rename External Reference to Reference

dmp-backend/core/src/main/java/eu/eudat/data/DmpReferenceEntity.java

@@ -8,8 +8,8 @@ import jakarta.persistence.Table;
 import java.util.UUID;
 
 @Entity
-@Table(name = "\"DmpExternalReference\"")
+@Table(name = "\"DmpReference\"")
-public class DmpExternalReferenceEntity {
+public class DmpReferenceEntity {
 
     @Id
     @Column(name = "id", columnDefinition = "uuid", updatable = false, nullable = false)

dmp-backend/core/src/main/java/eu/eudat/data/ReferenceEntity.java

@@ -12,8 +12,8 @@ import java.time.Instant;
 import java.util.UUID;
 
 @Entity
-@Table(name = "\"ExternalReference\"")
+@Table(name = "\"Reference\"")
-public class ExternalReferenceEntity {
+public class ReferenceEntity {
 
     @Id
     @Column(name = "id", columnDefinition = "uuid", updatable = false, nullable = false)

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

@@ -93,6 +93,9 @@ public class Dmp {
 
     public static final String _dmpDescriptions = "dmpDescriptions";
 
+    public static final String _dmpExternalReferences = "dmpExternalReferences";
+    private List<DmpReference> dmpReferences;
+
     public UUID getId() {
         return id;
     }
@@ -260,4 +263,12 @@ public class Dmp {
     public void setDmpDescriptions(List<Description> dmpDescriptions) {
         this.dmpDescriptions = dmpDescriptions;
     }
+
+    public List<DmpReference> getDmpExternalReferences() {
+        return dmpReferences;
+    }
+
+    public void setDmpExternalReferences(List<DmpReference> dmpReferences) {
+        this.dmpReferences = dmpReferences;
+    }
 }

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

@@ -34,9 +34,6 @@ public class DmpBlueprint {
     public final static String _hash = "hash";
     private String hash;
 
-    public static final String _dmpExternalReferences = "dmpExternalReferences";
-    private List<DmpExternalReference> dmpExternalReferences;
-
     public UUID getId() {
         return id;
     }
@@ -100,14 +97,6 @@ public class DmpBlueprint {
     public void setDefinition(Definition definition) {
         this.definition = definition;
     }
-
-    public List<DmpExternalReference> getDmpExternalReferences() {
-        return dmpExternalReferences;
-    }
-
-    public void setDmpExternalReferences(List<DmpExternalReference> dmpExternalReferences) {
-        this.dmpExternalReferences = dmpExternalReferences;
-    }
 }
 
 

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

@@ -2,15 +2,15 @@ package eu.eudat.model;
 
 import java.util.UUID;
 
-public class DmpExternalReference {
+public class DmpReference {
 
     private UUID id;
     public static final String _id = "id";
 
-    private DmpBlueprint dmp;
+    private Dmp dmp;
     public static final String _dmp = "dmp";
 
-    private ExternalReference externalReference;
+    private Reference reference;
     public static final String _externalReference = "externalReference";
 
     private String data;
@@ -24,20 +24,20 @@ public class DmpExternalReference {
         this.id = id;
     }
 
-    public DmpBlueprint getDmp() {
+    public Dmp getDmp() {
         return dmp;
     }
 
-    public void setDmp(DmpBlueprint dmp) {
+    public void setDmp(Dmp dmp) {
         this.dmp = dmp;
     }
 
-    public ExternalReference getExternalReference() {
+    public Reference getExternalReference() {
-        return externalReference;
+        return reference;
     }
 
-    public void setExternalReference(ExternalReference externalReference) {
+    public void setExternalReference(Reference reference) {
-        this.externalReference = externalReference;
+        this.reference = reference;
     }
 
     public String getData() {

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

@@ -8,7 +8,7 @@ import java.time.Instant;
 import java.util.List;
 import java.util.UUID;
 
-public class ExternalReference {
+public class Reference {
 
     private UUID id;
     public static final String _id = "id";
@@ -49,7 +49,7 @@ public class ExternalReference {
     //private UserInfo createdBy; ToDo
     //public static final String _createdBy = "createdBy";
 
-    private List<DmpExternalReference> dmpExternalReferences;
+    private List<DmpReference> dmpReferences;
     public static final String _dmpExternalReferences = "dmpExternalReferences";
 
     public UUID getId() {
@@ -148,11 +148,11 @@ public class ExternalReference {
         this.updatedAt = updatedAt;
     }
 
-    public List<DmpExternalReference> getDmpExternalReferences() {
+    public List<DmpReference> getDmpExternalReferences() {
-        return dmpExternalReferences;
+        return dmpReferences;
     }
 
-    public void setDmpExternalReferences(List<DmpExternalReference> dmpExternalReferences) {
+    public void setDmpExternalReferences(List<DmpReference> dmpReferences) {
-        this.dmpExternalReferences = dmpExternalReferences;
+        this.dmpReferences = dmpReferences;
     }
 }

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

@@ -6,14 +6,9 @@ import eu.eudat.commons.types.dmpblueprint.DefinitionEntity;
 import eu.eudat.convention.ConventionService;
 import eu.eudat.data.DmpBlueprintEntity;
 import eu.eudat.model.DmpBlueprint;
-import eu.eudat.model.DmpExternalReference;
-import eu.eudat.model.ExternalReference;
 import eu.eudat.model.builder.dmpblueprintdefinition.DefinitionBuilder;
-import eu.eudat.query.DmpExternalReferenceQuery;
 import gr.cite.tools.data.builder.BuilderFactory;
-import gr.cite.tools.data.query.QueryFactory;
 import gr.cite.tools.exception.MyApplicationException;
-import gr.cite.tools.fieldset.BaseFieldSet;
 import gr.cite.tools.fieldset.FieldSet;
 import gr.cite.tools.logging.DataLogEntry;
 import gr.cite.tools.logging.LoggerService;
@@ -24,24 +19,21 @@ import org.springframework.context.annotation.Scope;
 import org.springframework.stereotype.Component;
 
 import java.util.*;
-import java.util.stream.Collectors;
 
 @Component
 @Scope(value = ConfigurableBeanFactory.SCOPE_PROTOTYPE)
 public class DmpBlueprintBuilder extends BaseBuilder<DmpBlueprint, DmpBlueprintEntity> {
 
     private final BuilderFactory builderFactory;
-    private final QueryFactory queryFactory;
     private final XmlHandlingService xmlHandlingService;
     private EnumSet<AuthorizationFlags> authorize = EnumSet.of(AuthorizationFlags.None);
 
     @Autowired
     public DmpBlueprintBuilder(
             ConventionService conventionService,
-            BuilderFactory builderFactory, QueryFactory queryFactory, XmlHandlingService xmlHandlingService) {
+            BuilderFactory builderFactory, XmlHandlingService xmlHandlingService) {
         super(conventionService, new LoggerService(LoggerFactory.getLogger(DmpBlueprintBuilder.class)));
         this.builderFactory = builderFactory;
-        this.queryFactory = queryFactory;
         this.xmlHandlingService = xmlHandlingService;
     }
 
@@ -57,9 +49,6 @@ public class DmpBlueprintBuilder extends BaseBuilder<DmpBlueprint, DmpBlueprintE
         if (fields == null || data == null || fields.isEmpty())
             return new ArrayList<>();
         FieldSet definitionFields = fields.extractPrefixed(this.asPrefix(DmpBlueprint._definition));
-        FieldSet dmpExternalReferencesFields = fields.extractPrefixed(this.asPrefix(ExternalReference._dmpExternalReferences));
-        Map<UUID, List<DmpExternalReference>> dmpExternalReferenceMap = this.collectDmpExternalReferences(dmpExternalReferencesFields, data);
-
         List<DmpBlueprint> models = new ArrayList<>();
         for (DmpBlueprintEntity d : data) {
             DmpBlueprint m = new DmpBlueprint();
@@ -74,29 +63,9 @@ public class DmpBlueprintBuilder extends BaseBuilder<DmpBlueprint, DmpBlueprintE
                 DefinitionEntity definition = this.xmlHandlingService.xmlSerializableFromXmlSafe(DefinitionEntity.class, d.getDefinition());
                 m.setDefinition(this.builderFactory.builder(DefinitionBuilder.class).authorize(this.authorize).build(definitionFields, definition));
             }
-            if (dmpExternalReferenceMap != null && !dmpExternalReferenceMap.isEmpty() && dmpExternalReferenceMap.containsKey(d.getId())) m.setDmpExternalReferences(dmpExternalReferenceMap.get(d.getId()));
-            models.add(m);
             models.add(m);
         }
         this.logger.debug("build {} items", Optional.of(models).map(List::size).orElse(0));
         return models;
     }
-
-    private Map<UUID, List<DmpExternalReference>> collectDmpExternalReferences(FieldSet fields, List<DmpBlueprintEntity> datas) throws MyApplicationException {
-        if (fields.isEmpty() || datas.isEmpty()) return null;
-        this.logger.debug("checking related - {}", DmpExternalReference.class.getSimpleName());
-
-        Map<UUID, List<DmpExternalReference>> itemMap = null;
-        FieldSet clone = new BaseFieldSet(fields.getFields()).ensure(this.asIndexer(DmpExternalReference._dmp, DmpBlueprint._id));
-        DmpExternalReferenceQuery query = this.queryFactory.query(DmpExternalReferenceQuery.class).authorize(this.authorize).dmpIds(datas.stream().map(x -> x.getId()).distinct().collect(Collectors.toList()));
-        itemMap = this.builderFactory.builder(DmpExternalReferenceBuilder.class).authorize(this.authorize).authorize(this.authorize).asMasterKey(query, clone, x -> x.getDmp().getId());
-
-        if (!fields.hasField(this.asIndexer(DmpExternalReference._dmp, DmpBlueprint._id))) {
-            itemMap.values().stream().flatMap(List::stream).filter(x -> x != null && x.getDmp() != null).map(x -> {
-                x.getDmp().setId(null);
-                return x;
-            }).collect(Collectors.toList());
-        }
-        return itemMap;
-    }
 }

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

@@ -3,9 +3,9 @@ package eu.eudat.model.builder;
 import eu.eudat.authorization.AuthorizationFlags;
 import eu.eudat.convention.ConventionService;
 import eu.eudat.data.DmpEntity;
-import eu.eudat.model.Description;
+import eu.eudat.model.*;
-import eu.eudat.model.Dmp;
 import eu.eudat.query.DescriptionQuery;
+import eu.eudat.query.DmpReferenceQuery;
 import gr.cite.tools.data.builder.BuilderFactory;
 import gr.cite.tools.data.query.QueryFactory;
 import gr.cite.tools.exception.MyApplicationException;
@@ -57,6 +57,8 @@ public class DmpBuilder extends BaseBuilder<Dmp, DmpEntity> {
 
