diff --git a/frontend-js/src/main/js/ServerConnector.js b/frontend-js/src/main/js/ServerConnector.js
index 5dd2d408f4a7fb33a12f4d421890f80d4cee6ebe..a09ffb94f0f06043855c2276e63b96fffcfa6f09 100644
--- a/frontend-js/src/main/js/ServerConnector.js
+++ b/frontend-js/src/main/js/ServerConnector.js
@@ -1194,7 +1194,9 @@ ServerConnector.getOverlayById = function (overlayId, projectId) {
ServerConnector.getReactions = function (params) {
var self = this;
- var queryParams = {};
+ var queryParams = {
+ modelId: params.modelId
+ };
if (params.ids === undefined) {
params.ids = [];
}
diff --git a/frontend-js/src/main/js/gui/PluginDialog.js b/frontend-js/src/main/js/gui/PluginDialog.js
index 1133b62a4c9bd5849860dc7fe009fe00d623beba..fd351bac1583f542de07b0ec827cf139b45bf52f 100644
--- a/frontend-js/src/main/js/gui/PluginDialog.js
+++ b/frontend-js/src/main/js/gui/PluginDialog.js
@@ -1,7 +1,4 @@
"use strict";
-var Promise = require('bluebird');
-
-
var AbstractGuiElement = require('./AbstractGuiElement');
var GuiConnector = require('../GuiConnector');
var GuiUtils = require('./leftPanel/GuiUtils');
@@ -56,12 +53,10 @@ PluginDialog.prototype._createPluginGui = function () {
var pluginManager = self.getPluginManager();
var loadedPlugins = [];
- var processedPlugins = [];
var plugins = pluginManager.getPlugins();
var i;
for (i = 0; i < plugins.length; i++) {
loadedPlugins[plugins[i].getOptions().url] = true;
- processedPlugins[plugins[i].getOptions().url] = false;
}
for (i = 0; i < self._knownPlugins.length; i++) {
@@ -75,23 +70,7 @@ PluginDialog.prototype._createPluginGui = function () {
});
pluginUrl.readOnly = true;
var button;
- if (loadedPlugins[url]) {
- button = Functions.createElement({
- type: "button",
- content: "UNLOAD",
- onclick: function () {
- var promises = [];
- for (var i = 0; i < plugins.length; i++) {
- if (plugins[i].getOptions().url === $(this).data("url")) {
- promises.push(pluginManager.removePlugin(plugins[i]));
- }
- }
- return Promise.all(promises).then(function () {
- self.close();
- }).then(null, GuiConnector.alert);
- }
- });
- } else {
+ if (!loadedPlugins[url]) {
button = Functions.createElement({
type: "button",
content: "LOAD",
@@ -103,39 +82,33 @@ PluginDialog.prototype._createPluginGui = function () {
});
}
$(button).data("url", url);
- processedPlugins[url] = true;
pluginFormTab.appendChild(guiUtils.createTableRow([Functions.createElement({type: "span"}), pluginUrl, button]));
}
- for (url in loadedPlugins) {
- if (loadedPlugins.hasOwnProperty(url) && !processedPlugins[url]) {
- pluginUrl = Functions.createElement({
- type: "input",
- value: url,
- style: "color:#999999"
- });
- pluginUrl.readOnly = true;
- button = Functions.createElement({
- type: "button",
- content: "UNLOAD",
- onclick: function () {
- var promises = [];
- for (var i = 0; i < plugins.length; i++) {
- if (plugins[i].getOptions().url === $(this).data("url")) {
- promises.push(pluginManager.removePlugin(plugins[i]));
- }
- }
- return Promise.all(promises).then(function () {
- self.close();
- }).then(null, GuiConnector.alert);
- }
- });
-
- $(button).data("url", url);
+ for (i = 0; i < plugins.length; i++) {
+ var plugin = plugins[i];
+ var removePlugin = (function () {
+ var pluginToRemove = plugin;
+ return function () {
+ return pluginManager.removePlugin(pluginToRemove).then(function () {
+ self.close();
+ }).then(null, GuiConnector.alert);
+ }
+ })();
+ pluginUrl = Functions.createElement({
+ type: "input",
+ value: plugins[i].getOptions().url,
+ style: "color:#999999"
+ });
+ pluginUrl.readOnly = true;
+ button = Functions.createElement({
+ type: "button",
+ content: "UNLOAD",
+ onclick: removePlugin
+ });
- pluginFormTab.appendChild(guiUtils.createTableRow([Functions.createElement({type: "span"}), pluginUrl, button]));
+ pluginFormTab.appendChild(guiUtils.createTableRow([Functions.createElement({type: "span"}), pluginUrl, button]));
- }
}
};
@@ -173,8 +146,8 @@ PluginDialog.prototype.close = function () {
PluginDialog.prototype.destroy = function () {
var self = this;
var div = self.getElement();
- if ($(self.getElement()).hasClass("ui-dialog-content")) {
- $(self.getElement()).dialog("destroy");
+ if ($(div).hasClass("ui-dialog-content")) {
+ $(div).dialog("destroy");
}
};
diff --git a/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js b/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js
