X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=7aab4aeaf583cfe1449206d3a38bdf0d52c3f8d0;hb=5d501d5230ad1c42f1e17a485cb86a04ba8b538a;hp=e2477d9eab317abb2452fff15073bfd7a4f3770f;hpb=086115440f8e30fa1bfc881e00b94878b491fb89;p=jalview.git diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java index e2477d9..4a83b35 100755 --- a/src/jalview/bin/Cache.java +++ b/src/jalview/bin/Cache.java @@ -1,174 +1,1715 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program 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 2 - * of the License, or (at your option) any later version. - * - * This program 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA - */ -package jalview.bin; - -import java.io.*; - -import java.util.*; - -import java.net.*; - - -/** - * Stores and retrieves Jalview Application Properties - *

Current properties include: - *
logs.Axis.Level - one of the stringified Levels for log4j controlling the logging level for axis (used for web services) - *
logs.Castor.Level - one of the stringified Levels for log4j controlling the logging level for castor (used for serialization) - *
jalview.browser - used in the jalview.utils.browserLauncher class if it doesn't know what else to do. - *
SCREEN_WIDTH,SCREEN_HEIGHT,SCREEN_Y=285,SCREEN_X=371,SHOW_FULLSCREEN - * FONT_NAME,FONT_SIZE,FONT_STYLE,GAP_SYMBOL,LAST_DIRECTORY,USER_DEFINED_COLOUR - * SHOW_FULL_ID,SHOW_IDENTITY,SHOW_QUALITY,SHOW_ANNOTATIONS,SHOW_CONSERVATION, - * DEFAULT_COLOUR,DEFAULT_FILE_FORMAT,STARTUP_FILE,SHOW_STARTUP_FILE - - * @author $author$ - * @version $Revision$ - */ -public class Cache -{ - - /** Jalview Properties */ - public static Properties applicationProperties; - - /** Default file is ~/.jalview_properties */ - static String propertiesFile; - - /** Called when Jalview is started */ - public static void loadProperties(String propsFile) - { - applicationProperties = new Properties(); - propertiesFile = propsFile; - if (propsFile == null) - { - propertiesFile = System.getProperty("user.home") + "/.jalview_properties"; - } - - try - { - FileInputStream 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); - } - - // 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"; - } - - // jnlpVersion will be null if we're using InstallAnywhere - if(jnlpVersion==null) - { - try{ - java.net.URL url = new java.net.URL("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) - { jnlpVersion = codeVersion; } - } - - System.out.println("Version: "+codeVersion); - System.out.println("Latest : "+jnlpVersion); - - setProperty("LATEST_VERSION", jnlpVersion); - setProperty("VERSION", codeVersion); - } - - /** - * 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); - } - - /** - * 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 - { - FileOutputStream out = new FileOutputStream(propertiesFile); - - applicationProperties.setProperty(key, obj); - - applicationProperties.store(out, "---JalviewX Properties File---"); - out.close(); - } - catch (Exception ex) - { - } - - return obj; - } -} +/* + * 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 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.io.PrintWriter; +import java.io.StringWriter; +import java.net.Authenticator; +import java.net.PasswordAuthentication; +import java.net.URL; +import java.text.DateFormat; +import java.text.SimpleDateFormat; +import java.util.Arrays; +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 java.util.regex.Pattern; + +import javax.swing.LookAndFeel; +import javax.swing.UIManager; + +import org.apache.log4j.ConsoleAppender; +import org.apache.log4j.Level; +import org.apache.log4j.Logger; +import org.apache.log4j.SimpleLayout; + +import jalview.datamodel.PDBEntry; +import jalview.gui.Preferences; +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.ChannelProperties; +import jalview.util.ColorUtils; +import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.ws.sifts.SiftsSettings; + +/** + * 