def ready(self):
global world
global ontology
global graph
if world is None:
world = owlready2.World(filename=settings.FLONT_DB)
if ontology is None:
ontology = world.get_ontology(
"https://ontology.chalier.fr/flont").load()
if graph is None:
graph = world.as_rdflib_graph()
def rereason(G, filename):
world = owlready2.World()
with open(filename, 'wb') as f:
f.write(G.serialize(format='ntriples'))
on = world.get_ontology(f"file://./{filename}").load()
owlready2.sync_reasoner(world, infer_property_values=True)
G = world.as_rdflib_graph()
G.bind('rdf', RDF)
G.bind('owl', OWL)
G.bind('rdfs', RDFS)
G.bind('skos', SKOS)
G.bind('brick', BRICK)
G.bind('tag', TAG)
G.bind('bldg', BLDG)
return G
def __init__(self,
subfolder_id="000",
folder="IIMB_LARGE",
filename="onto.owl"):
""" Load an ontology from a given folder.
By extracting the default folder IIMB_LARGE, subfolders are of the
form 000, 001, 002, ..., 080. Each contains a file onto.owl with an
ontology in XML format.
This method intializes a Ontology object by loading the content of a
given folder.
"""
self.iri = os.path.join("file://", sys.path[0], folder, subfolder_id,
filename)
print("Loading ontology at", self.iri)
owl.Ontology.__init__(self, owl.World(), base_iri=self.iri + "#")
self.load()
import owlready2 as owl
import pathlib
# import rdflib
tpoPath = pathlib.Path('../TissuePhenomics.owl')
importsPath = pathlib.Path('..\imports')
clPath = importsPath / 'cl_import.owl'
# TPO
tpoWorld = owl.World()
if tpoPath.exists():
owl.onto_path.append(str(tpoPath.parent.resolve()))
owl.onto_path.append(str(importsPath.resolve()))
try:
tpo = tpoWorld.get_ontology(str(
tpoPath.resolve())).load(only_local=True)
except:
pass
else:
raise FileNotFoundError
# CL Imports
clWorld = owl.World()
if clPath.exists():
owl.onto_path.append(str(clPath.parent.resolve()))
owl.onto_path.append(str(importsPath.resolve()))
try:
cl = clWorld.get_ontology(str(clPath.resolve())).load(only_local=True)
except:
pass
else:
def GetOntology(cls, iri, doReasoner=False, cachePath=None):
iri_hash = cls.IRI_HASH.get(iri)
if iri_hash is None:
cls.IRI_HASH[iri] = iri_hash = hashlib.sha1(
iri.encode('utf-8')).hexdigest()
onto = cls.ONTO_CACHE.get(iri_hash)
if onto is None:
worldDB = cls.TermWorlds.get(iri_hash)
if worldDB is None:
worldDBPath = cls.GetWorldDBPath(iri_hash, cachePath)
# Activate this only if you want to save a copy of the ontologies
#ontologiesPath = os.path.join(cachePath,'ontologies')
#os.makedirs(ontologiesPath,exist_ok=True)
#owlready2.onto_path.append(ontologiesPath)
worldDB = owlready2.World(filename=worldDBPath,
exclusive=False)
cls.TermWorlds[iri_hash] = worldDB
# Trying to get the metadata useful for an optimal ontology download
metadataPath = cls.GetMetadataPath(iri_hash, cachePath)
if os.path.exists(metadataPath):
try:
with open(metadataPath, mode='r',
encoding='utf-8') as metadata_fh:
metadata = json.load(metadata_fh)
except:
# A corrupted cache should not disturb
metadata = {}
else:
metadata = {}
ontologyPath = cls.GetOntologyPath(iri_hash, cachePath)
gotPath, gotMetadata = download_file(iri, ontologyPath, metadata)
if gotPath:
gotMetadata['orig_url'] = iri
# Reading the ontology
with open(ontologyPath, mode="rb") as onto_fh:
onto = worldDB.get_ontology(iri).load(fileobj=onto_fh,
reload=True)
# Save the metadata
with open(metadataPath, mode="w",
encoding="utf-8") as metadata_fh:
json.dump(gotMetadata, metadata_fh)
# Re-save once the reasoner has run
if doReasoner:
worldDB.save()
owlready2.sync_reasoner(onto)
else:
onto = worldDB.get_ontology(iri).load()
worldDB.save()
# And now unlink the ontology (if exists)
if os.path.exists(ontologyPath):
os.unlink(ontologyPath)
cls.ONTO_CACHE[iri_hash] = onto
return onto
#!/usr/bin/env python3
import os, shutil
import owlready2
CachePath = '/tmp/onto'
shutil.rmtree(CachePath, ignore_errors=True)
os.makedirs(CachePath, exist_ok=True)
owlready2.onto_path.append(CachePath)
import time
w = owlready2.World(filename=os.path.join(CachePath, 'firstDirect.sqlite3'),
exclusive=False)
print("FirstDirect")
onto1 = w.get_ontology(
'https://raw.githubusercontent.com/inab/OEB-ontologies/master/oebDataFormats.owl'
).load()
w.save()
onto1.save()
res1 = onto1.search(label="participant")
import pprint
pprint.pprint(res1)
theRes = res1[0]
print("{0} => {1}".format(theRes.label, theRes.iri))
w = owlready2.World(filename=os.path.join(CachePath, 'firstIndirect1.sqlite3'),
exclusive=False)
print("FirstIndirect1")
#!/usr/bin/env python3
import os , shutil
import owlready2
CachePath = '/tmp/onto'
shutil.rmtree(CachePath,ignore_errors=True)
os.makedirs(CachePath,exist_ok=True)
owlready2.onto_path.append(CachePath)
import time
w = owlready2.World(filename='/tmp/onto/firstDirect.sqlite3', exclusive=False)
print("FirstDirect")
onto1 = w.get_ontology('https://raw.githubusercontent.com/inab/OEB-ontologies/master/oebDatasets.owl').load()
w.save()
onto1.save()
res1 = onto1.search(label = "participant")
import pprint
pprint.pprint(res1)
theRes = res1[0]
print("{0} => {1}".format(theRes.label,theRes.iri))
w = owlready2.World(filename='/tmp/onto/firstIndirect1.sqlite3', exclusive=False)
print("FirstIndirect1")
onto1 = w.get_ontology('https://w3id.org/oebDatasets/').load()
w.save()
onto1.save()
res1 = onto1.search(label = "participant")
'owlready2': {},
'reasonable': {},
}
# owlready2
import owlready2
for data_file in data_files:
print(f"Benching owlready2 on {data_file}")
all_samples['owlready2'][data_file] = []
for i in range(N):
g = rdflib.Graph()
load_file(g, data_file)
for ont_file in ontology_files:
load_file(g, ont_file)
g.serialize("_owlready2_input.ttl", format="ttl")
world = owlready2.World()
onto = world.get_ontology(f"file://./_owlready2_input.ttl").load()
t0 = time.time()
owlready2.sync_reasoner(world, infer_property_values=True)
G = world.as_rdflib_graph()
t1 = time.time()
print(f" owlready2: {data_file} took {t1-t0}")
all_samples['owlready2'][data_file].append({
'duration': t1 - t0,
'triples': len(G)
})
# OWLRL
import owlrl
for data_file in data_files:
print(f"Benching owlrl on {data_file}")
def load(self):
"""Load the ontology schema.
"""
uri = "file://" + os.path.join(os.getcwd(), self.folder, "schema.owl")
self.world = owlready2.World()
self.ontology = self.world.get_ontology(uri).load()