From 6dcf626ab3f32b045ded3fdb0aab4c1633196eb8 Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Tue, 9 Jun 2020 00:49:34 +0100
Subject: [PATCH] JAL-3628 Changed all file1.renameTo(file2) calls to
 Files.move(path1,path2,REPLACE_EXISTING) in
 jalview.io.BackupFiles. This fixes a problem in Windows
 with renameTo when destination file already exists.

---
 src/jalview/io/BackupFiles.java |   59 +++++++++++++++++++++++++++++----------
 1 file changed, 44 insertions(+), 15 deletions(-)

diff --git a/src/jalview/io/BackupFiles.java b/src/jalview/io/BackupFiles.java
index 0d5f92b..a41af4a 100644
--- a/src/jalview/io/BackupFiles.java
+++ b/src/jalview/io/BackupFiles.java
@@ -28,12 +28,21 @@ import jalview.util.Platform;
 
 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.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:
@@ -96,6 +105,10 @@ public class BackupFiles
   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));
@@ -107,7 +120,8 @@ public class BackupFiles
   {
     classInit();
     this.file = file;
-    BackupFilesPresetEntry bfpe = BackupFilesPresetEntry.getSavedBackupEntry();
+    BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
+            .getSavedBackupEntry();
     this.suffix = bfpe.suffix;
     this.noMax = bfpe.keepAll;
     this.max = bfpe.rollMax;
@@ -122,8 +136,8 @@ public class BackupFiles
       {
         String tempfilename = file.getName();
         File tempdir = file.getParentFile();
-        temp = File.createTempFile(tempfilename, TEMP_FILE_EXT + "_newfile",
-                tempdir);
+        temp = File.createTempFile(tempfilename,
+                TEMP_FILE_EXT + newTempFileSuffix, tempdir);
       }
       else
       {
@@ -210,7 +224,7 @@ public class BackupFiles
 
   public boolean renameTempFile()
   {
-    return tempFile.renameTo(file);
+    return moveFileToFile(tempFile, file);
   }
 
   // roll the backupfiles
@@ -272,7 +286,6 @@ public class BackupFiles
       {
         // backup style numbering
 
-
         int tempMax = noMax ? -1 : max;
         // noMax == true means no limits
         // look for first "gap" in backupFiles
@@ -288,7 +301,7 @@ public class BackupFiles
             tempMax = i;
           }
         }
-        
+
         File previousFile = null;
         File fileToBeDeleted = null;
         for (int n = tempMax; n > 0; n--)
@@ -318,7 +331,7 @@ public class BackupFiles
             {
               File oldestTempFile = nextTempFile(fileToBeDeleted.getName(),
                       dirFile);
-              
+
               if (fileToBeDeletedLMT > replacementFileLMT)
               {
                 String fileToBeDeletedLMTString = sdf
@@ -344,12 +357,12 @@ public class BackupFiles
                 }
                 else
                 {
-                  fileToBeDeleted.renameTo(oldestTempFile);
+                  moveFileToFile(fileToBeDeleted, oldestTempFile);
                 }
               }
               else
               {
-                fileToBeDeleted.renameTo(oldestTempFile);
+                moveFileToFile(fileToBeDeleted, oldestTempFile);
                 addDeleteFile(oldestTempFile);
               }
 
@@ -373,7 +386,7 @@ public class BackupFiles
           {
             if (previousFile != null)
             {
-              ret = ret && backupfile_n.renameTo(previousFile);
+              ret = ret && moveFileToFile(backupfile_n, previousFile);
             }
           }
 
@@ -463,7 +476,7 @@ public class BackupFiles
     String latestBackupFilename = dir + File.separatorChar
             + BackupFilenameParts.getBackupFilename(nextIndexNum, basename,
                     suffix, digits);
-    ret |= file.renameTo(new File(latestBackupFilename));
+    ret |= moveFileToFile(file, new File(latestBackupFilename));
 
     if (tidyUp)
     {
@@ -565,7 +578,6 @@ public class BackupFiles
               null, options, options[0]);
     }
 
-
     // return should be TRUE if file is to be deleted
     return (confirmButton == JvOptionPane.YES_OPTION);
   }
@@ -622,8 +634,7 @@ public class BackupFiles
   }
 
   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
@@ -662,7 +673,8 @@ public class BackupFiles
     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"));
       if (rename)
       {
         if (messageSB.length() > 0)
@@ -761,4 +773,21 @@ public class BackupFiles
     return ret;
   }
 
+  private 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;
+  }
 }
-- 
1.7.10.2