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  1. Project Clover database Thu Dec 4 2025 14:43:25 GMT
  2. Package jalview.io

File BackupFilesTest.java

 

Code metrics

48
164
21
1
494
352
47
0.29
7.81
21
2.24

Classes

Class Line # Actions
BackupFilesTest 47 164 47
0.836909983.7%
 

Contributing tests

This file is covered by 5 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.io;
22   
23    import java.io.File;
24    import java.io.IOException;
25    import java.nio.file.Files;
26    import java.nio.file.Path;
27    import java.nio.file.Paths;
28    import java.util.Arrays;
29    import java.util.Collections;
30    import java.util.Enumeration;
31    import java.util.HashMap;
32    import java.util.List;
33    import java.util.TreeMap;
34   
35    import org.testng.Assert;
36    import org.testng.annotations.AfterClass;
37    import org.testng.annotations.BeforeClass;
38    import org.testng.annotations.Test;
39   
40    import jalview.bin.Cache;
41    import jalview.datamodel.AlignmentI;
42    import jalview.datamodel.Sequence;
43    import jalview.datamodel.SequenceI;
44    import jalview.gui.AlignFrame;
45    import jalview.gui.JvOptionPane;
46   
 
47    public class BackupFilesTest
48    {
 
49  1 toggle @BeforeClass(alwaysRun = true)
50    public void setUpJvOptionPane()
51    {
52  1 JvOptionPane.setInteractiveMode(false);
53  1 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
54    }
55   
56    private static boolean actuallyDeleteTmpFiles = true;
57   
58    private static String testDir = "test/jalview/io";
59   
60    private static String testBasename = "backupfilestest";
61   
62    private static String testExt = ".fa";
63   
64    private static String testFilename = testBasename + testExt;
65   
66    private static String testFile = testDir + File.separatorChar
67    + testFilename;
68   
69    private static String newBasename = testBasename + "Temp";
70   
71    private static String newFilename = newBasename + testExt;
72   
73    private static String newFile = testDir + File.separatorChar
74    + newFilename;
75   
76    private static String sequenceName = "BACKUP_FILES";
77   
78    private static String sequenceDescription = "backupfiles";
79   
80    private static String sequenceData = "AAAARG";
81   
82    private static String suffix = "_BACKUPTEST-%n";
83   
84    private static int digits = 6;
85   
86    private static int rollMax = 2;
87   
88    private AlignFrame af;
89   
90    // read and save with backupfiles disabled
 
91  1 toggle @Test(groups = { "Functional" })
92    public void noBackupsEnabledTest() throws Exception
93    {
94    // set BACKUPFILES_ENABLED to false (i.e. turn off BackupFiles feature -- no
95    // backup files to be made when saving)
96  1 setBackupFilesOptions(false, true, true);
97   
98    // init the newFile and backups (i.e. make sure newFile exists on its own
99    // and has no backups
100  1 initNewFileForTesting();
101   
102    // now save again
103  1 save();
104   
105    // check no backup files
106  1 File[] backupFiles = getBackupFiles();
107  1 Assert.assertEquals(backupFiles.length, 0, "Number of backup files is "
108    + backupFiles.length + ", not " + 0);
109    }
110   
111    // save with no numbers in the backup file names
 
112  1 toggle @Test(groups = { "Functional" })
113    public void backupsEnabledSingleFileBackupTest() throws Exception
114    {
115    // Enable BackupFiles and set noMax so all backupfiles get kept
116  1 String mysuffix = "~";
117  1 BackupFilesPresetEntry bfpe = new BackupFilesPresetEntry(mysuffix, 1,
118    false, true, 1, false);
119  1 setBackupFilesOptions(true, false, true,
120    "test/jalview/io/testProps_singlefilebackup.jvprops", bfpe);
121   
122    // init the newFile and backups (i.e. make sure newFile exists on its own
123    // and has no backups)
124  1 initNewFileForTesting();
125  1 HashMap<Integer, String> correctindexmap = new HashMap<>();
126  1 correctindexmap.put(0, "backupfilestestTemp.fa~");
127   
128  1 save();
129  1 Assert.assertTrue(checkBackupFiles(correctindexmap, newFile, "~", 1));
130   
131    // and a second time -- see JAL-3628
132  1 save();
133  1 Assert.assertTrue(checkBackupFiles(correctindexmap, newFile, "~", 1));
134   
135  1 cleanupTmpFiles(newFile, "~", 1);
136    }
137   
138    // save keeping all backup files
 
