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Coverage Report

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

File BackupFiles.java

 

Coverage histogram

../../img/srcFileCovDistChart7.png
30% of files have more coverage

Code metrics

118
348
34
1
1,057
807
116
0.33
10.24
34
3.41

Classes

Class Line # Actions
BackupFiles 56 348 116
0.66666.6%
 

Contributing tests

This file is covered by 28 tests. .

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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.nio.file.StandardCopyOption;
29    import java.text.SimpleDateFormat;
30    import java.util.ArrayList;
31    import java.util.HashMap;
32    import java.util.List;
33    import java.util.Map;
34    import java.util.TreeMap;
35    import java.util.concurrent.CompletableFuture;
36    import java.util.concurrent.ExecutionException;
37    import java.util.concurrent.ExecutorService;
38    import java.util.concurrent.Executors;
39    import java.util.concurrent.Future;
40   
41    import jalview.bin.Cache;
42    import jalview.bin.Console;
43    import jalview.gui.Desktop;
44    import jalview.gui.JvOptionPane;
45    import jalview.util.MessageManager;
46    import jalview.util.Platform;
47   
48    /*
49    * BackupFiles used for manipulating (naming rolling/deleting) backup/version files when an alignment or project file is saved.
50    * User configurable options are:
51    * BACKUPFILES_ENABLED - boolean flag as to whether to use this mechanism or act as before, including overwriting files as saved.
52    * The rest of the options are now saved as BACKUPFILES_PRESET, BACKUPFILES_SAVED and BACKUPFILES_CUSTOM
53    * (see BackupFilesPresetEntry)
54    */
55   
 
56    public class BackupFiles
57    {
58   
59    // labels for saved params in Cache and .jalview_properties
60    public static final String NS = "BACKUPFILES";
61   
62    public static final String ENABLED = NS + "_ENABLED";
63   
64    public static final String NUM_PLACEHOLDER = "%n";
65   
66    private static final String DEFAULT_TEMP_FILE = "jalview_temp_file_" + NS;
67   
68    private static final String TEMP_FILE_EXT = ".tmp";
69   
70    // file - File object to be backed up and then updated (written over)
71    private File file;
72   
73    // enabled - default flag as to whether to do the backup file roll (if not
74    // defined in preferences)
75    private static boolean enabled;
76   
77    // confirmDelete - default flag as to whether to confirm with the user before
78    // deleting old backup/version files
79    private static boolean confirmDelete;
80   
81    // defaultSuffix - default template to use to append to basename of file
82    private String suffix;
83   
84    // noMax - flag to turn off a maximum number of files
85    private boolean noMax;
86   
87    // defaultMax - default max number of backup files
88    private int max;
89   
90    // defaultDigits - number of zero-led digits to use in the filename
91    private int digits;
92   
93    // reverseOrder - set to true to make newest (latest) files lowest number
94    // (like rolled log files)
95    private boolean reverseOrder;
96   
97    // temp saved file to become new saved file
98    private File tempFile;
99   
100    // flag set to see if file save to temp file was successful
101    private boolean tempFileWriteSuccess;
102   
103    // array of files to be deleted, with extra information
104    private ArrayList<File> deleteFiles = new ArrayList<>();
105   
106    // date formatting for modification times
107    private static final SimpleDateFormat sdf = new SimpleDateFormat(
108    "yyyy-MM-dd HH:mm:ss");
109   
110    private static final String newTempFileSuffix = "_newfile";
111   
112    private static final String oldTempFileSuffix = "_oldfile_tobedeleted";
113   
114    // thread pool used for completablefutures
115    private static final ExecutorService executorService = Executors
116    .newFixedThreadPool(3);
117   
118    private static List<BackupFiles> savesInProgress = new ArrayList<>();
119   
120    private CompletableFuture<Boolean> myFuture = null;
121   
 
122  100 toggle private boolean addSaveInProgress()
123    {
124  100 if (savesInProgress.contains(this))
125    {
126  0 return false;
127    }
128    else
129    {
130  100 this.setMyFuture();
131  100 savesInProgress.add(this);
132  100 return true;
133    }
134    }
135   
 
136  100 toggle private boolean removeSaveInProgress(boolean ret)
137    {
138  100 if (savesInProgress.contains(this))
139    {
140  100 this.getMyFuture().complete(ret);
141    // remove all occurrences
142  200 while (savesInProgress.remove(this))
143    {
144    }
145  100 return true;
146    }
147  0 return false;
148    }
149   
 
150  100 toggle private static CompletableFuture<Boolean> getNewFuture()
151    {
152  100 return new CompletableFuture<Boolean>()
153    {
154    };
155    }
156   
 
157  160 toggle private CompletableFuture<Boolean> getMyFuture()
158    {
159  160 return this.myFuture;
160    }
161   
 
