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-rw-r--r--src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager.java114
-rw-r--r--src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java2
-rw-r--r--src/uk/ac/ox/cs/pagoda/reasoner/IterativeRefinement.java26
-rw-r--r--src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java145
-rw-r--r--src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java12
-rw-r--r--src/uk/ac/ox/cs/pagoda/reasoner/RLUQueryReasoner.java4
-rw-r--r--src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxQueryEngine.java94
7 files changed, 202 insertions, 195 deletions
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager.java b/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager.java
index 409a2c9..ef9338a 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager.java
@@ -30,43 +30,42 @@ public class ConsistencyManager {
30 protected MyQueryReasoner m_reasoner; 30 protected MyQueryReasoner m_reasoner;
31 protected QueryManager m_queryManager; 31 protected QueryManager m_queryManager;
32 32
33 Timer t = new Timer(); 33 Timer t = new Timer();
34 QueryRecord fullQueryRecord;
35 QueryRecord[] botQueryRecords;
36 LinkedList<DLClause> toAddClauses;
37 boolean fragmentExtracted = false;
34 38
35 public ConsistencyManager(MyQueryReasoner reasoner) { 39 public ConsistencyManager(MyQueryReasoner reasoner) {
36 m_reasoner = reasoner; 40 m_reasoner = reasoner;
37 m_queryManager = reasoner.getQueryManager(); 41 m_queryManager = reasoner.getQueryManager();
38 } 42 }
39 43
40 QueryRecord fullQueryRecord;
41 QueryRecord[] botQueryRecords;
42
43 LinkedList<DLClause> toAddClauses;
44
45 boolean checkRLLowerBound() { 44 boolean checkRLLowerBound() {
46 fullQueryRecord = m_queryManager.create(QueryRecord.botQueryText, 0); 45 fullQueryRecord = m_queryManager.create(QueryRecord.botQueryText, 0);
47 AnswerTuples iter = null; 46 AnswerTuples iter = null;
48 47
49 try { 48 try {
50 iter = m_reasoner.rlLowerStore.evaluate(fullQueryRecord.getQueryText(), fullQueryRecord.getAnswerVariables()); 49 iter = m_reasoner.rlLowerStore.evaluate(fullQueryRecord.getQueryText(), fullQueryRecord.getAnswerVariables());
51 fullQueryRecord.updateLowerBoundAnswers(iter); 50 fullQueryRecord.updateLowerBoundAnswers(iter);
52 } finally { 51 } finally {
53 iter.dispose(); 52 iter.dispose();
54 } 53 }
55 54
56 if (fullQueryRecord.getNoOfSoundAnswers() > 0) { 55 if (fullQueryRecord.getNoOfSoundAnswers() > 0) {
57 Utility.logInfo("Answers to bottom in the lower bound: ", fullQueryRecord.outputSoundAnswerTuple()); 56 Utility.logInfo("Answers to bottom in the lower bound: ", fullQueryRecord.outputSoundAnswerTuple());
58 return false; 57 return false;
59 } 58 }
60 return true; 59 return true;
61 } 60 }
62 61
63 boolean checkELLowerBound() { 62 boolean checkELLowerBound() {
64 fullQueryRecord.updateLowerBoundAnswers(m_reasoner.elLowerStore.evaluate(fullQueryRecord.getQueryText(), fullQueryRecord.getAnswerVariables())); 63 fullQueryRecord.updateLowerBoundAnswers(m_reasoner.elLowerStore.evaluate(fullQueryRecord.getQueryText(), fullQueryRecord.getAnswerVariables()));
65 if (fullQueryRecord.getNoOfSoundAnswers() > 0) { 64 if (fullQueryRecord.getNoOfSoundAnswers() > 0) {
66 Utility.logInfo("Answers to bottom in the lower bound: ", fullQueryRecord.outputSoundAnswerTuple()); 65 Utility.logInfo("Answers to bottom in the lower bound: ", fullQueryRecord.outputSoundAnswerTuple());
67 return true; 66 return true;
68 } 67 }
69 return true; 68 return true;
70 } 69 }
71 70
72 boolean checkUpper(BasicQueryEngine upperStore) { 71 boolean checkUpper(BasicQueryEngine upperStore) {
@@ -91,65 +90,64 @@ public class ConsistencyManager {
91 fullQueryRecord.dispose(); 90 fullQueryRecord.dispose();
92 } 91 }
93 92
93// protected boolean unsatisfiability(double duration) {
94// fullQueryRecord.dispose();
95// Utility.logDebug("The ontology and dataset is unsatisfiable.");
96// return false;
97// }
98
99// protected boolean satisfiability(double duration) {
100// fullQueryRecord.dispose();
101// Utility.logDebug("The ontology and dataset is satisfiable.");
102// return true;
103// }
104
94 boolean check() { 105 boolean check() {
95// if (!checkRLLowerBound()) return false; 106// if (!checkRLLowerBound()) return false;
96// if (!checkELLowerBound()) return false; 107// if (!checkELLowerBound()) return false;
97// if (checkLazyUpper()) return true; 108// if (checkLazyUpper()) return true;
98 AnswerTuples iter = null; 109 AnswerTuples iter = null;
99 110
100 try { 111 try {
101 iter = m_reasoner.trackingStore.evaluate(fullQueryRecord.getQueryText(), fullQueryRecord.getAnswerVariables()); 112 iter =
113 m_reasoner.trackingStore.evaluate(fullQueryRecord.getQueryText(), fullQueryRecord.getAnswerVariables());
102 fullQueryRecord.updateUpperBoundAnswers(iter); 114 fullQueryRecord.updateUpperBoundAnswers(iter);
103 } finally { 115 } finally {
104 if (iter != null) iter.dispose(); 116 if(iter != null) iter.dispose();
105 } 117 }
106 118
107 if (fullQueryRecord.getNoOfCompleteAnswers() == 0) 119 if(fullQueryRecord.getNoOfCompleteAnswers() == 0)
108 return true; 120 return true;
109 121
110 extractBottomFragment(); 122 extractBottomFragment();
111 123
112 try { 124 try {
113 extractAxioms4Full(); 125 extractAxioms4Full();
114 } catch (OWLOntologyCreationException e) { 126 } catch(OWLOntologyCreationException e) {
115 e.printStackTrace(); 127 e.printStackTrace();
116 } 128 }
117// fullQueryRecord.saveRelevantClause(); 129// fullQueryRecord.saveRelevantClause();
118 130
119 boolean satisfiability; 131 boolean satisfiability;
120 132
121 Checker checker; 133 Checker checker;
122 for (QueryRecord r: getQueryRecords()) { 134 for(QueryRecord r : getQueryRecords()) {
123 // TODO to be removed ... 135 // TODO to be removed ...
