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Merge branch 'develop' of https://github.com/vivo-project/Vitro into develop

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This commit is contained in:
brianjlowe 2013-05-17 15:03:57 -04:00
commit eebb205723
52 changed files with 800 additions and 631 deletions
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12
webapp/src/edu/cornell/mannlib/vedit/controller/BaseEditController.java
View file

@ -25,6 +25,7 @@ import edu.cornell.mannlib.vedit.util.FormUtils;
import edu.cornell.mannlib.vitro.webapp.controller.Controllers;
import edu.cornell.mannlib.vitro.webapp.controller.VitroHttpServlet;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
@ -153,14 +154,13 @@ public class BaseEditController extends VitroHttpServlet {
}
}
protected String MODEL_ATTR_NAME = "jenaOntModel";
protected OntModel getOntModel( HttpServletRequest request, ServletContext ctx ) {
// TODO: JB - This method gets the UNION FULL model from the session, if there is one,
// TODO and the BASE_TBOX model otherwise.
OntModel ontModel = null;
try {
ontModel = (OntModel) request.getSession().getAttribute(MODEL_ATTR_NAME);
try {
ontModel = ModelAccess.on(request.getSession()).getJenaOntModel();
} catch (Exception e) {
// ignoring any problems here - we're not really expecting
// this attribute to be populated anyway

5
webapp/src/edu/cornell/mannlib/vitro/webapp/auth/identifier/common/IsBlacklisted.java
View file

@ -16,18 +16,19 @@ import org.apache.commons.lang.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.ontology.OntModel;
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.RDFNode;
import edu.cornell.mannlib.vitro.webapp.auth.identifier.Identifier;
import edu.cornell.mannlib.vitro.webapp.auth.identifier.IdentifierBundle;
import edu.cornell.mannlib.vitro.webapp.beans.Individual;
import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
/**
* The current user is blacklisted for this reason.
@ -152,7 +153,7 @@ public class IsBlacklisted extends AbstractCommonIdentifier implements
return NOT_BLACKLISTED;
}
Model model = (Model) context.getAttribute("jenaOntModel");
OntModel model = ModelAccess.on(context).getJenaOntModel();
queryString = queryString.replaceAll("\\?individualURI",
"<" + ind.getURI() + ">");

3
webapp/src/edu/cornell/mannlib/vitro/webapp/auth/policy/bean/PropertyRestrictionListener.java
View file

@ -13,6 +13,7 @@ import edu.cornell.mannlib.vedit.beans.EditProcessObject;
import edu.cornell.mannlib.vedit.listener.ChangeListener;
import edu.cornell.mannlib.vitro.webapp.beans.BaseResourceBean.RoleLevel;
import edu.cornell.mannlib.vitro.webapp.beans.Property;
import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
/**
* Add this ChangeListener to your EditProcessObject when modifying the
@ -90,7 +91,7 @@ public class PropertyRestrictionListener implements ChangeListener {
}
private void createAndSetBean() {
OntModel model = (OntModel) ctx.getAttribute("jenaOntModel");
OntModel model = ModelAccess.on(ctx).getJenaOntModel();
PropertyRestrictionPolicyHelper bean = PropertyRestrictionPolicyHelper
.createBean(model);
PropertyRestrictionPolicyHelper.setBean(ctx, bean);

3
webapp/src/edu/cornell/mannlib/vitro/webapp/auth/policy/bean/PropertyRestrictionPolicyHelper.java
View file

@ -26,6 +26,7 @@ import com.hp.hpl.jena.rdf.model.impl.Util;
import com.hp.hpl.jena.shared.Lock;
import edu.cornell.mannlib.vitro.webapp.beans.BaseResourceBean.RoleLevel;
import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
@ -344,7 +345,7 @@ public class PropertyRestrictionPolicyHelper {
StartupStatus ss = StartupStatus.getBean(ctx);
try {
OntModel model = (OntModel) ctx.getAttribute("jenaOntModel");
OntModel model = ModelAccess.on(ctx).getJenaOntModel();
if (model == null) {
throw new NullPointerException(
"jenaOntModel has not been initialized.");

5
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/FedoraDatastreamController.java
View file

@ -42,6 +42,7 @@ import edu.cornell.mannlib.vitro.webapp.beans.Individual;
import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement;
import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
import edu.cornell.mannlib.vitro.webapp.dao.IndividualDao;
import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
import edu.cornell.mannlib.vitro.webapp.filestorage.uploadrequest.FileUploadServletRequest;
@ -101,7 +102,7 @@ public class FedoraDatastreamController extends VitroHttpServlet implements Cons
log.debug("In doGet");
VitroRequest vreq = new VitroRequest(req);
OntModel sessionOntModel = (OntModel)vreq.getSession().getAttribute("jenaOntModel");
OntModel sessionOntModel = ModelAccess.on(vreq.getSession()).getJenaOntModel();
synchronized (FedoraDatastreamController.class) {
if( fedoraUrl == null ){
@ -231,7 +232,7 @@ public class FedoraDatastreamController extends VitroHttpServlet implements Cons
}
//check if fedora is on line
OntModel sessionOntModel = (OntModel)rawRequest.getSession().getAttribute("jenaOntModel");
OntModel sessionOntModel = ModelAccess.on(rawRequest.getSession()).getJenaOntModel();
synchronized (FedoraDatastreamController.class) {
if( fedoraUrl == null ){
setup( sessionOntModel, getServletContext() );

8
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/OntologyController.java
View file

@ -27,6 +27,7 @@ import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.shared.Lock;
import edu.cornell.mannlib.vitro.webapp.beans.ApplicationBean;
import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
import edu.cornell.mannlib.vitro.webapp.utils.jena.JenaOutputUtils;
import edu.cornell.mannlib.vitro.webapp.web.ContentType;
@ -127,12 +128,7 @@ public class OntologyController extends VitroHttpServlet{
String url = ontology;
OntModel ontModel = null;
HttpSession session = vreq.getSession(false);
if( session != null )
ontModel =(OntModel)session.getAttribute("jenaOntModel");
if( ontModel == null)
ontModel = (OntModel)getServletContext().getAttribute("jenaOntModel");
OntModel ontModel = ModelAccess.on(vreq.getSession()).getJenaOntModel();
boolean found = false;
Model newModel = ModelFactory.createDefaultModel();

29
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/VitroRequest.java
View file

@ -2,7 +2,6 @@
package edu.cornell.mannlib.vitro.webapp.controller;
import static edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary.DISPLAY_ONT_MODEL;
import java.util.Map;
@ -17,6 +16,8 @@ import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.query.Dataset;
import edu.cornell.mannlib.vitro.webapp.beans.ApplicationBean;
import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess.ModelID;
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.OntModelSelector;
@ -107,7 +108,7 @@ public class VitroRequest extends HttpServletRequestWrapper {
}
public void setJenaOntModel(OntModel ontModel) {
setAttribute("jenaOntModel", ontModel);
ModelAccess.on(this).setJenaOntModel(ontModel);
}
public void setOntModelSelector(OntModelSelector oms) {
@ -176,15 +177,7 @@ public class VitroRequest extends HttpServletRequestWrapper {
public OntModel getJenaOntModel() {
Object ontModel = getAttribute("jenaOntModel");
if (ontModel instanceof OntModel) {
return (OntModel) ontModel;
}
OntModel jenaOntModel = (OntModel)_req.getSession().getAttribute( JenaBaseDao.JENA_ONT_MODEL_ATTRIBUTE_NAME );
if ( jenaOntModel == null ) {
jenaOntModel = (OntModel)_req.getSession().getServletContext().getAttribute( JenaBaseDao.JENA_ONT_MODEL_ATTRIBUTE_NAME );
}
return jenaOntModel;
return ModelAccess.on(this).getJenaOntModel();
}
public OntModelSelector getOntModelSelector() {
@ -198,11 +191,7 @@ public class VitroRequest extends HttpServletRequestWrapper {
public OntModel getAssertionsOntModel() {
OntModel jenaOntModel = (OntModel)_req.getSession().getAttribute( JenaBaseDao.ASSERTIONS_ONT_MODEL_ATTRIBUTE_NAME );
if ( jenaOntModel == null ) {
jenaOntModel = (OntModel)_req.getSession().getServletContext().getAttribute( JenaBaseDao.ASSERTIONS_ONT_MODEL_ATTRIBUTE_NAME );
}
return jenaOntModel;
return ModelAccess.on(getSession()).getBaseOntModel();
}
public OntModel getInferenceOntModel() {
@ -215,13 +204,7 @@ public class VitroRequest extends HttpServletRequestWrapper {
//Get the display and editing configuration model
public OntModel getDisplayModel(){
Object value = _req.getAttribute(DISPLAY_ONT_MODEL);
if (value instanceof OntModel) {
return (OntModel) value;
} else {
log.error("No display model on the VitroRequest. Expecting an OntModel but found " + value);
return null;
}
return ModelAccess.on(_req).getDisplayModel();
}
/**

12
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/Authenticate.java
View file

@ -39,6 +39,7 @@ import edu.cornell.mannlib.vitro.webapp.controller.authenticate.LoginRedirector;
import edu.cornell.mannlib.vitro.webapp.controller.login.LoginProcessBean;
import edu.cornell.mannlib.vitro.webapp.controller.login.LoginProcessBean.Message;
import edu.cornell.mannlib.vitro.webapp.controller.login.LoginProcessBean.State;
import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
import edu.cornell.mannlib.vitro.webapp.dao.jena.LoginLogoutEvent;
public class Authenticate extends VitroHttpServlet {
@ -557,16 +558,7 @@ public class Authenticate extends VitroHttpServlet {
return;
}
OntModel jenaOntModel = (OntModel) session.getAttribute("jenaOntModel");
if (jenaOntModel == null) {
jenaOntModel = (OntModel) context.getAttribute("jenaOntModel");
}
if (jenaOntModel == null) {
log.error("Unable to notify audit model of login event "
+ "because no model could be found");
return;
}
OntModel jenaOntModel = ModelAccess.on(session).getJenaOntModel();
jenaOntModel.getBaseModel().notifyEvent(event);
}

3
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/NamespacePrefixOperationController.java
View file

@ -24,6 +24,7 @@ import edu.cornell.mannlib.vedit.beans.EditProcessObject;
import edu.cornell.mannlib.vedit.controller.BaseEditController;
import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
public class NamespacePrefixOperationController extends BaseEditController {
@ -68,7 +69,7 @@ public class NamespacePrefixOperationController extends BaseEditController {
if (request.getParameter("_cancel") == null) {
OntModel ontModel = (OntModel) getServletContext().getAttribute("jenaOntModel");
OntModel ontModel = ModelAccess.on(getServletContext()).getJenaOntModel();
String namespaceStr = request.getParameter("namespace");
String prefixStr = request.getParameter("prefix");

9
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/RefactorOperationController.java
View file

@ -7,7 +7,6 @@ import java.io.UnsupportedEncodingException;
import java.net.URLEncoder;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import javax.servlet.RequestDispatcher;
import javax.servlet.http.HttpServletRequest;
@ -40,7 +39,6 @@ import com.hp.hpl.jena.rdf.model.StmtIterator;
import com.hp.hpl.jena.shared.InvalidPropertyURIException;
import com.hp.hpl.jena.shared.Lock;
import com.hp.hpl.jena.util.ResourceUtils;
import com.hp.hpl.jena.util.iterator.ClosableIterator;
import com.hp.hpl.jena.util.iterator.ExtendedIterator;
import com.hp.hpl.jena.vocabulary.RDF;
@ -50,6 +48,7 @@ import edu.cornell.mannlib.vedit.controller.BaseEditController;
import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission;
import edu.cornell.mannlib.vitro.webapp.controller.Controllers;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
import edu.cornell.mannlib.vitro.webapp.dao.jena.event.EditEvent;
import edu.cornell.mannlib.vitro.webapp.servlet.setup.FileGraphSetup;
@ -74,7 +73,7 @@ public class RefactorOperationController extends BaseEditController {
request.setAttribute("title","Check Datatype Properties");
request.setAttribute("css", "<link rel=\"stylesheet\" type=\"text/css\" href=\""+vreq.getAppBean().getThemeDir()+"css/edit.css\"/>");
OntModel ontModel = (OntModel) getServletContext().getAttribute("baseOntModel");
OntModel ontModel = ModelAccess.on(getServletContext()).getBaseOntModel();
ontModel.enterCriticalSection(Lock.WRITE);
ArrayList<String> results = new ArrayList<String>();
@ -330,7 +329,7 @@ public class RefactorOperationController extends BaseEditController {
private void doMovePropertyStatements(VitroRequest request, HttpServletResponse response, EditProcessObject epo) {
String userURI = LoginStatusBean.getBean(request).getUserURI();
OntModel ontModel = ModelContext.getBaseOntModel(getServletContext());
OntModel ontModel = ModelAccess.on(getServletContext()).getBaseOntModel();
Model tempRetractModel = ModelFactory.createDefaultModel();
Model tempAddModel = ModelFactory.createDefaultModel();
@ -414,7 +413,7 @@ public class RefactorOperationController extends BaseEditController {
private void doMoveInstances(VitroRequest request, HttpServletResponse response, EditProcessObject epo) {
String userURI = LoginStatusBean.getBean(request).getUserURI();
OntModel ontModel = ModelContext.getBaseOntModel(getServletContext());
OntModel ontModel = ModelAccess.on(getServletContext()).getBaseOntModel();
String oldClassURIStr = (String) epo.getAttribute("VClassURI");
String newClassURIStr = (String) request.getParameter("NewVClassURI");

