2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
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;
33 import java.util.TreeMap;
35 import jalview.bin.Cache;
36 import jalview.gui.Desktop;
37 import jalview.gui.JvOptionPane;
38 import jalview.util.MessageManager;
41 * BackupFiles used for manipulating (naming rolling/deleting) backup/version files when an alignment or project file is saved.
42 * User configurable options are:
43 * BACKUPFILES_ENABLED - boolean flag as to whether to use this mechanism or act as before, including overwriting files as saved.
44 * The rest of the options are now saved as BACKUPFILES_PRESET, BACKUPFILES_SAVED and BACKUPFILES_CUSTOM
45 * (see BackupFilesPresetEntry)
48 public class BackupFiles
51 // labels for saved params in Cache and .jalview_properties
52 public static final String NS = "BACKUPFILES";
54 public static final String ENABLED = NS + "_ENABLED";
56 public static final String NUM_PLACEHOLDER = "%n";
58 private static final String DEFAULT_TEMP_FILE = "jalview_temp_file_" + NS;
60 private static final String TEMP_FILE_EXT = ".tmp";
62 // file - File object to be backed up and then updated (written over)
65 // enabled - default flag as to whether to do the backup file roll (if not
66 // defined in preferences)
67 private static boolean enabled;
69 // confirmDelete - default flag as to whether to confirm with the user before
70 // deleting old backup/version files
71 private static boolean confirmDelete;
73 // defaultSuffix - default template to use to append to basename of file
74 private String suffix;
76 // noMax - flag to turn off a maximum number of files
77 private boolean noMax;
79 // defaultMax - default max number of backup files
82 // defaultDigits - number of zero-led digits to use in the filename
85 // reverseOrder - set to true to make newest (latest) files lowest number
86 // (like rolled log files)
87 private boolean reverseOrder;
89 // temp saved file to become new saved file
90 private File tempFile;
92 // flag set to see if file save to temp file was successful
93 private boolean tempFileWriteSuccess;
95 // array of files to be deleted, with extra information
96 private ArrayList<File> deleteFiles = new ArrayList<>();
98 // date formatting for modification times
99 private static final SimpleDateFormat sdf = new SimpleDateFormat(
100 "yyyy-MM-dd HH:mm:ss");
102 private static final String newTempFileSuffix = "_newfile";
104 private static final String oldTempFileSuffix = "_oldfile_tobedeleted";
106 public BackupFiles(String filename)
108 this(new File(filename));
111 // first time defaults for SUFFIX, NO_MAX, ROLL_MAX, SUFFIX_DIGITS and
113 public BackupFiles(File file)
117 BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
118 .getSavedBackupEntry();
119 this.suffix = bfpe.suffix;
120 this.noMax = bfpe.keepAll;
121 this.max = bfpe.rollMax;
122 this.digits = bfpe.digits;
123 this.reverseOrder = bfpe.reverse;
125 // create a temp file to save new data in
131 String tempfilename = file.getName();
132 File tempdir = file.getParentFile();
133 temp = File.createTempFile(tempfilename,
134 TEMP_FILE_EXT + newTempFileSuffix, tempdir);
138 temp = File.createTempFile(DEFAULT_TEMP_FILE, TEMP_FILE_EXT);
140 } catch (IOException e)
143 "Could not create temp file to save into (IOException)");
144 } catch (Exception e)
146 Cache.log.error("Exception ctreating temp file for saving");
148 this.setTempFile(temp);
151 public static void classInit()
153 setEnabled(Cache.getDefault(ENABLED, true));
154 BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
155 .getSavedBackupEntry();
156 setConfirmDelete(bfpe.confirmDelete);
159 public static void setEnabled(boolean flag)
164 public static boolean getEnabled()
