added logging and instant execution support
This commit is contained in:
Navan Chauhan
parent
0bcccae1dd
commit
2f0d88120f
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@ -10,6 +10,23 @@ DB_USER = config['DATABASE']['USER']
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DB_PASSWORD = config['DATABASE']['PASSWORD']
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DB_NAME = config['DATABASE']['NAME']
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UPLOAD_FOLDER = config['FILES']['UPLOAD_FOLDER']
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LOG_FOLDER = config['FILES']['LOG_FOLDER']
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INSTANT_EXEC = config['EXECUTION']['INSTANT']
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if INSTANT_EXEC == 'True':
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INSTANT_EXEC = True
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else:
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INSTANT_EXEC = False
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LOG = True
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SAVE_LOGS = False
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if config['LOGS']['LOG'] == 'True':
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LOG = True
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if config['LOGS']['SAVE_LOGS'] == 'True':
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SAVE_LOGS = True
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else:
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LOG = False
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"""
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# Hardcoded Values
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78
app/views.py
78
app/views.py
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@ -10,14 +10,39 @@ from werkzeug.utils import secure_filename
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from random import choice, shuffle
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from string import digits, ascii_lowercase
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from pymed import PubMed
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from datetime import datetime
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from datetime import datetime,date
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import json
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import subprocess
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import logging
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import logzero
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from logzero import logger
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logzero.loglevel(logging.DEBUG)
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if app.config['SAVE_LOGS']:
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logFile = app.config['LOG_FOLDER'] + date.today().strftime("%m-%d-%y") + ".log"
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logzero.logfile(logFile, maxBytes=1e6, backupCount=3)
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import configparser
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misc = configparser.ConfigParser()
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misc.read('app/misc.ini')
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errors = misc['ERRORS']
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# Note: that when using Flask-WTF we need to import the Form Class that we created
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# in forms.py
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from .forms import MyForm, curieForm, statusForm, generateSMILES, PyMedSearch, dockSingleForm, generatePDBQTS
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def log(message,logType="INFO"):
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if app.config['LOG']:
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if logType == "INFO":
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logger.info(message)
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elif logType == "DEBUG":
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logger.debug(message)
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elif logType == "EXCEPTION":
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logger.exception(message)
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elif logType == "DANGER":
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logger.error(message)
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return None
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def gen_word(N, min_N_dig, min_N_low):
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choose_from = [digits]*min_N_dig + [ascii_lowercase]*min_N_low
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choose_from.extend([digits + ascii_lowercase] * (N-min_N_low-min_N_dig))
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@ -63,8 +88,8 @@ def pubmed():
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if request.method == 'POST' and form.validate_on_submit():
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q = form.query.data
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print(form)
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print(pubmed)
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log(form,"DEBUG")
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log(pubmed,"DEBUG")
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results = pubmed.query(q,max_results=100)
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search = []
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for x in results:
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@ -153,25 +178,28 @@ def generate_pdbqts():
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smiles = myform.smiles.data
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name = myform.name.data
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if (len(pdbId)==0) and (len(smiles)==0):
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print("Nothing Submitted!")
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log("Nothing Submitted!","WARNING")
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flash("Invalid Submission!",'danger')
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if len(smiles) != 0:
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try:
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import oddt
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except ImportError:
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return render_template('error.html',code="OD00",description=errors['OD00'])
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try:
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mol = oddt.toolkit.readstring('smi', smiles)
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except:
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return render_template('error.html',code="OD01",description="Could not convert SMILES to molecule, please check the SMILES")
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return render_template('error.html',code="OD01",description=errors['OD01'])
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try:
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mol.make3D()
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mol.calccharges()
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except:
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return render_template('error.html',code="OD02",description="Failed to add charges to molecule")
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return render_template('error.html',code="OD02",description=errors['OD02'])
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from oddt.docking.AutodockVina import write_vina_pdbqt
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try:
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write_vina_pdbqt(mol,'app',flexible=False)
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except:
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return render_template('error.html',code="OD03",description="Failed to write the converted PDBQT file")
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return render_template('error.html',code="OD03",description=errors['OD03'])
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path = ".pdbqt"
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if ".pdbqt" in name:
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fname = name
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@ -179,7 +207,10 @@ def generate_pdbqts():
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fname = name + ".pdbqt"
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return send_file(path,attachment_filename=fname,as_attachment=True)
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if len(pdbId) != 0:
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try:
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from plip.basic import config
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except ImportError:
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return render_template('error.html',code="PL00",description=errors['PL00'])
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from plip.exchange.webservices import fetch_pdb
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from plip.structure.preparation import create_folder_if_not_exists, extract_pdbid
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from plip.structure.preparation import tilde_expansion, PDBComplex
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@ -187,12 +218,15 @@ def generate_pdbqts():
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try:
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pdbfile, pdbid = fetch_pdb(pdbId.lower())
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except:
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return render_template('error.html',code="PL01",description="Failed to fetch the PDB, please check the PDB Code")
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return render_template('error.html',code="PL01",description=errors['PL01'])
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pdbpath = tilde_expansion('%s/%s.pdb' % (config.BASEPATH.rstrip('/'), pdbid))
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create_folder_if_not_exists(config.BASEPATH)
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with open(pdbpath, 'w') as g:
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g.write(pdbfile)
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try:
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import oddt
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except:
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return render_template('error.html',code="OD00",description=errors['OD00'])
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from oddt.docking.AutodockVina import write_vina_pdbqt
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try:
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receptor = next(oddt.toolkit.readfile("pdb",pdbpath.split("./")[1]))
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@ -204,7 +238,7 @@ def generate_pdbqts():
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try:
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path = write_vina_pdbqt(receptor,'app',flexible=False)
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except:
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return render_template('error.html',code="OD03",description="Failed to write the converted PDBQT file")
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return render_template('error.html',code="OD03",description=errors['OD03'])
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os.rename(path,"app/.pdbqt")
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path = ".pdbqt"
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fname = pdbId.upper() + ".pdqbt"
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@ -213,15 +247,14 @@ def generate_pdbqts():
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return render_template('pdbqt_form.html',form=myform)
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tfWorking = 0
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if tfWorking == -1:
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try:
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import tensorflow as tf
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import tensorrflow as tf
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tfWorking = 1
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except:
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print("Could not load tensorflow model :/")
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except Exception as e:
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log(e,"EXCEPTION")
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tfWorking = 0
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if tfWorking == 1:
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@ -231,7 +264,7 @@ if tfWorking == 1:
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config = process_config("app/prod/config.json")
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modeler = LSTMChem(config, session="generate")
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gen = LSTMChemGenerator(modeler)
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print("Testing Model")
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log("Heating up model","INFO")
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gen.sample(1)
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@app.route('/Generate', methods=['GET','POST'])
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@ -242,12 +275,13 @@ def generate():
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with open("./app/prod/config.json") as config:
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import json
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j = json.loads(config.read())
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print("Model Name:", j["exp_name"])
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log(("Model Name:", j["exp_name"]),"INFO")
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if request.method == 'POST' and form.validate_on_submit():
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print(tfWorking)
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log(tfWorking,"DEBUG")
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if tfWorking == 0:
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log("Failed to initialise model","DANGER")
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flash("Failed to initialise the model!","danger")
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else:
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result = gen.sample(form.n.data)
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@ -260,7 +294,7 @@ def dock_upload():
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form = curieForm()
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if request.method == 'POST' and form.validate_on_submit():
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print("Recieved task: ",form.description.data)
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log(("Recieved task: ",form.description.data),"DEBUG")
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description = form.description.data
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target = form.target.data
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ligand = form.ligand.data
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@ -287,13 +321,14 @@ def dock_upload():
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receptorName = secure_filename(target.filename)
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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) "
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jobID = gen_word(16, 1, 1)
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print("Submitted JobID: ",jobID)
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log(("Submitted JobID: ",jobID),"DEBUG")
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insert_tuple = (jobID,email,receptor,receptorName,ligandB,ligandName,description,config)
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mycursor.execute(sqlQuery,insert_tuple)
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mycon.commit()
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print("Description",description)
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log(("Description",description),"DEBUG")
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cwd = os.path.join(os.getcwd(),"app")
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if app.config['INSTANT_EXEC']:
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subprocess.Popen(['python3', 'dock-docker.py'],cwd=cwd)
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return render_template('display_result.html', filename="OwO", description=description,job=jobID)
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@ -305,7 +340,7 @@ def dock_upload_single():
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form = dockSingleForm()
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if request.method == 'POST' and form.validate_on_submit():
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print("Recieved task: ",form.description.data)
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log(("Recieved task: ",form.description.data),"DEBUG")
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description = form.description.data
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pdb = form.pdbID.data
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smile = form.smiles.data
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@ -323,9 +358,10 @@ def dock_upload_single():
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mycursor.execute(sqlQuery,insert_tuple)
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mycon.commit()
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print("Description",description)
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log(("Description",description),"DEBUG")
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cwd = os.path.join(os.getcwd(),"app")
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if app.config['INSTANT_EXEC']:
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subprocess.Popen(['python3', 'dock-single.py'],cwd=cwd)
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return render_template('display_result.html', filename="OwO", description=description,job=jobID)
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@ -12,9 +12,12 @@ EMAIL = navanchauhan@gmail.com
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PASSWORD = okrs shoc ahtk idui
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[LOGS]
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ERRORS = logs/errors.log
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INFO = data/info.log
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LOG = True
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SAVE_LOGS = False
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[FILES]
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UPLOAD_FOLDER = ./app/static/uploads
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TEMPLATES_FOLDER = templates
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LOG_FOLDER = ./app/logs/
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[EXECUTION]
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INSTANT = True
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