uploader/nice.py

#!/usr/bin/env python3
import asyncio
from collections import defaultdict
from pathlib import Path

from bs4 import BeautifulSoup
from local_file_picker import local_file_picker

from nicegui import ui, app, html, run, Client

from datetime import datetime

import zmq
import zmq.asyncio

from loguru import logger
import sys

from anonymiser import Anonymizer
import pydicom

import requests
import time

from multiprocessing import Manager, Queue, freeze_support

import watchfiles

from functools import partial


from typing import Optional

from fastapi import Request
from fastapi.responses import RedirectResponse
from starlette.middleware.base import BaseHTTPMiddleware
#import typer

#typer_app = typer.Typer()

#logger.add(sys.stderr, format="{time} {level} {message}", filter="my_module", level="INFO")

#async def pick_file() -> None:
#    result = await local_file_picker('~', multiple=True)
#    ui.notify(f'You chose {result}')
#    ui.html("<h2>Uploader tool</h2>")
#
#    ui.chat_message(f'{result}!',
#                name='Robot',
#                stamp='now',
#                avatar='https://robohash.org/ui')
#
#
#@ui.page('/')
#def index():
#    ui.html("<h2>Uploader tool</h2>")
#    ui.button('Choose file', on_click=pick_file, icon='folder')

SOCKET_PATH = 'tcp://localhost:9975'

EXPORT_PATH = Path("./test/export")
PROCESS_PATH = Path("./test/to_process")
ANON_PATH = Path("./test/anon")

EXPORT_PATH.mkdir(exist_ok=True, parents=True)
PROCESS_PATH.mkdir(exist_ok=True, parents=True)
EXPORT_PATH.mkdir(exist_ok=True, parents=True)

BASE_SITE_URL = "http://localhost:8000"
BASE_SITE_URL = "https://www.penracourses.org.uk"

LOGIN_URL = f"{BASE_SITE_URL}/accounts/login/"

LOGIN_SUCCESS = False

LOGGED_IN_USER = "None"


REFRESH_TRIGGERED = False

DELETE_FILES_ON_UPLOAD = False

rqst = None


use_zmq = True
loaded_files: dict = {}
loaded_series = defaultdict(list)
loaded_series_data = {}
uploaded_files: dict = {}
duplicate_series = set()


if use_zmq:
    context = zmq.asyncio.Context()
    socket = context.socket(zmq.PULL)
    #socket.bind('tcp://localhost:5575')
    try:
        socket.bind(SOCKET_PATH)
    except zmq.error.ZMQError as e:
        logger.debug("send reload")
        socket = context.socket(zmq.PUSH)
        socket.connect(SOCKET_PATH)
        socket.send_string("loaded")
        sys.exit(0)
        #app.shutdown()

    poller = zmq.asyncio.Poller()
    poller.register(socket, zmq.POLLIN)

    async def read_loop() -> None:
        while not app.is_stopped:
            events = await poller.poll()
            if socket in dict(events):
                data = await socket.recv()
                msg = data.decode()

                logger.debug(f'Received msg {msg}')

                match msg:
                    case "loaded":
                        for client in Client.instances.values():
                            if not client.has_socket_connection:
                                continue
                            with client:
                                ui.notify("Export done", color='positive')
                        
                        global REFRESH_TRIGGERED
                        REFRESH_TRIGGERED = True
                        logger.debug("loaded")

                        #with updates:
                        #    ui.item(f"{datetime.now().strftime('%H:%M:%S')} - {msg}")
                        #logger.debug("loaded")
                        #load_files_start()

                        
                    case _:
                        logger.error("invalid message")

anonymizer = Anonymizer(ANON_PATH)

async def upload_files_start(progress, upload_queue):
    global uploaded_files, duplicate_series
    progress.visible = True
    new_uploaded_files, upload_file_list, duplicate_file_list, failed, duplicate_series = await run.cpu_bound(upload_files, upload_queue, rqst)
    progress.visible = False

    uploaded_files.update(new_uploaded_files)

    ui.notify(f"Uploaded {len(upload_file_list)} files", color='positive')
    ui.notify(f"Duplicate {len(duplicate_file_list)} files", color='warning')
    ui.notify(f"Failed {len(failed)} files", color='negative')

    if DELETE_FILES_ON_UPLOAD:
        clear_anonymized_files()


    loaded_series_ui.refresh()
    loaded_files_ui.refresh()
    uploaded_files_ui.refresh()

