add references definition xml,builder, persist

dmp-backend/core/src/main/java/eu/eudat/audit/AuditableAction.java

@@ -36,9 +36,9 @@ public class AuditableAction {
     public static final EventId Description_Persist = new EventId(6002, "Description_Persist");
     public static final EventId Description_Delete = new EventId(6003, "Description_Delete");
 
-    public static final EventId External_Reference_Query = new EventId(7000, "External_Reference_Query");
-    public static final EventId External_Reference_Lookup = new EventId(7001, "External_Reference_Lookup");
-    public static final EventId External_Reference_Persist = new EventId(7002, "External_Reference_Persist");
-    public static final EventId External_Reference_Delete = new EventId(7003, "External_Reference_Delete");
+    public static final EventId Reference_Query = new EventId(7000, "Reference_Query");
+    public static final EventId Reference_Lookup = new EventId(7001, "Reference_Lookup");
+    public static final EventId Reference_Persist = new EventId(7002, "Reference_Persist");
+    public static final EventId Reference_Delete = new EventId(7003, "Reference_Delete");
 
 }

dmp-backend/core/src/main/java/eu/eudat/commons/enums/ReferenceFieldDataType.java

@@ -0,0 +1,27 @@
+package eu.eudat.commons.enums;
+
+import com.fasterxml.jackson.annotation.JsonValue;
+import eu.eudat.data.converters.enums.DatabaseEnum;
+
+import java.util.Map;
+
+public enum ReferenceFieldDataType implements DatabaseEnum<Short> {
+	Text((short) 0),
+	Date((short) 1);
+	private final Short value;
+
+	ReferenceFieldDataType(Short value) {
+		this.value = value;
+	}
+
+	@JsonValue
+	public Short getValue() {
+		return value;
+	}
+
+	private static final Map<Short, ReferenceFieldDataType> map = EnumUtils.getEnumValueMap(ReferenceFieldDataType.class);
+
+	public static ReferenceFieldDataType of(Short i) {
+		return map.get(i);
+	}
+}

dmp-backend/core/src/main/java/eu/eudat/commons/types/reference/DefinitionEntity.java

@@ -0,0 +1,22 @@
+package eu.eudat.commons.types.reference;
+
+import jakarta.xml.bind.annotation.*;
+
+import java.util.List;
+
+@XmlRootElement(name = "definition")
+@XmlAccessorType(XmlAccessType.FIELD)
+public class DefinitionEntity {
+	@XmlElementWrapper(name = "fields")
+	@XmlElement(name = "field")
+	private List<FieldEntity> fields;
+
+	public List<FieldEntity> getFields() {
+		return fields;
+	}
+
+	public void setFields(List<FieldEntity> fields) {
+		this.fields = fields;
+	}
+	
+}

dmp-backend/core/src/main/java/eu/eudat/commons/types/reference/FieldEntity.java

@@ -0,0 +1,47 @@
+package eu.eudat.commons.types.reference;
+
+import eu.eudat.commons.enums.ReferenceFieldDataType;
+import jakarta.xml.bind.annotation.XmlAccessType;
+import jakarta.xml.bind.annotation.XmlAccessorType;
+import jakarta.xml.bind.annotation.XmlAttribute;
+import jakarta.xml.bind.annotation.XmlRootElement;
+
+@XmlRootElement(name = "field")
+@XmlAccessorType(XmlAccessType.FIELD)
+public class FieldEntity {
+
+    @XmlAttribute(name = "code")
+    private String code;
+    @XmlAttribute(name = "dataType")
+    private ReferenceFieldDataType dataType;
+    @XmlAttribute(name = "value")
+    private String value;
+
+
+    public String getCode() {
+        return code;
+    }
+
+    public void setCode(String code) {
+        this.code = code;
+    }
+
+
+    public ReferenceFieldDataType getDataType() {
+        return dataType;
+    }
+
+    public void setDataType(ReferenceFieldDataType dataType) {
+        this.dataType = dataType;
+    }
+
+
+    public String getValue() {
+        return value;
+    }
+
+    public void setValue(String value) {
+        this.value = value;
+    }
+
+}

dmp-backend/core/src/main/java/eu/eudat/configurations/referencetype/ReferenceTypeConfiguration.java

@@ -0,0 +1,17 @@
+package eu.eudat.configurations.referencetype;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.context.properties.EnableConfigurationProperties;
+import org.springframework.context.annotation.Configuration;
+
+@Configuration
+@EnableConfigurationProperties({ReferenceTypeProperties.class})
+public class ReferenceTypeConfiguration {
+
+    private final ReferenceTypeProperties referenceTypeProperties;
+
+    @Autowired
+    public ReferenceTypeConfiguration(ReferenceTypeProperties referenceTypeProperties) {
+        this.referenceTypeProperties = referenceTypeProperties;
+    }
+}

dmp-backend/core/src/main/java/eu/eudat/configurations/referencetype/ReferenceTypeField.java

@@ -0,0 +1,24 @@
+package eu.eudat.configurations.referencetype;
+
+public class ReferenceTypeField {
+
+    String code;
+
+    String dataType;
+
+    public String getCode() {
+        return code;
+    }
+
+    public void setCode(String code) {
+        this.code = code;
+    }
+
+    public String getDataType() {
+        return dataType;
+    }
+
+    public void setDataType(String dataType) {
+        this.dataType = dataType;
+    }
+}

dmp-backend/core/src/main/java/eu/eudat/configurations/referencetype/ReferenceTypeProperties.java

