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;
23 public class CommandsTest
25 private static final String testfiles = "test/jalview/bin/argparser/testfiles";
27 @BeforeClass(alwaysRun = true)
28 public static void setUpBeforeClass() throws Exception
30 Cache.loadProperties("test/jalview/gui/quitProps.jvprops");
31 Date oneHourFromNow = new Date(
32 System.currentTimeMillis() + 3600 * 1000);
33 Cache.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED", oneHourFromNow);
36 @AfterClass(alwaysRun = true)
37 public static void resetProps()
39 Cache.loadProperties("test/jalview/testProps.jvprops");
42 @BeforeClass(alwaysRun = true)
43 public void setUpJvOptionPane()
45 JvOptionPane.setInteractiveMode(false);
46 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
49 @AfterMethod(alwaysRun = true)
50 public void tearDown()
52 if (Desktop.instance != null)
53 Desktop.instance.closeAll_actionPerformed(null);
56 /* --setprops is currently disabled so this test won't work
57 @Test(groups = "Functional")
58 public void setpropsTest()
60 final String MOSTLY_HARMLESS = "MOSTLY_HARMLESS";
61 String cmdLine = "--setprop=" + MOSTLY_HARMLESS + "=Earth";
62 String[] args = cmdLine.split("\\s+");
64 Assert.assertEquals(Cache.getDefault(MOSTLY_HARMLESS, "Magrathea"),
69 @Test(groups = "Functional", dataProvider = "cmdLines")
70 public void commandsOpenTest(String cmdLine, boolean cmdArgs,
71 int numFrames, String[] sequences)
73 String[] args = cmdLine.split("\\s+");
75 Commands cmds = Jalview.getInstance().getCommands();
76 Assert.assertNotNull(cmds);
77 Assert.assertEquals(cmds.commandArgsProvided(), cmdArgs,
78 "Commands were not provided in the args");
79 Assert.assertEquals(cmds.argsWereParsed(), cmdArgs,
80 "Overall command parse and operation is false");
82 Assert.assertEquals(Desktop.getAlignFrames().length, numFrames,
83 "Wrong number of AlignFrames");
85 if (sequences != null)
87 Set<String> openedSequenceNames = new HashSet<>();
88 AlignFrame[] afs = Desktop.getAlignFrames();
89 for (AlignFrame af : afs)
92 .addAll(af.getViewport().getAlignment().getSequenceNames());
94 for (String sequence : sequences)
96 Assert.assertTrue(openedSequenceNames.contains(sequence),
97 "Sequence '" + sequence
98 + "' was not found in opened alignment files: "
99 + cmdLine + ".\nOpened sequence names are:\n"
100 + String.join("\n", openedSequenceNames));
105 lookForSequenceName("THIS_SEQUENCE_ID_DOESN'T_EXIST"));
108 @Test(groups = "Functional", dataProvider = "argfileOutputFiles")
109 public void argFilesGlobAndSubstitutionsTest(String cmdLine,
110 String[] filenames) throws IOException
112 cleanupFiles(filenames);
113 String[] args = cmdLine.split("\\s+");
115 Commands cmds = Jalview.getInstance().getCommands();
116 Assert.assertNotNull(cmds);
117 File lastFile = null;
118 for (String filename : filenames)
120 File file = new File(filename);
121 Assert.assertTrue(file.exists(), "File '" + filename
122 + "' was not created by '" + cmdLine + "'");
123 Assert.assertTrue(file.isFile(), "File '" + filename
124 + "' is not a file from '" + cmdLine + "'");
125 Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
126 + "' has no content from '" + cmdLine + "'");
127 // make sure the successive output files get bigger!
128 if (lastFile != null)
130 Files.size(file.toPath()) > Files.size(lastFile.toPath()));
132 cleanupFiles(filenames);
136 @DataProvider(name = "argfileOutputFiles")
137 public Object[][] argfileOutputFiles()
139 return new Object[][] {
141 { "--argfile=" + testfiles + "/**/*.txt", new String[]
142 { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png",
143 testfiles + "/dir3/subdir/test0.png" } },
144 { "--argfile=" + testfiles + "/**/argfile.txt", new String[]
145 { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
146 { "--argfile=" + testfiles + "/dir*/argfile.txt", new String[]
147 { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
148 { "--initsubstitutions --append examples/uniref50.fa --image "
149 + testfiles + "/{basename}.png",
151 { testfiles + "/uniref50.png" } },
152 { "--append examples/uniref50.fa --nosubstitutions --image "
153 + testfiles + "/{basename}.png",
155 { testfiles + "/{basename}.png" } }
161 @DataProvider(name = "cmdLines")
162 public Object[][] cmdLines()
164 String[] someUniref50Seqs = new String[] { "FER_CAPAA", "FER_CAPAN",
165 "FER1_MAIZE", "FER1_SPIOL", "O80429_MAIZE" };
166 String[] t1 = new String[] { "TEST1" };
167 String[] t2 = new String[] { "TEST2" };
168 String[] t3 = new String[] { "TEST3" };
169 return new Object[][] {
172 { "--append=examples/uniref50.fa", true, 1, someUniref50Seqs },
173 { "--append examples/uniref50.fa", true, 1, someUniref50Seqs },
174 { "--append=examples/uniref50*.fa", true, 1, someUniref50Seqs },
175 // NOTE we cannot use shell expansion in tests, so list all files!