index acc4f48ffd840bed390b80fe526c4903365cb9be..d6ebbb214bda55b40fb90e0bddb5ac6090dbe514 100644
--- a/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js
+++ b/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js
@@ -534,7 +534,7 @@ GuiUtils.prototype.createTab = function (params) {
tabData.content.appendChild(contentDiv);
$(contentDiv).css("overflow", "auto");
- $(contentDiv).css("height", "calc(100vh - " + $(contentDiv).position().top + "px)");
+ $(contentDiv).css("height", "calc(100vh - " + $(contentDiv).offset().top + "px)");
return {
title: navLink,
diff --git a/frontend-js/src/main/js/map/data/MapModel.js b/frontend-js/src/main/js/map/data/MapModel.js
index 1e4e53b9f6ff0d03d8c6e9288c8078043b270ec9..000602857d2fa04286c5aa712fb26be8d9cbe6b4 100644
--- a/frontend-js/src/main/js/map/data/MapModel.js
+++ b/frontend-js/src/main/js/map/data/MapModel.js
@@ -746,7 +746,8 @@ MapModel.prototype.getReactionsForElements = function(elements, complete) {
var result = [];
return ServerConnector.getReactions({
- participantId : ids,
+ modelId: self.getId(),
+ participantId : ids
}).then(function(reactions) {
result = reactions;
@@ -781,7 +782,7 @@ MapModel.prototype.getCompartments = function() {
promise = ServerConnector.getAliases({
columns : "id,bounds,modelId",
type : "Compartment",
- modelId : self.getId(),
+ modelId : self.getId()
}).then(function(compartments) {
self._compartments = [];
for (var i = 0; i < compartments.length; i++) {
diff --git a/frontend-js/src/main/js/minerva.js b/frontend-js/src/main/js/minerva.js
index b2514003b69769e0fb3059dcebe9e361d3a492c5..71b007ad67a6e48c7b97fdd0b4538765c3c4668a 100644
--- a/frontend-js/src/main/js/minerva.js
+++ b/frontend-js/src/main/js/minerva.js
@@ -104,7 +104,7 @@ function createDivStructure(element) {
var splitBar = functions.createElement({
type: "div",
name: "minerva-plugin-split-bar",
- style: "width:5px;height:100%;clear: both;display: table-cell;vertical-align:top",
+ style: "width:5px;height:100%;clear: both;display: table-cell;vertical-align:top;border-left:1px dotted gray;cursor:col-resize",
content: " "
});
element.appendChild(splitBar);
@@ -206,7 +206,7 @@ function modifyParamsForTouchInterface(params) {
return params;
}
-function assignSplitBarHandler(customMap) {
+function assignSplitBarHandler(customMap, pluginManager) {
var splitBar = $('[name="minerva-plugin-split-bar"]');
var rightPanelDiv = $('[name="minerva-plugin-div"]');
var mouseDownHandler = function (e) {
@@ -215,6 +215,7 @@ function assignSplitBarHandler(customMap) {
var x = $("body").width() - e.pageX;
$(rightPanelDiv).css("width", x);
google.maps.event.trigger(customMap.getGoogleMap(), 'resize');
+ return pluginManager.callListeners("onResize");
};
$(splitBar).mousedown(function (e) {
e.preventDefault();
@@ -260,8 +261,6 @@ function create(params) {
customMap = new CustomMap(params);
- assignSplitBarHandler(customMap);
-
new DbOverlayCollection({
map: customMap
@@ -279,6 +278,7 @@ function create(params) {
configuration: params.getConfiguration()
});
leftPanel.setPluginManager(pluginManager);
+ assignSplitBarHandler(customMap, pluginManager);
topMenu = new TopMenu({
element: functions.getElementByName(element, "menuDiv"),
diff --git a/frontend-js/src/main/js/plugin/MinervaPluginProxy.js b/frontend-js/src/main/js/plugin/MinervaPluginProxy.js
index 59e9adb5876f52c70a4752bffd28d8c3646d68fc..7c3c39890d4fbc2f794b73206437b8203e94751d 100644
--- a/frontend-js/src/main/js/plugin/MinervaPluginProxy.js
+++ b/frontend-js/src/main/js/plugin/MinervaPluginProxy.js
@@ -236,15 +236,26 @@ function createProjectMap(options) {
return map.getVisibleDataOverlays();
},
addListener: function (param) {
- var dbOverlay = getOverlayByName(map, param.dbOverlayName);
+ var object = null;
+ var listenerWrapper = null;
+ if (param.dbOverlayName !== undefined) {
+ object = getOverlayByName(map, param.dbOverlayName);
+ listenerWrapper = function (e) {
+ return getFullElements(map, e.arg.identifiedElements).then(function (result) {
+ return param.callback(result);
+ });
+ };
+ } else if (param.object === "plugin") {
+ object = options.plugin;
+ listenerWrapper = function () {
+ return param.callback();
+ };
+ } else {
+ throw new Error("Invalid argument");
+ }
- var listenerWrapper = function (e) {
