diff --git a/frontend-js/src/main/js/gui/leftPanel/AbstractDbPanel.js b/frontend-js/src/main/js/gui/leftPanel/AbstractDbPanel.js
index 4ac01269f335e0baedb92c2ea2a709028e9c19b6..6589ecc001536d09984f33ac5cf8066afd8b2e58 100644
--- a/frontend-js/src/main/js/gui/leftPanel/AbstractDbPanel.js
+++ b/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: "));
diff --git a/frontend-js/src/main/js/gui/leftPanel/ChemicalPanel.js b/frontend-js/src/main/js/gui/leftPanel/ChemicalPanel.js
index de9406d698ed1966f9b4f7cd7d77443c22bf6b7a..35d60913fe28f1b620ed15f6df7d38d9914e3d4f 100644
--- a/frontend-js/src/main/js/gui/leftPanel/ChemicalPanel.js
+++ b/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());
}
diff --git a/frontend-js/src/main/js/gui/leftPanel/DrugPanel.js b/frontend-js/src/main/js/gui/leftPanel/DrugPanel.js
index b670a7842fa730157faf19d0adce4b4b84390cad..c7b0fe717e1662bcc78555a718618d6730416e83 100644
--- a/frontend-js/src/main/js/gui/leftPanel/DrugPanel.js
+++ b/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) {
diff --git a/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js b/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js
index 42486c427e2dc0b5915e1ce7e9f6adbb7cf98b06..f0b329d370adf6b29385f67650ab0d48846a6d23 100644
--- a/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js
+++ b/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()));
diff --git a/frontend-js/src/test/js/gui/leftPanel/GuiUtils-test.js b/frontend-js/src/test/js/gui/leftPanel/GuiUtils-test.js
index 04cf05a62215549c27bc659c429adf360f58c4b3..d8194e12f81cea7f59beb461c423734b99ee95dd 100644
--- a/frontend-js/src/test/js/gui/leftPanel/GuiUtils-test.js
+++ b/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");
+ });
+ });
+
+
});
diff --git a/frontend-js/src/test/js/helper.js b/frontend-js/src/test/js/helper.js
index d14e81dc155f412edd8950a0c4e7bceb79fcbae7..3464f548066c6f0598bc544f95408c286f19cf9d 100644
--- a/frontend-js/src/test/js/helper.js
+++ b/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;
diff --git a/frontend-js/src/test/js/map/window/AliasInfoWindow-test.js b/frontend-js/src/test/js/map/window/AliasInfoWindow-test.js
index c97b51f8d920187b5dda9444f8885efa9090a3b4..845f2bb295ce228d34b28cf3f3111074f7891c20 100644
--- a/frontend-js/src/test/js/map/window/AliasInfoWindow-test.js
+++ b/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);
-
});
});