JAL-1270 ensure before/after clauses have at least alwaysRun=true in them

diff --git a/test/jalview/datamodel/PDBEntryTest.java b/test/jalview/datamodel/PDBEntryTest.java
index 8a3b925..42bb091 100644 (file)
--- a/test/jalview/datamodel/PDBEntryTest.java
+++ b/test/jalview/datamodel/PDBEntryTest.java
@@ -34,7 +34,7 @@ public class PDBEntryTest
   {
   }
 
-  @AfterMethod
+  @AfterMethod(alwaysRun = true)
   public void tearDown() throws Exception
   {
   }

diff --git a/test/jalview/ext/ensembl/EnsemblCdnaTest.java b/test/jalview/ext/ensembl/EnsemblCdnaTest.java
index 90c38d4..fb7e143 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblCdnaTest.java
+++ b/test/jalview/ext/ensembl/EnsemblCdnaTest.java
@@ -21,13 +21,13 @@ import org.testng.annotations.Test;
 
 public class EnsemblCdnaTest
 {
-  @BeforeClass
+  @BeforeClass(alwaysRun = true)
   public void setUp()
   {
     SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
   }
 
-  @AfterClass
+  @AfterClass(alwaysRun = true)
   public void tearDown()
   {
     SequenceOntologyFactory.setInstance(null);

diff --git a/test/jalview/ext/ensembl/EnsemblCdsTest.java b/test/jalview/ext/ensembl/EnsemblCdsTest.java
index 183f933..5344575 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblCdsTest.java
+++ b/test/jalview/ext/ensembl/EnsemblCdsTest.java
@@ -20,13 +20,13 @@ import org.testng.annotations.Test;
 
 public class EnsemblCdsTest
 {
-  @BeforeClass
+  @BeforeClass(alwaysRun = true)
   public void setUp()
   {
     SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
   }
 
-  @AfterClass
+  @AfterClass(alwaysRun = true)
   public void tearDown()
   {
     SequenceOntologyFactory.setInstance(null);

diff --git a/test/jalview/ext/ensembl/EnsemblGeneTest.java b/test/jalview/ext/ensembl/EnsemblGeneTest.java
index 5cf296c..4e815d1 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblGeneTest.java
+++ b/test/jalview/ext/ensembl/EnsemblGeneTest.java
@@ -22,13 +22,13 @@ import org.testng.annotations.Test;
 
 public class EnsemblGeneTest
 {
-  @BeforeClass
+  @BeforeClass(alwaysRun = true)
   public void setUp()
   {
     SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
   }
 
-  @AfterClass
+  @AfterClass(alwaysRun = true)
   public void tearDown()
   {
     SequenceOntologyFactory.setInstance(null);

diff --git a/test/jalview/ext/ensembl/EnsemblGenomeTest.java b/test/jalview/ext/ensembl/EnsemblGenomeTest.java
index daad8b1..c711279 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblGenomeTest.java
+++ b/test/jalview/ext/ensembl/EnsemblGenomeTest.java
@@ -19,13 +19,13 @@ import org.testng.annotations.Test;
 
 public class EnsemblGenomeTest
 {
-  @BeforeClass
+  @BeforeClass(alwaysRun = true)
   public void setUp()
   {
     SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
   }
 
-  @AfterClass
+  @AfterClass(alwaysRun = true)
   public void tearDown()
   {
     SequenceOntologyFactory.setInstance(null);

diff --git a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
index 6ce8a3b..2d3948f 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;
@@ -109,13 +105,13 @@ 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);

diff --git a/test/jalview/ext/jmol/JmolViewerTest.java b/test/jalview/ext/jmol/JmolViewerTest.java
index c9b2980..10224fa 100644 (file)
--- a/test/jalview/ext/jmol/JmolViewerTest.java
+++ b/test/jalview/ext/jmol/JmolViewerTest.java
@@ -53,7 +53,7 @@ public class JmolViewerTest
   /**
    * @throws java.lang.Exception
    */
-  @AfterClass
+  @AfterClass(alwaysRun = true)
   public static void tearDownAfterClass() throws Exception
   {
     jalview.gui.Desktop.instance.closeAll_actionPerformed(null);

diff --git a/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java b/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
index cd28a2b..93a98b8 100644 (file)
--- a/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
+++ b/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
@@ -54,7 +54,7 @@ public class JalviewChimeraView
   /**
    * @throws java.lang.Exception
    */
-  @AfterClass
+  @AfterClass(alwaysRun = true)
   public static void tearDownAfterClass() throws Exception
   {
     jalview.gui.Desktop.instance.closeAll_actionPerformed(null);

diff --git a/test/jalview/ext/so/SequenceOntologyTest.java b/test/jalview/ext/so/SequenceOntologyTest.java
index be07485..1ebc42c 100644 (file)
--- a/test/jalview/ext/so/SequenceOntologyTest.java
+++ b/test/jalview/ext/so/SequenceOntologyTest.java
@@ -3,7 +3,6 @@ package jalview.ext.so;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertTrue;
 
