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 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;
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()
{
// 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");
switch (proxyType)
{
case PROXYTYPE_NONE:
- setProxyProperties(null, null, null, null, null, null, null, null);
+ clearProxyProperties();
break;
case PROXYTYPE_SYSTEM: // use system settings
resetProxyProperties();
String httpsHost = getDefault("PROXY_SERVER_HTTPS", httpHost);
String httpsPort = getDefault("PROXY_PORT_HTTPS", httpPort);
String httpUser = getDefault("PROXY_AUTH_USER", null);
- String httpPassword = getDefault("PROXY_AUTH_PASSWORD", null);
// https.proxyUser and https.proxyPassword are not able to be
- // independently set in Preferences yet
+ // independently set in Preferences yet (or http.nonProxyHosts)
String httpsUser = getDefault("PROXY_AUTH_USER_HTTPS", httpUser);
- String httpsPassword = getDefault("PROXY_AUTH_PASSWORD_HTTPS",
- httpPassword);
setProxyProperties(httpHost, httpPort, httpsHost, httpsPort, httpUser,
- httpPassword, httpsUser, httpsPassword);
+ proxyAuthPassword, httpsUser, proxyAuthPassword, "localhost");
break;
default:
String message = "Incorrect PROXY_TYPE - should be 'none' (clear proxy properties), 'false' (system settings), 'true' (custom settings): "
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);
}
}
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)
{
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)
{
.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")),
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: ");
}
// 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],
- startupProxyProperties[6], startupProxyProperties[7]);
+ 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=")
Cache.debug(sb.toString());
}
- public static void setProxyProperties(String httpHost, String httpPort,
- String httpsHost, String httpsPort, String httpUser,
- String httpPassword)
+ public static void setProxyPropertiesFromPreferences()
{
- setProxyProperties(httpHost, httpPort, httpsHost, httpsPort, httpUser,
- httpPassword, httpUser, httpPassword);
+ 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,
- String httpPassword, String httpsUser, String httpsPassword)
+ 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("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
{
+ char[] displayHttpPw = new char[httpPassword == null ? 0
+ : httpPassword.length];
+ Arrays.fill(displayHttpPw, '*');
+ Cache.debug("CACHE Proxy: setting new Authenticator with httpUser='"
+ + httpUser + "' httpPassword='" + displayHttpPw + "'");
Authenticator.setDefault(new Authenticator()
{
@Override
{
if (getRequestorType() == RequestorType.PROXY)
{
- 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))))
{
- if (getRequestingScheme().equalsIgnoreCase("http")
- && getRequestingHost().equalsIgnoreCase(httpHost)
- && getRequestingPort() == Integer.valueOf(httpPort))
+ // open Preferences -> Connections
+ String message = MessageManager
+ .getString("label.proxy_password_required");
+ Preferences.openPreferences(Preferences.CONNECTIONS_TAB,
+ message);
+ Preferences.getInstance()
+ .proxyAuthPasswordCheckHighlight(true, true);
+ }
+ else
+ {
+ try
{
- return new PasswordAuthentication(httpUser,
- httpPassword == null ? new char[] {}
- : httpPassword.toCharArray());
- }
- if (getRequestingScheme().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)
{
- return new PasswordAuthentication(httpsUser,
- httpsPassword == null ? new char[] {}
- : httpsPassword.toCharArray());
+ 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");
}
}
// non proxy request
+ Cache.debug("AUTHENTICATOR returning null");
return null;
}
});
// 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)
{
{
// reset the Authenticator to protect http.proxyUser and
// http.proxyPassword Just In Case
- Authenticator.setDefault(new Authenticator()
- {
- @Override
- protected PasswordAuthentication getPasswordAuthentication()
- {
- return 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.
+ */
+ Cache.debug("AUTHENTICATOR setting default Authenticator to null");
+ Authenticator.setDefault(null);
}
- // clear localhost from proxying unless nonProxyHosts already set (not
- // currently configurable in Preferences)
- String nonProxyHosts = startupProxyProperties[8];
- System.setProperty("http.nonProxyHosts",
- nonProxyHosts == null ? "localhost" : nonProxyHosts);
+ // 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)
}
}
- public final static int DEBUG = 10;
+ public final static int TRACE = 10;
- public final static int INFO = 20;
+ public final static int DEBUG = 20;
- public final static int WARN = 30;
+ public final static int INFO = 30;
- public final static int ERROR = 40;
+ 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 >= 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);
}
{
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);
{
println(ERROR, message);
}
-}
+}
\ No newline at end of file
git://source.jalview.org / jalview.git / blobdiff