diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/jena/JenaCsv2RdfController.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/jena/JenaCsv2RdfController.java index 1f51d023a..ea83c0cf5 100644 --- a/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/jena/JenaCsv2RdfController.java +++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/jena/JenaCsv2RdfController.java @@ -5,6 +5,7 @@ package edu.cornell.mannlib.vitro.webapp.controller.jena; import java.io.IOException; import java.io.InputStream; import java.net.URL; +import java.util.ArrayList; import java.util.LinkedList; import java.util.List; import java.util.Map; @@ -34,7 +35,6 @@ import edu.cornell.mannlib.vitro.webapp.utils.jena.JenaIngestUtils; public class JenaCsv2RdfController extends BaseEditController{ private static final String CSV2RDF_JSP = "/jenaIngest/csv2rdf.jsp"; - private static final String INGEST_MENU_JSP = "/jenaIngest/ingestMenu.jsp"; private static final String CSV2RDF_SELECT_URI_JSP = "/jenaIngest/csv2rdfSelectUri.jsp"; private static int maxFileSizeInBytes = 1024 * 1024 * 2000; //2000mb @@ -62,17 +62,20 @@ public class JenaCsv2RdfController extends BaseEditController{ if ("csv2rdf".equals(actionStr)) { String csvUrl = request.getParameter("csvUrl"); if (!csvUrl.isEmpty() || !filePath.isEmpty()) { - String[] sourceModel = new String[1]; - sourceModel[0] = doExecuteCsv2Rdf(request,fileStream,filePath); - Model model = ModelFactory.createDefaultModel(); + String destinationModelNameStr = request.getParameter( + "destinationModelName"); + Model csv2rdfResult = doExecuteCsv2Rdf( + request, fileStream, filePath); ModelMaker maker = getVitroJenaModelMaker(request); Boolean csv2rdf = true; JenaIngestUtils utils = new JenaIngestUtils(); - Map> propertyMap = utils.generatePropertyMap(sourceModel, model, maker); + List resultList = new ArrayList(); + resultList.add(csv2rdfResult); + Map> propertyMap = + utils.generatePropertyMap(resultList, maker); request.setAttribute("propertyMap",propertyMap); - getServletContext().setAttribute("sourceModel", sourceModel); - getServletContext().setAttribute("csv2rdf",csv2rdf); - request.setAttribute("destinationModelName", sourceModel[0]); + request.setAttribute("csv2rdf", csv2rdf); + request.setAttribute("destinationModelName", destinationModelNameStr); request.setAttribute("title","URI Select"); request.setAttribute("bodyJsp", CSV2RDF_SELECT_URI_JSP); } else { @@ -88,9 +91,7 @@ public class JenaCsv2RdfController extends BaseEditController{ try { rd.forward(request, response); } catch (Exception e) { - System.out.println(this.getClass().getName()+" could not forward to view."); - System.out.println(e.getMessage()); - System.out.println(e.getStackTrace()); + throw new RuntimeException(e); } } @@ -106,7 +107,7 @@ public class JenaCsv2RdfController extends BaseEditController{ return; } - public String doExecuteCsv2Rdf(VitroRequest vreq,FileItem fileStream, String filePath) { + public Model doExecuteCsv2Rdf(VitroRequest vreq, FileItem fileStream, String filePath) { char[] quoteChars = {'"'}; String namespace = ""; String tboxNamespace = vreq.getParameter("tboxNamespace"); @@ -139,25 +140,26 @@ public class JenaCsv2RdfController extends BaseEditController{ is = fileStream.getInputStream(); } catch (IOException e) { - System.out.println("IOException opening URL "+csvUrl); - return null; + throw new RuntimeException("Unable to access URL " + csvUrl); } Model[] models = null; try { - models = c2r.convertToRdf(is,vreq,destination); + models = c2r.convertToRdf( + is, vreq.getWebappDaoFactory(), destination); } catch (IOException e) { - System.out.println("IOException converting "+csvUrl+" to RDF"); + throw new RuntimeException( + "Unable to convert " + csvUrl + " to RDF"); } - if (destination != null) { - destination.add(models[0]); - } + // TODO: rework this + vreq.getSession().setAttribute("csv2rdfResult", models[0]); if (tboxDestination != null) { tboxDestination.add(models[1]); } - return destinationModelNameStr; + + return models[0]; } private Model getModel(String name, HttpServletRequest request) { diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/jena/JenaIngestController.