test/jalview/ext/ensembl/EnsemblXrefTest.java

   1 package jalview.ext.ensembl;
   2
   3 import static org.testng.AssertJUnit.assertEquals;
   4
   5 import jalview.datamodel.DBRefEntry;
   6
   7 import java.io.BufferedReader;
   8 import java.io.IOException;
   9 import java.io.StringReader;
  10 import java.net.URL;
  11 import java.util.List;
  12
  13 import org.testng.annotations.Test;
  14
  15 public class EnsemblXrefTest
  16 {
  17   //@formatter:off
  18   private static final String JSON =
  19           "[{\"primary_id\":\"CCDS5863\",\"dbname\":\"CCDS\"}," +
  20            "{\"primary_id\":\"P15056\",\"dbname\":\"Uniprot/SWISSPROT\",\"synonyms\":[\"C21\"]}," +
  21            "{\"primary_id\":\"GO:0000165\",\"dbname\":\"GO\"}]";
  22   //@formatter:on
  23
  24   @Test(groups = "Functional")
  25   public void testGetCrossReferences()
  26   {
  27     System.out.println(JSON);
  28     EnsemblXref testee = new EnsemblXref("http://rest.ensembl.org")
  29     {
  30       @Override
  31       protected BufferedReader getHttpResponse(URL url, List<String> ids)
  32               throws IOException
  33       {
  34         return new BufferedReader(new StringReader(JSON));
  35       }
  36     };
  37
  38     // synonyms and GO terms are not returned
  39     List<DBRefEntry> dbrefs = testee.getCrossReferences("ABCDE");
  40     assertEquals(2, dbrefs.size());
  41     assertEquals("CCDS", dbrefs.get(0).getSource());
  42     assertEquals("CCDS5863", dbrefs.get(0).getAccessionId());
  43     // Uniprot name should get converted to Jalview canonical form
  44     assertEquals("UNIPROT", dbrefs.get(1).getSource());
  45     assertEquals("P15056", dbrefs.get(1).getAccessionId());
  46   }
  47 }