From fe52bed04d064a2b85a9ebdef9b1c3a397a8063c Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 6 Jan 2017 19:15:55 +0100
Subject: [PATCH] first approach to search Db Ovelay
clicking on map access appropriate elements vi api
---
frontend-js/src/main/js/ServerConnector.js | 70 +-------
.../src/main/js/map/AbstractCustomMap.js | 10 +-
frontend-js/src/main/js/map/CustomMap.js | 159 +++++++++---------
.../src/main/js/map/data/IdentifiedElement.js | 33 ++--
frontend-js/src/main/js/map/data/MapModel.js | 3 +-
frontend-js/src/main/js/map/data/Reaction.js | 18 +-
.../main/js/map/overlay/CommentDbOverlay.js | 17 +-
.../main/js/map/overlay/OverlayCollection.js | 30 +++-
.../main/js/map/overlay/SearchDbOverlay.js | 106 ++++++++++++
frontend-js/src/main/js/minerva.js | 3 +
.../src/test/js/ServerConnector-mock.js | 12 --
frontend-js/src/test/js/google-map-mock.js | 40 ++++-
frontend-js/src/test/js/helper.js | 11 ++
frontend-js/src/test/js/map/CustomMap-test.js | 31 +++-
frontend-js/src/test/js/minerva-test.js | 18 ++
...lse&projectId=sample&token=MOCK_TOKEN_ID&} | 0
...102&projectId=sample&token=MOCK_TOKEN_ID&} | 0
...5781&projectId=sample&token=MOCK_TOKEN_ID& | 1 +
...5781&projectId=sample&token=MOCK_TOKEN_ID& | 1 +
...9180&projectId=sample&token=MOCK_TOKEN_ID& | 1 +
...9173&projectId=sample&token=MOCK_TOKEN_ID& | 1 +
...3515&projectId=sample&token=MOCK_TOKEN_ID& | 1 +
22 files changed, 375 insertions(+), 191 deletions(-)
create mode 100644 frontend-js/src/main/js/map/overlay/SearchDbOverlay.js
rename frontend-js/testFiles/apiCalls/comment/addComment/{content=&coordinates=2,12&elementId=&elementType=POINT&email=&modelId=102&name=&pinned=false&projectId=sample&token=MOCK_TOKEN_ID& => content=&coordinates=2.00,12.00&elementId=&elementType=POINT&email=&modelId=102&name=&pinned=false&projectId=sample&token=MOCK_TOKEN_ID&} (100%)
rename frontend-js/testFiles/apiCalls/project/getClosestElementsByCoordinates/{coordinates=2,12&modelId=102&projectId=sample&token=MOCK_TOKEN_ID& => coordinates=2.00,12.00&modelId=102&projectId=sample&token=MOCK_TOKEN_ID&} (100%)
create mode 100644 frontend-js/testFiles/apiCalls/project/getClosestElementsByCoordinates/coordinates=26547.33,39419.29&count=1&modelId=15781&projectId=sample&token=MOCK_TOKEN_ID&
create mode 100644 frontend-js/testFiles/apiCalls/project/getClosestElementsByCoordinates/coordinates=26547.33,40201.07&count=1&modelId=15781&projectId=sample&token=MOCK_TOKEN_ID&
create mode 100644 frontend-js/testFiles/apiCalls/project/getElements/columns=&id=329156,329162,329174,329180&projectId=sample&token=MOCK_TOKEN_ID&
create mode 100644 frontend-js/testFiles/apiCalls/project/getElements/columns=id,bounds,modelId&id=329173&projectId=sample&token=MOCK_TOKEN_ID&
create mode 100644 frontend-js/testFiles/apiCalls/project/getReactions/columns=&id=153515&projectId=sample&token=MOCK_TOKEN_ID&
diff --git a/frontend-js/src/main/js/ServerConnector.js b/frontend-js/src/main/js/ServerConnector.js
index 70b703de56..1de30ae567 100644
--- a/frontend-js/src/main/js/ServerConnector.js
+++ b/frontend-js/src/main/js/ServerConnector.js
@@ -43,13 +43,6 @@ ServerConnector.formIdentifier = "_gmapForm";
ServerConnector._customMap = null;
-/**
- * Sets search query that will be handled by server.
- */
-ServerConnector.setSearchQuery = function(value) {
- document.getElementById(ServerConnector.formIdentifier + ':mapParam').value = "" + value;
-};
-
/**
* Sets data mining query that will be handled by server.
*/
@@ -153,11 +146,6 @@ ServerConnector.updateOverlayCollection = function(overlayName, data, fitBounds)
}
};
-/**
- * Name of the overlay for 'search' overlay.
- */
-ServerConnector.SEARCH_OVERLAY_NAME = 'search';
-
/**
* Name of the overlay for 'data mining' overlay.
*/
@@ -178,30 +166,6 @@ ServerConnector.CHEMICAL_OVERLAY_NAME = 'chemical';
*/
ServerConnector.MI_RNA_OVERLAY_NAME = 'mirna';
-/**
- * Register 'search' overlay on the server.
- */
-ServerConnector.registerSearchOverlay = function() {
- _registerSearchOverlayCollection([ {
- name : "overlayName",
- value : ServerConnector.SEARCH_OVERLAY_NAME,
- } ]);
-};
-
-/**
- * Sends request to the server to refresh data in 'search' overlay.
- */
-ServerConnector.refreshSearchOverlay = function() {
- _refreshSearchOverlayCollection();
-};
-
-/**
- * Clear data related to 'search' overlay..
- */
-ServerConnector.clearSearchOverlay = function() {
- _clearSearchOverlayCollection();
-};
-
/**
* Register 'data mining' overlay on the server.
*/
@@ -351,15 +315,6 @@ ServerConnector.clearMiRnaOverlay = function() {
_clearMiRnaOverlayCollection();
};
-/**
- * Define pack of methods for 'search' overlay.
