Fix issues with xml import and issues with zenodo deposit

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

@@ -260,7 +260,7 @@ public class DMPs extends BaseController {
         if (files[0].getContentType().equals(APPLICATION_JSON.toString())) {
             this.dataManagementPlanManager.createFromRDA(files, principal, profiles);
         } else if (files[0].getContentType().equals(APPLICATION_ATOM_XML.toString()) || files[0].getContentType().equals(TEXT_XML.toString())) {
-            this.dataManagementPlanManager.createDmpFromXml(this.getApiContext(), files, principal);
+            this.dataManagementPlanManager.createDmpFromXml(files, principal, profiles);
         } else {
             return ResponseEntity.badRequest().body(new ResponseItem().status(ApiMessageCode.ERROR_MESSAGE).message("File format is not supported"));
         }

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

@@ -1476,7 +1476,7 @@ public class DataManagementPlanManager {
     * Data Import
     * */
 
-    public List<DmpImportModel> createDmpFromXml(ApiContext apiContext, MultipartFile[] files, Principal principal) throws IOException, JAXBException, Exception {
+    public List<DmpImportModel> createDmpFromXml(MultipartFile[] files, Principal principal, String[] profiles) throws IOException, JAXBException, Exception {
         List<DmpImportModel> dataManagementPlans = new ArrayList<>();
         // Jaxb approach.
         JAXBContext jaxbContext;
@@ -1532,16 +1532,26 @@ public class DataManagementPlanManager {
             projectEditor.setExistProject(project);
 
             List<eu.eudat.models.data.dmp.AssociatedProfile> associatedProfiles = new LinkedList<>();
-            for (AssociatedProfileImportModels a : dataManagementPlans.get(0).getProfilesImportModels()) {
+            if (profiles != null && profiles.length > 0) {
-                AssociatedProfile associatedProfile = new AssociatedProfile();
+                for (String profile : profiles) {
-                associatedProfile.setId(a.getId());
+                    DatasetProfile exProfile = apiContext.getOperationsContext().getDatabaseRepository().getDatasetProfileDao().find(UUID.fromString(profile));
-                associatedProfile.setLabel(a.getLabel());
+                    AssociatedProfile associatedProfile = new AssociatedProfile().fromData(exProfile);
                     associatedProfiles.add(associatedProfile);
                 }
+            }
+
+            for (AssociatedProfileImportModels a : dataManagementPlans.get(0).getProfilesImportModels()) {
+                try {
+                    DatasetProfile exProfile = apiContext.getOperationsContext().getDatabaseRepository().getDatasetProfileDao().find(a.getId());
+                    AssociatedProfile associatedProfile = new AssociatedProfile().fromData(exProfile);
+                    associatedProfiles.add(associatedProfile);
+                } catch (Exception ignored) {
+                }
+            }
             List<eu.eudat.models.data.dmp.Organisation> organisations = new ArrayList<>();
             for (OrganisationImportModel org : dataManagementPlans.get(0).getOrganisationImportModels()) {
                 eu.eudat.models.data.dmp.Organisation organisation = new eu.eudat.models.data.dmp.Organisation();
-                organisation.setLabel(org.getOrganaisationNameImport());
+                organisation.setName(org.getOrganaisationNameImport());
                 organisation.setReference(org.getOrganaisationReferenceImport());
                 organisation.setKey(organisation.getReference().split(":")[0]);
                 organisations.add(organisation);
@@ -1593,7 +1603,11 @@ public class DataManagementPlanManager {
             for (DatasetImportModels das: dataManagementPlans.get(0).getDatasetImportModels()) {
                 eu.eudat.data.entities.Dataset dataset = new eu.eudat.data.entities.Dataset();
                 dataset.setLabel(das.getName());
+                try {
                     dataset.setProfile(databaseRepository.getDatasetProfileDao().find(das.getProfile()));
+                } catch (Exception ignored) {
+                    dataset.setProfile(databaseRepository.getDatasetProfileDao().find(associatedProfiles.get(0).getId()));
+                }
                 dataset.setProperties(new ObjectMapper().writeValueAsString(das.getFieldImportModels()));
                 dataset.setStatus((short) 0);
                 dataset.setRegistries(new HashSet<>());
@@ -1972,6 +1986,9 @@ public class DataManagementPlanManager {
             i++;
         }
         dataBuilder.append("],\n");
+        if (dmp.getGrant().getReference() == null) {
+            dmp.getGrant().setReference("dmp:" + dmp.getGrant().getId());
+        }
         String grantReferenceHead = dmp.getGrant().getReference().split(":")[0];
         if (grantReferenceHead.equals("openaire")) {
             String grantReferenceTail = dmp.getGrant().getReference().split(":")[3];
@@ -1980,6 +1997,7 @@ public class DataManagementPlanManager {
             dataBuilder.append("        \"grants\": [{\n");
             dataBuilder.append("        \t\t\"id\": \"").append(finalId).append("\"\n}],\n");
         }
+
         dataBuilder.append("        \"creators\": [{\n");
         dataBuilder.append("        \t\t\"name\": \"").append(dmp.getUsers().stream().filter(userDMP -> userDMP.getRole().equals(UserDMP.UserDMPRoles.OWNER.getValue())).findFirst().get().getUser().getName()).append("\",\n");
         if (dmp.getOrganisations() != null && !dmp.getOrganisations().isEmpty()) {

