Use Jena 2.12.1 implementation of the rulesys reasoner

pom.xml

@@ -5,7 +5,7 @@
 	<name>baseCode</name>
 	<groupId>baseCode</groupId>
 	<artifactId>baseCode</artifactId>
-	<version>1.1.18</version>
+	<version>1.1.19</version>
 	<inceptionYear>2003</inceptionYear>
 	<description>
 		<![CDATA[Data structures, math and statistics tools, and utilities that are often needed across projects.]]>
@@ -347,6 +347,100 @@
 					</gitFlowConfig>
 				</configuration>
 			</plugin>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-dependency-plugin</artifactId>
+				<version>3.3.0</version>
+				<executions>
+					<execution>
+						<id>unpack-jena-rete-engine</id>
+						<phase>generate-sources</phase>
+						<goals>
+							<goal>unpack</goal>
+						</goals>
+						<configuration>
+							<artifactItems>
+								<artifactItem>
+									<groupId>org.apache.jena</groupId>
+									<artifactId>jena-core</artifactId>
+									<version>2.12.1</version>
+									<classifier>sources</classifier>
+									<outputDirectory>${project.build.directory}/generated-sources/jena-core</outputDirectory>
+									<includes>com/hp/hpl/jena/reasoner/rulesys/impl/*.java,com/hp/hpl/jena/graph/NodeFactory.java</includes>
+								</artifactItem>
+							</artifactItems>
+						</configuration>
+					</execution>
+				</executions>
+			</plugin>
+			<plugin>
+				<groupId>org.codehaus.mojo</groupId>
+				<artifactId>build-helper-maven-plugin</artifactId>
+				<version>3.3.0</version>
+				<executions>
+					<execution>
+						<phase>generate-sources</phase>
+						<goals>
+							<goal>add-source</goal>
+						</goals>
+						<configuration>
+							<!-- dependencies:unpack does not add a source root -->
+							<sources>${project.build.directory}/generated-sources/jena-core</sources>
+						</configuration>
+					</execution>
+				</executions>
+			</plugin>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-shade-plugin</artifactId>
+				<version>3.5.0</version>
+				<executions>
+					<execution>
+						<phase>package</phase>
+						<goals>
+							<goal>shade</goal>
+						</goals>
+						<configuration>
+							<artifactSet>
+								<includes>
+									<include>org.apache.jena:*</include>
+								</includes>
+							</artifactSet>
+							<filters>
+								<filter>
+									<artifact>org.apache.jena:*</artifact>
+									<includes>
+										<include>com/hp/hpl/jena/**/*</include>
+										<include>org/apache/jena/**/*</include>
+										<include>org/openjena/**/*</include>
+										<include>etc/**/*</include>
+										<include>vocabularies/**/*</include>
+									</includes>
+									<excludes>
+										<!-- this one we compiled ourselves -->
+										<exclude>com/hp/hpl/jena/reasoner/rulesys/impl/**/*</exclude>
+									</excludes>
+								</filter>
+							</filters>
+							<!-- relocate Jena under a private package name to prevent conflicts -->
+							<relocations>
+								<relocation>
+									<pattern>com.hp.hpl.jena</pattern>
+									<shadedPattern>ubic.basecode.ontology.jena.impl</shadedPattern>
+								</relocation>
+								<relocation>
+									<pattern>org.apache.jena</pattern>
+									<shadedPattern>ubic.basecode.ontology.jena.impl</shadedPattern>
+								</relocation>
+								<relocation>
+									<pattern>org.openjena</pattern>
+									<shadedPattern>ubic.basecode.ontology.jena.impl</shadedPattern>
+								</relocation>
+							</relocations>
+						</configuration>
+					</execution>
+				</executions>
+			</plugin>
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-compiler-plugin</artifactId>

