2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.ws.rest;
23 import static org.junit.Assert.assertNotNull;
24 import static org.junit.Assert.assertTrue;
28 import org.junit.Test;
30 import jalview.gui.AlignFrame;
31 import jalview.util.StringUtils;
37 public class ShmmrRSBSService
41 public void testShmmrService()
45 "Test Rsd Exchange using using default Shmmr service failed.",
46 testRsdExchange("Test using default Shmmr service",
47 RestClient.makeShmmrRestClient().service));
51 public void testShmmrServiceDataprep() throws Exception
53 RestClient _rc = RestClient.makeShmmrRestClient();
55 AlignFrame alf = new jalview.io.FileLoader(false)
56 .LoadFileWaitTillLoaded("examples/testdata/smad.fa",
57 jalview.io.FormatAdapter.FILE);
58 assertNotNull("Couldn't find test data.", alf);
59 alf.loadJalviewDataFile("examples/testdata/smad_groups.jva",
60 jalview.io.FormatAdapter.FILE, null, null);
62 "Couldn't load the test data's annotation file (should be 5 groups but found "
63 + alf.getViewport().getAlignment().getGroups().size()
64 + ").", alf.getViewport().getAlignment().getGroups()
67 RestClient rc = new RestClient(_rc.service, alf, true);
69 assertNotNull("Couldn't creat RestClient job.", rc);
70 jalview.bin.Cache.initLogger();
71 RestJob rjb = new RestJob(0, new RestJobThread(rc),
72 rc.av.getAlignment(), null);
73 rjb.setAlignmentForInputs(rc.service.getInputParams().values(),
74 rc.av.getAlignment());
75 for (Map.Entry<String, InputType> e : rc.service.getInputParams()
78 System.out.println("For Input '" + e.getKey() + ":\n"
79 + e.getValue().formatForInput(rjb).getContentLength());
83 private static boolean testRsdExchange(String desc, String servicestring)
87 RestServiceDescription newService = new RestServiceDescription(
89 if (!newService.isValid())
91 throw new Error("Failed to create service from '" + servicestring
92 + "'.\n" + newService.getInvalidMessage());
94 return testRsdExchange(desc, newService);
97 System.err.println("Failed for service (" + desc + "): "
104 private static boolean testRsdExchange(String desc,
105 RestServiceDescription service)
109 String fromservicetostring = service.toString();
110 RestServiceDescription newService = new RestServiceDescription(
111 fromservicetostring);
112 if (!newService.isValid())
114 throw new Error("Failed to create service from '"
115 + fromservicetostring + "'.\n"
116 + newService.getInvalidMessage());
119 if (!service.equals(newService))
121 System.err.println("Failed for service (" + desc + ").");
122 System.err.println("Original service and parsed service differ.");
123 System.err.println("Original: " + fromservicetostring);
124 System.err.println("Parsed : " + newService.toString());
127 } catch (Throwable x)
129 System.err.println("Failed for service (" + desc + "): "
130 + service.toString());