NIHVIVO-3481 fixed 'create classgroups automatically' option
This commit is contained in:
brianjlowe
parent
83c4e54a34
commit
549d489bac
2 changed files with 557 additions and 517 deletions
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@ -34,6 +34,7 @@ import edu.cornell.mannlib.vitro.webapp.controller.Controllers;
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import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
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import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.JenaModelUtils;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelector;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaSpecialModelMaker;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.event.BulkUpdateEvent;
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@ -41,156 +42,153 @@ import edu.cornell.mannlib.vitro.webapp.dao.jena.event.EditEvent;
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import edu.cornell.mannlib.vitro.webapp.filestorage.uploadrequest.FileUploadServletRequest;
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public class RDFUploadController extends BaseEditController {
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private static int maxFileSizeInBytes = 1024 * 1024 * 2000; //2000mb
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private static FileItem fileStream = null;
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private static final String INGEST_MENU_JSP = "/jenaIngest/ingestMenu.jsp";
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private static final String LOAD_RDF_DATA_JSP="/jenaIngest/loadRDFData.jsp";
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private static final String LIST_MODELS_JSP = "/jenaIngest/listModels.jsp";
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public void doPost(HttpServletRequest rawRequest,
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HttpServletResponse response) throws ServletException, IOException {
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public void doPost(HttpServletRequest rawRequest,
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HttpServletResponse response) throws ServletException, IOException {
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if (!isAuthorizedToDisplayPage(rawRequest, response, new Actions(
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new UseAdvancedDataToolsPages()))) {
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return;
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new UseAdvancedDataToolsPages()))) {
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return;
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}
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FileUploadServletRequest req = FileUploadServletRequest.parseRequest(
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FileUploadServletRequest req = FileUploadServletRequest.parseRequest(
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rawRequest, maxFileSizeInBytes);
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if (req.hasFileUploadException()) {
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forwardToFileUploadError(
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req.getFileUploadException().getLocalizedMessage(),
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if (req.hasFileUploadException()) {
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forwardToFileUploadError(
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req.getFileUploadException().getLocalizedMessage(),
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req, response);
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return;
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}
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return;
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}
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Map<String, List<FileItem>> fileStreams = req.getFiles();
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VitroRequest request = new VitroRequest(req);
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LoginStatusBean loginBean = LoginStatusBean.getBean(request);
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String modelName = req.getParameter("modelName");
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if(modelName!=null){
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loadRDF(req,request,response);
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return;
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}
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boolean remove = "remove".equals(request.getParameter("mode"));
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String verb = remove?"Removed":"Added";
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String languageStr = request.getParameter("language");
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boolean makeClassgroups =
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(request.getParameter("makeClassgroups") != null);
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// add directly to the ABox model without reading first into
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// a temporary in-memory model
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boolean directRead = ("directAddABox".equals(request.getParameter(
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Map<String, List<FileItem>> fileStreams = req.getFiles();
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VitroRequest request = new VitroRequest(req);
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LoginStatusBean loginBean = LoginStatusBean.getBean(request);
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String modelName = req.getParameter("modelName");
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if(modelName!=null){
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loadRDF(req,request,response);
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return;
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}
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boolean remove = "remove".equals(request.getParameter("mode"));
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String verb = remove?"Removed":"Added";
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String languageStr = request.getParameter("language");
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boolean makeClassgroups = ("true".equals(request.getParameter(
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"makeClassgroups")));
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// add directly to the ABox model without reading first into
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// a temporary in-memory model
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boolean directRead = ("directAddABox".equals(request.getParameter(
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"mode")));
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String uploadDesc ="";
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OntModel uploadModel = (directRead)
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? getABoxModel(request.getSession(), getServletContext())
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: ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
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/* ********************* GET RDF by URL ********************** */
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String RDFUrlStr = request.getParameter("rdfUrl");
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if (RDFUrlStr != null && RDFUrlStr.length() > 0) {
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try {
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uploadModel.enterCriticalSection(Lock.WRITE);
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try {
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uploadModel.read(RDFUrlStr, languageStr);
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// languageStr may be null and default would be RDF/XML
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} finally {
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uploadModel.leaveCriticalSection();
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}
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uploadDesc = verb + " RDF from " + RDFUrlStr;
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} catch (JenaException ex){
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forwardToFileUploadError("Could not parse file to " +
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String uploadDesc ="";
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OntModel uploadModel = (directRead)
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? getABoxModel(request.getSession(), getServletContext())
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: ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
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/* ********************* GET RDF by URL ********************** */
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String RDFUrlStr = request.getParameter("rdfUrl");
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if (RDFUrlStr != null && RDFUrlStr.length() > 0) {
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try {
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uploadModel.enterCriticalSection(Lock.WRITE);
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try {
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uploadModel.read(RDFUrlStr, languageStr);
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// languageStr may be null and default would be RDF/XML
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} finally {
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uploadModel.leaveCriticalSection();
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}
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uploadDesc = verb + " RDF from " + RDFUrlStr;
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} catch (JenaException ex){
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forwardToFileUploadError("Could not parse file to " +
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languageStr + ": " + ex.getMessage(), req, response);
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return;
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}catch (Exception e) {
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return;
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}catch (Exception e) {
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forwardToFileUploadError("Could not load from URL: " +
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e.getMessage(), req, response);
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e.getMessage(), req, response);
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return;
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}
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} else {
