Modified: incubator/stanbol/trunk/kres/eu.iksproject.kres.semion.reengineer.xml/src/main/java/eu/iksproject/kres/semion/reengineer/xml/XMLExtractor.java URL: http://svn.apache.org/viewvc/incubator/stanbol/trunk/kres/eu.iksproject.kres.semion.reengineer.xml/src/main/java/eu/iksproject/kres/semion/reengineer/xml/XMLExtractor.java?rev=1080180&r1=1080179&r2=1080180&view=diff ============================================================================== --- incubator/stanbol/trunk/kres/eu.iksproject.kres.semion.reengineer.xml/src/main/java/eu/iksproject/kres/semion/reengineer/xml/XMLExtractor.java (original) +++ incubator/stanbol/trunk/kres/eu.iksproject.kres.semion.reengineer.xml/src/main/java/eu/iksproject/kres/semion/reengineer/xml/XMLExtractor.java Thu Mar 10 10:55:30 2011 @@ -50,6 +50,7 @@ import org.xml.sax.SAXException; import eu.iksproject.kres.api.manager.DuplicateIDException; import eu.iksproject.kres.api.manager.KReSONManager; +import eu.iksproject.kres.api.manager.io.RootOntologyIRISource; import eu.iksproject.kres.api.manager.ontology.OntologyScope; import eu.iksproject.kres.api.manager.ontology.OntologyScopeFactory; import eu.iksproject.kres.api.manager.ontology.OntologySpaceFactory; @@ -73,7 +74,7 @@ import eu.iksproject.kres.ontologies.XSD * the {@link SemionReengineer} for XML data sources. * * @author andrea.nuzzolese - * + * */ @Component(immediate = true, metatype = true) @@ -84,30 +85,30 @@ public class XMLExtractor extends Semion public static final String _HOST_NAME_AND_PORT_DEFAULT = "localhost:8080"; public static final String _REENGINEERING_SCOPE_DEFAULT = "xml_reengineering"; public static final String _XML_REENGINEERING_SESSION_SPACE_DEFAULT = "/xml-reengineering-session-space"; - + @Property(value = _HOST_NAME_AND_PORT_DEFAULT) - public static final String HOST_NAME_AND_PORT = "host.name.port"; - + public static final String HOST_NAME_AND_PORT = "host.name.port"; + @Property(value = _REENGINEERING_SCOPE_DEFAULT) public static final String REENGINEERING_SCOPE = "xml.reengineering.scope"; @Property(value = _XML_REENGINEERING_SESSION_SPACE_DEFAULT) - public static final String XML_REENGINEERING_SESSION_SPACE = "http://kres.iks-project.eu/space/reengineering/db";; - + public static final String XML_REENGINEERING_SESSION_SPACE = "http://kres.iks-project.eu/space/reengineering/db";; + private IRI kReSSessionID; - + public final Logger log = LoggerFactory.getLogger(getClass()); - + @Reference KReSONManager onManager; - + @Reference SemionManager reengineeringManager; - + private OntologyScope scope; private IRI scopeIRI; private IRI spaceIRI; - + /** * This default constructor is <b>only</b> intended to be used by the OSGI * environment with Service Component Runtime support. @@ -119,9 +120,9 @@ public class XMLExtractor extends Semion * OSGI environment. */ public XMLExtractor() { - + } - + public XMLExtractor(SemionManager reengineeringManager, KReSONManager onManager, Dictionary<String, Object> configuration) { this(); @@ -129,7 +130,7 @@ public class XMLExtractor extends Semion this.onManager = onManager; activate(configuration); } - + /** * Used to configure an instance within an OSGi container. * @@ -155,26 +156,26 @@ public class XMLExtractor extends Semion if (hostPort == null) hostPort = _HOST_NAME_AND_PORT_DEFAULT; // TODO: Manage the other properties - + spaceIRI = IRI.create(XML_REENGINEERING_SESSION_SPACE); scopeIRI = IRI.create("http://"; + hostPort + "/kres/ontology/" + scopeID); - + reengineeringManager.bindReengineer(this); - + KReSSessionManager