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updating comments, and changed some methods from public to protected

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stellamit 2012-03-15 16:36:12 +00:00
parent 5e025d66af
commit cfe7e3b462
2 changed files with 82 additions and 75 deletions
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136
webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasoner.java
View file

@ -43,12 +43,12 @@ import edu.cornell.mannlib.vitro.webapp.dao.jena.event.BulkUpdateEvent;
* Allows for real-time incremental materialization or retraction of RDFS- * Allows for real-time incremental materialization or retraction of RDFS-
* style class and property subsumption based ABox inferences as statements * style class and property subsumption based ABox inferences as statements
* are added to or removed from the (ABox or TBox) knowledge base. * are added to or removed from the (ABox or TBox) knowledge base.
* @author sjm222
*/ */
public class SimpleReasoner extends StatementListener { public class SimpleReasoner extends StatementListener {
private static final Log log = LogFactory.getLog(SimpleReasoner.class); private static final Log log = LogFactory.getLog(SimpleReasoner.class);
//private static final MyTempLogger log = new MyTempLogger();
private OntModel tboxModel; // asserted and inferred TBox axioms private OntModel tboxModel; // asserted and inferred TBox axioms
private OntModel aboxModel; // ABox assertions private OntModel aboxModel; // ABox assertions
@ -120,9 +120,9 @@ public class SimpleReasoner extends StatementListener {
} }
/* /*
* Performs selected incremental ABox reasoning based * Performs incremental ABox reasoning based
* on the addition of a new statement (aka assertion) * on the addition of a new statement
* to the ABox. * (aka assertion) to the ABox.
*/ */
@Override @Override
public void addedStatement(Statement stmt) { public void addedStatement(Statement stmt) {
@ -142,7 +142,7 @@ public class SimpleReasoner extends StatementListener {
} }
/* /*
* Performs selected incremental ABox reasoning based * Performs incremental ABox reasoning based
* on the retraction of a statement (aka assertion) * on the retraction of a statement (aka assertion)
* from the ABox. * from the ABox.
*/ */
@ -160,7 +160,12 @@ public class SimpleReasoner extends StatementListener {
} }
} }
public synchronized void handleRemovedStatement(Statement stmt) {
/*
* Synchronized part of removedStatement. Interacts
* with DeltaComputer.
*/
protected synchronized void handleRemovedStatement(Statement stmt) {
if (batchMode1) { if (batchMode1) {
aBoxDeltaModeler1.removedStatement(stmt); aBoxDeltaModeler1.removedStatement(stmt);
@ -176,7 +181,7 @@ public class SimpleReasoner extends StatementListener {
} }
/* /*
* Performs incremental selected ABox reasoning based * Performs incremental ABox reasoning based
* on changes to the class hierarchy. * on changes to the class hierarchy.
* *
* Handles rdfs:subclassOf, owl:equivalentClass, * Handles rdfs:subclassOf, owl:equivalentClass,
@ -229,7 +234,7 @@ public class SimpleReasoner extends StatementListener {
} }
/* /*
* Performs incremental selected ABox reasoning based * Performs incremental ABox reasoning based
* on changes to the class hierarchy. * on changes to the class hierarchy.
* *
* Handles rdfs:subclassOf, owl:equivalentClass, * Handles rdfs:subclassOf, owl:equivalentClass,
@ -282,9 +287,9 @@ public class SimpleReasoner extends StatementListener {
} }
/* /*
* * This signature used when recomputing the whole ABox
*/ */
public void addedABoxTypeAssertion(Resource individual, Model inferenceModel, HashSet<String> unknownTypes) { protected void addedABoxTypeAssertion(Resource individual, Model inferenceModel, HashSet<String> unknownTypes) {
StmtIterator iter = null; StmtIterator iter = null;
@ -302,6 +307,7 @@ public class SimpleReasoner extends StatementListener {
aboxModel.leaveCriticalSection(); aboxModel.leaveCriticalSection();
} }
} }
/* /*
* Performs incremental reasoning based on a new type assertion * Performs incremental reasoning based on a new type assertion
* added to the ABox (assertion that an individual is of a certain * added to the ABox (assertion that an individual is of a certain
@ -309,9 +315,8 @@ public class SimpleReasoner extends StatementListener {
* *
* If it is added that B is of type A, then for each superclass of * If it is added that B is of type A, then for each superclass of
* A assert that B is of that type. * A assert that B is of that type.
