MaDgiK-CITE
/
argos
13
0
Fork 0
Code Issues Pull Requests Projects Releases 3 Wiki Activity

Dmp/Description changes

This commit is contained in:
Efstratios Giannopoulos 2023-12-06 18:33:01 +02:00
parent b9eba9edcb
commit c1b197ea30
6 changed files with 201 additions and 38 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

40
dmp-backend/core/src/main/java/eu/eudat/errorcode/ErrorThesaurusProperties.java
View File

@ -74,4 +74,44 @@ public class ErrorThesaurusProperties {
public void setDmpIsFinalized(ErrorDescription dmpIsFinalized) {
this.dmpIsFinalized = dmpIsFinalized;
}
private ErrorDescription dmpCanNotChange;
public ErrorDescription getDmpCanNotChange() {
return dmpCanNotChange;
}
public void setDmpCanNotChange(ErrorDescription dmpCanNotChange) {
this.dmpCanNotChange = dmpCanNotChange;
}
private ErrorDescription dmpDescriptionTemplateCanNotChange;
public ErrorDescription getDmpDescriptionTemplateCanNotChange() {
return dmpDescriptionTemplateCanNotChange;
}
public void setDmpDescriptionTemplateCanNotChange(ErrorDescription dmpDescriptionTemplateCanNotChange) {
this.dmpDescriptionTemplateCanNotChange = dmpDescriptionTemplateCanNotChange;
}
private ErrorDescription invalidDescriptionTemplate;
public ErrorDescription getInvalidDescriptionTemplate() {
return invalidDescriptionTemplate;
}
public void setInvalidDescriptionTemplate(ErrorDescription invalidDescriptionTemplate) {
this.invalidDescriptionTemplate = invalidDescriptionTemplate;
}
private ErrorDescription descriptionIsFinalized;
public ErrorDescription getDescriptionIsFinalized() {
return descriptionIsFinalized;
}
public void setDescriptionIsFinalized(ErrorDescription descriptionIsFinalized) {
this.descriptionIsFinalized = descriptionIsFinalized;
}
}

12
dmp-backend/core/src/main/java/eu/eudat/model/Dmp.java
View File

@ -99,6 +99,10 @@ public class Dmp {
public static final String _descriptions = "descriptions";
private List<EntityDoi> entityDois;
public static final String _entityDois = "entityDois";
public UUID getId() {
return id;
}
@ -274,4 +278,12 @@ public class Dmp {
public void setDescriptions(List<Description> descriptions) {
this.descriptions = descriptions;
}
public List<EntityDoi> getEntityDois() {
return entityDois;
}
public void setEntityDois(List<EntityDoi> entityDois) {
this.entityDois = entityDois;
}
}

25
dmp-backend/core/src/main/java/eu/eudat/model/builder/DmpBuilder.java
View File

@ -1,6 +1,7 @@
package eu.eudat.model.builder;
import eu.eudat.authorization.AuthorizationFlags;
import eu.eudat.commons.enums.EntityType;
import eu.eudat.convention.ConventionService;
import eu.eudat.data.DmpEntity;
import eu.eudat.model.*;
@ -54,6 +55,9 @@ public class DmpBuilder extends BaseBuilder<Dmp, DmpEntity> {
List<Dmp> models = new ArrayList<>();
FieldSet entityDoisFields = fields.extractPrefixed(this.asPrefix(Dmp._entityDois));
Map<UUID, List<EntityDoi>> entityDoisMap = this.collectEntityDois(entityDoisFields, data);
FieldSet dmpReferencesFields = fields.extractPrefixed(this.asPrefix(Dmp._dmpReferences));
Map<UUID, List<DmpReference>> dmpReferencesMap = this.collectDmpReferences(dmpReferencesFields, data);
@ -89,6 +93,7 @@ public class DmpBuilder extends BaseBuilder<Dmp, DmpEntity> {
if (fields.hasField(this.asIndexer(Dmp._hash))) m.setHash(this.hashValue(d.getUpdatedAt()));
if (!userFields.isEmpty() && userItemsMap != null && userItemsMap.containsKey(d.getCreatorId())) m.setCreator(userItemsMap.get(d.getCreatorId()));
if (!blueprintFields.isEmpty() && blueprintItemsMap != null && blueprintItemsMap.containsKey(d.getBlueprintId())) m.setBlueprint(blueprintItemsMap.get(d.getBlueprintId()));
if (entityDoisMap != null && !entityDoisMap.isEmpty() && entityDoisMap.containsKey(d.getId())) m.setEntityDois(entityDoisMap.get(d.getId()));
if (dmpReferencesMap != null && !dmpReferencesMap.isEmpty() && dmpReferencesMap.containsKey(d.getId())) m.setDmpReferences(dmpReferencesMap.get(d.getId()));
if (dmpUsersMap != null && !dmpUsersMap.isEmpty() && dmpUsersMap.containsKey(d.getId())) m.setDmpUsers(dmpUsersMap.get(d.getId()));
if (descriptionsMap != null && !descriptionsMap.isEmpty() && descriptionsMap.containsKey(d.getId())) m.setDescriptions(descriptionsMap.get(d.getId()));
@ -117,7 +122,25 @@ public class DmpBuilder extends BaseBuilder<Dmp, DmpEntity> {
return itemMap;
}
private Map<UUID, List<EntityDoi>> collectEntityDois(FieldSet fields, List<DmpEntity> data) throws MyApplicationException {
if (fields.isEmpty() || data.isEmpty()) return null;
this.logger.debug("checking related - {}", EntityDoi.class.getSimpleName());
Map<UUID, List<EntityDoi>> itemMap;
FieldSet clone = new BaseFieldSet(fields.getFields()).ensure(this.asIndexer(EntityDoi._entityId));
EntityDoiQuery query = this.queryFactory.query(EntityDoiQuery.class).authorize(this.authorize).types(EntityType.DMP).entityIds(data.stream().map(DmpEntity::getId).distinct().collect(Collectors.toList()));
itemMap = this.builderFactory.builder(EntityDoiBuilder.class).authorize(this.authorize).asMasterKey(query, clone, EntityDoi::getEntityId);
if (!fields.hasField(this.asIndexer(EntityDoi._entityId))) {
itemMap.values().stream().flatMap(List::stream).filter(x -> x != null && x.getEntityId() != null).peek(x -> {
x.setEntityId(null);
});
}
return itemMap;
}
private Map<UUID, DmpBlueprint> collectDmpBlueprints(FieldSet fields, List<DmpEntity> data) throws MyApplicationException {
if (fields.isEmpty() || data.isEmpty())
return null;

3
dmp-backend/core/src/main/java/eu/eudat/model/censorship/DmpCensor.java
View File

@ -46,6 +46,7 @@ public class DmpCensor extends BaseCensor {
this.censorFactory.censor(DmpReferenceCensor.class).censor(dmpReferencesFields, userId);
FieldSet creatorFields = fields.extractPrefixed(this.asIndexerPrefix(Dmp._creator));
this.censorFactory.censor(UserCensor.class).censor(creatorFields, userId);
FieldSet doisFields = fields.extractPrefixed(this.asIndexerPrefix(Dmp._entityDois));
this.censorFactory.censor(EntityDoiCensor.class).censor(doisFields, userId);
}
}

147
dmp-backend/core/src/main/java/eu/eudat/service/description/DescriptionServiceImpl.java
View File

@ -17,8 +17,7 @@ import eu.eudat.data.*;
import eu.eudat.errorcode.ErrorThesaurusProperties;
import eu.eudat.event.DescriptionTouchedEvent;
import eu.eudat.event.EventBroker;
import eu.eudat.model.Description;
import eu.eudat.model.DescriptionReference;
import eu.eudat.model.*;
import eu.eudat.model.builder.DescriptionBuilder;
import eu.eudat.model.deleter.DescriptionDeleter;
import eu.eudat.model.deleter.DescriptionReferenceDeleter;
@ -54,9 +53,7 @@ import org.springframework.stereotype.Service;
import javax.management.InvalidApplicationException;
import java.io.IOException;
import java.time.Instant;
import java.util.ArrayList;
import java.util.List;
import java.util.UUID;
import java.util.*;
import java.util.stream.Collectors;
@Service
@ -130,32 +127,104 @@ public class DescriptionServiceImpl implements DescriptionService {
data = this.entityManager.find(DescriptionEntity.class, model.getId());
if (data == null) throw new MyNotFoundException(messageSource.getMessage("General_ItemNotFound", new Object[]{model.getId(), Description.class.getSimpleName()}, LocaleContextHolder.getLocale()));
if (!this.conventionService.hashValue(data.getUpdatedAt()).equals(model.getHash())) throw new MyValidationException(this.errors.getHashConflict().getCode(), this.errors.getHashConflict().getMessage());
if (data.getStatus() == DescriptionStatus.Finalized) throw new MyForbiddenException("Can not update finalized template");
if (data.getStatus().equals(DescriptionStatus.Finalized)) throw new MyValidationException(this.errors.getDescriptionIsFinalized().getCode(), this.errors.getDescriptionIsFinalized().getMessage());
if (!data.getDmpId().equals(model.getDmpId())) throw new MyValidationException(this.errors.getDmpCanNotChange().getCode(), this.errors.getDmpCanNotChange().getMessage());
if (!data.getDmpDescriptionTemplateId().equals(model.getDmpDescriptionTemplateId())) throw new MyValidationException(this.errors.getDmpDescriptionTemplateCanNotChange().getCode(), this.errors.getDmpDescriptionTemplateCanNotChange().getMessage());
} else {
data = new DescriptionEntity();
data.setId(UUID.randomUUID());
data.setIsActive(IsActive.Active);
data.setCreatedAt(Instant.now());
data.setDmpId(model.getDmpId());
data.setDmpDescriptionTemplateId(model.getDmpDescriptionTemplateId());
}
DmpDescriptionTemplateEntity dmpDescriptionTemplate = this.entityManager.find(DmpDescriptionTemplateEntity.class, data.getDescriptionTemplateId());
if (dmpDescriptionTemplate == null) throw new MyNotFoundException(messageSource.getMessage("General_ItemNotFound", new Object[]{data.getDescriptionTemplateId(), DmpDescriptionTemplate.class.getSimpleName()}, LocaleContextHolder.getLocale()));
DescriptionTemplateEntity descriptionTemplateEntity = this.entityManager.find(DescriptionTemplateEntity.class, model.getDescriptionTemplateId());
if (descriptionTemplateEntity == null) throw new MyNotFoundException(messageSource.getMessage("General_ItemNotFound", new Object[]{model.getDescriptionTemplateId(), DescriptionTemplate.class.getSimpleName()}, LocaleContextHolder.getLocale()));
if (!dmpDescriptionTemplate.getDescriptionTemplateGroupId().equals(descriptionTemplateEntity.getGroupId())) throw new MyValidationException(this.errors.getInvalidDescriptionTemplate().getCode(), this.errors.getInvalidDescriptionTemplate().getMessage());
DmpEntity dmp = this.entityManager.find(DmpEntity.class, data.getDmpId());
if (dmp == null) throw new MyNotFoundException(messageSource.getMessage("General_ItemNotFound", new Object[]{data.getDmpId(), Dmp.class.getSimpleName()}, LocaleContextHolder.getLocale()));
if (dmp.getStatus().equals(DmpStatus.Finalized) && isUpdate) throw new MyValidationException(this.errors.getDmpIsFinalized().getCode(), this.errors.getDmpIsFinalized().getMessage());
data.setLabel(model.getLabel());
data.setProperties(this.jsonHandlingService.toJson(this.buildPropertyDefinitionEntity(model.getProperties())));
data.setStatus(model.getStatus());
data.setDescription(model.getDescription());
data.setDescriptionTemplateId(model.getDescriptionTemplateId());
data.setDmpDescriptionTemplateId(model.getDmpDescriptionTemplateId());
data.setUpdatedAt(Instant.now());
if (isUpdate) this.entityManager.merge(data);
else this.entityManager.persist(data);
this.persistTags(data.getId(), model.getTags());
this.persistDescriptionReferences(data.getId(), model.getReferences());
this.entityManager.flush();
if (isUpdate){
if (!data.getStatus() .equals(DescriptionStatus.Finalized)) {
//TODO
//this.sendNotification(dataset1, dataset1.getDmp(), userInfo, NotificationType.DATASET_MODIFIED);
} else {
//TODO
//this.sendNotification(dataset1, dataset1.getDmp(), userInfo, NotificationType.DATASET_MODIFIED_FINALISED);
}
}
//this.deleteOldFilesAndAddNew(datasetWizardModel, userInfo); //TODO
this.eventBroker.emit(new DescriptionTouchedEvent(data.getId()));
return this.builderFactory.builder(DescriptionBuilder.class).authorize(AuthorizationFlags.OwnerOrDmpAssociatedOrPermissionOrPublic).build(BaseFieldSet.build(fields, Description._id), data);
}
public void descriptionForce(DescriptionEntity description) throws Exception {
List<String> datasetProfileValidators = new LinkedList<>();
DescriptionTemplateEntity descriptionTemplateEntity = this.entityManager.find(DescriptionTemplateEntity.class, description.getDescriptionTemplateId());
if (descriptionTemplateEntity == null) throw new MyNotFoundException(messageSource.getMessage("General_ItemNotFound", new Object[]{description.getDescriptionTemplateId(), DescriptionTemplate.class.getSimpleName()}, LocaleContextHolder.getLocale()));
eu.eudat.commons.types.descriptiontemplate.DefinitionEntity definition = this.xmlHandlingService.fromXml(eu.eudat.commons.types.descriptiontemplate.DefinitionEntity.class, descriptionTemplateEntity.getDefinition());
// DocumentBuilderFactory builderFactory = DocumentBuilderFactory.newInstance();
// DocumentBuilder builder = builderFactory.newDocumentBuilder();
// Document xmlDocument = builder.parse(new ByteArrayInputStream(profile.getDefinition().getBytes()));
//
// XPath xPath = XPathFactory.newInstance().newXPath();
// String expression = "//validation/@type[.=1]/ancestor::field/@id";
// NodeList nodeList = (NodeList) xPath.compile(expression).evaluate(xmlDocument, XPathConstants.NODESET);
//
// for (int i = 0; i < nodeList.getLength(); i++) {
// Node node = nodeList.item(i);
// datasetProfileValidators.add(node.getNodeValue());
// }
//
// expression = "//validation/@type[.=1]/ancestor::fieldSet";
// nodeList = (NodeList) xPath.compile(expression).evaluate(xmlDocument, XPathConstants.NODESET);
//
//
// JSONObject obj = new JSONObject(description.getProperties());
// VisibilityRuleService visibilityRuleService = new VisibilityRuleServiceImpl();
// visibilityRuleService.setProperties(obj.toMap());
//
// description.setProfile(profile);
// PagedDatasetProfile pagedDatasetProfile = this.getPagedProfile(new DatasetWizardModel(), description);
// visibilityRuleService.buildVisibilityContext(pagedDatasetProfile.getRules());
//
//
// String failedField = null;
//
// for (String validator : datasetProfileValidators) {
// if (obj.has(validator) && isNullOrEmpty(obj.getString(validator)) && isElementVisible(nodeList, validator, visibilityRuleService)) {
// //throw new Exception("Field value of " + validator + " must be filled.");
// failedField = validator;
// break;
// }
// }
// return failedField;
}
@Override
public Description persistStatus(DescriptionStatusPersist model, FieldSet fields) {
logger.debug(new MapLogEntry("persisting data dmp").And("model", model).And("fields", fields));
@ -246,63 +315,69 @@ public class DescriptionServiceImpl implements DescriptionService {
this.deleterFactory.deleter(DescriptionTagDeleter.class).delete(toDelete);
}
private void persistDescriptionReferences(UUID id, List<DescriptionReferencePersist> persists) throws InvalidApplicationException {
if (persists == null) persists = new ArrayList<>();
private void persistDescriptionReferences(UUID id, List<DescriptionReferencePersist> models) throws InvalidApplicationException {
if (models == null) models = new ArrayList<>();
List<DescriptionReferenceEntity> items = this.queryFactory.query(DescriptionReferenceQuery.class).isActive(IsActive.Active).descriptionIds(id).collect();
List<ReferenceEntity> existingReferences = this.queryFactory.query(ReferenceQuery.class).isActive(IsActive.Active).ids(models.stream().filter(x-> this.conventionService.isValidGuid(x.getReference().getId())).map(x-> x.getReference().getId()).distinct().toList()).collect();
List<DescriptionReferenceEntity> existingItems = this.queryFactory.query(DescriptionReferenceQuery.class).isActive(IsActive.Active).descriptionIds(id).collect();
Map<UUID, ReferenceEntity> existingReferencesMap = this.queryFactory.query(ReferenceQuery.class).isActive(IsActive.Active).ids(persists.stream().filter(x-> x.getReference().getId() != null).map(x-> x.getReference().getId()).toList()).collect()
.stream()
.collect(Collectors.toMap(ReferenceEntity::getId, x-> x));;
List<UUID> updatedCreatedIds = new ArrayList<>();
for (DescriptionReferencePersist model : models) {
Boolean isUpdate = this.conventionService.isValidGuid(model.getId());
for (DescriptionReferencePersist persist : persists) {
Boolean isUpdate = this.conventionService.isValidGuid(persist.getId());
DescriptionReferenceEntity data;
if (isUpdate) {
data = items.stream().filter(x -> x.getId().equals(model.getId())).findFirst().orElse(null);
if (data == null) throw new MyNotFoundException(messageSource.getMessage("General_ItemNotFound", new Object[]{model.getId(), DescriptionReference.class.getSimpleName()}, LocaleContextHolder.getLocale()));
if (!this.conventionService.hashValue(data.getUpdatedAt()).equals(model.getHash())) throw new MyValidationException(this.errors.getHashConflict().getCode(), this.errors.getHashConflict().getMessage());
if (!data.getReferenceId().equals(model.getReference().getId())) throw new MyForbiddenException("Can not change reference of DescriptionReferenceEntity");
data = this.entityManager.find(DescriptionReferenceEntity.class, persist.getId());
if (data == null) throw new MyNotFoundException(messageSource.getMessage("General_ItemNotFound", new Object[]{persist.getId(), DescriptionReference.class.getSimpleName()}, LocaleContextHolder.getLocale()));
if (!this.conventionService.hashValue(data.getUpdatedAt()).equals(persist.getHash())) throw new MyValidationException(this.errors.getHashConflict().getCode(), this.errors.getHashConflict().getMessage());
if (!data.getReferenceId().equals(persist.getReference().getId())) throw new MyValidationException("reference can not changed");
} else {
data = new DescriptionReferenceEntity();
data.setId(UUID.randomUUID());
data.setIsActive(IsActive.Active);
data.setDescriptionId(id);
data.setCreatedAt(Instant.now());
data.setIsActive(IsActive.Active);
}
ReferenceEntity referenceEntity = this.persisReference(existingReferences, model.getReference());
data.setReferenceId(referenceEntity.getId());
data.setUpdatedAt(Instant.now());
ReferenceEntity reference = this.persistReference(existingReferencesMap, persist.getReference());
data.setReferenceId(reference.getId());
data.setUpdatedAt(Instant.now());
if (isUpdate) this.entityManager.merge(data);
else this.entityManager.persist(data);
updatedCreatedIds.add(data.getId());
}
List<DescriptionReferenceEntity> toDelete = items.stream().filter(x-> updatedCreatedIds.stream().noneMatch(y-> y.equals(x.getId()))).collect(Collectors.toList());
List<DescriptionReferenceEntity> toDelete = existingItems.stream().filter(x-> updatedCreatedIds.stream().noneMatch(y-> y.equals(x.getId()))).collect(Collectors.toList());
this.deleterFactory.deleter(DescriptionReferenceDeleter.class).delete(toDelete);
}
private ReferenceEntity persistReference(Map<UUID, ReferenceEntity> existingReferencesMap , ReferencePersist persist){
Boolean isUpdate = this.conventionService.isValidGuid(persist.getId());
private ReferenceEntity persisReference(List<ReferenceEntity> existingReferences, ReferencePersist model) throws InvalidApplicationException {
Boolean isUpdate = this.conventionService.isValidGuid(model.getId());
ReferenceEntity data;
if (isUpdate) {
data = existingReferences.stream().filter(x -> x.getId().equals(model.getId())).findFirst().orElse(null);
if (data == null) throw new MyNotFoundException(messageSource.getMessage("General_ItemNotFound", new Object[]{model.getId(), DescriptionReference.class.getSimpleName()}, LocaleContextHolder.getLocale()));
if (!this.conventionService.hashValue(data.getUpdatedAt()).equals(model.getHash())) throw new MyValidationException(this.errors.getHashConflict().getCode(), this.errors.getHashConflict().getMessage());
data = this.entityManager.find(ReferenceEntity.class, persist.getId());
if (data == null) throw new MyNotFoundException(messageSource.getMessage("General_ItemNotFound", new Object[]{persist.getId(), Reference.class.getSimpleName()}, LocaleContextHolder.getLocale()));
if (!this.conventionService.hashValue(data.getUpdatedAt()).equals(persist.getHash())) throw new MyValidationException(this.errors.getHashConflict().getCode(), this.errors.getHashConflict().getMessage());
} else {
data = new ReferenceEntity();
data.setId(UUID.randomUUID());
data.setIsActive(IsActive.Active);
data.setCreatedAt(Instant.now());
data.setIsActive(IsActive.Active);
}
data.setDefinition(this.xmlHandlingService.toXmlSafe(this.buildDefinitionEntity(persist.getDefinition())));
data.setUpdatedAt(Instant.now());
data.setReference(persist.getReference());
data.setAbbreviation(persist.getAbbreviation());
data.setSource(persist.getSource());
data.setSourceType(persist.getSourceType());
data.setUpdatedAt(Instant.now());
data.setDefinition(this.xmlHandlingService.toXmlSafe(this.buildDefinitionEntity(model.getDefinition())));
data.setUpdatedAt(Instant.now());
data.setReference(model.getReference());
data.setAbbreviation(model.getAbbreviation());
data.setSource(model.getSource());
data.setSourceType(model.getSourceType());
data.setUpdatedAt(Instant.now());
if (isUpdate) this.entityManager.merge(data);
else this.entityManager.persist(data);

12
dmp-backend/web/src/main/resources/config/errors.yml
View File

@ -35,3 +35,15 @@ error-thesaurus:
dmp-is-finalized:
code: 116
message: To perform this action you will need to revert DMP's finalisation
dmp-can-not-change:
code: 117
message: dmp can not change
dmp-description-template-can-not-change:
code: 118
message: dmp description template can not change
invalid-description-template:
code: 118
message: invalid description template id
description-is-finalized:
code: 119
message: To perform this action you will need to revert description finalisation