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/* **************** upload RDF from POST ********************* */
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if( fileStreams.get("rdfStream") != null
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&& fileStreams.get("rdfStream").size() > 0 ) {
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FileItem rdfStream = fileStreams.get("rdfStream").get(0);
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try {
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uploadModel.enterCriticalSection(Lock.WRITE);
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try {
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uploadModel.read(
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rdfStream.getInputStream(), null, languageStr);
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} finally {
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uploadModel.leaveCriticalSection();
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}
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uploadDesc = verb + " RDF from file " + rdfStream.getName();
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} catch (IOException e) {
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forwardToFileUploadError("Could not read file: " +
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e.getLocalizedMessage(), req, response);
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return;
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}catch (JenaException ex){
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forwardToFileUploadError("Could not parse file to " +
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languageStr + ": " + ex.getMessage(),
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req, response);
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return;
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}catch (Exception e) {
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forwardToFileUploadError("Could not load from file: " +
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e.getMessage(), req, response);
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return;
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}finally{
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rdfStream.delete();
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}
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}
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}
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/* ********** Do the model changes *********** */
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if( !directRead && uploadModel != null ){
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long tboxstmtCount = 0L;
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long aboxstmtCount = 0L;
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}
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} else {
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/* **************** upload RDF from POST ********************* */
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if( fileStreams.get("rdfStream") != null
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&& fileStreams.get("rdfStream").size() > 0 ) {
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FileItem rdfStream = fileStreams.get("rdfStream").get(0);
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try {
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uploadModel.enterCriticalSection(Lock.WRITE);
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try {
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uploadModel.read(
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rdfStream.getInputStream(), null, languageStr);
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} finally {
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uploadModel.leaveCriticalSection();
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}
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uploadDesc = verb + " RDF from file " + rdfStream.getName();
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} catch (IOException e) {
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forwardToFileUploadError("Could not read file: " +
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e.getLocalizedMessage(), req, response);
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return;
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}catch (JenaException ex){
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forwardToFileUploadError("Could not parse file to " +
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languageStr + ": " + ex.getMessage(),
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req, response);
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return;
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}catch (Exception e) {
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forwardToFileUploadError("Could not load from file: " +
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e.getMessage(), req, response);
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return;
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}finally{
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rdfStream.delete();
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}
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}
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}
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/* ********** Do the model changes *********** */
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if( !directRead && uploadModel != null ){
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long tboxstmtCount = 0L;
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long aboxstmtCount = 0L;
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JenaModelUtils xutil = new JenaModelUtils();
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OntModel tboxModel = getTBoxModel(
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request.getSession(), getServletContext());
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OntModel aboxModel = getABoxModel(
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request.getSession(), getServletContext());
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OntModel tboxChangeModel=null;
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Model aboxChangeModel=null;
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if (tboxModel != null) {
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boolean AGGRESSIVE = true;
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tboxChangeModel = xutil.extractTBox(uploadModel, AGGRESSIVE);
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// aggressively seek all statements that are part of the TBox
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tboxstmtCount = operateOnModel(
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request.getFullWebappDaoFactory(),
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tboxModel,tboxChangeModel,
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remove,
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makeClassgroups,
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loginBean.getUserURI());
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}
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if (aboxModel != null) {
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aboxChangeModel = uploadModel.remove(tboxChangeModel);
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aboxstmtCount = operateOnModel(
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request.getFullWebappDaoFactory(),
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aboxModel,
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aboxChangeModel,
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remove,
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makeClassgroups,
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loginBean.getUserURI());
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}
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request.setAttribute("uploadDesc", uploadDesc + ". " + verb + " " +
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JenaModelUtils xutil = new JenaModelUtils();
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OntModel tboxModel = getTBoxModel(
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request.getSession(), getServletContext());
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OntModel aboxModel = getABoxModel(
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request.getSession(), getServletContext());
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OntModel tboxChangeModel = null;
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Model aboxChangeModel = null;
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OntModelSelector ontModelSelector = ModelContext.getOntModelSelector(
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getServletContext());
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if (tboxModel != null) {
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boolean AGGRESSIVE = true;
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tboxChangeModel = xutil.extractTBox(uploadModel, AGGRESSIVE);
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// aggressively seek all statements that are part of the TBox
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tboxstmtCount = operateOnModel(request.getFullWebappDaoFactory(),
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tboxModel, tboxChangeModel, ontModelSelector,
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remove, makeClassgroups, loginBean.getUserURI());
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}
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if (aboxModel != null) {
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aboxChangeModel = uploadModel.remove(tboxChangeModel);
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aboxstmtCount = operateOnModel(request.getFullWebappDaoFactory(),
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aboxModel, aboxChangeModel, ontModelSelector,
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remove, makeClassgroups, loginBean.getUserURI());
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}
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request.setAttribute("uploadDesc", uploadDesc + ". " + verb + " " +
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(tboxstmtCount + aboxstmtCount) + " statements.");
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} else {
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request.setAttribute("uploadDesc", "RDF upload successful.");
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}
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} else {
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request.setAttribute("uploadDesc", "RDF upload successful.");
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}
