package jalview.ext.ensembl;
import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertTrue;
import jalview.datamodel.DBRefEntry;
import java.io.IOException;
import java.io.StringReader;
import java.net.URL;
-import java.util.Arrays;
import java.util.List;
import org.testng.annotations.Test;
//@formatter:off
private static final String JSON =
"[{\"primary_id\":\"CCDS5863\",\"dbname\":\"CCDS\"}," +
- "{\"primary_id\":\"P15056\",\"dbname\":\"Uniprot/SWISSPROT\"}]";
+ "{\"primary_id\":\"P15056\",\"dbname\":\"Uniprot/SWISSPROT\",\"synonyms\":[\"C21\"]}," +
+ "{\"primary_id\":\"GO:0000165\",\"dbname\":\"GO\"}]";
//@formatter:on
@Test(groups = "functional")
}
};
- /*
- * with no filter
- */
- List<DBRefEntry> dbrefs = testee.getCrossReferences("ABCDE", null);
+ // 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());
// Uniprot name should get converted to Jalview canonical form
assertEquals("UNIPROT", dbrefs.get(1).getSource());
assertEquals("P15056", dbrefs.get(1).getAccessionId());
-
- /*
- * filter for Uniprot only
- */
- dbrefs = testee.getCrossReferences(
- "ABCDE",
- Arrays.asList(new String[] { "Uniprot/SWISSPROT",
- "Uniprot/SPTREMBL" }));
- assertEquals(1, dbrefs.size());
- assertEquals("UNIPROT", dbrefs.get(0).getSource());
- assertEquals("P15056", dbrefs.get(0).getAccessionId());
-
- /*
- * filter for PDB only
- */
- dbrefs = testee.getCrossReferences("ABCDE",
- Arrays.asList(new String[] { "PDB" }));
- assertTrue(dbrefs.isEmpty());
}
}