3
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/listing/jena/NamespacesListingController.java
View file

@ -22,6 +22,7 @@ import edu.cornell.mannlib.vedit.controller.BaseEditController;
import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission;
import edu.cornell.mannlib.vitro.webapp.controller.Controllers;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
public class NamespacesListingController extends BaseEditController {
@ -34,7 +35,7 @@ public class NamespacesListingController extends BaseEditController {
VitroRequest vrequest = new VitroRequest(request);
OntModel ontModel = (OntModel) getServletContext().getAttribute("jenaOntModel");
OntModel ontModel = ModelAccess.on(getServletContext()).getJenaOntModel();
ArrayList results = new ArrayList();
request.setAttribute("results",results);

5
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/listing/jena/RestrictionsListingController.java
View file

@ -33,6 +33,7 @@ import edu.cornell.mannlib.vitro.webapp.beans.VClass;
import edu.cornell.mannlib.vitro.webapp.controller.Controllers;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.IndividualDao;
import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
import edu.cornell.mannlib.vitro.webapp.dao.ObjectPropertyDao;
import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
@ -51,8 +52,8 @@ public class RestrictionsListingController extends BaseEditController {
epo = super.createEpo(request);
OntModel ontModel = (OntModel) getServletContext().getAttribute("jenaOntModel");
OntModel ontModel = ModelAccess.on(getServletContext()).getJenaOntModel();
ObjectPropertyDao opDao = vrequest.getFullWebappDaoFactory().getObjectPropertyDao();
VClassDao vcDao = vrequest.getFullWebappDaoFactory().getVClassDao();
IndividualDao iDao = vrequest.getFullWebappDaoFactory().getIndividualDao();

19
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/jena/JenaAdminActions.java
View file

@ -47,6 +47,7 @@ import com.hp.hpl.jena.vocabulary.RDFS;
import edu.cornell.mannlib.vedit.controller.BaseEditController;
import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
public class JenaAdminActions extends BaseEditController {
@ -93,7 +94,7 @@ public class JenaAdminActions extends BaseEditController {
* @param response
*/
private void outputTbox(HttpServletResponse response) {
OntModel memoryModel = (OntModel) getServletContext().getAttribute("baseOntModel");
OntModel memoryModel = ModelAccess.on(getServletContext()).getBaseOntModel();
try {
OntModel tempOntModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_DL_MEM);
Property DescriptionProp = ResourceFactory.createProperty(VitroVocabulary.DESCRIPTION_ANNOT);
@ -171,7 +172,7 @@ public class JenaAdminActions extends BaseEditController {
private String testWriteXML() {
StringBuffer output = new StringBuffer();
output.append("<html><head><title>Test Write XML</title></head><body><pre>\n");
Model model = (Model) getServletContext().getAttribute("jenaOntModel");
OntModel model = ModelAccess.on(getServletContext()).getJenaOntModel();
Model tmp = ModelFactory.createDefaultModel();
boolean valid = true;
for (Statement stmt : ((List<Statement>)model.listStatements().toList()) ) {
@ -230,7 +231,7 @@ public class JenaAdminActions extends BaseEditController {
}
private void removeLongLiterals() {
OntModel memoryModel = (OntModel) getServletContext().getAttribute("jenaOntModel");
OntModel memoryModel = ModelAccess.on(getServletContext()).getJenaOntModel();
memoryModel.enterCriticalSection(Lock.WRITE);
try {
List<Statement> statementsToRemove = new LinkedList<Statement>();
@ -273,7 +274,7 @@ public class JenaAdminActions extends BaseEditController {
}
if (actionStr.equals("checkURIs")) {
OntModel memoryModel = (OntModel) getServletContext().getAttribute("jenaOntModel");
OntModel memoryModel = ModelAccess.on(getServletContext()).getJenaOntModel();
ClosableIterator stmtIt = memoryModel.listStatements();
try {
for (Iterator i = stmtIt; i.hasNext(); ) {
@ -305,7 +306,7 @@ public class JenaAdminActions extends BaseEditController {
if (actionStr.equals("output")) {
OntModel memoryModel = null;
if (request.getParameter("assertionsOnly") != null) {
memoryModel = (OntModel) getServletContext().getAttribute("baseOntModel");
memoryModel = ModelAccess.on(getServletContext()).getBaseOntModel();
System.out.println("baseOntModel");
} else if (request.getParameter("inferences") != null) {
memoryModel = (OntModel) getServletContext().getAttribute("inferenceOntModel");
@ -314,7 +315,7 @@ public class JenaAdminActions extends BaseEditController {
memoryModel = (OntModel) getServletContext().getAttribute("pelletOntModel");
System.out.println("pelletOntModel");
} else {
memoryModel = (OntModel) getServletContext().getAttribute("jenaOntModel");
memoryModel = ModelAccess.on(getServletContext()).getJenaOntModel();
System.out.println("jenaOntModel");
}
int subModelCount = 0;
@ -340,7 +341,7 @@ public class JenaAdminActions extends BaseEditController {
}
if (actionStr.equals("isIsomorphic")) {
OntModel memoryModel = (OntModel) getServletContext().getAttribute("jenaOntModel");
OntModel memoryModel = ModelAccess.on(getServletContext()).getJenaOntModel();
OntModel persistentModel = (OntModel) getServletContext().getAttribute("jenaPersistentOntModel");
if ((memoryModel != null) && (persistentModel != null)) {
long startTime = System.currentTimeMillis();
@ -363,7 +364,7 @@ public class JenaAdminActions extends BaseEditController {
log.trace((System.currentTimeMillis()-startTime)/1000+" seconds to check isomorphism");
}
} else if (actionStr.equals("removeUntypedResources")) {
OntModel memoryModel = (OntModel) getServletContext().getAttribute("jenaOntModel");
OntModel memoryModel = ModelAccess.on(getServletContext()).getJenaOntModel();
OntModel persistentModel = (OntModel) getServletContext().getAttribute("jenaPersistentOntModel");
ClosableIterator rIt = memoryModel.listSubjects();
clean(rIt,memoryModel);
@ -374,7 +375,7 @@ public class JenaAdminActions extends BaseEditController {
ClosableIterator ooIt = persistentModel.listObjects();
clean(oIt,persistentModel);
} else if (actionStr.equals("outputTaxonomy")) {
OntModel ontModel = (OntModel) getServletContext().getAttribute("baseOntModel");
OntModel ontModel = ModelAccess.on(getServletContext()).getBaseOntModel();
Model taxonomyModel = extractTaxonomy(ontModel);
try {
taxonomyModel.write(response.getOutputStream());

2
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/jena/JenaExportController.java
View file

@ -283,8 +283,6 @@ public class JenaExportController extends BaseEditController {
}
}
static final String FULL_ONT_MODEL_ATTR = "jenaOntModel";
static final String ASSERTIONS_ONT_MODEL_ATTR = "baseOntModel";
static final String INFERENCES_ONT_MODEL_ATTR = "inferenceOntModel";
static final String FULL_GRAPH = "?g";
static final String ASSERTIONS_GRAPH = "<http://vitro.mannlib.cornell.edu/default/vitro-kb-2>";

31
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/jena/JenaIngestController.java
View file

@ -67,6 +67,7 @@ import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission;
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.ModelAccess;
import edu.cornell.mannlib.vitro.webapp.dao.OntologyDao;
import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceGraph;
@ -80,7 +81,7 @@ import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase;
import edu.cornell.mannlib.vitro.webapp.servlet.setup.WebappDaoSetup;
import edu.cornell.mannlib.vitro.webapp.servlet.setup.ContentModelSetup;
import edu.cornell.mannlib.vitro.webapp.utils.SparqlQueryUtils;
import edu.cornell.mannlib.vitro.webapp.utils.jena.JenaIngestUtils;
import edu.cornell.mannlib.vitro.webapp.utils.jena.JenaIngestUtils.MergeResult;
@ -520,7 +521,7 @@ public class JenaIngestController extends BaseEditController {
vreq.setAttribute("title", "Choose Workflow Step");
vreq.setAttribute("bodyJsp", WORKFLOW_STEP_JSP);
} else {
OntModel jenaOntModel = (OntModel) getServletContext().getAttribute("jenaOntModel");
OntModel jenaOntModel = ModelAccess.on(getServletContext()).getJenaOntModel();
jenaOntModel.enterCriticalSection(Lock.READ);
List<Individual> savedQueryList = new LinkedList<Individual>();
try {
@ -537,7 +538,7 @@ public class JenaIngestController extends BaseEditController {
private void processExecuteSparqlRequest(VitroRequest vreq, ModelMaker maker, String modelType) {
String sparqlQueryStr = vreq.getParameter("sparqlQueryStr");
OntModel jenaOntModel = (OntModel) getServletContext().getAttribute("jenaOntModel");
OntModel jenaOntModel = ModelAccess.on(getServletContext()).getJenaOntModel();
jenaOntModel.enterCriticalSection(Lock.READ);
List<Individual> savedQueryList = new LinkedList<Individual>();
try {
@ -660,8 +661,7 @@ public class JenaIngestController extends BaseEditController {
/*
* get baseOnt and infOnt models
*/
OntModel baseOntModel = ModelContext.getBaseOntModel(
getServletContext());
OntModel baseOntModel = ModelAccess.on(getServletContext()).getBaseOntModel();
OntModel tboxOntModel = ModelContext.getUnionOntModelSelector(
getServletContext()).getTBoxModel();
@ -910,7 +910,7 @@ public class JenaIngestController extends BaseEditController {
}
private long doExecuteSparql(VitroRequest vreq) {
OntModel jenaOntModel = (OntModel) getServletContext().getAttribute("jenaOntModel");
OntModel jenaOntModel = ModelAccess.on(getServletContext()).getJenaOntModel();
OntModel source = null;
if ("pellet".equals(vreq.getParameter("reasoning"))) {
source = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
@ -984,7 +984,7 @@ public class JenaIngestController extends BaseEditController {
log.debug("Connecting to DB at "+jdbcUrl);
StoreDesc storeDesc = new StoreDesc(LayoutType.LayoutTripleNodesHash,dbTypeObj) ;
ServletContext ctx = vreq.getSession().getServletContext();
DataSource bds = WebappDaoSetup.makeBasicDataSource(
DataSource bds = ContentModelSetup.makeBasicDataSource(
driver, jdbcUrl, username, password, ctx);
try {
VitroJenaSDBModelMaker vsmm = new VitroJenaSDBModelMaker(storeDesc, bds);
@ -1193,8 +1193,7 @@ public class JenaIngestController extends BaseEditController {
Model baseOntModel = RDFServiceGraph.createRDFServiceModel
(new RDFServiceGraph(
rdfService, JenaDataSourceSetupBase.JENA_DB_MODEL));
OntModel ontModel = (OntModel)
getServletContext().getAttribute("jenaOntModel");
OntModel ontModel = ModelAccess.on(getServletContext()).getJenaOntModel();
List<String> urisToChange = new LinkedList<String>();
ontModel.enterCriticalSection(Lock.READ);
try {
@ -1312,19 +1311,9 @@ public class JenaIngestController extends BaseEditController {
public static Model getModel(String name, HttpServletRequest request, ServletContext context) {
if ("vitro:jenaOntModel".equals(name)) {
Object sessionOntModel = request.getSession().getAttribute("jenaOntModel");
if (sessionOntModel != null && sessionOntModel instanceof OntModel) {
return (OntModel) sessionOntModel;
} else {
return (OntModel) context.getAttribute("jenaOntModel");
}
return ModelAccess.on(request.getSession()).getJenaOntModel();
} else if ("vitro:baseOntModel".equals(name)) {
Object sessionOntModel = request.getSession().getAttribute("baseOntModel");
if (sessionOntModel != null && sessionOntModel instanceof OntModel) {
return (OntModel) sessionOntModel;
} else {
return (OntModel) context.getAttribute("baseOntModel");
}
return ModelAccess.on(request.getSession()).getBaseOntModel();
} else if ("vitro:inferenceOntModel".equals(name)) {
Object sessionOntModel = request.getSession().getAttribute("inferenceOntModel");
if (sessionOntModel != null && sessionOntModel instanceof OntModel) {

3
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/DisplayVocabulary.java
View file

