Merge remote-tracking branch 'origin/update-configs' into update-configs

# Conflicts:
#	dmp-backend/web/src/main/java/eu/eudat/logic/mapper/prefilling/PrefillingMapper.java

ELK.Docker/logstash/Dockerfile

@@ -16,5 +16,5 @@ FROM docker.elastic.co/logstash/logstash:${ELK_VERSION}
 
 # Add your logstash plugins setup here
 # Example: RUN logstash-plugin install logstash-filter-json
-RUN logstash-plugin update logstash-input-beats
-RUN logstash-plugin update logstash-filter-grok
+#RUN logstash-plugin update logstash-input-beats
+#RUN logstash-plugin update logstash-filter-grok

ELK.Docker/shared/config-elk/logstash/pipeline/open_dmp_send_to_elastic.conf

@@ -2,18 +2,11 @@ input {
 	pipeline { address => open_dmp_send_to_elastic }
 }
 
-filter {
-}
-
 output {   
 	elasticsearch {
 		hosts => "elasticsearch:9200"
-		user => elastic
-		password =>
 		index => "opendmp.logs"
-		#manage_template => true
-		#template => "/usr/share/logstash/templates/audit/openDMP.json"
-		#template_name => "cite.elas.openDMP-audit*" 
-		#template_overwrite => true
+		user => elastic
+		password => ""
 		}
 }

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

@@ -11,6 +11,8 @@ import eu.eudat.queryable.QueryableList;
 import eu.eudat.queryable.types.FieldSelectionType;
 import eu.eudat.queryable.types.SelectionField;
 import eu.eudat.types.grant.GrantStateType;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.scheduling.annotation.Async;
 import org.springframework.stereotype.Component;
@@ -25,6 +27,7 @@ import java.util.concurrent.CompletableFuture;
 
 @Component("datasetDao")
 public class DatasetDaoImpl extends DatabaseAccess<Dataset> implements DatasetDao {
+    private static final Logger logger = LoggerFactory.getLogger(DatasetDaoImpl.class);
 
     @Autowired
     public DatasetDaoImpl(DatabaseService<Dataset> databaseService) { super(databaseService); }
@@ -99,6 +102,7 @@ public class DatasetDaoImpl extends DatabaseAccess<Dataset> implements DatasetDa
 
     @Override
     public Dataset createOrUpdate(Dataset item) {
+        logger.info("I'm Here " + item.getLabel());
         return getDatabaseService().createOrUpdate(item, Dataset.class);
     }
 

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

@@ -11,7 +11,6 @@ import eu.eudat.types.grant.GrantStateType;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.scheduling.annotation.Async;
 import org.springframework.stereotype.Component;
-import schemasMicrosoftComOfficeOffice.LeftDocument;
 
 import javax.persistence.criteria.JoinType;
 import java.util.Date;

dmp-backend/elastic/src/main/java/eu/eudat/elastic/repository/ElasticRepository.java

@@ -17,6 +17,7 @@ import java.io.IOException;
  */
 public abstract class ElasticRepository<T extends ElasticEntity,C extends Criteria> implements Repository<T,C> {
     private static final Logger logger = LoggerFactory.getLogger(ElasticRepository.class);
+    private final ObjectMapper mapper;
     private RestHighLevelClient client;
 
     public RestHighLevelClient getClient() {
@@ -32,10 +33,10 @@ public abstract class ElasticRepository<T extends ElasticEntity,C extends Criter
             logger.warn("Unable to connect to Elastic Services");
             this.client = null;
         }
+        this.mapper = new ObjectMapper();
     }
 
     public  <T> T transformFromString(String value, Class<T> tClass) {
-        ObjectMapper mapper = new ObjectMapper();
         T item = null;
         try {
             item = mapper.readValue(value, tClass);

dmp-backend/pom.xml

@@ -10,7 +10,7 @@
     <parent>
         <groupId>org.springframework.boot</groupId>
         <artifactId>spring-boot-starter-parent</artifactId>
-        <version>2.5.2</version>
+        <version>2.6.6</version>
     </parent>
 
     <modules>
@@ -27,166 +27,168 @@
         <java.version>1.8</java.version>
 
         <dmp-backend-commons.version>0.0.1-SNAPSHOT</dmp-backend-commons.version>
-        <org.springframework.version>5.3.8</org.springframework.version>
+        <!--<org.springframework.version>5.3.8</org.springframework.version>-->
         <!-- 		<org.springframeweu.eudat.logic.securityrity.version>3.2.10.RELEASE</org.springframeweu.eudat.logic.securityrity.version> -->
-        <org.springframework.security.version>5.3.10.RELEASE</org.springframework.security.version>
+        <!--        <org.springframework.security.version>5.3.10.RELEASE</org.springframework.security.version>-->
         <!--<com.sun.jersey.version>1.19.1</com.sun.jersey.version>-->
         <!--
                 <org.apache.tomcat.tomcat-jdbc.version>7.0.35</org.apache.tomcat.tomcat-jdbc.version>
         -->
         <!--<com.fasterxml.jackson>2.9.0</com.fasterxml.jackson>-->
 
-        <hibernate.version>5.5.3.Final</hibernate.version>
+        <!--        <hibernate.version>5.5.3.Final</hibernate.version>-->
 
-        <commons-codec.version>1.9</commons-codec.version>
-        <org.junit.version>4.11</org.junit.version>
-        <log4j.version>1.2.17</log4j.version>
+        <!--        <commons-codec.version>1.9</commons-codec.version>-->
+        <!--        <org.junit.version>4.11</org.junit.version>-->
+        <!--        <log4j.version>1.2.17</log4j.version>-->
         <log4j2.version>2.15.0</log4j2.version>
-        <slf4j.version>1.7.12</slf4j.version>
+        <!--        <slf4j.version>1.7.12</slf4j.version>-->
         <!--<jetty.version>11.0.5
         </jetty.version>--> <!-- Adapt this to a version found on http://repo.maven.apache.org/maven2/org/eclipse/jetty/jetty-maven-plugin/ -->
-        <logback.version>1.2.3</logback.version>
+        <!--        <logback.version>1.2.3</logback.version>-->
         <!-- <javax.inject.version>1</javax.inject.version>-->
         <!--<javax.servlet.servlet-api.version>3.0.1</javax.servlet.servlet-api.version>-->
+        <apache.poi.version>5.2.2</apache.poi.version>
+        <jackson.version>2.12.3</jackson.version>
+        <elasticsearch.version>7.6.2</elasticsearch.version>
+        <jaxb.version>2.3.0</jaxb.version>
+        <caffeine.version>2.9.0</caffeine.version>
+        <google.api.version>1.33.4</google.api.version>
+        <json.path.version>2.4.0</json.path.version>
+        <postgresql.version>42.2.22</postgresql.version>
+        <social.facebook.version>2.0.3.RELEASE</social.facebook.version>
+        <social.linkedin.version>1.0.2.RELEASE</social.linkedin.version>
+        <social.twitter.version>1.1.2.RELEASE</social.twitter.version>
+        <apache.commons.lang3.version>3.12.0</apache.commons.lang3.version>
     </properties>
 
     <dependencies>
-
-        <dependency>
-            <groupId>org.json</groupId>
-            <artifactId>json</artifactId>
-            <version>20160810</version>
-        </dependency>
-        <dependency>
+        <!-- Core Spring Boot Dependencies -->
+        <!--<dependency>
             <groupId>org.springframework</groupId>
             <artifactId>spring-context-support</artifactId>
             <version>${org.springframework.version}</version>
-        </dependency>
+        </dependency>-->
         <dependency>
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter-data-jpa</artifactId>
         </dependency>
 
-        <!-- https://mvnrepository.com/artifact/org.elasticsearch/elasticsearch -->
-        <dependency>
-            <groupId>org.elasticsearch</groupId>
-            <artifactId>elasticsearch</artifactId>
-            <version>7.7.0</version>
-            <exclusions>
-                <exclusion>
-                    <groupId>org.apache.httpcomponents</groupId>
-                    <artifactId>httpclient</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>org.apache.httpcomponents</groupId>
-                    <artifactId>httpcore</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>org.apache.httpcomponents</groupId>
-                    <artifactId>httpcore-nio</artifactId>
-                </exclusion>
-            </exclusions>
-        </dependency>
-
-        <dependency>
-            <groupId>org.apache.httpcomponents</groupId>
-            <artifactId>httpclient</artifactId>
-            <version>4.5.12</version>
-        </dependency>
-
-        <dependency>
-            <groupId>org.apache.httpcomponents</groupId>
-            <artifactId>httpcore-nio</artifactId>
-            <version>4.4.13</version>
-        </dependency>
-
-        <dependency>
-            <groupId>org.apache.httpcomponents</groupId>
-            <artifactId>httpcore</artifactId>
-            <version>4.4.13</version>
-        </dependency>
-
-        <dependency>
-            <groupId>org.elasticsearch.client</groupId>
-            <artifactId>elasticsearch-rest-high-level-client</artifactId>
-            <version>7.6.0</version>
-        </dependency>
-        <dependency>
-            <groupId>org.hibernate</groupId>
-            <artifactId>hibernate-core</artifactId>
-            <version>${hibernate.version}</version>
-        </dependency>
-
         <dependency>
             <groupId>org.hibernate</groupId>
             <artifactId>hibernate-c3p0</artifactId>
             <version>${hibernate.version}</version>
         </dependency>
 
+        <!-- jdbc Driver -->
+        <dependency>
+            <groupId>org.postgresql</groupId>
+            <artifactId>postgresql</artifactId>
+            <version>${postgresql.version}</version>
+        </dependency>
+
+        <!-- Elasticsearch -->
+        <!-- https://mvnrepository.com/artifact/org.elasticsearch/elasticsearch -->
+        <dependency>
+            <groupId>org.elasticsearch</groupId>
+            <artifactId>elasticsearch</artifactId>
+            <version>${elasticsearch.version}</version>
+        </dependency>
+
+        <dependency>
+            <groupId>org.elasticsearch.client</groupId>
+            <artifactId>elasticsearch-rest-high-level-client</artifactId>
+            <version>${elasticsearch.version}</version>
+        </dependency>
+
+        <!-- Autocomplete cache -->
+        <dependency>
+            <groupId>com.github.ben-manes.caffeine</groupId>
+            <artifactId>caffeine</artifactId>
+            <version>${caffeine.version}</version>
+        </dependency>
+
+        <!-- Used for Google login ONLY -->
         <!-- https://mvnrepository.com/artifact/com.google.api-client/google-api-client -->
         <dependency>
             <groupId>com.google.api-client</groupId>
             <artifactId>google-api-client</artifactId>
-            <version>1.23.0</version>
+            <version>${google.api.version}</version>
         </dependency>
+
+        <!-- facebook Login -->
+        <dependency>
+            <groupId>org.springframework.social</groupId>
+            <artifactId>spring-social-facebook</artifactId>
+            <version>${social.facebook.version}</version>
+        </dependency>
+
+        <!-- linkedin Login -->
+        <dependency>
+            <groupId>org.springframework.social</groupId>
+            <artifactId>spring-social-linkedin</artifactId>
+            <version>${social.linkedin.version}</version>
+        </dependency>
+
+        <!-- twitter login-->
+        <dependency>
+            <groupId>org.springframework.social</groupId>
+            <artifactId>spring-social-twitter</artifactId>
+            <version>${social.twitter.version}</version>
+        </dependency>
+        <!-- Used for Remote Fetcher -->
         <!-- https://mvnrepository.com/artifact/com.jayway.jsonpath/json-path -->
         <dependency>
             <groupId>com.jayway.jsonpath</groupId>
             <artifactId>json-path</artifactId>
-            <version>2.4.0</version>
+            <version>${json.path.version}</version>
         </dependency>
 
-
-        <!-- https://mvnrepository.com/artifact/com.fasterxml.jackson.dataformat/jackson-dataformat-xml -->
-        <dependency>
-            <groupId>com.fasterxml.jackson.dataformat</groupId>
-            <artifactId>jackson-dataformat-xml</artifactId>
-            <version>2.12.3</version>
-        </dependency>
-
-
         <!-- https://mvnrepository.com/artifact/com.fasterxml.jackeu.eudat.corecore/jackeu.eudat.corecore -->
         <dependency>
             <groupId>com.fasterxml.jackson.core</groupId>
             <artifactId>jackson-core</artifactId>
-            <version>2.12.3</version>
+            <version>${jackson.version}</version>
         </dependency>
         <!-- https://mvnrepository.com/artifact/com.fasterxml.jackeu.eudat.corecore/jackson-databind -->
         <dependency>
             <groupId>com.fasterxml.jackson.core</groupId>
             <artifactId>jackson-databind</artifactId>
-            <version>2.12.3</version>
+            <version>${jackson.version}</version>
         </dependency>
 
-        <!-- g/a spring -->
-        <!-- https://mvnrepository.com/artifact/com.fasterxml.jackeu.eudat.corecore/jackson-databind -->
-
-
+        <dependency>
+            <groupId>com.fasterxml.jackson.core</groupId>
+            <artifactId>jackson-annotations</artifactId>
+            <version>${jackson.version}</version>
+        </dependency>
 
         <!-- Various libs -->
         <dependency>
             <groupId>org.apache.commons</groupId>
             <artifactId>commons-lang3</artifactId>
-            <version>3.5</version>
+            <version>${apache.commons.lang3.version}</version>
         </dependency>
+        <!-- Docx export -->
         <!-- https://mvnrepository.com/artifact/org.apache.poi/poi -->
         <dependency>
             <groupId>org.apache.poi</groupId>
             <artifactId>poi-ooxml</artifactId>
-            <version>4.0.0</version>
+            <version>${apache.poi.version}</version>
         </dependency>
 
         <dependency>
             <groupId>org.apache.poi</groupId>
             <artifactId>poi</artifactId>
-            <version>4.0.0</version>
+            <version>${apache.poi.version}</version>
         </dependency>
 
-        <!-- https://mvnrepository.com/artifact/org.apache.xmlgraphics/fop -->
+        <!-- Used for the HTML to DocX export -->
+        <!-- https://mvnrepository.com/artifact/fr.opensagres.xdocreport/org.apache.poi.xwpf.convereu.eudat.corecore -->
         <dependency>
-            <groupId>org.apache.xmlgraphics</groupId>
-            <artifactId>fop</artifactId>
-            <version>2.3</version>
+            <groupId>fr.opensagres.xdocreport</groupId>
+            <artifactId>org.apache.poi.xwpf.converter.core</artifactId>
+            <version>1.0.6</version>
         </dependency>
 
         <dependency>
@@ -194,77 +196,38 @@
             <artifactId>jsoup</artifactId>
             <version>1.14.3</version>
         </dependency>
-        <!-- https://mvnrepository.com/artifact/fr.opensagres.xdocreport/org.apache.poi.xwpf.converter.pdf -->
-        <dependency>
-            <groupId>fr.opensagres.xdocreport</groupId>
-            <artifactId>org.apache.poi.xwpf.converter.pdf</artifactId>
-            <version>1.0.6</version>
-        </dependency>
-        <!-- https://mvnrepository.com/artifact/fr.opensagres.xdocreport/org.apache.poi.xwpf.convereu.eudat.corecore -->
-        <dependency>
-            <groupId>fr.opensagres.xdocreport</groupId>
-            <artifactId>org.apache.poi.xwpf.converter.core</artifactId>
-            <version>1.0.6</version>
-        </dependency>
-        <!-- https://mvnrepository.com/artifact/fr.opensagres.xdocreport/fr.opensagres.xdocreport.itext.extension -->
-        <dependency>
-            <groupId>fr.opensagres.xdocreport</groupId>
-            <artifactId>fr.opensagres.xdocreport.itext.extension</artifactId>
-            <version>2.0.1</version>
-        </dependency>
-
-        <dependency>
-            <groupId>commons-io</groupId>
-            <artifactId>commons-io</artifactId>
-            <version>2.1</version>
-        </dependency>
-
-        <!--<dependency>
-            <groupId>org.hibernate</groupId>
-            <artifactId>hibernate-jpamodelgen</artifactId>
-        </dependency>-->
-
-        <dependency>
-            <groupId>org.elasticsearch.client</groupId>
-            <artifactId>transport</artifactId>
-            <version>7.6.0</version>
-        </dependency>
-
-        <!--<dependency>
-            <groupId>org.apache.logging.log4j</groupId>
-            <artifactId>log4j-to-slf4j</artifactId>
-            <version>2.8.2</version>
-        </dependency>-->
 
+        <!-- XML Binding for (mainly) the templates -->
         <!-- https://mvnrepository.com/artifact/javax.xml.bind/jaxb-api -->
         <dependency>
             <groupId>javax.xml.bind</groupId>
             <artifactId>jaxb-api</artifactId>
-            <version>2.3.1</version>
+            <version>${jaxb.version}</version>
         </dependency>
 
         <!-- https://mvnrepository.com/artifact/org.glassfish.jaxb/jaxb-core -->
         <dependency>
             <groupId>org.glassfish.jaxb</groupId>
             <artifactId>jaxb-core</artifactId>
-            <version>2.3.0</version>
+            <version>${jaxb.version}</version>
         </dependency>
 
         <!-- https://mvnrepository.com/artifact/org.glassfish.jaxb/jaxb-runtime -->
         <dependency>
             <groupId>org.glassfish.jaxb</groupId>
             <artifactId>jaxb-runtime</artifactId>
-            <version>2.3.1</version>
+            <version>${jaxb.version}</version>
         </dependency>
 
 
         <!-- https://mvnrepository.com/artifact/javax.annotation/javax.annotation-api -->
-        <dependency>
+        <!--<dependency>
             <groupId>javax.annotation</groupId>
             <artifactId>javax.annotation-api</artifactId>
             <version>1.3.1</version>
-        </dependency>
+        </dependency>-->
 
+        <!-- Model Validation -->
         <!-- https://mvnrepository.com/artifact/javax.validation/validation-api -->
         <dependency>
             <groupId>javax.validation</groupId>
@@ -272,37 +235,11 @@
             <version>2.0.1.Final</version>
         </dependency>
 
-
-        <!-- The client -->
-        <dependency>
-            <groupId>io.prometheus</groupId>
-            <artifactId>simpleclient</artifactId>
-            <version>0.11.0</version>
-        </dependency>
-        <!-- Hotspot JVM metrics-->
-        <dependency>
-            <groupId>io.prometheus</groupId>
-            <artifactId>simpleclient_hotspot</artifactId>
-            <version>0.11.0</version>
-        </dependency>
-        <!-- Exposition HTTPServer-->
-        <dependency>
-            <groupId>io.prometheus</groupId>
-            <artifactId>simpleclient_httpserver</artifactId>
-            <version>0.11.0</version>
-        </dependency>
-        <!-- Pushgateway exposition-->
-        <dependency>
-            <groupId>io.prometheus</groupId>
-            <artifactId>simpleclient_pushgateway</artifactId>
-            <version>0.11.0</version>
-        </dependency>
-
+        <!-- Prometheus Analytics -->
         <!-- https://mvnrepository.com/artifact/io.micrometer/micrometer-registry-prometheus -->
         <dependency>
             <groupId>io.micrometer</groupId>
             <artifactId>micrometer-registry-prometheus</artifactId>
-            <version>1.7.1</version>
         </dependency>
         <dependency>
             <groupId>org.springframework.boot</groupId>

dmp-backend/queryable/src/main/java/eu/eudat/queryable/collector/ProjectionField.java

@@ -1,7 +1,5 @@
 package eu.eudat.queryable.collector;
 
-import com.google.common.collect.Lists;
-
 import javax.persistence.Tuple;
 import java.util.*;
 import java.util.stream.Collectors;
@@ -68,7 +66,8 @@ public class ProjectionField {
 			list.add(current.parent.key);
 			current = current.parent;
 		}
-		return String.join(".", Lists.reverse(list));
+		Collections.reverse(list);
+		return String.join(".", list);
 	}
 
 	private Object createObject(List<Tuple> tuples, String field) {

dmp-backend/queryable/src/main/java/eu/eudat/queryable/jpa/hibernatequeryablelist/QueryableHibernateList.java

@@ -42,9 +42,12 @@ public class QueryableHibernateList<T extends DataEntity> implements QueryableLi
 	private String hint;
 	private Map<String, Join> joinsMap = new HashMap<>();
 
+	private final ObjectMapper mapper;
+
 	public QueryableHibernateList(EntityManager manager, Class<T> tClass) {
 		this.manager = manager;
 		this.tClass = tClass;
+		this.mapper = new ObjectMapper();
 	}
 
 	public QueryableHibernateList<T> setManager(EntityManager manager) {
@@ -246,7 +249,6 @@ public class QueryableHibernateList<T extends DataEntity> implements QueryableLi
 		if (!this.fields.isEmpty()) this.selectFields();
 		if (distinct) this.query.distinct(true);
 		//if (!this.fields.isEmpty()) this.query.multiselect(this.parseFields(this.fields));
-		ObjectMapper mapper = new ObjectMapper();
 		if (!this.fields.isEmpty()) return this.toListWithFields().stream().map(m -> mapper.convertValue(m, this.tClass)).collect(Collectors.toList());
 		return this.toListWithOutFields();
 	}

dmp-backend/web/pom.xml

@@ -50,7 +50,6 @@
         <dependency>
             <groupId>com.fasterxml.jackson.core</groupId>
             <artifactId>jackson-annotations</artifactId>
-            <version>2.12.3</version>
         </dependency>
 
         <!-- https://mvnrepository.com/artifact/org.springframework/spring-context -->
@@ -71,55 +70,45 @@
         <dependency>
             <groupId>com.github.ben-manes.caffeine</groupId>
             <artifactId>caffeine</artifactId>
-            <version>2.9.0</version>
         </dependency>
 
 
 
         <!-- https://mvnrepository.com/artifact/junit/junit -->
-        <dependency>
+        <!--<dependency>
             <groupId>org.junit.jupiter</groupId>
             <artifactId>junit-jupiter-api</artifactId>
             <version>5.7.2</version>
             <scope>test</scope>
-        </dependency>
+        </dependency>-->
 
-        <dependency>
-            <groupId>org.postgresql</groupId>
-            <artifactId>postgresql</artifactId>
-            <version>42.2.22</version>
-        </dependency>
-
-        <dependency>
+        <!--<dependency>
             <groupId>io.springfox</groupId>
             <artifactId>springfox-swagger-ui</artifactId>
             <version>3.0.0</version>
-        </dependency>
+        </dependency>-->
 
