merge recent revision from trunk
This commit is contained in:
brianjlowe
parent
b480cb2eea
commit
101de4614b
6 changed files with 1632 additions and 259 deletions
|
|
@ -0,0 +1,40 @@
|
|||
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
|
||||
|
||||
package edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.utils;
|
||||
|
||||
import java.lang.reflect.Constructor;
|
||||
import java.util.HashMap;
|
||||
import java.util.Map;
|
||||
|
||||
import javax.servlet.ServletContext;
|
||||
|
||||
import net.sf.json.JSONObject;
|
||||
|
||||
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.RDFNode;
|
||||
import com.hp.hpl.jena.rdf.model.ResourceFactory;
|
||||
import com.hp.hpl.jena.rdf.model.StmtIterator;
|
||||
|
||||
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
|
||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
|
||||
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.utils.ProcessDataGetterN3;
|
||||
import edu.cornell.mannlib.vitro.webapp.utils.dataGetter.DataGetter;
|
||||
|
||||
/*
|
||||
* This class determines what n3 should be returned for a particular data getter and can be overwritten or extended in VIVO.
|
||||
*/
|
||||
public class ProcessDataGetterN3Map {
|
||||
private static final Log log = LogFactory.getLog(ProcessDataGetterN3Map.class);
|
||||
public static HashMap<String, String> getDataGetterTypeToProcessorMap() {
|
||||
HashMap<String, String> map = new HashMap<String, String>();
|
||||
map.put("edu.cornell.mannlib.vitro.webapp.utils.dataGetter.SparqlQueryDataGetter", "edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.utils.ProcessSparqlDataGetterN3");
|
||||
map.put("edu.cornell.mannlib.vitro.webapp.utils.dataGetter.ClassGroupPageData", "edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.utils.ProcessClassGroupDataGetterN3");
|
||||
map.put("edu.cornell.mannlib.vitro.webapp.utils.dataGetter.IndividualsForClassesDataGetter", "edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.utils.ProcessIndividualsForClassesDataGetterN3");
|
||||
map.put("edu.cornell.mannlib.vitro.webapp.utils.dataGetter.FixedHTMLDataGetter", "edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.utils.ProcessFixedHTMLN3");
|
||||
|
||||
return map;
|
||||
}
|
||||
}
|
||||
|
|
@ -133,6 +133,8 @@ public class SimpleReasoner extends StatementListener {
|
|||
if (stmt.getPredicate().equals(RDF.type)) {
|
||||
addedABoxTypeAssertion(stmt, inferenceModel, new HashSet<String>());
|
||||
setMostSpecificTypes(stmt.getSubject(), inferenceModel, new HashSet<String>());
|
||||
} else if (stmt.getPredicate().equals(OWL.sameAs)) {
|
||||
addedABoxSameAsAssertion(stmt, inferenceModel);
|
||||
} else {
|
||||
addedABoxAssertion(stmt, inferenceModel);
|
||||
}
|
||||
|
|
@ -179,6 +181,8 @@ public class SimpleReasoner extends StatementListener {
|
|||
if (stmt.getPredicate().equals(RDF.type)) {
|
||||
removedABoxTypeAssertion(stmt, inferenceModel);
|
||||
setMostSpecificTypes(stmt.getSubject(), inferenceModel, new HashSet<String>());
|
||||
} else if (stmt.getPredicate().equals(OWL.sameAs)) {
|
||||
removedABoxSameAsAssertion(stmt, inferenceModel);
|
||||
} else {
|
||||
removedABoxAssertion(stmt, inferenceModel);
|
||||
}
|
||||
|
|
@ -360,11 +364,8 @@ public class SimpleReasoner extends StatementListener {
|
|||
protected void addedABoxTypeAssertion(Statement stmt, Model inferenceModel, HashSet<String> unknownTypes) {
|
||||
|
||||
tboxModel.enterCriticalSection(Lock.READ);
|
||||
|
||||
try {
|
||||
|
||||
OntClass cls = null;
|
||||
|
||||
if ( (stmt.getObject().asResource()).getURI() != null ) {
|
||||
|
||||
cls = tboxModel.getOntClass(stmt.getObject().asResource().getURI());
|
||||
|
|
@ -374,6 +375,8 @@ public class SimpleReasoner extends StatementListener {
|
|||
parents.addAll((cls.listEquivalentClasses()).toList());
|
||||
Iterator<OntClass> parentIt = parents.iterator();
|
||||
|
||||
if (parentIt.hasNext()) {
|
||||
List<Resource> sameIndividuals = getSameIndividuals(stmt.getSubject().asResource(), inferenceModel);
|
||||
while (parentIt.hasNext()) {
|
||||
OntClass parentClass = parentIt.next();
|
||||
|
||||
|
|
@ -389,9 +392,17 @@ public class SimpleReasoner extends StatementListener {
|
|||
inferenceModel.enterCriticalSection(Lock.WRITE);
|
||||
try {
|
||||
if (!inferenceModel.contains(infStmt) && !aboxModel.contains(infStmt)) {
|
||||
//log.debug("Adding this inferred statement: " + infStmt.toString() );
|
||||
inferenceModel.add(infStmt);
|
||||
}
|
||||
|
||||
Iterator<Resource> sameIter = sameIndividuals.iterator();
|
||||
while (sameIter.hasNext()) {
|
||||
Resource subject = sameIter.next();
|
||||
if (!inferenceModel.contains(subject,infStmt.getPredicate(),infStmt.getObject()) && !aboxModel.contains(subject,infStmt.getPredicate(),infStmt.getObject())) {
|
||||
inferenceModel.add(subject,infStmt.getPredicate(),infStmt.getObject());
|
||||
}
|
||||
}
|
||||
|
||||
} finally {
|
||||
inferenceModel.leaveCriticalSection();
|
||||
}
|
||||
|
|
@ -399,6 +410,7 @@ public class SimpleReasoner extends StatementListener {
|
|||
aboxModel.leaveCriticalSection();
|
||||
}
|
||||
}
|
||||
}
|
||||
} else {
|
||||
if ( !(stmt.getObject().asResource().getNameSpace()).equals(OWL.NS)) {
|
||||
if (!unknownTypes.contains(stmt.getObject().asResource().getURI())) {
|
||||
|
|
@ -418,24 +430,47 @@ public class SimpleReasoner extends StatementListener {
|
|||
}
|
||||
|
||||
/*
|
||||
* Performs incremental property-based reasoning.
|
||||
* Materializes inferences based on the owl:sameAs relationship.
|
||||
*
|
||||
* Materializes inferences based on the owl:inverseOf relationship.
|
||||
*
|
||||
* If it is added that x prop1 y, and prop2 is an inverseOf prop1
|
||||
* then add y prop2 x to the inference graph, if it is not already in
|
||||
* the assertions graph.
|
||||
* If it is added that x owl:sameAs y, then all asserted and inferred
|
||||
* statements about x will become inferred about y if they are not already
|
||||
* asserted about y, and vice versa.
|
||||
*/
|
||||
public void addedABoxAssertion(Statement stmt, Model inferenceModel) {
|
||||
public void addedABoxSameAsAssertion(Statement stmt, Model inferenceModel) {
|
||||
Resource subject = null;
|
||||
Resource object = null;
|
||||
|
||||
List<OntProperty> inverseProperties = getInverseProperties(stmt);
|
||||
Iterator<OntProperty> inverseIter = inverseProperties.iterator();
|
||||
if (stmt.getSubject().isResource()) {
|
||||
subject = stmt.getSubject().asResource();
|
||||
if (tboxModel.containsResource(subject) || subject.isAnon()) {
|
||||
log.debug("the subject of this sameAs statement is either in the tbox or an anonymous node, no reasoning will be done: " + stmtString(stmt));
|
||||
return;
|
||||
}
|
||||
} else {
|
||||
log.warn("the subject of this sameAs statement is not a resource, no reasoning will be done: " + stmtString(stmt));
|
||||
return;
|
||||
}
|
||||
|
||||
while (inverseIter.hasNext()) {
|
||||
Property inverseProp = inverseIter.next();
|
||||
if (stmt.getObject().isResource()) {
|
||||
object = stmt.getObject().asResource();
|
||||
if (tboxModel.containsResource(object) || object.isAnon()) {
|
||||
log.debug("the object of this sameAs statement is either in the tbox or an anonymous node, no reasoning will be done: " + stmtString(stmt));
|
||||
return;
|
||||
}
|
||||
} else {
|
||||
log.warn("the object of this sameAs statement is not a resource, no reasoning will be done: " + stmtString(stmt));
|
||||
return;
|
||||
}
|
||||
|
||||
Statement infStmt = ResourceFactory.createStatement(stmt.getObject().asResource(), inverseProp, stmt.getSubject());
|
||||
Model inferences = ModelFactory.createDefaultModel();
|
||||
inferences.add(generateSameAsInferences(subject, object, inferenceModel));
|
||||
inferences.add(generateSameAsInferences(object, subject, inferenceModel));
|
||||
inferences.add(object, OWL.sameAs, subject);
|
||||
|
||||
Iterator<Statement> infIter = inferences.listStatements();
|
||||
|
||||
while (infIter.hasNext()) {
|
||||
Statement infStmt = infIter.next();
|
||||
aboxModel.enterCriticalSection(Lock.READ);
|
||||
try {
|
||||
inferenceModel.enterCriticalSection(Lock.WRITE);
|
||||
|
|
@ -456,6 +491,214 @@ public class SimpleReasoner extends StatementListener {
|
|||
}
|
||||
}
|
||||
|
||||
/*
|
||||
* Create a model that contains every assertion about indB as exists for
|
||||
* indA in the Abox assertions or inference model
|
||||
*/
|
||||
public Model generateSameAsInferences(Resource indA, Resource indB, Model inferenceModel) {
|
||||
|
||||
Model inferences = ModelFactory.createDefaultModel();
|
||||
|
||||
OntModel unionModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
|
||||
unionModel.addSubModel(aboxModel);
|
||||
unionModel.addSubModel(inferenceModel);
|
||||
|
||||
aboxModel.enterCriticalSection(Lock.READ);
|
||||
try {
|
||||
Iterator<Statement> iter = unionModel.listStatements(indA, (Property) null, (RDFNode) null);
|
||||
|
||||
while (iter.hasNext()) {
|
||||
Statement stmt = iter.next();
|
||||
if (stmt.getObject() == null) continue;
|
||||
if (OWL.sameAs.equals(stmt.getPredicate()) && indB.equals(stmt.getObject())) continue;
|
||||
inferences.add(indB, stmt.getPredicate(), stmt.getObject());
|
||||
}
|
||||
} finally {
|
||||
aboxModel.leaveCriticalSection();
|
||||
}
|
||||
|
||||
return inferences;
|
||||
}
|
||||
|
||||
/*
|
||||
* Get a list of individuals the same as the given individual
|
||||
*/
|
||||
public List<Resource> getSameIndividuals(Resource ind, Model inferenceModel) {
|
||||
|
||||
OntModel unionModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
|
||||
unionModel.addSubModel(aboxModel);
|
||||
unionModel.addSubModel(inferenceModel);
|
||||
|
||||
ArrayList<Resource> sameIndividuals = new ArrayList<Resource>();
|
||||
aboxModel.enterCriticalSection(Lock.READ);
|
||||
inferenceModel.enterCriticalSection(Lock.READ);
|
||||
try {
|
||||
Iterator<Statement> iter = unionModel.listStatements(ind, OWL.sameAs, (RDFNode) null);
|
||||
|
||||
while (iter.hasNext()) {
|
||||
Statement stmt = iter.next();
|
||||
if (stmt.getObject() == null || !stmt.getObject().isResource() || stmt.getObject().asResource().getURI() == null) continue;
|
||||
sameIndividuals.add(stmt.getObject().asResource());
|
||||
}
|
||||
} finally {
|
||||
inferenceModel.leaveCriticalSection();
|
||||
aboxModel.leaveCriticalSection();
|
||||
}
|
||||
|
||||
return sameIndividuals;
|
||||
}
|
||||
|
||||
/*
|
||||
* Materializes inferences based on the owl:sameAs relationship.
