def get_files():
files_name = os.listdir(INSTANCES_FOLDER)
onto_base = get_ontology("/home/marjorie/Bureau/uploads/ontology/Tbox.owl").load()
if len(files_name) != 0:
for instance in files_name:
onto_base = get_ontology(INSTANCES_FOLDER + instance).load()
continue
def find_bad_smells_argparse(args):
if not (os.path.exists(P_ONTO_PATH) and os.path.isfile(P_ONTO_PATH)):
print('Ontology "%s" does not exist ...' %
os.path.basename(P_ONTO_PATH))
sys.exit(0)
get_ontology(P_ONTO_PATH).load()
find_bad_smells()
def test_parse_ontology():
"""
If the ontology does not contains any class the parse_ontology function should return []
If the ontology contains any class the parse_ontology function should return
a list with the ontology terms
"""
ontology = get_ontology('http://purl.obolibrary.org/obo/pizza.owl')
gene_ontology = get_ontology(
'http://www.geneontology.org/formats/oboInOwl#')
obo = get_ontology('http://purl.obolibrary.org/obo/')
ontology_terms = parse_ontology(ontology)
assert ontology_terms == []
with ontology:
class Pizza(Thing):
pass
class HawaiianPizza(Pizza):
pass
with obo:
class IAO_0000115(AnnotationProperty):
pass
with gene_ontology:
class hasExactSynonym(AnnotationProperty):
pass
Pizza.label = 'Pizza'
HawaiianPizza.label = 'Hawaiian Pizza'
Pizza.IAO_0000115.append('Italian dish')
HawaiianPizza.IAO_0000115.append(
'Controversial Italian dish with pineapple')
HawaiianPizza.hasExactSynonym.append('Ham and pineapple pizza')
ontology_terms = parse_ontology(ontology)
assert ontology_terms == [{
'ontologyId': 'pizza',
'ontologyTermId': 'Pizza',
'label': ['Pizza'],
'description': ['Italian dish'],
'synonyms': [],
'parents': ['Thing'],
'children': ['HawaiianPizza']
}, {
'ontologyId':
'pizza',
'ontologyTermId':
'HawaiianPizza',
'label': ['Hawaiian Pizza'],
'description': ['Controversial Italian dish with pineapple'],
'synonyms': ['Ham and pineapple pizza'],
'parents': ['Pizza'],
'children': []
}]
def load_ontology_modules():
global model_asset, model_fmea_iso, model_functional_system, model_iso
onto_path.append("./owl-files")
model_asset = get_ontology("asset.owl").load()
model_fmea_iso = get_ontology("fmea-iso.owl").load()
model_functional_system = get_ontology(
"functional-system-ontology.owl").load()
model_iso = get_ontology("LIS-14.owl").load()
return model_asset, model_fmea_iso, model_functional_system, model_iso
def parse(file: str):
onto = owl.get_ontology(file)
onto.load()
kb = get_kb(onto)
pbox_restrictions = pbox_parser.get_restrictions(onto)
return kb, pbox_restrictions
def main():
ontology = owl.get_ontology("./root-ontology.owl").load()
print()
for instrument in get_MIDI_instruments():
create_instrument_individual(ontology, instrument[1], instrument[0])
print_onto(ontology)
ontology.save("./root-ontology.owl")
def __init__(self, *args, onto_uri=None, **kwargs):
super().__init__(*args, **kwargs)
self.port = None
self.subgraph = None
self.bel_graph = None
self.url = "localhost:"
self.jid_domain = "@gtirouter.dsic.upv.es"
self.presence.approve_all = True
self.source = ColumnDataSource(dict(iterations=[], values=[]))
self.new_data = dict(iterations=[], values=[])
self.avail_contacts = {}
self.avail_observers = []
self.onto_uri = onto_uri
if onto_uri != None:
self.onto = owl.get_ontology(onto_uri).load()
print("Ontology: ", onto_uri)
self.bel_graph = nx.Graph()
self.bel_graph.add_nodes_from(list(self.onto.classes()))
print("Belief graph created from: ", list(self.onto.classes()))
print("Node: ", self.bel_graph.nodes())
self.avail_mutex = aioLock()
def loadOntology(self, reasoner=Reasoner.NONE, memory_java="10240"):
# self.world = World()
# Method from owlready
self.onto = get_ontology(self.urionto).load()
# self.onto = self.world.get_ontology(self.urionto).load()
# self.onto.load()
# self.classifiedOnto = get_ontology(self.urionto + '_classified')
owlready2.reasoning.JAVA_MEMORY = memory_java
owlready2.set_log_level(9)
if reasoner == Reasoner.PELLET:
try:
with self.onto: # it does add inferences to ontology
# Is this wrt data assertions? Check if necessary
# infer_property_values = True, infer_data_property_values = True
logging.info("Classifying ontology with Pellet...")
