425 lines
26 KiB
Java
425 lines
26 KiB
Java
package eu.old.eudat.migration;
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import com.fasterxml.jackson.core.JsonProcessingException;
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import eu.eudat.commons.JsonHandlingService;
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import eu.eudat.commons.XmlHandlingService;
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import eu.eudat.commons.enums.*;
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import eu.eudat.commons.types.dmp.DmpBlueprintValueEntity;
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import eu.eudat.commons.types.dmp.DmpContactEntity;
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import eu.eudat.commons.types.dmp.DmpPropertiesEntity;
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import eu.eudat.commons.types.dmpblueprint.ReferenceTypeFieldEntity;
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import eu.eudat.commons.types.dmpblueprint.SectionEntity;
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import eu.eudat.commons.types.dmpreference.DmpReferenceDataEntity;
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import eu.eudat.commons.types.reference.DefinitionEntity;
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import eu.eudat.commons.types.reference.FieldEntity;
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import eu.eudat.convention.ConventionService;
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import eu.eudat.data.*;
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import eu.eudat.model.DmpBlueprint;
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import eu.eudat.query.DmpBlueprintQuery;
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import eu.old.eudat.data.dao.entities.DMPDao;
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import eu.old.eudat.data.entities.*;
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import eu.old.eudat.logic.services.operations.DatabaseRepository;
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import eu.old.eudat.models.data.dmp.DataManagementPlan;
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import gr.cite.tools.data.query.QueryFactory;
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import gr.cite.tools.exception.MyApplicationException;
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import gr.cite.tools.fieldset.BaseFieldSet;
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import gr.cite.tools.logging.LoggerService;
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import jakarta.persistence.EntityManager;
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import jakarta.xml.bind.JAXBException;
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import org.slf4j.LoggerFactory;
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import org.springframework.core.env.Environment;
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import org.springframework.stereotype.Service;
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import org.xml.sax.SAXException;
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import javax.xml.parsers.ParserConfigurationException;
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import java.io.IOException;
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import java.time.Instant;
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import java.util.*;
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import java.util.stream.Collectors;
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@Service
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public class DmpMigrationService {
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private static final LoggerService logger = new LoggerService(LoggerFactory.getLogger(DmpMigrationService.class));
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private final DatabaseRepository databaseRepository;
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private final JsonHandlingService jsonHandlingService;
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private final EntityManager entityManager;
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private final ConventionService conventionService;
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private final XmlHandlingService xmlHandlingService;
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private final Environment environment;
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private final QueryFactory queryFactory;
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private static final int PageSize = 500;
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private static final boolean TestMode = false;
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public DmpMigrationService(DatabaseRepository databaseRepository, JsonHandlingService jsonHandlingService, EntityManager entityManager, ConventionService conventionService, XmlHandlingService xmlHandlingService, Environment environment, QueryFactory queryFactory) {
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this.databaseRepository = databaseRepository;
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this.jsonHandlingService = jsonHandlingService;
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this.entityManager = entityManager;
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this.conventionService = conventionService;
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this.xmlHandlingService = xmlHandlingService;
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this.environment = environment;
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this.queryFactory = queryFactory;
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}
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public void migrate() throws IOException, NoSuchFieldException, IllegalAccessException, JAXBException, ParserConfigurationException, InstantiationException, SAXException {
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DMPDao dmpDao = databaseRepository.getDmpDao();
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long total = dmpDao.asQueryable().count();
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logger.debug("Migrate Dmp Total : " + total);
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int page = 0;
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Map<String, UUID> licenseIdByName = new HashMap<>();
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List<DMP> items;
