X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=4891451cfc6dbdf3e6ab3ad6c713fdeae7177352;hb=80b889f0cca49103e1b20ed806755a0719789906;hp=6266b712eb791a65cd11092b3f029b83fdfdb808;hpb=9d2d179549fa20c2ea0d96198009a142c0d4fb65;p=jalview.git diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java index 6266b71..4891451 100755 --- a/src/jalview/bin/Cache.java +++ b/src/jalview/bin/Cache.java @@ -24,13 +24,21 @@ import java.awt.Color; import java.io.BufferedReader; import java.io.File; import java.io.FileInputStream; +import java.io.FileNotFoundException; import java.io.FileOutputStream; +import java.io.IOException; 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.ArrayList; +import java.util.Arrays; +import java.util.Collection; import java.util.Collections; import java.util.Date; import java.util.Enumeration; @@ -38,30 +46,23 @@ 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 org.apache.log4j.builders.appender.ConsoleAppenderBuilder; -import org.apache.logging.log4j.core.config.Configurator; -import org.apache.logging.log4j.core.config.builder.api.AppenderComponentBuilder; -import org.apache.logging.log4j.core.config.builder.api.ConfigurationBuilder; -import org.apache.logging.log4j.core.config.builder.api.ConfigurationBuilderFactory; -import org.apache.logging.log4j.core.config.builder.impl.BuiltConfiguration; - import jalview.datamodel.PDBEntry; +import jalview.gui.Preferences; import jalview.gui.UserDefinedColours; +import jalview.log.JLoggerLog4j; 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; /** @@ -281,7 +282,30 @@ public class Cache /** * Initialises the Jalview Application Log */ - public static Logger log; + + public final static String JALVIEW_LOGGER_NAME = "JalviewLogger"; + + // 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() @@ -294,58 +318,28 @@ public class Cache } }; + /* 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 = false; + private static final String fallbackPropertiesFile = ".jalview_properties"; + + private static boolean propsAreReadOnly = Platform.isJS(); - public static void initLogger() + public static boolean isPropsAreReadOnly() { - if (log != null) - { - return; - } - try - { - // TODO: redirect stdout and stderr here in order to grab the output of - // the log - ConfigurationBuilder builder = ConfigurationBuilderFactory.newConfigurationBuilder(); - AppenderComponentBuilder consoleApp = builder.newAppender("stderr", "Console"); - builder.add(consoleApp); - Configurator.initialize(builder.build()); - // 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("Jalview Debugging Output Follows."); - } catch (Exception ex) - { - System.err.println("Problems initializing the log4j system\n"); - ex.printStackTrace(System.err); - } + return propsAreReadOnly; + } + + public static void setPropsAreReadOnly(boolean propsAreReadOnly) + { + Cache.propsAreReadOnly = propsAreReadOnly; } + private final static String JS_PROPERTY_PREFIX = "jalview_"; + /** * Loads properties from the given properties file. Any existing properties * are first cleared. @@ -353,10 +347,18 @@ public class Cache public static void loadProperties(String propsFile) { propertiesFile = propsFile; - if (propsFile == null) + String releasePropertiesFile = null; + boolean defaultProperties = false; + if (propsFile == null && !propsAreReadOnly) { + String channelPrefsFilename = ChannelProperties + .getProperty("preferences.filename"); + String releasePrefsFilename = fallbackPropertiesFile; propertiesFile = System.getProperty("user.home") + File.separatorChar - + ".jalview_properties"; + + channelPrefsFilename; + releasePropertiesFile = System.getProperty("user.home") + + File.separatorChar + releasePrefsFilename; + defaultProperties = true; } else { @@ -364,65 +366,112 @@ public class Cache propsAreReadOnly = true; } - try + if (propertiesFile == null) + { // BH 2019 + Platform.readInfoProperties(JS_PROPERTY_PREFIX, + applicationProperties); + } + else { - 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; + InputStream fis; + try + { + // props