Package org.semanticweb.owlapi.model

Interface OWLOntologyManager

All Superinterfaces:
HasAddAxiom, HasAddAxioms, HasApplyChange, HasApplyChanges, HasContainsOntology, HasDataFactory, HasGetOntologies, HasGetOntologyById, HasOntologyChangeListeners, HasOntologyConfigurator, HasOntologyLoaderConfiguration, HasOntologyWriterConfiguration, HasRemoveAxiom, HasRemoveAxioms, OWLOntologySetProvider, Serializable
All Known Implementing Classes:
OWLOntologyManagerImpl
public interface OWLOntologyManager extends OWLOntologySetProvider, HasDataFactory, HasGetOntologyById, HasApplyChanges, HasApplyChange, HasAddAxioms, HasAddAxiom, HasRemoveAxioms, HasRemoveAxiom, HasContainsOntology, HasOntologyChangeListeners, HasOntologyConfigurator, HasOntologyLoaderConfiguration, HasOntologyWriterConfiguration, Serializable
An OWLOntologyManager manages a set of ontologies. It is the main point for creating, loading and accessing ontologies.
An OWLOntologyManager also manages the mapping between an ontology and its ontology document.
Since:
2.0.0
Author:
Matthew Horridge, The University Of Manchester, Bio-Health Informatics Group

  • Method Details

    • clearOntologies

      void clearOntologies()
      Clear all ontologies, listeners and maps from the manager. Leave injected factories, storers and parsers.

    • getOntologies

      default Set<OWLOntology> getOntologies(OWLAxiom axiom)
      Gets the ontologies that are managed by this manager that contain the specified axiom.
      Parameters:
      axiom - The axioms
      Returns:
      The set of ontologies such that for each ontology O the specified axiom is contained in O. The set that is returned is a copy; modifications to the returned set will not be reflected in this object.

    • ontologies

      default Stream<OWLOntology> ontologies(OWLAxiom axiom)
      Gets the ontologies that are managed by this manager that contain the specified axiom.
      Parameters:
      axiom - The axioms
      Returns:
      The stream of ontologies such that for each ontology O the specified axiom is contained in O.

    • getVersions

      @Deprecated default Set<OWLOntology> getVersions(IRI ontology)
      Deprecated.
      use versions(IRI)
      Gets the versions (if any) of the ontology that have the specified IRI
      Parameters:
      ontology - The ontology IRI
      Returns:
      The set of ontologies that have the specified ontology IRI.

    • versions

      default Stream<OWLOntology> versions(IRI ontology)
      Gets the versions (if any) of the ontology that have the specified IRI
      Parameters:
      ontology - The ontology IRI
      Returns:
      The set of ontologies that have the specified ontology IRI.

    • contains

      boolean contains(OWLOntology ontology)
      Parameters:
      ontology - ontology to check
      Returns:
      true if the ontology is contained

    • contains

      boolean contains(IRI ontologyIRI)
      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.
      Parameters:
      ontologyIRI - The IRI of the ontology to test for.
      Returns:
      true if there is an ontology with the specified IRI or version IRI, that is managed by this manager, otherwise false.

    • contains

      boolean contains(OWLOntologyID id)
      Determines if there is an ontology with the specified id that is managed by this manager; this method works only with non anonymous ids.
      Specified by:
      contains in interface HasContainsOntology
      Parameters:
      id - The id of the ontology to test for
      Returns:
      true if there is an ontology with the specified id that is managed by this manager, otherwise false.

    • containsVersion

      boolean containsVersion(IRI ontologyVersionIRI)
      Determines if there is an ontology with the specified version IRI, that is managed by this manager.
      Parameters:
      ontologyVersionIRI - The version IRI of the ontology to test for (the ontology IRI may be anything)
      Returns:
      true if there is an ontology with the specified version IRI, that is managed by this manager, otherwise false.

