Update Depedencies

dmp-backend/pom.xml

@@ -27,7 +27,7 @@
         <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>5.3.14</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>
         <!--<com.sun.jersey.version>1.19.1</com.sun.jersey.version>-->
@@ -36,27 +36,27 @@
 -->
         <!--<com.fasterxml.jackson>2.9.0</com.fasterxml.jackson>-->
 
-        <hibernate.version>5.5.3.Final</hibernate.version>
+        <hibernate.version>5.6.3.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>
-        <log4j2.version>2.15.0</log4j2.version>
+        <log4j2.version>2.17.0</log4j2.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>1.2.10</logback.version>
        <!-- <javax.inject.version>1</javax.inject.version>-->
         <!--<javax.servlet.servlet-api.version>3.0.1</javax.servlet.servlet-api.version>-->
     </properties>
 
     <dependencies>
 
-        <dependency>
+        <!--<dependency>
             <groupId>org.json</groupId>
             <artifactId>json</artifactId>
             <version>20160810</version>
-        </dependency>
+        </dependency>-->
         <dependency>
             <groupId>org.springframework</groupId>
             <artifactId>spring-context-support</artifactId>
@@ -91,19 +91,18 @@
         <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>
+            <version>4.4.15</version>
         </dependency>
 
         <dependency>
             <groupId>org.apache.httpcomponents</groupId>
             <artifactId>httpcore</artifactId>
-            <version>4.4.13</version>
+            <version>4.4.15</version>
         </dependency>
 
         <dependency>
@@ -127,13 +126,13 @@
         <dependency>
             <groupId>com.google.api-client</groupId>
             <artifactId>google-api-client</artifactId>
-            <version>1.23.0</version>
+            <version>1.33.0</version>
         </dependency>
         <!-- 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>2.6.0</version>
         </dependency>
 
 
@@ -141,7 +140,7 @@
         <dependency>
             <groupId>com.fasterxml.jackson.dataformat</groupId>
             <artifactId>jackson-dataformat-xml</artifactId>
-            <version>2.12.3</version>
+            <version>2.13.1</version>
         </dependency>
 
 
@@ -149,13 +148,13 @@
         <dependency>
             <groupId>com.fasterxml.jackson.core</groupId>
             <artifactId>jackson-core</artifactId>
-            <version>2.12.3</version>
+            <version>2.13.1</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>2.13.1</version>
         </dependency>
 
         <!-- g/a spring -->
@@ -167,26 +166,25 @@
         <dependency>
             <groupId>org.apache.commons</groupId>
             <artifactId>commons-lang3</artifactId>
-            <version>3.5</version>
         </dependency>
         <!-- https://mvnrepository.com/artifact/org.apache.poi/poi -->
         <dependency>
             <groupId>org.apache.poi</groupId>
             <artifactId>poi-ooxml</artifactId>
-            <version>4.0.0</version>
+            <version>5.0.0</version>
         </dependency>
 
         <dependency>
             <groupId>org.apache.poi</groupId>
             <artifactId>poi</artifactId>
-            <version>4.0.0</version>
+            <version>5.0.0</version>
         </dependency>
 
         <!-- https://mvnrepository.com/artifact/org.apache.xmlgraphics/fop -->
         <dependency>
             <groupId>org.apache.xmlgraphics</groupId>
             <artifactId>fop</artifactId>
-            <version>2.3</version>
+            <version>2.6</version>
         </dependency>
 
         <dependency>
@@ -210,13 +208,13 @@
         <dependency>
             <groupId>fr.opensagres.xdocreport</groupId>
             <artifactId>fr.opensagres.xdocreport.itext.extension</artifactId>
-            <version>2.0.1</version>
+            <version>2.0.2</version>
         </dependency>
 
         <dependency>
             <groupId>commons-io</groupId>
             <artifactId>commons-io</artifactId>
-            <version>2.1</version>
+            <version>2.11.0</version>
         </dependency>
 
         <!--<dependency>
@@ -247,14 +245,14 @@
         <dependency>
             <groupId>org.glassfish.jaxb</groupId>
             <artifactId>jaxb-core</artifactId>
-            <version>2.3.0</version>
+            <version>3.0.1</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>3.0.1</version>
         </dependency>
 
 
@@ -262,7 +260,6 @@
         <dependency>
             <groupId>javax.annotation</groupId>
             <artifactId>javax.annotation-api</artifactId>
-            <version>1.3.1</version>
         </dependency>
 
         <!-- https://mvnrepository.com/artifact/javax.validation/validation-api -->
@@ -277,32 +274,32 @@
         <dependency>
             <groupId>io.prometheus</groupId>
             <artifactId>simpleclient</artifactId>
-            <version>0.11.0</version>
+            <version>0.14.1</version>
         </dependency>
         <!-- Hotspot JVM metrics-->
         <dependency>
             <groupId>io.prometheus</groupId>
             <artifactId>simpleclient_hotspot</artifactId>
-            <version>0.11.0</version>
+            <version>0.14.1</version>
         </dependency>
         <!-- Exposition HTTPServer-->
         <dependency>
             <groupId>io.prometheus</groupId>
             <artifactId>simpleclient_httpserver</artifactId>
-            <version>0.11.0</version>
+            <version>0.14.1</version>
         </dependency>
         <!-- Pushgateway exposition-->
         <dependency>
             <groupId>io.prometheus</groupId>
             <artifactId>simpleclient_pushgateway</artifactId>
-            <version>0.11.0</version>
+            <version>0.14.1</version>
         </dependency>
 
         <!-- https://mvnrepository.com/artifact/io.micrometer/micrometer-registry-prometheus -->
         <dependency>
             <groupId>io.micrometer</groupId>
             <artifactId>micrometer-registry-prometheus</artifactId>
-            <version>1.7.1</version>
+            <version>1.8.1</version>
         </dependency>
         <dependency>
             <groupId>org.springframework.boot</groupId>

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;
@@ -19,9 +17,7 @@ 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;

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

@@ -52,7 +52,6 @@ public class UserInvitationController extends BaseController {
     public @ResponseBody
 //    ResponseEntity<ResponseItem<List<UserInfoInvitationModel>>> getUsers(Principal principal) throws IllegalAccessException, InstantiationException {
     ResponseEntity<ResponseItem<List<UserInfoInvitationModel>>> getUsers(Principal principal, @RequestBody UserInfoRequestItem userInfoRequestItem) throws IllegalAccessException, InstantiationException {
-        System.out.println(userInfoRequestItem.getCriteria().getLike());
 //        List<UserInfoInvitationModel> users = invitationsManager.getUsers(principal);
         List<UserInfoInvitationModel> users = invitationsManager.getUsersWithCriteria(principal, userInfoRequestItem);
         return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<List<UserInfoInvitationModel>>().status(ApiMessageCode.SUCCESS_MESSAGE).payload(users));

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

@@ -1,7 +1,6 @@
 package eu.eudat.logic.managers;
 