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"; + + /** + * 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; + + // save the proxy properties set at startup + public final static String[] startupProxyProperties = { + System.getProperty("http.proxyHost"), + System.getProperty("http.proxyPort"), + System.getProperty("https.proxyHost"), + System.getProperty("https.proxyPort"), + System.getProperty("http.proxyUser"), + System.getProperty("http.proxyPassword"), + System.getProperty("https.proxyUser"), + System.getProperty("https.proxyPassword"), + System.getProperty("http.nonProxyHosts") }; + + public final static String PROXYTYPE_NONE = "none"; + + // "false" and "true" for backward compatibility + public final static String PROXYTYPE_SYSTEM = "false"; + + public final static String PROXYTYPE_CUSTOM = "true"; + + // in-memory only storage of proxy password, safer to use char array + public static char[] proxyAuthPassword = null; + + /** 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())); + } + }; + + /* build Properties (not all saved to .jalview_properties) */ + public static Properties buildProperties = new Properties(); + + /** Default file is ~/.jalview_properties */ + static String propertiesFile; + + private static boolean propsAreReadOnly = Platform.isJS(); + + private final static String JS_PROPERTY_PREFIX = "jalview_"; + + 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()))); + // we shouldn't need to do this + org.apache.log4j.Logger.getRootLogger() + .setLevel(org.apache.log4j.Level.INFO); + + 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(ChannelProperties.getProperty("app_name") + + " 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 && !propsAreReadOnly) + { + propertiesFile = System.getProperty("user.home") + File.separatorChar + + ".jalview_properties"; + } + else + { + // don't corrupt the file we've been given. + propsAreReadOnly = true; + } + + if (propertiesFile == null) + { // BH 2019 + Platform.readInfoProperties(JS_PROPERTY_PREFIX, + applicationProperties); + } + else + { + try + { + InputStream fis; + try + { + fis = new 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); + } + } + + /* TO BE REPLACED WITH PROXY_TYPE SETTINGS + if (getDefault("USE_PROXY", false)) + { + String proxyServer = getDefault("PROXY_SERVER", ""), + proxyPort = getDefault("PROXY_PORT", "8080"); + } + */ + + // PROXY TYPE settings (now three options "none", "false", "true", but using + // backward compatible strings) + String proxyType = getDefault("USE_PROXY", PROXYTYPE_SYSTEM); + // default to upgrading old settings + switch (proxyType) + { + case PROXYTYPE_NONE: + clearProxyProperties(); + break; + case PROXYTYPE_SYSTEM: // use system settings + resetProxyProperties(); + break; + case PROXYTYPE_CUSTOM: // use specified proxy settings + String httpHost = getDefault("PROXY_SERVER", ""); + String httpPort = getDefault("PROXY_PORT", "8080"); + String httpsHost = getDefault("PROXY_SERVER_HTTPS", httpHost); + String httpsPort = getDefault("PROXY_PORT_HTTPS", httpPort); + String httpUser = getDefault("PROXY_AUTH_USER", null); + // https.proxyUser and https.proxyPassword are not able to be + // independently set in Preferences yet (or http.nonProxyHosts) + String httpsUser = getDefault("PROXY_AUTH_USER_HTTPS", httpUser); + setProxyProperties(httpHost, httpPort, httpsHost, httpsPort, httpUser, + proxyAuthPassword, httpsUser, proxyAuthPassword, "localhost"); + break; + default: + String message = "Incorrect PROXY_TYPE - should be 'none' (clear proxy properties), 'false' (system settings), 'true' (custom settings): " + + proxyType; + Cache.warn(message); + } + + // LOAD THE AUTHORS FROM THE authors.props file + String authorDetails = resolveResourceURLFor("/authors.props"); + + try + { + if (authorDetails != null) + { + URL localJarFileURL = new URL(authorDetails); + InputStream in = localJarFileURL.openStream(); + applicationProperties.load(in); + in.close(); + } + } catch (Exception