Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
RNAStructExportImport	66	97	30	0.00%	Show methods

Class RNAStructExportImport

Class RNAStructExportImport	Line # 66	Total Statements 97	Complexity 30	TOTAL Coverage 0.00%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	6969	2.02	1.01	0.0 0.00%
setUpBeforeClass() : void   setUpBeforeClass() : void	8888	21.021	5.05	0.0 0.00%
tearDownAfterClass() : void   tearDownAfterClass() : void	143143	6.06	3.03	0.0 0.00%
testRNAAliFoldValidStructure() : void   testRNAAliFoldValidStructure() : void	158158	10.010	5.05	0.0 0.00%
testRNAStructExport() : void   testRNAStructExport() : void	191191	7.07	3.03	0.0 0.00%
verifyAnnotationFileIO(String,AlignmentI) : void   verifyAnnotationFileIO(String,AlignmentI) : void	217217	12.012	2.02	0.0 0.00%
testRnaalifoldSettingsRecovery() : void   testRnaalifoldSettingsRecovery() : void	257257	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
25		import static org.testng.AssertJUnit.assertNotNull;
26		import static org.testng.AssertJUnit.assertTrue;
27
28		import jalview.bin.Cache;
29		import jalview.bin.Console;
30		import jalview.datamodel.AlignmentAnnotation;
31		import jalview.datamodel.AlignmentI;
32		import jalview.gui.JvOptionPane;
33		import jalview.io.AnnotationFile;
34		import jalview.io.DataSourceType;
35		import jalview.io.FileFormat;
36		import jalview.io.FormatAdapter;
37		import jalview.io.StockholmFileTest;
38		import jalview.project.Jalview2XML;
39		import jalview.ws.jws2.Jws2Discoverer;
40		import jalview.ws.jws2.RNAalifoldClient;
41		import jalview.ws.jws2.SequenceAnnotationWSClient;
42		import jalview.ws.jws2.jabaws2.Jws2Instance;
43		import jalview.ws.params.AutoCalcSetting;
44
45		import java.awt.Component;
46		import java.io.File;
47		import java.util.ArrayList;
48		import java.util.List;
49
50		import javax.swing.JMenu;
51		import javax.swing.JMenuItem;
52
53		import org.testng.Assert;
54		import org.testng.annotations.AfterClass;
55		import org.testng.annotations.BeforeClass;
56		import org.testng.annotations.Test;
57
58		import compbio.metadata.Argument;
59		import compbio.metadata.WrongParameterException;
60
61		/*
62		* All methods in this class are set to the Network group because setUpBeforeClass will fail
63		* if there is no network.
64		*/
65		@Test(singleThreaded = true)
		0% Uncovered Elements: 138 (138) Complexity: 30 Complexity Density: 0.31
66		public class RNAStructExportImport
67		{
68
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
69	0	@BeforeClass(alwaysRun = true)...
70		public void setUpJvOptionPane()
71		{
72	0	JvOptionPane.setInteractiveMode(false);
73	0	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
74		}
75
76		private static final String JAR_FILE_NAME = "testRnalifold_param.jar";
77
78		public static String testseqs = "examples/RF00031_folded.stk";
79
80		public static Jws2Discoverer disc;
81
82		public static Jws2Instance rnaalifoldws;
83
84		jalview.ws.jws2.RNAalifoldClient alifoldClient;
85
86		public static jalview.gui.AlignFrame af = null;
87
		0% Uncovered Elements: 29 (29) Complexity: 5 Complexity Density: 0.24
88	0	@BeforeClass(alwaysRun = true)...