         FieldSet dmpDescriptionsFields = fields.extractPrefixed(this.asPrefix(Dmp._dmpDescriptions));
         Map<UUID, List<Description>> dmpDescriptionsMap = this.collectDmpDescriptions(dmpDescriptionsFields, data);
+        FieldSet dmpReferencesFields = fields.extractPrefixed(this.asPrefix(Reference._dmpExternalReferences));
+        Map<UUID, List<DmpReference>> dmpReferenceMap = this.collectDmpReferences(dmpReferencesFields, data);
 
         for (DmpEntity d : data) {
             Dmp m = new Dmp();
@@ -96,6 +98,7 @@ public class DmpBuilder extends BaseBuilder<Dmp, DmpEntity> {
             if (!dmpDescriptionsFields.isEmpty() && dmpDescriptionsMap != null && dmpDescriptionsMap.containsKey(d.getId()))
                 m.setDmpDescriptions(dmpDescriptionsMap.get(d.getId()));
 
+            if (dmpReferenceMap != null && !dmpReferenceMap.isEmpty() && dmpReferenceMap.containsKey(d.getId())) m.setDmpExternalReferences(dmpReferenceMap.get(d.getId()));
             models.add(m);
         }
         this.logger.debug("build {} items", Optional.of(models).map(List::size).orElse(0));
@@ -123,4 +126,22 @@ public class DmpBuilder extends BaseBuilder<Dmp, DmpEntity> {
         return itemMap;
     }
 
+    private Map<UUID, List<DmpReference>> collectDmpReferences(FieldSet fields, List<DmpEntity> datas) throws MyApplicationException {
+        if (fields.isEmpty() || datas.isEmpty()) return null;
+        this.logger.debug("checking related - {}", DmpReference.class.getSimpleName());
+
+        Map<UUID, List<DmpReference>> itemMap = null;
+        FieldSet clone = new BaseFieldSet(fields.getFields()).ensure(this.asIndexer(DmpReference._dmp, Dmp._id));
+        DmpReferenceQuery query = this.queryFactory.query(DmpReferenceQuery.class).authorize(this.authorize).dmpIds(datas.stream().map(x -> x.getId()).distinct().collect(Collectors.toList()));
+        itemMap = this.builderFactory.builder(DmpReferenceBuilder.class).authorize(this.authorize).authorize(this.authorize).asMasterKey(query, clone, x -> x.getDmp().getId());
+
+        if (!fields.hasField(this.asIndexer(DmpReference._dmp, Dmp._id))) {
+            itemMap.values().stream().flatMap(List::stream).filter(x -> x != null && x.getDmp() != null).map(x -> {
+                x.getDmp().setId(null);
+                return x;
+            }).collect(Collectors.toList());
+        }
+        return itemMap;
+    }
+
 }

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

@@ -1,130 +0,0 @@
-package eu.eudat.model.builder;
-
-import eu.eudat.authorization.AuthorizationFlags;
-import eu.eudat.convention.ConventionService;
-import eu.eudat.data.DmpExternalReferenceEntity;
-import eu.eudat.model.DmpBlueprint;
-import eu.eudat.model.DmpExternalReference;
-import eu.eudat.model.ExternalReference;
-import eu.eudat.query.DmpBlueprintQuery;
-import eu.eudat.query.ExternalReferenceQuery;
-import gr.cite.tools.data.builder.BuilderFactory;
-import gr.cite.tools.data.query.QueryFactory;
-import gr.cite.tools.exception.MyApplicationException;
-import gr.cite.tools.fieldset.BaseFieldSet;
-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.*;
-import java.util.stream.Collectors;
-
-@Component
-@Scope(value = ConfigurableBeanFactory.SCOPE_PROTOTYPE)
-public class DmpExternalReferenceBuilder extends BaseBuilder<DmpExternalReference, DmpExternalReferenceEntity>{
-
-    private final BuilderFactory builderFactory;
-    private final QueryFactory queryFactory;
-    private EnumSet<AuthorizationFlags> authorize = EnumSet.of(AuthorizationFlags.None);
-
-    @Autowired
-    public DmpExternalReferenceBuilder(
-            ConventionService conventionService,
-            BuilderFactory builderFactory, QueryFactory queryFactory) {
-        super(conventionService, new LoggerService(LoggerFactory.getLogger(DmpExternalReferenceBuilder.class)));
-        this.builderFactory = builderFactory;
-        this.queryFactory = queryFactory;
-    }
-
-    public DmpExternalReferenceBuilder authorize(EnumSet<AuthorizationFlags> values) {
-        this.authorize = values;
-        return this;
-    }
-
-    @Override
-    public List<DmpExternalReference> build(FieldSet fields, List<DmpExternalReferenceEntity> 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<>();
-        FieldSet externalReferenceFields = fields.extractPrefixed(this.asPrefix(DmpExternalReference._externalReference));
-        Map<UUID, ExternalReference> externalReferenceItemsMap = this.collectExternalReferences(externalReferenceFields, data);
-
-        FieldSet dmpFields = fields.extractPrefixed(this.asPrefix(DmpExternalReference._dmp));
-        Map<UUID, DmpBlueprint> dmpBlueprintItemsMap = this.collectDmps(dmpFields, data);
-
-        List<DmpExternalReference> models = new ArrayList<>();
-        for (DmpExternalReferenceEntity d : data) {
-            DmpExternalReference m = new DmpExternalReference();
-            if (fields.hasField(this.asIndexer(DmpExternalReference._id))) m.setId(d.getId());
-            if (fields.hasField(this.asIndexer(DmpExternalReference._data))) m.setData(d.getData());
-            if(!externalReferenceFields.isEmpty() && externalReferenceItemsMap != null && externalReferenceItemsMap.containsKey(d.getReferenceId())){
-                m.setExternalReference(externalReferenceItemsMap.get(d.getReferenceId()));
-            }
-            if(!dmpFields.isEmpty() && dmpBlueprintItemsMap != null && dmpBlueprintItemsMap.containsKey(d.getDmpId())){
-                m.setDmp(dmpBlueprintItemsMap.get(d.getDmpId()));
-            }
-            models.add(m);
-        }
-        this.logger.debug("build {} items", Optional.of(models).map(List::size).orElse(0));
-        return models;
-    }
-
-    private Map<UUID, ExternalReference> collectExternalReferences(FieldSet fields, List<DmpExternalReferenceEntity> data) throws MyApplicationException {
-        if (fields.isEmpty() || data.isEmpty()) return null;
-        this.logger.debug("checking related - {}", ExternalReference.class.getSimpleName());
-
-        Map<UUID, ExternalReference> itemMap;
-        if (!fields.hasOtherField(this.asIndexer(ExternalReference._id))) {
-            itemMap = this.asEmpty(
-                    data.stream().map(x -> x.getReferenceId()).distinct().collect(Collectors.toList()),
-                    x -> {
-                        ExternalReference item = new ExternalReference();
-                        item.setId(x);
-                        return item;
-                    },
-                    ExternalReference::getId);
-        } else {
-            FieldSet clone = new BaseFieldSet(fields.getFields()).ensure(ExternalReference._id);
-            ExternalReferenceQuery q = this.queryFactory.query(ExternalReferenceQuery.class).authorize(this.authorize).ids(data.stream().map(x -> x.getReferenceId()).distinct().collect(Collectors.toList()));
-            itemMap = this.builderFactory.builder(ExternalReferenceBuilder.class).authorize(this.authorize).asForeignKey(q, clone, ExternalReference::getId);
-        }
-        if (!fields.hasField(ExternalReference._id)) {
-            itemMap.values().stream().filter(Objects::nonNull).peek(x -> x.setId(null)).collect(Collectors.toList());
-        }
-
-        return itemMap;
-    }
-
-    private Map<UUID, DmpBlueprint> collectDmps(FieldSet fields, List<DmpExternalReferenceEntity> data) throws MyApplicationException {
-        if (fields.isEmpty() || data.isEmpty()) return null;
-        this.logger.debug("checking related - {}", DmpBlueprint.class.getSimpleName());
-
-        Map<UUID, DmpBlueprint> itemMap;
-        if (!fields.hasOtherField(this.asIndexer(DmpBlueprint._id))) {
-            itemMap = this.asEmpty(
-                    data.stream().map(x -> x.getDmpId()).distinct().collect(Collectors.toList()),
-                    x -> {
-                        DmpBlueprint item = new DmpBlueprint();
-                        item.setId(x);
-                        return item;
-                    },
-                    DmpBlueprint::getId);
-        } else {
-            FieldSet clone = new BaseFieldSet(fields.getFields()).ensure(DmpBlueprint._id);
-            DmpBlueprintQuery q = this.queryFactory.query(DmpBlueprintQuery.class).authorize(this.authorize).ids(data.stream().map(x -> x.getDmpId()).distinct().collect(Collectors.toList()));
-            itemMap = this.builderFactory.builder(DmpBlueprintBuilder.class).authorize(this.authorize).asForeignKey(q, clone, DmpBlueprint::getId);
-        }
-        if (!fields.hasField(DmpBlueprint._id)) {
-            itemMap.values().stream().filter(Objects::nonNull).peek(x -> x.setId(null)).collect(Collectors.toList());
-        }
-
-        return itemMap;
-    }
-
-}

