Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
CommandLineOperations	45	97	35	0.781021978.1%	Show methods
CommandLineOperations.Worker	74	8	7	1.0100%	Show methods

Class CommandLineOperations

Class CommandLineOperations	Line # 45	Total Statements 97	Complexity 35	TOTAL Coverage 0.781021978.1%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4848	2.02	1.01	1.0 1.0100%
getClassPath() : String   getClassPath() : String	130130	12.012	4.04	0.75 0.7575%
getJalviewDesktopRunner(boolean,String,int) : Worker   getJalviewDesktopRunner(boolean,String,int) : Worker	159159	18.018	6.06	0.875 0.87587.5%
reportCurrentWorkingDirectory() : void   reportCurrentWorkingDirectory() : void	201201	5.05	2.02	0.8 0.880%
initialize() : void   initialize() : void	215215	1.01	1.01	1.0 1.0100%
setUpForHeadlessCommandLineInputOperations() : void   setUpForHeadlessCommandLineInputOperations() : void	221221	9.09	3.03	0.6923077 0.692307769.2%
run() : void   run() : void	258258	16.016	6.06	0.5 0.550%
setUpForCommandLineInputOperations() : void   setUpForCommandLineInputOperations() : void	242242	15.015	6.06	0.94736844 0.9473684494.7%
testAllInputOperations(String,String) : void   testAllInputOperations(String,String) : void	312312	1.01	1.01	1.0 1.0100%
testHeadlessModeOutputOperations(String,String,String,boolean,int,int) : void   testHeadlessModeOutputOperations(String,String,String,boolean,int,int) : void	319319	15.015	3.03	0.7058824 0.705882470.6%
getHeadlessModeInputParams() : Object[][]   getHeadlessModeInputParams() : Object[][]	349349	1.01	1.01	1.0 1.0100%
getHeadlessModeOutputParams() : Object[][]   getHeadlessModeOutputParams() : Object[][]	379379	2.02	1.01	1.0 1.0100%

 

Class CommandLineOperations.Worker

Class CommandLineOperations.Worker	Line # 74	Total Statements 8	Complexity 7	TOTAL Coverage 1.0100%
Worker(Process)   Worker(Process)	8484	1.01	1.01	1.0 1.0100%
run() : void   run() : void	8989	3.03	2.02	1.0 1.0100%
getOutputReader() : BufferedReader   getOutputReader() : BufferedReader	101101	1.01	1.01	1.0 1.0100%
setOutputReader(BufferedReader) : void   setOutputReader(BufferedReader) : void	106106	1.01	1.01	1.0 1.0100%
getErrorReader() : BufferedReader   getErrorReader() : BufferedReader	111111	1.01	1.01	1.0 1.0100%
setErrorReader(BufferedReader) : void   setErrorReader(BufferedReader) : void	116116	1.01	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.2781457	jalview.bin.CommandsTest.headlessOrGuiImageOutputTestjalview.bin.CommandsTest.headlessOrGuiImageOutputTest	1PASS

 

Source view

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.bin;
22
23		import static org.testng.Assert.assertNotNull;
24		import static org.testng.Assert.assertTrue;
25
26		import java.io.BufferedReader;
27		import java.io.File;
28		import java.io.IOException;
29		import java.io.InputStreamReader;
30		import java.nio.file.Path;
31		import java.nio.file.Paths;
32		import java.util.ArrayList;
33
34		import org.testng.Assert;
35		import org.testng.FileAssert;
36		import org.testng.annotations.BeforeClass;
37		import org.testng.annotations.DataProvider;
38		import org.testng.annotations.Test;
39
40		import io.github.classgraph.ClassGraph;
41		import io.github.classgraph.ModuleRef;
42		import io.github.classgraph.ScanResult;
43		import jalview.gui.JvOptionPane;
44
		78.1% Uncovered Elements: 30 (137) Complexity: 35 Complexity Density: 0.36
45		public class CommandLineOperations
46		{
47
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
48	1	@BeforeClass(alwaysRun = true)...
