update logging, db configurations

.gitignore

@@ -50,3 +50,4 @@ bin/
 openDMP/dmp-backend/uploads/
 openDMP/dmp-backend/tmp/
 storage/
+logs/

dmp-backend/core/src/main/java/eu/eudat/configurations/typedefinition/DataType.java

@@ -1,13 +0,0 @@
-package eu.eudat.configurations.typedefinition;
-
-public enum DataType {
-    TINY,
-    SHORT,
-    INTEGER,
-    LONG,
-    DOUBLE,
-    FLOAT,
-    DATE,
-    STRING,
-    TEXT
-}

dmp-backend/core/src/main/java/eu/eudat/configurations/typedefinition/DatabaseColumnType.java

@@ -1,5 +0,0 @@
-package eu.eudat.configurations.typedefinition;
-
-public interface DatabaseColumnType {
-    public String getType(DataType dt);
-}

dmp-backend/core/src/main/java/eu/eudat/configurations/typedefinition/PostgreSQLDatabaseColumnType.java

@@ -1,25 +0,0 @@
-package eu.eudat.configurations.typedefinition;
-
-public class PostgreSQLDatabaseColumnType implements DatabaseColumnType {
-
-    public String getType(DataType dt) {
-        switch (dt) {
-            case TINY:
-            case SHORT:
-            case INTEGER:
-                return "integer";
-            case LONG:
-                return "bigint";
-            case FLOAT:
-            case DOUBLE:
-                return "numeric";
-            case DATE:
-                return "timestamp";
-            case STRING:
-                return "character varying(250)";
-            case TEXT:
-                return "text";
-        }
-        return "character varying(250)";
-    }
-}

dmp-backend/core/src/main/java/eu/eudat/configurations/typedefinition/PostgreSQLEnumType.java

@@ -1,31 +0,0 @@
-package eu.eudat.configurations.typedefinition;
-
-import org.hibernate.HibernateException;
-import org.hibernate.engine.spi.SharedSessionContractImplementor;
-
-import java.sql.PreparedStatement;
-import java.sql.SQLException;
-import java.sql.Types;
-
-/**
- * @deprecated hibernate's abstract class is depricated and those type of conversions and checks
- * are done by hibernate itself
- */
-@Deprecated
-public class PostgreSQLEnumType extends org.hibernate.type.EnumType {
-
-    public void nullSafeSet(
-            PreparedStatement st,
-            Object value,
-            int index,
-            SharedSessionContractImplementor session)
-            throws HibernateException, SQLException {
-        st.setObject(
-                index,
-                value != null ?
-                        ((Enum) value).name() :
-                        null,
-                Types.OTHER
-        );
-    }
-}

dmp-backend/core/src/main/java/eu/eudat/configurations/typedefinition/UUIDType.java

@@ -1,118 +0,0 @@
-package eu.eudat.configurations.typedefinition;
-
-import org.hibernate.HibernateException;
-import org.hibernate.engine.spi.SharedSessionContractImplementor;
-import org.hibernate.usertype.UserType;
-
-import java.io.Serializable;
-import java.sql.PreparedStatement;
-import java.sql.ResultSet;
-import java.sql.SQLException;
-import java.sql.Types;
-import java.util.UUID;
-
-/**
- * Currently not used
- */
-public class UUIDType implements UserType<UUID> {
-    private final int[] sqlTypesSupported = new int[]{Types.NUMERIC};
-    private final String CAST_EXCEPTION_TEXT = " cannot be cast to a java.util.UUID";
-
-    public int[] sqlTypes() {
-        return sqlTypesSupported;
-    }
-
-    @Override
-    public int getSqlType() {
-        return sqlTypesSupported[0];
-    }
-
-    public Class<UUID> returnedClass() {
-        return UUID.class;
-    }
-
-    public boolean equals(UUID x, UUID y) throws HibernateException {
-        if (x == null) return y == null;
-        else return x.equals(y);
-    }
-
-    public int hashCode(UUID x) throws HibernateException {
-        return x == null ? -1 : x.hashCode();
-    }
-
-    @Override
-    public UUID nullSafeGet(ResultSet rs, int position, SharedSessionContractImplementor session, Object owner) throws SQLException {
-        assert (position >= 0);
-        Object value = rs.getObject(position);
-        if (value == null) return null;
-
-        UUID uuid = UUID.fromString(rs.getString(position));
-        return rs.wasNull() ? null : uuid;
-    }
-
-    public Object nullSafeGet(ResultSet rs, String[] names, Object owner) throws HibernateException, SQLException {
-        assert (names.length == 1);
-        Object value = rs.getObject(names[0]);
-        if (value == null) return null;
-
-        UUID uuid = UUID.fromString(rs.getString(names[0]));
-        return rs.wasNull() ? null : uuid;
-    }
-
-    public void nullSafeSet(PreparedStatement st, Object value, int index) throws HibernateException, SQLException {
-        if (value == null) {
-            st.setNull(index, Types.NULL);
-            return;
-        }
-
-        if (!UUID.class.isAssignableFrom(value.getClass()))
-            throw new HibernateException(value.getClass().toString() + CAST_EXCEPTION_TEXT);
-
-        UUID uuid = (UUID) value;
-        st.setObject(index, uuid, Types.OTHER);
-    }
-
-    public UUID deepCopy(UUID value) throws HibernateException {
-        if (value == null) return null;
-        return new UUID(value.getMostSignificantBits(), value.getLeastSignificantBits());
-    }
-
-    public boolean isMutable() {
-        return false;
-    }
-
-    public Serializable disassemble(UUID value) throws HibernateException {
-        return value;
-    }
-
-    public UUID assemble(Serializable cached, Object owner) throws HibernateException {
-        return (UUID) cached;
-    }
-
-    public UUID replace(UUID original, Object target, Object owner) throws HibernateException {
-        return original;
-    }
-
-//	public Object nullSafeGet(ResultSet rs, String[] names, SessionImplementor session, Object owner) 
-//			throws HibernateException, SQLException 
-//	{
-//		return nullSafeGet(rs, names, owner);
-//	}
-//
-//	public void nullSafeSet(PreparedStatement st, Object value, int index, SessionImplementor session) 
-//			throws HibernateException, SQLException 
-//	{
-//		nullSafeSet(st, value, index);
-//		
-//	}
-
-    public Object nullSafeGet(ResultSet rs, String[] names, SharedSessionContractImplementor session, Object owner)
-            throws HibernateException, SQLException {
-        return nullSafeGet(rs, names, owner);
-    }
-
-    public void nullSafeSet(PreparedStatement st, UUID value, int index, SharedSessionContractImplementor session)
-            throws HibernateException, SQLException {
-        nullSafeSet(st, value, index);
-    }
-}

dmp-backend/core/src/main/java/eu/eudat/configurations/typedefinition/XMLType.java