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do {
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items = dmpDao.asQueryable().orderBy((builder, root) -> builder.asc(root.get("created"))).orderBy((builder, root) -> builder.asc(root.get("ID"))).skip(page * PageSize).take(PageSize).toList();
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List<DMP> finalItems = items;
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List<DMP> groupDmps = dmpDao.asQueryable().where((builder, root) -> root.get("groupId").in(finalItems.stream().map(DMP::getGroupId).distinct().collect(Collectors.toList()))).toList();
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Map<UUID, List<DMP>> groupDmpMap = new HashMap<>();
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for (DMP dmp: groupDmps) {
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if (!groupDmpMap.containsKey(dmp.getGroupId())) groupDmpMap.put(dmp.getGroupId(), new ArrayList<>());
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groupDmpMap.get(dmp.getGroupId()).add(dmp);
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}
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if (items != null && !items.isEmpty()) {
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logger.debug("Migrate Dmp " + page * PageSize + " of " + total);
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List<DmpBlueprintEntity> dmpBlueprintEntities = this.queryFactory.query(DmpBlueprintQuery.class).ids(items.stream().filter(x-> x.getProfile() != null).map(x-> x.getProfile().getId()).distinct().collect(Collectors.toList())).collectAs(new BaseFieldSet().ensure(DmpBlueprint._definition).ensure(DmpBlueprint._id));
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Map<UUID, List<ReferenceTypeFieldEntity>> referenceTypeFieldsByDmpBlueprintId = new HashMap<>();
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for (DmpBlueprintEntity dmpBlueprintEntity : dmpBlueprintEntities) {
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eu.eudat.commons.types.dmpblueprint.DefinitionEntity definition = this.xmlHandlingService.fromXml(eu.eudat.commons.types.dmpblueprint.DefinitionEntity.class, dmpBlueprintEntity.getDefinition());
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List<ReferenceTypeFieldEntity> referenceTypeFieldEntities = definition.getSections().stream().filter(x-> x.getFields() != null).map(SectionEntity::getFields).flatMap(List::stream).filter(x-> x.getCategory().equals(DmpBlueprintFieldCategory.ReferenceType)).map(x-> (ReferenceTypeFieldEntity)x)
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.filter(x-> x.getReferenceTypeId().equals(ReferenceTypeIds.License) || x.getReferenceTypeId().equals(ReferenceTypeIds.Project) || x.getReferenceTypeId().equals(ReferenceTypeIds.Researcher)
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|| x.getReferenceTypeId().equals(ReferenceTypeIds.Grants) || x.getReferenceTypeId().equals(ReferenceTypeIds.Organizations) || x.getReferenceTypeId().equals(ReferenceTypeIds.Funder))
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.collect(Collectors.toList());
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referenceTypeFieldsByDmpBlueprintId.put(dmpBlueprintEntity.getId() , referenceTypeFieldEntities);
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}
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for (DMP item : items) {
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//entityManager.detach(item);
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DataManagementPlan model = new DataManagementPlan();
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model.fromDataModel(item);
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List<DMP> itemGroupDmps = groupDmpMap.get(item.getGroupId());
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DMP currentVersionDmp = itemGroupDmps.stream().filter(x-> DmpStatus.Finalized.getValue().equals(x.getStatus())).max(Comparator.comparing(DMP::getVersion)).orElse(null);
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DmpPropertiesEntity dmpProperties = new DmpPropertiesEntity();
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dmpProperties.setDmpBlueprintValues(new ArrayList<>());
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dmpProperties.setContacts(new ArrayList<>());
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DmpEntity data = new DmpEntity();
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data.setId(model.getId());
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data.setLabel(model.getLabel());
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data.setDescription(model.getDescription());
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if (model.getCreator() != null && model.getCreator().getId() != null) {
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data.setCreatorId(model.getCreator().getId());
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} else {
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for (DMP groupDmp: itemGroupDmps) {
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DataManagementPlan groupDmpModel = new DataManagementPlan();
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groupDmpModel.fromDataModel(groupDmp);
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if (groupDmpModel.getCreator() != null) {
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data.setCreatorId(groupDmpModel.getCreator().getId());
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break;
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}
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}
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}
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data.setGroupId(model.getGroupId());
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data.setVersion((short) model.getVersion());
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if (currentVersionDmp != null && currentVersionDmp.getId().equals(item.getId())){
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data.setVersionStatus(DmpVersionStatus.Current);
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} else {
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if (DmpStatus.Finalized.getValue().equals(item.getStatus())){
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if (currentVersionDmp == null) throw new MyApplicationException("Found Finalized Dmp out of the group ");
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data.setVersionStatus(DmpVersionStatus.Previous);