-import com.fasterxml.jackson.core.JsonParser;
+import com.fasterxml.jackson.core.JsonProcessingException;
-import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import eu.eudat.configurations.dynamicgrant.DynamicGrantConfiguration;
 import eu.eudat.configurations.dynamicgrant.entities.Property;
@@ -64,7 +63,6 @@ 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;
@@ -299,15 +297,21 @@ public class DataManagementPlanManager {
                       .filter(dataset -> !dataset.getStatus().equals(Dataset.Status.DELETED) && !dataset.getStatus().equals(Dataset.Status.CANCELED))
                       .forEach(dataset -> {
                           dataManagementPlan.getDatasets().stream().filter(datasetWizardModel -> datasetWizardModel.getId().equals(dataset.getId())).forEach(datasetWizardModel -> {
-                              DatasetWizardModel wizardModel = datasetManager.getSingle(datasetWizardModel.getId().toString(), principal);
+                              DatasetWizardModel wizardModel;
-                              datasetWizardModel.setDatasetProfileDefinition(wizardModel.getDatasetProfileDefinition());
+                              try {
-                              datasetWizardModel.setTags(wizardModel.getTags());
+                                  wizardModel = datasetManager.getSingle(datasetWizardModel.getId().toString(), principal);
+                                  datasetWizardModel.setDatasetProfileDefinition(wizardModel.getDatasetProfileDefinition());
+                                  datasetWizardModel.setTags(wizardModel.getTags());
+                              } catch (JsonProcessingException e) {
+                                  logger.error(e.getLocalizedMessage(), e);
+                              }
+
                           });
                       });
         if (isPublic) {
             dataManagementPlan.setDatasets(dataManagementPlan.getDatasets().stream().filter(dataset -> dataset.getStatus() == Dataset.Status.FINALISED.getValue()).collect(Collectors.toList()));
         }
-        Map dmpProperties = dataManagementPlanEntity.getDmpProperties() != null ? new org.json.JSONObject(dataManagementPlanEntity.getDmpProperties()).toMap() : null;
+        Map dmpProperties = dataManagementPlanEntity.getDmpProperties() != null ? apiContext.getObjectMapper().readValue(dataManagementPlanEntity.getDmpProperties(), HashMap.class) : null;
 
         if (dmpProperties != null && dataManagementPlan.getDynamicFields() != null)
             dataManagementPlan.getDynamicFields().forEach(item -> {
@@ -1305,10 +1309,11 @@ public class DataManagementPlanManager {
                      datasetDescriptionRun.setBold(true);
                      datasetDescriptionRun.setFontSize(12);
 
-                     PagedDatasetProfile pagedDatasetProfile = datasetManager.getPagedProfile(dataset, datasetEntity);
+                     PagedDatasetProfile pagedDatasetProfile = null;
-                     visibilityRuleService.setProperties(properties);
-                     visibilityRuleService.buildVisibilityContext(pagedDatasetProfile.getRules());
                      try {
+                         pagedDatasetProfile = datasetManager.getPagedProfile(dataset, datasetEntity);
+                        visibilityRuleService.setProperties(properties);
+                        visibilityRuleService.buildVisibilityContext(pagedDatasetProfile.getRules());
                          wordBuilder.build(document, pagedDatasetProfile, visibilityRuleService);
                      } catch (IOException e) {
                          logger.error(e.getMessage(), e);
@@ -1456,8 +1461,7 @@ public class DataManagementPlanManager {
             DatasetWizardModel datasetWizardModel = new DatasetWizardModel();
             Map<String, Object> properties = new HashMap<>();
             if (dataset.getProperties() != null) {
-                JSONObject jobject = new JSONObject(dataset.getProperties());
+                properties = apiContext.getObjectMapper().readValue(dataset.getProperties(), HashMap.class);
-                properties = jobject.toMap();
             }
             PagedDatasetProfile pagedDatasetProfile = datasetManager.getPagedProfile(datasetWizardModel, dataset);
             visibilityRuleService.setProperties(properties);
@@ -2017,7 +2021,7 @@ public class DataManagementPlanManager {
         headers.setAccept(Collections.singletonList(MediaType.APPLICATION_JSON));
         headers.setContentType(MediaType.APPLICATION_JSON);
         String createData = null;
-        Map<String, Object> extraProperties = dmp.getExtraProperties() != null ? new org.json.JSONObject(dmp.getExtraProperties()).toMap() : new HashMap<>();
+        Map<String, Object> extraProperties = dmp.getExtraProperties() != null ? apiContext.getObjectMapper().readValue(dmp.getExtraProperties(), HashMap.class) : new HashMap<>();
         StringBuilder dataBuilder = new StringBuilder();
         dataBuilder.append("{\n    \"metadata\": {\n");
         dataBuilder.append( "        \"title\": \"").append(dmp.getLabel()).append("\",\n");

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

@@ -1,5 +1,6 @@
 package eu.eudat.logic.managers;
 
+import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import eu.eudat.data.dao.criteria.*;
@@ -49,22 +50,19 @@ import eu.eudat.models.data.user.composite.PagedDatasetProfile;
 import eu.eudat.queryable.QueryableList;
 import eu.eudat.types.Authorities;
 import eu.eudat.types.MetricNames;
-import org.apache.commons.io.IOUtils;
 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;
 import org.springframework.core.env.Environment;
-import org.springframework.core.io.FileSystemResource;
+import org.springframework.http.HttpHeaders;
-import org.springframework.http.*;
+import org.springframework.http.HttpStatus;
+import org.springframework.http.MediaType;
+import org.springframework.http.ResponseEntity;
 import org.springframework.stereotype.Component;
-import org.springframework.util.LinkedMultiValueMap;
-import org.springframework.web.client.RestTemplate;
 import org.springframework.web.multipart.MultipartFile;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
@@ -91,8 +89,6 @@ import java.time.temporal.ChronoUnit;
 import java.util.*;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
-import java.util.zip.ZipEntry;
-import java.util.zip.ZipInputStream;
 
 @Component
 public class DatasetManager {
@@ -279,7 +275,7 @@ public class DatasetManager {
         return dataTable;
     }
 
-    public DatasetWizardModel getSingle(String id, Principal principal) {
+    public DatasetWizardModel getSingle(String id, Principal principal) throws JsonProcessingException {
         DatasetWizardModel dataset = new DatasetWizardModel();
         eu.eudat.data.entities.Dataset datasetEntity = databaseRepository.getDatasetDao().find(UUID.fromString(id), HintedModelFactory.getHint(DatasetWizardModel.class));
         if (datasetEntity.getDmp().getUsers()
@@ -380,12 +376,11 @@ public class DatasetManager {
         return databaseRepository.getDatasetDao().find(id);
     }
 
-    public PagedDatasetProfile getPagedProfile(DatasetWizardModel dataset, eu.eudat.data.entities.Dataset datasetEntity) {
+    public PagedDatasetProfile getPagedProfile(DatasetWizardModel dataset, eu.eudat.data.entities.Dataset datasetEntity) throws JsonProcessingException {
         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 = apiContext.getObjectMapper().readValue(datasetEntity.getProperties(), HashMap.class);
-            Map<String, Object> properties = jObject.toMap();
             datasetprofile.fromJsonObject(properties);
         }
         PagedDatasetProfile pagedDatasetProfile = new PagedDatasetProfile();
@@ -451,8 +446,7 @@ public class DatasetManager {
 
