HBASE-15118 Fix findbugs complaint in hbase-server

hbase-server/src/main/java/org/apache/hadoop/hbase/JMXListener.java

@@ -60,7 +60,7 @@ public class JMXListener implements Coprocessor {
    * only 1 JMX instance is allowed, otherwise there is port conflict even if
    * we only load regionserver coprocessor on master
    */
-  private static JMXConnectorServer jmxCS = null;
+  private static JMXConnectorServer JMX_CS = null;
 
   public static JMXServiceURL buildJMXServiceURL(int rmiRegistryPort,
       int rmiConnectorPort) throws IOException {
@@ -137,8 +137,13 @@ public class JMXListener implements Coprocessor {
 
     try {
       // Start the JMXListener with the connection string
-      jmxCS = JMXConnectorServerFactory.newJMXConnectorServer(serviceUrl, jmxEnv, mbs);
+      synchronized(JMXListener.class) {
-      jmxCS.start();
+        if (JMX_CS != null) {
+          throw new RuntimeException("Started by another thread?");
+        }
+        JMX_CS = JMXConnectorServerFactory.newJMXConnectorServer(serviceUrl, jmxEnv, mbs);
+        JMX_CS.start();
+      }
       LOG.info("ConnectorServer started!");
     } catch (IOException e) {
       LOG.error("fail to start connector server!", e);
@@ -148,10 +153,10 @@ public class JMXListener implements Coprocessor {
 
   public void stopConnectorServer() throws IOException {
     synchronized(JMXListener.class) {
-      if (jmxCS != null) {
+      if (JMX_CS != null) {
-        jmxCS.stop();
+        JMX_CS.stop();
         LOG.info("ConnectorServer stopped!");
-        jmxCS = null;
+        JMX_CS = null;
       }
     }
   }
@@ -186,7 +191,7 @@ public class JMXListener implements Coprocessor {
     }
 
     synchronized(JMXListener.class) {
-      if (jmxCS != null) {
+      if (JMX_CS != null) {
         LOG.info("JMXListener has been started at Registry port " + rmiRegistryPort);
       }
       else {

hbase-server/src/main/java/org/apache/hadoop/hbase/SizeCachedKeyValue.java

@@ -30,8 +30,8 @@ import org.apache.hadoop.hbase.util.Bytes;
  * See https://issues.apache.org/jira/browse/HBASE-13448
  */
 @InterfaceAudience.Private
+@edu.umd.cs.findbugs.annotations.SuppressWarnings(value="EQ_DOESNT_OVERRIDE_EQUALS")
 public class SizeCachedKeyValue extends KeyValue {
-
   private static final int HEAP_SIZE_OVERHEAD = Bytes.SIZEOF_SHORT + Bytes.SIZEOF_INT;
 
   private short rowLen;

hbase-server/src/main/java/org/apache/hadoop/hbase/coordination/ZKSplitLogManagerCoordination.java

@@ -175,7 +175,7 @@ public class ZKSplitLogManagerCoordination extends ZooKeeperListener implements
       return;
     }
     Task task = findOrCreateOrphanTask(path);
-    if (task.isOrphan() && (task.incarnation == 0)) {
+    if (task.isOrphan() && (task.incarnation.get() == 0)) {
       LOG.info("resubmitting unassigned orphan task " + path);
       // ignore failure to resubmit. The timeout-monitor will handle it later
       // albeit in a more crude fashion
@@ -228,7 +228,7 @@ public class ZKSplitLogManagerCoordination extends ZooKeeperListener implements
       version = -1;
     }
     LOG.info("resubmitting task " + path);
-    task.incarnation++;
+    task.incarnation.incrementAndGet();
     boolean result = resubmit(this.details.getServerName(), path, version);
     if (!result) {
       task.heartbeatNoDetails(EnvironmentEdgeManager.currentTime());

hbase-server/src/main/java/org/apache/hadoop/hbase/coordination/ZkSplitLogWorkerCoordination.java

@@ -78,7 +78,7 @@ public class ZkSplitLogWorkerCoordination extends ZooKeeperListener implements
   private TaskExecutor splitTaskExecutor;
 
   private final Object taskReadyLock = new Object();
-  volatile int taskReadySeq = 0;
+  private AtomicInteger taskReadySeq = new AtomicInteger(0);
   private volatile String currentTask = null;
   private int currentVersion;
   private volatile boolean shouldStop = false;
@@ -106,7 +106,7 @@ public class ZkSplitLogWorkerCoordination extends ZooKeeperListener implements
     if (path.equals(watcher.splitLogZNode)) {
       if (LOG.isTraceEnabled()) LOG.trace("tasks arrived or departed on " + path);
       synchronized (taskReadyLock) {
-        taskReadySeq++;
+        this.taskReadySeq.incrementAndGet();
         taskReadyLock.notify();
       }
     }
@@ -400,14 +400,14 @@ public class ZkSplitLogWorkerCoordination extends ZooKeeperListener implements
    * policy puts an upper-limit on the number of simultaneous log splitting that could be happening
    * in a cluster.
    * <p>
-   * Synchronization using {@link #taskReadyLock} ensures that it will try to grab every task that
+   * Synchronization using <code>taskReadyLock</code> ensures that it will try to grab every task
-   * has been put up
+   * that has been put up
    * @throws InterruptedException
    */
   @Override
   public void taskLoop() throws InterruptedException {
     while (!shouldStop) {
-      int seq_start = taskReadySeq;
+      int seq_start = taskReadySeq.get();
       List<String> paths = null;
       paths = getTaskList();
       if (paths == null) {
@@ -441,7 +441,7 @@ public class ZkSplitLogWorkerCoordination extends ZooKeeperListener implements
       }
       SplitLogCounters.tot_wkr_task_grabing.incrementAndGet();
       synchronized (taskReadyLock) {
-        while (seq_start == taskReadySeq) {
+        while (seq_start == taskReadySeq.get()) {
           taskReadyLock.wait(checkInterval);
           if (server != null) {
             // check to see if we have stale recovering regions in our internal memory state
@@ -527,7 +527,7 @@ public class ZkSplitLogWorkerCoordination extends ZooKeeperListener implements
 
   @Override
   public int getTaskReadySeq() {
-    return taskReadySeq;
+    return taskReadySeq.get();
   }
 
   @Override

hbase-server/src/main/java/org/apache/hadoop/hbase/http/jmx/JMXJsonServlet.java

@@ -149,6 +149,8 @@ public class JMXJsonServlet extends HttpServlet {
    *          The servlet response we are creating
    */
   @Override
+  @edu.umd.cs.findbugs.annotations.SuppressWarnings(value="XSS_REQUEST_PARAMETER_TO_SERVLET_WRITER",
+    justification="TODO: See HBASE-15122")
   public void doGet(HttpServletRequest request, HttpServletResponse response) {
     try {
       if (!HttpServer.isInstrumentationAccessAllowed(getServletContext(), request, response)) {

hbase-server/src/main/java/org/apache/hadoop/hbase/io/HFileLink.java

@@ -54,6 +54,8 @@ import org.apache.hadoop.hbase.util.Pair;
  * it fallbacks to the archived path.
  */
 @InterfaceAudience.Private
+@edu.umd.cs.findbugs.annotations.SuppressWarnings(value="EQ_DOESNT_OVERRIDE_EQUALS",
+  justification="To be fixed but warning suppressed for now")
 public class HFileLink extends FileLink {
   private static final Log LOG = LogFactory.getLog(HFileLink.class);
 

hbase-server/src/main/java/org/apache/hadoop/hbase/io/hfile/HFile.java

@@ -488,6 +488,8 @@ public class HFile {
    * @return an appropriate instance of HFileReader
    * @throws IOException If file is invalid, will throw CorruptHFileException flavored IOException
    */
+  @edu.umd.cs.findbugs.annotations.SuppressWarnings(value="SF_SWITCH_FALLTHROUGH",
+      justification="Intentional")
   private static Reader pickReaderVersion(Path path, FSDataInputStreamWrapper fsdis,
       long size, CacheConfig cacheConf, HFileSystem hfs, Configuration conf) throws IOException {
     FixedFileTrailer trailer = null;
@@ -498,7 +500,7 @@ public class HFile {
       switch (trailer.getMajorVersion()) {
       case 2:
         LOG.debug("Opening HFile v2 with v3 reader");
-        // Fall through.
+        // Fall through. FindBugs: SF_SWITCH_FALLTHROUGH
       case 3 :
         return new HFileReaderImpl(path, trailer, fsdis, size, cacheConf, hfs, conf);
       default:

hbase-server/src/main/java/org/apache/hadoop/hbase/io/hfile/HFileBlock.java

@@ -109,8 +109,8 @@ public class HFileBlock implements Cacheable {
      new byte[HConstants.HFILEBLOCK_HEADER_SIZE_NO_CHECKSUM];
 