170 public static void setConfirmDelete(boolean flag)
172 confirmDelete = flag;
175 public static boolean getConfirmDelete()
178 return confirmDelete;
181 // set, get and rename temp file into place
182 public void setTempFile(File temp)
184 this.tempFile = temp;
187 public File getTempFile()
192 public String getTempFilePath()
197 path = this.getTempFile().getCanonicalPath();
198 } catch (IOException e)
201 "IOException when getting Canonical Path of temp file '"
202 + this.getTempFile().getName() + "'");
207 public boolean setWriteSuccess(boolean flag)
209 boolean old = this.tempFileWriteSuccess;
210 this.tempFileWriteSuccess = flag;
214 public boolean getWriteSuccess()
216 return this.tempFileWriteSuccess;
219 public boolean renameTempFile()
221 return moveFileToFile(tempFile, file);
224 // roll the backupfiles
225 public boolean rollBackupFiles()
227 return this.rollBackupFiles(true);
230 public boolean rollBackupFiles(boolean tidyUp)
232 // file doesn't yet exist or backups are not enabled or template is null or
234 if ((!file.exists()) || (!enabled) || max < 0 || suffix == null
235 || suffix.length() == 0)
238 Cache.log.debug("BACKUPFILES rollBackupFiles nothing to do." + ", "
239 + "filename: " + (file != null ? file.getName() : "null")
240 + ", " + "file exists: " + file.exists() + ", " + "enabled: "
241 + enabled + ", " + "max: " + max + ", " + "suffix: '" + suffix
250 dirFile = file.getParentFile();
251 dir = dirFile.getCanonicalPath();
252 Cache.log.debug("BACKUPFILES: dir: " + dir);
253 } catch (Exception e)
256 "Could not get canonical path for file '" + file + "'");
259 String filename = file.getName();
260 String basename = filename;
263 // Create/move backups up one
267 // find existing backup files
268 BackupFilenameFilter bff = new BackupFilenameFilter(basename, suffix,
270 File[] backupFiles = dirFile.listFiles(bff);
271 int nextIndexNum = 0;
274 .debug("BACKUPFILES backupFiles.length: " + backupFiles.length);
275 if (backupFiles.length == 0)
277 // No other backup files. Just need to move existing file to backupfile_1
282 TreeMap<Integer, File> bfTreeMap = sortBackupFilesAsTreeMap(
283 backupFiles, basename);
284 // bfTreeMap now a sorted list of <Integer index>,<File backupfile>
289 // backup style numbering
291 int tempMax = noMax ? -1 : max;
292 // noMax == true means no limits
293 // look for first "gap" in backupFiles
294 // if tempMax is -1 at this stage just keep going until there's a gap,
295 // then hopefully tempMax gets set to the right index (a positive
296 // integer so the loop breaks)...
297 // why do I feel a little uneasy about this loop?..
298 for (int i = 1; tempMax < 0 || i <= max; i++)
300 if (!bfTreeMap.containsKey(i)) // first index without existent
307 File previousFile = null;
308 File fileToBeDeleted = null;
309 for (int n = tempMax; n > 0; n--)
311 String backupfilename = dir + File.separatorChar
312 + BackupFilenameParts.getBackupFilename(n, basename,
314 File backupfile_n = new File(backupfilename);
316 if (!backupfile_n.exists())
318 // no "oldest" file to delete
319 previousFile = backupfile_n;
320 fileToBeDeleted = null;
324 // check the modification time of this (backupfile_n) and the previous
325 // file (fileToBeDeleted) if the previous file is going to be deleted
326 if (fileToBeDeleted != null)
328 File replacementFile = backupfile_n;
329 long fileToBeDeletedLMT = fileToBeDeleted.lastModified();
330 long replacementFileLMT = replacementFile.lastModified();
334 File oldestTempFile = nextTempFile(fileToBeDeleted.getName(),
337 if (fileToBeDeletedLMT > replacementFileLMT)
339 String fileToBeDeletedLMTString = sdf
340 .format(fileToBeDeletedLMT);
341 String replacementFileLMTString = sdf
342 .format(replacementFileLMT);
343 Cache.log.warn("WARNING! I am set to delete backupfile "
