app.py

import concurrent.futures
import glob
import smtplib
from datetime import datetime, timedelta
import itertools
import textwrap
from email.mime.multipart import MIMEMultipart
from email.mime.text import MIMEText
from email.utils import formatdate, make_msgid
from math import pi
from time import sleep, time
from uuid import uuid4

import io
import os
from pathlib import Path
import sys

import pytz
from Bio import SeqIO
from Bio.Align import PairwiseAligner
from email_validator import validate_email, EmailNotValidError
import gradio as gr
import hydra
import pandas as pd
import requests
from markdown import markdown
from rdkit.Chem.PandasTools import _MolPlusFingerprint
from rdkit.Chem.rdMolDescriptors import CalcNumRotatableBonds, CalcNumHeavyAtoms, CalcNumAtoms, CalcTPSA
from requests.adapters import HTTPAdapter, Retry
from rdkit import Chem
from rdkit.Chem import RDConfig, Descriptors, Draw, Lipinski, Crippen, PandasTools
from rdkit.Chem.Scaffolds import MurckoScaffold
import seaborn as sns

from bokeh.models import Legend, NumberFormatter, BooleanFormatter, HTMLTemplateFormatter, LegendItem
from bokeh.palettes import Category20c_20
from bokeh.plotting import figure
from bokeh.transform import cumsum
from bokeh.resources import INLINE
import panel as pn

from apscheduler.schedulers.background import BackgroundScheduler
from tinydb import TinyDB, Query

import swifter
from tqdm.auto import tqdm

from deepscreen.data.dti import validate_seq_str, rdkit_canonicalize, FASTA_PAT, SMILES_PAT
from deepscreen.predict import predict

sys.path.append(os.path.join(RDConfig.RDContribDir, 'SA_Score'))
import sascorer

DATASET_MAX_LEN = 10_000
SERVER_DATA_DIR = os.getenv('DATA')  # '/data'
DB_EXPIRY = timedelta(hours=48).total_seconds()

CSS = """
.help-tip {
  position: absolute;
  display: inline-block;
  top: 16px;
  right: 0px;
  text-align: center;
  border-radius: 40%;
  /* border: 2px solid darkred; background-color: #8B0000;*/
  width: 24px;
  height: 24px;
  font-size: 16px;
  line-height: 26px;
  cursor: default;
  transition: all 0.5s cubic-bezier(0.55, 0, 0.1, 1);
  z-index: 100 !important;
}

.help-tip:hover {
  cursor: pointer;
  /*background-color: #ccc;*/
}

.help-tip:before {
  content: '?';
  font-weight: 700;
  color: #8B0000;
  z-index: 100 !important;
}

.help-tip p {
  visibility: hidden;
  opacity: 0;
  text-align: left;
  background-color: #EFDDE3;
  padding: 20px;
  width: 300px;
  position: absolute;
  border-radius: 4px;
  right: -4px;
  color: #494F5A;
  font-size: 13px;
  line-height: normal;
  transform: scale(0.7);
  transform-origin: 100% 0%;
  transition: all 0.5s cubic-bezier(0.55, 0, 0.1, 1);
  z-index: 100;
}

.help-tip:hover p {
  cursor: default;
  visibility: visible;
  opacity: 1;
  transform: scale(1.0);
}

.help-tip p:before {
  position: absolute;
  content: '';
  width: 0;
  height: 0;
  border: 6px solid transparent;
  border-bottom-color: #EFDDE3;
  right: 10px;
  top: -12px;
}

.help-tip p:after {
  width: 100%;
  height: 40px;
  content: '';
  position: absolute;
  top: -5px;
  left: 0;
  z-index: 101;
}

.upload_button {
  background-color: #008000;
}

.absolute {
  position: absolute;
}

.example {
padding: 0;
background: none;
border: none;
text-decoration: underline;
box-shadow: none;
text-align: left !important;
display: inline-block !important;
}

footer {
visibility: hidden
}

"""


class HelpTip:
    def __new__(cls, text):
        return gr.HTML(
            # elem_classes="absolute",
            value=f'<div class="help-tip"><p>{text}</p>',
        )


TASK_MAP = {
    'Compound-Protein Interaction': 'DTI',
    'Compound-Protein Binding Affinity': 'DTA',
}

TASK_METRIC_MAP = {
    'DTI': 'AUROC',
    'DTA': 'CI',
}

PRESET_MAP = {
    'DeepDTA': 'deep_dta',
    'DeepConvDTI': 'deep_conv_dti',
    'GraphDTA': 'graph_dta',
    'MGraphDTA': 'm_graph_dta',
    'HyperAttentionDTI': 'hyper_attention_dti',
    'MolTrans': 'mol_trans',
    'TransformerCPI': 'transformer_cpi',
    'TransformerCPI2': 'transformer_cpi_2',
    'DrugBAN': 'drug_ban',
    'DrugVQA-Seq': 'drug_vqa'
}

TARGET_FAMILY_MAP = {
    'General': 'general',
    'Kinase': 'kinase',
    'Non-Kinase Enzyme': 'non_kinase_enzyme',
    'Membrane Receptor': 'membrane_receptor',
    'Nuclear Receptor': 'nuclear_receptor',
    'Ion Channel': 'ion_channel',
    'Others': 'others',
}

TARGET_LIBRARY_MAP = {
    'DrugBank (Human)': 'drugbank_targets.csv',
    'ChEMBL33 (Human)': 'ChEMBL33_human_proteins.csv',
}

DRUG_LIBRARY_MAP = {
    'DrugBank (Human)': 'drugbank_compounds.csv',
    'Drug Repurposing Hub': 'drug_repurposing_hub.csv'
}

COLUMN_ALIASES = {
    'X1': 'Compound SMILES',
    'X2': 'Target FASTA',
    'ID1': 'Compound ID',
    'ID2': 'Target ID',
    'Y': 'Actual CPI/CPA',
    'Y^': 'Predicted CPI/CPA',
}

pd.set_option('display.float_format', '{:.3f}'.format)
PandasTools.molRepresentation = 'svg'
PandasTools.drawOptions = Draw.rdMolDraw2D.MolDrawOptions()
PandasTools.drawOptions.clearBackground = False
PandasTools.drawOptions.bondLineWidth = 1
PandasTools.drawOptions.explicitMethyl = True
PandasTools.drawOptions.singleColourWedgeBonds = True
PandasTools.drawOptions.useCDKAtomPalette()
PandasTools.molSize = (128, 80)

session = requests.Session()
ADAPTER = HTTPAdapter(max_retries=Retry(total=5, backoff_factor=0.1, status_forcelist=[500, 502, 503, 504]))
session.mount('http://', ADAPTER)
session.mount('https://', ADAPTER)

db = TinyDB(f'{SERVER_DATA_DIR}/db.json')
# Set all RUNNING jobs to FAILED at TinyDB initialization
Job = Query()
jobs = db.all()
for job in jobs:
    if job['status'] == 'RUNNING':
        db.update({'status': 'FAILED'}, Job.id == job['id'])

scheduler = BackgroundScheduler()


def remove_job_record(job_id):
    # Delete the job from the database
    db.remove(Job.id == job_id)
    # Delete the corresponding files
    files = glob.glob(f"/data/{job_id}*")
    for file_path in files:
        if os.path.exists(file_path):
            os.remove(file_path)


def check_expiry():
    Job = Query()
    jobs = db.all()

    for job in jobs:
        # Check if the job has expired
        if job['status'] != 'RUNNING':
            expiry_time = job['expiry_time'] if job['expiry_time'] is not None else job['start_time'] + DB_EXPIRY
            if expiry_time < time():
                # Delete the job from the database
                db.remove(Job.id == job['id'])
                # Delete the corresponding file
                files = glob.glob(f"/data/{job['id']}*")
                for file_path in files:
                    if os.path.exists(file_path):
                        os.remove(file_path)
        elif job['status'] == 'RUNNING' and time() - job['start_time'] > 4 * 60 * 60:  # 4 hours
            # Mark the job as failed
            db.update({'status': 'FAILED',
                       'error': 'Job has timed out by exceeding the maximum running time of 4 hours.'},
                      Job.id == job['id'])
            if job.get('email'):
                send_email(job)


scheduler.add_job(check_expiry, 'interval', hours=1)
scheduler.start()


def sa_score(mol):
    return sascorer.calculateScore(mol)


def mw(mol):
    return Chem.Descriptors.MolWt(mol)


def mr(mol):
    return Crippen.MolMR(mol)


def hbd(mol):
    return Lipinski.NumHDonors(mol)


def hba(mol):
    return Lipinski.NumHAcceptors(mol)


def logp(mol):
    return Crippen.MolLogP(mol)


def atom(mol):
    return CalcNumAtoms(mol)


def heavy_atom(mol):
    return CalcNumHeavyAtoms(mol)


def rotatable_bond(mol):
    return CalcNumRotatableBonds((mol))


def tpsa(mol):
    return CalcTPSA((mol))


def lipinski(mol):
    """
    Lipinski's rules:
    Hydrogen bond donors <= 5
    Hydrogen bond acceptors <= 10
    Molecular weight <= 500 daltons
    logP <= 5
    """
    if hbd(mol) > 5:
        return False
    elif hba(mol) > 10:
        return False
    elif mw(mol) > 500:
        return False
    elif logp(mol) > 5:
        return False
    else:
        return True


def reos(mol):
    """
    Rapid Elimination Of Swill filter:
    Molecular weight between 200 and 500
    LogP between -5.0 and +5.0
    H-bond donor count between 0 and 5
    H-bond acceptor count between 0 and 10
    Formal charge between -2 and +2
    Rotatable bond count between 0 and 8
    Heavy atom count between 15 and 50
    """
    if not 200 < mw(mol) < 500:
        return False
    elif not -5.0 < logp(mol) < 5.0:
        return False
    elif not 0 < hbd(mol) < 5:
        return False
    elif not 0 < hba(mol) < 10:
        return False
    elif not 0 < rotatable_bond(mol) < 8:
        return False
    elif not 15 < heavy_atom(mol) < 50:
        return False
    else:
        return True


def ghose(mol):
    """
    Ghose drug like filter:
    Molecular weight between 160 and 480
    LogP between -0.4 and +5.6
    Atom count between 20 and 70
    Molar refractivity between 40 and 130
    """
    if not 160 < mw(mol) < 480:
        return False
    elif not -0.4 < logp(mol) < 5.6:
        return False
    elif not 20 < atom(mol) < 70:
        return False
    elif not 40 < mr(mol) < 130:
        return False
    else:
        return True


def veber(mol):
    """
    The Veber filter is a rule of thumb filter for orally active drugs described in
    Veber et al., J Med Chem. 2002; 45(12): 2615-23.:
    Rotatable bonds <= 10
    Topological polar surface area <= 140
    """
    if not rotatable_bond(mol) <= 10:
        return False
    elif not tpsa(mol) <= 140:
        return False
    else:
        return True


def rule_of_three(mol):
    """
    Rule of Three filter (Congreve et al., Drug Discov. Today. 8 (19): 876–7, (2003).):
    Molecular weight <= 300
    LogP <= 3
    H-bond donor <= 3
    H-bond acceptor count <= 3
    Rotatable bond count <= 3
    """
    if not mw(mol) <= 300:
        return False
    elif not logp(mol) <= 3:
        return False
    elif not hbd(mol) <= 3:
        return False
    elif not hba(mol) <= 3:
        return False
    elif not rotatable_bond(mol) <= 3:
        return False
    else:
        return True