    • getOntologyIDsByVersion

      default Set<OWLOntologyID> getOntologyIDsByVersion(IRI ontologyVersionIRI)
      Gets a set of OWLOntologyIDs representing ontologies that are managed by this manager.
      Parameters:
      ontologyVersionIRI - The version IRI to match against all of the known ontologies.
      Returns:
      A set of OWLOntologyIDs where the version matches the given version or the empty set if none match. The set that is returned is a copy; modifications to the returned set will not be reflected in this object.

    • ontologyIDsByVersion

      Stream<OWLOntologyID> ontologyIDsByVersion(IRI ontologyVersionIRI)
      Gets a stream of OWLOntologyIDs representing ontologies that are managed by this manager.
      Parameters:
      ontologyVersionIRI - The version IRI to match against all of the known ontologies.
      Returns:
      A stream of OWLOntologyIDs where the version matches the given version or the empty set if none match.

    • getOntology

      @Nullable OWLOntology getOntology(IRI ontologyIRI)
      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.
      Parameters:
      ontologyIRI - The IRI of the ontology to be retrieved.
      Returns:
      The ontology that has the specified IRI, null if none found.

    • getOntology

      @Nullable OWLOntology getOntology(OWLOntologyID ontologyID)
      Description copied from interface: HasGetOntologyById
      Get a previously loaded/created ontology that has the specified ontology ID. For anonymous ids, this method tries to locate the ontology by document IRI.
      Specified by:
      getOntology in interface HasGetOntologyById
      Parameters:
      ontologyID - The ID of the ontology to retrieve.
      Returns:
      The ontology with the specified ID, or null if there is no ontology with the specified ID.

    • getImportedOntology

      @Nullable OWLOntology getImportedOntology(OWLImportsDeclaration declaration)
      Given an imports declaration, obtains the ontology that this import has been resolved to.
      Parameters:
      declaration - The declaration that points to the imported ontology.
      Returns:
      The ontology that the imports declaration resolves to, or 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

    • getDirectImports

      default Set<OWLOntology> getDirectImports(OWLOntology ontology)
      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
      Parameters:
      ontology - The ontology whose direct imports are to be retrieved.
      Returns:
      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. The set that is returned is a copy; modifications to the returned set will not be reflected in this object.

    • directImports

      Stream<OWLOntology> directImports(OWLOntology 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
      Parameters:
      ontology - The ontology whose direct imports are to be retrieved.
      Returns:
      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.

    • getImports

      default Set<OWLOntology> getImports(OWLOntology ontology)
      Gets the set of ontologies that are in the transitive closure of the directly imports relation.
      Parameters:
      ontology - The ontology whose imports are to be retrieved.
      Returns:
      A set of OWLOntology instances 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. The set that is returned is a copy; modifications to the returned set will not be reflected in this object.

    • imports

      Stream<OWLOntology> imports(OWLOntology ontology)
      Gets the stream of ontologies that are in the transitive closure of the directly imports relation.
      Parameters:
      ontology - The ontology whose imports are to be retrieved.
      Returns:
      Sorted stream of OWLOntologyies 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.

    • getImportsClosure

      default Set<OWLOntology> getImportsClosure(OWLOntology ontology)
      Gets the imports closure for the specified ontology.
      Parameters:
      ontology - The ontology whose imports closure is to be retrieved.
      Returns:
      A 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. The set that is returned is a copy; modifications to the returned set will not be reflected in this object.

    • importsClosure

      Stream<OWLOntology> importsClosure(OWLOntology ontology)
      Imports closure stream for the specified ontology.
      Parameters:
      ontology - The ontology whose imports closure is to be retrieved.
      Returns:
      Sorted stream of ontologies that contains the imports closure for the specified ontology. It includes the specified ontology.

    • getSortedImportsClosure

      List<OWLOntology> getSortedImportsClosure(OWLOntology ontology)
      Gets the topologically ordered imports closure.
      Parameters:
      ontology - The ontology whose imports closure is to be determined.
      Returns:
      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.