file provided as URL + 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) + { + String readPropertiesFile = propertiesFile; + // if we're using the usual properties file and the channel properties + // file doesn't exist, read .jalview_properties + // (but we'll still save to the channel properties file). + if (defaultProperties && (!new File(propertiesFile).exists()) + && (new File(releasePropertiesFile).exists())) + { + readPropertiesFile = releasePropertiesFile; + } + fis = new FileInputStream(readPropertiesFile); + } + applicationProperties.clear(); + applicationProperties.load(fis); + + // remove any old build properties + deleteBuildProperties(); + fis.close(); } catch (Exception ex) { - fis = null; - } - if (fis == null) - { - fis = new FileInputStream(propertiesFile); + System.out.println("Error reading properties file: " + ex); } - 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"); + } + */ - System.out.println("Using proxyServer: " + proxyServer - + " proxyPort: " + proxyPort); - - System.setProperty("http.proxyHost", proxyServer); - System.setProperty("http.proxyPort", proxyPort); + // 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; + Console.warn(message); } // LOAD THE AUTHORS FROM THE authors.props file + String authorDetails = resolveResourceURLFor("/authors.props"); + 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(); + 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"); @@ -433,27 +482,27 @@ public class Cache SiftsSettings .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false)); - SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache + SiftsSettings.setSiftDownloadDirectory(Cache .getDefault("sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR)); SiftsSettings.setFailSafePIDThreshold( - jalview.bin.Cache.getDefault("sifts_fail_safe_pid_threshold", + Cache.getDefault("sifts_fail_safe_pid_threshold", DEFAULT_FAIL_SAFE_PID_THRESHOLD)); SiftsSettings.setCacheThresholdInDays( - jalview.bin.Cache.getDefault("sifts_cache_threshold_in_days", + Cache.getDefault("sifts_cache_threshold_in_days", DEFAULT_CACHE_THRESHOLD_IN_DAYS)); IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL", "https://www.jalview.org/services/identifiers")); IdOrgSettings.setDownloadLocation(ID_ORG_FILE); - StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache - .getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT)); + StructureImportSettings.setDefaultStructureFileFormat( + Cache.getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT)); StructureImportSettings .setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER); // StructureImportSettings - // .setDefaultPDBFileParser(jalview.bin.Cache.getDefault( + // .setDefaultPDBFileParser(Cache.getDefault( // "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER)); String jnlpVersion = System.getProperty("jalview.version"); @@ -473,7 +522,8 @@ public class Cache @Override public void run() { - String buildPropertiesUrl = Cache.getAppbaseBuildProperties(); + String remoteBuildPropertiesUrl = Cache + .getAppbaseBuildProperties(); String orgtimeout = System .getProperty("sun.net.client.defaultConnectTimeout"); @@ -484,25 +534,29 @@ public class Cache + orgtimeout + " seconds."); } String remoteVersion = null; - try - { - System.setProperty("sun.net.client.defaultConnectTimeout", - "5000"); - java.net.URL url = new java.net.URL(buildPropertiesUrl); - - BufferedReader in = new BufferedReader( - new InputStreamReader(url.openStream())); - - Properties remoteBuildProperties = new Properties(); - remoteBuildProperties.load(in); - remoteVersion = remoteBuildProperties.getProperty("VERSION"); - } catch (Exception ex) + if (remoteBuildPropertiesUrl.startsWith("http")) { - System.out - .println("Non-fatal exception when checking version at " - + buildPropertiesUrl + ":"); - System.out.println(ex); - remoteVersion = getProperty("VERSION"); + try + { + System.setProperty("sun.net.client.defaultConnectTimeout", + "5000"); + + URL url = new 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); @@ -527,29 +581,76 @@ public class Cache } // LOAD USERDEFINED COLOURS - jalview.bin.Cache - .initUserColourSchemes(getProperty("USER_DEFINED_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 printV = codeInstallation == null; + boolean printVersion = codeInstallation == null; - // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar + /* + * read build properties - from the Jalview jar for a Java distribution, + * or from codebase file in test or JalviewJS context + */ try { - String buildDetails = "jar:".concat(Cache.class.getProtectionDomain() - .getCodeSource().getLocation().toString() - .concat("!/.build_properties")); - - java.net.URL localJarFileURL = new java.net.URL(buildDetails); - + String buildDetails = resolveResourceURLFor("/.build_properties"); + URL localJarFileURL = new URL(buildDetails); InputStream in = localJarFileURL.openStream(); - applicationProperties.load(in); + 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")); + } + if (buildProperties.getProperty("JAVA_COMPILE_VERSION", null) != null) + { + applicationProperties.put("JAVA_COMPILE_VERSION", + buildProperties.getProperty("JAVA_COMPILE_VERSION")); + } } catch (Exception ex) { System.out.println("Error reading build details: " + ex); @@ -570,10 +671,10 @@ public class Cache } setProperty("VERSION", codeVersion); new BuildDetails(codeVersion, null, codeInstallation); - if (printV && reportVersion) + if (printVersion && reportVersion) { - System.out.println( - "Jalview Version: " + codeVersion + codeInstallation); + System.out.println(ChannelProperties.getProperty("app_name") + + " Version: " + codeVersion + codeInstallation); } } @@ -599,7 +700,13 @@ public class Cache */ public static String getProperty(String key) { - return applicationProperties.getProperty(key); + String prop = applicationProperties.getProperty(key); + if (prop == null && Platform.isJS()) + { + prop = applicationProperties.getProperty(Platform.getUniqueAppletID() + + "_" + JS_PROPERTY_PREFIX + key); + } + return prop; } /** @@ -637,18 +744,13 @@ public class Cache } /** - * These methods are used when checking if the saved preference is different - * to the default setting + * 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 string = getProperty(property); - if (string != null) - { - return string; - } - - return def; + String value = getProperty(property); + return value == null ? def : value; } /** @@ -730,21 +832,21 @@ public class Cache if (jalview.jbgui.GDesktop.class.getClassLoader() .loadClass("uk.ac.vamsas.client.VorbaId") != null) { - jalview.bin.Cache.log.debug( + Console.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")); + JLoggerLog4j lvclient = JLoggerLog4j.getLogger("uk.ac.vamsas", + Console.getCachedLogLevel("logs.Vamsas.Level")); + JLoggerLog4j.addAppender(lvclient, Console.log, + JALVIEW_LOGGER_NAME); // Tell the user that debug is enabled - lvclient.debug("Jalview Vamsas Client Debugging Output Follows."); + 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"); + Console.debug("Vamsas Classes are not present"); } } return (vamsasJarsArePresent > 0); @@ -769,25 +871,25 @@ public class Cache if (Cache.class.getClassLoader() .loadClass("groovy.lang.GroovyObject") != null) { - jalview.bin.Cache.log.debug( + Console.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")); + JLoggerLog4j lgclient = JLoggerLog4j.getLogger("groovy", + Console.getCachedLogLevel("logs.Groovy.Level")); + JLoggerLog4j.addAppender(lgclient, Console.log, + JALVIEW_LOGGER_NAME); // Tell the user that debug is enabled - lgclient.debug("Jalview Groovy Client Debugging Output Follows."); + 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); + Console.debug("Groovy Classes are not present", e); } catch (Exception e) { groovyJarsArePresent = 0; - jalview.bin.Cache.log.debug("Groovy Classes are not present"); + Console.debug("Groovy Classes are not present"); } } return (groovyJarsArePresent > 0); @@ -821,7 +923,7 @@ public class Cache .loadClass("com.boxysystems.jgoogleanalytics.FocusPoint"); } catch (Exception e) { - log.debug( + Console.debug( "com.boxysystems.jgoogleanalytics package is not present - tracking not enabled."); tracker = null; jgoogleanalyticstracker = null; @@ -840,10 +942,9 @@ public class Cache .