162  100 toggle private void setMyFuture()
163    {
164  100 this.myFuture = getNewFuture();
165    }
166   
 
167  28 toggle public static boolean hasSavesInProgress()
168    {
169  28 boolean has = false;
170  28 for (CompletableFuture cf : savesInProgressCompletableFutures(true))
171    {
172  32 has |= !cf.isDone();
173    }
174  28 return has;
175    }
176   
 
177  5 toggle public static List<File> savesInProgressFiles(boolean all)
178    {
179  5 List<File> files = new ArrayList<>();
180  5 for (BackupFiles bfile : savesInProgress)
181    {
182  7 if (all || !bfile.getMyFuture().isDone())
183  5 files.add(bfile.getFile());
184    }
185  5 return files;
186    }
187   
 
188  37 toggle public static List<CompletableFuture<Boolean>> savesInProgressCompletableFutures(
189    boolean all)
190    {
191  37 List<CompletableFuture<Boolean>> cfs = new ArrayList<>();
192  37 for (BackupFiles bfile : savesInProgress)
193    {
194  44 if (all || !bfile.getMyFuture().isDone())
195  41 cfs.add(bfile.getMyFuture());
196    }
197  37 return cfs;
198    }
199   
 
200  0 toggle public static Future<Boolean> allSaved()
201    {
202  0 CompletableFuture<Boolean> f = new CompletableFuture<>();
203   
204  0 executorService.submit(() -> {
205  0 for (BackupFiles buf : savesInProgress)
206    {
207  0 boolean allSaved = true;
208  0 try
209    {
210  0 allSaved &= buf.getMyFuture().get();
211    } catch (InterruptedException e)
212    {
213  0 Console.debug("InterruptedException waiting for files to save",
214    e);
215    } catch (ExecutionException e)
216    {
217  0 Console.debug("ExecutionException waiting for files to save", e);
218    }
219  0 f.complete(allSaved);
220    }
221    });
222  0 return f;
223    }
224   
 
225  98 toggle public BackupFiles(String filename)
226    {
227  98 this(new File(filename));
228    }
229   
230    // first time defaults for SUFFIX, NO_MAX, ROLL_MAX, SUFFIX_DIGITS and
231    // REVERSE_ORDER
 
232  100 toggle public BackupFiles(File file)
233    {
234  100 classInit();
235  100 if (file.getParentFile() == null)
236    {
237    // filename probably in pwd represented with no parent -- fix it before
238    // it's a problem
239  0 file = file.getAbsoluteFile();
240    }
241  100 this.file = file;
242   
243    // add this file from the save in progress stack
244  100 addSaveInProgress();
245   
246  100 BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
247    .getSavedBackupEntry();
248  100 this.suffix = bfpe.suffix;
249  100 this.noMax = bfpe.keepAll;
250  100 this.max = bfpe.rollMax;
251  100 this.digits = bfpe.digits;
252  100 this.reverseOrder = bfpe.reverse;
253   
254    // create a temp file to save new data in
255  100 File temp = null;
256  100 try
257    {
258  100 if (file != null)
259    {
260  100 String tempfilename = file.getName();
261  100 File tempdir = file.getAbsoluteFile().getParentFile();
262  100 tempdir.mkdirs();
263  100 Console.trace(
264    "BACKUPFILES [file!=null] attempting to create temp file for "
265    + tempfilename + " in dir " + tempdir);
266  100 temp = File.createTempFile(tempfilename,
267    TEMP_FILE_EXT + newTempFileSuffix, tempdir);
268  100 Console.debug(
269    "BACKUPFILES using temp file " + temp.getAbsolutePath());
270    }
271    else
272    {
273  0 Console.trace(
274    "BACKUPFILES [file==null] attempting to create default temp file "
275    + DEFAULT_TEMP_FILE + " with extension "
276    + TEMP_FILE_EXT);
277  0 temp = File.createTempFile(DEFAULT_TEMP_FILE, TEMP_FILE_EXT);
278    }
279    } catch (IOException e)
280    {
281  0 Console.error("Could not create temp file to save to (IOException)");
282  0 Console.error(e.getMessage());
283  0 Console.debug(Cache.getStackTraceString(e));
284    } catch (Exception e)
285    {
286  0 Console.error("Exception creating temp file for saving");
287  0 Console.debug(Cache.getStackTraceString(e));
288    }
289  100 this.setTempFile(temp);
290    }
291   
 