124// r.saveRelevantOntology("bottom" + r.getQueryID() + ".owl"); 136// r.saveRelevantOntology("bottom" + r.getQueryID() + ".owl");
125 checker = new HermitSummaryFilter(r, true); // m_reasoner.factory.getSummarisedReasoner(r); 137 checker = new HermitSummaryFilter(r, true); // m_reasoner.factory.getSummarisedReasoner(r);
126 satisfiability = checker.isConsistent(); 138 satisfiability = checker.isConsistent();
127 checker.dispose(); 139 checker.dispose();
128 if (!satisfiability) return false; 140 if(!satisfiability) return false;
129 } 141 }
130 142
131// Checker checker = m_reasoner.factory.getSummarisedReasoner(fullQueryRecord); 143// Checker checker = m_reasoner.factory.getSummarisedReasoner(fullQueryRecord);
132// boolean satisfiable = checker.isConsistent(); 144// boolean satisfiable = checker.isConsistent();
133// checker.dispose(); 145// checker.dispose();
134// if (!satisfiable) return unsatisfiability(t.duration()); 146// if (!satisfiable) return unsatisfiability(t.duration());
135 147
136 return true; 148 return true;
137 } 149 }
138 150
139// protected boolean unsatisfiability(double duration) {
140// fullQueryRecord.dispose();
141// Utility.logDebug("The ontology and dataset is unsatisfiable.");
142// return false;
143// }
144
145// protected boolean satisfiability(double duration) {
146// fullQueryRecord.dispose();
147// Utility.logDebug("The ontology and dataset is satisfiable.");
148// return true;
149// }
150
151 boolean fragmentExtracted = false;
152
153 public void extractBottomFragment() { 151 public void extractBottomFragment() {
154 if (fragmentExtracted) return ; 152 if (fragmentExtracted) return ;
155 fragmentExtracted = true; 153 fragmentExtracted = true;
@@ -179,7 +177,7 @@ public class ConsistencyManager {
179 int[] group = new int[number - 1]; 177 int[] group = new int[number - 1];
180 for (int i = 0; i < number - 1; ++i) group[i] = i; 178 for (int i = 0; i < number - 1; ++i) group[i] = i;
181 for (int i = 0; i < number - 1; ++i) 179 for (int i = 0; i < number - 1; ++i)
182 if (tempQueryRecords[i].processed()) tempQueryRecords[i].dispose(); 180 if(tempQueryRecords[i].isProcessed()) tempQueryRecords[i].dispose();
183 else if (group[i] == i) { 181 else if (group[i] == i) {
184 ++bottomNumber; 182 ++bottomNumber;
185 record = tempQueryRecords[i]; 183 record = tempQueryRecords[i];
@@ -193,8 +191,8 @@ public class ConsistencyManager {
193 int bottomCounter = 0; 191 int bottomCounter = 0;
194 botQueryRecords = new QueryRecord[bottomNumber]; 192 botQueryRecords = new QueryRecord[bottomNumber];
195 Variable X = Variable.create("X"); 193 Variable X = Variable.create("X");
196 for (int i = 0; i < number - 1; ++i) 194 for (int i = 0; i < number - 1; ++i)
197 if (!tempQueryRecords[i].processed()) 195 if(!tempQueryRecords[i].isProcessed())
198 if (group[i] == i) { 196 if (group[i] == i) {
199 botQueryRecords[bottomCounter] = record = tempQueryRecords[i]; 197 botQueryRecords[bottomCounter] = record = tempQueryRecords[i];
200 record.resetInfo(QueryRecord.botQueryText.replace("Nothing", "Nothing_final" + (++bottomCounter)), 0, group[i] = bottomCounter); 198 record.resetInfo(QueryRecord.botQueryText.replace("Nothing", "Nothing_final" + (++bottomCounter)), 0, group[i] = bottomCounter);
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java
index 34742c8..c74ea58 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java
@@ -68,7 +68,7 @@ class ELHOUQueryReasoner extends QueryReasoner {
68 } 68 }
69 queryRecord.addProcessingTime(Step.UPPER_BOUND, t.duration()); 69 queryRecord.addProcessingTime(Step.UPPER_BOUND, t.duration());
70 70
71 if (queryRecord.processed()) { 71 if(queryRecord.isProcessed()) {
72 queryRecord.setDifficulty(Step.UPPER_BOUND); 72 queryRecord.setDifficulty(Step.UPPER_BOUND);
73 return; 73 return;
74 } 74 }
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/IterativeRefinement.java b/src/uk/ac/ox/cs/pagoda/reasoner/IterativeRefinement.java
index 447a92d..7847e7c 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/IterativeRefinement.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/IterativeRefinement.java
@@ -1,9 +1,6 @@
1package uk.ac.ox.cs.pagoda.reasoner; 1package uk.ac.ox.cs.pagoda.reasoner;
2 2
3import java.io.File;
4
5import org.semanticweb.owlapi.model.OWLOntology; 3import org.semanticweb.owlapi.model.OWLOntology;
6
7import uk.ac.ox.cs.pagoda.constraints.BottomStrategy; 4import uk.ac.ox.cs.pagoda.constraints.BottomStrategy;
8import uk.ac.ox.cs.pagoda.constraints.UpperUnaryBottom; 5import uk.ac.ox.cs.pagoda.constraints.UpperUnaryBottom;
