removing hardcoded values

testing updated github workflow

.github/workflows/test-database.yaml

@@ -1,29 +0,0 @@
-name: Test Database
-
-on: [push]
-
-jobs:
-  build:
-
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: [3.7]
-
-    steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install flake8 mysql-connector mysql
-    - name: Lint script with flake8
-      run: |
-        flake8 ./tests/dbTestFiller.py --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 ./tests/dbTestFiller.py --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Run Database-Filler script
-      run: cd tests && python dbTestFiller.py

tests/backendTest.py

@@ -1,6 +1,15 @@
 import mysql.connector as con
 
-mycon = con.connect(host="navanspi.duckdns.org",user="curieweb",password="curie-web-russian-54",port=3306,database="curie")
+import configparser
+config = configparser.ConfigParser()
+config.read('config.ini')
+
+try:
+    config['DATABASE']
+except KeyError:
+    config.read("../config.ini")
+
+mycon = con.connect(host=config['DATABASE']['HOST'],user=config['DATABASE']['USER'],password=config['DATABASE']['PASSWORD'],port=config['DATABASE']['PORT'],database=config['DATABASE']['NAME'])
 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
@@ -16,7 +25,7 @@ def email(compressedFile):
     from email.mime.base import MIMEBase 
     from email import encoders 
     
-    fromaddr = "navanchauhan@gmail.com"
+    fromaddr = config['SMTP']['EMAIL']
     toaddr = toEmail
     
     msg = MIMEMultipart()  
@@ -34,9 +43,9 @@ def email(compressedFile):
     p.add_header('Content-Disposition', "attachment; filename= %s" % filename) 
     msg.attach(p) 
     
-    s = smtplib.SMTP('smtp.gmail.com', 587) 
+    s = smtplib.SMTP(config['SMTP']['SERVER'], config['SMTP']['PORT']) 
     s.starttls() 
-    s.login(fromaddr, 'okrs shoc ahtk idui') 
+    s.login(fromaddr, config['SMTP']['PASSWORD']) 
     
     text = msg.as_string() 
     

tests/dbTestFiller.py

@@ -1,30 +1,14 @@
 import mysql.connector as con
-
-debug = False
-host = "navanspi.duckdns.org"
-done = 1
-
-if debug:
-    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()
-
+import configparser
+config = configparser.ConfigParser()
+config.read('config.ini')
 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!")
-
-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)
+    config['DATABASE']
+except KeyError:
+    config.read("../config.ini")
+mycon = con.connect(host=config['DATABASE']['HOST'],user=config['DATABASE']['USER'],password=config['DATABASE']['PASSWORD'],port=config['DATABASE']['PORT'],database=config['DATABASE']['NAME'])
+mycursor = mycon.cursor()
+done = 1
 
 def convertToBinaryData(filename):
     with open(filename, 'rb') as file:
@@ -36,27 +20,12 @@ receptor = convertToBinaryData("./files/6LU7.pdbqt")
 config = convertToBinaryData("./files/6LU7.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)
+jobID = "l9xo2isr98oepcia"
 
 insert_tuple = (jobID,"b5bmf.{curie-gh-ci}@inbox.testmail.app",receptor,receptorName,ligand,ligandName,config,done)
+mycursor.execute(sqlQuery,insert_tuple)
+print("Succesfuly submitted Job ID:",jobID)
 
-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,"b5bmf.{curie-gh-ci}@inbox.testmail.app",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")

tests/removeSample.py

@@ -0,0 +1,20 @@
+import mysql.connector as con
+import configparser
+config = configparser.ConfigParser()
+config.read('config.ini')
+
+try:
+    config['DATABASE']
+except KeyError:
+    config.read("../config.ini")
+
+mycon = con.connect(host=config['DATABASE']['HOST'],user=config['DATABASE']['USER'],password=config['DATABASE']['PASSWORD'],port=config['DATABASE']['PORT'],database=config['DATABASE']['NAME'])
+mycursor = mycon.cursor()
+
+print("Removing Test Query")
+jobID = "l9xo2isr98oepcia"
+q = 'delete from curieweb where id="%s"' % (jobID)
+mycursor.execute(q)
+mycon.commit()
+
+print("Database working perfectly")