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

@@ -0,0 +1,130 @@
+package eu.eudat.model.builder;
+
+import eu.eudat.authorization.AuthorizationFlags;
+import eu.eudat.convention.ConventionService;
+import eu.eudat.data.DmpReferenceEntity;
+import eu.eudat.model.Dmp;
+import eu.eudat.model.DmpReference;
+import eu.eudat.model.Reference;
+import eu.eudat.query.DmpQuery;
+import eu.eudat.query.ReferenceQuery;
+import gr.cite.tools.data.builder.BuilderFactory;
+import gr.cite.tools.data.query.QueryFactory;
+import gr.cite.tools.exception.MyApplicationException;
+import gr.cite.tools.fieldset.BaseFieldSet;
+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.*;
+import java.util.stream.Collectors;
+
+@Component
+@Scope(value = ConfigurableBeanFactory.SCOPE_PROTOTYPE)
+public class DmpReferenceBuilder extends BaseBuilder<DmpReference, DmpReferenceEntity>{
+
+    private final BuilderFactory builderFactory;
+    private final QueryFactory queryFactory;
+    private EnumSet<AuthorizationFlags> authorize = EnumSet.of(AuthorizationFlags.None);
+
+    @Autowired
+    public DmpReferenceBuilder(
+            ConventionService conventionService,
+            BuilderFactory builderFactory, QueryFactory queryFactory) {
+        super(conventionService, new LoggerService(LoggerFactory.getLogger(DmpReferenceBuilder.class)));
+        this.builderFactory = builderFactory;
+        this.queryFactory = queryFactory;
+    }
+
+    public DmpReferenceBuilder authorize(EnumSet<AuthorizationFlags> values) {
+        this.authorize = values;
+        return this;
+    }
+
+    @Override
+    public List<DmpReference> build(FieldSet fields, List<DmpReferenceEntity> 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<>();
+        FieldSet referenceFields = fields.extractPrefixed(this.asPrefix(DmpReference._externalReference));
+        Map<UUID, Reference> referenceItemsMap = this.collectReferences(referenceFields, data);
+
+        FieldSet dmpFields = fields.extractPrefixed(this.asPrefix(DmpReference._dmp));
+        Map<UUID, Dmp> dmpItemsMap = this.collectDmps(dmpFields, data);
+
+        List<DmpReference> models = new ArrayList<>();
+        for (DmpReferenceEntity d : data) {
+            DmpReference m = new DmpReference();
+            if (fields.hasField(this.asIndexer(DmpReference._id))) m.setId(d.getId());
+            if (fields.hasField(this.asIndexer(DmpReference._data))) m.setData(d.getData());
+            if(!referenceFields.isEmpty() && referenceItemsMap != null && referenceItemsMap.containsKey(d.getReferenceId())){
+                m.setExternalReference(referenceItemsMap.get(d.getReferenceId()));
+            }
+            if(!dmpFields.isEmpty() && dmpItemsMap != null && dmpItemsMap.containsKey(d.getDmpId())){
+                m.setDmp(dmpItemsMap.get(d.getDmpId()));
+            }
+            models.add(m);
+        }
+        this.logger.debug("build {} items", Optional.of(models).map(List::size).orElse(0));
+        return models;
+    }
+
+    private Map<UUID, Reference> collectReferences(FieldSet fields, List<DmpReferenceEntity> data) throws MyApplicationException {
+        if (fields.isEmpty() || data.isEmpty()) return null;
+        this.logger.debug("checking related - {}", Reference.class.getSimpleName());
+
+        Map<UUID, Reference> itemMap;
+        if (!fields.hasOtherField(this.asIndexer(Reference._id))) {
+            itemMap = this.asEmpty(
+                    data.stream().map(x -> x.getReferenceId()).distinct().collect(Collectors.toList()),
+                    x -> {
+                        Reference item = new Reference();
+                        item.setId(x);
+                        return item;
+                    },
+                    Reference::getId);
+        } else {
+            FieldSet clone = new BaseFieldSet(fields.getFields()).ensure(Reference._id);
+            ReferenceQuery q = this.queryFactory.query(ReferenceQuery.class).authorize(this.authorize).ids(data.stream().map(x -> x.getReferenceId()).distinct().collect(Collectors.toList()));
+            itemMap = this.builderFactory.builder(ReferenceBuilder.class).authorize(this.authorize).asForeignKey(q, clone, Reference::getId);
+        }
+        if (!fields.hasField(Reference._id)) {
+            itemMap.values().stream().filter(Objects::nonNull).peek(x -> x.setId(null)).collect(Collectors.toList());
+        }
+
+        return itemMap;
+    }
+
+    private Map<UUID, Dmp> collectDmps(FieldSet fields, List<DmpReferenceEntity> data) throws MyApplicationException {
+        if (fields.isEmpty() || data.isEmpty()) return null;
+        this.logger.debug("checking related - {}", Dmp.class.getSimpleName());
+
+        Map<UUID, Dmp> itemMap;
+        if (!fields.hasOtherField(this.asIndexer(Dmp._id))) {
+            itemMap = this.asEmpty(
+                    data.stream().map(x -> x.getDmpId()).distinct().collect(Collectors.toList()),
+                    x -> {
+                        Dmp item = new Dmp();
+                        item.setId(x);
+                        return item;
+                    },
+                    Dmp::getId);
+        } else {
+            FieldSet clone = new BaseFieldSet(fields.getFields()).ensure(Dmp._id);
+            DmpQuery q = this.queryFactory.query(DmpQuery.class).authorize(this.authorize).ids(data.stream().map(x -> x.getDmpId()).distinct().collect(Collectors.toList()));
+            itemMap = this.builderFactory.builder(DmpBuilder.class).authorize(this.authorize).asForeignKey(q, clone, Dmp::getId);
+        }
+        if (!fields.hasField(Dmp._id)) {
+            itemMap.values().stream().filter(Objects::nonNull).peek(x -> x.setId(null)).collect(Collectors.toList());
+        }
+
+        return itemMap;
+    }
+
+}

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

@@ -1,101 +0,0 @@
-package eu.eudat.model.builder;
-
-import eu.eudat.authorization.AuthorizationFlags;
-import eu.eudat.convention.ConventionService;
-import eu.eudat.data.ExternalReferenceEntity;
-import eu.eudat.model.DmpExternalReference;
-import eu.eudat.model.ExternalReference;
-import eu.eudat.query.DmpExternalReferenceQuery;
-import gr.cite.tools.data.builder.BuilderFactory;
-import gr.cite.tools.data.query.QueryFactory;
-import gr.cite.tools.exception.MyApplicationException;
-import gr.cite.tools.fieldset.BaseFieldSet;
-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.*;
-import java.util.stream.Collectors;
-
-@Component
-@Scope(value = ConfigurableBeanFactory.SCOPE_PROTOTYPE)
-public class ExternalReferenceBuilder extends BaseBuilder<ExternalReference, ExternalReferenceEntity>{
-
-    private final BuilderFactory builderFactory;
-    private final QueryFactory queryFactory;
-    private EnumSet<AuthorizationFlags> authorize = EnumSet.of(AuthorizationFlags.None);
-
-    @Autowired
-    public ExternalReferenceBuilder(
-            ConventionService conventionService,
-            BuilderFactory builderFactory, QueryFactory queryFactory) {
-        super(conventionService, new LoggerService(LoggerFactory.getLogger(ExternalReferenceBuilder.class)));
-        this.builderFactory = builderFactory;
-        this.queryFactory = queryFactory;
-    }
-
-    public ExternalReferenceBuilder authorize(EnumSet<AuthorizationFlags> values) {
-        this.authorize = values;
-        return this;
-    }
-
-    @Override
-    public List<ExternalReference> build(FieldSet fields, List<ExternalReferenceEntity> 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<>();
-
-        //FieldSet userInfoFields = fields.extractPrefixed(this.asPrefix(ExternalReference._createdBy));
-
-        FieldSet dmpExternalReferencesFields = fields.extractPrefixed(this.asPrefix(ExternalReference._dmpExternalReferences));
-        Map<UUID, List<DmpExternalReference>> dmpExternalReferenceMap = this.collectDmpExternalReferences(dmpExternalReferencesFields, data);
-
-        List<ExternalReference> models = new ArrayList<>();
-        for (ExternalReferenceEntity d : data) {
-            ExternalReference m = new ExternalReference();
-            if (fields.hasField(this.asIndexer(ExternalReference._id))) m.setId(d.getId());
-            if (fields.hasField(this.asIndexer(ExternalReference._label))) m.setLabel(d.getLabel());
-            if (fields.hasField(this.asIndexer(ExternalReference._createdAt))) m.setCreatedAt(d.getCreatedAt());
-            if (fields.hasField(this.asIndexer(ExternalReference._updatedAt))) m.setUpdatedAt(d.getUpdatedAt());
-            if (fields.hasField(this.asIndexer(ExternalReference._isActive))) m.setIsActive(d.getIsActive());
-            if (fields.hasField(this.asIndexer(ExternalReference._definition))) m.setReference(d.getDefinition());
-            if (fields.hasField(this.asIndexer(ExternalReference._reference))) m.setReference(d.getReference());
-            if (fields.hasField(this.asIndexer(ExternalReference._abbreviation))) m.setAbbreviation(d.getAbbreviation());
-            if (fields.hasField(this.asIndexer(ExternalReference._description))) m.setDescription(d.getDescription());
-            if (fields.hasField(this.asIndexer(ExternalReference._source))) m.setSource(d.getSource());
-            if (fields.hasField(this.asIndexer(ExternalReference._sourceType))) m.setSourceType(d.getSourceType());
-            if (fields.hasField(this.asIndexer(ExternalReference._type))) m.setType(d.getType());
-//            if (!userInfoFields.isEmpty() && d.getCreatedBy() != null){
-//                //ToDo
-//            }
-            if (!dmpExternalReferenceMap.isEmpty() && dmpExternalReferenceMap != null && dmpExternalReferenceMap.containsKey(d.getId())) m.setDmpExternalReferences(dmpExternalReferenceMap.get(d.getId()));
-            models.add(m);
-        }
-        this.logger.debug("build {} items", Optional.of(models).map(List::size).orElse(0));
-        return models;
-    }
-
-    private Map<UUID, List<DmpExternalReference>> collectDmpExternalReferences(FieldSet fields, List<ExternalReferenceEntity> datas) throws MyApplicationException {
-        if (fields.isEmpty() || datas.isEmpty()) return null;
-        this.logger.debug("checking related - {}", DmpExternalReference.class.getSimpleName());
-
-        Map<UUID, List<DmpExternalReference>> itemMap = null;
-        FieldSet clone = new BaseFieldSet(fields.getFields()).ensure(this.asIndexer(DmpExternalReference._externalReference, ExternalReference._id));
-        DmpExternalReferenceQuery query = this.queryFactory.query(DmpExternalReferenceQuery.class).authorize(this.authorize).referenceIds(datas.stream().map(x -> x.getId()).distinct().collect(Collectors.toList()));
-        itemMap = this.builderFactory.builder(DmpExternalReferenceBuilder.class).authorize(this.authorize).authorize(this.authorize).asMasterKey(query, clone, x -> x.getExternalReference().getId());
-
-        if (!fields.hasField(this.asIndexer(DmpExternalReference._externalReference, ExternalReference._id))) {
-            itemMap.values().stream().flatMap(List::stream).filter(x -> x != null && x.getExternalReference() != null).map(x -> {
-                x.getExternalReference().setId(null);
-                return x;
-            }).collect(Collectors.toList());
-        }
-        return itemMap;
-    }
-}

