import os import mysql.connector as con from mysql.connector.errors import InterfaceError GitHubWorkflow = True try: print(os.environ['GITHUB_ACTIONS']) except: GitHubWorkflow = False def returnValue(key): return os.environ[key] if GitHubWorkflow: host = returnValue("CURIE_HOST") db = returnValue("CURIE_DB") user = returnValue("CURIE_USER") port = returnValue("CURIE_PORT") password = returnValue("CURIE_PASSWORD") fromaddress = returnValue("CURIE_EMAIL") emailServer = returnValue("CURIE_EMAIL_SERVER") emailPort = returnValue("CURIE_EMAIL_PORT") emailPassword = returnValue("CURIE_EMAIL_PASSWORD") else: import configparser config = configparser.ConfigParser() config.read('config.ini') try: config['DATABASE'] except KeyError: config.read("../config.ini") v = config['DATABASE'] host = v['HOST'] db = v['NAME'] user = v['USER'] password = v['PASSWORD'] port = v['PORT'] fromaddress = config['SMTP']['EMAIL'] emailServer = config['SMTP']['SERVER'] emailPort = config['SMTP']['PORT'] emailPassword = config['SMTP']['PASSWORD'] try: mycon = con.connect(host=host,user=user,password=password,port=port,database=db) except InterfaceError: print("Could not connect to the database") sys.exit(1) mycursor = mycon.cursor() # If we are running the CI on an actual server, try using the 6LU7 Mpro and Geraniin Job ID because Eucalyptol fails sql_select_Query = 'select * from curieweb where id="l9xo2isr98oepcia" LIMIT 1' mycursor.execute(sql_select_Query) records = mycursor.fetchall() def email(compressedFile): import smtplib from email.mime.multipart import MIMEMultipart from email.mime.text import MIMEText from email.mime.base import MIMEBase from email import encoders fromaddr = fromaddress toaddr = toEmail msg = MIMEMultipart() msg['From'] = fromaddr msg['To'] = toaddr msg['Subject'] = "Curie Web Results for Job ID " + str(jobID) body = "Attached Zip contains the docked files, PLIP report and PyMOL Visualisations. If the ZIP file does not contain these files, please report this issue by replying to this email. Job was submitted on {} with the description {}".format(date, description) msg.attach(MIMEText(body, 'plain')) filename = "Curie_Web_Results_Job_ID_" + str(jobID) + ".zip" p = MIMEBase('application', 'octet-stream') with open((str(compressedFile) + ".zip"), "rb") as attachment: p.set_payload((attachment).read()) encoders.encode_base64(p) p.add_header('Content-Disposition', "attachment; filename= %s" % filename) msg.attach(p) s = smtplib.SMTP(emailServer, emailPort) s.starttls() s.login(fromaddr, emailPassword) text = msg.as_string() s.sendmail(fromaddr, toaddr, text) s.quit() receptor_name = "protein.pdbqt" ligand_name = "ligand.pdbqt" description = "Test" #print(records[0]) r = records[0] jobID = r[0] toEmail = r[1] targetB = r[2] if r[3] is not None: receptor_name = str(r[3]) if r[6] is not None: ligand_name = str(r[6]) ligandB = r[4] configB = r[7] date = r[8] if r[9] is not None: description = r[9] import os cd = os.getcwd() f = os.path.join(cd,"static/uploads") if ".pdbqt" not in receptor_name: receptor_name+=".pdbqt" if ".pdbqt" not in ligand_name: ligand_name+=".pdbqt" print(f) import tempfile from shutil import make_archive with tempfile.TemporaryDirectory() as directory: print('The created temporary directory is %s' % directory) os.chdir(directory) with open(receptor_name,"wb") as file: file.write(targetB) with open(ligand_name,"wb") as file: file.write(ligandB) with open("config.txt","wb") as file: file.write(configB) os.system("docker run --rm -v ${PWD}:/results -w /results -u $(id -u ${USER}):$(id -g ${USER}) navanchauhan/curie-cli -r %s -l %s -c config.txt -dpi" % (receptor_name,ligand_name)) z = "Curie_Web_Result_"+str(jobID) zi = os.path.join(f,z) make_archive(zi, 'zip', directory) email(zi) mycursor.execute('UPDATE curieweb set done=1 where id="%s"' % (jobID)) mycon.commit()