def setUp(self):
alchemist = AlchemyHandler()
alchemist.username = "******"
alchemist.password = "******"
alchemist.database = "test_db"
alchemist.connect()
alchemist.build_graph()
self.alchemist = alchemist
self.db_filter = Filter(alchemist=self.alchemist)
phageid = self.alchemist.get_column("phage.PhageID")
self.phageid = phageid
def build_alchemist(database, ask_database=True, config=None, dialect="mysql"):
if config is not None:
username = config["mysql"].get("user")
password = config["mysql"].get("password")
if not (username is None or password is None):
alchemist = AlchemyHandler(username=username, password=password,
dialect=dialect)
alchemist.connect(login_attempts=0, pipeline=True)
alchemist.database = database
alchemist.connect(ask_database=ask_database, pipeline=True)
return alchemist
alchemist = AlchemyHandler(database=database)
alchemist.connect(ask_database=ask_database, pipeline=True)
return alchemist
def setUp(self):
alchemist = AlchemyHandler()
alchemist.username=user
alchemist.password=pwd
alchemist.database=db
alchemist.connect()
self.alchemist = alchemist
self.db_filter = Filter(alchemist=self.alchemist)
self.phage = self.alchemist.metadata.tables["phage"]
self.gene = self.alchemist.metadata.tables["gene"]
self.trna = self.alchemist.metadata.tables["trna"]
self.PhageID = self.phage.c.PhageID
self.Cluster = self.phage.c.Cluster
self.Subcluster = self.phage.c.Subcluster
self.Notes = self.gene.c.Notes