@@ -1,95 +0,0 @@
-package eu.eudat.configurations.typedefinition;
-
-import org.hibernate.HibernateException;
-import org.hibernate.engine.spi.SharedSessionContractImplementor;
-import org.hibernate.usertype.UserType;
-
-import java.io.Serializable;
-import java.sql.PreparedStatement;
-import java.sql.ResultSet;
-import java.sql.SQLException;
-import java.sql.Types;
-
-/**
- * Store and retrieve a PostgreSQL "xml" column as a Java string.
- */
-public class XMLType implements UserType<String> {
-
-    private final int[] sqlTypesSupported = new int[]{Types.VARCHAR};
-
-    public int[] sqlTypes() {
-        return sqlTypesSupported;
-    }
-
-    @Override
-    public int getSqlType() {
-        return sqlTypesSupported[0];
-    }
-
-    public Class<String> returnedClass() {
-        return String.class;
-    }
-
-    public boolean equals(String x, String y) throws HibernateException {
-        if (x == null) {
-            return y == null;
-        } else {
-            return x.equals(y);
-        }
-    }
-
-    public int hashCode(String x) throws HibernateException {
-        return x == null ? -1 : x.hashCode();
-    }
-
-    @Override
-    public String nullSafeGet(ResultSet resultSet, int i, SharedSessionContractImplementor sharedSessionContractImplementor, Object o) throws SQLException {
-        assert (i >= 0);
-        String xmldoc = resultSet.getString(i);
-        return resultSet.wasNull() ? null : xmldoc;
-    }
-
-    public Object nullSafeGet(ResultSet rs, String[] names, Object owner) throws HibernateException, SQLException {
-        assert (names.length == 1);
-        String xmldoc = rs.getString(names[0]);
-        return rs.wasNull() ? null : xmldoc;
-    }
-
-    public void nullSafeSet(PreparedStatement st, Object value, int index) throws HibernateException, SQLException {
-        if (value == null) {
-            st.setNull(index, Types.OTHER);
-        } else {
-            st.setObject(index, value, Types.OTHER);
-        }
-    }
-
-    public String deepCopy(String value) throws HibernateException {
-        return value;
-    }
-
-    public boolean isMutable() {
-        return false;
-    }
-
-    public Serializable disassemble(String value) throws HibernateException {
-        return value;
-    }
-
-    public String assemble(Serializable cached, Object owner) throws HibernateException {
-        return (String) cached;
-    }
-
-    public String replace(String original, String target, Object owner) throws HibernateException {
-        return original;
-    }
-
-    public Object nullSafeGet(ResultSet rs, String[] names, SharedSessionContractImplementor session, Object owner)
-            throws HibernateException, SQLException {
-        return nullSafeGet(rs, names, owner);
-    }
-
-    public void nullSafeSet(PreparedStatement st, String value, int index, SharedSessionContractImplementor session) throws HibernateException, SQLException {
-        nullSafeSet(st, value, index);
-    }
-
-}

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

@@ -7,10 +7,10 @@ import eu.eudat.data.converters.enums.DescriptionTemplateStatusConverter;
 import eu.eudat.data.converters.enums.IsActiveConverter;
 import eu.eudat.queryable.queryableentity.DataEntity;
 import jakarta.persistence.*;
-import org.hibernate.annotations.Type;
 
 import java.time.Instant;
-import java.util.*;
+import java.util.List;
+import java.util.UUID;
 
 
 @Entity
@@ -26,8 +26,7 @@ public class DescriptionTemplateEntity implements DataEntity<DescriptionTemplate
     public static final String _label = "label";
     public static final int _labelLength = 250;
 
-    @Type(eu.eudat.configurations.typedefinition.XMLType.class)
+    @Column(name = "\"definition\"", nullable = false)
-    @Column(name = "\"definition\"", columnDefinition = "xml", nullable = false)
     private String definition;
     public static final String _definition = "definition";
 

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

@@ -3,22 +3,11 @@ package eu.eudat.data;
 
 import eu.eudat.commons.enums.DmpBlueprintStatus;
 import eu.eudat.commons.enums.IsActive;
-import eu.eudat.data.converters.DateToUTCConverter;
-import eu.eudat.data.converters.enums.DescriptionTemplateTypeStatusConverter;
 import eu.eudat.data.converters.enums.DmpBlueprintStatusConverter;
 import eu.eudat.data.converters.enums.IsActiveConverter;
-import eu.eudat.data.old.DMP;
-import eu.eudat.data.old.helpers.EntityBinder;
-import eu.eudat.queryable.queryableentity.DataEntity;
-import org.hibernate.annotations.GenericGenerator;
-import org.hibernate.annotations.Type;
-
 import jakarta.persistence.*;
 
 import java.time.Instant;
-import java.util.Date;
-import java.util.List;
-import java.util.Set;
 import java.util.UUID;
 
 
@@ -35,8 +24,7 @@ public class DmpBlueprintEntity {
     public static final String _label = "label";
     public static final int _labelLength = 250;
 
-    @Type(eu.eudat.configurations.typedefinition.XMLType.class)
+    @Column(name = "\"definition\"", nullable = true)
-    @Column(name = "\"definition\"", columnDefinition = "xml", nullable = true)
     private String definition;
     public static final String _definition = "definition";
 

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

@@ -9,6 +9,7 @@ import jakarta.persistence.*;
 import java.time.Instant;
 import java.util.UUID;
 
+@Entity
 @Table(name = "\"DmpUser\"")
 public class DmpUserEntity {
 

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

@@ -7,7 +7,6 @@ import eu.eudat.data.converters.enums.ReferenceSourceTypeConverter;
 import eu.eudat.data.converters.enums.ReferenceTypeConverter;
 import eu.eudat.data.converters.enums.IsActiveConverter;
 import jakarta.persistence.*;
-import org.hibernate.annotations.Type;
 
 import java.time.Instant;
 import java.util.UUID;
@@ -34,8 +33,7 @@ public class ReferenceEntity {
     private String description;
     public static final String _description = "description";
 
-    @Type(eu.eudat.configurations.typedefinition.XMLType.class)
+    @Column(name = "definition")
-    @Column(name = "definition", columnDefinition = "xml")
     private String definition;
     public static final String _definition = "definition";
 

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

@@ -3,7 +3,6 @@ package eu.eudat.data;
 import eu.eudat.commons.enums.IsActive;
 import eu.eudat.data.converters.enums.IsActiveConverter;
 import jakarta.persistence.*;
-import org.hibernate.annotations.Type;
 
 import java.time.Instant;
 import java.util.UUID;
@@ -25,8 +24,7 @@ public class ReferenceTypeEntity {
     private String code;
     public static final String _code = "code";
 
-    @Type(eu.eudat.configurations.typedefinition.XMLType.class)
+    @Column(name = "definition")
-    @Column(name = "definition", columnDefinition = "xml")
     private String definition;
     public static final String _definition = "definition";
 

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

@@ -1,16 +1,11 @@
 package eu.eudat.data;
 
 
-import eu.eudat.commons.enums.DescriptionTemplateStatus;
 import eu.eudat.commons.enums.IsActive;
-import eu.eudat.data.converters.enums.DescriptionTemplateStatusConverter;
 import eu.eudat.data.converters.enums.IsActiveConverter;
-import eu.eudat.queryable.queryableentity.DataEntity;
 import jakarta.persistence.*;
-import org.hibernate.annotations.Type;
 
 import java.time.Instant;
-import java.util.List;
 import java.util.UUID;
 
 

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

@@ -2,7 +2,6 @@ package eu.eudat.data.old;
 
 import eu.eudat.data.old.helpers.EntityBinder;
 import eu.eudat.queryable.queryableentity.DataEntity;
-import org.hibernate.annotations.GenericGenerator;
 
 import jakarta.persistence.*;
 import java.util.List;
@@ -65,7 +64,6 @@ public class Content implements DataEntity<Content, UUID> { //IGNORE ME
 
 	@Id
 	@GeneratedValue
-	@GenericGenerator(name = "uuid2", strategy = "uuid2")
 	@Column(name = "\"Id\"", updatable = false, nullable = false, columnDefinition = "BINARY(16)")
 	private UUID id;
 

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

@@ -6,7 +6,6 @@ import eu.eudat.data.DmpBlueprintEntity;
 import eu.eudat.data.EntityDoiEntity;
 import eu.eudat.data.converters.DateToUTCConverter;
 import eu.eudat.queryable.queryableentity.DataEntity;
-import org.hibernate.annotations.GenericGenerator;
 
 import jakarta.persistence.*;
 import java.util.*;
@@ -90,7 +89,6 @@ public class DMP implements DataEntity<DMP, UUID> {
 
