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Add support for OWL micro, mini and full reasoners
Add LanguageLevel so that one can configure the level of OWL supported. Remove unused getSpec() in AbstractOntologyService.
1 parent b796fc0 commit f6b3dd2

5 files changed

Lines changed: 111 additions & 26 deletions

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‎src/ubic/basecode/ontology/jena/AbstractOntologyMemoryBackedService.java‎

Lines changed: 41 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -15,6 +15,13 @@
1515
package ubic.basecode.ontology.jena;
1616

1717
import com.hp.hpl.jena.ontology.OntModelSpec;
18+
import com.hp.hpl.jena.ontology.ProfileRegistry;
19+
import com.hp.hpl.jena.rdf.model.ModelFactory;
20+
import com.hp.hpl.jena.reasoner.ReasonerFactory;
21+
import com.hp.hpl.jena.reasoner.rulesys.OWLFBRuleReasonerFactory;
22+
import com.hp.hpl.jena.reasoner.rulesys.OWLMicroReasonerFactory;
23+
import com.hp.hpl.jena.reasoner.rulesys.OWLMiniReasonerFactory;
24+
import com.hp.hpl.jena.reasoner.transitiveReasoner.TransitiveReasonerFactory;
1825
import ubic.basecode.ontology.model.OntologyModel;
1926
import ubic.basecode.util.Configuration;
2027

@@ -35,23 +42,50 @@ protected String getOntologyUrl() {
3542
}
3643

3744
@Override
38-
protected OntologyModel loadModel( boolean processImports, InferenceMode inferenceMode ) throws IOException {
39-
return new OntologyModelImpl( OntologyLoader.loadMemoryModel( this.getOntologyUrl(), this.getCacheName(), processImports, this.getSpec( inferenceMode ) ) );
45+
protected OntologyModel loadModel( boolean processImports, LanguageLevel languageLevel, InferenceMode inferenceMode ) throws IOException {
46+
return new OntologyModelImpl( OntologyLoader.loadMemoryModel( this.getOntologyUrl(), this.getCacheName(), processImports, this.getSpec( languageLevel, inferenceMode ) ) );
4047
}
4148

4249
@Override
43-
protected OntologyModel loadModelFromStream( InputStream is, boolean processImports, InferenceMode inferenceMode ) throws IOException {
44-
return new OntologyModelImpl( OntologyLoader.loadMemoryModel( is, this.getOntologyUrl(), processImports, this.getSpec( inferenceMode ) ) );
50+
protected OntologyModel loadModelFromStream( InputStream is, boolean processImports, LanguageLevel languageLevel, InferenceMode inferenceMode ) throws IOException {
51+
return new OntologyModelImpl( OntologyLoader.loadMemoryModel( is, this.getOntologyUrl(), processImports, this.getSpec( languageLevel, inferenceMode ) ) );
4552
}
4653

47-
private OntModelSpec getSpec( InferenceMode inferenceMode ) {
54+
private OntModelSpec getSpec( LanguageLevel languageLevel, InferenceMode inferenceMode ) {
55+
String profile;
56+
switch ( languageLevel ) {
57+
case FULL:
58+
profile = ProfileRegistry.OWL_LANG;
59+
break;
60+
case DL:
61+
profile = ProfileRegistry.OWL_DL_LANG;
62+
break;
63+
case LITE:
64+
profile = ProfileRegistry.OWL_LITE_LANG;
65+
break;
66+
default:
67+
throw new UnsupportedOperationException( String.format( "Unsupported OWL language level %s.", languageLevel ) );
68+
}
69+
ReasonerFactory reasonerFactory;
4870
switch ( inferenceMode ) {
71+
case FULL:
72+
reasonerFactory = OWLFBRuleReasonerFactory.theInstance();
73+
break;
74+
case MINI:
75+
reasonerFactory = OWLMiniReasonerFactory.theInstance();
76+
break;
77+
case MICRO:
78+
reasonerFactory = OWLMicroReasonerFactory.theInstance();
79+
break;
4980
case TRANSITIVE:
50-
return OntModelSpec.OWL_MEM_TRANS_INF;
81+
reasonerFactory = TransitiveReasonerFactory.theInstance();
82+
break;
5183
case NONE:
52-
return OntModelSpec.OWL_MEM;
84+
reasonerFactory = null;
85+
break;
5386
default:
5487
throw new UnsupportedOperationException( String.format( "Unsupported inference level %s.", inferenceMode ) );
5588
}
89+
return new OntModelSpec( ModelFactory.createMemModelMaker(), null, reasonerFactory, profile );
5690
}
5791
}