9import uk.ac.ox.cs.pagoda.multistage.MultiStageQueryEngine; 6import uk.ac.ox.cs.pagoda.multistage.MultiStageQueryEngine;
@@ -14,6 +11,8 @@ import uk.ac.ox.cs.pagoda.rules.GeneralProgram;
14import uk.ac.ox.cs.pagoda.tracking.QueryTracker; 11import uk.ac.ox.cs.pagoda.tracking.QueryTracker;
15import uk.ac.ox.cs.pagoda.util.Utility; 12import uk.ac.ox.cs.pagoda.util.Utility;
16 13
14import java.io.File;
15
17public class IterativeRefinement { 16public class IterativeRefinement {
18 17
19 private static final int depthLimit = 1; 18 private static final int depthLimit = 1;
@@ -23,16 +22,15 @@ public class IterativeRefinement {
23 BasicQueryEngine m_trackingStore; 22 BasicQueryEngine m_trackingStore;
24 QueryRecord[] botQueryRecords; 23 QueryRecord[] botQueryRecords;
25 24
26 int m_depth = 0; 25 int m_depth = 0;
27 26 String tempDataFile = "temp.ttl";
27
28 public IterativeRefinement(QueryRecord queryRecord, QueryTracker tracker, BasicQueryEngine trackingStore, QueryRecord[] botQueryRecords) { 28 public IterativeRefinement(QueryRecord queryRecord, QueryTracker tracker, BasicQueryEngine trackingStore, QueryRecord[] botQueryRecords) {
29 m_record = queryRecord; 29 m_record = queryRecord;
30 m_tracker = tracker; 30 m_tracker = tracker;
31 m_trackingStore = trackingStore; 31 m_trackingStore = trackingStore;
32 this.botQueryRecords = botQueryRecords; 32 this.botQueryRecords = botQueryRecords;
33 } 33 }
34
35 String tempDataFile = "temp.ttl";
36 34
37 public OWLOntology extractWithFullABox(String dataset, BottomStrategy upperBottom) { 35 public OWLOntology extractWithFullABox(String dataset, BottomStrategy upperBottom) {
38 GeneralProgram program; 36 GeneralProgram program;
@@ -58,8 +56,8 @@ public class IterativeRefinement {
58 } finally { 56 } finally {
59 tEngine.dispose(); 57 tEngine.dispose();
60 } 58 }
61 59
62 if (m_record.processed()) 60 if(m_record.isProcessed())
63 return null; 61 return null;
64 62
65 if (!update) break; 63 if (!update) break;
@@ -95,8 +93,8 @@ public class IterativeRefinement {
95 } finally { 93 } finally {
96 tEngine.dispose(); 94 tEngine.dispose();
97 } 95 }
98 96
99 if (m_record.processed()) 97 if(m_record.isProcessed())
100 return null; 98 return null;
101 99
102 if (!update) break; 100 if (!update) break;
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
index cc0e647..b5b9534 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
@@ -23,7 +23,6 @@ import uk.ac.ox.cs.pagoda.util.Utility;
23import uk.ac.ox.cs.pagoda.util.tuples.Tuple; 23import uk.ac.ox.cs.pagoda.util.tuples.Tuple;
24 24
25import java.util.Collection; 25import java.util.Collection;
26import java.util.HashMap;
27 26
28class MyQueryReasoner extends QueryReasoner { 27class MyQueryReasoner extends QueryReasoner {
29 28
@@ -33,7 +32,7 @@ class MyQueryReasoner extends QueryReasoner {
33// String additonalDataFile; 32// String additonalDataFile;
34 BasicQueryEngine rlLowerStore = null; 33 BasicQueryEngine rlLowerStore = null;
35 BasicQueryEngine lazyUpperStore = null; 34 BasicQueryEngine lazyUpperStore = null;
36 BasicQueryEngine limitedSkolemUpperStore; 35 // BasicQueryEngine limitedSkolemUpperStore;
37 OWLOntology elho_ontology; 36 OWLOntology elho_ontology;
38// boolean[] namedIndividuals_lazyUpper; 37// boolean[] namedIndividuals_lazyUpper;
39 KarmaQueryEngine elLowerStore = null; 38 KarmaQueryEngine elLowerStore = null;
@@ -99,7 +98,7 @@ class MyQueryReasoner extends QueryReasoner {
99 useUpperStores = multiStageTag && !program.getGeneral().isHorn(); 98 useUpperStores = multiStageTag && !program.getGeneral().isHorn();
100 if(useUpperStores) { 99 if(useUpperStores) {
101 lazyUpperStore = getUpperStore("lazy-upper-bound", true); 100 lazyUpperStore = getUpperStore("lazy-upper-bound", true);
102 limitedSkolemUpperStore = getUpperStore("limited-skolem-upper-bound", true); 101// limitedSkolemUpperStore = getUpperStore("limited-skolem-upper-bound", true);
103 } 102 }
104 103
105 importData(program.getAdditionalDataFile()); 104 importData(program.getAdditionalDataFile());
@@ -147,20 +146,20 @@ class MyQueryReasoner extends QueryReasoner {
147 Utility.logInfo("time for satisfiability checking: " + t.duration()); 146 Utility.logInfo("time for satisfiability checking: " + t.duration());
148 } 147 }
149 148
150 if(limitedSkolemUpperStore != null) { 149// if(limitedSkolemUpperStore != null) {
151 limitedSkolemUpperStore.importRDFData(name, datafile); 150// limitedSkolemUpperStore.importRDFData(name, datafile);
152 limitedSkolemUpperStore.materialise("saturate named individuals", originalMarkProgram); 151// limitedSkolemUpperStore.materialise("saturate named individuals", originalMarkProgram);