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

@@ -15,6 +15,13 @@
 package ubic.basecode.ontology.jena;
 
 import com.hp.hpl.jena.ontology.OntModelSpec;
+import com.hp.hpl.jena.ontology.ProfileRegistry;
+import com.hp.hpl.jena.rdf.model.ModelFactory;
+import com.hp.hpl.jena.reasoner.ReasonerFactory;
+import com.hp.hpl.jena.reasoner.rulesys.OWLFBRuleReasonerFactory;
+import com.hp.hpl.jena.reasoner.rulesys.OWLMicroReasonerFactory;
+import com.hp.hpl.jena.reasoner.rulesys.OWLMiniReasonerFactory;
+import com.hp.hpl.jena.reasoner.transitiveReasoner.TransitiveReasonerFactory;
 import ubic.basecode.ontology.model.OntologyModel;
 import ubic.basecode.util.Configuration;
 
@@ -35,23 +42,50 @@ protected String getOntologyUrl() {
     }
 
     @Override
-    protected OntologyModel loadModel( boolean processImports, InferenceMode inferenceMode ) throws IOException {
-        return new OntologyModelImpl( OntologyLoader.loadMemoryModel( this.getOntologyUrl(), this.getCacheName(), processImports, this.getSpec( inferenceMode ) ) );
+    protected OntologyModel loadModel( boolean processImports, LanguageLevel languageLevel, InferenceMode inferenceMode ) throws IOException {
+        return new OntologyModelImpl( OntologyLoader.loadMemoryModel( this.getOntologyUrl(), this.getCacheName(), processImports, this.getSpec( languageLevel, inferenceMode ) ) );
     }
 
     @Override
-    protected OntologyModel loadModelFromStream( InputStream is, boolean processImports, InferenceMode inferenceMode ) throws IOException {
-        return new OntologyModelImpl( OntologyLoader.loadMemoryModel( is, this.getOntologyUrl(), processImports, this.getSpec( inferenceMode ) ) );
+    protected OntologyModel loadModelFromStream( InputStream is, boolean processImports, LanguageLevel languageLevel, InferenceMode inferenceMode ) throws IOException {
+        return new OntologyModelImpl( OntologyLoader.loadMemoryModel( is, this.getOntologyUrl(), processImports, this.getSpec( languageLevel, inferenceMode ) ) );
     }
 
-    private OntModelSpec getSpec( InferenceMode inferenceMode ) {
+    private OntModelSpec getSpec( LanguageLevel languageLevel, InferenceMode inferenceMode ) {
+        String profile;
+        switch ( languageLevel ) {
+            case FULL:
+                profile = ProfileRegistry.OWL_LANG;
+                break;
+            case DL:
+                profile = ProfileRegistry.OWL_DL_LANG;
+                break;
+            case LITE:
+                profile = ProfileRegistry.OWL_LITE_LANG;
+                break;
+            default:
+                throw new UnsupportedOperationException( String.format( "Unsupported OWL language level %s.", languageLevel ) );
+        }
+        ReasonerFactory reasonerFactory;
         switch ( inferenceMode ) {
+            case FULL:
+                reasonerFactory = OWLFBRuleReasonerFactory.theInstance();
+                break;
+            case MINI:
+                reasonerFactory = OWLMiniReasonerFactory.theInstance();
+                break;
+            case MICRO:
+                reasonerFactory = OWLMicroReasonerFactory.theInstance();
+                break;
             case TRANSITIVE:
-                return OntModelSpec.OWL_MEM_TRANS_INF;
+                reasonerFactory = TransitiveReasonerFactory.theInstance();
+                break;
             case NONE:
-                return OntModelSpec.OWL_MEM;
+                reasonerFactory = null;
+                break;
             default:
                 throw new UnsupportedOperationException( String.format( "Unsupported inference level %s.", inferenceMode ) );
         }
+        return new OntModelSpec( ModelFactory.createMemModelMaker(), null, reasonerFactory, profile );
     }
 }

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

@@ -74,6 +74,7 @@ public abstract class AbstractOntologyService implements OntologyService {
     }
 
     /* settings (applicable for next initialization) */
+    private LanguageLevel nextLanguageLevel = LanguageLevel.FULL;
     private InferenceMode nextInferenceMode = InferenceMode.TRANSITIVE;
     private boolean nextProcessImports = true;
     private boolean nextSearchEnabled = true;
@@ -91,12 +92,30 @@ public abstract class AbstractOntologyService implements OntologyService {
     private Set<Restriction> additionalRestrictions;
     private boolean isInitialized = false;
     @Nullable
+    private LanguageLevel languageLevel = null;
+    @Nullable
     private InferenceMode inferenceMode = null;
     @Nullable
     private Boolean processImports = null;
     @Nullable
     private Boolean searchEnabled = null;
 
