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/* This file is part of the OWL API.
* The contents of this file are subject to the LGPL License, Version 3.0.
* Copyright 2014, The University of Manchester
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
* You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.
*
* Alternatively, the contents of this file may be used under the terms of the Apache License, Version 2.0 in which case, the provisions of the Apache License Version 2.0 are applicable instead of those above.
* Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
* Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. */
package org.semanticweb.owlapi.model;
import static org.semanticweb.owlapi.util.OWLAPIPreconditions.emptyOptional;
import static org.semanticweb.owlapi.util.OWLAPIPreconditions.optional;
import static org.semanticweb.owlapi.util.OWLAPIPreconditions.verifyNotNull;
import static org.semanticweb.owlapi.util.OWLAPIStreamUtils.asSet;
import java.io.File;
import java.io.InputStream;
import java.io.OutputStream;
import java.io.Serializable;
import java.util.Collection;
import java.util.List;
import java.util.Set;
import java.util.function.Supplier;
import java.util.stream.Stream;
import javax.annotation.Nullable;
import org.semanticweb.owlapi.io.FileDocumentSource;
import org.semanticweb.owlapi.io.IRIDocumentSource;
import org.semanticweb.owlapi.io.OWLOntologyDocumentSource;
import org.semanticweb.owlapi.io.OWLOntologyDocumentTarget;
import org.semanticweb.owlapi.io.OWLParserFactory;
import org.semanticweb.owlapi.io.StreamDocumentSource;
import org.semanticweb.owlapi.io.StreamDocumentTarget;
import org.semanticweb.owlapi.model.parameters.OntologyCopy;
import org.semanticweb.owlapi.util.PriorityCollection;
/**
* An {@code OWLOntologyManager} manages a set of ontologies. It is the main point for creating,
* loading and accessing ontologies.
* An {@code OWLOntologyManager} also manages the mapping betweem an ontology and its ontology
* document.
*
* @author Matthew Horridge, The University Of Manchester, Bio-Health Informatics Group
* @since 2.0.0
*/
public interface OWLOntologyManager extends OWLOntologySetProvider, HasDataFactory,
HasGetOntologyById, HasApplyChanges, HasApplyChange, HasAddAxioms, HasAddAxiom, HasRemoveAxioms,
HasRemoveAxiom, HasContainsOntology, HasOntologyChangeListeners, HasOntologyConfigurator,
HasOntologyLoaderConfiguration, HasOntologyWriterConfiguration, Serializable {
/**
* Clear all ontologies, listeners and maps from the manager. Leave injected factories, storers
* and parsers.
*/
public void clearOntologies();
/**
* Gets the ontologies that are managed by this manager that contain the specified axiom.
*
* @param axiom The axioms
* @return The set of ontologies such that for each ontology, O the specified axiom is contained
* in O.
* @deprecated use the stream method
*/
@Deprecated
default Set getOntologies(OWLAxiom axiom) {
return asSet(ontologies(axiom));
}
/**
* Gets the ontologies that are managed by this manager that contain the specified axiom.
*
* @param axiom The axioms
* @return The set of ontologies such that for each ontology, O the specified axiom is contained
* in O.
*/
default Stream ontologies(OWLAxiom axiom) {
return ontologies().filter(o -> o.containsAxiom(axiom));
}
/**
* Gets the versions (if any) of the ontology that have the specified IRI
*
* @param ontology The ontology IRI
* @return The set of ontologies that have the specified ontology IRI.
* @deprecated use {@link #versions(IRI)}
*/
@Deprecated
default Set getVersions(IRI ontology) {
return asSet(versions(ontology));
}
/**
* Gets the versions (if any) of the ontology that have the specified IRI
*
* @param ontology The ontology IRI
* @return The set of ontologies that have the specified ontology IRI.
*/
default Stream versions(IRI ontology) {
return ontologies().filter(o -> o.getOntologyID().matchOntology(ontology));
}
/**
* @param ontology ontology to check
* @return true if the ontology is contained
*/
boolean contains(OWLOntology ontology);
/**
* Determines if there is an ontology that has the specified ontology IRI, regardless of version
* IRI. If there is no ontology which has the input IRI as ontology IRI, the IRI is matched
* against the version IRI.
*
* @param ontologyIRI The IRI of the ontology to test for.
* @return {@code true} if there is an ontology with the specified IRI or version IRI, that is
* managed by this manager, otherwise {@code false}.
*/
boolean contains(IRI ontologyIRI);
/**
* Determines if there is an ontology with the specified id that is managed by this manager;
* this method works only with non anonymous ids.
*
* @param id The id of the ontology to test for
* @return {@code true} if there is an ontology with the specified id that is managed by this
* manager, otherwise {@code false}.
*/
@Override
boolean contains(OWLOntologyID id);
/**
* Determines if there is an ontology with the specified version IRI, that is managed by this
* manager.
*
* @param ontologyVersionIRI The version IRI of the ontology to test for (the ontology IRI may
* be anything)
* @return {@code true} if there is an ontology with the specified version IRI, that is managed
* by this manager, otherwise {@code false}.
*/
boolean containsVersion(IRI ontologyVersionIRI);
/**
* Gets a set of OWLOntologyIDs representing ontologies that are managed by this manager.
*
* @param ontologyVersionIRI The version IRI to match against all of the known ontologies.
* @return A set of OWLOntologyIDs where the version matches the given version or the empty set
* if none match.
* @deprecated use the stream method
*/
@Deprecated
default Set getOntologyIDsByVersion(IRI ontologyVersionIRI) {
return asSet(ontologyIDsByVersion(ontologyVersionIRI));
}
/**
* Gets a set of OWLOntologyIDs representing ontologies that are managed by this manager.
*
* @param ontologyVersionIRI The version IRI to match against all of the known ontologies.
* @return A set of OWLOntologyIDs where the version matches the given version or the empty set
* if none match.
