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package eu.dnetlib.data.objectstore.s3;
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import com.amazonaws.ClientConfiguration;
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import com.amazonaws.Protocol;
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import com.amazonaws.auth.AWSCredentials;
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import com.amazonaws.auth.AWSStaticCredentialsProvider;
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import com.amazonaws.auth.BasicAWSCredentials;
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import com.amazonaws.client.builder.AwsClientBuilder;
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import com.amazonaws.services.s3.AmazonS3;
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import com.amazonaws.services.s3.AmazonS3ClientBuilder;
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import com.amazonaws.services.s3.model.ListObjectsV2Request;
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import com.amazonaws.services.s3.model.ListObjectsV2Result;
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import com.amazonaws.services.s3.model.S3Object;
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import com.amazonaws.services.s3.model.S3ObjectSummary;
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import com.google.common.collect.Lists;
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import com.mongodb.client.MongoCollection;
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import com.mongodb.client.model.Filters;
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import eu.dnetlib.data.objectstore.modular.ObjectStoreRecord;
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import eu.dnetlib.data.objectstore.modular.connector.ObjectStore;
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import eu.dnetlib.data.objectstore.rmi.MetadataObjectRecord;
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import eu.dnetlib.data.objectstore.rmi.ObjectStoreFile;
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import eu.dnetlib.data.objectstore.rmi.ObjectStoreServiceException;
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import eu.dnetlib.enabling.resultset.ResultSetListener;
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import org.apache.commons.lang3.exception.ExceptionUtils;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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import org.bson.Document;
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import java.io.ByteArrayInputStream;
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import java.io.IOException;
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import java.io.InputStream;
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import java.nio.file.Files;
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import java.nio.file.Path;
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import java.nio.file.Paths;
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import java.nio.file.StandardCopyOption;
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import java.util.UUID;
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import java.util.concurrent.atomic.AtomicInteger;
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import java.util.regex.Pattern;
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public class S3ObjectStore implements ObjectStore {
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//CONSTANT VARIABLE NAME
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private static final String S3_REGION = "eu-west-3";
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private static final String URI_FIELD = "uri";
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private static final String ID_FIELD = "id";
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private static final String MIME_FIELD = "mime";
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private static final String ORIGINAL_OBJECT_FIELD = "originalObject";
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private static final String TIMESTAMP_FIELD = "timestamp";
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private static final String MD5_FIELD = "md5Sum";
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private static final String SIZE_FIELD = "size";
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private final String id;
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private final String interpretation;
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private final String s3AccessKey;
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private final String s3SecretKey;
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private final String s3EndPoint;
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private final String objectStoreBucket;
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private final String basePath;
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private final MongoCollection<Document> mongoCollection;
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// private AmazonS3 client;
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private static final Log log = LogFactory.getLog(S3ObjectStore.class);
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public S3ObjectStore(final String identifier, final String interpretation, final String s3AccessKey, final String s3SecretKey, final String s3EndPoint, final String objectStoreBucket, final MongoCollection<Document> mongoCollection, final String basePath) throws ObjectStoreServiceException {
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this.id = identifier;
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this.interpretation = interpretation;
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this.s3AccessKey = s3AccessKey;
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this.s3SecretKey = s3SecretKey;
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this.mongoCollection = mongoCollection;
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this.s3EndPoint = s3EndPoint;
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this.objectStoreBucket = objectStoreBucket;
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this.basePath = basePath;
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}
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private AmazonS3 initializeClient() throws ObjectStoreServiceException {
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try {
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final AWSCredentials credentials = new BasicAWSCredentials(this.s3AccessKey, this.s3SecretKey);
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final ClientConfiguration cfg = new ClientConfiguration().withProtocol(Protocol.HTTPS);
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final AmazonS3 s3 = AmazonS3ClientBuilder.standard().withCredentials(new AWSStaticCredentialsProvider(credentials))
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.withClientConfiguration(cfg)
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.withEndpointConfiguration(new AwsClientBuilder.EndpointConfiguration(this.s3EndPoint, S3_REGION))
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.build();
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if (s3 == null)
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throw new ObjectStoreServiceException("Cannot initialize s3 client because is NULL");
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return s3;
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} catch (Throwable e) {
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log.error("An Error happen on initialize client ", e);
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throw new ObjectStoreServiceException("Cannot initialize s3 client", e);
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}
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}
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@Override
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public String getId() {
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return this.id;
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}
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@Override
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public String getInterpretation() {
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return this.interpretation;
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}
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@Override
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public int feed(Iterable<ObjectStoreRecord> iterable, boolean upsert) throws ObjectStoreServiceException {
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final AtomicInteger count = new AtomicInteger();
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iterable.forEach(objectStoreRecord -> {
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try {
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feedObjectRecord(objectStoreRecord);
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count.incrementAndGet();
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} catch (ObjectStoreServiceException e) {
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log.error("Error on saving file in a temporary Folder");
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}
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});
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return count.intValue();
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}
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@Override
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public int feedMetadataRecord(Iterable<MetadataObjectRecord> iterable, boolean b) throws ObjectStoreServiceException {
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final AtomicInteger count = new AtomicInteger();
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iterable.forEach(mor -> {
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final ObjectStoreRecord r = new ObjectStoreRecord();
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r.setInputStream(new ByteArrayInputStream(mor.getRecord().getBytes()));
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final ObjectStoreFile fileMetadata = new ObjectStoreFile();
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fileMetadata.setObjectID(mor.getId());
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fileMetadata.setMimeType(mor.getMime());
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r.setFileMetadata(fileMetadata);
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try {
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feedObjectRecord(r);
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count.incrementAndGet();
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} catch (ObjectStoreServiceException e) {
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log.error("Unable to store record r", e);
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}
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});
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return count.intValue();
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}
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@Override
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public String feedObjectRecord(ObjectStoreRecord objectStoreRecord) throws ObjectStoreServiceException {
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final AmazonS3 client = initializeClient();
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try {
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long start = System.currentTimeMillis();
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final Path result = saveAndGenerateMD5(objectStoreRecord.getInputStream(), basePath);
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log.debug("Total time to download into fileSystem " + (System.currentTimeMillis() - start));
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if (result!= null) {
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log.debug("Saving object with ID: " + objectStoreRecord.getFileMetadata().getObjectID() + " on s3 ");
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client.putObject(objectStoreBucket, id + "/" + objectStoreRecord.getFileMetadata().getObjectID(), result.toFile());
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log.debug("Total time to put into the ObjectStore " + (System.currentTimeMillis() - start));
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log.debug("Deleting file");
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boolean deleteSuccess = Files.deleteIfExists(result);
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log.debug("Temporary file deleting success " + deleteSuccess);
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log.debug("Saved object on s3 ");
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final S3Object s3Object = client.getObject(objectStoreBucket ,id+ "/" + objectStoreRecord.getFileMetadata().getObjectID());
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double timestamp = System.currentTimeMillis();
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Document metadata = new Document()
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.append(ID_FIELD, objectStoreRecord.getFileMetadata().getObjectID())
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.append(MIME_FIELD, objectStoreRecord.getFileMetadata().getMimeType())
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.append(ORIGINAL_OBJECT_FIELD, objectStoreRecord.getFileMetadata().toJSON())
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.append(TIMESTAMP_FIELD, timestamp)
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.append(MD5_FIELD, s3Object.getObjectMetadata().getETag())
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.append(SIZE_FIELD, s3Object.getObjectMetadata().getContentLength())
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.append(URI_FIELD, String.format("s3://%s/%s/%s", objectStoreBucket, id, objectStoreRecord.getFileMetadata().getObjectID()));
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log.debug("saving metadata object to the collection: " + metadata.toString());
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start = System.currentTimeMillis();
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mongoCollection.insertOne(metadata);
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log.debug("Total time to save in Mongo " + (System.currentTimeMillis() - start));
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}
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} catch (Throwable e) {
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log.error("Error on put file in the objectStore", e);
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log.error(ExceptionUtils.getStackTrace(e));
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throw new ObjectStoreServiceException(e);
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}
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return null;
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}
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@Override
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public ResultSetListener deliver(final Long from, final Long until) throws ObjectStoreServiceException {
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S3ObjectStoreResultSetListener resultSet = new S3ObjectStoreResultSetListener();
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resultSet.setMongoCollection(this.mongoCollection);
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resultSet.setObjectStoreID(getId());
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resultSet.setFromDate(from);
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resultSet.setUntilDate(until);
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return resultSet;
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}
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@Override
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public ResultSetListener deliverIds(final Iterable<String> ids) throws ObjectStoreServiceException {
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S3ObjectStoreResultSetListener resultSet = new S3ObjectStoreResultSetListener();
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resultSet.setMongoCollection(this.mongoCollection);
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resultSet.setObjectStoreID(getId());
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resultSet.setRecords(Lists.newArrayList(ids));
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return resultSet;
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}
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@Override
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public ObjectStoreFile deliverObject(String objectId) throws ObjectStoreServiceException {
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Document resultQuery = this.mongoCollection.find(Filters.eq("id", objectId)).first();
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if (resultQuery!= null)
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return ObjectStoreS3Utility.build(resultQuery);
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else return null;
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}
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@Override
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public int getSize() throws ObjectStoreServiceException {
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return (int) this.mongoCollection.count();
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}
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@Override
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public void deleteObject(String objectId) throws ObjectStoreServiceException {
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final Document response =this.mongoCollection.findOneAndDelete(Filters.eq("id", objectId));
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if (response == null)
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throw new ObjectStoreServiceException("Error document not found with objectId: "+objectId);
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final AmazonS3 client = initializeClient();
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client.deleteObject(this.objectStoreBucket, String.format("%s/%s", this.id, response.get(ID_FIELD)));
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}
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@Override
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public String getObject(String objectId) throws ObjectStoreServiceException {
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Document response = this.mongoCollection.find(Filters.eq("id", objectId)).first();
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if (response == null || !response.containsKey(URI_FIELD))
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return null;
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return response.getString(URI_FIELD);
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}
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@Override
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public boolean existIDStartsWith(String startId) throws ObjectStoreServiceException {
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return this.mongoCollection.count(Filters.regex("id", Pattern.compile(startId))) > 0;
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}
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@Override
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public boolean dropContent() throws ObjectStoreServiceException {
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final AmazonS3 client = initializeClient();
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final ListObjectsV2Request req = new ListObjectsV2Request().withBucketName(objectStoreBucket).withPrefix(id);
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ListObjectsV2Result result;
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do {
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result = client.listObjectsV2(req);
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for (S3ObjectSummary objectSummary : result.getObjectSummaries()) {
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log.debug(String.format(" - %s (size: %d)\n", objectSummary.getKey(), objectSummary.getSize()));
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client.deleteObject(objectStoreBucket, objectSummary.getKey());
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log.debug("Object Deleted");
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}
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String token = result.getNextContinuationToken();
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log.debug("Next Continuation Token: " + token);
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req.setContinuationToken(token);
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} while (result.isTruncated());
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this.mongoCollection.drop();
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return true;
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}
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private static Path saveAndGenerateMD5(final InputStream inputStream, final String basePath) throws IOException {
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if (inputStream == null) return null;
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Path tempFile = Paths.get(basePath, UUID.randomUUID().toString());
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log.debug("Temp file On Default Location: " + tempFile.toString());
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long size = 0;
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try {
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Files.copy(inputStream, tempFile, StandardCopyOption.REPLACE_EXISTING);
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} catch (IOException e1) {
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log.error(e1);
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}
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return tempFile;
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}
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}
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