edu.stanford.smi.protegex.owl.jena.parser
Class ProtegeOWLParser

java.lang.Object
  edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser

public class ProtegeOWLParser

extends Object

An OWL parser that reads an OWL stream triple-by-triple and writes the corresponding Protege-OWL Triples into one or more TripleStores. The current implementation uses the Jena ARP parser for triple loading.

Author:

Holger Knublauch

Nested Class Summary

static interface	ProtegeOWLParser.ARPInvokation An interface needed as an abstraction of the various methods to invoke the Jena ARP (the various load methods with different parameters).
private class	ProtegeOWLParser.MyErrorHandler
private class	ProtegeOWLParser.MyNamespaceHandler
private class	ProtegeOWLParser.MyStatementHandler

Field Summary

private int	count
private String	currentDefaultNamespace The default namespace to use if the current file does not define one by itself.
private edu.stanford.smi.protege.model.Frame	currentType
private static int	errorLineNumber
private static URI	errorURI
static boolean	inUI A rather ugly flag that can be activated to prompt the user if a local file was found as a possible import redirection.
private boolean	isRDFList
private edu.stanford.smi.protege.model.KnowledgeBase	kb
private ProtegeOWLParserLogger	logger
private OWLModel	owlModel
private edu.stanford.smi.protege.model.Cls	owlNamedClassClass
private OWLModelPatcher	patcher
private String	prefixForDefaultNamespace
private RDFProperty	rdfFirstProperty
private RDFProperty	rdfRestProperty
private static String	RDFS_RESOURCE_URI
private RDFProperty	rdfTypeProperty
private TripleStore	tripleStore
private TripleStoreModel	tripleStoreModel
private Collection	tripleStores
private static UnresolvedImportHandler	unresolvedImportHandler
private Map	untypedResources
private URI2NameConverter	uri2NameConverter

Constructor Summary

ProtegeOWLParser(OWLModel owlModel, boolean incremental)

Method Summary

static void	addImport(JenaOWLModel owlModel, URI ontologyName) A convenience method that dynamically adds an import to a JenaOWLModel.
static void	addImport(JenaOWLModel owlModel, URI ontologyName, String prefixForDefaultNamespace) A convenience method that dynamically adds an import to a JenaOWLModel.
private void	addNamespaceToImports(String defaultNamespace, Set imports)
protected com.hp.hpl.jena.rdf.arp.ARP	createARP()
private void	createDefaultNamespace(TripleStore tripleStore)
private Object	createLiteralObject(com.hp.hpl.jena.rdf.arp.ALiteral node, RDFProperty property)
protected ProtegeOWLParserLogger	createLogger()
protected OWLModelPatcher	createPatcher()
private RDFResource	createRDFResource(String name)
private RDFSLiteral	createRDFSLiteral(com.hp.hpl.jena.rdf.arp.ALiteral literal, RDFProperty property)
protected URI2NameConverter	createURI2NameConverter(OWLModel owlModel, boolean incremental)
private RDFResource	findResource(String name)
static int	getErrorLineNumber()
static URI	getErrorURI() Gets the URI of the most recently parsed file.
protected String	getImplicitImport(String namespace)
static InputStream	getInputStream(URL url)
protected ProtegeOWLParserLogger	getLogger()
private RDFProperty	getRDFProperty(com.hp.hpl.jena.rdf.arp.AResource propertyNode)
private RDFResource	getRDFResource(com.hp.hpl.jena.rdf.arp.AResource aResource)
private static Repository	getRepository(OWLModel owlModel, TripleStore tripleStore, URI ontologyName)
private Collection	getUntypedResources() Gets all RDFResources that don't have any rdf:type.
void	loadTriples(InputStream is, String xmlBase, TripleStore tripleStore)
private void	populateUntypedResourcesMap()
private void	replaceNamespace(TripleStore tripleStore, RDFResource ontology, String prefix, String namespace)
private void	replaceTemporaryName(TripleStore tripleStore, RDFResource resource, String name, boolean isOntology)
private void	replaceTemporaryNames()
private void	replaceTemporaryNames(TripleStore tripleStore)
void	run(InputStream is, String uri)
void	run(Reader reader, String uri)
void	run(TripleStore tripleStore, String ontologyName, ProtegeOWLParser.ARPInvokation invokation)
void	run(URI uri)
void	run(URI uri, String defaultNamespace, TripleStore tripleStore) Deprecated.
void	run(URI uri, TripleStore tripleStore)
private boolean	runImplicitImport(RDFResource resource, Set imports, Collection untypedResources)
private boolean	runImplicitImports(Set imports) Applies some heuristics to resolve missing owl:imports, especially for RDF Schema files.
private void	runImport(String uri, Set imports) Imports the ontology that has the name specified by uri.
private void	runImports(TripleStore tripleStore, Set imports) Imports the ontologies that are objects of any owl:imports triples in the specified TripleStore.
void	setLogger(ProtegeOWLParserLogger logger)
private void	setPrefixForDefaultNamespace(String prefixForDefaultNamespace)
static void	setUnresolvedImportHandler(UnresolvedImportHandler handler)
void	setURI2NameConverter(URI2NameConverter converter)
void	setURLResolver(URIResolver urlResolver) Deprecated. This method no longer does anything.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