- */
-ServerConnector._overlayMethods[ServerConnector.SEARCH_OVERLAY_NAME] = {
- initFunction : ServerConnector.registerSearchOverlay,
- refreshFunction : ServerConnector.refreshSearchOverlay,
- clearFunction : ServerConnector.clearSearchOverlay,
-};
-
/**
* Define pack of methods for 'data minig' overlay.
*/
@@ -495,19 +450,6 @@ ServerConnector.addReactions = function(jsonReactions) {
this.getCustomMap().addReactions(jsonReactions);
};
-ServerConnector.searchByCoord = function(modelId, latLngCoordinates) {
- _searchByCoord([ {
- name : 'submodelId',
- value : modelId
- }, {
- name : 'latCoord',
- value : latLngCoordinates.lat()
- }, {
- name : 'lngCoord',
- value : latLngCoordinates.lng()
- } ]);
-};
-
ServerConnector.sendReferenceGenomeDetailRequest = function(type, version) {
logger.debug("Send request", type, version);
_sendReferenceGenomeDetailRequest([ {
@@ -726,7 +668,7 @@ ServerConnector.idsToString = function (ids) {
};
ServerConnector.pointToString = function (point) {
- return point.x+","+point.y;
+ return point.x.toFixed(2)+","+point.y.toFixed(2);
};
ServerConnector.columnsToString = function (columns) {
@@ -781,13 +723,15 @@ ServerConnector.getClosestElementsByCoordinatesUrl = function(params) {
var projectId = params.projectId;
var modelId = params.modelId;
var token = params.token;
+ var count = params.count;
return this.getApiUrl({type:"project",
method:"getClosestElementsByCoordinates",
params: {
projectId: projectId,
coordinates: coordinates,
- modelId: modelId,
+ modelId: modelId,
+ count: count,
token: token},
});
};
@@ -1020,13 +964,13 @@ ServerConnector.getSessionData = function(project) {
ServerConnector.getClosestElementsByCoordinates = function(params) {
var self = this;
- var projectId;
return new Promise(function(resolve, reject) {
return self.getProjectId(params.projectId).then(function(result) {
- projectId = result;
+ params.projectId = result;
return self.getToken();
}).then(function(token) {
- return self.readFile(self.getClosestElementsByCoordinatesUrl({projectId:projectId, token:token, modelId:params.modelId, coordinates: params.coordinates}));
+ params.token = token;
+ return self.readFile(self.getClosestElementsByCoordinatesUrl(params));
}).then(function(content) {
var array=JSON.parse(content);
var result = [];
diff --git a/frontend-js/src/main/js/map/AbstractCustomMap.js b/frontend-js/src/main/js/map/AbstractCustomMap.js
index 5263499926..7a70a061cc 100644
--- a/frontend-js/src/main/js/map/AbstractCustomMap.js
+++ b/frontend-js/src/main/js/map/AbstractCustomMap.js
@@ -313,7 +313,11 @@ AbstractCustomMap.prototype.registerMapClickEvents = function() {
// search event
google.maps.event.addListener(this.getGoogleMap(), 'click', function(mouseEvent) {
- ServerConnector.searchByCoord(self.getId(), mouseEvent.latLng);
+ var point = self.fromLatLngToPoint(mouseEvent.latLng);
+ var searchDb = customMap.getOverlayByName('search');
+ return searchDb.searchByCoordinates(self.getModel(), point).then(function() {
+ return customMap.updateOverlayCollection(searchDb, false);
+ }).catch(GuiConnector.alert);
});
// select last clicked map
@@ -685,8 +689,8 @@ AbstractCustomMap.prototype.getAliasVisibleLayoutsData = function(aliasId) {
for (var i = 0; i < layoutIds.length; i++) {
promises.push(this.getModel().getLayoutDataById(layoutIds[i]));
}
- return new Promise(function(resolve){
- return Promise.all(promises).then(function(layouts){
+ return new Promise(function(resolve) {
+ return Promise.all(promises).then(function(layouts) {
var result = [];
for (var i = 0; i < layouts.length; i++) {
var layout = layouts[i];
diff --git a/frontend-js/src/main/js/map/CustomMap.js b/frontend-js/src/main/js/map/CustomMap.js
index 9e3d6a61b5..689281d9de 100644
--- a/frontend-js/src/main/js/map/CustomMap.js
+++ b/frontend-js/src/main/js/map/CustomMap.js
@@ -16,6 +16,7 @@ var PointMarker = require('./marker/PointMarker');
var ReactionMarker = require('./marker/ReactionMarker');
var ReactionOverlay = require('./overlay/ReactionOverlay');
var ReferenceGenome = require('./data/ReferenceGenome');
+var SearchDbCollection = require('./overlay/SearchDbOverlay');
var Submap = require('./Submap');
var TouchMap = require('./TouchMap');
@@ -214,7 +215,9 @@ CustomMap.prototype.refreshOverlays = function() {
for ( var overlayName in this.overlayCollections) {
if (this.overlayCollections.hasOwnProperty(overlayName)) {
var collection = this.overlayCollections[overlayName];
- promises.push(collection.refresh());
+ if (!collection instanceof SearchDbCollection) {
+ promises.push(collection.refresh());
+ }
}
}
return Promise.all(promises);
@@ -549,25 +552,16 @@ CustomMap.prototype.refreshOverlayMarkers = function(overlay) {
if (overlay.reactionMarkers.hasOwnProperty(reactionKey) && overlay.reactionMarkers[reactionKey] !== undefined
&& overlay.reactionMarkers[reactionKey] !== null) {
var reactionOverlay = overlay.reactionMarkers[reactionKey];
- if (reactionOverlay.getReactionData() === null || reactionOverlay.getReactionData() === undefined) {
- reactionOverlay.getCustomMap().getModel().getReactionById(reactionOverlay.getId()).then(function(reactionData) {
- reactionOverlay.setReactionData(reactionData);
- reactionOverlay.init();
- reactionOverlay.show();
- updated = true;
- bounds = reactionOverlay.getBounds();
- boundsArray[reactionOverlay.getCustomMap().getId()].extend(bounds.getNorthEast());
- boundsArray[reactionOverlay.getCustomMap().getId()].extend(bounds.getSouthWest());
- });
- } else {
- bounds = reactionOverlay.getBounds();
- if (!this.isMarkerOptimization()) {
- reactionOverlay.hide();
- reactionOverlay.show();
- }
- boundsArray[reactionOverlay.getCustomMap().getId()].extend(bounds.getNorthEast());
- boundsArray[reactionOverlay.getCustomMap().getId()].extend(bounds.getSouthWest());
+ if (!reactionOverlay.isShown()) {
+ reactionOverlay.show();
+ }
+ bounds = reactionOverlay.getBounds();
+ if (!this.isMarkerOptimization()) {
+ reactionOverlay.hide();
+ reactionOverlay.show();