- return getFullElements(map, e.arg.identifiedElements).then(function (result) {
- return param.callback(result);
- });
- };
- dbOverlay.addListener(param.type, listenerWrapper);
- listenersData.push({listener: param.callback, wrapper: listenerWrapper, object: dbOverlay, type: param.type});
+ object.addListener(param.type, listenerWrapper);
+ listenersData.push({listener: param.callback, wrapper: listenerWrapper, object: object, type: param.type});
},
removeListener: function (param) {
var dbOverlay = getOverlayByName(map, param.dbOverlayName);
diff --git a/frontend-js/src/main/js/plugin/Plugin.js b/frontend-js/src/main/js/plugin/Plugin.js
index 960c24d71654c95fc9f0750b7a436edd0af86011..8b650459d264bfb185ccfb606ee2862cf156d23f 100644
--- a/frontend-js/src/main/js/plugin/Plugin.js
+++ b/frontend-js/src/main/js/plugin/Plugin.js
@@ -15,6 +15,7 @@ function Plugin(options) {
var self = this;
self.setOptions(options);
self.registerListenerType("onUnload");
+ self.registerListenerType("onResize");
}
Plugin.prototype = Object.create(ObjectWithListeners.prototype);
@@ -59,7 +60,7 @@ Plugin.prototype.load = function () {
var error = false;
try {
// noinspection JSUnusedLocalSymbols
- var define = function (pluginFunction) {
+ var minervaDefine = function (pluginFunction) {
try {
if (typeof pluginFunction === "function") {
pluginData = pluginFunction();
@@ -71,6 +72,7 @@ Plugin.prototype.load = function () {
map: options.map,
configuration: options.configuration,
element: options.element,
+ plugin: self,
pluginId: "plugin" + (pluginId++)
});
self.setLoadedPluginData(pluginData);
@@ -80,6 +82,7 @@ Plugin.prototype.load = function () {
error = e;
}
};
+ content += "//# sourceURL=" + options.url;
eval(content);
} catch (e) {
error = e;
@@ -91,6 +94,20 @@ Plugin.prototype.load = function () {
};
+Plugin.prototype.getMinWidth = function () {
+ var result = 0;
+ var data = this.getLoadedPluginData();
+ if (data.minWidth !== undefined) {
+ var value = 0;
+ if (typeof data.minWidth === "function") {
+ value = parseInt(data.minWidth());
+ } else {
+ value = parseInt(data.minWidth);
+ }
+ }
+ return value;
+};
+
Plugin.prototype.unload = function () {
var self = this;
return Promise.resolve().then(function () {
@@ -98,7 +115,7 @@ Plugin.prototype.unload = function () {
}).then(function () {
var removedListeners = self.getMinervaPluginProxy().project.map.removeAllListeners();
if (removedListeners.length > 0) {
- logger.warn("'"+self.getLoadedPluginData().getName() + "' plugin didn't remove all registered listeners");
+ logger.warn("'" + self.getLoadedPluginData().getName() + "' plugin didn't remove all registered listeners");
}
return self.callListeners("onUnload");
}).then(function () {
diff --git a/frontend-js/src/main/js/plugin/PluginManager.js b/frontend-js/src/main/js/plugin/PluginManager.js
index 0ff0e7fe05a944676765ac61727e5325464a8ca1..354e94906bb647f77e35306de26f772e63291fea 100644
--- a/frontend-js/src/main/js/plugin/PluginManager.js
+++ b/frontend-js/src/main/js/plugin/PluginManager.js
@@ -7,8 +7,8 @@ var GuiConnector = require('../GuiConnector');
var Promise = require("bluebird");
+// noinspection JSUnusedLocalSymbols
var logger = require('../logger');
-var Functions = require('../Functions');
function PluginManager(options) {
@@ -20,6 +20,15 @@ function PluginManager(options) {
self.setConfiguration(options.configuration);
self._plugins = [];
self._pluginOnResizeHandlers = {};
+
+ self.registerListenerType("onResize");
+ self.addListener("onResize", function () {
+ var promises = [];
+ for (var i = 0; i < self._plugins.length; i++) {
+ promises.push(self._plugins[i].callListeners("onResize"));
+ }
+ return Promise.resolve(promises);
+ });
}
PluginManager.prototype = Object.create(ObjectWithListeners.prototype);
@@ -71,7 +80,7 @@ PluginManager.prototype.addPlugin = function (options) {
configuration: self.getConfiguration(),
map: self.getMap()
});
- plugin.addListener("onUnload", function(){
+ plugin.addListener("onUnload", function () {
tabData.content.parentNode.removeChild(tabData.content);
tabData.title.parentNode.parentNode.removeChild(tabData.title.parentNode);
});
@@ -82,12 +91,14 @@ PluginManager.prototype.addPlugin = function (options) {
const tab = $(tabData.content);
tab.css('overflow', 'auto');
var adjustHeight = function () {