292  178 toggle private static void classInit()
293    {
294  178 Console.initLogger();
295  178 Console.trace("BACKUPFILES classInit");
296  178 boolean e = Cache.getDefault(ENABLED, !Platform.isJS());
297  178 setEnabled(e);
298  178 Console.trace("BACKUPFILES " + (e ? "enabled" : "disabled"));
299  178 BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
300    .getSavedBackupEntry();
301  178 Console.trace("BACKUPFILES preset scheme " + bfpe.toString());
302  178 setConfirmDelete(bfpe.confirmDelete);
303  178 Console.trace("BACKUPFILES confirm delete " + bfpe.confirmDelete);
304    }
305   
 
306  178 toggle public static void setEnabled(boolean flag)
307    {
308  178 enabled = flag;
309    }
310   
 
311  78 toggle public static boolean getEnabled()
312    {
313  78 classInit();
314  78 return enabled;
315    }
316   
 
317  178 toggle public static void setConfirmDelete(boolean flag)
318    {
319  178 confirmDelete = flag;
320    }
321   
 
322  0 toggle public static boolean getConfirmDelete()
323    {
324  0 classInit();
325  0 return confirmDelete;
326    }
327   
328    // set, get and rename temp file into place
 
329  100 toggle public void setTempFile(File temp)
330    {
331  100 this.tempFile = temp;
332    }
333   
 
334  192 toggle public File getTempFile()
335    {
336  192 return tempFile;
337    }
338   
 
339  190 toggle public String getTempFilePath()
340    {
341  190 String path = null;
342  190 try
343    {
344  190 path = this.getTempFile().getCanonicalPath();
345    } catch (IOException e)
346    {
347  0 Console.error("IOException when getting Canonical Path of temp file '"
348    + this.getTempFile().getName() + "'");
349  0 Console.debug(Cache.getStackTraceString(e));
350    }
351  190 return path;
352    }
353   
 
354  100 toggle public boolean setWriteSuccess(boolean flag)
355    {
356  100 boolean old = this.tempFileWriteSuccess;
357  100 this.tempFileWriteSuccess = flag;
358  100 return old;
359    }
360   
 
361  100 toggle public boolean getWriteSuccess()
362    {
363  100 return this.tempFileWriteSuccess;
364    }
365   
 
366  100 toggle public boolean renameTempFile()
367    {
368  100 return moveFileToFile(tempFile, file);
369    }
370   
371    // roll the backupfiles
 
372  0 toggle public boolean rollBackupFiles()
373    {
374  0 return this.rollBackupFiles(true);
375    }
376   
 