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/jena/JenaIngestController.java index 411cd9635..f51a79c2c 100644 --- a/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/jena/JenaIngestController.java +++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/jena/JenaIngestController.java @@ -11,6 +11,7 @@ import java.lang.reflect.Method; import java.sql.SQLException; import java.text.Collator; import java.util.ArrayList; +import java.util.Arrays; import java.util.Collections; import java.util.Comparator; import java.util.HashMap; @@ -68,7 +69,6 @@ import edu.cornell.mannlib.vitro.webapp.beans.Ontology; import edu.cornell.mannlib.vitro.webapp.controller.Controllers; import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest; import edu.cornell.mannlib.vitro.webapp.dao.OntologyDao; -import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory; import edu.cornell.mannlib.vitro.webapp.dao.jena.JenaBaseDao; import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext; import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaModelMaker; @@ -145,8 +145,6 @@ public class JenaIngestController extends BaseEditController { return; // don't attempt to display a JSP } else if("clearModel".equals(actionStr)) { processClearModelRequest(vreq, maker, modelType); - } else if("setWriteLayer".equals(actionStr)) { - processSetWriteLayerRequest(vreq, maker, modelType); } else if("attachModel".equals(actionStr)) { processAttachModelRequest(vreq, maker, modelType); } else if("detachModel".equals(actionStr)) { @@ -337,13 +335,13 @@ public class JenaIngestController extends BaseEditController { } catch (com.hp.hpl.jena.shared.CannotEncodeCharacterException cece) { // there's got to be a better way to do this byte[] badCharBytes = String.valueOf(cece.getBadChar()).getBytes(); - System.out.println("Cannot encode character with byte values: (decimal) "); + String errorMsg = "Cannot encode character with byte values: (decimal) "; for (int i=0; i> propertyMap = utils.generatePropertyMap(sourceModel, model, maker); - getServletContext().setAttribute("sourceModel",sourceModel); + if(sourceModel != null && sourceModel.length != 0) { + List sourceModelList = new ArrayList(); + for (int i = 0; i < sourceModel.length ; i++) { + Model m = maker.getModel(sourceModel[i]); + if (m != null) { + sourceModelList.add(m); + } + } + Map> propertyMap = + utils.generatePropertyMap(sourceModelList, maker); + List sourceModelNameList = Arrays.asList(sourceModel); + vreq.setAttribute("sourceModel",sourceModelNameList); vreq.setAttribute("propertyMap", propertyMap); + vreq.setAttribute("enablePropertyPatternURIs", !propertyMap.isEmpty()); vreq.setAttribute("title","URI Select"); vreq.setAttribute("bodyJsp",RENAME_BNODES_URI_SELECT_JSP); } else { @@ -421,12 +404,21 @@ public class JenaIngestController extends BaseEditController { String namespaceEtcStr = vreq.getParameter("namespaceEtcStr"); String pattern = vreq.getParameter("pattern"); String concatenate = vreq.getParameter("concatenate"); - String[] sourceModel = (String[])getServletContext().getAttribute("sourceModel"); - if(namespaceEtcStr!=null && !namespaceEtcStr.isEmpty()){ - if(concatenate.equals("integer")){ - doRenameBNodes(vreq,namespaceEtcStr, false, null, sourceModel); + String[] sourceModel = (String[]) vreq.getParameterValues("sourceModelName"); + if(namespaceEtcStr != null) { + if (namespaceEtcStr.isEmpty()) { + if ("true".equals(vreq.getParameter("csv2rdf"))) { + processCsv2rdfRequest(vreq, maker, modelType); + return; + } else { + vreq.setAttribute("errorMsg", "Please enter a value."); + processRenameBNodesRequest(vreq, maker, modelType); + return; + } } - else{ + if (concatenate.equals("integer")) { + doRenameBNodes(vreq,namespaceEtcStr, false, null, sourceModel); + } else { pattern = pattern.trim(); doRenameBNodes(vreq,namespaceEtcStr, true, pattern, sourceModel); } @@ -695,7 +687,7 @@ public class JenaIngestController extends BaseEditController { * calling method that does the merge operation. */ String result = utils.doMerge(uri1,uri2,baseOntModel,ontModel,infOntModel,usePrimaryLabelOnly); - getServletContext().setAttribute("leftoverModel", utils.getLeftOverModel()); + vreq.getSession().setAttribute("leftoverModel", utils.getLeftOverModel()); vreq.setAttribute("result",result); vreq.setAttribute("title","Merge Resources"); vreq.setAttribute("bodyJsp",MERGE_RESULT); @@ -710,15 +702,32 @@ public class JenaIngestController extends BaseEditController { HttpServletResponse response, ModelMaker maker, String modelType) { - String uri1 = vreq.getParameter("uri1"); - String uri2 = vreq.getParameter("uri2"); - if(uri1!=null){ - String result = doRename(uri1,uri2,response); - vreq.setAttribute("result",result); - vreq.setAttribute("title","Rename Resources"); - vreq.setAttribute("bodyJsp",RENAME_RESULT); - } - else{ + String oldNamespace = vreq.getParameter("oldNamespace"); + String newNamespace = vreq.getParameter("newNamespace"); + String errorMsg = ""; + if (oldNamespace != null) { + if (oldNamespace.isEmpty() && !newNamespace.isEmpty()) { + errorMsg = "Please enter the old namespace to be changed."; + } else if (!oldNamespace.isEmpty() && newNamespace.isEmpty()) { + errorMsg = "Please enter the new namespace."; + } else if (oldNamespace.isEmpty() && newNamespace.isEmpty()) { + errorMsg = "Please enter the namespaces."; + } else if (oldNamespace.equals(newNamespace)) { + errorMsg = "Please enter two different namespaces."; + } + if (!errorMsg.isEmpty()) { + vreq.setAttribute("errorMsg", errorMsg); + vreq.setAttribute("oldNamespace", oldNamespace); + vreq.setAttribute("newNamespace", newNamespace); + vreq.setAttribute("title","Rename Resource"); + vreq.setAttribute("bodyJsp",RENAME_RESOURCE); + } else { + String result = doRename(oldNamespace, newNamespace, response); + vreq.setAttribute("result",result); + vreq.setAttribute("title","Rename Resources"); + vreq.setAttribute("bodyJsp",RENAME_RESULT); + } + } else{ vreq.setAttribute("title","Rename Resource"); vreq.setAttribute("bodyJsp",RENAME_RESOURCE); } @@ -728,8 +737,8 @@ public class JenaIngestController extends BaseEditController { HttpServletResponse response, ModelMaker maker, String modelType) { - //Model lmodel = (Model)request.getSession().getAttribute("leftoverModel"); - Model lmodel = (Model)getServletContext().getAttribute("leftoverModel"); + + Model lmodel = (Model) vreq.getSession().getAttribute("leftoverModel"); response.setContentType("RDF/XML-ABBREV"); try { OutputStream outStream = response.getOutputStream(); @@ -745,7 +754,7 @@ public class JenaIngestController extends BaseEditController { private ModelMaker getVitroJenaModelMaker(HttpServletRequest request) { ModelMaker myVjmm = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker"); - myVjmm = (myVjmm == null) ? (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker") : myVjmm; + myVjmm = (myVjmm == null) ? (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker") : myVjmm; return new VitroJenaSpecialModelMaker(myVjmm, request); } @@ -783,7 +792,7 @@ public class JenaIngestController extends BaseEditController { private void doRemoveModel(String modelName, ModelMaker modelMaker) { //Try to detach first since it cause problems to remove an attached model. doDetachModel(modelName, modelMaker); - System.out.println("Removing "+modelName+" from webapp"); + log.debug("Removing " + modelName + " from webapp"); modelMaker.removeModel(modelName); } @@ -861,13 +870,28 @@ public class JenaIngestController extends BaseEditController { private void doRenameBNodes(VitroRequest vreq, String namespaceEtc, boolean patternBoolean, String pattern, String[] sourceModel) { OntModel source = ModelFactory.createOntologyModel(OntModelSpec.OWL_DL_MEM); String property = vreq.getParameter("property"); - Boolean csv2rdf = (Boolean)getServletContext().getAttribute("csv2rdf"); - for (int i=0; i urisToChange = new LinkedList(); ontModel.enterCriticalSection(Lock.READ); try { @@ -1272,37 +1250,22 @@ public class JenaIngestController extends BaseEditController { Matcher matcher = p.matcher(candidateString); newURIStr = matcher.replaceFirst(newNamespace); long time3 = System.currentTimeMillis(); - log.info("time to get new uri: " + + log.debug("time to get new uri: " + Long.toString(time3 - time2)); - log.info("Renaming "+ oldURIStr + " to " + newURIStr); + log.debug("Renaming "+ oldURIStr + " to " + newURIStr); ResourceUtils.renameResource(res,newURIStr); ResourceUtils.renameResource(infRes,newURIStr); long time4 = System.currentTimeMillis(); - log.info(" time to rename : " + Long.toString( time4 - time3)); - log.info(" time for one resource: " + + log.debug(" time to rename : " + Long.toString( time4 - time3)); + log.debug(" time for one resource: " + Long.toString( time4 -time1)); } finally { infOntModel.leaveCriticalSection(); ontModel.leaveCriticalSection(); baseOntModel.leaveCriticalSection(); } - try { - Thread.currentThread().sleep(200); - } catch (InterruptedException e) { - // TODO Auto-generated catch block - e.printStackTrace(); - } counter++; } - /*baseOntModel.enterCriticalSection(Lock.WRITE); - ontModel.enterCriticalSection(Lock.WRITE); - try{ - baseOntModel.getBaseModel().notifyEvent(new EditEvent(null,true)); - baseOntModel.getBaseModel().notifyEvent(new EditEvent(null,false)); - } finally { - ontModel.leaveCriticalSection(); - baseOntModel.leaveCriticalSection(); - }*/ result = counter.toString() + " resources renamed"; return result; } diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/utils/Csv2Rdf.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/utils/Csv2Rdf.java index 66f17bd05..769e53b0c 100644 --- a/webapp/src/edu/cornell/mannlib/vitro/webapp/utils/Csv2Rdf.java +++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/utils/Csv2Rdf.java @@ -60,7 +60,7 @@ public class Csv2Rdf { return convertToRdf(fis, null, null); } - public Model[] convertToRdf(InputStream fis,VitroRequest vreq, Model destination) throws IOException { + public Model[] convertToRdf(InputStream fis, WebappDaoFactory wadf, Model destination) throws IOException { OntModel ontModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM); OntModel tboxOntModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM); ontModel.addSubModel(tboxOntModel); @@ -70,8 +70,8 @@ public class Csv2Rdf { cReader.setSeperator(separatorChar); cReader.setQuoteCharacters(quoteChars); - URIGenerator