package eu.eudat.logic.services.references; import com.fasterxml.jackson.core.JsonProcessingException; import eu.eudat.authorization.AuthorizationFlags; import eu.eudat.authorization.Permission; import eu.eudat.commons.XmlHandlingService; import eu.eudat.commons.enums.IsActive; import eu.eudat.commons.enums.ReferenceType; import eu.eudat.commons.scope.user.UserScope; import eu.eudat.commons.types.reference.DefinitionEntity; import eu.eudat.commons.types.reference.FieldEntity; import eu.eudat.configurations.referencetype.ReferenceTypeProperties; import eu.eudat.convention.ConventionService; import eu.eudat.data.ReferenceEntity; import eu.eudat.data.dao.criteria.*; import eu.eudat.data.old.DataRepository; import eu.eudat.data.old.ExternalDataset; import eu.eudat.data.old.Registry; import eu.eudat.data.old.Service; import eu.eudat.logic.builders.model.criteria.ExternalDatasetCriteriaBuilder; import eu.eudat.logic.proxy.config.ExternalUrlCriteria; import eu.eudat.logic.proxy.config.exceptions.HugeResultSet; import eu.eudat.logic.proxy.config.exceptions.NoURLFound; import eu.eudat.logic.proxy.fetching.RemoteFetcher; import eu.eudat.logic.services.ApiContext; import eu.eudat.model.Reference; import eu.eudat.model.builder.ReferenceBuilder; import eu.eudat.model.builder.referencesearch.ReferenceSearchBuilder; import eu.eudat.model.deleter.ReferenceDeleter; import eu.eudat.model.persist.ReferencePersist; import eu.eudat.model.persist.referencedefinition.DefinitionPersist; import eu.eudat.model.persist.referencedefinition.FieldPersist; import eu.eudat.models.data.FetcherReference; import eu.eudat.query.ReferenceQuery; import eu.eudat.query.lookup.ReferenceSearchLookup; import eu.eudat.queryable.QueryableList; import gr.cite.commons.web.authz.service.AuthorizationService; import gr.cite.tools.data.builder.BuilderFactory; import gr.cite.tools.data.deleter.DeleterFactory; import gr.cite.tools.data.query.QueryFactory; import gr.cite.tools.exception.MyApplicationException; import gr.cite.tools.exception.MyForbiddenException; import gr.cite.tools.exception.MyNotFoundException; import gr.cite.tools.exception.MyValidationException; import gr.cite.tools.fieldset.BaseFieldSet; import gr.cite.tools.fieldset.FieldSet; import gr.cite.tools.logging.LoggerService; import gr.cite.tools.logging.MapLogEntry; import jakarta.persistence.EntityManager; import jakarta.xml.bind.JAXBException; import org.jetbrains.annotations.NotNull; import org.slf4j.LoggerFactory; import org.springframework.context.MessageSource; import org.springframework.context.i18n.LocaleContextHolder; import javax.management.InvalidApplicationException; import javax.xml.parsers.ParserConfigurationException; import javax.xml.transform.TransformerException; import java.time.Instant; import java.util.*; import java.util.stream.Collectors; @org.springframework.stereotype.Service public class ReferenceService { private static final LoggerService logger = new LoggerService(LoggerFactory.getLogger(ReferenceService.class)); private final ApiContext apiContext; private final UserScope userScope; private final RemoteFetcher remoteFetcher; private final EntityManager entityManager; private final AuthorizationService authorizationService; private final DeleterFactory deleterFactory; private final BuilderFactory builderFactory; private final ConventionService conventionService; private final MessageSource messageSource; private final QueryFactory queryFactory; private final XmlHandlingService xmlHandlingService; private final ReferenceTypeProperties referenceTypeProperties; public ReferenceService(ApiContext apiContext, UserScope userScope, RemoteFetcher remoteFetcher, EntityManager entityManager, AuthorizationService authorizationService, DeleterFactory deleterFactory, BuilderFactory builderFactory, ConventionService conventionService, MessageSource