JAL-1805 modified test setup's so the are ran for groups which requires them

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

diff --git a/test/jalview/io/AnnotatedPDBFileInputTest.java b/test/jalview/io/AnnotatedPDBFileInputTest.java
index 29d5549..31bfd9d 100644 (file)
--- a/test/jalview/io/AnnotatedPDBFileInputTest.java
+++ b/test/jalview/io/AnnotatedPDBFileInputTest.java
@@ -1,9 +1,10 @@
 package jalview.io;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotEquals;
-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.bin.Cache;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
@@ -15,12 +16,12 @@ import jalview.structure.StructureMapping;
 import jalview.structure.StructureSelectionManager;
 
 import java.io.File;
-import java.util.Vector;
 
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.BeforeClass;
-import org.junit.Test;
+import org.junit.Assert;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
 
 public class AnnotatedPDBFileInputTest
 {
@@ -31,18 +32,22 @@ public class AnnotatedPDBFileInputTest
 
   String pdbId;
 
-  @Before
+ @BeforeMethod(alwaysRun = true)
   public void setup() throws Exception
   {
+    Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
+            Boolean.TRUE.toString());
+    Cache.applicationProperties.setProperty("ADD_SS_ANN",
+            Boolean.TRUE.toString());
     FileLoader loader = new FileLoader(false);
     AlignFrame af = loader.LoadFileWaitTillLoaded(pdbStr,
             FormatAdapter.FILE);
     al = af.getViewport().getAlignment();
-    pdbId = ((PDBEntry) al.getSequenceAt(0).getDatasetSequence().getPDBId()
-            .get(0)).getId();
+    pdbId = al.getSequenceAt(0).getDatasetSequence().getPDBId()
+            .get(0).getId();
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void checkNoDuplicates()
   {
     // not strictly a requirement, but strange things may happen if multiple
@@ -55,14 +60,14 @@ public class AnnotatedPDBFileInputTest
     {
       for (int q = p + 1; q < avec.length; q++)
       {
-        assertNotEquals(
+        Assert.assertNotEquals(
                 "Found a duplicate annotation row " + avec[p].label,
                 avec[p], avec[q]);
       }
     }
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void checkPDBannotationSource()
   {
 
@@ -80,7 +85,7 @@ public class AnnotatedPDBFileInputTest
   /**
    * Check sequence features have been added
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void checkPDBSequenceFeatures()
   {
     StructureSelectionManager ssm = StructureSelectionManager
@@ -119,7 +124,7 @@ public class AnnotatedPDBFileInputTest
     assertEquals("TYR:314 1gaqC", sf[295].getDescription());
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void checkAnnotationWiring()
   {
     assertTrue(al.getAlignmentAnnotation() != null);
@@ -151,7 +156,7 @@ public class AnnotatedPDBFileInputTest
   /**
    * @throws java.lang.Exception
    */
-  @BeforeClass
+  @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
   {
     jalview.bin.Jalview.main(new String[]
@@ -168,7 +173,7 @@ public class AnnotatedPDBFileInputTest
 
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void testJalviewProjectRelocationAnnotation() throws Exception
   {
 
@@ -194,7 +199,7 @@ public class AnnotatedPDBFileInputTest
       }
       assertNotNull(sq.getPDBId());
       assertEquals("Expected only one PDB ID", sq.getPDBId().size(), 1);
-      for (PDBEntry pdbentry : (Vector<PDBEntry>) sq.getPDBId())
+      for (PDBEntry pdbentry : sq.getPDBId())
       {
         System.err.println("PDB Entry " + pdbentry.getId() + " "
                 + pdbentry.getFile());