new api call for get overlay detail data about element

frontend-js/src/main/js/ServerConnector.js

@@ -381,7 +381,13 @@ ServerConnector.getOverlayElementsUrl = function(queryParams, filterParams) {
 
 };
 
-ServerConnector.getFullOverlayElementUrl = function(params, token) {
+ServerConnector.getFullOverlayElementUrl = function(queryParams, filterParams) {
+
+  return this.getApiUrl({
+    url : this.getAliasesUrl(queryParams) + queryParams.id + "/",
+    params : filterParams,
+  });
+
   return this.getApiUrl({
     type : "overlay",
     method : "getOverlayElement",
@@ -426,11 +432,16 @@ ServerConnector.columnsToString = function(columns) {
   return columns;
 };
 
-ServerConnector.getModelsUrl = function(params) {
-  var modelId = this.getIdOrAsterisk(params.modelId);
+ServerConnector.getModelsUrl = function(queryParams) {
+  var modelId = this.getIdOrAsterisk(queryParams.modelId);
+  var overlayId = queryParams.overlayId;
+  var url = this.getProjectsUrl(queryParams);
+  if (overlayId !== undefined) {
+    url = this.getOverlayByIdUrl(queryParams);
+  }
 
   return this.getApiUrl({
-    url : this.getProjectsUrl(params) + "models/" + modelId + "/",
+    url : url + "models/" + modelId + "/",
   });
 };
 
@@ -846,12 +857,19 @@ ServerConnector.getFullOverlayElement = function(params) {
   var self = this;
   var token = null;
 
+  var queryParams = {
+    overlayId : params.overlay.getId(),
+    modelId : params.element.getModelId(),
+    id : params.element.getId(),
+  }
+  var filterParams = {};
+
   return self.getToken().then(function(result) {
-    token = result;
+    filterParams.token = result;
     return self.getProjectId(params.projectId);
   }).then(function(result) {
-    params.projectId = result;
-    return self.readFile(self.getFullOverlayElementUrl(params, token));
+    queryParams.projectId = result;
+    return self.readFile(self.getFullOverlayElementUrl(queryParams, filterParams));
   }).then(function(content) {
     var element = JSON.parse(content);
     var result = null;

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

@@ -44,17 +44,44 @@ public class OverlayController extends BaseController {
 		return overlayController.getOverlayById(token, projectId, overlayId);
 	}
 
-	@RequestMapping(value = "/projects/{projectId}/overlays/{overlayId}/bioEntities/", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
-	public List<Map<String, Object>> getOverlayElements(
-			@RequestParam(value = "token") String token, 
+	@RequestMapping(value = "/projects/{projectId}/overlays/{overlayId}/bioEntities/", method = { RequestMethod.GET },
+			produces = { MediaType.APPLICATION_JSON_VALUE })
+	public List<Map<String, Object>> getOverlayElements(//
+			@RequestParam(value = "token") String token, //
 			@PathVariable(value = "projectId") String projectId, //
 			@PathVariable(value = "overlayId") String overlayId, 
-			@RequestParam(value = "columns", defaultValue = "") String columns
-			)
+			@RequestParam(value = "columns", defaultValue = "") String columns)
 			throws SecurityException, QueryException {
 		return overlayController.getOverlayElements(token, projectId, Integer.valueOf(overlayId), columns);
 	}
 
