Merge branch 'features/mchmmer' into merge/wsinterfaces_mchmmer_JAL-3070_JAL-1950

[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 9b1dc19..6698ed1 100644 (file)
--- a/test/jalview/ws/jabaws/DisorderAnnotExportImport.java
+++ b/test/jalview/ws/jabaws/DisorderAnnotExportImport.java
@@ -69,16 +69,23 @@ 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();
-    iupreds = new ArrayList<Jws2Instance>();
+
+    while (disc.isRunning())
+    {
+      // don't get services until discoverer has finished
+      Thread.sleep(100);
+    }
+
+    iupreds = new ArrayList<>();
     for (Jws2Instance svc : disc.getServices())
     {
-      if (svc.getServiceTypeURI().toLowerCase().contains("iupredws"))
+      if (svc.getNameURI().toLowerCase().contains("iupredws"))
       {
         iupreds.add(svc);
       }
@@ -122,7 +129,7 @@ public class DisorderAnnotExportImport
     AlignmentI orig_alig = af.getViewport().getAlignment();
     // NOTE: Consensus annotation row cannot be exported and reimported
     // faithfully - so we remove them
-    List<AlignmentAnnotation> toremove = new ArrayList<AlignmentAnnotation>();
+    List<AlignmentAnnotation> toremove = new ArrayList<>();
     for (AlignmentAnnotation aa : orig_alig.getAlignmentAnnotation())
     {
       if (aa.autoCalculated)
@@ -170,7 +177,8 @@ 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)
     {