    • createOntology

      default OWLOntology createOntology() throws OWLOntologyCreationException
      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.
      Returns:
      The newly created ontology
      Throws:
      OWLOntologyCreationException - if there was a problem creating the ontology

    • createOntology

      default OWLOntology createOntology(Collection<OWLAxiom> axioms) throws OWLOntologyCreationException
      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.
      Parameters:
      axioms - The axioms that should be copied into the new ontology
      Returns:
      An ontology without an IRI that contains all of the specified axioms
      Throws:
      OWLOntologyCreationException - if there was a problem creating the new ontology.
      OWLOntologyChangeException - if there was a problem copying the axioms.

    • createOntology

      default OWLOntology createOntology(Stream<OWLAxiom> axioms) throws OWLOntologyCreationException
      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.
      Parameters:
      axioms - The axioms that should be copied into the new ontology
      Returns:
      An ontology without an IRI that contains all of the specified axioms
      Throws:
      OWLOntologyCreationException - if there was a problem creating the new ontology.
      OWLOntologyChangeException - if there was a problem copying the axioms.

    • createOntology

      default OWLOntology createOntology(Collection<OWLAxiom> axioms, IRI ontologyIRI) throws OWLOntologyCreationException
      Creates a new ontology that has the specified ontology IRI and is initialised to contain specific axioms.
      Parameters:
      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 OWLOntologyIRIMappers. 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 ontologyIRI.
      axioms - The axioms that should be copied into the new ontology
      Returns:
      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.
      OWLOntologyChangeException - if there was a problem copying the axioms.
      OWLOntologyAlreadyExistsException - if the manager already contains an ontology with the specified ontologyIRI.
      OWLOntologyDocumentAlreadyExistsException - if the specified ontologyIRI is mapped to a ontology document IRI for which there already exists a mapping in this manager.

    • createOntology

      OWLOntology createOntology(Stream<OWLAxiom> axioms, IRI ontologyIRI) throws OWLOntologyCreationException
      Creates a new ontology that has the specified ontology IRI and is initialised to contain specific axioms.
      Parameters:
      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 OWLOntologyIRIMappers. 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 ontologyIRI.
      axioms - The axioms that should be copied into the new ontology
      Returns:
      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.
      OWLOntologyChangeException - if there was a problem copying the axioms.
      OWLOntologyAlreadyExistsException - if the manager already contains an ontology with the specified ontologyIRI.
      OWLOntologyDocumentAlreadyExistsException - if the specified ontologyIRI is mapped to a ontology document IRI for which there already exists a mapping in this manager.

    • createOntology

      default OWLOntology createOntology(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 OWLOntologyIRIMappers. 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 ontologyIRI.
      Parameters:
      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 null then a default (in memory) implementation of the ontology will most likely be created.
      Returns:
      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.
      OWLOntologyAlreadyExistsException - if the manager already contains an ontology with the specified ontologyIRI (and no version IRI).
      OWLOntologyDocumentAlreadyExistsException - if the specified ontologyIRI is mapped to a ontology document IRI for which there already exists a mapping in this manager.

    • createOntology

      OWLOntology createOntology(OWLOntologyID ontologyID) throws OWLOntologyCreationException
      Creates a new (empty) ontology that has the specified ontology ID.
      Parameters:
      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 OWLOntologyIRIMappers. 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 ontologyIRI.
      Returns:
      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.
      OWLOntologyAlreadyExistsException - if the manager already contains an ontology with the specified ontologyID (and no version IRI).
      OWLOntologyDocumentAlreadyExistsException - if the specified ontologyID is mapped to a ontology document IRI for which there already exists a mapping in this manager.

    • createOntology

      default OWLOntology createOntology(IRI ontologyIRI, Collection<OWLOntology> 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 OWLOntologyIRIMappers. 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 ontologyIRI.
      Parameters:
      ontologyIRI - The IRI of the new ontology.
      ontologies - The ontologies whose axioms should be copied into the new ontology
      copyLogicalAxiomsOnly - If set to true only logical axioms are copied into the new ontology. If set to false then all axioms (including annotation axioms) are copied into the new ontology.
      Returns:
      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.
      OWLOntologyAlreadyExistsException - if the manager already contains an ontology with the specified ontologyIRI (and no ontology version IRI).
      OWLOntologyDocumentAlreadyExistsException - if the specified ontologyIRI is mapped to a ontology document IRI for which there already exists a mapping in this manager.

