removed extra files and changed zi to zipArchive

app/backend_test.py

@@ -1,99 +0,0 @@
-import mysql.connector as con
-
-mycon = con.connect(host="navanspi.duckdns.org",user="curieweb",password="curie-web-russian-54",port=3306,database="curie")
-mycursor = mycon.cursor()
-
-sql_select_Query = 'select * from curieweb where id="18u3r0chcf6nr6mj" LIMIT 1'
-mycursor.execute(sql_select_Query)
-
-records = mycursor.fetchall()
-
-def email(zi):
-    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 = "navanchauhan@gmail.com"
-    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"
-    attachment = open((str(zi) + ".zip"), "rb") 
-    p = MIMEBase('application', 'octet-stream') 
-    p.set_payload((attachment).read()) 
-    encoders.encode_base64(p) 
-    p.add_header('Content-Disposition', "attachment; filename= %s" % filename) 
-    msg.attach(p) 
-    
-    s = smtplib.SMTP('smtp.gmail.com', 587) 
-    s.starttls() 
-    s.login(fromaddr, 'ircd mday avbc tice') 
-    
-    text = msg.as_string() 
-    
-    s.sendmail(fromaddr, toaddr, text) 
-    s.quit() 
-
-receptor_name = "protein.pdbqt"
-ligand_name = "ligand.pdbqt"
-description = "Curie Web Task"
-
-#print(records[0])
-r = records[0]
-jobID = r[0]
-toEmail = r[1]
-targetB = r[2]
-if r[3] != None:
-    receptor_name = str(r[3])
-if r[6] != None:
-    ligand_name = str(r[6])
-ligandB = r[4]
-configB = r[7]
-date = r[8]
-if r[9] != None:
-    description = r[9]
-
-import os
-cd = os.getcwd()
-f = os.path.join(cd,"static/uploads")
-#t = os.path.join(f,"receptor",target)
-#r = os.path.join(f,"ligands",ligand)
-#c = os.path.join(f,"configs",config)
-print(f)
-import tempfile
-from shutil import copy
-from shutil import make_archive
-
-with tempfile.TemporaryDirectory() as directory:
-    print('The created temporary directory is %s' % directory)
-    os.chdir(directory)
-#    copy(t,os.getcwd())
-#    copy(r,os.getcwd())
-#    copy(c, os.getcwd())
-    file = open(receptor_name,"wb")
-    file.write(targetB)
-    file.close()
-    file = open(ligand_name,"wb")
-    file.write(ligandB)
-    file.close()
-    file = open("config.txt","wb")
-    file.write(configB)
-    file.close()
-    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))
-    #copy("report.pdf",f)
-    z = "Curie_Web_Result_"+str(jobID)
-    zi = os.path.join(f,z)
-    make_archive(zi, 'zip', directory)
-    #copy(("Curie_Web_Result_"+str(jobID)),f)
-    email(zi)
-    #print((str(zi) + ".zip"))
-    mycursor.execute('UPDATE curieweb set done=1 where id="%s"' % (jobID))
-    mycon.commit()    

app/create_table.py

@@ -1,17 +0,0 @@
-import mysql.connector as con
-
-mycon = con.connect(host="sql12.freesqldatabase.com",user="sql12352288",password="7X35JENbK3",port=3306,database="sql12352288")
-
-mycursor = mycon.cursor()
-
-try:
-    mycursor.execute("create table curie (id INT PRIMARY KEY, email VARCHAR(255), receptor VARCHAR(255), ligand VARCHAR(255), config VARCHAR(255), date DATE, description VARCHAR(255),done TINYINT DEFAULT 0)")
-except con.ProgrammingError:
-    print("Table Already Exists!")
-
-try:
-    mycursor.execute("insert into curie values (1,'navanchauhan@gmail.com','lu.pdbqt','test.pdbqt','owo.txt',CURDATE(),'CURIE WEB TASK',0)")
-except con.IntegrityError:
-    print("Duplicate Entry For Primary Key!")
-
-mycon.commit()

