diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java
index ced49d86ec0d0a3a8de3791e0fe7191e3c22d467..b343f67f1db7df65a5a46d67d28dcc489d090d83 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java
@@ -251,7 +251,7 @@ public class ModelAnnotatorTest extends AnnotationTestFunctions {
Reaction reaction = new Reaction();
reaction.addMiriamData(new MiriamData(MiriamType.PUBMED, "12345"));
List<ImproperAnnotations> result = modelAnnotator.findImproperAnnotations(reaction, list);
- assertEquals(0, result.size());
+ assertEquals("Unexpected improper annotations found: "+result, 0, result.size());
} catch (Exception e) {
e.printStackTrace();
throw e;
diff --git a/frontend-js/src/main/js/ServerConnector.js b/frontend-js/src/main/js/ServerConnector.js
index b104a2e9594062f4e1c88a3f90e6cf8d902f96a0..21c3c3ca56bc926bc58855ef363994536867b65d 100644
--- a/frontend-js/src/main/js/ServerConnector.js
+++ b/frontend-js/src/main/js/ServerConnector.js
@@ -1754,7 +1754,7 @@ ServerConnector.getSessionData = function (project) {
* @param {number} [params.count]
* @param {string[]} [params.type]
*
- * @returns {PromiseLike<IdentifiedElement[]>}
+ * @returns {PromiseLike<IdentifiedElement[]>|Promise<IdentifiedElement[]>}
*/
ServerConnector.getClosestElementsByCoordinates = function (params) {
var self = this;
diff --git a/frontend-js/src/main/js/map/overlay/AbstractDbOverlay.js b/frontend-js/src/main/js/map/overlay/AbstractDbOverlay.js
index 828dde5883177fab14ab5c3d23ad59d5d60153ce..46e8a6d43509b3c1f1253e1d6daaddb5b2c8fa2d 100644
--- a/frontend-js/src/main/js/map/overlay/AbstractDbOverlay.js
+++ b/frontend-js/src/main/js/map/overlay/AbstractDbOverlay.js
@@ -111,7 +111,7 @@ AbstractDbOverlay.prototype.encodeQuery = function (type, arg0, arg1, arg2) {
/**
*
* @param {string} query
- * @returns {any}
+ * @returns {Object}
*/
AbstractDbOverlay.prototype.decodeQuery = function (query) {
return JSON.parse(query);
@@ -231,6 +231,7 @@ AbstractDbOverlay.prototype.refresh = function () {
throw new Error("Refreshing shouldn't be called");
};
+// noinspection JSUnusedLocalSymbols
/**
*
* @param {IdentifiedElement} element
@@ -311,6 +312,14 @@ AbstractDbOverlay.prototype.getMap = function () {
return this._map;
};
+/**
+ *
+ * @returns {Configuration}
+ */
+AbstractDbOverlay.prototype.getConfiguration = function () {
+ return this.getMap().getConfiguration();
+};
+
/**
*
* @param {string} name
diff --git a/frontend-js/src/main/js/map/overlay/SearchDbOverlay.js b/frontend-js/src/main/js/map/overlay/SearchDbOverlay.js
index aba0743abf24bdebd69d926d7cb5705308649560..68c15f0929562f79e611c9f576ee69f54d96edf6 100644
--- a/frontend-js/src/main/js/map/overlay/SearchDbOverlay.js
+++ b/frontend-js/src/main/js/map/overlay/SearchDbOverlay.js
@@ -3,13 +3,16 @@
/* exported logger */
var logger = require('../../logger');
+var Functions = require('../../Functions');
var Promise = require("bluebird");
var AbstractDbOverlay = require('./AbstractDbOverlay');
var Alias = require('../data/Alias');
+var ConfigurationType = require('../../ConfigurationType');
var IdentifiedElement = require('../data/IdentifiedElement');
var InvalidArgumentException = require('../../InvalidArgumentError');
+var Point = require('../canvas/Point');
var Reaction = require('../data/Reaction');
var SearchBioEntityGroup = require('../data/SearchBioEntityGroup');
@@ -91,14 +94,45 @@ SearchDbOverlay.prototype.getElementsByQuery = function (query) {
});
};
+
+/**
+ *
+ * @param {Point} coordinates
+ * @param {IdentifiedElement} compartment
+ * @param {number} maxDistance
+ * @returns {Promise}
+ * @private
+ */
