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Merge branch 'maint-rel-1.6' into develop

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This commit is contained in:
hudajkhan 2013-12-05 16:21:34 -05:00
commit 05be6f36bc
22 changed files with 420 additions and 204 deletions
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5
webapp/src/edu/cornell/mannlib/vitro/webapp/beans/DataProperty.java
View file

@ -71,6 +71,11 @@ public class DataProperty extends Property implements Comparable<DataProperty>,
return domainClassURI;
}
@Override
public String getDomainVClassURI() {
return domainClassURI;
}
public void setDomainClassURI(String domainClassURI) {
this.domainClassURI = domainClassURI;
}

30
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/DatapropEditController.java
View file

@ -28,6 +28,7 @@ import edu.cornell.mannlib.vitro.webapp.controller.Controllers;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyDao;
import edu.cornell.mannlib.vitro.webapp.dao.PropertyGroupDao;
import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
public class DatapropEditController extends BaseEditController {
@ -45,7 +46,13 @@ public class DatapropEditController extends BaseEditController {
String datapropURI = request.getParameter("uri");
DataPropertyDao dpDao = vreq.getUnfilteredWebappDaoFactory().getDataPropertyDao();
DataPropertyDao dpDaoLangNeut = vreq.getLanguageNeutralWebappDaoFactory().getDataPropertyDao();
VClassDao vcDao = vreq.getLanguageNeutralWebappDaoFactory().getVClassDao();
VClassDao vcDaoWLang = vreq.getUnfilteredWebappDaoFactory().getVClassDao();
DataProperty dp = dpDao.getDataPropertyByURI(datapropURI);
DataProperty pLangNeut = dpDaoLangNeut.getDataPropertyByURI(request.getParameter("uri"));
PropertyGroupDao pgDao = vreq.getUnfilteredWebappDaoFactory().getPropertyGroupDao();
ArrayList results = new ArrayList();
@ -98,14 +105,21 @@ public class DatapropEditController extends BaseEditController {
//String parentPropertyStr = "<i>(datatype properties are not yet modeled in a property hierarchy)</i>"; // TODO - need multiple inheritance
//results.add(parentPropertyStr);
// TODO - need unionOf/intersectionOf-style domains for domain class
String domainStr="";
try {
VClass domainClass = getWebappDaoFactory().getVClassDao().getVClassByURI(dp.getDomainClassURI());
String domainLinkAnchor = (domainClass != null) ? domainClass.getPickListName() : dp.getDomainClassURI();
domainStr = (dp.getDomainClassURI() == null) ? "" : "<a href=\"vclassEdit?uri="+URLEncoder.encode(dp.getDomainClassURI(),"UTF-8")+"\">"+domainLinkAnchor+"</a>";
} catch (UnsupportedEncodingException e) {
log.error(e, e);
String domainStr = "";
if (pLangNeut.getDomainVClassURI() != null) {
VClass domainClass = vcDao.getVClassByURI(pLangNeut.getDomainVClassURI());
VClass domainWLang = vcDaoWLang.getVClassByURI(pLangNeut.getDomainVClassURI());
if (domainClass != null && domainClass.getURI() != null && domainClass.getPickListName() != null) {
try {
if (domainClass.isAnonymous()) {
domainStr = domainClass.getPickListName();
} else {
domainStr = "<a href=\"vclassEdit?uri="+URLEncoder.encode(domainClass.getURI(),"UTF-8")+"\">"+domainWLang.getPickListName()+"</a>";
}
} catch (UnsupportedEncodingException e) {
log.error(e, e);
}
}
}
results.add(domainStr); // column 6

23
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/PropertyEditController.java
View file

@ -27,6 +27,7 @@ import edu.cornell.mannlib.vitro.webapp.beans.PropertyGroup;
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.ModelAccess;
import edu.cornell.mannlib.vitro.webapp.dao.ObjectPropertyDao;
import edu.cornell.mannlib.vitro.webapp.dao.PropertyGroupDao;
import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
@ -47,10 +48,12 @@ public class PropertyEditController extends BaseEditController {
VitroRequest vreq = new VitroRequest(request);
ObjectPropertyDao propDao = vreq.getUnfilteredWebappDaoFactory().getObjectPropertyDao();
VClassDao vcDao = vreq.getUnfilteredWebappDaoFactory().getVClassDao();
ObjectPropertyDao propDaoLangNeut = vreq.getLanguageNeutralWebappDaoFactory().getObjectPropertyDao();
VClassDao vcDao = vreq.getLanguageNeutralWebappDaoFactory().getVClassDao();
VClassDao vcDaoWLang = vreq.getUnfilteredWebappDaoFactory().getVClassDao();
PropertyGroupDao pgDao = vreq.getUnfilteredWebappDaoFactory().getPropertyGroupDao();
DataPropertyDao dpDao = vreq.getUnfilteredWebappDaoFactory().getDataPropertyDao();
ObjectProperty p = (ObjectProperty)propDao.getObjectPropertyByURI(request.getParameter("uri"));
ObjectProperty p = propDao.getObjectPropertyByURI(request.getParameter("uri"));
ObjectProperty pLangNeut = propDaoLangNeut.getObjectPropertyByURI(request.getParameter("uri"));
request.setAttribute("property",p);
ArrayList<String> results = new ArrayList<String>();
@ -119,14 +122,15 @@ public class PropertyEditController extends BaseEditController {
results.add(p.getDomainPublic() == null ? "(no public label)" : p.getDomainPublic()); // column 6
String domainStr = "";
if (p.getDomainVClassURI() != null) {
VClass domainClass = vcDao.getVClassByURI(p.getDomainVClassURI());
if (pLangNeut.getDomainVClassURI() != null) {
VClass domainClass = vcDao.getVClassByURI(pLangNeut.getDomainVClassURI());
VClass domainWLang = vcDaoWLang.getVClassByURI(pLangNeut.getDomainVClassURI());
if (domainClass != null && domainClass.getURI() != null && domainClass.getPickListName() != null) {
try {
if (domainClass.isAnonymous()) {
domainStr = domainClass.getPickListName();
} else {
domainStr = "<a href=\"vclassEdit?uri="+URLEncoder.encode(domainClass.getURI(),"UTF-8")+"\">"+domainClass.getPickListName()+"</a>";
domainStr = "<a href=\"vclassEdit?uri="+URLEncoder.encode(domainClass.getURI(),"UTF-8")+"\">"+domainWLang.getPickListName()+"</a>";
}
} catch (UnsupportedEncodingException e) {
log.error(e, e);
@ -136,14 +140,15 @@ public class PropertyEditController extends BaseEditController {
results.add(domainStr); // column 7
String rangeStr = "";
if (p.getRangeVClassURI() != null) {
VClass rangeClass = vcDao.getVClassByURI(p.getRangeVClassURI());
if (pLangNeut.getRangeVClassURI() != null) {
VClass rangeClass = vcDao.getVClassByURI(pLangNeut.getRangeVClassURI());
VClass rangeWLang = vcDaoWLang.getVClassByURI(pLangNeut.getRangeVClassURI());
if (rangeClass != null && rangeClass.getURI() != null && rangeClass.getPickListName() != null) {
try {
if (rangeClass.isAnonymous()) {
rangeStr = rangeClass.getPickListName();
} else {
rangeStr = "<a href=\"vclassEdit?uri="+URLEncoder.encode(rangeClass.getURI(),"UTF-8")+"\">"+rangeClass.getPickListName()+"</a>";
rangeStr = "<a href=\"vclassEdit?uri="+URLEncoder.encode(rangeClass.getURI(),"UTF-8")+"\">"+rangeWLang.getPickListName()+"</a>";
}
} catch (UnsupportedEncodingException e) {
log.error(e, e);