}
+ boundsArray[reactionOverlay.getCustomMap().getId()].extend(bounds.getNorthEast());
+ boundsArray[reactionOverlay.getCustomMap().getId()].extend(bounds.getSouthWest());
}
}
@@ -1356,70 +1350,75 @@ CustomMap.prototype.renderOverlayCollection = function(overlayCollection, fitBou
fitBounds = overlayCollection.fitBounds;
overlayCollection = overlayCollection.overlayCollection;
}
+
+ var elements;
+
+ return overlayCollection.getIdentifiedElements().then(function(identifiedElements){
+ elements = identifiedElements;
+ var boundsArray = [];
+ boundsArray[self.getId()] = new google.maps.LatLngBounds();
+ for (var j = 0; j < self.submaps.length; j++) {
+ boundsArray[self.submaps[j].getId()] = new google.maps.LatLngBounds();
+ }
- var elements = overlayCollection.getIdentifiedElements();
-
- var boundsArray = [];
- boundsArray[this.getId()] = new google.maps.LatLngBounds();
- for (var j = 0; j < this.submaps.length; j++) {
- boundsArray[this.submaps[j].getId()] = new google.maps.LatLngBounds();
- }
-
- var bounds;
-
- return Promise.each(
- elements,
- function(element) {
- var model = self.getSubmodelById(element.modelId);
- if (element.getType() === "ALIAS") {
- if (overlayCollection.aliasMarkers[element.getId()] !== undefined) {
- logger.warn("More than one marker in " + overlayCollection.name + " for alias " + element.getId()
- + ". Skipping duplicates.");
- return null;
- } else {
- return model.getModel().getAliasById(element.getId()).then(function(aliasData) {
- var aliasMarker = new AliasMarker(element.getId(), element.icon, aliasData, model);
- overlayCollection.aliasMarkers[element.getId()] = aliasMarker;
- bounds = aliasMarker.getBounds();
+ var bounds;
+
+ return Promise.each(
+ elements,
+ function(element) {
+ var model = self.getSubmodelById(element.modelId);
+ if (element.getType() === "ALIAS") {
+ if (overlayCollection.aliasMarkers[element.getId()] !== undefined) {
+ logger.warn("More than one marker in " + overlayCollection.name + " for alias " + element.getId()
+ + ". Skipping duplicates.");
+ return null;
+ } else {
+ return model.getModel().getAliasById(element.getId()).then(function(aliasData) {
+ var aliasMarker = new AliasMarker(element.getId(), element.icon, aliasData, model);
+ overlayCollection.aliasMarkers[element.getId()] = aliasMarker;
+ bounds = aliasMarker.getBounds();
+ boundsArray[element.getModelId()].extend(bounds.getNorthEast());
+ boundsArray[element.getModelId()].extend(bounds.getSouthWest());
+ return aliasMarker;
+ });
+ }
+ } else if (element.getType() === "REACTION") {
+ return model.getModel().getReactionById(element.getId()).then(function(reactionData) {
+ var marker = null;
+ var icon = element.getIcon();
+
+ if (icon === null || icon === undefined) {
+ // this should happen when we visualize search data (there is
+ // no marker, but only flat overlay of the reaction lines)
+ //
+ marker = new ReactionOverlay(null, reactionData, model, false, element.getId());
+ } else {
+ // when we have icon defined (for instance when it comes from
+ // comment) then we don't want to have overlayed reaction lines
+ // but icon marker
+ marker = new ReactionMarker(element.getId(), icon, reactionData, model);
+ }
+ marker.show();
+ overlayCollection.reactionMarkers[element.getId()] = marker;
+ bounds = marker.getBounds();
boundsArray[element.getModelId()].extend(bounds.getNorthEast());
boundsArray[element.getModelId()].extend(bounds.getSouthWest());
- return aliasMarker;
+ return marker;
});
- }
- } else if (element.getType() === "REACTION") {
- return model.getModel().getReactionById(element.getId()).then(function(reactionData) {
- var marker = null;
- var icon = element.getIcon();
-
- if (icon === null || icon === undefined) {
- // this should happen when we visualize search data (there is
- // no marker, but only flat overlay of the reaction lines)
- //
- marker = new ReactionOverlay(null, reactionData, model, false, element.getId());
- } else {
- // when we have icon defined (for instance when it comes from
- // comment) then we don't want to have overlayed reaction lines
- // but icon marker
- marker = new ReactionMarker(element.getId(), icon, reactionData, model);
- }
- overlayCollection.reactionMarkers[element.getId()] = marker;
- bounds = marker.getBounds();
+ } else if (element.getType() === "POINT") {
+ var pointData = model.getModel().getPointDataByPoint(element.getPoint());
+ var pointMarker = new PointMarker(pointData, element.icon, model);
+ overlayCollection.pointMarkers[pointData.getId()] = pointMarker;
+ bounds = pointMarker.getBounds();
boundsArray[element.getModelId()].extend(bounds.getNorthEast());
boundsArray[element.getModelId()].extend(bounds.getSouthWest());
- return marker;
- });
- } else if (element.getType() === "POINT") {
- var pointData = model.getModel().getPointDataByPoint(element.getPoint());
- var pointMarker = new PointMarker(pointData, element.icon, model);
- overlayCollection.pointMarkers[pointData.getId()] = pointMarker;
- bounds = pointMarker.getBounds();
- boundsArray[element.getModelId()].extend(bounds.getNorthEast());
- boundsArray[element.getModelId()].extend(bounds.getSouthWest());
- return pointMarker;
- } else {
- throw new Error("Unknown type of the element in overlay: " + element.type);
- }
- }).then(function() {
+ return pointMarker;
+ } else {
+ throw new Error("Unknown type of the element in overlay: " + element.type);
+ }
+ });
+ }).then(function() {
+
for (var i = 0; i < elements.length; i++) {
var element = elements[i];
var infoWindow = self.getInfoWindowForIdentifiedElement(element);
@@ -1447,6 +1446,8 @@ CustomMap.prototype.renderOverlayCollection = function(overlayCollection, fitBou
});
+
+
};
/**
@@ -1646,6 +1647,10 @@ CustomMap.prototype.getOverlayDataForIdentifiedElement = function(identifiedElem
});
};
+CustomMap.prototype.getOverlayByName = function(name) {
+ return this.overlayCollections[name];
+};
+
/**
* Returns {@link AbstractInfoWindow} for element identified by the parameter.