ex) + { + System.out.println("Error reading author details: " + ex); + authorDetails = null; + } + if (authorDetails == null) + { + applicationProperties.remove("AUTHORS"); + applicationProperties.remove("AUTHORFNAMES"); + applicationProperties.remove("YEAR"); + } + + loadBuildProperties(false); + + 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); + + 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)); + + String jnlpVersion = System.getProperty("jalview.version"); + + // jnlpVersion will be null if a latest version check for the channel needs + // to be done + // 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 remoteBuildPropertiesUrl = Cache + .getAppbaseBuildProperties(); + + 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(remoteBuildPropertiesUrl); + + BufferedReader in = new BufferedReader( + new InputStreamReader(url.openStream())); + + Properties remoteBuildProperties = new Properties(); + remoteBuildProperties.load(in); + remoteVersion = remoteBuildProperties.getProperty("VERSION"); + } catch (Exception ex) + { + System.out + .println("Non-fatal exception when checking version at " + + remoteBuildPropertiesUrl + ":"); + 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"); + } + } + + // LOAD USERDEFINED COLOURS + Cache.initUserColourSchemes(getProperty("USER_DEFINED_COLOURS")); + jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER", + false); + } + + /** + * construct a resource URL for the given absolute resource pathname + * + * @param resourcePath + * @return + */ + private static String resolveResourceURLFor(String resourcePath) + { + String url = null; + if (Platform.isJS() || !Cache.class.getProtectionDomain() + .getCodeSource().getLocation().toString().endsWith(".jar")) + { + try + { + url = Cache.class.getResource(resourcePath).toString(); + } catch (Exception ex) + { + System.err.println("Failed to resolve resource " + resourcePath + + ": " + ex.getMessage()); + } + } + else + { + url = "jar:".concat(Cache.class.getProtectionDomain().getCodeSource() + .getLocation().toString().concat("!" + resourcePath)); + } + return url; + } + + public static void loadBuildProperties(boolean reportVersion) + { + String codeInstallation = getProperty("INSTALLATION"); + boolean printVersion = codeInstallation == null; + + /* + * read build properties - from the Jalview jar for a Java distribution, + * or from codebase file in test or JalviewJS context + */ + try + { + String buildDetails = resolveResourceURLFor("/.build_properties"); + URL localJarFileURL = new URL(buildDetails); + InputStream in = localJarFileURL.openStream(); + buildProperties.load(in); + in.close(); + if (buildProperties.getProperty("BUILD_DATE", null) != null) + { + applicationProperties.put("BUILD_DATE", + buildProperties.getProperty("BUILD_DATE")); + } + if (buildProperties.getProperty("INSTALLATION", null) != null) + { + applicationProperties.put("INSTALLATION", + buildProperties.getProperty("INSTALLATION")); + } + if (buildProperties.getProperty("VERSION", null) != null) + { + applicationProperties.put("VERSION", + buildProperties.getProperty("VERSION")); + } + } catch (Exception ex) + { + System.out.println("Error reading build details: " + ex); + applicationProperties.remove("VERSION"); + } + String codeVersion = getProperty("VERSION"); + codeInstallation = getProperty("INSTALLATION"); + + if (codeVersion == null) + { + // THIS SHOULD ONLY BE THE CASE WHEN TESTING!! + codeVersion = "Test"; + codeInstallation = ""; + } + else + { + codeInstallation = " (" + codeInstallation + ")"; + } + setProperty("VERSION", codeVersion); + new BuildDetails(codeVersion, null, codeInstallation); + if (printVersion && reportVersion) + { + System.out.println(ChannelProperties.getProperty("app_name") + + " Version: " + codeVersion + codeInstallation); + } + } + + 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) + { + String prop = applicationProperties.getProperty(key); + if (prop == null && Platform.isJS()) + { + prop = applicationProperties.getProperty(Platform.getUniqueAppletID() + + "_" + JS_PROPERTY_PREFIX + key); + } + return prop; + } + + /** + * 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; + } + + public static int getDefault(String property, int def) + { + String string = getProperty(property); + if (string != null) + { + try + { + def = Integer.parseInt(string); + } catch (NumberFormatException e) + { + System.out.println("Error parsing int property '" + property + + "' with value '" + string + "'"); + } + } + + return def; + } + + /** + * Answers the value of the given property, or the supplied default value if + * the property is not set + */ + public static String getDefault(String property, String def) + { + String value = getProperty(property); + return value == null ? def : value; + } + + /** + * 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 (propertiesFile != null && !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(ChannelProperties.getProperty("app_name") + + " 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(ChannelProperties.getProperty("app_name") + + " 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[] + { ChannelProperties.getProperty("app_name") + " 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; + } + + /** + * 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); + } + } + } + + /** + * Initial logging information helper for various versions output + * + * @param prefix + * @param value + * @param defaultValue + */ + private static void appendIfNotNull(StringBuilder sb, String prefix, + String value, String suffix, String defaultValue) + { + if (value == null && defaultValue == null) + { + return; + } + String line = prefix + (value != null ? value : defaultValue) + suffix; + sb.append(line); + } + + /** + * + * @return Jalview version, build details and JVM platform version for console + */ + public static String getVersionDetailsForConsole() + { + StringBuilder sb = new StringBuilder(); + sb.append(ChannelProperties.getProperty("app_name")) + .append(" Version: "); + sb.append(jalview.bin.Cache.getDefault("VERSION", "TEST")); + sb.append("\n"); + sb.append(ChannelProperties.getProperty("app_name")) + .append(" Installation: "); + sb.append(jalview.bin.Cache.getDefault("INSTALLATION", "unknown")); + sb.append("\n"); + sb.append("Build Date: "); + sb.append(jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")); + sb.append("\n"); + sb.append("Java version: "); + sb.append(System.getProperty("java.version")); + sb.append("\n"); + sb.append(System.getProperty("os.arch")); + sb.append(" "); + sb.append(System.getProperty("os.name")); + sb.append(" "); + sb.append(System.getProperty("os.version")); + sb.append("\n"); + appendIfNotNull(sb, "Install4j version: ", + System.getProperty("sys.install4jVersion"), "\n", null); + appendIfNotNull(sb, "Install4j template version: ", + System.getProperty("installer_template_version"), "\n", null); + appendIfNotNull(sb, "Launcher version: ", + System.getProperty("launcher_version"), "\n", null); + LookAndFeel laf = UIManager.getLookAndFeel(); + String lafName = laf == null ? "Not obtained" : laf.getName(); + String lafClass = laf == null ? "unknown" : laf.getClass().getName(); + sb.append("LookAndFeel: "); + sb.append(lafName); + sb.append(" ("); + sb.append(lafClass); + sb.append(")\n"); + // Not displayed in release version ( determined by possible version number + // regex 9[9.]*9[.-_a9]* ) + if (Pattern.matches("^\\d[\\d\\.]*\\d[\\.