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app.py
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import os
import flask
from flask import Flask, request, redirect, url_for, send_from_directory
from werkzeug.utils import secure_filename
import pandas as pd
from flask import send_file
import pubchempy as pcp
from zipfile import ZipFile
from collections import deque
UPLOAD_FOLDER = 'static/'
ALLOWED_EXTENSIONS = set(['xlsx'])
app = Flask(__name__)
app.config['UPLOAD_FOLDER'] = UPLOAD_FOLDER
def allowed_file(filename):
return '.' in filename and \
filename.rsplit('.', 1)[1] in ALLOWED_EXTENSIONS
def pipeline(list_of_compounds, opt):
files = []
no_result = []
for i in list_of_compounds:
try:
pcp.download('SDF', app.config['UPLOAD_FOLDER'] + i + opt + '.sdf', i, 'name', record_type=opt)
files.append(app.config['UPLOAD_FOLDER'] + i + opt + '.sdf')
except:
no_result.append(i)
return files, no_result
def return_files_tut(filename):
try:
return send_file(filename, attachment_filename='result.zip')
except Exception as e:
return str(e)
def zip_files(files):
with ZipFile(app.config['UPLOAD_FOLDER'] + 'files.zip', mode='w') as zf:
for f in files:
zf.write(f)
os.remove(f)
return app.config['UPLOAD_FOLDER'] + 'files.zip'
@app.route('/', methods=['GET', 'POST'])
def upload_file():
if request.method == 'POST':
option = request.form['options']
upfile = request.files['file']
if request.form['text']:
text = request.form['text']
list_of_compounds = text.split('\r\n')
files, no_result = pipeline(list_of_compounds, option)
zipped = zip_files(files)
return_files_tut(zipped)
return flask.render_template('results.html', x=len(files) + len(no_result), y=len(no_result))
if upfile and allowed_file(upfile.filename):
dir = app.config['UPLOAD_FOLDER']
for f in os.listdir(dir):
os.remove(os.path.join(dir, f))
filename = secure_filename(upfile.filename)
upfile.save(os.path.join(app.config['UPLOAD_FOLDER'], filename))
data = pd.read_excel(os.path.join(app.config['UPLOAD_FOLDER'], filename), header=None)
list_of_compounds = data[0][1:]
files, no_result = pipeline(list_of_compounds, option)
os.remove(os.path.join(app.config['UPLOAD_FOLDER'], filename))
zipped = zip_files(files)
return_files_tut(zipped)
print(files, no_result)
return flask.render_template('results.html', x = len(files) + len(no_result), y = len(no_result))
return flask.render_template('main.html')
if __name__ == "__main__":
app.run(port=5000, debug=True)