darna.py

##Sets up the flask server for viewing locally at {ip_address}:3001
#/* DARNA.HI
# * Copyright (c) 2023 Seapoe1809   <https://github.com/seapoe1809>
# * Copyright (c) 2023 pnmeka   <https://github.com/pnmeka>
# * 
# *
# *   This program is free software: you can redistribute it and/or modify
# *   it under the terms of the GNU General Public License as published by
# *   the Free Software Foundation, either version 3 of the License, or
# *   (at your option) any later version.
# *
# *   This program is distributed in the hope that it will be useful,
# *   but WITHOUT ANY WARRANTY; without even the implied warranty of
# *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# *   GNU General Public License for more details.
# *
# *   You should have received a copy of the GNU General Public License
# *   along with this program. If not, see <http://www.gnu.org/licenses/>.
# */
# Flask and extensions
from flask import Flask, render_template, send_file, send_from_directory, session, request, redirect, jsonify, url_for, Response, flash
from flask_login import LoginManager, UserMixin, login_user, logout_user, login_required, current_user
from flask_bcrypt import Bcrypt
from flask_sqlalchemy import SQLAlchemy

# Standard library
import os
import sqlite3
import json
import subprocess
from subprocess import run, CalledProcessError
import getpass
import webbrowser
from datetime import datetime, timedelta
from pathlib import Path
from functools import wraps
from urllib.parse import quote, unquote
import io

# Third-party packages
import requests
import qrcode
import pyzipper
import numpy as np
import matplotlib.pyplot as plt
from pdf2image import convert_from_path
from cryptography.fernet import Fernet

# DICOM handling
import pydicom
from pydicom.pixel_data_handlers.util import apply_voi_lut

# Local imports
import variables.variables as variables

##UPDATE ZIP PASSWORD HERE
create_zip_password = "2023"

app = Flask(__name__)
#app.config.update(
    #SESSION_COOKIE_SECURE=True,
    #SESSION_COOKIE_SAMESITE='None',
#)

# Initialize Flask extensions and Flask_login
bcrypt = Bcrypt(app)
login_manager = LoginManager()
login_manager.init_app(app)
login_manager.login_view = 'login'

#generates a app.secret_key that is variable and encrypted
key = Fernet.generate_key()
cipher_suite = Fernet(key)
app.secret_key = cipher_suite.encrypt(os.getcwd().encode())


# Configure static folder path
app.static_folder = 'static'

# Configure the SQLAlchemy part to use SQLite database
app.config['SQLALCHEMY_DATABASE_URI'] = 'sqlite:///users.db'
db = SQLAlchemy(app)

# Define User model, access
class User(db.Model, UserMixin):
    id = db.Column(db.Integer, primary_key=True)
    username = db.Column(db.String(80), unique=True)
    password = db.Column(db.String(120))

    def get_paths(self):
        base_path = os.getcwd()
        if self.username == 'ADMIN':
            folder_name = 'Health_files'
        elif self.username == 'USER1':
            folder_name = 'Health_files2'
        else:
            folder_name = f'Health_files_{self.username}'  # fallback

        folderpath = os.path.join(base_path, folder_name)
        APP_dir = os.path.join(base_path, 'install_module')
        ocr_files = os.path.join(folderpath, 'ocr_files')
        upload_dir = os.path.join(folderpath, 'upload')
        summary_dir = os.path.join(folderpath, 'summary')

        return {
            'HS_path': base_path,
            'folderpath': folderpath,
            'APP_dir': APP_dir,
            'ocr_files': ocr_files,
            'upload_dir': upload_dir,
            'summary_dir': summary_dir
            
        }

#importing variables from variables.py
# Label current dir and parent dir
HS_path = os.getcwd()
ip_address = variables.ip_address
APP_dir = f"{HS_path}/install_module"


@login_manager.user_loader
def load_user(user_id):
    return db.session.get(User, int(user_id))


