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authorFederico Igne <federico.igne@cs.ox.ac.uk>2022-05-10 18:17:06 +0100
committerFederico Igne <federico.igne@cs.ox.ac.uk>2022-05-11 12:34:47 +0100
commit17bd9beaf7f358a44e5bf36a5855fe6727d506dc (patch)
tree47e9310a0cff869d9ec017dcb2c81876407782c8 /src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
parent8651164cd632a5db310b457ce32d4fbc97bdc41c (diff)
downloadACQuA-17bd9beaf7f358a44e5bf36a5855fe6727d506dc.tar.gz
ACQuA-17bd9beaf7f358a44e5bf36a5855fe6727d506dc.zip
[pagoda] Move project to Scala
This commit includes a few changes: - The repository still uses Maven to manage dependency but it is now a Scala project. - The code has been ported from OWLAPI 3.4.10 to 5.1.20 - A proof of concept program using both RSAComb and PAGOdA has been added.
Diffstat (limited to 'src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java')
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1 files changed, 0 insertions, 472 deletions
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
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1package uk.ac.ox.cs.pagoda.reasoner;
2
3import org.semanticweb.karma2.profile.ELHOProfile;
4import org.semanticweb.owlapi.model.OWLOntology;
5import uk.ac.ox.cs.JRDFox.JRDFStoreException;
6import uk.ac.ox.cs.pagoda.multistage.MultiStageQueryEngine;
7import uk.ac.ox.cs.pagoda.owl.EqualitiesEliminator;
8import uk.ac.ox.cs.pagoda.owl.OWLHelper;
9import uk.ac.ox.cs.pagoda.query.AnswerTuples;
10import uk.ac.ox.cs.pagoda.query.GapByStore4ID;
11import uk.ac.ox.cs.pagoda.query.GapByStore4ID2;
12import uk.ac.ox.cs.pagoda.query.QueryRecord;
13import uk.ac.ox.cs.pagoda.query.QueryRecord.Step;
14import uk.ac.ox.cs.pagoda.reasoner.light.BasicQueryEngine;
15import uk.ac.ox.cs.pagoda.reasoner.light.KarmaQueryEngine;
16import uk.ac.ox.cs.pagoda.rules.DatalogProgram;
17import uk.ac.ox.cs.pagoda.summary.HermitSummaryFilter;
18import uk.ac.ox.cs.pagoda.tracking.QueryTracker;
19import uk.ac.ox.cs.pagoda.tracking.TrackingRuleEncoder;
20import uk.ac.ox.cs.pagoda.tracking.TrackingRuleEncoderDisjVar1;
21import uk.ac.ox.cs.pagoda.tracking.TrackingRuleEncoderWithGap;
22import uk.ac.ox.cs.pagoda.util.ExponentialInterpolation;
23import uk.ac.ox.cs.pagoda.util.PagodaProperties;
24import uk.ac.ox.cs.pagoda.util.Timer;
25import uk.ac.ox.cs.pagoda.util.Utility;
26import uk.ac.ox.cs.pagoda.util.disposable.DisposedException;
27import uk.ac.ox.cs.pagoda.util.tuples.Tuple;
28
29import java.util.Collection;
30import java.util.LinkedList;
31
32class MyQueryReasoner extends QueryReasoner {
33
34 OWLOntology ontology;
35 OWLOntology elho_ontology;
36 DatalogProgram program;
37
38 BasicQueryEngine rlLowerStore = null;
39 KarmaQueryEngine elLowerStore = null;
40 MultiStageQueryEngine lazyUpperStore = null;
41 MultiStageQueryEngine trackingStore = null;
42 TrackingRuleEncoder encoder;
43
44 private boolean equalityTag;
45 private Timer t = new Timer();
46
47 private Collection<String> predicatesWithGap = null;
48 private ConsistencyStatus isConsistent;
49 private ConsistencyManager consistency = new ConsistencyManager(this);
50// private int relevantOntologiesCounter = 0;
51
52 public MyQueryReasoner() {
53 setup(true);
54 }
55
56 public MyQueryReasoner(boolean multiStageTag, boolean considerEqualities) {
57 if(!multiStageTag)
58 throw new IllegalArgumentException(
59 "Value \"true\" for parameter \"multiStageTag\" is no longer supported");
60
61 setup(considerEqualities);
62 }
63
64 @Override
65 public void loadOntology(OWLOntology o) {
66 if(isDisposed()) throw new DisposedException();
67 if(!equalityTag) {
68 EqualitiesEliminator eliminator = new EqualitiesEliminator(o);
69 o = eliminator.getOutputOntology();
70 eliminator.save();
