fix bugs in rda json export when rda semantics don't correspond to valid dataset field input type

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

@@ -6,6 +6,7 @@ import java.util.stream.Collectors;
 import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.node.ArrayNode;
 import eu.eudat.logic.utilities.json.JavaToJson;
 import eu.eudat.models.rda.Cost;
 import eu.eudat.models.rda.PidSystem;
@@ -34,11 +35,14 @@ public class CostRDAMapper {
 			String rdaProperty = "";
 			JsonNode schematics = node.get("schematics");
 			if(schematics.isArray()){
+				int index = 0;
 				for(JsonNode schematic: schematics){
 					if(schematic.asText().startsWith("rda.dmp.cost")){
 						rdaProperty = schematic.asText();
+						((ArrayNode)schematics).remove(index);
 						break;
 					}
+					index++;
 				}
 			}
 			else{
@@ -64,12 +68,22 @@ public class CostRDAMapper {
 				rdaMap.put(key, rda);
 			}
 			if(rdaProperty.contains("value")){
-				rda.setValue(Double.valueOf(rdaValue));
+				try {
+					rda.setValue(Double.valueOf(rdaValue));
+				}
+				catch (NumberFormatException e) {
+					logger.warn("Dmp cost value " + rdaValue + " is not valid. Cost value will not be set.");
+				}
 			}
 			else if(rdaProperty.contains("currency_code")){
-				HashMap<String,String> result =
+				try {
-						new ObjectMapper().readValue(rdaValue, HashMap.class);
+					HashMap<String, String> result =
-				rda.setCurrencyCode(Cost.CurrencyCode.fromValue(result.get("value")));
+							new ObjectMapper().readValue(rdaValue, HashMap.class);
+					rda.setCurrencyCode(Cost.CurrencyCode.fromValue(result.get("value")));
+				}
+				catch (Exception e) {
+					logger.warn("Dmp cost currency code is not valid and will not be set.");
+				}
 			}
 			else if(rdaProperty.contains("title")){
 				Iterator<JsonNode> iter = node.get("value").elements();

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

@@ -2,6 +2,7 @@ package eu.eudat.models.rda.mapper;
 
 import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.node.ArrayNode;
 import eu.eudat.logic.utilities.json.JsonSearcher;
 import eu.eudat.models.rda.DatasetId;
 import org.slf4j.Logger;
@@ -30,11 +31,14 @@ public class DatasetIdRDAMapper {
 			String rdaProperty = "";
 			JsonNode schematics = node.get("schematics");
 			if(schematics.isArray()){
+				int index = 0;
 				for(JsonNode schematic: schematics){
 					if(schematic.asText().startsWith("rda.dataset.dataset_id")){
 						rdaProperty = schematic.asText();
+						((ArrayNode)schematics).remove(index);
 						break;
 					}
+					index++;
 				}
 			}
 			else{
@@ -76,7 +80,13 @@ public class DatasetIdRDAMapper {
 							rda.setIdentifier(value);
 							break;
 						case TYPE:
-							rda.setType(DatasetId.Type.fromValue(value));
+							try {
+								rda.setType(DatasetId.Type.fromValue(value));
+							}
+							catch (IllegalArgumentException e){
+								logger.warn("Type " + value + " from semantic rda.dataset.dataset_id.type was not found. Setting type to OTHER.");
+								rda.setType(DatasetId.Type.OTHER);
+							}
 							break;
 					}
 				}

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

@@ -3,6 +3,7 @@ package eu.eudat.models.rda.mapper;
 import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import eu.eudat.data.entities.DatasetProfile;
+import com.fasterxml.jackson.databind.node.ArrayNode;
 import eu.eudat.elastic.criteria.DatasetCriteria;
 import eu.eudat.elastic.entities.Tag;
 import eu.eudat.logic.managers.DatasetManager;
@@ -74,7 +75,14 @@ public class DatasetRDAMapper {
 			}
 			List<JsonNode> languageNodes = JsonSearcher.findNodes(datasetDescriptionObj, "schematics", "rda.dataset.language");
 			if (!languageNodes.isEmpty() && !languageNodes.get(0).get("value").asText().isEmpty()) {
-				rda.setLanguage(Language.fromValue(languageNodes.get(0).get("value").asText()));
+				String lang = languageNodes.get(0).get("value").asText();
+				try {
+					rda.setLanguage(Language.fromValue(lang));
+				}
+				catch (IllegalArgumentException e){
+					logger.warn("Language " + lang + " from semantic rda.dataset.language was not found. Setting '" + dataset.getProfile().getLanguage() +"' as language from the dataset profile.");
+					rda.setLanguage(LanguageRDAMapper.mapLanguageIsoToRDAIso(dataset.getProfile().getLanguage()));
+				}
 			} else {
 				rda.setLanguage(LanguageRDAMapper.mapLanguageIsoToRDAIso(dataset.getProfile().getLanguage()));
 			}
@@ -188,6 +196,7 @@ public class DatasetRDAMapper {
 						return Collections.singletonList(new Contributor());
 					}
 				}).flatMap(Collection::stream).collect(Collectors.toList()));
+				dmp.setContributor(dmp.getContributor().stream().filter(contributor -> contributor.getContributorId() != null && contributor.getName() != null).collect(Collectors.toList()));
 			}
 			List<JsonNode> costNodes = JsonSearcher.findNodes(datasetDescriptionObj, "schematics", "rda.dmp.cost");
 			if (!costNodes.isEmpty()) {
@@ -199,11 +208,14 @@ public class DatasetRDAMapper {
 					String rdaProperty = "";
 					JsonNode schematics = node.get("schematics");
 					if(schematics.isArray()){
+						int index = 0;
 						for(JsonNode schematic: schematics){
 							if(schematic.asText().startsWith("rda.dmp.ethical_issues")){
 								rdaProperty = schematic.asText();
+								((ArrayNode)schematics).remove(index);
 								break;
 							}
+							index++;
 						}
 					}
 					else{

