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 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 jalview.datamodel.PDBEntry;
import jalview.gui.Preferences;
import jalview.gui.UserDefinedColours;
-import jalview.jbgui.GPreferences;
+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;
* <li>FOLLOW_SELECTIONS (true) Controls whether a new alignment view should
* respond to selections made in other alignments containing the same sequences.
* </li>
+ * <li>SHOW_JWS2_SERVICES (true) when set to false, jalview will not
+ * auto-discover JABAWS services</li>
* <li>JWS2HOSTURLS comma-separated list of URLs to try for JABAWS services</li>
* <li>SHOW_WSDISCOVERY_ERRORS (true) Controls if the web service URL discovery
* warning dialog box is displayed.</li>
* when shading by annotation</li>
* <li>ANNOTATIONCOLOUR_MAX (red) Shade used for maximum value of annotation
* when shading by annotation</li>
- * <li>www.jalview.org (http://www.jalview.org) a property enabling all HTTP
- * requests to be redirected to a mirror of http://www.jalview.org</li>
+ * <li>www.jalview.org (https://www.jalview.org) a property enabling all HTTP
+ * requests to be redirected to a mirror of https://www.jalview.org</li>
* <li>FIGURE_AUTOIDWIDTH (false) Expand the left hand column of an exported
* alignment figure to accommodate even the longest sequence ID or annotation
* label.</li>
* <li>CHIMERA_PATH specify full path to Chimera program (if non-standard)</li>
* <li>ID_ORG_HOSTURL location of jalview service providing identifiers.org urls
* </li>
- *
+ * <li>NONEWS - when set disables Jalview News from automatically appearing</li>
+ * <li>NOHTMLTEMPLATES - when set, the
+ * https://github.com/jalview/exporter-templates/tree/master/biojs repository is
+ * not downloaded automatically</li>
+ * <li>NOIDENTIFIERSSERVICE - when set, jalview won't automatically download
+ * available URL linkouts via www.jalview.org/services/identifiers</li>
+ * <li>
* </ul>
* Deprecated settings:
* <ul>
/**
* 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 = {
}
};
+ /* 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 = Platform.isJS();
- private final static String JS_PROPERTY_PREFIX = "jalview_";
+ public static boolean isPropsAreReadOnly()
+ {
+ return propsAreReadOnly;
+ }
- public static void initLogger()
+ public static void setPropsAreReadOnly(boolean propsAreReadOnly)
{
- if (log != null)
- {
- return;
- }
- try
- {
- // TODO: redirect stdout and stderr here in order to grab the output of
- // the log
-
- ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
- "System.err");
- ap.setName("JalviewLogger");
- org.apache.log4j.Logger.getRootLogger().addAppender(ap); // catch all for
- // 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);
- }
+ Cache.propsAreReadOnly = propsAreReadOnly;
}
+ private final static String JS_PROPERTY_PREFIX = "jalview_";
+
/**
* Loads properties from the given properties file. Any existing properties
* are first cleared.
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
{
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);
default:
String message = "Incorrect PROXY_TYPE - should be 'none' (clear proxy properties), 'false' (system settings), 'true' (custom settings): "
+ proxyType;
- Cache.warn(message);
+ Console.warn(message);
}
// LOAD THE AUTHORS FROM THE authors.props file
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",
- "http://www.jalview.org/services/identifiers"));
+ "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");
class VersionChecker extends Thread
{
+
@Override
public void run()
{
+ String remoteBuildPropertiesUrl = Cache
+ .getAppbaseBuildProperties();
+
String orgtimeout = System
.getProperty("sun.net.client.defaultConnectTimeout");
if (orgtimeout == null)
+ orgtimeout + " seconds.");
}
String remoteVersion = null;
- try
+ if (remoteBuildPropertiesUrl.startsWith("http"))
{
- 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");
- BufferedReader in = new BufferedReader(
- new InputStreamReader(url.openStream()));
- String line = null;
- while ((line = in.readLine()) != null)
+ try
{
- if (line.indexOf("jalview.version") == -1)
- {
- continue;
- }
+ System.setProperty("sun.net.client.defaultConnectTimeout",
+ "5000");
+
+ URL url = new URL(remoteBuildPropertiesUrl);
+
+ BufferedReader in = new BufferedReader(
+ new InputStreamReader(url.openStream()));
- 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 "
+ + remoteBuildPropertiesUrl + ":");
+ System.out.println(ex);
+ remoteVersion = getProperty("VERSION");
}
- } catch (Exception ex)
- {
- System.out.println(
- "Non-fatal exception when checking version at www.jalview.org :");
- System.out.println(ex);
- remoteVersion = getProperty("VERSION");
}
System.setProperty("sun.net.client.defaultConnectTimeout",
orgtimeout);
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);
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);
}
}
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);
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);
.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;
.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[]
}
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.");
}
}
}
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;
{
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);
}
/**
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(" (");
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")))
+ if (Console.isDebugEnabled()
+ || !"release".equals(ChannelProperties.getProperty("channel")))
{
+ appendIfNotNull(sb, "Channel: ",
+ ChannelProperties.getProperty("channel"), "\n", null);
appendIfNotNull(sb, "Getdown appdir: ",
- System.getProperty("getdownappdir"), "\n", null);
+ System.getProperty("getdowninstanceappdir"), "\n", null);
+ appendIfNotNull(sb, "Getdown appbase: ",
+ System.getProperty("getdowninstanceappbase"), "\n", null);
appendIfNotNull(sb, "Java home: ", System.getProperty("java.home"),
"\n", "unknown");
}
{
// 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)
? " [" + startupProxyProperties[6] + "]"
: "");
- Cache.debug(sb.toString());
+ 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,
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, '*');
+ Console.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()
{
- if (getRequestorType() == RequestorType.PROXY)
+ @Override
+ protected PasswordAuthentication getPasswordAuthentication()
{
- String scheme = getRequestingScheme();
- boolean needProxyPasswordSet = false;
- if (customProxySet &&
- // we have a username but no password for the scheme being
- // requested
- (scheme.equalsIgnoreCase("http")
- && (httpUser != null && httpUser.length() > 0
- && (httpPassword == null
- || httpPassword.length == 0)))
- || (scheme.equalsIgnoreCase("https")
- && (httpsUser != null
- && httpsUser.length() > 0
- && (httpsPassword == null
- || httpsPassword.length == 0))))
- {
- // open Preferences -> Connections
- String message = MessageManager
- .getString("label.proxy_password_required");
- openPreferencesConnectionsForProxyPassword(message);
- }
- else
+ 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 (scheme.equalsIgnoreCase("http")
- && getRequestingHost().equalsIgnoreCase(httpHost)
- && getRequestingPort() == Integer
- .valueOf(httpPort))
+ // 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
{
- return new PasswordAuthentication(httpUser,
- httpPassword);
- }
- if (scheme.equalsIgnoreCase("https")
- && getRequestingHost().equalsIgnoreCase(httpsHost)
- && getRequestingPort() == Integer
- .valueOf(httpsPort))
+ 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)
{
- return new PasswordAuthentication(httpsUser,
- httpsPassword);
+ Console.error("Problem with proxy port values [http:"
+ + httpPort + ", https:" + httpsPort + "]");
}
- } catch (NumberFormatException e)
- {
- Cache.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;
}
- // non proxy request
- 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)
{
- Cache.error("Could not set default Authenticator");
- Cache.debug(getStackTraceString(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
- 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
+ *
+ */
+ {
+ 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);
}
- private static void openPreferencesConnectionsForProxyPassword(
- String message)
- {
- //
- Cache.info("Opening Preferences for proxy password");
- // Desktop.instance.preferences_actionPerformed(null);
- Preferences p = new Preferences(GPreferences.CONNECTIONS_TAB);
- p.grabFocus();
- }
-
public static void setOrClearSystemProperty(String key, char[] value)
{
setOrClearSystemProperty(key,
- (value == null) ? null : value.toString());
+ (value == null) ? null : new String(value));
}
public static void setOrClearSystemProperty(String key, String value)
}
}
- public final static int DEBUG = 10;
+ /**
+ * Getdown appbase methods
+ */
- public final static int INFO = 20;
+ private static final String releaseAppbase;
- public final static int WARN = 30;
+ private static String getdownAppbase;
- public final static int ERROR = 40;
+ private static String getdownDistDir;
- public static boolean println(int level, String message)
+ static
{
- if (Cache.log == null)
- {
- if (level >= ERROR)
- System.err.println(message);
- else
- System.out.println(message);
- return false;
- }
- if (level >= WARN)
- {
- Cache.log.warn(message);
- }
- else if (level >= INFO)
+ if (!Platform.isJS())
{
- Cache.log.info(message);
+ 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
{
- Cache.log.debug(message);
+ // 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";
}
- return true;
}
- public static void debug(String message)
+ // look for properties (passed in by getdown) otherwise default to release
+ private static void setGetdownAppbase()
{
- println(DEBUG, message);
- }
-
- public static void info(String message)
- {
- println(INFO, message);
+ 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 void warn(String message)
+ public static String getGetdownAppbase()
{
- println(WARN, message);
+ setGetdownAppbase();
+ return getdownAppbase;
}
- public static void error(String message)
+ public static String getAppbaseBuildProperties()
{
- println(ERROR, message);
+ String appbase = getGetdownAppbase();
+ return appbase + "/" + getdownDistDir + "/build_properties";
}
}