Dmp/Description changes

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

@@ -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;
+    }
 }

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

@@ -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;
+    }
 }

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

@@ -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()));
@@ -118,6 +123,24 @@ 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;

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

@@ -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);
     }
-
 }

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

@@ -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.*;
-import eu.eudat.model.DescriptionReference;
 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.*;
-import java.util.List;
-import java.util.UUID;
 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));
@@ -247,29 +316,34 @@ public class DescriptionServiceImpl implements DescriptionService {
         this.deleterFactory.deleter(DescriptionTagDeleter.class).delete(toDelete);
     }
     
-    private void persistDescriptionReferences(UUID id, List<DescriptionReferencePersist> models) throws InvalidApplicationException {
+    private void persistDescriptionReferences(UUID id, List<DescriptionReferencePersist> persists) throws InvalidApplicationException {
-        if (models == null) models = new ArrayList<>();
+        if (persists == null) persists = new ArrayList<>();
 
-        List<DescriptionReferenceEntity> items = this.queryFactory.query(DescriptionReferenceQuery.class).isActive(IsActive.Active).descriptionIds(id).collect();
+        List<DescriptionReferenceEntity> existingItems = 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();
+        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) {
+        for (DescriptionReferencePersist persist : persists) {
-            Boolean isUpdate = this.conventionService.isValidGuid(model.getId());
+            Boolean isUpdate = this.conventionService.isValidGuid(persist.getId());
+
             DescriptionReferenceEntity data;
             if (isUpdate) {
-                data = items.stream().filter(x -> x.getId().equals(model.getId())).findFirst().orElse(null);
+                data = this.entityManager.find(DescriptionReferenceEntity.class, persist.getId());
-                if (data == null) throw new MyNotFoundException(messageSource.getMessage("General_ItemNotFound", new Object[]{model.getId(), DescriptionReference.class.getSimpleName()}, LocaleContextHolder.getLocale()));
+                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(model.getHash())) throw new MyValidationException(this.errors.getHashConflict().getCode(), this.errors.getHashConflict().getMessage());
+                if (!this.conventionService.hashValue(data.getUpdatedAt()).equals(persist.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");
+                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());
+            ReferenceEntity reference = this.persistReference(existingReferencesMap, persist.getReference());
+            data.setReferenceId(reference.getId());
             data.setUpdatedAt(Instant.now());
             
             if (isUpdate) this.entityManager.merge(data);
@@ -277,32 +351,33 @@ public class DescriptionServiceImpl implements DescriptionService {
 
             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 persisReference(List<ReferenceEntity> existingReferences, ReferencePersist model) throws InvalidApplicationException {
+    private ReferenceEntity persistReference(Map<UUID, ReferenceEntity> existingReferencesMap , ReferencePersist persist){
-        Boolean isUpdate = this.conventionService.isValidGuid(model.getId());
+        Boolean isUpdate = this.conventionService.isValidGuid(persist.getId());
+
         ReferenceEntity data;
         if (isUpdate) {
-            data = existingReferences.stream().filter(x -> x.getId().equals(model.getId())).findFirst().orElse(null);
+            data = this.entityManager.find(ReferenceEntity.class, persist.getId());
-            if (data == null) throw new MyNotFoundException(messageSource.getMessage("General_ItemNotFound", new Object[]{model.getId(), DescriptionReference.class.getSimpleName()}, LocaleContextHolder.getLocale()));
+            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(model.getHash())) throw new MyValidationException(this.errors.getHashConflict().getCode(), this.errors.getHashConflict().getMessage());
+            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);

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

@@ -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