X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=1a4f3418168d75b6e5f16152c2c603126e40dc88;hb=1c721468246c2aafd86fc52d954512374f576b11;hp=353f449f1bdbfeffbc69998e69bfdbd3bdd02a34;hpb=b7d225fc8a17594a1ddacd775a819b9ffc70131b;p=jalview.git
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 353f449..1a4f341 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -47,14 +47,11 @@ 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.log.JLogger;
+import jalview.log.JLoggerLog4j;
import jalview.schemes.ColourSchemeLoader;
import jalview.schemes.ColourSchemes;
import jalview.schemes.UserColourScheme;
@@ -62,6 +59,7 @@ import jalview.structure.StructureImportSettings;
import jalview.urls.IdOrgSettings;
import jalview.util.ChannelProperties;
import jalview.util.ColorUtils;
+import jalview.util.Log4j;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.sifts.SiftsSettings;
@@ -182,8 +180,8 @@ import jalview.ws.sifts.SiftsSettings;
* when shading by annotation
* ANNOTATIONCOLOUR_MAX (red) Shade used for maximum value of annotation
* when shading by annotation
- * www.jalview.org (http://www.jalview.org) a property enabling all HTTP
- * requests to be redirected to a mirror of http://www.jalview.org
+ * www.jalview.org (https://www.jalview.org) a property enabling all HTTP
+ * requests to be redirected to a mirror of https://www.jalview.org
* FIGURE_AUTOIDWIDTH (false) Expand the left hand column of an exported
* alignment figure to accommodate even the longest sequence ID or annotation
* label.
@@ -275,7 +273,10 @@ public class Cache
/**
* 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 = {
@@ -320,52 +321,58 @@ public class Cache
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
{
- // 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
+ JLogger.LogLevel cachedLevel = getCachedLogLevel();
+ if (!Platform.isJS())
+ {
+ Log4j.init(cachedLevel);
+ }
// 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);
+ // 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
- jalview.bin.Cache.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;
}
}
@@ -511,27 +518,27 @@ public class Cache
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");
@@ -852,14 +859,11 @@ public class Cache
if (jalview.jbgui.GDesktop.class.getClassLoader()
.loadClass("uk.ac.vamsas.client.VorbaId") != null)
{
- jalview.bin.Cache.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 = 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",
+ 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.");
@@ -867,7 +871,7 @@ public class Cache
} catch (Exception e)
{
vamsasJarsArePresent = 0;
- jalview.bin.Cache.log.debug("Vamsas Classes are not present");
+ debug("Vamsas Classes are not present");
}
}
return (vamsasJarsArePresent > 0);
@@ -892,14 +896,11 @@ public class Cache
if (Cache.class.getClassLoader()
.loadClass("groovy.lang.GroovyObject") != null)
{
- jalview.bin.Cache.log.debug(
- "Found Groovy (groovy.lang.GroovyObject can be loaded)");
+ 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",
+ 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.");
@@ -907,11 +908,11 @@ public class Cache
} catch (Error e)
{
groovyJarsArePresent = 0;
- jalview.bin.Cache.log.debug("Groovy Classes are not present", e);
+ debug("Groovy Classes are not present", e);
} catch (Exception e)
{
groovyJarsArePresent = 0;
- jalview.bin.Cache.log.debug("Groovy Classes are not present");
+ debug("Groovy Classes are not present");
}
}
return (groovyJarsArePresent > 0);
@@ -945,8 +946,7 @@ public class Cache
.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;
@@ -965,9 +965,8 @@ public class Cache
{ 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[]
@@ -988,57 +987,24 @@ public class Cache
}
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.");
}
}
}
@@ -1060,8 +1026,7 @@ public class Cache
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;
}
@@ -1242,14 +1207,14 @@ public class Cache
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"));
@@ -1277,7 +1242,7 @@ public class Cache
// 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);
@@ -1297,7 +1262,7 @@ public class Cache
{
// 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)
@@ -1367,7 +1332,7 @@ public class Cache
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);
}
@@ -1375,7 +1340,7 @@ public class Cache
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),
@@ -1389,7 +1354,7 @@ public class Cache
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();
}
}
@@ -1476,8 +1441,8 @@ public class Cache
// open Preferences -> Connections
String message = MessageManager
.getString("label.proxy_password_required");
- Preferences.openPreferences(Preferences.CONNECTIONS_TAB,
- message);
+ Preferences.openPreferences(
+ Preferences.TabRef.CONNECTIONS_TAB, message);
Preferences.getInstance()
.proxyAuthPasswordCheckHighlight(true, true);
}
@@ -1588,73 +1553,174 @@ public class Cache
}
}
- public final static int TRACE = 10;
+ public static void trace(String message)
+ {
+ if (initLogger())
+ {
+ log.trace(message, null);
+ }
+ else
+ {
+ System.out.println(message);
+ }
+ }
- public final static int DEBUG = 20;
+ public static void trace(String message, Throwable t)
+ {
+ if (initLogger())
+ {
+ log.trace(message, t);
+ }
+ else
+ {
+ System.out.println(message);
+ t.printStackTrace();
+ }
+ }
- public final static int INFO = 30;
+ public static void debug(String message)
+ {
+ if (initLogger())
+ {
+ log.debug(message, null);
+ }
+ else
+ {
+ System.out.println(message);
+ }
- public final static int WARN = 40;
+ }
- public final static int ERROR = 50;
+ public static void debug(String message, Throwable t)
+ {
+ if (initLogger())
+ {
+ log.debug(message, t);
+ }
+ else
+ {
+ System.out.println(message);
+ t.printStackTrace();
+ }
+
+ }
- public static boolean println(int level, String message)
+ public static void info(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.info(message, null);
}
- if (level >= ERROR)
+ else
{
- Cache.log.error(message);
+ System.out.println(message);
}
- else if (level >= WARN)
+
+ }
+
+ public static void info(String message, Throwable t)
+ {
+ if (initLogger())
{
- Cache.log.warn(message);
+ log.info(message, t);
}
- else if (level >= INFO)
+ else
{
- Cache.log.info(message);
+ System.out.println(message);
+ t.printStackTrace();
}
- else if (level >= DEBUG)
+
+ }
+
+ public static void warn(String message)
+ {
+ if (initLogger())
{
- Cache.log.debug(message);
+ log.warn(message, null);
}
else
{
- Cache.log.trace(message);
+ System.out.println(message);
}
- return true;
+
}
- public static void trace(String message)
+ public static void warn(String message, Throwable t)
{
- println(TRACE, message);
+ if (initLogger())
+ {
+ log.warn(message, t);
+ }
+ else
+ {
+ System.out.println(message);
+ t.printStackTrace();
+ }
+
}
- public static void debug(String message)
+ public static void error(String message)
+ {
+ if (initLogger())
+ {
+ log.error(message, null);
+ }
+ else
+ {
+ System.err.println(message);
+ }
+
+ }
+
+ public static void error(String message, Throwable t)
{
- println(DEBUG, message);
+ if (initLogger())
+ {
+ log.error(message, t);
+ }
+ else
+ {
+ System.err.println(message);
+ t.printStackTrace(System.err);
+ }
+
}
- public static void info(String message)
+ public static void fatal(String message)
+ {
+ if (initLogger())
+ {
+ log.fatal(message, null);
+ }
+ else
+ {
+ System.err.println(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();
}
/**