count

private int count

currentDefaultNamespace

private String currentDefaultNamespace

The default namespace to use if the current file does not define one by itself. This is typically the file's URL (import URI).

currentType

private edu.stanford.smi.protege.model.Frame currentType

errorLineNumber

private static int errorLineNumber

errorURI

private static URI errorURI

inUI

public static boolean inUI

A rather ugly flag that can be activated to prompt the user if a local file was found as a possible import redirection.

isRDFList

private boolean isRDFList

kb

private edu.stanford.smi.protege.model.KnowledgeBase kb

logger

private ProtegeOWLParserLogger logger

owlNamedClassClass

private edu.stanford.smi.protege.model.Cls owlNamedClassClass

owlModel

private OWLModel owlModel

patcher

private OWLModelPatcher patcher

prefixForDefaultNamespace

private String prefixForDefaultNamespace

rdfFirstProperty

private RDFProperty rdfFirstProperty

rdfRestProperty

private RDFProperty rdfRestProperty

RDFS_RESOURCE_URI

private static final String RDFS_RESOURCE_URI

rdfTypeProperty

private RDFProperty rdfTypeProperty

tripleStore

private TripleStore tripleStore

tripleStoreModel

private TripleStoreModel tripleStoreModel

tripleStores

private Collection tripleStores

untypedResources

private Map untypedResources

uri2NameConverter

private URI2NameConverter uri2NameConverter

unresolvedImportHandler

private static UnresolvedImportHandler unresolvedImportHandler

Constructor Detail

ProtegeOWLParser

public ProtegeOWLParser(OWLModel owlModel,
                        boolean incremental)

Method Detail

setUnresolvedImportHandler

public static void setUnresolvedImportHandler(UnresolvedImportHandler handler)

addNamespaceToImports

private void addNamespaceToImports(String defaultNamespace,
                                   Set imports)

addImport

public static void addImport(JenaOWLModel owlModel,
                             URI ontologyName)
                      throws Exception

A convenience method that dynamically adds an import to a JenaOWLModel. This will immediately load the file into a new TripleStore. Prior to invoking this method, the caller should define a prefix for the expected namespace (e.g., URI + "#"). Following the call, the caller should add an import statement to an existing OWLOntology (usually the default ontology).

Parameters:

owlModel -

ontologyName - The name of the imported ontology.

Throws:

Exception

addImport

public static void addImport(JenaOWLModel owlModel,
                             URI ontologyName,
                             String prefixForDefaultNamespace)
                      throws Exception

A convenience method that dynamically adds an import to a JenaOWLModel. This will immediately load the file into a new TripleStore. Following the call, the caller should add an import statement to an existing OWLOntology (usually the default ontology).

