JAL-3691 automatic insertion of Locale.ROOT to toUpperCase() and toLowerCase() and...

[jalview.git] / test / jalview / ws / jabaws / DisorderAnnotExportImport.java

diff --git a/test/jalview/ws/jabaws/DisorderAnnotExportImport.java b/test/jalview/ws/jabaws/DisorderAnnotExportImport.java
index 85c075b..d13dc0f 100644 (file)
--- a/test/jalview/ws/jabaws/DisorderAnnotExportImport.java
+++ b/test/jalview/ws/jabaws/DisorderAnnotExportImport.java
@@ -20,12 +20,15 @@
  */
 package jalview.ws.jabaws;
 
+import java.util.Locale;
+
 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.gui.JvOptionPane;
 import jalview.io.AnnotationFile;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
@@ -43,9 +46,21 @@ import org.testng.annotations.AfterClass;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
-@Test(groups = { "External" })
+/*
+ * All methods in this class are set to the Network group because setUpBeforeClass will fail
+ * if there is no network.
+ */
+@Test(singleThreaded = true)
 public class DisorderAnnotExportImport
 {
+
+  @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;
@@ -56,16 +71,23 @@ public class DisorderAnnotExportImport
 
   public static jalview.gui.AlignFrame af = null;
 
-  @BeforeClass(inheritGroups = true)
+  @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
   {
     Cache.loadProperties("test/jalview/io/testProps.jvprops");
     Cache.initLogger();
     disc = JalviewJabawsTestUtils.getJabawsDiscoverer();
+
+    while (disc.isRunning())
+    {
+      // don't get services until discoverer has finished
+      Thread.sleep(100);
+    }
+
     iupreds = new ArrayList<Jws2Instance>();
     for (Jws2Instance svc : disc.getServices())
     {
-      if (svc.getServiceTypeURI().toLowerCase().contains("iupredws"))
+      if (svc.getServiceTypeURI().toLowerCase(Locale.ROOT).contains("iupredws"))
       {
         iupreds.add(svc);
       }
@@ -91,7 +113,7 @@ public class DisorderAnnotExportImport
   /**
    * test for patches to JAL-1294
    */
-  @Test
+  @Test(groups = { "External", "Network" })
   public void testDisorderAnnotExport()
   {
     disorderClient = new AADisorderClient(iupreds.get(0), af, null, null);
@@ -121,15 +143,15 @@ public class DisorderAnnotExportImport
     {
       orig_alig.deleteAnnotation(aa);
     }
-    testAnnotationFileIO("Testing IUPred Annotation IO", orig_alig);
+    checkAnnotationFileIO("Testing IUPred Annotation IO", orig_alig);
 
   }
 
-  public static void testAnnotationFileIO(String testname, AlignmentI al)
+  static void checkAnnotationFileIO(String testname, AlignmentI al)
   {
     try
     {
-      String aligfileout = FileFormat.Pfam.getAlignmentFile().print(
+      String aligfileout = FileFormat.Pfam.getWriter(al).print(
               al.getSequencesArray(), true);
       String anfileout = new AnnotationFile()
               .printAnnotationsForAlignment(al);
@@ -157,7 +179,8 @@ public class DisorderAnnotExportImport
                       DataSourceType.PASTE));
 
       // test for consistency in io
-      StockholmFileTest.testAlignmentEquivalence(al, al_new, true);
+      StockholmFileTest.testAlignmentEquivalence(al, al_new, true, false,
+              false);
       return;
     } catch (Exception e)
     {