71 }
72
73 ontology = o;
74 program = new DatalogProgram(ontology);
75// program.getLower().save();
76// program.getUpper().save();
77 program.getGeneral().save();
78
79 if(!program.getGeneral().isHorn())
80 lazyUpperStore = new MultiStageQueryEngine("lazy-upper-bound", true);
81
82 importData(program.getAdditionalDataFile());
83
84 elho_ontology = new ELHOProfile().getFragment(ontology);
85 elLowerStore.processOntology(elho_ontology);
86 }
87
88 public Collection<String> getPredicatesWithGap() {
89 if(isDisposed()) throw new DisposedException();
90 return predicatesWithGap;
91 }
92
93 @Override
94 public boolean preprocess() {
95 if(isDisposed()) throw new DisposedException();
96
97 t.reset();
98 Utility.logInfo("Preprocessing (and checking satisfiability)...");
99
100 String name = "data", datafile = getImportedData();
101 rlLowerStore.importRDFData(name, datafile);
102 rlLowerStore.materialise("lower program", program.getLower().toString());
103// program.getLower().save();
104 if(!consistency.checkRLLowerBound()) {
105 Utility.logDebug("time for satisfiability checking: " + t.duration());
106 isConsistent = ConsistencyStatus.INCONSISTENT;
107 return false;
108 }
109 Utility.logDebug("The number of sameAs assertions in RL lower store: " + rlLowerStore.getSameAsNumber());
110
111 String originalMarkProgram = OWLHelper.getOriginalMarkProgram(ontology);
112
113 elLowerStore.importRDFData(name, datafile);
114 elLowerStore.materialise("saturate named individuals", originalMarkProgram);
115 elLowerStore.materialise("lower program", program.getLower().toString());
116 elLowerStore.initialiseKarma();
117 if(!consistency.checkELLowerBound()) {
118 Utility.logDebug("time for satisfiability checking: " + t.duration());
119 isConsistent = ConsistencyStatus.INCONSISTENT;
120 return false;
121 }
122
123 if(lazyUpperStore != null) {
124 lazyUpperStore.importRDFData(name, datafile);
125 lazyUpperStore.materialise("saturate named individuals", originalMarkProgram);
126 int tag = lazyUpperStore.materialiseRestrictedly(program, null);
127 if(tag == -1) {
128 Utility.logDebug("time for satisfiability checking: " + t.duration());
129 isConsistent = ConsistencyStatus.INCONSISTENT;
130 return false;
131 }
132 else if(tag != 1) {
133 lazyUpperStore.dispose();
134 lazyUpperStore = null;
135 }
136 }
137 if(consistency.checkUpper(lazyUpperStore)) {
138 isConsistent = ConsistencyStatus.CONSISTENT;
139 Utility.logDebug("time for satisfiability checking: " + t.duration());
140 }
141
142 trackingStore.importRDFData(name, datafile);
143 trackingStore.materialise("saturate named individuals", originalMarkProgram);
144
145// materialiseFullUpper();
146// GapByStore4ID gap = new GapByStore4ID(trackingStore);
147 GapByStore4ID gap = new GapByStore4ID2(trackingStore, rlLowerStore);
148 trackingStore.materialiseFoldedly(program, gap);
149 predicatesWithGap = gap.getPredicatesWithGap();
150 gap.clear();
151
152 if(program.getGeneral().isHorn())
153 encoder = new TrackingRuleEncoderWithGap(program.getUpper(), trackingStore);
154 else
155 encoder = new TrackingRuleEncoderDisjVar1(program.getUpper(), trackingStore);
156// encoder = new TrackingRuleEncoderDisj1(program.getUpper(), trackingStore);
157// encoder = new TrackingRuleEncoderDisjVar2(program.getUpper(), trackingStore);
158// encoder = new TrackingRuleEncoderDisj2(program.getUpper(), trackingStore);
159
160 // TODO? add consistency check by Skolem-upper-bound
161
162 if(!isConsistent())
163 return false;
164
165 consistency.extractBottomFragment();
166
167 return true;
168 }
169
170 @Override
171 public boolean isConsistent() {
172 if(isDisposed()) throw new DisposedException();
173
174 if(isConsistent == ConsistencyStatus.UNCHECKED) {