         <!-- facebook Login -->
-        <dependency>
+        <!--<dependency>
             <groupId>org.springframework.social</groupId>
             <artifactId>spring-social-facebook</artifactId>
-            <version>2.0.3.RELEASE</version>
         </dependency>
 
-        <!-- linkedin Login -->
+        &lt;!&ndash; linkedin Login &ndash;&gt;
         <dependency>
             <groupId>org.springframework.social</groupId>
             <artifactId>spring-social-linkedin</artifactId>
-            <version>1.0.2.RELEASE</version>
         </dependency>
 
-        <!-- tweeter login-->
+        &lt;!&ndash; tweeter login&ndash;&gt;
         <dependency>
             <groupId>org.springframework.social</groupId>
             <artifactId>spring-social-twitter</artifactId>
-            <version>1.1.2.RELEASE</version>
-        </dependency>
-        <dependency>
+        </dependency>-->
+        <!--<dependency>
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter-tomcat</artifactId>
-        </dependency>
+        </dependency>-->
     </dependencies>
 
     <build>

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

@@ -1,30 +0,0 @@
-package eu.eudat.configurations;
-
-import com.fasterxml.jackson.annotation.JsonInclude;
-import com.fasterxml.jackson.databind.DeserializationFeature;
-import com.fasterxml.jackson.databind.Module;
-import com.fasterxml.jackson.databind.ObjectMapper;
-import com.fasterxml.jackson.databind.SerializationFeature;
-import com.fasterxml.jackson.databind.module.SimpleModule;
-import eu.eudat.criteria.entities.Criteria;
-import eu.eudat.criteria.serialzier.CriteriaSerializer;
-import org.springframework.context.annotation.Bean;
-import org.springframework.context.annotation.Configuration;
-
-import java.util.ArrayList;
-
-@Configuration
-public class JacksonConfiguration {
-	@Bean
-	public ObjectMapper buildObjectMapper() {
-
-		ArrayList<Module> modules = new ArrayList<>();
-		SimpleModule criteriaSerializerModule = new SimpleModule();
-		criteriaSerializerModule.addDeserializer(Criteria.class, new CriteriaSerializer());
-		modules.add(criteriaSerializerModule);
-
-		return new ObjectMapper()
-				.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false)
-				.registerModules(modules);
-	}
-}

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

@@ -1,37 +1,43 @@
 package eu.eudat.configurations;
 
-import eu.eudat.controllers.interceptors.RequestInterceptor;
 import eu.eudat.logic.handlers.PrincipalArgumentResolver;
 import eu.eudat.logic.services.ApiContext;
 import eu.eudat.logic.services.operations.authentication.AuthenticationService;
-import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Configuration;
+import org.springframework.core.env.Environment;
 import org.springframework.scheduling.annotation.EnableAsync;
 import org.springframework.scheduling.annotation.EnableScheduling;
 import org.springframework.web.method.support.HandlerMethodArgumentResolver;
+import org.springframework.web.servlet.config.annotation.CorsRegistry;
 import org.springframework.web.servlet.config.annotation.InterceptorRegistry;
-import org.springframework.web.servlet.config.annotation.WebMvcConfigurerAdapter;
+import org.springframework.web.servlet.config.annotation.WebMvcConfigurer;
 
 import java.util.List;
 
 @EnableAsync
 @Configuration
 @EnableScheduling
-public class WebMVCConfiguration extends WebMvcConfigurerAdapter {
+public class WebMVCConfiguration implements WebMvcConfigurer {
 
 	private ApiContext apiContext;
 
-	private AuthenticationService verifiedUserAuthenticationService;
-	private AuthenticationService nonVerifiedUserAuthenticationService;
+	private final AuthenticationService verifiedUserAuthenticationService;
+	private final AuthenticationService nonVerifiedUserAuthenticationService;
 
-	@Autowired
-	public WebMVCConfiguration(ApiContext apiContext, AuthenticationService verifiedUserAuthenticationService, AuthenticationService nonVerifiedUserAuthenticationService) {
+	private final Environment environment;
+
+	public WebMVCConfiguration(ApiContext apiContext, AuthenticationService verifiedUserAuthenticationService, AuthenticationService nonVerifiedUserAuthenticationService, Environment environment) {
 		this.apiContext = apiContext;
 		this.verifiedUserAuthenticationService = verifiedUserAuthenticationService;
 		this.nonVerifiedUserAuthenticationService = nonVerifiedUserAuthenticationService;
+		this.environment = environment;
+	}
+
+	@Override
+	public void addCorsMappings(CorsRegistry registry) {
+		registry.addMapping("/api/**").allowedOrigins(this.environment.getProperty("dmp.domain"));
 	}
 
-	@Autowired
 	@Override
 	public void addArgumentResolvers(List<HandlerMethodArgumentResolver> argumentResolvers) {
 		argumentResolvers.add(new PrincipalArgumentResolver(verifiedUserAuthenticationService, nonVerifiedUserAuthenticationService));

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

@@ -0,0 +1,9 @@
+package eu.eudat.configurations.file;
+
+import org.springframework.boot.context.properties.EnableConfigurationProperties;
+import org.springframework.context.annotation.Configuration;
+
+@Configuration
+@EnableConfigurationProperties({TmpProperties.class, PermProperties.class})
+public class FileTimeConfiguration {
+}

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

@@ -0,0 +1,17 @@
+package eu.eudat.configurations.file;
+
+import org.springframework.boot.context.properties.ConfigurationProperties;
+
+@ConfigurationProperties(prefix = "perm")
+public class PermProperties {
+
+    private TimeProperties time;
+
+    public TimeProperties getTime() {
+        return time;
+    }
+
+    public void setTime(TimeProperties time) {
+        this.time = time;
+    }
+}

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

@@ -0,0 +1,59 @@
+package eu.eudat.configurations.file;
+
+public class StartTimeProperties {
+    private Integer month;
+    private String dayOfWeekName;
+    private Integer dayOfWeek;
+
+    private Integer dayOfMonth;
+    private Integer hour;
+    private Integer minute;
+
+    public Integer getMonth() {
+        return month;
+    }
+
+    public void setMonth(Integer month) {
+        this.month = month;
+    }
+
+    public String getDayOfWeekName() {
+        return dayOfWeekName;
+    }
+
+    public void setDayOfWeekName(String dayOfWeekName) {
+        this.dayOfWeekName = dayOfWeekName;
+    }
+
+    public Integer getDayOfWeek() {
+        return dayOfWeek;
+    }
+
+    public void setDayOfWeek(Integer dayOfWeek) {
+        this.dayOfWeek = dayOfWeek;
+    }
+
+    public Integer getDayOfMonth() {
+        return dayOfMonth;
+    }
+
+    public void setDayOfMonth(Integer dayOfMonth) {
+        this.dayOfMonth = dayOfMonth;
+    }
+
+    public Integer getHour() {
+        return hour;
+    }
+
+    public void setHour(Integer hour) {
+        this.hour = hour;
+    }
+
+    public Integer getMinute() {
+        return minute;
+    }
+
+    public void setMinute(Integer minute) {
+        this.minute = minute;
+    }
+}

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

@@ -0,0 +1,33 @@
+package eu.eudat.configurations.file;
+
+import java.time.temporal.ChronoUnit;
+
+public class TimeProperties {
+    private Integer interval;
+    private ChronoUnit timeUnit;
+    private StartTimeProperties startTime;
+
+    public Integer getInterval() {
+        return interval;
+    }
+
+    public void setInterval(Integer interval) {
+        this.interval = interval;
+    }
+
+    public ChronoUnit getTimeUnit() {
+        return timeUnit;
+    }
+
+    public void setTimeUnit(ChronoUnit timeUnit) {
+        this.timeUnit = timeUnit;
+    }
+
+    public StartTimeProperties getStartTime() {
+        return startTime;
+    }
+
+    public void setStartTime(StartTimeProperties startTime) {
+        this.startTime = startTime;
+    }
+}

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

@@ -0,0 +1,17 @@
+package eu.eudat.configurations.file;
+
+import org.springframework.boot.context.properties.ConfigurationProperties;
+
+@ConfigurationProperties(prefix = "tmp")
+public class TmpProperties {
+
+    private TimeProperties time;
+
+    public TimeProperties getTime() {
+        return time;
+    }
+
+    public void setTime(TimeProperties time) {
+        this.time = time;
+    }
+}

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

@@ -38,7 +38,6 @@ import static eu.eudat.types.Authorities.ADMIN;
 import static eu.eudat.types.Authorities.DATASET_PROFILE_MANAGER;
 
 @RestController
-@CrossOrigin
 @RequestMapping(value = {"/api/admin/"})
 public class Admin extends BaseController {
 

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

@@ -18,7 +18,6 @@ import java.util.List;
  * Created by ikalyvas on 3/28/2018.
  */
 @RestController
-@CrossOrigin
 @RequestMapping(value = {"/api/common"})
 public class CommonController {
 

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

@@ -15,7 +15,6 @@ import org.springframework.web.bind.annotation.*;
 import javax.transaction.Transactional;
 
 @RestController
-@CrossOrigin
 @RequestMapping(value = "api/contactEmail")
 public class ContactEmail {
 	private static final Logger logger = LoggerFactory.getLogger(ContactEmail.class);

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

@@ -12,7 +12,6 @@ import org.springframework.web.bind.annotation.*;
 import java.util.List;
 
 @RestController
-@CrossOrigin
 @RequestMapping(value = "api/currency")
 public class CurrencyController {
 

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

@@ -31,7 +31,6 @@ import static eu.eudat.types.Authorities.ADMIN;
  * Created by ikalyvas on 3/21/2018.
  */
 @RestController
-@CrossOrigin
 @RequestMapping(value = {"/api/dmpprofile"})
 public class DMPProfileController extends BaseController {
 

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

@@ -62,7 +62,6 @@ import static org.springframework.http.MediaType.*;
 
 
 @RestController
-@CrossOrigin
 @RequestMapping(value = {"/api/dmps/"})
 public class DMPs extends BaseController {
     private static final Logger logger = LoggerFactory.getLogger(DMPs.class);

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

@@ -22,11 +22,10 @@ import java.io.IOException;
 import java.util.List;
 
 @RestController
-@CrossOrigin
 @RequestMapping(value = {"/api"})
 public class DashBoardController extends BaseController {
 
-    private DashBoardManager dashBoardManager;
+    private final DashBoardManager dashBoardManager;
     @Autowired
     public DashBoardController(ApiContext apiContext, DashBoardManager dashBoardManager) {
         super(apiContext);

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

@@ -19,7 +19,6 @@ import java.util.List;
 
 
 @RestController
-@CrossOrigin
 @RequestMapping(value = {"/api/external/datarepos"})
 public class DataRepositories extends BaseController {
 

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

@@ -9,9 +9,7 @@ import eu.eudat.models.data.components.commons.datafield.AutoCompleteData;
 import eu.eudat.models.data.externaldataset.ExternalAutocompleteFieldModel;
 import eu.eudat.models.data.helpers.common.AutoCompleteLookupItem;
 import eu.eudat.models.data.helpers.responses.ResponseItem;
-import eu.eudat.models.data.properties.PropertiesModel;
 import eu.eudat.models.data.security.Principal;
-import org.json.JSONObject;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.HttpStatus;
 import org.springframework.http.ResponseEntity;
@@ -19,15 +17,12 @@ import org.springframework.transaction.annotation.Transactional;
 import org.springframework.web.bind.annotation.*;
 
 import javax.xml.xpath.XPathExpressionException;
-import java.util.HashMap;
 import java.util.List;
-import java.util.Map;
 import java.util.UUID;
 
 import static eu.eudat.types.Authorities.ADMIN;
 
 @RestController
-@CrossOrigin
 @RequestMapping(value = {"/api"})
 public class DatasetProfileController extends BaseController {
 

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

@@ -17,7 +17,6 @@ import java.util.List;
 
 
 @RestController
-@CrossOrigin
 @RequestMapping(value = {"/api"})
 public class DatasetProfiles extends BaseController {
 

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

@@ -59,7 +59,6 @@ import static eu.eudat.types.Authorities.ANONYMOUS;
 
 
 @RestController
-@CrossOrigin
 @RequestMapping(value = {"/api/datasets/"})
 public class Datasets extends BaseController {
     private static final Logger logger = LoggerFactory.getLogger(Datasets.class);

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

@@ -16,7 +16,6 @@ import org.springframework.web.bind.annotation.*;
 import javax.transaction.Transactional;
 
 @RestController
-@CrossOrigin
 @RequestMapping(value = "api/emailConfirmation")
 public class EmailConfirmation {
 

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

@@ -18,7 +18,6 @@ import org.springframework.web.bind.annotation.*;
 import javax.transaction.Transactional;
 
 @RestController
-@CrossOrigin
 @RequestMapping(value = "api/emailMergeConfirmation")
 public class EmailMergeConfirmation {
 

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

@@ -24,7 +24,6 @@ import java.util.UUID;
 
 
 @RestController
-@CrossOrigin
 @RequestMapping(value = {"/api"})
 public class ExternalDatasets extends BaseController {
 

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

@@ -1,6 +1,6 @@
 package eu.eudat.controllers;
 
-import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import eu.eudat.data.entities.FileUpload;
@@ -12,14 +12,15 @@ import eu.eudat.logic.services.operations.DatabaseRepository;
 import eu.eudat.logic.utilities.documents.helpers.FileEnvelope;
 import eu.eudat.logic.utilities.json.JsonSearcher;
 import eu.eudat.models.HintedModelFactory;
+import eu.eudat.models.data.components.commons.datafield.UploadData;
 import eu.eudat.models.data.datasetwizard.DatasetWizardModel;
 import eu.eudat.models.data.helpers.responses.ResponseItem;
 import eu.eudat.models.data.security.Principal;
 import eu.eudat.types.ApiMessageCode;
 import eu.eudat.types.Authorities;
 import org.apache.poi.util.IOUtils;
-import org.json.JSONArray;
-import org.json.JSONObject;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.core.env.Environment;
 import org.springframework.http.HttpHeaders;
@@ -32,25 +33,28 @@ import org.springframework.web.multipart.MultipartFile;
 import javax.transaction.Transactional;
 import java.io.*;
 import java.nio.file.Files;
-import java.util.*;
-import java.util.concurrent.atomic.AtomicBoolean;
-import java.util.concurrent.atomic.AtomicReference;
+import java.util.HashSet;
+import java.util.NoSuchElementException;
+import java.util.Set;
+import java.util.UUID;
 import java.util.stream.Collectors;
 
 @RestController
-@CrossOrigin
 @RequestMapping(value = {"/api/file/"})
 public class FileController {
+    private static final Logger logger = LoggerFactory.getLogger(FileController.class);
 
     private DatasetProfileManager datasetProfileManager;
     private final Environment environment;
     private DatabaseRepository databaseRepository;
+    private final ObjectMapper objectMapper;
 
     @Autowired
     public FileController(DatasetProfileManager datasetProfileManager, Environment environment, ApiContext apiContext) {
         this.datasetProfileManager = datasetProfileManager;
         this.environment = environment;
         this.databaseRepository = apiContext.getOperationsContext().getDatabaseRepository();
+        this.objectMapper = apiContext.getUtilitiesService().getGenericObjectMapper();
     }
 
     @RequestMapping(method = RequestMethod.POST, value = {"/upload"})
@@ -62,57 +66,48 @@ public class FileController {
 
         eu.eudat.models.data.admin.composite.DatasetProfile datasetprofile = this.datasetProfileManager.getDatasetProfile(datasetProfileId);
 
-        ObjectMapper mapper = new ObjectMapper();
-        mapper.setSerializationInclusion(JsonInclude.Include.NON_NULL);
-        String json = mapper.writeValueAsString(datasetprofile.getSections());;
-        JsonNode propertiesJson = mapper.readTree(json);
+        String json = objectMapper.writeValueAsString(datasetprofile.getSections());
+        JsonNode propertiesJson = objectMapper.readTree(json);
         Set<JsonNode> fieldNodes = new HashSet<>();
         fieldNodes.addAll(JsonSearcher.findNodes(propertiesJson, "id", fieldId, false));
 
 //        AtomicReference<String> exceptionMessage = null;
-        AtomicBoolean acceptedFile = new AtomicBoolean(false);
-        fieldNodes.forEach(node -> {
+        Boolean acceptedFile = false;
+        for (JsonNode node : fieldNodes) {
             JsonNode data = node.get("data");
-            if (data != null && !data.toString().equals("\"\"") && !data.toString().equals("null")) {
-                String stringValue = data.toString().replaceAll("=", ":");
-                JSONObject dataObj = new JSONObject(stringValue);
-                Map<String, Object> dataMap = ((JSONObject) dataObj).toMap();
-                if(dataMap.get("maxFileSizeInMB") != null && !dataMap.get("maxFileSizeInMB").toString().equals("\"\"") && !dataMap.get("maxFileSizeInMB").toString().equals("null")) {
-                    if (file.getSize() <= Integer.parseInt(dataMap.get("maxFileSizeInMB").toString())*1048576) {
-                        acceptedFile.set(true);
-                    }
-//                    else {
-//                        exceptionMessage.set("The file is too large. Max file upload is " + dataMap.get("maxFileSizeInMB").toString() + " MB.");
-//                    }
-                }
-
-                if(acceptedFile.get() && data.get("types") != null && !data.get("types").toString().equals("\"\"") && !data.get("types").toString().equals("null")) {
-                    acceptedFile.set(false);
-
-                    JSONArray types = new JSONArray(data.get("types").toString());
-
-                    types.iterator().forEachRemaining(element -> {
-                        Map<String, Object> typesMap = ((JSONObject) element).toMap();
-                        if(typesMap.get("value") != null && !typesMap.get("value").toString().equals("\"\"") && !typesMap.get("value").toString().equals("null")) {
-                            if(file.getContentType().equals(typesMap.get("value").toString())) {
-                                acceptedFile.set(true);
+            try {
+                UploadData uploadData = objectMapper.treeToValue(data, UploadData.class);
+                if (uploadData != null) {
+                    if (uploadData.getMaxFileSizeInMB() != null) {
+                        if (file.getSize() <= (uploadData.getMaxFileSizeInMB() * Math.pow(1024, 2))) {
+                            acceptedFile = true;
                         }
                     }
-                    });
+                    if (acceptedFile && uploadData.getTypes() != null && !uploadData.getTypes().isEmpty()) {
+                        acceptedFile = false;
+                        for (UploadData.Option option : uploadData.getTypes()) {
+                            if (option.getValue() != null) {
+                                if (file.getContentType().equals(option.getValue())) {
+                                    acceptedFile = true;
+                                }
+                            }
+                        }
+                    }
+                }
+            } catch (JsonProcessingException e) {
+                logger.error(e.getLocalizedMessage(), e);
+            }
         }
 //                if(!acceptedFile.get()) {
 //                    exceptionMessage.set("The file type is not accepted.");
 //                }
-            }
-        });
 
-        if(!acceptedFile.get()) {
+        if (!acceptedFile) {
             return ResponseEntity.status(HttpStatus.BAD_REQUEST).body(new ResponseItem<String>().status(ApiMessageCode.ERROR_MESSAGE).message("The uploaded file is too large or has an unaccepted type"));
         }
 
 
         File convFile = new File(this.environment.getProperty("temp.temp") + uuid);
-        convFile.createNewFile();
         FileOutputStream fos = new FileOutputStream(convFile);
         fos.write(file.getBytes());
         fos.close();

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

@@ -16,7 +16,6 @@ import org.springframework.web.bind.annotation.*;
 import java.util.List;
 
 @RestController
-@CrossOrigin
 @RequestMapping(value = {"/api/funders/"})
 public class Funders extends BaseController {
 	private FunderManager funderManager;

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

@@ -28,7 +28,6 @@ import static eu.eudat.types.Authorities.ANONYMOUS;
 
 
 @RestController
-@CrossOrigin
 @RequestMapping(value = {"/api/grants/"})
 public class Grants extends BaseController {
     private GrantManager grantManager;

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

@@ -19,7 +19,6 @@ import java.util.List;
 
 
 @RestController
-@CrossOrigin
 @RequestMapping(value = {"/api/external/journals"})
 public class JournalsController extends BaseController {
 

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

@@ -15,7 +15,6 @@ import java.io.*;
 import java.util.UUID;
 
 @RestController
-@CrossOrigin
 @RequestMapping(value = {"/api/language/"})
 public class LanguageController {
 

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

@@ -17,7 +17,6 @@ import java.util.List;
 
 
 @RestController
-@CrossOrigin
 @RequestMapping(value = {"/api/external/licenses"})
 public class Licenses extends BaseController {
 

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

@@ -14,7 +14,6 @@ import org.springframework.web.bind.annotation.*;
 import java.util.UUID;
 
 @RestController
-@CrossOrigin
 @RequestMapping(value = {"/api/lock/"})
 public class LockController {
 

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

@@ -50,7 +50,6 @@ import java.security.GeneralSecurityException;
 
 
 @RestController
-@CrossOrigin
 @RequestMapping(value = "api/auth")
 public class Login {
     private static final Logger logger = LoggerFactory.getLogger(Login.class);

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

@@ -20,7 +20,6 @@ import java.util.List;
 
 
 @RestController
-@CrossOrigin
 @RequestMapping(value = {"/api"})
 public class Organisations extends BaseController {
 

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

@@ -14,7 +14,6 @@ import java.util.List;
 import java.util.UUID;
 
 @RestController
-@CrossOrigin
 @RequestMapping(value = {"/api"})
 public class Prefillings {
 

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

@@ -17,7 +17,6 @@ import org.springframework.web.bind.annotation.*;
 import java.util.List;
 
 @RestController
-@CrossOrigin
 @RequestMapping(value = {"/api/projects/"})
 public class Projects extends BaseController {
 	private ProjectManager projectManager;

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

@@ -17,7 +17,6 @@ import java.util.List;
 
 
 @RestController
-@CrossOrigin
 @RequestMapping(value = {"/api/external/pubrepos"})
 public class PubRepositoriesController extends BaseController {
 

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

@@ -17,7 +17,6 @@ import java.util.List;
 
 
 @RestController
-@CrossOrigin
 @RequestMapping(value = {"/api/external/publications"})
 public class PublicationsController extends BaseController {
 

