X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fjabaws%2FRNAStructExportImport.java;h=292a48a039e717ee26ac31f9febe06c2f23d3a2b;hb=cfb79b69d9fa44595560659bd95d1d1cd27677ad;hp=fbee3a7ef2bea12a13d6920b7566fb6d0f1926de;hpb=8b27085fa7fc5f2877e078421284c2636b85b8c6;p=jalview.git

diff --git a/test/jalview/ws/jabaws/RNAStructExportImport.java b/test/jalview/ws/jabaws/RNAStructExportImport.java
index fbee3a7..292a48a 100644
--- a/test/jalview/ws/jabaws/RNAStructExportImport.java
+++ b/test/jalview/ws/jabaws/RNAStructExportImport.java
@@ -26,14 +26,17 @@ 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.DataSourceType;
 import jalview.io.FileFormat;
 import jalview.io.FormatAdapter;
 import jalview.io.StockholmFileTest;
+import jalview.project.Jalview2XML;
+import jalview.ws.api.ServiceWithParameters;
+import jalview.ws.jws2.JabaParamStore;
 import jalview.ws.jws2.Jws2Discoverer;
-import jalview.ws.jws2.RNAalifoldClient;
+import jalview.ws.jws2.SeqAnnotationServiceCalcWorker;
 import jalview.ws.jws2.SequenceAnnotationWSClient;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.params.AutoCalcSetting;
@@ -54,8 +57,21 @@ 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
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   private static final String JAR_FILE_NAME = "testRnalifold_param.jar";
 
   public static String testseqs = "examples/RF00031_folded.stk";
@@ -64,7 +80,7 @@ public class RNAStructExportImport
 
   public static Jws2Instance rnaalifoldws;
 
-  jalview.ws.jws2.RNAalifoldClient alifoldClient;
+  SeqAnnotationServiceCalcWorker alifoldClient;
 
   public static jalview.gui.AlignFrame af = null;
 
@@ -75,12 +91,18 @@ public class RNAStructExportImport
     Cache.initLogger();
     disc = JalviewJabawsTestUtils.getJabawsDiscoverer(false);
 
-    for (Jws2Instance svc : disc.getServices())
+    while (disc.isRunning())
     {
+      // don't get services until discoverer has finished
+      Thread.sleep(100);
+    }
 
-      if (svc.getServiceTypeURI().toLowerCase().contains("rnaalifoldws"))
+    for (ServiceWithParameters svc : disc.getServices())
+    {
+
+      if (svc.getNameURI().toLowerCase().contains("rnaalifoldws"))
       {
-        rnaalifoldws = svc;
+        rnaalifoldws = (Jws2Instance) svc;
       }
     }
 
@@ -98,7 +120,7 @@ public class RNAStructExportImport
     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())
     {
@@ -130,11 +152,12 @@ public class RNAStructExportImport
     }
   }
 
-  @Test(groups = { "Functional" })
+  @Test(groups = { "Network" })
   public void testRNAAliFoldValidStructure()
   {
 
-    alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, null);
+    alifoldClient = new SeqAnnotationServiceCalcWorker(rnaalifoldws, af, null,
+            null);
 
     af.getViewport().getCalcManager().startWorker(alifoldClient);
 
@@ -163,11 +186,12 @@ public class RNAStructExportImport
     }
   }
 
-  @Test(groups = { "Functional" })
+  @Test(groups = { "Network" })
   public void testRNAStructExport()
   {
 
-    alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, null);
+    alifoldClient = new SeqAnnotationServiceCalcWorker(rnaalifoldws, af, null,
+            null);
 
     af.getViewport().getCalcManager().startWorker(alifoldClient);
 
@@ -182,17 +206,19 @@ 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. bug is JAL-3122
+    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 = FileFormat.Pfam.getAlignmentFile().print(
+      String aligfileout = FileFormat.Pfam.getWriter(null).print(
               al.getSequencesArray(), true);
 
       String anfileout = new AnnotationFile()
@@ -222,7 +248,8 @@ public class RNAStructExportImport
                       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)
     {
@@ -233,12 +260,12 @@ 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>();
-    for (Argument rg : (List<Argument>) rnaalifoldws
-            .getRunnerConfig().getArguments())
+    List<Argument> opts = new ArrayList<>();
+    for (Argument rg : (List<Argument>) rnaalifoldws.getRunnerConfig()
+            .getArguments())
     {
       if (rg.getDescription().contains("emperature"))
       {
@@ -257,7 +284,8 @@ public class RNAStructExportImport
         opts.add(rg);
       }
     }
-    alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, opts);
+    alifoldClient = new SeqAnnotationServiceCalcWorker(rnaalifoldws, af, null,
+            JabaParamStore.getJwsArgsfromJaba(opts));
 
     af.getViewport().getCalcManager().startWorker(alifoldClient);