89		public static void setUpBeforeClass() throws Exception
90		{
91	0	Cache.loadProperties("test/jalview/io/testProps.jvprops");
92	0	Console.initLogger();
93	0	disc = JalviewJabawsTestUtils.getJabawsDiscoverer(false);
94
95	0	while (disc.isRunning())
96		{
97		// don't get services until discoverer has finished
98	0	Thread.sleep(100);
99		}
100
101	0	for (Jws2Instance svc : disc.getServices())
102		{
103
104	0	if (svc.getServiceTypeURI().toLowerCase(Locale.ROOT)
105		.contains("rnaalifoldws"))
106		{
107	0	rnaalifoldws = svc;
108		}
109		}
110
111	0	System.out.println("State of rnaalifoldws: " + rnaalifoldws);
112
113	0	if (rnaalifoldws == null)
114		{
115	0	Assert.fail("no web service");
116		}
117
118	0	jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
119
120	0	af = fl.LoadFileWaitTillLoaded(testseqs,
121		jalview.io.DataSourceType.FILE);
122
123	0	assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
124
125		// remove any existing annotation
126	0	List<AlignmentAnnotation> aal = new ArrayList<>();
127	0	for (AlignmentAnnotation rna : af.getViewport().getAlignment()
128		.getAlignmentAnnotation())
129		{
130	0	if (rna.isRNA())
131		{
132	0	aal.add(rna);
133		}
134		}
135	0	for (AlignmentAnnotation rna : aal)
136		{
137	0	af.getViewport().getAlignment().deleteAnnotation(rna);
138		}
139	0	af.getViewport().alignmentChanged(af.alignPanel); // why is af.alignPanel
140		// public?
141		}
142
		0% Uncovered Elements: 10 (10) Complexity: 3 Complexity Density: 0.5
143	0	@AfterClass(alwaysRun = true)...
144		public static void tearDownAfterClass() throws Exception
145		{
146	0	if (af != null)
147		{
148	0	af.setVisible(false);
149	0	af.dispose();
150	0	File f = new File(JAR_FILE_NAME);
151	0	if (f.exists())
152		{
153	0	f.delete();
154		}
155		}
156		}
157
		0% Uncovered Elements: 16 (16) Complexity: 5 Complexity Density: 0.5 4-
158	0	@Test(groups = { "Network" })...
159		public void testRNAAliFoldValidStructure()
160		{
161
162	0	alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, null);
163
164	0	af.getViewport().getCalcManager().startWorker(alifoldClient);
165
166	0	do
167		{
168	0	try
169		{
170	0	Thread.sleep(50);
171		} catch (InterruptedException x)
172		{
173		}
174	0	} while (af.getViewport().getCalcManager().isWorking());
175
176	0	AlignmentI orig_alig = af.getViewport().getAlignment();
177	0	for (AlignmentAnnotation aa : orig_alig.getAlignmentAnnotation())
178		{
179	0	if (alifoldClient.involves(aa))
180		{
181	0	if (aa.isRNA())
182		{
183	0	assertTrue(
184		"Did not create valid structure from RNAALiFold prediction",
185		aa.isValidStruc());
186		}
187		}
188		}
189		}
190
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.43 4-
191	0	@Test(groups = { "Network" })...
192		public void testRNAStructExport()
193		{
194
195	0	alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, null);
196
197	0	af.getViewport().getCalcManager().startWorker(alifoldClient);
198
199	0	do
200		{
201	0	try
202		{
203	0	Thread.sleep(50);
204		} catch (InterruptedException x)
205		{
206		}
207	0	} while (af.getViewport().getCalcManager().isWorking());
208
209	0	AlignmentI orig_alig = af.getViewport().getAlignment();
210		// JBPNote: this assert fails (2.10.2) because the 'Reference Positions'
211		// annotation is mistakenly recognised as an RNA annotation row when read in
212		// as an annotation file.
213	0	verifyAnnotationFileIO("Testing RNAalifold Annotation IO", orig_alig);
214
215		}
216
		0% Uncovered Elements: 12 (12) Complexity: 2 Complexity Density: 0.17
217	0	static void verifyAnnotationFileIO(String testname, AlignmentI al)...
218		{
219	0	try
220		{
221		// what format would be appropriate for RNAalifold annotations?
222	0	String aligfileout = FileFormat.Pfam.getWriter(null)
223		.print(al.getSequencesArray(), true);
224
225	0	String anfileout = new AnnotationFile()
226		.printAnnotationsForAlignment(al);
227	0	assertNotNull("Test " + testname
228		+ "\nAlignment annotation file was not regenerated. Null string",
229		anfileout);
230	0	assertTrue("Test " + testname
231		+ "\nAlignment annotation file was not regenerated. Empty string",
232		anfileout.length() > "JALVIEW_ANNOTATION".length());
233
234	0	System.out.println(
235		"Output annotation file:\n" + anfileout + "\n<<EOF\n");
236
237		// again what format would be appropriate?
