X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Frest%2FShmmrRSBSService.java;h=c4430ad6fe5921f4652c2cc064e89e32d3f5c054;hb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;hp=05f7cd02e3e2cf2ad265c6b8385bb5f7ecbad510;hpb=89fdf2b589aadf46000d58306e0b50dc9ef1af74;p=jalview.git
diff --git a/test/jalview/ws/rest/ShmmrRSBSService.java b/test/jalview/ws/rest/ShmmrRSBSService.java
index 05f7cd0..c4430ad 100644
--- a/test/jalview/ws/rest/ShmmrRSBSService.java
+++ b/test/jalview/ws/rest/ShmmrRSBSService.java
@@ -1,28 +1,35 @@
-/**
+/*
+ * 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.
+ *
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.rest;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.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 org.junit.AfterClass;
-import org.junit.BeforeClass;
import org.junit.Test;
+import jalview.gui.AlignFrame;
+import jalview.util.StringUtils;
+
/**
* @author jimp
*
@@ -31,18 +38,6 @@ public class ShmmrRSBSService
{
@Test
- public void testSeparatorListToArrayForRestServiceDescriptions()
- {
- 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
- }
-
- @Test
public void testShmmrService()
{
@@ -51,27 +46,37 @@ public class ShmmrRSBSService
testRsdExchange("Test using default Shmmr service",
RestClient.makeShmmrRestClient().service));
}
+
@Test
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.FormatAdapter.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);
-
+ 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);
+
+ 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 e:rc.service.getInputParams().entrySet()) {
- System.out.println("For Input '"+e.getKey()+":\n"+e.getValue().formatForInput(rjb).getContentLength());
+ RestJob rjb = new RestJob(0, new RestJobThread(rc),
+ rc.av.getAlignment(), null);
+ rjb.setAlignmentForInputs(rc.service.getInputParams().values(),
+ rc.av.getAlignment());
+ for (Map.Entry e : rc.service.getInputParams()
+ .entrySet())
+ {
+ System.out.println("For Input '" + e.getKey() + ":\n"
+ + e.getValue().formatForInput(rjb).getContentLength());
}
}