMPLATE) if HAS_CONFIG else DEFAULT_BOILERPLATE_TEMPLATE
    
    with gr.Blocks(title="Patient Search Prototype", theme=theme, css=custom_css) as demo:
        
        with gr.Row(variant="panel"):
            with gr.Column(scale=4):
                gr.Markdown("""
                # 🔬 Patient Search Prototype
                **Find patients matching clinical criteria. Designed for clinical trial matching.**
                """)
            with gr.Column(scale=1):
                pass
        
        with gr.Tabs():
            # ============= TAB 1: SEARCH =============
            with gr.Tab("1️⃣ Search"):
                gr.Markdown("""
                ### Define Your Search Criteria
                Enter the clinical criteria to search for matching patients.
                """)
                
                with gr.Row():
                    with gr.Column():
                        clinical_space_input = gr.Textbox(
                            label="Clinical Criteria",
                            placeholder="Enter eligibility criteria...",
                            value=clinical_space_template,
                            lines=12,
                            info="Define age, sex, cancer type, histology, treatments, biomarkers, etc."
                        )
                    
                    with gr.Column():
                        boilerplate_input = gr.Textbox(
                            label="Boilerplate Exclusion Criteria",
                            placeholder="Enter boilerplate exclusions...",
                            value=boilerplate_template,
                            lines=12,
                            info="Common exclusions like organ dysfunction, infections, etc."
                        )
                
                gr.Markdown("---")
                
                with gr.Row():
                    with gr.Column(scale=1):
                        match_btn = gr.Button("🔍 Find Matching Patients", variant="primary", size="lg")
                    with gr.Column(scale=3):
                        with gr.Accordion("Search Settings", open=False):
                            top_k_check_slider = gr.Slider(
                                minimum=5, maximum=10000, value=500, step=50,
                                label="Patients to Check with Classifiers",
                                info="Number of top-ranked patients to run through eligibility/boilerplate models (larger queries take more time)"
                            )
                            eligibility_threshold_slider = gr.Slider(
                                minimum=0.0, maximum=1.0, value=0.5, step=0.05,
                                label="Eligibility Threshold",
                                info="Threshold for counting patients as 'eligible'"
                            )

                gr.Markdown("### 📊 Results")
                
                # Bottom line summary
                bottom_line_output = gr.Markdown(
                    value="*Run a search to see results*"
                )
                
                with gr.Row():
                    with gr.Column(scale=7):
                        results_df = gr.Dataframe(
                            label="Matched Patients",
                            interactive=False,
                            wrap=True,
                            datatype=["str", "markdown", "markdown", "str", "str"],
                            column_widths=["12%", "12%", "12%", "10%", "54%"]
                        )
                    
                    with gr.Column(scale=5):
                        patient_details = gr.Markdown(
                            label="Patient Details",
                            value="<div style='text-align: center; padding: 50px; color: #666;'>👈 Click on a patient row to see full details here</div>"
                        )
                
                # Request identified patients button
                with gr.Row():
                    request_btn = gr.Button("📋 Request Identified Patient List", variant="secondary")
                
                # Wire up matching
                match_btn.click(
                    fn=match_patients,
                    inputs=[clinical_space_input, boilerplate_input, top_k_check_slider, eligibility_threshold_slider],
                    outputs=[results_df, bottom_line_output]
                )
                
                results_df.select(
                    fn=get_patient_details,
                    inputs=[results_df],
                    outputs=[patient_details]
                )
                
                request_btn.click(
                    fn=request_identified_patients,
                    inputs=[],
                    outputs=[]
                )
            
            # ============= TAB 2: PATIENT DATABASE =============
            with gr.Tab("2️⃣ Patient Database"):
                gr.Markdown("### 📊 Patient Database Management")
                
                with gr.Row():
                    with gr.Column():
                        gr.Markdown("#### Load Pre-embedded Patients (Fast)")
                        preembed_prefix = gr.Textbox(
                            label="Pre-embedded Prefix",
                            placeholder="patient_embeddings",
                            value=getattr(config, 'PREEMBEDDED_PATIENTS', '') or "" if HAS_CONFIG else ""
                        )
                        preembed_btn = gr.Button("Load Pre-embedded", variant="secondary")
                    
                    with gr.Column():
                        gr.Markdown("#### Upload & Embed New Database")
                        patient_file = gr.File(
                            label="Upload Patient Database (Parquet/CSV/Excel)",
                            file_types=[".parquet", ".csv", ".xlsx", ".xls"]
                        )
                        patient_upload_btn = gr.Button("Process & Embed", variant="secondary")
                
