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JAL-3676 Documentation in Help for Java Console, Logging and Reporting Bugs
[jalview.git]
/
src
/
jalview
/
io
/
BackupFiles.java
diff --git
a/src/jalview/io/BackupFiles.java
b/src/jalview/io/BackupFiles.java
index
4f86f3d
..
2acd6cc
100644
(file)
--- a/
src/jalview/io/BackupFiles.java
+++ b/
src/jalview/io/BackupFiles.java
@@
-131,7
+131,7
@@
public class BackupFiles
{
String tempfilename = file.getName();
File tempdir = file.getParentFile();
{
String tempfilename = file.getName();
File tempdir = file.getParentFile();
- Cache.log.debug(
+ Cache.log.trace(
"BACKUPFILES [file!=null] attempting to create temp file for "
+ tempfilename + " in dir " + tempdir);
temp = File.createTempFile(tempfilename,
"BACKUPFILES [file!=null] attempting to create temp file for "
+ tempfilename + " in dir " + tempdir);
temp = File.createTempFile(tempfilename,
@@
-141,7
+141,7
@@
public class BackupFiles
}
else
{
}
else
{
- Cache.log.debug(
+ Cache.log.trace(
"BACKUPFILES [file==null] attempting to create default temp file "
+ DEFAULT_TEMP_FILE + " with extension "
+ TEMP_FILE_EXT);
"BACKUPFILES [file==null] attempting to create default temp file "
+ DEFAULT_TEMP_FILE + " with extension "
+ TEMP_FILE_EXT);
@@
-152,26
+152,27
@@
public class BackupFiles
Cache.log
.error("Could not create temp file to save to (IOException)");
Cache.log.error(e.getMessage());
Cache.log
.error("Could not create temp file to save to (IOException)");
Cache.log.error(e.getMessage());
- Cache.log.debug(e.getStackTrace());
+ Cache.log.debug(Cache.getStackTraceString(e));
} catch (Exception e)
{
Cache.log.error("Exception ctreating temp file for saving");
} catch (Exception e)
{
Cache.log.error("Exception ctreating temp file for saving");
- Cache.log.debug(e.getStackTrace());
+ Cache.log.debug(Cache.getStackTraceString(e));
}
this.setTempFile(temp);
}
public static void classInit()
{
}
this.setTempFile(temp);
}
public static void classInit()
{
- Cache.log.debug("BACKUPFILES classInit");
+ Cache.initLogger();
+ Cache.log.trace("BACKUPFILES classInit");
boolean e = Cache.getDefault(ENABLED, true);
setEnabled(e);
boolean e = Cache.getDefault(ENABLED, true);
setEnabled(e);
- Cache.log.debug("BACKUPFILES " + (e ? "enabled" : "disabled"));
+ Cache.log.trace("BACKUPFILES " + (e ? "enabled" : "disabled"));
BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
.getSavedBackupEntry();
BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
.getSavedBackupEntry();
- Cache.log.debug("BACKUPFILES preset scheme " + bfpe.toString());
+ Cache.log.trace("BACKUPFILES preset scheme " + bfpe.toString());
setConfirmDelete(bfpe.confirmDelete);
setConfirmDelete(bfpe.confirmDelete);
- Cache.log.debug("BACKUPFILES confirm delete " + bfpe.confirmDelete);
+ Cache.log.trace("BACKUPFILES confirm delete " + bfpe.confirmDelete);
}
public static void setEnabled(boolean flag)
}
public static void setEnabled(boolean flag)
@@
-218,7
+219,7
@@
public class BackupFiles
Cache.log.error(
"IOException when getting Canonical Path of temp file '"
+ this.getTempFile().getName() + "'");
Cache.log.error(
"IOException when getting Canonical Path of temp file '"
+ this.getTempFile().getName() + "'");
- Cache.log.debug(e.getStackTrace());
+ Cache.log.debug(Cache.getStackTraceString(e));
}
return path;
}
}
return path;
}
@@
-262,7
+263,7
@@
public class BackupFiles
return true;
}
return true;
}
- Cache.log.debug("BACKUPFILES rollBackupFiles starting");
