/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
import jalview.bin.Cache;
import jalview.gui.Desktop;
import jalview.gui.JvOptionPane;
import jalview.util.MessageManager;
import jalview.util.Platform;
import java.io.File;
import java.io.IOException;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Map;
import java.util.TreeMap;
/*
* BackupFiles used for manipulating (naming rolling/deleting) backup/version files when an alignment or project file is saved.
* User configurable options are:
* BACKUPFILES_ENABLED - boolean flag as to whether to use this mechanism or act as before, including overwriting files as saved.
* The rest of the options are now saved as BACKUPFILES_PRESET, BACKUPFILES_SAVED and BACKUPFILES_CUSTOM
* (see BackupFilesPresetEntry)
*/
public class BackupFiles
{
// labels for saved params in Cache and .jalview_properties
public static final String NS = "BACKUPFILES";
public static final String ENABLED = NS + "_ENABLED";
public static final String NUM_PLACEHOLDER = "%n";
private static final String DEFAULT_TEMP_FILE = "jalview_temp_file_" + NS;
private static final String TEMP_FILE_EXT = ".tmp";
// file - File object to be backed up and then updated (written over)
private File file;
// enabled - default flag as to whether to do the backup file roll (if not
// defined in preferences)
private static boolean enabled;
// confirmDelete - default flag as to whether to confirm with the user before
// deleting old backup/version files
private static boolean confirmDelete;
// defaultSuffix - default template to use to append to basename of file
private String suffix;
// noMax - flag to turn off a maximum number of files
private boolean noMax;
// defaultMax - default max number of backup files
private int max;
// defaultDigits - number of zero-led digits to use in the filename
private int digits;
// reverseOrder - set to true to make newest (latest) files lowest number
// (like rolled log files)
private boolean reverseOrder;
// temp saved file to become new saved file
private File tempFile;
// flag set to see if file save to temp file was successful
private boolean tempFileWriteSuccess;
// array of files to be deleted, with extra information
private ArrayList deleteFiles = new ArrayList<>();
// date formatting for modification times
private static final SimpleDateFormat sdf = new SimpleDateFormat(
"yyyy-MM-dd HH:mm:ss");
public BackupFiles(String filename)
{
this(new File(filename));
}
// first time defaults for SUFFIX, NO_MAX, ROLL_MAX, SUFFIX_DIGITS and
// REVERSE_ORDER
public BackupFiles(File file)
{
classInit();
this.file = file;
BackupFilesPresetEntry bfpe = BackupFilesPresetEntry.getSavedBackupEntry();
this.suffix = bfpe.suffix;
this.noMax = bfpe.keepAll;
this.max = bfpe.rollMax;
this.digits = bfpe.digits;
this.reverseOrder = bfpe.reverse;
// create a temp file to save new data in
File temp = null;
try
{
if (file != null)
{
String tempfilename = file.getName();
File tempdir = file.getParentFile();
temp = File.createTempFile(tempfilename, TEMP_FILE_EXT + "_newfile",
tempdir);
}
else
{
temp = File.createTempFile(DEFAULT_TEMP_FILE, TEMP_FILE_EXT);
}
} catch (IOException e)
{
System.out.println(
"Could not create temp file to save into (IOException)");
} catch (Exception e)
{
System.out.println("Exception ctreating temp file for saving");
}
this.setTempFile(temp);
}
public static void classInit()
{
setEnabled(Cache.getDefault(ENABLED, !Platform.isJS()));
BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
.getSavedBackupEntry();
setConfirmDelete(bfpe.confirmDelete);
}
public static void setEnabled(boolean flag)
{
enabled = flag;
}
public static boolean getEnabled()
{
classInit();
return enabled;
}
public static void setConfirmDelete(boolean flag)
{
confirmDelete = flag;
}
public static boolean getConfirmDelete()
{
classInit();
return confirmDelete;
}
// set, get and rename temp file into place
public void setTempFile(File temp)
{
this.tempFile = temp;
}
public File getTempFile()
{
return tempFile;
}
public String getTempFilePath()
{
String path = null;
try
{
path = this.getTempFile().getCanonicalPath();
} catch (IOException e)
{
System.out.println(
"IOException when getting Canonical Path of temp file '"
+ this.getTempFile().getName() + "'");
}
return path;
}
public boolean setWriteSuccess(boolean flag)
{
boolean old = this.tempFileWriteSuccess;
this.tempFileWriteSuccess = flag;
return old;
}
public boolean getWriteSuccess()
{
return this.tempFileWriteSuccess;
}
public boolean renameTempFile()
{
return tempFile.renameTo(file);
}
// roll the backupfiles
public boolean rollBackupFiles()
{
return this.rollBackupFiles(true);
}
public boolean rollBackupFiles(boolean tidyUp)
{
// file doesn't yet exist or backups are not enabled or template is null or
// empty
if ((!file.exists()) || (!enabled) || max < 0 || suffix == null
|| suffix.length() == 0)
{
// nothing to do
return true;
}
String dir = "";
File dirFile;
