package jalview.io;
import jalview.bin.Cache;
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
+import jalview.util.MessageManager;
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.
+ * BACKUPFILES_SUFFIX - a template to insert after the file extension. Use '%n' to be replaced by a 0-led SUFFIX_DIGITS long integer.
+ * BACKUPFILES_NO_MAX - flag to turn off setting a maximum number of backup files to keep.
+ * BACKUPFILES_ROLL_MAX - the maximum number of backupfiles to keep for any one alignment or project file.
+ * BACKUPFILES_SUFFIX_DIGITS - the number of digits to insert replace %n with (e.g. BACKUPFILES_SUFFIX_DIGITS = 3 would make "001", "002", etc)
+ * 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.
+ * BACKUPFILES_CONFIRM_DELETE_OLD - if true then prompt/confirm with the user when deleting older backup/version files.
+ */
public class BackupFiles
{
// labels for saved params in Cache and .jalview_properties
- private static String NS = "BACKUPFILES";
+ public static final String NS = "BACKUPFILES";
- public static String ENABLED = NS + "_ENABLED";
+ public static final String ENABLED = NS + "_ENABLED";
- public static String SUFFIX = NS + "_SUFFIX";
+ public static final String SUFFIX = NS + "_SUFFIX";
- public static String ROLL_MAX = NS + "_ROLL_MAX";
+ public static final String NO_MAX = NS + "_NO_MAX";
- public static String SUFFIX_DIGITS = NS + "_SUFFIX_DIGITS";
+ public static final String ROLL_MAX = NS + "_ROLL_MAX";
- protected static String NUM_PLACEHOLDER = "%n";
+ public static final String SUFFIX_DIGITS = NS + "_SUFFIX_DIGITS";
- public static String REVERSE_ORDER = NS + "_REVERSE_ORDER";
+ public static final String NUM_PLACEHOLDER = "%n";
- private static String DEFAULT_TEMP_FILE = "jalview_temp_file_" + NS;
+ public static final String REVERSE_ORDER = NS + "_REVERSE_ORDER";
+
+ public static final String CONFIRM_DELETE_OLD = NS
+ + "_CONFIRM_DELETE_OLD";
+
+ 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 boolean enabled;
+ 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;
// 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<DeleteFile> deleteFiles = new ArrayList<>();
+
+ // next backup filename
+ private File nextBackupFile;
+
+ // 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 ENABLED, SUFFIX, ROLL_MAX, SUFFIX_DIGITS and
+ // first time defaults for SUFFIX, NO_MAX, ROLL_MAX, SUFFIX_DIGITS and
// REVERSE_ORDER
public BackupFiles(File file)
{
- this(file, true, "-v" + NUM_PLACEHOLDER, 4, 3, false);
- }
-
- // set, get and rename temp file into place
- public void setTempFile(File temp)
- {
- this.tempFile = temp;
- }
-
- public File getTempFile()
- {
- return tempFile;
- }
-
- public boolean renameTempFile()
- {
- return tempFile.renameTo(file);
+ this(file, ".bak" + NUM_PLACEHOLDER, false, 3, 3, false);
}
- public BackupFiles(File file, boolean defaultEnabled,
- String defaultSuffix,
+ public BackupFiles(File file, String defaultSuffix, boolean defaultNoMax,
int defaultMax, int defaultDigits, boolean defaultReverseOrder)
{
+ classInit();
this.file = file;
- this.enabled = Cache.getDefault(ENABLED, defaultEnabled);
this.suffix = Cache.getDefault(SUFFIX, defaultSuffix);
+ this.noMax = Cache.getDefault(NO_MAX, defaultNoMax);
this.max = Cache.getDefault(ROLL_MAX, defaultMax);
this.digits = Cache.getDefault(SUFFIX_DIGITS, defaultDigits);
this.reverseOrder = Cache.getDefault(REVERSE_ORDER,
defaultReverseOrder);
-
+
// create a temp file to save new data in
- File temp;
+ File temp = null;
try
{
if (file != null)
