+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * 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 java.io.File;
import java.io.IOException;
+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.bin.Console;
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
/*
* 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
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";
private boolean tempFileWriteSuccess;
// array of files to be deleted, with extra information
- private ArrayList<DeleteFile> deleteFiles = new ArrayList<>();
-
- // next backup filename
- private File nextBackupFile;
+ private ArrayList<File> 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));
// 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;
{
String tempfilename = file.getName();
File tempdir = file.getParentFile();
- temp = File.createTempFile(tempfilename, TEMP_FILE_EXT, tempdir);
+ Console.trace(
+ "BACKUPFILES [file!=null] attempting to create temp file for "
+ + tempfilename + " in dir " + tempdir);
+ temp = File.createTempFile(tempfilename,
+ TEMP_FILE_EXT + newTempFileSuffix, tempdir);
+ Console.debug(
+ "BACKUPFILES using temp file " + temp.getAbsolutePath());
}
else
{
+ Console.trace(
+ "BACKUPFILES [file==null] attempting to create default temp file "
+ + DEFAULT_TEMP_FILE + " with extension "
+ + TEMP_FILE_EXT);
temp = File.createTempFile(DEFAULT_TEMP_FILE, TEMP_FILE_EXT);
}
} catch (IOException e)
{
- System.out.println(
- "Could not create temp file to save into (IOException)");
+ Console.error("Could not create temp file to save to (IOException)");
+ Console.error(e.getMessage());
+ Console.debug(Cache.getStackTraceString(e));
} catch (Exception e)
{
- System.out.println("Exception ctreating temp file for saving");
+ Console.error("Exception creating temp file for saving");
+ Console.debug(Cache.getStackTraceString(e));
}
this.setTempFile(temp);
}
public static void classInit()
{
- setEnabled(Cache.getDefault(ENABLED, true));
- setConfirmDelete(Cache.getDefault(CONFIRM_DELETE_OLD, true));
+ Console.initLogger();
+ Console.trace("BACKUPFILES classInit");
+ boolean e = Cache.getDefault(ENABLED, !Platform.isJS());
+ setEnabled(e);
+ Console.trace("BACKUPFILES " + (e ? "enabled" : "disabled"));
+ BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
+ .getSavedBackupEntry();
+ Console.trace("BACKUPFILES preset scheme " + bfpe.toString());
+ setConfirmDelete(bfpe.confirmDelete);
+ Console.trace("BACKUPFILES confirm delete " + bfpe.confirmDelete);
}
public static void setEnabled(boolean flag)
path = this.getTempFile().getCanonicalPath();
} catch (IOException e)
{
- System.out.println(
- "IOException when getting Canonical Path of temp file '"
- + this.getTempFile().getName() + "'");
+ Console.error("IOException when getting Canonical Path of temp file '"
+ + this.getTempFile().getName() + "'");
+ Console.debug(Cache.getStackTraceString(e));
}
return path;
}
public boolean renameTempFile()
{
- return tempFile.renameTo(file);
+ return moveFileToFile(tempFile, file);
}
// roll the backupfiles
|| suffix.length() == 0)
{
// nothing to do
+ Console.debug("BACKUPFILES rollBackupFiles nothing to do." + ", "
+ + "filename: " + (file != null ? file.getName() : "null")
+ + ", " + "file exists: " + file.exists() + ", " + "enabled: "
+ + enabled + ", " + "max: " + max + ", " + "suffix: '" + suffix
+ + "'");
return true;
}
+ Console.trace("BACKUPFILES rollBackupFiles starting");
+
String dir = "";
File dirFile;
try
{
dirFile = file.getParentFile();
dir = dirFile.getCanonicalPath();
+ Console.trace("BACKUPFILES dir: " + dir);
} catch (Exception e)
{
- System.out.println(
- "Could not get canonical path for file '" + file + "'");
+ Console.error("Could not get canonical path for file '" + file + "'");
+ Console.error(e.getMessage());
+ Console.debug(Cache.getStackTraceString(e));
return false;
}
String filename = file.getName();
String basename = filename;
+ Console.trace("BACKUPFILES filename is " + filename);
boolean ret = true;
// Create/move backups up one
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,
File[] backupFiles = dirFile.listFiles(bff);
int nextIndexNum = 0;
+ Console.trace("BACKUPFILES backupFiles.length: " + backupFiles.length);
if (backupFiles.length == 0)
{