175 isConsistent = consistency.check() ? ConsistencyStatus.CONSISTENT : ConsistencyStatus.INCONSISTENT;
176 Utility.logDebug("time for satisfiability checking: " + t.duration());
177 }
178 if(isConsistent == ConsistencyStatus.CONSISTENT) {
179 Utility.logInfo("The ontology is consistent!");
180 return true;
181 }
182 else {
183 Utility.logInfo("The ontology is inconsistent!");
184 return false;
185 }
186 }
187
188 @Override
189 public void evaluate(QueryRecord queryRecord) {
190 if(isDisposed()) throw new DisposedException();
191
192 if(queryLowerAndUpperBounds(queryRecord))
193 return;
194
195 OWLOntology relevantOntologySubset = extractRelevantOntologySubset(queryRecord);
196
197// queryRecord.saveRelevantOntology("/home/alessandro/Desktop/test-relevant-ontology-"+relevantOntologiesCounter+".owl");
198// relevantOntologiesCounter++;
199
200 if(properties.getSkolemUpperBound() == PagodaProperties.SkolemUpperBoundOptions.BEFORE_SUMMARISATION
201 && querySkolemisedRelevantSubset(relevantOntologySubset, queryRecord)) {
202 return;
203 }
204
205 Utility.logInfo(">> Summarisation <<");
206 HermitSummaryFilter summarisedChecker = new HermitSummaryFilter(queryRecord, properties.getToCallHermiT());
207 if(summarisedChecker.check(queryRecord.getGapAnswers()) == 0) {
208 summarisedChecker.dispose();
209 return;
210 }
211
212 if(properties.getSkolemUpperBound() == PagodaProperties.SkolemUpperBoundOptions.AFTER_SUMMARISATION
213 && querySkolemisedRelevantSubset(relevantOntologySubset, queryRecord)) {
214 summarisedChecker.dispose();
215 return;
216 }
217
218 Utility.logInfo(">> Full reasoning <<");
219 Timer t = new Timer();
220 summarisedChecker.checkByFullReasoner(queryRecord.getGapAnswers());
221 Utility.logDebug("Total time for full reasoner: " + t.duration());
222
223 if(properties.getToCallHermiT())
224 queryRecord.markAsProcessed();
225 summarisedChecker.dispose();
226 }
227
228 @Override
229 public void evaluateUpper(QueryRecord queryRecord) {
230 if(isDisposed()) throw new DisposedException();
231 // TODO? add new upper store
232 AnswerTuples rlAnswer = null;
233 boolean useFull = queryRecord.isBottom() || lazyUpperStore == null;
234 try {
235 rlAnswer =
236 (useFull ? trackingStore : lazyUpperStore).evaluate(queryRecord.getQueryText(), queryRecord.getAnswerVariables());
237 queryRecord.updateUpperBoundAnswers(rlAnswer, true);
238 } finally {
239 if(rlAnswer != null) rlAnswer.dispose();
240 }
241 }
242
243 @Override
244 public void dispose() {
245 super.dispose();
246
247 if(encoder != null) encoder.dispose();
248 if(rlLowerStore != null) rlLowerStore.dispose();
249 if(lazyUpperStore != null) lazyUpperStore.dispose();
250 if(elLowerStore != null) elLowerStore.dispose();
251 if(trackingStore != null) trackingStore.dispose();
252 if(consistency != null) consistency.dispose();
253 if(program != null) program.dispose();
254 }
255
256 private void setup(boolean considerEqualities) {
257 if(isDisposed()) throw new DisposedException();
258
259 isConsistent = ConsistencyStatus.UNCHECKED;
260 this.equalityTag = considerEqualities;
261
262 rlLowerStore = new BasicQueryEngine("rl-lower-bound");
263 elLowerStore = new KarmaQueryEngine("elho-lower-bound");
264
265 trackingStore = new MultiStageQueryEngine("tracking", false);
266 }
267
268 protected void internal_importDataFile(String name, String datafile) {
269// addDataFile(datafile);
270 rlLowerStore.importRDFData(name, datafile);
271 if(lazyUpperStore != null)
272 lazyUpperStore.importRDFData(name, datafile);
273 elLowerStore.importRDFData(name, datafile);
274 trackingStore.importRDFData(name, datafile);
275 }
276
277 /**
278 * It deals with blanks nodes differently from variables
279 * according to SPARQL semantics for OWL2 Entailment Regime.