         Map<String, Object> properties = new HashMap<>();
         if (datasetEntity.getProperties() != null) {
-            JSONObject jObject = new JSONObject(datasetEntity.getProperties());
+            properties = apiContext.getObjectMapper().readValue(datasetEntity.getProperties(), HashMap.class);
-            properties = jObject.toMap();
         }
 
         wordBuilder.addParagraphContent("Dataset Description", document, ParagraphStyle.HEADER2, BigInteger.ZERO);
@@ -484,8 +478,7 @@ public class DatasetManager {
 
         Map<String, Object> properties = new HashMap<>();
         if (dataset.getDatasetProfileDefinition() != null) {
-            JSONObject jObject = new JSONObject(propertiesModelToString(dataset.getDatasetProfileDefinition()));
+            properties = apiContext.getObjectMapper().readValue(propertiesModelToString(dataset.getDatasetProfileDefinition()), HashMap.class);
-            properties = jObject.toMap();
         }
 
         wordBuilder.addParagraphContent("Dataset Description", document, ParagraphStyle.HEADER2, BigInteger.ZERO);
@@ -542,8 +535,7 @@ public class DatasetManager {
             throw new UnauthorisedException();
         Map<String, Object> properties = new HashMap<>();
         if (datasetEntity.getProperties() != null) {
-            JSONObject jobject = new JSONObject(datasetEntity.getProperties());
+            properties = apiContext.getObjectMapper().readValue(datasetEntity.getProperties(), HashMap.class);
-            properties = jobject.toMap();
         }
         PagedDatasetProfile pagedDatasetProfile = getPagedProfile(dataset, datasetEntity);
         visibilityRuleService.setProperties(properties);
@@ -656,9 +648,9 @@ public class DatasetManager {
         nodeList = (NodeList) xPath.compile(expression).evaluate(xmlDocument, XPathConstants.NODESET);
 
 
-        JSONObject obj = new JSONObject(dataset.getProperties());
+        Map<String, Object> obj = apiContext.getObjectMapper().readValue(dataset.getProperties(), HashMap.class);
         VisibilityRuleService visibilityRuleService = this.apiContext.getUtilitiesService().getVisibilityRuleService();
-        visibilityRuleService.setProperties(obj.toMap());
+        visibilityRuleService.setProperties(obj);
 
         dataset.setProfile(profile);
         PagedDatasetProfile pagedDatasetProfile = this.getPagedProfile(new DatasetWizardModel(), dataset);
@@ -666,7 +658,7 @@ public class DatasetManager {
 
 
         for (String validator : datasetProfileValidators) {
-            if ((obj.has(validator) && (obj.getString(validator) == null || obj.getString(validator).trim().isEmpty())) && isElementVisible(nodeList, validator, visibilityRuleService)) {
+            if ((obj.containsKey(validator) && (obj.get(validator) == null || obj.get(validator).toString().trim().isEmpty())) && isElementVisible(nodeList, validator, visibilityRuleService)) {
                 throw new Exception("Field value of " + validator + " must be filled.");
             }
         }
@@ -695,11 +687,10 @@ public class DatasetManager {
         }
     }
 
-    private String propertiesModelToString(PagedDatasetProfile pagedDatasetProfile) {
+    private String propertiesModelToString(PagedDatasetProfile pagedDatasetProfile) throws JsonProcessingException {
         Map<String, Object> values = new LinkedHashMap<>();
         pagedDatasetProfile.toMap(values);
-        JSONObject jobject = new JSONObject(values);
+        return apiContext.getObjectMapper().writeValueAsString(values);
-        return jobject.toString();
     }
 
     public void updateTags(Dataset datasetEntity, List<Tag> tags) throws Exception {
@@ -908,12 +899,9 @@ 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.getObjectMapper().writeValueAsString(importMap));
         entity.setLabel(importFile.getOriginalFilename());
         DMP dmp = new DMP();
         dmp.setId(UUID.fromString(dmpId));
@@ -942,7 +930,7 @@ public class DatasetManager {
         // TODO: When tags functionality return.
     }
 
-    public DatasetWizardModel datasetUpdateProfile(String id) {
+    public DatasetWizardModel datasetUpdateProfile(String id) throws JsonProcessingException {
         DatasetWizardModel dataset = new DatasetWizardModel();
         eu.eudat.data.entities.Dataset datasetEntity = databaseRepository.getDatasetDao().find(UUID.fromString(id), HintedModelFactory.getHint(DatasetWizardModel.class));
         eu.eudat.elastic.entities.Dataset datasetElastic;
@@ -982,12 +970,11 @@ public class DatasetManager {
         return dataset;
     }
 
-    public PagedDatasetProfile getLatestDatasetProfile(Dataset datasetEntity, DatasetProfile profile) {
+    public PagedDatasetProfile getLatestDatasetProfile(Dataset datasetEntity, DatasetProfile profile) throws JsonProcessingException {
         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 = apiContext.getObjectMapper().readValue(datasetEntity.getProperties(), HashMap.class);
-            Map<String, Object> properties = jobject.toMap();
             datasetprofile.fromJsonObject(properties);
         }
         PagedDatasetProfile pagedDatasetProfile = new PagedDatasetProfile();
@@ -1053,11 +1040,20 @@ public class DatasetManager {
                 JsonNode value = node.get("value");
                 if (!value.toString().equals("\"\"")) {
                     String stringValue = value.toString().replaceAll("=", ":");
-                    JSONArray values = new JSONArray(stringValue);
+                    List<Map<String, Object>> values = null;
-                    values.iterator().forEachRemaining(element -> {
+                    try {
-                        Map<String, Object> data = ((JSONObject) element).toMap();
+                        values = apiContext.getObjectMapper().readValue(stringValue, LinkedList.class);
-                        this.addTag(tags, wizardModel.getTags(), data.get("id").toString(), data.get("name").toString());
+                    } catch (JsonProcessingException e) {
-                    });
+                        logger.error(e.getLocalizedMessage(), e);
+                    }
+                    if (values != null) {
+                        values.iterator().forEachRemaining(element -> {
+                            Map<String, Object> data = element;
+                            this.addTag(tags, wizardModel.getTags(), data.get("id").toString(), data.get("name").toString());
+                        });
+                    } else {
+                        this.addTag(tags, wizardModel.getTags(), "", value.asText());
+                    }
                 }
             });
         }

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;
@@ -133,7 +132,7 @@ public class UserManager {
 		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(new ObjectMapper().writeValueAsString(result));
 		apiContext.getOperationsContext().getDatabaseRepository().getUserInfoDao()
 				.createOrUpdate(userInfo);
 	}

dmp-backend/web/src/main/java/eu/eudat/logic/proxy/config/prefilling/PrefillingConfigMapAdapter.java