// No other backup files. Just need to move existing file to backupfile_1
+ Console.trace(
+ "BACKUPFILES no existing backup files, setting index to 1");
nextIndexNum = 1;
}
else
if (reverseOrder)
{
// backup style numbering
-
- File lastfile = null;
- File lastfiletobedeleted = null;
- String lastfiletobedeletedoriginalname = null;
+ Console.trace("BACKUPFILES rolling files in reverse order");
int tempMax = noMax ? -1 : max;
// noMax == true means no limits
tempMax = i;
}
}
-
+
+ File previousFile = null;
+ File fileToBeDeleted = null;
for (int n = tempMax; n > 0; n--)
{
String backupfilename = dir + File.separatorChar
if (!backupfile_n.exists())
{
// no "oldest" file to delete
- lastfile = backupfile_n;
- lastfiletobedeleted = null;
+ previousFile = backupfile_n;
+ fileToBeDeleted = null;
+ Console.trace("BACKUPFILES No oldest file to delete");
continue;
}
- // check the modification time of the previous file if it's going to
- // be deleted
- if (lastfiletobedeleted != null)
+ // 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)
{
- long oldLMT = lastfiletobedeleted.lastModified();
- long newLMT = backupfile_n.lastModified();
- if (oldLMT > newLMT)
+ File replacementFile = backupfile_n;
+ long fileToBeDeletedLMT = fileToBeDeleted.lastModified();
+ long replacementFileLMT = replacementFile.lastModified();
+ Console.trace("BACKUPFILES fileToBeDeleted is "
+ + fileToBeDeleted.getAbsolutePath());
+ Console.trace("BACKUPFILES replacementFile is "
+ + backupfile_n.getAbsolutePath());
+
+ try
+ {
+ File oldestTempFile = nextTempFile(fileToBeDeleted.getName(),
+ dirFile);
+
+ if (fileToBeDeletedLMT > replacementFileLMT)
+ {
+ String fileToBeDeletedLMTString = sdf
+ .format(fileToBeDeletedLMT);
+ String replacementFileLMTString = sdf
+ .format(replacementFileLMT);
+ Console.warn("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);
+ Console.trace("BACKUPFILES " + (delete ? "confirmed" : "not")
+ + " deleting file "
+ + fileToBeDeleted.getAbsolutePath()
+ + " which is newer than "
+ + replacementFile.getAbsolutePath());
+
+ if (delete)
+ {
+ // User has confirmed delete -- no need to add it to the list
+ fileToBeDeleted.delete();
+ }
+ else
+ {
+ Console.debug("BACKUPFILES moving "
+ + fileToBeDeleted.getAbsolutePath() + " to "
+ + oldestTempFile.getAbsolutePath());
+ moveFileToFile(fileToBeDeleted, oldestTempFile);
+ }
+ }
+ else
+ {
+ Console.debug("BACKUPFILES going to move "
+ + fileToBeDeleted.getAbsolutePath() + " to "
+ + oldestTempFile.getAbsolutePath());
+ moveFileToFile(fileToBeDeleted, oldestTempFile);
+ addDeleteFile(oldestTempFile);
+ }
+
+ } catch (Exception e)
{
- 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[]
- { lastfile.getName() }) + ")");
+ Console.error(
+ "Error occurred, probably making new temp file for '"
+ + fileToBeDeleted.getName() + "'");
+ Console.error(Cache.getStackTraceString(e));
}
// reset
- lastfiletobedeleted = null;
- lastfiletobedeletedoriginalname = null;
+ fileToBeDeleted = 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");
- }
+ fileToBeDeleted = backupfile_n;
}
else
{
- // Just In Case
- if (lastfile != null)
+ if (previousFile != null)
{
- ret = ret && backupfile_n.renameTo(lastfile);
+ // using boolean '&' instead of '&&' as don't want moveFileToFile
+ // attempt to be conditional (short-circuit)
+ ret = ret & moveFileToFile(backupfile_n, previousFile);
}
}
- lastfile = backupfile_n;
+ previousFile = backupfile_n;
}
// index to use for the latest backup
nextIndexNum = 1;
}
- else
+ else // not reverse numbering
{
// version style numbering (with earliest file deletion if max files
// reached)
bfTreeMap.values().toArray(backupFiles);
+ StringBuilder bfsb = new StringBuilder();
+ for (int i = 0; i < backupFiles.length; i++)
+ {
+ if (bfsb.length() > 0)
+ {
+ bfsb.append(", ");
+ }
+ bfsb.append(backupFiles[i].getName());
+ }
+ Console.trace("BACKUPFILES backupFiles: " + bfsb.toString());
// noMax == true means keep all backup files
if ((!noMax) && bfTreeMap.size() >= max)
{
+ Console.trace("BACKUPFILES noMax: " + noMax + ", " + "max: " + max
+ + ", " + "bfTreeMap.size(): " + bfTreeMap.size());
// need to delete some files to keep number of backups to designated
- // max
- int numToDelete = bfTreeMap.size() - max + 1;
+ // max.