+ Cache.log.trace("BACKUPFILES rollBackupFiles starting");
String dir = "";
File dirFile;
String dir = "";
File dirFile;
@@
-270,19
+271,19
@@
public class BackupFiles
{
dirFile = file.getParentFile();
dir = dirFile.getCanonicalPath();
{
dirFile = file.getParentFile();
dir = dirFile.getCanonicalPath();
- Cache.log.debug("BACKUPFILES dir: " + dir);
+ Cache.log.trace("BACKUPFILES dir: " + dir);
} catch (Exception e)
{
Cache.log.error(
"Could not get canonical path for file '" + file + "'");
Cache.log.error(e.getMessage());
} catch (Exception e)
{
Cache.log.error(
"Could not get canonical path for file '" + file + "'");
Cache.log.error(e.getMessage());
- Cache.log.debug(e.getStackTrace());
+ Cache.log.debug(Cache.getStackTraceString(e));
return false;
}
String filename = file.getName();
String basename = filename;
return false;
}
String filename = file.getName();
String basename = filename;
- Cache.log.debug("BACKUPFILES filename is " + filename);
+ Cache.log.trace("BACKUPFILES filename is " + filename);
boolean ret = true;
// Create/move backups up one
boolean ret = true;
// Create/move backups up one
@@
-295,11
+296,11
@@
public class BackupFiles
int nextIndexNum = 0;
Cache.log
int nextIndexNum = 0;
Cache.log
- .debug("BACKUPFILES backupFiles.length: " + backupFiles.length);
+ .trace("BACKUPFILES backupFiles.length: " + backupFiles.length);
if (backupFiles.length == 0)
{
// No other backup files. Just need to move existing file to backupfile_1
if (backupFiles.length == 0)
{
// No other backup files. Just need to move existing file to backupfile_1
- Cache.log.debug(
+ Cache.log.trace(
"BACKUPFILES no existing backup files, setting index to 1");
nextIndexNum = 1;
}
"BACKUPFILES no existing backup files, setting index to 1");
nextIndexNum = 1;
}
@@
-313,7
+314,7
@@
public class BackupFiles
if (reverseOrder)
{
// backup style numbering
if (reverseOrder)
{
// backup style numbering
- Cache.log.debug("BACKUPFILES rolling files in reverse order");
+ Cache.log.trace("BACKUPFILES rolling files in reverse order");
int tempMax = noMax ? -1 : max;
// noMax == true means no limits
int tempMax = noMax ? -1 : max;
// noMax == true means no limits
@@
-345,7
+346,7
@@
public class BackupFiles
// no "oldest" file to delete
previousFile = backupfile_n;
fileToBeDeleted = null;
// no "oldest" file to delete
previousFile = backupfile_n;
fileToBeDeleted = null;
- Cache.log.debug("BACKUPFILES No oldest file to delete");
+ Cache.log.trace("BACKUPFILES No oldest file to delete");
continue;
}
continue;
}
@@
-356,9
+357,9
@@
public class BackupFiles
File replacementFile = backupfile_n;
long fileToBeDeletedLMT = fileToBeDeleted.lastModified();
long replacementFileLMT = replacementFile.lastModified();
File replacementFile = backupfile_n;
long fileToBeDeletedLMT = fileToBeDeleted.lastModified();
long replacementFileLMT = replacementFile.lastModified();
- Cache.log.debug("BACKUPFILES fileToBeDeleted is "
+ Cache.log.trace("BACKUPFILES fileToBeDeleted is "
+ fileToBeDeleted.getAbsolutePath());
+ fileToBeDeleted.getAbsolutePath());
- Cache.log.debug("BACKUPFILES replacementFile is "
+ Cache.log.trace("BACKUPFILES replacementFile is "
+ backupfile_n.getAbsolutePath());
try
+ backupfile_n.getAbsolutePath());
try
@@
-383,7
+384,7
@@
public class BackupFiles
boolean delete = confirmNewerDeleteFile(fileToBeDeleted,
replacementFile, true);
boolean delete = confirmNewerDeleteFile(fileToBeDeleted,
replacementFile, true);
- Cache.log.debug("BACKUPFILES "
