aboutsummaryrefslogtreecommitdiff
path: root/src
diff options
context:
space:
mode:
authorRncLsn <rnc.lsn@gmail.com>2015-06-02 15:40:29 +0100
committerRncLsn <rnc.lsn@gmail.com>2015-06-02 15:40:29 +0100
commit691964863246bbf6ef9f72cc5e82c83df34f135a (patch)
tree98c9834f788ff320cabcfb29733890c5b40e024f /src
parent4b7253559c290b6fdd1c4122830f153fda85dd62 (diff)
downloadACQuA-691964863246bbf6ef9f72cc5e82c83df34f135a.tar.gz
ACQuA-691964863246bbf6ef9f72cc5e82c83df34f135a.zip
Working query-dependent semi-skolemised upper bound (tested on UOBM1 and LUBM1).
Diffstat (limited to 'src')
-rw-r--r--src/org/semanticweb/simpleETL/SimpleETL.java2
-rw-r--r--src/uk/ac/ox/cs/pagoda/multistage/MultiStageQueryEngine.java8
-rw-r--r--src/uk/ac/ox/cs/pagoda/multistage/StageQueryEngine.java2
-rw-r--r--src/uk/ac/ox/cs/pagoda/query/AnswerTuple.java30
-rw-r--r--src/uk/ac/ox/cs/pagoda/query/QueryRecord.java141
-rw-r--r--src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager.java2
-rw-r--r--src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java132
-rw-r--r--src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxQueryEngine.java2
-rw-r--r--src/uk/ac/ox/cs/pagoda/rules/Program.java2
-rw-r--r--src/uk/ac/ox/cs/pagoda/tracking/QueryTracker.java165
-rw-r--r--src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoder.java2
11 files changed, 255 insertions, 233 deletions
diff --git a/src/org/semanticweb/simpleETL/SimpleETL.java b/src/org/semanticweb/simpleETL/SimpleETL.java
index 5907b7b..cc91e1f 100644
--- a/src/org/semanticweb/simpleETL/SimpleETL.java
+++ b/src/org/semanticweb/simpleETL/SimpleETL.java
@@ -67,7 +67,7 @@ public class SimpleETL {
67 finally { 67 finally {
68 fos.close(); 68 fos.close();
69 } 69 }
70 Utility.logInfo("SimpleETL rewriting DONE: additional ontology data is saved in " + m_fileToExport + "."); 70 Utility.logDebug("SimpleETL rewriting DONE: additional ontology data is saved in " + m_fileToExport + ".");
71 } 71 }
72 72
73 public String getExportedFile() { 73 public String getExportedFile() {
diff --git a/src/uk/ac/ox/cs/pagoda/multistage/MultiStageQueryEngine.java b/src/uk/ac/ox/cs/pagoda/multistage/MultiStageQueryEngine.java
index b708bee..e1be6d2 100644
--- a/src/uk/ac/ox/cs/pagoda/multistage/MultiStageQueryEngine.java
+++ b/src/uk/ac/ox/cs/pagoda/multistage/MultiStageQueryEngine.java
@@ -82,7 +82,6 @@ public class MultiStageQueryEngine extends StageQueryEngine {
82 if(gap != null) 82 if(gap != null)
83 treatment.addAdditionalGapTuples(); 83 treatment.addAdditionalGapTuples();
84 String programName = "multi-stage upper program"; 84 String programName = "multi-stage upper program";
85 Utility.logInfo(name + " store is materialising " + programName + " ...");
86 Timer t = new Timer(); 85 Timer t = new Timer();
87 86
88 String datalogProgram = program.getDatalogRuleText(); 87 String datalogProgram = program.getDatalogRuleText();
@@ -101,7 +100,8 @@ public class MultiStageQueryEngine extends StageQueryEngine {
101 long oldTripleCount = store.getTriplesCount(); 100 long oldTripleCount = store.getTriplesCount();
102 101
103 subTimer.reset(); 102 subTimer.reset();
104 Utility.logInfo("Iteration " + ++iteration + ": "); 103 Utility.logInfo(name + " store is materialising " +
104 programName + "... (iteration " + ++iteration + ")");
105 105
106 incrementally = (iteration != 1); 106 incrementally = (iteration != 1);
107 107
@@ -143,8 +143,8 @@ public class MultiStageQueryEngine extends StageQueryEngine {
143 subTimer.reset(); 143 subTimer.reset();
144 if((violations = program.isIntegrated(this, incrementally)) == null || violations.size() == 0) { 144 if((violations = program.isIntegrated(this, incrementally)) == null || violations.size() == 0) {
145 store.clearRulesAndMakeFactsExplicit(); 145 store.clearRulesAndMakeFactsExplicit();
146 Utility.logInfo(name + " store after materialising " + programName + ": " + tripleCount + " (" + (tripleCount - tripleCountBeforeMat) + " new)"); 146 Utility.logDebug(name + " store after materialising " + programName + ": " + tripleCount + " (" + (tripleCount - tripleCountBeforeMat) + " new)");
147 Utility.logInfo(name + " store is DONE for multi-stage materialising in " + t.duration() + " seconds."); 147 Utility.logDebug(name + " store is DONE for multi-stage materialising in " + t.duration() + " seconds.");
148 return isValid() ? 1 : 0; 148 return isValid() ? 1 : 0;
149 } 149 }
150 Utility.logDebug("Time to detect violations: " + subTimer.duration()); 150 Utility.logDebug("Time to detect violations: " + subTimer.duration());
diff --git a/src/uk/ac/ox/cs/pagoda/multistage/StageQueryEngine.java b/src/uk/ac/ox/cs/pagoda/multistage/StageQueryEngine.java
index c8776fe..ffca55a 100644
--- a/src/uk/ac/ox/cs/pagoda/multistage/StageQueryEngine.java
+++ b/src/uk/ac/ox/cs/pagoda/multistage/StageQueryEngine.java
@@ -40,7 +40,7 @@ public abstract class StageQueryEngine extends BasicQueryEngine {
40 } 40 }
41 41
42 if (validMaterialisation) 42 if (validMaterialisation)
43 Utility.logInfo("The " + name + " store is valid."); 43 Utility.logDebug("The " + name + " store is valid.");
44 else 44 else
45 Utility.logInfo("The " + name + " store is not valid."); 45 Utility.logInfo("The " + name + " store is not valid.");
46 return validMaterialisation; 46 return validMaterialisation;
diff --git a/src/uk/ac/ox/cs/pagoda/query/AnswerTuple.java b/src/uk/ac/ox/cs/pagoda/query/AnswerTuple.java
index 78aced1..9a9d0de 100644
--- a/src/uk/ac/ox/cs/pagoda/query/AnswerTuple.java
+++ b/src/uk/ac/ox/cs/pagoda/query/AnswerTuple.java
@@ -16,14 +16,10 @@ import java.lang.reflect.Type;
16import java.util.HashMap; 16import java.util.HashMap;
17import java.util.Map; 17import java.util.Map;
18import java.util.StringTokenizer; 18import java.util.StringTokenizer;
19import java.util.regex.Matcher;
20import java.util.regex.Pattern;
21 19
22public class AnswerTuple { 20public class AnswerTuple {
23 21
24 public static final String SEPARATOR = "\t"; 22 public static final String SEPARATOR = "\t";
25 static final Pattern owlLiteralRegex =
26 Pattern.compile("^\"(?<lexicalForm>[^@]+(@(?<langTag>.+))?)\"(^^<(?<dataType>.+)>)?$");
27 String m_str = null; 23 String m_str = null;
28 GroundTerm[] m_tuple; 24 GroundTerm[] m_tuple;
29 25
@@ -158,32 +154,36 @@ public class AnswerTuple {
158 String tuplesString = json.getAsJsonPrimitive().getAsString(); 154 String tuplesString = json.getAsJsonPrimitive().getAsString();
159// StringTokenizer tokenizer = new StringTokenizer(tuplesString, SEPARATOR); 155// StringTokenizer tokenizer = new StringTokenizer(tuplesString, SEPARATOR);
