Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
CommandLineOperations	53	106	40	0.7878%	Show methods
CommandLineOperations.Worker	82	8	7	1.0100%	Show methods

Class CommandLineOperations

Class CommandLineOperations	Line # 53	Total Statements 106	Complexity 40	TOTAL Coverage 0.7878%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	5656	2.02	1.01	1.0 1.0100%
getClassPath() : String   getClassPath() : String	138138	12.012	4.04	0.75 0.7575%
getJalviewDesktopRunner(boolean,String,int) : Worker   getJalviewDesktopRunner(boolean,String,int) : Worker	167167	19.019	6.06	0.88 0.8888%
reportCurrentWorkingDirectory() : void   reportCurrentWorkingDirectory() : void	210210	5.05	2.02	0.8 0.880%
initialize() : void   initialize() : void	224224	1.01	1.01	1.0 1.0100%
setUpForHeadlessCommandLineInputOperations() : void   setUpForHeadlessCommandLineInputOperations() : void	230230	9.09	3.03	0.6923077 0.692307769.2%
run() : void   run() : void	267267	16.016	6.06	0.5 0.550%
setUpForCommandLineInputOperations() : void   setUpForCommandLineInputOperations() : void	251251	15.015	6.06	0.94736844 0.9473684494.7%
testAllInputOperations(String,String) : void   testAllInputOperations(String,String) : void	321321	1.01	1.01	1.0 1.0100%
testHeadlessModeOutputOperations(String,String,String,boolean,int,int,String) : void   testHeadlessModeOutputOperations(String,String,String,boolean,int,int,String) : void	328328	23.023	8.08	0.7241379 0.724137972.4%
getHeadlessModeInputParams() : Object[][]   getHeadlessModeInputParams() : Object[][]	380380	1.01	1.01	1.0 1.0100%
getHeadlessModeOutputParams() : Object[][]   getHeadlessModeOutputParams() : Object[][]	410410	2.02	1.01	1.0 1.0100%

 

Class CommandLineOperations.Worker

Class CommandLineOperations.Worker	Line # 82	Total Statements 8	Complexity 7	TOTAL Coverage 1.0100%
Worker(Process)   Worker(Process)	9292	1.01	1.01	1.0 1.0100%
run() : void   run() : void	9797	3.03	2.02	1.0 1.0100%
getOutputReader() : BufferedReader   getOutputReader() : BufferedReader	109109	1.01	1.01	1.0 1.0100%
setOutputReader(BufferedReader) : void   setOutputReader(BufferedReader) : void	114114	1.01	1.01	1.0 1.0100%
getErrorReader() : BufferedReader   getErrorReader() : BufferedReader	119119	1.01	1.01	1.0 1.0100%
setErrorReader(BufferedReader) : void   setErrorReader(BufferedReader) : void	124124	1.01	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.2621951	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.assertEquals;
24		import static org.testng.Assert.assertNotNull;
25		import static org.testng.Assert.assertTrue;
26
27		import java.io.BufferedReader;
28		import java.io.File;
29		import java.io.FileNotFoundException;
30		import java.io.IOException;
31		import java.io.InputStreamReader;
32		import java.nio.file.Path;
33		import java.nio.file.Paths;
34		import java.util.ArrayList;
35
36		import org.testng.Assert;
37		import org.testng.FileAssert;
38		import org.testng.annotations.BeforeClass;
39		import org.testng.annotations.DataProvider;
40		import org.testng.annotations.Test;
41
42		import io.github.classgraph.ClassGraph;
43		import io.github.classgraph.ModuleRef;
44		import io.github.classgraph.ScanResult;
45		import jalview.gui.JvOptionPane;
46		import jalview.io.DataSourceType;
47		import jalview.io.FileFormat;
48		import jalview.io.FileFormatException;
49		import jalview.io.FileFormatI;
50		import jalview.io.FileFormats;
51		import jalview.io.IdentifyFile;
52
		78% Uncovered Elements: 33 (150) Complexity: 40 Complexity Density: 0.38
53		public class CommandLineOperations
54		{
55
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
56	1	@BeforeClass(alwaysRun = true)...
