Improve OntologyService API

Add a public initialize() method to initialize an ontology service and
use that in the initialization thread.

Use a read-write lock for initializing and refreshing the ontology,
allowing more than one reader at a time.

Expose the initialization thread's properties via public method in
AbstractOntologyService.

Catch all possible exceptions in ontology initialization thread

Author: arteymix

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

@@ -1,97 +1,30 @@
 /*
  * The baseCode project
- * 
+ *
  * Copyright (c) 2013 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
- * 
+ *
  * http://www.apache.org/licenses/LICENSE-2.0
- * 
+ *
  * Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on
  * an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the
  * specific language governing permissions and limitations under the License.
  */
 package ubic.basecode.ontology.providers;
 
-import java.io.IOException;
-import java.io.InputStream;
-
-import ubic.basecode.ontology.OntologyLoader;
-import ubic.basecode.ontology.search.OntologyIndexer;
-
 import com.hp.hpl.jena.ontology.OntModel;
-import com.hp.hpl.jena.ontology.OntModelSpec;
+import ubic.basecode.ontology.OntologyLoader;
 
 /**
  * This class has some stuff that's specific to in-memory ontologies. Unlike database backed ontologies we don't use a
  * pool keeping only one instance of model in memory.
- * 
+ *
  * @author paul
  */
 public abstract class AbstractOntologyMemoryBackedService extends AbstractOntologyService {
 
-    /**
-     * For testing! Overrides normal way of loading the ontology. This does not index the ontology unless 'force' is
-     * true (if there is an existing index, it will be used)
-     * 
-     * @param  is
-     * @param  forceIndex  initialize the index. Otherwise it will only be initialized if it doesn't exist.
-     * @throws IOException
-     */
-    public synchronized void loadTermsInNameSpace( InputStream is, boolean forceIndex ) {
-        synchronized ( isInitialized ) {
-            this.indexReady.set( false );
-            this.modelReady.set( false );
-            this.isInitialized.set( false );
-            this.cacheReady.set( false );
-        }
-
-        if ( initializationThread.isAlive() ) {
-            log.warn( this.getOntologyName() + " initialization is already running, trying to cancel ..." );
-            initializationThread.cancel();
-
-            // wait for the thread to die.
-            int maxWait = 10;
-            int wait = 0;
-            while ( initializationThread.isAlive() ) {
-                try {
-                    Thread.sleep( 5000 );
-                    log.warn( "Waiting for auto-initialization to stop so manual initialization can begin ..." );
-                } catch ( InterruptedException e ) {
-                    // no-op.
-                }
-                if ( ++wait >= maxWait ) {
-                    log.error( "Got tired of waiting" );
-                    break;
-                }
-                if ( initializationThread.isInterrupted() ) {
-                    log.warn( "Got interrupt." );
-                    break;
-                }
-            }
-        }
-
-        if ( this.terms != null ) this.terms.clear();
-        if ( this.individuals != null ) this.individuals.clear();
-
-        this.model = OntologyLoader.loadMemoryModel( is, this.getOntologyUrl(), OntModelSpec.OWL_MEM );
-        this.index = OntologyIndexer.getSubjectIndex( getOntologyName() );
-        if ( index == null || forceIndex ) {
-            this.index = OntologyIndexer.indexOntology( getOntologyName(), model, true /* force */ );
-        }
-
-        addTerms( OntologyLoader.initialize( this.getOntologyUrl(), model ) );
-
-        synchronized ( isInitialized ) {
-            indexReady.set( this.index != null );
-            cacheReady.set( true );
-            modelReady.set( true );
-            isInitialized.set( true );
-        }
-        log.info( this.getClass().getSimpleName() + " ready" );
-    }
-
     @Override
     protected synchronized OntModel loadModel() {
         return OntologyLoader.loadMemoryModel( this.getOntologyUrl(), this.getOntologyName() );