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

@@ -108,7 +108,7 @@ public class DatasetRDAMapper {
 				for (int i = 0; i < keywordNodes.size(); i++) {
 					rda.setAdditionalProperty("keyword" + (i + 1),  keywordNodes.get(i).get("id").asText());
 				}
-			} else {
+			} else if (apiContext.getOperationsContext().getElasticRepository().getDatasetRepository().exists()) {
 				List<String> tags = apiContext.getOperationsContext().getElasticRepository().getDatasetRepository().findDocument(dataset.getId().toString()).getTags().stream().map(Tag::getName).collect(Collectors.toList());
 				rda.setKeyword(tags);
 			}

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

@@ -6,11 +6,13 @@ import eu.eudat.data.entities.Grant;
 import eu.eudat.logic.services.ApiContext;
 import eu.eudat.models.rda.Funding;
 
+import javax.transaction.Transactional;
 import java.util.Date;
 import java.util.UUID;
 
 public class FundingRDAMapper {
 
+	@Transactional
 	public static Funding toRDA(Grant grant) {
 		Funding rda = new Funding();
 		String referencePrefix;
@@ -22,9 +24,13 @@ public class FundingRDAMapper {
 		} else {
 			rda.setFunderId(FunderIdRDAMapper.toRDA(grant.getFunder().getId()));
 		}
+		if (grant.getReference() != null) {
 			referencePrefix = grant.getReference().split(":")[0];
 			shortReference = grant.getReference().substring(referencePrefix.length() + 1);
 			rda.setGrantId(GrantIdRDAMapper.toRDA(shortReference));
+		} else {
+			rda.setGrantId(GrantIdRDAMapper.toRDA(grant.getId().toString()));
+		}
 		return rda;
 	}
 

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

@@ -4,13 +4,19 @@ import eu.eudat.data.entities.Funder;
 import eu.eudat.data.entities.Grant;
 import eu.eudat.logic.services.ApiContext;
 import eu.eudat.models.rda.Project;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
+import javax.transaction.Transactional;
 import java.util.*;
 
 public class ProjectRDAMapper {
+	private final static Logger logger = LoggerFactory.getLogger(ProjectRDAMapper.class);
 
+	@Transactional
 	public static Project toRDA(eu.eudat.data.entities.Project project, Grant grant) {
 		Project rda = new Project();
+		try {
 			rda.setTitle(project.getLabel());
 			rda.setDescription(project.getDescription());
 			if (project.getStartdate() != null) {
@@ -24,6 +30,9 @@ public class ProjectRDAMapper {
 			if (rda.getTitle() == null) {
 				throw new IllegalArgumentException("Project Title is missing");
 			}
+		} catch (Exception e) {
+			logger.error(e.getLocalizedMessage(), e);
+		}
 
 		return rda;
 	}