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

package eu.eudat.logic.managers;

import com.fasterxml.jackson.databind.ObjectMapper;
import eu.eudat.configurations.dynamicproject.DynamicProjectConfiguration;
import eu.eudat.configurations.dynamicproject.entities.Property;
import eu.eudat.data.dao.criteria.*;
import eu.eudat.data.dao.entities.*;
import eu.eudat.data.entities.Organisation;
import eu.eudat.data.entities.Researcher;
import eu.eudat.data.entities.*;
import eu.eudat.data.query.items.item.dmp.DataManagementPlanCriteriaRequest;
import eu.eudat.data.query.items.table.dmp.DataManagementPlanTableRequest;
import eu.eudat.data.query.items.table.dmp.DataManagmentPlanPublicTableRequest;
import eu.eudat.exceptions.datamanagementplan.DMPNewVersionException;
import eu.eudat.exceptions.datamanagementplan.DMPWithDatasetsDeleteException;
import eu.eudat.exceptions.security.UnauthorisedException;
import eu.eudat.logic.builders.entity.UserInfoBuilder;
import eu.eudat.logic.services.ApiContext;
import eu.eudat.logic.services.forms.VisibilityRuleService;
import eu.eudat.logic.services.operations.DatabaseRepository;
import eu.eudat.logic.services.utilities.UtilitiesService;
import eu.eudat.logic.utilities.builders.XmlBuilder;
import eu.eudat.logic.utilities.documents.helpers.FileEnvelope;
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.models.HintedModelFactory;
import eu.eudat.models.data.datasetwizard.DatasetWizardModel;
import eu.eudat.models.data.dmp.*;
import eu.eudat.models.data.dynamicfields.DynamicFieldWithValue;
import eu.eudat.models.data.entities.xmlmodels.dmpprofiledefinition.DataManagementPlanProfile;
import eu.eudat.models.data.entities.xmlmodels.dmpprofiledefinition.Field;
import eu.eudat.models.data.helpermodels.Tuple;
import eu.eudat.models.data.helpers.common.DataTableData;
import eu.eudat.models.data.listingmodels.DataManagementPlanListingModel;
import eu.eudat.models.data.listingmodels.DataManagementPlanOverviewModel;
import eu.eudat.models.data.listingmodels.DatasetListingModel;
import eu.eudat.models.data.listingmodels.UserInfoListingModel;
import eu.eudat.models.data.security.Principal;
import eu.eudat.models.data.user.composite.PagedDatasetProfile;
import eu.eudat.models.data.userinfo.UserListingModel;
import eu.eudat.queryable.QueryableList;
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.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 javax.xml.bind.JAXBContext;
import javax.xml.bind.JAXBException;
import javax.xml.bind.Unmarshaller;
import java.io.*;
import java.math.BigInteger;
import java.net.URL;
import java.nio.file.Files;
import java.nio.file.Paths;
import java.util.*;
import java.util.concurrent.CompletableFuture;
import java.util.stream.Collectors;

@Component
public class DataManagementPlanManager {

    private ApiContext apiContext;
    private DatasetManager datasetManager;
    private UtilitiesService utilitiesService;
    private DatabaseRepository databaseRepository;
    private Environment environment;

    @Autowired
    public DataManagementPlanManager(ApiContext apiContext, DatasetManager datasetManager, Environment environment) {
        this.apiContext = apiContext;
        this.datasetManager = datasetManager;
        this.utilitiesService = apiContext.getUtilitiesService();
        this.databaseRepository = apiContext.getOperationsContext().getDatabaseRepository();
        this.environment = environment;
    }

    public DataTableData<DataManagementPlanListingModel> getPaged(DataManagementPlanTableRequest dataManagementPlanTableRequest, Principal principal, String fieldsGroup) throws Exception {
        UUID principalID = principal.getId();
        QueryableList<DMP> items = apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().getWithCriteria(dataManagementPlanTableRequest.getCriteria());
        QueryableList<DMP> authItems = apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().getAuthenticated(items, principalID);
        QueryableList<DMP> pagedItems = PaginationManager.applyPaging(authItems, dataManagementPlanTableRequest);

