X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=353f449f1bdbfeffbc69998e69bfdbd3bdd02a34;hb=b7d225fc8a17594a1ddacd775a819b9ffc70131b;hp=40fccb0e61bd06e4d4100a6207544c4501a4c315;hpb=b9bf3044b32b62771648842169f79ca8e7050c7f;p=jalview.git diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java index 40fccb0..353f449 100755 --- a/src/jalview/bin/Cache.java +++ b/src/jalview/bin/Cache.java @@ -29,9 +29,12 @@ 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; @@ -50,13 +53,16 @@ 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; @@ -271,6 +277,28 @@ public class Cache */ 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() { @@ -282,6 +310,9 @@ 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; @@ -329,7 +360,8 @@ public class Cache // 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."); + jalview.bin.Cache.log.debug(ChannelProperties.getProperty("app_name") + + " Debugging Output Follows."); } catch (Exception ex) { System.err.println("Problems initializing the log4j system\n"); @@ -344,10 +376,18 @@ public class Cache public static void loadProperties(String propsFile) { propertiesFile = propsFile; + String releasePropertiesFile = null; + boolean defaultProperties = false; if (propsFile == null && !propsAreReadOnly) { + String channelPrefsFilename = ChannelProperties + .getProperty("preferences.filename"); + String releasePrefsFilename = ".jalview_properties"; propertiesFile = System.getProperty("user.home") + File.separatorChar - + ".jalview_properties"; + + channelPrefsFilename; + releasePropertiesFile = System.getProperty("user.home") + + File.separatorChar + releasePrefsFilename; + defaultProperties = true; } else { @@ -367,20 +407,29 @@ public class Cache 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) { - fis = new FileInputStream(propertiesFile); + 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); @@ -394,16 +443,43 @@ public class Cache 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; + Cache.warn(message); } // LOAD THE AUTHORS FROM THE authors.props file @@ -471,9 +547,13 @@ public class Cache class VersionChecker extends Thread { + @Override public void run() { + String remoteBuildPropertiesUrl = Cache + .getAppbaseBuildProperties(); + String orgtimeout = System .getProperty("sun.net.client.defaultConnectTimeout"); if (orgtimeout == null) @@ -487,28 +567,19 @@ public class Cache { 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"); + java.net.URL url = new java.net.URL(remoteBuildPropertiesUrl); + 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; - } + Properties remoteBuildProperties = new Properties(); + remoteBuildProperties.load(in); + remoteVersion = remoteBuildProperties.getProperty("VERSION"); } catch (Exception ex) { - System.out.println( - "Non-fatal exception when checking version at www.jalview.org :"); + System.out + .println("Non-fatal exception when checking version at " + + remoteBuildPropertiesUrl + ":"); System.out.println(ex); remoteVersion = getProperty("VERSION"); } @@ -583,8 +654,23 @@ public class Cache 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")); + } } catch (Exception ex) { System.out.println("Error reading build details: " + ex); @@ -607,8 +693,8 @@ public class Cache new BuildDetails(codeVersion, null, codeInstallation); if (printVersion && reportVersion) { - System.out.println( - "Jalview Version: " + codeVersion + codeInstallation); + System.out.println(ChannelProperties.getProperty("app_name") + + " Version: " + codeVersion + codeInstallation); } } @@ -775,7 +861,8 @@ public class Cache lvclient.addAppender(log.getAppender("JalviewLogger")); // 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) { @@ -814,7 +901,8 @@ public class Cache lgclient.addAppender(log.getAppender("JalviewLogger")); // 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) { @@ -876,7 +964,7 @@ public class Cache .getConstructor(new Class[] { String.class, String.class, String.class }) .newInstance(new Object[] - { "Jalview Desktop", + { ChannelProperties.getProperty("app_name") + " Desktop", (vrs = jalview.bin.Cache.getProperty("VERSION") + "_" + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")), @@ -1152,10 +1240,12 @@ public class Cache public static String getVersionDetailsForConsole() { StringBuilder sb = new StringBuilder(); - sb.append("Jalview Version: "); + sb.append(ChannelProperties.getProperty("app_name")) + .append(" Version: "); sb.append(jalview.bin.Cache.getDefault("VERSION", "TEST")); sb.append("\n"); - sb.append("Jalview Installation: "); + sb.append(ChannelProperties.getProperty("app_name")) + .append(" Installation: "); sb.append(jalview.bin.Cache.getDefault("INSTALLATION", "unknown")); sb.append("\n"); sb.append("Build Date: "); @@ -1191,6 +1281,8 @@ public class Cache { 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"); } @@ -1215,4 +1307,426 @@ public class Cache 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"; + } }