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‎owlapy/owlapi_adaptor.py‎

Lines changed: 87 additions & 88 deletions
Original file line numberDiff line numberDiff line change
@@ -6,23 +6,69 @@
66
from owlapy.iri import IRI
77
from owlapy.owl_individual import OWLNamedIndividual
88
from owlapy.render import owl_expression_to_manchester
9+
from typing import List
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10-
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# TODO:What are the downsides of start() close() fashion ?:
1211
class OWLAPIAdaptor:
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"""
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A class to interface with the OWL API using the HermiT reasoner, enabling ontology management,
14+
reasoning, and parsing class expressions in Manchester OWL Syntax.
15+
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Attributes:
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path (str): The file path to the ontology.
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name_reasoner (str): The reasoner to be used, default is "HermiT".
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manager: The OWL ontology manager.
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ontology: The loaded OWL ontology.
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reasoner: The HermiT reasoner for the ontology.
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parser: The Manchester OWL Syntax parser.
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renderer: The Manchester OWL Syntax renderer.
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__is_open (bool): Flag to check if the JVM is open.
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"""
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def __init__(self, path: str, name_reasoner: str = "HermiT"):
27+
"""
28+
Initialize the OWLAPIAdaptor with a path to an ontology and a reasoner name.
29+
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Args:
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path (str): The file path to the ontology.
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name_reasoner (str, optional): The reasoner to be used. Defaults to "HermiT".
1333
14-
def __init__(self, path: str, reasoner: str = "HermiT"):
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Raises:
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AssertionError: If the provided reasoner name is not implemented.
36+
"""
1537
self.path = path
16-
assert reasoner in ["HermiT"], f"{reasoner} is not implemented. Please use HermiT"
17-
self.reasoner = reasoner
38+
assert name_reasoner in ["HermiT"], f"{name_reasoner} is not implemented. Please use HermiT"
39+
self.name_reasoner = name_reasoner
40+
# Attributes are initialized as JVMStarted is started
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# () Manager is needed to load an ontology
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self.manager = None
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# () Load a local ontology using the manager
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self.ontology = None
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# () Create a HermiT reasoner for the loaded ontology
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self.reasoner = None
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self.parser = None
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# () A manchester renderer to render owlapi ce to manchester syntax
49+
self.renderer = None
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self.open()
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self.__is_open = True
1852

1953
def __exit__(self, exc_type, exc_val, exc_tb):
2054
"""Shuts down the java virtual machine hosted by jpype."""
21-
if jpype.isJVMStarted() and not jpype.isThreadAttachedToJVM():
22-
jpype.shutdownJVM()
55+
self.close()
2356

2457
def __enter__(self):
25-
"""Initialization via the `with` statement"""
58+
"""
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Initialization via the `with` statement.
60+
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Returns:
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OWLAPIAdaptor: The current instance.
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"""
64+
if not self.__is_open:
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self.open()
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return self
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def open(self):
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"""
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Start the JVM with jar dependencies, import necessary OWL API dependencies, and initialize attributes.
71+
"""
2672
if not jpype.isJVMStarted():
2773
# Start a java virtual machine using the dependencies in the respective folder:
2874
if os.getcwd()[-6:] == "owlapy":
@@ -36,7 +82,7 @@ def __enter__(self):
3682
# Import Java classes
3783
from org.semanticweb.owlapi.apibinding import OWLManager
3884
from java.io import File
39-
if self.reasoner == "HermiT":
85+
if self.name_reasoner == "HermiT":
4086
from org.semanticweb.HermiT import ReasonerFactory
4187
else:
4288
raise NotImplementedError("Not implemented")
@@ -60,105 +106,58 @@ def __enter__(self):
60106
bidi_provider = BidirectionalShortFormProviderAdapter(self.manager, ontology_set, SimpleShortFormProvider())
61107
entity_checker = ShortFormEntityChecker(bidi_provider)
62108
self.parser = ManchesterOWLSyntaxClassExpressionParser(self.manager.getOWLDataFactory(), entity_checker)
63-
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# A manchester renderer to render owlapi ce to manchester syntax
65110
self.renderer = ManchesterOWLSyntaxOWLObjectRendererImpl()
66111

67-
return self
112+
def close(self, *args, **kwargs) -> None:
113+
"""Shuts down the java virtual machine hosted by jpype."""
114+
if jpype.isJVMStarted() and not jpype.isThreadAttachedToJVM():
115+
jpype.shutdownJVM()
116+
self.__is_open = False
68117

69118
def convert_to_owlapi(self, ce: OWLClassExpression):
70-
""" Converts an owlapy ce to an owlapi ce.
119+
"""
120+
Converts an OWLAPY class expression to an OWLAPI class expression.
71121
72-
Args:
73-
ce (OWLClassExpression): class expression in owlapy format to be converted.
122+
Args:
123+
ce (OWLClassExpression): The class expression in OWLAPY format to be converted.
74124
75-
Return:
76-
Class expression in owlapi format.
125+
Returns:
126+
The class expression in OWLAPI format.
77127
"""
78128
return self.parser.parse(owl_expression_to_manchester(ce))
79129