     @Id
     @GeneratedValue
-    @GenericGenerator(name = "uuid2", strategy = "uuid2")
     @Column(name = "\"ID\"", updatable = false, nullable = false, columnDefinition = "BINARY(16)")
     private UUID id;
 

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

@@ -2,7 +2,6 @@ package eu.eudat.data.old;
 
 import eu.eudat.data.DescriptionTemplateEntity;
 import eu.eudat.queryable.queryableentity.DataEntity;
-import org.hibernate.annotations.GenericGenerator;
 
 import jakarta.persistence.*;
 import java.util.List;
@@ -14,7 +13,6 @@ public class DMPDatasetProfile implements DataEntity<DMPDatasetProfile, UUID> {
 
     @Id
     @GeneratedValue
-    @GenericGenerator(name = "uuid2", strategy = "uuid2")
     @Column(name = "\"ID\"", updatable = false, nullable = false, columnDefinition = "BINARY(16)")
     private UUID id;
 

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

@@ -1,8 +1,6 @@
 package eu.eudat.data.old;
 
 
-import org.hibernate.annotations.GenericGenerator;
-
 import jakarta.persistence.*;
 import java.io.Serializable;
 import java.util.UUID;
@@ -14,7 +12,6 @@ public class DMPOrganisation {
 
     @Id
     @GeneratedValue
-    @GenericGenerator(name = "uuid2", strategy = "uuid2")
     @Column(name = "\"ID\"", updatable = false, nullable = false, columnDefinition = "BINARY(16)")
     private UUID id;
 

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

@@ -1,8 +1,6 @@
 package eu.eudat.data.old;
 
 
-import org.hibernate.annotations.GenericGenerator;
-import org.hibernate.annotations.Type;
 
 import jakarta.persistence.*;
 import java.util.UUID;
@@ -14,7 +12,6 @@ public class DMPResearcher {
 
     @Id
     @GeneratedValue
-    @GenericGenerator(name = "uuid2", strategy = "uuid2")
     @Column(name = "\"ID\"", updatable = false, nullable = false, columnDefinition = "BINARY(16)")
     private UUID id;
 

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

@@ -3,13 +3,11 @@ package eu.eudat.data.old;
 
 import eu.eudat.data.old.helpers.EntityBinder;
 import eu.eudat.queryable.queryableentity.DataEntity;
-import org.hibernate.annotations.Type;
 
 import jakarta.persistence.*;
 import java.io.Serializable;
 import java.util.Date;
 import java.util.List;
-import java.util.Set;
 import java.util.UUID;
 
 @Entity
@@ -32,8 +30,7 @@ public class DataRepository implements Serializable, DataEntity<DataRepository,
 	@Column(name = "\"Uri\"")
 	private String uri;
 
-	@Type(eu.eudat.configurations.typedefinition.XMLType.class)
+	@Column(name = "\"Definition\"")
-	@Column(name = "\"Definition\"", columnDefinition = "xml")
 	private String definition;
 
 	@Column(name = "\"Status\"", nullable = false)

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

@@ -2,7 +2,6 @@ package eu.eudat.data.old;
 
 import eu.eudat.data.converters.DateToUTCConverter;
 import eu.eudat.queryable.queryableentity.DataEntity;
-import org.hibernate.annotations.GenericGenerator;
 
 import jakarta.persistence.*;
 import java.util.Date;
@@ -15,7 +14,6 @@ public class EmailConfirmation implements DataEntity<EmailConfirmation, UUID> {
 
 	@Id
 	@GeneratedValue
-	@GenericGenerator(name = "uuid2", strategy = "uuid2")
 	@Column(name = "\"ID\"", updatable = false, nullable = false)
 	private UUID id;
 

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

@@ -1,7 +1,6 @@
 package eu.eudat.data.old;
 
 import eu.eudat.queryable.queryableentity.DataEntity;
-import org.hibernate.annotations.Type;
 
 import jakarta.persistence.*;
 import java.util.Date;
@@ -73,12 +72,10 @@ public class Funder implements DataEntity<Funder, UUID> {
 	@Column(name = "\"Label\"")
 	private String label;
 
-	@Type(eu.eudat.configurations.typedefinition.XMLType.class)
+	@Column(name = "\"Reference\"", nullable = true)
-	@Column(name = "\"Reference\"", columnDefinition = "xml", nullable = true)
 	private String reference;
 
-	@Type(eu.eudat.configurations.typedefinition.XMLType.class)
+	@Column(name = "\"Definition\"", nullable = true)
-	@Column(name = "\"Definition\"", columnDefinition = "xml", nullable = true)
 	private String definition;
 
 	@Column(name = "\"Status\"", nullable = false)

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

@@ -4,7 +4,6 @@ package eu.eudat.data.old;
 import eu.eudat.data.converters.DateToUTCConverter;
 import eu.eudat.data.old.helpers.EntityBinder;
 import eu.eudat.queryable.queryableentity.DataEntity;
-import org.hibernate.annotations.Type;
 
 import jakarta.persistence.*;
 import java.util.*;
@@ -101,7 +100,6 @@ public class Grant implements DataEntity<Grant, UUID> {
 	@Column(name = "\"Uri\"")
 	private String uri;
 
-	@Type(eu.eudat.configurations.typedefinition.XMLType.class)
 	@Column(name = "\"Definition\"", columnDefinition = "xml", nullable = true)
 	private String definition;
 

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

@@ -2,8 +2,6 @@ package eu.eudat.data.old;
 
 import eu.eudat.data.old.helpers.EntityBinder;
 import eu.eudat.queryable.queryableentity.DataEntity;
-import org.hibernate.annotations.GenericGenerator;
-import org.hibernate.annotations.Type;
 
 import jakarta.persistence.*;
 import java.util.List;
@@ -16,7 +14,6 @@ public class Invitation implements DataEntity<Invitation, UUID> {
 
 	@Id
 	@GeneratedValue
-	@GenericGenerator(name = "uuid2", strategy = "uuid2")
 	@Column(name = "\"Id\"", updatable = false, nullable = false)
 	private UUID id;
 
@@ -37,8 +34,7 @@ public class Invitation implements DataEntity<Invitation, UUID> {
 	@Column(name = "\"AcceptedInvitation\"", nullable = false)
 	private boolean acceptedInvitation;
 
-	@Type(eu.eudat.configurations.typedefinition.XMLType.class)
+	@Column(name = "\"Properties\"", nullable = true)
-	@Column(name = "\"Properties\"", columnDefinition = "xml", nullable = true)
 	private String properties;
 
 	public UUID getId() {

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

@@ -3,7 +3,6 @@ package eu.eudat.data.old;
 import eu.eudat.data.converters.DateToUTCConverter;
 import eu.eudat.data.old.helpers.EntityBinder;
 import eu.eudat.queryable.queryableentity.DataEntity;
-import org.hibernate.annotations.GenericGenerator;
 
 import jakarta.persistence.*;
 import java.util.Date;
@@ -16,7 +15,6 @@ public class Lock implements DataEntity<Lock, UUID> {
 
 	@Id
 	@GeneratedValue
-	@GenericGenerator(name = "uuid2", strategy = "uuid2")
 	@Column(name = "id", updatable = false, nullable = false, columnDefinition = "BINARY(16)")
 	private UUID id;
 

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

@@ -5,7 +5,6 @@ import eu.eudat.commons.enums.old.notification.ContactType;
 import eu.eudat.commons.enums.old.notification.NotificationType;
 import eu.eudat.commons.enums.old.notification.NotifyState;
 import eu.eudat.queryable.queryableentity.DataEntity;
-import org.hibernate.annotations.GenericGenerator;
 
 import jakarta.persistence.*;
 import java.util.Date;
@@ -18,7 +17,6 @@ public class Notification implements DataEntity<Notification, UUID> {
 
