fixed some bugs in windows server

4 files changed, 137 insertions, 80 deletions

diff --git a/test/uk/ac/ox/cs/jrdfox/Tester.java b/test/uk/ac/ox/cs/jrdfox/Tester.java
index 00476d6..94f5401 100644
--- a/test/uk/ac/ox/cs/jrdfox/Tester.java
+++ b/test/uk/ac/ox/cs/jrdfox/Tester.java
@@ -2,44 +2,137 @@ package uk.ac.ox.cs.jrdfox;
 
 import java.io.File;
 
+import org.semanticweb.owlapi.model.OWLOntology;
+
 import uk.ac.ox.cs.JRDFox.JRDFStoreException;
 import uk.ac.ox.cs.JRDFox.Prefixes;
 import uk.ac.ox.cs.JRDFox.store.DataStore;
+import uk.ac.ox.cs.JRDFox.store.DataStore.UpdateType;
 import uk.ac.ox.cs.JRDFox.store.Parameters;
+import uk.ac.ox.cs.JRDFox.store.TripleStatus;
 import uk.ac.ox.cs.JRDFox.store.TupleIterator;
+import uk.ac.ox.cs.JRDFox.store.DataStore.StoreType;
+import uk.ac.ox.cs.pagoda.owl.OWLHelper;
+import uk.ac.ox.cs.pagoda.reasoner.light.RDFoxQueryEngine;
+import uk.ac.ox.cs.pagoda.util.Namespace;
 import uk.ac.ox.cs.pagoda.util.Timer;
 
 public class Tester {
         
-        public static void main(String[] args) {
+        public static void main(String[] args) throws JRDFStoreException {
+                Tester tester = new Tester();
+                tester.testCrash();
+        }
+        
+        private void evaluate_againstIDs(String queryText) throws JRDFStoreException {
+                int number = 0; 
+                Timer t = new Timer(); 
+                TupleIterator iter = null; 
                 try {
-                        (new Tester()).test();;
-                } catch (JRDFStoreException e) {
-                        // TODO Auto-generated catch block
-                        e.printStackTrace();
+                        iter = store.compileQuery(queryText, prefixes, parameters, TripleStatus.TUPLE_STATUS_IDB.union(TripleStatus.TUPLE_STATUS_EDB), TripleStatus.TUPLE_STATUS_IDB);
+                        for (long multi = iter.open(); multi != 0; multi = iter.getNext()) 
+                                ++number; 
+                } finally {
+                        if (iter != null) iter.dispose();
                 }
+                System.out.println(number); 
+                System.out.println(t.duration());
+
         }
-        
+
         DataStore store; 
         Prefixes prefixes = new Prefixes(); 
         Parameters parameters; 
         
         public Tester() {
                 try {
-                        store = new DataStore(new File("lazy-upper-bound"));
+                        store = new DataStore(StoreType.NarrowParallelHead);
+                        store.setNumberOfThreads(RDFoxQueryEngine.matNoOfThreads);
+                        store.initialize();
+                        System.out.println("data store created.");
                 } catch (JRDFStoreException e) {
                         e.printStackTrace();
                 }
-                parameters = new Parameters(); 
+                parameters = new Parameters();
                 parameters.m_allAnswersInRoot = true; 
-                parameters.m_useBushy = true;
-                
+                parameters.m_useBushy = true; 
+        }
+        
+        public Tester(String path) {
+                try {
+                        store = new DataStore(new File(path));
+                } catch (JRDFStoreException e) {
+                        e.printStackTrace();
+                }
+                parameters = new Parameters(); 
+//              parameters.m_allAnswersInRoot = true; 
+//              parameters.m_useBushy = true;
+        }
+        
+        public void applyReasoning(boolean incremental) {
+                Timer t = new Timer(); 
+                try {
+                        store.applyReasoning(incremental);
+                } catch (JRDFStoreException e) {
+                        e.printStackTrace();
+                }  
+                System.out.println("reasoning done: " + t.duration()); 
         }
         