377  100 toggle public boolean rollBackupFiles(boolean tidyUp)
378    {
379    // file doesn't yet exist or backups are not enabled or template is null or
380    // empty
381  100 if ((!file.exists()) || (!enabled) || max < 0 || suffix == null
382    || suffix.length() == 0)
383    {
384    // nothing to do
385  62 Console.debug("BACKUPFILES rollBackupFiles nothing to do." + ", "
386  62 + "filename: " + (file != null ? file.getName() : "null")
387    + ", " + "file exists: " + file.exists() + ", " + "enabled: "
388    + enabled + ", " + "max: " + max + ", " + "suffix: '" + suffix
389    + "'");
390  62 return true;
391    }
392   
393  38 Console.trace("BACKUPFILES rollBackupFiles starting");
394   
395  38 String dir = "";
396  38 File dirFile;
397  38 try
398    {
399  38 dirFile = file.getParentFile();
400  38 dir = dirFile.getCanonicalPath();
401  38 Console.trace("BACKUPFILES dir: " + dir);
402    } catch (Exception e)
403    {
404  0 Console.error("Could not get canonical path for file '" + file + "'");
405  0 Console.error(e.getMessage());
406  0 Console.debug(Cache.getStackTraceString(e));
407  0 return false;
408    }
409  38 String filename = file.getName();
410  38 String basename = filename;
411   
412  38 Console.trace("BACKUPFILES filename is " + filename);
413  38 boolean ret = true;
414    // Create/move backups up one
415   
416  38 deleteFiles.clear();
417   
418    // find existing backup files
419  38 BackupFilenameFilter bff = new BackupFilenameFilter(basename, suffix,
420    digits);
421  38 File[] backupFiles = dirFile.listFiles(bff);
422  38 int nextIndexNum = 0;
423   
424  38 Console.trace("BACKUPFILES backupFiles.length: " + backupFiles.length);
425  38 if (backupFiles.length == 0)
426    {
427    // No other backup files. Just need to move existing file to backupfile_1
428  10 Console.trace(
429    "BACKUPFILES no existing backup files, setting index to 1");
430  10 nextIndexNum = 1;
431    }
432    else
433    {
434  28 TreeMap<Integer, File> bfTreeMap = sortBackupFilesAsTreeMap(
435    backupFiles, basename);
436    // bfTreeMap now a sorted list of <Integer index>,<File backupfile>
437    // mappings
438   
439  28 if (reverseOrder)
440    {
441    // backup style numbering
442  9 Console.trace("BACKUPFILES rolling files in reverse order");
443   
444  9 int tempMax = noMax ? -1 : max;
445    // noMax == true means no limits
446    // look for first "gap" in backupFiles
447    // if tempMax is -1 at this stage just keep going until there's a gap,
448    // then hopefully tempMax gets set to the right index (a positive
449    // integer so the loop breaks)...
450    // why do I feel a little uneasy about this loop?..
451  27 for (int i = 1; tempMax < 0 || i <= max; i++)
452    {
453  18 if (!bfTreeMap.containsKey(i)) // first index without existent
454    // backupfile
455    {
456  1 tempMax = i;
457    }
458    }
459   
460  9 File previousFile = null;
461  9 File fileToBeDeleted = null;
462  27 for (int n = tempMax; n > 0; n--)
463    {
464  18 String backupfilename = dir + File.separatorChar
465    + BackupFilenameParts.getBackupFilename(n, basename,
466    suffix, digits);
467  18 File backupfile_n = new File(backupfilename);
468   
469  18 if (!backupfile_n.exists())
470    {
471    // no "oldest" file to delete
472  1 previousFile = backupfile_n;
473  1 fileToBeDeleted = null;
474  1 Console.trace("BACKUPFILES No oldest file to delete");
475  1 continue;
476    }
477   
478    // check the modification time of this (backupfile_n) and the previous
479    // file (fileToBeDeleted) if the previous file is going to be deleted
480  17 if (fileToBeDeleted != null)
481    {
482  8 File replacementFile = backupfile_n;
483  8 long fileToBeDeletedLMT = fileToBeDeleted.lastModified();
484  8 long replacementFileLMT = replacementFile.lastModified();
485  8 Console.trace("BACKUPFILES fileToBeDeleted is "
486    + fileToBeDeleted.getAbsolutePath());
487  8 Console.trace("BACKUPFILES replacementFile is "
488    + backupfile_n.getAbsolutePath());
489   
490  8 try
491    {
492  8 File oldestTempFile = nextTempFile(fileToBeDeleted.getName(),
493    dirFile);
494   
495  8 if (fileToBeDeletedLMT > replacementFileLMT)
496    {
497  0 String fileToBeDeletedLMTString = sdf
498    .format(fileToBeDeletedLMT);
499  0 String replacementFileLMTString = sdf
500    .format(replacementFileLMT);
501  0 Console.warn("WARNING! I am set to delete backupfile "
502    + fileToBeDeleted.getName()
503    + " has modification time "
504    + fileToBeDeletedLMTString
505    + " which is newer than its replacement "
506    + replacementFile.getName()
507    + " with modification time "
508    + replacementFileLMTString);
509   
510  0 boolean delete = confirmNewerDeleteFile(fileToBeDeleted,
511    replacementFile, true);
512  0 Console.trace("BACKUPFILES "
513  0 + (delete ? "confirmed" : "not") + " deleting file "
514    + fileToBeDeleted.getAbsolutePath()
515    + " which is newer than "
516    + replacementFile.getAbsolutePath());
517   
518  0 if (delete)
519    {
520    // User has confirmed delete -- no need to add it to the list
521  0 fileToBeDeleted.delete();
522    }
523    else
524    {
525  0 Console.debug("BACKUPFILES moving "
526    + fileToBeDeleted.getAbsolutePath() + " to "
527    + oldestTempFile.getAbsolutePath());
528  0 moveFileToFile(fileToBeDeleted, oldestTempFile);