*
*/ */
public void addedABoxTypeAssertion(Statement stmt, Model inferenceModel, HashSet<String> unknownTypes) { protected void addedABoxTypeAssertion(Statement stmt, Model inferenceModel, HashSet<String> unknownTypes) {
tboxModel.enterCriticalSection(Lock.READ); tboxModel.enterCriticalSection(Lock.READ);
@ -377,13 +382,10 @@ public class SimpleReasoner extends StatementListener {
* that B is of that type. * that B is of that type.
* *
*/ */
public void removedABoxTypeAssertion(Statement stmt, Model inferenceModel) { protected void removedABoxTypeAssertion(Statement stmt, Model inferenceModel) {
tboxModel.enterCriticalSection(Lock.READ); tboxModel.enterCriticalSection(Lock.READ);
// convert this method to use generic resources - not get ontclass, not cls.listSuperClasses...
// use model contains if want to log warning about type owl class
try { try {
OntClass cls = null; OntClass cls = null;
@ -431,7 +433,6 @@ public class SimpleReasoner extends StatementListener {
inferenceModel.enterCriticalSection(Lock.WRITE); inferenceModel.enterCriticalSection(Lock.WRITE);
try { try {
if (inferenceModel.contains(infStmt)) { if (inferenceModel.contains(infStmt)) {
//log.debug("Removing this inferred statement: " + infStmt.toString() + " - " + infStmt.getSubject().toString() + " - " + infStmt.getPredicate().toString() + " - " + infStmt.getObject().toString());
inferenceModel.remove(infStmt); inferenceModel.remove(infStmt);
} }
} finally { } finally {
@ -454,7 +455,7 @@ public class SimpleReasoner extends StatementListener {
// Returns true if it is entailed by class subsumption that // Returns true if it is entailed by class subsumption that
// subject is of type cls; otherwise returns false. // subject is of type cls; otherwise returns false.
public boolean entailedType(Resource subject, OntClass cls) { protected boolean entailedType(Resource subject, OntClass cls) {
aboxModel.enterCriticalSection(Lock.READ); aboxModel.enterCriticalSection(Lock.READ);
tboxModel.enterCriticalSection(Lock.READ); tboxModel.enterCriticalSection(Lock.READ);
@ -485,9 +486,9 @@ public class SimpleReasoner extends StatementListener {
/* /*
* If it is added that B is a subClass of A, then for each * If it is added that B is a subClass of A, then for each
* individual that is typed as B, either in the ABox or in the * individual that is typed as B, either in the ABox or in the
* inferred model, assert that it is of type A. * inferred model, infer that it is of type A.
*/ */
public void addedSubClass(OntClass subClass, OntClass superClass, Model inferenceModel) { protected void addedSubClass(OntClass subClass, OntClass superClass, Model inferenceModel) {
log.debug("subClass = " + subClass.getURI() + " superClass = " + superClass.getURI()); log.debug("subClass = " + subClass.getURI() + " superClass = " + superClass.getURI());
OntModel unionModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM); OntModel unionModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
unionModel.addSubModel(aboxModel); unionModel.addSubModel(aboxModel);
@ -530,7 +531,7 @@ public class SimpleReasoner extends StatementListener {
* UNLESS the individual is of some type C that is a subClass * UNLESS the individual is of some type C that is a subClass
* of A (including A itself) * of A (including A itself)
*/ */
public void removedSubClass(OntClass subClass, OntClass superClass, Model inferenceModel) { protected void removedSubClass(OntClass subClass, OntClass superClass, Model inferenceModel) {
OntModel unionModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM); OntModel unionModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
unionModel.addSubModel(aboxModel); unionModel.addSubModel(aboxModel);
unionModel.addSubModel(inferenceModel); unionModel.addSubModel(inferenceModel);
@ -567,10 +568,10 @@ public class SimpleReasoner extends StatementListener {
/* /*
* Find the most specific types (classes) of an individual and * Find the most specific types (classes) of an individual and
* indicate them for the individual with the core:mostSpecificType * indicate them for the individual with the mostSpecificType
* annotation. * annotation.