*
diff --git a/frontend-js/src/main/js/map/data/IdentifiedElement.js b/frontend-js/src/main/js/map/data/IdentifiedElement.js
index 4b849f949b..5f4730bad2 100644
--- a/frontend-js/src/main/js/map/data/IdentifiedElement.js
+++ b/frontend-js/src/main/js/map/data/IdentifiedElement.js
@@ -21,15 +21,15 @@ function IdentifiedElement(javaObject) {
if (javaObject instanceof Alias) {
this.setId(javaObject.getId());
this.setModelId(javaObject.getModelId());
- this.type = "ALIAS";
+ this.setType("ALIAS");
} else if (javaObject instanceof Reaction) {
this.setId(javaObject.getId());
this.setModelId(javaObject.getModelId());
- this.type = "REACTION";
+ this.setType("REACTION");
} else if (javaObject instanceof PointData) {
this.setId(javaObject.getId());
this.setModelId(javaObject.getModelId());
- this.type = "POINT";
+ this.setType("POINT");
} else {
// identifier of the object to visualize
if (javaObject.objectId === undefined) {
@@ -38,19 +38,14 @@ function IdentifiedElement(javaObject) {
this.setId(javaObject.objectId);
}
// which marker should be used to show this object
- this.icon = javaObject.icon;
+ this.setIcon(javaObject.icon);
// on which model the element is located
this.setModelId(javaObject.modelId);
// what kind of object we are talking about
- this.type = javaObject.type;
+ this.setType(javaObject.type);
}
- if (this.type === undefined || this.type === null) {
- throw new Error("Type not defined for element: " + javaObject);
- }
-
- this.type = this.type.toUpperCase();
- if (this.type === "POINT") {
+ if (this.getType() === "POINT") {
var tmp = this.getId();
if (tmp.indexOf("Point2D.Double") >= 0) {
tmp = tmp.replace("Point2D.Double", "");
@@ -63,8 +58,8 @@ function IdentifiedElement(javaObject) {
var x = parseFloat(tmp[0]).toFixed(2);
var y = parseFloat(tmp[1]).toFixed(2);
this._point = new google.maps.Point(x, y);
- } else if (this.type !== "ALIAS" && this.type !== "REACTION") {
- throw new Error("Unknown type of identified element: " + this.type);
+ } else if (this.getType() !== "ALIAS" && this.getType() !== "REACTION") {
+ throw new Error("Unknown type of identified element: " + this.getType());
}
if (this.getId() === undefined || this.getId() === null) {
@@ -137,6 +132,14 @@ IdentifiedElement.prototype.getType = function() {
return this.type;
};
+IdentifiedElement.prototype.setType = function(type) {
+ if (type === undefined || type === null) {
+ throw new Error("Type not defined");
+ }
+
+ this.type = type.toUpperCase();
+};
+
/**
* Returns icon that should be used for visualization.