26
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ListDatatypePropertiesController.java
View file

@ -20,6 +20,7 @@ import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission;
import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.Actions;
import edu.cornell.mannlib.vitro.webapp.beans.DataProperty;
import edu.cornell.mannlib.vitro.webapp.beans.Datatype;
import edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty;
import edu.cornell.mannlib.vitro.webapp.beans.PropertyGroup;
import edu.cornell.mannlib.vitro.webapp.beans.VClass;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
@ -57,7 +58,9 @@ public class ListDatatypePropertiesController extends FreemarkerHttpServlet {
String ontologyUri = vreq.getParameter("ontologyUri");
DataPropertyDao dao = vreq.getUnfilteredWebappDaoFactory().getDataPropertyDao();
DataPropertyDao dpDaoLangNeut = vreq.getLanguageNeutralWebappDaoFactory().getDataPropertyDao();
VClassDao vcDao = vreq.getUnfilteredWebappDaoFactory().getVClassDao();
VClassDao vcDaoLangNeut = vreq.getLanguageNeutralWebappDaoFactory().getVClassDao();
DatatypeDao dDao = vreq.getUnfilteredWebappDaoFactory().getDatatypeDao();
PropertyGroupDao pgDao = vreq.getUnfilteredWebappDaoFactory().getPropertyGroupDao();
@ -132,8 +135,11 @@ public class ListDatatypePropertiesController extends FreemarkerHttpServlet {
}
}
*/
VClass vc = (prop.getDomainClassURI() != null) ? vcDao.getVClassByURI(prop.getDomainClassURI()) : null;
String domainStr = (vc != null) ? vc.getPickListName() : "";
DataProperty dpLangNeut = dpDaoLangNeut.getDataPropertyByURI(prop.getURI());
if(dpLangNeut == null) {
dpLangNeut = prop;
}
String domainStr = getVClassNameFromURI(dpLangNeut.getDomainVClassURI(), vcDao, vcDaoLangNeut);
json += "\"domainVClass\": " + JSONUtils.quote(domainStr) + ", " ;
Datatype rangeDatatype = dDao.getDatatypeByURI(prop.getRangeDatatypeURI());
@ -156,4 +162,20 @@ public class ListDatatypePropertiesController extends FreemarkerHttpServlet {
}
return new TemplateResponseValues(TEMPLATE_NAME, body);
}
private String getVClassNameFromURI(String vclassURI, VClassDao vcDao, VClassDao vcDaoLangNeut) {
if(vclassURI == null) {
return "";
}
VClass vclass = vcDaoLangNeut.getVClassByURI(vclassURI);
if(vclass == null) {
return "";
}
if(vclass.isAnonymous()) {
return vclass.getPickListName();
} else {
VClass vclassWLang = vcDao.getVClassByURI(vclassURI);
return (vclassWLang != null) ? vclassWLang.getPickListName() : vclass.getPickListName();
}
}
}

28
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ListPropertyWebappsController.java
View file