#@app.before_first_request
def create_users():
    db.create_all()
    admin = User(username='ADMIN', password=bcrypt.generate_password_hash('health').decode('utf-8'))
    user1 = User(username='USER1', password=bcrypt.generate_password_hash('wellness').decode('utf-8'))
    db.session.add(admin)
    db.session.add(user1)
    db.session.commit()
    
@app.route('/login', methods=['GET', 'POST'])
def login():
    error_message = None
    if request.method == 'POST':
        username = request.form['username']
        password = request.form['password']
        user = User.query.filter_by(username=username).first()

        if user and bcrypt.check_password_hash(user.password, password):
            login_user(user)

            if username == "ADMIN":
                session['folderpath'] = f"{os.getcwd()}/Health_files"
            elif username == "USER1":
                session['folderpath'] = f"{os.getcwd()}/Health_files2"

            return redirect(url_for('protected'))
        else:
            error_message = "Password ⚠️"

    return render_template('login.html', error_message=error_message)

@app.route('/protected')
@login_required
def protected():
    return redirect(url_for('home'))

@login_manager.unauthorized_handler
def unauthorized():
    return render_template('login.html')

@app.route('/logout')
@login_required
def logout():
    logout_user()
    return redirect('/login')
    
@app.route('/shutdown')
@login_required
def shutdown():
    messages = []

    # Attempt to gracefully shut down the mainapp.py process
    try:
        subprocess.run(["pkill", "-f", "python.*darnabot.py"], check=True)
        messages.append("mainapp.py shut down successfully.")
        subprocess.run(["pkill", "-f", "python.*darna.py"], check=True)
        messages.append("app2.py shut down successfully.")
    except subprocess.CalledProcessError as e:
        messages.append(f"Failed to shut down processes: {e}")
    # List of ports to shut down processes on
    ports = [3001, 3012]
    
    for port in ports:
        try:
            pid = subprocess.check_output(["lsof", "-t", "-i:{}".format(port)]).decode().strip()
            if pid:
                # Splitting PIDs in case multiple PIDs are found
                pids = pid.split('\n')
                for pid in pids:
                    subprocess.run(["kill", pid], check=True)
                messages.append(f"Process on port {port} shut down successfully.")
            else:
                messages.append(f"No process found on port {port}.")
        except subprocess.CalledProcessError:
            try:
                # If the first kill fails, attempt a forceful kill
                for pid in pids:
                    subprocess.run(["kill", "-9", pid], check=True)
                messages.append(f"Process on port {port} force-killed successfully.")
            except subprocess.CalledProcessError as e:
                messages.append(f"Forceful kill failed on port {port}: {e}")

    return ' '.join(messages)
    

@app.route('/')
def home():
    if current_user.is_authenticated:
        # User is logged in
        return render_template('index.html')
    else:
        # User is not logged in
        return redirect(url_for('login'))


#making links for folder directory and files
@app.route('/folder')
@login_required
def folder_index():

    folder_path = session.get('folderpath')
    if folder_path is None:
        return "No folder path set in the session, please log in again.", 400

    files = []
    files = os.listdir(folder_path)

    file_links = []

    for filename in files:
        file_path = os.path.join(folder_path, filename)
        is_directory = os.path.isdir(file_path)

        if is_directory:
            file_links.append({'filename': filename, 'path': f'/folder/{filename}', 'is_folder': True})
        else:
            file_links.append({'filename': filename, 'path': f'/{filename}', 'is_folder': False})

    return render_template('folder_index.html', files=file_links)

#serving files from folder directory
@app.route('/<path:filename>')
@login_required
def serve_file(filename):
    if not current_user.is_authenticated:
        return redirect('/login')
    
    folderpath = session.get('folderpath')
    decoded_filename = unquote(filename)
    return send_from_directory(folderpath, decoded_filename, as_attachment=False)

#making file links in subdirectory    
@app.route('/folder/<path:subfolder>')
@login_required
def subfolder_index(subfolder):
    
    folderpath = session.get('folderpath')
    folder_path = os.path.join(folderpath, subfolder)

    files = []
    if os.path.exists(folder_path):
        files = os.listdir(folder_path)

    file_links = []

    for filename in files:
        file_path = os.path.join(folder_path, filename)
        is_directory = os.path.isdir(file_path)

        if is_directory:
            file_links.append({'filename': filename, 'path': f'/folder/{subfolder}/{filename}', 'is_folder': True})
        else:
            file_links.append({'filename': filename, 'path': f'/folder/{subfolder}/{filename}', 'is_folder': False})

    return render_template('folder_index.html', files=file_links)

