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  1. Project Clover database Wed Jun 18 2025 15:09:16 BST
  2. Package jalview.bin.argparser

File ArgParserTest.java

 

Code metrics

38
149
23
2
822
652
45
0.3
6.48
11.5
1.96

Classes

Class Line # Actions
ArgParserTest 43 141 42
0.919191991.9%
ArgParserTest.ArgAndValues 777 8 3
0.916666791.7%
 

Contributing tests

This file is covered by 65 tests. .

Source view

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.argparser;
22   
23    import java.io.File;
24    import java.io.IOException;
25    import java.util.ArrayList;
26    import java.util.Arrays;
27    import java.util.HashSet;
28    import java.util.List;
29    import java.util.Properties;
30   
31    import org.apache.logging.log4j.util.Strings;
32    import org.testng.Assert;
33    import org.testng.annotations.AfterClass;
34    import org.testng.annotations.AfterMethod;
35    import org.testng.annotations.DataProvider;
36    import org.testng.annotations.Test;
37   
38    import jalview.bin.Cache;
39    import jalview.bin.Console;
40    import jalview.gui.Desktop;
41   
42    @Test(singleThreaded = true)
 
43    public class ArgParserTest
44    {
 
45  1 toggle @AfterClass(alwaysRun = true)
46    public static void resetProps()
47    {
48  1 Cache.loadProperties("test/jalview/testProps.jvprops");
49    }
50   
 
51  71 toggle @AfterMethod(alwaysRun = true)
52    public void tearDown()
53    {
54  71 if (Desktop.instance != null)
55  71 Desktop.instance.closeAll_actionPerformed(null);
56    }
57   
 
58  10 toggle @Test(groups = "Functional", dataProvider = "argLines")
59    public void parseArgsTest(String commandLineArgs, Arg a, String other)
60    {
61  10 String[] args = commandLineArgs.split("\\s+");
62  10 ArgParser argparser = new ArgParser(args);
63    }
64   
 
65  7 toggle @Test(groups = "Functional", dataProvider = "argSubValsAndLinkedIds")
66    public void parseSubValsAndLinkedIdsTest(String commandLineArgs,
67    String linkedId, Arg a, String subvalKey, String value,
68    boolean trueOrFalse)
69    {
70  7 String[] args = commandLineArgs.split("\\s+");
71  7 ArgParser argparser = new ArgParser(args);
72  7 ArgValuesMap avm = argparser.getLinkedArgs(linkedId);
73  7 ArgValue av = avm.getArgValue(a);
74  7 SubVals sv = av.getSubVals();
75  7 String testString = null;
76  7 if (subvalKey.equals("GETINDEX"))
77    {
78  2 testString = String.valueOf(sv.getIndex());
79    }
80    else
81    {
82  5 testString = sv.get(subvalKey);
83    }
84  7 if (trueOrFalse)
85    {
86  4 Assert.assertEquals(testString, value);
87    }
88    else
89    {
90  3 Assert.assertNotEquals(testString, value);
91    }
92    }
93   
 
94  24 toggle @Test(
95    groups = "Functional",
96    dataProvider = "argAutoIndexAndSubstitutions")
97    public void parseAutoIndexAndSubstitutionsTest(String commandLineArgs,
98    String linkedId, Arg a, String filename)
99    {
100    // { "--append=filename0 --new --append=filename1", "JALVIEW:1",
101    // Arg.OPEN, "filename1" },
102  24 String[] args = commandLineArgs.split("\\s+");
103  24 ArgParser argparser = new ArgParser(args);
104  24 ArgValuesMap avm = argparser.getLinkedArgs(linkedId);
105  24 ArgValue av = avm.getArgValue(a);
106  24 Assert.assertEquals(av.getValue(), filename);
107    }
108   
 
109  10 toggle @Test(groups = "Functional", dataProvider = "argLines")
110    public void bootstrapArgsTest(String commandLineArgs, Arg a, String other)
111    {
112  10 String[] args = commandLineArgs.split("\\s+");
113  10 BootstrapArgs b = BootstrapArgs.getBootstrapArgs(args);
114   
115  10 Assert.assertTrue(b.contains(a));
116  10 if (a == Arg.PROPS)
117    {
118  1 Properties bP = Cache.bootstrapProperties(b.getValue(Arg.PROPS));
119  1 Assert.assertNotNull(bP);
120  1 Assert.assertTrue(other.equals(bP.get(Cache.BOOTSTRAP_TEST)));
121  1 Assert.assertFalse(bP.contains("NOT" + Cache.BOOTSTRAP_TEST));
122    }
123  9 else if (a == Arg.ARGFILE)
124    {
125  7 List<String> filenames = b.getValueList(a);
126  7 boolean found = false;
127  7 for (String s : filenames)
128    {
129  13 File f = new File(s);
130  13 File fo = new File(other);
131  13 try
132    {
133  13 if (fo.getCanonicalPath().equals(f.getCanonicalPath()))
134    {
135  7 found = true;
136  7 break;
137    }
138    } catch (IOException e)
139    {
140    }
141    }
142  7 Assert.assertTrue(found,
143    "File '" + other + "' not found in shell expanded glob '"
144    + commandLineArgs + "'");
145    }
146    }
147   
 
