package jalview.ext.ensembl;

import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;

import jalview.datamodel.DBRefEntry;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.StringReader;
import java.net.URL;
import java.util.List;

import org.testng.annotations.Test;

public class EnsemblXrefTest
{
  //@formatter:off
  private static final String JSON = 
          "[{\"primary_id\":\"CCDS5863\",\"dbname\":\"CCDS\"}," +
           "{\"primary_id\":\"P15056\",\"dbname\":\"Uniprot/SWISSPROT\",\"synonyms\":[\"C21\"]}," +
           "{\"primary_id\":\"GO:0000165\",\"dbname\":\"GO\"}]";
  //@formatter:on

  @Test(groups = "Functional")
  public void testGetCrossReferences()
  {
    String dbName = "ENSEMBL";
    String dbVers = "0.6.2b1";
    System.out.println(JSON);
    EnsemblXref testee = new EnsemblXref("http://rest.ensembl.org", dbName,
            dbVers)
    {
      @Override
      protected BufferedReader getHttpResponse(URL url, List<String> ids)
              throws IOException
      {
        return new BufferedReader(new StringReader(JSON));
      }
    };

    // synonyms and GO terms are not returned
    List<DBRefEntry> dbrefs = testee.getCrossReferences("ABCDE");
    assertEquals(2, dbrefs.size());
    assertEquals("CCDS", dbrefs.get(0).getSource());
    assertEquals("CCDS5863", dbrefs.get(0).getAccessionId());
    assertFalse(dbrefs.get(0).isPrimary());
    assertEquals(dbName + ":" + dbVers, dbrefs.get(0).getVersion());
    // Uniprot name should get converted to Jalview canonical form
    assertEquals("UNIPROT", dbrefs.get(1).getSource());
    assertEquals("P15056", dbrefs.get(1).getAccessionId());
    assertEquals(dbName + ":" + dbVers, dbrefs.get(1).getVersion());
    assertFalse(dbrefs.get(1).isPrimary());
  }
}