Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
RNAStructExportImport	67	97	30	0.00%	Show methods

Class RNAStructExportImport

Class RNAStructExportImport	Line # 67	Total Statements 97	Complexity 30	TOTAL Coverage 0.00%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	7070	2.02	1.01	0.0 0.00%
setUpBeforeClass() : void   setUpBeforeClass() : void	8989	21.021	5.05	0.0 0.00%
tearDownAfterClass() : void   tearDownAfterClass() : void	144144	6.06	3.03	0.0 0.00%
testRNAAliFoldValidStructure() : void   testRNAAliFoldValidStructure() : void	159159	10.010	5.05	0.0 0.00%
testRNAStructExport() : void   testRNAStructExport() : void	193193	7.07	3.03	0.0 0.00%
verifyAnnotationFileIO(String,AlignmentI) : void   verifyAnnotationFileIO(String,AlignmentI) : void	220220	12.012	2.02	0.0 0.00%
testRnaalifoldSettingsRecovery() : void   testRnaalifoldSettingsRecovery() : void	260260	39.039	11.011	0.0 0.00%

 

Contributing tests

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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.jabaws;
22
23		import java.util.Locale;
24		import static org.testng.AssertJUnit.assertNotNull;
25		import static org.testng.AssertJUnit.assertTrue;
26
27		import jalview.bin.Cache;
28		import jalview.bin.Console;
29		import jalview.datamodel.AlignmentAnnotation;
30		import jalview.datamodel.AlignmentI;
31		import jalview.gui.JvOptionPane;
32		import jalview.io.AnnotationFile;
33		import jalview.io.DataSourceType;
34		import jalview.io.FileFormat;
35		import jalview.io.FormatAdapter;
36		import jalview.io.StockholmFileTest;
37		import jalview.project.Jalview2XML;
38		import jalview.ws.api.ServiceWithParameters;
39		import jalview.ws.jws2.JabaParamStore;
40		import jalview.ws.jws2.Jws2Discoverer;
41		import jalview.ws.jws2.SeqAnnotationServiceCalcWorker;
42		import jalview.ws.jws2.SequenceAnnotationWSClient;
43		import jalview.ws.jws2.jabaws2.Jws2Instance;
44		import jalview.ws.params.AutoCalcSetting;
45
46		import java.awt.Component;
47		import java.io.File;
48		import java.util.ArrayList;
49		import java.util.List;
50
51		import javax.swing.JMenu;
52		import javax.swing.JMenuItem;
53
54		import org.testng.Assert;
55		import org.testng.annotations.AfterClass;
56		import org.testng.annotations.BeforeClass;
57		import org.testng.annotations.Test;
58
59		import compbio.metadata.Argument;
60		import compbio.metadata.WrongParameterException;
61
62		/*
63		* All methods in this class are set to the Network group because setUpBeforeClass will fail
64		* if there is no network.
65		*/
66		@Test(singleThreaded = true)
		0% Uncovered Elements: 138 (138) Complexity: 30 Complexity Density: 0.31
67		public class RNAStructExportImport
68		{
69
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
70	0	@BeforeClass(alwaysRun = true)...
71		public void setUpJvOptionPane()
72		{
73	0	JvOptionPane.setInteractiveMode(false);
74	0	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
75		}
76
77		private static final String JAR_FILE_NAME = "testRnalifold_param.jar";
78
79		public static String testseqs = "examples/RF00031_folded.stk";
80
81		public static Jws2Discoverer disc;
82
83		public static Jws2Instance rnaalifoldws;
84
85		SeqAnnotationServiceCalcWorker alifoldClient;
86
87		public static jalview.gui.AlignFrame af = null;
88
		0% Uncovered Elements: 29 (29) Complexity: 5 Complexity Density: 0.24
89	0	@BeforeClass(alwaysRun = true)...
90		public static void setUpBeforeClass() throws Exception
91		{
92	0	Cache.loadProperties("test/jalview/io/testProps.jvprops");
93	0	Console.initLogger();
94	0	disc = JalviewJabawsTestUtils.getJabawsDiscoverer(false);
95
96	0	while (disc.isRunning())
97		{
98		// don't get services until discoverer has finished
99	0	Thread.sleep(100);
100		}
101