@@ -23,7 +23,6 @@ public class PrefillingConfigMapAdapter extends XmlAdapter<Object, Map<String, P
             String id = element.getChildNodes().item(i).getAttributes().getNamedItem("id").getNodeValue();
             PrefillingConfig prefillingConfig = (PrefillingConfig) jaxbUnmarshaller.unmarshal(element.getChildNodes().item(i));
             prefillingConfig = configMap.put(id, prefillingConfig);
-            System.out.println(prefillingConfig);
         }
         return configMap;
     }

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

@@ -1,7 +1,7 @@
 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.apache.commons.codec.binary.Base64;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.core.env.Environment;
 import org.springframework.http.HttpEntity;

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, new GsonFactory())
 				.setAudience(Collections.singletonList(environment.getProperty("google.login.clientId")))
 				.build();
 	}

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

@@ -1,5 +1,6 @@
 package eu.eudat.logic.services;
 
+import com.fasterxml.jackson.databind.ObjectMapper;
 import eu.eudat.logic.services.helpers.HelpersService;
 import eu.eudat.logic.services.operations.OperationsContext;
 import eu.eudat.logic.services.utilities.UtilitiesService;
@@ -11,4 +12,6 @@ public interface ApiContext {
     OperationsContext getOperationsContext();
 
     UtilitiesService getUtilitiesService();
+
+    ObjectMapper getObjectMapper();
 }

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

@@ -1,5 +1,6 @@
 package eu.eudat.logic.services;
 
+import com.fasterxml.jackson.databind.ObjectMapper;
 import eu.eudat.logic.services.helpers.HelpersService;
 import eu.eudat.logic.services.operations.OperationsContext;
 import eu.eudat.logic.services.utilities.UtilitiesService;
@@ -9,6 +10,7 @@ import org.springframework.stereotype.Service;
 
 @Service("apiContext")
 public class ApiContextImpl implements ApiContext {
+    private static final ObjectMapper mapper = new ObjectMapper();
 
     private OperationsContext operationsContext;
     private HelpersService helpersService;
@@ -35,4 +37,9 @@ public class ApiContextImpl implements ApiContext {
     public UtilitiesService getUtilitiesService() {
         return utilitiesService;
     }
+
+    @Override
+    public ObjectMapper getObjectMapper() {
+        return mapper;
+    }
 }

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;
@@ -164,25 +164,31 @@ public abstract class AbstractAuthenticationService implements AuthenticationSer
 			apiContext.getOperationsContext().getDatabaseRepository().getUserRoleDao().createOrUpdate(role);
 
 		} else {
-			Map<String, Object> additionalInfo = userInfo.getAdditionalinfo() != null ?
+			Map<String, Object> additionalInfo = null;
-					new JSONObject(userInfo.getAdditionalinfo()).toMap() : new HashMap<>();
+			try {
-			if (profile.getAvatarUrl() != null && !profile.getAvatarUrl().isEmpty() && !profile.getAvatarUrl().equals("null")) {
+				additionalInfo = userInfo.getAdditionalinfo() != null ?
-				additionalInfo.put("avatarUrl", profile.getAvatarUrl());
+						apiContext.getObjectMapper().readValue(userInfo.getAdditionalinfo(), HashMap.class) : new HashMap<>();
+				if (profile.getAvatarUrl() != null && !profile.getAvatarUrl().isEmpty() && !profile.getAvatarUrl().equals("null")) {
+					additionalInfo.put("avatarUrl", profile.getAvatarUrl());
+				}
+				if (profile.getZenodoId() != null && !profile.getZenodoId().isEmpty() && !profile.getZenodoId().equals("null")) {
+					additionalInfo.put("zenodoToken", profile.getZenodoId());
+				}
+				if (profile.getZenodoExpire() != null) {
+					additionalInfo.put("expirationDate", Instant.now().plusSeconds(profile.getZenodoExpire()).toEpochMilli());
+				}
+				if (profile.getZenodoRefresh() != null) {
+					additionalInfo.put("zenodoRefresh", profile.getZenodoRefresh());
+				}
+				if (profile.getProvider() == TokenValidatorFactoryImpl.LoginProvider.ZENODO) {
+					additionalInfo.put("zenodoEmail", profile.getEmail());
+				}
+				userInfo.setLastloggedin(new Date());
+				userInfo.setAdditionalinfo(apiContext.getObjectMapper().writeValueAsString(additionalInfo));
+			} catch (JsonProcessingException e) {
+				logger.error(e.getLocalizedMessage(), e);
 			}
-			if (profile.getZenodoId() != null && !profile.getZenodoId().isEmpty() && !profile.getZenodoId().equals("null")) {
+
-				additionalInfo.put("zenodoToken", profile.getZenodoId());
-			}
-			if (profile.getZenodoExpire() != null) {
-				additionalInfo.put("expirationDate", Instant.now().plusSeconds(profile.getZenodoExpire()).toEpochMilli());
-			}
-			if (profile.getZenodoRefresh() != null) {
-				additionalInfo.put("zenodoRefresh", profile.getZenodoRefresh());
-			}
-			if (profile.getProvider() == TokenValidatorFactoryImpl.LoginProvider.ZENODO) {
-				additionalInfo.put("zenodoEmail", profile.getEmail());
-			}
-			userInfo.setLastloggedin(new Date());
-			userInfo.setAdditionalinfo(new JSONObject(additionalInfo).toString());
 			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/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/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 +9,20 @@ 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 Logger logger = LoggerFactory.getLogger(DataManagementPlan.class);
     private UUID id;
     private String label;
     private UUID groupId;
@@ -233,67 +237,72 @@ public class DataManagementPlan implements DataModel<DMP, DataManagementPlan> {
 
