Use pending file during save

.github/build.sh

@@ -1,3 +1,5 @@
 #!/bin/sh
+export DISPLAY=:99
+sudo Xvfb -ac :99 -screen 0 1280x1024x24 > /dev/null 2>&1 &
 curl -fsLO https://raw.githubusercontent.com/scijava/scijava-scripts/main/ci-build.sh
 sh ci-build.sh

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

@@ -28,6 +28,8 @@
  */
 package org.mastodon.mamut.io.project;
 
+import org.apache.commons.io.FileUtils;
+
 import java.io.Closeable;
 import java.io.File;
 import java.io.FileInputStream;
@@ -36,6 +38,8 @@
 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.Arrays;
 import java.util.Collection;
 import java.util.Collections;
@@ -333,29 +337,37 @@ public void close() throws IOException
 
 	private class WriteToDirectory implements ProjectWriter
 	{
+		private final File pendingDirectory;
+
+		private WriteToDirectory()
+		{
+			pendingDirectory = new File( projectRoot.getParent(), projectRoot.getName() + "_pending" );
+			if ( !pendingDirectory.exists() )
+				pendingDirectory.mkdir();
+		}
 
 		@Override
 		public OutputStream getProjectXmlOutputStream() throws FileNotFoundException
 		{
-			return new FileOutputStream( new File( projectRoot, PROJECT_FILE_NAME ) );
+			return new FileOutputStream( new File( pendingDirectory, PROJECT_FILE_NAME ) );
 		}
 
 		@Override
 		public OutputStream getRawModelOutputStream() throws FileNotFoundException
 		{
-			return new FileOutputStream( new File( projectRoot, RAW_MODEL_FILE_NAME ) );
+			return new FileOutputStream( new File( pendingDirectory, RAW_MODEL_FILE_NAME ) );
 		}
 
 		@Override
 		public OutputStream getRawTagsOutputStream() throws FileNotFoundException
 		{
-			return new FileOutputStream( new File( projectRoot, RAW_TAGS_FILE_NAME ) );
+			return new FileOutputStream( new File( pendingDirectory, RAW_TAGS_FILE_NAME ) );
 		}
 
 		@Override
 		public OutputStream getFeatureOutputStream( final String featureKey ) throws IOException
 		{
-			final File featureFolder = new File( projectRoot, FEATURE_FOLDER_NAME );
+			final File featureFolder = new File( pendingDirectory, FEATURE_FOLDER_NAME );
 			if ( !featureFolder.exists() )
 				featureFolder.mkdir();
 			return new FileOutputStream( new File( featureFolder, featureKey + ".raw" ) );
@@ -364,27 +376,34 @@ public OutputStream getFeatureOutputStream( final String featureKey ) throws IOE
 		@Override
 		public OutputStream getGuiOutputStream() throws IOException
 		{
-			return new FileOutputStream( new File( projectRoot, GUI_FILE_NAME ) );
+			return new FileOutputStream( new File( pendingDirectory, GUI_FILE_NAME ) );
 		}
 
 		@Override
 		public OutputStream getBackupDatasetXmlOutputStream() throws IOException
 		{
-			return new FileOutputStream( new File( projectRoot, BACKUP_DATASET_XML_FILE_NAME ) );
+			return new FileOutputStream( new File( pendingDirectory, BACKUP_DATASET_XML_FILE_NAME ) );
 		}
 
 		@Override
 		public void close() throws IOException
-		{}
+		{
+			FileUtils.deleteDirectory( projectRoot );
+			Files.move( pendingDirectory.toPath(), projectRoot.toPath(), StandardCopyOption.REPLACE_EXISTING );
+		}
 	}
 
 	private class WriteToZip implements ProjectWriter
 	{
 		private final WriteZip zip;
 
