Properly formatted the enumerations on the CommonDataElements.

src/main/java/eu/hbp/mip/controllers/PathologiesAPI.java

@@ -15,8 +15,6 @@ import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RequestMethod;
 import org.springframework.web.bind.annotation.RestController;
 
-import java.io.IOException;
-import java.net.ConnectException;
 import java.util.*;
 
 import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@@ -49,17 +47,14 @@ public class PathologiesAPI {
         Logger logger = new Logger(activeUserService.getActiveUser().getUsername(), "(GET) /pathologies");
         logger.LogUserAction("Loading pathologies ...");
 
-        Map<String, List<PathologyDTO.PathologyDatasetDTO>> datasetsPerPathology = getMIPEngineDatasetsPerPathology(logger);
-        System.out.println(datasetsPerPathology);
+        Map<String, List<PathologyDTO.EnumerationDTO>> datasetsPerPathology = getMIPEngineDatasetsPerPathology(logger);
 
         Map<String, MIPEngineAttributesDTO> mipEnginePathologyAttributes = getMIPEnginePathologyAttributes(logger);
-        System.out.println(mipEnginePathologyAttributes);
 
         List<PathologyDTO> pathologyDTOS = new ArrayList<>();
         for (String pathology : mipEnginePathologyAttributes.keySet()) {
             pathologyDTOS.add(new PathologyDTO(pathology, mipEnginePathologyAttributes.get(pathology), datasetsPerPathology.get(pathology)));
         }
-        System.out.println(pathologyDTOS);
 
         // If authentication is disabled return everything
         if (!authenticationIsEnabled) {
@@ -71,7 +66,7 @@ public class PathologiesAPI {
         return ResponseEntity.ok().body(gson.toJson(ClaimUtils.getAuthorizedPathologies(logger, authentication, pathologyDTOS)));
     }
 
-    public Map<String, List<PathologyDTO.PathologyDatasetDTO>> getMIPEngineDatasetsPerPathology(Logger logger) {
+    public Map<String, List<PathologyDTO.EnumerationDTO>> getMIPEngineDatasetsPerPathology(Logger logger) {
         Map<String, Map<String, MetadataHierarchyDTO.CommonDataElement>> mipEngineCDEsMetadata;
         // Get MIPEngine algorithms
         try {
@@ -87,15 +82,17 @@ public class PathologiesAPI {
             return null;
         }
 
-        Map<String, List<PathologyDTO.PathologyDatasetDTO>> datasetsPerPathology = new HashMap<>();
+        Map<String, List<PathologyDTO.EnumerationDTO>> datasetsPerPathology = new HashMap<>();
 
         mipEngineCDEsMetadata.forEach( (pathology, cdePerDataset) ->  {
-            List<PathologyDTO.PathologyDatasetDTO> pathologyDatasetDTOS = new ArrayList<>();
-            cdePerDataset.forEach((dataset, cde) ->  pathologyDatasetDTOS.add(new PathologyDTO.PathologyDatasetDTO(dataset, cde.getLabel())));
+            List<PathologyDTO.EnumerationDTO> pathologyDatasetDTOS = new ArrayList<>();
+            Map datasetEnumerations = (Map) cdePerDataset.get("dataset").getEnumerations();
+            datasetEnumerations.forEach((code, label) ->  pathologyDatasetDTOS.add(new PathologyDTO.EnumerationDTO((String) code, (String) label)));
             datasetsPerPathology.put(pathology, pathologyDatasetDTOS);
         });
 
 
+
         return datasetsPerPathology;
     }
 
@@ -115,6 +112,14 @@ public class PathologiesAPI {
             return null;
         }
 
-        return mipEnginePathologyAttributes;
+        Map<String, MIPEngineAttributesDTO> mipEnginePathologyAttributesWithProperEnums = new HashMap<>();
+        for (Map.Entry<String, MIPEngineAttributesDTO> entry : mipEnginePathologyAttributes.entrySet()) {
+            String pathology = entry.getKey();
+            MIPEngineAttributesDTO attributes = entry.getValue();
+            attributes.updateAttributesWithProperEnums();
+            mipEnginePathologyAttributesWithProperEnums.put(pathology, attributes);
+        }
+
+        return mipEnginePathologyAttributesWithProperEnums;
     }
 }

src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAttributesDTO.java

 package eu.hbp.mip.models.DTOs;
 
 import com.google.gson.annotations.SerializedName;
-import eu.hbp.mip.models.DTOs.MetadataHierarchyDTO;
 import lombok.AllArgsConstructor;
 import lombok.Data;
 
+import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
@@ -17,4 +18,19 @@ public class MIPEngineAttributesDTO {
     @SerializedName("tags")
     private Object tags;
 
+    public void updateAttributesWithProperEnums(){
+        Map<String, List<MetadataHierarchyDTO>> updated_properties = new HashMap<>();
+        for (Map.Entry<String, List<MetadataHierarchyDTO>> entry : this.properties.entrySet()) {
+            String pathology = entry.getKey();
+            List<MetadataHierarchyDTO> hierarchyDTOS = entry.getValue();
+            List<MetadataHierarchyDTO> updatedHierarchyDTOS = new ArrayList<>();
+
+            for (MetadataHierarchyDTO hierarchyDTO : hierarchyDTOS) {
+                hierarchyDTO.updateGroupWithProperEnums();
+                updatedHierarchyDTOS.add(hierarchyDTO);
+            }
+            updated_properties.put(pathology,updatedHierarchyDTOS);
+        }
+        this.properties = updated_properties;
+    }
 }

src/main/java/eu/hbp/mip/models/DTOs/MetadataHierarchyDTO.java

@@ -4,9 +4,9 @@ import com.google.gson.annotations.SerializedName;
 import lombok.AllArgsConstructor;
 import lombok.Data;
 
