Add an option to enable imports per-ontology

Author: arteymix

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

@@ -27,13 +27,17 @@
  */
 public abstract class AbstractOntologyMemoryBackedService extends AbstractOntologyService {
 
+    protected boolean getProcessImport() {
+        return true;
+    }
+
     @Override
     protected OntModel loadModel() {
-        return OntologyLoader.loadMemoryModel( this.getOntologyUrl(), this.getOntologyName() );
+        return OntologyLoader.loadMemoryModel( this.getOntologyUrl(), this.getOntologyName(), this.getProcessImport() );
     }
 
     @Override
     protected OntModel loadModelFromStream( InputStream is ) {
-        return OntologyLoader.loadMemoryModel( is, this.getOntologyUrl() );
+        return OntologyLoader.loadMemoryModel( is, this.getOntologyUrl(), this.getProcessImport() );
     }
 }

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

@@ -21,6 +21,7 @@
 import com.hp.hpl.jena.ontology.OntModel;
 import com.hp.hpl.jena.ontology.OntModelSpec;
 import com.hp.hpl.jena.rdf.model.*;
+import com.hp.hpl.jena.shared.CannotCreateException;
 import com.hp.hpl.jena.shared.JenaException;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.lang3.StringUtils;
@@ -50,22 +51,30 @@ public 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 ) {
+        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 ) {
-        OntModel model = getMemoryModel( url );
+    public static OntModel loadMemoryModel( InputStream is, String url, boolean processImports ) {
+        OntModel model = getMemoryModel( url, processImports );
         model.read( is, null );
         return model;
     }
 
     /**
      * Load an ontology into memory. Use this type of model when fast access is critical and memory is available.
      *
-     * @see #loadMemoryModel(String, String)
+     * @see #loadMemoryModel(String, String, boolean)
      */
     public static OntModel loadMemoryModel( String url ) {
-        return loadMemoryModel( url, null );
+        return loadMemoryModel( url, null, true );
+    }
+
+    public static OntModel loadMemoryModel( String url, @Nullable String cacheName ) {
+        return loadMemoryModel( url, cacheName, true );
     }
 
     /**
@@ -77,10 +86,10 @@ public static OntModel loadMemoryModel( String url ) {
      * @param url       a URL where the OWL file is stored
      * @param cacheName unique name of this ontology, will be used to load from disk in case of failed url connection
      */
-    public static OntModel loadMemoryModel( String url, @Nullable String cacheName ) {
+    public static OntModel loadMemoryModel( String url, @Nullable String cacheName, boolean processImports ) {
         StopWatch timer = new StopWatch();
         timer.start();
-        OntModel model = getMemoryModel( url );
+        OntModel model = getMemoryModel( url, processImports );
 
         URLConnection urlc = openConnection( url );
 
@@ -187,12 +196,12 @@ public static void deleteOldCache( String cacheName ) {
     /**
      * Get model that is entirely in memory.
      */
-    private static OntModel getMemoryModel( String url ) {
+    private static OntModel getMemoryModel( String url, boolean processImports ) {
         OntModelSpec spec = new OntModelSpec( OntModelSpec.OWL_MEM_TRANS_INF );
         ModelMaker maker = ModelFactory.createMemModelMaker();
         Model base = maker.createModel( url, false );
         spec.setImportModelMaker( maker );
-        spec.getDocumentManager().setProcessImports( true );
+        spec.getDocumentManager().setProcessImports( processImports );
         spec.setImportModelGetter( new ModelGetter() {
             @Override
             public Model getModel( String URL ) {
@@ -207,7 +216,7 @@ public Model getModel( String URL, ModelReader loadIfAbsent ) {
                     try ( InputStream in = urlc.getInputStream() ) {
                         return model.read( in, URL );
                     } catch ( JenaException | IOException e ) {
-                        log.error( String.format( "Failed to resolve import %s for %s: %s.", URL, url, e.getMessage() ) );
+                        throw new CannotCreateException( String.format( "Failed to resolve import %s for %s.", URL, url ), e );
                     }
                 }
                 return loadIfAbsent.readModel( model, URL );