+SearchDbOverlay.prototype._returnCompartmentIfClickOnBorder = function (coordinates, compartment, maxDistance) {
+ var model = this.getMap().getSubmapById(compartment.getModelId()).getModel();
+
+ return model.getByIdentifiedElement(compartment).then(function (result) {
+ var p1 = new Point(result.getX(), result.getY());
+ var p2 = new Point(result.getX() + result.getWidth(), result.getY());
+ var p3 = new Point(result.getX() + result.getWidth(), result.getY() + result.getHeight());
+ var p4 = new Point(result.getX(), result.getY() + result.getHeight());
+ var distance = Functions.distance(coordinates, {start: p1, end: p2});
+ distance = Math.min(distance, Functions.distance(coordinates, {start: p2, end: p3}));
+ distance = Math.min(distance, Functions.distance(coordinates, {start: p3, end: p4}));
+ distance = Math.min(distance, Functions.distance(coordinates, {start: p4, end: p1}));
+
+ if (maxDistance>distance) {
+ return compartment;
+ } else {
+ return undefined;
+ }
+ });
+};
+
/**
*
* @param {IdentifiedElement} identifiedElement
* @param {number} zoomLevel
+ * @param {Point} coordinates
* @returns {Promise}
* @private
*/
-SearchDbOverlay.prototype._getFirstVisibleParentOrObject = function (identifiedElement, zoomLevel) {
+SearchDbOverlay.prototype._getFirstVisibleParentOrObject = function (identifiedElement, zoomLevel, coordinates) {
if (identifiedElement === undefined) {
return Promise.resolve();
}
@@ -109,7 +143,8 @@ SearchDbOverlay.prototype._getFirstVisibleParentOrObject = function (identifiedE
if (fullElement instanceof Alias) {
//transparent compartments shouldn't be clickable
if (fullElement.getTransparencyLevel() <= zoomLevel && fullElement.getType() === "Compartment") {
- return undefined;
+ var maxDistance = self.computeMaxDistance(model, zoomLevel);
+ return self._returnCompartmentIfClickOnBorder(coordinates, identifiedElement, maxDistance);
}
}
return identifiedElement;
@@ -128,7 +163,7 @@ SearchDbOverlay.prototype._getFirstVisibleParentOrObject = function (identifiedE
type: "ALIAS",
modelId: identifiedElement.getModelId()
});
- return self._getFirstVisibleParentOrObject(parent, zoomLevel);
+ return self._getFirstVisibleParentOrObject(parent, zoomLevel, coordinates);
} else {
logger.warn("Cannot find visible parent for object. (zoomLevel=" + zoomLevel + ")");
logger.warn(fullElement);
@@ -138,12 +173,58 @@ SearchDbOverlay.prototype._getFirstVisibleParentOrObject = function (identifiedE
});
};
+/**
+ *
+ * @param {MapModel} model
+ * @param {number} zoom
+ * @returns {number}
+ */
+SearchDbOverlay.prototype.computeMaxDistance = function (model, zoom) {
+ var distance = parseFloat(this.getConfiguration().getOption(ConfigurationType.SEARCH_DISTANCE).getValue());
+ var maxZoom = model.getMaxZoom();
+ var zoomDiff = maxZoom - zoom;
+ for (var i = 0; i < zoomDiff; i++) {
+ distance = distance * 1.5;
+ }
+ return distance;
+};
+
+/**
+ *
+ * @param {Point} coordinates
+ * @param {number} zoom
+ * @param {MapModel} model
+ * @param {number} maxDistance
+ * @returns {PromiseLike<T | never> | Promise<T | never>}
+ */
+SearchDbOverlay.prototype.findCompartmentByCoordinates = function (coordinates, zoom, model, maxDistance) {
+ var self = this;
+ return ServerConnector.getClosestElementsByCoordinates({
+ modelId: model.getId(),
+ coordinates: coordinates,
+ count: 1,
+ type: ["Compartment"]
+ }).then(function (elements) {
+ var nestedOverlay = "Pathways and compartments";
+ if (elements.length === 0) {
+ return undefined;
+ } else {
+ if (self.getMap().getBackgroundDataOverlay().getName() === nestedOverlay) {
+ return self._getFirstVisibleParentOrObject(elements[0], zoom - model.getMinZoom(), coordinates);
+ } else {
+ return self._returnCompartmentIfClickOnBorder(coordinates, elements[0], maxDistance);
+ }
+ }
+ });
+};
+
/**
*
* @param {Object} params
* @param {number} params.modelId
* @param {Point} params.coordinates
* @param {number} params.zoom
+ * @param {boolean} [params.fitBounds]
* @returns {Promise| PromiseLike}
*/
SearchDbOverlay.prototype.searchByCoordinates = function (params) {
@@ -167,31 +248,23 @@ SearchDbOverlay.prototype.searchByCoordinates = function (params) {
});
} else {
var searchResult = null;
- var maxDistance;
var map = self.getMap().getSubmapById(modelId);
if (map === null) {
return Promise.reject(new InvalidArgumentException("model doesn't exist for modelId: " + modelId));
}
var model = map.getModel();
- return ServerConnector.getMaxSearchDistance().then(function (distance) {
- var maxZoom = model.getMaxZoom();
- var zoomDiff = maxZoom - zoom;
- for (var i = 0; i < zoomDiff; i++) {
- distance = distance * 1.5;
- }
- maxDistance = distance;
- return ServerConnector.getClosestElementsByCoordinates({
- modelId: modelId,
- coordinates: coordinates,
- count: 1
- });
+ var maxDistance = self.computeMaxDistance(model, zoom);
+ return ServerConnector.getClosestElementsByCoordinates({
+ modelId: modelId,
+ coordinates: coordinates,
+ count: 1
}).then(function (elements) {
var nestedOverlay = "Pathways and compartments";
if (elements.length === 0) {
return undefined;
} else {
if (self.getMap().getBackgroundDataOverlay().getName() === nestedOverlay) {
- return self._getFirstVisibleParentOrObject(elements[0], zoom - model.getMinZoom());
+ return self._getFirstVisibleParentOrObject(elements[0], zoom - model.getMinZoom(), coordinates);
} else {
return elements[0];
}
@@ -224,23 +297,7 @@ SearchDbOverlay.prototype.searchByCoordinates = function (params) {
if (distance <= maxDistance) {
self._elementsByQuery[query] = searchResult;
} else {
- return ServerConnector.getClosestElementsByCoordinates({
- modelId: modelId,
- coordinates: coordinates,
- count: 1,
- type: ["Compartment"]
- }).then(function (elements) {
- var nestedOverlay = "Pathways and compartments";
- if (elements.length === 0) {
- return undefined;
- } else {
- if (self.getMap().getBackgroundDataOverlay().getName() === nestedOverlay) {
- return self._getFirstVisibleParentOrObject(elements[0], zoom - model.getMinZoom());
- } else {
- return undefined;
- }
- }
- }).then(function (visibleObject) {
+ return self.findCompartmentByCoordinates(coordinates, zoom, model, maxDistance).then(function (visibleObject) {
if (visibleObject !== undefined) {
self._elementsByQuery[query] = [visibleObject];
} else {
@@ -372,7 +429,7 @@ SearchDbOverlay.prototype.getIdentifiedElements = function () {
/**
*
* @param element
- * @returns {Promise<BioEntity[]>}
+ * @returns {Promise<BioEntity>}
*/
SearchDbOverlay.prototype.getDetailDataByIdentifiedElement = function (element) {
if (element.getType() === "POINT") {
diff --git a/frontend-js/src/test/js/helper.js b/frontend-js/src/test/js/helper.js
index 7d7fb45b1ff4f1023dcc6f4e2f5905a3121d025e..ab4c42c742d31a8ddbdfe2f3cfc6cb7af7cb7a2b 100644
--- a/frontend-js/src/test/js/helper.js
+++ b/frontend-js/src/test/js/helper.js
@@ -462,7 +462,7 @@ Helper.prototype.createAbstractCustomMap = function () {
/**
*
- * @param project
+ * @param {Project} [project]
* @returns {CustomMap}
*/
Helper.prototype.createCustomMap = function (project) {
diff --git a/frontend-js/src/test/js/map/overlay/SearchDbOverlay-test.js b/frontend-js/src/test/js/map/overlay/SearchDbOverlay-test.js
index f88dfeda4cdd0a634c2d59dab25d5956d588e91e..1ff3665b028863ea6d0ebbcbc82ee0437ef61eec 100644
