Curie-Web/app/views.py

"""
Flask Documentation:     http://flask.pocoo.org/docs/
Jinja2 Documentation:    http://jinja.pocoo.org/2/documentation/
Werkzeug Documentation:  http://werkzeug.pocoo.org/documentation/
"""
import os
from app import app
from flask import render_template, request, flash, send_file
from werkzeug.utils import secure_filename
from random import choice, shuffle
from string import digits, ascii_lowercase
from pymed import PubMed
from datetime import datetime,date
import json
import subprocess

import logging
import logzero
from logzero import logger
logzero.loglevel(logging.DEBUG)
if app.config['SAVE_LOGS']:
    logFile = app.config['LOG_FOLDER'] + date.today().strftime("%m-%d-%y") + ".log"
    logzero.logfile(logFile, maxBytes=1e6, backupCount=3)

import configparser
misc = configparser.ConfigParser()
misc.read('app/misc.ini')
errors = misc['ERRORS']

# Note: that when using Flask-WTF we need to import the Form Class that we created
# in forms.py
from .forms import MyForm, curieForm, statusForm, generateSMILES, PyMedSearch, dockSingleForm, generatePDBQTS

def log(message,logType="INFO"):
    if app.config['LOG']:
        if logType == "INFO":
            logger.info(message)
        elif logType == "DEBUG":
            logger.debug(message)
        elif logType == "EXCEPTION":
            logger.exception(message)
        elif logType == "DANGER":
            logger.error(message)
    return None

def gen_word(N, min_N_dig, min_N_low):
    choose_from = [digits]*min_N_dig + [ascii_lowercase]*min_N_low
    choose_from.extend([digits + ascii_lowercase] * (N-min_N_low-min_N_dig))
    chars = [choice(bet) for bet in choose_from]
    shuffle(chars)
    return ''.join(chars)

def convertToBinaryData(filename):
    # Convert digital data to binary format
    with open(filename, 'rb') as file:
        binaryData = file.read()
    return binaryData

###
# Routing for your application.
###

@app.route('/')
def home():
    """Render website's home page."""
    return render_template('home.html')

@app.route('/About')
def about():
    """Render about page."""
    return render_template('about.html')

@app.route('/Editor')
def editor():
    """Render Molecular Editor"""
    return render_template('molecule_editor.html')

@app.route('/Visualise')
def visualise():
    """Render visualisation page."""
    return render_template('visualise.html')    

@app.route('/Search',methods=['GET','POST'])
def pubmed():
    """Query PubMed"""
    form = PyMedSearch()
    pubmed = PubMed(tool="Curie", email="navanchauhan@gmail.com")

    if request.method == 'POST' and form.validate_on_submit():
        q = form.query.data
        log(form,"DEBUG")
        log(pubmed,"DEBUG")
        results = pubmed.query(q,max_results=100) 
        search = []
        for x in results:
            search.append(x.toDict())

        return render_template('search.html',result=search,form=form)
    
    flash_errors(form)
    return render_template('search.html',form=form)

@app.route('/Status',methods=['GET','POST'])
def status():
    taskStatusForm = statusForm()

    if request.method == 'POST':
        if taskStatusForm.validate_on_submit():
            jobID = taskStatusForm.jobID.data
            import mysql.connector as con
            mycon = con.connect(host=app.config['DB_HOST'],user=app.config['DB_USER'],password=app.config['DB_PASSWORD'],port=app.config['DB_PORT'],database=app.config['DB_NAME'])
            mycursor = mycon.cursor()
            sqlQuery = 'select id, protein_name, ligand_name, date, description, done, pdb from curieweb where id="%s"' % (jobID)
            mycursor.execute(sqlQuery)
            records = mycursor.fetchall()
            if records == []:
                return render_template('job_status_error.html',job=jobID)
            r = records[0]
            protein_name = r[1]
            ligand_name = r[2]
            date = r[3]
            description = r[4]
            done = r[5]
            if done==1:
                done="Completed"
            elif done==0:
                done="Queued"
            if protein_name == None:
                protein_name = r[6]
                
            PDFReport = "./app/static/uploads/reports/" + str(jobID) + ".pdf"
            AndroidModel = "/static/uploads/3DModels/" + str(jobID) + ".gltf"
            iOSModel = "/static/uploads/3DModels/" + str(jobID) + ".usdz"

            return render_template('job_status.html',ID=jobID,pn=protein_name,ln=ligand_name,subDate=date,desc=description,status=done,PDFReport=PDFReport,AndroidModel=AndroidModel,iOSModel=iOSModel)
        flash_errors(taskStatusForm)
    return render_template('job_status_form.html',form=taskStatusForm)
        
@app.route('/basic-form', methods=['GET', 'POST'])
def basic_form():
    if request.method == 'POST':
        firstname = request.form['firstname']
        lastname = request.form['lastname']
        email = request.form['email']

        return render_template('result.html',
                               firstname=firstname,
                               lastname=lastname,
                               email=email)

    return render_template('form.html')

