def __init__(self):
handlers = [(r"^/ajax/([a-z]*)/(.*)", AjaxHandler),
(r"^/substance/(.*)", SimpleHtmlHandlerWithId),
(r"^/run/(.*)", RunSparkHandler),
(r"^/mzimage/([^/]*)\.png", MZImageHandler),
(r"^/mzimage/([^/]*)/([^/]*)\.png", MZImageParamHandler),
(r"^/jobs/", SimpleHtmlHandler),
(r"^/datasets/", SimpleHtmlHandler),
(r"^/fullresults/(.*)", SimpleHtmlHandlerWithId),
(r"/", IndexHandler)]
settings = dict(static_path=path.join(os.path.dirname(__file__),
"static"),
debug=True)
config_db = dict(host="/var/run/postgresql/",
db="ims",
user="******",
password="")
tornado.web.Application.__init__(self, handlers, **settings)
# Have one global connection to the blog DB across all handlers
self.db = tornpsql.Connection(config_db['host'], config_db['db'],
config_db['user'], config_db['password'],
5432)
self.conf = SparkConf().setMaster("local[2]").setAppName(
"IMS Webserver v0.2").set("spark.ui.showConsoleProgress", "false")
self.sc = SparkContext(conf=self.conf)
self.status = self.sc.statusTracker()
self.max_jobid = self.db.get("SELECT max(id) as maxid FROM jobs").maxid
self.max_jobid = int(self.max_jobid) if self.max_jobid != None else 0
self.jobs = {}
def run(self):
db = tornpsql.Connection(database='tornpsql')
pubsub = db.pubsub()
pubsub.subscribe(('example', 'other', 'exit', 'unsub', 'unsuball'))
for notify in pubsub.listen():
if notify.channel == 'exit':
db.close()
break
elif notify.channel == 'unsub':
pubsub.unsubscribe(('example', ))
elif notify.channel == 'unsuball':
pubsub.unsubscribe()
else:
db.query(
"insert into notices (channel, payload) values (%s, %s);",
notify.channel, notify.payload)
def __init__(self):
routes = [
(r"/", handlers.MainHandler),
(r"/mpg",handlers.MpgHandler),
(r"/mpg-view",handlers.MpgViewHandler),
(r"/pi",handlers.PiHandler),
(r"/login", handlers.LoginHandler),
(r"/logout", handlers.LogoutHandler),
(r"/signup", handlers.SignupHandler),
(r"/.*", handlers.MainHandler),
]
# connects to database
self.db = tornpsql.Connection()
settings = dict(
template_path=os.path.join(os.path.dirname(__file__), "templates"),
static_path=os.path.join(os.path.dirname(__file__), "static"),
debug=(os.getenv("DEBUG")=='true'),
cookie_secret=os.getenv("COOKIE_SECRET")
)
tornado.web.Application.__init__(self, routes, **settings)
def __init__(self, debug=False):
"""Initializes handlers, including the spark handler, sets up database connection."""
handlers = [
(r"/", misc.IndexHandler),
(r"/auth", auth.AuthenticateClient),
(r"/feedback-rating", feedback.FeedbackRating),
(r"/feedback-comment", feedback.FeedbackComment),
# (r"/static/(.*)", tornado.web.StaticFileHandler, {"path": path.join(path.dirname(__file__), "static")}),
(r"^/results_table/(.*)", results_table.ResultsTableHandler),
(r"^/mzimage2/([^/]+)/([^/]+)/([^/]+)/([^/]+)/([^/]+)/([^/]+)",
iso_image_gen.AggIsoImgPngHandler),
(r"^/mzimage2/([^/]+)/([^/]+)/([^/]+)/([^/]+)/([^/]+)/([^/]+)/([^/]+)",
iso_image_gen.IsoImgPngHandler),
(r"^/spectrum_line_chart_data/([^/]+)/([^/]+)/([^/]+)/([^/]+)",
misc.SpectrumLineChartHandler),
(r"^/sf_peak_mzs/([^/]+)/([^/]+)/([^/]+)/([^/]+)",
misc.SFPeakMZsHandler),
(r"^/min_max_int/([^/]+)/([^/]+)/([^/]+)/([^/]+)",
misc.MinMaxIntHandler),
]
settings = dict(static_path=path.join(path.dirname(__file__),
'static'),
template_path=path.join(path.dirname(__file__),
'html'),
cookie_secret='59x6wj71r6462o16PSFsouy5QnaviACW',
debug=debug,
compress_response=True)
config_db = config["db"]
tornado.web.Application.__init__(self, handlers, **settings)
# Have one global connection to the blog DB across all handlers
self.db = tornpsql.Connection(config_db['host'], config_db['database'],
config_db['user'], config_db['password'],
5432)
# hack needed to overcome sending expensive query every time results table is filtered or sorted
self.adducts = [
row['adduct'] for row in self.db.query(
'select distinct(target_add) as adduct from target_decoy_add')
]
def test_connection_from_url(self):
"can connect from the os.getenv('DATABASE_URL')"
db = tornpsql.Connection()
self.assertTrue(db.get("select true as connected").connected)
def test_connection_via_url(self):
"can test connect with args"
db = tornpsql.Connection(os.getenv("ALTERNATE_DATABASE_URL"))
self.assertTrue(db.get("select true as connected").connected)
def test_connection_args(self):
"test connect with args"
db = tornpsql.Connection("127.0.0.1", "tornpsql", os.getenv("postgres", None))
self.assertTrue(db.get("select true as connected").connected)
def setUpClass(self):
try:
self.db = tornpsql.Connection(database="tornpsql")
except:
pass
def __init__(self, *a, **k):
Inquiry.__init__(self, *a, **k)
self.db = tornpsql.Connection(
os.getenv("PSQL", "postgres://peak:@localhost:5432/inquiry"))
def setUpClass(self):
PubSubThread()
self.db = tornpsql.Connection(database="tornpsql")