‎src/ubic/basecode/ontology/jena/AbstractOntologyService.java‎

Lines changed: 24 additions & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -74,6 +74,7 @@ public abstract class AbstractOntologyService implements OntologyService {
7474
}
7575

7676
/* settings (applicable for next initialization) */
77+
private LanguageLevel nextLanguageLevel = LanguageLevel.FULL;
7778
private InferenceMode nextInferenceMode = InferenceMode.TRANSITIVE;
7879
private boolean nextProcessImports = true;
7980
private boolean nextSearchEnabled = true;
@@ -91,12 +92,30 @@ public abstract class AbstractOntologyService implements OntologyService {
9192
private Set<Restriction> additionalRestrictions;
9293
private boolean isInitialized = false;
9394
@Nullable
95+
private LanguageLevel languageLevel = null;
96+
@Nullable
9497
private InferenceMode inferenceMode = null;
9598
@Nullable
9699
private Boolean processImports = null;
97100
@Nullable
98101
private Boolean searchEnabled = null;
99102

103+
@Override
104+
public LanguageLevel getLanguageLevel() {
105+
Lock lock = rwLock.readLock();
106+
try {
107+
lock.lock();
108+
return this.languageLevel != null ? this.languageLevel : nextLanguageLevel;
109+
} finally {
110+
lock.unlock();
111+
}
112+
}
113+
114+
@Override
115+
public void setLanguageLevel( LanguageLevel languageLevel ) {
116+
this.nextLanguageLevel = languageLevel;
117+
}
118+
100119
@Override
101120
public InferenceMode getInferenceMode() {
102121
Lock lock = rwLock.readLock();
@@ -162,6 +181,7 @@ private void initialize( @Nullable InputStream stream, boolean forceLoad, boolea
162181
String ontologyUrl = getOntologyUrl();
163182
String ontologyName = getOntologyName();
164183
String cacheName = getCacheName();
184+
LanguageLevel languageLevel = nextLanguageLevel;
165185
InferenceMode inferenceMode = nextInferenceMode;
166186
boolean processImports = nextProcessImports;
167187
boolean searchEnabled = nextSearchEnabled;
@@ -196,7 +216,7 @@ private void initialize( @Nullable InputStream stream, boolean forceLoad, boolea
196216
return;
197217

198218
try {
199-
OntologyModel m = stream != null ? loadModelFromStream( stream, processImports, inferenceMode ) : loadModel( processImports, inferenceMode ); // can take a while.
219+
OntologyModel m = stream != null ? loadModelFromStream( stream, processImports, languageLevel, inferenceMode ) : loadModel( processImports, languageLevel, inferenceMode ); // can take a while.
200220
if ( m instanceof OntologyModelImpl ) {
201221
model = ( ( OntologyModelImpl ) m ).getOntModel();
202222
} else {
@@ -254,6 +274,7 @@ private void initialize( @Nullable InputStream stream, boolean forceLoad, boolea
254274
this.additionalRestrictions = additionalRestrictions;
255275
this.index = index;
256276
this.isInitialized = true;
277+
this.languageLevel = languageLevel;
257278
this.inferenceMode = inferenceMode;
258279
this.processImports = processImports;
259280
this.searchEnabled = searchEnabled;
@@ -615,13 +636,13 @@ public void waitForInitializationThread() throws InterruptedException {
615636
* Delegates the call as to load the model into memory or leave it on disk. Simply delegates to either
616637
* OntologyLoader.loadMemoryModel( url ); OR OntologyLoader.loadPersistentModel( url, spec );
617638
*/
618-
protected abstract OntologyModel loadModel( boolean processImports, InferenceMode inferenceMode ) throws IOException;
639+
protected abstract OntologyModel loadModel( boolean processImports, LanguageLevel languageLevel, InferenceMode inferenceMode ) throws IOException;
619640

620641

621642
/**
622643
* Load a model from a given input stream.
623644
*/
624-
protected abstract OntologyModel loadModelFromStream( InputStream stream, boolean processImports, InferenceMode inferenceMode ) throws IOException;
645+
protected abstract OntologyModel loadModelFromStream( InputStream stream, boolean processImports, LanguageLevel languageLevel, InferenceMode inferenceMode ) throws IOException;
625646