@ -59,8 +59,10 @@ public class ListPropertyWebappsController extends FreemarkerHttpServlet {
String ontologyUri = vreq.getParameter("ontologyUri");
ObjectPropertyDao dao = vreq.getUnfilteredWebappDaoFactory().getObjectPropertyDao();
ObjectPropertyDao opDaoLangNeut = vreq.getLanguageNeutralWebappDaoFactory().getObjectPropertyDao();
PropertyInstanceDao piDao = vreq.getLanguageNeutralWebappDaoFactory().getPropertyInstanceDao();
VClassDao vcDao = vreq.getUnfilteredWebappDaoFactory().getVClassDao();
VClassDao vcDaoLangNeut = vreq.getLanguageNeutralWebappDaoFactory().getVClassDao();
PropertyGroupDao pgDao = vreq.getUnfilteredWebappDaoFactory().getPropertyGroupDao();
String vclassURI = vreq.getParameter("vclassUri");
@ -160,12 +162,14 @@ public class ListPropertyWebappsController extends FreemarkerHttpServlet {
json += "\"data\": { \"internalName\": " + JSONUtils.quote(prop.getLocalNameWithPrefix()) + ", ";
VClass vc = (prop.getDomainVClassURI() != null) ? vcDao.getVClassByURI(prop.getDomainVClassURI()) : null;
String domainStr = (vc != null) ? vc.getPickListName() : "";
ObjectProperty opLangNeut = opDaoLangNeut.getObjectPropertyByURI(prop.getURI());
if(opLangNeut == null) {
opLangNeut = prop;
}
String domainStr = getVClassNameFromURI(opLangNeut.getDomainVClassURI(), vcDao, vcDaoLangNeut);
json += "\"domainVClass\": " + JSONUtils.quote(domainStr) + ", " ;
vc = (prop.getRangeVClassURI() != null) ? vcDao.getVClassByURI(prop.getRangeVClassURI()) : null;
String rangeStr = (vc != null) ? vc.getPickListName() : "";
String rangeStr = getVClassNameFromURI(opLangNeut.getRangeVClassURI(), vcDao, vcDaoLangNeut);
json += "\"rangeVClass\": " + JSONUtils.quote(rangeStr) + ", " ;
if (prop.getGroupURI() != null) {
@ -186,4 +190,20 @@ public class ListPropertyWebappsController extends FreemarkerHttpServlet {
return new TemplateResponseValues(TEMPLATE_NAME, body);
}
private String getVClassNameFromURI(String vclassURI, VClassDao vcDao, VClassDao vcDaoLangNeut) {
if(vclassURI == null) {
return "";
}
VClass vclass = vcDaoLangNeut.getVClassByURI(vclassURI);
if(vclass == null) {
return "";
}
if(vclass.isAnonymous()) {
return vclass.getPickListName();
} else {
VClass vclassWLang = vcDao.getVClassByURI(vclassURI);
return (vclassWLang != null) ? vclassWLang.getPickListName() : vclass.getPickListName();
}
}
}

36
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ShowDataPropertyHierarchyController.java
View file

@ -21,6 +21,7 @@ import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission;
import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.Actions;
import edu.cornell.mannlib.vitro.webapp.beans.DataProperty;
import edu.cornell.mannlib.vitro.webapp.beans.Datatype;
import edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty;
import edu.cornell.mannlib.vitro.webapp.beans.PropertyGroup;
import edu.cornell.mannlib.vitro.webapp.beans.VClass;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
@ -40,7 +41,9 @@ public class ShowDataPropertyHierarchyController extends FreemarkerHttpServlet {
private int MAXDEPTH = 5;
private DataPropertyDao dpDao = null;
private DataPropertyDao dpDaoLangNeut = null;
private VClassDao vcDao = null;
private VClassDao vcDaoLangNeut = null;
private PropertyGroupDao pgDao = null;
private DatatypeDao dDao = null;
@ -77,7 +80,9 @@ public class ShowDataPropertyHierarchyController extends FreemarkerHttpServlet {
body.put("propertyType", "data");
dpDao = vreq.getUnfilteredAssertionsWebappDaoFactory().getDataPropertyDao();
dpDaoLangNeut = vreq.getLanguageNeutralWebappDaoFactory().getDataPropertyDao();
vcDao = vreq.getUnfilteredAssertionsWebappDaoFactory().getVClassDao();
vcDaoLangNeut = vreq.getLanguageNeutralWebappDaoFactory().getVClassDao();
pgDao = vreq.getUnfilteredAssertionsWebappDaoFactory().getPropertyGroupDao();
dDao = vreq.getUnfilteredAssertionsWebappDaoFactory().getDatatypeDao();
@ -217,15 +222,14 @@ public class ShowDataPropertyHierarchyController extends FreemarkerHttpServlet {
tempString += "\"data\": { \"internalName\": " + JSONUtils.quote(
dp.getPickListName()) + ", ";
VClass tmp = null;
DataProperty dpLangNeut = dpDaoLangNeut.getDataPropertyByURI(dp.getURI());
if(dpLangNeut == null) {
dpLangNeut = dp;
}
String domainStr = getVClassNameFromURI(dpLangNeut.getDomainVClassURI(), vcDao, vcDaoLangNeut);
try {
tempString += "\"domainVClass\": " + JSONUtils.quote(
((tmp = vcDao.getVClassByURI(dp.getDomainClassURI())) != null
&& (tmp.getPickListName() == null))
? ""
: vcDao.getVClassByURI(
dp.getDomainClassURI())
.getPickListName()) + ", " ;
tempString += "\"domainVClass\": " + JSONUtils.quote(domainStr) + ", " ;
} catch (NullPointerException e) {
tempString += "\"domainVClass\": \"\",";
}
@ -249,4 +253,20 @@ public class ShowDataPropertyHierarchyController extends FreemarkerHttpServlet {
return tempString;
}
private String getVClassNameFromURI(String vclassURI, VClassDao vcDao, VClassDao vcDaoLangNeut) {
if(vclassURI == null) {
return "";
}
VClass vclass = vcDaoLangNeut.getVClassByURI(vclassURI);
if(vclass == null) {
return "";
}
if(vclass.isAnonymous()) {
return vclass.getPickListName();
} else {
VClass vclassWLang = vcDao.getVClassByURI(vclassURI);
return (vclassWLang != null) ? vclassWLang.getPickListName() : vclass.getPickListName();
}
}
}

45
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ShowObjectPropertyHierarchyController.java
View file