uriGen = (vreq != null && destination != null) - ? new RandomURIGenerator(vreq, destination) + URIGenerator uriGen = (wadf != null && destination != null) + ? new RandomURIGenerator(wadf, destination) : new SequentialURIGenerator(); List fileRows = cReader.parse(fis); @@ -115,12 +115,12 @@ public class Csv2Rdf { private class RandomURIGenerator implements URIGenerator { - private VitroRequest vreq; + private WebappDaoFactory wadf; private Model destination; private Random random = new Random(System.currentTimeMillis()); - public RandomURIGenerator(VitroRequest vreq, Model destination) { - this.vreq = vreq; + public RandomURIGenerator(WebappDaoFactory webappDaoFactory, Model destination) { + this.wadf = webappDaoFactory; this.destination = destination; } @@ -132,7 +132,7 @@ public class Csv2Rdf { if(namespace!=null && !namespace.isEmpty()){ while( uriIsGood == false && attempts < 30 ){ uri = namespace+individualNameBase+random.nextInt( Math.min(Integer.MAX_VALUE,(int)Math.pow(2,attempts + 13)) ); - String errMsg = vreq.getWebappDaoFactory().checkURI(uri); + String errMsg = wadf.checkURI(uri); Resource res = ResourceFactory.createResource(uri); inDestination = destination.contains(res, null); if( errMsg != null && !inDestination) diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/utils/jena/JenaIngestUtils.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/utils/jena/JenaIngestUtils.java index 48eeabca6..68f2af94d 100644 --- a/webapp/src/edu/cornell/mannlib/vitro/webapp/utils/jena/JenaIngestUtils.java +++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/utils/jena/JenaIngestUtils.java @@ -173,7 +173,11 @@ public class JenaIngestUtils { if (stmt != null) { Resource outRes = stmt.getSubject(); if(stmt.getObject().isLiteral()){ - ResourceUtils.renameResource(outRes,namespaceEtc+pattern+"_"+stmt.getObject().toString()); + String value = ((Literal) stmt.getObject()).getLexicalForm(); + String suffix = (pattern.contains("$$$")) + ? pattern.replace("$$$", value) + : pattern + value; + ResourceUtils.renameResource(outRes, namespaceEtc + suffix); } doneSet.add(res.getId().toString()); } @@ -191,70 +195,58 @@ public class JenaIngestUtils { } - public Map generatePropertyMap(String[] sourceModel, Model model, ModelMaker maker){ + public Map> generatePropertyMap(List sourceModels, ModelMaker maker){ Map> propertyMap = Collections.synchronizedMap(new HashMap>()); Set doneList = new HashSet(); - if(sourceModel!=null && sourceModel.length!=0){ - for(String modelName : sourceModel){ - if(modelName != null){ - model = maker.getModel(modelName); - ClosableIterator cItr = model.listSubjects(); - while(cItr.hasNext()){ - Resource res = (Resource) cItr.next(); - if(res.isAnon() && !doneList.contains(res.getId())){ - - doneList.add(res.getId().toString()); - StmtIterator stmtItr = model.listStatements(res, (Property)null, (RDFNode)null); - while(stmtItr.hasNext()){ - Statement stmt = stmtItr.next(); - if(!stmt.getObject().isResource()){ - if(propertyMap.containsKey(stmt.getPredicate().getURI())){ - LinkedList linkList = propertyMap.get(stmt.getPredicate().getURI()); - linkList.add(stmt.getObject().toString()); - - } - else{ - propertyMap.put(stmt.getPredicate().getURI(), new LinkedList()); - LinkedList linkList = propertyMap.get(stmt.getPredicate().getURI()); - linkList.add(stmt.getObject().toString()); - - } - - } - + for(Model model : sourceModels) { + ClosableIterator cItr = model.listSubjects(); + while(cItr.hasNext()){ + Resource res = (Resource) cItr.next(); + if(res.isAnon() && !doneList.contains(res.getId())){ + doneList.add(res.getId().toString()); + StmtIterator stmtItr = model.listStatements(res, (Property)null, (RDFNode)null); + while(stmtItr.hasNext()){ + Statement stmt = stmtItr.next(); + if(!stmt.getObject().isResource()){ + if(propertyMap.containsKey(stmt.getPredicate().getURI())){ + LinkedList linkList = propertyMap.get(stmt.getPredicate().getURI()); + linkList.add(stmt.getObject().toString()); } - } + else{ + propertyMap.put(stmt.getPredicate().getURI(), new LinkedList()); + LinkedList linkList = propertyMap.get(stmt.getPredicate().getURI()); + linkList.add(stmt.getObject().toString()); + } + } } - cItr = model.listObjects(); - while(cItr.hasNext()){ - RDFNode rdfn = (RDFNode) cItr.next(); - if(rdfn.isResource()){ - Resource res = (Resource)rdfn; - if(res.isAnon() && !doneList.contains(res.getId())){ - doneList.add(res.getId().toString()); - StmtIterator stmtItr = model.listStatements(res, (Property)null, (RDFNode)null); - while(stmtItr.hasNext()){ - Statement stmt = stmtItr.next(); - if(!stmt.getObject().isResource()){ - if(propertyMap.containsKey(stmt.getPredicate().getURI())){ - LinkedList linkList = propertyMap.get(stmt.getPredicate().getURI()); - linkList.add(stmt.getObject().toString()); - - } - else{ - propertyMap.put(stmt.getPredicate().getURI(), new