|
||||
*
|
||||
* If it is removed that x is sameAs y, then remove y sameAs x from
|
||||
* the inference graph and then recompute the inferences for x and
|
||||
* y based on their respective assertions. that x owl:sameAs y, then all asserted and inferred
|
||||
*/
|
||||
public void removedABoxSameAsAssertion(Statement stmt, Model inferenceModel) {
|
||||
|
||||
Resource subject = null;
|
||||
Resource object = null;
|
||||
|
||||
if (stmt.getSubject().isResource()) {
|
||||
subject = stmt.getSubject().asResource();
|
||||
if (tboxModel.containsResource(subject) || subject.isAnon()) {
|
||||
log.debug("the subject of this removed sameAs statement is either in the tbox or an anonymous node, no reasoning will be done: " + stmtString(stmt));
|
||||
return;
|
||||
}
|
||||
} else {
|
||||
log.warn("the subject of this removed sameAs statement is not a resource, no reasoning will be done: " + stmtString(stmt));
|
||||
return;
|
||||
}
|
||||
|
||||
if (stmt.getObject().isResource()) {
|
||||
object = stmt.getObject().asResource();
|
||||
if (tboxModel.containsResource(object) || object.isAnon()) {
|
||||
log.debug("the object of this removed sameAs statement is either in the tbox or an anonymous node, no reasoning will be done: " + stmtString(stmt));
|
||||
return;
|
||||
}
|
||||
} else {
|
||||
log.warn("the object of this removed sameAs statement is not a resource, no reasoning will be done: " + stmtString(stmt));
|
||||
return;
|
||||
}
|
||||
|
||||
inferenceModel.enterCriticalSection(Lock.WRITE);
|
||||
try {
|
||||
if (inferenceModel.contains(stmt)) {
|
||||
inferenceModel.remove(stmt);
|
||||
}
|
||||
|
||||
if (!inferenceModel.contains(object, OWL.sameAs, subject) && !aboxModel.contains(object, OWL.sameAs, subject) ) {
|
||||
inferenceModel.add(object, OWL.sameAs, subject);
|
||||
}
|
||||
} finally {
|
||||
inferenceModel.leaveCriticalSection();
|
||||
}
|
||||
|
||||
recomputeInferencesForIndividual(subject, inferenceModel);
|
||||
recomputeInferencesForIndividual(object, inferenceModel);
|
||||
}
|
||||
|
||||
/*
|
||||
* Recompute inferences for individual
|
||||
*/
|
||||
public void recomputeInferencesForIndividual(Resource ind, Model inferenceModel) {
|
||||
|
||||
Model inferencesToRemove = ModelFactory.createDefaultModel();
|
||||
|
||||
inferenceModel.enterCriticalSection(Lock.READ);
|
||||
try {
|
||||
Iterator<Statement> iter = inferenceModel.listStatements(ind, (Property) null, (RDFNode) null);
|
||||
|
||||
while (iter.hasNext()) {
|
||||
inferencesToRemove.add(iter.next());
|
||||
}
|
||||
} finally {
|
||||
inferenceModel.leaveCriticalSection();
|
||||
}
|
||||
|
||||
inferenceModel.enterCriticalSection(Lock.WRITE);
|
||||
try {
|
||||
inferenceModel.remove(inferencesToRemove);
|
||||
} finally {
|
||||
inferenceModel.leaveCriticalSection();
|
||||
}
|
||||
|
||||
Iterator<Statement> iter = null;
|
||||
aboxModel.enterCriticalSection(Lock.WRITE);
|
||||
try {
|
||||
iter = aboxModel.listStatements(ind, (Property) null, (RDFNode) null);
|
||||
} finally {
|
||||
aboxModel.leaveCriticalSection();
|
||||
}
|
||||
|
||||
while (iter.hasNext()) {
|
||||
addedStatement(iter.next());
|
||||
}
|
||||
|
||||
return;
|
||||
}
|
||||
|
||||
/*
|
||||
* Performs incremental property-based reasoning.
|
||||
*
|
||||
* Materializes inferences based on the owl:inverseOf relationship.
|
||||
*
|
||||
* If it is added that x prop1 y, and prop2 is an inverseOf prop1
|
||||
* then add y prop2 x to the inference graph, if it is not already in
|
||||
* the assertions graph.
|
||||
*/
|
||||
public void addedABoxAssertion(Statement stmt, Model inferenceModel) {
|
||||
List<Resource> sameIndividuals = getSameIndividuals(stmt.getSubject().asResource(), inferenceModel);
|
||||
List<OntProperty> inverseProperties = getInverseProperties(stmt);
|
||||
Iterator<OntProperty> inverseIter = inverseProperties.iterator();
|
||||
|
||||
while (inverseIter.hasNext()) {
|
||||
Property inverseProp = inverseIter.next();
|
||||
|
||||
Statement infStmt = ResourceFactory.createStatement(stmt.getObject().asResource(), inverseProp, stmt.getSubject());
|
||||
|
||||
aboxModel.enterCriticalSection(Lock.READ);
|
||||
try {
|
||||
inferenceModel.enterCriticalSection(Lock.WRITE);
|
||||
try {
|
||||
if (!inferenceModel.contains(infStmt) && !aboxModel.contains(infStmt) ) {
|
||||
inferenceModel.add(infStmt);
|
||||
}
|
||||
|
||||
Iterator<Resource> sameIter = sameIndividuals.iterator();
|
||||
while (sameIter.hasNext()) {
|
||||
Resource subject = sameIter.next();
|
||||
if (!inferenceModel.contains(subject,infStmt.getPredicate(),infStmt.getObject()) && !aboxModel.contains(subject,infStmt.getPredicate(),infStmt.getObject())) {
|
||||
inferenceModel.add(subject,infStmt.getPredicate(),infStmt.getObject());
|
||||
}
|
||||
}
|
||||
} finally {
|
||||
inferenceModel.leaveCriticalSection();
|
||||
}
|
||||
} finally {
|
||||
aboxModel.leaveCriticalSection();
|
||||
}
|
||||
}
|
||||
|
||||
inferenceModel.enterCriticalSection(Lock.WRITE);
|
||||
try {
|
||||
if (inferenceModel.contains(stmt)) {
|
||||
inferenceModel.remove(stmt);
|
||||
}
|
||||
|
||||
Iterator<Resource> sameIter = sameIndividuals.iterator();
|
||||
while (sameIter.hasNext()) {
|
||||
Resource subject = sameIter.next();
|
||||
if (!inferenceModel.contains(subject,stmt.getPredicate(),stmt.getObject()) && !aboxModel.contains(subject,stmt.getPredicate(),stmt.getObject())) {
|
||||
inferenceModel.add(subject,stmt.getPredicate(),stmt.getObject());
|
||||
}
|
||||
}
|
||||
} finally {
|
||||
inferenceModel.leaveCriticalSection();
|
||||
}
|
||||
}
|
||||
|
||||
/*
|
||||
* If it is removed that B is of type A, then for each superclass of A remove
|
||||
* the inferred statement that B is of that type UNLESS it is otherwise entailed
|
||||
|
|
@ -484,7 +727,6 @@ public class SimpleReasoner extends StatementListener {
|
|||
} finally {
|
||||
inferenceModel.leaveCriticalSection();
|
||||
}
|
||||
|
||||
return;
|
||||
}
|
||||
|
||||
|
|
@ -543,6 +785,8 @@ public class SimpleReasoner extends StatementListener {
|
|||
* this removed statement.