49		public void setUpJvOptionPane()
50		{
51	1	JvOptionPane.setInteractiveMode(false);
52	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
53		}
54
55		// Note longer timeout needed on full test run than on individual tests
56		private static final int TEST_TIMEOUT = 15000;
57
58		private static final int SETUP_TIMEOUT = 9500;
59
60		private static final int MINFILESIZE_SMALL = 2096;
61
62		private static final int MINFILESIZE_BIG = 4096;
63
64		private ArrayList<String> successfulCMDs = new ArrayList<>();
65
66		/***
67		* from
68		* http://stackoverflow.com/questions/808276/how-to-add-a-timeout-value-when
69		* -using-javas-runtime-exec
70		*
71		* @author jimp
72		*
73		*/
		100% Uncovered Elements: 0 (14) Complexity: 7 Complexity Density: 0.88
74		public static class Worker extends Thread
75		{
76		private final Process process;
77
78		private BufferedReader outputReader;
79
80		private BufferedReader errorReader;
81
82		private Integer exit;
83
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
84	20	private Worker(Process process)...
85		{
86	20	this.process = process;
87		}
88
		100% Uncovered Elements: 0 (3) Complexity: 2 Complexity Density: 0.67
89	20	@Override...
90		public void run()
91		{
92	20	try
93		{
94	20	exit = process.waitFor();
95		} catch (InterruptedException ignore)
96		{
97	1	return;
98		}
99		}
100
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
101	55	public BufferedReader getOutputReader()...
102		{
103	55	return outputReader;
104		}
105
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
106	20	public void setOutputReader(BufferedReader outputReader)...
107		{
108	20	this.outputReader = outputReader;
109		}
110
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
111	12	public BufferedReader getErrorReader()...
112		{
113	12	return errorReader;
114		}
115
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
116	20	public void setErrorReader(BufferedReader errorReader)...
117		{
118	20	this.errorReader = errorReader;
119		}
120		}
121
122		private static ClassGraph scanner = null;
123
124		private static String classpath = null;
125
126		private static String modules = null;
127
128		private static String java_exe = null;
129
		75% Uncovered Elements: 4 (16) Complexity: 4 Complexity Density: 0.33
130	20	public synchronized static String getClassPath()...
131		{
132	20	if (scanner == null)
133		{
134	2	scanner = new ClassGraph();
135	2	ScanResult scan = scanner.scan();
136	2	classpath = scan.getClasspath();
137	2	modules = "";
138	2	for (ModuleRef mr : scan.getModules())
139		{
140	0	modules.concat(mr.getName());
141		}
142	2	java_exe = System.getProperty("java.home") + File.separator + "bin"
143		+ File.separator + "java";
144
145		}
146	20	while (classpath == null)
147		{
148	0	try
149		{
150	0	Thread.sleep(10);
151		} catch (InterruptedException x)
152		{
153
154		}
155		}
156	20	return classpath;
157		}
158
		87.5% Uncovered Elements: 3 (24) Complexity: 6 Complexity Density: 0.33
159	20	public static Worker getJalviewDesktopRunner(boolean withAwt, String cmd,...