messageSource, QueryFactory queryFactory, XmlHandlingService xmlHandlingService, ReferenceTypeProperties referenceTypeProperties) { this.apiContext = apiContext; this.userScope = userScope; this.remoteFetcher = remoteFetcher; this.entityManager = entityManager; this.authorizationService = authorizationService; this.deleterFactory = deleterFactory; this.builderFactory = builderFactory; this.conventionService = conventionService; this.messageSource = messageSource; this.queryFactory = queryFactory; this.xmlHandlingService = xmlHandlingService; this.referenceTypeProperties = referenceTypeProperties; } public Reference persist(ReferencePersist model, FieldSet fields) throws MyForbiddenException, MyValidationException, MyApplicationException, MyNotFoundException, InvalidApplicationException, JAXBException, JsonProcessingException, TransformerException, ParserConfigurationException { logger.debug(new MapLogEntry("persisting data").And("model", model).And("fields", fields)); this.authorizationService.authorizeForce(Permission.EditDmpBlueprint); Boolean isUpdate = this.conventionService.isValidGuid(model.getId()); ReferenceEntity data; if (isUpdate) { data = this.entityManager.find(ReferenceEntity.class, model.getId()); if (data == null) throw new MyNotFoundException(messageSource.getMessage("General_ItemNotFound", new Object[]{model.getId(), Reference.class.getSimpleName()}, LocaleContextHolder.getLocale())); } else { data = new ReferenceEntity(); data.setId(UUID.randomUUID()); data.setIsActive(IsActive.Active); data.setCreatedAt(Instant.now()); } data.setLabel(model.getLabel()); data.setType(model.getType()); data.setDescription(model.getDescription()); data.setDefinition(this.xmlHandlingService.toXmlSafe(this.buildDefinitionEntity(model.getDefinition()))); data.setUpdatedAt(Instant.now()); data.setReference(model.getReference()); data.setAbbreviation(model.getAbbreviation()); data.setSource(model.getSource()); data.setSourceType(model.getSourceType()); if (isUpdate) this.entityManager.merge(data); else this.entityManager.persist(data); this.entityManager.flush(); return this.builderFactory.builder(ReferenceBuilder.class).authorize(AuthorizationFlags.OwnerOrPermission).build(BaseFieldSet.build(fields, Reference._id), data); } private @NotNull DefinitionEntity buildDefinitionEntity(DefinitionPersist persist){ DefinitionEntity data = new DefinitionEntity(); if (persist == null) return data; if (!this.conventionService.isListNullOrEmpty(persist.getFields())){ data.setFields(new ArrayList<>()); for (FieldPersist fieldPersist: persist.getFields()) { data.getFields().add(this.buildFieldEntity(fieldPersist)); } } return data; } private @NotNull FieldEntity buildFieldEntity(FieldPersist persist){ FieldEntity data = new FieldEntity(); if (persist == null) return data; data.setCode(persist.getCode()); data.setDataType(persist.getDataType()); data.setCode(persist.getCode()); return data; } public void deleteAndSave(UUID id) throws MyForbiddenException, InvalidApplicationException { logger.debug("deleting : {}", id); this.authorizationService.authorizeForce(Permission.DeleteReference); this.deleterFactory.deleter(ReferenceDeleter.class).deleteAndSaveByIds(List.of(id)); } // public List searchReference(ReferenceType externalType, String query, String type) throws HugeResultSet, NoURLFound, InvalidApplicationException { // ExternalUrlCriteria externalUrlCriteria = new ExternalUrlCriteria(query); // // List> remoteRepos = this.apiContext.getOperationsContext().getRemoteFetcher().get(externalType, externalUrlCriteria, type); // // List list = this.fetchFromDb(externalType, query, type, remoteRepos); // // list.addAll(remoteRepos.stream().map(FetcherReference::fromRemoteModel).toList()); // list = list.stream().filter(x -> x.getName().toLowerCase().contains(query.toLowerCase())).collect(Collectors.toList()); // list.sort(Comparator.comparing(FetcherReference::getName)); // return list; // } public List searchReference(ReferenceSearchLookup lookup) throws HugeResultSet, NoURLFound, InvalidApplicationException { ExternalUrlCriteria externalUrlCriteria = new ExternalUrlCriteria(lookup.getLike()); List> remoteRepos = this.apiContext.getOperationsContext().getRemoteFetcher().get(lookup.getType(), externalUrlCriteria, lookup.getKey()); List externalModels = this.builderFactory.builder(ReferenceSearchBuilder.class).authorize(AuthorizationFlags.OwnerOrPermission).build(lookup.getProject(), remoteRepos); List models = this.fetchFromDb(lookup); models.addAll(externalModels); models = models.stream().filter(x -> x.getLabel().toLowerCase().contains(lookup.getLike().toLowerCase())).collect(Collectors.toList()); models.sort(Comparator.comparing(Reference::getLabel)); return models; } private List fetchFromDb(ReferenceSearchLookup lookup){ List fields = Arrays.asList(Reference._id, Reference._label, Reference._description, Reference._abbreviation, Reference._source, Reference._isActive, Reference._createdAt, Reference._updatedAt, Reference._type, Reference._definition, Reference._reference, Reference._sourceType ); lookup.setProject(new BaseFieldSet(fields)); ReferenceQuery query = lookup.enrich(this.queryFactory).authorize(AuthorizationFlags.OwnerOrPermission); List datas = query.collectAs(lookup.getProject()); return this.builderFactory.builder(ReferenceBuilder.class).authorize(AuthorizationFlags.OwnerOrPermission).build(lookup.getProject(), datas); } // private List fetchFromDb(ReferenceType externalType, String query, String type, List> remoteRepos) throws InvalidApplicationException { // List list = new LinkedList<>(); // switch (externalType) { // case DataRepositories: // case PubRepositories: // case Journals: { // DataRepositoryCriteria criteria = new DataRepositoryCriteria(); // if (!query.isEmpty()) criteria.setLike(query); // criteria.setCreationUserId(this.userScope.getUserId()); // if (type.equals("")) { // List dataRepositoryList = (this.apiContext.getOperationsContext().getDatabaseRepository().getDataRepositoryDao().getWithCriteria(criteria)).toList(); // list = dataRepositoryList.stream().map(item -> new FetcherReference().fromDataRepository(item)).collect(Collectors.toList()); // } // } // case Registries: { // RegistryCriteria criteria = new RegistryCriteria(); // if (!query.isEmpty()) criteria.setLike(query); // criteria.setCreationUserId(this.userScope.getUserId()); // if (type.equals("")) { // List registryList = (this.apiContext.getOperationsContext().getDatabaseRepository().getRegistryDao().getWithCriteria(criteria)).toList(); // list = registryList.stream().map(item -> new FetcherReference().fromRegistry(item)).collect(Collectors.toList()); // } // } // case Services: // { // ServiceCriteria criteria = new ServiceCriteria(); // // if (!query.isEmpty()) criteria.setLike(query); // criteria.setCreationUserId(this.userScope.getUserId()); // // if (type.equals("")) { // List serviceList = (this.apiContext.getOperationsContext().getDatabaseRepository().getServiceDao().getWithCriteria(criteria)).toList(); // list = serviceList.stream().map(item -> new FetcherReference().fromService(item)).collect(Collectors.toList()); // } // } // case Datasets:{ // // ExternalDatasetCriteria criteria = apiContext.getOperationsContext().getBuilderFactory().getBuilder(ExternalDatasetCriteriaBuilder.class).like(query).build(); // // criteria.setCreationUserId(this.userScope.getUserId()); // QueryableList items = apiContext.getOperationsContext().getDatabaseRepository().getExternalDatasetDao().getWithCriteria(criteria); // // list = items.select(item -> new FetcherReference().fromDataset(item)); // } // case Taxonomies: // case Publications: // case Licenses: // break; // } // // return list; // } }