- tab.css('height', 'calc( 100vh - ' + tab.position().top + 'px )');
+ tab.css('height', 'calc( 100vh - ' + tab.offset().top + 'px )');
};
self._pluginOnResizeHandlers[plugin.getPluginId()] = adjustHeight;
GuiConnector.addWindowResizeEvent(adjustHeight);
adjustHeight();
+ return self.adjustMinWidth();
+ }).then(function () {
return plugin;
});
};
@@ -98,9 +109,12 @@ PluginManager.prototype.createTabForPlugin = function () {
var guiUtils = new GuiUtils(self.getConfiguration());
if (tabData === undefined) {
self.getElement().style.width = "300px";
+ self.getElement().style.maxWidth = "600px";
+ self.getElement().style.minWidth = "150px";
self.getElement().style.height = "100%";
self._tabData = guiUtils.createTabDiv({element: self.getElement(), id: "plugin_tab"});
tabData = self._tabData;
+ $(tabData.content).css('position', 'relative');
}
return guiUtils.createTab({
title: "",
@@ -108,6 +122,27 @@ PluginManager.prototype.createTabForPlugin = function () {
tabData: tabData
});
};
+PluginManager.prototype.adjustMinWidth = function () {
+ var self = this;
+ var oldVal = self.getElement().style.minWidth;
+ var minWidth = 150;
+ var i;
+ for (i = 0; i < self._plugins.length; i++) {
+ var plugin = self._plugins[i];
+ var value = plugin.getMinWidth();
+ if (value > minWidth) {
+ minWidth = value;
+ }
+ }
+ var newVal = minWidth + "px";
+ self.getElement().style.minWidth = newVal;
+ if (newVal !== oldVal) {
+ return self.callListeners("onResize");
+ } else {
+ return Promise.resolve();
+ }
+};
+
PluginManager.prototype.removePlugin = function (plugin) {
var self = this;
var found = false;
@@ -121,7 +156,9 @@ PluginManager.prototype.removePlugin = function (plugin) {
return Promise.reject(new Error("Plugin not registered"));
}
GuiConnector.removeWindowResizeEvent(self._pluginOnResizeHandlers[plugin.getPluginId()]);
- return plugin.unload();
+ return plugin.unload().then(function () {
+ return self.adjustMinWidth();
+ });
};
PluginManager.prototype.destroy = function () {
diff --git a/frontend-js/src/test/js/ServerConnector-test.js b/frontend-js/src/test/js/ServerConnector-test.js
index 754d45cfdcef8efcb6937c016ecb2edd9d1020c5..7b844e1e805d8a2e16a1a9bfec32bd3f9b3afd07 100644
--- a/frontend-js/src/test/js/ServerConnector-test.js
+++ b/frontend-js/src/test/js/ServerConnector-test.js
@@ -153,7 +153,7 @@ describe('ServerConnector', function () {
var modelId = 15781;
return ServerConnector.getImageDownloadUrl({
modelId: modelId,
- handlerClass: "lcsb.mapviewer.converter.graphics.PngImageGenerator",
+ handlerClass: "lcsb.mapviewer.converter.graphics.PngImageGenerator"
}).then(function (url) {
assert.ok(url);
assert.ok(url.indexOf(modelId) >= 0);
@@ -165,7 +165,7 @@ describe('ServerConnector', function () {
var modelId = 15781;
return ServerConnector.getModelDownloadUrl({
modelId: modelId,
- handlerClass: "lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser",
+ handlerClass: "lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser"
}).then(function (url) {
assert.ok(url);
assert.ok(url.indexOf(modelId) >= 0);
@@ -195,13 +195,13 @@ describe('ServerConnector', function () {
it('removeOverlay', function () {
return ServerConnector.removeOverlay({
- overlayId: 17296,
+ overlayId: 17296
});
});
it('removeComment', function () {
return ServerConnector.removeComment({
- commentId: 4290,
+ commentId: 4290
});
});
@@ -230,7 +230,7 @@ describe('ServerConnector', function () {
it('getModelDownloadUrl', function () {
return ServerConnector.getModelDownloadUrl({
- backgroundOverlayId: "cv14081",
+ backgroundOverlayId: "cv14081"
}).then(function (url) {
assert.ok(url);
});
@@ -305,16 +305,16 @@ describe('ServerConnector', function () {
describe('returnUserOrSystemColor ', function () {
it('user has empty color', function () {
- var systemColor = {};
+ var systemColor = "0000FF";
return ServerConnector.returnUserOrSystemColor("", Promise.resolve(systemColor)).then(function (result) {
- assert.ok(result = systemColor);
+ assert.ok(255, result);
});
});
it('user has defined color', function () {
- var userColor = {};
- var systemColor = {};
+ var userColor = "000001";
+ var systemColor = "000010";
return ServerConnector.returnUserOrSystemColor(userColor, Promise.resolve(systemColor)).then(function (result) {
- assert.ok(result = userColor);