sync_reasoner_pellet(
) # it does add inferences to ontology
unsat = len(list(self.onto.inconsistent_classes()))
logging.info("Ontology successfully classified.")
if unsat > 0:
logging.warning(
f"There are {str(unsat)} unsatisfiable classes: {list(self.onto.inconsistent_classes())}"
)
except Exception:
logging.info("Classifying with Pellet failed.")
elif reasoner == Reasoner.HERMIT:
try:
with self.onto: # it does add inferences to ontology
logging.info("Classifying ontology with HermiT...")
sync_reasoner() # HermiT doe snot work very well....
unsat = len(list(self.onto.inconsistent_classes()))
logging.info("Ontology successfully classified.")
if unsat > 0:
logging.warning(
f"There are {str(unsat)} unsatisfiable classes: {list(self.onto.inconsistent_classes())}"
)
return f"{str(unsat)} unsatisfiable classes: {list(self.onto.inconsistent_classes())}"
except Exception:
logging.info("Classifying with HermiT failed.")
# End Classification
# report problem with unsat (Nothing not declared....)
# print(list(self.onto.inconsistent_classes()))
self.graph = default_world.as_rdflib_graph()
logging.info("There are {} triples in the ontology".format(
len(self.graph)))
def test_templateDriver(self):
"""Function to test the TemplateDriver functionality of the templating
engine. Validates that the 'cv' template can be rendered.
"""
# Importing CV template
cv_template = precis.templating.PrecisTemplate(
template_folder=TestConfig.template_cv
)
# Loading user ontology
user_ont = get_ontology(TestConfig.sample_rdf_data).load()
# Casting to RDFLib graph (for template driver)
user_graph = default_world.as_rdflib_graph()
# Loading user preferences (for the template)
user_prefs = open(TestConfig.template_prefs, 'r')
# Instantiating template driver
driver = precis.templating.TemplateDriver(
template=cv_template,
user_ont=user_ont,
user_graph=user_graph,
user_prefs=user_prefs
)
with open(TestConfig.template_cv_out, 'w') as f:
f.write(driver.buildTemplate())
def init_onto():
import owlready2 as ow
import pandas as pd
onto = ow.get_ontology(main_onto_name)
vivoNS = onto.get_namespace("http://vivoweb.org/ontology/core")
onto.load()
return onto, vivoNS
def updateConcepts(docId, ontoId, concepts):
log("Call to updateConcepts()")
import coruja_database
ontopath = coruja_database.getOntology(str(ontoId))
import owlready2
owlready2.default_world.ontologies.clear()
onto = owlready2.get_ontology("file://" + ontopath)
log("updateConcepts(): Onto world debug after load: " +
str(onto.world.ontologies))
try:
onto.load()
log("updateConcepts(): Load ontology " + ontopath)
except:
log("updateConcepts(): Error loading ontology " + ontopath)
return 0
log("updateConcepts(): Onto world debug: " + str(onto.world.ontologies))
log("updateConcepts(): Searching for " + onto.base_iri + str(docId))
status = 1
result = onto.search(iri=onto.base_iri + str(docId))
if (len(result) > 0):
document = result[0]
ontoConcepts = document.documentHasConcept
keepConcepts = []
if len(ontoConcepts) > 0:
for concept in ontoConcepts:
if concept.name in concepts:
keepConcepts.append(concept)
else:
log("updateConcepts(): Deleting concept: " + concept.name)
document.documentHasConcept = keepConcepts
else:
log("updateConcepts(): No concepts found")
status = 0
else:
status = 0
log("updateConcepts(): Document not found id=" + str(docId))
if status == 1:
try:
onto_file = open(ontopath, 'wb+')
#onto.save(file=ontopath, format="rdfxml")
onto.save(file=onto_file, format="rdfxml")
onto_file.flush()
onto_file.close()
del onto_file
log("updateConcepts(): Saved ontology to " + ontopath)
except:
log("updateConcepts(): Error saving ontology " + ontopath)
status = 0
else:
log("updateConcepts(): Empty ontology loaded " + ontopath)
try:
log("updateConcepts(): Destroying ontology " + onto.base_iri)
onto.destroy()
del onto
del owlready2
except:
log("updateConcepts(): Error destroying ontology:" + onto.base_iri)
gc.collect()
return status
def get_all_child_cells():
"""
Args:
cell_cls (dict): dict of cell type name : ontology thing
Returns a dict of cell type : list of child cell types.