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} else {
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data.setVersionStatus(DmpVersionStatus.NotFinalized);
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}
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}
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if (model.getCreated() != null)
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data.setCreatedAt(model.getCreated().toInstant());
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if (model.getModified() != null)
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data.setUpdatedAt(model.getModified().toInstant());
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if (model.getFinalized() != null)
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data.setFinalizedAt(model.getFinalized().toInstant());
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data.setBlueprintId(model.getProfile().getId());
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if (model.getExtraProperties() != null) {
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if (model.getExtraProperties().containsKey("language") && model.getExtraProperties().get("language") != null)
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data.setLanguage((String) model.getExtraProperties().get("language"));
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if (model.getExtraProperties().containsKey("visible") && model.getExtraProperties().get("visible") != null)
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data.setAccessType((boolean) model.getExtraProperties().get("visible") ? DmpAccessType.Public : DmpAccessType.Restricted);
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if (model.getExtraProperties().containsKey("contact") && model.getExtraProperties().get("contact") != null) {
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DmpContactEntity contactEntity = new DmpContactEntity();
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contactEntity.setUserId(UUID.fromString((String)model.getExtraProperties().get("contact")));
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dmpProperties.getContacts().add(contactEntity);
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}
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}
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if (model.getProperties() != null) {
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model.getProperties().forEach((key,val) -> {
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DmpBlueprintValueEntity valueEntity = new DmpBlueprintValueEntity();
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valueEntity.setFieldId(UUID.fromString(key));
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valueEntity.setValue((String) val);
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dmpProperties.getDmpBlueprintValues().add(valueEntity);
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});
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}
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if (model.getStatus() == 99) {
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data.setIsActive(IsActive.Inactive);
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data.setStatus(DmpStatus.Draft);
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} else {
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data.setIsActive(IsActive.Active);
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data.setStatus(DmpStatus.of((short) model.getStatus()));
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}
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data.setProperties(jsonHandlingService.toJson(dmpProperties));
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if (data.getAccessType() == null && item.getStatus().equals(DmpStatus.Finalized.getValue())) {
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logger.warn("AccessType not found set to default for dmp " + item.getId());
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data.setAccessType(item.isPublic() ? DmpAccessType.Public : DmpAccessType.Restricted);
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}
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if ((data.getLanguage() == null || data.getLanguage().isBlank()) && item.getStatus().equals(DmpStatus.Finalized.getValue())) {
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logger.warn("Language not found set to default for dmp " + item.getId());
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data.setLanguage("en");
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}
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if (data.getCreatorId() == null){
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throw new MyApplicationException("Migration skipped creator not found " + item.getId());
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}
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this.entityManager.persist(data);
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this.entityManager.flush();
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boolean shouldCreateOwner = item.getUsers() == null || item.getUsers().stream().noneMatch(x-> x.getUser() != null && data.getCreatorId().equals(x.getUser().getId()) && DmpUserRole.Owner.getValue().equals(x.getRole().shortValue()));
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if (shouldCreateOwner) {
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DmpUserEntity dmpUserEntity = new DmpUserEntity();
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dmpUserEntity.setId(UUID.randomUUID());
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dmpUserEntity.setDmpId(data.getId());
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dmpUserEntity.setUserId(data.getCreatorId());
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dmpUserEntity.setRole(DmpUserRole.Owner);
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dmpUserEntity.setCreatedAt(data.getCreatedAt());
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dmpUserEntity.setUpdatedAt(data.getCreatedAt());
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dmpUserEntity.setIsActive(IsActive.Active);
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this.entityManager.persist(dmpUserEntity);
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this.entityManager.flush();
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}