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

@@ -0,0 +1,101 @@
+package eu.eudat.model.builder;
+
+import eu.eudat.authorization.AuthorizationFlags;
+import eu.eudat.convention.ConventionService;
+import eu.eudat.data.ReferenceEntity;
+import eu.eudat.model.DmpReference;
+import eu.eudat.model.Reference;
+import eu.eudat.query.DmpReferenceQuery;
+import gr.cite.tools.data.builder.BuilderFactory;
+import gr.cite.tools.data.query.QueryFactory;
+import gr.cite.tools.exception.MyApplicationException;
+import gr.cite.tools.fieldset.BaseFieldSet;
+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.*;
+import java.util.stream.Collectors;
+
+@Component
+@Scope(value = ConfigurableBeanFactory.SCOPE_PROTOTYPE)
+public class ReferenceBuilder extends BaseBuilder<Reference, ReferenceEntity>{
+
+    private final BuilderFactory builderFactory;
+    private final QueryFactory queryFactory;
+    private EnumSet<AuthorizationFlags> authorize = EnumSet.of(AuthorizationFlags.None);
+
+    @Autowired
+    public ReferenceBuilder(
+            ConventionService conventionService,
+            BuilderFactory builderFactory, QueryFactory queryFactory) {
+        super(conventionService, new LoggerService(LoggerFactory.getLogger(ReferenceBuilder.class)));
+        this.builderFactory = builderFactory;
+        this.queryFactory = queryFactory;
+    }
+
+    public ReferenceBuilder authorize(EnumSet<AuthorizationFlags> values) {
+        this.authorize = values;
+        return this;
+    }
+
+    @Override
+    public List<Reference> build(FieldSet fields, List<ReferenceEntity> 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<>();
+
+        //FieldSet userInfoFields = fields.extractPrefixed(this.asPrefix(ExternalReference._createdBy));
+
+        FieldSet dmpReferencesFields = fields.extractPrefixed(this.asPrefix(Reference._dmpExternalReferences));
+        Map<UUID, List<DmpReference>> dmpReferenceMap = this.collectDmpReferences(dmpReferencesFields, data);
+
+        List<Reference> models = new ArrayList<>();
+        for (ReferenceEntity d : data) {
+            Reference m = new Reference();
+            if (fields.hasField(this.asIndexer(Reference._id))) m.setId(d.getId());
+            if (fields.hasField(this.asIndexer(Reference._label))) m.setLabel(d.getLabel());
+            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 (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());
+            if (fields.hasField(this.asIndexer(Reference._source))) m.setSource(d.getSource());
+            if (fields.hasField(this.asIndexer(Reference._sourceType))) m.setSourceType(d.getSourceType());
+            if (fields.hasField(this.asIndexer(Reference._type))) m.setType(d.getType());
+//            if (!userInfoFields.isEmpty() && d.getCreatedBy() != null){
+//                //ToDo
+//            }
+            if (!dmpReferenceMap.isEmpty() && dmpReferenceMap != null && dmpReferenceMap.containsKey(d.getId())) m.setDmpExternalReferences(dmpReferenceMap.get(d.getId()));
+            models.add(m);
+        }
+        this.logger.debug("build {} items", Optional.of(models).map(List::size).orElse(0));
+        return models;
+    }
+
+    private Map<UUID, List<DmpReference>> collectDmpReferences(FieldSet fields, List<ReferenceEntity> datas) throws MyApplicationException {
+        if (fields.isEmpty() || datas.isEmpty()) return null;
+        this.logger.debug("checking related - {}", DmpReference.class.getSimpleName());
+
+        Map<UUID, List<DmpReference>> itemMap = null;
+        FieldSet clone = new BaseFieldSet(fields.getFields()).ensure(this.asIndexer(DmpReference._externalReference, Reference._id));
+        DmpReferenceQuery query = this.queryFactory.query(DmpReferenceQuery.class).authorize(this.authorize).referenceIds(datas.stream().map(x -> x.getId()).distinct().collect(Collectors.toList()));
+        itemMap = this.builderFactory.builder(DmpReferenceBuilder.class).authorize(this.authorize).authorize(this.authorize).asMasterKey(query, clone, x -> x.getExternalReference().getId());
+
+        if (!fields.hasField(this.asIndexer(DmpReference._externalReference, Reference._id))) {
+            itemMap.values().stream().flatMap(List::stream).filter(x -> x != null && x.getExternalReference() != null).map(x -> {
+                x.getExternalReference().setId(null);
+                return x;
+            }).collect(Collectors.toList());
+        }
+        return itemMap;
+    }
+}

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

@@ -41,8 +41,6 @@ public class DmpBlueprintCensor extends BaseCensor {
         this.authService.authorizeForce(Permission.BrowseDmpBlueprint);
         FieldSet definitionFields = fields.extractPrefixed(this.asIndexerPrefix(DmpBlueprint._definition));
         this.censorFactory.censor(DefinitionCensor.class).censor(definitionFields, userId);
-        FieldSet dmpExternalReferencesFields = fields.extractPrefixed(this.asIndexerPrefix(DmpBlueprint._dmpExternalReferences));
-        this.censorFactory.censor(DmpExternalReferenceCensor.class).censor(dmpExternalReferencesFields, userId);
     }
 
 }

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

@@ -42,6 +42,8 @@ public class DmpCensor extends BaseCensor {
 
         FieldSet dmpDescriptionsFields = fields.extractPrefixed(this.asIndexerPrefix(Dmp._dmpDescriptions));
         this.censorFactory.censor(DescriptionCensor.class).censor(dmpDescriptionsFields, userId);
+        FieldSet dmpExternalReferencesFields = fields.extractPrefixed(this.asIndexerPrefix(Dmp._dmpExternalReferences));
+        this.censorFactory.censor(DmpReferenceCensor.class).censor(dmpExternalReferencesFields, userId);
     }
 
 }

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

@@ -2,7 +2,7 @@ package eu.eudat.model.censorship;
 
 import eu.eudat.authorization.Permission;
 import eu.eudat.convention.ConventionService;
-import eu.eudat.model.DmpExternalReference;
+import eu.eudat.model.DmpReference;
 import gr.cite.commons.web.authz.service.AuthorizationService;
 import gr.cite.tools.data.censor.CensorFactory;
 import gr.cite.tools.fieldset.FieldSet;
@@ -17,14 +17,14 @@ import java.util.UUID;
 
 @Component
 @Scope(value = ConfigurableBeanFactory.SCOPE_PROTOTYPE)
-public class DmpExternalReferenceCensor extends BaseCensor {
+public class DmpReferenceCensor extends BaseCensor {
 
-    private static final LoggerService logger = new LoggerService(LoggerFactory.getLogger(DmpExternalReferenceCensor.class));
+    private static final LoggerService logger = new LoggerService(LoggerFactory.getLogger(DmpReferenceCensor.class));
 
     protected final AuthorizationService authService;
     protected final CensorFactory censorFactory;
 
-    public DmpExternalReferenceCensor(ConventionService conventionService,
+    public DmpReferenceCensor(ConventionService conventionService,
                               AuthorizationService authService,
                               CensorFactory censorFactory) {
         super(conventionService);
@@ -38,10 +38,10 @@ public class DmpExternalReferenceCensor extends BaseCensor {
             return;
 
         this.authService.authorizeForce(Permission.BrowseDmpExternalReference);
-        FieldSet dmpFields = fields.extractPrefixed(this.asIndexerPrefix(DmpExternalReference._dmp));
+        FieldSet dmpFields = fields.extractPrefixed(this.asIndexerPrefix(DmpReference._dmp));
-        this.censorFactory.censor(DmpBlueprintCensor.class).censor(dmpFields, userId);
+        this.censorFactory.censor(DmpCensor.class).censor(dmpFields, userId);
-        FieldSet externalReferenceFields = fields.extractPrefixed(this.asIndexerPrefix(DmpExternalReference._externalReference));
+        FieldSet externalReferenceFields = fields.extractPrefixed(this.asIndexerPrefix(DmpReference._externalReference));
-        this.censorFactory.censor(ExternalReferenceCensor.class).censor(externalReferenceFields, userId);
+        this.censorFactory.censor(ReferenceCensor.class).censor(externalReferenceFields, userId);
     }
 
 }

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

@@ -2,7 +2,7 @@ package eu.eudat.model.censorship;
 
 import eu.eudat.authorization.Permission;
 import eu.eudat.convention.ConventionService;
-import eu.eudat.model.ExternalReference;
+import eu.eudat.model.Reference;
 import gr.cite.commons.web.authz.service.AuthorizationService;
 import gr.cite.tools.data.censor.CensorFactory;
 import gr.cite.tools.fieldset.FieldSet;
@@ -17,14 +17,14 @@ import java.util.UUID;
 
 @Component
 @Scope(value = ConfigurableBeanFactory.SCOPE_PROTOTYPE)
-public class ExternalReferenceCensor extends BaseCensor {
+public class ReferenceCensor extends BaseCensor {
 
-    private static final LoggerService logger = new LoggerService(LoggerFactory.getLogger(ExternalReferenceCensor.class));
+    private static final LoggerService logger = new LoggerService(LoggerFactory.getLogger(ReferenceCensor.class));
 
     protected final AuthorizationService authService;
     protected final CensorFactory censorFactory;
 
-    public ExternalReferenceCensor(ConventionService conventionService,
+    public ReferenceCensor(ConventionService conventionService,
                            AuthorizationService authService,
                            CensorFactory censorFactory) {
         super(conventionService);
@@ -38,8 +38,8 @@ public class ExternalReferenceCensor extends BaseCensor {
             return;
 
         this.authService.authorizeForce(Permission.BrowseExternalReference);
-        FieldSet dmpExternalReferencesFields = fields.extractPrefixed(this.asIndexerPrefix(ExternalReference._dmpExternalReferences));
+        FieldSet dmpExternalReferencesFields = fields.extractPrefixed(this.asIndexerPrefix(Reference._dmpExternalReferences));
-        this.censorFactory.censor(DmpExternalReferenceCensor.class).censor(dmpExternalReferencesFields, userId);
+        this.censorFactory.censor(DmpReferenceCensor.class).censor(dmpExternalReferencesFields, userId);
         //ToDo
         //FieldSet definitionFields = fields.extractPrefixed(this.asIndexerPrefix(ExternalReference._createdBy));
         //this.censorFactory.censor(UserInfo.class).censor(definitionFields, userId);

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

@@ -1,7 +1,7 @@
 package eu.eudat.model.deleter;
 
-import eu.eudat.data.DmpExternalReferenceEntity;
+import eu.eudat.data.DmpReferenceEntity;
-import eu.eudat.query.DmpExternalReferenceQuery;
+import eu.eudat.query.DmpReferenceQuery;
 import gr.cite.tools.data.deleter.Deleter;
 import gr.cite.tools.data.deleter.DeleterFactory;
 import gr.cite.tools.data.query.QueryFactory;
@@ -21,9 +21,9 @@ import java.util.UUID;
 