160		int timeout)
161		{
162		// Note: JAL-3065 - don't include quotes for lib/* because the arguments are
163		// not expanded by the shell
164	20	String classpath = getClassPath();
165	20	String _cmd = java_exe + " "
166	20	+ (withAwt ? "-Djava.awt.headless=true" : "") + " -classpath "
167		+ classpath
168	20	+ (modules.length() > 2 ? "--add-modules=\"" + modules + "\""
169		: "")
170		+ " jalview.bin.Jalview ";
171	20	Process ls2_proc = null;
172	20	Worker worker = null;
173	20	try
174		{
175	20	ls2_proc = Runtime.getRuntime().exec(_cmd + cmd);
176		} catch (Throwable e1)
177		{
178	0	e1.printStackTrace();
179		}
180	20	if (ls2_proc != null)
181		{
182	20	BufferedReader outputReader = new BufferedReader(
183		new InputStreamReader(ls2_proc.getInputStream()));
184	20	BufferedReader errorReader = new BufferedReader(
185		new InputStreamReader(ls2_proc.getErrorStream()));
186	20	worker = new CommandLineOperations.Worker(ls2_proc);
187	20	worker.start();
188	20	try
189		{
190	20	worker.join(timeout);
191		} catch (InterruptedException e)
192		{
193	1	System.err.println("Thread interrupted");
194		}
195	20	worker.setOutputReader(outputReader);
196	20	worker.setErrorReader(errorReader);
197		}
198	20	return worker;
199		}
200
		80% Uncovered Elements: 1 (5) Complexity: 2 Complexity Density: 0.4
201	1	@Test(groups = { "Functional" })...
202		public void reportCurrentWorkingDirectory()
203		{
204	1	try
205		{
206	1	Path currentRelativePath = Paths.get("");
207	1	String s = currentRelativePath.toAbsolutePath().toString();
208	1	System.out.println("Test CWD is " + s);
209		} catch (Exception q)
210		{
211	0	q.printStackTrace();
212		}
213		}
214
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
215	1	@BeforeClass(alwaysRun = true)...
216		public void initialize()
217		{
218	1	new CommandLineOperations();
219		}
220
		69.2% Uncovered Elements: 4 (13) Complexity: 3 Complexity Density: 0.33
221	1	@BeforeClass(alwaysRun = true)...
222		public void setUpForHeadlessCommandLineInputOperations()
223		throws IOException
224		{
225	1	String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props test/jalview/bin/testProps.jvprops -colour zappo "
226		+ "-jabaws http://www.compbio.dundee.ac.uk/jabaws -nosortbytree "
227		+ "-features examples/testdata/plantfdx.features -annotations examples/testdata/plantfdx.annotations -tree examples/testdata/uniref50_test_tree";
228	1	Worker worker = getJalviewDesktopRunner(true, cmds, SETUP_TIMEOUT);
229	1	String ln = null;
230	?	while ((ln = worker.getOutputReader().readLine()) != null)
231		{
232	22	System.out.println("STDOUT: " + ln);
233	22	successfulCMDs.add(ln);
234		}
235	?	while ((ln = worker.getErrorReader().readLine()) != null)
236		{
237	10	System.err.println("STDERR: " + ln);
238	10	successfulCMDs.add(ln);
239		}
240		}
241
		94.7% Uncovered Elements: 1 (19) Complexity: 6 Complexity Density: 0.4
242	1	@BeforeClass(alwaysRun = true)...
243		public void setUpForCommandLineInputOperations() throws IOException
244		{
245	1	String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats";
246	1	final Worker worker = getJalviewDesktopRunner(false, cmds,
247		SETUP_TIMEOUT);
248
249		// number of lines expected on STDERR when Jalview starts up normally
250		// may need to adjust this if Jalview is excessively noisy ?
251	1	final int STDOUT_SETUPLINES = 50;
252	1	final int STDERR_SETUPLINES = 50;
253
254		// thread monitors stderr - bails after SETUP_TIMEOUT or when
255		// STDERR_SETUPLINES have been read
256	1	Thread runner = new Thread(new Runnable()
257		{
		50% Uncovered Elements: 12 (24) Complexity: 6 Complexity Density: 0.38
258	1	@Override...
