overlayId is numeric

rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayController.java

@@ -53,7 +53,7 @@ public class OverlayController extends BaseController {
   @GetMapping(value = "/{overlayId}/")
   public Map<String, Object> getOverlayById(
       @PathVariable(value = "projectId") String projectId,
-      @PathVariable(value = "overlayId") String overlayId) throws QueryException {
+      @PathVariable(value = "overlayId") Integer overlayId) throws QueryException {
     return overlayRestImp.getOverlayById(projectId, overlayId);
   }
 
@@ -64,7 +64,7 @@ public class OverlayController extends BaseController {
   @GetMapping(value = "/{overlayId}/models/{modelId}/bioEntities/")
   public List<Map<String, Object>> getOverlayElements(
       @PathVariable(value = "projectId") String projectId,
-      @PathVariable(value = "overlayId") String overlayId,
+      @PathVariable(value = "overlayId") Integer overlayId,
       @RequestParam(value = "columns", defaultValue = "") String columns) throws QueryException {
     return overlayRestImp.getOverlayElements(projectId, Integer.valueOf(overlayId), columns);
   }
@@ -77,7 +77,7 @@ public class OverlayController extends BaseController {
   public Map<String, Object> getFullReaction(
       @PathVariable(value = "projectId") String projectId,
       @PathVariable(value = "modelId") String modelId,
-      @PathVariable(value = "overlayId") String overlayId,
+      @PathVariable(value = "overlayId") Integer overlayId,
       @PathVariable(value = "reactionId") String reactionId,
       @RequestParam(value = "columns", defaultValue = "") String columns)
       throws QueryException, NumberFormatException, ObjectNotFoundException {
@@ -93,7 +93,7 @@ public class OverlayController extends BaseController {
   public Map<String, Object> getFullSpecies(
       @PathVariable(value = "projectId") String projectId,
       @PathVariable(value = "modelId") String modelId,
-      @PathVariable(value = "overlayId") String overlayId,
+      @PathVariable(value = "overlayId") Integer overlayId,
       @PathVariable(value = "elementId") String reactionId,
       @RequestParam(value = "columns", defaultValue = "") String columns)
       throws QueryException, NumberFormatException, ObjectNotFoundException {
@@ -126,7 +126,7 @@ public class OverlayController extends BaseController {
   @DeleteMapping(value = "/{overlayId}")
   public Map<String, Object> removeOverlay(
       @PathVariable(value = "projectId") String projectId,
-      @PathVariable(value = "overlayId") String overlayId) throws QueryException, IOException {
+      @PathVariable(value = "overlayId") Integer overlayId) throws QueryException, IOException {
     return overlayRestImp.removeOverlay(projectId, overlayId);
   }
 
@@ -136,7 +136,7 @@ public class OverlayController extends BaseController {
   @PatchMapping(value = "/{overlayId}")
   public Map<String, Object> updateOverlay(
       @RequestBody String body,
-      @PathVariable(value = "overlayId") String overlayId,
+      @PathVariable(value = "overlayId") Integer overlayId,
       @PathVariable(value = "projectId") String projectId)
       throws QueryException, IOException {
     Map<String, Object> node = parseBody(body);
@@ -151,7 +151,7 @@ public class OverlayController extends BaseController {
   @GetMapping(value = "/{overlayId}:downloadSource")
   public ResponseEntity<byte[]> getOverlaySource(
       @PathVariable(value = "projectId") String projectId,
-      @PathVariable(value = "overlayId") String overlayId)
+      @PathVariable(value = "overlayId") Integer overlayId)
       throws QueryException {
 
     FileEntry file = overlayRestImp.getOverlaySource(projectId, overlayId);

rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java

@@ -147,28 +147,27 @@ public class OverlayRestImpl extends BaseRestImpl {
     return result;
   }
 
-  public Map<String, Object> getOverlayById(String projectId, String overlayId)
+  public Map<String, Object> getOverlayById(String projectId, Integer overlayId)
       throws QueryException {
     Model model = getModelService().getLastModelByProjectId(projectId);
     if (model == null) {
       throw new QueryException("Project with given id doesn't exist");
     }
-    Layout overlay = layoutService.getLayoutById(Integer.valueOf(overlayId));
+    Layout overlay = layoutService.getLayoutById(overlayId);
     if (overlay == null) {
       throw new QueryException("Overlay with given id doesn't exist");
     }
     return overlayToMap(overlay);
   }
 