+ assert.ok(1, result);
});
});
});
diff --git a/frontend-js/src/test/js/gui/OptionsMenu-test.js b/frontend-js/src/test/js/gui/OptionsMenu-test.js
index 416b1dc307e4a4b85ca2d8d35b4f6617e5c5700a..58e741d7332de438f3e87227a410ec88150da3f9 100644
--- a/frontend-js/src/test/js/gui/OptionsMenu-test.js
+++ b/frontend-js/src/test/js/gui/OptionsMenu-test.js
@@ -47,5 +47,4 @@ describe('OptionsMenu', function () {
return pluginManager.destroy();
});
});
-})
-;
+});
diff --git a/frontend-js/src/test/js/plugin/PluginManager-test.js b/frontend-js/src/test/js/plugin/PluginManager-test.js
index 61d8ac2df925f77b5b8f9fe3bceb686641a030e7..f37e2cfeee5c2c6e391f57eb9ca6e1ac156e8d09 100644
--- a/frontend-js/src/test/js/plugin/PluginManager-test.js
+++ b/frontend-js/src/test/js/plugin/PluginManager-test.js
@@ -7,6 +7,8 @@ require("../mocha-config");
var Plugin = require('../../../main/js/plugin/Plugin');
var PluginManager = require('../../../main/js/plugin/PluginManager');
+var ProxyAccessPlugin = require('./ProxyAccessPlugin');
+
var logger = require('../logger');
var assert = require('assert');
@@ -38,6 +40,27 @@ describe('PluginManager', function () {
assert.equal(1, manager.getPlugins().length);
});
});
+ it('with min width', function () {
+ var manager = new PluginManager(createParams());
+ return manager.addPlugin({url: "./testFiles/plugin/min-width.js"}).then(function () {
+ assert.equal("200px", $(manager.getElement()).css("min-width"));
+ });
+ });
+ it('with onResize listener', function () {
+ var manager = new PluginManager(createParams());
+ var plugin = new ProxyAccessPlugin({});
+ var listenerCalled = false;
+ return manager.addPlugin(plugin).then(function () {
+ plugin.getMinervaPluginProxy().project.map.addListener({
+ object: "plugin", type: "onResize", callback: function () {
+ listenerCalled = true;
+ }
+ });
+ return manager.addPlugin({url: "./testFiles/plugin/min-width.js"});
+ }).then(function () {
+ assert.ok(listenerCalled);
+ });
+ });
it('after removal', function () {
var manager = new PluginManager(createParams());
return manager.addPlugin({url: "./testFiles/plugin/empty.js"}).then(function (plugin) {
diff --git a/frontend-js/src/test/js/plugin/ProxyAccessPlugin.js b/frontend-js/src/test/js/plugin/ProxyAccessPlugin.js
index 1dfe2df922218b584fda055dd9b971c4c1ef1437..696549ef59ca79472fa1082f85f7ed6735fe1350 100644
--- a/frontend-js/src/test/js/plugin/ProxyAccessPlugin.js
+++ b/frontend-js/src/test/js/plugin/ProxyAccessPlugin.js
@@ -8,13 +8,17 @@ var Promise = require('bluebird');
var logger = require('../logger');
function ProxyAccessPlugin(options) {
+ Plugin.call(this);
}
ProxyAccessPlugin.prototype = Object.create(Plugin.prototype);
ProxyAccessPlugin.prototype.constructor = ProxyAccessPlugin;
ProxyAccessPlugin.prototype.setOptions = function (options) {
- this.setMinervaPluginProxy(new MinervaPluginProxy(options));
+ if (options !== undefined) {
+ options.plugin = this;
+ this.setMinervaPluginProxy(new MinervaPluginProxy(options));
+ }
};
ProxyAccessPlugin.prototype.load = function () {
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/reactions/participantId=329156,329157,329158,329159,329160,329161,329162,329163,329164,329165,329166,329167,329168,329169,329170,329171,329172,329173,329174,329175,329176,329177,329178,329179,329180,329181,329182,329183,329184,329185&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities/reactions/participantId=329156,329157,329158,329159,329160,329161,329162,329163,329164,329165,329166,329167,329168,329169,329170,329171,329172,329173,329174,329175,329176,329177,329178,329179,329180,329181,329182,329183,329184,329185&token=MOCK_TOKEN_ID&
similarity index 100%
rename from frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/reactions/participantId=329156,329157,329158,329159,329160,329161,329162,329163,329164,329165,329166,329167,329168,329169,329170,329171,329172,329173,329174,329175,329176,329177,329178,329179,329180,329181,329182,329183,329184,329185&token=MOCK_TOKEN_ID&
rename to frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities/reactions/participantId=329156,329157,329158,329159,329160,329161,329162,329163,329164,329165,329166,329167,329168,329169,329170,329171,329172,329173,329174,329175,329176,329177,329178,329179,329180,329181,329182,329183,329184,329185&token=MOCK_TOKEN_ID&