    
@app.route('/folder/<path:subfolder>/<path:nested_subfolder>/<path:filename>')
@app.route('/folder/<path:subfolder>/<path:filename>')
@login_required
def serve_file_or_subfolder(subfolder, filename, nested_subfolder=''):
    
    folderpath = session.get('folderpath')
    folder_path = os.path.join(folderpath, subfolder, nested_subfolder)

    decoded_filename = unquote(filename)

    if os.path.isdir(os.path.join(folder_path, decoded_filename)):
        # Render subfolder index
        files = os.listdir(os.path.join(folder_path, decoded_filename))
        file_links = []

        for file in files:
            file_path = os.path.join(folder_path, decoded_filename, file)
            is_directory = os.path.isdir(file_path)

            if is_directory:
                file_links.append({'filename': file, 'path': f'/folder/{subfolder}/{nested_subfolder}/{decoded_filename}/{file}', 'is_folder': True})
            else:
                file_links.append({'filename': file, 'path': f'/folder/{subfolder}/{nested_subfolder}/{decoded_filename}/{file}', 'is_folder': False})

        return render_template('folder_index.html', files=file_links)
    else:
        # Serve file
        return send_from_directory(folder_path, decoded_filename, as_attachment=False)



@app.route('/zip_summary', methods=['POST'])
@login_required
def zip_summary():
    folderpath = session.get('folderpath')
    folder = folderpath
    zip_password = f'{create_zip_password}'.encode('utf-8')  # PASSWORD TO YOUR CHOICE HERE FOR ZIP ENCRYPT
    folder_to_zip = f'{folder}/summary'
    zip_filename = f'{folder}/my_summary.zip'

    try:
        with pyzipper.AESZipFile(zip_filename,
                                'w',
                                compression=pyzipper.ZIP_DEFLATED,
                                encryption=pyzipper.WZ_AES) as zipf:
            zipf.setpassword(zip_password)
            for root, _, files in os.walk(folder_to_zip):
                for file in files:
                    zipf.write(os.path.join(root, file),
                               os.path.relpath(os.path.join(root, file),
                                               folder_to_zip))
        return render_template('success.html', message="ZIP file created and encrypted.")
    except Exception as e:
        return render_template('error.html', message=str(e))

#The Following 3 sections are removed in ver 2.2 as sudo in app is security risk    


#the following are to chart your medications and past medical history in fhir format
@app.route('/chart')
@login_required
def chart():
    chart_json_url = url_for('custom_static', filename='chart.json')
    #vitals_json_url = url_for('custom_static', filename='vitals.json')
    return render_template('chart.html', chart_json_url=chart_json_url)


  
@app.route('/save-edits', methods=['POST'])
@login_required
def save_edits():
    folderpath = session.get('folderpath', '')
    destination_dir3 = os.path.join(folderpath, 'summary')
    file_path = os.path.join(destination_dir3, 'chart.json')
    updatedData = request.json  # Get the updated data from the request
    try:
        with open(file_path, 'w') as jsonFile:
            json.dump(updatedData, jsonFile, indent=4)
        return jsonify({"status": "success", "message": "Data saved successfully"})
    except Exception as e:
        return jsonify({"status": "error", "message": str(e)}), 500 

#Portal access viewer in Sky        
@app.route('/pabv')
def pabv():
    if current_user.is_authenticated:
        # User is logged in
        return render_template('pabv.html')
    else:
        # User is not logged in
        return redirect(url_for('login'))   

#Launches the darnabot with user ID
@app.route('/gradio_user')
@login_required
def gradio_user():
    user_id = current_user.id  # Get the user's ID
    current_ip = request.host.split(':')[0]  # Extract the IP
    return redirect(f"http://{current_ip}:3012?user={user_id}")
           