LinkedList()); - LinkedList linkList = propertyMap.get(stmt.getPredicate().getURI()); - linkList.add(stmt.getObject().toString()); - - } - } - } - } - } - } - cItr.close(); } } + cItr = model.listObjects(); + while(cItr.hasNext()){ + RDFNode rdfn = (RDFNode) cItr.next(); + if(rdfn.isResource()){ + Resource res = (Resource)rdfn; + if(res.isAnon() && !doneList.contains(res.getId())){ + doneList.add(res.getId().toString()); + StmtIterator stmtItr = model.listStatements(res, (Property)null, (RDFNode)null); + while(stmtItr.hasNext()){ + Statement stmt = stmtItr.next(); + if(!stmt.getObject().isResource()){ + if(propertyMap.containsKey(stmt.getPredicate().getURI())){ + LinkedList linkList = propertyMap.get(stmt.getPredicate().getURI()); + linkList.add(stmt.getObject().toString()); + } + else{ + propertyMap.put(stmt.getPredicate().getURI(), new LinkedList()); + LinkedList linkList = propertyMap.get(stmt.getPredicate().getURI()); + linkList.add(stmt.getObject().toString()); + } + } + } + } + } + } + cItr.close(); } return propertyMap; } diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/utils/jena/SesameSyncUtils.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/utils/jena/SesameSyncUtils.java index 96ef68acc..9875e5238 100644 --- a/webapp/src/edu/cornell/mannlib/vitro/webapp/utils/jena/SesameSyncUtils.java +++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/utils/jena/SesameSyncUtils.java @@ -6,6 +6,8 @@ import java.io.IOException; import java.io.OutputStream; import java.io.PipedInputStream; import java.io.PipedOutputStream; +import java.util.ArrayList; +import java.util.List; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; @@ -18,7 +20,16 @@ import org.openrdf.repository.http.HTTPRepository; import org.openrdf.rio.RDFFormat; import org.openrdf.rio.RDFParseException; +import com.hp.hpl.jena.query.Query; +import com.hp.hpl.jena.query.QueryExecution; +import com.hp.hpl.jena.query.QueryExecutionFactory; +import com.hp.hpl.jena.query.QueryFactory; +import com.hp.hpl.jena.query.QuerySolution; +import com.hp.hpl.jena.query.ResultSet; import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.ModelFactory; +import com.hp.hpl.jena.rdf.model.RDFNode; +import com.hp.hpl.jena.vocabulary.OWL; public class SesameSyncUtils { @@ -42,11 +53,16 @@ public class SesameSyncUtils { } else { myConn.clear(); } - + PipedInputStream in = new PipedInputStream(); PipedOutputStream out = new PipedOutputStream(in); + + + try { - new Thread(new JenaOutputter(jenaModel, out), "SesameSyncUtilities.JenaOutputter").start(); + + new Thread(new JenaOutputter(jenaModel, out, myConn), "SesameSyncUtilities.JenaOutputter").start(); + if (contextRes != null) { myConn.add(in,"http://example.org/base/", RDFFormat.NTRIPLES, contextRes); } else { @@ -69,19 +85,62 @@ public class SesameSyncUtils { } + private List getIndividualURIs(Model model) { + List individualURIs = new ArrayList(); + String queryStr = "SELECT DISTINCT ?s WHERE { \n" + + " ?s a <" + OWL.Thing.getURI() + "> \n" + + "}"; + Query query = QueryFactory.create(queryStr); + QueryExecution qe = QueryExecutionFactory.create(query, model); + try { + ResultSet rs = qe.execSelect(); + while (rs.hasNext()) { + QuerySolution qsoln = rs.nextSolution(); + String individualURI = qsoln.getResource("s").getURI(); + if (individualURI != null) { + individualURIs.add(individualURI); + } + } + } finally { + qe.close(); + } + return individualURIs; + } + private class JenaOutputter implements Runnable { private Model model; private OutputStream out; + private RepositoryConnection rconn; - public JenaOutputter(Model model, OutputStream out) { + public JenaOutputter(Model model, OutputStream out, RepositoryConnection rconn) { this.model = model; this.out = out; + this.rconn = rconn; } public void run() { + Model t = ModelFactory.createDefaultModel(); try { - model.write(out, "N-TRIPLE"); + List individualURIs = getIndividualURIs(model); + log.info(individualURIs.size() + " individuals to send to Sesame"); + int i = 0; + for (String individualURI : individualURIs) { + t.removeAll(); + t.add(model.listStatements( + model.getResource( + individualURI), null, (RDFNode) null)); + t.write(out, "N-TRIPLE"); + i++; + if (i % 100 == 0) { + try { + rconn.commit(); + } catch (Throwable e) { + log.error(e, e); + } + log.info(i + " individuals sent to Sesame"); + } + } } finally { try { out.flush(); diff --git a/webapp/web/jenaIngest/csv2rdf.jsp b/webapp/web/jenaIngest/csv2rdf.jsp index 41f7f0657..11d24440d 100644 --- a/webapp/web/jenaIngest/csv2rdf.jsp +++ b/webapp/web/jenaIngest/csv2rdf.jsp @@ -17,7 +17,7 @@ ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker"); if (maker == null) { - maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker"); + maker = (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker"); } %> @@ -36,15 +36,27 @@

