/* * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) * Copyright (C) $$Year-Rel$$ The Jalview Authors * * 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 . * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.bin; import jalview.datamodel.PDBEntry; import jalview.gui.UserDefinedColours; import jalview.schemes.ColourSchemeLoader; import jalview.schemes.ColourSchemes; import jalview.schemes.UserColourScheme; import jalview.structure.StructureImportSettings; import jalview.urls.IdOrgSettings; import jalview.util.ColorUtils; import jalview.ws.dbsources.das.api.DasSourceRegistryI; import jalview.ws.dbsources.das.datamodel.DasSourceRegistry; import jalview.ws.sifts.SiftsSettings; import java.awt.Color; import java.io.BufferedReader; import java.io.File; import java.io.FileInputStream; import java.io.FileOutputStream; import java.io.InputStream; import java.io.InputStreamReader; import java.text.DateFormat; import java.text.SimpleDateFormat; import java.util.Collections; import java.util.Date; import java.util.Enumeration; import java.util.Locale; import java.util.Properties; import java.util.StringTokenizer; import java.util.TreeSet; import org.apache.log4j.ConsoleAppender; import org.apache.log4j.Level; import org.apache.log4j.Logger; import org.apache.log4j.SimpleLayout; /** * 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"; /** * Sifts settings */ public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System .getProperty("user.home") + File.separatorChar + ".sifts_downloads" + File.separatorChar; private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2"; private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30"; /** * Identifiers.org download settings */ private static final String ID_ORG_FILE = System.getProperty("user.home") + File.separatorChar + ".identifiers.org.ids.json"; /** * Allowed values are PDB or mmCIF */ private final static String PDB_DOWNLOAD_FORMAT = PDBEntry.Type.MMCIF .toString(); private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.StructureParser.JMOL_PARSER .toString(); /* * a date formatter using a fixed (rather than the user's) locale; * this ensures that date properties can be written and re-read successfully * even if the user changes their locale setting */ private static final DateFormat date_format = SimpleDateFormat .getDateTimeInstance(SimpleDateFormat.MEDIUM, SimpleDateFormat.MEDIUM, Locale.UK); /** * Initialises the Jalview Application Log */ public static Logger log; /** Jalview Properties */ public static Properties applicationProperties = new Properties() { // override results in properties output in alphabetical order @Override public synchronized Enumeration keys() { return Collections.enumeration(new TreeSet<>(super.keySet())); } }; /** 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); } } /** * Loads properties from the given properties file. Any existing properties * are first cleared. */ 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.clear(); applicationProperties.load(fis); // remove any old build properties deleteBuildProperties(); fis.close(); } catch (Exception ex) { System.out.println("Error reading properties file: " + ex); } if (getDefault("USE_PROXY", false)) { String proxyServer = getDefault("PROXY_SERVER", ""), proxyPort = getDefault("PROXY_PORT", "8080"); System.out.println("Using proxyServer: " + proxyServer + " proxyPort: " + proxyPort); System.setProperty("http.proxyHost", proxyServer); System.setProperty("http.proxyPort", proxyPort); } // 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"); String codeInstallation = getProperty("INSTALLATION"); if (codeVersion == null) { // THIS SHOULD ONLY BE THE CASE WHEN TESTING!! codeVersion = "Test"; jnlpVersion = "Test"; codeInstallation = ""; } else { codeInstallation = " (" + codeInstallation + ")"; } new BuildDetails(codeVersion, null, codeInstallation); SiftsSettings .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false)); SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache .getDefault("sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR)); SiftsSettings.setFailSafePIDThreshold( jalview.bin.Cache.getDefault("sifts_fail_safe_pid_threshold", DEFAULT_FAIL_SAFE_PID_THRESHOLD)); SiftsSettings.setCacheThresholdInDays( jalview.bin.Cache.getDefault("sifts_cache_threshold_in_days", DEFAULT_CACHE_THRESHOLD_IN_DAYS)); IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL", "http://www.jalview.org/services/identifiers")); IdOrgSettings.setDownloadLocation(ID_ORG_FILE); System.out .println("Jalview Version: " + codeVersion + codeInstallation); StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache .getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT)); StructureImportSettings .setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER); // StructureImportSettings // .setDefaultPDBFileParser(jalview.bin.Cache.getDefault( // "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER)); // 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 { @Override 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 remoteVersion = 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("\"")); remoteVersion = line; break; } } catch (Exception ex) { System.out.println( "Non-fatal exception when checking version at www.jalview.org :"); System.out.println(ex); remoteVersion = getProperty("VERSION"); } System.setProperty("sun.net.client.defaultConnectTimeout", orgtimeout); setProperty("LATEST_VERSION", remoteVersion); } } 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.bin.Cache .initUserColourSchemes(getProperty("USER_DEFINED_COLOURS")); jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER", false); } private static void deleteBuildProperties() { applicationProperties.remove("LATEST_VERSION"); applicationProperties.remove("VERSION"); applicationProperties.remove("AUTHORS"); applicationProperties.remove("AUTHORFNAMES"); applicationProperties.remove("YEAR"); applicationProperties.remove("BUILD_DATE"); applicationProperties.remove("INSTALLATION"); } /** * 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 previous value of property (or null) */ public static Object setProperty(String key, String obj) { Object oldValue = null; try { oldValue = 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 oldValue; } /** * 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 = ColorUtils.parseColourString(colprop); if (col == null) { log.warn("Couldn't parse '" + colprop + "' as a colour for " + property); } 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)); } /** * Stores a formatted date in a jalview property, using a fixed locale. * * @param propertyName * @param date * @return the formatted date string */ public static String setDateProperty(String propertyName, Date date) { String formatted = date_format.format(date); setProperty(propertyName, formatted); return formatted; } /** * Reads a date stored in a Jalview property, parses it (using a fixed locale * format) and returns as a Date, or null if parsing fails * * @param propertyName * @return * */ public static Date getDateProperty(String propertyName) { String val = getProperty(propertyName); if (val != null) { try { return date_format.parse(val); } catch (Exception ex) { System.err.println("Invalid or corrupt date in property '" + propertyName + "' : 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; } /** * Set the specified value, or remove it if null or empty. Does not save the * properties file. * * @param propName * @param value */ public static void setOrRemove(String propName, String value) { if (propName == null) { return; } if (value == null || value.trim().length() < 1) { Cache.applicationProperties.remove(propName); } else { Cache.applicationProperties.setProperty(propName, value); } } /** * Loads in user colour schemes from files. * * @param files * a '|'-delimited list of file paths */ public static void initUserColourSchemes(String files) { if (files == null || files.length() == 0) { return; } // In case colours can't be loaded, we'll remove them // from the default list here. StringBuffer coloursFound = new StringBuffer(); StringTokenizer st = new StringTokenizer(files, "|"); while (st.hasMoreElements()) { String file = st.nextToken(); try { UserColourScheme ucs = ColourSchemeLoader.loadColourScheme(file); if (ucs != null) { if (coloursFound.length() > 0) { coloursFound.append("|"); } coloursFound.append(file); ColourSchemes.getInstance().registerColourScheme(ucs); } } catch (Exception ex) { System.out.println("Error loading User ColourFile\n" + ex); } } if (!files.equals(coloursFound.toString())) { if (coloursFound.toString().length() > 1) { setProperty(UserDefinedColours.USER_DEFINED_COLOURS, coloursFound.toString()); } else { applicationProperties .remove(UserDefinedColours.USER_DEFINED_COLOURS); } } } }