Java tutorial
/* * Copyright (c) 2007-2012 The Broad Institute, Inc. * SOFTWARE COPYRIGHT NOTICE * This software and its documentation are the copyright of the Broad Institute, Inc. All rights are reserved. * * This software is supplied without any warranty or guaranteed support whatsoever. The Broad Institute is not responsible for its use, misuse, or functionality. * * This software is licensed under the terms of the GNU Lesser General Public License (LGPL), * Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php. */ package org.broad.igv; import org.apache.commons.io.FileUtils; import org.apache.log4j.*; import org.broad.igv.exceptions.DataLoadException; import org.broad.igv.ui.util.FileDialogUtils; import org.broad.igv.ui.util.MessageUtils; import org.broad.igv.util.RuntimeUtils; import javax.swing.*; import javax.swing.filechooser.FileSystemView; import java.io.File; import java.io.IOException; import java.util.prefs.Preferences; /** * @author Jim Robinson * @date 3/19/12 */ public class DirectoryManager { private static Logger log = Logger.getLogger(DirectoryManager.class); private static File USER_HOME; private static File USER_DIRECTORY; // FileSystemView.getFileSystemView().getDefaultDirectory(); private static File IGV_DIRECTORY; // The IGV application directory private static File GENOME_CACHE_DIRECTORY; private static File GENE_LIST_DIRECTORY; private static File BAM_CACHE_DIRECTORY; final public static String IGV_DIR_USERPREF = "igvDir"; private static File getUserHome() { if (USER_HOME == null) { String userHomeString = System.getProperty("user.home"); USER_HOME = new File(userHomeString); } return USER_HOME; } /** * The user directory. On Mac and Linux this should be the user home directory. On Windows platforms this * is the "My Documents" directory. */ public static synchronized File getUserDirectory() { if (USER_DIRECTORY == null) { System.out.print("Fetching user directory... "); USER_DIRECTORY = FileSystemView.getFileSystemView().getDefaultDirectory(); //Mostly for testing, in some environments USER_DIRECTORY can be null if (USER_DIRECTORY == null) { USER_DIRECTORY = getUserHome(); } } return USER_DIRECTORY; } public static File getIgvDirectory() { if (IGV_DIRECTORY == null) { // Hack for known Java / Windows bug. Attempt to remvoe (possible) read-only bit from user directory if (System.getProperty("os.name").startsWith("Windows")) { try { Runtime.getRuntime().exec("attrib -r \"" + getUserDirectory().getAbsolutePath() + "\""); } catch (Exception e) { // We tried } } IGV_DIRECTORY = getIgvDirectoryOverride(); // If still null, try the default place if (IGV_DIRECTORY == null) { File rootDir = getUserHome(); IGV_DIRECTORY = new File(rootDir, "igv"); if (!IGV_DIRECTORY.exists()) { // See if a pre-2.1 release directory exists, if so copy it File legacyDirectory = null; try { legacyDirectory = getLegacyIGVDirectory(); if (legacyDirectory.exists()) { log.info("Copying " + legacyDirectory + " => " + IGV_DIRECTORY); FileUtils.copyDirectory(legacyDirectory, IGV_DIRECTORY); } } catch (IOException e) { log.error("Error copying igv directory " + legacyDirectory + " => " + IGV_DIRECTORY, e); } } if (!IGV_DIRECTORY.exists()) { try { boolean wasSuccessful = IGV_DIRECTORY.mkdir(); if (!wasSuccessful) { System.err.println("Failed to create user directory!"); IGV_DIRECTORY = null; } } catch (Exception e) { log.error("Error creating igv directory", e); } } } // The IGV directory either doesn't exist or isn't writeable. This situation can arise with Windows Vista // and Windows 7 due to a Java bug (http://bugs.sun.com/view_bug.do?bug_id=4787931) if (IGV_DIRECTORY == null || !IGV_DIRECTORY.exists() || !canWrite(IGV_DIRECTORY)) { if (Globals.isHeadless() || Globals.isSuppressMessages()) { System.err.println("Cannot write to igv directory: " + IGV_DIRECTORY.getAbsolutePath()); IGV_DIRECTORY = (new File(".")).getParentFile(); } else { int option = JOptionPane.showConfirmDialog(null, "<html>The default IGV directory (" + IGV_DIRECTORY + ") " + "cannot be accessed. Click Yes to choose a new folder or No to exit.