Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ShmmrRSBSService	39	42	11	0.509090950.9%	Show methods

Class ShmmrRSBSService

Class ShmmrRSBSService	Line # 39	Total Statements 42	Complexity 11	TOTAL Coverage 0.509090950.9%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4242	2.02	1.01	1.0 1.0100%
testShmmrService() : void   testShmmrService() : void	4949	1.01	1.01	1.0 1.0100%
testShmmrServiceDataprep() : void   testShmmrServiceDataprep() : void	5959	13.013	1.01	1.0 1.0100%
testRsdExchange(String,String) : boolean   testRsdExchange(String,String) : boolean	9292	8.08	3.03	0.0 0.00%
testRsdExchange(String,RestServiceDescription) : boolean   testRsdExchange(String,RestServiceDescription) : boolean	113113	18.018	5.05	0.33333334 0.3333333433.3%

 

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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		import jalview.ws.rest.clientdefs.ShmrRestClient;
29
30		import java.util.Map;
31
32		import org.testng.annotations.BeforeClass;
33		import org.testng.annotations.Test;
34
35		/**
36		* @author jimp
37		*
38		*/
		50.9% Uncovered Elements: 27 (55) Complexity: 11 Complexity Density: 0.26
39		public class ShmmrRSBSService
40		{
41
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
42	1	@BeforeClass(alwaysRun = true)...
43		public void setUpJvOptionPane()
44		{
45	1	JvOptionPane.setInteractiveMode(false);
46	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
47		}
48
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
49	1	@Test(groups = { "Functional" })...
50		public void testShmmrService()
51		{
52
53	1	assertTrue(
54		"Test Rsd Exchange using using default Shmmr service failed.",
55		testRsdExchange("Test using default Shmmr service",
56		ShmrRestClient.makeShmmrRestClient().service));
57		}
58
		100% Uncovered Elements: 0 (13) Complexity: 1 Complexity Density: 0.08
59	1	@Test(groups = { "Functional" })...
60		public void testShmmrServiceDataprep() throws Exception
61		{
62	1	RestClient _rc = ShmrRestClient.makeShmmrRestClient();
63	1	assertNotNull(_rc);
64	1	AlignFrame alf = new jalview.io.FileLoader(false)
65		.LoadFileWaitTillLoaded("examples/testdata/smad.fa",
66		jalview.io.DataSourceType.FILE);
67	1	assertNotNull("Couldn't find test data.", alf);
68	1	alf.loadJalviewDataFile("examples/testdata/smad_groups.jva",
69		jalview.io.DataSourceType.FILE, null, null);
70	1	assertTrue(
71		"Couldn't load the test data's annotation file (should be 5 groups but found "
72		+ alf.getViewport().getAlignment().getGroups().size()
73		+ ").",
74		alf.getViewport().getAlignment().getGroups().size() == 5);
75
76	1	RestClient rc = new RestClient(_rc.service, alf, true);
77
78	1	assertNotNull("Couldn't creat RestClient job.", rc);
79	1	jalview.bin.Console.initLogger();
80	1	RestJob rjb = new RestJob(0, new RestJobThread(rc),
81		rc.av.getAlignment(), null);
82	1	rjb.setAlignmentForInputs(rc.service.getInputParams().values(),
83		rc.av.getAlignment());
84	1	for (Map.Entry<String, InputType> e : rc.service.getInputParams()
85		.entrySet())
86		{
87	2	System.out.println("For Input '" + e.getKey() + ":\n"
88		+ e.getValue().formatForInput(rjb).getContentLength());
89		}
90		}
91
		0% Uncovered Elements: 10 (10) Complexity: 3 Complexity Density: 0.38
92	0	private static boolean testRsdExchange(String desc, String servicestring)...
93		{
94	0	try
95		{
96	0	RestServiceDescription newService = new RestServiceDescription(
97		servicestring);
98	0	if (!newService.isValid())
99		{
100	0	throw new Error("Failed to create service from '" + servicestring
101		+ "'.\n" + newService.getInvalidMessage());
102		}
103	0	return testRsdExchange(desc, newService);
104		} catch (Throwable x)
105		{
106	0	System.err.println(
107		"Failed for service (" + desc + "): " + servicestring);
108	0	x.printStackTrace();
109	0	return false;
110		}
111		}
112
		33.3% Uncovered Elements: 16 (24) Complexity: 5 Complexity Density: 0.28
113	1	private static boolean testRsdExchange(String desc,...
114		RestServiceDescription service)
115		{
116	1	try
117		{
118	1	String fromservicetostring = service.toString();
119	1	RestServiceDescription newService = new RestServiceDescription(
120		fromservicetostring);
121	1	if (!newService.isValid())
122		{
123	0	throw new Error(
124		"Failed to create service from '" + fromservicetostring
125		+ "'.\n" + newService.getInvalidMessage());
126		}
127
128	1	if (!service.equals(newService))
129		{
130	0	System.err.println("Failed for service (" + desc + ").");
131	0	if (fromservicetostring.equals(newService.toString()))
132		{
133	0	System.err.println(
134		"Description strings are equivalent: fault during RestServiceDescription.equals()");
135	0	return false;
136		}
137	0	System.err.println("Original service and parsed service differ.");
138	0	System.err.println("Original: " + fromservicetostring);
139	0	System.err.println("Parsed : " + newService.toString());
140	0	return false;
141		}
142		} catch (Throwable x)
143		{
144	0	System.err.println(
145		"Failed for service (" + desc + "): " + service.toString());
146	0	x.printStackTrace();
147	0	return false;
148		}
149	1	return true;
150		}
151
152		}