57		public void setUpJvOptionPane()
58		{
59	1	JvOptionPane.setInteractiveMode(false);
60	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
61		}
62
63		// Note longer timeout needed on full test run than on individual tests
64		private static final int TEST_TIMEOUT = 15000;
65
66		private static final int SETUP_TIMEOUT = 9500;
67
68		private static final int MINFILESIZE_SMALL = 2096;
69
70		private static final int MINFILESIZE_BIG = 4096;
71
72		private ArrayList<String> successfulCMDs = new ArrayList<>();
73
74		/***
75		* from
76		* http://stackoverflow.com/questions/808276/how-to-add-a-timeout-value-when
77		* -using-javas-runtime-exec
78		*
79		* @author jimp
80		*
81		*/
		100% Uncovered Elements: 0 (14) Complexity: 7 Complexity Density: 0.88
82		public static class Worker extends Thread
83		{
84		private final Process process;
85
86		private BufferedReader outputReader;
87
88		private BufferedReader errorReader;
89
90		private Integer exit;
91
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
92	20	private Worker(Process process)...
93		{
94	20	this.process = process;
95		}
96
		100% Uncovered Elements: 0 (3) Complexity: 2 Complexity Density: 0.67
97	20	@Override...
98		public void run()
99		{
100	20	try
101		{
102	20	exit = process.waitFor();
103		} catch (InterruptedException ignore)
104		{
105	1	return;
106		}
107		}
108
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
109	44	public BufferedReader getOutputReader()...
110		{
111	44	return outputReader;
112		}
113
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
114	20	public void setOutputReader(BufferedReader outputReader)...
115		{
116	20	this.outputReader = outputReader;
117		}
118
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
119	20	public BufferedReader getErrorReader()...
120		{
121	20	return errorReader;
122		}
123
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
124	20	public void setErrorReader(BufferedReader errorReader)...
125		{
126	20	this.errorReader = errorReader;
127		}
128		}
129
130		private static ClassGraph scanner = null;
131
132		private static String classpath = null;
133
134		private static String modules = null;
135
136		private static String java_exe = null;
137
		75% Uncovered Elements: 4 (16) Complexity: 4 Complexity Density: 0.33
138	20	public synchronized static String getClassPath()...
139		{
140	20	if (scanner == null)
141		{
142	2	scanner = new ClassGraph();
143	2	ScanResult scan = scanner.scan();
144	2	classpath = scan.getClasspath();
145	2	modules = "";
146	2	for (ModuleRef mr : scan.getModules())
147		{
148	0	modules.concat(mr.getName());
149		}
150	2	java_exe = System.getProperty("java.home") + File.separator + "bin"
151		+ File.separator + "java";
152
153		}
154	20	while (classpath == null)
155		{
156	0	try
157		{
158	0	Thread.sleep(10);
159		} catch (InterruptedException x)
160		{
161
162		}
163		}
164	20	return classpath;
165		}
166
		88% Uncovered Elements: 3 (25) Complexity: 6 Complexity Density: 0.32
167	20	public static Worker getJalviewDesktopRunner(boolean withAwt, String cmd,...
168		int timeout)
169		{
170		// Note: JAL-3065 - don't include quotes for lib/* because the arguments are
171		// not expanded by the shell
172	20	String classpath = getClassPath();
173	20	String _cmd = java_exe + " "
174	20	+ (withAwt ? "-Djava.awt.headless=true" : "") + " -classpath "
175		+ classpath
176	20	+ (modules.length() > 2 ? "--add-modules=\"" + modules + "\""
177		: "")
178		+ " jalview.bin.Jalview ";
179	20	System.out.println("COMMAND EXECUTED: " + _cmd + cmd);
180	20	Process ls2_proc = null;
181	20	Worker worker = null;
182	20	try
183		{
184	20	ls2_proc = Runtime.getRuntime().exec(_cmd + cmd);
185		} catch (Throwable e1)
186		{
187	0	e1.printStackTrace();
188		}
189	20	if (ls2_proc != null)
190		{
191	20	BufferedReader outputReader = new BufferedReader(
192		new InputStreamReader(ls2_proc.getInputStream()));
193	20	BufferedReader errorReader = new BufferedReader(
194		new InputStreamReader(ls2_proc.getErrorStream()));
195	20	worker = new CommandLineOperations.Worker(ls2_proc);
196	20	worker.start();
197	20	try
198		{
199	20	worker.join(timeout);
200		} catch (InterruptedException e)
201		{
202	1	System.err.println("Thread interrupted");
203		}
204	20	worker.setOutputReader(outputReader);
205	20	worker.setErrorReader(errorReader);
206		}
207	20	return worker;
208		}
209
		80% Uncovered Elements: 1 (5) Complexity: 2 Complexity Density: 0.4
210	1	@Test(groups = { "Functional" })...