async def load_files_start(progress_bar, queue):
    global loaded_files, loaded_series, loaded_series_data
    progress_bar.visible = True
    new_loaded_files, new_loaded_series, new_loaded_series_data = await run.cpu_bound(load_files, queue)

    loaded_files.update(new_loaded_files)
    loaded_series.update(new_loaded_series)
    loaded_series_data.update(new_loaded_series_data)

    progress_bar.visible = False
    #load_series_view(loaded_series, loaded_series_data)
    loaded_series_ui.refresh()
    loaded_files_ui.refresh()

async def reload_anonymized_start(progress_bar, queue):
    global loaded_files, loaded_series, loaded_series_data
    progress_bar.visible = True
    loaded_files, loaded_series, loaded_series_data = await run.cpu_bound(reload_anonymized, queue)
    progress_bar.visible = False
    #load_series_view(loaded_series, loaded_series_data)
    loaded_series_ui.refresh()
    loaded_files_ui.refresh()

@ui.refreshable
def user_info_ui():
    global LOGGED_IN_USER
    user_label = ui.label(f"User: {LOGGED_IN_USER}")
    #user_label.bind_visibility_from(globals(), "LOGIN_SUCCESS")

@ui.refreshable
def loaded_series_ui() -> None:
    global loaded_series, loaded_series_data

    series_title = ui.label('Series to upload').classes("text-h3")
    series_title.visible = False

    series = ui.row()

    #def load_series_view(loaded_series, loaded_series_data):
    logger.debug("load series view")
    logger.debug(loaded_series)
    for key in loaded_series:
        logger.debug(f"load series: {key}")
        with series:
            with ui.card():
                ui.label(loaded_series_data[key][0])
                ui.label(loaded_series_data[key][1])
                ui.label(f"Images: {len(loaded_series[key])}")

    if loaded_series:
        series_title.visible = True

@ui.refreshable
def loaded_files_ui() -> None:
    with ui.expansion('Loaded files', icon='drive_folder_upload').classes('w-full'):
        ui.label(f"Items: {len(loaded_files)}")
        with ui.list():
            for file, data in loaded_files.items():
                ui.item(f"{file} - {data[0]} - {data[1]}")


@ui.refreshable
def uploaded_files_ui() -> None:
    with ui.expansion('Uploaded files', icon='file_upload').classes('w-full'):
        ui.label(f"Items: {len(uploaded_files)}")
        with ui.list():
            for series in duplicate_series:
                ui.item(f"Duplicate series: {series}", on_click=lambda: ui.navigate.to(f'{BASE_SITE_URL}{series}', new_tab=True)).classes("text-red-500")
        with ui.list():
            for file, data in uploaded_files.items():
                ui.item(f"{file} - {data}")

def load_files(q: Queue):
    loaded_files: dict = {}
    loaded_series = defaultdict(list)
    loaded_series_data = {}
    # Move files
    src_path = EXPORT_PATH

    to_process = []
    for file in src_path.iterdir():
        logger.debug(f"Moving {file} to {PROCESS_PATH}")

        file_to_process = PROCESS_PATH / file.name
        file.rename(file_to_process)

        to_process.append(file_to_process)

    to_process_len = len(to_process)
    for n, file in enumerate(to_process):
        dataset, output_file = anonymizer.anonymize_file(file, remove_original=True)
        #with processed_files:
        #    ui.item(f"{datetime.now().strftime('%H:%M:%S')} - {file.name} -> {output_file.name}")

        loaded_files[output_file] = (dataset.StudyDescription, dataset.SeriesDescription, str(dataset.SeriesInstanceUID))

        loaded_series[dataset.SeriesInstanceUID].append(output_file)
        loaded_series_data[dataset.SeriesInstanceUID] = (dataset.StudyDescription, dataset.SeriesDescription)

        q.put_nowait((n + 1) / to_process_len)

        #time.sleep(0.01)

    return loaded_files, loaded_series, loaded_series_data 



def reload_anonymized(q: Queue):
    loaded_files = {}
    loaded_series = defaultdict(list)
    loaded_series_data = {}

    #processed_files.clear()


    to_process = list(ANON_PATH.glob("*.dcm"))
    to_process_len = len(to_process)
    for n, file in enumerate(to_process):
        with pydicom.dcmread(file) as dataset:
            loaded_files[file] = (dataset.StudyDescription, dataset.SeriesDescription, str(dataset.SeriesInstanceUID))

            loaded_series[dataset.SeriesInstanceUID].append(file)
            loaded_series_data[dataset.SeriesInstanceUID] = (dataset.StudyDescription, dataset.SeriesDescription)

