Merge branch 'dmp-refactoring' of code-repo.d4science.org:MaDgiK-CITE/argos into dmp-refactoring

backend/core/src/main/java/org/opencdmp/service/description/DescriptionService.java

@@ -8,7 +8,6 @@ import gr.cite.tools.fieldset.FieldSet;
 import jakarta.xml.bind.JAXBException;
 import org.opencdmp.commonmodels.models.description.DescriptionModel;
 import org.opencdmp.commons.types.description.importexport.DescriptionImportExport;
-import org.opencdmp.data.DmpDescriptionTemplateEntity;
 import org.opencdmp.data.StorageFileEntity;
 import org.opencdmp.model.DescriptionValidationResult;
 import org.opencdmp.model.StorageFile;
@@ -55,6 +54,6 @@ public interface DescriptionService {
 
     Description importXml(DescriptionImportExport descriptionXml, UUID dmpId, FieldSet fields) throws MyForbiddenException, MyNotFoundException, JAXBException, ParserConfigurationException, TransformerException, InvalidApplicationException, IOException, InstantiationException, IllegalAccessException, SAXException;
 
-    Description importCommonModel(DescriptionModel model, UUID dmpId, List<DmpDescriptionTemplateEntity> dmpDescriptionTemplates, FieldSet fields) throws MyForbiddenException, MyNotFoundException, InvalidApplicationException, IOException, JAXBException, ParserConfigurationException, TransformerException, InstantiationException, IllegalAccessException, SAXException;
+    Description importCommonModel(DescriptionModel model, UUID dmpId, FieldSet fields) throws MyForbiddenException, MyNotFoundException, InvalidApplicationException, IOException, JAXBException, ParserConfigurationException, TransformerException, InstantiationException, IllegalAccessException, SAXException;
 
 }

backend/core/src/main/java/org/opencdmp/service/description/DescriptionServiceImpl.java

@@ -1500,13 +1500,11 @@ public class DescriptionServiceImpl implements DescriptionService {
     //region Import Common Model 
 
     @Override
-    public Description importCommonModel(DescriptionModel model, UUID dmpId, List<DmpDescriptionTemplateEntity> dmpDescriptionTemplates, FieldSet fields) throws MyForbiddenException, MyNotFoundException, InvalidApplicationException, IOException, JAXBException, ParserConfigurationException, TransformerException, InstantiationException, IllegalAccessException, SAXException {
+    public Description importCommonModel(DescriptionModel model, UUID dmpId, FieldSet fields) throws MyForbiddenException, MyNotFoundException, InvalidApplicationException, IOException, JAXBException, ParserConfigurationException, TransformerException, InstantiationException, IllegalAccessException, SAXException {
         logger.debug(new MapLogEntry("import description").And("dmpId", dmpId).And("fields", fields));
         if (model == null) throw new IllegalArgumentException ("model");
         if (dmpId == null) throw new IllegalArgumentException ("dmpId");
 
-        if (this.conventionService.isListNullOrEmpty(dmpDescriptionTemplates)) throw new MyValidationException(this.errors.getImportDescriptionWithoutDmpDescriptionTemplate().getCode(), this.errors.getImportDescriptionWithoutDmpDescriptionTemplate().getMessage());
-
         DescriptionPersist persist = new DescriptionPersist();
         persist.setLabel(model.getLabel());
         persist.setDescription(model.getDescription());