         public void dispose() {
                 store.dispose();
         }
         
+        public void testCrash() throws JRDFStoreException {
+//              DataStore lowerStore = new DataStore(StoreType.NarrowParallelHead);
+//              lowerStore.setNumberOfThreads(RDFoxQueryEngine.matNoOfThreads);
+//              lowerStore.initialize();
+//              System.out.println("lower data store created.");
+                OWLOntology ontology = OWLHelper.loadOntology("data/fly/fly_anatomy_XP_with_GJ_FC_individuals.owl");
+                System.out.println("ontology loaded ... " + ontology.getAxiomCount());
+                
+                store.importTurtleFile(new File("testcase/fly.ttl"));
+                System.out.println("data loaded. " + store.getTriplesCount());
+                
+                store.importRules(new File[] {new File("testcase/lower.dlog")});
+                System.out.println("rules loaded. " + store.getTriplesCount());
+                
+                store.applyReasoning();
+                System.out.println("materialised. " + store.getTriplesCount());
+                
+                store.clearRulesAndMakeFactsExplicit();
+                
+                store.importRules(new File[] {new File("testcase/multi.dlog")});
+                System.out.println("rules loaded. " + store.getTriplesCount());
+                
+                store.applyReasoning();
+                System.out.println("materialised. " + store.getTriplesCount());
+                
+                store.makeFactsExplicit();
+                
+                store.importTurtleFiles(new File[] {new File("testcase/first.ttl")}, UpdateType.ScheduleForAddition);
+                System.out.println("first data loaded. " + store.getTriplesCount());
+                
+                store.applyReasoning(true);
+                System.out.println("incremental reasoning done. " + store.getTriplesCount());
+                
+                store.clearRulesAndMakeFactsExplicit();
+                
+                store.importTurtleFiles(new File[] {new File("testcase/second.ttl")}, UpdateType.ScheduleForAddition);
+                store.importRules(new File[] {new File("testcase/tracking.dlog")}, UpdateType.ScheduleForAddition);
+                store.applyReasoning(true);
+                System.out.println("incremental reasoning done. " + store.getTriplesCount());
+                
+                evaluate_againstIDs("select distinct ?z where { ?x <" + Namespace.RDF_TYPE + "> ?z . }");
+                System.out.println("done."); 
+//              tester.applyReasoning(true);
+//              tester.evaluate_againstIDs("select distinct ?z where { ?x <" + Namespace.RDF_TYPE + "> ?z . }");
+//              System.out.println("done."); 
+                
+                store.dispose();
+//              lowerStore.dispose();
+        }
+        
         public void test() throws JRDFStoreException {
                 evaluate("PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> " 
                                 + "SELECT distinct ?x WHERE { "
@@ -82,18 +175,18 @@ public class Tester {
                                 + "?z benchmark:isHeadOf <http://www.Department0.University0.edu> . "
                                 + "?z benchmark:like ?y . "
                                 + "?y a <http://www.cs.ox.ac.uk/PAGOdA/auxiliary#Original> }"); 
-}
+        }
         
         public void evaluate(String query) throws JRDFStoreException {
-                TupleIterator iter = store.compileQuery(query, prefixes, parameters);
-                
                 int number = 0; 
                 Timer t = new Timer(); 
+                TupleIterator iter = null; 
                 try {
+                        iter = store.compileQuery(query, prefixes, parameters);
                         for (long multi = iter.open(); multi != 0; multi = iter.getNext()) 
                                 ++number; 
                 } finally {
-                        iter.dispose();
+                        if (iter != null) iter.dispose();
                 }
                 System.out.println(number); 
                 System.out.println(t.duration());
diff --git a/test/uk/ac/ox/cs/pagoda/junit/JAIR_Scalability.java b/test/uk/ac/ox/cs/pagoda/junit/JAIR_Scalability.java
index 5bd3134..5e2b1d7 100644
--- a/test/uk/ac/ox/cs/pagoda/junit/JAIR_Scalability.java
+++ b/test/uk/ac/ox/cs/pagoda/junit/JAIR_Scalability.java
@@ -3,6 +3,7 @@ package uk.ac.ox.cs.pagoda.junit;
 import org.junit.Test;
 
 import uk.ac.ox.cs.pagoda.tester.PagodaTester;
+import uk.ac.ox.cs.pagoda.util.Properties;
 
 public class JAIR_Scalability {
         
@@ -78,7 +79,7 @@ public class JAIR_Scalability {
         }
         
         public static void main(String... args) {
-                PagodaTester.ShellMode = true; 
+                Properties.ShellModeDefault = true; 
                 new JAIR_Scalability().testUniProt(50, false);
         }
 
diff --git a/test/uk/ac/ox/cs/pagoda/tester/ORETester.java b/test/uk/ac/ox/cs/pagoda/tester/ORETester.java
index 1092d6f..ae58ba9 100644
--- a/test/uk/ac/ox/cs/pagoda/tester/ORETester.java
+++ b/test/uk/ac/ox/cs/pagoda/tester/ORETester.java
@@ -1,9 +1,7 @@
 package uk.ac.ox.cs.pagoda.tester;
 