80130
def convert_from_owlapi(self, ce, namespace: str) -> OWLClassExpression:
81-
"""Converts an owlapi ce to an owlapy ce.
131+
"""
132+
Converts an OWLAPI class expression to an OWLAPY class expression.
82133
83-
Args:
84-
ce: Class expression in owlapi format.
85-
namespace: Ontology's namespace where class expression belongs.
134+
Args:
135+
ce: The class expression in OWLAPI format.
136+
namespace (str): The ontology's namespace where the class expression belongs.
86137
87-
Return:
88-
Class expression in owlapy format.
138+
Returns:
139+
OWLClassExpression: The class expression in OWLAPY format.
89140
"""
90141
return manchester_to_owl_expression(str(self.renderer.render(ce)), namespace)
91142

92-
def instances(self, ce: OWLClassExpression):
93-
""" Get the instances for a given class expression using HermiT.
94-
Args:
95-
ce: Class expression in owlapy format.
143+
def instances(self, ce: OWLClassExpression)->List[OWLNamedIndividual]:
144+
"""
145+
Get the instances for a given class expression using HermiT.
146+
147+
Args:
148+
ce (OWLClassExpression): The class expression in OWLAPY format.
96149
97-
Return:
98-
Individuals which are classified by the given class expression.
150+
Returns:
151+
list: A list of individuals classified by the given class expression.
99152
"""
100153
inds = self.reasoner.getInstances(self.convert_to_owlapi(ce), False).getFlattened()
101154
return [OWLNamedIndividual(IRI.create(str(ind)[1:-1])) for ind in inds]
102155

103156
def has_consistent_ontology(self) -> bool:
104-
""" Check if the used ontology is consistent."""
105-
return self.reasoner.isConsistent()
106-
107-
108-
class DemoOWLAPIAdaptor(OWLAPIAdaptor):
109-
110-
def __init__(self, *args, **kwargs):
111-
112-
super().__init__(*args, **kwargs)
113-
self.__start()
114-
115-
@staticmethod
116-
def close(*args, **kwargs):
117-
"""Shuts down the java virtual machine hosted by jpype."""
118-
if jpype.isJVMStarted() and not jpype.isThreadAttachedToJVM():
119-
jpype.shutdownJVM()
120-
121-
def __start(self):
122-
"""Initialization via the `with` statement"""
123-
if not jpype.isJVMStarted():
124-
# Start a java virtual machine using the dependencies in the respective folder:
125-
if os.getcwd()[-6:] == "owlapy":
126-
jar_folder = "jar_dependencies"
127-
else:
128-
jar_folder = "../jar_dependencies"
129-
jar_files = [os.path.join(jar_folder, f) for f in os.listdir(jar_folder) if f.endswith('.jar')]
130-
# Starting JVM.
131-
jpype.startJVM(classpath=jar_files)
132-
133-
# Import Java classes
134-
from org.semanticweb.owlapi.apibinding import OWLManager
135-
from java.io import File
136-
if self.reasoner == "HermiT":
137-
from org.semanticweb.HermiT import ReasonerFactory
138-
else:
139-
raise NotImplementedError("Not implemented")
140-
141-
from org.semanticweb.owlapi.manchestersyntax.parser import ManchesterOWLSyntaxClassExpressionParser
142-
from org.semanticweb.owlapi.util import BidirectionalShortFormProviderAdapter, SimpleShortFormProvider
143-
from org.semanticweb.owlapi.expression import ShortFormEntityChecker
144-
from java.util import HashSet
145-
from org.semanticweb.owlapi.manchestersyntax.renderer import ManchesterOWLSyntaxOWLObjectRendererImpl
146-
147-
# () Manager is needed to load an ontology
148-
self.manager = OWLManager.createOWLOntologyManager()
149-
# () Load a local ontology using the manager
150-
self.ontology = self.manager.loadOntologyFromOntologyDocument(File(self.path))
151-
# () Create a HermiT reasoner for the loaded ontology
152-
self.reasoner = ReasonerFactory().createReasoner(self.ontology)
153-
154-
# () Create a manchester parser and all the necessary attributes for parsing manchester syntax string to owlapi ce
155-
ontology_set = HashSet()
156-
ontology_set.add(self.ontology)
157-
bidi_provider = BidirectionalShortFormProviderAdapter(self.manager, ontology_set, SimpleShortFormProvider())
158-
entity_checker = ShortFormEntityChecker(bidi_provider)
159-
self.parser = ManchesterOWLSyntaxClassExpressionParser(self.manager.getOWLDataFactory(), entity_checker)
160-
161-
# A manchester renderer to render owlapi ce to manchester syntax
162-
self.renderer = ManchesterOWLSyntaxOWLObjectRendererImpl()
157+
"""
158+
Check if the used ontology is consistent.
163159
164-
return self
160+
Returns:
161+
bool: True if the ontology is consistent, False otherwise.
162+
"""
163+
return self.reasoner.isConsistent()

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