 @Component
 @Scope(value = ConfigurableBeanFactory.SCOPE_PROTOTYPE)
-public class DmpExternalReferenceDeleter implements Deleter {
+public class DmpReferenceDeleter implements Deleter {
 
-    private static final LoggerService logger = new LoggerService(LoggerFactory.getLogger(DmpExternalReferenceDeleter.class));
+    private static final LoggerService logger = new LoggerService(LoggerFactory.getLogger(DmpReferenceDeleter.class));
     private final EntityManager entityManager;
 
     protected final QueryFactory queryFactory;
@@ -31,7 +31,7 @@ public class DmpExternalReferenceDeleter implements Deleter {
     protected final DeleterFactory deleterFactory;
 
     @Autowired
-    public DmpExternalReferenceDeleter(
+    public DmpReferenceDeleter(
             EntityManager entityManager,
             QueryFactory queryFactory,
             DeleterFactory deleterFactory
@@ -43,12 +43,12 @@ public class DmpExternalReferenceDeleter implements Deleter {
 
     public void deleteAndSaveByIds(List<UUID> ids) throws InvalidApplicationException {
         logger.debug(new MapLogEntry("collecting to delete").And("count", Optional.ofNullable(ids).map(List::size).orElse(0)).And("ids", ids));
-        List<DmpExternalReferenceEntity> data = this.queryFactory.query(DmpExternalReferenceQuery.class).ids(ids).collect();
+        List<DmpReferenceEntity> data = this.queryFactory.query(DmpReferenceQuery.class).ids(ids).collect();
         logger.trace("retrieved {} items", Optional.ofNullable(data).map(List::size).orElse(0));
         this.deleteAndSave(data);
     }
 
-    public void deleteAndSave(List<DmpExternalReferenceEntity> data) throws InvalidApplicationException {
+    public void deleteAndSave(List<DmpReferenceEntity> data) throws InvalidApplicationException {
         logger.debug("will delete {} items", Optional.ofNullable(data).map(List::size).orElse(0));
         this.delete(data);
         logger.trace("saving changes");
@@ -56,12 +56,12 @@ public class DmpExternalReferenceDeleter implements Deleter {
         logger.trace("changes saved");
     }
 
-    public void delete(List<DmpExternalReferenceEntity> data) throws InvalidApplicationException {
+    public void delete(List<DmpReferenceEntity> data) throws InvalidApplicationException {
         logger.debug("will delete {} items", Optional.ofNullable(data).map(List::size).orElse(0));
         if (data == null || data.isEmpty())
             return;
 
-        for (DmpExternalReferenceEntity item : data) {
+        for (DmpReferenceEntity item : data) {
             logger.trace("deleting item {}", item.getId());
             logger.trace("updating item");
             this.entityManager.merge(item);

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

@@ -1,8 +1,8 @@
 package eu.eudat.model.deleter;
 
 import eu.eudat.commons.enums.IsActive;
-import eu.eudat.data.ExternalReferenceEntity;
+import eu.eudat.data.ReferenceEntity;
-import eu.eudat.query.ExternalReferenceQuery;
+import eu.eudat.query.ReferenceQuery;
 import gr.cite.tools.data.deleter.Deleter;
 import gr.cite.tools.data.deleter.DeleterFactory;
 import gr.cite.tools.data.query.QueryFactory;
@@ -23,9 +23,9 @@ import java.util.UUID;
 
 @Component
 @Scope(value = ConfigurableBeanFactory.SCOPE_PROTOTYPE)
-public class ExternalReferenceDeleter implements Deleter {
+public class ReferenceDeleter implements Deleter {
 
-    private static final LoggerService logger = new LoggerService(LoggerFactory.getLogger(ExternalReferenceDeleter.class));
+    private static final LoggerService logger = new LoggerService(LoggerFactory.getLogger(ReferenceDeleter.class));
     private final EntityManager entityManager;
 
     protected final QueryFactory queryFactory;
@@ -33,7 +33,7 @@ public class ExternalReferenceDeleter implements Deleter {
     protected final DeleterFactory deleterFactory;
 
     @Autowired
-    public ExternalReferenceDeleter(
+    public ReferenceDeleter(
             EntityManager entityManager,
             QueryFactory queryFactory,
             DeleterFactory deleterFactory
@@ -45,12 +45,12 @@ public class ExternalReferenceDeleter implements Deleter {
 
     public void deleteAndSaveByIds(List<UUID> ids) throws InvalidApplicationException {
         logger.debug(new MapLogEntry("collecting to delete").And("count", Optional.ofNullable(ids).map(List::size).orElse(0)).And("ids", ids));
-        List<ExternalReferenceEntity> data = this.queryFactory.query(ExternalReferenceQuery.class).ids(ids).collect();
+        List<ReferenceEntity> data = this.queryFactory.query(ReferenceQuery.class).ids(ids).collect();
         logger.trace("retrieved {} items", Optional.ofNullable(data).map(List::size).orElse(0));
         this.deleteAndSave(data);
     }
 
-    public void deleteAndSave(List<ExternalReferenceEntity> data) throws InvalidApplicationException {
+    public void deleteAndSave(List<ReferenceEntity> data) throws InvalidApplicationException {
         logger.debug("will delete {} items", Optional.ofNullable(data).map(List::size).orElse(0));
         this.delete(data);
         logger.trace("saving changes");
@@ -58,14 +58,14 @@ public class ExternalReferenceDeleter implements Deleter {
         logger.trace("changes saved");
     }
 
-    public void delete(List<ExternalReferenceEntity> data) throws InvalidApplicationException {
+    public void delete(List<ReferenceEntity> data) throws InvalidApplicationException {
         logger.debug("will delete {} items", Optional.ofNullable(data).map(List::size).orElse(0));
         if (data == null || data.isEmpty())
             return;
 
         Instant now = Instant.now();
 
-        for (ExternalReferenceEntity item : data) {
+        for (ReferenceEntity item : data) {
             logger.trace("deleting item {}", item.getId());
             item.setIsActive(IsActive.Inactive);
             item.setUpdatedAt(now);

dmp-backend/core/src/main/java/eu/eudat/query/DmpReferenceQuery.java

@@ -2,7 +2,7 @@ package eu.eudat.query;
 
 import eu.eudat.authorization.AuthorizationFlags;
 import eu.eudat.commons.scope.user.UserScope;
-import eu.eudat.data.DmpExternalReferenceEntity;
+import eu.eudat.data.DmpReferenceEntity;
 import gr.cite.commons.web.authz.service.AuthorizationService;
 import gr.cite.tools.data.query.FieldResolver;
 import gr.cite.tools.data.query.QueryBase;
@@ -18,7 +18,7 @@ import java.util.*;
 
 @Component
 @Scope(value = ConfigurableBeanFactory.SCOPE_PROTOTYPE)
-public class DmpExternalReferenceQuery extends QueryBase<DmpExternalReferenceEntity> {
+public class DmpReferenceQuery extends QueryBase<DmpReferenceEntity> {
 
     private Collection<UUID> ids;
 
@@ -29,52 +29,52 @@ public class DmpExternalReferenceQuery extends QueryBase<DmpExternalReferenceEnt
     private EnumSet<AuthorizationFlags> authorize = EnumSet.of(AuthorizationFlags.None);
 
 
-    public DmpExternalReferenceQuery ids(UUID value) {
+    public DmpReferenceQuery ids(UUID value) {
         this.ids = List.of(value);
         return this;
     }
 
-    public DmpExternalReferenceQuery ids(UUID... value) {
+    public DmpReferenceQuery ids(UUID... value) {
         this.ids = Arrays.asList(value);
         return this;
     }
 
-    public DmpExternalReferenceQuery ids(Collection<UUID> values) {
+    public DmpReferenceQuery ids(Collection<UUID> values) {
         this.ids = values;
         return this;
     }
 
-    public DmpExternalReferenceQuery dmpIds(UUID value) {
+    public DmpReferenceQuery dmpIds(UUID value) {
         this.dmpIds = List.of(value);
         return this;
     }
 
-    public DmpExternalReferenceQuery dmpIds(UUID... value) {
+    public DmpReferenceQuery dmpIds(UUID... value) {
         this.dmpIds = Arrays.asList(value);
         return this;
     }
 
-    public DmpExternalReferenceQuery dmpIds(Collection<UUID> values) {
+    public DmpReferenceQuery dmpIds(Collection<UUID> values) {
         this.dmpIds = values;
         return this;
     }
 
-    public DmpExternalReferenceQuery referenceIds(UUID value) {
+    public DmpReferenceQuery referenceIds(UUID value) {
         this.referenceIds = List.of(value);
         return this;
     }
 
-    public DmpExternalReferenceQuery referenceIds(UUID... value) {
+    public DmpReferenceQuery referenceIds(UUID... value) {
         this.referenceIds = Arrays.asList(value);
         return this;
     }
 
-    public DmpExternalReferenceQuery referenceIds(Collection<UUID> values) {
+    public DmpReferenceQuery referenceIds(Collection<UUID> values) {
         this.referenceIds = values;
         return this;
     }
 
-    public DmpExternalReferenceQuery authorize(EnumSet<AuthorizationFlags> values) {
+    public DmpReferenceQuery authorize(EnumSet<AuthorizationFlags> values) {
         this.authorize = values;
         return this;
     }
@@ -83,7 +83,7 @@ public class DmpExternalReferenceQuery extends QueryBase<DmpExternalReferenceEnt
 
     private final AuthorizationService authService;
 
-    public DmpExternalReferenceQuery(
+    public DmpReferenceQuery(
             UserScope userScope,
             AuthorizationService authService
     ) {
@@ -92,8 +92,8 @@ public class DmpExternalReferenceQuery extends QueryBase<DmpExternalReferenceEnt
     }
 
     @Override
-    protected Class<DmpExternalReferenceEntity> entityClass() {
+    protected Class<DmpReferenceEntity> entityClass() {
-        return DmpExternalReferenceEntity.class;
+        return DmpReferenceEntity.class;
     }
 