*
@@ -146,4 +149,8 @@ IdentifiedElement.prototype.getIcon = function() {
return this.icon;
};
+IdentifiedElement.prototype.setIcon = function(icon) {
+ this.icon = icon;
+};
+
module.exports = IdentifiedElement;
diff --git a/frontend-js/src/main/js/map/data/MapModel.js b/frontend-js/src/main/js/map/data/MapModel.js
index 6201f0a402..c7370e2973 100644
--- a/frontend-js/src/main/js/map/data/MapModel.js
+++ b/frontend-js/src/main/js/map/data/MapModel.js
@@ -177,7 +177,7 @@ MapModel.prototype.getReactionById = function(id, complete) {
MapModel.prototype.getCompleteReactionById = function(id) {
var self = this;
return new Promise(function(resolve) {
- if (self._reactions[id]!==undefined && self._reactions[id].isComplete()) {
+ if (self._reactions[id] instanceof Reaction && self._reactions[id].isComplete()) {
resolve(self._reactions[id]);
} else {
var result;
@@ -296,7 +296,6 @@ MapModel.prototype.getMissingElements = function(elements) {
}
}
-
return new Promise(function(resolve, reject) {
Promise.all([reactionPromise, aliasPromise]).then(function(values) {
var result = [], i;
diff --git a/frontend-js/src/main/js/map/data/Reaction.js b/frontend-js/src/main/js/map/data/Reaction.js
index 8b6aae5848..395353c819 100644
--- a/frontend-js/src/main/js/map/data/Reaction.js
+++ b/frontend-js/src/main/js/map/data/Reaction.js
@@ -39,7 +39,7 @@ function Reaction(javaObject) {
}
this.setCenter(javaObject.centerPoint);
this.setModelId(javaObject.modelId);
- this.setCompletness(false);
+ this.setIsComplete(false);
this.update(javaObject);
}
}
@@ -112,12 +112,12 @@ Reaction.prototype.update = function(javaObject) {
}
};
-Reaction.prototype.getCompletness = function() {
- return this._completness;
+Reaction.prototype.isComplete = function() {
+ return this._complete;
};
-Reaction.prototype.setCompletness = function(completness) {
- this._completness = completness;
+Reaction.prototype.setIsComplete = function(complete) {
+ this._complete = complete;
};
Reaction.prototype.getReactionId = function() {
@@ -144,6 +144,14 @@ Reaction.prototype.getProducts = function() {
return this._products;
};
+Reaction.prototype.getElements = function() {
+ var result = [];
+ result = result.concat(this.getReactants());
+ result = result.concat(this.getProducts());
+ result = result.concat(this.getModifiers());
+ return result;
+};
+
Reaction.prototype.setModifiers = function(modifiers) {
this._modifiers = modifiers;
};
diff --git a/frontend-js/src/main/js/map/overlay/CommentDbOverlay.js b/frontend-js/src/main/js/map/overlay/CommentDbOverlay.js
index 41df64f1cc..abbbec7715 100644
--- a/frontend-js/src/main/js/map/overlay/CommentDbOverlay.js
+++ b/frontend-js/src/main/js/map/overlay/CommentDbOverlay.js
@@ -43,14 +43,17 @@ CommentDbOverlay.prototype._getDetailArrayByIdentifiedElement = function(element
CommentDbOverlay.prototype.getIdentifiedElements = function(){
- var result = [];
- for (var i=0;i<this.elements.length;i++) {
- //we return only elements that are pinned to the map and weren't removed
- if (!this.elements[i].isRemoved()) {
- result.push(this.elements[i].getIdentifiedElement());
+ var self = this;
+ return new Promise(function(resolve){
+ var result = [];
+ for (var i=0;i<self.elements.length;i++) {
+ // we return only elements that are pinned to the map and weren't removed
+ if (!self.elements[i].isRemoved()) {
+ result.push(self.elements[i].getIdentifiedElement());
+ }
}
- }
- return result;
+ resolve(result);
+ });
};
diff --git a/frontend-js/src/main/js/map/overlay/OverlayCollection.js b/frontend-js/src/main/js/map/overlay/OverlayCollection.js
index c1fff1bcb6..0679d67318 100644
--- a/frontend-js/src/main/js/map/overlay/OverlayCollection.js
+++ b/frontend-js/src/main/js/map/overlay/OverlayCollection.js
@@ -236,8 +236,34 @@ OverlayCollection.prototype.setAllowGeneralSearch = function(allowGeneralSearch)
}
};
-OverlayCollection.prototype.getIdentifiedElements = function(){
- return this.elements;
+OverlayCollection.prototype.getIdentifiedElements = function() {
+ var self = this;
+ return new Promise(function(resolve) {
+ resolve(self.elements);
+ });
+};
+
+OverlayCollection.prototype.setIconType = function(iconType) {
+ return this._iconType = iconType;
+};
+OverlayCollection.prototype.setIconStart = function(iconStart) {
+ return this._iconStart = iconStart;
+};
+
+OverlayCollection.IconColors = [ "red", "blue", "green", "purple", "yellow", "pink", "paleblue", "brown", "orange" ];
+
+OverlayCollection.prototype.getColor = function(colorId) {
+ var id = colorId + this._iconStart;
+ id %= OverlayCollection.IconColors.length;
+ return OverlayCollection.IconColors[id];
+}
+
+OverlayCollection.prototype.getIcon = function(colorId, id) {
+ if (id >= 100) {
+ id = 1;
+ }
+ var color = this.getColor(colorId);
+ return "marker/" + this._iconType + "/" + this._iconType + "_" + color + "_" + id + ".png";
};
module.exports = OverlayCollection;
diff --git a/frontend-js/src/main/js/map/overlay/SearchDbOverlay.js b/frontend-js/src/main/js/map/overlay/SearchDbOverlay.js
new file mode 100644
index 0000000000..be7537e826
--- /dev/null
+++ b/frontend-js/src/main/js/map/overlay/SearchDbOverlay.js
@@ -0,0 +1,106 @@
+"use strict";
+
+var Promise = require("bluebird");
+
+var Alias = require('../data/Alias');