kReSSessionManager = onManager.getSessionManager(); KReSSession kReSSession = kReSSessionManager.createSession(); - + kReSSessionID = kReSSession.getID(); - + OntologyScopeFactory ontologyScopeFactory = onManager .getOntologyScopeFactory(); - + ScopeRegistry scopeRegistry = onManager.getScopeRegistry(); OntologySpaceFactory ontologySpaceFactory = onManager .getOntologySpaceFactory(); - + scope = null; try { log.info("Semion XMLEtractor : created scope with IRI " @@ -183,13 +184,14 @@ public class XMLExtractor extends Semion OWLOntologyManager ontologyManager = OWLManager .createOWLOntologyManager(); OWLOntology owlOntology = ontologyManager.createOntology(iri); - + System.out.println("Created ONTOLOGY OWL"); - + scope = ontologyScopeFactory.createOntologyScope(scopeIRI, - new OntologyInputSourceOXML()); + new RootOntologyIRISource(IRI.create(XML_OWL.URI)) + /* new OntologyInputSourceOXML() */); // scope.setUp(); - + scopeRegistry.registerScope(scope); } catch (DuplicateIDException e) { log.info("Semion DBExtractor : already existing scope for IRI " @@ -211,11 +213,11 @@ public class XMLExtractor extends Semion scopeRegistry.setScopeActive(scopeIRI, true); } - + log.info("Activated KReS Semion RDB Reengineer"); - } - - @Override + } + + @Override public boolean canPerformReengineering(DataSource dataSource) { if (dataSource.getDataSourceType() == ReengineerType.XML) return true; @@ -229,20 +231,20 @@ public class XMLExtractor extends Semion return true; } else { return false; - } - } - + } + } + @Override public boolean canPerformReengineering(OWLOntology schemaOntology) { - + OWLDataFactory factory = onManager.getOwlFactory(); - + OWLClass dataSourceClass = factory.getOWLClass(Semion_OWL.DataSource); Set<OWLIndividual> individuals = dataSourceClass .getIndividuals(schemaOntology); - + int hasDataSourceType = -1; - + if (individuals != null && individuals.size() == 1) { for (OWLIndividual individual : individuals) { OWLDataProperty hasDataSourceTypeProperty = factory @@ -251,36 +253,36 @@ public class XMLExtractor extends Semion hasDataSourceTypeProperty, schemaOntology); if (values != null && values.size() == 1) { for (OWLLiteral value : values) { - try { + try { Integer valueInteger = Integer.valueOf(value .getLiteral()); hasDataSourceType = valueInteger.intValue(); } catch (NumberFormatException e) { } + } + } } } - } - } - + if (hasDataSourceType == getReengineerType()) { return true; } else { return false; } - } - - @Override + } + + @Override public boolean canPerformReengineering(String dataSourceType) throws UnsupportedReengineerException { return canPerformReengineering(ReengineerType.getType(dataSourceType)); - } - + } + private IRI createElementResource(String ns, String schemaNS, Element element, String parentName, Integer id, OWLOntologyManager manager, OWLDataFactory factory, OWLOntology dataOntology) { - + IRI elementResourceIRI; OWLClassAssertionAxiom elementResource; if (id == null) { @@ -292,23 +294,23 @@ public class XMLExtractor extends Semion + element.getLocalName() + "_" + id.toString()); elementResource = createOWLClassAssertionAxiom(factory, XML_OWL.XMLElement, elementResourceIRI); - } + } manager.applyChange(new AddAxiom(dataOntology, elementResource)); - + String schemaElementName = element.getLocalName(); - + IRI elementDeclarationIRI = IRI.create(schemaNS + schemaElementName); - + manager.applyChange(new AddAxiom(dataOntology, createOWLObjectPropertyAssertionAxiom(factory, XML_OWL.hasElementDeclaration, elementResourceIRI, elementDeclarationIRI))); - + NamedNodeMap