153 int tag = limitedSkolemUpperStore.materialiseSkolemly(program, null); 152// int tag = limitedSkolemUpperStore.materialiseSkolemly(program, null);
154 if(tag != 1) { 153// if(tag != 1) {
155 limitedSkolemUpperStore.dispose(); 154// limitedSkolemUpperStore.dispose();
156 limitedSkolemUpperStore = null; 155// limitedSkolemUpperStore = null;
157 } 156// }
158 if(tag == -1) return false; 157// if(tag == -1) return false;
159 } 158// }
160 if(satisfiable == SatisfiabilityStatus.UNCHECKED && consistency.checkUpper(limitedSkolemUpperStore)) { 159// if(satisfiable == SatisfiabilityStatus.UNCHECKED && consistency.checkUpper(limitedSkolemUpperStore)) {
161 satisfiable = SatisfiabilityStatus.SATISFIABLE; 160// satisfiable = SatisfiabilityStatus.SATISFIABLE;
162 Utility.logInfo("time for satisfiability checking: " + t.duration()); 161// Utility.logInfo("time for satisfiability checking: " + t.duration());
163 } 162// }
164 163
165 trackingStore.importRDFData(name, datafile); 164 trackingStore.importRDFData(name, datafile);
166 trackingStore.materialise("saturate named individuals", originalMarkProgram); 165 trackingStore.materialise("saturate named individuals", originalMarkProgram);
@@ -214,7 +213,7 @@ class MyQueryReasoner extends QueryReasoner {
214 queryUpperBound(upperStore, queryRecord, queryRecord.getQueryText(), queryRecord.getAnswerVariables()); 213 queryUpperBound(upperStore, queryRecord, queryRecord.getQueryText(), queryRecord.getAnswerVariables());
215 214
216 queryRecord.addProcessingTime(step, t.duration()); 215 queryRecord.addProcessingTime(step, t.duration());
217 if(queryRecord.processed()) { 216 if(queryRecord.isProcessed()) {
218 queryRecord.setDifficulty(step); 217 queryRecord.setDifficulty(step);
219 return true; 218 return true;
220 } 219 }
@@ -224,7 +223,7 @@ class MyQueryReasoner extends QueryReasoner {
224 /** 223 /**
225 * Returns the part of the ontology relevant for Hermit, while computing the bound answers. 224 * Returns the part of the ontology relevant for Hermit, while computing the bound answers.
226 * */ 225 * */
227 private OWLOntology relevantPart(QueryRecord queryRecord) { 226 private boolean queryBounds(QueryRecord queryRecord) {
228 AnswerTuples rlAnswer = null, elAnswer = null; 227 AnswerTuples rlAnswer = null, elAnswer = null;
229 228
230 t.reset(); 229 t.reset();
@@ -243,15 +242,15 @@ class MyQueryReasoner extends QueryReasoner {
243 242
244 Utility.logDebug("Tracking store"); 243 Utility.logDebug("Tracking store");
245 if(queryUpperStore(trackingStore, queryRecord, extendedQueryTexts, Step.SIMPLE_UPPER_BOUND)) 244 if(queryUpperStore(trackingStore, queryRecord, extendedQueryTexts, Step.SIMPLE_UPPER_BOUND))
246 return null; 245 return true;
247 246
248 if(!queryRecord.isBottom()) { 247 if(!queryRecord.isBottom()) {
249 Utility.logDebug("Lazy store"); 248 Utility.logDebug("Lazy store");
250 if(lazyUpperStore != null && queryUpperStore(lazyUpperStore, queryRecord, extendedQueryTexts, Step.LAZY_UPPER_BOUND)) 249 if(lazyUpperStore != null && queryUpperStore(lazyUpperStore, queryRecord, extendedQueryTexts, Step.LAZY_UPPER_BOUND))
251 return null; 250 return true;
252 Utility.logDebug("Skolem store"); 251// Utility.logDebug("Skolem store");
253 if(limitedSkolemUpperStore != null && queryUpperStore(limitedSkolemUpperStore, queryRecord, extendedQueryTexts, Step.L_SKOLEM_UPPER_BOUND)) 252// if(limitedSkolemUpperStore != null && queryUpperStore(limitedSkolemUpperStore, queryRecord, extendedQueryTexts, Step.L_SKOLEM_UPPER_BOUND))
254 return null; 253// return null;
255 } 254 }
256 255
257 t.reset(); 256 t.reset();
@@ -266,52 +265,23 @@ class MyQueryReasoner extends QueryReasoner {
266 } 265 }
267 queryRecord.addProcessingTime(Step.EL_LOWER_BOUND, t.duration()); 266 queryRecord.addProcessingTime(Step.EL_LOWER_BOUND, t.duration());
268 267
269 if (queryRecord.processed()) { 268 if(queryRecord.isProcessed()) {
270 queryRecord.setDifficulty(Step.EL_LOWER_BOUND); 269 queryRecord.setDifficulty(Step.EL_LOWER_BOUND);
271 return null; 270 return true;
272 } 271 }
273 272
273 return false;
274 }
275
276 private OWLOntology extractRelevantOntologySubset(QueryRecord queryRecord) {
274 t.reset(); 277 t.reset();
275 278
276 QueryTracker tracker = new QueryTracker(encoder, rlLowerStore, queryRecord); 279 QueryTracker tracker = new QueryTracker(encoder, rlLowerStore, queryRecord);
280 OWLOntology relevantOntologySubset = tracker.extract(trackingStore, consistency.getQueryRecords(), true);
277 281
278 OWLOntology knowledgeBase;
279 t.reset();
