diff options
| -rw-r--r-- | app/__init__.py | 17 | ||||
| -rw-r--r-- | app/views.py | 88 | ||||
| -rw-r--r-- | config.ini | 9 |
3 files changed, 85 insertions, 29 deletions
diff --git a/app/__init__.py b/app/__init__.py index 8a397ec..b405e40 100644 --- a/app/__init__.py +++ b/app/__init__.py @@ -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 diff --git a/app/views.py b/app/views.py index 1e6b269..c296f68 100644 --- a/app/views.py +++ b/app/views.py @@ -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) @@ -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
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