    • createOntology

      OWLOntology createOntology(IRI ontologyIRI, Stream<OWLOntology> 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 OWLOntologyIRIMappers. 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 ontologyIRI.
      Parameters:
      ontologyIRI - The IRI of the new ontology.
      ontologies - The ontologies whose axioms should be copied into the new ontology
      copyLogicalAxiomsOnly - If set to true only logical axioms are copied into the new ontology. If set to false then all axioms (including annotation axioms) are copied into the new ontology.
      Returns:
      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.
      OWLOntologyAlreadyExistsException - if the manager already contains an ontology with the specified ontologyIRI (and no ontology version IRI).
      OWLOntologyDocumentAlreadyExistsException - if the specified ontologyIRI is mapped to a ontology document IRI for which there already exists a mapping in this manager.

    • createOntology

      default OWLOntology createOntology(IRI ontologyIRI, Collection<OWLOntology> ontologies) 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 OWLOntologyIRIMappers. 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 ontologyIRI.
      Parameters:
      ontologyIRI - The IRI of the new ontology.
      ontologies - The ontologies whose axioms should be copied into the new ontology
      Returns:
      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.
      OWLOntologyAlreadyExistsException - if the manager already contains an ontology with the specified ontologyIRI (and no version IRI).
      OWLOntologyDocumentAlreadyExistsException - if the specified ontologyIRI is mapped to a ontology document IRI for which there already exists a mapping in this manager.

    • copyOntology

      OWLOntology copyOntology(OWLOntology toCopy, OntologyCopy settings) throws OWLOntologyCreationException
      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 across format and document IRI, MOVE to remove the ontology from its previous manager.
      Parameters:
      toCopy - ontology to copy
      settings - settings for the copy
      Returns:
      copied ontology. This is the same object as toCopy only for MOVE copies
      Throws:
      OWLOntologyCreationException - if this manager cannot add the new ontology

    • loadOntology

      OWLOntology loadOntology(IRI ontologyIRI) throws OWLOntologyCreationException
      Loads an ontology that is assumed to have the specified 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 OWLOntologyIRIMapper objects. By default, if no custom OWLOntologyIRIMappers have been registered using the getIRIMappers() PriorityCollection PriorityCollection.add(Serializable...) method, or no mapping can be found, the ontology document IRI is taken to be the specified ontology IRI.
      Parameters:
      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).
      Returns:
      The OWLOntology representation of the ontology that was loaded.
      Throws:
      OWLOntologyCreationException - If there was a problem in creating and loading the ontology.
      UnparsableOntologyException - if the ontology was being parsed from a document and the document contained syntax errors.
      UnloadableImportException - if the ontology imports ontologies and one of the imports could not be loaded for what ever reason. If the MissingImportHandlingStrategy is set to MissingImportHandlingStrategy.SILENT then this exception will not be thrown. The UnloadableImportException contains information about the import declaration that triggered the import and the cause of this exception is an OWLOntologyCreationException which contains information about why the import could not be loaded.
      OWLOntologyCreationIOException - if there was an IOException when trying to load the ontology.
      OWLOntologyAlreadyExistsException - if the manager already contains an ontology with the specified ontologyIRI (where the ontology doesn't have a version IRI).
      OWLOntologyDocumentAlreadyExistsException - if the specified ontologyIRI is mapped to a ontology document IRI for which there already exists a mapping in this manager.

    • loadOntologyFromOntologyDocument

      default OWLOntology loadOntologyFromOntologyDocument(IRI documentIRI) throws OWLOntologyCreationException
      Loads an ontology from an ontology document specified by an IRI. In contrast the the loadOntology(IRI) method, no mapping is performed on the specified IRI.
      Parameters:
      documentIRI - The ontology document IRI where the ontology will be loaded from.
      Returns:
      The ontology that was loaded.
      Throws:
      OWLOntologyCreationException - If there was a problem in creating and loading the ontology.
      UnparsableOntologyException - if the ontology was being parsed from a document and the document contained syntax errors.
      UnloadableImportException - if the ontology imports ontologies and one of the imports could not be loaded for what ever reason. If the MissingImportHandlingStrategy is set to MissingImportHandlingStrategy.SILENT then this exception will not be thrown. The UnloadableImportException contains information about the import declaration that triggered the import and the cause of this exception is an OWLOntologyCreationException which contains information about why the import could not be loaded.
      OWLOntologyCreationIOException - if there was an IOException when trying to load the ontology.
      OWLOntologyDocumentAlreadyExistsException - if the specified documentIRI is already the document IRI for a loaded ontology.
      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 documentIRI.

