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.testng.AssertJUnit.assertNotNull;
24 import static org.testng.AssertJUnit.assertTrue;
26 import jalview.gui.AlignFrame;
30 import org.testng.annotations.Test;
36 public class ShmmrRSBSService
39 @Test(groups = { "Functional" })
40 public void testShmmrService()
44 "Test Rsd Exchange using using default Shmmr service failed.",
45 testRsdExchange("Test using default Shmmr service",
46 RestClient.makeShmmrRestClient().service));
49 @Test(groups = { "Functional" })
50 public void testShmmrServiceDataprep() throws Exception
52 RestClient _rc = RestClient.makeShmmrRestClient();
54 AlignFrame alf = new jalview.io.FileLoader(false)
55 .LoadFileWaitTillLoaded("examples/testdata/smad.fa",
56 jalview.io.FormatAdapter.FILE);
57 assertNotNull("Couldn't find test data.", alf);
58 alf.loadJalviewDataFile("examples/testdata/smad_groups.jva",
59 jalview.io.FormatAdapter.FILE, null, null);
61 "Couldn't load the test data's annotation file (should be 5 groups but found "
62 + alf.getViewport().getAlignment().getGroups().size()
63 + ").", alf.getViewport().getAlignment().getGroups()
66 RestClient rc = new RestClient(_rc.service, alf, true);
68 assertNotNull("Couldn't creat RestClient job.", rc);
69 jalview.bin.Cache.initLogger();
70 RestJob rjb = new RestJob(0, new RestJobThread(rc),
71 rc.av.getAlignment(), null);
72 rjb.setAlignmentForInputs(rc.service.getInputParams().values(),
73 rc.av.getAlignment());
74 for (Map.Entry<String, InputType> e : rc.service.getInputParams()
77 System.out.println("For Input '" + e.getKey() + ":\n"
78 + e.getValue().formatForInput(rjb).getContentLength());
82 private static boolean testRsdExchange(String desc, String servicestring)
86 RestServiceDescription newService = new RestServiceDescription(
88 if (!newService.isValid())
90 throw new Error("Failed to create service from '" + servicestring
91 + "'.\n" + newService.getInvalidMessage());
93 return testRsdExchange(desc, newService);
96 System.err.println("Failed for service (" + desc + "): "
103 private static boolean testRsdExchange(String desc,
104 RestServiceDescription service)
108 String fromservicetostring = service.toString();
109 RestServiceDescription newService = new RestServiceDescription(
110 fromservicetostring);
111 if (!newService.isValid())
113 throw new Error("Failed to create service from '"
114 + fromservicetostring + "'.\n"
115 + newService.getInvalidMessage());
118 if (!service.equals(newService))
120 System.err.println("Failed for service (" + desc + ").");
121 System.err.println("Original service and parsed service differ.");
122 System.err.println("Original: " + fromservicetostring);
123 System.err.println("Parsed : " + newService.toString());
126 } catch (Throwable x)
128 System.err.println("Failed for service (" + desc + "): "
129 + service.toString());