/* * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * * You should have received a copy of the GNU General Public License along with Jalview. If not, see . */ package jalview.bin; import jalview.ws.dbsources.das.api.DasSourceRegistryI; import jalview.ws.dbsources.das.datamodel.DasSourceRegistry; import java.awt.Color; import java.io.*; import java.text.DateFormat; import java.text.SimpleDateFormat; import java.util.*; import org.apache.log4j.*; /** * Stores and retrieves Jalview Application Properties Lists and fields within * list entries are separated by '|' symbols unless otherwise stated (|) clauses * are alternative values for a tag.
*
* Current properties include: * * Deprecated settings: * * @author $author$ * @version $Revision$ */ public class Cache { /** * property giving log4j level for CASTOR loggers */ public static final String CASTORLOGLEVEL = "logs.Castor.level"; /** * property giving log4j level for AXIS loggers */ public static final String AXISLOGLEVEL = "logs.Axis.level"; /** * property giving log4j level for Jalview Log */ public static final String JALVIEWLOGLEVEL = "logs.Jalview.level"; public static final String DAS_LOCAL_SOURCE = "DAS_LOCAL_SOURCE"; public static final String DAS_REGISTRY_URL = "DAS_REGISTRY_URL"; public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE"; /** * Initialises the Jalview Application Log */ public static Logger log; /** Jalview Properties */ public static Properties applicationProperties = new Properties(); /** Default file is ~/.jalview_properties */ static String propertiesFile; private static boolean propsAreReadOnly=false; public static void initLogger() { if (log != null) { return; } try { // TODO: redirect stdout and stderr here in order to grab the output of // the log ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(), "System.err"); ap.setName("JalviewLogger"); org.apache.log4j.Logger.getRootLogger().addAppender(ap); // catch all for // log output Logger laxis = Logger.getLogger("org.apache.axis"); Logger lcastor = Logger.getLogger("org.exolab.castor"); jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview"); laxis.setLevel(Level.toLevel(Cache.getDefault("logs.Axis.Level", Level.INFO.toString()))); lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level", Level.INFO.toString()))); lcastor = Logger.getLogger("org.exolab.castor.xml"); lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level", Level.INFO.toString()))); // lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller"); // lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level", // Level.INFO.toString()))); jalview.bin.Cache.log.setLevel(Level.toLevel(Cache.getDefault( "logs.Jalview.level", Level.INFO.toString()))); // laxis.addAppender(ap); // lcastor.addAppender(ap); // jalview.bin.Cache.log.addAppender(ap); // Tell the user that debug is enabled jalview.bin.Cache.log.debug("Jalview Debugging Output Follows."); } catch (Exception ex) { System.err.println("Problems initializing the log4j system\n"); ex.printStackTrace(System.err); } } /** Called when Jalview is started */ public static void loadProperties(String propsFile) { propertiesFile = propsFile; if (propsFile == null) { propertiesFile = System.getProperty("user.home") + File.separatorChar + ".jalview_properties"; } else { // don't corrupt the file we've been given. propsAreReadOnly = true; } try { InputStream fis; try { fis = new java.net.URL(propertiesFile).openStream(); System.out.println("Loading jalview properties from : " + propertiesFile); System.out .println("Disabling Jalview writing to user's local properties file."); propsAreReadOnly = true; } catch (Exception ex) { fis = null; } if (fis == null) { fis = new FileInputStream(propertiesFile); } applicationProperties.load(fis); applicationProperties.remove("LATEST_VERSION"); applicationProperties.remove("VERSION"); fis.close(); } catch (Exception ex) { System.out.println("Error reading properties file: " + ex); } if (getDefault("USE_PROXY", false)) { System.out.println("Using proxyServer: " + getDefault("PROXY_SERVER", null) + " proxyPort: " + getDefault("PROXY_PORT", null)); System.setProperty("http.proxyHost", getDefault("PROXY_SERVER", null)); System.setProperty("http.proxyPort", getDefault("PROXY_PORT", null)); } // LOAD THE AUTHORS FROM THE authors.props file try { String authorDetails = "jar:".concat(Cache.class.getProtectionDomain() .getCodeSource().getLocation().toString() .concat("!