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

@@ -4,6 +4,7 @@ import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.JsonMappingException;
 import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.node.ArrayNode;
 import eu.eudat.logic.utilities.helpers.MyStringUtils;
 import eu.eudat.logic.utilities.json.JavaToJson;
 import eu.eudat.logic.utilities.json.JsonSearcher;
@@ -74,8 +75,13 @@ public class DistributionRDAMapper {
 							}
 							break;
 						case DATA_ACCESS:
-							rda.setDataAccess(Distribution.DataAccess.fromValue(rdaValue));
+							try {
-							rda.setAdditionalProperty(ImportPropertyName.DATA_ACCESS.getName(), node.get("id").asText());
+								rda.setDataAccess(Distribution.DataAccess.fromValue(rdaValue));
+								rda.setAdditionalProperty(ImportPropertyName.DATA_ACCESS.getName(), node.get("id").asText());
+							}
+							catch (IllegalArgumentException e) {
+								logger.warn("Distribution data access " + rdaValue + " from semantic distribution.data_access is not valid. Data access will not be set set.");
+							}
 							break;
 						case BYTE_SIZE:
 							rda.setByteSize(Integer.parseInt(rdaValue));
@@ -376,11 +382,14 @@ public class DistributionRDAMapper {
 		String rdaProperty = "";
 		JsonNode schematics = node.get("schematics");
 		if(schematics.isArray()){
+			int index = 0;
 			for(JsonNode schematic: schematics){
 				if(schematic.asText().startsWith("rda.dataset.distribution")){
 					rdaProperty = schematic.asText();
+					((ArrayNode)schematics).remove(index);
 					break;
 				}
+				index++;
 			}
 		}
 		return rdaProperty;

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

@@ -3,7 +3,6 @@ package eu.eudat.models.rda.mapper;
 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;