529    }
530    }
531    else
532    {
533  8 Console.debug("BACKUPFILES going to move "
534    + fileToBeDeleted.getAbsolutePath() + " to "
535    + oldestTempFile.getAbsolutePath());
536  8 moveFileToFile(fileToBeDeleted, oldestTempFile);
537  8 addDeleteFile(oldestTempFile);
538    }
539   
540    } catch (Exception e)
541    {
542  0 Console.error(
543    "Error occurred, probably making new temp file for '"
544    + fileToBeDeleted.getName() + "'");
545  0 Console.error(Cache.getStackTraceString(e));
546    }
547   
548    // reset
549  8 fileToBeDeleted = null;
550    }
551   
552  17 if (!noMax && n == tempMax && backupfile_n.exists())
553    {
554  8 fileToBeDeleted = backupfile_n;
555    }
556    else
557    {
558  9 if (previousFile != null)
559    {
560    // using boolean '&' instead of '&&' as don't want moveFileToFile
561    // attempt to be conditional (short-circuit)
562  9 ret = ret & moveFileToFile(backupfile_n, previousFile);
563    }
564    }
565   
566  17 previousFile = backupfile_n;
567    }
568   
569    // index to use for the latest backup
570  9 nextIndexNum = 1;
571    }
572    else // not reverse numbering
573    {
574    // version style numbering (with earliest file deletion if max files
575    // reached)
576   
577  19 bfTreeMap.values().toArray(backupFiles);
578  19 StringBuilder bfsb = new StringBuilder();
579  82 for (int i = 0; i < backupFiles.length; i++)
580    {
581  63 if (bfsb.length() > 0)
582    {
583  44 bfsb.append(", ");
584    }
585  63 bfsb.append(backupFiles[i].getName());
586    }
587  19 Console.trace("BACKUPFILES backupFiles: " + bfsb.toString());
588   
589    // noMax == true means keep all backup files
590  19 if ((!noMax) && bfTreeMap.size() >= max)
591    {
592  8 Console.trace("BACKUPFILES noMax: " + noMax + ", " + "max: " + max
593    + ", " + "bfTreeMap.size(): " + bfTreeMap.size());
594    // need to delete some files to keep number of backups to designated
595    // max.
596    // Note that if the suffix is not numbered then do not delete any
597    // backup files later or we'll delete the new backup file (there can
598    // be only one).
599  8 int numToDelete = suffix.indexOf(NUM_PLACEHOLDER) > -1
600    ? bfTreeMap.size() - max + 1
601    : 0;
602  8 Console.trace("BACKUPFILES numToDelete: " + numToDelete);
603    // the "replacement" file is the latest backup file being kept (it's
604    // not replacing though)
605  8 File replacementFile = numToDelete < backupFiles.length
606    ? backupFiles[numToDelete]
607    : null;
608  16 for (int i = 0; i < numToDelete; i++)
609    {
610    // check the deletion files for modification time of the last
611    // backupfile being saved
612  8 File fileToBeDeleted = backupFiles[i];
613  8 boolean delete = true;
614   
615  8 Console.trace(
616    "BACKUPFILES fileToBeDeleted: " + fileToBeDeleted);
617   
618  8 boolean newer = false;
619  8 if (replacementFile != null)
620    {
621  8 long fileToBeDeletedLMT = fileToBeDeleted.lastModified();
622  8 long replacementFileLMT = replacementFile != null
623    ? replacementFile.lastModified()
624    : Long.MAX_VALUE;
625  8 if (fileToBeDeletedLMT > replacementFileLMT)
626    {
627  0 String fileToBeDeletedLMTString = sdf
628    .format(fileToBeDeletedLMT);
629  0 String replacementFileLMTString = sdf
630    .format(replacementFileLMT);
631   
632  0 Console.warn("WARNING! I am set to delete backupfile '"
633    + fileToBeDeleted.getName()
634    + "' has modification time "
635    + fileToBeDeletedLMTString
636    + " which is newer than the oldest backupfile being kept '"
637    + replacementFile.getName()
638    + "' with modification time "
639    + replacementFileLMTString);
640   
641  0 delete = confirmNewerDeleteFile(fileToBeDeleted,
642    replacementFile, false);
643  0 if (delete)
644    {
645    // User has confirmed delete -- no need to add it to the list
646  0 fileToBeDeleted.delete();
647  0 Console.debug("BACKUPFILES deleting fileToBeDeleted: "
648    + fileToBeDeleted);
649  0 delete = false;
650    }
651    else
652    {
653    // keeping file, nothing to do!
654  0 Console.debug("BACKUPFILES keeping fileToBeDeleted: "
655    + fileToBeDeleted);
656    }
657    }
658    }
659  8 if (delete)
660    {
661  8 addDeleteFile(fileToBeDeleted);
662  8 Console.debug("BACKUPFILES addDeleteFile(fileToBeDeleted): "
663    + fileToBeDeleted);
664    }
665   
666    }
667   
668    }
669   
670  19 nextIndexNum = bfTreeMap.lastKey() + 1;
671    }
672    }
673   
674    // Let's make the new backup file!! yay, got there at last!
675  38 String latestBackupFilename = dir + File.separatorChar
676    + BackupFilenameParts.getBackupFilename(nextIndexNum, basename,
677    suffix, digits);
678  38 Console.trace("BACKUPFILES Moving old file [" + file
679    + "] to latestBackupFilename [" + latestBackupFilename + "]");
680    // using boolean '&' instead of '&&' as don't want moveFileToFile attempt to
681    // be conditional (short-circuit)
682  38 ret = ret & moveFileToFile(file, new File(latestBackupFilename));
683  38 Console.debug(
684    "BACKUPFILES moving " + file + " to " + latestBackupFilename
685  38 + " was " + (ret ? "" : "NOT ") + "successful");
686  38 if (tidyUp)
687    {
688  0 Console.debug("BACKUPFILES tidying up files");
689  0 tidyUpFiles();
690    }
691   
692  38 return ret;
693    }
694   
 