@ -39,7 +39,9 @@ public class ShowObjectPropertyHierarchyController extends FreemarkerHttpServlet
private int MAXDEPTH = 5;
private ObjectPropertyDao opDao = null;
private ObjectPropertyDao opDaoLangNeut = null;
private VClassDao vcDao = null;
private VClassDao vcDaoLangNeut = null;
private PropertyGroupDao pgDao = null;
private int previous_posn = 0;
@ -75,7 +77,9 @@ public class ShowObjectPropertyHierarchyController extends FreemarkerHttpServlet
body.put("propertyType", "object");
opDao = vreq.getUnfilteredAssertionsWebappDaoFactory().getObjectPropertyDao();
opDaoLangNeut = vreq.getLanguageNeutralWebappDaoFactory().getObjectPropertyDao();
vcDao = vreq.getUnfilteredAssertionsWebappDaoFactory().getVClassDao();
vcDaoLangNeut = vreq.getLanguageNeutralWebappDaoFactory().getVClassDao();
pgDao = vreq.getUnfilteredAssertionsWebappDaoFactory().getPropertyGroupDao();
String json = new String();
@ -213,29 +217,20 @@ public class ShowObjectPropertyHierarchyController extends FreemarkerHttpServlet
tempString += "\"data\": { \"internalName\": " + JSONUtils.quote(
op.getLocalNameWithPrefix()) + ", ";
VClass tmp = null;
ObjectProperty opLangNeut = opDaoLangNeut.getObjectPropertyByURI(op.getURI());
if(opLangNeut == null) {
opLangNeut = op;
}
String domainStr = getVClassNameFromURI(opLangNeut.getDomainVClassURI(), vcDao, vcDaoLangNeut);
String rangeStr = getVClassNameFromURI(opLangNeut.getRangeVClassURI(), vcDao, vcDaoLangNeut);
try {
tempString += "\"domainVClass\": " + JSONUtils.quote(
((tmp = vcDao.getVClassByURI(
op.getDomainVClassURI())) != null
&& (tmp.getPickListName() == null))
? ""
: vcDao.getVClassByURI(
op.getDomainVClassURI())
.getPickListName()) + ", " ;
tempString += "\"domainVClass\": " + JSONUtils.quote(domainStr) + ", " ;
} catch (NullPointerException e) {
tempString += "\"domainVClass\": \"\",";
}
try {
tempString += "\"rangeVClass\": " + JSONUtils.quote(
((tmp = vcDao.getVClassByURI(
op.getRangeVClassURI())) != null
&& (tmp.getPickListName() == null))
? ""
: vcDao.getVClassByURI(
op.getRangeVClassURI())
.getPickListName()) + ", " ;
tempString += "\"rangeVClass\": " + JSONUtils.quote(rangeStr) + ", " ;
} catch (NullPointerException e) {
tempString += "\"rangeVClass\": \"\",";
}
@ -253,6 +248,22 @@ public class ShowObjectPropertyHierarchyController extends FreemarkerHttpServlet
return tempString;
}
private String getVClassNameFromURI(String vclassURI, VClassDao vcDao, VClassDao vcDaoLangNeut) {
if(vclassURI == null) {
return "";
}
VClass vclass = vcDaoLangNeut.getVClassByURI(vclassURI);
if(vclass == null) {
return "";
}
if(vclass.isAnonymous()) {
return vclass.getPickListName();
} else {
VClass vclassWLang = vcDao.getVClassByURI(vclassURI);
return (vclassWLang != null) ? vclassWLang.getPickListName() : vclass.getPickListName();
}
}
public static class ObjectPropertyAlphaComparator implements Comparator<ObjectProperty> {
Collator collator;

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

@ -183,7 +183,7 @@ public class DataPropertyDaoJena extends PropertyDaoJena implements
dp.setPickListName(getWebappDaoFactory().makePickListName(dp));
Resource dRes = op.getDomain();
if (dRes != null) {
dp.setDomainClassURI(dRes.getURI());
dp.setDomainClassURI(dRes.isAnon()? PSEUDO_BNODE_NS + dRes.getId().toString() : dRes.getURI());
}
Resource rRes = op.getRange();
if (rRes != null) {

1
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/VClassDaoJena.java
View file

@ -192,6 +192,7 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
return getLabelOrId(cls);
}
} catch (Exception e) {
log.error(e, e);
return "???";
} finally {
cls.getModel().leaveCriticalSection();

190
webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/ABoxRecomputer.java
View file