     @Override
@@ -105,19 +105,19 @@ public class DmpExternalReferenceQuery extends QueryBase<DmpExternalReferenceEnt
     protected <X, Y> Predicate applyFilters(QueryContext<X, Y> queryContext) {
         List<Predicate> predicates = new ArrayList<>();
         if (this.ids != null) {
-            CriteriaBuilder.In<UUID> inClause = queryContext.CriteriaBuilder.in(queryContext.Root.get(DmpExternalReferenceEntity._id));
+            CriteriaBuilder.In<UUID> inClause = queryContext.CriteriaBuilder.in(queryContext.Root.get(DmpReferenceEntity._id));
             for (UUID item : this.ids)
                 inClause.value(item);
             predicates.add(inClause);
         }
         if (this.dmpIds != null) {
-            CriteriaBuilder.In<UUID> inClause = queryContext.CriteriaBuilder.in(queryContext.Root.get(DmpExternalReferenceEntity._dmpId));
+            CriteriaBuilder.In<UUID> inClause = queryContext.CriteriaBuilder.in(queryContext.Root.get(DmpReferenceEntity._dmpId));
             for (UUID item : this.ids)
                 inClause.value(item);
             predicates.add(inClause);
         }
         if (this.referenceIds != null) {
-            CriteriaBuilder.In<UUID> inClause = queryContext.CriteriaBuilder.in(queryContext.Root.get(DmpExternalReferenceEntity._referenceId));
+            CriteriaBuilder.In<UUID> inClause = queryContext.CriteriaBuilder.in(queryContext.Root.get(DmpReferenceEntity._referenceId));
             for (UUID item : this.ids)
                 inClause.value(item);
             predicates.add(inClause);
@@ -131,21 +131,21 @@ public class DmpExternalReferenceQuery extends QueryBase<DmpExternalReferenceEnt
     }
 
     @Override
-    protected DmpExternalReferenceEntity convert(Tuple tuple, Set<String> columns) {
+    protected DmpReferenceEntity convert(Tuple tuple, Set<String> columns) {
-        DmpExternalReferenceEntity item = new DmpExternalReferenceEntity();
+        DmpReferenceEntity item = new DmpReferenceEntity();
-        item.setId(QueryBase.convertSafe(tuple, columns, DmpExternalReferenceEntity._id, UUID.class));
+        item.setId(QueryBase.convertSafe(tuple, columns, DmpReferenceEntity._id, UUID.class));
-        item.setReferenceId(QueryBase.convertSafe(tuple, columns, DmpExternalReferenceEntity._dmpId, UUID.class));
+        item.setReferenceId(QueryBase.convertSafe(tuple, columns, DmpReferenceEntity._dmpId, UUID.class));
-        item.setReferenceId(QueryBase.convertSafe(tuple, columns, DmpExternalReferenceEntity._referenceId, UUID.class));
+        item.setReferenceId(QueryBase.convertSafe(tuple, columns, DmpReferenceEntity._referenceId, UUID.class));
-        item.setData(QueryBase.convertSafe(tuple, columns, DmpExternalReferenceEntity._data, String.class));
+        item.setData(QueryBase.convertSafe(tuple, columns, DmpReferenceEntity._data, String.class));
         return item;
     }
 
     @Override
     protected String fieldNameOf(FieldResolver item) {
-        if (item.match(DmpExternalReferenceEntity._id)) return DmpExternalReferenceEntity._id;
+        if (item.match(DmpReferenceEntity._id)) return DmpReferenceEntity._id;
-        else if (item.prefix(DmpExternalReferenceEntity._dmpId)) return DmpExternalReferenceEntity._dmpId;
+        else if (item.prefix(DmpReferenceEntity._dmpId)) return DmpReferenceEntity._dmpId;
-        else if (item.prefix(DmpExternalReferenceEntity._referenceId)) return DmpExternalReferenceEntity._referenceId;
+        else if (item.prefix(DmpReferenceEntity._referenceId)) return DmpReferenceEntity._referenceId;
-        else if (item.match(DmpExternalReferenceEntity._data)) return DmpExternalReferenceEntity._data;
+        else if (item.match(DmpReferenceEntity._data)) return DmpReferenceEntity._data;
         else return null;
     }
 

dmp-backend/core/src/main/java/eu/eudat/query/ReferenceQuery.java

@@ -5,8 +5,7 @@ import eu.eudat.commons.enums.ExternalReferencesType;
 import eu.eudat.commons.enums.IsActive;
 import eu.eudat.commons.enums.SourceType;
 import eu.eudat.commons.scope.user.UserScope;
-import eu.eudat.data.DmpBlueprintEntity;
+import eu.eudat.data.ReferenceEntity;
-import eu.eudat.data.ExternalReferenceEntity;
 import gr.cite.commons.web.authz.service.AuthorizationService;
 import gr.cite.tools.data.query.FieldResolver;
 import gr.cite.tools.data.query.QueryBase;
@@ -23,7 +22,7 @@ import java.util.*;
 
 @Component
 @Scope(value = ConfigurableBeanFactory.SCOPE_PROTOTYPE)
-public class ExternalReferenceQuery extends QueryBase<ExternalReferenceEntity> {
+public class ReferenceQuery extends QueryBase<ReferenceEntity> {
 
     private String like;
 
@@ -39,87 +38,87 @@ public class ExternalReferenceQuery extends QueryBase<ExternalReferenceEntity> {
 
     private EnumSet<AuthorizationFlags> authorize = EnumSet.of(AuthorizationFlags.None);
 
-    public ExternalReferenceQuery like(String value) {
+    public ReferenceQuery like(String value) {
         this.like = value;
         return this;
     }
 
-    public ExternalReferenceQuery ids(UUID value) {
+    public ReferenceQuery ids(UUID value) {
         this.ids = List.of(value);
         return this;
     }
 
-    public ExternalReferenceQuery ids(UUID... value) {
+    public ReferenceQuery ids(UUID... value) {
         this.ids = Arrays.asList(value);
         return this;
     }
 
-    public ExternalReferenceQuery ids(Collection<UUID> values) {
+    public ReferenceQuery ids(Collection<UUID> values) {
         this.ids = values;
         return this;
     }
 
-    public ExternalReferenceQuery isActive(IsActive value) {
+    public ReferenceQuery isActive(IsActive value) {
         this.isActives = List.of(value);
         return this;
     }
 
-    public ExternalReferenceQuery isActive(IsActive... value) {
+    public ReferenceQuery isActive(IsActive... value) {
         this.isActives = Arrays.asList(value);
         return this;
     }
 
-    public ExternalReferenceQuery isActive(Collection<IsActive> values) {
+    public ReferenceQuery isActive(Collection<IsActive> values) {
         this.isActives = values;
         return this;
     }
 
-    public ExternalReferenceQuery externalReferenceTypes(ExternalReferencesType value) {
+    public ReferenceQuery externalReferenceTypes(ExternalReferencesType value) {
         this.externalReferenceTypes = List.of(value);
         return this;
     }
 
-    public ExternalReferenceQuery externalReferenceTypes(ExternalReferencesType... value) {
+    public ReferenceQuery externalReferenceTypes(ExternalReferencesType... value) {
         this.externalReferenceTypes = Arrays.asList(value);
         return this;
     }
 
-    public ExternalReferenceQuery externalReferenceTypes(Collection<ExternalReferencesType> values) {
+    public ReferenceQuery externalReferenceTypes(Collection<ExternalReferencesType> values) {
         this.externalReferenceTypes = values;
         return this;
     }
 
-    public ExternalReferenceQuery excludedIds(Collection<UUID> values) {
+    public ReferenceQuery excludedIds(Collection<UUID> values) {
         this.excludedIds = values;
         return this;
     }
 
-    public ExternalReferenceQuery excludedIds(UUID value) {
+    public ReferenceQuery excludedIds(UUID value) {
         this.excludedIds = List.of(value);
         return this;
     }
 
-    public ExternalReferenceQuery excludedIds(UUID... value) {
+    public ReferenceQuery excludedIds(UUID... value) {
         this.excludedIds = Arrays.asList(value);
         return this;
     }
 
-    public ExternalReferenceQuery sourceTypes(SourceType value) {
+    public ReferenceQuery sourceTypes(SourceType value) {
         this.sourceTypes = List.of(value);
         return this;
     }
 
-    public ExternalReferenceQuery sourceTypes(SourceType... value) {
+    public ReferenceQuery sourceTypes(SourceType... value) {
         this.sourceTypes = Arrays.asList(value);
         return this;
     }
 
-    public ExternalReferenceQuery sourceTypes(Collection<SourceType> values) {
+    public ReferenceQuery sourceTypes(Collection<SourceType> values) {
         this.sourceTypes = values;
         return this;
     }
 
-    public ExternalReferenceQuery authorize(EnumSet<AuthorizationFlags> values) {
+    public ReferenceQuery authorize(EnumSet<AuthorizationFlags> values) {
         this.authorize = values;
         return this;
     }
@@ -128,7 +127,7 @@ public class ExternalReferenceQuery extends QueryBase<ExternalReferenceEntity> {
 
     private final AuthorizationService authService;
 
-    public ExternalReferenceQuery(
+    public ReferenceQuery(
             UserScope userScope,
             AuthorizationService authService
     ) {
@@ -137,8 +136,8 @@ public class ExternalReferenceQuery extends QueryBase<ExternalReferenceEntity> {
     }
 
     @Override
-    protected Class<ExternalReferenceEntity> entityClass() {
+    protected Class<ReferenceEntity> entityClass() {
-        return ExternalReferenceEntity.class;
+        return ReferenceEntity.class;
     }
 