namedNodeMap = element.getAttributes(); if (namedNodeMap != null) { for (int i = 0, j = namedNodeMap.getLength(); i < j; i++) { Node node = namedNodeMap.item(i); - + String attributeName = node.getNodeName(); String attributeValue = node.getTextContent(); @@ -319,8 +321,8 @@ public class XMLExtractor extends Semion elementLocalName = elementNames[1]; } else { elementLocalName = elementNames[0]; - } - + } + IRI xmlAttributeIRI = IRI.create(ns + elementLocalName + attributeName); System.out.println("Attribute: " + ns + elementLocalName @@ -328,7 +330,7 @@ public class XMLExtractor extends Semion OWLClassAssertionAxiom xmlAttribute = createOWLClassAssertionAxiom( factory, XML_OWL.XMLAttribute, xmlAttributeIRI); manager.addAxiom(dataOntology, xmlAttribute); - + manager.addAxiom(dataOntology, createOWLDataPropertyAssertionAxiom(factory, XML_OWL.nodeName, xmlAttributeIRI, @@ -349,31 +351,31 @@ public class XMLExtractor extends Semion createOWLObjectPropertyAssertionAxiom(factory, XML_OWL.hasXMLAttribute, elementResourceIRI, xmlAttributeIRI)); - + + } } - } - + return elementResourceIRI; } - + @Override public OWLOntology dataReengineering(String graphNS, IRI outputIRI, DataSource dataSource, final OWLOntology schemaOntology) throws ReengineeringException { - + OWLOntology ontology = null; - + System.out.println("Starting XML Reengineering"); OWLOntologyManager ontologyManager = onManager.getOwlCacheManager(); OWLDataFactory factory = onManager.getOwlFactory(); - + IRI schemaOntologyIRI = schemaOntology.getOntologyID().getOntologyIRI(); - + OWLOntology localDataOntology = null; - - System.out.println("XML output IRI: "+outputIRI); - if(schemaOntology != null){ - if(outputIRI != null){ + + System.out.println("XML output IRI: " + outputIRI); + if (schemaOntology != null) { + if (outputIRI != null) { try { localDataOntology = ontologyManager .createOntology(outputIRI); @@ -386,53 +388,53 @@ public class XMLExtractor extends Semion localDataOntology = ontologyManager.createOntology(); } catch (OWLOntologyCreationException e) { throw new ReengineeringException(); - } + } } - + final OWLOntology dataOntology = localDataOntology; - + OWLImportsDeclaration importsDeclaration = factory .getOWLImportsDeclaration(IRI.create(XML_OWL.URI)); - + ontologyManager.applyChange(new AddImport(dataOntology, importsDeclaration)); - + graphNS = graphNS.replace("#", ""); String schemaNS = graphNS + "/schema#"; ; String dataNS = graphNS + "#"; - + OWLClass dataSourceOwlClass = factory .getOWLClass(Semion_OWL.DataSource); - + Set<OWLIndividual> individuals = dataSourceOwlClass .getIndividuals(schemaOntology); - + DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance(); dbf.setNamespaceAware(true); DocumentBuilder db; try { db = dbf.newDocumentBuilder(); - + InputStream xmlStream = (InputStream) dataSource .getDataSource(); - + Document dom = db.parse(xmlStream); - + Element documentElement = dom.getDocumentElement(); - + String nodeName = documentElement.getNodeName(); - + IRI rootElementIRI = createElementResource(dataNS, schemaNS, documentElement, null, null, ontologyManager, factory, dataOntology); - + iterateChildren(dataNS, schemaNS, rootElementIRI, documentElement, ontologyManager, factory, dataOntology); - + } catch (ParserConfigurationException e) { // TODO Auto-generated catch block - e.printStackTrace(); + e.printStackTrace(); } catch (SAXException e) { // TODO Auto-generated catch block e.printStackTrace(); @@ -440,11 +442,11 @@ public class