backend/core/src/main/java/org/opencdmp/service/dmp/DmpServiceImpl.java

@@ -27,6 +27,7 @@ import org.opencdmp.commonmodels.models.description.DescriptionModel;
 import org.opencdmp.commonmodels.models.dmp.DmpBlueprintValueModel;
 import org.opencdmp.commonmodels.models.dmp.DmpContactModel;
 import org.opencdmp.commonmodels.models.dmp.DmpModel;
+import org.opencdmp.commonmodels.models.dmp.DmpPropertiesModel;
 import org.opencdmp.commonmodels.models.dmpblueprint.ExtraFieldModel;
 import org.opencdmp.commonmodels.models.dmpblueprint.FieldModel;
 import org.opencdmp.commonmodels.models.dmpblueprint.ReferenceTypeFieldModel;
@@ -2070,50 +2071,46 @@ public class DmpServiceImpl implements DmpService {
         persist.setLanguage(model.getLanguage());
         persist.setUsers(this.commonModelToDmpUsersPersist(model));
         persist.setBlueprint(this.commonModelDmpBlueprintToPersist(model));
-
-        
-        persist.setProperties(this.commonDmpPropertiesToPersist(model));
-
-        if (!this.conventionService.isListNullOrEmpty(model.getDescriptionTemplates())) {
-            List<DmpDescriptionTemplatePersist> descriptionTemplates = new ArrayList<>();
-            for (DmpDescriptionTemplateModel descriptionTemplate : model.getDescriptionTemplates()) {
-                descriptionTemplates.add(this.commonDmpDescriptionTemplateToPersist(descriptionTemplate));
-            }
-            persist.setDescriptionTemplates(descriptionTemplates);
-        }
+        persist.setDescriptionTemplates(this.commonModelDmpDescriptionTemplatesToPersist(model)); //TODO maybe we should create templates if not exists
+        persist.setProperties(this.commonModelDmpPropertiesToPersist(model));
 
         this.validatorFactory.validator(DmpPersist.DmpPersistValidator.class).validateForce(persist);
         Dmp dmp = this.persist(persist, BaseFieldSet.build(fields, Dmp._id, Dmp._hash));
         if (dmp == null) throw new MyApplicationException("Error creating dmp");
 
-        if (!this.conventionService.isListNullOrEmpty(model.getDescriptions())) {
-            List<DmpDescriptionTemplateEntity> dmpDescriptionTemplates = this.queryFactory.query(DmpDescriptionTemplateQuery.class).disableTracking()
-                    .isActive(IsActive.Active)
-                    .dmpIds(dmp.getId())
-                    .collect();
-
+        if (!this.conventionService.isListNullOrEmpty(model.getDescriptions())){
             for (DescriptionModel description: model.getDescriptions()){
-                this.descriptionService.importCommonModel(description, dmp.getId(), dmpDescriptionTemplates, fields != null ? fields.extractPrefixed(this.conventionService.asPrefix(Dmp._description)) : null);
+                this.descriptionService.importCommonModel(description, dmp.getId(), fields != null ? fields.extractPrefixed(this.conventionService.asPrefix(Dmp._description)) : null);
             }
         }
 
+
         return dmp;
     }
 
-    private List<DmpUserPersist> commonModelToDmpUsersPersist(DmpModel model){
-        if (!this.conventionService.isListNullOrEmpty(model.getUsers())) {
-            List<UserEntity> users = this.queryFactory.query(UserQuery.class).disableTracking().ids(model.getUsers().stream().map(DmpUserModel::getUser).toList().stream().map(UserModel::getId).filter(Objects::nonNull).distinct().toList()).isActive(IsActive.Active).collect();
-            List<UUID> userIds = users == null ? new ArrayList<>() : users.stream().map(UserEntity::getId).collect(Collectors.toList());
-
-            List<DmpUserPersist> dmpUsers = new ArrayList<>();
-            for (DmpUserModel user : model.getUsers()) {
-                dmpUsers.add(this.commonDmpUserToPersist(user, userIds));
+    private  List<DmpDescriptionTemplatePersist> commonModelDmpDescriptionTemplatesToPersist(DmpModel commonModel){
+        if (!this.conventionService.isListNullOrEmpty(commonModel.getDescriptionTemplates())) {
+            List<DmpDescriptionTemplatePersist> descriptionTemplates = new ArrayList<>();
+            for (DmpDescriptionTemplateModel descriptionTemplate : commonModel.getDescriptionTemplates()) {
+                descriptionTemplates.add(this.commonModelDmpDescriptionTemplateToPersist(descriptionTemplate));
             }
-            return dmpUsers;
+            return descriptionTemplates.stream().filter(Objects::nonNull).toList();
         }
         return null;
     }
 