@ -119,9 +119,6 @@ public class DisplayVocabulary {
public static final String CONTEXT_DISPLAY_TBOX = "displayOntModelTBOX";
public static final String CONTEXT_DISPLAY_DISPLAY = "displayOntModelDisplayModel";
/** Key for display model in request, session or context attributes */
public static final String DISPLAY_ONT_MODEL = "displayOntModel";
//URL for menu management
public static final String PROCESS_MENU_MANAGEMENT_URL = "/menuManagementEdit";
public static final String REORDER_MENU_URL = PROCESS_MENU_MANAGEMENT_URL + "?cmd=Reorder&" + SWITCH_TO_DISPLAY_MODEL + "=true";

301
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/ModelAccess.java Normal file
View file

@ -0,0 +1,301 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
package edu.cornell.mannlib.vitro.webapp.dao;
import java.util.HashMap;
import java.util.Map;
import javax.servlet.ServletContext;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpSession;
import com.hp.hpl.jena.ontology.OntModel;
/**
* Hierarchical storage for models. TODO
*/
public class ModelAccess {
/** These attributes should only be accessed through this class. */
private static final String ATTRIBUTE_NAME = ModelAccess.class.getName();
public enum ModelID {
APPLICATION_METADATA,
USER_ACCOUNTS,
DISPLAY, DISPLAY_DISPLAY, DISPLAY_TBOX,
BASE_ABOX, BASE_TBOX, BASE_FULL,
INFERRED_ABOX, INFERRED_TBOX, INFERRED_FULL,
UNION_ABOX, UNION_TBOX, UNION_FULL
}
// ----------------------------------------------------------------------
// Factory methods
// ----------------------------------------------------------------------
public static ModelAccess on(HttpServletRequest req) {
Object o = req.getAttribute(ATTRIBUTE_NAME);
if (o instanceof ModelAccess) {
return (ModelAccess) o;
} else {
ModelAccess parent = on(req.getSession());
ModelAccess ma = new ModelAccess(parent);
req.setAttribute(ATTRIBUTE_NAME, ma);
return ma;
}
}
public static ModelAccess on(HttpSession session) {
Object o = session.getAttribute(ATTRIBUTE_NAME);
if (o instanceof ModelAccess) {
return (ModelAccess) o;
} else {
ModelAccess parent = on(session.getServletContext());
ModelAccess ma = new ModelAccess(parent);
session.setAttribute(ATTRIBUTE_NAME, ma);
return ma;
}
}
public static ModelAccess on(ServletContext ctx) {
Object o = ctx.getAttribute(ATTRIBUTE_NAME);
if (o instanceof ModelAccess) {
return (ModelAccess) o;
} else {
ModelAccess ma = new ModelAccess(null);
ctx.setAttribute(ATTRIBUTE_NAME, ma);
return ma;
}
}
// ----------------------------------------------------------------------
// Instance methods
// ----------------------------------------------------------------------
private final ModelAccess parent;
private final Map<String, OntModel> modelMap = new HashMap<>();
public ModelAccess(ModelAccess parent) {
this.parent = parent;
}
public void setUserAccountsModel(OntModel m) {
setOntModel(ModelID.USER_ACCOUNTS, m);
}
public OntModel getUserAccountsModel() {
return getOntModel(ModelID.USER_ACCOUNTS);
}
public void setDisplayModel(OntModel m) {
setOntModel(ModelID.DISPLAY, m);
}
public OntModel getDisplayModel() {
return getOntModel(ModelID.DISPLAY);
}
public void setJenaOntModel(OntModel m) {
setOntModel(ModelID.UNION_FULL, m);
}
public OntModel getJenaOntModel() {
return getOntModel(ModelID.UNION_FULL);
}
public void setBaseOntModel(OntModel m) {
setOntModel(ModelID.BASE_FULL, m);
}
public OntModel getBaseOntModel() {
return getOntModel(ModelID.BASE_FULL);
}
// public OntModel getDisplayTboxOntModel() {
// throw new RuntimeException(
// "ModelAccess.getDisplayTboxOntModel not implemented.");
// }
//
// public OntModel getDisplayModelDisplayOntModel() {
// throw new RuntimeException(
// "ModelAccess.getDisplayModelDisplayOntModel not implemented.");
// }
//
// public OntModelSelector getOntModelSelector() {
// return getUnionOntModelSelector();
// }
//
// public OntModelSelector getBaseOntModelSelector() {
// return new FacadeOntModelSelector(this, ModelID.BASE_ABOX,
// ModelID.BASE_TBOX, ModelID.BASE_FULL);
// }
//
// public OntModelSelector getInferenceOntModelSelector() {
// return new FacadeOntModelSelector(this, ModelID.INFERRED_ABOX,
// ModelID.INFERRED_TBOX, ModelID.INFERRED_FULL);
// }
//
// public OntModelSelector getUnionOntModelSelector() {
// return new FacadeOntModelSelector(this, ModelID.UNION_ABOX,
// ModelID.UNION_TBOX, ModelID.UNION_FULL);
// }
//
// private static class FacadeOntModelSelector implements OntModelSelector {
// private final ModelAccess parent;
// private final ModelID aboxID;
// private final ModelID tboxID;
// private final ModelID fullID;
//
// public FacadeOntModelSelector(ModelAccess parent, ModelID aboxID,
// ModelID tboxID, ModelID fullID) {
// this.parent = parent;
// this.aboxID = aboxID;
// this.tboxID = tboxID;
// this.fullID = fullID;
// }
//
// @Override
// public OntModel getABoxModel() {
// return parent.getOntModel(aboxID);
// }
//
// @Override
// public OntModel getTBoxModel() {
// return parent.getOntModel(tboxID);
// }
//
// @Override
// public OntModel getTBoxModel(String ontologyURI) {
// return parent.getOntModel(tboxID);
// }
//
// @Override
// public OntModel getFullModel() {
// return parent.getOntModel(fullID);
// }
//
// @Override
// public OntModel getApplicationMetadataModel() {
// return parent.getOntModel(ModelID.APPLICATION_METADATA);
// }
//
// @Override
// public OntModel getUserAccountsModel() {
// return parent.getOntModel(ModelID.USER_ACCOUNTS);
// }
//
// @Override
// public OntModel getDisplayModel() {
// return parent.getOntModel(ModelID.DISPLAY);
// }
// }
/**
* <pre>
* From ModelContext
*
* public static OntModelSelector getOntModelSelector(ServletContext ctx) {
* return (OntModelSelector) ctx.getAttribute(ONT_MODEL_SELECTOR);
* }
*
* public static void setOntModelSelector(OntModelSelector oms, ServletContext ctx) {
* ctx.setAttribute(ONT_MODEL_SELECTOR, oms);
* }
*
* public static OntModelSelector getUnionOntModelSelector(ServletContext ctx) {
* return (OntModelSelector) ctx.getAttribute(UNION_ONT_MODEL_SELECTOR);
* }
*
* public static void setUnionOntModelSelector(OntModelSelector oms, ServletContext ctx) {
* ctx.setAttribute(UNION_ONT_MODEL_SELECTOR, oms);
* }
*
* public static OntModelSelector getBaseOntModelSelector(ServletContext ctx) {
* return (OntModelSelector) ctx.getAttribute(BASE_ONT_MODEL_SELECTOR);
* }
*
* public static void setBaseOntModelSelector(OntModelSelector oms, ServletContext ctx) {
* ctx.setAttribute(BASE_ONT_MODEL_SELECTOR, oms);
* }
*
* public static OntModelSelector getInferenceOntModelSelector(ServletContext ctx) {
* return (OntModelSelector) ctx.getAttribute(INFERENCE_ONT_MODEL_SELECTOR);
* }
*
* public static void setInferenceOntModelSelector(OntModelSelector oms, ServletContext ctx) {
* ctx.setAttribute(INFERENCE_ONT_MODEL_SELECTOR, oms);
* }
*
* public static OntModel getInferenceOntModel(ServletContext ctx) {
* return (OntModel) ctx.getAttribute(INFERENCE_ONT_MODEL);
* }
*
* public static void setInferenceOntModel(OntModel ontModel, ServletContext ctx) {
* ctx.setAttribute(INFERENCE_ONT_MODEL, ontModel);
* }
*
* </pre>
*/
/**
* <pre>
* VitroRequest.getAssertionsWebappDaoFactory()
* VitroRequest.getDeductionsWebappDaoFactory()
* VitroRequest.getFullWebappDaoFactory()
* VitroRequest.getRDFService()
* VitroRequest.getUnfilteredRDFService()
* VitroRequest.getWebappDaoFactory()
* VitroRequest.getWriteModel()
* VitroRequest.getJenaOntModel()
* VitroRequest.setJenaOntModel()
* ModelContext.getBaseOntModelSelector()
* ModelContext.getInferenceOntModel()
* ModelContext.getInferenceOntModelSelector()
* ModelContext.getOntModelSelector()
* ModelContext.getUnionOntModelSelector()
* OntModelSelector.getAboxModel
* OntModelSelector.getApplicationMetadataModel()
* OntModelSelector.getFullModel()
* OntModelSelector.getTBoxModel()
* OntModelSelector.getTBoxModel(ontologyURI)
* OntModelSelector.getUserAccountsModel()
* VitroModelSource.getModel(URL)
* VitroModelSource.getModel(URL, loadIfAbsent)
* VitroModelSource.openModel(name)
* VitroModelSource.openModelIfPresent(string)
* ServletContext.getAttribute("assertionsWebappDaoFactory")
* ServletContext.getAttribute("baseOntModelSelector")
* ServletContext.getAttribute("jenaPersistentOntModel")
* ServletContext.getAttribute("pelletOntModel")
* ServletContext.getAttribute("webappDaoFactory")
* VitroJenaModelMaker
* VitroJenaSpecialModelMaker
* JenaDataSourceSetupBase.getApplicationDataSource(ctx)
* JenaDataSourceSetupBase.getStartupDataset()
* HttpSession.getAttribute("jenaAuditModel")
* </pre>
*/
public void setOntModel(ModelID id, OntModel ontModel) {
String key = id.toString();
if (ontModel == null) {
modelMap.remove(key);
} else {
modelMap.put(key, ontModel);
}
}
public OntModel getOntModel(ModelID id) {
String key = id.toString();
if (modelMap.containsKey(key)) {
return modelMap.get(key);
} else if (parent != null) {
return parent.getOntModel(id);
} else {
return null;
}
}
}

2
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/JenaBaseDao.java
View file

@ -54,8 +54,6 @@ public class JenaBaseDao extends JenaBaseDaoCon {
public static final boolean KEEP_ONLY_IF_TRUE = true; //used for updatePropertyBooleanValue()
public static final boolean KEEP_ONLY_IF_FALSE = false; //used for updatePropertyBooleanValue()
public static final String JENA_ONT_MODEL_ATTRIBUTE_NAME = "jenaOntModel";
public static final String ASSERTIONS_ONT_MODEL_ATTRIBUTE_NAME = "baseOntModel";
public static final String INFERENCE_ONT_MODEL_ATTRIBUTE_NAME = "inferenceOntModel";
protected static final Log log = LogFactory.getLog(JenaBaseDao.class.getName());

25
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/ModelContext.java
View file

@ -10,7 +10,6 @@ import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.rdf.model.ModelChangedListener;
import edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
@ -23,8 +22,6 @@ public class ModelContext {
private static final String BASE_ONT_MODEL_SELECTOR = "baseOntModelSelector";
private static final String INFERENCE_ONT_MODEL_SELECTOR = "inferenceOntModelSelector";
private static final String JENA_ONT_MODEL = "jenaOntModel";
private static final String BASE_ONT_MODEL = "baseOntModel";
private static final String INFERENCE_ONT_MODEL = "inferenceOntModel";
public ModelContext() {}
@ -61,22 +58,6 @@ public class ModelContext {
ctx.setAttribute(INFERENCE_ONT_MODEL_SELECTOR, oms);
}
public static OntModel getJenaOntModel(ServletContext ctx) {
return (OntModel) ctx.getAttribute(JENA_ONT_MODEL);
}
public static void setJenaOntModel(OntModel ontModel, ServletContext ctx) {
ctx.setAttribute(JENA_ONT_MODEL, ontModel);
}
public static OntModel getBaseOntModel(ServletContext ctx) {
return (OntModel) ctx.getAttribute(BASE_ONT_MODEL);
}
public static void setBaseOntModel(OntModel ontModel, ServletContext ctx) {
ctx.setAttribute(BASE_ONT_MODEL, ontModel);
}
public static OntModel getInferenceOntModel(ServletContext ctx) {
return (OntModel) ctx.getAttribute(INFERENCE_ONT_MODEL);
}
@ -113,10 +94,4 @@ public class ModelContext {
}
public static OntModel getDisplayModel(ServletContext ctx){
return(OntModel) ctx.getAttribute( DisplayVocabulary.DISPLAY_ONT_MODEL );
}
public static void setDisplayModel(OntModel ontModel, ServletContext ctx){
ctx.setAttribute(DisplayVocabulary.DISPLAY_ONT_MODEL,ontModel);
}
}

3
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/VClassGroupCache.java
View file