Or upload a file from your computer:

+

+

This tool will automatically generate a mini ontology to represent the + data in the CSV file. A property will be produced for each column in the + spreadsheet, based on the text in the header for that column.

In what + namespace should these properties be created?

-

Namespace in which to generate class and properties

+

Namespace in which to generate properties

+

+

Each row in the spreadsheet will produce an resource. Each of these + resources will be a member of a class in the namespace selected above.

+

What should the local name of this class be? This is normally a word or two + in "camel case" starting with an uppercase letter. (For example, if the + spreadsheet represents a list of faculty members, you might enter + "FacultyMember" on the next line.)

-

Class Name for Resources

+

Class Local Name for Resources

-

Destination Model

+

Model in which to save the converted spreadsheet data

-

Destination Model for TBox

+

Model in which to save the automatically-generated ontology

+ +

+

The data in the CSV file will initially be represented using blank + nodes (RDF resources without URIs). You will choose how to assign + URIs to these resources in the next step.

diff --git a/webapp/web/jenaIngest/csv2rdfSelectUri.jsp b/webapp/web/jenaIngest/csv2rdfSelectUri.jsp index 9de19e4dd..5ed8172e6 100644 --- a/webapp/web/jenaIngest/csv2rdfSelectUri.jsp +++ b/webapp/web/jenaIngest/csv2rdfSelectUri.jsp @@ -1,5 +1,8 @@ <%-- $This file is distributed under the terms of the license in /doc/license.txt$ --%> +<%@ taglib uri="http://java.sun.com/jstl/core" prefix="c"%> +<%@ taglib prefix="vitro" uri="/WEB-INF/tlds/VitroUtils.tld" %> + <%@ page import="com.hp.hpl.jena.ontology.Individual" %> <%@ page import="com.hp.hpl.jena.ontology.OntModel" %> <%@ page import="com.hp.hpl.jena.rdf.model.ModelMaker" %> @@ -13,8 +16,7 @@ <%@ page import="java.util.Set" %> <%@ page import="java.util.Map.Entry" %> -<%@taglib prefix="vitro" uri="/WEB-INF/tlds/VitroUtils.tld" %> -<%@page import="edu.cornell.mannlib.vitro.webapp.auth.requestedAction.usepages.UseAdvancedDataToolsPages" %> +<%@ page import="edu.cornell.mannlib.vitro.webapp.auth.requestedAction.usepages.UseAdvancedDataToolsPages" %> <% request.setAttribute("requestedActions", new UseAdvancedDataToolsPages()); %> @@ -22,7 +24,7 @@ ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker"); if (maker == null) { - maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker"); + maker = (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker"); } %> @@ -46,16 +48,18 @@ function disableProperties(){