160 StringTokenizer tokenizer = new StringTokenizer(tuplesString); 156 StringTokenizer tokenizer = new StringTokenizer(tuplesString);
161 GroundTerm[] terms = new GroundTerm[tokenizer.countTokens()]; 157 int tokensCount = tokenizer.countTokens();
158 GroundTerm[] terms = new GroundTerm[tokensCount];
162 159
163 // TODO test parsing 160 // TODO test parsing
164 for (int i = 0; i < tokenizer.countTokens(); i++) { 161 for(int i = 0; i < tokensCount; i++) {
165 String token = tokenizer.nextToken(); 162 String token = tokenizer.nextToken();
166 if (token.charAt(0) == '<') { 163 if (token.charAt(0) == '<') {
167 terms[i] = uk.ac.ox.cs.JRDFox.model.Individual.create(token.substring(1,token.length()-1)); 164 terms[i] = uk.ac.ox.cs.JRDFox.model.Individual.create(token.substring(1,token.length()-1));
168 } 165 }
169 else if (token.charAt(0) == '"') { 166 else if (token.charAt(0) == '"') {
170 Matcher matcher = owlLiteralRegex.matcher(token); 167 Datatype datatype;
171 if(matcher.matches()) { 168 String lexicalForm;
172 String lexicalForm = matcher.group("lexicalForm"); 169 if(token.contains("^^")) {
173 String dataTypeIRI = matcher.group("dataType"); 170 String[] lexicalFormAndType = token.split("^^");
174 Datatype dataType; 171 lexicalForm = lexicalFormAndType[0];
175 if(dataTypeIRI == null || dataTypeIRI.isEmpty()) dataType = Datatype.RDF_PLAIN_LITERAL; 172 datatype = Datatype.value(lexicalFormAndType[1]);
176 else dataType = uk.ac.ox.cs.JRDFox.model.Datatype.value(dataTypeIRI);
177 terms[i] = uk.ac.ox.cs.JRDFox.model.Literal.create(lexicalForm, dataType);
178 } 173 }
179 else { 174 else {
180 throw new IllegalArgumentException("The given json does not represent a valid AnswerTuple"); 175 lexicalForm = token.substring(1, token.length() - 1);
176 // TODO check
177// datatype = token.contains("@") ? Datatype.RDF_PLAIN_LITERAL : Datatype.XSD_STRING;
178 datatype = Datatype.XSD_STRING;
181 } 179 }
180 terms[i] = uk.ac.ox.cs.JRDFox.model.Literal.create(lexicalForm, datatype);
182 } 181 }
183 else { 182 else {
184 terms[i] = uk.ac.ox.cs.JRDFox.model.BlankNode.create(token); 183 terms[i] = uk.ac.ox.cs.JRDFox.model.BlankNode.create(token);
185 } 184 }
186 } 185 }
186
187 return new AnswerTuple(terms); 187 return new AnswerTuple(terms);
188 } 188 }
189 } 189 }
diff --git a/src/uk/ac/ox/cs/pagoda/query/QueryRecord.java b/src/uk/ac/ox/cs/pagoda/query/QueryRecord.java
index 742b7da..516a461 100644
--- a/src/uk/ac/ox/cs/pagoda/query/QueryRecord.java
+++ b/src/uk/ac/ox/cs/pagoda/query/QueryRecord.java
@@ -135,74 +135,16 @@ public class QueryRecord extends Disposable {
135 return updateUpperBoundAnswers(answerTuples, false); 135 return updateUpperBoundAnswers(answerTuples, false);
136 } 136 }
137 137
138 public boolean updateUpperBoundAnswers(AnswerTuples answerTuples, boolean toCheckAux) { 138 public boolean checkUpperBoundAnswers(AnswerTuples answerTuples) {
139 if(isDisposed()) throw new DisposedException(); 139 if(isDisposed()) throw new DisposedException();
140 140
141 if(!(answerTuples instanceof RDFoxAnswerTuples)) { 141 return updateUpperBoundAnswers(answerTuples, true, false);
142 String msg = "The upper bound must be computed by RDFox!"; 142 }
143 Utility.logError(msg);
144 throw new IllegalArgumentException(msg);
145 }
146
147 RDFoxAnswerTuples rdfoxAnswerTuples = (RDFoxAnswerTuples) answerTuples;
148
149 Set<AnswerTuple> candidateGapAnswerTuples = new HashSet<AnswerTuple>();
150 AnswerTuple tuple;
151 for(; rdfoxAnswerTuples.isValid(); rdfoxAnswerTuples.moveNext()) {
152 tuple = rdfoxAnswerTuples.getTuple();
153 if(isBottom() || !tuple.hasAnonymousIndividual())
154 if((!toCheckAux || !tuple.hasAuxPredicate()) && !soundAnswerTuples.contains(tuple))
155 candidateGapAnswerTuples.add(tuple);
156 }
157
158 /*** START: debugging ***/
159 if(PagodaProperties.isDebuggingMode()) {
160 if(rdfoxAnswerTuples.getArity() != getAnswerVariables().length)
161 throw new IllegalArgumentException(
162 "The arity of answers (" + rdfoxAnswerTuples.getArity() + ") " +
163 "is different from the number of answer variables (" +
164 getAnswerVariables().length + ")");
165
166 Set<AnswerTuple> namedAnswerTuples = new HashSet<>();
167 rdfoxAnswerTuples.reset();
168 for(; rdfoxAnswerTuples.isValid(); rdfoxAnswerTuples.moveNext()) {
169 tuple = rdfoxAnswerTuples.getTuple();
170// if(isBottom() || !tuple.hasAnonymousIndividual()) {
171 namedAnswerTuples.add(tuple);
172// }
173 }
174 HashSet<AnswerTuple> difference = new HashSet<>(soundAnswerTuples);
175 difference.removeAll(namedAnswerTuples);
176 if(!difference.isEmpty())
177 throw new IllegalArgumentException("The upper bound does not contain the lower bound! Missing answers: " + difference
178 .size());
179 }
180 /*** END: debugging ***/
181
182 boolean update;
183 if(gapAnswerTuples == null) {
184 gapAnswerTuples = candidateGapAnswerTuples;
185 update = true;
186 }
187 else {
188 update = gapAnswerTuples.retainAll(candidateGapAnswerTuples);
189 }
190
191 if(update)
192 Utility.logInfo("Upper bound answers updated: " + getNumberOfAnswers());
193 else
194 Utility.logInfo("Upper bound answers unchanged");
195 143
196 return update; 144 public boolean updateUpperBoundAnswers(AnswerTuples answerTuples, boolean toCheckAux) {
145 if(isDisposed()) throw new DisposedException();
197 146
198// boolean update = false; 147 return updateUpperBoundAnswers(answerTuples, toCheckAux, true);
199// for(Iterator<AnswerTuple> iter = gapAnswerTuples.iterator(); iter.hasNext(); ) {
200// tuple = iter.next();
201// if(!candidateGapAnswerTuples.contains(tuple)) {
202// iter.remove();
203// update = true;
204// }
205// }
206 } 148 }
207 149
208 public int getNumberOfAnswers() { 150 public int getNumberOfAnswers() {
@@ -713,6 +655,77 @@ public class QueryRecord extends Disposable {
713 return Objects.hash(queryText, soundAnswerTuples); 655 return Objects.hash(queryText, soundAnswerTuples);
714 } 656 }
715 657
658 private boolean updateUpperBoundAnswers(AnswerTuples answerTuples, boolean toCheckAux, boolean _check_containment) {
659 if(!(answerTuples instanceof RDFoxAnswerTuples)) {
660 String msg = "The upper bound must be computed by RDFox!";
661 Utility.logError(msg);
662 throw new IllegalArgumentException(msg);
663 }
664
665 RDFoxAnswerTuples rdfoxAnswerTuples = (RDFoxAnswerTuples) answerTuples;
666
667 Set<AnswerTuple> candidateGapAnswerTuples = new HashSet<AnswerTuple>();
668 AnswerTuple tuple;
