diff --git a/commons/src/main/java/lcsb/mapviewer/common/geometry/ColorParser.java b/commons/src/main/java/lcsb/mapviewer/common/geometry/ColorParser.java
index f76dce4edb7f08ab22821bdf6633a1e4a7bff89a..f78e460818ca7672354874b712036e714d35a789 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/geometry/ColorParser.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/geometry/ColorParser.java
@@ -1,6 +1,8 @@
package lcsb.mapviewer.common.geometry;
import java.awt.Color;
+import java.util.HashMap;
+import java.util.Map;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
@@ -56,4 +58,17 @@ public class ColorParser {
Integer.valueOf(string.substring(COLOR_SUBSTRING_START_BLUE, COLOR_STRING_LENGTH), HEX_BASE));
}
}
+
+ /**
+ * Converts color into list of atributes.
+ *
+ * @param color color to convert
+ * @return map with list of color attributes
+ */
+ public Map<String, Object> colorToMap(Color color) {
+ Map<String, Object> result = new HashMap<>();
+ result.put("alpha", color.getAlpha());
+ result.put("rgb", color.getRGB());
+ return result;
+ }
}
diff --git a/frontend-js/src/main/js/Functions.js b/frontend-js/src/main/js/Functions.js
index de976d6f3778f44c0acde57220c832bea03b711a..c2594abb1575f2dc79df84ec36093fc7b7c2b701 100644
--- a/frontend-js/src/main/js/Functions.js
+++ b/frontend-js/src/main/js/Functions.js
@@ -170,7 +170,7 @@ Functions.overlayToColor = function(elementOverlay) {
if (elementOverlay === null || elementOverlay === undefined) {
return Promise.reject("elementOverlay cannot be null!");
} else if (elementOverlay.color !== undefined && elementOverlay.color !== null) {
- return Promise.resolve(self.intToColorString(elementOverlay.color.value));
+ return Promise.resolve(self.intToColorString(elementOverlay.color.rgb));
} else {
var ratio = 0;
var promiseColor = null;
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 0c2c7a6ea47a6108c58a00903ded58abedae174d..ec6bb96897cb4a0c4b6f3a8223ea59bc6be51813 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
@@ -47,11 +47,6 @@ public class OverlayRestImpl extends BaseRestImpl {
*/
private Logger logger = Logger.getLogger(OverlayRestImpl.class);
- @Autowired
- private IUserService userService;
-
- @Autowired
- private IModelService modelService;
@Autowired
private ILayoutService layoutService;
@@ -60,31 +55,14 @@ public class OverlayRestImpl extends BaseRestImpl {
private LayoutDao layoutDao;
public List<LayoutView> getOverlayList(String token, String projectId) throws SecurityException, QueryException {
- AuthenticationToken authenticationToken = userService.getToken(token);
- Model model = modelService.getLastModelByProjectId(projectId, authenticationToken);
+ AuthenticationToken authenticationToken = getUserService().getToken(token);
+ Model model = getModelService().getLastModelByProjectId(projectId, authenticationToken);
if (model == null) {
throw new QueryException("Project with given id doesn't exist");
}
return layoutService.getCustomLayouts(model, token);
}
- /**
- * @return the userService
- * @see #userService
- */
- public IUserService getUserService() {
- return userService;
- }
-
- /**
- * @param userService
- * the userService to set
- * @see #userService
- */
- public void setUserService(IUserService userService) {
- this.userService = userService;
- }
-
/**
* @return the layoutService
* @see #layoutService
@@ -102,28 +80,11 @@ public class OverlayRestImpl extends BaseRestImpl {
this.layoutService = layoutService;
}
- /**
- * @return the modelService
- * @see #modelService
- */
- public IModelService getModelService() {
- return modelService;
- }
-
- /**
- * @param modelService
- * the modelService to set
- * @see #modelService
- */
- public void setModelService(IModelService modelService) {
- this.modelService = modelService;
- }
-
public List<Map<String, Object>> getOverlayElements(String token, String projectId, int overlayId, String columns) throws QueryException, SecurityException {
List<Map<String, Object>> result = new ArrayList<>();
- AuthenticationToken authenticationToken = userService.getToken(token);
+ AuthenticationToken authenticationToken = getUserService().getToken(token);
- Model model = modelService.getLastModelByProjectId(projectId, authenticationToken);
+ Model model = getModelService().getLastModelByProjectId(projectId, authenticationToken);
if (model == null) {
throw new QueryException("Project with given id doesn't exist");
}
@@ -146,8 +107,8 @@ public class OverlayRestImpl extends BaseRestImpl {
}
public LayoutView getOverlayById(String token, String projectId, String overlayId) throws SecurityException, QueryException {
- AuthenticationToken authenticationToken = userService.getToken(token);
- Model model = modelService.getLastModelByProjectId(projectId, authenticationToken);
+ AuthenticationToken authenticationToken = getUserService().getToken(token);
+ Model model = getModelService().getLastModelByProjectId(projectId, authenticationToken);
if (model == null) {
throw new QueryException("Project with given id doesn't exist");
}
@@ -155,8 +116,8 @@ public class OverlayRestImpl extends BaseRestImpl {
