Fully read and write buffers from/into channels

Update places where ByteBuffers were not fully written or read.
Most affected from change set was IdContainer that had both problems
and any of those can potentially cause id file corruption (real or "heisen")

Add additional checks into NativeLabelScanStoreMigrator and CountsMigrator
that will check that stores are in "store ok" state before performing
migration.

community/kernel/src/main/java/org/neo4j/kernel/impl/index/IndexConfigStore.java

@@ -295,7 +295,7 @@ private void write( File file )
         try
         {
             channel = fileSystem.open( file, "rw" );
-            channel.write( ByteBuffer.wrap( MAGICK ) );
+            channel.writeAll( ByteBuffer.wrap( MAGICK ) );
             IoPrimitiveUtils.writeInt( channel, buffer( 4 ), VERSION );
             writeMap( channel, nodeConfig );
             writeMap( channel, relConfig );

community/kernel/src/main/java/org/neo4j/kernel/impl/store/id/IdContainer.java

@@ -137,11 +137,11 @@ private long readAndValidateHeader() throws IOException
     private static long readAndValidate( StoreChannel channel, File fileName ) throws IOException
     {
         ByteBuffer buffer = ByteBuffer.allocate( HEADER_SIZE );
-        int read = channel.read( buffer );
-        if ( read != HEADER_SIZE )
+        int totalBytesRead = readBuffer( channel, buffer );
+        if ( totalBytesRead != HEADER_SIZE )
         {
             throw new InvalidIdGeneratorException(
-                    "Unable to read header, bytes read: " + read );
+                    "Unable to read header, bytes read: " + totalBytesRead );
         }
         buffer.flip();
         byte storageStatus = buffer.get();
@@ -174,7 +174,7 @@ private void markAsSticky() throws IOException
         ByteBuffer buffer = ByteBuffer.allocate( Byte.BYTES );
         buffer.put( STICKY_GENERATOR ).flip();
         fileChannel.position( 0 );
-        fileChannel.write( buffer );
+        fileChannel.writeAll( buffer );
         fileChannel.force( false );
     }
 
@@ -184,7 +184,7 @@ private void markAsCleanlyClosed(  ) throws IOException
         ByteBuffer buffer = ByteBuffer.allocate( Byte.BYTES );
         buffer.put( CLEAN_GENERATOR ).flip();
         fileChannel.position( 0 );
-        fileChannel.write( buffer );
+        fileChannel.writeAll( buffer );
     }
 
     public void close( long highId )
@@ -218,7 +218,7 @@ private void writeHeader( long highId ) throws IOException
         ByteBuffer buffer = ByteBuffer.allocate( HEADER_SIZE );
         buffer.put( STICKY_GENERATOR ).putLong( highId ).flip();
         fileChannel.position( 0 );
-        fileChannel.write( buffer );
+        fileChannel.writeAll( buffer );
     }
 
     public void delete()
@@ -305,7 +305,7 @@ public static void createEmptyIdFile( FileSystemAbstraction fs, File file, long
             channel.truncate( 0 );
             ByteBuffer buffer = ByteBuffer.allocate( HEADER_SIZE );
             buffer.put( CLEAN_GENERATOR ).putLong( highId ).flip();
-            channel.write( buffer );
+            channel.writeAll( buffer );
             channel.force( false );
         }
         catch ( IOException e )
@@ -314,6 +314,22 @@ public static void createEmptyIdFile( FileSystemAbstraction fs, File file, long
         }
     }
 
+    private static int readBuffer( StoreChannel channel, ByteBuffer buffer ) throws IOException
+    {
+        int totalBytesRead = 0;
+        int currentBytesRead;
+        do
+        {
+            currentBytesRead = channel.read( buffer );
+            if ( currentBytesRead > 0 )
+            {
+                totalBytesRead += currentBytesRead;
+            }
+        }
+        while ( buffer.hasRemaining() && currentBytesRead >= 0 );
+        return totalBytesRead;
+    }
+
     @Override
     public String toString()
     {

community/kernel/src/main/java/org/neo4j/kernel/impl/storemigration/participant/CountsMigrator.java

@@ -163,6 +163,7 @@ private void rebuildCountsFromScratch( File storeDirToReadFrom, File migrationDi
                 .openNeoStores( StoreType.NODE, StoreType.RELATIONSHIP, StoreType.LABEL_TOKEN,
                         StoreType.RELATIONSHIP_TYPE_TOKEN ) )
         {
+            neoStores.verifyStoreOk();
             NodeStore nodeStore = neoStores.getNodeStore();
             RelationshipStore relationshipStore = neoStores.getRelationshipStore();
             try ( Lifespan life = new Lifespan() )

community/kernel/src/main/java/org/neo4j/kernel/impl/storemigration/participant/NativeLabelScanStoreMigrator.java

@@ -73,6 +73,7 @@ public void migrate( File storeDir, File migrationDir, MigrationProgressMonitor.
             try ( NeoStores neoStores = storeFactory.openAllNeoStores();
                     Lifespan lifespan = new Lifespan() )
             {
+                neoStores.verifyStoreOk();
                 // Remove any existing file to ensure we always do migration
                 deleteNativeIndexFile( migrationDir );
 

community/kernel/src/main/java/org/neo4j/kernel/impl/transaction/log/entry/LogHeaderWriter.java

@@ -66,7 +66,7 @@ public static void writeLogHeader( StoreChannel channel, long logVersion, long p
     {
         ByteBuffer buffer = ByteBuffer.allocate( LOG_HEADER_SIZE );
         writeLogHeader( buffer, logVersion, previousLastCommittedTxId );
-        channel.write( buffer );
+        channel.writeAll( buffer );
     }
 
     public static long encodeLogVersion( long logVersion )

community/kernel/src/test/java/org/neo4j/kernel/impl/store/id/IdContainerTest.java

@@ -19,13 +19,17 @@
  */
 package org.neo4j.kernel.impl.store.id;
 
-import java.io.File;
-
 import org.junit.Before;
 import org.junit.Rule;
 import org.junit.Test;
 
+import java.io.File;
+import java.io.IOException;
+import java.nio.ByteBuffer;
+
+import org.neo4j.io.fs.DefaultFileSystemAbstraction;
 import org.neo4j.io.fs.FileSystemAbstraction;
+import org.neo4j.io.fs.StoreFileChannel;
 import org.neo4j.kernel.impl.store.InvalidIdGeneratorException;
 import org.neo4j.test.rule.TestDirectory;
 import org.neo4j.test.rule.fs.DefaultFileSystemRule;
@@ -171,8 +175,61 @@ public void shouldReturnTrueOnInitIfAProperFileWasThere() throws Exception
         assertTrue( idContainer.init() );
     }
 
+    @Test
+    public void idContainerReadWriteBySingleByte() throws IOException
+    {
+        SingleByteFileSystemAbstraction fileSystem = new SingleByteFileSystemAbstraction();
+        IdContainer idContainer = new IdContainer( fileSystem, file, 100, false );
+        idContainer.init();
+        idContainer.close( 100 );
+
+        idContainer = new IdContainer( fileSystem, file, 100, false );
+        idContainer.init();
+        assertEquals( 100, idContainer.getInitialHighId() );
+        fileSystem.close();
+    }
+
     private void createEmptyFile()
     {
         IdContainer.createEmptyIdFile( fs, file, 42, false );
     }
+
+    private static class SingleByteFileSystemAbstraction extends DefaultFileSystemAbstraction
+    {
+        @Override
+        public StoreFileChannel open( File fileName, String mode ) throws IOException
+        {
+            return new SingleByteBufferChannel( super.open( fileName, mode ) );
+        }
+    }
+
+    private static class SingleByteBufferChannel extends StoreFileChannel
+    {
+
+        SingleByteBufferChannel( StoreFileChannel channel )
+        {
+            super( channel );
+        }
+
+        @Override
+        public int write( ByteBuffer src ) throws IOException
+        {
+            byte b = src.get();
+            ByteBuffer byteBuffer = ByteBuffer.wrap( new byte[]{b} );
+            return super.write( byteBuffer );
+        }
+
+        @Override
+        public int read( ByteBuffer dst ) throws IOException
+        {
+            ByteBuffer byteBuffer = ByteBuffer.allocate( 1 );
+            int read = super.read( byteBuffer );
+            if ( read > 0 )
+            {
+                byteBuffer.flip();
+                dst.put( byteBuffer.get() );
+            }
+            return read;
+        }
+    }
 }

community/kernel/src/test/java/org/neo4j/kernel/impl/storemigration/participant/NativeLabelScanStoreMigratorTest.java

@@ -43,7 +43,9 @@
 import org.neo4j.kernel.configuration.Config;
 import org.neo4j.kernel.impl.api.scan.FullStoreChangeStream;
 import org.neo4j.kernel.impl.index.labelscan.NativeLabelScanStore;
+import org.neo4j.kernel.impl.store.InvalidIdGeneratorException;
 import org.neo4j.kernel.impl.store.MetaDataStore;
+import org.neo4j.kernel.impl.store.StoreFile;
 import org.neo4j.kernel.impl.store.format.standard.StandardV2_3;
 import org.neo4j.kernel.impl.store.format.standard.StandardV3_2;
 import org.neo4j.kernel.impl.storemigration.monitoring.MigrationProgressMonitor;
@@ -100,7 +102,7 @@ public void setUp() throws Exception
     @Test
     public void skipMigrationIfNativeIndexExist() throws Exception
     {
-        ByteBuffer sourceBuffer = writeNativeIndexFile( nativeLabelIndex, new byte[]{1, 2, 3} );
+        ByteBuffer sourceBuffer = writeFile( nativeLabelIndex, new byte[]{1, 2, 3} );
 
         indexMigrator.migrate( storeDir, migrationDir, progressMonitor, StandardV3_2.STORE_VERSION, StandardV3_2.STORE_VERSION );
         indexMigrator.moveMigratedFiles( migrationDir, storeDir, StandardV3_2.STORE_VERSION, StandardV3_2.STORE_VERSION );
@@ -110,6 +112,16 @@ public void skipMigrationIfNativeIndexExist() throws Exception
         assertTrue( fileSystem.fileExists( luceneLabelScanStore ) );
     }
 
+    @Test( expected = InvalidIdGeneratorException.class )
+    public void failMigrationWhenNodeIdFileIsBroken() throws Exception
+    {
+        prepareEmpty23Database();
+        File nodeIdFile = new File( storeDir, StoreFile.NODE_STORE.storeFileName() + ".id" );
+        writeFile( nodeIdFile, new byte[]{1, 2, 3} );
+
+        indexMigrator.migrate( storeDir, migrationDir, progressMonitor, StandardV3_2.STORE_VERSION, StandardV3_2.STORE_VERSION );
+    }
+
     @Test
     public void clearMigrationDirFromAnyLabelScanStoreBeforeMigrating() throws Exception
     {
@@ -143,7 +155,7 @@ public void moveCreatedNativeLabelIndexBackToStoreDirectory() throws IOException
         prepareEmpty23Database();
         indexMigrator.migrate( storeDir, migrationDir, progressMonitor, StandardV2_3.STORE_VERSION, StandardV3_2.STORE_VERSION );
         File migrationNativeIndex = new File( migrationDir, NativeLabelScanStore.FILE_NAME );
-        ByteBuffer migratedFileContent = writeNativeIndexFile( migrationNativeIndex, new byte[]{5, 4, 3, 2, 1} );
+        ByteBuffer migratedFileContent = writeFile( migrationNativeIndex, new byte[]{5, 4, 3, 2, 1} );
 
         indexMigrator.moveMigratedFiles( migrationDir, storeDir, StandardV2_3.STORE_VERSION, StandardV3_2.STORE_VERSION );
 
@@ -219,7 +231,7 @@ private void assertNoContentInNativeLabelScanStore( File dir )
         }
     }
 
-    private ByteBuffer writeNativeIndexFile( File file, byte[] content ) throws IOException
+    private ByteBuffer writeFile( File file, byte[] content ) throws IOException
     {
         ByteBuffer sourceBuffer = ByteBuffer.wrap( content );
         storeFileContent( file, sourceBuffer );
@@ -271,9 +283,9 @@ private ByteBuffer readFileContent( File nativeLabelIndex, int length ) throws I
         }
     }
 
-    private void storeFileContent( File nativeLabelIndex, ByteBuffer sourceBuffer ) throws IOException
+    private void storeFileContent( File file, ByteBuffer sourceBuffer ) throws IOException
     {
-        try ( StoreChannel storeChannel = fileSystem.create( nativeLabelIndex ) )
+        try ( StoreChannel storeChannel = fileSystem.create( file ) )
         {
             storeChannel.write( sourceBuffer );
         }

community/lucene-index/src/main/java/org/neo4j/kernel/api/impl/index/storage/FailureStorage.java

@@ -70,7 +70,7 @@ public synchronized void reserveForIndex() throws IOException
         File failureFile = failureFile();
         try ( StoreChannel channel = fs.create( failureFile ) )
         {
-            channel.write( ByteBuffer.wrap( new byte[MAX_FAILURE_SIZE] ) );
+            channel.writeAll( ByteBuffer.wrap( new byte[MAX_FAILURE_SIZE] ) );
             channel.force( true );
         }
     }
@@ -120,7 +120,7 @@ public synchronized void storeIndexFailure( String failure ) throws IOException
             channel.position( lengthOf( existingData ) );
 
             byte[] data = UTF8.encode( failure );
-            channel.write( ByteBuffer.wrap( data, 0, Math.min( data.length, MAX_FAILURE_SIZE ) ) );
+            channel.writeAll( ByteBuffer.wrap( data, 0, Math.min( data.length, MAX_FAILURE_SIZE ) ) );
 
             channel.force( true );
             channel.close();