argos/dmp-migration-tool/web/src/main/java/eu/old/eudat/migration/DatasetMigrationService.java

1106 lines
78 KiB
Java

package eu.old.eudat.migration;
import eu.eudat.commons.JsonHandlingService;
import eu.eudat.commons.XmlHandlingService;
import eu.eudat.commons.enums.*;
import eu.eudat.commons.types.description.*;
import eu.eudat.commons.types.descriptiontemplate.FieldSetEntity;
import eu.eudat.commons.types.descriptiontemplate.fielddata.ReferenceTypeDataEntity;
import eu.eudat.commons.types.dmpblueprint.DefinitionEntity;
import eu.eudat.commons.types.externalfetcher.ExternalFetcherApiSourceConfigurationEntity;
import eu.eudat.commons.types.referencetype.ReferenceTypeDefinitionEntity;
import eu.eudat.convention.ConventionService;
import eu.eudat.data.*;
import eu.eudat.model.Dmp;
import eu.eudat.model.Reference;
import eu.eudat.model.ReferenceType;
import eu.eudat.query.*;
import eu.old.eudat.data.dao.entities.DatasetDao;
import eu.old.eudat.data.entities.Dataset;
import eu.old.eudat.logic.services.operations.DatabaseRepository;
import gr.cite.tools.data.query.QueryFactory;
import gr.cite.tools.exception.MyApplicationException;
import gr.cite.tools.fieldset.BaseFieldSet;
import gr.cite.tools.logging.LoggerService;
import jakarta.persistence.EntityManager;
import jakarta.xml.bind.JAXBException;
import org.json.JSONObject;
import org.slf4j.LoggerFactory;
import org.springframework.stereotype.Service;
import org.xml.sax.SAXException;
import javax.xml.parsers.ParserConfigurationException;
import java.io.IOException;
import java.time.Instant;
import java.time.LocalDate;
import java.time.ZoneOffset;
import java.time.format.DateTimeParseException;
import java.util.*;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.util.stream.Collectors;
@Service
public class DatasetMigrationService {
private static final LoggerService logger = new LoggerService(LoggerFactory.getLogger(DmpDatasetProfileMigrationService.class));
private final DatabaseRepository databaseRepository;
private final JsonHandlingService jsonHandlingService;
private final QueryFactory queryFactory;
private final XmlHandlingService xmlHandlingService;
private static final int PageSize = 500;
private static final boolean TestMode = false;
private final EntityManager entityManager;
private final ConventionService conventionService;
private final MigrationTools migrationTools;
public DatasetMigrationService(DatabaseRepository databaseRepository, JsonHandlingService jsonHandlingService, QueryFactory queryFactory, XmlHandlingService xmlHandlingService, EntityManager entityManager, ConventionService conventionService, MigrationTools migrationTools) {
this.databaseRepository = databaseRepository;
this.jsonHandlingService = jsonHandlingService;
this.queryFactory = queryFactory;
this.xmlHandlingService = xmlHandlingService;
this.entityManager = entityManager;
this.conventionService = conventionService;
this.migrationTools = migrationTools;
}
public void migrate() throws IOException, JAXBException, ParserConfigurationException, InstantiationException, IllegalAccessException, SAXException {
DatasetDao datasetDao = databaseRepository.getDatasetDao();
long total = datasetDao.asQueryable().count();
logger.debug("Migrate Dataset Total : " + total);
int page = 0;
Map<UUID, ReferenceTypeDefinitionEntity> referenceTypeDefinitionEntityMap = new HashMap<>();
List<ReferenceTypeEntity> referenceTypes = this.queryFactory.query(ReferenceTypeQuery.class).collectAs(new BaseFieldSet().ensure(ReferenceType._id).ensure(ReferenceType._definition));
for (ReferenceTypeEntity referenceType : referenceTypes){
referenceTypeDefinitionEntityMap.put(referenceType.getId(), this.xmlHandlingService.fromXml(ReferenceTypeDefinitionEntity.class, referenceType.getDefinition()));
}
Map<ReferenceKey, ReferenceEntity> referenceMap = new HashMap<>();
List<ReferenceEntity> references = this.queryFactory.query(ReferenceQuery.class).collectAs(new BaseFieldSet().ensure(Reference._id).ensure(Reference._source).ensure(Reference._type).ensure(Reference._reference));
for (ReferenceEntity reference : references){
if (reference.getCreatedById() == null) referenceMap.put(new ReferenceKey(reference), reference);
}
List<Dataset> items;
do {
items = datasetDao.asQueryable().orderBy((builder, root) -> builder.asc(root.get("created"))).orderBy((builder, root) -> builder.asc(root.get("ID"))).skip(page * PageSize).take(PageSize).toList();
if (items != null && !items.isEmpty()) {
logger.debug("Migrate Dataset " + page * PageSize + " of " + total);
List<DmpBlueprintEntity> dmpBlueprints = this.queryFactory.query(DmpBlueprintQuery.class).ids(items.stream().map(x-> x.getDmp().getProfile().getId()).distinct().toList()).collect();
Map<UUID, DefinitionEntity> dmpBlueprintsMap = new HashMap<>();
for (DmpBlueprintEntity dmpBlueprint : dmpBlueprints) {
DefinitionEntity definitionEntity = this.xmlHandlingService.fromXml(DefinitionEntity.class, dmpBlueprint.getDefinition());
dmpBlueprintsMap.put(dmpBlueprint.getId(), definitionEntity);
}
List<DmpDescriptionTemplateEntity> dmpDescriptionTemplateEntities = this.queryFactory.query(DmpDescriptionTemplateQuery.class).dmpIds(items.stream().map(x-> x.getDmp().getId()).distinct().toList()).collect();
List<DescriptionTemplateEntity> descriptionTemplates = this.queryFactory.query(DescriptionTemplateQuery.class).ids(items.stream().map(x-> x.getProfile().getId()).distinct().toList()).collect();
Map<UUID, UUID> creatorsByDmp = this.queryFactory.query(DmpQuery.class).ids(items.stream().map(x-> x.getDmp().getId()).distinct().toList()).collectAs(new BaseFieldSet().ensure(Dmp._id).ensure(Dmp._creator)).stream().collect(Collectors.toMap(DmpEntity::getId, DmpEntity::getCreatorId));
Map<UUID, eu.eudat.commons.types.descriptiontemplate.DefinitionEntity> descriptionTemplateDefinitionMap = new HashMap<>();
for (DescriptionTemplateEntity descriptionTemplateEntity : descriptionTemplates){
descriptionTemplateDefinitionMap.put(descriptionTemplateEntity.getId(), this.xmlHandlingService.fromXml(eu.eudat.commons.types.descriptiontemplate.DefinitionEntity.class, descriptionTemplateEntity.getDefinition()));
}
for (Dataset item : items) {
DefinitionEntity definition = dmpBlueprintsMap.getOrDefault(item.getDmp().getProfile().getId(), null);
if (definition == null || definition.getSections() == null || definition.getSections().size() <= item.getDmpSectionIndex()) {
throw new MyApplicationException("Migrate Dataset " + item.getId() + " cannot found section id for section " + item.getDmpSectionIndex());
}
UUID sectionId = definition.getSections().get(item.getDmpSectionIndex()).getId();
if (sectionId == null) {
throw new MyApplicationException("Migrate Dataset " + item.getId() + " cannot found section id for section " + item.getDmpSectionIndex());
}
List<DmpDescriptionTemplateEntity> itemDescriptionTemplates = this.getOrCreateDmpDescriptionTemplateEntity(item, sectionId, dmpDescriptionTemplateEntities);
if (itemDescriptionTemplates.size() > 1) {
throw new MyApplicationException("Migrate Dataset " + item.getId() + " multiple DmpDescriptionTemplateEntity for section " + item.getDmpSectionIndex());
}
DescriptionEntity data = new DescriptionEntity();
data.setId(item.getId());
data.setDescription(item.getDescription());
if (item.getCreator() != null) {
data.setCreatedById(item.getCreator().getId());
} else {
data.setCreatedById(creatorsByDmp.getOrDefault(item.getDmp().getId(), null));
}
data.setDmpId(item.getDmp().getId());
data.setLabel(item.getLabel());
data.setDmpDescriptionTemplateId(itemDescriptionTemplates.getFirst().getId());
data.setDescriptionTemplateId(item.getProfile().getId());
data.setCreatedAt(item.getCreated() != null ? item.getCreated().toInstant() : Instant.now());
data.setUpdatedAt(item.getModified() != null ? item.getModified().toInstant() : Instant.now());
if (item.getFinalizedAt() != null)
data.setFinalizedAt(item.getFinalizedAt().toInstant());
if (item.getStatus() == 99) {
data.setIsActive(IsActive.Inactive);