+ Cache.log.trace("BACKUPFILES "
+ (delete ? "confirmed" : "not") + " deleting file "
+ fileToBeDeleted.getAbsolutePath()
+ " which is newer than "
+ (delete ? "confirmed" : "not") + " deleting file "
+ fileToBeDeleted.getAbsolutePath()
+ " which is newer than "
@@
-416,7
+417,7
@@
public class BackupFiles
Cache.log.error(
"Error occurred, probably making new temp file for '"
+ fileToBeDeleted.getName() + "'");
Cache.log.error(
"Error occurred, probably making new temp file for '"
+ fileToBeDeleted.getName() + "'");
- Cache.log.error(e.getStackTrace());
+ Cache.log.error(Cache.getStackTraceString(e));
}
// reset
}
// reset
@@
-431,7
+432,9
@@
public class BackupFiles
{
if (previousFile != null)
{
{
if (previousFile != null)
{
- ret = ret && moveFileToFile(backupfile_n, previousFile);
+ // using boolean '&' instead of '&&' as don't want moveFileToFile
+ // attempt to be conditional (short-circuit)
+ ret = ret & moveFileToFile(backupfile_n, previousFile);
}
}
}
}
@@
-456,12
+459,12
@@
public class BackupFiles
}
bfsb.append(backupFiles[i].getName());
}
}
bfsb.append(backupFiles[i].getName());
}
- Cache.log.debug("BACKUPFILES backupFiles: " + bfsb.toString());
+ Cache.log.trace("BACKUPFILES backupFiles: " + bfsb.toString());
// noMax == true means keep all backup files
if ((!noMax) && bfTreeMap.size() >= max)
{
// noMax == true means keep all backup files
if ((!noMax) && bfTreeMap.size() >= max)
{
- Cache.log.debug("BACKUPFILES noMax: " + noMax + ", " + "max: "
+ Cache.log.trace("BACKUPFILES noMax: " + noMax + ", " + "max: "
+ max + ", " + "bfTreeMap.size(): " + bfTreeMap.size());
// need to delete some files to keep number of backups to designated
// max.
+ max + ", " + "bfTreeMap.size(): " + bfTreeMap.size());
// need to delete some files to keep number of backups to designated
// max.
@@
-471,7
+474,7
@@
public class BackupFiles
int numToDelete = suffix.indexOf(NUM_PLACEHOLDER) > -1
? bfTreeMap.size() - max + 1
: 0;
int numToDelete = suffix.indexOf(NUM_PLACEHOLDER) > -1
? bfTreeMap.size() - max + 1
: 0;
- Cache.log.debug("BACKUPFILES numToDelete: " + numToDelete);
+ Cache.log.trace("BACKUPFILES numToDelete: " + numToDelete);
// the "replacement" file is the latest backup file being kept (it's
// not replacing though)
File replacementFile = numToDelete < backupFiles.length
// the "replacement" file is the latest backup file being kept (it's
// not replacing though)
File replacementFile = numToDelete < backupFiles.length
@@
-484,7
+487,7
@@
public class BackupFiles
File fileToBeDeleted = backupFiles[i];
boolean delete = true;
File fileToBeDeleted = backupFiles[i];
boolean delete = true;
- Cache.log.debug(
+ Cache.log.trace(
"BACKUPFILES fileToBeDeleted: " + fileToBeDeleted);
boolean newer = false;
"BACKUPFILES fileToBeDeleted: " + fileToBeDeleted);
boolean newer = false;
@@
-547,9
+550,11
@@
public class BackupFiles
String latestBackupFilename = dir + File.separatorChar
+ BackupFilenameParts.getBackupFilename(nextIndexNum, basename,
suffix, digits);
String latestBackupFilename = dir + File.separatorChar
+ BackupFilenameParts.getBackupFilename(nextIndexNum, basename,
suffix, digits);
- Cache.log.debug("BACKUPFILES Moving old file [" + file
+ Cache.log.trace("BACKUPFILES Moving old file [" + file
+ "] to latestBackupFilename [" + latestBackupFilename + "]");
+ "] to latestBackupFilename [" + latestBackupFilename + "]");
- ret |= moveFileToFile(file, new File(latestBackupFilename));
+ // using boolean '&' instead of '&&' as don't want moveFileToFile attempt to