     @Override
     public DataManagementPlan fromDataModel(DMP entity) {
-        this.id = entity.getId();
+        try {
-        this.profile = entity.getProfile() != null ? new Tuple<UUID, String>(entity.getProfile().getId(), entity.getProfile().getLabel()) : null;
+            ObjectMapper objectMapper = new ObjectMapper();
-        this.organisations = entity.getOrganisations() != null ? entity.getOrganisations().stream().map(item -> new Organisation().fromDataModel(item)).collect(Collectors.toList()) : new ArrayList<>();
+            this.id = entity.getId();
-        this.researchers = entity.getResearchers() != null ? entity.getResearchers().stream().map(item -> new Researcher().fromDataModel(item)).collect(Collectors.toList()): new ArrayList<>();
+            this.profile = entity.getProfile() != null ? new Tuple<UUID, String>(entity.getProfile().getId(), entity.getProfile().getLabel()) : null;
-        this.version = entity.getVersion();
+            this.organisations = entity.getOrganisations() != null ? entity.getOrganisations().stream().map(item -> new Organisation().fromDataModel(item)).collect(Collectors.toList()) : new ArrayList<>();
-        this.groupId = this.groupId == null ? null : entity.getGroupId();
+            this.researchers = entity.getResearchers() != null ? entity.getResearchers().stream().map(item -> new Researcher().fromDataModel(item)).collect(Collectors.toList()): new ArrayList<>();
-        this.label = entity.getLabel();
+            this.version = entity.getVersion();
-        this.grant = new Grant();
+            this.groupId = this.groupId == null ? null : entity.getGroupId();
-        this.properties = entity.getProperties() != null ? new org.json.JSONObject(entity.getProperties()).toMap() : null;
+            this.label = entity.getLabel();
-        this.grant.fromDataModel(entity.getGrant());
+            this.grant = new Grant();
-        this.creator = new eu.eudat.models.data.userinfo.UserInfo();
+            this.properties = entity.getProperties() != null ? objectMapper.readValue(entity.getProperties(), HashMap.class) : null;
-        this.groupId = entity.getGroupId();
+            this.grant.fromDataModel(entity.getGrant());
-        this.lockable = entity.getDataset() != null && entity.getDataset().stream().findAny().isPresent();
+            this.creator = new eu.eudat.models.data.userinfo.UserInfo();
-        this.definition = entity.getProfile() == null ? null : new DataManagementPlanProfile().fromXml(XmlBuilder.fromXml(entity.getProfile().getDefinition()).getDocumentElement());
+            this.groupId = entity.getGroupId();
-        if (this.definition != null && this.definition.getFields() != null && !this.definition.getFields().isEmpty() && this.properties != null) {
+            this.lockable = entity.getDataset() != null && entity.getDataset().stream().findAny().isPresent();
-            this.definition.getFields().forEach(item -> {
+            this.definition = entity.getProfile() == null ? null : new DataManagementPlanProfile().fromXml(XmlBuilder.fromXml(entity.getProfile().getDefinition()).getDocumentElement());
-                Optional<Map<String, Object>> fieldOptional = ((List<Map<String, Object>>) this.properties.get("fields")).stream().filter(field -> field.get("id").equals(item.getId().toString())).findFirst();
+            if (this.definition != null && this.definition.getFields() != null && !this.definition.getFields().isEmpty() && this.properties != null) {
-                if (fieldOptional.isPresent()) item.setValue(fieldOptional.get().get("value"));
+                this.definition.getFields().forEach(item -> {
-            });
+                    Optional<Map<String, Object>> fieldOptional = ((List<Map<String, Object>>) this.properties.get("fields")).stream().filter(field -> field.get("id").equals(item.getId().toString())).findFirst();
-        }
+                    if (fieldOptional.isPresent()) item.setValue(fieldOptional.get().get("value"));
-        if (entity.getUsers() != null && entity.getUsers().stream().anyMatch(userDMP -> userDMP.getRole().equals(UserDMP.UserDMPRoles.OWNER.getValue())))
+                });
-            this.creator.fromDataModel(entity.getUsers().stream().filter(user -> user.getRole().equals(UserDMP.UserDMPRoles.OWNER.getValue())).findFirst().get().getUser());
-
-        if (entity.getAssociatedDmps() != null && !entity.getAssociatedDmps().isEmpty()) {
-            this.profiles = new LinkedList<>();
-            for (DatasetProfile datasetProfile: entity.getAssociatedDmps()) {
-                AssociatedProfile associatedProfile = new AssociatedProfile().fromData(datasetProfile);
-                this.profiles.add(associatedProfile);
             }
-        }
+            if (entity.getUsers() != null && entity.getUsers().stream().anyMatch(userDMP -> userDMP.getRole().equals(UserDMP.UserDMPRoles.OWNER.getValue())))
-        if (entity.getDataset() != null) {
+                this.creator.fromDataModel(entity.getUsers().stream().filter(user -> user.getRole().equals(UserDMP.UserDMPRoles.OWNER.getValue())).findFirst().get().getUser());
-            if (entity.isPublic()) {
+
-                this.datasets = entity.getDataset().stream()
+            if (entity.getAssociatedDmps() != null && !entity.getAssociatedDmps().isEmpty()) {
-                                      .filter(dataset -> !dataset.getStatus().equals(Dataset.Status.DELETED.getValue()) && !dataset.getStatus().equals(Dataset.Status.CANCELED.getValue()) && !dataset.getStatus().equals(Dataset.Status.SAVED.getValue()))
+                this.profiles = new LinkedList<>();
-                                      .map(x -> new DatasetWizardModel().fromDataModelNoDmp(x)).collect(Collectors.toList());
+                for (DatasetProfile datasetProfile: entity.getAssociatedDmps()) {
-            } else {
+                    AssociatedProfile associatedProfile = new AssociatedProfile().fromData(datasetProfile);
-                this.datasets = entity.getDataset().stream()
+                    this.profiles.add(associatedProfile);
-                                      .filter(dataset -> !dataset.getStatus().equals(Dataset.Status.DELETED.getValue()) && !dataset.getStatus().equals(Dataset.Status.CANCELED.getValue()))
+                }
-                                      .map(x -> new DatasetWizardModel().fromDataModelNoDmp(x)).collect(Collectors.toList());
             }
-        }
+            if (entity.getDataset() != null) {
-        this.modified = entity.getModified();
+                if (entity.isPublic()) {
-        this.created = entity.getCreated();
+                    this.datasets = entity.getDataset().stream()
-        this.description = entity.getDescription();
+                                          .filter(dataset -> !dataset.getStatus().equals(Dataset.Status.DELETED.getValue()) && !dataset.getStatus().equals(Dataset.Status.CANCELED.getValue()) && !dataset.getStatus().equals(Dataset.Status.SAVED.getValue()))
-        this.status = entity.getStatus();
+                                          .map(x -> new DatasetWizardModel().fromDataModelNoDmp(x)).collect(Collectors.toList());
-        this.associatedUsers = entity.getUsers() != null ? entity.getUsers().stream().map(item -> new UserListingModel().fromDataModel(item.getUser())).collect(Collectors.toList()) : new ArrayList<>();
+                } else {
-        this.users = entity.getUsers() != null ? entity.getUsers().stream().map(item -> new UserInfoListingModel().fromDataModel(item)).collect(Collectors.toList()) : new ArrayList<>();
+                    this.datasets = entity.getDataset().stream()
-        this.doi = entity.getDoi();
+                                          .filter(dataset -> !dataset.getStatus().equals(Dataset.Status.DELETED.getValue()) && !dataset.getStatus().equals(Dataset.Status.CANCELED.getValue()))
+                                          .map(x -> new DatasetWizardModel().fromDataModelNoDmp(x)).collect(Collectors.toList());
+                }
+            }
+            this.modified = entity.getModified();
+            this.created = entity.getCreated();
+            this.description = entity.getDescription();
+            this.status = entity.getStatus();
+            this.associatedUsers = entity.getUsers() != null ? entity.getUsers().stream().map(item -> new UserListingModel().fromDataModel(item.getUser())).collect(Collectors.toList()) : new ArrayList<>();
+            this.users = entity.getUsers() != null ? entity.getUsers().stream().map(item -> new UserInfoListingModel().fromDataModel(item)).collect(Collectors.toList()) : new ArrayList<>();
+            this.doi = entity.getDoi();
 
