/*
 * The Gemma project
 * 
 * Copyright (c) 2007 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.gemma.ontology;

import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;

import java.util.Collection;

import org.junit.Test;
import org.springframework.beans.factory.annotation.Autowired;

import ubic.basecode.ontology.model.OntologyTerm;
import ubic.gemma.model.common.description.Characteristic;
import ubic.gemma.testing.BaseSpringContextTest;

/**
 * @author paul
 * @version $Id$
 */
public class OntologyServiceTest extends BaseSpringContextTest {

    @Autowired
    OntologyService os;

    /**
     * This test can fail if the db isn't initialized public void testListAvailableOntologies() throws Exception {
     * Collection<Ontology> name = OntologyService.listAvailableOntologies(); assertTrue( name.size() > 0 ); }
     */
    @Test
    public final void testFindExactMatch() throws Exception {
        os.getMgedOntologyService().startInitializationThread( true );
        int c = 0;
        while ( !os.getMgedOntologyService().isOntologyLoaded() ) {
            Thread.sleep( 10000 );
            log.info( "Waiting for Ontology to load" );
            if ( ++c > 10 ) {
                fail( "Ontology load timeout" );
            }
        }

        Collection<Characteristic> name = os.findExactTerm( "male",
                "http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Sex", null );
        for ( Characteristic characteristic : name ) {
            log.info( characteristic );
        }
        assertTrue( name.size() > 0 );
    }

    @Test
    public void testObsolete() throws Exception {
        os.getDiseaseOntologyService().startInitializationThread( true );
        int c = 0;

        while ( !os.getDiseaseOntologyService().isOntologyLoaded() ) {
            Thread.sleep( 10000 );
            log.info( "Waiting for DiseaseOntology to load" );
            if ( ++c > 10 ) {
                fail( "Ontology load timeout" );
            }
        }

        OntologyTerm t1 = os.getTerm( "http://purl.org/obo/owl/DOID#DOID_0050001" );
        assertNotNull( t1 );

        // Actinomadura madurae infectious disease
        assertTrue( os.isObsolete( "http://purl.org/obo/owl/DOID#DOID_0050001" ) );

        // inflammatory diarrhea, not obolete as of May 2012.
        assertNotNull( os.getTerm( "http://purl.org/obo/owl/DOID#DOID_0050132" ) );
        assertTrue( !os.isObsolete( "http://purl.org/obo/owl/DOID#DOID_0050132" ) );

    }
}

@@ -1528,32 +1528,101 @@
 ows Exception %7B%0A
+        if ( !os.getMgedOntologyService().isOntologyLoaded() ) %7B%0A    
         os.getMg
@@ -1676,32 +1676,36 @@
 true );%0A        
+ 
+   
 int c = 0;%0A     
@@ -1699,16 +1699,20 @@
  c = 0;%0A
+    
         
@@ -1775,32 +1775,36 @@
 ) %7B%0A            
+    
 Thread.sleep( 10
@@ -1814,32 +1814,36 @@
  );%0A            
+   
+ 
 log.info( %22Waiti
@@ -1874,32 +1874,36 @@
  );%0A            
+    
 if ( ++c %3E 10 ) 
@@ -1912,32 +1912,36 @@
                 
+  
+  
 fail( %22Ontology 
@@ -1949,32 +1949,50 @@
 oad timeout%22 );%0A
+                %7D%0A
             %7D%0A  
@@ -1981,32 +1981,32 @@
 %7D%0A            %7D%0A
+
         %7D%0A%0A     
@@ -1991,33 +1991,32 @@
     %7D%0A        %7D%0A
-%0A
         Collecti

put back extra check (why matters?)