data.setStatus(DescriptionStatus.Canceled);
} else {
data.setIsActive(IsActive.Active);
data.setStatus(DescriptionStatus.of(item.getStatus()));
}
eu.eudat.commons.types.descriptiontemplate.DefinitionEntity descriptionTemplateDefinitionEntity = descriptionTemplateDefinitionMap.getOrDefault(item.getProfile().getId(), null);
data.setProperties(this.jsonHandlingService.toJson(this.buildPropertyDefinitionEntity(item, descriptionTemplateDefinitionEntity, referenceTypeDefinitionEntityMap, referenceMap)));
if (data.getCreatedById() == null){
throw new MyApplicationException("Migration skipped creator not found " + item.getId());
}
this.entityManager.persist(data);
this.entityManager.flush();
}
page++;
}
} while (items != null && !items.isEmpty() && !TestMode);
}
private List<DmpDescriptionTemplateEntity> getOrCreateDmpDescriptionTemplateEntity(Dataset item, UUID sectionId, List<DmpDescriptionTemplateEntity> dmpDescriptionTemplateEntities){
List<DmpDescriptionTemplateEntity> itemDescriptionTemplates = dmpDescriptionTemplateEntities.stream().filter(x-> x.getDescriptionTemplateGroupId().equals(item.getProfile().getGroupId()) && x.getDmpId().equals(item.getDmp().getId()) && x.getSectionId().equals(sectionId)).toList();
if (itemDescriptionTemplates.isEmpty()) {
logger.warn("Migrate Dataset " + item.getId() + " cannot found DmpDescriptionTemplateEntity for section " + item.getDmpSectionIndex());
if (dmpDescriptionTemplateEntities.stream().anyMatch(x -> x.getDmpId().equals(item.getDmp().getId()) && x.getSectionId().equals(sectionId))) {
DmpDescriptionTemplateEntity dmpDescriptionTemplateEntity = new DmpDescriptionTemplateEntity();
dmpDescriptionTemplateEntity.setId(UUID.randomUUID());
dmpDescriptionTemplateEntity.setDescriptionTemplateGroupId(item.getProfile().getGroupId());
dmpDescriptionTemplateEntity.setDmpId(item.getDmp().getId());
dmpDescriptionTemplateEntity.setCreatedAt(item.getCreated() != null ? item.getCreated().toInstant() : Instant.now());
dmpDescriptionTemplateEntity.setUpdatedAt(item.getModified() != null ? item.getModified().toInstant() : Instant.now());
dmpDescriptionTemplateEntity.setSectionId(sectionId);
dmpDescriptionTemplateEntity.setIsActive(IsActive.Active);
this.entityManager.persist(dmpDescriptionTemplateEntity);
itemDescriptionTemplates = List.of(dmpDescriptionTemplateEntity);
} else {
throw new MyApplicationException("Migrate Dataset " + item.getId() + " " + item.getLabel() + " cannot found DmpDescriptionTemplateEntity for section " + item.getDmpSectionIndex());
}
}
return itemDescriptionTemplates;
}
private PropertyDefinitionEntity buildPropertyDefinitionEntity(Dataset item, eu.eudat.commons.types.descriptiontemplate.DefinitionEntity descriptionTemplateDefinitionEntity, Map<UUID, ReferenceTypeDefinitionEntity> referenceTypeDefinitionEntityMap, Map<ReferenceKey, ReferenceEntity> referenceMap) {
if (this.conventionService.isNullOrEmpty(item.getProperties())) return null;
JSONObject jObject = new JSONObject(item.getProperties());
Map<String, Object> properties = jObject.toMap();
PropertyDefinitionEntity propertyDefinitionEntity = new PropertyDefinitionEntity();
propertyDefinitionEntity.setFieldSets(new HashMap<>());
List<FieldSetEntity> fieldSetEntities = descriptionTemplateDefinitionEntity.getAllFieldSets();
for (String key : properties.keySet()) {
if (key.toLowerCase(Locale.ROOT).trim().startsWith("commentfieldvalue")){
if (properties.get(key) != null && this.conventionService.isNullOrEmpty(properties.get(key).toString())) { continue; }
FieldSetEntity currentFieldSet = fieldSetEntities.stream().filter(x-> x.getId().equals(key.trim().substring("commentfieldvalue".length()))).findFirst().orElse(null);
if (currentFieldSet == null) {
logger.error("Migrate Dataset " + item.getId() + " " + item.getLabel() + " Field set " + key + " not found for comment " + properties.get(key).toString());
continue;
}
this.addSimpleCommentField(propertyDefinitionEntity, currentFieldSet, properties.get(key).toString());
} else {
if (!key.toLowerCase(Locale.ROOT).trim().startsWith("multiple_")) {
FieldSetEntity currentFieldSet = null;
eu.eudat.commons.types.descriptiontemplate.FieldEntity currentField = null;
for (FieldSetEntity fieldSetEntity : fieldSetEntities) {
List<eu.eudat.commons.types.descriptiontemplate.FieldEntity> fieldEntities = fieldSetEntity.getFieldById(key.trim());
if (!fieldEntities.isEmpty()) {
currentFieldSet = fieldSetEntity;
currentField = fieldEntities.getFirst();
}
}
if (currentField == null) {
logger.error("Migrate Dataset " + item.getId() + " " + item.getLabel() + " Field set not found for field " + key + " " + properties.get(key).toString());
continue;
}
this.addSimpleField(item, propertyDefinitionEntity, currentFieldSet, currentField, properties, referenceTypeDefinitionEntityMap, referenceMap);
}
}
}
this.addMultipleField(item, properties, descriptionTemplateDefinitionEntity, propertyDefinitionEntity, referenceTypeDefinitionEntityMap, referenceMap);
for (PropertyDefinitionFieldSetEntity fieldSetEntity : propertyDefinitionEntity.getFieldSets().values()){
int newOrdinal = 0;
for (PropertyDefinitionFieldSetItemEntity propertyDefinitionFieldSetItemEntity : fieldSetEntity.getItems().stream().filter(x-> x.getOrdinal() >= 0).sorted(Comparator.comparingInt(PropertyDefinitionFieldSetItemEntity::getOrdinal)).toList()){
propertyDefinitionFieldSetItemEntity.setOrdinal(newOrdinal);
newOrdinal++;
}
for (PropertyDefinitionFieldSetItemEntity propertyDefinitionFieldSetItemEntity : fieldSetEntity.getItems().stream().filter(x-> x.getOrdinal() < 0).sorted(Comparator.comparingInt(PropertyDefinitionFieldSetItemEntity::getOrdinal)).toList()){
propertyDefinitionFieldSetItemEntity.setOrdinal(newOrdinal);
newOrdinal++;
}
}
return propertyDefinitionEntity;
}
private void addMultipleField(Dataset item, Map<String, Object> properties, eu.eudat.commons.types.descriptiontemplate.DefinitionEntity descriptionTemplateDefinitionEntity, PropertyDefinitionEntity propertyDefinitionEntity, Map<UUID, ReferenceTypeDefinitionEntity> referenceTypeDefinitionEntityMap, Map<ReferenceKey, ReferenceEntity> referenceMap){
Map<MultipleFieldKey, Integer> groupOrdinalMapping = new HashMap<>();
for (String key : properties.keySet()) {
if (key.trim().toLowerCase(Locale.ROOT).startsWith("multiple_")) {
String newKey = key.trim().substring("multiple_".length());
String[] keyParts = newKey.split("_");
if (keyParts.length > 4 && newKey.contains("_multiple_")){
String[] multiParts = newKey.split("_multiple_");
if (multiParts.length == 2){
newKey = multiParts[0] + "_" + multiParts[1].split("_")[multiParts[1].split("_").length - 1];
keyParts = newKey.split("_");
}
}
String fieldSetId = "";
String groupId = "";
int ordinal = Integer.MIN_VALUE;
String fieldId = "";
if (keyParts.length == 4) {
fieldSetId = keyParts[0].trim();
groupId = keyParts[1].trim();
fieldId = keyParts[3].trim();
} else if (keyParts.length == 3) {
fieldSetId = keyParts[0].trim();
groupId = keyParts[1].trim();
fieldId = keyParts[2].trim();
} else {
throw new MyApplicationException("Migrate Dataset " + item.getId() + " " + item.getLabel() + " Field group key has invalid format " + key + " " + properties.get(key).toString());
}
try {
if (keyParts.length == 4) ordinal = Integer.parseInt(keyParts[2].trim());
} catch (Exception e){
throw new MyApplicationException("Migrate Dataset " + item.getId() + " " + item.getLabel() + " Field group key has invalid format " + key + " " + properties.get(key).toString());
}
eu.eudat.commons.types.descriptiontemplate.FieldEntity currentField = descriptionTemplateDefinitionEntity.getFieldById(fieldId).stream().findFirst().orElse(null);
if (currentField == null) {
logger.warn("Migrate Dataset " + item.getId() + " " + item.getLabel() + " Field set not found for field " + key + " " + properties.get(key).toString());
continue;
}
PropertyDefinitionFieldSetEntity propertyDefinitionFieldSetEntity = propertyDefinitionEntity.getFieldSets().getOrDefault(fieldSetId, null);
if (propertyDefinitionFieldSetEntity == null) {
