pathways with glyphs and z-index <0 are not clickable

CHANGELOG

@@ -21,7 +21,10 @@ minerva (15.1.0) unstable; urgency=medium
     raised if images are not referenced in coords.txt file (#1308)
   * Small improvement: hitting enter after filling credentials automatically
     tries to log in (#1312)
-  * Small improvement: rest API provides information about element glyph
+  * Small improvement: rest API provides information about element glyph and z
+    index
+  * Small improvement: pathways with glyphs and z index below 0 are not
+    clickable (#1314)
   * Bug fix: export to image from selected polygon contained all elements
     inside rectangle bounded by the polygon coordinates (#1096)
   * Bug fix: continuous refreshing list of project when uploading/removing

frontend-js/src/main/js/map/data/Alias.js

@@ -23,6 +23,7 @@ function Alias(javaObject) {
   if (javaObject.bounds !== undefined) {
     this.setX(javaObject.bounds.x);
     this.setY(javaObject.bounds.y);
+    this.setZ(javaObject.bounds.z);
     this.setWidth(javaObject.bounds.width);
     this.setHeight(javaObject.bounds.height);
   }
@@ -79,8 +80,11 @@ Alias.prototype.update = function (javaObject) {
     this.setInitialAmount(javaObject.getInitialAmount());
     this.setInitialConcentration(javaObject.getInitialConcentration());
 
+    this.setGlyph(javaObject.getGlyph());
+
     this.setX(javaObject.getX());
     this.setY(javaObject.getY());
+    this.setZ(javaObject.getZ());
     this.setWidth(javaObject.getWidth());
     this.setHeight(javaObject.getHeight());
 
@@ -113,10 +117,12 @@ Alias.prototype.update = function (javaObject) {
     this.setInitialAmount(javaObject.initialAmount);
     this.setInitialConcentration(javaObject.initialConcentration);
 
+    this.setGlyph(javaObject.glyph);
 
     if (javaObject.bounds !== undefined) {
       this.setX(javaObject.bounds.x);
       this.setY(javaObject.bounds.y);
+      this.setZ(javaObject.bounds.z);
       this.setWidth(javaObject.bounds.width);
       this.setHeight(javaObject.bounds.height);
     }
@@ -256,6 +262,24 @@ Alias.prototype.getY = function () {
   return this.y;
 };
 
+/**
+ *
+ * @param {number}  z
+ */
+Alias.prototype.setZ = function (z) {
+  if (z !== undefined) {
+    this.z = z;
+  }
+};
+
+/**
+ *
+ * @returns {number}
+ */
+Alias.prototype.getZ = function () {
+  return this.z;
+};
+
 /**
  *
  * @param {number} elementId
@@ -400,4 +424,20 @@ Alias.prototype.getCenter = function () {
   return new Point(this.getX() + this.getWidth() / 2, this.getY() + this.getHeight() / 2);
 };
 
+/**
+ *
+ * @returns {Object}
+ */
+Alias.prototype.getGlyph = function () {
+  return this._glyph;
+};
+
+/**
+ *
+ * @param {Object} glyph
+ */
+Alias.prototype.setGlyph = function (glyph) {
+  this._glyph = glyph;
+};
+
 module.exports = Alias;

frontend-js/src/main/js/map/overlay/SearchDbOverlay.js

@@ -228,6 +228,17 @@ SearchDbOverlay.prototype.findCompartmentByCoordinates = function (coordinates,
         }
       });
     }
+  }).then(function (result) {
+    if (result !== undefined) {
+      return model.getAliasById(result.getId(), true).then(function (alias) {
+        //pathways with glyph and z index below 0 should not be clickable
+        if (alias.getType() === "Pathway" && alias.getZ() < 0 && alias.getGlyph() !== null) {
+          return undefined;
+        } else {
+          return result;
+        }
+      });
+    }
   });
 };
 
@@ -295,6 +306,13 @@ SearchDbOverlay.prototype.searchByCoordinates = function (params) {
               searchResult.push(new IdentifiedElement(reactionElements[i]));
             }
           });
+        } else {
+          return model.getAliasById(searchResult[0].getId(), true).then(function (alias) {
+            //pathways with glyph and z index below 0 should not be clickable
+            if (alias.getType() === "Pathway" && alias.getZ() < 0 && alias.getGlyph() !== null) {
+              searchResult = [];
+            }
+          });
         }
       } else {
         searchResult = [];

rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java

@@ -212,7 +212,7 @@ public class ElementsRestImpl extends BaseRestImpl {
         }
         break;
       case "bounds":
-        value = createBounds(element.getX(), element.getY(), element.getWidth(), element.getHeight());
+        value = createBounds(element.getX(), element.getY(),element.getZ(), element.getWidth(), element.getHeight());
         break;
       case "glyph":
         value = createGlyph(element.getGlyph());
@@ -321,10 +321,11 @@ public class ElementsRestImpl extends BaseRestImpl {
     return result;
   }
 
-  private Map<String, Object> createBounds(Double x, Double y, Double width, Double height) {
+  private Map<String, Object> createBounds(Double x, Double y, Integer z, Double width, Double height) {
     Map<String, Object> result = new TreeMap<>();
     result.put("x", x);
     result.put("y", y);
+    result.put("z", z);
     result.put("width", width);
     result.put("height", height);
     return result;