211		public void reportCurrentWorkingDirectory()
212		{
213	1	try
214		{
215	1	Path currentRelativePath = Paths.get("");
216	1	String s = currentRelativePath.toAbsolutePath().toString();
217	1	System.out.println("Test CWD is " + s);
218		} catch (Exception q)
219		{
220	0	q.printStackTrace();
221		}
222		}
223
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
224	1	@BeforeClass(alwaysRun = true)...
225		public void initialize()
226		{
227	1	new CommandLineOperations();
228		}
229
		69.2% Uncovered Elements: 4 (13) Complexity: 3 Complexity Density: 0.33
230	1	@BeforeClass(alwaysRun = true)...
231		public void setUpForHeadlessCommandLineInputOperations()
232		throws IOException
233		{
234	1	String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props test/jalview/bin/testProps.jvprops -colour zappo "
235		+ "-jabaws http://www.compbio.dundee.ac.uk/jabaws -nosortbytree "
236		+ "-features examples/testdata/plantfdx.features -annotations examples/testdata/plantfdx.annotations -tree examples/testdata/uniref50_test_tree";
237	1	Worker worker = getJalviewDesktopRunner(true, cmds, SETUP_TIMEOUT);
238	1	String ln = null;
239	?	while ((ln = worker.getOutputReader().readLine()) != null)
240		{
241	22	System.out.println("STDOUT: " + ln);
242	22	successfulCMDs.add(ln);
243		}
244	?	while ((ln = worker.getErrorReader().readLine()) != null)
245		{
246	18	System.err.println("STDERR: " + ln);
247	18	successfulCMDs.add(ln);
248		}
249		}
250
		94.7% Uncovered Elements: 1 (19) Complexity: 6 Complexity Density: 0.4
251	1	@BeforeClass(alwaysRun = true)...
252		public void setUpForCommandLineInputOperations() throws IOException
253		{
254	1	String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats";
255	1	final Worker worker = getJalviewDesktopRunner(false, cmds,
256		SETUP_TIMEOUT);
257
258		// number of lines expected on STDERR when Jalview starts up normally
259		// may need to adjust this if Jalview is excessively noisy ?
260	1	final int STDOUT_SETUPLINES = 50;
261	1	final int STDERR_SETUPLINES = 50;
262
263		// thread monitors stderr - bails after SETUP_TIMEOUT or when
264		// STDERR_SETUPLINES have been read
265	1	Thread runner = new Thread(new Runnable()
266		{
		50% Uncovered Elements: 12 (24) Complexity: 6 Complexity Density: 0.38
267	1	@Override...
268		public void run()
269		{
270	1	String ln = null;
271	1	int stdoutcount = 0;
272	1	int stderrcount = 0;
273	1	try
274		{
275	?	while ((ln = worker.getOutputReader().readLine()) != null)
276		{
277	20	System.out.println(ln);
278	20	successfulCMDs.add(ln);
279	20	if (++stdoutcount > STDOUT_SETUPLINES)
280		{
281	0	break;
282		}
283		}
284	?	while ((ln = worker.getErrorReader().readLine()) != null)
285		{
286	0	System.err.println(ln);
287	0	successfulCMDs.add(ln);
288	0	if (++stderrcount > STDERR_SETUPLINES)
289		{
290	0	break;
291		}
292		}
293		} catch (Exception e)
294		{
295	1	System.err.println(
296		"Unexpected Exception reading stderr from the Jalview process");
297	1	e.printStackTrace();
298		}
299		}
300		});
301	1	long t = System.currentTimeMillis() + SETUP_TIMEOUT;
302	1	runner.start();
303	20	while (!runner.isInterrupted() && System.currentTimeMillis() < t)
304		{
305	19	try
306		{
307	19	Thread.sleep(500);
308		} catch (InterruptedException e)
309		{
310		}
311		}
312	1	runner.interrupt();
313	1	if (worker != null && worker.exit == null)
314		{
315	1	worker.interrupt();
316	1	Thread.currentThread().interrupt();
317	1	worker.process.destroy();
318		}
319		}
320
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
321	11	@Test(groups = { "Functional" }, dataProvider = "allInputOperationsData")...
