*/
package jalview.io;
-
import java.io.File;
import java.io.IOException;
import java.nio.file.Files;
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:
private static final String newTempFileSuffix = "_newfile";
private static final String oldTempFileSuffix = "_oldfile_tobedeleted";
+
public BackupFiles(String filename)
{
this(new File(filename));
{
String tempfilename = file.getName();
File tempdir = file.getParentFile();
- Cache.trace(
+ Console.trace(
"BACKUPFILES [file!=null] attempting to create temp file for "
+ tempfilename + " in dir " + tempdir);
temp = File.createTempFile(tempfilename,
TEMP_FILE_EXT + newTempFileSuffix, tempdir);
- Cache.debug(
+ Console.debug(
"BACKUPFILES using temp file " + temp.getAbsolutePath());
}
else
{
- Cache.trace(
+ Console.trace(
"BACKUPFILES [file==null] attempting to create default temp file "
+ DEFAULT_TEMP_FILE + " with extension "
+ TEMP_FILE_EXT);
}
} catch (IOException e)
{
- Cache.error("Could not create temp file to save to (IOException)");
- Cache.error(e.getMessage());
- Cache.debug(Cache.getStackTraceString(e));
+ Console.error("Could not create temp file to save to (IOException)");
+ Console.error(e.getMessage());
+ Console.debug(Cache.getStackTraceString(e));
} catch (Exception e)
{
- Cache.error("Exception creating temp file for saving");
- Cache.debug(Cache.getStackTraceString(e));
+ Console.error("Exception creating temp file for saving");
+ Console.debug(Cache.getStackTraceString(e));
}
this.setTempFile(temp);
}
public static void classInit()
{
- Cache.initLogger();
- Cache.trace("BACKUPFILES classInit");
+ Console.initLogger();
+ Console.trace("BACKUPFILES classInit");
boolean e = Cache.getDefault(ENABLED, !Platform.isJS());
setEnabled(e);
- Cache.trace("BACKUPFILES " + (e ? "enabled" : "disabled"));
+ Console.trace("BACKUPFILES " + (e ? "enabled" : "disabled"));
BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
.getSavedBackupEntry();
- Cache.trace("BACKUPFILES preset scheme " + bfpe.toString());
+ Console.trace("BACKUPFILES preset scheme " + bfpe.toString());
setConfirmDelete(bfpe.confirmDelete);
- Cache.trace("BACKUPFILES confirm delete " + bfpe.confirmDelete);
+ Console.trace("BACKUPFILES confirm delete " + bfpe.confirmDelete);
}
public static void setEnabled(boolean flag)
path = this.getTempFile().getCanonicalPath();
} catch (IOException e)
{
- Cache.error("IOException when getting Canonical Path of temp file '"
+ Console.error("IOException when getting Canonical Path of temp file '"
+ this.getTempFile().getName() + "'");
- Cache.debug(Cache.getStackTraceString(e));
+ Console.debug(Cache.getStackTraceString(e));
}
return path;
}
|| suffix.length() == 0)
{
// nothing to do
- Cache.debug("BACKUPFILES rollBackupFiles 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;
}
- Cache.trace("BACKUPFILES rollBackupFiles starting");
+ Console.trace("BACKUPFILES rollBackupFiles starting");
+
String dir = "";
File dirFile;
try
{
dirFile = file.getParentFile();
dir = dirFile.getCanonicalPath();
- Cache.trace("BACKUPFILES dir: " + dir);
+ Console.trace("BACKUPFILES dir: " + dir);
} catch (Exception e)
{
- Cache.error("Could not get canonical path for file '" + file + "'");
- Cache.error(e.getMessage());
- Cache.debug(Cache.getStackTraceString(e));
+ 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;
- Cache.trace("BACKUPFILES filename is " + filename);
+ Console.trace("BACKUPFILES filename is " + filename);
boolean ret = true;
// Create/move backups up one
File[] backupFiles = dirFile.listFiles(bff);
int nextIndexNum = 0;
- Cache.trace("BACKUPFILES backupFiles.length: " + backupFiles.length);