@ -107,6 +107,9 @@ public class ABoxRecomputer {
}
}
// don't check for existing inferences in the rebuild model
private boolean DO_CHECK = true;
/*
* Recompute the entire ABox inference graph. The new
* inference graph is built in a separate model and
@ -132,11 +135,13 @@ public class ABoxRecomputer {
log.info("Recomputing inferences for " + individuals.size() + " individuals");
long start = System.currentTimeMillis();
for (String individualURI : individuals) {
Resource individual = ResourceFactory.createResource(individualURI);
try {
addedABoxTypeAssertion(individual, inferenceRebuildModel, unknownTypes);
addedABoxTypeAssertion(individual, inferenceRebuildModel, unknownTypes, DO_CHECK);
simpleReasoner.setMostSpecificTypes(individual, inferenceRebuildModel, unknownTypes);
List<ReasonerPlugin> pluginList = simpleReasoner.getPluginList();
if (pluginList.size() > 0) {
@ -165,8 +170,11 @@ public class ABoxRecomputer {
}
numStmts++;
if ((numStmts % 10000) == 0) {
log.info("Still computing class subsumption ABox inferences...");
if ((numStmts % 1000) == 0) {
log.info("Still computing class subsumption ABox inferences ("
+ numStmts + "/" + individuals.size() + " individuals)");
log.info((System.currentTimeMillis() - start) / 1000 + " ms per individual");
start = System.currentTimeMillis();
}
if (stopRequested) {
@ -275,7 +283,7 @@ public class ABoxRecomputer {
log.info("Finished computing sameAs ABox inferences");
try {
if (updateInferenceModel(inferenceRebuildModel)) {
if (updateInferenceModel(inferenceRebuildModel, individuals)) {
log.info("a stopRequested signal was received during updateInferenceModel. Halting Processing.");
return;
}
@ -366,7 +374,13 @@ public class ABoxRecomputer {
}
protected void addedABoxTypeAssertion(Resource individual, Model inferenceModel, HashSet<String> unknownTypes) {
protected void addedABoxTypeAssertion(Resource individual, Model inferenceModel,
HashSet<String> unknownTypes) {
addedABoxTypeAssertion(individual, inferenceModel, unknownTypes, true);
}
protected void addedABoxTypeAssertion(Resource individual, Model inferenceModel,
HashSet<String> unknownTypes, boolean checkRedundancy) {
StmtIterator iter = null;
@ -376,7 +390,8 @@ public class ABoxRecomputer {
while (iter.hasNext()) {
Statement stmt = iter.next();
simpleReasoner.addedABoxTypeAssertion(stmt, inferenceModel, unknownTypes);
simpleReasoner.addedABoxTypeAssertion(
stmt, inferenceModel, unknownTypes, checkRedundancy);
}
} finally {
if (iter != null) {
@ -388,125 +403,72 @@ public class ABoxRecomputer {
/*
* reconcile a set of inferences into the application inference model
*/
protected boolean updateInferenceModel(Model inferenceRebuildModel) {
protected boolean updateInferenceModel(Model inferenceRebuildModel,
Collection<String> individuals) {
log.info("Updating ABox inference model");
Iterator<Statement> iter = null;
log.info("Updating ABox inference model");
// Remove everything from the current inference model that is not
// in the recomputed inference model
int num = 0;
scratchpadModel.enterCriticalSection(Lock.WRITE);
scratchpadModel.removeAll();
log.info("Updating ABox inference model (checking for outdated inferences)");
try {
inferenceModel.enterCriticalSection(Lock.READ);
// Remove everything from the current inference model that is not
// in the recomputed inference model
int num = 0;
scratchpadModel.enterCriticalSection(Lock.WRITE);
scratchpadModel.removeAll();
Model rebuild = ModelFactory.createDefaultModel();
Model existing = ModelFactory.createDefaultModel();
try {
iter = listModelStatements(inferenceModel, JenaDataSourceSetupBase.JENA_INF_MODEL);
while (iter.hasNext()) {
Statement stmt = iter.next();
if (!inferenceRebuildModel.contains(stmt)) {
scratchpadModel.add(stmt);
}
long start = System.currentTimeMillis();
num++;
if ((num % 10000) == 0) {
log.info("Still updating ABox inference model (checking for outdated inferences)...");
}
for (String individualURI : individuals) {
rebuild.removeAll();
existing.removeAll();
Resource subjInd = ResourceFactory.createResource(individualURI);
inferenceModel.enterCriticalSection(Lock.READ);
try {
existing.add(inferenceModel.listStatements(subjInd, null, (RDFNode) null));
} finally {
inferenceModel.leaveCriticalSection();
}
inferenceRebuildModel.enterCriticalSection(Lock.READ);
try {
rebuild.add(inferenceRebuildModel.listStatements(subjInd, null, (RDFNode) null));
} finally {
inferenceRebuildModel.leaveCriticalSection();
}
if (stopRequested) {
return true;
}
}
} finally {
// if (iter != null) {
// iter.close();
// }
inferenceModel.leaveCriticalSection();
}
Model retractions = existing.difference(rebuild);
Model additions = rebuild.difference(existing);
try {
iter = listModelStatements(scratchpadModel, SimpleReasonerSetup.JENA_INF_MODEL_SCRATCHPAD);
while (iter.hasNext()) {
Statement stmt = iter.next();
inferenceModel.enterCriticalSection(Lock.WRITE);
try {
inferenceModel.remove(retractions);
inferenceModel.add(additions);
} finally {
inferenceModel.leaveCriticalSection();
}
// skip statements with blank nodes to avoid excessive deletion
if (stmt.getSubject().isAnon() || stmt.getObject().isAnon()) {
continue;
}
inferenceRebuildModel.enterCriticalSection(Lock.WRITE);
try {
inferenceRebuildModel.remove(rebuild);
} finally {
inferenceRebuildModel.leaveCriticalSection();
}
inferenceModel.enterCriticalSection(Lock.WRITE);
try {
inferenceModel.remove(stmt);
} finally {
inferenceModel.leaveCriticalSection();
}
}
} finally {
// if (iter != null) {
// iter.close();
// }
}
num++;
if ((num % 1000) == 0) {
log.info("Still updating ABox inference model (" +
+ num + "/" + individuals.size() + " individuals)");
log.info((System.currentTimeMillis() - start) / 1000 + " ms per individual");
start = System.currentTimeMillis();
}
// Add everything from the recomputed inference model that is not already
// in the current inference model to the current inference model.
try {
scratchpadModel.removeAll();
log.info("Updating ABox inference model (adding any new inferences)");
iter = listModelStatements(inferenceRebuildModel, SimpleReasonerSetup.JENA_INF_MODEL_REBUILD);
if (stopRequested) {
return true;
}
while (iter.hasNext()) {
Statement stmt = iter.next();
}
inferenceModel.enterCriticalSection(Lock.READ);
try {
if (!inferenceModel.contains(stmt)) {
scratchpadModel.add(stmt);
}
} finally {
inferenceModel.leaveCriticalSection();
}
num++;
if ((num % 10000) == 0) {
log.info("Still updating ABox inference model (adding any new inferences)...");
}
if (stopRequested) {
return true;
}
}
} finally {
// if (iter != null) {
// iter.close();
// }
}
iter = listModelStatements(scratchpadModel, SimpleReasonerSetup.JENA_INF_MODEL_SCRATCHPAD);
try {
while (iter.hasNext()) {
Statement stmt = iter.next();
inferenceModel.enterCriticalSection(Lock.WRITE);
try {
inferenceModel.add(stmt);
} finally {
inferenceModel.leaveCriticalSection();
}
}
} finally {
// if (iter != null) {
// iter.close();
// }
}
} finally {
scratchpadModel.removeAll();
scratchpadModel.leaveCriticalSection();
}
log.info("ABox inference model updated");
return false;
log.info("ABox inference model updated");
return false;
}
private Iterator<Statement> listModelStatements(Model model, String graphURI) {