# def smarts_filter():
#     alerts = Chem.MolFromSmarts("enter one smart here")
#     detected_alerts = []
#     for smiles in data['X1']:
#         mol = Chem.MolFromSmiles(smiles)
#         detected_alerts.append(mol.HasSubstructMatch(alerts))


SCORE_MAP = {
    'SAscore': sa_score,
    'LogP': logp,
    'Molecular Weight': mw,
    'Number of Heavy Atoms': heavy_atom,
    'Molar Refractivity': mr,
    'H-Bond Donor Count': hbd,
    'H-Bond Acceptor Count': hba,
    'Rotatable Bond Count': rotatable_bond,
    'Topological Polar Surface Area': tpsa,
}

FILTER_MAP = {
    # TODO support number_of_violations
    'REOS': reos,
    "Lipinski's Rule of Five": lipinski,
    'Ghose': ghose,
    'Rule of Three': rule_of_three,
    'Veber': veber,
    # 'PAINS': pains,
}


def validate_columns(df, mandatory_cols):
    missing_cols = [col for col in mandatory_cols if col not in df.columns]
    if missing_cols:
        error_message = (f"The following mandatory columns are missing "
                         f"in the uploaded dataset: {str(mandatory_cols).strip('[]')}.")
        raise ValueError(error_message)
    else:
        return


def process_target_fasta(sequence):
    try:
        if sequence:
            lines = sequence.strip().split("\n")
            if lines[0].startswith(">"):
                lines = lines[1:]
            return ''.join(lines).split(">")[0]
            # record = list(SeqIO.parse(io.StringIO(sequence), "fasta"))[0]
            # return str(record.seq)
        else:
            raise ValueError('Empty FASTA sequence.')
    except Exception as e:
        raise gr.Error(f'Failed to process FASTA due to error: {str(e)}')


def send_email(job_info):
    if job_info.get('email'):
        try:
            email_serv = os.getenv('EMAIL_SERV')
            email_port = os.getenv('EMAIL_PORT')
            email_addr = os.getenv('EMAIL_ADDR')
            email_pass = os.getenv('EMAIL_PASS')
            email_form = os.getenv('EMAIL_FORM')
            email_subj = os.getenv('EMAIL_SUBJ')

            for key, value in job_info.items():
                if key.endswith("time") and value:
                    job_info[key] = datetime.fromtimestamp(value).strftime("%Y-%m-%d %H:%M:%S")

            server = smtplib.SMTP(email_serv, int(email_port))
            # server.starttls()

            server.login(email_addr, email_pass)
            msg = MIMEMultipart("alternative")
            msg["From"] = email_addr
            msg["To"] = job_info['email']
            msg["Subject"] = email_subj.format(**job_info)
            msg["Date"] = formatdate(localtime=True)
            msg["Message-ID"] = make_msgid()

            msg.attach(MIMEText(markdown(email_form.format(**job_info)), 'html'))
            msg.attach(MIMEText(email_form.format(**job_info), 'plain'))

            server.sendmail(email_addr, job_info['email'], msg.as_string())
            server.quit()
            gr.Info('Email notification sent successfully.')
        except Exception as e:
            gr.Warning('Failed to send email notification due to error: ' + str(e))


def check_user_running_job(email, request):
    message = ("You already have a running prediction job (ID: {id}) under this {reason}. "
               "Please wait for it to complete before submitting another job.")
    try:
        # with open('jobs.json', 'r') as f:  # /data/
        #     # Load the JSON data from the file
        #     jobs = json.load(f)
        #
        # for job_id, job_info in jobs.items():
        #     # check if a job is running for the email
        #     if email:
        #         if job_info["email"] == email and job_info["status"] == "running":
        #             return message.format(id=job_id, reason="email")
        #     # check if a job is running for the session
        #     elif request.cookies:
        #         for key, value in job_info["cookies"].items() and job_info["status"] == "running":
        #             if key in request.cookies and request.cookies[key] == value:
        #                 return message.format(id=job_id, reason="session")
        #     # check if a job is running for the IP
        #     else:
        #         if job_info["IP"] == request.client.host and job_info["status"] == "running":
        #             return message.format(id=job_id, reason="IP")
        # check if a job is running for the email
        Job = Query()
        if email:
            job = db.search((Job.email == email) & (Job.status == "RUNNING"))
            if job:
                return message.format(id=job[0]['id'], reason="email")
        # check if a job is running for the session
        elif request.cookies:
            for key, value in request.cookies.items():
                job = db.search((Job.cookies[key] == value) & (Job.status == "RUNNING"))
                if job:
                    return message.format(id=job[0]['id'], reason="session")
        # check if a job is running for the IP
        else:
            job = db.search((Job.IP == request.client.host) & (Job.status == "RUNNING"))
            if job:
                return message.format(id=job[0]['id'], reason="IP")

        return False
    except Exception as e:
        raise gr.Error(f'Failed to validate user running jobs due to error: {str(e)}')


def get_timezone_by_ip(ip):
    try:
        data = session.get(f'http://ip-api.com/json/{ip}').json()
        return data['timezone']
    except Exception:
        return 'UTC'


def ts_to_str(ts, timezone_str):
    if isinstance(ts, str):
        return ts
    local_tz = pytz.timezone(timezone_str)
    dt = datetime.fromtimestamp(ts)
    dt = dt.replace(tzinfo=pytz.utc)  # Set the datetime object to UTC
    localized_dt = dt.astimezone(local_tz)  # Convert the datetime object to the desired timezone
    return localized_dt.strftime('%Y-%m-%d %H:%M:%S (%Z%z)')


def lookup_job(job_id):
    gr.Info('Start querying the job database...')
    stop = False
    while not stop:
        try:
            Job = Query()
            jobs = db.search((Job.id == job_id))
            if jobs:
                job = jobs[0]
                job_status = job['status']
                job_type = job['type']
                error = job['error']
                start_time = ts_to_str(job['start_time'], get_timezone_by_ip(job['ip']))
                if job.get('end_time'):
                    end_time = ts_to_str(job['end_time'], get_timezone_by_ip(job['ip']))
                if job.get('expiry_time'):
                    expiry_time = ts_to_str(job['expiry_time'], get_timezone_by_ip(job['ip']))
                if job_status == "RUNNING":
                    sleep(5)
                    yield {
                        pred_lookup_status: f'''
Your **{job_type}** job (ID: {job_id}) started at 
**{start_time}** and is **RUNNING...**

It might take a few minutes up to a few hours depending on the prediction dataset, the model, and the queue status.
You may keep the page open and wait for the completion, or close the page and revisit later to look up the job status 
using the job id. You will also receive an email notification once the job is done.
''',
                        pred_lookup_btn: gr.Button(visible=False),
                        pred_lookup_stop_btn: gr.Button(visible=True)
                    }
                if job_status == "COMPLETED":
                    stop = True
                    msg = f"Your {job_type} job (ID: {job_id}) has been **COMPLETED**"
                    msg += f" at {end_time}" if job.get('end_time') else ""
                    msg += f" and the results will expire by {expiry_time}." if job.get('expiry_time') else "."
                    msg += f' Redirecting to the report page...'

                    gr.Info(msg)
                    yield {
                        pred_lookup_status: msg,
                        pred_lookup_btn: gr.Button(visible=True),
                        pred_lookup_stop_btn: gr.Button(visible=False),
                        tabs: gr.Tabs(selected='Chemical Property Report'),
                        file_for_report: job['output_file']
                    }
                if job_status == "FAILED":
                    stop = True
                    msg = f'Your {job_type} job (ID: {job_id}) has **FAILED**'
                    msg += f' at {end_time}' if job.get('end_time') else ''
                    msg += f' due to error: {error}.' if job.get('expiry_time') else '.'
                    gr.Info(msg)
                    yield {
                        pred_lookup_status: msg,
                        pred_lookup_btn: gr.Button(visible=True),
                        pred_lookup_stop_btn: gr.Button(visible=False),
                        tabs: gr.Tabs(selected='Prediction Status Lookup'),
                    }
            else:
                stop = True
                msg = f'Job ID {job_id} not found.'
                gr.Info(msg)
                yield {
                    pred_lookup_status: msg,
                    pred_lookup_btn: gr.Button(visible=True),
                    pred_lookup_stop_btn: gr.Button(visible=False),
                    tabs: gr.Tabs(selected='Prediction Status Lookup'),
                }

        except Exception as e:
            raise gr.Error(f'Failed to retrieve job status due to error: {str(e)}')


def submit_predict(predict_filepath, task, preset, target_family, state):
    job_id = state['id']
    status = "RUNNING"
    error = None
    task_file_abbr = {'Compound-Protein Interaction': 'CPI', 'Compound-Protein Binding Affinity': 'CPA'}
    predictions_file = None
    try:
        target_family = TARGET_FAMILY_MAP[target_family]

        predictions_file = f'{SERVER_DATA_DIR}/{job_id}_{task_file_abbr[task]}_{preset}_{target_family}_predictions.csv'

        task = TASK_MAP[task]
        preset = PRESET_MAP[preset]

        prediction_df = pd.DataFrame()
        cfg = hydra.compose(
            config_name="webserver_inference",
            overrides=[f"task={task}",
                       f"preset={preset}",
                       f"ckpt_path=resources/checkpoints/{preset}-{task}-{target_family}.ckpt",
                       f"data.data_file='{str(predict_filepath)}'"])
        # with concurrent.futures.ThreadPoolExecutor() as executor:
        #     future = executor.submit(predict, cfg)
        #     try:
        #         predictions, _ = future.result(timeout=4*60*60)
        #     except concurrent.futures.TimeoutError:
        #         raise gr.Error("Prediction timed out.")
        predictions, _ = predict(cfg)
        predictions = [pd.DataFrame(prediction) for prediction in predictions]
        prediction_df = pd.concat([prediction_df, pd.concat(predictions, ignore_index=True)])
        prediction_df.set_index('N', inplace=True)
        orig_df = pd.read_csv(
            predict_filepath,
            usecols=lambda x: x not in ['X1', 'ID1', 'Compound', 'Scaffold', 'Scaffold SMILES',
                                        'X2', 'ID2',
                                        'Y', 'Y^']
        )
        prediction_df = pd.merge(prediction_df, orig_df, left_index=True, right_index=True, how='left')

        prediction_df.to_csv(predictions_file)
        status = "COMPLETED"

        return {run_state: False}

    except Exception as e:
        gr.Warning(f"Prediction job failed due to error: {str(e)}")
        status = "FAILED"
        predictions_file = None
        error = str(e)
        return {run_state: False}

