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
  }
 
  /**