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CommandLineOperations | 45 | 97 | 35 | ||
CommandLineOperations.Worker | 74 | 8 | 7 |
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 | ||
45 | public class CommandLineOperations | |
46 | { | |
47 | ||
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 | */ | |
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 | ||
84 | 20 | private Worker(Process process) |
85 | { | |
86 | 20 | this.process = process; |
87 | } | |
88 | ||
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 | ||
101 | 55 | public BufferedReader getOutputReader() |
102 | { | |
103 | 55 | return outputReader; |
104 | } | |
105 | ||
106 | 20 | public void setOutputReader(BufferedReader outputReader) |
107 | { | |
108 | 20 | this.outputReader = outputReader; |
109 | } | |
110 | ||
111 | 11 | public BufferedReader getErrorReader() |
112 | { | |
113 | 11 | return errorReader; |
114 | } | |
115 | ||
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 | ||
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 | ||
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 | ||
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 | ||
215 | 1 | @BeforeClass(alwaysRun = true) |
216 | public void initialize() | |
217 | { | |
218 | 1 | new CommandLineOperations(); |
219 | } | |
220 | ||
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 | 9 | System.err.println("STDERR: " + ln); |
238 | 9 | successfulCMDs.add(ln); |
239 | } | |
240 | } | |
241 | ||
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 | { | |
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 | ||
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 | ||
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 | ||
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 | ||
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 | } |