695  8 toggle private static File nextTempFile(String filename, File dirFile)
696    throws IOException
697    {
698  8 File temp = null;
699  8 COUNT: for (int i = 1; i < 1000; i++)
700    {
701  8 File trythis = new File(dirFile,
702    filename + '~' + Integer.toString(i));
703  8 if (!trythis.exists())
704    {
705  8 temp = trythis;
706  8 break COUNT;
707    }
708   
709    }
710  8 if (temp == null)
711    {
712  0 temp = File.createTempFile(filename, TEMP_FILE_EXT, dirFile);
713    }
714  8 return temp;
715    }
716   
 
717  100 toggle private void tidyUpFiles()
718    {
719  100 deleteOldFiles();
720    }
721   
 
722  0 toggle private static boolean confirmNewerDeleteFile(File fileToBeDeleted,
723    File replacementFile, boolean replace)
724    {
725  0 StringBuilder messageSB = new StringBuilder();
726   
727  0 File ftbd = fileToBeDeleted;
728  0 String ftbdLMT = sdf.format(ftbd.lastModified());
729  0 String ftbdSize = Long.toString(ftbd.length());
730   
731  0 File rf = replacementFile;
732  0 String rfLMT = sdf.format(rf.lastModified());
733  0 String rfSize = Long.toString(rf.length());
734   
735  0 int confirmButton = JvOptionPane.NO_OPTION;
736  0 if (replace)
737    {
738  0 File saveFile = null;
739  0 try
740    {
741  0 saveFile = nextTempFile(ftbd.getName(), ftbd.getParentFile());
742    } catch (Exception e)
743    {
744  0 Console.error(
745    "Error when confirming to keep backup file newer than other backup files.");
746  0 e.printStackTrace();
747    }
748  0 messageSB.append(MessageManager.formatMessage(
749    "label.newerdelete_replacement_line", new String[]
750    { ftbd.getName(), rf.getName(), ftbdLMT, rfLMT, ftbdSize,
751    rfSize }));
752    // "Backup file\n''{0}''\t(modified {2}, size {4})\nis to be deleted and
753    // replaced by apparently older file \n''{1}''\t(modified {3}, size
754    // {5}).""
755  0 messageSB.append("\n\n");
756  0 messageSB.append(MessageManager.formatMessage(
757    "label.confirm_deletion_or_rename", new String[]
758    { ftbd.getName(), saveFile.getName() }));
759    // "Confirm deletion of ''{0}'' or rename to ''{1}''?"
760  0 String[] options = new String[] {
761    MessageManager.getString("label.delete"),
762    MessageManager.getString("label.rename") };
763   
764    // TODO enable JvOptionPane to behave appropriately when batch/headless
765  0 confirmButton = Platform.isHeadless() ? JvOptionPane.YES_OPTION
766    : JvOptionPane.showOptionDialog(Desktop.getDesktopPane(),
767    messageSB.toString(),
768    MessageManager.getString(
769    "label.backupfiles_confirm_delete"),
770    JvOptionPane.YES_NO_OPTION,
771    JvOptionPane.WARNING_MESSAGE, null, options,
772    options[0]);
773    }
774    else
775    {
776  0 messageSB.append(MessageManager
777    .formatMessage("label.newerdelete_line", new String[]
778    { ftbd.getName(), rf.getName(), ftbdLMT, rfLMT, ftbdSize,
779    rfSize }));
780    // "Backup file\n''{0}''\t(modified {2}, size {4})\nis to be deleted but
781    // is newer than the oldest remaining backup file \n''{1}''\t(modified
782    // {3}, size {5})."
783  0 messageSB.append("\n\n");
784  0 messageSB.append(MessageManager
785    .formatMessage("label.confirm_deletion", new String[]
786    { ftbd.getName() }));
787    // "Confirm deletion of ''{0}''?"
788  0 String[] options = new String[] {
789    MessageManager.getString("label.delete"),
790    MessageManager.getString("label.keep") };
791   
792  0 confirmButton = Platform.isHeadless() ? JvOptionPane.YES_OPTION
793    : JvOptionPane.showOptionDialog(Desktop.getDesktopPane(),
794    messageSB.toString(),
795    MessageManager.getString("label.backupfiles_confirm_delete"),
796    JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
797    null, options, options[0]);
798    }
799   
800    // return should be TRUE if file is to be deleted
801  0 return (confirmButton == JvOptionPane.YES_OPTION);
802    }
803   
 