/authors.props")); java.net.URL localJarFileURL = new java.net.URL(authorDetails); InputStream in = localJarFileURL.openStream(); applicationProperties.load(in); in.close(); } catch (Exception ex) { System.out.println("Error reading author details: " + ex); applicationProperties.remove("AUTHORS"); applicationProperties.remove("AUTHORFNAMES"); applicationProperties.remove("YEAR"); } // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar // MUST FOLLOW READING OF LOCAL PROPERTIES FILE AS THE // VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW try { String buildDetails = "jar:".concat(Cache.class.getProtectionDomain() .getCodeSource().getLocation().toString() .concat("!/.build_properties")); java.net.URL localJarFileURL = new java.net.URL(buildDetails); InputStream in = localJarFileURL.openStream(); applicationProperties.load(in); in.close(); } catch (Exception ex) { System.out.println("Error reading build details: " + ex); applicationProperties.remove("VERSION"); } String jnlpVersion = System.getProperty("jalview.version"); String codeVersion = getProperty("VERSION"); if (codeVersion == null) { // THIS SHOULD ONLY BE THE CASE WHEN TESTING!! codeVersion = "Test"; jnlpVersion = "Test"; } System.out.println("Jalview Version: " + codeVersion); // jnlpVersion will be null if we're using InstallAnywhere // Dont do this check if running in headless mode if (jnlpVersion == null && getDefault("VERSION_CHECK", true) && (System.getProperty("java.awt.headless") == null || System .getProperty("java.awt.headless").equals("false"))) { class VersionChecker extends Thread { public void run() { String orgtimeout = System .getProperty("sun.net.client.defaultConnectTimeout"); if (orgtimeout == null) { orgtimeout = "30"; System.out.println("# INFO: Setting default net timeout to " + orgtimeout + " seconds."); } String jnlpVersion = null; try { System.setProperty("sun.net.client.defaultConnectTimeout", "5000"); java.net.URL url = new java.net.URL( Cache.getDefault("www.jalview.org", "http://www.jalview.org")+"/webstart/jalview.jnlp"); BufferedReader in = new BufferedReader(new InputStreamReader( url.openStream())); String line = null; while ((line = in.readLine()) != null) { if (line.indexOf("jalview.version") == -1) { continue; } line = line.substring(line.indexOf("value=") + 7); line = line.substring(0, line.lastIndexOf("\"")); jnlpVersion = line; break; } } catch (Exception ex) { System.out .println("Non-fatal exceptions when checking version at www.jalview.org :"); System.out.println(ex); jnlpVersion = getProperty("VERSION"); } System.setProperty("sun.net.client.defaultConnectTimeout", orgtimeout); setProperty("LATEST_VERSION", jnlpVersion); } } VersionChecker vc = new VersionChecker(); vc.start(); } else { if (jnlpVersion != null) { setProperty("LATEST_VERSION", jnlpVersion); } else { applicationProperties.remove("LATEST_VERSION"); } } setProperty("VERSION", codeVersion); // LOAD USERDEFINED COLOURS jalview.gui.UserDefinedColours .initUserColourSchemes(getProperty("USER_DEFINED_COLOURS")); jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER", false); } /** * Gets Jalview application property of given key. Returns null if key not * found * * @param key * Name of property * * @return Property value */ public static String getProperty(String key) { return applicationProperties.getProperty(key); } /** * These methods are used when checking if the saved preference is different * to the default setting */ public static boolean getDefault(String property, boolean def) { String string = getProperty(property); if (string != null) { def = Boolean.valueOf(string).booleanValue(); } return def; } /** * These methods are used when checking