|
||||
*/
|
||||
public void removedABoxAssertion(Statement stmt, Model inferenceModel) {
|
||||
|
||||
List<Resource> sameIndividuals = getSameIndividuals(stmt.getSubject().asResource(), inferenceModel);
|
||||
List<OntProperty> inverseProperties = getInverseProperties(stmt);
|
||||
Iterator<OntProperty> inverseIter = inverseProperties.iterator();
|
||||
|
||||
|
|
@ -553,19 +797,40 @@ public class SimpleReasoner extends StatementListener {
|
|||
|
||||
inferenceModel.enterCriticalSection(Lock.WRITE);
|
||||
try {
|
||||
if (!entailedInverseStmt(infStmt) && inferenceModel.contains(infStmt)) {
|
||||
if (!entailedStatement(infStmt) && inferenceModel.contains(infStmt)) {
|
||||
inferenceModel.remove(infStmt);
|
||||
}
|
||||
|
||||
// if a statement has been removed that is otherwise entailed,
|
||||
// add it to the inference graph.
|
||||
if (entailedInverseStmt(stmt) && !inferenceModel.contains(stmt)) {
|
||||
inferenceModel.add(stmt);
|
||||
Iterator<Resource> sameIter = sameIndividuals.iterator();
|
||||
while (sameIter.hasNext()) {
|
||||
Statement infStmtSame = ResourceFactory.createStatement(sameIter.next(), infStmt.getPredicate(), infStmt.getObject());
|
||||
if (!entailedStatement(infStmtSame) && inferenceModel.contains(infStmtSame)) {
|
||||
inferenceModel.remove(infStmtSame);
|
||||
}
|
||||
}
|
||||
} finally {
|
||||
inferenceModel.leaveCriticalSection();
|
||||
}
|
||||
}
|
||||
|
||||
inferenceModel.enterCriticalSection(Lock.WRITE);
|
||||
try {
|
||||
// if a statement has been removed that is otherwise entailed,
|
||||
// add it to the inference graph.
|
||||
if (entailedStatement(stmt) && !inferenceModel.contains(stmt)) {
|
||||
inferenceModel.add(stmt);
|
||||
}
|
||||
|
||||
Iterator<Resource> sameIter = sameIndividuals.iterator();
|
||||
while (sameIter.hasNext()) {
|
||||
Statement stmtSame = ResourceFactory.createStatement(sameIter.next(), stmt.getPredicate(), stmt.getObject());
|
||||
if (!entailedStatement(stmtSame) && inferenceModel.contains(stmtSame)) {
|
||||
inferenceModel.remove(stmtSame);
|
||||
}
|
||||
}
|
||||
} finally {
|
||||
inferenceModel.leaveCriticalSection();
|
||||
}
|
||||
}
|
||||
|
||||
// Returns true if it is entailed by class subsumption that
|
||||
|
|
@ -600,22 +865,25 @@ public class SimpleReasoner extends StatementListener {
|
|||
}
|
||||
|
||||
// Returns true if the triple is entailed by inverse property
|
||||
// reasoning; otherwise returns false.
|
||||
protected boolean entailedInverseStmt(Statement stmt) {
|
||||
ExtendedIterator <? extends OntProperty> iter = null;
|
||||
// reasoning or sameAs reasoning; otherwise returns false.
|
||||
protected boolean entailedStatement(Statement stmt) {
|
||||
|
||||
List<OntProperty> inverses = new ArrayList<OntProperty>();
|
||||
|
||||
tboxModel.enterCriticalSection(Lock.READ);
|
||||
try {
|
||||
OntProperty prop = tboxModel.getOntProperty(stmt.getPredicate().asResource().getURI());
|
||||
iter = prop.listInverse();
|
||||
inverses.addAll(prop.listInverse().toList());
|
||||
} finally {
|
||||
tboxModel.leaveCriticalSection();
|
||||
}
|
||||
|
||||
Iterator<OntProperty> oIter = inverses.iterator();
|
||||
if (oIter.hasNext()) {
|
||||
aboxModel.enterCriticalSection(Lock.READ);
|
||||
try {
|
||||
while (iter.hasNext()) {
|
||||
Property invProp = iter.next();
|
||||
while (oIter.hasNext()) {
|
||||
Property invProp = oIter.next();
|
||||
|
||||
// not reasoning on properties in the OWL, RDF or RDFS namespace
|
||||
if ((invProp.getNameSpace()).equals(OWL.NS) ||
|
||||
|
|
@ -629,12 +897,31 @@ public class SimpleReasoner extends StatementListener {
|
|||
return true;
|
||||
}
|
||||
}
|
||||
return false;
|
||||
} finally {
|
||||
aboxModel.leaveCriticalSection();
|
||||
}
|
||||
}
|
||||
|
||||
List<Resource> sameIndividuals = getSameIndividuals(stmt.getSubject().asResource(),inferenceModel);
|
||||
Iterator<Resource> rIter = sameIndividuals.iterator();
|
||||
if (rIter.hasNext()) {
|
||||
aboxModel.enterCriticalSection(Lock.READ);
|
||||
try {
|
||||
while (rIter.hasNext()) {
|
||||
Resource subject = rIter.next();
|
||||
|
||||
if (aboxModel.contains(subject, stmt.getPredicate(), stmt.getObject())) {
|
||||
return true;
|
||||
}
|
||||
}
|
||||
} finally {
|
||||
aboxModel.leaveCriticalSection();
|
||||
}
|
||||
}
|
||||
|
||||
return false;
|
||||
}
|
||||
|
||||
/*
|
||||
* Returns a list of properties that are inverses of the property
|
||||
* in the given statement.
|
||||
|
|
@ -800,12 +1087,21 @@ public class SimpleReasoner extends StatementListener {
|
|||
|
||||
while (iter.hasNext()) {
|
||||
Statement infStmt = iter.next();
|
||||
List<Resource> sameIndividuals = getSameIndividuals(infStmt.getSubject().asResource(), inferenceModel);
|
||||
|
||||
inferenceModel.enterCriticalSection(Lock.WRITE);
|
||||
try {
|
||||
if (!inferenceModel.contains(infStmt) && !aboxModel.contains(infStmt)) {
|
||||
inferenceModel.add(infStmt);
|
||||
}
|
||||
|
||||
Iterator<Resource> sameIter = sameIndividuals.iterator();
|
||||
while (sameIter.hasNext()) {
|
||||
Resource subject = sameIter.next();
|
||||
if (!inferenceModel.contains(subject,infStmt.getPredicate(),infStmt.getObject()) && !aboxModel.contains(subject,infStmt.getPredicate(),infStmt.getObject())) {
|
||||
inferenceModel.add(subject,infStmt.getPredicate(),infStmt.getObject());
|
||||
}
|
||||
}
|
||||
} finally {
|
||||
inferenceModel.leaveCriticalSection();
|
||||
}
|
||||
|
|
@ -862,7 +1158,7 @@ public class SimpleReasoner extends StatementListener {
|
|||
while (iter.hasNext()) {
|
||||
Statement infStmt = iter.next();
|
||||
|
||||
if (entailedInverseStmt(infStmt)) {
|
||||
if (entailedStatement(infStmt)) {
|
||||
continue;
|
||||
}
|
||||
|
||||
|
|
@ -1051,19 +1347,18 @@ public class SimpleReasoner extends StatementListener {
|
|||
* inference models.
