def _configure_datatypes_registry( self, installed_repository_manager=None ):
from galaxy.datatypes import registry
# Create an empty datatypes registry.
self.datatypes_registry = registry.Registry()
if installed_repository_manager:
# Load proprietary datatypes defined in datatypes_conf.xml files in all installed tool shed repositories. We
# load proprietary datatypes before datatypes in the distribution because Galaxy's default sniffers include some
# generic sniffers (eg text,xml) which catch anything, so it's impossible for proprietary sniffers to be used.
# However, if there is a conflict (2 datatypes with the same extension) between a proprietary datatype and a datatype
# in the Galaxy distribution, the datatype in the Galaxy distribution will take precedence. If there is a conflict
# between 2 proprietary datatypes, the datatype from the repository that was installed earliest will take precedence.
installed_repository_manager.load_proprietary_datatypes()
# Load the data types in the Galaxy distribution, which are defined in self.config.datatypes_config.
self.datatypes_registry.load_datatypes( self.config.root, self.config.datatypes_config )
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)
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)