if the saved preference is different * to the default setting */ public static String getDefault(String property, String def) { String string = getProperty(property); if (string != null) { return string; } return def; } /** * Stores property in the file "HOME_DIR/.jalview_properties" * * @param key * Name of object * @param obj * String value of property * * @return String value of property */ public static String setProperty(String key, String obj) { try { applicationProperties.setProperty(key, obj); if (!propsAreReadOnly) { FileOutputStream out = new FileOutputStream(propertiesFile); applicationProperties.store(out, "---JalviewX Properties File---"); out.close(); } } catch (Exception ex) { System.out.println("Error setting property: " + key + " " + obj + "\n" + ex); } return obj; } /** * remove the specified property from the jalview properties file * * @param string */ public static void removeProperty(String string) { applicationProperties.remove(string); saveProperties(); } /** * save the properties to the jalview properties path */ public static void saveProperties() { if (!propsAreReadOnly) { try { FileOutputStream out = new FileOutputStream(propertiesFile); applicationProperties.store(out, "---JalviewX Properties File---"); out.close(); } catch (Exception ex) { System.out.println("Error saving properties: " + ex); } } } /** * internal vamsas class discovery state */ private static int vamsasJarsArePresent = -1; /** * Searches for vamsas client classes on class path. * * @return true if vamsas client is present on classpath */ public static boolean vamsasJarsPresent() { if (vamsasJarsArePresent == -1) { try { if (jalview.jbgui.GDesktop.class.getClassLoader().loadClass( "uk.ac.vamsas.client.VorbaId") != null) { jalview.bin.Cache.log .debug("Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)"); vamsasJarsArePresent = 1; Logger lvclient = Logger.getLogger("uk.ac.vamsas"); lvclient.setLevel(Level.toLevel(Cache.getDefault( "logs.Vamsas.Level", Level.INFO.toString()))); lvclient.addAppender(log.getAppender("JalviewLogger")); // Tell the user that debug is enabled lvclient.debug("Jalview Vamsas Client Debugging Output Follows."); } } catch (Exception e) { vamsasJarsArePresent = 0; jalview.bin.Cache.log.debug("Vamsas Classes are not present"); } } return (vamsasJarsArePresent > 0); } /** * internal vamsas class discovery state */ private static int groovyJarsArePresent = -1; /** * Searches for vamsas client classes on class path. * * @return true if vamsas client is present on classpath */ public static boolean groovyJarsPresent() { if (groovyJarsArePresent == -1) { try { if (Cache.class.getClassLoader().loadClass( "groovy.lang.GroovyObject") != null) { jalview.bin.Cache.log .debug("Found Groovy (groovy.lang.GroovyObject can be loaded)"); groovyJarsArePresent = 1; Logger lgclient = Logger.getLogger("groovy"); lgclient.setLevel(Level.toLevel(Cache.getDefault( "logs.Groovy.Level", Level.INFO.toString()))); lgclient.addAppender(log.getAppender("JalviewLogger")); // Tell the user that debug is enabled lgclient.debug("Jalview Groovy Client Debugging Output Follows."); } } catch (Error e) { groovyJarsArePresent = 0; jalview.bin.Cache.log.debug("Groovy Classes are not present", e); } catch (Exception e) { groovyJarsArePresent = 0; jalview.bin.Cache.log.debug("Groovy Classes are not present"); } } return (groovyJarsArePresent > 0); } /** * GA tracker object - actually JGoogleAnalyticsTracker null if tracking not * enabled. */ protected static Object tracker = null; protected static Class trackerfocus = null; protected static Class jgoogleanalyticstracker = null; /** * Initialise the google tracker if it is not done already. */ public static void initGoogleTracker() { if (tracker == null) { if (jgoogleanalyticstracker == null) { // try to get the tracker class try { jgoogleanalyticstracker = Cache.class .getClassLoader() .loadClass( "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker"); trackerfocus = Cache.class.getClassLoader().loadClass( "com.boxysystems.jgoogleanalytics.FocusPoint"); } catch (Exception e) { log.debug("com.boxysystems.jgoogleanalytics package is not present - tracking not enabled."); tracker = null; jgoogleanalyticstracker = null; trackerfocus = null; return; } } // now initialise tracker Exception re = null, ex = null; Error err = null; String vrs = "No Version Accessible"; try { // Google analytics tracking code for Library Finder tracker = jgoogleanalyticstracker.getConstructor(new Class[] { String.class, String.class, String.class }).newInstance( new Object[] { "Jalview Desktop", (vrs = jalview.bin.Cache.getProperty("VERSION") + "_" + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")), "UA-9060947-1" }); jgoogleanalyticstracker.getMethod("trackAsynchronously", new Class[] { trackerfocus }).invoke(tracker, new Object[] { trackerfocus.getConstructor(new Class[] { String.class }).newInstance(new Object[] { "Application Started." }) }); } catch (RuntimeException e) { re = e; } catch (Exception e) { ex = e; } catch (Error e) { err = e; } if (re != null || ex != null || err != null) { if (log != null) { if (re != null) log.debug("Caught runtime exception in googletracker init:", re); if (ex != null) log.warn( "Failed to initialise GoogleTracker for Jalview Desktop with version " + vrs, ex); if (err != null) log.error( "Whilst initing GoogleTracker for Jalview Desktop version " + vrs, err); } else { if (re != null) { System.err .println("Debug: Caught runtime exception in googletracker init:" + vrs); re.printStackTrace(); } if (ex != null) { System.err .println("Warning: Failed to initialise GoogleTracker for Jalview Desktop with version " + vrs); ex.printStackTrace(); } if (err != null) { System.err .println("ERROR: Whilst initing GoogleTracker for Jalview Desktop version " + vrs); err.printStackTrace(); } } } else { log.debug("Successfully initialised tracker."); } } } /** * get the user's default colour if available * @param property * @param defcolour * @return */ public static Color getDefaultColour(String property, Color defcolour) { String colprop = getProperty(property); if (colprop==null) { return defcolour; } Color col = jalview.schemes.ColourSchemeProperty.getAWTColorFromName(colprop); if (col==null) { try { col = new jalview.schemes.UserColourScheme(colprop).findColour('A'); } catch (Exception ex) { log.warn("Couldn't parse '"+colprop+"' as a colour for "+property); col=null; } } return (col==null) ? defcolour: col; } /** * store a colour as a Jalview user default property * @param property * @param colour */ public static void setColourProperty(String property, Color colour) { setProperty(property, jalview.util.Format .getHexString(colour)); } public static final DateFormat date_format = SimpleDateFormat.getDateTimeInstance(); /** * store a date in a jalview property * @param string * @param time */ public static void setDateProperty(String property, Date time) { setProperty(property, date_format.format(time)); } /** * read a date stored in a jalview property * @param property * @return valid date as stored by setDateProperty, or null * */ public static Date getDateProperty(String property) { String val = getProperty(property); if (val!=null) { try { return date_format.parse(val); } catch (Exception ex) { System.err.println("Invalid or corrupt date in property '"+property+"' : value was '"+val+"'"); } } return null; } /** * get and parse a property as an integer. send any parsing problems to System.err * @param property * @return null or Integer */ public static Integer getIntegerProperty(String property) { String val=getProperty(property); if (val!=null && (val=val.trim()).length()>0) { try { return Integer.valueOf(val); } catch (NumberFormatException x) { System.err.println("Invalid integer in property '"+property+"' (value was '"+val+"')"); } } return null; } private static DasSourceRegistryI sourceRegistry=null; /** * initialise and .. * @return instance of the das source registry */ public static DasSourceRegistryI getDasSourceRegistry() { if (sourceRegistry==null) { sourceRegistry = new DasSourceRegistry(); } return sourceRegistry; } }