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

@@ -3,6 +3,7 @@ package eu.eudat.models.rda.mapper;
 import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.node.ArrayNode;
 import eu.eudat.logic.utilities.helpers.MyStringUtils;
 import eu.eudat.models.rda.Host;
 import eu.eudat.models.rda.PidSystem;
@@ -22,11 +23,14 @@ public class HostRDAMapper {
 			String rdaProperty = "";
 			JsonNode schematics = node.get("schematics");
 			if(schematics.isArray()){
+				int index = 0;
 				for(JsonNode schematic: schematics){
 					if(schematic.asText().startsWith("rda.dataset.distribution.host")){
 						rdaProperty = schematic.asText();
+						((ArrayNode)schematics).remove(index);
 						break;
 					}
+					index++;
 				}
 			}
 			else{
@@ -55,8 +59,13 @@ public class HostRDAMapper {
 									rda.setAdditionalProperty(ImportPropertyName.BACKUP_TYPE.getName(), node.get("id").asText());
 									break;
 								case CERTIFIED_WITH:
-									rda.setCertifiedWith(Host.CertifiedWith.fromValue(rdaValue));
+									try {
-									rda.setAdditionalProperty(ImportPropertyName.CERTIFIED_WITH.getName(), node.get("id").asText());
+										rda.setCertifiedWith(Host.CertifiedWith.fromValue(rdaValue));
+										rda.setAdditionalProperty(ImportPropertyName.CERTIFIED_WITH.getName(), node.get("id").asText());
+									}
+									catch (IllegalArgumentException e) {
+										logger.warn("Distribution host certified with " + rdaValue + "from semantic distribution.host.certified_with is not valid. Certified_with will not be set set.");
+									}
 									break;
 								case DESCRIPTION:
 									rda.setDescription(rdaValue);
@@ -70,8 +79,13 @@ public class HostRDAMapper {
 											logger.warn(e.getLocalizedMessage() + ". Try to pass value as is");
 										}
 									}
-									rda.setGeoLocation(Host.GeoLocation.fromValue(rdaValue));
+									try {
-									rda.setAdditionalProperty(ImportPropertyName.GEO_LOCATION.getName(), node.get("id").asText());
+										rda.setGeoLocation(Host.GeoLocation.fromValue(rdaValue));
+										rda.setAdditionalProperty(ImportPropertyName.GEO_LOCATION.getName(), node.get("id").asText());
+									}
+									catch (IllegalArgumentException e) {
+										logger.warn("Distribution host geo location " + rdaValue + "from semantic distribution.host.geo_location is not valid. Geo location will not be set set.");
+									}
 									break;
 								case PID_SYSTEM:
 									try{
@@ -101,8 +115,13 @@ public class HostRDAMapper {
 									rda.setAdditionalProperty(ImportPropertyName.STORAGE_TYPE.getName(), node.get("id").asText());
 									break;
 								case SUPPORT_VERSIONING:
-									rda.setSupportVersioning(Host.SupportVersioning.fromValue(rdaValue));
+									try {
-									rda.setAdditionalProperty(ImportPropertyName.SUPPORT_VERSIONING.getName(), node.get("id").asText());
+										rda.setSupportVersioning(Host.SupportVersioning.fromValue(rdaValue));
+										rda.setAdditionalProperty(ImportPropertyName.SUPPORT_VERSIONING.getName(), node.get("id").asText());
+									}
+									catch (IllegalArgumentException e) {
+										logger.warn("Distribution host support versioning " + rdaValue + "from semantic distribution.host.support_versioning is not valid. Support versioning will not be set set.");
+									}
 									break;
 								case TITLE:
 									rda.setTitle(rdaValue);

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

@@ -1,6 +1,7 @@
 package eu.eudat.models.rda.mapper;
 
 import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.node.ArrayNode;
 import eu.eudat.logic.utilities.json.JsonSearcher;
 import eu.eudat.models.rda.License;
 import org.slf4j.Logger;
@@ -20,11 +21,14 @@ public class LicenseRDAMapper {
 			String rdaProperty = "";
 			JsonNode schematics = node.get("schematics");
 			if(schematics.isArray()){
+				int index = 0;
 				for(JsonNode schematic: schematics){
 					if(schematic.asText().startsWith("rda.dataset.distribution.license")){
 						rdaProperty = schematic.asText();
+						((ArrayNode)schematics).remove(index);
 						break;
 					}
+					index++;
 				}
 			}
 			else{

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

@@ -23,11 +23,14 @@ public class MetadataRDAMapper {
 			String rdaProperty = "";
 			JsonNode schematics = node.get("schematics");
 			if(schematics.isArray()){
+				int index = 0;
 				for(JsonNode schematic: schematics){
 					if(schematic.asText().startsWith("rda.dataset.metadata")){
 						rdaProperty = schematic.asText();
+						((ArrayNode)schematics).remove(index);
 						break;
 					}
+					index++;
 				}
 			}
 			else{

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

@@ -1,6 +1,7 @@
 package eu.eudat.models.rda.mapper;
 
 import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.node.ArrayNode;
 import eu.eudat.logic.utilities.helpers.MyStringUtils;
 import eu.eudat.models.rda.SecurityAndPrivacy;
 import org.slf4j.Logger;
@@ -19,11 +20,14 @@ public class SecurityAndPrivacyRDAMapper {
 			String rdaProperty = "";
 			JsonNode schematics = node.get("schematics");
 			if(schematics.isArray()){
+				int index = 0;
 				for(JsonNode schematic: schematics){
 					if(schematic.asText().startsWith("rda.dataset.security_and_privacy")){
 						rdaProperty = schematic.asText();
+						((ArrayNode)schematics).remove(index);
 						break;
 					}
+					index++;
 				}
 			}
 			else{

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

@@ -1,6 +1,7 @@
 package eu.eudat.models.rda.mapper;
 
 import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.node.ArrayNode;
 import eu.eudat.logic.utilities.helpers.MyStringUtils;
 import eu.eudat.models.rda.TechnicalResource;
 import org.slf4j.Logger;
@@ -19,11 +20,14 @@ public class TechnicalResourceRDAMapper {
 			String rdaProperty = "";
 			JsonNode schematics = node.get("schematics");
 			if(schematics.isArray()){
+				int index = 0;
 				for(JsonNode schematic: schematics){
 					if(schematic.asText().startsWith("rda.dataset.technical_resource")){
 						rdaProperty = schematic.asText();
+						((ArrayNode)schematics).remove(index);
 						break;
 					}
+					index++;
 				}
 			}
 			else{