2
webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/ReasonerPlugin.java
View file

@ -12,6 +12,8 @@ public interface ReasonerPlugin {
public boolean isInterestedInRemovedStatement(Statement stmt);
public boolean isConfigurationOnlyPlugin();
public void addedABoxStatement(Statement stmt,
Model aboxAssertionsModel,
Model aboxInferencesModel,

28
webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasoner.java
View file

@ -162,6 +162,10 @@ public class SimpleReasoner extends StatementListener {
this.doSameAs = tf;
}
public boolean getSameAsEnabled() {
return this.doSameAs;
}
/*
* Performs incremental ABox reasoning based
* on the addition of a new statement
@ -343,6 +347,12 @@ public class SimpleReasoner extends StatementListener {
changedTBoxStatement(stmt, false);
}
protected void addedABoxTypeAssertion(Statement stmt,
Model inferenceModel,
HashSet<String> unknownTypes) {
addedABoxTypeAssertion(stmt, inferenceModel, unknownTypes, true);
}
/**
* Performs incremental reasoning based on a new type assertion
* added to the ABox (assertion that an individual is of a certain
@ -353,7 +363,8 @@ public class SimpleReasoner extends StatementListener {
*/
protected void addedABoxTypeAssertion(Statement stmt,
Model inferenceModel,
HashSet<String> unknownTypes) {
HashSet<String> unknownTypes,
boolean checkRedundancy) {
tboxModel.enterCriticalSection(Lock.READ);
try {
@ -379,7 +390,7 @@ public class SimpleReasoner extends StatementListener {
Statement infStmt =
ResourceFactory.createStatement(stmt.getSubject(),
RDF.type, parentClass);
addInference(infStmt,inferenceModel,true);
addInference(infStmt, inferenceModel, true, checkRedundancy);
}
}
} else {
@ -1189,13 +1200,20 @@ public class SimpleReasoner extends StatementListener {
addInference(infStmt,inferenceModel,true);
}
protected void addInference(Statement infStmt, Model inferenceModel, boolean handleSameAs) {
protected void addInference(Statement infStmt, Model inferenceModel,
boolean handleSameAs) {
addInference(infStmt, inferenceModel, handleSameAs, true);
}
protected void addInference(Statement infStmt, Model inferenceModel,
boolean handleSameAs, boolean checkRedundancy) {
aboxModel.enterCriticalSection(Lock.READ);
try {
inferenceModel.enterCriticalSection(Lock.WRITE);
try {
if (!inferenceModel.contains(infStmt) && !aboxModel.contains(infStmt)) {
if (!checkRedundancy
|| (!inferenceModel.contains(infStmt) && !aboxModel.contains(infStmt))) {
inferenceModel.add(infStmt);
}
@ -1732,8 +1750,6 @@ public class SimpleReasoner extends StatementListener {
}
}
/**
* Utility method for logging
*/

6
webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/plugin/DisableSameAs.java
View file

@ -15,7 +15,7 @@ import edu.cornell.mannlib.vitro.webapp.reasoner.SimpleReasoner;
/**
* Disables sameAs in associated SimpleReasoner.
*/
public abstract class DisableSameAs implements ReasonerPlugin {
public class DisableSameAs implements ReasonerPlugin {
private static final Log log = LogFactory.getLog(DisableSameAs.class);
@ -27,6 +27,10 @@ public abstract class DisableSameAs implements ReasonerPlugin {
log.info("owl:sameAs disabled in SimpleReasoner.");
}
public boolean isConfigurationOnlyPlugin() {
return true;
}
public SimpleReasoner getSimpleReasoner() {
return this.simpleReasoner;
}

4
webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/plugin/SimpleBridgingRule.java
View file

@ -62,6 +62,10 @@ public abstract class SimpleBridgingRule implements ReasonerPlugin {
}
public boolean isConfigurationOnlyPlugin() {
return false;
}
public boolean isInterestedInAddedStatement(Statement stmt) {
return isRelevantPredicate(stmt);
}

4
webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/plugin/SimplePropertyAndTypeRule.java
View file

@ -36,6 +36,10 @@ public abstract class SimplePropertyAndTypeRule implements ReasonerPlugin {
INFERRED_PROP = ResourceFactory.createProperty(inferredProp);
}
public boolean isConfigurationOnlyPlugin() {
return false;
}
public boolean isInterestedInAddedStatement(Statement stmt) {
return (RDF.type.equals(stmt.getPredicate()) || isRelevantPredicate(stmt));
}

5
webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/SimpleReasonerSetup.java
View file