148  1 toggle @Test(groups = "Functional", dataProvider = "argFiles")
149    public void argFilesTest(String commandLineArgs, Arg a, String other)
150    {
151  1 String[] args = commandLineArgs.split("\\s+");
152  1 BootstrapArgs b = BootstrapArgs.getBootstrapArgs(args);
153   
154  1 Assert.assertTrue(b.contains(a));
155  1 Assert.assertFalse(b.contains(Arg.APPEND));
156  1 if (a == Arg.PROPS)
157    {
158  0 Properties bP = Cache.bootstrapProperties(b.getValue(Arg.PROPS));
159  0 Assert.assertTrue("true".equals(bP.get(Cache.BOOTSTRAP_TEST)));
160    }
161    }
162   
 
163  0 toggle @DataProvider(name = "argLinesNotworking")
164    public Object[][] argLinesTest()
165    {
166  0 return new Object[][] {
167    // can't use this one yet as it doesn't get shell glob expanded by the
168    // test
169    { "--argfile test/jalview/bin/argparser/testfiles/argfile*.txt",
170    Arg.ARGFILE,
171    "test/jalview/bin/argparser/testfiles/argfile0.txt" }, };
172    }
173   
 
174  2 toggle @DataProvider(name = "argLines")
175    public Object[][] argLines()
176    {
177  2 return new Object[][] { {
178    "--append=test/jalview/bin/argparser/testfiles/test1.fa --props=test/jalview/bin/argparser/testfiles/testProps.jvprops",
179    Arg.PROPS, "true" },
180    { "--debug --append=test/jalview/bin/argparser/testfiles/test1.fa",
181    Arg.DEBUG, null },
182    { "--append=test/jalview/bin/argparser/testfiles/test1.fa --headless",
183    Arg.HEADLESS, null },
184   
185    { "--argfile test/jalview/bin/argparser/testfiles/argfile0.txt",
186    Arg.ARGFILE,
187    "test/jalview/bin/argparser/testfiles/argfile0.txt" },
188    // these next three are what a shell glob expansion would look like
189    { "--argfile test/jalview/bin/argparser/testfiles/argfile0.txt test/jalview/bin/argparser/testfiles/argfile1.txt test/jalview/bin/argparser/testfiles/argfile2.txt",
190    Arg.ARGFILE,
191    "test/jalview/bin/argparser/testfiles/argfile0.txt" },
192    { "--argfile test/jalview/bin/argparser/testfiles/argfile0.txt test/jalview/bin/argparser/testfiles/argfile1.txt test/jalview/bin/argparser/testfiles/argfile2.txt",
193    Arg.ARGFILE,
194    "test/jalview/bin/argparser/testfiles/argfile1.txt" },
195    { "--argfile test/jalview/bin/argparser/testfiles/argfile0.txt test/jalview/bin/argparser/testfiles/argfile1.txt test/jalview/bin/argparser/testfiles/argfile2.txt",
196    Arg.ARGFILE,
197    "test/jalview/bin/argparser/testfiles/argfile2.txt" },
198    { "--argfile=test/jalview/bin/argparser/testfiles/argfile*.txt",
199    Arg.ARGFILE,
200    "test/jalview/bin/argparser/testfiles/argfile0.txt" },
201    { "--argfile=test/jalview/bin/argparser/testfiles/argfile*.txt",
202    Arg.ARGFILE,
203    "test/jalview/bin/argparser/testfiles/argfile1.txt" },
204    { "--argfile=test/jalview/bin/argparser/testfiles/argfile*.txt",
205    Arg.ARGFILE,
206    "test/jalview/bin/argparser/testfiles/argfile2.txt" } };
207    }
208   
 
