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From chir...@apache.org
Subject svn commit: r805550 - in /activemq/trunk/kahadb/src/main/java/org/apache/kahadb: index/BTreeVisitor.java journal/DataFile.java journal/DataFileAccessor.java journal/Journal.java util/ByteSequence.java util/SequenceSet.java
Date Tue, 18 Aug 2009 19:44:22 GMT
Author: chirino
Date: Tue Aug 18 19:44:22 2009
New Revision: 805550

URL: http://svn.apache.org/viewvc?rev=805550&view=rev
Log:
- Journal will now check the data files for data corruption if checkForCorruptionOnStartup
option is enabled.
  - The corrupted journal records can be inspected via DataFile.getCorruptedBlocks()
- An OR and AND BTreeVisitor is now supported to support running more complex queries against
the BTree


Modified:
    activemq/trunk/kahadb/src/main/java/org/apache/kahadb/index/BTreeVisitor.java
    activemq/trunk/kahadb/src/main/java/org/apache/kahadb/journal/DataFile.java
    activemq/trunk/kahadb/src/main/java/org/apache/kahadb/journal/DataFileAccessor.java
    activemq/trunk/kahadb/src/main/java/org/apache/kahadb/journal/Journal.java
    activemq/trunk/kahadb/src/main/java/org/apache/kahadb/util/ByteSequence.java
    activemq/trunk/kahadb/src/main/java/org/apache/kahadb/util/SequenceSet.java

Modified: activemq/trunk/kahadb/src/main/java/org/apache/kahadb/index/BTreeVisitor.java
URL: http://svn.apache.org/viewvc/activemq/trunk/kahadb/src/main/java/org/apache/kahadb/index/BTreeVisitor.java?rev=805550&r1=805549&r2=805550&view=diff
==============================================================================
--- activemq/trunk/kahadb/src/main/java/org/apache/kahadb/index/BTreeVisitor.java (original)
+++ activemq/trunk/kahadb/src/main/java/org/apache/kahadb/index/BTreeVisitor.java Tue Aug
18 19:44:22 2009
@@ -25,7 +25,7 @@
  * @param <Value>
  */
 public interface BTreeVisitor<Key,Value> {
-    
+
     /**
      * Do you want to visit the range of BTree entries between the first and and second key?
      * 
@@ -34,7 +34,7 @@
      * @return true if you want to visit the values between the first and second key.
      */
     boolean isInterestedInKeysBetween(Key first, Key second);
-    
+
     /**
      * The keys and values of a BTree leaf node.
      * 
@@ -42,32 +42,111 @@
      * @param values
      */
     void visit(List<Key> keys, List<Value> values);
-    
-    
-    abstract class GTVisitor<Key extends Comparable<Key>, Value> implements BTreeVisitor<Key,
Value>{
-		final private Key value;
-
-		public GTVisitor(Key value) {
-			this.value = value;
-		}
 
-		public boolean isInterestedInKeysBetween(Key first, Key second) {
-        	return second==null || second.compareTo(value)>0;
-		}
+    public interface Predicate<Key> {
+        boolean isInterestedInKeysBetween(Key first, Key second);
+        boolean isInterestedInKey(Key key);
+    }
 
+    abstract class PredicateVisitor<Key, Value> implements BTreeVisitor<Key, Value>,
Predicate<Key> {
 		public void visit(List<Key> keys, List<Value> values) {
 			for( int i=0; i < keys.size(); i++) {
 				Key key = keys.get(i);
-				if( key.compareTo(value)>0 ) {
+				if( isInterestedInKey(key) ) {
 					matched(key, values.get(i));
 				}
 			}
 		}
 
-		abstract protected void matched(Key key, Value value);
+		protected void matched(Key key, Value value) {
+        }
     }
-    
-    abstract class BetweenVisitor<Key extends Comparable<Key>, Value> implements
BTreeVisitor<Key, Value>{
+
+    class OrVisitor<Key, Value> extends PredicateVisitor<Key, Value> {
+        private final List<Predicate<Key>> conditions;
+
+        public OrVisitor(List<Predicate<Key>> conditions) {
+            this.conditions = conditions;
+        }
+
+		public boolean isInterestedInKeysBetween(Key first, Key second) {
+            for (Predicate<Key> condition : conditions) {
+                if( condition.isInterestedInKeysBetween(first, second) ) {
+                    return true;
+                }
+            }
+            return false;
+		}
+
+        public boolean isInterestedInKey(Key key) {
+            for (Predicate<Key> condition : conditions) {
+                if( condition.isInterestedInKey(key) ) {
+                    return true;
+                }
+            }
+            return false;
+        }
+
+        @Override
+        public String toString() {
+            StringBuilder sb = new StringBuilder();
+            boolean first=true;
+            for (Predicate<Key> condition : conditions) {
+                if( !first ) {
+                    sb.append(" OR ");
+                }
+                first=false;
+                sb.append("(");
+                sb.append(condition);
+                sb.append(")");
+            }
+            return sb.toString();
+        }
+    }
+
+    class AndVisitor<Key, Value> extends PredicateVisitor<Key, Value> {
+        private final List<Predicate<Key>> conditions;
+
+        public AndVisitor(List<Predicate<Key>> conditions) {
+            this.conditions = conditions;
+        }
+
+		public boolean isInterestedInKeysBetween(Key first, Key second) {
+            for (Predicate<Key> condition : conditions) {
+                if( !condition.isInterestedInKeysBetween(first, second) ) {
+                    return false;
+                }
+            }
+            return true;
+		}
+
+        public boolean isInterestedInKey(Key key) {
+            for (Predicate<Key> condition : conditions) {
+                if( !condition.isInterestedInKey(key) ) {
+                    return false;
+                }
+            }
+            return true;
+        }
+
+        @Override
+        public String toString() {
+            StringBuilder sb = new StringBuilder();
+            boolean first=true;
+            for (Predicate<Key> condition : conditions) {
+                if( !first ) {
+                    sb.append(" AND ");
+                }
+                first=false;
+                sb.append("(");
+                sb.append(condition);
+                sb.append(")");
+            }
+            return sb.toString();
+        }
+    }
+
+    class BetweenVisitor<Key extends Comparable<Key>, Value> extends PredicateVisitor<Key,
Value> {
 		private final Key first;
         private final Key last;
 
@@ -81,19 +160,38 @@
                    && (first==null || first.compareTo(last)<0);
 		}
 
-		public void visit(List<Key> keys, List<Value> values) {
-			for( int i=0; i < keys.size(); i++) {
-				Key key = keys.get(i);
-				if( key.compareTo(first)>=0 && key.compareTo(last)<0 ) {
-					matched(key, values.get(i));
-				}
-			}
+        public boolean isInterestedInKey(Key key) {
+            return key.compareTo(first) >=0 && key.compareTo(last) <0;
+        }
+
+        @Override
+        public String toString() {
+            return first+" <= key < "+last;
+        }
+    }
+
+    class GTVisitor<Key extends Comparable<Key>, Value> extends PredicateVisitor<Key,
Value> {
+		final private Key value;
+
+		public GTVisitor(Key value) {
+			this.value = value;
+		}
+
+		public boolean isInterestedInKeysBetween(Key first, Key second) {
+        	return second==null || second.compareTo(value)>0;
 		}
 
-		abstract protected void matched(Key key, Value value);
+        public boolean isInterestedInKey(Key key) {
+            return key.compareTo(value)>0;
+        }
+
+        @Override
+        public String toString() {
+            return "key > "+ value;
+        }
     }
 
-    abstract class GTEVisitor<Key extends Comparable<Key>, Value> implements
BTreeVisitor<Key, Value>{
+    class GTEVisitor<Key extends Comparable<Key>, Value> extends PredicateVisitor<Key,
Value> {
 		final private Key value;
 
 		public GTEVisitor(Key value) {
@@ -104,19 +202,17 @@
         	return second==null || second.compareTo(value)>=0;
 		}
 
-		public void visit(List<Key> keys, List<Value> values) {
-			for( int i=0; i < keys.size(); i++) {
-				Key key = keys.get(i);
-				if( key.compareTo(value)>=0 ) {
-					matched(key, values.get(i));
-				}
-			}
-		}
+        public boolean isInterestedInKey(Key key) {
+            return key.compareTo(value)>=0;
+        }
 
-		abstract protected void matched(Key key, Value value);
+        @Override
+        public String toString() {
+            return "key >= "+ value;
+        }
     }
     
-    abstract class LTVisitor<Key extends Comparable<Key>, Value> implements BTreeVisitor<Key,
Value>{
+    class LTVisitor<Key extends Comparable<Key>, Value> extends PredicateVisitor<Key,
Value> {
 		final private Key value;
 
 		public LTVisitor(Key value) {
@@ -127,19 +223,17 @@
         	return first==null || first.compareTo(value)<0;
 		}
 
-		public void visit(List<Key> keys, List<Value> values) {
-			for( int i=0; i < keys.size(); i++) {
-				Key key = keys.get(i);
-				if( key.compareTo(value)<0 ) {
-					matched(key, values.get(i));
-				}
-			}
-		}
+        public boolean isInterestedInKey(Key key) {
+            return key.compareTo(value)<0;
+        }
 
-		abstract protected void matched(Key key, Value value);
+        @Override
+        public String toString() {
+            return "key < "+ value;
+        }
     }
     
-    abstract class LTEVisitor<Key extends Comparable<Key>, Value> implements
BTreeVisitor<Key, Value>{
+    class LTEVisitor<Key extends Comparable<Key>, Value> extends PredicateVisitor<Key,
Value> {
 		final private Key value;
 
 		public LTEVisitor(Key value) {
@@ -150,15 +244,13 @@
         	return first==null || first.compareTo(value)<=0;
 		}
 
-		public void visit(List<Key> keys, List<Value> values) {
-			for( int i=0; i < keys.size(); i++) {
-				Key key = keys.get(i);
-				if( key.compareTo(value)<=0 ) {
-					matched(key, values.get(i));
-				}
-			}
-		}
+        public boolean isInterestedInKey(Key key) {
+            return key.compareTo(value)<=0;
+        }
 
-		abstract protected void matched(Key key, Value value);
+        @Override
+        public String toString() {
+            return "key <= "+ value;
+        }
     }
 }
\ No newline at end of file

Modified: activemq/trunk/kahadb/src/main/java/org/apache/kahadb/journal/DataFile.java
URL: http://svn.apache.org/viewvc/activemq/trunk/kahadb/src/main/java/org/apache/kahadb/journal/DataFile.java?rev=805550&r1=805549&r2=805550&view=diff
==============================================================================
--- activemq/trunk/kahadb/src/main/java/org/apache/kahadb/journal/DataFile.java (original)
+++ activemq/trunk/kahadb/src/main/java/org/apache/kahadb/journal/DataFile.java Tue Aug 18
19:44:22 2009
@@ -22,6 +22,7 @@
 
 import org.apache.kahadb.util.IOHelper;
 import org.apache.kahadb.util.LinkedNode;
+import org.apache.kahadb.util.SequenceSet;
 
 /**
  * DataFile
@@ -33,6 +34,7 @@
     protected final File file;
     protected final Integer dataFileId;
     protected int length;
+    protected final SequenceSet corruptedBlocks = new SequenceSet();
 
     DataFile(File file, int number, int preferedSize) {
         this.file = file;
@@ -80,6 +82,10 @@
         IOHelper.moveFile(file,targetDirectory);
     }
 
+    public SequenceSet getCorruptedBlocks() {
+        return corruptedBlocks;
+    }
+    
     public int compareTo(DataFile df) {
         return dataFileId - df.dataFileId;
     }

Modified: activemq/trunk/kahadb/src/main/java/org/apache/kahadb/journal/DataFileAccessor.java
URL: http://svn.apache.org/viewvc/activemq/trunk/kahadb/src/main/java/org/apache/kahadb/journal/DataFileAccessor.java?rev=805550&r1=805549&r2=805550&view=diff
==============================================================================
--- activemq/trunk/kahadb/src/main/java/org/apache/kahadb/journal/DataFileAccessor.java (original)
+++ activemq/trunk/kahadb/src/main/java/org/apache/kahadb/journal/DataFileAccessor.java Tue
Aug 18 19:44:22 2009
@@ -95,11 +95,16 @@
         }
     }
     
-    public void read(long offset, byte data[]) throws IOException {
+    public void readFully(long offset, byte data[]) throws IOException {
        file.seek(offset);
        file.readFully(data);
     }
 
+    public int read(long offset, byte data[]) throws IOException {
+       file.seek(offset);
+       return file.read(data);
+    }
+
     public void readLocationDetails(Location location) throws IOException {
         WriteCommand asyncWrite = (WriteCommand)inflightWrites.get(new WriteKey(location));
         if (asyncWrite != null) {

Modified: activemq/trunk/kahadb/src/main/java/org/apache/kahadb/journal/Journal.java
URL: http://svn.apache.org/viewvc/activemq/trunk/kahadb/src/main/java/org/apache/kahadb/journal/Journal.java?rev=805550&r1=805549&r2=805550&view=diff
==============================================================================
--- activemq/trunk/kahadb/src/main/java/org/apache/kahadb/journal/Journal.java (original)
+++ activemq/trunk/kahadb/src/main/java/org/apache/kahadb/journal/Journal.java Tue Aug 18
19:44:22 2009
@@ -20,15 +20,7 @@
 import java.io.FilenameFilter;
 import java.io.IOException;
 import java.io.UnsupportedEncodingException;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.TreeMap;
+import java.util.*;
 import java.util.concurrent.ConcurrentHashMap;
 import java.util.concurrent.atomic.AtomicLong;
 import java.util.concurrent.atomic.AtomicReference;
@@ -39,10 +31,7 @@
 import org.apache.commons.logging.LogFactory;
 import org.apache.kahadb.journal.DataFileAppender.WriteCommand;
 import org.apache.kahadb.journal.DataFileAppender.WriteKey;
-import org.apache.kahadb.util.ByteSequence;
-import org.apache.kahadb.util.DataByteArrayInputStream;
-import org.apache.kahadb.util.LinkedNodeList;
-import org.apache.kahadb.util.Scheduler;
+import org.apache.kahadb.util.*;
 
 /**
  * Manages DataFiles
@@ -61,7 +50,22 @@
     // Batch Control Item holds a 4 byte size of the batch and a 8 byte checksum of the batch.

     public static final byte[] BATCH_CONTROL_RECORD_MAGIC = bytes("WRITE BATCH");
     public static final int BATCH_CONTROL_RECORD_SIZE = RECORD_HEAD_SPACE+BATCH_CONTROL_RECORD_MAGIC.length+4+8;
-    
+    public static final byte[] BATCH_CONTROL_RECORD_HEADER = createBatchControlRecordHeader();
+
+    private static byte[] createBatchControlRecordHeader() {
+        try {
+            DataByteArrayOutputStream os = new DataByteArrayOutputStream();
+            os.writeInt(BATCH_CONTROL_RECORD_SIZE);
+            os.writeByte(BATCH_CONTROL_RECORD_TYPE);
+            os.write(BATCH_CONTROL_RECORD_MAGIC);
+            ByteSequence sequence = os.toByteSequence();
+            sequence.compact();
+            return sequence.getData();
+        } catch (IOException e) {
+            throw new RuntimeException("Could not create batch control record header.");
+        }
+    }
+
     public static final String DEFAULT_DIRECTORY = ".";
     public static final String DEFAULT_ARCHIVE_DIRECTORY = "data-archive";
     public static final String DEFAULT_FILE_PREFIX = "db-";
@@ -96,6 +100,7 @@
     protected boolean archiveDataLogs;
 	private ReplicationTarget replicationTarget;
     protected boolean checksum;
+    protected boolean checkForCorruptionOnStartup;
 
     public synchronized void start() throws IOException {
         if (started) {
@@ -137,17 +142,20 @@
             for (DataFile df : l) {
                 dataFiles.addLast(df);
                 fileByFileMap.put(df.getFile(), df);
+
+                if( isCheckForCorruptionOnStartup() ) {
+                    lastAppendLocation.set(recoveryCheck(df));
+                }
             }
         }
 
     	getCurrentWriteFile();
-        try {
-        	Location l = recoveryCheck(dataFiles.getTail());
-            lastAppendLocation.set(l);
-        } catch (IOException e) {
-            LOG.warn("recovery check failed", e);
+
+        if( lastAppendLocation.get()==null ) {
+            DataFile df = dataFiles.getTail();
+            lastAppendLocation.set(recoveryCheck(df));
         }
-        
+
         cleanupTask = new Runnable() {
             public void run() {
                 cleanup();
@@ -177,56 +185,108 @@
     	DataFileAccessor reader = accessorPool.openDataFileAccessor(dataFile);
         try {
             while( true ) {
-	        	reader.read(location.getOffset(), controlRecord);
-	        	controlIs.restart();
-	        	
-	        	// Assert that it's  a batch record.
-	        	if( controlIs.readInt() != BATCH_CONTROL_RECORD_SIZE ) {
-	        		break;
-	        	}
-	        	if( controlIs.readByte() != BATCH_CONTROL_RECORD_TYPE ) {
-	        		break;
-	        	}
-	        	for( int i=0; i < BATCH_CONTROL_RECORD_MAGIC.length; i++ ) {
-	        		if( controlIs.readByte() != BATCH_CONTROL_RECORD_MAGIC[i] ) {
-	        			break;
-	        		}
-	        	}
-	        	
-	        	int size = controlIs.readInt();
-	        	if( size > MAX_BATCH_SIZE ) {
-	        		break;
-	        	}
-	        	
-	        	if( isChecksum() ) {
-		        	
-	        		long expectedChecksum = controlIs.readLong();	        	
-		        	
-	        		byte data[] = new byte[size];
-		        	reader.read(location.getOffset()+BATCH_CONTROL_RECORD_SIZE, data);
-		        	
-		        	Checksum checksum = new Adler32();
-	                checksum.update(data, 0, data.length);
-	                
-	                if( expectedChecksum!=checksum.getValue() ) {
-	                	break;
-	                }
-	                
-	        	}
-                
-	        	
-                location.setOffset(location.getOffset()+BATCH_CONTROL_RECORD_SIZE+size);
+                int size = checkBatchRecord(reader, location.getOffset());
+                if ( size>=0 ) {
+                    location.setOffset(location.getOffset()+BATCH_CONTROL_RECORD_SIZE+size);
+                } else {
+
+                    // Perhaps it's just some corruption... scan through the file to find
the next valid batch record.  We
+                    // may have subsequent valid batch records.
+                    int nextOffset = findNextBatchRecord(reader, location.getOffset()+1);
+                    if( nextOffset >=0 ) {
+                        Sequence sequence = new Sequence(location.getOffset(), nextOffset
- 1);
+                        LOG.info("Corrupt journal records found in '"+dataFile.getFile()+"'
between offsets: "+sequence);
+                        dataFile.corruptedBlocks.add(sequence);
+                        location.setOffset(nextOffset);
+                    } else {
+                        break;
+                    }
+                }
             }
             
         } catch (IOException e) {
 		} finally {
             accessorPool.closeDataFileAccessor(reader);
         }
-        
+
         dataFile.setLength(location.getOffset());
+
+        if( !dataFile.corruptedBlocks.isEmpty() ) {
+            // Is the end of the data file corrupted?
+            if( dataFile.corruptedBlocks.getTail().getLast()+1 == location.getOffset() )
{
+                dataFile.setLength((int) dataFile.corruptedBlocks.removeLastSequence().getFirst());
+            }
+        }
+
         return location;
     }
 
+    private int findNextBatchRecord(DataFileAccessor reader, int offset) throws IOException
{
+        ByteSequence header = new ByteSequence(BATCH_CONTROL_RECORD_HEADER);
+        byte data[] = new byte[1024*4];
+        ByteSequence bs = new ByteSequence(data, 0, reader.read(offset, data));
+
+        int pos = 0;
+        while( true ) {
+            pos = bs.indexOf(header, pos);
+            if( pos >= 0 ) {
+                return offset+pos;
+            } else {
+                // need to load the next data chunck in..
+                if( bs.length != data.length ) {
+                    // If we had a short read then we were at EOF
+                    return -1;
+                }
+                offset += bs.length-BATCH_CONTROL_RECORD_HEADER.length;
+                bs = new ByteSequence(data, 0, reader.read(offset, data));
+                pos=0;
+            }
+        }
+    }
+
+
+    public int checkBatchRecord(DataFileAccessor reader, int offset) throws IOException {
+        byte controlRecord[] = new byte[BATCH_CONTROL_RECORD_SIZE];
+        DataByteArrayInputStream controlIs = new DataByteArrayInputStream(controlRecord);
+
+        reader.readFully(offset, controlRecord);
+
+        // Assert that it's  a batch record.
+        for( int i=0; i < BATCH_CONTROL_RECORD_HEADER.length; i++ ) {
+            if( controlIs.readByte() != BATCH_CONTROL_RECORD_HEADER[i] ) {
+                return -1;
+            }
+        }
+
+        int size = controlIs.readInt();
+        if( size > MAX_BATCH_SIZE ) {
+            return -1;
+        }
+
+        if( isChecksum() ) {
+
+            long expectedChecksum = controlIs.readLong();
+            if( expectedChecksum == 0 ) {
+                // Checksuming was not enabled when the record was stored.
+                // we can't validate the record :(
+                return size;
+            }
+
+            byte data[] = new byte[size];
+            reader.readFully(offset+BATCH_CONTROL_RECORD_SIZE, data);
+
+            Checksum checksum = new Adler32();
+            checksum.update(data, 0, data.length);
+
+            if( expectedChecksum!=checksum.getValue() ) {
+                return -1;
+            }
+
+        }
+        return size;
+    }
+
+
 	void addToTotalLength(int size) {
 		totalLength.addAndGet(size);
 	}
@@ -640,5 +700,11 @@
 		this.checksum = checksumWrites;
 	}
 
+    public boolean isCheckForCorruptionOnStartup() {
+        return checkForCorruptionOnStartup;
+    }
 
+    public void setCheckForCorruptionOnStartup(boolean checkForCorruptionOnStartup) {
+        this.checkForCorruptionOnStartup = checkForCorruptionOnStartup;
+    }
 }

Modified: activemq/trunk/kahadb/src/main/java/org/apache/kahadb/util/ByteSequence.java
URL: http://svn.apache.org/viewvc/activemq/trunk/kahadb/src/main/java/org/apache/kahadb/util/ByteSequence.java?rev=805550&r1=805549&r2=805550&view=diff
==============================================================================
--- activemq/trunk/kahadb/src/main/java/org/apache/kahadb/util/ByteSequence.java (original)
+++ activemq/trunk/kahadb/src/main/java/org/apache/kahadb/util/ByteSequence.java Tue Aug 18
19:44:22 2009
@@ -71,4 +71,35 @@
         }
     }
 
+    public int indexOf(ByteSequence needle, int pos) {
+        int max = length - needle.length;
+        for (int i = pos; i < max; i++) {
+            if (matches(needle, i)) {
+                return i;
+            }
+        }
+        return -1;
+    }
+
+    private boolean matches(ByteSequence needle, int pos) {
+        for (int i = 0; i < needle.length; i++) {
+            if( data[offset + pos+ i] != needle.data[needle.offset + i] ) {
+                return false;
+            }
+        }
+        return true;
+    }
+
+    private byte getByte(int i) {
+        return data[offset+i];
+    }
+
+    final public int indexOf(byte value, int pos) {
+        for (int i = pos; i < length; i++) {
+            if (data[offset + i] == value) {
+                return i;
+            }
+        }
+        return -1;
+    }
 }

Modified: activemq/trunk/kahadb/src/main/java/org/apache/kahadb/util/SequenceSet.java
URL: http://svn.apache.org/viewvc/activemq/trunk/kahadb/src/main/java/org/apache/kahadb/util/SequenceSet.java?rev=805550&r1=805549&r2=805550&view=diff
==============================================================================
--- activemq/trunk/kahadb/src/main/java/org/apache/kahadb/util/SequenceSet.java (original)
+++ activemq/trunk/kahadb/src/main/java/org/apache/kahadb/util/SequenceSet.java Tue Aug 18
19:44:22 2009
@@ -175,7 +175,18 @@
         Sequence rc = removeFirstSequence(1);
         return rc.first;
     }
-    
+
+
+    public Sequence removeLastSequence() {
+        if (isEmpty()) {
+            return null;
+        }
+
+        Sequence rc = getTail();
+        rc.unlink();
+        return rc;
+    }
+
     /**
      * Removes and returns the first sequence that is count range large.
      *



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