        #with processed_files:
        #    ui.item(f"{datetime.now().strftime('%H:%M:%S')} - {file.name} -> Reloaded")


        q.put_nowait(f"{(n + 1) / to_process_len * 100:.0f}%")
        logger.debug(file)

        #time.sleep(0.01)
    
    logger.debug("end reload")
    logger.debug(loaded_files)
    logger.debug(loaded_series)
    logger.debug("-----")

    return loaded_files, loaded_series, loaded_series_data 

def clear_anonymized_files():
    for file in ANON_PATH.iterdir():
        if file.is_file():
            file.unlink()

    logger.debug("Deleted all files in ANON_PATH")

    return

def upload_files(q, rqst):
    #global rqst#, uploaded_files

    uploaded_files = {}

    files_to_upload = []
    for file in ANON_PATH.iterdir():
        files_to_upload.append(("files", open(str(file), "rb")))

    if not files_to_upload:
        ui.notify('No files to upload', color='negative')
        return

    # chunck files
    n = 10
    chunked_files = [
        files_to_upload[i : i + n] for i in range(0, len(files_to_upload), n)
    ]


    upload_file_list = []
    duplicate_file_list = []
    failed = []
    duplicate_series = set()

    logger.debug("START UPLOAD")
    logger.debug(files_to_upload)

    to_process_len = len(chunked_files)

    for n, files in enumerate(chunked_files):

        def upload_files_(files):
            rqst.headers["X-CSRFToken"] = rqst.cookies["csrftoken"]
            # print(self.rqst.headers)
            # print(self.rqst.cookies)
            resp = rqst.post(
                f"{BASE_SITE_URL}/api/atlas/upload_dicom",
                # data=data,
                files=files,
            )

            logger.debug(f"Resp: {resp}")
            logger.debug(f"{resp.content}")
            return resp

        # progress_dialog.Update(n, f"Uploading batch {n}/{len(chunked_files)}")

        logger.debug(f"n: {n}")
        # try to upload the files

        for i in range(3):
            resp = upload_files_(files)
            if resp.status_code == 200:
                upload_file_list.extend(resp.json()["uploaded"])
                duplicate_file_list.extend(resp.json()["duplicates"])
                failed.extend(resp.json()["failed"])
                duplicate_series.update(resp.json()["duplicate_series"])

                break

            logger.error(f"i: {i}")
            logger.debug(f"n: {n} fail (attempt {i})")

        q.put_nowait((n + 1) / to_process_len)
        # progress_dialog.Destroy()
    print(upload_file_list)
    print("dup", duplicate_file_list)
    print("failed", failed)

    for f, hash in upload_file_list:
        uploaded_files[f] = "success"

    for f, hash in duplicate_file_list:
        uploaded_files[f] = "duplicate"

    for f in failed:
        uploaded_files[f] = "failed"


    return uploaded_files, upload_file_list, duplicate_file_list, failed, duplicate_series







@ui.page('/login')
def login() -> Optional[RedirectResponse]:
    dark = ui.dark_mode()
    dark.enable()
    def try_login() -> None:  # local function to avoid passing username and password as arguments
        logger.debug(username.value)
        #if passwords.get(username.value) == password.value:
        #    app.storage.user.update({'username': username.value, 'authenticated': True})
        #    ui.navigate.to(app.storage.user.get('referrer_path', '/'))  # go back to where the user wanted to go
        #else:
        #    ui.notify('Wrong username or password', color='negative')
        user = username.value
        pw = password.value

        global rqst, LOGIN_SUCCESS, LOGGED_IN_USER
        rqst = requests.session()
        try: 
            rsp = rqst.get(LOGIN_URL)
        except requests.exceptions.ConnectionError:
            ui.notify('Connection error!', color='negative')
            return

        token = (
            BeautifulSoup(rsp.content, "html.parser").find("input").attrs["value"]
        )  # , attr={"name": "csrfmiddlewaretoken"}).attrs("value")

