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Commit e2f6baa9 authored by Piotr Gawron's avatar Piotr Gawron
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extracting common interface for targeting database from drug 

this interface can be used by rna chemicals later
parent 545ecb8d
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frontend-js/src/main/js/gui/DrugPanel.js
View file @ e2f6baa9
......@@ -107,7 +107,7 @@ DrugPanel.prototype.addResultTab = function(query, elements) {
contentElement.appendChild(contentDiv);
contentDiv.appendChild(this.createDrugHeader(elements.drug));
contentDiv.appendChild(this.createDrugHeader(elements.element));
var tableDiv = document.createElement("table");
tableDiv.className = "table table-bordered";
......
frontend-js/src/main/js/map/overlay/AbstractDbOverlay.js
View file @ e2f6baa9
......@@ -18,7 +18,6 @@ function AbstractDbOverlay(params) {
this._elementsByQuery = [];
this._drugsByQuery = [];
this.registerListenerType('onSearch');
this.registerListenerType('onTargetVisibilityChange');
......@@ -97,8 +96,6 @@ AbstractDbOverlay.prototype.searchNamesByTarget = function(element) {
var self = this;
var query = self.encodeQuery(AbstractDbOverlay.QueryType.SEARCH_BY_TARGET, element);
ServerConnector.getSessionData().setQuery({type:self.getName(),query:query});
return new Promise(function(resolve, reject) {
if (self._elementsByQuery[query] !== undefined) {
resolve(self._elementsByQuery[query]);
......@@ -156,7 +153,7 @@ AbstractDbOverlay.prototype.searchByEncodedQuery = function(originalQuery) {
if (query.type === AbstractDbOverlay.QueryType.SEARCH_BY_QUERY) {
return this.searchByQuery(query.query, query.perfect);
} else if (query.type === AbstractDbOverlay.QueryType.SEARCH_BY_TARGET) {
return this.searchByTarget(query.target);
return this.searchNamesByTarget(query.target);
} else if (query.type === AbstractDbOverlay.QueryType.SEARCH_BY_COORDINATES) {
return this.searchByCoordinates(query.modelId, query.coordinates);
} else {
......@@ -168,32 +165,4 @@ AbstractDbOverlay.prototype.clear = function() {
return this.searchByQuery("");
};
AbstractDbOverlay.prototype.getDetailDataByIdentifiedElement = function(element, general) {
var self = this;
if (general) {
return self.searchNamesByTarget(element);
} else {
return new Promise(function(resolve){
var result =[];
var queries =self.getQueries();
for (var i=0;i<queries.length;i++) {
var drugs = self._drugsByQuery[queries[i]];
for (var j=0;j<drugs.length;j++){
var drug = drugs[j];
var targets = drug.getTargets();
for (var k=0;k<targets.length;k++) {
var elements = targets[k].getTargetElements();
for (var l=0;l<elements.length;l++) {
if (element.equals(elements[l])) {
result.push(drug.getName());
}
}
}
}
}
resolve(result);
});
}
};
module.exports = AbstractDbOverlay;
frontend-js/src/main/js/map/overlay/AbstractTargettingDbOverlay.js 0 → 100644
View file @ e2f6baa9
"use strict";
var logger = require('../../logger');
var Promise = require("bluebird");
var IdentifiedElement = require('../data/IdentifiedElement');
var AbstractDbOverlay = require('./AbstractDbOverlay');
var ServerConnector = require('../../ServerConnector');
function AbstractTargettingDbOverlay(params) {
// call super constructor
AbstractDbOverlay.call(this, params);
}
AbstractTargettingDbOverlay.prototype = Object.create(AbstractDbOverlay.prototype);
AbstractTargettingDbOverlay.prototype.constructor = AbstractTargettingDbOverlay;
AbstractTargettingDbOverlay.prototype.getElementsByQuery = function(query) {