+ // Note that if the suffix is not numbered then do not delete any
+ // backup files later or we'll delete the new backup file (there can
+ // be only one).
+ int numToDelete = suffix.indexOf(NUM_PLACEHOLDER) > -1
+ ? bfTreeMap.size() - max + 1
+ : 0;
+ Console.trace("BACKUPFILES numToDelete: " + 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++)
{
- addDeleteFile(backupFiles[i], null, true, false, null);
+ // check the deletion files for modification time of the last
+ // backupfile being saved
+ File fileToBeDeleted = backupFiles[i];
+ boolean delete = true;
+
+ Console.trace("BACKUPFILES fileToBeDeleted: " + fileToBeDeleted);
+
+ 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);
+
+ Console.warn("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();
+ Console.debug("BACKUPFILES deleting fileToBeDeleted: "
+ + fileToBeDeleted);
+ delete = false;
+ }
+ else
+ {
+ // keeping file, nothing to do!
+ Console.debug("BACKUPFILES keeping fileToBeDeleted: "
+ + fileToBeDeleted);
+ }
+ }
+ }
+ if (delete)
+ {
+ addDeleteFile(fileToBeDeleted);
+ Console.debug("BACKUPFILES addDeleteFile(fileToBeDeleted): "
+ + fileToBeDeleted);
+ }
+
}
}
nextIndexNum = bfTreeMap.lastKey() + 1;
-
}
}
String latestBackupFilename = dir + File.separatorChar
+ BackupFilenameParts.getBackupFilename(nextIndexNum, basename,
suffix, digits);
- nextBackupFile = new File(latestBackupFilename);
- ret |= file.renameTo(nextBackupFile);
-
+ Console.trace("BACKUPFILES Moving old file [" + file
+ + "] to latestBackupFilename [" + latestBackupFilename + "]");
+ // using boolean '&' instead of '&&' as don't want moveFileToFile attempt to
+ // be conditional (short-circuit)
+ ret = ret & moveFileToFile(file, new File(latestBackupFilename));
+ Console.debug("BACKUPFILES moving " + file + " to " + latestBackupFilename
+ + " was " + (ret ? "" : "NOT ") + "successful");
if (tidyUp)
{
+ Console.debug("BACKUPFILES tidying up files");
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 void deleteOldFiles()
+ private static boolean confirmNewerDeleteFile(File fileToBeDeleted,
+ File replacementFile, boolean replace)
{
- if (deleteFiles != null && !deleteFiles.isEmpty())
- {
- boolean confirm = confirmDelete;
- // delete old backup/version files
+ StringBuilder messageSB = new StringBuilder();
- // check for newer files
- boolean newerDelete = hasNewerDeleteFile();
- StringBuilder newerDeleteSB = null;
- if (newerDelete)
+ 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
{
- newerDeleteSB = new StringBuilder();
- for (int i = 0; i < deleteFiles.size(); i++)
- {
- DeleteFile df = deleteFiles.get(i);
- if (df.newer && df.delete)
- {
- 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;
- }
- }
+ saveFile = nextTempFile(ftbd.getName(), ftbd.getParentFile());
+ } catch (Exception e)
+ {
+ Console.error(
+ "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 }));
+ // "Backup file\n''{0}''\t(modified {2}, size {4})\nis to be deleted and
+ // replaced by apparently older file \n''{1}''\t(modified {3}, size
+ // {5}).""