propertyDefinitionFieldSetEntity = new PropertyDefinitionFieldSetEntity();
propertyDefinitionFieldSetEntity.setItems(new ArrayList<>());
propertyDefinitionEntity.getFieldSets().put(fieldId, propertyDefinitionFieldSetEntity);
}
if (ordinal == Integer.MIN_VALUE) {
if (groupOrdinalMapping.containsKey(new MultipleFieldKey(fieldSetId, groupId))){
ordinal = groupOrdinalMapping.get(new MultipleFieldKey(fieldSetId, groupId));
} else {
ordinal = propertyDefinitionFieldSetEntity.getItems().stream().filter(x-> !x.getFields().isEmpty()).map(PropertyDefinitionFieldSetItemEntity::getOrdinal).min(Comparator.comparing(x -> x)).orElse(-1) - 1;
ordinal = Math.min(ordinal, -1);
}
}
if (!groupOrdinalMapping.containsKey(new MultipleFieldKey(fieldSetId, groupId))){
groupOrdinalMapping.put(new MultipleFieldKey(fieldSetId, groupId), ordinal);
} else {
if (groupOrdinalMapping.get(new MultipleFieldKey(fieldSetId, groupId)) != ordinal) throw new MyApplicationException("Invalid multiple key ordinal " + key);
}
this.addMultipleField(item, propertyDefinitionFieldSetEntity, ordinal, currentField, properties, referenceTypeDefinitionEntityMap, referenceMap);
}
}
}
private void addMultipleField(Dataset item, PropertyDefinitionFieldSetEntity propertyDefinitionFieldSetEntity, int ordinal, eu.eudat.commons.types.descriptiontemplate.FieldEntity currentField, Map<String, Object> properties, Map<UUID, ReferenceTypeDefinitionEntity> referenceTypeDefinitionEntityMap, Map<ReferenceKey, ReferenceEntity> referenceMap){
PropertyDefinitionFieldSetItemEntity propertyDefinitionFieldSetItemEntity = propertyDefinitionFieldSetEntity.getItems().stream().filter(x-> x.getOrdinal() == ordinal).findFirst().orElse(null);
if (propertyDefinitionFieldSetItemEntity == null){
propertyDefinitionFieldSetItemEntity = new PropertyDefinitionFieldSetItemEntity();
propertyDefinitionFieldSetItemEntity.setFields(new HashMap<>());
propertyDefinitionFieldSetItemEntity.setOrdinal(ordinal);
propertyDefinitionFieldSetEntity.getItems().add(propertyDefinitionFieldSetItemEntity);
}
propertyDefinitionFieldSetItemEntity.getFields().put(currentField.getId(), this.buildField(item, currentField, properties, referenceTypeDefinitionEntityMap, referenceMap));
}
private void addSimpleField(Dataset item, PropertyDefinitionEntity propertyDefinitionEntity, FieldSetEntity currentFieldSet, eu.eudat.commons.types.descriptiontemplate.FieldEntity currentField, Map<String, Object> properties, Map<UUID, ReferenceTypeDefinitionEntity> referenceTypeDefinitionEntityMap, Map<ReferenceKey, ReferenceEntity> referenceMap){
PropertyDefinitionFieldSetEntity propertyDefinitionFieldSetEntity = propertyDefinitionEntity.getFieldSets().getOrDefault(currentFieldSet.getId(), null);
if (propertyDefinitionFieldSetEntity == null) {
propertyDefinitionFieldSetEntity = new PropertyDefinitionFieldSetEntity();
propertyDefinitionFieldSetEntity.setItems(new ArrayList<>());
propertyDefinitionEntity.getFieldSets().put(currentFieldSet.getId(), propertyDefinitionFieldSetEntity);
}
PropertyDefinitionFieldSetItemEntity propertyDefinitionFieldSetItemEntity = null;
if (this.conventionService.isListNullOrEmpty(propertyDefinitionFieldSetEntity.getItems())){
propertyDefinitionFieldSetItemEntity = new PropertyDefinitionFieldSetItemEntity();
propertyDefinitionFieldSetItemEntity.setFields(new HashMap<>());
propertyDefinitionFieldSetItemEntity.setOrdinal(0);
propertyDefinitionFieldSetEntity.getItems().add(propertyDefinitionFieldSetItemEntity);
} else {
propertyDefinitionFieldSetItemEntity = propertyDefinitionFieldSetEntity.getItems().getFirst();
}
propertyDefinitionFieldSetItemEntity.getFields().put(currentField.getId(), this.buildField(item, currentField, properties, referenceTypeDefinitionEntityMap, referenceMap));
}
private void addSimpleCommentField(PropertyDefinitionEntity propertyDefinitionEntity, FieldSetEntity currentFieldSet, String comment){
PropertyDefinitionFieldSetEntity propertyDefinitionFieldSetEntity = propertyDefinitionEntity.getFieldSets().getOrDefault(currentFieldSet.getId(), null);
if (propertyDefinitionFieldSetEntity == null) {
propertyDefinitionFieldSetEntity = new PropertyDefinitionFieldSetEntity();
propertyDefinitionFieldSetEntity.setItems(new ArrayList<>());
propertyDefinitionEntity.getFieldSets().put(currentFieldSet.getId(), propertyDefinitionFieldSetEntity);
}
PropertyDefinitionFieldSetItemEntity propertyDefinitionFieldSetItemEntity = null;
if (this.conventionService.isListNullOrEmpty(propertyDefinitionFieldSetEntity.getItems())){
propertyDefinitionFieldSetItemEntity = new PropertyDefinitionFieldSetItemEntity();
propertyDefinitionFieldSetItemEntity.setFields(new HashMap<>());
propertyDefinitionFieldSetItemEntity.setOrdinal(0);
propertyDefinitionFieldSetEntity.getItems().add(propertyDefinitionFieldSetItemEntity);
} else {
propertyDefinitionFieldSetItemEntity = propertyDefinitionFieldSetEntity.getItems().getFirst();
}
propertyDefinitionFieldSetItemEntity.setComment(comment);
}
private FieldEntity buildField(Dataset item, eu.eudat.commons.types.descriptiontemplate.FieldEntity currentField, Map<String, Object> properties, Map<UUID, ReferenceTypeDefinitionEntity> referenceTypeDefinitionEntityMap, Map<ReferenceKey, ReferenceEntity> referenceMap){
FieldEntity fieldEntity = new FieldEntity();
String textValue = properties.get(currentField.getId()) != null ? properties.get(currentField.getId()).toString() : null;
if (textValue == null || textValue.isEmpty()) return fieldEntity;
switch (currentField.getData().getFieldType()){
case FREE_TEXT, TEXT_AREA, RICH_TEXT_AREA, RADIO_BOX -> fieldEntity.setTextValue(textValue.trim());
case CHECK_BOX, BOOLEAN_DECISION -> fieldEntity.setTextValue(textValue.trim().toLowerCase(Locale.ROOT));
case DATE_PICKER -> {
Instant instant = null;
if(!this.conventionService.isNullOrEmpty(textValue)) {
try {
instant = Instant.parse(textValue);
} catch (DateTimeParseException ex) {
instant = LocalDate.parse(textValue).atStartOfDay().toInstant(ZoneOffset.UTC);
}
}
fieldEntity.setDateValue(instant);
}
case SELECT -> {
if(!this.conventionService.isNullOrEmpty(textValue)) {
String[] valuesParsed = migrationTools.tryParseJsonAsObjectString(String[].class, textValue);
fieldEntity.setTextListValue(valuesParsed == null ? List.of(textValue) : Arrays.stream(valuesParsed).toList());
}
}
case DATASET_IDENTIFIER, VALIDATION -> {
if(!this.conventionService.isNullOrEmpty(textValue)) {
ExternalIdentifierEntity externalIdentifierEntity = migrationTools.tryParseJsonAsObjectString(ExternalIdentifierEntity.class, textValue);
if (externalIdentifierEntity == null) throw new MyApplicationException("Could not parse dataset External Identifier : " + textValue);
fieldEntity.setExternalIdentifier(externalIdentifierEntity);
}
}
case UPLOAD -> {
if(!this.conventionService.isNullOrEmpty(textValue)) {
Map<String, String> valuesParsed = migrationTools.tryParseJsonAsObjectString(Map.class, textValue);
if (valuesParsed == null) {
valuesParsed = (Map<String, String>) properties.get(currentField.getId());
}
if (valuesParsed == null) throw new MyApplicationException("Could not parse upload : " + textValue);
String id = valuesParsed.getOrDefault("id", null);
if (id == null) throw new MyApplicationException("Could not parse upload : " + textValue);
fieldEntity.setTextValue(UUID.fromString(id).toString());
}
}
case CURRENCY -> {
if(!this.conventionService.isNullOrEmpty(textValue)) {
Currency currency = migrationTools.tryParseJsonAsObjectString(Currency.class, textValue);
if (currency == null && textValue.toUpperCase(Locale.ROOT).contains("EUR")) {
currency = new Currency();
currency.setName("Euro");
currency.setValue("EUR");
}
if (currency == null && textValue.toUpperCase(Locale.ROOT).contains("US DOLLAR")) {
currency = new Currency();
currency.setName("US DOLLAR");
currency.setValue("USD");
}
if (currency == null) throw new MyApplicationException("Could not parse Currency : " + textValue);
//TODO: {"name":"Euro","value":"EUR"} what we want to keep ?
