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 private static final String png1 = testfiles + "/dir1/test1.png";
29 private static final String png2 = testfiles + "/dir2/test1.png";
31 @BeforeClass(alwaysRun = true)
32 public static void setUpBeforeClass() throws Exception
34 Cache.loadProperties("test/jalview/gui/quitProps.jvprops");
35 Date oneHourFromNow = new Date(
36 System.currentTimeMillis() + 3600 * 1000);
37 Cache.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED", oneHourFromNow);
40 @AfterClass(alwaysRun = true)
41 public static void resetProps()
43 Cache.loadProperties("test/jalview/testProps.jvprops");
46 @BeforeClass(alwaysRun = true)
47 public void setUpJvOptionPane()
49 JvOptionPane.setInteractiveMode(false);
50 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
53 @AfterMethod(alwaysRun = true)
54 public void tearDown()
56 if (Desktop.instance != null)
57 Desktop.instance.closeAll_actionPerformed(null);
60 /* --setprops is currently disabled so this test won't work
61 @Test(groups = "Functional")
62 public void setpropsTest()
64 final String MOSTLY_HARMLESS = "MOSTLY_HARMLESS";
65 String cmdLine = "--setprop=" + MOSTLY_HARMLESS + "=Earth";
66 String[] args = cmdLine.split("\\s+");
68 Assert.assertEquals(Cache.getDefault(MOSTLY_HARMLESS, "Magrathea"),
73 @Test(groups = "Functional", dataProvider = "cmdLines")
74 public void commandsOpenTest(String cmdLine, boolean cmdArgs,
75 int numFrames, String[] sequences)
77 String[] args = cmdLine.split("\\s+");
79 Commands cmds = Jalview.getInstance().getCommands();
80 Assert.assertNotNull(cmds);
81 Assert.assertEquals(cmds.commandArgsProvided(), cmdArgs,
82 "Commands were not provided in the args");
83 Assert.assertEquals(cmds.argsWereParsed(), cmdArgs,
84 "Overall command parse and operation is false");
86 Assert.assertEquals(Desktop.getAlignFrames().length, numFrames,
87 "Wrong number of AlignFrames");
89 if (sequences != null)
91 Set<String> openedSequenceNames = new HashSet<>();
92 AlignFrame[] afs = Desktop.getAlignFrames();
93 for (AlignFrame af : afs)
96 .addAll(af.getViewport().getAlignment().getSequenceNames());
98 for (String sequence : sequences)
100 Assert.assertTrue(openedSequenceNames.contains(sequence),
101 "Sequence '" + sequence
102 + "' was not found in opened alignment files: "
103 + cmdLine + ".\nOpened sequence names are:\n"
104 + String.join("\n", openedSequenceNames));
109 lookForSequenceName("THIS_SEQUENCE_ID_DOESN'T_EXIST"));
112 @Test(groups = "Functional", dataProvider = "argfileOutputFiles")
113 public void argFilesGlobAndSubstitutionsTest(String cmdLine,
114 String[] filenames) throws IOException
116 cleanupFiles(filenames);
117 String[] args = cmdLine.split("\\s+");
119 Commands cmds = Jalview.getInstance().getCommands();
120 Assert.assertNotNull(cmds);
121 File lastFile = null;
122 for (String filename : filenames)
124 File file = new File(filename);
125 Assert.assertTrue(file.exists(), "File '" + filename
126 + "' was not created by '" + cmdLine + "'");
127 Assert.assertTrue(file.isFile(), "File '" + filename
128 + "' is not a file from '" + cmdLine + "'");
129 Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
130 + "' has no content from '" + cmdLine + "'");
131 // make sure the successive output files get bigger!