280// if (program.getGeneral().isHorn()) {
281// knowledgebase = tracker.extract(lazyUpperStore, consistency.getQueryRecords(), true);
282// queryRecord.addProcessingTime(Step.Fragment, t.duration());
283// return knowledgebase;
284// }
285// else {
286 knowledgeBase = tracker.extract(trackingStore, consistency.getQueryRecords(), true);
287 queryRecord.addProcessingTime(Step.FRAGMENT, t.duration()); 282 queryRecord.addProcessingTime(Step.FRAGMENT, t.duration());
288// }
289
290 if(knowledgeBase.isEmpty() || queryRecord.isBottom())
291 return knowledgeBase;
292
293 if(program.getGeneral().isHorn()) return knowledgeBase;
294 283
295// t.reset(); 284 return relevantOntologySubset;
296// if (queryRecord.isHorn() && lazyUpperStore != null) {
297//// knowledgebase = tracker.extract(lazyUpperStore, consistency.getQueryRecords(), true);
298// } else if (queryRecord.getArity() < 3) {
299// IterativeRefinement iterativeRefinement = new IterativeRefinement(queryRecord, tracker, trackingStore, consistency.getQueryRecords());
300// knowledgebase = iterativeRefinement.extractWithFullABox(importedData.toString(), program.getUpperBottomStrategy());
301// }
302//
303// queryRecord.addProcessingTime(Step.FRAGMENT_REFINEMENT, t.duration());
304//
305// if (knowledgebase == null)
306// queryRecord.setDifficulty(Step.FRAGMENT_REFINEMENT);
307
308 return knowledgeBase;
309 }
310
311 private String toJsonKeyValuePair(String key, Object value) {
312 HashMap<String, Object> map = new HashMap<>();
313 map.put(key, value);
314 return QueryRecord.GsonCreator.getInstance().toJson(map);
315 } 285 }
316 286
317 private void queryUpperBound(BasicQueryEngine upperStore, QueryRecord queryRecord, String queryText, String[] answerVariables) { 287 private void queryUpperBound(BasicQueryEngine upperStore, QueryRecord queryRecord, String queryText, String[] answerVariables) {
@@ -323,35 +293,59 @@ class MyQueryReasoner extends QueryReasoner {
323 queryRecord.updateUpperBoundAnswers(rlAnswer); 293 queryRecord.updateUpperBoundAnswers(rlAnswer);
324 } finally { 294 } finally {
325 if(rlAnswer != null) rlAnswer.dispose(); 295 if(rlAnswer != null) rlAnswer.dispose();
326 rlAnswer = null;
327 } 296 }
328 } 297 }
329 298
330// int counter = 0;
331
332 @Override 299 @Override
333 public void evaluate(QueryRecord queryRecord) { 300 public void evaluate(QueryRecord queryRecord) {
334 OWLOntology knowledgeBase = relevantPart(queryRecord); 301 if(queryBounds(queryRecord))
335
336 if(knowledgeBase == null) {
337 Utility.logDebug("Difficulty of this query: " + queryRecord.getDifficulty());
338 return; 302 return;
339 }
340 303
341 int aBoxCount = knowledgeBase.getABoxAxioms(true).size(); 304 OWLOntology relevantOntologySubset = extractRelevantOntologySubset(queryRecord);
342 Utility.logDebug("ABox axioms: " + aBoxCount + " TBox axioms: " + (knowledgeBase.getAxiomCount() - aBoxCount)); 305
306 int aBoxCount = relevantOntologySubset.getABoxAxioms(true).size();
307 Utility.logInfo("Relevant ontology subset: ABox_axioms=" + aBoxCount + " TBox_axioms=" + (relevantOntologySubset
308 .getAxiomCount() - aBoxCount));
343// queryRecord.saveRelevantOntology("fragment_query" + queryRecord.getQueryID() + ".owl"); 309// queryRecord.saveRelevantOntology("fragment_query" + queryRecord.getQueryID() + ".owl");
344 310
311 if(querySkolemisedRelevantSubset(relevantOntologySubset, queryRecord))
312 return;
313
345 Timer t = new Timer(); 314 Timer t = new Timer();
346 Checker summarisedChecker = new HermitSummaryFilter(queryRecord, properties.getToCallHermiT()); 315 Checker summarisedChecker = new HermitSummaryFilter(queryRecord, properties.getToCallHermiT());
347// int validNumber =
348 summarisedChecker.check(queryRecord.getGapAnswers()); 316 summarisedChecker.check(queryRecord.getGapAnswers());
349 summarisedChecker.dispose(); 317 summarisedChecker.dispose();
350 Utility.logDebug("Total time for full reasoner: " + t.duration()); 318 Utility.logDebug("Total time for full reasoner: " + t.duration());
351// if (validNumber == 0) {
352 queryRecord.markAsProcessed(); 319 queryRecord.markAsProcessed();
353 Utility.logDebug("Difficulty of this query: " + queryRecord.getDifficulty()); 320 Utility.logDebug("Difficulty of this query: " + queryRecord.getDifficulty());
354// } 321 }
322
323 private boolean querySkolemisedRelevantSubset(OWLOntology relevantSubset, QueryRecord queryRecord) {
324 MultiStageQueryEngine relevantStore =
325 new MultiStageQueryEngine("Relevant-store", true); // checkValidity is true
326 DatalogProgram relevantProgram = new DatalogProgram(relevantSubset, false); // toClassify is false
