More cleanups

Eliminate AbstractOntologyMemoryBackedService and introduce two abstract
class in the providers package: one for built-in baseCode ontologies and
another for general use.

Author: arteymix

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

@@ -20,12 +20,14 @@
 package ubic.basecode.ontology.jena;
 
 import com.hp.hpl.jena.ontology.*;
-import com.hp.hpl.jena.rdf.model.NodeIterator;
-import com.hp.hpl.jena.rdf.model.Property;
-import com.hp.hpl.jena.rdf.model.Resource;
-import com.hp.hpl.jena.rdf.model.ResourceFactory;
+import com.hp.hpl.jena.rdf.model.*;
 import com.hp.hpl.jena.rdfxml.xmlinput.ARPErrorNumbers;
 import com.hp.hpl.jena.rdfxml.xmlinput.ParseException;
+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 com.hp.hpl.jena.util.iterator.ExtendedIterator;
 import com.hp.hpl.jena.vocabulary.DC_11;
 import org.apache.commons.lang3.RandomStringUtils;
@@ -40,7 +42,6 @@
 import ubic.basecode.ontology.providers.OntologyService;
 import ubic.basecode.ontology.search.OntologySearchException;
 import ubic.basecode.ontology.search.OntologySearchResult;
-import ubic.basecode.util.Configuration;
 
 import javax.annotation.Nullable;
 import java.io.IOException;
@@ -472,13 +473,8 @@ public Set<OntologyTerm> getChildren( Collection<OntologyTerm> terms, boolean di
 
     @Override
     public boolean isEnabled() {
-        // quick path: just lookup the configuration
-        String configParameter = "load." + getOntologyName();
-        if ( Boolean.TRUE.equals( Configuration.getBoolean( configParameter ) ) ) {
-            return true;
-        }
         // could have forced, without setting config
-        return getState().isPresent();
+        return isOntologyEnabled() || isOntologyLoaded() || isInitializationThreadAlive();
     }
 
     @Override
@@ -549,25 +545,69 @@ public void waitForInitializationThread() throws InterruptedException {
     protected abstract String getOntologyUrl();
 
     /**
-     * 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, LanguageLevel languageLevel, InferenceMode inferenceMode ) throws IOException;
-
-
-    /**
-     * Load a model from a given input stream.
+     * Indicate if this ontology is enabled.
      */
-    protected abstract OntologyModel loadModelFromStream( InputStream stream, boolean processImports, LanguageLevel languageLevel, InferenceMode inferenceMode ) throws IOException;
+    protected abstract boolean isOntologyEnabled();
 
     /**
      * A name for caching this ontology, or null to disable caching.
      * <p>
      * Note that if null is returned, the ontology will not have full-text search capabilities.
      */
     @Nullable
-    protected String getCacheName() {
-        return getOntologyName();
+    protected abstract String getCacheName();
+
+    /**
+     * 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 OntologyModel loadModel( boolean processImports, LanguageLevel languageLevel, InferenceMode inferenceMode ) throws IOException {
+        return new OntologyModelImpl( OntologyLoader.loadMemoryModel( this.getOntologyUrl(), this.getCacheName(), processImports, this.getSpec( languageLevel, inferenceMode ) ) );
+    }
+
+    /**
+     * Load a model from a given input stream.
+     */
+    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( 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:
+                reasonerFactory = TransitiveReasonerFactory.theInstance();
+                break;
+            case NONE:
+                reasonerFactory = null;
+                break;
+            default:
+                throw new UnsupportedOperationException( String.format( "Unsupported inference level %s.", inferenceMode ) );
+        }
+        return new OntModelSpec( ModelFactory.createMemModelMaker(), null, reasonerFactory, profile );
     }
 
     @Override

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

@@ -52,18 +52,18 @@ class OntologyLoader {
     private static final String OLD_CACHE_SUFFIX = ".old";
     private static final String TMP_CACHE_SUFFIX = ".tmp";
 
-    public static OntModel loadMemoryModel( InputStream is, String url ) throws JenaException {
+    public static OntModel loadMemoryModel( InputStream is, String url ) throws JenaException, IOException {
         return loadMemoryModel( is, url, true );
     }
 
     /**
      * Load an ontology into memory. Use this type of model when fast access is critical and memory is available.
      */
-    public static OntModel loadMemoryModel( InputStream is, String url, boolean processImports ) throws JenaException {
+    public static OntModel loadMemoryModel( InputStream is, String url, boolean processImports ) throws JenaException, IOException {
         return loadMemoryModel( is, url, processImports, OntModelSpec.OWL_MEM_TRANS_INF );
     }
 