@app.route('/wtform', methods=['GET', 'POST'])
def wtform():
    myform = MyForm()

    if request.method == 'POST':
        if myform.validate_on_submit():
            # Note the difference when retrieving form data using Flask-WTF
            # Here we use myform.firstname.data instead of request.form['firstname']
            firstname = myform.firstname.data
            lastname = myform.lastname.data
            email = myform.email.data

            flash('You have successfully filled out the form', 'success')
            return render_template('result.html', firstname=firstname, lastname=lastname, email=email)

        flash_errors(myform)
    return render_template('wtform.html', form=myform)

@app.route('/PDBQTs',methods=['GET','POST'])
def generate_pdbqts():
    myform = generatePDBQTS()

    if request.method == 'POST':
        if myform.validate_on_submit():
            pdbId = myform.pdb.data
            smiles = myform.smiles.data
            name = myform.name.data
            if (len(pdbId)==0) and (len(smiles)==0):
                log("Nothing Submitted!","WARNING")
                flash("Invalid Submission!",'danger')
            if len(smiles) != 0:
                try:
                    import oddt
                except ImportError:
                    return render_template('error.html',code="OD00",description=errors['OD00'])
                try:
                    mol = oddt.toolkit.readstring('smi', smiles)
                except:
                    return render_template('error.html',code="OD01",description=errors['OD01'])
                try:
                    mol.make3D()
                    mol.calccharges()
                except:
                    return render_template('error.html',code="OD02",description=errors['OD02'])
                from oddt.docking.AutodockVina import write_vina_pdbqt
                
                try:
                    write_vina_pdbqt(mol,'app',flexible=False)
                except:
                    return render_template('error.html',code="OD03",description=errors['OD03'])
                path = ".pdbqt"
                if ".pdbqt" in name:
                    fname = name
                else:
                    fname = name + ".pdbqt"
                return send_file(path,attachment_filename=fname,as_attachment=True)
            if len(pdbId) != 0:
                try:
                    from plip.basic import config
                except ImportError:
                    return render_template('error.html',code="PL00",description=errors['PL00'])
                from plip.exchange.webservices import fetch_pdb
                from plip.structure.preparation import create_folder_if_not_exists, extract_pdbid
                from plip.structure.preparation import tilde_expansion, PDBComplex

                try:
                    pdbfile, pdbid = fetch_pdb(pdbId.lower())
                except:
                    return render_template('error.html',code="PL01",description=errors['PL01'])
                pdbpath = tilde_expansion('%s/%s.pdb' % (config.BASEPATH.rstrip('/'), pdbid))
                create_folder_if_not_exists(config.BASEPATH)
                with open(pdbpath, 'w') as g:
                    g.write(pdbfile)
                try:
                    import oddt
                except:
                    return render_template('error.html',code="OD00",description=errors['OD00'])
                from oddt.docking.AutodockVina import write_vina_pdbqt
                try:
                    receptor = next(oddt.toolkit.readfile("pdb",pdbpath.split("./")[1]))
                    receptor.calccharges()
                except Exception:
                    receptor = next(oddt.toolkits.rdk.readfile("pdb",pdbpath.split("./")[1]))
                    receptor.calccharges()

                try:
                    path = write_vina_pdbqt(receptor,'app',flexible=False)
                except:
                    return render_template('error.html',code="OD03",description=errors['OD03'])
                os.rename(path,"app/.pdbqt")
                path = ".pdbqt"
                fname = pdbId.upper() + ".pdqbt"
                return send_file(path,attachment_filename=fname,as_attachment=True) 
        flash_errors(myform)
    return render_template('pdbqt_form.html',form=myform)
            

tfWorking = 0
if app.config['LSTM']:
    try:
        import tensorflow as tf
        tfWorking = 1
    except Exception as e:
        log(e,"EXCEPTION")
        tfWorking = 0

if tfWorking == 1:
    from lstm_chem.utils.config import process_config
    from lstm_chem.model import LSTMChem
    from lstm_chem.generator import LSTMChemGenerator
    config = process_config("app/prod/config.json")
    modeler = LSTMChem(config, session="generate")
    gen = LSTMChemGenerator(modeler)
    log("Heating up model","INFO")
    gen.sample(1)

@app.route('/Generate', methods=['GET','POST'])
def generate():
    """Generate novel drugs"""
    form = generateSMILES()

    with open("./app/prod/config.json") as config:
        import json
        j = json.loads(config.read())
        log(("Model Name:", j["exp_name"]),"INFO")
    

    if request.method == 'POST' and form.validate_on_submit():
        log(tfWorking,"DEBUG")
        if tfWorking == 0:
            log("Failed to initialise model","DANGER")   
            flash("Failed to initialise the model!","danger")
        else:
            result = gen.sample(form.n.data)
            return render_template('generate.html',expName=j["exp_name"],epochs=j["num_epochs"],optimizer=j["optimizer"].capitalize(), form=form,result=result)

    return render_template('generate.html',expName=j["exp_name"],epochs=j["num_epochs"],optimizer=j["optimizer"].capitalize(), form=form)