XMLExtractor extends Semion // TODO Auto-generated catch block e.printStackTrace(); } - + OWLOntologyManager man = OWLManager.createOWLOntologyManager(); - + OWLOntologySetProvider provider = new OWLOntologySetProvider() { - + @Override public Set<OWLOntology> getOntologies() { Set<OWLOntology> ontologies = new HashSet<OWLOntology>(); @@ -454,30 +456,30 @@ public class XMLExtractor extends Semion } }; OWLOntologyMerger merger = new OWLOntologyMerger(provider); - + try { ontology = merger.createMergedOntology(man, outputIRI); } catch (OWLOntologyCreationException e) { e.printStackTrace(); } } - + return ontology; } - + private OWLOntology dataReengineering(String graphNS, IRI outputIRI, Document dom, OWLOntology schemaOntology) throws ReengineeringException { - + OWLOntologyManager ontologyManager = onManager.getOwlCacheManager(); OWLDataFactory factory = onManager.getOwlFactory(); - + IRI schemaOntologyIRI = schemaOntology.getOntologyID().getOntologyIRI(); - + OWLOntology dataOntology = null; - - if(schemaOntology != null){ - if(outputIRI != null){ + + if (schemaOntology != null) { + if (outputIRI != null) { try { dataOntology = ontologyManager.createOntology(outputIRI); } catch (OWLOntologyCreationException e) { @@ -488,86 +490,86 @@ public class XMLExtractor extends Semion dataOntology = ontologyManager.createOntology(); } catch (OWLOntologyCreationException e) { throw new ReengineeringException(); - } + } } - + OWLImportsDeclaration importsDeclaration = factory .getOWLImportsDeclaration(schemaOntologyIRI); - + ontologyManager.applyChange(new AddImport(dataOntology, importsDeclaration)); - + String schemaNS = graphNS + "/schema#"; ; String dataNS = graphNS + "#"; ; - + OWLClass dataSourceOwlClass = factory .getOWLClass(Semion_OWL.DataSource); - + Set<OWLIndividual> individuals = dataSourceOwlClass .getIndividuals(schemaOntology); - + DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance(); dbf.setNamespaceAware(true); DocumentBuilder db; try { db = dbf.newDocumentBuilder(); - + Element documentElement = dom.getDocumentElement(); - + String nodeName = documentElement.getNodeName(); - + IRI rootElementIRI = createElementResource(dataNS, schemaNS, documentElement, null, null, ontologyManager, factory, dataOntology); - + iterateChildren(dataNS, schemaNS, rootElementIRI, documentElement, ontologyManager, factory, dataOntology); - + } catch (ParserConfigurationException e) { // TODO Auto-generated catch block - e.printStackTrace(); - } + e.printStackTrace(); + } } - + return dataOntology; } - + @Deactivate protected void deactivate(ComponentContext context) { log.info("in " + XMLExtractor.class + " deactivate with context " + context); reengineeringManager.unbindReengineer(this); } - + @Override public int getReengineerType() { return ReengineerType.XML; - } - + } + private OntologyScope getScope() { OntologyScope ontologyScope = null; - + ScopeRegistry scopeRegistry = onManager.getScopeRegistry(); - + if (scopeRegistry.isScopeActive(scopeIRI)) { ontologyScope = scopeRegistry.getScope(scopeIRI); - } - + } + return ontologyScope; } - + private void iterateChildren(String dataNS, String schemaNS, IRI parentResource, Node parentElement, OWLOntologyManager manager, OWLDataFactory factory, OWLOntology dataOntology) { - + NodeList children = parentElement.getChildNodes(); if (children != null) { for (int i = 0, j = children.getLength(); i < j; i++) { Node child = children.item(i); if (child instanceof Element) { - + String[] parentNames = parentResource.toString().split("#"); String