\\-\\w]*$", + jalview.bin.Cache.getDefault("VERSION", "TEST"))) + { + appendIfNotNull(sb, "Getdown appdir: ", + System.getProperty("getdownappdir"), "\n", null); + appendIfNotNull(sb, "Getdown appbase: ", + System.getProperty("getdownappbase"), "\n", null); + appendIfNotNull(sb, "Java home: ", System.getProperty("java.home"), + "\n", "unknown"); + } + return sb.toString(); + } + + /** + * + * @return build details as reported in splashscreen + */ + public static String getBuildDetailsForSplash() + { + // consider returning more human friendly info + // eg 'built from Source' or update channel + return jalview.bin.Cache.getDefault("INSTALLATION", "unknown"); + } + + public static String getStackTraceString(Throwable t) + { + StringWriter sw = new StringWriter(); + PrintWriter pw = new PrintWriter(sw); + t.printStackTrace(pw); + return sw.toString(); + } + + // proxy properties methods + public static void clearProxyProperties() + { + setProxyProperties(null, null, null, null, null, null, null, null, + null); + } + + public static void resetProxyProperties() + { + setProxyProperties(startupProxyProperties[0], startupProxyProperties[1], + startupProxyProperties[2], startupProxyProperties[3], + startupProxyProperties[4], + startupProxyProperties[5] == null ? null + : startupProxyProperties[5].toCharArray(), + startupProxyProperties[6], + startupProxyProperties[7] == null ? null + : startupProxyProperties[7].toCharArray(), + startupProxyProperties[8]); + StringBuilder sb = new StringBuilder(); + sb.append("Setting proxy properties to: http.proxyHost=") + .append(startupProxyProperties[0]).append(", http.proxyPort=") + .append(startupProxyProperties[1]) + .append(startupProxyProperties[4] != null + && !startupProxyProperties[4].isEmpty() + ? " [" + startupProxyProperties[4] + "]" + : "") + .append(", https.proxyHost=").append(startupProxyProperties[2]) + .append(", https.proxyPort=").append(startupProxyProperties[3]) + .append(startupProxyProperties[6] != null + && !startupProxyProperties[6].isEmpty() + ? " [" + startupProxyProperties[6] + "]" + : ""); + + Cache.debug(sb.toString()); + } + + public static void setProxyPropertiesFromPreferences() + { + setProxyPropertiesFromPreferences(Cache.PROXYTYPE_SYSTEM); + } + + public static void setProxyPropertiesFromPreferences( + String previousProxyType) + { + String proxyType = Cache.getDefault("USE_PROXY", + Cache.PROXYTYPE_SYSTEM); + if (previousProxyType != null + && !proxyType.equals(Cache.PROXYTYPE_CUSTOM) // always apply + // customProxy + && proxyType.equals(previousProxyType)) + { + // no change + return; + } + switch (proxyType) + { + case Cache.PROXYTYPE_NONE: + if (!previousProxyType.equals(proxyType)) + { + Cache.log.info("Setting no proxy settings"); + Cache.setProxyProperties(null, null, null, null, null, null, null, + null, null); + } + break; + case Cache.PROXYTYPE_CUSTOM: + // always re-set a custom proxy -- it might have changed, particularly + // password + Cache.log.info("Setting custom proxy settings"); + boolean proxyAuthSet = Cache.getDefault("PROXY_AUTH", false); + Cache.setProxyProperties(Cache.getDefault("PROXY_SERVER", null), + Cache.getDefault("PROXY_PORT", null), + Cache.getDefault("PROXY_SERVER_HTTPS", null), + Cache.getDefault("PROXY_PORT_HTTPS", null), + proxyAuthSet ? Cache.getDefault("PROXY_AUTH_USERNAME", "") + : null, + proxyAuthSet ? Cache.proxyAuthPassword : null, + proxyAuthSet ? Cache.getDefault("PROXY_AUTH_USERNAME", "") + : null, + proxyAuthSet ? Cache.proxyAuthPassword : null, "localhost"); + break; + default: // system proxy settings by default + Cache.log.info("Setting system proxy settings"); + Cache.resetProxyProperties(); + } + } + + public static void setProxyProperties(String httpHost, String httpPort, + String httpsHost, String httpsPort, String httpUser, + char[] httpPassword, String httpsUser, char[] httpsPassword, + String nonProxyHosts) + { + setOrClearSystemProperty("http.proxyHost", httpHost); + setOrClearSystemProperty("http.proxyPort", httpPort); + setOrClearSystemProperty("https.proxyHost", httpsHost); + setOrClearSystemProperty("https.proxyPort", httpsPort); + setOrClearSystemProperty("http.proxyUser", httpUser); + setOrClearSystemProperty("https.proxyUser", httpsUser); + // note: passwords for http.proxyPassword and https.proxyPassword are sent + // via the Authenticator, properties do not need to be set + + // are we using a custom proxy (password prompt might be required)? + boolean customProxySet = getDefault("USE_PROXY", PROXYTYPE_SYSTEM) + .equals(PROXYTYPE_CUSTOM); + + /* + * A bug in Java means the AuthCache does not get reset, so once it has working credentials, + * it never asks for more, so changing the Authenticator has no effect (as getPasswordAuthentication() + * is not re-called). + * This could lead to password leak to a hostile proxy server, so I'm putting in a hack to clear + * the AuthCache. + * see https://www.generacodice.com/en/articolo/154918/Reset-the-Authenticator-credentials + * ... + * Turns out this is only accessible in Java 8, and not in Java 9 onwards, so commenting out + */ + /* + try + { + sun.net.www.protocol.http.AuthCacheValue + .setAuthCache(new sun.net.www.protocol.http.AuthCacheImpl()); + } catch (Throwable t) + { + Cache.error(t.getMessage()); + Cache.debug(getStackTraceString(t)); + } + */ + + if (httpUser != null || httpsUser != null) + { + try + { + char[] displayHttpPw = new char[httpPassword == null ? 0 + : httpPassword.length]; + Arrays.fill(displayHttpPw, '*'); + Cache.debug("CACHE Proxy: setting new Authenticator with httpUser='" + + httpUser + "' httpPassword='" + displayHttpPw + "'"); + if (!Platform.isJS()) + /* * + * java.net.Authenticator not implemented in SwingJS yet + * + * @j2sIgnore + * + */ + { + Authenticator.setDefault(new Authenticator() + { + @Override + protected PasswordAuthentication getPasswordAuthentication() + { + if (getRequestorType() == RequestorType.PROXY) + { + String protocol = getRequestingProtocol(); + boolean needProxyPasswordSet = false; + if (customProxySet && + // we have a username but no password for the scheme being + // requested + (protocol.equalsIgnoreCase("http") + && (httpUser != null && httpUser.length() > 0 + && (httpPassword == null + || httpPassword.length == 0))) + || (protocol.equalsIgnoreCase("https") + && (httpsUser != null + && httpsUser.length() > 0 + && (httpsPassword == null + || httpsPassword.length == 0)))) + { + // open Preferences -> Connections + String message = MessageManager + .getString("label.proxy_password_required"); + Preferences.openPreferences(Preferences.CONNECTIONS_TAB, + message); + Preferences.getInstance() + .proxyAuthPasswordCheckHighlight(true, true); + } + else + { + try + { + if (protocol.equalsIgnoreCase("http") + && getRequestingHost() + .equalsIgnoreCase(httpHost) + && getRequestingPort() == Integer + .valueOf(httpPort)) + { + Cache.debug( + "AUTHENTICATOR returning PasswordAuthentication(\"" + + httpUser + "\", '" + + new String(displayHttpPw) + "')"); + return new PasswordAuthentication(httpUser, + httpPassword); + } + if (protocol.equalsIgnoreCase("https") + && getRequestingHost() + .equalsIgnoreCase(httpsHost) + && getRequestingPort() == Integer + .valueOf(httpsPort)) + { + char[] displayHttpsPw = new char[httpPassword.length]; + Arrays.fill(displayHttpsPw, '*'); + Cache.debug( + "AUTHENTICATOR returning PasswordAuthentication(\"" + + httpsUser + "\", '" + displayHttpsPw + + "'"); + return new PasswordAuthentication(httpsUser, + httpsPassword); + } + } catch (NumberFormatException e) + { + Cache.error("Problem with proxy port values [http:" + + httpPort + ", https:" + httpsPort + "]"); + } + Cache.debug( + "AUTHENTICATOR after trying to get PasswordAuthentication"); + } + } + // non proxy request + Cache.debug("AUTHENTICATOR returning null"); + return null; + } + }); + } // end of j2sIgnore for java.net.Authenticator + + // required to re-enable basic authentication (should be okay for a + // local proxy) + Cache.debug( + "AUTHENTICATOR setting property 'jdk.http.auth.tunneling.disabledSchemes' to \"\""); + System.setProperty("jdk.http.auth.tunneling.disabledSchemes", ""); + } catch (SecurityException e) + { + Cache.error("Could not set default Authenticator"); + Cache.debug(getStackTraceString(e)); + } + } + else + { + // reset the Authenticator to protect http.proxyUser and + // http.proxyPassword