4 import java.io.IOException;
5 import java.nio.file.Files;
7 import java.util.HashSet;
10 import org.testng.Assert;
11 import org.testng.annotations.AfterClass;
12 import org.testng.annotations.AfterMethod;
13 import org.testng.annotations.BeforeClass;
14 import org.testng.annotations.DataProvider;
15 import org.testng.annotations.Test;
17 import jalview.gui.AlignFrame;
18 import jalview.gui.Desktop;
19 import jalview.gui.JvOptionPane;
20 import jalview.util.ArrayUtils;
22 public class CommandsTest
24 private static final String testfiles = "test/jalview/bin/argparser/testfiles";
26 @BeforeClass(alwaysRun = true)
27 public static void setUpBeforeClass() throws Exception
29 Cache.loadProperties("test/jalview/gui/quitProps.jvprops");
30 Date oneHourFromNow = new Date(
31 System.currentTimeMillis() + 3600 * 1000);
32 Cache.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED", oneHourFromNow);
35 @AfterClass(alwaysRun = true)
36 public static void resetProps()
38 Cache.loadProperties("test/jalview/testProps.jvprops");
41 @BeforeClass(alwaysRun = true)
42 public void setUpJvOptionPane()
44 JvOptionPane.setInteractiveMode(false);
45 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
48 @AfterMethod(alwaysRun = true)
49 public void tearDown()
51 Desktop.closeDesktop();
54 public static void callJalviewMain(String[] args) {
55 if (Jalview.getInstance()!=null) {
56 Jalview.getInstance().doMain(args);
62 /* --setprops is currently disabled so this test won't work
63 @Test(groups = "Functional")
64 public void setpropsTest()
66 final String MOSTLY_HARMLESS = "MOSTLY_HARMLESS";
67 String cmdLine = "--setprop=" + MOSTLY_HARMLESS + "=Earth";
68 String[] args = cmdLine.split("\\s+");
70 Assert.assertEquals(Cache.getDefault(MOSTLY_HARMLESS, "Magrathea"),
75 @Test(groups = "Functional", dataProvider = "cmdLines")
76 public void commandsOpenTest(String cmdLine, boolean cmdArgs,
77 int numFrames, String[] sequences)
81 String[] args = (cmdLine + " --gui").split("\\s+");
82 callJalviewMain(args);
83 Commands cmds = Jalview.getInstance().getCommands();
84 Assert.assertNotNull(cmds);
85 Assert.assertEquals(cmds.commandArgsProvided(), cmdArgs,
86 "Commands were not provided in the args");
87 Assert.assertEquals(cmds.argsWereParsed(), cmdArgs,
88 "Overall command parse and operation is false");
90 Assert.assertEquals(Desktop.getAlignFrames().length, numFrames,
91 "Wrong number of AlignFrames");
93 if (sequences != null)
95 Set<String> openedSequenceNames = new HashSet<>();
96 AlignFrame[] afs = Desktop.getAlignFrames();
97 for (AlignFrame af : afs)
99 openedSequenceNames.addAll(
100 af.getViewport().getAlignment().getSequenceNames());
102 for (String sequence : sequences)
104 Assert.assertTrue(openedSequenceNames.contains(sequence),
105 "Sequence '" + sequence
106 + "' was not found in opened alignment files: "
107 + cmdLine + ".\nOpened sequence names are:\n"
108 + String.join("\n", openedSequenceNames));
113 lookForSequenceName("THIS_SEQUENCE_ID_DOESN'T_EXIST"));
114 } catch (Exception x)
116 Assert.fail("Unexpected exception during commandsOpenTest", x);
124 @Test(groups = {"Functional","testTask1"}, dataProvider = "structureImageOutputFiles")
125 public void structureImageOutputTest(String cmdLine, String[] filenames)
128 cleanupFiles(filenames);
129 String[] args = (cmdLine + " --gui").split("\\s+");
132 callJalviewMain(args);
133 Commands cmds = Jalview.getInstance().getCommands();
134 Assert.assertNotNull(cmds);
135 File lastFile = null;
136 for (String filename : filenames)
138 File file = new File(filename);
139 Assert.assertTrue(file.exists(), "File '" + filename
140 + "' was not created by '" + cmdLine + "'");
141 Assert.assertTrue(file.isFile(), "File '" + filename
142 + "' is not a file from '" + cmdLine + "'");
143 Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
144 + "' has no content from '" + cmdLine + "'");
145 // make sure the successive output files get bigger!
