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/
Curie-Web
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added logging and instant execution support

This commit is contained in:
Navan Chauhan 2020-09-10 12:04:25 +05:30
parent 0bcccae1dd
commit 2f0d88120f
3 changed files with 85 additions and 29 deletions
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17
app/__init__.py
View File

@ -10,6 +10,23 @@ DB_USER = config['DATABASE']['USER']
DB_PASSWORD = config['DATABASE']['PASSWORD']
DB_NAME = config['DATABASE']['NAME']
UPLOAD_FOLDER = config['FILES']['UPLOAD_FOLDER']
LOG_FOLDER = config['FILES']['LOG_FOLDER']
INSTANT_EXEC = config['EXECUTION']['INSTANT']
if INSTANT_EXEC == 'True':
INSTANT_EXEC = True
else:
INSTANT_EXEC = False
LOG = True
SAVE_LOGS = False
if config['LOGS']['LOG'] == 'True':
LOG = True
if config['LOGS']['SAVE_LOGS'] == 'True':
SAVE_LOGS = True
else:
LOG = False
"""
# Hardcoded Values

88
app/views.py
View File

@ -10,14 +10,39 @@ 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
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))
@ -63,8 +88,8 @@ def pubmed():
if request.method == 'POST' and form.validate_on_submit():
q = form.query.data
print(form)
print(pubmed)
log(form,"DEBUG")
log(pubmed,"DEBUG")
results = pubmed.query(q,max_results=100)
search = []
for x in results:
@ -153,25 +178,28 @@ def generate_pdbqts():
smiles = myform.smiles.data
name = myform.name.data
if (len(pdbId)==0) and (len(smiles)==0):
print("Nothing Submitted!")
log("Nothing Submitted!","WARNING")
flash("Invalid Submission!",'danger')
if len(smiles) != 0:
import oddt
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="Could not convert SMILES to molecule, please check the SMILES")
return render_template('error.html',code="OD01",description=errors['OD01'])
try:
mol.make3D()
mol.calccharges()
except:
return render_template('error.html',code="OD02",description="Failed to add charges to molecule")
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="Failed to write the converted PDBQT file")
return render_template('error.html',code="OD03",description=errors['OD03'])
path = ".pdbqt"
if ".pdbqt" in name:
fname = name
@ -179,7 +207,10 @@ def generate_pdbqts():
fname = name + ".pdbqt"
return send_file(path,attachment_filename=fname,as_attachment=True)
if len(pdbId) != 0:
from plip.basic import config
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
@ -187,12 +218,15 @@ def generate_pdbqts():
try:
pdbfile, pdbid = fetch_pdb(pdbId.lower())
except:
return render_template('error.html',code="PL01",description="Failed to fetch the PDB, please check the PDB Code")
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)
import oddt
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]))
@ -204,7 +238,7 @@ def generate_pdbqts():
try:
path = write_vina_pdbqt(receptor,'app',flexible=False)
except:
return render_template('error.html',code="OD03",description="Failed to write the converted PDBQT file")
return render_template('error.html',code="OD03",description=errors['OD03'])
os.rename(path,"app/.pdbqt")
path = ".pdbqt"
fname = pdbId.upper() + ".pdqbt"
@ -213,15 +247,14 @@ def generate_pdbqts():
return render_template('pdbqt_form.html',form=myform)
tfWorking = 0
if tfWorking == -1:
try:
import tensorflow as tf
import tensorrflow as tf
tfWorking = 1
except:
print("Could not load tensorflow model :/")
except Exception as e:
log(e,"EXCEPTION")
tfWorking = 0
if tfWorking == 1:
@ -231,7 +264,7 @@ if tfWorking == 1:
config = process_config("app/prod/config.json")
modeler = LSTMChem(config, session="generate")
gen = LSTMChemGenerator(modeler)
print("Testing Model")
log("Heating up model","INFO")
gen.sample(1)
@app.route('/Generate', methods=['GET','POST'])
@ -242,12 +275,13 @@ def generate():
with open("./app/prod/config.json") as config:
import json
j = json.loads(config.read())
print("Model Name:", j["exp_name"])
log(("Model Name:", j["exp_name"]),"INFO")
if request.method == 'POST' and form.validate_on_submit():
print(tfWorking)
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)
@ -260,7 +294,7 @@ def dock_upload():
form = curieForm()
if request.method == 'POST' and form.validate_on_submit():
print("Recieved task: ",form.description.data)
log(("Recieved task: ",form.description.data),"DEBUG")
description = form.description.data
target = form.target.data
ligand = form.ligand.data
@ -287,14 +321,15 @@ def dock_upload():
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)
log(("Submitted JobID: ",jobID),"DEBUG")
insert_tuple = (jobID,email,receptor,receptorName,ligandB,ligandName,description,config)
mycursor.execute(sqlQuery,insert_tuple)
mycon.commit()
print("Description",description)
log(("Description",description),"DEBUG")
cwd = os.path.join(os.getcwd(),"app")
subprocess.Popen(['python3', 'dock-docker.py'],cwd=cwd)
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)
@ -305,7 +340,7 @@ def dock_upload_single():
form = dockSingleForm()
if request.method == 'POST' and form.validate_on_submit():
print("Recieved task: ",form.description.data)
log(("Recieved task: ",form.description.data),"DEBUG")
description = form.description.data
pdb = form.pdbID.data
smile = form.smiles.data
@ -323,10 +358,11 @@ def dock_upload_single():
mycursor.execute(sqlQuery,insert_tuple)
mycon.commit()
print("Description",description)
log(("Description",description),"DEBUG")
cwd = os.path.join(os.getcwd(),"app")
subprocess.Popen(['python3', 'dock-single.py'],cwd=cwd)
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)

9
config.ini
View File

@ -12,9 +12,12 @@ EMAIL = navanchauhan@gmail.com
PASSWORD = okrs shoc ahtk idui
[LOGS]
ERRORS = logs/errors.log
INFO = data/info.log
LOG = True
SAVE_LOGS = False
[FILES]
UPLOAD_FOLDER = ./app/static/uploads
TEMPLATES_FOLDER = templates
LOG_FOLDER = ./app/logs/
[EXECUTION]
INSTANT = True