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

@@ -26,7 +26,6 @@ import javax.validation.Valid;
 import java.util.UUID;
 
 @RestController
-@CrossOrigin
 @RequestMapping(value = {"/api/quick-wizard/"})
 public class QuickWizardController extends BaseController {
 

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

@@ -19,7 +19,6 @@ import java.util.List;
 
 
 @RestController
-@CrossOrigin
 @RequestMapping(value = {"/api"})
 public class Registries extends BaseController {
 

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

@@ -21,7 +21,6 @@ import java.util.Map;
 
 
 @RestController
-@CrossOrigin
 @RequestMapping(value = {"/api/researchers"})
 
 public class Researchers extends BaseController {

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

@@ -19,7 +19,6 @@ import java.util.List;
 
 
 @RestController
-@CrossOrigin
 @RequestMapping(value = {"/api"})
 public class Services extends BaseController {
 

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

@@ -25,7 +25,6 @@ import java.util.stream.Collectors;
  * Created by ikalyvas on 7/5/2018.
  */
 @RestController
-@CrossOrigin
 @RequestMapping(value = {"/api"})
 public class TagController extends BaseController {
 

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

@@ -17,7 +17,6 @@ import java.util.List;
 
 
 @RestController
-@CrossOrigin
 @RequestMapping(value = {"/api/external/taxonomies"})
 public class TaxonomiesController extends BaseController {
 

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

@@ -26,7 +26,6 @@ import java.util.stream.Stream;
 import static eu.eudat.types.Authorities.ADMIN;
 
 @RestController
-@CrossOrigin
 @RequestMapping(value = {"/api/userguide/"})
 public class UserGuideController {
 

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

@@ -22,7 +22,6 @@ import java.util.UUID;
 
 @RequestMapping("api/invite/")
 @RestController
-@CrossOrigin
 public class UserInvitationController extends BaseController {
 
     private InvitationsManager invitationsManager;

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

@@ -31,7 +31,6 @@ import static eu.eudat.types.Authorities.ADMIN;
 
 
 @RestController
-@CrossOrigin
 @RequestMapping(value = "api/user")
 public class Users extends BaseController {
 

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

@@ -20,7 +20,6 @@ import java.util.List;
 
 
 @RestController
-@CrossOrigin
 @RequestMapping(value = {"/api"})
 public class Validation extends BaseController {
 

dmp-backend/web/src/main/java/eu/eudat/controllers/controllerhandler/ControllerErrorHandler.java

@@ -6,6 +6,7 @@ import eu.eudat.models.data.security.Principal;
 import eu.eudat.types.ApiMessageCode;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import org.springframework.core.annotation.Order;
 import org.springframework.http.HttpStatus;
 import org.springframework.web.bind.annotation.ControllerAdvice;
 import org.springframework.web.bind.annotation.ExceptionHandler;
@@ -18,7 +19,7 @@ import javax.annotation.Priority;
  * Created by ikalyvas on 6/12/2018.
  */
 @ControllerAdvice
-@Priority(5)
+@Order(5)
 public class ControllerErrorHandler {
     private static final Logger logger = LoggerFactory.getLogger(ControllerErrorHandler.class);
 

dmp-backend/web/src/main/java/eu/eudat/controllers/controllerhandler/ControllerUnauthorisedHandler.java

@@ -4,6 +4,7 @@ import eu.eudat.exceptions.security.UnauthorisedException;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.core.annotation.Order;
 import org.springframework.http.HttpStatus;
 import org.springframework.web.bind.annotation.ControllerAdvice;
 import org.springframework.web.bind.annotation.ExceptionHandler;
@@ -16,7 +17,7 @@ import javax.annotation.Priority;
  * Created by ikalyvas on 6/12/2018.
  */
 @ControllerAdvice
-@Priority(4)
+@Order(4)
 public class ControllerUnauthorisedHandler {
     private static final Logger logger = LoggerFactory.getLogger(ControllerUnauthorisedHandler.class);
 

dmp-backend/web/src/main/java/eu/eudat/logic/managers/DashBoardManager.java

@@ -56,8 +56,8 @@ public class DashBoardManager {
             {"publishedAt", Comparator.comparing(o -> ((RecentActivityModel) o).getPublishedAt(), Comparator.nullsLast(Comparator.naturalOrder())).reversed()}
     }).collect(Collectors.toMap(data -> (String) data[0], data -> (Comparator<RecentActivityModel>) data[1]));
 
-    private ApiContext apiContext;
-    private DatabaseRepository databaseRepository;
+    private final ApiContext apiContext;
+    private final DatabaseRepository databaseRepository;
     private final DataManagementPlanManager dataManagementPlanManager;
     private final DatasetManager datasetManager;
 
@@ -152,21 +152,14 @@ public class DashBoardManager {
 
         List<Integer> roles = new LinkedList<>();
         if ((dmps == null || dmps == 0L) && (datasets == null || datasets == 0L)) {
-            CompletableFuture dmpFuture = dataManagementPlanRepository.getAuthenticated(dataManagementPlanRepository.getWithCriteria(dataManagementPlanCriteria), principal.getId(), roles).distinct().countAsync()
-                    .whenComplete((dmpsStats, throwable) -> statistics.setTotalDataManagementPlanCount(dmpsStats));
-            CompletableFuture datasetFuture = datasetRepository.getAuthenticated( datasetRepository.getWithCriteria(datasetCriteria), user, roles).distinct().countAsync()
-                    .whenComplete((datasetsStats, throwable) -> statistics.setTotalDataSetCount(datasetsStats));
-            CompletableFuture.allOf(dmpFuture, datasetFuture).join();
+            statistics.setTotalDataManagementPlanCount(dataManagementPlanRepository.getAuthenticated(dataManagementPlanRepository.getWithCriteria(dataManagementPlanCriteria), principal.getId(), roles).distinct().count());
+            statistics.setTotalDataSetCount(datasetRepository.getAuthenticated(datasetRepository.getWithCriteria(datasetCriteria), user, roles).distinct().count());
         } else {
             statistics.setTotalDataManagementPlanCount(dmps);
             statistics.setTotalDataSetCount(datasets);
         }
-        CompletableFuture grantFuture = grantRepository.getAuthenticated(grantRepository.getWithCriteria(grantCriteria), user).countAsync()
-                .whenComplete((grantsStats, throwable) -> statistics.setTotalGrantCount(grantsStats));
-        CompletableFuture orgnanisationFuture = organisationRepository.getAuthenticated(organisationRepository.getWithCriteria(organisationCriteria).withHint("organisationRecentActivity"), user).countAsync()
-                .whenComplete((organisationStats, throwable) -> statistics.setTotalOrganisationCount(organisationStats));
-
-        CompletableFuture.allOf( grantFuture, orgnanisationFuture).join();
+        statistics.setTotalGrantCount(grantRepository.getAuthenticated(grantRepository.getWithCriteria(grantCriteria), user).count());
+        statistics.setTotalOrganisationCount(organisationRepository.getAuthenticated(organisationRepository.getWithCriteria(organisationCriteria).withHint("organisationRecentActivity"), user).count());
         return statistics;
     }
 

dmp-backend/web/src/main/java/eu/eudat/logic/managers/DataManagementPlanManager.java

@@ -65,7 +65,6 @@ import eu.eudat.types.MetricNames;
 import org.apache.poi.xwpf.usermodel.XWPFDocument;
 import org.apache.poi.xwpf.usermodel.XWPFParagraph;
 import org.apache.poi.xwpf.usermodel.XWPFRun;
-import org.json.JSONObject;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -97,7 +96,6 @@ import java.util.stream.Stream;
 @Component
 public class DataManagementPlanManager {
     private static final Logger logger = LoggerFactory.getLogger(DataManagementPlanManager.class);
-    private static final ObjectMapper objectMapper = new ObjectMapper();
 
     private final Map<NotificationType, String> notificationPaths = Stream.of(new Object[][]{
             {NotificationType.DMP_MODIFIED, "/plans/edit"},
@@ -106,12 +104,12 @@ public class DataManagementPlanManager {
             {NotificationType.DMP_MODIFIED_FINALISED, "/plans/edit"}
     }).collect(Collectors.toMap(data -> (NotificationType) data[0], data -> (String) data[1]));
 
-    private ApiContext apiContext;
-    private DatasetManager datasetManager;
-    private DatabaseRepository databaseRepository;
-    private Environment environment;
-    private RDAManager rdaManager;
-    private UserManager userManager;
+    private final ApiContext apiContext;
+    private final DatasetManager datasetManager;
+    private final DatabaseRepository databaseRepository;
+    private final Environment environment;
+    private final RDAManager rdaManager;
+    private final UserManager userManager;
     private final MetricsManager metricsManager;
     private final ConfigLoader configLoader;
 
@@ -125,6 +123,7 @@ public class DataManagementPlanManager {
         this.userManager = userManager;
         this.metricsManager = metricsManager;
         this.configLoader = configLoader;
+
     }
 
     /*
@@ -318,7 +317,7 @@ public class DataManagementPlanManager {
         } else {
             dataManagementPlan.fromDataModelNoDatasets(dataManagementPlanEntity);
         }
-        Map dmpProperties = dataManagementPlanEntity.getDmpProperties() != null ? new org.json.JSONObject(dataManagementPlanEntity.getDmpProperties()).toMap() : null;
+        Map dmpProperties = dataManagementPlanEntity.getDmpProperties() != null ? apiContext.getUtilitiesService().getGenericObjectMapper().readValue(dataManagementPlanEntity.getDmpProperties(), LinkedHashMap.class) : null;
 
         if (dmpProperties != null && dataManagementPlan.getDynamicFields() != null)
             dataManagementPlan.getDynamicFields().forEach(item -> {
@@ -1474,8 +1473,8 @@ public class DataManagementPlanManager {
             DatasetWizardModel datasetWizardModel = new DatasetWizardModel();
             Map<String, Object> properties = new HashMap<>();
             if (dataset.getProperties() != null) {
-                JSONObject jobject = new JSONObject(dataset.getProperties());
-                properties = jobject.toMap();
+                properties = apiContext.getUtilitiesService().getGenericObjectMapper().readValue(dataset.getProperties(), LinkedHashMap.class);
+                ;
             }
             PagedDatasetProfile pagedDatasetProfile = datasetManager.getPagedProfile(datasetWizardModel, dataset);
             visibilityRuleService.setProperties(properties);
@@ -1763,9 +1762,9 @@ public class DataManagementPlanManager {
             UserInfo me = apiContext.getOperationsContext().getDatabaseRepository().getUserInfoDao().find(principal.getId());
             dmp.setModified(new Date());
             dmp.setCreator(me);
-            Map<String, String> extraProperties = objectMapper.readValue(dmp.getExtraProperties(), HashMap.class);
+            Map<String, String> extraProperties = apiContext.getUtilitiesService().getGenericObjectMapper().readValue(dmp.getExtraProperties(), HashMap.class);
             extraProperties.put("contact", me.getId().toString());
-            dmp.setExtraProperties(objectMapper.writeValueAsString(extraProperties));
+            dmp.setExtraProperties(apiContext.getUtilitiesService().getGenericObjectMapper().writeValueAsString(extraProperties));
             dmp.setVersion(0);
             dmp.setStatus((short)0);
             dmp.setGroupId(UUID.randomUUID());
@@ -2043,7 +2042,7 @@ public class DataManagementPlanManager {
         headers.setContentType(MediaType.APPLICATION_JSON);
         ZenodoDeposit deposit = DMPToZenodoMapper.fromDMP(dmp, environment, configLoader);
         //if (Objects.requireNonNull(environment.getProperty("spring.profiles.active")).contains("devel")) {
-            String json = objectMapper.writerWithDefaultPrettyPrinter().writeValueAsString(deposit);
+        String json = apiContext.getUtilitiesService().getGenericObjectMapper().writerWithDefaultPrettyPrinter().writeValueAsString(deposit);
             logger.info(json);
         //}
         HttpEntity<ZenodoDeposit> request = new HttpEntity<>(deposit, headers);

dmp-backend/web/src/main/java/eu/eudat/logic/managers/DatasetManager.java

@@ -4,6 +4,8 @@ import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.type.CollectionType;
+import com.fasterxml.jackson.databind.type.TypeFactory;
 import eu.eudat.data.dao.criteria.*;
 import eu.eudat.data.dao.entities.DataRepositoryDao;
 import eu.eudat.data.dao.entities.DatasetDao;
@@ -56,8 +58,6 @@ import org.apache.poi.xwpf.extractor.XWPFWordExtractor;
 import org.apache.poi.xwpf.usermodel.XWPFDocument;
 import org.apache.poi.xwpf.usermodel.XWPFParagraph;
 import org.apache.poi.xwpf.usermodel.XWPFRun;
-import org.json.JSONArray;
-import org.json.JSONObject;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -103,13 +103,13 @@ public class DatasetManager {
             {NotificationType.DATASET_MODIFIED_FINALISED, "/datasets/edit"}
     }).collect(Collectors.toMap(data -> (NotificationType) data[0], data -> (String) data[1]));
 
-    private ApiContext apiContext;
-    private DatabaseRepository databaseRepository;
-    private DatasetRepository datasetRepository;
-    private BuilderFactory builderFactory;
-    private UserManager userManager;
-    private ConfigLoader configLoader;
-    private Environment environment;
+    private final ApiContext apiContext;
+    private final DatabaseRepository databaseRepository;
+    private final DatasetRepository datasetRepository;
+    private final BuilderFactory builderFactory;
+    private final UserManager userManager;
+    private final ConfigLoader configLoader;
+    private final Environment environment;
     private final MetricsManager metricsManager;
     private final FileManager fileManager;
 
@@ -168,20 +168,14 @@ public class DatasetManager {
             datasets = null;
         }
 
-        UserInfo userInfo = builderFactory.getBuilder(UserInfoBuilder.class).id(principal.getId()).build();
+
 //        QueryableList<eu.eudat.data.entities.Dataset> items = databaseRepository.getDatasetDao().getWithCriteria(datasetTableRequest.getCriteria()).withHint(HintedModelFactory.getHint(DatasetListingModel.class));
         QueryableList<eu.eudat.data.entities.Dataset> items;
-        if (datasets != null) {
-
-            if (!datasets.isEmpty()) {
+        if (datasets != null && !datasets.isEmpty()) {
             //items = databaseRepository.getDatasetDao().asQueryable().withHint(HintedModelFactory.getHint(DatasetListingModel.class));
             final List<UUID> datasetIds = datasets.stream().map(datasetE -> UUID.fromString(datasetE.getId())).distinct().collect(Collectors.toList());
             items = databaseRepository.getDatasetDao().filterFromElastic(datasetTableRequest.getCriteria(), datasetIds).withHint(HintedModelFactory.getHint(DatasetListingModel.class));//.withFields(Collections.singletonList("id"));
             //items.where((builder, root) -> root.get("id").in(datasetIds));
-            } else {
-                items = databaseRepository.getDatasetDao().getWithCriteria(datasetTableRequest.getCriteria()).withHint(HintedModelFactory.getHint(DatasetListingModel.class));//.withFields(Collections.singletonList("id"));
-                //items.where((builder, root) -> root.get("id").in(new UUID[]{UUID.randomUUID()}));
-            }
         } else {
             items = databaseRepository.getDatasetDao().getWithCriteria(datasetTableRequest.getCriteria()).withHint(HintedModelFactory.getHint(DatasetListingModel.class));//.withFields(Collections.singletonList("id"));
         }
@@ -192,11 +186,11 @@ public class DatasetManager {
             if (principal.getId() == null) {
                 throw new UnauthorisedException("You are not allowed to access those datasets");
             }
+            UserInfo userInfo = apiContext.getOperationsContext().getDatabaseRepository().getUserInfoDao().find(principal.getId());//builderFactory.getBuilder(UserInfoBuilder.class).id(principal.getId()).build();
             if (datasetTableRequest.getCriteria().getRole() != null) {
                 roles.add(datasetTableRequest.getCriteria().getRole());
             }
             authItems = databaseRepository.getDatasetDao().getAuthenticated(items, userInfo, roles).distinct();
-            pagedItems = PaginationManager.applyPaging(authItems, datasetTableRequest);
         } else {
             if (principal.getId() != null && datasetTableRequest.getCriteria().getRole() != null) {
                 items.where((builder, root) -> {
@@ -204,12 +198,12 @@ public class DatasetManager {
                     return builder.and(builder.equal(userJoin.join("user", JoinType.LEFT).get("id"), principal.getId()), builder.equal(userJoin.get("role"), datasetTableRequest.getCriteria().getRole()));
                 });
             }
-            String[] strings = new String[1];
+            //String[] strings = new String[1];
             //strings[0] = "-dmp:publishedAt|join|";
             //datasetTableRequest.getOrderings().setFields(strings);
             authItems = items;
-            pagedItems = PaginationManager.applyPaging(items, datasetTableRequest);
         }
+        pagedItems = PaginationManager.applyPaging(authItems, datasetTableRequest);
         DataTableData<DatasetListingModel> dataTable = new DataTableData<>();
 
 
@@ -387,8 +381,12 @@ public class DatasetManager {
         eu.eudat.models.data.user.composite.DatasetProfile datasetprofile = userManager.generateDatasetProfileModel(datasetEntity.getProfile());
         datasetprofile.setStatus(dataset.getStatus());
         if (datasetEntity.getProperties() != null) {
-            JSONObject jObject = new JSONObject(datasetEntity.getProperties());
-            Map<String, Object> properties = jObject.toMap();
+            Map<String, Object> properties = null;
+            try {
+                properties = apiContext.getUtilitiesService().getGenericObjectMapper().readValue(datasetEntity.getProperties(), LinkedHashMap.class);
+            } catch (JsonProcessingException e) {
+                logger.error(e.getLocalizedMessage(), e);
+            }
             datasetprofile.fromJsonObject(properties);
         }
         PagedDatasetProfile pagedDatasetProfile = new PagedDatasetProfile();
@@ -456,8 +454,7 @@ public class DatasetManager {
 
         Map<String, Object> properties = new HashMap<>();
         if (datasetEntity.getProperties() != null) {
-            JSONObject jObject = new JSONObject(datasetEntity.getProperties());
-            properties = jObject.toMap();
+            properties = apiContext.getUtilitiesService().getGenericObjectMapper().readValue(datasetEntity.getProperties(), LinkedHashMap.class);
         }
 
         wordBuilder.addParagraphContent("Dataset Description", document, ParagraphStyle.HEADER2, BigInteger.ZERO);
@@ -489,8 +486,7 @@ public class DatasetManager {
 
         Map<String, Object> properties = new HashMap<>();
         if (dataset.getDatasetProfileDefinition() != null) {
-            JSONObject jObject = new JSONObject(propertiesModelToString(dataset.getDatasetProfileDefinition()));
-            properties = jObject.toMap();
+            properties = apiContext.getUtilitiesService().getGenericObjectMapper().readValue(propertiesModelToString(dataset.getDatasetProfileDefinition()), LinkedHashMap.class);
         }
 
         wordBuilder.addParagraphContent("Dataset Description", document, ParagraphStyle.HEADER2, BigInteger.ZERO);
@@ -547,8 +543,7 @@ public class DatasetManager {
             throw new UnauthorisedException();
         Map<String, Object> properties = new HashMap<>();
         if (datasetEntity.getProperties() != null) {
-            JSONObject jobject = new JSONObject(datasetEntity.getProperties());
-            properties = jobject.toMap();
+            properties = apiContext.getUtilitiesService().getGenericObjectMapper().readValue(datasetEntity.getProperties(), LinkedHashMap.class);
         }
         PagedDatasetProfile pagedDatasetProfile = getPagedProfile(dataset, datasetEntity);
         visibilityRuleService.setProperties(properties);
@@ -609,6 +604,7 @@ public class DatasetManager {
 //        datasetWizardModel.setDatasetProfileDefinition(getPagedProfile(datasetWizardModel, dataset1));
         UUID dmpId = dataset1.getDmp().getId();
         dataset1.getDmp().setUsers(new HashSet<>(apiContext.getOperationsContext().getDatabaseRepository().getUserDmpDao().asQueryable().where((builder, root) -> builder.equal(root.get("dmp").get("id"), dmpId)).toList()));
+        this.deleteOldFilesAndAddNew(datasetWizardModel, userInfo);
         updateTags(dataset1, datasetWizardModel.getTags());
         if (sendNotification) {
             if (dataset1.getStatus() != Dataset.Status.FINALISED.getValue()) {
@@ -618,9 +614,6 @@ public class DatasetManager {
             }
         }
 
-        this.deleteOldFilesAndAddNew(datasetWizardModel, userInfo);
-
-
         return dataset1;
     }
 
@@ -631,7 +624,7 @@ public class DatasetManager {
 
         ObjectMapper mapper = new ObjectMapper();
         mapper.setSerializationInclusion(JsonInclude.Include.NON_NULL);
-        String json = mapper.writeValueAsString(datasetWizardModel.getDatasetProfileDefinition());;
+        String json = mapper.writeValueAsString(datasetWizardModel.getDatasetProfileDefinition());
         JsonNode propertiesJson = mapper.readTree(json);
 
         Set<JsonNode> uploadNodes = new HashSet<>();
@@ -641,8 +634,12 @@ public class DatasetManager {
             JsonNode value = node.get("value");
             if (value != null && !value.toString().equals("\"\"") && !value.toString().equals("null")) {
                 String stringValue = value.toString().replaceAll("=", ":");
-                JSONObject values = new JSONObject(stringValue);
-                Map<String, Object> data = ((JSONObject) values).toMap();
+                Map<String, Object> data = null;
+                try {
+                    data = apiContext.getUtilitiesService().getGenericObjectMapper().readValue(stringValue, LinkedHashMap.class);
+                } catch (JsonProcessingException e) {
+                    logger.error(e.getLocalizedMessage(), e);
+                }
 
                 int index = fileUploadIds.indexOf(data.get("id").toString());
                 if (index != -1) {
@@ -657,9 +654,7 @@ public class DatasetManager {
         });
 
         // old files in DB that are not contained anymore in the Dataset -> mark them as Deleted
-        fileUploads.forEach(fileUpload -> {
-            fileManager.markOldFileAsDeleted(fileUpload);
-        });
+        fileUploads.forEach(fileManager::markOldFileAsDeleted);
     }
 
     private void sendNotification(Dataset dataset, DMP dmp, UserInfo user, NotificationType notificationType) {
@@ -707,9 +702,9 @@ public class DatasetManager {
         nodeList = (NodeList) xPath.compile(expression).evaluate(xmlDocument, XPathConstants.NODESET);
 
