X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fjabaws%2FDisorderAnnotExportImport.java;h=4602e9364b2e7f7ff7d8c8c8590fbb9c0ca6a2e3;hb=3f4b01ff53be81b3a04a9893f9bd2a93dbee0a6f;hp=71fc82959779cea7041346dd30bf3d87bae211dd;hpb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;p=jalview.git

diff --git a/test/jalview/ws/jabaws/DisorderAnnotExportImport.java b/test/jalview/ws/jabaws/DisorderAnnotExportImport.java
index 71fc829..4602e93 100644
--- a/test/jalview/ws/jabaws/DisorderAnnotExportImport.java
+++ b/test/jalview/ws/jabaws/DisorderAnnotExportImport.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,17 +20,24 @@
  */
 package jalview.ws.jabaws;
 
+import java.util.Locale;
 import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.bin.Cache;
+import jalview.bin.Console;
 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;
+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;
@@ -38,31 +45,57 @@ import java.util.List;
 import org.testng.Assert;
 import org.testng.annotations.AfterClass;
 import org.testng.annotations.BeforeClass;
+import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
-@Test(groups = { "Network" })
+/*
+ * 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
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   public static String testseqs = "examples/uniref50.fa";
 
   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
   {
-
-    jalview.bin.Cache.initLogger();
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
+    Console.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.startDiscoverer();
+    while (disc2.isRunning())
     {
-      if (svc.getServiceTypeURI().toLowerCase().contains("iupredws"))
+      Thread.sleep(100);
+    }
+    iupreds = new ArrayList<>();
+    for (ServiceWithParameters svc : disc2.getServices())
+    {
+      if (svc.getNameURI().toLowerCase().contains("iupred"))
       {
         iupreds.add(svc);
       }
@@ -70,7 +103,8 @@ 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);
   }
 
@@ -84,14 +118,29 @@ public class DisorderAnnotExportImport
       af = null;
     }
   }
+  
+  @DataProvider(name="getIuPreds",parallel = false)
+  public static ServiceWithParameters[][] getIuPreds()
+  {
+    ServiceWithParameters[][] services = new ServiceWithParameters[iupreds
+            .size()][1];
+
+    int i = 0;
+    for (ServiceWithParameters iupred : iupreds)
+    {
+      services[i++][0] = iupred;
+    }
+    return services;
+  }
 
   /**
    * test for patches to JAL-1294
    */
-  @Test
-  public void testDisorderAnnotExport()
+  @Test(groups = { "External", "Network" },dataProvider = "getIuPreds")
+  public void testDisorderAnnotExport(ServiceWithParameters iuPred)
   {
-    disorderClient = new AADisorderClient(iupreds.get(0), af, null, null);
+    disorderClient = new SeqAnnotationServiceCalcWorker(iuPred, af, null,
+            null);
     af.getViewport().getCalcManager().startWorker(disorderClient);
     do
     {
@@ -106,7 +155,7 @@ 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)
@@ -118,50 +167,44 @@ public class DisorderAnnotExportImport
     {
       orig_alig.deleteAnnotation(aa);
     }
-    testAnnotationFileIO("Testing IUPred Annotation IO", orig_alig);
+    checkAnnotationFileIO("Testing IUPred Annotation IO", orig_alig);
 
   }
 
-  public static void testAnnotationFileIO(String testname, AlignmentI al)
+  static void checkAnnotationFileIO(String testname, AlignmentI al)
   {
     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(
-              "Test "
-                      + testname
-                      + "\nAlignment annotation file was not regenerated. Null string",
+      assertTrue("Test " + testname
+              + "\nAlignment annotation file was not regenerated. Null string",
               anfileout != null);
-      assertTrue(
-              "Test "
-                      + testname
-                      + "\nAlignment annotation file was not regenerated. Empty string",
+      assertTrue("Test " + testname
+              + "\nAlignment annotation file was not regenerated. Empty string",
               anfileout.length() > "JALVIEW_ANNOTATION".length());
 
-      System.out.println("Output annotation file:\n" + anfileout
-              + "\n<<EOF\n");
+      System.out.println(
+              "Output annotation file:\n" + anfileout + "\n<<EOF\n");
 
       AlignmentI al_new = new FormatAdapter().readFile(aligfileout,
-              FormatAdapter.PASTE, "PFAM");
-      assertTrue(
-              "Test "
-                      + testname
-                      + "\nregenerated annotation file did not annotate alignment.",
+              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)
     {
       e.printStackTrace();
     }
-    Assert.fail("Test "
-            + testname
+    Assert.fail("Test " + testname
             + "\nCouldn't complete Annotation file roundtrip input/output/input test.");
   }