Add transactional to makeFinalize on DMP and remove jackson parsing when depositing to zenodo

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

@@ -7,6 +7,7 @@ import eu.eudat.queryable.queryableentity.DataEntity;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 
+import javax.transaction.Transactional;
 import java.util.Set;
 
 
@@ -28,6 +29,7 @@ public class DatabaseService<T extends DataEntity> {
         return this.databaseCtx.getQueryable(tClass);
     }
 
+    @Transactional
     public T createOrUpdate(T item, Class<T> tClass) {
         return this.databaseCtx.createOrUpdate(item, tClass);
     }

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

@@ -16,6 +16,7 @@ import org.springframework.stereotype.Component;
 
 import javax.persistence.criteria.Join;
 import javax.persistence.criteria.JoinType;
+import javax.transaction.Transactional;
 import java.util.Arrays;
 import java.util.Date;
 import java.util.List;
@@ -106,6 +107,7 @@ public class DMPDaoImpl extends DatabaseAccess<DMP> implements DMPDao {
 	}
 
 	@Override
+	@Transactional
 	public DMP createOrUpdate(DMP item) {
 		return this.getDatabaseService().createOrUpdate(item, DMP.class);
 	}

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

@@ -79,6 +79,7 @@ import org.springframework.web.multipart.MultipartFile;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
 
+import javax.transaction.Transactional;
 import javax.xml.bind.JAXBContext;
 import javax.xml.bind.JAXBException;
 import javax.xml.bind.Unmarshaller;
@@ -1034,6 +1035,7 @@ public class DataManagementPlanManager {
         }
     }
 
+    @Transactional
     public void makeFinalize(UUID id, Principal principal, DatasetsToBeFinalized datasetsToBeFinalized) throws Exception {
         DMP dmp = this.apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().find(id);
         if (!isUserOwnerOfDmp(dmp, principal))
@@ -2093,10 +2095,10 @@ public class DataManagementPlanManager {
         }
         dataBuilder.append("    }\n").append("}");
         createData = dataBuilder.toString();
-        ObjectMapper mapper = new ObjectMapper();
+        /*ObjectMapper mapper = new ObjectMapper();
         mapper.configure(JsonParser.Feature.ALLOW_UNQUOTED_CONTROL_CHARS, true);
-        JsonNode createDataJSON = mapper.readTree(createData);
+        JsonNode createDataJSON = mapper.readTree(createData);*/
-        HttpEntity<JsonNode> request = new HttpEntity<>(createDataJSON, headers);
+        HttpEntity<String> request = new HttpEntity<>(createData, headers);
         Map createResponse = null;
         LinkedHashMap<String, String> links = null;
         String previousDOI = this.getPreviousDOI(dmp.getGroupId(), dmp.getId());