-    public static OntModel loadMemoryModel( InputStream is, String url, boolean processImports, OntModelSpec spec ) throws JenaException {
+    public static OntModel loadMemoryModel( InputStream is, String url, boolean processImports, OntModelSpec spec ) throws JenaException, IOException {
         OntModel model = getMemoryModel( url, processImports, spec );
         model.read( is, null );
         return model;

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

@@ -0,0 +1,48 @@
+package ubic.basecode.ontology.providers;
+
+import ubic.basecode.util.Configuration;
+
+import javax.annotation.Nullable;
+
+/**
+ * Base class for all ontologies built-in to the baseCode project.
+ * <p>
+ * The ontologies that subclass this will honor settings in the {@code basecode.properties} file for loading and
+ * locating the ontology.
+ *
+ * @author poirigui
+ */
+public abstract class AbstractBaseCodeOntologyService extends AbstractOntologyService {
+
+    private final String name;
+    private final String cacheName;
+
+    /**
+     * Intentionally package-private constructor.
+     */
+    AbstractBaseCodeOntologyService( String name, String cacheName ) {
+        this.name = name;
+        this.cacheName = cacheName;
+    }
+
+    @Override
+    protected String getOntologyName() {
+        return name;
+    }
+
+    @Override
+    protected String getOntologyUrl() {
+        return Configuration.getString( "url." + cacheName );
+    }
+
+    @Override
+    protected boolean isOntologyEnabled() {
+        return Boolean.TRUE.equals( Configuration.getBoolean( "load." + cacheName ) );
+    }
+
+    @Nullable
+    @Override
+    public String getCacheName() {
+        return cacheName;
+    }
+}

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

@@ -0,0 +1,9 @@
+package ubic.basecode.ontology.providers;
+
+/**
+ * Base class for all ontology services.
+ * <p>
+ * The actual implementation is provided by the {@code ubic.basecode.ontology.jena} package.
+ */
+public abstract class AbstractOntologyService extends ubic.basecode.ontology.jena.AbstractOntologyService {
+}

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

@@ -1,8 +1,8 @@
 /*
  * The baseCode project
- * 
+ *
  * Copyright (c) 2010 University of British Columbia
- * 
+ *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * You may obtain a copy of the License at
@@ -19,26 +19,14 @@
 
 package ubic.basecode.ontology.providers;
 
-import ubic.basecode.ontology.jena.AbstractOntologyMemoryBackedService;
-import ubic.basecode.util.Configuration;
-
 /**
- * See http://www.obofoundry.org/cgi-bin/detail.cgi?id=CLO
- * 
+ * <a href="https://obofoundry.org/ontology/clo.html">Cell Line Ontology</a>
+ *
  * @author paul
- * 
  */
-public class CellLineOntologyService extends AbstractOntologyMemoryBackedService {
-
-    private static final String ONTOLOGY_URL = "url.cellLineOntology";
-
-    @Override
-    protected String getOntologyName() {
-        return "cellLineOntology";
-    }
+public class CellLineOntologyService extends AbstractBaseCodeOntologyService {
 
-    @Override
-    protected String getOntologyUrl() {
-        return Configuration.getString( ONTOLOGY_URL );
+    public CellLineOntologyService() {
+        super( "Cell Line Ontology", "cellLineOntology" );
     }
 }

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

@@ -1,8 +1,8 @@
 /*
  * The baseCode project
- * 
+ *
  * Copyright (c) 2010 University of British Columbia
- * 
+ *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * You may obtain a copy of the License at
@@ -19,26 +19,14 @@
 
 package ubic.basecode.ontology.providers;
 
-import ubic.basecode.ontology.jena.AbstractOntologyMemoryBackedService;
-import ubic.basecode.util.Configuration;
-
 /**
- * See http://www.obofoundry.org/cgi-bin/detail.cgi?id=cell
- * 
+ * <a href="https://obofoundry.org/ontology/cl.html">Cell Ontology</a>
+ *
  * @author paul
- * 
  */
-public class CellTypeOntologyService extends AbstractOntologyMemoryBackedService {
-
-    private static final String ONTOLOGY_URL = "url.cellTypeOntology";
-
-    @Override
-    protected String getOntologyName() {
-        return "cellTypeOntology";
-    }
+public class CellTypeOntologyService extends AbstractBaseCodeOntologyService {
 
-    @Override
-    protected String getOntologyUrl() {
-        return Configuration.getString( ONTOLOGY_URL );
+    public CellTypeOntologyService() {
+        super( "Cell Ontology", "cellTypeOntology" );
     }
-}
+}