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RequestDispatcher rd = request.getRequestDispatcher(
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Controllers.BASIC_JSP);
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Controllers.BASIC_JSP);
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request.setAttribute(
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"bodyJsp", "/templates/edit/specific/upload_rdf_result.jsp");
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"bodyJsp", "/templates/edit/specific/upload_rdf_result.jsp");
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request.setAttribute("title","Ingest RDF Data");
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try {
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@ -200,31 +198,31 @@ public class RDFUploadController extends BaseEditController {
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}
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}
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public void loadRDF(FileUploadServletRequest req,
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public void loadRDF(FileUploadServletRequest req,
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VitroRequest request,
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HttpServletResponse response)
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throws ServletException, IOException {
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Map<String, List<FileItem>> fileStreams = req.getFiles();
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String filePath = fileStreams.get("filePath").get(0).getName();
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fileStream = fileStreams.get("filePath").get(0);
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String modelName = req.getParameter("modelName");
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String docLoc = req.getParameter("docLoc");
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String languageStr = request.getParameter("language");
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ModelMaker maker = getVitroJenaModelMaker(request);
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if (docLoc!=null && modelName != null) {
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doLoadRDFData(modelName,docLoc,filePath,languageStr,maker);
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//request.setAttribute("title","Ingest Menu");
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//request.setAttribute("bodyJsp",INGEST_MENU_JSP);
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request.setAttribute("title","Available Models");
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request.setAttribute("bodyJsp",LIST_MODELS_JSP);
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} else {
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request.setAttribute("title","Load RDF Data");
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request.setAttribute("bodyJsp",LOAD_RDF_DATA_JSP);
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}
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RequestDispatcher rd = request.getRequestDispatcher(
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Controllers.BASIC_JSP);
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Map<String, List<FileItem>> fileStreams = req.getFiles();
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String filePath = fileStreams.get("filePath").get(0).getName();
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fileStream = fileStreams.get("filePath").get(0);
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String modelName = req.getParameter("modelName");
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String docLoc = req.getParameter("docLoc");
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String languageStr = request.getParameter("language");
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ModelMaker maker = getVitroJenaModelMaker(request);
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if (docLoc!=null && modelName != null) {
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doLoadRDFData(modelName,docLoc,filePath,languageStr,maker);
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//request.setAttribute("title","Ingest Menu");
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//request.setAttribute("bodyJsp",INGEST_MENU_JSP);
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request.setAttribute("title","Available Models");
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request.setAttribute("bodyJsp",LIST_MODELS_JSP);
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} else {
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request.setAttribute("title","Load RDF Data");
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request.setAttribute("bodyJsp",LOAD_RDF_DATA_JSP);
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}
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RequestDispatcher rd = request.getRequestDispatcher(
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Controllers.BASIC_JSP);
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try {
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rd.forward(request, response);
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@ -233,40 +231,54 @@ public class RDFUploadController extends BaseEditController {
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log.error(errMsg, e);
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throw new ServletException(errMsg, e);
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}
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}
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}
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private long operateOnModel(WebappDaoFactory webappDaoFactory,
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OntModel mainModel,
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Model changesModel,
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boolean remove,
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boolean makeClassgroups,
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String userURI) {
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OntModel mainModel,
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Model changesModel,
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OntModelSelector ontModelSelector,
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boolean remove,
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boolean makeClassgroups,
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String userURI) {
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EditEvent startEvent = null, endEvent = null;
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if (remove) {
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startEvent = new BulkUpdateEvent(userURI, true);
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endEvent = new BulkUpdateEvent(userURI, false);
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} else {
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startEvent = new EditEvent(userURI, true);
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endEvent = new EditEvent(userURI, false);
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}
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Model[] classgroupModel = null;
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if (makeClassgroups) {
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classgroupModel = JenaModelUtils.makeClassGroupsFromRootClasses(
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webappDaoFactory, changesModel);
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OntModel appMetadataModel = ontModelSelector
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.getApplicationMetadataModel();
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appMetadataModel.enterCriticalSection(Lock.WRITE);
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try {
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appMetadataModel.add(classgroupModel[0]);
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} finally {
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appMetadataModel.leaveCriticalSection();
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}
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}
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mainModel.enterCriticalSection(Lock.WRITE);
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try {
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EditEvent startEvent = null, endEvent = null;
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if (remove) {
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startEvent = new BulkUpdateEvent(userURI, true);
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endEvent = new BulkUpdateEvent(userURI, false);
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} else {
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startEvent = new EditEvent(userURI, true);
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endEvent = new EditEvent(userURI, false);
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}
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mainModel.getBaseModel().notifyEvent(startEvent);
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try {
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if (makeClassgroups) {
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Model classgroupModel =
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JenaModelUtils.makeClassGroupsFromRootClasses(
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webappDaoFactory, changesModel, changesModel);
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mainModel.add(classgroupModel);
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}
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try {
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if (remove) {
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mainModel.remove(changesModel);
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} else {
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mainModel.add(changesModel);
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if (classgroupModel != null) {
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mainModel.add(classgroupModel[1]);
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}
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}
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} finally {
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mainModel.getBaseModel().notifyEvent(endEvent);
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@ -279,45 +291,45 @@ public class RDFUploadController extends BaseEditController {
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private void doLoadRDFData(String modelName,
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String docLoc,
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String filePath,
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String language,