<br>" + "This folder will be used to create the 'igv' directory", "IGV Directory Error", JOptionPane.YES_NO_OPTION); if (option == JOptionPane.YES_OPTION) { File parentDirectory = FileDialogUtils .chooseDirectory("Select a location for the igv directory", null); if (parentDirectory != null) { IGV_DIRECTORY = new File(parentDirectory, "igv"); IGV_DIRECTORY.mkdir(); Preferences prefs = Preferences.userNodeForPackage(Globals.class); prefs.put(IGV_DIR_USERPREF, IGV_DIRECTORY.getAbsolutePath()); } } } } if (IGV_DIRECTORY == null || !IGV_DIRECTORY.canRead()) { throw new DataLoadException("Cannot read from user directory", IGV_DIRECTORY.getAbsolutePath()); } else if (!canWrite(IGV_DIRECTORY)) { throw new DataLoadException("Cannot write to user directory", IGV_DIRECTORY.getAbsolutePath()); } log.info("IGV Directory: " + IGV_DIRECTORY.getAbsolutePath()); } return IGV_DIRECTORY; } private static File getIgvDirectoryOverride() { Preferences userPrefs = null; File override = null; try { // See if an override location has been specified. This is stored with the Java Preferences API userPrefs = Preferences.userNodeForPackage(Globals.class); String userDir = userPrefs.get(IGV_DIR_USERPREF, null); if (userDir != null) { override = new File(userDir); if (!override.exists()) { override = null; userPrefs.remove(IGV_DIR_USERPREF); } } } catch (Exception e) { userPrefs.remove(IGV_DIR_USERPREF); override = null; System.err.println("Error creating user directory"); e.printStackTrace(); } return override; } public static File getGenomeCacheDirectory() { if (GENOME_CACHE_DIRECTORY == null) { //Create the Genome Cache GENOME_CACHE_DIRECTORY = new File(getIgvDirectory(), "genomes"); if (!GENOME_CACHE_DIRECTORY.exists()) { GENOME_CACHE_DIRECTORY.mkdir(); } if (!GENOME_CACHE_DIRECTORY.canRead()) { throw new DataLoadException("Cannot read from user directory", GENOME_CACHE_DIRECTORY.getAbsolutePath()); } else if (!GENOME_CACHE_DIRECTORY.canWrite()) { throw new DataLoadException("Cannot write to user directory", GENOME_CACHE_DIRECTORY.getAbsolutePath()); } } return GENOME_CACHE_DIRECTORY; } public static File getGeneListDirectory() { if (GENE_LIST_DIRECTORY == null) { GENE_LIST_DIRECTORY = new File(getIgvDirectory(), "lists"); if (!GENE_LIST_DIRECTORY.exists()) { GENE_LIST_DIRECTORY.mkdir(); } if (!GENE_LIST_DIRECTORY.canRead()) { throw new DataLoadException("Cannot read from user directory", GENE_LIST_DIRECTORY.getAbsolutePath()); } else if (!GENE_LIST_DIRECTORY.canWrite()) { throw new DataLoadException("Cannot write to user directory", GENE_LIST_DIRECTORY.getAbsolutePath()); } } return GENE_LIST_DIRECTORY; } public static synchronized File getCacheDirectory() { if (BAM_CACHE_DIRECTORY == null) { File defaultDir = getIgvDirectory(); if (defaultDir.exists()) { BAM_CACHE_DIRECTORY = new File(defaultDir, "bam"); if (!BAM_CACHE_DIRECTORY.exists()) { BAM_CACHE_DIRECTORY.mkdir(); } } } return BAM_CACHE_DIRECTORY; } public static synchronized File getSamDirectory() { File samDir = new File(DirectoryManager.getIgvDirectory(), "sam"); if (!samDir.exists()) { samDir.mkdir(); } return samDir; } public static synchronized File getLogFile() throws IOException { File logFile = new File(getIgvDirectory(), "igv.log"); if (!logFile.exists()) { logFile.createNewFile(); } return logFile; } /** * Return the user preferences property file ("~/igv/prefs.properties"). * * @return */ public static synchronized File getPreferencesFile() { File igvDirectoy = getIgvDirectory(); File igvPropertyFile = new File(igvDirectoy, "prefs.properties"); // If the property file doesn't exist, try the "legacy" location. This should only make a difference for Macs if (!igvPropertyFile.exists()) { File oldFile = getLegacyPreferencesFile(); if (oldFile.exists()) { try { // Copy contents to new location. Leave oldFile in place for compatibility with earlier IGV releases FileUtils.copyFile(oldFile, igvPropertyFile); } catch (IOException e) { log.error("Error copy property file from: " + oldFile + " to: " + igvPropertyFile, e); } } } if (!igvPropertyFile.exists()) { try { igvPropertyFile.createNewFile(); } catch (IOException e) { log.error("Could not create property file: " + igvPropertyFile, e); } } return igvPropertyFile; } /** * Move the "igv" directory to a new location, copying all contents. Returns True if the directory * is successfully moved, irrespective of any errors that might occur later (e.g. when attempting to * remove the old directory). * * @param newIGVDirectory * @return True if the directory