ufal/s3-check-etag (#537)

* Temp commit - upload a file by uploading 50MB parts

* Added uploading the file by parts - for every part is computed checksum and compared with UploadPartResult's ETag. This feature could be enabled or disabled by cfg.

* Undo S3BitStoreService changes

* Fixed checkstyle issues

* Prettify the code

* Changed cfg property to be better understandable and file size is converted into constant.

dspace-api/src/main/java/org/dspace/storage/bitstore/SyncS3BitStoreService.java

@@ -12,12 +12,22 @@
 import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
+import java.io.OutputStream;
 import java.security.DigestInputStream;
 import java.security.MessageDigest;
 import java.security.NoSuchAlgorithmException;
+import java.util.ArrayList;
+import java.util.List;
 
 import com.amazonaws.AmazonClientException;
+import com.amazonaws.services.s3.model.CompleteMultipartUploadRequest;
+import com.amazonaws.services.s3.model.InitiateMultipartUploadRequest;
+import com.amazonaws.services.s3.model.PartETag;
+import com.amazonaws.services.s3.model.UploadPartRequest;
+import com.amazonaws.services.s3.model.UploadPartResult;
 import com.amazonaws.services.s3.transfer.Upload;
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.dspace.content.Bitstream;
@@ -38,6 +48,16 @@ public class SyncS3BitStoreService extends S3BitStoreService {
     private static final Logger log = LogManager.getLogger(SyncS3BitStoreService.class);
     private boolean syncEnabled = false;
 
+    /**
+     * The uploading file is divided into parts and each part is uploaded separately. The size of the part is 50 MB.
+     */
+    private static final long UPLOAD_FILE_PART_SIZE = 50 * 1024 * 1024; // 50 MB
+
+    /**
+     * Upload large file by parts - check the checksum of every part
+     */
+    private boolean uploadByParts = false;
+
     @Autowired(required = true)
     DSBitStoreService dsBitStoreService;
 
@@ -48,9 +68,29 @@ public SyncS3BitStoreService() {
         super();
     }
 
+    /**
+     * Define syncEnabled and uploadByParts in the constructor - this values won't be overridden by the configuration
+     *
+     * @param syncEnabled   if true, the file will be uploaded to the local assetstore
+     * @param uploadByParts if true, the file will be uploaded by parts
+     */
+    public SyncS3BitStoreService(boolean syncEnabled, boolean uploadByParts) {
+        super();
+        this.syncEnabled = syncEnabled;
+        this.uploadByParts = uploadByParts;
+    }
+
     public void init() throws IOException {
         super.init();
-        syncEnabled = configurationService.getBooleanProperty("sync.storage.service.enabled", false);
+
+        // The syncEnabled and uploadByParts could be set to true in the constructor,
+        // do not override them by the configuration in this case
+        if (!syncEnabled) {
+            syncEnabled = configurationService.getBooleanProperty("sync.storage.service.enabled", false);
+        }
+        if (!uploadByParts) {
+            uploadByParts = configurationService.getBooleanProperty("s3.upload.by.parts.enabled", false);
+        }
     }
 
     @Override
@@ -66,9 +106,11 @@ public void put(Bitstream bitstream, InputStream in) throws IOException {
             Utils.bufferedCopy(dis, fos);
             in.close();
 
-            Upload upload = tm.upload(getBucketName(), key, scratchFile);
-
-            upload.waitForUploadResult();
+            if (uploadByParts) {
+                uploadByParts(key, scratchFile);
+            } else {
+                uploadFluently(key, scratchFile);
+            }
 
             bitstream.setSizeBytes(scratchFile.length());
             // we cannot use the S3 ETAG here as it could be not a MD5 in case of multipart upload (large files) or if
@@ -119,6 +161,7 @@ public void remove(Bitstream bitstream) throws IOException {
 
     /**
      * Create a new file in the assetstore if it does not exist
+     *
      * @param localFile
      * @throws IOException
      */
@@ -137,4 +180,116 @@ private void createFileIfNotExist(File localFile) throws IOException {
                     " was not created");
         }
     }
+
+    /**
+     * Upload a file fluently. The file is uploaded in a single request.
+     *
+     * @param key the bitstream's internalId
+     * @param scratchFile the file to upload
+     * @throws InterruptedException if the S3 upload is interrupted
+     */
+    private void uploadFluently(String key, File scratchFile) throws InterruptedException {
+        Upload upload = tm.upload(getBucketName(), key, scratchFile);
+
+        upload.waitForUploadResult();
+    }
+
+    /**
+     * Upload a file by parts. The file is divided into parts and each part is uploaded separately.
+     * The checksum of each part is checked. If the checksum does not match, the file is not uploaded.
+     *
+     * @param key the bitstream's internalId
+     * @param scratchFile the file to upload
+     * @throws IOException if an I/O error occurs
+     */
+    private void uploadByParts(String key, File scratchFile) throws IOException {
+        // Initialize MessageDigest for computing checksum
+        MessageDigest digest;
+        try {
+            digest = MessageDigest.getInstance("MD5");
+        } catch (Exception e) {
+            throw new RuntimeException("MD5 algorithm not available", e);
+        }
+
+        // Initiate multipart upload
+        InitiateMultipartUploadRequest initiateRequest = new InitiateMultipartUploadRequest(getBucketName(), key);
+        String uploadId = this.s3Service.initiateMultipartUpload(initiateRequest).getUploadId();
+
+        // Create a list to hold the ETags for individual parts
+        List<PartETag> partETags = new ArrayList<>();
+
+        try {
+            // Upload parts
+            File file = new File(scratchFile.getPath());
+            long fileLength = file.length();
+            long remainingBytes = fileLength;
+            int partNumber = 1;
+
+            while (remainingBytes > 0) {
+                long bytesToUpload = Math.min(UPLOAD_FILE_PART_SIZE, remainingBytes);
+
+                // Calculate the checksum for the part
+                String partChecksum = calculatePartChecksum(file, fileLength - remainingBytes, bytesToUpload, digest);
+
+                UploadPartRequest uploadRequest = new UploadPartRequest()
+                        .withBucketName(this.getBucketName())
+                        .withKey(key)
+                        .withUploadId(uploadId)
+                        .withPartNumber(partNumber)
+                        .withFile(file)
+                        .withFileOffset(fileLength - remainingBytes)
+                        .withPartSize(bytesToUpload);
+
+                // Upload the part
+                UploadPartResult uploadPartResponse = this.s3Service.uploadPart(uploadRequest);
+
+                // Collect the ETag for the part
+                partETags.add(uploadPartResponse.getPartETag());
+
+                // Compare checksums - local with ETag
+                if (!StringUtils.equals(uploadPartResponse.getETag(), partChecksum)) {
+                    String errorMessage = "Checksums do not match error: The locally computed checksum does " +
+                            "not match with the ETag from the UploadPartResult. Local checksum: " + partChecksum +
+                            ", ETag: " + uploadPartResponse.getETag() + ", partNumber: " + partNumber;
+                    log.error(errorMessage);
+                    throw new IOException(errorMessage);
+                }
+
+                remainingBytes -= bytesToUpload;
+                partNumber++;
+            }
+
+            // Complete the multipart upload
+            CompleteMultipartUploadRequest completeRequest = new CompleteMultipartUploadRequest(this.getBucketName(),
+                    key, uploadId, partETags);
+            this.s3Service.completeMultipartUpload(completeRequest);
+        } catch (AmazonClientException e) {
+            log.error("Cannot upload the file by parts because: ", e);
+        }
+    }
+
+    /**
+     * Calculate the checksum of the specified part of the file (Multipart upload)
+     *
+     * @param file the uploading file
+     * @param offset the offset in the file
+     * @param length the length of the part
+     * @param digest the message digest for computing the checksum
+     * @return the checksum of the part
+     * @throws IOException if an I/O error occurs
+     */
+    public static String calculatePartChecksum(File file, long offset, long length, MessageDigest digest)
+            throws IOException {
+        try (FileInputStream fis = new FileInputStream(file);
+             DigestInputStream dis = new DigestInputStream(fis, digest)) {
+            // Skip to the specified offset
+            fis.skip(offset);
+
+            // Read the specified length
+            IOUtils.copyLarge(dis, OutputStream.nullOutputStream(), 0, length);
+
+            // Convert the digest to a hex string
+            return Utils.toHex(digest.digest());
+        }
+    }
 }

dspace/config/clarin-dspace.cfg

@@ -246,6 +246,8 @@ file.preview.enabled = false
 ### Storage service ###
 # Synchronization is NOT enabled by default
 sync.storage.service.enabled = true
+# Upload large file by parts - check the checksum of every part
+s3.upload.by.parts.enabled = true
 
 
 ### The build version is stored in the specific file ###