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ModelMaker modelMaker) {
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Model m = modelMaker.getModel(modelName);
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m.enterCriticalSection(Lock.WRITE);
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try {
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if ( (docLoc != null) && (docLoc.length()>0) ) {
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m.read(docLoc, language);
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} else if ( (filePath != null) && (filePath.length()>0) ) {
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File file = new File(filePath);
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File[] files;
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if (file.isDirectory()) {
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files = file.listFiles();
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} else {
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files = new File[1];
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files[0] = file;
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}
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for (int i=0; i<files.length; i++) {
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File currentFile = files[i];
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log.debug("Reading file " + currentFile.getName());
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try {
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m.read(fileStream.getInputStream(), null, language);
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fileStream.delete();
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} catch (IOException ioe) {
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String errMsg = "Error loading RDF from " +
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currentFile.getName();
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log.error(errMsg, ioe);
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throw new RuntimeException(errMsg, ioe);
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}
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}
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}
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} finally {
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m.leaveCriticalSection();
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}
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}
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String filePath,
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String language,
|
||||
ModelMaker modelMaker) {
|
||||
Model m = modelMaker.getModel(modelName);
|
||||
m.enterCriticalSection(Lock.WRITE);
|
||||
try {
|
||||
if ( (docLoc != null) && (docLoc.length()>0) ) {
|
||||
m.read(docLoc, language);
|
||||
} else if ( (filePath != null) && (filePath.length()>0) ) {
|
||||
File file = new File(filePath);
|
||||
File[] files;
|
||||
if (file.isDirectory()) {
|
||||
files = file.listFiles();
|
||||
} else {
|
||||
files = new File[1];
|
||||
files[0] = file;
|
||||
}
|
||||
for (int i=0; i<files.length; i++) {
|
||||
File currentFile = files[i];
|
||||
log.debug("Reading file " + currentFile.getName());
|
||||
try {
|
||||
m.read(fileStream.getInputStream(), null, language);
|
||||
fileStream.delete();
|
||||
} catch (IOException ioe) {
|
||||
String errMsg = "Error loading RDF from " +
|
||||
currentFile.getName();
|
||||
log.error(errMsg, ioe);
|
||||
throw new RuntimeException(errMsg, ioe);
|
||||
}
|
||||
}
|
||||
}
|
||||
} finally {
|
||||
m.leaveCriticalSection();
|
||||
}
|
||||
}
|
||||
|
||||
private void forwardToFileUploadError( String errrorMsg ,
|
||||
HttpServletRequest req,
|
||||
HttpServletResponse response)
|
||||
HttpServletResponse response)
|
||||
throws ServletException{
|
||||
VitroRequest vreq = new VitroRequest(req);
|
||||
req.setAttribute("title","RDF Upload Error ");
|
||||
|
|
@ -332,21 +344,21 @@ public class RDFUploadController extends BaseEditController {
|
|||
try {
|
||||
rd.forward(req, response);
|
||||
} catch (IOException e1) {
|
||||
log.error(e1);
|
||||
log.error(e1);
|
||||
throw new ServletException(e1);
|
||||
}
|
||||
return;
|
||||
}
|
||||
|
||||
private ModelMaker getVitroJenaModelMaker(HttpServletRequest request) {
|
||||
ModelMaker myVjmm = (ModelMaker) request.getSession().getAttribute(
|
||||
"vitroJenaModelMaker");
|
||||
myVjmm = (myVjmm == null)
|
||||
ModelMaker myVjmm = (ModelMaker) request.getSession().getAttribute(
|
||||
"vitroJenaModelMaker");
|
||||
myVjmm = (myVjmm == null)
|
||||
? (ModelMaker) getServletContext().getAttribute(
|
||||
"vitroJenaModelMaker")
|
||||
"vitroJenaModelMaker")
|
||||
: myVjmm;
|
||||
return new VitroJenaSpecialModelMaker(myVjmm, request);
|
||||
}
|
||||
return new VitroJenaSpecialModelMaker(myVjmm, request);
|
||||
}
|
||||
|
||||
private OntModel getABoxModel(HttpSession session, ServletContext ctx) {
|
||||
if (session != null
|
||||
|
|
@ -374,6 +386,6 @@ public class RDFUploadController extends BaseEditController {
|
|||
}
|
||||
}
|
||||
|
||||
private static final Log log = LogFactory.getLog(
|
||||
RDFUploadController.class.getName());
|
||||
private static final Log log = LogFactory.getLog(
|
||||
RDFUploadController.class.getName());
|
||||
}
|
||||
|
|
|
|||
|
|
@ -11,7 +11,6 @@ import java.util.Set;
|
|||
import org.apache.commons.logging.Log;
|
||||
import org.apache.commons.logging.LogFactory;
|
||||
|
||||
import com.hp.hpl.jena.datatypes.xsd.XSDDatatype;
|
||||
import com.hp.hpl.jena.ontology.Individual;
|
||||
import com.hp.hpl.jena.ontology.OntClass;
|
||||
import com.hp.hpl.jena.ontology.OntModel;
|
||||
|
|
@ -25,6 +24,7 @@ import com.hp.hpl.jena.query.QueryFactory;
|
|||
import com.hp.hpl.jena.rdf.model.Model;
|
||||
import com.hp.hpl.jena.rdf.model.ModelFactory;
|
||||
import com.hp.hpl.jena.rdf.model.Property;
|
||||
import com.hp.hpl.jena.rdf.model.RDFNode;
|
||||
import com.hp.hpl.jena.rdf.model.Resource;
|
||||
import com.hp.hpl.jena.rdf.model.ResourceFactory;
|
||||
import com.hp.hpl.jena.shared.Lock;
|
||||
|
|
@ -38,259 +38,287 @@ import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
|
|||
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactoryConfig;
|
||||
|
||||
public class JenaModelUtils {
|
||||
|
||||
private static final Log log = LogFactory.getLog(JenaModelUtils.class.getName());
|
||||
|
||||
private static final Log log = LogFactory.getLog(JenaModelUtils.class.getName());
|
||||
|
||||
private static final Set<String> nonIndividualTypeURIs ;
|
||||
|
||||
static {
|
||||
nonIndividualTypeURIs = new HashSet<String>();
|
||||
nonIndividualTypeURIs.add(OWL.Class.getURI());
|
||||
nonIndividualTypeURIs.add(OWL.Restriction.getURI());
|
||||
nonIndividualTypeURIs.add(OWL.ObjectProperty.getURI());
|
||||
nonIndividualTypeURIs.add(OWL.DatatypeProperty.getURI());
|
||||
nonIndividualTypeURIs.add(OWL.AnnotationProperty.getURI());
|
||||
nonIndividualTypeURIs.add(OWL.Ontology.getURI());
|
||||
nonIndividualTypeURIs.add(RDFS.Class.getURI());
|
||||
nonIndividualTypeURIs.add(RDF.Property.getURI());
|
||||
}
|
||||
|
||||
public synchronized static void makeClassGroupsFromRootClasses(WebappDaoFactory wadf, Model ontModel) {
|
||||
makeClassGroupsFromRootClasses(wadf, ontModel, ontModel);
|
||||
}
|
||||
|
||||
public synchronized static OntModel makeClassGroupsFromRootClasses(WebappDaoFactory wadf, Model baseModel, Model vitroInternalsSubmodel) {
|
||||
OntModel ontModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_DL_MEM,baseModel);
|
||||
OntModel modelForClassgroups = ModelFactory.createOntologyModel(OntModelSpec.OWL_DL_MEM);
|
||||
SimpleOntModelSelector oms = new SimpleOntModelSelector();
|
||||
oms.setTBoxModel(ontModel);
|
||||
oms.setApplicationMetadataModel(modelForClassgroups);
|
||||
WebappDaoFactoryConfig config = new WebappDaoFactoryConfig();
|
||||
config.setDefaultNamespace(wadf.getDefaultNamespace());
|
||||
WebappDaoFactory myWebappDaoFactory = new WebappDaoFactoryJena(
|
||||
new SimpleOntModelSelector(ontModel), config, null);
|
||||
OntModel tempModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_DL_MEM);
|
||||
Resource classGroupClass = ResourceFactory.createResource(VitroVocabulary.CLASSGROUP);
|
||||
Property inClassGroupProperty = ResourceFactory.createProperty(VitroVocabulary.IN_CLASSGROUP);
|
||||
ontModel.enterCriticalSection(Lock.READ);
|
||||
try {
|
||||
try {
|
||||
for (Iterator rootClassIt = myWebappDaoFactory.getVClassDao().getRootClasses().iterator(); rootClassIt.hasNext(); ) {
|
||||
VClass rootClass = (VClass) rootClassIt.next();
|
||||
Individual classGroup = tempModel.createIndividual(wadf.getDefaultNamespace()+"vitroClassGroup"+rootClass.getLocalName(), classGroupClass);
|
||||
classGroup.addProperty(tempModel.getProperty(VitroVocabulary.DISPLAY_RANK_ANNOT),"50",XSDDatatype.XSDint);
|
||||
classGroup.setLabel(rootClass.getName(),null);
|
||||
OntClass rootClassOntClass = ontModel.getOntClass(rootClass.getURI());
|
||||
tempModel.add(rootClassOntClass, inClassGroupProperty, classGroup);
|
||||
for (Iterator childIt = myWebappDaoFactory.getVClassDao().getAllSubClassURIs(rootClass.getURI()).iterator(); childIt.hasNext(); ) {
|
||||
String childURI = (String) childIt.next();
|
||||
OntClass childClass = ontModel.getOntClass(childURI);
|
||||
childClass.addProperty(inClassGroupProperty, classGroup);
|
||||
}
|
||||
}
|
||||
} catch (Exception e) {
|
||||
log.error("Unable to create class groups automatically based on class hierarchy");
|
||||
}
|
||||
vitroInternalsSubmodel.enterCriticalSection(Lock.WRITE);
|
||||
try {
|
||||
vitroInternalsSubmodel.add(tempModel);
|
||||
} finally {
|
||||
vitroInternalsSubmodel.leaveCriticalSection();
|
||||
}
|
||||
} finally {
|
||||
ontModel.leaveCriticalSection();
|
||||
}
|
||||
return modelForClassgroups;
|
||||
}
|
||||
|
||||
private final OntModelSpec DEFAULT_ONT_MODEL_SPEC = OntModelSpec.OWL_MEM;
|
||||
private final boolean NORMAL = false;
|
||||
private final boolean AGGRESSIVE = true;
|
||||
private static final Set<String> nonIndividualTypeURIs ;
|
||||
|
||||
static {
|
||||
nonIndividualTypeURIs = new HashSet<String>();
|
||||
nonIndividualTypeURIs.add(OWL.Class.getURI());
|
||||
nonIndividualTypeURIs.add(OWL.Restriction.getURI());
|
||||
nonIndividualTypeURIs.add(OWL.ObjectProperty.getURI());
|
||||
nonIndividualTypeURIs.add(OWL.DatatypeProperty.getURI());
|
||||
nonIndividualTypeURIs.add(OWL.AnnotationProperty.getURI());
|
||||
nonIndividualTypeURIs.add(OWL.Ontology.getURI());
|
||||
nonIndividualTypeURIs.add(RDFS.Class.getURI());
|
||||
nonIndividualTypeURIs.add(RDF.Property.getURI());
|
||||
}
|
||||
|
||||
/**
|
||||
* Creates a set of vitro:ClassGroup resources for each root class in
|
||||
* an ontology. Also creates annotations to place each root class and all
|
||||
* of its children in the appropriate groups. In the case of multiple
|
||||
* inheritance, classgroup assignment will be arbitrary.
