Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ParameterUtilsTest	54	54	13	0.00%	Show methods

Class ParameterUtilsTest

Class ParameterUtilsTest	Line # 54	Total Statements 54	Complexity 13	TOTAL Coverage 0.00%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	5757	2.02	1.01	0.0 0.00%
setUpBeforeClass() : void   setUpBeforeClass() : void	7272	4.04	1.01	0.0 0.00%
testWriteParameterSet() : void   testWriteParameterSet() : void	8181	27.027	6.06	0.0 0.00%
isForTesting(UIinfo) : boolean   isForTesting(UIinfo) : boolean	136136	1.01	1.01	0.0 0.00%
testCopyOption() : void   testCopyOption() : void	142142	10.010	2.02	0.0 0.00%
testCopyParameter() : void   testCopyParameter() : void	167167	10.010	2.02	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.jws2;
22
23		import java.util.Locale;
24		import static org.testng.AssertJUnit.assertEquals;
25		import static org.testng.AssertJUnit.assertFalse;
26		import static org.testng.AssertJUnit.assertTrue;
27
28		import jalview.bin.Cache;
29		import jalview.bin.Console;
30		import jalview.gui.JvOptionPane;
31		import jalview.ws.api.ServiceWithParameters;
32		import jalview.ws.api.UIinfo;
33		import jalview.ws.jabaws.JalviewJabawsTestUtils;
34		import jalview.ws.jws2.jabaws2.Jws2Instance;
35
36		import java.util.ArrayList;
37		import java.util.Iterator;
38		import java.util.List;
39
40		import org.testng.annotations.BeforeClass;
41		import org.testng.annotations.Test;
42
43		import compbio.metadata.Option;
44		import compbio.metadata.Parameter;
45		import compbio.metadata.Preset;
46		import compbio.metadata.PresetManager;
47		import compbio.metadata.WrongParameterException;
48
49		/*
50		* All methods in this class are set to the Network group because setUpBeforeClass will fail
51		* if there is no network.
52		*/
53		@Test(singleThreaded = true)
		0% Uncovered Elements: 72 (72) Complexity: 13 Complexity Density: 0.24
54		public class ParameterUtilsTest
55		{
56
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
57	0	@BeforeClass(alwaysRun = true)...
58		public void setUpJvOptionPane()
59		{
60	0	JvOptionPane.setInteractiveMode(false);
61	0	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
62		}
63
64		/*
65		* To limit tests to specify services, add them to this list; leave list empty
66		* to test all
67		*/
68		private static List<String> serviceTests = new ArrayList<>();
69
70		private static Jws2Discoverer disc = null;
71
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
72	0	@BeforeClass(alwaysRun = true)...
73		public static void setUpBeforeClass() throws Exception
74		{
75	0	serviceTests.add("AAConWS".toLowerCase(Locale.ROOT));
76	0	Cache.loadProperties("test/jalview/io/testProps.jvprops");
77	0	Console.initLogger();
78	0	disc = JalviewJabawsTestUtils.getJabawsDiscoverer();
79		}
80
		0% Uncovered Elements: 35 (35) Complexity: 6 Complexity Density: 0.22 4-
81	0	@Test(groups = { "Network" })...
82		public void testWriteParameterSet() throws WrongParameterException
83		{
84	0	for (ServiceWithParameters _service : disc.getServices())
85		{
86	0	if (isForTesting(_service))
87		{
88	0	Jws2Instance service = (Jws2Instance) _service;
89
90	0	List<Preset> prl = null;
91	0	PresetManager prman = service.getPresets();
92	0	if (prman == null)
93		{
94	0	continue;
95		}
96	0	prl = prman.getPresets();
97	0	if (prl == null)
98		{
99	0	continue;
100		}
101	0	for (Preset pr : prl)
102		{
103	0	List<String> writeparam = null;
104	0	List<String> readparam = null;
105	0	writeparam = ParameterUtils.writeParameterSet(
106		pr.getArguments(service.getRunnerConfig()), " ");
107	0	List<Option> pset = ParameterUtils.processParameters(writeparam,
108		service.getRunnerConfig(), " ");
109	0	readparam = ParameterUtils.writeParameterSet(pset, " ");
110	0	Iterator<String> o = pr.getOptions().iterator();
111	0	Iterator<String> s = writeparam.iterator();
112	0	Iterator<String> t = readparam.iterator();
113	0	boolean failed = false;
114	0	while (s.hasNext() && t.hasNext())
115		{
116	0	String on = o.next();
117	0	String sn = s.next();
118	0	String st = t.next();
119	0	final String errorMsg = "Original was " + on + " Phase 1 wrote "
120		+ sn + "\tPhase 2 wrote " + st;
121	0	assertEquals(errorMsg, sn, st);
122	0	assertEquals(errorMsg, sn, on);
123		}
124		}
125		}
126		}
127		}
128
129		/**
130		* Returns true if the service is in the list of the ones we chose to test,
131		* _or_ the list is empty (test all)
132		*
133		* @param service
134		* @return
135		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
136	0	public boolean isForTesting(UIinfo service)...
137		{
138	0	return serviceTests.size() == 0 || serviceTests
139		.contains(service.getServiceType().toLowerCase(Locale.ROOT));
140		}
141
		0% Uncovered Elements: 12 (12) Complexity: 2 Complexity Density: 0.2 4-
142	0	@Test(groups = { "Network" })...
143		public void testCopyOption()
144		{
145	0	for (ServiceWithParameters _service : disc.getServices())
146		{
147	0	if (isForTesting(_service))
148		{
149	0	Jws2Instance service = (Jws2Instance) _service;
150	0	List<Option<?>> options = service.getRunnerConfig().getOptions();
151	0	for (Option<?> o : options)
152		{
153	0	System.out.println("Testing copyOption for option " + o.getName()
154		+ " of " + service.getActionText());
155	0	Option<?> cpy = ParameterUtils.copyOption(o);
156	0	assertTrue(cpy.equals(o));
157	0	assertEquals(cpy.getName(), o.getName());
158	0	assertFalse(cpy == o);
159		// todo more assertions?
160		}
161		}
162		}
163		}
164
165		/**
166		*/
		0% Uncovered Elements: 12 (12) Complexity: 2 Complexity Density: 0.2 4-
167	0	@Test(groups = { "Network" })...
168		public void testCopyParameter()
169		{
170	0	for (ServiceWithParameters _service : disc.getServices())
171		{
172	0	if (isForTesting(_service))
173		{
174	0	Jws2Instance service = (Jws2Instance) _service;
175	0	List<Parameter> parameters = service.getRunnerConfig()
176		.getParameters();
177	0	for (Parameter o : parameters)
178		{
179	0	System.out.println("Testing copyParameter for parameter "
180		+ o.getName() + " of " + service.getActionText());
181	0	Parameter cpy = ParameterUtils.copyParameter(o);
182	0	assertTrue(cpy.equals(o));
183	0	assertFalse(cpy == o);
184	0	assertEquals(cpy.getName(), o.getName());
185		// todo more assertions?
186		}
187		}
188		}
189		}
190		}