*/
Stream ontologyIDsByVersion(IRI ontologyVersionIRI);
/**
* Gets a previously loaded/created ontology that has the specified ontology IRI, regardless of
* version IRI. If there is no ontology which has the input IRI as ontology IRI, the IRI is
* matched against the version IRI.
*
* @param ontologyIRI The IRI of the ontology to be retrieved.
* @return The ontology that has the specified IRI, {@code null} if none found.
*/
@Nullable
OWLOntology getOntology(IRI ontologyIRI);
@Nullable
@Override
OWLOntology getOntology(OWLOntologyID ontologyID);
/**
* Given an imports declaration, obtains the ontology that this import has been resolved to.
*
* @param declaration The declaration that points to the imported ontology.
* @return The ontology that the imports declaration resolves to, or {@code null} if the imports
* declaration could not be resolved to an ontology, because the ontology was not loaded
* or has been removed from this manager
*/
@Nullable
OWLOntology getImportedOntology(OWLImportsDeclaration declaration);
/**
* Gets the set of loaded ontologies that the specified ontology is related to via the
* directlyImports relation as defined in Section 3.4 of the OWL 2 Structural specification
*
* @param ontology The ontology whose direct imports are to be retrieved.
* @return The set of loaded ontologies that the specified ontology is related to via
* the directlyImports relation. If the ontology is not managed by this manager then the
* empty set will be returned.
* @deprecated use the stream method
*/
@Deprecated
default Set getDirectImports(OWLOntology ontology) {
return asSet(directImports(ontology));
}
/**
* Stream of loaded ontologies that the specified ontology is related to via the
* directlyImports relation as defined in Section 3.4 of the OWL 2 Structural specification
*
* @param ontology The ontology whose direct imports are to be retrieved.
* @return Stream of loaded ontologies that the specified ontology is related to via
* the directlyImports relation. If the ontology is not managed by this manager then the
* empty set will be returned.
*/
Stream directImports(OWLOntology ontology);
/**
* Gets the set of ontologies that are in the transitive closure of the directly imports
* relation.
*
* @param ontology The ontology whose imports are to be retrieved.
* @return A set of {@code OWLOntology}ies that are in the transitive closure of the directly
* imports relation of this ontology. If, for what ever reason, an imported ontology
* could not be loaded, then it will not be contained in the returned set of ontologies.
* If the ontology is not managed by this manager then the empty set will be returned.
* @deprecated use the stream method
*/
@Deprecated
default Set getImports(OWLOntology ontology) {
return asSet(imports(ontology));
}
/**
* Gets the stream of ontologies that are in the transitive closure of the directly imports
* relation.
*
* @param ontology The ontology whose imports are to be retrieved.
* @return Sorted stream of {@code OWLOntology}ies that are in the transitive closure of the
* directly imports relation of this ontology. If, for what ever reason, an imported
* ontology could not be loaded, then it will not be contained in the returned set of
* ontologies. If the ontology is not managed by this manager then the empty set will be
* returned.
*/
Stream imports(OWLOntology ontology);
/**
* Gets the imports closure for the specified ontology.
*
* @param ontology The ontology whose imports closure is to be retrieved.
* @return A {@code Set} of ontologies that contains the imports closure for the specified
* ontology. This set will also include the specified ontology. Example: if A imports B
* and B imports C, then calling this method with A will return the set consisting of A,
* B and C. If, for what ever reason, an imported ontology could not be loaded, then it
* will not be contained in the returned set of ontologies. If the ontology is not
* managed by this manager then the empty set will be returned.
* @deprecated use the stream method
*/
@Deprecated
default Set getImportsClosure(OWLOntology ontology) {
return asSet(importsClosure(ontology));
}
/**
* Imports closure stream for the specified ontology.
*
* @param ontology The ontology whose imports closure is to be retrieved.
* @return Sorted stream of ontologies that contains the imports closure for the specified
* ontology. It includes the specified ontology.
*/
Stream importsClosure(OWLOntology ontology);
/**
* Gets the topologically ordered imports closure.
*
* @param ontology The ontology whose imports closure is to be determined.
* @return A list that represents a topological ordering of the imports closure. The first
* element in the list will be the specified ontology. If the ontology is not managed by
* this manager then an empty list will be returned.
*/
List getSortedImportsClosure(OWLOntology ontology);
// Ontology change
// Ontology creation
/**
* Creates a new (empty) ontology that does not have an ontology IRI (and therefore does not
* have a version IRI). A document IRI will automatically be generated.
*
* @return The newly created ontology
* @throws OWLOntologyCreationException if there was a problem creating the ontology
*/
default OWLOntology createOntology() throws OWLOntologyCreationException {
// Brand new ontology without a URI
return createOntology(new OWLOntologyID());
}
/**
* Creates a new ontology that is initialised to contain specific axioms. The ontology will not
* have an IRI. The document IRI of the created ontology will be auto-generated.
*
* @param axioms The axioms that should be copied into the new ontology
* @return An ontology without an IRI that contains all of the specified axioms
* @throws OWLOntologyCreationException if there was a problem creating the new ontology.
* @throws OWLOntologyChangeException if there was a problem copying the axioms.
*/
default OWLOntology createOntology(Collection axioms)
throws OWLOntologyCreationException {
return createOntology(axioms, IRI.getNextDocumentIRI("urn:unnamed:ontology#ont"));
}
/**
* Creates a new ontology that is initialised to contain specific axioms. The ontology will not
* have an IRI. The document IRI of the created ontology will be auto-generated.
*
* @param axioms The axioms that should be copied into the new ontology
* @return An ontology without an IRI that contains all of the specified axioms
* @throws OWLOntologyCreationException if there was a problem creating the new ontology.
* @throws OWLOntologyChangeException if there was a problem copying the axioms.