fieldEntity.setTextValue(currency.getName());
}
}
case TAGS -> {
if(!this.conventionService.isNullOrEmpty(textValue)) {
Tag[] tags = migrationTools.tryParseJsonAsObjectString(Tag[].class, textValue);
if (tags == null) {
Tag tag = migrationTools.tryParseJsonAsObjectString(Tag.class, textValue);
if (tag != null) tags = List.of(tag).toArray(Tag[]::new);
}
if (tags == null) tags = this.jsonHandlingService.fromJsonSafe(Tag[].class, migrationTools.cleanTagString(textValue));
if (tags == null) throw new MyApplicationException("Could not parse tag : " + textValue);
fieldEntity.setTextListValue(Arrays.stream(tags).toList().stream().map(Tag::getName).toList());
}
}
case INTERNAL_ENTRIES_DMPS -> throw new MyApplicationException("Found INTERNAL_ENTRIES_DMPS into description");
case INTERNAL_ENTRIES_DESCRIPTIONS -> throw new MyApplicationException("Found INTERNAL_ENTRIES_DMPS into description");
case REFERENCE_TYPES -> {
if(!this.conventionService.isNullOrEmpty(textValue)) { //TODO
Map<String, Object>[] references = migrationTools.tryParseJsonAsObjectString(Map[].class, textValue);
ReferenceTypeDataEntity referenceTypeDataEntity = (ReferenceTypeDataEntity)currentField.getData();
if (referenceTypeDataEntity == null) throw new MyApplicationException("Could not parse description template reference : " + textValue);
if (references == null) {
Map<String, Object> reference = migrationTools.tryParseJsonAsObjectString(Map.class, textValue);
if (reference != null) references = List.of(reference).toArray(Map[]::new);
}
if (references == null && !textValue.contains("{") && !textValue.contains("[") ) {
if (!textValue.contains(",")) {
Map<String, Object> ref = new HashMap<>();
ref.put("name", textValue);
if (!ReferenceTypeIds.KnownReferenceTypeIds.contains(referenceTypeDataEntity.getReferenceTypeId())) {
ReferenceTypeDefinitionEntity referenceTypeDefinition = referenceTypeDefinitionEntityMap.getOrDefault(referenceTypeDataEntity.getReferenceTypeId(), null);
if (referenceTypeDefinition == null) throw new MyApplicationException("Could not find reference type for reference : " + this.jsonHandlingService.toJsonSafe(textValue));
if (this.conventionService.isListNullOrEmpty(referenceTypeDefinition.getSources())) throw new MyApplicationException("Could not find reference source for reference : " + this.jsonHandlingService.toJsonSafe(textValue));
if (referenceTypeDefinition.getSources().size() > 1) throw new MyApplicationException("Multiple reference source for reference : " + this.jsonHandlingService.toJsonSafe(textValue));
ref.put("source", referenceTypeDefinition.getSources().getFirst().getKey());
} else if (ReferenceTypeIds.DataRepositories.equals(referenceTypeDataEntity.getReferenceTypeId())) {
ref.put("source", "openaire");
} else if (ReferenceTypeIds.Services.equals(referenceTypeDataEntity.getReferenceTypeId())) {
ref.put("source", "eosc");
} else if (ReferenceTypeIds.Registries.equals(referenceTypeDataEntity.getReferenceTypeId())) {
ref.put("source", "rda-metadata-schemes");
} else if (ReferenceTypeIds.Organizations.equals(referenceTypeDataEntity.getReferenceTypeId())) {
ref.put("source", "openaire");
} else if (ReferenceTypeIds.Datasets.equals(referenceTypeDataEntity.getReferenceTypeId())) {
ref.put("source", "openaire");
} else if (ReferenceTypeIds.Journal.equals(referenceTypeDataEntity.getReferenceTypeId())) {
ref.put("source", "openaire");
} else if (ReferenceTypeIds.License.equals(referenceTypeDataEntity.getReferenceTypeId())) {
ref.put("source", "opendefinition");
} else if (ReferenceTypeIds.PubRepositories.equals(referenceTypeDataEntity.getReferenceTypeId())) {
ref.put("source", "opendefinition");
} else if (ReferenceTypeIds.Researcher.equals(referenceTypeDataEntity.getReferenceTypeId())) {
Matcher pattern = Pattern.compile("\\((.*?)\\)").matcher(textValue);
if (pattern.find()) {
String matchedString = pattern.group(0);
ref.put("name", textValue.replace(matchedString, "").trim());
matchedString = matchedString.substring(1, matchedString.length() - 1);
ref.put("source", matchedString.split(":")[0]);
ref.put("id", matchedString.split(":")[1]);
} else {
ref.put("name", textValue);
ref.put("source", "orcid");
}
}
if (ref.containsKey("source")) references = List.of(ref).toArray(new Map[1]);
} else {
String source = null;
if (!ReferenceTypeIds.KnownReferenceTypeIds.contains(referenceTypeDataEntity.getReferenceTypeId())) {
ReferenceTypeDefinitionEntity referenceTypeDefinition = referenceTypeDefinitionEntityMap.getOrDefault(referenceTypeDataEntity.getReferenceTypeId(), null);
if (referenceTypeDefinition == null) throw new MyApplicationException("Could not find reference type for reference : " + this.jsonHandlingService.toJsonSafe(textValue));
if (this.conventionService.isListNullOrEmpty(referenceTypeDefinition.getSources())) throw new MyApplicationException("Could not find reference source for reference : " + this.jsonHandlingService.toJsonSafe(textValue));
//if (referenceTypeDefinition.getSources().size() > 1) throw new MyApplicationException("Multiple reference source for reference : " + this.jsonHandlingService.toJsonSafe(textValue));
source = referenceTypeDefinition.getSources().getFirst().getKey();
String[] parts = null;
if (textValue.startsWith("[\"")){
parts = migrationTools.tryParseJsonAsObjectString(String[].class, textValue);
} else{
if (textValue.startsWith("[")) textValue = textValue.substring(1).trim();
if (textValue.endsWith("]")) textValue = textValue.substring(0, textValue.length() -1).trim();
parts = textValue.split(",");
}
if (parts != null) {
List<Map<String, Object>> items = new ArrayList<>();
for (String part : parts) {
if (this.conventionService.isNullOrEmpty(part)) continue;
part = part.trim().replace(",", "").trim();
if (this.conventionService.isNullOrEmpty(part) || part.equals("null")) continue;
Map<String, Object> ref = new HashMap<>();
ref.put("name", part);
ref.put("source", source);
items.add(ref);
}
if (items.isEmpty()) break;
references = items.toArray(new Map[items.size()]);
}
}
}
}
if (references == null && !ReferenceTypeIds.KnownReferenceTypeIds.contains(referenceTypeDataEntity.getReferenceTypeId())){
if (textValue.equalsIgnoreCase("[\"dublin core\",\"{\\\"id\\\":\\\"metadataschema:rd-alliance/dublin-core\\\",\\\"label\\\":\\\"Dublin Core\\\",\\\"source\\\":\\\"\\\",\\\"uri\\\":\\\"http://dublincore.org\\\"}\"]")){
Map<String, Object> ref = new HashMap<>();
ref.put("name", "Dublin Core");
ref.put("source", "metadataschema");
ref.put("id", "rd-alliance/dublin-core");
ref.put("uri", "http://dublincore.org");
references = List.of(ref).toArray(new Map[1]);
} else if (textValue.equalsIgnoreCase("[\"Datacite\",\"{\\\"id\\\":\\\"metadataschema:rd-alliance/datacite-metadata-schema\\\",\\\"label\\\":\\\"DataCite Metadata Schema\\\",\\\"source\\\":\\\"\\\",\\\"uri\\\":\\\"http://schema.datacite.org\\\"}\"]")){
Map<String, Object> ref = new HashMap<>();
ref.put("name", "DataCite Metadata Schema");
ref.put("source", "metadataschema");
ref.put("id", "rd-alliance/datacite-metadata-schema");
ref.put("uri", "http://schema.datacite.org");
references = List.of(ref).toArray(new Map[1]);
} else if (textValue.equalsIgnoreCase("[\" .\"]")) {
break;
} else if (textValue.equalsIgnoreCase("[INT]")) {
ReferenceTypeDefinitionEntity referenceTypeDefinition = referenceTypeDefinitionEntityMap.getOrDefault(referenceTypeDataEntity.getReferenceTypeId(), null);
if (referenceTypeDefinition == null) throw new MyApplicationException("Could not find reference type for reference : " + this.jsonHandlingService.toJsonSafe(textValue));
