/*
 * The Gemma 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
 *
 *       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.loader.protein;

import static org.junit.Assert.assertEquals;
import static org.junit.Assert.fail;

import org.junit.Before;
import org.junit.Test;

import ubic.gemma.model.common.description.DatabaseEntry;

/**
 * Test to ensure string links are set correctly in gemma and that evidence codes for interactions are correctly set.
 * 
 * @author ldonnison
 * @version $Id$
 */
public class ProteinLinkOutFormatterTest {
    
    private ProteinLinkOutFormatter formatter= null;
    DatabaseEntry entry = DatabaseEntry.Factory.newInstance();
    private static String accession =  "9606.ENSP00000293813%0D9606.ENSP00000360616";
    private static String url =  "http://string-db.org/version_8_2/newstring_cgi/show_network_section.pl?identifier";
    private static String baseFormattedUrl = url.concat("s=").concat(accession);
    
    @Before
    public void setUp() throws Exception {        
        formatter = new ProteinLinkOutFormatter();      
        entry.setUri( url + "=" );       
        entry.setAccession( accession );
    }
   

    @Test
    public void testGetStringProteinProteinInteractionLinkFormatted() {
        String urlForString = formatter.getStringProteinProteinInteractionLinkGemmaDefault( entry );    
        String defaultUrl = (baseFormattedUrl.concat("&required_score=150"));
        assertEquals(defaultUrl, urlForString);
        System.out.println(defaultUrl);
    }

    @Test
    public void testGetStringProteinProteinInteractionLinkDefault() {
        String urlForString = formatter.getStringProteinProteinInteractionLinkFormatted( entry, "20", "420" );
        String defaultUrl = (baseFormattedUrl.concat( "&limit=20" ).concat("&required_score=420"));
        assertEquals(defaultUrl, urlForString);
        System.out.println(defaultUrl);
        
        
    }

    @Test
    public void testGetEvidenceDisplayText() {
        byte[] bytes = new byte[]{0,0,0,0,1,0,1};
        try {
            String evidenceText = formatter.getEvidenceDisplayText( bytes );
            assertEquals("Experimental:TextMining",evidenceText );
            
        } catch ( Exception e ) {           
            e.printStackTrace();
            fail();
        }
        
    }

}

Test to check string links are correctly formatted and evidence codes
Test to check string links are correctly formatted and evidence codes