+    private DmpDescriptionTemplatePersist commonModelDmpDescriptionTemplateToPersist(DmpDescriptionTemplateModel commonModel) {
+        if (commonModel == null)
+            return null;
+
+        DmpDescriptionTemplatePersist persist = new DmpDescriptionTemplatePersist();
+
+        persist.setDescriptionTemplateGroupId(commonModel.getDescriptionTemplateGroupId());
+        persist.setSectionId(commonModel.getSectionId());
+
+        return persist;
+    }
+    
     private UUID commonModelDmpBlueprintToPersist(DmpModel dmpXml) throws JAXBException, InvalidApplicationException, ParserConfigurationException, IOException, TransformerException, InstantiationException, IllegalAccessException, SAXException {
         if (dmpXml.getDmpBlueprint() != null){
             DmpBlueprintEntity dmpBlueprintEntity = this.queryFactory.query(DmpBlueprintQuery.class).disableTracking().ids(dmpXml.getDmpBlueprint().getId()).first();
@@ -2128,158 +2125,175 @@ public class DmpServiceImpl implements DmpService {
         return null;
     }
 
-    private DmpPropertiesPersist commonDmpPropertiesToPersist(DmpModel model) {
-        if (model == null)
-            return null;
+    private DmpPropertiesPersist commonModelDmpPropertiesToPersist(DmpModel commonModel) {
+        if (commonModel == null || commonModel.getProperties() == null) return null;
 
         DmpPropertiesPersist persist = new DmpPropertiesPersist();
+        persist.setContacts(this.commonModelToDmpContactPersist(commonModel.getProperties()));
+        persist.setDmpBlueprintValues(this.commonModelToDmpBlueprintValuePersist(commonModel));
 
-        List<DmpContactPersist> contacts = new ArrayList<>();
-        if (model.getProperties() != null && !this.conventionService.isListNullOrEmpty(model.getProperties().getContacts())) {
-            for (DmpContactModel contact : model.getProperties().getContacts()) {
-                contacts.add(this.commonDmpContactToPersist(contact));
+        return persist;
+    }  
+    
+    private List<DmpContactPersist> commonModelToDmpContactPersist(DmpPropertiesModel commonModel){
+        if (!this.conventionService.isListNullOrEmpty(commonModel.getContacts())) {
+            List<DmpContactPersist> contacts = new ArrayList<>();
+            for (DmpContactModel contact : commonModel.getContacts()) {
+                contacts.add(this.commonModelDmpContactToPersist(contact));
             }
+            return contacts;
         }
+        return null;
+    }
 
