migration fixes
This commit is contained in:
parent
c27e98acd8
commit
33d9bab4bf
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@ -489,6 +489,16 @@ public class DatasetMigrationService {
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ref.put("source", "opendefinition");
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} else if (ReferenceTypeIds.PubRepositories.equals(referenceTypeDataEntity.getReferenceTypeId())) {
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ref.put("source", "opendefinition");
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} else if (ReferenceTypeIds.Grants.equals(referenceTypeDataEntity.getReferenceTypeId())) {
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ref.put("source", "openaire");
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} else if (ReferenceTypeIds.Project.equals(referenceTypeDataEntity.getReferenceTypeId())) {
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ref.put("source", "project");
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} else if (ReferenceTypeIds.Taxonomy.equals(referenceTypeDataEntity.getReferenceTypeId())) {
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ref.put("source", "taxonomy");
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} else if (ReferenceTypeIds.Publication.equals(referenceTypeDataEntity.getReferenceTypeId())) {
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ref.put("source", "openaire");
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} else if (ReferenceTypeIds.Currency.equals(referenceTypeDataEntity.getReferenceTypeId())) {
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ref.put("source", "currencies");
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} else if (ReferenceTypeIds.Researcher.equals(referenceTypeDataEntity.getReferenceTypeId())) {
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Matcher pattern = Pattern.compile("\\((.*?)\\)").matcher(textValue);
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if (pattern.find()) {
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@ -504,40 +514,37 @@ public class DatasetMigrationService {
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}
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if (ref.containsKey("source")) references = List.of(ref).toArray(new Map[1]);
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} else {
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String source = null;
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if (!ReferenceTypeIds.KnownReferenceTypeIds.contains(referenceTypeDataEntity.getReferenceTypeId())) {
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ReferenceTypeDefinitionEntity referenceTypeDefinition = referenceTypeDefinitionEntityMap.getOrDefault(referenceTypeDataEntity.getReferenceTypeId(), null);
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if (referenceTypeDefinition == null) throw new MyApplicationException("Could not find reference type for reference : " + this.jsonHandlingService.toJsonSafe(textValue));
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if (this.conventionService.isListNullOrEmpty(referenceTypeDefinition.getSources())) throw new MyApplicationException("Could not find reference source for reference : " + this.jsonHandlingService.toJsonSafe(textValue));
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//if (referenceTypeDefinition.getSources().size() > 1) throw new MyApplicationException("Multiple reference source for reference : " + this.jsonHandlingService.toJsonSafe(textValue));
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source = referenceTypeDefinition.getSources().getFirst().getKey();
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String[] parts = null;
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if (textValue.startsWith("[\"")){
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parts = migrationTools.tryParseJsonAsObjectString(String[].class, textValue);
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} else{
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if (textValue.startsWith("[")) textValue = textValue.substring(1).trim();
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if (textValue.endsWith("]")) textValue = textValue.substring(0, textValue.length() -1).trim();
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parts = textValue.split(",");
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}
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if (parts != null) {
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List<Map<String, Object>> items = new ArrayList<>();
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for (String part : parts) {
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if (this.conventionService.isNullOrEmpty(part)) continue;
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part = part.trim().replace(",", "").trim();
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if (this.conventionService.isNullOrEmpty(part) || part.equals("null")) continue;
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Map<String, Object> ref = new HashMap<>();
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ref.put("name", part);
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ref.put("source", source);
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items.add(ref);
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}
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if (items.isEmpty()) break;
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references = items.toArray(new Map[items.size()]);
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ReferenceTypeDefinitionEntity referenceTypeDefinition = referenceTypeDefinitionEntityMap.getOrDefault(referenceTypeDataEntity.getReferenceTypeId(), null);
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if (referenceTypeDefinition == null) throw new MyApplicationException("Could not find reference type for reference : " + this.jsonHandlingService.toJsonSafe(textValue));
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if (this.conventionService.isListNullOrEmpty(referenceTypeDefinition.getSources())) throw new MyApplicationException("Could not find reference source for reference : " + this.jsonHandlingService.toJsonSafe(textValue));
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//if (referenceTypeDefinition.getSources().size() > 1) throw new MyApplicationException("Multiple reference source for reference : " + this.jsonHandlingService.toJsonSafe(textValue));
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String source = referenceTypeDefinition.getSources().getFirst().getKey();
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String[] parts = null;
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if (textValue.startsWith("[\"")){
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parts = migrationTools.tryParseJsonAsObjectString(String[].class, textValue);
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} else{
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if (textValue.startsWith("[")) textValue = textValue.substring(1).trim();
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if (textValue.endsWith("]")) textValue = textValue.substring(0, textValue.length() -1).trim();
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parts = textValue.split(",");
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}
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if (parts != null) {
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List<Map<String, Object>> items = new ArrayList<>();
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for (String part : parts) {
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if (this.conventionService.isNullOrEmpty(part)) continue;
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part = part.trim().replace(",", "").trim();
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if (this.conventionService.isNullOrEmpty(part) || part.equals("null")) continue;
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Map<String, Object> ref = new HashMap<>();
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ref.put("name", part);
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ref.put("source", source);
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items.add(ref);
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}
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if (items.isEmpty()) break;
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references = items.toArray(new Map[items.size()]);
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}
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}
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}
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if (references == null && !ReferenceTypeIds.KnownReferenceTypeIds.contains(referenceTypeDataEntity.getReferenceTypeId())){
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if (references == null){
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if (textValue.equalsIgnoreCase("[\"dublin core\",\"{\\\"id\\\":\\\"metadataschema:rd-alliance/dublin-core\\\",\\\"label\\\":\\\"Dublin Core\\\",\\\"source\\\":\\\"\\\",\\\"uri\\\":\\\"http://dublincore.org\\\"}\"]")){
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Map<String, Object> ref = new HashMap<>();
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@ -733,8 +740,7 @@ public class DatasetMigrationService {
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if (this.conventionService.isNullOrEmpty(data.getLabel())) data.setLabel(data.getReference());
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if (this.conventionService.isNullOrEmpty(data.getSource()) &&
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referenceTypeDefinition.getSources().size() == 1 &&
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!ReferenceTypeIds.KnownReferenceTypeIds.contains(referenceTypeDataEntity.getReferenceTypeId())) {
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referenceTypeDefinition.getSources().size() == 1) {
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data.setSource(referenceTypeDefinition.getSources().getFirst().getKey());
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}
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if (this.conventionService.isNullOrEmpty(data.getLabel()) || data.getLabel().equals("null")){
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@ -742,7 +748,7 @@ public class DatasetMigrationService {
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return null;
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}
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if (this.conventionService.isNullOrEmpty(data.getSource())) throw new MyApplicationException("Migrate Dataset " + dataset.getId() + " " + dataset.getLabel() + " Source not found source for reference : " + referenceTypeDataEntity.getReferenceTypeId() + " " + this.jsonHandlingService.toJsonSafe(item)); //TODO
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if (this.conventionService.isNullOrEmpty(data.getSource())) throw new MyApplicationException("Migrate Dataset " + dataset.getId() + " " + dataset.getLabel() + " Source not found source for reference : " + referenceTypeDataEntity.getReferenceTypeId() + " " + this.jsonHandlingService.toJsonSafe(item)); //TODO
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if (this.conventionService.isNullOrEmpty(data.getReference())) {
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data.setReference(this.queryFactory.query(ReferenceQuery.class).sources(data.getSource()).like(data.getLabel()).typeIds(data.getTypeId()).sourceTypes(ReferenceSourceType.External).collectAs(new BaseFieldSet().ensure(Reference._reference, Reference._label))
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@ -14,6 +14,7 @@ import eu.eudat.data.ReferenceTypeEntity;
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import eu.eudat.data.converters.enums.DatabaseEnum;
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import eu.eudat.model.DescriptionTemplate;
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import eu.eudat.query.DescriptionTemplateQuery;
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import eu.eudat.query.ReferenceTypeQuery;
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import eu.old.eudat.logic.services.helpers.HelpersService;
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import eu.old.eudat.logic.utilities.builders.XmlBuilder;
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import eu.old.eudat.models.data.components.commons.Multiplicity;
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@ -28,6 +29,7 @@ import gr.cite.tools.logging.LoggerService;
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import jakarta.persistence.EntityManager;
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import jakarta.ws.rs.NotSupportedException;
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import jakarta.xml.bind.JAXBException;
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import org.elasticsearch.common.inject.Guice;
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import org.jetbrains.annotations.NotNull;
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import org.slf4j.LoggerFactory;
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import org.springframework.http.MediaType;
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@ -75,6 +77,7 @@ public class DescriptionTemplateXmlMigrationService {
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int page = 0;
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Map<String, ReferenceTypeEntity> referenceTypeEntityMap = new HashMap<>();
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Map<UUID, ReferenceTypeEntity> knownReferenceEntities = this.queryFactory.query(ReferenceTypeQuery.class).ids(ReferenceTypeIds.KnownReferenceTypeIds).collect().stream().collect(Collectors.toMap(ReferenceTypeEntity::getId, x-> x));
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List<DescriptionTemplateEntity> items;
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do {
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DescriptionTemplateQuery query = this.queryFactory.query(DescriptionTemplateQuery.class);
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@ -99,7 +102,7 @@ public class DescriptionTemplateXmlMigrationService {
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logger.error("Migrate DescriptionTemplate " + item.getId() + " failed read xml");
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throw new MyApplicationException("Migrate DescriptionTemplate " + item.getId() + " failed read xml");
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}
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item.setDefinition(this.xmlHandlingService.toXml(this.buildDefinitionEntity(viewStyleModel, referenceTypeEntityMap)));
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item.setDefinition(this.xmlHandlingService.toXml(this.buildDefinitionEntity(viewStyleModel, referenceTypeEntityMap, knownReferenceEntities)));
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this.entityManager.merge(item);
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}
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@ -115,7 +118,7 @@ public class DescriptionTemplateXmlMigrationService {
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this.entityManager.flush();
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}
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private @NotNull DefinitionEntity buildDefinitionEntity(ViewStyleModel persist, Map<String, ReferenceTypeEntity> referenceTypeEntityMap) throws URISyntaxException {
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private @NotNull DefinitionEntity buildDefinitionEntity(ViewStyleModel persist, Map<String, ReferenceTypeEntity> referenceTypeEntityMap, Map<UUID, ReferenceTypeEntity> knownReferenceEntities) throws URISyntaxException {
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DefinitionEntity data = new DefinitionEntity();
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if (persist == null)
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return data;
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@ -123,14 +126,14 @@ public class DescriptionTemplateXmlMigrationService {
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Map<String, List<Section>> sectionPerPage = mapSectionsToPage(persist);
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data.setPages(new ArrayList<>());
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for (Page pagePersist : persist.getPages()) {
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data.getPages().add(this.buildPageEntity(pagePersist, sectionPerPage.get(pagePersist.getId()), referenceTypeEntityMap));
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data.getPages().add(this.buildPageEntity(pagePersist, sectionPerPage.get(pagePersist.getId()), referenceTypeEntityMap, knownReferenceEntities));
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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 persist, Map<String, ReferenceTypeEntity> referenceTypeEntityMap) throws URISyntaxException {
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private @NotNull SectionEntity buildSectionEntity(Section persist, Map<String, ReferenceTypeEntity> referenceTypeEntityMap, Map<UUID, ReferenceTypeEntity> knownReferenceEntities) throws URISyntaxException {
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SectionEntity data = new SectionEntity();
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if (persist == null)
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return data;
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@ -146,21 +149,21 @@ public class DescriptionTemplateXmlMigrationService {
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if (!this.conventionService.isListNullOrEmpty(persist.getSections())) {
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data.setSections(new ArrayList<>());
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for (Section sectionPersist : persist.getSections()) {
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data.getSections().add(this.buildSectionEntity(sectionPersist, referenceTypeEntityMap));
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data.getSections().add(this.buildSectionEntity(sectionPersist, referenceTypeEntityMap, knownReferenceEntities));
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}
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}
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if (!this.conventionService.isListNullOrEmpty(persist.getFieldSets())) {
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data.setFieldSets(new ArrayList<>());
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for (FieldSet fieldSetPersist : persist.getFieldSets()) {
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data.getFieldSets().add(this.buildFieldSetEntity(fieldSetPersist, referenceTypeEntityMap));
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data.getFieldSets().add(this.buildFieldSetEntity(fieldSetPersist, referenceTypeEntityMap, knownReferenceEntities));
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}
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}
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return data;
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}
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private @NotNull FieldSetEntity buildFieldSetEntity(FieldSet persist, Map<String, ReferenceTypeEntity> referenceTypeEntityMap) throws URISyntaxException {
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private @NotNull FieldSetEntity buildFieldSetEntity(FieldSet persist, Map<String, ReferenceTypeEntity> referenceTypeEntityMap, Map<UUID, ReferenceTypeEntity> knownReferenceEntities) throws URISyntaxException {
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FieldSetEntity data = new FieldSetEntity();
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if (persist == null)
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return data;
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@ -180,13 +183,13 @@ public class DescriptionTemplateXmlMigrationService {
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if (!this.conventionService.isListNullOrEmpty(persist.getFields())) {
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data.setFields(new ArrayList<>());
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for (Field fieldPersist : persist.getFields()) {
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data.getFields().add(this.buildFieldEntity(fieldPersist, referenceTypeEntityMap));
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data.getFields().add(this.buildFieldEntity(fieldPersist, referenceTypeEntityMap, knownReferenceEntities));
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}
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}
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return data;
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}
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private @NotNull FieldEntity buildFieldEntity(Field persist, Map<String, ReferenceTypeEntity> referenceTypeEntityMap) throws URISyntaxException {
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private @NotNull FieldEntity buildFieldEntity(Field persist, Map<String, ReferenceTypeEntity> referenceTypeEntityMap, Map<UUID, ReferenceTypeEntity> knownReferenceEntities) throws URISyntaxException {
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FieldEntity data = new FieldEntity();
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if (persist == null)
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return data;
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@ -213,7 +216,7 @@ public class DescriptionTemplateXmlMigrationService {
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}).toList());
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data.setIncludeInExport(persist.getExport());
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if (persist.getData() != null) {
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data.setData(this.buildFieldDataEntity(persist.getData(), persist.getViewStyle().getRenderStyle(), referenceTypeEntityMap));
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data.setData(this.buildFieldDataEntity(persist.getData(), persist.getViewStyle().getRenderStyle(), referenceTypeEntityMap, knownReferenceEntities));
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if (persist.getViewStyle().getRenderStyle().equals("externalDatasets")){
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FieldDataExternalDatasetType type = null;
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try {
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@ -239,7 +242,7 @@ public class DescriptionTemplateXmlMigrationService {
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return data;
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}
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private BaseFieldDataEntity buildFieldDataEntity(FieldData<?> persist, String renderStyle, Map<String, ReferenceTypeEntity> referenceTypeEntityMap) throws URISyntaxException {
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private BaseFieldDataEntity buildFieldDataEntity(FieldData<?> persist, String renderStyle, Map<String, ReferenceTypeEntity> referenceTypeEntityMap, Map<UUID, ReferenceTypeEntity> knownReferenceEntities) throws URISyntaxException {
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if (renderStyle.equals("checkBox")){
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return this.buildLabelDataEntity(persist.getLabel(), FieldType.CHECK_BOX);
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}
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@ -369,7 +372,7 @@ public class DescriptionTemplateXmlMigrationService {
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return data;
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}
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case "autocomplete":{
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ReferenceTypeEntity referenceType = this.resolveReferenceTypeEntityAutoCompleteData(((AutoCompleteData)persist), referenceTypeEntityMap);
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ReferenceTypeEntity referenceType = this.resolveReferenceTypeEntityAutoCompleteData(((AutoCompleteData)persist), referenceTypeEntityMap, knownReferenceEntities);
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return this.buildReferenceTypeDataEntity(persist.getLabel(), ((AutoCompleteData)persist).getMultiAutoComplete(), referenceType.getId());
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}
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}
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@ -461,7 +464,7 @@ public class DescriptionTemplateXmlMigrationService {
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private @NotNull PageEntity buildPageEntity(Page persist, List<Section> sections, Map<String, ReferenceTypeEntity> referenceTypeEntityMap) throws URISyntaxException {
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private @NotNull PageEntity buildPageEntity(Page persist, List<Section> sections, Map<String, ReferenceTypeEntity> referenceTypeEntityMap, Map<UUID, ReferenceTypeEntity> knownReferenceEntities) throws URISyntaxException {
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PageEntity data = new PageEntity();
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if (persist == null)
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return data;
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@ -473,7 +476,7 @@ public class DescriptionTemplateXmlMigrationService {
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if (!this.conventionService.isListNullOrEmpty(sections)) {
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data.setSections(new ArrayList<>());
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for (Section sectionPersist : sections) {
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data.getSections().add(this.buildSectionEntity(sectionPersist, referenceTypeEntityMap));
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data.getSections().add(this.buildSectionEntity(sectionPersist, referenceTypeEntityMap, knownReferenceEntities));
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}
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}
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return data;
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@ -511,10 +514,13 @@ public class DescriptionTemplateXmlMigrationService {
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}
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}
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public ReferenceTypeEntity resolveReferenceTypeEntityAutoCompleteData(AutoCompleteData persist, Map<String, ReferenceTypeEntity> referenceTypeEntityMap) throws URISyntaxException {
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public ReferenceTypeEntity resolveReferenceTypeEntityAutoCompleteData(AutoCompleteData persist, Map<String, ReferenceTypeEntity> referenceTypeEntityMap, Map<UUID, ReferenceTypeEntity> knownReferenceEntities) throws URISyntaxException {
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ReferenceTypeDefinitionEntity definitionEntity = this.buildReferenceTypeDefinitionEntity(persist);
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String hash = this.referenceTypeCalculatedHash(definitionEntity);
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ReferenceTypeEntity data = referenceTypeEntityMap.getOrDefault(hash, null);
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ReferenceTypeEntity data = this.getReferenceTypeEntityByUrl(definitionEntity, knownReferenceEntities);
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if (data == null){
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data = referenceTypeEntityMap.getOrDefault(hash, null);
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}
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if (data == null) {
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data = new ReferenceTypeEntity();
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data.setId(UUID.randomUUID());
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@ -529,6 +535,26 @@ public class DescriptionTemplateXmlMigrationService {
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return data;
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}
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private ReferenceTypeEntity getReferenceTypeEntityByUrl(ReferenceTypeDefinitionEntity definitionEntity, Map<UUID, ReferenceTypeEntity> knownReferenceEntities){
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if (definitionEntity == null || this.conventionService.isListNullOrEmpty(definitionEntity.getSources()) || definitionEntity.getSources().size() != 1) return null;
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ExternalFetcherApiSourceConfigurationEntity externalFetcherApiSourceConfigurationEntity = (ExternalFetcherApiSourceConfigurationEntity)definitionEntity.getSources().getFirst();
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if (externalFetcherApiSourceConfigurationEntity == null || this.conventionService.isNullOrEmpty(externalFetcherApiSourceConfigurationEntity.getUrl())) return null;
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if (externalFetcherApiSourceConfigurationEntity.getUrl().trim().toLowerCase(Locale.ROOT).equals("https://eestore.paas2.uninett.no/api/license/".trim().toLowerCase(Locale.ROOT))) return knownReferenceEntities.get(ReferenceTypeIds.License);
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else if (externalFetcherApiSourceConfigurationEntity.getUrl().trim().toLowerCase(Locale.ROOT).equals("https://zenodo.org/api/licenses".trim().toLowerCase(Locale.ROOT))) return knownReferenceEntities.get(ReferenceTypeIds.License);
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else if (externalFetcherApiSourceConfigurationEntity.getUrl().trim().toLowerCase(Locale.ROOT).equals("https://zenodo.org/api/licenses?q={like}".trim().toLowerCase(Locale.ROOT))) return knownReferenceEntities.get(ReferenceTypeIds.License);
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else if (externalFetcherApiSourceConfigurationEntity.getUrl().trim().toLowerCase(Locale.ROOT).equals("http://api.openaire.eu/search/publications".trim().toLowerCase(Locale.ROOT))) return knownReferenceEntities.get(ReferenceTypeIds.Publication);
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else if (externalFetcherApiSourceConfigurationEntity.getUrl().trim().toLowerCase(Locale.ROOT).equals("http://api.openaire.eu/search/publications?format=json&title={like}".trim().toLowerCase(Locale.ROOT))) return knownReferenceEntities.get(ReferenceTypeIds.Publication);
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else if (externalFetcherApiSourceConfigurationEntity.getUrl().trim().toLowerCase(Locale.ROOT).equals("https://services.openaire.eu/openaire/ds/searchdetails/{page}/{pageSize}?requestSortBy=id&order=ASCENDING".trim().toLowerCase(Locale.ROOT))) return knownReferenceEntities.get(ReferenceTypeIds.Publication);
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else if (externalFetcherApiSourceConfigurationEntity.getUrl().trim().toLowerCase(Locale.ROOT).equals("https://eestore.paas2.uninett.no/api/datarepo/".trim().toLowerCase(Locale.ROOT))) return knownReferenceEntities.get(ReferenceTypeIds.DataRepositories);
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else if (externalFetcherApiSourceConfigurationEntity.getUrl().trim().toLowerCase(Locale.ROOT).equals("https://services.openaire.eu/search/v2/api/datasources?q={like}&fq=datasourcetypeuiname".trim().toLowerCase(Locale.ROOT))) return knownReferenceEntities.get(ReferenceTypeIds.DataRepositories);
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else if (externalFetcherApiSourceConfigurationEntity.getUrl().trim().toLowerCase(Locale.ROOT).equals("https://services.openaire.eu/search/v2/api/resources?query=oaftype exact datasource and {like} and ( datasourcetypeuiid = \"pubsrepository::journal\" or datasourcetypeuiid = \"aggregator::pubsrepository::journals\")&page=0&size=60&format=json".trim().toLowerCase(Locale.ROOT))) return knownReferenceEntities.get(ReferenceTypeIds.Journal);
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else if (externalFetcherApiSourceConfigurationEntity.getUrl().trim().toLowerCase(Locale.ROOT).equals("https://eestore.paas2.uninett.no/api/metadataschema/".trim().toLowerCase(Locale.ROOT))) return knownReferenceEntities.get(ReferenceTypeIds.Registries);
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else if (externalFetcherApiSourceConfigurationEntity.getUrl().trim().toLowerCase(Locale.ROOT).equals("https://eestore.paas2.uninett.no/api/taxonomy/".trim().toLowerCase(Locale.ROOT))) return knownReferenceEntities.get(ReferenceTypeIds.Taxonomy);
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return null;
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}
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public String referenceTypeCalculatedHash(ReferenceTypeDefinitionEntity definitionEntity) {
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List<String> sourceKeys = new ArrayList<>();
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if (definitionEntity.getSources() != null){
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@ -90,29 +90,29 @@ public class MigrationController {
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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, InvalidApplicationException, TransformerException, URISyntaxException {
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//Reference
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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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this.grantMigrationService.migrate();
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this.organizationMigrationService.migrate();
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this.projectMigrationService.migrate();
|
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this.registryMigrationService.migrate();
|
||||
this.researcherMigrationService.migrate();
|
||||
this.serviceMigrationService.migrate();
|
||||
// //Reference
|
||||
// this.dataRepositoryMigrationService.migrate();
|
||||
// this.externalDatasetMigrationService.migrate();
|
||||
// this.funderMigrationService.migrate();
|
||||
// this.grantMigrationService.migrate();
|
||||
// this.organizationMigrationService.migrate();
|
||||
// this.projectMigrationService.migrate();
|
||||
// this.registryMigrationService.migrate();
|
||||
// this.researcherMigrationService.migrate();
|
||||
// this.serviceMigrationService.migrate();
|
||||
//
|
||||
// //User
|
||||
// this.userContactInfoMigrationService.migrate();
|
||||
// this.userMigrationService.migrate();
|
||||
//
|
||||
// //XML recreate
|
||||
// this.dmpBlueprintXmlMigrationService.migrate();
|
||||
// this.descriptionTemplateXmlMigrationService.migrate();
|
||||
|
||||
//User
|
||||
this.userContactInfoMigrationService.migrate();
|
||||
this.userMigrationService.migrate();
|
||||
|
||||
//XML recreate
|
||||
this.dmpBlueprintXmlMigrationService.migrate();
|
||||
this.descriptionTemplateXmlMigrationService.migrate();
|
||||
|
||||
//Dmp
|
||||
this.dmpMigrationService.migrate();
|
||||
this.dmpDatasetProfileMigrationService.migrate();
|
||||
this.dmpUserMigrationService.migrate();
|
||||
// //Dmp
|
||||
// this.dmpMigrationService.migrate();
|
||||
// this.dmpDatasetProfileMigrationService.migrate();
|
||||
// this.dmpUserMigrationService.migrate();
|
||||
|
||||
//Description
|
||||
this.datasetMigrationService.migrate();
|
||||
|
|
|
|||
Loading…
Reference in New Issue