From 4491c406071757a359bd796c38179021cb391a1c Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 20 Jan 2017 15:19:13 +0100
Subject: [PATCH] MiRna Overlay Db implemented
---
frontend-js/src/main/js/ServerConnector.js | 81 +++++++++++++++++++
frontend-js/src/main/js/SessionData.js | 16 ++++
frontend-js/src/main/js/SessionObjectType.js | 1 +
frontend-js/src/main/js/map/data/MiRna.js | 40 +++++++++
.../src/main/js/map/overlay/MiRnaDbOverlay.js | 31 +++++++
frontend-js/src/test/js/helper.js | 16 ++++
.../js/map/overlay/MiRnaDbOverlay-test.js | 62 ++++++++++++++
...query=hsa-miR-125a-3p&token=MOCK_TOKEN_ID& | 1 +
...9170&targetType=ALIAS&token=MOCK_TOKEN_ID& | 1 +
9 files changed, 249 insertions(+)
create mode 100644 frontend-js/src/main/js/map/data/MiRna.js
create mode 100644 frontend-js/src/main/js/map/overlay/MiRnaDbOverlay.js
create mode 100644 frontend-js/src/test/js/map/overlay/MiRnaDbOverlay-test.js
create mode 100644 frontend-js/testFiles/apiCalls/miRna/getMiRnasByQuery/projectId=sample&query=hsa-miR-125a-3p&token=MOCK_TOKEN_ID&
create mode 100644 frontend-js/testFiles/apiCalls/miRna/getMiRnasByTarget/columns=name&projectId=sample&targetId=329170&targetType=ALIAS&token=MOCK_TOKEN_ID&
diff --git a/frontend-js/src/main/js/ServerConnector.js b/frontend-js/src/main/js/ServerConnector.js
index 4088ad4b7a..a2c861e1fe 100644
--- a/frontend-js/src/main/js/ServerConnector.js
+++ b/frontend-js/src/main/js/ServerConnector.js
@@ -16,6 +16,7 @@ var IdentifiedElement= require('./map/data/IdentifiedElement');
var LayoutAlias = require('./map/data/LayoutAlias');
var LayoutData = require('./map/data/LayoutData');
var LayoutReaction = require('./map/data/LayoutReaction');
+var MiRna = require('./map/data/MiRna');
var Project = require('./map/data/Project');
var Reaction = require('./map/data/Reaction');
var SessionData = require('./SessionData');
@@ -690,6 +691,41 @@ ServerConnector.getDrugsByTargetUrl = function(params) {
});
};
+ServerConnector.getMiRnasByQueryUrl = function(params) {
+ var query = params.query;
+ var projectId = params.projectId;
+ var token = params.token;
+
+ return this.getApiUrl({type:"miRna",
+ method:"getMiRnasByQuery",
+ params: {
+ projectId: projectId,
+ query: query,
+ token: token},
+ });
+};
+
+ServerConnector.getMiRnasByTargetUrl = function(params) {
+ var query = params.query;
+ var projectId = params.projectId;
+ var token = params.token;
+ var columns = this.idsToString(params.columns);
+ var targetId = params.target.getId();
+ var targetType = params.target.getType();
+
+ return this.getApiUrl({type:"miRna",
+ method:"getMiRnasByTarget",
+ params: {
+ projectId: projectId,
+ query: query,
+ columns: columns,
+ token: token,
+ targetId: targetId,
+ targetType: targetType,
+ },
+ });
+};
+
ServerConnector.getChemicalsByQueryUrl = function(params) {
var query = params.query;
var projectId = params.projectId;
@@ -1012,6 +1048,28 @@ ServerConnector.getDrugsByQuery = function(params) {
});
};
+ServerConnector.getMiRnasByQuery = function(params) {
+ var self = this;
+ return new Promise(function(resolve, reject) {
+ return self.getProjectId(params.projectId).then(function(result) {
+ params.projectId = result;
+ return self.getToken();
+ }).then(function(token) {
+ params.token = token;
+ return self.readFile(self.getMiRnasByQueryUrl(params));
+ }).then(function(content) {
+ var array=JSON.parse(content);
+ var result = [];
+ for (var i = 0; i < array.length; i++) {
+ result.push(new MiRna(array[i]));
+ }
+ resolve(result);
+ }).catch(function(exception){
+ reject(exception);
+ });
+ });
+};
+
ServerConnector.getChemicalsByQuery = function(params) {
var self = this;
return new Promise(function(resolve, reject) {
@@ -1057,6 +1115,29 @@ ServerConnector.getDrugNamesByTarget = function(params) {
});
};
+ServerConnector.getMiRnaNamesByTarget = function(params) {
+ var self = this;
+ params.columns = ["name"];
+ return new Promise(function(resolve, reject) {
+ return self.getProjectId(params.projectId).then(function(result) {
+ params.projectId = result;
+ return self.getToken();
+ }).then(function(token) {
+ params.token = token;
+ return self.readFile(self.getMiRnasByTargetUrl(params));
+ }).then(function(content) {
+ var result = [];
+ var object = JSON.parse(content);
+ for (var i=0;i<object.length;i++){
+ result.push(object[i].name);
+ }
+ resolve(result);
+ }).catch(function(exception){
+ reject(exception);
+ });
+ });
+};
+
ServerConnector.getChemicalNamesByTarget = function(params) {
var self = this;
params.columns = ["name"];
diff --git a/frontend-js/src/main/js/SessionData.js b/frontend-js/src/main/js/SessionData.js
index 392790edef..2b9c36db3d 100644
--- a/frontend-js/src/main/js/SessionData.js
+++ b/frontend-js/src/main/js/SessionData.js
@@ -36,6 +36,8 @@ SessionData.prototype.setQuery = function(param) {
this.setSearchQuery(param.query);
} else if (param.type === "chemical") {
this.setChemicalQuery(param.query);
+ } else if (param.type === "mirna") {
+ this.setMiRnaQuery(param.query);
} else {
throw new Error("Invalid query type: " + param.type);
}
@@ -64,6 +66,20 @@ SessionData.prototype.getDrugQuery = function() {
return result;
};
+SessionData.prototype.setMiRnaQuery = function(value) {
+ var key = this.getKey(SessionObjectType.MI_RNA_QUERY);
+ Cookies.set(key, JSON.stringify(value));
+};
+
+SessionData.prototype.getMiRnaQuery = function() {
+ var key = this.getKey(SessionObjectType.MI_RNA_QUERY);
+ var result = Cookies.get(key);
+ if (result !== undefined) {
+ result = JSON.parse(result);
+ }
+ return result;
+};
+
SessionData.prototype.setChemicalQuery = function(value) {
var key = this.getKey(SessionObjectType.CHEMICAL_QUERY);
Cookies.set(key, JSON.stringify(value));
diff --git a/frontend-js/src/main/js/SessionObjectType.js b/frontend-js/src/main/js/SessionObjectType.js
index 616d9e6621..911929e6dd 100644
--- a/frontend-js/src/main/js/SessionObjectType.js
+++ b/frontend-js/src/main/js/SessionObjectType.js
@@ -3,6 +3,7 @@
var SessionObjectType = {
CHEMICAL_QUERY : "CHEMICAL_QUERY",
DRUG_QUERY : "DRUG_QUERY",
+ MI_RNA_QUERY : "MI_RNA_QUERY",
SHOW_COMMENT : "SHOW_COMMENT",
SELECTED_BACKGROUND_OVERLAY : "SELECTED_BACKGROUND_OVERLAY",
SEARCH_QUERY : "SEARCH_QUERY",
diff --git a/frontend-js/src/main/js/map/data/MiRna.js b/frontend-js/src/main/js/map/data/MiRna.js
new file mode 100644
index 0000000000..2b8f60c887
--- /dev/null
+++ b/frontend-js/src/main/js/map/data/MiRna.js
@@ -0,0 +1,40 @@
+"use strict";
+
+var Target = require("./Target");
+
+function MiRna(javaObject) {
+ if (javaObject !== undefined) {
+ this.setName(javaObject.name);
+ this.setId(javaObject.id);
+ this.setTargets(javaObject.targets);
+ }
+}
+
+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;
+};
+
+module.exports = MiRna;
diff --git a/frontend-js/src/main/js/map/overlay/MiRnaDbOverlay.js b/frontend-js/src/main/js/map/overlay/MiRnaDbOverlay.js
new file mode 100644
index 0000000000..23e5d9c33f
--- /dev/null
+++ b/frontend-js/src/main/js/map/overlay/MiRnaDbOverlay.js
@@ -0,0 +1,31 @@
+"use strict";
+
+var logger = require('../../logger');
+
+var Promise = require("bluebird");
+
+var IdentifiedElement = require('../data/IdentifiedElement');
+var AbstractTargettingDbOverlay = require('./AbstractTargettingDbOverlay');
+
+var ServerConnector = require('../../ServerConnector');
+
+function MiRnaDbOverlay(params) {
+ params.iconType= "target";
+ params.iconColorStart = 2;
+ // call super constructor
+ AbstractTargettingDbOverlay.call(this, params);
+
+}
+
+MiRnaDbOverlay.prototype = Object.create(AbstractTargettingDbOverlay.prototype);
+MiRnaDbOverlay.prototype.constructor = MiRnaDbOverlay;
+
+MiRnaDbOverlay.prototype.getNamesByTargetFromServer = function(param) {
+ return ServerConnector.getMiRnaNamesByTarget(param);
+}
+
+MiRnaDbOverlay.prototype.getElementsByQueryFromServer = function(param) {
+ return ServerConnector.getMiRnasByQuery(param);
+}
+
+module.exports = MiRnaDbOverlay;
diff --git a/frontend-js/src/test/js/helper.js b/frontend-js/src/test/js/helper.js
index 52fb8a8766..6ca84dd1e2 100644
--- a/frontend-js/src/test/js/helper.js
+++ b/frontend-js/src/test/js/helper.js
@@ -14,6 +14,7 @@ var IdentifiedElement = require("../../main/js/map/data/IdentifiedElement");
var LayoutAlias = require("../../main/js/map/data/LayoutAlias");
var LayoutData = require("../../main/js/map/data/LayoutData");
var LayoutReaction = require("../../main/js/map/data/LayoutReaction");
+var MiRnaDbOverlay = require("../../main/js/map/overlay/MiRnaDbOverlay");
var Model = require("../../main/js/map/data/MapModel");
var OverlayCollection = require("../../main/js/map/overlay/OverlayCollection");
var Project = require("../../main/js/map/data/Project");
@@ -36,6 +37,10 @@ Helper.prototype.createChemicalTab = function() {
return this.createPanelTab("chemicalTab");
};
+Helper.prototype.createMiRnaTab = function() {
+ return this.createPanelTab("mirnaTab");
+};
+
Helper.prototype.createPanelTab = function(id) {
var result = document.createElement("div");
result.id = id;
@@ -115,6 +120,17 @@ Helper.prototype.createChemicalDbOverlay = function(map) {
return result;
};
+Helper.prototype.createMiRnaDbOverlay = function(map) {
+ var result = new MiRnaDbOverlay({
+ map : map,
+ name : "mirna",
+ allowGeneralSearch : true,
+ allowSearchById : true,
+ });
+ map.registerSource(result);
+ return result;
+};
+
Helper.prototype.createComment = function(element) {
var elementType = "ALIAS";
var elementId = this.idCounter++;
diff --git a/frontend-js/src/test/js/map/overlay/MiRnaDbOverlay-test.js b/frontend-js/src/test/js/map/overlay/MiRnaDbOverlay-test.js
new file mode 100644
index 0000000000..4e5efe554e
--- /dev/null
+++ b/frontend-js/src/test/js/map/overlay/MiRnaDbOverlay-test.js
@@ -0,0 +1,62 @@
+"use strict";
+
+var Helper = require('../../Helper');
+
+var logger = require('../../logger');
+
+var IdentifiedElement = require('../../../../main/js/map/data/IdentifiedElement');
+var MiRnaDbOverlay = require('../../../../main/js/map/overlay/MiRnaDbOverlay');
+
+var assert = require('assert');
+
+describe('MiRnaDbOverlay', function() {
+ var helper;
+ before(function() {
+ helper = new Helper();
+ });
+
+ it("constructor 1", function() {
+ var map = helper.createCustomMap();
+ var oc = new MiRnaDbOverlay({
+ map : map,
+ name : 'miRna'
+ });
+ assert.ok(oc);
+ assert.equal(oc.getName(), 'miRna');
+
+ assert.equal(logger.getWarnings.length, 0);
+ });
+
+ it("searchByQuery", function() {
+ var map = helper.createCustomMap();
+ map.getModel().setId(15781);
+ var searchDb = helper.createMiRnaDbOverlay(map);
+ return searchDb.searchByQuery("hsa-miR-125a-3p").then(function(miRnas) {
+ assert.equal(miRnas.length, 1);
+ assert.equal(searchDb.getQueries().length, 1);
+ return searchDb.getElementsByQuery(searchDb.getQueries()[0]);
+ }).then(function(elements) {
+ assert.equal(elements.length, 3);
+ return searchDb.getIdentifiedElements();
+ }).then(function(elements) {
+ assert.equal(elements.length, 0);
+ });
+ });
+
+ it("searchNamesByTarget", function() {
+ var map = helper.createCustomMap();
+ map.getModel().setId(15781);
+ var searchDb = helper.createMiRnaDbOverlay(map);
+
+ var target = new IdentifiedElement({
+ type : "ALIAS",
+ id : 329170,
+ modelId : 15781,
+ });
+
+ return searchDb.searchNamesByTarget(target).then(function(miRnaNames) {
+ assert.equal(miRnaNames.length, 0);
+ });
+ });
+
+});
diff --git a/frontend-js/testFiles/apiCalls/miRna/getMiRnasByQuery/projectId=sample&query=hsa-miR-125a-3p&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/miRna/getMiRnasByQuery/projectId=sample&query=hsa-miR-125a-3p&token=MOCK_TOKEN_ID&
new file mode 100644
index 0000000000..ad629e97ae
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/miRna/getMiRnasByQuery/projectId=sample&query=hsa-miR-125a-3p&token=MOCK_TOKEN_ID&
@@ -0,0 +1 @@
+[{"name":"hsa-miR-125a-3p","id":"hsa-miR-125a-3p","targets":[{"targetElements":[],"references":[{"title":"microRNA-125a-3p reduces cell proliferation and migration by targeting Fyn.","authors":["Ninio-Many L"," Grossman H"," Shomron N"," Chuderland D"," Shalgi R."],"journal":"Journal of cell science","year":2013,"link":"http://www.ncbi.nlm.nih.gov/pubmed/23606749","id":"23606749","citationCount":6}],"name":"FYN","targetParticipants":[{"name":"FYN","type":"HGNC Symbol","link":"http://www.genenames.org/cgi-bin/gene_symbol_report?match\u003dFYN","idObject":0}]},{"targetElements":[],"references":[{"title":"MicroRNA-125a inhibits cell growth by targeting glypican-4.","authors":["Feng C"," Li J"," Ruan J"," Ding K."],"journal":"Glycoconjugate journal","year":2012,"link":"http://www.ncbi.nlm.nih.gov/pubmed/22644326","id":"22644326","citationCount":4}],"name":"GPC4","targetParticipants":[{"name":"GPC4","type":"HGNC Symbol","link":"http://www.genenames.org/cgi-bin/gene_symbol_report?match\u003dGPC4","idObject":0}]},{"targetElements":[],"references":[{"title":"MiRNA-125a-3p is a negative regulator of the RhoA-actomyosin pathway in A549 cells.","authors":["Huang B"," Luo W"," Sun L"," Zhang Q"," Jiang L"," Chang J"," Qiu X"," Wang E."],"journal":"International journal of oncology","year":2013,"link":"http://www.ncbi.nlm.nih.gov/pubmed/23525486","id":"23525486","citationCount":4}],"name":"RHOA","targetParticipants":[{"name":"RHOA","type":"HGNC Symbol","link":"http://www.genenames.org/cgi-bin/gene_symbol_report?match\u003dRHOA","idObject":0}]}]}]
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/miRna/getMiRnasByTarget/columns=name&projectId=sample&targetId=329170&targetType=ALIAS&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/miRna/getMiRnasByTarget/columns=name&projectId=sample&targetId=329170&targetType=ALIAS&token=MOCK_TOKEN_ID&
new file mode 100644
index 0000000000..0637a088a0
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/miRna/getMiRnasByTarget/columns=name&projectId=sample&targetId=329170&targetType=ALIAS&token=MOCK_TOKEN_ID&
@@ -0,0 +1 @@
+[]
\ No newline at end of file
--
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