refresh data overlay should hide data overlays that were removed

CHANGELOG

 minerva (14.0.9) stable; urgency=medium
   * Bug fix: simultanous export to SBML of more than one file could result in
     500 Internal Server Error (#1110)
+  * Bug fix: refresh data overlay did not hide data overlays that were removed
+    and selected (#1097)
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 3 Feb 2020 15:00:00 +0200
 

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

@@ -1882,7 +1882,7 @@ ServerConnector.getOverlayById = function (overlayId, projectId) {
     return self.sendGetRequest(self.getOverlayByIdUrl(queryParams, filterParams));
   }).then(function (content) {
     return new DataOverlay(JSON.parse(content));
-  });
+  }).catch(self.processNetworkError);
 };
 
 /**

frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js

@@ -608,6 +608,17 @@ OverlayPanel.prototype.refresh = function (showDefault) {
       }
     }
     return Promise.all(promises);
+  }).then(function () {
+    return self.getMap().getVisibleDataOverlays();
+  }).then(function (visibleDataOverlays) {
+    var promises = [];
+    for (var i = 0; i < visibleDataOverlays.length; i++) {
+      var overlay = visibleDataOverlays[i];
+      if (self.getProject().getDataOverlayById(overlay.getId()) === undefined) {
+        promises.push(self.getMap().hideDataOverlay(overlay.getId()));
+      }
+    }
+    return Promise.all(promises);
   }).then(function () {
     return self.getMap().redrawSelectedDataOverlays();
   });

frontend-js/src/main/js/map/CustomMap.js

@@ -1317,15 +1317,33 @@ CustomMap.prototype.destroy = function () {
  * @returns {Promise<DataOverlay[]>}
  */
 CustomMap.prototype.getVisibleDataOverlays = function () {
+  var self = this;
+
   var dataOverlayPromises = [];
 
-  for (var key in this._selectedOverlays) {
-    if (this._selectedOverlays.hasOwnProperty(key) && this._selectedOverlays[key] === true) {
-      dataOverlayPromises.push(this.getProject().getDataOverlayById(parseInt(key)));
+  for (var key in self._selectedOverlays) {
+    if (self._selectedOverlays.hasOwnProperty(key) && self._selectedOverlays[key] === true) {
+      dataOverlayPromises.push(function () {
+        var id = parseInt(key);
+        return self.getProject().getDataOverlayById(id).then(function (overlay) {
+          if (overlay === null) {
+            self._selectedOverlays[id] = false;
+            return self.hideSelectedLayout(id).then(function () {
+              return overlay;
+            })
+          } else {
+            return overlay;
+          }
+        });
+      }());
     }
   }
 
   return Promise.all(dataOverlayPromises).then(function (overlays) {
+    overlays = overlays.filter(function (overlay) {
+      return overlay != null;
+    });
+
     overlays.sort(function (dataOverlay1, dataOverlay2) {
       if (dataOverlay1.getOrder() < dataOverlay2.getOrder())
         return -1;

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

@@ -536,8 +536,12 @@ Project.prototype.getDataOverlayById = function (overlayId) {
     return Promise.resolve(self._dataOverlays[overlayId]);
   } else {
     return ServerConnector.getOverlayById(overlayId).then(function (overlay) {
-      self.addDataOverlay(overlay, false);
-      return self._dataOverlays[overlayId];
+      if (overlay !== null) {
+        self.addDataOverlay(overlay, false);
+        return self._dataOverlays[overlayId];
+      } else {
+        return null;
+      }
     });
   }
 };

frontend-js/src/test/js/map/CustomMap-test.js

@@ -548,7 +548,7 @@ describe('CustomMap', function () {
     return map.openInfoWindowForIdentifiedElement(ie, marker).then(function () {
       infoWindow = map.getInfoWindowForIdentifiedElement(ie);
       assert.ok(infoWindow);
-    }).finally(function(){
+    }).finally(function () {
       return map.destroy();
     });
 
@@ -975,7 +975,7 @@ describe('CustomMap', function () {
       var map = new CustomMap(options);
       return map.init().then(function () {
         assert.fail();
-      }).catch(function(e){
+      }).catch(function (e) {
         assert.ok(e instanceof ValidationError);
       });
     });
@@ -999,6 +999,26 @@ describe('CustomMap', function () {
 
   });
 
+  it("get visible data overlays with removed overlay", function () {
+    var project = helper.createProject();
+    var overlay1 = helper.createOverlay();
+    overlay1.setInputDataAvailable(true);
+    project.addDataOverlay(overlay1);
+
+    var options = helper.createCustomMapOptions(project);
+    ServerConnector.getSessionData(options.getProject()).setVisibleOverlays([overlay1.getId()]);
+    var map = new CustomMap(options);
+    return map.init().then(function () {
+      map._selectedOverlays[-1] = true;
+      map.selectedLayoutOverlays[-1] = [];
+      return map.getVisibleDataOverlays();
+    }).then(function (overlays) {
+      assert.equal(1, overlays.length);
+      assert.notOk(map._selectedOverlays[-1]);
+      map.destroy();
+    })
+  });
+
   it("center button", function () {
     var options = helper.createCustomMapOptions();
     var map = new CustomMap(options);

frontend-js/src/test/js/map/data/Project-test.js

@@ -48,11 +48,8 @@ describe('Project', function () {
     var project = helper.createProject();
     var overlay = helper.createOverlay();
 
-    return project.getDataOverlayById(overlay.getId()).then(function () {
-      assert.ok(false, 'expected rejection');
-    }, function (exception) {
-      assert.ok(exception);
-
+    return project.getDataOverlayById(overlay.getId()).then(function (result) {
+      assert.equal(null, result);
       project.addDataOverlay(overlay);
 
       return project.getDataOverlayById(overlay.getId()).then(function (overlayResult) {