# Keep the original custom_static function 
@app.route('/custom_static/<filename>')
@login_required
def custom_static(filename):
    folderpath = session.get('folderpath', '')
    directory = os.path.join(folderpath, 'summary')
    return send_from_directory(directory, filename)

"""
#view dicom files in Health files    
@app.route('/summary/', methods=['GET'])
@login_required
def dicom_files():
    folderpath = session.get('folderpath', '')
    directory = os.path.join(folderpath, 'summary')

    # Lists to store file names
    pdf_files = []
    xml_files = []
    dicom_files = []

    # Scan directory and categorize files by extension
    for f in os.listdir(directory):
        if f.lower().endswith(('.pdf', '.PDF')):
            pdf_files.append(f)
        elif f.lower().endswith(('.xml', '.XML')):
            xml_files.append(f)
        elif f.lower().endswith(('.dcm', '.dicom', '.DCM')):
            dicom_files.append(f)

    # Pass the lists to the template
    print(pdf_files)
    print(dicom_files)
    return render_template('summary.html', pdf_files=pdf_files, xml_files=xml_files, dicom_files=dicom_files)


@app.route('/summary/<filename>')
@login_required
def display_file(filename):
    folderpath = session.get('folderpath', '')
    directory = os.path.join(folderpath, 'summary')
    file_path = os.path.join(directory, filename)

    # Handle DICOM files
    if filename.lower().endswith(('.dcm', '.dicom', '.DCM')):
        # Load the DICOM file to compute max_slice
        dicom_data = pydicom.dcmread(file_path)
        
        # Ensure it's a multi-dimensional dataset to calculate max_slice
        if dicom_data.pixel_array.ndim > 2:
            max_slice = dicom_data.pixel_array.shape[0] - 1
        else:
            max_slice = 0  # Handle single-slice (2D) DICOM images as well

        return render_template('view_dicom.html', filename=filename, max_slice=max_slice)

    # Directly serve PDF files
    if filename.lower().endswith('.pdf'):
        return send_from_directory(directory, filename, mimetype='application/pdf')

    # Directly serve XML files
    elif filename.lower().endswith('.xml'):
        return send_from_directory(directory, filename, mimetype='application/xml')

    # Fallback for unsupported file types
    return 'Unsupported file type', 404
"""
#view structured data with AI metadata
import os
import sqlite3
import json
from datetime import datetime
from pathlib import Path
from flask import render_template, send_from_directory, session, request
import pydicom
from functools import wraps


def get_db_connection(db_path):
    """Create a database connection to medical_records.db"""
    conn = sqlite3.connect(db_path)
    conn.row_factory = sqlite3.Row
    return conn

def format_file_size(size_in_bytes):
    """Convert bytes to human readable format"""
    for unit in ['B', 'KB', 'MB', 'GB']:
        if size_in_bytes < 1024.0:
            return f"{size_in_bytes:.1f} {unit}"
        size_in_bytes /= 1024.0
    return f"{size_in_bytes:.1f} TB"

def format_date(date_string):
    """Format date string to readable format"""
    try:
        dt = datetime.fromisoformat(date_string)
        return dt.strftime("%B %d, %Y at %I:%M %p")
    except:
        return date_string

def format_json_metadata(json_string):
    """Format JSON string for display"""
    try:
        if json_string:
            data = json.loads(json_string)
            return json.dumps(data, indent=2)
        return None
    except:
        return json_string

def search_files(search_term, folderpath):
    """Search files across all fields with folder path filtering"""
    # Get the summary directory path
    db_path = f"{folderpath}/medical_records.db"
    print("db_path", db_path)
    
    # Check if database exists
    if not os.path.exists(db_path):
        raise FileNotFoundError(f"Database not found at {db_path}")
    
    conn = get_db_connection(db_path)
    cursor = conn.cursor()
    