"""
from owlready2 import get_ontology, default_world
cl_db_dir = os.path.join(PATH, 'data', 'cl.db')
default_world.set_backend(filename=cl_db_dir)
conn = sqlite3.connect(DB_DIR)
C = conn.cursor()
C.execute('SELECT * FROM cell_cl')
results = C.fetchall()
cell_cl = {r[0]: r[1] for r in results}
conn.close()
# open cell ontology
onto = get_ontology('cl.owl').load()
# http://owlready.8326.n8.nabble.com/Accessing-class-by-its-name-in-owlready2-td457.html
namespace = onto.get_namespace("http://purl.obolibrary.org/obo/")
cell_cls = dict()
for cell, cl in cell_cl.items():
cell_cls[cell] = namespace[cl]
cl_cells = {cl.get_name(cl) : cell for cell, cl in cell_cls.items()}
cells_children = dict()
for cell_name, cl in cell_cls.items():
children = list(cl.descendants())
cells_children[cell_name] = []
for child in children:
child_name = child.get_name(child)
if child_name in cl_cells:
cell_type = cl_cells[child.get_name(child)]
cells_children[cell_name].append(cell_type)
return cells_children
def addDocumentConceptsToOntology(docid, path, concepts):
import owlready2
onto = owlready2.get_ontology("file://" + path)
onto.load()
class Concept(owlready2.Thing):
namespace = onto
class Document(owlready2.Thing):
namespace = onto
currentDocument = Document(docid)
class documentHasConcept(owlready2.ObjectProperty):
namespace = onto
domain = [Document]
range = [Concept]
for concept in concepts:
currentConcept = Concept(concept)
currentDocument.documentHasConcept.append(currentConcept)
onto_file = open(path, 'wb+')
try:
onto.save(file=onto_file, format="rdfxml")
onto.destroy()
del onto
return True
except:
onto.destroy()
del onto
return False
def load_ontologies(ontology_arguments):
"""Loads the ontologies provided as a list of OntologyArgument.
Also loads all indirectly imported ontologies. Each ontology is prefixed
with the specified prefix (OntologyArgument.prefix) or with a generated
prefix (generate_prefix). The manually specified prefixes take precedence.
Args:
ontology_arguments: A list of OntologyArguments.
Returns:
A tuple, the first value is a list of loaded ontologies (owlready2
objects), the second value is the map of ontology names to the
prefix.
"""
ontology_prefix_map = {'owl': 'owl'}
ontologies = []
for ontology in ontology_arguments:
onto = owlready2.get_ontology(ontology.uri).load(reload=True)
ontologies.append(onto)
ontology_prefix_map[onto.ontology.name] = ontology.prefix
for ontology in ontologies:
for imported_ontology in ontology.indirectly_imported_ontologies():
onto_name = imported_ontology.ontology.name
if onto_name not in ontology_prefix_map:
ontologies.append(imported_ontology)
ontology_prefix_map[onto_name] = generate_prefix(onto_name)
return ontologies, ontology_prefix_map
def processOntodict(ontodict, ontopath, mtype):
log("Call to processOntodict() with ontopath: " + ontopath)
import owlready2
onto = owlready2.get_ontology("file://" + ontopath)
onto.load()
#class Concept(Thing):
# namespace = onto
#class Document(Thing):
# namespace = onto
clases = ontodict['clases']
concepts = ontodict['concepts']
if mtype == 1:
log("Generating clases...")