+	@RequestMapping(value = "/projects/{projectId}/overlays/{overlayId}/models/{modelId}/bioEntities/reactions/{reactionId}/", method = { RequestMethod.GET },
+			produces = { MediaType.APPLICATION_JSON_VALUE })
+	public Map<String, Object> getFullReaction(//
+			@RequestParam(value = "token") String token, //
+			@PathVariable(value = "projectId") String projectId, //
+			@PathVariable(value = "modelId") String modelId, //
+			@PathVariable(value = "overlayId") String overlayId, //
+			@PathVariable(value = "reactionId") String reactionId, //
+			@RequestParam(value = "columns", defaultValue = "") String columns //
+			) throws SecurityException, QueryException {
+		return overlayController
+				.getOverlayElement(token, projectId, Integer.valueOf(modelId), Integer.valueOf(overlayId), Integer.valueOf(reactionId), "REACTION", columns);
+	}
+	@RequestMapping(value = "/projects/{projectId}/overlays/{overlayId}/models/{modelId}/bioEntities/elements/{elementId}/", method = { RequestMethod.GET },
+			produces = { MediaType.APPLICATION_JSON_VALUE })
+	public Map<String, Object> getFullSpecies(//
+			@RequestParam(value = "token") String token, //
+			@PathVariable(value = "projectId") String projectId, //
+			@PathVariable(value = "modelId") String modelId, //
+			@PathVariable(value = "overlayId") String overlayId, //
+			@PathVariable(value = "elementId") String reactionId, //
+			@RequestParam(value = "columns", defaultValue = "") String columns //
+			) throws SecurityException, QueryException {
+		return overlayController
+				.getOverlayElement(token, projectId, Integer.valueOf(modelId), Integer.valueOf(overlayId), Integer.valueOf(reactionId), "ALIAS", columns);
+	}
+
 	@RequestMapping(value = "/overlay/getOverlayTypes", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
 	public List<Map<String, Object>> getOverlayTypes(@RequestParam(value = "token") String token) throws SecurityException, QueryException {
 		return overlayController.getOverlayTypes(token);
@@ -97,15 +124,6 @@ public class OverlayController extends BaseController {
 				.body(file.getFileContent());
 	}
 
-	@RequestMapping(value = "/overlay/getOverlayElement", method = { RequestMethod.GET, RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
-	public Map<String, Object> getFullElement(@RequestParam(value = "token") String token, @RequestParam(value = "projectId") String projectId,
-			@RequestParam(value = "modelId") String modelId, @RequestParam(value = "overlayId") String overlayId,
-			@RequestParam(value = "elementId") String elementId, @RequestParam(value = "elementType") String elementType,
-			@RequestParam(value = "columns", defaultValue = "") String columns) throws SecurityException, QueryException {
-		return overlayController
-				.getOverlayElement(token, projectId, Integer.valueOf(modelId), Integer.valueOf(overlayId), Integer.valueOf(elementId), elementType, columns);
-	}
-
 	/**
 	 * @return the overlayController
 	 * @see #overlayController

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

@@ -29,6 +29,7 @@ import lcsb.mapviewer.services.interfaces.IModelService;
 import lcsb.mapviewer.services.interfaces.IUserService;
 import lcsb.mapviewer.services.search.data.ElementIdentifier.ElementIdentifierType;
 import lcsb.mapviewer.services.search.layout.FullLayoutAliasView;
+import lcsb.mapviewer.services.search.layout.FullLayoutReactionView;
 import lcsb.mapviewer.services.search.layout.LightLayoutAliasView;
 import lcsb.mapviewer.services.search.layout.LightLayoutReactionView;
 import lcsb.mapviewer.services.utils.data.ColorSchemaType;
@@ -288,6 +289,11 @@ public class OverlayRestImpl extends BaseRestImpl {
 			result.put("type", ElementIdentifierType.ALIAS);
 			result.put("overlayContent", layoutAliasView);
 			return result;
+		} else if (ElementIdentifierType.REACTION.getJsName().equals(elementType)) {
+			FullLayoutReactionView layoutAliasView = layoutService.getFullReactionForLayout(model, elementId, overlayId, authenticationToken);
+			result.put("type", ElementIdentifierType.REACTION);
+			result.put("overlayContent", layoutAliasView);
+			return result;
 		} else {
 			throw new QueryException("Unknown element type: " + elementType);
 		}

