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"""
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
from werkzeug.utils import secure_filename
from random import choice, shuffle
from string import digits, ascii_lowercase
# Note: that when using Flask-WTF we need to import the Form Class that we created
# in forms.py
from .forms import MyForm, curieForm
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('/Visualise')
def visualise():
"""Render visualisation page."""
return render_template('visualise.html')
@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('/dock', methods=['GET', 'POST'])
def dock_upload():
form = curieForm()
if request.method == 'POST' and form.validate_on_submit():
print("Recieved task: ",form.description.data)
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)
print("Submitted JobID: ",jobID)
insert_tuple = (jobID,email,receptor,receptorName,ligandB,ligandName,description,config)
mycursor.execute(sqlQuery,insert_tuple)
mycon.commit()
print("Description",description)
return render_template('display_result.html', filename="OwO", description=description,job=jobID)
flash_errors(form)
return render_template('dock_upload.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")
|