    # First, let's check what paths are actually in the database
    # (You can remove this debug code later)
    cursor.execute("SELECT DISTINCT file_path FROM files LIMIT 5")
    sample_paths = cursor.fetchall()
    print("Sample paths in DB:", sample_paths)
    
    if not search_term:
        # Return all files if no search term
        # Remove the file_path filter since we're already using the correct database
        query = """
        SELECT 
            filename,
            file_path,
            file_size,
            file_type,
            upload_date,
            embedded_metadata,
            ai_metadata
        FROM files
        WHERE filename != '.db' 
        AND filename != 'chart.json'
        AND filename != 'medical_records.db'
        ORDER BY upload_date DESC
        """
        cursor.execute(query)
    else:
        # Search across all relevant fields
        query = '''
            SELECT 
                filename,
                file_path,
                file_size,
                file_type,
                upload_date,
                embedded_metadata,
                ai_metadata
            FROM files 
            WHERE (filename LIKE ? 
            OR embedded_metadata LIKE ? 
            OR ai_metadata LIKE ?)
            AND filename != '.db' 
            AND filename != 'chart.json'
            AND filename != 'medical_records.db'
            ORDER BY upload_date DESC
        '''
        search_pattern = f"%{search_term}%"
        cursor.execute(query, [search_pattern, search_pattern, search_pattern])
    
    files = cursor.fetchall()
    conn.close()
    
    # Convert to list of dictionaries and add formatted fields
    file_list = []
    for file in files:
        file_dict = dict(file)
        
        # Add formatted versions
        file_dict['file_size_formatted'] = format_file_size(file_dict.get('file_size', 0))
        file_dict['upload_date_formatted'] = format_date(file_dict.get('upload_date', ''))
        file_dict['embedded_metadata_formatted'] = format_json_metadata(file_dict.get('embedded_metadata', ''))
        file_dict['ai_metadata_formatted'] = format_json_metadata(file_dict.get('ai_metadata', ''))
        
        file_list.append(file_dict)
    
    return file_list

def categorize_files_from_db(files):
    """Categorize files from database based on their extensions"""
    categories = {
        'pdf_files': [],
        'xml_files': [],
        'dicom_files': [],
        'image_files': [],
        'other_files': []
    }
    
    # Define file extensions for each category
    pdf_extensions = {'.pdf'}
    xml_extensions = {'.xml'}
    dicom_extensions = {'.dcm', '.dicom'}
    image_extensions = {'.jpg', '.jpeg', '.png', '.gif', '.bmp', '.tiff', '.svg', '.webp'}
    
    for file in files:
        filename = file['filename'].lower()
        extension = Path(filename).suffix.lower()
        
        if extension in pdf_extensions:
            categories['pdf_files'].append(file)
        elif extension in xml_extensions:
            categories['xml_files'].append(file)
        elif extension in dicom_extensions:
            categories['dicom_files'].append(file)
        elif extension in image_extensions:
            categories['image_files'].append(file)
        else:
            categories['other_files'].append(file)
    
    return categories

# View dicom files in Health files - MAIN SUMMARY ROUTE
@app.route('/summary/', methods=['GET'])
@login_required
def dicom_files():
    """Main summary page with search functionality"""
    folderpath = session.get('folderpath', '')
    directory = os.path.join(folderpath, 'summary')
    
    # Get search term from query parameters
    search_term = request.args.get('search', '').strip()
    
    # Try database first, then fallback to filesystem
    use_database = False
    total_results = 0
    
    try:
        # Check if database exists and try to use it
        db_path = f"{directory}/medical_records.db"
        if os.path.exists(db_path):
            # Try to get files from database
            if search_term:
                files = search_files(search_term, directory)

            else:
                files = search_files(None, directory)  # Get all files
            
            # Categorize files from database
            categories = categorize_files_from_db(files)
            
            # Calculate total results
            total_results = len(files)
            use_database = True
            
            # Extract the categorized files
            pdf_files = categories['pdf_files']
            xml_files = categories['xml_files']
            dicom_files = categories['dicom_files']
            image_files = categories['image_files']
            other_files = categories['other_files']
        else:
            raise FileNotFoundError("Database not found, using filesystem")
            
    except Exception as e:
        # Fallback to filesystem if database fails
        print(f"Database error, falling back to filesystem: {str(e)}")
        