Select URI prefix

-

URIs will be constructed from the following string:

+

URIs will be constructed using the following base string:

-

You can concatenate above string with random integer OR your own pattern based on values of one of the properties (Properties will be enabled in the dropdown)

+

Each resource will be assigned a URI by taking the above string and + adding either a random integer, or a string based on the value of one of the + the properties of the resource

- No, concatenate with random integer + Use random integer

- Yes, concatenate with my pattern + Use pattern based on values of <% Map> propertyMap = (Map) request.getAttribute("propertyMap"); @@ -75,12 +79,16 @@ function disableProperties(){ %>

-

Enter your pattern that will prefix property value with an underscore eg. depID_$$$ where depID is your pattern and $$$ is the property value.

+

Enter a pattern using $$$ as the placeholder for the value of the property selected above.

+

For example, entering dept_$$$ might generate URIs with endings such as dept_Art or dept_Classics.

- <%String modelName = (String) request.getAttribute("destinationModelName"); %> + + - + + + diff --git a/webapp/web/jenaIngest/executeWorkflow.jsp b/webapp/web/jenaIngest/executeWorkflow.jsp index a6a1e68fe..55e964be0 100644 --- a/webapp/web/jenaIngest/executeWorkflow.jsp +++ b/webapp/web/jenaIngest/executeWorkflow.jsp @@ -17,7 +17,7 @@ ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker"); if (maker == null) { - maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker"); + maker = (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker"); } %> diff --git a/webapp/web/jenaIngest/generateTBox.jsp b/webapp/web/jenaIngest/generateTBox.jsp index 53ff8bfcd..fe435284c 100644 --- a/webapp/web/jenaIngest/generateTBox.jsp +++ b/webapp/web/jenaIngest/generateTBox.jsp @@ -17,7 +17,7 @@ ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker"); if (maker == null) { - maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker"); + maker = (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker"); } %> diff --git a/webapp/web/jenaIngest/mergeResources.jsp b/webapp/web/jenaIngest/mergeResources.jsp index 966c2100e..31ef13595 100644 --- a/webapp/web/jenaIngest/mergeResources.jsp +++ b/webapp/web/jenaIngest/mergeResources.jsp @@ -16,7 +16,7 @@ ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker"); if (maker == null) { - maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker"); + maker = (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker"); } %> @@ -46,4 +46,4 @@ Retain rdfs:labels only from Primary Resource

- \ No newline at end of file + diff --git a/webapp/web/jenaIngest/permanentURI.jsp b/webapp/web/jenaIngest/permanentURI.jsp index 1b6416032..481d2df38 100644 --- a/webapp/web/jenaIngest/permanentURI.jsp +++ b/webapp/web/jenaIngest/permanentURI.jsp @@ -16,7 +16,7 @@ ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker"); if (maker == null) { - maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker"); + maker = (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker"); } %> @@ -63,4 +63,4 @@ Or <%String defaultNamespace = (String)request.getAttribute("defaultNamespace");

- \ No newline at end of file + diff --git a/webapp/web/jenaIngest/processStrings.jsp b/webapp/web/jenaIngest/processStrings.jsp index 0bb67a7c9..47d4376d2 100644 --- a/webapp/web/jenaIngest/processStrings.jsp +++ b/webapp/web/jenaIngest/processStrings.jsp @@ -17,7 +17,7 @@ ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker"); if (maker == null) { - maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker"); + maker = (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker"); } %> diff --git a/webapp/web/jenaIngest/renameBNodes.jsp b/webapp/web/jenaIngest/renameBNodes.jsp index 69e8a984f..191f3e7b1 100644 --- a/webapp/web/jenaIngest/renameBNodes.jsp +++ b/webapp/web/jenaIngest/renameBNodes.jsp @@ -17,7 +17,7 @@ ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker"); if (maker == null) { - maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker"); + maker = (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker"); } %> diff --git a/webapp/web/jenaIngest/renameBNodesURISelect.jsp b/webapp/web/jenaIngest/renameBNodesURISelect.jsp index 938dd0cb7..8b92dee23 100644 --- a/webapp/web/jenaIngest/renameBNodesURISelect.jsp +++ b/webapp/web/jenaIngest/renameBNodesURISelect.jsp @@ -12,6 +12,7 @@ <%@ page import="java.util.HashMap" %> <%@ page import="java.util.Set" %> <%@ page import="java.util.Map.Entry" %> +<%@ taglib uri="http://java.sun.com/jstl/core" prefix="c"%> <%@taglib prefix="vitro" uri="/WEB-INF/tlds/VitroUtils.tld" %> <%@page import="edu.cornell.mannlib.vitro.webapp.auth.requestedAction.usepages.UseAdvancedDataToolsPages" %> @@ -22,12 +23,11 @@ ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker"); if (maker == null) { - maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker"); + maker = (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker"); } %> - -

Ingest Menu > Change Namespace of Resources

@@ -25,9 +24,13 @@ they will be updated to this format.