    finally:
        Job = Query()
        job_query = (Job.id == job_id)

        end_time = time()
        expiry_time = end_time + DB_EXPIRY

        db.update({'end_time': end_time,
                   'expiry_time': expiry_time,
                   'status': status,
                   'error': error,
                   'input_file': predict_filepath,
                   'output_file': predictions_file},
                  job_query)
        if job_info := db.search(job_query)[0]:
            if job_info.get('email'):
                send_email(job_info)


def update_df(file, progress=gr.Progress(track_tqdm=True)):
    if file and Path(file).is_file():
        task = None
        if "_CPI_" in str(file):
            task = 'Compound-Protein Interaction'
        elif "_CPA_" in str(file):
            task = 'Compound-Protein Binding Affinity'

        df = pd.read_csv(file)
        if 'N' in df.columns:
            df.set_index('N', inplace=True)
        if not any(col in ['X1', 'X2'] for col in df.columns):
            gr.Warning("At least one of columns `X1` and `X2` must be in the uploaded dataset.")
            return {analyze_btn: gr.Button(interactive=False)}
        if 'X1' in df.columns:
            df['Scaffold SMILES'] = df['X1'].swifter.progress_bar(
                desc=f"Calculating scaffold...").apply(MurckoScaffold.MurckoScaffoldSmilesFromSmiles)
            df['Scaffold'] = df['Scaffold SMILES'].swifter.progress_bar(
                desc='Generating scaffold graphs...').apply(
                lambda smiles: _MolPlusFingerprint(Chem.MolFromSmiles(smiles)))
            # Add a new column with RDKit molecule objects
            if 'Compound' not in df.columns or df['Compound'].dtype != 'object':
                df['Compound'] = df['X1'].swifter.progress_bar(
                    desc='Generating molecular graphs...').apply(
                    lambda smiles: _MolPlusFingerprint(Chem.MolFromSmiles(smiles)))

        # DF_FOR_REPORT = df.copy()

        # pie_chart = None
        # value = None
        # if 'Y^' in DF_FOR_REPORT.columns:
        #     value = 'Y^'
        # elif 'Y' in DF_FOR_REPORT.columns:
        #     value = 'Y'

        # if value:
        #     if DF_FOR_REPORT['X1'].nunique() > 1 >= DF_FOR_REPORT['X2'].nunique():
        #         pie_chart = create_pie_chart(DF_FOR_REPORT, category='Scaffold SMILES', value=value, top_k=100)
        #     elif DF_FOR_REPORT['X2'].nunique() > 1 >= DF_FOR_REPORT['X1'].nunique():
        #         pie_chart = create_pie_chart(DF_FOR_REPORT, category='Target family', value=value, top_k=100)

        return {html_report: create_html_report(df, file=None, task=task),
                raw_df: df,
                report_df: df.copy(),
                analyze_btn: gr.Button(interactive=True),
                report_task: task}  # pie_chart
    else:
        return {analyze_btn: gr.Button(interactive=False)}


def create_html_report(df, file=None, task=None, progress=gr.Progress(track_tqdm=True)):
    df_html = df.copy(deep=True)
    column_aliases = COLUMN_ALIASES.copy()
    cols_left = list(pd.Index(
        ['ID1', 'Compound', 'Scaffold', 'Scaffold SMILES', 'ID2', 'Y', 'Y^']).intersection(df_html.columns))
    cols_right = list(pd.Index(['X1', 'X2']).intersection(df_html.columns))
    df_html = df_html[cols_left + (df_html.columns.drop(cols_left + cols_right).tolist()) + cols_right]

    if isinstance(task, str):
        column_aliases.update({
            'Y': 'Actual Interaction Probability' if task == 'Compound-Protein Interaction'
            else 'Actual Binding Affinity',
            'Y^': 'Predicted Interaction Probability' if task == 'Compound-Protein Interaction'
            else 'Predicted Binding Affinity'
        })

    ascending = True if column_aliases['Y^'] == 'Predicted Binding Affinity' else False
    df_html = df_html.sort_values(
        [col for col in ['Y', 'Y^'] if col in df_html.columns], ascending=ascending
    )

    if not file:
        df_html = df_html.iloc[:31]

    # Remove repeated info for one-against-N tasks to save visual and physical space
    job = 'Chemical Property'
    unique_entity = 'Unique Entity'
    unique_df = None
    category = None
    columns_unique = None
    if 'X1' in df_html.columns and 'X2' in df_html.columns:
        n_compound = df_html['X1'].nunique()
        n_protein = df_html['X2'].nunique()

        if n_compound == 1 and n_protein >= 2:
            unique_entity = 'Compound of Interest'
            if any(col in df_html.columns for col in ['Y^', 'Y']):
                job = 'Target Protein Identification'
                category = 'Target Family'
            columns_unique = df_html.columns.isin(['X1', 'ID1', 'Scaffold', 'Compound', 'Scaffold SMILES']
                                                  + list(FILTER_MAP.keys()) + list(SCORE_MAP.keys()))

        elif n_compound >= 2 and n_protein == 1:
            unique_entity = 'Target of Interest'
            if any(col in df_html.columns for col in ['Y^', 'Y']):
                job = 'Drug Hit Screening'
                category = 'Scaffold SMILES'
            columns_unique = df_html.columns.isin(['X2', 'ID2'])

        elif 'Y^' in df_html.columns:
            job = 'Interaction Pair Inference'
    if 'Compound' in df_html.columns:
        df_html['Compound'] = df_html['Compound'].swifter.progress_bar(
            desc='Generating compound graph...').apply(
            lambda x: PandasTools.PrintAsImageString(x) if not pd.isna(x) else x)
    if 'Scaffold' in df_html.columns:
        df_html['Scaffold'] = df_html['Scaffold'].swifter.progress_bar(
            desc='Generating scaffold graph...').apply(
            lambda x: PandasTools.PrintAsImageString(x) if not pd.isna(x) else x)

    df_html.rename(columns=column_aliases, inplace=True)
    df_html.index.name = 'Index'
    if 'Target FASTA' in df_html.columns:
        df_html['Target FASTA'] = df_html['Target FASTA'].swifter.progress_bar(
            desc='Processing FASTA...').apply(
            lambda x: wrap_text(x) if not pd.isna(x) else x)

    num_cols = df_html.select_dtypes('number').columns
    num_col_colors = sns.color_palette('husl', len(num_cols))
    bool_cols = df_html.select_dtypes(bool).columns
    bool_col_colors = {True: 'lightgreen', False: 'lightpink'}

    if columns_unique is not None:
        unique_df = df_html.loc[:, columns_unique].iloc[[0]].copy()
        df_html = df_html.loc[:, ~columns_unique]

    if not file:
        if 'Compound ID' in df_html.columns:
            df_html.drop(['Compound SMILES'], axis=1, inplace=True)
        if 'Target ID' in df_html.columns:
            df_html.drop(['Target FASTA'], axis=1, inplace=True)
        if 'Target FASTA' in df_html.columns:
            df_html['Target FASTA'] = df_html['Target FASTA'].swifter.progress_bar(
                desc='Processing FASTA...').apply(
                lambda x: wrap_text(x) if not pd.isna(x) else x)
        if 'Scaffold SMILES' in df_html.columns:
            df_html.drop(['Scaffold SMILES'], axis=1, inplace=True)
        styled_df = df_html.style.format(precision=3)

        for i, col in enumerate(num_cols):
            if col in df_html.columns:
                if col not in ['Predicted Binding Affinity', 'Actual Binding Affinity']:
                    styled_df = styled_df.background_gradient(
                        subset=[col], cmap=sns.light_palette(num_col_colors[i], as_cmap=True))
                else:
                    styled_df = styled_df.background_gradient(
                        subset=[col], cmap=sns.light_palette(num_col_colors[i], as_cmap=True).reversed())

        if any(df_html.columns.isin(bool_cols)):
            styled_df.applymap(lambda val: f'background-color: {bool_col_colors[val]}', subset=bool_cols)

        table_html = styled_df.to_html()
        unique_html = ''
        if unique_df is not None:
            if 'Target FASTA' in unique_df.columns:
                unique_df['Target FASTA'] = unique_df['Target FASTA'].str.replace('\n', '<br>')
            if any(unique_df.columns.isin(bool_cols)):
                unique_df = unique_df.style.applymap(
                    lambda val: f"background-color: {bool_col_colors[val]}", subset=bool_cols)
            unique_html = (f'<div style="font-family: Courier !important;">'
                           f'{unique_df.to_html(escape=False, index=False)}</div>')

        return (f'<div style="font-size: 16px; font-weight: bold;">{job} Report Preview (Top 30 Records)</div>'
                f'<div style="overflow-x:auto; font-family: Courier !important;">{unique_html}</div>'
                f'<div style="overflow:auto; height: 300px; font-family: Courier !important;">{table_html}</div>')

    else:
        bool_formatters = {col: BooleanFormatter() for col in bool_cols}
        float_formatters = {col: NumberFormatter(format='0.000') for col in df_html.select_dtypes('floating').columns}
        other_formatters = {
            'Predicted Interaction Probability': {'type': 'progress', 'max': 1.0, 'legend': True},
            'Actual Interaction Probability': {'type': 'progress', 'max': 1.0, 'legend': True},
            'Compound': HTMLTemplateFormatter(template='<div class="image-zoom-viewer"><%= value %></div>'),
            'Scaffold': HTMLTemplateFormatter(template='<div class="image-zoom-viewer"><%= value %></div>'),
            'Target FASTA': {'type': 'textarea', 'width': 60},
            'Target ID': HTMLTemplateFormatter(
                template='<a href="<% '
                         'if (/^[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}$/.test(value)) '
                         '{ %>https://www.uniprot.org/uniprotkb/<%= value %><% } '
                         'else { %>https://www.uniprot.org/uniprotkb?query=<%= value %><% } '
                         '%>" target="_blank"><%= value %></a>'),
            'Compound ID': HTMLTemplateFormatter(
                template='<a href="https://pubchem.ncbi.nlm.nih.gov/compound/<%= value %>" '
                         'target="_blank"><%= value %></a>')
        }
        formatters = {**bool_formatters, **float_formatters, **other_formatters}

        # html = df.to_html(file)
        # return html

        report_table = pn.widgets.Tabulator(
            df_html, formatters=formatters,
            frozen_columns=['Index', 'Target ID', 'Compound ID', 'Compound', 'Scaffold'],
            disabled=True, sizing_mode='stretch_both', pagination='local', page_size=30)

        for i, col in enumerate(num_cols):
            if col not in ['Predicted Binding Affinity', 'Actual Binding Affinity']:
                if col not in ['Predicted Interaction Probability', 'Actual Interaction Probability']:
                    report_table.style.background_gradient(
                        subset=df_html.columns == col, cmap=sns.light_palette(num_col_colors[i], as_cmap=True))
                else:
                    continue
            else:
                report_table.style.background_gradient(
                    subset=df_html.columns == col, cmap=sns.light_palette(num_col_colors[i], as_cmap=True).reversed())

        pie_charts = {}
        for y in df_html.columns.intersection(['Predicted Interaction Probability', 'Actual Interaction Probability',
                                               'Predicted Binding Affinity', 'Actual Binding Affinity']):
            pie_charts[y] = []
            for k in [10, 30, 100]:
                if k < len(df_html):
                    pie_charts[y].append(create_pie_chart(df_html, category=category, value=y, top_k=k))
            pie_charts[y].append(create_pie_chart(df_html, category=category, value=y, top_k=len(df_html)))