        # Lists to store file names (original method)
        pdf_files = []
        xml_files = []
        dicom_files = []
        image_files = []
        other_files = []
        
        # Scan directory and categorize files by extension
        if os.path.exists(directory):
            for f in os.listdir(directory):
                # Skip database files
                if f in ['medical_records.db', '.db', 'chart.json']:
                    continue
                    
                # Create file dict for compatibility with template
                file_dict = {'filename': f}
                
                if f.lower().endswith(('.pdf', '.PDF')):
                    pdf_files.append(file_dict)
                elif f.lower().endswith(('.xml', '.XML')):
                    xml_files.append(file_dict)
                elif f.lower().endswith(('.dcm', '.dicom', '.DCM')):
                    dicom_files.append(file_dict)
                elif f.lower().endswith(('.jpg', '.jpeg', '.png', '.gif', '.bmp', '.tiff', '.svg', '.webp')):
                    image_files.append(file_dict)
                else:
                    # Other files
                    other_files.append(file_dict)
        
        use_database = False
        search_term = None
        total_results = len(pdf_files) + len(xml_files) + len(dicom_files) + len(image_files) + len(other_files)
    
    # Debug prints (like original)
    print(f"PDF files: {len(pdf_files)}")
    print(f"DICOM files: {len(dicom_files)}")
    print(f"Using database: {use_database}")
    
    # Pass the lists to the template
    return render_template('summary.html', 
                         pdf_files=pdf_files, 
                         xml_files=xml_files, 
                         dicom_files=dicom_files,
                         image_files=image_files,
                         other_files=other_files,
                         search_term=search_term,
                         total_results=total_results,
                         use_database=use_database)

@app.route('/summary/<filename>')
@login_required
def display_file(filename):
    """Display individual file"""
    folderpath = session.get('folderpath', '')
    directory = os.path.join(folderpath, 'summary')
    file_path = os.path.join(directory, filename)
    
    # Handle DICOM files
    if filename.lower().endswith(('.dcm', '.dicom', '.DCM')):
        # Load the DICOM file to compute max_slice
        dicom_data = pydicom.dcmread(file_path)
        
        # Ensure it's a multi-dimensional dataset to calculate max_slice
        if dicom_data.pixel_array.ndim > 2:
            max_slice = dicom_data.pixel_array.shape[0] - 1
        else:
            max_slice = 0  # Handle single-slice (2D) DICOM images as well
        return render_template('view_dicom.html', filename=filename, max_slice=max_slice)
    
    # Directly serve PDF files
    if filename.lower().endswith('.pdf'):
        return send_from_directory(directory, filename, mimetype='application/pdf')
    
    # Directly serve XML files
    elif filename.lower().endswith('.xml'):
        return send_from_directory(directory, filename, mimetype='application/xml')
    
    # Serve image files
    elif filename.lower().endswith(('.jpg', '.jpeg', '.png', '.gif', '.bmp', '.tiff', '.svg', '.webp')):
        # Determine appropriate mimetype
        extension = Path(filename).suffix.lower()
        mimetypes = {
            '.jpg': 'image/jpeg',
            '.jpeg': 'image/jpeg',
            '.png': 'image/png',
            '.gif': 'image/gif',
            '.bmp': 'image/bmp',
            '.tiff': 'image/tiff',
            '.svg': 'image/svg+xml',
            '.webp': 'image/webp'
        }
        return send_from_directory(directory, filename, mimetype=mimetypes.get(extension, 'application/octet-stream'))
    
    # Fallback for unsupported file types
    return 'Unsupported file type', 404
####End og AI metadata view

@app.route('/dicom/slice/<filename>/<int:slice_index>')
@login_required
def serve_dicom_slice(filename, slice_index):
    folderpath = session.get('folderpath', '')
    directory = os.path.join(folderpath, 'summary')
    dicom_file_path = os.path.join(directory, filename)
    
    dicom_data = pydicom.dcmread(dicom_file_path)
    image_3d = apply_voi_lut(dicom_data.pixel_array, dicom_data)
    
