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