|
||||
* @param wadf
|
||||
* @param tboxModel containing ontology classes
|
||||
* @return resultArray of OntModels, where resultArray[0] is the model containing
|
||||
* the triples about the classgroups, and resultArray[1] is the model containing
|
||||
* annotation triples assigning ontology classes to classgroups.
|
||||
*/
|
||||
public synchronized static OntModel[] makeClassGroupsFromRootClasses(
|
||||
WebappDaoFactory wadf, Model tboxModel) {
|
||||
|
||||
OntModel ontModel = ModelFactory.createOntologyModel(
|
||||
OntModelSpec.OWL_DL_MEM, tboxModel);
|
||||
OntModel modelForClassgroups = ModelFactory.createOntologyModel(
|
||||
OntModelSpec.OWL_DL_MEM);
|
||||
OntModel modelForClassgroupAnnotations = ModelFactory.createOntologyModel(
|
||||
OntModelSpec.OWL_DL_MEM);
|
||||
SimpleOntModelSelector oms = new SimpleOntModelSelector();
|
||||
oms.setTBoxModel(ontModel);
|
||||
oms.setApplicationMetadataModel(modelForClassgroups);
|
||||
WebappDaoFactoryConfig config = new WebappDaoFactoryConfig();
|
||||
config.setDefaultNamespace(wadf.getDefaultNamespace());
|
||||
WebappDaoFactory myWebappDaoFactory = new WebappDaoFactoryJena(
|
||||
new SimpleOntModelSelector(ontModel), config, null);
|
||||
|
||||
Resource classGroupClass = ResourceFactory.createResource(
|
||||
VitroVocabulary.CLASSGROUP);
|
||||
Property inClassGroupProperty = ResourceFactory.createProperty(
|
||||
VitroVocabulary.IN_CLASSGROUP);
|
||||
|
||||
ontModel.enterCriticalSection(Lock.READ);
|
||||
try {
|
||||
try {
|
||||
for (Iterator rootClassIt = myWebappDaoFactory.getVClassDao()
|
||||
.getRootClasses().iterator(); rootClassIt.hasNext(); ) {
|
||||
VClass rootClass = (VClass) rootClassIt.next();
|
||||
|
||||
Individual classGroup = modelForClassgroups.createIndividual(
|
||||
wadf.getDefaultNamespace() + "vitroClassGroup" +
|
||||
rootClass.getLocalName(), classGroupClass);
|
||||
classGroup.setLabel(rootClass.getName(), null);
|
||||
|
||||
Resource rootClassRes = modelForClassgroupAnnotations.getResource(
|
||||
rootClass.getURI());
|
||||
modelForClassgroupAnnotations.add(
|
||||
rootClassRes, inClassGroupProperty, classGroup);
|
||||
for (Iterator<String> childIt = myWebappDaoFactory.getVClassDao()
|
||||
.getAllSubClassURIs(rootClass.getURI()).iterator();
|
||||
childIt.hasNext(); ) {
|
||||
String childURI = (String) childIt.next();
|
||||
Resource childClass = modelForClassgroupAnnotations
|
||||
.getResource(childURI);
|
||||
if (!modelForClassgroupAnnotations.contains(
|
||||
childClass, inClassGroupProperty, (RDFNode) null)) {
|
||||
childClass.addProperty(inClassGroupProperty, classGroup);
|
||||
}
|
||||
}
|
||||
}
|
||||
} catch (Exception e) {
|
||||
String errMsg = "Unable to create class groups automatically " +
|
||||
"based on class hierarchy";
|
||||
log.error(errMsg, e);
|
||||
throw new RuntimeException(errMsg, e);
|
||||
}
|
||||
} finally {
|
||||
ontModel.leaveCriticalSection();
|
||||
}
|
||||
OntModel[] resultArray = new OntModel[2];
|
||||
resultArray[0] = modelForClassgroups;
|
||||
resultArray[1] = modelForClassgroupAnnotations;
|
||||
return resultArray;
|
||||
}
|
||||
|
||||
private final OntModelSpec DEFAULT_ONT_MODEL_SPEC = OntModelSpec.OWL_MEM;
|
||||
private final boolean NORMAL = false;
|
||||
private final boolean AGGRESSIVE = true;
|
||||
|
||||
|
||||
public OntModel extractTBox( Model inputModel ) {
|
||||
return extractTBox(inputModel, null);
|
||||
}
|
||||
|
||||
public OntModel extractTBox( Model inputModel, boolean MODE ) {
|
||||
Dataset dataset = DatasetFactory.create(inputModel);
|
||||
public OntModel extractTBox( Model inputModel ) {
|
||||
return extractTBox(inputModel, null);
|
||||
}
|
||||
|
||||
public OntModel extractTBox( Model inputModel, boolean MODE ) {
|
||||
Dataset dataset = DatasetFactory.create(inputModel);
|
||||
return extractTBox(dataset, null, null, MODE);
|
||||
}
|
||||
|
||||
public OntModel extractTBox( Model inputModel, String namespace ) {
|
||||
Dataset dataset = DatasetFactory.create(inputModel);
|
||||
|
||||
public OntModel extractTBox( Model inputModel, String namespace ) {
|
||||
Dataset dataset = DatasetFactory.create(inputModel);
|
||||
return extractTBox( dataset, namespace, null, NORMAL );
|
||||
}
|
||||
|
||||
public OntModel extractTBox( Dataset dataset, String namespace, String graphURI) {
|
||||
return extractTBox( dataset, namespace, graphURI, NORMAL);
|
||||
}
|
||||
|
||||
public OntModel extractTBox( Dataset dataset, String namespace, String graphURI, boolean mode ) {
|
||||
OntModel tboxModel = ModelFactory.createOntologyModel(DEFAULT_ONT_MODEL_SPEC);
|
||||
|
||||
List<String> queryStrList = new LinkedList<String>();
|
||||
|
||||
// Use SPARQL DESCRIBE queries to extract the RDF for named ontology entities
|
||||
|
||||
queryStrList.add( makeDescribeQueryStr( OWL.Class.getURI(), namespace, graphURI ) );
|
||||
queryStrList.add( makeDescribeQueryStr( OWL.Restriction.getURI(), namespace, graphURI ) );
|
||||
queryStrList.add( makeDescribeQueryStr( OWL.ObjectProperty.getURI(), namespace, graphURI ) );
|
||||
queryStrList.add( makeDescribeQueryStr( OWL.DatatypeProperty.getURI(), namespace, graphURI ) );
|
||||
queryStrList.add( makeDescribeQueryStr( OWL.AnnotationProperty.getURI(), namespace, graphURI ) );
|
||||
// if we're using to a hash namespace, the URI of the Ontology resource will be
|
||||
// that namespace minus the final hash mark.
