diff --git a/frontend-js/src/main/js/ServerConnector.js b/frontend-js/src/main/js/ServerConnector.js
index 3ff7d7b652efe21ab982898d1d40ffa2bf7f1031..e93a5625b17d5f0548e5c73f34277a9338a56680 100644
--- a/frontend-js/src/main/js/ServerConnector.js
+++ b/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;
diff --git a/frontend-js/testFiles/apiCalls/overlay/getOverlayElement/elementId=329163&elementType=ALIAS&modelId=15781&overlayId=18076&projectId=sample&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/overlays/18076/models/15781/bioEntities/elements/329163/token=MOCK_TOKEN_ID&
similarity index 100%
rename from frontend-js/testFiles/apiCalls/overlay/getOverlayElement/elementId=329163&elementType=ALIAS&modelId=15781&overlayId=18076&projectId=sample&token=MOCK_TOKEN_ID&
rename to frontend-js/testFiles/apiCalls/projects/sample/overlays/18076/models/15781/bioEntities/elements/329163/token=MOCK_TOKEN_ID&
diff --git a/frontend-js/testFiles/apiCalls/overlay/getOverlayElement/elementId=329163&elementType=ALIAS&modelId=15781&overlayId=18077&projectId=sample&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/overlays/18077/models/15781/bioEntities/elements/329163/token=MOCK_TOKEN_ID&
similarity index 100%
rename from frontend-js/testFiles/apiCalls/overlay/getOverlayElement/elementId=329163&elementType=ALIAS&modelId=15781&overlayId=18077&projectId=sample&token=MOCK_TOKEN_ID&
rename to frontend-js/testFiles/apiCalls/projects/sample/overlays/18077/models/15781/bioEntities/elements/329163/token=MOCK_TOKEN_ID&
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayController.java
index a40438e46cec76de5649c4e86c10f999fb5681a1..8196f53e14f688ae1438aef11980cc1bf326c097 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayController.java
+++ b/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
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java
index bf6a0040511c3e7b0528a538214bf0085e079f8c..aef38648ff446f6437d2ffd5d703cc5794ab6c37 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java
+++ b/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);
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java b/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
index 08d1314773be8b3f220302fdf91f2ed7b0044e9f..5ebe9bb4cf4984cb40b050b18240ad02a4009c1e 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
+++ b/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);
+ }
+ }
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/ILayoutService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/ILayoutService.java
index f5a1b1ca8c20d253922b6659f76035cddc590bd5..207b7d3d29b4881451eb48bf3f5761e548da75b9 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/ILayoutService.java
+++ b/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.
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/layout/FullLayoutReactionView.java b/service/src/main/java/lcsb/mapviewer/services/search/layout/FullLayoutReactionView.java
new file mode 100644
index 0000000000000000000000000000000000000000..126b8493872e024db5b495721ead6b687423e119
--- /dev/null
+++ b/service/src/main/java/lcsb/mapviewer/services/search/layout/FullLayoutReactionView.java
@@ -0,0 +1,15 @@
+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;
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/layout/FullLayoutReactionViewFactory.java b/service/src/main/java/lcsb/mapviewer/services/search/layout/FullLayoutReactionViewFactory.java
new file mode 100644
index 0000000000000000000000000000000000000000..de40e6e11aef70a289ca1b9a97baea9ccbe008ed
--- /dev/null
+++ b/service/src/main/java/lcsb/mapviewer/services/search/layout/FullLayoutReactionViewFactory.java
@@ -0,0 +1,39 @@
+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);
+ }
+}