@ -31,6 +31,7 @@ import com.hp.hpl.jena.vocabulary.RDFS;
import edu.cornell.mannlib.vitro.webapp.beans.VClass;
import edu.cornell.mannlib.vitro.webapp.beans.VClassGroup;
import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
import edu.cornell.mannlib.vitro.webapp.dao.VClassGroupDao;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
@ -494,7 +495,7 @@ public class VClassGroupCache implements IndexingEventListener {
} else if(VitroVocabulary.DISPLAY_RANK.equals(stmt.getPredicate().getURI())){
requestCacheUpdate();
} else {
OntModel jenaOntModel = ModelContext.getJenaOntModel(context);
OntModel jenaOntModel = ModelAccess.on(context).getJenaOntModel();
if( isClassNameChange(stmt, jenaOntModel) ) {
requestCacheUpdate();
}

17
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/VitroJenaModelMaker.java
View file

@ -27,6 +27,7 @@ import com.hp.hpl.jena.util.iterator.ExtendedIterator;
import com.hp.hpl.jena.util.iterator.WrappedIterator;
import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase;
/**
@ -311,21 +312,9 @@ public class VitroJenaModelMaker implements ModelMaker {
private Model getSpecialModel(String modelName) {
if (request != null) {
if ("vitro:jenaOntModel".equals(modelName)) {
Object sessionOntModel = request.getSession().getAttribute("jenaOntModel");
if (sessionOntModel != null && sessionOntModel instanceof OntModel) {
log.debug("Returning jenaOntModel from session");
return (OntModel) sessionOntModel;
} else {
log.debug("Returning jenaOntModel from context");
return (OntModel) request.getSession().getServletContext().getAttribute("jenaOntModel");
}
return ModelAccess.on(request.getSession()).getJenaOntModel();
} else if ("vitro:baseOntModel".equals(modelName)) {
Object sessionOntModel = request.getSession().getAttribute("baseOntModel");
if (sessionOntModel != null && sessionOntModel instanceof OntModel) {
return (OntModel) sessionOntModel;
} else {
return (OntModel) request.getSession().getServletContext().getAttribute("baseOntModel");
}
return ModelAccess.on(request.getSession()).getBaseOntModel();
} else if ("vitro:inferenceOntModel".equals(modelName)) {
Object sessionOntModel = request.getSession().getAttribute("inferenceOntModel");
if (sessionOntModel != null && sessionOntModel instanceof OntModel) {

18
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/VitroJenaSpecialModelMaker.java
View file

@ -14,6 +14,8 @@ import com.hp.hpl.jena.rdf.model.ModelMaker;
import com.hp.hpl.jena.rdf.model.ModelReader;
import com.hp.hpl.jena.util.iterator.ExtendedIterator;
import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
/**
* Wraps a model maker and returns Models from the servlet context when
* certain model URIs are requested
@ -115,21 +117,9 @@ public class VitroJenaSpecialModelMaker implements ModelMaker {
private Model getSpecialModel(String modelName) {
if (request != null) {
if ("vitro:jenaOntModel".equals(modelName)) {
Object sessionOntModel = request.getSession().getAttribute("jenaOntModel");
if (sessionOntModel != null && sessionOntModel instanceof OntModel) {
log.debug("Returning jenaOntModel from session");
return (OntModel) sessionOntModel;
} else {
log.debug("Returning jenaOntModel from context");
return (OntModel) request.getSession().getServletContext().getAttribute("jenaOntModel");
}
return ModelAccess.on(request.getSession()).getJenaOntModel();
} else if ("vitro:baseOntModel".equals(modelName)) {
Object sessionOntModel = request.getSession().getAttribute("baseOntModel");
if (sessionOntModel != null && sessionOntModel instanceof OntModel) {
return (OntModel) sessionOntModel;
} else {
return (OntModel) request.getSession().getServletContext().getAttribute("baseOntModel");
}
return ModelAccess.on(request.getSession()).getBaseOntModel();
} else if ("vitro:inferenceOntModel".equals(modelName)) {
Object sessionOntModel = request.getSession().getAttribute("inferenceOntModel");
if (sessionOntModel != null && sessionOntModel instanceof OntModel) {

5
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/VitroModelSource.java
View file

@ -10,6 +10,7 @@ import com.hp.hpl.jena.rdf.model.ModelReader;
import com.hp.hpl.jena.rdf.model.ModelSource;
import edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary;
import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
/**
* ModelSource that will handle specially named Vitro models such
@ -106,11 +107,11 @@ public class VitroModelSource implements ModelSource {
private Model getNamedModel( ModelName pmn ){
switch( pmn ){
case ABOX:
return (Model) context.getAttribute("jenaOntModel");
return ModelAccess.on(context).getJenaOntModel();
case TBOX:
return (Model) context.getAttribute("tboxmodel???");
case DISPLAY:
return (Model) context.getAttribute(DisplayVocabulary.DISPLAY_ONT_MODEL );
return ModelAccess.on(context).getDisplayModel();
case DISPLAY_TBOX:
return (Model) context.getAttribute(DisplayVocabulary.CONTEXT_DISPLAY_TBOX);
case DISPLAY_DISPLAY:

5
webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/VTwo/EditConfigurationUtils.java
View file

@ -14,8 +14,8 @@ import javax.servlet.http.HttpSession;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.rdf.model.Model;
import edu.cornell.mannlib.vitro.webapp.beans.DataProperty;
import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatement;
@ -23,6 +23,7 @@ import edu.cornell.mannlib.vitro.webapp.beans.Individual;
import edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.FreemarkerConfigurationLoader;
import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.fields.FieldVTwo;
@ -189,7 +190,7 @@ public class EditConfigurationUtils {
public static DataPropertyStatement getDataPropertyStatement(VitroRequest vreq, HttpSession session, Integer dataHash, String predicateUri) {
DataPropertyStatement dps = null;
if( dataHash != 0) {
Model model = (Model)session.getServletContext().getAttribute("jenaOntModel");
OntModel model = ModelAccess.on(session.getServletContext()).getJenaOntModel();
dps = RdfLiteralHash.getPropertyStmtByHash(EditConfigurationUtils.getSubjectUri(vreq), predicateUri, dataHash, model);
}
return dps;

8
webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/BaseEditConfigurationGenerator.java
View file

@ -4,8 +4,6 @@ package edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.generators
import java.util.ArrayList;
import java.util.List;
import javax.servlet.ServletContext;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpSession;
import org.apache.commons.lang.StringUtils;
@ -13,13 +11,11 @@ import org.apache.commons.lang.StringUtils;
import com.hp.hpl.jena.ontology.OntModel;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary;
import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationUtils;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationVTwo;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.IdModelSelector;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.ModelSelector;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.StandardModelSelector;
import edu.cornell.mannlib.vitro.webapp.filters.VitroRequestPrep;
public abstract class BaseEditConfigurationGenerator implements EditConfigurationGenerator {
@ -66,7 +62,7 @@ public abstract class BaseEditConfigurationGenerator implements EditConfiguratio
//setup the model selectors for query, write and display models on editConfig
setupModelSelectorsFromVitroRequest(vreq, editConfig);
OntModel queryModel = vreq.getJenaOntModel(); // (OntModel)vreq.getAttribute("jenaOntModel");
OntModel queryModel = ModelAccess.on(vreq).getJenaOntModel();
if( editConfig.getSubjectUri() == null)
editConfig.setSubjectUri( EditConfigurationUtils.getSubjectUri(vreq));

4
webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/DefaultAddMissingIndividualFormGenerator.java
View file

@ -14,6 +14,7 @@ import org.apache.commons.lang.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.rdf.model.Model;
@ -21,6 +22,7 @@ import edu.cornell.mannlib.vitro.webapp.beans.Individual;
import edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty;
import edu.cornell.mannlib.vitro.webapp.beans.VClass;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationUtils;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationVTwo;
@ -350,7 +352,7 @@ public class DefaultAddMissingIndividualFormGenerator implements EditConfigurati
private void prepareForUpdate(VitroRequest vreq, HttpSession session, EditConfigurationVTwo editConfiguration) {
//Here, retrieve model from
Model model = (Model) session.getServletContext().getAttribute("jenaOntModel");
OntModel model = ModelAccess.on(session.getServletContext()).getJenaOntModel();
//if object property
if(EditConfigurationUtils.isObjectProperty(EditConfigurationUtils.getPredicateUri(vreq), vreq)){
Individual objectIndividual = EditConfigurationUtils.getObjectIndividual(vreq);

18
webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/DefaultObjectPropertyFormGenerator.java
View file

@ -31,6 +31,7 @@ import edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty;
import edu.cornell.mannlib.vitro.webapp.beans.VClass;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary;
import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationUtils;
@ -377,7 +378,7 @@ public class DefaultObjectPropertyFormGenerator implements EditConfigurationGene
private void prepareForUpdate(VitroRequest vreq, HttpSession session, EditConfigurationVTwo editConfiguration) {
//Here, retrieve model from
Model model = (Model) session.getServletContext().getAttribute("jenaOntModel");
OntModel model = ModelAccess.on(session.getServletContext()).getJenaOntModel();
//if object property
if(EditConfigurationUtils.isObjectProperty(EditConfigurationUtils.getPredicateUri(vreq), vreq)){
Individual objectIndividual = EditConfigurationUtils.getObjectIndividual(vreq);
@ -408,16 +409,11 @@ public class DefaultObjectPropertyFormGenerator implements EditConfigurationGene
if(isSelectFromExisting(vreq)) {
// set ProhibitedFromSearch object so picklist doesn't show
// individuals from classes that should be hidden from list views
//TODO: Check how model is retrieved
OntModel displayOntModel =
(OntModel) session.getServletContext()
.getAttribute(DISPLAY_ONT_MODEL);
if (displayOntModel != null) {
ProhibitedFromSearch pfs = new ProhibitedFromSearch(
DisplayVocabulary.SEARCH_INDEX_URI, displayOntModel);
if( editConfig != null )
editConfig.setProhibitedFromSearch(pfs);
}
OntModel displayOntModel = ModelAccess.on(session).getDisplayModel();
ProhibitedFromSearch pfs = new ProhibitedFromSearch(
DisplayVocabulary.SEARCH_INDEX_URI, displayOntModel);
if( editConfig != null )
editConfig.setProhibitedFromSearch(pfs);
}
}

8
webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/ManagePageGenerator.java
View file

@ -33,6 +33,7 @@ import com.hp.hpl.jena.vocabulary.XSD;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder;
import edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary;
import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationUtils;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationVTwo;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.fields.FieldVTwo;
@ -207,7 +208,7 @@ public class ManagePageGenerator extends BaseEditConfigurationGenerator implemen
void prepare(VitroRequest vreq, EditConfigurationVTwo editConfig) {
//setup the model selectors for query, write and display models on editConfig
setupModelSelectorsFromVitroRequest(vreq, editConfig);
OntModel queryModel = (OntModel)vreq.getAttribute("jenaOntModel");
OntModel queryModel = ModelAccess.on(vreq).getJenaOntModel();
if (editConfig.isParamUpdate()) {
editConfig.prepareForParamUpdate(queryModel);
@ -224,7 +225,7 @@ public class ManagePageGenerator extends BaseEditConfigurationGenerator implemen
if (editConfig.isParamUpdate()) {
//setup the model selectors for query, write and display models on editConfig
setupModelSelectorsFromVitroRequest(vreq, editConfig);
OntModel queryModel = (OntModel)vreq.getAttribute("jenaOntModel");
OntModel queryModel = ModelAccess.on(vreq).getJenaOntModel();
retrieveExistingDataGetterInfo(context, editConfig, queryModel);
}
@ -589,7 +590,8 @@ private String getExistingIsSelfContainedTemplateQuery() {
int maxMenuPosition = 0;
Literal menuPosition = null;
setupModelSelectorsFromVitroRequest(vreq, editConfig);
OntModel queryModel = (OntModel)vreq.getAttribute("jenaOntModel");
OntModel queryModel = ModelAccess.on(vreq).getJenaOntModel();
String maxMenuPositionQuery = getMaxMenuPositionQueryString();
QueryExecution qe = null;
try{

5
webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/NewIndividualFormGenerator.java
View file

@ -10,13 +10,14 @@ import java.util.Map;
import javax.servlet.http.HttpSession;
import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.vocabulary.RDFS;
import com.hp.hpl.jena.vocabulary.XSD;
import edu.cornell.mannlib.vitro.webapp.beans.VClass;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationUtils;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationVTwo;
@ -239,7 +240,7 @@ public class NewIndividualFormGenerator implements EditConfigurationGenerator {
private void prepareForUpdate(VitroRequest vreq, HttpSession session, EditConfigurationVTwo editConfiguration) {
//Here, retrieve model from
Model model = (Model) session.getServletContext().getAttribute("jenaOntModel");
OntModel model = ModelAccess.on(session.getServletContext()).getJenaOntModel();
//This form is always doing a non-update
editConfiguration.prepareForNonUpdate( model );

4
webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/RDFSLabelGenerator.java
View file

