1. Project Clover database Fri Dec 6 2024 13:47:14 GMT
  2. Package jalview.ws.rest

File ShmmrRSBSService.java

 

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Classes

Class
Line #
Actions
ShmmrRSBSService 38 39 10
0.5656%
 

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1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
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.
11    *
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.
16    *
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.
20    */
21    package jalview.ws.rest;
22   
23    import static org.testng.AssertJUnit.assertNotNull;
24    import static org.testng.AssertJUnit.assertTrue;
25   
26    import jalview.gui.AlignFrame;
27    import jalview.gui.JvOptionPane;
28   
29    import java.util.Map;
30   
31    import org.testng.annotations.BeforeClass;
32    import org.testng.annotations.Test;
33   
34    /**
35    * @author jimp
36    *
37    */
 
38    public class ShmmrRSBSService
39    {
40   
 
41  1 toggle @BeforeClass(alwaysRun = true)
42    public void setUpJvOptionPane()
43    {
44  1 JvOptionPane.setInteractiveMode(false);
45  1 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
46    }
47   
 
48  1 toggle @Test(groups = { "Functional" })
49    public void testShmmrService()
50    {
51   
52  1 assertTrue(
53    "Test Rsd Exchange using using default Shmmr service failed.",
54    testRsdExchange("Test using default Shmmr service",
55    RestClient.makeShmmrRestClient().service));
56    }
57   
 
58  1 toggle @Test(groups = { "Functional" })
59    public void testShmmrServiceDataprep() throws Exception
60    {
61  1 RestClient _rc = RestClient.makeShmmrRestClient();
62  1 assertNotNull(_rc);
63  1 AlignFrame alf = new jalview.io.FileLoader(false)
64    .LoadFileWaitTillLoaded("examples/testdata/smad.fa",
65    jalview.io.DataSourceType.FILE);
66  1 assertNotNull("Couldn't find test data.", alf);
67  1 alf.loadJalviewDataFile("examples/testdata/smad_groups.jva",
68    jalview.io.DataSourceType.FILE, null, null);
69  1 assertTrue(
70    "Couldn't load the test data's annotation file (should be 5 groups but found "
71    + alf.getViewport().getAlignment().getGroups().size()
72    + ").",
73    alf.getViewport().getAlignment().getGroups().size() == 5);
74   
75  1 RestClient rc = new RestClient(_rc.service, alf, true);
76   
77  1 assertNotNull("Couldn't creat RestClient job.", rc);
78  1 jalview.bin.Console.initLogger();
79  1 RestJob rjb = new RestJob(0, new RestJobThread(rc),
80    rc.av.getAlignment(), null);
81  1 rjb.setAlignmentForInputs(rc.service.getInputParams().values(),
82    rc.av.getAlignment());
83  1 for (Map.Entry<String, InputType> e : rc.service.getInputParams()
84    .entrySet())
85    {
86  2 System.out.println("For Input '" + e.getKey() + ":\n"
87    + e.getValue().formatForInput(rjb).getContentLength());
88    }
89    }
90   
 
91  0 toggle private static boolean testRsdExchange(String desc, String servicestring)
92    {
93  0 try
94    {
95  0 RestServiceDescription newService = new RestServiceDescription(
96    servicestring);
97  0 if (!newService.isValid())
98    {
99  0 throw new Error("Failed to create service from '" + servicestring
100    + "'.\n" + newService.getInvalidMessage());
101    }
102  0 return testRsdExchange(desc, newService);
103    } catch (Throwable x)
104    {
105  0 System.err.println(
106    "Failed for service (" + desc + "): " + servicestring);
107  0 x.printStackTrace();
108  0 return false;
109    }
110    }
111   
 
112  1 toggle private static boolean testRsdExchange(String desc,
113    RestServiceDescription service)
114    {
115  1 try
116    {
117  1 String fromservicetostring = service.toString();
118  1 RestServiceDescription newService = new RestServiceDescription(
119    fromservicetostring);
120  1 if (!newService.isValid())
121    {
122  0 throw new Error(
123    "Failed to create service from '" + fromservicetostring
124    + "'.\n" + newService.getInvalidMessage());
125    }
126   
127  1 if (!service.equals(newService))
128    {
129  0 System.err.println("Failed for service (" + desc + ").");
130  0 System.err.println("Original service and parsed service differ.");
131  0 System.err.println("Original: " + fromservicetostring);
132  0 System.err.println("Parsed : " + newService.toString());
133  0 return false;
134    }
135    } catch (Throwable x)
136    {
137  0 System.err.println(
138    "Failed for service (" + desc + "): " + service.toString());
139  0 x.printStackTrace();
140  0 return false;
141    }
142  1 return true;
143    }
144   
145    }