    • loadOntologyFromOntologyDocument

      default OWLOntology loadOntologyFromOntologyDocument(File file) throws OWLOntologyCreationException
      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.
      Parameters:
      file - The file that contains a representation of an ontology
      Returns:
      The ontology that was parsed from the file.
      Throws:
      OWLOntologyCreationException - If there was a problem in creating and loading the ontology.
      UnparsableOntologyException - if the ontology could not be parsed.
      UnloadableImportException - if the ontology imports ontologies and one of the imports could not be loaded for what ever reason. If the MissingImportHandlingStrategy is set to MissingImportHandlingStrategy.SILENT then this exception will not be thrown. The UnloadableImportException contains information about the import declaration that triggered the import and the cause of this exception is an OWLOntologyCreationException which contains information about why the import could not be loaded.
      OWLOntologyCreationIOException - if there was an IOException when trying to load the ontology.
      OWLOntologyDocumentAlreadyExistsException - if the IRI of the specified file is already the document IRI for a loaded ontology.
      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 documentIRI.

    • loadOntologyFromOntologyDocument

      default OWLOntology loadOntologyFromOntologyDocument(InputStream inputStream) throws OWLOntologyCreationException
      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.
      Parameters:
      inputStream - The input stream that can be used to obtain a representation of an ontology
      Returns:
      The ontology that was parsed from the input stream.
      Throws:
      OWLOntologyCreationException - If there was a problem in creating and loading the ontology.
      UnparsableOntologyException - if the ontology could not be parsed.
      UnloadableImportException - if the ontology imports ontologies and one of the imports could not be loaded for what ever reason. If the MissingImportHandlingStrategy is set to MissingImportHandlingStrategy.SILENT then this exception will not be thrown. The UnloadableImportException contains information about the import declaration that triggered the import and the cause of this exception is an OWLOntologyCreationException which contains information about why the import could not be loaded.
      OWLOntologyCreationIOException - if there was an IOException when trying to load the ontology.
      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.

    • loadOntologyFromOntologyDocument

      default OWLOntology loadOntologyFromOntologyDocument(OWLOntologyDocumentSource documentSource) throws OWLOntologyCreationException
      A convenience method that load an ontology from an input source.
      Parameters:
      documentSource - The input source that describes where the ontology should be loaded from.
      Returns:
      The ontology that was loaded.
      Throws:
      OWLOntologyCreationException - If there was a problem in creating and loading the ontology.
      UnparsableOntologyException - if the ontology was being parsed from a document and the document contained syntax errors.
      UnloadableImportException - if the ontology imports ontologies and one of the imports could not be loaded for what ever reason. If the MissingImportHandlingStrategy is set to MissingImportHandlingStrategy.SILENT then this exception will not be thrown. The UnloadableImportException contains information about the import declaration that triggered the import and the cause of this exception is an OWLOntologyCreationException which contains information about why the import could not be loaded.
      OWLOntologyCreationIOException - if there was an IOException when trying to load the ontology.
      OWLOntologyDocumentAlreadyExistsException - if the document IRI of the input source is already the document IRI for a loaded ontology.
      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.