                patient_status = gr.Textbox(
                    label="Status",
                    interactive=False,
                    value=state.auto_load_status.get("patients", "No patients loaded")
                )
                
                patient_preview = gr.Dataframe(
                    label="Patient Preview (first 10)",
                    value=state.patient_preview_df,
                    wrap=True
                )
                
                preembed_btn.click(
                    fn=load_preembedded_patients,
                    inputs=[preembed_prefix],
                    outputs=[patient_status, patient_preview]
                )
                
                patient_upload_btn.click(
                    fn=load_and_embed_patients,
                    inputs=[patient_file],
                    outputs=[patient_status, patient_preview]
                )
            
            # ============= TAB 3: MODEL CONFIGURATION =============
            with gr.Tab("3️⃣ Model Configuration"):
                gr.Markdown("### 🧠 Model Management")
                
                status_msg = """
                **Config file detected** - Models will auto-load on startup.
                """ if HAS_CONFIG else """
                **No config file found** - Please load models manually below.
                """
                gr.Info(status_msg)
                
                with gr.Group():
                    with gr.Row():
                        with gr.Column():
                            embedder_input = gr.Textbox(
                                label="Embedder Model", 
                                placeholder="Qwen/Qwen3-Embedding-0.6B",
                                value=config.MODEL_CONFIG.get("embedder", "") if HAS_CONFIG else ""
                            )
                            embedder_btn = gr.Button("Load Embedder")
                            embedder_status = gr.Textbox(
                                label="Status", 
                                interactive=False, 
                                value=state.auto_load_status.get("embedder", ""),
                                elem_classes=["model-status"]
                            )
                            embedder_warning = gr.Textbox(visible=False)
                        
                        with gr.Column():
                            trial_checker_input = gr.Textbox(
                                label="Trial Checker Model", 
                                placeholder="answerdotai/ModernBERT-large",
                                value=config.MODEL_CONFIG.get("trial_checker", "") if HAS_CONFIG else ""
                            )
                            trial_checker_btn = gr.Button("Load Trial Checker")
                            trial_checker_status = gr.Textbox(
                                label="Status", 
                                interactive=False, 
                                value=state.auto_load_status.get("trial_checker", ""),
                                elem_classes=["model-status"]
                            )
                
                with gr.Row():
                    with gr.Column(scale=1):
                        boilerplate_checker_input = gr.Textbox(
                            label="Boilerplate Checker Model", 
                            placeholder="answerdotai/ModernBERT-large",
                            value=config.MODEL_CONFIG.get("boilerplate_checker", "") if HAS_CONFIG else ""
                        )
                        boilerplate_checker_btn = gr.Button("Load Boilerplate Checker")
                        boilerplate_checker_status = gr.Textbox(
                            label="Status", 
                            interactive=False, 
                            value=state.auto_load_status.get("boilerplate_checker", ""),
                            elem_classes=["model-status"]
                        )
                    with gr.Column(scale=1):
                        pass
                
                # Wire up model loading
                embedder_btn.click(
                    fn=load_embedder_model, 
                    inputs=[embedder_input], 
                    outputs=[embedder_status, gr.Textbox(visible=False), embedder_warning]
                )
                trial_checker_btn.click(
                    fn=load_trial_checker, 
                    inputs=[trial_checker_input], 
                    outputs=[trial_checker_status, gr.Textbox(visible=False)]
                )
                boilerplate_checker_btn.click(
                    fn=load_boilerplate_checker, 
                    inputs=[boilerplate_checker_input], 
                    outputs=[boilerplate_checker_status, gr.Textbox(visible=False)]
                )
    
    return demo


# ============================================================================
# MAIN
# ============================================================================

if __name__ == "__main__":
    print(f"Device: {state.device}")
    print(f"GPU Available: {torch.cuda.is_available()}")
    if torch.cuda.is_available():
        print(f"GPU Count: {torch.cuda.device_count()}")
    
    # Auto-load models from config if available
    if HAS_CONFIG:
        auto_load_models_from_config()
        
        # Auto-load patients after embedder is ready
        if state.embedder_model is not None or (hasattr(config, 'PREEMBEDDED_PATIENTS') and config.PREEMBEDDED_PATIENTS):
            auto_load_patients_from_config()
    
    demo = create_interface()
    demo.launch(
        server_name="0.0.0.0",
        share=False
    )