669 for(; rdfoxAnswerTuples.isValid(); rdfoxAnswerTuples.moveNext()) {
670 tuple = rdfoxAnswerTuples.getTuple();
671 if(isBottom() || !tuple.hasAnonymousIndividual())
672 if((!toCheckAux || !tuple.hasAuxPredicate()) && !soundAnswerTuples.contains(tuple))
673 candidateGapAnswerTuples.add(tuple);
674 }
675
676 /*** START: debugging ***/
677 if(PagodaProperties.isDebuggingMode() && _check_containment) {
678 if(rdfoxAnswerTuples.getArity() != getAnswerVariables().length)
679 throw new IllegalArgumentException(
680 "The arity of answers (" + rdfoxAnswerTuples.getArity() + ") " +
681 "is different from the number of answer variables (" +
682 getAnswerVariables().length + ")");
683
684 Set<AnswerTuple> namedAnswerTuples = new HashSet<>();
685 rdfoxAnswerTuples.reset();
686 int numberOfAnswers = 0;
687 for(; rdfoxAnswerTuples.isValid(); rdfoxAnswerTuples.moveNext()) {
688 tuple = rdfoxAnswerTuples.getTuple();
689// if(isBottom() || !tuple.hasAnonymousIndividual()) {
690 namedAnswerTuples.add(tuple);
691// }
692 numberOfAnswers++;
693 }
694 Utility.logDebug("The number of answers returned by an upper bound: " + numberOfAnswers);
695 HashSet<AnswerTuple> difference = new HashSet<>(soundAnswerTuples);
696 difference.removeAll(namedAnswerTuples);
697 if(!difference.isEmpty())
698 throw new IllegalArgumentException("The upper bound does not contain the lower bound! Missing answers: " + difference
699 .size());
700 }
701 /*** END: debugging ***/
702
703 boolean update;
704 if(gapAnswerTuples == null) {
705 gapAnswerTuples = candidateGapAnswerTuples;
706 update = true;
707 }
708 else {
709 update = gapAnswerTuples.retainAll(candidateGapAnswerTuples);
710 }
711
712 if(update)
713 Utility.logInfo("Upper bound answers updated: " + getNumberOfAnswers());
714 else
715 Utility.logInfo("Upper bound answers unchanged");
716
717 return update;
718
719// boolean update = false;
720// for(Iterator<AnswerTuple> iter = gapAnswerTuples.iterator(); iter.hasNext(); ) {
721// tuple = iter.next();
722// if(!candidateGapAnswerTuples.contains(tuple)) {
723// iter.remove();
724// update = true;
725// }
726// }
727 }
728
716 public enum Step { 729 public enum Step {
717 LOWER_BOUND, 730 LOWER_BOUND,
718 UPPER_BOUND, 731 UPPER_BOUND,
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager.java b/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager.java
index b4a1775..453b5ca 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager.java
@@ -128,7 +128,7 @@ public class ConsistencyManager extends Disposable {
128 store.applyReasoning(true); 128 store.applyReasoning(true);
129 tripleCount = store.getTriplesCount(); 129 tripleCount = store.getTriplesCount();
130 130
131 Utility.logInfo("tracking store after materialising tracking program: " + tripleCount + " (" + (tripleCount - oldTripleCount) + " new)", 131 Utility.logDebug("tracking store after materialising tracking program: " + tripleCount + " (" + (tripleCount - oldTripleCount) + " new)",
132 "tracking store finished the materialisation of tracking program in " + t1.duration() + " seconds."); 132 "tracking store finished the materialisation of tracking program in " + t1.duration() + " seconds.");
133 133
134 extractAxioms(); 134 extractAxioms();
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
index 8445713..acdb8a3 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
@@ -31,42 +31,29 @@ class MyQueryReasoner extends QueryReasoner {
31 OWLOntology ontology; 31 OWLOntology ontology;
32 DatalogProgram program; 32 DatalogProgram program;
33 33
34 // String additonalDataFile;
35 BasicQueryEngine rlLowerStore = null; 34 BasicQueryEngine rlLowerStore = null;
36 BasicQueryEngine lazyUpperStore = null; 35 BasicQueryEngine lazyUpperStore = null;
37 MultiStageQueryEngine limitedSkolemUpperStore; 36 // MultiStageQueryEngine limitedSkolemUpperStore;
38 OWLOntology elho_ontology; 37 OWLOntology elho_ontology;
39 // boolean[] namedIndividuals_lazyUpper;
40 KarmaQueryEngine elLowerStore = null; 38 KarmaQueryEngine elLowerStore = null;
41 BasicQueryEngine trackingStore = null; 39 BasicQueryEngine trackingStore = null;
42 // boolean[] namedIndividuals_tracking;
43 TrackingRuleEncoder encoder; 40 TrackingRuleEncoder encoder;
44 private boolean equalityTag; 41 private boolean equalityTag;
45 private boolean multiStageTag;
46 private Timer t = new Timer(); 42 private Timer t = new Timer();
47 private Collection<String> predicatesWithGap = null; 43 private Collection<String> predicatesWithGap = null;
48 private SatisfiabilityStatus satisfiable; 44 private SatisfiabilityStatus satisfiable;
49 private ConsistencyManager consistency = new ConsistencyManager(this); 45 private ConsistencyManager consistency = new ConsistencyManager(this);
50 private boolean useUpperStores = false;
51 46
52 public MyQueryReasoner() { 47 public MyQueryReasoner() {
53 setup(true, true); 48 setup(true);
54 } 49 }
55 50
56 public MyQueryReasoner(boolean multiStageTag, boolean considerEqualities) { 51 public MyQueryReasoner(boolean multiStageTag, boolean considerEqualities) {
57 setup(multiStageTag, considerEqualities); 52 if(!multiStageTag)
58 } 53 throw new IllegalArgumentException(
54 "Value \"true\" for parameter \"multiStageTag\" is no longer supported");
59 55
60 public void setup(boolean multiStageTag, boolean considerEqualities) { 56 setup(considerEqualities);
61 if(isDisposed()) throw new DisposedException();
62 satisfiable = SatisfiabilityStatus.UNCHECKED;
63 this.multiStageTag = multiStageTag;
64 this.equalityTag = considerEqualities;
65
66 rlLowerStore = new BasicQueryEngine("rl-lower-bound");
67 elLowerStore = new KarmaQueryEngine("elho-lower-bound");
68
69 trackingStore = getUpperStore("tracking", false);
70 } 57 }
71 58
72 @Override 59 @Override
@@ -84,11 +71,8 @@ class MyQueryReasoner extends QueryReasoner {
84// program.getUpper().save(); 71// program.getUpper().save();
85// program.getGeneral().save(); 72// program.getGeneral().save();
86 73
87 useUpperStores = multiStageTag && !program.getGeneral().isHorn(); 74 if(!program.getGeneral().isHorn())
88 if(useUpperStores) { 75 lazyUpperStore = new MultiStageQueryEngine("lazy-upper-bound", true);
89 lazyUpperStore = getUpperStore("lazy-upper-bound", true);
90 limitedSkolemUpperStore = new MultiStageQueryEngine("limited-skolem-upper-bound", true);
91 }
92 76
93 importData(program.getAdditionalDataFile()); 77 importData(program.getAdditionalDataFile());
94 78
@@ -104,15 +88,16 @@ class MyQueryReasoner extends QueryReasoner {
104 @Override 88 @Override