-        if (entity.getProject() != null) {
+            if (entity.getProject() != null) {
-            this.project = new Project();
+                this.project = new Project();
-            this.project = new Project().fromDataModel(entity.getProject());
+                this.project = new Project().fromDataModel(entity.getProject());
-        }
+            }
 
-        if (entity.getGrant().getFunder() != null) {
+            if (entity.getGrant().getFunder() != null) {
-            this.funder = new Funder();
+                this.funder = new Funder();
-            this.funder.fromDataModel(entity.getGrant().getFunder());
+                this.funder.fromDataModel(entity.getGrant().getFunder());
-        }
+            }
-        this.isPublic = entity.isPublic();
+            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(), HashMap.class) : null;
+        } catch (JsonProcessingException e) {
+            logger.error(e.getMessage(), e);
+        }
 
         return this;
     }
@@ -342,54 +351,59 @@ public class DataManagementPlan implements DataModel<DMP, DataManagementPlan> {
     }
 
     public DataManagementPlan fromDataModelNoDatasets(DMP entity) {
-        this.id = entity.getId();
+        try {
-        this.profile = entity.getProfile() != null ? new Tuple<UUID, String>(entity.getProfile().getId(), entity.getProfile().getLabel()) : null;
+            ObjectMapper objectMapper = new ObjectMapper();
-        this.organisations = entity.getOrganisations() != null ? entity.getOrganisations().stream().map(item -> new Organisation().fromDataModel(item)).collect(Collectors.toList()) : new ArrayList<>();
+            this.id = entity.getId();
-        this.researchers = entity.getResearchers() != null ? entity.getResearchers().stream().filter(Objects::nonNull).map(item -> new Researcher().fromDataModel(item)).collect(Collectors.toList()) : new ArrayList<>();
+            this.profile = entity.getProfile() != null ? new Tuple<UUID, String>(entity.getProfile().getId(), entity.getProfile().getLabel()) : null;
-        this.version = entity.getVersion();
+            this.organisations = entity.getOrganisations() != null ? entity.getOrganisations().stream().map(item -> new Organisation().fromDataModel(item)).collect(Collectors.toList()) : new ArrayList<>();
-        this.label = entity.getLabel();
+            this.researchers = entity.getResearchers() != null ? entity.getResearchers().stream().filter(Objects::nonNull).map(item -> new Researcher().fromDataModel(item)).collect(Collectors.toList()) : new ArrayList<>();
-        this.grant = new Grant();
+            this.version = entity.getVersion();
-        this.properties = entity.getProperties() != null ? new org.json.JSONObject(entity.getProperties()).toMap() : null;
+            this.label = entity.getLabel();
-        this.creator = new eu.eudat.models.data.userinfo.UserInfo();
+            this.grant = new Grant();
-        this.groupId = entity.getGroupId();
+            this.properties = entity.getProperties() != null ? objectMapper.readValue(entity.getProperties(), HashMap.class) : null;
-        this.lockable = entity.getDataset() != null && entity.getDataset().stream().findAny().isPresent();
+            this.creator = new eu.eudat.models.data.userinfo.UserInfo();
-        this.definition = entity.getProfile() == null ? null : new DataManagementPlanProfile().fromXml(XmlBuilder.fromXml(entity.getProfile().getDefinition()).getDocumentElement());
+            this.groupId = entity.getGroupId();
-        if (this.definition != null && this.definition.getFields() != null && !this.definition.getFields().isEmpty() && this.properties != null) {
+            this.lockable = entity.getDataset() != null && entity.getDataset().stream().findAny().isPresent();
-            this.definition.getFields().forEach(item -> {
+            this.definition = entity.getProfile() == null ? null : new DataManagementPlanProfile().fromXml(XmlBuilder.fromXml(entity.getProfile().getDefinition()).getDocumentElement());
-                Optional<Map<String, Object>> fieldOptional = ((List<Map<String, Object>>) this.properties.get("fields")).stream().filter(field -> field.get("id").equals(item.getId().toString())).findFirst();
+            if (this.definition != null && this.definition.getFields() != null && !this.definition.getFields().isEmpty() && this.properties != null) {
-                fieldOptional.ifPresent(stringObjectMap -> item.setValue(stringObjectMap.get("value")));
+                this.definition.getFields().forEach(item -> {
-            });
+                    Optional<Map<String, Object>> fieldOptional = ((List<Map<String, Object>>) this.properties.get("fields")).stream().filter(field -> field.get("id").equals(item.getId().toString())).findFirst();
-        }
+                    fieldOptional.ifPresent(stringObjectMap -> item.setValue(stringObjectMap.get("value")));
-        if (entity.getUsers() != null && entity.getUsers().stream().anyMatch(userDMP -> userDMP.getRole().equals(UserDMP.UserDMPRoles.OWNER.getValue())))
+                });
-            this.creator.fromDataModel(entity.getUsers().stream().filter(user -> user.getRole().equals(UserDMP.UserDMPRoles.OWNER.getValue())).findFirst().get().getUser());
-
-        if (entity.getAssociatedDmps() != null && !entity.getAssociatedDmps().isEmpty()) {
-            this.profiles = new LinkedList<>();
-            for (DatasetProfile datasetProfile: entity.getAssociatedDmps()) {
-                AssociatedProfile associatedProfile = new AssociatedProfile().fromData(datasetProfile);
-                this.profiles.add(associatedProfile);
             }
-        }
+            if (entity.getUsers() != null && entity.getUsers().stream().anyMatch(userDMP -> userDMP.getRole().equals(UserDMP.UserDMPRoles.OWNER.getValue())))
-        this.modified = entity.getModified();
+                this.creator.fromDataModel(entity.getUsers().stream().filter(user -> user.getRole().equals(UserDMP.UserDMPRoles.OWNER.getValue())).findFirst().get().getUser());
-        this.created = entity.getCreated();
-        this.description = entity.getDescription();
-        this.status = entity.getStatus();
-        this.associatedUsers = entity.getUsers() != null ? entity.getUsers().stream().map(item -> new UserListingModel().fromDataModel(item.getUser())).collect(Collectors.toList()) : new ArrayList<>();
-        this.users = entity.getUsers() != null ? entity.getUsers().stream().map(item -> new UserInfoListingModel().fromDataModel(item)).collect(Collectors.toList()) : new ArrayList<>();
-        this.doi = entity.getDoi();
-        this.grant.fromDataModel(entity.getGrant());
 
