Merge remote-tracking branch 'origin/dmp-refactoring' into dmp-refactoring

This commit is contained in:
George Kalampokis 2024-02-06 16:20:45 +02:00
commit fbe9683842
14 changed files with 1 additions and 548 deletions

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@ -1,128 +0,0 @@
package eu.eudat.data.old;
import eu.eudat.data.UserEntity;
import eu.eudat.data.converters.DateToUTCConverter;
import eu.eudat.data.old.helpers.EntityBinder;
import eu.eudat.data.old.queryableentity.DataEntity;
import jakarta.persistence.*;
import java.util.Date;
import java.util.List;
import java.util.UUID;
import java.util.stream.Collectors;
@Entity
@Table(name = "\"FileUpload\"")
public class FileUpload implements DataEntity<FileUpload, UUID> {
public enum EntityType {
DATASET, DMP
}
@Id
@Column(name = "\"ID\"", updatable = false, nullable = false, columnDefinition = "BINARY(16)")
private UUID id;
@Column(name = "\"Name\"", nullable = false)
private String name;
@Column(name = "\"FileType\"", nullable = false)
private String fileType;
@Column(name = "\"EntityId\"", nullable = false)
private UUID entityId;
@Enumerated(EnumType.STRING)
@Column(name = "\"EntityType\"", nullable = false)
private EntityType entityType;
@Column(name = "\"CreatedAt\"", nullable = false)
@Convert(converter = DateToUTCConverter.class)
private Date createdAt;
@Column(name = "\"IsDeleted\"", nullable = false)
private Boolean isDeleted;
@ManyToOne(fetch = FetchType.LAZY)
@JoinColumn(name = "\"Creator\"")
private UserEntity creator;
public UUID getId() {
return id;
}
public void setId(UUID id) {
this.id = id;
}
public String getName() {
return name;
}
public void setName(String name) {
this.name = name;
}
public String getFileType() {
return fileType;
}
public void setFileType(String fileType) {
this.fileType = fileType;
}
public UUID getEntityId() {
return entityId;
}
public void setEntityId(UUID entityId) {
this.entityId = entityId;
}
public EntityType getEntityType() {
return entityType;
}
public void setEntityType(EntityType entityType) {
this.entityType = entityType;
}
public Date getCreatedAt() {
return createdAt;
}
public void setCreatedAt(Date createdAt) {
this.createdAt = createdAt;
}
public Boolean getIsDeleted() {
return isDeleted;
}
public void setIsDeleted(Boolean isDeleted) {
this.isDeleted = isDeleted;
}
public UserEntity getCreator() {
return creator;
}
public void setCreator(UserEntity creator) {
this.creator = creator;
}
@Override
public void update(FileUpload file) {
this.name = file.getName();
this.fileType = file.getFileType();
this.entityId = file.getEntityId();
this.entityType = file.getEntityType();
this.createdAt = file.getCreatedAt();
this.isDeleted = file.getIsDeleted();
this.creator = file.getCreator();
}
@Override
public UUID getKeys() {
return this.id;
}
@Override
public FileUpload buildFromTuple(List<Tuple> tuple, List<String> fields, String base) {
String currentBase = base.isEmpty() ? "" : base + ".";
if (fields.contains(currentBase + "id")) this.id = EntityBinder.fromTuple(tuple, currentBase + "id");
// this.creator = tuple.stream().map(x -> new UserEntity().buildFromTuple(tuple, fields , base.isEmpty() ? "creator" : base + "." + "creator")).collect(Collectors.toList()).get(0);
return this;
}
}

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@ -1,12 +0,0 @@
package eu.eudat.data.dao.entities;
import eu.eudat.data.dao.DatabaseAccessLayer;
import eu.eudat.data.old.FileUpload;
import javax.management.InvalidApplicationException;
import java.util.List;
import java.util.UUID;
public interface FileUploadDao extends DatabaseAccessLayer<FileUpload, UUID> {
List<FileUpload> getFileUploads(UUID entityId) throws InvalidApplicationException;
}

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@ -1,57 +0,0 @@
package eu.eudat.data.dao.entities;
import eu.eudat.data.dao.DatabaseAccess;
import eu.eudat.data.dao.databaselayer.service.DatabaseService;
import eu.eudat.data.old.FileUpload;
import eu.eudat.queryable.QueryableList;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;
import javax.management.InvalidApplicationException;
import java.util.List;
import java.util.UUID;
import java.util.concurrent.CompletableFuture;
@Component("FileUploadDao")
public class FileUploadDaoImpl extends DatabaseAccess<FileUpload> implements FileUploadDao {
@Autowired
public FileUploadDaoImpl(DatabaseService<FileUpload> databaseService) {
super(databaseService);
}
@Override
public FileUpload createOrUpdate(FileUpload item) {
return getDatabaseService().createOrUpdate(item, FileUpload.class);
}
//
@Override
public CompletableFuture<FileUpload> createOrUpdateAsync(FileUpload item) {
return CompletableFuture.supplyAsync(() -> this.createOrUpdate(item));
}
@Override
public FileUpload find(UUID id) throws InvalidApplicationException {
return getDatabaseService().getQueryable(FileUpload.class).where((builder, root) -> builder.equal(root.get("id"), id)).getSingle();
}
@Override
public List<FileUpload> getFileUploads(UUID entityId) throws InvalidApplicationException {
return this.getDatabaseService().getQueryable(FileUpload.class).where((builder, root) -> builder.equal(root.get("entityId"), entityId)).toList();
}
@Override
public FileUpload find(UUID id, String hint) {
return null;
}
@Override
public void delete(FileUpload item) {
this.getDatabaseService().delete(item);
}
@Override
public QueryableList<FileUpload> asQueryable() {
return this.getDatabaseService().getQueryable(FileUpload.class);
}
}

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@ -2,7 +2,6 @@ package eu.eudat.data.query.definition;
import eu.eudat.data.dao.criteria.Criteria;
import eu.eudat.queryable.QueryableList;
import eu.eudat.data.old.queryableentity.DataEntity;
/**
* Created by ikalyvas on 3/21/2018.

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@ -1,183 +0,0 @@
package eu.eudat.controllers;
import eu.eudat.authorization.AuthorizationFlags;
import eu.eudat.authorization.Permission;
import eu.eudat.commons.XmlHandlingService;
import eu.eudat.commons.enums.DmpAccessType;
import eu.eudat.commons.enums.FieldType;
import eu.eudat.commons.enums.IsActive;
import eu.eudat.commons.scope.user.UserScope;
import eu.eudat.commons.types.descriptiontemplate.DefinitionEntity;
import eu.eudat.commons.types.descriptiontemplate.FieldEntity;
import eu.eudat.commons.types.descriptiontemplate.fielddata.UploadDataEntity;
import eu.eudat.data.DescriptionEntity;
import eu.eudat.data.DescriptionTemplateEntity;
import eu.eudat.data.DmpEntity;
import eu.eudat.data.old.FileUpload;
import eu.eudat.exceptions.security.UnauthorisedException;
import eu.eudat.logic.managers.DatasetProfileManager;
import eu.eudat.logic.services.ApiContext;
import eu.eudat.logic.services.operations.DatabaseRepository;
import eu.eudat.model.file.FileEnvelope;
import eu.eudat.models.HintedModelFactory;
import eu.eudat.models.data.helpers.responses.ResponseItem;
import eu.eudat.query.DescriptionQuery;
import eu.eudat.query.DescriptionTemplateQuery;
import eu.eudat.query.DmpDescriptionTemplateQuery;
import eu.eudat.query.DmpQuery;
import eu.eudat.types.ApiMessageCode;
import gr.cite.commons.web.authz.service.AuthorizationService;
import gr.cite.tools.data.query.QueryFactory;
import jakarta.transaction.Transactional;
import jakarta.xml.bind.JAXBException;
import org.apache.poi.util.IOUtils;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.core.env.Environment;
import org.springframework.http.HttpHeaders;
import org.springframework.http.HttpStatus;
import org.springframework.http.MediaType;
import org.springframework.http.ResponseEntity;
import org.springframework.util.unit.DataSize;
import org.springframework.web.bind.annotation.*;
import org.springframework.web.multipart.MultipartFile;
import org.xml.sax.SAXException;
import javax.management.InvalidApplicationException;
import javax.xml.parsers.ParserConfigurationException;
import java.io.*;
import java.nio.file.Files;
import java.util.*;
import java.util.concurrent.atomic.AtomicBoolean;
@RestController
@CrossOrigin
@RequestMapping(value = {"/api/file/"})
public class FileController {
private DatasetProfileManager datasetProfileManager;
private final Environment environment;
private DatabaseRepository databaseRepository;
private final AuthorizationService authorizationService;
private final UserScope userScope;
private final QueryFactory queryFactory;
private final XmlHandlingService xmlHandlingService;
@Autowired
public FileController(DatasetProfileManager datasetProfileManager, Environment environment, ApiContext apiContext, AuthorizationService authorizationService, UserScope userScope, QueryFactory queryFactory, XmlHandlingService xmlHandlingService) {
this.datasetProfileManager = datasetProfileManager;
this.environment = environment;
this.databaseRepository = apiContext.getOperationsContext().getDatabaseRepository();
this.authorizationService = authorizationService;
this.userScope = userScope;
this.queryFactory = queryFactory;
this.xmlHandlingService = xmlHandlingService;
}
@RequestMapping(method = RequestMethod.POST, value = {"/upload"})
public ResponseEntity<ResponseItem<String>> upload(
@RequestParam("file") MultipartFile file, @RequestParam("datasetProfileId") String datasetProfileId, @RequestParam("fieldId") String fieldId)
throws IllegalAccessException, IOException, InvalidApplicationException, JAXBException, ParserConfigurationException, InstantiationException, SAXException {
this.authorizationService.authorizeForce(Permission.AdminRole, Permission.ManagerRole, Permission.UserRole);
String uuid = UUID.randomUUID().toString();
DescriptionTemplateEntity descriptionTemplate = this.queryFactory.query(DescriptionTemplateQuery.class).ids(UUID.fromString(datasetProfileId)).authorize(AuthorizationFlags.OwnerOrDmpAssociatedOrPermissionOrPublic).first();
DefinitionEntity definition = descriptionTemplate == null ? null : this.xmlHandlingService.fromXml(DefinitionEntity.class, descriptionTemplate.getDefinition());
AtomicBoolean acceptedFile = new AtomicBoolean(false);
List<FieldEntity> fieldEntities = definition != null ? definition.getFieldById(fieldId).stream().filter(x -> x != null && x.getData() != null && x.getData().getFieldType().equals(FieldType.UPLOAD)).toList() : new ArrayList<>();
fieldEntities.forEach(x-> {
UploadDataEntity uploadDataEntity = (UploadDataEntity)x.getData();
if (DataSize.ofBytes(file.getSize()).equals(DataSize.ofMegabytes(uploadDataEntity.getMaxFileSizeInMB()))) {
acceptedFile.set(true);
}
if(acceptedFile.get() && uploadDataEntity.getTypes() != null && !uploadDataEntity.getTypes().isEmpty()) {
acceptedFile.set(false);
for (UploadDataEntity.UploadDataOptionEntity option: uploadDataEntity.getTypes()) {
if(Objects.equals(file.getContentType(), option.getValue())) {
acceptedFile.set(true);
}
}
}
});
if(!acceptedFile.get()) {
return ResponseEntity.status(HttpStatus.BAD_REQUEST).body(new ResponseItem<String>().status(ApiMessageCode.ERROR_MESSAGE).message("The uploaded file is too large or has an unaccepted type"));
}
File convFile = new File(this.environment.getProperty("temp.temp") + uuid);
convFile.createNewFile();
FileOutputStream fos = new FileOutputStream(convFile);
fos.write(file.getBytes());
fos.close();
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<String>().payload(uuid)
.status(ApiMessageCode.SUCCESS_MESSAGE).message(""));
}
@RequestMapping(method = RequestMethod.POST, value = {"/delete-temp"})
public ResponseEntity<ResponseItem<String>> upload(@RequestBody String filename) throws IllegalAccessException, IOException {
File convFile = new File(this.environment.getProperty("temp.temp") + filename);
// Boolean deleted = convFile.delete();
Boolean deleted = Files.deleteIfExists(convFile.toPath());
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<String>().payload(deleted.toString())
.status(ApiMessageCode.SUCCESS_MESSAGE).message(""));
}
@Transactional
@RequestMapping(method = RequestMethod.GET, value = {"{id}"}, produces = "application/json")
public @ResponseBody
ResponseEntity download(@PathVariable String id) throws IOException, InvalidApplicationException {
this.authorizationService.authorizeForce(Permission.AdminRole, Permission.ManagerRole, Permission.UserRole, Permission.AnonymousRole);
FileUpload fileUpload = databaseRepository.getFileUploadDao().find(UUID.fromString(id));
if(fileUpload == null) {
throw new NoSuchElementException("File with id "+id+" not found");
}
if(fileUpload.getEntityType().name().equals(FileUpload.EntityType.DATASET.name())) {
DescriptionEntity descriptionEntityEntity = this.queryFactory.query(DescriptionQuery.class).ids(fileUpload.getEntityId()).first();
if (descriptionEntityEntity == null) {
throw new NoSuchElementException("No dataset with id " + fileUpload.getEntityId() + " found. This dataset was related to the file with id " + id);
}
DmpEntity dmp = this.queryFactory.query(DmpQuery.class).ids(this.queryFactory.query(DmpDescriptionTemplateQuery.class).ids(descriptionEntityEntity.getDmpDescriptionTemplateId()).isActive(IsActive.Active).first().getDmpId()).first();
if (!dmp.getAccessType().equals(DmpAccessType.Public)
//TODO
// && dmp.getUsers()
// .stream().filter(userInfo -> this.userScope.getUserIdSafe().equals(userInfo.getUser().getId()))
// .collect(Collectors.toList()).size() == 0
)
throw new UnauthorisedException();
}
FileEnvelope fileEnvelope = new FileEnvelope();
fileEnvelope.setFilename(fileUpload.getName());
File exportFile = new File(this.environment.getProperty("file.storage") + id);
fileEnvelope.setFile(exportFile);
InputStream resource = new FileInputStream(fileEnvelope.getFile());
HttpHeaders responseHeaders = new HttpHeaders();
responseHeaders.setContentLength(fileEnvelope.getFile().length());
responseHeaders.setContentType(MediaType.APPLICATION_OCTET_STREAM);
String fileName = fileEnvelope.getFilename().replace(" ", "_").replace(",", "_");
responseHeaders.set("Content-Disposition", "attachment;filename=" + fileName);
responseHeaders.set("Access-Control-Expose-Headers", "Content-Disposition");
responseHeaders.set("Cache-Control", "no-store");
responseHeaders.get("Access-Control-Expose-Headers").add("Content-Type");
byte[] content = IOUtils.toByteArray(resource);
resource.close();
return new ResponseEntity<>(content,
responseHeaders,
HttpStatus.OK);
}
}

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@ -6,7 +6,6 @@ import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.ObjectReader;
import com.fasterxml.jackson.databind.node.JsonNodeType;
import eu.eudat.criteria.entities.Criteria;
import eu.eudat.logic.services.operations.DatabaseRepository;
import java.io.IOException;
import java.util.*;

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@ -6,8 +6,6 @@ import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.ObjectReader;
import com.fasterxml.jackson.databind.node.JsonNodeType;
import eu.eudat.criteria.entities.Criteria;
import eu.eudat.logic.services.operations.DatabaseRepository;
import eu.eudat.model.User;
import eu.eudat.query.UserQuery;
import java.io.IOException;
@ -58,10 +56,4 @@ public class UserCriteria {
return new LinkedList<>(fields);
}
public UserQuery buildQuery(DatabaseRepository dao) {
List<String> fields = this.buildFields("");
// UserQuery query = new UserQuery(dao.getUserInfoDao(), fields);
// if (this.id != null) query.setId(this.id.getValue());
return null;
}
}

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@ -8,7 +8,6 @@ import eu.eudat.logic.proxy.config.configloaders.ConfigLoader;
import eu.eudat.service.remotefetcher.config.entities.GeneralUrls;
import eu.eudat.service.remotefetcher.RemoteFetcherService;
import eu.eudat.logic.services.ApiContext;
import eu.eudat.logic.services.operations.DatabaseRepository;
import eu.eudat.service.remotefetcher.models.ExternalAutocompleteFieldResult;
import eu.eudat.service.remotefetcher.config.AuthenticationConfiguration;
import eu.eudat.service.remotefetcher.config.DataFieldsUrlConfiguration;
@ -39,13 +38,11 @@ public class DatasetProfileManager {
private static final Logger logger = LoggerFactory.getLogger(DatasetProfileManager.class);
private static final List<String> cache = new ArrayList<>();
private final DatabaseRepository databaseRepository;
private final ConfigLoader configLoader;
private final RemoteFetcherService remoteFetcherService;
@Autowired
public DatasetProfileManager(ApiContext apiContext, ConfigLoader configLoader, RemoteFetcherService remoteFetcherService) {
this.databaseRepository = apiContext.getOperationsContext().getDatabaseRepository();
this.configLoader = configLoader;
this.remoteFetcherService = remoteFetcherService;
}

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@ -1,96 +0,0 @@
package eu.eudat.logic.managers;
import eu.eudat.data.old.FileUpload;
import eu.eudat.data.UserEntity;
import eu.eudat.logic.services.ApiContext;
import eu.eudat.logic.services.operations.DatabaseRepository;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.core.env.Environment;
import org.springframework.stereotype.Component;
import javax.management.InvalidApplicationException;
import java.io.File;
import java.io.IOException;
import java.nio.file.Files;
import java.util.Date;
import java.util.List;
import java.util.UUID;
@Component
public class FileManager {
private static final Logger logger = LoggerFactory.getLogger(FileManager.class);
private ApiContext apiContext;
private DatabaseRepository databaseRepository;
private Environment environment;
@Autowired
public FileManager(ApiContext apiContext, Environment environment) {
this.apiContext = apiContext;
this.databaseRepository = apiContext.getOperationsContext().getDatabaseRepository();
this.environment = environment;
}
public String moveFromTmpToStorage(String filename) {
File tempFile = new File(this.environment.getProperty("temp.temp") + filename);
File newFile = new File(this.environment.getProperty("file.storage") + filename);
try {
return Files.move(tempFile.toPath(), newFile.toPath()).toString();
} catch (IOException e) {
e.printStackTrace();
}
return null;
}
public boolean deleteFromStorage(String filename) {
File toBeDeletedFile = new File(this.environment.getProperty("file.storage") + filename);
// toBeDeletedFile.delete();
try {
return Files.deleteIfExists(toBeDeletedFile.toPath());
} catch (IOException e) {
e.printStackTrace();
}
return false;
}
public void markOldFileAsDeleted(FileUpload fileUpload) {
fileUpload.setIsDeleted(true);
databaseRepository.getFileUploadDao().createOrUpdate(fileUpload);
}
public List<FileUpload> getFileUploadsForEntityId(String entityId) throws InvalidApplicationException {
return databaseRepository.getFileUploadDao().asQueryable()
.where((builder, root) -> builder.equal(root.get("entityId"), entityId)).toList();
}
public List<FileUpload> getCurrentFileUploadsForEntityId(UUID entityId) throws InvalidApplicationException {
return databaseRepository.getFileUploadDao().asQueryable()
.where((builder, root) -> builder.and(
builder.equal(root.get("entityId"), entityId),
builder.equal(root.get("isDeleted"), false))).toList();
}
public void markAllFilesOfEntityIdAsDeleted(UUID entityId) throws InvalidApplicationException {
List<FileUpload> fileUploads = this.getCurrentFileUploadsForEntityId(entityId);
fileUploads.forEach(fileUpload -> {
this.markOldFileAsDeleted(fileUpload);
});
}
public void createFile(String id, String fileName, String fileType, String entityId, FileUpload.EntityType entityType, UserEntity userInfo) {
FileUpload fileUpload = new FileUpload();
fileUpload.setId(UUID.fromString(id));
fileUpload.setName(fileName);
fileUpload.setFileType(fileType);
fileUpload.setEntityId(UUID.fromString(entityId));
fileUpload.setEntityType(entityType);
fileUpload.setCreatedAt(new Date());
fileUpload.setIsDeleted(false);
fileUpload.setCreator(userInfo);
databaseRepository.getFileUploadDao().createOrUpdate(fileUpload);
this.moveFromTmpToStorage(fileUpload.getId().toString());
}
}

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@ -1,10 +0,0 @@
package eu.eudat.logic.services.operations;
import eu.eudat.data.dao.entities.*;
public interface DatabaseRepository {
FileUploadDao getFileUploadDao();
<T> void detachEntity(T entity);
}

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@ -1,38 +0,0 @@
package eu.eudat.logic.services.operations;
import eu.eudat.data.dao.entities.*;
import jakarta.persistence.EntityManager;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
@Service("databaseRepository")
public class DatabaseRepositoryImpl implements DatabaseRepository {
private FileUploadDao fileUploadDao;
private EntityManager entityManager;
@Autowired
public void setEntityManager(EntityManager entityManager) {
this.entityManager = entityManager;
}
@Override
public FileUploadDao getFileUploadDao() {
return fileUploadDao;
}
@Autowired
public void setFileUploadDao(FileUploadDao fileUploadDao) {
this.fileUploadDao = fileUploadDao;
}
public <T> void detachEntity(T entity) {
this.entityManager.detach(entity);
}
}

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@ -9,8 +9,6 @@ import org.springframework.context.ApplicationContext;
*/
public interface OperationsContext {
DatabaseRepository getDatabaseRepository();
ApplicationContext getApplicationContext();
BuilderFactory getBuilderFactory();

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@ -12,7 +12,6 @@ import org.springframework.stereotype.Service;
@Service("operationsContext")
public class OperationsContextImpl implements OperationsContext {
private final DatabaseRepository databaseRepository;
private final ApplicationContext applicationContext;
private final RemoteFetcherService remoteFetcherService;
private final BuilderFactory builderFactory;
@ -20,9 +19,8 @@ public class OperationsContextImpl implements OperationsContext {
// private final ElasticRepository elasticRepository;
@Autowired
public OperationsContextImpl(DatabaseRepository databaseRepository, ApplicationContext applicationContext, RemoteFetcherService remoteFetcherService
public OperationsContextImpl(ApplicationContext applicationContext, RemoteFetcherService remoteFetcherService
, BuilderFactory builderFactory/*FileStorageService fileStorageService, ElasticRepository elasticRepository*/) {
this.databaseRepository = databaseRepository;
this.applicationContext = applicationContext;
this.remoteFetcherService = remoteFetcherService;
this.builderFactory = builderFactory;
@ -30,11 +28,6 @@ public class OperationsContextImpl implements OperationsContext {
// this.elasticRepository = elasticRepository;
}
@Override
public DatabaseRepository getDatabaseRepository() {
return databaseRepository;
}
@Override
public ApplicationContext getApplicationContext() {
return applicationContext;

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@ -1,6 +1,5 @@
package eu.eudat.models.data;
import eu.eudat.data.old.*;
import java.util.Map;