-        Map<UUID, DmpBlueprintValuePersist> dmpBlueprintValues = new HashMap<>();
-
-        if (model.getDmpBlueprint() != null && model.getDmpBlueprint().getDefinition() != null && !this.conventionService.isListNullOrEmpty(model.getDmpBlueprint().getDefinition().getSections())) {
-            List<SectionModel> sections = model.getDmpBlueprint().getDefinition().getSections();
+    private Map<UUID, DmpBlueprintValuePersist> commonModelToDmpBlueprintValuePersist(DmpModel commonModel){
+        if (commonModel.getDmpBlueprint() != null && commonModel.getDmpBlueprint().getDefinition() != null && !this.conventionService.isListNullOrEmpty(commonModel.getDmpBlueprint().getDefinition().getSections())) {
+            Map<UUID, DmpBlueprintValuePersist> dmpBlueprintValues = new HashMap<>();
+            List<SectionModel> sections = commonModel.getDmpBlueprint().getDefinition().getSections();
             if (!this.conventionService.isListNullOrEmpty(sections)){
-                for (SectionModel section : model.getDmpBlueprint().getDefinition().getSections()) {
-                    if (!this.conventionService.isListNullOrEmpty(section.getFields()) && !this.conventionService.isListNullOrEmpty(model.getReferences())){
+                for (SectionModel section : sections) {
+                    if (!this.conventionService.isListNullOrEmpty(section.getFields())){
                         for (FieldModel field : section.getFields()) {
                             // reference
                             if (field.getCategory().equals(org.opencdmp.commonmodels.enums.DmpBlueprintFieldCategory.ReferenceType)){
                                 ReferenceTypeFieldModel referenceField = (ReferenceTypeFieldModel) field;
-                                List<DmpReferenceModel> dmpReferencesByField = model.getReferences().stream().filter(x -> x.getData() != null && x.getData().getBlueprintFieldId().equals(referenceField.getId())).collect(Collectors.toList());
+                                List<DmpReferenceModel> dmpReferencesByField = commonModel.getReferences().stream().filter(x -> x.getData() != null && x.getData().getBlueprintFieldId().equals(referenceField.getId())).collect(Collectors.toList());
                                 if (!this.conventionService.isListNullOrEmpty(dmpReferencesByField)){
-                                    dmpBlueprintValues.put(referenceField.getId(), this.commonDmpReferenceFieldToDmpBlueprintValuePersist(referenceField, dmpReferencesByField));
+                                    dmpBlueprintValues.put(referenceField.getId(), this.commonModelDmpReferenceFieldToDmpBlueprintValuePersist(referenceField, dmpReferencesByField));
                                 }
                             } else {
                                 // custom fields
-                                if (field.getCategory().equals(org.opencdmp.commonmodels.enums.DmpBlueprintFieldCategory.Extra) && model.getProperties() != null && this.conventionService.isListNullOrEmpty(model.getProperties().getDmpBlueprintValues())){
-                                    DmpBlueprintValueModel dmpBlueprintValueModel = model.getProperties().getDmpBlueprintValues().stream().filter(x -> x.getFieldId().equals(field.getId())).findFirst().orElse(null);
+                                if (field.getCategory().equals(org.opencdmp.commonmodels.enums.DmpBlueprintFieldCategory.Extra) && commonModel.getProperties() != null && this.conventionService.isListNullOrEmpty(commonModel.getProperties().getDmpBlueprintValues())){
+                                    DmpBlueprintValueModel dmpBlueprintValueModel = commonModel.getProperties().getDmpBlueprintValues().stream().filter(x -> x.getFieldId().equals(field.getId())).findFirst().orElse(null);
                                     ExtraFieldModel extraFieldModel = (ExtraFieldModel) field;
-                                    if (dmpBlueprintValueModel != null) dmpBlueprintValues.put(dmpBlueprintValueModel.getFieldId(), this.commonDmpBlueprintValueToPersist(dmpBlueprintValueModel, extraFieldModel));
+                                    if (dmpBlueprintValueModel != null) dmpBlueprintValues.put(dmpBlueprintValueModel.getFieldId(), this.commonModelDmpBlueprintValueToPersist(dmpBlueprintValueModel, extraFieldModel));
                                 }
                             }
                         }
                     }
                 }
             }
-
+            return dmpBlueprintValues;
         }
-
-        persist.setContacts(contacts);
-        persist.setDmpBlueprintValues(dmpBlueprintValues);
-
-        return persist;
+        return null;
     }
     
-    private DmpBlueprintValuePersist commonDmpReferenceFieldToDmpBlueprintValuePersist(ReferenceTypeFieldModel model, List<DmpReferenceModel> dmpReferences) {
-        if (model == null || this.conventionService.isListNullOrEmpty(dmpReferences))
+    private DmpBlueprintValuePersist commonModelDmpReferenceFieldToDmpBlueprintValuePersist(ReferenceTypeFieldModel model, List<DmpReferenceModel> dmpReferences) {
+        if (model == null || this.conventionService.isListNullOrEmpty(dmpReferences) || model.getReferenceType() == null)
             return null;
 
+        ReferenceTypeEntity referenceTypeEntity = this.queryFactory.query(ReferenceTypeQuery.class).ids(model.getReferenceType().getId()).first();//TODO: optimize
+        if (referenceTypeEntity == null) referenceTypeEntity = this.queryFactory.query(ReferenceTypeQuery.class).codes(model.getReferenceType().getCode()).first();
+        if (referenceTypeEntity == null) throw new MyNotFoundException(this.messageSource.getMessage("General_ItemNotFound", new Object[]{model.getReferenceType().getCode(), ReferenceType.class.getSimpleName()}, LocaleContextHolder.getLocale()));
+
         DmpBlueprintValuePersist persist = new DmpBlueprintValuePersist();
 