 
-        JSONObject obj = new JSONObject(dataset.getProperties());
+        Map<String, Object> obj = apiContext.getUtilitiesService().getGenericObjectMapper().readValue(dataset.getProperties(), LinkedHashMap.class);
         VisibilityRuleService visibilityRuleService = new VisibilityRuleServiceImpl();
-        visibilityRuleService.setProperties(obj.toMap());
+        visibilityRuleService.setProperties(obj);
 
         dataset.setProfile(profile);
         PagedDatasetProfile pagedDatasetProfile = this.getPagedProfile(new DatasetWizardModel(), dataset);
@@ -719,7 +714,7 @@ public class DatasetManager {
         String failedField = null;
 
         for (String validator : datasetProfileValidators) {
-            if (obj.has(validator) && isNullOrEmpty(obj.getString(validator)) && isElementVisible(nodeList, validator, visibilityRuleService)) {
+            if (obj.containsKey(validator) && isNullOrEmpty(obj.get(validator).toString()) && isElementVisible(nodeList, validator, visibilityRuleService)) {
                 //throw new Exception("Field value of " + validator + " must be filled.");
                 failedField = validator;
                 break;
@@ -759,8 +754,12 @@ public class DatasetManager {
     private String propertiesModelToString(PagedDatasetProfile pagedDatasetProfile) {
         Map<String, Object> values = new LinkedHashMap<>();
         pagedDatasetProfile.toMap(values);
-        JSONObject jobject = new JSONObject(values);
-        return jobject.toString();
+        try {
+            return apiContext.getUtilitiesService().getGenericObjectMapper().writeValueAsString(values);
+        } catch (JsonProcessingException e) {
+            logger.error(e.getLocalizedMessage(), e);
+        }
+        return null;
     }
 
     public void updateTags(Dataset datasetEntity, List<Tag> tags) throws Exception {
@@ -969,12 +968,9 @@ public class DatasetManager {
                                                 )))))
                 .collect(Collectors.toMap(DatasetImportField::getId, DatasetImportField::getValue));
 
-        // Transforms map into json file.
-        JSONObject jsonDatasetProperties = new JSONObject(importMap);
-
         // Creates the entity data set to save.
         eu.eudat.data.entities.Dataset entity = new Dataset();
-        entity.setProperties(jsonDatasetProperties.toString());
+        entity.setProperties(apiContext.getUtilitiesService().getGenericObjectMapper().writeValueAsString(importMap));
         entity.setLabel(importFile.getOriginalFilename());
         DMP dmp = new DMP();
         dmp.setId(UUID.fromString(dmpId));
@@ -1047,8 +1043,12 @@ public class DatasetManager {
         eu.eudat.models.data.user.composite.DatasetProfile datasetprofile = userManager.generateDatasetProfileModel(profile);
         datasetprofile.setStatus(datasetEntity.getStatus());
         if (datasetEntity.getProperties() != null) {
-            JSONObject jobject = new JSONObject(datasetEntity.getProperties());
-            Map<String, Object> properties = jobject.toMap();
+            Map<String, Object> properties = null;
+            try {
+                properties = apiContext.getUtilitiesService().getGenericObjectMapper().readValue(datasetEntity.getProperties(), LinkedHashMap.class);
+            } catch (JsonProcessingException e) {
+                logger.error(e.getLocalizedMessage(), e);
+            }
             datasetprofile.fromJsonObject(properties);
         }
         PagedDatasetProfile pagedDatasetProfile = new PagedDatasetProfile();
@@ -1117,11 +1117,15 @@ public class DatasetManager {
                 JsonNode value = node.get("value");
                 if (!value.toString().equals("\"\"") && !value.toString().equals("null") && value.toString().startsWith("[")) {
                     String stringValue = value.toString().replaceAll("=", ":");
-                    JSONArray values = new JSONArray(stringValue);
-                    values.iterator().forEachRemaining(element -> {
-                        Map<String, Object> data = ((JSONObject) element).toMap();
-                        this.addTag(tags, wizardModel.getTags(), data.get("id").toString(), data.get("name").toString());
-                    });
+                    List<Tag> values = null;
+                    try {
+                        CollectionType tagCollection = TypeFactory.defaultInstance().constructCollectionType(LinkedList.class, Tag.class);
+                        values = apiContext.getUtilitiesService().getGenericObjectMapper().readValue(stringValue, tagCollection);
+                        values.iterator().forEachRemaining(element -> this.addTag(tags, wizardModel.getTags(), element.getId(), element.getName()));
+                    } catch (JsonProcessingException e) {
+                        logger.error(e.getLocalizedMessage(), e);
+                    }
+
                 } else {
                     List<String> values = Arrays.asList(value.textValue().split(", "));
                     List<Tag> tagValues = values.stream().map(stringValue -> new Tag(stringValue, stringValue)).collect(Collectors.toList());

dmp-backend/web/src/main/java/eu/eudat/logic/managers/FileManager.java

@@ -60,6 +60,10 @@ public class FileManager {
         databaseRepository.getFileUploadDao().createOrUpdate(fileUpload);
     }
 
+    public List<FileUpload> getDeletedFileUploads() {
+        return databaseRepository.getFileUploadDao().asQueryable().where(((builder, root) -> builder.equal(root.get("isDeleted"), true))).toList();
+    }
+
     public List<FileUpload> getFileUploadsForEntityId(String entityId) {
         return databaseRepository.getFileUploadDao().asQueryable()
                 .where((builder, root) -> builder.equal(root.get("entityId"), entityId)).toList();
@@ -74,9 +78,7 @@ public class FileManager {
 
     public void markAllFilesOfEntityIdAsDeleted(UUID entityId) {
         List<FileUpload> fileUploads = this.getCurrentFileUploadsForEntityId(entityId);
-        fileUploads.forEach(fileUpload -> {
-            this.markOldFileAsDeleted(fileUpload);
-        });
+        fileUploads.forEach(this::markOldFileAsDeleted);
     }
 
     public void createFile(String id, String fileName, String fileType, String entityId, FileUpload.EntityType entityType, UserInfo userInfo) {

dmp-backend/web/src/main/java/eu/eudat/logic/managers/UserManager.java

@@ -33,7 +33,6 @@ import eu.eudat.models.data.userinfo.UserProfile;
 import eu.eudat.queryable.QueryableList;
 import eu.eudat.types.Authorities;
 
-import org.json.JSONObject;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -129,11 +128,11 @@ public class UserManager {
 		eu.eudat.data.entities.UserInfo userInfo = apiContext.getOperationsContext().getDatabaseRepository().getUserInfoDao().find(principal.getId());
 		apiContext.getOperationsContext().getDatabaseRepository().detachEntity(userInfo);
 		HashMap<String, Object> result =
-				new ObjectMapper().readValue(userInfo.getAdditionalinfo(), HashMap.class);
+                apiContext.getUtilitiesService().getGenericObjectMapper().readValue(userInfo.getAdditionalinfo(), HashMap.class);
 		userInfo.setName(settings.entrySet().stream().filter(entry -> entry.getKey().equals("name")).filter(Objects::nonNull).map(entry -> entry.getValue().toString()).findFirst().orElse(userInfo.getName()));
 		settings.remove("name");
         result.putAll(settings);
-		userInfo.setAdditionalinfo(new JSONObject(result).toString());
+        userInfo.setAdditionalinfo(apiContext.getUtilitiesService().getGenericObjectMapper().writeValueAsString(result));
         apiContext.getOperationsContext().getDatabaseRepository().getUserInfoDao()
                 .createOrUpdate(userInfo);
 	}

dmp-backend/web/src/main/java/eu/eudat/logic/mapper/prefilling/PrefillingMapper.java

@@ -24,7 +24,7 @@ import eu.eudat.models.data.datasetprofile.RenderStyle;
 import eu.eudat.models.data.datasetwizard.DatasetWizardModel;
 import eu.eudat.models.data.externaldataset.ExternalAutocompleteFieldModel;
 import eu.eudat.models.data.license.LicenseModel;
-import org.json.JSONObject;
+
 
 import java.lang.reflect.InvocationTargetException;
 import java.lang.reflect.Method;
@@ -35,6 +35,7 @@ import java.util.stream.Collectors;
 
 public class PrefillingMapper {
     private static final ObjectMapper mapper = new ObjectMapper().configure(DeserializationFeature.ACCEPT_SINGLE_VALUE_AS_ARRAY, true);
+    private static final List<String> tagDelimiters = Arrays.asList(", ", "; ");
 
     public static DatasetWizardModel mapPrefilledEntityToDatasetWizard(Map<String, Object> prefilledEntity, PrefillingGet prefillingGet, String type,
                                                                        DatasetProfile profile, DatasetManager datasetManager, LicenseManager licenseManager) throws Exception {
@@ -155,10 +156,10 @@ public class PrefillingMapper {
                         properties.put(id, mapper.valueToTree(parseTags(parsedValue)).toString());
                         break;
                     case DATASET_IDENTIFIER:
-                        JSONObject datasetID = new JSONObject();
-                        datasetID.put("identifier", parsedValue);
+                        Map<String, String> datasetId = new LinkedHashMap<>();
+                        datasetId.put("identifier", parsedValue);
                         if (type.equals("zenodo")) {
-                            datasetID.put("type", "doi");
+                            datasetId.put("type", "doi");
                         }
                         properties.put(id, datasetID.toString());
                         break;
@@ -225,13 +226,23 @@ public class PrefillingMapper {
     }
 
     private static List<Tag> parseTags(String value) throws JsonProcessingException {
+
         if (value == null || value.isEmpty())
             return new LinkedList<>();
-        String[] rawTags = value.split(", ");
+        String[] rawTags = null;
+        for (String tagDelim : tagDelimiters) {
+            rawTags = value.split(tagDelim);
+            if (rawTags.length > 1) {
+                break;
+            }
+        }
+        if (rawTags != null) {
             List<Tag> parsedTags = new LinkedList<>();
             for (String rawTag : rawTags) {
                 parsedTags.add(new Tag(rawTag, rawTag));
             }
             return parsedTags;
         }
+        return null;
+    }
 }

dmp-backend/web/src/main/java/eu/eudat/logic/proxy/Proxy.java

@@ -11,7 +11,6 @@ import java.net.*;
 
 
 @RestController
-@CrossOrigin
 public class Proxy {
 
     private String allowedHost;

dmp-backend/web/src/main/java/eu/eudat/logic/security/customproviders/B2Access/B2AccessCustomProviderImpl.java

@@ -1,6 +1,5 @@
 package eu.eudat.logic.security.customproviders.B2Access;
 
-import com.google.api.client.repackaged.org.apache.commons.codec.binary.Base64;
 import eu.eudat.logic.security.validators.b2access.helpers.B2AccessResponseToken;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.core.env.Environment;
@@ -14,6 +13,7 @@ import org.springframework.util.MultiValueMap;
 import org.springframework.web.client.RestTemplate;
 
 import java.nio.charset.Charset;
+import java.util.Base64;
 import java.util.Map;
 
 @Component("b2AccessCustomProvider")
@@ -60,8 +60,7 @@ public class B2AccessCustomProviderImpl implements B2AccessCustomProvider {
     private HttpHeaders createBasicAuthHeaders(String username, String password) {
         return new HttpHeaders() {{
             String auth = username + ":" + password;
-            byte[] encodedAuth = Base64.encodeBase64(
-                    auth.getBytes(Charset.forName("US-ASCII")));
+            byte[] encodedAuth = Base64.getEncoder().encode(auth.getBytes(Charset.forName("US-ASCII")));
             String authHeader = "Basic " + new String(encodedAuth);
             set("Authorization", authHeader);
         }};

dmp-backend/web/src/main/java/eu/eudat/logic/security/validators/google/GoogleTokenValidator.java

@@ -5,7 +5,7 @@ import com.google.api.client.googleapis.auth.oauth2.GoogleIdToken.Payload;
 import com.google.api.client.googleapis.auth.oauth2.GoogleIdTokenVerifier;
 import com.google.api.client.http.HttpTransport;
 import com.google.api.client.http.javanet.NetHttpTransport;
-import com.google.api.client.json.jackson2.JacksonFactory;
+import com.google.api.client.json.gson.GsonFactory;
 import eu.eudat.logic.security.validators.TokenValidator;
 import eu.eudat.logic.security.validators.TokenValidatorFactoryImpl;
 import eu.eudat.logic.services.operations.authentication.AuthenticationService;
@@ -29,7 +29,7 @@ public class GoogleTokenValidator implements TokenValidator {
 	@Autowired
 	public GoogleTokenValidator(Environment environment, AuthenticationService nonVerifiedUserAuthenticationService) {
 		this.nonVerifiedUserAuthenticationService = nonVerifiedUserAuthenticationService;
-		verifier = new GoogleIdTokenVerifier.Builder(transport, JacksonFactory.getDefaultInstance())
+        verifier = new GoogleIdTokenVerifier.Builder(transport, GsonFactory.getDefaultInstance())
                 .setAudience(Collections.singletonList(environment.getProperty("google.login.clientId")))
                 .build();
 	}

dmp-backend/web/src/main/java/eu/eudat/logic/services/operations/authentication/AbstractAuthenticationService.java

@@ -1,5 +1,6 @@
 package eu.eudat.logic.services.operations.authentication;
 
+import com.fasterxml.jackson.core.JsonProcessingException;
 import eu.eudat.data.entities.Credential;
 import eu.eudat.data.entities.UserInfo;
 import eu.eudat.data.entities.UserRole;
@@ -14,7 +15,6 @@ import eu.eudat.models.data.login.Credentials;
 import eu.eudat.models.data.loginprovider.LoginProviderUser;
 import eu.eudat.models.data.security.Principal;
 import eu.eudat.types.Authorities;
-import org.json.JSONObject;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.core.env.Environment;
@@ -164,8 +164,13 @@ public abstract class AbstractAuthenticationService implements AuthenticationSer
 			apiContext.getOperationsContext().getDatabaseRepository().getUserRoleDao().createOrUpdate(role);
 
 		} else {
-			Map<String, Object> additionalInfo = userInfo.getAdditionalinfo() != null ?
-					new JSONObject(userInfo.getAdditionalinfo()).toMap() : new HashMap<>();
+			Map<String, Object> additionalInfo = null;
+			try {
+				additionalInfo = userInfo.getAdditionalinfo() != null ?
+						apiContext.getUtilitiesService().getGenericObjectMapper().readValue(userInfo.getAdditionalinfo(), LinkedHashMap.class) : new HashMap<>();
+			} catch (JsonProcessingException e) {
+				logger.error(e.getLocalizedMessage(), e);
+			}
 			if (profile.getAvatarUrl() != null && !profile.getAvatarUrl().isEmpty() && !profile.getAvatarUrl().equals("null")) {
 				additionalInfo.put("avatarUrl", profile.getAvatarUrl());
 			}
@@ -182,7 +187,11 @@ public abstract class AbstractAuthenticationService implements AuthenticationSer
 				additionalInfo.put("zenodoEmail", profile.getEmail());
 			}
 			userInfo.setLastloggedin(new Date());
-			userInfo.setAdditionalinfo(new JSONObject(additionalInfo).toString());
+			try {
+				userInfo.setAdditionalinfo(apiContext.getUtilitiesService().getGenericObjectMapper().writeValueAsString(additionalInfo));
+			} catch (JsonProcessingException e) {
+				logger.error(e.getLocalizedMessage(), e);
+			}
 			Set<Credential> credentials = userInfo.getCredentials();
 			if (credentials.contains(credential)) {
 				Credential oldCredential = credentials.stream().filter(item -> credential.getProvider().equals(item.getProvider())).findFirst().get();

dmp-backend/web/src/main/java/eu/eudat/logic/services/operations/authentication/VerifiedUserAuthenticationService.java

@@ -1,27 +1,21 @@
 package eu.eudat.logic.services.operations.authentication;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
-import eu.eudat.data.entities.Credential;
 import eu.eudat.data.entities.UserInfo;
 import eu.eudat.data.entities.UserRole;
 import eu.eudat.data.entities.UserToken;
 import eu.eudat.exceptions.security.NullEmailException;
-import eu.eudat.logic.builders.entity.CredentialBuilder;
-import eu.eudat.logic.builders.entity.UserInfoBuilder;
-import eu.eudat.logic.builders.entity.UserTokenBuilder;
 import eu.eudat.logic.builders.model.models.PrincipalBuilder;
-import eu.eudat.logic.security.validators.TokenValidatorFactoryImpl;
 import eu.eudat.logic.services.ApiContext;
-import eu.eudat.models.data.login.Credentials;
-import eu.eudat.models.data.loginprovider.LoginProviderUser;
 import eu.eudat.models.data.security.Principal;
 import eu.eudat.types.Authorities;
-import org.json.JSONObject;
 import org.springframework.core.env.Environment;
 import org.springframework.stereotype.Service;
 
 import java.time.Instant;
-import java.util.*;
+import java.util.Date;
+import java.util.HashSet;
+import java.util.List;
 
 
 @Service("verifiedUserAuthenticationService")

dmp-backend/web/src/main/java/eu/eudat/logic/services/utilities/MailServiceImpl.java

@@ -1,7 +1,6 @@
 package eu.eudat.logic.services.utilities;
 
 import eu.eudat.models.data.mail.SimpleMail;
-import org.apache.commons.io.IOUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -17,10 +16,15 @@ import javax.mail.MessagingException;
 import javax.mail.internet.MimeBodyPart;
 import javax.mail.internet.MimeMessage;
 import javax.mail.internet.MimeMultipart;
-import java.io.*;
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.nio.charset.StandardCharsets;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.UUID;
+import java.util.stream.Collectors;
 
 
 @Service("mailService")
@@ -84,10 +88,11 @@ public class MailServiceImpl implements MailService {
         Resource resource = applicationContext.getResource(resourceTemplate);
         try {
             InputStream inputStream = resource.getInputStream();
-            StringWriter writer = new StringWriter();
-            IOUtils.copy(inputStream, writer, "UTF-8");
+            String tempate = new BufferedReader(
+                    new InputStreamReader(inputStream, StandardCharsets.UTF_8)
+            ).lines().collect(Collectors.joining("\n"));
             inputStream.close();
-            return writer.toString();
+            return tempate;
         } catch (IOException e) {
             logger.error(e.getMessage(), e);
         }

dmp-backend/web/src/main/java/eu/eudat/logic/services/utilities/UtilitiesService.java

@@ -1,5 +1,6 @@
 package eu.eudat.logic.services.utilities;
 
+import com.fasterxml.jackson.databind.ObjectMapper;
 import eu.eudat.logic.services.forms.VisibilityRuleService;
 
 /**
@@ -12,4 +13,6 @@ public interface UtilitiesService {
     MailService getMailService();
 
     ConfirmationEmailService getConfirmationEmailService();
+
+    ObjectMapper getGenericObjectMapper();
 }

dmp-backend/web/src/main/java/eu/eudat/logic/services/utilities/UtilitiesServiceImpl.java

@@ -1,5 +1,6 @@
 package eu.eudat.logic.services.utilities;
 
+import com.fasterxml.jackson.databind.ObjectMapper;
 import eu.eudat.logic.services.forms.VisibilityRuleService;
 import eu.eudat.logic.services.forms.VisibilityRuleServiceImpl;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -14,12 +15,14 @@ public class UtilitiesServiceImpl implements UtilitiesService {
     private InvitationService invitationService;
     private MailService mailService;
     private ConfirmationEmailService confirmationEmailService;
+    private final ObjectMapper objectMapper;
 
     @Autowired
     public UtilitiesServiceImpl(InvitationService invitationService, MailService mailService, ConfirmationEmailService confirmationEmailService) {
         this.invitationService = invitationService;
         this.mailService = mailService;
         this.confirmationEmailService = confirmationEmailService;
+        this.objectMapper = new ObjectMapper();
     }
 
     @Override
@@ -27,6 +30,11 @@ public class UtilitiesServiceImpl implements UtilitiesService {
         return confirmationEmailService;
     }
 
+    @Override
+    public ObjectMapper getGenericObjectMapper() {
+        return this.objectMapper;
+    }
+
     @Override
     public InvitationService getInvitationService() {
         return invitationService;

dmp-backend/web/src/main/java/eu/eudat/logic/utilities/builders/ModelBuilder.java

@@ -1,5 +1,6 @@
 package eu.eudat.logic.utilities.builders;
 
+import eu.eudat.logic.utilities.helpers.FieldFactory;
 import eu.eudat.models.data.entities.xmlmodels.datasetprofiledefinition.DatabaseViewStyleDefinition;
 import eu.eudat.models.data.components.commons.datafield.*;
 import eu.eudat.models.data.entities.xmlmodels.modeldefinition.DatabaseModelDefinition;
@@ -20,9 +21,7 @@ public class ModelBuilder {
         for (U item : items) {
             try {
                 list.add(item.toDatabaseDefinition(clazz.newInstance()));
-            } catch (InstantiationException e) {
-                logger.error(e.getMessage(), e);
-            } catch (IllegalAccessException e) {
+            } catch (InstantiationException | IllegalAccessException e) {
                 logger.error(e.getMessage(), e);
             }
         }
@@ -34,9 +33,7 @@ public class ModelBuilder {
         for (U item : items) {
             try {
                 list.add(item.toDatabaseDefinition(clazz.newInstance()));
-            } catch (InstantiationException e) {
-                logger.error(e.getMessage(), e);
-            } catch (IllegalAccessException e) {
+            } catch (InstantiationException | IllegalAccessException e) {
                 logger.error(e.getMessage(), e);
             }
         }
@@ -50,64 +47,71 @@ public class ModelBuilder {
                 U modelItem = clazz.newInstance();
                 modelItem.fromDatabaseDefinition(item);
                 list.add(modelItem);
-            } catch (InstantiationException e) {
-                logger.error(e.getMessage(), e);
-            } catch (IllegalAccessException e) {
+            } catch (InstantiationException | IllegalAccessException e) {
                 logger.error(e.getMessage(), e);
             }
         }
         return list;
     }
 