is successfully moved, false otherwise */ public static Boolean moveIGVDirectory(final File newIGVDirectory) { if (newIGVDirectory.equals(IGV_DIRECTORY)) { return false; // Nothing to do } if (IGV_DIRECTORY != null && IGV_DIRECTORY.exists()) { File oldDirectory = IGV_DIRECTORY; try { log.info("Moving igv directory from " + oldDirectory.getParent() + " to " + newIGVDirectory.getAbsolutePath()); FileUtils.copyDirectory(IGV_DIRECTORY, newIGVDirectory); IGV_DIRECTORY = newIGVDirectory; // Store location of new directory in Java preferences node (not pref.properties) Preferences prefs = Preferences.userNodeForPackage(Globals.class); prefs.put(IGV_DIR_USERPREF, newIGVDirectory.getAbsolutePath()); // Update preference manager with new file location PreferenceManager.getInstance().setPrefsFile(getPreferencesFile().getAbsolutePath()); } catch (IOException e) { log.error("Error copying IGV directory", e); MessageUtils.showMessage("<html>Error moving IGV directory:<br/> nbsp;" + e.getMessage()); return false; } // Restart the log LogManager.shutdown(); initializeLog(); // Try to delete the old directory try { deleteDirectory(oldDirectory); } catch (IOException e) { log.error("An error was encountered deleting the previous IGV directory", e); MessageUtils.showMessage("<html>An error was encountered deleting the previous IGV directory (" + e.getMessage() + "):<br> nbsp;nbsp;" + oldDirectory.getAbsolutePath() + "<br>Remaining files should be manually deleted."); } } GENOME_CACHE_DIRECTORY = null; GENE_LIST_DIRECTORY = null; BAM_CACHE_DIRECTORY = null; return true; } /** * Delete the directory and all contents recursively. The apache FileUtils is hanging on Linux. * * @param oldDirectory * @throws IOException */ private static void deleteDirectory(File oldDirectory) throws IOException { if (Globals.IS_LINUX || Globals.IS_MAC) { //System.out.println("Deleting: " + oldDirectory); String result = RuntimeUtils.executeShellCommand("rm -rf " + oldDirectory.getAbsolutePath(), null, null); if (result != null && result.trim().length() > 0) { log.info("Response from 'rm -rf': " + result); } } else { // The apache commons FileUtils is not working reliably org.broad.igv.util.FileUtils.deleteDir(oldDirectory); } } /** * Return the pre 2.1 release properties file. This may or may not exist. * * @return */ private static synchronized File getLegacyPreferencesFile() { File rootDir = getLegacyIGVDirectory(); return new File(rootDir, "prefs.properties"); } /** * REturn the pre 2.1 release IGV directory. This differs from the current location only for Macs. * * @return */ private static File getLegacyIGVDirectory() { File rootDir = getUserHome(); if (Globals.IS_MAC) { rootDir = new File(rootDir, ".igv"); } else { rootDir = new File(rootDir, "igv"); } return rootDir; } private static boolean canWrite(File directory) { // There are bugs in the Windows Java JVM that can cause user directories to be non-writable (target fix is // Java 7). The only way to know if the directory is writable for sure is to try to write something. if (Globals.IS_WINDOWS) { File testFile = null; try { testFile = new File(directory, "igv332415dsfjdsklt.testfile"); if (testFile.exists()) { testFile.delete(); } testFile.deleteOnExit(); testFile.createNewFile(); return testFile.exists(); } catch (IOException e) { return false; } finally { if (testFile.exists()) { testFile.delete(); } } } else { return directory.canWrite(); } } public static void initializeLog() { Logger logger = Logger.getRootLogger(); PatternLayout layout = new PatternLayout(); layout.setConversionPattern("%p [%d{ISO8601}] [%F:%L] %m%n"); // Create a log file that is ready to have text appended to it try { File logFile = getLogFile(); RollingFileAppender appender = new RollingFileAppender(); appender.setName("IGV_ROLLING_APPENDER"); appender.setFile(logFile.getAbsolutePath()); appender.setThreshold(Level.ALL); appender.setMaxFileSize("1000KB"); appender.setMaxBackupIndex(1); appender.setLayout(layout); appender.setAppend(true); appender.activateOptions(); logger.addAppender(appender); } catch (IOException e) { // Can't create log file, just log to console System.err.println("Error creating log file"); e.printStackTrace(); ConsoleAppender consoleAppender = new ConsoleAppender(); logger.addAppender(consoleAppender); } } }