@ -104,7 +104,10 @@ public class SimpleReasonerSetup implements ServletContextListener {
ReasonerPlugin plugin = (ReasonerPlugin) Class.forName(
classname).getConstructors()[0].newInstance();
plugin.setSimpleReasoner(simpleReasoner);
pluginList.add(plugin);
if (!plugin.isConfigurationOnlyPlugin()) {
pluginList.add(plugin);
log.info("adding reasoner plugin " + plugin.getClass().getName());
}
} catch(Throwable t) {
ss.info(this, "Could not instantiate reasoner plugin " + classname);
}

21
webapp/test/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasonerInversePropertyTest.java
View file

@ -14,6 +14,7 @@ import com.hp.hpl.jena.ontology.OntProperty;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.vocabulary.OWL;
import edu.cornell.mannlib.vitro.testing.AbstractTestClass;
import edu.cornell.mannlib.vitro.webapp.utils.threads.VitroBackgroundThread;
@ -431,10 +432,10 @@ public class SimpleReasonerInversePropertyTest extends AbstractTestClass {
tBox.register(simpleReasonerTBoxListener);
// add abox data
Resource a = aBox.createResource("http://test.vivo/a");
Resource b = aBox.createResource("http://test.vivo/b");
Resource c = aBox.createResource("http://test.vivo/c");
Resource d = aBox.createResource("http://test.vivo/d");
Resource a = aBox.createIndividual("http://test.vivo/a", OWL.Thing);
Resource b = aBox.createIndividual("http://test.vivo/b", OWL.Thing);
Resource c = aBox.createIndividual("http://test.vivo/c", OWL.Thing);
Resource d = aBox.createIndividual("http://test.vivo/d", OWL.Thing);
aBox.add(a,P,b);
aBox.add(c,P,d);
@ -496,8 +497,8 @@ public class SimpleReasonerInversePropertyTest extends AbstractTestClass {
tBox.register(simpleReasonerTBoxListener);
// add statements to the abox and verify inference
Resource c = aBox.createResource("http://test.vivo/c");
Resource d = aBox.createResource("http://test.vivo/d");
Resource c = aBox.createIndividual("http://test.vivo/c", OWL.Thing);
Resource d = aBox.createIndividual("http://test.vivo/d", OWL.Thing);
aBox.add(c,P,d);
Assert.assertTrue(inf.contains(d,Q,c));
@ -555,10 +556,10 @@ public class SimpleReasonerInversePropertyTest extends AbstractTestClass {
aBox.register(simpleReasoner);
// abox statements
Resource a = aBox.createResource("http://test.vivo/a");
Resource b = aBox.createResource("http://test.vivo/b");
Resource c = aBox.createResource("http://test.vivo/c");
Resource d = aBox.createResource("http://test.vivo/d");
Resource a = aBox.createIndividual("http://test.vivo/a", OWL.Thing);
Resource b = aBox.createIndividual("http://test.vivo/b", OWL.Thing);
Resource c = aBox.createIndividual("http://test.vivo/c", OWL.Thing);
Resource d = aBox.createIndividual("http://test.vivo/d", OWL.Thing);
aBox.add(a,P,b);
aBox.add(c,X,d);

8
webapp/test/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasonerSameAsTest.java
View file

@ -782,10 +782,10 @@ public class SimpleReasonerSameAsTest extends AbstractTestClass {
aBox.register(simpleReasoner);
// Individuals a, b, c and d
Resource a = aBox.createResource("http://test.vivo/a");
Resource b = aBox.createResource("http://test.vivo/b");
Resource c = aBox.createResource("http://test.vivo/c");
Resource d = aBox.createResource("http://test.vivo/d");
Resource a = aBox.createIndividual("http://test.vivo/a", OWL.Thing);
Resource b = aBox.createIndividual("http://test.vivo/b", OWL.Thing);
Resource c = aBox.createIndividual("http://test.vivo/c", OWL.Thing);
Resource d = aBox.createIndividual("http://test.vivo/d", OWL.Thing);
aBox.add(a,P,c);
aBox.add(a,S,literal1);

2
webapp/web/i18n/all.properties
View file

@ -697,6 +697,7 @@ select_existing_collaborator = Select an existing Collaborator for {0}
selected = Selected
change_selection = change selection
there_are_no_entries_for_selection = There are no entries in the system from which to select.
the_range_class_does_not_exist= The range class for this property does not exist in the system.
editing_prohibited = This property is currently configured to prohibit editing.
confirm_entry_deletion_from = Are you sure you want to delete the following entry from
@ -752,6 +753,7 @@ custom_template_containing_content = Custom template containing all content
a_menu_page = This is a menu page
menu_item_name = Menu Item Name
if_blank_page_title_used = If left blank, the page title will be used.
multiple_content_default_template_error = With multiple content types, you must specify a custom template.
label = label
no_classes_to_select = There are no Classes in the system from which to select.

45
webapp/web/js/menupage/pageManagementUtils.js
View file

@ -205,13 +205,15 @@ var pageManagementUtils = {
//Also clear custom template value so as not to submit it
pageManagementUtils.clearInputs(pageManagementUtils.customTemplate);
pageManagementUtils.rightSideDiv.show();
pageManagementUtils.disablePageSave();
//Check to see if there is already content on page, in which case save should be enabled
var pageContentSections = $("section[class='pageContent']");
if(pageContentSections.length == 0) {
pageManagementUtils.disablePageSave();
}
});
this.customTemplateRadio.click( function() {
pageManagementUtils.customTemplate.removeClass('hidden');
pageManagementUtils.rightSideDiv.show();
pageManagementUtils.disablePageSave();
pageManagementUtils.handleSelectCustomTemplate();
});
this.selfContainedTemplateRadio.click( function() {
@ -265,6 +267,16 @@ var pageManagementUtils = {
});
},
handleSelectCustomTemplate: function() {
pageManagementUtils.customTemplate.removeClass('hidden');
pageManagementUtils.rightSideDiv.show();
//Check to see if there is already content on page, in which case save should be enabled
var pageContentSections = $("section[class='pageContent']");
if(pageContentSections.length == 0) {
pageManagementUtils.disablePageSave();
}
},
handleClickDone:function() {
var selectedType = pageManagementUtils.contentTypeSelect.val();
var selectedTypeText = $("#typeSelect option:selected").text();
@ -392,6 +404,9 @@ var pageManagementUtils = {
pageManagementUtils.adjustSaveButtonHeight();
//Disable save button until the user has clicked done or cancel from the addition
pageManagementUtils.disablePageSave();
//If the default template is selected, there is already content on the page, and the user is selecting new content
//display alert message that they must select a custom template and select
pageManagementUtils.checkTemplateForMultipleContent(_this.contentTypeSelect.val());
},
disablePageSave:function() {
pageManagementUtils.pageSaveButton.attr("disabled", "disabled");
@ -430,6 +445,21 @@ var pageManagementUtils = {
$el.find("select option:eq(0)").attr("selected", "selected");
},
checkTemplateForMultipleContent:function(contentTypeSelected) {
if(contentTypeSelected != "") {
var pageContentSections = $("section[class='pageContent']");
var selectedTemplateValue = $('input:radio[name=selectedTemplate]:checked').val();
//A new section hasn't been added yet so check to see if there is at least one content type already on page
if(selectedTemplateValue == "default" && pageContentSections.length >= 1) {
//alert the user that they should be picking custom template instead
alert(pageManagementUtils.multipleContentWithDefaultTemplateError);
//pick custom template
$('input:radio[name=selectedTemplate][value="custom"]').attr("checked", true);
pageManagementUtils.handleSelectCustomTemplate();
}
}
},
//Clone content area
//When adding a new content type, this function will copy the values from the new content form and generate
//the content for the new section containing the content
@ -874,7 +904,12 @@ var pageManagementUtils = {
if(pageContentSections.length == 0) {
validationErrorMsg = pageManagementUtils.selectContentType + " <br /> ";
} else {
//For each, based on type, validate if a validation function exists
//If there are multiple content types, and the default template option is selected, then display error message
var selectedTemplateValue = $('input:radio[name=selectedTemplate]:checked').val();
if(selectedTemplateValue == "default") {
validationErrorMsg += pageManagementUtils.multipleContentWithDefaultTemplateError;
}
//For each, based on type, validate if a validation function exists
$.each(pageContentSections, function(i) {
if(pageManagementUtils.processDataGetterUtils != null) {
var dataGetterType = pageManagementUtils.processDataGetterUtils.selectDataGetterType($(this));

84
webapp/web/templates/freemarker/body/menupage/menupage--exampleMultipleContentTypes.ftl Normal file
View file

@ -0,0 +1,84 @@
<#-- $This file is distributed under the terms of the license in /doc/license.txt$ -->
<#--This is an example of including multiple content types in the same template, this combines the default templates for Fixed HTML, Class groups and Solr Individuals in one template-->
<#include "menupage-checkForData.ftl">
<#--Fixed HTML portion-->
<#--Note that variableName is employed by both the fixed html and sparql query templates, this is used to store the
actual name of the variable that is used to store either the fixed html or sparql query results. If combining fixed html
and sparql query results in a custom template, the template can utilize the actual variable name e.g. "query results" instead of how
variableName is used below.-->
<#assign htmlExists = false/>
<#if variableName?has_content>
<#assign htmlExists = true />
</#if>
<#if htmlExists>
${.globals[variableName]}
<#else>
${i18n().no_html_specified}
</#if>
<#--Class grou section-->
<#if !noData>
<section id="menupage-intro" role="region">
<h2>${page.title}</h2>
</section>
<#include "menupage-browse.ftl">
${stylesheets.add('<link rel="stylesheet" href="${urls.base}/css/menupage/menupage.css" />')}
<#include "menupage-scripts.ftl">
<#else>
${noDataNotification}
</#if>
<#--Solr Individuals section-->
<#import "lib-list.ftl" as l>
<#include "individualList-checkForData.ftl">
${stylesheets.add('<link rel="stylesheet" href="${urls.base}/css/browseIndex.css" />')}
<section class="individualList">
<h2>${title}
</h2>
<#if subtitle?has_content>
<h4>${subtitle}</h4>
</#if>
<#if (!noData)>
<#if errorMessage?has_content>
<p>${errorMessage}</p>
<#else>
<#assign pagination>
<#if (pages?has_content && pages?size > 1)>
${i18n().pages}:
<ul class="pagination">
<#list pages as page>
<#if page.selected>
<li class="selectedNavPage">${page.text}</li>
<#else>
<#-- RY Ideally the urls would be generated by the controller; see search-pagedResults.ftl -->
<li><a href="${urls.base}/individuallist?${page.param}&vclassId=${vclassId?url}" title="${i18n().page_text}">${page.text}</a></li>
</#if>
</#list>
</ul>
</#if>
</#assign>
${pagination}
<ul>
<#list individuals as individual>
<li>
<@shortView uri=individual.uri viewContext="index" />
</li>
</#list>
</ul>
${pagination}
</#if>
<#else>
${noDataNotification}
</#if>
</section> <!-- .individualList -->

3
webapp/web/templates/freemarker/edit/forms/pageManagement.ftl
View file

@ -189,7 +189,8 @@
supplyPrettyUrl: '${i18n().supply_url}',
startUrlWithSlash: '${i18n().start_url_with_slash}',
supplyTemplate: '${i18n().supply_template}',
selectContentType: '${i18n().select_content_type}'
selectContentType: '${i18n().select_content_type}',
multipleContentWithDefaultTemplateError: '${i18n().multiple_content_default_template_error}'
};
</script>