-import java.util.Hashtable;
+import java.util.ArrayList;
 import java.util.List;
-import java.util.Optional;
+import java.util.Map;
 
 @Data
 @AllArgsConstructor
@@ -19,15 +19,15 @@ public class MetadataHierarchyDTO {
     private String code;
 
     @SerializedName("groups")
-    private Object groups;
+    private List<MetadataHierarchyDTO> groups;
 
     @SerializedName("label")
     private String label;
     @Data
     @AllArgsConstructor
     public static class CommonDataElement {
-        @SerializedName("isCategorical")
-        private Boolean isCategorical;
+        @SerializedName("is_categorical")
+        private Boolean is_categorical;
 
         @SerializedName("code")
         private String code;
@@ -53,5 +53,46 @@ public class MetadataHierarchyDTO {
         @SerializedName("methodology")
         private String methodology;
 
+        @SerializedName("min")
+        private String min;
+
+        @SerializedName("max")
+        private String max;
+
+        private void updateEnumerations(){
+            if (this.enumerations != null){
+                Map old_enumeration = (Map) this.enumerations;
+                List<PathologyDTO.EnumerationDTO> enumerationDTOS = new ArrayList<>();
+                old_enumeration.forEach((cdeCode, cdeLabel) -> {
+                    enumerationDTOS.add(new PathologyDTO.EnumerationDTO((String) cdeCode, (String) cdeLabel));
+                });
+                setEnumerations(enumerationDTOS);
+            }
+        }
+    }
+
+    public void updateVariableWithProperEnums(){
+        List<CommonDataElement> updated_variables = new ArrayList<>();
+        this.variables.forEach(commonDataElement -> {
+            commonDataElement.updateEnumerations();
+            updated_variables.add(commonDataElement);
+        });
+        setVariables(updated_variables);
+    }
+
+    public void updateGroupWithProperEnums(){
+        List<MetadataHierarchyDTO> updated_groups = new ArrayList<>();
+        for (MetadataHierarchyDTO hierarchyDTO : this.groups) {
+
+            if (hierarchyDTO.getVariables() != null) {
+                hierarchyDTO.updateVariableWithProperEnums();
+            }
+
+            if (hierarchyDTO.getGroups() != null) {
+                hierarchyDTO.updateGroupWithProperEnums();
+            }
+            updated_groups.add(hierarchyDTO);
+        }
+        this.groups = updated_groups;
     }
 }

src/main/java/eu/hbp/mip/models/DTOs/PathologyDTO.java

@@ -6,7 +6,6 @@ import lombok.Data;
 
 import java.util.Arrays;
 import java.util.List;
-import java.util.Optional;
 
 @Data
 @AllArgsConstructor
@@ -26,14 +25,14 @@ public class PathologyDTO {
     private MetadataHierarchyDTO metadataHierarchyDTO;
 
     @SerializedName("datasets")
-    private List<PathologyDatasetDTO> datasets;
+    private List<EnumerationDTO> datasets;
 
     public PathologyDTO(){
 
     }
 
 
-    public PathologyDTO(String pathology, MIPEngineAttributesDTO mipEngineAttributesDTO, List<PathologyDatasetDTO> pathologyDatasetDTOS) {
+    public PathologyDTO(String pathology, MIPEngineAttributesDTO mipEngineAttributesDTO, List<EnumerationDTO> pathologyDatasetDTOS) {
         MetadataHierarchyDTO metadataHierarchyDTO = mipEngineAttributesDTO.getProperties().get("cdes").get(0);
         List<MetadataHierarchyDTO.CommonDataElement> variables = metadataHierarchyDTO.getVariables();
         variables.stream().filter(cde -> cde.getCode().equals("dataset")).
@@ -50,7 +49,7 @@ public class PathologyDTO {
 
     @Data
     @AllArgsConstructor
-    public static class PathologyDatasetDTO {
+    public static class EnumerationDTO {
         @SerializedName("code")
         private String code;
 

src/main/java/eu/hbp/mip/utils/ClaimUtils.java

@@ -68,8 +68,8 @@ public class ClaimUtils {
 
         List<PathologyDTO> userPathologies = new ArrayList<>();
         for (PathologyDTO curPathology : allPathologies) {
-            List<PathologyDTO.PathologyDatasetDTO> userPathologyDatasets = new ArrayList<>();
-            for (PathologyDTO.PathologyDatasetDTO dataset : curPathology.getDatasets()) {
+            List<PathologyDTO.EnumerationDTO> userPathologyDatasets = new ArrayList<>();
+            for (PathologyDTO.EnumerationDTO dataset : curPathology.getDatasets()) {
                 if (hasRoleAccess(authorities, ClaimUtils.getDatasetClaim(dataset.getCode()), logger)) {
                     logger.LogUserAction("Added dataset: " + dataset.getCode());
                     userPathologyDatasets.add(dataset);