{
String tempfilename = file.getName();
File tempdir = file.getParentFile();
- temp = File.createTempFile(tempfilename, ".tmp", tempdir);
+ temp = File.createTempFile(tempfilename, TEMP_FILE_EXT, tempdir);
}
else
{
- temp = File.createTempFile(DEFAULT_TEMP_FILE, ".tmp");
- setTempFile(temp);
+ temp = File.createTempFile(DEFAULT_TEMP_FILE, TEMP_FILE_EXT);
}
} catch (IOException e)
{
{
System.out.println("Exception ctreating temp file for saving");
}
+ this.setTempFile(temp);
+ }
+
+ public static void classInit()
+ {
+ setEnabled(Cache.getDefault(ENABLED, true));
+ setConfirmDelete(Cache.getDefault(CONFIRM_DELETE_OLD, true));
+ }
+
+ 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);
+ }
- // file doesn't yet exist or backups are not enabled
- if ((!file.exists()) || (!enabled) || (max < 1))
+ 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;
}
- // split filename up to insert suffix template in the right place. template
- // and backupMax can be set in .jalview_properties
String dir = "";
File dirFile;
try
}
String filename = file.getName();
String basename = filename;
- String extension = "";
- int dotcharpos = filename.lastIndexOf('.');
- // don't split of filenames with the last '.' at the very beginning or
- // very end of the filename
- if ((dotcharpos > 0) && (dotcharpos < filename.length() - 1))
- {
- basename = filename.substring(0, dotcharpos);
- extension = filename.substring(dotcharpos); // NOTE this includes the '.'
- }
boolean ret = true;
// Create/move backups up one
- String numString = null;
- File lastfile = null;
- if (reverseOrder)
+ deleteFiles.clear();
+ //File[] oldFilesToDelete = null;
+ //File[] newerOldFilesToDelete = null; // put files with newer modification
+ // timestamps in here to warn the user!
+
+ // find existing backup files
+ BackupFilenameFilter bff = new BackupFilenameFilter(basename, suffix,
+ digits);
+ File[] backupFiles = dirFile.listFiles(bff);
+ int nextIndexNum = 0;
+
+ if (backupFiles.length == 0)
{
- // backup style numbering
- for (int m = 0; m < max; m++)
+ // No other backup files. Just need to move existing file to backupfile_1
+ nextIndexNum = 1;
+ }
+ else
+ {
+ TreeMap<Integer, File> bfTreeMap = sortBackupFilesAsTreeMap(
+ backupFiles, basename);
+ // bfTreeMap now a sorted list of <Integer index>,<File backupfile>
+ // mappings
+
+ if (reverseOrder)
{
- int n = max - m;
- numString = String.format("%0" + digits + "d", n);
- String backupSuffix = suffix.replaceAll(NUM_PLACEHOLDER, numString);
- String backupfilename = dir + File.separatorChar + basename
- + backupSuffix + extension;
- File backupfile_n = new File(backupfilename);
-
- if (!backupfile_n.exists())
+ // backup style numbering
+
+ File lastfile = null;
+ File lastfiletobedeleted = null;
+ String lastfiletobedeletedoriginalname = null;
+
+ 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;
+ }
+ }
+
+ 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
+ lastfile = backupfile_n;
+ lastfiletobedeleted = null;
+ continue;
+ }
+
+ // check the modification time of the previous file if it's going to
+ // be deleted
+ if (lastfiletobedeleted != null)
+ {
+ long oldLMT = lastfiletobedeleted.lastModified();
+ long newLMT = backupfile_n.lastModified();
+ if (oldLMT > newLMT)
+ {
+ String oldLMTString = sdf
+ .format(lastfiletobedeleted.lastModified());
+ String newLMTString = sdf.format(backupfile_n.lastModified());
+ System.out.println("WARNING! I am set to delete backupfile "
+ + lastfiletobedeleted.getName() + " (was '"