}
public FileEntry getOverlaySource(String token, String projectId, String overlayId) throws SecurityException, QueryException {
- AuthenticationToken authenticationToken = userService.getToken(token);
- Model model = modelService.getLastModelByProjectId(projectId, authenticationToken);
+ AuthenticationToken authenticationToken = getUserService().getToken(token);
+ Model model = getModelService().getLastModelByProjectId(projectId, authenticationToken);
if (model == null) {
throw new QueryException("Project with given id doesn't exist");
}
@@ -175,8 +136,8 @@ public class OverlayRestImpl extends BaseRestImpl {
}
public LayoutView updateOverlay(String token, String projectId, String overlayId, Map<String, Object> overlayData) throws QueryException, SecurityException {
- AuthenticationToken authenticationToken = userService.getToken(token);
- Model model = modelService.getLastModelByProjectId(projectId, authenticationToken);
+ AuthenticationToken authenticationToken = getUserService().getToken(token);
+ Model model = getModelService().getLastModelByProjectId(projectId, authenticationToken);
if (model == null) {
throw new QueryException("Project with given id doesn't exist");
}
@@ -184,7 +145,7 @@ public class OverlayRestImpl extends BaseRestImpl {
throw new QueryException("overlay field cannot be undefined");
}
Project project = model.getProject();
- boolean isAdmin = userService.userHasPrivilege(authenticationToken, PrivilegeType.LAYOUT_MANAGEMENT, project);
+ boolean isAdmin = getUserService().userHasPrivilege(authenticationToken, PrivilegeType.LAYOUT_MANAGEMENT, project);
try {
Integer id = Integer.valueOf(overlayId);
Layout layout = layoutService.getLayoutDataById(id, authenticationToken);
@@ -208,8 +169,8 @@ public class OverlayRestImpl extends BaseRestImpl {
}
public Map<String, Object> removeOverlay(String token, String projectId, String overlayId) throws QueryException, SecurityException, IOException {
- AuthenticationToken authenticationToken = userService.getToken(token);
- Model model = modelService.getLastModelByProjectId(projectId, authenticationToken);
+ AuthenticationToken authenticationToken = getUserService().getToken(token);
+ Model model = getModelService().getLastModelByProjectId(projectId, authenticationToken);
if (model == null) {
throw new ObjectNotFoundException("Project with given id doesn't exist");
}
@@ -249,12 +210,12 @@ public class OverlayRestImpl extends BaseRestImpl {
public LayoutView addOverlay(String token, String projectId, String name, String description, String content, String filename, String type)
throws SecurityException, QueryException, IOException {
- AuthenticationToken authenticationToken = userService.getToken(token);
- User user = userService.getUserByToken(token);
+ AuthenticationToken authenticationToken = getUserService().getToken(token);
+ User user = getUserService().getUserByToken(token);
if (Configuration.ANONYMOUS_LOGIN.equals(user.getLogin())) {
throw new SecurityException("You have no privileges to add overlay");
}
- Model model = modelService.getLastModelByProjectId(projectId, authenticationToken);
+ Model model = getModelService().getLastModelByProjectId(projectId, authenticationToken);
if (model == null) {
throw new QueryException("Project with given id doesn't exist");
}
@@ -284,9 +245,9 @@ public class OverlayRestImpl extends BaseRestImpl {
public Map<String, Object> getOverlayElement(String token, String projectId, Integer modelId, Integer overlayId, Integer elementId, String elementType,
String columns) throws QueryException, SecurityException {
- AuthenticationToken authenticationToken = userService.getToken(token);
+ AuthenticationToken authenticationToken = getUserService().getToken(token);
- Model topModel = modelService.getLastModelByProjectId(projectId, authenticationToken);
+ Model topModel = getModelService().getLastModelByProjectId(projectId, authenticationToken);
if (topModel == null) {
throw new QueryException("Project with given id doesn't exist");
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/layout/FullLayoutAliasViewFactory.java b/service/src/main/java/lcsb/mapviewer/services/search/layout/FullLayoutAliasViewFactory.java
index e42bc74452ab802039cdd8f87ac09afeb0eff40f..c08811bee4ad4a6f7c1f75b4fd60143f0e862d03 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/layout/FullLayoutAliasViewFactory.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/layout/FullLayoutAliasViewFactory.java
@@ -5,6 +5,7 @@ import org.apache.log4j.Logger;
import com.google.gson.Gson;
import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.geometry.ColorParser;
import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.layout.GeneVariationColorSchema;
import lcsb.mapviewer.model.map.species.Element;
@@ -18,18 +19,26 @@ import lcsb.mapviewer.services.utils.data.ColorSchemaType;
*
*/
public class FullLayoutAliasViewFactory extends ElementViewFactory<Pair<Element, ColorSchema>, FullLayoutAliasView> {
+
+ /**
+ * Parser to map color into object that can be returned to client side.