    # Selecting the requested slice
    try:
        image_slice = image_3d[slice_index]
    except IndexError:
        return "Slice index out of range", 400
    
    # Normalize and convert to uint8
    image_slice = np.interp(image_slice, (image_slice.min(), image_slice.max()), (0, 255))
    image_slice = image_slice.astype(np.uint8)
    
    # Convert to PNG
    buf = io.BytesIO()
    plt.imsave(buf, image_slice, cmap='gray', format='png')
    buf.seek(0)
    
    return send_file(buf, mimetype='image/png')  
          

@app.route('/upload', methods=['GET', 'POST'])
@login_required
def upload_file():
    folderpath = session.get('folderpath', '')
    destination_dir1 = os.path.join(folderpath, 'ocr_files')
    upload_dir = os.path.join(folderpath, 'upload')
    destination_dir3 = os.path.join(folderpath, 'summary')

    if request.method == 'POST':
        file_type = request.form.get('Type')
        file = request.files.get('File')

        if file:
            filename = file.filename
            file_path1 = os.path.join(destination_dir1 if file_type == 'HL_File' else folderpath, filename)
            file.save(file_path1)  # Save the file temporarily

            try:
                # Run clamscan on the uploaded file
                result = subprocess.run(['clamscan', '-r', file_path1], capture_output=True, text=True, check=True)

                if "Infected files: 0" in result.stdout:
                    if file_type == 'HL_File':
                        file_path2 = os.path.join(destination_dir3, filename)
                        # Use subprocess to copy the file
                        if os.name == 'posix':  # Unix-based system
                            subprocess.run(['cp', file_path1, file_path2], check=True)
                        elif os.name == 'nt':  # Windows
                            subprocess.run(['copy', file_path1, file_path2], shell=True, check=True)
                    return render_template('success.html')
                else:
                    os.remove(file_path1)  # Remove the infected file
                    return render_template('upload.html', message='File is infected!')

            except subprocess.CalledProcessError as e:
                print(f"An error occurred during file operation: {e}")
                os.remove(file_path1)  # Ensure the source file is removed in case of error
                return render_template('upload.html', message='An error occurred during file processing!')

            except Exception as e:
                print(f"An error occurred: {e}")
                if file_type == 'HL_File':
                    file_path2 = os.path.join(destination_dir3, filename)
                    # Use subprocess to copy the file
                    if os.name == 'posix':  # Unix-based system
                        subprocess.run(['cp', file_path1, file_path2], check=True)
                    elif os.name == 'nt':  # Windows
                        subprocess.run(['cmd', '/c', 'copy', file_path1, file_path2], check=True)
                return render_template('success.html')  # Proceed if ClamAV scan is not performed

    return render_template('upload.html')

@app.route('/connect_nc')
@login_required
def connect_nc():
    url = request.remote_addr
    client_ip = request.remote_addr
    if url == '127.0.0.1':
        url = f"http://{ip_address}:3001"  
    else:
        url = f"http://{url}:3001"
    print(url)
    qr = qrcode.QRCode()
    qr.add_data(url)
    qr.make()
    image = qr.make_image()
    image.save(f'{HS_path}/static/qrcode.png')
    return render_template('connect_nc.html')
 
#update password in connect_nc   
@app.route('/register', methods=['GET', 'POST'])
@login_required
def register():
    if request.method == 'POST':
        # Get the new password from the form
        new_password = request.form['password']
        
        # Hash the new password
        hashed_new_password = bcrypt.generate_password_hash(new_password).decode('utf-8')
        
        # Look up the current user in your database
        user = User.query.filter_by(username=current_user.username).first()
        
        if user:
            # Update the password in the database
            user.password = hashed_new_password
            db.session.commit()
            
            flash('Password change successful. You can now log in.')
            return redirect(url_for('login'))
        else:
            flash('Error: User not found.')
            return redirect(url_for('register'))

    return render_template('register.html')
   