app/dbTestFiller.py

@@ -1,69 +0,0 @@
-import mysql.connector as con
-
-debug = False
-host = "navanspi.duckdns.org"
-done = 1
-
-if debug != False:
-    host = "192.168.1.6"
-    done = 0
-
-mycon = con.connect(host=host,user="curieweb",password="curie-web-russian-54",port=3306,database="curie")
-mycursor = mycon.cursor()
-
-try:
-    mycursor.execute("create table curieweb (    id varchar(16) primary key, email nvarchar(255) NOT NULL,   protein LONGBLOB NOT NULL, protein_name VARCHAR(255),  ligand_pdbqt LONGBLOB,   ligand_smile VARCHAR(255),   ligand_name VARCHAR(255),   config LONGBLOB NOT NULL, date DATE, description VARCHAR(255),   done TINYINT DEFAULT 0)")
-except con.ProgrammingError:
-    print("Table Already Exists!")
-
-#try:
-#    mycursor.execute("insert into curieweb values (1,'navanchauhan@gmail.com','lu.pdbqt','test.pdbqt','owo.txt',CURDATE(),'CURIE WEB TASK',0)")
-#except con.IntegrityError:
-#    print("Duplicate Entry For Primary Key!")
-
-from random import choice, shuffle
-from string import digits, ascii_lowercase
-
-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))
-    chars = [choice(bet) for bet in choose_from]
-    shuffle(chars)
-    return ''.join(chars)
-
-def convertToBinaryData(filename):
-    with open(filename, 'rb') as file:
-        binaryData = file.read()
-    return binaryData
-
-from os.path import basename
-
-ligand = convertToBinaryData("./static/uploads/ligands/test.pdbqt")
-receptor = convertToBinaryData("static/uploads/receptor/lu.pdbqt")
-config = convertToBinaryData("static/uploads/configs/owo.txt")
-ligandName = "Eucalyptol"
-receptorName = "6LU7"
-
-sqlQuery = "insert into curieweb (id, email, protein, protein_name, ligand_pdbqt, ligand_name,date, config,done) values (%s,%s,%s,%s,%s,%s,CURDATE(),%s,%s) "
-
-jobID = gen_word(16, 1, 1)
-print("Succesfuly submitted Job ID:",jobID)
-
-insert_tuple = (jobID,"navanchauhan@gmail.com",receptor,receptorName,ligand,ligandName,config,done)
-
-try:
-    mycursor.execute(sqlQuery,insert_tuple)
-except con.IntegrityError:
-    print("Oops, Collision occured. Generating new Job ID and trying again.")
-    jobID = gen_word(16, 1, 1)
-    insert_tuple = (jobID,"navanchauhan@gmail.com",receptor,receptorName,ligand,ligandName,config,done)
-    mycursor.execute(sqlQuery,insert_tuple)
-
-print("Removing Test Query")
-
-q = 'delete from curieweb where id="%s"' % (jobID)
-mycursor.execute(q)
-
-mycon.commit()
-
-print("Database working perfectly")

app/dock_docker.py

@@ -8,7 +8,7 @@ mycursor.execute(sql_select_Query)
 
 records = mycursor.fetchall()
 
-def email(zi):
+def email(zipArchive):
     import smtplib 
     from email.mime.multipart import MIMEMultipart 
     from email.mime.text import MIMEText 
@@ -26,7 +26,7 @@ def email(zi):
     
     msg.attach(MIMEText(body, 'plain')) 
     filename = "Curie_Web_Results_Job_ID_" + str(jobID) + ".zip"
-    attachment = open((str(zi) + ".zip"), "rb") 
+    attachment = open((str(zipArchive) + ".zip"), "rb") 
     p = MIMEBase('application', 'octet-stream') 
     p.set_payload((attachment).read()) 
     encoders.encode_base64(p) 

app/test.py

@@ -1,5 +0,0 @@
-import mysql.connector as con
-mycon = con.connect(host="sql12.freesqldatabase.com",user="sql12352288",password="7X35JENbK3",port=3306,database="sql12352288")
-mycursor = mycon.cursor()
-mycursor.execute("SELECT COUNT(*) FROM curie")
-id = mycursor.fetchall()[0][0]