         persist.setFieldId(model.getId());
         if (model.getMultipleSelect()){
             List<ReferencePersist> references = new ArrayList<>();
             for (DmpReferenceModel dmpReference : dmpReferences) {
-                references.add(this.commonDmpReferenceToReferencePersist(dmpReference.getReference()));
+                references.add(this.commonDmpReferenceToReferencePersist(dmpReference.getReference(), referenceTypeEntity));
             }
             persist.setReferences(references);
         } else {
-            persist.setReference(this.commonDmpReferenceToReferencePersist(dmpReferences.getFirst().getReference()));
+            persist.setReference(this.commonDmpReferenceToReferencePersist(dmpReferences.getFirst().getReference(), referenceTypeEntity));
         }
 
         return persist;
     }
 
-    private ReferencePersist commonDmpReferenceToReferencePersist(ReferenceModel model) {
-        if (model == null)
-            return null;
+    private ReferencePersist commonDmpReferenceToReferencePersist(ReferenceModel model, ReferenceTypeEntity referenceTypeEntity) {
+        if (!referenceTypeEntity.getCode().equals(model.getType().getCode())) throw new MyApplicationException("Invalid reference for field " + model.getId());
+        
+        if (this.conventionService.isNullOrEmpty(model.getLabel()) && this.conventionService.isNullOrEmpty(model.getReference())) throw new MyApplicationException("Dmp Reference without label and reference id ");
+
+        ReferenceEntity referenceEntity = this.queryFactory.query(ReferenceQuery.class).ids(model.getId()).first(); //TODO: optimize
+        if (referenceEntity == null) referenceEntity = this.queryFactory.query(ReferenceQuery.class).references(model.getReference()).typeIds(referenceTypeEntity.getId()).sources(model.getSource()).first();
 
         ReferencePersist persist = new ReferencePersist();
 
-        persist.setId(model.getId());
-        persist.setLabel(model.getLabel());
-        persist.setDescription(model.getDescription());
-        persist.setReference(model.getReference());
-        persist.setAbbreviation(model.getAbbreviation());
-        persist.setSource(model.getSource());
-        switch (model.getSourceType()){
-            case Internal -> persist.setSourceType(ReferenceSourceType.Internal);
-            case External -> persist.setSourceType(ReferenceSourceType.External);
-            default -> throw new MyApplicationException("Unrecognized Type " + model.getSourceType().getValue());
+        persist.setTypeId(referenceTypeEntity.getId());
+        if (referenceEntity == null) {
+            persist.setLabel(model.getLabel());
+            persist.setReference(model.getReference());
+            persist.setSource("internal");
+            persist.setSourceType(ReferenceSourceType.Internal);
+        } else {
+            persist.setId(referenceEntity.getId());
+            persist.setLabel(referenceEntity.getLabel());
+            persist.setReference(referenceEntity.getReference());
+            persist.setSource(referenceEntity.getSource());
+            persist.setSourceType(referenceEntity.getSourceType());
+            persist.setAbbreviation(referenceEntity.getAbbreviation());
+            persist.setDescription(referenceEntity.getDescription());
+            persist.setHash(this.conventionService.hashValue(referenceEntity.getUpdatedAt()));
         }
-
         return persist;
     }
 
-    private DmpBlueprintValuePersist commonDmpBlueprintValueToPersist(DmpBlueprintValueModel model, ExtraFieldModel extraFieldModel) {
-        if (model == null || extraFieldModel == null)
+    private DmpBlueprintValuePersist commonModelDmpBlueprintValueToPersist(DmpBlueprintValueModel commonModel, ExtraFieldModel extraFieldModel) {
+        if (commonModel == null || extraFieldModel == null)
             return null;
-
         DmpBlueprintValuePersist persist = new DmpBlueprintValuePersist();
 
-        persist.setFieldId(model.getFieldId());
-        if (extraFieldModel.getDataType().equals(org.opencdmp.commonmodels.enums.DmpBlueprintExtraFieldDataType.Date)){
-            persist.setDateValue(model.getDateValue());
-        } else if (extraFieldModel.getDataType().equals(org.opencdmp.commonmodels.enums.DmpBlueprintExtraFieldDataType.Number)){
-            persist.setNumberValue(model.getNumberValue());
-        } else {
-            persist.setFieldValue(model.getValue());
+        persist.setFieldId(commonModel.getFieldId());
+        switch (extraFieldModel.getDataType()){
+            case Date ->  persist.setDateValue(commonModel.getDateValue());
+            case Number ->  persist.setNumberValue(commonModel.getNumberValue());
+            case Text, RichTex ->  persist.setFieldValue(commonModel.getValue());
+            default -> throw new MyApplicationException("unrecognized type " + extraFieldModel.getDataType());
         }
 
         return persist;
     }
 
-    private DmpDescriptionTemplatePersist commonDmpDescriptionTemplateToPersist(DmpDescriptionTemplateModel model) {
-        if (model == null)
-            return null;
+    private List<DmpUserPersist> commonModelToDmpUsersPersist(DmpModel commonModel){
+        if (!this.conventionService.isListNullOrEmpty(commonModel.getUsers())) {
+            List<UserEntity> users = this.queryFactory.query(UserQuery.class).disableTracking().ids(commonModel.getUsers().stream().map(DmpUserModel::getUser).filter(Objects::nonNull).map(UserModel::getId).filter(Objects::nonNull).distinct().toList()).isActive(IsActive.Active).collect();
+            List<UUID> userIds = users == null ? new ArrayList<>() : users.stream().map(UserEntity::getId).collect(Collectors.toList());
 
-        DmpDescriptionTemplatePersist persist = new DmpDescriptionTemplatePersist();
-
-        persist.setDescriptionTemplateGroupId(model.getDescriptionTemplateGroupId());
-        persist.setSectionId(model.getSectionId());
-
-        return persist;
+            List<DmpUserPersist> dmpUsers = new ArrayList<>();
+            for (DmpUserModel user : commonModel.getUsers()) {
+                dmpUsers.add(this.commonModelDmpUserToPersist(user, userIds));
+            }
+            return dmpUsers;
+        }
+        return null;
     }
 
-    private DmpUserPersist commonDmpUserToPersist(DmpUserModel model, List<UUID> userIds) {
-        if (model == null)
+
+    private DmpUserPersist commonModelDmpUserToPersist(DmpUserModel commonModel, List<UUID> userIds) {
+        if (commonModel == null)
             return null;
 
-        if (model.getUser() != null && model.getUser().getId() != null && !userIds.isEmpty() && userIds.contains(model.getUser().getId())) {
+        if (commonModel.getUser() != null && commonModel.getUser().getId() != null && !userIds.isEmpty() && userIds.contains(commonModel.getUser().getId())) {
             DmpUserPersist persist = new DmpUserPersist();
 
-            persist.setUser(model.getUser().getId());
+            persist.setUser(commonModel.getUser().getId());
 
-            switch (model.getRole()){
+            switch (commonModel.getRole()){
                 case Owner -> persist.setRole(DmpUserRole.Owner);
                 case Viewer -> persist.setRole(DmpUserRole.Viewer);
                 case DescriptionContributor -> persist.setRole(DmpUserRole.DescriptionContributor);
                 case Reviewer -> persist.setRole(DmpUserRole.Reviewer);
-                default -> throw new MyApplicationException("Unrecognized Type " + model.getRole().getValue());
+                default -> throw new MyApplicationException("Unrecognized Type " + commonModel.getRole().getValue());
             }
-            persist.setSectionId(model.getSectionId());
+            persist.setSectionId(commonModel.getSectionId());
             return persist;
         }
 
         return null;
     }
 
-    private DmpContactPersist commonDmpContactToPersist(DmpContactModel model) {
-        if (model == null)
+    private DmpContactPersist commonModelDmpContactToPersist(DmpContactModel commonModel) {
+        if (commonModel == null)
             return null;
 
         DmpContactPersist persist = new DmpContactPersist();
 
-        persist.setEmail(model.getEmail());
-        persist.setFirstName(model.getEmail());
-        persist.setLastName(model.getLastName());
+        persist.setEmail(commonModel.getEmail());
+        persist.setFirstName(commonModel.getEmail());
+        persist.setLastName(commonModel.getLastName());
 
         return persist;
     }