-import jalview.ext.so.SequenceOntology;
 import jalview.io.gff.SequenceOntologyFactory;
 import jalview.io.gff.SequenceOntologyI;
 
@@ -15,7 +14,7 @@ public class SequenceOntologyTest
 {
   private SequenceOntologyI so;
 
-  @BeforeClass
+  @BeforeClass(alwaysRun = true)
   public void setUp() {
     long now = System.currentTimeMillis();
     SequenceOntologyFactory.setInstance(new SequenceOntology());
@@ -25,7 +24,7 @@ public class SequenceOntologyTest
     so = SequenceOntologyFactory.getInstance();
   }
 
-  @AfterClass
+  @AfterClass(alwaysRun = true)
   public void tearDown()
   {
     SequenceOntologyFactory.setInstance(null);

diff --git a/test/jalview/fts/service/pdb/PDBFTSPanelTest.java b/test/jalview/fts/service/pdb/PDBFTSPanelTest.java
index ac1d304..69792bb 100644 (file)
--- a/test/jalview/fts/service/pdb/PDBFTSPanelTest.java
+++ b/test/jalview/fts/service/pdb/PDBFTSPanelTest.java
@@ -23,8 +23,6 @@ package jalview.fts.service.pdb;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertTrue;
 
-import jalview.fts.service.pdb.PDBFTSPanel;
-
 import javax.swing.JInternalFrame;
 import javax.swing.JTextField;
 
@@ -40,7 +38,7 @@ public class PDBFTSPanelTest
   {
   }
 
-  @AfterMethod
+  @AfterMethod(alwaysRun = true)
   public void tearDown() throws Exception
   {
   }

diff --git a/test/jalview/fts/service/pdb/PDBFTSRestClientTest.java b/test/jalview/fts/service/pdb/PDBFTSRestClientTest.java
index ebc0405..ed248bb 100644 (file)
--- a/test/jalview/fts/service/pdb/PDBFTSRestClientTest.java
+++ b/test/jalview/fts/service/pdb/PDBFTSRestClientTest.java
@@ -59,7 +59,7 @@ public class PDBFTSRestClientTest
   {
   }
 
-  @AfterMethod
+  @AfterMethod(alwaysRun = true)
   public void tearDown() throws Exception
   {
   }

diff --git a/test/jalview/gui/JAL1353bugdemo.java b/test/jalview/gui/JAL1353bugdemo.java
index ff8c179..9d0cedb 100644 (file)
--- a/test/jalview/gui/JAL1353bugdemo.java
+++ b/test/jalview/gui/JAL1353bugdemo.java
@@ -47,7 +47,7 @@ public class JAL1353bugdemo
   {
   }
 
-  @AfterClass
+  @AfterClass(alwaysRun = true)
   public static void tearDownAfterClass() throws Exception
   {
   }

diff --git a/test/jalview/gui/PaintRefresherTest.java b/test/jalview/gui/PaintRefresherTest.java
index 52eadcb..212bcce 100644 (file)
--- a/test/jalview/gui/PaintRefresherTest.java
+++ b/test/jalview/gui/PaintRefresherTest.java
@@ -48,7 +48,7 @@ public class PaintRefresherTest
     PaintRefresher.components.clear();
   }
 
-  @AfterMethod
+  @AfterMethod(alwaysRun = true)
   public void tearDown()
   {
     PaintRefresher.components.clear();

diff --git a/test/jalview/gui/StructureChooserTest.java b/test/jalview/gui/StructureChooserTest.java
index ae6bf38..da2cde5 100644 (file)
--- a/test/jalview/gui/StructureChooserTest.java
+++ b/test/jalview/gui/StructureChooserTest.java
@@ -60,7 +60,7 @@ public class StructureChooserTest
     seq.setPDBId(pdbIds);
   }
 
-  @AfterMethod
+  @AfterMethod(alwaysRun = true)
   public void tearDown() throws Exception
   {
     seq = null;

diff --git a/test/jalview/io/AnnotatedPDBFileInputTest.java b/test/jalview/io/AnnotatedPDBFileInputTest.java
index c472576..62d76a2 100644 (file)
--- a/test/jalview/io/AnnotatedPDBFileInputTest.java
+++ b/test/jalview/io/AnnotatedPDBFileInputTest.java
@@ -180,7 +180,7 @@ public class AnnotatedPDBFileInputTest
   /**
    * @throws java.lang.Exception
    */
-  @AfterClass
+  @AfterClass(alwaysRun = true)
   public static void tearDownAfterClass() throws Exception
   {
     jalview.gui.Desktop.instance.closeAll_actionPerformed(null);

diff --git a/test/jalview/io/FileIOTester.java b/test/jalview/io/FileIOTester.java
index cde1cbc..2eb3703 100644 (file)
--- a/test/jalview/io/FileIOTester.java
+++ b/test/jalview/io/FileIOTester.java
@@ -46,7 +46,7 @@ public class FileIOTester
   /**
    * @throws java.lang.Exception
    */
-  @AfterClass
+  @AfterClass(alwaysRun = true)
   public static void tearDownAfterClass() throws Exception
   {
   }

diff --git a/test/jalview/io/JSONFileTest.java b/test/jalview/io/JSONFileTest.java
index d327134..93fb12b 100644 (file)
--- a/test/jalview/io/JSONFileTest.java
+++ b/test/jalview/io/JSONFileTest.java
@@ -262,7 +262,7 @@ public class JSONFileTest
     passedCount = 0;
   }
 
