def create_ontology(handle=None, **args): ont = None logging.info( "Determining strategy to load '{}' into memory...".format(handle)) if handle.find("+") > -1: handles = handle.split("+") onts = [create_ontology(ont) for ont in handles] ont = onts.pop() ont.merge(onts) return ont # TODO: consider replacing with plugin architecture if handle.find(".") > 0 and os.path.isfile(handle): logging.info("Fetching obograph-json file from filesystem") ont = translate_file_to_ontology(handle, **args) elif handle.startswith("obo:"): logging.info("Fetching from OBO PURL") if handle.find(".") == -1: if handle == 'chebi' or handle == 'ncbitaxon' or handle == 'pr': handle += '.obo' logging.info("using obo for large ontology: {}".format(handle)) else: handle += '.owl' fn = '/tmp/' + handle if not os.path.isfile(fn): url = handle.replace("obo:", "http://purl.obolibrary.org/obo/") cmd = ['owltools', url, '-o', '-f', 'json', fn] cp = subprocess.run(cmd, check=True) logging.info(cp) else: logging.info("using cached file: " + fn) g = obograph_util.convert_json_file(fn) ont = Ontology(handle=handle, payload=g) elif handle.startswith("wdq:"): from ontobio.sparql.wikidata_ontology import EagerWikidataOntology logging.info("Fetching from Wikidata") ont = EagerWikidataOntology(handle=handle) elif handle.startswith("skos:"): fn = handle.replace('skos:', '') from ontobio.sparql.skos import Skos logging.info("Fetching from Skos file") skos = Skos() ont = skos.process_file(fn) elif handle.startswith("scigraph:"): from ontobio.neo.scigraph_ontology import RemoteScigraphOntology logging.info("Fetching from SciGraph") ont = RemoteScigraphOntology(handle=handle) elif handle.startswith("http:"): logging.info("Fetching from Web PURL: " + handle) encoded = hashlib.sha256(handle.encode()).hexdigest() #encoded = binascii.hexlify(bytes(handle, 'utf-8')) #base64.b64encode(bytes(handle, 'utf-8')) logging.info(" encoded: " + str(encoded)) fn = '/tmp/' + encoded if not os.path.isfile(fn): cmd = ['owltools', handle, '-o', '-f', 'json', fn] cp = subprocess.run(cmd, check=True) logging.info(cp) else: logging.info("using cached file: " + fn) g = obograph_util.convert_json_file(fn) ont = Ontology(handle=handle, payload=g) else: logging.info("Fetching from SPARQL") ont = EagerRemoteSparqlOntology(handle=handle) #g = get_digraph(handle, None, True) return ont