804  100 toggle private void deleteOldFiles()
805    {
806  100 if (deleteFiles != null && !deleteFiles.isEmpty())
807    {
808  16 boolean doDelete = false;
809  16 StringBuilder messageSB = null;
810  16 if (confirmDelete && deleteFiles.size() > 0)
811    {
812  0 messageSB = new StringBuilder();
813  0 messageSB.append(MessageManager
814    .getString("label.backupfiles_confirm_delete_old_files"));
815    // "Delete the following older backup files? (see the Backups tab in
816    // Preferences for more options)"
817  0 for (int i = 0; i < deleteFiles.size(); i++)
818    {
819  0 File df = deleteFiles.get(i);
820  0 messageSB.append("\n");
821  0 messageSB.append(df.getName());
822  0 messageSB.append(" ");
823  0 messageSB.append(MessageManager.formatMessage("label.file_info",
824    new String[]
825    { sdf.format(df.lastModified()),
826    Long.toString(df.length()) }));
827    // "(modified {0}, size {1})"
828    }
829   
830  0 int confirmButton = Platform.isHeadless() ? JvOptionPane.YES_OPTION
831    : JvOptionPane.showConfirmDialog(Desktop.getDesktopPane(),
832    messageSB.toString(),
833    MessageManager.getString(
834    "label.backupfiles_confirm_delete"),
835    // "Confirm delete"
836    JvOptionPane.YES_NO_OPTION,
837    JvOptionPane.WARNING_MESSAGE);
838   
839  0 doDelete = (confirmButton == JvOptionPane.YES_OPTION);
840    }
841    else
842    {
843  16 doDelete = true;
844    }
845   
846  16 if (doDelete)
847    {
848  32 for (int i = 0; i < deleteFiles.size(); i++)
849    {
850  16 File fileToDelete = deleteFiles.get(i);
851  16 Console.trace("BACKUPFILES about to delete fileToDelete:"
852    + fileToDelete);
853  16 fileToDelete.delete();
854  16 Console.warn("deleted '" + fileToDelete.getName() + "'");
855    }
856    }
857   
858    }
859   
860  100 deleteFiles.clear();
861    }
862   
 
863  28 toggle private TreeMap<Integer, File> sortBackupFilesAsTreeMap(
864    File[] backupFiles, String basename)
865    {
866    // sort the backup files (based on integer found in the suffix) using a
867    // precomputed Hashmap for speed
868  28 Map<Integer, File> bfHashMap = new HashMap<>();
869  108 for (int i = 0; i < backupFiles.length; i++)
870    {
871  80 File f = backupFiles[i];
872  80 BackupFilenameParts bfp = new BackupFilenameParts(f, basename, suffix,
873    digits);
874  80 bfHashMap.put(bfp.indexNum(), f);
875    }
876  28 TreeMap<Integer, File> bfTreeMap = new TreeMap<>();
877  28 bfTreeMap.putAll(bfHashMap);
878  28 return bfTreeMap;
879    }
880   
 
881  100 toggle public boolean rollBackupsAndRenameTempFile()
882    {
883  100 boolean write = this.getWriteSuccess();
884   
885  100 boolean roll = false;
886  100 boolean rename = false;
887  100 if (write)
888    {
889  100 roll = this.rollBackupFiles(false); // tidyUpFiles at the end
890  100 rename = this.renameTempFile();
891    }
892   
893    /*
894    * Not sure that this confirmation is desirable. By this stage the new file is
895    * already written successfully, but something (e.g. disk full) has happened while
896    * trying to roll the backup files, and most likely the filename needed will already
897    * be vacant so renaming the temp file is nearly always correct!
898    */
899  100 boolean okay = roll && rename;
900  100 if (!okay)
901    {
902  0 StringBuilder messageSB = new StringBuilder();
903  0 messageSB.append(MessageManager.getString(
904    "label.backupfiles_confirm_save_file_backupfiles_roll_wrong"));
905    // "Something possibly went wrong with the backups of this file."
906  0 if (rename)
907    {
908  0 if (messageSB.length() > 0)
909    {
910  0 messageSB.append("\n");
911    }
912  0 messageSB.append(MessageManager.getString(
913    "label.backupfiles_confirm_save_new_saved_file_ok"));
914    // "The new saved file seems okay."
915    }
916    else
917    {
918  0 if (messageSB.length() > 0)
919    {
920  0 messageSB.append("\n");
921    }
922  0 messageSB.append(MessageManager.getString(
923    "label.backupfiles_confirm_save_new_saved_file_not_ok"));
924    // "The new saved file might not be okay."
925    }
926  0 if (messageSB.length() > 0)
927    {
928  0 messageSB.append("\n");
929    }
930  0 messageSB
931    .append(MessageManager.getString("label.continue_operation"));
932   
933  0 int confirmButton = Platform.isHeadless() ? JvOptionPane.OK_OPTION
934    : JvOptionPane.showConfirmDialog(Desktop.getDesktopPane(),
935    messageSB.toString(),
936    MessageManager.getString(
937    "label.backupfiles_confirm_save_file"),
938    // "Confirm save file"
939    JvOptionPane.OK_OPTION, JvOptionPane.WARNING_MESSAGE);
940  0 okay = confirmButton == JvOptionPane.OK_OPTION;
941    }
942  100 if (okay)
943    {
944  100 tidyUpFiles();
945    }
946   
947    // remove this file from the save in progress stack
948  100 removeSaveInProgress(rename);
949   
950  100 return rename;
951    }
952   
 
953  21 toggle public static TreeMap<Integer, File> getBackupFilesAsTreeMap(
954    String fileName, String suffix, int digits)
955    {
956  21 File[] backupFiles = null;
957   
958  21 File file = new File(fileName);
959   
960  21 File dirFile;
961  21 try
962    {
963  21 dirFile = file.getParentFile();
964    } catch (Exception e)
965    {
966  0 Console.error("Could not get canonical path for file '" + file + "'");
967  0 return new TreeMap<>();
968    }
969   
970  21 String filename = file.getName();
971  21 String basename = filename;
972   
973    // find existing backup files
974  21 BackupFilenameFilter bff = new BackupFilenameFilter(basename, suffix,
975    digits);
976  21 backupFiles = dirFile.listFiles(bff); // is clone needed?
977   
978    // sort the backup files (based on integer found in the suffix) using a
979    // precomputed Hashmap for speed
980  21 Map<Integer, File> bfHashMap = new HashMap<>();
981  91 for (int i = 0; i < backupFiles.length; i++)
982    {
983  70 File f = backupFiles[i];
984  70 BackupFilenameParts bfp = new BackupFilenameParts(f, basename, suffix,
985    digits);
986  70 bfHashMap.put(bfp.indexNum(), f);
987    }
988  21 TreeMap<Integer, File> bfTreeMap = new TreeMap<>();
989  21 bfTreeMap.putAll(bfHashMap);
990   
991  21 return bfTreeMap;
992    }
993   
994    /*
995    private boolean addDeleteFile(File fileToBeDeleted, File originalFile,
996    boolean delete, boolean newer)
997    {
998    return addDeleteFile(fileToBeDeleted, originalFile, null, delete, newer);
999    }
1000    */
 
1001  16 toggle private boolean addDeleteFile(File fileToBeDeleted)
1002    {
1003  16 boolean ret = false;
1004  16 int pos = deleteFiles.indexOf(fileToBeDeleted);
1005  16 if (pos > -1)
1006    {
1007  0 Console.debug("BACKUPFILES not adding file "
1008    + fileToBeDeleted.getAbsolutePath()
1009    + " to the delete list (already at index" + pos + ")");
1010  0 return true;
1011    }
1012    else
1013    {
1014  16 Console.debug("BACKUPFILES adding file "
1015    + fileToBeDeleted.getAbsolutePath() + " to the delete list");
1016  16 deleteFiles.add(fileToBeDeleted);
1017    }
1018  16 return ret;
1019    }
1020   
 
1021  5 toggle public File getFile()
1022    {
1023  5 return file;
1024    }
1025   
 
1026  155 toggle public static boolean moveFileToFile(File oldFile, File newFile)
1027    {
1028  155 Console.initLogger();
1029  155 boolean ret = false;
1030  155 Path oldPath = Paths.get(oldFile.getAbsolutePath());
1031  155 Path newPath = Paths.get(newFile.getAbsolutePath());
1032  155 try
1033    {
1034    // delete destination file - not usually necessary but Just In Case...
1035  155 Console.trace("BACKUPFILES deleting " + newFile.getAbsolutePath());
1036  155 newFile.delete();
1037  155 Console.trace("BACKUPFILES moving " + oldFile.getAbsolutePath()
1038    + " to " + newFile.getAbsolutePath());
1039  155 Files.move(oldPath, newPath, StandardCopyOption.REPLACE_EXISTING);
1040  155 ret = true;
1041  155 Console.trace("BACKUPFILES move seems to have succeeded");
1042    } catch (IOException e)
1043    {
1044  0 Console.warn("Could not move file '" + oldPath.toString() + "' to '"
1045    + newPath.toString() + "'");
1046  0 Console.error(e.getMessage());
1047  0 Console.debug(Cache.getStackTraceString(e));
1048  0 ret = false;
1049    } catch (Exception e)
1050    {
1051  0 Console.error(e.getMessage());
1052  0 Console.debug(Cache.getStackTraceString(e));
1053  0 ret = false;
1054    }
1055  155 return ret;
1056    }
1057    }
  • 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.