Parameters:

owlModel -

ontologyName -

prefixForDefaultNamespace - an (optional) prefix that shall be used for the the default namespace of the directly imported ontology

Throws:

Exception

getRepository

private static Repository getRepository(OWLModel owlModel,
                                        TripleStore tripleStore,
                                        URI ontologyName)

createARP

protected com.hp.hpl.jena.rdf.arp.ARP createARP()

createDefaultNamespace

private void createDefaultNamespace(TripleStore tripleStore)

createLiteralObject

private Object createLiteralObject(com.hp.hpl.jena.rdf.arp.ALiteral node,
                                   RDFProperty property)

createLogger

protected ProtegeOWLParserLogger createLogger()

createPatcher

protected OWLModelPatcher createPatcher()

createRDFSLiteral

private RDFSLiteral createRDFSLiteral(com.hp.hpl.jena.rdf.arp.ALiteral literal,
                                      RDFProperty property)

createRDFResource

private RDFResource createRDFResource(String name)

createURI2NameConverter

protected URI2NameConverter createURI2NameConverter(OWLModel owlModel,
                                                    boolean incremental)

getErrorLineNumber

public static int getErrorLineNumber()

getErrorURI

public static URI getErrorURI()

Gets the URI of the most recently parsed file. This can be used to diagnose where an exception has occured

Returns:

the URI or null

findResource

private RDFResource findResource(String name)

getImplicitImport

protected String getImplicitImport(String namespace)

getLogger

protected ProtegeOWLParserLogger getLogger()

getRDFProperty

private RDFProperty getRDFProperty(com.hp.hpl.jena.rdf.arp.AResource propertyNode)

getRDFResource

private RDFResource getRDFResource(com.hp.hpl.jena.rdf.arp.AResource aResource)

getUntypedResources

private Collection getUntypedResources()

Gets all RDFResources that don't have any rdf:type.

Returns:

the untyped resources

populateUntypedResourcesMap

private void populateUntypedResourcesMap()

replaceNamespace

private void replaceNamespace(TripleStore tripleStore,
                              RDFResource ontology,
                              String prefix,
                              String namespace)

replaceTemporaryNames

private void replaceTemporaryNames()

replaceTemporaryNames

private void replaceTemporaryNames(TripleStore tripleStore)

replaceTemporaryName

private void replaceTemporaryName(TripleStore tripleStore,
                                  RDFResource resource,
                                  String name,
                                  boolean isOntology)

run

public void run(URI uri,
                TripleStore tripleStore)
         throws Exception

Throws:

Exception

loadTriples

public void loadTriples(InputStream is,
                        String xmlBase,
                        TripleStore tripleStore)
                 throws Exception

Throws:

Exception

run

public void run(URI uri,
                String defaultNamespace,
                TripleStore tripleStore)
         throws Exception

Deprecated.

Throws:

Exception

run

public void run(TripleStore tripleStore,
                String ontologyName,
                ProtegeOWLParser.ARPInvokation invokation)
         throws Exception

Throws:

Exception

runImplicitImports

private boolean runImplicitImports(Set imports)
                            throws IOException,
                                   SAXException

Applies some heuristics to resolve missing owl:imports, especially for RDF Schema files.

Throws:

IOException

SAXException

runImplicitImport

private boolean runImplicitImport(RDFResource resource,
                                  Set imports,
                                  Collection untypedResources)
                           throws SAXException,
                                  IOException

Throws:

SAXException

IOException

runImports

private void runImports(TripleStore tripleStore,
                        Set imports)
                 throws SAXException,
                        IOException

Imports the ontologies that are objects of any owl:imports triples in the specified TripleStore. Ontologies that have already been imported will not be imported again.

Throws:

SAXException

IOException

runImport

private void runImport(String uri,
                       Set imports)
                throws SAXException,
                       IOException

Imports the ontology that has the name specified by uri.

Parameters:

uri - The name of the ontology to be imported.

imports - A Set that contains a list of strings that represent the names of the ontologies that have already been imported.

Throws:

SAXException

IOException

run

public void run(InputStream is,
                String uri)
         throws Exception

Throws:

Exception

run

public void run(Reader reader,
                String uri)
         throws Exception

Throws:

Exception

run

public void run(URI uri)
         throws Exception

Throws:

Exception

setLogger

public void setLogger(ProtegeOWLParserLogger logger)

setPrefixForDefaultNamespace

private void setPrefixForDefaultNamespace(String prefixForDefaultNamespace)

setURI2NameConverter

public void setURI2NameConverter(URI2NameConverter converter)

setURLResolver

public void setURLResolver(URIResolver urlResolver)

Deprecated. This method no longer does anything.

getInputStream

public static InputStream getInputStream(URL url)
                                  throws IOException

Throws:

IOException