     @Override
@@ -150,36 +149,36 @@ public class ExternalReferenceQuery extends QueryBase<ExternalReferenceEntity> {
     protected <X, Y> Predicate applyFilters(QueryContext<X, Y> queryContext) {
         List<Predicate> predicates = new ArrayList<>();
         if (this.ids != null) {
-            CriteriaBuilder.In<UUID> inClause = queryContext.CriteriaBuilder.in(queryContext.Root.get(ExternalReferenceEntity._id));
+            CriteriaBuilder.In<UUID> inClause = queryContext.CriteriaBuilder.in(queryContext.Root.get(ReferenceEntity._id));
             for (UUID item : this.ids)
                 inClause.value(item);
             predicates.add(inClause);
         }
         if (this.like != null && !this.like.isEmpty()) {
-            predicates.add(queryContext.CriteriaBuilder.or(queryContext.CriteriaBuilder.like(queryContext.Root.get(ExternalReferenceEntity._label), this.like),
+            predicates.add(queryContext.CriteriaBuilder.or(queryContext.CriteriaBuilder.like(queryContext.Root.get(ReferenceEntity._label), this.like),
-                    queryContext.CriteriaBuilder.like(queryContext.Root.get(ExternalReferenceEntity._description), this.like)
+                    queryContext.CriteriaBuilder.like(queryContext.Root.get(ReferenceEntity._description), this.like)
             ));
         }
         if (this.isActives != null) {
-            CriteriaBuilder.In<IsActive> inClause = queryContext.CriteriaBuilder.in(queryContext.Root.get(ExternalReferenceEntity._isActive));
+            CriteriaBuilder.In<IsActive> inClause = queryContext.CriteriaBuilder.in(queryContext.Root.get(ReferenceEntity._isActive));
             for (IsActive item : this.isActives)
                 inClause.value(item);
             predicates.add(inClause);
         }
         if (this.sourceTypes != null) {
-            CriteriaBuilder.In<SourceType> inClause = queryContext.CriteriaBuilder.in(queryContext.Root.get(ExternalReferenceEntity._sourceType));
+            CriteriaBuilder.In<SourceType> inClause = queryContext.CriteriaBuilder.in(queryContext.Root.get(ReferenceEntity._sourceType));
             for (SourceType item : this.sourceTypes)
                 inClause.value(item);
             predicates.add(inClause);
         }
         if (this.externalReferenceTypes != null) {
-            CriteriaBuilder.In<ExternalReferencesType> inClause = queryContext.CriteriaBuilder.in(queryContext.Root.get(ExternalReferenceEntity._type));
+            CriteriaBuilder.In<ExternalReferencesType> inClause = queryContext.CriteriaBuilder.in(queryContext.Root.get(ReferenceEntity._type));
             for (ExternalReferencesType item : this.externalReferenceTypes)
                 inClause.value(item);
             predicates.add(inClause);
         }
         if (this.excludedIds != null) {
-            CriteriaBuilder.In<UUID> notInClause = queryContext.CriteriaBuilder.in(queryContext.Root.get(ExternalReferenceEntity._id));
+            CriteriaBuilder.In<UUID> notInClause = queryContext.CriteriaBuilder.in(queryContext.Root.get(ReferenceEntity._id));
             for (UUID item : this.excludedIds)
                 notInClause.value(item);
             predicates.add(notInClause.not());
@@ -193,38 +192,38 @@ public class ExternalReferenceQuery extends QueryBase<ExternalReferenceEntity> {
     }
 
     @Override
-    protected ExternalReferenceEntity convert(Tuple tuple, Set<String> columns) {
+    protected ReferenceEntity convert(Tuple tuple, Set<String> columns) {
-        ExternalReferenceEntity item = new ExternalReferenceEntity();
+        ReferenceEntity item = new ReferenceEntity();
-        item.setId(QueryBase.convertSafe(tuple, columns, ExternalReferenceEntity._id, UUID.class));
+        item.setId(QueryBase.convertSafe(tuple, columns, ReferenceEntity._id, UUID.class));
-        item.setLabel(QueryBase.convertSafe(tuple, columns, ExternalReferenceEntity._label, String.class));
+        item.setLabel(QueryBase.convertSafe(tuple, columns, ReferenceEntity._label, String.class));
-        item.setDescription(QueryBase.convertSafe(tuple, columns, ExternalReferenceEntity._description, String.class));
+        item.setDescription(QueryBase.convertSafe(tuple, columns, ReferenceEntity._description, String.class));
-        item.setCreatedAt(QueryBase.convertSafe(tuple, columns, ExternalReferenceEntity._createdAt, Instant.class));
+        item.setCreatedAt(QueryBase.convertSafe(tuple, columns, ReferenceEntity._createdAt, Instant.class));
-        item.setUpdatedAt(QueryBase.convertSafe(tuple, columns, ExternalReferenceEntity._updatedAt, Instant.class));
+        item.setUpdatedAt(QueryBase.convertSafe(tuple, columns, ReferenceEntity._updatedAt, Instant.class));
-        item.setIsActive(QueryBase.convertSafe(tuple, columns, ExternalReferenceEntity._isActive, IsActive.class));
+        item.setIsActive(QueryBase.convertSafe(tuple, columns, ReferenceEntity._isActive, IsActive.class));
-        item.setDefinition(QueryBase.convertSafe(tuple, columns, ExternalReferenceEntity._definition, String.class));
+        item.setDefinition(QueryBase.convertSafe(tuple, columns, ReferenceEntity._definition, String.class));
-        item.setAbbreviation(QueryBase.convertSafe(tuple, columns, ExternalReferenceEntity._abbreviation, String.class));
+        item.setAbbreviation(QueryBase.convertSafe(tuple, columns, ReferenceEntity._abbreviation, String.class));
-        item.setReference(QueryBase.convertSafe(tuple, columns, ExternalReferenceEntity._reference, String.class));
+        item.setReference(QueryBase.convertSafe(tuple, columns, ReferenceEntity._reference, String.class));
-        item.setSource(QueryBase.convertSafe(tuple, columns, ExternalReferenceEntity._source, String.class));
+        item.setSource(QueryBase.convertSafe(tuple, columns, ReferenceEntity._source, String.class));
-        item.setSourceType(QueryBase.convertSafe(tuple, columns, ExternalReferenceEntity._sourceType, SourceType.class));
+        item.setSourceType(QueryBase.convertSafe(tuple, columns, ReferenceEntity._sourceType, SourceType.class));
-        item.setType(QueryBase.convertSafe(tuple, columns, ExternalReferenceEntity._type, ExternalReferencesType.class));
+        item.setType(QueryBase.convertSafe(tuple, columns, ReferenceEntity._type, ExternalReferencesType.class));
-        item.setCreatedBy(QueryBase.convertSafe(tuple, columns, ExternalReferenceEntity._createdBy, UUID.class));
+        item.setCreatedBy(QueryBase.convertSafe(tuple, columns, ReferenceEntity._createdBy, UUID.class));
         return item;
     }
 
     @Override
     protected String fieldNameOf(FieldResolver item) {
-        if (item.match(ExternalReferenceEntity._id)) return ExternalReferenceEntity._id;
+        if (item.match(ReferenceEntity._id)) return ReferenceEntity._id;
-        else if (item.match(ExternalReferenceEntity._label)) return ExternalReferenceEntity._label;
+        else if (item.match(ReferenceEntity._label)) return ReferenceEntity._label;
-        else if (item.match(ExternalReferenceEntity._description)) return ExternalReferenceEntity._description;
+        else if (item.match(ReferenceEntity._description)) return ReferenceEntity._description;
-        else if (item.match(ExternalReferenceEntity._createdAt)) return ExternalReferenceEntity._createdAt;
+        else if (item.match(ReferenceEntity._createdAt)) return ReferenceEntity._createdAt;
-        else if (item.match(ExternalReferenceEntity._updatedAt)) return ExternalReferenceEntity._updatedAt;
+        else if (item.match(ReferenceEntity._updatedAt)) return ReferenceEntity._updatedAt;
-        else if (item.match(ExternalReferenceEntity._isActive)) return ExternalReferenceEntity._isActive;
+        else if (item.match(ReferenceEntity._isActive)) return ReferenceEntity._isActive;
-        else if (item.match(ExternalReferenceEntity._definition)) return ExternalReferenceEntity._definition;
+        else if (item.match(ReferenceEntity._definition)) return ReferenceEntity._definition;
-        else if (item.match(ExternalReferenceEntity._abbreviation)) return ExternalReferenceEntity._abbreviation;
+        else if (item.match(ReferenceEntity._abbreviation)) return ReferenceEntity._abbreviation;
-        else if (item.match(ExternalReferenceEntity._reference)) return ExternalReferenceEntity._reference;
+        else if (item.match(ReferenceEntity._reference)) return ReferenceEntity._reference;
-        else if (item.match(ExternalReferenceEntity._source)) return ExternalReferenceEntity._source;
+        else if (item.match(ReferenceEntity._source)) return ReferenceEntity._source;
-        else if (item.match(ExternalReferenceEntity._sourceType)) return ExternalReferenceEntity._sourceType;
+        else if (item.match(ReferenceEntity._sourceType)) return ReferenceEntity._sourceType;
-        else if (item.match(ExternalReferenceEntity._type)) return ExternalReferenceEntity._type;
+        else if (item.match(ReferenceEntity._type)) return ReferenceEntity._type;
         //else if (item.prefix(ExternalReferenceEntity._createdBy)) return ExternalReferenceEntity._createdBy;
         else return null;
     }

dmp-backend/core/src/main/java/eu/eudat/query/lookup/DmpReferenceLookup.java

@@ -1,13 +1,13 @@
 package eu.eudat.query.lookup;
 
-import eu.eudat.query.DmpExternalReferenceQuery;
+import eu.eudat.query.DmpReferenceQuery;
 import gr.cite.tools.data.query.Lookup;
 import gr.cite.tools.data.query.QueryFactory;
 
 import java.util.Collection;
 import java.util.UUID;
 
-public class DmpExternalReferenceLookup extends Lookup {
+public class DmpReferenceLookup extends Lookup {
 
     private Collection<UUID> ids;
 
@@ -16,8 +16,8 @@ public class DmpExternalReferenceLookup extends Lookup {
     private Collection<UUID> referenceIds;
 
 
-    public DmpExternalReferenceQuery enrich(QueryFactory queryFactory) {
+    public DmpReferenceQuery enrich(QueryFactory queryFactory) {
-        DmpExternalReferenceQuery query = queryFactory.query(DmpExternalReferenceQuery.class);
+        DmpReferenceQuery query = queryFactory.query(DmpReferenceQuery.class);
         if (this.ids != null) query.ids(this.ids);
         if (this.dmpIds != null) query.dmpIds(this.dmpIds);
         if (this.referenceIds != null) query.referenceIds(this.referenceIds);

dmp-backend/core/src/main/java/eu/eudat/query/lookup/ReferenceLookup.java

@@ -3,7 +3,7 @@ package eu.eudat.query.lookup;
 import eu.eudat.commons.enums.ExternalReferencesType;
 import eu.eudat.commons.enums.IsActive;
 import eu.eudat.commons.enums.SourceType;
-import eu.eudat.query.ExternalReferenceQuery;
+import eu.eudat.query.ReferenceQuery;
 import gr.cite.tools.data.query.Lookup;
 import gr.cite.tools.data.query.QueryFactory;
 
@@ -11,7 +11,7 @@ import java.util.Collection;
 import java.util.List;
 import java.util.UUID;
 
-public class ExternalReferenceLookup extends Lookup {
+public class ReferenceLookup extends Lookup {
 
     private String like;
 
@@ -73,8 +73,8 @@ public class ExternalReferenceLookup extends Lookup {
         this.externalReferenceTypes = externalReferenceTypes;
     }
 
-    public ExternalReferenceQuery enrich(QueryFactory queryFactory) {
+    public ReferenceQuery enrich(QueryFactory queryFactory) {
-        ExternalReferenceQuery query = queryFactory.query(ExternalReferenceQuery.class);
+        ReferenceQuery query = queryFactory.query(ReferenceQuery.class);
         if (this.like != null) query.like(this.like);
         if (this.isActive != null) query.isActive(this.isActive);
         if (this.externalReferenceTypes != null) query.externalReferenceTypes(this.externalReferenceTypes);

