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