+ Console.trace("BACKUPFILES backupFiles.length: " + backupFiles.length);
if (backupFiles.length == 0)
{
// No other backup files. Just need to move existing file to backupfile_1
- Cache.trace(
+ Console.trace(
"BACKUPFILES no existing backup files, setting index to 1");
nextIndexNum = 1;
}
if (reverseOrder)
{
// backup style numbering
-
- Cache.trace("BACKUPFILES rolling files in reverse order");
+ 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--)
// no "oldest" file to delete
previousFile = backupfile_n;
fileToBeDeleted = null;
- Cache.trace("BACKUPFILES No oldest file to delete");
+ Console.trace("BACKUPFILES No oldest file to delete");
continue;
}
File replacementFile = backupfile_n;
long fileToBeDeletedLMT = fileToBeDeleted.lastModified();
long replacementFileLMT = replacementFile.lastModified();
- Cache.trace("BACKUPFILES fileToBeDeleted is "
+ Console.trace("BACKUPFILES fileToBeDeleted is "
+ fileToBeDeleted.getAbsolutePath());
- Cache.trace("BACKUPFILES replacementFile is "
+ 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);
- Cache.warn("WARNING! I am set to delete backupfile "
+ Console.warn("WARNING! I am set to delete backupfile "
+ fileToBeDeleted.getName()
+ " has modification time "
+ fileToBeDeletedLMTString
boolean delete = confirmNewerDeleteFile(fileToBeDeleted,
replacementFile, true);
- Cache.trace("BACKUPFILES " + (delete ? "confirmed" : "not")
- + " deleting file "
+ Console.trace("BACKUPFILES "
+ + (delete ? "confirmed" : "not") + " deleting file "
+ fileToBeDeleted.getAbsolutePath()
+ " which is newer than "
+ replacementFile.getAbsolutePath());
}
else
{
- Cache.debug("BACKUPFILES moving "
+ Console.debug("BACKUPFILES moving "
+ fileToBeDeleted.getAbsolutePath() + " to "
+ oldestTempFile.getAbsolutePath());
moveFileToFile(fileToBeDeleted, oldestTempFile);
}
else
{
- Cache.debug("BACKUPFILES going to move "
+ Console.debug("BACKUPFILES going to move "
+ fileToBeDeleted.getAbsolutePath() + " to "
+ oldestTempFile.getAbsolutePath());
moveFileToFile(fileToBeDeleted, oldestTempFile);
} catch (Exception e)
{
- Cache.error(
+ Console.error(
"Error occurred, probably making new temp file for '"
+ fileToBeDeleted.getName() + "'");
- Cache.error(Cache.getStackTraceString(e));
+ Console.error(Cache.getStackTraceString(e));
}
// reset
}
bfsb.append(backupFiles[i].getName());
}
- Cache.trace("BACKUPFILES backupFiles: " + bfsb.toString());
+ Console.trace("BACKUPFILES backupFiles: " + bfsb.toString());
// noMax == true means keep all backup files
if ((!noMax) && bfTreeMap.size() >= max)
{
- Cache.trace("BACKUPFILES noMax: " + noMax + ", " + "max: " + 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 = suffix.indexOf(NUM_PLACEHOLDER) > -1
? bfTreeMap.size() - max + 1
: 0;
- Cache.trace("BACKUPFILES numToDelete: " + numToDelete);
+ 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
File fileToBeDeleted = backupFiles[i];
boolean delete = true;
- Cache.trace("BACKUPFILES fileToBeDeleted: " + fileToBeDeleted);
+ Console.trace(
+ "BACKUPFILES fileToBeDeleted: " + fileToBeDeleted);
+
boolean newer = false;
if (replacementFile != null)
{
String replacementFileLMTString = sdf
.format(replacementFileLMT);
- Cache.warn("WARNING! I am set to delete backupfile '"
+ Console.warn("WARNING! I am set to delete backupfile '"
+ fileToBeDeleted.getName()
+ "' has modification time "
+ fileToBeDeletedLMTString
{
// User has confirmed delete -- no need to add it to the list
fileToBeDeleted.delete();
- Cache.debug("BACKUPFILES deleting fileToBeDeleted: "
+ Console.debug("BACKUPFILES deleting fileToBeDeleted: "
+ fileToBeDeleted);
delete = false;
}
else
{
// keeping file, nothing to do!
