NIHVIVO-874 Merge 5357 from the branch.

webapp/src/edu/cornell/mannlib/vitro/webapp/filestorage/updater/AllThumbsAdjuster.java

@@ -12,11 +12,12 @@ import com.hp.hpl.jena.rdf.model.Resource;
  * Adjust any individual that has a thumbnail with no main image.
  */
 public class AllThumbsAdjuster extends FsuScanner {
-	protected final File imageDirectory;
+	private ImageDirectoryWithBackup imageDirectoryWithBackup;
 
 	public AllThumbsAdjuster(FSUController controller) {
 		super(controller);
-		this.imageDirectory = controller.getImageDirectory();
+		this.imageDirectoryWithBackup = controller
+				.getImageDirectoryWithBackup();
 	}
 
 	/**
@@ -56,8 +57,9 @@ public class AllThumbsAdjuster extends FsuScanner {
 				+ "' to match the thumbnail at '" + thumbFilename + "'");
 
 		try {
-			File thumbFile = new File(imageDirectory, thumbFilename);
+			File thumbFile = imageDirectoryWithBackup
-			File mainFile = new File(imageDirectory, mainFilename);
+					.getExistingFile(thumbFilename);
+			File mainFile = imageDirectoryWithBackup.getNewfile(mainFilename);
 			mainFile = checkNameConflicts(mainFile);
 			FileUtil.copyFile(thumbFile, mainFile);
 

webapp/src/edu/cornell/mannlib/vitro/webapp/filestorage/updater/DeadEndPropertyRemover.java

@@ -16,11 +16,12 @@ import com.hp.hpl.jena.rdf.model.Statement;
  * don't actually exist.
  */
 public class DeadEndPropertyRemover extends FsuScanner {
-	protected final File imageDirectory;
+	private ImageDirectoryWithBackup imageDirectoryWithBackup;
 
 	public DeadEndPropertyRemover(FSUController controller) {
 		super(controller);
-		this.imageDirectory = controller.getImageDirectory();
+		this.imageDirectoryWithBackup = controller
+				.getImageDirectoryWithBackup();
 	}
 
 	/**
@@ -58,16 +59,18 @@ public class DeadEndPropertyRemover extends FsuScanner {
 		for (Statement stmt : getStatements(resource, prop)) {
 			RDFNode node = stmt.getObject();
 			if (node.isLiteral()) {
-				String filename = ((Literal)node).getString();
+				String filename = ((Literal) node).getString();
-				File file = new File(imageDirectory, filename);
+				File file = imageDirectoryWithBackup.getExistingFile(filename);
 				if (!file.exists()) {
-					updateLog.warn(resource, "removing link to " + label + " '"
+					updateLog.warn(
-							+ filename + "': file does not exist at '"
+							resource,
-							+ file.getAbsolutePath() + "'.");
+							"removing link to " + label + " '" + filename
+									+ "': file does not exist at '"
+									+ file.getAbsolutePath() + "'.");
 					model.remove(stmt);
 				}
 			}
 		}
 	}
-	
+
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/filestorage/updater/FSUController.java

@@ -20,8 +20,8 @@ public interface FSUController {
 	/** The update log. */
 	FSULog getUpdateLog();
 
-	/** The directory where the old-style images were stored. */
+	/** The place to find or to create image files. */
-	File getImageDirectory();
+	ImageDirectoryWithBackup getImageDirectoryWithBackup();
 
 	/** The file storage system. */
 	FileStorage getFileStorage();

webapp/src/edu/cornell/mannlib/vitro/webapp/filestorage/updater/FileStorageUpdater.java