+var IdentifiedElement = require('../data/IdentifiedElement');
+var OverlayCollection = require('./OverlayCollection');
+
+var logger = require('../../logger');
+
+function SearchDbOverlay(params) {
+ // call super constructor
+ OverlayCollection.call(this, params);
+
+ this.setIconType("marker");
+ this.setIconStart(0);
+ this._elementsByQuery = [];
+}
+
+SearchDbOverlay.prototype = Object.create(OverlayCollection.prototype);
+SearchDbOverlay.prototype.constructor = SearchDbOverlay;
+
+SearchDbOverlay.QueryType = {
+ SEARCH_BY_COORDINATES : "SEARCH_BY_COORDINATES",
+ SEARCH_BY_QUERY : "SEARCH_BY_QUERY",
+};
+
+function encodeQuery(type, model, arg){
+ if (type === SearchDbOverlay.QueryType.SEARCH_BY_COORDINATES) {
+ return type + "_"+model.getId()+"_"+arg.x+","+arg.y;
+ } else {
+ throw new Error("Unknown query type: "+type);
+ }
+}
+
+SearchDbOverlay.prototype.searchByCoordinates = function(model, coordinates) {
+ var self = this;
+ return new Promise(function(resolve, reject) {
+ var query = encodeQuery(SearchDbOverlay.QueryType.SEARCH_BY_COORDINATES, model, coordinates);
+ self.setQueries([query]);
+
+ if (self._elementsByQuery[query] !== undefined) {
+ resolve(self._elementsByQuery[query]);
+ } else {
+ return ServerConnector.getClosestElementsByCoordinates({
+ modelId:model.getId(), coordinates: coordinates, count: 1
+ }).then(function(elements) {
+ self._elementsByQuery[query] = elements;
+ if (elements[0].getType()==="REACTION") {
+ var model = self.getMap().getSubmodelById(elements[0].getModelId()).getModel();
+ return model.getReactionById(elements[0].getId(), true).then(function(reaction){
+ var i=0;
+ var reactionElements = reaction.getElements();
+ for (i=0;i<reactionElements.length;i++) {
+ self._elementsByQuery[query].push(new IdentifiedElement(reactionElements[i]));
+ }
+ resolve(self._elementsByQuery[query]);
+ }).catch(reject);
+ } else {
+ resolve(self._elementsByQuery[query]);
+ }
+ }).catch(reject);
+ }
+ });
+};
+
+SearchDbOverlay.prototype.setQueries = function(queries){
+ this._queries = queries;
+};
+
+SearchDbOverlay.prototype.getQueries = function(){
+ return this._queries ;
+};
+
+SearchDbOverlay.prototype.getIdentifiedElements = function(){
+ var self = this;
+
+ return new Promise(function(resolve){
+ var queries = self.getQueries();
+ var result = [];
+ for (var i=0;i<queries.length;i++) {
+ var query = queries[i];
+ var elements = self._elementsByQuery[query];
+
+ var iconCounter =1;
+ for (var j=0;j<elements.length;j++) {
+ var element = elements[j];
+ var ie = new IdentifiedElement(element);
+ if (element.getType() === "ALIAS") {
+ ie.setIcon(self.getIcon(i, iconCounter++));
+ } else if (element.getType() !== "REACTION") {
+ throw new Error("Unknown element type: "+element.getType());
+ }
+ result.push(ie);
+ }
+ }
+ resolve(result);
+ });
+};
+
+SearchDbOverlay.prototype.refresh = function(){
+ throw new Error("Refreshing shouldn't be called");
+};
+
+
+module.exports = SearchDbOverlay;
diff --git a/frontend-js/src/main/js/minerva.js b/frontend-js/src/main/js/minerva.js
index 3aab0b86ef..daf8c324d7 100644
--- a/frontend-js/src/main/js/minerva.js
+++ b/frontend-js/src/main/js/minerva.js
@@ -5,6 +5,7 @@ var functions = require('./Functions');
var CommentDbOverlay = require('./map/overlay/CommentDbOverlay');
var CustomMap = require('./map/CustomMap');
var OverlayCollection = require('./map/overlay/OverlayCollection');
+var SearchDbOverlay = require('./map/overlay/SearchDbOverlay');
var OriginalGuiConnector = require('./GuiConnector');
var OriginalServerConnector = require('./ServerConnector');
@@ -75,6 +76,8 @@ function create(params) {
var collection = null;
if (collectionParams.name === "comment") {
collection = new CommentDbOverlay(collectionParams);
+ } else if (collectionParams.name === "search") {
+ collection = new SearchDbOverlay(collectionParams);
} else {
collection = new OverlayCollection(collectionParams);
}
diff --git a/frontend-js/src/test/js/ServerConnector-mock.js b/frontend-js/src/test/js/ServerConnector-mock.js
index 0f84b28d5a..1819d39311 100644
--- a/frontend-js/src/test/js/ServerConnector-mock.js
+++ b/frontend-js/src/test/js/ServerConnector-mock.js
@@ -108,18 +108,6 @@ ServerConnectorMock.sendOverlayDetailDataRequest = function(overlayName, identif
ServerConnectorMock.callListeners("onSendOverlayDetailDataRequest", overlayName, identifiedElement);
};
-ServerConnectorMock.searchByCoord = function(modelId, latLngCoordinates) {
- ServerConnectorMock.callListeners("onSearchByCoord", [ modelId, latLngCoordinates ]);
-};
-
-ServerConnectorMock.setCustomMap = function(customMap) {
- this._customMap = customMap;
-};
-
-ServerConnectorMock.getCustomMap = function() {
- return this._customMap;
-};
-
ServerConnectorMock.addOverlayCollection = function(overlay) {
logger.debug("Adding overlay: " + overlay);
};
diff --git a/frontend-js/src/test/js/google-map-mock.js b/frontend-js/src/test/js/google-map-mock.js
index 949e0a8474..da21005981 100644
--- a/frontend-js/src/test/js/google-map-mock.js
+++ b/frontend-js/src/test/js/google-map-mock.js
@@ -15,12 +15,14 @@ var google = {
object.addEventListener(type, fun);
},
trigger : function(object, type, param) {
+ var promises = [];
for (var i = 0; i < google.maps.event._data.length; i++) {
var e = google.maps.event._data[i];
