diff --git a/webapp/ontologies/system/vitro-0.7.owl b/webapp/ontologies/system/vitro-0.7.owl index 648c9bf28..33fff74e6 100644 --- a/webapp/ontologies/system/vitro-0.7.owl +++ b/webapp/ontologies/system/vitro-0.7.owl @@ -134,9 +134,6 @@ xmlns:vitro="&vitro;" - - - diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasoner.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasoner.java index b292703c0..88cc95b2a 100644 --- a/webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasoner.java +++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasoner.java @@ -100,8 +100,8 @@ public class SimpleReasoner extends StatementListener { try { if (stmt.getPredicate().equals(RDF.type)) { - addedABoxTypeAssertion(stmt, inferenceModel); - setMostSpecificTypes(stmt.getSubject(), inferenceModel); + addedABoxTypeAssertion(stmt, inferenceModel, new HashSet()); + setMostSpecificTypes(stmt.getSubject(), inferenceModel, new HashSet()); } /* uncomment this to enable subproperty/equivalent property inferencing. sjm222 5/13/2011 else { @@ -110,7 +110,7 @@ public class SimpleReasoner extends StatementListener { */ } catch (Exception e) { // 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 { if (stmt.getPredicate().equals(RDF.type)) { removedABoxTypeAssertion(stmt, inferenceModel); - setMostSpecificTypes(stmt.getSubject(), inferenceModel); + setMostSpecificTypes(stmt.getSubject(), inferenceModel, new HashSet()); } /* uncomment this to enable subproperty/equivalent property inferencing. sjm222 5/13/2011 else { @@ -134,7 +134,7 @@ public class SimpleReasoner extends StatementListener { */ } catch (Exception e) { // 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) { // 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) { // 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. * */ - public void addedABoxTypeAssertion(Statement stmt, Model inferenceModel) { - - //System.out.println("sjm: addedABoxTypeAssertion: " + stmtString(stmt)); + public void addedABoxTypeAssertion(Statement stmt, Model inferenceModel, HashSet unknownTypes) { + tboxModel.enterCriticalSection(Lock.READ); try { @@ -298,9 +297,9 @@ public class SimpleReasoner extends StatementListener { OntClass cls = null; if ( (stmt.getObject().asResource()).getURI() != null ) { + cls = tboxModel.getOntClass(stmt.getObject().asResource().getURI()); - - if (cls != null) { + if (cls != null) { List parents = (cls.listSuperClasses(false)).toList(); parents.addAll((cls.listEquivalentClasses()).toList()); @@ -327,8 +326,13 @@ public class SimpleReasoner extends StatementListener { } } } else { - 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 ( !(stmt.getObject().asResource().getNameSpace()).equals(OWL.NS)) { + 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 { log.warn("The object of this rdf:type assertion has a null URI: " + stmtString(stmt)); @@ -405,9 +409,7 @@ public class SimpleReasoner extends StatementListener { */ public void removedABoxTypeAssertion(Statement stmt, Model inferenceModel) { - - //System.out.println("sjm: removedABoxTypeAssertion: " + stmtString(stmt)); - + tboxModel.enterCriticalSection(Lock.READ); // convert this method to use generic resources - not get ontclass, not cls.listSuperClasses... @@ -454,7 +456,8 @@ public class SimpleReasoner extends StatementListener { } } } 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 { 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)) { inferenceModel.add(infStmt); - setMostSpecificTypes(infStmt.getSubject(), inferenceModel); + setMostSpecificTypes(infStmt.getSubject(), inferenceModel, new HashSet()); } } } finally { @@ -641,7 +644,7 @@ public class SimpleReasoner extends StatementListener { if (inferenceModel.contains(infStmt)) { inferenceModel.remove(infStmt); - setMostSpecificTypes(infStmt.getSubject(), inferenceModel); + setMostSpecificTypes(infStmt.getSubject(), inferenceModel, new HashSet()); } } } finally { @@ -744,13 +747,12 @@ public class SimpleReasoner extends StatementListener { * indicate them for the individual with the core:mostSpecificType * annotation. */ - public void setMostSpecificTypes(Resource individual, Model inferenceModel) { - - //System.out.println("sjm: setMostSpecificTypes called for individual " + individual.getURI()); + public void setMostSpecificTypes(Resource individual, Model inferenceModel, HashSet unknownTypes) { + inferenceModel.enterCriticalSection(Lock.WRITE); aboxModel.enterCriticalSection(Lock.READ); tboxModel.enterCriticalSection(Lock.READ); - + try { OntModel unionModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM); unionModel.addSubModel(aboxModel); @@ -780,8 +782,11 @@ public class SimpleReasoner extends StatementListener { if (ontClass == null) { 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: " + - (stmt.getObject().asResource()).getURI() + "\nstatement is: " + stmtString(stmt)); + 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 mostSpecificType computation will be done based on type assertions of this type."); + } } continue; } @@ -914,20 +919,29 @@ public class SimpleReasoner extends StatementListener { */ public synchronized void recomputeABox() { + HashSet unknownTypes = new HashSet(); + // recompute the inferences inferenceRebuildModel.enterCriticalSection(Lock.WRITE); aboxModel.enterCriticalSection(Lock.WRITE); tboxModel.enterCriticalSection(Lock.READ); try { + log.info("Computing class-based ABox inferences"); inferenceRebuildModel.removeAll(); StmtIterator iter = aboxModel.listStatements((Resource) null, RDF.type, (RDFNode) null); - log.info("Computing class-based ABox inferences"); + int numStmts = 0; + while (iter.hasNext()) { Statement stmt = iter.next(); - addedABoxTypeAssertion(stmt, inferenceRebuildModel); - setMostSpecificTypes(stmt.getSubject(), inferenceRebuildModel); + addedABoxTypeAssertion(stmt, inferenceRebuildModel, unknownTypes); + setMostSpecificTypes(stmt.getSubject(), inferenceRebuildModel, unknownTypes); + + numStmts++; + if ((numStmts % 8000) == 0) { + log.info("Still computing class-based ABox inferences..."); + } } /* @@ -984,14 +998,16 @@ public class SimpleReasoner extends StatementListener { inferenceRebuildModel.leaveCriticalSection(); } - + log.info("Finished computing class-based ABox inferences"); + // reflect the recomputed inferences into the application inference // model. inferenceRebuildModel.enterCriticalSection(Lock.WRITE); scratchpadModel.enterCriticalSection(Lock.WRITE); log.info("Updating ABox inference model"); // Remove everything from the current inference model that is not - // in the recomputed inference model + // in the recomputed inference model + int num = 0; try { inferenceModel.enterCriticalSection(Lock.READ); @@ -1002,8 +1018,13 @@ public class SimpleReasoner extends StatementListener { while (iter.hasNext()) { Statement stmt = iter.next(); 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) { 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)) { scratchpadModel.add(stmt); } + + num++; + if ((num % 8000) == 0) { + log.info("Still updating ABox inference model (adding new inferences)..."); + } } } catch (Exception 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() { + HashSet unknownTypes = new HashSet(); + // recompute the inferences inferenceRebuildModel.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); log.info("Computing mostSpecificType annotations"); + int numStmts = 0; + while (iter.hasNext()) { 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) { log.error("Exception while recomputing ABox inference model", e); @@ -1088,12 +1123,13 @@ public class SimpleReasoner extends StatementListener { inferenceRebuildModel.leaveCriticalSection(); } + log.info("Finished computing mostSpecificType annotations"); // reflect the recomputed inferences into the application inference // model. inferenceRebuildModel.enterCriticalSection(Lock.WRITE); scratchpadModel.enterCriticalSection(Lock.WRITE); - log.info("Updating ABox inference model"); + log.info("Updating ABox inference model with mostSpecificType annotations"); try { // Add everything from the recomputed inference model that is not already @@ -1103,12 +1139,19 @@ public class SimpleReasoner extends StatementListener { try { scratchpadModel.removeAll(); StmtIterator iter = inferenceRebuildModel.listStatements(); + + int numStmts = 0; while (iter.hasNext()) { Statement stmt = iter.next(); if (!inferenceModel.contains(stmt)) { scratchpadModel.add(stmt); } + + numStmts++; + if ((numStmts % 8000) == 0) { + log.info("Still updating ABox inference model with mostSpecificType annotations..."); + } } } catch (Exception 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(); } - log.info("ABox inference model updated"); + log.info("ABox inference model updated with mostSpecificType annotations"); } public static SimpleReasoner getSimpleReasonerFromServletContext(ServletContext ctx) { diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/SimpleReasonerSetup.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/SimpleReasonerSetup.java index e5b29c07d..eb7f5c5d8 100644 --- a/webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/SimpleReasonerSetup.java +++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/SimpleReasonerSetup.java @@ -42,7 +42,6 @@ public class SimpleReasonerSetup implements ServletContextListener { try { // set up Pellet reasoning for the TBox - OntModelSelector assertionsOms = ModelContext.getBaseOntModelSelector(sce.getServletContext()); OntModelSelector inferencesOms = ModelContext.getInferenceOntModelSelector(sce.getServletContext()); OntModelSelector unionOms = ModelContext.getUnionOntModelSelector(sce.getServletContext()); @@ -110,9 +109,9 @@ public class SimpleReasonerSetup implements ServletContextListener { sleeps++; } - simpleReasoner.recompute(); + new Thread(new ABoxRecomputer(simpleReasoner,false)).start(); } else if ( isMSTComputeRequired(sce.getServletContext()) ) { - log.info("most specific type computation required"); + log.info("mostSpecificType computation required"); int sleeps = 0; while (sleeps < 1000 && pelletListener.isReasoning()) { @@ -123,7 +122,7 @@ public class SimpleReasonerSetup implements ServletContextListener { sleeps++; } - simpleReasoner.recomputeMostSpecificType(); + new Thread(new ABoxRecomputer(simpleReasoner,true)).start(); } assertionsOms.getTBoxModel().register(new SimpleReasonerTBoxListener(simpleReasoner)); @@ -163,4 +162,23 @@ public class SimpleReasonerSetup implements ServletContextListener { private static boolean isMSTComputeRequired(ServletContext ctx) { 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(); + } + } + } }