-		WriteToZip() throws IOException
+		private final File pendingFile;
+
+		private 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 +446,7 @@ public OutputStream getBackupDatasetXmlOutputStream() throws IOException
 		public void close() throws IOException
 		{
 			zip.close();
+			Files.move( pendingFile.toPath(), projectRoot.toPath(), StandardCopyOption.REPLACE_EXISTING );
 		}
 	}
 }

src/test/java/org/mastodon/mamut/io/ProjectSaverTest.java

@@ -0,0 +1,97 @@
+package org.mastodon.mamut.io;
+
+import ij.ImagePlus;
+import net.imagej.ImgPlus;
+import net.imagej.axis.Axes;
+import net.imagej.axis.AxisType;
+import net.imglib2.img.Img;
+import net.imglib2.img.array.ArrayImgs;
+import net.imglib2.img.display.imagej.ImgToVirtualStack;
+import net.imglib2.type.numeric.real.FloatType;
+import org.junit.Test;
+import org.mastodon.mamut.ProjectModel;
+import org.mastodon.mamut.io.project.MamutProject;
+import org.mastodon.mamut.model.Model;
+import org.mastodon.views.bdv.SharedBigDataViewerData;
+import org.scijava.Context;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.util.Objects;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+
+public class ProjectSaverTest
+{
+	@Test
+	public void testSaveProjectToZip() throws IOException
+	{
+		try (Context context = new Context())
+		{
+			Model model = new Model();
+			Img< FloatType > image = ArrayImgs.floats( 1, 1, 1 );
+			File mastodonFile = File.createTempFile( "test", ".mastodon" );
+			ProjectModel appModel = wrapAsAppModel( image, model, context, mastodonFile );
+			ProjectSaver.saveProject( mastodonFile, appModel );
+			assertNotNull( mastodonFile );
+			assertTrue( mastodonFile.exists() );
+			assertTrue( mastodonFile.isFile() );
+			assertTrue( mastodonFile.length() > 0 );
+			assertEquals( mastodonFile, appModel.getProject().getProjectRoot() );
+
+			ProjectSaver.saveProject( mastodonFile, appModel ); // Overwrite again
+			assertTrue( mastodonFile.exists() );
+			assertTrue( mastodonFile.isFile() );
+			assertTrue( mastodonFile.length() > 0 );
+			assertEquals( mastodonFile, appModel.getProject().getProjectRoot() );
+		}
+	}
+
+	@Test
+	public void testSaveProjectToDirectory() throws IOException
+	{
+		try (Context context = new Context())
+		{
+			Model model = new Model();
+			Img< FloatType > image = ArrayImgs.floats( 1, 1, 1 );
+			File mastodonDirectory = Files.createTempDirectory( "test" ).toFile();
+			ProjectModel appModel = wrapAsAppModel( image, model, context, mastodonDirectory );
+			ProjectSaver.saveProject( mastodonDirectory, appModel );
+			assertNotNull( mastodonDirectory );
+			assertTrue( mastodonDirectory.exists() );
+			assertTrue( mastodonDirectory.isDirectory() );
+			assertEquals( mastodonDirectory, appModel.getProject().getProjectRoot() );
+			File[] files = mastodonDirectory.listFiles();
+			assertNotNull( files );
+			assertEquals( 6, files.length );
+
+			ProjectSaver.saveProject( mastodonDirectory, appModel ); // Overwrite again
+			assertTrue( mastodonDirectory.exists() );
+			assertTrue( mastodonDirectory.isDirectory() );
+			assertEquals( mastodonDirectory, appModel.getProject().getProjectRoot() );
+			files = mastodonDirectory.listFiles();
+			assertNotNull( files );
+			assertEquals( 6, files.length );
+		}
+	}
+
+	private static ProjectModel wrapAsAppModel( final Img< FloatType > image, final Model model, final Context context, final File file )
+			throws IOException
+	{
+		final SharedBigDataViewerData sharedBigDataViewerData = asSharedBdvDataXyz( image );
+		MamutProject mamutProject = new MamutProject( file );
+		File datasetXmlFile = File.createTempFile( "test", ".xml" );
+		mamutProject.setDatasetXmlFile( datasetXmlFile );
+		return ProjectModel.create( context, model, sharedBigDataViewerData, mamutProject );
+	}
+
+	private static SharedBigDataViewerData asSharedBdvDataXyz( final Img< FloatType > image1 )
+	{
+		final ImagePlus image =
+				ImgToVirtualStack.wrap( new ImgPlus<>( image1, "image", new AxisType[] { Axes.X, Axes.Y, Axes.Z, Axes.TIME } ) );
+		return Objects.requireNonNull( SharedBigDataViewerData.fromImagePlus( image ) );
+	}
+}