[NO ISSUE][STO] Force Checkpoints/Index Metadata Files to Disk

- user model changes: no
- storage format changes: no
- interface changes: no

Details:
- Ensure the system checkpoint file is forced to disk.
- Ensure index metadata files and checkpoints are forced
  to disk.

Change-Id: I27ab8ed39e23760b514640d77532a1dc24a97992
Reviewed-on: https://asterix-gerrit.ics.uci.edu/c/asterixdb/+/3943
Integration-Tests: Jenkins <jenkins@fulliautomatix.ics.uci.edu>
Tested-by: Jenkins <jenkins@fulliautomatix.ics.uci.edu>
Reviewed-by: Murtadha Hubail <mhubail@apache.org>
Reviewed-by: Michael Blow <mblow@apache.org>
diff --git a/asterixdb/asterix-app/src/main/java/org/apache/asterix/app/nc/IndexCheckpointManager.java b/asterixdb/asterix-app/src/main/java/org/apache/asterix/app/nc/IndexCheckpointManager.java
index 420585a..54647f8 100644
--- a/asterixdb/asterix-app/src/main/java/org/apache/asterix/app/nc/IndexCheckpointManager.java
+++ b/asterixdb/asterix-app/src/main/java/org/apache/asterix/app/nc/IndexCheckpointManager.java
@@ -36,6 +36,7 @@
 import org.apache.asterix.common.utils.StorageConstants;
 import org.apache.hyracks.api.exceptions.HyracksDataException;
 import org.apache.hyracks.util.annotations.ThreadSafe;
+import org.apache.hyracks.util.file.FileUtil;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 
@@ -191,9 +192,7 @@
                 if (checkpointPath.toFile().exists()) {
                     Files.delete(checkpointPath);
                 }
-                try (BufferedWriter writer = Files.newBufferedWriter(checkpointPath)) {
-                    writer.write(checkpoint.asJson());
-                }
+                FileUtil.writeAndForce(checkpointPath, checkpoint.asJson().getBytes());
                 // ensure it was written correctly by reading it
                 read(checkpointPath);
                 return;
diff --git a/asterixdb/asterix-transactions/src/main/java/org/apache/asterix/transaction/management/resource/PersistentLocalResourceRepository.java b/asterixdb/asterix-transactions/src/main/java/org/apache/asterix/transaction/management/resource/PersistentLocalResourceRepository.java
index aef7bbd..9f5300e 100644
--- a/asterixdb/asterix-transactions/src/main/java/org/apache/asterix/transaction/management/resource/PersistentLocalResourceRepository.java
+++ b/asterixdb/asterix-transactions/src/main/java/org/apache/asterix/transaction/management/resource/PersistentLocalResourceRepository.java
@@ -71,6 +71,7 @@
 import org.apache.hyracks.storage.common.ILocalResourceRepository;
 import org.apache.hyracks.storage.common.LocalResource;
 import org.apache.hyracks.util.ExitUtil;
+import org.apache.hyracks.util.file.FileUtil;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 
@@ -194,8 +195,7 @@
         try {
             createResourceFileMask(resourceFile);
             byte[] bytes = OBJECT_MAPPER.writeValueAsBytes(resource.toJson(persistedResourceRegistry));
-            final Path path = Paths.get(resourceFile.getAbsolutePath());
-            Files.write(path, bytes);
+            FileUtil.writeAndForce(Paths.get(resourceFile.getAbsolutePath()), bytes);
             indexCheckpointManagerProvider.get(DatasetResourceReference.of(resource)).init(Long.MIN_VALUE, 0,
                     LSMComponentId.EMPTY_INDEX_LAST_COMPONENT_ID.getMaxId());
             deleteResourceFileMask(resourceFile);
diff --git a/asterixdb/asterix-transactions/src/main/java/org/apache/asterix/transaction/management/service/recovery/AbstractCheckpointManager.java b/asterixdb/asterix-transactions/src/main/java/org/apache/asterix/transaction/management/service/recovery/AbstractCheckpointManager.java
index 81002be..717af81 100644
--- a/asterixdb/asterix-transactions/src/main/java/org/apache/asterix/transaction/management/service/recovery/AbstractCheckpointManager.java
+++ b/asterixdb/asterix-transactions/src/main/java/org/apache/asterix/transaction/management/service/recovery/AbstractCheckpointManager.java
@@ -22,11 +22,11 @@
 import java.io.FilenameFilter;
 import java.io.IOException;
 import java.io.OutputStream;
+import java.io.RandomAccessFile;
 import java.nio.channels.ClosedByInterruptException;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
-import java.nio.file.StandardOpenOption;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
@@ -42,6 +42,8 @@
 import org.apache.asterix.common.utils.StorageConstants;
 import org.apache.hyracks.api.exceptions.HyracksDataException;
 import org.apache.hyracks.api.io.IPersistedResourceRegistry;
+import org.apache.hyracks.api.util.IoUtil;
+import org.apache.hyracks.util.file.FileUtil;
 import org.apache.logging.log4j.Level;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
@@ -172,8 +174,11 @@
         }
         // Write checkpoint file to disk
         try {
+            if (path.toFile().exists()) {
+                IoUtil.delete(path);
+            }
             byte[] bytes = OBJECT_MAPPER.writeValueAsBytes(checkpoint.toJson(persistedResourceRegistry));
-            Files.write(path, bytes, StandardOpenOption.CREATE, StandardOpenOption.TRUNCATE_EXISTING);
+            FileUtil.writeAndForce(path, bytes);
             readCheckpoint(path);
         } catch (IOException e) {
             LOGGER.log(Level.ERROR, "Failed to write checkpoint to disk", e);
diff --git a/hyracks-fullstack/hyracks/hyracks-util/src/main/java/org/apache/hyracks/util/file/FileUtil.java b/hyracks-fullstack/hyracks/hyracks-util/src/main/java/org/apache/hyracks/util/file/FileUtil.java
index 443640a..fe60653 100644
--- a/hyracks-fullstack/hyracks/hyracks-util/src/main/java/org/apache/hyracks/util/file/FileUtil.java
+++ b/hyracks-fullstack/hyracks/hyracks-util/src/main/java/org/apache/hyracks/util/file/FileUtil.java
@@ -20,6 +20,8 @@
 
 import java.io.File;
 import java.io.IOException;
+import java.io.RandomAccessFile;
+import java.nio.file.Path;
 import java.util.regex.Pattern;
 
 import org.apache.commons.io.FileUtils;
@@ -86,4 +88,11 @@
             }
         }
     }
+
+    public static void writeAndForce(Path path, byte[] data) throws IOException {
+        try (RandomAccessFile raf = new RandomAccessFile(path.toFile(), "rw");) {
+            raf.write(data);
+            raf.getChannel().force(true);
+        }
+    }
 }