        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(ds -> !ds.getStatus().equals(Dataset.Status.DELETED.getValue())).collect(Collectors.toList()).stream()
                                        .filter(dataset -> dataset.getDmp().getUsers().stream().filter(userDMP -> userDMP.getRole().equals(UserDMP.UserDMPRoles.OWNER.getValue())).findFirst().get().getUser().getId().equals(principalID)
                                        || dataset.isPublic()
                                        || 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{
            itemsFuture = pagedItems
                    .selectAsync(item ->  new DataManagementPlanListingModel().fromDataModel(item))
                    .whenComplete((resultList, throwable) -> dataTable.setData(resultList));
        }

        CompletableFuture countFuture = authItems.countAsync().whenComplete((count, throwable) -> {
            dataTable.setTotalCount(count);
        });
        CompletableFuture.allOf(itemsFuture, countFuture).join();
        return dataTable;
    }

    public DataTableData<DataManagementPlanListingModel> getPaged(DataManagmentPlanPublicTableRequest dataManagementPlanPublicTableRequest, String fieldsGroup) throws Exception {
        dataManagementPlanPublicTableRequest.setQuery(databaseRepository.getDmpDao().asQueryable().withHint(HintedModelFactory.getHint(DataManagementPlanListingModel.class)));
        QueryableList<DMP> items = dataManagementPlanPublicTableRequest.applyCriteria();
        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 getWordDocument(String id) throws InstantiationException, IllegalAccessException, IOException {
        WordBuilder wordBuilder = new WordBuilder();
        VisibilityRuleService visibilityRuleService = this.utilitiesService.getVisibilityRuleService();
        DatasetWizardModel dataset = new DatasetWizardModel();
        String fileUrl = environment.getProperty("configuration.h2020template");
        InputStream is = new URL(Paths.get(fileUrl).toUri().toURL().toString()).openStream();
        XWPFDocument document = new XWPFDocument(is);

        eu.eudat.data.entities.DMP dmpEntity = databaseRepository.getDmpDao().find(UUID.fromString(id));

        // Space above DMP title.
        XWPFParagraph parAboveDmpTitle = document.createParagraph();
        XWPFParagraph parAboveDmpTitle1 = document.createParagraph();
        XWPFParagraph parAboveDmpTitle2 = document.createParagraph();
        XWPFParagraph parAboveDmpTitle3 = document.createParagraph();

        // DMP title custom style.
        //wordBuilder.addParagraphContent(dmpEntity.getLabel(), document, ParagraphStyle.TITLE, BigInteger.ZERO);
        XWPFParagraph dmpLabelParagraph = document.createParagraph();
        XWPFRun run = dmpLabelParagraph.createRun();
        run.setText(dmpEntity.getLabel());
        run.setBold(true);
        run.setFontSize(20);

        // Space below DMP title.
        XWPFParagraph parBelowDmpTitle = document.createParagraph();

        wordBuilder.addParagraphContent(dmpEntity.getDescription(), document, ParagraphStyle.TEXT, BigInteger.ZERO);

        wordBuilder.addParagraphContent("Organisations", document, ParagraphStyle.HEADER2, BigInteger.ZERO);
        if (dmpEntity.getOrganisations().size() > 0) {
            wordBuilder.addParagraphContent(dmpEntity.getOrganisations().stream().map(x -> x.getLabel()).collect(Collectors.joining(", "))
                    , document, ParagraphStyle.TEXT, BigInteger.ZERO);
        }

        wordBuilder.addParagraphContent("Researchers", document, ParagraphStyle.HEADER2, BigInteger.ZERO);
        if (dmpEntity.getResearchers().size() > 0) {
            wordBuilder.addParagraphContent(dmpEntity.getResearchers().stream().map(x -> x.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.TITLE, BigInteger.ZERO);
        dmpEntity.getDataset().stream().forEach(datasetEntity -> {
            Map<String, Object> properties = new HashMap<>();
            if (datasetEntity.getProperties() != null) {
                JSONObject jobject = new JSONObject(datasetEntity.getProperties());
                properties = jobject.toMap();
            }