238	0	AlignmentI al_new = new FormatAdapter().readFile(aligfileout,
239		DataSourceType.PASTE, FileFormat.Pfam);
240	0	assertTrue("Test " + testname
241		+ "\nregenerated annotation file did not annotate alignment.",
242		new AnnotationFile().readAnnotationFile(al_new, anfileout,
243		DataSourceType.PASTE));
244
245		// test for consistency in io
246	0	StockholmFileTest.testAlignmentEquivalence(al, al_new, false, false,
247		false);
248	0	return;
249		} catch (Exception e)
250		{
251	0	e.printStackTrace();
252		}
253	0	Assert.fail("Test " + testname
254		+ "\nCouldn't complete Annotation file roundtrip input/output/input test.");
255		}
256
		0% Uncovered Elements: 53 (53) Complexity: 11 Complexity Density: 0.28 4-
257	0	@Test(groups = { "Network" })...
258		public void testRnaalifoldSettingsRecovery()
259		{
260	0	List<Argument> opts = new ArrayList<>();
261	0	for (Argument rg : (List<Argument>) rnaalifoldws.getRunnerConfig()
262		.getArguments())
263		{
264	0	if (rg.getDescription().contains("emperature"))
265		{
266	0	try
267		{
268	0	rg.setValue("292");
269		} catch (WrongParameterException q)
270		{
271	0	Assert.fail("Couldn't set the temperature parameter "
272		+ q.getStackTrace());
273		}
274	0	opts.add(rg);
275		}
276	0	if (rg.getDescription().contains("max"))
277		{
278	0	opts.add(rg);
279		}
280		}
281	0	alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, opts);
282
283	0	af.getViewport().getCalcManager().startWorker(alifoldClient);
284
285	0	do
286		{
287	0	try
288		{
289	0	Thread.sleep(50);
290		} catch (InterruptedException x)
291		{
292		}
293	0	;
294	0	} while (af.getViewport().getCalcManager().isWorking());
295	0	AutoCalcSetting oldacs = af.getViewport()
296		.getCalcIdSettingsFor(alifoldClient.getCalcId());
297	0	String oldsettings = oldacs.getWsParamFile();
298		// write out parameters
299	0	jalview.gui.AlignFrame nalf = null;
300	0	assertTrue("Couldn't write out the Jar file", new Jalview2XML(false)
301		.saveAlignment(af, JAR_FILE_NAME, "trial parameter writeout"));
302	0	assertTrue("Couldn't read back the Jar file",
303		(nalf = new Jalview2XML(false)
304		.loadJalviewAlign(JAR_FILE_NAME)) != null);
305	0	if (nalf != null)
306		{
307	0	AutoCalcSetting acs = af.getViewport()
308		.getCalcIdSettingsFor(alifoldClient.getCalcId());
309	0	assertTrue("Calc ID settings not recovered from viewport stash",
310		acs.equals(oldacs));
311	0	assertTrue(
312		"Serialised Calc ID settings not identical to those recovered from viewport stash",
313		acs.getWsParamFile().equals(oldsettings));
314	0	JMenu nmenu = new JMenu();
315	0	new SequenceAnnotationWSClient().attachWSMenuEntry(nmenu,
316		rnaalifoldws, af);
317	0	assertTrue("Couldn't get menu entry for service",
318		nmenu.getItemCount() > 0);
319	0	for (Component itm : nmenu.getMenuComponents())
320		{
321	0	if (itm instanceof JMenuItem)
322		{
323	0	JMenuItem i = (JMenuItem) itm;
324	0	if (i.getText().equals(
325		rnaalifoldws.getAlignAnalysisUI().getAAconToggle()))
326		{
327	0	i.doClick();
328	0	break;
329		}
330		}
331		}
332	0	while (af.getViewport().isCalcInProgress())
333		{
334	0	try
335		{
336	0	Thread.sleep(200);
337		} catch (Exception x)
338		{
339		}
340	0	;
341		}
342	0	AutoCalcSetting acs2 = af.getViewport()
343		.getCalcIdSettingsFor(alifoldClient.getCalcId());
344	0	assertTrue(
345		"Calc ID settings after recalculation has not been recovered.",
346		acs2.getWsParamFile().equals(oldsettings));
347		}
348		}
349		}