Merge branch '373-source-of-annotation' into 'master'

Resolve "source of annotation"

Closes #373

See merge request piotr.gawron/minerva!279

frontend-js/src/main/js/gui/leftPanel/AbstractDbPanel.js

@@ -312,10 +312,12 @@ AbstractPanel.prototype.createTargetRow = function (target, icon) {
   descColumn.appendChild(guiUtils.createParamLine("Name: ", target.getName()));
   descColumn.appendChild(guiUtils.createAnnotations("Elements: ", target.getTargetParticipants(), {
     showType: false,
-    inline: true
+    inline: true,
+    groupAnnotations: false
   }));
   descColumn.appendChild(guiUtils.createAnnotations("References: ", target.getReferences(), {
-    showType: false
+    showType: false,
+    groupAnnotations: false
   }));
   if (submaps.length > 0) {
     descColumn.appendChild(guiUtils.createLabel("Available in submaps: "));

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

@@ -42,7 +42,7 @@ ChemicalPanel.prototype.createPreamble = function (chemical) {
     result.appendChild(guiUtils.createArrayParamLine("Synonyms: ", chemical.getSynonyms()));
     result.appendChild(guiUtils.createParamLine("Direct Evidence: ", chemical.getDirectEvidence()));
     result.appendChild(guiUtils
-      .createAnnotations("Direct Evidence Publications: ", chemical.getDirectEvidenceReferences()));
+      .createAnnotations("Direct Evidence Publications: ", chemical.getDirectEvidenceReferences(), {groupAnnotations: false}));
     result.appendChild(guiUtils.createAnnotations("Sources: ", chemical.getReferences()));
     result.appendChild(guiUtils.createNewLine());
   }

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

@@ -11,17 +11,18 @@ var PanelControlElementType = require('../PanelControlElementType');
 function DrugPanel(params) {
   params.panelName = "drug";
   params.helpTip = '<p>source: <a target="_drugbank" href="http://www.drugbank.ca/">DrugBank</a> and '
-      + '<a target="_drugbank" href="https://www.ebi.ac.uk/chembl/">ChEMBL</a></p>'
-      + "<p>use of drug names, synonyms and brand names is supported<p>separate multiple search by semicolon</p>";
-  params.placeholder  = "drug, synonym, brand name";
-  
+    + '<a target="_drugbank" href="https://www.ebi.ac.uk/chembl/">ChEMBL</a></p>'
+    + "<p>use of drug names, synonyms and brand names is supported<p>separate multiple search by semicolon</p>";
+  params.placeholder = "drug, synonym, brand name";
+
   AbstractDbPanel.call(this, params);
   this.getControlElement(PanelControlElementType.SEARCH_LABEL).innerHTML = "SEARCH FOR TARGETS OF:";
 }
+
 DrugPanel.prototype = Object.create(AbstractDbPanel.prototype);
 DrugPanel.prototype.constructor = DrugPanel;
 
-DrugPanel.prototype.createPreamble = function(drug) {
+DrugPanel.prototype.createPreamble = function (drug) {
   var self = this;
   var guiUtils = self.getGuiUtils();
   var result = document.createElement("div");
@@ -33,24 +34,24 @@ DrugPanel.prototype.createPreamble = function(drug) {
     result.appendChild(guiUtils.createArrayParamLine("Synonyms: ", drug.getSynonyms()));
     result.appendChild(guiUtils.createArrayParamLine("Brand names: ", drug.getBrandNames()));
     result.appendChild(guiUtils.createParamLine("Blood brain barrier: ", drug.getBloodBrainBarrier()));
-    result.appendChild(guiUtils.createAnnotations("Sources: ", drug.getReferences()));
+    result.appendChild(guiUtils.createAnnotations("Sources: ", drug.getReferences(), {groupAnnotations: false}));
     result.appendChild(guiUtils.createNewLine());
   }
 
   return result;
 };
 
-DrugPanel.prototype.createTableElement = function(target, icon) {
+DrugPanel.prototype.createTableElement = function (target, icon) {
   return this.createTargetRow(target, icon);
 };
 
-DrugPanel.prototype.searchByQuery = function() {
+DrugPanel.prototype.searchByQuery = function () {
   var self = this;
   var query = self.getControlElement(PanelControlElementType.SEARCH_INPUT).value;
   return self.getOverlayDb().searchByQuery(query);
 };
 