            // Custom style for the Dataset title.
            //wordBuilder.addParagraphContent("Title: " + datasetEntity.getLabel(), document, ParagraphStyle.HEADER1, BigInteger.ZERO);
            XWPFParagraph datasetLabelParagraph = document.createParagraph();

            XWPFRun runDatasetTitle1 = datasetLabelParagraph.createRun();
            runDatasetTitle1.setText("Title: ");
            runDatasetTitle1.setBold(true);
            runDatasetTitle1.setFontSize(12);

            XWPFRun runDatasetTitle = datasetLabelParagraph.createRun();
            runDatasetTitle.setText(datasetEntity.getLabel());
            runDatasetTitle.setColor("2E75B6");
            runDatasetTitle.setBold(true);
            runDatasetTitle.setFontSize(12);

            wordBuilder.addParagraphContent(datasetEntity.getDescription(), document, ParagraphStyle.TEXT, BigInteger.ZERO);
            wordBuilder.addParagraphContent("Dataset Description", document, ParagraphStyle.HEADER1, BigInteger.ZERO);
            PagedDatasetProfile pagedDatasetProfile = datasetManager.getPagedProfile(dataset, datasetEntity);
            visibilityRuleService.setProperties(properties);
            visibilityRuleService.buildVisibilityContext(pagedDatasetProfile.getRules());
            try {
                wordBuilder.build(document, pagedDatasetProfile, visibilityRuleService);
            } catch (IOException e) {
                e.printStackTrace();
            }
            // Page break at the end of the Dataset.
            XWPFParagraph parBreakDataset = document.createParagraph();
        });
        String fileName = dmpEntity.getLabel();
        fileName = fileName.replaceAll("[^a-zA-Z0-9+ ]", "");
        File exportFile = new File(environment.getProperty("configuration.exportUrl") + fileName + ".docx");
        FileOutputStream out = new FileOutputStream(exportFile);
        document.write(out);
        out.close();

        return exportFile;
    }

    /*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 getSingle(String id, Principal principal, DynamicProjectConfiguration dynamicProjectConfiguration) throws InstantiationException, IllegalAccessException {
        DMP dataManagementPlanEntity = databaseRepository.getDmpDao().find(UUID.fromString(id));
        if (dataManagementPlanEntity.getUsers().stream().filter(userInfo -> userInfo.getUser().getId() == principal.getId()).collect(Collectors.toList()).size() == 0)
            throw new UnauthorisedException();
        eu.eudat.models.data.dmp.DataManagementPlan datamanagementPlan = new eu.eudat.models.data.dmp.DataManagementPlan();
        datamanagementPlan.fromDataModel(dataManagementPlanEntity);
        Map dmpProperties = dataManagementPlanEntity.getDmpProperties() != null ? new org.json.JSONObject(dataManagementPlanEntity.getDmpProperties()).toMap() : null;
        datamanagementPlan.setDynamicFields(dynamicProjectConfiguration.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;
    }

    public DataManagementPlanOverviewModel getOverviewSingle(String id, Principal principal) throws InstantiationException, IllegalAccessException {
        DMP dataManagementPlanEntity = databaseRepository.getDmpDao().find(UUID.fromString(id));
        if (dataManagementPlanEntity.getUsers()
                .stream().filter(userInfo -> userInfo.getUser().getId() == principal.getId())
                .collect(Collectors.toList()).size() == 0)
            throw new UnauthorisedException();
        DataManagementPlanOverviewModel datamanagementPlan = new DataManagementPlanOverviewModel();
        datamanagementPlan.fromDataModelDatasets(dataManagementPlanEntity);

        /*Map dmpProperties = dataManagementPlanEntity.getDmpProperties() != null ? new org.json.JSONObject(dataManagementPlanEntity.getDmpProperties()).toMap() : null;
        datamanagementPlan.setDynamicFields(dynamicProjectConfiguration.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;
    }

    public eu.eudat.models.data.dmp.DataManagementPlan getSinglePublic(String id, DynamicProjectConfiguration dynamicProjectConfiguration) 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(dynamicProjectConfiguration.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 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));
        QueryableList<DMP> authenticatedItems = dmpsRepository.getAuthenticated(items, principalID);
        List<eu.eudat.models.data.dmp.DataManagementPlan> datamanagementPlans = authenticatedItems.select(item -> new DataManagementPlan().fromDataModel(item));
        return datamanagementPlans;
    }

    public List<Tuple<String, String>> getDynamicFields(String id, DynamicProjectConfiguration dynamicProjectConfiguration, 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 = dynamicProjectConfiguration.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 void createOrUpdate(ApiContext apiContext, DataManagementPlan dataManagementPlan, Principal principal) throws Exception {

        DMP newDmp = dataManagementPlan.toDataModel();
        UserInfo user = apiContext.getOperationsContext().getDatabaseRepository().getUserInfoDao().find(principal.getId());
        //newDmp.setCreator(user);

        createOrganisationsIfTheyDontExist(newDmp, apiContext.getOperationsContext().getDatabaseRepository().getOrganisationDao());
        createResearchersIfTheyDontExist(newDmp, apiContext.getOperationsContext().getDatabaseRepository().getResearcherDao());
        createProjectIfItDoesntExist(newDmp, apiContext.getOperationsContext().getDatabaseRepository().getProjectDao(), user);

        try {
            DMP dmp = apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().find(dataManagementPlan.getId());
            newDmp.setCreated(dmp.getCreated());
            if (dmp.getUsers().stream().filter(userInfo -> userInfo.getUser().getId() == principal.getId())
                    .collect(Collectors.toList()).size() == 0) {
                List<UserDMP> userDMPList = dmp.getUsers().stream().collect(Collectors.toList());
                for (UserInfoListingModel userInfoListingModel : dataManagementPlan.getUsers()) {
                    for(UserDMP userDMP : userDMPList) {
                        if (!(userDMP.getUser().getId().equals(userInfoListingModel.getId()))) {
                            apiContext.getOperationsContext().getDatabaseRepository().getUserDmpDao().delete(userDMP);
                        }
                    }
                }
            }
        } catch (Exception e) {
            newDmp.setCreated(new Date());
        }

        newDmp = apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().createOrUpdate(newDmp);

        if (dataManagementPlan.getStatus() == DMP.DMPStatus.FINALISED.getValue()) {
            apiContext.getOperationsContext().getDatabaseRepository().getDatasetDao()
                    .asQueryable().where((builder, root) -> root.get("id").in(dataManagementPlan.getDatasets()
                    .stream().map(x -> UUID.fromString(x.getId())).collect(Collectors.toList())))
                    .update(root -> root.<Integer>get("status"), Dataset.Status.FINALISED.getValue());
        }

        if (dataManagementPlan.getAssociatedUsers().size() == 0)
            assignUser(newDmp, user, apiContext);
    }

    public void assignUser(DMP dmp, UserInfo userInfo, ApiContext apiContext) {
        UserDMP userDMP = new UserDMP();
        userDMP.setDmp(dmp);
        userDMP.setUser(userInfo);
        userDMP.setRole(UserDMP.UserDMPRoles.OWNER.getValue());
        apiContext.getOperationsContext().getDatabaseRepository().getUserDmpDao().createOrUpdate(userDMP);
    }

    public void newVersion(UUID uuid, DataManagementPlanNewVersionModel dataManagementPlan, Principal principal) throws Exception {
        DMP oldDmp = apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().find(uuid);

        DataManagementPlanCriteria criteria = new DataManagementPlanCriteria();
        LinkedList<UUID> list = new LinkedList<>();
        list.push(oldDmp.getGroupId());
        criteria.setGroupIds(list);
        criteria.setAllVersions(false);
        QueryableList<DMP> dataManagementPlanQueryableList = apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().getWithCriteria(criteria);
        List<DMP> latestVersionDMP = dataManagementPlanQueryableList.toList();

        if(latestVersionDMP.get(0).getVersion().equals(oldDmp.getVersion())){
            DMP newDmp = dataManagementPlan.toDataModel();
            createOrganisationsIfTheyDontExist(newDmp, apiContext.getOperationsContext().getDatabaseRepository().getOrganisationDao());
            createResearchersIfTheyDontExist(newDmp, apiContext.getOperationsContext().getDatabaseRepository().getResearcherDao());
            UserInfo user = apiContext.getOperationsContext().getBuilderFactory().getBuilder(UserInfoBuilder.class).id(principal.getId()).build();
            createProjectIfItDoesntExist(newDmp, apiContext.getOperationsContext().getDatabaseRepository().getProjectDao(), user);

            newDmp.setGroupId(oldDmp.getGroupId());
            newDmp.setVersion(oldDmp.getVersion() + 1);
            newDmp.setId(null);
            newDmp = apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().createOrUpdate(newDmp);

            // Assign creator.
            UserDMP userDMP = new UserDMP();
            userDMP.setDmp(newDmp);
            userDMP.setUser(user);
            userDMP.setRole((UserDMP.UserDMPRoles.OWNER.getValue()));
            apiContext.getOperationsContext().getDatabaseRepository().getUserDmpDao().createOrUpdate(userDMP);

            copyDatasets(newDmp, apiContext.getOperationsContext().getDatabaseRepository().getDatasetDao());
        } else {
            throw new DMPNewVersionException("Version to update not the latest.");
        }
    }

    public void clone(UUID uuid, DataManagementPlanNewVersionModel dataManagementPlan, Principal principal) throws Exception {
        DMP newDmp = dataManagementPlan.toDataModel();
        createOrganisationsIfTheyDontExist(newDmp, apiContext.getOperationsContext().getDatabaseRepository().getOrganisationDao());
        createResearchersIfTheyDontExist(newDmp, apiContext.getOperationsContext().getDatabaseRepository().getResearcherDao());
        UserInfo user = apiContext.getOperationsContext().getBuilderFactory().getBuilder(UserInfoBuilder.class).id(principal.getId()).build();
        createProjectIfItDoesntExist(newDmp, apiContext.getOperationsContext().getDatabaseRepository().getProjectDao(), user);

        newDmp.setGroupId(UUID.randomUUID());
        newDmp.setVersion(0);
        newDmp.setId(null);
        newDmp = apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().createOrUpdate(newDmp);

        // Assign creator.
        UserDMP userDMP = new UserDMP();
        userDMP.setDmp(newDmp);
        userDMP.setUser(user);
        userDMP.setRole((UserDMP.UserDMPRoles.OWNER.getValue()));
        apiContext.getOperationsContext().getDatabaseRepository().getUserDmpDao().createOrUpdate(userDMP);
        copyDatasets(newDmp, apiContext.getOperationsContext().getDatabaseRepository().getDatasetDao());
    }

    public void delete(UUID uuid) throws DMPWithDatasetsDeleteException {
        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");
        DMP oldDmp = apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().find(uuid);
        oldDmp.setStatus(DMP.DMPStatus.DELETED.getValue());
        apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().createOrUpdate(oldDmp);
    }

    private void createResearchersIfTheyDontExist(DMP newDmp, ResearcherDao researcherRepository) {
        if (newDmp.getResearchers() != null && !newDmp.getResearchers().isEmpty()) {
            for (eu.eudat.data.entities.Researcher researcher : newDmp.getResearchers()) {
                ResearcherCriteria criteria = new ResearcherCriteria();
                criteria.setLike(researcher.getReference());
                List<eu.eudat.data.entities.Researcher> entries = researcherRepository.getWithCriteria(criteria).toList();
                if (entries != null && !entries.isEmpty()) researcher.setId(entries.get(0).getId());
                else researcher = researcherRepository.createOrUpdate(researcher);
            }
        }
    }

    private void createOrganisationsIfTheyDontExist(DMP newDmp, OrganisationDao organisationRepository) {
        if (newDmp.getOrganisations() != null && !newDmp.getOrganisations().isEmpty()) {
            for (eu.eudat.data.entities.Organisation organisation : newDmp.getOrganisations()) {
                OrganisationCriteria criteria = new OrganisationCriteria();
                criteria.setLike(organisation.getReference());
                List<eu.eudat.data.entities.Organisation> entries = organisationRepository.getWithCriteria(criteria).toList();
                if (entries != null && !entries.isEmpty()) organisation.setId(entries.get(0).getId());
                else organisation = organisationRepository.createOrUpdate(organisation);
            }
        }
    }

    private void createProjectIfItDoesntExist(DMP newDmp, ProjectDao projectDao, UserInfo userInfo) {
        if (newDmp.getProject() != null) {
            Project project = newDmp.getProject();
            ProjectCriteria criteria = new ProjectCriteria();
            criteria.setReference(project.getReference());
            eu.eudat.data.entities.Project projectEntity = projectDao.getWithCriteria(criteria).getSingleOrDefault();
            if (projectEntity != null) project.setId(projectEntity.getId());
            else {
                project.setType(Project.ProjectType.EXTERNAL.getValue());
                projectDao.createOrUpdate(project);
            }
        }
    }

    private void copyDatasets(DMP newDmp, DatasetDao datasetDao) {
        List<CompletableFuture<Dataset>> futures = new LinkedList<>();
        for (Dataset dataset : newDmp.getDataset()) {
            datasetDao.asQueryable().withHint(HintedModelFactory.getHint(DatasetListingModel.class)).where((builder, root) -> builder.equal(root.get("id"), dataset.getId())).getSingleAsync()
                    .thenApplyAsync(entityDataset -> {
                        Dataset newDataset = new Dataset();
                        newDataset.update(entityDataset);
                        newDataset.setDmp(newDmp);
                        newDataset.setStatus(Dataset.Status.SAVED.getValue());
                        if (newDataset.getDatasetDataRepositories() != null) {
                            newDataset.setDatasetDataRepositories(newDataset.getDatasetDataRepositories().stream().map(item -> {
                                DataRepository dataRepository = new DataRepository();
                                dataRepository.setId(item.getId());

                                DatasetDataRepository datasetDataRepository = new DatasetDataRepository();
                                datasetDataRepository.setDataRepository(dataRepository);
                                datasetDataRepository.setDataset(newDataset);
                                return datasetDataRepository;
                            }).collect(Collectors.toSet()));
                        }

                        if (newDataset.getDatasetExternalDatasets() != null) {
                            newDataset.setDatasetExternalDatasets(newDataset.getDatasetExternalDatasets().stream().map(item -> {
                                ExternalDataset externalDataset = new ExternalDataset();
                                externalDataset.setId(item.getId());
                                DatasetExternalDataset datasetExternalDataset = new DatasetExternalDataset();
                                datasetExternalDataset.setExternalDataset(externalDataset);
                                datasetExternalDataset.setDataset(newDataset);
                                return datasetExternalDataset;
                            }).collect(Collectors.toSet()));
                        }

                        if (newDataset.getRegistries() != null) {
                            newDataset.setRegistries(newDataset.getRegistries().stream().map(item -> {
                                Registry registry = new Registry();
                                registry.setId(item.getId());
                                return registry;
                            }).collect(Collectors.toSet()));
                        }

                        if (newDataset.getServices() != null) {
                            newDataset.setServices(newDataset.getServices().stream().map(item -> {
                                Service service = new Service();
                                service.setId(item.getId());
                                DatasetService datasetService = new DatasetService();
                                datasetService.setService(service);
                                datasetService.setDataset(newDataset);
                                return datasetService;
                            }).collect(Collectors.toSet()));
                        }
                        newDataset.setCreated(new Date());
                        return newDataset;
                    }).thenApplyAsync(item -> {
                futures.add(datasetDao.createOrUpdateAsync(item));
                return futures;
            }).join();

        }
    }

    public FileEnvelope getXmlDocument(String id) throws InstantiationException, IllegalAccessException, IOException {
        ExportXmlBuilder xmlBuilder = new ExportXmlBuilder();
        VisibilityRuleService visibilityRuleService = utilitiesService.getVisibilityRuleService();
        eu.eudat.data.entities.DMP dmp = databaseRepository.getDmpDao().find(UUID.fromString(id));
        List<Dataset> datasets = dmp.getDataset().stream().collect(Collectors.toList());
        String fileName = dmp.getLabel();
        fileName = fileName.replaceAll("[^a-zA-Z0-9+ ]", "");
        File xmlFile = new File(fileName + ".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);

        DMPProfile dmpProfile = dmp.getProfile();
        Element dmpProfileElement = xmlDoc.createElement("dmpProfile");
        Element dmpProfileName = xmlDoc.createElement("dmpProfileName");
        if (!(dmpProfile == null)){
            dmpProfileName.setTextContent(dmpProfile.getLabel());
            dmpProfileElement.appendChild(dmpProfileName);
            Element dmpProfileId = xmlDoc.createElement("dmpProfileId");
            dmpProfileId.setTextContent(dmpProfile.getId().toString());
            dmpProfileElement.appendChild(dmpProfileId);
            Element values = xmlDoc.createElement("values");
            values.setTextContent(dmpProfile.getDefinition());
            dmpProfileElement.appendChild(values);
        }
        dmpElement.appendChild(dmpProfileElement);

        Element project = xmlDoc.createElement("project");
        Element label = xmlDoc.createElement("label");
        label.setTextContent(dmp.getProject().getLabel());
        project.appendChild(label);
        Element projectId = xmlDoc.createElement("id");
        projectId.setTextContent(dmp.getProject().getId().toString());
        project.appendChild(projectId);
        dmpElement.appendChild(project);
        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 datasetsElement = xmlDoc.createElement("datasets");

        for (Dataset dataset : datasets) {
            Element datasetElement = xmlDoc.createElement("dataset");

            DatasetWizardModel datasetWizardModel = new DatasetWizardModel();
            Map<String, Object> properties = new HashMap<>();
            if (dataset.getProperties() != null) {
                JSONObject jobject = new JSONObject(dataset.getProperties());
                properties = jobject.toMap();
            }
            PagedDatasetProfile pagedDatasetProfile = datasetManager.getPagedProfile(datasetWizardModel, dataset);
            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.
        for (DatasetProfile datasetProfile : dmp.getAssociatedDmps()) {
            Element profile = xmlDoc.createElement("profile");
            Element profileLabel = xmlDoc.createElement("profilelabel");
            profileLabel.setTextContent(datasetProfile.getLabel());
            profile.appendChild(profileLabel);
            Element profileId = xmlDoc.createElement("profileId");
            profileId.setTextContent(datasetProfile.getId().toString());
            profile.appendChild(profileId);
            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);
        fileEnvelope.setFilename(dmp.getLabel());

        return fileEnvelope;
    }

    public ResponseEntity<byte[]>  getRDAJsonDocument(String id) throws IOException {
        eu.eudat.data.entities.DMP dmp = databaseRepository.getDmpDao().find(UUID.fromString(id));
        DmpRDAExportModel dmpExport = new DmpRDAExportModel().fromDataModel(dmp);
        RDAExportModel rdaExportModel = new RDAExportModel();
        rdaExportModel.setDmp(dmpExport);

        ObjectMapper mapper = new ObjectMapper();
        String fileName = dmp.getLabel();
        fileName = fileName.replaceAll("[^a-zA-Z0-9+ ]", "");
        File file = new File(fileName);
        try {
            mapper.writeValue(file, rdaExportModel);
        }
        catch (IOException e) {
            e.printStackTrace();
        }

        InputStream resource = new FileInputStream(file);
        HttpHeaders responseHeaders = new HttpHeaders();
        responseHeaders.setContentLength(file.length());
        responseHeaders.setContentType(MediaType.APPLICATION_OCTET_STREAM);
        responseHeaders.set("Content-Disposition", "attachment;filename=" + file.getName());
        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.toPath());
        return new ResponseEntity<>(content, responseHeaders, HttpStatus.OK);
    }

    public ResponseEntity<byte[]> getDocument(String id, String contentType) throws InstantiationException, IllegalAccessException, IOException {
        File file;
        switch (contentType){
            case "application/xml":
                file = getXmlDocument(id).getFile();
                break;
            case "application/msword":
                file = getWordDocument(id);
                break;
            /*case "application/pdf":
                file = getPdfDocument(id);
                break;*/
            default:
                file = getXmlDocument(id).getFile();
        }
        InputStream resource = new FileInputStream(file);
        HttpHeaders responseHeaders = new HttpHeaders();
        responseHeaders.setContentLength(file.length());
        responseHeaders.setContentType(MediaType.APPLICATION_OCTET_STREAM);
        responseHeaders.set("Content-Disposition", "attachment;filename=" + file.getName());
        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.toPath());
        return new ResponseEntity<>(content,
                responseHeaders,
                HttpStatus.OK);
    }

    public List<DmpImportModel> createDmpFromXml( ApiContext apiContext, MultipartFile[] files, Principal principal) 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){
                ex.printStackTrace();
            }
            // TODO Iterate through the list of dataManagmentPlans.
            // Creates new dataManagmentPlan to fill it with the data model that was parsed from the xml.
            // Creates properties.
            DataManagementPlan dm = new DataManagementPlan();
            DataManagementPlanProfile dmpProfile = new DataManagementPlanProfile();

            List<Field> fieldList = new LinkedList<>();
            Field field = new Field();
            field.setLabel(dataManagementPlans.get(0).getDmpProfile().getDmpProfileName());
            field.setId(dataManagementPlans.get(0).getDmpProfile().getDmpProfileId());

            fieldList.add(field);
            dmpProfile.setFields(fieldList);

            /*Tuple tuple = new Tuple();
            tuple.setId(dataManagementPlans.get(0).getDmpProfile().getDmpProfileId());
            tuple.setLabel(dataManagementPlans.get(0).getDmpProfile().getDmpProfileName());*/
            eu.eudat.models.data.project.Project project = new eu.eudat.models.data.project.Project();
            ProjectImportModels projectImport = dataManagementPlans.get(0).getProjectImport();
            project.setId(projectImport.getId());
            project.setLabel(projectImport.getLabel());
            project.setAbbreviation(projectImport.getAbbreviation());
            project.setDescription(projectImport.getDescription());
            List<eu.eudat.models.data.dmp.AssociatedProfile> associatedProfiles = new LinkedList<>();
            for(AssociatedProfileImportModels a : dataManagementPlans.get(0).getProfilesImportModels()) {
                AssociatedProfile associatedProfile = new AssociatedProfile();
                associatedProfile.setId(a.getId());
                associatedProfile.setLabel(a.getLabel());
                associatedProfiles.add(associatedProfile);
            }
            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.setLabel(org.getOrganaisationNameImport());
                organisation.setId(org.getOrganaisationReferenceImport());
                organisations.add(organisation);
            }
            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.setId(res.getResearcherImportReference());
                researchers.add(researcher);
            }

            List<UserListingModel> associatedUsers = new LinkedList<>();
            List<DynamicFieldWithValue> dynamicFields = new LinkedList<>();

            // Sets properties.
            dm.setLabel(files[0].getOriginalFilename());  // Sets label.
            dm.setProject(project);  //Sets project property.
            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);

            createOrUpdate(apiContext, dm, principal);

            System.out.println(dm);
        }

        return dataManagementPlans;
    }
}