105 public boolean preprocess() { 89 public boolean preprocess() {
106 if(isDisposed()) throw new DisposedException(); 90 if(isDisposed()) throw new DisposedException();
91
107 t.reset(); 92 t.reset();
108 Utility.logInfo("Preprocessing... checking satisfiability... "); 93 Utility.logInfo("Preprocessing (and checking satisfiability)...");
109 94
110 String name = "data", datafile = importedData.toString(); 95 String name = "data", datafile = importedData.toString();
111 rlLowerStore.importRDFData(name, datafile); 96 rlLowerStore.importRDFData(name, datafile);
112 rlLowerStore.materialise("lower program", program.getLower().toString()); 97 rlLowerStore.materialise("lower program", program.getLower().toString());
113// program.getLower().save(); 98// program.getLower().save();
114 if(!consistency.checkRLLowerBound()) return false; 99 if(!consistency.checkRLLowerBound()) return false;
115 Utility.logInfo("The number of sameAs assertions in RL lower store: " + rlLowerStore.getSameAsNumber()); 100 Utility.logDebug("The number of sameAs assertions in RL lower store: " + rlLowerStore.getSameAsNumber());
116 101
117 String originalMarkProgram = OWLHelper.getOriginalMarkProgram(ontology); 102 String originalMarkProgram = OWLHelper.getOriginalMarkProgram(ontology);
118 103
@@ -134,22 +119,7 @@ class MyQueryReasoner extends QueryReasoner {
134 } 119 }
135 if(consistency.checkUpper(lazyUpperStore)) { 120 if(consistency.checkUpper(lazyUpperStore)) {
136 satisfiable = SatisfiabilityStatus.SATISFIABLE; 121 satisfiable = SatisfiabilityStatus.SATISFIABLE;
137 Utility.logInfo("time for satisfiability checking: " + t.duration()); 122 Utility.logDebug("time for satisfiability checking: " + t.duration());
138 }
139
140 if(limitedSkolemUpperStore != null) {
141 limitedSkolemUpperStore.importRDFData(name, datafile);
142 limitedSkolemUpperStore.materialise("saturate named individuals", originalMarkProgram);
143 int tag = limitedSkolemUpperStore.materialiseSkolemly(program, null);
144 if(tag != 1) {
145 limitedSkolemUpperStore.dispose();
146 limitedSkolemUpperStore = null;
147 }
148 if(tag == -1) return false;
149 }
150 if(satisfiable == SatisfiabilityStatus.UNCHECKED && consistency.checkUpper(limitedSkolemUpperStore)) {
151 satisfiable = SatisfiabilityStatus.SATISFIABLE;
152 Utility.logInfo("time for satisfiability checking: " + t.duration());
153 } 123 }
154 124
155 trackingStore.importRDFData(name, datafile); 125 trackingStore.importRDFData(name, datafile);
@@ -194,14 +164,11 @@ class MyQueryReasoner extends QueryReasoner {
194 @Override 164 @Override
195 public void evaluate(QueryRecord queryRecord) { 165 public void evaluate(QueryRecord queryRecord) {
196 if(isDisposed()) throw new DisposedException(); 166 if(isDisposed()) throw new DisposedException();
197 if(queryBounds(queryRecord)) 167
168 if(queryLowerAndUpperBounds(queryRecord))
198 return; 169 return;
199 170
200 OWLOntology relevantOntologySubset = extractRelevantOntologySubset(queryRecord); 171 OWLOntology relevantOntologySubset = extractRelevantOntologySubset(queryRecord);
201
202 int aBoxCount = relevantOntologySubset.getABoxAxioms(true).size();
203 Utility.logInfo("Relevant ontology subset: ABox_axioms=" + aBoxCount + " TBox_axioms=" + (relevantOntologySubset
204 .getAxiomCount() - aBoxCount));
205// queryRecord.saveRelevantOntology("fragment_query" + queryRecord.getQueryID() + ".owl"); 172// queryRecord.saveRelevantOntology("fragment_query" + queryRecord.getQueryID() + ".owl");
206 173
207 if(querySkolemisedRelevantSubset(relevantOntologySubset, queryRecord)) 174 if(querySkolemisedRelevantSubset(relevantOntologySubset, queryRecord))
@@ -240,16 +207,18 @@ class MyQueryReasoner extends QueryReasoner {
240 if(lazyUpperStore != null) lazyUpperStore.dispose(); 207 if(lazyUpperStore != null) lazyUpperStore.dispose();
241 if(elLowerStore != null) elLowerStore.dispose(); 208 if(elLowerStore != null) elLowerStore.dispose();
242 if(trackingStore != null) trackingStore.dispose(); 209 if(trackingStore != null) trackingStore.dispose();
243 if(limitedSkolemUpperStore != null) limitedSkolemUpperStore.dispose(); 210// if(limitedSkolemUpperStore != null) limitedSkolemUpperStore.dispose();
244
245 } 211 }
246 212
247 private BasicQueryEngine getUpperStore(String name, boolean checkValidity) { 213 private void setup(boolean considerEqualities) {
248 if(multiStageTag) 214 if(isDisposed()) throw new DisposedException();
249 return new MultiStageQueryEngine(name, checkValidity); 215 satisfiable = SatisfiabilityStatus.UNCHECKED;
250// return new TwoStageQueryEngine(name, checkValidity); 216 this.equalityTag = considerEqualities;
251 else 217
252 return new BasicQueryEngine(name); 218 rlLowerStore = new BasicQueryEngine("rl-lower-bound");
219 elLowerStore = new KarmaQueryEngine("elho-lower-bound");
220
221 trackingStore = new MultiStageQueryEngine("tracking", false);
253 } 222 }
254 223
255 protected void internal_importDataFile(String name, String datafile) { 224 protected void internal_importDataFile(String name, String datafile) {
@@ -284,10 +253,37 @@ class MyQueryReasoner extends QueryReasoner {
284 return false; 253 return false;
285 } 254 }
286 255
256 private boolean checkGapAnswers(BasicQueryEngine relevantStore, QueryRecord queryRecord) {
257 Tuple<String> extendedQueries = queryRecord.getExtendedQueryText();
258 if(queryRecord.hasNonAnsDistinguishedVariables())
259 checkGapAnswers(relevantStore, queryRecord, extendedQueries.get(0), queryRecord.getAnswerVariables());
260 else
261 checkGapAnswers(relevantStore, queryRecord, queryRecord.getQueryText(), queryRecord.getAnswerVariables());
262
263 queryRecord.addProcessingTime(Step.L_SKOLEM_UPPER_BOUND, t.duration());
264 if(queryRecord.isProcessed()) {
265 queryRecord.setDifficulty(Step.L_SKOLEM_UPPER_BOUND);
266 return true;
267 }
268 return false;
269 }
270
271 private void checkGapAnswers(BasicQueryEngine relevantStore, QueryRecord queryRecord, String queryText, String[] answerVariables) {
272 AnswerTuples rlAnswer = null;
273 try {
274 Utility.logDebug(queryText);
275 rlAnswer = relevantStore.evaluate(queryText, answerVariables);
276 Utility.logDebug(t.duration());
277 queryRecord.checkUpperBoundAnswers(rlAnswer);
278 } finally {
279 if(rlAnswer != null) rlAnswer.dispose();
280 }
281 }
282
287 /** 283 /**
288 * Returns the part of the ontology relevant for Hermit, while computing the bound answers. 284 * Returns the part of the ontology relevant for Hermit, while computing the bound answers.