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")), + { ChannelProperties.getProperty("app_name") + " Desktop", + (vrs = Cache.getProperty("VERSION") + "_" + + Cache.getDefault("BUILD_DATE", "unknown")), "UA-9060947-1" }); jgoogleanalyticstracker .getMethod("trackAsynchronously", new Class[] @@ -864,57 +965,29 @@ public class Cache } if (re != null || ex != null || err != null) { - if (log != null) + if (re != 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); - } + Console.debug("Caught runtime exception in googletracker init:", + re); } - else + if (ex != null) { - 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(); - } + Console.warn( + "Failed to initialise GoogleTracker for Jalview Desktop with version " + + vrs, + ex); + } + if (err != null) + { + Console.error( + "Whilst initing GoogleTracker for Jalview Desktop version " + + vrs, + err); } } else { - log.debug("Successfully initialised tracker."); + Console.debug("Successfully initialised tracker."); } } } @@ -936,7 +1009,7 @@ public class Cache Color col = ColorUtils.parseColourString(colprop); if (col == null) { - log.warn("Couldn't parse '" + colprop + "' as a colour for " + Console.warn("Couldn't parse '" + colprop + "' as a colour for " + property); } return (col == null) ? defcolour : col; @@ -1105,8 +1178,11 @@ public class Cache { return; } - String line = prefix + (value != null ? value : defaultValue) + suffix; - sb.append(line); + if (prefix != null) + sb.append(prefix); + sb.append(value == null ? defaultValue : value); + if (suffix != null) + sb.append(suffix); } /** @@ -1116,18 +1192,21 @@ public class Cache public static String getVersionDetailsForConsole() { StringBuilder sb = new StringBuilder(); - sb.append("Jalview Version: "); - sb.append(jalview.bin.Cache.getDefault("VERSION", "TEST")); + sb.append(ChannelProperties.getProperty("app_name")) + .append(" Version: "); + sb.append(Cache.getDefault("VERSION", "TEST")); sb.append("\n"); - sb.append("Jalview Installation: "); - sb.append(jalview.bin.Cache.getDefault("INSTALLATION", "unknown")); + sb.append(ChannelProperties.getProperty("app_name")) + .append(" Installation: "); + sb.append(Cache.getDefault("INSTALLATION", "unknown")); sb.append("\n"); sb.append("Build Date: "); - sb.append(jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")); + sb.append(Cache.getDefault("BUILD_DATE", "unknown")); sb.append("\n"); sb.append("Java version: "); sb.append(System.getProperty("java.version")); sb.append("\n"); + sb.append("Java platform: "); sb.append(System.getProperty("os.arch")); sb.append(" "); sb.append(System.getProperty("os.name")); @@ -1148,17 +1227,19 @@ public class Cache 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, "Channel: ", + ChannelProperties.getProperty("channel"), "\n", null); + if (Console.isDebugEnabled() + || !"release".equals(ChannelProperties.getProperty("channel"))) { appendIfNotNull(sb, "Getdown appdir: ", - System.getProperty("getdownappdir"), "\n", null); + System.getProperty("getdowninstanceappdir"), "\n", null); appendIfNotNull(sb, "Getdown appbase: ", - System.getProperty("getdownappbase"), "\n", null); + System.getProperty("getdowninstanceappbase"), "\n", null); appendIfNotNull(sb, "Java home: ", System.getProperty("java.home"), "\n", "unknown"); + appendIfNotNull(sb, "Preferences file: ", propertiesFile, "\n", + "unknown"); } return sb.toString(); } @@ -1171,7 +1252,7 @@ public class Cache { // consider returning more human friendly info // eg 'built from Source' or update channel - return jalview.bin.Cache.getDefault("INSTALLATION", "unknown"); + return Cache.getDefault("INSTALLATION", "unknown"); } public static String getStackTraceString(Throwable t) @@ -1182,6 +1263,290 @@ public class Cache 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] + "]" + : ""); + + Console.