first working chemical panel

frontend-js/src/main/js/ServerConnector.js

@@ -8,6 +8,7 @@ var request = require('request');
 
 
 var Alias = require('./map/data/Alias');
+var Chemical = require('./map/data/Chemical');
 var Comment = require('./map/data/Comment');
 var Drug = require('./map/data/Drug');
 var ConfigurationType = require('./ConfigurationType');
@@ -180,43 +181,6 @@ ServerConnector.clearDataMiningOverlay = function() {
   _clearMissingConnectionOverlayCollection();
 };
 
-ServerConnector.registerChemicalOverlay = function() {
-  _registerChemicalOverlayCollection([ {
-    name : "overlayName",
-    value : ServerConnector.CHEMICAL_OVERLAY_NAME,
-  } ]);
-};
-
-ServerConnector.requestChemicalDetailDataFunction = function(identfiedElement, id) {
-  _requestChemicalDetailDataFunction([ {
-    name : "searchResultIdentifier",
-    value : id,
-  }, {
-    name : "objectIdentifier",
-    value : identfiedElement.getId(),
-  }, {
-    name : "modelIdentifier",
-    value : identfiedElement.getModelId(),
-  }, {
-    name : "type",
-    value : identfiedElement.getType(),
-  } ]);
-};
-
-/**
- * Sends request to the server to refresh data in 'drug' overlay.
- */
-ServerConnector.refreshChemicalOverlay = function() {
-  _refreshChemicalOverlayCollection();
-};
-
-/**
- * Clear data related to 'chemical' overlay.
- */
-ServerConnector.clearChemicalOverlay = function() {
-  _clearChemicalOverlayCollection();
-};
-
 /**
  * Clear data related to 'data mining' overlay.
  */
@@ -273,16 +237,6 @@ ServerConnector._overlayMethods[ServerConnector.DATA_MINING_OVERLAY_NAME] = {
     clearFunction : ServerConnector.clearDataMiningOverlay,
 };
 
-/**
- * Define pack of methods for 'chemical' overlay.
- */
-ServerConnector._overlayMethods[ServerConnector.CHEMICAL_OVERLAY_NAME] = {
-    initFunction : ServerConnector.registerChemicalOverlay,
-    refreshFunction : ServerConnector.refreshChemicalOverlay,
-    clearFunction : ServerConnector.clearChemicalOverlay,
-    requestDetailDataFunction : ServerConnector.requestChemicalDetailDataFunction,
-};
-
 ServerConnector._overlayMethods[ServerConnector.MI_RNA_OVERLAY_NAME] = {
     initFunction : ServerConnector.registerMiRnaOverlay,
     refreshFunction : ServerConnector.refreshMiRnaOverlay,
@@ -299,7 +253,7 @@ ServerConnector.sendClearRequest = function(overlayName) {
     } else {
       logger.warn("Clear function for " + overlayName + " doesn't exist");
     }
-  } else if (overlayName==="search" || overlayName==="comment" || overlayName ==="drug"){
+  } else if (overlayName==="search" || overlayName==="comment" || overlayName ==="drug"|| overlayName ==="chemical"){
     logger.warn("Send clear request for overlay that doesn't support it: "+overlayName);
   } else {
     throw new Error("[Clear function] Unknown overlay: ", overlayName);
@@ -1071,7 +1025,7 @@ ServerConnector.getChemicalsByQuery = function(params) {
       var array=JSON.parse(content);
       var result = [];
       for (var i = 0; i < array.length; i++) {
-        result.push(new Drug(array[i]));
+        result.push(new Chemical(array[i]));
       }
       resolve(result);
     }).catch(function(exception){

frontend-js/src/main/js/gui/AbstractPanel.js

@@ -461,4 +461,40 @@ AbstractPanel.prototype.addResultTab = function(query, elements) {
   }
 };
 