if (this.conventionService.isListNullOrEmpty(referenceTypeDefinition.getSources())) throw new MyApplicationException("Could not find reference source for reference : " + this.jsonHandlingService.toJsonSafe(textValue));
//if (referenceTypeDefinition.getSources().size() > 1) throw new MyApplicationException("Multiple reference source for reference : " + this.jsonHandlingService.toJsonSafe(textValue));
Map<String, Object> ref = new HashMap<>();
ref.put("name", "INT");
ref.put("source", referenceTypeDefinition.getSources().getFirst().getKey());
references = List.of(ref).toArray(new Map[1]);
}
}
if (references == null && ReferenceTypeIds.Researcher.equals(referenceTypeDataEntity.getReferenceTypeId())){
if (textValue.equals("[\"-\"]")){
break;
} else if (textValue.startsWith("[\"") && !textValue.startsWith("[\"{") && textValue.contains(",")){
references = migrationTools.tryParseJsonAsObjectString(Map[].class, textValue.replace(textValue.substring(1, textValue.indexOf(",") + 1), ""));
} else if (textValue.contains(",") && !textValue.contains("{") && !textValue.contains("[") ){
String[] parts = textValue.split(",");
List<Map<String, Object>> items = new ArrayList<>();
for (String part : parts){
if (this.conventionService.isNullOrEmpty(part)) continue;
part = part.trim().replace(",", "").trim();
if (this.conventionService.isNullOrEmpty(part) || part.equals("null")) continue;
Matcher pattern = Pattern.compile("\\((.*?)\\)").matcher(part);
Map<String, Object> ref = new HashMap<>();
if (pattern.find()){
String matchedString = pattern.group(0);
ref.put("name", part.replace(matchedString, "").trim());
matchedString = matchedString.substring(1, matchedString.length() - 1);
ref.put("source", matchedString.split(":")[0]);
ref.put("id", matchedString.split(":")[1]);
}else {
ref.put("name", part);
ref.put("source", "orcid");
}
items.add(ref);
}
if (items.isEmpty()) break;
references = items.toArray(new Map[items.size()]);
}
}
if (references == null && (ReferenceTypeIds.Datasets.equals(referenceTypeDataEntity.getReferenceTypeId())
|| ReferenceTypeIds.DataRepositories.equals(referenceTypeDataEntity.getReferenceTypeId())
|| ReferenceTypeIds.Services.equals(referenceTypeDataEntity.getReferenceTypeId())
|| ReferenceTypeIds.License.equals(referenceTypeDataEntity.getReferenceTypeId()))){
textValue = textValue.trim();
if (textValue.equals("[\".\"]")){
break;
} else if (!textValue.contains("{")) {
String[] parts = null;
if (textValue.startsWith("[\"")){
parts = migrationTools.tryParseJsonAsObjectString(String[].class, textValue);
} else{
if (textValue.startsWith("[")) textValue = textValue.substring(1).trim();
if (textValue.endsWith("]")) textValue = textValue.substring(0, textValue.length() -1).trim();
parts = textValue.split(",");
}
if (parts != null) {
List<Map<String, Object>> items = new ArrayList<>();
for (String part : parts) {
if (this.conventionService.isNullOrEmpty(part)) continue;
part = part.trim().replace(",", "").trim();
if (this.conventionService.isNullOrEmpty(part) || part.equals("null")) continue;
Map<String, Object> ref = new HashMap<>();
ref.put("name", part);
if (ReferenceTypeIds.Services.equals(referenceTypeDataEntity.getReferenceTypeId())) ref.put("source", "eosc");
else if (ReferenceTypeIds.License.equals(referenceTypeDataEntity.getReferenceTypeId())) ref.put("source", "opendefinition");
else ref.put("source", "openaire");
items.add(ref);
}
if (items.isEmpty()) break;
references = items.toArray(new Map[items.size()]);
}
}
}
if (references == null){
throw new MyApplicationException("Migrate Dataset " + item.getId() + " " + item.getCreated() + " " + item.getLabel() + " Could not parse reference : " + referenceTypeDataEntity.getReferenceTypeId() + " with value " + textValue);
}
fieldEntity.setTextListValue(new ArrayList<>());
for (Map<String, Object> reference : references){
ReferenceEntity referenceEntity = this.geReferenceEntity(item, reference, referenceTypeDefinitionEntityMap, referenceTypeDataEntity, referenceMap);
if (referenceEntity != null) fieldEntity.getTextListValue().add(referenceEntity.getId().toString());
}
}
}
}
return fieldEntity;
}
private ReferenceEntity geReferenceEntity(Dataset dataset, Map<String, Object> item, Map<UUID, ReferenceTypeDefinitionEntity> referenceTypeDefinitionEntityMap, ReferenceTypeDataEntity referenceTypeDataEntity, Map<ReferenceKey, ReferenceEntity> referenceMap){
ReferenceTypeDefinitionEntity referenceTypeDefinition = referenceTypeDefinitionEntityMap.getOrDefault(referenceTypeDataEntity.getReferenceTypeId(), null);
if (referenceTypeDefinition == null) throw new MyApplicationException("Could not find reference type for reference : " + this.jsonHandlingService.toJsonSafe(item));
if (this.conventionService.isListNullOrEmpty(referenceTypeDefinition.getSources())) throw new MyApplicationException("Could not find reference source for reference : " + this.jsonHandlingService.toJsonSafe(item));
ReferenceEntity data = new ReferenceEntity();
if (item.containsKey("name")) data.setLabel((String) item.get("name"));
if (this.conventionService.isNullOrEmpty(data.getLabel()) && item.containsKey("label")) data.setLabel((String) item.get("label"));
if (item.containsKey("abbreviation")) data.setAbbreviation((String) item.get("abbreviation"));
if (item.containsKey("pid")) data.setReference((String)item.get("pid"));
if (item.containsKey("key")) data.setSource((String)item.get("key"));
if (this.conventionService.isNullOrEmpty(data.getSource()) && item.containsKey("source")) data.setSource((String) item.get("source"));
if (item.containsKey("reference") && !this.conventionService.isNullOrEmpty(((String)item.get("reference")))){
if (((String)item.get("reference")).contains(":")) {
String[] referenceParts = ((String)item.get("reference")).split(":", 2);
if (this.conventionService.isNullOrEmpty(data.getReference())) data.setReference(referenceParts[1]);
if (this.conventionService.isNullOrEmpty(data.getSource())) data.setSource(referenceParts[0]);
}
else if (this.conventionService.isNullOrEmpty(data.getReference())) data.setReference(((String)item.get("reference")));
}
if (item.containsKey("tag") && !this.conventionService.isNullOrEmpty(((String)item.get("tag")))){
if (((String)item.get("tag")).equalsIgnoreCase("openaire")) {
if (this.conventionService.isNullOrEmpty(data.getSource())) data.setSource("openaire");
} else if (((String)item.get("tag")).equalsIgnoreCase("Open Definition")) {
if (this.conventionService.isNullOrEmpty(data.getSource())) data.setSource("opendefinition");
} else if (((String)item.get("tag")).equalsIgnoreCase("RDA Metadata Schemes")) {
if (this.conventionService.isNullOrEmpty(data.getSource())) data.setSource("rda-metadata-schemes");
} else if (((String)item.get("tag")).equalsIgnoreCase("OpenAIRE publication repositories 1")) {
if (this.conventionService.isNullOrEmpty(data.getSource())) data.setSource("openaire");
} else if (((String)item.get("tag")).equalsIgnoreCase("OpenAIRE publication repositories 2")) {
if (this.conventionService.isNullOrEmpty(data.getSource())) data.setSource("openaire");
} else if (((String)item.get("tag")).equalsIgnoreCase("OpenAIRE publication repositories 3")) {
if (this.conventionService.isNullOrEmpty(data.getSource())) data.setSource("openaire");
} else if (((String)item.get("tag")).equalsIgnoreCase("OpenAIRE Journals")) {
if (this.conventionService.isNullOrEmpty(data.getSource())) data.setSource("openaire");
} else if (((String)item.get("tag")).equalsIgnoreCase("OpenAIRE Alternative")) {
if (this.conventionService.isNullOrEmpty(data.getSource())) data.setSource("openaire");
}else if (((String)item.get("tag")).equalsIgnoreCase("Taxonomies")) {