209  1 toggle @DataProvider(name = "argSubValsAndLinkedIds")
210    public Object[][] argSubValsAndLinkedIds()
211    {
212  1 return new Object[][] {
213    //
214    /*
215    */
216    { "--debug --append=[hi]test/jalview/bin/argparser/testfiles/test1.fa",
217    "JALVIEW:0", Arg.APPEND, "hi", "true", true },
218    { "--append[linkedId1]=[new,hello=world,1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
219    "linkedId1", Arg.APPEND, "new", "true", true },
220    { "--append[linkedId2]=[new,hello=world,1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
221    "linkedId2", Arg.APPEND, "hello", "world", true },
222    { "--append[linkedId3]=[new,hello=world,1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
223    "linkedId3", Arg.APPEND, "GETINDEX", "1", true },
224    { "--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",
225    "linkedId5", Arg.APPEND, "new", "true", false },
226    { "--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",
227    "linkedId5", Arg.APPEND, "hello", "world", false },
228    { "--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",
229    "linkedId7", Arg.APPEND, "GETINDEX", "0", false },
230    /*
231    */
232    //
233    };
234    }
235   
 
236  1 toggle @DataProvider(name = "argAutoIndexAndSubstitutions")
237    public Object[][] argAutoIndexAndSubstitutions()
238    {
239  1 return new Object[][] {
240    //
241    /*
242    */
243    { "--append=filename0 --append=filename1", "JALVIEW:0", Arg.APPEND,
244    "filename0" },
245    { "--append=filename0 --new --append=filename1", "JALVIEW:1",
246    Arg.APPEND, "filename1" },
247    { "--append=filename0 --new --new --append=filename2", "JALVIEW:0",
248    Arg.APPEND, "filename0" },
249    { "--append=filename0 --new --new --append=filename2", "JALVIEW:2",
250    Arg.APPEND, "filename2" },
251    { "--append[linkA-{n}]=filenameA0 --append[linkA-{++n}]=filenameA1",
252    "linkA-0", Arg.APPEND, "filenameA0" },
253    { "--append[linkB-{n}]=filenameB0 --append[linkB-{++n}]=filenameB1",
254    "linkB-1", Arg.APPEND, "filenameB1" },
255    { "--append[linkC-{n}]=filenameC0 --image[linkC-{n}]=outputC{n}.txt",
256    "linkC-0", Arg.IMAGE, "outputC{n}.txt" },
257    { "--append[linkD-{n}]=filenameD0 --substitutions --image[linkD-{n}]=outputD{n}.txt",
258    "linkD-0", Arg.IMAGE, "outputD0.txt" },
259    { "--append[linkE-{n}]=filenameE0 --substitutions --image[linkE-{n}]=output-E{n}.txt --nil[{++n}] --image[linkE-{n}]=outputE{n}.txt",
260    "linkE-0", Arg.IMAGE, "output-E0.txt" },
261    { "--append[linkF-{n}]=filenameF0 --substitutions --image[linkF-{n}]=output-F{n}.txt --nil[{++n}] --image[linkF-{n}]=outputF{n}.txt",
262    "linkF-1", Arg.IMAGE, "outputF1.txt" },
263    { "--append[linkG-{n}]=filenameG0 --substitutions --image[linkG-{n}]=output-G{n}.txt --nil[{++n}] --nosubstitutions --image[linkG-{n}]=outputG{n}.txt",
264    "linkG-1", Arg.IMAGE, "outputG{n}.txt" },
265    { "--append[linkH-{n}]=filenameH0 --substitutions --image[linkH-{n}]=output-H{n}.txt --nil[{++n}] --nosubstitutions --image[linkH-{n}]=outputH{n}.txt",
266    "linkH-0", Arg.IMAGE, "output-H0.txt" },
267    { "--open=filename0 --append=filename1", "JALVIEW:0", Arg.OPEN,
268    "filename0" },
269    { "--open=filename0 --new --append=filename1", "JALVIEW:1",
270    Arg.APPEND, "filename1" },
271    { "--open=filename0 --new --new --append=filename2", "JALVIEW:0",
272    Arg.OPEN, "filename0" },
273    { "--open=filename0 --new --new --append=filename2", "JALVIEW:2",
274    Arg.APPEND, "filename2" },
275    { "--open[linkA-{n}]=filenameA0 --append[linkA-{++n}]=filenameA1",
276    "linkA-0", Arg.OPEN, "filenameA0" },
277    { "--open[linkB-{n}]=filenameB0 --append[linkB-{++n}]=filenameB1",
278    "linkB-1", Arg.APPEND, "filenameB1" },
279    { "--open[linkC-{n}]=filenameC0 --image[linkC-{n}]=outputC{n}.txt",
280    "linkC-0", Arg.IMAGE, "outputC{n}.txt" },
281    { "--open[linkD-{n}]=filenameD0 --substitutions --image[linkD-{n}]=outputD{n}.txt",
282    "linkD-0", Arg.IMAGE, "outputD0.txt" },
283    { "--open[linkE-{n}]=filenameE0 --substitutions --image[linkE-{n}]=output-E{n}.txt --nil[{++n}] --image[linkE-{n}]=outputE{n}.txt",
284    "linkE-0", Arg.IMAGE, "output-E0.txt" },
285    { "--open[linkF-{n}]=filenameF0 --substitutions --image[linkF-{n}]=output-F{n}.txt --nil[{++n}] --image[linkF-{n}]=outputF{n}.txt",
286    "linkF-1", Arg.IMAGE, "outputF1.txt" },
287    { "--open[linkG-{n}]=filenameG0 --substitutions --image[linkG-{n}]=output-G{n}.txt --nil[{++n}] --nosubstitutions --image[linkG-{n}]=outputG{n}.txt",
288    "linkG-1", Arg.IMAGE, "outputG{n}.txt" },
289    { "--open[linkH-{n}]=filenameH0 --substitutions --image[linkH-{n}]=output-H{n}.txt --nil[{++n}] --nosubstitutions --image[linkH-{n}]=outputH{n}.txt",
290    "linkH-0", Arg.IMAGE, "output-H0.txt" },
291    /*
292    */
293   
294    //
295    };
296    }
297   
 