if (e.object === object && e.type === type) {
- e.fun(param);
+ promises.push(e.fun(param));
}
}
+ return Promise.all(promises);
},
},
drawing : {
@@ -61,15 +63,44 @@ var google = {
};
},
LatLngBounds : function(ne, sw) {
+ var data = {
+ ne : ne,
+ sw : sw
+ };
return {
getSouthWest : function() {
- return sw;
+ return data.sw;
},
getNorthEast : function() {
- return ne;
+ return data.ne;
+ },
+ isEmpty : function() {
+ return ne === sw || (data.ne.lat() === sw.lat() && data.ne.lng() === sw.lng());
},
- extend : function() {
+ extend : function(arg) {
+ if (data.sw === undefined) {
+ data.sw = arg;
+ } else {
+ if (arg.lng() < data.sw.lng()) {
+ data.sw.longitude = arg.lng();
+ }
+ if (arg.lat() < data.sw.lat()) {
+ data.sw.longitude = arg.lng();
+ }
+ }
+ if (data.ne === undefined) {
+ data.ne = arg;
+ } else {
+ if (arg.lng() > data.ne.lng()) {
+ data.ne.longitude = arg.lng();
+ }
+
+ if (arg.lat() > data.ne.lat()) {
+ data.ne.longitude = arg.lng();
+ }
+ }
},
+
};
},
OverlayView : function() {
@@ -97,6 +128,7 @@ var google = {
},
Marker : function(options) {
this.options = options;
+ this.position = options.position;
this.getMap = function() {
return this.options.map;
};
diff --git a/frontend-js/src/test/js/helper.js b/frontend-js/src/test/js/helper.js
index 7a61d23de1..b7001fdb64 100644
--- a/frontend-js/src/test/js/helper.js
+++ b/frontend-js/src/test/js/helper.js
@@ -16,6 +16,7 @@ var Model = require("../../main/js/map/data/MapModel");
var OverlayCollection = require("../../main/js/map/overlay/OverlayCollection");
var Project = require("../../main/js/map/data/Project");
var Reaction = require("../../main/js/map/data/Reaction");
+var SearchDbOverlay = require("../../main/js/map/overlay/SearchDbOverlay");
function Helper() {
this.idCounter = 1000000;
@@ -30,6 +31,16 @@ Helper.prototype.createCommentDbOverlay = function(map) {
return result;
};
+Helper.prototype.createSearchDbOverlay = function(map) {
+ var result = new SearchDbOverlay({
+ map : map,
+ name : "search",
+ });
+ return result;
+};
+
+
+
Helper.prototype.createDrugDbOverlay = function(map) {
var result = this.createDbOverlay(map);
result.setName('drug');
diff --git a/frontend-js/src/test/js/map/CustomMap-test.js b/frontend-js/src/test/js/map/CustomMap-test.js
index c7d46c095a..3eebf279e5 100644
--- a/frontend-js/src/test/js/map/CustomMap-test.js
+++ b/frontend-js/src/test/js/map/CustomMap-test.js
@@ -467,18 +467,43 @@ describe('CustomMap', function() {
assert.equal(map.getId(), map.getActiveSubmapId());
});
+
it("left click on map", function() {
var map = helper.createCustomMap();
-
+ map.getModel().setId(15781);
+
+ var searchOverlay = helper.createSearchDbOverlay(map);
+
var mev = {
stop : null,
latLng : new google.maps.LatLng(40.0, -90.0)
};
assert.notOk(map.getActiveSubmapId());
- google.maps.event.trigger(map.getGoogleMap(), 'click', mev);
- assert.equal(map.getId(), map.getActiveSubmapId());
+ return google.maps.event.trigger(map.getGoogleMap(), 'click', mev).then(function(){
+ assert.equal(map.getId(), map.getActiveSubmapId());
+ assert.ok(searchOverlay.aliasMarkers[329173]);
+ });
+ });
+ it("left click on reaction", function() {
+ var map = helper.createCustomMap();
+ map.getModel().setId(15781);
+
+ var searchOverlay = helper.createSearchDbOverlay(map);
+
+ var mev = {
+ stop : null,
+ latLng : new google.maps.LatLng(42.0, -90.0)
+ };
+
+ assert.notOk(map.getActiveSubmapId());
+ return google.maps.event.trigger(map.getGoogleMap(), 'click', mev).then(function(){
+ assert.equal(map.getId(), map.getActiveSubmapId());
+ assert.ok(searchOverlay.reactionMarkers[153515]);
+ assert.ok(searchOverlay.reactionMarkers[153515].isShown());
+ assert.ok(searchOverlay.aliasMarkers[329162]);
+ });
});
it("create polygon through drawingManager", function() {
diff --git a/frontend-js/src/test/js/minerva-test.js b/frontend-js/src/test/js/minerva-test.js
index f2252c102d..7dc361355f 100644
--- a/frontend-js/src/test/js/minerva-test.js
+++ b/frontend-js/src/test/js/minerva-test.js
@@ -126,4 +126,22 @@ describe('minerva global', function() {
assert.ok(result);
});
});
+
+ it('create with search overlay', function() {
+ var project = helper.createProject();
+ project.getModel().setId(15781);
+ var map = helper.createGoogleMap();
+
+ var options = {
+ map : map,
+ project : project,
+ dataCollections : [ {
+ name : "search"
+ } ],
+ };
+
+ return minerva.create(options).then(function(result) {
+ assert.ok(result);
+ });
+ });
});
diff --git a/frontend-js/testFiles/apiCalls/comment/addComment/content=&coordinates=2,12&elementId=&elementType=POINT&email=&modelId=102&name=&pinned=false&projectId=sample&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/comment/addComment/content=&coordinates=2.00,12.00&elementId=&elementType=POINT&email=&modelId=102&name=&pinned=false&projectId=sample&token=MOCK_TOKEN_ID&
similarity index 100%
rename from frontend-js/testFiles/apiCalls/comment/addComment/content=&coordinates=2,12&elementId=&elementType=POINT&email=&modelId=102&name=&pinned=false&projectId=sample&token=MOCK_TOKEN_ID&
rename to frontend-js/testFiles/apiCalls/comment/addComment/content=&coordinates=2.00,12.00&elementId=&elementType=POINT&email=&modelId=102&name=&pinned=false&projectId=sample&token=MOCK_TOKEN_ID&
