diff --git a/frontend-js/src/main/js/ServerConnector.js b/frontend-js/src/main/js/ServerConnector.js index bfde71174a8acc063017f8e2a50899b2825b1ae6..be1e48a07a4d4eb4d202ebfd10f5bb3e7f8101c8 100644 --- a/frontend-js/src/main/js/ServerConnector.js +++ b/frontend-js/src/main/js/ServerConnector.js @@ -736,6 +736,41 @@ ServerConnector.getDrugsByTargetUrl = function(params) { }); }; +ServerConnector.getChemicalsByQueryUrl = function(params) { + var query = params.query; + var projectId = params.projectId; + var token = params.token; + + return this.getApiUrl({type:"chemical", + method:"getChemicalsByQuery", + params: { + projectId: projectId, + query: query, + token: token}, + }); +}; + +ServerConnector.getChemicalsByTargetUrl = 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:"chemical", + method:"getChemicalsByTarget", + params: { + projectId: projectId, + query: query, + columns: columns, + token: token, + targetId: targetId, + targetType: targetType, + }, + }); +}; + ServerConnector.getConfigurationParam = function(paramId) { var self = this; return new Promise(function(resolve, reject) { @@ -1023,6 +1058,28 @@ ServerConnector.getDrugsByQuery = function(params) { }); }; +ServerConnector.getChemicalsByQuery = 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.getChemicalsByQueryUrl(params)); + }).then(function(content) { + var array=JSON.parse(content); + var result = []; + for (var i = 0; i < array.length; i++) { + result.push(new Drug(array[i])); + } + resolve(result); + }).catch(function(exception){ + reject(exception); + }); + }); +}; + ServerConnector.getDrugNamesByTarget = function(params) { var self = this; params.columns = ["name"]; @@ -1046,6 +1103,29 @@ ServerConnector.getDrugNamesByTarget = function(params) { }); }; +ServerConnector.getChemicalNamesByTarget = 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.getChemicalsByTargetUrl(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.addComment = function(params) { var self = this; return new Promise(function(resolve, reject) { diff --git a/frontend-js/src/main/js/SessionData.js b/frontend-js/src/main/js/SessionData.js index 7c58c887b95e14baaf14f596582a65dd5a5fe6d0..392790edefa78eb57aa95e2da226a121e9059325 100644 --- a/frontend-js/src/main/js/SessionData.js +++ b/frontend-js/src/main/js/SessionData.js @@ -34,6 +34,8 @@ SessionData.prototype.setQuery = function(param) { this.setDrugQuery(param.query); } else if (param.type === "search") { this.setSearchQuery(param.query); + } else if (param.type === "chemical") { + this.setChemicalQuery(param.query); } else { throw new Error("Invalid query type: " + param.type); } @@ -62,6 +64,20 @@ SessionData.prototype.getDrugQuery = function() { return result; }; +SessionData.prototype.setChemicalQuery = function(value) { + var key = this.getKey(SessionObjectType.CHEMICAL_QUERY); + Cookies.set(key, JSON.stringify(value)); +}; + +SessionData.prototype.getChemicalQuery = function() { + var key = this.getKey(SessionObjectType.CHEMICAL_QUERY); + var result = Cookies.get(key); + if (result !== undefined) { + result = JSON.parse(result); + } + return result; +}; + SessionData.prototype.setShowComments = function(value) { var key = this.getKey(SessionObjectType.SHOW_COMMENT); Cookies.set(key, value + ""); diff --git a/frontend-js/src/main/js/SessionObjectType.js b/frontend-js/src/main/js/SessionObjectType.js index 1148eb5d079c1854b965997d27644e57d79909fd..616d9e66218ea2a073de15dc9d80b874bdb873b0 100644 --- a/frontend-js/src/main/js/SessionObjectType.js +++ b/frontend-js/src/main/js/SessionObjectType.js @@ -1,6 +1,7 @@ "use strict"; var SessionObjectType = { + CHEMICAL_QUERY : "CHEMICAL_QUERY", DRUG_QUERY : "DRUG_QUERY", SHOW_COMMENT : "SHOW_COMMENT", SELECTED_BACKGROUND_OVERLAY : "SELECTED_BACKGROUND_OVERLAY", diff --git a/frontend-js/src/main/js/map/overlay/ChemicalDbOverlay.js b/frontend-js/src/main/js/map/overlay/ChemicalDbOverlay.js new file mode 100644 index 0000000000000000000000000000000000000000..19e3fcfa2bf8f68bd413f31c1646a59b9113a9db --- /dev/null +++ b/frontend-js/src/main/js/map/overlay/ChemicalDbOverlay.