diff options
| -rw-r--r-- | .github/workflows/test-database.yaml | 29 | ||||
| -rw-r--r-- | tests/backendTest.py | 17 | ||||
| -rw-r--r-- | tests/dbTestFiller.py | 55 | ||||
| -rw-r--r-- | tests/removeSample.py | 20 |
4 files changed, 45 insertions, 76 deletions
diff --git a/.github/workflows/test-database.yaml b/.github/workflows/test-database.yaml deleted file mode 100644 index 36d00cb..0000000 --- a/.github/workflows/test-database.yaml +++ /dev/null @@ -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 diff --git a/tests/backendTest.py b/tests/backendTest.py index d172033..0965e0a 100644 --- a/tests/backendTest.py +++ b/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() diff --git a/tests/dbTestFiller.py b/tests/dbTestFiller.py index e56ea5c..02d51de 100644 --- a/tests/dbTestFiller.py +++ b/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") diff --git a/tests/removeSample.py b/tests/removeSample.py new file mode 100644 index 0000000..d054f60 --- /dev/null +++ b/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")
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