1 package jalview.bin.argparser;
4 import java.io.IOException;
6 import java.util.Properties;
8 import org.testng.Assert;
9 import org.testng.annotations.AfterClass;
10 import org.testng.annotations.AfterMethod;
11 import org.testng.annotations.DataProvider;
12 import org.testng.annotations.Test;
14 import jalview.bin.Cache;
15 import jalview.gui.Desktop;
17 @Test(singleThreaded = true)
18 public class ArgParserTest
20 @AfterClass(alwaysRun = true)
21 public static void resetProps()
23 Cache.loadProperties("test/jalview/testProps.jvprops");
26 @AfterMethod(alwaysRun = true)
27 public void tearDown()
29 if (Desktop.instance != null)
30 Desktop.instance.closeAll_actionPerformed(null);
33 @Test(groups = "Functional", dataProvider = "argLines")
34 public void parseArgsTest(String commandLineArgs, Arg a, String other)
36 String[] args = commandLineArgs.split("\\s+");
37 ArgParser argparser = new ArgParser(args);
40 @Test(groups = "Functional", dataProvider = "argSubValsAndLinkedIds")
41 public void parseSubValsAndLinkedIdsTest(String commandLineArgs,
42 String linkedId, Arg a, String subvalKey, String value,
45 String[] args = commandLineArgs.split("\\s+");
46 ArgParser argparser = new ArgParser(args);
47 ArgValuesMap avm = argparser.getLinkedArgs(linkedId);
48 ArgValue av = avm.getArgValue(a);
49 SubVals sv = av.getSubVals();
50 String testString = null;
51 if (subvalKey.equals("GETINDEX"))
53 testString = String.valueOf(sv.getIndex());
57 testString = sv.get(subvalKey);
61 Assert.assertEquals(testString, value);
65 Assert.assertNotEquals(testString, value);
70 groups = "Functional",
71 dataProvider = "argAutoIndexAndSubstitutions")
72 public void parseAutoIndexAndSubstitutionsTest(String commandLineArgs,
73 String linkedId, Arg a, String filename)
75 // { "--append=filename0 --new --append=filename1", "JALVIEW:1",
76 // Arg.OPEN, "filename1" },
77 String[] args = commandLineArgs.split("\\s+");
78 ArgParser argparser = new ArgParser(args);
79 ArgValuesMap avm = argparser.getLinkedArgs(linkedId);
80 ArgValue av = avm.getArgValue(a);
81 Assert.assertEquals(av.getValue(), filename);
84 @Test(groups = "Functional", dataProvider = "argLines")
85 public void bootstrapArgsTest(String commandLineArgs, Arg a, String other)
87 String[] args = commandLineArgs.split("\\s+");
88 BootstrapArgs b = BootstrapArgs.getBootstrapArgs(args);
90 Assert.assertTrue(b.contains(a));
93 Properties bP = Cache.bootstrapProperties(b.get(Arg.PROPS));
94 Assert.assertNotNull(bP);
95 Assert.assertTrue(other.equals(bP.get(Cache.BOOTSTRAP_TEST)));
96 Assert.assertFalse(bP.contains("NOT" + Cache.BOOTSTRAP_TEST));
98 else if (a == Arg.ARGFILE)
100 List<String> filenames = b.getValueList(a);
101 boolean found = false;
102 for (String s : filenames)
104 File f = new File(s);
105 File fo = new File(other);
108 if (fo.getCanonicalPath().equals(f.getCanonicalPath()))
113 } catch (IOException e)
117 Assert.assertTrue(found,
118 "File '" + other + "' not found in shell expanded glob '"
119 + commandLineArgs + "'");
123 @Test(groups = "Functional", dataProvider = "argFiles")
124 public void argFilesTest(String commandLineArgs, Arg a, String other)
126 String[] args = commandLineArgs.split("\\s+");
127 BootstrapArgs b = BootstrapArgs.getBootstrapArgs(args);
129 Assert.assertTrue(b.contains(a));
130 Assert.assertFalse(b.contains(Arg.APPEND));
133 Properties bP = Cache.bootstrapProperties(b.get(Arg.PROPS));
134 Assert.assertTrue("true".equals(bP.get(Cache.BOOTSTRAP_TEST)));
138 @DataProvider(name = "argLinesNotworking")
139 public Object[][] argLinesTest()
141 return new Object[][] {
142 // can't use this one yet as it doesn't get shell glob expanded by the
144 { "--argfile test/jalview/bin/argparser/testfiles/argfile*.txt",
146 "test/jalview/bin/argparser/testfiles/argfile0.txt" }, };
149 @DataProvider(name = "argLines")
150 public Object[][] argLines()
152 return new Object[][] { {
153 "--append=test/jalview/bin/argparser/testfiles/test1.fa --props=test/jalview/bin/argparser/testfiles/testProps.jvprops",
155 { "--debug --append=test/jalview/bin/argparser/testfiles/test1.fa",