+ // be conditional (short-circuit)
+ ret = ret & moveFileToFile(file, new File(latestBackupFilename));
Cache.log.debug(
"BACKUPFILES moving " + file + " to " + latestBackupFilename
+ " was " + (ret ? "" : "NOT ") + "successful");
Cache.log.debug(
"BACKUPFILES moving " + file + " to " + latestBackupFilename
+ " was " + (ret ? "" : "NOT ") + "successful");
@@
-721,10
+726,10
@@
public class BackupFiles
for (int i = 0; i < deleteFiles.size(); i++)
{
File fileToDelete = deleteFiles.get(i);
for (int i = 0; i < deleteFiles.size(); i++)
{
File fileToDelete = deleteFiles.get(i);
- Cache.log.debug(
- "BACKUPFILES deleting fileToDelete:" + fileToDelete);
+ Cache.log.trace("BACKUPFILES about to delete fileToDelete:"
+ + fileToDelete);
fileToDelete.delete();
fileToDelete.delete();
- Cache.log.warn("deleting '" + fileToDelete.getName() + "'");
+ Cache.log.warn("deleted '" + fileToDelete.getName() + "'");
}
}
}
}
@@
-772,7
+777,6
@@
public class BackupFiles
boolean okay = roll && rename;
if (!okay)
{
boolean okay = roll && rename;
if (!okay)
{
- boolean yesno = false;
StringBuilder messageSB = new StringBuilder();
messageSB.append(MessageManager.getString(
"label.backupfiles_confirm_save_file_backupfiles_roll_wrong"));
StringBuilder messageSB = new StringBuilder();
messageSB.append(MessageManager.getString(
"label.backupfiles_confirm_save_file_backupfiles_roll_wrong"));
@@
-797,6
+801,12
@@
public class BackupFiles
"label.backupfiles_confirm_save_new_saved_file_not_ok"));
// "The new saved file might not be okay."
}
"label.backupfiles_confirm_save_new_saved_file_not_ok"));
// "The new saved file might not be okay."
}
+ 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,
int confirmButton = Platform.isHeadless() ? JvOptionPane.OK_OPTION
: JvOptionPane.showConfirmDialog(Desktop.desktop,
@@
-886,30
+896,31
@@
public class BackupFiles
public static boolean moveFileToFile(File oldFile, File newFile)
{
public static boolean moveFileToFile(File oldFile, File newFile)
{
+ Cache.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...
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.log.debug("BACKUPFILES deleting " + newFile.getAbsolutePath());
+ Cache.log.trace("BACKUPFILES deleting " + newFile.getAbsolutePath());
newFile.delete();
newFile.delete();
- Cache.log.debug("BACKUPFILES moving " + oldFile.getAbsolutePath()
+ Cache.log.trace("BACKUPFILES moving " + oldFile.getAbsolutePath()
+ " to " + newFile.getAbsolutePath());
Files.move(oldPath, newPath, StandardCopyOption.REPLACE_EXISTING);
ret = true;
+ " to " + newFile.getAbsolutePath());
Files.move(oldPath, newPath, StandardCopyOption.REPLACE_EXISTING);
ret = true;
- Cache.log.debug("BACKUPFILES move seems to have succeeded");
+ Cache.log.trace("BACKUPFILES move seems to have succeeded");
} catch (IOException e)
{
Cache.log.warn("Could not move file '" + oldPath.toString() + "' to '"
+ newPath.toString() + "'");
Cache.log.error(e.getMessage());
} catch (IOException e)
{
Cache.log.warn("Could not move file '" + oldPath.toString() + "' to '"
+ newPath.toString() + "'");
Cache.log.error(e.getMessage());
- Cache.log.debug(e.getStackTrace());
+ Cache.log.debug(Cache.getStackTraceString(e));
ret = false;
} catch (Exception e)
{
Cache.log.error(e.getMessage());
ret = false;
} catch (Exception e)
{
Cache.log.error(e.getMessage());
- Cache.log.debug(e.getStackTrace());
+ Cache.log.debug(Cache.getStackTraceString(e));
ret = false;
}
return ret;
ret = false;
}
return ret;