Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ParameterUtilsTest	53	51	13	0.00%	Show methods

Class ParameterUtilsTest

Class ParameterUtilsTest	Line # 53	Total Statements 51	Complexity 13	TOTAL Coverage 0.00%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	5656	2.02	1.01	0.0 0.00%
setUpBeforeClass() : void   setUpBeforeClass() : void	7171	4.04	1.01	0.0 0.00%
testWriteParameterSet() : void   testWriteParameterSet() : void	8080	26.026	6.06	0.0 0.00%
isForTesting(Jws2Instance) : boolean   isForTesting(Jws2Instance) : boolean	134134	1.01	1.01	0.0 0.00%
testCopyOption() : void   testCopyOption() : void	140140	9.09	2.02	0.0 0.00%
testCopyParameter() : void   testCopyParameter() : void	164164	9.09	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
25		import static org.testng.AssertJUnit.assertEquals;
26		import static org.testng.AssertJUnit.assertFalse;
27		import static org.testng.AssertJUnit.assertTrue;
28
29		import jalview.bin.Cache;
30		import jalview.bin.Console;
31		import jalview.gui.JvOptionPane;
32		import jalview.ws.jabaws.JalviewJabawsTestUtils;
33		import jalview.ws.jws2.jabaws2.Jws2Instance;
34
35		import java.util.ArrayList;
36		import java.util.Iterator;
37		import java.util.List;
38
39		import org.testng.annotations.BeforeClass;
40		import org.testng.annotations.Test;
41
42		import compbio.metadata.Option;
43		import compbio.metadata.Parameter;
44		import compbio.metadata.Preset;
45		import compbio.metadata.PresetManager;
46		import compbio.metadata.WrongParameterException;
47
48		/*
49		* All methods in this class are set to the Network group because setUpBeforeClass will fail
50		* if there is no network.
51		*/
52		@Test(singleThreaded = true)
		0% Uncovered Elements: 69 (69) Complexity: 13 Complexity Density: 0.25
53		public class ParameterUtilsTest
54		{
55
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
56	0	@BeforeClass(alwaysRun = true)...
57		public void setUpJvOptionPane()
58		{
59	0	JvOptionPane.setInteractiveMode(false);
60	0	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
61		}
62
63		/*
64		* To limit tests to specify services, add them to this list; leave list empty
65		* to test all
66		*/
67		private static List<String> serviceTests = new ArrayList<String>();
68
69		private static Jws2Discoverer disc = null;
70
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
71	0	@BeforeClass(alwaysRun = true)...
72		public static void setUpBeforeClass() throws Exception
73		{
74	0	serviceTests.add("AAConWS".toLowerCase(Locale.ROOT));
75	0	Cache.loadProperties("test/jalview/io/testProps.jvprops");
76	0	Console.initLogger();
77	0	disc = JalviewJabawsTestUtils.getJabawsDiscoverer();
78		}
79
		0% Uncovered Elements: 34 (34) Complexity: 6 Complexity Density: 0.23 4-
80	0	@Test(groups = { "Network" })...
81		public void testWriteParameterSet() throws WrongParameterException
82		{
83	0	for (Jws2Instance service : disc.getServices())
84		{
85	0	if (isForTesting(service))
86		{
87
88	0	List<Preset> prl = null;
89	0	PresetManager prman = service.getPresets();
90	0	if (prman == null)
91		{
92	0	continue;
93		}
94	0	prl = prman.getPresets();
95	0	if (prl == null)
96		{
97	0	continue;
98		}
99	0	for (Preset pr : prl)
100		{
101	0	List<String> writeparam = null;
102	0	List<String> readparam = null;
103	0	writeparam = ParameterUtils.writeParameterSet(
104		pr.getArguments(service.getRunnerConfig()), " ");
105	0	List<Option> pset = ParameterUtils.processParameters(writeparam,
106		service.getRunnerConfig(), " ");
107	0	readparam = ParameterUtils.writeParameterSet(pset, " ");
108	0	Iterator<String> o = pr.getOptions().iterator();
109	0	Iterator<String> s = writeparam.iterator();
110	0	Iterator<String> t = readparam.iterator();
111	0	boolean failed = false;
112	0	while (s.hasNext() && t.hasNext())
113		{
114	0	String on = o.next();
115	0	String sn = s.next();
116	0	String st = t.next();
117	0	final String errorMsg = "Original was " + on + " Phase 1 wrote "
118		+ sn + "\tPhase 2 wrote " + st;
119	0	assertEquals(errorMsg, sn, st);
120	0	assertEquals(errorMsg, sn, on);
121		}
122		}
123		}
124		}
125		}
126
127		/**
128		* Returns true if the service is in the list of the ones we chose to test,
129		* _or_ the list is empty (test all)
130		*
131		* @param service
132		* @return
133		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
134	0	public boolean isForTesting(Jws2Instance service)...
135		{
136	0	return serviceTests.size() == 0 || serviceTests
137		.contains(service.serviceType.toLowerCase(Locale.ROOT));
138		}
139
		0% Uncovered Elements: 11 (11) Complexity: 2 Complexity Density: 0.22 4-
140	0	@Test(groups = { "Network" })...
141		public void testCopyOption()
142		{
143	0	for (Jws2Instance service : disc.getServices())
144		{
145	0	if (isForTesting(service))
146		{
147	0	List<Option<?>> options = service.getRunnerConfig().getOptions();
148	0	for (Option<?> o : options)
149		{
150	0	System.out.println("Testing copyOption for option " + o.getName()
151		+ " of " + service.getActionText());
152	0	Option<?> cpy = ParameterUtils.copyOption(o);
153	0	assertTrue(cpy.equals(o));
154	0	assertEquals(cpy.getName(), o.getName());
155	0	assertFalse(cpy == o);
156		// todo more assertions?
157		}
158		}
159		}
160		}
161
162		/**
163		*/
		0% Uncovered Elements: 11 (11) Complexity: 2 Complexity Density: 0.22 4-
164	0	@Test(groups = { "Network" })...
165		public void testCopyParameter()
166		{
167	0	for (Jws2Instance service : disc.getServices())
168		{
169	0	if (isForTesting(service))
170		{
171	0	List<Parameter> parameters = service.getRunnerConfig()
172		.getParameters();
173	0	for (Parameter o : parameters)
174		{
175	0	System.out.println("Testing copyParameter for parameter "
176		+ o.getName() + " of " + service.getActionText());
177	0	Parameter cpy = ParameterUtils.copyParameter(o);
178	0	assertTrue(cpy.equals(o));
179	0	assertFalse(cpy == o);
180	0	assertEquals(cpy.getName(), o.getName());
181		// todo more assertions?
182		}
183		}
184		}
185		}
186		}