146 if (lastFile != null)
147 Assert.assertTrue(Files.size(file.toPath()) > Files
148 .size(lastFile.toPath()));
150 } catch (Exception x)
152 Assert.fail("Unexpected exception during structureImageOutputTest",
156 cleanupFiles(filenames);
161 @Test(groups = "Functional", dataProvider = "argfileOutputFiles")
162 public void argFilesGlobAndSubstitutionsTest(String cmdLine,
163 String[] filenames) throws IOException
165 cleanupFiles(filenames);
166 String[] args = (cmdLine + " --gui").split("\\s+");
168 callJalviewMain(args);
169 Commands cmds = Jalview.getInstance().getCommands();
170 Assert.assertNotNull(cmds);
171 File lastFile = null;
172 for (String filename : filenames)
174 File file = new File(filename);
175 Assert.assertTrue(file.exists(), "File '" + filename
176 + "' was not created by '" + cmdLine + "'");
177 Assert.assertTrue(file.isFile(), "File '" + filename
178 + "' is not a file from '" + cmdLine + "'");
179 Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
180 + "' has no content from '" + cmdLine + "'");
181 // make sure the successive output files get bigger!
182 if (lastFile != null)
184 Files.size(file.toPath()) > Files.size(lastFile.toPath()));
186 } catch (Exception x)
188 Assert.fail("Unexpected exception during argFilesGlobAndSubstitutions",
192 cleanupFiles(filenames);
197 @DataProvider(name = "structureImageOutputFiles")
198 public Object[][] structureImageOutputFiles()
200 return new Object[][] {
202 { "--gui --nonews --nosplash --open=./examples/test_fab41.result/sample.a2m "
203 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
204 + "--structureimage=" + testfiles + "/structureimage1.png "
205 + "--open=./examples/test_fab41.result/sample.a2m "
206 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
207 + "--structureimage=" + testfiles
208 + "/structureimage2.png --structureimagescale=1.5"
209 + "--open=./examples/test_fab41.result/sample.a2m "
210 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
211 + "--structureimage=" + testfiles
212 + "/structureimage3.png --structureimagescale=2.0",
214 { testfiles + "/structureimage1.png",
215 testfiles + "/structureimage2.png",
216 testfiles + "/structureimage3.png" } },
218 { "--headless --noquit --open=./examples/test_fab41.result/sample.a2m "
219 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
220 + "--structureimage=" + testfiles + "/structureimage1.png "
221 + "--open=./examples/test_fab41.result/sample.a2m "
222 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
223 + "--structureimage=" + testfiles
224 + "/structureimage2.png --structureimagescale=1.5"
225 + "--open=./examples/test_fab41.result/sample.a2m "
226 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
227 + "--structureimage=" + testfiles
228 + "/structureimage3.png --structureimagescale=2.0",
230 { testfiles + "/structureimage1.png",
231 testfiles + "/structureimage2.png",
232 testfiles + "/structureimage3.png" } },
239 @DataProvider(name = "argfileOutputFiles")
240 public Object[][] argfileOutputFiles()
242 return new Object[][] {
244 { "--gui --argfile=" + testfiles + "/**/*.txt", new String[]
245 { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png",
246 testfiles + "/dir3/subdir/test0.png" } },
247 { "--gui --argfile=" + testfiles + "/**/argfile.txt", new String[]
248 { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
249 { "--gui --argfile=" + testfiles + "/dir*/argfile.txt", new String[]
250 { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
251 { "--gui --initsubstitutions --append examples/uniref50.fa --image "
252 + testfiles + "/{basename}.png",
254 { testfiles + "/uniref50.png" } },
255 { "--gui --append examples/uniref50.fa --nosubstitutions --image "
256 + testfiles + "/{basename}.png",
258 { testfiles + "/{basename}.png" } }
264 @DataProvider(name = "cmdLines")
265 public Object[][] cmdLines()
267 String[] someUniref50Seqs = new String[] { "FER_CAPAA", "FER_CAPAN",
268 "FER1_MAIZE", "FER1_SPIOL", "O80429_MAIZE" };
269 String[] t1 = new String[] { "TEST1" };
270 String[] t2 = new String[] { "TEST2" };
271 String[] t3 = new String[] { "TEST3" };
272 return new Object[][] {
275 { "--append=examples/uniref50.fa", true, 1, someUniref50Seqs },
276 { "--append examples/uniref50.fa", true, 1, someUniref50Seqs },
277 { "--append=examples/uniref50*.fa", true, 1, someUniref50Seqs },
278 // NOTE we cannot use shell expansion in tests, so list all files!