try
{
dirFile = file.getParentFile();
dir = dirFile.getCanonicalPath();
} catch (Exception e)
{
System.out.println(
"Could not get canonical path for file '" + file + "'");
return false;
}
String filename = file.getName();
String basename = filename;
boolean ret = true;
// Create/move backups up one
deleteFiles.clear();
// find existing backup files
BackupFilenameFilter bff = new BackupFilenameFilter(basename, suffix,
digits);
File[] backupFiles = dirFile.listFiles(bff);
int nextIndexNum = 0;
if (backupFiles.length == 0)
{
// No other backup files. Just need to move existing file to backupfile_1
nextIndexNum = 1;
}
else
{
TreeMap bfTreeMap = sortBackupFilesAsTreeMap(
backupFiles, basename);
// bfTreeMap now a sorted list of ,
// mappings
if (reverseOrder)
{
// backup style numbering
int tempMax = noMax ? -1 : max;
// noMax == true means no limits
// look for first "gap" in backupFiles
// if tempMax is -1 at this stage just keep going until there's a gap,
// then hopefully tempMax gets set to the right index (a positive
// integer so the loop breaks)...
// why do I feel a little uneasy about this loop?..
for (int i = 1; tempMax < 0 || i <= max; i++)
{
if (!bfTreeMap.containsKey(i)) // first index without existent
// backupfile
{
tempMax = i;
}
}
File previousFile = null;
File fileToBeDeleted = null;
for (int n = tempMax; n > 0; n--)
{
String backupfilename = dir + File.separatorChar
+ BackupFilenameParts.getBackupFilename(n, basename,
suffix, digits);
File backupfile_n = new File(backupfilename);
if (!backupfile_n.exists())
{
// no "oldest" file to delete
previousFile = backupfile_n;
fileToBeDeleted = null;
continue;
}
// check the modification time of this (backupfile_n) and the previous
// file (fileToBeDeleted) if the previous file is going to be deleted
if (fileToBeDeleted != null)
{
File replacementFile = backupfile_n;
long fileToBeDeletedLMT = fileToBeDeleted.lastModified();
long replacementFileLMT = replacementFile.lastModified();
try
{
File oldestTempFile = nextTempFile(fileToBeDeleted.getName(),
dirFile);
if (fileToBeDeletedLMT > replacementFileLMT)
{
String fileToBeDeletedLMTString = sdf
.format(fileToBeDeletedLMT);
String replacementFileLMTString = sdf
.format(replacementFileLMT);
System.out.println("WARNING! I am set to delete backupfile "
+ fileToBeDeleted.getName()
+ " has modification time "
+ fileToBeDeletedLMTString
+ " which is newer than its replacement "
+ replacementFile.getName()
+ " with modification time "
+ replacementFileLMTString);
boolean delete = confirmNewerDeleteFile(fileToBeDeleted,
replacementFile, true);
if (delete)
{
// User has confirmed delete -- no need to add it to the list
fileToBeDeleted.delete();
}
else
{
fileToBeDeleted.renameTo(oldestTempFile);
}
}
else
{
fileToBeDeleted.renameTo(oldestTempFile);
addDeleteFile(oldestTempFile);
}
} catch (Exception e)
{
System.out.println(
"Error occurred, probably making new temp file for '"
+ fileToBeDeleted.getName() + "'");
e.printStackTrace();
}
// reset
fileToBeDeleted = null;
}
if (!noMax && n == tempMax && backupfile_n.exists())
{
fileToBeDeleted = backupfile_n;
}
else
{
if (previousFile != null)
{
ret = ret && backupfile_n.renameTo(previousFile);
}
}
previousFile = backupfile_n;
}
// index to use for the latest backup
nextIndexNum = 1;
}
else
{
// version style numbering (with earliest file deletion if max files
// reached)
bfTreeMap.values().toArray(backupFiles);
// noMax == true means keep all backup files
if ((!noMax) && bfTreeMap.size() >= max)
{
// need to delete some files to keep number of backups to designated
// max
int numToDelete = bfTreeMap.size() - max + 1;
// the "replacement" file is the latest backup file being kept (it's
// not replacing though)
File replacementFile = numToDelete < backupFiles.length
? backupFiles[numToDelete]
: null;
for (int i = 0; i < numToDelete; i++)
{
// check the deletion files for modification time of the last
// backupfile being saved
File fileToBeDeleted = backupFiles[i];
boolean delete = true;
boolean newer = false;
if (replacementFile != null)
{
long fileToBeDeletedLMT = fileToBeDeleted.lastModified();
long replacementFileLMT = replacementFile != null
? replacementFile.lastModified()
: Long.MAX_VALUE;
if (fileToBeDeletedLMT > replacementFileLMT)
{
String fileToBeDeletedLMTString = sdf
.format(fileToBeDeletedLMT);
String replacementFileLMTString = sdf
.format(replacementFileLMT);
System.out
.println("WARNING! I am set to delete backupfile '"
+ fileToBeDeleted.getName()
+ "' has modification time "
+ fileToBeDeletedLMTString
+ " which is newer than the oldest backupfile being kept '"
+ replacementFile.getName()
+ "' with modification time "
+ replacementFileLMTString);
delete = confirmNewerDeleteFile(fileToBeDeleted,
replacementFile, false);
if (delete)
{
// User has confirmed delete -- no need to add it to the list
fileToBeDeleted.delete();
delete = false;
}
else
{
// keeping file, nothing to do!
