X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fensembl%2FEnsemblXrefTest.java;h=9ef2843d707350ea4b0b2b9b43cfd84712b3972f;hb=0afb50988743f5b902ad985793d55104e419da85;hp=50734233a5b1fcc73d3a275c2e6296d05e440e6a;hpb=b40bbf24867e2f44c40e9af6cf43bdfee29c337c;p=jalview.git
diff --git a/test/jalview/ext/ensembl/EnsemblXrefTest.java b/test/jalview/ext/ensembl/EnsemblXrefTest.java
index 5073423..9ef2843 100644
--- a/test/jalview/ext/ensembl/EnsemblXrefTest.java
+++ b/test/jalview/ext/ensembl/EnsemblXrefTest.java
@@ -1,7 +1,27 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.ext.ensembl;
import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertTrue;
+import static org.testng.AssertJUnit.assertFalse;
import jalview.datamodel.DBRefEntry;
@@ -9,7 +29,6 @@ import java.io.BufferedReader;
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;
@@ -19,14 +38,18 @@ public class EnsemblXrefTest
//@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")
+ @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")
+ EnsemblXref testee = new EnsemblXref("http://rest.ensembl.org", dbName,
+ dbVers)
{
@Override
protected BufferedReader getHttpResponse(URL url, List ids)
@@ -36,33 +59,17 @@ public class EnsemblXrefTest
}
};
- /*
- * with no filter
- */
- List dbrefs = testee.getCrossReferences("ABCDE", null);
+ // synonyms and GO terms are not returned
+ List dbrefs = testee.getCrossReferences("ABCDE");
assertEquals(2, dbrefs.size());
assertEquals("CCDS", dbrefs.get(0).getSource());
assertEquals("CCDS5863", dbrefs.get(0).getAccessionId());
+ assertFalse(dbrefs.get(0).isPrimaryCandidate());
+ 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());
-
- /*
- * 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());
+ assertEquals(dbName + ":" + dbVers, dbrefs.get(1).getVersion());
+ assertFalse(dbrefs.get(1).isPrimaryCandidate());
}
}