327
328// relevantStore.importRDFData("data", importedData.toString()); // 2 answers more
329 relevantStore.importDataFromABoxOf(relevantSubset);
330
331 int materialisationResult = relevantStore.materialiseSkolemly(relevantProgram, null);
332 if(materialisationResult != 1)
333 throw new RuntimeException("Skolemised materialisation error"); // TODO check consistency
334// relevantStore.materialiseRestrictedly(relevantProgram, null); // it has been tried
335
336 return queryUpperStore(relevantStore, queryRecord, queryRecord.getExtendedQueryText(), Step.L_SKOLEM_UPPER_BOUND);
337
338 // the following has been tried
339// Tuple<String> extendedQueryText = queryRecord.getExtendedQueryText();
340// if(queryRecord.hasNonAnsDistinguishedVariables()) {
341// queryUpperBound(relevantStore, queryRecord, extendedQueryText.get(0), queryRecord.getAnswerVariables());
342// queryUpperBound(relevantStore, queryRecord, extendedQueryText.get(1), queryRecord.getDistinguishedVariables());
343// }
344// else
345// queryUpperBound(relevantStore, queryRecord, queryRecord.getQueryText(), queryRecord.getAnswerVariables());
346//
347// return queryRecord.isProcessed();
348
355 } 349 }
356 350
357 @Override 351 @Override
@@ -375,7 +369,8 @@ class MyQueryReasoner extends QueryReasoner {
375 if (lazyUpperStore != null) lazyUpperStore.dispose(); 369 if (lazyUpperStore != null) lazyUpperStore.dispose();
376 if (elLowerStore != null) elLowerStore.dispose(); 370 if (elLowerStore != null) elLowerStore.dispose();
377 if (trackingStore != null) trackingStore.dispose(); 371 if (trackingStore != null) trackingStore.dispose();
378 if(limitedSkolemUpperStore != null) limitedSkolemUpperStore.dispose(); 372
373// if(limitedSkolemUpperStore != null) limitedSkolemUpperStore.dispose();
379 super.dispose(); 374 super.dispose();
380 } 375 }
381 376
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java
index 64945e8..118c1b2 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java
@@ -147,7 +147,7 @@ PagodaProperties properties;
147 if (forFacetGeneration) { 147 if (forFacetGeneration) {
148 QueryRecord record = m_queryManager.create(queryText); 148 QueryRecord record = m_queryManager.create(queryText);
149 Utility.logInfo("---------- start evaluating upper bound for Query " + record.getQueryID() + " ----------", queryText); 149 Utility.logInfo("---------- start evaluating upper bound for Query " + record.getQueryID() + " ----------", queryText);
150 if(!record.processed()) 150 if(!record.isProcessed())
151 evaluateUpper(record); 151 evaluateUpper(record);
152// AnswerTuples tuples = record.getUpperBoundAnswers(); 152// AnswerTuples tuples = record.getUpperBoundAnswers();
153// for (AnswerTuple tuple; tuples.isValid(); tuples.moveNext()) { 153// for (AnswerTuple tuple; tuples.isValid(); tuples.moveNext()) {
@@ -167,7 +167,7 @@ PagodaProperties properties;
167 public AnswerTuples evaluate(String queryText) { 167 public AnswerTuples evaluate(String queryText) {
168 QueryRecord record = m_queryManager.create(queryText); 168 QueryRecord record = m_queryManager.create(queryText);
169 Utility.logInfo("---------- start evaluating Query " + record.getQueryID() + " ----------", queryText); 169 Utility.logInfo("---------- start evaluating Query " + record.getQueryID() + " ----------", queryText);
170 if(!record.processed()) 170 if(!record.isProcessed())
171 evaluate(record); 171 evaluate(record);
172 AnswerTuples answer = record.getAnswers(); 172 AnswerTuples answer = record.getAnswers();
173 record.dispose(); 173 record.dispose();
@@ -178,7 +178,7 @@ PagodaProperties properties;
178 public void evaluate_shell(String queryText) { 178 public void evaluate_shell(String queryText) {
179 QueryRecord record = m_queryManager.create(queryText); 179 QueryRecord record = m_queryManager.create(queryText);
180 Utility.logInfo("---------- start evaluating Query " + record.getQueryID() + " ----------", queryText); 180 Utility.logInfo("---------- start evaluating Query " + record.getQueryID() + " ----------", queryText);
181 if(!record.processed()) 181 if(!record.isProcessed())
182 evaluate(record); 182 evaluate(record);
183 Utility.logInfo("Answers to this query: ", record.outputSoundAnswerTuple()); 183 Utility.logInfo("Answers to this query: ", record.outputSoundAnswerTuple());
184 record.dispose(); 184 record.dispose();
@@ -206,12 +206,12 @@ PagodaProperties properties;
206// if (Integer.parseInt(record.getQueryID()) != 218) continue; 206// if (Integer.parseInt(record.getQueryID()) != 218) continue;
