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 94a5fe0..6698ed1 100644 (file)
--- a/test/jalview/ws/jabaws/DisorderAnnotExportImport.java
+++ b/test/jalview/ws/jabaws/DisorderAnnotExportImport.java
@@ -28,6 +28,8 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.gui.JvOptionPane;
 import jalview.io.AnnotationFile;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
 import jalview.io.FormatAdapter;
 import jalview.io.StockholmFileTest;
 import jalview.ws.jws2.AADisorderClient;
@@ -42,7 +44,11 @@ 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
 {
 
@@ -63,16 +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);
       }
@@ -80,7 +93,7 @@ public class DisorderAnnotExportImport
     assertTrue("Couldn't discover any IUPred services to use to test.",
             iupreds.size() > 0);
     jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
-    af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.FormatAdapter.FILE);
+    af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.DataSourceType.FILE);
     assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
   }
 
@@ -98,7 +111,7 @@ 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);
@@ -116,7 +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)
@@ -136,8 +149,8 @@ public class DisorderAnnotExportImport
   {
     try
     {
-      String aligfileout = new FormatAdapter().formatSequences("PFAM",
-              al.getSequencesArray());
+      String aligfileout = FileFormat.Pfam.getWriter(al).print(
+              al.getSequencesArray(), true);
       String anfileout = new AnnotationFile()
               .printAnnotationsForAlignment(al);
       assertTrue(
@@ -155,16 +168,17 @@ public class DisorderAnnotExportImport
               + "\n<<EOF\n");
 
       AlignmentI al_new = new FormatAdapter().readFile(aligfileout,
-              FormatAdapter.PASTE, "PFAM");
+              DataSourceType.PASTE, FileFormat.Pfam);
       assertTrue(
               "Test "
                       + testname
                       + "\nregenerated annotation file did not annotate alignment.",
               new AnnotationFile().readAnnotationFile(al_new, anfileout,
-                      FormatAdapter.PASTE));
+                      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)
     {