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.assertTrue;
   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.Arrays;
  13 import java.util.List;
  14
  15 import org.testng.annotations.Test;
  16
  17 public class EnsemblXrefTest
  18 {
  19   //@formatter:off
  20   private static final String JSON =
  21           "[{\"primary_id\":\"CCDS5863\",\"dbname\":\"CCDS\"}," +
  22            "{\"primary_id\":\"P15056\",\"dbname\":\"Uniprot/SWISSPROT\"}]";
  23   //@formatter:on
  24
  25   @Test(groups = "functional")
  26   public void testGetCrossReferences()
  27   {
  28     System.out.println(JSON);
  29     EnsemblXref testee = new EnsemblXref("http://rest.ensembl.org")
  30     {
  31       @Override
  32       protected BufferedReader getHttpResponse(URL url, List<String> ids)
  33               throws IOException
  34       {
  35         return new BufferedReader(new StringReader(JSON));
  36       }
  37     };
  38
  39     /*
  40      * with no filter
  41      */
  42     List<DBRefEntry> dbrefs = testee.getCrossReferences("ABCDE", null);
  43     assertEquals(2, dbrefs.size());
  44     assertEquals("CCDS", dbrefs.get(0).getSource());
  45     assertEquals("CCDS5863", dbrefs.get(0).getAccessionId());
  46     // Uniprot name should get converted to Jalview canonical form
  47     assertEquals("UNIPROT", dbrefs.get(1).getSource());
  48     assertEquals("P15056", dbrefs.get(1).getAccessionId());
  49
  50     /*
  51      * filter for Uniprot only
  52      */
  53     dbrefs = testee.getCrossReferences(
  54             "ABCDE",
  55             Arrays.asList(new String[] { "Uniprot/SWISSPROT",
  56                 "Uniprot/SPTREMBL" }));
  57     assertEquals(1, dbrefs.size());
  58     assertEquals("UNIPROT", dbrefs.get(0).getSource());
  59     assertEquals("P15056", dbrefs.get(0).getAccessionId());
  60
  61     /*
  62      * filter for PDB only
  63      */
  64     dbrefs = testee.getCrossReferences("ABCDE",
  65             Arrays.asList(new String[] { "PDB" }));
  66     assertTrue(dbrefs.isEmpty());
  67   }
  68 }