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licenseIdByName = this.migrateLicense(item, model, licenseIdByName, referenceTypeFieldsByDmpBlueprintId.getOrDefault(data.getBlueprintId(), null));
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this.migrateOrganizations(item, referenceTypeFieldsByDmpBlueprintId.getOrDefault(data.getBlueprintId(), null));
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this.migrateResearchers(item, referenceTypeFieldsByDmpBlueprintId.getOrDefault(data.getBlueprintId(), null));
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this.migrateProjects(item, referenceTypeFieldsByDmpBlueprintId.getOrDefault(data.getBlueprintId(), null));
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this.migrateGrantAndFunder(item, referenceTypeFieldsByDmpBlueprintId.getOrDefault(data.getBlueprintId(), null));
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}
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page++;
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}
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} while (items != null && !items.isEmpty() && !TestMode);
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}
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private void migrateOrganizations(DMP item, List<ReferenceTypeFieldEntity> referenceTypeFieldEntities){
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Set<Organisation> organisations = item.getOrganisations();
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if (organisations == null || organisations.isEmpty()) return;
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if (referenceTypeFieldEntities == null) {
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throw new MyApplicationException("Migration failed Blueprint not found " + item.getProfile().getId());
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}
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ReferenceTypeFieldEntity referenceTypeFieldEntity = referenceTypeFieldEntities.stream().filter(x-> x.getReferenceTypeId().equals(ReferenceTypeIds.Organizations)).findFirst().orElse(null);
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if (referenceTypeFieldEntity == null) {
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throw new MyApplicationException("Migration failed Organizations field not found " + item.getId());
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}
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for (Organisation organisation : organisations) {
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DmpReferenceEntity data = new DmpReferenceEntity();
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data.setId(UUID.randomUUID());
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data.setDmpId(item.getId());
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data.setReferenceId(organisation.getId());
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data.setCreatedAt(item.getCreated() != null ? item.getCreated().toInstant() : Instant.now());
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data.setUpdatedAt(item.getModified() != null ? item.getModified().toInstant() : Instant.now());
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data.setData(this.jsonHandlingService.toJsonSafe(this.buildDmpReferenceDataEntity(referenceTypeFieldEntity)));
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data.setIsActive(IsActive.Active);
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this.entityManager.persist(data);
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}
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}
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private void migrateProjects(DMP item, List<ReferenceTypeFieldEntity> referenceTypeFieldEntities){
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Project project = item.getProject();
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if (project == null) return;
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if (referenceTypeFieldEntities == null) {
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throw new MyApplicationException("Migration failed Blueprint not found " + item.getProfile().getId());
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}
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ReferenceTypeFieldEntity referenceTypeFieldEntity = referenceTypeFieldEntities.stream().filter(x-> x.getReferenceTypeId().equals(ReferenceTypeIds.Project)).findFirst().orElse(null);
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if (referenceTypeFieldEntity == null) {
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throw new MyApplicationException("Migration failed Project field not found " + item.getId());
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}
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DmpReferenceEntity data = new DmpReferenceEntity();
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data.setId(UUID.randomUUID());
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data.setDmpId(item.getId());
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data.setReferenceId(project.getId());
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data.setCreatedAt(item.getCreated() != null ? item.getCreated().toInstant() : Instant.now());
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data.setUpdatedAt(item.getModified() != null ? item.getModified().toInstant() : Instant.now());
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data.setIsActive(IsActive.Active);
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data.setData(this.jsonHandlingService.toJsonSafe(this.buildDmpReferenceDataEntity(referenceTypeFieldEntity)));
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this.entityManager.persist(data);
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}
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private void migrateResearchers(DMP item, List<ReferenceTypeFieldEntity> referenceTypeFieldEntities){
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Set<Researcher> researchers = item.getResearchers();
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if (researchers == null || researchers.isEmpty()) return;
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if (referenceTypeFieldEntities == null) {
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throw new MyApplicationException("Migration failed Blueprint not found " + item.getProfile().getId());
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}