@ -13,6 +13,7 @@ import javax.servlet.http.HttpSession;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.vocabulary.XSD;
@ -21,6 +22,7 @@ import edu.cornell.mannlib.vitro.webapp.beans.DataProperty;
import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatement;
import edu.cornell.mannlib.vitro.webapp.beans.Individual;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationUtils;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationVTwo;
@ -297,7 +299,7 @@ public class RDFSLabelGenerator implements EditConfigurationGenerator {
private void prepareForUpdate(VitroRequest vreq, HttpSession session, EditConfigurationVTwo editConfiguration) {
//Here, retrieve model from
Model model = (Model) session.getServletContext().getAttribute("jenaOntModel");
OntModel model = ModelAccess.on(session.getServletContext()).getJenaOntModel();
if( editConfiguration.isDataPropertyUpdate() ){
editConfiguration.prepareForDataPropUpdate(model, vreq.getWebappDaoFactory().getDataPropertyDao());
}

32
webapp/src/edu/cornell/mannlib/vitro/webapp/filters/VitroRequestPrep.java
View file

@ -4,14 +4,12 @@ package edu.cornell.mannlib.vitro.webapp.filters;
import static edu.cornell.mannlib.vitro.webapp.controller.VitroRequest.SPECIAL_WRITE_MODEL;
import static edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary.CONTEXT_DISPLAY_TBOX;
import static edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary.DISPLAY_ONT_MODEL;
import static edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary.SWITCH_TO_DISPLAY_MODEL;
import static edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary.USE_DISPLAY_MODEL_PARAM;
import static edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary.USE_MODEL_PARAM;
import static edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary.USE_TBOX_MODEL_PARAM;
import java.io.IOException;
import java.util.List;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
@ -42,20 +40,19 @@ import edu.cornell.mannlib.vitro.webapp.auth.policy.ServletPolicyList;
import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
import edu.cornell.mannlib.vitro.webapp.controller.VitroHttpServlet;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess.ModelID;
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
import edu.cornell.mannlib.vitro.webapp.dao.filtering.WebappDaoFactoryFiltering;
import edu.cornell.mannlib.vitro.webapp.dao.filtering.filters.FilterFactory;
import edu.cornell.mannlib.vitro.webapp.dao.filtering.filters.HideFromDisplayByPolicyFilter;
import edu.cornell.mannlib.vitro.webapp.dao.filtering.filters.VitroFilters;
import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceGraph;
import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroModelSource;
import edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactoryJena;
import edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactorySDB;
import edu.cornell.mannlib.vitro.webapp.rdfservice.filter.LanguageFilteringRDFService;
import edu.cornell.mannlib.vitro.webapp.rdfservice.filter.LanguageFilteringUtils;
import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.model.RDFServiceModel;
import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase;
/**
@ -138,21 +135,14 @@ public class VitroRequestPrep implements Filter {
log.debug("Found a WebappDaoFactory in the session and using it for this request");
}
// Set up the DisplayModel, with language filtering if appropriate.
OntModel displayModel;
Object displayModelObject = req.getSession().getAttribute(DISPLAY_ONT_MODEL);
if (displayModelObject instanceof OntModel) {
displayModel = (OntModel) displayModelObject;
} else {
displayModel = (OntModel) _context.getAttribute(DISPLAY_ONT_MODEL);
}
if (Boolean.valueOf(ConfigurationProperties.getBean(vreq).getProperty(
"RDFService.languageFilter", "true"))) {
displayModel = LanguageFilteringUtils.wrapOntModelInALanguageFilter(displayModel, req);
// Set up the DisplayModel with language filtering, if appropriate.
ConfigurationProperties props = ConfigurationProperties.getBean(req);
Boolean languageFilteringEnabled = Boolean.valueOf(props.getProperty("RDFService.languageFilter", "true"));
if (languageFilteringEnabled) {
OntModel displayModel = ModelAccess.on(req.getSession()).getDisplayModel();
OntModel filteredDisplayModel = LanguageFilteringUtils.wrapOntModelInALanguageFilter(displayModel, req);
ModelAccess.on(req).setDisplayModel(filteredDisplayModel);
}
vreq.setAttribute(DISPLAY_ONT_MODEL, displayModel);
//Do model switching and replace the WebappDaoFactory with
//a different version if requested by parameters
@ -245,7 +235,7 @@ public class VitroRequestPrep implements Filter {
// If they asked for the display model, give it to them.
if (isParameterPresent(vreq, SWITCH_TO_DISPLAY_MODEL)) {
OntModel mainOntModel = (OntModel)_context.getAttribute( DISPLAY_ONT_MODEL);
OntModel mainOntModel = ModelAccess.on(_context).getDisplayModel();
OntModel tboxOntModel = (OntModel) _context.getAttribute(CONTEXT_DISPLAY_TBOX);
setSpecialWriteModel(vreq, mainOntModel);
@ -323,7 +313,7 @@ public class VitroRequestPrep implements Filter {
private void setSpecialWriteModel(VitroRequest vreq, OntModel mainOntModel) {
if (mainOntModel != null) {
vreq.setAttribute("jenaOntModel", mainOntModel);
ModelAccess.on(vreq).setJenaOntModel(mainOntModel);
vreq.setAttribute(SPECIAL_WRITE_MODEL, mainOntModel);
}
}

12
webapp/src/edu/cornell/mannlib/vitro/webapp/search/solr/SolrSetup.java
View file

@ -2,7 +2,6 @@
package edu.cornell.mannlib.vitro.webapp.search.solr;
import java.io.File;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.ArrayList;
@ -11,19 +10,16 @@ import java.util.List;
import javax.servlet.ServletContext;
import javax.servlet.ServletContextEvent;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.solr.client.solrj.SolrServer;
import org.apache.solr.client.solrj.impl.CommonsHttpSolrServer;
import org.apache.solr.client.solrj.impl.XMLResponseParser;
import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.vocabulary.OWL;
import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
import edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary;
import edu.cornell.mannlib.vitro.webapp.dao.IndividualDao;
import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
import edu.cornell.mannlib.vitro.webapp.dao.filtering.WebappDaoFactoryFiltering;
@ -31,8 +27,6 @@ import edu.cornell.mannlib.vitro.webapp.dao.filtering.filters.VitroFilterUtils;
import edu.cornell.mannlib.vitro.webapp.dao.filtering.filters.VitroFilters;
import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
import edu.cornell.mannlib.vitro.webapp.search.beans.FileBasedProhibitedFromSearch;
import edu.cornell.mannlib.vitro.webapp.search.beans.ProhibitedFromSearch;
import edu.cornell.mannlib.vitro.webapp.search.beans.StatementToURIsToUpdate;
import edu.cornell.mannlib.vitro.webapp.search.indexing.AdditionalURIsForContextNodes;
import edu.cornell.mannlib.vitro.webapp.search.indexing.AdditionalURIsForDataProperties;
@ -119,8 +113,8 @@ public class SolrSetup implements javax.servlet.ServletContextListener{
context.setAttribute(SOLR_SERVER, server);
/* set up the individual to solr doc translation */
OntModel jenaOntModel = ModelContext.getJenaOntModel(context);
Model displayModel = ModelContext.getDisplayModel(context);
OntModel jenaOntModel = ModelAccess.on(context).getJenaOntModel();
OntModel displayModel = ModelAccess.on(context).getDisplayModel();
/* try to get context attribute DocumentModifiers
* and use that as the start of the list of DocumentModifier

7
webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/ApplicationModelSetup.java
View file

@ -9,7 +9,6 @@ import javax.servlet.ServletContextEvent;
import javax.servlet.ServletContextListener;
import javax.sql.DataSource;
import org.apache.commons.dbcp.BasicDataSource;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.joda.time.DateTime;
@ -23,7 +22,7 @@ import com.hp.hpl.jena.query.QueryFactory;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelSynchronizer;
import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
@ -63,8 +62,8 @@ implements ServletContextListener {
}
OntModel displayModel = ModelFactory.createOntologyModel(MEM_ONT_MODEL_SPEC);
displayModel.add(displayDbModel);
displayModel.getBaseModel().register(new ModelSynchronizer(displayDbModel));
ModelContext.setDisplayModel(displayModel, ctx);
displayModel.getBaseModel().register(new ModelSynchronizer(displayDbModel));
ModelAccess.on(ctx).setDisplayModel(displayModel);
//at each startup load all RDF files from directory to sub-models of display model
initializeDisplayLoadedAtStartup(ctx, displayModel);

10
webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/AssembleModelsSetup.java
View file

@ -22,6 +22,7 @@ import com.hp.hpl.jena.rdf.model.ResourceFactory;
import com.hp.hpl.jena.util.iterator.ExtendedIterator;
import com.hp.hpl.jena.vocabulary.RDF;
import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelSynchronizer;
/**
@ -42,14 +43,7 @@ public class AssembleModelsSetup implements ServletContextListener {
private String SYNTAX = "N3";
public void contextInitialized(ServletContextEvent sce) {
OntModel jenaOntModel = null;
try {
jenaOntModel = (OntModel) sce.getServletContext().getAttribute("baseOntModel");
} catch (Exception e) {
log.error("No baseOntModel found to which to attach assembled models");
return;
}
OntModel jenaOntModel = ModelAccess.on(sce.getServletContext()).getBaseOntModel();
// read assemblers out of assemblers directory
Set pathSet = sce.getServletContext().getResourcePaths(ASSEMBLERS_DIR_PATH);
for (String path : (Set<String>)pathSet) {

297
webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/ContentModelSetup.java Normal file
View file