*/
default OWLOntology createOntology(Stream axioms)
throws OWLOntologyCreationException {
return createOntology(axioms, IRI.getNextDocumentIRI("urn:unnamed:ontology#ont"));
}
/**
* Creates a new ontology that has the specified ontology IRI and is initialised to contain
* specific axioms.
*
* @param ontologyIRI The IRI of the new ontology.
* The ontology document IRI of the created ontology will be set to the value returned by
* any installed {@link org.semanticweb.owlapi.model.OWLOntologyIRIMapper}s. If no
* mappers are installed or the ontology IRI was not mapped to a document IRI by any of
* the installed mappers, then the ontology document IRI will be set to the value of
* {@code ontologyIRI}.
* @param axioms The axioms that should be copied into the new ontology
* @return An ontology that has the specified IRI and contains all of the specified axioms
* @throws OWLOntologyCreationException if there was a problem creating the new ontology, if the
* new ontology already exists in this manager.
* @throws OWLOntologyChangeException if there was a problem copying the axioms.
* @throws OWLOntologyAlreadyExistsException if the manager already contains an ontology with
* the specified {@code ontologyIRI}.
* @throws OWLOntologyDocumentAlreadyExistsException if the specified {@code ontologyIRI} is
* mapped to a ontology document IRI for which there already exists a mapping in this
* manager.
*/
default OWLOntology createOntology(Collection axioms, IRI ontologyIRI)
throws OWLOntologyCreationException {
return createOntology(axioms.stream(), ontologyIRI);
}
/**
* Creates a new ontology that has the specified ontology IRI and is initialised to contain
* specific axioms.
*
* @param ontologyIRI The IRI of the new ontology.
* The ontology document IRI of the created ontology will be set to the value returned by
* any installed {@link org.semanticweb.owlapi.model.OWLOntologyIRIMapper}s. If no
* mappers are installed or the ontology IRI was not mapped to a document IRI by any of
* the installed mappers, then the ontology document IRI will be set to the value of
* {@code ontologyIRI}.
* @param axioms The axioms that should be copied into the new ontology
* @return An ontology that has the specified IRI and contains all of the specified axioms
* @throws OWLOntologyCreationException if there was a problem creating the new ontology, if the
* new ontology already exists in this manager.
* @throws OWLOntologyChangeException if there was a problem copying the axioms.
* @throws OWLOntologyAlreadyExistsException if the manager already contains an ontology with
* the specified {@code ontologyIRI}.
* @throws OWLOntologyDocumentAlreadyExistsException if the specified {@code ontologyIRI} is
* mapped to a ontology document IRI for which there already exists a mapping in this
* manager.
*/
OWLOntology createOntology(Stream axioms, IRI ontologyIRI)
throws OWLOntologyCreationException;
/**
* Creates a new (empty) ontology that has the specified ontology IRI (and no version IRI).
* The ontology document IRI of the created ontology will be set to the value returned by any
* installed {@link org.semanticweb.owlapi.model.OWLOntologyIRIMapper}s. If no mappers are
* installed or the ontology IRI was not mapped to a document IRI by any of the installed
* mappers, then the ontology document IRI will be set to the value of {@code ontologyIRI}.
*
* @param ontologyIRI The IRI of the ontology to be created. The ontology IRI will be mapped to
* a document IRI in order to determine the type of ontology factory that will be used to
* create the ontology. If this mapping is {@code null} then a default (in memory)
* implementation of the ontology will most likely be created.
* @return The newly created ontology, or if an ontology with the specified IRI already exists
* then this existing ontology will be returned.
* @throws OWLOntologyCreationException If the ontology could not be created.
* @throws OWLOntologyAlreadyExistsException if the manager already contains an ontology with
* the specified {@code ontologyIRI} (and no version IRI).
* @throws OWLOntologyDocumentAlreadyExistsException if the specified {@code ontologyIRI} is
* mapped to a ontology document IRI for which there already exists a mapping in this
* manager.
*/
default OWLOntology createOntology(IRI ontologyIRI) throws OWLOntologyCreationException {
return createOntology(new OWLOntologyID(optional(ontologyIRI), emptyOptional(IRI.class)));
}
/**
* Creates a new (empty) ontology that has the specified ontology ID.
*
* @param ontologyID The ID of the ontology to be created.
* The ontology document IRI of the created ontology will be set to the value returned by
* any installed {@link org.semanticweb.owlapi.model.OWLOntologyIRIMapper}s. If no
* mappers are installed or the ontology IRI was not mapped to a document IRI by any of
* the installed mappers, then the ontology document IRI will be set to the value of
* {@code ontologyIRI}.
* @return The newly created ontology, or if an ontology with the specified IRI already exists
* then this existing ontology will be returned.
* @throws OWLOntologyCreationException If the ontology could not be created.
* @throws OWLOntologyAlreadyExistsException if the manager already contains an ontology with
* the specified {@code ontologyID} (and no version IRI).
* @throws OWLOntologyDocumentAlreadyExistsException if the specified {@code ontologyID} is
* mapped to a ontology document IRI for which there already exists a mapping in this
* manager.
*/
OWLOntology createOntology(OWLOntologyID ontologyID) throws OWLOntologyCreationException;
/**
* Creates a new ontology that has the specified ontology IRI and is initialised to contain the
* axioms that are contained in the specified ontologies. Note that the specified ontologies
* need not be managed by this manager.
* The ontology document IRI of the created ontology will be set to the value returned by any
* installed {@link org.semanticweb.owlapi.model.OWLOntologyIRIMapper}s. If no mappers are
* installed or the ontology IRI was not mapped to a document IRI by any of the installed
* mappers, then the ontology document IRI will be set to the value of {@code ontologyIRI}.
*
* @param ontologyIRI The IRI of the new ontology.
* @param ontologies The ontologies whose axioms should be copied into the new ontology
* @param copyLogicalAxiomsOnly If set to {@code true} only logical axioms are copied into the
* new ontology. If set to {@code false} then all axioms (including annotation axioms)
* are copied into the new ontology.