207 Utility.logInfo("---------- start evaluating Query " + record.getQueryID() + " ----------", 207 Utility.logInfo("---------- start evaluating Query " + record.getQueryID() + " ----------",
208 record.getQueryText()); 208 record.getQueryText());
209 if (!record.processed()) { 209 if(!record.isProcessed()) {
210 t.reset(); 210 t.reset();
211 if (!record.processed()) 211 if(!record.isProcessed())
212 evaluate(record); 212 evaluate(record);
213 Utility.logInfo("Total time to answer this query: " + t.duration()); 213 Utility.logInfo("Total time to answer this query: " + t.duration());
214 if (!fullReasoner && !record.processed()) { 214 if(!fullReasoner && !record.isProcessed()) {
215 Utility.logInfo("The query has not been fully answered in " + t.duration() + " seconds."); 215 Utility.logInfo("The query has not been fully answered in " + t.duration() + " seconds.");
216 continue; 216 continue;
217 } 217 }
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/RLUQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/RLUQueryReasoner.java
index bdef436..547140a 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/RLUQueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/RLUQueryReasoner.java
@@ -53,8 +53,8 @@ class RLUQueryReasoner extends QueryReasoner {
53 if (ans != null) ans.dispose(); 53 if (ans != null) ans.dispose();
54 } 54 }
55 queryRecord.addProcessingTime(Step.UPPER_BOUND, t.duration()); 55 queryRecord.addProcessingTime(Step.UPPER_BOUND, t.duration());
56 56
57 if (queryRecord.processed()) 57 if(queryRecord.isProcessed())
58 queryRecord.setDifficulty(Step.UPPER_BOUND); 58 queryRecord.setDifficulty(Step.UPPER_BOUND);
59 } 59 }
60 60
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 63773d9..61500f5 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxQueryEngine.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxQueryEngine.java
@@ -1,5 +1,7 @@
1package uk.ac.ox.cs.pagoda.reasoner.light; 1package uk.ac.ox.cs.pagoda.reasoner.light;
2 2
3import org.semanticweb.owlapi.model.OWLOntology;
4import org.semanticweb.owlapi.model.OWLOntologyCreationException;
3import uk.ac.ox.cs.JRDFox.JRDFStoreException; 5import uk.ac.ox.cs.JRDFox.JRDFStoreException;
4import uk.ac.ox.cs.JRDFox.Prefixes; 6import uk.ac.ox.cs.JRDFox.Prefixes;
5import uk.ac.ox.cs.JRDFox.store.DataStore; 7import uk.ac.ox.cs.JRDFox.store.DataStore;
@@ -18,32 +20,44 @@ import java.util.Collection;
18public abstract class RDFoxQueryEngine implements QueryEngine { 20public abstract class RDFoxQueryEngine implements QueryEngine {
19 21
20 public static final int matNoOfThreads = Runtime.getRuntime().availableProcessors() * 2; 22 public static final int matNoOfThreads = Runtime.getRuntime().availableProcessors() * 2;
21
22 public String getName() {
23 return name;
24 }
25
26 protected String name; 23 protected String name;
27 protected Prefixes prefixes = MyPrefixes.PAGOdAPrefixes.getRDFoxPrefixes(); 24 protected Prefixes prefixes = MyPrefixes.PAGOdAPrefixes.getRDFoxPrefixes();
28 25
29 public RDFoxQueryEngine(String name) { 26 public RDFoxQueryEngine(String name) {
30 this.name = name; 27 this.name = name;
31 } 28 }
32 29
33 public abstract DataStore getDataStore(); 30 public static DataStore createDataStore() {
31 DataStore instance = null;
32 try {
33// instance = new DataStore("par-head-n");
34 instance = new DataStore(StoreType.NarrowParallelHead);
35 instance.setNumberOfThreads(matNoOfThreads);
36 instance.initialize();
37 } catch(JRDFStoreException e) {
38 e.printStackTrace();
39 }
40 return instance;
41 }
34 42
35 public abstract void dispose(); 43 public String getName() {
44 return name;
45 }
36 46
47 public abstract DataStore getDataStore();
48
49 public abstract void dispose();
50
37 public void importRDFData(String fileName, String importedFile) { 51 public void importRDFData(String fileName, String importedFile) {
38 if (importedFile == null || importedFile.isEmpty()) return ; 52 if(importedFile == null || importedFile.isEmpty()) return;
39 Timer t = new Timer(); 53 Timer t = new Timer();
40 DataStore store = getDataStore(); 54 DataStore store = getDataStore();
41 try { 55 try {
42 long oldTripleCount = store.getTriplesCount(), tripleCount; 56 long oldTripleCount = store.getTriplesCount(), tripleCount;
43 for (String file: importedFile.split(QueryReasoner.ImportDataFileSeparator)) { 57 for (String file: importedFile.split(QueryReasoner.ImportDataFileSeparator)) {
44 store.importTurtleFile(new File(file), prefixes); 58 store.importTurtleFile(new File(file), prefixes);
45 } 59 }
46 tripleCount = store.getTriplesCount(); 60 tripleCount = store.getTriplesCount();