- Cache.debug("BACKUPFILES keeping fileToBeDeleted: "
+ Console.debug("BACKUPFILES keeping fileToBeDeleted: "
+ fileToBeDeleted);
}
}
if (delete)
{
addDeleteFile(fileToBeDeleted);
- Cache.debug("BACKUPFILES addDeleteFile(fileToBeDeleted): "
+ Console.debug("BACKUPFILES addDeleteFile(fileToBeDeleted): "
+ fileToBeDeleted);
}
String latestBackupFilename = dir + File.separatorChar
+ BackupFilenameParts.getBackupFilename(nextIndexNum, basename,
suffix, digits);
- Cache.trace("BACKUPFILES Moving old file [" + file
+ 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));
- Cache.debug("BACKUPFILES moving " + file + " to " + latestBackupFilename
- + " was " + (ret ? "" : "NOT ") + "successful");
-
+ Console.debug(
+ "BACKUPFILES moving " + file + " to " + latestBackupFilename
+ + " was " + (ret ? "" : "NOT ") + "successful");
if (tidyUp)
{
- Cache.debug("BACKUPFILES tidying up files");
+ Console.debug("BACKUPFILES tidying up files");
tidyUpFiles();
}
saveFile = nextTempFile(ftbd.getName(), ftbd.getParentFile());
} catch (Exception e)
{
- Cache.error(
+ Console.error(
"Error when confirming to keep backup file newer than other backup files.");
e.printStackTrace();
}
null, options, options[0]);
}
-
// return should be TRUE if file is to be deleted
return (confirmButton == JvOptionPane.YES_OPTION);
}
}
int confirmButton = Platform.isHeadless() ? JvOptionPane.YES_OPTION
- : JvOptionPane.showConfirmDialog(Desktop.getDesktopPane(),
+ : JvOptionPane.showConfirmDialog(Desktop.getDesktopPane(),
messageSB.toString(),
MessageManager.getString(
"label.backupfiles_confirm_delete"),
for (int i = 0; i < deleteFiles.size(); i++)
{
File fileToDelete = deleteFiles.get(i);
- Cache.trace("BACKUPFILES about to delete fileToDelete:"
+ Console.trace("BACKUPFILES about to delete fileToDelete:"
+ fileToDelete);
fileToDelete.delete();
- Cache.warn("deleted '" + fileToDelete.getName() + "'");
+ Console.warn("deleted '" + fileToDelete.getName() + "'");
}
}
dirFile = file.getParentFile();
} catch (Exception e)
{
- Cache.error("Could not get canonical path for file '" + file + "'");
+ Console.error("Could not get canonical path for file '" + file + "'");
return new TreeMap<>();
}
int pos = deleteFiles.indexOf(fileToBeDeleted);
if (pos > -1)
{
- Cache.debug("BACKUPFILES not adding file "
+ Console.debug("BACKUPFILES not adding file "
+ fileToBeDeleted.getAbsolutePath()
+ " to the delete list (already at index" + pos + ")");
return true;
}
else
{
- Cache.debug("BACKUPFILES adding file "
+ Console.debug("BACKUPFILES adding file "
+ fileToBeDeleted.getAbsolutePath() + " to the delete list");
deleteFiles.add(fileToBeDeleted);
}
public static boolean moveFileToFile(File oldFile, File newFile)
{
- Cache.initLogger();
+ Console.initLogger();
boolean ret = false;
Path oldPath = Paths.get(oldFile.getAbsolutePath());
Path newPath = Paths.get(newFile.getAbsolutePath());
try
{
// delete destination file - not usually necessary but Just In Case...
- Cache.trace("BACKUPFILES deleting " + newFile.getAbsolutePath());
+ Console.trace("BACKUPFILES deleting " + newFile.getAbsolutePath());
newFile.delete();
- Cache.trace("BACKUPFILES moving " + oldFile.getAbsolutePath() + " to "
- + newFile.getAbsolutePath());
+ Console.trace("BACKUPFILES moving " + oldFile.getAbsolutePath()
+ + " to " + newFile.getAbsolutePath());
Files.move(oldPath, newPath, StandardCopyOption.REPLACE_EXISTING);
ret = true;
- Cache.trace("BACKUPFILES move seems to have succeeded");
+ Console.trace("BACKUPFILES move seems to have succeeded");
} catch (IOException e)
{
- Cache.warn("Could not move file '" + oldPath.toString() + "' to '"
+ Console.warn("Could not move file '" + oldPath.toString() + "' to '"
+ newPath.toString() + "'");
- Cache.error(e.getMessage());
- Cache.debug(Cache.getStackTraceString(e));
+ Console.error(e.getMessage());
+ Console.debug(Cache.getStackTraceString(e));
ret = false;
} catch (Exception e)
{
- Cache.error(e.getMessage());
- Cache.debug(Cache.getStackTraceString(e));
+ Console.error(e.getMessage());
+ Console.debug(Cache.getStackTraceString(e));
ret = false;
}
return ret;
git://source.jalview.org / jalview.git / blobdiff