+AbstractPanel.prototype.createTargetRow = function(target, icon) {
+  var self = this;
+  var result = document.createElement("tr");
+  var iconColumn = document.createElement("td");
+  iconColumn.style.width = "20px";
+  iconColumn.style.verticalAlign = "middle";
+  iconColumn.style.textAlign = "center";
+  result.appendChild(iconColumn);
+  if (target.getTargetElements().length > 0) {
+    iconColumn.appendChild(self.createIcon(icon));
+    var checkbox = document.createElement('input');
+    checkbox.type = "checkbox";
+    checkbox.checked = target.isVisible();
+    checkbox.onclick = function() {
+      target.setIsVisible(!target.isVisible());
+      self.getOverlayDb().callListeners("onTargetVisibilityChange");
+    };
+
+    iconColumn.appendChild(checkbox);
+  }
+
+  var descColumn = document.createElement("td");
+  result.appendChild(descColumn);
+
+  descColumn.appendChild(self.createParamLine("Name: ", target.getName()));
+  descColumn.appendChild(self.createAnnotations("Elements: ", target.getTargetParticipants(), {
+    showType : false,
+    inline : true
+  }));
+  descColumn.appendChild(self.createAnnotations("References: ", target.getReferences(), {
+    showType : false,
+  }));
+  return result;
+};
+
+
 module.exports = AbstractPanel;

frontend-js/src/main/js/gui/ChemicalPanel.js

+"use strict";
+
+/* exported logger */
+var logger = require('../logger');
+
+var AbstractPanel = require('./AbstractPanel');
+
+function ChemicalPanel(params) {
+  params.panelName = "chemical";
+  AbstractPanel.call(this, params);
+}
+ChemicalPanel.prototype = Object.create(AbstractPanel.prototype);
+ChemicalPanel.prototype.constructor = ChemicalPanel;
+
+ChemicalPanel.prototype.createPreamble = function(chemical) {
+  var self = this;
+  var result = document.createElement("div");
+  if (chemical === undefined || chemical.getName() === undefined) {
+    result.appendChild(self.createLabel("NOT FOUND"));
+  } else {
+    result.appendChild(self.createParamLine("Chemical: ", chemical.getName()));
+    result.appendChild(self.createParamLine("Description: ", chemical.getDescription()));
+    result.appendChild(self.createArrayParamLine("Synonyms: ", chemical.getSynonyms()));
+    result.appendChild(self.createParamLine("Direct Evidence: ", chemical.getDirectEvidence()));
+    result.appendChild(self.createAnnotations("Directe Evidence Publications: ", chemical.getDirectEvidenceReferences()));
+    result.appendChild(self.createAnnotations("Sources: ", chemical.getReferences()));
+    result.appendChild(self.createNewLine());
+  }
+
+  return result;
+};
+
+ChemicalPanel.prototype.createTableElement = function(target, icon) {
+  return this.createTargetRow(target, icon);
+};
+
+ChemicalPanel.prototype.searchByQuery = function() {
+  var self = this;
+  var query = self.getSearchInput().value;
+  return self.getOverlayDb().searchByQuery(query);
+};
+
+module.exports = ChemicalPanel;

frontend-js/src/main/js/gui/DrugPanel.js

@@ -31,41 +31,9 @@ DrugPanel.prototype.createPreamble = function(drug) {
 };
 