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ReferenceTypeFieldEntity referenceTypeFieldEntity = referenceTypeFieldEntities.stream().filter(x-> x.getReferenceTypeId().equals(ReferenceTypeIds.Researcher)).findFirst().orElse(null);
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if (referenceTypeFieldEntity == null) {
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throw new MyApplicationException("Migration failed Researchers field not found " + item.getId());
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}
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for (Researcher researcher : researchers) {
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DmpReferenceEntity data = new DmpReferenceEntity();
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data.setId(UUID.randomUUID());
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data.setDmpId(item.getId());
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data.setReferenceId(researcher.getId());
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data.setCreatedAt(item.getCreated() != null ? item.getCreated().toInstant() : Instant.now());
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data.setUpdatedAt(item.getModified() != null ? item.getModified().toInstant() : Instant.now());
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data.setData(this.jsonHandlingService.toJsonSafe(this.buildDmpReferenceDataEntity(referenceTypeFieldEntity)));
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data.setIsActive(IsActive.Active);
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this.entityManager.persist(data);
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}
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}
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private void migrateGrantAndFunder(DMP item, List<ReferenceTypeFieldEntity> referenceTypeFieldEntities){
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Grant grant = item.getGrant();
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if (grant == null) return;
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if (referenceTypeFieldEntities == null) {
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throw new MyApplicationException("Migration failed Blueprint not found " + item.getProfile().getId());
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}
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ReferenceTypeFieldEntity referenceTypeFieldEntity = referenceTypeFieldEntities.stream().filter(x-> x.getReferenceTypeId().equals(ReferenceTypeIds.Grants)).findFirst().orElse(null);
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if (referenceTypeFieldEntity == null) {
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throw new MyApplicationException("Migration failed Grant field not found " + item.getId());
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}
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DmpReferenceEntity data = new DmpReferenceEntity();
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data.setId(UUID.randomUUID());
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data.setDmpId(item.getId());
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data.setReferenceId(grant.getId());
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data.setCreatedAt(item.getCreated() != null ? item.getCreated().toInstant() : Instant.now());
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data.setUpdatedAt(item.getModified() != null ? item.getModified().toInstant() : Instant.now());
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data.setData(this.jsonHandlingService.toJsonSafe(this.buildDmpReferenceDataEntity(referenceTypeFieldEntity)));
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data.setIsActive(IsActive.Active);
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this.entityManager.persist(data);
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if (grant.getFunder() != null){
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ReferenceTypeFieldEntity funderField = referenceTypeFieldEntities.stream().filter(x-> x.getReferenceTypeId().equals(ReferenceTypeIds.Funder)).findFirst().orElse(null);
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if (funderField == null) {
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throw new MyApplicationException("Migration failed Funder field not found " + item.getId());
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}
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DmpReferenceEntity founder = new DmpReferenceEntity();
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founder.setId(UUID.randomUUID());
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founder.setDmpId(item.getId());
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founder.setReferenceId(grant.getFunder().getId());
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founder.setCreatedAt(item.getCreated() != null ? item.getCreated().toInstant() : Instant.now());
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founder.setUpdatedAt(item.getModified() != null ? item.getModified().toInstant() : Instant.now());
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founder.setData(this.jsonHandlingService.toJsonSafe(this.buildDmpReferenceDataEntity(funderField)));
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founder.setIsActive(IsActive.Active);
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this.entityManager.persist(founder);
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}
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}
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private Map<String, UUID> migrateLicense(DMP item, DataManagementPlan model, Map<String, UUID> licenseIdByName, List<ReferenceTypeFieldEntity> referenceTypeFieldEntities) throws JsonProcessingException {
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if (model.getExtraProperties() != null) {
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if (model.getExtraProperties().containsKey("license") && model.getExtraProperties().get("license") != null) {
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if (referenceTypeFieldEntities == null) {
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throw new MyApplicationException("Migration failed Blueprint not found " + item.getProfile().getId());
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}
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ReferenceTypeFieldEntity referenceTypeFieldEntity = referenceTypeFieldEntities.stream().filter(x-> x.getReferenceTypeId().equals(ReferenceTypeIds.License)).findFirst().orElse(null);