parentLocalName; if (parentNames.length == 2) { @@ -575,7 +577,7 @@ public class XMLExtractor extends Semion } else { parentLocalName = parentNames[0]; } - + IRI childResource = createElementResource(dataNS, schemaNS, (Element) child, parentLocalName, Integer .valueOf(i), manager, factory, dataOntology); @@ -595,7 +597,7 @@ public class XMLExtractor extends Semion String textContent = child.getNodeValue(); if (textContent != null) { textContent = textContent.trim(); - + if (!textContent.equals("")) { log.info("VALUE : " + textContent); manager.applyChange(new AddAxiom(dataOntology, @@ -608,40 +610,40 @@ public class XMLExtractor extends Semion } } } - + @Override public OWLOntology reengineering(String graphNS, IRI outputIRI, DataSource dataSource) throws ReengineeringException { InputStream dataSourceAsStream = (InputStream) dataSource .getDataSource(); - + InputStreamReader isr = new InputStreamReader(dataSourceAsStream); BufferedReader reader = new BufferedReader(isr); final StringBuilder stringBuilder1 = new StringBuilder(); final StringBuilder stringBuilder2 = new StringBuilder(); - + OutputStream out = new OutputStream() { - - @Override + + @Override public void write(byte[] bytes) throws IOException { for (byte b : bytes) { stringBuilder1.append((char) b); stringBuilder2.append((char) b); - } - } - - @Override + } + } + + @Override public void write(int arg0) throws IOException { stringBuilder1.append((char) arg0); stringBuilder2.append((char) arg0); - + } - + }; - + String line = ""; - try{ + try { while ((line = reader.readLine()) != null) { out.write(line.getBytes()); } @@ -650,15 +652,15 @@ public class XMLExtractor extends Semion // TODO Auto-generated catch block e1.printStackTrace(); } - + final ByteArrayOutputStream buff1 = new ByteArrayOutputStream(); try { buff1.write(stringBuilder1.toString().getBytes()); } catch (IOException e) { // TODO Auto-generated catch block e.printStackTrace(); - } - + } + final ByteArrayOutputStream buff2 = new ByteArrayOutputStream(); try { buff2.write(stringBuilder2.toString().getBytes()); @@ -666,7 +668,7 @@ public class XMLExtractor extends Semion // TODO Auto-generated catch block e.printStackTrace(); } - + DataSource ds1 = new DataSource() { @Override @@ -674,22 +676,22 @@ public class XMLExtractor extends Semion ByteArrayInputStream byteArr = new ByteArrayInputStream(buff1 .toByteArray()); return byteArr; - + } - + @Override public int getDataSourceType() { // TODO Auto-generated method stub return ReengineerType.XML; } - + @Override public String getID() { // TODO Auto-generated method stub return null; - } + } }; - + DataSource ds2 = new DataSource() { @Override @@ -697,14 +699,14 @@ public class XMLExtractor extends Semion ByteArrayInputStream byteArr = new ByteArrayInputStream(buff2 .toByteArray()); return byteArr; - - } - + + } + @Override public int getDataSourceType() { // TODO Auto-generated method stub return ReengineerType.XML; - } + } @Override public String getID() { @@ -712,9 +714,9 @@ public class XMLExtractor extends Semion return null; } }; - + OWLOntology schemaOntology; - + System.out.println("XML outputIRI : " + outputIRI); if (outputIRI != null && !outputIRI.equals("")) { IRI schemaIRI = IRI.create(outputIRI.toString() + "/schema"); @@ -725,7 +727,7 @@ public class XMLExtractor extends Semion } OWLOntology ontology = dataReengineering(graphNS, outputIRI, ds2, schemaOntology); - + try { onManager.getOwlCacheManager().saveOntology(ontology, System.out); } catch (OWLOntologyStorageException e) {
