changes in dmp deposit model

dmp-backend/web/src/main/java/eu/eudat/logic/security/repositorydeposit/mapper/DMPToDepositMapper.java

@@ -1,29 +1,45 @@
 package eu.eudat.logic.security.repositorydeposit.mapper;
 
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.JsonMappingException;
+import com.fasterxml.jackson.databind.ObjectMapper;
 import eu.eudat.data.entities.*;
 import eu.eudat.depositinterface.models.*;
-import org.springframework.http.ResponseEntity;
+import eu.eudat.logic.utilities.builders.XmlBuilder;
+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.io.File;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
 import java.util.stream.Collectors;
 
 public class DMPToDepositMapper {
 
-    public static DMPDepositModel fromDMP(DMP entity, File pdfFile, String fileName, ResponseEntity<byte[]> jsonFile, File supportingFilesZip, String previousDOI) {
+    private static final Logger logger = LoggerFactory.getLogger(DMPToDepositMapper.class);
+    private static final ObjectMapper mapper = new ObjectMapper();
+
+    public static DMPDepositModel fromDMP(DMP entity, FileEnvelope pdfFile, FileEnvelope jsonFile, File supportingFilesZip, String previousDOI) {
         DMPDepositModel deposit = new DMPDepositModel();
         deposit.setId(entity.getId());
         deposit.setVersion(entity.getVersion());
         deposit.setLabel(entity.getLabel());
         deposit.setDescription(entity.getDescription());
         deposit.setPublic(entity.isPublic());
+        deposit.setDatasets(entity.getDataset().stream().map(DMPToDepositMapper::fromDataset).collect(Collectors.toList()));
         deposit.setUsers(entity.getUsers().stream().map(DMPToDepositMapper::fromUserDMP).collect(Collectors.toSet()));
         deposit.setOrganisations(entity.getOrganisations().stream().map(DMPToDepositMapper::fromOrganisation).collect(Collectors.toSet()));
         deposit.setResearchers(entity.getResearchers().stream().map(DMPToDepositMapper::fromResearcher).collect(Collectors.toSet()));
         deposit.setGrant(fromGrant(entity.getGrant()));
 
         deposit.setPdfFile(pdfFile);
-        deposit.setPdfFileName(fileName);
+        deposit.setRdaJsonFile(jsonFile);
-        deposit.setRdaJson(jsonFile);
         deposit.setSupportingFilesZip(supportingFilesZip);
         deposit.setPreviousDOI(previousDOI);
 
@@ -31,6 +47,54 @@ public class DMPToDepositMapper {
         return deposit;
     }
 
+    private static DatasetDepositModel fromDataset(Dataset entity){
+        DatasetDepositModel deposit = new DatasetDepositModel();
+        deposit.setLabel(entity.getLabel());
+        deposit.setDescription(entity.getDescription());
+        deposit.setProfileDefinition(entity.getProfile().getDefinition());
+        deposit.setProperties(entity.getProperties());
+        deposit.setFields(fromDefinitionAndProperties(deposit.getProfileDefinition(), deposit.getProperties()));
+        return deposit;
+    }
+
+    private static List<DatasetFieldsDepositModel> fromDefinitionAndProperties(String definition, String properties){
+        List<DatasetFieldsDepositModel> deposit = new ArrayList<>();
+        try {
+
+            Map<String, Object> datasetAnswers = mapper.readValue(properties, HashMap.class);
+
+            Document document = XmlBuilder.fromXml(definition);
+            XPathFactory xpathFactory = XPathFactory.newInstance();
+            XPath xpath = xpathFactory.newXPath();
+            XPathExpression expr = xpath.compile("//schematics");
+            NodeList schematics = (NodeList) expr.evaluate(document, XPathConstants.NODESET);
+            for (int i = 0; i < schematics.getLength(); i++) {
+                Node schematicsNode = schematics.item(i);
+                NodeList schematicsList = schematicsNode.getChildNodes();
+                DatasetFieldsDepositModel fieldDeposit = new DatasetFieldsDepositModel();
+                List<String> schematicsDeposit = new ArrayList<>();
+                if(schematicsList != null){
+                    for(int j = 0; j < schematicsList.getLength(); j++){
+                        Node schematic = schematicsList.item(j);
+                        if(schematic.getTextContent().matches(".*\\w+.*")) {
+                            schematicsDeposit.add(schematic.getTextContent());
+                        }
+                    }
+                }
+                fieldDeposit.setSchematics(schematicsDeposit);
+                String fieldId = schematicsNode.getParentNode().getAttributes().getNamedItem("id").getNodeValue();
+                String value = (String) datasetAnswers.get(fieldId);
+                fieldDeposit.setValue(value);
+                deposit.add(fieldDeposit);
+            }
+        }
+        catch (XPathExpressionException | JsonProcessingException ex){
+            logger.error(ex.getMessage(), ex);
+            return null;
+        }
+        return deposit;
+    }
+
     private static UserDMPDepositModel fromUserDMP(UserDMP entity){
         UserDMPDepositModel deposit = new UserDMPDepositModel();
         deposit.setUser(fromUserInfo(entity.getUser()));