* @return An ontology that has the specified IRI and contains all of the axioms that are
* contained in the specified ontologies possibly minus all non-logical axioms
* @throws OWLOntologyCreationException if there was a problem creating the new ontology, if the
* new ontology already exists in this manager.
* @throws OWLOntologyAlreadyExistsException if the manager already contains an ontology with
* the specified {@code ontologyIRI} (and no ontology version IRI).
* @throws OWLOntologyDocumentAlreadyExistsException if the specified {@code ontologyIRI} is
* mapped to a ontology document IRI for which there already exists a mapping in this
* manager.
*/
default OWLOntology createOntology(IRI ontologyIRI, Collection ontologies,
boolean copyLogicalAxiomsOnly) throws OWLOntologyCreationException {
return createOntology(ontologyIRI, ontologies.stream(), copyLogicalAxiomsOnly);
}
/**
* Creates a new ontology that has the specified ontology IRI and is initialised to contain the
* axioms that are contained in the specified ontologies. Note that the specified ontologies
* need not be managed by this manager.
* The ontology document IRI of the created ontology will be set to the value returned by any
* installed {@link org.semanticweb.owlapi.model.OWLOntologyIRIMapper}s. If no mappers are
* installed or the ontology IRI was not mapped to a document IRI by any of the installed
* mappers, then the ontology document IRI will be set to the value of {@code ontologyIRI}.
*
* @param ontologyIRI The IRI of the new ontology.
* @param ontologies The ontologies whose axioms should be copied into the new ontology
* @param copyLogicalAxiomsOnly If set to {@code true} only logical axioms are copied into the
* new ontology. If set to {@code false} then all axioms (including annotation axioms)
* are copied into the new ontology.
* @return An ontology that has the specified IRI and contains all of the axioms that are
* contained in the specified ontologies possibly minus all non-logical axioms
* @throws OWLOntologyCreationException if there was a problem creating the new ontology, if the
* new ontology already exists in this manager.
* @throws OWLOntologyAlreadyExistsException if the manager already contains an ontology with
* the specified {@code ontologyIRI} (and no ontology version IRI).
* @throws OWLOntologyDocumentAlreadyExistsException if the specified {@code ontologyIRI} is
* mapped to a ontology document IRI for which there already exists a mapping in this
* manager.
*/
OWLOntology createOntology(IRI ontologyIRI, Stream ontologies,
boolean copyLogicalAxiomsOnly) throws OWLOntologyCreationException;
/**
* Creates a new ontology that has the specified ontology IRI and is initialised to contain the
* axioms that are contained in the specified ontologies. Note that the specified ontologies
* need not be managed by this manager.
* The ontology document IRI of the created ontology will be set to the value returned by any
* installed {@link org.semanticweb.owlapi.model.OWLOntologyIRIMapper}s. If no mappers are
* installed or the ontology IRI was not mapped to a document IRI by any of the installed
* mappers, then the ontology document IRI will be set to the value of {@code ontologyIRI}.
*
* @param ontologyIRI The IRI of the new ontology.
* @param ontologies The ontologies whose axioms should be copied into the new ontology
* @return An ontology that has the specified IRI and contains all of the axioms that are
* contained in the specified ontologies
* @throws OWLOntologyCreationException if there was a problem creating the new ontology, if the
* new ontology already exists in this manager.
* @throws OWLOntologyAlreadyExistsException if the manager already contains an ontology with
* the specified {@code ontologyIRI} (and no version IRI).
* @throws OWLOntologyDocumentAlreadyExistsException if the specified {@code ontologyIRI} is
* mapped to a ontology document IRI for which there already exists a mapping in this
* manager.
*/
default OWLOntology createOntology(IRI ontologyIRI, Collection ontologies)
throws OWLOntologyCreationException {
return createOntology(ontologyIRI, ontologies, false);
}
/**
* Copy an ontology from another manager to this one. The returned OWLOntology will return this
* manager when getOWLOntologyManager() is invoked. The copy mode is defined by the OntologyCopy
* parameter: SHALLOW for simply creating a new ontology containing the same axioms and same id,
* DEEP for copying actoss format and document IRI, MOVE to remove the ontology from its
* previous manager.
*
* @param toCopy ontology to copy
* @param settings settings for the copy
* @return copied ontology. This is the same object as toCopy only for MOVE copies
* @throws OWLOntologyCreationException if this manager cannot add the new ontology
*/
OWLOntology copyOntology(OWLOntology toCopy, OntologyCopy settings)
throws OWLOntologyCreationException;
// Loading
/**
* Loads an ontology that is assumed to have the specified {@code ontologyIRI} as its IRI or
* version IRI.
* The ontology IRI will be mapped to an ontology document IRI. The mapping will be determined
* using one of the loaded {@link OWLOntologyIRIMapper} objects. By default, if no custom
* {@code OWLOntologyIRIMapper}s have been registered using the {@link #getIRIMappers()}
* PriorityCollection {@link PriorityCollection#add(Serializable...)} method, or no mapping can
* be found, the ontology document IRI is taken to be the specified ontology IRI.
*
* @param ontologyIRI The IRI that identifies the ontology. It is expected that the ontology
* will also have this IRI (although the OWL API will tolerated situations where this is
* not the case).
* @return The {@code OWLOntology} representation of the ontology that was loaded.
* @throws OWLOntologyCreationException If there was a problem in creating and loading the
* ontology.
* @throws org.semanticweb.owlapi.io.UnparsableOntologyException if the ontology was being
* parsed from a document and the document contained syntax errors.
* @throws UnloadableImportException if the ontology imports ontologies and one of the imports
* could not be loaded for what ever reason. If the
* {@link MissingImportHandlingStrategy} is set to
* {@link MissingImportHandlingStrategy#SILENT} then this exception will not be thrown.