139  1 toggle @Test(groups = { "Functional" })
140    public void backupsEnabledNoRollMaxTest() throws Exception
141    {
142    // Enable BackupFiles and set noMax so all backupfiles get kept
143  1 setBackupFilesOptions(true, false, true);
144   
145    // init the newFile and backups (i.e. make sure newFile exists on its own
146    // and has no backups)
147  1 initNewFileForTesting();
148   
149    // now save a few times again. No rollMax so should have more than two
150    // backup files
151  1 int numSaves = 10;
152  11 for (int i = 0; i < numSaves; i++)
153    {
154  10 save();
155    }
156   
157    // check 10 backup files
158  1 HashMap<Integer, String> correctindexmap = new HashMap<>();
159  1 correctindexmap.put(1, "backupfilestestTemp.fa_BACKUPTEST-000001");
160  1 correctindexmap.put(2, "backupfilestestTemp.fa_BACKUPTEST-000002");
161  1 correctindexmap.put(3, "backupfilestestTemp.fa_BACKUPTEST-000003");
162  1 correctindexmap.put(4, "backupfilestestTemp.fa_BACKUPTEST-000004");
163  1 correctindexmap.put(5, "backupfilestestTemp.fa_BACKUPTEST-000005");
164  1 correctindexmap.put(6, "backupfilestestTemp.fa_BACKUPTEST-000006");
165  1 correctindexmap.put(7, "backupfilestestTemp.fa_BACKUPTEST-000007");
166  1 correctindexmap.put(8, "backupfilestestTemp.fa_BACKUPTEST-000008");
167  1 correctindexmap.put(9, "backupfilestestTemp.fa_BACKUPTEST-000009");
168  1 correctindexmap.put(10, "backupfilestestTemp.fa_BACKUPTEST-000010");
169  1 HashMap<Integer, String> wrongindexmap = new HashMap<>();
170  1 wrongindexmap.put(1, "backupfilestestTemp.fa_BACKUPTEST-1");
171  1 wrongindexmap.put(2, "backupfilestestTemp.fa_BACKUPTEST-000002");
172  1 wrongindexmap.put(3, "backupfilestestTemp.fa_BACKUPTEST-000003");
173  1 wrongindexmap.put(4, "backupfilestestTemp.fa_BACKUPTEST-000004");
174  1 wrongindexmap.put(5, "backupfilestestTemp.fa_BACKUPTEST-000005");
175  1 wrongindexmap.put(6, "backupfilestestTemp.fa_BACKUPTEST-000006");
176  1 wrongindexmap.put(7, "backupfilestestTemp.fa_BACKUPTEST-000007");
177  1 wrongindexmap.put(8, "backupfilestestTemp.fa_BACKUPTEST-000008");
178  1 wrongindexmap.put(9, "backupfilestestTemp.fa_BACKUPTEST-000009");
179  1 wrongindexmap.put(10, "backupfilestestTemp.fa_BACKUPTEST-000010");
180  1 int[] indexes2 = { 3, 4, 5, 6, 7, 8, 9, 10 };
181  1 int[] indexes3 = { 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 };
182  1 Assert.assertTrue(checkBackupFiles(correctindexmap));
183  1 Assert.assertFalse(checkBackupFiles(wrongindexmap));
184  1 Assert.assertFalse(checkBackupFiles(indexes2));
185  1 Assert.assertFalse(checkBackupFiles(indexes3));
186    }
187   
188    // save keeping only the last rollMax (2) backup files
 
