import javax.swing.LookAndFeel;
import javax.swing.UIManager;
-import org.apache.logging.log4j.Level;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.core.config.Configurator;
-import org.apache.logging.log4j.core.config.builder.api.AppenderComponentBuilder;
-import org.apache.logging.log4j.core.config.builder.api.ConfigurationBuilder;
-import org.apache.logging.log4j.core.config.builder.api.ConfigurationBuilderFactory;
-import org.apache.logging.log4j.core.config.builder.impl.BuiltConfiguration;
-
import jalview.datamodel.PDBEntry;
import jalview.gui.Preferences;
import jalview.gui.UserDefinedColours;
+import jalview.log.JLogger;
+import jalview.log.JLoggerLog4j;
import jalview.schemes.ColourSchemeLoader;
import jalview.schemes.ColourSchemes;
import jalview.schemes.UserColourScheme;
/**
* Initialises the Jalview Application Log
*/
- public static Logger log;
+
+ public final static String JALVIEW_LOGGER_NAME = "JalviewLogger";
+
+ public static JLoggerLog4j log;
// save the proxy properties set at startup
public final static String[] startupProxyProperties = {
private final static String JS_PROPERTY_PREFIX = "jalview_";
- public static void initLogger()
+ public final static String LOGGING_TEST_MESSAGE = "Logging to STDERR";
+
+ public static JLogger.LogLevel getCachedLogLevel()
+ {
+ return getCachedLogLevel(JALVIEWLOGLEVEL);
+ }
+
+ public static JLogger.LogLevel getCachedLogLevel(String key)
+ {
+ return JLogger.toLevel(Cache.getDefault(key, "INFO"));
+ }
+
+ public static boolean initLogger()
{
if (log != null)
{
- return;
+ return true;
}
try
{
- // configure the root logger to stderr
- ConfigurationBuilder<BuiltConfiguration> builder = ConfigurationBuilderFactory
- .newConfigurationBuilder();
- AppenderComponentBuilder consoleApp = builder.newAppender("stderr",
- "Console");
- builder.add(consoleApp);
- Configurator.initialize(builder.build());
+ JLogger.LogLevel cachedLevel = getCachedLogLevel();
+ if (!Platform.isJS())
+ {
+ Log4j.init(cachedLevel);
+ }
// log output
- Logger laxis = LogManager.getLogger("org.apache.axis");
- log = LogManager.getLogger("jalview.bin.Jalview");
-
- Log4j.setLevel(laxis, Level.toLevel(
- Cache.getDefault("logs.Axis.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
- Log4j.setRootLevel(Level.INFO);
-
- Log4j.setLevel(log, Level.toLevel(Cache
- .getDefault("logs.Jalview.level", Level.INFO.toString())));
- // laxis.addAppender(ap);
- // lcastor.addAppender(ap);
- // jalview.bin.Cache.log.addAppender(ap);
+ // is laxis used? Does getLogger do anything without a Logger object?
+ // Logger laxis = Log4j.getLogger("org.apache.axis", myLevel);
+ JLoggerLog4j.getLogger("org.apache.axis", cachedLevel);
+
+ // The main application logger
+ log = JLoggerLog4j.getLogger(JALVIEW_LOGGER_NAME, cachedLevel);
+ } catch (NoClassDefFoundError e)
+ {
+ System.err.println("Could not initialise the logger framework");
+ e.printStackTrace();
+ }
+
+ // Test message
+ if (log != null)
+ {
+ // Logging test message should got through the logger object
+ if (log.loggerExists())
+ log.debug(LOGGING_TEST_MESSAGE);
// Tell the user that debug is enabled
- log.debug(ChannelProperties.getProperty("app_name")
+ Cache.debug(ChannelProperties.getProperty("app_name")
+ " Debugging Output Follows.");
- } catch (Exception ex)
+ return true;
+ }
+ else
{
- System.err.println("Problems initializing the log4j system\n");
- ex.printStackTrace(System.err);
+ return false;
}
}
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",
"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");
if (jalview.jbgui.GDesktop.class.getClassLoader()
.loadClass("uk.ac.vamsas.client.VorbaId") != null)
{
- log.debug(
- "Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
+ debug("Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
vamsasJarsArePresent = 1;
- Logger lvclient = LogManager.getLogger("uk.ac.vamsas");