* The {@code UnloadableImportException} contains information about the import
* declaration that triggered the import and the cause of this exception is an {@code
* OWLOntologyCreationException} which contains information about why the import could not be
* loaded.
* @throws org.semanticweb.owlapi.io.OWLOntologyCreationIOException if there was an {@code
* IOException} when trying to load the ontology.
* @throws OWLOntologyAlreadyExistsException if the manager already contains an ontology with
* the specified {@code ontologyIRI} (where the ontology doesn't have a version IRI).
* @throws OWLOntologyDocumentAlreadyExistsException if the specified {@code ontologyIRI} is
* mapped to a ontology document IRI for which there already exists a mapping in this
* manager.
*/
OWLOntology loadOntology(IRI ontologyIRI) throws OWLOntologyCreationException;
/**
* Loads an ontology from an ontology document specified by an IRI. In contrast the the
* {@link #loadOntology(IRI)} method, no mapping is performed on the specified IRI.
*
* @param documentIRI The ontology document IRI where the ontology will be loaded from.
* @return The ontology that was loaded.
* @throws OWLOntologyCreationException If there was a problem in creating and loading the
* ontology.
* @throws org.semanticweb.owlapi.io.UnparsableOntologyException if the ontology was being
* parsed from a document and the document contained syntax errors.
* @throws UnloadableImportException if the ontology imports ontologies and one of the imports
* could not be loaded for what ever reason. If the
* {@link MissingImportHandlingStrategy} is set to
* {@link MissingImportHandlingStrategy#SILENT} then this exception will not be thrown.
* The {@code UnloadableImportException} contains information about the import
* declaration that triggered the import and the cause of this exception is an {@code
* OWLOntologyCreationException} which contains information about why the import could not be
* loaded.
* @throws org.semanticweb.owlapi.io.OWLOntologyCreationIOException if there was an {@code
* IOException} when trying to load the ontology.
* @throws OWLOntologyDocumentAlreadyExistsException if the specified {@code documentIRI} is
* already the document IRI for a loaded ontology.
* @throws OWLOntologyAlreadyExistsException if the manager already contains an ontology whose
* ontology IRI and version IRI is the same as the ontology IRI and version IRI of the
* ontology contained in the document pointed to by {@code documentIRI}.
*/
default OWLOntology loadOntologyFromOntologyDocument(IRI documentIRI)
throws OWLOntologyCreationException {
// Ontology URI not known in advance
return loadOntologyFromOntologyDocument(new IRIDocumentSource(documentIRI, null, null),
getOntologyLoaderConfiguration());
}
/**
* Loads an ontology from an ontology document contained in a local file. The loaded ontology
* will be assigned a document IRI that corresponds to the file IRI.
*
* @param file The file that contains a representation of an ontology
* @return The ontology that was parsed from the file.
* @throws OWLOntologyCreationException If there was a problem in creating and loading the
* ontology.
* @throws org.semanticweb.owlapi.io.UnparsableOntologyException if the ontology could not be
* parsed.
* @throws UnloadableImportException if the ontology imports ontologies and one of the imports
* could not be loaded for what ever reason. If the
* {@link MissingImportHandlingStrategy} is set to
* {@link MissingImportHandlingStrategy#SILENT} then this exception will not be thrown.
* The {@code UnloadableImportException} contains information about the import
* declaration that triggered the import and the cause of this exception is an {@code
* OWLOntologyCreationException} which contains information about why the import could not be
* loaded.
* @throws org.semanticweb.owlapi.io.OWLOntologyCreationIOException if there was an {@code
* IOException} when trying to load the ontology.
* @throws OWLOntologyDocumentAlreadyExistsException if the IRI of the specified file is already
* the document IRI for a loaded ontology.
* @throws OWLOntologyAlreadyExistsException if the manager already contains an ontology whose
* ontology IRI and version IRI is the same as the ontology IRI and version IRI of the
* ontology contained in the document pointed to by {@code documentIRI}.
*/
default OWLOntology loadOntologyFromOntologyDocument(File file)
throws OWLOntologyCreationException {
return loadOntologyFromOntologyDocument(new FileDocumentSource(file));
}
/**
* Loads an ontology from an ontology document obtained from an input stream. The loaded
* ontology will be assigned an auto-generated document IRI with "inputstream" as its scheme.
*
* @param inputStream The input stream that can be used to obtain a representation of an
* ontology
* @return The ontology that was parsed from the input stream.
* @throws OWLOntologyCreationException If there was a problem in creating and loading the
* ontology.
* @throws org.semanticweb.owlapi.io.UnparsableOntologyException if the ontology could not be
* parsed.
* @throws UnloadableImportException if the ontology imports ontologies and one of the imports
* could not be loaded for what ever reason. If the
* {@link MissingImportHandlingStrategy} is set to
* {@link MissingImportHandlingStrategy#SILENT} then this exception will not be thrown.
* The {@code UnloadableImportException} contains information about the import
* declaration that triggered the import and the cause of this exception is an {@code
* OWLOntologyCreationException} which contains information about why the import could not be
* loaded.
* @throws org.semanticweb.owlapi.io.OWLOntologyCreationIOException if there was an {@code
* IOException} when trying to load the ontology.
* @throws OWLOntologyAlreadyExistsException if the manager already contains an ontology whose
* ontology IRI and version IRI is the same as the ontology IRI and version IRI of the
* ontology obtained from parsing the content of the input stream.
*/
default OWLOntology loadOntologyFromOntologyDocument(InputStream inputStream)
throws OWLOntologyCreationException {
return loadOntologyFromOntologyDocument(new StreamDocumentSource(inputStream));
}
/**
* A convenience method that load an ontology from an input source.
*
* @param documentSource The input source that describes where the ontology should be loaded
* from.
* @return The ontology that was loaded.
* @throws OWLOntologyCreationException If there was a problem in creating and loading the
* ontology.
* @throws org.semanticweb.owlapi.io.UnparsableOntologyException if the ontology was being
* parsed from a document and the document contained syntax errors.