    • loadOntologyFromOntologyDocument

      OWLOntology loadOntologyFromOntologyDocument(OWLOntologyDocumentSource documentSource, OWLOntologyLoaderConfiguration config) throws OWLOntologyCreationException
      A convenience method that load an ontology from an input source with specified configuration.
      Parameters:
      documentSource - The input source that describes where the ontology should be loaded from.
      config - the configuration to use
      Returns:
      The ontology that was loaded.
      Throws:
      OWLOntologyCreationException - If there was a problem in creating and loading the ontology.
      UnparsableOntologyException - if the ontology was being parsed from a document and the document contained syntax errors.
      UnloadableImportException - if the ontology imports ontologies and one of the imports could not be loaded for what ever reason. If the MissingImportHandlingStrategy is set to MissingImportHandlingStrategy.SILENT then this exception will not be thrown. The UnloadableImportException contains information about the import declaration that triggered the import and the cause of this exception is an OWLOntologyCreationException which contains information about why the import could not be loaded.
      OWLOntologyCreationIOException - if there was an IOException when trying to load the ontology.
      OWLOntologyDocumentAlreadyExistsException - if the document IRI of the input source is already the document IRI for a loaded ontology.
      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.

    • removeOntology

      default void removeOntology(OWLOntology ontology)
      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.
      Parameters:
      ontology - The ontology to be removed. If this manager does not manage the ontology then nothing happens.

    • removeOntology

      void removeOntology(OWLOntologyID ontologyID)
      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.
      Parameters:
      ontologyID - The ontology to be removed. If this manager does not manage the ontology then nothing happens.

    • getOntologyDocumentIRI

      IRI getOntologyDocumentIRI(OWLOntology ontology)
      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.
      Parameters:
      ontology - The ontology whose document IRI is to be obtained.
      Returns:
      The document IRI of the ontology.
      Throws:
      UnknownOWLOntologyException - If the specified ontology is not managed by this manager.

    • setOntologyDocumentIRI

      void setOntologyDocumentIRI(OWLOntology ontology, IRI documentIRI)
      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.
      Parameters:
      ontology - The ontology that has already been loaded.
      documentIRI - The new ontology document IRI
      Throws:
      UnknownOWLOntologyException - If the specified ontology is not managed by this manager.

    • getOntologyFormat

      @Nullable OWLDocumentFormat getOntologyFormat(OWLOntology ontology)
      Gets the ontology format for the specified ontology.
      Parameters:
      ontology - The ontology whose format is to be obtained.
      Returns:
      The format of the ontology, or null if the ontology has no format (e.g., programmatically created ontology)

    • getNonnullOntologyFormat

      default OWLDocumentFormat getNonnullOntologyFormat(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 getOntologyFormat(OWLOntology).
      Parameters:
      ontology - The ontology whose format is to be obtained.
      Returns:
      The format of the ontology

    • setOntologyFormat

      void setOntologyFormat(OWLOntology ontology, OWLDocumentFormat ontologyFormat)
      Sets the format for the specified ontology.
      Parameters:
      ontology - The ontology whose format is to be set.
      ontologyFormat - The format for the specified ontology.
      Throws:
      UnknownOWLOntologyException - If the specified ontology is not managed by this manager.

    • saveOntology

      default void saveOntology(OWLOntology ontology) throws OWLOntologyStorageException
      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.
      Parameters:
      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.
      UnknownOWLOntologyException - if this manager does not manage the specified ontology

    • saveOntology

      default void saveOntology(OWLOntology ontology, IRI documentIRI) throws OWLOntologyStorageException
      Saves the specified ontology, using the specified document IRI to determine where/how the ontology should be saved.
      Parameters:
      ontology - The ontology to be saved.
      documentIRI - The document IRI where the ontology should be saved to
      Throws:
      OWLOntologyStorageException - If the ontology cannot be saved
      UnknownOWLOntologyException - if the specified ontology is not managed by this manager.

    • saveOntology

      default void saveOntology(OWLOntology ontology, OutputStream outputStream) throws OWLOntologyStorageException
      Saves the specified ontology, to the specified output stream
      Parameters:
      ontology - The ontology to be saved.
      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
      UnknownOWLOntologyException - if this manager does not manage the specified ontology.