        # Remove keys with empty values
        pie_charts = {k: v for k, v in pie_charts.items() if any(v)}

        pn_css = """
        .tabulator {
            font-family: Courier New !important;
            font-weight: normal !important;
            font-size: 12px !important;
        }
        
        .tabulator-cell {
            overflow: visible !important;
        }
        
        .tabulator-cell:hover {
            z-index: 1000 !important;
        }
        
        .tabulator-cell.tabulator-frozen:hover {
            z-index: 1000 !important;
        }
        
        .image-zoom-viewer {
            display: inline-block;
            overflow: visible; 
            z-index: 1000;
        }
        
        .image-zoom-viewer::after {
            content: "";
            top: 0;
            left: 0;
            width: 100%;
            height: 100%;
            pointer-events: none;
        }
        
        .image-zoom-viewer:hover::after {
            pointer-events: all;
        }
        
        /* When hovering over the container, scale its child (the SVG) */
        .tabulator-cell:hover .image-zoom-viewer svg {
            padding: 3px;
            position: absolute; 
            background-color: rgba(250, 250, 250, 0.854);
            box-shadow: 0 0 10px rgba(0, 0, 0, 0.618);
            border-radius: 3px;
            transform: scale(3); /* Scale up the SVG */
            transition: transform 0.3s ease;
            pointer-events: none; /* Prevents the SVG from blocking mouse interactions */
            z-index: 1000;
        }
        
        .image-zoom-viewer svg {
            display: block; /* SVG is a block-level element for proper scaling */
            z-index: 1000;
        }
        
        .image-zoom-viewer:hover {
            z-index: 1000;
        }
        """

        pn.extension(raw_css=[pn_css])

        template = pn.template.VanillaTemplate(
            title=f'DeepSEQreen {job} Report',
            sidebar=[],
            favicon='deepseqreen.svg',
            logo='deepseqreen.svg',
            header_background='#F3F5F7',
            header_color='#4372c4',
            busy_indicator=None,
        )

        stats_pane = pn.Row()
        if unique_df is not None:
            unique_table = pn.widgets.Tabulator(unique_df, formatters=formatters, sizing_mode='stretch_width',
                                                show_index=False, disabled=True,
                                                frozen_columns=['Compound ID', 'Compound', 'Scaffold'])
            # if pie_charts:
            #     unique_table.width = 640
            stats_pane.append(pn.Column(f'### {unique_entity}', unique_table))
        if pie_charts:
            for score_name, figure_list in pie_charts.items():
                stats_pane.append(
                    pn.Column(f'### {category} by Top {score_name}',
                              pn.Tabs(*figure_list, tabs_location='above'))
                    # pn.Card(pn.Row(v), title=f'{category} by Top {k}')
                )

        if stats_pane:
            template.main.append(pn.Card(stats_pane,
                                         sizing_mode='stretch_width', title='Summary Statistics', margin=10))

        template.main.append(
            pn.Card(report_table, title=f'{job} Results',  # width=1200,
                    margin=10)
        )

        template.save(file, resources=INLINE)
        return file


def create_pie_chart(df, category, value, top_k):
    if category not in df or value not in df:
        return
    top_k_df = df.nlargest(top_k, value)
    category_counts = top_k_df[category].value_counts()
    data = pd.DataFrame({category: category_counts.index, 'value': category_counts.values})

    data['proportion'] = data['value'] / data['value'].sum()
    # Merge rows with proportion less than 0.2% into one row
    mask = data['proportion'] < 0.002
    if any(mask):
        merged_row = data[mask].sum()
        merged_row[category] = '...'
        data = pd.concat([data[~mask], pd.DataFrame(merged_row).T])
    data['angle'] = data['proportion'] * 2 * pi

    color_dict = {cat: color for cat, color in
                  zip(df[category].unique(),
                      (Category20c_20 * (len(df[category].unique()) // 20 + 1))[:len(df[category].unique())])}
    color_dict['...'] = '#636363'
    data['color'] = data[category].map(color_dict)

    tooltips = [
        (f"{category}", f"@{{{category}}}"),
        ("Count", "@value"),
        ("Percentage", "@proportion{0.0%}")
    ]

    if category == 'Scaffold SMILES':
        data = data.merge(top_k_df[['Scaffold SMILES', 'Scaffold']].drop_duplicates(), how='left',
                          left_on='Scaffold SMILES', right_on='Scaffold SMILES')
        tooltips.append(("Scaffold", "<div>@{Scaffold}{safe}</div>"))
    p = figure(height=384, width=960, name=f"Top {top_k}" if top_k < len(df) else 'All', sizing_mode='stretch_height',
               toolbar_location=None, tools="hover", tooltips=tooltips, x_range=(-0.4, 0.4))

    def truncate_label(label, max_length=60):
        return label if len(label) <= max_length else label[:max_length] + "..."

    data['legend_field'] = data[category].apply(truncate_label)

    p.add_layout(Legend(padding=0, margin=0), 'right')
    p.wedge(x=0, y=1, radius=0.3,
            start_angle=cumsum('angle', include_zero=True), end_angle=cumsum('angle'),
            line_color="white", fill_color='color', legend_field='legend_field', source=data)

    # Limit the number of legend items to 20 and add "..." if there are more than 20 items
    if len(p.legend.items) > 20:
        new_legend_items = p.legend.items[:20]
        new_legend_items.append(LegendItem(label="..."))
        p.legend.items = new_legend_items

    p.legend.label_text_font_size = "10pt"
    p.legend.label_text_font = "courier"
    p.axis.axis_label = None
    p.axis.visible = False
    p.grid.grid_line_color = None
    p.outline_line_width = 0
    p.min_border = 0
    p.margin = 0

    return p


def submit_report(df, score_list, filter_list, task, progress=gr.Progress(track_tqdm=True)):
    df_report = df.copy()
    try:
        for filter_name in filter_list:
            df_report[filter_name] = df_report['Compound'].swifter.progress_bar(
                desc=f"Calculating {filter_name}").apply(
                lambda x: FILTER_MAP[filter_name](x) if not pd.isna(x) else x)

        for score_name in score_list:
            df_report[score_name] = df_report['Compound'].swifter.progress_bar(
                desc=f"Calculating {score_name}").apply(
                lambda x: SCORE_MAP[score_name](x) if not pd.isna(x) else x)

        # pie_chart = None
        # value = None
        # if 'Y^' in df.columns:
        #     value = 'Y^'
        # elif 'Y' in df.columns:
        #     value = 'Y'
        #
        # if value:
        #     if df['X1'].nunique() > 1 >= df['X2'].nunique():
        #         pie_chart = create_pie_chart(df, category='Scaffold SMILES', value=value, top_k=100)
        #     elif df['X2'].nunique() > 1 >= df['X1'].nunique():
        #         pie_chart = create_pie_chart(df, category='Target family', value=value, top_k=100)

        return (create_html_report(df_report, file=None, task=task), df_report,
                gr.File(visible=False), gr.File(visible=False))

    except Exception as e:
        gr.Warning(f'Failed to report results due to error: {str(e)}')
        return None, None, None, None


def wrap_text(text, line_length=60):
    if isinstance(text, str):
        wrapper = textwrap.TextWrapper(width=line_length)
        if text.startswith('>'):
            sections = text.split('>')
            wrapped_sections = []
            for section in sections:
                if not section:
                    continue
                lines = section.split('\n')
                seq_header = lines[0]
                wrapped_seq = wrapper.fill(''.join(lines[1:]))
                wrapped_sections.append(f">{seq_header}\n{wrapped_seq}")
            return '\n'.join(wrapped_sections)
        else:
            return wrapper.fill(text)
    else:
        return text


def unwrap_text(text):
    return text.strip.replece('\n', '')


def drug_library_from_sdf(sdf_path):
    return PandasTools.LoadSDF(
        sdf_path,
        smilesName='X1', molColName='Compound', includeFingerprints=True
    )


def process_target_library_upload(library_upload):
    if library_upload.endswith('.csv'):
        df = pd.read_csv(library_upload)
    elif library_upload.endswith('.fasta'):
        df = target_library_from_fasta(library_upload)
    else:
        raise gr.Error('Currently only CSV and FASTA files are supported as target libraries.')
    validate_columns(df, ['X2'])
    return df


def process_drug_library_upload(library_upload):
    if library_upload.endswith('.csv'):
        df = pd.read_csv(library_upload)
    elif library_upload.endswith('.sdf'):
        df = drug_library_from_sdf(library_upload)
    else:
        raise gr.Error('Currently only CSV and SDF files are supported as drug libraries.')
    validate_columns(df, ['X1'])
    return df


def target_library_from_fasta(fasta_path):
    records = list(SeqIO.parse(fasta_path, "fasta"))
    id2 = [record.id for record in records]
    seq = [str(record.seq) for record in records]
    df = pd.DataFrame({'ID2': id2, 'X2': seq})
    return df


theme = gr.themes.Base(spacing_size="sm", text_size='md', font=gr.themes.GoogleFont("Roboto")).set(
    background_fill_primary='#eef3f9',
    background_fill_secondary='white',
    checkbox_label_background_fill='#eef3f9',
    checkbox_label_background_fill_hover='#dfe6f0',
    checkbox_background_color='white',
    checkbox_border_color='#4372c4',
    border_color_primary='#4372c4',
    border_color_accent='#2e6ab5',
    button_primary_background_fill='#2e6ab4',
    button_primary_text_color='white',
    body_text_color='#28496F',
    block_background_fill='#fbfcfd',
    block_title_text_color='#28496F',
    block_label_text_color='#28496F',
    block_info_text_color='#505358',
    block_border_color=None,
    # input_border_color='#4372c4',
    # panel_border_color='#4372c4',
    input_background_fill='#F1F2F4',
)

with gr.Blocks(theme=theme, title='DeepSEQreen', css=CSS, delete_cache=(3600, 48 * 3600)) as demo:
    run_state = gr.State(value=False)
    screen_flag = gr.State(value=False)
    identify_flag = gr.State(value=False)
    infer_flag = gr.State(value=False)

    with gr.Tabs() as tabs:
        with gr.TabItem(label='Drug Hit Screening', id='Drug Hit Screening'):
            gr.Markdown('''
            # <center>Drug Hit Screening</center>
            