}
}
}
if (delete)
{
addDeleteFile(fileToBeDeleted);
}
}
}
nextIndexNum = bfTreeMap.lastKey() + 1;
}
}
// Let's make the new backup file!! yay, got there at last!
String latestBackupFilename = dir + File.separatorChar
+ BackupFilenameParts.getBackupFilename(nextIndexNum, basename,
suffix, digits);
ret |= file.renameTo(new File(latestBackupFilename));
if (tidyUp)
{
tidyUpFiles();
}
return ret;
}
private static File nextTempFile(String filename, File dirFile)
throws IOException
{
File temp = null;
COUNT: for (int i = 1; i < 1000; i++)
{
File trythis = new File(dirFile,
filename + '~' + Integer.toString(i));
if (!trythis.exists())
{
temp = trythis;
break COUNT;
}
}
if (temp == null)
{
temp = File.createTempFile(filename, TEMP_FILE_EXT, dirFile);
}
return temp;
}
private void tidyUpFiles()
{
deleteOldFiles();
}
private static boolean confirmNewerDeleteFile(File fileToBeDeleted,
File replacementFile, boolean replace)
{
StringBuilder messageSB = new StringBuilder();
File ftbd = fileToBeDeleted;
String ftbdLMT = sdf.format(ftbd.lastModified());
String ftbdSize = Long.toString(ftbd.length());
File rf = replacementFile;
String rfLMT = sdf.format(rf.lastModified());
String rfSize = Long.toString(rf.length());
int confirmButton = JvOptionPane.NO_OPTION;
if (replace)
{
File saveFile = null;
try
{
saveFile = nextTempFile(ftbd.getName(), ftbd.getParentFile());
} catch (Exception e)
{
System.out.println(
"Error when confirming to keep backup file newer than other backup files.");
e.printStackTrace();
}
messageSB.append(MessageManager.formatMessage(
"label.newerdelete_replacement_line", new String[]
{ ftbd.getName(), rf.getName(), ftbdLMT, rfLMT, ftbdSize,
rfSize }));
messageSB.append("\n\n");
messageSB.append(MessageManager.formatMessage(
"label.confirm_deletion_or_rename", new String[]
{ ftbd.getName(), saveFile.getName() }));
String[] options = new String[] {
MessageManager.getString("label.delete"),
MessageManager.getString("label.rename") };
confirmButton = JvOptionPane.showOptionDialog(Desktop.desktop,
messageSB.toString(),
MessageManager.getString("label.backupfiles_confirm_delete"),
JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
null, options, options[0]);
}
else
{
messageSB.append(MessageManager
.formatMessage("label.newerdelete_line", new String[]
{ ftbd.getName(), rf.getName(), ftbdLMT, rfLMT, ftbdSize,
rfSize }));
messageSB.append("\n\n");
messageSB.append(MessageManager
.formatMessage("label.confirm_deletion", new String[]
{ ftbd.getName() }));
String[] options = new String[] {
MessageManager.getString("label.delete"),
MessageManager.getString("label.keep") };
confirmButton = JvOptionPane.showOptionDialog(Desktop.desktop,
messageSB.toString(),
MessageManager.getString("label.backupfiles_confirm_delete"),
JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
null, options, options[0]);
}
// return should be TRUE if file is to be deleted
return (confirmButton == JvOptionPane.YES_OPTION);
}
private void deleteOldFiles()
{
if (deleteFiles != null && !deleteFiles.isEmpty())
{
boolean doDelete = false;
StringBuilder messageSB = null;
if (confirmDelete && deleteFiles.size() > 0)
{
messageSB = new StringBuilder();
messageSB.append(MessageManager
.getString("label.backupfiles_confirm_delete_old_files"));
for (int i = 0; i < deleteFiles.size(); i++)
{
File df = deleteFiles.get(i);
messageSB.append("\n");
messageSB.append(df.getName());
messageSB.append(" ");
messageSB.append(MessageManager.formatMessage("label.file_info",
new String[]
{ sdf.format(df.lastModified()),
Long.toString(df.length()) }));
}
int confirmButton = JvOptionPane.showConfirmDialog(Desktop.desktop,
messageSB.toString(),