*/ */
public void setMostSpecificTypes(Resource individual, Model inferenceModel, HashSet<String> unknownTypes) { protected void setMostSpecificTypes(Resource individual, Model inferenceModel, HashSet<String> unknownTypes) {
tboxModel.enterCriticalSection(Lock.READ); tboxModel.enterCriticalSection(Lock.READ);
aboxModel.enterCriticalSection(Lock.READ); aboxModel.enterCriticalSection(Lock.READ);
@ -665,13 +666,13 @@ public class SimpleReasoner extends StatementListener {
return; return;
} }
public void setMostSpecificTypes(Resource individual, HashSet<String> typeURIs, Model inferenceModel) { protected void setMostSpecificTypes(Resource individual, HashSet<String> typeURIs, Model inferenceModel) {
inferenceModel.enterCriticalSection(Lock.WRITE); inferenceModel.enterCriticalSection(Lock.WRITE);
try { try {
Model retractions = ModelFactory.createDefaultModel(); Model retractions = ModelFactory.createDefaultModel();
// remove obsolete most-specific-type assertions // remove obsolete mostSpecificType assertions
StmtIterator iter = inferenceModel.listStatements(individual, mostSpecificType, (RDFNode) null); StmtIterator iter = inferenceModel.listStatements(individual, mostSpecificType, (RDFNode) null);
while (iter.hasNext()) { while (iter.hasNext()) {
@ -689,7 +690,7 @@ public class SimpleReasoner extends StatementListener {
inferenceModel.remove(retractions); inferenceModel.remove(retractions);
// add new most-specific-type assertions // add new mostSpecificType assertions
Iterator<String> typeIter = typeURIs.iterator(); Iterator<String> typeIter = typeURIs.iterator();
while (typeIter.hasNext()) { while (typeIter.hasNext()) {
@ -707,12 +708,12 @@ public class SimpleReasoner extends StatementListener {
return; return;
} }
private boolean recomputing = false;
/** /**
* Returns true if the reasoner is in the process of recomputing all * Returns true if the reasoner is in the process of recomputing all
* inferences. * inferences.
*/ */
private boolean recomputing = false;
public boolean isRecomputing() { public boolean isRecomputing() {
return recomputing; return recomputing;
} }
@ -731,14 +732,14 @@ public class SimpleReasoner extends StatementListener {
/* /*
* Recompute the entire ABox inference graph. The new * Recompute the entire ABox inference graph. The new
* inference graph is built up in a separate model and * inference graph is built in a separate model and
* then reconciled with the inference graph used by the * then reconciled with the inference graph in active
* application. The model reconciliation must be done * use. The model reconciliation must be done
* without reading the whole inference models into * without reading the whole inference models into
* memory in order to support very large ABox * memory in order to support very large ABox
* inference models. * inference models.
*/ */
public synchronized void recomputeABox() { protected synchronized void recomputeABox() {
HashSet<String> unknownTypes = new HashSet<String>(); HashSet<String> unknownTypes = new HashSet<String>();
@ -799,8 +800,8 @@ public class SimpleReasoner extends StatementListener {
log.info("Finished computing class-based ABox inferences"); log.info("Finished computing class-based ABox inferences");
// reflect the recomputed inferences into the application inference // reflect the recomputed inferences into the application
// model. // inference model.