 DrugPanel.prototype.createTableElement = function(target, icon) {
-  var self = this;
-  var result = document.createElement("tr");
-  var iconColumn = document.createElement("td");
-  iconColumn.style.width = "20px";
-  iconColumn.style.verticalAlign = "middle";
-  iconColumn.style.textAlign = "center";
-  result.appendChild(iconColumn);
-  if (target.getTargetElements().length > 0) {
-    iconColumn.appendChild(self.createIcon(icon));
-    var checkbox = document.createElement('input');
-    checkbox.type = "checkbox";
-    checkbox.checked = target.isVisible();
-    checkbox.onclick = function() {
-      target.setIsVisible(!target.isVisible());
-      self.getOverlayDb().callListeners("onTargetVisibilityChange");
-    };
-
-    iconColumn.appendChild(checkbox);
-  }
-
-  var descColumn = document.createElement("td");
-  result.appendChild(descColumn);
-
-  descColumn.appendChild(self.createParamLine("Name: ", target.getName()));
-  descColumn.appendChild(self.createAnnotations("Elements: ", target.getTargetParticipants(), {
-    showType : false,
-    inline : true
-  }));
-  descColumn.appendChild(self.createAnnotations("References: ", target.getReferences(), {
-    showType : false,
-  }));
-  return result;
+  return this.createTargetRow(target, icon);
 };
 
-
 DrugPanel.prototype.searchByQuery = function() {
   var self = this;
   var query = self.getSearchInput().value;

frontend-js/src/main/js/map/CustomMap.js

@@ -10,7 +10,7 @@ var AliasMarker = require('./marker/AliasMarker');
 var CommentDialog = require('../gui/CommentDialog');
 var ControlType = require('./ControlType');
 var CustomMapOptions = require('./CustomMapOptions');
-var DrugDbCollection = require('./overlay/DrugDbOverlay');
+var CommentDbCollection = require('./overlay/CommentDbOverlay');
 var IdentifiedElement = require('./data/IdentifiedElement');
 var OverlayCollection = require('./overlay/OverlayCollection');
 var PointMarker = require('./marker/PointMarker');
@@ -206,7 +206,7 @@ CustomMap.prototype.refreshOverlays = function() {
   for ( var overlayName in this.overlayCollections) {
     if (this.overlayCollections.hasOwnProperty(overlayName)) {
       var collection = this.overlayCollections[overlayName];
-      if (!(collection instanceof SearchDbCollection)&&!(collection instanceof DrugDbCollection)) {
+      if ((collection instanceof CommentDbCollection) || (collection.constructor.name==="OverlayCollection")) {
         promises.push(collection.refresh());
       }
     }
@@ -439,7 +439,7 @@ CustomMap.prototype.registerSource = function(overlayCollection) {
       return self.updateOverlayCollection(overlayCollection, false);
     });
   }
-  if (overlayCollection.getName() === "drug") {
+  if (overlayCollection.getName() === "drug" || overlayCollection.getName() === "chemical") {
     overlayCollection.addListener("onSearch", function() {
       return self.updateOverlayCollection(overlayCollection, false);
     });

frontend-js/src/main/js/map/data/Chemical.js

+"use strict";
+
+var Target = require("./Target");
+
+function Chemical(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.setDirectEvidence = function(directeEvidence) {
+  this._directeEvidence = directeEvidence;
+};
+
+Chemical.prototype.getDirectEvidence = function() {
+  return this._directeEvidence;
+};
+
+Chemical.prototype.setDirectEvidenceReferences = function(directeEvidenceReferences) {
+  this._directeEvidenceReferences = directeEvidenceReferences;
+};
+
+Chemical.prototype.getDirectEvidenceReferences = function() {
+  return this._directEvidenceReferences;
+};
+
+Chemical.prototype.setBrandNames = function(brandNames) {
+  this._brandNames = brandNames;
+};
+
+Chemical.prototype.getBrandNames = function() {
+  return this._brandNames;
+};
+
+Chemical.prototype.setReferences = function(references) {
+  this._references = references;
+};
+
+Chemical.prototype.getReferences = function() {
+  return this._references;
+};
+
+Chemical.prototype.setSynonyms = function(synonyms) {
+  this._synonyms = synonyms;
+};
+
+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;
+};
+
+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;
+};
+
+Chemical.prototype.getBloodBrainBarrier = function() {
+  return this._bloodBrainBarrier;
+};
+
+module.exports = Chemical;

frontend-js/src/main/js/minerva.js

@@ -3,6 +3,8 @@
 var functions = require('./Functions');
 
