Resolve "data overlays should provide entries for submaps in anchors"

Closes #1962 (closed)

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

@@ -45,6 +45,7 @@ import lcsb.mapviewer.model.cache.UploadedFileEntry;
 import lcsb.mapviewer.model.map.BioEntity;
 import lcsb.mapviewer.model.map.MiriamData;
 import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
+import lcsb.mapviewer.model.map.model.ElementSubmodelConnection;
 import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.model.ModelData;
 import lcsb.mapviewer.model.map.reaction.Reaction;
@@ -58,9 +59,11 @@ import lcsb.mapviewer.model.overlay.GenericDataOverlayEntry;
 import lcsb.mapviewer.model.overlay.InvalidDataOverlayException;
 import lcsb.mapviewer.model.user.User;
 import lcsb.mapviewer.persist.dao.map.DataOverlayDao;
+import lcsb.mapviewer.persist.dao.map.species.ElementProperty;
 import lcsb.mapviewer.services.ObjectNotFoundException;
 import lcsb.mapviewer.services.QueryException;
 import lcsb.mapviewer.services.interfaces.IDataOverlayService;
+import lcsb.mapviewer.services.interfaces.IElementService;
 import lcsb.mapviewer.services.interfaces.IModelService;
 import lcsb.mapviewer.services.interfaces.IUserService;
 import lcsb.mapviewer.services.utils.EmailSender;
@@ -83,6 +86,9 @@ public class DataOverlayService implements IDataOverlayService {
   @Autowired
   private IModelService modelService;
 
+  @Autowired
+  private IElementService elementService;
+
   private ExecutorService jobQueue;
 
   public DataOverlayService() {
@@ -475,7 +481,7 @@ public class DataOverlayService implements IDataOverlayService {
 
   @Override
   public List<Pair<? extends BioEntity, DataOverlayEntry>> getBioEntitiesForDataOverlay(final String projectId, final int mapId,
-      final Integer overlayId, final boolean fetchLazy) throws QueryException {
+      final Integer overlayId, final boolean fetchLazy, final boolean includeIndirect) throws QueryException {
     ModelData map = modelService.getModelByMapId(projectId, mapId);
     getOverlayByIdNotNull(projectId, overlayId);
 
@@ -491,9 +497,34 @@ public class DataOverlayService implements IDataOverlayService {
       }
       result.stream().forEach(initializeLazy());
     }
+    if (includeIndirect) {
+      Map<ElementProperty, List<? extends Object>> properties = new HashMap<>();
+      properties.put(ElementProperty.MAP, Arrays.asList(map));
+      properties.put(ElementProperty.SUBMAP_CONNECTION, Arrays.asList(Boolean.TRUE));
+
+      List<Element> elements = elementService.getElementsByFilter(properties, true);
+
+      for (Element element : elements) {
+        ElementSubmodelConnection connection = element.getSubmodel();
+        List<Pair<? extends BioEntity, DataOverlayEntry>> listForSubmap = new ArrayList<>();
+        listForSubmap.addAll(dataOverlayDao.getElementsForModels(overlayId, Arrays.asList(connection.getSubmodel())));
+        listForSubmap.addAll(dataOverlayDao.getReactionsForModels(overlayId, Arrays.asList(connection.getSubmodel())));
+
+        for (Pair<? extends BioEntity, DataOverlayEntry> pair : listForSubmap) {
+          result.add(new Pair<BioEntity, DataOverlayEntry>(element, pair.getRight()));
+        }
+      }
+      result.stream().forEach(initializeLazy());
+    }
     return result;
   }
 
+  @Override
+  public List<Pair<? extends BioEntity, DataOverlayEntry>> getBioEntitiesForDataOverlay(final String projectId, final int mapId,
+      final Integer overlayId, final boolean fetchLazy) throws QueryException {
+    return getBioEntitiesForDataOverlay(projectId, mapId, overlayId, fetchLazy, false);
+  }
+
   @Override
   public List<Pair<Element, DataOverlayEntry>> getFullElementForDataOverlay(final String projectId, final int mapId, final Integer id,
       final int overlayId, final boolean fetchLazy) throws QueryException {