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Merge branch 'maint-rel-1.6' into develop

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This commit is contained in:
brianjlowe 2013-12-04 16:34:38 -05:00
commit 6637a54252
9 changed files with 144 additions and 148 deletions
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212
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;
}
@ -365,8 +373,14 @@ 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");
// 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();
log.info("Updating ABox inference model");
Iterator<Statement> iter = null;
// 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);
try {
iter = listModelStatements(inferenceModel, JenaDataSourceSetupBase.JENA_INF_MODEL);
while (iter.hasNext()) {
Statement stmt = iter.next();
if (!inferenceRebuildModel.contains(stmt)) {
scratchpadModel.add(stmt);
}
num++;
if ((num % 10000) == 0) {
log.info("Still updating ABox inference model (checking for outdated inferences)...");
}
if (stopRequested) {
return true;
}
}
} finally {
// if (iter != null) {
// iter.close();
// }
inferenceModel.leaveCriticalSection();
}
try {
iter = listModelStatements(scratchpadModel, SimpleReasonerSetup.JENA_INF_MODEL_SCRATCHPAD);
while (iter.hasNext()) {
Statement stmt = iter.next();
// skip statements with blank nodes to avoid excessive deletion
if (stmt.getSubject().isAnon() || stmt.getObject().isAnon()) {
continue;
}
inferenceModel.enterCriticalSection(Lock.WRITE);
try {
inferenceModel.remove(stmt);
} finally {
inferenceModel.leaveCriticalSection();
}
}
} finally {
// if (iter != null) {
// iter.close();
// }
}
// 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);
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;
long start = System.currentTimeMillis();
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();
}
Model retractions = existing.difference(rebuild);
Model additions = rebuild.difference(existing);
inferenceModel.enterCriticalSection(Lock.WRITE);
try {
inferenceModel.remove(retractions);
inferenceModel.add(additions);
} finally {
inferenceModel.leaveCriticalSection();
}
inferenceRebuildModel.enterCriticalSection(Lock.WRITE);
try {
inferenceRebuildModel.remove(rebuild);
} finally {
inferenceRebuildModel.leaveCriticalSection();
}
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();
}
if (stopRequested) {
return true;
}
}
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,

30
webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasoner.java
View file

@ -161,6 +161,10 @@ public class SimpleReasoner extends StatementListener {
public void setSameAsEnabled( boolean tf){
this.doSameAs = tf;
}
public boolean getSameAsEnabled() {
return this.doSameAs;
}
/*
* Performs incremental ABox reasoning based
@ -342,6 +346,12 @@ public class SimpleReasoner extends StatementListener {
public void removedTBoxStatement(Statement stmt) {
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
@ -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);
}
@ -1730,9 +1748,7 @@ public class SimpleReasoner extends StatementListener {
log.info("ending DeltaComputer.run. batchMode = " + batchMode);
}
}
}
/**
* 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);