189  1 toggle @Test(groups = { "Functional" })
190    public void backupsEnabledRollMaxTest() throws Exception
191    {
192    // Enable BackupFiles and set noMax so all backupfiles get kept
193  1 setBackupFilesOptions(true, false, false);
194   
195    // init the newFile and backups (i.e. make sure newFile exists on its own
196    // and has no backups)
197  1 initNewFileForTesting();
198   
199    // now save a few times again. No rollMax so should have more than two
200    // backup files
201  1 int numSaves = 10;
202  11 for (int i = 0; i < numSaves; i++)
203    {
204  10 save();
205    }
206   
207    // check there are "rollMax" backup files and they are all saved correctly
208    // check 10 backup files
209  1 HashMap<Integer, String> correctindexmap = new HashMap<>();
210  1 correctindexmap.put(9, "backupfilestestTemp.fa_BACKUPTEST-000009");
211  1 correctindexmap.put(10, "backupfilestestTemp.fa_BACKUPTEST-000010");
212  1 int[] indexes2 = { 10 };
213  1 int[] indexes3 = { 8, 9, 10 };
214  1 Assert.assertTrue(checkBackupFiles(correctindexmap));
215  1 Assert.assertFalse(checkBackupFiles(indexes2));
216  1 Assert.assertFalse(checkBackupFiles(indexes3));
217    }
218   
219    // save keeping only the last rollMax (2) backup files
 
220  1 toggle @Test(groups = { "Functional" })
221    public void backupsEnabledReverseRollMaxTest() throws Exception
222    {
223    // Enable BackupFiles and set noMax so all backupfiles get kept
224  1 setBackupFilesOptions(true, true, false);
225   
226    // init the newFile and backups (i.e. make sure newFile exists on its own
227    // and has no backups)
228  1 initNewFileForTesting();
229   
230    // now save a few times again. No rollMax so should have more than two
231    // backup files
232  1 int numSaves = 10;
233  11 for (int i = 0; i < numSaves; i++)
234    {
235  10 save();
236    }
237   
238    // check there are "rollMax" backup files and they are all saved correctly
239    // check 10 backup files
240  1 HashMap<Integer, String> correctindexmap = new HashMap<>();
241  1 correctindexmap.put(1, "backupfilestestTemp.fa_BACKUPTEST-000001");
242  1 correctindexmap.put(2, "backupfilestestTemp.fa_BACKUPTEST-000002");
243  1 int[] indexes2 = { 1 };
244  1 int[] indexes3 = { 1, 2, 3 };
245  1 Assert.assertTrue(checkBackupFiles(correctindexmap));
246  1 Assert.assertFalse(checkBackupFiles(indexes2));
247  1 Assert.assertFalse(checkBackupFiles(indexes3));
248    }
249   
 
250  0 toggle private void setBackupFilesOptions()
251    {
252  0 setBackupFilesOptions(true, false, false);
253    }
254   
 
255  4 toggle private void setBackupFilesOptions(boolean enabled, boolean reverse,
256    boolean noMax)
257    {
258  4 BackupFilesPresetEntry bfpe = new BackupFilesPresetEntry(suffix, digits,
259    reverse, noMax, rollMax, false);
260  4 setBackupFilesOptions(enabled, reverse, noMax,
261    "test/jalview/io/testProps.jvprops", bfpe);
262    }
263   
 
