JAL-2189 format tests

[jalview.git] / test / jalview / ext / ensembl / EnsemblSeqProxyTest.java

diff --git a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
index 6df479c..3ca4553 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
+++ b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
@@ -6,7 +6,6 @@ import static org.testng.AssertJUnit.assertTrue;
 import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
 
 import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.io.AppletFormatAdapter;
@@ -16,10 +15,7 @@ import jalview.io.gff.SequenceOntologyFactory;
 import jalview.io.gff.SequenceOntologyLite;
 
 import java.lang.reflect.Method;
-import java.net.MalformedURLException;
-import java.net.URL;
 import java.util.Arrays;
-import java.util.List;
 
 import org.testng.Assert;
 import org.testng.annotations.AfterClass;
@@ -27,7 +23,6 @@ import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
-
 public class EnsemblSeqProxyTest
 {
   private static final Object[][] allSeqs = new Object[][] {
@@ -109,13 +104,13 @@ public class EnsemblSeqProxyTest
                   + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
                   + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH" } };
 
-  @BeforeClass
+  @BeforeClass(alwaysRun = true)
   public void setUp()
   {
     SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
   }
 
-  @AfterClass
+  @AfterClass(alwaysRun = true)
   public void tearDown()
   {
     SequenceOntologyFactory.setInstance(null);
@@ -129,12 +124,11 @@ public class EnsemblSeqProxyTest
   }
 
   @Test(dataProvider = "ens_seqs", suiteName = "live")
-  public void testGetOneSeqs(EnsemblRestClient proxy, String sq, String fastasq)
-          throws Exception
+  public void testGetOneSeqs(EnsemblRestClient proxy, String sq,
+          String fastasq) throws Exception
   {
     FileParse fp = proxy.getSequenceReader(Arrays
-            .asList(new String[]
-    { sq }));
+            .asList(new String[] { sq }));
     SequenceI[] sqs = new FastaFile(fp).getSeqsAsArray();
     FastaFile trueRes = new FastaFile(fastasq, AppletFormatAdapter.PASTE);
     SequenceI[] trueSqs = trueRes.getSeqsAsArray();
@@ -156,63 +150,8 @@ public class EnsemblSeqProxyTest
               "Sequences differ for " + tr.getName() + "\n" + "Exp:"
                       + tr.getSequenceAsString() + "\n" + "Got:"
                       + rseq[0].getSequenceAsString());
-  
-    }
-  }
-
-  @Test(suiteName = "live")
-  public void testLiveCheckEnsembl()
-  {
-    EnsemblRestClient sf = new EnsemblRestClient()
-    {
-
-      @Override
-      public String getDbName()
-      {
-        // TODO Auto-generated method stub
-        return null;
-      }
-
-      @Override
-      public AlignmentI getSequenceRecords(String queries) throws Exception
-      {
-        // TODO Auto-generated method stub
-        return null;
-      }
 
-      @Override
-      protected URL getUrl(List<String> ids) throws MalformedURLException
-      {
-        // TODO Auto-generated method stub
-        return null;
-      }
-
-      @Override
-      protected boolean useGetRequest()
-      {
-        // TODO Auto-generated method stub
-        return false;
-      }
-
-      @Override
-      protected String getRequestMimeType(boolean b)
-      {
-        // TODO Auto-generated method stub
-        return null;
-      }
-
-      @Override
-      protected String getResponseMimeType()
-      {
-        // TODO Auto-generated method stub
-        return null;
-      }
-
-    };
-    boolean isAvailable = sf.isEnsemblAvailable();
-    System.out.println("Ensembl is "
-            + (isAvailable ? "UP!"
-                    : "DOWN or unreachable ******************* BAD!"));
+    }
   }
 
   @Test(groups = "Functional")
@@ -267,7 +206,8 @@ public class EnsemblSeqProxyTest
     sb = new StringBuilder();
     EnsemblSeqProxy.reverseComplementAllele(sb, "-GATt"); // revcomp=aATC-
     EnsemblSeqProxy.reverseComplementAllele(sb, "hgmd_mutation");
-    assertEquals("aATC-,hgmd_mutation", sb.toString());
+    EnsemblSeqProxy.reverseComplementAllele(sb, "PhenCode_variation");
+    assertEquals("aATC-,hgmd_mutation,PhenCode_variation", sb.toString());
   }
 
   /**