implementation of ChemicalDbOverlay

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) {

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 + "");

frontend-js/src/main/js/SessionObjectType.js

 "use strict";
 
 var SessionObjectType = {
+  CHEMICAL_QUERY : "CHEMICAL_QUERY",
   DRUG_QUERY : "DRUG_QUERY",
   SHOW_COMMENT : "SHOW_COMMENT",
   SELECTED_BACKGROUND_OVERLAY : "SELECTED_BACKGROUND_OVERLAY",

frontend-js/src/main/js/map/overlay/ChemicalDbOverlay.js

+"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;

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++;

frontend-js/src/test/js/map/overlay/ChemicalDbOverlay-test.js

+"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);
+    });
+  });
+
+});

frontend-js/testFiles/apiCalls/chemical/getChemicalsByTarget/columns=name&projectId=sample&targetId=329170&targetType=ALIAS&token=MOCK_TOKEN_ID&

+[]
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