 	@Id
 	@GeneratedValue
-	@GenericGenerator(name = "uuid2", strategy = "uuid2")
 	@Column(name = "id", updatable = false, nullable = false, columnDefinition = "BINARY(16)")
 	private UUID id;
 

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

@@ -3,8 +3,6 @@ package eu.eudat.data.old;
 import eu.eudat.data.converters.DateToUTCConverter;
 import eu.eudat.data.old.helpers.EntityBinder;
 import eu.eudat.queryable.queryableentity.DataEntity;
-import org.hibernate.annotations.GenericGenerator;
-import org.hibernate.annotations.Type;
 
 import jakarta.persistence.*;
 import java.io.Serializable;
@@ -25,7 +23,6 @@ public class Organisation implements Serializable, DataEntity<Organisation,UUID>
 
     @Id
     @GeneratedValue
-    @GenericGenerator(name = "uuid2", strategy = "uuid2")
     @Column(name = "\"ID\"", updatable = false, nullable = false, columnDefinition = "BINARY(16)")
     private UUID id;
 
@@ -35,15 +32,13 @@ public class Organisation implements Serializable, DataEntity<Organisation,UUID>
     @Column(name = "\"Abbreviation\"")
     private String abbreviation;
 
-    @Type(eu.eudat.configurations.typedefinition.XMLType.class)
+    @Column(name = "\"Reference\"", nullable = true)
-    @Column(name = "\"Reference\"", columnDefinition = "xml", nullable = true)
     private String reference;
 
     @Column(name = "\"Uri\"")
     private String uri;
 
-    @Type(eu.eudat.configurations.typedefinition.XMLType.class)
+    @Column(name = "\"Definition\"", nullable = true)
-    @Column(name = "\"Definition\"", columnDefinition = "xml", nullable = true)
     private String definition;
 
     @OneToMany(fetch = FetchType.LAZY)

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

@@ -3,7 +3,6 @@ package eu.eudat.data.old;
 import eu.eudat.data.converters.DateToUTCConverter;
 import eu.eudat.data.old.helpers.EntityBinder;
 import eu.eudat.queryable.queryableentity.DataEntity;
-import org.hibernate.annotations.Type;
 
 import jakarta.persistence.*;
 import java.util.*;
@@ -80,14 +79,13 @@ public class Project implements DataEntity<Project, UUID> {
 	@Column(name = "\"Abbreviation\"")
 	private String abbreviation;
 
-	@Column(name = "\"Reference\"", columnDefinition = "xml", nullable = true)
+	@Column(name = "\"Reference\"", nullable = true)
 	private String reference;
 
 	@Column(name = "\"Uri\"")
 	private String uri;
 
-	@Type(eu.eudat.configurations.typedefinition.XMLType.class)
+	@Column(name = "\"Definition\"", nullable = true)
-	@Column(name = "\"Definition\"", columnDefinition = "xml", nullable = true)
 	private String definition;
 
 	@Column(name = "\"StartDate\"", nullable = false)

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

@@ -5,7 +5,6 @@ import eu.eudat.data.DescriptionEntity;
 import eu.eudat.data.converters.DateToUTCConverter;
 import eu.eudat.data.old.helpers.EntityBinder;
 import eu.eudat.queryable.queryableentity.DataEntity;
-import org.hibernate.annotations.Type;
 
 import jakarta.persistence.*;
 import java.util.Date;
@@ -34,8 +33,7 @@ public class Registry implements DataEntity<Registry, UUID> {
 	@Column(name = "\"Uri\"")
 	private String uri;
 
-	@Type(eu.eudat.configurations.typedefinition.XMLType.class)
+	@Column(name = "\"Definition\"", nullable = true)
-	@Column(name = "\"Definition\"", columnDefinition = "xml", nullable = true)
 	private String definition;
 
 	@Transient

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

@@ -4,7 +4,6 @@ package eu.eudat.data.old;
 import eu.eudat.data.converters.DateToUTCConverter;
 import eu.eudat.data.old.helpers.EntityBinder;
 import eu.eudat.queryable.queryableentity.DataEntity;
-import org.hibernate.annotations.Type;
 
 import jakarta.persistence.*;
 import java.util.Date;
@@ -18,8 +17,6 @@ import java.util.UUID;
 public class Researcher implements DataEntity<Researcher, UUID> {
 
 	@Id
-	/*@GeneratedValue
-	@GenericGenerator(name = "uuid2", strategy = "uuid2")*/
 	@Column(name = "\"ID\"", updatable = false, nullable = false, columnDefinition = "BINARY(16)")
 	private UUID id;
 
@@ -32,12 +29,10 @@ public class Researcher implements DataEntity<Researcher, UUID> {
 	@Column(name = "\"PrimaryEmail\"")
 	private String primaryEmail;
 
-	@Type(eu.eudat.configurations.typedefinition.XMLType.class)
+	@Column(name = "\"Definition\"", nullable = true)
-	@Column(name = "\"Definition\"", columnDefinition = "xml", nullable = true)
 	private String definition;
 
-	@Type(eu.eudat.configurations.typedefinition.XMLType.class)
+	@Column(name = "\"Reference\"", nullable = true)
-	@Column(name = "\"Reference\"", columnDefinition = "xml", nullable = true)
 	private String reference;
 
 

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

@@ -3,7 +3,6 @@ package eu.eudat.data.old;
 
 import eu.eudat.data.converters.DateToUTCConverter;
 import eu.eudat.queryable.queryableentity.DataEntity;
-import org.hibernate.annotations.Type;
 
 import jakarta.persistence.*;
 import java.util.Date;
@@ -32,8 +31,7 @@ public class Service implements DataEntity<Service, UUID> {
 	@Column(name = "\"Uri\"")
 	private String uri;
 
-	@Type(eu.eudat.configurations.typedefinition.XMLType.class)
+	@Column(name = "\"Definition\"", nullable = false)
-	@Column(name = "\"Definition\"", columnDefinition = "xml", nullable = false)
 	private String definition;
 
 	@Column(name = "\"Status\"", nullable = false)

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

@@ -2,7 +2,6 @@ package eu.eudat.data.old;
 
 import eu.eudat.data.old.helpers.EntityBinder;
 import eu.eudat.queryable.queryableentity.DataEntity;
-import org.hibernate.annotations.GenericGenerator;
 
 import jakarta.persistence.*;
 import java.util.LinkedList;
@@ -49,7 +48,6 @@ public class UserDMP implements DataEntity<UserDMP, UUID> {
 
 	@Id
 	@GeneratedValue
-	@GenericGenerator(name = "uuid2", strategy = "uuid2")
 	@Column(name = "id", updatable = false, nullable = false, columnDefinition = "BINARY(16)")
 	private UUID id;
 

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

@@ -4,8 +4,6 @@ import eu.eudat.data.CredentialEntity;
 import eu.eudat.data.converters.DateToUTCConverter;
 import eu.eudat.data.old.helpers.EntityBinder;
 import eu.eudat.queryable.queryableentity.DataEntity;
-import org.hibernate.annotations.GenericGenerator;
-import org.hibernate.annotations.Type;
 
 import jakarta.persistence.*;
 import java.util.*;
@@ -22,7 +20,6 @@ public class UserInfo implements DataEntity<UserInfo, UUID> {
 