280 * <p>
281 * In particular variables are matched only against named individuals,
282 * and blank nodes against named and anonymous individuals.
283 */
284 private boolean queryUpperStore(BasicQueryEngine upperStore, QueryRecord queryRecord,
285 Tuple<String> extendedQuery, Step step) {
286 t.reset();
287
288 Utility.logDebug("First query type");
289 queryUpperBound(upperStore, queryRecord, queryRecord.getQueryText(), queryRecord.getAnswerVariables());
290 if(!queryRecord.isProcessed() && !queryRecord.getQueryText().equals(extendedQuery.get(0))) {
291 Utility.logDebug("Second query type");
292 queryUpperBound(upperStore, queryRecord, extendedQuery.get(0), queryRecord.getAnswerVariables());
293 }
294 if(!queryRecord.isProcessed() && queryRecord.hasNonAnsDistinguishedVariables()) {
295 Utility.logDebug("Third query type");
296 queryUpperBound(upperStore, queryRecord, extendedQuery.get(1), queryRecord.getDistinguishedVariables());
297 }
298
299 queryRecord.addProcessingTime(step, t.duration());
300 if(queryRecord.isProcessed()) {
301 queryRecord.setDifficulty(step);
302 return true;
303 }
304 return false;
305 }
306
307 /**
308 * Returns the part of the ontology relevant for Hermit, while computing the bound answers.
309 */
310 private boolean queryLowerAndUpperBounds(QueryRecord queryRecord) {
311
312 Utility.logInfo(">> Base bounds <<");
313
314 AnswerTuples rlAnswer = null, elAnswer = null;
315
316 t.reset();
317 try {
318 rlAnswer = rlLowerStore.evaluate(queryRecord.getQueryText(), queryRecord.getAnswerVariables());
319 Utility.logDebug(t.duration());
320 queryRecord.updateLowerBoundAnswers(rlAnswer);
321 } finally {
322 if(rlAnswer != null) rlAnswer.dispose();
323 }
324 queryRecord.addProcessingTime(Step.LOWER_BOUND, t.duration());
325
326 Tuple<String> extendedQueryTexts = queryRecord.getExtendedQueryText();
327
328 if(properties.getUseAlwaysSimpleUpperBound() || lazyUpperStore == null) {
329 Utility.logDebug("Tracking store");
330 if(queryUpperStore(trackingStore, queryRecord, extendedQueryTexts, Step.SIMPLE_UPPER_BOUND))
331 return true;
332 }
333
334 if(!queryRecord.isBottom()) {
335 Utility.logDebug("Lazy store");
336 if(lazyUpperStore != null && queryUpperStore(lazyUpperStore, queryRecord, extendedQueryTexts, Step.LAZY_UPPER_BOUND))
337 return true;
338 }
339
340 t.reset();
341 try {
342 elAnswer = elLowerStore.evaluate(extendedQueryTexts.get(0),
343 queryRecord.getAnswerVariables(),
344 queryRecord.getLowerBoundAnswers());
345 Utility.logDebug(t.duration());
346 queryRecord.updateLowerBoundAnswers(elAnswer);
347 } finally {
348 if(elAnswer != null) elAnswer.dispose();
349 }
350 queryRecord.addProcessingTime(Step.EL_LOWER_BOUND, t.duration());
351
352 if(queryRecord.isProcessed()) {
353 queryRecord.setDifficulty(Step.EL_LOWER_BOUND);
354 return true;
355 }
356
357 return false;
358 }
359
360 private OWLOntology extractRelevantOntologySubset(QueryRecord queryRecord) {
361 Utility.logInfo(">> Relevant ontology-subset extraction <<");
362
363 t.reset();
364
365 QueryTracker tracker = new QueryTracker(encoder, rlLowerStore, queryRecord);
366 OWLOntology relevantOntologySubset = tracker.extract(trackingStore, consistency.getQueryRecords(), true);
367
368 queryRecord.addProcessingTime(Step.FRAGMENT, t.duration());
369
370 int numOfABoxAxioms = relevantOntologySubset.getABoxAxioms(true).size();
371 int numOfTBoxAxioms = relevantOntologySubset.getAxiomCount() - numOfABoxAxioms;
372 Utility.logInfo("Relevant ontology-subset has been extracted: |ABox|="
373 + numOfABoxAxioms + ", |TBox|=" + numOfTBoxAxioms);
374
375 return relevantOntologySubset;
376 }
377
378 private void queryUpperBound(BasicQueryEngine upperStore, QueryRecord queryRecord, String queryText, String[] answerVariables) {
379 AnswerTuples rlAnswer = null;
380 try {
381 Utility.logDebug(queryText);
382 rlAnswer = upperStore.evaluate(queryText, answerVariables);
383 Utility.logDebug(t.duration());
384 queryRecord.updateUpperBoundAnswers(rlAnswer);
385 } finally {
386 if(rlAnswer != null) rlAnswer.dispose();
387 }
388 }
389
390 private boolean querySkolemisedRelevantSubset(OWLOntology relevantSubset, QueryRecord queryRecord) {
391 Utility.logInfo(">> Semi-Skolemisation <<");
392 t.reset();
393
394 DatalogProgram relevantProgram = new DatalogProgram(relevantSubset);
395
396 MultiStageQueryEngine relevantStore =
397 new MultiStageQueryEngine("Relevant-store", true); // checkValidity is true
398
399 relevantStore.importDataFromABoxOf(relevantSubset);
400 String relevantOriginalMarkProgram = OWLHelper.getOriginalMarkProgram(relevantSubset);
401
402 relevantStore.materialise("Mark original individuals", relevantOriginalMarkProgram);
403
404 boolean isFullyProcessed = false;
405 LinkedList<Tuple<Long>> lastTwoTriplesCounts = new LinkedList<>();
406 for (int currentMaxTermDepth = 1; !isFullyProcessed; currentMaxTermDepth++) {
407
408 if(currentMaxTermDepth > properties.getSkolemDepth()) {
409 Utility.logInfo("Maximum term depth reached");
410 break;
411 }
412
413 if(lastTwoTriplesCounts.size() == 2) {
414 if(lastTwoTriplesCounts.get(0).get(1).equals(lastTwoTriplesCounts.get(1).get(1)))
415 break;
416
417 ExponentialInterpolation interpolation = new ExponentialInterpolation(lastTwoTriplesCounts.get(0).get(0),
418 lastTwoTriplesCounts.get(0).get(1),
419 lastTwoTriplesCounts.get(1).get(0),
420 lastTwoTriplesCounts.get(1).get(1));
421 double triplesEstimate = interpolation.computeValue(currentMaxTermDepth);
422
423 Utility.logDebug("Estimate of the number of triples:" + triplesEstimate);
424
425 // exit condition if the query is not fully answered
426 if(triplesEstimate > properties.getMaxTriplesInSkolemStore()) {
427 Utility.logInfo("Interrupting Semi-Skolemisation because of triples count limit");
428 break;
429 }
430 }
431
432 Utility.logInfo("Trying with maximum depth " + currentMaxTermDepth);
433
434 int materialisationTag = relevantStore.materialiseSkolemly(relevantProgram, null,
435 currentMaxTermDepth);
436 queryRecord.addProcessingTime(Step.SKOLEM_UPPER_BOUND, t.duration());
437 if(materialisationTag == -1) {
438 relevantStore.dispose();
439 throw new Error("A consistent ontology has turned out to be " +
440 "inconsistent in the Skolemises-relevant-upper-store");
441 }
442 else if(materialisationTag != 1) {
443 Utility.logInfo("Semi-Skolemised relevant upper store cannot be employed");
444 break;
445 }
446
447 Utility.logInfo("Querying semi-Skolemised upper store...");
448 isFullyProcessed = queryUpperStore(relevantStore, queryRecord,
449 queryRecord.getExtendedQueryText(),
450 Step.SKOLEM_UPPER_BOUND);
451
452 try {
453 lastTwoTriplesCounts.add
454 (new Tuple<>((long) currentMaxTermDepth, relevantStore.getStoreSize()));
455 } catch (JRDFStoreException e) {
456 e.printStackTrace();
457 break;
458 }
459 if(lastTwoTriplesCounts.size() > 2)
460 lastTwoTriplesCounts.remove();
461
462 Utility.logDebug("Last two triples counts:" + lastTwoTriplesCounts);
463 }
464
465 relevantStore.dispose();
466 Utility.logInfo("Semi-Skolemised relevant upper store has been evaluated");
467 return isFullyProcessed;
468 }
469
470 private enum ConsistencyStatus {CONSISTENT, INCONSISTENT, UNCHECKED}
471
472}
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