344 + fileToBeDeleted.getName()
345 + " has modification time "
346 + fileToBeDeletedLMTString
347 + " which is newer than its replacement "
348 + replacementFile.getName()
349 + " with modification time "
350 + replacementFileLMTString);
352 boolean delete = confirmNewerDeleteFile(fileToBeDeleted,
353 replacementFile, true);
357 // User has confirmed delete -- no need to add it to the list
358 fileToBeDeleted.delete();
362 moveFileToFile(fileToBeDeleted, oldestTempFile);
367 moveFileToFile(fileToBeDeleted, oldestTempFile);
368 addDeleteFile(oldestTempFile);
371 } catch (Exception e)
374 "Error occurred, probably making new temp file for '"
375 + fileToBeDeleted.getName() + "'");
376 Cache.log.error(e.getStackTrace());
380 fileToBeDeleted = null;
383 if (!noMax && n == tempMax && backupfile_n.exists())
385 fileToBeDeleted = backupfile_n;
389 if (previousFile != null)
391 ret = ret && moveFileToFile(backupfile_n, previousFile);
395 previousFile = backupfile_n;
398 // index to use for the latest backup
401 else // not reverse numbering
403 // version style numbering (with earliest file deletion if max files
406 bfTreeMap.values().toArray(backupFiles);
407 StringBuilder bfsb = new StringBuilder();
408 for (int i = 0; i < backupFiles.length; i++)
410 if (bfsb.length() > 0)
414 bfsb.append(backupFiles[i].getName());
416 Cache.log.debug("BACKUPFILES backupFiles: " + bfsb.toString());
418 // noMax == true means keep all backup files
419 if ((!noMax) && bfTreeMap.size() >= max)
421 Cache.log.debug("BACKUPFILES noMax: " + noMax + ", " + "max: "
422 + max + ", " + "bfTreeMap.size(): " + bfTreeMap.size());
423 // need to delete some files to keep number of backups to designated
425 // Note that if the suffix is not numbered then do not delete any
426 // backup files later or we'll delete the new backup file (there can
428 int numToDelete = suffix.indexOf(NUM_PLACEHOLDER) > -1
429 ? bfTreeMap.size() - max + 1
431 Cache.log.debug("BACKUPFILES numToDelete: " + numToDelete);
432 // the "replacement" file is the latest backup file being kept (it's
433 // not replacing though)
434 File replacementFile = numToDelete < backupFiles.length
435 ? backupFiles[numToDelete]
437 for (int i = 0; i < numToDelete; i++)
439 // check the deletion files for modification time of the last
440 // backupfile being saved
441 File fileToBeDeleted = backupFiles[i];
442 boolean delete = true;
445 "BACKUPFILES fileToBeDeleted: " + fileToBeDeleted);
447 boolean newer = false;
448 if (replacementFile != null)
450 long fileToBeDeletedLMT = fileToBeDeleted.lastModified();
451 long replacementFileLMT = replacementFile != null
452 ? replacementFile.lastModified()
454 if (fileToBeDeletedLMT > replacementFileLMT)
456 String fileToBeDeletedLMTString = sdf
457 .format(fileToBeDeletedLMT);
458 String replacementFileLMTString = sdf
459 .format(replacementFileLMT);
461 Cache.log.warn("WARNING! I am set to delete backupfile '"
462 + fileToBeDeleted.getName()
463 + "' has modification time "
464 + fileToBeDeletedLMTString
465 + " which is newer than the oldest backupfile being kept '"
466 + replacementFile.getName()
467 + "' with modification time "
468 + replacementFileLMTString);
470 delete = confirmNewerDeleteFile(fileToBeDeleted,
471 replacementFile, false);
474 // User has confirmed delete -- no need to add it to the list
475 fileToBeDeleted.delete();
476 Cache.log.debug("BACKUPFILES deleting fileToBeDeleted: "
482 // keeping file, nothing to do!
483 Cache.log.debug("BACKUPFILES keeping fileToBeDeleted: "
490 addDeleteFile(fileToBeDeleted);
491 Cache.log.debug("BACKUPFILES addDeleteFile(fileToBeDelted): "
499 nextIndexNum = bfTreeMap.lastKey() + 1;
503 // Let's make the new backup file!! yay, got there at last!
504 String latestBackupFilename = dir + File.separatorChar
505 + BackupFilenameParts.getBackupFilename(nextIndexNum, basename,
507 Cache.log.debug("BACKUPFILES Moving old file [" + file
508 + "] to latestBackupFilename [" + latestBackupFilename + "]");
509 ret |= moveFileToFile(file, new File(latestBackupFilename));
510 Cache.log.debug("BACKUPFILES moving " + latestBackupFilename + " to "
511 + file + " was " + (ret ? "" : "NOT ") + "successful");
515 Cache.log.debug("BACKUPFILES tidying up files");
522 private static File nextTempFile(String filename, File dirFile)
526 COUNT: for (int i = 1; i < 1000; i++)
528 File trythis = new File(dirFile,
529 filename + '~' + Integer.toString(i));
530 if (!trythis.exists())
539 temp = File.createTempFile(filename, TEMP_FILE_EXT, dirFile);
544 private void tidyUpFiles()
549 private static boolean confirmNewerDeleteFile(File fileToBeDeleted,
550 File replacementFile, boolean replace)
552 StringBuilder messageSB = new StringBuilder();
554 File ftbd = fileToBeDeleted;
555 String ftbdLMT = sdf.format(ftbd.lastModified());
556 String ftbdSize = Long.toString(ftbd.length());
558 File rf = replacementFile;
559 String rfLMT = sdf.format(rf.lastModified());
560 String rfSize = Long.toString(rf.length());
562 int confirmButton = JvOptionPane.NO_OPTION;
565 File saveFile = null;
568 saveFile = nextTempFile(ftbd.getName(), ftbd.getParentFile());
569 } catch (Exception e)
572 "Error when confirming to keep backup file newer than other backup files.");
575 messageSB.append(MessageManager.formatMessage(
576 "label.newerdelete_replacement_line", new String[]
577 { ftbd.getName(), rf.getName(), ftbdLMT, rfLMT, ftbdSize,
579 // "Backup file\n''{0}''\t(modified {2}, size {4})\nis to be deleted and
580 // replaced by apparently older file \n''{1}''\t(modified {3}, size
582 messageSB.append("\n\n");
583 messageSB.append(MessageManager.formatMessage(
584 "label.confirm_deletion_or_rename", new String[]
585 { ftbd.getName(), saveFile.getName() }));
586 // "Confirm deletion of ''{0}'' or rename to ''{1}''?"
587 String[] options = new String[] {
588 MessageManager.getString("label.delete"),
589 MessageManager.getString("label.rename") };
591 confirmButton = JvOptionPane.showOptionDialog(Desktop.desktop,
592 messageSB.toString(),
593 MessageManager.getString("label.backupfiles_confirm_delete"),
595 JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
596 null, options, options[0]);
600 messageSB.append(MessageManager
601 .formatMessage("label.newerdelete_line", new String[]
602 { ftbd.getName(), rf.getName(), ftbdLMT, rfLMT, ftbdSize,
604 // "Backup file\n''{0}''\t(modified {2}, size {4})\nis to be deleted but
605 // is newer than the oldest remaining backup file \n''{1}''\t(modified
607 messageSB.append("\n\n");
608 messageSB.append(MessageManager
609 .formatMessage("label.confirm_deletion", new String[]
610 { ftbd.getName() }));
611 // "Confirm deletion of ''{0}''?"
612 String[] options = new String[] {
613 MessageManager.getString("label.delete"),
614 MessageManager.getString("label.keep") };
616 confirmButton = JvOptionPane.showOptionDialog(Desktop.desktop,
617 messageSB.toString(),
618 MessageManager.getString("label.backupfiles_confirm_delete"),
620 JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
621 null, options, options[0]);
624 // return should be TRUE if file is to be deleted
625 return (confirmButton == JvOptionPane.YES_OPTION);
628 private void deleteOldFiles()
630 if (deleteFiles != null && !deleteFiles.isEmpty())
632 boolean doDelete = false;
633 StringBuilder messageSB = null;
634 if (confirmDelete && deleteFiles.size() > 0)
636 messageSB = new StringBuilder();
637 messageSB.append(MessageManager
638 .getString("label.backupfiles_confirm_delete_old_files"));
639 // "Delete the following older backup files? (see the Backups tab in
640 // Preferences for more options)"
641 for (int i = 0; i < deleteFiles.size(); i++)
643 File df = deleteFiles.get(i);
644 messageSB.append("\n");
645 messageSB.append(df.getName());
646 messageSB.append(" ");
647 messageSB.append(MessageManager.formatMessage("label.file_info",
649 { sdf.format(df.lastModified()),
650 Long.toString(df.length()) }));
651 // "(modified {0}, size {1})"
654 int confirmButton = JvOptionPane.showConfirmDialog(Desktop.desktop,
655 messageSB.toString(),
657 .getString("label.backupfiles_confirm_delete"),
659 JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE);
661 doDelete = (confirmButton == JvOptionPane.YES_OPTION);
670 for (int i = 0; i < deleteFiles.size(); i++)
672 File fileToDelete = deleteFiles.get(i);
674 "BACKUPFILES deleting fileToDelete:" + fileToDelete);
675 fileToDelete.delete();
676 Cache.log.warn("deleting '" + fileToDelete.getName() + "'");
685 private TreeMap<Integer, File> sortBackupFilesAsTreeMap(
686 File[] backupFiles, String basename)
688 // sort the backup files (based on integer found in the suffix) using a
689 // precomputed Hashmap for speed
690 Map<Integer, File> bfHashMap = new HashMap<>();
691 for (int i = 0; i < backupFiles.length; i++)
693 File f = backupFiles[i];
694 BackupFilenameParts bfp = new BackupFilenameParts(f, basename, suffix,
696 bfHashMap.put(bfp.indexNum(), f);
698 TreeMap<Integer, File> bfTreeMap = new TreeMap<>();
699 bfTreeMap.putAll(bfHashMap);
703 public boolean rollBackupsAndRenameTempFile()
705 boolean write = this.getWriteSuccess();
707 boolean roll = false;
708 boolean rename = false;
711 roll = this.rollBackupFiles(false); // tidyUpFiles at the end
712 rename = this.renameTempFile();
716 * Not sure that this confirmation is desirable. By this stage the new file is
717 * already written successfully, but something (e.g. disk full) has happened while
718 * trying to roll the backup files, and most likely the filename needed will already
719 * be vacant so renaming the temp file is nearly always correct!
721 boolean okay = roll && rename;
724 boolean yesno = false;
725 StringBuilder messageSB = new StringBuilder();
726 messageSB.append(MessageManager.getString(
727 "label.backupfiles_confirm_save_file_backupfiles_roll_wrong"));
728 // "Something possibly went wrong with the backups of this file."
731 if (messageSB.length() > 0)
733 messageSB.append("\n");
735 messageSB.append(MessageManager.getString(
736 "label.backupfiles_confirm_save_new_saved_file_ok"));
737 // "The new saved file seems okay."
741 if (messageSB.length() > 0)
743 messageSB.append("\n");
745 messageSB.append(MessageManager.getString(
746 "label.backupfiles_confirm_save_new_saved_file_not_ok"));
747 // "The new saved file might not be okay."
750 int confirmButton = JvOptionPane.showConfirmDialog(Desktop.desktop,
751 messageSB.toString(),
753 .getString("label.backupfiles_confirm_save_file"),
754 // "Confirm save file"
755 JvOptionPane.OK_OPTION, JvOptionPane.WARNING_MESSAGE);
756 okay = confirmButton == JvOptionPane.OK_OPTION;
766 public static TreeMap<Integer, File> getBackupFilesAsTreeMap(
767 String fileName, String suffix, int digits)
769 File[] backupFiles = null;
771 File file = new File(fileName);
776 dirFile = file.getParentFile();
777 } catch (Exception e)
780 "Could not get canonical path for file '" + file + "'");
781 return new TreeMap<>();
784 String filename = file.getName();
785 String basename = filename;
787 // find existing backup files
788 BackupFilenameFilter bff = new BackupFilenameFilter(basename, suffix,
790 backupFiles = dirFile.listFiles(bff); // is clone needed?
792 // sort the backup files (based on integer found in the suffix) using a
793 // precomputed Hashmap for speed
794 Map<Integer, File> bfHashMap = new HashMap<>();
795 for (int i = 0; i < backupFiles.length; i++)
797 File f = backupFiles[i];
798 BackupFilenameParts bfp = new BackupFilenameParts(f, basename, suffix,
800 bfHashMap.put(bfp.indexNum(), f);
802 TreeMap<Integer, File> bfTreeMap = new TreeMap<>();
803 bfTreeMap.putAll(bfHashMap);
809 private boolean addDeleteFile(File fileToBeDeleted, File originalFile,
810 boolean delete, boolean newer)
812 return addDeleteFile(fileToBeDeleted, originalFile, null, delete, newer);
815 private boolean addDeleteFile(File fileToBeDeleted)
818 int pos = deleteFiles.indexOf(fileToBeDeleted);
825 deleteFiles.add(fileToBeDeleted);
830 public static boolean moveFileToFile(File oldFile, File newFile)
833 Path oldPath = Paths.get(oldFile.getAbsolutePath());
834 Path newPath = Paths.get(newFile.getAbsolutePath());
837 // delete destination file - not usually necessary but Just In Case...
839 Files.move(oldPath, newPath, StandardCopyOption.REPLACE_EXISTING);
841 } catch (IOException e)
843 Cache.log.warn("Could not move file '" + oldPath.toString() + "' to '"
844 + newPath.toString() + "'");
845 Cache.log.error(e.getStackTrace());
847 } catch (Exception e)
849 Cache.log.error(e.getMessage());
850 Cache.log.error(e.getStackTrace());