for classkey, classelem in clases.items():
ontoclass = classkey.title()
with onto:
NewClass = owlready2.types.new_class(ontoclass,
(onto.Concept, ),
kwds={})
for elem in classelem:
NewClass(elem.lower())
for concept in concepts:
docid = concept[1]
conceptname = concept[0]
with onto:
currentDocumentSearch = onto.search(iri=onto.base_iri + str(docid))
if len(currentDocumentSearch) > 0:
currentDocument = currentDocumentSearch[0]
else:
currentDocument = onto.Document(docid)
currentConceptSearch = onto.search(iri=onto.base_iri +
conceptname.lower())
if len(currentConceptSearch):
currentConcept = currentConceptSearch[0]
else:
currentConcept = onto.Concept(conceptname.lower())
currentDocument.documentHasConcept.append(currentConcept)
currentConcept.conceptInDocument.append(currentDocument)
onto_file = open(ontopath, 'wb+')
try:
onto.save(file=onto_file, format="rdfxml")
log("Saved file to path " + ontopath)
onto_file.close()
log("Call to destroy ontolgy: " + ontopath)
onto.destroy()
del onto
del owlready2
return True
except:
log("Error saving ontology, destroying object: " + ontopath)
onto.destroy()
del onto
del owlready2
return False
def insert_relations(specific_relations):
"""insert connected_to relations into onto"""
onto = get_ontology(IRI).load()
with onto:
for i in specific_relations:
onto[str(i[0]).split('.')[-1]].specifically_connected_to.\
append(onto[str(i[1]).split('.')[-1]])
onto.save(file=ONTOFILE)
def populate_from_uberon(self):
from owlready2 import get_ontology
o = get_ontology("file:///Users/andrew/Data/uberon.owl").load()
RegionalPartOfBrain = o.search(
iri="http://purl.obolibrary.org/obo/UBERON_0002616")[0]
parts_of_brain = o.search(subclass_of=RegionalPartOfBrain)
for cls in parts_of_brain:
print(cls.label[0], cls.iri)
def init_onto(onto_path):
"""Helper: read ontology file & run default reasoner.
"""
onto_path = 'file://' + onto_path
onto = owl.get_ontology(onto_path).load()
print('Loaded owl file at:', onto_path)
owl.sync_reasoner()
return onto
def get_scansion_graph(scansion):
"""Transform a scansion dictionary into a compliant LOD graph.
:param scansion: Dictionary with a Rantanplan-like scansion analysis
:return: RDFLib Graph with the individuals from scansion
"""
structural_onto = get_ontology(ONTOLOGIES["structural"]).load()
onto = add_structural_individuals(scansion, structural_onto)
return onto_to_graph(onto)
def dynamically_create_instances(iri, output, input_list):
"""create instances from list"""
onto = get_ontology(iri).load()
for i in input_list[1:]:
my_instance = getattr(onto, i[1])(i[0])
if i[2]:
my_instance.comment.append(i[2])
onto.save(file=output)
def __init__(self):
owl.onto_path.append("data/external_data")
self.ontology = owl.get_ontology("ontology.owl").load()
self.ontology_classes = set(self.ontology.classes())
self.lexicon = {}
for ontology_class in self.ontology_classes:
self.lexicon[ontology_class] = ontology_class.lex
def dynamically_create_classes(iri, output, input_list):
"""create classes from list"""
onto = get_ontology(iri).load()
with onto:
for i in input_list[1:]:
my_class = types.new_class(i[0], (getattr(onto, i[1]), ))
if i[2]:
my_class.comment.append(i[2])
onto.save(file=output)
def handle(self, *args, **options):
ontology = get_ontology(options['path_to_owl_file']).load()
self.process_option(options['import_categories'], ontology)
self.process_option(options['import_audiences'], ontology)
if not any([options['import_categories'], options['import_audiences']
]):
self.stderr.write(
'Specify --categories and/or --audiences to import onotologies.'