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/reactions/participantId=329167&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities/reactions/participantId=329167&token=MOCK_TOKEN_ID&
similarity index 100%
rename from frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/reactions/participantId=329167&token=MOCK_TOKEN_ID&
rename to frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities/reactions/participantId=329167&token=MOCK_TOKEN_ID&
diff --git a/frontend-js/testFiles/plugin-invalid/invalid_register.js b/frontend-js/testFiles/plugin-invalid/invalid_register.js
index f8b555f8c9aecccb91ace2d921e8964e8006ed11..607f1da2c32f227008e6e9c346d3ff580f499de2 100644
--- a/frontend-js/testFiles/plugin-invalid/invalid_register.js
+++ b/frontend-js/testFiles/plugin-invalid/invalid_register.js
@@ -1,4 +1,4 @@
-define(function () {
+minervaDefine(function () {
return {
register: function (object) {
throw new Error("Let's crash");
diff --git a/frontend-js/testFiles/plugin-invalid/unclean-unregister.js b/frontend-js/testFiles/plugin-invalid/unclean-unregister.js
index a309c06a475b6ef5d444021d31eade224eea8e91..a7c00e2c55824505ed6740963cab18960fd29d72 100644
--- a/frontend-js/testFiles/plugin-invalid/unclean-unregister.js
+++ b/frontend-js/testFiles/plugin-invalid/unclean-unregister.js
@@ -1,4 +1,4 @@
-define(function () {
+minervaDefine(function () {
return {
register: function (minervaObject) {
options = {
diff --git a/frontend-js/testFiles/plugin/empty-without-function.js b/frontend-js/testFiles/plugin/empty-without-function.js
index bafb6d13a6cf3b927941251b270111f11b70ffc2..e0b51b2161304fbaa3663e497b8f42deb0e8decb 100644
--- a/frontend-js/testFiles/plugin/empty-without-function.js
+++ b/frontend-js/testFiles/plugin/empty-without-function.js
@@ -1,4 +1,4 @@
-define({
+minervaDefine({
register: function (object) {
console.log("registering test plugin");
},
diff --git a/frontend-js/testFiles/plugin/empty.js b/frontend-js/testFiles/plugin/empty.js
index a3fd24885e527b3933a46efdf362b82fbd403fbf..a8e14229f38ebf43e61642799887410b9a2364b3 100644
--- a/frontend-js/testFiles/plugin/empty.js
+++ b/frontend-js/testFiles/plugin/empty.js
@@ -1,4 +1,4 @@
-define(function () {
+minervaDefine(function () {
return {
register: function (object) {
console.log("registering test plugin");
diff --git a/frontend-js/testFiles/plugin/highlight-something.js b/frontend-js/testFiles/plugin/highlight-something.js
index 985dec3860a6168245a2aa536fc3c15870438d95..be4c1edce0ed6594e08030917ac295713fb56194 100644
--- a/frontend-js/testFiles/plugin/highlight-something.js
+++ b/frontend-js/testFiles/plugin/highlight-something.js
@@ -1,4 +1,4 @@
-define(function () {
+minervaDefine(function () {
return {
register: function (minervaObject) {
minervaObject.element.innerHTML = "<div><button id='show'>highlight something</button></div>";
diff --git a/frontend-js/testFiles/plugin/min-width.js b/frontend-js/testFiles/plugin/min-width.js
new file mode 100644
index 0000000000000000000000000000000000000000..6752a72ac12e72440fa02ebfc298762965bae2ef
--- /dev/null
+++ b/frontend-js/testFiles/plugin/min-width.js
@@ -0,0 +1,25 @@
+minervaDefine(function () {
+ return {
+ register: function (object) {
+ console.log("registering test plugin with min width");
+ object.project.map.addListener({
+ object: "plugin", type: "onResize", callback: function () {
+ console.log("Resize of plugin tab called");
+ }
+ });
+
+ },
+ unregister: function () {
+ console.log("unregistering test plugin");
+ },
+ getName: function () {
+ return "test plugin";
+ },
+ minWidth: function () {
+ return 200;
+ },
+ getVersion: function () {
+ return "0.0.1";
+ }
+ };
+});
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsRestImpl.java
index 276e9256cc39ca0e194e842316b157438e5c6a15..d8a8ed17ac8d9e7a93c5dfd817f5d74e295ad6da 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsRestImpl.java
@@ -28,167 +28,168 @@ import lcsb.mapviewer.services.search.data.LightReactionView;
@Transactional(value = "txManager")
public class ReactionsRestImpl extends BaseRestImpl {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(ReactionsRestImpl.class);
-
- @Autowired
- private IUserService userService;
-
- @Autowired
- private IModelService modelService;
-
- /**
- * @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;
- }