 var AbstractDbOverlay = require('./map/overlay/AbstractDbOverlay');
+var ChemicalDbOverlay = require('./map/overlay/ChemicalDbOverlay');
+var ChemicalPanel = require('./gui/ChemicalPanel');
 var CommentDbOverlay = require('./map/overlay/CommentDbOverlay');
 var ControlType = require('./map/ControlType');
 var CustomMap = require('./map/CustomMap');
@@ -120,6 +122,13 @@ function create(params) {
           element : document.getElementById("drugTab"),
           customMap : result
         });
+      } else if (collectionParams.name === "chemical") {
+        collection = new ChemicalDbOverlay(collectionParams);
+        result.registerSource(collection);
+        new ChemicalPanel({
+          element : document.getElementById("chemicalTab"),
+          customMap : result
+        });
       } else {
         collection = new OverlayCollection(collectionParams);
         result.registerSource(collection);

frontend-js/src/test/js/gui/ChemicalPanel-test.js

+"use strict";
+
+var Helper = require('../helper');
+
+require("../mocha-config.js");
+
+var Chemical = require('../../../main/js/map/data/Chemical');
+var ChemicalPanel = require('../../../main/js/gui/ChemicalPanel');
+
+
+var chai = require('chai');
+var assert = chai.assert;
+var logger = require('../logger');
+
+describe('ChemicalPanel', function() {
+
+  var helper;
+  before(function() {
+    helper = new Helper();
+  });
+
+  it('contructor', function() {
+    var div = helper.createChemicalTab();
+
+    var map = helper.createCustomMap();
+    helper.createChemicalDbOverlay(map);
+
+    new ChemicalPanel({
+      element : div,
+      customMap : map
+    });
+    assert.equal(logger.getWarnings().length, 0);
+  });
+
+  it('createChemicaleader for empty', function() {
+    var div = helper.createChemicalTab();
+
+    var map = helper.createCustomMap();
+    helper.createChemicalDbOverlay(map);
+
+    var panel = new ChemicalPanel({
+      element : div,
+      customMap : map
+    });
+
+    assert.ok(panel.createPreamble().innerHTML.indexOf("NOT FOUND") > 0);
+  });
+
+  it('createChemicaleader for empty', function() {
+    var div = helper.createChemicalTab();
+
+    var map = helper.createCustomMap();
+    helper.createChemicalDbOverlay(map);
+
+    var panel = new ChemicalPanel({
+      element : div,
+      customMap : map
+    });
+
+    assert.ok(panel.createPreamble(new Chemical()).innerHTML.indexOf("NOT FOUND") > 0);
+  });
+
+  it('on searchResults changed', function() {
+    var div = helper.createChemicalTab();
+    var map = helper.createCustomMap();
+    map.getModel().setId(15781);
+    var chemicalDbOverlay = helper.createChemicalDbOverlay(map);
+
+    new ChemicalPanel({
+      element : div,
+      customMap : map
+    });
+
+    return chemicalDbOverlay.searchByQuery("rotenone").then(function() {
+      assert.equal(logger.getWarnings().length, 0);
+      assert.ok(div.innerHTML.indexOf("marker/mechanism") >= 0);
+    });
+  });
+
+  it('searchByQuery', function() {
+    var div = helper.createChemicalTab();
+    var map = helper.createCustomMap();
+    map.getModel().setId(15781);
+    helper.createChemicalDbOverlay(map);
+
+    var panel = new ChemicalPanel({
+      element : div,
+      customMap : map
+    });
+
+    panel.getSearchInput().value = "rotenone";
+
+    return panel.searchByQuery().then(function() {
+      assert.equal(logger.getWarnings().length, 0);
+      assert.ok(div.innerHTML.indexOf("Rotenone ") >= 0);
+    });
+  });
+
+});

frontend-js/src/test/js/helper.js

@@ -32,6 +32,10 @@ Helper.prototype.createDrugTab = function() {
   return this.createPanelTab("drugTab");
 };
 