626647
/**
627648
* A name for caching this ontology, or null to disable caching.
@@ -633,17 +654,6 @@ protected String getCacheName() {
633654
return getOntologyName();
634655
}
635656

636-
private OntModelSpec getSpec( InferenceMode inferenceMode ) {
637-
switch ( inferenceMode ) {
638-
case TRANSITIVE:
639-
return OntModelSpec.OWL_MEM_TRANS_INF;
640-
case NONE:
641-
return OntModelSpec.OWL_MEM;
642-
default:
643-
throw new UnsupportedOperationException( String.format( "Unsupported inference level %s.", inferenceMode ) );
644-
}
645-
}
646-
647657
@Override
648658
public void index( boolean force ) {
649659
String cacheName = getCacheName();

‎src/ubic/basecode/ontology/providers/MedicOntologyService.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -52,12 +52,12 @@ protected String getOntologyUrl() {
5252
}
5353

5454
@Override
55-
protected OntologyModel loadModel( boolean processImports, InferenceMode inferenceMode ) {
55+
protected OntologyModel loadModel( boolean processImports, LanguageLevel languageLevel, InferenceMode inferenceMode ) {
5656
try ( InputStream is = this.getClass().getResourceAsStream( MEDIC_ONTOLOGY_FILE ) ) {
5757
if ( is == null ) {
5858
throw new RuntimeException( String.format( "The MEDIC ontology was not found in classpath at %s.", MEDIC_ONTOLOGY_FILE ) );
5959
}
60-
return loadModelFromStream( new GZIPInputStream( is ), processImports, inferenceMode );
60+
return loadModelFromStream( new GZIPInputStream( is ), processImports, languageLevel, inferenceMode );
6161
} catch ( IOException e ) {
6262
throw new RuntimeException( e );
6363
}

‎src/ubic/basecode/ontology/providers/NIFSTDOntologyService.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -43,12 +43,12 @@ protected String getOntologyUrl() {
4343
}
4444

4545
@Override
46-
protected OntologyModel loadModel( boolean processImports, InferenceMode inferenceMode ) {
46+
protected OntologyModel loadModel( boolean processImports, LanguageLevel languageLevel, InferenceMode inferenceMode ) {
4747
try ( InputStream stream = getClass().getResourceAsStream( NIFSTD_ONTOLOGY_FILE ) ) {
4848
if ( stream == null ) {
4949
throw new RuntimeException( String.format( "The NIF ontology was not found in classpath at %s.", NIFSTD_ONTOLOGY_FILE ) );
5050
}
51-
return loadModelFromStream( new GZIPInputStream( stream ), processImports, inferenceMode );
51+
return loadModelFromStream( new GZIPInputStream( stream ), processImports, languageLevel, inferenceMode );
5252
} catch ( IOException e ) {
5353
throw new RuntimeException( e );
5454
}

‎src/ubic/basecode/ontology/providers/OntologyService.java‎

Lines changed: 42 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -16,9 +16,50 @@ public interface OntologyService {
1616

1717
void setProcessImports( boolean processImports );
1818

19+
enum LanguageLevel {
20+
/**
21+
* The full OWL language.
22+
*/
23+
FULL,
24+
/**
25+
* OWL-DL
26+
*/
27+
DL,
28+
/**
29+
* OWL/Lite
30+
*/
31+
LITE
32+
}
33+
34+
LanguageLevel getLanguageLevel();
35+
36+
void setLanguageLevel( LanguageLevel languageLevel );
37+
1938
enum InferenceMode {
39+
/**
40+
* No inference is supported, only the axioms defined in the ontology are considered.
41+
*/
2042
NONE,
21-
TRANSITIVE
43+
/**
44+
* Only basic inference is supported for {@code subClassOf} and {@code subPropertyOf}.
45+
* <p>
46+
* This is the fastest inference mode.
47+
*/
48+
TRANSITIVE,
49+
/**
50+
* Very limited inference.
51+
*/
52+
MICRO,
53+
/**
54+
* Limited inference.
55+
*/
56+
MINI,
57+
/**
58+
* Complete inference.
59+
* <p>
60+
* This is the slowest inference mode.
61+
*/
62+
FULL
2263
}
2364

2465
/**

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