-DrugPanel.prototype.init = function() {
+DrugPanel.prototype.init = function () {
   var query = ServerConnector.getSessionData().getDrugQuery();
   if (query !== undefined) {
     return this.getOverlayDb().searchByEncodedQuery(query);
@@ -60,7 +61,7 @@ DrugPanel.prototype.init = function() {
 };
 
 DrugPanel.prototype.destroy = function () {
-    return Promise.resolve();
+  return Promise.resolve();
 };
 
 DrugPanel.prototype.getAutocomplete = function (query) {

frontend-js/src/main/js/gui/leftPanel/GuiUtils.js

@@ -3,7 +3,7 @@
 /* exported logger */
 
 var Alias = require('../../map/data/Alias');
-var ConfigurationType= require('../../ConfigurationType');
+var ConfigurationType = require('../../ConfigurationType');
 
 var GuiConnector = require('../../GuiConnector');
 var AbstractGuiElement = require('../AbstractGuiElement');
@@ -171,52 +171,20 @@ GuiUtils.prototype.createAnnotations = function (label, value, options) {
   return result;
 };
 
-GuiUtils.prototype.createAnnotationList = function (annotations, options) {
-  var showType = true;
-  var inline = false;
-  if (options !== undefined) {
-    if (options.showType !== undefined) {
-      showType = options.showType;
-    }
-    if (options.inline !== undefined) {
-      inline = options.inline;
-    }
-  }
-
-  var self = this;
-  var result = document.createElement("div");
-
-  var annotators = this.getConfiguration().getAnnotators();
-  var annotatorsClassMapping = {};
-  for (var i = 0; i < annotators.length; i++) {
-    annotatorsClassMapping[annotators[i].getClassName()] = annotators[i];
-  }
-
-  var grouppedAnnotations = {};
-  for (var i = 0; i < annotations.length; i++) {
-    var clazz = annotations[i].getAnnotatorClassName();
-    if (!(clazz in grouppedAnnotations)) grouppedAnnotations[clazz] = [];
-    grouppedAnnotations[clazz].push(annotations[i])
-  }
-
-  // = annotatorClasName ? annotatorsClassMapping[annotatorClasName].getName() : "Annotated by curator";
-
-  var cntAnnotations = 0;
-
-  Object.keys(grouppedAnnotations).sort().forEach(function (annotatorClass) {
-
-    // var desc = grouppedAnnotations.keys()[i];
-    var groupContainer = (inline ? document.createElement("span") : document.createElement("div"));
-    var descContainer = (inline ? document.createElement("span") : document.createElement("div"));
-
-    var annotatorName = annotatorClass ? annotatorsClassMapping[annotatorClass].getName() : "Annotated by curator";
+function createGroupContainer(inline, annotatorClass, annotatorsClassMapping, groupAnnotations) {
+  var automaticallyAnnotated = !(annotatorClass === undefined || annotatorClass === "undefined" || annotatorClass === null || annotatorClass === "");
+// var desc = grouppedAnnotations.keys()[i];
+  var groupContainer = (inline ? document.createElement("span") : document.createElement("div"));
+  var descContainer = (inline ? document.createElement("span") : document.createElement("div"));
 
+  if (groupAnnotations) {
+    var annotatorName = automaticallyAnnotated ? annotatorsClassMapping[annotatorClass].getName() : "Annotated by curator";
     if (inline) {
       descContainer.innerHTML = annotatorName + ': ';
     } else {
       descContainer.innerHTML = annotatorName;
 
-      if (annotatorClass) {
+      if (automaticallyAnnotated) {
         var annotatorDescription = annotatorsClassMapping[annotatorClass].getDescription();
         if (annotatorDescription) {
           var tooltipContainer = Functions.createElement({
@@ -239,6 +207,57 @@ GuiUtils.prototype.createAnnotationList = function (annotations, options) {
     descContainer.className = "minerva-annotation-group-header";
     if (!inline) groupContainer.className = "minerva-annotation-group";
     groupContainer.appendChild(descContainer);
+  }
+  return groupContainer;
+}
+
+GuiUtils.prototype.createAnnotationList = function (annotations, options) {
+  var showType = true;
+  var inline = false;
+  var groupAnnotations = true;
+  if (options !== undefined) {
+    if (options.showType !== undefined) {
+      showType = options.showType;
+    }
+    if (options.inline !== undefined) {
+      inline = options.inline;
+    }
+    if (options.groupAnnotations !== undefined) {
+      groupAnnotations = options.groupAnnotations;
+    }
+  }
+
+  var self = this;
+  var result = document.createElement("div");
+
+  var annotators = this.getConfiguration().getAnnotators();
+  var annotatorsClassMapping = {};
+  var grouppedAnnotations = {};
+  if (groupAnnotations) {
+    for (var i = 0; i < annotators.length; i++) {
+      annotatorsClassMapping[annotators[i].getClassName()] = annotators[i];
+    }
+
+    for (var i = 0; i < annotations.length; i++) {
+      var clazz = annotations[i].getAnnotatorClassName();
+      if (!(clazz in grouppedAnnotations)) grouppedAnnotations[clazz] = [];
+      grouppedAnnotations[clazz].push(annotations[i])
+    }
+  } else {
+    annotatorsClassMapping["undefined"] = {
+      getName: function () {
+        return ""
+      }
+    };
+    grouppedAnnotations["undefined"] = annotations;
+  }
+
+  // = annotatorClasName ? annotatorsClassMapping[annotatorClasName].getName() : "Annotated by curator";
+
+  var cntAnnotations = 0;
+
+  Object.keys(grouppedAnnotations).sort().forEach(function (annotatorClass) {
+    var groupContainer = createGroupContainer(inline, annotatorClass, annotatorsClassMapping, groupAnnotations);
 
     if (inline) {
       var par = document.createElement("span");
@@ -434,7 +453,7 @@ GuiUtils.prototype.createReactionElement = function (params) {
     div.appendChild(self.createNewLine());
   }
 
-  if (self.getConfiguration().getOption(ConfigurationType.SHOW_REACTION_TYPE).getValue().toLowerCase()==="true") {
+  if (self.getConfiguration().getOption(ConfigurationType.SHOW_REACTION_TYPE).getValue().toLowerCase() === "true") {
     div.appendChild(self.createParamLine("Type: ", reaction.getType()));
   }
   div.appendChild(self.createParamLine("Symbol: ", reaction.getSymbol()));

frontend-js/src/test/js/gui/leftPanel/GuiUtils-test.js

@@ -201,4 +201,21 @@ describe('GuiUtils', function () {
     button.onclick();
     $(".ui-dialog-titlebar-close").click();
   });
+
+  describe('createAnnotationList', function () {
+    it('default', function () {
+      var guiUtils = new GuiUtils(helper.getConfiguration());
+      var annotation = helper.createAnnotation();
+      var element = guiUtils.createAnnotationList([annotation]);
+      assert.ok(element.innerHTML.indexOf("Annotated by curator") >= 0);
+    });
+    it('without annotator type separation', function () {
+      var guiUtils = new GuiUtils(helper.getConfiguration());
+      var annotation = helper.createAnnotation();
+      var element = guiUtils.createAnnotationList([annotation], {groupAnnotations: false});
+      assert.equal(element.innerHTML.indexOf("Annotated by curator"), -1, "annotator type description shouldn't be visible");
+    });
+  });
+
+
 });

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

@@ -6,6 +6,7 @@ var logger = require('./logger');
 
 var Alias = require("../../main/js/map/data/Alias");
 var AbstractCustomMap = require("../../main/js/map/AbstractCustomMap");
+var Annotation = require("../../main/js/map/data/Annotation");
 var ChemicalDbOverlay = require("../../main/js/map/overlay/ChemicalDbOverlay");
 var Comment = require("../../main/js/map/data/Comment");
 var CommentDbOverlay = require("../../main/js/map/overlay/CommentDbOverlay");
@@ -465,6 +466,14 @@ Helper.prototype.triggerJqueryEvent = function (element, eventType) {
   return Promise.all(promises);
 };
 
+Helper.prototype.createAnnotation = function () {
+  return new Annotation({
+    resource: "10.1038%2Fnpjsba.2016.20",
+    link: "http://doi.org/10.1038%2Fnpjsba.2016.20",
+    id: this.idCounter++,
+    type: "DOI"
+  });
+};
 
 Helper.EPSILON = 1e-6;
 

frontend-js/src/test/js/map/window/AliasInfoWindow-test.js

@@ -124,9 +124,7 @@ describe('AliasInfoWindow', function () {
     }).then(function (data) {
       var overlayDiv = aliasWindow.createOverlayInfoDiv(oc, data);
       assert.ok(functions.isDomElement(overlayDiv));
-      logger.debug(overlayDiv.innerHTML);
       assert.ok(overlayDiv.innerHTML.indexOf('NADH') >= 0);
-
     });
   });