log.info("Updating ABox inference model"); log.info("Updating ABox inference model");
StmtIterator iter = null; StmtIterator iter = null;
@ -913,23 +914,16 @@ public class SimpleReasoner extends StatementListener {
log.info("ABox inference model updated"); log.info("ABox inference model updated");
} }
public synchronized boolean isABoxReasoningAsynchronous() { /*
if (batchMode1 || batchMode2) { * Get the URIs for all individuals in the system
return true; */
} else { protected ArrayList<String> getAllIndividualURIs() {
return false;
}
}
public ArrayList<String> getAllIndividualURIs() {
String queryString = "select distinct ?subject where {?subject <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?type}"; String queryString = "select distinct ?subject where {?subject <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?type}";
return getIndividualURIs(queryString); return getIndividualURIs(queryString);
} }
public ArrayList<String> getIndividualURIs(String queryString) { protected ArrayList<String> getIndividualURIs(String queryString) {
ArrayList<String> individuals = new ArrayList<String>(); ArrayList<String> individuals = new ArrayList<String>();
aboxModel.enterCriticalSection(Lock.READ); aboxModel.enterCriticalSection(Lock.READ);
@ -960,6 +954,19 @@ public class SimpleReasoner extends StatementListener {
return individuals; return individuals;
} }
// system-configured reasoning modules (plugins)
public boolean isInterestedInRemovedStatement(Statement stmt) {
if (stmt.getPredicate().equals(RDF.type)) return true;
for (ReasonerPlugin plugin : getPluginList()) {
if (plugin.isInterestedInRemovedStatement(stmt)) return true;
}
return false;
}
protected void doPlugins(ModelUpdate.Operation op, Statement stmt) { protected void doPlugins(ModelUpdate.Operation op, Statement stmt) {
for (ReasonerPlugin plugin : getPluginList()) { for (ReasonerPlugin plugin : getPluginList()) {
@ -983,29 +990,16 @@ public class SimpleReasoner extends StatementListener {
} }
} }
public boolean isInterestedInRemovedStatement(Statement stmt) {
if (stmt.getPredicate().equals(RDF.type)) return true;
for (ReasonerPlugin plugin : getPluginList()) {
if (plugin.isInterestedInRemovedStatement(stmt)) return true;
}
return false;
}
//TODO remove this for 1.5
public synchronized void computeMostSpecificType() {
}
/** /**
* This is called when the system shuts down. * This is called when the application shuts down.
*/ */
public void setStopRequested() { public void setStopRequested() {
this.stopRequested = true; this.stopRequested = true;
} }
/*
* Utility method for logging
*/
public static String stmtString(Statement statement) { public static String stmtString(Statement statement) {
return " [subject = " + statement.getSubject().getURI() + return " [subject = " + statement.getSubject().getURI() +
"] [property = " + statement.getPredicate().getURI() + "] [property = " + statement.getPredicate().getURI() +
@ -1013,6 +1007,20 @@ public class SimpleReasoner extends StatementListener {
: ((Resource)statement.getObject()).getURI() + " (Resource)") + "]"; : ((Resource)statement.getObject()).getURI() + " (Resource)") + "]";
} }
// DeltaComputer
/*
* Asynchronous reasoning mode (DeltaComputer) is used in the case of batch removals.
*/
public synchronized boolean isABoxReasoningAsynchronous() {
if (batchMode1 || batchMode2) {
return true;
} else {
return false;
}
}
private volatile boolean deltaComputerProcessing = false; private volatile boolean deltaComputerProcessing = false;
private int eventCount = 0; private int eventCount = 0;
@ -1083,7 +1091,7 @@ public class SimpleReasoner extends StatementListener {
} }
} }
} else { } else {
log.warn("unexpected condition, invoked when batchMode1 and batchMode2 were both false"); log.warn("unexpected condition, invoked when batchMode1 and batchMode2 are both false");
deltaComputerProcessing = false; deltaComputerProcessing = false;
} }

7
webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasonerTBoxListener.java
View file

@ -13,12 +13,11 @@ import com.hp.hpl.jena.rdf.model.Statement;
import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase; import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase;
import edu.cornell.mannlib.vitro.webapp.utils.threads.VitroBackgroundThread; import edu.cornell.mannlib.vitro.webapp.utils.threads.VitroBackgroundThread;
/** /**
* Route notification of changes to TBox to the incremental ABox reasoner. * Route notification of changes to TBox to the incremental ABox reasoner.
* The incremental ABox reasoner handles only subclass, superclass * The incremental ABox reasoner handles only subClass and
* and equivalent class axioms. * equivalentClass class axioms. Reasoning dones as a result of TBox
* * changes is always done in a separate thread.
*/ */
public class SimpleReasonerTBoxListener extends StatementListener { public class SimpleReasonerTBoxListener extends StatementListener {