-import org.semanticweb.owlapi.model.OWLOntology;
-
-import uk.ac.ox.cs.pagoda.owl.OWLHelper;
 import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner;
+import uk.ac.ox.cs.pagoda.util.Properties;
 
 public class ORETester {
 
@@ -13,17 +11,11 @@ public class ORETester {
 //              args = new String[] { "/home/yzhou/krr-nas-share/Yujiao/ontologies/ORE2014/DL/wine_nodatatype.owl" };
                 
 //              args = new String[] { "/home/yzhou/krr-nas-share/Yujiao/ontologies/ORE2014/EL/b7700fe1-103b-4b32-a21c-f6604a763ba5_t-cell.owl" };
-                args = new String[] { "/home/yzhou/krr-nas-share/Yujiao/ontologies/ORE2014/EL/baa29363-f93c-4285-827e-0e2380c82efc_cations.n3" };
-                
+//              args = new String[] { "/home/yzhou/krr-nas-share/Yujiao/ontologies/ORE2014/EL/baa29363-f93c-4285-827e-0e2380c82efc_cations.n3" };
                 
-                OWLOntology ontology = OWLHelper.loadOntology(args[0]);
-                QueryReasoner pagoda = QueryReasoner.getInstance(ontology);
-                System.out.println(pagoda); 
-                pagoda.loadOntology(ontology);
-                if (pagoda.preprocess())
-                        System.out.println("The ontology is consistent!"); 
-                else 
-                        System.out.println("The ontology is inconsistent!"); 
+                Properties properties = new Properties("config/sys.conf"); 
+                QueryReasoner pagoda = QueryReasoner.getInstance(properties);
+                pagoda.dispose();
         }
         
 }
diff --git a/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java b/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java
index d754a70..48a2a51 100644
--- a/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java
+++ b/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java
@@ -5,13 +5,10 @@ import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.util.Scanner;
 
-import org.semanticweb.owlapi.model.OWLOntology;
-
-import uk.ac.ox.cs.pagoda.owl.OWLHelper;
 import uk.ac.ox.cs.pagoda.query.AnswerTuple;
 import uk.ac.ox.cs.pagoda.query.AnswerTuples;
 import uk.ac.ox.cs.pagoda.reasoner.*; 
-import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner.Type; 
+import uk.ac.ox.cs.pagoda.util.Properties;
 import uk.ac.ox.cs.pagoda.util.Timer;
 import uk.ac.ox.cs.pagoda.util.Utility;
 
@@ -93,8 +90,6 @@ public class PagodaTester {
         public static final String atlas_abox = onto_dir + "bio2rdf/atlas/graph sampling/sample_1.nt"; 
         public static final String atlas_queries = onto_dir + "bio2rdf/atlas/queries/atomic_one.sparql"; 
         
-        public static boolean ShellMode = false; 
-        
         public static void main(String... args) {
                 if (args.length == 0) {
 //                      args = new String[] {test_tbox, test_abox, test_query};
@@ -109,7 +104,7 @@ public class PagodaTester {
 //                      args = new String[] {"../SemFacet/WebContent/WEB-INF/data/dbpedia.owl", "../SemFacet/WebContent/WEB-INF/data/dbpediaA.nt", null}; 
 //                      args = new String[] {"../core/WebContent/WEB-INF/data/fly.owl", "../core/WebContent/WEB-INF/data/fly-data.nt", null}; 
 //                      args = new String[] {"data/lubm/univ-bench.owl", "data/lubm/lubm1.ttl", "data/lubm/lubm.sparql", "lubm.ans"}; 
-                        args = new String[] {"data/uobm/univ-bench-dl.owl", "data/uobm/uobm1.ttl", "data/uobm/uobm.sparql", "uobm.ans"}; 
+//                      args = new String[] {"data/uobm/univ-bench-dl.owl", "data/uobm/uobm1.ttl", "data/uobm/uobm.sparql", "uobm.ans"}; 
 //                      args = new String[] {"data/fly/fly_anatomy_XP_with_GJ_FC_individuals.owl", "data/fly/fly.sparql", "fly.ans"}; 
 //                      args = new String[] {bioModels_tbox, bioModels_abox, bioModels_queries}; 
 //                      args = new String[] {chembl_tbox, chembl_abox, chembl_queries};
@@ -124,66 +119,42 @@ public class PagodaTester {
 //                      args[2] = args[2].replace(".sparql", "_pellet.sparql");
                 }
 
