X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FBackupFiles.java;h=1c8525b2de5987b135c6972da80620522470c718;hb=31df3f13e3ab1ac158ec576d691fa860e9f6dd4b;hp=65232fd16cde68a349d682d2b100337d67decb64;hpb=db80eb8e1acf352e72a33e1e3825d40f7c6e4046;p=jalview.git
diff --git a/src/jalview/io/BackupFiles.java b/src/jalview/io/BackupFiles.java
index 65232fd..1c8525b 100644
--- a/src/jalview/io/BackupFiles.java
+++ b/src/jalview/io/BackupFiles.java
@@ -1,27 +1,54 @@
+/*
+ * 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.util.Arrays;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.nio.file.StandardCopyOption;
+import java.text.SimpleDateFormat;
+import java.util.ArrayList;
import java.util.HashMap;
import java.util.Map;
import java.util.TreeMap;
+import jalview.bin.Cache;
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
+import jalview.util.MessageManager;
+
/*
* 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.
+ * The rest of the options are now saved as BACKUPFILES_PRESET, BACKUPFILES_SAVED and BACKUPFILES_CUSTOM
+ * (see BackupFilesPresetEntry)
*/
public class BackupFiles
@@ -32,21 +59,8 @@ public class BackupFiles
public static final String ENABLED = NS + "_ENABLED";
- public static final String SUFFIX = NS + "_SUFFIX";
-
- public static final String NO_MAX = NS + "_NO_MAX";
-
- public static final String ROLL_MAX = NS + "_ROLL_MAX";
-
- public static final String SUFFIX_DIGITS = NS + "_SUFFIX_DIGITS";
-
public static final String NUM_PLACEHOLDER = "%n";
- 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";
@@ -84,6 +98,17 @@ public class BackupFiles
// 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");
+
+ private static final String newTempFileSuffix = "_newfile";
+
+ private static final String oldTempFileSuffix = "_oldfile_tobedeleted";
+
public BackupFiles(String filename)
{
this(new File(filename));
@@ -93,20 +118,15 @@ public class BackupFiles
// REVERSE_ORDER
public BackupFiles(File file)
{
- this(file, ".bak" + NUM_PLACEHOLDER, false, 3, 3, false);
- }
-
- public BackupFiles(File file, String defaultSuffix, boolean defaultNoMax,
- int defaultMax, int defaultDigits, boolean defaultReverseOrder)
- {
classInit();
this.file = file;
- 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);
+ 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;
@@ -116,7 +136,8 @@ public class BackupFiles
{
String tempfilename = file.getName();
File tempdir = file.getParentFile();
- temp = File.createTempFile(tempfilename, TEMP_FILE_EXT, tempdir);
+ temp = File.createTempFile(tempfilename,
+ TEMP_FILE_EXT + newTempFileSuffix, tempdir);
}
else
{
@@ -135,8 +156,10 @@ public class BackupFiles
public static void classInit()
{
- setEnabled(Cache.getDefault(ENABLED, true));
- setConfirmDelete(Cache.getDefault(CONFIRM_DELETE_OLD, true));
+ setEnabled(Cache.getDefault(ENABLED, !Platform.isJS()));
+ BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
+ .getSavedBackupEntry();
+ setConfirmDelete(bfpe.confirmDelete);
}
public static void setEnabled(boolean flag)
@@ -201,13 +224,17 @@ public class BackupFiles
public boolean renameTempFile()
{
- return tempFile.renameTo(file);
+ return moveFileToFile(tempFile, 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
@@ -235,14 +262,13 @@ public class BackupFiles
boolean ret = true;
// Create/move backups up one
- File[] oldFilesToDelete = null;
+ deleteFiles.clear();
// find existing backup files
BackupFilenameFilter bff = new BackupFilenameFilter(basename, suffix,
digits);
File[] backupFiles = dirFile.listFiles(bff);
int nextIndexNum = 0;
- String confirmDeleteExtraInfo = null;
if (backupFiles.length == 0)
{
@@ -253,12 +279,13 @@ public class BackupFiles
{
TreeMap bfTreeMap = sortBackupFilesAsTreeMap(