-  public FileEntry getOverlaySource(String projectId, String overlayId)
+  public FileEntry getOverlaySource(String projectId, Integer overlayId)
       throws QueryException {
     Model model = getModelService().getLastModelByProjectId(projectId);
     if (model == null) {
       throw new QueryException("Project with given id doesn't exist");
     }
     try {
-      int id = Integer.parseInt(overlayId);
-      Layout layout = layoutService.getLayoutById(id);
+      Layout layout = layoutService.getLayoutById(overlayId);
       if (layout == null) {
         throw new QueryException("Invalid overlay id");
       }
@@ -180,13 +179,12 @@ public class OverlayRestImpl extends BaseRestImpl {
     }
   }
 
-  public Map<String, Object> updateOverlay(String overlayId, Map<String, Object> overlayData) throws QueryException {
+  public Map<String, Object> updateOverlay(Integer overlayId, Map<String, Object> overlayData) throws QueryException {
     if (overlayData == null) {
       throw new QueryException("overlay field cannot be undefined");
     }
     try {
-      int id = Integer.parseInt(overlayId);
-      Layout layout = layoutService.getLayoutById(id);
+      Layout layout = layoutService.getLayoutById(overlayId);
       if (layout == null) {
         throw new ObjectNotFoundException("overlay doesn't exist");
       }
@@ -232,15 +230,14 @@ public class OverlayRestImpl extends BaseRestImpl {
     }
   }
 
-  public Map<String, Object> removeOverlay(String projectId, String overlayId)
+  public Map<String, Object> removeOverlay(String projectId, Integer overlayId)
       throws QueryException, IOException {
     Project project = getProjectService().getProjectByProjectId(projectId);
     if (project == null) {
       throw new ObjectNotFoundException("Project with given id doesn't exist");
     }
     try {
-      int id = Integer.parseInt(overlayId);
-      Layout layout = layoutService.getLayoutById(id);
+      Layout layout = layoutService.getLayoutById(overlayId);
       if (layout == null) {
         throw new ObjectNotFoundException("Overlay doesn't exist");
       }
@@ -321,7 +318,7 @@ public class OverlayRestImpl extends BaseRestImpl {
       layout.setOrderIndex(count);
       layoutService.updateLayout(layout);
 
-      return getOverlayById(projectId, layout.getId() + "");
+      return getOverlayById(projectId, layout.getId());
     } catch (InvalidColorSchemaException e) {
       throw new QueryException(e.getMessage(), e);
     }

rest-api/src/test/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImplTest.java

@@ -66,7 +66,7 @@ public class OverlayRestImplTest extends RestTestFunctions {
       Map<String, Object> result = overlayRest.addOverlay(projectId, "x", "desc", "s1", null, null,
           ColorSchemaType.GENERIC.name(), "true", null);
 
-      String id = result.get("idObject").toString();
+      Integer id = Integer.valueOf(result.get("idObject").toString());
       Map<String, Object> data = new HashMap<>();
       data.put("name", "xyz");
       result = overlayRest.updateOverlay(id, data);
@@ -84,7 +84,7 @@ public class OverlayRestImplTest extends RestTestFunctions {
       Map<String, Object> result = overlayRest.addOverlay(projectId, "x", "desc", "s1", null, null,
           ColorSchemaType.GENERIC.name(), "true", null);
 
-      String id = result.get("idObject").toString();
+      Integer id = Integer.valueOf(result.get("idObject").toString());
       Map<String, Object> data = new HashMap<>();
       data.put("name", "");
       result = overlayRest.updateOverlay(id, data);

service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java

@@ -469,7 +469,7 @@ public class LayoutService implements ILayoutService {
   }
 
   @Override
-  public Layout getLayoutById(int overlayId) {
+  public Layout getLayoutById(Integer overlayId) {
     return layoutDao.getById(overlayId);
   }
 

service/src/main/java/lcsb/mapviewer/services/interfaces/ILayoutService.java

@@ -142,7 +142,7 @@ public interface ILayoutService {
    */
   List<Layout> getLayoutsByProject(Project project);
 
-  Layout getLayoutById(int overlayId);
+  Layout getLayoutById(Integer overlayId);
 
   void setLayoutDao(LayoutDao layoutDao);