-        if (entity.getProject() != null) {
+            if (entity.getAssociatedDmps() != null && !entity.getAssociatedDmps().isEmpty()) {
-            this.project = new Project();
+                this.profiles = new LinkedList<>();
-            this.project = new Project().fromDataModel(entity.getProject());
+                for (DatasetProfile datasetProfile: entity.getAssociatedDmps()) {
-        }
+                    AssociatedProfile associatedProfile = new AssociatedProfile().fromData(datasetProfile);
-        if (entity.getGrant().getFunder() != null) {
+                    this.profiles.add(associatedProfile);
-            this.funder = new Funder();
+                }
-            this.funder.fromDataModel(entity.getGrant().getFunder());
+            }
-        }
+            this.modified = entity.getModified();
-        this.isPublic = entity.isPublic();
+            this.created = entity.getCreated();
+            this.description = entity.getDescription();
+            this.status = entity.getStatus();
+            this.associatedUsers = entity.getUsers() != null ? entity.getUsers().stream().map(item -> new UserListingModel().fromDataModel(item.getUser())).collect(Collectors.toList()) : new ArrayList<>();
+            this.users = entity.getUsers() != null ? entity.getUsers().stream().map(item -> new UserInfoListingModel().fromDataModel(item)).collect(Collectors.toList()) : new ArrayList<>();
+            this.doi = entity.getDoi();
+            this.grant.fromDataModel(entity.getGrant());
 
-        this.extraProperties = entity.getExtraProperties() != null ? new org.json.JSONObject(entity.getExtraProperties()).toMap() : null;
+            if (entity.getProject() != null) {
+                this.project = new Project();
+                this.project = new Project().fromDataModel(entity.getProject());
+            }
+            if (entity.getGrant().getFunder() != null) {
+                this.funder = new Funder();
+                this.funder.fromDataModel(entity.getGrant().getFunder());
+            }
+            this.isPublic = entity.isPublic();
+
+            this.extraProperties = entity.getExtraProperties() != null ? objectMapper.readValue(entity.getExtraProperties(), HashMap.class) : null;
+        } catch (JsonProcessingException e) {
+            logger.error(e.getMessage(), e);
+        }
 
         return this;
     }

dmp-backend/web/src/main/java/eu/eudat/models/data/dmp/DataManagementPlanEditorModel.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 +9,20 @@ 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.FunderDMPEditorModel;
-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.GrantDMPEditorModel;
+import eu.eudat.models.data.helpermodels.Tuple;
+import eu.eudat.models.data.listingmodels.UserInfoListingModel;
 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 Logger logger = LoggerFactory.getLogger(DataManagementPlan.class);
     private UUID id;
     private String label;
     private UUID groupId;
@@ -224,50 +228,54 @@ public class DataManagementPlanEditorModel implements DataModel<DMP, DataManagem
 
     @Override
     public DataManagementPlanEditorModel fromDataModel(DMP entity) {
-        this.id = entity.getId();
+        try {
-        this.profile = entity.getProfile() != null ? new Tuple<UUID, String>(entity.getProfile().getId(), entity.getProfile().getLabel()) : null;
+            ObjectMapper objectMapper = new ObjectMapper();
-        this.organisations = entity.getOrganisations().stream().map(item -> new Organisation().fromDataModel(item)).collect(Collectors.toList());
+            this.id = entity.getId();
-        this.researchers = entity.getResearchers().stream().map(item -> new Researcher().fromDataModel(item)).collect(Collectors.toList());
+            this.profile = entity.getProfile() != null ? new Tuple<UUID, String>(entity.getProfile().getId(), entity.getProfile().getLabel()) : null;
-        this.version = entity.getVersion();
+            this.organisations = entity.getOrganisations().stream().map(item -> new Organisation().fromDataModel(item)).collect(Collectors.toList());
-        this.groupId = this.groupId == null ? null : entity.getGroupId();
+            this.researchers = entity.getResearchers().stream().map(item -> new Researcher().fromDataModel(item)).collect(Collectors.toList());
-        this.label = entity.getLabel();
+            this.version = entity.getVersion();
-        this.grant = new GrantDMPEditorModel();
+            this.groupId = this.groupId == null ? null : entity.getGroupId();
-        this.properties = entity.getProperties() != null ? new org.json.JSONObject(entity.getProperties()).toMap() : null;
+            this.label = entity.getLabel();
-        this.grant.getExistGrant().fromDataModel(entity.getGrant());
+            this.grant = new GrantDMPEditorModel();
-        this.grant.getExistGrant().setSource("");
+            this.properties = entity.getProperties() != null ? objectMapper.readValue(entity.getProperties(), HashMap.class) : null;
-        this.creator = new eu.eudat.models.data.userinfo.UserInfo();
+            this.grant.getExistGrant().fromDataModel(entity.getGrant());
-        this.groupId = entity.getGroupId();
+            this.grant.getExistGrant().setSource("");
-        this.lockable = entity.getDataset().stream().findAny().isPresent();
+            this.creator = new eu.eudat.models.data.userinfo.UserInfo();
-        this.definition = entity.getProfile() == null ? null : new DataManagementPlanProfile().fromXml(XmlBuilder.fromXml(entity.getProfile().getDefinition()).getDocumentElement());
+            this.groupId = entity.getGroupId();
-        if (this.definition != null && this.definition.getFields() != null && !this.definition.getFields().isEmpty() && this.properties != null) {
+            this.lockable = entity.getDataset().stream().findAny().isPresent();
-            this.definition.getFields().forEach(item -> {
+            this.definition = entity.getProfile() == null ? null : new DataManagementPlanProfile().fromXml(XmlBuilder.fromXml(entity.getProfile().getDefinition()).getDocumentElement());
-                Optional<Map<String, Object>> fieldOptional = ((List<Map<String, Object>>) this.properties.get("fields")).stream().filter(field -> field.get("id").equals(item.getId().toString())).findFirst();
+            if (this.definition != null && this.definition.getFields() != null && !this.definition.getFields().isEmpty() && this.properties != null) {
-                if (fieldOptional.isPresent()) item.setValue(fieldOptional.get().get("value"));
+                this.definition.getFields().forEach(item -> {
-            });
+                    Optional<Map<String, Object>> fieldOptional = ((List<Map<String, Object>>) this.properties.get("fields")).stream().filter(field -> field.get("id").equals(item.getId().toString())).findFirst();
-        }
+                    if (fieldOptional.isPresent()) item.setValue(fieldOptional.get().get("value"));
-        if (entity.getUsers().stream().anyMatch(userDMP -> userDMP.getRole().equals(UserDMP.UserDMPRoles.OWNER.getValue())))
+                });
-            this.creator.fromDataModel(entity.getUsers().stream().filter(user -> user.getRole().equals(UserDMP.UserDMPRoles.OWNER.getValue())).findFirst().get().getUser());
-
-        if (entity.getAssociatedDmps() != null && !entity.getAssociatedDmps().isEmpty()) {
-            this.profiles = new LinkedList<>();
-            for (DatasetProfile datasetProfile: entity.getAssociatedDmps()) {
-                AssociatedProfile associatedProfile = new AssociatedProfile().fromData(datasetProfile);
-                this.profiles.add(associatedProfile);
             }
-        }
+            if (entity.getUsers().stream().anyMatch(userDMP -> userDMP.getRole().equals(UserDMP.UserDMPRoles.OWNER.getValue())))
-        this.datasets = entity.getDataset().stream().map(item -> new DatasetWizardModel().fromDataModelNoDmp(item)).collect(Collectors.toList());
+                this.creator.fromDataModel(entity.getUsers().stream().filter(user -> user.getRole().equals(UserDMP.UserDMPRoles.OWNER.getValue())).findFirst().get().getUser());
-        this.modified = entity.getModified();
-        this.created = entity.getCreated();
-        this.description = entity.getDescription();
-        this.status = entity.getStatus();
-        this.project = new ProjectDMPEditorModel();
-        this.project.getExistProject().fromDataModel(entity.getProject());
-        this.associatedUsers = entity.getUsers().stream().map(item -> new UserListingModel().fromDataModel(item.getUser())).collect(Collectors.toList());
-        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;
 