@@ -106,18 +106,21 @@ public class FileStorageUpdater implements FSUController {
 
 	private final FileStorage fileStorage;
 	private final FileModelHelper fileModelHelper;
-	private final File imageDirectory;
+	private final ImageDirectoryWithBackup imageDirectoryWithBackup;
 	private final File upgradeDirectory;
 
 	private FSULog updateLog;
 
 	public FileStorageUpdater(WebappDaoFactory wadf, Model model,
-			FileStorage fileStorage, File uploadDirectory) {
+			FileStorage fileStorage, File uploadDirectory,
+			File webappImageDirectory) {
 		this.model = model;
 		this.fileStorage = fileStorage;
 		this.fileModelHelper = new FileModelHelper(wadf);
-		this.imageDirectory = new File(uploadDirectory, "images");
 		this.upgradeDirectory = new File(uploadDirectory, "upgrade");
+
+		this.imageDirectoryWithBackup = new ImageDirectoryWithBackup(new File(
+				uploadDirectory, "images"), webappImageDirectory);
 	}
 
 	/**
@@ -176,7 +179,7 @@ public class FileStorageUpdater implements FSUController {
 			// Clean out the old image directory, separating into files which
 			// were translated, and files for which we found no reference.
 			new ImageDirectoryCleaner(this).clean(translatedFiles);
-			
+
 			updateLog.section("File Storage update is complete.");
 		} finally {
 			updateLog.close();
@@ -256,9 +259,8 @@ public class FileStorageUpdater implements FSUController {
 	}
 
 	@Override
-	public File getImageDirectory() {
+	public ImageDirectoryWithBackup getImageDirectoryWithBackup() {
-		return this.imageDirectory;
+		return this.imageDirectoryWithBackup;
-
 	}
 
 	@Override

webapp/src/edu/cornell/mannlib/vitro/webapp/filestorage/updater/ImageDirectoryCleaner.java

@@ -12,13 +12,15 @@ import java.util.Collection;
  * referenced.
  */
 public class ImageDirectoryCleaner extends FsuScanner {
-	protected final File imageDirectory;
+	private final ImageDirectoryWithBackup imageDirectoryWithBackup;
 	protected final File translatedDirectory;
 	protected final File unreferencedDirectory;
 
 	public ImageDirectoryCleaner(FSUController controller) {
 		super(controller);
-		this.imageDirectory = controller.getImageDirectory();
+		this.imageDirectoryWithBackup = controller
+				.getImageDirectoryWithBackup();
+
 		this.translatedDirectory = controller.getTranslatedDirectory();
 		this.unreferencedDirectory = controller.getUnreferencedDirectory();
 	}
@@ -33,7 +35,8 @@ public class ImageDirectoryCleaner extends FsuScanner {
 
 		updateLog.section("Cleaning the old image directory of "
 				+ "files that were not referenced.");
-		removeRemainingFiles(imageDirectory);
+		removeRemainingFiles(imageDirectoryWithBackup
+				.getPrimaryImageDirectory());
 	}
 
 	/**
@@ -41,15 +44,22 @@ public class ImageDirectoryCleaner extends FsuScanner {
 	 */
 	private void removeTranslatedFiles(Collection<String> translatedFiles) {
 		for (String path : translatedFiles) {
-			updateLog.log("moving image file '" + path
+			File oldFile = new File(
-					+ "' to the 'translated' directory.");
+					imageDirectoryWithBackup.getPrimaryImageDirectory(), path);
-			File oldFile = new File(imageDirectory, path);
+			if (oldFile.exists()) {
-			File deletedFile = new File(translatedDirectory, path);
+				updateLog.log("moving image file '" + path
-			try {
+						+ "' to the 'translated' directory.");
-				FileUtil.moveFile(oldFile, deletedFile);
+				File deletedFile = new File(translatedDirectory, path);
-			} catch (IOException e) {
+				try {
-				updateLog.error("Failed to move translated file '"
+					FileUtil.moveFile(oldFile, deletedFile);
-						+ oldFile.getAbsolutePath() + "'");
+				} catch (IOException e) {
+					updateLog.error("Failed to move translated file '"
+							+ oldFile.getAbsolutePath() + "'");
+				}
+			} else {
+				updateLog.log("Not moving image file '" + path
+						+ "' to the 'translated' directory -- "
+						+ "found it in the backup directory.");
 			}
 		}
 	}
@@ -73,8 +83,9 @@ public class ImageDirectoryCleaner extends FsuScanner {
 				}
 			}
 		} catch (IOException e) {
-			updateLog.error("Failed to clean images directory '"
+			updateLog.error(
-					+ directory.getAbsolutePath() + "'", e);
+					"Failed to clean images directory '"
+							+ directory.getAbsolutePath() + "'", e);
 		}
 	}
 