-  @AfterTest
+  @AfterTest(alwaysRun = true)
   public void tearDown() throws Exception
   {
     testJsonFile = null;

diff --git a/test/jalview/io/Jalview2xmlTests.java b/test/jalview/io/Jalview2xmlTests.java
index b45cd2a..00d4ee0 100644 (file)
--- a/test/jalview/io/Jalview2xmlTests.java
+++ b/test/jalview/io/Jalview2xmlTests.java
@@ -62,7 +62,7 @@ public class Jalview2xmlTests
   /**
    * @throws java.lang.Exception
    */
-  @AfterClass
+  @AfterClass(alwaysRun = true)
   public static void tearDownAfterClass() throws Exception
   {
     jalview.gui.Desktop.instance.closeAll_actionPerformed(null);

diff --git a/test/jalview/io/JalviewExportPropertiesTests.java b/test/jalview/io/JalviewExportPropertiesTests.java
index ab3d9df..164c259 100644 (file)
--- a/test/jalview/io/JalviewExportPropertiesTests.java
+++ b/test/jalview/io/JalviewExportPropertiesTests.java
@@ -52,7 +52,7 @@ public class JalviewExportPropertiesTests
   /**
    * @throws java.lang.Exception
    */
-  @AfterClass
+  @AfterClass(alwaysRun = true)
   public static void tearDownAfterClass() throws Exception
   {
     jalview.gui.Desktop.instance.closeAll_actionPerformed(null);

diff --git a/test/jalview/io/NewickFileTests.java b/test/jalview/io/NewickFileTests.java
index d8e21c4..f89f58b 100644 (file)
--- a/test/jalview/io/NewickFileTests.java
+++ b/test/jalview/io/NewickFileTests.java
@@ -172,7 +172,7 @@ public class NewickFileTests
   /**
    * @throws java.lang.Exception
    */
-  @AfterClass
+  @AfterClass(alwaysRun = true)
   public static void tearDownAfterClass() throws Exception
   {
   }

diff --git a/test/jalview/io/RNAMLfileTest.java b/test/jalview/io/RNAMLfileTest.java
index d41446b..c084792 100644 (file)
--- a/test/jalview/io/RNAMLfileTest.java
+++ b/test/jalview/io/RNAMLfileTest.java
@@ -34,7 +34,7 @@ public class RNAMLfileTest
   {
   }
 
-  @AfterClass
+  @AfterClass(alwaysRun = true)
   public static void tearDownAfterClass() throws Exception
   {
   }

diff --git a/test/jalview/ws/jabaws/JalviewJabawsTestUtils.java b/test/jalview/ws/jabaws/JalviewJabawsTestUtils.java
index 46feebc..4550fe8 100644 (file)
--- a/test/jalview/ws/jabaws/JalviewJabawsTestUtils.java
+++ b/test/jalview/ws/jabaws/JalviewJabawsTestUtils.java
@@ -37,7 +37,7 @@ public class JalviewJabawsTestUtils
   {
   }
 
-  @AfterClass
+  @AfterClass(alwaysRun = true)
   public static void tearDownAfterClass() throws Exception
   {
   }

diff --git a/test/jalview/ws/jabaws/JpredJabaStructExportImport.java b/test/jalview/ws/jabaws/JpredJabaStructExportImport.java
index afb24c4..9398d18 100644 (file)
--- a/test/jalview/ws/jabaws/JpredJabaStructExportImport.java
+++ b/test/jalview/ws/jabaws/JpredJabaStructExportImport.java
@@ -84,7 +84,7 @@ public class JpredJabaStructExportImport
     assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
   }
 
-  @AfterClass
+  @AfterClass(alwaysRun = true)
   public static void tearDownAfterClass() throws Exception
   {
     if (af != null)

diff --git a/test/jalview/ws/jabaws/RNAStructExportImport.java b/test/jalview/ws/jabaws/RNAStructExportImport.java
index b57e5d0..24578f1 100644 (file)
--- a/test/jalview/ws/jabaws/RNAStructExportImport.java
+++ b/test/jalview/ws/jabaws/RNAStructExportImport.java
@@ -108,7 +108,7 @@ public class RNAStructExportImport
                                                       // public?
   }
 
-  @AfterClass
+  @AfterClass(alwaysRun = true)
   public static void tearDownAfterClass() throws Exception
   {
     if (af != null)

diff --git a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
index 63b1b9c..341d9ef 100644 (file)
--- a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
+++ b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
@@ -62,7 +62,7 @@ public class DbRefFetcherTest
   /**
    * @throws java.lang.Exception
    */
-  @AfterClass
+  @AfterClass(alwaysRun = true)
   public static void tearDownAfterClass() throws Exception
   {
   }