 	@Id
 	@GeneratedValue
-	@GenericGenerator(name = "uuid2", strategy = "uuid2")
 	@Column(name = "id", updatable = false, nullable = false, columnDefinition = "BINARY(16)")
 	private UUID id;
 	public final static String _id = "id";
@@ -65,7 +62,6 @@ public class UserInfo implements DataEntity<UserInfo, UUID> {
 	public final static String _lastloggedin = "lastloggedin";
 
 
-	@Type(eu.eudat.configurations.typedefinition.XMLType.class)
 	@Column(name = "additionalinfo", nullable = true)
 	private String additionalinfo;
 	public final static String _additionalinfo = "additionalinfo";

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

@@ -2,7 +2,6 @@ package eu.eudat.data.old;
 
 import eu.eudat.data.old.helpers.EntityBinder;
 import eu.eudat.queryable.queryableentity.DataEntity;
-import org.hibernate.annotations.GenericGenerator;
 
 import jakarta.persistence.*;
 import java.util.List;
@@ -15,7 +14,6 @@ public class UserRole implements DataEntity<UserRole, UUID> {
 
 	@Id
 	@GeneratedValue
-	@GenericGenerator(name = "uuid2", strategy = "uuid2")
 	@Column(name = "\"Id\"", updatable = false, nullable = false, columnDefinition = "BINARY(16)")
 	private UUID id;
 

dmp-backend/core/src/main/java/eu/eudat/model/mapper/deposit/DMPToDepositMapper.java

@@ -6,9 +6,9 @@ import eu.eudat.data.DescriptionEntity;
 import eu.eudat.data.old.*;
 import eu.eudat.depositinterface.models.*;
 import eu.eudat.commons.types.xml.XmlBuilder;
-import jakarta.transaction.Transactional;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import org.springframework.transaction.annotation.Transactional;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
 import org.w3c.dom.Node;

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

@@ -24,9 +24,7 @@ import java.util.*;
 @Component
 @Scope(value = ConfigurableBeanFactory.SCOPE_PROTOTYPE)
 public class DescriptionQuery extends QueryBase<DescriptionEntity> {
-
     private String like;
-
     private Collection<UUID> ids;
     private DmpDescriptionTemplateQuery dmpDescriptionTemplateQuery;
     private Collection<UUID> excludedIds;
@@ -61,8 +59,6 @@ public class DescriptionQuery extends QueryBase<DescriptionEntity> {
         return this;
     }
 
-
-
     public DescriptionQuery dmpDescriptionTemplateSubQuery(DmpDescriptionTemplateQuery subQuery) {
         this.dmpDescriptionTemplateQuery = subQuery;
         return this;

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

@@ -4,6 +4,7 @@ import eu.eudat.authorization.AuthorizationFlags;
 import eu.eudat.commons.enums.IsActive;
 import eu.eudat.data.DescriptionEntity;
 import eu.eudat.data.DmpDescriptionTemplateEntity;
+import eu.eudat.data.DmpEntity;
 import eu.eudat.model.DmpDescriptionTemplate;
 import gr.cite.tools.data.query.FieldResolver;
 import gr.cite.tools.data.query.QueryBase;
@@ -11,6 +12,7 @@ import gr.cite.tools.data.query.QueryContext;
 import jakarta.persistence.Tuple;
 import jakarta.persistence.criteria.CriteriaBuilder;
 import jakarta.persistence.criteria.Predicate;
+import jakarta.persistence.criteria.Subquery;
 import org.springframework.beans.factory.config.ConfigurableBeanFactory;
 import org.springframework.context.annotation.Scope;
 import org.springframework.stereotype.Component;
@@ -25,6 +27,7 @@ public class DmpDescriptionTemplateQuery extends QueryBase<DmpDescriptionTemplat
     private Collection<UUID> ids;
 
     private Collection<UUID> dmpIds;
+    private DmpQuery dmpQuery;
 
     private Collection<UUID> descriptionTemplateIds;
 
@@ -95,6 +98,11 @@ public class DmpDescriptionTemplateQuery extends QueryBase<DmpDescriptionTemplat
         return this;
     }    
     
+    public DmpDescriptionTemplateQuery dmpSubQuery(DmpQuery subQuery) {
+        this.dmpQuery = subQuery;
+        return this;
+    }
+
     public DmpDescriptionTemplateQuery descriptionTemplateIds(UUID value) {
         this.descriptionTemplateIds = List.of(value);
         return this;
@@ -126,7 +134,7 @@ public class DmpDescriptionTemplateQuery extends QueryBase<DmpDescriptionTemplat
 
     @Override
     protected Boolean isFalseQuery() {
-        return this.isEmpty(this.ids) || this.isEmpty(this.excludedIds) || this.isEmpty(this.isActives) || this.isEmpty(this.dmpIds) || this.isEmpty(this.descriptionTemplateIds);
+        return this.isEmpty(this.ids)|| this.isFalseQuery(this.dmpQuery) || this.isEmpty(this.excludedIds) || this.isEmpty(this.isActives) || this.isEmpty(this.dmpIds) || this.isEmpty(this.descriptionTemplateIds);
     }
 
     @Override
@@ -139,11 +147,16 @@ public class DmpDescriptionTemplateQuery extends QueryBase<DmpDescriptionTemplat
             predicates.add(inClause);
         }
         if (this.excludedIds != null) {
-            CriteriaBuilder.In<UUID> notInClause = queryContext.CriteriaBuilder.in(queryContext.Root.get(DescriptionEntity._id));
+            CriteriaBuilder.In<UUID> notInClause = queryContext.CriteriaBuilder.in(queryContext.Root.get(DmpDescriptionTemplateEntity._id));
             for (UUID item : this.excludedIds)
                 notInClause.value(item);
             predicates.add(notInClause.not());
         }
+        if (this.dmpQuery != null) {
+            Subquery<DmpEntity> subQuery = queryContext.Query.subquery(this.dmpQuery.entityClass());
+            this.applySubQuery(this.dmpQuery, queryContext.CriteriaBuilder, subQuery);
+            predicates.add(queryContext.CriteriaBuilder.in(queryContext.Root.get(DmpDescriptionTemplateEntity._dmpId)).value(subQuery));
+        }
         if (this.dmpIds != null) {
             CriteriaBuilder.In<UUID> inClause = queryContext.CriteriaBuilder.in(queryContext.Root.get(DmpDescriptionTemplateEntity._dmpId));
             for (UUID item : this.dmpIds)

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

@@ -1,8 +1,12 @@
 package eu.eudat.query;
 
 import eu.eudat.authorization.AuthorizationFlags;
+import eu.eudat.authorization.Permission;
+import eu.eudat.commons.enums.DmpAccessType;
 import eu.eudat.commons.enums.DmpUserRole;
 import eu.eudat.commons.scope.user.UserScope;
+import eu.eudat.data.DmpDescriptionTemplateEntity;
+import eu.eudat.data.DmpEntity;
 import eu.eudat.data.DmpUserEntity;
 import eu.eudat.model.DmpUser;
 import gr.cite.commons.web.authz.service.AuthorizationService;
@@ -12,6 +16,7 @@ import gr.cite.tools.data.query.QueryContext;
 import jakarta.persistence.Tuple;
 import jakarta.persistence.criteria.CriteriaBuilder;
 import jakarta.persistence.criteria.Predicate;
+import jakarta.persistence.criteria.Subquery;
 import org.springframework.beans.factory.config.ConfigurableBeanFactory;
 import org.springframework.context.annotation.Scope;
 import org.springframework.stereotype.Component;
@@ -121,6 +126,26 @@ public class DmpUserQuery extends QueryBase<DmpUserEntity> {
         return this.isEmpty(this.ids) || this.isEmpty(this.dmpIds) || this.isEmpty(this.userIds);
     }
 