47 Utility.logDebug(name + " store after importing " + fileName + ": " + tripleCount + " (" + (tripleCount - oldTripleCount) + " new)"); 61 Utility.logDebug(name + " store after importing " + fileName + ": " + tripleCount + " (" + (tripleCount - oldTripleCount) + " new)");
48 store.clearRulesAndMakeFactsExplicit(); 62 store.clearRulesAndMakeFactsExplicit();
49 } catch (JRDFStoreException e) { 63 } catch (JRDFStoreException e) {
@@ -51,17 +65,32 @@ public abstract class RDFoxQueryEngine implements QueryEngine {
51 } 65 }
52 Utility.logDebug(name + " store finished importing " + fileName + " in " + t.duration() + " seconds."); 66 Utility.logDebug(name + " store finished importing " + fileName + " in " + t.duration() + " seconds.");
53 } 67 }
54 68
69 public void importDataFromABoxOf(OWLOntology ontology) {
70 DataStore store = getDataStore();
71 try {
72 long prevTriplesCount = store.getTriplesCount();
73 store.importOntology(ontology.getOWLOntologyManager().createOntology(ontology.getABoxAxioms(true)));
74 long loadedTriples = store.getTriplesCount() - prevTriplesCount;
75 Utility.logInfo(name + ": loaded " + loadedTriples + " triples from " + ontology.getABoxAxioms(true)
76 .size() + " ABox axioms");
77 } catch(JRDFStoreException | OWLOntologyCreationException e) {
78 e.printStackTrace();
79 System.exit(1);
80 }
81
82 }
83
55 public void materialise(String programName, String programText) { 84 public void materialise(String programName, String programText) {
56 if (programText == null) return ; 85 if(programText == null) return;
57 Timer t = new Timer(); 86 Timer t = new Timer();
58 DataStore store = getDataStore(); 87 DataStore store = getDataStore();
59 try { 88 try {
60 long oldTripleCount = store.getTriplesCount(), tripleCount; 89 long oldTripleCount = store.getTriplesCount(), tripleCount;
61// store.addRules(new String[] {programText}); 90// store.addRules(new String[] {programText});
62 store.importRules(programText); 91 store.importRules(programText);
63 store.applyReasoning(); 92 store.applyReasoning();
64 tripleCount = store.getTriplesCount(); 93 tripleCount = store.getTriplesCount();
65 Utility.logDebug(name + " store after materialising " + programName + ": " + tripleCount + " (" + (tripleCount - oldTripleCount) + " new)"); 94 Utility.logDebug(name + " store after materialising " + programName + ": " + tripleCount + " (" + (tripleCount - oldTripleCount) + " new)");
66 store.clearRulesAndMakeFactsExplicit(); 95 store.clearRulesAndMakeFactsExplicit();
67 } catch (JRDFStoreException e) { 96 } catch (JRDFStoreException e) {
@@ -74,17 +103,17 @@ public abstract class RDFoxQueryEngine implements QueryEngine {
74 public void evaluate(Collection<String> queryTexts, String answerFile) { 103 public void evaluate(Collection<String> queryTexts, String answerFile) {
75 if (queryTexts == null) 104 if (queryTexts == null)
76 return ; 105 return ;
77 106
78 int queryID = 0; 107 int queryID = 0;
79 AnswerTuplesWriter answerWriter = new AnswerTuplesWriter(answerFile); 108 AnswerTuplesWriter answerWriter = new AnswerTuplesWriter(answerFile);
80 AnswerTuples answerTuples; 109 AnswerTuples answerTuples;
81 Timer t = new Timer(); 110 Timer t = new Timer();
82 try { 111 try {
83 for (String query: queryTexts) { 112 for (String query: queryTexts) {
84 t.reset(); 113 t.reset();
85 answerTuples = null; 114 answerTuples = null;
86 try { 115 try {
87 answerTuples = evaluate(query); 116 answerTuples = evaluate(query);
88 Utility.logDebug("time to answer Query " + ++queryID + ": " + t.duration()); 117 Utility.logDebug("time to answer Query " + ++queryID + ": " + t.duration());
89 answerWriter.write(answerTuples.getAnswerVariables(), answerTuples); 118 answerWriter.write(answerTuples.getAnswerVariables(), answerTuples);
90 } finally { 119 } finally {
@@ -94,22 +123,9 @@ public abstract class RDFoxQueryEngine implements QueryEngine {
94 } finally { 123 } finally {
95 answerWriter.close(); 124 answerWriter.close();
96 } 125 }
97 126
98 Utility.logDebug("done computing query answers by RDFox."); 127 Utility.logDebug("done computing query answers by RDFox.");
99 128
100 }
101
102 public static DataStore createDataStore() {
103 DataStore instance = null;
104 try {
105// instance = new DataStore("par-head-n");
106 instance = new DataStore(StoreType.NarrowParallelHead);
107 instance.setNumberOfThreads(matNoOfThreads);
108 instance.initialize();
109 } catch (JRDFStoreException e) {
110 e.printStackTrace();
111 }
112 return instance;
113 } 129 }
114 130
115} 131}
generated by cgit v1.2.3 (git 2.25.1) at 2025-11-06 02:01:42 +0000