This tool operates on the main web application model only, not on any of the additional Jena models.

+ +

${errorMsg}

+ +
-

Old namespace:

-

New namespace:

+

Old namespace:

+

New namespace:

\ No newline at end of file diff --git a/webapp/web/jenaIngest/smushSingleModel.jsp b/webapp/web/jenaIngest/smushSingleModel.jsp index 1509ec2be..58fb3de57 100644 --- a/webapp/web/jenaIngest/smushSingleModel.jsp +++ b/webapp/web/jenaIngest/smushSingleModel.jsp @@ -17,7 +17,7 @@ ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker"); if (maker == null) { - maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker"); + maker = (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker"); } %> diff --git a/webapp/web/jenaIngest/sparqlConstruct.jsp b/webapp/web/jenaIngest/sparqlConstruct.jsp index 8651819f0..b5e3da4b1 100644 --- a/webapp/web/jenaIngest/sparqlConstruct.jsp +++ b/webapp/web/jenaIngest/sparqlConstruct.jsp @@ -19,7 +19,7 @@ ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker"); if (maker == null) { - maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker"); + maker = (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker"); } %> @@ -188,4 +188,4 @@ PREFIX <%=prefixText%>: <<%=urlText%>><%}}%>

include Pellet OWL-DL reasoning

- \ No newline at end of file + diff --git a/webapp/web/jenaIngest/splitPropertyValues.jsp b/webapp/web/jenaIngest/splitPropertyValues.jsp index 8bf1dbe6c..2dde5dc82 100644 --- a/webapp/web/jenaIngest/splitPropertyValues.jsp +++ b/webapp/web/jenaIngest/splitPropertyValues.jsp @@ -17,7 +17,7 @@ ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker"); if (maker == null) { - maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker"); + maker = (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker"); } %> diff --git a/webapp/web/jenaIngest/subtractModels.jsp b/webapp/web/jenaIngest/subtractModels.jsp index 888579056..0aa3026c4 100644 --- a/webapp/web/jenaIngest/subtractModels.jsp +++ b/webapp/web/jenaIngest/subtractModels.jsp @@ -17,7 +17,7 @@ ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker"); if (maker == null) { - maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker"); + maker = (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker"); } %> diff --git a/webapp/web/jenaIngest/xmlFileUpload.jsp b/webapp/web/jenaIngest/xmlFileUpload.jsp index 3aafaff0e..bc91a4248 100644 --- a/webapp/web/jenaIngest/xmlFileUpload.jsp +++ b/webapp/web/jenaIngest/xmlFileUpload.jsp @@ -14,7 +14,7 @@ ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker"); if (maker == null) { - maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker"); + maker = (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker"); } %> diff --git a/webapp/web/js/jenaIngest/ingestUtils.js b/webapp/web/js/jenaIngest/ingestUtils.js deleted file mode 100644 index c2998172c..000000000 --- a/webapp/web/js/jenaIngest/ingestUtils.js +++ /dev/null @@ -1,28 +0,0 @@ -/* $This file is distributed under the terms of the license in /doc/license.txt$ */ - - - -$(document).ready(function(){ - - $('#takeuri').submit(function() { - if ($('#uri1').val() == '') { - alert('Please enter a value for Individual URI 1.'); - return false; - } - if ($('#uri2').val() == '') { - alert('Please enter a value for Individual URI 2.'); - return false; - } - if (!$('#uri1').val().match(/\/$/)) { - $('#uri1').val($('#uri1').val() + "/"); - } - if (!$('#uri2').val().match(/\/$/)) { - $('#uri2').val($('#uri2').val() + "/"); - } - if ($('#uri1').val() == $('#uri2').val()){ - alert('Primary and duplicate URI cannot be same.'); - return false; - } - }); - -}); \ No newline at end of file diff --git a/webapp/web/js/jenaIngest/renameNode.js b/webapp/web/js/jenaIngest/renameNode.js deleted file mode 100644 index 2a61923ec..000000000 --- a/webapp/web/js/jenaIngest/renameNode.js +++ /dev/null @@ -1,14 +0,0 @@ -/* $This file is distributed under the terms of the license in /doc/license.txt$ */ - - - -$(document).ready(function(){ - - $('#takeuri').submit(function() { - if ($('#namespace').val() == '') { - alert('Please enter URI prefix.'); - return false; - } - }); - -}); \ No newline at end of file