* @throws UnloadableImportException if the ontology imports ontologies and one of the imports
* could not be loaded for what ever reason. If the
* {@link MissingImportHandlingStrategy} is set to
* {@link MissingImportHandlingStrategy#SILENT} then this exception will not be thrown.
* The {@code UnloadableImportException} contains information about the import
* declaration that triggered the import and the cause of this exception is an {@code
* OWLOntologyCreationException} which contains information about why the import could not be
* loaded.
* @throws org.semanticweb.owlapi.io.OWLOntologyCreationIOException if there was an {@code
* IOException} when trying to load the ontology.
* @throws OWLOntologyDocumentAlreadyExistsException if the document IRI of the input source is
* already the document IRI for a loaded ontology.
* @throws OWLOntologyAlreadyExistsException if the manager already contains an ontology whose
* ontology IRI and version IRI is the same as the ontology IRI and version IRI of the
* ontology contained in the document represented by the input source.
*/
default OWLOntology loadOntologyFromOntologyDocument(OWLOntologyDocumentSource documentSource)
throws OWLOntologyCreationException {
// Ontology URI not known in advance
return loadOntologyFromOntologyDocument(documentSource, getOntologyLoaderConfiguration());
}
/**
* A convenience method that load an ontology from an input source with specified configuration.
*
* @param documentSource The input source that describes where the ontology should be loaded
* from.
* @param config the configuration to use
* @return The ontology that was loaded.
* @throws OWLOntologyCreationException If there was a problem in creating and loading the
* ontology.
* @throws org.semanticweb.owlapi.io.UnparsableOntologyException if the ontology was being
* parsed from a document and the document contained syntax errors.
* @throws UnloadableImportException if the ontology imports ontologies and one of the imports
* could not be loaded for what ever reason. If the
* {@link MissingImportHandlingStrategy} is set to
* {@link MissingImportHandlingStrategy#SILENT} then this exception will not be thrown.
* The {@code UnloadableImportException} contains information about the import
* declaration that triggered the import and the cause of this exception is an {@code
* OWLOntologyCreationException} which contains information about why the import could not be
* loaded.
* @throws org.semanticweb.owlapi.io.OWLOntologyCreationIOException if there was an {@code
* IOException} when trying to load the ontology.
* @throws OWLOntologyDocumentAlreadyExistsException if the document IRI of the input source is
* already the document IRI for a loaded ontology.
* @throws OWLOntologyAlreadyExistsException if the manager already contains an ontology whose
* ontology IRI and version IRI is the same as the ontology IRI and version IRI of the
* ontology contained in the document represented by the input source.
*/
OWLOntology loadOntologyFromOntologyDocument(OWLOntologyDocumentSource documentSource,
OWLOntologyLoaderConfiguration config) throws OWLOntologyCreationException;
/**
* Attempts to remove an ontology. The ontology which is identified by the specified IRI is
* removed regardless of whether it is referenced by other ontologies via imports statements.
*
* @param ontology The ontology to be removed. If this manager does not manage the ontology then
* nothing happens.
*/
default void removeOntology(OWLOntology ontology) {
removeOntology(ontology.getOntologyID());
}
/**
* Attempts to remove an ontology. The ontology which is identified by the specified IRI is
* removed regardless of whether it is referenced by other ontologies via imports statements.
*
* @param ontologyID The ontology to be removed. If this manager does not manage the ontology
* then nothing happens.
*/
void removeOntology(OWLOntologyID ontologyID);
/**
* Gets the document IRI for a given ontology. This will either be the document IRI from where
* the ontology was obtained from during loading, or the document IRI which was specified (via a
* mapper) when the (empty) ontology was created. Note that this may not correspond to the first
* document IRI found in the list of mappings from ontology IRI to document IRI. The reason for
* this is that it might not have been possible to load the ontology from the first document IRI
* found in the mapping table.
*
* @param ontology The ontology whose document IRI is to be obtained.
* @return The document IRI of the ontology.
* @throws UnknownOWLOntologyException If the specified ontology is not managed by this manager.
*/
IRI getOntologyDocumentIRI(OWLOntology ontology);
/**
* Overrides the current document IRI for a given ontology. This method does not alter the IRI
* mappers which are installed, but alters the actual document IRI of an ontology that has
* already been loaded.
*
* @param ontology The ontology that has already been loaded.
* @param documentIRI The new ontology document IRI
* @throws UnknownOWLOntologyException If the specified ontology is not managed by this manager.
*/
void setOntologyDocumentIRI(OWLOntology ontology, IRI documentIRI);
/**
* Gets the ontology format for the specified ontology.
*
* @param ontology The ontology whose format is to be obtained.
* @return The format of the ontology, or {@code null} if the ontology has no format (e.g.,
* programmatically created ontology)
*/
@Nullable
OWLDocumentFormat getOntologyFormat(OWLOntology ontology);
/**
* Gets the ontology format for the specified ontology, ensuring it is not null (an error is
* thrown if the ontology has no format). Do not use this method to check if an ontology has a
* format associated with it; prefer {@link #getOntologyFormat(OWLOntology)}.
*
* @param ontology The ontology whose format is to be obtained.
* @return The format of the ontology
*/
default OWLDocumentFormat getNonnullOntologyFormat(OWLOntology ontology) {
return verifyNotNull(getOntologyFormat(ontology),
(Supplier) () -> "There is no format specified for ontology "
+ ontology.getOntologyID()
+ ", the ontology format needs to be set before saving or specified in the save call");
}
/**
* Sets the format for the specified ontology.
*
* @param ontology The ontology whose format is to be set.
* @param ontologyFormat The format for the specified ontology.
* @throws UnknownOWLOntologyException If the specified ontology is not managed by this manager.