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)) + { + Console.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 + Console.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 + Console.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, '*'); + Console.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.TabRef.CONNECTIONS_TAB, message); + Preferences.getInstance() + .proxyAuthPasswordCheckHighlight(true, true); + } + else + { + try + { + if (protocol.equalsIgnoreCase("http") + && getRequestingHost() + .equalsIgnoreCase(httpHost) + && getRequestingPort() == Integer + .valueOf(httpPort)) + { + Console.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, '*'); + Console.debug( + "AUTHENTICATOR returning PasswordAuthentication(\"" + + httpsUser + "\", '" + displayHttpsPw + + "'"); + return new PasswordAuthentication(httpsUser, + httpsPassword); + } + } catch (NumberFormatException e) + { + Console.error("Problem with proxy port values [http:" + + httpPort + ", https:" + httpsPort + "]"); + } + Console.debug( + "AUTHENTICATOR after trying to get PasswordAuthentication"); + } + } + // non proxy request + Console.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) + Console.debug( + "AUTHENTICATOR setting property 'jdk.http.auth.tunneling.disabledSchemes' to \"\""); + System.setProperty("jdk.http.auth.tunneling.disabledSchemes", ""); + } catch (SecurityException e) + { + Console.error("Could not set default Authenticator"); + Console.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 + * + */ + { + Console.debug( + "AUTHENTICATOR setting default Authenticator to null"); + Authenticator.setDefault(null); + } + } + + // nonProxyHosts not currently configurable in Preferences + Console.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); + } + } + /** * Getdown appbase methods */ @@ -1194,11 +1559,22 @@ public class Cache static { - 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"; + 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 @@ -1212,6 +1588,11 @@ public class Cache String distDir = System.getProperty("getdowndistdir"); if (appbase == null) { + appbase = buildProperties.getProperty("GETDOWNAPPBASE"); + distDir = buildProperties.getProperty("GETDOWNAPPDISTDIR"); + } + if (appbase == null) + { appbase = releaseAppbase; distDir = "release"; } @@ -1238,4 +1619,61 @@ public class Cache String appbase = getGetdownAppbase(); return appbase + "/" + getdownDistDir + "/build_properties"; } + + private static final Collection bootstrapProperties = new ArrayList<>( + Arrays.asList(JALVIEWLOGLEVEL)); + + public static Properties bootstrapProperties(String filename) + { + Properties bootstrapProps = new Properties(); + File file = null; + if (filename != null) + { + file = new File(filename); + } + if (file == null || !file.exists()) + { + String channelPrefsFilename = ChannelProperties + .getProperty("preferences.filename"); + String propertiesFilename = System.getProperty("user.home") + + File.separatorChar + channelPrefsFilename; + file = new File(propertiesFilename); + } + if (file == null || !file.exists()) + { + String releasePrefsFilename = fallbackPropertiesFile; + String releasePropertiesFilename = System.getProperty("user.home") + + File.separatorChar + releasePrefsFilename; + file = new File(releasePropertiesFilename); + } + + if (filename == null || !file.exists()) + { + System.err.println("Could not load bootstrap preferences file '" + + filename + "'"); + return null; + } + + try + { + FileInputStream in = new FileInputStream(file.getAbsoluteFile()); + Properties props = new Properties(); + props.load(in); + for (String prop : bootstrapProperties) + { + if (props.containsKey(prop)) + bootstrapProps.put(prop, props.getProperty(prop)); + } + } catch (FileNotFoundException e) + { + System.err.println("Could not find bootstrap preferences file '" + + file.getAbsolutePath() + "'"); + } catch (IOException e) + { + System.err.println( + "IOException when loading bootstrap preferences file '" + + file.getAbsolutePath() + "'"); + } + return bootstrapProps; + } }