@app.route('/pi')
@login_required
def pi():
    with open('install_module/templates/index2.html', 'r') as f:
        content = f.read()
    return Response(content, content_type='text/html')

"""        
@app.route('/analyze', methods=['GET', 'POST'])
@login_required
def analyze():

    if request.method == 'POST':
        age = request.form['age']
        sex = request.form['sex']
        ignore_words = request.form['ignore-words']
        print(f"Age: {age}")
        print(f"Sex: {sex}")
        print(f"Ignore Words: {ignore_words}")
        formatted_ignore_words = ignore_words.replace(' ', '|')

        content = f"age = '{age}'\nsex = '{sex}'\nignore_words = '{formatted_ignore_words}'\n"
        file_path = f"{HS_path}/variables/variables2.py"

        try:
            with open(file_path, 'w') as file:
                file.write(content)
        except Exception as e:
            print(f"Error writing to variables2.py: {str(e)}")
            return str(e)

        # Run the analyze script asynchronously using nohup and pass session cookie
        folderpath = session.get('folderpath')
        env_vars = os.environ.copy()
        env_vars['FOLDERPATH'] = folderpath
        command = f'python3 {HS_path}/analyze.py'
        #command = f'nohup python3 {HS_path}/analyze.py > /dev/null 2>&1 &'
        #subprocess.Popen(command, shell=True, env=env_vars)
        print("Process time is 3 minutes")
        try:
            subprocess.Popen(command, shell=True, env=env_vars)
        except Exception as e:
            print(f"Error running analyze.py: {str(e)}")
            return str(e)

        return render_template('success.html', message="Process time is 3 minutes")

    return render_template('analyze.html', submitted=True)

"""
    
@app.route('/install_module/<path:filename>')
@login_required
def serve_install_module(filename):
    return send_from_directory('install_module', filename)
     
@app.route('/install')
@login_required
def install():
    print("Inside /install")
    app_name_file = request.args.get('app_name_file') + '.js'
    app_folder = request.args.get('app_folder')
    session['app_name_file']= app_name_file
    app_name = session.get('app_name_file', '').replace('.js', '')
    
    print(f"Session variables: {session}")

    # Additional logic to process the app_name_file and app_folder if needed
    return render_template('install.html', app_name_file=app_name_file, app_folder=app_folder)


@app.route('/execute_script', methods=['GET', 'POST'])
@login_required
# executes the install script
def execute_script():
    try:
        print("Inside /execute_script")
        
        # List of allowed app names
        allowed_app_names = ['Ibs_Module', 'Immunization_Tracker', 'Weight_Tracker', 'Tailscale', 'Dock', 'Strep_Module', 'Anxiety_Module']
        
        app_name = session.get('app_name_file', '').replace('.js', '')
        if not app_name:
            return jsonify(success=False, error="Missing app_name")
        
        # Validate app_name
        if app_name not in allowed_app_names:
            return jsonify(success=False, error=f"Invalid app_name. Allowed values are: {', '.join(allowed_app_names)}")
        
        app_name_file = session['app_name_file']
        # import ip_address from variables and pass to env_var to install app_name
        url = f"http://{ip_address}"
        env_vars = os.environ.copy()
        env_vars['URL'] = url
        cmd = ['python3', f'install_module/{app_name}/{app_name}.py']
        print(cmd)
        proc = subprocess.Popen(cmd, env=env_vars, stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.PIPE, universal_newlines=True)
        stdout, stderr = proc.communicate()
        if proc.returncode == 0:
            return jsonify(success=True, message="Please Refresh App")
        else:
            print(f'Subprocess output: {stdout}')
            print(f'Subprocess error: {stderr}')
            return jsonify(success=False, error="Non-zero return code")
        print(f"Session variables: {session}")
    except Exception as e:
        return jsonify(success=False, error=str(e))

 
@app.errorhandler(404)
@login_required
def page_not_found(error):
    print("Error 404 Encountered")
    return render_template('errors.html', error_message='Page not found'), 404

        
if __name__== '__main__':
    app.run('0.0.0.0', port=3001)
    print("server is running at http://localhost:3001")