+    @Override
+    protected <X, Y> Predicate applyAuthZ(QueryContext<X, Y> queryContext) {
+        if (this.authorize.contains(AuthorizationFlags.None)) return null;
+        if (this.authorize.contains(AuthorizationFlags.Permission) && this.authService.authorize(Permission.BrowseDmp)) return null;
+        UUID ownerId = null;
+        if (this.authorize.contains(AuthorizationFlags.Owner)) ownerId = this.userScope.getUserIdSafe();
+
+        List<Predicate> predicates = new ArrayList<>();
+        if (ownerId != null) {
+            predicates.add(queryContext.CriteriaBuilder.equal(queryContext.Root.get(DmpUserEntity._user), ownerId));
+            
+        }
+        if (predicates.size() > 0) {
+            Predicate[] predicatesArray = predicates.toArray(new Predicate[0]);
+            return queryContext.CriteriaBuilder.and(predicatesArray);
+        } else {
+            return queryContext.CriteriaBuilder.or(); //Creates a false query
+        }
+    }
+    
     @Override
     protected <X, Y> Predicate applyFilters(QueryContext<X, Y> queryContext) {
         List<Predicate> predicates = new ArrayList<>();

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

@@ -15,6 +15,7 @@ public class DmpDescriptionTemplateLookup extends Lookup {
     private List<UUID> ids;
     private List<UUID> dmpIds;
     private List<UUID> descriptionTemplateIds;
+    private DmpLookup dmpSubQuery;
 
     private List<UUID> excludedIds;
 
@@ -60,6 +61,14 @@ public class DmpDescriptionTemplateLookup extends Lookup {
         this.descriptionTemplateIds = descriptionTemplateIds;
     }
 
+    public DmpLookup getDmpSubQuery() {
+        return dmpSubQuery;
+    }
+
+    public void setDmpSubQuery(DmpLookup dmpSubQuery) {
+        this.dmpSubQuery = dmpSubQuery;
+    }
+
     public DmpDescriptionTemplateQuery enrich(QueryFactory queryFactory) {
         DmpDescriptionTemplateQuery query = queryFactory.query(DmpDescriptionTemplateQuery.class);
         if (this.ids != null) query.ids(this.ids);
@@ -67,6 +76,7 @@ public class DmpDescriptionTemplateLookup extends Lookup {
         if (this.descriptionTemplateIds != null) query.ids(this.descriptionTemplateIds);
         if (this.excludedIds != null) query.excludedIds(this.excludedIds);
         if (this.isActive != null) query.isActive(this.isActive);
+        if (this.dmpSubQuery != null) query.dmpSubQuery(this.dmpSubQuery.enrich(queryFactory));
 
         this.enrichCommon(query);
 

dmp-backend/data/src/main/java/eu/eudat/data/dao/databaselayer/service/DatabaseService.java

@@ -6,8 +6,8 @@ import eu.eudat.queryable.QueryableList;
 import eu.eudat.queryable.queryableentity.DataEntity;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
+import org.springframework.transaction.annotation.Transactional;
 
-import jakarta.transaction.Transactional;
 import java.util.Set;
 
 

dmp-backend/data/src/main/java/eu/eudat/data/dao/entities/DMPDaoImpl.java

@@ -12,10 +12,10 @@ import eu.eudat.queryable.types.SelectionField;
 import eu.eudat.types.grant.GrantStateType;
 import jakarta.persistence.criteria.Join;
 import jakarta.persistence.criteria.JoinType;
-import jakarta.transaction.Transactional;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.scheduling.annotation.Async;
 import org.springframework.stereotype.Component;
+import org.springframework.transaction.annotation.Transactional;
 
 import javax.management.InvalidApplicationException;
 import java.util.Arrays;

dmp-backend/pom.xml

@@ -99,6 +99,7 @@
         <dependency>
             <groupId>org.hibernate.orm</groupId>
             <artifactId>hibernate-core</artifactId>
+            <version>6.3.1.Final</version>
         </dependency>
 
         <dependency>

dmp-backend/web/pom.xml

@@ -102,7 +102,10 @@
         <dependency>
             <groupId>org.postgresql</groupId>
             <artifactId>postgresql</artifactId>
-            <version>42.6.0</version>
+        </dependency>
+        <dependency>
+            <groupId>org.hibernate.orm</groupId>
+            <artifactId>hibernate-core</artifactId>
         </dependency>
 
         <!--<dependency>

dmp-backend/web/src/main/java/eu/eudat/EuDatApplication.java

@@ -22,6 +22,8 @@ import org.springframework.scheduling.annotation.EnableAsync;
         "gr.cite.tools", 
         "gr.cite.commons"
 })
+@EntityScan({
+        "eu.eudat.data"})
 @EnableAsync
 public class EuDatApplication extends SpringBootServletInitializer {
 

dmp-backend/web/src/main/java/eu/eudat/configurations/DevelDatabaseConfiguration.java

@@ -1,73 +0,0 @@
-package eu.eudat.configurations;
-
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.boot.context.properties.ConfigurationProperties;
-import org.springframework.boot.jdbc.DataSourceBuilder;
-import org.springframework.context.annotation.*;
-import org.springframework.core.env.Environment;
-import org.springframework.dao.annotation.PersistenceExceptionTranslationPostProcessor;
-import org.springframework.orm.jpa.JpaTransactionManager;
-import org.springframework.orm.jpa.JpaVendorAdapter;
-import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
-import org.springframework.orm.jpa.vendor.HibernateJpaVendorAdapter;
-import org.springframework.transaction.PlatformTransactionManager;
-import org.springframework.transaction.annotation.EnableTransactionManagement;
-
-import jakarta.persistence.EntityManagerFactory;
-
-import javax.sql.DataSource;
-import java.util.Properties;
-
-@Configuration
-@EnableTransactionManagement
-@Profile("devel")
-@ComponentScan(basePackages = {"eu.eudat.data"})
-public class DevelDatabaseConfiguration {
-
-    @Autowired
-    private Environment env;
-
-    @Bean
-    public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
-        LocalContainerEntityManagerFactoryBean em = new LocalContainerEntityManagerFactoryBean();
-        em.setDataSource(dataSource());
-        em.setPackagesToScan("eu.eudat.data");
-        JpaVendorAdapter vendorAdapter = new HibernateJpaVendorAdapter();
-        em.setJpaVendorAdapter(vendorAdapter);
-        em.setJpaProperties(additionalProperties());
-        return em;
-    }
-
-    @Bean
-    @Primary
-    @ConfigurationProperties(prefix = "spring.datasource")
-    public DataSource dataSource() {
-        return DataSourceBuilder
-                .create()
-                .username(env.getProperty("database.username"))
-                .password(env.getProperty("database.password"))
-                .url(env.getProperty("database.url"))
-                .driverClassName(env.getProperty("database.driver-class-name"))
-                .build();
-    }
-
-    @Bean
-    public PlatformTransactionManager transactionManager(EntityManagerFactory emf) {
-        JpaTransactionManager transactionManager = new JpaTransactionManager();
-        transactionManager.setEntityManagerFactory(emf);
-        return transactionManager;
-    }
-
-    @Bean
-    public PersistenceExceptionTranslationPostProcessor exceptionTranslation() {
-        return new PersistenceExceptionTranslationPostProcessor();
-    }
-
-    private Properties additionalProperties() {
-        Properties properties = new Properties();
-        properties.setProperty("hibernate.dialect", "org.hibernate.dialect.PostgreSQLDialect");
-        properties.setProperty("hibernate.show_sql", "false");
-        properties.setProperty("hibernate.temp.use_jdbc_metadata_defaults", "false");
-        return properties;
-    }
-}

dmp-backend/web/src/main/java/eu/eudat/configurations/ProductionDatabaseConfiguration.java