259		public void run()
260		{
261	1	String ln = null;
262	1	int stdoutcount = 0;
263	1	int stderrcount = 0;
264	1	try
265		{
266	?	while ((ln = worker.getOutputReader().readLine()) != null)
267		{
268	31	System.out.println(ln);
269	31	successfulCMDs.add(ln);
270	31	if (++stdoutcount > STDOUT_SETUPLINES)
271		{
272	0	break;
273		}
274		}
275	?	while ((ln = worker.getErrorReader().readLine()) != null)
276		{
277	0	System.err.println(ln);
278	0	successfulCMDs.add(ln);
279	0	if (++stderrcount > STDERR_SETUPLINES)
280		{
281	0	break;
282		}
283		}
284		} catch (Exception e)
285		{
286	1	System.err.println(
287		"Unexpected Exception reading stderr from the Jalview process");
288	1	e.printStackTrace();
289		}
290		}
291		});
292	1	long t = System.currentTimeMillis() + SETUP_TIMEOUT;
293	1	runner.start();
294	20	while (!runner.isInterrupted() && System.currentTimeMillis() < t)
295		{
296	19	try
297		{
298	19	Thread.sleep(500);
299		} catch (InterruptedException e)
300		{
301		}
302		}
303	1	runner.interrupt();
304	1	if (worker != null && worker.exit == null)
305		{
306	1	worker.interrupt();
307	1	Thread.currentThread().interrupt();
308	1	worker.process.destroy();
309		}
310		}
311
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
312	11	@Test(groups = { "Functional" }, dataProvider = "allInputOperationsData")...
313		public void testAllInputOperations(String expectedString,
314		String failureMsg)
315		{
316	11	Assert.assertTrue(successfulCMDs.contains(expectedString), failureMsg);
317		}
318
		70.6% Uncovered Elements: 5 (17) Complexity: 3 Complexity Density: 0.2
319	16	@Test(...
320		groups =
321		{ "Functional" },
322		dataProvider = "headlessModeOutputOperationsData")
323		public void testHeadlessModeOutputOperations(String harg, String type,
324		String fileName, boolean withAWT, int expectedMinFileSize,
325		int timeout)
326		{
327	16	String cmd = harg + type + " " + fileName;
328		// System.out.println(">>>>>>>>>>>>>>>> Command : " + cmd);
329	16	File file = new File(fileName);
330	16	file.deleteOnExit();
331	16	Worker worker = getJalviewDesktopRunner(withAWT, cmd, timeout);
332	16	assertNotNull(worker, "worker is null");
333	16	String msg = "Didn't create an output" + type + " file.[" + harg + "]";
334	16	assertTrue(file.exists(), msg);
335	16	FileAssert.assertFile(file, msg);
336	16	FileAssert.assertMinLength(file, expectedMinFileSize);
337	16	if (worker != null && worker.exit == null)
338		{
339	0	worker.interrupt();
340	0	Thread.currentThread().interrupt();
341	0	worker.process.destroy();
342	0	Assert.fail("Jalview did not exit after " + type
343		+ " generation (try running test again to verify - timeout at "
344		+ timeout + "ms). [" + harg + "]");
345		}
346	16	file.delete();
347		}
348
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
349	1	@DataProvider(name = "allInputOperationsData")...
350		public Object[][] getHeadlessModeInputParams()
351		{
352	1	return new Object[][] {
353		// headless mode input operations
354		{ "CMD [-colour zappo] executed successfully!",
355		"Failed command : -colour zappo" },
356		{ "CMD [-props test/jalview/bin/testProps.jvprops] executed successfully!",
357		"Failed command : -props File" },
358		{ "CMD [-sortbytree] executed successfully!",
359		"Failed command : -sortbytree" },
360		{ "CMD [-jabaws http://www.compbio.dundee.ac.uk/jabaws] executed successfully!",
361		"Failed command : -jabaws http://www.compbio.dundee.ac.uk/jabaws" },
362		{ "CMD [-open examples/uniref50.fa] executed successfully!",
363		"Failed command : -open examples/uniref50.fa" },
364		{ "CMD [-nosortbytree] executed successfully!",
365		"Failed command : -nosortbytree" },
366		{ "CMD [-features examples/testdata/plantfdx.features] executed successfully!",
367		"Failed command : -features examples/testdata/plantfdx.features" },
368		{ "CMD [-annotations examples/testdata/plantfdx.annotations] executed successfully!",
369		"Failed command : -annotations examples/testdata/plantfdx.annotations" },
370		{ "CMD [-tree examples/testdata/uniref50_test_tree] executed successfully!",
371		"Failed command : -tree examples/testdata/uniref50_test_tree" },
372		// non headless mode input operations
373		{ "CMD [-nousagestats] executed successfully!",
374		"Failed command : -nousagestats" },
375		{ "CMD [-noquestionnaire] executed successfully!",
376		"Failed command : -noquestionnaire" } };
377		}
378
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
379	1	@DataProvider(name = "headlessModeOutputOperationsData")...
380		public static Object[][] getHeadlessModeOutputParams()
381		{
382		// JBPNote: I'm not clear why need to specify full path for output file
383		// when running tests on build server, but we will keep this patch for now
384		// since it works.
385		// https://issues.jalview.org/browse/JAL-1889?focusedCommentId=21609&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-21609
386	1	String workingDir = "test/jalview/bin/";
387	1	return new Object[][] {
388		//
389		{ "nodisplay -open examples/uniref50.fa", " -eps",
390		workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG,
391		TEST_TIMEOUT },
392		{ "nodisplay -open examples/uniref50.fa", " -eps",
393		workingDir + "test_uniref50_out.eps", false, MINFILESIZE_BIG,
394		TEST_TIMEOUT },
395		{ "nogui -open examples/uniref50.fa", " -eps",
396		workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG,
397		TEST_TIMEOUT },
398		{ "nogui -open examples/uniref50.fa", " -eps",
399		workingDir + "test_uniref50_out.eps", false, MINFILESIZE_BIG,
400		TEST_TIMEOUT },
401		{ "headless -open examples/uniref50.fa", " -eps",
402		workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG,
403		TEST_TIMEOUT },
404		{ "headless -open examples/uniref50.fa", " -svg",
405		workingDir + "test_uniref50_out.svg", false, MINFILESIZE_BIG,
406		TEST_TIMEOUT },
407		{ "headless -open examples/uniref50.fa", " -png",
408		workingDir + "test_uniref50_out.png", true, MINFILESIZE_BIG,
409		TEST_TIMEOUT },
410		{ "headless -open examples/uniref50.fa", " -html",
411		workingDir + "test_uniref50_out.html", true, MINFILESIZE_BIG,
412		TEST_TIMEOUT },
413		{ "headless -open examples/uniref50.fa", " -fasta",
414		workingDir + "test_uniref50_out.mfa", true, MINFILESIZE_SMALL,
415		TEST_TIMEOUT },
416		{ "headless -open examples/uniref50.fa", " -clustal",
417		workingDir + "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
418		TEST_TIMEOUT },
419		{ "headless -open examples/uniref50.fa", " -msf",
420		workingDir + "test_uniref50_out.msf", true, MINFILESIZE_SMALL,
421		TEST_TIMEOUT },
422		{ "headless -open examples/uniref50.fa", " -pileup",
423		workingDir + "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
424		TEST_TIMEOUT },
425		{ "headless -open examples/uniref50.fa", " -pir",
426		workingDir + "test_uniref50_out.pir", true, MINFILESIZE_SMALL,
427		TEST_TIMEOUT },
428		{ "headless -open examples/uniref50.fa", " -pfam",
429		workingDir + "test_uniref50_out.pfam", true, MINFILESIZE_SMALL,
430		TEST_TIMEOUT },
431		{ "headless -open examples/uniref50.fa", " -blc",
432		workingDir + "test_uniref50_out.blc", true, MINFILESIZE_SMALL,
433		TEST_TIMEOUT },
434		{ "headless -open examples/uniref50.fa", " -jalview",
435		workingDir + "test_uniref50_out.jvp", true, MINFILESIZE_SMALL,
436		TEST_TIMEOUT },
437		//
438		};
439		}
440		}