132 if (lastFile != null)
134 Files.size(file.toPath()) > Files.size(lastFile.toPath()));
136 cleanupFiles(filenames);
140 @DataProvider(name = "argfileOutputFiles")
141 public Object[][] argfileOutputFiles()
143 return new Object[][] {
145 { "--argfile=" + testfiles + "/**/*.txt", new String[]
146 { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png",
147 testfiles + "/dir3/subdir/test0.png" } },
148 { "--argfile=" + testfiles + "/**/argfile.txt", new String[]
149 { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
150 { "--argfile=" + testfiles + "/dir*/argfile.txt", new String[]
151 { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
152 { "--initsubstitutions --append examples/uniref50.fa --image "
153 + testfiles + "/{basename}.png",
155 { testfiles + "/uniref50.png" } },
156 { "--append examples/uniref50.fa --nosubstitutions --image "
157 + testfiles + "/{basename}.png",
159 { testfiles + "/{basename}.png" } }
165 @DataProvider(name = "cmdLines")
166 public Object[][] cmdLines()
168 String[] someUniref50Seqs = new String[] { "FER_CAPAA", "FER_CAPAN",
169 "FER1_MAIZE", "FER1_SPIOL", "O80429_MAIZE" };
170 String[] t1 = new String[] { "TEST1" };
171 String[] t2 = new String[] { "TEST2" };
172 String[] t3 = new String[] { "TEST3" };
173 return new Object[][] {
176 { "--append=examples/uniref50.fa", true, 1, someUniref50Seqs },
177 { "--append examples/uniref50.fa", true, 1, someUniref50Seqs },
178 { "--append=examples/uniref50*.fa", true, 1, someUniref50Seqs },
179 // NOTE we cannot use shell expansion in tests, so list all files!
180 { "--append examples/uniref50.fa examples/uniref50_mz.fa", true, 1,
182 { "--append=[new]examples/uniref50*.fa", true, 2,
184 { "--open=examples/uniref50*.fa", true, 2, someUniref50Seqs },
185 { "examples/uniref50.fa", true, 1, someUniref50Seqs },
186 { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2,
187 ArrayUtils.concatArrays(someUniref50Seqs, t1) },
188 { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2, t1 },
189 { "--argfile=" + testfiles + "/argfile0.txt", true, 1,
190 ArrayUtils.concatArrays(t1, t3) },
191 { "--argfile=" + testfiles + "/argfile*.txt", true, 5,
192 ArrayUtils.concatArrays(t1, t2, t3) },
193 { "--argfile=" + testfiles + "/argfile.autocounter", true, 3,
194 ArrayUtils.concatArrays(t1, t2) } };
198 public static boolean lookForSequenceName(String sequenceName)
200 AlignFrame[] afs = Desktop.getAlignFrames();
201 for (AlignFrame af : afs)
203 for (String name : af.getViewport().getAlignment().getSequenceNames())
205 if (sequenceName.equals(name))
214 public static void cleanupFiles(String[] filenames)
216 for (String filename : filenames)
218 File file = new File(filename);
226 @Test(groups = "Functional", dataProvider = "allLinkedIdsData")
227 public void allLinkedIdsTest(String cmdLine, String[] filenames)
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);
241 @DataProvider(name = "allLinkedIdsData")
242 public Object[][] allLinkedIdsData()
244 return new Object[][] {
247 { "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --output={dirname}/{basename}.stk --close",
248 Arg.OUTPUT, new String[]
249 { "test/jalview/bin/argparser/testfiles/test1.stk",
250 "test/jalview/bin/argparser/testfiles/test2.stk",
251 "test/jalview/bin/argparser/testfiles/test3.stk", } },
253 { "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
255 { "test/jalview/bin/argparser/testfiles/test1.png",
256 "test/jalview/bin/argparser/testfiles/test2.png",
257 "test/jalview/bin/argparser/testfiles/test3.png", } },
258 { "--open=test/jalview/bin/argparser/testfiles/*.fa --all --output={dirname}/{basename}.stk --close",
260 { "test/jalview/bin/argparser/testfiles/test1.stk",
261 "test/jalview/bin/argparser/testfiles/test2.stk",
262 "test/jalview/bin/argparser/testfiles/test3.stk", } },