322		public void testAllInputOperations(String expectedString,
323		String failureMsg)
324		{
325	11	Assert.assertTrue(successfulCMDs.contains(expectedString), failureMsg);
326		}
327
		72.4% Uncovered Elements: 8 (29) Complexity: 8 Complexity Density: 0.35
328	16	@Test(...
329		groups =
330		{ "Functional", "testben" },
331		dataProvider = "headlessModeOutputOperationsData")
332		public void testHeadlessModeOutputOperations(String harg, String type,
333		String fileName, boolean withAWT, int expectedMinFileSize,
334		int timeout, String fileFormatType)
335		{
336	16	String cmd = harg + type + " " + fileName;
337		// System.out.println(">>>>>>>>>>>>>>>> Command : " + cmd);
338	16	File file = new File(fileName);
339	16	file.deleteOnExit();
340	16	Worker worker = getJalviewDesktopRunner(withAWT, cmd, timeout);
341	16	assertNotNull(worker, "worker is null");
342	16	String msg = "Didn't create an output" + type + " file.[" + harg + "]";
343	16	assertTrue(file.exists(), msg);
344	16	FileAssert.assertFile(file, msg);
345	16	FileAssert.assertMinLength(file, expectedMinFileSize);
346	16	if (fileFormatType != null && fileFormatType.length() > 0)
347		{
348	8	FileFormatI format = FileFormats.getInstance()
349		.forName(fileFormatType);
350	8	if (format != null)
351		{
352	8	try
353		{
354	8	FileFormatI exportedType = new IdentifyFile()
355		.identify(file.getAbsolutePath(), DataSourceType.FILE);
356	8	assertEquals(exportedType, format,
357		"Exported file type was wrong");
358		} catch (FileFormatException e)
359		{
360	0	Assert.fail("Couldn't identify file " + file
361		+ " as an alignment format", e);
362		} catch (FileNotFoundException e)
363		{
364	0	Assert.fail("Couldn't locate file " + file, e);
365		}
366		}
367		}
368	16	if (worker != null && worker.exit == null)
369		{
370	0	worker.interrupt();
371	0	Thread.currentThread().interrupt();
372	0	worker.process.destroy();
373	0	Assert.fail("Jalview did not exit after " + type
374		+ " generation (try running test again to verify - timeout at "
375		+ timeout + "ms). [" + harg + "]");
376		}
377	16	file.delete();
378		}
379
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
380	1	@DataProvider(name = "allInputOperationsData")...
381		public Object[][] getHeadlessModeInputParams()
382		{
383	1	return new Object[][] {
384		// headless mode input operations
385		{ "CMD [-colour zappo] executed successfully!",
386		"Failed command : -colour zappo" },
387		{ "CMD [-props test/jalview/bin/testProps.jvprops] executed successfully!",
388		"Failed command : -props File" },
389		{ "CMD [-sortbytree] executed successfully!",
390		"Failed command : -sortbytree" },
391		{ "CMD [-jabaws http://www.compbio.dundee.ac.uk/jabaws] executed successfully!",
392		"Failed command : -jabaws http://www.compbio.dundee.ac.uk/jabaws" },
393		{ "CMD [-open examples/uniref50.fa] executed successfully!",
394		"Failed command : -open examples/uniref50.fa" },
395		{ "CMD [-nosortbytree] executed successfully!",
396		"Failed command : -nosortbytree" },
397		{ "CMD [-features examples/testdata/plantfdx.features] executed successfully!",
398		"Failed command : -features examples/testdata/plantfdx.features" },
399		{ "CMD [-annotations examples/testdata/plantfdx.annotations] executed successfully!",
400		"Failed command : -annotations examples/testdata/plantfdx.annotations" },
401		{ "CMD [-tree examples/testdata/uniref50_test_tree] executed successfully!",
402		"Failed command : -tree examples/testdata/uniref50_test_tree" },
403		// non headless mode input operations
404		{ "CMD [-nousagestats] executed successfully!",
405		"Failed command : -nousagestats" },
406		{ "CMD [-noquestionnaire] executed successfully!",
407		"Failed command : -noquestionnaire" } };
408		}
409
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
410	1	@DataProvider(name = "headlessModeOutputOperationsData")...