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

@@ -60,6 +60,8 @@ import lcsb.mapviewer.services.interfaces.ILogService.LogParams;
 import lcsb.mapviewer.services.interfaces.IUserService;
 import lcsb.mapviewer.services.search.layout.FullLayoutAliasView;
 import lcsb.mapviewer.services.search.layout.FullLayoutAliasViewFactory;
+import lcsb.mapviewer.services.search.layout.FullLayoutReactionView;
+import lcsb.mapviewer.services.search.layout.FullLayoutReactionViewFactory;
 import lcsb.mapviewer.services.search.layout.LightLayoutAliasView;
 import lcsb.mapviewer.services.search.layout.LightLayoutAliasViewFactory;
 import lcsb.mapviewer.services.search.layout.LightLayoutReactionView;
@@ -1075,4 +1077,30 @@ public class LayoutService implements ILayoutService {
 			throw new InvalidStateException(e);
 		}
 	}
+
+	@Override
+	public FullLayoutReactionView getFullReactionForLayout(Model model, Integer id, int layoutId, AuthenticationToken token) throws SecurityException {
+		try {
+			ColorSchemaReader reader = new ColorSchemaReader();
+			Collection<ColorSchema> schemas;
+			schemas = reader.readColorSchema(getInputDataForLayout(layoutId, token));
+			// colors here are not important
+			ColorModelCommand command = new ColorModelCommand(model, schemas, new ColorExtractor(Color.BLACK, Color.BLACK));
+			FullLayoutReactionViewFactory factory = new FullLayoutReactionViewFactory();
+
+			for (Map.Entry<Object, ColorSchema> entry : command.getModifiedElements().entrySet()) {
+				if (entry.getKey() instanceof Reaction) {
+					Reaction alias = (Reaction) entry.getKey();
+					if (id.equals(alias.getId())) {
+						return factory.create(new Pair<Reaction, ColorSchema>(alias, entry.getValue()));
+					}
+				}
+			}
+			return null;
+		} catch (InvalidColorSchemaException e) {
+			throw new InvalidStateException(e);
+		} catch (IOException e) {
+			throw new InvalidStateException(e);
+		}
+	}
 }

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

@@ -16,6 +16,7 @@ import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.user.User;
 import lcsb.mapviewer.services.SecurityException;
 import lcsb.mapviewer.services.search.layout.FullLayoutAliasView;
+import lcsb.mapviewer.services.search.layout.FullLayoutReactionView;
 import lcsb.mapviewer.services.search.layout.LightLayoutAliasView;
 import lcsb.mapviewer.services.search.layout.LightLayoutReactionView;
 import lcsb.mapviewer.services.utils.EmailSender;
@@ -502,6 +503,8 @@ public interface ILayoutService {
 			throws SecurityException;
 
 	FullLayoutAliasView getFullAliasForLayout(Model model, Integer id, int layoutId, AuthenticationToken token) throws SecurityException;
+	
+	FullLayoutReactionView getFullReactionForLayout(Model model, Integer id, int layoutId, AuthenticationToken token) throws SecurityException;
 
 	/**
 	 * Returns {@link EmailSender} used by the service.

service/src/main/java/lcsb/mapviewer/services/search/layout/FullLayoutReactionView.java

+package lcsb.mapviewer.services.search.layout;
+
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+public class FullLayoutReactionView extends LightLayoutReactionView {
+
+	public FullLayoutReactionView(Reaction reaction) {
+		super(reaction);
+	}
+
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = 1L;
+}

service/src/main/java/lcsb/mapviewer/services/search/layout/FullLayoutReactionViewFactory.java

+package lcsb.mapviewer.services.search.layout;
+
+import org.apache.log4j.Logger;
+
+import com.google.gson.Gson;
+
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.services.search.ElementViewFactory;
+
+/**
+ * Factory class for {@link LightLayoutReactionView} class.
+ * 
+ * @author Piotr Gawron
+ * 
+ */
+public class FullLayoutReactionViewFactory extends ElementViewFactory<Pair<Reaction, ColorSchema>, FullLayoutReactionView> {
+	/**
+	 * Default class logger.
+	 */
+	@SuppressWarnings("unused")
+	private static Logger logger = Logger.getLogger(FullLayoutReactionViewFactory.class);
+
+	@Override
+	public FullLayoutReactionView create(Pair<Reaction, ColorSchema> pair) {
+		FullLayoutReactionView result = new FullLayoutReactionView(pair.getLeft());
+		result.setColor(pair.getRight().getColor());
+		result.setValue(pair.getRight().getValue());
+		result.setWidth(pair.getRight().getLineWidth());
+		result.setReverse(pair.getRight().getReverseReaction());
+		return result;
+	}
+
+	@Override
+	public String createGson(FullLayoutReactionView object) {
+		return new Gson().toJson(object);
+	}
+}