@@ -0,0 +1,163 @@
+package eu.eudat.configurations.referencetype;
+
+import eu.eudat.model.persist.referencedefinition.DefinitionPersist;
+import org.springframework.boot.context.properties.ConfigurationProperties;
+import org.springframework.boot.context.properties.bind.ConstructorBinding;
+
+import java.util.List;
+import java.util.Map;
+
+@ConfigurationProperties(prefix = "reference-type")
+public class ReferenceTypeProperties {
+
+    private Map<String, List<ReferenceTypeField>> grant;
+    private Map<String, List<ReferenceTypeField>> funder;
+    private Map<String, List<ReferenceTypeField>> researcher;
+    private Map<String, List<ReferenceTypeField>> service;
+    private Map<String, List<ReferenceTypeField>> registry;
+    private Map<String, List<ReferenceTypeField>> project;
+    private Map<String, List<ReferenceTypeField>> organisation;
+    private Map<String, List<ReferenceTypeField>> dataset;
+    private Map<String, List<ReferenceTypeField>> dataRepository;
+    private Map<String, List<ReferenceTypeField>> pubRepository;
+    private Map<String, List<ReferenceTypeField>> journal;
+    private Map<String, List<ReferenceTypeField>> publication;
+    private Map<String, List<ReferenceTypeField>> licence;
+    private Map<String, List<ReferenceTypeField>> taxonomy;
+
+    @ConstructorBinding
+    public ReferenceTypeProperties(Map<String, List<ReferenceTypeField>> grant, Map<String, List<ReferenceTypeField>> funder,
+                                   Map<String, List<ReferenceTypeField>> researcher, Map<String, List<ReferenceTypeField>> service,
+                                   Map<String, List<ReferenceTypeField>> registry, Map<String, List<ReferenceTypeField>> project,
+                                   Map<String, List<ReferenceTypeField>> organisation, Map<String, List<ReferenceTypeField>> dataset,
+                                   Map<String, List<ReferenceTypeField>> dataRepository, Map<String, List<ReferenceTypeField>> pubRepository,
+                                   Map<String, List<ReferenceTypeField>> journal, Map<String, List<ReferenceTypeField>> publication,
+                                   Map<String, List<ReferenceTypeField>> licence, Map<String, List<ReferenceTypeField>> taxonomy) {
+        this.grant = grant;
+        this.funder = funder;
+        this.researcher = researcher;
+        this.service = service;
+        this.registry = registry;
+        this.project = project;
+        this.organisation = organisation;
+        this.dataset = dataset;
+        this.dataRepository = dataRepository;
+        this.pubRepository = pubRepository;
+        this.journal = journal;
+        this.publication = publication;
+        this.licence = licence;
+        this.taxonomy = taxonomy;
+    }
+
+    public Map<String, List<ReferenceTypeField>> getGrant() {
+        return grant;
+    }
+
+    public void setGrant(Map<String, List<ReferenceTypeField>> grant) {
+        this.grant = grant;
+    }
+
+    public Map<String, List<ReferenceTypeField>> getFunder() {
+        return funder;
+    }
+
+    public void setFunder(Map<String, List<ReferenceTypeField>> funder) {
+        this.funder = funder;
+    }
+
+    public Map<String, List<ReferenceTypeField>> getResearcher() {
+        return researcher;
+    }
+
+    public void setResearcher(Map<String, List<ReferenceTypeField>> researcher) {
+        this.researcher = researcher;
+    }
+
+    public Map<String, List<ReferenceTypeField>> getService() {
+        return service;
+    }
+
+    public void setService(Map<String, List<ReferenceTypeField>> service) {
+        this.service = service;
+    }
+
+    public Map<String, List<ReferenceTypeField>> getRegistry() {
+        return registry;
+    }
+
+    public void setRegistry(Map<String, List<ReferenceTypeField>> registry) {
+        this.registry = registry;
+    }
+
+    public Map<String, List<ReferenceTypeField>> getProject() {
+        return project;
+    }
+
+    public void setProject(Map<String, List<ReferenceTypeField>> project) {
+        this.project = project;
+    }
+
+    public Map<String, List<ReferenceTypeField>> getOrganisation() {
+        return organisation;
+    }
+
+    public void setOrganisation(Map<String, List<ReferenceTypeField>> organisation) {
+        this.organisation = organisation;
+    }
+
+    public Map<String, List<ReferenceTypeField>> getDataset() {
+        return dataset;
+    }
+
+    public void setDataset(Map<String, List<ReferenceTypeField>> dataset) {
+        this.dataset = dataset;
+    }
+
+    public Map<String, List<ReferenceTypeField>> getDataRepository() {
+        return dataRepository;
+    }
+
+    public void setDataRepository(Map<String, List<ReferenceTypeField>> dataRepository) {
+        this.dataRepository = dataRepository;
+    }
+
+    public Map<String, List<ReferenceTypeField>> getPubRepository() {
+        return pubRepository;
+    }
+
+    public void setPubRepository(Map<String, List<ReferenceTypeField>> pubRepository) {
+        this.pubRepository = pubRepository;
+    }
+
+    public Map<String, List<ReferenceTypeField>> getJournal() {
+        return journal;
+    }
+
+    public void setJournal(Map<String, List<ReferenceTypeField>> journal) {
+        this.journal = journal;
+    }
+
+    public Map<String, List<ReferenceTypeField>> getPublication() {
+        return publication;
+    }
+
+    public void setPublication(Map<String, List<ReferenceTypeField>> publication) {
+        this.publication = publication;
+    }
+
+    public Map<String, List<ReferenceTypeField>> getLicence() {
+        return licence;
+    }
+
+    public void setLicence(Map<String, List<ReferenceTypeField>> licence) {
+        this.licence = licence;
+    }
+
+    public Map<String, List<ReferenceTypeField>> getTaxonomy() {
+        return taxonomy;
+    }
+
+    public void setTaxonomy(Map<String, List<ReferenceTypeField>> taxonomy) {
+        this.taxonomy = taxonomy;
+    }
+}

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

@@ -3,6 +3,7 @@ package eu.eudat.model;
 import eu.eudat.commons.enums.ReferenceType;
 import eu.eudat.commons.enums.IsActive;
 import eu.eudat.commons.enums.SourceType;
+import eu.eudat.model.referencedefinition.Definition;
 
 import java.time.Instant;
 import java.util.List;
@@ -22,7 +23,7 @@ public class Reference {
     private String description;
     public static final String _description = "description";
 
-    private String definition;
+    private Definition definition;
     public static final String _definition = "definition";
 
     private String reference;
@@ -84,11 +85,11 @@ public class Reference {
         this.description = description;
     }
 
-    public String getDefinition() {
+    public Definition getDefinition() {
         return definition;
     }
 
-    public void setDefinition(String definition) {
+    public void setDefinition(Definition definition) {
         this.definition = definition;
     }
 

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

@@ -1,10 +1,13 @@
 package eu.eudat.model.builder;
 
 import eu.eudat.authorization.AuthorizationFlags;
+import eu.eudat.commons.XmlHandlingService;
+import eu.eudat.commons.types.reference.DefinitionEntity;
 import eu.eudat.convention.ConventionService;
 import eu.eudat.data.ReferenceEntity;
 import eu.eudat.model.DmpReference;
 import eu.eudat.model.Reference;
+import eu.eudat.model.builder.referencedefinition.DefinitionBuilder;
 import eu.eudat.query.DmpReferenceQuery;
 import gr.cite.tools.data.builder.BuilderFactory;
 import gr.cite.tools.data.query.QueryFactory;
@@ -28,15 +31,17 @@ public class ReferenceBuilder extends BaseBuilder<Reference, ReferenceEntity>{
 
     private final BuilderFactory builderFactory;
     private final QueryFactory queryFactory;
+    private final XmlHandlingService xmlHandlingService;
     private EnumSet<AuthorizationFlags> authorize = EnumSet.of(AuthorizationFlags.None);
 
     @Autowired
     public ReferenceBuilder(
             ConventionService conventionService,
-            BuilderFactory builderFactory, QueryFactory queryFactory) {
+            BuilderFactory builderFactory, QueryFactory queryFactory, XmlHandlingService xmlHandlingService) {
         super(conventionService, new LoggerService(LoggerFactory.getLogger(ReferenceBuilder.class)));
         this.builderFactory = builderFactory;
         this.queryFactory = queryFactory;
+        this.xmlHandlingService = xmlHandlingService;
     }
 
     public ReferenceBuilder authorize(EnumSet<AuthorizationFlags> values) {
@@ -51,7 +56,8 @@ public class ReferenceBuilder extends BaseBuilder<Reference, ReferenceEntity>{
         if (fields == null || data == null || fields.isEmpty())
             return new ArrayList<>();
 
-        //FieldSet userInfoFields = fields.extractPrefixed(this.asPrefix(Reference._createdBy));
+        //ToDo FieldSet userInfoFields = fields.extractPrefixed(this.asPrefix(Reference._createdBy));
+        FieldSet definitionFields = fields.extractPrefixed(this.asPrefix(Reference._definition));
 
         FieldSet dmpReferencesFields = fields.extractPrefixed(this.asPrefix(Reference._dmpReferences));
         Map<UUID, List<DmpReference>> dmpReferenceMap = this.collectDmpReferences(dmpReferencesFields, data);
@@ -64,7 +70,10 @@ public class ReferenceBuilder extends BaseBuilder<Reference, ReferenceEntity>{
             if (fields.hasField(this.asIndexer(Reference._createdAt))) m.setCreatedAt(d.getCreatedAt());
             if (fields.hasField(this.asIndexer(Reference._updatedAt))) m.setUpdatedAt(d.getUpdatedAt());
             if (fields.hasField(this.asIndexer(Reference._isActive))) m.setIsActive(d.getIsActive());
-            if (fields.hasField(this.asIndexer(Reference._definition))) m.setReference(d.getDefinition());
+            if (!definitionFields.isEmpty() && d.getDefinition() != null){
+                DefinitionEntity definition = this.xmlHandlingService.fromXmlSafe(DefinitionEntity.class, d.getDefinition());
+                m.setDefinition(this.builderFactory.builder(DefinitionBuilder.class).authorize(this.authorize).build(definitionFields, definition));
+            }
             if (fields.hasField(this.asIndexer(Reference._reference))) m.setReference(d.getReference());
             if (fields.hasField(this.asIndexer(Reference._abbreviation))) m.setAbbreviation(d.getAbbreviation());
             if (fields.hasField(this.asIndexer(Reference._description))) m.setDescription(d.getDescription());

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

@@ -0,0 +1,59 @@
+package eu.eudat.model.builder.referencedefinition;
+
+import eu.eudat.authorization.AuthorizationFlags;
+import eu.eudat.commons.types.reference.DefinitionEntity;
+import eu.eudat.convention.ConventionService;
+import eu.eudat.model.builder.BaseBuilder;
+import eu.eudat.model.referencedefinition.Definition;
+import gr.cite.tools.data.builder.BuilderFactory;
+import gr.cite.tools.exception.MyApplicationException;
+import gr.cite.tools.fieldset.FieldSet;
+import gr.cite.tools.logging.DataLogEntry;
+import gr.cite.tools.logging.LoggerService;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.config.ConfigurableBeanFactory;
+import org.springframework.context.annotation.Scope;
+import org.springframework.stereotype.Component;
+
+import java.util.*;
+
+@Component
+@Scope(value = ConfigurableBeanFactory.SCOPE_PROTOTYPE)
+public class DefinitionBuilder extends BaseBuilder<Definition, DefinitionEntity> {
+
+    private final BuilderFactory builderFactory;
+    private EnumSet<AuthorizationFlags> authorize = EnumSet.of(AuthorizationFlags.None);
+
+    @Autowired
+    public DefinitionBuilder(
+            ConventionService conventionService, BuilderFactory builderFactory) {
+        super(conventionService, new LoggerService(LoggerFactory.getLogger(DefinitionBuilder.class)));
+        this.builderFactory = builderFactory;
+    }
+
+    public DefinitionBuilder authorize(EnumSet<AuthorizationFlags> values) {
+        this.authorize = values;
+        return this;
+    }
+
+    @Override
+    public List<Definition> build(FieldSet fields, List<DefinitionEntity> data) throws MyApplicationException {
+        this.logger.debug("building for {} items requesting {} fields", Optional.ofNullable(data).map(List::size).orElse(0), Optional.ofNullable(fields).map(FieldSet::getFields).map(Set::size).orElse(0));
+        this.logger.trace(new DataLogEntry("requested fields", fields));
+        if (fields == null || data == null || fields.isEmpty())
+            return new ArrayList<>();
+
+        //Not Bulk Build because is XML no interaction with db
+        FieldSet definitionFields = fields.extractPrefixed(this.asPrefix(Definition._fields));
+        
+        List<Definition> models = new ArrayList<>();
+        for (DefinitionEntity d : data) {
+            Definition m = new Definition();
+            if (!definitionFields.isEmpty() && d.getFields() != null) m.setFields(this.builderFactory.builder(FieldBuilder.class).authorize(this.authorize).build(definitionFields, d.getFields()));
+            models.add(m);
+        }
+        this.logger.debug("build {} items", Optional.of(models).map(List::size).orElse(0));
+        return models;
+    }
+}

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

@@ -0,0 +1,59 @@
+package eu.eudat.model.builder.referencedefinition;
+
+import eu.eudat.authorization.AuthorizationFlags;
+import eu.eudat.commons.types.reference.FieldEntity;
+import eu.eudat.convention.ConventionService;
+import eu.eudat.model.builder.BaseBuilder;
+import eu.eudat.model.referencedefinition.Field;
+import gr.cite.tools.data.builder.BuilderFactory;
+import gr.cite.tools.exception.MyApplicationException;
+import gr.cite.tools.fieldset.FieldSet;
+import gr.cite.tools.logging.DataLogEntry;
+import gr.cite.tools.logging.LoggerService;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.config.ConfigurableBeanFactory;
+import org.springframework.context.annotation.Scope;
+import org.springframework.stereotype.Component;
+
+import java.util.*;
+
+@Component
+@Scope(value = ConfigurableBeanFactory.SCOPE_PROTOTYPE)
+public class FieldBuilder extends BaseBuilder<Field, FieldEntity> {
+
+    private final BuilderFactory builderFactory;
+    private EnumSet<AuthorizationFlags> authorize = EnumSet.of(AuthorizationFlags.None);
+
+    @Autowired
+    public FieldBuilder(
+            ConventionService conventionService, BuilderFactory builderFactory) {
+        super(conventionService, new LoggerService(LoggerFactory.getLogger(FieldBuilder.class)));
+        this.builderFactory = builderFactory;
+    }
+
+    public FieldBuilder authorize(EnumSet<AuthorizationFlags> values) {
+        this.authorize = values;
+        return this;
+    }
+
+    @Override
+    public List<Field> build(FieldSet fields, List<FieldEntity> data) throws MyApplicationException {
+        this.logger.debug("building for {} items requesting {} fields", Optional.ofNullable(data).map(List::size).orElse(0), Optional.ofNullable(fields).map(FieldSet::getFields).map(Set::size).orElse(0));
+        this.logger.trace(new DataLogEntry("requested fields", fields));
+        if (fields == null || data == null || fields.isEmpty())
+            return new ArrayList<>();
+
+        List<Field> models = new ArrayList<>();
+        for (FieldEntity d : data) {
+            Field m = new Field();
+            if (fields.hasField(this.asIndexer(Field._code))) m.setCode(d.getCode());
+            if (fields.hasField(this.asIndexer(Field._dataType))) m.setDataType(d.getDataType());
+            if (fields.hasField(this.asIndexer(Field._value))) m.setValue(d.getValue());
+
+            models.add(m);
+        }
+        this.logger.debug("build {} items", Optional.of(models).map(List::size).orElse(0));
+        return models;
+    }
+}

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

@@ -0,0 +1,123 @@
+package eu.eudat.model.persist;
+
+import eu.eudat.commons.enums.ReferenceType;
+import eu.eudat.commons.enums.SourceType;
+import eu.eudat.commons.validation.FieldNotNullIfOtherSet;
+import eu.eudat.commons.validation.ValidEnum;
+import eu.eudat.commons.validation.ValidId;
+import eu.eudat.model.persist.referencedefinition.DefinitionPersist;
+import jakarta.validation.Valid;
+import jakarta.validation.constraints.NotEmpty;
+import jakarta.validation.constraints.NotNull;
+import jakarta.validation.constraints.Size;
+
+import java.util.UUID;
+
+@FieldNotNullIfOtherSet(message = "{validation.hashempty}")
+public class ReferencePersist {
+
+    @ValidId(message = "{validation.invalidid}")
+    private UUID id;
+
+    @NotNull(message = "{validation.empty}")
+    @NotEmpty(message = "{validation.empty}")
+    @Size(max = 250, message = "{validation.largerthanmax}")
+    private String label;
+
+    @ValidEnum(message = "{validation.empty}")
+    private ReferenceType type;
+
+    private String description;
+
+    @Valid
+    private DefinitionPersist definition;
+
+    @NotNull(message = "{validation.empty}")
+    @NotEmpty(message = "{validation.empty}")
+    @Size(max = 1024, message = "{validation.largerthanmax}")
+    private String reference;
+
+    @Size(max = 50, message = "{validation.largerthanmax}")
+    private String abbreviation;
+
+    @Size(max = 1024, message = "{validation.largerthanmax}")
+    private String source;
+
+    @ValidEnum(message = "{validation.empty}")
+    private SourceType sourceType;
+
+    //private UserInfoPersist createdBy; ToDo
+
+
+    public UUID getId() {
+        return id;
+    }
+
+    public void setId(UUID id) {
+        this.id = id;
+    }
+
+    public String getLabel() {
+        return label;
+    }
+
+    public void setLabel(String label) {
+        this.label = label;
+    }
+
+    public ReferenceType getType() {
+        return type;
+    }
+
+    public void setType(ReferenceType type) {
+        this.type = type;
+    }
+
+    public String getDescription() {
+        return description;
+    }
+
+    public void setDescription(String description) {
+        this.description = description;
+    }
+
+    public DefinitionPersist getDefinition() {
+        return definition;
+    }
+
+    public void setDefinition(DefinitionPersist definition) {
+        this.definition = definition;
+    }
+
+    public String getReference() {
+        return reference;
+    }
+
+    public void setReference(String reference) {
+        this.reference = reference;
+    }
+
+    public String getAbbreviation() {
+        return abbreviation;
+    }
+
+    public void setAbbreviation(String abbreviation) {
+        this.abbreviation = abbreviation;
+    }
+
+    public String getSource() {
+        return source;
+    }
+
+    public void setSource(String source) {
+        this.source = source;
+    }
+
+    public SourceType getSourceType() {
+        return sourceType;
+    }
+
+    public void setSourceType(SourceType sourceType) {
+        this.sourceType = sourceType;
+    }
+}

dmp-backend/core/src/main/java/eu/eudat/model/persist/referencedefinition/DefinitionPersist.java

@@ -0,0 +1,21 @@
+package eu.eudat.model.persist.referencedefinition;
+
+import jakarta.validation.Valid;
+import jakarta.validation.constraints.NotNull;
+
+import java.util.List;
+
+public class DefinitionPersist {
+
+	@NotNull(message = "{validation.empty}")
+	@Valid
+	private List<FieldPersist> fields = null;
+
+	public List<FieldPersist> getFields() {
+		return fields;
+	}
+
+	public void setFields(List<FieldPersist> fields) {
+		this.fields = fields;
+	}
+}

dmp-backend/core/src/main/java/eu/eudat/model/persist/referencedefinition/FieldPersist.java

@@ -0,0 +1,47 @@
+package eu.eudat.model.persist.referencedefinition;
+
+import eu.eudat.commons.enums.ReferenceFieldDataType;
+import eu.eudat.commons.validation.ValidEnum;
+
+import jakarta.validation.constraints.NotEmpty;
+import jakarta.validation.constraints.NotNull;
+
+public class FieldPersist {
+
+	@NotNull(message = "{validation.empty}")
+	@NotEmpty(message = "{validation.empty}")
+	private String code = null;
+
+	@ValidEnum(message = "{validation.empty}")
+	private ReferenceFieldDataType dataType;
+
+	@NotNull(message = "{validation.empty}")
+	@NotEmpty(message = "{validation.empty}")
+	private String value = null;
+
+	public String getCode() {
+		return code;
+	}
+
+	public void setCode(String code) {
+		this.code = code;
+	}
+
+	public ReferenceFieldDataType getDataType() {
+		return dataType;
+	}
+
+	public void setDataType(ReferenceFieldDataType dataType) {
+		this.dataType = dataType;
+	}
+
+	public String getValue() {
+		return value;
+	}
+
+	public void setValue(String value) {
+		this.value = value;
+	}
+}
+
+

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

@@ -0,0 +1,17 @@
+package eu.eudat.model.referencedefinition;
+
+import java.util.List;
+
+public class Definition {
+
+	public final static String _fields = "fields";
+	private List<Field> fields;
+
+	public List<Field> getFields() {
+		return fields;
+	}
+
+	public void setFields(List<Field> fields) {
+		this.fields = fields;
+	}
+}

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

@@ -0,0 +1,39 @@
+package eu.eudat.model.referencedefinition;
+
+import eu.eudat.commons.enums.ReferenceFieldDataType;
+
+public class Field {
+
+	public final static String _code = "code";
+	private String code;
+
+	public final static String _dataType = "dataType";
+	private ReferenceFieldDataType dataType;
+
+	public final static String _value = "value";
+	private String value;
+
+	public String getCode() {
+		return code;
+	}
+
+	public void setCode(String code) {
+		this.code = code;
+	}
+
+	public ReferenceFieldDataType getDataType() {
+		return dataType;
+	}
+
+	public void setDataType(ReferenceFieldDataType dataType) {
+		this.dataType = dataType;
+	}
+
+	public String getValue() {
+		return value;
+	}
+
+	public void setValue(String value) {
+		this.value = value;
+	}
+}

dmp-backend/data/src/main/java/eu/eudat/data/dao/criteria/ReferenceCriteria.java

@@ -0,0 +1,17 @@
+package eu.eudat.data.dao.criteria;
+
+import eu.eudat.data.ReferenceEntity;
+
+import java.util.UUID;
+
+public class ReferenceCriteria extends Criteria<ReferenceEntity>{
+
+    private UUID creationUserId;
+
+    public UUID getCreationUserId() {
+        return creationUserId;
+    }
+    public void setCreationUserId(UUID creationUserId) {
+        this.creationUserId = creationUserId;
+    }
+}

dmp-backend/web/src/main/java/eu/eudat/controllers/v2/ReferenceController.java

@@ -1,5 +1,6 @@
 package eu.eudat.controllers.v2;
 
+import com.fasterxml.jackson.core.JsonProcessingException;
 import eu.eudat.audit.AuditableAction;
 import eu.eudat.authorization.AuthorizationFlags;
 import eu.eudat.authorization.Permission;
@@ -13,6 +14,7 @@ import eu.eudat.logic.services.references.ReferenceService;
 import eu.eudat.model.Reference;
 import eu.eudat.model.builder.ReferenceBuilder;
 import eu.eudat.model.censorship.ReferenceCensor;
+import eu.eudat.model.persist.ReferencePersist;
 import eu.eudat.model.result.QueryResult;
 import eu.eudat.models.data.FetcherReference;
 import eu.eudat.models.data.helpers.responses.ResponseItem;
@@ -30,7 +32,9 @@ import gr.cite.tools.exception.MyNotFoundException;
 import gr.cite.tools.fieldset.FieldSet;
 import gr.cite.tools.logging.LoggerService;
 import gr.cite.tools.logging.MapLogEntry;
+import gr.cite.tools.validation.MyValidate;
 import jakarta.transaction.Transactional;
+import jakarta.xml.bind.JAXBException;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.MessageSource;
@@ -40,6 +44,8 @@ import org.springframework.http.ResponseEntity;
 import org.springframework.web.bind.annotation.*;
 
 import javax.management.InvalidApplicationException;
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.transform.TransformerException;
 import java.util.AbstractMap;
 import java.util.List;
 import java.util.Map;
@@ -88,7 +94,7 @@ public class ReferenceController extends BaseController {
         List<Reference> models = this.builderFactory.builder(ReferenceBuilder.class).authorize(AuthorizationFlags.OwnerOrPermission).build(lookup.getProject(), datas);
         long count = (lookup.getMetadata() != null && lookup.getMetadata().getCountAll()) ? query.count() : models.size();
 
-        this.auditService.track(AuditableAction.External_Reference_Query, "lookup", lookup);
+        this.auditService.track(AuditableAction.Reference_Query, "lookup", lookup);
 
         return new QueryResult(models, count);
     }
@@ -104,7 +110,7 @@ public class ReferenceController extends BaseController {
         if (model == null)
             throw new MyNotFoundException(messageSource.getMessage("General_ItemNotFound", new Object[]{id, Reference.class.getSimpleName()}, LocaleContextHolder.getLocale()));
 
-        this.auditService.track(AuditableAction.External_Reference_Lookup, Map.ofEntries(
+        this.auditService.track(AuditableAction.Reference_Lookup, Map.ofEntries(
                 new AbstractMap.SimpleEntry<String, Object>("id", id),
                 new AbstractMap.SimpleEntry<String, Object>("fields", fieldSet)
         ));
@@ -112,6 +118,22 @@ public class ReferenceController extends BaseController {
         return model;
     }
 
+    @PostMapping("persist")
+    @Transactional
+    public Reference persist(@MyValidate @RequestBody ReferencePersist model, FieldSet fieldSet) throws MyApplicationException, MyForbiddenException, MyNotFoundException, InvalidApplicationException, JAXBException, ParserConfigurationException, JsonProcessingException, TransformerException {
+        logger.debug(new MapLogEntry("persisting" + Reference.class.getSimpleName()).And("model", model).And("fieldSet", fieldSet));
+        this.censorFactory.censor(ReferenceCensor.class).censor(fieldSet, null);
+
+        Reference persisted = this.referenceService.persist(model, fieldSet);
+
+        this.auditService.track(AuditableAction.Reference_Persist, Map.ofEntries(
+                new AbstractMap.SimpleEntry<String, Object>("model", model),
+                new AbstractMap.SimpleEntry<String, Object>("fields", fieldSet)
+        ));
+        //this.auditService.trackIdentity(AuditableAction.IdentityTracking_Action);
+        return persisted;
+    }
+
     @GetMapping(path = {"search/{externalType}"}, produces = "application/json")
     public @ResponseBody ResponseEntity<ResponseItem<List<FetcherReference>>> searchReference(@PathVariable(value = "externalType") int externalType,
                                                                                               @RequestParam(value = "query", required = false) String query,
@@ -131,7 +153,7 @@ public class ReferenceController extends BaseController {
 
         this.referenceService.deleteAndSave(id);
 
-        this.auditService.track(AuditableAction.External_Reference_Delete, "id", id);
+        this.auditService.track(AuditableAction.Reference_Delete, "id", id);
     }
 
 
@@ -145,27 +167,4 @@ public class ReferenceController extends BaseController {
 //        return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<ExternalReference>().payload(newExternalReference).status(ApiMessageCode.SUCCESS_MESSAGE));
 //    }
 
-
-
-
-//    @GetMapping(path = {"{externalType}"}, produces = "application/json")
-//    public @ResponseBody ResponseEntity<ResponseItem<List<ExternalReference2>>> listExternalReferecnes2(@RequestParam(value = "externalType") String externalType, @RequestParam(value = "query", required = false) String query,
-//                                                                                                        @RequestParam(value = "type", required = false) String type
-//    ) throws HugeResultSet, NoURLFound, InvalidApplicationException {
-//        this.authorizationService.authorizeForce(Permission.AuthenticatedRole);
-//        
-//        List<ExternalReference2> externalReferences = this.externalReferencesService.getExternalReference2(externalType, query, type);
-//        return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<List<ExternalReference2>>().status(ApiMessageCode.NO_MESSAGE).payload(externalReferences));
-//    }
-//
-//    @Transactional
-//    @PostMapping(value = {"{externalType}/persist"}, consumes = "application/json", produces = "application/json")
-//    public @ResponseBody
-//    ResponseEntity<ResponseItem<ExternalReference2>> create(@RequestBody ExternalReference2 externalReference) throws Exception {
-//        this.authorizationService.authorizeForce(Permission.AuthenticatedRole);
-//        
-//        ExternalReference2 newExternalReference = this.externalReferencesService.create(externalReference);
-//        return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<ExternalReference2>().payload(newExternalReference).status(ApiMessageCode.SUCCESS_MESSAGE));
-//    }
-
 }

dmp-backend/web/src/main/java/eu/eudat/logic/services/references/ReferenceService.java

@@ -1,13 +1,18 @@
 package eu.eudat.logic.services.references;
 
+import com.fasterxml.jackson.core.JsonProcessingException;
+import eu.eudat.authorization.AuthorizationFlags;
 import eu.eudat.authorization.Permission;
+import eu.eudat.commons.XmlHandlingService;
+import eu.eudat.commons.enums.IsActive;
 import eu.eudat.commons.enums.ReferenceType;
 import eu.eudat.commons.scope.user.UserScope;
+import eu.eudat.commons.types.reference.DefinitionEntity;
+import eu.eudat.commons.types.reference.FieldEntity;
+import eu.eudat.configurations.referencetype.ReferenceTypeProperties;
 import eu.eudat.convention.ConventionService;
-import eu.eudat.data.dao.criteria.DataRepositoryCriteria;
-import eu.eudat.data.dao.criteria.ExternalDatasetCriteria;
-import eu.eudat.data.dao.criteria.RegistryCriteria;
-import eu.eudat.data.dao.criteria.ServiceCriteria;
+import eu.eudat.data.ReferenceEntity;
+import eu.eudat.data.dao.criteria.*;
 import eu.eudat.data.old.DataRepository;
 import eu.eudat.data.old.ExternalDataset;
 import eu.eudat.data.old.Registry;
@@ -18,20 +23,37 @@ import eu.eudat.logic.proxy.config.exceptions.HugeResultSet;
 import eu.eudat.logic.proxy.config.exceptions.NoURLFound;
 import eu.eudat.logic.proxy.fetching.RemoteFetcher;
 import eu.eudat.logic.services.ApiContext;
+import eu.eudat.model.Reference;
+import eu.eudat.model.builder.ReferenceBuilder;
 import eu.eudat.model.deleter.ReferenceDeleter;
+import eu.eudat.model.persist.ReferencePersist;
+import eu.eudat.model.persist.referencedefinition.DefinitionPersist;
+import eu.eudat.model.persist.referencedefinition.FieldPersist;
 import eu.eudat.models.data.FetcherReference;
 import eu.eudat.queryable.QueryableList;
 import gr.cite.commons.web.authz.service.AuthorizationService;
 import gr.cite.tools.data.builder.BuilderFactory;
 import gr.cite.tools.data.deleter.DeleterFactory;
 import gr.cite.tools.data.query.QueryFactory;
+import gr.cite.tools.exception.MyApplicationException;
 import gr.cite.tools.exception.MyForbiddenException;
+import gr.cite.tools.exception.MyNotFoundException;
+import gr.cite.tools.exception.MyValidationException;
+import gr.cite.tools.fieldset.BaseFieldSet;
+import gr.cite.tools.fieldset.FieldSet;
 import gr.cite.tools.logging.LoggerService;
+import gr.cite.tools.logging.MapLogEntry;
 import jakarta.persistence.EntityManager;
+import jakarta.xml.bind.JAXBException;
+import org.jetbrains.annotations.NotNull;
 import org.slf4j.LoggerFactory;
 import org.springframework.context.MessageSource;
+import org.springframework.context.i18n.LocaleContextHolder;
 
 import javax.management.InvalidApplicationException;
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.transform.TransformerException;
+import java.time.Instant;
 import java.util.*;
 import java.util.stream.Collectors;
 
@@ -49,6 +71,8 @@ public class ReferenceService {
     private final ConventionService conventionService;
     private final MessageSource messageSource;
     private final QueryFactory queryFactory;
+    private final XmlHandlingService xmlHandlingService;
+    private final ReferenceTypeProperties referenceTypeProperties;
 
     public ReferenceService(ApiContext apiContext,
                             UserScope userScope,
@@ -59,7 +83,9 @@ public class ReferenceService {
                             BuilderFactory builderFactory,
                             ConventionService conventionService,
                             MessageSource messageSource,
-                            QueryFactory queryFactory) {
+                            QueryFactory queryFactory,
+                            XmlHandlingService xmlHandlingService,
+                            ReferenceTypeProperties referenceTypeProperties) {
         this.apiContext = apiContext;
         this.userScope = userScope;
         this.remoteFetcher = remoteFetcher;
@@ -70,6 +96,68 @@ public class ReferenceService {
         this.conventionService = conventionService;
         this.messageSource = messageSource;
         this.queryFactory = queryFactory;
+        this.xmlHandlingService = xmlHandlingService;
+        this.referenceTypeProperties = referenceTypeProperties;
+    }
+
+    public Reference persist(ReferencePersist model, FieldSet fields) throws MyForbiddenException, MyValidationException, MyApplicationException, MyNotFoundException, InvalidApplicationException, JAXBException, JsonProcessingException, TransformerException, ParserConfigurationException {
+        logger.debug(new MapLogEntry("persisting data").And("model", model).And("fields", fields));
+
+        this.authorizationService.authorizeForce(Permission.EditDmpBlueprint);
+
+        Boolean isUpdate = this.conventionService.isValidGuid(model.getId());
+
+        ReferenceEntity data;
+        if (isUpdate) {
+            data = this.entityManager.find(ReferenceEntity.class, model.getId());
+            if (data == null)
+                throw new MyNotFoundException(messageSource.getMessage("General_ItemNotFound", new Object[]{model.getId(), Reference.class.getSimpleName()}, LocaleContextHolder.getLocale()));
+        } else {
+            data = new ReferenceEntity();
+            data.setId(UUID.randomUUID());
+            data.setIsActive(IsActive.Active);
+            data.setCreatedAt(Instant.now());
+        }
+
+        data.setLabel(model.getLabel());
+        data.setType(model.getType());
+        data.setDescription(model.getDescription());
+        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());
+
+        if (isUpdate) this.entityManager.merge(data);
+        else  this.entityManager.persist(data);
+
+        this.entityManager.flush();
+
+        return this.builderFactory.builder(ReferenceBuilder.class).authorize(AuthorizationFlags.OwnerOrPermission).build(BaseFieldSet.build(fields, Reference._id), data);
+    }
+
+    private @NotNull DefinitionEntity buildDefinitionEntity(DefinitionPersist persist){
+        DefinitionEntity data = new DefinitionEntity();
+        if (persist == null) return data;
+        if (!this.conventionService.isListNullOrEmpty(persist.getFields())){
+            data.setFields(new ArrayList<>());
+            for (FieldPersist fieldPersist: persist.getFields()) {
+                data.getFields().add(this.buildFieldEntity(fieldPersist));
+            }
+        }
+
+        return data;
+    }
+
+    private @NotNull FieldEntity buildFieldEntity(FieldPersist persist){
+        FieldEntity data = new FieldEntity();
+        if (persist == null) return data;
+
+        data.setCode(persist.getCode());
+        data.setDataType(persist.getDataType());
+        data.setCode(persist.getCode());
+
+        return data;
     }
 
     public void deleteAndSave(UUID id) throws MyForbiddenException, InvalidApplicationException {
@@ -80,27 +168,13 @@ public class ReferenceService {
         this.deleterFactory.deleter(ReferenceDeleter.class).deleteAndSaveByIds(List.of(id));
     }
 
-    // external references:
-    //    taxonomies,
-    //    licenses,
-    //    publications,
-    //    journals,
-    //    pubRepositories,
-    //    dataRepositories
-    //    registries,
-    //    services
     public List<FetcherReference> searchReference(ReferenceType externalType, String query, String type) throws HugeResultSet, NoURLFound, InvalidApplicationException {
         ExternalUrlCriteria externalUrlCriteria = new ExternalUrlCriteria(query);
 
