X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=adfd206a14f34a588cb589d31eb1c500ffc656df;hb=ec45a7f3c872496cc282806938e2b9d6e023f935;hp=aa9c0305e73112aa5182110dbd5e92d6303b13d2;hpb=aebe4cc0bfa4c9780bb6010fbd86cfb84fe3d2dd;p=jalview.git

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index aa9c030..adfd206 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -47,20 +47,10 @@ 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 org.apache.log4j.builders.appender.ConsoleAppenderBuilder;
-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.JLoggerLog4j;
 import jalview.schemes.ColourSchemeLoader;
 import jalview.schemes.ColourSchemes;
 import jalview.schemes.UserColourScheme;
@@ -209,6 +199,7 @@ import jalview.ws.sifts.SiftsSettings;
  * <li>ID_ORG_HOSTURL location of jalview service providing identifiers.org urls
  * </li>
  * 
+ * <li>NONEWS - when set disables Jalview News from automatically appearing</li>
  * </ul>
  * Deprecated settings:
  * <ul>
@@ -281,7 +272,8 @@ public class Cache
   /**
    * 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 = {
@@ -326,56 +318,9 @@ public class Cache
 
   private final static String JS_PROPERTY_PREFIX = "jalview_";
 
-  public static void initLogger()
-  {
-    if (log != null)
-    {
-      return;
-    }
-    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());
-      // 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(ChannelProperties.getProperty("app_name")
-              + " Debugging Output Follows.");
-    } catch (Exception ex)
-    {
-      System.err.println("Problems initializing the log4j system\n");
-      ex.printStackTrace(System.err);
-    }
-  }
-
   /**
-   * Loads properties from the given properties file. Any existing properties are
-   * first cleared.
+   * Loads properties from the given properties file. Any existing properties
+   * are first cleared.
    */
   public static void loadProperties(String propsFile)
   {
@@ -483,7 +428,7 @@ public class Cache
     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
@@ -515,27 +460,27 @@ 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",
             "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");
@@ -714,10 +659,11 @@ public class Cache
   }
 
   /**
-   * Gets Jalview application property of given key. Returns null if key not found
+   * Gets Jalview application property of given key. Returns null if key not
+   * found
    * 
    * @param key
-   *              Name of property
+   *          Name of property
    * 
    * @return Property value
    */
@@ -733,8 +679,8 @@ public class Cache
   }
 
   /**
-   * These methods are used when checking if the saved preference is different to
-   * the default setting
+   * These methods are used when checking if the saved preference is different
+   * to the default setting
    */
 
   public static boolean getDefault(String property, boolean def)
@@ -767,8 +713,8 @@ public class Cache
   }
 
   /**
-   * Answers the value of the given property, or the supplied default value if the
-   * property is not set
+   * Answers the value of the given property, or the supplied default value if
+   * the property is not set
    */
   public static String getDefault(String property, String def)
   {
@@ -780,9 +726,9 @@ public class Cache
    * Stores property in the file "HOME_DIR/.jalview_properties"
    * 
    * @param key
-   *              Name of object
+   *          Name of object
    * @param obj
-   *              String value of property
+   *          String value of property
    * 
    * @return previous value of property (or null)
    */
@@ -855,14 +801,11 @@ 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)");
+          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(ChannelProperties.getProperty("app_name")
                   + " Vamsas Client Debugging Output Follows.");
@@ -870,7 +813,7 @@ public class Cache
       } 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);
@@ -895,14 +838,11 @@ 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)");
+          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(ChannelProperties.getProperty("app_name")
                   + " Groovy Client Debugging Output Follows.");
@@ -910,11 +850,11 @@ public class Cache
       } 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);
@@ -948,8 +888,7 @@ public class Cache
                   .loadClass("com.boxysystems.jgoogleanalytics.FocusPoint");
         } catch (Exception e)
         {
-          log.debug(
-                  "com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
+          Console.debug("com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
           tracker = null;
           jgoogleanalyticstracker = null;
           trackerfocus = null;
@@ -968,9 +907,8 @@ 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[]
@@ -991,57 +929,24 @@ 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);
-          }
+          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.");
       }
     }
   }
@@ -1063,8 +968,7 @@ public class Cache
     Color col = ColorUtils.parseColourString(colprop);
     if (col == null)
     {
-      log.warn("Couldn't parse '" + colprop + "' as a colour for "
-              + property);
+      Console.warn("Couldn't parse '" + colprop + "' as a colour for " + property);
     }
     return (col == null) ? defcolour : col;
   }
@@ -1170,7 +1074,7 @@ public class Cache
    * Loads in user colour schemes from files.
    * 
    * @param files
-   *                a '|'-delimited list of file paths
+   *          a '|'-delimited list of file paths
    */
   public static void initUserColourSchemes(String files)
   {
@@ -1245,14 +1149,14 @@ 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"));
@@ -1280,7 +1184,7 @@ 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);
@@ -1300,7 +1204,7 @@ 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)
@@ -1344,7 +1248,7 @@ public class Cache
                             ? " [" + startupProxyProperties[6] + "]"
                             : "");
 
-    Cache.debug(sb.toString());
+    Console.debug(sb.toString());
   }
 
   public static void setProxyPropertiesFromPreferences()
@@ -1370,7 +1274,7 @@ public class Cache
     case Cache.PROXYTYPE_NONE:
       if (!previousProxyType.equals(proxyType))
       {
-        Cache.log.info("Setting no proxy settings");
+        Console.info("Setting no proxy settings");
         Cache.setProxyProperties(null, null, null, null, null, null, null,
                 null, null);
       }
@@ -1378,7 +1282,7 @@ 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");
+      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),
@@ -1392,7 +1296,7 @@ public class Cache
               proxyAuthSet ? Cache.proxyAuthPassword : null, "localhost");
       break;
     default: // system proxy settings by default
-      Cache.log.info("Setting system proxy settings");
+      Console.info("Setting system proxy settings");
       Cache.resetProxyProperties();
     }
   }
@@ -1444,7 +1348,7 @@ public class Cache
         char[] displayHttpPw = new char[httpPassword == null ? 0
                 : httpPassword.length];
         Arrays.fill(displayHttpPw, '*');
-        Cache.debug("CACHE Proxy: setting new Authenticator with httpUser='"
+        Console.debug("CACHE Proxy: setting new Authenticator with httpUser='"
                 + httpUser + "' httpPassword='" + displayHttpPw + "'");
         if (!Platform.isJS())
         /* *
@@ -1494,7 +1398,7 @@ public class Cache
                             && getRequestingPort() == Integer
                                     .valueOf(httpPort))
                     {
-                      Cache.debug(
+                      Console.debug(
                               "AUTHENTICATOR returning PasswordAuthentication(\""
                                       + httpUser + "\", '"
                                       + new String(displayHttpPw) + "')");
@@ -1509,7 +1413,7 @@ public class Cache
                     {
                       char[] displayHttpsPw = new char[httpPassword.length];
                       Arrays.fill(displayHttpsPw, '*');
-                      Cache.debug(
+                      Console.debug(
                               "AUTHENTICATOR returning PasswordAuthentication(\""
                                       + httpsUser + "\", '" + displayHttpsPw
                                       + "'");
@@ -1518,15 +1422,15 @@ public class Cache
                     }
                   } catch (NumberFormatException e)
                   {
-                    Cache.error("Problem with proxy port values [http:"
+                    Console.error("Problem with proxy port values [http:"
                             + httpPort + ", https:" + httpsPort + "]");
                   }
-                  Cache.debug(
+                  Console.debug(
                           "AUTHENTICATOR after trying to get PasswordAuthentication");
                 }
               }
               // non proxy request
-              Cache.debug("AUTHENTICATOR returning null");
+              Console.debug("AUTHENTICATOR returning null");
               return null;
             }
           });
@@ -1534,13 +1438,13 @@ public class Cache
 
         // required to re-enable basic authentication (should be okay for a
         // local proxy)
-        Cache.debug(
+        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
@@ -1558,13 +1462,13 @@ public class Cache
        * 
        */
       {
-        Cache.debug("AUTHENTICATOR setting default Authenticator to null");
+        Console.debug("AUTHENTICATOR setting default Authenticator to null");
         Authenticator.setDefault(null);
       }
     }
 
     // nonProxyHosts not currently configurable in Preferences
-    Cache.debug("AUTHENTICATOR setting property 'http.nonProxyHosts' to \""
+    Console.debug("AUTHENTICATOR setting property 'http.nonProxyHosts' to \""
             + nonProxyHosts + "\"");
     setOrClearSystemProperty("http.nonProxyHosts", nonProxyHosts);
   }
@@ -1591,75 +1495,6 @@ public class Cache
     }
   }
 
-  public final static int TRACE = 10;
-
-  public final static int DEBUG = 20;
-
-  public final static int INFO = 30;
-
-  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 >= WARN)
-        System.err.println(message);
-      else if (level >= INFO)
-        System.out.println(message);
-      // not printing debug or trace messages
-      return false;
-    }
-    if (level >= ERROR)
-    {
-      Cache.log.error(message);
-    }
-    else if (level >= WARN)
-    {
-      Cache.log.warn(message);
-    }
-    else if (level >= INFO)
-    {
-      Cache.log.info(message);
-    }
-    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);
-  }
-
-  public static void info(String message)
-  {
-    println(INFO, message);
-  }
-
-  public static void warn(String message)
-  {
-    println(WARN, message);
-  }
-
-  public static void error(String message)
-  {
-    println(ERROR, message);
-  }
-
   /**
    * Getdown appbase methods
    */