+Helper.prototype.createChemicalTab = function() {
+  return this.createPanelTab("chemicalTab");
+};
+
 Helper.prototype.createPanelTab = function(id) {
   var result = document.createElement("div");
   result.id = id;

frontend-js/src/test/js/minerva-test.js

@@ -23,11 +23,15 @@ describe('minerva global', function() {
     
     global.drugTab = helper.createDrugTab();
     document.body.appendChild(global.drugTab);
+    
+    global.chemicalTab = helper.createChemicalTab();
+    document.body.appendChild(global.chemicalTab);
   });
 
   afterEach(function() {
     document.body.removeChild(global.searchTab);
     document.body.removeChild(global.drugTab);
+    document.body.removeChild(global.chemicalTab);
   });
 
   it('create', function() {
@@ -149,6 +153,20 @@ describe('minerva global', function() {
     });
   });
 
+  it('create with chemical overlay', function() {
+    var project = helper.createProject();
+    project.getModel().setId(15781);
+
+    var options = helper.createOptions(project);
+    options.dataCollections.push({
+      name : "chemical"
+    });
+
+    return minerva.create(options).then(function(result) {
+      assert.ok(result);
+    });
+  });
+
   it('create with search overlay and GET search param', function() {
     GuiConnector.getParams["search"] = "s1";
 

rest-api/src/main/java/lcsb/mapviewer/api/chemical/ChemicalRestImpl.java

@@ -207,9 +207,8 @@ public class ChemicalRestImpl {
 			columnsSet.add("description");
 			columnsSet.add("synonyms");
 			columnsSet.add("id");
-			columnsSet.add("directevidencereferences");
-			columnsSet.add("description");
-			columnsSet.add("directevidence");
+			columnsSet.add("directEvidenceReferences");
+			columnsSet.add("directEvidence");
 			columnsSet.add("targets");
 		} else {
 			for (String str : columns.split(",")) {

service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalService.java

@@ -195,7 +195,7 @@ public class ChemicalService implements IChemicalService {
 			throw new InvalidArgumentException("diseaseID cannot be null");
 		}
 		if (name == null || name.isEmpty()) {
-			throw new InvalidArgumentException("name cannot be null");
+			return null;
 		}
 		MiriamData id = null;
 		List<Chemical> result = new ArrayList<Chemical>();

web/src/main/webapp/WEB-INF/components/map/chemicalPanel.xhtml

@@ -6,132 +6,39 @@
 	xmlns:cc="http://java.sun.com/jsf/composite/pfcomp"
 	xmlns:p="http://primefaces.org/ui">
 
-<h:outputStylesheet library="css" name="chemical.css" />
+<h:outputStylesheet library="css" name="global.css" />
+
+<div id="chemicalTab">
+	<div name="searchQuery" class="searchPanel">	
+				<table cellpadding="4" style="width:100%">
+								<tbody>
+												<tr>
+																<td>FIND TARGETS:</td>
+												</tr>
+												<tr>
+																<td>
+																		<input name="searchInput" class="input-field typeahead" autocomplete="off"/>
+																</td>
+																<td>
+																		<a name="searchButton" href="#">
+																						<img src="resources/images/icons/search.png"/>
+																		</a>
+																</td>
+												</tr>
+								</tbody>
+				</table>
+	</div>
+
+	<div name="searchResults" class="tabbable boxed parentTabs">
+    <ul class="nav nav-tabs">
+        <li class="active"><a href="#set1"/></li>
+    </ul>
+    <div class="tab-content">
+        <div class="tab-pane fade active in" id="set1">
+				</div>
+    </div>
+	</div>
+</div>
 
-<h:form id="chemicalForm" class="chemicalPanel">
-
-	<h:panelGrid id="chemicalSearchComponent" columns="2" cellpadding="4"
-		style="width:100%;" disabled="true"