@ -0,0 +1,297 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
package edu.cornell.mannlib.vitro.webapp.servlet.setup;
import static edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactorySDB.SDBDatasetMode.ASSERTIONS_ONLY;
import static edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactorySDB.SDBDatasetMode.INFERENCES_ONLY;
import java.util.ArrayList;
import java.util.List;
import javax.servlet.ServletContext;
import javax.servlet.ServletContextEvent;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.graph.BulkUpdateHandler;
import com.hp.hpl.jena.graph.Graph;
import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.ontology.OntModelSpec;
import com.hp.hpl.jena.query.Dataset;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.ResIterator;
import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.shared.Lock;
import com.hp.hpl.jena.util.ResourceUtils;
import com.hp.hpl.jena.vocabulary.RDF;
import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess.ModelID;
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactoryConfig;
import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelSynchronizer;
import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelectorImpl;
import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceDataset;
import edu.cornell.mannlib.vitro.webapp.dao.jena.SpecialBulkUpdateHandlerGraph;
import edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactorySDB;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceFactory;
import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
import edu.cornell.mannlib.vitro.webapp.utils.jena.InitialJenaModelUtils;
/**
* Sets up the content models, OntModelSelectors and webapp DAO factories.
*/
public class ContentModelSetup extends JenaDataSourceSetupBase
implements javax.servlet.ServletContextListener {
private static final Log log = LogFactory.getLog(ContentModelSetup.class);
@Override
public void contextInitialized(ServletContextEvent sce) {
ServletContext ctx = sce.getServletContext();
StartupStatus ss = StartupStatus.getBean(ctx);
long begin = System.currentTimeMillis();
setUpJenaDataSource(ctx);
ss.info(this, secondsSince(begin) + " seconds to set up models and DAO factories");
}
private void setUpJenaDataSource(ServletContext ctx) {
RDFServiceFactory rdfServiceFactory = RDFServiceUtils.getRDFServiceFactory(ctx);
RDFService rdfService = rdfServiceFactory.getRDFService();
Dataset dataset = new RDFServiceDataset(rdfService);
setStartupDataset(dataset, ctx);
OntModel applicationMetadataModel = createdMemoryMappedModel(dataset, JENA_APPLICATION_METADATA_MODEL, "application metadata model");
if (applicationMetadataModel.size()== 0) {
JenaDataSourceSetupBase.thisIsFirstStartup();
}
OntModel userAccountsModel = ModelAccess.on(ctx).getUserAccountsModel();
OntModel displayModel = ModelAccess.on(ctx).getDisplayModel();
OntModel baseABoxModel = createNamedModelFromDataset(dataset, JENA_DB_MODEL);
OntModel inferenceABoxModel = createNamedModelFromDataset(dataset, JENA_INF_MODEL);
OntModel baseTBoxModel = createdMemoryMappedModel(dataset, JENA_TBOX_ASSERTIONS_MODEL, "tbox assertions");
OntModel inferenceTBoxModel = createdMemoryMappedModel(dataset, JENA_TBOX_INF_MODEL, "tbox inferences");
OntModel unionABoxModel = createCombinedBulkUpdatingModel(baseABoxModel, inferenceABoxModel);
OntModel unionTBoxModel = createCombinedBulkUpdatingModel(baseTBoxModel, inferenceTBoxModel);
if (isFirstStartup()) {
loadInitialApplicationMetadataModel(applicationMetadataModel, ctx);
loadDataFromFilesystem(baseABoxModel, baseTBoxModel, applicationMetadataModel, ctx);
}
log.info("Setting up union models");
OntModel baseFullModel = createCombinedBulkUpdatingModel(baseABoxModel, baseTBoxModel);
OntModel inferenceFullModel = createCombinedModel(inferenceABoxModel, inferenceTBoxModel);
OntModel unionFullModel = ModelFactory.createOntologyModel(DB_ONT_MODEL_SPEC, dataset.getDefaultModel());
ModelAccess.on(ctx).setOntModel(ModelID.APPLICATION_METADATA, applicationMetadataModel);
ModelAccess.on(ctx).setOntModel(ModelID.USER_ACCOUNTS, userAccountsModel);
ModelAccess.on(ctx).setOntModel(ModelID.DISPLAY, displayModel);
ModelAccess.on(ctx).setOntModel(ModelID.BASE_ABOX, baseABoxModel);
ModelAccess.on(ctx).setOntModel(ModelID.BASE_TBOX, baseTBoxModel);
ModelAccess.on(ctx).setOntModel(ModelID.BASE_FULL, baseFullModel);
ModelAccess.on(ctx).setOntModel(ModelID.INFERRED_ABOX, inferenceABoxModel);
ModelAccess.on(ctx).setOntModel(ModelID.INFERRED_TBOX, inferenceTBoxModel);
ModelAccess.on(ctx).setOntModel(ModelID.INFERRED_FULL, inferenceFullModel);
ModelAccess.on(ctx).setOntModel(ModelID.UNION_ABOX, unionABoxModel);
ModelAccess.on(ctx).setOntModel(ModelID.UNION_TBOX, unionTBoxModel);
ModelAccess.on(ctx).setOntModel(ModelID.UNION_FULL, unionFullModel);
ModelContext.setInferenceOntModel(inferenceFullModel, ctx);
checkForNamespaceMismatch( applicationMetadataModel, ctx );
OntModelSelectorImpl baseOms = new OntModelSelectorImpl();
baseOms.setApplicationMetadataModel(applicationMetadataModel);
baseOms.setUserAccountsModel(userAccountsModel);
baseOms.setDisplayModel(displayModel);
baseOms.setABoxModel(baseABoxModel);
baseOms.setTBoxModel(baseTBoxModel);
baseOms.setFullModel(baseFullModel);
OntModelSelectorImpl inferenceOms = new OntModelSelectorImpl();
inferenceOms.setApplicationMetadataModel(applicationMetadataModel);
inferenceOms.setUserAccountsModel(userAccountsModel);
inferenceOms.setDisplayModel(displayModel);
inferenceOms.setABoxModel(inferenceABoxModel);
inferenceOms.setTBoxModel(inferenceTBoxModel);
inferenceOms.setFullModel(inferenceFullModel);
OntModelSelectorImpl unionOms = new OntModelSelectorImpl();
unionOms.setApplicationMetadataModel(applicationMetadataModel);
unionOms.setUserAccountsModel(userAccountsModel);
unionOms.setDisplayModel(displayModel);
unionOms.setABoxModel(unionABoxModel);
unionOms.setTBoxModel(unionTBoxModel);
unionOms.setFullModel(unionFullModel);
ModelContext.setOntModelSelector(unionOms, ctx);
ModelContext.setUnionOntModelSelector(unionOms, ctx); // assertions and inferences
ModelContext.setBaseOntModelSelector(baseOms, ctx); // assertions
ModelContext.setInferenceOntModelSelector(inferenceOms, ctx); // inferences
log.info("Setting up DAO factories");
WebappDaoFactoryConfig config = new WebappDaoFactoryConfig();
config.setDefaultNamespace(getDefaultNamespace(ctx));
WebappDaoFactory baseWadf = new WebappDaoFactorySDB(rdfService, baseOms, config, ASSERTIONS_ONLY);
ctx.setAttribute("assertionsWebappDaoFactory",baseWadf);
WebappDaoFactory infWadf = new WebappDaoFactorySDB(rdfService, inferenceOms, config, INFERENCES_ONLY);
ctx.setAttribute("deductionsWebappDaoFactory", infWadf);
WebappDaoFactory wadf = new WebappDaoFactorySDB(rdfService, unionOms, config);
ctx.setAttribute("webappDaoFactory",wadf);
log.info("Model makers set up");
ctx.setAttribute("defaultNamespace", getDefaultNamespace(ctx));
}
private OntModel createNamedModelFromDataset(Dataset dataset, String name) {
return ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM, dataset.getNamedModel(name));
}
private OntModel createdMemoryMappedModel(Dataset dataset, String name, String label) {
try {
Model dbModel = dataset.getNamedModel(name);
OntModel memoryModel = ModelFactory.createOntologyModel(MEM_ONT_MODEL_SPEC);
if (dbModel != null) {
long begin = System.currentTimeMillis();
log.info("Copying cached " + label + " into memory");
memoryModel.add(dbModel);
log.info(secondsSince(begin) + " seconds to load " + label);
memoryModel.getBaseModel().register(new ModelSynchronizer(dbModel));
}
return memoryModel;
} catch (Throwable e) {
throw new RuntimeException("Unable to load " + label + " from DB", e);
}
}
private OntModel createCombinedModel(OntModel oneModel, OntModel otherModel) {
return ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM,
ModelFactory.createUnion(oneModel, otherModel));
}
private OntModel createCombinedBulkUpdatingModel(OntModel baseModel,
OntModel otherModel) {
BulkUpdateHandler bulkUpdateHandler = baseModel.getGraph().getBulkUpdateHandler();
Graph unionGraph = ModelFactory.createUnion(baseModel, otherModel).getGraph();
Model unionModel = ModelFactory.createModelForGraph(
new SpecialBulkUpdateHandlerGraph(unionGraph, bulkUpdateHandler));
return ModelFactory.createOntologyModel(MEM_ONT_MODEL_SPEC, unionModel);
}
private void loadInitialApplicationMetadataModel(OntModel applicationMetadataModel,
ServletContext ctx) {
try {
applicationMetadataModel.add(
InitialJenaModelUtils.loadInitialModel(ctx, getDefaultNamespace(ctx)));
} catch (Throwable e) {
throw new RuntimeException("Unable to load application metadata model cache from DB", e);
}
}
private void loadDataFromFilesystem(OntModel baseABoxModel, OntModel baseTBoxModel, OntModel applicationMetadataModel,
ServletContext ctx) {
Long startTime = System.currentTimeMillis();
log.info("Initializing models from RDF files");
readOntologyFilesInPathSet(USER_ABOX_PATH, ctx, baseABoxModel);
readOntologyFilesInPathSet(USER_TBOX_PATH, ctx, baseTBoxModel);
readOntologyFilesInPathSet(USER_APPMETA_PATH, ctx, applicationMetadataModel);
log.debug(((System.currentTimeMillis() - startTime) / 1000)
+ " seconds to read RDF files ");
}
private long secondsSince(long startTime) {
return (System.currentTimeMillis() - startTime) / 1000;
}
/* ===================================================================== */
/**
* If we find a "portal1" portal (and we should), its URI should use the
* default namespace.
*/
private void checkForNamespaceMismatch(OntModel model, ServletContext ctx) {
String expectedNamespace = getDefaultNamespace(ctx);
List<Resource> portals = getPortal1s(model);
if(!portals.isEmpty() && noPortalForNamespace(
portals, expectedNamespace)) {
// There really should be only one portal 1, but if there happen to
// be multiple, just arbitrarily pick the first in the list.
Resource portal = portals.get(0);
String oldNamespace = portal.getNameSpace();
renamePortal(portal, expectedNamespace, model);
StartupStatus ss = StartupStatus.getBean(ctx);
ss.warning(this, "\nThe default namespace has been changed \n" +
"from " + oldNamespace +
"\nto " + expectedNamespace + ".\n" +
"The application will function normally, but " +
"any individuals in the \n" + oldNamespace + " " +
"namespace will need to have their URIs \n" +
"changed in order to be served as linked data. " +
"You can use the Ingest Tools \nto change the " +
"URIs for a batch of resources.");
}
}
private List<Resource> getPortal1s(Model model) {
List<Resource> portals = new ArrayList<Resource>();
try {
model.enterCriticalSection(Lock.READ);
ResIterator portalIt = model.listResourcesWithProperty(
RDF.type, PORTAL);
while (portalIt.hasNext()) {
Resource portal = portalIt.nextResource();
if ("portal1".equals(portal.getLocalName())) {
portals.add(portal);
}
}
} finally {
model.leaveCriticalSection();
}
return portals;
}
private boolean noPortalForNamespace(List<Resource> portals, String expectedNamespace) {
for (Resource portal : portals) {
if(expectedNamespace.equals(portal.getNameSpace())) {
return false;
}
}
return true;
}
private void renamePortal(Resource portal, String namespace, Model model) {
model.enterCriticalSection(Lock.WRITE);
try {
ResourceUtils.renameResource(portal, namespace + portal.getLocalName());
} finally {
model.leaveCriticalSection();
}
}
/* ===================================================================== */
@Override
public void contextDestroyed(ServletContextEvent sce) {
// Nothing to do.
}
}

2
webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/JenaDataSourceSetupBase.java
View file

@ -471,7 +471,7 @@ public class JenaDataSourceSetupBase extends JenaBaseDaoCon {
} else if (TripleStoreType.SDB.equals(type)) {
StoreDesc storeDesc = new StoreDesc(
LayoutType.LayoutTripleNodesHash, DatabaseType.fetch(dbtypeStr));
DataSource bds = WebappDaoSetup.makeC3poDataSource(
DataSource bds = ContentModelSetup.makeC3poDataSource(
getDbDriverClassName(ctx), jdbcUrl, username, password, ctx);
// DataSource bds = WebappDaoSetup.makeBasicDataSource(
// getDbDriverClassName(ctx), jdbcUrl, username, password, ctx);

54
webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/ModelMakerSetup.java Normal file
View file

@ -0,0 +1,54 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
package edu.cornell.mannlib.vitro.webapp.servlet.setup;
import javax.servlet.ServletContext;
import javax.servlet.ServletContextEvent;
import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceModelMaker;
import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaModelMaker;
import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroModelSource;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceFactory;
import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
/**
* Sets up the content models, OntModelSelectors and webapp DAO factories.
*/
public class ModelMakerSetup extends JenaDataSourceSetupBase
implements javax.servlet.ServletContextListener {
@Override
public void contextInitialized(ServletContextEvent sce) {
ServletContext ctx = sce.getServletContext();
StartupStatus ss = StartupStatus.getBean(ctx);
long begin = System.currentTimeMillis();
RDFServiceFactory rdfServiceFactory = RDFServiceUtils.getRDFServiceFactory(ctx);
makeModelMakerFromConnectionProperties(TripleStoreType.RDB, ctx);
VitroJenaModelMaker vjmm = getVitroJenaModelMaker();
setVitroJenaModelMaker(vjmm, ctx);
makeModelMakerFromConnectionProperties(TripleStoreType.SDB, ctx);
RDFServiceModelMaker vsmm = new RDFServiceModelMaker(rdfServiceFactory);
setVitroJenaSDBModelMaker(vsmm, ctx);
//bdc34: I have no reason for vsmm vs vjmm.
//I don't know what are the implications of this choice.
setVitroModelSource( new VitroModelSource(vsmm,ctx), ctx);
ss.info(this, secondsSince(begin) + " seconds to set up models and DAO factories");
}
private long secondsSince(long startTime) {
return (System.currentTimeMillis() - startTime) / 1000;
}
/* ===================================================================== */
@Override
public void contextDestroyed(ServletContextEvent sce) {
// Nothing to do.
}
}

4
webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/PropertyMaskingSetup.java
View file

@ -13,15 +13,15 @@ import net.sf.jga.fn.UnaryFunctor;
import com.hp.hpl.jena.ontology.OntModel;
import edu.cornell.mannlib.vitro.webapp.beans.Property;
import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
import edu.cornell.mannlib.vitro.webapp.dao.filtering.filters.EntityPropertyListFilter;
import edu.cornell.mannlib.vitro.webapp.dao.jena.JenaBaseDao;
public class PropertyMaskingSetup implements ServletContextListener {
private final static String ENTITY_PROPERTY_LIST_FILTER_ATTR_NAME = "entityPropertyListFilter";
public void contextInitialized(ServletContextEvent sce) {
OntModel jenaOntModel = (OntModel) sce.getServletContext().getAttribute(JenaBaseDao.JENA_ONT_MODEL_ATTRIBUTE_NAME);
OntModel jenaOntModel = ModelAccess.on(sce.getServletContext()).getJenaOntModel();
sce.getServletContext().setAttribute(ENTITY_PROPERTY_LIST_FILTER_ATTR_NAME, new EntityPropertyListFilter(jenaOntModel));
}

3
webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/RunSparqlConstructs.java
View file

@ -28,6 +28,7 @@ import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.util.ResourceUtils;
import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
public class RunSparqlConstructs implements ServletContextListener {
@ -46,7 +47,7 @@ public class RunSparqlConstructs implements ServletContextListener {
String namespace = (wadf != null && wadf.getDefaultNamespace() != null)
? wadf.getDefaultNamespace() : DEFAULT_DEFAULT_NAMESPACE;
OntModel baseOntModel = (OntModel) sce.getServletContext().getAttribute("baseOntModel");
OntModel baseOntModel = ModelAccess.on(sce.getServletContext()).getBaseOntModel();
Model anonModel = ModelFactory.createDefaultModel();
Model namedModel = ModelFactory.createDefaultModel();