            <center>
            To predict interactions or binding affinities of a single target against a compound library.
            </center>
            ''')
            with gr.Row():
                with gr.Column():
                    HelpTip(
                        "Enter (paste) a amino acid sequence below manually or upload a FASTA file. "
                        "If multiple entities are in the FASTA, only the first will be used. "
                        "Alternatively, enter a Uniprot ID or gene symbol with organism and click Query for "
                        "the sequence."
                    )
                    target_input_type = gr.Dropdown(
                        label='Step 1. Select Target Input Type and Input',
                        choices=['Sequence', 'UniProt ID', 'Gene symbol'],
                        info='Enter (paste) a FASTA string below manually or upload a FASTA file.',
                        value='Sequence',
                        scale=4, interactive=True
                    )

            with gr.Row():
                target_id = gr.Textbox(show_label=False, visible=False,
                                       interactive=True, scale=4,
                                       info='Enter a UniProt ID and query.')
                target_gene = gr.Textbox(
                    show_label=False, visible=False,
                    interactive=True, scale=4,
                    info='Enter a gene symbol and query. The first record is used by default.')
                target_organism = gr.Textbox(
                    info='Organism scientific name (default: Homo sapiens).',
                    placeholder='Homo sapiens', show_label=False,
                    visible=False, interactive=True, scale=4, )
                target_upload_btn = gr.UploadButton(label='Upload a FASTA File', type='binary',
                                                    visible=True, variant='primary',
                                                    size='lg')
                target_paste_markdown = gr.Button(value='OR Paste Your Sequence Below',
                                                  variant='secondary')
                target_query_btn = gr.Button(value='Query the Sequence', variant='primary',
                                             visible=False, scale=4)
            # with gr.Row():
            #     example_uniprot = gr.Button(value='Example: Q16539', elem_classes='example', visible=False)
            #     example_gene = gr.Button(value='Example: MAPK14', elem_classes='example', visible=False)
            example_fasta = gr.Button(value='Example: MAPK14 (Q16539)', elem_classes='example')
            target_fasta = gr.Code(label='Input or Display FASTA', interactive=True, lines=5)
            # with gr.Row():
            #     with gr.Column():
            # with gr.Column():
            #     gr.File(label='Example FASTA file',
            #             value='data/examples/MAPK14.fasta', interactive=False)

            with gr.Row():
                with gr.Column(min_width=200):
                    HelpTip(
                        "Click Auto-detect to identify the protein family using sequence alignment. "
                        "This optional step allows applying a family-specific model instead of a all-family "
                        "model (general). "
                        "Manually select general if the alignment results are unsatisfactory."
                    )
                    drug_screen_target_family = gr.Dropdown(
                        choices=list(TARGET_FAMILY_MAP.keys()),
                        value='General',
                        label='Step 2. Select Target Family (Optional)', interactive=True)
                    target_family_detect_btn = gr.Button(value='OR Let Us Auto-Detect for You',
                                                         variant='primary')
                with gr.Column(min_width=200):
                    HelpTip(
                        "Interaction prediction provides you binding probability score between the target of "
                        "interest and each compound in the library, "
                        "while affinity prediction directly estimates their binding strength measured using "
                        "IC50."
                    )
                    drug_screen_task = gr.Dropdown(
                        list(TASK_MAP.keys()),
                        label='Step 3. Select a Prediction Task',
                        value='Compound-Protein Interaction')
                with gr.Column(min_width=200):
                    HelpTip(
                        "Select your preferred model, or click Recommend for the best-performing model based "
                        "on the selected task, family, and whether the target was trained. "
                        "Please refer to documentation for detailed benchmark results."
                    )
                    drug_screen_preset = gr.Dropdown(
                        list(PRESET_MAP.keys()),
                        label='Step 4. Select a Preset Model')
                    screen_preset_recommend_btn = gr.Button(
                        value='OR Let Us Recommend for You', variant='primary')

            with gr.Row():
                with gr.Column():
                    HelpTip(
                        "Select a preset compound library (e.g., DrugBank). "
                        "Alternatively, upload a CSV file with a column named X1 containing compound SMILES, "
                        "or use an SDF file (Max. 10,000 compounds per task). Example CSV and SDF files are "
                        "provided below and can be downloaded by clicking the lower right corner."
                    )
                    drug_library = gr.Dropdown(
                        label='Step 5. Select a Preset Compound Library',
                        choices=list(DRUG_LIBRARY_MAP.keys()))
                    with gr.Row():
                        gr.File(label='Example SDF compound library',
                                value='data/examples/compound_library.sdf', interactive=False)
                        gr.File(label='Example CSV compound library',
                                value='data/examples/compound_library.csv', interactive=False)
                    drug_library_upload_btn = gr.UploadButton(
                        label='OR Upload Your Own Library', variant='primary')
                    drug_library_upload = gr.File(label='Custom compound library file', visible=False)
            with gr.Row():
                with gr.Column():
                    drug_screen_email = gr.Textbox(
                        label='Step 6. Input Your Email Address (Optional)',
                        info="Your email address will be used to notify you of the status of your job. "
                             "If you cannot receive the email, please check your spam/junk folder."
                    )

            with gr.Row(visible=True):
                with gr.Column():
                    # drug_screen_clr_btn = gr.ClearButton(size='lg')
                    drug_screen_btn = gr.Button(value='SUBMIT THE SCREENING JOB', variant='primary', size='lg')
            # TODO Modify the pd df directly with df['X2'] = target

        screen_data_for_predict = gr.File(visible=False, file_count="single", type='filepath')

        with gr.TabItem(label='Target Protein Identification', id='Target Protein Identification'):
            gr.Markdown('''
            # <center>Target Protein Identification</center>
            
            <center>
            To predict interactions or binding affinities of a single compound against a protein library.
            </center>
            ''')
            with gr.Column() as identify_page:
                with gr.Row():
                    with gr.Column():
                        HelpTip(
                            "Enter (paste) a compound SMILES below manually or upload a SDF file. "
                            "If multiple entities are in the SDF, only the first will be used. "
                            "SMILES can be obtained by searching for the compound of interest in databases such "
                            "as NCBI, PubChem and and ChEMBL."
                        )
                        compound_type = gr.Dropdown(
                            label='Step 1. Select Compound Input Type and Input',
                            choices=['SMILES', 'SDF'],
                            info='Enter (paste) an SMILES string or upload an SDF file to convert to SMILES.',
                            value='SMILES',
                            interactive=True)
                        compound_upload_btn = gr.UploadButton(
                            label='OR Upload a SDF File', variant='primary', type='binary', visible=False)

                compound_smiles = gr.Code(label='Input or Display Compound SMILES', interactive=True, lines=5)
                example_drug = gr.Button(value='Example: Aspirin', elem_classes='example')

                with gr.Row():
                    with gr.Column(visible=False):
                        HelpTip(
                            "By default, models trained on all protein families (general) will be applied. "
                            # "If the proteins in the target library of interest all belong to the same protein "
                            # "family, manually selecting the family is supported."
                        )
                        target_identify_target_family = gr.Dropdown(
                            choices=['General'], value='General',
                            label='Target Family')

                with gr.Row():
                    with gr.Column():
                        HelpTip(
                            "Interaction prediction provides you binding probability score between the target of "
                            "interest and each compound in the library, while affinity prediction directly "
                            "estimates their binding strength measured using IC50."
                        )
                        target_identify_task = gr.Dropdown(
                            list(TASK_MAP.keys()),
                            label='Step 2. Select a Prediction Task',
                            value='Compound-Protein Interaction')

                    with gr.Column():
                        HelpTip(
                            "Select your preferred model, or click Recommend for the best-performing model based "
                            "on the selected task and whether the compound was trained. By default, General-trained "
                            "model is used for Target Protein Identification. "
                            "Please refer to the documentation for detailed benchmark results."
                        )
                        target_identify_preset = gr.Dropdown(
                            list(PRESET_MAP.keys()),
                            label='Step 3. Select a Preset Model')
                        identify_preset_recommend_btn = gr.Button(value='OR Let Us Recommend for You',
                                                                  variant='primary')
                with gr.Row():
                    with gr.Column():
                        HelpTip(
                            "Select a preset target library (e.g., ChEMBL33_human_proteins). "
                            "Alternatively, upload a CSV file with a column named X2 containing target protein "
                            "sequences, or use an FASTA file (Max. 10,000 targets per task). "
                            "Example CSV and SDF files are provided below "
                            "and can be downloaded by clicking the lower right corner."
                        )
                        target_library = gr.Dropdown(
                            label='Step 4. Select a Preset Target Library',
                            choices=list(TARGET_LIBRARY_MAP.keys()))
                        with gr.Row():
                            gr.File(label='Example FASTA target library',
                                    value='data/examples/target_library.fasta', interactive=False)
                            gr.File(label='Example CSV target library',
                                    value='data/examples/target_library.csv', interactive=False)
                        target_library_upload_btn = gr.UploadButton(
                            label='OR Upload Your Own Library', variant='primary')
                        target_library_upload = gr.File(label='Custom target library file', visible=False)

                with gr.Row():
                    with gr.Column():
                        target_identify_email = gr.Textbox(
                            label='Step 5. Input Your Email Address (Optional)',
                            info="Your email address will be used to notify you of the status of your job. "
                                 "If you cannot receive the email, please check your spam/junk folder."
                        )

                with gr.Row(visible=True):
                    # target_identify_clr_btn = gr.ClearButton(size='lg')
                    target_identify_btn = gr.Button(value='SUBMIT THE IDENTIFICATION JOB', variant='primary',
                                                    size='lg')

            identify_data_for_predict = gr.File(visible=False, file_count="single", type='filepath')

        with gr.TabItem(label='Interaction Pair Inference', id='Interaction Pair Inference'):
            gr.Markdown('''
            # <center>Interaction Pair Inference</center>
            