|
||||
*/
|
||||
protected synchronized void recomputeABox() {
|
||||
HashSet<String> unknownTypes = new HashSet<String>();
|
||||
|
||||
// recompute the inferences
|
||||
// recompute class subsumption inferences
|
||||
inferenceRebuildModel.enterCriticalSection(Lock.WRITE);
|
||||
try {
|
||||
log.info("Computing ABox inferences.");
|
||||
HashSet<String> unknownTypes = new HashSet<String>();
|
||||
inferenceRebuildModel.removeAll();
|
||||
|
||||
log.info("Computing class subsumtion ABox inferences.");
|
||||
int numStmts = 0;
|
||||
ArrayList<String> individuals = this.getAllIndividualURIs();
|
||||
|
||||
for (String individualURI : individuals) {
|
||||
|
||||
Resource individual = ResourceFactory.createResource(individualURI);
|
||||
|
||||
try {
|
||||
|
|
@ -1091,7 +1386,7 @@ public class SimpleReasoner extends StatementListener {
|
|||
|
||||
numStmts++;
|
||||
if ((numStmts % 10000) == 0) {
|
||||
log.info("Still computing class-based ABox inferences...");
|
||||
log.info("Still computing class subsumption ABox inferences...");
|
||||
}
|
||||
|
||||
if (stopRequested) {
|
||||
|
|
@ -1100,8 +1395,9 @@ public class SimpleReasoner extends StatementListener {
|
|||
}
|
||||
}
|
||||
|
||||
log.info("Finished computing class-based ABox inferences");
|
||||
log.info("Finished computing class subsumption ABox inferences");
|
||||
|
||||
log.info("Computing inverse property ABox inferences");
|
||||
Iterator<Statement> invStatements = null;
|
||||
tboxModel.enterCriticalSection(Lock.READ);
|
||||
try {
|
||||
|
|
@ -1110,18 +1406,21 @@ public class SimpleReasoner extends StatementListener {
|
|||
tboxModel.leaveCriticalSection();
|
||||
}
|
||||
|
||||
numStmts = 0;
|
||||
while (invStatements.hasNext()) {
|
||||
Statement stmt = invStatements.next();
|
||||
|
||||
try {
|
||||
OntProperty prop1 = tboxModel.getOntProperty((stmt.getSubject()).getURI());
|
||||
if (prop1 == null) {
|
||||
//TODO make sure not to print out a million of these for the same property
|
||||
log.debug("didn't find subject property in the tbox: " + (stmt.getSubject()).getURI());
|
||||
continue;
|
||||
}
|
||||
|
||||
OntProperty prop2 = tboxModel.getOntProperty(((Resource)stmt.getObject()).getURI());
|
||||
if (prop2 == null) {
|
||||
//TODO make sure not to print out a million of these for the same property
|
||||
log.debug("didn't find object property in the tbox: " + ((Resource)stmt.getObject()).getURI());
|
||||
continue;
|
||||
}
|
||||
|
|
@ -1142,7 +1441,7 @@ public class SimpleReasoner extends StatementListener {
|
|||
|
||||
numStmts++;
|
||||
if ((numStmts % 10000) == 0) {
|
||||
log.info("Still computing property-based ABox inferences...");
|
||||
log.info("Still computing inverse property ABox inferences...");
|
||||
}
|
||||
|
||||
if (stopRequested) {
|
||||
|
|
@ -1150,26 +1449,80 @@ public class SimpleReasoner extends StatementListener {
|
|||
return;
|
||||
}
|
||||
}
|
||||
|
||||
log.info("Finished computing inverse property ABox inferences");
|
||||
|
||||
log.info("Computing sameAs ABox inferences");
|
||||
|
||||
Iterator<Statement> sameAsStatements = null;
|
||||
aboxModel.enterCriticalSection(Lock.READ);
|
||||
try {
|
||||
sameAsStatements = aboxModel.listStatements((Resource) null, OWL.sameAs, (Resource) null);
|
||||
} finally {
|
||||
aboxModel.leaveCriticalSection();
|
||||
}
|
||||
|
||||
numStmts = 0;
|
||||
while (sameAsStatements.hasNext()) {
|
||||
Statement stmt = sameAsStatements.next();
|
||||
|
||||
try {
|
||||
addedABoxSameAsAssertion(stmt, inferenceRebuildModel);
|
||||
} catch (NullPointerException npe) {
|
||||
log.error("a NullPointerException was received while recomputing the ABox inferences. Halting inference computation.");
|
||||
return;
|
||||
} catch (JenaException je) {
|
||||
if (je.getMessage().equals("Statement models must no be null")) {
|
||||
log.error("Exception while recomputing ABox inference model. Halting inference computation.", je);
|
||||
return;
|
||||
}
|
||||
log.error("Exception while recomputing ABox inference model: ", je);
|
||||
} catch (Exception e) {
|
||||
log.error("Exception while recomputing ABox inference model", e);
|
||||
inferenceRebuildModel.removeAll(); // don't do this in the finally, it's needed in the case
|
||||
// where there isn't an exception
|
||||
log.error("Exception while recomputing ABox inference model: ", e);
|
||||
}
|
||||
|
||||
numStmts++;
|
||||
if ((numStmts % 10000) == 0) {
|
||||
log.info("Still computing sameAs ABox inferences...");
|
||||
}
|
||||
|
||||
if (stopRequested) {
|
||||
log.info("a stopRequested signal was received during recomputeABox. Halting Processing.");
|
||||
return;
|
||||
}
|
||||
}
|
||||
log.info("Finished computing sameAs ABox inferences");
|
||||
|
||||
try {
|
||||
if (updateInferenceModel(inferenceRebuildModel)) {
|
||||
log.info("a stopRequested signal was received during updateInferenceModel. Halting Processing.");
|
||||
return;
|
||||
}
|
||||
} catch (Exception e) {
|
||||
log.error("Exception while reconciling the current and recomputed ABox inference model for class subsumption inferences. Halting processing." , e);
|
||||
inferenceRebuildModel.removeAll();
|
||||
return;
|
||||
}
|
||||
} catch (Exception e) {
|
||||
log.error("Exception while recomputing ABox inferences. Halting processing.", e);
|
||||
inferenceRebuildModel.removeAll();
|
||||
return;
|
||||
} finally {
|
||||
inferenceRebuildModel.leaveCriticalSection();
|
||||
}
|
||||
}
|
||||
|
||||
log.info("Finished computing property-based ABox inferences");
|
||||
/*
|
||||
* reconcile a set of inferences into the application inference model
|
||||
*/
|
||||
protected synchronized boolean updateInferenceModel(Model inferenceRebuildModel) {
|
||||
|
||||
// reflect the recomputed inferences into the application
|
||||
// inference model.
|
||||
log.info("Updating ABox inference model");
|
||||
StmtIterator iter = null;
|
||||
|
||||
// Remove everything from the current inference model that is not
|
||||
// in the recomputed inference model
|
||||
int num = 0;
|
||||
inferenceRebuildModel.enterCriticalSection(Lock.WRITE);
|
||||
scratchpadModel.enterCriticalSection(Lock.WRITE);
|
||||
try {
|
||||
inferenceModel.enterCriticalSection(Lock.READ);
|
||||
|
|
@ -1189,18 +1542,15 @@ public class SimpleReasoner extends StatementListener {
|
|||
}
|
||||
|
||||
if (stopRequested) {
|
||||
log.info("a stopRequested signal was received during recomputeABox. Halting Processing.");
|
||||
return;
|
||||
return true;
|
||||
}
|
||||
}
|
||||
} catch (Exception e) {
|
||||
log.error("Exception while reconciling the current and recomputed ABox inference models", e);
|
||||
return;
|
||||
} finally {
|
||||
iter.close();
|
||||
inferenceModel.leaveCriticalSection();
|
||||
}
|
||||
|
||||
try {
|
||||
iter = scratchpadModel.listStatements();
|
||||
while (iter.hasNext()) {
|
||||
Statement stmt = iter.next();
|
||||
|
|
@ -1208,12 +1558,13 @@ public class SimpleReasoner extends StatementListener {
|
|||
inferenceModel.enterCriticalSection(Lock.WRITE);
|
||||
try {
|
||||
inferenceModel.remove(stmt);
|
||||
} catch (Exception e) {
|
||||
log.error("Exception while reconciling the current and recomputed ABox inference models", e);
|
||||
} finally {
|
||||
inferenceModel.leaveCriticalSection();
|
||||
}
|
||||
}
|
||||
} finally {
|
||||
iter.close();
|
||||
}
|
||||
|
||||
// Add everything from the recomputed inference model that is not already
|
||||
// in the current inference model to the current inference model.
|
||||
|
|
@ -1239,13 +1590,9 @@ public class SimpleReasoner extends StatementListener {
|
|||
}
|
||||
|
||||
if (stopRequested) {
|
||||
log.info("a stopRequested signal was received during recomputeABox. Halting Processing.");
|
||||
return;
|
||||
return true;
|
||||
}
|
||||
}
|
||||
} catch (Exception e) {
|
||||
log.error("Exception while reconciling the current and recomputed ABox inference models", e);
|
||||
return;
|
||||
} finally {
|
||||
iter.close();
|
||||
}
|
||||
|
|
@ -1257,24 +1604,19 @@ public class SimpleReasoner extends StatementListener {
|
|||
inferenceModel.enterCriticalSection(Lock.WRITE);
|
||||
try {
|
||||
inferenceModel.add(stmt);
|
||||
} catch (Exception e) {
|
||||
log.error("Exception while reconciling the current and recomputed ABox inference models", e);
|
||||
return;
|
||||
} finally {
|
||||
inferenceModel.leaveCriticalSection();
|
||||
}
|
||||
}
|
||||
} finally {
|
||||
iter.close();
|
||||
inferenceRebuildModel.removeAll();
|
||||
scratchpadModel.removeAll();
|
||||
inferenceRebuildModel.leaveCriticalSection();
|
||||
scratchpadModel.leaveCriticalSection();
|
||||
}
|
||||
|
||||
log.info("ABox inference model updated");
|
||||
return false;
|
||||
}
|
||||
|
||||
/*
|
||||
* Get the URIs for all individuals in the system
|
||||
*/
|
||||
|
|
@ -1492,7 +1834,6 @@ public class SimpleReasoner extends StatementListener {
|
|||
log.info("started computing inferences for batch " + qualifier + " updates");
|
||||
iter = retractions.listStatements();
|
||||
|
||||
|
||||
while (iter.hasNext() && !stopRequested) {
|
||||
Statement stmt = iter.next();
|
||||
num++;
|
||||
|
|
|
|||
564
webapp/src/edu/ucsf/vitro/opensocial/OpenSocialSmokeTests.java
Normal file
564
webapp/src/edu/ucsf/vitro/opensocial/OpenSocialSmokeTests.java
Normal file
|
|
@ -0,0 +1,564 @@
|
|||
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
|
||||
|
||||
package edu.ucsf.vitro.opensocial;
|
||||
|
||||
import java.io.File;
|
||||
import java.io.InputStream;
|
||||
import java.net.Socket;
|
||||
import java.net.SocketTimeoutException;
|
||||
import java.net.URL;
|
||||
import java.sql.Connection;
|
||||
import java.sql.ResultSet;
|
||||
import java.sql.SQLException;
|
||||
import java.sql.Statement;
|
||||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
|
||||
import javax.servlet.ServletContext;
|
||||
import javax.servlet.ServletContextEvent;
|
||||
import javax.servlet.ServletContextListener;
|
||||
|
||||
import org.apache.commons.dbcp.BasicDataSource;
|
||||
import org.apache.commons.httpclient.HttpClient;
|
||||
import org.apache.commons.httpclient.HttpStatus;
|
||||
import org.apache.commons.httpclient.methods.GetMethod;
|
||||
import org.apache.commons.lang.StringUtils;
|
||||
import org.apache.commons.logging.Log;
|
||||
import org.apache.commons.logging.LogFactory;
|
||||
|
||||
import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
|
||||
import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
|
||||
import edu.cornell.mannlib.vitro.webapp.utils.threads.VitroBackgroundThread;
|
||||
|
||||
/**
|
||||
* Do some quick checks to see whether the OpenSocial stuff is configured and
|
||||
* working.
|
||||
*/
|
||||
public class OpenSocialSmokeTests implements ServletContextListener {
|
||||
private static final String PROPERTY_SHINDIG_URL = "OpenSocial.shindigURL";
|
||||
private static final String PROPERTY_SHINDIG_TOKEN_KEY_FILE = "OpenSocial.tokenKeyFile";
|
||||
private static final String PROPERTY_SHINDIG_TOKEN_SERVICE = "OpenSocial.tokenService";
|
||||
|
||||
private static final String PROPERTY_DB_DRIVER = "VitroConnection.DataSource.driver";
|
||||
private static final String PROPERTY_DB_JDBC_URL = "VitroConnection.DataSource.url";
|
||||
private static final String PROPERTY_DB_USERNAME = "VitroConnection.DataSource.username";
|
||||
private static final String PROPERTY_DB_PASSWORD = "VitroConnection.DataSource.password";
|
||||
|
||||
private static final String FILENAME_SHINDIG_PROPERTIES = "shindig.orng.properties";
|
||||
|
||||
/*
|
||||
* If a connection fails in the tester thread, how long do we wait before
|
||||
* trying again?
|
||||
*/
|
||||
private static final long SLEEP_INTERVAL = 10000; // 10 seconds
|
||||
|
||||
private ServletContext ctx;
|
||||
private ConfigurationProperties configProps;
|
||||
private List<Warning> warnings = new ArrayList<Warning>();
|
||||
|
||||
private String shindigBaseUrl;
|
||||
private String tokenServiceHost;
|
||||
private int tokenServicePort;
|
||||
|
||||
/**
|
||||
* When the system starts up, run the tests.
|
||||
*/
|
||||
@Override
|
||||
public void contextInitialized(ServletContextEvent sce) {
|
||||
ctx = sce.getServletContext();
|
||||
StartupStatus ss = StartupStatus.getBean(ctx);
|
||||
configProps = ConfigurationProperties.getBean(ctx);
|
||||
|
||||
/*
|
||||
* If OpenSocial is not configured in deploy.properties, skip the tests.
|
||||
*/
|
||||
if (!configurationPresent()) {
|
||||
ss.info(this, "The OpenSocial connection is not configured.");
|
||||
return;
|
||||
}
|
||||
|
||||
/*
|
||||
* Run all of the non-threaded tests. If any fail, skip the threaded
|
||||
* tests.
|
||||
*/
|
||||
checkDatabaseTables();
|
||||
checkShindigConfigFile();
|
||||
checkTokenKeyFile();
|
||||
checkTokenServiceInfo();
|
||||
if (!warnings.isEmpty()) {
|
||||
for (Warning w : warnings) {
|
||||
w.warn(ss);
|
||||
}
|
||||
return;
|
||||
}
|
||||
|
||||
/*
|
||||
* Run the threaded tests.
|
||||
*/
|
||||
ss.info(this, "Starting threads for OpenSocial smoke tests");
|
||||
new ShindigTestThread(this, ss, shindigBaseUrl).start();
|
||||
new TokenServiceTestThread(this, ss, tokenServiceHost, tokenServicePort)
|
||||
.start();
|
||||
}
|
||||
|
||||
/**
|
||||
* Get the base URL for the Shindig server. If none, then the whole thing is
|
||||
* disabled.
|
||||
*/
|
||||
private boolean configurationPresent() {
|
||||
String shindigUrl = configProps.getProperty(PROPERTY_SHINDIG_URL);
|
||||
if (StringUtils.isNotEmpty(shindigUrl)) {
|
||||
this.shindigBaseUrl = shindigUrl;
|
||||
return true;
|
||||
} else {
|
||||
return false;
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Check that we can connect to the database, and query one of the Shindig
|
||||
* tables.
|
||||
*/
|
||||
private void checkDatabaseTables() {
|
||||
BasicDataSource dataSource = null;
|
||||
Connection conn = null;
|
||||
Statement stmt = null;
|
||||
ResultSet rset = null;
|
||||
try {
|
||||
dataSource = new BasicDataSource();
|
||||
dataSource.setDriverClassName(getProperty(PROPERTY_DB_DRIVER));
|
||||
dataSource.setUrl(getProperty(PROPERTY_DB_JDBC_URL));
|
||||
dataSource.setUsername(getProperty(PROPERTY_DB_USERNAME));
|
||||
dataSource.setPassword(getProperty(PROPERTY_DB_PASSWORD));
|
||||
|
||||
conn = dataSource.getConnection();
|
||||
stmt = conn.createStatement();
|
||||
rset = stmt.executeQuery("select * from shindig_apps");
|
||||
} catch (NoSuchPropertyException e) {
|
||||
warnings.add(new Warning(e.getMessage()));
|
||||
} catch (SQLException e) {
|
||||
if (e.getMessage().contains("doesn't exist")) {
|
||||
warnings.add(new Warning("The Shindig tables don't exist "
|
||||
+ "in the database. Was shindig_orng_tables.sql "
|
||||
+ "run to set them up?", e));
|
||||
} else {
|
||||
warnings.add(new Warning(
|
||||
"Can't access the Shindig database tables", e));
|
||||
}
|
||||
} finally {
|
||||
try {
|
||||
if (rset != null) {
|
||||
rset.close();
|
||||
}
|
||||
} catch (Exception e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
try {
|
||||
if (stmt != null) {
|
||||
stmt.close();
|
||||
}
|
||||
} catch (Exception e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
try {
|
||||
if (conn != null) {
|
||||
conn.close();
|
||||
}
|
||||
} catch (Exception e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Check that the Shindig configuration file is present in the classpath.
|
||||
*/
|
||||
private void checkShindigConfigFile() {
|
||||
URL url = this.getClass()
|
||||
.getResource("/" + FILENAME_SHINDIG_PROPERTIES);
|
||||
if (url == null) {
|
||||
String message = "Can't find the '" + FILENAME_SHINDIG_PROPERTIES
|
||||
+ "' file in the classpath. ";
|
||||
message += "Has the Tomcat classpath been set to include the "
|
||||
+ "Shindig config directory? "
|
||||
+ "(inside the Vitro home directory) ";
|
||||
message += "Was the openSocial build script run? "
|
||||
+ "('ant -file openSocialBuild.xml')";
|
||||
warnings.add(new Warning(message));
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Check that the Token Key file has been specified in deploy.properties,
|
||||
* and that it actually does exist.
|
||||
*/
|
||||
private void checkTokenKeyFile() {
|
||||
try {
|
||||
String tokenFilename = getProperty(PROPERTY_SHINDIG_TOKEN_KEY_FILE);
|
||||
File tokenFile = new File(tokenFilename);
|
||||
if (!tokenFile.exists()) {
|
||||
warnings.add(new Warning(
|
||||
"Token key file for Shindig does not exist: '"
|
||||
+ tokenFilename + "'"));
|
||||
} else if (!tokenFile.isFile()) {
|
||||
warnings.add(new Warning(
|
||||
"Token key file for Shindig is not a file: '"
|
||||
+ tokenFilename + "'"));
|
||||
}
|
||||
} catch (NoSuchPropertyException e) {
|
||||
warnings.add(new Warning(e.getMessage()));
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Get the Token Service info from deploy.properties. It must be in the form
|
||||
* of host:port, and may not refer to localhost.
|
||||
*/
|
||||
private void checkTokenServiceInfo() {
|
||||
String tsInfo = configProps.getProperty(PROPERTY_SHINDIG_TOKEN_SERVICE);
|
||||
if (StringUtils.isEmpty(tsInfo)) {
|
||||
warnings.add(new Warning("There is no value for '"
|
||||
+ PROPERTY_SHINDIG_TOKEN_SERVICE + "' in deploy.properties"));
|
||||
return;
|
||||
}
|
||||
|
||||
/*
|
||||
* If the parameter is invalid, use this message.
|
||||
*/
|
||||
String warningText = "The '" + PROPERTY_SHINDIG_TOKEN_SERVICE
|
||||
+ "' parameter is set to \"" + tsInfo
|
||||
+ "\". It must be in the form [hostname]:[port]. "
|
||||
+ "For example, \"myhost.mydomain.edu:8777\". "
|
||||
+ "The hostname may be an IP address, "
|
||||
+ "but it may not be \"localhost\" or \"127.0.0.1\"";
|
||||
|
||||
int firstColon = tsInfo.indexOf(':');
|
||||
if (firstColon <= 0) {
|
||||
warnings.add(new Warning(warningText));
|
||||
return;
|
||||
}
|
||||
|
||||
int lastColon = tsInfo.lastIndexOf(':');
|
||||
if (firstColon != lastColon) {
|
||||
warnings.add(new Warning(warningText));
|
||||
return;
|
||||
}
|
||||
|
||||
tokenServiceHost = tsInfo.substring(0, firstColon);
|
||||
if (("localhost".equals(tokenServiceHost))
|
||||
|| ("127.0.0.1".equals(tokenServiceHost))) {
|
||||
warnings.add(new Warning(warningText));
|
||||
return;
|
||||
}
|
||||
|
||||
try {
|
||||
tokenServicePort = Integer.parseInt(tsInfo
|
||||
.substring(firstColon + 1));
|
||||
} catch (Exception e) { // probably a NumberFormatException
|
||||
warnings.add(new Warning(warningText, e));
|
||||
}
|
||||
}
|
||||
|
||||
private String getProperty(String key) throws NoSuchPropertyException {
|
||||
String value = configProps.getProperty(key);
|
||||
if (StringUtils.isEmpty(value)) {
|
||||
throw new NoSuchPropertyException(key);
|
||||
} else {
|
||||
return value;
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
public void contextDestroyed(ServletContextEvent sce) {
|
||||
// nothing to destroy
|
||||
}
|
||||
|
||||
// ----------------------------------------------------------------------
|
||||
// Helper classes
|
||||
// ----------------------------------------------------------------------
|
||||
|
||||
private static class NoSuchPropertyException extends Exception {
|
||||
NoSuchPropertyException(String key) {
|
||||
super("There is no value for '" + key + "' in deploy.properties");
|
||||
}
|
||||
}
|
||||
|
||||
private class Warning {
|
||||
private final String message;
|
||||
private final Throwable cause;
|
||||
|
||||
Warning(String message) {
|
||||
this.message = message;
|
||||
this.cause = null;
|
||||
}
|
||||
|
||||
Warning(String message, Throwable cause) {
|
||||
this.message = message;
|
||||
this.cause = cause;
|
||||
}
|
||||
|
||||
void warn(StartupStatus ss) {
|
||||
if (cause == null) {
|
||||
ss.warning(OpenSocialSmokeTests.this, message);
|
||||
} else {
|
||||
ss.warning(OpenSocialSmokeTests.this, message, cause);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
private static class ShindigTestThread extends VitroBackgroundThread {
|
||||
private final OpenSocialSmokeTests listener;
|
||||
private final StartupStatus ss;
|
||||
private final String shindigBaseUrl;
|
||||
|
||||
public ShindigTestThread(OpenSocialSmokeTests listener,
|
||||
StartupStatus ss, String shindigBaseUrl) {
|
||||
super("OpenSocialSmokeTest.ShindigTestThread");
|
||||
this.listener = listener;
|
||||
this.ss = ss;
|
||||
this.shindigBaseUrl = shindigBaseUrl;
|
||||
}
|
||||
|
||||
@Override
|
||||
public void run() {
|
||||
try {
|
||||
new ShindigTester(shindigBaseUrl).connect();
|
||||
ss.info(listener, "Shindig service responds to a REST query.");
|
||||
} catch (ShindigTesterException e) {
|
||||
String message = e.getMessage();
|
||||
Throwable cause = e.getCause();
|
||||
if (cause == null) {
|
||||
ss.warning(listener, message);
|
||||
} else {
|
||||
ss.warning(listener, message, cause);
|
||||
}
|
||||
return;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
private static class ShindigTester {
|
||||
// Use the parent's log
|
||||
private static final Log log = LogFactory
|
||||
.getLog(OpenSocialSmokeTests.class);
|
||||
|
||||
/** Pretend that there is an HTTP status code for this. */
|
||||
private static final int SOCKET_TIMEOUT_STATUS = -500;
|
||||
|
||||
private final String shindigBaseUrl;
|
||||
private final HttpClient httpClient = new HttpClient();
|
||||
|
||||
private int statusCode = Integer.MIN_VALUE;
|
||||
|
||||
public ShindigTester(String shindigBaseUrl) {
|
||||
this.shindigBaseUrl = shindigBaseUrl;
|
||||
}
|
||||
|
||||
public void connect() throws ShindigTesterException {
|
||||
testConnection();
|
||||
|
||||
if (!isDone()) {
|
||||
sleep();
|
||||
testConnection();
|
||||
}
|
||||
|
||||
if (!isDone()) {
|
||||
sleep();
|
||||
testConnection();
|
||||
}
|
||||
|
||||
if (statusCode != HttpStatus.SC_OK) {
|
||||
throw new ShindigTesterException(statusCode);
|
||||
}
|
||||
}
|
||||
|
||||
private void testConnection() throws ShindigTesterException {
|
||||
String shindigTestUrl = shindigBaseUrl + "/rest/activities";
|
||||
GetMethod method = new GetMethod(shindigTestUrl);
|
||||
try {
|
||||
log.debug("Trying to connect to Shindig");
|
||||
statusCode = httpClient.executeMethod(method);
|
||||
log.debug("HTTP status was " + statusCode);
|
||||
|
||||
// clear the buffer.
|
||||
InputStream stream = method.getResponseBodyAsStream();
|
||||
stream.close();
|
||||
} catch (SocketTimeoutException e) {
|
||||
// Catch the exception so we can retry this.
|
||||
// Save the status so we know why we failed.
|
||||
statusCode = SOCKET_TIMEOUT_STATUS;
|
||||
} catch (Exception e) {
|
||||
throw new ShindigTesterException(e);
|
||||
} finally {
|
||||
method.releaseConnection();
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Stop trying to connect if we succeed, or if we receive an error that
|
||||
* won't change on retry.
|
||||
*/
|
||||
private boolean isDone() {
|
||||
return (statusCode == HttpStatus.SC_OK)
|
||||
|| (statusCode == HttpStatus.SC_FORBIDDEN);
|
||||
}
|
||||
|
||||
private void sleep() {
|
||||
try {
|
||||
Thread.sleep(SLEEP_INTERVAL);
|
||||
} catch (InterruptedException e) {
|
||||
e.printStackTrace(); // Should never happen
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
protected static class ShindigTesterException extends Exception {
|
||||
private final int httpStatusCode;
|
||||
|
||||
protected ShindigTesterException(Integer httpStatusCode) {
|
||||
super("Failed to connect to the Shindig service. "
|
||||
+ "status code was " + httpStatusCode);
|
||||
this.httpStatusCode = httpStatusCode;
|
||||
}
|
||||
|
||||
protected ShindigTesterException(Throwable cause) {
|
||||
super("Failed to connect to the Shindig service.", cause);
|
||||
this.httpStatusCode = Integer.MIN_VALUE;
|
||||
}
|
||||
|
||||
protected int getHttpStatusCode() {
|
||||
return httpStatusCode;
|
||||
}
|
||||
}
|
||||
|
||||
private static class TokenServiceTestThread extends VitroBackgroundThread {
|
||||
private final OpenSocialSmokeTests listener;
|
||||
private final StartupStatus ss;
|
||||
private final String tokenServiceHost;
|
||||
private final int tokenServicePort;
|
||||
|
||||
public TokenServiceTestThread(OpenSocialSmokeTests listener,
|
||||
StartupStatus ss, String tokenServiceHost, int tokenServicePort) {
|
||||
super("OpenSocialSmokeTest.TokenServiceTestThread");
|
||||
this.listener = listener;
|
||||
this.ss = ss;
|
||||
this.tokenServiceHost = tokenServiceHost;
|
||||
this.tokenServicePort = tokenServicePort;
|
||||
}
|
||||
|
||||
@Override
|
||||
public void run() {
|
||||
try {
|
||||
new TokenServiceTester(tokenServiceHost, tokenServicePort)
|
||||
.connect();
|
||||
ss.info(listener,
|
||||
"Shindig security token service responds to a request.");
|
||||
} catch (TokenServiceTesterException e) {
|
||||
String message = e.getMessage();
|
||||
Throwable cause = e.getCause();
|
||||
if (cause == null) {
|
||||
ss.warning(listener, message);
|
||||
} else {
|
||||
ss.warning(listener, message, cause);
|
||||
}
|
||||
return;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
protected static class TokenServiceTester {
|
||||
// Use the parent's log
|
||||
private static final Log log = LogFactory
|
||||
.getLog(OpenSocialSmokeTests.class);
|
||||
|
||||
private final String host;
|
||||
private final int port;
|
||||
|
||||
private Object problem;
|
||||
|
||||
public TokenServiceTester(String host, int port) {
|
||||
this.host = host;
|
||||
this.port = port;
|
||||
}
|
||||
|
||||
public void connect() throws TokenServiceTesterException {
|
||||
testConnection();
|
||||
|
||||
if (!isDone()) {
|
||||
sleep();
|
||||
testConnection();
|
||||
}
|
||||
|
||||
if (!isDone()) {
|
||||
sleep();
|
||||
testConnection();
|
||||
}
|
||||
|
||||
if (problem instanceof Throwable) {
|
||||
throw new TokenServiceTesterException(
|
||||
"Test of the Shindig token service failed.",
|
||||
(Throwable) problem);
|
||||
} else if (problem instanceof String) {
|
||||
throw new TokenServiceTesterException((String) problem);
|
||||
}
|
||||
}
|
||||
|
||||
private void testConnection() {
|
||||
try {
|
||||
log.debug("Connecting to the token service");
|
||||
Socket s = new Socket(host, port);
|
||||
|
||||
s.getOutputStream().write("c=default\n".getBytes());
|
||||
|
||||
int byteCount = 0;
|
||||
int totalBytecount = 0;
|
||||
byte[] buffer = new byte[8192];
|
||||
|
||||
// The following will block until the page is transmitted.
|
||||
InputStream inputStream = s.getInputStream();
|
||||
while ((byteCount = inputStream.read(buffer)) > 0) {
|
||||
totalBytecount += byteCount;
|
||||
}
|
||||
|
||||
if (totalBytecount == 0) {
|
||||
log.debug("Received an empty response.");
|
||||
problem = "The Shindig security token service responded to a test, but the response was empty.";
|
||||
} else {
|
||||
log.debug("Recieved the token.");
|
||||
problem = null;
|
||||
}
|
||||
} catch (Exception e) {
|
||||
log.debug("Problem with the token service", e);
|
||||
problem = e;
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Stop trying to connect if we succeed, or if we receive an error that
|
||||
* won't change on retry.
|
||||
*/
|
||||
private boolean isDone() {
|
||||
return ((problem == null) || (problem instanceof String));
|
||||
}
|
||||
|
||||
private void sleep() {
|
||||
try {
|
||||
Thread.sleep(SLEEP_INTERVAL);
|
||||
} catch (InterruptedException e) {
|
||||
e.printStackTrace(); // Should never happen
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
protected static class TokenServiceTesterException extends Exception {
|
||||
protected TokenServiceTesterException(String message) {
|
||||
super(message);
|
||||
}
|
||||
|
||||
protected TokenServiceTesterException(String message, Throwable cause) {
|
||||
super(message, cause);
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -18,7 +18,7 @@ import com.hp.hpl.jena.rdf.model.Resource;
|
|||
import edu.cornell.mannlib.vitro.testing.AbstractTestClass;
|
||||
import edu.cornell.mannlib.vitro.webapp.utils.threads.VitroBackgroundThread;
|
||||
|
||||
public class SimpleReasonerPropertyTest extends AbstractTestClass {
|
||||
public class SimpleReasonerInversePropertyTest extends AbstractTestClass {
|
||||
|
||||
long delay = 50;
|
||||
|
||||
|
|
@ -439,8 +439,6 @@ public class SimpleReasonerPropertyTest extends AbstractTestClass {
|
|||
|
||||
SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf);
|
||||
aBox.register(simpleReasoner);
|
||||
SimpleReasonerTBoxListener simpleReasonerTBoxListener = getTBoxListener(simpleReasoner);
|
||||
tBox.register(simpleReasonerTBoxListener);
|
||||
// Individuals a, b, c and d
|
||||
Resource a = aBox.createResource("http://test.vivo/a");
|
||||
Resource b = aBox.createResource("http://test.vivo/b");
|
||||
|
|
@ -460,8 +458,6 @@ public class SimpleReasonerPropertyTest extends AbstractTestClass {
|
|||
// Verify inferences
|
||||
Assert.assertTrue(inf.contains(b,Q,a));
|
||||
Assert.assertTrue(inf.contains(d,Y,c));
|
||||
|
||||
simpleReasonerTBoxListener.setStopRequested();
|
||||
}
|
||||
|
||||
//==================================== Utility methods ====================
|
||||
|
|
@ -0,0 +1,430 @@
|
|||
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
|
||||
|
||||
package edu.cornell.mannlib.vitro.webapp.reasoner;
|
||||
|
||||
import org.apache.log4j.Level;
|
||||
import org.junit.Assert;
|
||||
import org.junit.Before;
|
||||
import org.junit.Test;
|
||||
import org.mindswap.pellet.jena.PelletReasonerFactory;
|
||||
|
||||
import com.hp.hpl.jena.ontology.OntClass;
|
||||
import com.hp.hpl.jena.ontology.OntModel;
|
||||
import com.hp.hpl.jena.ontology.OntModelSpec;
|
||||
import com.hp.hpl.jena.ontology.OntProperty;
|
||||
import com.hp.hpl.jena.rdf.model.Literal;
|
||||
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 com.hp.hpl.jena.vocabulary.RDF;
|
||||
|
||||
import edu.cornell.mannlib.vitro.testing.AbstractTestClass;
|
||||
import edu.cornell.mannlib.vitro.webapp.utils.threads.VitroBackgroundThread;
|
||||
|
||||
public class SimpleReasonerSameAsTest extends AbstractTestClass {
|
||||
|
||||
long delay = 50;
|
||||
|
||||
@Before
|
||||
public void suppressErrorOutput() {
|
||||
suppressSyserr();
|
||||
//Turn off log messages to console
|
||||
setLoggerLevel(SimpleReasoner.class, Level.OFF);
|
||||
setLoggerLevel(SimpleReasonerTBoxListener.class, Level.OFF);
|
||||
}
|
||||
|
||||
/*
|
||||
* basic scenario of adding an abox sameAs assertion
|
||||
//*/
|
||||
@Test
|
||||
public void addSameAsABoxAssertion1() {
|
||||
|
||||
OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
|
||||
|
||||
OntProperty P = tBox.createObjectProperty("http://test.vivo/P");
|
||||
P.setLabel("property P", "en-US");
|
||||
|
||||
OntProperty Q = tBox.createObjectProperty("http://test.vivo/Q");
|
||||
Q.setLabel("property Q", "en-US");
|
||||
|
||||
OntProperty S = tBox.createDatatypeProperty("http://test.vivo/");
|
||||
S.setLabel("property S", "en-US");
|
||||
|
||||
OntProperty T = tBox.createDatatypeProperty("http://test.vivo/");
|
||||
T.setLabel("property T", "en-US");
|
||||
|
||||
Literal literal1 = tBox.createLiteral("Literal value 1");
|
||||
Literal literal2 = tBox.createLiteral("Literal value 2");
|
||||
|
||||
// this is the model to receive inferences
|
||||
Model inf = ModelFactory.createDefaultModel();
|
||||
|
||||
// create an ABox and register the SimpleReasoner listener with it
|
||||
OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
|
||||
aBox.register(new SimpleReasoner(tBox, aBox, inf));
|
||||
|
||||
// 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");
|
||||
|
||||
aBox.add(a,P,c);
|
||||
aBox.add(a,S,literal1);
|
||||
aBox.add(b,Q,d);
|
||||
aBox.add(b,T,literal2);
|
||||
aBox.add(a,OWL.sameAs,b);
|
||||
|
||||
Assert.assertTrue(inf.contains(b,OWL.sameAs,a));
|
||||
Assert.assertTrue(inf.contains(b,P,c));
|
||||
Assert.assertTrue(inf.contains(b,S,literal1));
|
||||
Assert.assertTrue(inf.contains(a,Q,d));
|
||||
Assert.assertTrue(inf.contains(a,T,literal2));
|
||||
|
||||
Assert.assertFalse(aBox.contains(b,OWL.sameAs,a));
|
||||
Assert.assertFalse(aBox.contains(b,P,c));
|
||||
Assert.assertFalse(aBox.contains(b,S,literal1));
|
||||
Assert.assertFalse(aBox.contains(a,Q,d));
|
||||
Assert.assertFalse(aBox.contains(a,T,literal2));
|
||||
}
|
||||
|
||||
/*
|
||||
* basic scenario of removing an abox sameAs assertion
|
||||
*/
|
||||
@Test
|
||||
public void removeSameAsABoxAssertion1() {
|
||||
|
||||
OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
|
||||
|
||||
OntProperty P = tBox.createObjectProperty("http://test.vivo/P");
|
||||
P.setLabel("property P", "en-US");
|
||||
|
||||
OntProperty Q = tBox.createObjectProperty("http://test.vivo/Q");
|
||||
Q.setLabel("property Q", "en-US");
|
||||
|
||||
OntProperty S = tBox.createDatatypeProperty("http://test.vivo/");
|
||||
S.setLabel("property S", "en-US");
|
||||
|
||||
OntProperty T = tBox.createDatatypeProperty("http://test.vivo/");
|
||||
T.setLabel("property T", "en-US");
|
||||
|
||||
Literal literal1 = tBox.createLiteral("Literal value 1");
|
||||
Literal literal2 = tBox.createLiteral("Literal value 2");
|
||||
|
||||
// this is the model to receive inferences
|
||||
Model inf = ModelFactory.createDefaultModel();
|
||||
|
||||
// create an ABox and register the SimpleReasoner listener with it
|
||||
OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
|
||||
aBox.register(new SimpleReasoner(tBox, aBox, inf));
|
||||
|
||||
// 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");
|
||||
|
||||
aBox.add(a,P,c);
|
||||
aBox.add(a,S,literal1);
|
||||
aBox.add(b,Q,d);
|
||||
aBox.add(b,T,literal2);
|
||||
aBox.add(a,OWL.sameAs,b);
|
||||
|
||||
Assert.assertTrue(inf.contains(b,OWL.sameAs,a));
|
||||
Assert.assertTrue(inf.contains(b,P,c));
|
||||
Assert.assertTrue(inf.contains(b,S,literal1));
|
||||
Assert.assertTrue(inf.contains(a,Q,d));
|
||||
Assert.assertTrue(inf.contains(a,T,literal2));
|
||||
|
||||
aBox.remove(a,OWL.sameAs,b);
|
||||
|
||||
Assert.assertFalse(inf.contains(b,OWL.sameAs,a));
|
||||
Assert.assertFalse(inf.contains(b,P,c));
|
||||
Assert.assertFalse(inf.contains(b,S,literal1));
|
||||
Assert.assertFalse(inf.contains(a,Q,d));
|
||||
Assert.assertFalse(inf.contains(a,T,literal2));
|
||||
}
|
||||
|
||||
/*
|
||||
* basic scenario of adding an abox assertion for
|
||||
* an individual is sameAs another.
|
||||
*/
|
||||
@Test
|
||||
public void addABoxAssertion1() {
|
||||
|
||||
OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
|
||||
|
||||
OntProperty P = tBox.createObjectProperty("http://test.vivo/P");
|
||||
P.setLabel("property P", "en-US");
|
||||
|
||||
OntProperty Q = tBox.createObjectProperty("http://test.vivo/Q");
|
||||
Q.setLabel("property Q", "en-US");
|
||||
|
||||
OntProperty S = tBox.createDatatypeProperty("http://test.vivo/");
|
||||
S.setLabel("property S", "en-US");
|
||||
|
||||
OntProperty T = tBox.createDatatypeProperty("http://test.vivo/");
|
||||
T.setLabel("property T", "en-US");
|
||||
|
||||
Literal literal1 = tBox.createLiteral("Literal value 1");
|
||||
Literal literal2 = tBox.createLiteral("Literal value 2");
|
||||
|
||||
// this is the model to receive inferences
|
||||
Model inf = ModelFactory.createDefaultModel();
|
||||
|
||||
// create an ABox and register the SimpleReasoner listener with it
|
||||
OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
|
||||
aBox.register(new SimpleReasoner(tBox, aBox, inf));
|
||||
|
||||
// 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");
|
||||
|
||||
aBox.add(a,OWL.sameAs,b);
|
||||
|
||||
Assert.assertTrue(inf.contains(b,OWL.sameAs,a));
|
||||
|
||||
aBox.add(a,P,c);
|
||||
aBox.add(a,S,literal1);
|
||||
aBox.add(b,Q,d);
|
||||
aBox.add(b,T,literal2);
|
||||
|
||||
Assert.assertTrue(inf.contains(b,P,c));
|
||||
Assert.assertTrue(inf.contains(b,S,literal1));
|
||||
Assert.assertTrue(inf.contains(a,Q,d));
|
||||
Assert.assertTrue(inf.contains(a,T,literal2));
|
||||
}
|
||||
|
||||
/*
|
||||
* adding abox assertion for individuals that are sameAs
|
||||
* each other.