- Log4j.setLevel(lvclient, Level.toLevel(Cache
- .getDefault("logs.Vamsas.Level", Level.INFO.toString())));
-
- Log4j.addAppender(lvclient, log, "JalviewLogger");
+ JLoggerLog4j lvclient = JLoggerLog4j.getLogger("uk.ac.vamsas",
+ getCachedLogLevel("logs.Vamsas.Level"));
+ JLoggerLog4j.addAppender(lvclient, log, JALVIEW_LOGGER_NAME);
// Tell the user that debug is enabled
lvclient.debug(ChannelProperties.getProperty("app_name")
+ " Vamsas Client Debugging Output Follows.");
} catch (Exception e)
{
vamsasJarsArePresent = 0;
- log.debug("Vamsas Classes are not present");
+ debug("Vamsas Classes are not present");
}
}
return (vamsasJarsArePresent > 0);
if (Cache.class.getClassLoader()
.loadClass("groovy.lang.GroovyObject") != null)
{
- log.debug(
- "Found Groovy (groovy.lang.GroovyObject can be loaded)");
+ debug("Found Groovy (groovy.lang.GroovyObject can be loaded)");
groovyJarsArePresent = 1;
- Logger lgclient = LogManager.getLogger("groovy");
- Log4j.setLevel(lgclient, Level.toLevel(Cache
- .getDefault("logs.Groovy.Level", Level.INFO.toString())));
-
- Log4j.addAppender(lgclient, log, "JalviewLogger");
+ JLoggerLog4j lgclient = JLoggerLog4j.getLogger("groovy",
+ getCachedLogLevel("logs.Groovy.Level"));
+ JLoggerLog4j.addAppender(lgclient, log, JALVIEW_LOGGER_NAME);
// Tell the user that debug is enabled
lgclient.debug(ChannelProperties.getProperty("app_name")
+ " Groovy Client Debugging Output Follows.");
} catch (Error e)
{
groovyJarsArePresent = 0;
- log.debug("Groovy Classes are not present", e);
+ debug("Groovy Classes are not present", e);
} catch (Exception e)
{
groovyJarsArePresent = 0;
- log.debug("Groovy Classes are not present");
+ debug("Groovy Classes are not present");
}
}
return (groovyJarsArePresent > 0);
.loadClass("com.boxysystems.jgoogleanalytics.FocusPoint");
} catch (Exception e)
{
- log.debug(
- "com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
+ debug("com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
tracker = null;
jgoogleanalyticstracker = null;
trackerfocus = null;
{ String.class, String.class, String.class })
.newInstance(new Object[]
{ ChannelProperties.getProperty("app_name") + " Desktop",
- (vrs = jalview.bin.Cache.getProperty("VERSION") + "_"
- + jalview.bin.Cache.getDefault("BUILD_DATE",
- "unknown")),
+ (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);
- }
+ 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();
- }
+ warn("Failed to initialise GoogleTracker for Jalview Desktop with version "
+ + vrs, ex);
+ }
+ if (err != null)
+ {
+ error("Whilst initing GoogleTracker for Jalview Desktop version "
+ + vrs, err);
}
}
else
{
- log.debug("Successfully initialised tracker.");
+ debug("Successfully initialised tracker.");
}
}
}
Color col = ColorUtils.parseColourString(colprop);
if (col == null)
{
- log.warn("Couldn't parse '" + colprop + "' as a colour for "
- + property);
+ warn("Couldn't parse '" + colprop + "' as a colour for " + property);
}
return (col == null) ? defcolour : col;
}
StringBuilder sb = new StringBuilder();
sb.append(ChannelProperties.getProperty("app_name"))
.append(" Version: ");
- sb.append(jalview.bin.Cache.getDefault("VERSION", "TEST"));
+ sb.append(Cache.getDefault("VERSION", "TEST"));
sb.append("\n");
sb.append(ChannelProperties.getProperty("app_name"))
.append(" Installation: ");
- sb.append(jalview.bin.Cache.getDefault("INSTALLATION", "unknown"));
+ 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"));
// 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")))
+ Cache.getDefault("VERSION", "TEST")))
{
appendIfNotNull(sb, "Getdown appdir: ",
System.getProperty("getdownappdir"), "\n", null);
{
// 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)
case Cache.PROXYTYPE_NONE:
if (!previousProxyType.equals(proxyType))
{
- Cache.log.info("Setting no proxy settings");
+ Cache.info("Setting no proxy settings");