3
webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/UpdateKnowledgeBase.java
View file

@ -32,6 +32,7 @@ import com.hp.hpl.jena.vocabulary.RDF;
import com.hp.hpl.jena.vocabulary.RDFS;
import edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary;
import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
import edu.cornell.mannlib.vitro.webapp.ontology.update.KnowledgeBaseUpdater;
@ -106,7 +107,7 @@ public class UpdateKnowledgeBase implements ServletContextListener {
settings.setUnionOntModelSelector(ModelContext.getUnionOntModelSelector(ctx));
boolean tryMigrateDisplay = true;
try {
settings.setDisplayModel(ModelContext.getDisplayModel(ctx));
settings.setDisplayModel(ModelAccess.on(ctx).getDisplayModel());
OntModel oldTBoxModel = loadModelFromDirectory(ctx.getRealPath(OLD_TBOX_MODEL_DIR));
settings.setOldTBoxModel(oldTBoxModel);
OntModel newTBoxModel = loadModelFromDirectory(ctx.getRealPath(NEW_TBOX_MODEL_DIR));

4
webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/UserModelSetup.java
View file

@ -6,7 +6,6 @@ import javax.servlet.ServletContextEvent;
import javax.servlet.ServletContextListener;
import javax.sql.DataSource;
import org.apache.commons.dbcp.BasicDataSource;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
@ -14,6 +13,7 @@ import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelSynchronizer;
import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
@ -65,7 +65,7 @@ public class UserModelSetup extends JenaDataSourceSetupBase
userAccountsModel.add(userAccountsDbModel);
userAccountsModel.getBaseModel().register(
new ModelSynchronizer(userAccountsDbModel));
ctx.setAttribute("userAccountsOntModel", userAccountsModel);
ModelAccess.on(ctx).setUserAccountsModel(userAccountsModel);
} catch (Throwable t) {
log.error("Unable to load user accounts model from DB", t);

385
webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/WebappDaoSetup.java
View file

@ -1,385 +0,0 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
package edu.cornell.mannlib.vitro.webapp.servlet.setup;
import static edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary.DISPLAY_ONT_MODEL;
import java.util.ArrayList;
import java.util.List;
import javax.servlet.ServletContext;
import javax.servlet.ServletContextEvent;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.ontology.OntModelSpec;
import com.hp.hpl.jena.query.Dataset;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.ResIterator;
import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.rdf.model.ResourceFactory;
import com.hp.hpl.jena.rdf.model.Statement;
import com.hp.hpl.jena.shared.Lock;
import com.hp.hpl.jena.util.ResourceUtils;
import com.hp.hpl.jena.util.iterator.ClosableIterator;
import com.hp.hpl.jena.vocabulary.RDF;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactoryConfig;
import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelSynchronizer;
import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelector;
import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelectorImpl;
import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceDataset;
import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceModelMaker;
import edu.cornell.mannlib.vitro.webapp.dao.jena.SpecialBulkUpdateHandlerGraph;
import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaModelMaker;
import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroModelSource;
import edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactorySDB;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceFactory;
import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
import edu.cornell.mannlib.vitro.webapp.utils.jena.InitialJenaModelUtils;
/**
* Primarily sets up webapp DAO factories.
*/
public class WebappDaoSetup extends JenaDataSourceSetupBase
implements javax.servlet.ServletContextListener {
private static final Log log = LogFactory.getLog(WebappDaoSetup.class);
@Override
public void contextInitialized(ServletContextEvent sce) {
ServletContext ctx = sce.getServletContext();
StartupStatus ss = StartupStatus.getBean(ctx);
try {
long startTime = System.currentTimeMillis();
setUpJenaDataSource(ctx, ss);
log.info((System.currentTimeMillis() - startTime) / 1000 +
" seconds to set up models and DAO factories");
} catch (Throwable t) {
log.error("Throwable in " + this.getClass().getName(), t);
ss.fatal(this, "Throwable in " + this.getClass().getName(), t);
}
}
private void setUpJenaDataSource(ServletContext ctx, StartupStatus ss) {
OntModelSelectorImpl baseOms = new OntModelSelectorImpl();
OntModelSelectorImpl inferenceOms = new OntModelSelectorImpl();
OntModelSelectorImpl unionOms = new OntModelSelectorImpl();
OntModel userAccountsModel = ontModelFromContextAttribute(
ctx, "userAccountsOntModel");
baseOms.setUserAccountsModel(userAccountsModel);
inferenceOms.setUserAccountsModel(userAccountsModel);
unionOms.setUserAccountsModel(userAccountsModel);
OntModel displayModel = ontModelFromContextAttribute(
ctx,DISPLAY_ONT_MODEL);
baseOms.setDisplayModel(displayModel);
inferenceOms.setDisplayModel(displayModel);
unionOms.setDisplayModel(displayModel);
RDFServiceFactory rdfServiceFactory = RDFServiceUtils.getRDFServiceFactory(ctx);
RDFService rdfService = rdfServiceFactory.getRDFService();
Dataset dataset = new RDFServiceDataset(rdfService);
setStartupDataset(dataset, ctx);
// ABox assertions
baseOms.setABoxModel(ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM, dataset.getNamedModel(JenaDataSourceSetupBase.JENA_DB_MODEL)));
// ABox inferences
inferenceOms.setABoxModel(ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM, dataset.getNamedModel(JenaDataSourceSetupBase.JENA_INF_MODEL)));
// TBox assertions
try {
Model tboxAssertionsDB = dataset.getNamedModel(
JENA_TBOX_ASSERTIONS_MODEL);
OntModel tboxAssertions = ModelFactory.createOntologyModel(
MEM_ONT_MODEL_SPEC);
if (tboxAssertionsDB != null) {
long startTime = System.currentTimeMillis();
log.info("Copying cached tbox assertions into memory");
tboxAssertions.add(tboxAssertionsDB);
log.info((System.currentTimeMillis() - startTime)/ 1000 + " seconds to load tbox assertions");
tboxAssertions.getBaseModel().register(new ModelSynchronizer(tboxAssertionsDB));
}
baseOms.setTBoxModel(tboxAssertions);
} catch (Throwable e) {
log.error("Unable to load tbox assertion cache from DB", e);
throw new RuntimeException(e);
}
// TBox inferences
try {
Model tboxInferencesDB = dataset.getNamedModel(JENA_TBOX_INF_MODEL);
OntModel tboxInferences = ModelFactory.createOntologyModel(
MEM_ONT_MODEL_SPEC);
if (tboxInferencesDB != null) {
long startTime = System.currentTimeMillis();
log.info(
"Copying cached tbox inferences into memory");
tboxInferences.add(tboxInferencesDB);
System.out.println((System.currentTimeMillis() - startTime)
/ 1000 + " seconds to load tbox inferences");
tboxInferences.getBaseModel().register(new ModelSynchronizer(
tboxInferencesDB));
}
inferenceOms.setTBoxModel(tboxInferences);
} catch (Throwable e) {
log.error("Unable to load tbox inference cache from DB", e);
throw new RuntimeException(e);
}
// union ABox
Model m = ModelFactory.createUnion(
baseOms.getABoxModel(), inferenceOms.getABoxModel());
m = ModelFactory.createModelForGraph(
new SpecialBulkUpdateHandlerGraph(
m.getGraph(),
baseOms.getABoxModel().getGraph().getBulkUpdateHandler()));
OntModel unionABoxModel = ModelFactory.createOntologyModel(
MEM_ONT_MODEL_SPEC, m);
unionOms.setABoxModel(unionABoxModel);
// union TBox
m = ModelFactory.createUnion(baseOms.getTBoxModel(), inferenceOms.getTBoxModel());
m = ModelFactory.createModelForGraph(
new SpecialBulkUpdateHandlerGraph(
m.getGraph(),
baseOms.getTBoxModel().getGraph().getBulkUpdateHandler()));
OntModel unionTBoxModel = ModelFactory.createOntologyModel(
MEM_ONT_MODEL_SPEC, m);
unionOms.setTBoxModel(unionTBoxModel);
// Application metadata model is cached in memory.
try {
Model applicationMetadataModelDB = dataset.getNamedModel(
JENA_APPLICATION_METADATA_MODEL);
OntModel applicationMetadataModel =
ModelFactory.createOntologyModel(MEM_ONT_MODEL_SPEC);
long startTime = System.currentTimeMillis();
System.out.println(
"Copying cached application metadata model into memory");
applicationMetadataModel.add(applicationMetadataModelDB);
System.out.println((System.currentTimeMillis() - startTime)
/ 1000 + " seconds to load application metadata model " +
"assertions of size " + applicationMetadataModel.size());
applicationMetadataModel.getBaseModel().register(
new ModelSynchronizer(applicationMetadataModelDB));
if (applicationMetadataModel.size()== 0 /* isFirstStartup() */) {
JenaDataSourceSetupBase.thisIsFirstStartup();
applicationMetadataModel.add(
InitialJenaModelUtils.loadInitialModel(
ctx, getDefaultNamespace(ctx)));
}
baseOms.setApplicationMetadataModel(applicationMetadataModel);
inferenceOms.setApplicationMetadataModel(
baseOms.getApplicationMetadataModel());
unionOms.setApplicationMetadataModel(
baseOms.getApplicationMetadataModel());
} catch (Throwable e) {
log.error("Unable to load application metadata model cache from DB"
, e);
throw new RuntimeException(e);
}
checkForNamespaceMismatch( baseOms.getApplicationMetadataModel(), ctx );
if (isFirstStartup()) {
loadDataFromFilesystem(baseOms, ctx);
}
log.info("Setting up union models and DAO factories");
// create TBox + ABox union models and set up webapp DAO factories
Model baseDynamicUnion = ModelFactory.createUnion(baseOms.getABoxModel(),
baseOms.getTBoxModel());
baseDynamicUnion = ModelFactory.createModelForGraph(
new SpecialBulkUpdateHandlerGraph(
baseDynamicUnion.getGraph(),
baseOms.getABoxModel().getGraph().getBulkUpdateHandler()) );
OntModel baseUnion = ModelFactory.createOntologyModel(
OntModelSpec.OWL_MEM, baseDynamicUnion);
baseOms.setFullModel(baseUnion);
ModelContext.setBaseOntModel(baseOms.getFullModel(), ctx);
WebappDaoFactoryConfig config = new WebappDaoFactoryConfig();
config.setDefaultNamespace(getDefaultNamespace(ctx));
WebappDaoFactory baseWadf = new WebappDaoFactorySDB(
rdfService, baseOms, config,
WebappDaoFactorySDB.SDBDatasetMode.ASSERTIONS_ONLY);
ctx.setAttribute("assertionsWebappDaoFactory",baseWadf);
OntModel inferenceUnion = ModelFactory.createOntologyModel(
OntModelSpec.OWL_MEM,
ModelFactory.createUnion(
inferenceOms.getABoxModel(),
inferenceOms.getTBoxModel()));
inferenceOms.setFullModel(inferenceUnion);
ModelContext.setInferenceOntModel(inferenceOms.getFullModel(), ctx);
WebappDaoFactory infWadf = new WebappDaoFactorySDB(
rdfService, inferenceOms, config,
WebappDaoFactorySDB.SDBDatasetMode.INFERENCES_ONLY);
ctx.setAttribute("deductionsWebappDaoFactory", infWadf);
OntModel masterUnion = ModelFactory.createOntologyModel(
DB_ONT_MODEL_SPEC, dataset.getDefaultModel());
unionOms.setFullModel(masterUnion);
ctx.setAttribute("jenaOntModel", masterUnion);
WebappDaoFactory wadf = new WebappDaoFactorySDB(
rdfService, unionOms, config);
ctx.setAttribute("webappDaoFactory",wadf);
ModelContext.setOntModelSelector(unionOms, ctx);
ModelContext.setUnionOntModelSelector(unionOms, ctx);
// assertions and inferences
ModelContext.setBaseOntModelSelector(baseOms, ctx);
// assertions
ModelContext.setInferenceOntModelSelector(inferenceOms, ctx);
// inferences
ctx.setAttribute("defaultNamespace", getDefaultNamespace(ctx));
makeModelMakerFromConnectionProperties(TripleStoreType.RDB, ctx);
VitroJenaModelMaker vjmm = getVitroJenaModelMaker();
setVitroJenaModelMaker(vjmm, ctx);
makeModelMakerFromConnectionProperties(TripleStoreType.SDB, ctx);
RDFServiceModelMaker vsmm = new RDFServiceModelMaker(rdfServiceFactory);
setVitroJenaSDBModelMaker(vsmm, ctx);
//bdc34: I have no reason for vsmm vs vjmm.
//I don't know what are the implications of this choice.
setVitroModelSource( new VitroModelSource(vsmm,ctx), ctx);
log.info("Model makers set up");
}
/**
* If we find a "portal1" portal (and we should), its URI should use the
* default namespace.
*/
private void checkForNamespaceMismatch(OntModel model, ServletContext ctx) {
String expectedNamespace = getDefaultNamespace(ctx);
List<Resource> portals = getPortal1s(model);
if(!portals.isEmpty() && noPortalForNamespace(
portals, expectedNamespace)) {
// There really should be only one portal 1, but if there happen to
// be multiple, just arbitrarily pick the first in the list.
Resource portal = portals.get(0);
String oldNamespace = portal.getNameSpace();
renamePortal(portal, expectedNamespace, model);
StartupStatus ss = StartupStatus.getBean(ctx);
ss.warning(this, "\nThe default namespace has been changed \n" +
"from " + oldNamespace +
"\nto " + expectedNamespace + ".\n" +
"The application will function normally, but " +
"any individuals in the \n" + oldNamespace + " " +
"namespace will need to have their URIs \n" +
"changed in order to be served as linked data. " +
"You can use the Ingest Tools \nto change the " +
"URIs for a batch of resources.");
}
}
private List<Resource> getPortal1s(Model model) {
List<Resource> portals = new ArrayList<Resource>();
try {
model.enterCriticalSection(Lock.READ);
ResIterator portalIt = model.listResourcesWithProperty(
RDF.type, PORTAL);
while (portalIt.hasNext()) {
Resource portal = portalIt.nextResource();
if ("portal1".equals(portal.getLocalName())) {
portals.add(portal);
}
}
} finally {
model.leaveCriticalSection();
}
return portals;
}
private boolean noPortalForNamespace(List<Resource> portals,
String expectedNamespace) {
for (Resource portal : portals) {
if(expectedNamespace.equals(portal.getNameSpace())) {
return false;
}
}
return true;
}
private void renamePortal(Resource portal, String namespace, Model model) {
model.enterCriticalSection(Lock.WRITE);
try {
ResourceUtils.renameResource(
portal, namespace + portal.getLocalName());
} finally {
model.leaveCriticalSection();
}
}
/* ===================================================================== */
@Override
public void contextDestroyed(ServletContextEvent sce) {
// Nothing to do.
}
private boolean isEmpty(Model model) {
ClosableIterator<Statement> closeIt = model.listStatements(
null, RDF.type, ResourceFactory.createResource(
VitroVocabulary.PORTAL));
try {
if (closeIt.hasNext()) {
return false;
} else {
return true;
}
} finally {
closeIt.close();
}
}
private void loadDataFromFilesystem(OntModelSelector baseOms,
ServletContext ctx) {
Long startTime = System.currentTimeMillis();
log.info("Initializing models from RDF files");
readOntologyFilesInPathSet(USER_ABOX_PATH, ctx, baseOms.getABoxModel());
readOntologyFilesInPathSet(USER_TBOX_PATH, ctx, baseOms.getTBoxModel());
readOntologyFilesInPathSet(
USER_APPMETA_PATH, ctx, baseOms.getApplicationMetadataModel());
log.debug(((System.currentTimeMillis() - startTime) / 1000)
+ " seconds to read RDF files ");
}
}

