X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fjabaws%2FJpredJabaStructExportImport.java;h=22cdd4c819f67cb048979a74c3e2465818d2bfd1;hb=5f4e1e4c330b045e9c8bce28ee132a0fca3834d8;hp=baf06546db53e7636d4f43a6ec55a0ab6a0ab29a;hpb=5f326a3fc836403095b2a5038261a0e75f8d170f;p=jalview.git

diff --git a/test/jalview/ws/jabaws/JpredJabaStructExportImport.java b/test/jalview/ws/jabaws/JpredJabaStructExportImport.java
index baf0654..22cdd4c 100644
--- a/test/jalview/ws/jabaws/JpredJabaStructExportImport.java
+++ b/test/jalview/ws/jabaws/JpredJabaStructExportImport.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,11 +20,13 @@
  */
 package jalview.ws.jabaws;
 
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.gui.Jalview2XML;
+import jalview.gui.JvOptionPane;
 import jalview.io.AnnotationFile;
 import jalview.io.FormatAdapter;
 import jalview.io.StockholmFileTest;
@@ -42,15 +44,24 @@ import java.util.List;
 import javax.swing.JMenu;
 import javax.swing.JMenuItem;
 
-import org.junit.AfterClass;
-import org.junit.BeforeClass;
-import org.junit.Test;
+import org.testng.Assert;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
 
 import compbio.metadata.Argument;
 import compbio.metadata.WrongParameterException;
 
 public class JpredJabaStructExportImport
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   public static String testseqs = "examples/uniref50.fa";
 
   public static Jws2Discoverer disc;
@@ -61,16 +72,15 @@ public class JpredJabaStructExportImport
 
   public static jalview.gui.AlignFrame af = null;
 
-  @BeforeClass
+  @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
   {
-
-    jalview.bin.Cache.initLogger();
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
+    Cache.initLogger();
     disc = JalviewJabawsTestUtils.getJabawsDiscoverer(false);
 
     for (Jws2Instance svc : disc.getServices())
     {
-
       if (svc.getServiceTypeURI().toLowerCase().contains("jpred"))
       {
         jpredws = svc;
@@ -78,21 +88,13 @@ public class JpredJabaStructExportImport
     }
 
     System.out.println("State of jpredws: " + jpredws);
-
-    if (jpredws == null)
-    {
-      System.exit(0);
-    }
-
+    Assert.assertNotNull(jpredws, "jpredws is null!");
     jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
-
     af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.FormatAdapter.FILE);
-
     assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
-
   }
 
-  @AfterClass
+  @AfterClass(alwaysRun = true)
   public static void tearDownAfterClass() throws Exception
   {
     if (af != null)
@@ -102,7 +104,7 @@ public class JpredJabaStructExportImport
     }
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void testJPredStructOneSeqOnly()
   {
     af.selectAllSequenceMenuItem_actionPerformed(null);
@@ -143,7 +145,7 @@ public class JpredJabaStructExportImport
         if (!success)
         {
           jpredClient.cancelCurrentJob();
-          fail("Jpred Client didn't run with hardwired default parameters.");
+          Assert.fail("Jpred Client didn't run with hardwired default parameters.");
         }
 
       } catch (InterruptedException x)
@@ -154,7 +156,7 @@ public class JpredJabaStructExportImport
 
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void testJPredStructExport()
   {
 
@@ -214,21 +216,21 @@ public class JpredJabaStructExportImport
                       FormatAdapter.PASTE));
 
       // test for consistency in io
-      StockholmFileTest.testAlignmentEquivalence(al, al_new);
+      StockholmFileTest.testAlignmentEquivalence(al, al_new, false);
       return;
     } catch (Exception e)
     {
       e.printStackTrace();
     }
-    fail("Test "
+    Assert.fail("Test "
             + testname
             + "\nCouldn't complete Annotation file roundtrip input/output/input test.");
   }
 
-  // @Test
+  @Test(groups = { "Functional" })
   public void testJpredwsSettingsRecovery()
   {
-    fail("not implemnented");
+    Assert.fail("not implemnented");
     List<compbio.metadata.Argument> opts = new ArrayList<compbio.metadata.Argument>();
     for (compbio.metadata.Argument rg : (List<compbio.metadata.Argument>) jpredws
             .getRunnerConfig().getArguments())
@@ -240,7 +242,7 @@ public class JpredJabaStructExportImport
           rg.setValue("292");
         } catch (WrongParameterException q)
         {
-          fail("Couldn't set the temperature parameter "
+          Assert.fail("Couldn't set the temperature parameter "
                   + q.getStackTrace());
         }
         opts.add(rg);
@@ -270,10 +272,10 @@ public class JpredJabaStructExportImport
     // write out parameters
     jalview.gui.AlignFrame nalf = null;
     assertTrue("Couldn't write out the Jar file",
-            new Jalview2XML(false).SaveAlignment(af,
+            new Jalview2XML(false).saveAlignment(af,
                     "testJPredWS_param.jar", "trial parameter writeout"));
     assertTrue("Couldn't read back the Jar file", (nalf = new Jalview2XML(
-            false).LoadJalviewAlign("testJpredWS_param.jar")) != null);
+            false).loadJalviewAlign("testJpredWS_param.jar")) != null);
     if (nalf != null)
     {
       AutoCalcSetting acs = af.getViewport().getCalcIdSettingsFor(