Cache.setProxyProperties(null, null, null, null, null, null, null,
null, null);
}
case Cache.PROXYTYPE_CUSTOM:
// always re-set a custom proxy -- it might have changed, particularly
// password
- Cache.log.info("Setting custom proxy settings");
+ Cache.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.proxyAuthPassword : null, "localhost");
break;
default: // system proxy settings by default
- Cache.log.info("Setting system proxy settings");
+ Cache.info("Setting system proxy settings");
Cache.resetProxyProperties();
}
}
}
}
- public final static int TRACE = 10;
+ public static void trace(String message)
+ {
+ if (initLogger())
+ {
+ log.trace(message, null);
+ }
+ else
+ {
+ System.out.println(message);
+ }
+ }
+
+ public static void trace(String message, Throwable t)
+ {
+ if (initLogger())
+ {
+ log.trace(message, t);
+ }
+ else
+ {
+ System.out.println(message);
+ t.printStackTrace();
+ }
+ }
+
+ public static void debug(String message)
+ {
+ if (initLogger())
+ {
+ log.debug(message, null);
+ }
+ else
+ {
+ System.out.println(message);
+ }
+
+ }
+
+ public static void debug(String message, Throwable t)
+ {
+ if (initLogger())
+ {
+ log.debug(message, t);
+ }
+ else
+ {
+ System.out.println(message);
+ t.printStackTrace();
+ }
+
+ }
- public final static int DEBUG = 20;
+ public static void info(String message)
+ {
+ if (initLogger())
+ {
+ log.info(message, null);
+ }
+ else
+ {
+ System.out.println(message);
+ }
- public final static int INFO = 30;
+ }
- public final static int WARN = 40;
+ public static void info(String message, Throwable t)
+ {
+ if (initLogger())
+ {
+ log.info(message, t);
+ }
+ else
+ {
+ System.out.println(message);
+ t.printStackTrace();
+ }
- public final static int ERROR = 50;
+ }
- public static boolean println(int level, String message)
+ public static void warn(String message)
{
- if (Cache.log == null)
+ if (initLogger())
{
- if (level >= WARN)
- System.err.println(message);
- else if (level >= INFO)
- System.out.println(message);
- // not printing debug or trace messages
- return false;
+ log.warn(message, null);
}
- if (level >= ERROR)
+ else
{
- Cache.log.error(message);
+ System.out.println(message);
}
- else if (level >= WARN)
+
+ }
+
+ public static void warn(String message, Throwable t)
+ {
+ if (initLogger())
{
- Cache.log.warn(message);
+ log.warn(message, t);
}
- else if (level >= INFO)
+ else
{
- Cache.log.info(message);
+ System.out.println(message);
+ t.printStackTrace();
}
- else if (level >= DEBUG)
+
+ }
+
+ public static void error(String message)
+ {
+ if (initLogger())
{
- Cache.log.debug(message);
+ log.error(message, null);
}
else
{
- Cache.log.trace(message);
+ System.err.println(message);
}
- return true;
+
}
- public static void trace(String message)
+ public static void error(String message, Throwable t)
{
- println(TRACE, message);
+ if (initLogger())
+ {
+ log.error(message, t);
+ }
+ else
+ {
+ System.err.println(message);
+ t.printStackTrace(System.err);
+ }
+
}
- public static void debug(String message)
+ public static void fatal(String message)
{
- println(DEBUG, message);
+ if (initLogger())
+ {
+ log.fatal(message, null);
+ }
+ else
+ {
+ System.err.println(message);
+ }
+
}
- public static void info(String message)
+ public static void fatal(String message, Throwable t)
{
- println(INFO, message);
+ if (initLogger())
+ {
+ log.fatal(message, t);
+ }
+ else
+ {
+ System.err.println(message);
+ t.printStackTrace(System.err);
+ }
+
}
- public static void warn(String message)
+ public static boolean isDebugEnabled()
{
- println(WARN, message);
+ return log == null ? false : log.isDebugEnabled();
}
- public static void error(String message)
+ public static boolean isTraceEnabled()
{
- println(ERROR, message);
+ return log == null ? false : log.isTraceEnabled();
}
/**
git://source.jalview.org / jalview.git / blobdiff