diff --git a/frontend-js/testFiles/apiCalls/project/getClosestElementsByCoordinates/coordinates=2,12&modelId=102&projectId=sample&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/project/getClosestElementsByCoordinates/coordinates=2.00,12.00&modelId=102&projectId=sample&token=MOCK_TOKEN_ID&
similarity index 100%
rename from frontend-js/testFiles/apiCalls/project/getClosestElementsByCoordinates/coordinates=2,12&modelId=102&projectId=sample&token=MOCK_TOKEN_ID&
rename to frontend-js/testFiles/apiCalls/project/getClosestElementsByCoordinates/coordinates=2.00,12.00&modelId=102&projectId=sample&token=MOCK_TOKEN_ID&
diff --git a/frontend-js/testFiles/apiCalls/project/getClosestElementsByCoordinates/coordinates=26547.33,39419.29&count=1&modelId=15781&projectId=sample&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/project/getClosestElementsByCoordinates/coordinates=26547.33,39419.29&count=1&modelId=15781&projectId=sample&token=MOCK_TOKEN_ID&
new file mode 100644
index 0000000000..189815b72b
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/project/getClosestElementsByCoordinates/coordinates=26547.33,39419.29&count=1&modelId=15781&projectId=sample&token=MOCK_TOKEN_ID&
@@ -0,0 +1 @@
+[{"modelId":15781,"id":153515,"type":"REACTION"}]
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/project/getClosestElementsByCoordinates/coordinates=26547.33,40201.07&count=1&modelId=15781&projectId=sample&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/project/getClosestElementsByCoordinates/coordinates=26547.33,40201.07&count=1&modelId=15781&projectId=sample&token=MOCK_TOKEN_ID&
new file mode 100644
index 0000000000..410f869e59
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/project/getClosestElementsByCoordinates/coordinates=26547.33,40201.07&count=1&modelId=15781&projectId=sample&token=MOCK_TOKEN_ID&
@@ -0,0 +1 @@
+[{"modelId":15781,"id":329173,"type":"ALIAS"}]
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/project/getElements/columns=&id=329156,329162,329174,329180&projectId=sample&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/project/getElements/columns=&id=329156,329162,329174,329180&projectId=sample&token=MOCK_TOKEN_ID&
new file mode 100644
index 0000000000..50f4f50347
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/project/getElements/columns=&id=329156,329162,329174,329180&projectId=sample&token=MOCK_TOKEN_ID&
@@ -0,0 +1 @@
+[{"formerSymbols":[],"references":[],"modelId":15781,"synonyms":[],"description":"","type":"Protein","name":"s22","bounds":{"x":918.0,"y":427.0,"width":80.0,"height":40.0},"id":329162},{"formerSymbols":[],"references":[],"modelId":15781,"synonyms":[],"description":"","type":"Protein","name":"s22","bounds":{"x":712.0,"y":384.0,"width":80.0,"height":40.0},"id":329174},{"formerSymbols":[],"references":[],"modelId":15781,"synonyms":[],"description":"","type":"Simple molecule","name":"GDP","bounds":{"x":959.0,"y":271.0,"width":70.0,"height":25.0},"id":329156},{"formerSymbols":[],"references":[],"modelId":15781,"synonyms":[],"description":"","type":"Simple molecule","name":"GTP","bounds":{"x":849.0,"y":309.0,"width":70.0,"height":25.0},"id":329180}]
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/project/getElements/columns=id,bounds,modelId&id=329173&projectId=sample&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/project/getElements/columns=id,bounds,modelId&id=329173&projectId=sample&token=MOCK_TOKEN_ID&
new file mode 100644
index 0000000000..3cd9b0d710
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/project/getElements/columns=id,bounds,modelId&id=329173&projectId=sample&token=MOCK_TOKEN_ID&
@@ -0,0 +1 @@
+[{"modelId":15781,"bounds":{"x":12.0,"y":6.0,"width":80.0,"height":40.0},"id":329173}]
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/project/getReactions/columns=&id=153515&projectId=sample&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/project/getReactions/columns=&id=153515&projectId=sample&token=MOCK_TOKEN_ID&
new file mode 100644
index 0000000000..35ab17dc8b
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/project/getReactions/columns=&id=153515&projectId=sample&token=MOCK_TOKEN_ID&
@@ -0,0 +1 @@
+[{"modelId":15781,"reactants":"329174,329180","reactionId":"re26","id":153515,"type":"State transition","lines":[{"start":{"x":792.0,"y":404.0},"end":{"x":868.3333333333338,"y":377.9999999999997},"type":"START"},{"start":{"x":868.3333333333338,"y":377.9999999999997},"end":{"x":893.6666666666671,"y":378.00000000000017},"type":"MIDDLE"},{"start":{"x":884.0,"y":334.0},"end":{"x":893.6666666666671,"y":378.00000000000017},"type":"START"},{"start":{"x":931.666666666667,"y":378.0000000000009},"end":{"x":918.0,"y":447.0},"type":"END"},{"start":{"x":906.3333333333337,"y":378.00000000000045},"end":{"x":931.666666666667,"y":378.0000000000009},"type":"MIDDLE"},{"start":{"x":906.3333333333337,"y":378.00000000000045},"end":{"x":994.0,"y":296.0},"type":"END"},{"start":{"x":893.6666666666671,"y":378.00000000000017},"end":{"x":896.0000000000005,"y":378.0000000000003},"type":"MIDDLE"},{"start":{"x":906.3333333333337,"y":378.00000000000045},"end":{"x":904.0000000000005,"y":378.0000000000004},"type":"MIDDLE"}],"modifiers":"","centerPoint":{"x":900.0000000000005,"y":378.00000000000034},"products":"329162,329156"}]
\ No newline at end of file
--
GitLab