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15 package ubic.basecode.ontology.model;
16
17 import java.util.Collection;
18 import java.util.HashSet;
19 import java.util.Set;
20
21 import org.apache.commons.lang3.ObjectUtils;
22
23 import com.hp.hpl.jena.ontology.AllValuesFromRestriction;
24 import com.hp.hpl.jena.ontology.ConversionException;
25 import com.hp.hpl.jena.ontology.Individual;
26 import com.hp.hpl.jena.ontology.OntClass;
27 import com.hp.hpl.jena.ontology.OntProperty;
28 import com.hp.hpl.jena.ontology.OntResource;
29 import com.hp.hpl.jena.ontology.Restriction;
30 import com.hp.hpl.jena.ontology.SomeValuesFromRestriction;
31 import com.hp.hpl.jena.rdf.model.Property;
32 import com.hp.hpl.jena.rdf.model.RDFNode;
33 import com.hp.hpl.jena.rdf.model.Resource;
34 import com.hp.hpl.jena.rdf.model.ResourceFactory;
35 import com.hp.hpl.jena.rdf.model.Statement;
36 import com.hp.hpl.jena.rdf.model.StmtIterator;
37 import com.hp.hpl.jena.util.iterator.ExtendedIterator;
38
39
40
41
42
43
44 public class OntologyTermImpl extends AbstractOntologyResource implements OntologyTerm {
45
46 private static final String HAS_ALTERNATE_ID = "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId";
47 private static final String NOTHING = "http://www.w3.org/2002/07/owl#Nothing";
48 private static Set<String> REJECT_PARENT_URI = new HashSet<>();
49
50
51
52
53 private static final long serialVersionUID = 1L;
54
55
56
57
58 private static final boolean USE_PROPER_PART_RESTRICTIONS = true;
59 static {
60 REJECT_PARENT_URI.add( "http://www.ifomis.org/bfo/1.1/snap#IndependentContinuant" );
61 REJECT_PARENT_URI.add( "http://www.ifomis.org/bfo/1.1/snap#Continuant" );
62 REJECT_PARENT_URI.add( "http://www.ifomis.org/bfo/1.1/snap#MaterialEntity" );
63
64
65 REJECT_PARENT_URI.add( "http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl#birnlex_6" );
66 }
67
68 private String label = null;
69 private String localName = null;
70
71 private transient OntClass ontResource = null;
72
73 public OntologyTermImpl( OntClass resource ) {
74 this.ontResource = resource;
75 if ( ontResource != null ) {
76 this.label = ontResource.getLabel( "EN" );
77 if ( this.label == null ) this.label = ontResource.getLabel( null );
78 this.localName = ontResource.getLocalName();
79 }
80 }
81
82 @Override
83 public boolean equals( Object obj ) {
84 if ( this == obj ) return true;
85
86 if ( !super.equals( obj ) ) return false;
87 if ( getClass() != obj.getClass() ) return false;
88
89 final OntologyTermImpl that = ( OntologyTermImpl ) obj;
90 if ( this.getUri() != null ) {
91 return ObjectUtils.equals( this.getUri(), that.getUri() );
92 }
93 return ObjectUtils.equals( this.getTerm(), that.getTerm() );
94 }
95
96 @Override
97 public Collection<String> getAlternativeIds() {
98 Collection<String> results = new HashSet<>();
99
100 Property alternate = ResourceFactory.createProperty( HAS_ALTERNATE_ID );
101 for ( StmtIterator it = this.ontResource.listProperties( alternate ); it.hasNext(); ) {
102 Statement statement = it.next();
103 results.add( statement.asTriple().getMatchObject().getLiteralLexicalForm() );
104 }
105
106 return results;
107
108 }
109
110 @Override
111 public Collection<AnnotationProperty> getAnnotations() {
112 Collection<AnnotationProperty> annots = new HashSet<>();
113 StmtIterator iterator = ontResource.listProperties();
114
115 while ( iterator.hasNext() ) {
116 Statement state = iterator.next();