8
webapp/src/edu/cornell/mannlib/vitro/webapp/utils/ApplicationConfigurationOntologyUtils.java
View file

@ -5,6 +5,8 @@ package edu.cornell.mannlib.vitro.webapp.utils;
import java.util.ArrayList;
import java.util.List;
import javax.servlet.ServletContext;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
@ -21,6 +23,7 @@ import com.hp.hpl.jena.rdf.model.Resource;
import edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
public class ApplicationConfigurationOntologyUtils {
@ -28,8 +31,9 @@ public class ApplicationConfigurationOntologyUtils {
private static final Log log = LogFactory.getLog(ApplicationConfigurationOntologyUtils.class);
public static List<ObjectProperty> getAdditionalFauxSubpropertiesForList(List<ObjectProperty> propList, VitroRequest vreq) {
Model displayModel = ModelContext.getDisplayModel(vreq.getSession().getServletContext());
Model tboxModel = ModelContext.getUnionOntModelSelector(vreq.getSession().getServletContext()).getTBoxModel();
ServletContext ctx = vreq.getSession().getServletContext();
Model displayModel = ModelAccess.on(ctx).getDisplayModel();
Model tboxModel = ModelContext.getUnionOntModelSelector(ctx).getTBoxModel();
return getAdditionalFauxSubpropertiesForList(propList, displayModel, tboxModel);
}

8
webapp/src/edu/cornell/mannlib/vitro/webapp/utils/dataGetter/DataGetterBase.java
View file

@ -1,8 +1,6 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
package edu.cornell.mannlib.vitro.webapp.utils.dataGetter;
import java.util.Map;
import javax.servlet.ServletContext;
import org.apache.commons.lang.StringUtils;
@ -11,9 +9,7 @@ import com.hp.hpl.jena.rdf.model.Model;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.controller.jena.JenaIngestController;
import edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary;
import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaModelMaker;
import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaSDBModelMaker;
import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
public abstract class DataGetterBase implements DataGetter {
@ -29,7 +25,7 @@ public abstract class DataGetterBase implements DataGetter {
}else if( REQUEST_JENA_ONT_MODEL.equals(modelName)){
return vreq.getJenaOntModel();
}else if( CONTEXT_DISPLAY_MODEL.equals(modelName)){
return (Model)context.getAttribute( DisplayVocabulary.DISPLAY_ONT_MODEL);
return ModelAccess.on(context).getDisplayModel();
}else if( ! StringUtils.isEmpty( modelName)){
Model model = JenaIngestController.getModel( modelName, vreq, context);
if( model == null )

4
webapp/web/WEB-INF/resources/startup_listeners.txt
View file

@ -20,8 +20,8 @@ edu.cornell.mannlib.vitro.webapp.servlet.setup.RDFServiceSetup
edu.cornell.mannlib.vitro.webapp.servlet.setup.ApplicationModelSetup
edu.cornell.mannlib.vitro.webapp.servlet.setup.UserModelSetup
edu.cornell.mannlib.vitro.webapp.servlet.setup.WebappDaoSetup
edu.cornell.mannlib.vitro.webapp.servlet.setup.ContentModelSetup
edu.cornell.mannlib.vitro.webapp.servlet.setup.ModelMakerSetup
edu.cornell.mannlib.vitro.webapp.servlet.setup.UpdateKnowledgeBase

3
webapp/web/admin/conceptRepair.jsp
View file

@ -3,6 +3,7 @@
<%@ taglib prefix="c" uri="http://java.sun.com/jsp/jstl/core" %>
<%@ page import="edu.cornell.mannlib.vitro.webapp.controller.Controllers" %>
<%@ page import="edu.cornell.mannlib.vitro.webapp.dao.ModelAccess"%>
<%@taglib prefix="vitro" uri="/WEB-INF/tlds/VitroUtils.tld" %>
<%@page import="edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission" %>
@ -21,7 +22,7 @@
" FILTER(afn:bnode(?bnode) = \"" + conceptIdStr + "\")\n" +
"}";
OntModel ontModel = (OntModel) getServletContext().getAttribute("baseOntModel");
OntModel ontModel = ModelAccess.on(getServletContext()).getBaseOntModel();
Model conceptDescription = ModelFactory.createDefaultModel();
try {
ontModel.enterCriticalSection(Lock.READ);

5
webapp/web/admin/removeBadRestrictions.jsp
View file

@ -4,12 +4,13 @@
<%@taglib prefix="vitro" uri="/WEB-INF/tlds/VitroUtils.tld" %>
<%@page import="edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission" %>
<%@page import="edu.cornell.mannlib.vitro.webapp.dao.ModelAccess"%>
<% request.setAttribute("requestedActions", SimplePermission.USE_MISCELLANEOUS_CURATOR_PAGES.ACTION); %>
<vitro:confirmAuthorization />
<%
if (request.getParameter("execute") != null) {
OntModel ontModel = (OntModel) getServletContext().getAttribute(JenaBaseDao.ASSERTIONS_ONT_MODEL_ATTRIBUTE_NAME);
OntModel ontModel = ModelAccess.on(getServletContext()).getBaseOntModel();
int results = doRemoval(ontModel);
request.setAttribute("removalCount", results);
}
@ -66,7 +67,7 @@
" FILTER(afn:bnode(?bnode) = \"" + bnodeId + "\")\n" +
"}";
OntModel ontModel = (OntModel) getServletContext().getAttribute("baseOntModel");
OntModel ontModel = ModelAccess.on(getServletContext()).getBaseOntModel();
Model conceptDescription = ModelFactory.createDefaultModel();
try {
ontModel.enterCriticalSection(Lock.READ);

3
webapp/web/admin/removeResourceDescription.jsp
View file

@ -6,6 +6,7 @@
<%@taglib prefix="vitro" uri="/WEB-INF/tlds/VitroUtils.tld" %>
<%@page import="edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission" %>
<%@page import="edu.cornell.mannlib.vitro.webapp.dao.ModelAccess"%>
<% request.setAttribute("requestedActions", SimplePermission.USE_MISCELLANEOUS_CURATOR_PAGES.ACTION); %>
<vitro:confirmAuthorization />
@ -16,7 +17,7 @@
String describeQueryStr =
"DESCRIBE <" + resourceURIStr + ">";
OntModel ontModel = (OntModel) getServletContext().getAttribute("baseOntModel");
OntModel ontModel = ModelAccess.on(getServletContext()).getBaseOntModel();
Model resourceDescription = ModelFactory.createDefaultModel();
try {
ontModel.enterCriticalSection(Lock.READ);

3
webapp/web/admin/syncSesame.jsp
View file

@ -7,6 +7,7 @@
<%@page import="edu.cornell.mannlib.vitro.webapp.dao.jena.JenaModelUtils"%>
<%@page import="com.hp.hpl.jena.rdf.model.Model"%>
<%@page import="edu.cornell.mannlib.vitro.webapp.dao.jena.JenaBaseDao"%>
<%@page import="edu.cornell.mannlib.vitro.webapp.dao.ModelAccess"%>
<%@page import="java.io.InputStream"%>
<%@page import="java.util.Properties"%>
<%@ page import="edu.cornell.mannlib.vitro.webapp.controller.Controllers" %>
@ -54,7 +55,7 @@
}
String contextId = sesameProperties.getProperty(SESAME_CONTEXT);
Model fullModel = (Model) getServletContext().getAttribute(JenaBaseDao.JENA_ONT_MODEL_ATTRIBUTE_NAME);
Model fullModel = ModelAccess.on(getServletContext()).getJenaOntModel();
// Copy the model to avoid locking the main model during sync. Assumes enough memory.
Model copyModel = ModelFactory.createDefaultModel();
fullModel.enterCriticalSection(Lock.READ);

3
webapp/web/jenaIngest/executeWorkflow.jsp
View file

@ -3,6 +3,7 @@
<%@ 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" %>
<%@ page import="edu.cornell.mannlib.vitro.webapp.dao.ModelAccess"%>
<%@ page import="com.hp.hpl.jena.shared.Lock" %>
<%@ page import="java.util.Iterator" %>
<%@ page import="java.util.List" %>
@ -23,7 +24,7 @@
<select name="workflowURI">
<%
OntModel jenaOntModel = (OntModel) getServletContext().getAttribute("jenaOntModel");
OntModel jenaOntModel = ModelAccess.on(getServletContext()).getJenaOntModel();
jenaOntModel.enterCriticalSection(Lock.READ);
try {
List savedQueries = (List) request.getAttribute("workflows");

3
webapp/web/jenaIngest/sparqlConstruct.jsp
View file

@ -3,6 +3,7 @@
<%@ 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"%>
<%@ page import="edu.cornell.mannlib.vitro.webapp.dao.ModelAccess"%>
<%@ page import="com.hp.hpl.jena.shared.Lock"%>
<%@ page import="java.util.Iterator"%>
<%@ page import="java.util.List"%>
@ -46,7 +47,7 @@
<h3>SPARQL Query <select name="savedQuery">
<option value="">select saved query</option>
<%
OntModel jenaOntModel = (OntModel) getServletContext().getAttribute("jenaOntModel");
OntModel jenaOntModel = ModelAccess.on(getServletContext()).getJenaOntModel();
jenaOntModel.enterCriticalSection(Lock.READ);
try {
List savedQueries = (List) request.getAttribute("savedQueries");

3
webapp/web/jenaIngest/workflowStep.jsp
View file

@ -3,6 +3,7 @@
<%@ 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" %>
<%@ page import="edu.cornell.mannlib.vitro.webapp.dao.ModelAccess"%>
<%@ page import="com.hp.hpl.jena.shared.Lock" %>
<%@ page import="java.util.Iterator" %>
<%@ page import="java.util.List" %>
@ -25,7 +26,7 @@
<select name="workflowStepURI">
<%
OntModel jenaOntModel = (OntModel) getServletContext().getAttribute("jenaOntModel");
OntModel jenaOntModel = ModelAccess.on(getServletContext()).getJenaOntModel();
jenaOntModel.enterCriticalSection(Lock.READ);
try {
List workflowSteps = (List) request.getAttribute("workflowSteps");