migration changes
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package eu.old.eudat.migration;
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import eu.eudat.commons.XmlHandlingService;
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import eu.eudat.commons.enums.DmpBlueprintExtraFieldDataType;
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import eu.eudat.commons.enums.DmpBlueprintFieldCategory;
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import eu.eudat.commons.enums.DmpBlueprintSystemFieldType;
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import eu.eudat.commons.types.dmpblueprint.*;
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import eu.eudat.convention.ConventionService;
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import eu.eudat.data.DescriptionTemplateEntity;
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import eu.eudat.data.DmpBlueprintEntity;
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import eu.eudat.model.DmpBlueprint;
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import eu.eudat.query.DescriptionTemplateQuery;
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import eu.eudat.query.DmpBlueprintQuery;
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import eu.old.eudat.logic.utilities.builders.XmlBuilder;
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import eu.old.eudat.models.data.entities.xmlmodels.dmpprofiledefinition.*;
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import eu.old.eudat.models.data.entities.xmlmodels.dmpprofiledefinition.types.FieldCategory;
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import gr.cite.tools.data.query.Ordering;
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import gr.cite.tools.data.query.Paging;
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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.jetbrains.annotations.NotNull;
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import org.slf4j.LoggerFactory;
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import org.springframework.stereotype.Service;
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import org.w3c.dom.Document;
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import org.xml.sax.SAXException;
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import javax.management.InvalidApplicationException;
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import javax.xml.parsers.ParserConfigurationException;
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import javax.xml.transform.TransformerException;
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import java.io.IOException;
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import java.util.*;
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@Service
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public class DmpBlueprintMigrationService {
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private static final LoggerService logger = new LoggerService(LoggerFactory.getLogger(DmpBlueprintMigrationService.class));
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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 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 DmpBlueprintMigrationService(EntityManager entityManager, ConventionService conventionService, XmlHandlingService xmlHandlingService, QueryFactory queryFactory) {
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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.queryFactory = queryFactory;
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}
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public void migrate() throws IOException, NoSuchFieldException, IllegalAccessException, JAXBException, ParserConfigurationException, InstantiationException, SAXException, InvalidApplicationException, TransformerException {
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long total = this.queryFactory.query(DmpBlueprintQuery.class).count();
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logger.debug("Migrate DmpBlueprint Total : " + total);
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int page = 0;
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Map<String, UUID> licenseIdByName = new HashMap<>();
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List<DmpBlueprintEntity> items;
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List<DescriptionTemplateEntity> descriptionTemplateEntities = this.queryFactory.query(DescriptionTemplateQuery.class).collectAs(new BaseFieldSet().ensure(eu.eudat.model.DescriptionTemplate._id).ensure(eu.eudat.model.DescriptionTemplate._groupId));
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Map<UUID, UUID> descriptionTemplateGroupMap = new HashMap<>();
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for (DescriptionTemplateEntity descriptionTemplateEntity: descriptionTemplateEntities) {
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descriptionTemplateGroupMap.put(descriptionTemplateEntity.getId(), descriptionTemplateEntity.getGroupId());
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}
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do {
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DmpBlueprintQuery query = this.queryFactory.query(DmpBlueprintQuery.class);
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query.setOrder(new Ordering().addDescending(DmpBlueprint._createdAt));
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query.setPage(new Paging(page * PageSize, PageSize));
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items = query.collect();
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if (items != null && !items.isEmpty()) {
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logger.debug("Migrate DmpBlueprint " + page * PageSize + " of " + total);
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for (DmpBlueprintEntity item : items) {
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if (this.conventionService.isNullOrEmpty(item.getDefinition())) continue;
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Document document = XmlBuilder.fromXml(item.getDefinition());
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if (document == null){
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logger.error("Migrate DmpBlueprint " + item.getId() + " failed read xml");
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continue;
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}
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DataManagementPlanBlueprint dataManagementPlanBlueprint =new DataManagementPlanBlueprint().fromXml(document.getDocumentElement());
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item.setDefinition(this.xmlHandlingService.toXml(this.buildDefinitionEntity(dataManagementPlanBlueprint, descriptionTemplateGroupMap)));
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this.entityManager.merge(item);
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this.entityManager.flush();
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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 @NotNull eu.eudat.commons.types.dmpblueprint.DefinitionEntity buildDefinitionEntity(DataManagementPlanBlueprint dataManagementPlanBlueprint, Map<UUID, UUID> descriptionTemplateGroupMap ) {
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eu.eudat.commons.types.dmpblueprint.DefinitionEntity data = new DefinitionEntity();
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if (dataManagementPlanBlueprint == null)
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return data;
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if (!this.conventionService.isListNullOrEmpty(dataManagementPlanBlueprint.getSections())) {
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data.setSections(new ArrayList<>());
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for (Section section : dataManagementPlanBlueprint.getSections()) {
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data.getSections().add(this.buildSectionEntity(section, descriptionTemplateGroupMap));
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}
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}
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return data;
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}
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private @NotNull SectionEntity buildSectionEntity(Section itm, Map<UUID, UUID> descriptionTemplateGroupMap ) {
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SectionEntity data = new SectionEntity();
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if (itm == null)
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return data;
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data.setId(itm.getId());
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data.setDescription(itm.getDescription());
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data.setLabel(itm.getLabel());
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data.setOrdinal(itm.getOrdinal());
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data.setHasTemplates(itm.getHasTemplates());
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if (!this.conventionService.isListNullOrEmpty(itm.getFields())) {
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data.setFields(new ArrayList<>());
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for (FieldModel fieldModel : itm.getFields()) {
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data.getFields().add(this.buildExtraFieldEntity(fieldModel));
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}
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}
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if (!this.conventionService.isListNullOrEmpty(itm.getDescriptionTemplates())) {
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data.setDescriptionTemplates(new ArrayList<>());
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for (DescriptionTemplate descriptionTemplate : itm.getDescriptionTemplates()) {
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data.getDescriptionTemplates().add(this.buildDescriptionTemplateEntity(descriptionTemplate, descriptionTemplateGroupMap));
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}
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}
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return data;
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}
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private @NotNull eu.eudat.commons.types.dmpblueprint.DescriptionTemplateEntity buildDescriptionTemplateEntity(DescriptionTemplate itm, Map<UUID, UUID> descriptionTemplateGroupMap ) {
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eu.eudat.commons.types.dmpblueprint.DescriptionTemplateEntity data = new eu.eudat.commons.types.dmpblueprint.DescriptionTemplateEntity();
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if (itm == null)
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return data;
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UUID groupId = descriptionTemplateGroupMap.getOrDefault(itm.getDescriptionTemplateId(), null);
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if (groupId == null){
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logger.error("Migrate DmpBlueprint, DescriptionTemplate " + itm.getDescriptionTemplateId() + " group not found");
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data.setDescriptionTemplateGroupId(itm.getDescriptionTemplateId());
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} else {
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data.setDescriptionTemplateGroupId(groupId);
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}
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data.setLabel(itm.getLabel());
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data.setMaxMultiplicity(itm.getMaxMultiplicity());
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data.setMinMultiplicity(itm.getMinMultiplicity());
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return data;
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}
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private @NotNull eu.eudat.commons.types.dmpblueprint.FieldEntity buildExtraFieldEntity(FieldModel itm) {
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if (itm == null)
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return new ExtraFieldEntity();
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FieldEntity data;
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if (FieldCategory.EXTRA.equals(itm.getCategory())) {
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ExtraFieldEntity dataTyped = new ExtraFieldEntity();
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ExtraField extraField = itm.toExtraField();
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switch (extraField.getType()){
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case TEXT -> dataTyped.setType(DmpBlueprintExtraFieldDataType.Text);
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case DATE -> dataTyped.setType(DmpBlueprintExtraFieldDataType.Date);
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case NUMBER -> dataTyped.setType(DmpBlueprintExtraFieldDataType.Number);
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case RICH_TEXT -> dataTyped.setType(DmpBlueprintExtraFieldDataType.RichTex);
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default -> throw new MyApplicationException("Type not found " + extraField.getType());
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}
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dataTyped.setRequired(extraField.getRequired());
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data = dataTyped;
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} else {
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SystemFieldEntity dataTyped = new SystemFieldEntity();
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SystemField systemField = itm.toSystemField();
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switch (systemField.getType()){
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case TEXT -> dataTyped.setType(DmpBlueprintSystemFieldType.Text);
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case ACCESS_RIGHTS -> dataTyped.setType(DmpBlueprintSystemFieldType.AccessRights);
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case CONTACT -> dataTyped.setType(DmpBlueprintSystemFieldType.Contact);
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case FUNDER -> dataTyped.setType(DmpBlueprintSystemFieldType.Funder);
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case GRANT -> dataTyped.setType(DmpBlueprintSystemFieldType.Grant);
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case HTML_TEXT -> dataTyped.setType(DmpBlueprintSystemFieldType.HtmlText);
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case LANGUAGE -> dataTyped.setType(DmpBlueprintSystemFieldType.Language);
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case LICENSE -> dataTyped.setType(DmpBlueprintSystemFieldType.License);
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case ORGANIZATIONS -> dataTyped.setType(DmpBlueprintSystemFieldType.Organizations);
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case PROJECT -> dataTyped.setType(DmpBlueprintSystemFieldType.Project);
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case RESEARCHERS -> dataTyped.setType(DmpBlueprintSystemFieldType.Researchers);
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default -> throw new MyApplicationException("Type not found " + systemField.getType());
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}
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dataTyped.setRequired(systemField.isRequired());
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data = dataTyped;
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}
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data.setId(itm.getId());
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switch (itm.getCategory()){
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case EXTRA -> data.setCategory(DmpBlueprintFieldCategory.Extra);
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case SYSTEM -> data.setCategory(DmpBlueprintFieldCategory.System);
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default -> throw new MyApplicationException("Type not found " + itm.getCategory());
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}
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data.setLabel(itm.getLabel());
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data.setPlaceholder(itm.getPlaceholder());
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data.setDescription(itm.getDescription());
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data.setOrdinal(itm.getOrdinal());
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return data;
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}
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}
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@ -11,7 +11,9 @@ import org.springframework.web.bind.annotation.RequestMapping;
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import org.springframework.web.bind.annotation.RestController;
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import org.xml.sax.SAXException;
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import javax.management.InvalidApplicationException;
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import javax.xml.parsers.ParserConfigurationException;
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import javax.xml.transform.TransformerException;
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import java.io.IOException;
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@Api(tags = "Migration")
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@ -37,23 +39,26 @@ public class MigrationController {
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private final UserContactInfoMigrationService userContactInfoMigrationService;
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private final DmpUserMigrationService dmpUserMigrationService;
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private final UserMigrationService userMigrationService;
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private final DmpBlueprintMigrationService dmpBlueprintMigrationService;
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public MigrationController(
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DmpMigrationService dmpMigrationService,
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DatasetMigrationService datasetMigrationService,
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DmpDatasetProfileMigrationService dmpDatasetProfileMigrationService,
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DataRepositoryMigrationService dataRepositoryMigrationService,
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ExternalDatasetMigrationService externalDatasetMigrationService,
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FunderMigrationService funderMigrationService,
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GrantMigrationService grantMigrationService,
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ProjectMigrationService projectMigrationService,
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RegistryMigrationService registryMigrationService,
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ResearcherMigrationService researcherMigrationService,
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ServiceMigrationService serviceMigrationService, TagMigrationService tagMigrationService,
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OrganizationMigrationService organizationMigrationService,
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ReferenceMigrationService referenceMigrationService,
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UserContactInfoMigrationService userContactInfoMigrationService,
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DmpUserMigrationService dmpUserMigrationService, UserMigrationService userMigrationService) {
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DmpMigrationService dmpMigrationService,
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DatasetMigrationService datasetMigrationService,
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DmpDatasetProfileMigrationService dmpDatasetProfileMigrationService,
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DataRepositoryMigrationService dataRepositoryMigrationService,
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ExternalDatasetMigrationService externalDatasetMigrationService,
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FunderMigrationService funderMigrationService,
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GrantMigrationService grantMigrationService,
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ProjectMigrationService projectMigrationService,
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RegistryMigrationService registryMigrationService,
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ResearcherMigrationService researcherMigrationService,
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ServiceMigrationService serviceMigrationService, TagMigrationService tagMigrationService,
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OrganizationMigrationService organizationMigrationService,
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ReferenceMigrationService referenceMigrationService,
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UserContactInfoMigrationService userContactInfoMigrationService,
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DmpUserMigrationService dmpUserMigrationService,
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UserMigrationService userMigrationService,
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DmpBlueprintMigrationService dmpBlueprintMigrationService) {
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this.dmpMigrationService = dmpMigrationService;
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this.datasetMigrationService = datasetMigrationService;
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this.dmpDatasetProfileMigrationService = dmpDatasetProfileMigrationService;
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@ -71,11 +76,12 @@ public class MigrationController {
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this.userContactInfoMigrationService = userContactInfoMigrationService;
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this.dmpUserMigrationService = dmpUserMigrationService;
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this.userMigrationService = userMigrationService;
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this.dmpBlueprintMigrationService = dmpBlueprintMigrationService;
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}
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@GetMapping("all")
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@Transactional
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public boolean migrateAll() throws IOException, JAXBException, ParserConfigurationException, InstantiationException, IllegalAccessException, SAXException, NoSuchFieldException {
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public boolean migrateAll() throws IOException, JAXBException, ParserConfigurationException, InstantiationException, IllegalAccessException, SAXException, NoSuchFieldException, InvalidApplicationException, TransformerException {
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this.dataRepositoryMigrationService.migrate();
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this.externalDatasetMigrationService.migrate();
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this.funderMigrationService.migrate();
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@ -97,9 +103,20 @@ public class MigrationController {
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this.userContactInfoMigrationService.migrate();
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this.userMigrationService.migrate();
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//XML recreate
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this.dmpBlueprintMigrationService.migrate();
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return true;
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}
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@GetMapping("dmp-blueprints")
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@Transactional
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public boolean migrateDmpBlueprint() throws JAXBException, InvalidApplicationException, IOException, ParserConfigurationException, NoSuchFieldException, TransformerException, IllegalAccessException, InstantiationException, SAXException {
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this.dmpBlueprintMigrationService.migrate();
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return true;
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}
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@GetMapping("contacts")
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@Transactional
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public boolean migrateContacts() {
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