Ensure that the project files are only overwritten, when the saving p…

…rocess was successful and not interrupted

* Strategy to achieve this:
 * When saving the mastodon project files, they are first saved to projectfile_pending
 * When saving was successful, projectfile gets overwritten with projectfile_pending
 * In the past, it has been observed that *.mastodon files were corrupted and could not be read anymore
 * Typical saving times for a project range from ~0.2s to ~2s (depending on project size, attributes, etc.). Not very long, but long enough to kill mastodon during the saving process.

src/main/java/org/mastodon/mamut/io/project/MamutProject.java

@@ -28,6 +28,8 @@
  */
 package org.mastodon.mamut.io.project;
 
+import org.apache.commons.lang3.tuple.Pair;
+
 import java.io.Closeable;
 import java.io.File;
 import java.io.FileInputStream;
@@ -36,6 +38,9 @@
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
+import java.nio.file.Files;
+import java.nio.file.StandardCopyOption;
+import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
 import java.util.Collections;
@@ -334,22 +339,31 @@ public void close() throws IOException
 	private class WriteToDirectory implements ProjectWriter
 	{
 
+		private final List< Pair< File, File > > files;
+
+		private WriteToDirectory()
+		{
+			files = new ArrayList<>();
+		}
+
 		@Override
 		public OutputStream getProjectXmlOutputStream() throws FileNotFoundException
 		{
-			return new FileOutputStream( new File( projectRoot, PROJECT_FILE_NAME ) );
+			return new FileOutputStream( getPendingFile( PROJECT_FILE_NAME ) );
 		}
 
 		@Override
 		public OutputStream getRawModelOutputStream() throws FileNotFoundException
 		{
-			return new FileOutputStream( new File( projectRoot, RAW_MODEL_FILE_NAME ) );
+
+			return new FileOutputStream( getPendingFile( RAW_MODEL_FILE_NAME ) );
 		}
 
 		@Override
 		public OutputStream getRawTagsOutputStream() throws FileNotFoundException
 		{
-			return new FileOutputStream( new File( projectRoot, RAW_TAGS_FILE_NAME ) );
+
+			return new FileOutputStream( getPendingFile( RAW_TAGS_FILE_NAME ) );
 		}
 
 		@Override
@@ -358,33 +372,55 @@ public OutputStream getFeatureOutputStream( final String featureKey ) throws IOE
 			final File featureFolder = new File( projectRoot, FEATURE_FOLDER_NAME );
 			if ( !featureFolder.exists() )
 				featureFolder.mkdir();
-			return new FileOutputStream( new File( featureFolder, featureKey + ".raw" ) );
+			return new FileOutputStream( getPendingFile( featureFolder, featureKey + ".raw" ) );
 		}
 
 		@Override
 		public OutputStream getGuiOutputStream() throws IOException
 		{
-			return new FileOutputStream( new File( projectRoot, GUI_FILE_NAME ) );
+			return new FileOutputStream( getPendingFile( GUI_FILE_NAME ) );
 		}
 
 		@Override
 		public OutputStream getBackupDatasetXmlOutputStream() throws IOException
 		{
-			return new FileOutputStream( new File( projectRoot, BACKUP_DATASET_XML_FILE_NAME ) );
+			return new FileOutputStream( getPendingFile( BACKUP_DATASET_XML_FILE_NAME ) );
 		}
 
 		@Override
 		public void close() throws IOException
-		{}
+		{
+			for ( final Pair< File, File > pair : files )
+				Files.move( pair.getLeft().toPath(), pair.getRight().toPath(), StandardCopyOption.REPLACE_EXISTING );
+		}
+
+		private File getPendingFile( final File parent, final String fileName )
+		{
+			String suffix = "_pending";
+			File pendingFile = new File( parent, fileName + suffix );
+			File targetFile = new File( parent, fileName );
+			files.add( Pair.of( pendingFile, targetFile ) );
+			return pendingFile;
+		}
+
+		private File getPendingFile( final String fileName )
+		{
+			return getPendingFile( projectRoot, fileName );
+		}
+
 	}
 
 	private class WriteToZip implements ProjectWriter
 	{
 		private final WriteZip zip;
 
+		private final File pendingFile;
+
 		WriteToZip() throws IOException
 		{
-			zip = new WriteZip( projectRoot );
+			String suffix = "_pending";
+			pendingFile = new File( projectRoot.getParent(), projectRoot.getName() + suffix );
+			zip = new WriteZip( pendingFile );
 		}
 
 		@Override
@@ -427,6 +463,7 @@ public OutputStream getBackupDatasetXmlOutputStream() throws IOException
 		public void close() throws IOException
 		{
 			zip.close();
+			Files.move( pendingFile.toPath(), projectRoot.toPath(), StandardCopyOption.REPLACE_EXISTING );
 		}
 	}
 }