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 ChemicalDbOverlay(params) { + params.iconType= "ball"; + params.iconColorStart = 1; + // call super constructor + AbstractTargettingDbOverlay.call(this, params); + +} + +ChemicalDbOverlay.prototype = Object.create(AbstractTargettingDbOverlay.prototype); +ChemicalDbOverlay.prototype.constructor = ChemicalDbOverlay; + +ChemicalDbOverlay.prototype.getNamesByTargetFromServer = function(param) { + return ServerConnector.getChemicalNamesByTarget(param); +} + +ChemicalDbOverlay.prototype.getElementsByQueryFromServer = function(param) { + return ServerConnector.getChemicalsByQuery(param); +} + +module.exports = ChemicalDbOverlay; diff --git a/frontend-js/src/test/js/helper.js b/frontend-js/src/test/js/helper.js index 3d75b1b79544808bdd1670b5444dcaf4ebc9e973..1d4ac957d7a33108d3cb23ed14adb70da28b9996 100644 --- a/frontend-js/src/test/js/helper.js +++ b/frontend-js/src/test/js/helper.js @@ -4,6 +4,7 @@ require("./mocha-config"); var Alias = require("../../main/js/map/data/Alias"); var AbstractCustomMap = require("../../main/js/map/AbstractCustomMap"); +var ChemicalDbOverlay = require("../../main/js/map/overlay/ChemicalDbOverlay"); var Comment = require("../../main/js/map/data/Comment"); var CommentDbOverlay = require("../../main/js/map/overlay/CommentDbOverlay"); var CustomMap = require("../../main/js/map/CustomMap"); @@ -99,6 +100,17 @@ Helper.prototype.createDrugDbOverlay = function(map) { return result; }; +Helper.prototype.createChemicalDbOverlay = function(map) { + var result = new ChemicalDbOverlay({ + map : map, + name : "chemical", + 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/ChemicalDbOverlay-test.js b/frontend-js/src/test/js/map/overlay/ChemicalDbOverlay-test.js new file mode 100644 index 0000000000000000000000000000000000000000..f73b9ebddc27671462a8b94a0ba5275f45cd1307 --- /dev/null +++ b/frontend-js/src/test/js/map/overlay/ChemicalDbOverlay-test.js @@ -0,0 +1,65 @@ +"use strict"; + +var Helper = require('../../Helper'); + +var logger = require('../../logger'); + +var IdentifiedElement = require('../../../../main/js/map/data/IdentifiedElement'); +var ChemicalDbOverlay = require('../../../../main/js/map/overlay/ChemicalDbOverlay'); + +var assert = require('assert'); + +describe('ChemicalDbOverlay', function() { + var helper; + before(function() { + helper = new Helper(); + }); + + it("constructor 1", function() { + var map = helper.createCustomMap(); + var oc = new ChemicalDbOverlay({ + map : map, + name : 'chemical' + }); + assert.ok(oc); + assert.equal(oc.getName(), 'chemical'); + + assert.equal(logger.getWarnings.length, 0); + }); + + it("searchByQuery", function() { + var map = helper.createCustomMap(); + map.getModel().setId(15781); + var searchDb = helper.createChemicalDbOverlay(map); + return searchDb.searchByQuery("rotenone").then(function(chemicals) { + assert.equal(chemicals.length, 1); + assert.equal(searchDb.getQueries().length, 1); + return searchDb.getElementsByQuery(searchDb.getQueries()[0]); + }).then(function(elements) { + //these are targets + assert.ok(elements.length>0); + var chemical = elements.element; + assert.equal(chemical.getName(), "Rotenone"); + 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.createChemicalDbOverlay(map); + + var target = new IdentifiedElement({ + type : "ALIAS", + id : 329170, + modelId : 15781, + }); + + return searchDb.searchNamesByTarget(target).then(function(chemicalNames) { + assert.equal(chemicalNames.length, 0); + }); + }); + +}); diff --git a/frontend-js/testFiles/apiCalls/chemical/getChemicalsByQuery/projectId=sample&query=rotenone&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/chemical/getChemicalsByQuery/projectId=sample&query=rotenone&token=MOCK_TOKEN_ID& new file mode 100644 index 0000000000000000000000000000000000000000..8f223c5699efb05be5f4230652eea8e83227f8ae --- /dev/null +++ b/frontend-js/testFiles/apiCalls/chemical/getChemicalsByQuery/projectId=sample&query=rotenone&token=MOCK_TOKEN_ID& @@ -0,0 +1 @@ +[{"directevidence":"marker/mechanism","references":[{"name":"D012402","type":"Toxicogenomic Chemical","link":"http://ctdbase.org/detail.go?type\u003dchem\u0026acc\u003dD012402","idObject":0},{"name":"83-79-4","type":"Chemical Abstracts Service","link":"http://commonchemistry.org/ChemicalDetail.aspx?ref\u003d83-79-4","idObject":0}],"synonyms":[],"directevidencereferences":[],"name":"Rotenone","description":"A botanical insecticide that is an inhibitor of mitochondrial electron transport.","id":"Rotenone","targets":[{"targetElements":[],"references":[{"title":"In vitro search for synergy between flavonoids and epirubicin on multidrug-resistant cancer cells.","authors":["Gyémánt N"," Tanaka M"," Antus S"," Hohmann J"," Csuka O"," Mándoky L"," Molnár J."],"journal":"In vivo (Athens, Greece)","year":2005,"link":"http://www.ncbi.nlm.nih.gov/pubmed/15796199","id":"15796199","citationCount":14}],"name":"ABCB1","targetParticipants":[{"name":"ABCB1","type":"HGNC 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