""" 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('error.html',code="DB01",description=errors['DB01']) 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 = "/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 if len(pdb) != 4: return render_template("error.html",code="CW01",description=errors['CW01']) 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('/.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.route('/debug-sentry') def trigger_error(): division_by_zero = 1 / 0 @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")