if (this.conventionService.isNullOrEmpty(data.getSource())) data.setSource("taxonomy");
} else if (((String)item.get("tag")).equalsIgnoreCase("OpenAIRE Publications")) {
if (this.conventionService.isNullOrEmpty(data.getSource())) data.setSource("openaire");
} else if (((String)item.get("tag")).equalsIgnoreCase("EOSC Providers")) {
if (this.conventionService.isNullOrEmpty(data.getSource())) data.setSource("eosc");
} else if (((String)item.get("tag")).equalsIgnoreCase("ORCID")) {
if (this.conventionService.isNullOrEmpty(data.getSource())) data.setSource("orcid");
} else if (((String)item.get("tag")).equalsIgnoreCase("Zenodo")) {
if (this.conventionService.isNullOrEmpty(data.getSource())) data.setSource("zenodo");
}
}
if (this.conventionService.isNullOrEmpty(data.getReference()) && item.containsKey("id") && !this.conventionService.isNullOrEmpty(((String)item.get("id")))) {
if (((String)item.get("id")).startsWith("datarepo:re3data/")) {
if (this.conventionService.isNullOrEmpty(data.getReference())) data.setReference(((String)item.get("id")).substring("datarepo:re3data/".length()));
if (this.conventionService.isNullOrEmpty(data.getSource())) data.setSource("re3data");
}
else if (this.conventionService.isNullOrEmpty(data.getReference())) data.setReference(((String)item.get("id")));
data.setReference((String)item.get("id"));
}
data.setId(UUID.randomUUID());
data.setCreatedAt(Instant.now());
data.setUpdatedAt(Instant.now());
data.setSourceType(ReferenceSourceType.External);
data.setTypeId(referenceTypeDataEntity.getReferenceTypeId());
data.setIsActive(IsActive.Active);
eu.eudat.commons.types.reference.DefinitionEntity definitionEntity = new eu.eudat.commons.types.reference.DefinitionEntity();
definitionEntity.setFields(new ArrayList<>());
for (Map.Entry<String, Object> entries : item.entrySet()){
if (entries.getValue() != null && !entries.getKey().equals("name") && !entries.getKey().equals("label")&& !entries.getKey().equals("abbreviation")
&& !entries.getKey().equals("id") && !entries.getKey().equals("key") && !entries.getKey().equals("pid")&& !entries.getKey().equals("source")) {
eu.eudat.commons.types.reference.FieldEntity field = new eu.eudat.commons.types.reference.FieldEntity();
field.setCode(entries.getKey());
field.setDataType(ReferenceFieldDataType.Text);
field.setValue(entries.getValue().toString());
definitionEntity.getFields().add(field);
}
}
if (!this.conventionService.isListNullOrEmpty(definitionEntity.getFields())) data.setDefinition(this.xmlHandlingService.toXmlSafe(definitionEntity));
if (this.conventionService.isNullOrEmpty(data.getLabel())) data.setLabel(data.getReference());
if (this.conventionService.isNullOrEmpty(data.getSource()) &&
referenceTypeDefinition.getSources().size() == 1 &&
!ReferenceTypeIds.KnownReferenceTypeIds.contains(referenceTypeDataEntity.getReferenceTypeId())) {
data.setSource(referenceTypeDefinition.getSources().getFirst().getKey());
}
if (this.conventionService.isNullOrEmpty(data.getLabel()) || data.getLabel().equals("null")){
logger.warn("Migrate Dataset " + dataset.getId() + " " + dataset.getLabel() + " no label for the reference : " + referenceTypeDataEntity.getReferenceTypeId() + " " + this.jsonHandlingService.toJsonSafe(item)); //TODO
return null;
}
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
if (this.conventionService.isNullOrEmpty(data.getReference())) {
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))
.stream().filter(x-> x.getLabel().equals(data.getLabel())).map(ReferenceEntity::getReference).findFirst().orElse(null));//TODO
}
if (this.conventionService.isNullOrEmpty(data.getReference())) {
if (referenceTypeDefinition.getSources().stream().filter(x-> x.getType().equals(ExternalFetcherSourceType.API)).map(x-> (ExternalFetcherApiSourceConfigurationEntity)x).anyMatch(x-> x.getUrl().toLowerCase(Locale.ROOT).contains("eestore.paas2.uninett.no"))){
if (data.getLabel().equalsIgnoreCase("Attribution 4.0 International")){
data.setReference("CC-BY-4.0");
} else if (data.getLabel().equalsIgnoreCase("Attribution-NonCommercial 4.0 International")){
data.setReference("CC-BY-NC-4.0");
} else if (data.getLabel().equalsIgnoreCase("Attribution-NonCommercial-NoDerivatives 4.0 International")){
data.setReference("CC-BY-NC-ND-4.0");
} else if (data.getLabel().equalsIgnoreCase("Attribution-NoDerivatives 4.0 International")){
data.setReference("CC-BY-ND-4.0");
} else if (data.getLabel().equalsIgnoreCase("Attribution-NonCommercial-ShareAlike 4.0 International") ){
data.setReference("CC-BY-NC-SA-4.0");
}
} if (data.getTypeId().equals(ReferenceTypeIds.License) && data.getSource().equalsIgnoreCase("OpenAIRE")){
if (data.getLabel().equalsIgnoreCase("Academic Free License 3.0")){
data.setReference("AFL-3.0");
} else if (data.getLabel().equalsIgnoreCase("Attribution Assurance Licenses")){
data.setReference("AFL-3.0");
}
} else if (data.getTypeId().equals(ReferenceTypeIds.Datasets) && data.getSource().equalsIgnoreCase("OpenAIRE")) {
if (data.getLabel().equalsIgnoreCase("Bulk RNA-seq U2OS cells treated with small molecules") && data.getSource().equalsIgnoreCase("OpenAIRE")){
data.setReference("50|_____OmicsDI::7fc1bcd133082463ec1948b82f1ad0ee");
} else if (data.getLabel().equalsIgnoreCase("Genome-wide effect of the microenvironment over the Galectin-7 regulation network in HeLa and SiHa tumors in nude mice.")){
data.setReference("50|_____OmicsDI::4e0de948bf961b96dbdef82797b5a8dc");
}
// else if (data.getLabel().equalsIgnoreCase("other")){
// data.setReference(data.getId().toString().replace("-", "").toLowerCase(Locale.ROOT));
// data.setSourceType(ReferenceSourceType.Internal);
// if (dataset.getCreator() != null) data.setCreatedById(dataset.getCreator().getId());
// } else if (data.getLabel().equalsIgnoreCase("none")){
// data.setReference(data.getId().toString().replace("-", "").toLowerCase(Locale.ROOT));
// data.setSourceType(ReferenceSourceType.Internal);
// if (dataset.getCreator() != null) data.setCreatedById(dataset.getCreator().getId());
// } else if (data.getLabel().equalsIgnoreCase("to be clarified later")){
// data.setReference(data.getId().toString().replace("-", "").toLowerCase(Locale.ROOT));
// data.setSourceType(ReferenceSourceType.Internal);
// if (dataset.getCreator() != null) data.setCreatedById(dataset.getCreator().getId());
// } else if (data.getLabel().equalsIgnoreCase("articles")){
// data.setReference(data.getId().toString().replace("-", "").toLowerCase(Locale.ROOT));
// data.setSourceType(ReferenceSourceType.Internal);
// if (dataset.getCreator() != null) data.setCreatedById(dataset.getCreator().getId());
// } else if (data.getLabel().equalsIgnoreCase("Freistilringen")){
// data.setReference(data.getId().toString().replace("-", "").toLowerCase(Locale.ROOT));
// data.setSourceType(ReferenceSourceType.Internal);
// if (dataset.getCreator() != null) data.setCreatedById(dataset.getCreator().getId());
// }
else if (data.getLabel().equalsIgnoreCase("Randomized Phase 3 Trial of ALIMTA (Pemetrexed) and Carboplatin versus Etoposide and Carboplatin in Extensive-Stage Small Cell Lung Cancer")){
data.setReference("50|datacite____::1df6f72ab95712d5f26ecb43b2d1d303");
}
} else if (data.getTypeId().equals(ReferenceTypeIds.DataRepositories) && data.getSource().equalsIgnoreCase("OpenAIRE")) {
if (data.getLabel().equalsIgnoreCase("INPTDAT")){
data.setReference("re3data_____::r3d100013120");
} if (data.getLabel().equalsIgnoreCase("OpenAPC Global Initiative")){
data.setReference("apc_________::openapc");
} else if (data.getLabel().equalsIgnoreCase("Human Gene and Protein Database")){
data.setReference("fairsharing_::1592");
} else if (data.getLabel().equalsIgnoreCase("Bacterial protein tYrosine Kinase database")){
data.setReference("fairsharing_::1557");
}
// else if (data.getLabel().equalsIgnoreCase("other")){
// data.setReference(data.getId().toString().replace("-", "").toLowerCase(Locale.ROOT));
// data.setSourceType(ReferenceSourceType.Internal);
// if (dataset.getCreator() != null) data.setCreatedById(dataset.getCreator().getId());
// } else if (data.getLabel().equalsIgnoreCase("Zenodo")){
// data.setReference(data.getId().toString().replace("-", "").toLowerCase(Locale.ROOT));
// data.setSourceType(ReferenceSourceType.Internal);
// if (dataset.getCreator() != null) data.setCreatedById(dataset.getCreator().getId());
// } else if (data.getLabel().equalsIgnoreCase("Zenado")){
// data.setReference(data.getId().toString().replace("-", "").toLowerCase(Locale.ROOT));
// data.setSourceType(ReferenceSourceType.Internal);
// if (dataset.getCreator() != null) data.setCreatedById(dataset.getCreator().getId());
// } else if (data.getLabel().equalsIgnoreCase("none")){
// data.setReference(data.getId().toString().replace("-", "").toLowerCase(Locale.ROOT));
// data.setSourceType(ReferenceSourceType.Internal);
// if (dataset.getCreator() != null) data.setCreatedById(dataset.getCreator().getId());
// } else if (data.getLabel().equalsIgnoreCase("articles")){
// data.setReference(data.getId().toString().replace("-", "").toLowerCase(Locale.ROOT));
// data.setSourceType(ReferenceSourceType.Internal);
// if (dataset.getCreator() != null) data.setCreatedById(dataset.getCreator().getId());
// } else if (data.getLabel().equalsIgnoreCase("https://github.com/sisyphe-re/riot_rpl_udp_scenarios")){
// data.setReference(data.getId().toString().replace("-", "").toLowerCase(Locale.ROOT));
// data.setSourceType(ReferenceSourceType.Internal);
// if (dataset.getCreator() != null) data.setCreatedById(dataset.getCreator().getId());
// } else else if (data.getLabel().equalsIgnoreCase("Cool data")){
// data.setReference(data.getId().toString().replace("-", "").toLowerCase(Locale.ROOT));
// data.setSourceType(ReferenceSourceType.Internal);
// if (dataset.getCreator() != null) data.setCreatedById(dataset.getCreator().getId());
// } else if (data.getLabel().equalsIgnoreCase("Raw data")){
// data.setReference(data.getId().toString().replace("-", "").toLowerCase(Locale.ROOT));
// data.setSourceType(ReferenceSourceType.Internal);
// if (dataset.getCreator() != null) data.setCreatedById(dataset.getCreator().getId());
// } else if (data.getLabel().equalsIgnoreCase("Repository hosted by Zenodo")){
// data.setReference(data.getId().toString().replace("-", "").toLowerCase(Locale.ROOT));
// data.setSourceType(ReferenceSourceType.Internal);
// if (dataset.getCreator() != null) data.setCreatedById(dataset.getCreator().getId());
// } else if (data.getLabel().equalsIgnoreCase("ICPSR - Interuniversity Consortium for Political and Social Research")){
// data.setReference(data.getId().toString().replace("-", "").toLowerCase(Locale.ROOT));
// data.setSourceType(ReferenceSourceType.Internal);
// if (dataset.getCreator() != null) data.setCreatedById(dataset.getCreator().getId());
// } else if (data.getLabel().equalsIgnoreCase("XC7 pharmaceutical development IPF")){
// data.setReference(data.getId().toString().replace("-", "").toLowerCase(Locale.ROOT));
// data.setSourceType(ReferenceSourceType.Internal);
// if (dataset.getCreator() != null) data.setCreatedById(dataset.getCreator().getId());
// } else if (data.getLabel().equalsIgnoreCase("nct")){
// data.setReference(data.getId().toString().replace("-", "").toLowerCase(Locale.ROOT));
// data.setSourceType(ReferenceSourceType.Internal);
// if (dataset.getCreator() != null) data.setCreatedById(dataset.getCreator().getId());
// } else if (data.getLabel().equalsIgnoreCase("UK Data Service")){
// data.setReference(data.getId().toString().replace("-", "").toLowerCase(Locale.ROOT));
// data.setSourceType(ReferenceSourceType.Internal);
// if (dataset.getCreator() != null) data.setCreatedById(dataset.getCreator().getId());
// } else if (data.getLabel().equalsIgnoreCase("figshare")){
// data.setReference(data.getId().toString().replace("-", "").toLowerCase(Locale.ROOT));
// data.setSourceType(ReferenceSourceType.Internal);
// if (dataset.getCreator() != null) data.setCreatedById(dataset.getCreator().getId());
// } else if (data.getLabel().equalsIgnoreCase("University of Strathclyde")){
// data.setReference(data.getId().toString().replace("-", "").toLowerCase(Locale.ROOT));
// data.setSourceType(ReferenceSourceType.Internal);
// if (dataset.getCreator() != null) data.setCreatedById(dataset.getCreator().getId());
// }
} else if (data.getTypeId().equals(ReferenceTypeIds.Services) && data.getSource().equalsIgnoreCase("eosc")) {
// if (data.getLabel().equalsIgnoreCase("website")){
// data.setReference(data.getId().toString().replace("-", "").toLowerCase(Locale.ROOT));
// data.setSourceType(ReferenceSourceType.Internal);
// if (dataset.getCreator() != null) data.setCreatedById(dataset.getCreator().getId());
// } else if (data.getLabel().equalsIgnoreCase("integration1")){
// data.setReference(data.getId().toString().replace("-", "").toLowerCase(Locale.ROOT));
// data.setSourceType(ReferenceSourceType.Internal);
// if (dataset.getCreator() != null) data.setCreatedById(dataset.getCreator().getId());
// } else if (data.getLabel().equalsIgnoreCase("SeaDataNet Common Data Index (CDI)")){
// data.setReference(data.getId().toString().replace("-", "").toLowerCase(Locale.ROOT));
// data.setSourceType(ReferenceSourceType.Internal);
// if (dataset.getCreator() != null) data.setCreatedById(dataset.getCreator().getId());
// } else if (data.getLabel().equalsIgnoreCase("Europeana APIs")){
// data.setReference(data.getId().toString().replace("-", "").toLowerCase(Locale.ROOT));
// data.setSourceType(ReferenceSourceType.Internal);
// if (dataset.getCreator() != null) data.setCreatedById(dataset.getCreator().getId());
// } else if (data.getLabel().equalsIgnoreCase("Imaging at Plentzia Marine Station-UPV/EHU")){
// data.setReference(data.getId().toString().replace("-", "").toLowerCase(Locale.ROOT));
// data.setSourceType(ReferenceSourceType.Internal);
// if (dataset.getCreator() != null) data.setCreatedById(dataset.getCreator().getId());
// } else if (data.getLabel().equalsIgnoreCase("Spectroscopy")){
// data.setReference(data.getId().toString().replace("-", "").toLowerCase(Locale.ROOT));
// data.setSourceType(ReferenceSourceType.Internal);
// if (dataset.getCreator() != null) data.setCreatedById(dataset.getCreator().getId());
// } else if (data.getLabel().equalsIgnoreCase("Library services at Stazione Zoologica Anton Dohrn")){
// data.setReference(data.getId().toString().replace("-", "").toLowerCase(Locale.ROOT));
// data.setSourceType(ReferenceSourceType.Internal);
// if (dataset.getCreator() != null) data.setCreatedById(dataset.getCreator().getId());
// } else if (data.getLabel().equalsIgnoreCase("PRACE Training Portal")){
// data.setReference(data.getId().toString().replace("-", "").toLowerCase(Locale.ROOT));
// data.setSourceType(ReferenceSourceType.Internal);
// if (dataset.getCreator() != null) data.setCreatedById(dataset.getCreator().getId());
// } else if (data.getLabel().equalsIgnoreCase("DARIAH Science Gateway")){
// data.setReference(data.getId().toString().replace("-", "").toLowerCase(Locale.ROOT));
// data.setSourceType(ReferenceSourceType.Internal);
// if (dataset.getCreator() != null) data.setCreatedById(dataset.getCreator().getId());
// } else if (data.getLabel().equalsIgnoreCase("Finding Anisotropy Tensor")){
