X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FBackupFiles.java;fp=src%2Fjalview%2Fio%2FBackupFiles.java;h=7bb5d310dcaf2066e2298294728dd7fd32ae2c55;hb=ca8504cf9d10874dce9f07cf7a9d933853fe0dd0;hp=0000000000000000000000000000000000000000;hpb=775e7bc104584e88dddcea73fbf02c66f5200c16;p=jalview.git

diff --git a/src/jalview/io/BackupFiles.java b/src/jalview/io/BackupFiles.java
new file mode 100644
index 0000000..7bb5d31
--- /dev/null
+++ b/src/jalview/io/BackupFiles.java
@@ -0,0 +1,743 @@
+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.
+ * The rest of the options are now saved as BACKUPFILES_PRESET, BACKUPFILES_SAVED and BACKUPFILES_CUSTOM
+ * (see BackupFilesPresetEntry)
+ */
+
+public class BackupFiles
+{
+
+  // labels for saved params in Cache and .jalview_properties
+  public static final String NS = "BACKUPFILES";
+
+  public static final String ENABLED = NS + "_ENABLED";
+
+  public static final String NUM_PLACEHOLDER = "%n";
+
+  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 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;
+
+  // defaultDigits - number of zero-led digits to use in the filename
+  private int digits;
+
+  // reverseOrder - set to true to make newest (latest) files lowest number
+  // (like rolled log files)
+  private boolean reverseOrder;
+
+  // 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<File> deleteFiles = new ArrayList<>();
+
+  // 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 SUFFIX, NO_MAX, ROLL_MAX, SUFFIX_DIGITS and
+  // REVERSE_ORDER
+  public BackupFiles(File file)
+  {
+    classInit();
+    this.file = file;
+    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;
+    try
+    {
+      if (file != null)
+      {
+        String tempfilename = file.getName();
+        File tempdir = file.getParentFile();
+        temp = File.createTempFile(tempfilename, TEMP_FILE_EXT + "_newfile",
+                tempdir);
+      }
+      else
+      {
+        temp = File.createTempFile(DEFAULT_TEMP_FILE, TEMP_FILE_EXT);
+      }
+    } catch (IOException e)
+    {
+      System.out.println(
+              "Could not create temp file to save into (IOException)");
+    } catch (Exception e)
+    {
+      System.out.println("Exception ctreating temp file for saving");
+    }
+    this.setTempFile(temp);
+  }
+
+  public static void classInit()
+  {
+    setEnabled(Cache.getDefault(ENABLED, true));
+    BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
+            .getSavedBackupEntry();
+    setConfirmDelete(bfpe.confirmDelete);
+  }
+
+  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);
+  }
+
+  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;
+    }
+
+    String dir = "";
+    File dirFile;
+    try
+    {
+      dirFile = file.getParentFile();
+      dir = dirFile.getCanonicalPath();
+    } catch (Exception e)
+    {
+      System.out.println(
+              "Could not get canonical path for file '" + file + "'");
+      return false;
+    }
+    String filename = file.getName();
+    String basename = filename;
+
+    boolean ret = true;
+    // Create/move backups up one
+
+    deleteFiles.clear();
+
+    // find existing backup files
+    BackupFilenameFilter bff = new BackupFilenameFilter(basename, suffix,
+            digits);
+    File[] backupFiles = dirFile.listFiles(bff);
+    int nextIndexNum = 0;
+
+    if (backupFiles.length == 0)
+    {
+      // 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)
+      {
+        // backup style numbering
+
+
+        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;
+          }
+        }
+        
+        File previousFile = null;
+        File fileToBeDeleted = null;
+        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
+            previousFile = backupfile_n;
+            fileToBeDeleted = null;
+            continue;
+          }
+
+          // 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)
+          {
+            File replacementFile = backupfile_n;
+            long fileToBeDeletedLMT = fileToBeDeleted.lastModified();
+            long replacementFileLMT = replacementFile.lastModified();
+
+            try
+            {
+              File oldestTempFile = nextTempFile(fileToBeDeleted.getName(),
+                      dirFile);
+              
+              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
+                {
+                  fileToBeDeleted.renameTo(oldestTempFile);
+                }
+              }
+              else
+              {
+                fileToBeDeleted.renameTo(oldestTempFile);
+                addDeleteFile(oldestTempFile);
+              }
+
+            } catch (Exception e)
+            {
+              System.out.println(
+                      "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
+          {
+            if (previousFile != null)
+            {
+              ret = ret && backupfile_n.renameTo(previousFile);
+            }
+          }
+
+          previousFile = backupfile_n;
+        }
+
+        // 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;
+          // 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;
+      }
+    }
+
+    // Let's make the new backup file!! yay, got there at last!
+    String latestBackupFilename = dir + File.separatorChar
+            + BackupFilenameParts.getBackupFilename(nextIndexNum, basename,
+                    suffix, digits);
+    ret |= file.renameTo(new File(latestBackupFilename));
+
+    if (tidyUp)
+    {
+      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 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
+    {
+      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);
+  }
+
+  private void deleteOldFiles()
+  {
+    if (deleteFiles != null && !deleteFiles.isEmpty())
+    {
+      boolean doDelete = false;
+      StringBuilder messageSB = null;
+      if (confirmDelete && deleteFiles.size() > 0)
+      {
+        messageSB = new StringBuilder();
+        messageSB.append(MessageManager
+                .getString("label.backupfiles_confirm_delete_old_files"));
+        for (int i = 0; i < deleteFiles.size(); i++)
+        {
+          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 confirmButton = JvOptionPane.showConfirmDialog(Desktop.desktop,
+                messageSB.toString(),
+                MessageManager
+                        .getString("label.backupfiles_confirm_delete"),
+                JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE);
+
+        doDelete = (confirmButton == JvOptionPane.YES_OPTION);
+      }
+      else
+      {
+        doDelete = true;
+      }
+
+      if (doDelete)
+      {
+        for (int i = 0; i < deleteFiles.size(); i++)
+        {
+          File fileToDelete = deleteFiles.get(i);
+          fileToDelete.delete();
+          System.out.println("DELETING '" + fileToDelete.getName() + "'");
+        }
+      }
+
+    }
+
+    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
+    {
+      dirFile = file.getParentFile();
+    } catch (Exception e)
+    {
+      System.out.println(
+              "Could not get canonical path for file '" + file + "'");
+      return new TreeMap<>();
+    }
+
+    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 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;
+  }
+
+}