+ messageSB.append("\n\n");
+ messageSB.append(MessageManager.formatMessage(
+ "label.confirm_deletion_or_rename", new String[]
+ { ftbd.getName(), saveFile.getName() }));
+ // "Confirm deletion of ''{0}'' or rename to ''{1}''?"
+ String[] options = new String[] {
+ MessageManager.getString("label.delete"),
+ MessageManager.getString("label.rename") };
+
+ confirmButton = Platform.isHeadless() ? JvOptionPane.YES_OPTION
+ : JvOptionPane.showOptionDialog(Desktop.desktop,
+ messageSB.toString(),
+ MessageManager.getString(
+ "label.backupfiles_confirm_delete"),
+ // "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 }));
+ // "Backup file\n''{0}''\t(modified {2}, size {4})\nis to be deleted but
+ // is newer than the oldest remaining backup file \n''{1}''\t(modified
+ // {3}, size {5})."
+ messageSB.append("\n\n");
+ messageSB.append(MessageManager
+ .formatMessage("label.confirm_deletion", new String[]
+ { ftbd.getName() }));
+ // "Confirm deletion of ''{0}''?"
+ String[] options = new String[] {
+ MessageManager.getString("label.delete"),
+ MessageManager.getString("label.keep") };
+
+ confirmButton = Platform.isHeadless() ? JvOptionPane.YES_OPTION
+ : JvOptionPane.showOptionDialog(Desktop.desktop,
+ messageSB.toString(),
+ MessageManager.getString(
+ "label.backupfiles_confirm_delete"),
+ // "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 deleteSB = null;
+ StringBuilder messageSB = null;
if (confirmDelete && deleteFiles.size() > 0)
{
- deleteSB = new StringBuilder();
- deleteSB.append(MessageManager
+ messageSB = new StringBuilder();
+ messageSB.append(MessageManager
.getString("label.backupfiles_confirm_delete_old_files"));
+ // "Delete the following older backup files? (see the Backups tab in
+ // Preferences for more options)"
for (int i = 0; i < deleteFiles.size(); i++)
{
- DeleteFile df = deleteFiles.get(i);
- if (!df.delete)
- {
- 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)
- {
+ File df = deleteFiles.get(i);
messageSB.append("\n");
- messageSB.append(newerDeleteSB);
+ messageSB.append(df.getName());
+ messageSB.append(" ");
+ messageSB.append(MessageManager.formatMessage("label.file_info",
+ new String[]
+ { sdf.format(df.lastModified()),
+ Long.toString(df.length()) }));
+ // "(modified {0}, size {1})"
}
- int confirmButton = JvOptionPane.showConfirmDialog(Desktop.desktop,
- messageSB.toString(),
- MessageManager
- .getString("label.backupfiles_confirm_delete"),
- JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE);
+ int confirmButton = Platform.isHeadless() ? JvOptionPane.YES_OPTION
+ : JvOptionPane.showConfirmDialog(Desktop.desktop,
+ messageSB.toString(),
+ MessageManager.getString(
+ "label.backupfiles_confirm_delete"),
+ // "Confirm delete"
+ JvOptionPane.YES_NO_OPTION,
+ JvOptionPane.WARNING_MESSAGE);
doDelete = (confirmButton == JvOptionPane.YES_OPTION);
}
{
for (int i = 0; i < deleteFiles.size(); i++)
{
- File fileToDelete = deleteFiles.get(i).oldFile;
+ File fileToDelete = deleteFiles.get(i);
+ Console.trace("BACKUPFILES about to delete fileToDelete:"
+ + fileToDelete);
fileToDelete.delete();
- // System.out.println("DELETING '" + fileToDelete.getName() +
- // "'");
+ Console.warn("deleted '" + fileToDelete.getName() + "'");
}
}
}
private TreeMap<Integer, File> sortBackupFilesAsTreeMap(
- File[] backupFiles,
- String basename)
+ File[] backupFiles, String basename)
{
// sort the backup files (based on integer found in the suffix) using a
// precomputed Hashmap for speed
boolean rename = false;
if (write)
{
- roll = this.rollBackupFiles(false);
+ roll = this.rollBackupFiles(false); // tidyUpFiles at the end
rename = this.renameTempFile();
}
if (!okay)
{
StringBuilder messageSB = new StringBuilder();
- messageSB.append(MessageManager.getString( "label.backupfiles_confirm_save_file_backupfiles_roll_wrong"));
+ messageSB.append(MessageManager.getString(
+ "label.backupfiles_confirm_save_file_backupfiles_roll_wrong"));
+ // "Something possibly went wrong with the backups of this file."
if (rename)
{
if (messageSB.length() > 0)
}
messageSB.append(MessageManager.getString(
"label.backupfiles_confirm_save_new_saved_file_ok"));
+ // "The new saved file seems okay."
