From d627c4fed8558fdd353e71183d6a0fb6290c9ef9 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Thu, 8 Feb 2018 14:32:17 +0100
Subject: [PATCH] reaction contains kinetic law info
---
.../src/main/js/map/data/KineticLaw.js | 31 +++++++
frontend-js/src/main/js/map/data/Reaction.js | 20 ++++-
.../src/test/js/map/data/KineticLaw-test.js | 25 ++++++
.../src/test/js/map/data/Reaction-test.js | 82 +++++++++++--------
4 files changed, 121 insertions(+), 37 deletions(-)
create mode 100644 frontend-js/src/main/js/map/data/KineticLaw.js
create mode 100644 frontend-js/src/test/js/map/data/KineticLaw-test.js
diff --git a/frontend-js/src/main/js/map/data/KineticLaw.js b/frontend-js/src/main/js/map/data/KineticLaw.js
new file mode 100644
index 0000000000..81133f5dc6
--- /dev/null
+++ b/frontend-js/src/main/js/map/data/KineticLaw.js
@@ -0,0 +1,31 @@
+"use strict";
+
+function KineticLaw(jsonObject) {
+ var self = this;
+ self.setParameterIds(jsonObject.parameterIds);
+ self.setFunctionIds(jsonObject.functionIds);
+ self.setDefinition(jsonObject.definition);
+}
+
+KineticLaw.prototype.setParameterIds = function (parameterIds) {
+ this._parameterIds = parameterIds;
+};
+KineticLaw.prototype.getParameterIds = function () {
+ return this._parameterIds;
+};
+
+KineticLaw.prototype.setFunctionIds = function (functionIds) {
+ this._functionIds = functionIds;
+};
+KineticLaw.prototype.getFunctionIds = function () {
+ return this._functionIds;
+};
+
+KineticLaw.prototype.setDefinition = function (definition) {
+ this._definition = definition;
+};
+KineticLaw.prototype.getDefinition = function () {
+ return this._definition;
+};
+
+module.exports = KineticLaw;
diff --git a/frontend-js/src/main/js/map/data/Reaction.js b/frontend-js/src/main/js/map/data/Reaction.js
index e43e94c88b..a8883197e8 100644
--- a/frontend-js/src/main/js/map/data/Reaction.js
+++ b/frontend-js/src/main/js/map/data/Reaction.js
@@ -4,6 +4,7 @@
var Alias = require('./Alias');
var BioEntity = require("./BioEntity");
+var KineticLaw = require("./KineticLaw");
var logger = require('../../logger');
@@ -79,7 +80,7 @@ Reaction.prototype.getEndLines = function () {
Reaction.prototype.setCenter = function (center) {
if (center === null || center === undefined) {
- throw new Error("Setting undefined center: ", center);
+ throw new Error("Setting undefined center: " + center);
}
this._center = center;
};
@@ -103,22 +104,26 @@ Reaction.prototype.update = function (javaObject) {
this.setReferences(javaObject.references);
this.setType(javaObject.type);
- if (javaObject.reactants !== "") {
+ if (javaObject.reactants !== "" && javaObject.reactants !== undefined) {
this.setReactants(javaObject.reactants.split(","));
} else {
this.setReactants([]);
}
- if (javaObject.products !== "") {
+ if (javaObject.products !== "" && javaObject.products !== undefined) {
this.setProducts(javaObject.products.split(","));
} else {
this.setProducts([]);
}
- if (javaObject.modifiers !== "") {
+ if (javaObject.modifiers !== "" && javaObject.modifiers !== undefined) {
this.setModifiers(javaObject.modifiers.split(","));
} else {
this.setModifiers([]);
}
+ if (javaObject.kineticLaw !== undefined && javaObject.kineticLaw !== null) {
+ this.setKineticLaw(new KineticLaw(javaObject.kineticLaw));
+ }
+
this.setHierarchyVisibilityLevel(javaObject.hierarchyVisibilityLevel);
this.setIsComplete(true);
};
@@ -219,4 +224,11 @@ Reaction.prototype.getModifiers = function () {
return this._modifiers;
};
+Reaction.prototype.setKineticLaw = function (kineticLaw) {
+ this._kineticLaw = kineticLaw;
+};
+Reaction.prototype.getKineticLaw = function () {
+ return this._kineticLaw;
+};
+
module.exports = Reaction;
diff --git a/frontend-js/src/test/js/map/data/KineticLaw-test.js b/frontend-js/src/test/js/map/data/KineticLaw-test.js
new file mode 100644
index 0000000000..ea819abb40
--- /dev/null
+++ b/frontend-js/src/test/js/map/data/KineticLaw-test.js
@@ -0,0 +1,25 @@
+"use strict";
+
+var KineticLaw = require('../../../../main/js/map/data/KineticLaw');
+var chai = require('chai');
+var assert = chai.assert;
+var logger = require('../../logger');
+
+describe('Comment', function () {
+ beforeEach(function () {
+ logger.flushBuffer();
+ });
+
+ it("constructor", function () {
+ var kineticLaw = new KineticLaw({
+ "parameterIds": [],
+ "definition": '<math xmlns="http://www.w3.org/1998/Math/MathML">' +
+ '<apply xmlns="http://www.w3.org/1998/Math/MathML">' +
+ '<divide/><apply><times/><ci>ca1</ci><apply><plus/><ci>sa1</ci><ci>sa2</ci></apply></apply><cn type=\"integer\"> 2 </cn>' +
+ '</apply></math>',
+ "functionIds": []
+ });
+ assert.ok(kineticLaw);
+ assert.ok(kineticLaw.getDefinition().indexOf("apply") >= 0);
+ });
+});
diff --git a/frontend-js/src/test/js/map/data/Reaction-test.js b/frontend-js/src/test/js/map/data/Reaction-test.js
index c1d97443cd..f6050668e5 100644
--- a/frontend-js/src/test/js/map/data/Reaction-test.js
+++ b/frontend-js/src/test/js/map/data/Reaction-test.js
@@ -3,47 +3,63 @@
require("../../mocha-config.js");
var Reaction = require('../../../../main/js/map/data/Reaction');
+var KineticLaw = require('../../../../main/js/map/data/KineticLaw');
var assert = require('assert');
var logger = require('../../logger');
describe('Reaction', function () {
- it("constructor from invalid", function () {
- var javaObject = {
- lines: [{
- start: Object,
- end: Object,
- type: "UNK"
- }]
-
- };
- try {
- new Reaction(javaObject);
- } catch (exception) {
- assert.ok(exception.message.indexOf("Unknown line type") >= 0);
- }
- });
- it("constructor from invalid 2", function () {
- var javaObject = {
- lines: []
+ describe("constructor", function () {
+ it("invalid line type", function () {
+ var javaObject = {
+ lines: [{
+ start: Object,
+ end: Object,
+ type: "UNK"
+ }]
+ };
+ try {
+ new Reaction(javaObject);
+ } catch (exception) {
+ assert.ok(exception.message.indexOf("Unknown line type") >= 0);
+ }
+ });
+ it("invalid center point", function () {
+ var javaObject = {
+ lines: []
+ };
+ try {
+ new Reaction(javaObject);
+ } catch (exception) {
+ assert.ok(exception.message.indexOf("undefined center") >= 0);
+ }
+ });
- };
- try {
- new Reaction(javaObject);
- } catch (exception) {
- assert.ok(exception.message.indexOf("undefined center") >= 0);
- }
- });
- it("constructor from Reaction", function () {
- var reaction = helper.createReaction();
- var reaction2 = new Reaction(reaction);
- assert.equal(reaction2.getId(), reaction.getId());
- assert.equal(reaction2.getCenter(), reaction.getCenter());
- assert.equal(reaction2.getModelId(), reaction.getModelId());
- assert.deepEqual(reaction2.getLines(), reaction.getLines());
- assert.equal(logger.getWarnings().length, 0);
+ it("from Reaction", function () {
+ var reaction = helper.createReaction();
+ var reaction2 = new Reaction(reaction);
+ assert.equal(reaction2.getId(), reaction.getId());
+ assert.equal(reaction2.getCenter(), reaction.getCenter());
+ assert.equal(reaction2.getModelId(), reaction.getModelId());
+ assert.deepEqual(reaction2.getLines(), reaction.getLines());
+ assert.equal(logger.getWarnings().length, 0);
+ });
+
+ it("with empty Kinetics", function () {
+ var javaObject = {
+ reactionId: "re1",
+ references: [],
+ type: "",
+ lines: [],
+ centerPoint: {x: 0, y: 0},
+ kineticLaw: {}
+ };
+ var reaction = new Reaction(javaObject);
+ assert.ok(reaction.getKineticLaw() instanceof KineticLaw);
+ });
+
});
});
--
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