)
def getConcepts(documentId, ontoId):
import coruja_database
import time
log("Call to getConcepts(): docid = " + str(documentId) + " - ontid = " +
str(ontoId))
result = []
ontopath = coruja_database.getOntology(str(ontoId))
#Read temp file
tmpFilename = config.OntologyDir + str(int(time.time())) + "_tmp.owl"
copyfile(ontopath, tmpFilename)
log("getConcepts(): Copied ontology from " + ontopath + " to " +
tmpFilename)
import owlready2
owlready2.default_world.ontologies.clear()
getConceptsOnto = owlready2.get_ontology("file://" + tmpFilename)
log("getConcepts(): Onto world debug before load: " +
str(getConceptsOnto.world.ontologies))
#getConceptsOnto = get_ontology("file://" + ontopath)
try:
getConceptsOnto.load()
log("getConcepts(): Load ontology :" + tmpFilename)
#log("getConcepts(): Load ontology :" + ontopath)
except:
log("getConcepts(): Error loading ontology " + tmpFilename)
#log("getConcepts(): Error loading ontology " + ontopath)
return result
documents = getConceptsOnto.search(iri=getConceptsOnto.base_iri +
str(documentId))
log("getConcepts(): Onto world debug: " +
str(getConceptsOnto.world.ontologies))
if len(documents) > 0:
document = documents[0]
log("getConcepts(): Document found " + document.iri)
concepts = document.documentHasConcept
for concept in concepts:
if concept not in result:
result.append(concept.name)
if len(concepts) > 0:
log("getConcepts(): Concepts found: " + str(len(concepts)))
else:
log("getConcepts(): No concepts found.")
else:
log("No document found. docid = " + str(documentId))
os.remove(tmpFilename)
log("getConcepts(): Deleting temp file " + tmpFilename)
log("getConcepts(): Trying to destroy " + getConceptsOnto.base_iri)
try:
getConceptsOnto.destroy()
del getConceptsOnto
del owlready2
log("getConcepts(): Ontology destroyed")
except:
log("getConcepts(): Can not destroy ontology loaded")
gc.collect()
return result
def load_ontology():
print('Ontology loading...')
onto_path.append('ontology/')
onto_path.append('ontology/judo-master')
onto_path.append('ontology/lkif-core-master/')
onto = get_ontology(
'http://www.semanticweb.org/marko/ontologies/2020/3/lcr_onto.owl'
).load()
return onto
def __init__(self, onto_filename):
"""
Load ontology from file.
onto_filename: str,
"""
import owlready2 as owl
self._onto = owl.get_ontology(onto_filename).load()
def get_hpo_synonyms():
ont = owlready2.get_ontology(config.hpo_file)
ont.load()
g = owlready2.default_world.as_rdflib_graph()
hpo_ontology_syns = g.query(config.hpo_syns_statement,
initNs=HPO.hp_namespaces)
g.close()
results = [[id, synonym.toPython().lower()]
for (id, synonym) in hpo_ontology_syns]
return results
def read_ontology(path):
onto = get_ontology(path)
onto.load()
# Read classes
classes = []
for cl in onto.classes():
classes.append(str(cl).split('.')[1].lower())
return classes
def populate_ontology_argparse(args):
if args.source is None or not os.path.exists(args.source):
print('Enter a valid path to a directory containing java files...')
sys.exit(0)
elif not (os.path.exists(ONTO_PATH) and os.path.isfile(ONTO_PATH)):
print('Ontology "%s" does not exist ...' % os.path.basename(ONTO_PATH))
sys.exit(0)
onto = owlready2.get_ontology(ONTO_PATH).load()
populate_ontology(onto=onto, source=args.source)
def __init__(self, *args, **kwargs):
# Running superclass initialization
super(TestOntQuery, self).__init__(*args, **kwargs)
# Loading ontology
self.ont = get_ontology(TestConfig.sample_rdf_data).load()
# Casting to graph
self.graph = default_world.as_rdflib_graph()
# Instantiating OntQuery for tests
self.query = precis.OntQuery(ont=self.ont, graph=self.graph)