-                int ontoIndex = 0, dataIndex = 1, queryIndex = 2;
-
-                if (args.length > dataIndex && args[dataIndex] != null && args[dataIndex].endsWith(".sparql")) {
-                        String[] inputArgs = args;
-                        args = new String[inputArgs.length + 1];
-                        for (int i = 0; i < dataIndex; ++i)
-                                args[i] = inputArgs[i];
-                        args[dataIndex] = null;
-                        args[queryIndex] = inputArgs[dataIndex];
-                        for (int i = dataIndex + 1; i < inputArgs.length; ++i)
-                                args[i + 1] = inputArgs[i]; 
-                }
-
-                StringBuilder info = new StringBuilder(); 
-                info.append("System started with \n");
-                for (int i = 0; i < args.length; ++i)
-                        info.append("Arg " + (i + 1) + ": " + args[i] + "\n"); 
-                Utility.logInfo(info);
-
-//              Utility.redirectCurrentOut("temp.out");
-
-                OWLOntology ontology = OWLHelper.loadOntology(args[ontoIndex]);
-                
-                QueryReasoner pagoda = QueryReasoner.getInstance(Type.Full, ontology, true, true); 
-//              QueryReasoner pagoda = QueryReasoner.getInstance(Type.ELHOU, ontology, true, true);
+                Properties properties = new Properties("config/uobm.conf"); 
                 
-//              QueryReasoner pagoda = QueryReasoner.getInstanceForSemFacet(ontology);
-//              QueryReasoner pagoda = QueryReasoner.getHermiTReasoner(false); 
+                int index = 0; 
+                if (args.length > index) properties.setOntologyPath(args[index++]);   
+                if (args.length > index && (args[index].endsWith(".ttl") || args[index].endsWith(".nt"))) properties.setDataPath(args[index++]);   
+                if (args.length > index && args[index].endsWith(".sparql")) properties.setQueryPath(args[index++]);   
+                if (args.length > index && !args[index].startsWith("-")) properties.setAnswerPath(args[index++]);   
+                if (args.length > index) properties.setToClassify(Boolean.parseBoolean(args[index++].substring(1)));   
+                if (args.length > index) properties.setToCallHermiT(Boolean.parseBoolean(args[index++].substring(1)));   
+        
+                QueryReasoner pagoda = null; 
                 
-//              PagodaTester tester = new PagodaTester(pagoda);
-                String ansFile = args.length > 3 ? args[3] : null; 
                 try {
                         Timer t = new Timer();
-                        pagoda.loadOntology(ontology);
-                        pagoda.importData(args[dataIndex]);
-                        if (!pagoda.preprocess())
-                                return;
+                        pagoda = QueryReasoner.getInstance(properties); 
+                        if (pagoda == null) return;
+                        
                         Utility.logInfo("Preprocessing Done in " + t.duration() + " seconds.");
-//                      tester.printPredicatesWithGap(); 
-//                      tester.testSemFacetQueries();
-//                      tester.testSomeFlyQueries();
-//                      tester.testISGQueries();
-//                      tester.testReactomeQueries(); 
-                        if (args[queryIndex] != null)
-                                for (String queryFile: args[queryIndex].split(";"))
-                                        pagoda.evaluate(pagoda.getQueryManager().collectQueryRecords(queryFile), ansFile);
-
-                        if (ShellMode)
+                        
+                        if (properties.getQueryPath() != null)
+                                for (String queryFile: properties.getQueryPath().split(";"))
+                                        pagoda.evaluate(pagoda.getQueryManager().collectQueryRecords(queryFile), properties.getAnswerPath());
+
+                        if (properties.getShellMode())
                                 try {
                                         evaluateConsoleQuery(pagoda);
                                 } catch (IOException e) {
                                         e.printStackTrace();
                                 } 
                 } finally {
-                        pagoda.dispose();
+                        if (pagoda != null) pagoda.dispose();
                 }
 
                 Utility.closeCurrentOut();
                 
-                if (ShellMode) System.exit(0);
+                if (properties.getShellMode()) System.exit(0);
         }
         
 //      private void printPredicatesWithGap() {