|
||||
if ( namespace != null && namespace.endsWith("#") ) {
|
||||
queryStrList.add( makeDescribeQueryStr( OWL.Ontology.getURI(), namespace.substring(0,namespace.length()-1), graphURI ) );
|
||||
} else {
|
||||
queryStrList.add( makeDescribeQueryStr( OWL.Ontology.getURI(), namespace, graphURI ) );
|
||||
}
|
||||
|
||||
// Perform the SPARQL DESCRIBEs
|
||||
for ( String queryStr : queryStrList ) {
|
||||
Query tboxSparqlQuery = QueryFactory.create(queryStr);
|
||||
QueryExecution qe = QueryExecutionFactory.create(tboxSparqlQuery,dataset);
|
||||
try {
|
||||
dataset.getLock().enterCriticalSection(Lock.READ);
|
||||
qe.execDescribe(tboxModel);
|
||||
} finally {
|
||||
dataset.getLock().leaveCriticalSection();
|
||||
}
|
||||
}
|
||||
|
||||
// Perform possibly-redundant extraction to try ensure we don't miss
|
||||
// individual axioms floating around. We still might miss things;
|
||||
// this approach isn't perfect.
|
||||
if (mode = AGGRESSIVE) {
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, RDFS.subClassOf));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, RDFS.subPropertyOf));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, OWL.equivalentClass));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, OWL.unionOf));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, OWL.intersectionOf));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, OWL.complementOf));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, OWL.onProperty));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, OWL.allValuesFrom));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, OWL.someValuesFrom));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, OWL.hasValue));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, OWL.minCardinality));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, OWL.maxCardinality));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, OWL.cardinality));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, OWL.disjointWith));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, ResourceFactory.createResource(
|
||||
VitroVocabulary.DISPLAY_LIMIT)));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, ResourceFactory.createResource(
|
||||
}
|
||||
|
||||
public OntModel extractTBox( Dataset dataset, String namespace, String graphURI) {
|
||||
return extractTBox( dataset, namespace, graphURI, NORMAL);
|
||||
}
|
||||
|
||||
public OntModel extractTBox( Dataset dataset, String namespace, String graphURI, boolean mode ) {
|
||||
OntModel tboxModel = ModelFactory.createOntologyModel(DEFAULT_ONT_MODEL_SPEC);
|
||||
|
||||
List<String> queryStrList = new LinkedList<String>();
|
||||
|
||||
// Use SPARQL DESCRIBE queries to extract the RDF for named ontology entities
|
||||
|
||||
queryStrList.add( makeDescribeQueryStr( OWL.Class.getURI(), namespace, graphURI ) );
|
||||
queryStrList.add( makeDescribeQueryStr( OWL.Restriction.getURI(), namespace, graphURI ) );
|
||||
queryStrList.add( makeDescribeQueryStr( OWL.ObjectProperty.getURI(), namespace, graphURI ) );
|
||||
queryStrList.add( makeDescribeQueryStr( OWL.DatatypeProperty.getURI(), namespace, graphURI ) );
|
||||
queryStrList.add( makeDescribeQueryStr( OWL.AnnotationProperty.getURI(), namespace, graphURI ) );
|
||||
// if we're using to a hash namespace, the URI of the Ontology resource will be
|
||||
// that namespace minus the final hash mark.
|
||||
if ( namespace != null && namespace.endsWith("#") ) {
|
||||
queryStrList.add( makeDescribeQueryStr( OWL.Ontology.getURI(), namespace.substring(0,namespace.length()-1), graphURI ) );
|
||||
} else {
|
||||
queryStrList.add( makeDescribeQueryStr( OWL.Ontology.getURI(), namespace, graphURI ) );
|
||||
}
|
||||
|
||||
// Perform the SPARQL DESCRIBEs
|
||||
for ( String queryStr : queryStrList ) {
|
||||
Query tboxSparqlQuery = QueryFactory.create(queryStr);
|
||||
QueryExecution qe = QueryExecutionFactory.create(tboxSparqlQuery,dataset);
|
||||
try {
|
||||
dataset.getLock().enterCriticalSection(Lock.READ);
|
||||
qe.execDescribe(tboxModel);
|
||||
} finally {
|
||||
dataset.getLock().leaveCriticalSection();
|
||||
}
|
||||
}
|
||||
|
||||
// Perform possibly-redundant extraction to try ensure we don't miss
|
||||
// individual axioms floating around. We still might miss things;
|
||||
// this approach isn't perfect.
|
||||
if (mode = AGGRESSIVE) {
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, RDFS.subClassOf));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, RDFS.subPropertyOf));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, OWL.equivalentClass));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, OWL.unionOf));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, OWL.intersectionOf));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, OWL.complementOf));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, OWL.onProperty));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, OWL.allValuesFrom));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, OWL.someValuesFrom));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, OWL.hasValue));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, OWL.minCardinality));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, OWL.maxCardinality));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, OWL.cardinality));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, OWL.disjointWith));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, ResourceFactory.createResource(
|
||||
VitroVocabulary.DISPLAY_LIMIT)));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, ResourceFactory.createResource(
|
||||
VitroVocabulary.DISPLAY_RANK_ANNOT)));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, ResourceFactory.createResource(
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, ResourceFactory.createResource(
|
||||
VitroVocabulary.IN_CLASSGROUP)));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, ResourceFactory.createResource(
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, ResourceFactory.createResource(
|
||||
VitroVocabulary.IN_CLASSGROUP)));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, ResourceFactory.createResource(
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, ResourceFactory.createResource(
|
||||
VitroVocabulary.PROPERTY_INPROPERTYGROUPANNOT)));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, ResourceFactory.createResource(
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, ResourceFactory.createResource(
|
||||
VitroVocabulary.PROHIBITED_FROM_UPDATE_BELOW_ROLE_LEVEL_ANNOT)));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, ResourceFactory.createResource(
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, ResourceFactory.createResource(
|
||||
VitroVocabulary.HIDDEN_FROM_DISPLAY_BELOW_ROLE_LEVEL_ANNOT)));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, ResourceFactory.createResource(
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, ResourceFactory.createResource(
|
||||
VitroVocabulary.DESCRIPTION_ANNOT)));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, ResourceFactory.createResource(
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, ResourceFactory.createResource(
|
||||
VitroVocabulary.SHORTDEF)));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, ResourceFactory.createResource(
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, ResourceFactory.createResource(
|
||||
VitroVocabulary.EXAMPLE_ANNOT)));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, ResourceFactory.createResource(
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, ResourceFactory.createResource(
|
||||
VitroVocabulary.vitroURI + "extendedLinkedData")));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, ResourceFactory.createResource(
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, ResourceFactory.createResource(
|
||||
VitroVocabulary.PROPERTY_OFFERCREATENEWOPTIONANNOT)));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, ResourceFactory.createResource(
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, ResourceFactory.createResource(
|
||||