157 { "--append=test/jalview/bin/argparser/testfiles/test1.fa --headless",
158 Arg.HEADLESS, null },
160 { "--argfile test/jalview/bin/argparser/testfiles/argfile0.txt",
162 "test/jalview/bin/argparser/testfiles/argfile0.txt" },
163 // these next three are what a shell glob expansion would look like
164 { "--argfile test/jalview/bin/argparser/testfiles/argfile0.txt test/jalview/bin/argparser/testfiles/argfile1.txt test/jalview/bin/argparser/testfiles/argfile2.txt",
166 "test/jalview/bin/argparser/testfiles/argfile0.txt" },
167 { "--argfile test/jalview/bin/argparser/testfiles/argfile0.txt test/jalview/bin/argparser/testfiles/argfile1.txt test/jalview/bin/argparser/testfiles/argfile2.txt",
169 "test/jalview/bin/argparser/testfiles/argfile1.txt" },
170 { "--argfile test/jalview/bin/argparser/testfiles/argfile0.txt test/jalview/bin/argparser/testfiles/argfile1.txt test/jalview/bin/argparser/testfiles/argfile2.txt",
172 "test/jalview/bin/argparser/testfiles/argfile2.txt" },
173 { "--argfile=test/jalview/bin/argparser/testfiles/argfile*.txt",
175 "test/jalview/bin/argparser/testfiles/argfile0.txt" },
176 { "--argfile=test/jalview/bin/argparser/testfiles/argfile*.txt",
178 "test/jalview/bin/argparser/testfiles/argfile1.txt" },
179 { "--argfile=test/jalview/bin/argparser/testfiles/argfile*.txt",
181 "test/jalview/bin/argparser/testfiles/argfile2.txt" } };
184 @DataProvider(name = "argSubValsAndLinkedIds")
185 public Object[][] argSubValsAndLinkedIds()
187 return new Object[][] { {
188 "--debug --append=[hi]test/jalview/bin/argparser/testfiles/test1.fa",
189 "JALVIEW:0", Arg.APPEND, "hi", "true", true },
190 { "--append[linkedId1]=[new,hello=world,1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
191 "linkedId1", Arg.APPEND, "new", "true", true },
192 { "--append[linkedId2]=[new,hello=world,1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
193 "linkedId2", Arg.APPEND, "hello", "world", true },
194 { "--append[linkedId3]=[new,hello=world,1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
195 "linkedId3", Arg.APPEND, "GETINDEX", "1", true },
196 { "--append[linkedId4]=[new,hello=world,1]test/jalview/bin/argparser/testfiles/test1.fa --append[linkedId5]=[notnew;hello=world;1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
197 "linkedId5", Arg.APPEND, "new", "true", false },
198 { "--append[linkedId5]=[new,hello=worlddomination,1]test/jalview/bin/argparser/testfiles/test1.fa --append[linkedId2]=[new;hello=world;1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
199 "linkedId5", Arg.APPEND, "hello", "world", false },
200 { "--append[linkedId6]=[new,hello=world,0]test/jalview/bin/argparser/testfiles/test1.fa --append[linkedId7]=[new;hello=world;1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
201 "linkedId7", Arg.APPEND, "GETINDEX", "0", false }, };
204 @DataProvider(name = "argAutoIndexAndSubstitutions")
205 public Object[][] argAutoIndexAndSubstitutions()
207 return new Object[][] {
211 { "--append=filename0 --append=filename1", "JALVIEW:0", Arg.APPEND,
213 { "--append=filename0 --new --append=filename1", "JALVIEW:1",
214 Arg.APPEND, "filename1" },
215 { "--append=filename0 --new --new --append=filename2", "JALVIEW:0",
216 Arg.APPEND, "filename0" },
217 { "--append=filename0 --new --new --append=filename2", "JALVIEW:2",
218 Arg.APPEND, "filename2" },
219 { "--append[linkA-{n}]=filenameA0 --append[linkA-{++n}]=filenameA1",
220 "linkA-0", Arg.APPEND, "filenameA0" },
221 { "--append[linkB-{n}]=filenameB0 --append[linkB-{++n}]=filenameB1",
222 "linkB-1", Arg.APPEND, "filenameB1" },
223 { "--append[linkC-{n}]=filenameC0 --image[linkC-{n}]=outputC{n}.txt",
224 "linkC-0", Arg.IMAGE, "outputC{n}.txt" },
225 { "--append[linkD-{n}]=filenameD0 --substitutions --image[linkD-{n}]=outputD{n}.txt",
226 "linkD-0", Arg.IMAGE, "outputD0.txt" },
227 { "--append[linkE-{n}]=filenameE0 --substitutions --image[linkE-{n}]=output-E{n}.txt --nil[{++n}] --image[linkE-{n}]=outputE{n}.txt",
228 "linkE-0", Arg.IMAGE, "output-E0.txt" },
229 { "--append[linkF-{n}]=filenameF0 --substitutions --image[linkF-{n}]=output-F{n}.txt --nil[{++n}] --image[linkF-{n}]=outputF{n}.txt",