   // How to get the estimate correctly? if it is a singleBB?
-  public static final int MULTI_BYTE_BUFFER_HEAP_SIZE = (int) ClassSize.estimateBase(
+  public static final int MULTI_BYTE_BUFFER_HEAP_SIZE =
-      new MultiByteBuff(ByteBuffer.wrap(new byte[0], 0, 0)).getClass(), false);
+      (int)ClassSize.estimateBase(MultiByteBuff.class, false);
 
   // meta.usesHBaseChecksum+offset+nextBlockOnDiskSizeWithHeader
   public static final int EXTRA_SERIALIZATION_SPACE = Bytes.SIZEOF_BYTE + Bytes.SIZEOF_INT

hbase-server/src/main/java/org/apache/hadoop/hbase/io/hfile/HFileReaderImpl.java

@@ -23,6 +23,7 @@ import java.nio.ByteBuffer;
 import java.security.Key;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.concurrent.atomic.AtomicInteger;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
@@ -473,7 +474,7 @@ public class HFileReaderImpl implements HFile.Reader, Configurable {
     private int currMemstoreTSLen;
     private long currMemstoreTS;
     // Updated but never read?
-    protected volatile int blockFetches;
+    protected AtomicInteger blockFetches = new AtomicInteger(0);
     protected final HFile.Reader reader;
     private int currTagsLen;
     // buffer backed keyonlyKV
@@ -877,6 +878,8 @@ public class HFileReaderImpl implements HFile.Reader, Configurable {
      * @return the next block, or null if there are no more data blocks
      * @throws IOException
      */
+    @edu.umd.cs.findbugs.annotations.SuppressWarnings(value="NP_NULL_ON_SOME_PATH",
+        justification="Yeah, unnecessary null check; could do w/ clean up")
     protected HFileBlock readNextDataBlock() throws IOException {
       long lastDataBlockOffset = reader.getTrailer().getLastDataBlockOffset();
       if (curBlock == null)
@@ -885,8 +888,9 @@ public class HFileReaderImpl implements HFile.Reader, Configurable {
       HFileBlock block = this.curBlock;
 
       do {
-        if (block.getOffset() >= lastDataBlockOffset)
+        if (block.getOffset() >= lastDataBlockOffset) {
           return null;
+        }
 
         if (block.getOffset() < 0) {
           throw new IOException("Invalid block file offset: " + block);
@@ -898,7 +902,7 @@ public class HFileReaderImpl implements HFile.Reader, Configurable {
             + block.getOnDiskSizeWithHeader(),
             block.getNextBlockOnDiskSizeWithHeader(), cacheBlocks, pread,
             isCompaction, true, null, getEffectiveDataBlockEncoding());
-        if (block != null && !block.getBlockType().isData()) {
+        if (block != null && !block.getBlockType().isData()) { // Findbugs: NP_NULL_ON_SOME_PATH
           // Whatever block we read we will be returning it unless
           // it is a datablock. Just in case the blocks are non data blocks
           reader.returnBlock(block);
@@ -1228,7 +1232,7 @@ public class HFileReaderImpl implements HFile.Reader, Configurable {
       updateCurrBlockRef(newBlock);
       blockBuffer = newBlock.getBufferWithoutHeader();
       readKeyValueLen();
-      blockFetches++;
+      blockFetches.incrementAndGet();
 
       // Reset the next indexed key
       this.nextIndexedKey = null;
@@ -1667,7 +1671,7 @@ public class HFileReaderImpl implements HFile.Reader, Configurable {
       updateCurrBlockRef(newBlock);
       ByteBuff encodedBuffer = getEncodedBuffer(newBlock);
       seeker.setCurrentBuffer(encodedBuffer);
-      blockFetches++;
+      blockFetches.incrementAndGet();
 
       // Reset the next indexed key
       this.nextIndexedKey = null;

hbase-server/src/main/java/org/apache/hadoop/hbase/io/hfile/HFileWriterImpl.java

@@ -354,7 +354,7 @@ public class HFileWriterImpl implements HFile.Writer {
     // (table,startrow,hash) so can't be treated as plain byte arrays. Just skip
     // out without
     // trying to do this optimization.
-    if (comparator != null && comparator instanceof MetaCellComparator) {
+    if (comparator instanceof MetaCellComparator) {
       return right;
     }
     int diff = comparator.compareRows(left, right);

hbase-server/src/main/java/org/apache/hadoop/hbase/ipc/RpcServer.java

@@ -322,6 +322,8 @@ public class RpcServer implements RpcServerInterface, ConfigurationObserver {
     private long responseBlockSize = 0;
     private boolean retryImmediatelySupported;
 
+    @edu.umd.cs.findbugs.annotations.SuppressWarnings(value="NP_NULL_ON_SOME_PATH",
+        justification="Can't figure why this complaint is happening... see below")
     Call(int id, final BlockingService service, final MethodDescriptor md, RequestHeader header,
          Message param, CellScanner cellScanner, Connection connection, Responder responder,
          long size, TraceInfo tinfo, final InetAddress remoteAddress) {
@@ -339,15 +341,18 @@ public class RpcServer implements RpcServerInterface, ConfigurationObserver {
       this.isError = false;
       this.size = size;
       this.tinfo = tinfo;
-      this.user = connection == null ? null : connection.user;
+      this.user = connection == null? null: connection.user; // FindBugs: NP_NULL_ON_SOME_PATH
       this.remoteAddress = remoteAddress;
-      this.retryImmediatelySupported = connection.retryImmediatelySupported;
+      this.retryImmediatelySupported =
+          connection == null? null: connection.retryImmediatelySupported;
     }
 
     /**
      * Call is done. Execution happened and we returned results to client. It is now safe to
      * cleanup.
      */
+    @edu.umd.cs.findbugs.annotations.SuppressWarnings(value="IS2_INCONSISTENT_SYNC",
+        justification="Presume the lock on processing request held by caller is protection enough")
     void done() {
       if (this.cellBlock != null && reservoir != null) {
         // Return buffer to reservoir now we are done with it.
@@ -599,7 +604,7 @@ public class RpcServer implements RpcServerInterface, ConfigurationObserver {
     }
 
     @Override
-    public void setCallBack(RpcCallback callback) {
+    public synchronized void setCallBack(RpcCallback callback) {
       this.callback = callback;
     }
 
@@ -779,6 +784,9 @@ public class RpcServer implements RpcServerInterface, ConfigurationObserver {
     }
 
     @Override
+    @edu.umd.cs.findbugs.annotations.SuppressWarnings(value="IS2_INCONSISTENT_SYNC",
+      justification="selector access is not synchronized; seems fine but concerned changing " +
+        "it will have per impact")
     public void run() {
       LOG.info(getName() + ": starting");
       while (running) {
@@ -1280,15 +1288,14 @@ public class RpcServer implements RpcServerInterface, ConfigurationObserver {
     private boolean useWrap = false;
     // Fake 'call' for failed authorization response
     private static final int AUTHORIZATION_FAILED_CALLID = -1;
-    private final Call authFailedCall =
+    private final Call authFailedCall = new Call(AUTHORIZATION_FAILED_CALLID, null, null, null,
-      new Call(AUTHORIZATION_FAILED_CALLID, null, null, null, null, null, this, null, 0, null,
+        null, null, this, null, 0, null, null);
-        null);
     private ByteArrayOutputStream authFailedResponse =
         new ByteArrayOutputStream();
     // Fake 'call' for SASL context setup
     private static final int SASL_CALLID = -33;
-    private final Call saslCall =
+    private final Call saslCall = new Call(SASL_CALLID, null, null, null, null, null, this, null,
-      new Call(SASL_CALLID, this.service, null, null, null, null, this, null, 0, null, null);
+        0, null, null);
 
     // was authentication allowed with a fallback to simple auth
     private boolean authenticatedWithFallback;
@@ -2177,7 +2184,7 @@ public class RpcServer implements RpcServerInterface, ConfigurationObserver {
   }
 
   @Override
-  public void refreshAuthManager(PolicyProvider pp) {
+  public synchronized void refreshAuthManager(PolicyProvider pp) {
     // Ignore warnings that this should be accessed in a static way instead of via an instance;
     // it'll break if you go via static route.
     this.authManager.refresh(this.conf, pp);
@@ -2403,7 +2410,8 @@ public class RpcServer implements RpcServerInterface, ConfigurationObserver {
    * @throws org.apache.hadoop.security.authorize.AuthorizationException
    *         when the client isn't authorized to talk the protocol
    */
-  public void authorize(UserGroupInformation user, ConnectionHeader connection, InetAddress addr)
+  public synchronized void authorize(UserGroupInformation user, ConnectionHeader connection,
+      InetAddress addr)
   throws AuthorizationException {
     if (authorize) {
       Class<?> c = getServiceInterface(services, connection.getServiceName());

hbase-server/src/main/java/org/apache/hadoop/hbase/mapreduce/HashTable.java

@@ -32,7 +32,6 @@ import org.apache.commons.logging.LogFactory;
 import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.conf.Configured;
 import org.apache.hadoop.fs.FSDataInputStream;
-import org.apache.hadoop.fs.FSDataOutputStream;
 import org.apache.hadoop.fs.FileSystem;
 import org.apache.hadoop.fs.Path;
 import org.apache.hadoop.hbase.Cell;
@@ -135,17 +134,18 @@ public class HashTable extends Configured implements Tool {
         p.setProperty("endTimestamp", Long.toString(endTime));
       }
       
