sys.path.insert( 1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib'))) from galaxy.datatypes.registry import Registry from galaxy.model import * # noqa from galaxy.model import set_datatypes_registry # More explicit than `*` import from galaxy.model.mapping import init from galaxy.model.orm.scripts import get_config if sys.version_info > (3, ): long = int registry = Registry() registry.load_datatypes() set_datatypes_registry(registry) db_url = get_config(sys.argv)['db_url'] sa_session = init('/tmp/', db_url).context # Helper function for debugging sqlalchemy queries... # http://stackoverflow.com/questions/5631078/sqlalchemy-print-the-actual-query def printquery(statement, bind=None): """ Print a query, with values filled in for debugging purposes *only* for security, you should always separate queries from their values please also note that this function is quite slow """ import sqlalchemy.orm if isinstance(statement, sqlalchemy.orm.Query):
def init_datatypes(self): datatypes_registry = registry.Registry() datatypes_registry.load_datatypes() model.set_datatypes_registry(datatypes_registry) self.datatypes_registry = datatypes_registry
def init_datatypes( self ): datatypes_registry = registry.Registry() datatypes_registry.load_datatypes() model.set_datatypes_registry( datatypes_registry )
def init_datatypes(self): datatypes_registry = registry.Registry() datatypes_registry.load_datatypes() model.set_datatypes_registry(datatypes_registry) datatypes_registry.set_external_metadata_tool = MockSetExternalTool() self.datatypes_registry = datatypes_registry
def datatypes_registry(): r = registry.Registry() r.load_datatypes() set_datatypes_registry(r)
from sqlalchemy.sql import label # noqa sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib'))) from galaxy.datatypes.registry import Registry from galaxy.model import * # noqa from galaxy.model import set_datatypes_registry # More explicit than `*` import from galaxy.model.mapping import init from galaxy.model.orm.scripts import get_config if sys.version_info > (3,): long = int registry = Registry() registry.load_datatypes() set_datatypes_registry(registry) db_url = get_config(sys.argv)['db_url'] sa_session = init('/tmp/', db_url).context # Helper function for debugging sqlalchemy queries... # http://stackoverflow.com/questions/5631078/sqlalchemy-print-the-actual-query def printquery(statement, bind=None): """ Print a query, with values filled in for debugging purposes *only* for security, you should always separate queries from their values please also note that this function is quite slow """ import sqlalchemy.orm if isinstance(statement, sqlalchemy.orm.Query):