230 "linkF-1", Arg.IMAGE, "outputF1.txt" },
231 { "--append[linkG-{n}]=filenameG0 --substitutions --image[linkG-{n}]=output-G{n}.txt --nil[{++n}] --nosubstitutions --image[linkG-{n}]=outputG{n}.txt",
232 "linkG-1", Arg.IMAGE, "outputG{n}.txt" },
233 { "--append[linkH-{n}]=filenameH0 --substitutions --image[linkH-{n}]=output-H{n}.txt --nil[{++n}] --nosubstitutions --image[linkH-{n}]=outputH{n}.txt",
234 "linkH-0", Arg.IMAGE, "output-H0.txt" },
235 { "--open=filename0 --append=filename1", "JALVIEW:0", Arg.OPEN,
237 { "--open=filename0 --new --append=filename1", "JALVIEW:1",
238 Arg.APPEND, "filename1" },
239 { "--open=filename0 --new --new --append=filename2", "JALVIEW:0",
240 Arg.OPEN, "filename0" },
241 { "--open=filename0 --new --new --append=filename2", "JALVIEW:2",
242 Arg.APPEND, "filename2" },
243 { "--open[linkA-{n}]=filenameA0 --append[linkA-{++n}]=filenameA1",
244 "linkA-0", Arg.OPEN, "filenameA0" },
245 { "--open[linkB-{n}]=filenameB0 --append[linkB-{++n}]=filenameB1",
246 "linkB-1", Arg.APPEND, "filenameB1" },
247 { "--open[linkC-{n}]=filenameC0 --image[linkC-{n}]=outputC{n}.txt",
248 "linkC-0", Arg.IMAGE, "outputC{n}.txt" },
249 { "--open[linkD-{n}]=filenameD0 --substitutions --image[linkD-{n}]=outputD{n}.txt",
250 "linkD-0", Arg.IMAGE, "outputD0.txt" },
251 { "--open[linkE-{n}]=filenameE0 --substitutions --image[linkE-{n}]=output-E{n}.txt --nil[{++n}] --image[linkE-{n}]=outputE{n}.txt",
252 "linkE-0", Arg.IMAGE, "output-E0.txt" },
253 { "--open[linkF-{n}]=filenameF0 --substitutions --image[linkF-{n}]=output-F{n}.txt --nil[{++n}] --image[linkF-{n}]=outputF{n}.txt",
254 "linkF-1", Arg.IMAGE, "outputF1.txt" },
255 { "--open[linkG-{n}]=filenameG0 --substitutions --image[linkG-{n}]=output-G{n}.txt --nil[{++n}] --nosubstitutions --image[linkG-{n}]=outputG{n}.txt",
256 "linkG-1", Arg.IMAGE, "outputG{n}.txt" },
257 { "--open[linkH-{n}]=filenameH0 --substitutions --image[linkH-{n}]=output-H{n}.txt --nil[{++n}] --nosubstitutions --image[linkH-{n}]=outputH{n}.txt",
258 "linkH-0", Arg.IMAGE, "output-H0.txt" },
266 @DataProvider(name = "argFiles")
267 public Object[][] argFiles()
269 return new Object[][] { {
270 "--argfile=test/jalview/bin/argparser/testfiles/argfile0.txt --open=shouldntbeabootstrap",
271 Arg.ARGFILE, "test/jalview/bin/argfiles/testfiles/test1.fa" } };
274 @Test(groups = "Functional", dataProvider = "allLinkedIdsData")
275 public void allLinkedIdsTest(String commandLineArgs, Arg a,
276 String[] values, String[] nonvalues)
278 String[] args = commandLineArgs.split("\\s+");
279 ArgParser argparser = new ArgParser(args);
281 int num = values.length;
282 List<String> linkedIds = argparser.getLinkedIds();
283 Assert.assertEquals(linkedIds.size(), num,
284 "Wrong number of linkedIds: " + linkedIds.toString());
285 for (int i = 0; i < num; i++)
287 String value = values[i];
288 String linkedId = linkedIds.get(i);
289 ArgValuesMap avm = argparser.getLinkedArgs(linkedId);
292 Assert.assertTrue(avm.containsArg(a),
293 "Arg value for " + a.argString()
294 + " not applied correctly to linkedId '" + linkedId
299 ArgValues avs = avm.getArgValues(a);
300 ArgValue av = avs.getArgValue();
301 String v = av.getValue();
302 value = new File(value).getAbsolutePath();
303 Assert.assertEquals(v, value, "Arg value for " + a.argString()
304 + " not applied correctly to linkedId '" + linkedId + "'");
310 @DataProvider(name = "allLinkedIdsData")
311 public Object[][] allLinkedIdsData()
313 return new Object[][] {
317 { "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
318 Arg.CLOSE, new String[]
319 { null, null, null },
321 { "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --output={dirname}/{basename}.stk --close",
322 Arg.OUTPUT, new String[]
323 { "test/jalview/bin/argparser/testfiles/test1.stk",
324 "test/jalview/bin/argparser/testfiles/test2.stk",
325 "test/jalview/bin/argparser/testfiles/test3.stk", },
327 { "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
328 Arg.IMAGE, new String[]
329 { "test/jalview/bin/argparser/testfiles/test1.png",
330 "test/jalview/bin/argparser/testfiles/test2.png",
331 "test/jalview/bin/argparser/testfiles/test3.png", },