+ + lastfiletobedeletedoriginalname + "')"
+ + " has modification time "
+ + oldLMTString
+ + " which is newer than its replacement "
+ + backupfile_n.getName() + " with modification time "
+ + newLMTString);
+
+ addDeleteFile(lastfiletobedeleted, backupfile_n, true, true,
+ " (" + MessageManager.formatMessage(
+ "label.was_previous", new String[]
+ { backupfile_n.getName() }) + ")");
+ }
+
+ // reset
+ lastfiletobedeleted = null;
+ lastfiletobedeletedoriginalname = null;
+ }
+
+ if (!noMax && n == tempMax && backupfile_n.exists())
+ {
+ // move the largest (max) rolled file to a temp file and add to the
+ // delete list
+ try
+ {
+ File temp = File.createTempFile(backupfilename, TEMP_FILE_EXT,
+ dirFile);
+ backupfile_n.renameTo(temp);
+
+ String message = "(" + MessageManager
+ .formatMessage("label.was_previous", new String[]
+ { backupfile_n.getName() }) + ")";
+ addDeleteFile(temp, backupfile_n, true, false, message);
+
+ lastfiletobedeleted = temp;
+ } catch (IOException e)
+ {
+ System.out.println(
+ "IOException when creating temporary file for backupfilename");
+ }
+ }
+ else
+ {
+ // Just In Case
+ if (lastfile != null)
+ {
+ ret = ret && backupfile_n.renameTo(lastfile);
+ }
+ }
+
lastfile = backupfile_n;
- continue;
}
- if (m == 0)
- { // Move the max backup to /tmp instead of deleting (Just In
- // Case)
- String tmpfile = "tmp-" + backupfile_n.getName();
- try
+ // 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;
+ for (int i = 0; i < numToDelete; i++)
{
- File tmpFile = File.createTempFile(tmpfile, ".tmp");
- ret = ret && backupfile_n.renameTo(tmpFile);
- } catch (IOException e)
+ addDeleteFile(backupFiles[i], null, true, false, null);
+ }
+
+ }
+
+ 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);
+ nextBackupFile = new File(latestBackupFilename);
+ ret |= file.renameTo(nextBackupFile);
+
+ if (tidyUp)
+ {
+ tidyUpFiles();
+ }
+
+ return ret;
+ }
+
+ private void tidyUpFiles()
+ {
+ deleteOldFiles();
+ }
+
+ private void deleteOldFiles()
+ {
+ if (deleteFiles != null && !deleteFiles.isEmpty())
+ {
+ boolean confirm = confirmDelete;
+ // delete old backup/version files
+
+ // check for newer files
+ boolean newerDelete = hasNewerDeleteFile();
+ StringBuilder newerDeleteSB = null;
+ if (newerDelete)
+ {
+ newerDeleteSB = new StringBuilder();
+ for (int i = 0; i < deleteFiles.size(); i++)
+ {
+ DeleteFile df = deleteFiles.get(i);
+ if (df.newer && df.delete)
{
- System.out.println(
- "Could not create temp file '" + tmpfile + ".tmp'");
+ String oldName = df.oldFile.getName();
+ String oldLMT = sdf.format(df.oldFile.lastModified());
+ String newLMT = sdf.format(df.newFile.lastModified());
+ if (newerDeleteSB.length() > 0)
+ {
+ newerDeleteSB.append("\n");
+ }
+ newerDeleteSB.append(
+ MessageManager.formatMessage("label.newerdelete_line",
+ new String[]
+ { oldName, oldLMT, df.newFile.getName(),
+ newLMT })
+ );
+ if (df.info != null
+ && df.info.length() > 0)
+ {
+ newerDeleteSB.append(" ");
+ newerDeleteSB.append(df.info);
+ }
+ confirm = true;
}
}
- else
+ }
+
+ boolean doDelete = false;
+ StringBuilder deleteSB = null;
+ if (confirmDelete && deleteFiles.size() > 0)
+ {
+ deleteSB = new StringBuilder();
+ deleteSB.append(MessageManager
+ .getString("label.backupfiles_confirm_delete_old_files"));
+ for (int i = 0; i < deleteFiles.size(); i++)
{
- // Just In Case
- if (lastfile != null)
+ DeleteFile df = deleteFiles.get(i);
+ if (!df.delete)
{
- ret = ret && backupfile_n.renameTo(lastfile);
+ break;
}
+ deleteSB.append("\n");