backupFiles, basename);
+ // bfTreeMap now a sorted list of ,
+ // mappings
if (reverseOrder)
{
// backup style numbering
- File lastfile = null;
int tempMax = noMax ? -1 : max;
// noMax == true means no limits
// look for first "gap" in backupFiles
@@ -275,10 +302,10 @@ public class BackupFiles
}
}
- // for (int m = 0; m < tempMax; m++)
+ File previousFile = null;
+ File fileToBeDeleted = null;
for (int n = tempMax; n > 0; n--)
{
- // int n = tempMax - m;
String backupfilename = dir + File.separatorChar
+ BackupFilenameParts.getBackupFilename(n, basename,
suffix, digits);
@@ -286,40 +313,84 @@ public class BackupFiles
if (!backupfile_n.exists())
{
- lastfile = backupfile_n;
+ // no "oldest" file to delete
+ previousFile = backupfile_n;
+ fileToBeDeleted = null;
continue;
}
- // if (m == 0 && backupfile_n.exists())
- if ((!noMax) && n == tempMax && backupfile_n.exists())
+ // 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)
{
- // move the largest (max) rolled file to a temp file and add to the
- // delete list
+ File replacementFile = backupfile_n;
+ long fileToBeDeletedLMT = fileToBeDeleted.lastModified();
+ long replacementFileLMT = replacementFile.lastModified();
+
try
{
- File temp = File.createTempFile(backupfilename, TEMP_FILE_EXT,
+ File oldestTempFile = nextTempFile(fileToBeDeleted.getName(),
dirFile);
- backupfile_n.renameTo(temp);
- oldFilesToDelete = new File[] { temp };
- confirmDeleteExtraInfo = "(was " + backupfile_n.getName()
- + ")";
- } catch (IOException e)
+ 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
+ {
+ moveFileToFile(fileToBeDeleted, oldestTempFile);
+ }
+ }
+ else
+ {
+ moveFileToFile(fileToBeDeleted, oldestTempFile);
+ addDeleteFile(oldestTempFile);
+ }
+
+ } catch (Exception e)
{
System.out.println(
- "IOException when creating temporary file for backupfilename");
+ "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
{
- // Just In Case
- if (lastfile != null)
+ if (previousFile != null)
{
- ret = ret && backupfile_n.renameTo(lastfile);
+ ret = ret && moveFileToFile(backupfile_n, previousFile);
}
}
- lastfile = backupfile_n;
+ previousFile = backupfile_n;
}
// index to use for the latest backup
@@ -338,82 +409,232 @@ public class BackupFiles
// need to delete some files to keep number of backups to designated
// max
int numToDelete = bfTreeMap.size() - max + 1;
- oldFilesToDelete = Arrays.copyOfRange(backupFiles, 0,
- numToDelete);
+ // 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;
-
}
}
- deleteOldFiles(oldFilesToDelete, confirmDeleteExtraInfo);
-
// Let's make the new backup file!! yay, got there at last!
String latestBackupFilename = dir + File.separatorChar
+ BackupFilenameParts.getBackupFilename(nextIndexNum, basename,
suffix, digits);
- File latestBackupFile = new File(latestBackupFilename);
- ret = ret && file.renameTo(latestBackupFile);
+ ret |= moveFileToFile(file, new File(latestBackupFilename));
+
+ if (tidyUp)
+ {
+ tidyUpFiles();
+ }
return ret;
}
- private void deleteOldFiles(File[] oldFilesToDelete,
- String confirmDeleteExtraInfo)
+ private static File nextTempFile(String filename, File dirFile)
+ throws IOException
{
- if (oldFilesToDelete != null && oldFilesToDelete.length > 0)
+ 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
{
- // delete old backup/version files
+ 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);
+ }
- boolean delete = false;
- if (confirmDelete)
+ private void deleteOldFiles()
+ {
+ if (deleteFiles != null && !deleteFiles.isEmpty())
+ {
+ boolean doDelete = false;
+ StringBuilder messageSB = null;
+ if (confirmDelete && deleteFiles.size() > 0)
{
- // Object[] confirmMessageArray = {};
- StringBuilder confirmMessage = new StringBuilder();