            <center>To predict interactions or binding affinities between up to 
            10,000 paired compound-protein data.</center>
            ''')
            HelpTip(
                "A custom interation pair dataset can be a CSV file with 2 required columns "
                "(X1 for smiles and X2 for sequences) "
                "and optionally 2 ID columns (ID1 for compound ID and ID2 for target ID), "
                "or generated from a FASTA file containing multiple "
                "sequences and a SDF file containing multiple compounds. "
                "Currently, a maximum of 10,000 pairs is supported, "
                "which means that the size of CSV file or "
                "the product of the two library sizes should not exceed 10,000."
            )
            infer_type = gr.Dropdown(
                choices=['Upload a CSV file containing paired compound-protein data',
                         'Upload a compound library and a target library'],
                label='Step 1. Select Pair Input Type and Input',
                value='Upload a CSV file containing paired compound-protein data')
            with gr.Column() as pair_upload:
                gr.File(label="Example CSV dataset",
                        value="data/examples/interaction_pair_inference.csv",
                        interactive=False)
                with gr.Row():
                    infer_csv_prompt = gr.Button(
                        value="Upload Your Own Dataset Below",
                        variant='secondary')
                with gr.Column():
                    infer_pair = gr.File(
                        label='Upload CSV File Containing Paired Records',
                        file_count="single", type='filepath', visible=True)
            with gr.Column(visible=False) as pair_generate:
                with gr.Row():
                    gr.File(label='Example SDF compound library',
                            value='data/examples/compound_library.sdf', interactive=False)
                    gr.File(label='Example FASTA target library',
                            value='data/examples/target_library.fasta', interactive=False)
                with gr.Row():
                    gr.File(label='Example CSV compound library',
                            value='data/examples/compound_library.csv', interactive=False)
                    gr.File(label='Example CSV target library',
                            value='data/examples/target_library.csv', interactive=False)
                with gr.Row():
                    infer_library_prompt = gr.Button(
                        value="Upload Your Own Libraries Below",
                        visible=False, variant='secondary')
                with gr.Row():
                    infer_drug = gr.File(label='Upload SDF/CSV File Containing Multiple Compounds',
                                         file_count="single", type='filepath')
                    infer_target = gr.File(label='Upload FASTA/CSV File Containing Multiple Targets',
                                           file_count="single", type='filepath')

            with gr.Row():
                with gr.Column(min_width=200):
                    HelpTip(
                        "By default, models trained on all protein families (general) will be applied. "
                        "If the proteins in the target library of interest "
                        "all belong to the same protein family, manually selecting the family is supported."
                    )
                    pair_infer_target_family = gr.Dropdown(
                        choices=list(TARGET_FAMILY_MAP.keys()),
                        value='General',
                        label='Step 2. Select Target Family (Optional)')

                with gr.Column(min_width=200):
                    HelpTip(
                        "Interaction prediction provides you binding probability score "
                        "between the target of interest and each compound in the library, "
                        "while affinity prediction directly estimates their binding strength "
                        "measured using IC50."
                    )
                    pair_infer_task = gr.Dropdown(
                        list(TASK_MAP.keys()),
                        label='Step 3. Select a Prediction Task',
                        value='Compound-Protein Interaction')

                with gr.Column(min_width=200):
                    HelpTip("Select your preferred model. "
                            "Please refer to documentation for detailed benchmark results."
                            )
                    pair_infer_preset = gr.Dropdown(
                        list(PRESET_MAP.keys()),
                        label='Step 4. Select a Preset Model')
                    # infer_preset_recommend_btn = gr.Button(value='OR Let Us Recommend for You',
                    #                                        variant='primary')

            with gr.Row():
                pair_infer_email = gr.Textbox(
                    label='Step 5. Input Your Email Address (Optional)',
                    info="Your email address will be used to notify you of the status of your job. "
                         "If you cannot receive the email, please check your spam/junk folder.")

            with gr.Row(visible=True):
                # pair_infer_clr_btn = gr.ClearButton(size='lg')
                pair_infer_btn = gr.Button(value='SUBMIT THE INFERENCE JOB', variant='primary', size='lg')

            infer_data_for_predict = gr.File(file_count="single", type='filepath', visible=False)

        with gr.TabItem(label='Chemical Property Report', id='Chemical Property Report'):
            gr.Markdown('''
            # <center>Chemical Property Report</center>
      
            To compute chemical properties for the predictions of Drug Hit Screening, 
            Target Protein Identification, and Interaction Pair Inference. 
            
            You may also upload your own dataset using a CSV file containing 
            one required column `X1` for compound SMILES. 
            
            The page shows only a preview report displaying at most 30 records 
            (with top predicted CPI/CPA if reporting results from a prediction job). 
            
            Please first `Preview` the report, then `Generate` and download a CSV report 
            or an interactive HTML report below if you wish to access the full report.
            ''')
            with gr.Row():
                with gr.Column():
                    file_for_report = gr.File(interactive=True, type='filepath')
                    report_task = gr.Dropdown(list(TASK_MAP.keys()), visible=False, value=None,
                                              label='Specify the Task Labels in the Upload Dataset')
                raw_df = gr.State(value=pd.DataFrame())
                report_df = gr.State(value=pd.DataFrame())
                scores = gr.CheckboxGroup(list(SCORE_MAP.keys()), label='Scores')
                filters = gr.CheckboxGroup(list(FILTER_MAP.keys()), label='Filters')

            with gr.Row():
                # clear_btn = gr.ClearButton(size='lg')
                analyze_btn = gr.Button('Preview Top 30 Records', variant='primary', size='lg',
                                        interactive=False)

            with gr.Row():
                with gr.Column(scale=3):
                    html_report = gr.HTML()  # label='Results', visible=True)
                ranking_pie_chart = gr.Plot(visible=False)

            with gr.Row():
                with gr.Column():
                    csv_generate = gr.Button(value='Generate CSV Report',
                                             interactive=False, variant='primary')
                    csv_download_file = gr.File(label='Download CSV Report', visible=False)
                with gr.Column():
                    html_generate = gr.Button(value='Generate HTML Report',
                                              interactive=False, variant='primary')
                    html_download_file = gr.File(label='Download HTML Report', visible=False)

        with gr.TabItem(label='Prediction Status Lookup', id='Prediction Status Lookup'):
            gr.Markdown('''
            # <center>Prediction Status Lookup</center>
            
            To check the status of an in-progress or historical job using the job ID and retrieve the predictions 
            if the job has completed. Note that predictions are only kept for 48 hours upon job completion.
            
            You will be redirected to Chemical Property Report for carrying out further analysis and 
            generating the full report if the job is done. If the Lookup fails to respond, please come back 
            in five minutes, refresh the page, and try again. 
            ''')
            with gr.Column():
                pred_lookup_id = gr.Textbox(
                    label='Input Your Job ID', placeholder='e.g., e9dfd149-3f5c-48a6-b797-c27d027611ac',
                    info="Your job ID is a UUID4 string that you receive after submitting a job on the "
                         "page or in the email notification.")
                pred_lookup_btn = gr.Button(value='Lookup the Job Status', variant='primary', visible=True)
                pred_lookup_stop_btn = gr.Button(value='Stop Tracking', variant='stop', visible=False)
                pred_lookup_status = gr.Markdown()

                # retrieve_email = gr.Textbox(label='Step 2. Input Your Email Address', placeholder='e.g.,


    def target_input_type_select(input_type):
        match input_type:
            case 'UniProt ID':
                return [gr.Dropdown(info=''),
                        gr.UploadButton(visible=False),
                        gr.Textbox(visible=True, value=''),
                        gr.Textbox(visible=False, value=''),
                        gr.Textbox(visible=False, value=''),
                        gr.Button(visible=True),
                        gr.Code(value=''),
                        gr.Button(visible=False)]
            case 'Gene symbol':
                return [gr.Dropdown(info=''),
                        gr.UploadButton(visible=False),
                        gr.Textbox(visible=False, value=''),
                        gr.Textbox(visible=True, value=''),
                        gr.Textbox(visible=True, value=''),
                        gr.Button(visible=True),
                        gr.Code(value=''),
                        gr.Button(visible=False)]
            case 'Sequence':
                return [gr.Dropdown(info='Enter (paste) a FASTA string below manually or upload a FASTA file.'),
                        gr.UploadButton(visible=True),
                        gr.Textbox(visible=False, value=''),
                        gr.Textbox(visible=False, value=''),
                        gr.Textbox(visible=False, value=''),
                        gr.Button(visible=False),
                        gr.Code(value=''),
                        gr.Button(visible=True)]


    target_input_type.select(
        fn=target_input_type_select,
        inputs=target_input_type,
        outputs=[
            target_input_type, target_upload_btn,
            target_id, target_gene, target_organism, target_query_btn,
            target_fasta, target_paste_markdown
        ],
        show_progress='hidden'
    )


    def uniprot_query(input_type, uid, gene, organism='Human'):
        uniprot_endpoint = 'https://rest.uniprot.org/uniprotkb/{query}'
        fasta_rec = ''

        match input_type:
            case 'UniProt ID':
                query = f"{uid.strip()}.fasta"
            case 'Gene symbol':
                organism = organism if organism else 'Human'
                query = f'search?query=organism_name:{organism.strip()}+AND+gene:{gene.strip()}&format=fasta'

        try:
            fasta = session.get(uniprot_endpoint.format(query=query))
            fasta.raise_for_status()
            if fasta.text:
                fasta_rec = next(SeqIO.parse(io.StringIO(fasta.text), format='fasta'))
                fasta_rec = f">{fasta_rec.description}\n{fasta_rec.seq}"

        except Exception as e:
            raise gr.Warning(f"Failed to query FASTA from UniProt database due to {str(e)}")
        finally:
            return fasta_rec


    def process_fasta_upload(fasta_upload):
        fasta = ''
        try:
            fasta = fasta_upload.decode()
        except Exception as e:
            gr.Warning(f"Please upload a valid FASTA file. Error: {str(e)}")
            return fasta


    target_upload_btn.upload(fn=process_fasta_upload, inputs=target_upload_btn, outputs=target_fasta)
    target_query_btn.click(uniprot_query,
                           inputs=[target_input_type, target_id, target_gene, target_organism],
                           outputs=target_fasta)


    def target_family_detect(fasta, progress=gr.Progress(track_tqdm=True)):
        try:
            aligner = PairwiseAligner(scoring='blastp', mode='local')
            alignment_df = pd.read_csv('data/target_libraries/ChEMBL33_all_spe_single_prot_info.csv')

            def align_score(query):
                return aligner.align(process_target_fasta(fasta), query).score

            alignment_df['score'] = alignment_df['X2'].swifter.progress_bar(
                desc="Detecting protein family of the target...").apply(align_score)
            row = alignment_df.loc[alignment_df['score'].idxmax()]
            return gr.Dropdown(value=row['protein_family'].capitalize(),
                               info=f"Reason: Best BLASTP score ({row['score']}) "
                                    f"with {row['ID2']} from family {row['protein_family']}")
        except Exception as e:
            gr.Warning("Failed to detect the protein family due to error: " + str(e))


    target_family_detect_btn.click(fn=target_family_detect, inputs=target_fasta, outputs=drug_screen_target_family)