298  1 toggle @DataProvider(name = "argFiles")
299    public Object[][] argFiles()
300    {
301  1 return new Object[][] { {
302    "--argfile=test/jalview/bin/argparser/testfiles/argfile0.txt --open=shouldntbeabootstrap",
303    Arg.ARGFILE, "test/jalview/bin/argfiles/testfiles/test1.fa" } };
304    }
305   
 
306  3 toggle @Test(groups = "Functional", dataProvider = "allLinkedIdsData")
307    public void allLinkedIdsTest(String pwd, String commandLineArgs, Arg a,
308    String[] values, String[] nonvalues)
309    {
310  3 String userDir = System.getProperty("user.dir");
311  3 if (pwd != null)
312    {
313  0 File pwdFile = new File(pwd);
314  0 System.setProperty("user.dir", pwdFile.getAbsolutePath());
315    }
316  3 String[] args = commandLineArgs.split("\\s+");
317  3 ArgParser argparser = new ArgParser(args);
318   
319  3 int num = values.length;
320  3 List<String> linkedIds = argparser.getLinkedIds();
321  3 Assert.assertEquals(linkedIds.size(), num,
322    "Wrong number of linkedIds: " + linkedIds.toString());
323  12 for (int i = 0; i < num; i++)
324    {
325  9 String value = values[i];
326  9 String linkedId = linkedIds.get(i);
327  9 ArgValuesMap avm = argparser.getLinkedArgs(linkedId);
328  9 if (value == null)
329    {
330  3 Assert.assertTrue(avm.containsArg(a),
331    "Arg value for " + a.argString()
332    + " not applied correctly to linkedId '" + linkedId
333    + "'");
334    }
335    else
336    {
337  6 ArgValues avs = avm.getArgValues(a);
338  6 ArgValue av = avs.getArgValue();
339  6 String v = av.getValue();
340  6 value = new File(value).getPath();
341  6 Assert.assertEquals(v, value, "Arg value for " + a.argString()
342    + " not applied correctly to linkedId '" + linkedId + "'");
343    }
344    }
345   
346  3 System.setProperty("user.dir", userDir);
347    }
348   
 
349  1 toggle @DataProvider(name = "allLinkedIdsData")
350    public Object[][] allLinkedIdsData()
351    {
352  1 return new Object[][] {
353    //
354    /*
355    */
356    { null,
357    "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
358    Arg.CLOSE, new String[]
359    { null, null, null },
360    null },
361    { null,
362    "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --output={dirname}/{basename}.stk --close",
363    Arg.OUTPUT, new String[]
364    { "test/jalview/bin/argparser/testfiles/test1.stk",
365    "test/jalview/bin/argparser/testfiles/test2.stk",
366    "test/jalview/bin/argparser/testfiles/test3.stk", },
367    null },
368    { null,
369    "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
370    Arg.IMAGE, new String[]
371    { "test/jalview/bin/argparser/testfiles/test1.png",
372    "test/jalview/bin/argparser/testfiles/test2.png",
373    "test/jalview/bin/argparser/testfiles/test3.png", },
374    null },
375    /*
376    * Find a way to change pwd reliably -- need to match "*.fa" against some files!
377    { "test/jalview/bin/argparser/testfiles",
378   
379    "--open=*.fa --image={dirname}/{basename}.png --close",
380    Arg.IMAGE, new String[]
381    { "./test1.png", "./test2.png", "./test3.png", }, null },
382    */
383    //
384    };
385    }
386   
 
