test/jalview/ext/ensembl/EnsemblXrefTest.java

   1 package jalview.ext.ensembl;
   2
   3 import static org.testng.AssertJUnit.assertEquals;
   4 import static org.testng.AssertJUnit.assertFalse;
   5
   6 import jalview.datamodel.DBRefEntry;
   7
   8 import java.io.BufferedReader;
   9 import java.io.IOException;
  10 import java.io.StringReader;
  11 import java.net.URL;
  12 import java.util.List;
  13
  14 import org.testng.annotations.Test;
  15
  16 public class EnsemblXrefTest
  17 {
  18   //@formatter:off
  19   private static final String JSON =
  20           "[{\"primary_id\":\"CCDS5863\",\"dbname\":\"CCDS\"}," +
  21            "{\"primary_id\":\"P15056\",\"dbname\":\"Uniprot/SWISSPROT\",\"synonyms\":[\"C21\"]}," +
  22            "{\"primary_id\":\"GO:0000165\",\"dbname\":\"GO\"}]";
  23   //@formatter:on
  24
  25   @Test(groups = "Functional")
  26   public void testGetCrossReferences()
  27   {
  28     String dbName = "ENSEMBL";
  29     String dbVers = "0.6.2b1";
  30     System.out.println(JSON);
  31     EnsemblXref testee = new EnsemblXref("http://rest.ensembl.org", dbName,
  32             dbVers)
  33     {
  34       @Override
  35       protected BufferedReader getHttpResponse(URL url, List<String> ids)
  36               throws IOException
  37       {
  38         return new BufferedReader(new StringReader(JSON));
  39       }
  40     };
  41
  42     // synonyms and GO terms are not returned
  43     List<DBRefEntry> dbrefs = testee.getCrossReferences("ABCDE");
  44     assertEquals(2, dbrefs.size());
  45     assertEquals("CCDS", dbrefs.get(0).getSource());
  46     assertEquals("CCDS5863", dbrefs.get(0).getAccessionId());
  47     assertFalse(dbrefs.get(0).isPrimaryCandidate());
  48     assertEquals(dbName + ":" + dbVers, dbrefs.get(0).getVersion());
  49     // Uniprot name should get converted to Jalview canonical form
  50     assertEquals("UNIPROT", dbrefs.get(1).getSource());
  51     assertEquals("P15056", dbrefs.get(1).getAccessionId());
  52     assertEquals(dbName + ":" + dbVers, dbrefs.get(1).getVersion());
  53     assertFalse(dbrefs.get(1).isPrimaryCandidate());
  54   }
  55 }