-      FSDataOutputStream out = fs.create(path);
+      try (OutputStreamWriter osw = new OutputStreamWriter(fs.create(path), Charsets.UTF_8)) {
-      p.store(new OutputStreamWriter(out, Charsets.UTF_8), null);
+        p.store(osw, null);
-      out.close();
+      }
     }
 
     void readPropertiesFile(FileSystem fs, Path path) throws IOException {
-      FSDataInputStream in = fs.open(path);
       Properties p = new Properties();
-      p.load(new InputStreamReader(in, Charsets.UTF_8));
+      try (FSDataInputStream in = fs.open(path)) {
-      in.close();
+        try (InputStreamReader isr = new InputStreamReader(in, Charsets.UTF_8)) {
-      
+          p.load(isr);
+        }
+      }
       tableName = p.getProperty("table");
       families = p.getProperty("columnFamilies");
       batchSize = Long.parseLong(p.getProperty("targetBatchSize"));

hbase-server/src/main/java/org/apache/hadoop/hbase/mapreduce/Import.java

@@ -142,6 +142,8 @@ public class Import extends Configured implements Tool {
     }
 
     @Override
+    @edu.umd.cs.findbugs.annotations.SuppressWarnings(value="EQ_COMPARETO_USE_OBJECT_EQUALS",
+      justification="This is wrong, yes, but we should be purging Writables, not fixing them")
     public int compareTo(KeyValueWritableComparable o) {
       return CellComparator.COMPARATOR.compare(this.kv, ((KeyValueWritableComparable)o).kv);
     }
@@ -249,6 +251,8 @@ public class Import extends Configured implements Tool {
   /**
    * A mapper that just writes out KeyValues.
    */
+  @edu.umd.cs.findbugs.annotations.SuppressWarnings(value="EQ_COMPARETO_USE_OBJECT_EQUALS",
+      justification="Writables are going away and this has been this way forever")
   public static class KeyValueImporter extends TableMapper<ImmutableBytesWritable, KeyValue> {
     private Map<byte[], byte[]> cfRenameMap;
     private Filter filter;

hbase-server/src/main/java/org/apache/hadoop/hbase/mapreduce/ImportTsv.java

@@ -107,7 +107,7 @@ public class ImportTsv extends Configured implements Tool {
    * If table didn't exist and was created in dry-run mode, this flag is
    * flipped to delete it when MR ends.
    */
-  private static boolean dryRunTableCreated;
+  private static boolean DRY_RUN_TABLE_CREATED;
 
   public static class TsvParser {
     /**
@@ -475,8 +475,7 @@ public class ImportTsv extends Configured implements Tool {
 
         // See if a non-default Mapper was set
         String mapperClassName = conf.get(MAPPER_CONF_KEY);
-        Class mapperClass =
+        Class mapperClass = mapperClassName != null? Class.forName(mapperClassName): DEFAULT_MAPPER;
-          mapperClassName != null ? Class.forName(mapperClassName) : DEFAULT_MAPPER;
 
         TableName tableName = TableName.valueOf(args[0]);
         Path inputDir = new Path(args[1]);
@@ -504,7 +503,9 @@ public class ImportTsv extends Configured implements Tool {
               createTable(admin, tableName, columns);
               if (isDryRun) {
                 LOG.warn("Dry run: Table will be deleted at end of dry run.");
-                  dryRunTableCreated = true;
+                synchronized (ImportTsv.class) {
+                  DRY_RUN_TABLE_CREATED = true;
+                }
               }
             } else {
               String errorMsg =
@@ -616,7 +617,8 @@ public class ImportTsv extends Configured implements Tool {
       }
       admin.deleteTable(tableName);
     } catch (IOException e) {
-      LOG.error(format("***Dry run: Failed to delete table '%s'.***\n%s", tableName, e.toString()));
+      LOG.error(format("***Dry run: Failed to delete table '%s'.***%n%s", tableName,
+          e.toString()));
       return;
     }
     LOG.info(format("Dry run: Deleted table '%s'.", tableName));
@@ -658,7 +660,7 @@ public class ImportTsv extends Configured implements Tool {
       "input data. Another special column" + TsvParser.TIMESTAMPKEY_COLUMN_SPEC +
       " designates that this column should be\n" +
       "used as timestamp for each record. Unlike " + TsvParser.ROWKEY_COLUMN_SPEC + ", " +
-      TsvParser.TIMESTAMPKEY_COLUMN_SPEC + " is optional.\n" +
+      TsvParser.TIMESTAMPKEY_COLUMN_SPEC + " is optional." + "\n" +
       "You must specify at most one column as timestamp key for each imported record.\n" +
       "Record with invalid timestamps (blank, non-numeric) will be treated as bad record.\n" +
       "Note: if you use this option, then '" + TIMESTAMP_CONF_KEY + "' option will be ignored.\n" +
@@ -767,10 +769,16 @@ public class ImportTsv extends Configured implements Tool {
     // system time
     getConf().setLong(TIMESTAMP_CONF_KEY, timstamp);
 
-    dryRunTableCreated = false;
+    synchronized (ImportTsv.class) {
+      DRY_RUN_TABLE_CREATED = false;
+    }
     Job job = createSubmittableJob(getConf(), args);
     boolean success = job.waitForCompletion(true);
-    if (dryRunTableCreated) {
+    boolean delete = false;
+    synchronized (ImportTsv.class) {
+      delete = DRY_RUN_TABLE_CREATED;
+    }
+    if (delete) {
       deleteTable(getConf(), args);
     }
     return success ? 0 : 1;

hbase-server/src/main/java/org/apache/hadoop/hbase/mapreduce/MultiTableInputFormatBase.java

@@ -110,10 +110,8 @@ public abstract class MultiTableInputFormatBase extends
         @Override
         public void close() throws IOException {
           trr.close();
-          if (connection != null) {
           connection.close();
         }
-        }
 
         @Override
         public ImmutableBytesWritable getCurrentKey() throws IOException, InterruptedException {
@@ -145,9 +143,7 @@ public abstract class MultiTableInputFormatBase extends
       // If there is an exception make sure that all
       // resources are closed and released.
       trr.close();
-      if (connection != null) {
       connection.close();
-      }
       throw ioe;
     }
   }

hbase-server/src/main/java/org/apache/hadoop/hbase/mapreduce/MultithreadedTableMapper.java

@@ -230,6 +230,8 @@ public class MultithreadedTableMapper<K2, V2> extends TableMapper<K2, V2> {
     }
   }
 
+  @edu.umd.cs.findbugs.annotations.SuppressWarnings(value="REC_CATCH_EXCEPTION",
+      justification="Don't understand why FB is complaining about this one. We do throw exception")
   private class MapRunner implements Runnable {
     private Mapper<ImmutableBytesWritable, Result, K2,V2> mapper;
     private Context subcontext;
@@ -280,7 +282,7 @@ public class MultithreadedTableMapper<K2, V2> extends TableMapper<K2, V2> {
           Class<?> wrappedMapperClass = Class.forName("org.apache.hadoop.mapreduce.lib.map.WrappedMapper");
           Method getMapContext = wrappedMapperClass.getMethod("getMapContext", MapContext.class);
           subcontext = (Context) getMapContext.invoke(wrappedMapperClass.newInstance(), mc);
-        } catch (Exception ee) {
+        } catch (Exception ee) { // FindBugs: REC_CATCH_EXCEPTION
           // rethrow as IOE
           throw new IOException(e);
         }

hbase-server/src/main/java/org/apache/hadoop/hbase/mapreduce/TableInputFormat.java

@@ -111,6 +111,8 @@ implements Configurable {
    *   org.apache.hadoop.conf.Configuration)
    */
   @Override
+  @edu.umd.cs.findbugs.annotations.SuppressWarnings(value="REC_CATCH_EXCEPTION",
+    justification="Intentional")
   public void setConf(Configuration configuration) {
     this.conf = configuration;
 

hbase-server/src/main/java/org/apache/hadoop/hbase/master/AssignmentManager.java

@@ -2174,6 +2174,9 @@ public class AssignmentManager {
     }
   }
 
+  @edu.umd.cs.findbugs.annotations.SuppressWarnings(
+      value="AT_OPERATION_SEQUENCE_ON_CONCURRENT_ABSTRACTION",
+      justification="Worth fixing but not the end of the world.")
   private String onRegionFailedOpen(final RegionState current,
       final HRegionInfo hri, final ServerName serverName) {
     // The region must be opening on this server.
@@ -2189,6 +2192,7 @@ public class AssignmentManager {
     }
 