    # target_fasta.focus(fn=wrap_text, inputs=target_fasta, outputs=target_fasta, show_progress='hidden')
    target_fasta.blur(fn=wrap_text, inputs=target_fasta, outputs=target_fasta, show_progress='hidden')

    drug_library_upload_btn.upload(fn=lambda x: [
        x.name, gr.Dropdown(value=Path(x.name).name, choices=list(DRUG_LIBRARY_MAP.keys()) + [Path(x.name).name])
    ], inputs=drug_library_upload_btn, outputs=[drug_library_upload, drug_library])


    def example_fill(input_type):
        return {target_id: 'Q16539',
                target_gene: 'MAPK14',
                target_organism: 'Human',
                target_fasta: """
>sp|Q16539|MK14_HUMAN Mitogen-activated protein kinase 14 OS=Homo sapiens OX=9606 GN=MAPK14 PE=1 SV=3
MSQERPTFYRQELNKTIWEVPERYQNLSPVGSGAYGSVCAAFDTKTGLRVAVKKLSRPFQ
SIIHAKRTYRELRLLKHMKHENVIGLLDVFTPARSLEEFNDVYLVTHLMGADLNNIVKCQ
KLTDDHVQFLIYQILRGLKYIHSADIIHRDLKPSNLAVNEDCELKILDFGLARHTDDEMT
GYVATRWYRAPEIMLNWMHYNQTVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILRLVG
TPGAELLKKISSESARNYIQSLTQMPKMNFANVFIGANPLAVDLLEKMLVLDSDKRITAA
QALAHAYFAQYHDPDDEPVADPYDQSFESRDLLIDEWKSLTYDEVISFVPPPLDQEEMES
"""}


    example_fasta.click(fn=example_fill, inputs=target_input_type, outputs=[
        target_id, target_gene, target_organism, target_fasta], show_progress='hidden')


    def screen_recommend_model(fasta, family, task):
        task = TASK_MAP[task]
        score = TASK_METRIC_MAP[task]
        benchmark_df = pd.read_csv(f'data/benchmarks/{task}_test_metrics.csv')

        if not fasta:
            gr.Warning('Please enter a valid FASTA for model recommendation.')
            return [None, family]

        if family == 'General':
            seen_targets = pd.read_csv(
                f'data/benchmarks/seen_targets/all_families_full_{task.lower()}_random_split.csv')
            if process_target_fasta(fasta) in seen_targets['X2'].values:
                scenario = "Seen Target"
            else:
                scenario = "Unseen Target"
            filtered_df = benchmark_df[(benchmark_df['Family'] == 'All Families')
                                       & (benchmark_df['Scenario'] == scenario)
                                       & (benchmark_df['Type'] == 'General')]

        else:
            seen_targets_general = pd.read_csv(
                f'data/benchmarks/seen_targets/all_families_full_{task.lower()}_random_split.csv')
            if process_target_fasta(fasta) in seen_targets_general['X2'].values:
                scenario_general = "Seen Target"
            else:
                scenario_general = "Unseen Target"

            seen_targets_family = pd.read_csv(
                f'data/benchmarks/seen_targets/{TARGET_FAMILY_MAP[family]}_{task.lower()}_random_split.csv')
            if process_target_fasta(fasta) in seen_targets_family['X2'].values:
                scenario_family = "Seen Target"
            else:
                scenario_family = "Unseen Target"

            filtered_df_general = benchmark_df[(benchmark_df['Family'] == family)
                                               & (benchmark_df['Scenario'] == scenario_general)
                                               & (benchmark_df['Type'] == 'General')]
            filtered_df_family = benchmark_df[(benchmark_df['Family'] == family)
                                              & (benchmark_df['Scenario'] == scenario_family)
                                              & (benchmark_df['Type'] == 'Family')]
            filtered_df = pd.concat([filtered_df_general, filtered_df_family])

        row = filtered_df.loc[filtered_df[score].idxmax()]

        return {drug_screen_preset:
                    gr.Dropdown(value=row['Model'],
                                info=f"Reason: {row['Scenario']} in training; we recommend the {row['Type']}-trained "
                                     f"model with the best {score} ({float(row[score]):.3f}) "
                                     f"in the {row['Scenario']} scenario on {row['Family']}."),
                drug_screen_target_family:
                    gr.Dropdown(value='General') if row['Type'] == 'General' else gr.Dropdown(value=family)}


    screen_preset_recommend_btn.click(fn=screen_recommend_model,
                                      inputs=[target_fasta, drug_screen_target_family, drug_screen_task],
                                      outputs=[drug_screen_preset, drug_screen_target_family], show_progress='hidden')


    def compound_input_type_select(input_type):
        match input_type:
            case 'SMILES':
                return gr.Button(visible=False)
            case 'SDF':
                return gr.Button(visible=True)


    compound_type.select(fn=compound_input_type_select,
                         inputs=compound_type, outputs=compound_upload_btn, show_progress='hidden')


    def compound_upload_process(input_type, input_upload):
        smiles = ''
        try:
            match input_type:
                case 'SMILES':
                    smiles = input_upload.decode()
                case 'SDF':
                    suppl = Chem.ForwardSDMolSupplier(io.BytesIO(input_upload))
                    smiles = Chem.MolToSmiles(next(suppl))
        except Exception as e:
            gr.Warning(f"Please upload a valid {input_type} file. Error: {str(e)}")
        return smiles


    compound_upload_btn.upload(fn=compound_upload_process,
                               inputs=[compound_type, compound_upload_btn],
                               outputs=compound_smiles)

    example_drug.click(fn=lambda: 'CC(=O)Oc1ccccc1C(=O)O', outputs=compound_smiles, show_progress='hidden')

    target_library_upload_btn.upload(fn=lambda x: [
        x.name, gr.Dropdown(value=Path(x.name).name, choices=list(TARGET_LIBRARY_MAP.keys()) + [Path(x.name).name])
    ], inputs=target_library_upload_btn, outputs=[target_library_upload, target_library])


    def identify_recommend_model(smiles, task):
        task = TASK_MAP[task]
        score = TASK_METRIC_MAP[task]
        benchmark_df = pd.read_csv(f'data/benchmarks/{task}_test_metrics.csv')

        if not smiles:
            gr.Warning('Please enter a valid SMILES for model recommendation.')
            return None

        seen_drugs = pd.read_csv(
            f'data/benchmarks/seen_drugs/all_families_full_{task.lower()}_random_split.csv')
        if rdkit_canonicalize(smiles) in seen_drugs['X1'].values:
            scenario = "Seen Compound"
        else:
            scenario = "Unseen Compound"

        filtered_df = benchmark_df[(benchmark_df['Family'] == 'All Families')
                                   & (benchmark_df['Scenario'] == scenario)
                                   & (benchmark_df['Type'] == 'General')]

        row = filtered_df.loc[filtered_df[score].idxmax()]

        return gr.Dropdown(value=row['Model'],
                           info=f"Reason: {scenario} in training; choosing the model "
                                f"with the best {score} ({float(row[score]):3f}) "
                                f"in the {scenario} scenario.")


    identify_preset_recommend_btn.click(fn=identify_recommend_model,
                                        inputs=[compound_smiles, target_identify_task],
                                        outputs=target_identify_preset, show_progress='hidden')


    def infer_type_change(upload_type):
        match upload_type:
            case "Upload a compound library and a target library":
                return {
                    pair_upload: gr.Column(visible=False),
                    pair_generate: gr.Column(visible=True),
                    infer_pair: None,
                    infer_drug: None,
                    infer_target: None,
                    infer_csv_prompt: gr.Button(visible=False),
                    infer_library_prompt: gr.Button(visible=True),
                }
        match upload_type:
            case "Upload a CSV file containing paired compound-protein data":
                return {
                    pair_upload: gr.Column(visible=True),
                    pair_generate: gr.Column(visible=False),
                    infer_pair: None,
                    infer_drug: None,
                    infer_target: None,
                    infer_csv_prompt: gr.Button(visible=True),
                    infer_library_prompt: gr.Button(visible=False),
                }


    infer_type.select(fn=infer_type_change, inputs=infer_type,
                      outputs=[pair_upload, pair_generate, infer_pair, infer_drug, infer_target,
                               infer_csv_prompt, infer_library_prompt],
                      show_progress='hidden')


    def common_input_validate(state, preset, email, request):
        gr.Info('Start processing inputs...')
        if not preset:
            raise gr.Error('Please select a model.')

        if email:
            try:
                email_info = validate_email(email, check_deliverability=False)
                email = email_info.normalized
            except EmailNotValidError as e:
                raise gr.Error(f"Invalid email address: {str(e)}.")

        if state:
            raise gr.Error(f"You already have a running prediction job (ID: {state['id']}) under this session. "
                           "Please wait for it to complete before submitting another job.")

        if check := check_user_running_job(email, request):
            raise gr.Error(check)

        return state, preset, email


    def common_job_initiate(job_id, job_type, email, request, task):
        gr.Info('Finished processing inputs. Initiating the prediction job... '
                'You will be redirected to Prediction Status Lookup after the job is submitted.')
        job_info = {'id': job_id,
                    'type': job_type,
                    'task': task,
                    'status': 'RUNNING',
                    'email': email,
                    'ip': str(request.client.host),
                    'cookies': dict(request.cookies),
                    'start_time': time(),
                    'end_time': None,
                    'expiry_time': None,
                    'error': None}
        db.insert(job_info)
        return job_info


    def drug_screen_validate(fasta, library, library_upload, preset, task, email, state,
                             request: gr.Request, progress=gr.Progress(track_tqdm=True)):
        state, preset, email = common_input_validate(state, preset, email, request)

        fasta = process_target_fasta(fasta)
        err = validate_seq_str(fasta, FASTA_PAT)
        if err:
            raise gr.Error(f'Found error(s) in your Target FASTA input: {err}')
        if not library:
            raise gr.Error('Please select or upload a compound library.')
        if library in DRUG_LIBRARY_MAP.keys():
            screen_df = pd.read_csv(Path('data/drug_libraries', DRUG_LIBRARY_MAP[library]))
        else:
            screen_df = process_drug_library_upload(library_upload)
            if len(screen_df) >= DATASET_MAX_LEN:
                raise gr.Error(f'The uploaded compound library has more records '
                               f'than the allowed maximum {DATASET_MAX_LEN}.')

        screen_df['X2'] = fasta

        job_id = str(uuid4())
        temp_file = Path(f'{SERVER_DATA_DIR}/{job_id}_input.csv').resolve()
        screen_df.to_csv(temp_file, index=False)
        if temp_file.is_file():
            job_info = common_job_initiate(job_id, 'Drug Hit Screening', email, request, task)
            return {screen_data_for_predict: str(temp_file),
                    run_state: job_info}
        else:
            raise gr.Error('System failed to create temporary files. Please try again later.')


    def target_identify_validate(smiles, library, library_upload, preset, task, email, state,
                                 request: gr.Request, progress=gr.Progress(track_tqdm=True)):
        state, preset, email = common_input_validate(state, preset, email, request)

        smiles = smiles.strip()
        err = validate_seq_str(smiles, SMILES_PAT)
        if err:
            raise gr.Error(f'Found error(s) in your Compound SMILES input: {err}')
        if not library:
            raise gr.Error('Please select or upload a target library.')
        if library in TARGET_LIBRARY_MAP.keys():
            identify_df = pd.read_csv(Path('data/target_libraries', TARGET_LIBRARY_MAP[library]))
        else:
            identify_df = process_target_library_upload(library_upload)
            if len(identify_df) >= DATASET_MAX_LEN:
                raise gr.Error(f'The uploaded target library has more records '
                               f'than the allowed maximum {DATASET_MAX_LEN}.')
        identify_df['X1'] = smiles

        job_id = str(uuid4())
        temp_file = Path(f'{SERVER_DATA_DIR}/{job_id}_input.csv').resolve()
        identify_df.to_csv(temp_file, index=False)
        if temp_file.is_file():
            job_info = common_job_initiate(job_id, 'Target Protein Identification', email, request, task)
            return {identify_data_for_predict: str(temp_file),
                    run_state: job_info}
        else:
            raise gr.Error('System failed to create temporary files. Please try again later.')