102	0	for (ServiceWithParameters svc : disc.getServices())
103		{
104
105	0	if (svc.getServiceType().toLowerCase(Locale.ROOT)
106		.contains("rnaalifoldws"))
107		{
108	0	rnaalifoldws = (Jws2Instance) svc;
109		}
110		}
111
112	0	System.out.println("State of rnaalifoldws: " + rnaalifoldws);
113
114	0	if (rnaalifoldws == null)
115		{
116	0	Assert.fail("no web service");
117		}
118
119	0	jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
120
121	0	af = fl.LoadFileWaitTillLoaded(testseqs,
122		jalview.io.DataSourceType.FILE);
123
124	0	assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
125
126		// remove any existing annotation
127	0	List<AlignmentAnnotation> aal = new ArrayList<>();
128	0	for (AlignmentAnnotation rna : af.getViewport().getAlignment()
129		.getAlignmentAnnotation())
130		{
131	0	if (rna.isRNA())
132		{
133	0	aal.add(rna);
134		}
135		}
136	0	for (AlignmentAnnotation rna : aal)
137		{
138	0	af.getViewport().getAlignment().deleteAnnotation(rna);
139		}
140	0	af.getViewport().alignmentChanged(af.alignPanel); // why is af.alignPanel
141		// public?
142		}
143
		0% Uncovered Elements: 10 (10) Complexity: 3 Complexity Density: 0.5
144	0	@AfterClass(alwaysRun = true)...
145		public static void tearDownAfterClass() throws Exception
146		{
147	0	if (af != null)
148		{
149	0	af.setVisible(false);
150	0	af.dispose();
151	0	File f = new File(JAR_FILE_NAME);
152	0	if (f.exists())
153		{
154	0	f.delete();
155		}
156		}
157		}
158
		0% Uncovered Elements: 16 (16) Complexity: 5 Complexity Density: 0.5 4-
159	0	@Test(groups = { "Network" })...
160		public void testRNAAliFoldValidStructure()
161		{
162
163	0	alifoldClient = new SeqAnnotationServiceCalcWorker(rnaalifoldws, af, null,
164		null);
165
166	0	af.getViewport().getCalcManager().startWorker(alifoldClient);
167
168	0	do
169		{
170	0	try
171		{
172	0	Thread.sleep(50);
173		} catch (InterruptedException x)
174		{
175		}
176	0	} while (af.getViewport().getCalcManager().isWorking());
177
178	0	AlignmentI orig_alig = af.getViewport().getAlignment();
179	0	for (AlignmentAnnotation aa : orig_alig.getAlignmentAnnotation())
180		{
181	0	if (alifoldClient.involves(aa))
182		{
183	0	if (aa.isRNA())
184		{
185	0	assertTrue(
186		"Did not create valid structure from RNAALiFold prediction",
187		aa.isValidStruc());
188		}
189		}
190		}
191		}
192
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.43 4-
193	0	@Test(groups = { "Network" })...
194		public void testRNAStructExport()
195		{
196
197	0	alifoldClient = new SeqAnnotationServiceCalcWorker(rnaalifoldws, af, null,
198		null);
199
200	0	af.getViewport().getCalcManager().startWorker(alifoldClient);
201
202	0	do
203		{
204	0	try
205		{
206	0	Thread.sleep(50);
207		} catch (InterruptedException x)
208		{
209		}
210	0	} while (af.getViewport().getCalcManager().isWorking());
211
212	0	AlignmentI orig_alig = af.getViewport().getAlignment();
213		// JBPNote: this assert fails (2.10.2) because the 'Reference Positions'
214		// annotation is mistakenly recognised as an RNA annotation row when read in
215		// as an annotation file. bug is JAL-3122
216	0	verifyAnnotationFileIO("Testing RNAalifold Annotation IO", orig_alig);
217
218		}
219
		0% Uncovered Elements: 12 (12) Complexity: 2 Complexity Density: 0.17
220	0	static void verifyAnnotationFileIO(String testname, AlignmentI al)...
221		{
222	0	try
223		{
224		// what format would be appropriate for RNAalifold annotations?
225	0	String aligfileout = FileFormat.Pfam.getWriter(null)
226		.print(al.getSequencesArray(), true);
227
228	0	String anfileout = new AnnotationFile()
229		.printAnnotationsForAlignment(al);
230	0	assertNotNull("Test " + testname
231		+ "\nAlignment annotation file was not regenerated. Null string",
232		anfileout);
233	0	assertTrue("Test " + testname
