User specific pathologies.json based on roles.

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

@@ -110,8 +110,8 @@ public class ExperimentApi {
         UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Run algorithm", "Running the algorithm...");
 
         // --- Validating proper access rights on the datasets  ---
-        String allowedDatasets = authentication.getAuthorities().toString();
-        UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Authorities", allowedDatasets.toString());
+        String userRoles = authentication.getAuthorities().toString();
+        UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Authorities", userRoles);
 
         // Getting the dataset from the experiment parameters
         String experimentDatasets = null;
@@ -131,7 +131,7 @@ public class ExperimentApi {
 
         for (String dataset : experimentDatasets.split(",")) {
             String datasetRole = "role_" + dataset;
-            if (!allowedDatasets.toLowerCase().contains(datasetRole.toLowerCase())) {
+            if (!userRoles.toLowerCase().contains(datasetRole.toLowerCase())) {
                 UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Run algorithm",
                         "You are not allowed to use dataset: " + dataset);
                 return ResponseEntity.status(403).body("You are not allowed to use dataset: " + dataset);

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

@@ -4,13 +4,18 @@
 
 package eu.hbp.mip.controllers;
 
-import com.fasterxml.jackson.core.type.TypeReference;
+import com.google.gson.Gson;
+import com.google.gson.reflect.TypeToken;
+import eu.hbp.mip.model.PathologyDTO;
+import eu.hbp.mip.model.PathologyDTO.PathologyDatasetDTO;
 import eu.hbp.mip.model.UserInfo;
 import eu.hbp.mip.utils.CustomResourceLoader;
+import eu.hbp.mip.utils.UserActionLogging;
 import io.swagger.annotations.Api;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.core.io.Resource;
-import org.springframework.core.io.ResourceLoader;
+import org.springframework.http.ResponseEntity;
+import org.springframework.security.core.Authentication;
 import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RequestMethod;
 import org.springframework.web.bind.annotation.RestController;
@@ -19,7 +24,9 @@ import java.io.ByteArrayOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.nio.charset.StandardCharsets;
-import eu.hbp.mip.utils.UserActionLogging;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
 
 import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
 
@@ -28,28 +35,69 @@ import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
 @Api(value = "/pathologies")
 public class PathologiesApi {
 
+    private static final Gson gson = new Gson();
+
     @Autowired
     private UserInfo userInfo;
 
-    @RequestMapping(name = "/pathologies", method = RequestMethod.GET)
-    public String getPathologies() {
-		UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "load the pathologies", "");
-		
-        return loadPathologies();
-    }
-
     @Autowired
     private CustomResourceLoader resourceLoader;
-    private String loadPathologies() {
 
-        Resource resource  = resourceLoader.getResource("file:/opt/portal/api/pathologies.json");
-        String result;
+    @RequestMapping(name = "/pathologies", method = RequestMethod.GET)
+    public ResponseEntity<String> getPathologies(Authentication authentication) {
+        UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Load all the pathologies", "");
+
+        Resource resource = resourceLoader.getResource("file:/opt/portal/api/pathologies.json");
+        List<PathologyDTO> allPathologies;
         try {
-            result = convertInputStreamToString(resource.getInputStream());
+            allPathologies = gson.fromJson(convertInputStreamToString(resource.getInputStream()), new TypeToken<List<PathologyDTO>>() {
+            }.getType());
         } catch (IOException e) {
-            result = "{\"error\" : \"The pathologies.json file could not be read.\"}";
+            return ResponseEntity.badRequest().body("{\"error\" : \"The pathologies.json file could not be read.\"}");
         }
-        return result;
+
+        // --- Providing only the allowed pathologies/datasets to the user  ---
+        UserActionLogging.LogUserAction(userInfo.getUser().getUsername(),
+                "Load all the pathologies", "Filter out the unauthorised datasets.");
+
+        List<String> userRoles = Arrays.asList(authentication.getAuthorities().toString().toLowerCase()
+                .replaceAll("[\\s+\\]\\[]","").split(","));
+
+        UserActionLogging.LogUserAction(userInfo.getUser().getUsername(),
+                "Load all the pathologies", "Authorities : " + authentication.getAuthorities().toString());
+
+        UserActionLogging.LogUserAction(userInfo.getUser().getUsername(),
+                "Load all the pathologies", "Authorities: " + userRoles);
+
+        List<PathologyDTO> userPathologies = new ArrayList<>();
+        for (PathologyDTO curPathology : allPathologies) {
+            UserActionLogging.LogUserAction(userInfo.getUser().getUsername(),
+                    "Load all the pathologies", "Pathology: " + curPathology);
+
+            List<PathologyDatasetDTO> userPathologyDatasets = new ArrayList<PathologyDatasetDTO>();
+            for (PathologyDatasetDTO dataset : curPathology.getDatasets()) {
+                if(userRoles.contains("role_" + dataset.getCode())){
+                    userPathologyDatasets.add(dataset);
+                }
+            }
+
+            UserActionLogging.LogUserAction(userInfo.getUser().getUsername(),
+                    "Load all the pathologies", "User Pathologies size: " + userPathologyDatasets.size());
+
+            if(userPathologyDatasets.size() > 0){
+                UserActionLogging.LogUserAction(userInfo.getUser().getUsername(),
+                        "Load all the pathologies", "Added the pathology");
+
+                PathologyDTO userPathology = new PathologyDTO();
+                userPathology.setCode(curPathology.getCode());
+                userPathology.setLabel(curPathology.getLabel());
+                userPathology.setMetadataHierarchy(curPathology.getMetadataHierarchy());
+                userPathology.setDatasets(userPathologyDatasets);
+                userPathologies.add(userPathology);
+            }
+        }
+
+        return ResponseEntity.ok().body(gson.toJson(userPathologies));
     }
 
     // Pure Java

src/main/java/eu/hbp/mip/model/PathologyDTO.java

+package eu.hbp.mip.model;
+
+import com.google.gson.annotations.SerializedName;
+
+import java.util.List;
+
+public class PathologyDTO {
+
+    public String getCode() {
+        return code;
+    }
+
+    public void setCode(String code) {
+        this.code = code;
+    }
+
+    public String getLabel() {
+        return label;
+    }
+
+    public void setLabel(String label) {
+        this.label = label;
+    }
+
+    public Object getMetadataHierarchy() {
+        return metadataHierarchy;
+    }
+
+    public void setMetadataHierarchy(Object metadataHierarchy) {
+        this.metadataHierarchy = metadataHierarchy;
+    }
+
+    public List<PathologyDatasetDTO> getDatasets() {
+        return datasets;
+    }
+
+    public void setDatasets(List<PathologyDatasetDTO> datasets) {
+        this.datasets = datasets;
+    }
+
+    @SerializedName("code")
+    private String code;
+
+    @SerializedName("label")
+    private String label;
+
+    @SerializedName("metadataHierarchy")
+    private Object metadataHierarchy;
+
+    @SerializedName("datasets")
+    private List<PathologyDatasetDTO> datasets;
+
+    public static class PathologyDatasetDTO {
+        @SerializedName("code")
+        private String code;
+
+        @SerializedName("label")
+        private String label;
+
+        public String getCode() {
+            return code;
+        }
+
+        public void setCode(String code) {
+            this.code = code;
+        }
+
+        public String getLabel() {
+            return label;
+        }
+
+        public void setLabel(String label) {
+            this.label = label;
+        }
+    }
+
+}