@@ -1,76 +0,0 @@
-package eu.eudat.configurations;
-
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.context.annotation.Bean;
-import org.springframework.context.annotation.ComponentScan;
-import org.springframework.context.annotation.Configuration;
-import org.springframework.context.annotation.Profile;
-import org.springframework.core.env.Environment;
-import org.springframework.dao.annotation.PersistenceExceptionTranslationPostProcessor;
-import org.springframework.jdbc.datasource.DriverManagerDataSource;
-import org.springframework.orm.jpa.JpaTransactionManager;
-import org.springframework.orm.jpa.JpaVendorAdapter;
-import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
-import org.springframework.orm.jpa.vendor.HibernateJpaVendorAdapter;
-import org.springframework.transaction.PlatformTransactionManager;
-import org.springframework.transaction.annotation.EnableTransactionManagement;
-
-import jakarta.persistence.EntityManagerFactory;
-import javax.sql.DataSource;
-import java.util.Properties;
-
-/**
- * Created by ikalyvas on 2/9/2018.
- */
-@Configuration
-@EnableTransactionManagement
-@Profile({ "production", "staging", "docker" })
-@ComponentScan(basePackages = {"eu.eudat.data.entities"})
-public class ProductionDatabaseConfiguration {
-
-    @Autowired
-    private Environment env;
-
-    @Bean
-    public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
-        LocalContainerEntityManagerFactoryBean em = new LocalContainerEntityManagerFactoryBean();
-        em.setDataSource(dataSource());
-        em.setPackagesToScan(new String[]{"eu.eudat.data.entities"});
-        JpaVendorAdapter vendorAdapter = new HibernateJpaVendorAdapter();
-        em.setJpaVendorAdapter(vendorAdapter);
-        em.setJpaProperties(additionalProperties());
-
-        return em;
-    }
-
-    @Bean
-    public DataSource dataSource() {
-        DriverManagerDataSource dataSource = new DriverManagerDataSource();
-        dataSource.setDriverClassName(env.getProperty("database.driver-class-name"));
-        dataSource.setUrl(env.getProperty("database.url"));
-        dataSource.setUsername(env.getProperty("database.username"));
-        dataSource.setPassword(env.getProperty("database.password"));
-        return dataSource;
-    }
-
-    @Bean
-    public PlatformTransactionManager transactionManager(EntityManagerFactory emf) {
-        JpaTransactionManager transactionManager = new JpaTransactionManager();
-        transactionManager.setEntityManagerFactory(emf);
-
-        return transactionManager;
-    }
-
-    @Bean
-    public PersistenceExceptionTranslationPostProcessor exceptionTranslation() {
-        return new PersistenceExceptionTranslationPostProcessor();
-    }
-
-    private Properties additionalProperties() {
-        Properties properties = new Properties();
-        properties.setProperty("hibernate.dialect", "org.hibernate.dialect.PostgreSQL92Dialect");
-        properties.setProperty("hibernate.show_sql", "true");
-        properties.setProperty("hibernate.temp.use_jdbc_metadata_defaults", "false");
-        return properties;
-    }
-}

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

@@ -1,2 +0,0 @@
-audit:
-  enable: false

dmp-backend/web/src/main/resources/config/db-devel.yml

@@ -3,3 +3,8 @@ spring:
     maxIdle: 10
     minIdle: 5
     maxActive: 10
+  jpa:
+    show-sql: true
+    properties:
+      hibernate:
+        format_sql: true

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

@@ -1,6 +1,27 @@
-database:
+#database:
-  driver-class-name: org.postgresql.Driver
+#  driver-class-name: org.postgresql.Driver
-  lock-fail-interval: 120000
+#  lock-fail-interval: 120000
+#  url: ${DB_URL:}
+#  username: ${DB_USER:}
+#  password: ${DB_PASS:}
+spring:
+  jpa:
+    properties:
+      hibernate:
+        ddl-auto: validate
+        dialect: org.hibernate.dialect.PostgreSQLDialect
+    hibernate:
+      naming:
+        physical-strategy: org.hibernate.boot.model.naming.PhysicalNamingStrategyStandardImpl
+        implicit-strategy: org.springframework.boot.orm.jpa.hibernate.SpringImplicitNamingStrategy
+  datasource:
     url: ${DB_URL:}
     username: ${DB_USER:}
     password: ${DB_PASS:}
+    driver-class-name: org.postgresql.Driver
+    hikari:
+      connection-timeout: 30000
+      minimum-idle: 3
+      maximum-pool-size: 10
+      idle-timeout: 600000
+      max-lifetime: 1800000

dmp-backend/web/src/main/resources/config/logging-devel.yml

@@ -0,0 +1,36 @@
+logging:
+  config: classpath:logging/logback-${spring.profiles.active}.xml
+  context:
+    request:
+      requestIdKey: req.id
+      requestRemoteHostKey: req.remoteHost
+      requestUriKey: req.requestURI
+      requestQueryStringKey: req.queryString
+      requestUrlKey : req.requestURL
+      requestMethodKey: req.method
+      requestUserAgentKey: req.userAgent
+      requestForwardedForKey: req.xForwardedFor
+      requestSchemeKey: req.scheme
+      requestRemoteAddressKey: req.remoteAddr
+      requestRemotePortKey: req.remotePort
+      requestRemoteUserKey: req.remoteUser
+    principal:
+      subjectKey: usr.subject
+      nameKey: usr.name
+      clientKey: usr.client
+audit:
+  enable: true
+  requestRemoteHostKey: req.remoteHost
+  requestUriKey: req.requestURI
+  requestQueryStringKey: req.queryString
+  requestUrlKey : req.requestURL
+  requestMethodKey: req.method
+  requestUserAgentKey: req.userAgent
+  requestForwardedForKey: req.xForwardedFor
+  requestSchemeKey: req.scheme
+  requestRemoteAddressKey: req.remoteAddr
+  requestRemotePortKey: req.remotePort
+  requestRemoteUserKey: req.remoteUser
+  principalSubjectKey: usr.subject
+  principalNameKey: usr.name
+  principalClientKey: usr.client

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

@@ -1,2 +1,35 @@
 logging:
-  config: classpath:logging/logback-${spring.profiles.active}.xml
+  context:
+    request:
+      requestIdKey: req.id
+      requestRemoteHostKey: req.remoteHost
+      requestUriKey: req.requestURI
+      requestQueryStringKey: req.queryString
+      requestUrlKey : req.requestURL
+      requestMethodKey: req.method
+      requestUserAgentKey: req.userAgent
+      requestForwardedForKey: req.xForwardedFor
+      requestSchemeKey: req.scheme
+      requestRemoteAddressKey: req.remoteAddr
+      requestRemotePortKey: req.remotePort
+      requestRemoteUserKey: req.remoteUser
+    principal:
+      subjectKey: usr.subject
+      nameKey: usr.name
+      clientKey: usr.client
+audit:
+  enable: true
+  requestRemoteHostKey: req.remoteHost
+  requestUriKey: req.requestURI
+  requestQueryStringKey: req.queryString
+  requestUrlKey : req.requestURL
+  requestMethodKey: req.method
+  requestUserAgentKey: req.userAgent
+  requestForwardedForKey: req.xForwardedFor
+  requestSchemeKey: req.scheme
+  requestRemoteAddressKey: req.remoteAddr
+  requestRemotePortKey: req.remotePort
+  requestRemoteUserKey: req.remoteUser
+  principalSubjectKey: usr.subject
+  principalNameKey: usr.name
+  principalClientKey: usr.client

dmp-backend/web/src/main/resources/logging/logback-devel.xml

@@ -1,33 +1,66 @@
 <configuration debug="true">
     <include resource="org/springframework/boot/logging/logback/defaults.xml"/>
     <appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender">
-        <encoder>
+        <encoder class="ch.qos.logback.classic.encoder.PatternLayoutEncoder">
-            <pattern>${CONSOLE_LOG_PATTERN}</pattern>
+            <Pattern>%date{ISO8601} [%thread] %-5level %logger{36} [%X{req.id}] - %message%n</Pattern>
         </encoder>
     </appender>
 