--- a/frontend-js/src/test/js/map/overlay/SearchDbOverlay-test.js
+++ b/frontend-js/src/test/js/map/overlay/SearchDbOverlay-test.js
@@ -153,6 +153,28 @@ describe('SearchDbOverlay', function () {
});
});
+ it("on compartment border", function () {
+ helper.setUrl("http://test/?id=complex_model_with_submaps");
+ var map;
+ return ServerConnector.getProject().then(function (project) {
+ map = helper.createCustomMap(project);
+ return map.openDataOverlay(14961);
+ }).then(function () {
+
+ var searchDb = helper.createSearchDbOverlay(map);
+
+ var searchParams = {
+ modelId: map.getModel().getId(),
+ coordinates: new Point(104.36, 182.81),
+ zoom: 4
+ };
+ return searchDb.searchByCoordinates(searchParams);
+ }).then(function (result) {
+ assert.equal(result.length, 1);
+ });
+
+ });
+
it("on hidden nested object", function () {
return ServerConnector.getProject().then(function (project) {
@@ -242,4 +264,5 @@ describe('SearchDbOverlay', function () {
});
-});
+})
+;
diff --git a/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/16728/bioEntities.search/coordinates=104.36,182.81&count=1&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/16728/bioEntities.search/coordinates=104.36,182.81&count=1&token=MOCK_TOKEN_ID&
new file mode 100644
index 0000000000000000000000000000000000000000..efcec7f8da674b402d62d9b674c5bfc256cc12ea
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/16728/bioEntities.search/coordinates=104.36,182.81&count=1&token=MOCK_TOKEN_ID&
@@ -0,0 +1 @@
+[{"id":345331,"modelId":16728,"type":"ALIAS"}]
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/16728/bioEntities.search/coordinates=104.36,182.81&count=1&type=Compartment&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/16728/bioEntities.search/coordinates=104.36,182.81&count=1&type=Compartment&token=MOCK_TOKEN_ID&
new file mode 100644
index 0000000000000000000000000000000000000000..46a291bd26e929ef7376e3ca227948f78c85d741
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/16728/bioEntities.search/coordinates=104.36,182.81&count=1&type=Compartment&token=MOCK_TOKEN_ID&
@@ -0,0 +1 @@
+[{"id":345323,"modelId":16728,"type":"ALIAS"}]
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId,linkedSubmodel&id=345323&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId,linkedSubmodel&id=345323&token=MOCK_TOKEN_ID&
new file mode 100644
index 0000000000000000000000000000000000000000..392b44d0f9c421325d6eec0f73a72fb35c40b658
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId,linkedSubmodel&id=345323&token=MOCK_TOKEN_ID&
@@ -0,0 +1 @@
+[{"bounds":{"height":142.0,"width":144.0,"x":35.0,"y":45.0},"id":345323,"linkedSubmodel":null,"modelId":16728}]
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/id=345323&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/id=345323&token=MOCK_TOKEN_ID&
new file mode 100644
index 0000000000000000000000000000000000000000..10efe849d6ce6ecef22eeb1cfedfc94ef7ec6d99
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/id=345323&token=MOCK_TOKEN_ID&
@@ -0,0 +1 @@
+[{"abbreviation":null,"boundaryCondition":null,"bounds":{"height":142.0,"width":144.0,"x":35.0,"y":45.0},"compartmentId":null,"complexId":null,"constant":null,"elementId":"ca1","formerSymbols":[],"formula":null,"fullName":null,"hierarchyVisibilityLevel":"0","id":345323,"initialAmount":null,"initialConcentration":null,"linkedSubmodel":null,"modelId":16728,"name":"c1","notes":"","other":{"modifications":[],"structuralState":null,"structures":{}},"references":[],"symbol":null,"synonyms":[],"transparencyLevel":"2","type":"Compartment"}]
\ No newline at end of file