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/
Curie-Web
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added github action and local tests

This commit is contained in:
Navan Chauhan 2020-09-22 18:13:35 +05:30
parent 9ef980067d
commit a9c8e275e5
3 changed files with 143 additions and 27 deletions
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60
tests/backendTest.py
View File

@ -1,17 +1,50 @@
import os
import mysql.connector as con import mysql.connector as con
from mysql.connector.errors import InterfaceError from mysql.connector.errors import InterfaceError
import sys
import configparser GitHubWorkflow = True
config = configparser.ConfigParser()
config.read('config.ini')
try: try:
config['DATABASE'] print(os.environ['GITHUB_ACTIONS'])
except KeyError: except:
config.read("../config.ini") 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")
fromaddr = returnValue("CURIE_EMAIL")
emailServer = returnValue("CURIE_EMAIL_SERVER")
emailPort = returnValye("CURIE_EMAIL_PORT")
emailPassword = returnValye("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']
fromaddr = config['SMTP']['EMAIL']
emailServer = config['SMTP']['SERVER']
emailPort = config['SMTP']['PORT']
emailPassword = config['SMTP']['PASSWORD']
try: try:
mycon = con.connect(host=config['DATABASE']['HOST'],user=config['DATABASE']['USER'],password=config['DATABASE']['PASSWORD'],port=config['DATABASE']['PORT'],database=config['DATABASE']['NAME']) mycon = con.connect(host=host,user=user,password=password,port=port,database=db)
except InterfaceError: except InterfaceError:
print("Could not connect to the database") print("Could not connect to the database")
sys.exit(1) sys.exit(1)
@ -30,7 +63,7 @@ def email(compressedFile):
from email.mime.base import MIMEBase from email.mime.base import MIMEBase
from email import encoders from email import encoders
fromaddr = config['SMTP']['EMAIL'] fromaddr = fromaddr
toaddr = toEmail toaddr = toEmail
msg = MIMEMultipart() msg = MIMEMultipart()
@ -48,9 +81,9 @@ def email(compressedFile):
p.add_header('Content-Disposition', "attachment; filename= %s" % filename) p.add_header('Content-Disposition', "attachment; filename= %s" % filename)
msg.attach(p) msg.attach(p)
s = smtplib.SMTP(config['SMTP']['SERVER'], config['SMTP']['PORT']) s = smtplib.SMTP(emailServer, emailPort)
s.starttls() s.starttls()
s.login(fromaddr, config['SMTP']['PASSWORD']) s.login(fromaddr, emailPassword)
text = msg.as_string() text = msg.as_string()
@ -59,7 +92,7 @@ def email(compressedFile):
receptor_name = "protein.pdbqt" receptor_name = "protein.pdbqt"
ligand_name = "ligand.pdbqt" ligand_name = "ligand.pdbqt"
description = "GitHub Action Test" description = "Test"
#print(records[0]) #print(records[0])
r = records[0] r = records[0]
@ -103,6 +136,7 @@ with tempfile.TemporaryDirectory() as directory:
z = "Curie_Web_Result_"+str(jobID) z = "Curie_Web_Result_"+str(jobID)
zi = os.path.join(f,z) zi = os.path.join(f,z)
make_archive(zi, 'zip', directory) make_archive(zi, 'zip', directory)
#email(zi) email(zi)
mycursor.execute('UPDATE curieweb set done=1 where id="%s"' % (jobID)) mycursor.execute('UPDATE curieweb set done=1 where id="%s"' % (jobID))
mycon.commit() mycon.commit()

56
tests/dbTestFiller.py
View File

@ -1,12 +1,54 @@
import os
import mysql.connector as con import mysql.connector as con
import configparser from mysql.connector.errors import InterfaceError
config = configparser.ConfigParser()
config.read('config.ini') GitHubWorkflow = True
try: try:
config['DATABASE'] print(os.environ['GITHUB_ACTIONS'])
except KeyError: except:
config.read("../config.ini") GitHubWorkflow = False
mycon = con.connect(host=config['DATABASE']['HOST'],user=config['DATABASE']['USER'],password=config['DATABASE']['PASSWORD'],port=config['DATABASE']['PORT'],database=config['DATABASE']['NAME'])
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")
fromaddr = returnValue("CURIE_EMAIL")
emailServer = returnValue("CURIE_EMAIL_SERVER")
emailPort = returnValye("CURIE_EMAIL_PORT")
emailPassword = returnValye("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']
fromaddr = 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() mycursor = mycon.cursor()
done = 1 done = 1

54
tests/removeSample.py
View File

@ -1,14 +1,54 @@
import os
import mysql.connector as con import mysql.connector as con
import configparser from mysql.connector.errors import InterfaceError
config = configparser.ConfigParser()
config.read('config.ini') GitHubWorkflow = True
try: try:
config['DATABASE'] print(os.environ['GITHUB_ACTIONS'])
except KeyError: except:
config.read("../config.ini") 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")
fromaddr = returnValue("CURIE_EMAIL")
emailServer = returnValue("CURIE_EMAIL_SERVER")
emailPort = returnValye("CURIE_EMAIL_PORT")
emailPassword = returnValye("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']
fromaddr = 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)
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() mycursor = mycon.cursor()
print("Removing Test Query") print("Removing Test Query")