X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=50db03b7c228c9448627e8528e613f075577d034;hb=2ea1b352349a737f513131873551bfb7899d812f;hp=8269f32c66d4813c9f92a5baf8a3c094fa717833;hpb=7664ccad29d55ad2355d72feeac23d8bdd49a2a7;p=jalview.git diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java index 8269f32..50db03b 100755 --- a/src/jalview/bin/Cache.java +++ b/src/jalview/bin/Cache.java @@ -34,6 +34,7 @@ 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; @@ -54,12 +55,12 @@ import org.apache.log4j.SimpleLayout; import jalview.datamodel.PDBEntry; import jalview.gui.Preferences; import jalview.gui.UserDefinedColours; -import jalview.jbgui.GPreferences; 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; @@ -309,6 +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; @@ -356,7 +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"); @@ -525,9 +530,12 @@ public class Cache class VersionChecker extends Thread { + @Override public void run() { + String buildPropertiesUrl = Cache.getAppbaseBuildProperties(); + String orgtimeout = System .getProperty("sun.net.client.defaultConnectTimeout"); if (orgtimeout == null) @@ -541,28 +549,19 @@ 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(buildPropertiesUrl); + 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 " + + buildPropertiesUrl + ":"); System.out.println(ex); remoteVersion = getProperty("VERSION"); } @@ -637,8 +636,13 @@ 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(); + applicationProperties.put("BUILD_DATE", + buildProperties.get("BUILD_DATE")); + applicationProperties.put("INSTALLATION", + buildProperties.get("INSTALLATION")); + applicationProperties.put("VERSION", buildProperties.get("VERSION")); } catch (Exception ex) { System.out.println("Error reading build details: " + ex); @@ -661,8 +665,8 @@ 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); } } @@ -829,7 +833,8 @@ 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) { @@ -868,7 +873,8 @@ 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) { @@ -930,7 +936,7 @@ 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")), @@ -1206,10 +1212,12 @@ 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: "); @@ -1245,6 +1253,8 @@ 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"); } @@ -1316,17 +1326,28 @@ public class Cache { String proxyType = Cache.getDefault("USE_PROXY", Cache.PROXYTYPE_SYSTEM); - if (proxyType.equals(Cache.PROXYTYPE_NONE)) + if (previousProxyType != null + && !proxyType.equals(Cache.PROXYTYPE_CUSTOM) // always apply + // customProxy + && proxyType.equals(previousProxyType)) { - if (!previousProxyType.equals(proxyType)) - Cache.log.info("Setting no proxy settings"); - Cache.setProxyProperties(null, null, null, null, null, null, null, - null, null); + // no change + return; } - else if (proxyType.equals(Cache.PROXYTYPE_CUSTOM)) + switch (proxyType) { + case Cache.PROXYTYPE_NONE: if (!previousProxyType.equals(proxyType)) - Cache.log.info("Setting custom proxy settings"); + { + 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), @@ -1338,11 +1359,9 @@ public class Cache proxyAuthSet ? Cache.getDefault("PROXY_AUTH_USERNAME", "") : null, proxyAuthSet ? Cache.proxyAuthPassword : null, "localhost"); - } - else // systemProxy should be selected and is sensible default anyway - { - if (!previousProxyType.equals(proxyType)) - Cache.log.info("Setting system proxy settings"); + break; + default: // system proxy settings by default + Cache.log.info("Setting system proxy settings"); Cache.resetProxyProperties(); } } @@ -1357,103 +1376,135 @@ public class Cache setOrClearSystemProperty("https.proxyHost", httpsHost); setOrClearSystemProperty("https.proxyPort", httpsPort); setOrClearSystemProperty("http.proxyUser", httpUser); - setOrClearSystemProperty("http.proxyPassword", httpPassword); setOrClearSystemProperty("https.proxyUser", httpsUser); - setOrClearSystemProperty("https.proxyPassword", httpsPassword); + // 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 { - Authenticator.setDefault(new Authenticator() + 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 + * + */ { - @Override - protected PasswordAuthentication getPasswordAuthentication() + Authenticator.setDefault(new Authenticator() { - Cache.debug( - "*** START PasswordAuthentication.getPasswordAuthentication()"); - Cache.debug("*** getRequestorType()=" + getRequestorType()); - if (getRequestorType() == RequestorType.PROXY) + @Override + protected PasswordAuthentication getPasswordAuthentication() { - String protocol = getRequestingProtocol(); - boolean needProxyPasswordSet = false; - Cache.debug("*** customProxySet = " + customProxySet); - Cache.debug("*** protocol = " + protocol); - Cache.debug("*** httpUser = " + httpUser); - Cache.debug( - "*** httpPassword = \"" + (httpPassword == null ? null - : new String(httpPassword)) + "\""); - Cache.debug("*** httpsUser = " + httpsUser); - Cache.debug("*** httpsPassword = \"" - + (httpsPassword == null ? null - : new String(httpsPassword)) - + "\""); - 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)))) + if (getRequestorType() == RequestorType.PROXY) { - // open Preferences -> Connections - String message = MessageManager - .getString("label.proxy_password_required"); - Cache.debug("***+ TRYING TO OPEN PREFERENCES"); - openPreferencesConnectionsForProxyPassword(message); - Cache.debug("***+ AFTER TRYING TO OPEN PREFERENCES"); - } - else - { - Cache.debug("***+ TRYING TO GET PASSWORDAUTHENTICATION"); - try + 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 { - if (protocol.equalsIgnoreCase("http") - && getRequestingHost().equalsIgnoreCase(httpHost) - && getRequestingPort() == Integer - .valueOf(httpPort)) + try { - Cache.debug("***+ RETURNING PasswordAuthentication(\"" - + httpUser + "\", \"" + new String(httpPassword) - + "\""); - return new PasswordAuthentication(httpUser, - httpPassword); - } - if (protocol.equalsIgnoreCase("https") - && getRequestingHost().equalsIgnoreCase(httpsHost) - && getRequestingPort() == Integer - .valueOf(httpsPort)) + 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.debug("***+ RETURNING PasswordAuthentication(\"" - + httpsUser + "\", \"" + httpsPassword + "\""); - return new PasswordAuthentication(httpsUser, - httpsPassword); + Cache.error("Problem with proxy port values [http:" + + httpPort + ", https:" + httpsPort + "]"); } - } catch (NumberFormatException e) - { - Cache.error("Problem with proxy port values [http:" - + httpPort + ", https:" + httpsPort + "]"); + Cache.debug( + "AUTHENTICATOR after trying to get PasswordAuthentication"); } - Cache.debug( - "***+ AFTER TRYING TO GET PASSWORDAUTHENTICATION"); } + // non proxy request + Cache.debug("AUTHENTICATOR returning null"); + return null; } - // non proxy request - Cache.debug("***+ 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( - "***+ Setting jdk.http.auth.tunneling.disabledSchemes to ''"); + "AUTHENTICATOR setting property 'jdk.http.auth.tunneling.disabledSchemes' to \"\""); System.setProperty("jdk.http.auth.tunneling.disabledSchemes", ""); } catch (SecurityException e) { @@ -1465,27 +1516,28 @@ public class Cache { // reset the Authenticator to protect http.proxyUser and // http.proxyPassword Just In Case - Cache.debug("***+ Setting default Authenticator to null"); - Authenticator.setDefault(null); + /* 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("***+ Setting http.nonProxyHosts property to \"" + Cache.debug("AUTHENTICATOR setting property 'http.nonProxyHosts' to \"" + nonProxyHosts + "\""); setOrClearSystemProperty("http.nonProxyHosts", nonProxyHosts); } - private static void openPreferencesConnectionsForProxyPassword( - String message) - { - // - Cache.info("Opening Preferences for proxy password"); - // Desktop.instance.preferences_actionPerformed(null); - Cache.debug("***+########## TRYING TO OPEN PREFERENCES: " + message); - Preferences p = new Preferences(GPreferences.CONNECTIONS_TAB, message); - p.grabFocus(); - } - public static void setOrClearSystemProperty(String key, char[] value) { setOrClearSystemProperty(key, @@ -1508,25 +1560,32 @@ public class Cache } } - public final static int DEBUG = 10; + public final static int TRACE = 10; + + public final static int DEBUG = 20; - public final static int INFO = 20; + public final static int INFO = 30; - public final static int WARN = 30; + public final static int WARN = 40; - public final static int ERROR = 40; + public final static int ERROR = 50; public static boolean println(int level, String message) { if (Cache.log == null) { - if (level >= ERROR) + if (level >= WARN) System.err.println(message); - else + else if (level >= INFO) System.out.println(message); + // not printing debug or trace messages return false; } - if (level >= WARN) + if (level >= ERROR) + { + Cache.log.error(message); + } + else if (level >= WARN) { Cache.log.warn(message); } @@ -1534,13 +1593,22 @@ public class Cache { Cache.log.info(message); } - else + 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); @@ -1560,4 +1628,66 @@ public class Cache { println(ERROR, message); } + + /** + * Getdown appbase methods + */ + + private static final String releaseAppbase; + + private static String getdownAppbase; + + private static String getdownDistDir; + + 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"; + } + + // 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"; + } }