X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fjabaws%2FRNAStructExportImport.java;h=889c0038462c86fcb7307196dcbc14fd6c6b295b;hb=bc18effe68ba80213a6d03ca7e6175adc6be71d6;hp=418e8275c7801717b13b835f86c70983e1de82ad;hpb=5f4e1e4c330b045e9c8bce28ee132a0fca3834d8;p=jalview.git

diff --git a/test/jalview/ws/jabaws/RNAStructExportImport.java b/test/jalview/ws/jabaws/RNAStructExportImport.java
index 418e827..889c003 100644
--- a/test/jalview/ws/jabaws/RNAStructExportImport.java
+++ b/test/jalview/ws/jabaws/RNAStructExportImport.java
@@ -26,12 +26,13 @@ import static org.testng.AssertJUnit.assertTrue;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
-import jalview.gui.Jalview2XML;
 import jalview.gui.JvOptionPane;
 import jalview.io.AnnotationFile;
-import jalview.io.FileLoader;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
 import jalview.io.FormatAdapter;
 import jalview.io.StockholmFileTest;
+import jalview.project.Jalview2XML;
 import jalview.ws.jws2.Jws2Discoverer;
 import jalview.ws.jws2.RNAalifoldClient;
 import jalview.ws.jws2.SequenceAnnotationWSClient;
@@ -54,6 +55,11 @@ import org.testng.annotations.Test;
 import compbio.metadata.Argument;
 import compbio.metadata.WrongParameterException;
 
+/*
+ * 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 RNAStructExportImport
 {
 
@@ -83,6 +89,12 @@ public class RNAStructExportImport
     Cache.initLogger();
     disc = JalviewJabawsTestUtils.getJabawsDiscoverer(false);
 
+    while (disc.isRunning())
+    {
+      // don't get services until discoverer has finished
+      Thread.sleep(100);
+    }
+
     for (Jws2Instance svc : disc.getServices())
     {
 
@@ -99,14 +111,14 @@ public class RNAStructExportImport
       Assert.fail("no web service");
     }
 
-    FileLoader fl = new FileLoader(false);
+    jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
 
-    af = fl.LoadFileWaitTillLoaded(testseqs, FormatAdapter.FILE);
+    af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.DataSourceType.FILE);
 
     assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
 
     // remove any existing annotation
-    List<AlignmentAnnotation> aal = new ArrayList<AlignmentAnnotation>();
+    List<AlignmentAnnotation> aal = new ArrayList<>();
     for (AlignmentAnnotation rna : af.getViewport().getAlignment()
             .getAlignmentAnnotation())
     {
@@ -138,7 +150,7 @@ public class RNAStructExportImport
     }
   }
 
-  @Test(groups = { "Functional" })
+  @Test(groups = { "Network" })
   public void testRNAAliFoldValidStructure()
   {
 
@@ -171,7 +183,7 @@ public class RNAStructExportImport
     }
   }
 
-  @Test(groups = { "Functional" })
+  @Test(groups = { "Network" })
   public void testRNAStructExport()
   {
 
@@ -190,18 +202,20 @@ public class RNAStructExportImport
     } while (af.getViewport().getCalcManager().isWorking());
 
     AlignmentI orig_alig = af.getViewport().getAlignment();
-
-    testAnnotationFileIO("Testing RNAalifold Annotation IO", orig_alig);
+    // JBPNote: this assert fails (2.10.2) because the 'Reference Positions'
+    // annotation is mistakenly recognised as an RNA annotation row when read in
+    // as an annotation file.
+    verifyAnnotationFileIO("Testing RNAalifold Annotation IO", orig_alig);
 
   }
 
-  public static void testAnnotationFileIO(String testname, AlignmentI al)
+  static void verifyAnnotationFileIO(String testname, AlignmentI al)
   {
     try
     {
       // what format would be appropriate for RNAalifold annotations?
-      String aligfileout = new FormatAdapter().formatSequences("PFAM",
-              al.getSequencesArray());
+      String aligfileout = FileFormat.Pfam.getWriter(null).print(
+              al.getSequencesArray(), true);
 
       String anfileout = new AnnotationFile()
               .printAnnotationsForAlignment(al);
@@ -221,16 +235,17 @@ public class RNAStructExportImport
 
       // again what format would be appropriate?
       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, false);
+      StockholmFileTest.testAlignmentEquivalence(al, al_new, false, false,
+              false);
       return;
     } catch (Exception e)
     {
@@ -241,10 +256,10 @@ public class RNAStructExportImport
             + "\nCouldn't complete Annotation file roundtrip input/output/input test.");
   }
 
-  @Test(groups = { "Functional" })
+  @Test(groups = { "Network" })
   public void testRnaalifoldSettingsRecovery()
   {
-    List<Argument> opts = new ArrayList<Argument>();
+    List<Argument> opts = new ArrayList<>();
     for (Argument rg : (List<Argument>) rnaalifoldws.getRunnerConfig()
             .getArguments())
     {