@@ -89,8 +100,9 @@ public class ImageDirectoryCleaner extends FsuScanner {
 			File newFile = new File(targetDirectory, file.getName());
 			FileUtil.moveFile(file, newFile);
 		} catch (IOException e) {
-			updateLog.error("Can't move unreferenced file '"
+			updateLog.error(
-					+ file.getAbsolutePath() + "'", e);
+					"Can't move unreferenced file '" + file.getAbsolutePath()
+							+ "'", e);
 		}
 	}
 
@@ -99,7 +111,8 @@ public class ImageDirectoryCleaner extends FsuScanner {
 	 * corresponding directory in the "unreferenced" area.
 	 */
 	private File makeCorrespondingDirectory(File directory) throws IOException {
-		String imagesPath = imageDirectory.getAbsolutePath();
+		String imagesPath = imageDirectoryWithBackup.getPrimaryImageDirectory()
+				.getAbsolutePath();
 		String thisPath = directory.getAbsolutePath();
 
 		if (!thisPath.startsWith(imagesPath)) {

webapp/src/edu/cornell/mannlib/vitro/webapp/filestorage/updater/ImageDirectoryWithBackup.java

@@ -0,0 +1,77 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+package edu.cornell.mannlib.vitro.webapp.filestorage.updater;
+
+import java.io.File;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
+/**
+ * A way to look for files in TOMCAT_WEBAPP/vivo/images, if they are not found
+ * in upload.directory/images.
+ */
+public class ImageDirectoryWithBackup {
+	private static final Log log = LogFactory
+			.getLog(ImageDirectoryWithBackup.class);
+
+	/** The primary image directory, where we do most of the manipulation. */
+	private final File uploadImageDirectory;
+
+	/**
+	 * If we are looking for a file and don't find it in the primary directory,
+	 * look for it here.
+	 */
+	private final File webappImageDirectory;
+
+	/**
+	 * Be careful! webappImageDirectory may be null.
+	 */
+	public ImageDirectoryWithBackup(File uploadImageDirectory,
+			File webappImageDirectory) {
+		this.uploadImageDirectory = uploadImageDirectory;
+		this.webappImageDirectory = webappImageDirectory;
+	}
+
+	/**
+	 * When looking to read a file, start by looking in the
+	 * {@link #uploadImageDirectory}.
+	 * 
+	 * If the file isn't found there, look in the {@link #webappImageDirectory}
+	 * as a fallback.
+	 * 
+	 * If not there either, return the pointer to the nonexistent file in the
+	 * {@link #uploadImageDirectory}.
+	 */
+	File getExistingFile(String relativePath) {
+		File file1 = new File(uploadImageDirectory, relativePath);
+		if (file1.exists()) {
+			log.trace("Found file: " + file1.getAbsolutePath());
+			return file1;
+		}
+		if (webappImageDirectory != null) {
+			File file2 = new File(webappImageDirectory, relativePath);
+			if (file2.exists()) {
+				log.trace("Found file: " + file2.getAbsolutePath());
+				return file2;
+			}
+		}
+		log.trace("Didn't find file: " + file1.getAbsolutePath());
+		return file1;
+	}
+
+	/**
+	 * New files will always be created in the primary directory.
+	 */
+	File getNewfile(String relativePath) {
+		return new File(uploadImageDirectory, relativePath);
+	}
+
+	/**
+	 * You can get a direct reference to the primary image directory, but it
+	 * should only be used for directory-base operations, like final cleanup.
+	 */
+	public File getPrimaryImageDirectory() {
+		return uploadImageDirectory;
+	}
+}

webapp/src/edu/cornell/mannlib/vitro/webapp/filestorage/updater/ImageSchemaTranslater.java

