JAL-1805 test envirionment separation

[jalview.git] / test / jalview / io / Jalview2xmlTests.java

diff --git a/test/jalview/io/Jalview2xmlTests.java b/test/jalview/io/Jalview2xmlTests.java
index 8b83934..c03dd71 100644 (file)
--- a/test/jalview/io/Jalview2xmlTests.java
+++ b/test/jalview/io/Jalview2xmlTests.java
@@ -20,10 +20,11 @@
  */
 package jalview.io;
 
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
+import static org.testng.AssertJUnit.assertTrue;
+
 import jalview.api.AlignmentViewPanel;
 import jalview.api.ViewStyleI;
+import jalview.bin.Cache;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
@@ -34,10 +35,11 @@ import jalview.schemes.ColourSchemeI;
 
 import java.io.File;
 
-import org.junit.AfterClass;
-import org.junit.Assert;
-import org.junit.BeforeClass;
-import org.junit.Test;
+import org.testng.Assert;
+import org.testng.AssertJUnit;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
 
 public class Jalview2xmlTests
 {
@@ -81,7 +83,7 @@ public class Jalview2xmlTests
     return numdsann;
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void testRNAStructureRecovery() throws Exception
   {
     String inFile = "examples/RF00031_folded.stk";
@@ -116,7 +118,7 @@ public class Jalview2xmlTests
             af.getViewport().getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void testTCoffeeScores() throws Exception
   {
     String inFile = "examples/uniref50.fa", inAnnot = "examples/uniref50.score_ascii";
@@ -152,7 +154,7 @@ public class Jalview2xmlTests
             .println("T-Coffee score shading successfully recovered from project.");
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void testColourByAnnotScores() throws Exception
   {
     String inFile = "examples/uniref50.fa", inAnnot = "examples/testdata/uniref50_iupred.jva";
@@ -238,7 +240,7 @@ public class Jalview2xmlTests
             .println("Per sequence (Group) colourscheme successfully applied and recovered.");
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void gatherViewsHere() throws Exception
   {
     int origCount = Desktop.getAlignFrames() == null ? 0 : Desktop
@@ -251,9 +253,13 @@ public class Jalview2xmlTests
 
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void viewRefPdbAnnotation() throws Exception
   {
+    Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
+            Boolean.TRUE.toString());
+    Cache.applicationProperties.setProperty("ADD_SS_ANN",
+            Boolean.TRUE.toString());
     AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
             "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
     assertTrue("Didn't read in the example file correctly.", af != null);
@@ -299,7 +305,7 @@ public class Jalview2xmlTests
           }
           catch (NullPointerException q)
           {
-            fail("Mismatch of alignment annotations at position " + p
+            Assert.fail("Mismatch of alignment annotations at position " + p
                     + " Ref seq ann: " + refan.annotations[p]
                     + " alignment " + alaa.annotations[p]);
           }
@@ -309,12 +315,12 @@ public class Jalview2xmlTests
     
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void testCopyViewSettings() throws Exception
   {
     AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
             "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
-    Assert.assertTrue("Didn't read in the example file correctly.", af != null);
+    assertTrue("Didn't read in the example file correctly.", af != null);
     AlignmentViewPanel sps = null, groups = null;
     for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels())
     {
@@ -332,10 +338,10 @@ public class Jalview2xmlTests
 
     ViewStyleI structureStyle = sps.getAlignViewport().getViewStyle();
     ViewStyleI groupStyle = groups.getAlignViewport().getViewStyle();
-    Assert.assertFalse(structureStyle.sameStyle(groupStyle));
+    AssertJUnit.assertFalse(structureStyle.sameStyle(groupStyle));
 
     groups.getAlignViewport().setViewStyle(structureStyle);
-    Assert.assertFalse(groupStyle.sameStyle(groups.getAlignViewport()
+    AssertJUnit.assertFalse(groupStyle.sameStyle(groups.getAlignViewport()
             .getViewStyle()));
     Assert.assertTrue(structureStyle.sameStyle(groups.getAlignViewport()
             .getViewStyle()));