MessageManager
.getString("label.backupfiles_confirm_delete"),
JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE);
doDelete = (confirmButton == JvOptionPane.YES_OPTION);
}
else
{
doDelete = true;
}
if (doDelete)
{
for (int i = 0; i < deleteFiles.size(); i++)
{
File fileToDelete = deleteFiles.get(i);
fileToDelete.delete();
System.out.println("DELETING '" + fileToDelete.getName() + "'");
}
}
}
deleteFiles.clear();
}
private TreeMap sortBackupFilesAsTreeMap(
File[] backupFiles,
String basename)
{
// sort the backup files (based on integer found in the suffix) using a
// precomputed Hashmap for speed
Map bfHashMap = new HashMap<>();
for (int i = 0; i < backupFiles.length; i++)
{
File f = backupFiles[i];
BackupFilenameParts bfp = new BackupFilenameParts(f, basename, suffix,
digits);
bfHashMap.put(bfp.indexNum(), f);
}
TreeMap bfTreeMap = new TreeMap<>();
bfTreeMap.putAll(bfHashMap);
return bfTreeMap;
}
public boolean rollBackupsAndRenameTempFile()
{
boolean write = this.getWriteSuccess();
boolean roll = false;
boolean rename = false;
if (write)
{
roll = this.rollBackupFiles(false);
rename = this.renameTempFile();
}
/*
* Not sure that this confirmation is desirable. By this stage the new file is
* already written successfully, but something (e.g. disk full) has happened while
* trying to roll the backup files, and most likely the filename needed will already
* be vacant so renaming the temp file is nearly always correct!
*/
boolean okay = roll && rename;
if (!okay)
{
StringBuilder messageSB = new StringBuilder();
messageSB.append(MessageManager.getString( "label.backupfiles_confirm_save_file_backupfiles_roll_wrong"));
if (rename)
{
if (messageSB.length() > 0)
{
messageSB.append("\n");
}
messageSB.append(MessageManager.getString(
"label.backupfiles_confirm_save_new_saved_file_ok"));
}
else
{
if (messageSB.length() > 0)
{
messageSB.append("\n");
}
messageSB.append(MessageManager.getString(
"label.backupfiles_confirm_save_new_saved_file_not_ok"));
}
int confirmButton = JvOptionPane.showConfirmDialog(Desktop.desktop,
messageSB.toString(),
MessageManager
.getString("label.backupfiles_confirm_save_file"),
JvOptionPane.OK_OPTION, JvOptionPane.WARNING_MESSAGE);
okay = confirmButton == JvOptionPane.OK_OPTION;
}
if (okay)
{
tidyUpFiles();
}
return rename;
}
public static TreeMap getBackupFilesAsTreeMap(
String fileName, String suffix, int digits)
{
File[] backupFiles = null;
File file = new File(fileName);
File dirFile;
try
{
dirFile = file.getParentFile();
} catch (Exception e)
{
System.out.println(
"Could not get canonical path for file '" + file + "'");
return new TreeMap<>();
}
String filename = file.getName();
String basename = filename;
// find existing backup files
BackupFilenameFilter bff = new BackupFilenameFilter(basename, suffix,
digits);
backupFiles = dirFile.listFiles(bff); // is clone needed?
// sort the backup files (based on integer found in the suffix) using a
// precomputed Hashmap for speed
Map bfHashMap = new HashMap<>();
for (int i = 0; i < backupFiles.length; i++)
{
File f = backupFiles[i];
BackupFilenameParts bfp = new BackupFilenameParts(f, basename, suffix,
digits);
bfHashMap.put(bfp.indexNum(), f);
}
TreeMap bfTreeMap = new TreeMap<>();
bfTreeMap.putAll(bfHashMap);
return bfTreeMap;
}
/*
private boolean addDeleteFile(File fileToBeDeleted, File originalFile,
boolean delete, boolean newer)
{
return addDeleteFile(fileToBeDeleted, originalFile, null, delete, newer);
}
*/
private boolean addDeleteFile(File fileToBeDeleted)
{
boolean ret = false;
int pos = deleteFiles.indexOf(fileToBeDeleted);
if (pos > -1)
{
return true;
}
else
{
deleteFiles.add(fileToBeDeleted);
}
return ret;
}
}