*/
void setOntologyFormat(OWLOntology ontology, OWLDocumentFormat ontologyFormat);
/**
* Saves the specified ontology. The ontology will be saved to the location that it was loaded
* from, or if it was created programmatically, it will be saved to the location specified by an
* ontology IRI mapper at creation time. The ontology will be saved in the same format which it
* was loaded from, or the default ontology format if the ontology was created programmatically.
*
* @param ontology The ontology to be saved.
* @throws OWLOntologyStorageException An exception will be thrown if there is a problem with
* saving the ontology, or the ontology can't be saved in the format it was loaded from.
* @throws UnknownOWLOntologyException if this manager does not manage the specified ontology
*/
default void saveOntology(OWLOntology ontology) throws OWLOntologyStorageException {
saveOntology(ontology, getNonnullOntologyFormat(ontology));
}
/**
* Saves the specified ontology, using the specified document IRI to determine where/how the
* ontology should be saved.
*
* @param ontology The ontology to be saved.
* @param documentIRI The document IRI where the ontology should be saved to
* @throws OWLOntologyStorageException If the ontology cannot be saved
* @throws UnknownOWLOntologyException if the specified ontology is not managed by this manager.
*/
default void saveOntology(OWLOntology ontology, IRI documentIRI)
throws OWLOntologyStorageException {
saveOntology(ontology, getNonnullOntologyFormat(ontology), documentIRI);
}
/**
* Saves the specified ontology, to the specified output stream
*
* @param ontology The ontology to be saved.
* @param outputStream The output stream where the ontology will be saved to
* @throws OWLOntologyStorageException If there was a problem saving this ontology to the
* specified output stream
* @throws UnknownOWLOntologyException if this manager does not manage the specified ontology.
*/
default void saveOntology(OWLOntology ontology, OutputStream outputStream)
throws OWLOntologyStorageException {
saveOntology(ontology, new StreamDocumentTarget(outputStream));
}
/**
* Saves the specified ontology in the specified ontology format to its document URI.
*
* @param ontology The ontology to be saved.
* @param ontologyFormat The format in which the ontology should be saved.
* @throws OWLOntologyStorageException If the ontology cannot be saved.
* @throws UnknownOWLOntologyException if the specified ontology is not managed by this manager
*/
default void saveOntology(OWLOntology ontology, OWLDocumentFormat ontologyFormat)
throws OWLOntologyStorageException {
saveOntology(ontology, ontologyFormat, getOntologyDocumentIRI(ontology));
}
/**
* Saves the specified ontology to the specified document IRI in the specified ontology format.
*
* @param ontology The ontology to be saved
* @param ontologyFormat The format in which to save the ontology
* @param documentIRI The document IRI where the ontology should be saved to
* @throws OWLOntologyStorageException If the ontology could not be saved.
* @throws UnknownOWLOntologyException if the specified ontology is not managed by the manager.
*/
void saveOntology(OWLOntology ontology, OWLDocumentFormat ontologyFormat, IRI documentIRI)
throws OWLOntologyStorageException;
/**
* Saves the specified ontology to the specified output stream in the specified ontology format.
*
* @param ontology The ontology to be saved
* @param ontologyFormat The format in which to save the ontology
* @param outputStream The output stream where the ontology will be saved to.
* @throws OWLOntologyStorageException If the ontology could not be saved.
* @throws UnknownOWLOntologyException if the specified ontology is not managed by the manager.
*/
default void saveOntology(OWLOntology ontology, OWLDocumentFormat ontologyFormat,
OutputStream outputStream) throws OWLOntologyStorageException {
saveOntology(ontology, ontologyFormat, new StreamDocumentTarget(outputStream));
}
/**
* Saves the specified ontology to the specified
* {@link org.semanticweb.owlapi.io.OWLOntologyDocumentTarget}.
*
* @param ontology The ontology to be saved.
* @param documentTarget The output target where the ontology will be saved to.
* @throws OWLOntologyStorageException If the ontology could not be saved.
* @throws UnknownOWLOntologyException if the specified ontology is not managed by this manager.
*/
default void saveOntology(OWLOntology ontology, OWLOntologyDocumentTarget documentTarget)
throws OWLOntologyStorageException {
saveOntology(ontology, getNonnullOntologyFormat(ontology), documentTarget);
}
/**
* Saves the specified ontology to the specified output target in the specified ontology format.
*
* @param ontology The ontology to be saved.
* @param ontologyFormat The output format in which to save the ontology
* @param documentTarget The output target where the ontology will be saved to
* @throws OWLOntologyStorageException If the ontology could not be saved.
* @throws UnknownOWLOntologyException If the specified ontology is not managed by this manager.
*/
void saveOntology(OWLOntology ontology, OWLDocumentFormat ontologyFormat,
OWLOntologyDocumentTarget documentTarget) throws OWLOntologyStorageException;
/**
* Add an IRI mapper to the manager
*
* @param mapper the mapper to add
* @deprecated use getIRIMappers().add() instead
*/
@Deprecated
void addIRIMapper(OWLOntologyIRIMapper mapper);
/**
* Remove an IRI mapper from the manager
*
* @param mapper the mapper to remove
* @deprecated use getIRIMappers().remove() instead
*/
@Deprecated
void removeIRIMapper(OWLOntologyIRIMapper mapper);
/**
* Clear the manager mappers
*
* @deprecated use getIRIMappers().clear() instead
*/
@Deprecated
void clearIRIMappers();
/**
* Add astorer to the manager
*
* @param storer the storer to add
* @deprecated use getOntologyStorers().add() instead
*/
@Deprecated
void addOntologyStorer(OWLStorerFactory storer);
/**
* Remove a storer from the manager
*
* @param storer the storer to remove
* @deprecated use getOntologyStorers().remove() instead
*/
@Deprecated
void removeOntologyStorer(OWLStorerFactory storer);
/**
* Clear the manager storers
*
* @deprecated use getOntologyStorers().clear() instead
*/
@Deprecated
void clearOntologyStorers();
/**
* @return the collection of IRI mappers. This allows for iteration and modification of the
* list.