+    @Override
+    public LanguageLevel getLanguageLevel() {
+        Lock lock = rwLock.readLock();
+        try {
+            lock.lock();
+            return this.languageLevel != null ? this.languageLevel : nextLanguageLevel;
+        } finally {
+            lock.unlock();
+        }
+    }
+
+    @Override
+    public void setLanguageLevel( LanguageLevel languageLevel ) {
+        this.nextLanguageLevel = languageLevel;
+    }
+
     @Override
     public InferenceMode getInferenceMode() {
         Lock lock = rwLock.readLock();
@@ -162,6 +181,7 @@ private void initialize( @Nullable InputStream stream, boolean forceLoad, boolea
         String ontologyUrl = getOntologyUrl();
         String ontologyName = getOntologyName();
         String cacheName = getCacheName();
+        LanguageLevel languageLevel = nextLanguageLevel;
         InferenceMode inferenceMode = nextInferenceMode;
         boolean processImports = nextProcessImports;
         boolean searchEnabled = nextSearchEnabled;
@@ -196,7 +216,7 @@ private void initialize( @Nullable InputStream stream, boolean forceLoad, boolea
             return;
 
         try {
-            OntologyModel m = stream != null ? loadModelFromStream( stream, processImports, inferenceMode ) : loadModel( processImports, inferenceMode ); // can take a while.
+            OntologyModel m = stream != null ? loadModelFromStream( stream, processImports, languageLevel, inferenceMode ) : loadModel( processImports, languageLevel, inferenceMode ); // can take a while.
             if ( m instanceof OntologyModelImpl ) {
                 model = ( ( OntologyModelImpl ) m ).getOntModel();
             } else {
@@ -254,6 +274,7 @@ private void initialize( @Nullable InputStream stream, boolean forceLoad, boolea
             this.additionalRestrictions = additionalRestrictions;
             this.index = index;
             this.isInitialized = true;
+            this.languageLevel = languageLevel;
             this.inferenceMode = inferenceMode;
             this.processImports = processImports;
             this.searchEnabled = searchEnabled;
@@ -615,13 +636,13 @@ public void waitForInitializationThread() throws InterruptedException {
      * Delegates the call as to load the model into memory or leave it on disk. Simply delegates to either
      * OntologyLoader.loadMemoryModel( url ); OR OntologyLoader.loadPersistentModel( url, spec );
      */
-    protected abstract OntologyModel loadModel( boolean processImports, InferenceMode inferenceMode ) throws IOException;
+    protected abstract OntologyModel loadModel( boolean processImports, LanguageLevel languageLevel, InferenceMode inferenceMode ) throws IOException;
 
 
     /**
      * Load a model from a given input stream.
      */
-    protected abstract OntologyModel loadModelFromStream( InputStream stream, boolean processImports, InferenceMode inferenceMode ) throws IOException;
+    protected abstract OntologyModel loadModelFromStream( InputStream stream, boolean processImports, LanguageLevel languageLevel, InferenceMode inferenceMode ) throws IOException;
 
     /**
      * A name for caching this ontology, or null to disable caching.
@@ -633,17 +654,6 @@ protected String getCacheName() {
         return getOntologyName();
     }
 
-    private OntModelSpec getSpec( InferenceMode inferenceMode ) {
-        switch ( inferenceMode ) {
-            case TRANSITIVE:
-                return OntModelSpec.OWL_MEM_TRANS_INF;
-            case NONE:
-                return OntModelSpec.OWL_MEM;
-            default:
-                throw new UnsupportedOperationException( String.format( "Unsupported inference level %s.", inferenceMode ) );
-        }
-    }
-
     @Override
     public void index( boolean force ) {
         String cacheName = getCacheName();
@@ -743,7 +753,8 @@ public void loadTermsInNameSpace( InputStream is, boolean forceIndex ) {
 
