Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ShmmrRSBSService	38	39	10	0.00%	Show methods

Class ShmmrRSBSService

Class ShmmrRSBSService	Line # 38	Total Statements 39	Complexity 10	TOTAL Coverage 0.00%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4141	2.02	1.01	0.0 0.00%
testShmmrService() : void   testShmmrService() : void	4848	1.01	1.01	0.0 0.00%
testShmmrServiceDataprep() : void   testShmmrServiceDataprep() : void	5858	13.013	1.01	0.0 0.00%
testRsdExchange(String,String) : boolean   testRsdExchange(String,String) : boolean	9191	8.08	3.03	0.0 0.00%
testRsdExchange(String,RestServiceDescription) : boolean   testRsdExchange(String,RestServiceDescription) : boolean	112112	15.015	4.04	0.0 0.00%

 

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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		*/
		0% Uncovered Elements: 50 (50) Complexity: 10 Complexity Density: 0.26
38		public class ShmmrRSBSService
39		{
40
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
41	0	@BeforeClass(alwaysRun = true)...
42		public void setUpJvOptionPane()
43		{
44	0	JvOptionPane.setInteractiveMode(false);
45	0	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
46		}
47
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
48	0	@Test(groups = { "Functional" })...
49		public void testShmmrService()
50		{
51
52	0	assertTrue(
53		"Test Rsd Exchange using using default Shmmr service failed.",
54		testRsdExchange("Test using default Shmmr service",
55		RestClient.makeShmmrRestClient().service));
56		}
57
		0% Uncovered Elements: 13 (13) Complexity: 1 Complexity Density: 0.08
58	0	@Test(groups = { "Functional" })...
59		public void testShmmrServiceDataprep() throws Exception
60		{
61	0	RestClient _rc = RestClient.makeShmmrRestClient();
62	0	assertNotNull(_rc);
63	0	AlignFrame alf = new jalview.io.FileLoader(false)
64		.LoadFileWaitTillLoaded("examples/testdata/smad.fa",
65		jalview.io.DataSourceType.FILE);
66	0	assertNotNull("Couldn't find test data.", alf);
67	0	alf.loadJalviewDataFile("examples/testdata/smad_groups.jva",
68		jalview.io.DataSourceType.FILE, null, null);
69	0	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	0	RestClient rc = new RestClient(_rc.service, alf, true);
76
77	0	assertNotNull("Couldn't creat RestClient job.", rc);
78	0	jalview.bin.Console.initLogger();
79	0	RestJob rjb = new RestJob(0, new RestJobThread(rc),
80		rc.av.getAlignment(), null);
81	0	rjb.setAlignmentForInputs(rc.service.getInputParams().values(),
82		rc.av.getAlignment());
83	0	for (Map.Entry<String, InputType> e : rc.service.getInputParams()
84		.entrySet())
85		{
86	0	System.out.println("For Input '" + e.getKey() + ":\n"
87		+ e.getValue().formatForInput(rjb).getContentLength());
88		}
89		}
90
		0% Uncovered Elements: 10 (10) Complexity: 3 Complexity Density: 0.38
91	0	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
		0% Uncovered Elements: 19 (19) Complexity: 4 Complexity Density: 0.27
112	0	private static boolean testRsdExchange(String desc,...
113		RestServiceDescription service)
114		{
115	0	try
116		{
117	0	String fromservicetostring = service.toString();
118	0	RestServiceDescription newService = new RestServiceDescription(
119		fromservicetostring);
120	0	if (!newService.isValid())
121		{
122	0	throw new Error(
123		"Failed to create service from '" + fromservicetostring
124		+ "'.\n" + newService.getInvalidMessage());
125		}
126
127	0	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	0	return true;
143		}
144
145		}