    • saveOntology

      default void saveOntology(OWLOntology ontology, OWLDocumentFormat ontologyFormat) throws OWLOntologyStorageException
      Saves the specified ontology in the specified ontology format to its document URI.
      Parameters:
      ontology - The ontology to be saved.
      ontologyFormat - The format in which the ontology should be saved.
      Throws:
      OWLOntologyStorageException - If the ontology cannot be saved.
      UnknownOWLOntologyException - if the specified ontology is not managed by this manager

    • saveOntology

      void saveOntology(OWLOntology ontology, OWLDocumentFormat ontologyFormat, IRI documentIRI) throws OWLOntologyStorageException
      Saves the specified ontology to the specified document IRI in the specified ontology format.
      Parameters:
      ontology - The ontology to be saved
      ontologyFormat - The format in which to save the ontology
      documentIRI - The document IRI where the ontology should be saved to
      Throws:
      OWLOntologyStorageException - If the ontology could not be saved.
      UnknownOWLOntologyException - if the specified ontology is not managed by the manager.

    • saveOntology

      default void saveOntology(OWLOntology ontology, OWLDocumentFormat ontologyFormat, OutputStream outputStream) throws OWLOntologyStorageException
      Saves the specified ontology to the specified output stream in the specified ontology format.
      Parameters:
      ontology - The ontology to be saved
      ontologyFormat - The format in which to save the ontology
      outputStream - The output stream where the ontology will be saved to.
      Throws:
      OWLOntologyStorageException - If the ontology could not be saved.
      UnknownOWLOntologyException - if the specified ontology is not managed by the manager.

    • saveOntology

      default void saveOntology(OWLOntology ontology, OWLOntologyDocumentTarget documentTarget) throws OWLOntologyStorageException
      Saves the specified ontology to the specified OWLOntologyDocumentTarget.
      Parameters:
      ontology - The ontology to be saved.
      documentTarget - The output target where the ontology will be saved to.
      Throws:
      OWLOntologyStorageException - If the ontology could not be saved.
      UnknownOWLOntologyException - if the specified ontology is not managed by this manager.

    • saveOntology

      void saveOntology(OWLOntology ontology, OWLDocumentFormat ontologyFormat, OWLOntologyDocumentTarget documentTarget) throws OWLOntologyStorageException
      Saves the specified ontology to the specified output target in the specified ontology format.
      Parameters:
      ontology - The ontology to be saved.
      ontologyFormat - The output format in which to save the ontology
      documentTarget - The output target where the ontology will be saved to
      Throws:
      OWLOntologyStorageException - If the ontology could not be saved.
      UnknownOWLOntologyException - If the specified ontology is not managed by this manager.

    • addIRIMapper

      @Deprecated void addIRIMapper(OWLOntologyIRIMapper mapper)
      Deprecated.
      use getIRIMappers().add() instead
      Add an IRI mapper to the manager
      Parameters:
      mapper - the mapper to add

    • removeIRIMapper

      @Deprecated void removeIRIMapper(OWLOntologyIRIMapper mapper)
      Deprecated.
      use getIRIMappers().remove() instead
      Remove an IRI mapper from the manager
      Parameters:
      mapper - the mapper to remove

    • clearIRIMappers

      @Deprecated void clearIRIMappers()
      Deprecated.
      use getIRIMappers().clear() instead
      Clear the manager mappers

    • addOntologyStorer

      @Deprecated void addOntologyStorer(OWLStorerFactory storer)
      Deprecated.
      use getOntologyStorers().add() instead
      Add a storer to the manager
      Parameters:
      storer - the storer to add

    • removeOntologyStorer

      @Deprecated void removeOntologyStorer(OWLStorerFactory storer)
      Deprecated.
      use getOntologyStorers().remove() instead
      Remove a storer from the manager
      Parameters:
      storer - the storer to remove

    • clearOntologyStorers

      @Deprecated void clearOntologyStorers()
      Deprecated.
      use getOntologyStorers().clear() instead
      Clear the manager storers

    • getIRIMappers

      PriorityCollection<OWLOntologyIRIMapper> getIRIMappers()
      Returns:
      the collection of IRI mappers. This allows for iteration and modification of the list.