     String encodedName = hri.getEncodedName();
+    // FindBugs: AT_OPERATION_SEQUENCE_ON_CONCURRENT_ABSTRACTION Worth fixing!!!
     AtomicInteger failedOpenCount = failedOpenTracker.get(encodedName);
     if (failedOpenCount == null) {
       failedOpenCount = new AtomicInteger();

hbase-server/src/main/java/org/apache/hadoop/hbase/master/ExpiredMobFileCleanerChore.java

@@ -61,6 +61,8 @@ public class ExpiredMobFileCleanerChore extends ScheduledChore {
   }
 
   @Override
+  @edu.umd.cs.findbugs.annotations.SuppressWarnings(value="REC_CATCH_EXCEPTION",
+    justification="Intentional")
   protected void chore() {
     try {
       TableDescriptors htds = master.getTableDescriptors();

hbase-server/src/main/java/org/apache/hadoop/hbase/master/RegionStates.java

@@ -424,8 +424,6 @@ public class RegionStates {
       if (!serverName.equals(oldServerName)) {
         if (LOG.isDebugEnabled()) {
           LOG.debug("Onlined " + hri.getShortNameToLog() + " on " + serverName);
-        } else {
-          LOG.debug("Onlined " + hri.getShortNameToLog() + " on " + serverName);
         }
         addToServerHoldings(serverName, hri);
         addToReplicaMapping(hri);

hbase-server/src/main/java/org/apache/hadoop/hbase/master/SplitLogManager.java

@@ -643,7 +643,7 @@ public class SplitLogManager {
     public volatile ServerName cur_worker_name;
     public volatile TaskBatch batch;
     public volatile TerminationStatus status;
-    public volatile int incarnation;
+    public volatile AtomicInteger incarnation = new AtomicInteger(0);
     public final AtomicInteger unforcedResubmits = new AtomicInteger();
     public volatile boolean resubmitThresholdReached;
 
@@ -655,7 +655,6 @@ public class SplitLogManager {
     }
 
     public Task() {
-      incarnation = 0;
       last_version = -1;
       status = IN_PROGRESS;
       setUnassigned();

hbase-server/src/main/java/org/apache/hadoop/hbase/master/TableNamespaceManager.java

@@ -65,12 +65,15 @@ import com.google.common.collect.Sets;
  * is likely to go aways anyways.
  */
 @InterfaceAudience.Private
+@edu.umd.cs.findbugs.annotations.SuppressWarnings(value="IS2_INCONSISTENT_SYNC",
+  justification="TODO: synchronize access on nsTable but it is done in tiers above and this " +
+    "class is going away/shrinking")
 public class TableNamespaceManager {
   private static final Log LOG = LogFactory.getLog(TableNamespaceManager.class);
 
   private Configuration conf;
   private MasterServices masterServices;
-  private Table nsTable = null;
+  private Table nsTable = null; // FindBugs: IS2_INCONSISTENT_SYNC TODO: Access is not synchronized
   private ZKNamespaceManager zkNamespaceManager;
   private boolean initialized;
 

hbase-server/src/main/java/org/apache/hadoop/hbase/master/balancer/BaseLoadBalancer.java

@@ -554,17 +554,21 @@ public abstract class BaseLoadBalancer implements LoadBalancer {
       switch (action.type) {
       case NULL: break;
       case ASSIGN_REGION:
+        // FindBugs: Having the assert quietens FB BC_UNCONFIRMED_CAST warnings
+        assert action instanceof AssignRegionAction: action.getClass();
         AssignRegionAction ar = (AssignRegionAction) action;
         regionsPerServer[ar.server] = addRegion(regionsPerServer[ar.server], ar.region);
         regionMoved(ar.region, -1, ar.server);
         break;
       case MOVE_REGION:
+        assert action instanceof MoveRegionAction: action.getClass();
         MoveRegionAction mra = (MoveRegionAction) action;
         regionsPerServer[mra.fromServer] = removeRegion(regionsPerServer[mra.fromServer], mra.region);
         regionsPerServer[mra.toServer] = addRegion(regionsPerServer[mra.toServer], mra.region);
         regionMoved(mra.region, mra.fromServer, mra.toServer);
         break;
       case SWAP_REGIONS:
+        assert action instanceof SwapRegionsAction: action.getClass();
         SwapRegionsAction a = (SwapRegionsAction) action;
         regionsPerServer[a.fromServer] = replaceRegion(regionsPerServer[a.fromServer], a.fromRegion, a.toRegion);
         regionsPerServer[a.toServer] = replaceRegion(regionsPerServer[a.toServer], a.toRegion, a.fromRegion);
@@ -1095,7 +1099,7 @@ public abstract class BaseLoadBalancer implements LoadBalancer {
   }
 
   @Override
-  public void setClusterStatus(ClusterStatus st) {
+  public synchronized void setClusterStatus(ClusterStatus st) {
     this.clusterStatus = st;
     regionFinder.setClusterStatus(st);
   }

hbase-server/src/main/java/org/apache/hadoop/hbase/master/balancer/StochasticLoadBalancer.java

@@ -94,6 +94,8 @@ import org.apache.hadoop.hbase.util.EnvironmentEdgeManager;
  * so that the balancer gets the full picture of all loads on the cluster.</p>
  */
 @InterfaceAudience.LimitedPrivate(HBaseInterfaceAudience.CONFIG)
+@edu.umd.cs.findbugs.annotations.SuppressWarnings(value="IS2_INCONSISTENT_SYNC",
+  justification="Complaint is about costFunctions not being synchronized; not end of the world")
 public class StochasticLoadBalancer extends BaseLoadBalancer {
 
   protected static final String STEPS_PER_REGION_KEY =
@@ -119,7 +121,7 @@ public class StochasticLoadBalancer extends BaseLoadBalancer {
 
   private CandidateGenerator[] candidateGenerators;
   private CostFromRegionLoadFunction[] regionLoadFunctions;
-  private CostFunction[] costFunctions;
+  private CostFunction[] costFunctions; // FindBugs: Wants this protected; IS2_INCONSISTENT_SYNC
 
   // to save and report costs to JMX
   private Double curOverallCost = 0d;

hbase-server/src/main/java/org/apache/hadoop/hbase/master/cleaner/HFileLinkCleaner.java

@@ -96,7 +96,7 @@ public class HFileLinkCleaner extends BaseHFileCleanerDelegate {
   }
 
   @Override
-  public void setConf(Configuration conf) {
+  public synchronized void setConf(Configuration conf) {
     super.setConf(conf);
 
     // setup filesystem

hbase-server/src/main/java/org/apache/hadoop/hbase/master/snapshot/TakeSnapshotHandler.java

@@ -154,6 +154,8 @@ public abstract class TakeSnapshotHandler extends EventHandler implements Snapsh
    * call should get implemented for each snapshot flavor.
    */
   @Override
+  @edu.umd.cs.findbugs.annotations.SuppressWarnings(value="REC_CATCH_EXCEPTION",
+    justification="Intentional")
   public void process() {
     String msg = "Running " + snapshot.getType() + " table snapshot " + snapshot.getName() + " "
         + eventType + " on table " + snapshotTable;
@@ -205,7 +207,7 @@ public abstract class TakeSnapshotHandler extends EventHandler implements Snapsh
       status.markComplete(msg);
       LOG.info(msg);
       metricsSnapshot.addSnapshot(status.getCompletionTimestamp() - status.getStartTime());
-    } catch (Exception e) {
+    } catch (Exception e) { // FindBugs: REC_CATCH_EXCEPTION
       status.abort("Failed to complete snapshot " + snapshot.getName() + " on table " +
           snapshotTable + " because " + e.getMessage());
       String reason = "Failed taking snapshot " + ClientSnapshotDescriptionUtils.toString(snapshot)

hbase-server/src/main/java/org/apache/hadoop/hbase/mob/ExpiredMobFileCleaner.java

@@ -89,6 +89,8 @@ public class ExpiredMobFileCleaner extends Configured implements Tool {
     System.err.println(" familyName       The column family name");
   }
 
+  @edu.umd.cs.findbugs.annotations.SuppressWarnings(value="REC_CATCH_EXCEPTION",
+      justification="Intentional")
   public int run(String[] args) throws Exception {
     if (args.length != 2) {
       printUsage();

hbase-server/src/main/java/org/apache/hadoop/hbase/monitoring/MonitoredRPCHandlerImpl.java

