JAL-1805 test envirionment separation

[jalview.git] / test / jalview / ws / seqfetcher / DbRefFetcherTest.java

diff --git a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
index afaadbb..abaa7ec 100644 (file)
--- a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
+++ b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
@@ -20,9 +20,10 @@
  */
 package jalview.ws.seqfetcher;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertTrue;
+
 import jalview.analysis.CrossRef;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
@@ -33,9 +34,9 @@ import jalview.ws.SequenceFetcher;
 import java.util.ArrayList;
 import java.util.List;
 
-import org.junit.AfterClass;
-import org.junit.BeforeClass;
-import org.junit.Test;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
 
 /**
  * @author jimp
@@ -50,6 +51,7 @@ public class DbRefFetcherTest
   @BeforeClass
   public static void setUpBeforeClass() throws Exception
   {
+    jalview.bin.Cache.initLogger();
   }
 
   /**
@@ -60,7 +62,7 @@ public class DbRefFetcherTest
   {
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void testStandardProtDbs()
   {
     String[] defdb = DBRefSource.PROTEINDBS;
@@ -97,18 +99,40 @@ public class DbRefFetcherTest
             uniprot != null && i < 2);
   }
 
-  @Test
+  @Test(groups =
+  { "External" })
   public void testEmblUniprotProductRecovery() throws Exception
   {
     String retrievalId = "CAA23748"; // "V00488";
     DbSourceProxy embl = new SequenceFetcher().getSourceProxy(DBRefSource.EMBL).get(0);
-    assertNotNull("Couldn't find the EMBL retrieval client",embl);
+    assertNotNull("Couldn't find the EMBL retrieval client", embl);
+    verifyProteinNucleotideXref(retrievalId, embl);
+  }
+
+  @Test(groups =
+  { "External" })
+  public void testEmblCDSUniprotProductRecovery() throws Exception
+  {
+    String retrievalId = "AAH29712";
+    DbSourceProxy embl = new SequenceFetcher().getSourceProxy(
+            DBRefSource.EMBLCDS).get(0);
+    assertNotNull("Couldn't find the EMBL retrieval client", embl);
+    verifyProteinNucleotideXref(retrievalId, embl);
+  }
+
+  private void verifyProteinNucleotideXref(String retrievalId,
+          DbSourceProxy embl) throws Exception
+  {
     AlignmentI alsq = embl.getSequenceRecords(retrievalId);
     assertNotNull("Couldn't find the EMBL record " + retrievalId, alsq);
     assertEquals("Didn't retrieve right number of records", 1, alsq.getHeight());
     DBRefEntry[] dr = DBRefUtils.selectRefs(alsq.getSequenceAt(0).getDBRef(), DBRefSource.PROTEINSEQ);
     assertNotNull(dr);
     assertEquals("Expected a single Uniprot cross reference", 1, dr.length);
+    assertEquals("Expected cross refernce map to be one amino acid", dr[0]
+            .getMap().getMappedWidth(), 1);
+    assertEquals("Expected local refernce map to be 3 nucleotides", dr[0]
+            .getMap().getWidth(), 3);
     AlignmentI sprods = CrossRef.findXrefSequences(alsq.getSequencesArray(), true, dr[0].getSource(), alsq.getDataset());
     assertNotNull(
             "Couldn't recover cross reference sequence from dataset. Was it ever added ?",