more aggressive checks for the locking, and some more documentation

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3404 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java

@@ -168,9 +168,9 @@ public class TribbleRMDTrackBuilder extends PluginManager<FeatureCodec> implemen
      */
     private static LinearIndex writeIndexToDisk(File inputFile, FeatureCodec codec, boolean onDisk, File indexFile, boolean obtainedLock) throws IOException {
         LinearIndexCreator create = new LinearIndexCreator(inputFile, codec);
-        LinearIndex index = create.createIndex();
+        LinearIndex index = create.createIndex(null); // we don't want to write initially, so we pass in null
 
-        // if the index doesn't exist, and we can write to the directory, and we got a lock, write to the disk
+        // if the index doesn't exist, and we can write to the directory, and we got a lock: write to the disk
         if (indexFile.getParentFile().canWrite() &&
                 (!indexFile.exists() || indexFile.canWrite()) &&
                 onDisk &&
@@ -182,7 +182,7 @@ public class TribbleRMDTrackBuilder extends PluginManager<FeatureCodec> implemen
         // we can't write it to disk, just store it in memory
         else {
             // if they wanted to write, let them know we couldn't
-            if (onDisk) logger.warn("Unable to write to " + indexFile + " for the index file, creating index in memory only");
+            if (onDisk) logger.info("Unable to write to " + indexFile + " for the index file, creating index in memory only");
             return index;
         }
     }

java/src/org/broadinstitute/sting/utils/file/FSLock.java

@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.utils.file;
 
+import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.io.File;
@@ -13,9 +14,19 @@ import java.nio.channels.FileLock;
  * a quick implementation of a file based lock, using the Java NIO classes
  */
 public class FSLock {
+    // connect to the logger
+    private static Logger logger = Logger.getLogger(FSLock.class);
+
+    // the lock string
     private static final String lockString = ".lock";
+
+    // the file we're attempting to lock
     private final File lockFile;
+
+    // the file lock
     private FileLock lock = null;
+
+    // the file channel we open
     FileChannel fc = null;
 
     /**
@@ -32,20 +43,22 @@ public class FSLock {
      *
      * @return boolean true if we obtained a lock
      */
-    public boolean lock() {
+    public synchronized boolean lock() {
         if (lock != null) throw new IllegalStateException("Unable to lock on file " + lockFile + " there is already a lock active");
-        if (lockFile.exists()) {
+
-            System.err.println("exits!!"); 
+        // if the file already exists, or we can't write to the parent directory, return false
+        if (lockFile.exists() || !lockFile.getParentFile().canWrite())
             return false;
-        }
         try {
             fc = new RandomAccessFile(lockFile,"rw").getChannel();
-            lock = fc.lock();
+            lock = fc.tryLock();
             return lock != null && lock.isValid();
         } catch (FileNotFoundException e) {
-            throw new StingException("Unable to create lock file named " + lockFile,e);
+            logger.info("Unable to create lock file (due to no file found exception), file = " + lockFile,e);
+            return false;
         } catch (IOException e) {
-            throw new StingException("Unable to create lock file named " + lockFile,e);
+            logger.info("Unable to create lock file (due to IO exception), file = " + lockFile,e);
+            return false;
         }
     }