387  14 toggle @Test(groups = "Functional", dataProvider = "bootstrapArgsData")
388    public void bootstrapArgsValuesAndHeadlessModeTest(String commandLineArgs,
389    Arg a, String valS, boolean valB, boolean headlessValue)
390    {
391  14 String[] args = commandLineArgs.split("\\s+");
392  14 BootstrapArgs bsa = BootstrapArgs.getBootstrapArgs(args);
393  14 if (a != null)
394    {
395  6 if (valS != null)
396    {
397  1 Assert.assertEquals(bsa.getValue(a), valS,
398    "BootstrapArg " + a.argString()
399    + " value does not match expected '" + valS + "'");
400    }
401    else
402    {
403  5 Assert.assertEquals(bsa.getBoolean(a), valB,
404    "Boolean/Unary value of BootstrapArg " + a.argString()
405    + "' is not the expected '" + valB + "'");
406    }
407    }
408   
409  14 boolean isHeadless = bsa.isHeadless();
410  14 Assert.assertEquals(isHeadless, headlessValue,
411    "Assumed headless setting '" + isHeadless + "' is wrong.");
412    }
413   
 
414  1 toggle @DataProvider(name = "bootstrapArgsData")
415    public Object[][] bootstrapArgsData()
416    {
417  1 return new Object[][] {
418    /*
419    * cmdline args
420    * Arg (null if only testing headless)
421    * String value if there is one (null otherwise)
422    * boolean value if String value is null
423    * expected value of isHeadless()
424    */
425    /*
426    */
427    { "--open thisway.fa --output thatway.fa --jabaws https://forwardsandbackwards.com/",
428    Arg.JABAWS, "https://forwardsandbackwards.com/", false, true },
429    { "--help-all --open thisway.fa --output thatway.fa --jabaws https://forwardsandbackwards.com/",
430    Arg.HELP, null, true, true },
431    { "--help-all --nonews --open thisway.fa --output thatway.fa --jabaws https://forwardsandbackwards.com/",
432    Arg.NEWS, null, false, true },
433    { "--help --nonews --open thisway.fa --output thatway.fa --jabaws https://forwardsandbackwards.com/",
434    Arg.NEWS, null, false, true },
435    { "--help-opening --nonews --open thisway.fa --output thatway.fa --jabaws https://forwardsandbackwards.com/",
436    Arg.NEWS, null, false, true },
437    { "--nonews --open thisway.fa --output thatway.fa --jabaws https://forwardsandbackwards.com/",
438    Arg.NEWS, null, false, true },
439    { "--open thisway.fa --image thatway.png", null, null, false,
440    true },
441    { "--open thisway.fa --output thatway.png", null, null, false,
442    true },
443    { "--open thisway.fa --image thatway.png --noheadless", null, null,
444    false, false },
445    { "--open thisway.fa --output thatway.png --noheadless", null, null,
446    false, false },
447    { "--open thisway.fa --image thatway.png --gui", null, null, false,
448    false },
449    { "--open thisway.fa --output thatway.png --gui", null, null, false,
450    false },
451    // --gui takes precedence
452    { "--open thisway.fa --image thatway.png --gui --headless", null,
453    null, false, false },
454    { "--open thisway.fa --output thatway.png --gui --headless", null,
455    null, false, false },
456    //
457    };
458    }
459   
 
460  2 toggle @Test(groups = "Functional", dataProvider = "argsWithinTypesData")
461    public void checkArgsWithinTypesTest(String commandLineArgs,
462    Object[] stuff)
463    {
464  2 String linkedId = "JALVIEW:0";
465  2 String[] args = commandLineArgs.split("\\s+");
466  2 ArgParser argparser = new ArgParser(args);
467  2 ArgValuesMap avm = argparser.getLinkedArgs(linkedId);
468   
469  2 ArgAndValues avals = (ArgAndValues) stuff[0];
470   
471  2 Object[] moreStuff = (Object[]) stuff[1];
472   
473  2 ArgAndValues[] subAv = (ArgAndValues[]) moreStuff[0];
474   
475  2 Object[] secondaryArgAndAuxStuff = (Object[]) stuff[2];
476   
477    // Now look at the argparser
478   
479  2 Arg primaryArg = avals.arg;
480   
481  2 List<ArgValue> parsed_ArgValues = avm.getArgValueList(primaryArg);
482   
483  2 Assert.assertTrue(
484    areEqualSets(avals.values,
485    ArgValuesMap.toValues(parsed_ArgValues)),
486    "Primary arg (" + primaryArg.toString()
487    + ") does not have the expected values. Expected "
488    + avals.values + " and got "
489    + ArgValuesMap.toValues(parsed_ArgValues));
490   
491  7 for (int i = 0; i < parsed_ArgValues.size(); i++)
492    {
493  5 ArgValue parsed_ArgValue = parsed_ArgValues.get(i);
494  5 String value = avals.values.get(i);
495   
496  5 Console.debug("- primary arg '" + primaryArg + "' = '" + value + "'");
497   
498  5 Assert.assertEquals(parsed_ArgValue.getValue(), value,
499    "Primary arg value not as expected");
500   
501  5 ArgAndValues[] aux_avals = (ArgAndValues[]) moreStuff[i];
502   
503  5 for (ArgAndValues aux_aval : aux_avals)
504    {
505  10 Arg auxArg = aux_aval.arg;
506  10 List<String> auxValues = aux_aval.values;
507   
508  10 String parsed_auxValue = avm.getFromSubValArgOrPref(auxArg,
509    ArgValuesMap.Position.AFTER, parsed_ArgValue, null, null,
510    null, null);
511   
512  10 if (auxValues.isEmpty())
513    {
514  2 Assert.assertTrue(parsed_auxValue == null,
515    "Not expecting to parse a value for '" + auxArg
516    + "' but found '" + parsed_auxValue + "'");
517    }
518   
519  10 for (String auxValue : auxValues)
520    {
521   
522  8 Console.debug("- + primary aux arg '" + auxArg + "' = '"
523    + auxValue + "'");
524   
525  8 Assert.assertEquals(parsed_auxValue, auxValue,
526    "Primary auxiliary arg (" + auxArg.toString()
527    + ") values do not match");
528   
529    }
530    }
531   
532    // Now for the secondary args
533  5 Object[] secondaryStuff = (Object[]) secondaryArgAndAuxStuff[i];
534  5 ArgAndValues secondaryArgAndValues = (ArgAndValues) secondaryStuff[0];
535  5 Arg secondaryArg = secondaryArgAndValues.arg;
536  5 List<String> secondaryValues = secondaryArgAndValues.values;
537   
538  5 List<ArgValue> parsed_secondaryArgValues = avm
539    .getArgValueListFromSubValOrArg(parsed_ArgValue, secondaryArg,
540    null);
541   
542  5 Assert.assertTrue(
543    areEqualSets(secondaryValues,
544    ArgValuesMap.toValues(parsed_secondaryArgValues)),
545    "Secondary arg (" + secondaryArg.toString()
546    + ") does not have the expected values");
547   
548  5 Object[] secondaryMoreStuff = (Object[]) secondaryStuff[1];
549   
550  18 for (int j = 0; j < parsed_secondaryArgValues.size(); j++)
551    {
552  13 ArgValue parsed_secondaryArgValue = parsed_secondaryArgValues
553    .get(j);
554  13 String secondary_value = secondaryValues.get(j);
555   
556  13 Console.debug("-- secondary arg '" + secondaryArg + "' = '"
557    + secondary_value + "'");
558   
559  13 Assert.assertEquals(parsed_secondaryArgValue.getValue(),
560    secondary_value, "Secondary arg value not as expected");
561   
562  13 ArgAndValues[] secondary_aux_avals = (ArgAndValues[]) secondaryMoreStuff[j];
563   
564  13 for (ArgAndValues secondary_aux_aval : secondary_aux_avals)
565    {
566  35 Arg secondary_auxArg = secondary_aux_aval.arg;
567  35 List<String> secondary_auxValues = secondary_aux_aval.values;
568   
569  35 String parsed_secondary_auxValue = avm.getValueFromSubValOrArg(
570    parsed_secondaryArgValue, secondary_auxArg, null);
571   
572  35 if (secondary_auxValues.isEmpty())
573    {
574  1 Assert.assertTrue(parsed_secondary_auxValue == null,
575    "Not expecting to parse a value for '"
576    + secondary_auxArg + "' but found '"
577    + parsed_secondary_auxValue + "'");
578    }
579   
580  35 for (String secondary_auxValue : secondary_auxValues)
581    {
582  34 Console.debug("-- + secondary aux arg '" + secondary_auxArg
583    + "' for value '" + secondary_auxValue + "'");
584   
585  34 Assert.assertEquals(parsed_secondary_auxValue,
586    secondary_auxValue,
587    "Secondary auxiliary arg ("
588    + secondary_auxArg.toString()
589    + ") values do not match");
590    }
591    }
592    }
593    }
594    }
595   
 
596  1 toggle @DataProvider(name = "argsWithinTypesData")
597    public Object[][] argsWithinTypesData()
598    {
599  1 return new Object[][] {
600    /*
601    * { cmdline args },
602    * {
603    * { Primary Arg, Secondary Args },
604    * { { Secondary Arg => { Values } } }
605    * },
606    */
607    /*
608    */
609    { //
610    // commandLineArgs
611    "--open=alignment.fa --structure=structure0.pdb"
612    // structureimage0a and structureimage args
613    + " --structureimage=image0a.png --bgcolour=bg0a --imagecolour=col0a"
614    // structureimage0b and structureimage args
615    + " --structureimage=image0b.png --bgcolour=bg0b --imagecolour=col0b"
616    // more structure args
617    + " --structureviewer=sv0 --paematrix=pae0" //
618    // structure1
619    + " --structure=structure1.pdb"
620    // structure args
621    + " --structureviewer=sv1 --paematrix=pae1"
622    // structureimage1a with NO structureimage args
623    // (see `--all --bgcolour=pineapple` later)
624    + " --structureimage=image1a.png"
625    // structureimage1b and structureimage args
626    + " --structureimage=image1b.png --bgcolour=bg1b --imagecolour=col1b"
627    // --all args, should apply to structureimage1a only
628    + " --all --bgcolour=pineapple" //
629    ,
630    // stuff
631    new Object[]
632    {
633    // avals (0) and (1)
634    av(Arg.STRUCTURE, "structure0.pdb", "structure1.pdb"),
635    // moreStuff (0) and (1)
636    new ArgAndValues[][]
637    { //
638    { av(Arg.STRUCTUREVIEWER, "sv0"),
639    av(Arg.PAEMATRIX, "pae0") },
640    { av(Arg.STRUCTUREVIEWER, "sv1"),
641    av(Arg.PAEMATRIX, "pae1") } //
642    },
643    // secondaryArgAndAuxStuff
644    // (same size as values of avals)
645    new Object[][]
646    {
647    // secondaryStuff (0)
648    {
649    // secondaryArgAndValues (a) and (b)
650    av(Arg.STRUCTUREIMAGE, "image0a.png",
651    "image0b.png"),
652    // secondaryMoreStuff
653    // (same size as values of secondaryArgAndValues)
654    new ArgAndValues[][]
655    {
656    // secondary_aux_avals (a)
657    { av(Arg.BGCOLOUR, "bg0a"),
658    av(Arg.IMAGECOLOUR, "col0a") },
659    // secondary_aux_avals (b)
660    { av(Arg.BGCOLOUR, "bg0b"),
661    av(Arg.IMAGECOLOUR, "col0b") }, //
662    }, //
663    },
664    // secondaryStuff (1)
665    {
666    // secondaryArgAndValues (a) and (b)
667    av(Arg.STRUCTUREIMAGE, "image1a.png",
668    "image1b.png"),
669    // secondaryMoreStuff
670    new ArgAndValues[][]
671    {
672    // secondary_aux_avals (a)
673    { av(Arg.BGCOLOUR, "pineapple"),
674    av(Arg.IMAGECOLOUR) },
675    // secondary_aux_avals (b)
676    { av(Arg.BGCOLOUR, "bg1b"),
677    av(Arg.IMAGECOLOUR, "col1b") }, //
678    }, //
679    }, //
680    } //
681    } //
682    }, //
683    { //
684    "--open=alignment.fa --wrap --colour=gecose-flower"
685    // structure0
686    + " --structure=structure0.pdb"
687    + " --structureimage=image0a.png --bgcolour=bg0a --scale=3"
688    + " --structureimage=image0b.png --imagecolour=col0b --scale=4"
689    + " --structureviewer=sv0 --paematrix=pae0" //
690    + " --structureimage=image0c.png"
691    // structure1
692    + " --structure=structure1.pdb"
693    + " --structureviewer=sv1 --paematrix=pae1"
694    + " --structureimage=image1a.png"
695    + " --structureimage=image1b.png --bgcolour=bg1b --imagecolour=col1b"
696    + " --structureimage=image1c.png --bgcolour=bg1c --imagecolour=col1c --scale=5"
697    + " --structureimage=image1d.png --imagecolour=col1d --scale=6"
698    + " --structureimage=image1e.png --bgcolour=bg1e"
699    // structure2
700    + " --structure=structure2.pdb"
701    + " --structureimage=image2a.png --bgcolour=bg2a --scale=23"
702    + " --all --bgcolour=pineapple --imagecolour=banana --scale=2" //
703    ,
704    // stuff
705    new Object[]
706    { av(Arg.STRUCTURE, "structure0.pdb", "structure1.pdb",
707    "structure2.pdb"),
708    new ArgAndValues[][]
709    { //
710    { av(Arg.STRUCTUREVIEWER, "sv0"),
711    av(Arg.PAEMATRIX, "pae0") },
712    { av(Arg.STRUCTUREVIEWER, "sv1"),
713    av(Arg.PAEMATRIX, "pae1") },
714    { av(Arg.STRUCTUREVIEWER), av(Arg.PAEMATRIX) } //
715    }, //
716    new Object[][]
717    { //
718    { //
719    av(Arg.STRUCTUREIMAGE, "image0a.png", "image0b.png",
720    "image0c.png"), //
721    new ArgAndValues[][]
722    { //
723    { av(Arg.BGCOLOUR, "bg0a"),
724    av(Arg.IMAGECOLOUR, "banana"),
725    av(Arg.SCALE, "3") },
726    { av(Arg.BGCOLOUR, "pineapple"),
727    av(Arg.IMAGECOLOUR, "col0b"),
728    av(Arg.SCALE, "4") },
729    { av(Arg.BGCOLOUR, "pineapple"),
730    av(Arg.IMAGECOLOUR, "banana"),
731    av(Arg.SCALE, "2") }, //
732    }, //
733    }, //
734    { //
735    av(Arg.STRUCTUREIMAGE, "image1a.png", "image1b.png",
736    "image1c.png", "image1d.png",
737    "image1e.png"),
738    new ArgAndValues[][]
739    { //
740    { av(Arg.BGCOLOUR, "pineapple"),
741    av(Arg.IMAGECOLOUR, "banana"),
742    av(Arg.SCALE, "2") },
743    { av(Arg.BGCOLOUR, "bg1b"),
744    av(Arg.IMAGECOLOUR, "col1b"),
745    av(Arg.SCALE, "2") },
746    { av(Arg.BGCOLOUR, "bg1c"),
747    av(Arg.IMAGECOLOUR, "col1c"),
748    av(Arg.SCALE, "5") },
749    { av(Arg.BGCOLOUR, "pineapple"),
750    av(Arg.IMAGECOLOUR, "col1d"),
751    av(Arg.SCALE, "6") },
752    { av(Arg.BGCOLOUR, "bg1e"),
753    av(Arg.IMAGECOLOUR, "banana"),
754    av(Arg.SCALE, "2") } //
755    }, //
756    }, //
757    { //
758    av(Arg.STRUCTUREIMAGE, "image2a.png"),
759    new ArgAndValues[][]
760    { //
761    { av(Arg.BGCOLOUR, "bg2a"),
762    av(Arg.IMAGECOLOUR, "banana"),
763    av(Arg.SCALE, "23") }, //
764    }, //
765    }, //
766    } //
767    } //
768    } //
769    };
770    }
771   
 
772  52 toggle protected ArgAndValues av(Arg a, String... vals)
773    {
774  52 return new ArgAndValues(a, vals);
775    }
776   
 
777    protected class ArgAndValues
778    {
779    protected Arg arg;
780   
781    protected List<String> values;
782   
 
783  52 toggle ArgAndValues(Arg a, String... vals)
784    {
785  52 arg = a;
786  52 values = vals == null ? new ArrayList<String>() : Arrays.asList(vals);
787    }
788   
 
789  312 toggle @Override
790    public String toString()
791    {
792  312 StringBuilder sb = new StringBuilder();
793  312 sb.append(arg.argString());
794  312 sb.append("\n");
795  312 sb.append(Strings.join(values, ','));
796  312 sb.append("\n");
797  312 return sb.toString();
798    }
799    }
800   
 
801  0 toggle private static boolean areEqualSets(String[] strArray,
802    List<String> strList)
803    {
804  0 return areEqualSets(Arrays.asList(strArray), strList);
805    }
806   
 
807  7 toggle private static boolean areEqualSets(List<String> l1, List<String> l2)
808    {
809  7 if (l1 == null && l2 == null)
810    {
811  0 Console.info(
812    "Comparing null lists, should be okay but you might want to know");
813  0 return true;
814    }
815  7 if (l1 == null || l2 == null)
816    {
817  0 return false;
818    }
819  7 return new HashSet<String>(l1).equals(new HashSet<String>(l2));
820    }
821   
822    }
  • Report generated by OpenClover v 4.4.1 on Wed Jun 18 2025 15:16:08 BST using coverage data from Wed Jun 18 2025 15:15:57 BST.
  • OpenClover is free and open-source software.