-    public <U> FieldData<U> toFieldData(Object data, String type, Element dataElement) {
-        if (type.equals("combobox")) {
+    public FieldData toFieldData(Object data, String type, Element dataElement) {
+        if (dataElement != null && dataElement.hasAttribute("type")) {
+            logger.info("Type " + type + " SubType " + dataElement.getAttribute("type"));
+            return FieldFactory.fromData(type, data, dataElement.getAttribute("type"));
+        }
+        return FieldFactory.fromData(type, data);
+        /*if (type.equals("combobox")) {
             if (dataElement != null) {
                 if (dataElement.getAttribute("type").equals("autocomplete")) {
-                    return (FieldData<U>) new AutoCompleteData().fromData(data);
+                    return new AutoCompleteData().fromData(data);
                 } else if (dataElement.getAttribute("type").equals("wordlist"))
-                    return (FieldData<U>) new WordListData().fromData(data);
+                    return new WordListData().fromData(data);
             }
         }
         if (type.equals("internalDmpEntities")) {
             if (dataElement != null) {
                 if (dataElement.getAttribute("type").equals("researchers")) {
-                    return (FieldData<U>) new ResearchersAutoCompleteData().fromData(data);
+                    return new ResearchersAutoCompleteData().fromData(data);
                 }
 				else if (dataElement.getAttribute("type").equals("datasets"))
-					return (FieldData<U>) new DatasetsAutoCompleteData().fromData(data);
+					return new DatasetsAutoCompleteData().fromData(data);
 				else if (dataElement.getAttribute("type").equals("dmps"))
-					return (FieldData<U>) new DMPsAutoCompleteData().fromData(data);
+					return new DMPsAutoCompleteData().fromData(data);
             }
         }
-        if (type.equals("booleanDecision")) return (FieldData<U>) new BooleanDecisionData().fromData(data);
-        if (type.equals("radiobox")) return (FieldData<U>) new RadioBoxData().fromData(data);
-        if (type.equals("checkBox")) return (FieldData<U>) new CheckBoxData().fromData(data);
-        if (type.equals("freetext")) return (FieldData<U>) new FreeTextData().fromData(data);
-        if (type.equals("textarea")) return (FieldData<U>) new TextAreaData().fromData(data);
-        if (type.equals("richTextarea")) return (FieldData<U>) new RichTextAreaData().fromData(data);
-        if (type.equals("upload")) return (FieldData<U>) new UploadData().fromData(data);
+        if (type.equals("booleanDecision")) return new BooleanDecisionData().fromData(data);
+        if (type.equals("radiobox")) return new RadioBoxData().fromData(data);
+        if (type.equals("checkBox")) return new CheckBoxData().fromData(data);
+        if (type.equals("freetext")) return new FreeTextData().fromData(data);
+        if (type.equals("textarea")) return new TextAreaData().fromData(data);
+        if (type.equals("richTextarea")) return new RichTextAreaData().fromData(data);
+        if (type.equals("upload")) return new UploadData().fromData(data);
 //        if (type.equals("table")) return (FieldData<U>) new TableData().fromData(data);
-        if (type.equals("datePicker")) return (FieldData<U>) new DatePickerData().fromData(data);
-        if (type.equals("externalDatasets")) return (FieldData<U>) new ExternalDatasetsData().fromData(data);
-        if (type.equals("dataRepositories")) return (FieldData<U>) new DataRepositoriesData().fromData(data);
-        if (type.equals("pubRepositories")) return (FieldData<U>) new DataRepositoriesData().fromData(data);
-        if (type.equals("journalRepositories")) return (FieldData<U>) new DataRepositoriesData().fromData(data);
-        if (type.equals("taxonomies")) return (FieldData<U>) new TaxonomiesData().fromData(data);
-        if (type.equals("licenses")) return (FieldData<U>) new LicensesData().fromData(data);
-        if (type.equals("publications")) return (FieldData<U>) new PublicationsData().fromData(data);
-        if (type.equals("registries")) return (FieldData<U>) new RegistriesData().fromData(data);
-        if (type.equals("services")) return (FieldData<U>) new ServicesData().fromData(data);
-        if (type.equals("tags")) return (FieldData<U>) new TagsData().fromData(data);
-        if (type.equals("researchers")) return (FieldData<U>) new ResearcherData().fromData(data);
-        if (type.equals("organizations")) return (FieldData<U>) new OrganizationsData().fromData(data);
-        if (type.equals("datasetIdentifier")) return (FieldData<U>) new DatasetIdentifierData().fromData(data);
-        if (type.equals("currency")) return (FieldData<U>) new CurrencyData().fromData(data);
-        if (type.equals("validation")) return (FieldData<U>) new ValidationData().fromData(data);
-        return null;
+        if (type.equals("datePicker")) return new DatePickerData().fromData(data);
+        if (type.equals("externalDatasets")) return new ExternalDatasetsData().fromData(data);
+        if (type.equals("dataRepositories")) return new DataRepositoriesData().fromData(data);
+        if (type.equals("pubRepositories")) return new DataRepositoriesData().fromData(data);
+        if (type.equals("journalRepositories")) return new DataRepositoriesData().fromData(data);
+        if (type.equals("taxonomies")) return new TaxonomiesData().fromData(data);
+        if (type.equals("licenses")) return new LicensesData().fromData(data);
+        if (type.equals("publications")) return new PublicationsData().fromData(data);
+        if (type.equals("registries")) return new RegistriesData().fromData(data);
+        if (type.equals("services")) return new ServicesData().fromData(data);
+        if (type.equals("tags")) return new TagsData().fromData(data);
+        if (type.equals("researchers")) return new ResearcherData().fromData(data);
+        if (type.equals("organizations")) return new OrganizationsData().fromData(data);
+        if (type.equals("datasetIdentifier")) return new DatasetIdentifierData().fromData(data);
+        if (type.equals("currency")) return new CurrencyData().fromData(data);
+        if (type.equals("validation")) return new ValidationData().fromData(data);*/
+        //return null;
     }
 
-    public <U> FieldData<U> toFieldData(Object data, String type) {
-        if (type.equals("combobox")) {
+    public FieldData toFieldData(Object data, String type) {
+        if (data != null && ((Map<String, Object>) data).containsKey("type")) {
+            return FieldFactory.fromData(type, data, (String) ((Map<String, Object>) data).get("type"));
+        }
+        return FieldFactory.fromData(type, data);
+        /*if (type.equals("combobox")) {
             String comboboxType = (String) ((Map<String, Object>) data).get("type");
             if (comboboxType.equals("autocomplete")) {
                 return (FieldData<U>) new AutoCompleteData().fromData(data);
@@ -150,6 +154,6 @@ public class ModelBuilder {
         if (type.equals("datasetIdentifier")) return (FieldData<U>) new DatasetIdentifierData().fromData(data);
         if (type.equals("currency")) return (FieldData<U>) new CurrencyData().fromData(data);
         if (type.equals("validation")) return (FieldData<U>) new ValidationData().fromData(data);
-        return null;
+        return null;*/
     }
 }

dmp-backend/web/src/main/java/eu/eudat/logic/utilities/documents/pdf/PDFUtils.java

@@ -1,7 +1,6 @@
 package eu.eudat.logic.utilities.documents.pdf;
 
 import eu.eudat.logic.utilities.documents.helpers.FileEnvelope;
-import org.apache.commons.io.IOUtils;
 import org.springframework.core.env.Environment;
 import org.springframework.core.io.FileSystemResource;
 import org.springframework.http.HttpEntity;
@@ -36,7 +35,8 @@ public class PDFUtils {
 
         File resultPdf = new File(environment.getProperty("temp.temp") + uuid + ".pdf");
         FileOutputStream output = new FileOutputStream(resultPdf);
-        IOUtils.write(queueResult, output);
+        output.write(queueResult);
+        output.flush();
         output.close();
         Files.deleteIfExists(file.getFile().toPath());
 

dmp-backend/web/src/main/java/eu/eudat/logic/utilities/documents/word/WordBuilder.java

@@ -1,5 +1,6 @@
 package eu.eudat.logic.utilities.documents.word;
 
+import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.DeserializationFeature;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import eu.eudat.logic.services.forms.VisibilityRuleService;
@@ -15,11 +16,12 @@ import eu.eudat.models.data.user.composite.PagedDatasetProfile;
 import org.apache.poi.openxml4j.exceptions.InvalidFormatException;
 import org.apache.poi.util.Units;
 import org.apache.poi.xwpf.usermodel.*;
-import org.json.JSONArray;
-import org.json.JSONException;
 import org.jsoup.Jsoup;
 import org.jsoup.nodes.Document;
-import org.openxmlformats.schemas.wordprocessingml.x2006.main.*;
+import org.openxmlformats.schemas.wordprocessingml.x2006.main.CTAbstractNum;
+import org.openxmlformats.schemas.wordprocessingml.x2006.main.CTDecimalNumber;
+import org.openxmlformats.schemas.wordprocessingml.x2006.main.CTLvl;
+import org.openxmlformats.schemas.wordprocessingml.x2006.main.STNumberFormat;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.core.env.Environment;
@@ -55,16 +57,17 @@ public class WordBuilder {
             }
     ).collect(Collectors.toMap(objects -> (String) objects[0], o -> (Integer) o[1]));
 
-    private Map<ParagraphStyle, ApplierWithValue<XWPFDocument, Object, XWPFParagraph>> options = new HashMap<>();
-    private CTAbstractNum cTAbstractNum;
+    private final Map<ParagraphStyle, ApplierWithValue<XWPFDocument, Object, XWPFParagraph>> options = new HashMap<>();
+    private final CTAbstractNum cTAbstractNum;
     private BigInteger numId;
     private Integer indent;
-    private static final ObjectMapper mapper = new ObjectMapper();
+    private final ObjectMapper mapper;
 
     public WordBuilder(Environment environment) {
         this.cTAbstractNum = CTAbstractNum.Factory.newInstance();
         this.cTAbstractNum.setAbstractNumId(BigInteger.valueOf(1));
         this.indent = 0;
+        this.mapper = new ObjectMapper();
         this.buildOptions(environment);
     }
 
@@ -164,7 +167,7 @@ public class WordBuilder {
             int format;
             format = IMAGE_TYPE_MAP.getOrDefault(fileType, 0);
             try {
-                FileInputStream image = new FileInputStream(environment.getProperty("file.storage") + imageId);
+
                 ImageInputStream iis = ImageIO.createImageInputStream(new File(environment.getProperty("file.storage") + imageId));
                 Iterator<ImageReader> readers = ImageIO.getImageReaders(iis);
                 if (readers.hasNext()) {
@@ -176,17 +179,17 @@ public class WordBuilder {
 
                     float ratio = initialImageHeight / (float) initialImageWidth;
 
-                    int marginLeftInDXA = mainDocumentPart.getDocument().getBody().getSectPr().getPgMar().getLeft().intValue();
-                    int marginRightInDXA = mainDocumentPart.getDocument().getBody().getSectPr().getPgMar().getRight().intValue();
-                    int pageWidthInDXA = mainDocumentPart.getDocument().getBody().getSectPr().getPgSz().getW().intValue();
+                    int marginLeftInDXA = ((BigInteger) mainDocumentPart.getDocument().getBody().getSectPr().getPgMar().getLeft()).intValue();
+                    int marginRightInDXA = ((BigInteger) mainDocumentPart.getDocument().getBody().getSectPr().getPgMar().getRight()).intValue();
+                    int pageWidthInDXA = ((BigInteger) mainDocumentPart.getDocument().getBody().getSectPr().getPgSz().getW()).intValue();
                     int pageWidth = Math.round((pageWidthInDXA - marginLeftInDXA - marginRightInDXA) / (float) 20); // /20 converts dxa to points
 
                     int imageWidth = Math.round(initialImageWidth * (float) 0.75);    // *0.75 converts pixels to points
                     int width = Math.min(imageWidth, pageWidth);
 
-                    int marginTopInDXA = mainDocumentPart.getDocument().getBody().getSectPr().getPgMar().getTop().intValue();
-                    int marginBottomInDXA = mainDocumentPart.getDocument().getBody().getSectPr().getPgMar().getBottom().intValue();
-                    int pageHeightInDXA = mainDocumentPart.getDocument().getBody().getSectPr().getPgSz().getH().intValue();
+                    int marginTopInDXA = ((BigInteger) mainDocumentPart.getDocument().getBody().getSectPr().getPgMar().getTop()).intValue();
+                    int marginBottomInDXA = ((BigInteger) mainDocumentPart.getDocument().getBody().getSectPr().getPgMar().getBottom()).intValue();
+                    int pageHeightInDXA = ((BigInteger) mainDocumentPart.getDocument().getBody().getSectPr().getPgSz().getH()).intValue();
                     int pageHeight = Math.round((pageHeightInDXA - marginTopInDXA - marginBottomInDXA) / (float) 20);    // /20 converts dxa to points
 
                     int imageHeight = Math.round(initialImageHeight * ((float) 0.75));  // *0.75 converts pixels to points
@@ -197,7 +200,7 @@ public class WordBuilder {
                         height = Math.min(imageHeight, pageHeight);
                         width = Math.round(height / ratio);
                     }
-
+                    FileInputStream image = new FileInputStream(environment.getProperty("file.storage") + imageId);
                     run.addPicture(image, format, fileName, Units.toEMU(width), Units.toEMU(height));
                     paragraph.setPageBreak(false);
                 }
@@ -380,16 +383,16 @@ public class WordBuilder {
             return null;
         }
         try {
-            JSONArray array = new JSONArray(JavaToJson.objectStringToJson(format));
+            List<Map<String, Object>> array = this.mapper.readValue(JavaToJson.objectStringToJson(format), ArrayList.class);
             StringBuilder multipleFormats = new StringBuilder();
-            for (int i = 0; i < array.length(); i++) {
-                multipleFormats.append(array.getJSONObject(i).getString(attribute)).append(", ");
+            for (Map<String, Object> node : array) {
+                multipleFormats.append(node.get(attribute)).append(", ");
             }
             if (multipleFormats.length() > 0) {
                 multipleFormats.setLength(multipleFormats.length() - 2);
             }
             return multipleFormats.toString();
-        } catch (JSONException e) {
+        } catch (JsonProcessingException e) {
             return format;
         }
     }

dmp-backend/web/src/main/java/eu/eudat/logic/utilities/documents/xml/ExportXmlBuilder.java

@@ -1,7 +1,6 @@
 package eu.eudat.logic.utilities.documents.xml;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
-import com.fasterxml.jackson.databind.exc.MismatchedInputException;
 import eu.eudat.logic.services.forms.VisibilityRuleService;
 import eu.eudat.logic.utilities.builders.XmlBuilder;
 import eu.eudat.models.data.components.commons.datafield.ExternalDatasetsData;
@@ -10,8 +9,6 @@ import eu.eudat.models.data.user.components.datasetprofile.FieldSet;
 import eu.eudat.models.data.user.components.datasetprofile.Section;
 import eu.eudat.models.data.user.composite.DatasetProfilePage;
 import eu.eudat.models.data.user.composite.PagedDatasetProfile;
-import org.json.JSONArray;
-import org.json.JSONException;
 import org.springframework.core.env.Environment;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;

dmp-backend/web/src/main/java/eu/eudat/logic/utilities/helpers/FieldFactory.java

@@ -0,0 +1,63 @@
+package eu.eudat.logic.utilities.helpers;
+
+import eu.eudat.models.data.components.commons.datafield.*;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.lang.reflect.Modifier;
+import java.util.Map;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+
+public class FieldFactory {
+    private static final Logger logger = LoggerFactory.getLogger(FieldFactory.class);
+    private static final Map<String, Class<? extends FieldData>> fieldMap = Stream.of(new Object[][]{
+            {"combobox", ComboBoxData.class},
+            {"autocomplete", AutoCompleteData.class},
+            {"wordlist", WordListData.class},
+            {"internalDmpEntities", InternalDmpEntitiesData.class},
+            {"researchers", ResearcherData.class},
+            {"datasets", DatasetsAutoCompleteData.class},
+            {"dmps", DMPsAutoCompleteData.class},
+            {"booleanDecision", BooleanDecisionData.class},
+            {"radiobox", RadioBoxData.class},
+            {"checkBox", CheckBoxData.class},
+            {"freetext", FreeTextData.class},
+            {"textarea", TextAreaData.class},
+            {"richTextarea", RichTextAreaData.class},
+            {"upload", UploadData.class},
+            {"datePicker", DatePickerData.class},
+            {"externalDatasets", ExternalDatasetsData.class},
+            {"dataRepositories", DataRepositoriesData.class},
+            {"pubRepositories", DataRepositoriesData.class},
+            {"journalRepositories", DataRepositoriesData.class},
+            {"taxonomies", TaxonomiesData.class},
+            {"licenses", LicensesData.class},
+            {"publications", PublicationsData.class},
+            {"registries", RegistriesData.class},
+            {"services", ServicesData.class},
+            {"tags", TagsData.class},
+            {"organizations", OrganizationsData.class},
+            {"datasetIdentifier", DatasetIdentifierData.class},
+            {"currency", CurrencyData.class},
+            {"validation", ValidationData.class}
+    }).collect(Collectors.toMap(data -> (String) data[0], data -> (Class<? extends FieldData>) data[1]));
+
+    public static FieldData fromData(String type, Object data, String subType) {
+        if (Modifier.isAbstract(fieldMap.get(type).getModifiers())) {
+            return fromData(subType, data);
+        } else {
+            return fromData(type, data);
+        }
+    }
+
+    public static FieldData fromData(String type, Object data) {
+        try {
+            return (FieldData) fieldMap.get(type).newInstance().fromData(data);
+        } catch (InstantiationException | IllegalAccessException e) {
+            logger.error(e.getMessage(), e);
+        }
+        return null;
+    }
+
+}

dmp-backend/web/src/main/java/eu/eudat/logic/utilities/schedule/file/FileCleanUpJobs.java

@@ -0,0 +1,120 @@
+package eu.eudat.logic.utilities.schedule.file;
+
+import eu.eudat.configurations.file.PermProperties;
+import eu.eudat.configurations.file.TimeProperties;
+import eu.eudat.configurations.file.TmpProperties;
+import eu.eudat.data.entities.FileUpload;
+import eu.eudat.logic.managers.FileManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.core.env.Environment;
+import org.springframework.scheduling.annotation.Scheduled;
+import org.springframework.stereotype.Component;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Objects;
+import java.util.stream.Collectors;
+
+@Component
+public class FileCleanUpJobs {
+    private static final Logger logger = LoggerFactory.getLogger(FileCleanUpJobs.class);
+
+    private final FileManager fileManager;
+    private final Environment environment;
+
+    @Autowired
+    public FileCleanUpJobs(FileManager fileManager, Environment environment, PermProperties permProperties, TmpProperties tmpProperties) {
+        this.fileManager = fileManager;
+        this.environment = environment;
+        if (permProperties != null) {
+            System.getProperties().put("perm.cron", createCron(permProperties.getTime()));
+        }
+        if (tmpProperties != null) {
+            System.getProperties().put("temp.cron", createCron(tmpProperties.getTime()));
+        }
+
+    }
+
+    @Scheduled(cron = "${perm.cron}")
+    public void deleteUnusedPermFiles() {
+        logger.info("Start deleting unused permanent files");
+        List<FileUpload> fileUploads = fileManager.getDeletedFileUploads();
+        try {
+            List<Path> tempFilePaths = Files.walk(Paths.get(Objects.requireNonNull(environment.getProperty("file.storage")))).filter(Files::isRegularFile).collect(Collectors.toList());
+            for (Path tempFilePath : tempFilePaths) {
+                if (fileUploads.stream().map(FileUpload::getId).anyMatch(uuid -> tempFilePath.endsWith(uuid.toString()))) {
+                    Files.deleteIfExists(tempFilePath);
+                }
+            }
+            logger.info("Unused permanent files have been successfully deleted");
+        } catch (IOException e) {
+            logger.error(e.getLocalizedMessage(), e);
+        }
+    }
+
+    @Scheduled(cron = "${temp.cron}")
+    public void deleteTempFiles() {
+        logger.info("Start deleting temporary files");
+        try {
+            List<Path> tempFilePaths = Files.walk(Paths.get(Objects.requireNonNull(environment.getProperty("temp.temp")))).filter(Files::isRegularFile).collect(Collectors.toList());
+            for (Path tempFilePath : tempFilePaths) {
+                Files.deleteIfExists(tempFilePath);
+            }
+            logger.info("Temporary files have been successfully deleted");
+        } catch (IOException e) {
+            logger.error(e.getLocalizedMessage(), e);
+        }
+    }
+
+    private String createCron(TimeProperties timeProperties) {
+        List<String> cronList = new LinkedList<>();
+        cronList.add("0");
+        switch (timeProperties.getTimeUnit()) {
+            case MINUTES:
+                cronList.add("0/" + timeProperties.getInterval());
+                break;
+            case HOURS:
+                cronList.add(toSafeString(timeProperties.getStartTime().getMinute()));
+                cronList.add("0/" + timeProperties.getInterval());
+                break;
+            case DAYS:
+                cronList.add(toSafeString(timeProperties.getStartTime().getMinute()));
+                cronList.add(toSafeString(timeProperties.getStartTime().getHour()));
+                cronList.add("*/" + timeProperties.getInterval());
+                break;
+            case MONTHS:
+                cronList.add(toSafeString(timeProperties.getStartTime().getMinute()));
+                cronList.add(toSafeString(timeProperties.getStartTime().getHour()));
+                cronList.add(toSafeString(timeProperties.getStartTime().getDayOfMonth(), "1"));
+                cronList.add("*/" + timeProperties.getInterval());
+                break;
+            case WEEKS:
+                cronList.add(toSafeString(timeProperties.getStartTime().getMinute()));
+                cronList.add(toSafeString(timeProperties.getStartTime().getHour()));
+                cronList.add("*/" + (timeProperties.getInterval() * 7));
+                cronList.add("*");
+                cronList.add(toSafeString(timeProperties.getStartTime().getDayOfWeek(), "1"));
+                break;
+        }
+        if (cronList.size() < 6) {
+            for (int i = cronList.size(); i < 6; i++) {
+                cronList.add("*");
+            }
+        }
+        return String.join(" ", cronList);
+    }
+
+    private String toSafeString(Object object) {
+        return toSafeString(object, "0");
+    }
+
+    private String toSafeString(Object object, String defaultValue) {
+        return object != null ? object.toString() : defaultValue;
+    }
+}

dmp-backend/web/src/main/java/eu/eudat/logic/utilities/schedule/notification/NotificationScheduleJob.java