- confirmMessage.append(MessageManager
+ messageSB = new StringBuilder();
+ messageSB.append(MessageManager
.getString("label.backupfiles_confirm_delete_old_files"));
- for (File f : oldFilesToDelete)
- {
- confirmMessage.append("\n");
- confirmMessage.append(f.getName());
- }
- if (confirmDeleteExtraInfo != null
- && confirmDeleteExtraInfo.length() > 0)
+ for (int i = 0; i < deleteFiles.size(); i++)
{
- confirmMessage.append("\n");
- confirmMessage.append(confirmDeleteExtraInfo);
+ 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 confirm = JvOptionPane.showConfirmDialog(Desktop.desktop,
- confirmMessage.toString(),
+
+ int confirmButton = JvOptionPane.showConfirmDialog(Desktop.desktop,
+ messageSB.toString(),
MessageManager
.getString("label.backupfiles_confirm_delete"),
JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE);
- delete = (confirm == JvOptionPane.YES_OPTION);
+ doDelete = (confirmButton == JvOptionPane.YES_OPTION);
}
else
{
- delete = true;
+ doDelete = true;
}
- if (delete)
+ if (doDelete)
{
- for (int i = 0; i < oldFilesToDelete.length; i++)
+ for (int i = 0; i < deleteFiles.size(); i++)
{
- File fileToDelete = oldFilesToDelete[i];
+ File fileToDelete = deleteFiles.get(i);
fileToDelete.delete();
- // System.out.println("DELETING '" + fileToDelete.getName() +
- // "'");
+ System.out.println("DELETING '" + fileToDelete.getName() + "'");
}
}
}
+
+ deleteFiles.clear();
}
- private TreeMap sortBackupFilesAsTreeMap(File[] backupFiles,
- String basename)
+ private TreeMap sortBackupFilesAsTreeMap(
+ File[] backupFiles, String basename)
{
// sort the backup files (based on integer found in the suffix) using a
// precomputed Hashmap for speed
@@ -435,13 +656,11 @@ public class BackupFiles
boolean write = this.getWriteSuccess();
boolean roll = false;
+ boolean rename = false;
if (write)
{
- roll = this.rollBackupFiles();
- }
- else
- {
- return false;
+ roll = this.rollBackupFiles(false);
+ rename = this.renameTempFile();
}
/*
@@ -450,25 +669,41 @@ public class BackupFiles
* 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!
*/
- if (!roll)
+ boolean okay = roll && rename;
+ if (!okay)
{
- int confirm = JvOptionPane.showConfirmDialog(Desktop.desktop,
- MessageManager.getString(
- "label.backupfiles_confirm_save_file_backupfiles_roll_wrong"),
- MessageManager
- .getString("label.backupfiles_confirm_save_file"),
- JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE);
-
- if (confirm == JvOptionPane.YES_OPTION)
+ StringBuilder messageSB = new StringBuilder();
+ messageSB.append(MessageManager.getString(
+ "label.backupfiles_confirm_save_file_backupfiles_roll_wrong"));
+ if (rename)
{
- roll = true;
+ 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"));
}
- }
- boolean rename = false;
- if (roll)
+ 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)
{
- rename = this.renameTempFile();
+ tidyUpFiles();
}
return rename;
@@ -481,12 +716,10 @@ public class BackupFiles
File file = new File(fileName);
- String dir = "";
File dirFile;
try
{
dirFile = file.getParentFile();
- dir = dirFile.getCanonicalPath();
} catch (Exception e)
{
System.out.println(
@@ -518,4 +751,43 @@ public class BackupFiles
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;
+ }
+
+ public static boolean moveFileToFile(File oldFile, File newFile)
+ {
+ boolean ret = false;
+ Path oldPath = Paths.get(oldFile.getAbsolutePath());
+ Path newPath = Paths.get(newFile.getAbsolutePath());
+ try
+ {
+ Files.move(oldPath, newPath, StandardCopyOption.REPLACE_EXISTING);
+ ret = true;
+ } catch (IOException e)
+ {
+ Cache.log.warn("Could not move file '" + oldPath.toString() + "' to '"
+ + newPath.toString() + "'");
+ ret = false;
+ }
+ return ret;
+ }
}