Just In Case + /* as noted above, due to bug in java this doesn't work if the sun.net.www.protocol.http.AuthCache + * has working credentials. No workaround for Java 11. + */ + if (!Platform.isJS()) + /* * + * java.net.Authenticator not implemented in SwingJS yet + * + * @j2sIgnore + * + */ + { + Cache.debug("AUTHENTICATOR setting default Authenticator to null"); + Authenticator.setDefault(null); + } + } + + // nonProxyHosts not currently configurable in Preferences + Cache.debug("AUTHENTICATOR setting property 'http.nonProxyHosts' to \"" + + nonProxyHosts + "\""); + setOrClearSystemProperty("http.nonProxyHosts", nonProxyHosts); + } + + public static void setOrClearSystemProperty(String key, char[] value) + { + setOrClearSystemProperty(key, + (value == null) ? null : new String(value)); + } + + public static void setOrClearSystemProperty(String key, String value) + { + if (key == null) + { + return; + } + if (value == null) + { + System.clearProperty(key); + } + else + { + System.setProperty(key, value); + } + } + + public final static int TRACE = 10; + + public final static int DEBUG = 20; + + public final static int INFO = 30; + + public final static int WARN = 40; + + public final static int ERROR = 50; + + public static boolean println(int level, String message) + { + if (Cache.log == null) + { + if (level >= WARN) + System.err.println(message); + else if (level >= INFO) + System.out.println(message); + // not printing debug or trace messages + return false; + } + if (level >= ERROR) + { + Cache.log.error(message); + } + else if (level >= WARN) + { + Cache.log.warn(message); + } + else if (level >= INFO) + { + Cache.log.info(message); + } + else if (level >= DEBUG) + { + Cache.log.debug(message); + } + else + { + Cache.log.trace(message); + } + return true; + } + + public static void trace(String message) + { + println(TRACE, message); + } + + public static void debug(String message) + { + println(DEBUG, message); + } + + public static void info(String message) + { + println(INFO, message); + } + + public static void warn(String message) + { + println(WARN, message); + } + + public static void error(String message) + { + println(ERROR, message); + } + + /** + * Getdown appbase methods + */ + + private static final String releaseAppbase; + + private static String getdownAppbase; + + private static String getdownDistDir; + + static + { + if (!Platform.isJS()) + { + Float specversion = Float + .parseFloat(System.getProperty("java.specification.version")); + releaseAppbase = (specversion < 9) + ? "https://www.jalview.org/getdown/release/1.8" + : "https://www.jalview.org/getdown/release/11"; + } + else + { + // this value currenly made up, can be changed to URL that will be + // "https://www.jalview.org/jalview-js/swingjs/j2s/build_properties" + releaseAppbase = "https://www.jalview.org/jalview-js"; + getdownAppbase = releaseAppbase; + getdownDistDir = "/swingjs/j2s"; + } + } + + // look for properties (passed in by getdown) otherwise default to release + private static void setGetdownAppbase() + { + if (getdownAppbase != null) + { + return; + } + String appbase = System.getProperty("getdownappbase"); + String distDir = System.getProperty("getdowndistdir"); + if (appbase == null) + { + appbase = buildProperties.getProperty("GETDOWNAPPBASE"); + distDir = buildProperties.getProperty("GETDOWNAPPDISTDIR"); + } + if (appbase == null) + { + appbase = releaseAppbase; + distDir = "release"; + } + if (appbase.endsWith("/")) + { + appbase = appbase.substring(0, appbase.length() - 1); + } + if (distDir == null) + { + distDir = appbase.equals(releaseAppbase) ? "release" : "alt"; + } + getdownAppbase = appbase; + getdownDistDir = distDir; + } + + public static String getGetdownAppbase() + { + setGetdownAppbase(); + return getdownAppbase; + } + + public static String getAppbaseBuildProperties() + { + String appbase = getGetdownAppbase(); + return appbase + "/" + getdownDistDir + "/build_properties"; + } +}