-
- public List<Map<String, Object>> getReactions(String projectId, String id, String columns, String modelId, String token, String participantElementId)
- throws UserAccessException, SecurityException {
- Model model = modelService.getLastModelByProjectId(projectId, userService.getToken(token));
- Set<Integer> ids = new HashSet<>();
- if (!id.equals("")) {
- for (String str : id.split(",")) {
- ids.add(Integer.valueOf(str));
- }
- }
- Set<Element> elementSet = new HashSet<>();
- if (!participantElementId.equals("")) {
- for (String str : participantElementId.split(",")) {
- elementSet.add(model.getElementByDbId(Integer.valueOf(str)));
- }
- }
- Set<String> columnsSet = createReactionColumnSet(columns);
-
- List<Map<String, Object>> result = new ArrayList<>();
-
- List<Model> models = getModels(projectId, modelId, token);
-
- for (Model model2 : models) {
- for (Reaction reaction : model2.getReactions()) {
- if (ids.size() == 0 || ids.contains(reaction.getId())) {
- if (elementSet.size() == 0 || reactionContainsElement(reaction, elementSet)) {
- result.add(preparedReaction(reaction, columnsSet));
- }
- }
- }
- }
-
- return result;
- }
-
- private boolean reactionContainsElement(Reaction reaction, Set<Element> elementSet) {
- for (Element element : elementSet) {
- if (reaction.containsElement(element)) {
- return true;
- }
- }
- return false;
- }
-
- private Map<String, Object> preparedReaction(Reaction reaction, Set<String> columnsSet) {
- Map<String, Object> result = new HashMap<>();
- for (String string : columnsSet) {
- String column = string.toLowerCase();
- Object value = null;
- if (column.equals("id") || column.equals("idobject")) {
- value = reaction.getId();
- } else if (column.equals("modelid")) {
- value = reaction.getModelData().getId();
- } else if (column.equals("reactionid")) {
- value = reaction.getIdReaction();
- } else if (column.equals("name")) {
- value = reaction.getName();
- } else if (column.equals("centerpoint")) {
- value = reaction.getCenterPoint();
- } else if (column.equals("products")) {
- List<Integer> ids = new ArrayList<>();
- for (Product product : reaction.getProducts()) {
- ids.add(product.getElement().getId());
- }
- value = StringUtils.join(ids, ",");
- } else if (column.equals("reactants")) {
- List<Integer> ids = new ArrayList<>();
- for (Reactant reactant : reaction.getReactants()) {
- ids.add(reactant.getElement().getId());
- }
- value = StringUtils.join(ids, ",");
- } else if (column.equals("modifiers")) {
- List<Integer> ids = new ArrayList<>();
- for (Modifier product : reaction.getModifiers()) {
- ids.add(product.getElement().getId());
- }
- value = StringUtils.join(ids, ",");
- } else if (column.equals("type")) {
- value = reaction.getStringType();
- } else if (column.equals("hierarchyvisibilitylevel")) {
- value = reaction.getVisibilityLevel();
- } else if (column.equals("lines")) {
- value = new LightReactionView(reaction).getLines();
- } else if (column.equals("notes")) {
- value = reaction.getNotes();
- } else if (column.equals("references")) {
- value = createAnnotations(reaction.getMiriamData());
- } else {
- value = "Unknown column";
- }
- result.put(string, value);
- }
- return result;
- }
-
- private Set<String> createReactionColumnSet(String columns) {
- Set<String> columnsSet = new HashSet<>();
- if (columns.equals("")) {
- columnsSet.add("id");
- columnsSet.add("reactionId");
- columnsSet.add("modelId");
- columnsSet.add("type");
- columnsSet.add("lines");
- columnsSet.add("centerPoint");
- columnsSet.add("products");
- columnsSet.add("reactants");
- columnsSet.add("modifiers");
- columnsSet.add("hierarchyVisibilityLevel");
- columnsSet.add("references");
- columnsSet.add("notes");
- } else {
- for (String str : columns.split(",")) {
- columnsSet.add(str);
- }
- }
- return columnsSet;
- }
-
- /**
- * @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;
- }
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(ReactionsRestImpl.class);
+
+ @Autowired
+ private IUserService userService;
+
+ @Autowired
+ private IModelService modelService;
+
+ /**
+ * @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;
+ }
+
+ public List<Map<String, Object>> getReactions(String projectId, String id, String columns, String modelId,
+ String token, String participantElementId) throws UserAccessException, SecurityException {
+ Set<Integer> ids = new HashSet<>();
+ if (!id.equals("")) {
+ for (String str : id.split(",")) {
+ ids.add(Integer.valueOf(str));
+ }
+ }
+ List<Model> models = getModels(projectId, modelId, token);
+
+ Set<Element> elementSet = new HashSet<>();
+ if (!participantElementId.equals("")) {
+ for (String str : participantElementId.split(",")) {
+ for (Model model : models) {
+ elementSet.add(model.getElementByDbId(Integer.valueOf(str)));
+ }
+ }
+ }
+ Set<String> columnsSet = createReactionColumnSet(columns);
+
+ List<Map<String, Object>> result = new ArrayList<>();
+
+ for (Model model2 : models) {
+ for (Reaction reaction : model2.getReactions()) {
+ if (ids.size() == 0 || ids.contains(reaction.getId())) {
+ if (elementSet.size() == 0 || reactionContainsElement(reaction, elementSet)) {
+ result.add(preparedReaction(reaction, columnsSet));
+ }
+ }
+ }
+ }
+
+ return result;
+ }
+
+ private boolean reactionContainsElement(Reaction reaction, Set<Element> elementSet) {
+ for (Element element : elementSet) {
+ if (reaction.containsElement(element)) {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ private Map<String, Object> preparedReaction(Reaction reaction, Set<String> columnsSet) {
+ Map<String, Object> result = new HashMap<>();
+ for (String string : columnsSet) {
+ String column = string.toLowerCase();
+ Object value = null;
+ if (column.equals("id") || column.equals("idobject")) {
+ value = reaction.getId();
+ } else if (column.equals("modelid")) {
+ value = reaction.getModelData().getId();
+ } else if (column.equals("reactionid")) {
+ value = reaction.getIdReaction();
+ } else if (column.equals("name")) {
+ value = reaction.getName();
+ } else if (column.equals("centerpoint")) {
+ value = reaction.getCenterPoint();
+ } else if (column.equals("products")) {
+ List<Integer> ids = new ArrayList<>();
+ for (Product product : reaction.getProducts()) {
+ ids.add(product.getElement().getId());
+ }
+ value = StringUtils.join(ids, ",");
+ } else if (column.equals("reactants")) {
+ List<Integer> ids = new ArrayList<>();
+ for (Reactant reactant : reaction.getReactants()) {
+ ids.add(reactant.getElement().getId());
+ }
+ value = StringUtils.join(ids, ",");
+ } else if (column.equals("modifiers")) {
+ List<Integer> ids = new ArrayList<>();
+ for (Modifier product : reaction.getModifiers()) {
+ ids.add(product.getElement().getId());
+ }
+ value = StringUtils.join(ids, ",");
+ } else if (column.equals("type")) {
+ value = reaction.getStringType();
+ } else if (column.equals("hierarchyvisibilitylevel")) {
+ value = reaction.getVisibilityLevel();
+ } else if (column.equals("lines")) {
+ value = new LightReactionView(reaction).getLines();
+ } else if (column.equals("notes")) {
+ value = reaction.getNotes();
+ } else if (column.equals("references")) {
+ value = createAnnotations(reaction.getMiriamData());
+ } else {
+ value = "Unknown column";
+ }
+ result.put(string, value);
+ }
+ return result;
+ }
+
+ private Set<String> createReactionColumnSet(String columns) {
+ Set<String> columnsSet = new HashSet<>();
+ if (columns.equals("")) {
+ columnsSet.add("id");
+ columnsSet.add("reactionId");
+ columnsSet.add("modelId");
+ columnsSet.add("type");
+ columnsSet.add("lines");
+ columnsSet.add("centerPoint");
+ columnsSet.add("products");
+ columnsSet.add("reactants");
+ columnsSet.add("modifiers");
+ columnsSet.add("hierarchyVisibilityLevel");
+ columnsSet.add("references");
+ columnsSet.add("notes");
+ } else {
+ for (String str : columns.split(",")) {
+ columnsSet.add(str);
+ }
+ }
+ return columnsSet;
+ }
+
+ /**
+ * @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;
+ }
}
diff --git a/web/src/main/webapp/resources/js/plugins/empty.js b/web/src/main/webapp/resources/js/plugins/empty.js
deleted file mode 100644
index a3fd24885e527b3933a46efdf362b82fbd403fbf..0000000000000000000000000000000000000000
--- a/web/src/main/webapp/resources/js/plugins/empty.js
+++ /dev/null
@@ -1,16 +0,0 @@
-define(function () {
- return {
- register: function (object) {
- console.log("registering test plugin");
- },
- unregister: function () {
- console.log("unregistering test plugin");
- },
- getName: function () {
- return "test plugin";
- },
- getVersion: function () {
- return "0.0.1";
- }
- };
-});
\ No newline at end of file