// data.setReference(data.getId().toString().replace("-", "").toLowerCase(Locale.ROOT));
// data.setSourceType(ReferenceSourceType.Internal);
// if (dataset.getCreator() != null) data.setCreatedById(dataset.getCreator().getId());
// } else if (data.getLabel().equalsIgnoreCase("Imaging at University of Bergen-SLRC")){
// data.setReference(data.getId().toString().replace("-", "").toLowerCase(Locale.ROOT));
// data.setSourceType(ReferenceSourceType.Internal);
// if (dataset.getCreator() != null) data.setCreatedById(dataset.getCreator().getId());
// } else if (data.getLabel().equalsIgnoreCase("Training facilities at Toralla Marine Science Station - Vigo University Marine Research Centre")){
// data.setReference(data.getId().toString().replace("-", "").toLowerCase(Locale.ROOT));
// data.setSourceType(ReferenceSourceType.Internal);
// if (dataset.getCreator() != null) data.setCreatedById(dataset.getCreator().getId());
// } else if (data.getLabel().equalsIgnoreCase("Zenodo")){
// data.setReference(data.getId().toString().replace("-", "").toLowerCase(Locale.ROOT));
// data.setSourceType(ReferenceSourceType.Internal);
// if (dataset.getCreator() != null) data.setCreatedById(dataset.getCreator().getId());
// } else if (data.getLabel().equalsIgnoreCase("Digital Commons")){
// data.setReference(data.getId().toString().replace("-", "").toLowerCase(Locale.ROOT));
// data.setSourceType(ReferenceSourceType.Internal);
// if (dataset.getCreator() != null) data.setCreatedById(dataset.getCreator().getId());
// }
}else if (data.getTypeId().equals(ReferenceTypeIds.Registries) && data.getSource().equalsIgnoreCase("rda-metadata-schemes")) {
// if (data.getLabel().equalsIgnoreCase("DataCite Metadata Schema")){
// data.setReference(data.getId().toString().replace("-", "").toLowerCase(Locale.ROOT));
// data.setSourceType(ReferenceSourceType.Internal);
// if (dataset.getCreator() != null) data.setCreatedById(dataset.getCreator().getId());
// } else if (data.getLabel().equalsIgnoreCase("AgMES (Agricultural Metadata Element Set)")){
// data.setReference(data.getId().toString().replace("-", "").toLowerCase(Locale.ROOT));
// data.setSourceType(ReferenceSourceType.Internal);
// if (dataset.getCreator() != null) data.setCreatedById(dataset.getCreator().getId());
// }
} else if (data.getTypeId().equals(ReferenceTypeIds.Organizations) && data.getSource().equalsIgnoreCase("OpenAIRE")) {
if (data.getLabel().equalsIgnoreCase("Programa de Pós-Graduação em Ciência da Informação Ibict/UFRJ")){
data.setReference("pending_org_::f20d38c291e7d4a7a11d08481eebac44");
} else if (data.getLabel().equalsIgnoreCase("Applied Decision Science (United States)")){
data.setReference("openorgs____::0000093299");
} else if (data.getLabel().equalsIgnoreCase("BIODOL THERAPEUTICS")){
data.setReference("pending_org_::4c550b2917a6fc395bdb79eccdafe950");
} else if (data.getLabel().equalsIgnoreCase("OKKO")){
data.setReference("pending_org_::37ddf98c5fd2d6373fd315b0371fd4ac");
} else if (data.getLabel().equalsIgnoreCase("Health Research Board")){
data.setReference("openorgs____::0000006166");
} else if (data.getLabel().equalsIgnoreCase("Vidzeme University of Applied Sciences")){
data.setReference("openorgs____::0000029719");
}
// else if (data.getLabel().equalsIgnoreCase("Other Lab")){
// data.setReference(data.getId().toString().replace("-", "").toLowerCase(Locale.ROOT));
// data.setSourceType(ReferenceSourceType.Internal);
// if (dataset.getCreator() != null) data.setCreatedById(dataset.getCreator().getId());
// } else if (data.getLabel().equalsIgnoreCase("ATS APPLIED TECH SYSTEMS LTD")){
// data.setReference(data.getId().toString().replace("-", "").toLowerCase(Locale.ROOT));
// data.setSourceType(ReferenceSourceType.Internal);
// if (dataset.getCreator() != null) data.setCreatedById(dataset.getCreator().getId());
// } else if (data.getLabel().equalsIgnoreCase("Universidade Nova de Lisboa Centro de Linguística")){
// data.setReference(data.getId().toString().replace("-", "").toLowerCase(Locale.ROOT));
// data.setSourceType(ReferenceSourceType.Internal);
// if (dataset.getCreator() != null) data.setCreatedById(dataset.getCreator().getId());
// }
} else if (data.getTypeId().equals(ReferenceTypeIds.Researcher)){
if (data.getLabel().equalsIgnoreCase("Radosław Cichocki")){
data.setReference("0000-0002-4667-8445");
} else if (data.getLabel().equalsIgnoreCase("Kiranmai Uppuluri")){
data.setReference(data.getId().toString().replace("-", "").toLowerCase(Locale.ROOT));
data.setSourceType(ReferenceSourceType.Internal);
if (dataset.getCreator() != null) data.setCreatedById(dataset.getCreator().getId());
}
}
}
if (this.conventionService.isNullOrEmpty(data.getReference())) {
data.setReference(data.getId().toString().replace("-", "").toLowerCase(Locale.ROOT));
data.setSourceType(ReferenceSourceType.Internal);
data.setSource("Internal");
if (dataset.getCreator() != null) data.setCreatedById(dataset.getCreator().getId());
logger.warn("Migrate Dataset " + dataset.getId() + " " + dataset.getLabel() + " reference auto created as internal " + referenceTypeDataEntity.getReferenceTypeId() + " for value " + this.jsonHandlingService.toJsonSafe(item));
}
ReferenceEntity existingEntity = referenceMap.getOrDefault(new ReferenceKey(data), null);
if(existingEntity == null){
if (data.getCreatedById() != null) referenceMap.put(new ReferenceKey(data), data);
this.entityManager.persist(data);
return data;
} else {
return existingEntity;
}
}
public static class Currency{
private String name;
private String value;
public String getName() {
return name;
}
public void setName(String name) {
this.name = name;
}
public String getValue() {
return value;
}
public void setValue(String value) {
this.value = value;
}
}
public static class Tag{
private String id;
private String name;
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public String getName() {
return name;
}
public void setName(String name) {
this.name = name;
}
}
public static class MultipleFieldKey{
private final String fieldSetId;
private final String groupKey;
private final int hashCode;
public MultipleFieldKey(String fieldSetId, String groupKey) {
this.fieldSetId = fieldSetId;
this.groupKey = groupKey;
this.hashCode = Objects.hash(this.fieldSetId, this.groupKey);
}
public String getFieldSetId() {
return fieldSetId;
}
public String getGroupKey() {
return groupKey;
}
@Override
public boolean equals(Object o) {
if (this == o)
return true;
if (o == null || getClass() != o.getClass())
return false;
MultipleFieldKey that = (MultipleFieldKey) o;
return Objects.equals(fieldSetId, that.getFieldSetId()) && Objects.equals(groupKey, that.getGroupKey());
}
@Override
public int hashCode() {
return this.hashCode;
}
}
public static class ReferenceKey {
private final UUID type;
private final String source;
private final String reference;
private final int hashCode;
public ReferenceKey(ReferenceEntity reference) {
this.type = reference.getTypeId();
this.source = reference.getSource().trim();
this.reference = reference.getReference().trim();
hashCode = Objects.hash(this.type, this.source, this.reference);
}
public UUID getType() {
return type;
}
public String getSource() {
return source;
}
public String getReference() {
return reference;
}
@Override
public boolean equals(Object o) {
if (this == o)
return true;
if (o == null || getClass() != o.getClass())
return false;
ReferenceKey that = (ReferenceKey) o;
return Objects.equals(type, that.getType()) && Objects.equals(source, that.getSource()) && Objects.equals(reference, that.getReference());
}
@Override
public int hashCode() {
return this.hashCode;
}
}
}