-        List<Map<String, String>> remoteRepos = null;
-        if (externalType.equals(ReferenceType.Datasets)){
-            remoteRepos = remoteFetcher.getDatasets(externalUrlCriteria, type);
-        }else {
-            remoteRepos = this.apiContext.getOperationsContext().getRemoteFetcher().get(externalType, externalUrlCriteria, type);
-        }
+        List<Map<String, String>> remoteRepos = this.apiContext.getOperationsContext().getRemoteFetcher().get(externalType, externalUrlCriteria, type);
 
         List<FetcherReference> list = this.fetchFromDb(externalType, query, type, remoteRepos);
-        
+
         list.addAll(remoteRepos.stream().map(FetcherReference::fromRemoteModel).toList());
         list = list.stream().filter(x -> x.getName().toLowerCase().contains(query.toLowerCase())).collect(Collectors.toList());
         list.sort(Comparator.comparing(FetcherReference::getName));
@@ -136,7 +210,7 @@ public class ReferenceService {
 
                 if (!query.isEmpty()) criteria.setLike(query);
                 criteria.setCreationUserId(this.userScope.getUserId());
-    
+
                 if (type.equals("")) {
                     List<Service> serviceList = (this.apiContext.getOperationsContext().getDatabaseRepository().getServiceDao().getWithCriteria(criteria)).toList();
                    list = serviceList.stream().map(item -> new FetcherReference().fromService(item)).collect(Collectors.toList());
@@ -156,7 +230,7 @@ public class ReferenceService {
             case Licenses:
                 break;
         }
-        
+
         return list;
     }
 

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

@@ -18,4 +18,5 @@ spring:
       optional:classpath:config/cors.yml[.yml], optional:classpath:config/cors-${spring.profiles.active}.yml[.yml], optional:file:../config/cors-${spring.profiles.active}.yml[.yml],
       optional:classpath:config/swagger.yml[.yml], optional:classpath:config/swagger-${spring.profiles.active}.yml[.yml], optional:file:../config/swagger-${spring.profiles.active}.yml[.yml],
       optional:classpath:config/deposit.yml[.yml], optional:classpath:config/deposit-${spring.profiles.active}.yml[.yml], optional:file:../config/deposit-${spring.profiles.active}.yml[.yml],
-      optional:classpath:config/errors.yml[.yml], optional:classpath:config/errors-${spring.profiles.active}.yml[.yml], optional:file:../config/errors-${spring.profiles.active}.yml[.yml]
+      optional:classpath:config/errors.yml[.yml], optional:classpath:config/errors-${spring.profiles.active}.yml[.yml], optional:file:../config/errors-${spring.profiles.active}.yml[.yml],
+      optional:classpath:config/reference-type.yml[.yml], optional:classpath:config/reference-type-${spring.profiles.active}.yml[.yml], optional:file:../config/reference-type-${spring.profiles.active}.yml[.yml]

dmp-backend/web/src/main/resources/config/reference-type.yml

@@ -0,0 +1,65 @@
+reference-type:
+  grant:
+    fields:
+      - code: startDate
+        dataType: date
+      - code: endDate
+        dataType: date
+  funder:
+    fields:
+      - code: uri
+        dataType: text
+  researcher:
+    fields:
+      - code: firstName
+        dataType: text
+      - code: lastName
+        dataType: text
+      - code: uri
+        dataType: text
+  service:
+    fields:
+      - code: uri
+        dataType: text
+  registry:
+    fields:
+      - code: uri
+        dataType: text
+  project:
+    fields:
+      - code: startDate
+        dataType: date
+      - code: endDate
+        dataType: date
+  organisation:
+    fields:
+      - code: pid
+        dataType: text
+      - code: uri
+        dataType: text
+      - code: pidTypeField
+        dataType: text
+  dataset:
+    fields:
+      - code: pid
+        dataType: text
+      - code: pidTypeField
+        dataType: text
+  dataRepository:
+    fields:
+  pubRepository:
+    fields:
+  journal:
+    fields:
+  publication:
+    fields:
+      - code: pid
+        dataType: text
+      - code: pidTypeField
+        dataType: text
+  licence:
+    fields:
+      - code: uri
+        dataType: text
+  taxonomy:
+    fields:

dmp-frontend/src/app/core/common/enum/reference-field-data-type.ts

@@ -0,0 +1,4 @@
+export enum ReferenceFieldDataType {
+	Text = 0,
+	Date = 1
+}

dmp-frontend/src/app/core/model/reference/reference.ts

@@ -3,13 +3,14 @@ import { IsActive } from "@app/core/common/enum/is-active.enum";
 import { SourceType } from "@app/core/common/enum/source-type";
 import { UUID } from "crypto";
 import { DmpModel } from "../dmp/dmp";
+import { ReferenceFieldDataType } from "@app/core/common/enum/reference-field-data-type";
 
 export interface Reference {
 	id: UUID;
     label: string;
     type: ReferenceType;
     description: string;
-    definition: string;
+    definition: Definition;
     reference: string;
     abbreviation: string;
     source: string;
@@ -20,13 +21,26 @@ export interface Reference {
     dmpReferences: DmpReference[];
 }
 
+export interface Definition {
+	fields: Field[];
+}
+
+export interface Field {
+	code: string;
+    dataType: ReferenceFieldDataType;
+    value: string;
+}
+
 export interface DmpReference {
 	id: UUID;
     dmp: DmpModel;
     reference: Reference;
     data: string;
+    createdAt: Date;
+    updatedAt: Date;
 }
 
+// old fetcher
 export interface FetcherReference {
 	id: string;
     name: string;
@@ -42,4 +56,29 @@ export interface FetcherReference {
     firstName: string;
     lastName: string;
     tag: string;
+}
+
+
+// Persist
+
+export interface ReferencePersist {
+	id: UUID;
+    label: string;
+    type: ReferenceType;
+    description: string;
+    definition: DefinitionPersist;
+    reference: string;
+    abbreviation: string;
+    source: string;
+    sourceType: SourceType;
+}
+
+export interface DefinitionPersist {
+	fields?: FieldPersist[];
+}
+
+export interface FieldPersist {
+	code: string;
+    dataType: ReferenceFieldDataType;
+    value: string;
 }