def check_queue(ip, port):
app = Flask(__name__)
app.config['SERVER_NAME'] = conf.SERVER_NAME
app.add_url_rule('/pathfinder/download/<uuid>', 'download', download)
with app.app_context():
db = get_db()
cur = db.cursor()
cur.execute('select * from job where status == ?', ('R',))
numjobs = 0
mail = None
for row in cur.fetchall():
uuid, email, date, status = row
# finished?
pid = int(open(os.path.join(get_job_folder(uuid), 'run.pid'), 'r').read())
if pid_exists(pid):
numjobs += 1
else:
mail = Mail(app)
msg = Message('[PathFinder] Your job is finished.', sender='*****@*****.**', recipients=[email, '*****@*****.**'])
if os.path.exists(os.path.join(get_job_folder(uuid), 'pathway.pdb')):
cur.execute('update job set status = ? where uuid = ?', ('F',uuid))
msg.body = render_template('email.tpl', uuid=uuid, has_error=False)
msg.attach('pathway.pdb', 'text/pdb', open(os.path.join(get_job_folder(uuid), 'pathway.pdb')).read())
else:
cur.execute('update job set status = ? where uuid = ?', ('E',uuid))
msg.body = render_template('email.tpl', uuid=uuid, has_error=True)
if numjobs < NUMJOBS_CONCUR:
cur.execute('select * from job where status == ?', ('Q',))
for row in cur.fetchall():
uuid, email, date, status = row
newpid = client(ip, port, "SPAWN:%s" % uuid)
open(os.path.join(get_job_folder(uuid), 'run.pid'), 'w').write(newpid)
cur.execute('update job set status = ? where uuid = ?', ('R',uuid))
numjobs += 1
if numjobs >= NUMJOBS_CONCUR: break
db.commit()
db.close()
if mail:
try:
mail.send(msg)
except:
pass
def handle_spawn(self, uuid):
cwd = os.getcwd()
os.chdir(get_job_folder(uuid))
os.system('/bin/csh ./run.com > run.out')
if __name__ == "__main__":
app = Flask(__name__, template_folder=os.path.join(conf.BASEDIR, 'templates'))
app.config['SERVER_NAME'] = conf.SERVER_NAME
app.add_url_rule('/anmpathway.cgi/download/<uuid>/<filename>', 'download', download)
app.add_url_rule('/anmpathway.cgi/download/<uuid>', 'download', download)
app.add_url_rule('/anmpathway.cgi/status/<uuid>', 'status', status)
mail = None
with app.app_context():
db = get_db()
cur = db.cursor()
cur.execute('select * from job where uuid == ?', (uuid,))
uuid, email, date, status = cur.fetchone()
open(os.path.join(get_job_folder(uuid), 'run.pid'), 'w').write(str(os.getpid()))
cur.execute('update job set status = ? where uuid = ?', ('R',uuid))
db.commit()
mail = Mail(app)
msg = Message('[ANMPathway] Your job has started.', sender=conf.ADMIN_EMAIL, recipients=[email], bcc=[conf.ADMIN_EMAIL, conf.EXTRA_EMAIL])
msg.html = render_template('email_started.tpl', uuid=uuid)
mail.send(msg)
etime = time.time()
cwd = os.getcwd()
os.chdir(get_job_folder(uuid))
os.system('/bin/csh ./run.com > run.out')
etime = time.time() - etime
mail = Mail(app)