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

@@ -5,19 +5,19 @@ import eu.eudat.authorization.AuthorizationFlags;
 import eu.eudat.authorization.Permission;
 import eu.eudat.commons.enums.ExternalReferencesType;
 import eu.eudat.controllers.BaseController;
-import eu.eudat.data.ExternalReferenceEntity;
+import eu.eudat.data.ReferenceEntity;
 import eu.eudat.logic.proxy.config.exceptions.HugeResultSet;
 import eu.eudat.logic.proxy.config.exceptions.NoURLFound;
 import eu.eudat.logic.services.ApiContext;
-import eu.eudat.logic.services.externalreferences.ExternalReferenceService;
+import eu.eudat.logic.services.references.ReferenceService;
-import eu.eudat.model.ExternalReference;
+import eu.eudat.model.Reference;
-import eu.eudat.model.builder.ExternalReferenceBuilder;
+import eu.eudat.model.builder.ReferenceBuilder;
-import eu.eudat.model.censorship.ExternalReferenceCensor;
+import eu.eudat.model.censorship.ReferenceCensor;
 import eu.eudat.model.result.QueryResult;
 import eu.eudat.models.data.FetcherExternalReference;
 import eu.eudat.models.data.helpers.responses.ResponseItem;
-import eu.eudat.query.ExternalReferenceQuery;
+import eu.eudat.query.ReferenceQuery;
-import eu.eudat.query.lookup.ExternalReferenceLookup;
+import eu.eudat.query.lookup.ReferenceLookup;
 import eu.eudat.types.ApiMessageCode;
 import gr.cite.commons.web.authz.service.AuthorizationService;
 import gr.cite.tools.auditing.AuditService;
@@ -47,29 +47,29 @@ import java.util.UUID;
 
 @RestController
 @RequestMapping(path = {"api/external-references"})
-public class ExternalReferenceController extends BaseController {
+public class ReferenceController extends BaseController {
 
-    private static final LoggerService logger = new LoggerService(LoggerFactory.getLogger(ExternalReferenceController.class));
+    private static final LoggerService logger = new LoggerService(LoggerFactory.getLogger(ReferenceController.class));
     private final BuilderFactory builderFactory;
     private final AuditService auditService;
-    private final ExternalReferenceService externalReferenceService;
+    private final ReferenceService referenceService;
     private final CensorFactory censorFactory;
     private final QueryFactory queryFactory;
     private final MessageSource messageSource;
     private final AuthorizationService authorizationService;
 
     @Autowired
-    public ExternalReferenceController(
+    public ReferenceController(
             ApiContext apiContext,
             BuilderFactory builderFactory,
-            ExternalReferenceService externalReferenceService,
+            ReferenceService referenceService,
             AuditService auditService,
             CensorFactory censorFactory,
             QueryFactory queryFactory,
             MessageSource messageSource, AuthorizationService authorizationService) {
         super(apiContext);
         this.builderFactory = builderFactory;
-        this.externalReferenceService = externalReferenceService;
+        this.referenceService = referenceService;
         this.auditService = auditService;
         this.censorFactory = censorFactory;
         this.queryFactory = queryFactory;
@@ -78,14 +78,14 @@ public class ExternalReferenceController extends BaseController {
     }
 
     @PostMapping("query")
-    public QueryResult<ExternalReference> query(@RequestBody ExternalReferenceLookup lookup) throws MyApplicationException, MyForbiddenException {
+    public QueryResult<Reference> query(@RequestBody ReferenceLookup lookup) throws MyApplicationException, MyForbiddenException {
-        logger.debug("querying {}", ExternalReference.class.getSimpleName());
+        logger.debug("querying {}", Reference.class.getSimpleName());
 
-        this.censorFactory.censor(ExternalReferenceCensor.class).censor(lookup.getProject(), null);
+        this.censorFactory.censor(ReferenceCensor.class).censor(lookup.getProject(), null);
 
-        ExternalReferenceQuery query = lookup.enrich(this.queryFactory).authorize(AuthorizationFlags.OwnerOrPermission);
+        ReferenceQuery query = lookup.enrich(this.queryFactory).authorize(AuthorizationFlags.OwnerOrPermission);
-        List<ExternalReferenceEntity> datas = query.collectAs(lookup.getProject());
+        List<ReferenceEntity> datas = query.collectAs(lookup.getProject());
-        List<ExternalReference> models = this.builderFactory.builder(ExternalReferenceBuilder.class).authorize(AuthorizationFlags.OwnerOrPermission).build(lookup.getProject(), datas);
+        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);
@@ -94,15 +94,15 @@ public class ExternalReferenceController extends BaseController {
     }
 
     @GetMapping("{id}")
-    public ExternalReference get(@PathVariable("id") UUID id, FieldSet fieldSet) throws MyApplicationException, MyForbiddenException, MyNotFoundException {
+    public Reference get(@PathVariable("id") UUID id, FieldSet fieldSet) throws MyApplicationException, MyForbiddenException, MyNotFoundException {
-        logger.debug(new MapLogEntry("retrieving" + eu.eudat.model.ExternalReference.class.getSimpleName()).And("id", id).And("fields", fieldSet));
+        logger.debug(new MapLogEntry("retrieving" + Reference.class.getSimpleName()).And("id", id).And("fields", fieldSet));
 
-        this.censorFactory.censor(ExternalReferenceCensor.class).censor(fieldSet, null);
+        this.censorFactory.censor(ReferenceCensor.class).censor(fieldSet, null);
 
-        ExternalReferenceQuery query = this.queryFactory.query(ExternalReferenceQuery.class).authorize(AuthorizationFlags.OwnerOrPermission).ids(id);
+        ReferenceQuery query = this.queryFactory.query(ReferenceQuery.class).authorize(AuthorizationFlags.OwnerOrPermission).ids(id);
-        ExternalReference model = this.builderFactory.builder(ExternalReferenceBuilder.class).authorize(AuthorizationFlags.OwnerOrPermission).build(fieldSet, query.firstAs(fieldSet));
+        Reference model = this.builderFactory.builder(ReferenceBuilder.class).authorize(AuthorizationFlags.OwnerOrPermission).build(fieldSet, query.firstAs(fieldSet));
         if (model == null)
-            throw new MyNotFoundException(messageSource.getMessage("General_ItemNotFound", new Object[]{id, eu.eudat.model.ExternalReference.class.getSimpleName()}, LocaleContextHolder.getLocale()));
+            throw new MyNotFoundException(messageSource.getMessage("General_ItemNotFound", new Object[]{id, Reference.class.getSimpleName()}, LocaleContextHolder.getLocale()));
 
         this.auditService.track(AuditableAction.External_Reference_Lookup, Map.ofEntries(
                 new AbstractMap.SimpleEntry<String, Object>("id", id),
@@ -120,16 +120,16 @@ public class ExternalReferenceController extends BaseController {
         this.authorizationService.authorizeForce(Permission.AuthenticatedRole);
         ExternalReferencesType externalReferencesType = ExternalReferencesType.of((short) externalType);
 
-        List<FetcherExternalReference> fetcherExternalReferences = this.externalReferenceService.searchExternalReference(externalReferencesType, query, type);
+        List<FetcherExternalReference> fetcherExternalReferences = this.referenceService.searchExternalReference(externalReferencesType, query, type);
         return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<List<FetcherExternalReference>>().status(ApiMessageCode.NO_MESSAGE).payload(fetcherExternalReferences));
     }
 
     @DeleteMapping("{id}")
     @Transactional
     public void delete(@PathVariable("id") UUID id) throws MyForbiddenException, InvalidApplicationException {
-        logger.debug(new MapLogEntry("retrieving" +  ExternalReference.class.getSimpleName()).And("id", id));
+        logger.debug(new MapLogEntry("retrieving" +  Reference.class.getSimpleName()).And("id", id));
 
-        this.externalReferenceService.deleteAndSave(id);
+        this.referenceService.deleteAndSave(id);
 
         this.auditService.track(AuditableAction.External_Reference_Delete, "id", id);
     }

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

@@ -1,4 +1,4 @@
-package eu.eudat.logic.services.externalreferences;
+package eu.eudat.logic.services.references;
 
 import gr.cite.tools.cache.CacheOptions;
 import org.springframework.boot.context.properties.ConfigurationProperties;

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

@@ -1,4 +1,4 @@
-package eu.eudat.logic.services.externalreferences;
+package eu.eudat.logic.services.references;
 
 import eu.eudat.logic.proxy.config.ExternalUrlCriteria;
 import gr.cite.tools.cache.CacheService;

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

@@ -1,4 +1,4 @@
-package eu.eudat.logic.services.externalreferences;
+package eu.eudat.logic.services.references;
 
 import eu.eudat.authorization.Permission;
 import eu.eudat.commons.enums.ExternalReferencesType;
@@ -18,7 +18,7 @@ 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.deleter.ExternalReferenceDeleter;
+import eu.eudat.model.deleter.ReferenceDeleter;
 import eu.eudat.models.data.FetcherExternalReference;
 import eu.eudat.queryable.QueryableList;
 import gr.cite.commons.web.authz.service.AuthorizationService;
@@ -36,9 +36,9 @@ import java.util.*;
 import java.util.stream.Collectors;
 
 @org.springframework.stereotype.Service
-public class ExternalReferenceService {
+public class ReferenceService {
 
-    private static final LoggerService logger = new LoggerService(LoggerFactory.getLogger(ExternalReferenceService.class));
+    private static final LoggerService logger = new LoggerService(LoggerFactory.getLogger(ReferenceService.class));
     private final ApiContext apiContext;
     private final UserScope userScope;
     private final RemoteFetcher remoteFetcher;
@@ -50,7 +50,7 @@ public class ExternalReferenceService {
     private final MessageSource messageSource;
     private final QueryFactory queryFactory;
 
-    public ExternalReferenceService(ApiContext apiContext,
+    public ReferenceService(ApiContext apiContext,
                             UserScope userScope,
                             RemoteFetcher remoteFetcher,
                             EntityManager entityManager,
@@ -77,7 +77,7 @@ public class ExternalReferenceService {
 
         this.authorizationService.authorizeForce(Permission.DeleteExternalReference);
 
-        this.deleterFactory.deleter(ExternalReferenceDeleter.class).deleteAndSaveByIds(List.of(id));
+        this.deleterFactory.deleter(ReferenceDeleter.class).deleteAndSaveByIds(List.of(id));
     }
 
     // external references: