From 1f85699ba6d339211595bf82e0fbb583960fde8c Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Thu, 20 Jul 2017 18:00:12 +0200
Subject: [PATCH] drug, mirna and checmical have common interface
---
frontend-js/src/main/js/map/data/Chemical.js | 36 +++--------------
frontend-js/src/main/js/map/data/Drug.js | 35 +++-------------
frontend-js/src/main/js/map/data/MiRna.js | 35 ++--------------
.../main/js/map/data/TargettingStructure.js | 40 +++++++++++++++++++
.../overlay/AbstractTargettingDbOverlay.js | 18 ++++++++-
.../main/js/map/window/AbstractInfoWindow.js | 38 ++++++------------
.../test/js/gui/leftPanel/GuiUtils-test.js | 1 -
.../js/map/window/AliasInfoWindow-test.js | 8 ++++
8 files changed, 92 insertions(+), 119 deletions(-)
create mode 100644 frontend-js/src/main/js/map/data/TargettingStructure.js
diff --git a/frontend-js/src/main/js/map/data/Chemical.js b/frontend-js/src/main/js/map/data/Chemical.js
index de0fe4ec01..10fb8b1946 100644
--- a/frontend-js/src/main/js/map/data/Chemical.js
+++ b/frontend-js/src/main/js/map/data/Chemical.js
@@ -1,22 +1,25 @@
"use strict";
var Annotation = require("./Annotation");
+
var Target = require("./Target");
+var TargettingStructure = require("./TargettingStructure");
function Chemical(javaObject) {
+ TargettingStructure.call(this, javaObject);
if (javaObject !== undefined) {
- this.setName(javaObject.name);
this.setReferences(javaObject.references);
this.setDescription(javaObject.description);
this.setSynonyms(javaObject.synonyms);
- this.setId(javaObject.id);
- this.setTargets(javaObject.targets);
this.setDirectEvidence(javaObject.directEvidence);
this.setDirectEvidenceReferences(javaObject.directEvidenceReferences);
}
}
+Chemical.prototype = Object.create(TargettingStructure.prototype);
+Chemical.prototype.constructor = Chemical;
+
Chemical.prototype.setDirectEvidence = function(directeEvidence) {
this._directeEvidence = directeEvidence;
};
@@ -63,22 +66,6 @@ Chemical.prototype.getSynonyms = function() {
return this._synonyms;
};
-Chemical.prototype.setName = function(name) {
- this._name = name;
-};
-
-Chemical.prototype.getName = function() {
- return this._name;
-};
-
-Chemical.prototype.setId = function(id) {
- this._id = id;
-};
-
-Chemical.prototype.getId = function() {
- return this._id;
-};
-
Chemical.prototype.setDescription = function(description) {
this._description = description;
};
@@ -87,17 +74,6 @@ Chemical.prototype.getDescription = function() {
return this._description;
};
-Chemical.prototype.setTargets = function(targets) {
- this._targets = [];
- for (var i = 0; i < targets.length; i++) {
- this._targets.push(new Target(targets[i]));
- }
-};
-
-Chemical.prototype.getTargets = function() {
- return this._targets;
-};
-
Chemical.prototype.setBloodBrainBarrier = function(bloodBrainBarrier) {
this._bloodBrainBarrier = bloodBrainBarrier;
};
diff --git a/frontend-js/src/main/js/map/data/Drug.js b/frontend-js/src/main/js/map/data/Drug.js
index 9391dbc8a3..b737199fd4 100644
--- a/frontend-js/src/main/js/map/data/Drug.js
+++ b/frontend-js/src/main/js/map/data/Drug.js
@@ -2,20 +2,22 @@
var Annotation = require("./Annotation");
var Target = require("./Target");
+var TargettingStructure = require("./TargettingStructure");
function Drug(javaObject) {
+ TargettingStructure.call(this, javaObject);
if (javaObject !== undefined) {
this.setBrandNames(javaObject.brandNames);
this.setReferences(javaObject.references);
this.setSynonyms(javaObject.synonyms);
- this.setName(javaObject.name);
- this.setId(javaObject.id);
this.setDescription(javaObject.description);
- this.setTargets(javaObject.targets);
this.setBloodBrainBarrier(javaObject.bloodBrainBarrier);
}
}
+Drug.prototype = Object.create(TargettingStructure.prototype);
+Drug.prototype.constructor = Drug;
+
Drug.prototype.setBrandNames = function(brandNames) {
this._brandNames = brandNames;
};
@@ -43,22 +45,6 @@ Drug.prototype.getSynonyms = function() {
return this._synonyms;
};
-Drug.prototype.setName = function(name) {
- this._name = name;
-};
-
-Drug.prototype.getName = function() {
- return this._name;
-};
-
-Drug.prototype.setId = function(id) {
- this._id = id;
-};
-
-Drug.prototype.getId = function() {
- return this._id;
-};
-
Drug.prototype.setDescription = function(description) {
this._description = description;
};
@@ -67,17 +53,6 @@ Drug.prototype.getDescription = function() {
return this._description;
};
-Drug.prototype.setTargets = function(targets) {
- this._targets = [];
- for (var i = 0; i < targets.length; i++) {
- this._targets.push(new Target(targets[i]));
- }
-};
-
-Drug.prototype.getTargets = function() {
- return this._targets;
-};
-
Drug.prototype.setBloodBrainBarrier = function(bloodBrainBarrier) {
this._bloodBrainBarrier = bloodBrainBarrier;
};
diff --git a/frontend-js/src/main/js/map/data/MiRna.js b/frontend-js/src/main/js/map/data/MiRna.js
index 2b8f60c887..6c09ac419b 100644
--- a/frontend-js/src/main/js/map/data/MiRna.js
+++ b/frontend-js/src/main/js/map/data/MiRna.js
@@ -1,40 +1,13 @@
"use strict";
var Target = require("./Target");
+var TargettingStructure = require("./TargettingStructure");
function MiRna(javaObject) {
- if (javaObject !== undefined) {
- this.setName(javaObject.name);
- this.setId(javaObject.id);
- this.setTargets(javaObject.targets);
- }
+ TargettingStructure.call(this, javaObject);
}
-MiRna.prototype.setName = function(name) {
- this._name = name;
-};
-
-MiRna.prototype.getName = function() {
- return this._name;
-};
-
-MiRna.prototype.setId = function(id) {
- this._id = id;
-};
-
-MiRna.prototype.getId = function() {
- return this._id;
-};
-
-MiRna.prototype.setTargets = function(targets) {
- this._targets = [];
- for (var i = 0; i < targets.length; i++) {
- this._targets.push(new Target(targets[i]));
- }
-};
-
-MiRna.prototype.getTargets = function() {
- return this._targets;
-};
+MiRna.prototype = Object.create(TargettingStructure.prototype);
+MiRna.prototype.constructor = MiRna;
module.exports = MiRna;
diff --git a/frontend-js/src/main/js/map/data/TargettingStructure.js b/frontend-js/src/main/js/map/data/TargettingStructure.js
new file mode 100644
index 0000000000..c313ff3985
--- /dev/null
+++ b/frontend-js/src/main/js/map/data/TargettingStructure.js
@@ -0,0 +1,40 @@
+"use strict";
+
+var Target = require("./Target");
+
+function TargettingStructure(javaObject) {
+ if (javaObject !== undefined) {
+ this.setName(javaObject.name);
+ this.setId(javaObject.id);
+ this.setTargets(javaObject.targets);
+ }
+}
+
+TargettingStructure.prototype.setName = function(name) {
+ this._name = name;
+};
+
+TargettingStructure.prototype.getName = function() {
+ return this._name;
+};
+
+TargettingStructure.prototype.setId = function(id) {
+ this._id = id;
+};
+
+TargettingStructure.prototype.getId = function() {
+ return this._id;
+};
+
+TargettingStructure.prototype.setTargets = function(targets) {
+ this._targets = [];
+ for (var i = 0; i < targets.length; i++) {
+ this._targets.push(new Target(targets[i]));
+ }
+};
+
+TargettingStructure.prototype.getTargets = function() {
+ return this._targets;
+};
+
+module.exports = TargettingStructure;
diff --git a/frontend-js/src/main/js/map/overlay/AbstractTargettingDbOverlay.js b/frontend-js/src/main/js/map/overlay/AbstractTargettingDbOverlay.js
index f7b7b1eff6..9d0fa57f97 100644
--- a/frontend-js/src/main/js/map/overlay/AbstractTargettingDbOverlay.js
+++ b/frontend-js/src/main/js/map/overlay/AbstractTargettingDbOverlay.js
@@ -114,7 +114,21 @@ AbstractTargettingDbOverlay.prototype.getIdentifiedElements = function() {
AbstractTargettingDbOverlay.prototype.getDetailDataByIdentifiedElement = function(element, general) {
var self = this;
if (general) {
- return self.searchNamesByTarget(element);
+ return self.searchNamesByTarget(element).then(function(names) {
+ var promises = [];
+ names.forEach(function(name) {
+ promises.push(self.searchBySingleQuery(name));
+ })
+ return Promise.all(promises);
+ }).then(function(drugs) {
+ var result = [];
+ drugs.forEach(function(drugList) {
+ drugList.forEach(function(drug) {
+ result.push(drug);
+ })
+ });
+ return result;
+ });
} else {
return new Promise(function(resolve) {
var result = [];
@@ -131,7 +145,7 @@ AbstractTargettingDbOverlay.prototype.getDetailDataByIdentifiedElement = functio
var elements = targets[k].getTargetElements();
for (var l = 0; l < elements.length; l++) {
if (element.equals(elements[l])) {
- result.push(drug.getName());
+ result.push(drug);
}
}
}
diff --git a/frontend-js/src/main/js/map/window/AbstractInfoWindow.js b/frontend-js/src/main/js/map/window/AbstractInfoWindow.js
index d9f2caf8a2..ba14cb62b1 100644
--- a/frontend-js/src/main/js/map/window/AbstractInfoWindow.js
+++ b/frontend-js/src/main/js/map/window/AbstractInfoWindow.js
@@ -442,14 +442,8 @@ AbstractInfoWindow.prototype._createTargetInfoDiv = function(overlay, data, name
count = 0;
for ( var dataId in data) {
- if (data.hasOwnProperty(dataId) && data[dataId] !== undefined && data[dataId] !== null) {
- // if we have empty array, it means that we got data from server and it's
- // empty
- if (Object.prototype.toString.call(data[dataId]) === '[object Array]') {
- continue;
- } else {
- count++;
- }
+ if (data.hasOwnProperty(dataId)) {
+ count++;
}
}
@@ -458,25 +452,19 @@ AbstractInfoWindow.prototype._createTargetInfoDiv = function(overlay, data, name
table.appendChild(row);
for ( var searchId in data) {
- if (data.hasOwnProperty(searchId) && data[searchId] !== undefined && data[searchId] !== null) {
- // if we have empty array, it means that we got data from server and
- // it's
- // empty
- if (Object.prototype.toString.call(data[searchId]) === '[object Array]') {
- continue;
+ if (data.hasOwnProperty(searchId)) {
+ row = document.createElement("tr");
+ cell = document.createElement("td");
+ if (typeof data[searchId] === "string") {
+ cell.innerHTML = data[searchId];
+ } else if (typeof data[searchId].getName === "function") {
+ cell.innerHTML = data[searchId].getName();
} else {
- row = document.createElement("tr");
- cell = document.createElement("td");
- if (typeof data[searchId] === "string") {
- cell.innerHTML = data[searchId];
- } else {
- cell.innerHTML = searchId;
- }
-
- row.appendChild(cell);
- table.appendChild(row);
- count++;
+ cell.innerHTML = searchId;
}
+ row.appendChild(cell);
+ table.appendChild(row);
+ count++;
}
}
if (count === 0) {
diff --git a/frontend-js/src/test/js/gui/leftPanel/GuiUtils-test.js b/frontend-js/src/test/js/gui/leftPanel/GuiUtils-test.js
index 6617b629b7..5e0492f2f6 100644
--- a/frontend-js/src/test/js/gui/leftPanel/GuiUtils-test.js
+++ b/frontend-js/src/test/js/gui/leftPanel/GuiUtils-test.js
@@ -101,7 +101,6 @@ describe('GuiUtils', function() {
var res = utils.createPostTranslationalModifications("label", alias.getOther("modifications"));
assert.ok(res.innerHTML);
assert.ok(res.innerHTML.indexOf("phosphorylated") >= 0);
- logger.debug(res.innerHTML);
});
describe('createReactionElement', function() {
diff --git a/frontend-js/src/test/js/map/window/AliasInfoWindow-test.js b/frontend-js/src/test/js/map/window/AliasInfoWindow-test.js
index 7010e8351e..158e53b6c3 100644
--- a/frontend-js/src/test/js/map/window/AliasInfoWindow-test.js
+++ b/frontend-js/src/test/js/map/window/AliasInfoWindow-test.js
@@ -7,6 +7,7 @@ var functions = require('../../../../main/js/Functions');
var Helper = require('../../Helper');
var Alias = require('../../../../main/js/map/data/Alias');
+var Drug = require('../../../../main/js/map/data/Drug');
var AliasInfoWindow = require('../../../../main/js/map/window/AliasInfoWindow');
var IdentifiedElement = require('../../../../main/js/map/data/IdentifiedElement');
var LayoutData = require('../../../../main/js/map/data/LayoutData');
@@ -80,6 +81,13 @@ describe('AliasInfoWindow', function() {
oc.searchNamesByTarget = function() {
return Promise.resolve([ "xField" ]);
};
+ oc.getElementsByQueryFromServer = function() {
+ return Promise.resolve([ new Drug({
+ name : "xField",
+ references : [],
+ targets : [],
+ }) ]);
+ }
return oc.getDetailDataByIdentifiedElement(new IdentifiedElement(alias), true).then(function(data) {
var overlayDiv = aliasWindow.createOverlayInfoDiv(oc, data);
--
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