@@ -26,13 +26,14 @@ import edu.cornell.mannlib.vitro.webapp.filestorage.backend.FileStorage;
  * yet, in case someone else is referring to them also.
  */
 public class ImageSchemaTranslater extends FsuScanner {
-	protected final File imageDirectory;
+	private final ImageDirectoryWithBackup imageDirectoryWithBackup;
 	protected final FileModelHelper fileModelHelper;
 	protected final FileStorage fileStorage;
 
 	public ImageSchemaTranslater(FSUController controller) {
 		super(controller);
-		this.imageDirectory = controller.getImageDirectory();
+		this.imageDirectoryWithBackup = controller
+				.getImageDirectoryWithBackup();
 		this.fileStorage = controller.getFileStorage();
 		this.fileModelHelper = controller.getFileModelHelper();
 	}
@@ -126,7 +127,7 @@ public class ImageSchemaTranslater extends FsuScanner {
 	 */
 	private Individual translateFile(Resource resource, String path,
 			String label) {
-		File oldFile = new File(imageDirectory, path);
+		File oldFile = imageDirectoryWithBackup.getExistingFile(path);
 		String filename = getSimpleFilename(path);
 		String mimeType = guessMimeType(resource, filename);
 

webapp/src/edu/cornell/mannlib/vitro/webapp/filestorage/updater/NoThumbsAdjuster.java

@@ -17,11 +17,12 @@ import com.hp.hpl.jena.rdf.model.Resource;
  * Adjust any individual that has a main image but no thumbnail.
  */
 public class NoThumbsAdjuster extends FsuScanner {
-	protected final File imageDirectory;
+	private ImageDirectoryWithBackup imageDirectoryWithBackup;
 
 	public NoThumbsAdjuster(FSUController controller) {
 		super(controller);
-		this.imageDirectory = controller.getImageDirectory();
+		this.imageDirectoryWithBackup = controller
+				.getImageDirectoryWithBackup();
 	}
 
 	/**
@@ -59,8 +60,8 @@ public class NoThumbsAdjuster extends FsuScanner {
 		updateLog.log(resource, "creating a thumbnail at '" + thumbFilename
 				+ "' from the main image at '" + mainFilename + "'");
 
-		File mainFile = new File(imageDirectory, mainFilename);
+		File mainFile = imageDirectoryWithBackup.getExistingFile(mainFilename);
-		File thumbFile = new File(imageDirectory, thumbFilename);
+		File thumbFile = imageDirectoryWithBackup.getNewfile(thumbFilename);
 		thumbFile = checkNameConflicts(thumbFile);
 		try {
 			generateThumbnailImage(mainFile, thumbFile,

webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/UpdateUploadedFiles.java

@@ -17,7 +17,6 @@ import com.hp.hpl.jena.ontology.OntModel;
 
 import edu.cornell.mannlib.vitro.webapp.ConfigurationProperties;
 import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
-import edu.cornell.mannlib.vitro.webapp.dao.jena.JenaBaseDao;
 import edu.cornell.mannlib.vitro.webapp.filestorage.backend.FileStorage;
 import edu.cornell.mannlib.vitro.webapp.filestorage.backend.FileStorageSetup;
 import edu.cornell.mannlib.vitro.webapp.filestorage.updater.FileStorageUpdater;
@@ -97,8 +96,12 @@ public class UpdateUploadedFiles implements ServletContextListener {
 						+ "' does not exist.");
 			}
 
+			String webappImagePath = ctx.getRealPath("images");
+			File webappImageDirectory = (webappImagePath == null) ? null
+					: new File(webappImagePath);
+
 			FileStorageUpdater fsu = new FileStorageUpdater(wadf, jenaOntModel,
-					fileStorage, uploadDirectory);
+					fileStorage, uploadDirectory, webappImageDirectory);
 			fsu.update();
 		} catch (Exception e) {
 			log.error("Unknown problem", e);