+ */
+ private ColorParser parser = new ColorParser();
+
/**
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(FullLayoutAliasViewFactory.class);
+ private static Logger logger = Logger.getLogger(FullLayoutAliasViewFactory.class);
@Override
public FullLayoutAliasView create(Pair<Element, ColorSchema> pair) {
ColorSchema schema = pair.getRight();
FullLayoutAliasView result = new FullLayoutAliasView(pair.getLeft());
- result.setColor(schema.getColor());
+ if (schema.getColor() != null) {
+ result.setColor(parser.colorToMap(schema.getColor()));
+ }
result.setValue(schema.getValue());
result.setDescription(schema.getDescription());
if (schema instanceof GeneVariationColorSchema) {
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/layout/LightLayoutAliasView.java b/service/src/main/java/lcsb/mapviewer/services/search/layout/LightLayoutAliasView.java
index bf8008175a72d11552548b7fc551cbeb968cf229..f4f8d5a612377b1428936b3d377afa5d1e692486 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/layout/LightLayoutAliasView.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/layout/LightLayoutAliasView.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.services.search.layout;
-import java.awt.Color;
+import java.util.Map;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.services.search.ElementView;
@@ -18,17 +18,17 @@ public class LightLayoutAliasView extends ElementView {
/**
*
*/
- private static final long serialVersionUID = 1L;
+ private static final long serialVersionUID = 1L;
/**
* Value used to highlight {@link Element} in a a layout.
*/
- private Double value;
+ private Double value;
/**
* Color used to highlight {@link Element} in a layout.
*/
- private Color color;
+ private Map<String, Object> color;
/**
* Default constructor.
@@ -68,7 +68,7 @@ public class LightLayoutAliasView extends ElementView {
* @return the color
* @see #color
*/
- public Color getColor() {
+ public Map<String, Object> getColor() {
return color;
}
@@ -77,7 +77,7 @@ public class LightLayoutAliasView extends ElementView {
* the color to set
* @see #color
*/
- public void setColor(Color color) {
+ public void setColor(Map<String, Object> color) {
this.color = color;
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/layout/LightLayoutAliasViewFactory.java b/service/src/main/java/lcsb/mapviewer/services/search/layout/LightLayoutAliasViewFactory.java
index 0f37f3a0afe17a79edab2d9858bb2aed061e0d71..910a1b5a474907361138f8dbb12f91f18c58cc61 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/layout/LightLayoutAliasViewFactory.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/layout/LightLayoutAliasViewFactory.java
@@ -5,6 +5,7 @@ import org.apache.log4j.Logger;
import com.google.gson.Gson;
import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.geometry.ColorParser;
import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.services.search.ElementViewFactory;
@@ -16,16 +17,25 @@ import lcsb.mapviewer.services.search.ElementViewFactory;
*
*/
public class LightLayoutAliasViewFactory extends ElementViewFactory<Pair<Element, ColorSchema>, LightLayoutAliasView> {
+
+ /**
+ * Parser to map color into object that can be returned to client side.
+ */
+
+ private ColorParser parser = new ColorParser();
+
/**
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(LightLayoutAliasViewFactory.class);
+ private static Logger logger = Logger.getLogger(LightLayoutAliasViewFactory.class);
@Override
public LightLayoutAliasView create(Pair<Element, ColorSchema> pair) {
LightLayoutAliasView result = new LightLayoutAliasView(pair.getLeft());
- result.setColor(pair.getRight().getColor());
+ if (pair.getRight().getColor() != null) {
+ result.setColor(parser.colorToMap(pair.getRight().getColor()));
+ }
result.setValue(pair.getRight().getValue());
return result;
}