289 */ 285 */
290 private boolean queryBounds(QueryRecord queryRecord) { 286 private boolean queryLowerAndUpperBounds(QueryRecord queryRecord) {
291 AnswerTuples rlAnswer = null, elAnswer = null; 287 AnswerTuples rlAnswer = null, elAnswer = null;
292 288
293 t.reset(); 289 t.reset();
@@ -312,9 +308,6 @@ class MyQueryReasoner extends QueryReasoner {
312 Utility.logDebug("Lazy store"); 308 Utility.logDebug("Lazy store");
313 if(lazyUpperStore != null && queryUpperStore(lazyUpperStore, queryRecord, extendedQueryTexts, Step.LAZY_UPPER_BOUND)) 309 if(lazyUpperStore != null && queryUpperStore(lazyUpperStore, queryRecord, extendedQueryTexts, Step.LAZY_UPPER_BOUND))
314 return true; 310 return true;
315// Utility.logDebug("Skolem store");
316// if(limitedSkolemUpperStore != null && queryUpperStore(limitedSkolemUpperStore, queryRecord, extendedQueryTexts, Step.L_SKOLEM_UPPER_BOUND))
317// return null;
318 } 311 }
319 312
320 t.reset(); 313 t.reset();
@@ -338,6 +331,8 @@ class MyQueryReasoner extends QueryReasoner {
338 } 331 }
339 332
340 private OWLOntology extractRelevantOntologySubset(QueryRecord queryRecord) { 333 private OWLOntology extractRelevantOntologySubset(QueryRecord queryRecord) {
334 Utility.logInfo("Extracting relevant ontology-subset...");
335
341 t.reset(); 336 t.reset();
342 337
343 QueryTracker tracker = new QueryTracker(encoder, rlLowerStore, queryRecord); 338 QueryTracker tracker = new QueryTracker(encoder, rlLowerStore, queryRecord);
@@ -345,6 +340,14 @@ class MyQueryReasoner extends QueryReasoner {
345 340
346 queryRecord.addProcessingTime(Step.FRAGMENT, t.duration()); 341 queryRecord.addProcessingTime(Step.FRAGMENT, t.duration());
347 342
343 // just statistics
344 int numOfABoxAxioms = relevantOntologySubset.getABoxAxioms(true).size();
345 int numOfTBoxAxioms = relevantOntologySubset.getAxiomCount() - numOfABoxAxioms;
346 int originalNumOfABoxAxioms = ontology.getABoxAxioms(true).size();
347 int originalNumOfTBoxAxioms = ontology.getAxiomCount() - originalNumOfABoxAxioms;
348 Utility.logInfo("Relevant ontology-subset has been extracted: |ABox|="
349 + numOfABoxAxioms + ", |TBox|=" + numOfTBoxAxioms);
350
348 return relevantOntologySubset; 351 return relevantOntologySubset;
349 } 352 }
350 353
@@ -361,22 +364,23 @@ class MyQueryReasoner extends QueryReasoner {
361 } 364 }
362 365
363 private boolean querySkolemisedRelevantSubset(OWLOntology relevantSubset, QueryRecord queryRecord) { 366 private boolean querySkolemisedRelevantSubset(OWLOntology relevantSubset, QueryRecord queryRecord) {
367 Utility.logInfo("Evaluating semi-Skolemised relevant upper store...");
368
364 DatalogProgram relevantProgram = new DatalogProgram(relevantSubset, false); // toClassify is false 369 DatalogProgram relevantProgram = new DatalogProgram(relevantSubset, false); // toClassify is false
365 370
366 MultiStageQueryEngine relevantStore = 371 MultiStageQueryEngine relevantStore =
367 new MultiStageQueryEngine("Relevant-store", true); // checkValidity is true 372 new MultiStageQueryEngine("Relevant-store", true); // checkValidity is true
368// relevantStore.importRDFData("data", relevantProgram.getAdditionalDataFile()); // tried, doesn't work 373
369 relevantStore.importDataFromABoxOf(relevantSubset); 374 relevantStore.importDataFromABoxOf(relevantSubset);
370 375
371 int materialisationResult = relevantStore.materialiseSkolemly(relevantProgram, null); 376 int materialisationResult = relevantStore.materialiseSkolemly(relevantProgram, null);
372// int materialisationResult = relevantStore.materialiseRestrictedly(relevantProgram, null); // DOESN'T WORK!!!
373 if(materialisationResult != 1) 377 if(materialisationResult != 1)
374 throw new RuntimeException("Skolemised materialisation error"); // TODO check consistency 378 throw new RuntimeException("Skolemised materialisation error"); // TODO check consistency
375// relevantStore.materialiseRestrictedly(relevantProgram, null); // it has been tried
376 379
377 return queryUpperStore(relevantStore, queryRecord, queryRecord.getExtendedQueryText(), Step.L_SKOLEM_UPPER_BOUND); 380 boolean isFullyProcessed = checkGapAnswers(relevantStore, queryRecord);
378 381
379// return queryUpperStore(limitedSkolemUpperStore, queryRecord, queryRecord.getExtendedQueryText(), Step.L_SKOLEM_UPPER_BOUND); 382 Utility.logInfo("Semi-Skolemised relevant upper store has been evaluated");
383 return isFullyProcessed;
380 } 384 }
381 385
382 enum SatisfiabilityStatus {SATISFIABLE, UNSATISFIABLE, UNCHECKED} 386 enum SatisfiabilityStatus {SATISFIABLE, UNSATISFIABLE, UNCHECKED}
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxQueryEngine.java b/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxQueryEngine.java
index f835ba9..8b22919 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxQueryEngine.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxQueryEngine.java
@@ -74,7 +74,7 @@ public abstract class RDFoxQueryEngine extends QueryEngine {
74 long prevTriplesCount = store.getTriplesCount(); 74 long prevTriplesCount = store.getTriplesCount();
75 store.importOntology(ontology.getOWLOntologyManager().createOntology(ontology.getABoxAxioms(true))); 75 store.importOntology(ontology.getOWLOntologyManager().createOntology(ontology.getABoxAxioms(true)));
76 long loadedTriples = store.getTriplesCount() - prevTriplesCount; 76 long loadedTriples = store.getTriplesCount() - prevTriplesCount;
77 Utility.logInfo(name + ": loaded " + loadedTriples + " triples from " + ontology.getABoxAxioms(true) 77 Utility.logDebug(name + ": loaded " + loadedTriples + " triples from " + ontology.getABoxAxioms(true)
78 .size() + " ABox axioms"); 78 .size() + " ABox axioms");
79 } catch(JRDFStoreException | OWLOntologyCreationException e) { 79 } catch(JRDFStoreException | OWLOntologyCreationException e) {
80 e.printStackTrace(); 80 e.printStackTrace();
diff --git a/src/uk/ac/ox/cs/pagoda/rules/Program.java b/src/uk/ac/ox/cs/pagoda/rules/Program.java
index 4e147bb..afc32d4 100644
--- a/src/uk/ac/ox/cs/pagoda/rules/Program.java
+++ b/src/uk/ac/ox/cs/pagoda/rules/Program.java
@@ -106,7 +106,7 @@ protected PredicateDependency dependencyGraph;
106 clauses.addAll(botStrategy.process(botRelated)); 106 clauses.addAll(botStrategy.process(botRelated));
107 107
108 if(this instanceof GeneralProgram) 108 if(this instanceof GeneralProgram)
109 Utility.logInfo("The number of rules: " + (clauses.size() - 1)); 109 Utility.logDebug("The number of rules: " + (clauses.size() - 1));
110 } 110 }
111 111
112 @Override 112 @Override
diff --git a/src/uk/ac/ox/cs/pagoda/tracking/QueryTracker.java b/src/uk/ac/ox/cs/pagoda/tracking/QueryTracker.java
index d2d041f..27d3a53 100644
--- a/src/uk/ac/ox/cs/pagoda/tracking/QueryTracker.java
+++ b/src/uk/ac/ox/cs/pagoda/tracking/QueryTracker.java
@@ -73,7 +73,7 @@ public class QueryTracker {
73 store.applyReasoning(incrementally); 73 store.applyReasoning(incrementally);
74 tripleCount = store.getTriplesCount(); 74 tripleCount = store.getTriplesCount();
75 75
76 Utility.logInfo("tracking store after materialising tracking program: " 76 Utility.logDebug("tracking store after materialising tracking program: "
77 + tripleCount 77 + tripleCount
78 + " (" 78 + " ("
79 + (tripleCount - oldTripleCount) 79 + (tripleCount - oldTripleCount)
@@ -149,28 +149,47 @@ public class QueryTracker {
149 149
150 } 150 }
151 151
152 public void addRelatedAxiomsAndClauses(QueryRecord[] botQueryRecords) {
153 LinkedList<QueryRecord> toAddedRecords = new LinkedList<QueryRecord>();
154
155 for(QueryRecord botQueryRecord : botQueryRecords)
156 if(overlappingDisjunctiveClauses(botQueryRecord) != null)
157 toAddedRecords.add(botQueryRecord);
158
159 for(QueryRecord botQueryRecord : toAddedRecords) {
160 m_manager.addAxioms(m_record.getRelevantOntology(), botQueryRecord.getRelevantOntology().getAxioms());
161 for(DLClause clause : botQueryRecord.getRelevantClauses())
162 m_record.addRelevantClauses(clause);
163 }
164
165 if(!toAddedRecords.isEmpty())
166 Utility.logDebug("Part of bottom fragments is added for this query.");
167 else
168 Utility.logDebug("None of bottom fragments is added for this query.");
169 }
170
152 private int extractBinaryTuples(BasicQueryEngine trackingStore, OWLDataFactory factory, Set<String> binaryPredicates) { 171 private int extractBinaryTuples(BasicQueryEngine trackingStore, OWLDataFactory factory, Set<String> binaryPredicates) {
153 OWLOntology fragment = m_record.getRelevantOntology(); 172 OWLOntology fragment = m_record.getRelevantOntology();
154 int count; 173 int count;
155 int aboxAxiomCounter = 0; 174 int aboxAxiomCounter = 0;
156 Resource sub, obj; 175 Resource sub, obj;
157 OWLAxiom aboxAxiom; 176 OWLAxiom aboxAxiom;
158 String trackingIRI; 177 String trackingIRI;
159 Set<Integer> trackedIDEqualities = new HashSet<Integer>(); 178 Set<Integer> trackedIDEqualities = new HashSet<Integer>();
160 Set<String> trackedEntityEqualities = new HashSet<String>(); 179 Set<String> trackedEntityEqualities = new HashSet<String>();
161 TupleIterator trackingAnswers, lowerAnswers; 180 TupleIterator trackingAnswers, lowerAnswers;
162 181
163 for (Iterator<String> iter = binaryPredicates.iterator(); iter.hasNext(); ) { 182 for (Iterator<String> iter = binaryPredicates.iterator(); iter.hasNext(); ) {
164 trackingIRI = iter.next(); 183 trackingIRI = iter.next();
165 String propIRI = m_encoder.getOriginalPredicate(trackingIRI); 184 String propIRI = m_encoder.getOriginalPredicate(trackingIRI);
166 if (propIRI == null) continue; 185 if(propIRI == null) continue;
167 if (!propIRI.equals(Namespace.EQUALITY_QUOTED)) continue; 186 if (!propIRI.equals(Namespace.EQUALITY_QUOTED)) continue;
168 trackingAnswers = null; 187 trackingAnswers = null;
169 try { 188 try {
170 trackingAnswers = trackingStore.internal_evaluateAgainstIDBs(getSPARQLQuery4Binary(trackingIRI)); 189 trackingAnswers = trackingStore.internal_evaluateAgainstIDBs(getSPARQLQuery4Binary(trackingIRI));
171 for (long multi = trackingAnswers.open(); multi != 0; multi = trackingAnswers.getNext()) { 190 for (long multi = trackingAnswers.open(); multi != 0; multi = trackingAnswers.getNext()) {
172 if (trackingAnswers.getResourceID(0) != trackingAnswers.getResourceID(1)) { 191 if (trackingAnswers.getResourceID(0) != trackingAnswers.getResourceID(1)) {
173 for (int i = 0; i < 2; ++i) 192 for(int i = 0; i < 2; ++i)
174 if (trackedIDEqualities.add(trackingAnswers.getResourceID(i))) { 193 if (trackedIDEqualities.add(trackingAnswers.getResourceID(i))) {
175 trackedEntityEqualities.add(trackingAnswers.getResource(i).m_lexicalForm); 194 trackedEntityEqualities.add(trackingAnswers.getResource(i).m_lexicalForm);
176 } 195 }
@@ -179,71 +198,74 @@ public class QueryTracker {
179 } catch (JRDFStoreException e) { 198 } catch (JRDFStoreException e) {
180 e.printStackTrace(); 199 e.printStackTrace();
181 } finally { 200 } finally {
182 if (trackingAnswers != null) trackingAnswers.dispose(); 201 if(trackingAnswers != null) trackingAnswers.dispose();
183 } 202 }
184 iter.remove(); 203 iter.remove();
185 break; 204 break;
186 } 205 }
187 206
188 String sub_rep, obj_rep; 207 String sub_rep, obj_rep;
189 208
190 for (Iterator<String> iter = binaryPredicates.iterator(); iter.hasNext(); ) { 209 for (Iterator<String> iter = binaryPredicates.iterator(); iter.hasNext(); ) {
191 trackingIRI = iter.next(); 210 trackingIRI = iter.next();
192 count = 0; 211 count = 0;
193 String propIRI = m_encoder.getOriginalPredicate(trackingIRI); 212 String propIRI = m_encoder.getOriginalPredicate(trackingIRI);
194 if (propIRI == null) continue; 213 if(propIRI == null) continue;
195 iter.remove(); 214 iter.remove();
196 lowerAnswers = null; trackingAnswers = null; 215 lowerAnswers = null;
216 trackingAnswers = null;
197 Set<String> lower = new HashSet<String>(); 217 Set<String> lower = new HashSet<String>();
198 OWLObject prop = null; 218 OWLObject prop = null;
199 try { 219 try {
200 trackingAnswers = trackingStore.internal_evaluateAgainstIDBs(getSPARQLQuery4Binary(trackingIRI)); 220 trackingAnswers = trackingStore.internal_evaluateAgainstIDBs(getSPARQLQuery4Binary(trackingIRI));
201 trackingAnswers.open(); 221 trackingAnswers.open();
202 if (trackingAnswers.getMultiplicity() == 0) continue; 222 if(trackingAnswers.getMultiplicity() == 0) continue;
203 223
204 lowerAnswers = m_dataStore.internal_evaluateNotExpanded(getSPARQLQuery4Binary(propIRI)); 224 lowerAnswers = m_dataStore.internal_evaluateNotExpanded(getSPARQLQuery4Binary(propIRI));
205 lowerAnswers.open(); 225 lowerAnswers.open();
206 if (lowerAnswers.getMultiplicity() == 0) continue; 226 if(lowerAnswers.getMultiplicity() == 0) continue;
207 227
208 StringBuilder builder = new StringBuilder(); 228 StringBuilder builder = new StringBuilder();
209 for (long multi = lowerAnswers.getMultiplicity(); multi != 0; multi = lowerAnswers.getNext()) { 229 for (long multi = lowerAnswers.getMultiplicity(); multi != 0; multi = lowerAnswers.getNext()) {
210 sub = lowerAnswers.getResource(0); 230 sub = lowerAnswers.getResource(0);
211 obj = lowerAnswers.getResource(1); 231 obj = lowerAnswers.getResource(1);
212 builder.setLength(0); 232 builder.setLength(0);
213 builder.append(equalityGroups.find(sub.m_lexicalForm)).append(AnswerTuple.SEPARATOR).append(equalityGroups.find(obj.m_lexicalForm)); 233 builder.append(equalityGroups.find(sub.m_lexicalForm))
234 .append(AnswerTuple.SEPARATOR)
235 .append(equalityGroups.find(obj.m_lexicalForm));
214 lower.add(builder.toString()); 236 lower.add(builder.toString());
215 } 237 }
216 238
217 for (long multi = trackingAnswers.getMultiplicity(); multi != 0; multi = trackingAnswers.getNext()) { 239 for (long multi = trackingAnswers.getMultiplicity(); multi != 0; multi = trackingAnswers.getNext()) {
218 sub = trackingAnswers.getResource(0); 240 sub = trackingAnswers.getResource(0);
219 obj = trackingAnswers.getResource(1); 241 obj = trackingAnswers.getResource(1);
220 builder.setLength(0); 242 builder.setLength(0);
221 sub_rep = equalityGroups.find(sub.m_lexicalForm); 243 sub_rep = equalityGroups.find(sub.m_lexicalForm);
222 obj_rep = equalityGroups.find(obj.m_lexicalForm); 244 obj_rep = equalityGroups.find(obj.m_lexicalForm);
223 if (!sub_rep.equals(sub.m_lexicalForm) || !obj_rep.equals(obj.m_lexicalForm)) continue; 245 if (!sub_rep.equals(sub.m_lexicalForm) || !obj_rep.equals(obj.m_lexicalForm)) continue;
224 246
225 builder.append(sub_rep).append(AnswerTuple.SEPARATOR).append(obj_rep); 247 builder.append(sub_rep).append(AnswerTuple.SEPARATOR).append(obj_rep);
226 if (lower.contains(builder.toString())) { 248 if (lower.contains(builder.toString())) {
227 OWLObject owlObj = getOWLObject(obj, factory); 249 OWLObject owlObj = getOWLObject(obj, factory);
228 if (owlObj instanceof OWLIndividual) { 250 if (owlObj instanceof OWLIndividual) {
229 if (prop == null) 251 if (prop == null)
230 prop = factory.getOWLObjectProperty(IRI.create(propIRI.startsWith("<") ? OWLHelper.removeAngles(propIRI) : propIRI)); 252 prop = factory.getOWLObjectProperty(IRI.create(propIRI.startsWith("<") ? OWLHelper.removeAngles(propIRI) : propIRI));
231 aboxAxiom = factory.getOWLObjectPropertyAssertionAxiom( 253 aboxAxiom = factory.getOWLObjectPropertyAssertionAxiom(
232 (OWLObjectProperty) prop, 254 (OWLObjectProperty) prop,
233 factory.getOWLNamedIndividual(IRI.create(sub_rep)), 255 factory.getOWLNamedIndividual(IRI.create(sub_rep)),
234 factory.getOWLNamedIndividual(IRI.create(obj_rep))); 256 factory.getOWLNamedIndividual(IRI.create(obj_rep)));
235 } 257 }
236 else if (owlObj instanceof OWLLiteral) { 258 else if (owlObj instanceof OWLLiteral) {
237 if (prop == null) 259 if (prop == null)
238 prop = factory.getOWLDataProperty(IRI.create(propIRI.startsWith("<") ? OWLHelper.removeAngles(propIRI) : propIRI)); 260 prop = factory.getOWLDataProperty(IRI.create(propIRI.startsWith("<") ? OWLHelper.removeAngles(propIRI) : propIRI));
239 aboxAxiom = factory.getOWLDataPropertyAssertionAxiom( 261 aboxAxiom = factory.getOWLDataPropertyAssertionAxiom(
240 (OWLDataProperty) prop, 262 (OWLDataProperty) prop,
241 factory.getOWLNamedIndividual(IRI.create(sub_rep)), 263 factory.getOWLNamedIndividual(IRI.create(sub_rep)),
242 (OWLLiteral) owlObj); 264 (OWLLiteral) owlObj);
243 } 265 }
244 else { 266 else {
245 Utility.logError("There might be an error here ... "); 267 Utility.logError("There might be an error here ... ");
246 continue; 268 continue;
247 } 269 }
248 if (!fragment.containsAxiom(aboxAxiom)) { 270 if (!fragment.containsAxiom(aboxAxiom)) {
249 m_manager.addAxiom(fragment, aboxAxiom); 271 m_manager.addAxiom(fragment, aboxAxiom);
@@ -259,30 +281,30 @@ public class QueryTracker {
259 if (lowerAnswers != null) lowerAnswers.dispose(); 281 if (lowerAnswers != null) lowerAnswers.dispose();
260 lower.clear(); 282 lower.clear();
261 } 283 }
262 Utility.logDebug("property: " + propIRI + " " + count); 284 Utility.logDebug("property: " + propIRI + " " + count);
263 } 285 }
264 286
265 count = 0; 287 count = 0;
266 String value; 288 String value;
267 OWLObjectProperty sameAs = factory.getOWLObjectProperty(IRI.create(Namespace.EQUALITY)); 289 OWLObjectProperty sameAs = factory.getOWLObjectProperty(IRI.create(Namespace.EQUALITY));
268 for (String key: equalityGroups.keySet()) { 290 for (String key: equalityGroups.keySet()) {
269 if (!trackedEntityEqualities.contains(key)) continue; 291 if(!trackedEntityEqualities.contains(key)) continue;
270 value = equalityGroups.find(key); 292 value = equalityGroups.find(key);
271 m_manager.addAxiom(fragment, factory.getOWLObjectPropertyAssertionAxiom( 293 m_manager.addAxiom(fragment, factory.getOWLObjectPropertyAssertionAxiom(
272 sameAs, 294 sameAs,
273 factory.getOWLNamedIndividual(IRI.create(key)), 295 factory.getOWLNamedIndividual(IRI.create(key)),
274 factory.getOWLNamedIndividual(IRI.create(value)))); 296 factory.getOWLNamedIndividual(IRI.create(value))));
275 ++aboxAxiomCounter; 297 ++aboxAxiomCounter;
276 ++count; 298 ++count;
277 } 299 }
278 Utility.logDebug("property: " + Namespace.EQUALITY_QUOTED + " " + count); 300 Utility.logDebug("property: " + Namespace.EQUALITY_QUOTED + " " + count);
279 301
280 trackedEntityEqualities.clear(); 302 trackedEntityEqualities.clear();
281 trackedIDEqualities.clear(); 303 trackedIDEqualities.clear();
282 Utility.logTrace(Namespace.EQUALITY_QUOTED + " " + count); 304 Utility.logTrace(Namespace.EQUALITY_QUOTED + " " + count);
283 305
284 Utility.logDebug("ABox extraction Done"); 306 Utility.logDebug("ABox extraction Done");
285 return aboxAxiomCounter; 307 return aboxAxiomCounter;
286 } 308 }
287 309
288 private OWLObject getOWLObject(Resource rdfoxTerm, OWLDataFactory factory) { 310 private OWLObject getOWLObject(Resource rdfoxTerm, OWLDataFactory factory) {
@@ -298,15 +320,17 @@ public class QueryTracker {
298// rdfoxTerm.m_datatype.equals(Datatype.XSD_UNSIGNED_BYTE)) 320// rdfoxTerm.m_datatype.equals(Datatype.XSD_UNSIGNED_BYTE))
299 if (rdfoxTerm.m_datatype.equals(Datatype.XSD_DATE)) 321 if (rdfoxTerm.m_datatype.equals(Datatype.XSD_DATE))
300 return factory.getOWLLiteral(rdfoxTerm.m_lexicalForm, factory.getOWLDatatype(IRI.create(Namespace.XSD_STRING))); 322 return factory.getOWLLiteral(rdfoxTerm.m_lexicalForm, factory.getOWLDatatype(IRI.create(Namespace.XSD_STRING)));
301 323
302 else return factory.getOWLLiteral(rdfoxTerm.m_lexicalForm, factory.getOWLDatatype(IRI.create(rdfoxTerm.m_datatype.getIRI()))); 324 else
325 return factory.getOWLLiteral(rdfoxTerm.m_lexicalForm, factory.getOWLDatatype(IRI.create(rdfoxTerm.m_datatype
326 .getIRI())));
303 } 327 }
304 328
305 private int extractUnaryTuples(BasicQueryEngine trackingStore, OWLDataFactory factory, Set<String> unaryPredicates) { 329 private int extractUnaryTuples(BasicQueryEngine trackingStore, OWLDataFactory factory, Set<String> unaryPredicates) {
306 OWLOntology fragment = m_record.getRelevantOntology(); 330 OWLOntology fragment = m_record.getRelevantOntology();
307 int count; 331 int count;
308 int aboxAxiomCounter = 0; 332 int aboxAxiomCounter = 0;
309 String answer; 333 String answer;
310 OWLAxiom aboxAxiom; 334 OWLAxiom aboxAxiom;
311 for (String trackingIRI : unaryPredicates) { 335 for (String trackingIRI : unaryPredicates) {
312 count = 0; 336 count = 0;
@@ -319,12 +343,12 @@ public class QueryTracker {
319 try { 343 try {
320 answers = trackingStore.internal_evaluateAgainstIDBs(getSPARQLQuery4Unary(trackingIRI)); 344 answers = trackingStore.internal_evaluateAgainstIDBs(getSPARQLQuery4Unary(trackingIRI));
321 answers.open(); 345 answers.open();
322 if (answers.getMultiplicity() == 0) continue; 346 if(answers.getMultiplicity() == 0) continue;
323 347
324 lowerAnswers = m_dataStore.internal_evaluateNotExpanded(getSPARQLQuery4Unary(clsIRI)); 348 lowerAnswers = m_dataStore.internal_evaluateNotExpanded(getSPARQLQuery4Unary(clsIRI));
325 lowerAnswers.open(); 349 lowerAnswers.open();
326 if (lowerAnswers.getMultiplicity() == 0) continue; 350 if (lowerAnswers.getMultiplicity() == 0) continue;
327 351
328 for (long multi = lowerAnswers.getMultiplicity(); multi != 0; multi = lowerAnswers.getNext()) 352 for (long multi = lowerAnswers.getMultiplicity(); multi != 0; multi = lowerAnswers.getNext())
329 lower.add(equalityGroups.find(lowerAnswers.getResource(0).m_lexicalForm)); 353 lower.add(equalityGroups.find(lowerAnswers.getResource(0).m_lexicalForm));
330 354
@@ -386,25 +410,6 @@ public class QueryTracker {
386 } 410 }
387 } 411 }
388 412
389 public void addRelatedAxiomsAndClauses(QueryRecord[] botQueryRecords) {
390 LinkedList<QueryRecord> toAddedRecords = new LinkedList<QueryRecord>();
391
392 for (QueryRecord botQueryRecord : botQueryRecords)
393 if (overlappingDisjunctiveClauses(botQueryRecord) != null)
394 toAddedRecords.add(botQueryRecord);
395
396 for (QueryRecord botQueryRecord : toAddedRecords) {
397 m_manager.addAxioms(m_record.getRelevantOntology(), botQueryRecord.getRelevantOntology().getAxioms());
398 for (DLClause clause : botQueryRecord.getRelevantClauses())
399 m_record.addRelevantClauses(clause);
400 }
401
402 if (!toAddedRecords.isEmpty())
403 Utility.logDebug("Part of bottom fragments is added for this query.");
404 else
405 Utility.logDebug("None of bottom fragments is added for this query.");
406 }
407
408 private Set<DLClause> overlappingDisjunctiveClauses( 413 private Set<DLClause> overlappingDisjunctiveClauses(
409 QueryRecord botQueryRecord) { 414 QueryRecord botQueryRecord) {
410 if (m_tBoxAxioms == null) 415 if (m_tBoxAxioms == null)
diff --git a/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoder.java b/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoder.java
index d8ebc55..d05731a 100644
--- a/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoder.java
+++ b/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoder.java
@@ -311,7 +311,7 @@ public abstract class TrackingRuleEncoder extends Disposable {
311 } 311 }
312 } 312 }
313 313
314 Utility.logInfo(addedData.size() + " triples are added into the store."); 314 Utility.logDebug(addedData.size() + " triples are added into the store.");
315 } 315 }
316 316
317 protected DLPredicate getGapDLPredicate(DLPredicate dlPredicate) { 317 protected DLPredicate getGapDLPredicate(DLPredicate dlPredicate) {
generated by cgit v1.2.3 (git 2.25.1) at 2025-11-05 10:43:34 +0000