Redo some logging

Should have better logging during startup, same everywhere else

Author: Jacob Silterra

src/log4j.properties

@@ -14,6 +14,15 @@
 #e.g. java -jar -Xmx2g -Dlog4j.configuration=log4j_debug.properties igv.jar
 log4j.rootLogger=INFO, stdout
 
+log4j.appender.stdout.Target=System.out
 log4j.appender.stdout=org.apache.log4j.ConsoleAppender
 log4j.appender.stdout.layout=org.apache.log4j.PatternLayout
 log4j.appender.stdout.layout.ConversionPattern=%p [%d{ISO8601}]  [%F:%L] [%t]  %m%n
+
+#Don't want to double log, so we aren't using this now
+log4j.appender.stderr.Threshold=ERROR
+log4j.appender.stderr.Target=System.err
+log4j.appender.stderr=org.apache.log4j.ConsoleAppender
+log4j.appender.stderr.layout=org.apache.log4j.PatternLayout
+log4j.appender.stderr.layout.ConversionPattern=%p [%d{ISO8601}]  [%F:%L] [%t]  %m%n
+

src/log4j_all.properties

@@ -11,7 +11,15 @@
 
 log4j.rootLogger=ALL, stdout
 
+log4j.appender.stdout.Target=System.out
 log4j.appender.stdout=org.apache.log4j.ConsoleAppender
 log4j.appender.stdout.layout=org.apache.log4j.PatternLayout
 log4j.appender.stdout.layout.ConversionPattern=%p [%d{ISO8601}]  [%F:%L] [%t]  %m%n
 
+#Don't want to double log, so we aren't using this now
+log4j.appender.stderr.Threshold=ERROR
+log4j.appender.stderr.Target=System.err
+log4j.appender.stderr=org.apache.log4j.ConsoleAppender
+log4j.appender.stderr.layout=org.apache.log4j.PatternLayout
+log4j.appender.stderr.layout.ConversionPattern=%p [%d{ISO8601}]  [%F:%L] [%t]  %m%n
+

src/log4j_debug.properties

@@ -11,7 +11,14 @@
 
 log4j.rootLogger=DEBUG, stdout
 
+log4j.appender.stdout.Target=System.out
 log4j.appender.stdout=org.apache.log4j.ConsoleAppender
 log4j.appender.stdout.layout=org.apache.log4j.PatternLayout
 log4j.appender.stdout.layout.ConversionPattern=%p [%d{ISO8601}]  [%F:%L] [%t]  %m%n
 
+#Don't want to double log, so we aren't using this now
+log4j.appender.stderr.Threshold=ERROR
+log4j.appender.stderr.Target=System.err
+log4j.appender.stderr=org.apache.log4j.ConsoleAppender
+log4j.appender.stderr.layout=org.apache.log4j.PatternLayout
+log4j.appender.stderr.layout.ConversionPattern=%p [%d{ISO8601}]  [%F:%L] [%t]  %m%n

src/org/broad/igv/DirectoryManager.java

@@ -55,7 +55,7 @@ private static File getUserHome() {
      */
     public static synchronized File getUserDirectory() {
         if (USER_DIRECTORY == null) {
-            System.out.print("Fetching user directory... ");
+            log.info("Fetching user directory... ");
             USER_DIRECTORY = FileSystemView.getFileSystemView().getDefaultDirectory();
             //Mostly for testing, in some environments USER_DIRECTORY can be null
             if (USER_DIRECTORY == null) {
@@ -104,7 +104,7 @@ public static File getIgvDirectory() {
                     try {
                         boolean wasSuccessful = IGV_DIRECTORY.mkdir();
                         if (!wasSuccessful) {
-                            System.err.println("Failed to create user directory!");
+                            log.error("Failed to create user directory!");
                             IGV_DIRECTORY = null;
                         }
                     } catch (Exception e) {
@@ -168,8 +168,7 @@ private static File getIgvDirectoryOverride() {
         } catch (Exception e) {
             userPrefs.remove(IGV_DIR_USERPREF);
             override = null;
-            System.err.println("Error creating user directory");
-            e.printStackTrace();
+            log.error("Error creating user directory", e);
         }
         return override;
     }
@@ -412,35 +411,32 @@ private static boolean canWrite(File directory) {
     public static void initializeLog() {
 
         Logger logger = Logger.getRootLogger();
-        ConsoleAppender consoleAppender = new ConsoleAppender();
-        //Add console appender so we at least do some logging, somewhere,
-        //during this initialization process
         PatternLayout layout = new PatternLayout();
         layout.setConversionPattern("%p [%d{ISO8601}] [%F:%L]  %m%n");
-        consoleAppender.setLayout(layout);
-        consoleAppender.setThreshold(Level.ALL);
-        logger.addAppender(consoleAppender);
 
+        //Temp appender just used while initializing log
+        //If something goes wrong here we want a log of it
+        ConsoleAppender tempAppender = new ConsoleAppender(layout, "System.err");
+        logger.addAppender(tempAppender);
 
         // Create a log file that is ready to have text appended to it
         try {
             File logFile = getLogFile();
             RollingFileAppender appender = new RollingFileAppender();
             appender.setName("IGV_ROLLING_APPENDER");
             appender.setFile(logFile.getAbsolutePath());
+            //Will actually inherit from root logger
             appender.setThreshold(Level.ALL);
             appender.setMaxFileSize("1000KB");
             appender.setMaxBackupIndex(1);
             appender.setLayout(layout);
             appender.setAppend(true);
             appender.activateOptions();
             logger.addAppender(appender);
-            //If we make it here, we don't need to log to console
-            logger.removeAppender(consoleAppender);
+            logger.removeAppender(tempAppender);
         } catch (IOException e) {
-            // Can't create log file, just log to console
-            System.err.println("Error creating log file");
-            e.printStackTrace();
+            // Can't create log file, just log to console as set in log4j.properties
+            log.error("Error creating log file", e);
         }
     }
 }