VitroVocabulary.PROPERTY_COLLATEBYSUBCLASSANNOT)));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, ResourceFactory.createResource(
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, ResourceFactory.createResource(
|
||||
VitroVocabulary.PROPERTY_CUSTOM_LIST_VIEW_ANNOT)));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, ResourceFactory.createResource(
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, ResourceFactory.createResource(
|
||||
VitroVocabulary.PROPERTY_CUSTOMDISPLAYVIEWANNOT)));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, ResourceFactory.createResource(
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, ResourceFactory.createResource(
|
||||
VitroVocabulary.PROPERTY_CUSTOMENTRYFORMANNOT)));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, ResourceFactory.createResource(
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, ResourceFactory.createResource(
|
||||
VitroVocabulary.PROPERTY_CUSTOMSEARCHVIEWANNOT)));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, ResourceFactory.createResource(
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, ResourceFactory.createResource(
|
||||
VitroVocabulary.PROPERTY_CUSTOMSHORTVIEWANNOT)));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, ResourceFactory.createResource(
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, ResourceFactory.createResource(
|
||||
VitroVocabulary.PROPERTY_ENTITYSORTDIRECTION)));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, ResourceFactory.createResource(
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, ResourceFactory.createResource(
|
||||
VitroVocabulary.PROPERTY_ENTITYSORTFIELD)));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, ResourceFactory.createResource(
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, ResourceFactory.createResource(
|
||||
VitroVocabulary.PROPERTY_OBJECTINDIVIDUALSORTPROPERTY)));
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, ResourceFactory.createResource(
|
||||
tboxModel.add(construct(dataset, namespace, graphURI, ResourceFactory.createResource(
|
||||
VitroVocabulary.PROPERTY_SELECTFROMEXISTINGANNOT)));
|
||||
}
|
||||
return tboxModel;
|
||||
}
|
||||
|
||||
private Model construct(Dataset dataset,
|
||||
String namespace,
|
||||
String graphURI,
|
||||
Resource property) {
|
||||
dataset.getLock().enterCriticalSection(Lock.READ);
|
||||
try {
|
||||
StringBuffer buff = new StringBuffer();
|
||||
buff.append("PREFIX afn: <http://jena.hpl.hp.com/ARQ/function#> \n")
|
||||
.append("CONSTRUCT { \n")
|
||||
.append(" ?res <" + property.getURI() + "> ?o } WHERE { \n");
|
||||
if (graphURI != null) {
|
||||
buff.append(" GRAPH " + graphURI + " { \n");
|
||||
}
|
||||
buff.append(" ?res <" + property.getURI() + "> ?o \n");
|
||||
buff.append(getNamespaceFilter(namespace));
|
||||
if (graphURI != null) {
|
||||
buff.append(" } \n");
|
||||
}
|
||||
buff.append("}");
|
||||
Query constructProp = QueryFactory.create(buff.toString());
|
||||
QueryExecution qe = QueryExecutionFactory.create(constructProp, dataset);
|
||||
try {
|
||||
return qe.execConstruct();
|
||||
} finally {
|
||||
qe.close();
|
||||
}
|
||||
} finally {
|
||||
dataset.getLock().leaveCriticalSection();
|
||||
}
|
||||
}
|
||||
|
||||
private String makeDescribeQueryStr( String typeURI, String namespace ) {
|
||||
return makeDescribeQueryStr( typeURI, namespace, null );
|
||||
}
|
||||
|
||||
private String makeDescribeQueryStr( String typeURI, String namespace, String graphURI ) {
|
||||
|
||||
StringBuffer describeQueryStrBuff = new StringBuffer()
|
||||
.append("PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> \n")
|
||||
.append("PREFIX afn: <http://jena.hpl.hp.com/ARQ/function#> \n")
|
||||
.append("DESCRIBE ?res WHERE { \n");
|
||||
if (graphURI != null) {
|
||||
describeQueryStrBuff
|
||||
.append("GRAPH " + graphURI + "{ \n");
|
||||
}
|
||||
describeQueryStrBuff
|
||||
.append(" ?res rdf:type <").append(typeURI).append("> . \n");
|
||||
|
||||
describeQueryStrBuff
|
||||
.append(" FILTER (!isBlank(?res)) \n")
|
||||
|
||||
.append(getNamespaceFilter(namespace));
|
||||
|
||||
if (graphURI != null) {
|
||||
describeQueryStrBuff
|
||||
.append("} \n");
|
||||
}
|
||||
|
||||
describeQueryStrBuff.append("} \n");
|
||||
|
||||
return describeQueryStrBuff.toString();
|
||||
|
||||
}
|
||||
|
||||
private String getNamespaceFilter(String namespace) {
|
||||
StringBuffer buff = new StringBuffer();
|
||||
if (namespace == null) {
|
||||
}
|
||||
return tboxModel;
|
||||
}
|
||||
|
||||
private Model construct(Dataset dataset,
|
||||
String namespace,
|
||||
String graphURI,
|
||||
Resource property) {
|
||||
dataset.getLock().enterCriticalSection(Lock.READ);
|
||||
try {
|
||||
StringBuffer buff = new StringBuffer();
|
||||
buff.append("PREFIX afn: <http://jena.hpl.hp.com/ARQ/function#> \n")
|
||||
.append("CONSTRUCT { \n")
|
||||
.append(" ?res <" + property.getURI() + "> ?o } WHERE { \n");
|
||||
if (graphURI != null) {
|
||||
buff.append(" GRAPH " + graphURI + " { \n");
|
||||
}
|
||||
buff.append(" ?res <" + property.getURI() + "> ?o \n");
|
||||
buff.append(getNamespaceFilter(namespace));
|
||||
if (graphURI != null) {
|
||||
buff.append(" } \n");
|
||||
}
|
||||
buff.append("}");
|
||||
Query constructProp = QueryFactory.create(buff.toString());
|
||||
QueryExecution qe = QueryExecutionFactory.create(constructProp, dataset);
|
||||
try {
|
||||
return qe.execConstruct();
|
||||
} finally {
|
||||
qe.close();
|
||||
}
|
||||
} finally {
|
||||
dataset.getLock().leaveCriticalSection();
|
||||
}
|
||||
}
|
||||
|
||||
private String makeDescribeQueryStr( String typeURI, String namespace ) {
|
||||
return makeDescribeQueryStr( typeURI, namespace, null );
|
||||
}
|
||||
|
||||
private String makeDescribeQueryStr( String typeURI, String namespace, String graphURI ) {
|
||||
|
||||
StringBuffer describeQueryStrBuff = new StringBuffer()
|
||||
.append("PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> \n")
|
||||
.append("PREFIX afn: <http://jena.hpl.hp.com/ARQ/function#> \n")
|
||||
.append("DESCRIBE ?res WHERE { \n");
|
||||
if (graphURI != null) {
|
||||
describeQueryStrBuff
|
||||
.append("GRAPH " + graphURI + "{ \n");
|
||||
}
|
||||
describeQueryStrBuff
|
||||
.append(" ?res rdf:type <").append(typeURI).append("> . \n");
|
||||
|
||||
describeQueryStrBuff
|
||||
.append(" FILTER (!isBlank(?res)) \n")
|
||||
|
||||
.append(getNamespaceFilter(namespace));
|
||||
|
||||
if (graphURI != null) {
|
||||
describeQueryStrBuff
|
||||
.append("} \n");
|
||||
}
|
||||
|
||||
describeQueryStrBuff.append("} \n");
|
||||
|
||||
return describeQueryStrBuff.toString();
|
||||
|
||||
}
|
||||
|
||||
private String getNamespaceFilter(String namespace) {
|
||||
StringBuffer buff = new StringBuffer();
|
||||
if (namespace == null) {
|
||||
// exclude resources in the Vitro internal namespace or in the
|
||||
// OWL namespace, but allow all others
|
||||
buff
|
||||
|
|
@ -307,73 +335,73 @@ public class JenaModelUtils {
|
|||
.append(namespace)
|
||||
.append("\")) \n");
|
||||
}
|
||||
return buff.toString();
|
||||
}
|
||||
|
||||
public Model extractABox(Model inputModel){
|
||||
Dataset dataset = DatasetFactory.create(inputModel);
|
||||
return extractABox(dataset, null, null);
|
||||
}
|
||||
|
||||
public Model extractABox( Dataset unionDataset, Dataset baseOrInfDataset, String graphURI ) {
|
||||
|
||||
Model aboxModel = ModelFactory.createDefaultModel();
|
||||
return buff.toString();
|
||||
}
|
||||
|
||||
public Model extractABox(Model inputModel){
|
||||
Dataset dataset = DatasetFactory.create(inputModel);
|
||||
return extractABox(dataset, null, null);
|
||||
}
|
||||
|
||||
public Model extractABox( Dataset unionDataset, Dataset baseOrInfDataset, String graphURI ) {
|
||||
|
||||
Model aboxModel = ModelFactory.createDefaultModel();
|
||||
|
||||
// iterate through all classes and DESCRIBE each of their instances
|
||||
// Note that this could be simplified if we knew that the model was a
|
||||
// reasoning model: we could then simply describe all instances of
|
||||
// owl:Thing.
