JAL-3949 - refactor logging from jalview.bin.Cache to jalview.bin.Console

[jalview.git] / test / jalview / ws / rest / ShmmrRSBSService.java

diff --git a/test/jalview/ws/rest/ShmmrRSBSService.java b/test/jalview/ws/rest/ShmmrRSBSService.java
index 4c9e3de..a9668a9 100644 (file)
--- a/test/jalview/ws/rest/ShmmrRSBSService.java
+++ b/test/jalview/ws/rest/ShmmrRSBSService.java
@@ -1,42 +1,35 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 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.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.ws.rest;
 
-import static org.junit.Assert.*;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertTrue;
 
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Map;
-
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.AlignmentView;
 import jalview.gui.AlignFrame;
-import jalview.io.FileParse;
-import jalview.ws.rest.InputType;
-import jalview.ws.rest.params.SeqGroupIndexVector;
+import jalview.gui.JvOptionPane;
 
-import org.junit.AfterClass;
-import org.junit.BeforeClass;
-import org.junit.Test;
+import java.util.Map;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
 
 /**
  * @author jimp
@@ -45,19 +38,14 @@ import org.junit.Test;
 public class ShmmrRSBSService
 {
 
-  @Test
-  public void testSeparatorListToArrayForRestServiceDescriptions()
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
   {
-    assertTrue(
-            "separatorListToArray is faulty.",
-            RestServiceDescription.separatorListToArray(
-                    "foo=',',min='foo',max='1,2,3',fa=','", ",").length == 4);
-    assertTrue("separatorListToArray is faulty.",
-            RestServiceDescription.separatorListToArray(
-                    "minsize='2', sep=','", ",").length != 2); // probably should come as 2
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void testShmmrService()
   {
 
@@ -66,27 +54,37 @@ public class ShmmrRSBSService
             testRsdExchange("Test using default Shmmr service",
                     RestClient.makeShmmrRestClient().service));
   }
-  @Test
+
+  @Test(groups = { "Functional" })
   public void testShmmrServiceDataprep() throws Exception
   {
     RestClient _rc = RestClient.makeShmmrRestClient();
     assertNotNull(_rc);
-    AlignFrame alf = new jalview.io.FileLoader(false).LoadFileWaitTillLoaded("examples/testdata/smad.fa", jalview.io.FormatAdapter.FILE);
-    assertNotNull("Couldn't find test data.",alf);
+    AlignFrame alf = new jalview.io.FileLoader(false)
+            .LoadFileWaitTillLoaded("examples/testdata/smad.fa",
+                    jalview.io.DataSourceType.FILE);
+    assertNotNull("Couldn't find test data.", alf);
     alf.loadJalviewDataFile("examples/testdata/smad_groups.jva",
-            jalview.io.FormatAdapter.FILE, null, null);
-    assertTrue("Couldn't load the test data's annotation file (should be 5 groups but found "+alf.getViewport().getAlignment().getGroups().size()+").", alf.getViewport().getAlignment().getGroups().size()==5);
-    
+            jalview.io.DataSourceType.FILE, null, null);
+    assertTrue(
+            "Couldn't load the test data's annotation file (should be 5 groups but found "
+                    + alf.getViewport().getAlignment().getGroups().size()
+                    + ").", alf.getViewport().getAlignment().getGroups()
+                    .size() == 5);
+
     RestClient rc = new RestClient(_rc.service, alf, true);
-    
-    
-    
-    assertNotNull("Couldn't creat RestClient job.",rc);
-    jalview.bin.Cache.initLogger();
-    RestJob rjb = new RestJob(0, new RestJobThread(rc),rc.av.getAlignment(),null);
-    rjb.setAlignmentForInputs(rc.service.getInputParams().values(), rc.av.getAlignment());
-    for (Map.Entry<String,InputType> e:rc.service.getInputParams().entrySet()) {
-      System.out.println("For Input '"+e.getKey()+":\n"+e.getValue().formatForInput(rjb).getContentLength());
+
+    assertNotNull("Couldn't creat RestClient job.", rc);
+    jalview.bin.Console.initLogger();
+    RestJob rjb = new RestJob(0, new RestJobThread(rc),
+            rc.av.getAlignment(), null);
+    rjb.setAlignmentForInputs(rc.service.getInputParams().values(),
+            rc.av.getAlignment());
+    for (Map.Entry<String, InputType> e : rc.service.getInputParams()
+            .entrySet())
+    {
+      System.out.println("For Input '" + e.getKey() + ":\n"
+              + e.getValue().formatForInput(rjb).getContentLength());
     }
   }