From c1b73c88cd3239e2ebbadaf6132e4b4a79484edb Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Thu, 20 Dec 2018 15:26:23 +0100
Subject: [PATCH] export of reactions allows filtering by reaction type
---
frontend-js/src/main/js/Configuration.js | 19 +++++++++
.../main/js/gui/export/AbstractExportPanel.js | 23 ++++++++---
.../main/js/gui/export/NetworkExportPanel.js | 39 ++++++++++++++-----
.../js/gui/export/ElementExportPanel-test.js | 8 +++-
4 files changed, 72 insertions(+), 17 deletions(-)
diff --git a/frontend-js/src/main/js/Configuration.js b/frontend-js/src/main/js/Configuration.js
index 230456ab5f..e0245933d5 100644
--- a/frontend-js/src/main/js/Configuration.js
+++ b/frontend-js/src/main/js/Configuration.js
@@ -322,6 +322,25 @@ Configuration.prototype.getSimpleElementTypeNames = function () {
return result;
};
+/**
+ *
+ * @return {string[]}
+ */
+Configuration.prototype.getReactionTypeNames = function () {
+ var classesToBeExcluded = {};
+ var i;
+ for (i = 0; i < this._reactionTypes.length; i++) {
+ classesToBeExcluded[this._reactionTypes[i].parentClass] = true;
+ }
+ var result = [];
+ for (i = 0; i < this._reactionTypes.length; i++) {
+ if (classesToBeExcluded[this._reactionTypes[i].className] === undefined) {
+ result.push(this._reactionTypes[i].name);
+ }
+ }
+ return result;
+};
+
/**
*
* @param {BioEntityType[]} reactionTypes
diff --git a/frontend-js/src/main/js/gui/export/AbstractExportPanel.js b/frontend-js/src/main/js/gui/export/AbstractExportPanel.js
index 39cfcd95e1..345bac1d52 100644
--- a/frontend-js/src/main/js/gui/export/AbstractExportPanel.js
+++ b/frontend-js/src/main/js/gui/export/AbstractExportPanel.js
@@ -135,17 +135,21 @@ AbstractExportPanel.prototype.createDualListbox = function (selectElement) {
/**
*
* @param {BioEntityType[]} elementTypes
+ * @param {string} [panelName]
* @returns {HTMLElement}
* @protected
*/
-AbstractExportPanel.prototype._createSelectTypeDiv = function (elementTypes) {
+AbstractExportPanel.prototype._createSelectTypeDiv = function (elementTypes, panelName) {
+ if (panelName === undefined) {
+ panelName = " TYPE:";
+ }
var typeDiv = Functions.createElement({
type: "div",
name: "typeSelectDiv"
});
typeDiv.appendChild(Functions.createElement({
type: "h4",
- content: " TYPE:"
+ content: panelName
}));
var choicesContainer = Functions.createElement({
type: "ul",
@@ -181,12 +185,16 @@ AbstractExportPanel.prototype._createSelectTypeDiv = function (elementTypes) {
/**
*
+ * @param {HTMLElement} [htmlElement]
* @returns {Promise<BioEntityType[]>}
*/
-AbstractExportPanel.prototype.getSelectedTypes = function () {
+AbstractExportPanel.prototype.getSelectedTypes = function (htmlElement) {
var self = this;
+ if (htmlElement === undefined) {
+ htmlElement = self.getElement();
+ }
- var div = $("div[name='typeSelectDiv']", $(self.getElement()))[0];
+ var div = $("div[name='typeSelectDiv']", $(htmlElement))[0];
var result = [];
var selectedAll = false;
$(":checked", $(div)).each(function (index, element) {
@@ -196,8 +204,11 @@ AbstractExportPanel.prototype.getSelectedTypes = function () {
result.push(element.value);
});
if (selectedAll) {
- return ServerConnector.getConfiguration().then(function (configuration) {
- return configuration.getSimpleElementTypeNames();
+ result = [];
+ $("input[type='checkbox']", $(div)).each(function (index, element) {
+ if (element.value !== "ALL") {
+ result.push(element.value);
+ }
});
}
diff --git a/frontend-js/src/main/js/gui/export/NetworkExportPanel.js b/frontend-js/src/main/js/gui/export/NetworkExportPanel.js
index b681dad5c9..cc5941f297 100644
--- a/frontend-js/src/main/js/gui/export/NetworkExportPanel.js
+++ b/frontend-js/src/main/js/gui/export/NetworkExportPanel.js
@@ -7,6 +7,7 @@ var AbstractExportPanel = require('./AbstractExportPanel');
var Promise = require("bluebird");
// noinspection JSUnusedLocalSymbols
var logger = require('../../logger');
+var Functions = require('../../Functions');
var GuiMessageError = require('../GuiMessageError');
var Alias = require('../../map/data/Alias');
@@ -39,8 +40,12 @@ NetworkExportPanel.prototype.init = function () {
var self = this;
var element = self.getElement();
var configuration = self.getConfiguration();
- var typeDiv = self._createSelectTypeDiv(configuration.getElementTypes());
- element.appendChild(typeDiv);
+ var elementTypeDiv = Functions.createElement({type: "div", name: "elementTypes"});
+ elementTypeDiv.appendChild(self._createSelectTypeDiv(configuration.getElementTypes(), "Element type"));
+ element.appendChild(elementTypeDiv);
+ var reactionTypeDiv = Functions.createElement({type: "div", name: "reactionTypes"});
+ reactionTypeDiv.appendChild(self._createSelectTypeDiv(configuration.getReactionTypes(), "Reaction type"));
+ element.appendChild(reactionTypeDiv);
element.appendChild(self._createSelectColumnDiv(self.getAllColumns()));
return self.getServerConnector().getProjectStatistics(self.getProject().getProjectId()).then(function (statistics) {
return self._createMiriamTypeDiv(statistics.getReactionAnnotations());
@@ -118,6 +123,10 @@ NetworkExportPanel.prototype.getAllColumns = function () {
"columnName": "subsystem",
"method": "getSubsystem",
"name": "Subsystem"
+ }, {
+ "columnName": "type",
+ "method": "getType",
+ "name": "Reaction type"
}]);
};
@@ -125,9 +134,13 @@ NetworkExportPanel.prototype.getAllColumns = function () {
*
* @param {Reaction} reaction
* @param {Object<string,boolean>} elementIds
+ * @param {string[]} reactionTypes
* @returns {boolean}
*/
-function matchReaction(reaction, elementIds) {
+function matchReaction(reaction, elementIds, reactionTypes) {
+ if ($.inArray(reaction.getType(), reactionTypes) === -1) {
+ return false;
+ }
var count = 0;
reaction.getElements().forEach(function (element) {
if (elementIds[element.getId()]) {
@@ -143,18 +156,26 @@ function matchReaction(reaction, elementIds) {
*/
NetworkExportPanel.prototype.createResponseString = function () {
var self = this;
- var types, miriamTypes;
+ var elementTypes, reactionTypes, miriamTypes;
var includedCompartmentIds = [];
var excludedCompartmentIds = [];
var models = self.getProject().getModels();
var elementIds = [];
var reactions = [];
- return self.getSelectedTypes().then(function (result) {
+ var elementTypesDiv = $("[name='elementTypes']", self.getElement())[0];
+ var reactionTypesDiv = $("[name='reactionTypes']", self.getElement())[0];
+ return self.getSelectedTypes(elementTypesDiv).then(function (result) {
+ if (result.length === 0) {
+ return Promise.reject(new GuiMessageError("You must select at least one element type"));
+ }
+ elementTypes = result;
+ return self.getSelectedTypes(reactionTypesDiv);
+ }).then(function (result) {
if (result.length === 0) {
- return Promise.reject(new GuiMessageError("You must select at least one type"));
+ return Promise.reject(new GuiMessageError("You must select at least one reaction type"));
}
- types = result;
+ reactionTypes = result;
return self.getSelectedIncludedCompartments();
}).then(function (result) {
result.forEach(function (compartment) {
@@ -169,7 +190,7 @@ NetworkExportPanel.prototype.createResponseString = function () {
var promises = [];
for (var i = 0; i < models.length; i++) {
promises.push(models[i].getAliases({
- type: types,
+ type: elementTypes,
complete: true,
includedCompartmentIds: includedCompartmentIds,
excludedCompartmentIds: excludedCompartmentIds
@@ -189,7 +210,7 @@ NetworkExportPanel.prototype.createResponseString = function () {
for (var i = 0; i < models.length; i++) {
for (var j = 0; j < reactionsByModel[i].length; j++) {
var reaction = reactionsByModel[i][j];
- if (matchReaction(reaction, elementIds)) {
+ if (matchReaction(reaction, elementIds, reactionTypes)) {
reactions.push(reaction);
}
}
diff --git a/frontend-js/src/test/js/gui/export/ElementExportPanel-test.js b/frontend-js/src/test/js/gui/export/ElementExportPanel-test.js
index be02659da4..65a91982ef 100644
--- a/frontend-js/src/test/js/gui/export/ElementExportPanel-test.js
+++ b/frontend-js/src/test/js/gui/export/ElementExportPanel-test.js
@@ -42,9 +42,13 @@ describe('ElementExportPanel', function () {
it('select all', function () {
var exportObject;
var project;
- var elementTypes;
- elementTypes = helper.getConfiguration().getSimpleElementTypeNames();
+ function onlyUnique(value, index, self) {
+ return self.indexOf(value) === index;
+ }
+
+ var elementTypes = helper.getConfiguration().getSimpleElementTypeNames().filter(onlyUnique);
+
return ServerConnector.getProject().then(function (result) {
project = result;
exportObject = createExportPanel(project);
--
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