117 OntResource res = state.getPredicate().as( OntResource.class );
118 if ( res.isAnnotationProperty() ) {
119 com.hp.hpl.jena.ontology.AnnotationProperty p = res.asAnnotationProperty();
120 RDFNode n = state.getObject();
121 annots.add( new AnnotationPropertyImpl( p, n ) );
122 }
123 }
124 return annots;
125 }
126
127 @Override
128 public Collection<OntologyTerm> getChildren( boolean direct ) {
129 Collection<OntologyTerm> result = new HashSet<>();
130 getChildren( direct, result );
131 return result;
132 }
133
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137
138
139 @Override
140 public String getComment() {
141 String comment = this.ontResource.getComment( null );
142 return comment == null ? "" : comment;
143 }
144
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148
149
150 @Override
151 public Collection<OntologyIndividual> getIndividuals() {
152 return getIndividuals( true );
153 }
154
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158
159 @Override
160 public Collection<OntologyIndividual> getIndividuals( boolean direct ) {
161 Collection<OntologyIndividual> inds = new HashSet<>();
162 ExtendedIterator<? extends OntResource> iterator = this.ontResource.listInstances( direct );
163 while ( iterator.hasNext() ) {
164 Individual i = ( Individual ) iterator.next();
165 inds.add( new OntologyIndividualImpl( i ) );
166 }
167 return inds;
168 }
169
170 @Override
171 public String getLabel() {
172 return label;
173 }
174
175 @Override
176 public String getLocalName() {
177 return this.localName;
178 }
179
180 @Override
181 public Object getModel() {
182 return ontResource.getModel();
183 }
184
185 @Override
186 public Collection<OntologyTerm> getParents( boolean direct ) {
187 Collection<OntologyTerm> result = new HashSet<>();
188 this.getParents( direct, result );
189 return result;
190 }
191
192
193
194
195 @Override
196 public Collection<OntologyRestriction> getRestrictions() {
197
198
199
200 Collection<OntologyRestriction> result = new HashSet<>();
201 ExtendedIterator<OntClass> iterator = ontResource.listSuperClasses( false );
202 while ( iterator.hasNext() ) {
203 OntClass c = iterator.next();
204 Restriction r = null;
205 try {
206 r = c.asRestriction();
207 result.add( RestrictionFactory.asRestriction( r ) );
208 } catch ( Exception e ) {
209
210 }
211
212 }
213
214
215 iterator = ontResource.listSuperClasses( false );
216 while ( iterator.hasNext() ) {
217 OntClass c = iterator.next();
218
219 try {
220 c.asRestriction();
221 } catch ( Exception e ) {
222
223 ExtendedIterator<OntClass> supClassesIt = c.listSuperClasses( false );
224 loop: while ( supClassesIt.hasNext() ) {
225 OntClass sc = supClassesIt.next();
226 Restriction sr = null;
227 try {
228 sr = sc.asRestriction();
229
230
231 OntologyRestriction candidateRestriction = RestrictionFactory.asRestriction( sr );
232 for ( OntologyRestriction restr : result ) {
233 if ( restr.getRestrictionOn().equals( candidateRestriction.getRestrictionOn() ) )
234 continue loop;
235 }
236 result.add( candidateRestriction );
237
238 } catch ( Exception ex ) {
239
240 }
241 }
242 }
243
244 }
245
246 return result;
247 }
248
249
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251
252
253
254 @Override
255 public String getTerm() {
256 String res = null;
257 if ( this.label != null ) {
258 res = this.label;
259 } else if ( this.localName != null ) {
260 res = localName;