+            if (entity.getAssociatedDmps() != null && !entity.getAssociatedDmps().isEmpty()) {
+                this.profiles = new LinkedList<>();
+                for (DatasetProfile datasetProfile: entity.getAssociatedDmps()) {
+                    AssociatedProfile associatedProfile = new AssociatedProfile().fromData(datasetProfile);
+                    this.profiles.add(associatedProfile);
+                }
+            }
+            this.datasets = entity.getDataset().stream().map(item -> new DatasetWizardModel().fromDataModelNoDmp(item)).collect(Collectors.toList());
+            this.modified = entity.getModified();
+            this.created = entity.getCreated();
+            this.description = entity.getDescription();
+            this.status = entity.getStatus();
+            this.project = new ProjectDMPEditorModel();
+            this.project.getExistProject().fromDataModel(entity.getProject());
+            this.associatedUsers = entity.getUsers().stream().map(item -> new UserListingModel().fromDataModel(item.getUser())).collect(Collectors.toList());
+            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 ? objectMapper.readValue(entity.getExtraProperties(), HashMap.class) : null;
+        } catch (JsonProcessingException e) {
+            logger.error(e.getMessage(), 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

@@ -11,9 +11,6 @@ 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;
 
@@ -205,7 +202,7 @@ public class Field implements Comparable, PropertiesModelBuilder, ViewStyleDefin
             ObjectMapper mapper = new ObjectMapper();
             List<String> stringList = mapper.readValue(properties.get(this.id).toString(), LinkedList.class);
             this.value = stringList;
-        } catch (JSONException | NullPointerException | IOException e) {
+        } catch ( NullPointerException | IOException e) {
             this.value = (String) properties.get(this.id);
         }
         this.multiplicityItems = new LinkedList<>();

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

@@ -1,24 +1,31 @@
 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.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.stream.Collectors;
+
 public class CostRDAMapper {
 	private static final Logger logger = LoggerFactory.getLogger(DatasetRDAMapper.class);
 	
 	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();
+		Map<String, Object> code;
-		rda.setCurrencyCode(Cost.CurrencyCode.fromValue((String) code.get("value")));
+		try {
+			code = new ObjectMapper().readValue((String) cost.get("code"), HashMap.class);
+			rda.setCurrencyCode(Cost.CurrencyCode.fromValue((String) code.get("value")));
+		} catch (JsonProcessingException e) {
+			logger.error(e.getLocalizedMessage(), e);
+		}
 		rda.setDescription((String) cost.get("description"));
 		if (cost.get("title") == null) {
 			throw new IllegalArgumentException("Cost Title is missing");

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

@@ -12,7 +12,6 @@ import eu.eudat.logic.utilities.json.JsonSearcher;
 import eu.eudat.models.data.datasetprofile.DatasetProfileOverviewModel;
 import eu.eudat.models.data.datasetwizard.DatasetWizardModel;
 import eu.eudat.models.rda.*;
-import org.json.JSONObject;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -52,8 +51,7 @@ public class DatasetRDAMapper {
 		rda.setDescription(dataset.getDescription());
 		rda.setAdditionalProperty("template", dataset.getProfile().getId());
 		try {
-			JSONObject jObject = new JSONObject(dataset.getProperties());
+			Map<String, Object> templateIdsToValues = apiContext.getObjectMapper().readValue(dataset.getProperties(), HashMap.class);
-			Map<String, Object> templateIdsToValues = jObject.toMap();
 			DatasetWizardModel datasetWizardModel = new DatasetWizardModel().fromDataModel(dataset);
 			datasetWizardModel.setDatasetProfileDefinition(datasetManager.getPagedProfile(datasetWizardModel, dataset));
 			ObjectMapper mapper = new ObjectMapper();

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

@@ -1,12 +1,14 @@
 package eu.eudat.models.rda.mapper;
 
+import com.fasterxml.jackson.core.JsonProcessingException;
 import eu.eudat.data.entities.*;
 import eu.eudat.logic.services.ApiContext;
 import eu.eudat.logic.utilities.helpers.StreamDistinctBy;
-import eu.eudat.models.rda.Cost;
 import eu.eudat.models.rda.Dmp;
 import eu.eudat.models.rda.DmpId;
 import net.minidev.json.JSONObject;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Component;
 
@@ -17,6 +19,7 @@ import java.util.stream.Collectors;
 
 @Component
 public class DmpRDAMapper {
+	private static final Logger logger = LoggerFactory.getLogger(DmpRDAMapper.class);
 
 	private DatasetRDAMapper datasetRDAMapper;
 	private ApiContext apiContext;
@@ -34,17 +37,22 @@ public class DmpRDAMapper {
 		if (dmp.getDataset() == null || dmp.getDataset().isEmpty()) {
 			throw new IllegalArgumentException("DMP has no Datasets");
 		}
-		Map<String, Object> extraProperties;
+		Map<String, Object> extraProperties = null;
 		if (dmp.getExtraProperties() == null) {
 			throw new IllegalArgumentException("DMP is missing language and contact properties");
 		} else {
-			extraProperties = new org.json.JSONObject(dmp.getExtraProperties()).toMap();
+			try {
-			/*if (extraProperties.get("language") == null) {
+				extraProperties = apiContext.getObjectMapper().readValue(dmp.getExtraProperties(), HashMap.class);
+				/*if (extraProperties.get("language") == null) {
 				throw new IllegalArgumentException("DMP must have it's language property defined");
 			}*/
-			if (extraProperties.get("contact") == null) {
+				if (extraProperties.get("contact") == null) {
-				throw new IllegalArgumentException("DMP must have it's contact property defined");
+					throw new IllegalArgumentException("DMP must have it's contact property defined");
+				}
+			} catch (JsonProcessingException e) {
+				logger.error(e.getLocalizedMessage(), e);
 			}
+
 		}
 		Dmp rda = new Dmp();
 		if (dmp.getDoi() != null && !dmp.getDoi().isEmpty()) {
@@ -66,7 +74,7 @@ public class DmpRDAMapper {
 		rda.setModified(dmp.getModified());
 		rda.setTitle(dmp.getLabel());
 
-		if (!extraProperties.isEmpty()) {
+		if (extraProperties != null && !extraProperties.isEmpty()) {
 			if (extraProperties.get("ethicalIssues") != null) {
 				rda.setEthicalIssuesExist(Dmp.EthicalIssuesExist.fromValue(extraProperties.get("ethicalIssues").toString()));
 			} else {