264  5 toggle private void setBackupFilesOptions(boolean enabled, boolean reverse,
265    boolean noMax, String propsFile, BackupFilesPresetEntry bfpe)
266    {
267  5 Cache.loadProperties(propsFile);
268   
269  5 Cache.setPropertyNoSave(BackupFiles.ENABLED,
270    Boolean.toString(enabled));
271  5 Cache.setPropertyNoSave(
272    BackupFilesPresetEntry.SAVEDCONFIG, bfpe.toString());
273    /*
274    Cache.setPropertyNoSave(BackupFiles.ENABLED,
275    Boolean.toString(enabled));
276    Cache.setPropertyNoSave(BackupFiles.SUFFIX, suffix);
277    Cache.setPropertyNoSave(BackupFiles.SUFFIX_DIGITS,
278    Integer.toString(digits));
279    Cache.setPropertyNoSave(BackupFiles.REVERSE_ORDER,
280    Boolean.toString(reverse));
281    Cache.setPropertyNoSave(BackupFiles.NO_MAX,
282    Boolean.toString(noMax));
283    Cache.setPropertyNoSave(BackupFiles.ROLL_MAX,
284    Integer.toString(rollMax));
285    Cache.setPropertyNoSave(BackupFiles.CONFIRM_DELETE_OLD,
286    "false");
287    */
288    }
289   
 
290  33 toggle private void save()
291    {
292  33 if (af != null)
293    {
294  33 af.saveAlignment(newFile, jalview.io.FileFormat.Fasta);
295    }
296    }
297   
298    // this runs cleanTmpFiles and then writes the newFile once as a starting
299    // point for all tests
 
300  5 toggle private void initNewFileForTesting() throws Exception
301    {
302  5 cleanupTmpFiles();
303   
304  5 AppletFormatAdapter afa = new AppletFormatAdapter();
305  5 AlignmentI al = afa.readFile(testFile, DataSourceType.FILE,
306    jalview.io.FileFormat.Fasta);
307  5 List<SequenceI> l = al.getSequences();
308   
309    // check this is right
310  5 if (l.size() != 1)
311    {
312  0 throw new Exception("single sequence from '" + testFile
313    + "' not read in correctly (should be a single short sequence). List<SequenceI> size is wrong.");
314    }
315  5 SequenceI s = l.get(0);
316  5 Sequence ref = new Sequence(sequenceName, sequenceData);
317  5 ref.setDescription(sequenceDescription);
318  5 if (!sequencesEqual(s, ref))
319    {
320  0 throw new Exception("single sequence from '" + testFile
321    + "' not read in correctly (should be a single short sequence). SequenceI name, description or data is wrong.");
322    }
323    // save alignment file to new filename -- this doesn't test backups disabled
324    // yet as this file shouldn't already exist
325  5 af = new AlignFrame(al, 0, 0);
326  5 af.saveAlignment(newFile, jalview.io.FileFormat.Fasta);
327    }
328   
329    // this deletes the newFile (if it exists) and any saved backup file for it
 
330  6 toggle @AfterClass(alwaysRun = true)
331    private void cleanupTmpFiles()
332    {
333  6 cleanupTmpFiles(newFile, suffix, digits);
334    }
335   
 
336  8 toggle protected static void cleanupTmpFiles(String file, String mysuffix,
337    int mydigits)
338    {
339  8 File newfile = new File(file);
340  8 if (newfile.exists())
341    {
342  6 newfile.delete();
343    }
344  8 File[] tmpFiles = getBackupFiles(file, mysuffix, mydigits);
345  24 for (int i = 0; i < tmpFiles.length; i++)
346    {
347  16 if (actuallyDeleteTmpFiles)
348    {
349  16 tmpFiles[i].delete();
350    }
351    else
352    {
353  0 System.out.println("Pretending to delete " + tmpFiles[i].getPath());
354    }
355    }
356    }
357   
 
358  9 toggle private static File[] getBackupFiles(String f, String s, int i)
359    {
360  9 TreeMap<Integer, File> bfTreeMap = BackupFiles
361    .getBackupFilesAsTreeMap(f, s, i);
362  9 File[] backupFiles = new File[bfTreeMap.size()];
363  9 bfTreeMap.values().toArray(backupFiles);
364  9 return backupFiles;
365    }
366   
 
367  1 toggle private static File[] getBackupFiles()
368    {
369  1 return getBackupFiles(newFile, suffix, digits);
370    }
371   
 
372  4 toggle private static boolean checkBackupFiles(HashMap<Integer, String> indexmap)
373    throws IOException
374    {
375  4 return checkBackupFiles(indexmap, newFile, suffix, digits);
376    }
377   
 
378  6 toggle private static boolean checkBackupFiles(HashMap<Integer, String> indexmap,
379    String file, String mysuffix, int mydigits) throws IOException
380    {
381  6 TreeMap<Integer, File> map = BackupFiles.getBackupFilesAsTreeMap(file,
382    mysuffix, mydigits);
383  6 Enumeration<Integer> indexesenum = Collections
384    .enumeration(indexmap.keySet());
385  22 while (indexesenum.hasMoreElements())
386    {
387  17 int i = indexesenum.nextElement();
388  17 String indexfilename = indexmap.get(i);
389  17 if (!map.containsKey(i))
390    {
391  0 return false;
392    }
393  17 File f = map.get(i);
394  17 if (!filesContentEqual(newFile, f.getPath()))
395    {
396  0 return false;
397    }
398  17 map.remove(i);
399  17 if (f == null)
400    {
401  0 return false;
402    }
403  17 if (!f.getName().equals(indexfilename))
404    {
405  1 return false;
406    }
407    }
408    // should be nothing left in map
409  5 if (map.size() > 0)
410    {
411  0 return false;
412    }
413   
414  5 return true;
415    }
416   
 
417  6 toggle private static boolean checkBackupFiles(int[] indexes) throws IOException
418    {
419  6 TreeMap<Integer, File> map = BackupFiles
420    .getBackupFilesAsTreeMap(newFile, suffix, digits);
421  28 for (int m = 0; m < indexes.length; m++)
422    {
423  25 int i = indexes[m];
424  25 if (!map.containsKey(i))
425    {
426  3 return false;
427    }
428  22 File f = map.get(i);
429  22 if (!filesContentEqual(newFile, f.getPath()))
430    {
431  0 return false;
432    }
433  22 map.remove(i);
434  22 if (f == null)
435    {
436  0 return false;
437    }
438    // check the filename -- although this uses the same code to forumulate
439    // the filename so not much of a test!
440  22 String filename = BackupFilenameParts.getBackupFilename(i,
441    newBasename + testExt, suffix, digits);
442  22 if (!filename.equals(f.getName()))
443    {
444  0 System.out.println("Supposed filename '" + filename
445    + "' not equal to actual filename '" + f.getName() + "'");
446  0 return false;
447    }
448    }
449    // should be nothing left in map
450  3 if (map.size() > 0)
451    {
452  3 return false;
453    }
454   
455  0 return true;
456    }
457   
 
458  0 toggle private static String[] getBackupFilesAsStrings()
459    {
460  0 File[] files = getBackupFiles(newFile, suffix, digits);
461  0 String[] filenames = new String[files.length];
462  0 for (int i = 0; i < files.length; i++)
463    {
464  0 filenames[i] = files[i].getPath();
465    }
466  0 return filenames;
467    }
468   
 
469  5 toggle public static boolean sequencesEqual(SequenceI s1, SequenceI s2)
470    {
471  5 if (s1 == null && s2 == null)
472    {
473  0 return true;
474    }
475  5 else if (s1 == null || s2 == null)
476    {
477  0 return false;
478    }
479  5 return (s1.getName().equals(s2.getName())
480    && s1.getDescription().equals(s2.getDescription())
481    && Arrays.equals(s1.getSequence(), s2.getSequence()));
482    }
483   
 
484  39 toggle public static boolean filesContentEqual(String fileName1,
485    String fileName2) throws IOException
486    {
487  39 Path file1 = Paths.get(fileName1);
488  39 Path file2 = Paths.get(fileName2);
489  39 byte[] bytes1 = Files.readAllBytes(file1);
490  39 byte[] bytes2 = Files.readAllBytes(file2);
491  39 return Arrays.equals(bytes1, bytes2);
492    }
493   
494    }
  • Report generated by OpenClover v 4.4.1 on Thu Dec 4 2025 14:53:28 GMT using coverage data from Thu Dec 4 2025 14:53:14 GMT.
  • OpenClover is free and open-source software.