}
else
{
}
messageSB.append(MessageManager.getString(
"label.backupfiles_confirm_save_new_saved_file_not_ok"));
+ // "The new saved file might not be okay."
}
-
- int confirmButton = JvOptionPane.showConfirmDialog(Desktop.desktop,
- messageSB.toString(),
- MessageManager
- .getString("label.backupfiles_confirm_save_file"),
- JvOptionPane.OK_OPTION, JvOptionPane.WARNING_MESSAGE);
+ if (messageSB.length() > 0)
+ {
+ messageSB.append("\n");
+ }
+ messageSB
+ .append(MessageManager.getString("label.continue_operation"));
+
+ int confirmButton = Platform.isHeadless() ? JvOptionPane.OK_OPTION
+ : JvOptionPane.showConfirmDialog(Desktop.desktop,
+ messageSB.toString(),
+ MessageManager.getString(
+ "label.backupfiles_confirm_save_file"),
+ // "Confirm save file"
+ JvOptionPane.OK_OPTION, JvOptionPane.WARNING_MESSAGE);
okay = confirmButton == JvOptionPane.OK_OPTION;
}
if (okay)
dirFile = file.getParentFile();
} catch (Exception e)
{
- System.out.println(
- "Could not get canonical path for file '" + file + "'");
+ Console.error("Could not get canonical path for file '" + file + "'");
return new TreeMap<>();
}
return bfTreeMap;
}
- private boolean addDeleteFile(File oldFile, File newFile, boolean delete,
- boolean newer, String info)
+ /*
+ 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(oldFile);
+ int pos = deleteFiles.indexOf(fileToBeDeleted);
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;
+ Console.debug("BACKUPFILES not adding file "
+ + fileToBeDeleted.getAbsolutePath()
+ + " to the delete list (already at index" + pos + ")");
+ return true;
}
else
{
- deleteFiles
- .add(new DeleteFile(oldFile, newFile, delete, newer, info));
+ Console.debug("BACKUPFILES adding file "
+ + fileToBeDeleted.getAbsolutePath() + " to the delete list");
+ deleteFiles.add(fileToBeDeleted);
}
return ret;
}
- private boolean hasNewerDeleteFile()
+ public static boolean moveFileToFile(File oldFile, File newFile)
{
- for (int i = 0; i < deleteFiles.size(); i++)
+ Console.initLogger();
+ boolean ret = false;
+ Path oldPath = Paths.get(oldFile.getAbsolutePath());
+ Path newPath = Paths.get(newFile.getAbsolutePath());
+ try
{
- DeleteFile df = deleteFiles.get(i);
- if (df.newer)
- {
- return true;
- }
+ // delete destination file - not usually necessary but Just In Case...
+ Console.trace("BACKUPFILES deleting " + newFile.getAbsolutePath());
+ newFile.delete();
+ Console.trace("BACKUPFILES moving " + oldFile.getAbsolutePath() + " to "
+ + newFile.getAbsolutePath());
+ Files.move(oldPath, newPath, StandardCopyOption.REPLACE_EXISTING);
+ ret = true;
+ Console.trace("BACKUPFILES move seems to have succeeded");
+ } catch (IOException e)
+ {
+ Console.warn("Could not move file '" + oldPath.toString() + "' to '"
+ + newPath.toString() + "'");
+ Console.error(e.getMessage());
+ Console.debug(Cache.getStackTraceString(e));
+ ret = false;
+ } catch (Exception e)
+ {
+ Console.error(e.getMessage());
+ Console.debug(Cache.getStackTraceString(e));
+ ret = false;
}
- 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);
+ return ret;
}
}
git://source.jalview.org / jalview.git / blobdiff