     @Override
     public String toString() {
-        return String.format( "%s [%s]", getOntologyName(), getOntologyUrl() );
+        return String.format( "%s [url=%s] [language level=%s] [inference mode=%s] [imports=%b] [search=%b]",
+                getOntologyName(), getOntologyUrl(), getLanguageLevel(), getInferenceMode(), getProcessImports(), isSearchEnabled() );
     }
 
     private Set<OntClass> getOntClassesFromTerms( Collection<OntologyTerm> terms ) {

src/ubic/basecode/ontology/model/OntologyResource.java

@@ -19,7 +19,6 @@
 package ubic.basecode.ontology.model;
 
 import javax.annotation.Nullable;
-import java.io.Serializable;
 
 /**
  * @author pavlidis

src/ubic/basecode/ontology/model/OntologyTermSimple.java

@@ -15,6 +15,7 @@
 package ubic.basecode.ontology.model;
 
 import javax.annotation.Nullable;
+import java.io.Serializable;
 import java.util.Collection;
 import java.util.Comparator;
 import java.util.Objects;
@@ -25,8 +26,8 @@
  *
  * @author Paul
  */
-
-public class OntologyTermSimple implements OntologyTerm {
+@SuppressWarnings("unused")
+public class OntologyTermSimple implements OntologyTerm, Serializable {
 
     /**
      *

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

@@ -52,12 +52,12 @@ protected String getOntologyUrl() {
     }
 
     @Override
-    protected OntologyModel loadModel( boolean processImports, InferenceMode inferenceMode ) {
+    protected OntologyModel loadModel( boolean processImports, LanguageLevel languageLevel, InferenceMode inferenceMode ) {
         try ( InputStream is = this.getClass().getResourceAsStream( MEDIC_ONTOLOGY_FILE ) ) {
             if ( is == null ) {
                 throw new RuntimeException( String.format( "The MEDIC ontology was not found in classpath at %s.", MEDIC_ONTOLOGY_FILE ) );
             }
-            return loadModelFromStream( new GZIPInputStream( is ), processImports, inferenceMode );
+            return loadModelFromStream( new GZIPInputStream( is ), processImports, languageLevel, inferenceMode );
         } catch ( IOException e ) {
             throw new RuntimeException( e );
         }

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

@@ -43,12 +43,12 @@ protected String getOntologyUrl() {
     }
 
     @Override
-    protected OntologyModel loadModel( boolean processImports, InferenceMode inferenceMode ) {
+    protected OntologyModel loadModel( boolean processImports, LanguageLevel languageLevel, InferenceMode inferenceMode ) {
         try ( InputStream stream = getClass().getResourceAsStream( NIFSTD_ONTOLOGY_FILE ) ) {
             if ( stream == null ) {
                 throw new RuntimeException( String.format( "The NIF ontology was not found in classpath at %s.", NIFSTD_ONTOLOGY_FILE ) );
             }
-            return loadModelFromStream( new GZIPInputStream( stream ), processImports, inferenceMode );
+            return loadModelFromStream( new GZIPInputStream( stream ), processImports, languageLevel, inferenceMode );
         } catch ( IOException e ) {
             throw new RuntimeException( e );
         }

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

@@ -16,9 +16,50 @@ public interface OntologyService {
 
     void setProcessImports( boolean processImports );
 
+    enum LanguageLevel {
+        /**
+         * The full OWL language.
+         */
+        FULL,
+        /**
+         * OWL-DL
+         */
+        DL,
+        /**
+         * OWL/Lite
+         */
+        LITE
+    }
+
+    LanguageLevel getLanguageLevel();
+
+    void setLanguageLevel( LanguageLevel languageLevel );
+
     enum InferenceMode {
+        /**
+         * No inference is supported, only the axioms defined in the ontology are considered.
+         */
         NONE,
-        TRANSITIVE
+        /**
+         * Only basic inference is supported for {@code subClassOf} and {@code subPropertyOf}.
+         * <p>
+         * This is the fastest inference mode.
+         */
+        TRANSITIVE,
+        /**
+         * Very limited inference.
+         */
+        MICRO,
+        /**
+         * Limited inference.
+         */
+        MINI,
+        /**
+         * Complete inference.
+         * <p>
+         * This is the slowest inference mode.
+         */
+        FULL
     }
 
     /**