@@ -20,8 +20,8 @@ import java.util.concurrent.CompletableFuture;
 public class NotificationScheduleJob {
     private static final Logger logger = LoggerFactory.getLogger(NotificationScheduleJob.class);
 
-	private ApiContext apiContext;
-	private NotificationManager notificationManager;
+    private final ApiContext apiContext;
+    private final NotificationManager notificationManager;
 
     @Autowired
     public NotificationScheduleJob(ApiContext apiContext, NotificationManager notificationManager) {

dmp-backend/web/src/main/java/eu/eudat/models/data/components/commons/datafield/FieldData.java

@@ -1,5 +1,6 @@
 package eu.eudat.models.data.components.commons.datafield;
 
+import eu.eudat.logic.utilities.helpers.FieldFactory;
 import eu.eudat.logic.utilities.interfaces.XmlSerializable;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
@@ -21,6 +22,10 @@ public abstract class FieldData<T> implements XmlSerializable<T> {
         return null;
     }
 
+    public T fromData(Object data, String subType) {
+        return (T) FieldFactory.fromData(subType, data);
+    }
+
     public Object toData() {
         return null;
     }

dmp-backend/web/src/main/java/eu/eudat/models/data/components/commons/datafield/UploadData.java

@@ -13,7 +13,7 @@ import java.util.Map;
 
 
 public class UploadData extends FieldData<UploadData> {
-    public class Option implements XmlSerializable<UploadData.Option> {
+    public static class Option implements XmlSerializable<UploadData.Option> {
         private String label;
         private String value;
 
@@ -77,7 +77,7 @@ public class UploadData extends FieldData<UploadData> {
         if (data != null) {
             List<Map<String, String>> types = ((Map<String, List<Map<String, String>>>) data).get("types");
             for (Map<String, String> map : types) {
-                UploadData.Option newOption = new UploadData.Option();
+                UploadData.Option newOption = new Option();
                 newOption.setLabel(map.get("label"));
                 newOption.setValue(map.get("value"));
                 this.types.add(newOption);
@@ -125,7 +125,7 @@ public class UploadData extends FieldData<UploadData> {
             for (int temp = 0; temp < optionElements.getLength(); temp++) {
                 Node optionElement = optionElements.item(temp);
                 if (optionElement.getNodeType() == Node.ELEMENT_NODE) {
-                    this.types.add(new UploadData.Option().fromXml((Element) optionElement));
+                    this.types.add(new Option().fromXml((Element) optionElement));
                 }
             }
         }

dmp-backend/web/src/main/java/eu/eudat/models/data/dmp/DataManagementPlan.java

@@ -1,5 +1,7 @@
 package eu.eudat.models.data.dmp;
 
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.ObjectMapper;
 import eu.eudat.data.entities.*;
 import eu.eudat.logic.utilities.builders.XmlBuilder;
 import eu.eudat.models.DataModel;
@@ -7,18 +9,21 @@ import eu.eudat.models.data.datasetwizard.DatasetWizardModel;
 import eu.eudat.models.data.dynamicfields.DynamicFieldWithValue;
 import eu.eudat.models.data.entities.xmlmodels.dmpprofiledefinition.DataManagementPlanProfile;
 import eu.eudat.models.data.funder.Funder;
-import eu.eudat.models.data.helpermodels.Tuple;
-import eu.eudat.models.data.listingmodels.DatasetListingModel;
-import eu.eudat.models.data.listingmodels.UserInfoListingModel;
 import eu.eudat.models.data.grant.Grant;
+import eu.eudat.models.data.helpermodels.Tuple;
+import eu.eudat.models.data.listingmodels.UserInfoListingModel;
 import eu.eudat.models.data.project.Project;
 import eu.eudat.models.data.userinfo.UserListingModel;
 import net.minidev.json.JSONObject;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import java.util.*;
 import java.util.stream.Collectors;
 
 public class DataManagementPlan implements DataModel<DMP, DataManagementPlan> {
+    private static final ObjectMapper objectMapper = new ObjectMapper();
+    private static final Logger logger = LoggerFactory.getLogger(DataManagementPlan.class);
     private UUID id;
     private String label;
     private UUID groupId;
@@ -233,6 +238,7 @@ public class DataManagementPlan implements DataModel<DMP, DataManagementPlan> {
 
     @Override
     public DataManagementPlan fromDataModel(DMP entity) {
+        try {
             this.id = entity.getId();
             this.profile = entity.getProfile() != null ? new Tuple<UUID, String>(entity.getProfile().getId(), entity.getProfile().getLabel()) : null;
             this.organisations = entity.getOrganisations() != null ? entity.getOrganisations().stream().map(item -> new Organisation().fromDataModel(item)).collect(Collectors.toList()) : new ArrayList<>();
@@ -241,7 +247,7 @@ public class DataManagementPlan implements DataModel<DMP, DataManagementPlan> {
             this.groupId = this.groupId == null ? null : entity.getGroupId();
             this.label = entity.getLabel();
             this.grant = new Grant();
-        this.properties = entity.getProperties() != null ? new org.json.JSONObject(entity.getProperties()).toMap() : null;
+            this.properties = entity.getProperties() != null ? objectMapper.readValue(entity.getProperties(), LinkedHashMap.class) : null;
             this.grant.fromDataModel(entity.getGrant());
             this.creator = new eu.eudat.models.data.userinfo.UserInfo();
             this.groupId = entity.getGroupId();
@@ -293,7 +299,10 @@ public class DataManagementPlan implements DataModel<DMP, DataManagementPlan> {
             }
             this.isPublic = entity.isPublic();
 
-        this.extraProperties = entity.getExtraProperties() != null ? new org.json.JSONObject(entity.getExtraProperties()).toMap() : null;
+            this.extraProperties = entity.getExtraProperties() != null ? objectMapper.readValue(entity.getExtraProperties(), LinkedHashMap.class) : null;
+        } catch (JsonProcessingException e) {
+            logger.error(e.getLocalizedMessage(), e);
+        }
 
         return this;
     }
@@ -342,6 +351,7 @@ public class DataManagementPlan implements DataModel<DMP, DataManagementPlan> {
     }
 
     public DataManagementPlan fromDataModelNoDatasets(DMP entity) {
+        try {
             this.id = entity.getId();
             this.profile = entity.getProfile() != null ? new Tuple<UUID, String>(entity.getProfile().getId(), entity.getProfile().getLabel()) : null;
             this.organisations = entity.getOrganisations() != null ? entity.getOrganisations().stream().map(item -> new Organisation().fromDataModel(item)).collect(Collectors.toList()) : new ArrayList<>();
@@ -349,7 +359,7 @@ public class DataManagementPlan implements DataModel<DMP, DataManagementPlan> {
             this.version = entity.getVersion();
             this.label = entity.getLabel();
             this.grant = new Grant();
-        this.properties = entity.getProperties() != null ? new org.json.JSONObject(entity.getProperties()).toMap() : null;
+            this.properties = entity.getProperties() != null ? objectMapper.readValue(entity.getProperties(), LinkedHashMap.class) : null;
             this.creator = new eu.eudat.models.data.userinfo.UserInfo();
             this.groupId = entity.getGroupId();
             this.lockable = entity.getDataset() != null && entity.getDataset().stream().findAny().isPresent();
@@ -389,7 +399,10 @@ public class DataManagementPlan implements DataModel<DMP, DataManagementPlan> {
             }
             this.isPublic = entity.isPublic();
 
-        this.extraProperties = entity.getExtraProperties() != null ? new org.json.JSONObject(entity.getExtraProperties()).toMap() : null;
+            this.extraProperties = entity.getExtraProperties() != null ? objectMapper.readValue(entity.getExtraProperties(), LinkedHashMap.class) : null;
+        } catch (JsonProcessingException e) {
+            logger.error(e.getLocalizedMessage(), e);
+        }
 
         return this;
     }

dmp-backend/web/src/main/java/eu/eudat/models/data/dmp/DataManagementPlanEditorModel.java

@@ -1,5 +1,8 @@
 package eu.eudat.models.data.dmp;
 
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.JsonMappingException;
+import com.fasterxml.jackson.databind.ObjectMapper;
 import eu.eudat.data.entities.*;
 import eu.eudat.logic.utilities.builders.XmlBuilder;
 import eu.eudat.models.DataModel;
@@ -14,11 +17,15 @@ import eu.eudat.models.data.grant.GrantDMPEditorModel;
 import eu.eudat.models.data.project.ProjectDMPEditorModel;
 import eu.eudat.models.data.userinfo.UserListingModel;
 import net.minidev.json.JSONObject;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import java.util.*;
 import java.util.stream.Collectors;
 
 public class DataManagementPlanEditorModel implements DataModel<DMP, DataManagementPlanEditorModel> {
+    private static final ObjectMapper objectMapper = new ObjectMapper();
+    private static final Logger logger = LoggerFactory.getLogger(DataManagementPlanEditorModel.class);
     private UUID id;
     private String label;
     private UUID groupId;
@@ -224,6 +231,7 @@ public class DataManagementPlanEditorModel implements DataModel<DMP, DataManagem
 
     @Override
     public DataManagementPlanEditorModel fromDataModel(DMP entity) {
+        try {
             this.id = entity.getId();
             this.profile = entity.getProfile() != null ? new Tuple<UUID, String>(entity.getProfile().getId(), entity.getProfile().getLabel()) : null;
             this.organisations = entity.getOrganisations().stream().map(item -> new Organisation().fromDataModel(item)).collect(Collectors.toList());
@@ -232,7 +240,7 @@ public class DataManagementPlanEditorModel implements DataModel<DMP, DataManagem
             this.groupId = this.groupId == null ? null : entity.getGroupId();
             this.label = entity.getLabel();
             this.grant = new GrantDMPEditorModel();
-        this.properties = entity.getProperties() != null ? new org.json.JSONObject(entity.getProperties()).toMap() : null;
+            this.properties = entity.getProperties() != null ? objectMapper.readValue(entity.getProperties(), LinkedHashMap.class) : null;
             this.grant.getExistGrant().fromDataModel(entity.getGrant());
             this.grant.getExistGrant().setSource("");
             this.creator = new eu.eudat.models.data.userinfo.UserInfo();
@@ -266,7 +274,10 @@ public class DataManagementPlanEditorModel implements DataModel<DMP, DataManagem
             this.users = entity.getUsers().stream().map(item -> new UserInfoListingModel().fromDataModel(item)).collect(Collectors.toList());
             this.funder = new FunderDMPEditorModel();
             this.funder.getExistFunder().fromDataModel(entity.getGrant().getFunder());
-        this.extraProperties = entity.getExtraProperties() != null ? new org.json.JSONObject(entity.getExtraProperties()).toMap() : null;
+            this.extraProperties = entity.getExtraProperties() != null ? objectMapper.readValue(entity.getExtraProperties(), LinkedHashMap.class) : null;
+        } catch (JsonProcessingException e) {
+            logger.error(e.getLocalizedMessage(), e);
+        }
 
         return this;
     }

dmp-backend/web/src/main/java/eu/eudat/models/data/rda/ContactRDAExportModel.java

@@ -1,44 +0,0 @@
-package eu.eudat.models.data.rda;
-
-import eu.eudat.data.entities.UserInfo;
-
-public class ContactRDAExportModel {
-    private String mbox;
-    private String name;
-    private IdRDAExportModel contact_id;
-
-    public String getMbox() {
-        return mbox;
-    }
-    public void setMbox(String mbox) {
-        this.mbox = mbox;
-    }
-
-    public String getName() {
-        return name;
-    }
-    public void setName(String name) {
-        this.name = name;
-    }
-
-    public IdRDAExportModel getContact_id() {
-        return contact_id;
-    }
-    public void setContact_id(IdRDAExportModel contact_id) {
-        this.contact_id = contact_id;
-    }
-
-    public ContactRDAExportModel fromDataModel(UserInfo entity) {
-        ContactRDAExportModel contact = new ContactRDAExportModel();
-        contact.mbox = entity.getEmail();
-        contact.name = entity.getName();
-        // TODO: we should use a contact_id and not our UUID.
-        if (!entity.getId().toString().isEmpty()) {
-            contact.contact_id = new IdRDAExportModel(entity.getId().toString(), "other");
-        }
-        else {
-            contact.contact_id = null;
-        }
-        return contact;
-    }
-}

dmp-backend/web/src/main/java/eu/eudat/models/data/rda/DatasetDistributionRDAExportModel.java

@@ -1,93 +0,0 @@
-package eu.eudat.models.data.rda;
-
-import com.fasterxml.jackson.annotation.JsonIgnore;
-
-import java.util.List;
-
-public class DatasetDistributionRDAExportModel {
-	private String access_url;
-	private String available_till;
-	private String byte_size;
-	private String data_access; // Allowed values: open / shared / closed
-	private String description;
-	private String download_url;
-	private List<String> format; // Format according to: https://www.iana.org/assignments/media-types/media-types.xhtml if appropriate, otherwise use the common name for this format
-	private HostRDAExportModel host;
-	private List<LicenseRDAExportModel> license;
-	private String title;
-
-	public String getAccess_url() {
-		return access_url;
-	}
-	public void setAccess_url(String access_url) {
-		this.access_url = access_url;
-	}
-
-	public String getAvailable_till() {
-		return available_till;
-	}
-	public void setAvailable_till(String available_till) {
-		this.available_till = available_till;
-	}
-
-	public String getByte_size() {
-		return byte_size;
-	}
-	public void setByte_size(String byte_size) {
-		this.byte_size = byte_size;
-	}
-
-	public String getData_access() {
-		return data_access;
-	}
-	public void setData_access(String data_access) {
-		this.data_access = data_access;
-	}
-
-	public String getDescription() {
-		return description;
-	}
-	public void setDescription(String description) {
-		this.description = description;
-	}
-
-	public String getDownload_url() {
-		return download_url;
-	}
-	public void setDownload_url(String download_url) {
-		this.download_url = download_url;
-	}
-
-	public List<String> getFormat() {
-		return format;
-	}
-	public void setFormat(List<String> format) {
-		this.format = format;
-	}
-
-	public HostRDAExportModel getHost() {
-		return host;
-	}
-	public void setHost(HostRDAExportModel host) {
-		this.host = host;
-	}
-
-	public List<LicenseRDAExportModel> getLicense() {
-		return license;
-	}
-	public void setLicense(List<LicenseRDAExportModel> license) {
-		this.license = license;
-	}
-
-	public String getTitle() {
-		return title;
-	}
-	public void setTitle(String title) {
-		this.title = title;
-	}
-
-	@JsonIgnore
-	public boolean isValid() {
-		return title != null || data_access != null;
-	}
-}

dmp-backend/web/src/main/java/eu/eudat/models/data/rda/DatasetMetadataRDAExportModel.java

@@ -1,47 +0,0 @@
-package eu.eudat.models.data.rda;
-
-import com.fasterxml.jackson.annotation.JsonIgnore;
-
-public class DatasetMetadataRDAExportModel {
-	private String description; // Not mandatory.
-	private String language;
-	private IdRDAExportModel metadata_standard_id;
-
-	public String getDescription() {
-		return description;
-	}
-	public void setDescription(String description) {
-		this.description = description;
-	}
-
-	public String getLanguage() {
-		return language;
-	}
-	public void setLanguage(String language) {
-		this.language = language;
-	}
-
-	public IdRDAExportModel getMetadata_standard_id() {
-		return metadata_standard_id;
-	}
-	public void setMetadata_standard_id(IdRDAExportModel metadata_standard_id) {
-		this.metadata_standard_id = metadata_standard_id;
-	}
-
-	public DatasetMetadataRDAExportModel fromDataModel(String key, Object value) {
-		DatasetMetadataRDAExportModel metadataRDAExportModel = new DatasetMetadataRDAExportModel();
-		if (key.contains("metadata_standard_id"))
-			metadataRDAExportModel.setMetadata_standard_id(new IdRDAExportModel(value.toString(), "other"));
-		else if (key.contains("language"))
-			metadataRDAExportModel.setLanguage(value.toString());
-		else if (key.contains("description"))
-			metadataRDAExportModel.setDescription(value.toString());
-
-		return metadataRDAExportModel;
-	}
-
-	@JsonIgnore
-	public boolean isValid() {
-		return description != null || language != null || metadata_standard_id != null;
-	}
-}

dmp-backend/web/src/main/java/eu/eudat/models/data/rda/DatasetRDAExportModel.java