261 } else if ( this.getUri() != null ) {
262 res = this.getUri();
263 } else {
264 res = ontResource.toString();
265 }
266 return res;
267 }
268
269 @Override
270 public String getUri() {
271 return this.ontResource.getURI();
272 }
273
274 @Override
275 public int hashCode() {
276 if ( ontResource == null ) {
277 log.warn( "ontResource is null in hashCode()" );
278 return 0;
279 }
280
281 if ( this.getUri() != null ) {
282 return this.getUri().hashCode();
283 }
284 return this.getTerm().hashCode();
285 }
286
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290
291
292 @Override
293 public boolean isRoot() {
294 return !this.ontResource.listSuperClasses( true ).hasNext();
295 }
296
297
298
299
300
301
302 @Override
303 public boolean isTermObsolete() {
304
305 Collection<OntologyTerm> parentsOntologyTerm = getParents( false );
306
307
308
309
310 for ( OntologyTerm parentOntologyTerm : parentsOntologyTerm ) {
311
312 if ( parentOntologyTerm.getLocalName() != null
313 && parentOntologyTerm.getLocalName().equalsIgnoreCase( "ObsoleteClass" ) ) {
314 return true;
315 }
316
317
318 if ( parentOntologyTerm.getUri() == null ) {
319
320 continue;
321 }
322
323 if ( parentOntologyTerm.getUri() != null
324 && parentOntologyTerm.getUri().equalsIgnoreCase(
325 "http://bioontology.org/projects/ontologies/birnlex#_birnlex_retired_class" )
326 || parentOntologyTerm
327 .getUri()
328 .equalsIgnoreCase(
329 "http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#_birnlex_retired_class" ) ) {
330 return true;
331 }
332 }
333
334
335 StmtIterator iterator = ontResource.listProperties();
336
337 while ( iterator.hasNext() ) {
338 Statement state = iterator.next();
339 if ( state.getPredicate() == null ) continue;
340 OntResource res = state.getPredicate().as( OntResource.class );
341 if ( res.isAnnotationProperty() ) {
342 com.hp.hpl.jena.ontology.AnnotationProperty p = res.asAnnotationProperty();
343 RDFNode n = state.getObject();
344
345 if ( p.getLocalName().equalsIgnoreCase( "deprecated" ) ) {
346 if ( n.toString().indexOf( "true" ) != -1 ) {
347 return true;
348 }
349 break;
350 }
351 }
352 }
353 return false;
354 }
355
356 @Override
357 public String toString() {
358 String res = null;
359 if ( this.getTerm() != null ) {
360 res = this.getTerm();
361 if ( this.localName != null && !this.getTerm().equals( this.localName ) ) {
362 res = res + " [" + this.localName + "]";
363 }
364 } else if ( this.localName != null ) {
365 res = localName;
366 } else if ( this.getUri() != null ) {
367 res = this.getUri();
368 } else {
369 res = ontResource.toString();
370 }
371 return res;
372 }
373
374 protected OntologyTerm fromOntClass( OntClass ontClass ) {
375 return new OntologyTermImpl( ontClass );
376 }
377
378
379
380
381
382 private void getChildren( boolean direct, Collection<OntologyTerm> work ) {
383
384
385 ExtendedIterator<OntClass> iterator = ontResource.listSubClasses( true );
386 while ( iterator.hasNext() ) {
387 OntClass c = iterator.next();
388
389
390 if ( c.getURI() == null || c.getURI().equals( NOTHING ) ) continue;
391
392 if ( USE_PROPER_PART_RESTRICTIONS && c.isRestriction() ) {
393
394 Restriction restriction = c.asRestriction();
395
396 OntProperty onProperty = restriction.getOnProperty();
397
398 if ( !onProperty.getURI().equals( "http://www.obofoundry.org/ro/ro.owl#has_proper_part" ) ) {
399 continue;
400 }
401
402 Resource r = getRestrictionValue( restriction );
403 if ( r == null ) continue;
404
405 OntologyTerm child = fromOntClass( ( OntClass ) r );
406
407
408 if ( !work.contains( child ) ) {
409 work.add( child );
410 if ( !direct ) ( ( OntologyTermImpl ) child ).getChildren( false, work );
411 }
412 } else {
413 OntologyTerm child = this.fromOntClass( c );
414 work.add( child );
415 if ( !direct ) ( ( OntologyTermImpl ) child ).getChildren( false, work );
416 }
417
418 }
419
420 if ( USE_PROPER_PART_RESTRICTIONS ) {
421 ExtendedIterator<OntClass> sciterator = this.ontResource.listSuperClasses( true );
422 while ( sciterator.hasNext() ) {
423 OntClass c = sciterator.next();
424 if ( !c.isRestriction() ) {
425 continue;
426 }
427
428 Restriction restriction = c.asRestriction();
429
430 try {
431 OntProperty onProperty = restriction.getOnProperty();
432 if ( !onProperty.getURI().equals( "http://www.obofoundry.org/ro/ro.owl#has_proper_part" ) ) {
433 continue;
434 }
435 } catch ( ConversionException e ) {
436 continue;
437 }
438
439 Resource r = getRestrictionValue( restriction );
440 if ( r == null ) continue;
441
442
443
444
445
446
447
448 OntologyTerm child = fromOntClass( ( OntClass ) r );
449 if ( !work.contains( child ) ) {
450 work.add( child );
451 if ( !direct ) ( ( OntologyTermImpl ) child ).getChildren( false, work );
452 }
453
454 }
455 }
456 }
457
458
459
460
461
462 private void getParents( boolean direct, Collection<OntologyTerm> work ) {
463 assert work != null;
464 if ( !ontResource.isClass() ) {
465 return;
466 }
467
468 ExtendedIterator<OntClass> iterator = ontResource.listSuperClasses( true );
469
470 while ( iterator.hasNext() ) {
471
472 try {
473 OntClass c = iterator.next();
474
475 if ( USE_PROPER_PART_RESTRICTIONS && c.isRestriction() ) {
476 Restriction restriction = c.asRestriction();
477
478 OntProperty onProperty = restriction.getOnProperty();
479
480 assert onProperty != null;
481
482
483 if ( !onProperty.getURI().equals( "http://www.obofoundry.org/ro/ro.owl#proper_part_of" ) ) {
484 continue;
485 }
486
487 Resource r = getRestrictionValue( restriction );
488
489 if ( r == null ) continue;
490
491 assert r != null;
492 if ( log.isDebugEnabled() ) log.debug( " Some from:" + r + " " + onProperty.getURI() );
493
494 OntologyTerm parent = fromOntClass( ( OntClass ) r );
495
496 if ( REJECT_PARENT_URI.contains( parent.getUri() ) ) continue;
497
498
499 if ( !work.contains( parent ) ) {
500 work.add( parent );
501 if ( !direct ) ( ( OntologyTermImpl ) parent ).getParents( direct, work );
502 }
503
504 } else {
505
506 OntologyTerm parent = this.fromOntClass( c );
507
508 if ( REJECT_PARENT_URI.contains( parent.getUri() ) ) continue;
509
510 if ( !work.contains( parent ) ) {
511 work.add( parent );
512 if ( !direct ) {
513
514 ( ( OntologyTermImpl ) parent ).getParents( direct, work );
515 }
516 }
517 }
518 } catch ( ConversionException e ) {
519 if ( log.isDebugEnabled() ) log.debug( e.getMessage() );
520 continue;
521 }
522
523 }
524 }
525
526 private Resource getRestrictionValue( Restriction restriction ) {
527 Resource r = null;
528
529 if ( restriction.isSomeValuesFromRestriction() ) {
530 SomeValuesFromRestriction some = restriction.asSomeValuesFromRestriction();
531 r = some.getSomeValuesFrom();
532 } else if ( restriction.isAllValuesFromRestriction() ) {
533 AllValuesFromRestriction allValues = restriction.asAllValuesFromRestriction();
534 r = allValues.getAllValuesFrom();
535 }
536 return r;
537 }
538
539 }