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if (referenceTypeFieldEntity == null) {
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throw new MyApplicationException("Migration failed License field not found " + item.getId());
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}
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Object license = model.getExtraProperties().get("license");
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HashMap<String, String> licenseMap = this.jsonHandlingService.mapFromJson(this.jsonHandlingService.toJson(license));
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ReferenceEntity referenceEntity = new ReferenceEntity();
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String licensePid;
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if (licenseMap.containsKey("pid") && licenseMap.get("pid") != null) {
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licensePid = licenseMap.get("pid");
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referenceEntity.setReference(licensePid);
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}
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else return licenseIdByName;
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boolean licenseExists = licenseIdByName.containsKey(licensePid);
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if (!licenseExists) {
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DefinitionEntity definitionEntity = new DefinitionEntity();
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List<FieldEntity> fields = new ArrayList<>();
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if (licenseMap.containsKey("name")) {
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referenceEntity.setLabel(licenseMap.get("name"));
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}
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if (licenseMap.containsKey("pid")) {
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if (!this.conventionService.isNullOrEmpty(licensePid)){
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FieldEntity fieldEntity = new FieldEntity();
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fieldEntity.setCode("pid");
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fieldEntity.setDataType(ReferenceFieldDataType.Text);
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fieldEntity.setValue(licensePid);
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fields.add(fieldEntity);
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}
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}
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if (licenseMap.containsKey("tag")) {
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if (!this.conventionService.isNullOrEmpty(licenseMap.get("tag"))){
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FieldEntity fieldEntity = new FieldEntity();
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fieldEntity.setCode("tag");
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fieldEntity.setDataType(ReferenceFieldDataType.Text);
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fieldEntity.setValue(licenseMap.get("tag"));
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fields.add(fieldEntity);
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}
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}
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if (licenseMap.containsKey("uri")) {
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if (!this.conventionService.isNullOrEmpty(licenseMap.get("uri"))){
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FieldEntity fieldEntity = new FieldEntity();
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fieldEntity.setCode("uri");
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fieldEntity.setDataType(ReferenceFieldDataType.Text);
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fieldEntity.setValue(licenseMap.get("uri"));
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fields.add(fieldEntity);
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}
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}
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if (licenseMap.containsKey("abbreviation")) {
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referenceEntity.setAbbreviation(licenseMap.get("abbreviation"));
|
|
}
|
|
if (licenseMap.containsKey("created") && licenseMap.get("created") != null) {
|
|
referenceEntity.setUpdatedAt(Instant.parse(licenseMap.get("created")));
|
|
} else {
|
|
referenceEntity.setCreatedAt(item.getCreated() == null ? Instant.now() : item.getCreated().toInstant());
|
|
}
|
|
if (licenseMap.containsKey("modified") && licenseMap.get("modified") != null) {
|
|
referenceEntity.setUpdatedAt(Instant.parse(licenseMap.get("modified")));
|
|
} else {
|
|
referenceEntity.setUpdatedAt(item.getModified() == null ? Instant.now() : item.getModified().toInstant());
|
|
}
|
|
referenceEntity.setId(UUID.randomUUID());
|
|
referenceEntity.setSourceType(ReferenceSourceType.External);
|
|
referenceEntity.setSource(this.environment.getProperty("migration.default-license-source", "null"));
|
|
referenceEntity.setTypeId(ReferenceTypeIds.License);
|
|
referenceEntity.setIsActive(IsActive.Active);
|
|
definitionEntity.setFields(fields);
|
|
referenceEntity.setDefinition(this.xmlHandlingService.toXmlSafe(definitionEntity));
|
|
|
|
licenseIdByName.put(licensePid, referenceEntity.getId());
|
|
}
|
|
|
|
DmpReferenceEntity dmpReferenceEntity = new DmpReferenceEntity();
|
|
dmpReferenceEntity.setId(UUID.randomUUID());
|
|
dmpReferenceEntity.setDmpId(item.getId());
|
|
dmpReferenceEntity.setReferenceId(licenseIdByName.get(licensePid));
|
|
dmpReferenceEntity.setCreatedAt(Instant.now());
|
|
dmpReferenceEntity.setUpdatedAt(Instant.now());
|
|
dmpReferenceEntity.setData(this.jsonHandlingService.toJsonSafe(this.buildDmpReferenceDataEntity(referenceTypeFieldEntity)));
|
|
dmpReferenceEntity.setIsActive(IsActive.Active);
|
|
|
|
if (!licenseExists) entityManager.persist(referenceEntity);
|
|
entityManager.persist(dmpReferenceEntity);
|
|
}
|
|
}
|
|
|
|
return licenseIdByName;
|
|
}
|
|
|
|
private DmpReferenceDataEntity buildDmpReferenceDataEntity(ReferenceTypeFieldEntity referenceTypeFieldEntity){
|
|
DmpReferenceDataEntity data = new DmpReferenceDataEntity();
|
|
data.setBlueprintFieldId(referenceTypeFieldEntity.getId());
|
|
return data;
|
|
}
|
|
|
|
}
|