279 { "--append examples/uniref50.fa examples/uniref50_mz.fa", true, 1,
281 { "--append=[new]examples/uniref50*.fa", true, 2,
283 { "--open=examples/uniref50*.fa", true, 2, someUniref50Seqs },
284 { "examples/uniref50.fa", true, 1, someUniref50Seqs },
285 { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2,
286 ArrayUtils.concatArrays(someUniref50Seqs, t1) },
287 { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2, t1 },
288 { "--gui --argfile=" + testfiles + "/argfile0.txt", true, 1,
289 ArrayUtils.concatArrays(t1, t3) },
290 { "--gui --argfile=" + testfiles + "/argfile*.txt", true, 5,
291 ArrayUtils.concatArrays(t1, t2, t3) },
292 { "--gui --argfile=" + testfiles + "/argfile.autocounter", true, 3,
293 ArrayUtils.concatArrays(t1, t2) } };
297 public static boolean lookForSequenceName(String sequenceName)
299 AlignFrame[] afs = Desktop.getAlignFrames();
300 for (AlignFrame af : afs)
302 for (String name : af.getViewport().getAlignment().getSequenceNames())
304 if (sequenceName.equals(name))
313 public static void cleanupFiles(String[] filenames)
315 for (String filename : filenames)
317 File file = new File(filename);
326 groups = "Functional",
327 dataProvider = "allLinkedIdsData",
328 singleThreaded = true)
329 public void allLinkedIdsTest(String cmdLine, String[] filenames,
330 String[] nonfilenames)
332 String[] args = (cmdLine + " --gui").split("\\s+");
333 callJalviewMain(args);
334 Commands cmds = Jalview.getInstance().getCommands();
335 Assert.assertNotNull(cmds);
336 for (String filename : filenames)
338 Assert.assertTrue(new File(filename).exists(),
339 "File '" + filename + "' was not created");
341 cleanupFiles(filenames);
342 if (nonfilenames != null)
344 for (String nonfilename : nonfilenames)
346 File nonfile = new File(nonfilename);
347 Assert.assertFalse(nonfile.exists(),
348 "File " + nonfilename + " exists when it shouldn't!");
353 @DataProvider(name = "allLinkedIdsData")
354 public Object[][] allLinkedIdsData()
356 return new Object[][] {
360 { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --output={dirname}/{basename}.stk --close",
362 { "test/jalview/bin/argparser/testfiles/test1.stk",
363 "test/jalview/bin/argparser/testfiles/test2.stk",
364 "test/jalview/bin/argparser/testfiles/test3.stk", },
366 { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
368 { "test/jalview/bin/argparser/testfiles/test1.png",
369 "test/jalview/bin/argparser/testfiles/test2.png",
370 "test/jalview/bin/argparser/testfiles/test3.png", },
372 { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --all --output={dirname}/{basename}.stk --close",
374 { "test/jalview/bin/argparser/testfiles/test1.stk",
375 "test/jalview/bin/argparser/testfiles/test2.stk",
376 "test/jalview/bin/argparser/testfiles/test3.stk", },
378 { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
379 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
380 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
381 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
382 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
383 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
384 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
385 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
386 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
387 { "--gui --open=test/jalview/bin/argparser/**/*.fa --all --output={dirname}/{basename}.stk --close",
389 { "test/jalview/bin/argparser/testfiles/test1.stk",
390 "test/jalview/bin/argparser/testfiles/test2.stk",
391 "test/jalview/bin/argparser/testfiles/test3.stk",
392 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
393 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
394 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
395 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
396 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
397 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
398 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
399 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
400 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
402 { "--gui --open=test/jalview/bin/argparser/**/*.fa --output=*.stk --close",
404 { "test/jalview/bin/argparser/testfiles/test1.stk",
405 "test/jalview/bin/argparser/testfiles/test2.stk",
406 "test/jalview/bin/argparser/testfiles/test3.stk",
407 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
408 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
409 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
410 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
411 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
412 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
413 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
414 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
415 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
417 { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=*.stk --close",
419 { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
420 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
421 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
422 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
423 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
425 { "test/jalview/bin/argparser/testfiles/test1.stk",
426 "test/jalview/bin/argparser/testfiles/test2.stk",
427 "test/jalview/bin/argparser/testfiles/test3.stk",
428 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
429 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
430 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
431 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
432 { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=open*.stk --close",
434 { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
435 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
436 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
438 { "test/jalview/bin/argparser/testfiles/test1.stk",
439 "test/jalview/bin/argparser/testfiles/test2.stk",
440 "test/jalview/bin/argparser/testfiles/test3.stk",
441 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
442 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
443 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
444 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
445 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
446 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
447 { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --opened --output={dirname}/{basename}.stk --close",
449 { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
450 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
451 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
453 { "test/jalview/bin/argparser/testfiles/test1.stk",
454 "test/jalview/bin/argparser/testfiles/test2.stk",
455 "test/jalview/bin/argparser/testfiles/test3.stk",
456 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
457 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
458 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
459 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
460 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
461 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
462 { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --output open*.stk --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=open*.aln --close",
464 { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
465 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
466 "test/jalview/bin/argparser/testfiles/dir2/test1.aln",
467 "test/jalview/bin/argparser/testfiles/dir2/test2.aln",
468 "test/jalview/bin/argparser/testfiles/dir2/test3.aln", },
470 { "test/jalview/bin/argparser/testfiles/test1.stk",
471 "test/jalview/bin/argparser/testfiles/test2.stk",
472 "test/jalview/bin/argparser/testfiles/test3.stk",
473 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
474 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
475 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
476 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
477 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
478 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
479 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
480 "test/jalview/bin/argparser/testfiles/test1.aln",
481 "test/jalview/bin/argparser/testfiles/test2.aln",
482 "test/jalview/bin/argparser/testfiles/test3.aln",
483 "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
484 "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
485 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
486 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
487 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
488 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, },