def __init__(self,
greentConf=None,
config_file=os.path.join(os.path.dirname(__file__),
"rosetta.yml"),
delete_type_graph=False,
init_db=False,
build_indexes=False,
debug=False):
""" The constructor loads the config file an prepares the type graph.
If delete_type_graph flag is true, the graph is deleted entirely.
If the init_db flag is true, the type_graph will be loaded from the config file. """
self.debug = False
logger.debug("-- rosetta init.")
self.service_context = ServiceContext(greentConf)
self.core = self.service_context.core
""" Load configuration. """
with open(config_file, 'r') as stream:
self.config = yaml.load(stream)
self.operators = self.config["@operators"]
self.type_checks = self.config["@type_checks"]
# Abbreviation
self.cache = self.service_context.cache # core.service_context.cache
""" Initialize type graph. """
self.type_graph = TypeGraph(self.service_context, debug=debug)
self.synonymizer = Synonymizer(self.type_graph.concept_model, self)
""" Merge identifiers.org vocabulary into Rosetta vocab. """
self.identifiers = Identifiers()
if delete_type_graph:
logger.debug("--Deleting type graph")
self.type_graph.delete_all()
if init_db:
""" Initialize type graph metadata. """
'''
for k, v in self.identifiers.vocab.items():
if isinstance(v, str):
self.type_graph.find_or_create(k, v)
'''
self.type_graph.find_or_create_list(self.identifiers.vocab.items())
# self.configure_local_operators ()
self.type_graph.configure_operators(self.operators.items())
# self.configure_translator_registry ()
self.type_graph.cast_edges(self.type_checks)
if build_indexes:
"""Create neo4j indices for identifier on different labels"""
self.type_graph.create_constraints()
def __init__(self):
self.context = service_context = ServiceContext(
config=os.environ.get('greent.conf'))
self.generic_ont = GenericOntology(self.context, '')
