JAL-3070 jaba/slivka independent tests for disorder and AACon services

[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..8454e03 100644 (file)
--- a/test/jalview/ws/jabaws/DisorderAnnotExportImport.java
+++ b/test/jalview/ws/jabaws/DisorderAnnotExportImport.java
@@ -32,9 +32,10 @@ import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
 import jalview.io.FormatAdapter;
 import jalview.io.StockholmFileTest;
-import jalview.ws.jws2.AADisorderClient;
+import jalview.ws.api.ServiceWithParameters;
 import jalview.ws.jws2.Jws2Discoverer;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.jws2.SeqAnnotationServiceCalcWorker;
+import jalview.ws.slivkaws.SlivkaWSDiscoverer;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -63,22 +64,30 @@ public class DisorderAnnotExportImport
 
   public static Jws2Discoverer disc;
 
-  public static List<Jws2Instance> iupreds;
+  public static List<ServiceWithParameters> iupreds;
 
-  jalview.ws.jws2.AADisorderClient disorderClient;
+  jalview.ws.jws2.SeqAnnotationServiceCalcWorker disorderClient;
 
   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>();
-    for (Jws2Instance svc : disc.getServices())
+
+    while (disc.isRunning())
+    {
+      // don't get services until discoverer has finished
+      Thread.sleep(100);
+    }
+    SlivkaWSDiscoverer disc2 = SlivkaWSDiscoverer.getInstance();
+    disc2.run();
+    iupreds = new ArrayList<>();
+    for (ServiceWithParameters svc : disc2.getServices())
     {
-      if (svc.getServiceTypeURI().toLowerCase().contains("iupredws"))
+      if (svc.getNameURI().toLowerCase().contains("iupred"))
       {
         iupreds.add(svc);
       }
@@ -107,7 +116,8 @@ public class DisorderAnnotExportImport
   @Test(groups = { "External", "Network" })
   public void testDisorderAnnotExport()
   {
-    disorderClient = new AADisorderClient(iupreds.get(0), af, null, null);
+    disorderClient = new SeqAnnotationServiceCalcWorker(iupreds.get(0), af, null,
+            null);
     af.getViewport().getCalcManager().startWorker(disorderClient);
     do
     {
@@ -122,7 +132,7 @@ 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 +180,8 @@ 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)
     {