-    <appender name="FILE" class="ch.qos.logback.core.rolling.RollingFileAppender">
+    <appender name="TROUBLESHOOTING" class="ch.qos.logback.core.rolling.RollingFileAppender">
-        <file>${user.home}/openDMP/logs/openDMP.log</file>
+        <file>logs/logging.log</file>
         <rollingPolicy class="ch.qos.logback.core.rolling.TimeBasedRollingPolicy">
-            <fileNamePattern>${user.home}/openDMP/logs/openDMP-%d{yyyy-MM-dd}.%i.log</fileNamePattern>
+            <fileNamePattern>logs/logging.%d{yyyy-MM-dd}.%i.log</fileNamePattern>
             <timeBasedFileNamingAndTriggeringPolicy class="ch.qos.logback.core.rolling.SizeAndTimeBasedFNATP">
                 <maxFileSize>100MB</maxFileSize>
             </timeBasedFileNamingAndTriggeringPolicy>
-            <maxHistory>30</maxHistory>
+            <maxHistory>15</maxHistory>
-            <totalSizeCap>3GB</totalSizeCap>
         </rollingPolicy>
-        <encoder>
+        <encoder class="ch.qos.logback.classic.encoder.PatternLayoutEncoder">
-            <pattern>${FILE_LOG_PATTERN}</pattern>
+            <Pattern>%date{ISO8601} [%thread] %-5level %logger{36} [%X{req.id}] - %message%n</Pattern>
         </encoder>
     </appender>
 
-    <logger name="eu.eudat" level="DEBUG" additivity="false">
+    <appender name="AUDITING" class="ch.qos.logback.core.rolling.RollingFileAppender">
-        <appender-ref ref="FILE"/>
+        <file>logs/auditing.log</file>
+        <rollingPolicy class="ch.qos.logback.core.rolling.TimeBasedRollingPolicy">
+            <fileNamePattern>logs/auditing.%d{yyyy-MM-dd}.%i.log</fileNamePattern>
+            <timeBasedFileNamingAndTriggeringPolicy class="ch.qos.logback.core.rolling.SizeAndTimeBasedFNATP">
+                <maxFileSize>100MB</maxFileSize>
+            </timeBasedFileNamingAndTriggeringPolicy>
+            <maxHistory>15</maxHistory>
+        </rollingPolicy>
+        <encoder class="ch.qos.logback.classic.encoder.PatternLayoutEncoder">
+            <Pattern>%date{ISO8601} - %X{req.id} - %message%n</Pattern>
+        </encoder>
+    </appender>
+
+
+    <logger name="org.springframework.web" level="INFO" additivity="false">
+        <appender-ref ref="TROUBLESHOOTING"/>
         <appender-ref ref="STDOUT"/>
     </logger>
-
+    <logger name="org.hibernate" level="INFO" additivity="false">
-    <root level="info" additivity="false">
+        <appender-ref ref="TROUBLESHOOTING"/>
-        <appender-ref ref="FILE"/>
+        <appender-ref ref="STDOUT"/>
+    </logger>
+    <logger name="gr.cite" level="DEBUG" additivity="false">
+        <appender-ref ref="TROUBLESHOOTING"/>
+        <appender-ref ref="STDOUT"/>
+    </logger>
+    <logger name="eu.eudat" level="DEBUG" additivity="false">
+        <appender-ref ref="TROUBLESHOOTING"/>
+        <appender-ref ref="STDOUT"/>
+    </logger>
+    <logger name="org.springframework.data.elasticsearch.client.WIRE" level="TRACE" additivity="false">
+        <appender-ref ref="TROUBLESHOOTING"/>
+        <appender-ref ref="STDOUT"/>
+    </logger>
+    <logger name="audit" level="INFO" additivity="false">
+        <appender-ref ref="AUDITING"/>
+        <appender-ref ref="STDOUT"/>
+    </logger>
+    <root level="info">
+        <appender-ref ref="TROUBLESHOOTING"/>
         <appender-ref ref="STDOUT"/>
     </root>
 </configuration>

dmp-backend/web/src/main/resources/logging/logback-docker.xml

@@ -1,33 +0,0 @@
-<configuration debug="false">
-    <include resource="org/springframework/boot/logging/logback/defaults.xml"/>
-    <appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender">
-        <encoder>
-            <pattern>${CONSOLE_LOG_PATTERN}</pattern>
-        </encoder>
-    </appender>
-
-    <appender name="FILE" class="ch.qos.logback.core.rolling.RollingFileAppender">
-        <file>logs/openDMP.log</file>
-        <rollingPolicy class="ch.qos.logback.core.rolling.TimeBasedRollingPolicy">
-            <fileNamePattern>logs/openDMP-%d{yyyy-MM-dd}.%i.log</fileNamePattern>
-            <timeBasedFileNamingAndTriggeringPolicy class="ch.qos.logback.core.rolling.SizeAndTimeBasedFNATP">
-                <maxFileSize>100MB</maxFileSize>
-            </timeBasedFileNamingAndTriggeringPolicy>
-            <maxHistory>30</maxHistory>
-            <totalSizeCap>3GB</totalSizeCap>
-        </rollingPolicy>
-        <encoder>
-            <pattern>${FILE_LOG_PATTERN}</pattern>
-        </encoder>
-    </appender>
-
-    <logger name="eu.eudat" level="DEBUG" additivity="false">
-        <appender-ref ref="FILE"/>
-        <appender-ref ref="STDOUT"/>
-    </logger>
-
-    <root level="info" additivity="false">
-        <appender-ref ref="FILE"/>
-        <appender-ref ref="STDOUT"/>
-    </root>
-</configuration>

dmp-backend/web/src/main/resources/logging/logback-production.xml

@@ -1,33 +0,0 @@
-<configuration debug="false">
-    <include resource="org/springframework/boot/logging/logback/defaults.xml"/>
-    <appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender">
-        <encoder>
-            <pattern>${CONSOLE_LOG_PATTERN}</pattern>
-        </encoder>
-    </appender>
-
-    <appender name="FILE" class="ch.qos.logback.core.rolling.RollingFileAppender">
-        <file>logs/openDMP.log</file>
-        <rollingPolicy class="ch.qos.logback.core.rolling.TimeBasedRollingPolicy">
-            <fileNamePattern>logs/openDMP-%d{yyyy-MM-dd}.%i.log</fileNamePattern>
-            <timeBasedFileNamingAndTriggeringPolicy class="ch.qos.logback.core.rolling.SizeAndTimeBasedFNATP">
-                <maxFileSize>100MB</maxFileSize>
-            </timeBasedFileNamingAndTriggeringPolicy>
-            <maxHistory>30</maxHistory>
-            <totalSizeCap>3GB</totalSizeCap>
-        </rollingPolicy>
-        <encoder>
-            <pattern>${FILE_LOG_PATTERN}</pattern>
-        </encoder>
-    </appender>
-
-    <logger name="eu.eudat" level="INFO" additivity="false">
-        <appender-ref ref="FILE"/>
-        <appender-ref ref="STDOUT"/>
-    </logger>
-
-    <root level="info" additivity="false">
-        <appender-ref ref="FILE"/>
-        <appender-ref ref="STDOUT"/>
-    </root>
-</configuration>