3 import jalview.bin.Cache;
4 import jalview.gui.Desktop;
5 import jalview.gui.JvOptionPane;
6 import jalview.util.MessageManager;
9 import java.io.IOException;
10 import java.util.Arrays;
11 import java.util.HashMap;
12 import java.util.TreeMap;
15 * BackupFiles used for manipulating (naming rolling/deleting) backup/version files when an alignment or project file is saved.
16 * User configurable options are:
17 * BACKUPFILES_ENABLED - boolean flag as to whether to use this mechanism or act as before, including overwriting files as saved.
18 * BACKUPFILES_SUFFIX - a template to insert just before the file extension. Use '%n' to be replaced by a 0-led SUFFIX_DIGITS long integer.
19 * BACKUPFILES_NO_MAX - flag to turn off setting a maximum number of backup files to keep.
20 * BACKUPFILES_ROLL_MAX - the maximum number of backupfiles to keep for any one alignment or project file.
21 * BACKUPFILES_SUFFIX_DIGITS - the number of digits to insert replace %n with (e.g. BACKUPFILES_SUFFIX_DIGITS = 3 would make "001", "002", etc)
22 * BACKUPFILES_REVERSE_ORDER - if true then "logfile" style numbering and file rolling will occur. If false then ever-increasing version numbering will occur, but old files will still be deleted if there are more than ROLL_MAX backup files.
23 * BACKUPFILES_CONFIRM_DELETE_OLD - if true then prompt/confirm with the user when deleting older backup/version files.
26 public class BackupFiles
29 // labels for saved params in Cache and .jalview_properties
30 private static String NS = "BACKUPFILES";
32 public static String ENABLED = NS + "_ENABLED";
34 public static String SUFFIX = NS + "_SUFFIX";
36 public static String NO_MAX = NS + "_NO_MAX";
38 public static String ROLL_MAX = NS + "_ROLL_MAX";
40 public static String SUFFIX_DIGITS = NS + "_SUFFIX_DIGITS";
42 protected static String NUM_PLACEHOLDER = "%n";
44 public static String REVERSE_ORDER = NS + "_REVERSE_ORDER";
46 public static String CONFIRM_DELETE_OLD = NS + "_CONFIRM_DELETE_OLD";
48 private static String DEFAULT_TEMP_FILE = "jalview_temp_file_" + NS;
50 // file - File object to be backed up and then updated (written over)
53 // enabled - default flag as to whether to do the backup file roll (if not
54 // defined in preferences)
55 private static boolean enabled;
57 // confirmDelete - default flag as to whether to confirm with the user before
58 // deleting old backup/version files
59 private static boolean confirmDelete;
61 // defaultSuffix - default template to use to append to basename of file
62 private String suffix;
64 // noMax - flag to turn off a maximum number of files
65 private boolean noMax;
67 // defaultMax - default max number of backup files
70 // defaultDigits - number of zero-led digits to use in the filename
73 // reverseOrder - set to true to make newest (latest) files lowest number
74 // (like rolled log files)
75 private boolean reverseOrder;
77 // temp saved file to become new saved file
78 private File tempFile;
80 // flag set to see if file save to temp file was successful
81 private boolean tempFileWriteSuccess;
83 public BackupFiles(String filename)
85 this(new File(filename));
88 // first time defaults for SUFFIX, NO_MAX, ROLL_MAX, SUFFIX_DIGITS and
90 public BackupFiles(File file)
92 this(file, "-v" + NUM_PLACEHOLDER, false, 4, 3, false);
95 public BackupFiles(File file,
96 String defaultSuffix, boolean defaultNoMax, int defaultMax,
98 boolean defaultReverseOrder)
102 this.suffix = Cache.getDefault(SUFFIX, defaultSuffix);
103 this.noMax = Cache.getDefault(NO_MAX, defaultNoMax);
104 this.max = Cache.getDefault(ROLL_MAX, defaultMax);
105 this.digits = Cache.getDefault(SUFFIX_DIGITS, defaultDigits);
106 this.reverseOrder = Cache.getDefault(REVERSE_ORDER,
107 defaultReverseOrder);
109 // create a temp file to save new data in
115 String tempfilename = file.getName();
116 File tempdir = file.getParentFile();
117 temp = File.createTempFile(tempfilename, ".tmp", tempdir);
121 temp = File.createTempFile(DEFAULT_TEMP_FILE, ".tmp");
123 } catch (IOException e)
126 "Could not create temp file to save into (IOException)");
127 } catch (Exception e)
129 System.out.println("Exception ctreating temp file for saving");
131 this.setTempFile(temp);
134 public static void classInit()
136 setEnabled(Cache.getDefault(ENABLED, true));
137 setConfirmDelete(Cache.getDefault(CONFIRM_DELETE_OLD, true));
140 public static void setEnabled(boolean flag)
145 public static boolean getEnabled()
151 public static void setConfirmDelete(boolean flag)
153 confirmDelete = flag;
156 public static boolean getConfirmDelete()
159 return confirmDelete;
162 // set, get and rename temp file into place
163 public void setTempFile(File temp)
165 this.tempFile = temp;
168 public File getTempFile()
173 public String getTempFilePath()
178 path = this.getTempFile().getCanonicalPath();
179 } catch (IOException e)
182 "IOException when getting Canonical Path of temp file '"
183 + this.getTempFile().getName() + "'");
188 public static String getNumPlaceHolder()
190 return NUM_PLACEHOLDER;
193 public boolean setWriteSuccess(boolean flag)
195 boolean old = this.tempFileWriteSuccess;
196 this.tempFileWriteSuccess = flag;
200 public boolean getWriteSuccess()
202 return this.tempFileWriteSuccess;
205 public boolean renameTempFile()
207 return tempFile.renameTo(file);
211 // roll the backupfiles
212 public boolean rollBackupFiles()
215 // file doesn't yet exist or backups are not enabled
216 if ((!file.exists()) || (!enabled) || (max < 0))
222 // split filename up to insert suffix template in the right place. template
223 // and backupMax can be set in .jalview_properties
228 dirFile = file.getParentFile();
229 dir = dirFile.getCanonicalPath();
230 } catch (Exception e)
233 "Could not get canonical path for file '" + file + "'");
236 String filename = file.getName();
237 String basename = filename;
238 String extension = "";
239 int dotcharpos = filename.lastIndexOf('.');
240 // don't split of filenames with the last '.' at the very beginning or
241 // very end of the filename
242 if ((dotcharpos > 0) && (dotcharpos < filename.length() - 1))
244 basename = filename.substring(0, dotcharpos);
245 extension = filename.substring(dotcharpos); // NOTE this includes the '.'
249 // Create/move backups up one
251 File[] oldFilesToDelete = null;
253 // find existing backup files
254 BackupFilenameFilter bff = new BackupFilenameFilter(basename, suffix,
257 File[] backupFiles = dirFile.listFiles(bff);
258 int nextIndexNum = 0;
259 String confirmDeleteExtraInfo = null;
261 if (backupFiles.length == 0)
263 // No other backup files. Just need to move existing file to backupfile_1
269 // sort the backup files (based on integer found in the suffix) using a
270 // precomputed Hashmap for speed
271 HashMap<Integer, File> bfHashMap = new HashMap<>();
272 for (int i = 0; i < backupFiles.length; i++)
274 File f = backupFiles[i];
275 BackupFilenameParts bfp = new BackupFilenameParts(f, basename, suffix, digits, extension);
276 bfHashMap.put(bfp.indexNum(), f);
278 TreeMap<Integer, File> bfTreeMap = new TreeMap<>();
279 bfTreeMap.putAll(bfHashMap);
283 // backup style numbering
285 File lastfile = null;
286 int tempMax = noMax ? -1 : max;
287 // noMax == true means no limits
288 // look for first "gap" in backupFiles
289 // if tempMax is -1 at this stage just keep going until there's a gap,
290 // then hopefully tempMax gets set to the right index (a positive
291 // integer so the loop breaks)...
292 // why do I feel a little uneasy about this loop?..
293 for (int i = 1; tempMax < 0 || i <= max; i++)
295 if (!bfTreeMap.containsKey(i)) // first index without existent
302 // for (int m = 0; m < tempMax; m++)
303 for (int n = tempMax; n > 0; n--)
305 // int n = tempMax - m;
306 String backupfilename = dir + File.separatorChar
307 + BackupFilenameFilter.getBackupFilename(n, basename,
308 suffix, digits, extension);
309 File backupfile_n = new File(backupfilename);
311 if (!backupfile_n.exists())
313 lastfile = backupfile_n;
317 // if (m == 0 && backupfile_n.exists())
318 if ((!noMax) && n == tempMax && backupfile_n.exists())
320 // move the largest (max) rolled file to a temp file and add to the delete list
323 File temp = File.createTempFile(backupfilename, ".tmp",
325 backupfile_n.renameTo(temp);
327 oldFilesToDelete = new File[] { temp };
328 confirmDeleteExtraInfo = "(was " + backupfile_n.getName()
330 } catch (IOException e)
333 "IOException when creating temporary file for backupfilename");
339 if (lastfile != null)
341 ret = ret && backupfile_n.renameTo(lastfile);
345 lastfile = backupfile_n;
348 // index to use for the latest backup
353 // version style numbering (with earliest file deletion if max files
357 bfTreeMap.values().toArray(backupFiles);
359 // noMax == true means keep all backup files
360 if ((!noMax) && bfTreeMap.size() >= max)
362 // need to delete some files to keep number of backups to designated
364 int numToDelete = bfTreeMap.size() - max + 1;
365 oldFilesToDelete = Arrays.copyOfRange(backupFiles, 0,
370 nextIndexNum = bfTreeMap.lastKey() + 1;
375 if (oldFilesToDelete != null && oldFilesToDelete.length > 0)
377 // delete old backup/version files
379 boolean delete = false;
382 // Object[] confirmMessageArray = {};
383 StringBuilder confirmMessage = new StringBuilder();
384 confirmMessage.append(MessageManager
385 .getString("label.backupfiles_confirm_delete_old_files"));
386 for (File f : oldFilesToDelete)
388 confirmMessage.append("\n");
389 confirmMessage.append(f.getName());
391 if (confirmDeleteExtraInfo != null
392 && confirmDeleteExtraInfo.length() > 0)
394 confirmMessage.append("\n");
395 confirmMessage.append(confirmDeleteExtraInfo);
397 int confirm = JvOptionPane.showConfirmDialog(Desktop.desktop,
398 confirmMessage.toString(),
400 .getString("label.backupfiles_confirm_delete"),
401 JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE);
403 delete = (confirm == JvOptionPane.YES_OPTION);
412 for (int i = 0; i < oldFilesToDelete.length; i++)
414 File fileToDelete = oldFilesToDelete[i];
415 fileToDelete.delete();
416 // System.out.println("DELETING '" + fileToDelete.getName() +
423 // Let's make the new backup file!! yay, got there at last!
424 String latestBackupFilename = dir + File.separatorChar
425 + BackupFilenameFilter.getBackupFilename(nextIndexNum, basename,
426 suffix, digits, extension);
427 File latestBackupFile = new File(latestBackupFilename);
428 ret = ret && file.renameTo(latestBackupFile);
433 public boolean rollBackupsAndRenameTempFile()
435 boolean write = this.getWriteSuccess();
437 boolean roll = false;
439 roll = this.rollBackupFiles();
445 * Not sure that this confirmation is desirable. By this stage the new file is
446 * already written successfully, but something (e.g. disk full) has happened while
447 * trying to roll the backup files, and most likely the filename needed will already
448 * be vacant so renaming the temp file is nearly always correct!
452 int confirm = JvOptionPane.showConfirmDialog(Desktop.desktop,
453 MessageManager.getString(
454 "label.backupfiles_confirm_save_file_backupfiles_roll_wrong"),
455 MessageManager.getString("label.backupfiles_confirm_save_file"),
456 JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE);
458 if (confirm == JvOptionPane.YES_OPTION)
464 boolean rename = false;
467 rename = this.renameTempFile();
473 public static TreeMap<Integer, File> lsBackupFilesAsTreeMap(
475 String suffix, int digits)
477 File[] backupFiles = null;
479 File file = new File(fileName);
485 dirFile = file.getParentFile();
486 dir = dirFile.getCanonicalPath();
487 } catch (Exception e)
490 "Could not get canonical path for file '" + file + "'");
491 return new TreeMap<>();
494 String filename = file.getName();
495 String basename = filename;
496 String extension = "";
497 int dotcharpos = filename.lastIndexOf('.');
498 // don't split of filenames with the last '.' at the very beginning or
499 // very end of the filename
500 if ((dotcharpos > 0) && (dotcharpos < filename.length() - 1))
502 basename = filename.substring(0, dotcharpos);
503 extension = filename.substring(dotcharpos); // NOTE this includes the '.'
506 // find existing backup files
507 BackupFilenameFilter bff = new BackupFilenameFilter(basename, suffix, digits, extension);
508 backupFiles = dirFile.listFiles(bff); // is clone needed?
510 // sort the backup files (based on integer found in the suffix) using a
511 // precomputed Hashmap for speed
512 HashMap<Integer, File> bfHashMap = new HashMap<>();
513 for (int i = 0; i < backupFiles.length; i++)
515 File f = backupFiles[i];
516 BackupFilenameParts bfp = new BackupFilenameParts(f, basename, suffix,
518 bfHashMap.put(bfp.indexNum(), f);
520 TreeMap<Integer, File> bfTreeMap = new TreeMap<>();
521 bfTreeMap.putAll(bfHashMap);
526 public static File[] lsBackupFiles(String fileName, String suffix,
529 TreeMap<Integer, File> bfTreeMap = lsBackupFilesAsTreeMap(fileName,
531 File[] backupFiles = new File[bfTreeMap.size()];
532 bfTreeMap.values().toArray(backupFiles);