working on logging citations to file

src/dr/app/beast/BeastMain.java

@@ -37,6 +37,7 @@
 import dr.inference.mcmcmc.MCMCMC;
 import dr.inference.mcmcmc.MCMCMCOptions;
 import dr.math.MathUtils;
+import dr.util.CitationLogHandler;
 import dr.util.ErrorLogHandler;
 import dr.util.MessageLogHandler;
 import dr.util.Version;
@@ -135,15 +136,18 @@ public boolean isLoggable(LogRecord record) {
             });
             infoLogger.addHandler(errorHandler);
 
-            FileOutputStream citationStream = null;
-            if (System.getProperty("citations.filename") != null) {
-                citationStream = new FileOutputStream(System.getProperty("citations.filename"));
-
-            } else {
-                citationStream = new FileOutputStream(fileName.substring(0, fileName.toLowerCase().indexOf(".xml")) + CITATION_FILE_SUFFIX);
+            if (Boolean.parseBoolean(System.getProperty("output_citations"))) {
+                FileOutputStream citationStream = null;
+                if (System.getProperty("citations.filename") != null) {
+                    citationStream = new FileOutputStream(System.getProperty("citations.filename"));
+                } else {
+                    citationStream = new FileOutputStream(fileName.substring(0, fileName.toLowerCase().indexOf(".xml")) + CITATION_FILE_SUFFIX);
+                }
+                //Handler citationHandler = new MessageLogHandler(citationStream);
+                Handler citationHandler = CitationLogHandler.getHandler(citationStream);
+                //Logger.getLogger("dr.app.beast").addHandler(citationHandler);
+                Logger.getLogger("dr.util").addHandler(citationHandler);
             }
-            Handler citationHandler = new MessageLogHandler(citationStream);
-            Logger.getLogger("dr.app.beast").addHandler(citationHandler);
 
             logger.setUseParentHandlers(false);
 
@@ -158,7 +162,6 @@ public boolean isLoggable(LogRecord record) {
             messageHandler.setLevel(Level.WARNING);
             errorLogger.addHandler(messageHandler);
 
-
             PluginLoader.loadPlugins(parser);
 
             // Install the checkpointer. This creates a factory that returns
@@ -417,7 +420,7 @@ public static void main(String[] args) throws java.io.IOException {
                         new Arguments.Option("force_resume", "Force resuming from a saved state"),
 
                         new Arguments.StringOption("citations_file", "FILENAME", "Specify a filename to write a citation list to"),
-                        //new Arguments.Option("citations_off", "Turn off writing citations to file"),
+                        new Arguments.Option("citations_off", "Turn off writing citations to file"),
                         new Arguments.StringOption("plugins_dir", "FILENAME", "Specify a directory to load plugins from, multiple can be separated with ':' "),
 
                         new Arguments.Option("version", "Print the version and credits and stop"),
@@ -700,6 +703,11 @@ public void uncaughtException(Thread t, Throwable e) {
                      arguments.getStringOption("plugins_dir")+":"+System.getProperty("beast.plugins.dir"));
         }
 
+        if (arguments.hasOption("citations_off")) {
+            System.setProperty("output_citations", Boolean.FALSE.toString());
+        } else {
+            System.setProperty("output_citations", Boolean.TRUE.toString());
+        }
 
         if (!usingSMC) {
             // ignore these other options

src/dr/app/beast/BeastParser.java

@@ -25,7 +25,6 @@
 
 package dr.app.beast;
 
-import beagle.BeagleInfo;
 import dr.util.Citation;
 import dr.util.Pair;
 import dr.util.Version;
@@ -209,7 +208,8 @@ private void loadProperties(Class c, String parsersFile, boolean verbose, boolea
 
     @Override
     protected void executingRunnable() {
-        Logger.getLogger("dr.app.beast").info("\nCitations for this analysis: ");
+        //Logger.getLogger("dr.app.beast").info("\nCitations for this analysis: ");
+        Logger.getLogger("dr.util").info("\nCitations for this analysis: ");
 
         Map<String, Set<Pair<String, String>>> categoryMap = new LinkedHashMap<String, Set<Pair<String, String>>>();
 
@@ -226,22 +226,22 @@ protected void executingRunnable() {
         }
 
         for (String category : categoryMap.keySet()) {
-            Logger.getLogger("dr.app.beast").info("\n"+category.toUpperCase());
+            Logger.getLogger("dr.util").info("\n"+category.toUpperCase());
             Set<Pair<String, String>> pairSet = categoryMap.get(category);
 
             for (Pair<String, String>keyPair : pairSet) {
-                Logger.getLogger("dr.app.beast").info(keyPair.second + ":");
+                Logger.getLogger("dr.util").info(keyPair.second + ":");
 
                 for (Citation citation : getCitationStore().get(keyPair)) {
-                    Logger.getLogger("dr.app.beast").info("\t" + citation.toString());
+                    Logger.getLogger("dr.util").info("\t" + citation.toString());
                 }
             }
         }
 
         // clear the citation store so all the same citations don't get cited again
         getCitationStore().clear();
 
-        Logger.getLogger("dr.app.beast").info("\n");
+        Logger.getLogger("dr.util").info("\n");
 
     }
 

src/dr/util/CitationLogHandler.java

@@ -0,0 +1,70 @@
+/*
+ * ErrorLogHandler.java
+ *
+ * Copyright (c) 2002-2015 Alexei Drummond, Andrew Rambaut and Marc Suchard
+ *
+ * This file is part of BEAST.
+ * See the NOTICE file distributed with this work for additional
+ * information regarding copyright ownership and licensing.
+ *
+ * BEAST is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as
+ * published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ *  BEAST is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with BEAST; if not, write to the
+ * Free Software Foundation, Inc., 51 Franklin St, Fifth Floor,
+ * Boston, MA  02110-1301  USA
+ */
+
+package dr.util;
+
+import java.io.OutputStream;
+import java.util.logging.Formatter;
+import java.util.logging.LogRecord;
+import java.util.logging.StreamHandler;
+
+public class CitationLogHandler extends StreamHandler {
+    private static final CitationLogHandler INSTANCE = new CitationLogHandler();
+    private final MessageLogFormatter citationFormatter = new MessageLogFormatter();
+
+    public static CitationLogHandler getHandler(OutputStream stream) {
+        INSTANCE.setFormatter(INSTANCE.citationFormatter);
+        INSTANCE.setOutputStream(stream);
+        return INSTANCE;
+    }
+
+    public static void closeHandler() {
+        INSTANCE.close();
+    }
+
+    private class MessageLogFormatter extends Formatter {
+
+        // Line separator string.  This is the value of the line.separator
+        // property at the moment that the SimpleFormatter was created.
+        private final String lineSeparator = System.getProperty("line.separator");
+
+        // AR - is there a reason why this was used? It causes warnings at compile
+//        private final String lineSeparator = (String) java.security.AccessController.doPrivileged(
+//                new sun.security.action.GetPropertyAction("line.separator"));
+
+        /**
+         * Format the given LogRecord.
+         * @param record the log record to be formatted.
+         * @return a formatted log record
+         */
+        public synchronized String format(LogRecord record) {
+            final StringBuffer sb = new StringBuffer();
+            sb.append(formatMessage(record));
+            sb.append(lineSeparator);
+            return sb.toString();
+        }
+    }
+
+}

src/dr/xml/XMLParser.java

@@ -262,7 +262,6 @@ private Object convert(Element e, Class target, XMLObject parent, boolean run, b
 
             if (verbose) System.out.println("  Restoring idref=" + idref);
 
-
             return new Reference(restoredXMLObject);
 
         } else {
@@ -379,6 +378,9 @@ private Object convert(Element e, Class target, XMLObject parent, boolean run, b
 
                     executingRunnable();
 
+                    //close citationHandler
+                    CitationLogHandler.closeHandler();
+
                     if (obj instanceof Spawnable && !((Spawnable) obj).getSpawnable()) {
                         ((Spawnable) obj).run();
                     } else {