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argos/dmp-backend/web/src/main/java/eu/eudat/logic/managers/DataManagementPlanManager.java

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package eu.eudat.logic.managers;
import com.fasterxml.jackson.core.type.TypeReference;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.eudat.commons.XmlHandlingService;
import eu.eudat.commons.enums.*;
import eu.eudat.commons.scope.user.UserScope;
import eu.eudat.commons.types.dmpblueprint.*;
import eu.eudat.data.*;
import eu.eudat.data.dao.criteria.*;
import eu.eudat.data.dao.entities.*;
import eu.eudat.data.old.*;
import eu.eudat.data.query.items.table.dataset.DatasetTableRequest;
import eu.eudat.data.query.items.table.datasetprofile.DatasetProfileTableRequestItem;
import eu.eudat.data.query.items.table.dmp.DataManagementPlanTableRequest;
//import eu.eudat.depositinterface.models.DmpDepositModel;
import eu.eudat.exceptions.datamanagementplan.DMPNewVersionException;
import eu.eudat.exceptions.datamanagementplan.DMPWithDatasetsDeleteException;
import eu.eudat.exceptions.security.ForbiddenException;
import eu.eudat.exceptions.security.UnauthorisedException;
import eu.eudat.logic.builders.entity.UserInfoBuilder;
import eu.eudat.logic.proxy.config.configloaders.ConfigLoader;
import eu.eudat.model.DmpUser;
import eu.eudat.logic.services.ApiContext;
import eu.eudat.logic.services.forms.VisibilityRuleService;
import eu.eudat.logic.services.forms.VisibilityRuleServiceImpl;
import eu.eudat.logic.services.operations.DatabaseRepository;
import eu.eudat.commons.types.xml.XmlBuilder;
import eu.eudat.model.EntityDoi;
import eu.eudat.model.file.FileEnvelope;
import eu.eudat.query.*;
import eu.eudat.logic.utilities.documents.types.ParagraphStyle;
import eu.eudat.logic.utilities.documents.word.WordBuilder;
import eu.eudat.logic.utilities.documents.xml.ExportXmlBuilder;
import eu.eudat.model.persist.deposit.DepositRequest;
import eu.eudat.models.HintedModelFactory;
import eu.eudat.models.data.dataset.DatasetOverviewModel;
import eu.eudat.models.data.datasetprofile.DatasetProfileListingModel;
import eu.eudat.models.data.datasetwizard.DatasetWizardModel;
import eu.eudat.models.data.datasetwizard.DatasetsToBeFinalized;
import eu.eudat.models.data.dmp.*;
import eu.eudat.models.data.dynamicfields.DynamicFieldWithValue;
import eu.eudat.models.data.helpermodels.Tuple;
import eu.eudat.models.data.helpers.common.DataTableData;
import eu.eudat.models.data.listingmodels.*;
import eu.eudat.models.data.user.composite.PagedDatasetProfile;
import eu.eudat.queryable.QueryableList;
import eu.eudat.service.deposit.DepositService;
import eu.eudat.service.dmpblueprint.DmpBlueprintService;
import eu.eudat.types.MetricNames;
import gr.cite.commons.web.authz.service.AuthorizationService;
import gr.cite.tools.data.query.QueryFactory;
import org.apache.poi.xwpf.usermodel.XWPFDocument;
import org.apache.poi.xwpf.usermodel.XWPFParagraph;
import org.apache.poi.xwpf.usermodel.XWPFRun;
import org.json.JSONObject;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.core.env.Environment;
import org.springframework.http.*;
import org.springframework.stereotype.Component;
import org.springframework.web.client.RestTemplate;
import org.springframework.web.multipart.MultipartFile;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import jakarta.transaction.Transactional;
import jakarta.xml.bind.JAXBContext;
import jakarta.xml.bind.JAXBException;
import jakarta.xml.bind.Unmarshaller;
import javax.management.InvalidApplicationException;
import java.io.*;
import java.math.BigInteger;
import java.nio.file.Files;
import java.time.Instant;
import java.time.temporal.ChronoUnit;
import java.util.*;
import java.util.concurrent.CompletableFuture;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import java.util.zip.ZipEntry;
import java.util.zip.ZipOutputStream;
@Component
public class DataManagementPlanManager {
private static final Logger logger = LoggerFactory.getLogger(DataManagementPlanManager.class);
private final ObjectMapper objectMapper;
// private final Map<NotificationType, String> notificationPaths = Stream.of(new Object[][] {
// {NotificationType.DMP_MODIFIED, "/plans/edit"},
// {NotificationType.DMP_PUBLISH, "/plans/publicEdit"},
// {NotificationType.DMP_FINALISED, "/plans/edit"},
// {NotificationType.DMP_MODIFIED_FINALISED, "/plans/edit"}
// }).collect(Collectors.toMap(data -> (NotificationType) data[0], data -> (String) data[1]));
private ApiContext apiContext;
private DatasetManager datasetManager;
private DatabaseRepository databaseRepository;
private Environment environment;
private RDAManager rdaManager;
private final MetricsManager metricsManager;
private final ConfigLoader configLoader;
private DepositService repositoriesDeposit;
private final UserScope userScope;
private final AuthorizationService authorizationService;
private final DmpBlueprintService dmpBlueprintService;
private final QueryFactory queryFactory;
private final XmlHandlingService xmlHandlingService;
@Autowired
public DataManagementPlanManager(XmlHandlingService xmlHandlingService, ApiContext apiContext, DatasetManager datasetManager, Environment environment, RDAManager rdaManager,
MetricsManager metricsManager, ConfigLoader configLoader, DepositService repositoriesDeposit, UserScope userScope, AuthorizationService authorizationService, DmpBlueprintService dmpBlueprintService, QueryFactory queryFactory) {
this.xmlHandlingService = xmlHandlingService;
this.apiContext = apiContext;
this.datasetManager = datasetManager;
this.databaseRepository = apiContext.getOperationsContext().getDatabaseRepository();
this.environment = environment;
this.rdaManager = rdaManager;
this.metricsManager = metricsManager;
this.configLoader = configLoader;
this.userScope = userScope;
this.authorizationService = authorizationService;
this.dmpBlueprintService = dmpBlueprintService;
this.queryFactory = queryFactory;
this.objectMapper = new ObjectMapper();
this.repositoriesDeposit = repositoriesDeposit;
}
/*
* Data Retrieval
* */
public DataTableData<DataManagementPlanListingModel> getPaged(DataManagementPlanTableRequest dataManagementPlanTableRequest, String fieldsGroup) throws Exception {
UUID principalID = userScope.getUserIdSafe();
// List<Dmp> dmps = null;
QueryableList<DmpEntity> items = null;
QueryableList<DmpEntity> authItems = null;
Long totalData = 0L;
// if (apiContext.getOperationsContext().getElasticRepository().getDmpRepository() != null) { //TODO
// try {
// DmpCriteria criteria = DmpCriteriaMapper.toElasticCriteria(dataManagementPlanTableRequest.getCriteria(), principalID);
// criteria.setOffset(dataManagementPlanTableRequest.getOffset());
// criteria.setSize(dataManagementPlanTableRequest.getLength());
// criteria.setSortCriteria(DmpCriteriaMapper.toElasticSorting(dataManagementPlanTableRequest.getOrderings()));
//
// dmps = apiContext.getOperationsContext().getElasticRepository().getDmpRepository().query(criteria);
// if (dmps != null && !dmps.isEmpty()) {
// List<Dmp> finalDmps = dmps;
// items = apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().asQueryable().where((builder, root) -> root.get("id").in(finalDmps.stream().map(Dmp::getId).collect(Collectors.toList())));
// PaginationManager.applyOrder(items, dataManagementPlanTableRequest);
// totalData = apiContext.getOperationsContext().getElasticRepository().getDmpRepository().count(criteria);
// }
// } catch (Exception ex) {
// logger.warn(ex.getMessage(), ex);
// items = null;
// }
// }
if (items == null) {
items = apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().getWithCriteria(dataManagementPlanTableRequest.getCriteria());
}
List<Integer> roles = new LinkedList<>();
if (!dataManagementPlanTableRequest.getCriteria().isOnlyPublic()) {
if (dataManagementPlanTableRequest.getCriteria().getRole() != null)
roles.add(dataManagementPlanTableRequest.getCriteria().getRole());
authItems = apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().getAuthenticated(items, principalID, roles);
} else {
authItems = items;
}
// if (dmps == null) {
totalData = authItems.count();
items = PaginationManager.applyPaging(authItems, dataManagementPlanTableRequest);
// } else {
// items = authItems;
// }
DataTableData<DataManagementPlanListingModel> dataTable = new DataTableData<>();
if (fieldsGroup.equals("listing")) {
if (!dataManagementPlanTableRequest.getCriteria().isOnlyPublic()) {
List<DmpEntity> dmps1 = items.withHint(HintedModelFactory.getHint(DataManagementPlanListingModel.class))
.distinct().toList();
dataTable.setData(dmps1.stream().map(dmp -> {
DatasetCriteria datasetCriteria = new DatasetCriteria();
datasetCriteria.setDmpIds(Collections.singletonList(dmp.getId()));
datasetCriteria.setAllVersions(dataManagementPlanTableRequest.getCriteria().getAllVersions());
datasetCriteria.setIsPublic(dataManagementPlanTableRequest.getCriteria().getIsPublic());
datasetCriteria.setGroupIds(Collections.singletonList(dmp.getGroupId()));
// try { //TODO
// dmp.setDataset(retrieveRelevantDatasets(datasetCriteria, principalID));
// } catch (InvalidApplicationException e) {
// throw new RuntimeException(e);
// }
return new DataManagementPlanListingModel().fromDataModelDatasets(dmp);
}).collect(Collectors.toList()));
/*.selectAsync(item -> {
item.setDataset(
item.getDataset().stream()
.filter(dataset -> !dataset.getStatus().equals(Dataset.Status.DELETED.getValue()) && !dataset.getStatus().equals(Dataset.Status.CANCELED.getValue())).collect(Collectors.toList()).stream()
*//*.filter(dataset -> dataset.getDmp().getUsers().stream()
.filter(x -> x.getUser().getId().equals(principalID))
.collect(Collectors.toList()).size() > 0)*//*
.collect(Collectors.toSet()));
return new DataManagementPlanListingModel().fromDataModelDatasets(item);
})
.whenComplete((resultList, throwable) -> dataTable.setData(resultList));*/
} else {
List<DmpEntity> dmps1 = items.withHint(HintedModelFactory.getHint(DataManagementPlanListingModel.class))
.distinct().toList();
dataTable.setData(dmps1.stream().map(dmp -> {
DatasetCriteria datasetCriteria = new DatasetCriteria();
datasetCriteria.setDmpIds(Collections.singletonList(dmp.getId()));
datasetCriteria.setIsPublic(true);
datasetCriteria.setAllVersions(dataManagementPlanTableRequest.getCriteria().getAllVersions());
datasetCriteria.setGroupIds(Collections.singletonList(dmp.getGroupId()));
// try { //TODO
// dmp.setDataset(retrieveRelevantDatasets(datasetCriteria));
// } catch (InvalidApplicationException e) {
// throw new RuntimeException(e);
// }
return new DataManagementPlanListingModel().fromDataModelDatasets(dmp);
}).collect(Collectors.toList()));
/*.selectAsync(item -> {
item.setDataset(
item.getDataset().stream()
.filter(dataset -> dataset.getStatus().equals(Dataset.Status.FINALISED.getValue())).collect(Collectors.toSet()));
return new DataManagementPlanListingModel().fromDataModelDatasets(item);
})
.whenComplete((resultList, throwable) -> dataTable.setData(resultList));*/
}
} else if (fieldsGroup.equals("autocomplete")) {
dataTable.setData(items
.distinct()
.select(item -> new DataManagementPlanListingModel().fromDataModelAutoComplete(item)));
} else {
dataTable.setData(items
.distinct()
.select(item -> new DataManagementPlanListingModel().fromDataModelAssociatedProfiles(item)));
}
//CompletableFuture countFuture = authItems.distinct().countAsync().whenComplete((count, throwable) -> dataTable.setTotalCount(count));
dataTable.setTotalCount(totalData);
//CompletableFuture.allOf(itemsFuture).join();
return dataTable;
}
private Set<DescriptionEntity> retrieveRelevantDatasets(DatasetCriteria datasetCriteria) throws InvalidApplicationException {
return retrieveRelevantDatasets(datasetCriteria, null);
}
private Set<DescriptionEntity> retrieveRelevantDatasets (DatasetCriteria datasetCriteria, UUID principal) throws InvalidApplicationException {
QueryableList<DescriptionEntity> datasetItems = apiContext.getOperationsContext().getDatabaseRepository().getDatasetDao().getWithCriteria(datasetCriteria)
.orderBy((builder, root) -> builder.desc(root.get("modified")));
if (principal != null) {
UserEntity userInfo = this.queryFactory.query(UserQuery.class).ids(principal).first();
List<Integer> roles = new ArrayList<>();
roles.add(0);
roles.add(1);
datasetItems = apiContext.getOperationsContext().getDatabaseRepository().getDatasetDao().getAuthenticated(datasetItems, userInfo, roles);
}
Long maxDatasets = datasetItems.distinct().count();
DatasetTableRequest datasetTableRequest = new DatasetTableRequest();
datasetTableRequest.setOffset(0);
datasetTableRequest.setLength(3);
Set<DescriptionEntity> datasetsSet = new LinkedHashSet<>();
try {
datasetItems = PaginationManager.applyPaging(datasetItems, datasetTableRequest);
List<DescriptionEntity> descriptionEntities = datasetItems.distinct().toList();
datasetsSet.addAll(descriptionEntities);
for (int i = 0; i < maxDatasets - descriptionEntities.size(); i++) {
DescriptionEntity fakedataset = new DescriptionEntity();
fakedataset.setId(UUID.randomUUID());
datasetsSet.add(fakedataset);
}
} catch (Exception e) {
logger.error(e.getMessage(), e);
}
return datasetsSet;
}
public eu.eudat.models.data.dmp.DataManagementPlan getSingle(String id, boolean isPublic, boolean includeDatasets) throws Exception {
eu.eudat.models.data.dmp.DataManagementPlan dataManagementPlan = new eu.eudat.models.data.dmp.DataManagementPlan();
DmpEntity dataManagementPlanEntity = databaseRepository.getDmpDao().find(UUID.fromString(id));
if (!isPublic && !this.userScope.isSet()) {
throw new UnauthorisedException();
//TODO
} else if (!isPublic /*&& (dataManagementPlanEntity.getUsers().stream().noneMatch(userInfo -> this.userScope.getUserIdSafe().equals(userInfo.getUser().getId())))*/ ) {
if (!dataManagementPlanEntity.getAccessType().equals(DmpAccessType.Public)) {
throw new UnauthorisedException();
}
} else if (isPublic && !dataManagementPlanEntity.getAccessType().equals(DmpAccessType.Public)) {
throw new ForbiddenException("Selected DMP is not public");
}
if (includeDatasets) {
dataManagementPlan.fromDataModel(dataManagementPlanEntity);
dataManagementPlan.getDatasets().forEach(datasetWizardModel -> datasetWizardModel.setDescription(null));
dataManagementPlan.setDatasets(dataManagementPlan.getDatasets().stream().sorted(Comparator.comparing(DatasetWizardModel::getCreated).reversed()).collect(Collectors.toList()));
//List<Dataset> datasetEnities = new ArrayList<>(dataManagementPlanEntity.getDataset());
/*for (int i = 0; i < datasetEnities.size(); i++) {
for (int j = i; j < dataManagementPlan.getDatasets().size(); j++) {
if (dataManagementPlan.getDatasets().get(j).getId().equals(datasetEnities.get(i).getId())) {
dataManagementPlan.getDatasets().get(j).setDatasetProfileDefinition(datasetManager.getPagedProfile(dataManagementPlan.getDatasets().get(j), datasetEnities.get(i)));
break;
}
}
}*/
/*datasetEnities.stream()
.filter(dataset -> !dataset.getStatus().equals(Dataset.Status.DELETED) && !dataset.getStatus().equals(Dataset.Status.CANCELED))
.forEach(dataset -> {
dataManagementPlan.getDatasets().stream().filter(datasetWizardModel -> datasetWizardModel.getId().equals(dataset.getId())).forEach(datasetWizardModel -> {
DatasetWizardModel wizardModel = datasetManager.getSingle(datasetWizardModel.getId().toString(), principal);
datasetWizardModel.setDatasetProfileDefinition(wizardModel.getDatasetProfileDefinition());
datasetWizardModel.setTags(wizardModel.getTags());
});
});*/
if (isPublic) {
dataManagementPlan.setDatasets(dataManagementPlan.getDatasets().stream().filter(dataset -> dataset.getStatus() == DescriptionStatus.Finalized).collect(Collectors.toList()));
}
} else {
dataManagementPlan.fromDataModelNoDatasets(dataManagementPlanEntity);
}
Map dmpProperties = new HashMap();//TODO dataManagementPlanEntity.getDmpProperties() != null ? new org.json.JSONObject(dataManagementPlanEntity.getDmpProperties()).toMap() : null;
if (dmpProperties != null && dataManagementPlan.getDynamicFields() != null)
dataManagementPlan.getDynamicFields().forEach(item -> {
Map<String, String> properties = (Map<String, String>) dmpProperties.get(item.getId());
if (properties != null)
item.setValue(new Tuple<>(properties.get("id"), properties.get("label")));
});
return dataManagementPlan;
}
public DataManagementPlanOverviewModel getOverviewSingle(String id, boolean isPublic) throws Exception {
DmpEntity dataManagementPlanEntity = databaseRepository.getDmpDao().find(UUID.fromString(id));
if (dataManagementPlanEntity.getIsActive().equals(IsActive.Inactive)) {
throw new Exception("DMP is deleted.");
}
if (!isPublic && !this.userScope.isSet()) {
throw new UnauthorisedException();
} else
if (!isPublic //&& dataManagementPlanEntity.getUsers() //TODO
// .stream().noneMatch(userInfo -> userInfo.getUser().getId().equals(this.userScope.getUserIdSafe()))
) {
throw new UnauthorisedException();
} else if (isPublic && !dataManagementPlanEntity.getAccessType().equals(DmpAccessType.Public)) {
throw new ForbiddenException("Selected DMP is not public");
}
DataManagementPlanOverviewModel datamanagementPlan = new DataManagementPlanOverviewModel();
datamanagementPlan.fromDataModelDatasets(dataManagementPlanEntity);
datamanagementPlan.setDatasets(datamanagementPlan.getDatasets().stream().sorted(Comparator.comparing(DatasetOverviewModel::getCreated).reversed()).collect(Collectors.toList()));
if (isPublic) {
datamanagementPlan.setDatasets(datamanagementPlan.getDatasets().stream().filter(dataset -> dataset.getStatus() == DescriptionStatus.Finalized).collect(Collectors.toList()));
}
return datamanagementPlan;
}
// public List<Tuple<String, String>> getDynamicFields(String id, DynamicGrantConfiguration dynamicGrantConfiguration, DynamicFieldsCriteria criteria) throws IllegalAccessException, InstantiationException {
// List<Tuple<String, String>> result = new LinkedList<>();
// RestTemplate restTemplate = new RestTemplate();
// HttpHeaders headers = new HttpHeaders();
// headers.setAccept(Collections.singletonList(MediaType.APPLICATION_JSON));
// headers.setContentType(MediaType.APPLICATION_JSON);
// HttpEntity<String> entity = new HttpEntity<>("parameters", headers);
//
// Property property = dynamicGrantConfiguration.getConfiguration().getConfigurationProperties().stream()
// .filter(item -> item.getId().equals(id)).findFirst().orElse(null);
// StringBuilder stringBuilder = new StringBuilder();
// if (criteria.getLike() != null) stringBuilder.append("?search=" + criteria.getLike());
// if (property.getDependencies() != null && !property.getDependencies().isEmpty() && criteria.getDynamicFields() != null && !criteria.getDynamicFields().isEmpty()) {
// property.getDependencies().stream().forEach(item -> {
// DynamicFieldsCriteria.DynamicFieldDependencyCriteria dependencyCriteria = criteria.getDynamicFields().stream().filter(dfield -> dfield.getProperty().equals(item.getId()))
// .findFirst().orElse(null);
// if (dependencyCriteria != null) {
// if (criteria.getLike() != null || property.getDependencies().indexOf(item) > 0)
// stringBuilder.append("&");
// stringBuilder.append(item.getQueryProperty() + "=" + dependencyCriteria.getValue());
// }
// });
//
// ResponseEntity<ArrayList> response = restTemplate.exchange(property.getSourceUrl() + stringBuilder.toString(), HttpMethod.GET, entity, ArrayList.class);
// response.getBody().forEach(item -> {
// Tuple<String, String> tuple = new Tuple<>();
// tuple.setId((String) (((Map<String, Object>) item).get(property.getExternalFieldId())));
// tuple.setLabel((String) (((Map<String, Object>) item).get(property.getExternalFieldLabel())));
// result.add(tuple);
// });
//
// } else {
// ResponseEntity<ArrayList> response = restTemplate.exchange(property.getSourceUrl() + stringBuilder.toString(), HttpMethod.GET, entity, ArrayList.class);
// response.getBody().forEach(item -> {
// Tuple<String, String> tuple = new Tuple<>();
// tuple.setId((String) (((Map<String, Object>) item).get(property.getExternalFieldId())));
// tuple.setLabel((String) (((Map<String, Object>) item).get(property.getExternalFieldLabel())));
// result.add(tuple);
// });
// }
// return result;
// }
public DataTableData<DatasetProfileListingModel> getDatasetProfilesUsedByDMP(DatasetProfileTableRequestItem datasetProfileTableRequestItem) throws InvalidApplicationException {
datasetProfileTableRequestItem.getCriteria().setFilter(DatasetProfileCriteria.DatasetProfileFilter.DMPs.getValue());
datasetProfileTableRequestItem.getCriteria().setUserId(this.userScope.getUserId());
QueryableList<eu.eudat.data.DescriptionTemplateEntity> items = apiContext.getOperationsContext().getDatabaseRepository().getDatasetProfileDao().getWithCriteria(datasetProfileTableRequestItem.getCriteria());
List<DatasetProfileListingModel> listingModels = items.select(item -> new DatasetProfileListingModel().fromDataModel(item));
DataTableData<DatasetProfileListingModel> data = new DataTableData<>();
data.setData(listingModels);
data.setTotalCount((long) listingModels.size());
return data;
}
public List<VersionListingModel> getAllVersions(String groupId, Boolean isPublic) throws InvalidApplicationException {
UUID principalId = this.userScope.getUserIdSafe();
List<VersionListingModel> versions = new ArrayList<>();
QueryableList<DmpEntity> items = null;
QueryableList<DmpEntity> authItems = null;
List<Integer> roles = new LinkedList<>();
DataManagementPlanCriteria criteria = new DataManagementPlanCriteria();
criteria.setGroupIds(Collections.singletonList(UUID.fromString(groupId)));
criteria.setAllVersions(true);
criteria.setIsPublic(isPublic);
criteria.setOnlyPublic(isPublic);
items = apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().getWithCriteria(criteria);
if (!isPublic) {
authItems = apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().getAuthenticated(items, principalId, roles);
} else {
authItems = items;
}
CompletableFuture<List<VersionListingModel>> versionFuture = authItems.withHint(HintedModelFactory.getHint(VersionListingModel.class))
.orderBy(((builder, root) -> builder.desc(root.get("version"))))
.selectAsync(item -> new VersionListingModel().fromDataModel(item))
.whenComplete(((versionListingModels, throwable) -> versions.addAll(versionListingModels)));
CompletableFuture.allOf(versionFuture).join();
return versions;
}
/*
* Data Management
* */
@Transactional
public DmpEntity createOrUpdate(DataManagementPlanEditorModel dataManagementPlan) throws Exception {
boolean setNotification = false;
if (dataManagementPlan.getId() != null) {
DmpEntity dmp1 = apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().find(dataManagementPlan.getId());
Instant dbTime = dmp1.getUpdatedAt().truncatedTo(ChronoUnit.SECONDS);
Instant modelTime = dmp1.getUpdatedAt().truncatedTo(ChronoUnit.SECONDS);
if (!isUserOwnerOfDmp(dmp1)) {
throw new Exception("User not being the creator is not authorized to edit this DMP.");
}
if (dbTime.toEpochMilli() != modelTime.toEpochMilli()) {
throw new Exception("Another user have already edit that DMP.");
}
DatasetCriteria datasetCriteria = new DatasetCriteria();
datasetCriteria.setDmpIds(List.of(dmp1.getId()));
List<DescriptionEntity> descriptionEntityList = this.databaseRepository.getDatasetDao().getWithCriteria(datasetCriteria).toList().stream().filter(dataset -> dataset.getIsActive() != IsActive.Inactive).collect(Collectors.toList());
for (DescriptionEntity descriptionEntity : descriptionEntityList) {
if (dataManagementPlan.getProfiles().stream().filter(associatedProfile -> descriptionEntity.getDescriptionTemplateId().equals(associatedProfile.getDescriptionTemplateId())).findAny().orElse(null) == null)
throw new Exception("Dataset Template for Dataset Description is missing from the DMP.");
}
if (dataManagementPlan.getStatus() == DmpStatus.Finalized.getValue() && dmp1.getStatus().equals(DmpStatus.Finalized.getValue() ))
throw new Exception("DMP is finalized, therefore cannot be edited.");
setNotification = true;
} else {
metricsManager.increaseValue(MetricNames.DMP, 1, MetricNames.DRAFT);
}
DmpEntity newDmp = dataManagementPlan.toDataModel();
if(dataManagementPlan.getProfile() != null){
newDmp.setBlueprintId(dataManagementPlan.getProfile().getId());
}
if (newDmp.getStatus().equals(DmpStatus.Finalized)) {
checkDmpValidationRules(newDmp);
}
UserEntity user = this.queryFactory.query(UserQuery.class).ids(this.userScope.getUserId()).first();
newDmp.setCreatorId(user.getId());
DmpBlueprintEntity dmpBlueprint = this.queryFactory.query(DmpBlueprintQuery.class).ids(newDmp.getBlueprintId()).first();
// if(this.dmpBlueprintService.fieldInBlueprint(dmpBlueprint, DmpBlueprintSystemFieldType.Organizations)) {
// createOrganisationsIfTheyDontExist(newDmp, apiContext.getOperationsContext().getDatabaseRepository().getOrganisationDao());
// }
// if(this.dmpBlueprintService.fieldInBlueprint(dmpBlueprint, DmpBlueprintSystemFieldType.Researchers)) {
// createResearchersIfTheyDontExist(newDmp, apiContext.getOperationsContext().getDatabaseRepository().getResearcherDao(), user);
// } //TODO
// if(this.dmpBlueprintService.fieldInBlueprint(dmpBlueprint, DmpBlueprintSystemFieldType.Funder)) {
// createFunderIfItDoesntExist(newDmp, apiContext.getOperationsContext().getDatabaseRepository().getFunderDao());
// }/TODO
// if(this.dmpBlueprintService.fieldInBlueprint(dmpBlueprint, DmpBlueprintSystemFieldType.Grant)) {
// createGrantIfItDoesntExist(newDmp, apiContext.getOperationsContext().getDatabaseRepository().getGrantDao());
// if(this.dmpBlueprintService.fieldInBlueprint(dmpBlueprint, DmpBlueprintSystemFieldType.Project)) {
//// if (newDmp.getProject() != null && newDmp.getGrant() != null && (newDmp.getProject().getLabel() == null || newDmp.getProject().getLabel().trim().isEmpty())) { //TODO
//// newDmp.setProject(newDmp.getProject().projectFromGrant(newDmp.getGrant()));
//// }
//// createProjectIfItDoesntExist(newDmp, apiContext.getOperationsContext().getDatabaseRepository().getProjectDao()); //TODO
// }
// }
DmpEntity dmp;
if (dataManagementPlan.getId() != null) {
dmp = apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().find(dataManagementPlan.getId());
} else dmp = new DmpEntity();
newDmp.setCreatedAt(dmp.getCreatedAt() == null ? Instant.now() : dmp.getCreatedAt());
DmpEntity finalNewDmp = newDmp;
if (this.queryFactory.query(DmpUserQuery.class).dmpIds(finalNewDmp.getId()).collect() != null &&
this.queryFactory.query(DmpUserQuery.class).dmpIds(finalNewDmp.getId()).collect().stream().filter(userInfo -> this.userScope.getUserIdSafe().equals(userInfo.getUserId()))
.collect(Collectors.toList()).size() == 0) {
List<DmpUserEntity> userDMPList = new ArrayList<>(this.queryFactory.query(DmpUserQuery.class).dmpIds(finalNewDmp.getId()).collect());
for (DmpUser userInfoListingModel : dataManagementPlan.getUsers()) {
for (DmpUserEntity userDMP : userDMPList) {
if (!(userDMP.getUserId().equals(userInfoListingModel.getId()))) {
// apiContext.getOperationsContext().getDatabaseRepository().getUserDmpDao().delete(userDMP);
}
}
}
}
if(this.dmpBlueprintService.fieldInBlueprint(dmpBlueprint, DmpBlueprintSystemFieldType.Grant)) {
// if (newDmp.getGrant() != null && newDmp.getGrant().getType().equals(Grant.GrantType.INTERNAL.getValue())) {
// checkIfUserCanEditGrant(newDmp, user);
// }//TODO
assignGrandUserIfInternal(newDmp, user);
}
if(this.dmpBlueprintService.fieldInBlueprint(dmpBlueprint, DmpBlueprintSystemFieldType.Funder)) {
assignFunderUserIfInternal(newDmp, user);
}
if(this.dmpBlueprintService.fieldInBlueprint(dmpBlueprint, DmpBlueprintSystemFieldType.Project)) {
assignProjectUserIfInternal(newDmp, user);
}
if(newDmp.getId() != null){
// for(DMPDatasetProfile dmpDatasetProfile : newDmp.getAssociatedDmps()){ //TODO
// apiContext.getOperationsContext().getDatabaseRepository().getDmpDatasetProfileDao().createOrUpdate(dmpDatasetProfile);
// }
}
if(this.dmpBlueprintService.fieldInBlueprint(dmpBlueprint, DmpBlueprintSystemFieldType.Grant)) {
// if (newDmp.getGrant() != null) { //TODO
// apiContext.getOperationsContext().getDatabaseRepository().getGrantDao().createOrUpdate(newDmp.getGrant());
// }
}
newDmp = apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().createOrUpdate(newDmp);
// for(DMPDatasetProfile dmpDatasetProfile : newDmp.getAssociatedDmps()){ //TODO
// apiContext.getOperationsContext().getDatabaseRepository().getDmpDatasetProfileDao().createOrUpdate(dmpDatasetProfile);
// }
if (dataManagementPlan.getUsers() != null && !dataManagementPlan.getUsers().isEmpty()) {
clearUsers(newDmp);
for (DmpUser userListing : dataManagementPlan.getUsers()) {
UserEntity tempUser = this.queryFactory.query(UserQuery.class).ids(userListing.getId()).first();
assignUser(dmp, tempUser, userListing.getRole());
}
}
// Dataset manipulation for when the DMP is set to be finalized.
if (dataManagementPlan.getStatus() == DmpStatus.Finalized.getValue()) {
if (dataManagementPlan.getDatasetsToBeFinalized() != null && !dataManagementPlan.getDatasetsToBeFinalized().isEmpty()) {
apiContext.getOperationsContext().getDatabaseRepository().getDatasetDao()
.asQueryable().where((builder, root) -> root.get("id").in(dataManagementPlan.getDatasetsToBeFinalized()))
.update(root -> root.<Integer>get("status"), DescriptionStatus.Finalized);
apiContext.getOperationsContext().getDatabaseRepository().getDatasetDao()
.asQueryable().where((builder, root) -> root.get("id").in(dataManagementPlan.getDatasetsToBeFinalized()))
.update(root -> root.<Date>get("finalizedat"), new Date());
List<UUID> datasetsToBeCanceled = new LinkedList<>();
for (DatasetWizardModel dataset : dataManagementPlan.getDatasets()) {
if (!(dataset.getStatus() == DescriptionStatus.Finalized) && !dataManagementPlan.getDatasetsToBeFinalized().contains(dataset.getId())) {
datasetsToBeCanceled.add(UUID.fromString(dataset.getId().toString()));
}
}
if (!datasetsToBeCanceled.isEmpty())
apiContext.getOperationsContext().getDatabaseRepository().getDatasetDao()
.asQueryable().where((builder, root) -> root.get("id").in(datasetsToBeCanceled))
.update(root -> root.<Integer>get("status"), DescriptionStatus.Canceled);
} else {
List<UUID> datasetsToBeCanceled = new LinkedList<>();
for (DatasetWizardModel dataset : dataManagementPlan.getDatasets()) {
if (!(dataset.getStatus() == DescriptionStatus.Finalized)) {
datasetsToBeCanceled.add(dataset.getId());
}
}
if (!datasetsToBeCanceled.isEmpty())
apiContext.getOperationsContext().getDatabaseRepository().getDatasetDao()
.asQueryable().where((builder, root) -> root.get("id").in(datasetsToBeCanceled))
.update(root -> root.<Integer>get("status"), DescriptionStatus.Canceled);
}
}
// if (dataManagementPlan.getAssociatedUsers().size() == 0)
// assignUser(newDmp, user);
UUID dmpId = newDmp.getId();
//TODO
// newDmp.setUsers(new HashSet<>(apiContext.getOperationsContext().getDatabaseRepository().getUserDmpDao().asQueryable().where((builder, root) -> builder.equal(root.get("dmp").get("id"), dmpId)).toList()));
//this.updateIndex(newDmp); //TODO
if (setNotification) {
if (newDmp.getStatus().equals(DmpStatus.Finalized.getValue())) {
this.sendNotification(newDmp, user/*, NotificationType.DMP_MODIFIED*/);
} else {
this.sendNotification(newDmp, user/*, , NotificationType.DMP_MODIFIED_FINALISED*/);
}
}
return newDmp;
}
public DmpEntity createOrUpdateWithDatasets(DataManagementPlanEditorModel dataManagementPlan) throws Exception {
if (dataManagementPlan.getId() != null) {
DmpEntity dmp1 = apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().find(dataManagementPlan.getId());
Instant dbTime = dmp1.getUpdatedAt().truncatedTo(ChronoUnit.SECONDS);
Instant modelTime = Instant.ofEpochMilli(dataManagementPlan.getModified().getTime()).truncatedTo(ChronoUnit.SECONDS);
if (!isUserOwnerOfDmp(dmp1)) {
throw new Exception("User not being the creator is not authorized to edit this DMP.");
}
if (dbTime.toEpochMilli() != modelTime.toEpochMilli()) {
throw new Exception("Another user have already edit that DMP.");
}
for (DatasetWizardModel dataset : dataManagementPlan.getDatasets()) {
if (dataManagementPlan.getProfiles().stream().filter(associatedProfile -> dataset.getProfile().getId().equals(associatedProfile.getDescriptionTemplateId())).findAny().orElse(null) == null)
throw new Exception("Dataset Template for Dataset Description is missing from the DMP.");
}
if (dataManagementPlan.getStatus() == (int) DmpStatus.Finalized.getValue() && dmp1.getStatus().equals(DmpStatus.Finalized.getValue()))
throw new Exception("DMP is finalized, therefore cannot be edited.");
} else {
metricsManager.increaseValue(MetricNames.DMP, 1, MetricNames.DRAFT);
}
List<DescriptionEntity> descriptionEntities = new ArrayList<>();
DmpEntity tempDMP = dataManagementPlan.toDataModel();
if (tempDMP.getStatus().equals(DmpStatus.Finalized)) {
checkDmpValidationRules(tempDMP);
}
UserEntity user = this.queryFactory.query(UserQuery.class).ids(this.userScope.getUserId()).first();
DmpBlueprintEntity dmpBlueprint = this.queryFactory.query(DmpBlueprintQuery.class).ids(tempDMP.getBlueprintId()).first();
// if(this.dmpBlueprintService.fieldInBlueprint(dmpBlueprint, DmpBlueprintSystemFieldType.Organizations)) {
// createOrganisationsIfTheyDontExist(tempDMP, apiContext.getOperationsContext().getDatabaseRepository().getOrganisationDao());
// }
// if(this.dmpBlueprintService.fieldInBlueprint(dmpBlueprint, DmpBlueprintSystemFieldType.Researchers)) {
// createResearchersIfTheyDontExist(tempDMP, apiContext.getOperationsContext().getDatabaseRepository().getResearcherDao(), user);
// }
// if(this.dmpBlueprintService.fieldInBlueprint(dmpBlueprint, DmpBlueprintSystemFieldType.Funder)) {
// createFunderIfItDoesntExist(tempDMP, apiContext.getOperationsContext().getDatabaseRepository().getFunderDao());
// }
// if(this.dmpBlueprintService.fieldInBlueprint(dmpBlueprint, DmpBlueprintSystemFieldType.Grant)) {
// createGrantIfItDoesntExist(tempDMP, apiContext.getOperationsContext().getDatabaseRepository().getGrantDao());
// }//TODO
DmpEntity result = createOrUpdate(dataManagementPlan);
for (DatasetWizardModel datasetWizardModel: dataManagementPlan.getDatasets()) {
datasetWizardModel.setDmp(new DataManagementPlan().fromDataModel(result));
DescriptionEntity descriptionEntity = datasetManager.createOrUpdate(datasetWizardModel);
descriptionEntities.add(descriptionEntity);
}
UUID dmpId = result.getId();
//result.setUsers(new HashSet<>(apiContext.getOperationsContext().getDatabaseRepository().getUserDmpDao().asQueryable().where((builder, root) -> builder.equal(root.get("dmp").get("id"), dmpId)).toList())); //TODO
//this.updateIndex(result); //TODO
return result;
}
public UUID newVersion(UUID uuid, DataManagementPlanNewVersionModel dataManagementPlan) throws Exception {
DmpEntity oldDmp = databaseRepository.getDmpDao().find(uuid);
if (!isUserOwnerOfDmp(oldDmp)) {
throw new Exception("User not being the creator is not authorized to perform this action.");
}
DataManagementPlanCriteria criteria = new DataManagementPlanCriteria();
LinkedList<UUID> list = new LinkedList<>();
list.push(oldDmp.getGroupId());
criteria.setGroupIds(list);
criteria.setAllVersions(false);
QueryableList<DmpEntity> dataManagementPlanQueryableList = databaseRepository.getDmpDao().getWithCriteria(criteria);
List<DmpEntity> latestVersionDMP = dataManagementPlanQueryableList.toList();
if (latestVersionDMP.get(0).getVersion().equals(oldDmp.getVersion())) {
DmpEntity newDmp = dataManagementPlan.toDataModel();
newDmp.setBlueprintId(oldDmp.getBlueprintId());
newDmp.setProperties(oldDmp.getProperties());
newDmp.setProperties(oldDmp.getProperties());
UserEntity user = apiContext.getOperationsContext().getBuilderFactory().getBuilder(UserInfoBuilder.class).id(this.userScope.getUserId()).build();
newDmp.setCreatorId(user.getId());
DmpBlueprintEntity dmpBlueprint = this.queryFactory.query(DmpBlueprintQuery.class).ids(newDmp.getBlueprintId()).first();
// if(this.dmpBlueprintService.fieldInBlueprint(dmpBlueprint, DmpBlueprintSystemFieldType.Organizations)) {
// createOrganisationsIfTheyDontExist(newDmp, databaseRepository.getOrganisationDao());
// }
// if(this.dmpBlueprintService.fieldInBlueprint(dmpBlueprint, DmpBlueprintSystemFieldType.Researchers)) {
// createResearchersIfTheyDontExist(newDmp, databaseRepository.getResearcherDao(), user);
// }//TODO
// if(this.dmpBlueprintService.fieldInBlueprint(dmpBlueprint, DmpBlueprintSystemFieldType.Funder)) {
// createFunderIfItDoesntExist(newDmp, databaseRepository.getFunderDao());
// }//TODO
// if(this.dmpBlueprintService.fieldInBlueprint(dmpBlueprint, DmpBlueprintSystemFieldType.Grant)) {
// createGrantIfItDoesntExist(newDmp, databaseRepository.getGrantDao());
// if(this.dmpBlueprintService.fieldInBlueprint(dmpBlueprint, DmpBlueprintSystemFieldType.Project)) {
// //TODO
//// if (newDmp.getProject() != null && newDmp.getGrant() != null && (newDmp.getProject().getLabel() == null || newDmp.getProject().getLabel().trim().isEmpty())) {
//// newDmp.setProject(newDmp.getProject().projectFromGrant(newDmp.getGrant()));
//// }
//// createProjectIfItDoesntExist(newDmp, databaseRepository.getProjectDao()); //TODO
// }
// }//TODO
newDmp.setGroupId(oldDmp.getGroupId());
newDmp.setVersion((short)(oldDmp.getVersion() + 1));
newDmp.setId(null);
if(this.dmpBlueprintService.fieldInBlueprint(dmpBlueprint, DmpBlueprintSystemFieldType.Grant)) {
//TODO
// if (newDmp.getGrant() != null && newDmp.getGrant().getType().equals(Grant.GrantType.INTERNAL.getValue())) {
// checkIfUserCanEditGrant(newDmp, user);
// }
assignGrandUserIfInternal(newDmp, user);
}
if(this.dmpBlueprintService.fieldInBlueprint(dmpBlueprint, DmpBlueprintSystemFieldType.Funder)) {
assignFunderUserIfInternal(newDmp, user);
}
if(this.dmpBlueprintService.fieldInBlueprint(dmpBlueprint, DmpBlueprintSystemFieldType.Project)) {
assignProjectUserIfInternal(newDmp, user);
}
if(this.dmpBlueprintService.fieldInBlueprint(dmpBlueprint, DmpBlueprintSystemFieldType.Grant)) {
//TODO
// if (newDmp.getGrant() != null) {
// if (newDmp.getGrant().getStartdate() == null) {
// newDmp.getGrant().setStartdate(new Date());
// }
// if (newDmp.getGrant().getEnddate() == null) {
// newDmp.getGrant().setEnddate(Date.from(Instant.now().plus(365, ChronoUnit.DAYS)));
// }
// databaseRepository.getGrantDao().createOrUpdate(newDmp.getGrant());
// }
}
DmpEntity tempDmp = databaseRepository.getDmpDao().createOrUpdate(newDmp);
newDmp.setId(tempDmp.getId());
//TODO
// for(DMPDatasetProfile dmpDatasetProfile : newDmp.getAssociatedDmps()){
// apiContext.getOperationsContext().getDatabaseRepository().getDmpDatasetProfileDao().createOrUpdate(dmpDatasetProfile);
// }
// Assign creator.
//assignUser(newDmp, user);
copyDatasets(newDmp, databaseRepository.getDatasetDao());
this.queryFactory.query(DmpUserQuery.class).dmpIds(oldDmp.getId()).collect()
.stream().forEach(userDMP -> {
DmpUserEntity temp = new DmpUserEntity();
temp.setUserId(userDMP.getUserId());
temp.setRole(userDMP.getRole());
temp.setDmpId(newDmp.getId());
// apiContext.getOperationsContext().getDatabaseRepository().getUserDmpDao().createOrUpdate(temp);
});
//TODO
//newDmp.setUsers(new HashSet<>(databaseRepository.getUserDmpDao().asQueryable().where((builder, root) -> builder.equal(root.get("dmp").get("id"), newDmp.getId())).toList()));
DatasetCriteria criteria1 = new DatasetCriteria();
criteria1.setDmpIds(Collections.singletonList(newDmp.getId()));
//TODO
//newDmp.setDataset(new HashSet<>(databaseRepository.getDatasetDao().getWithCriteria(criteria1).toList()));
this.updateGroupIndex(newDmp.getGroupId());
return newDmp.getId();
} else {
throw new DMPNewVersionException("Version to update not the latest.");
}
}
public UUID clone(UUID uuid, DataManagementPlanNewVersionModel dataManagementPlan) throws Exception {
DmpEntity oldDmp = databaseRepository.getDmpDao().find(uuid);
DmpEntity newDmp = dataManagementPlan.toDataModel();
newDmp.setBlueprintId(oldDmp.getBlueprintId());
newDmp.setProperties(oldDmp.getProperties());
newDmp.setProperties(oldDmp.getProperties());
UserEntity user = apiContext.getOperationsContext().getBuilderFactory().getBuilder(UserInfoBuilder.class).id(this.userScope.getUserId()).build();
newDmp.setCreatorId(user.getId());
DmpBlueprintEntity dmpBlueprint = this.queryFactory.query(DmpBlueprintQuery.class).ids(newDmp.getBlueprintId()).first();
// if(this.dmpBlueprintService.fieldInBlueprint(dmpBlueprint, DmpBlueprintSystemFieldType.Organizations)) {
// createOrganisationsIfTheyDontExist(newDmp, databaseRepository.getOrganisationDao());
// }
// if(this.dmpBlueprintService.fieldInBlueprint(dmpBlueprint, DmpBlueprintSystemFieldType.Researchers)) {
// createResearchersIfTheyDontExist(newDmp, databaseRepository.getResearcherDao(), user);
// }
// if(this.dmpBlueprintService.fieldInBlueprint(dmpBlueprint, DmpBlueprintSystemFieldType.Funder)) {
// createFunderIfItDoesntExist(newDmp, databaseRepository.getFunderDao());
// }
// if(this.dmpBlueprintService.fieldInBlueprint(dmpBlueprint, DmpBlueprintSystemFieldType.Grant)) {
// createGrantIfItDoesntExist(newDmp, databaseRepository.getGrantDao());
// //TODO
//// if(this.dmpBlueprintService.fieldInBlueprint(newDmp.getProfile(), DmpBlueprintSystemFieldType.Project)) {
//// if (newDmp.getProject() != null && newDmp.getGrant() != null && (newDmp.getProject().getLabel() == null || newDmp.getProject().getLabel().trim().isEmpty())) {
//// newDmp.setProject(newDmp.getProject().projectFromGrant(newDmp.getGrant()));
//// }
//// createProjectIfItDoesntExist(newDmp, databaseRepository.getProjectDao());
//// }
// }//TODO
newDmp.setGroupId(UUID.randomUUID());
newDmp.setVersion((short)0);
newDmp.setId(null);
if(this.dmpBlueprintService.fieldInBlueprint(dmpBlueprint, DmpBlueprintSystemFieldType.Grant)) {
//TODO
// if (newDmp.getGrant() != null && newDmp.getGrant().getType().equals(Grant.GrantType.INTERNAL.getValue())) {
// checkIfUserCanEditGrant(newDmp, user);
// }
assignGrandUserIfInternal(newDmp, user);
}
if(this.dmpBlueprintService.fieldInBlueprint(dmpBlueprint, DmpBlueprintSystemFieldType.Funder)) {
assignFunderUserIfInternal(newDmp, user);
}
if(this.dmpBlueprintService.fieldInBlueprint(dmpBlueprint, DmpBlueprintSystemFieldType.Project)) {
assignProjectUserIfInternal(newDmp, user);
}
if(this.dmpBlueprintService.fieldInBlueprint(dmpBlueprint, DmpBlueprintSystemFieldType.Grant)) {
//TODO
// if (newDmp.getGrant() != null) {
// databaseRepository.getGrantDao().createOrUpdate(newDmp.getGrant());
// }
}
DmpEntity tempDmp = databaseRepository.getDmpDao().createOrUpdate(newDmp);
newDmp.setId(tempDmp.getId());
//TODO
// for(DMPDatasetProfile dmpDatasetProfile : newDmp.getAssociatedDmps()){
// apiContext.getOperationsContext().getDatabaseRepository().getDmpDatasetProfileDao().createOrUpdate(dmpDatasetProfile);
// }
assignUser(newDmp, user);
copyDatasets(newDmp, databaseRepository.getDatasetDao());
//TODO
// newDmp.setUsers(new HashSet<>(databaseRepository.getUserDmpDao().asQueryable().where((builder, root) -> builder.equal(root.get("dmp").get("id"), newDmp.getId())).toList()));
DatasetCriteria criteria1 = new DatasetCriteria();
criteria1.setDmpIds(Collections.singletonList(newDmp.getId()));
//TODO
// newDmp.setDataset(new HashSet<>(databaseRepository.getDatasetDao().getWithCriteria(criteria1).toList()));
UUID dmpId = newDmp.getId();
//TODO
// newDmp.setUsers(new HashSet<>(apiContext.getOperationsContext().getDatabaseRepository().getUserDmpDao().asQueryable().where((builder, root) -> builder.equal(root.get("dmp").get("id"), dmpId)).toList()));
//this.updateIndex(newDmp); //TODO
metricsManager.increaseValue(MetricNames.DMP, 1, MetricNames.DRAFT);
return newDmp.getId();
}
public void delete(UUID uuid) throws DMPWithDatasetsDeleteException, IOException, InvalidApplicationException {
DatasetCriteria criteria = new DatasetCriteria();
List<UUID> dmpIds = Collections.singletonList(uuid);
criteria.setDmpIds(dmpIds);
if (apiContext.getOperationsContext().getDatabaseRepository().getDatasetDao().getWithCriteria(criteria).toList().size() > 0)
throw new DMPWithDatasetsDeleteException("You cannot Remove Datamanagement Plan with Datasets");
DmpEntity oldDmp = apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().find(uuid);
switch (oldDmp.getStatus()) {
case Draft:
metricsManager.decreaseValue(MetricNames.DMP, 1, MetricNames.DRAFT);
break;
case Finalized:
//TODO
// if (oldDmp.getDois() != null && !oldDmp.getDois().isEmpty()) {
// metricsManager.decreaseValue(MetricNames.DMP, 1, MetricNames.DOIED);
// }
// if (oldDmp.isPublic()) {
// metricsManager.decreaseValue(MetricNames.DMP, 1, MetricNames.PUBLISHED);
// }
metricsManager.decreaseValue(MetricNames.DMP, 1, MetricNames.FINALIZED);
break;
}
oldDmp.setIsActive(IsActive.Inactive);
apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().createOrUpdate(oldDmp);
UUID dmpId = oldDmp.getId();
// oldDmp.setUsers(new HashSet<>(apiContext.getOperationsContext().getDatabaseRepository().getUserDmpDao().asQueryable().where((builder, root) -> builder.equal(root.get("dmp").get("id"), dmpId)).toList())); //TODO
// this.updateIndex(oldDmp); //TODO
DataManagementPlanCriteria criteria1 = new DataManagementPlanCriteria();
criteria1.setAllVersions(true);
criteria1.setGroupIds(Collections.singletonList(oldDmp.getGroupId()));
apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().getWithCriteria(criteria1).toList().forEach(dmp -> {
//TODO
// try {
// UUID tdmpId = dmp.getId();
// //TODO
// //dmp.setUsers(new HashSet<>(apiContext.getOperationsContext().getDatabaseRepository().getUserDmpDao().asQueryable().where((builder, root) -> builder.equal(root.get("dmp").get("id"), tdmpId)).toList()));
// //this.updateIndex(dmp); //TODO
// } catch (InvalidApplicationException e) {
// logger.error(e.getMessage(), e);
// }
// for (DescriptionEntity descriptionEntity : dmp.getDataset()) {
//
// try {
// List<Tag> tags = new ArrayList<>();
// eu.eudat.elastic.entities.Dataset elastic = apiContext.getOperationsContext().getElasticRepository().getDatasetRepository().findDocument(descriptionEntity.getId().toString());
// if (elastic != null) {
// tags = elastic.getTags();
// }
// //descriptionEntity.setDmpId(dmp.getId()); //TODO
// this.datasetManager.updateTags(descriptionEntity, tags);
// } catch (Exception e) {
// logger.error(e.getMessage(), e);
// }
// }
});
}
// private void createResearchersIfTheyDontExist(DmpEntity newDmp, ResearcherDao researcherRepository, UserEntity user) throws InvalidApplicationException {
// if (newDmp.getResearchers() != null && !newDmp.getResearchers().isEmpty()) { //TODO
// for (eu.eudat.data.old.Researcher researcher : newDmp.getResearchers()) {
// ResearcherCriteria criteria = new ResearcherCriteria();
// criteria.setReference(researcher.getReference());
// List<eu.eudat.data.old.Researcher> entries = researcherRepository.getWithCriteria(criteria).toList();
// if (entries != null && !entries.isEmpty()) researcher.setId(entries.get(0).getId());
// else {
// researcher.setCreationUser(user);
// researcherRepository.createOrUpdate(researcher);
// metricsManager.increaseValue(MetricNames.RESEARCHER, 1, null);
// }
// }
// }
// }
// private void createOrganisationsIfTheyDontExist(DmpEntity newDmp, OrganisationDao organisationRepository) throws InvalidApplicationException {
// if (newDmp.getOrganisations() != null && !newDmp.getOrganisations().isEmpty()) { //TODO
// for (Organisation organisation : newDmp.getOrganisations()) {
// boolean createNew = false;
// if (organisation.getReference() != null) {
// OrganisationCriteria criteria = new OrganisationCriteria();
// criteria.setLike(organisation.getReference());
// List<eu.eudat.data.old.Organisation> entries = organisationRepository.getWithCriteria(criteria).toList();
// if (entries != null && !entries.isEmpty()) organisation.setId(entries.get(0).getId());
// else createNew = true;
// } else {
// createNew = true;
// }
//
// if (createNew) {
// if (organisation.getReference() == null) {
// organisation.setReference("Internal:" + UUID.randomUUID().toString());
// }
// organisationRepository.createOrUpdate(organisation);
// }
// }
// }
// }
// private void createGrantIfItDoesntExist(DmpEntity newDmp, GrantDao grantDao) throws InvalidApplicationException {
// if (newDmp.getGrant() != null) { //TODO
// Grant grant = newDmp.getGrant();
// GrantCriteria criteria = new GrantCriteria();
// if (grant.getReference() != null) {
// criteria.setReference(grant.getReference());
// Grant grantEntity = grantDao.getWithCriteria(criteria).toList().stream().max(Comparator.comparing(grant1 -> grant1.getModified().getTime())).orElse(null);
// if (grantEntity != null) grant.setId(grantEntity.getId());
// else {
// grant.setType(Grant.GrantType.EXTERNAL.getValue());
// grant.setCreationUser(null);
// if (grant.getStartdate() == null) {
// grant.setStartdate(new Date());
// }
// if (grant.getEnddate() == null) {
// grant.setEnddate(Date.from(Instant.now().plus(365, ChronoUnit.DAYS)));
// }
// grantDao.createOrUpdate(grant);
// }
// }
// else {
// grant.setType(Grant.GrantType.EXTERNAL.getValue());
// grant.setCreationUser(null);
// grantDao.createOrUpdate(grant);
// }
// }
// }
// private void createFunderIfItDoesntExist(DmpEntity newDmp, FunderDao funderDao) throws InvalidApplicationException {
// if (newDmp.getGrant() != null && newDmp.getGrant().getFunder() != null) { //TODO
// Funder funder = newDmp.getGrant().getFunder();
// FunderCriteria criteria = new FunderCriteria();
// if (funder.getReference() != null) {
// criteria.setReference(funder.getReference());
// Funder funderEntity = funderDao.getWithCritetia(criteria).toList().stream().max(Comparator.comparing(funder1 -> funder1.getModified().getTime())).orElse(null);
// if (funderEntity != null) funder.setId(funderEntity.getId());
// else {
// funderDao.createOrUpdate(funder);
// }
// }
// else {
// funderDao.createOrUpdate(funder);
// }
// }
// }
// private void createProjectIfItDoesntExist(DmpEntity newDmp, ProjectDao projectDao) throws InvalidApplicationException { //TODO
// if (newDmp.getProject() != null) {
// Project project = newDmp.getProject();
// ProjectCriteria criteria = new ProjectCriteria();
// if (project.getReference() != null) {
// criteria.setReference(project.getReference());
// Project projectEntity = projectDao.getWithCritetia(criteria).toList().stream().max(Comparator.comparing(project1 -> project1.getModified().getTime())).orElse(null);
// if (projectEntity != null) project.setId(projectEntity.getId());
// else {
// createExternalProject(project, projectDao);
// }
// }
// else {
// createExternalProject(project, projectDao);
// }
// }
// }
//
// private void createExternalProject(Project project, ProjectDao projectDao) {
// if (project.getStartdate() == null) project.setStartdate(new Date());
// if (project.getEnddate() == null) project.setEnddate(new Date());
// project.setType(Project.ProjectType.EXTERNAL.getValue());
// if (project.getId() == null) project.setId(UUID.randomUUID());
// projectDao.createOrUpdate(project);
// metricsManager.increaseValue(MetricNames.PROJECT, 1, null);
// }
private void copyDatasets(DmpEntity newDmp, DatasetDao datasetDao) throws InvalidApplicationException {
List<CompletableFuture<DescriptionEntity>> futures = new LinkedList<>();
DatasetCriteria datasetCriteria = new DatasetCriteria();
datasetCriteria.setDmpIds(List.of(newDmp.getId()));
for (DescriptionEntity descriptionEntity : this.databaseRepository.getDatasetDao().getWithCriteria(datasetCriteria).toList()) {
DescriptionEntity tempDescriptionEntity = datasetDao.find(descriptionEntity.getId());
//TODO
// try {
// List<Tag> tags = new ArrayList<>();
// eu.eudat.elastic.entities.Dataset elastic = apiContext.getOperationsContext().getElasticRepository().getDatasetRepository().findDocument(descriptionEntity.getId().toString());
// if (elastic != null) {
// tags = elastic.getTags();
// }
// //TODO
// //UUID dmpId = tempDescriptionEntity.getDmpId();
// //tempDescriptionEntity.getDmp().setUsers(new HashSet<>(apiContext.getOperationsContext().getDatabaseRepository().getUserDmpDao().asQueryable().where((builder, root) -> builder.equal(root.get("dmp").get("id"), dmpId)).toList()));
// this.datasetManager.updateTags(tempDescriptionEntity, tags);
// } catch (Exception e) {
// logger.error(e.getMessage(), e);
// }
datasetDao.asQueryable().withHint(HintedModelFactory.getHint(DatasetListingModel.class)).where((builder, root) -> builder.equal(root.get("id"), descriptionEntity.getId())).getSingleAsync()
.thenApplyAsync(entityDataset -> {
DescriptionEntity newDescriptionEntity = new DescriptionEntity();
newDescriptionEntity.update(entityDataset);
newDescriptionEntity.setStatus(DescriptionStatus.Draft);
//TODO
//newDescriptionEntity.setDmpId(newDmp.getId());
// if (newDescriptionEntity.getDatasetDataRepositories() != null) {
// newDescriptionEntity.setDatasetDataRepositories(newDescriptionEntity.getDatasetDataRepositories().stream().map(item -> {
// DataRepository dataRepository = new DataRepository();
// dataRepository.setId(item.getDataRepository().getId());
//
// DatasetDataRepository datasetDataRepository = new DatasetDataRepository();
// datasetDataRepository.setDataRepository(dataRepository);
// datasetDataRepository.setDataset(newDescriptionEntity);
// datasetDataRepository.setData(item.getData());
// return datasetDataRepository;
// }).collect(Collectors.toSet()));
// }
//
// if (newDescriptionEntity.getDatasetExternalDatasets() != null) {
// newDescriptionEntity.setDatasetExternalDatasets(newDescriptionEntity.getDatasetExternalDatasets().stream().map(item -> {
// ExternalDataset externalDataset = new ExternalDataset();
// externalDataset.setId(item.getExternalDataset().getId());
// DatasetExternalDataset datasetExternalDataset = new DatasetExternalDataset();
// datasetExternalDataset.setExternalDataset(externalDataset);
// datasetExternalDataset.setDataset(newDescriptionEntity);
// datasetExternalDataset.setData(item.getData());
// return datasetExternalDataset;
// }).collect(Collectors.toSet()));
// }
//
// if (newDescriptionEntity.getRegistries() != null) {
// newDescriptionEntity.setRegistries(newDescriptionEntity.getRegistries().stream().map(item -> {
// Registry registry = new Registry();
// registry.setId(item.getId());
// return registry;
// }).collect(Collectors.toSet()));
// }
//
// if (newDescriptionEntity.getServices() != null) {
// newDescriptionEntity.setServices(newDescriptionEntity.getServices().stream().map(item -> {
// Service service = new Service();
// service.setId(item.getId());
// DatasetService datasetService = new DatasetService();
// datasetService.setService(service);
// datasetService.setDataset(newDescriptionEntity);
// datasetService.setData(item.getData());
// return datasetService;
// }).collect(Collectors.toSet()));
// }
newDescriptionEntity.setCreatedAt(Instant.now());
return newDescriptionEntity;
}).thenApplyAsync(item -> {
futures.add(datasetDao.createOrUpdateAsync(item).whenComplete(((dataset1, throwable) -> {
DmpEntity dmp = null;
try {
dmp = this.apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().find(this.queryFactory.query(DmpDescriptionTemplateQuery.class).ids(dataset1.getDmpDescriptionTemplateId()).isActive(IsActive.Active).first().getDmpId());
} catch (InvalidApplicationException e) {
throw new RuntimeException(e);
}
metricsManager.increaseValue(MetricNames.DATASET, 1, MetricNames.DRAFT);
//TODO
// eu.eudat.elastic.entities.Dataset datasetElastic = new eu.eudat.elastic.entities.Dataset();
// datasetElastic.setId(dataset1.getId().toString());
// datasetElastic.setLabel(dataset1.getLabel());
// datasetElastic.setDescription(dataset1.getDescription());
// datasetElastic.setTemplate(this.queryFactory.query(DmpDescriptionTemplateQuery.class).ids(dataset1.getDmpDescriptionTemplateId()).isActive(IsActive.Active).first().getDescriptionTemplateId());
// datasetElastic.setDmp(dmp.getId());
// datasetElastic.setStatus(dataset1.getStatus().getValue());
// datasetElastic.setGroup(dmp.getGroupId());
// if(this.dmpBlueprintService.fieldInBlueprint(dmp.getProfile(), DmpBlueprintSystemFieldType.Grant)) {
// datasetElastic.setGrant(dmp.getGrant().getId());
// }
// if (dmp.getUsers() != null) {
// datasetElastic.setCollaborators(dmp.getUsers().stream().map(user -> {
// Collaborator collaborator = new Collaborator();
// collaborator.setId(user.getId().toString());
// collaborator.setRole(user.getRole());
// // collaborator.setName(user.getUser().getName());
// return collaborator;
// }).collect(Collectors.toList()));
// }
// datasetElastic.setLastVersion(true);
// datasetElastic.setLastPublicVersion(false);
// if (dmp.getOrganisations() != null) {
// datasetElastic.setOrganizations(dmp.getOrganisations().stream().map(org -> {
// Organization organization = new Organization();
// organization.setId(org.getId().toString());
// organization.setName(org.getLabel());
// return organization;
// }).collect(Collectors.toList()));
// }
// datasetElastic.setPublic(dmp.isPublic());
// if(this.dmpBlueprintService.fieldInBlueprint(dmp.getProfile(), DmpBlueprintSystemFieldType.Grant)) {
// datasetElastic.setGrantStatus(dmp.getGrant().getStatus());
// }
//
// try {
// eu.eudat.elastic.entities.Dataset oldDatasetElastic = apiContext.getOperationsContext().getElasticRepository().getDatasetRepository().findDocument(descriptionEntity.getId().toString());
// if (oldDatasetElastic != null) {
// datasetElastic.setTags(oldDatasetElastic.getTags());
// }
// datasetElastic.setFormData(this.datasetManager.getWordDocumentText(dataset1));
// apiContext.getOperationsContext().getElasticRepository().getDatasetRepository().createOrUpdate(datasetElastic);
// } catch (Exception e) {
// logger.error(e.getMessage(), e);
// }
})));
return futures;
}).join();
}
}
public void makePublic(UUID id) throws Exception {
DmpEntity dmp = this.apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().find(id);
// Check if dmp is finalized and if user is owner.
if (!isUserOwnerOfDmp(dmp))
throw new Exception("User does not have the privilege to do this action.");
if (!dmp.getStatus().equals(DmpStatus.Finalized))
throw new Exception("DMP is not finalized");
dmp.setAccessType(DmpAccessType.Public);
apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().createOrUpdate(dmp);
UUID dmpId = dmp.getId();
// dmp.setUsers(new HashSet<>(apiContext.getOperationsContext().getDatabaseRepository().getUserDmpDao().asQueryable().where((builder, root) -> builder.equal(root.get("dmp").get("id"), dmpId)).toList())); //TODO
//this.updateIndex(dmp); //TODO
metricsManager.increaseValue(MetricNames.DMP, 1, MetricNames.PUBLISHED);
DataManagementPlanCriteria criteria = new DataManagementPlanCriteria();
criteria.setGroupIds(Collections.singletonList(dmp.getGroupId()));
criteria.setAllVersions(true);
apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().getWithCriteria(criteria).toList().stream().forEach(dmp1 -> {
// dmp1.getDataset().forEach(dataset -> {
//TODO
// try {
// List<Tag> tags = new ArrayList<>();
// eu.eudat.elastic.entities.Dataset elastic = apiContext.getOperationsContext().getElasticRepository().getDatasetRepository().findDocument(dataset.getId().toString());
// if (elastic != null) {
// tags = elastic.getTags();
// }
// //TODO
// //UUID tmdmpId = dataset.getDmpId();
// //dataset.getDmp().setUsers(new HashSet<>(apiContext.getOperationsContext().getDatabaseRepository().getUserDmpDao().asQueryable().where((builder, root) -> builder.equal(root.get("dmp").get("id"), tmdmpId)).toList()));
// this.datasetManager.updateTags(dataset, tags);
// metricsManager.increaseValue(MetricNames.DATASET, 1, MetricNames.PUBLISHED);
// } catch (Exception e) {
// logger.error(e.getMessage(), e);
// }
// });
});
UserEntity user = this.queryFactory.query(UserQuery.class).ids(this.userScope.getUserId()).first();
sendNotification(dmp, user/*, , NotificationType.DMP_PUBLISH*/);
}
@Transactional
public void makeFinalize(UUID id, DatasetsToBeFinalized datasetsToBeFinalized) throws Exception {
DmpEntity dmp = this.apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().find(id);
if (!isUserOwnerOfDmp(dmp))
throw new Exception("User does not have the privilege to do this action.");
if (dmp.getStatus().equals(DmpStatus.Finalized))
throw new Exception("DMP is already finalized");
List<DescriptionEntity> indexDescriptionEntities = new ArrayList<>();
if (datasetsToBeFinalized != null && datasetsToBeFinalized.getUuids() != null && !datasetsToBeFinalized.getUuids().isEmpty()) {
List<DescriptionEntity> finalizedDescriptionEntities = apiContext.getOperationsContext().getDatabaseRepository().getDatasetDao()
.asQueryable().where((builder, root) -> root.get("id").in(datasetsToBeFinalized.getUuids()))
.toList();
for (DescriptionEntity descriptionEntity : finalizedDescriptionEntities) {
DescriptionStatus status = descriptionEntity.getStatus();
Instant finalizedDate = descriptionEntity.getFinalizedAt();
descriptionEntity.setStatus(DescriptionStatus.Finalized);
descriptionEntity.setFinalizedAt(Instant.now());
DatasetWizardModel wizardModel = new DatasetWizardModel();
wizardModel = wizardModel.fromDataModel(descriptionEntity);
wizardModel.setDatasetProfileDefinition(this.datasetManager.getPagedProfile(wizardModel, descriptionEntity));
try {
datasetManager.createOrUpdate(wizardModel);
} catch (Exception e) {
descriptionEntity.setStatus(status);
descriptionEntity.setFinalizedAt(finalizedDate);
throw e;
}
descriptionEntity.setUpdatedAt(Instant.now());
}
/*apiContext.getOperationsContext().getDatabaseRepository().getDatasetDao()
.asQueryable().where((builder, root) -> root.get("id").in(datasetsToBeFinalized.getUuids()))
.update(root -> root.<Date>get("finalizedAt"), new Date());*/
//List<Dataset> finalizedDatasets = dmp.getDataset().stream().filter(dataset -> datasetsToBeFinalized.getUuids().contains(dataset.getId())).collect(Collectors.toList());
/* finalizedDatasets.forEach(dataset ->{
dataset.setStatus(Dataset.Status.FINALISED.getValue());
dataset.setFinalizedAt(new Date());
dataset.setModified(new Date());
} );*/
indexDescriptionEntities.addAll(finalizedDescriptionEntities);
List<UUID> datasetsToBeCanceled = new LinkedList<>();
DatasetCriteria datasetCriteria = new DatasetCriteria();
datasetCriteria.setDmpIds(List.of(dmp.getId()));
List<DescriptionEntity> descriptionEntityList = this.databaseRepository.getDatasetDao().getWithCriteria(datasetCriteria).toList().stream().collect(Collectors.toList());
for (DescriptionEntity descriptionEntity : descriptionEntityList) {
if (!descriptionEntity.getStatus().equals(DescriptionStatus.Finalized) && !datasetsToBeFinalized.getUuids().contains(descriptionEntity.getId())) {
datasetsToBeCanceled.add(descriptionEntity.getId());
}
}
if (!datasetsToBeCanceled.isEmpty()) {
apiContext.getOperationsContext().getDatabaseRepository().getDatasetDao()
.asQueryable().where((builder, root) -> root.get("id").in(datasetsToBeCanceled))
.update(root -> root.<Integer>get("status"), DescriptionStatus.Canceled);
List<DescriptionEntity> cancelledDescriptionEntities = descriptionEntityList.stream().filter(dataset -> datasetsToBeCanceled.contains(dataset.getId())).collect(Collectors.toList());
cancelledDescriptionEntities.forEach(dataset -> dataset.setStatus(DescriptionStatus.Canceled));
indexDescriptionEntities.addAll(cancelledDescriptionEntities);
}
} else {
List<UUID> datasetsToBeCanceled = new LinkedList<>();
DatasetCriteria datasetCriteria = new DatasetCriteria();
datasetCriteria.setDmpIds(List.of(dmp.getId()));
List<DescriptionEntity> descriptionEntityList = this.databaseRepository.getDatasetDao().getWithCriteria(datasetCriteria).toList().stream().collect(Collectors.toList());
for (DescriptionEntity descriptionEntity : descriptionEntityList) {
if (!descriptionEntity.getStatus().equals(DescriptionStatus.Finalized)) {
datasetsToBeCanceled.add(descriptionEntity.getId());
}
}
if (!datasetsToBeCanceled.isEmpty()) {
apiContext.getOperationsContext().getDatabaseRepository().getDatasetDao()
.asQueryable().where((builder, root) -> root.get("id").in(datasetsToBeCanceled))
.update(root -> root.<Integer>get("status"), DescriptionStatus.Canceled);
List<DescriptionEntity> cancelledDescriptionEntities = descriptionEntityList.stream().filter(dataset -> datasetsToBeCanceled.contains(dataset.getId())).collect(Collectors.toList());
cancelledDescriptionEntities.forEach(dataset -> dataset.setStatus(DescriptionStatus.Canceled));
indexDescriptionEntities.addAll(cancelledDescriptionEntities);
}
}
dmp.setStatus(DmpStatus.Finalized);
apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().createOrUpdate(dmp);
UUID dmpId = dmp.getId();
// dmp.setUsers(new HashSet<>(apiContext.getOperationsContext().getDatabaseRepository().getUserDmpDao().asQueryable().where((builder, root) -> builder.equal(root.get("dmp").get("id"), dmpId)).toList())); //TODO
//this.updateIndex(dmp); //TODO
UserEntity user = this.queryFactory.query(UserQuery.class).ids(this.userScope.getUserId()).first();
sendNotification(dmp, user/*, , NotificationType.DMP_FINALISED*/);
metricsManager.decreaseValue(MetricNames.DMP, 1, MetricNames.DRAFT);
metricsManager.increaseValue(MetricNames.DMP, 1, MetricNames.FINALIZED);
//this.updateDatasetsIndex(indexDescriptionEntities); //TODO
metricsManager.decreaseValue(MetricNames.DATASET, indexDescriptionEntities.size(), MetricNames.DRAFT);
metricsManager.increaseValue(MetricNames.DATASET, indexDescriptionEntities.size(), MetricNames.FINALIZED);
}
public void undoFinalize(UUID id) throws Exception {
DmpEntity dmp = this.apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().find(id);
if (!isUserOwnerOfDmp(dmp))
throw new Exception("User does not have the privilege to do this action.");
if (dmp.getIsActive().equals(IsActive.Inactive))
throw new Exception("DMP is already Active");
if (dmp.getAccessType().equals(DmpAccessType.Public))
throw new Exception("DMP is publicly available");
// if (!dmp.getDois().isEmpty())//TODO
// throw new Exception("DMP is deposited");
dmp.setStatus(DmpStatus.Draft);
apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().createOrUpdate(dmp);
UUID dmpId = dmp.getId();
// dmp.setUsers(new HashSet<>(apiContext.getOperationsContext().getDatabaseRepository().getUserDmpDao().asQueryable().where((builder, root) -> builder.equal(root.get("dmp").get("id"), dmpId)).toList())); //TODO
//this.updateIndex(dmp); //TODO
metricsManager.decreaseValue(MetricNames.DMP, 1, MetricNames.FINALIZED);
metricsManager.increaseValue(MetricNames.DMP, 1, MetricNames.DRAFT);
}
public void updateUsers(UUID id, List<DmpUser> users) throws Exception {
DmpEntity dmp = this.apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().find(id);
if (!isUserOwnerOfDmp(dmp))
throw new Exception("User does not have the privilege to do this action.");
clearUsers(dmp);
for (DmpUser userListing : users) {
UserEntity tempUser = this.queryFactory.query(UserQuery.class).ids(userListing.getId()).first();
assignUser(dmp, tempUser, userListing.getRole());
}
}
/*
* Export Data
* */
public FileEnvelope getWordDocument(String id, ConfigLoader configLoader) throws IOException, InvalidApplicationException {
return this.getWordDocument(id, configLoader, true);
}
public FileEnvelope getWordDocument(String id, ConfigLoader configLoader, Boolean versioned) throws IOException, InvalidApplicationException {
WordBuilder wordBuilder = new WordBuilder(this.environment, configLoader);
VisibilityRuleService visibilityRuleService = new VisibilityRuleServiceImpl();
DatasetWizardModel dataset = new DatasetWizardModel();
XWPFDocument document = configLoader.getDocument();
DmpEntity dmpEntity = databaseRepository.getDmpDao().find(UUID.fromString(id));
if (!dmpEntity.getAccessType().equals(DmpAccessType.Public)
//TODO && dmpEntity.getUsers().stream().filter(userInfo -> userInfo.getUser().getId().equals(this.userScope.getUserIdSafe())).collect(Collectors.toList()).size() == 0
)
throw new UnauthorisedException();
wordBuilder.fillFirstPage(dmpEntity, null, document, false);
// int powered_pos = document.getParagraphs().size() - 3;
int powered_pos = wordBuilder.findPosOfPoweredBy(document);
XWPFParagraph powered_par = null;
XWPFParagraph argos_img_par = null;
if(powered_pos != -1) {
powered_par = document.getParagraphArray(powered_pos);
argos_img_par = document.getParagraphArray(powered_pos + 1);
}
// // DMP info on top of the document.
// wordBuilder.addParagraphContent("Data Management Plan Information", document, ParagraphStyle.HEADER1, BigInteger.ZERO);
// // DMP title custom style.
// wordBuilder.addParagraphContent(dmpEntity.getLabel(), document, ParagraphStyle.HEADER2, BigInteger.ZERO);
// wordBuilder.addParagraphContent(dmpEntity.getDescription(), document, ParagraphStyle.HTML, BigInteger.ZERO);
//
// wordBuilder.addParagraphContent("Funder", document, ParagraphStyle.HEADER3, BigInteger.ZERO);
// if (dmpEntity.getGrant().getFunder() != null)
// wordBuilder.addParagraphContent(dmpEntity.getGrant().getFunder().getLabel(), document, ParagraphStyle.TEXT, BigInteger.ZERO);
//
// wordBuilder.addParagraphContent("Grant", document, ParagraphStyle.HEADER3, BigInteger.ZERO);
// wordBuilder.addParagraphContent(dmpEntity.getGrant().getLabel(), document, ParagraphStyle.TEXT, BigInteger.ZERO);
//
// wordBuilder.addParagraphContent("Organisations", document, ParagraphStyle.HEADER3, BigInteger.ZERO);
// if (dmpEntity.getOrganisations().size() > 0) {
// wordBuilder.addParagraphContent(dmpEntity.getOrganisations().stream().map(Organisation::getLabel).collect(Collectors.joining(", "))
// , document, ParagraphStyle.TEXT, BigInteger.ZERO);
// }
//
// wordBuilder.addParagraphContent("Researchers", document, ParagraphStyle.HEADER3, BigInteger.ZERO);
// if (dmpEntity.getResearchers().size() > 0) {
// wordBuilder.addParagraphContent(dmpEntity.getResearchers().stream().map(Researcher::getLabel).collect(Collectors.joining(", "))
// , document, ParagraphStyle.TEXT, BigInteger.ZERO);
// }
//
// /*wordBuilder.addParagraphContent("DMP Profile", document, ParagraphStyle.HEADER2, BigInteger.ZERO);
// if (dmpEntity.getProfile() != null){
// wordBuilder.addParagraphContent(dmpEntity.getProfile().getLabel(), document, ParagraphStyle.TEXT, BigInteger.ZERO);
// }*/
//
// // Page break at the end of the DMP title.
// XWPFParagraph parBreakDMP = document.createParagraph();
// parBreakDMP.setPageBreak(true);
//
// wordBuilder.addParagraphContent("Datasets", document, ParagraphStyle.HEADER1, BigInteger.ZERO);
// // Space below Datasets.
// XWPFParagraph parBreakDatasets = document.createParagraph();
DefinitionEntity dmpBlueprint = this.xmlHandlingService.fromXmlSafe(DefinitionEntity.class, this.queryFactory.query(DmpBlueprintQuery.class).ids(dmpEntity.getBlueprintId()).first().getDefinition());
for(SectionEntity section: dmpBlueprint.getSections()){
wordBuilder.addParagraphContent("Section " + section.getOrdinal(), document, ParagraphStyle.HEADER1, BigInteger.ZERO, 0);
XWPFParagraph sectionInfoParagraph = document.createParagraph();
sectionInfoParagraph.setSpacingBetween(1.0);
XWPFRun runSectionTitle = sectionInfoParagraph.createRun();
runSectionTitle.setText("Title: ");
runSectionTitle.setColor("000000");
XWPFRun runSectionTitleText = sectionInfoParagraph.createRun();
runSectionTitleText.setText(section.getLabel());
runSectionTitleText.setColor("116a78");
XWPFParagraph sectionDescriptionParagraph = document.createParagraph();
XWPFRun runSectionDescription = sectionDescriptionParagraph.createRun();
runSectionDescription.setText("Description: ");
runSectionDescription.setColor("000000");
XWPFRun runSectionDescriptionText = sectionDescriptionParagraph.createRun();
runSectionDescriptionText.setText(section.getDescription());
runSectionDescriptionText.setColor("116a78");
wordBuilder.addParagraphContent("Section Fields", document, ParagraphStyle.HEADER2, BigInteger.ZERO, 0);
section.getFields().sort(Comparator.comparingInt(FieldEntity::getOrdinal));
for(FieldEntity field: section.getFields()){
if(field.getCategory() == DmpBlueprintFieldCategory.System){
SystemFieldEntity systemField = (SystemFieldEntity) field;
XWPFParagraph systemFieldParagraph = document.createParagraph();
systemFieldParagraph.setSpacingBetween(1.0);
XWPFRun runSyStemFieldTitle = systemFieldParagraph.createRun();
runSyStemFieldTitle.setText("Title: ");
runSyStemFieldTitle.setColor("000000");
XWPFRun runSystemFieldTitleText = systemFieldParagraph.createRun();
runSystemFieldTitleText.setText(systemField.getLabel());
runSystemFieldTitleText.setColor("116a78");
if(systemField.getDescription() != null && !systemField.getDescription().isEmpty()){
XWPFParagraph systemFieldDescription = document.createParagraph();
systemFieldDescription.setSpacingBetween(1.0);
XWPFRun runSyStemFieldDescription = systemFieldDescription.createRun();
runSyStemFieldDescription.setText("Description: ");
runSyStemFieldDescription.setColor("000000");
XWPFRun runSystemFieldDescriptionText = systemFieldDescription.createRun();
runSystemFieldDescriptionText.setText(systemField.getDescription());
runSystemFieldDescriptionText.setColor("116a78");
}
XWPFParagraph systemFieldInput = document.createParagraph();
systemFieldInput.setSpacingBetween(1.0);
XWPFRun runInput = systemFieldInput.createRun();
runInput.setText("Input: ");
runInput.setColor("000000");
switch (systemField.getType()) {
case Text:
XWPFRun runTitle = systemFieldInput.createRun();
runTitle.setText(dmpEntity.getLabel());
runTitle.setColor("116a78");
break;
case HtmlText:
XWPFRun runDescription = systemFieldInput.createRun();
runDescription.setText(dmpEntity.getDescription());
runDescription.setColor("116a78");
break;
case Researchers:
//TODO
// for(Researcher researcher: dmpEntity.getResearchers()){
// XWPFRun runResearcher = systemFieldInput.createRun();
// runResearcher.setText("• " + researcher.getLabel());
// runResearcher.setColor("116a78");
// }
break;
//TODO
// case Organizations:
//
// for(Organisation organisation: dmpEntity.getOrganisations()){
// XWPFRun runOrganisation = systemFieldInput.createRun();
// runOrganisation.setText("• " + organisation.getLabel());
// runOrganisation.setColor("116a78");
// }
// break;
// case Language:
// XWPFRun runLanguage = systemFieldInput.createRun();
// runLanguage.setText(objectMapper.readValue(dmpEntity.getExtraProperties(), HashMap.class).get("language").toString());
// runLanguage.setColor("116a78");
// break;
// case Contact:
// XWPFRun runContact = systemFieldInput.createRun();
// runContact.setText(dmpEntity.getCreator().getName());
// runContact.setColor("116a78");
// break;
// case Funder:
// if (dmpEntity.getGrant() != null && dmpEntity.getGrant().getFunder() != null) {
// XWPFRun runFunder = systemFieldInput.createRun();
// runFunder.setText(dmpEntity.getGrant().getFunder().getLabel());
// runFunder.setColor("116a78");
// }
// break;
// case Grant:
// if (dmpEntity.getGrant() != null) {
// XWPFRun runGrant = systemFieldInput.createRun();
// runGrant.setText(dmpEntity.getGrant().getLabel());
// runGrant.setColor("116a78");
// }
// break;
// case Project:
// if (dmpEntity.getProject() != null ) {
// XWPFRun runProject = systemFieldInput.createRun();
// runProject.setText(dmpEntity.getProject().getLabel());
// runProject.setColor("116a78");
// }
// break;
// case License:
// Map extraProperties = objectMapper.readValue(dmpEntity.getExtraProperties(), HashMap.class);
// if (extraProperties.containsKey("license")) {
// XWPFRun runLicense = systemFieldInput.createRun();
// runLicense.setText(extraProperties.get("license").toString());
// runLicense.setColor("116a78");
// }
// break;
// case AccessRights:
// Map extraPropertiesMap = objectMapper.readValue(dmpEntity.getExtraProperties(), HashMap.class);
// if (extraPropertiesMap.containsKey("visible")) {
// XWPFRun runAccessRights = systemFieldInput.createRun();
// runAccessRights.setText(extraPropertiesMap.get("visible").toString());
// runAccessRights.setColor("116a78");
// }
// break;
}
document.createParagraph();
}
else if(field.getCategory() == DmpBlueprintFieldCategory.Extra){
ExtraFieldEntity extraField = (ExtraFieldEntity)field;
XWPFParagraph extraFieldParagraph = document.createParagraph();
extraFieldParagraph.setSpacingBetween(1.0);
XWPFRun runExtraFieldLabel = extraFieldParagraph.createRun();
runExtraFieldLabel.setText(extraField.getLabel());
runExtraFieldLabel.setColor("116a78");
if(extraField.getDescription() != null && !extraField.getDescription().isEmpty()){
XWPFRun runExtraFieldDescription = extraFieldParagraph.createRun();
runExtraFieldDescription.setText(extraField.getDescription());
runExtraFieldDescription.setColor("116a78");
}
XWPFRun runExtraFieldInput = extraFieldParagraph.createRun();
Map dmpProperties = objectMapper.readValue(dmpEntity.getProperties(), HashMap.class);
if (dmpProperties.containsKey(field.getId()) && dmpProperties.get(field.getId()) != null) {
runExtraFieldInput.setText((String) dmpProperties.get(field.getId()));
}
runExtraFieldInput.setColor("116a78");
}
}
if(!section.getDescriptionTemplates().isEmpty()){
wordBuilder.addParagraphContent("Section descriptions", document, ParagraphStyle.HEADER2, BigInteger.ZERO, 0);
wordBuilder.addParagraphContent("Description Templates", document, ParagraphStyle.HEADER4, BigInteger.ZERO, 0);
for(eu.eudat.commons.types.dmpblueprint.DescriptionTemplateEntity descriptionTemplateEntity : section.getDescriptionTemplates()){
XWPFParagraph templateParagraph = document.createParagraph();
XWPFRun runTemplateLabel = templateParagraph.createRun();
runTemplateLabel.setText("• " + descriptionTemplateEntity.getLabel());
runTemplateLabel.setColor("116a78");
}
final Boolean isFinalized = dmpEntity.getStatus().equals(DmpStatus.Finalized);
final Boolean isPublic = dmpEntity.getAccessType().equals(DmpAccessType.Public);
DatasetCriteria datasetCriteria = new DatasetCriteria();
datasetCriteria.setDmpIds(Collections.singletonList(dmpEntity.getId()));
List<DescriptionEntity> descriptionEntityList = this.databaseRepository.getDatasetDao().getWithCriteria(datasetCriteria).toList().stream().collect(Collectors.toList());
descriptionEntityList.stream()
.filter(item -> item.getStatus() != DescriptionStatus.Canceled)
.filter(item -> item.getIsActive() != IsActive.Inactive)
.filter(item -> !isPublic && !isFinalized || item.getStatus() == DescriptionStatus.Finalized)
//.filter(item -> item.getDmpSectionIndex().equals(section.getOrdinal() - 1)) //TODO
.sorted(Comparator.comparing(DescriptionEntity::getCreatedAt))
.forEach(datasetEntity -> {
Map<String, Object> properties = new HashMap<>();
if (datasetEntity.getProperties() != null) {
//ObjectMapper objectMapper = new ObjectMapper();
try {
properties = objectMapper.readValue(datasetEntity.getProperties(), LinkedHashMap.class);
} catch (IOException e) {
logger.error(e.getLocalizedMessage(), e);
}
/*JSONObject jObject = new JSONObject(datasetEntity.getProperties());
properties = jObject.toMap();*/
}
// Dataset Description custom style.
XWPFParagraph datasetDescriptionParagraph = document.createParagraph();
datasetDescriptionParagraph.setStyle("Heading4");
datasetDescriptionParagraph.setSpacingBetween(1.5);
XWPFRun datasetDescriptionRun = datasetDescriptionParagraph.createRun();
datasetDescriptionRun.setText("Dataset Description");
//datasetDescriptionRun.setColor("2E75B6");
//datasetDescriptionRun.setBold(true);
datasetDescriptionRun.setFontSize(15);
// Custom style for the Dataset title.
//wordBuilder.addParagraphContent("Title: " + datasetEntity.getLabel(), document, ParagraphStyle.HEADER1, BigInteger.ZERO);
XWPFParagraph datasetLabelParagraph = document.createParagraph();
// datasetLabelParagraph.setStyle("Heading2");
datasetLabelParagraph.setSpacingBetween(1.0);
XWPFRun runDatasetTitle1 = datasetLabelParagraph.createRun();
runDatasetTitle1.setText("Title: ");
runDatasetTitle1.setColor("000000");
//runDatasetTitle1.setBold(true);
//runDatasetTitle1.setFontSize(12);
XWPFRun runDatasetTitle = datasetLabelParagraph.createRun();
runDatasetTitle.setText(datasetEntity.getLabel());
runDatasetTitle.setColor("116a78");
//runDatasetTitle.setBold(true);
//runDatasetTitle.setFontSize(12);
XWPFParagraph datasetTemplateParagraph = document.createParagraph();
// datasetTemplateParagraph.setStyle("Heading3");
XWPFRun runDatasetTemplate1 = datasetTemplateParagraph.createRun();
runDatasetTemplate1.setText("Template: ");
runDatasetTemplate1.setColor("000000");
//runDatasetTemplate1.setBold(true);
//runDatasetTemplate1.setFontSize(12);
XWPFRun runDatasetTemplate = datasetTemplateParagraph.createRun();
runDatasetTemplate.setText(this.queryFactory.query(DescriptionTemplateQuery.class).ids(datasetEntity.getDescriptionTemplateId()).first().getLabel());
runDatasetTemplate.setColor("116a78");
//runDatasetTemplate.setBold(true);
//runDatasetTemplate.setFontSize(12);
// /*XWPFParagraph externalReferencesParagraph = document.createParagraph();
// externalReferencesParagraph.setStyle("Heading3");
// XWPFRun externalReferencesRun = externalReferencesParagraph.createRun();
// externalReferencesRun.setText("External References");
// externalReferencesRun.setColor("2E75B6");
// externalReferencesRun.setBold(true);
// externalReferencesRun.setFontSize(12);
//
// wordBuilder.addParagraphContent("Data Repositories", document, ParagraphStyle.HEADER4, BigInteger.ZERO);
// if (datasetEntity.getDatasetDataRepositories().size() > 0) {
// wordBuilder.addParagraphContent(datasetEntity.getDatasetDataRepositories().stream().map(DatasetDataRepository::getDataRepository).map(DataRepository::getLabel).collect(Collectors.joining(", "))
// , document, ParagraphStyle.TEXT, BigInteger.ZERO);
// }
// wordBuilder.addParagraphContent("External Datasets", document, ParagraphStyle.HEADER4, BigInteger.ZERO);
// if (datasetEntity.getDatasetExternalDatasets().size() > 0) {
// wordBuilder.addParagraphContent(datasetEntity.getDatasetExternalDatasets().stream().map(DatasetExternalDataset::getExternalDataset).map(ExternalDataset::getLabel).collect(Collectors.joining(", "))
// , document, ParagraphStyle.TEXT, BigInteger.ZERO);
// }
// wordBuilder.addParagraphContent("Registries", document, ParagraphStyle.HEADER4, BigInteger.ZERO);
// if (datasetEntity.getRegistries().size() > 0) {
// wordBuilder.addParagraphContent(datasetEntity.getRegistries().stream().map(Registry::getLabel).collect(Collectors.joining(", "))
// , document, ParagraphStyle.TEXT, BigInteger.ZERO);
// }
// wordBuilder.addParagraphContent("Services", document, ParagraphStyle.HEADER4, BigInteger.ZERO);
// if (datasetEntity.getServices().size() > 0) {
// wordBuilder.addParagraphContent(datasetEntity.getServices().stream().map(DatasetService::getService).map(Service::getLabel).collect(Collectors.joining(", "))
// , document, ParagraphStyle.TEXT, BigInteger.ZERO);
// }
// *//*wordBuilder.addParagraphContent("Tags", document, ParagraphStyle.HEADER3, BigInteger.ZERO);
// if (datasetEntity.().size() > 0) {
// wordBuilder.addParagraphContent(datasetEntity.getServices().stream().map(DatasetService::getService).map(Service::getLabel).collect(Collectors.joining(", "))
// , document, ParagraphStyle.HEADER4, BigInteger.ZERO);
// }*/
//
//
XWPFParagraph datasetDescParagraph = document.createParagraph();
XWPFRun runDatasetDescription1 = datasetDescParagraph.createRun();
runDatasetDescription1.setText("Description: ");
runDatasetDescription1.setColor("000000");
XWPFRun runDatasetDescription = datasetDescParagraph.createRun();
runDatasetDescription.setText(this.queryFactory.query(DescriptionTemplateQuery.class).ids(datasetEntity.getDescriptionTemplateId()).first().getLabel());
runDatasetDescription.setColor("116a78");
//wordBuilder.addParagraphContent(datasetEntity.getDescription(), document, ParagraphStyle.HTML, BigInteger.ZERO, 0);
document.createParagraph();
PagedDatasetProfile pagedDatasetProfile = datasetManager.getPagedProfile(dataset, datasetEntity);
visibilityRuleService.setProperties(properties);
visibilityRuleService.buildVisibilityContext(pagedDatasetProfile.getRules());
try {
wordBuilder.build(document, pagedDatasetProfile, visibilityRuleService);
} catch (IOException e) {
logger.error(e.getMessage(), e);
}
// Page break at the end of the Dataset.
XWPFParagraph parBreakDataset = document.createParagraph();
parBreakDataset.setPageBreak(true);
});
}
}
// // Removes the top empty headings.
// for (int i = 0; i < 6; i++) {
// document.removeBodyElement(0);
// }
if(powered_pos != -1) {
document.getLastParagraph().setPageBreak(false);
document.createParagraph();
document.setParagraph(powered_par, document.getParagraphs().size() - 1);
document.createParagraph();
document.setParagraph(argos_img_par, document.getParagraphs().size() - 1);
document.removeBodyElement(powered_pos + 1);
document.removeBodyElement(powered_pos + 1);
}
wordBuilder.fillFooter(dmpEntity, null, document, false);
String fileName ="";
//TODO
// if (dmpEntity.getGrant() != null && dmpEntity.getGrant().getLabel() != null) {
// fileName = "DMP_" + dmpEntity.getGrant().getLabel();
// }
// else {
// fileName = "DMP_" + dmpEntity.getLabel();
// }
// if (versioned) {
// fileName += "_" + dmpEntity.getVersion();
// }
// fileName = fileName.replaceAll("[^a-zA-Z0-9+ ]", "");
FileEnvelope exportEnvelope = new FileEnvelope();
exportEnvelope.setFilename(fileName + ".docx");
String uuid = UUID.randomUUID().toString();
File exportFile = new File(this.environment.getProperty("temp.temp") + uuid + ".docx");
FileOutputStream out = new FileOutputStream(exportFile);
document.write(out);
out.close();
exportEnvelope.setFile(exportFile);
return exportEnvelope;
}
private FileEnvelope getXmlDocument(String id) throws IOException, InvalidApplicationException {
ExportXmlBuilder xmlBuilder = new ExportXmlBuilder();
VisibilityRuleService visibilityRuleService = new VisibilityRuleServiceImpl();
DmpEntity dmp = databaseRepository.getDmpDao().find(UUID.fromString(id));
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();
final Boolean isFinalized = dmp.getStatus().equals(DmpStatus.Finalized);
final Boolean isPublic = dmp.getAccessType().equals(DmpAccessType.Public);
DatasetCriteria datasetCriteria = new DatasetCriteria();
datasetCriteria.setDmpIds(List.of(dmp.getId()));
List<DescriptionEntity> descriptionEntityList = this.databaseRepository.getDatasetDao().getWithCriteria(datasetCriteria).toList().stream().filter(dataset -> dataset.getIsActive() != IsActive.Inactive).collect(Collectors.toList());
List<DescriptionEntity> descriptionEntities = descriptionEntityList.stream()
.filter(dataset -> dataset.getIsActive() != IsActive.Inactive &&
dataset.getStatus() != DescriptionStatus.Canceled)
.filter(dataset -> !isPublic && !isFinalized || dataset.getStatus() == DescriptionStatus.Finalized)
.collect(Collectors.toList());
/*String fileName = dmp.getLabel();
fileName = fileName.replaceAll("[^a-zA-Z0-9+ ]", "");*/
String uuid = UUID.randomUUID().toString();
File xmlFile = new File(this.environment.getProperty("temp.temp") + uuid + ".xml");
BufferedWriter writer = new BufferedWriter(new FileWriter(xmlFile, true));
Document xmlDoc = XmlBuilder.getDocument();
Element dmpElement = xmlDoc.createElement("dmp");
Element dmpDescription = xmlDoc.createElement("description");
dmpDescription.setTextContent(dmp.getDescription());
dmpElement.appendChild(dmpDescription);
Element dmpName = xmlDoc.createElement("dmpName");
dmpName.setTextContent(dmp.getLabel());
dmpElement.appendChild(dmpName);
//TODO
// if (dmp.getExtraProperties() != null && !dmp.getExtraProperties().isEmpty()) {
// Map<String, Object> extraProperties = new ObjectMapper().readValue(dmp.getExtraProperties(), HashMap.class);
// Element language = xmlDoc.createElement("language");
// language.setTextContent(extraProperties.get("language") != null ? extraProperties.get("language").toString() : null);
// dmpElement.appendChild(language);
// Element visibility = xmlDoc.createElement("visibility");
// visibility.setTextContent(extraProperties.get("visible") != null ? extraProperties.get("visible").toString() : null);
// dmpElement.appendChild(visibility);
// Element publicDate = xmlDoc.createElement("publicDate");
// publicDate.setTextContent(extraProperties.get("publicDate") != null ? extraProperties.get("publicDate").toString() : null);
// dmpElement.appendChild(publicDate);
// Element costs = xmlDoc.createElement("costs");
// costs.setTextContent(extraProperties.get("costs") != null ? extraProperties.get("costs").toString() : null);
// dmpElement.appendChild(costs);
// }
DmpBlueprintEntity dmpBlueprint = this.queryFactory.query(DmpBlueprintQuery.class).ids(dmp.getBlueprintId()).first();
Element dmpProfileElement = xmlDoc.createElement("dmpProfile");
Element dmpProfileName = xmlDoc.createElement("dmpProfileName");
if (!(dmpBlueprint == null)) {
dmpProfileName.setTextContent(dmpBlueprint.getLabel());
dmpProfileElement.appendChild(dmpProfileName);
Element dmpProfileId = xmlDoc.createElement("dmpProfileId");
dmpProfileId.setTextContent(dmpBlueprint.getId().toString());
dmpProfileElement.appendChild(dmpProfileId);
// Element values = xmlDoc.createElement("values");
// values.setTextContent(dmpProfile.getDefinition());
// dmpProfileElement.appendChild(values);
}
dmpElement.appendChild(dmpProfileElement);
Element dmpContactElement = xmlDoc.createElement("contact");
Element dmpContactName = xmlDoc.createElement("name");
Element dmpContactEmail = xmlDoc.createElement("email");
if(dmp.getCreatorId() != null){
dmpContactName.setTextContent(this.queryFactory.query(UserQuery.class).ids(dmp.getCreatorId()).first().getName());
//TODO dmpContactEmail.setTextContent(this.databaseRepository.getUserInfoDao().find(dmp.getCreator()).getEmail());
}
else{
Iterator<DmpUserEntity> users = new ArrayList<DmpUserEntity>().iterator(); //TODO dmp.getUsers().iterator();
if(users.hasNext()){
DmpUserEntity creator = users.next();
dmpContactName.setTextContent(this.queryFactory.query(UserQuery.class).ids(creator.getUserId()).first().getName());
//TODO .setTextContent(this.databaseRepository.getUserInfoDao().find(creator.getUser()).getEmail());
}
}
dmpContactElement.appendChild(dmpContactName);
dmpContactElement.appendChild(dmpContactEmail);
dmpElement.appendChild(dmpContactElement);
Element dmpContributorsElement = xmlDoc.createElement("contributors");
Iterator<DmpUserEntity> users = new ArrayList<DmpUserEntity>().iterator(); //TODO dmp.getUsers().iterator();
while(users.hasNext()){
Element dmpContributorElement = xmlDoc.createElement("contributor");
Element dmpContributorName = xmlDoc.createElement("name");
Element dmpContributorEmail= xmlDoc.createElement("email");
DmpUserEntity contributor = users.next();
dmpContributorName.setTextContent(this.queryFactory.query(UserQuery.class).ids(contributor.getUserId()).first().getName());
//TODO dmpContributorEmail.setTextContent(this.databaseRepository.getUserInfoDao().find(contributor.getUser()).getEmail());
dmpContributorElement.appendChild(dmpContributorName);
dmpContributorElement.appendChild(dmpContributorEmail);
dmpContributorsElement.appendChild(dmpContributorElement);
}
dmpElement.appendChild(dmpContributorsElement);
// Funder.
Element funder = xmlDoc.createElement("funder");
if (this.dmpBlueprintService.fieldInBlueprint(this.queryFactory.query(DmpBlueprintQuery.class).ids(dmp.getBlueprintId()).first(), DmpBlueprintSystemFieldType.Grant) && this.dmpBlueprintService.fieldInBlueprint(this.queryFactory.query(DmpBlueprintQuery.class).ids(dmp.getBlueprintId()).first(), DmpBlueprintSystemFieldType.Funder)) {
Element funderLabel = xmlDoc.createElement("label");
Element funderId = xmlDoc.createElement("id");
//TODO
// funderLabel.setTextContent(dmp.getGrant().getFunder().getLabel());
// funderId.setTextContent(dmp.getGrant().getFunder().getId().toString());
// funder.appendChild(funderLabel);
// funder.appendChild(funderId);
// if (dmp.getGrant().getFunder().getReference() != null) {
// String referencePrefix = dmp.getGrant().getFunder().getReference().split(":")[0];
// String shortReference = dmp.getGrant().getFunder().getReference().substring(referencePrefix.length() + 1);
// Element funderReference = xmlDoc.createElement("reference");
// funderReference.setTextContent(shortReference);
// funder.appendChild(funderReference);
// }
}
dmpElement.appendChild(funder);
// Grant.
Element grant = xmlDoc.createElement("grant");
if (this.dmpBlueprintService.fieldInBlueprint(this.queryFactory.query(DmpBlueprintQuery.class).ids(dmp.getBlueprintId()).first(), DmpBlueprintSystemFieldType.Grant)) {
Element grantLabel = xmlDoc.createElement("label");
Element grantId = xmlDoc.createElement("id");
//TODO
// grantLabel.setTextContent(dmp.getGrant().getLabel());
// grantId.setTextContent(dmp.getGrant().getId().toString());
// grant.appendChild(grantLabel);
// grant.appendChild(grantId);
// if (dmp.getGrant().getReference() != null) {
// String referencePrefix = dmp.getGrant().getReference().split(":")[0];
// String shortReference = dmp.getGrant().getReference().substring(referencePrefix.length() + 1);
// Element grantReference = xmlDoc.createElement("reference");
// grantReference.setTextContent(shortReference);
// grant.appendChild(grantReference);
// }
}
dmpElement.appendChild(grant);
// Project.
Element project = xmlDoc.createElement("project");
if (this.dmpBlueprintService.fieldInBlueprint(this.queryFactory.query(DmpBlueprintQuery.class).ids(dmp.getBlueprintId()).first(), DmpBlueprintSystemFieldType.Project)) {
Element projectId = xmlDoc.createElement("id");
Element projectLabel = xmlDoc.createElement("label");
Element projectDescription = xmlDoc.createElement("description");
Element projectStartDate = xmlDoc.createElement("start");
Element projectEndDate = xmlDoc.createElement("end");
//TODO
// projectId.setTextContent(dmp.getProject().getId().toString());
// projectLabel.setTextContent(dmp.getProject().getLabel());
// projectDescription.setTextContent(dmp.getProject().getDescription());
// projectStartDate.setTextContent(dmp.getProject().getStartdate().toString());
// projectEndDate.setTextContent(dmp.getProject().getEnddate().toString());
project.appendChild(projectId);
project.appendChild(projectLabel);
project.appendChild(projectDescription);
project.appendChild(projectStartDate);
project.appendChild(projectEndDate);
}
dmpElement.appendChild(project);
//TODO
// Element organisationsElement = xmlDoc.createElement("organisations");
// for (Organisation organisation : dmp.getOrganisations()) {
// Element organisationElement = xmlDoc.createElement("organisation");
// Element organisationNameElement = xmlDoc.createElement("name");
// organisationNameElement.setTextContent(organisation.getLabel());
// Element organisationReferenceElement = xmlDoc.createElement("reference");
// organisationReferenceElement.setTextContent(organisation.getReference());
// organisationElement.appendChild(organisationNameElement);
// organisationElement.appendChild(organisationReferenceElement);
// organisationsElement.appendChild(organisationElement);
// }
// dmpElement.appendChild(organisationsElement);
//
// Element researchersElement = xmlDoc.createElement("researchers");
// for (Researcher researcher : dmp.getResearchers()) {
// Element researcherElement = xmlDoc.createElement("researcher");
// Element researcherNameElement = xmlDoc.createElement("name");
// researcherNameElement.setTextContent(researcher.getLabel());
// Element researcherReferenceElement = xmlDoc.createElement("reference");
// researcherReferenceElement.setTextContent(researcher.getReference());
// researcherElement.appendChild(researcherNameElement);
// researcherElement.appendChild(researcherReferenceElement);
// researchersElement.appendChild(researcherElement);
// }
// dmpElement.appendChild(researchersElement);
Element extraFields = xmlDoc.createElement("extraFields");
Map<String, Object> dmpProperties = new ObjectMapper().readValue(dmp.getProperties(), new TypeReference<Map<String, Object>>() {});
DefinitionEntity blueprint = new DefinitionEntity(); //new DefinitionEntity().fromXml(XmlBuilder.fromXml(this.queryFactory.query(DmpBlueprintQuery.class).ids(dmp.getBlueprintId()).first().getDefinition()).getDocumentElement());
blueprint.getSections().forEach(section -> {
section.getFields().forEach(fieldModel -> {
if (fieldModel.getCategory() == DmpBlueprintFieldCategory.Extra) {
Element extraField = xmlDoc.createElement("extraField");
Element extraFieldId = xmlDoc.createElement("id");
extraFieldId.setTextContent(fieldModel.getId().toString());
Element extraFieldLabel = xmlDoc.createElement("label");
extraFieldLabel.setTextContent(fieldModel.getLabel());
Element extraFieldValue = xmlDoc.createElement("value");
Object value = dmpProperties.get(fieldModel.getId().toString());
if (value != null) {
extraFieldValue.setTextContent((String) value);
}
extraField.appendChild(extraFieldId);
extraField.appendChild(extraFieldLabel);
extraField.appendChild(extraFieldValue);
extraFields.appendChild(extraField);
}
});
});
dmpElement.appendChild(extraFields);
Element datasetsElement = xmlDoc.createElement("datasets");
for (DescriptionEntity descriptionEntity : descriptionEntities) {
Element datasetElement = xmlDoc.createElement("dataset");
datasetElement.setAttribute("name", descriptionEntity.getLabel());
Element datasetDescriptionElement = xmlDoc.createElement("description");
datasetElement.appendChild(datasetDescriptionElement);
datasetDescriptionElement.setTextContent(descriptionEntity.getDescription());
//TODO
// Element datasetDmpSectionIndex = xmlDoc.createElement("dmpSectionIndex");
// datasetElement.appendChild(datasetDmpSectionIndex);
// datasetDmpSectionIndex.setTextContent(String.valueOf(descriptionEntity.getDmpSectionIndex()));
Element datsetProfileElement = xmlDoc.createElement("profile-id");
datasetElement.appendChild(datsetProfileElement);
datsetProfileElement.setTextContent(descriptionEntity.getDescriptionTemplateId().toString());
Element datsetProfileLabelElement = xmlDoc.createElement("profile-label");
datasetElement.appendChild(datsetProfileLabelElement);
datsetProfileLabelElement.setTextContent(this.queryFactory.query(DescriptionTemplateQuery.class).ids(descriptionEntity.getDescriptionTemplateId()).first().getLabel());
DatasetWizardModel datasetWizardModel = new DatasetWizardModel();
Map<String, Object> properties = new HashMap<>();
if (descriptionEntity.getProperties() != null) {
JSONObject jobject = new JSONObject(descriptionEntity.getProperties());
properties = jobject.toMap();
}
PagedDatasetProfile pagedDatasetProfile = datasetManager.getPagedProfile(datasetWizardModel, descriptionEntity);
visibilityRuleService.setProperties(properties);
visibilityRuleService.buildVisibilityContext(pagedDatasetProfile.getRules());
datasetElement.appendChild(xmlBuilder.createPages(pagedDatasetProfile.getPages(), visibilityRuleService, xmlDoc));
datasetsElement.appendChild(datasetElement);
}
Element profiles = xmlDoc.createElement("profiles");
// Get DatasetProfiles from DMP to add to XML.
//TODO
// for (DMPDatasetProfile dmpDescriptionProfile : dmp.getAssociatedDmps()) {
// DescriptionTemplateEntity descriptionTemplateEntity = dmpDescriptionProfile.getDatasetprofile();
// Element profile = xmlDoc.createElement("profile");
// Element profileId = xmlDoc.createElement("profileId");
// profileId.setTextContent(descriptionTemplateEntity.getId().toString());
// profile.appendChild(profileId);
// Element profileGroupId = xmlDoc.createElement("profileGroupId");
// profileGroupId.setTextContent(descriptionTemplateEntity.getGroupId().toString());
// profile.appendChild(profileGroupId);
// Element profileLabel = xmlDoc.createElement("profileLabel");
// profileLabel.setTextContent(descriptionTemplateEntity.getLabel());
// profile.appendChild(profileLabel);
// Element profileVersion = xmlDoc.createElement("profileVersion");
// profileVersion.setTextContent(String.valueOf(descriptionTemplateEntity.getVersion()));
// profile.appendChild(profileVersion);
// Element profileInSections = xmlDoc.createElement("profileInSections");
// Map<String, Object> data = new ObjectMapper().readValue(dmpDescriptionProfile.getData(), new TypeReference<Map<String, Object>>() {});
// List<Integer> sections = (List<Integer>) data.get("dmpSectionIndex");
// for(int section: sections) {
// Element profileInSection = xmlDoc.createElement("section");
// profileInSection.setTextContent(String.valueOf(section));
// profileInSections.appendChild(profileInSection);
// }
// profile.appendChild(profileInSections);
// profiles.appendChild(profile);
// }
dmpElement.appendChild(profiles);
dmpElement.appendChild(datasetsElement);
xmlDoc.appendChild(dmpElement);
String xml = XmlBuilder.generateXml(xmlDoc);
writer.write(xml);
writer.close();
FileEnvelope fileEnvelope = new FileEnvelope();
fileEnvelope.setFile(xmlFile);
//TODO
// if (dmp.getGrant() != null && dmp.getGrant().getLabel() != null) {
// fileEnvelope.setFilename("DMP_" + dmp.getGrant().getLabel() + "_" + dmp.getVersion() + ".xml");
// }
// else {
// fileEnvelope.setFilename("DMP_" + dmp.getLabel() + "_" + dmp.getVersion() + ".xml");
// }
return fileEnvelope;
}
@Transactional
public FileEnvelope getRDAJsonDocument(String id) throws Exception {
DmpEntity dmp = databaseRepository.getDmpDao().find(UUID.fromString(id));
if (!dmp.getAccessType().equals(DmpAccessType.Public)
//TODO && dmp.getUsers().stream().noneMatch(userInfo -> this.userScope.getUserIdSafe().equals(userInfo.getUser().getId()))
)
throw new UnauthorisedException();
final boolean isFinalized = dmp.getStatus() == DmpStatus.Finalized;
final boolean isPublic = dmp.getAccessType().equals(DmpAccessType.Public);
//TODO
// dmp.setDataset(dmp.getDataset().stream()
// .filter(dataset -> dataset.getIsActive() != IsActive.Inactive &&
// dataset.getStatus() != DescriptionStatus.Canceled)
// .filter(dataset -> !isPublic && !isFinalized || dataset.getStatus() == DescriptionStatus.Finalized)
// .collect(Collectors.toSet()));
String result = rdaManager.convertToRDA(dmp);
String fileName = "";
//TODO
// if (dmp.getGrant() != null && dmp.getGrant().getLabel() != null) {
// fileName = "DMP_" + dmp.getGrant().getLabel() + "_" + dmp.getVersion();
// }
// else {
// fileName = "DMP_" + dmp.getLabel() + "_" + dmp.getVersion();
// }
fileName = fileName.replaceAll("[^a-zA-Z0-9+ ]", "").replace(" ", "_").replace(",", "_");
String uuid = UUID.randomUUID().toString();
File file = new File(this.environment.getProperty("temp.temp") + uuid + ".json");
OutputStream output = new FileOutputStream(file);
try {
output.write(result.getBytes());
output.flush();
output.close();
} catch (IOException e) {
logger.error(e.getMessage(), e);
}
FileEnvelope rdaJsonDocument = new FileEnvelope();
rdaJsonDocument.setFilename(fileName + ".json");
rdaJsonDocument.setFile(file);
return rdaJsonDocument;
}
public ResponseEntity<byte[]> getDocument(String id, String contentType, ConfigLoader configLoader) throws InstantiationException, IllegalAccessException, IOException, InvalidApplicationException {
FileEnvelope file;
switch (contentType) {
case "application/xml":
file = getXmlDocument(id);
break;
case "application/msword":
file = getWordDocument(id, configLoader);
break;
default:
file = getXmlDocument(id);
}
String fileName = file.getFilename().replace(" ", "_").replace(",", "_");
InputStream resource = new FileInputStream(file.getFile());
HttpHeaders responseHeaders = new HttpHeaders();
responseHeaders.setContentLength(file.getFile().length());
responseHeaders.setContentType(MediaType.APPLICATION_OCTET_STREAM);
responseHeaders.set("Content-Disposition", "attachment;filename=" + fileName);
responseHeaders.set("Access-Control-Expose-Headers", "Content-Disposition");
responseHeaders.get("Access-Control-Expose-Headers").add("Content-Type");
byte[] content = org.apache.poi.util.IOUtils.toByteArray(resource);
resource.close();
Files.deleteIfExists(file.getFile().toPath());
return new ResponseEntity<>(content,
responseHeaders,
HttpStatus.OK);
}
/*
* Data Import
* */
public List<DmpImportModel> createDmpFromXml(MultipartFile[] files, String[] profiles) throws IOException, JAXBException, Exception {
List<DmpImportModel> dataManagementPlans = new ArrayList<>();
// Jaxb approach.
JAXBContext jaxbContext;
for (MultipartFile multipartFile : Arrays.asList(files)) { // Gets one item from the array.
try {
InputStream in = multipartFile.getInputStream(); // Transforms item to InputStream.
jaxbContext = JAXBContext.newInstance(DmpImportModel.class);
Unmarshaller jaxbUnmarshaller = jaxbContext.createUnmarshaller();
DmpImportModel dmpImportModel = (DmpImportModel) jaxbUnmarshaller.unmarshal(in);
dataManagementPlans.add(dmpImportModel);
} catch (IOException | JAXBException ex) {
logger.error(ex.getMessage(), ex);
}
// TODO Iterate through the list of dataManagementPlans.
// Creates new dataManagementPlan to fill it with the data model that was parsed from the xml.
// Creates properties.
DataManagementPlanEditorModel dm = new DataManagementPlanEditorModel();
DmpProfileImportModel dmpProfileImportModel = dataManagementPlans.get(0).getDmpProfile();
Tuple<UUID, String> tupleProfile = new Tuple<>();
if (dmpProfileImportModel != null) {
tupleProfile.setId(dmpProfileImportModel.getDmpProfileId());
tupleProfile.setLabel(dmpProfileImportModel.getDmpProfileName());
}
else {
tupleProfile.setId(UUID.fromString("86635178-36a6-484f-9057-a934e4eeecd5"));
tupleProfile.setLabel("Dmp Default Blueprint");
}
dm.setProfile(tupleProfile);
Map<String, Object> dmpPropertiesMap = new HashMap<>();
if (dataManagementPlans.get(0).getExtraFieldsImportModels() != null) {
for (ExtraFieldsImportModels extraField: dataManagementPlans.get(0).getExtraFieldsImportModels()) {
dmpPropertiesMap.put(extraField.getId(), extraField.getValue());
}
}
dm.setProperties(dmpPropertiesMap);
//TODO
// if (this.dmpBlueprintService.fieldInBlueprint(dmpProfileImportModel.getDmpProfileId(), DmpBlueprintSystemFieldType.Funder)) {
// eu.eudat.models.data.funder.Funder funder = new eu.eudat.models.data.funder.Funder();
// FunderImportModels funderImport = dataManagementPlans.get(0).getFunderImportModels();
// funder.setId(funderImport.getId());
// funder.setLabel(funderImport.getLabel());
// FunderDMPEditorModel funderEditor = new FunderDMPEditorModel();
// funderEditor.setExistFunder(funder);
//
// dm.setFunder(funderEditor);
// }
//TODO
// if (this.dmpBlueprintService.fieldInBlueprint(dmpProfileImportModel.getDmpProfileId(), DmpBlueprintSystemFieldType.Grant)) {
// eu.eudat.models.data.grant.Grant grant = new eu.eudat.models.data.grant.Grant();
// GrantImportModels grantImport = dataManagementPlans.get(0).getGrantImport();
// grant.setId(grantImport.getId());
// grant.setLabel(grantImport.getLabel());
// grant.setAbbreviation(grantImport.getAbbreviation());
// grant.setDescription(grantImport.getDescription());
// GrantDMPEditorModel grantEditor = new GrantDMPEditorModel();
// grantEditor.setExistGrant(grant);
//
// dm.setGrant(grantEditor);
// }
//TODO
// if (this.dmpBlueprintService.fieldInBlueprint(dmpProfileImportModel.getDmpProfileId(), DmpBlueprintSystemFieldType.Project)) {
// eu.eudat.models.data.project.Project project = new eu.eudat.models.data.project.Project();
// ProjectImportModels projectImport = dataManagementPlans.get(0).getProjectImportModels();
// project.setId(projectImport.getId());
// project.setLabel(projectImport.getLabel());
// ProjectDMPEditorModel projectEditor = new ProjectDMPEditorModel();
// projectEditor.setExistProject(project);
//
// dm.setProject(projectEditor);
// }
List<eu.eudat.models.data.dmp.AssociatedProfile> associatedProfiles = new LinkedList<>();
// if (profiles != null && profiles.length > 0) {
// for (String profile : profiles) {
// DescriptionTemplate exProfile = apiContext.getOperationsContext().getDatabaseRepository().getDatasetProfileDao().find(UUID.fromString(profile));
// AssociatedProfile associatedProfile = new AssociatedProfile().fromData(exProfile);
// associatedProfiles.add(associatedProfile);
// }
// }
for (AssociatedProfileImportModels a : dataManagementPlans.get(0).getProfilesImportModels()) {
try {
eu.eudat.data.DescriptionTemplateEntity exProfile = apiContext.getOperationsContext().getDatabaseRepository().getDatasetProfileDao().find(a.getId());
AssociatedProfile associatedProfile = new AssociatedProfile().fromData(exProfile);
Map<String, Object> data = new HashMap<>();
List<Integer> sections = new ArrayList<>(a.getSection());
data.put("dmpSectionIndex", sections);
associatedProfile.setData(data);
associatedProfiles.add(associatedProfile);
} catch (Exception ignored) {
}
}
// List<eu.eudat.models.data.dmp.Organisation> organisations = new ArrayList<>();
// for (OrganisationImportModel org : dataManagementPlans.get(0).getOrganisationImportModels()) {
// eu.eudat.models.data.dmp.Organisation organisation = new eu.eudat.models.data.dmp.Organisation();
// organisation.setName(org.getOrganaisationNameImport());
// organisation.setReference(org.getOrganaisationReferenceImport());
// organisation.setKey(organisation.getReference().split(":")[0]);
// organisations.add(organisation);
// }//TODO
// List<eu.eudat.models.data.dmp.Researcher> researchers = new LinkedList<>();
// for (ResearcherImportModels res : dataManagementPlans.get(0).getResearchersImportModels()) {
// eu.eudat.models.data.dmp.Researcher researcher = new eu.eudat.models.data.dmp.Researcher();
// researcher.setLabel(res.getResearcherImportName());
// researcher.setName(res.getResearcherImportName());
// researcher.setReference(res.getResearcherImportReference());
// researcher.setKey(researcher.getReference().split(":")[0]);
// researchers.add(researcher);
// } //TODO
//List<UserListingModel> associatedUsers = new LinkedList<>();
List<DynamicFieldWithValue> dynamicFields = new LinkedList<>();
// Sets properties.
dm.setLabel(files[0].getOriginalFilename()); // Sets label.
dm.setDescription(dataManagementPlans.get(0).getDescriptionImport()); // Sets description property.
dm.setProfiles(associatedProfiles);
// dm.setOrganisations(organisations); // Sets organisations property.
// dm.setResearchers(researchers); // Sets researchers property.
//dm.setAssociatedUsers(associatedUsers); // Sets associatedUsers property.
dm.setDynamicFields(dynamicFields); // Sets dynamicFields property.
//dm.setDefinition(dmpProfile);
//ObjectMapper mapper = new ObjectMapper();
Map<String, Object> extraPropertiesMap = new HashMap<>();
if (dataManagementPlans.get(0).getLanguage() != null) {
extraPropertiesMap.put("language", dataManagementPlans.get(0).getLanguage());
}
if (dataManagementPlans.get(0).getVisibility() != null) {
extraPropertiesMap.put("visible", dataManagementPlans.get(0).getVisibility());
}
if (dataManagementPlans.get(0).getPublicDate() != null) {
extraPropertiesMap.put("publicDate", dataManagementPlans.get(0).getPublicDate());
}
if (dataManagementPlans.get(0).getCosts() != null && !dataManagementPlans.get(0).getCosts().isEmpty()) {
extraPropertiesMap.put("costs", objectMapper.readValue(dataManagementPlans.get(0).getCosts(), ArrayList.class));
}
dm.setExtraProperties(extraPropertiesMap);
//createOrUpdate(apiContext, dm, principal);
DmpEntity dmp = this.createOrUpdate(dm);
// if (dmp.getOrganisations() == null) { //TODO
// dmp.setOrganisations(new HashSet<>());
// }
// if (dmp.getResearchers() == null) {
// dmp.setResearchers(new HashSet<>());
// }
// if (dmp.getDataset() == null) {
// dmp.setDataset(new HashSet<>());
// }
// if (dmp.getUsers() == null) {
// dmp.setUsers(new HashSet<>());
// }
// if (dmp.getAssociatedDmps() == null) {
// dmp.setAssociatedDmps(new HashSet<>());
// }
List<DatasetListingModel> datasets = new LinkedList<>();
for (DatasetImportModels das: dataManagementPlans.get(0).getDatasetImportModels()) {
DescriptionEntity descriptionEntity = new DescriptionEntity();
descriptionEntity.setLabel(das.getName());
//TODO
// descriptionEntity.setDmpSectionIndex(das.getDmpSectionIndex());
// try {
// descriptionEntity.setDescriptionTemplateId(das.getProfile());
// } catch (Exception ignored) {
// descriptionEntity.setDescriptionTemplateId(associatedProfiles.get(0).getDescriptionTemplateId());
// }
// descriptionEntity.setDmpId(dmp.getId());
descriptionEntity.setProperties(objectMapper.writeValueAsString(das.getFieldImportModels()));
descriptionEntity.setStatus(DescriptionStatus.Draft);
// descriptionEntity.setRegistries(new HashSet<>());
// descriptionEntity.setDatasetDataRepositories(new HashSet<>());
// descriptionEntity.setServices(new HashSet<>());
// descriptionEntity.setDatasetExternalDatasets(new HashSet<>());
DatasetWizardModel datasetWizard = new DatasetWizardModel();
datasetWizard.setDatasetProfileDefinition(this.datasetManager.getPagedProfile(datasetWizard, descriptionEntity));
datasetWizard.fromDataModel(descriptionEntity);
this.datasetManager.createOrUpdate(datasetWizard);
// datasets.add(new DatasetListingModel().fromDataModel(dataset));
}
}
return dataManagementPlans;
}
public List<DmpEntity> createFromRDA(MultipartFile[] files, String[] profiles) throws IOException, InvalidApplicationException {
if (!this.userScope.isSet()) {
throw new UnauthorisedException("No user is logged in");
}
List<DmpEntity> result = new ArrayList<>();
for (MultipartFile file: files) {
DmpEntity dmp = rdaManager.convertToEntity(new String(file.getBytes(), "UTF-8"), profiles);
dmp.setLabel(file.getOriginalFilename());
UserEntity me = this.queryFactory.query(UserQuery.class).ids(dmp.getCreatorId()).first();
dmp.setUpdatedAt(Instant.now());
dmp.setCreatorId(me.getId());
//TODO
// Map<String, String> extraProperties = objectMapper.readValue(dmp.getExtraProperties(), HashMap.class);
// extraProperties.put("contact", me.getId().toString());
// dmp.setExtraProperties(objectMapper.writeValueAsString(extraProperties));
// dmp.setVersion(0);
// dmp.setStatus((short)0);
// dmp.setGroupId(UUID.randomUUID());
// if (dmp.getResearchers() != null && !dmp.getResearchers().isEmpty()) {
// dmp.getResearchers().stream().filter(Objects::nonNull).forEach(researcher -> {
// researcher.setId(UUID.randomUUID());
// researcher.setCreated(new Date());
// researcher.setModified(new Date());
// researcher.setStatus((short) 0);
// apiContext.getOperationsContext().getDatabaseRepository().getResearcherDao().createOrUpdate(researcher);
// });
// }
// databaseRepository.getDmpDao().createOrUpdate(dmp);
// assignUser(dmp, me);
// //TODO
//// if (this.apiContext.getOperationsContext().getElasticRepository().getDmpRepository().getClient() != null) {
//// UUID dmpId = dmp.getId();
//// dmp.setUsers(new HashSet<>(apiContext.getOperationsContext().getDatabaseRepository().getUserDmpDao().asQueryable().where((builder, root) -> builder.equal(root.get("dmp").get("id"), dmpId)).toList()));
//// this.updateIndex(dmp);
//// }
// dmp.getDataset().forEach(dataset -> {
// dataset.setStatus(DescriptionStatus.Draft);
// dataset.setCreatedAt(Instant.now());
// dataset.setUpdatedAt(Instant.now());
// //dataset.setDmpId(dmp.getId()); //TODO
// dataset = databaseRepository.getDatasetDao().createOrUpdate(dataset);
//// dataset.setRegistries(new HashSet<>());
//// dataset.setDatasetDataRepositories(new HashSet<>());
//// dataset.setDatasetExternalDatasets(new HashSet<>());
//// dataset.setServices(new HashSet<>());
// if (dmp.getOrganisations() == null) {
// dmp.setOrganisations(new HashSet<>());
// }
// if (dmp.getResearchers() == null) {
// dmp.setResearchers(new HashSet<>());
// }
// try {
// dmp.setUsers(new HashSet<>(apiContext.getOperationsContext().getDatabaseRepository().getUserDmpDao().asQueryable().where((builder, root) -> builder.equal(root.get("dmp").get("id"), dmp.getId())).toList()));
// } catch (InvalidApplicationException e) {
// throw new RuntimeException(e);
// }
//TODO
// try {
// List<Tag> tags = new ArrayList<>();
// eu.eudat.elastic.entities.Dataset elastic = apiContext.getOperationsContext().getElasticRepository().getDatasetRepository().findDocument(dataset.getId().toString());
// DatasetWizardModel datasetWizardModel = new DatasetWizardModel().fromDataModel(dataset);
// if (elastic != null) {
// tags = elastic.getTags();
// datasetWizardModel.setTags(tags);
// }
// datasetManager.getTagsFromProfile(datasetWizardModel, dataset);
// datasetManager.updateTags(dataset, datasetWizardModel.getTags());
// } catch (Exception e) {
// logger.error(e.getMessage(), e);
// }
// });
result.add(dmp);
}
return result;
}
/*
* Data assignments
* */
private void assignUser(DmpEntity dmp, UserEntity userInfo) {
this.assignUser(dmp, userInfo, DmpUserRole.Owner);
}
private void assignUser(DmpEntity dmp, UserEntity userInfo, DmpUserRole role) {
DmpUserEntity userDMP = new DmpUserEntity();
userDMP.setDmpId(dmp.getId());
userDMP.setUserId(userInfo.getId());
userDMP.setRole(role);
// databaseRepository.getUserDmpDao().createOrUpdate(userDMP);
}
private void clearUsers(DmpEntity dmp) throws InvalidApplicationException {
List<DmpUserEntity> userDMPs = this.queryFactory.query(DmpUserQuery.class).dmpIds(dmp.getId()).collect();
// userDMPs.forEach(userDMP -> apiContext.getOperationsContext().getDatabaseRepository().getUserDmpDao().delete(userDMP));
}
private void assignGrandUserIfInternal(DmpEntity dmp, UserEntity user) {
//TODO
// if (dmp.getGrant() != null && dmp.getGrant().getCreationUser() == null && (dmp.getGrant().getReference() != null && dmp.getGrant().getReference().startsWith("dmp:"))) {
// dmp.getGrant().setCreationUser(user);
// }
}
private void assignFunderUserIfInternal(DmpEntity dmp, UserEntity user) {
//TODO
// if (dmp.getGrant() != null && dmp.getGrant().getFunder() != null && dmp.getGrant().getFunder().getCreationUser() == null && ( dmp.getGrant().getFunder().getReference() != null && dmp.getGrant().getFunder().getReference().startsWith("dmp:"))) {
// dmp.getGrant().getFunder().setCreationUser(user);
// }
}
private void assignProjectUserIfInternal(DmpEntity dmp, UserEntity user) {
//TODO
// if (dmp.getProject() != null && dmp.getProject().getCreationUser() == null && (dmp.getProject().getReference() != null && dmp.getProject().getReference().startsWith("dmp:"))) {
// dmp.getProject().setCreationUser(user);
// }
}
/*
* Data Index
* */
private void updateGroupIndex(UUID groupId) throws InvalidApplicationException {
DataManagementPlanCriteria criteria = new DataManagementPlanCriteria();
criteria.setGroupIds(Collections.singletonList(groupId));
criteria.setAllVersions(true);
List<DmpEntity> dmps = databaseRepository.getDmpDao().getWithCriteria(criteria).toList();
for (DmpEntity dmp: dmps) {
// try { //TODO
// if (dmp.getUsers() == null) {
// UUID dmpId = dmp.getId();
// dmp.setUsers(new HashSet<>(apiContext.getOperationsContext().getDatabaseRepository().getUserDmpDao().asQueryable().where((builder, root) -> builder.equal(root.get("dmp").get("id"), dmpId)).toList()));
// }
//// this.updateIndex(dmp); //TODO
// } catch (InvalidApplicationException e) {
// logger.error(e.getMessage(), e);
// }
}
}
// private void updateDatasetsIndex(List<DescriptionEntity> descriptionEntities) {
// descriptionEntities.forEach(dataset -> {
// List<Tag> tags = new ArrayList<>();
// eu.eudat.elastic.entities.Dataset elastic = null;
// try {
// elastic = apiContext.getOperationsContext().getElasticRepository().getDatasetRepository().findDocument(dataset.getId().toString());
// if (elastic != null) {
// tags = elastic.getTags();
// }
// //TODO
// //UUID dmpId = dataset.getDmpId();
// //dataset.getDmp().setUsers(new HashSet<>(apiContext.getOperationsContext().getDatabaseRepository().getUserDmpDao().asQueryable().where((builder, root) -> builder.equal(root.get("dmp").get("id"), dmpId)).toList()));
// this.datasetManager.updateTags(dataset, tags);
// } catch (Exception e) {
// logger.error(e.getMessage(), e);
// }
//
// });
// }
// public void updateIndex(DMP dmp) throws IOException, InvalidApplicationException {
// DmpMapper mapper = new DmpMapper(apiContext, datasetManager);
// Dmp elastic = mapper.toElastic(dmp);
// apiContext.getOperationsContext().getElasticRepository().getDmpRepository().createOrUpdate(elastic);
// }
//
// public void generateIndex() throws InvalidApplicationException {
// if (this.authorizationService.authorize(Permission.AdminRole)) {
// if (apiContext.getOperationsContext().getElasticRepository().getDmpRepository().createIndex()) {
// List<DMP> dmps = apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().asQueryable().toList();
// dmps.forEach(dmp -> {
// try {
// UUID dmpId = dmp.getId();
// dmp.setUsers(new HashSet<>(apiContext.getOperationsContext().getDatabaseRepository().getUserDmpDao().asQueryable().where((builder, root) -> builder.equal(root.get("dmp").get("id"), dmpId)).toList()));
// this.updateIndex(dmp);
// } catch (IOException | InvalidApplicationException e) {
// logger.error(e.getMessage(), e);
// }
// });
// }
// }
// }
// public void clearIndex() throws IOException {
// if (this.authorizationService.authorize(Permission.AdminRole)) {
// apiContext.getOperationsContext().getElasticRepository().getDmpRepository().clear();
// }
// }
/*
* Data Checkup
* */
private void checkIfUserCanEditGrant(DmpEntity dmp, UserEntity user) throws Exception{
// if (dmp.getGrant() != null && dmp.getGrant().getId() != null) { //TODO
// Grant grant = apiContext.getOperationsContext().getDatabaseRepository().getGrantDao().find(dmp.getGrant().getId());
// if (grant.getFunder() != null && dmp.getGrant().getFunder() != null
// && !grant.getFunder().getId().equals(dmp.getGrant().getFunder().getId())) {
// if (grant.getCreationUser() == null) {
// throw new Exception("Grant has no user, therefore, cannot be edited.");
// }
// if (!grant.getCreationUser().getId().equals(user.getId())) {
// throw new Exception("User is not the owner of the Grant, therefore, cannot edit it.");
// }
// }
// }
}
private void checkDmpValidationRules(DmpEntity dmp) throws Exception {
if (dmp.getLabel() == null || dmp.getLabel().trim().isEmpty()) {
throw new Exception("DMP has no label.");
}
//TODO
// if (dmp.getAssociatedDmps().size() == 0) {
// throw new Exception("DMP does not contain Dataset Templates.");
// }
// if (dmp.getGrant() == null) {
// throw new Exception("DMP has no Grant assigned.");
// }
}
private boolean isUserOwnerOfDmp(DmpEntity dmp) throws InvalidApplicationException {
return this.userScope.isSet() ;
//TODO && (dmp.getUsers().stream().filter(userDMP -> userDMP.getRole().equals(UserDMP.UserDMPRoles.OWNER.getValue())).map(userDMP -> userDMP.getUser().getId())).collect(Collectors.toList()).contains(this.userScope.getUserId();
}
/*
* DOI Generation
* */
private String getPreviousDOI(UUID groupId, UUID selfId, String repositoryId) throws InvalidApplicationException {
DataManagementPlanCriteria criteria = new DataManagementPlanCriteria();
List<UUID> groupIds = new ArrayList<>();
groupIds.add(groupId);
criteria.setGroupIds(groupIds);
criteria.setAllVersions(true);
List<DmpEntity> dmps = this.databaseRepository.getDmpDao().getWithCriteria(criteria).toList();
dmps.sort((DmpEntity d1, DmpEntity d2) -> d2.getVersion() - d1.getVersion());
for (DmpEntity dmp: dmps) {
if (!dmp.getId().equals(selfId)) {
// if (dmp.getDois() != null && !dmp.getDois().isEmpty()) { //TODO
// for (Iterator<EntityDoiEntity> it = dmp.getDois().iterator(); it.hasNext(); ) {
// EntityDoiEntity entityDoi = it.next();
// if(entityDoi.getRepositoryId().equals(repositoryId)){
// return entityDoi.getDoi();
// }
// }
// }
}
}
return null;
}
@Transactional
public EntityDoi createDoi(DepositRequest depositRequest) throws Exception {
DmpEntity dmp = this.apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().find(depositRequest.getDmpId());
if (!isUserOwnerOfDmp(dmp))
throw new Exception("User is not authorized to invoke this action");
if (!dmp.getStatus().equals(DmpStatus.Finalized))
throw new Exception("DMP is not finalized");
/*if (dmp.getDoi() != null)
throw new Exception("DMP already has a DOI");*/
FileEnvelope file = getWordDocument(depositRequest.getDmpId().toString(), configLoader);
String name = file.getFilename().substring(0, file.getFilename().length() - 5).replaceAll("[^a-zA-Z0-9_+ ]", "").replace(" ", "_").replace(",", "_");
byte[] pdfFile = null; //PDFUtils.convertToPDF(file, environment); //TODO
// eu.eudat.depositinterface.models.FileEnvelope pdfEnvelope = new eu.eudat.depositinterface.models.FileEnvelope();
// pdfEnvelope.setFile(pdfFile);
// pdfEnvelope.setFilename(name + ".pdf");
// eu.eudat.depositinterface.models.FileEnvelope rdaJsonFile = new eu.eudat.depositinterface.models.FileEnvelope();
try {
FileEnvelope rdaJsonDocument = getRDAJsonDocument(depositRequest.getDmpId().toString());
//rdaJsonFile.setFile(rdaJsonDocument.getFile()); //TODO
// rdaJsonFile.setFilename(rdaJsonDocument.getFilename());
} catch (Exception e) {
logger.error(e.getMessage(), e);
}
String previousDOI = this.getPreviousDOI(dmp.getGroupId(), dmp.getId(), depositRequest.getRepositoryId());
File supportingFilesZip = this.createSupportingFilesZip(dmp);
// DmpDepositModel dmpDepositModel = new DmpDepositModel(); // DMPToDepositMapper.fromDMP(dmp, pdfEnvelope, rdaJsonFile, supportingFilesZip, previousDOI);//TODO
String finalDoi = null;
try {
finalDoi = this.repositoriesDeposit.deposit(depositRequest).getDoi();
} catch (Exception e) {
logger.error(e.getMessage(), e);
return null;
}
EntityDoi doiModel = null;
if (finalDoi != null) {
EntityDoiEntity doiEntity = new EntityDoiEntity();
doiEntity.setId(UUID.randomUUID());
doiEntity.setEntityType(EntityType.DMP);
doiEntity.setDoi(finalDoi);
doiEntity.setRepositoryId(depositRequest.getRepositoryId());
doiEntity.setCreatedAt(Instant.now());
doiEntity.setUpdatedAt(Instant.now());
doiEntity.setEntityId(dmp.getId());
//TODO: Save doi
// apiContext.getOperationsContext().getDatabaseRepository().getEntityDoiDao().createOrUpdate(doiEntity);
// dmp.getDois().add(doiEntity);
apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().createOrUpdate(dmp);
doiModel = new EntityDoi();//.fromDataModel(doiEntity); //TODO
}
if(supportingFilesZip != null) {
Files.deleteIfExists(supportingFilesZip.toPath());
}
// Files.deleteIfExists(rdaJsonFile.getFile().toPath()); //TODO
// Files.deleteIfExists(pdfFile.toPath());
// Files.deleteIfExists(file.getFile().toPath());
return doiModel;
}
private File createSupportingFilesZip(DmpEntity dmp) throws IOException, InvalidApplicationException {
FileOutputStream fout = new FileOutputStream(this.environment.getProperty("temp.temp") + "supportingFiles.zip");
ZipOutputStream zout = new ZipOutputStream(fout);
boolean hasFileUploaded = false;
Set<DescriptionEntity> descriptionEntities = new HashSet<>(); //TODO dmp.getDataset();
for (DescriptionEntity descriptionEntity : descriptionEntities) {
List<FileUpload> files = this.apiContext.getOperationsContext().getDatabaseRepository().getFileUploadDao().getFileUploads(descriptionEntity.getId());
for (FileUpload f : files) {
if(!f.getIsDeleted()){
File exportFile = new File(this.environment.getProperty("file.storage") + f.getId());
String filename = f.getName().replace(" ", "_").replace(",", "_");
byte[] content = Files.readAllBytes(exportFile.toPath());
ZipEntry ze = new ZipEntry(filename);
zout.putNextEntry(ze);
zout.write(content, 0, content.length);
zout.closeEntry();
hasFileUploaded = true;
}
}
}
zout.close();
if(!hasFileUploaded){
Files.deleteIfExists(new File(this.environment.getProperty("temp.temp") + "supportingFiles.zip").toPath());
}
return hasFileUploaded ? new File(this.environment.getProperty("temp.temp") + "supportingFiles.zip") : null;
}
/*
* Misc
* */
private void sendNotification(DmpEntity dmp, UserEntity user/*, NotificationType notificationType*/) throws InvalidApplicationException {
List<DmpUserEntity> userDMPS = this.queryFactory.query(DmpUserQuery.class).dmpIds(dmp.getId()).collect();
for (DmpUserEntity userDMP : userDMPS) {
if (!userDMP.getUserId().equals(user.getId())) {
// Notification notification = new Notification(); //TODO
// notification.setUserId(user);
// notification.setType(notificationType);
// notification.setNotifyState(NotifyState.PENDING);
// notification.setIsActive(ActiveStatus.ACTIVE);
// notification.setData("{" +
// "\"userId\": \"" + userDMP.getId() + "\"" +
//// ", \"id\": \"" + userDMP.getDmp().getId() + "\"" + //TODO
//// ", \"name\": \"" + userDMP.getDmp().getLabel() + "\"" +
// ", \"path\": \"" + notificationPaths.get(notificationType) +"\"" +
// "}");
// notification.setCreatedAt(new Date());
// notification.setUpdatedAt(notification.getCreatedAt());
// notification.setContactTypeHint(ContactType.EMAIL);
// //notification.setContactHint(userDMP.getUser().getEmail()); //TODO
// databaseRepository.getNotificationDao().createOrUpdate(notification);
}
}
}
/*public DataTableData<DataManagementPlanListingModel> getPublicPaged(DataManagmentPlanPublicTableRequest dataManagementPlanPublicTableRequest, String fieldsGroup, Principal principal) throws Exception {
dataManagementPlanPublicTableRequest.setQuery(databaseRepository.getDmpDao().asQueryable().withHint(HintedModelFactory.getHint(DataManagementPlanListingModel.class)));
QueryableList<DMP> items = dataManagementPlanPublicTableRequest.applyCriteria();
if (principal.getId() != null && dataManagementPlanPublicTableRequest.getCriteria().getRole() != null) {
items.where((builder, root) -> {
Join userJoin = root.join("users", JoinType.LEFT);
return builder.and(builder.equal(userJoin.join("user", JoinType.LEFT).get("id"), principal.getId()), builder.equal(userJoin.get("role"), dataManagementPlanPublicTableRequest.getCriteria().getRole()));
});
}
QueryableList<DMP> pagedItems = PaginationManager.applyPaging(items, dataManagementPlanPublicTableRequest);
DataTableData<DataManagementPlanListingModel> dataTable = new DataTableData<>();
CompletableFuture itemsFuture;
if (fieldsGroup.equals("listing")) {
itemsFuture = pagedItems.withHint(HintedModelFactory.getHint(DataManagementPlanListingModel.class))
.selectAsync(item -> {
item.setDataset(
item.getDataset().stream()
.filter(dataset -> dataset.getStatus().equals(Dataset.Status.FINALISED.getValue())).collect(Collectors.toSet()));
return new DataManagementPlanListingModel().fromDataModelDatasets(item);
})
.whenComplete((resultList, throwable) -> dataTable.setData(resultList));
} else {
itemsFuture = pagedItems
.selectAsync(item -> new DataManagementPlanListingModel().fromDataModel(item))
.whenComplete((resultList, throwable) -> dataTable.setData(resultList));
}
CompletableFuture countFuture = items.countAsync().whenComplete((count, throwable) -> {
dataTable.setTotalCount(count);
});
CompletableFuture.allOf(itemsFuture, countFuture).join();
return dataTable;
}
*/
/*public void unlock(UUID uuid) throws Exception {
apiContext.getOperationsContext().getDatabaseRepository().getDmpDao()
.asQueryable().where((builder, root) -> builder.equal(root.get("id"), uuid))
.update(root -> root.get("status"), DMP.DMPStatus.ACTIVE.getValue());
return;
}*/
/*public File getPdfDocument(String id) throws InstantiationException, IllegalAccessException, InterruptedException, IOException {
File file = this.getWordDocument(id);
String fileName = file.getName();
if (fileName.endsWith(".docx")){
fileName = fileName.substring(0, fileName.length() - 5);
}
return this.datasetManager.convertToPDF(file, environment, fileName);
}*/
/*public eu.eudat.models.data.dmp.DataManagementPlan getSinglePublic(String id, DynamicGrantConfiguration dynamicGrantConfiguration) throws Exception {
DMP dataManagementPlanEntity = databaseRepository.getDmpDao().find(UUID.fromString(id));
if (dataManagementPlanEntity != null && dataManagementPlanEntity.getStatus() == 1) {
eu.eudat.models.data.dmp.DataManagementPlan datamanagementPlan = new eu.eudat.models.data.dmp.DataManagementPlan();
datamanagementPlan.fromDataModel(dataManagementPlanEntity);
datamanagementPlan.setDatasets(datamanagementPlan.getDatasets().stream().filter(dataset -> dataset.getStatus() == Dataset.Status.FINALISED.getValue()).collect(Collectors.toList()));
Map dmpProperties = dataManagementPlanEntity.getDmpProperties() != null ? new org.json.JSONObject(dataManagementPlanEntity.getDmpProperties()).toMap() : null;
// datamanagementPlan.setDynamicFields(dynamicGrantConfiguration.getFields().stream().map(item -> {
// DynamicFieldWithValue fieldWithValue = new DynamicFieldWithValue();
// fieldWithValue.setId(item.getId());
// fieldWithValue.setDependencies(item.getDependencies());
// fieldWithValue.setName(item.getName());
// fieldWithValue.setQueryProperty(item.getQueryProperty());
// fieldWithValue.setRequired(item.getRequired());
// return fieldWithValue;
// }).collect(Collectors.toList()));
if (dmpProperties != null && datamanagementPlan.getDynamicFields() != null)
datamanagementPlan.getDynamicFields().forEach(item -> {
Map<String, String> properties = (Map<String, String>) dmpProperties.get(item.getId());
if (properties != null)
item.setValue(new Tuple<>(properties.get("id"), properties.get("label")));
});
return datamanagementPlan;
} else {
throw new Exception("Selected DMP is not public");
}
}
public DataManagementPlanOverviewModel getOverviewSinglePublic(String id) throws Exception {
DMP dataManagementPlanEntity = databaseRepository.getDmpDao().find(UUID.fromString(id));
if (dataManagementPlanEntity != null && dataManagementPlanEntity.getStatus() == 1) {
DataManagementPlanOverviewModel datamanagementPlan = new DataManagementPlanOverviewModel();
datamanagementPlan.fromDataModelDatasets(dataManagementPlanEntity);
datamanagementPlan.setDatasets(datamanagementPlan.getDatasets().stream().filter(dataset -> dataset.getStatus() == Dataset.Status.FINALISED.getValue()).collect(Collectors.toList()));
return datamanagementPlan;
} else {
throw new Exception("Selected DMP is not public");
}
}*/
/*public List<DataManagementPlan> getWithCriteria(DMPDao dmpsRepository, DataManagementPlanCriteriaRequest dataManagementPlanCriteria, Principal principal) throws IllegalAccessException, InstantiationException {
UUID principalID = principal.getId();
QueryableList<DMP> items = dmpsRepository.getWithCriteria(dataManagementPlanCriteria.getCriteria()).withHint(HintedModelFactory.getHint(DataManagementPlan.class));
List<Integer> roles = new LinkedList<>();
QueryableList<DMP> authenticatedItems = dmpsRepository.getAuthenticated(items, principalID, roles);
List<eu.eudat.models.data.dmp.DataManagementPlan> datamanagementPlans = authenticatedItems.select(item -> new DataManagementPlan().fromDataModel(item));
return datamanagementPlans;
}*/
}
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