@app.route('/Dock', methods=['GET', 'POST'])
def dock_upload():
    form = curieForm()

    if request.method == 'POST' and form.validate_on_submit():
        log(("Recieved task: ",form.description.data),"DEBUG")
        description = form.description.data
        target = form.target.data
        ligand = form.ligand.data
        cx,cy,cz = str(form.center_x.data), str(form.center_y.data), str(form.center_z.data)
        sx,sy,sz = str(form.size_x.data), str(form.size_y.data), str(form.size_z.data)
        email = form.email.data

        import mysql.connector as con
        mycon = con.connect(host=app.config['DB_HOST'],user=app.config['DB_USER'],password=app.config['DB_PASSWORD'],port=app.config['DB_PORT'],database=app.config['DB_NAME'])
        mycursor = mycon.cursor()

        import tempfile
        with tempfile.TemporaryDirectory() as directory:
            os.chdir(directory)
            target.save(secure_filename(target.filename))
            ligand.save(secure_filename(ligand.filename))
            buffer = "center_x="+cx+"\ncenter_y="+cy+"\ncenter_z="+cz+"\nsize_x="+sx+"\nsize_y="+sy+"\nsize_z="+sz
            with open("config.txt","w") as f:
                f.write(buffer)
            ligandB = convertToBinaryData(secure_filename(ligand.filename))
            receptor = convertToBinaryData(secure_filename(target.filename))
            config = convertToBinaryData("config.txt")
            ligandName = secure_filename(ligand.filename)
            receptorName = secure_filename(target.filename)
            sqlQuery = "insert into curieweb (id, email, protein, protein_name, ligand_pdbqt, ligand_name,date, description, config) values (%s,%s,%s,%s,%s,%s,CURDATE(),%s,%s) "
            jobID = gen_word(16, 1, 1)
            log(("Submitted JobID: ",jobID),"DEBUG")
            insert_tuple = (jobID,email,receptor,receptorName,ligandB,ligandName,description,config)
            mycursor.execute(sqlQuery,insert_tuple)
            mycon.commit()

        log(("Description",description),"DEBUG")
        cwd = os.path.join(os.getcwd(),"app")
        if app.config['INSTANT_EXEC']:
            subprocess.Popen(['python3', 'dock-docker.py'],cwd=cwd)
        return render_template('display_result.html', filename="OwO", description=description,job=jobID)

    flash_errors(form)
    return render_template('dock_upload.html', form=form)

@app.route('/Dock-Single', methods=['GET', 'POST'])
def dock_upload_single():
    form = dockSingleForm()

    if request.method == 'POST' and form.validate_on_submit():
        log(("Recieved task: ",form.description.data),"DEBUG")
        description = form.description.data
        pdb = form.pdbID.data
        smile = form.smiles.data
        name = form.name.data
        email = form.email.data

        import mysql.connector as con
        mycon = con.connect(host=app.config['DB_HOST'],user=app.config['DB_USER'],password=app.config['DB_PASSWORD'],port=app.config['DB_PORT'],database=app.config['DB_NAME'])
        mycursor = mycon.cursor()

        sqlQuery = "insert into curieweb (id, email, pdb, ligand_smile, ligand_name, date, description) values (%s,%s,%s,%s,%s,CURDATE(),%s) "
        jobID = gen_word(16, 1, 1)

        insert_tuple = (jobID,email,pdb,smile,name,description)
        mycursor.execute(sqlQuery,insert_tuple)
        mycon.commit()
        
        log(("Description",description),"DEBUG")

        cwd = os.path.join(os.getcwd(),"app")
        if app.config['INSTANT_EXEC']:
            subprocess.Popen(['python3', 'dock-single.py'],cwd=cwd)
        
        return render_template('display_result.html', filename="OwO", description=description,job=jobID)

    flash_errors(form)
    return render_template('dock_upload_single.html', form=form)

###
# The functions below should be applicable to all Flask apps.
###

# Flash errors from the form if validation fails
def flash_errors(form):
    for field, errors in form.errors.items():
        for error in errors:
            flash(u"Error in the %s field - %s" % (
                getattr(form, field).label.text,
                error
            ), 'danger')

@app.route('/<file_name>.txt')
def send_text_file(file_name):
    """Send your static text file."""
    file_dot_text = file_name + '.txt'
    return app.send_static_file(file_dot_text)


@app.after_request
def add_header(response):
    """
    Add headers to both force latest IE rendering engine or Chrome Frame,
    and also to cache the rendered page for 10 minutes.
    """
    response.headers['X-UA-Compatible'] = 'IE=Edge,chrome=1'
    response.headers['Cache-Control'] = 'public, max-age=0'
    return response


@app.errorhandler(404)
def page_not_found(error):
    """Custom 404 page."""
    return render_template('404.html'), 404


if __name__ == '__main__':
    app.run(debug=True, host="0.0.0.0", port="8080")