    def pair_infer_validate(drug_target_pair_upload, drug_upload, target_upload, preset, task, email, state,
                            request: gr.Request, progress=gr.Progress(track_tqdm=True)):
        state, preset, email = common_input_validate(state, preset, email, request)

        job_id = str(uuid4())
        if drug_target_pair_upload:
            infer_df = pd.read_csv(drug_target_pair_upload)
            validate_columns(infer_df, ['X1', 'X2'])

            infer_df['X1_ERR'] = infer_df['X1'].swifter.progress_bar(desc="Validating SMILES...").apply(
                validate_seq_str, regex=SMILES_PAT)
            if not infer_df['X1_ERR'].isna().all():
                raise ValueError(
                    f"Encountered invalid SMILES:\n{infer_df[~infer_df['X1_ERR'].isna()][['X1', 'X1_ERR']]}")

            infer_df['X2_ERR'] = infer_df['X2'].swifter.progress_bar(desc="Validating FASTA...").apply(
                validate_seq_str, regex=FASTA_PAT)
            if not infer_df['X2_ERR'].isna().all():
                raise ValueError(
                    f"Encountered invalid FASTA:\n{infer_df[~infer_df['X2_ERR'].isna()][['X2', 'X2_ERR']]}")

            temp_file = Path(drug_target_pair_upload).resolve()

        elif drug_upload and target_upload:
            drug_df = process_drug_library_upload(drug_upload)
            target_df = process_target_library_upload(target_upload)

            drug_df.drop_duplicates(subset=['X1'], inplace=True)
            target_df.drop_duplicates(subset=['X2'], inplace=True)

            infer_df = pd.DataFrame(list(itertools.product(drug_df['X1'], target_df['X2'])),
                                    columns=['X1', 'X2'])
            infer_df = infer_df.merge(drug_df, on='X1').merge(target_df, on='X2')

            if len(infer_df) >= DATASET_MAX_LEN:
                raise gr.Error(f'The uploaded/generated compound-protein pair dataset has more records '
                               f'than the allowed maximum {DATASET_MAX_LEN}.')

            temp_file = Path(f'{SERVER_DATA_DIR}/{job_id}_input.csv').resolve()
            infer_df.to_csv(temp_file, index=False)

        else:
            raise gr.Error('Should upload a compound-protein pair dataset, or '
                           'upload both a compound library and a target library.')

        if temp_file.is_file():
            job_info = common_job_initiate(job_id, 'Interaction Pair Inference', email, request, task)
            return {infer_data_for_predict: str(temp_file),
                    run_state: job_info}
        else:
            raise gr.Error('System failed to create temporary files. Please try again later.')

    def fill_job_id(job_info):
        try:
            return job_info['id']
        except Exception as e:
            gr.Warning(f'Failed to fetch job ID due to error: {str(e)}')
            return ''


    drug_screen_click = drug_screen_btn.click(
        fn=drug_screen_validate,
        inputs=[target_fasta, drug_library, drug_library_upload, drug_screen_preset, drug_screen_task,
                drug_screen_email, run_state],
        outputs=[screen_data_for_predict, run_state],
        concurrency_limit=2,
    )

    drug_screen_lookup = drug_screen_click.success(
        fn=lambda: gr.Tabs(selected='Prediction Status Lookup'), outputs=[tabs],
    ).then(
        fn=fill_job_id, inputs=[run_state], outputs=[pred_lookup_id]
    ).then(
        fn=lookup_job,
        inputs=[pred_lookup_id],
        outputs=[pred_lookup_status, pred_lookup_btn, pred_lookup_stop_btn, tabs, file_for_report],
        show_progress='minimal',
        concurrency_limit=100,
    )

    drug_screen_click.success(
        fn=send_email,
        inputs=[run_state]
    )

    drug_screen_click.success(
        fn=submit_predict,
        inputs=[screen_data_for_predict, drug_screen_task, drug_screen_preset,
                drug_screen_target_family, run_state, ],
        outputs=[run_state, ]
    )

    target_identify_click = target_identify_btn.click(
        fn=target_identify_validate,
        inputs=[compound_smiles, target_library, target_library_upload, target_identify_preset, target_identify_task,
                target_identify_email, run_state],
        outputs=[identify_data_for_predict, run_state],
        concurrency_limit=2,
    )

    target_identify_lookup = target_identify_click.success(
        fn=lambda: gr.Tabs(selected='Prediction Status Lookup'), outputs=[tabs],
    ).then(
        fn=fill_job_id, inputs=[run_state], outputs=[pred_lookup_id]
    ).then(
        fn=lookup_job,
        inputs=[pred_lookup_id],
        outputs=[pred_lookup_status, pred_lookup_btn, pred_lookup_stop_btn, tabs, file_for_report],
        show_progress='minimal',
        concurrency_limit=100
    )

    target_identify_click.success(
        fn=send_email,
        inputs=[run_state]
    )

    target_identify_click.success(
        fn=submit_predict,
        inputs=[identify_data_for_predict, target_identify_task, target_identify_preset,
                target_identify_target_family, run_state, ],  # , target_identify_email],
        outputs=[run_state, ]
    )

    pair_infer_click = pair_infer_btn.click(
        fn=pair_infer_validate,
        inputs=[infer_pair, infer_drug, infer_target, pair_infer_preset, pair_infer_task,
                pair_infer_email, run_state],
        outputs=[infer_data_for_predict, run_state],
        concurrency_limit=2,
    )

    pair_infer_lookup = pair_infer_click.success(
        fn=lambda: gr.Tabs(selected='Prediction Status Lookup'), outputs=[tabs],
    ).then(
        fn=fill_job_id, inputs=[run_state], outputs=[pred_lookup_id]
    ).then(
        fn=lookup_job,
        inputs=[pred_lookup_id],
        outputs=[pred_lookup_status, pred_lookup_btn, pred_lookup_stop_btn, tabs, file_for_report],
        show_progress='minimal',
        concurrency_limit=100
    )

    pair_infer_click.success(
        fn=send_email,
        inputs=[run_state]
    )

    pair_infer_click.success(
        fn=submit_predict,
        inputs=[infer_data_for_predict, pair_infer_task, pair_infer_preset,
                pair_infer_target_family, run_state, ],  # , pair_infer_email],
        outputs=[run_state, ]
    )

    pred_lookup_click = pred_lookup_btn.click(
        fn=lookup_job,
        inputs=[pred_lookup_id],
        outputs=[pred_lookup_status, pred_lookup_btn, pred_lookup_stop_btn, tabs, file_for_report],
        show_progress='minimal',
        cancels=[drug_screen_lookup, target_identify_lookup, pair_infer_lookup],
        concurrency_limit=100,
    )

    pred_lookup_stop_btn.click(
        fn=lambda: [gr.Button(visible=True), gr.Button(visible=False)],
        outputs=[pred_lookup_btn, pred_lookup_stop_btn],
        cancels=[pred_lookup_click, drug_screen_lookup, target_identify_lookup, pair_infer_lookup],
        concurrency_limit=None,
    )


    def inquire_task(df):
        if 'Y' in df.columns:
            label = 'actual CPI/CPA labels (`Y`)'
        elif 'Y^' in df.columns:
            label = 'predicted CPI/CPA labels (`Y^`)'
        else:
            return {analyze_btn: gr.Button(interactive=True),
                    csv_generate: gr.Button(interactive=True),
                    html_generate: gr.Button(interactive=True)}

        return {report_task: gr.Dropdown(visible=True,
                                         info=f'Found {label} in your uploaded dataset. '
                                              'Is it compound-protein interaction or binding affinity?'),
                html_report: '',
                analyze_btn: gr.Button(interactive=False),
                csv_generate: gr.Button(interactive=False),
                html_generate: gr.Button(interactive=False)}


    report_df_change = file_for_report.change(
        fn=update_df, inputs=file_for_report, outputs=[html_report, raw_df, report_df, analyze_btn, report_task],
        concurrency_limit=100,
    )

    file_for_report.upload(
        fn=update_df, inputs=file_for_report, outputs=[html_report, raw_df, report_df, analyze_btn, report_task],
        cancels=[report_df_change],
        concurrency_limit=100,
    ).then(
        fn=inquire_task, inputs=[raw_df],
        outputs=[report_task, html_report, analyze_btn, csv_generate, html_generate],
    )

    file_for_report.clear(
        fn=lambda: [gr.Button(interactive=False)] * 3 +
                   [gr.File(visible=False, value=None)] * 2 +
                   [gr.Dropdown(visible=False, value=None),
                    gr.HTML(visible=False)],
        outputs=[
            csv_generate, html_generate, analyze_btn, csv_download_file, html_download_file, report_task, html_report
        ]
    )

    analyze_btn.click(
        fn=submit_report, inputs=[raw_df, scores, filters, report_task], outputs=[
            html_report, report_df, csv_download_file, html_download_file]
    ).success(
        fn=lambda: [gr.Button(interactive=True)] * 2,
        outputs=[csv_generate, html_generate],
        concurrency_limit=100,
    )

    report_task.select(fn=lambda: gr.Button(interactive=True),
                       outputs=analyze_btn)


    def create_csv_report_file(df, file_report, progress=gr.Progress(track_tqdm=True)):
        try:
            now = datetime.now().strftime("%Y-%m-%d_%H-%M-%S")
            filename = f"/data/{Path(file_report.name).stem}_DeepSEQreen_report_{now}.csv"
            df.drop(labels=['Compound', 'Scaffold'], axis=1).to_csv(filename, index=False)

            return gr.File(filename)
        except Exception as e:
            gr.Warning(f"Failed to generate CSV due to error: {str(e)}")
            return None


    def create_html_report_file(df, file_report, task, progress=gr.Progress(track_tqdm=True)):
        try:
            now = datetime.now().strftime("%Y-%m-%d_%H-%M-%S")
            filename = f"/data/{Path(file_report.name).stem}_DeepSEQreen_report_{now}.html"
            create_html_report(df, filename, task)
            return gr.File(filename, visible=True)
        except Exception as e:
            gr.Warning(f"Failed to generate HTML due to error: {str(e)}")
            return None


    html_report.change(lambda: [gr.Button(visible=True)] * 2, outputs=[csv_generate, html_generate])
    csv_generate.click(
        lambda: [gr.Button(visible=False), gr.File(visible=True)], outputs=[csv_generate, csv_download_file],
    ).then(fn=create_csv_report_file, inputs=[report_df, file_for_report],
           outputs=csv_download_file, show_progress='full')
    html_generate.click(
        lambda: [gr.Button(visible=False), gr.File(visible=True)], outputs=[html_generate, html_download_file],
    ).then(fn=create_html_report_file, inputs=[report_df, file_for_report, report_task],
           outputs=html_download_file, show_progress='full')

if __name__ == "__main__":
    hydra.initialize(version_base="1.3", config_path="configs", job_name="webserver_inference")
    demo.queue(default_concurrency_limit=None, max_size=10).launch(show_api=False)