|
||||
// iterate through all classes and DESCRIBE each of their instances
|
||||
// Note that this could be simplified if we knew that the model was a
|
||||
// reasoning model: we could then simply describe all instances of
|
||||
// owl:Thing.
|
||||
|
||||
//OntModel ontModel = ( inputModel instanceof OntModel )
|
||||
//? (OntModel)inputModel
|
||||
//: ModelFactory.createOntologyModel( DEFAULT_ONT_MODEL_SPEC, inputModel );
|
||||
OntModel ontModel = extractTBox(unionDataset, null, graphURI);
|
||||
|
||||
try {
|
||||
ontModel.enterCriticalSection(Lock.READ);
|
||||
Iterator classIt = ontModel.listNamedClasses();
|
||||
QueryExecution qe = null;
|
||||
while ( classIt.hasNext() ) {
|
||||
|
||||
OntClass ontClass = (OntClass) classIt.next();
|
||||
//if ( !(ontClass.getNameSpace().startsWith(OWL.getURI()) )
|
||||
// && !(ontClass.getNameSpace().startsWith(VitroVocabulary.vitroURI)) ) {
|
||||
if(!(ontClass.getNameSpace().startsWith(OWL.getURI()))){
|
||||
|
||||
String queryStr = makeDescribeQueryStr( ontClass.getURI(), null, graphURI );
|
||||
|
||||
Query aboxSparqlQuery = QueryFactory.create(queryStr);
|
||||
if(baseOrInfDataset != null){
|
||||
qe = QueryExecutionFactory.create(aboxSparqlQuery,baseOrInfDataset);
|
||||
}
|
||||
else{
|
||||
qe = QueryExecutionFactory.create(aboxSparqlQuery,unionDataset);
|
||||
}
|
||||
if(baseOrInfDataset != null){
|
||||
try {
|
||||
baseOrInfDataset.getLock().enterCriticalSection(Lock.READ);
|
||||
qe.execDescribe(aboxModel); // puts the statements about each resource into aboxModel.
|
||||
} finally {
|
||||
baseOrInfDataset.getLock().leaveCriticalSection();
|
||||
}
|
||||
}
|
||||
else{
|
||||
try {
|
||||
unionDataset.getLock().enterCriticalSection(Lock.READ);
|
||||
qe.execDescribe(aboxModel); // puts the statements about each resource into aboxModel.
|
||||
} finally {
|
||||
unionDataset.getLock().leaveCriticalSection();
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
} finally {
|
||||
ontModel.leaveCriticalSection();
|
||||
}
|
||||
|
||||
return aboxModel;
|
||||
|
||||
}
|
||||
|
||||
//OntModel ontModel = ( inputModel instanceof OntModel )
|
||||
//? (OntModel)inputModel
|
||||
//: ModelFactory.createOntologyModel( DEFAULT_ONT_MODEL_SPEC, inputModel );
|
||||
OntModel ontModel = extractTBox(unionDataset, null, graphURI);
|
||||
|
||||
try {
|
||||
ontModel.enterCriticalSection(Lock.READ);
|
||||
Iterator classIt = ontModel.listNamedClasses();
|
||||
QueryExecution qe = null;
|
||||
while ( classIt.hasNext() ) {
|
||||
|
||||
OntClass ontClass = (OntClass) classIt.next();
|
||||
//if ( !(ontClass.getNameSpace().startsWith(OWL.getURI()) )
|
||||
// && !(ontClass.getNameSpace().startsWith(VitroVocabulary.vitroURI)) ) {
|
||||
if(!(ontClass.getNameSpace().startsWith(OWL.getURI()))){
|
||||
|
||||
String queryStr = makeDescribeQueryStr( ontClass.getURI(), null, graphURI );
|
||||
|
||||
Query aboxSparqlQuery = QueryFactory.create(queryStr);
|
||||
if(baseOrInfDataset != null){
|
||||
qe = QueryExecutionFactory.create(aboxSparqlQuery,baseOrInfDataset);
|
||||
}
|
||||
else{
|
||||
qe = QueryExecutionFactory.create(aboxSparqlQuery,unionDataset);
|
||||
}
|
||||
if(baseOrInfDataset != null){
|
||||
try {
|
||||
baseOrInfDataset.getLock().enterCriticalSection(Lock.READ);
|
||||
qe.execDescribe(aboxModel); // puts the statements about each resource into aboxModel.
|
||||
} finally {
|
||||
baseOrInfDataset.getLock().leaveCriticalSection();
|
||||
}
|
||||
}
|
||||
else{
|
||||
try {
|
||||
unionDataset.getLock().enterCriticalSection(Lock.READ);
|
||||
qe.execDescribe(aboxModel); // puts the statements about each resource into aboxModel.
|
||||
} finally {
|
||||
unionDataset.getLock().leaveCriticalSection();
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
} finally {
|
||||
ontModel.leaveCriticalSection();
|
||||
}
|
||||
|
||||
return aboxModel;
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue