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NIHVIVO-2766 (abox recompute in separate thread)

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stellamit 2011-07-08 20:32:09 +00:00
parent 94ae938900
commit c492a4c397
3 changed files with 100 additions and 42 deletions
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3
webapp/ontologies/system/vitro-0.7.owl
View file

@ -134,9 +134,6 @@ xmlns:vitro="&vitro;"
<rdf:Description rdf:about="http://vitro.mannlib.cornell.edu/ns/vitro/0.7#shortDef"> <rdf:Description rdf:about="http://vitro.mannlib.cornell.edu/ns/vitro/0.7#shortDef">
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#AnnotationProperty"/> <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#AnnotationProperty"/>
</rdf:Description> </rdf:Description>
<rdf:Description rdf:about="http://vitro.mannlib.cornell.edu/ns/vitro/0.7#DependentResource">
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Class"/>
</rdf:Description>
<rdf:Description rdf:about="http://vitro.mannlib.cornell.edu/ns/vitro/0.7#publicDescriptionAnnot"> <rdf:Description rdf:about="http://vitro.mannlib.cornell.edu/ns/vitro/0.7#publicDescriptionAnnot">
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#AnnotationProperty"/> <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#AnnotationProperty"/>
</rdf:Description> </rdf:Description>

99
webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasoner.java
View file

@ -100,8 +100,8 @@ public class SimpleReasoner extends StatementListener {
try { try {
if (stmt.getPredicate().equals(RDF.type)) { if (stmt.getPredicate().equals(RDF.type)) {
addedABoxTypeAssertion(stmt, inferenceModel); addedABoxTypeAssertion(stmt, inferenceModel, new HashSet<String>());
setMostSpecificTypes(stmt.getSubject(), inferenceModel); setMostSpecificTypes(stmt.getSubject(), inferenceModel, new HashSet<String>());
} }
/* uncomment this to enable subproperty/equivalent property inferencing. sjm222 5/13/2011 /* uncomment this to enable subproperty/equivalent property inferencing. sjm222 5/13/2011
else { else {
@ -110,7 +110,7 @@ public class SimpleReasoner extends StatementListener {
*/ */
} catch (Exception e) { } catch (Exception e) {
// don't stop the edit if there's an exception // don't stop the edit if there's an exception
log.error("Exception while adding inferences: ", e); log.error("Exception while adding inferences: " + e.getMessage());
} }
} }
@ -125,7 +125,7 @@ public class SimpleReasoner extends StatementListener {
try { try {
if (stmt.getPredicate().equals(RDF.type)) { if (stmt.getPredicate().equals(RDF.type)) {
removedABoxTypeAssertion(stmt, inferenceModel); removedABoxTypeAssertion(stmt, inferenceModel);
setMostSpecificTypes(stmt.getSubject(), inferenceModel); setMostSpecificTypes(stmt.getSubject(), inferenceModel, new HashSet<String>());
} }
/* uncomment this to enable subproperty/equivalent property inferencing. sjm222 5/13/2011 /* uncomment this to enable subproperty/equivalent property inferencing. sjm222 5/13/2011
else { else {
@ -134,7 +134,7 @@ public class SimpleReasoner extends StatementListener {
*/ */
} catch (Exception e) { } catch (Exception e) {
// don't stop the edit if there's an exception // don't stop the edit if there's an exception
log.error("Exception while retracting inferences: ", e); log.error("Exception while retracting inferences: " + e.getMessage());
} }
} }
@ -207,7 +207,7 @@ public class SimpleReasoner extends StatementListener {
} catch (Exception e) { } catch (Exception e) {
// don't stop the edit if there's an exception // don't stop the edit if there's an exception
log.error("Exception while adding inference(s): ", e); log.error("Exception while adding inference(s): " + e.getMessage());
} }
} }
@ -275,7 +275,7 @@ public class SimpleReasoner extends StatementListener {
*/ */
} catch (Exception e) { } catch (Exception e) {
// don't stop the edit if there's an exception // don't stop the edit if there's an exception
log.error("Exception while removing inference(s): ", e); log.error("Exception while removing inference(s): " + e.getMessage());
} }
} }
@ -288,9 +288,8 @@ public class SimpleReasoner extends StatementListener {
* A assert that B is of that type. * A assert that B is of that type.
* *
*/ */
public void addedABoxTypeAssertion(Statement stmt, Model inferenceModel) { public void addedABoxTypeAssertion(Statement stmt, Model inferenceModel, HashSet<String> unknownTypes) {
//System.out.println("sjm: addedABoxTypeAssertion: " + stmtString(stmt));
tboxModel.enterCriticalSection(Lock.READ); tboxModel.enterCriticalSection(Lock.READ);
try { try {
@ -298,9 +297,9 @@ public class SimpleReasoner extends StatementListener {
OntClass cls = null; OntClass cls = null;
if ( (stmt.getObject().asResource()).getURI() != null ) { if ( (stmt.getObject().asResource()).getURI() != null ) {
cls = tboxModel.getOntClass(stmt.getObject().asResource().getURI());
if (cls != null) { cls = tboxModel.getOntClass(stmt.getObject().asResource().getURI());
if (cls != null) {
List<OntClass> parents = (cls.listSuperClasses(false)).toList(); List<OntClass> parents = (cls.listSuperClasses(false)).toList();
parents.addAll((cls.listEquivalentClasses()).toList()); parents.addAll((cls.listEquivalentClasses()).toList());
@ -327,8 +326,13 @@ public class SimpleReasoner extends StatementListener {
} }
} }
} else { } else {
if ( !(stmt.getObject().asResource().getNameSpace()).equals(OWL.NS)) if ( !(stmt.getObject().asResource().getNameSpace()).equals(OWL.NS)) {
log.warn("Didn't find target class (the object of the added rdf:type statement) in the TBox"); if (!unknownTypes.contains(stmt.getObject().asResource().getURI())) {
unknownTypes.add(stmt.getObject().asResource().getURI());
log.warn("Didn't find the target class (the object of an added rdf:type statement) in the TBox: " +
(stmt.getObject().asResource()).getURI() + ". No class subsumption reasoning will be done based on type assertions of this type.");
}
}
} }
} else { } else {
log.warn("The object of this rdf:type assertion has a null URI: " + stmtString(stmt)); log.warn("The object of this rdf:type assertion has a null URI: " + stmtString(stmt));
@ -406,8 +410,6 @@ public class SimpleReasoner extends StatementListener {
public void removedABoxTypeAssertion(Statement stmt, Model inferenceModel) { public void removedABoxTypeAssertion(Statement stmt, Model inferenceModel) {
//System.out.println("sjm: removedABoxTypeAssertion: " + stmtString(stmt));
tboxModel.enterCriticalSection(Lock.READ); tboxModel.enterCriticalSection(Lock.READ);
// convert this method to use generic resources - not get ontclass, not cls.listSuperClasses... // convert this method to use generic resources - not get ontclass, not cls.listSuperClasses...
@ -454,7 +456,8 @@ public class SimpleReasoner extends StatementListener {
} }
} }
} else { } else {
log.warn("Didn't find target class (the object of the removed rdf:type statement) in the TBox: " + ((Resource)stmt.getObject()).getURI()); log.warn("Didn't find target class (the object of the removed rdf:type statement) in the TBox: "
+ ((Resource)stmt.getObject()).getURI() + ". No class subsumption reasoning will be performed based on the removal of this assertion.");
} }
} else { } else {
log.warn("The object of this rdf:type assertion has a null URI: " + stmtString(stmt)); log.warn("The object of this rdf:type assertion has a null URI: " + stmtString(stmt));
@ -598,7 +601,7 @@ public class SimpleReasoner extends StatementListener {
if (!inferenceModel.contains(infStmt)) { if (!inferenceModel.contains(infStmt)) {
inferenceModel.add(infStmt); inferenceModel.add(infStmt);
setMostSpecificTypes(infStmt.getSubject(), inferenceModel); setMostSpecificTypes(infStmt.getSubject(), inferenceModel, new HashSet<String>());
} }
} }
} finally { } finally {
@ -641,7 +644,7 @@ public class SimpleReasoner extends StatementListener {
if (inferenceModel.contains(infStmt)) { if (inferenceModel.contains(infStmt)) {
inferenceModel.remove(infStmt); inferenceModel.remove(infStmt);
setMostSpecificTypes(infStmt.getSubject(), inferenceModel); setMostSpecificTypes(infStmt.getSubject(), inferenceModel, new HashSet<String>());
} }
} }
} finally { } finally {
@ -744,9 +747,8 @@ public class SimpleReasoner extends StatementListener {
* indicate them for the individual with the core:mostSpecificType * indicate them for the individual with the core:mostSpecificType
* annotation. * annotation.
*/ */
public void setMostSpecificTypes(Resource individual, Model inferenceModel) { public void setMostSpecificTypes(Resource individual, Model inferenceModel, HashSet<String> unknownTypes) {
//System.out.println("sjm: setMostSpecificTypes called for individual " + individual.getURI());
inferenceModel.enterCriticalSection(Lock.WRITE); inferenceModel.enterCriticalSection(Lock.WRITE);
aboxModel.enterCriticalSection(Lock.READ); aboxModel.enterCriticalSection(Lock.READ);
tboxModel.enterCriticalSection(Lock.READ); tboxModel.enterCriticalSection(Lock.READ);
@ -780,8 +782,11 @@ public class SimpleReasoner extends StatementListener {
if (ontClass == null) { if (ontClass == null) {
if ( !(stmt.getObject().asResource().getNameSpace()).equals(OWL.NS)) { if ( !(stmt.getObject().asResource().getNameSpace()).equals(OWL.NS)) {
log.warn("(setMostSpecificType) Didn't find target class (the object of the added rdf:type statement) in the TBox: " + if (!unknownTypes.contains(stmt.getObject().asResource().getURI())) {
(stmt.getObject().asResource()).getURI() + "\nstatement is: " + stmtString(stmt)); unknownTypes.add(stmt.getObject().asResource().getURI());
log.warn("Didn't find the target class (the object of an added rdf:type statement) in the TBox: " +
(stmt.getObject().asResource()).getURI() + ". No mostSpecificType computation will be done based on type assertions of this type.");
}
} }
continue; continue;
} }
@ -914,20 +919,29 @@ public class SimpleReasoner extends StatementListener {
*/ */
public synchronized void recomputeABox() { public synchronized void recomputeABox() {
HashSet<String> unknownTypes = new HashSet<String>();
// recompute the inferences // recompute the inferences
inferenceRebuildModel.enterCriticalSection(Lock.WRITE); inferenceRebuildModel.enterCriticalSection(Lock.WRITE);
aboxModel.enterCriticalSection(Lock.WRITE); aboxModel.enterCriticalSection(Lock.WRITE);
tboxModel.enterCriticalSection(Lock.READ); tboxModel.enterCriticalSection(Lock.READ);
try { try {
log.info("Computing class-based ABox inferences");
inferenceRebuildModel.removeAll(); inferenceRebuildModel.removeAll();
StmtIterator iter = aboxModel.listStatements((Resource) null, RDF.type, (RDFNode) null); StmtIterator iter = aboxModel.listStatements((Resource) null, RDF.type, (RDFNode) null);
log.info("Computing class-based ABox inferences"); int numStmts = 0;
while (iter.hasNext()) { while (iter.hasNext()) {
Statement stmt = iter.next(); Statement stmt = iter.next();
addedABoxTypeAssertion(stmt, inferenceRebuildModel); addedABoxTypeAssertion(stmt, inferenceRebuildModel, unknownTypes);
setMostSpecificTypes(stmt.getSubject(), inferenceRebuildModel); setMostSpecificTypes(stmt.getSubject(), inferenceRebuildModel, unknownTypes);
numStmts++;
if ((numStmts % 8000) == 0) {
log.info("Still computing class-based ABox inferences...");
}
} }
/* /*
@ -984,6 +998,7 @@ public class SimpleReasoner extends StatementListener {
inferenceRebuildModel.leaveCriticalSection(); inferenceRebuildModel.leaveCriticalSection();
} }
log.info("Finished computing class-based ABox inferences");
// reflect the recomputed inferences into the application inference // reflect the recomputed inferences into the application inference
// model. // model.
@ -992,6 +1007,7 @@ public class SimpleReasoner extends StatementListener {
log.info("Updating ABox inference model"); log.info("Updating ABox inference model");
// Remove everything from the current inference model that is not // Remove everything from the current inference model that is not
// in the recomputed inference model // in the recomputed inference model
int num = 0;
try { try {
inferenceModel.enterCriticalSection(Lock.READ); inferenceModel.enterCriticalSection(Lock.READ);
@ -1004,6 +1020,11 @@ public class SimpleReasoner extends StatementListener {
if (!inferenceRebuildModel.contains(stmt)) { if (!inferenceRebuildModel.contains(stmt)) {
scratchpadModel.add(stmt); scratchpadModel.add(stmt);
} }
num++;
if ((num % 8000) == 0) {
log.info("Still updating ABox inference model (removing outdated inferences)...");
}
} }
} catch (Exception e) { } catch (Exception e) {
log.error("Exception while reconciling the current and recomputed ABox inference models", e); log.error("Exception while reconciling the current and recomputed ABox inference models", e);
@ -1033,6 +1054,11 @@ public class SimpleReasoner extends StatementListener {
if (!inferenceModel.contains(stmt)) { if (!inferenceModel.contains(stmt)) {
scratchpadModel.add(stmt); scratchpadModel.add(stmt);
} }
num++;
if ((num % 8000) == 0) {
log.info("Still updating ABox inference model (adding new inferences)...");
}
} }
} catch (Exception e) { } catch (Exception e) {
log.error("Exception while reconciling the current and recomputed ABox inference models", e); log.error("Exception while reconciling the current and recomputed ABox inference models", e);
@ -1063,6 +1089,8 @@ public class SimpleReasoner extends StatementListener {
*/ */
public synchronized void recomputeMostSpecificType() { public synchronized void recomputeMostSpecificType() {
HashSet<String> unknownTypes = new HashSet<String>();
// recompute the inferences // recompute the inferences
inferenceRebuildModel.enterCriticalSection(Lock.WRITE); inferenceRebuildModel.enterCriticalSection(Lock.WRITE);
aboxModel.enterCriticalSection(Lock.WRITE); aboxModel.enterCriticalSection(Lock.WRITE);
@ -1073,9 +1101,16 @@ public class SimpleReasoner extends StatementListener {
StmtIterator iter = aboxModel.listStatements((Resource) null, RDF.type, (RDFNode) null); StmtIterator iter = aboxModel.listStatements((Resource) null, RDF.type, (RDFNode) null);
log.info("Computing mostSpecificType annotations"); log.info("Computing mostSpecificType annotations");
int numStmts = 0;
while (iter.hasNext()) { while (iter.hasNext()) {
Statement stmt = iter.next(); Statement stmt = iter.next();
setMostSpecificTypes(stmt.getSubject(), inferenceRebuildModel); setMostSpecificTypes(stmt.getSubject(), inferenceRebuildModel, unknownTypes);
numStmts++;
if ((numStmts % 8000) == 0) {
log.info("Still computing mostSpecificType annotations...");
}
} }
} catch (Exception e) { } catch (Exception e) {
log.error("Exception while recomputing ABox inference model", e); log.error("Exception while recomputing ABox inference model", e);
@ -1088,12 +1123,13 @@ public class SimpleReasoner extends StatementListener {
inferenceRebuildModel.leaveCriticalSection(); inferenceRebuildModel.leaveCriticalSection();
} }
log.info("Finished computing mostSpecificType annotations");
// reflect the recomputed inferences into the application inference // reflect the recomputed inferences into the application inference
// model. // model.
inferenceRebuildModel.enterCriticalSection(Lock.WRITE); inferenceRebuildModel.enterCriticalSection(Lock.WRITE);
scratchpadModel.enterCriticalSection(Lock.WRITE); scratchpadModel.enterCriticalSection(Lock.WRITE);
log.info("Updating ABox inference model"); log.info("Updating ABox inference model with mostSpecificType annotations");
try { try {
// Add everything from the recomputed inference model that is not already // Add everything from the recomputed inference model that is not already
@ -1104,11 +1140,18 @@ public class SimpleReasoner extends StatementListener {
scratchpadModel.removeAll(); scratchpadModel.removeAll();
StmtIterator iter = inferenceRebuildModel.listStatements(); StmtIterator iter = inferenceRebuildModel.listStatements();
int numStmts = 0;
while (iter.hasNext()) { while (iter.hasNext()) {
Statement stmt = iter.next(); Statement stmt = iter.next();
if (!inferenceModel.contains(stmt)) { if (!inferenceModel.contains(stmt)) {
scratchpadModel.add(stmt); scratchpadModel.add(stmt);
} }
numStmts++;
if ((numStmts % 8000) == 0) {
log.info("Still updating ABox inference model with mostSpecificType annotations...");
}
} }
} catch (Exception e) { } catch (Exception e) {
log.error("Exception while reconciling the current and recomputed ABox inference models", e); log.error("Exception while reconciling the current and recomputed ABox inference models", e);
@ -1131,7 +1174,7 @@ public class SimpleReasoner extends StatementListener {
scratchpadModel.leaveCriticalSection(); scratchpadModel.leaveCriticalSection();
} }
log.info("ABox inference model updated"); log.info("ABox inference model updated with mostSpecificType annotations");
} }
public static SimpleReasoner getSimpleReasonerFromServletContext(ServletContext ctx) { public static SimpleReasoner getSimpleReasonerFromServletContext(ServletContext ctx) {

26
webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/SimpleReasonerSetup.java
View file

@ -42,7 +42,6 @@ public class SimpleReasonerSetup implements ServletContextListener {
try { try {
// set up Pellet reasoning for the TBox // set up Pellet reasoning for the TBox
OntModelSelector assertionsOms = ModelContext.getBaseOntModelSelector(sce.getServletContext()); OntModelSelector assertionsOms = ModelContext.getBaseOntModelSelector(sce.getServletContext());
OntModelSelector inferencesOms = ModelContext.getInferenceOntModelSelector(sce.getServletContext()); OntModelSelector inferencesOms = ModelContext.getInferenceOntModelSelector(sce.getServletContext());
OntModelSelector unionOms = ModelContext.getUnionOntModelSelector(sce.getServletContext()); OntModelSelector unionOms = ModelContext.getUnionOntModelSelector(sce.getServletContext());
@ -110,9 +109,9 @@ public class SimpleReasonerSetup implements ServletContextListener {
sleeps++; sleeps++;
} }
simpleReasoner.recompute(); new Thread(new ABoxRecomputer(simpleReasoner,false)).start();
} else if ( isMSTComputeRequired(sce.getServletContext()) ) { } else if ( isMSTComputeRequired(sce.getServletContext()) ) {
log.info("most specific type computation required"); log.info("mostSpecificType computation required");
int sleeps = 0; int sleeps = 0;
while (sleeps < 1000 && pelletListener.isReasoning()) { while (sleeps < 1000 && pelletListener.isReasoning()) {
@ -123,7 +122,7 @@ public class SimpleReasonerSetup implements ServletContextListener {
sleeps++; sleeps++;
} }
simpleReasoner.recomputeMostSpecificType(); new Thread(new ABoxRecomputer(simpleReasoner,true)).start();
} }
assertionsOms.getTBoxModel().register(new SimpleReasonerTBoxListener(simpleReasoner)); assertionsOms.getTBoxModel().register(new SimpleReasonerTBoxListener(simpleReasoner));
@ -163,4 +162,23 @@ public class SimpleReasonerSetup implements ServletContextListener {
private static boolean isMSTComputeRequired(ServletContext ctx) { private static boolean isMSTComputeRequired(ServletContext ctx) {
return (ctx.getAttribute(MSTCOMPUTE_REQUIRED_ATTR) != null); return (ctx.getAttribute(MSTCOMPUTE_REQUIRED_ATTR) != null);
} }
private class ABoxRecomputer implements Runnable {
private SimpleReasoner simpleReasoner;
private boolean justMST;
public ABoxRecomputer(SimpleReasoner simpleReasoner, boolean justMST) {
this.simpleReasoner = simpleReasoner;
this.justMST = justMST;
}
public void run() {
if (justMST) {
simpleReasoner.recomputeMostSpecificType();
} else {
simpleReasoner.recompute();
}
}
}
} }