234		+ "\nAlignment annotation file was not regenerated. Empty string",
235		anfileout.length() > "JALVIEW_ANNOTATION".length());
236
237	0	System.out.println(
238		"Output annotation file:\n" + anfileout + "\n<<EOF\n");
239
240		// again what format would be appropriate?
241	0	AlignmentI al_new = new FormatAdapter().readFile(aligfileout,
242		DataSourceType.PASTE, FileFormat.Pfam);
243	0	assertTrue("Test " + testname
244		+ "\nregenerated annotation file did not annotate alignment.",
245		new AnnotationFile().readAnnotationFile(al_new, anfileout,
246		DataSourceType.PASTE));
247
248		// test for consistency in io
249	0	StockholmFileTest.testAlignmentEquivalence(al, al_new, false, false,
250		false);
251	0	return;
252		} catch (Exception e)
253		{
254	0	e.printStackTrace();
255		}
256	0	Assert.fail("Test " + testname
257		+ "\nCouldn't complete Annotation file roundtrip input/output/input test.");
258		}
259
		0% Uncovered Elements: 53 (53) Complexity: 11 Complexity Density: 0.28 4-
260	0	@Test(groups = { "Network" })...
261		public void testRnaalifoldSettingsRecovery()
262		{
263	0	List<Argument> opts = new ArrayList<>();
264	0	for (Argument rg : (List<Argument>) rnaalifoldws.getRunnerConfig()
265		.getArguments())
266		{
267	0	if (rg.getDescription().contains("emperature"))
268		{
269	0	try
270		{
271	0	rg.setValue("292");
272		} catch (WrongParameterException q)
273		{
274	0	Assert.fail("Couldn't set the temperature parameter "
275		+ q.getStackTrace());
276		}
277	0	opts.add(rg);
278		}
279	0	if (rg.getDescription().contains("max"))
280		{
281	0	opts.add(rg);
282		}
283		}
284	0	alifoldClient = new SeqAnnotationServiceCalcWorker(rnaalifoldws, af, null,
285		JabaParamStore.getJwsArgsfromJaba(opts));
286
287	0	af.getViewport().getCalcManager().startWorker(alifoldClient);
288
289	0	do
290		{
291	0	try
292		{
293	0	Thread.sleep(50);
294		} catch (InterruptedException x)
295		{
296		}
297	0	;
298	0	} while (af.getViewport().getCalcManager().isWorking());
299	0	AutoCalcSetting oldacs = af.getViewport()
300		.getCalcIdSettingsFor(alifoldClient.getCalcId());
301	0	String oldsettings = oldacs.getWsParamFile();
302		// write out parameters
303	0	jalview.gui.AlignFrame nalf = null;
304	0	assertTrue("Couldn't write out the Jar file", new Jalview2XML(false)
305		.saveAlignment(af, JAR_FILE_NAME, "trial parameter writeout"));
306	0	assertTrue("Couldn't read back the Jar file",
307		(nalf = new Jalview2XML(false)
308		.loadJalviewAlign(JAR_FILE_NAME)) != null);
309	0	if (nalf != null)
310		{
311	0	AutoCalcSetting acs = af.getViewport()
312		.getCalcIdSettingsFor(alifoldClient.getCalcId());
313	0	assertTrue("Calc ID settings not recovered from viewport stash",
314		acs.equals(oldacs));
315	0	assertTrue(
316		"Serialised Calc ID settings not identical to those recovered from viewport stash",
317		acs.getWsParamFile().equals(oldsettings));
318	0	JMenu nmenu = new JMenu();
319	0	new SequenceAnnotationWSClient().attachWSMenuEntry(nmenu,
320		rnaalifoldws, af);
321	0	assertTrue("Couldn't get menu entry for service",
322		nmenu.getItemCount() > 0);
323	0	for (Component itm : nmenu.getMenuComponents())
324		{
325	0	if (itm instanceof JMenuItem)
326		{
327	0	JMenuItem i = (JMenuItem) itm;
328	0	if (i.getText().equals(
329		rnaalifoldws.getAlignAnalysisUI().getAAconToggle()))
330		{
331	0	i.doClick();
332	0	break;
333		}
334		}
335		}
336	0	while (af.getViewport().isCalcInProgress())
337		{
338	0	try
339		{
340	0	Thread.sleep(200);
341		} catch (Exception x)
342		{
343		}
344	0	;
345		}
346	0	AutoCalcSetting acs2 = af.getViewport()
347		.getCalcIdSettingsFor(alifoldClient.getCalcId());
348	0	assertTrue(
349		"Calc ID settings after recalculation has not been recovered.",
350		acs2.getWsParamFile().equals(oldsettings));
351		}
352		}
353		}