|
||||
*/
|
||||
@Test
|
||||
public void addABoxAssertion2() {
|
||||
OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
|
||||
|
||||
OntClass classA = tBox.createClass("http://test.vivo/A");
|
||||
classA.setLabel("class A", "en-US");
|
||||
|
||||
OntClass classB = tBox.createClass("http://test.vivo/B");
|
||||
classB.setLabel("class B", "en-US");
|
||||
|
||||
classA.addSubClass(classB);
|
||||
|
||||
OntProperty desc = tBox.createDatatypeProperty("http://test.vivo/desc");
|
||||
desc.setLabel("property desc", "en-US");
|
||||
|
||||
Literal desc1 = tBox.createLiteral("individual 1");
|
||||
Literal desc2 = tBox.createLiteral("individual 2");
|
||||
|
||||
// this is the model to receive inferences
|
||||
Model inf = ModelFactory.createDefaultModel();
|
||||
|
||||
// create an ABox and register the SimpleReasoner listener with it
|
||||
OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
|
||||
aBox.register(new SimpleReasoner(tBox, aBox, inf));
|
||||
|
||||
// Individuals a and b
|
||||
Resource a = aBox.createResource("http://test.vivo/a");
|
||||
Resource b = aBox.createResource("http://test.vivo/b");
|
||||
|
||||
aBox.add(a,desc,desc1);
|
||||
aBox.add(b,desc,desc2);
|
||||
aBox.add(a,OWL.sameAs,b);
|
||||
aBox.add(a, RDF.type, classB);
|
||||
|
||||
Assert.assertTrue(inf.contains(a,desc,desc2));
|
||||
Assert.assertTrue(inf.contains(a,RDF.type,classA));
|
||||
Assert.assertTrue(inf.contains(b,desc,desc1));
|
||||
Assert.assertTrue(inf.contains(b,OWL.sameAs,a));
|
||||
Assert.assertTrue(inf.contains(b,RDF.type,classB));
|
||||
Assert.assertTrue(inf.contains(b,RDF.type,classA));
|
||||
}
|
||||
|
||||
/*
|
||||
* basic scenario of removing an abox assertion for
|
||||
* an individual is sameAs another.
|
||||
*/
|
||||
@Test
|
||||
public void removeABoxAssertion1() {
|
||||
|
||||
OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
|
||||
|
||||
OntProperty P = tBox.createObjectProperty("http://test.vivo/P");
|
||||
P.setLabel("property P", "en-US");
|
||||
|
||||
OntProperty Q = tBox.createObjectProperty("http://test.vivo/Q");
|
||||
Q.setLabel("property Q", "en-US");
|
||||
|
||||
OntProperty S = tBox.createDatatypeProperty("http://test.vivo/");
|
||||
S.setLabel("property S", "en-US");
|
||||
|
||||
OntProperty T = tBox.createDatatypeProperty("http://test.vivo/");
|
||||
T.setLabel("property T", "en-US");
|
||||
|
||||
Literal literal1 = tBox.createLiteral("Literal value 1");
|
||||
Literal literal2 = tBox.createLiteral("Literal value 2");
|
||||
|
||||
// this is the model to receive inferences
|
||||
Model inf = ModelFactory.createDefaultModel();
|
||||
|
||||
// create an ABox and register the SimpleReasoner listener with it
|
||||
OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
|
||||
aBox.register(new SimpleReasoner(tBox, aBox, inf));
|
||||
|
||||
// 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");
|
||||
|
||||
aBox.add(a,P,c);
|
||||
aBox.add(a,S,literal1);
|
||||
aBox.add(b,Q,d);
|
||||
aBox.add(b,T,literal2);
|
||||
aBox.add(a,OWL.sameAs,b);
|
||||
|
||||
aBox.remove(a,P,c);
|
||||
aBox.remove(a,S,literal1);
|
||||
|
||||
Assert.assertFalse(inf.contains(b,P,c));
|
||||
Assert.assertFalse(inf.contains(b,S,literal1));
|
||||
}
|
||||
|
||||
/*
|
||||
* adding an inverseOf assertion for individuals who are sameAs
|
||||
* each other.
|
||||
*/
|
||||
@Test
|
||||
public void addTBoxInverseAssertion1() throws InterruptedException {
|
||||
|
||||
// Create TBox, ABox and Inference models and register
|
||||
// the ABox reasoner listeners with the ABox and TBox
|
||||
// Pellet will compute TBox inferences
|
||||
|
||||
OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
|
||||
|
||||
OntProperty P = tBox.createOntProperty("http://test.vivo/P");
|
||||
P.setLabel("property P", "en-US");
|
||||
|
||||
OntProperty Q = tBox.createOntProperty("http://test.vivo/Q");
|
||||
Q.setLabel("property Q", "en-US");
|
||||
|
||||
OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
|
||||
Model inf = ModelFactory.createDefaultModel();
|
||||
|
||||
SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf);
|
||||
aBox.register(simpleReasoner);
|
||||
SimpleReasonerTBoxListener simpleReasonerTBoxListener = getTBoxListener(simpleReasoner);
|
||||
tBox.register(simpleReasonerTBoxListener);
|
||||
|
||||
// Individuals a and b
|
||||
Resource a = aBox.createResource("http://test.vivo/a");
|
||||
Resource b = aBox.createResource("http://test.vivo/b");
|
||||
|
||||
// abox statements
|
||||
aBox.add(a,P,b);
|
||||
aBox.add(a, OWL.sameAs,b);
|
||||
|
||||
// Assert P and Q as inverses and wait for SimpleReasoner TBox
|
||||
// thread to end
|
||||
|
||||
Q.addInverseOf(P);
|
||||
|
||||
tBox.rebind();
|
||||
tBox.prepare();
|
||||
|
||||
while (!VitroBackgroundThread.getLivingThreads().isEmpty()) {
|
||||
Thread.sleep(delay);
|
||||
}
|
||||
|
||||
// Verify inferences
|
||||
Assert.assertTrue(inf.contains(b,Q,a));
|
||||
Assert.assertTrue(inf.contains(b,OWL.sameAs,a));
|
||||
Assert.assertTrue(inf.contains(b,P,b));
|
||||
Assert.assertTrue(inf.contains(a,Q,a));
|
||||
simpleReasonerTBoxListener.setStopRequested();
|
||||
}
|
||||
|
||||
/*
|
||||
* Basic scenario around recomputing the ABox inferences
|
||||
*/
|
||||
@Test
|
||||
public void recomputeABox1() throws InterruptedException {
|
||||
|
||||
OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
|
||||
|
||||
OntProperty P = tBox.createObjectProperty("http://test.vivo/P");
|
||||
P.setLabel("property P", "en-US");
|
||||
|
||||
OntProperty Q = tBox.createObjectProperty("http://test.vivo/Q");
|
||||
Q.setLabel("property Q", "en-US");
|
||||
|
||||
OntProperty S = tBox.createDatatypeProperty("http://test.vivo/");
|
||||
S.setLabel("property S", "en-US");
|
||||
|
||||
OntProperty T = tBox.createDatatypeProperty("http://test.vivo/");
|
||||
T.setLabel("property T", "en-US");
|
||||
|
||||
Literal literal1 = tBox.createLiteral("Literal value 1");
|
||||
Literal literal2 = tBox.createLiteral("Literal value 2");
|
||||
|
||||
// this is the model to receive inferences
|
||||
Model inf = ModelFactory.createDefaultModel();
|
||||
|
||||
// create an ABox and register the SimpleReasoner listener with it
|
||||
OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
|
||||
SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf);
|
||||
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");
|
||||
|
||||
aBox.add(a,P,c);
|
||||
aBox.add(a,S,literal1);
|
||||
aBox.add(b,Q,d);
|
||||
aBox.add(b,T,literal2);
|
||||
aBox.add(a,OWL.sameAs,b);
|
||||
|
||||
simpleReasoner.recompute();
|
||||
|
||||
while (simpleReasoner.isRecomputing()) {
|
||||
Thread.sleep(delay);
|
||||
}
|
||||
|
||||
// Verify inferences
|
||||
Assert.assertTrue(inf.contains(b,OWL.sameAs,a));
|
||||
Assert.assertTrue(inf.contains(b,P,c));
|
||||
Assert.assertTrue(inf.contains(b,S,literal1));
|
||||
Assert.assertTrue(inf.contains(a,Q,d));
|
||||
Assert.assertTrue(inf.contains(a,T,literal2));
|
||||
}
|
||||
|
||||
//==================================== Utility methods ====================
|
||||
SimpleReasonerTBoxListener getTBoxListener(SimpleReasoner simpleReasoner) {
|
||||
return new SimpleReasonerTBoxListener(simpleReasoner, new Exception().getStackTrace()[1].getMethodName());
|
||||
}
|
||||
|
||||
// To help in debugging the unit test
|
||||
void printModel(Model model, String modelName) {
|
||||
|
||||
System.out.println("\nThe " + modelName + " model has " + model.size() + " statements:");
|
||||
System.out.println("---------------------------------------------------------------------");
|
||||
model.write(System.out);
|
||||
}
|
||||
|
||||
// To help in debugging the unit test
|
||||
void printModel(OntModel ontModel, String modelName) {
|
||||
|
||||
System.out.println("\nThe " + modelName + " model has " + ontModel.size() + " statements:");
|
||||
System.out.println("---------------------------------------------------------------------");
|
||||
ontModel.writeAll(System.out,"N3",null);
|
||||
|
||||
}
|
||||
}
|
||||
|
|
@ -54,6 +54,8 @@ edu.cornell.mannlib.vitro.webapp.auth.policy.RestrictHomeMenuItemEditingPolicy$S
|
|||
|
||||
edu.cornell.mannlib.vitro.webapp.services.shortview.ShortViewServiceSetup
|
||||
|
||||
edu.ucsf.vitro.opensocial.OpenSocialSmokeTests
|
||||
|
||||
# The Solr index uses a "public" permission, so the PropertyRestrictionPolicyHelper
|
||||
# and the PermissionRegistry must already be set up.
|
||||
edu.cornell.mannlib.vitro.webapp.search.solr.SolrSetup
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue