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

package eu.eudat.logic.managers;

import eu.eudat.configurations.dynamicproject.DynamicProjectConfiguration;
import eu.eudat.configurations.dynamicproject.entities.Property;
import eu.eudat.data.dao.criteria.DynamicFieldsCriteria;
import eu.eudat.data.dao.criteria.OrganisationCriteria;
import eu.eudat.data.dao.criteria.ProjectCriteria;
import eu.eudat.data.dao.criteria.ResearcherCriteria;
import eu.eudat.data.dao.entities.*;
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.exceptions.datamanagementplan.DMPWithDatasetsException;
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.utilities.builders.XmlBuilder;
import eu.eudat.logic.utilities.documents.helpers.FileEnvelope;
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.DataManagementPlan;
import eu.eudat.models.data.dmp.DataManagementPlanNewVersionModel;
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.DataManagementPlanListingModel;
import eu.eudat.models.data.listingmodels.DatasetListingModel;
import eu.eudat.models.data.security.Principal;
import eu.eudat.models.data.user.composite.PagedDatasetProfile;
import eu.eudat.queryable.QueryableList;
import org.json.JSONObject;
import org.springframework.http.*;
import org.springframework.web.client.RestTemplate;
import org.w3c.dom.Document;
import org.w3c.dom.Element;

import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.util.*;
import java.util.concurrent.CompletableFuture;
import java.util.stream.Collectors;

public class DataManagementPlanManager {

    public DataTableData<DataManagementPlanListingModel> getPaged(ApiContext apiContext, DataManagementPlanTableRequest dataManagementPlanTableRequest, Principal principal) throws Exception {
        UserInfo userInfo = new UserInfo();
        userInfo.setId(principal.getId());
        QueryableList<DMP> items = apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().getWithCriteria(dataManagementPlanTableRequest.getCriteria()).withHint(HintedModelFactory.getHint(DataManagementPlanListingModel.class));
        QueryableList<DMP> authItems = apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().getAuthenticated(items, userInfo);
        QueryableList<DMP> pagedItems = PaginationManager.applyPaging(authItems, dataManagementPlanTableRequest);

        DataTableData<DataManagementPlanListingModel> dataTable = new DataTableData<>();

        CompletableFuture itemsFuture = pagedItems.withHint(HintedModelFactory.getHint(DataManagementPlanListingModel.class))
                .selectAsync(item -> {
                    item.setDataset(
                            item.getDataset().stream()
                                    .filter(dataset -> dataset.getDmp().getCreator().getId().equals(userInfo.getId())
                                            || dataset.isPublic()
                                            || dataset.getDmp().getUsers().stream()
                                            .filter(x -> x.getId().equals(userInfo.getId())).collect(Collectors.toList()).size() > 0).collect(Collectors.toSet()));
                    return 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 eu.eudat.models.data.dmp.DataManagementPlan getSingle(DMPDao dmpsRepository, String id, Principal principal, DynamicProjectConfiguration dynamicProjectConfiguration) throws InstantiationException, IllegalAccessException {
        DMP dataManagementPlanEntity = dmpsRepository.find(UUID.fromString(id));
        if (dataManagementPlanEntity.getCreator().getId() != principal.getId() && dataManagementPlanEntity.getUsers().stream().filter(userInfo -> userInfo.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<String, String>(properties.get("id"), properties.get("label")));
            });
        return datamanagementPlan;
    }

    public List<DataManagementPlan> getWithCriteria(DMPDao dmpsRepository, DataManagementPlanCriteriaRequest dataManagementPlanCriteria, Principal principal) throws IllegalAccessException, InstantiationException {
        UserInfo userInfo = new UserInfo();
        userInfo.setId(principal.getId());
        QueryableList<DMP> items = dmpsRepository.getWithCriteria(dataManagementPlanCriteria.getCriteria()).withHint(HintedModelFactory.getHint(DataManagementPlan.class));
        QueryableList<DMP> authenticatedItems = dmpsRepository.getAuthenticated(items, userInfo);
        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 static void createOrUpdate(ApiContext apiContext, DataManagementPlan 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().getDatabaseRepository().getUserInfoDao().find(principal.getId());
        createProjectIfItDoesntExist(newDmp, apiContext.getOperationsContext().getDatabaseRepository().getProjectDao(), user);
        newDmp.setCreator(user);
        newDmp = apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().createOrUpdate(newDmp);
        if (dataManagementPlan.getAssociatedUsers().stream().filter(item -> item.getId() == principal.getId()).collect(Collectors.toList()).size() == 0)
            assignUser(newDmp, user, apiContext);
    }

    public static 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 static void newVersion(ApiContext apiContext, UUID uuid, DataManagementPlanNewVersionModel dataManagementPlan, Principal principal) throws Exception {
        DMP oldDmp = apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().find(uuid);
        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.setCreator(user);
        newDmp.setGroupId(oldDmp.getGroupId());
        newDmp.setVersion(oldDmp.getVersion() + 1);
        newDmp.setId(null);
        newDmp = apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().createOrUpdate(newDmp);
        copyDatasets(newDmp, apiContext.getOperationsContext().getDatabaseRepository().getDatasetDao());
    }

    public static void clone(ApiContext apiContext, 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.setCreator(user);
        newDmp.setGroupId(UUID.randomUUID());
        newDmp.setVersion(0);
        newDmp.setId(null);
        newDmp = apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().createOrUpdate(newDmp);
        copyDatasets(newDmp, apiContext.getOperationsContext().getDatabaseRepository().getDatasetDao());
    }

    public static void delete(ApiContext apiContext, UUID uuid) throws DMPWithDatasetsException {
        DMP oldDmp = apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().find(uuid);
        if (oldDmp.getDataset().size() > 0)
            throw new DMPWithDatasetsException("You cannot Remove Datamanagement Plan with Datasets");
        oldDmp.setStatus(DMP.DMPStatus.DELETED.getValue());
        apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().createOrUpdate(oldDmp);
    }

    private static 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 static 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 static 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 static 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(DMPDao dmpRepository, String id, VisibilityRuleService visibilityRuleService) throws InstantiationException, IllegalAccessException, IOException {
        ExportXmlBuilder xmlBuilder = new ExportXmlBuilder();
        eu.eudat.data.entities.DMP dmp = dmpRepository.find(UUID.fromString(id));
        List<Dataset> datasets = dmp.getDataset().stream().collect(Collectors.toList());
        File xmlFile = new File(UUID.randomUUID() + ".xml");
        BufferedWriter writer = new BufferedWriter(new FileWriter(xmlFile, true));
        Document xmlDoc = XmlBuilder.getDocument();
        Element root = xmlDoc.createElement("root");
        Element dmpElement = xmlDoc.createElement("dmp");
        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 = new DatasetManager().getPagedProfile(datasetWizardModel, dataset);
            visibilityRuleService.setProperties(properties);
            visibilityRuleService.buildVisibilityContext(pagedDatasetProfile.getRules());
            datasetElement.appendChild(xmlBuilder.createPages(pagedDatasetProfile.getPages(), visibilityRuleService, xmlDoc));
            datasetsElement.appendChild(datasetElement);
        }
        dmpElement.appendChild(datasetsElement);
        root.appendChild(dmpElement);
        xmlDoc.appendChild(root);
        String xml = XmlBuilder.generateXml(xmlDoc);
        writer.write(xml);
        writer.close();
        FileEnvelope fileEnvelope = new FileEnvelope();
        fileEnvelope.setFile(xmlFile);
        fileEnvelope.setFilename(dmp.getLabel());
        return fileEnvelope;
    }

}