@@ -1,474 +0,0 @@
-package eu.eudat.models.data.rda;
-
-import com.fasterxml.jackson.core.JsonProcessingException;
-import com.fasterxml.jackson.databind.DeserializationFeature;
-import com.fasterxml.jackson.databind.ObjectMapper;
-import com.jayway.jsonpath.JsonPath;
-import eu.eudat.data.entities.Dataset;
-import eu.eudat.logic.managers.DatasetManager;
-import eu.eudat.logic.utilities.builders.XmlBuilder;
-import eu.eudat.models.data.security.Principal;
-import org.json.JSONArray;
-import org.json.JSONObject;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.w3c.dom.Document;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-
-import javax.xml.xpath.*;
-import java.text.DateFormat;
-import java.util.*;
-
-import static java.util.stream.Collectors.groupingBy;
-
-public class DatasetRDAExportModel {
-	private static final Logger logger = LoggerFactory.getLogger(DatasetRDAExportModel.class);
-
-	private static final ObjectMapper mapper = new ObjectMapper().configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
-	private Map<String, String> multiplicityIdToFieldSetId = new HashMap<>();
-
-	private List<String> data_quality_assurance;
-	private IdRDAExportModel dataset_id;
-	private String description;
-	private List<DatasetDistributionRDAExportModel> distribution;
-	private String issued; // Created Date, could also use finalized one.
-	private List<String> keyword;
-	private String language;
-	private List<DatasetMetadataRDAExportModel> metadata;
-	private String personal_data; // Allowed Values: yes no unknown.
-	private String preservation_statement;
-	private List<DatasetSecurityAndPrivacyRDAExportModel> security_and_privacy;
-	private String sensitive_data; // Allowed Values: yes no unknown.
-	private List<DatasetTechnicalResourceRDAExportModel> technical_resource;
-	private String title;
-	private String type; // Type according to: http://vocabularies.coar-repositories.org/pubby/resource_type.html
-
-	public List<String> getData_quality_assurance() {
-		return data_quality_assurance;
-	}
-	public void setData_quality_assurance(List<String> data_quality_assurance) {
-		this.data_quality_assurance = data_quality_assurance;
-	}
-
-	public IdRDAExportModel getDataset_id() {
-		return dataset_id;
-	}
-	public void setDataset_id(IdRDAExportModel dataset_id) {
-		this.dataset_id = dataset_id;
-	}
-
-	public String getDescription() {
-		return description;
-	}
-	public void setDescription(String description) {
-		this.description = description;
-	}
-
-	public List<DatasetDistributionRDAExportModel> getDistribution() {
-		return distribution;
-	}
-	public void setDistribution(List<DatasetDistributionRDAExportModel> distribution) {
-		this.distribution = distribution;
-	}
-
-	public String getIssued() {
-		return issued;
-	}
-	public void setIssued(String issued) {
-		this.issued = issued;
-	}
-
-	public List<String> getKeyword() {
-		return keyword;
-	}
-	public void setKeyword(List<String> keyword) {
-		this.keyword = keyword;
-	}
-
-	public String getLanguage() {
-		return language;
-	}
-	public void setLanguage(String language) {
-		this.language = language;
-	}
-
-	public List<DatasetMetadataRDAExportModel> getMetadata() {
-		return metadata;
-	}
-	public void setMetadata(List<DatasetMetadataRDAExportModel> metadata) {
-		this.metadata = metadata;
-	}
-
-	public String getPersonal_data() {
-		return personal_data;
-	}
-	public void setPersonal_data(String personal_data) {
-		this.personal_data = personal_data;
-	}
-
-	public String getPreservation_statement() {
-		return preservation_statement;
-	}
-	public void setPreservation_statement(String preservation_statement) {
-		this.preservation_statement = preservation_statement;
-	}
-
-	public List<DatasetSecurityAndPrivacyRDAExportModel> getSecurity_and_privacy() {
-		return security_and_privacy;
-	}
-	public void setSecurity_and_privacy(List<DatasetSecurityAndPrivacyRDAExportModel> security_and_privacy) {
-		this.security_and_privacy = security_and_privacy;
-	}
-
-	public String getSensitive_data() {
-		return sensitive_data;
-	}
-	public void setSensitive_data(String sensitive_data) {
-		this.sensitive_data = sensitive_data;
-	}
-
-	public List<DatasetTechnicalResourceRDAExportModel> getTechnical_resource() {
-		return technical_resource;
-	}
-	public void setTechnical_resource(List<DatasetTechnicalResourceRDAExportModel> technical_resource) {
-		this.technical_resource = technical_resource;
-	}
-
-	public String getTitle() {
-		return title;
-	}
-	public void setTitle(String title) {
-		this.title = title;
-	}
-
-	public String getType() {
-		return type;
-	}
-	public void setType(String type) {
-		this.type = type;
-	}
-
-
-	public DatasetRDAExportModel fromDataModel(Dataset dataset, DatasetManager datasetManager, Principal principal) {
-		// Map of template Ids to rda values.
-		JSONObject jObject = new JSONObject(dataset.getProperties());
-		Map<String, Object> templateIdsToValues = jObject.toMap();
-
-		/*--------- Building dataset rda export model ---------*/
-		DatasetRDAExportModel datasetRDAExportModel = new DatasetRDAExportModel();
-		datasetRDAExportModel.setDataset_id(new IdRDAExportModel(dataset.getId().toString(), "other"));
-		if (dataset.getDescription() != null) datasetRDAExportModel.setDescription(dataset.getDescription().replace("\n", " "));
-		datasetRDAExportModel.setIssued(DateFormat.getDateInstance(DateFormat.SHORT).format(dataset.getCreated()));
-		datasetRDAExportModel.setLanguage("en"); // mock data
-		datasetRDAExportModel.setTitle(dataset.getLabel());
-
-		// Transform the answered dataset description to json so we can parse it and fill the rda model.
-		JSONObject datasetDescriptionJson = null;
-		try {
-			String jsonResult = mapper.writeValueAsString(datasetManager.getSingle(dataset.getId().toString(), principal).getDatasetProfileDefinition());
-			datasetDescriptionJson = new JSONObject(jsonResult);
-		} catch (JsonProcessingException e) {
-			logger.error(e.getMessage(), e);
-		}
-		setMultiplicityIdToFieldSetId(datasetDescriptionJson);
-
-		/*--------- Building personal data. ---------*/
-		String personalData = buildSingleProperties("dataset.personal_data", datasetDescriptionJson, templateIdsToValues);
-		if (personalData != null) {
-			datasetRDAExportModel.setPersonal_data(personalData);
-		} else {
-			datasetRDAExportModel.setPersonal_data("unknown");
-		}
-
-		/*--------- Building preservation statement. ---------*/
-		datasetRDAExportModel.setPreservation_statement(buildSingleProperties("dataset.preservation_statement", datasetDescriptionJson, templateIdsToValues));
-
-		/*--------- Building sensitive data. ---------*/
-		String sensitiveData = buildSingleProperties("dataset.sensitive_data", datasetDescriptionJson, templateIdsToValues);
-		if (personalData != null) {
-			datasetRDAExportModel.setSensitive_data(sensitiveData);
-		} else {
-			datasetRDAExportModel.setSensitive_data("unknown");
-		}
-
-		/*--------- Building type. ---------*/
-		datasetRDAExportModel.setType(buildSingleProperties("dataset.type", datasetDescriptionJson, templateIdsToValues));
-
-		/*--------- Building data_quality_assurance. ---------*/
-		datasetRDAExportModel.setData_quality_assurance(buildDataQualityAssurance(datasetDescriptionJson, templateIdsToValues, dataset.getProfile().getDefinition()));
-
-		/*--------- Building distribution. ---------*/
-		datasetRDAExportModel.setDistribution(buildDistribution(datasetDescriptionJson, templateIdsToValues, dataset.getProfile().getDefinition()));
-
-		/*--------- Building keywords. ---------*/
-		datasetRDAExportModel.setKeyword(buildKeywords(datasetDescriptionJson, templateIdsToValues, dataset.getProfile().getDefinition()));
-
-		/*--------- Building metadata items. ---------*/
-		datasetRDAExportModel.setMetadata(buildMetadata(datasetDescriptionJson, templateIdsToValues, dataset.getProfile().getDefinition()));
-
-		/*--------- Building security and privacy items. ---------*/
-		datasetRDAExportModel.setSecurity_and_privacy(buildSecurityAndPrivacy(datasetDescriptionJson, templateIdsToValues, dataset.getProfile().getDefinition()));
-
-		/*--------- Building technical_resource. ---------*/
-		datasetRDAExportModel.setTechnical_resource(buildTechnicalResource(datasetDescriptionJson, templateIdsToValues, dataset.getProfile().getDefinition()));
-
-		return datasetRDAExportModel;
-	}
-
-	private String buildSingleProperties(String rdaKey, JSONObject datasetDescriptionJson, Map<String, Object> templateIdsToValues) {
-		String expression = "$..fields[*][?(@.rdaProperty == \"" + rdaKey + "\" )].id";
-		List<String> list = jsonValueListFromExpression(datasetDescriptionJson, expression);
-		if (!list.isEmpty()) {
-			return templateIdsToValues.get(list.get(0)).toString();
-		} else {
-			return null;
-		}
-	}
-
-	private List<String> buildDataQualityAssurance(JSONObject datasetDescriptionJson, Map<String, Object> templateIdsToValues, String datasetProfileDefinition) {
-		List<RdaField> dataQualityFields = getRDAFieldsFromJson(datasetDescriptionJson, new String[]{"dataset.data_quality_assurance"}, datasetProfileDefinition);
-		for (RdaField rdaField : dataQualityFields) {
-			rdaField.setRdaValue(templateIdsToValues.get(rdaField.getFieldId()).toString());
-		}
-		List<String> dataQualityAssuranceList = new LinkedList<>();
-		for (RdaField rdaField : dataQualityFields) {
-			dataQualityAssuranceList.add(rdaField.getRdaValue());
-		}
-
-		return dataQualityAssuranceList;
-	}
-
-	private List<DatasetDistributionRDAExportModel> buildDistribution(JSONObject datasetDescriptionJson, Map<String, Object> templateIdsToValues, String datasetProfileDefinition) {
-		DatasetDistributionRDAExportModel distributionModel = new DatasetDistributionRDAExportModel();
-		distributionModel.setAccess_url(buildSingleProperties("dataset.distribution.access_url", datasetDescriptionJson, templateIdsToValues));
-		distributionModel.setAvailable_till(buildSingleProperties("dataset.distribution.available_till", datasetDescriptionJson, templateIdsToValues));
-		distributionModel.setByte_size(buildSingleProperties("dataset.distribution.byte_size", datasetDescriptionJson, templateIdsToValues));
-		distributionModel.setData_access(buildSingleProperties("dataset.distribution.data_access", datasetDescriptionJson, templateIdsToValues));
-		distributionModel.setDescription(buildSingleProperties("dataset.distribution.description", datasetDescriptionJson, templateIdsToValues));
-		distributionModel.setDownload_url(buildSingleProperties("dataset.distribution.download_url", datasetDescriptionJson, templateIdsToValues));
-		distributionModel.setTitle(buildSingleProperties("dataset.distribution.title", datasetDescriptionJson, templateIdsToValues));
-
-		/*--------- Building format. ---------*/
-
-
-		// We currently support the return of only one distribution.
-		List<DatasetDistributionRDAExportModel> distributionList = new LinkedList<>();
-		if (distributionModel.isValid()) {
-			distributionList.add(distributionModel);
-		} else {
-			DatasetDistributionRDAExportModel model = new DatasetDistributionRDAExportModel();
-			model.setDescription("Distribution data was not valid");
-			distributionList.add(model);
-		}
-
-		return distributionList;
-	}
-
-	private List<String> buildKeywords(JSONObject datasetDescriptionJson, Map<String, Object> templateIdsToValues, String datasetProfileDefinition) {
-		List<RdaField> keywordFields = getRDAFieldsFromJson(datasetDescriptionJson, new String[]{"dataset.keyword"}, datasetProfileDefinition);
-		for (RdaField rdaField : keywordFields) {
-			rdaField.setRdaValue(templateIdsToValues.get(rdaField.getFieldId()).toString());
-		}
-		List<String> keywordsList = new LinkedList<>();
-		for (RdaField rdaField : keywordFields) {
-			keywordsList.add(rdaField.getRdaValue());
-		}
-
-		return keywordsList;
-	}
-
-	private List<DatasetMetadataRDAExportModel> buildMetadata(JSONObject datasetDescriptionJson, Map<String, Object> templateIdsToValues, String datasetProfileDefinition) {
-		List<RdaField> metadataFields = getRDAFieldsFromJson(datasetDescriptionJson,
-				new String[]{"dataset.metadata.metadata_standard_id.type", "dataset.metadata.metadata_standard_id.identifier", "dataset.metadata.description", "dataset.metadata.language", "dataset.metadata.metadata_standard_id"},
-				datasetProfileDefinition);
-
-		// Adding rdaValue and FieldSetIds on metadataFields.
-		for (RdaField rdaField : metadataFields) {
-			rdaField.setRdaValue(templateIdsToValues.get(rdaField.getFieldId()).toString());
-		}
-		// Group metadataFields based on their field set id.
-		Map<String, List<RdaField>> groupedMetadataFields = metadataFields.stream().collect(groupingBy(RdaField::getFieldSetId));
-
-		// Creating the metadata.
-		List<DatasetMetadataRDAExportModel> metadataRDAExportModelList = new LinkedList<>();
-		for (String fieldSetId : groupedMetadataFields.keySet()) {
-			DatasetMetadataRDAExportModel metadataRda = new DatasetMetadataRDAExportModel();
-			for (RdaField rdaField : groupedMetadataFields.get(fieldSetId)) {
-				if (rdaField.getRdaProperty().equals("dataset.metadata.metadata_standard_id.identifier")) {
-					if (metadataRda.getMetadata_standard_id() != null) {
-						metadataRda.getMetadata_standard_id().setIdentifier(rdaField.getRdaValue());
-					} else {
-						metadataRda.setMetadata_standard_id(new IdRDAExportModel(rdaField.getRdaValue(), "other"));
-					}
-				}
-				if (rdaField.getRdaProperty().equals("dataset.metadata.metadata_standard_id.type")) {
-					if (metadataRda.getMetadata_standard_id() != null) {
-						metadataRda.getMetadata_standard_id().setType(rdaField.getRdaValue());
-					} else {
-						metadataRda.setMetadata_standard_id(new IdRDAExportModel("", rdaField.getRdaValue()));
-					}
-				}
-				if (rdaField.getRdaProperty().equals("dataset.metadata.description")) {
-					metadataRda.setDescription(rdaField.getRdaValue());
-				}
-				if (rdaField.getRdaProperty().equals("dataset.metadata.language")) {
-					metadataRda.setLanguage(rdaField.getRdaValue());
-				}
-				if (rdaField.getRdaProperty().equals("dataset.metadata.metadata_standard_id") && !rdaField.getRdaValue().isEmpty()) {
-					JSONArray jsonArray = new JSONArray(rdaField.getRdaValue());
-					for (int i = 0; i < jsonArray.length(); i++) {
-						JSONObject jsonObject = jsonArray.getJSONObject(i);
-						Map<String, Object> jsonObjectMap = jsonObject.toMap();
-						DatasetMetadataRDAExportModel metadataRda1 = new DatasetMetadataRDAExportModel();
-//						metadataRda1.setMetadata_standard_id(new IdRDAExportModel(jsonObjectMap.get("label").toString(), jsonObjectMap.get("source").toString()));
-						metadataRda1.setMetadata_standard_id(new IdRDAExportModel(jsonObjectMap.get("uri").toString(), "url"));
-						metadataRDAExportModelList.add(metadataRda1);
-					}
-				}
-			}
-			if (metadataRda.isValid()) {
-				metadataRDAExportModelList.add(metadataRda);
-			}
-		}
-
-		return new LinkedList<>(metadataRDAExportModelList);
-	}
-
-	private List<DatasetSecurityAndPrivacyRDAExportModel> buildSecurityAndPrivacy(JSONObject datasetDescriptionJson, Map<String, Object> templateIdsToValues, String datasetProfileDefinition) {
-		List<RdaField> secAndPrFields = getRDAFieldsFromJson(
-				datasetDescriptionJson,
-				new String[]{"dataset.security_and_privacy.description", "dataset.security_and_privacy.title", "dataset.security_and_privacy"},
-				datasetProfileDefinition);
-		for (RdaField rdaField : secAndPrFields) {
-			rdaField.setRdaValue(templateIdsToValues.get(rdaField.getFieldId()).toString());
-		}
-		Map<String, List<RdaField>> groupedSecurityAndPrivacyFields = secAndPrFields.stream().collect(groupingBy(RdaField::getFieldSetId));
-
-		List<DatasetSecurityAndPrivacyRDAExportModel> securityAndPrivacyRDAExportModelList = new LinkedList<>();
-		for (String fieldSetId : groupedSecurityAndPrivacyFields.keySet()) {
-			DatasetSecurityAndPrivacyRDAExportModel securityAndPrivacyModel = new DatasetSecurityAndPrivacyRDAExportModel();
-			for (RdaField rdaField : groupedSecurityAndPrivacyFields.get(fieldSetId)) {
-				if (rdaField.getRdaProperty().equals("dataset.security_and_privacy.description")) {
-					securityAndPrivacyModel.setDescription(rdaField.getRdaValue());
-				}
-				if (rdaField.getRdaProperty().equals("dataset.security_and_privacy.title")) {
-					securityAndPrivacyModel.setTitle(rdaField.getRdaValue());
-				}
-				if (rdaField.getRdaProperty().equals("dataset.security_and_privacy")) {
-					JSONArray jsonArray = new JSONArray(rdaField.getRdaValue());
-					for (int i = 0; i < jsonArray.length(); i++) {
-						JSONObject jsonObject = jsonArray.getJSONObject(i);
-						Map<String, Object> jsonObjectMap = jsonObject.toMap();
-						DatasetSecurityAndPrivacyRDAExportModel secAndPrivacy = new DatasetSecurityAndPrivacyRDAExportModel(jsonObjectMap.get("label").toString(), jsonObjectMap.get("source").toString());
-						securityAndPrivacyRDAExportModelList.add(secAndPrivacy);
-					}
-				}
-			}
-			securityAndPrivacyRDAExportModelList.add(securityAndPrivacyModel);
-		}
-
-		return securityAndPrivacyRDAExportModelList;
-	}
-
-	private List<DatasetTechnicalResourceRDAExportModel> buildTechnicalResource(JSONObject datasetDescriptionJson, Map<String, Object> templateIdsToValues, String datasetProfileDefinition) {
-		List<RdaField> dataQualityFields = getRDAFieldsFromJson(datasetDescriptionJson,
-				new String[]{"dataset.technical_resource.technical_resource", "dataset.technical_resource.technical_resource.description", "dataset.technical_resource.technical_resource.name"},
-				datasetProfileDefinition);
-		for (RdaField rdaField : dataQualityFields) {
-			rdaField.setRdaValue(templateIdsToValues.get(rdaField.getFieldId()).toString());
-		}
-		List<DatasetTechnicalResourceRDAExportModel> technicalResourceList = new LinkedList<>();
-		Map<String, List<RdaField>> groupedDataQualityFields = dataQualityFields.stream().collect(groupingBy(RdaField::getFieldSetId));
-		for (String fieldSetId : groupedDataQualityFields.keySet()) {
-			DatasetTechnicalResourceRDAExportModel technicalResourceModel = new DatasetTechnicalResourceRDAExportModel();
-			for (RdaField rdaField : groupedDataQualityFields.get(fieldSetId)) {
-				if (rdaField.getRdaProperty().equals("dataset.technical_resource.technical_resource.description")) {
-					technicalResourceModel.setDescription(rdaField.getRdaValue());
-				}
-				if (rdaField.getRdaProperty().equals("dataset.technical_resource.technical_resource.name")) {
-					technicalResourceModel.setName(rdaField.getRdaValue());
-				}
-				if (rdaField.getRdaProperty().equals("dataset.security_and_privacy")) {
-					JSONArray jsonArray = new JSONArray(rdaField.getRdaValue());
-					for (int i = 0; i < jsonArray.length(); i++) {
-						JSONObject jsonObject = jsonArray.getJSONObject(i);
-						Map<String, Object> jsonObjectMap = jsonObject.toMap();
-						DatasetTechnicalResourceRDAExportModel technicalResource = new DatasetTechnicalResourceRDAExportModel(jsonObjectMap.get("label").toString(), jsonObjectMap.get("label").toString());
-						technicalResourceList.add(technicalResource);
-					}
-				}
-			}
-			technicalResourceList.add(technicalResourceModel);
-		}
-
-		return technicalResourceList;
-	}
-
-	private void setMultiplicityIdToFieldSetId(JSONObject json) {
-		String multiplicityItemsFieldSetIdExp = "$..multiplicityItems[*].id";
-		List<String> multiplicityItemsFieldSetIdList = jsonValueListFromExpression(json, multiplicityItemsFieldSetIdExp);
-		for (String fieldSetId : multiplicityItemsFieldSetIdList) {
-			String fieldsFromFieldSetIdExp = "$..multiplicityItems[*][?(@.id == \""+ fieldSetId +"\")].fields[*].id";
-			List<String> fieldsIdList = jsonValueListFromExpression(json, fieldsFromFieldSetIdExp);
-			for (String fieldId : fieldsIdList) {
-				this.multiplicityIdToFieldSetId.put(fieldId, fieldSetId);
-			}
-		}
-	}
-
-	private List<RdaField> getRDAFieldsFromJson(JSONObject json, String[] rdaKey, String datasetProfileDefinition) {
-		List<RdaField> rdaFields = new LinkedList<>();
-		for (String key : rdaKey) {
-			String fieldIdExpression = "$..fields[*][?(@.rdaProperty == \"" + key + "\" )].id";
-			List<String> listFromExpression = jsonValueListFromExpression(json, fieldIdExpression);
-			for (String fieldId : listFromExpression) {
-				RdaField rdaField = new RdaField();
-				rdaField.setRdaProperty(key);
-				rdaField.setFieldId(fieldId);
-				if (fieldId.startsWith("multiple_")) {
-					rdaField.setFieldSetId(this.multiplicityIdToFieldSetId.get(fieldId));
-				} else {
-					rdaField.setFieldSetId(getFieldSetIdForFieldFromXML(datasetProfileDefinition, fieldId));
-				}
-				rdaFields.add(rdaField);
-			}
-		}
-		return rdaFields;
-	}
-
-	private List<String> jsonValueListFromExpression(JSONObject json, String expression) {
-		net.minidev.json.JSONArray jsonArray = JsonPath.parse(json.toString()).read(expression);
-		List<String> valueList = new LinkedList<>();
-		for (Object o : jsonArray) {
-			valueList.add(o.toString());
-		}
-		return valueList;
-	}
-
-	private String getFieldSetIdForFieldFromXML(String datasetProfileDefinition, String fieldId) {
-		String fieldSetIdExpression = "//field[@id ='" + fieldId + "']/ancestor::fieldSet/@id";
-		List<String> listFromExpression = xmlValueListFromExpression(datasetProfileDefinition, fieldSetIdExpression);
-		if (listFromExpression.size() == 1) return listFromExpression.get(0);
-		return null;
-	}
-
-	private List<String> xmlValueListFromExpression(String xml, String expression) {
-		List<String> valuesList = new LinkedList<>();
-		Document document = XmlBuilder.fromXml(xml);
-		XPathFactory xpathFactory = XPathFactory.newInstance();
-		XPath xpath = xpathFactory.newXPath();
-		try {
-			XPathExpression expr = xpath.compile(expression);
-			NodeList nodeList = (NodeList) expr.evaluate(document, XPathConstants.NODESET);
-			for (int i = 0; i < nodeList.getLength(); i++) {
-				Node node = nodeList.item(i);
-				valuesList.add(node.getNodeValue());
-			}
-		} catch (XPathExpressionException e) {
-			logger.error(e.getMessage(), e);
-		}
-
-		return valuesList;
-	}
-}

dmp-backend/web/src/main/java/eu/eudat/models/data/rda/DatasetSecurityAndPrivacyRDAExportModel.java

@@ -1,29 +0,0 @@
-package eu.eudat.models.data.rda;
-
-public class DatasetSecurityAndPrivacyRDAExportModel {
-	private String description;
-	private String title;
-
-	public DatasetSecurityAndPrivacyRDAExportModel() {
-
-	}
-
-	public DatasetSecurityAndPrivacyRDAExportModel(String description, String title) {
-		this.description = description;
-		this.title = title;
-	}
-
-	public String getDescription() {
-		return description;
-	}
-	public void setDescription(String description) {
-		this.description = description;
-	}
-
-	public String getTitle() {
-		return title;
-	}
-	public void setTitle(String title) {
-		this.title = title;
-	}
-}

dmp-backend/web/src/main/java/eu/eudat/models/data/rda/DatasetTechnicalResourceRDAExportModel.java

@@ -1,28 +0,0 @@
-package eu.eudat.models.data.rda;
-
-public class DatasetTechnicalResourceRDAExportModel {
-	private String description;
-	private String name;
-
-	public String getDescription() {
-		return description;
-	}
-	public void setDescription(String description) {
-		this.description = description;
-	}
-
-	public String getName() {
-		return name;
-	}
-	public void setName(String name) {
-		this.name = name;
-	}
-
-	public DatasetTechnicalResourceRDAExportModel(String description, String name) {
-		this.description = description;
-		this.name = name;
-	}
-
-	public DatasetTechnicalResourceRDAExportModel() {
-	}
-}

dmp-backend/web/src/main/java/eu/eudat/models/data/rda/DmpContributorRDAExportModel.java

@@ -1,52 +0,0 @@
-package eu.eudat.models.data.rda;
-
-import eu.eudat.data.entities.UserInfo;
-
-import java.util.LinkedList;
-import java.util.List;
-
-public class DmpContributorRDAExportModel {
-	private IdRDAExportModel contributor_id;
-	private String mbox;
-	private String name;
-	private List<String> role;
-
-	public IdRDAExportModel getContributor_id() {
-		return contributor_id;
-	}
-	public void setContributor_id(IdRDAExportModel contributor_id) {
-		this.contributor_id = contributor_id;
-	}
-
-	public String getMbox() {
-		return mbox;
-	}
-	public void setMbox(String mbox) {
-		this.mbox = mbox;
-	}
-
-	public String getName() {
-		return name;
-	}
-	public void setName(String name) {
-		this.name = name;
-	}
-
-	public List<String> getRole() {
-		return role;
-	}
-	public void setRole(List<String> role) {
-		this.role = role;
-	}
-
-	public DmpContributorRDAExportModel fromDataModel(UserInfo user, String role) {
-		DmpContributorRDAExportModel contributor = new DmpContributorRDAExportModel();
-		contributor.contributor_id = new IdRDAExportModel(user.getId().toString(), "other");
-		contributor.mbox = user.getEmail();
-		contributor.name = user.getName();
-		contributor.role = new LinkedList<>();
-		contributor.role.add(role);
-
-		return contributor;
-	}
-}

dmp-backend/web/src/main/java/eu/eudat/models/data/rda/DmpCostRDAExportModel.java

@@ -1,36 +0,0 @@
-package eu.eudat.models.data.rda;
-
-public class DmpCostRDAExportModel {
-	private String currency_code; //Allowed values defined by ISO 4217.
-	private String description;
-	private String title;
-	private String value;
-
-	public String getCurrency_code() {
-		return currency_code;
-	}
-	public void setCurrency_code(String currency_code) {
-		this.currency_code = currency_code;
-	}
-
-	public String getDescription() {
-		return description;
-	}
-	public void setDescription(String description) {
-		this.description = description;
-	}
-
-	public String getTitle() {
-		return title;
-	}
-	public void setTitle(String title) {
-		this.title = title;
-	}
-
-	public String getValue() {
-		return value;
-	}
-	public void setValue(String value) {
-		this.value = value;
-	}
-}

dmp-backend/web/src/main/java/eu/eudat/models/data/rda/DmpRDAExportModel.java

@@ -1,164 +0,0 @@
-package eu.eudat.models.data.rda;
-
-import eu.eudat.data.entities.DMP;
-import eu.eudat.data.entities.Dataset;
-import eu.eudat.data.entities.UserDMP;
-import eu.eudat.data.entities.UserInfo;
-import eu.eudat.logic.managers.DatasetManager;
-import eu.eudat.models.data.security.Principal;
-
-import java.text.DateFormat;
-import java.text.SimpleDateFormat;
-import java.util.Date;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.stream.Collectors;
-
-public class DmpRDAExportModel {
-    private ContactRDAExportModel contact;
-    private List<DmpContributorRDAExportModel> contributor;
-    private List<DmpCostRDAExportModel> cost;
-    private String created;
-    private List<DatasetRDAExportModel> dataset;
-    private String description;
-    private IdRDAExportModel dmp_id;
-    private String ethical_issues_description;
-    private String ethical_issues_exist; // Allowed Values: yes no unknown.
-    private String ethical_issues_report;
-    private String language;
-    private String modified;
-    private ProjectRDAExportModel project;
-    private String title;
-
-    public ContactRDAExportModel getContact() {
-        return contact;
-    }
-    public void setContact(ContactRDAExportModel contact) {
-        this.contact = contact;
-    }
-
-    public List<DmpContributorRDAExportModel> getContributor() {
-        return contributor;
-    }
-    public void setContributor(List<DmpContributorRDAExportModel> contributor) {
-        this.contributor = contributor;
-    }
-
-    public List<DmpCostRDAExportModel> getCost() {
-        return cost;
-    }
-    public void setCost(List<DmpCostRDAExportModel> cost) {
-        this.cost = cost;
-    }
-
-    public String getCreated() {
-        return created;
-    }
-    public void setCreated(String created) {
-        this.created = created;
-    }
-
-    public List<DatasetRDAExportModel> getDataset() {
-        return dataset;
-    }
-    public void setDataset(List<DatasetRDAExportModel> dataset) {
-        this.dataset = dataset;
-    }
-
-    public String getDescription() {
-        return description;
-    }
-    public void setDescription(String description) {
-        this.description = description;
-    }
-
-    public IdRDAExportModel getDmp_id() {
-        return dmp_id;
-    }
-    public void setDmp_id(IdRDAExportModel dmp_id) {
-        this.dmp_id = dmp_id;
-    }
-
-    public String getEthical_issues_description() {
-        return ethical_issues_description;
-    }
-    public void setEthical_issues_description(String ethical_issues_description) {
-        this.ethical_issues_description = ethical_issues_description;
-    }
-
-    public String getEthical_issues_exist() {
-        return ethical_issues_exist;
-    }
-    public void setEthical_issues_exist(String ethical_issues_exist) {
-        this.ethical_issues_exist = ethical_issues_exist;
-    }
-
-    public String getEthical_issues_report() {
-        return ethical_issues_report;
-    }
-    public void setEthical_issues_report(String ethical_issues_report) {
-        this.ethical_issues_report = ethical_issues_report;
-    }
-
-    public String getLanguage() {
-        return language;
-    }
-    public void setLanguage(String language) {
-        this.language = language;
-    }
-
-    public String getModified() {
-        return modified;
-    }
-    public void setModified(String modified) {
-        this.modified = modified;
-    }
-
-    public ProjectRDAExportModel getProject() {
-        return project;
-    }
-    public void setProject(ProjectRDAExportModel project) {
-        this.project = project;
-    }
-
-    public String getTitle() {
-        return title;
-    }
-    public void setTitle(String title) {
-        this.title = title;
-    }
-
-    public DmpRDAExportModel fromDataModel(DMP entity, DatasetManager datasetManager, Principal principal) {
-        DmpRDAExportModel dmpRda = new DmpRDAExportModel();
-        dmpRda.contact = new ContactRDAExportModel().fromDataModel(entity.getUsers().stream().filter(x -> x.getRole().equals(UserDMP.UserDMPRoles.OWNER.getValue())).findFirst().get().getUser());
-    	if (entity.getUsers().stream().anyMatch(x -> x.getRole().equals(UserDMP.UserDMPRoles.USER.getValue()))) {
-            dmpRda.contributor = new LinkedList<>();
-    	    for (UserDMP userdmp : entity.getUsers().stream().filter(x -> x.getRole().equals(UserDMP.UserDMPRoles.USER.getValue())).collect(Collectors.toList())) {
-                dmpRda.contributor.add(new DmpContributorRDAExportModel().fromDataModel(userdmp.getUser(), UserDMP.UserDMPRoles.fromInteger(userdmp.getRole()).toString()));
-            }
-        }
-        dmpRda.cost = null;
-        SimpleDateFormat formatter = new SimpleDateFormat("dd-MM-yyyy");
-        dmpRda.created = formatter.format(entity.getCreated());
-        dmpRda.dataset = new LinkedList<>();
-        for (Dataset dataset : entity.getDataset()) {
-            if (dataset.getStatus() != Dataset.Status.DELETED.getValue() && dataset.getStatus() != Dataset.Status.CANCELED.getValue())
-                dmpRda.dataset.add(new DatasetRDAExportModel().fromDataModel(dataset, datasetManager, principal));
-        }
-        dmpRda.description = entity.getDescription().replace("\n", " ");
-        if (entity.getDoi() != null) {
-            dmpRda.dmp_id = new IdRDAExportModel(entity.getDoi(), "zenodo");
-        }
-        else {
-            dmpRda.dmp_id = new IdRDAExportModel(entity.getId().toString(), "other");
-        }
-        // Mock up data on "language" and "ethical_issues_*" for now.
-        dmpRda.ethical_issues_exist = "unknown";
-        dmpRda.language = "en";
-        dmpRda.modified = formatter.format(new Date());
-        dmpRda.project = new ProjectRDAExportModel().fromDataModel(entity.getGrant());
-        dmpRda.title = entity.getLabel();
-
-        return dmpRda;
-    }
-}

dmp-backend/web/src/main/java/eu/eudat/models/data/rda/FundingRDAExportModel.java

@@ -1,43 +0,0 @@
-package eu.eudat.models.data.rda;
-
-import eu.eudat.data.entities.Funder;
-import eu.eudat.data.entities.Grant;
-
-public class FundingRDAExportModel {
-	private IdRDAExportModel funder_id;
-	private IdRDAExportModel grant_id;
-	private String funding_status;
-
-	public IdRDAExportModel getFunder_id() {
-		return funder_id;
-	}
-	public void setFunder_id(IdRDAExportModel funder_id) {
-		this.funder_id = funder_id;
-	}
-
-	public IdRDAExportModel getGrant_id() {
-		return grant_id;
-	}
-	public void setGrant_id(IdRDAExportModel grant_id) {
-		this.grant_id = grant_id;
-	}
-
-	public String getFunding_status() {
-		return funding_status;
-	}
-	public void setFunding_status(String funding_status) {
-		this.funding_status = funding_status;
-	}
-
-	public FundingRDAExportModel fromDataModel(Funder funder, Grant grant) {
-		FundingRDAExportModel funding = new FundingRDAExportModel();
-		funding.funding_status = "planned"; // mock data
-		if (funder != null) {
-			funding.funder_id = new IdRDAExportModel(funder.getReference(), "other");
-		}
-		if (grant != null) {
-			funding.grant_id = new IdRDAExportModel(grant.getReference(), "other");
-		}
-		return funding;
-	}
-}

dmp-backend/web/src/main/java/eu/eudat/models/data/rda/HostRDAExportModel.java

@@ -1,86 +0,0 @@
-package eu.eudat.models.data.rda;
-
-import java.util.List;
-
-public class HostRDAExportModel {
-	private String availability;
-	private String backup__frequency;
-	private String backup_type;
-	private String certified_with; // Repository certified with one the following standards: DIN31644 / DINI-Zertifikat / DSA / ISO16363 / ISO16919 /TRAC / WDS / CoreTrustSeal
-	private String description;
-	private String geo_location;  // Physical location of the data expressed using ISO 3166-1 country code.
-	private List<String> pid_system; // PID System: ark arxiv bibcode doi ean13 eissn handle igsn isbn issn istc lissn lsid pmid purl upc url urn other
-	private String storage_type;
-	private String support_versioning; // Allowed values: yes / no / unknown
-	private String title;
-
-	public String getAvailability() {
-		return availability;
-	}
-	public void setAvailability(String availability) {
-		this.availability = availability;
-	}
-
-	public String getBackup__frequency() {
-		return backup__frequency;
-	}
-	public void setBackup__frequency(String backup__frequency) {
-		this.backup__frequency = backup__frequency;
-	}
-
-	public String getBackup_type() {
-		return backup_type;
-	}
-	public void setBackup_type(String backup_type) {
-		this.backup_type = backup_type;
-	}
-
-	public String getCertified_with() {
-		return certified_with;
-	}
-	public void setCertified_with(String certified_with) {
-		this.certified_with = certified_with;
-	}
-
-	public String getDescription() {
-		return description;
-	}
-	public void setDescription(String description) {
-		this.description = description;
-	}
-
-	public String getGeo_location() {
-		return geo_location;
-	}
-	public void setGeo_location(String geo_location) {
-		this.geo_location = geo_location;
-	}
-
-	public List<String> getPid_system() {
-		return pid_system;
-	}
-	public void setPid_system(List<String> pid_system) {
-		this.pid_system = pid_system;
-	}
-
-	public String getStorage_type() {
-		return storage_type;
-	}
-	public void setStorage_type(String storage_type) {
-		this.storage_type = storage_type;
-	}
-
-	public String getSupport_versioning() {
-		return support_versioning;
-	}
-	public void setSupport_versioning(String support_versioning) {
-		this.support_versioning = support_versioning;
-	}
-
-	public String getTitle() {
-		return title;
-	}
-	public void setTitle(String title) {
-		this.title = title;
-	}
-}

dmp-backend/web/src/main/java/eu/eudat/models/data/rda/IdRDAExportModel.java

@@ -1,25 +0,0 @@
-package eu.eudat.models.data.rda;
-
-public class IdRDAExportModel {
-	private String identifier;
-	private String type;
-
-	public String getIdentifier() {
-		return identifier;
-	}
-	public void setIdentifier(String identifier) {
-		this.identifier = identifier;
-	}
-
-	public String getType() {
-		return type;
-	}
-	public void setType(String type) {
-		this.type = type;
-	}
-
-	IdRDAExportModel(String identifier, String type) {
-		this.identifier = identifier;
-		this.type = type;
-	}
-}

dmp-backend/web/src/main/java/eu/eudat/models/data/rda/LicenseRDAExportModel.java

@@ -1,20 +0,0 @@
-package eu.eudat.models.data.rda;
-
-public class LicenseRDAExportModel {
-	private String license_ref;
-	private String start_date; // If date is set in the future, it indicates embargo period.
-
-	public String getLicense_ref() {
-		return license_ref;
-	}
-	public void setLicense_ref(String license_ref) {
-		this.license_ref = license_ref;
-	}
-
-	public String getStart_date() {
-		return start_date;
-	}
-	public void setStart_date(String start_date) {
-		this.start_date = start_date;
-	}
-}

dmp-backend/web/src/main/java/eu/eudat/models/data/rda/ProjectRDAExportModel.java

@@ -1,54 +0,0 @@
-package eu.eudat.models.data.rda;
-
-import eu.eudat.data.entities.Grant;
-
-import java.util.Date;
-
-public class ProjectRDAExportModel {
-	private String title;
-	private String description;
-	private Date project_start;
-	private Date project_end;
-	private FundingRDAExportModel funding;
-
-	public String getTitle() {
-		return title;
-	}
-	public void setTitle(String title) {
-		this.title = title;
-	}
-
-	public String getDescription() {
-		return description;
-	}
-	public void setDescription(String description) {
-		this.description = description;
-	}
-
-	public Date getProject_start() {
-		return project_start;
-	}
-	public void setProject_start(Date project_start) {
-		this.project_start = project_start;
-	}
-
-	public Date getProject_end() {
-		return project_end;
-	}
-	public void setProject_end(Date project_end) {
-		this.project_end = project_end;
-	}
-
-	public FundingRDAExportModel getFunding() {
-		return funding;
-	}
-	public void setFunding(FundingRDAExportModel funding) {
-		this.funding = funding;
-	}
-
-
-	public ProjectRDAExportModel fromDataModel(Grant grant) {
-		this.funding = new FundingRDAExportModel().fromDataModel(grant.getFunder(), grant);
-		return this;
-	}
-}

dmp-backend/web/src/main/java/eu/eudat/models/data/rda/RDAExportModel.java

@@ -1,25 +0,0 @@
-package eu.eudat.models.data.rda;
-
-import eu.eudat.data.entities.DMP;
-import eu.eudat.data.entities.Dataset;
-import eu.eudat.logic.managers.DatasetManager;
-import eu.eudat.models.data.security.Principal;
-
-import java.util.LinkedList;
-import java.util.List;
-
-public class RDAExportModel {
-    private DmpRDAExportModel dmp;
-
-    public DmpRDAExportModel getDmp() {
-        return dmp;
-    }
-    public void setDmp(DmpRDAExportModel dmp) {
-        this.dmp = dmp;
-    }
-
-    public RDAExportModel fromDataModel(DMP dmp, DatasetManager datasetManager, Principal principal) {
-        this.dmp = new DmpRDAExportModel().fromDataModel(dmp, datasetManager, principal);
-        return this;
-    }
-}

dmp-backend/web/src/main/java/eu/eudat/models/data/rda/RdaField.java

@@ -1,36 +0,0 @@
-package eu.eudat.models.data.rda;
-
-public class RdaField {
-	private String rdaProperty;
-	private String rdaValue;
-	private String fieldId;
-	private String fieldSetId;
-
-	public String getRdaProperty() {
-		return rdaProperty;
-	}
-	public void setRdaProperty(String rdaProperty) {
-		this.rdaProperty = rdaProperty;
-	}
-
-	public String getRdaValue() {
-		return rdaValue;
-	}
-	public void setRdaValue(String rdaValue) {
-		this.rdaValue = rdaValue;
-	}
-
-	public String getFieldId() {
-		return fieldId;
-	}
-	public void setFieldId(String fieldId) {
-		this.fieldId = fieldId;
-	}
-
-	public String getFieldSetId() {
-		return fieldSetId;
-	}
-	public void setFieldSetId(String fieldSetId) {
-		this.fieldSetId = fieldSetId;
-	}
-}

dmp-backend/web/src/main/java/eu/eudat/models/data/user/components/datasetprofile/Field.java

@@ -2,18 +2,14 @@ package eu.eudat.models.data.user.components.datasetprofile;
 
 import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.ObjectMapper;
+import eu.eudat.logic.utilities.builders.ModelBuilder;
+import eu.eudat.logic.utilities.interfaces.ViewStyleDefinition;
 import eu.eudat.models.data.components.commons.DefaultValue;
 import eu.eudat.models.data.components.commons.Multiplicity;
 import eu.eudat.models.data.components.commons.ViewStyle;
 import eu.eudat.models.data.components.commons.Visibility;
 import eu.eudat.models.data.properties.PropertiesGenerator;
 import eu.eudat.models.data.user.composite.PropertiesModelBuilder;
-import eu.eudat.logic.utilities.interfaces.ViewStyleDefinition;
-import eu.eudat.logic.utilities.builders.ModelBuilder;
-
-import org.json.JSONArray;
-import org.json.JSONException;
-import org.json.JSONObject;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -26,6 +22,7 @@ import java.util.stream.Collectors;
 
 public class Field implements Comparable, PropertiesModelBuilder, ViewStyleDefinition<eu.eudat.models.data.entities.xmlmodels.datasetprofiledefinition.Field>, PropertiesGenerator {
     private static final Logger logger = LoggerFactory.getLogger(Field.class);
+    private static final ObjectMapper objectMapper = new ObjectMapper();
     private String id;
     private Integer ordinal;
     private Object value;
@@ -205,10 +202,9 @@ public class Field implements Comparable, PropertiesModelBuilder, ViewStyleDefin
     @Override
     public void fromJsonObject(Map<String, Object> properties) {
         try {
-            ObjectMapper mapper = new ObjectMapper();
-            List<String> stringList = mapper.readValue(properties.get(this.id).toString(), LinkedList.class);
+            List<String> stringList = objectMapper.readValue(properties.get(this.id).toString(), LinkedList.class);
             this.value = stringList;
-        } catch (JSONException | NullPointerException | IOException e) {
+        } catch (NullPointerException | IOException e) {
             try {
                 this.value = (String) properties.get(this.id);
             } catch (ClassCastException ce) {

dmp-backend/web/src/main/java/eu/eudat/models/data/user/components/datasetprofile/FieldSet.java

@@ -175,12 +175,12 @@ public class FieldSet implements Comparable, PropertiesModelBuilder, ViewStyleDe
 
     private FieldSet CloneForMultiplicity2(List<String> key, Map<String, Object> properties,String[] ids, int index){
         FieldSet newFieldSet = new FieldSet();
-        newFieldSet.id = ids[0]+"_"+ids[1]+"_"+ids[2] + (ids.length > 4 ? "_" + ids[3] : "");
+        newFieldSet.id = ids[0] + "_" + ids[1] + "_" + ids[2] + (ids.length > 3 && !ids[ids.length - 1].isEmpty() ? "_" + ids[ids.length - 1] : "");
         newFieldSet.description = this.description;
         newFieldSet.extendedDescription = this.extendedDescription;
         newFieldSet.additionalInformation=this.additionalInformation;
         newFieldSet.title = this.title;
-        newFieldSet.ordinal = ids.length > 4 ? Integer.valueOf(ids[3]) : this.ordinal;
+        newFieldSet.ordinal = ids.length > 3 && !ids[ids.length - 1].isEmpty() && ids[ids.length - 1].matches("[0-9]+") ? Integer.valueOf(ids[ids.length - 1]) : this.ordinal;
         newFieldSet.fields = new LinkedList();
 
         for (Field field: this.fields) {

dmp-backend/web/src/main/java/eu/eudat/models/deposit/zenodo/mapper/DMPToZenodoMapper.java

@@ -1,11 +1,15 @@
 package eu.eudat.models.deposit.zenodo.mapper;
 
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.ObjectMapper;
 import eu.eudat.data.entities.DMP;
 import eu.eudat.data.entities.Organisation;
 import eu.eudat.data.entities.UserDMP;
 import eu.eudat.logic.proxy.config.DOIFunder;
 import eu.eudat.logic.proxy.config.configloaders.ConfigLoader;
 import eu.eudat.models.deposit.zenodo.*;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.core.env.Environment;
 
 import java.time.Instant;
@@ -13,9 +17,16 @@ import java.util.*;
 import java.util.stream.Collectors;
 
 public class DMPToZenodoMapper {
+    private static final ObjectMapper objectmapper = new ObjectMapper();
+    private static final Logger logger = LoggerFactory.getLogger(DMPToZenodoMapper.class);
 
     public static ZenodoDeposit fromDMP(DMP dmp, Environment environment, ConfigLoader configLoader) {
-        Map<String, Object> extraProperties = dmp.getExtraProperties() != null ? new org.json.JSONObject(dmp.getExtraProperties()).toMap() : new HashMap<>();
+        Map<String, Object> extraProperties = null;
+        try {
+            extraProperties = dmp.getExtraProperties() != null ? objectmapper.readValue(dmp.getExtraProperties(), LinkedHashMap.class) : new HashMap<>();
+        } catch (JsonProcessingException e) {
+            logger.error(e.getLocalizedMessage(), e);
+        }
         ZenodoDeposit deposit = new ZenodoDeposit();
         deposit.setMetadata(new ZenodoDepositMetadata());
         deposit.getMetadata().setTitle(dmp.getLabel());
@@ -26,11 +37,11 @@ public class DMPToZenodoMapper {
         ZenodoComunity community = new ZenodoComunity();
         community.setIdentifier(environment.getProperty("zenodo.community"));
         deposit.getMetadata().setCommunities(Collections.singletonList(community));
-        if (extraProperties.get("visible") == null) {
+        if (extraProperties != null && extraProperties.get("visible") == null) {
             deposit.getMetadata().setAccessRight(ZenodoAccessRight.RESTRICTED);
             deposit.getMetadata().setAccessConditions("");
         } else {
-            if (((Boolean) extraProperties.get("visible"))) {
+            if (extraProperties != null && ((Boolean) extraProperties.get("visible"))) {
                 Instant publicationDate = Instant.parse(extraProperties.get("publicDate").toString());
                 if (publicationDate.isBefore(Instant.now())) {
                     deposit.getMetadata().setAccessRight(ZenodoAccessRight.OPEN);

dmp-backend/web/src/main/java/eu/eudat/models/rda/mapper/CostRDAMapper.java

@@ -1,23 +1,23 @@
 package eu.eudat.models.rda.mapper;
 
-import java.util.*;
-import java.util.stream.Collectors;
-
 import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.ObjectMapper;
-import eu.eudat.logic.utilities.json.JavaToJson;
 import eu.eudat.models.rda.Cost;
-import eu.eudat.models.rda.PidSystem;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.util.*;
+import java.util.stream.Collectors;
+
 public class CostRDAMapper {
 	private static final Logger logger = LoggerFactory.getLogger(DatasetRDAMapper.class);
+	private static final ObjectMapper objectMapper = new ObjectMapper();
 
 	public static Cost toRDA(Map<String, Object> cost) {
 		Cost rda = new Cost();
-		Map<String, Object> code = new org.json.JSONObject((String) cost.get("code")).toMap();
+		try {
+			Map<String, Object> code = objectMapper.readValue((String) cost.get("code"), LinkedHashMap.class);
 			rda.setCurrencyCode(Cost.CurrencyCode.fromValue((String) code.get("value")));
 			rda.setDescription((String) cost.get("description"));
 			if (cost.get("title") == null) {
@@ -25,6 +25,9 @@ public class CostRDAMapper {
 			}
 			rda.setTitle((String) cost.get("title"));
 			rda.setValue(((Integer) cost.get("value")).doubleValue());
+		} catch (JsonProcessingException e) {
+			logger.error(e.getLocalizedMessage(), e);
+		}
 		return rda;
 	}
 
@@ -56,7 +59,7 @@ public class CostRDAMapper {
 			}
 			else if(rdaProperty.contains("currency_code")){
 				HashMap<String, String> result =
-						new ObjectMapper().readValue(rdaValue, HashMap.class);
+						objectMapper.readValue(rdaValue, HashMap.class);
 				rda.setCurrencyCode(Cost.CurrencyCode.fromValue(result.get("value")));
 			}
 			else if(rdaProperty.contains("title")){