@@ -98,7 +98,7 @@ public class MonitoredRPCHandlerImpl extends MonitoredTaskImpl
    * by this Handler.
    * @return a string representing the method call without parameters
    */
-  public String getRPC() {
+  public synchronized String getRPC() {
     return getRPC(false);
   }
 
@@ -166,7 +166,7 @@ public class MonitoredRPCHandlerImpl extends MonitoredTaskImpl
    * @return true if the monitored handler is currently servicing an RPC call
    * to a database command.
    */
-  public boolean isOperationRunning() {
+  public synchronized boolean isOperationRunning() {
     if(!isRPCRunning()) {
       return false;
     }
@@ -212,7 +212,7 @@ public class MonitoredRPCHandlerImpl extends MonitoredTaskImpl
   }
 
   @Override
-  public void markComplete(String status) {
+  public synchronized void markComplete(String status) {
     super.markComplete(status);
     this.params = null;
     this.packet = null;

hbase-server/src/main/java/org/apache/hadoop/hbase/quotas/QuotaState.java

@@ -28,6 +28,9 @@ import org.apache.hadoop.hbase.util.EnvironmentEdgeManager;
  */
 @InterfaceAudience.Private
 @InterfaceStability.Evolving
+@edu.umd.cs.findbugs.annotations.SuppressWarnings(value="IS2_INCONSISTENT_SYNC",
+  justification="FindBugs seems confused; says globalLimiter and lastUpdate " +
+  "are mostly synchronized...but to me it looks like they are totally synchronized")
 public class QuotaState {
   protected long lastUpdate = 0;
   protected long lastQuery = 0;
@@ -77,7 +80,7 @@ public class QuotaState {
    * Setup the global quota information.
    * (This operation is part of the QuotaState setup)
    */
-  public void setQuotas(final Quotas quotas) {
+  public synchronized void setQuotas(final Quotas quotas) {
     if (quotas.hasThrottle()) {
       globalLimiter = QuotaLimiterFactory.fromThrottle(quotas.getThrottle());
     } else {

hbase-server/src/main/java/org/apache/hadoop/hbase/quotas/RateLimiter.java

@@ -45,6 +45,9 @@ import com.google.common.annotations.VisibleForTesting;
  */
 @InterfaceAudience.Private
 @InterfaceStability.Evolving
+@edu.umd.cs.findbugs.annotations.SuppressWarnings(value="IS2_INCONSISTENT_SYNC",
+  justification="FindBugs seems confused; says limit and tlimit " +
+  "are mostly synchronized...but to me it looks like they are totally synchronized")
 public abstract class RateLimiter {
   public static final String QUOTA_RATE_LIMITER_CONF_KEY = "hbase.quota.rate.limiter";
   private long tunit = 1000;           // Timeunit factor for translating to ms.
@@ -73,7 +76,7 @@ public abstract class RateLimiter {
    * @param limit The max value available resource units can be refilled to.
    * @param timeUnit Timeunit factor for translating to ms.
    */
-  public void set(final long limit, final TimeUnit timeUnit) {
+  public synchronized void set(final long limit, final TimeUnit timeUnit) {
     switch (timeUnit) {
     case MILLISECONDS:
       tunit = 1;
@@ -99,10 +102,11 @@ public abstract class RateLimiter {
 
   public String toString() {
     String rateLimiter = this.getClass().getSimpleName();
-    if (limit == Long.MAX_VALUE) {
+    if (getLimit() == Long.MAX_VALUE) {
       return rateLimiter + "(Bypass)";
     }
-    return rateLimiter + "(avail=" + avail + " limit=" + limit + " tunit=" + tunit + ")";
+    return rateLimiter + "(avail=" + getAvailable() + " limit=" + getLimit() +
+        " tunit=" + getTimeUnitInMillis() + ")";
   }
 
   /**
@@ -120,7 +124,7 @@ public abstract class RateLimiter {
   }
 
   public synchronized boolean isBypass() {
-    return limit == Long.MAX_VALUE;
+    return getLimit() == Long.MAX_VALUE;
   }
 
   public synchronized long getLimit() {
@@ -131,7 +135,7 @@ public abstract class RateLimiter {
     return avail;
   }
 
-  protected long getTimeUnitInMillis() {
+  protected synchronized long getTimeUnitInMillis() {
     return tunit;
   }
 
@@ -195,7 +199,7 @@ public abstract class RateLimiter {
    */
   public synchronized long waitInterval(final long amount) {
     // TODO Handle over quota?
-    return (amount <= avail) ? 0 : getWaitInterval(limit, avail, amount);
+    return (amount <= avail) ? 0 : getWaitInterval(getLimit(), avail, amount);
   }
 
   // These two method are for strictly testing purpose only

hbase-server/src/main/java/org/apache/hadoop/hbase/quotas/UserQuotaState.java

@@ -34,6 +34,9 @@ import org.apache.hadoop.hbase.util.EnvironmentEdgeManager;
  */
 @InterfaceAudience.Private
 @InterfaceStability.Evolving
+@edu.umd.cs.findbugs.annotations.SuppressWarnings(value="IS2_INCONSISTENT_SYNC",
+  justification="FindBugs seems confused; says bypassGlobals, namepaceLimiters, and " +
+    "tableLimiters are mostly synchronized...but to me it looks like they are totally synchronized")
 public class UserQuotaState extends QuotaState {
   private Map<String, QuotaLimiter> namespaceLimiters = null;
   private Map<TableName, QuotaLimiter> tableLimiters = null;
@@ -96,7 +99,7 @@ public class UserQuotaState extends QuotaState {
   }
 
   @Override
-  public void setQuotas(final Quotas quotas) {
+  public synchronized void setQuotas(final Quotas quotas) {
     super.setQuotas(quotas);
     bypassGlobals = quotas.getBypassGlobals();
   }
@@ -105,7 +108,7 @@ public class UserQuotaState extends QuotaState {
    * Add the quota information of the specified table.
    * (This operation is part of the QuotaState setup)
    */
-  public void setQuotas(final TableName table, Quotas quotas) {
+  public synchronized void setQuotas(final TableName table, Quotas quotas) {
     tableLimiters = setLimiter(tableLimiters, table, quotas);
   }
 

hbase-server/src/main/java/org/apache/hadoop/hbase/regionserver/HRegion.java

@@ -393,7 +393,7 @@ public class HRegion implements HeapSize, PropagatingConfigurationObserver, Regi
     // Set when a flush has been requested.
     volatile boolean flushRequested = false;
     // Number of compactions running.
-    volatile int compacting = 0;
+    AtomicInteger compacting = new AtomicInteger(0);
     // Gets set in close. If set, cannot compact or flush again.
     volatile boolean writesEnabled = true;
     // Set if region is read-only
@@ -824,7 +824,7 @@ public class HRegion implements HeapSize, PropagatingConfigurationObserver, Regi
 
     this.writestate.setReadOnly(ServerRegionReplicaUtil.isReadOnly(this));
     this.writestate.flushRequested = false;
-    this.writestate.compacting = 0;
+    this.writestate.compacting.set(0);
 
     if (this.writestate.writesEnabled) {
       // Remove temporary data left over from old regions
@@ -1368,6 +1368,8 @@ public class HRegion implements HeapSize, PropagatingConfigurationObserver, Regi
     this.closing.set(closing);
   }
 
+  @edu.umd.cs.findbugs.annotations.SuppressWarnings(value="UL_UNRELEASED_LOCK_EXCEPTION_PATH",
+      justification="I think FindBugs is confused")
   private Map<byte[], List<StoreFile>> doClose(final boolean abort, MonitoredTask status)
       throws IOException {
     if (isClosed()) {
@@ -1405,7 +1407,7 @@ public class HRegion implements HeapSize, PropagatingConfigurationObserver, Regi
     }
 
     // block waiting for the lock for closing
-    lock.writeLock().lock();
+    lock.writeLock().lock(); // FindBugs: Complains UL_UNRELEASED_LOCK_EXCEPTION_PATH but seems fine
     this.closing.set(true);
     status.setStatus("Disabling writes for close");
     try {
@@ -1537,7 +1539,7 @@ public class HRegion implements HeapSize, PropagatingConfigurationObserver, Regi
       }
       boolean interrupted = false;
       try {
-        while (writestate.compacting > 0 || writestate.flushing) {
+        while (writestate.compacting.get() > 0 || writestate.flushing) {
           LOG.debug("waiting for " + writestate.compacting + " compactions"
             + (writestate.flushing ? " & cache flush" : "") + " to complete for region " + this);
           try {
@@ -1894,7 +1896,7 @@ public class HRegion implements HeapSize, PropagatingConfigurationObserver, Regi
         synchronized (writestate) {
           if (writestate.writesEnabled) {
             wasStateSet = true;
-            ++writestate.compacting;
+            writestate.compacting.incrementAndGet();
           } else {
             String msg = "NOT compacting region " + this + ". Writes disabled.";
             LOG.info(msg);
@@ -1920,8 +1922,8 @@ public class HRegion implements HeapSize, PropagatingConfigurationObserver, Regi
       } finally {
         if (wasStateSet) {
           synchronized (writestate) {
-            --writestate.compacting;
+            writestate.compacting.decrementAndGet();
-            if (writestate.compacting <= 0) {
+            if (writestate.compacting.get() <= 0) {
               writestate.notifyAll();
             }
           }
@@ -2164,6 +2166,8 @@ public class HRegion implements HeapSize, PropagatingConfigurationObserver, Regi
     }
   }
 
+  @edu.umd.cs.findbugs.annotations.SuppressWarnings(value="DLS_DEAD_LOCAL_STORE",
+      justification="FindBugs seems confused about trxId")
   protected PrepareFlushResult internalPrepareFlushCache(final WAL wal, final long myseqid,
       final Collection<Store> storesToFlush, MonitoredTask status, boolean writeFlushWalMarker)
   throws IOException {
@@ -2395,6 +2399,8 @@ public class HRegion implements HeapSize, PropagatingConfigurationObserver, Regi
     return false;
   }
 
+  @edu.umd.cs.findbugs.annotations.SuppressWarnings(value="NN_NAKED_NOTIFY",
+      justification="Intentional; notify is about completed flush")
   protected FlushResult internalFlushCacheAndCommit(
         final WAL wal, MonitoredTask status, final PrepareFlushResult prepareResult,
         final Collection<Store> storesToFlush)
@@ -4448,6 +4454,8 @@ public class HRegion implements HeapSize, PropagatingConfigurationObserver, Regi
   }
 
   @VisibleForTesting
+  @edu.umd.cs.findbugs.annotations.SuppressWarnings(value="NN_NAKED_NOTIFY",
+    justification="Intentional; post memstore flush")
   void replayWALFlushCommitMarker(FlushDescriptor flush) throws IOException {
     MonitoredTask status = TaskMonitor.get().createStatus("Committing flush " + this);
 
@@ -4684,6 +4692,8 @@ public class HRegion implements HeapSize, PropagatingConfigurationObserver, Regi
     return prepareFlushResult;
   }
 
+  @edu.umd.cs.findbugs.annotations.SuppressWarnings(value="NN_NAKED_NOTIFY",
+      justification="Intentional; cleared the memstore")
   void replayWALRegionEventMarker(RegionEventDescriptor regionEvent) throws IOException {
     checkTargetRegion(regionEvent.getEncodedRegionName().toByteArray(),
       "RegionEvent marker from WAL ", regionEvent);
@@ -4914,6 +4924,8 @@ public class HRegion implements HeapSize, PropagatingConfigurationObserver, Regi
     return refreshStoreFiles(false);
   }
 
+  @edu.umd.cs.findbugs.annotations.SuppressWarnings(value="NN_NAKED_NOTIFY",
+      justification="Notify is about post replay. Intentional")
   protected boolean refreshStoreFiles(boolean force) throws IOException {
     if (!force && ServerRegionReplicaUtil.isDefaultReplica(this.getRegionInfo())) {
       return false; // if primary nothing to do
@@ -7838,6 +7850,8 @@ public class HRegion implements HeapSize, PropagatingConfigurationObserver, Regi
   }
 
   @Override
+  @edu.umd.cs.findbugs.annotations.SuppressWarnings(value="SF_SWITCH_FALLTHROUGH",
+    justification="Intentional")
   public void startRegionOperation(Operation op) throws IOException {
     switch (op) {
     case GET:  // read operations

hbase-server/src/main/java/org/apache/hadoop/hbase/regionserver/LruHashMap.java

@@ -189,7 +189,7 @@ implements HeapSize, Map<K,V> {
    *
    * @return currently available bytes
    */
-  public long getMemFree() {
+  public synchronized long getMemFree() {
     return memFree;
   }
 
@@ -208,7 +208,7 @@ implements HeapSize, Map<K,V> {
    * @return currently used memory in bytes
    */
   public long getMemUsed() {
-    return (memTotal - memFree); // FindBugs IS2_INCONSISTENT_SYNC
+    return (memTotal - getMemFree()); // FindBugs IS2_INCONSISTENT_SYNC
   }
 
   /**
@@ -227,7 +227,7 @@ implements HeapSize, Map<K,V> {
    *
    * @return number of misses
    */
-  public long getMissCount() {
+  public synchronized long getMissCount() {
     return missCount; // FindBugs IS2_INCONSISTENT_SYNC
   }
 
@@ -239,7 +239,7 @@ implements HeapSize, Map<K,V> {
    */
   public double getHitRatio() {
     return (double)((double)hitCount/
-      ((double)(hitCount+missCount)));
+      ((double)(hitCount + getMissCount())));
   }
 
   /**
@@ -269,7 +269,7 @@ implements HeapSize, Map<K,V> {
    * @return memory usage of map in bytes
    */
   public long heapSize() {
-    return (memTotal - memFree);
+    return (memTotal - getMemFree());
   }
 
   //--------------------------------------------------------------------------
@@ -824,6 +824,8 @@ implements HeapSize, Map<K,V> {
    *
    * @return Set of entries in hash
    */
+  @edu.umd.cs.findbugs.annotations.SuppressWarnings(value="IS2_INCONSISTENT_SYNC",
+      justification="Unused debugging function that reads only")
   public Set<Entry<K,V>> entryTableSet() {
     Set<Entry<K,V>> entrySet = new HashSet<Entry<K,V>>();
     Entry [] table = entries; // FindBugs IS2_INCONSISTENT_SYNC

hbase-server/src/main/java/org/apache/hadoop/hbase/regionserver/MemStoreChunkPool.java

@@ -60,7 +60,7 @@ public class MemStoreChunkPool {
   final static float POOL_INITIAL_SIZE_DEFAULT = 0.0f;
 
   // Static reference to the MemStoreChunkPool
-  private static MemStoreChunkPool globalInstance;
+  private static MemStoreChunkPool GLOBAL_INSTANCE;
   /** Boolean whether we have disabled the memstore chunk pool entirely. */
   static boolean chunkPoolDisabled = false;
 
@@ -179,12 +179,14 @@ public class MemStoreChunkPool {
    * @param conf
    * @return the global MemStoreChunkPool instance
    */
+  @edu.umd.cs.findbugs.annotations.SuppressWarnings(value="DC_DOUBLECHECK",
+      justification="Intentional")
   static MemStoreChunkPool getPool(Configuration conf) {
-    if (globalInstance != null) return globalInstance;
+    if (GLOBAL_INSTANCE != null) return GLOBAL_INSTANCE;
 
     synchronized (MemStoreChunkPool.class) {
       if (chunkPoolDisabled) return null;
-      if (globalInstance != null) return globalInstance;
+      if (GLOBAL_INSTANCE != null) return GLOBAL_INSTANCE;
       float poolSizePercentage = conf.getFloat(CHUNK_POOL_MAXSIZE_KEY, POOL_MAX_SIZE_DEFAULT);
       if (poolSizePercentage <= 0) {
         chunkPoolDisabled = true;
@@ -210,8 +212,8 @@ public class MemStoreChunkPool {
       int initialCount = (int) (initialCountPercentage * maxCount);
       LOG.info("Allocating MemStoreChunkPool with chunk size " + StringUtils.byteDesc(chunkSize)
           + ", max count " + maxCount + ", initial count " + initialCount);
-      globalInstance = new MemStoreChunkPool(conf, chunkSize, maxCount, initialCount);
+      GLOBAL_INSTANCE = new MemStoreChunkPool(conf, chunkSize, maxCount, initialCount);
-      return globalInstance;
+      return GLOBAL_INSTANCE;
     }
   }
 

hbase-server/src/main/java/org/apache/hadoop/hbase/regionserver/RegionServerCoprocessorHost.java

@@ -278,6 +278,8 @@ public class RegionServerCoprocessorHost extends
 
     private RegionServerServices regionServerServices;
 
+    @edu.umd.cs.findbugs.annotations.SuppressWarnings(value="BC_UNCONFIRMED_CAST",
+        justification="Intentional; FB has trouble detecting isAssignableFrom")
     public RegionServerEnvironment(final Class<?> implClass,
         final Coprocessor impl, final int priority, final int seq,
         final Configuration conf, final RegionServerServices services) {
@@ -285,7 +287,7 @@ public class RegionServerCoprocessorHost extends
       this.regionServerServices = services;
       for (Object itf : ClassUtils.getAllInterfaces(implClass)) {
         Class<?> c = (Class<?>) itf;
-        if (SingletonCoprocessorService.class.isAssignableFrom(c)) {
+        if (SingletonCoprocessorService.class.isAssignableFrom(c)) {// FindBugs: BC_UNCONFIRMED_CAST
           this.regionServerServices.registerService(
             ((SingletonCoprocessorService) impl).getService());
           break;

hbase-server/src/main/java/org/apache/hadoop/hbase/regionserver/StoreFile.java

@@ -30,7 +30,6 @@ import java.util.SortedSet;
 import java.util.UUID;
 import java.util.concurrent.atomic.AtomicBoolean;
 import java.util.concurrent.atomic.AtomicInteger;
-import java.util.concurrent.locks.ReentrantReadWriteLock;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
@@ -38,11 +37,11 @@ import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.fs.FileSystem;
 import org.apache.hadoop.fs.Path;
 import org.apache.hadoop.hbase.Cell;
+import org.apache.hadoop.hbase.CellComparator;
 import org.apache.hadoop.hbase.CellUtil;
 import org.apache.hadoop.hbase.HConstants;
 import org.apache.hadoop.hbase.HDFSBlocksDistribution;
 import org.apache.hadoop.hbase.KeyValue;
-import org.apache.hadoop.hbase.CellComparator;
 import org.apache.hadoop.hbase.KeyValueUtil;
 import org.apache.hadoop.hbase.classification.InterfaceAudience;
 import org.apache.hadoop.hbase.client.Scan;
@@ -51,6 +50,7 @@ import org.apache.hadoop.hbase.io.TimeRange;
 import org.apache.hadoop.hbase.io.hfile.BlockType;
 import org.apache.hadoop.hbase.io.hfile.CacheConfig;
 import org.apache.hadoop.hbase.io.hfile.HFile;
+import org.apache.hadoop.hbase.io.hfile.HFileBlock;
 import org.apache.hadoop.hbase.io.hfile.HFileContext;
 import org.apache.hadoop.hbase.io.hfile.HFileScanner;
 import org.apache.hadoop.hbase.nio.ByteBuff;
@@ -61,7 +61,6 @@ import org.apache.hadoop.hbase.util.BloomFilterWriter;
 import org.apache.hadoop.hbase.util.Bytes;
 import org.apache.hadoop.hbase.util.Writables;
 import org.apache.hadoop.io.WritableUtils;
-import org.apache.hadoop.hbase.io.hfile.HFileBlock;
 
 import com.google.common.annotations.VisibleForTesting;
 import com.google.common.base.Function;
@@ -623,6 +622,8 @@ public class StoreFile {
     return false;
   }
 
+  @edu.umd.cs.findbugs.annotations.SuppressWarnings(value="ICAST_INTEGER_MULTIPLY_CAST_TO_LONG",
+      justification="Will not overflow")
   public static class WriterBuilder {
     private final Configuration conf;
     private final CacheConfig cacheConf;
@@ -635,7 +636,6 @@ public class StoreFile {
     private Path filePath;
     private InetSocketAddress[] favoredNodes;
     private HFileContext fileContext;
-    private boolean shouldDropCacheBehind = false;
 
     public WriterBuilder(Configuration conf, CacheConfig cacheConf,
         FileSystem fs) {
@@ -703,8 +703,8 @@ public class StoreFile {
       return this;
     }
 
-    public WriterBuilder withShouldDropCacheBehind(boolean shouldDropCacheBehind) {
+    public WriterBuilder withShouldDropCacheBehind(boolean shouldDropCacheBehind/*NOT USED!!*/) {
-      this.shouldDropCacheBehind = shouldDropCacheBehind;
+      // TODO: HAS NO EFFECT!!! FIX!!
       return this;
     }
     /**
@@ -807,9 +807,6 @@ public class StoreFile {
     private Cell lastDeleteFamilyCell = null;
     private long deleteFamilyCnt = 0;
 
-    /** Bytes per Checksum */
-    protected int bytesPerChecksum;
-
     TimeRangeTracker timeRangeTracker = new TimeRangeTracker();
     /* isTimeRangeTrackerSet keeps track if the timeRange has already been set
      * When flushing a memstore, we set TimeRange and use this variable to

hbase-server/src/main/java/org/apache/hadoop/hbase/regionserver/TimeRangeTracker.java

@@ -91,6 +91,8 @@ public class TimeRangeTracker implements Writable {
    * If required, update the current TimestampRange to include timestamp
    * @param timestamp the timestamp value to include
    */
+  @edu.umd.cs.findbugs.annotations.SuppressWarnings(value="MT_CORRECTNESS",
+      justification="Intentional")
   void includeTimestamp(final long timestamp) {
     // Do test outside of synchronization block.  Synchronization in here can be problematic
     // when many threads writing one Store -- they can all pile up trying to add in here.

hbase-server/src/main/java/org/apache/hadoop/hbase/regionserver/compactions/Compactor.java

@@ -332,7 +332,7 @@ public abstract class Compactor {
 
     throughputController.start(compactionName);
     KeyValueScanner kvs = (scanner instanceof KeyValueScanner)? (KeyValueScanner)scanner : null;
-    int minFilesToCompact = Math.max(2,
+    long minFilesToCompact = Math.max(2L,
         conf.getInt(CompactionConfiguration.HBASE_HSTORE_COMPACTION_MIN_KEY,
             /* old name */ conf.getInt("hbase.hstore.compactionThreshold", 3)));
     long shippedCallSizeLimit = (long) minFilesToCompact * HConstants.DEFAULT_BLOCKSIZE;

hbase-server/src/main/java/org/apache/hadoop/hbase/replication/HBaseReplicationEndpoint.java

@@ -43,18 +43,20 @@ import org.apache.zookeeper.KeeperException.SessionExpiredException;
  * target cluster is an HBase cluster.
  */
 @InterfaceAudience.Private
+@edu.umd.cs.findbugs.annotations.SuppressWarnings(value="MT_CORRECTNESS",
+  justification="Thinks zkw needs to be synchronized access but should be fine as is.")
 public abstract class HBaseReplicationEndpoint extends BaseReplicationEndpoint
   implements Abortable {
 
   private static final Log LOG = LogFactory.getLog(HBaseReplicationEndpoint.class);
 
-  private ZooKeeperWatcher zkw = null;
+  private ZooKeeperWatcher zkw = null; // FindBugs: MT_CORRECTNESS
 
   private List<ServerName> regionServers = new ArrayList<ServerName>(0);
-  private volatile long lastRegionServerUpdate;
+  private long lastRegionServerUpdate;
 
   protected void disconnect() {
-    if (zkw != null){
+    if (zkw != null) {
       zkw.close();
     }
   }
@@ -181,7 +183,7 @@ public abstract class HBaseReplicationEndpoint extends BaseReplicationEndpoint
    * Set the list of region servers for that peer
    * @param regionServers list of addresses for the region servers
    */
-  public void setRegionServers(List<ServerName> regionServers) {
+  public synchronized void setRegionServers(List<ServerName> regionServers) {
     this.regionServers = regionServers;
     lastRegionServerUpdate = System.currentTimeMillis();
   }

hbase-server/src/main/java/org/apache/hadoop/hbase/replication/regionserver/RegionReplicaReplicationEndpoint.java

@@ -115,7 +115,7 @@ public class RegionReplicaReplicationEndpoint extends HBaseReplicationEndpoint {
    * Skips the entries which has original seqId. Only entries persisted via distributed log replay
    * have their original seq Id fields set.
    */
-  private class SkipReplayedEditsFilter extends BaseWALEntryFilter {
+  private static class SkipReplayedEditsFilter extends BaseWALEntryFilter {
     @Override
     public Entry filter(Entry entry) {
       // if orig seq id is set, skip replaying the entry

hbase-server/src/main/java/org/apache/hadoop/hbase/security/access/SecureBulkLoadEndpoint.java

@@ -280,7 +280,6 @@ public class SecureBulkLoadEndpoint extends SecureBulkLoadService
             Configuration conf = env.getConfiguration();
             fs = FileSystem.get(conf);
             for(Pair<byte[], String> el: familyPaths) {
-              Path p = new Path(el.getSecond());
               Path stageFamily = new Path(bulkToken, Bytes.toString(el.getFirst()));
               if(!fs.exists(stageFamily)) {
                 fs.mkdirs(stageFamily);

hbase-server/src/main/java/org/apache/hadoop/hbase/security/access/TableAuthManager.java

@@ -336,12 +336,6 @@ public class TableAuthManager implements Closeable {
     return false;
   }
 
-  private boolean authorize(List<TablePermission> perms,
-                            TableName table, byte[] family,
-                            Permission.Action action) {
-    return authorize(perms, table, family, null, action);
-  }
-
   private boolean authorize(List<TablePermission> perms,
                             TableName table, byte[] family,
                             byte[] qualifier, Permission.Action action) {

hbase-server/src/main/java/org/apache/hadoop/hbase/security/token/AuthenticationTokenSecretManager.java

@@ -124,7 +124,7 @@ public class AuthenticationTokenSecretManager
   }
 
   @Override
-  protected byte[] createPassword(AuthenticationTokenIdentifier identifier) {
+  protected synchronized byte[] createPassword(AuthenticationTokenIdentifier identifier) {
     long now = EnvironmentEdgeManager.currentTime();
     AuthenticationKey secretKey = currentKey;
     identifier.setKeyId(secretKey.getKeyId());
@@ -229,7 +229,7 @@ public class AuthenticationTokenSecretManager
     return true;
   }
 
-  AuthenticationKey getCurrentKey() {
+  synchronized AuthenticationKey getCurrentKey() {
     return currentKey;
   }
 
@@ -338,8 +338,11 @@ public class AuthenticationTokenSecretManager
 
         // clear any expired
         removeExpiredKeys();
-
+        long localLastKeyUpdate;
-        if (lastKeyUpdate + keyUpdateInterval < now) {
+        synchronized (this) {
+          localLastKeyUpdate = lastKeyUpdate;
+        }
+        if (localLastKeyUpdate + keyUpdateInterval < now) {
           // roll a new master key
           rollCurrentKey();
         }

hbase-server/src/main/java/org/apache/hadoop/hbase/security/visibility/VisibilityController.java

@@ -274,8 +274,10 @@ public class VisibilityController extends BaseMasterAndRegionObserver implements
     // Read the entire labels table and populate the zk
     if (e.getEnvironment().getRegion().getRegionInfo().getTable().equals(LABELS_TABLE_NAME)) {
       this.labelsRegion = true;
+      synchronized (this) {
         this.accessControllerAvailable = CoprocessorHost.getLoadedCoprocessors()
           .contains(AccessController.class.getName());
+      }
       // Defer the init of VisibilityLabelService on labels region until it is in recovering state.
       if (!e.getEnvironment().getRegion().isRecovering()) {
         initVisibilityLabelService(e.getEnvironment());

hbase-server/src/main/java/org/apache/hadoop/hbase/snapshot/ExportSnapshot.java

@@ -643,7 +643,6 @@ public class ExportSnapshot extends Configured implements Tool {
     @Override
     public List<InputSplit> getSplits(JobContext context) throws IOException, InterruptedException {
       Configuration conf = context.getConfiguration();
-      String snapshotName = conf.get(CONF_SNAPSHOT_NAME);
       Path snapshotDir = new Path(conf.get(CONF_SNAPSHOT_DIR));
       FileSystem fs = FileSystem.get(snapshotDir.toUri(), conf);
 

hbase-server/src/main/java/org/apache/hadoop/hbase/snapshot/SnapshotInfo.java

@@ -280,6 +280,8 @@ public final class SnapshotInfo extends Configured implements Tool {
   private SnapshotManifest snapshotManifest;
 
   @Override
+  @edu.umd.cs.findbugs.annotations.SuppressWarnings(value="REC_CATCH_EXCEPTION",
+    justification="Intentional")
   public int run(String[] args) throws IOException, InterruptedException {
     final Configuration conf = getConf();
     boolean listSnapshots = false;
@@ -317,7 +319,7 @@ public final class SnapshotInfo extends Configured implements Tool {
           printUsageAndExit();
         }
       } catch (Exception e) {
-        printUsageAndExit();
+        printUsageAndExit(); // FindBugs: REC_CATCH_EXCEPTION
       }
     }
 

hbase-server/src/main/java/org/apache/hadoop/hbase/util/HBaseFsck.java

@@ -3564,9 +3564,8 @@ public class HBaseFsck extends Configured implements Closeable {
       this.metaEntry = metaEntry;
     }
 
-    public int getReplicaId() {
+    public synchronized int getReplicaId() {
-      if (metaEntry != null) return metaEntry.getReplicaId();
+      return metaEntry != null? metaEntry.getReplicaId(): deployedReplicaId;
-      return deployedReplicaId;
     }
 
     public synchronized void addServer(HRegionInfo hri, ServerName server) {

hbase-server/src/main/java/org/apache/hadoop/hbase/util/IdReadWriteLock.java

@@ -68,12 +68,17 @@ public class IdReadWriteLock {
   /** For testing */
   @VisibleForTesting
   int purgeAndGetEntryPoolSize() {
-    System.gc();
+    gc();
     Threads.sleep(200);
     lockPool.purge();
     return lockPool.size();
   }
 
+  @edu.umd.cs.findbugs.annotations.SuppressWarnings(value="DM_GC", justification="Intentional")
+  private void gc() {
+    System.gc();
+  }
+
   @VisibleForTesting
   public void waitForWaiters(long id, int numWaiters) throws InterruptedException {
     for (ReentrantReadWriteLock readWriteLock;;) {

hbase-server/src/main/java/org/apache/hadoop/hbase/util/MetaUtils.java

@@ -104,11 +104,8 @@ public class MetaUtils {
    * @return HRegion for meta region
    * @throws IOException e
    */
-  public HRegion getMetaRegion() throws IOException {
+  public synchronized HRegion getMetaRegion() throws IOException {
-    if (this.metaRegion == null) {
+    return this.metaRegion == null? openMetaRegion(): this.metaRegion;
-      openMetaRegion();
-    }
-    return this.metaRegion;
   }
 
   /**

hbase-server/src/main/java/org/apache/hadoop/hbase/util/RegionMover.java

@@ -455,9 +455,11 @@ public class RegionMover extends AbstractHBaseTool {
     }
   }
 
+  @edu.umd.cs.findbugs.annotations.SuppressWarnings(value="DLS_DEAD_LOCAL_STORE",
+      justification="FB is wrong; its size is read")
   private void unloadRegions(Admin admin, String server, ArrayList<String> regionServers,
       boolean ack, List<HRegionInfo> movedRegions) throws Exception {
-    List<HRegionInfo> regionsToMove = new ArrayList<HRegionInfo>();
+    List<HRegionInfo> regionsToMove = new ArrayList<HRegionInfo>();// FindBugs: DLS_DEAD_LOCAL_STORE
     regionsToMove = getRegions(this.conf, server);
     if (regionsToMove.size() == 0) {
       LOG.info("No Regions to move....Quitting now");
@@ -597,7 +599,7 @@ public class RegionMover extends AbstractHBaseTool {
    * Move Regions without Acknowledging.Usefule in case of RS shutdown as we might want to shut the
    * RS down anyways and not abort on a stuck region. Improves movement performance
    */
-  private class MoveWithoutAck implements Callable<Boolean> {
+  private static class MoveWithoutAck implements Callable<Boolean> {
     private Admin admin;
     private HRegionInfo region;
     private String targetServer;
@@ -764,7 +766,7 @@ public class RegionMover extends AbstractHBaseTool {
       try {
         br = new BufferedReader(new FileReader(f));
         while ((line = br.readLine()) != null) {
-          line.trim();
+          line = line.trim();
           if (!line.equals("")) {
             excludeServers.add(line);
           }

hbase-server/src/main/java/org/apache/hadoop/hbase/util/SortedList.java

@@ -46,6 +46,8 @@ import java.util.RandomAccess;
  * <p>
  * Iterators are read-only. They cannot be used to remove elements.
  */
+@edu.umd.cs.findbugs.annotations.SuppressWarnings(value="UG_SYNC_SET_UNSYNC_GET",
+  justification="TODO: synchronization in here needs review!!!")
 public class SortedList<E> implements List<E>, RandomAccess {
   private volatile List<E> list;
   private final Comparator<? super E> comparator;
@@ -80,7 +82,7 @@ public class SortedList<E> implements List<E>, RandomAccess {
    * method to get a reference for iterating over using the RandomAccess
    * pattern.
    */
-  public List<E> get() {
+  public List<E> get() { // FindBugs: UG_SYNC_SET_UNSYNC_GET complaint. Fix!!
     return list;
   }
 
@@ -185,7 +187,7 @@ public class SortedList<E> implements List<E>, RandomAccess {
   }
 
   @Override
-  public E get(int index) {
+  public synchronized E get(int index) {
     return list.get(index);
   }
 

hbase-server/src/test/java/org/apache/hadoop/hbase/master/TestSplitLogManager.java

@@ -345,7 +345,7 @@ public class TestSplitLogManager {
     assertTrue(task == task2);
     LOG.debug("task = " + task);
     assertEquals(1L, tot_mgr_resubmit.get());
-    assertEquals(1, task.incarnation);
+    assertEquals(1, task.incarnation.get());
     assertEquals(0, task.unforcedResubmits.get());
     assertTrue(task.isOrphan());
     assertTrue(task.isUnassigned());