        # token = rsp.cookies["csrftoken"]
        # header = {"X-CSRFToken": token}
        # cookies = {"csrftoken": token}

        data = {
            "username": user,
            "password": pw,
            "csrfmiddlewaretoken": token,
            "next": "/",
        }

        rqst.headers["Referer"] = LOGIN_URL

        rsp = rqst.post(
            LOGIN_URL,
            data=data,
            # headers=header,
            # cookies=cookies
        )

        print(rsp.content)

        soup = BeautifulSoup(rsp.content, "html.parser")

        if soup.find("button") and soup.find("button").find(string="Login"):
            print("login fail")
            pass
        else:
            print("login success")
            LOGIN_SUCCESS = True
            LOGGED_IN_USER = user
            user_info_ui.refresh()
            #user_label.clear()
            #user_label.text = f"User: {user}"
        # print(rqst.headers)

        rqst.headers["X-CSRFToken"] = token

        print(rqst.headers)
        print(rqst.cookies)
        new = rqst.get(f"{BASE_SITE_URL}/accounts/api/atlas/get_cases_user")


        if LOGIN_SUCCESS:
            ui.notify('Logged in!', color='positive')
            ui.navigate.to("/")
            #login_button.visible = False
            pass
            #self.parent.upload_button.Enable()
            #self.parent.login_button.Hide()
            #self.parent.panel.Layout()
            #self.Destroy()

            # self.parent.login_button.SetBackgroundColour(wx.BLUE)
            # self.parent.login_button.SetForegroundColour(wx.WHITE)
        else:
            ui.notify('Wrong username or password', color='negative')
            pass
            #self.login_fail()

    #if app.storage.user.get('authenticated', False):
    #    return RedirectResponse('/')
    with ui.card().classes('absolute-center'):
        username = ui.input('Username').on('keydown.enter', try_login)
        password = ui.input('Password', password=True, password_toggle_button=True).on('keydown.enter', try_login)
        ui.button('Log in', on_click=try_login)
    return None

@ui.page('/')
def main_page():


    dark = ui.dark_mode()
    dark.enable()
    ui.page_title('Uploader tool')
    ui.label('Uploader tool').classes("text-h2")

    user_info_ui()

    login_button = ui.button("LOGIN", on_click=lambda: ui.navigate.to("/login"))
    login_button.bind_visibility_from(globals(), "LOGIN_SUCCESS", backward=lambda v: not v)

    updates = ui.list()

    loaded_series_ui()






#    typer_app()
    # Create a queue to communicate with the heavy computation process
    queue = Manager().Queue()
    # Update the progress bar on the main process
    ui.timer(0.1, callback=lambda: progressbar.set_value(queue.get() if not queue.empty() else progressbar.value))

    # Create a queue to communicate with the heavy computation process
    upload_queue = Manager().Queue()
    # Update the progress bar on the main process
    ui.timer(0.1, callback=lambda: upload_progressbar.set_value(upload_queue.get() if not upload_queue.empty() else upload_progressbar.value))




    upload_progress = ui.row().classes("w-full place-content-center bg-blue-900")

    with upload_progress:
        ui.label("Uploading files")
        upload_progressbar = ui.linear_progress(value=0).props('instant-feedback')
    upload_progress.visible = False

    upload_button = ui.button("Upload", on_click=partial(upload_files_start, upload_progress, upload_queue))
    upload_button.bind_visibility_from(globals(), "LOGIN_SUCCESS")

    anon_progress = ui.row().classes("w-full place-content-center bg-blue-900")

    with anon_progress:
        ui.label("Anonymizing files")
        progressbar = ui.linear_progress(value=0).props('instant-feedback')
    anon_progress.visible = False

    with ui.expansion('Extra', icon='build').classes('w-full'):
        ui.button("Load files", on_click=partial(load_files_start, anon_progress, queue))
        ui.button("Reload anon", on_click=partial(reload_anonymized_start, anon_progress, queue))

    with ui.expansion('File status', icon='view_list').classes('w-full'):
        loaded_files_ui()
        uploaded_files_ui()

        #with ui.expansion('Processed files!', icon='work').classes('w-full'):
        #    processed_files = ui.list()

    with ui.expansion("Settings", icon="settings").classes("w-full"):
        ui.label("Settings").classes("text-h4")
        ui.label(f"Export path: {EXPORT_PATH}")
        ui.label(f"Process path: {PROCESS_PATH}")
        ui.label(f"Anon path: {ANON_PATH}")
        ui.button("Clear anon path", on_click=clear_anonymized_files).tooltip("Delete all files in ANON_PATH")


    

    ui.notify("Welcome to the uploader tool", color='positive')

    async def watch_for_refresh():
        global REFRESH_TRIGGERED
        while not app.is_stopped:
            if REFRESH_TRIGGERED:
                REFRESH_TRIGGERED = False
                await load_files_start(anon_progress, queue)
            await asyncio.sleep(1)

    asyncio.create_task(watch_for_refresh())

if __name__ in {"__main__", "__mp_main__"}:
    freeze_support()

    if use_zmq:
        app.on_startup(read_loop)

    ui.run(storage_secret="123456", reload=False, show=False)