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

@@ -32,15 +32,21 @@ public class GenericOntologyService extends AbstractOntologyMemoryBackedService
     private final String url;
     private final String name;
     private final boolean cache;
+    private final boolean processImports;
 
     public GenericOntologyService( String name, String url ) {
         this( name, url, false );
     }
 
     public GenericOntologyService( String name, String url, boolean cache ) {
+        this( name, url, cache, true );
+    }
+
+    public GenericOntologyService( String name, String url, boolean cache, boolean processImports ) {
         this.name = name;
         this.url = url;
         this.cache = cache;
+        this.processImports = processImports;
     }
 
     @Override
@@ -57,4 +63,9 @@ protected String getOntologyUrl() {
     protected String getCacheName() {
         return this.cache ? this.name : null;
     }
+
+    @Override
+    protected boolean getProcessImport() {
+        return processImports;
+    }
 }

test/ubic/basecode/ontology/providers/AbstractOntologyServiceTest.java

@@ -95,7 +95,7 @@ public void testInitializeInBackgroundThread() throws InterruptedException {
     }
 
     private GenericOntologyService createService( String name, String resourceURL, boolean cache ) {
-        GenericOntologyService s = new GenericOntologyService( name, resourceURL, cache );
+        GenericOntologyService s = new GenericOntologyService( name, resourceURL, cache, false );
         s.initialize( true, false );
         return s;
     }

test/ubic/basecode/ontology/search/OntologySearchTest.java

@@ -59,7 +59,7 @@ public static void setUpUberon() throws IOException {
     @Test
     public final void testIndexing() throws Exception {
         InputStream is = new GZIPInputStream( requireNonNull( this.getClass().getResourceAsStream( "/data/mged.owl.gz" ) ) );
-        OntModel model = OntologyLoader.loadMemoryModel( is, "owl-test" );
+        OntModel model = OntologyLoader.loadMemoryModel( is, "owl-test", false );
 
         SearchIndex index = OntologyIndexer.indexOntology( "MGEDTEST", model, true );
 
@@ -168,7 +168,7 @@ public final void testOmitDefinitions2() throws Exception {
         OntModel model;
         try ( InputStream is = this.getClass().getResourceAsStream( "/data/nif.organism.test.owl.xml" ) ) {
             assertNotNull( is );
-            model = OntologyLoader.loadMemoryModel( is, "NIFORG_TEST" );
+            model = OntologyLoader.loadMemoryModel( is, "NIFORG_TEST", false );
         }
 
         SearchIndex index = OntologyIndexer.indexOntology( "NIFORG_TEST", model, true );
@@ -228,7 +228,7 @@ public final void testOmitDefinitions3() throws Exception {
     public final void testOmitDefinitions4() throws Exception {
         InputStream is = new GZIPInputStream( requireNonNull( this.getClass().getResourceAsStream( "/data/NIF-GrossAnatomy.owl.gz" ) ) );
 
-        OntModel model = OntologyLoader.loadMemoryModel( is, "NIFAN_TEST2" );
+        OntModel model = OntologyLoader.loadMemoryModel( is, "NIFAN_TEST2", false );
         is.close();
 
         SearchIndex index = OntologyIndexer.indexOntology( "NIFAN_TEST2", model, true );
@@ -268,7 +268,7 @@ public void testScore() throws OntologySearchException {
     @Test
     public final void testPersistence() throws Exception {
         InputStream is = new GZIPInputStream( requireNonNull( this.getClass().getResourceAsStream( "/data/mged.owl.gz" ) ) );
-        OntModel model = OntologyLoader.loadMemoryModel( is, "owl-test" );
+        OntModel model = OntologyLoader.loadMemoryModel( is, "owl-test", false );
 
         SearchIndex index = OntologyIndexer.indexOntology( "MGEDTEST", model, false );
         index.close();