    • setIRIMappers

      void setIRIMappers(Set<OWLOntologyIRIMapper> mappers)
      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.
      Parameters:
      mappers - the mappers to be injected

    • getOntologyParsers

      PriorityCollection<OWLParserFactory> getOntologyParsers()
      Returns:
      the collection of parsers. This allows for iteration and modification of the list.

    • setOntologyParsers

      void setOntologyParsers(Set<OWLParserFactory> parsers)
      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.
      Parameters:
      parsers - the factories to be injected

    • getOntologyFactories

      PriorityCollection<OWLOntologyFactory> getOntologyFactories()
      Returns:
      the collection of ontology factories. This allows for iteration and modification of the list.

    • setOntologyFactories

      void setOntologyFactories(Set<OWLOntologyFactory> factories)
      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.
      Parameters:
      factories - the factories to be injected

    • getOntologyStorers

      PriorityCollection<OWLStorerFactory> getOntologyStorers()
      Returns:
      the collection of storers. This allows for iteration and modification of the list.

    • setOntologyStorers

      void setOntologyStorers(Set<OWLStorerFactory> storers)
      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.
      Parameters:
      storers - The storers to be used

    • addOntologyChangeListener

      void addOntologyChangeListener(OWLOntologyChangeListener listener, OWLOntologyChangeBroadcastStrategy strategy)
      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.
      Parameters:
      listener - The listener to be added.
      strategy - The strategy that should be used for broadcasting changes to the listener.

    • addImpendingOntologyChangeListener

      void addImpendingOntologyChangeListener(ImpendingOWLOntologyChangeListener listener)
      Parameters:
      listener - the listener to add

    • removeImpendingOntologyChangeListener

      void removeImpendingOntologyChangeListener(ImpendingOWLOntologyChangeListener listener)
      Parameters:
      listener - the listener to remove

    • addOntologyChangesVetoedListener

      void addOntologyChangesVetoedListener(OWLOntologyChangesVetoedListener listener)
      Parameters:
      listener - the listener to add

    • removeOntologyChangesVetoedListener

      void removeOntologyChangesVetoedListener(OWLOntologyChangesVetoedListener listener)
      Parameters:
      listener - the listener to remove

    • setDefaultChangeBroadcastStrategy

      void setDefaultChangeBroadcastStrategy(OWLOntologyChangeBroadcastStrategy strategy)
      Sets the default strategy that is used to broadcast ontology changes.
      Parameters:
      strategy - The strategy to be used for broadcasting changes. This strategy will override any previously set broadcast strategy.
      See Also:

    • makeLoadImportRequest

      default void makeLoadImportRequest(OWLImportsDeclaration declaration)
      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.
      Parameters:
      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.

    • makeLoadImportRequest

      void makeLoadImportRequest(OWLImportsDeclaration declaration, OWLOntologyLoaderConfiguration configuration)
      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.
      Parameters:
      declaration - The declaration that describes the import to be loaded.
      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.

    • addMissingImportListener

      void addMissingImportListener(MissingImportListener listener)
      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.
      Parameters:
      listener - The listener to be added.

    • removeMissingImportListener

      void removeMissingImportListener(MissingImportListener listener)
      Removes a previously added missing import listener.
      Parameters:
      listener - The listener to be removed.

    • addOntologyLoaderListener

      void addOntologyLoaderListener(OWLOntologyLoaderListener listener)
      Adds an ontology loaded listener to this manager.
      Parameters:
      listener - The listener to be added.

    • removeOntologyLoaderListener

      void removeOntologyLoaderListener(OWLOntologyLoaderListener listener)
      Removes a previously added ontology loaded listener.
      Parameters:
      listener - The listener to be removed.

    • addOntologyChangeProgessListener

      void addOntologyChangeProgessListener(OWLOntologyChangeProgressListener listener)
      Adds an ontology change progress listener.
      Parameters:
      listener - The listener to be added.

    • removeOntologyChangeProgessListener

      void removeOntologyChangeProgessListener(OWLOntologyChangeProgressListener listener)
      Removes a previously added ontology change listener.
      Parameters:
      listener - The listener to be removed.