+ deleteSB.append(df.oldFile.getName());
+ if (df.info != null
+ && df.info.length() > 0)
+ {
+ deleteSB.append("\n");
+ deleteSB.append(df.info);
+ }
+ }
+ confirm = true;
+ }
+
+ if (confirm)
+ {
+ StringBuilder messageSB = new StringBuilder();
+ if (deleteSB != null && deleteSB.length() > 0)
+ {
+ messageSB.append(deleteSB);
}
+ if (newerDeleteSB != null && newerDeleteSB.length() > 0)
+ {
+ messageSB.append("\n");
+ messageSB.append(newerDeleteSB);
+ }
+
+ int confirmButton = JvOptionPane.showConfirmDialog(Desktop.desktop,
+ messageSB.toString(),
+ MessageManager
+ .getString("label.backupfiles_confirm_delete"),
+ JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE);
- lastfile = backupfile_n;
+ doDelete = (confirmButton == JvOptionPane.YES_OPTION);
+ }
+ else
+ {
+ doDelete = true;
+ }
+
+ if (doDelete)
+ {
+ for (int i = 0; i < deleteFiles.size(); i++)
+ {
+ File fileToDelete = deleteFiles.get(i).oldFile;
+ fileToDelete.delete();
+ // System.out.println("DELETING '" + fileToDelete.getName() +
+ // "'");
+ }
}
- // now actually backup the important file!
- ret = ret && file.renameTo(lastfile);
}
- else
+
+ deleteFiles.clear();
+ }
+
+ private TreeMap<Integer, File> sortBackupFilesAsTreeMap(
+ File[] backupFiles,
+ String basename)
+ {
+ // sort the backup files (based on integer found in the suffix) using a
+ // precomputed Hashmap for speed
+ Map<Integer, File> 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<Integer, File> 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<Integer, File> getBackupFilesAsTreeMap(
+ String fileName, String suffix, int digits)
+ {
+ File[] backupFiles = null;
+
+ File file = new File(fileName);
+
+ File dirFile;
+ try
{
- // version style numbering (with earliest file deletion if max files
- // reached)
+ dirFile = file.getParentFile();
+ } catch (Exception e)
+ {
+ System.out.println(
+ "Could not get canonical path for file '" + file + "'");
+ return new TreeMap<>();
+ }
- // find existing backup files
- BackupFileFilter bff = new BackupFileFilter(basename, suffix, digits,
- extension);
- File[] backupFiles = dirFile.listFiles(bff);
+ 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<Integer, File> 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<Integer, File> bfTreeMap = new TreeMap<>();
+ bfTreeMap.putAll(bfHashMap);
+ return bfTreeMap;
+ }
+
+ private boolean addDeleteFile(File oldFile, File newFile, boolean delete,
+ boolean newer, String info)
+ {
+ boolean ret = false;
+ int pos = deleteFiles.indexOf(oldFile);
+ if (pos > -1)
+ {
+ DeleteFile df = deleteFiles.get(pos);
+ if (newFile != null)
+ {
+ df.newFile = newFile;
+ }
+ df.delete |= delete;
+ df.newer |= newer;
+ df.info += ';' + info;
+ ret = true;
+ }
+ else
+ {
+ deleteFiles
+ .add(new DeleteFile(oldFile, newFile, delete, newer, info));
+ }
return ret;
}
+ private boolean hasNewerDeleteFile()
+ {
+ for (int i = 0; i < deleteFiles.size(); i++)
+ {
+ DeleteFile df = deleteFiles.get(i);
+ if (df.newer)
+ {
+ return true;
+ }
+ }
+ return false;
+ }
}
+class DeleteFile
+{
+ protected File oldFile;
+
+ protected File newFile;
+
+ protected boolean delete;
+
+ protected boolean newer;
+
+ protected String info;
+
+ protected DeleteFile(File oldFile, File newFile, boolean delete,
+ boolean newer, String info)
+ {
+ this.oldFile = oldFile;
+ this.newFile = newFile;
+ this.delete = delete;
+ this.newer = newer;
+ this.info = info;
+ }
+
+ public boolean equals(File file)
+ {
+ return this.oldFile.equals(file);
+ }
+}
git://source.jalview.org / jalview.git / blobdiff