var self = this;
return new Promise(function(resolve){
var i;
var queryId = null;
var queries =self.getQueries();
for (i=0;i<queries.length;i++) {
if (queries[i]===query) {
queryId = i;
}
}
if (queryId===null) {
throw new Error("Invalid query: "+query);
}
var colourId = queryId;
var elements = self._elementsByQuery[query];
var result = [];
if (elements.length>0) {
if (elements.length>1) {
logger.warn("More than one element per query not implemented");
}
var element = elements[0];
result.element = element;
var iconCounter = 1;
for (i=0; i<element.getTargets().length; i++) {
var target = element.getTargets()[i];
var icon = self.getIcon(colourId, iconCounter++);
if (target.getTargetElements().length===0) {
icon = null;
}
result.push({target:target, icon:icon});
}
}
resolve(result);
});
};
AbstractTargettingDbOverlay.prototype.searchBySingleQuery = function(originalQuery) {
var self = this;
return new Promise(function(resolve, reject) {
var query = self.encodeQuery(AbstractDbOverlay.QueryType.SEARCH_BY_QUERY, originalQuery);
if (self._elementsByQuery[query] !== undefined) {
resolve(self._elementsByQuery[query]);
} else {
return self.getElementsByQueryFromServer({
query:originalQuery
}).then(function(elements) {
self._elementsByQuery[query] = elements;
var identifiedElements = [];
for (var i=0;i<elements.length;i++) {
var targets = elements[i].getTargets();
for (var j=0;j<targets.length;j++) {
var target = targets[j];
for (var k=0;k<target.targetElements;k++) {
identifiedElements.push(new IdentifiedElement(target.targetElements[i]));
}
}
}
return self.getMap().fetchIdentifiedElements(identifiedElements, true);
}).then(function(){
resolve(self._elementsByQuery[query]);
}).catch(reject);
}
});
};
AbstractTargettingDbOverlay.prototype.getIdentifiedElements = function(){
var self = this;
return new Promise(function(resolve){
var queries = self.getQueries();
var result = [];
var colourId = 0;
for (var i=0;i<queries.length;i++) {
var query = queries[i];
var elements = self._elementsByQuery[query];
for (var j=0;j<elements.length;j++) {
var element = elements[j];
var targetElements = self.createIdentifiedElementsForTargetingClass(element, colourId);
result.push.apply(result, targetElements);
colourId++;
}
}
resolve(result);
});
};
AbstractTargettingDbOverlay.prototype.getDetailDataByIdentifiedElement = function(element, general) {
var self = this;
if (general) {
return self.searchNamesByTarget(element);
} else {
return new Promise(function(resolve){
var result =[];
var queries =self.getQueries();
for (var i=0;i<queries.length;i++) {
var drugs = self._elementsByQuery[queries[i]];
for (var j=0;j<drugs.length;j++){
var drug = drugs[j];
var targets = drug.getTargets();
for (var k=0;k<targets.length;k++) {
var elements = targets[k].getTargetElements();
for (var l=0;l<elements.length;l++) {
if (element.equals(elements[l])) {
result.push(drug.getName());
}
}
}
}
}
resolve(result);
});
}
};
module.exports = AbstractTargettingDbOverlay;
frontend-js/src/main/js/map/overlay/DrugDbOverlay.js
View file @ e2f6baa9
......@@ -5,7 +5,7 @@ var logger = require('../../logger');
var Promise = require("bluebird");
var IdentifiedElement = require('../data/IdentifiedElement');
var AbstractDbOverlay = require('./AbstractDbOverlay');
var AbstractTargettingDbOverlay = require('./AbstractTargettingDbOverlay');
var ServerConnector = require('../../ServerConnector');
......@@ -13,137 +13,19 @@ function DrugDbOverlay(params) {
params.iconType= "drug";
params.iconColorStart = 5