411		public static Object[][] getHeadlessModeOutputParams()
412		{
413		// JBPNote: I'm not clear why need to specify full path for output file
414		// when running tests on build server, but we will keep this patch for now
415		// since it works.
416		// https://issues.jalview.org/browse/JAL-1889?focusedCommentId=21609&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-21609
417	1	String workingDir = "test/jalview/bin/";
418	1	return new Object[][] {
419		//
420		{ "nodisplay -open examples/uniref50.fa", " -eps",
421		workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG,
422		TEST_TIMEOUT, null },
423		{ "nodisplay -open examples/uniref50.fa", " -eps",
424		workingDir + "test_uniref50_out.eps", false, MINFILESIZE_BIG,
425		TEST_TIMEOUT, null },
426		{ "nogui -open examples/uniref50.fa", " -eps",
427		workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG,
428		TEST_TIMEOUT, null },
429		{ "nogui -open examples/uniref50.fa", " -eps",
430		workingDir + "test_uniref50_out.eps", false, MINFILESIZE_BIG,
431		TEST_TIMEOUT, null },
432		{ "headless -open examples/uniref50.fa", " -eps",
433		workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG,
434		TEST_TIMEOUT, null },
435		{ "headless -open examples/uniref50.fa", " -svg",
436		workingDir + "test_uniref50_out.svg", false, MINFILESIZE_BIG,
437		TEST_TIMEOUT, null },
438		{ "headless -open examples/uniref50.fa", " -png",
439		workingDir + "test_uniref50_out.png", true, MINFILESIZE_BIG,
440		TEST_TIMEOUT, null },
441		{ "headless -open examples/uniref50.fa", " -html",
442		workingDir + "test_uniref50_out.html", true, MINFILESIZE_BIG,
443		TEST_TIMEOUT, null },
444		{ "headless -open examples/uniref50.fa", " -fasta",
445		workingDir + "test_uniref50_out.mfa", true, MINFILESIZE_SMALL,
446		TEST_TIMEOUT, FileFormat.Fasta.toString() },
447		{ "headless -open examples/uniref50.fa", " -clustal",
448		workingDir + "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
449		TEST_TIMEOUT, FileFormat.Clustal.toString() },
450		{ "headless -open examples/uniref50.fa", " -msf",
451		workingDir + "test_uniref50_out.msf", true, MINFILESIZE_SMALL,
452		TEST_TIMEOUT, FileFormat.MSF.toString() },
453		{ "headless -open examples/uniref50.fa", " -pileup",
454		workingDir + "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
455		TEST_TIMEOUT, FileFormat.Pileup.toString() },
456		{ "headless -open examples/uniref50.fa", " -pir",
457		workingDir + "test_uniref50_out.pir", true, MINFILESIZE_SMALL,
458		TEST_TIMEOUT, FileFormat.PIR.toString() },
459		{ "headless -open examples/uniref50.fa", " -pfam",
460		workingDir + "test_uniref50_out.pfam", true, MINFILESIZE_SMALL,
461		TEST_TIMEOUT, FileFormat.Pfam.toString() },
462		{ "headless -open examples/uniref50.fa", " -blc",
463		workingDir + "test_uniref50_out.blc", true, MINFILESIZE_SMALL,
464		TEST_TIMEOUT, FileFormat.BLC.toString() },
465		{ "headless -open examples/uniref50.fa", " -jalview",
466		workingDir + "test_uniref50_out.jvp", true, MINFILESIZE_SMALL,
467		TEST_TIMEOUT, FileFormat.Jalview.toString() },
468		//
469		};
470		}
471		}