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 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;
// 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");
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: ");
{
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),
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();
}
}
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
protected PasswordAuthentication getPasswordAuthentication()
{
- Cache.debug(
- "*** START PasswordAuthentication.getPasswordAuthentication()");
- Cache.debug("*** getRequestorType()=" + getRequestorType());
if (getRequestorType() == RequestorType.PROXY)
{
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
// 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");
+ Preferences.openPreferences(Preferences.CONNECTIONS_TAB,
+ message);
+ Preferences.getInstance()
+ .proxyAuthPasswordCheckHighlight(true, true);
}
else
{
- Cache.debug("***+ TRYING TO GET PASSWORDAUTHENTICATION");
try
{
if (protocol.equalsIgnoreCase("http")
&& getRequestingPort() == Integer
.valueOf(httpPort))
{
- Cache.debug("***+ RETURNING PasswordAuthentication(\""
- + httpUser + "\", \"" + new String(httpPassword)
- + "\"");
+ Cache.debug(
+ "AUTHENTICATOR returning PasswordAuthentication(\""
+ + httpUser + "\", '"
+ + new String(displayHttpPw) + "')");
return new PasswordAuthentication(httpUser,
httpPassword);
}
&& getRequestingPort() == Integer
.valueOf(httpsPort))
{
- Cache.debug("***+ RETURNING PasswordAuthentication(\""
- + httpsUser + "\", \"" + httpsPassword + "\"");
+ char[] displayHttpsPw = new char[httpPassword.length];
+ Arrays.fill(displayHttpsPw, '*');
+ Cache.debug(
+ "AUTHENTICATOR returning PasswordAuthentication(\""
+ + httpsUser + "\", '" + displayHttpsPw
+ + "'");
return new PasswordAuthentication(httpsUser,
httpsPassword);
}
+ httpPort + ", https:" + httpsPort + "]");
}
Cache.debug(
- "***+ AFTER TRYING TO GET PASSWORDAUTHENTICATION");
+ "AUTHENTICATOR after trying to get PasswordAuthentication");
}
}
// non proxy request
- Cache.debug("***+ Returning null");
+ Cache.debug("AUTHENTICATOR returning null");
return null;
}
});
// 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)
{
{
// reset the Authenticator to protect http.proxyUser and
// http.proxyPassword Just In Case
- Cache.debug("***+ Setting default Authenticator to 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);
}
// 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,
}
}
- 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