// call super constructor
AbstractDbOverlay.call(this, params);
AbstractTargettingDbOverlay.call(this, params);
}
DrugDbOverlay.prototype = Object.create(AbstractDbOverlay.prototype);
DrugDbOverlay.prototype = Object.create(AbstractTargettingDbOverlay.prototype);
DrugDbOverlay.prototype.constructor = DrugDbOverlay;
DrugDbOverlay.prototype.getElementsByQuery = function(query) {
var self = this;
return new Promise(function(resolve){
var i;
var queryId = null;
var queries =self.getQueries();
for (i=0;i<queries.length;i++) {
if (queries[i]===query) {
queryId = i;
}
}
if (queryId===null) {
throw new Error("Invalid query: "+query);
}
var colourId = queryId;
var drugs = self._drugsByQuery[query];
var result = [];
if (drugs.length>0) {
if (drugs.length>1) {
logger.warn("More than one drug per query not implemented");
}
var drug = drugs[0];
result.drug = drug;
var iconCounter = 1;
for (i=0; i<drug.getTargets().length; i++) {
var target = drug.getTargets()[i];
var icon = self.getIcon(colourId, iconCounter++);
if (target.getTargetElements().length===0) {
icon = null;
}
result.push({target:target, icon:icon});
}
}
resolve(result);
});
};
DrugDbOverlay.prototype.searchBySingleQuery = function(originalQuery) {
var self = this;
return new Promise(function(resolve, reject) {
var query = self.encodeQuery(AbstractDbOverlay.QueryType.SEARCH_BY_QUERY, originalQuery);
if (self._elementsByQuery[query] !== undefined) {
resolve(self._elementsByQuery[query]);
} else {
return ServerConnector.getDrugsByQuery({
query:originalQuery
}).then(function(drugs) {
self._drugsByQuery[query] = drugs;
var result = [];
for (var i=0;i<drugs.length;i++) {
var targets = drugs[i].getTargets();
for (var j=0;j<targets.length;j++) {
var target = targets[j];
for (var k=0;k<target.targetElements;k++) {
result.push(new IdentifiedElement(target.targetElements[i]));
}
}
}
self._elementsByQuery[query]=result;
return self.getMap().fetchIdentifiedElements(result, true);
}).then(function(){
resolve(self._elementsByQuery[query]);
}).catch(reject);
}
});
};
DrugDbOverlay.prototype.getIdentifiedElements = function(){
var self = this;
return new Promise(function(resolve){
var queries = self.getQueries();
var result = [];
var colourId = 0;
for (var i=0;i<queries.length;i++) {
var query = queries[i];
var drugs = self._drugsByQuery[query];
for (var j=0;j<drugs.length;j++) {
var drug = drugs[j];
var drugElements = self.createIdentifiedElementsForTargetingClass(drug, colourId);
result.push.apply(result, drugElements);
colourId++;
}
}
resolve(result);
});
};
DrugDbOverlay.prototype.getNamesByTargetFromServer = function(param) {
return ServerConnector.getDrugNamesByTarget(param);
}
DrugDbOverlay.prototype.getDetailDataByIdentifiedElement = function(element, general) {
var self = this;
if (general) {
return self.searchNamesByTarget(element);
} else {
return new Promise(function(resolve){
var result =[];
var queries =self.getQueries();
for (var i=0;i<queries.length;i++) {
var drugs = self._drugsByQuery[queries[i]];
for (var j=0;j<drugs.length;j++){
var drug = drugs[j];
var targets = drug.getTargets();
for (var k=0;k<targets.length;k++) {
var elements = targets[k].getTargetElements();
for (var l=0;l<elements.length;l++) {
if (element.equals(elements[l])) {
result.push(drug.getName());
}
}
}
}
}
resolve(result);
});
}
};
DrugDbOverlay.prototype.getElementsByQueryFromServer = function(param) {
return ServerConnector.getDrugsByQuery(param);
}
module.exports = DrugDbOverlay;
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