176 { "--append examples/uniref50.fa examples/uniref50_mz.fa", true, 1,
178 { "--append=[new]examples/uniref50*.fa", true, 2,
180 { "--open=examples/uniref50*.fa", true, 2, someUniref50Seqs },
181 { "examples/uniref50.fa", true, 1, someUniref50Seqs },
182 { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2,
183 ArrayUtils.concatArrays(someUniref50Seqs, t1) },
184 { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2, t1 },
185 { "--argfile=" + testfiles + "/argfile0.txt", true, 1,
186 ArrayUtils.concatArrays(t1, t3) },
187 { "--argfile=" + testfiles + "/argfile*.txt", true, 5,
188 ArrayUtils.concatArrays(t1, t2, t3) },
189 { "--argfile=" + testfiles + "/argfile.autocounter", true, 3,
190 ArrayUtils.concatArrays(t1, t2) } };
194 public static boolean lookForSequenceName(String sequenceName)
196 AlignFrame[] afs = Desktop.getAlignFrames();
197 for (AlignFrame af : afs)
199 for (String name : af.getViewport().getAlignment().getSequenceNames())
201 if (sequenceName.equals(name))
210 public static void cleanupFiles(String[] filenames)
212 for (String filename : filenames)
214 File file = new File(filename);
223 groups = "Functional",
224 dataProvider = "allLinkedIdsData",
225 singleThreaded = true)
226 public void allLinkedIdsTest(String cmdLine, String[] filenames,
227 String[] nonfilenames)
229 String[] args = cmdLine.split("\\s+");
231 Commands cmds = Jalview.getInstance().getCommands();
232 Assert.assertNotNull(cmds);
233 for (String filename : filenames)
235 Assert.assertTrue(new File(filename).exists(),
236 "File '" + filename + "' was not created");
238 cleanupFiles(filenames);
239 if (nonfilenames != null)
241 for (String nonfilename : nonfilenames)
243 File nonfile = new File(nonfilename);
244 Assert.assertFalse(nonfile.exists(),
245 "File " + nonfilename + " exists when it shouldn't!");
250 @DataProvider(name = "allLinkedIdsData")
251 public Object[][] allLinkedIdsData()
253 return new Object[][] {
257 { "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --output={dirname}/{basename}.stk --close",
259 { "test/jalview/bin/argparser/testfiles/test1.stk",
260 "test/jalview/bin/argparser/testfiles/test2.stk",
261 "test/jalview/bin/argparser/testfiles/test3.stk", },
263 { "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
265 { "test/jalview/bin/argparser/testfiles/test1.png",
266 "test/jalview/bin/argparser/testfiles/test2.png",
267 "test/jalview/bin/argparser/testfiles/test3.png", },
269 { "--open=test/jalview/bin/argparser/testfiles/*.fa --all --output={dirname}/{basename}.stk --close",
271 { "test/jalview/bin/argparser/testfiles/test1.stk",
272 "test/jalview/bin/argparser/testfiles/test2.stk",
273 "test/jalview/bin/argparser/testfiles/test3.stk", },
275 { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
276 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
277 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
278 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
279 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
280 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
281 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
282 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
283 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
284 { "--open=test/jalview/bin/argparser/**/*.fa --all --output={dirname}/{basename}.stk --close",
286 { "test/jalview/bin/argparser/testfiles/test1.stk",
287 "test/jalview/bin/argparser/testfiles/test2.stk",
288 "test/jalview/bin/argparser/testfiles/test3.stk",
289 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
290 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
291 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
292 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
293 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
294 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
295 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
296 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
297 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
299 { "--open=test/jalview/bin/argparser/**/*.fa --output=*.stk --close",
301 { "test/jalview/bin/argparser/testfiles/test1.stk",
302 "test/jalview/bin/argparser/testfiles/test2.stk",
303 "test/jalview/bin/argparser/testfiles/test3.stk",
304 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
305 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
306 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
307 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
308 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
309 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
310 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
311 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
312 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
314 { "--open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=*.stk --close",
316 { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
317 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
318 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
319 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
320 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
322 { "test/jalview/bin/argparser/testfiles/test1.stk",
323 "test/jalview/bin/argparser/testfiles/test2.stk",
324 "test/jalview/bin/argparser/testfiles/test3.stk",
325 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
326 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
327 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
328 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
329 { "--open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=open*.stk --close",
331 { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
332 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
333 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
335 { "test/jalview/bin/argparser/testfiles/test1.stk",
336 "test/jalview/bin/argparser/testfiles/test2.stk",
337 "test/jalview/bin/argparser/testfiles/test3.stk",
338 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
339 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
340 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
341 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
342 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
343 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
344 { "--open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --opened --output={dirname}/{basename}.stk --close",
346 { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
347 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
348 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
350 { "test/jalview/bin/argparser/testfiles/test1.stk",
351 "test/jalview/bin/argparser/testfiles/test2.stk",
352 "test/jalview/bin/argparser/testfiles/test3.stk",
353 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
354 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
355 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
356 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
357 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
358 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
359 { "--open=test/jalview/bin/argparser/testfiles/dir1/*.fa --output open*.stk --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=open*.aln --close",
361 { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
362 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
363 "test/jalview/bin/argparser/testfiles/dir2/test1.aln",
364 "test/jalview/bin/argparser/testfiles/dir2/test2.aln",
365 "test/jalview/bin/argparser/testfiles/dir2/test3.aln", },
367 { "test/jalview/bin/argparser/testfiles/test1.stk",
368 "test/jalview/bin/argparser/testfiles/test2.stk",
369 "test/jalview/bin/argparser/testfiles/test3.stk",
370 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
371 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
372 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
373 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
374 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
375 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
376 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
377 "test/jalview/bin/argparser/testfiles/test1.aln",
378 "test/jalview/bin/argparser/testfiles/test2.aln",
379 "test/jalview/bin/argparser/testfiles/test3.aln",
380 "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
381 "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
382 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
383 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
384 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
385 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, },