*/
PriorityCollection getIRIMappers();
/**
* Set the collection of IRI mappers. The mappers are used to obtain ontology document IRIs for
* ontology IRIs. If their type is annotated with a HasPriority type, this will be used to
* decide the order they are used. Otherwise, the order in which the collection is iterated will
* determine the order in which the mappers are used.
*
* @param mappers the mappers to be injected
*/
void setIRIMappers(Set mappers);
/**
* @return the collection of parsers. This allows for iteration and modification of the list.
*/
PriorityCollection getOntologyParsers();
/**
* Set the collection of parsers. If the parsers are annotated with a HasPriority type, this
* will be used to decide the order they are used. Otherwise, the order in which the collection
* is iterated will determine the order in which the parsers are used.
*
* @param parsers the factories to be injected
*/
void setOntologyParsers(Set parsers);
/**
* @return the collection of ontology factories. This allows for iteration and modification of
* the list.
*/
PriorityCollection getOntologyFactories();
/**
* Set the collection of ontology factories. If the factories are annotated with a HasPriority
* type, this will be used to decide the order they are used. Otherwise, the order in which the
* collection is iterated will determine the order in which the parsers are used.
*
* @param factories the factories to be injected
*/
void setOntologyFactories(Set factories);
/**
* @return the collection of storers. This allows for iteration and modification of the list.
*/
PriorityCollection getOntologyStorers();
/**
* Set the list of ontology storers. If their type is annotated with a HasPriority type, this
* will be used to decide the order they are used. Otherwise, the order in which the collection
* is iterated will determine the order in which the storers are used.
*
* @param storers The storers to be used
*/
void setOntologyStorers(Set storers);
/**
* Adds an ontology change listener, which listens to ontology changes. An ontology change
* broadcast strategy must be specified, which determines the changes that are broadcast to the
* listener.
*
* @param listener The listener to be added.
* @param strategy The strategy that should be used for broadcasting changes to the listener.
*/
void addOntologyChangeListener(OWLOntologyChangeListener listener,
OWLOntologyChangeBroadcastStrategy strategy);
/**
* @param listener the listener to add
*/
void addImpendingOntologyChangeListener(ImpendingOWLOntologyChangeListener listener);
/**
* @param listener the listener to remove
*/
void removeImpendingOntologyChangeListener(ImpendingOWLOntologyChangeListener listener);
/**
* @param listener the listener to add
*/
void addOntologyChangesVetoedListener(OWLOntologyChangesVetoedListener listener);
/**
* @param listener the listener to remove
*/
void removeOntologyChangesVetoedListener(OWLOntologyChangesVetoedListener listener);
/**
* Sets the default strategy that is used to broadcast ontology changes.
*
* @param strategy The strategy to be used for broadcasting changes. This strategy will override
* any previously set broadcast strategy.
* @see org.semanticweb.owlapi.model.DefaultChangeBroadcastStrategy
* @see org.semanticweb.owlapi.model.EDTChangeBroadcastStrategy
*/
void setDefaultChangeBroadcastStrategy(OWLOntologyChangeBroadcastStrategy strategy);
/**
* Requests that the manager loads an imported ontology that is described by an imports
* statement. This method is generally used by parsers and other kinds of loaders. For simply
* loading an ontology, use the loadOntologyXXX methods. The method respects the list of ignored
* imports in the specified configuration. In other words, if this methods is called for an
* ignored import as specified by the configuration object then the import won't be loaded. The
* ontology loader configuration used is the default one for this manager.
*
* @param declaration The declaration that describes the import to be loaded.
* @throws UnloadableImportException if there was a problem creating and loading the import and
* silent missing imports handling is not turned on. If silent missing import handling
* is turned on then this exception will not be thrown.
*/
default void makeLoadImportRequest(OWLImportsDeclaration declaration) {
makeLoadImportRequest(declaration, getOntologyLoaderConfiguration());
}
/**
* Requests that the manager loads an imported ontology that is described by an imports
* statement. This method is generally used by parsers and other kinds of loaders. For simply
* loading an ontology, use the loadOntologyXXX methods. The method respects the list of ignored
* imports in the specified configuration. In other words, if this methods is called for an
* ignored import as specified by the configuration object then the import won't be loaded.
*
* @param declaration The declaration that describes the import to be loaded.
* @param configuration The configuration object that passes arguments to the mechanism used for
* loading.
* @throws UnloadableImportException if there was a problem creating and loading the import and
* silent missing imports handling is not turned on. If silent missing import handling
* is turned on then this exception will not be thrown.
*/
void makeLoadImportRequest(OWLImportsDeclaration declaration,
OWLOntologyLoaderConfiguration configuration);
/**
* In the case where silent missing imports handling is enabled, a listener can be attached via
* this method so that there is a mechanism that allows clients to be informed of the reason
* when an import cannot be loaded.
*
* @param listener The listener to be added.
*/
void addMissingImportListener(MissingImportListener listener);
/**
* Removes a previously added missing import listener.
*
* @param listener The listener to be removed.
*/
void removeMissingImportListener(MissingImportListener listener);
/**
* Adds an ontology loaded listener to this manager.
*
* @param listener The listener to be added.
*/
void addOntologyLoaderListener(OWLOntologyLoaderListener listener);
/**
* Removes a previously added ontology loaded listener.
*
* @param listener The listener to be removed.
*/
void removeOntologyLoaderListener(OWLOntologyLoaderListener listener);
/**
* Adds an ontology change progress listener.
*
* @param listener The listener to be added.
*/
void addOntologyChangeProgessListener(OWLOntologyChangeProgressListener listener);
/**
* Removes a previously added ontology change listener.
*
* @param listener The listener to be removed.
*/
void removeOntologyChangeProgessListener(OWLOntologyChangeProgressListener listener);
}
