diff --git a/frontend-js/src/main/js/gui/leftPanel/GenericSearchPanel.js b/frontend-js/src/main/js/gui/leftPanel/GenericSearchPanel.js
index 30faa341b633ce1991ada5dc038ed710a36f6b43..931d88743cb4d3bbbc23cc1ed577d39d26de896d 100644
--- a/frontend-js/src/main/js/gui/leftPanel/GenericSearchPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/GenericSearchPanel.js
@@ -9,6 +9,7 @@ var Alias = require('../../map/data/Alias');
var InvalidArgumentError = require('../../InvalidArgumentError');
var PanelControlElementType = require('../PanelControlElementType');
var Reaction = require('../../map/data/Reaction');
+var SearchBioEntityGroup = require('../../map/data/SearchBioEntityGroup');
// noinspection JSUnusedLocalSymbols
var logger = require('../../logger');
@@ -52,6 +53,8 @@ GenericSearchPanel.prototype.createTableElement = function (element, icon) {
return this.createAliasElement(element, icon);
} else if (element instanceof Reaction) {
return this.createReactionElement(element);
+ } else if (element instanceof SearchBioEntityGroup) {
+ return this.createSearchBioEntityGroupElement(element);
} else {
throw new Error("Unknown element type: " + element.constructor.name);
}
@@ -95,6 +98,21 @@ GenericSearchPanel.prototype.createAliasElement = function (alias, icon) {
return result;
};
+GenericSearchPanel.prototype.createSearchBioEntityGroupElement = function (group, icon) {
+ var self = this;
+ var guiUtils = self.getGuiUtils();
+
+ var result = document.createElement("tr");
+ var td = document.createElement("td");
+ result.appendChild(td);
+ var div = guiUtils.createSearchBioEntityGroupElement(group);
+
+ div.appendChild(guiUtils.createSeparator());
+ td.appendChild(div);
+
+ return result;
+};
+
GenericSearchPanel.prototype.searchByQuery = function () {
var self = this;
var query = this.getControlElement(PanelControlElementType.SEARCH_INPUT).value;
@@ -123,7 +141,7 @@ GenericSearchPanel.prototype.refreshSearchAutocomplete = function () {
GenericSearchPanel.prototype.init = function () {
var query = ServerConnector.getSessionData().getSearchQuery();
if (query !== undefined) {
- return this.getOverlayDb().searchByEncodedQuery(query, false).catch(function(error){
+ return this.getOverlayDb().searchByEncodedQuery(query, false).catch(function (error) {
if (error instanceof InvalidArgumentError) {
logger.warn(error.message);
} else {
diff --git a/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js b/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js
index 09fc55fa0769c2beab7a7cb6ced8db7b91a92841..f677c943f01e13bba742df4afb0fdadf9afef67c 100644
--- a/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js
+++ b/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js
@@ -2,6 +2,8 @@
/* exported logger */
+var Alias = require('../../map/data/Alias');
+
var GuiConnector = require('../../GuiConnector');
var AbstractGuiElement = require('../AbstractGuiElement');
var Functions = require('../../Functions');
@@ -185,7 +187,7 @@ GuiUtils.prototype.createAnnotationList = function (annotations, options) {
var annotators = this.getConfiguration().getAnnotators();
var annotatorsClassMapping = {};
for (var i = 0; i < annotators.length; i++) {
- annotatorsClassMapping[annotators[i].getClassName()] = annotators[i];
+ annotatorsClassMapping[annotators[i].getClassName()] = annotators[i];
}
var grouppedAnnotations = {};
@@ -198,8 +200,8 @@ GuiUtils.prototype.createAnnotationList = function (annotations, options) {
// = annotatorClasName ? annotatorsClassMapping[annotatorClasName].getName() : "Annotated by curator";
var cntAnnotations = 0;
-
- Object.keys(grouppedAnnotations).sort().forEach(function(annotatorClass){
+
+ Object.keys(grouppedAnnotations).sort().forEach(function (annotatorClass) {
// var desc = grouppedAnnotations.keys()[i];
var groupContainer = (inline ? document.createElement("span") : document.createElement("div"));
@@ -210,16 +212,16 @@ GuiUtils.prototype.createAnnotationList = function (annotations, options) {
if (inline) {
descContainer.innerHTML = annotatorName + ': ';
} else {
- descContainer.innerHTML = annotatorName;
-
+ descContainer.innerHTML = annotatorName;
+
if (annotatorClass) {
var annotatorDescription = annotatorsClassMapping[annotatorClass].getDescription();
if (annotatorDescription) {
var tooltipContainer = Functions.createElement({
- type: "span"
+ type: "span"
});
tooltipContainer.appendChild(Functions.createElement({
- type: "span",
+ type: "span",
className: "glyphicon glyphicon-question-sign tooltip-icon"
}));
tooltipContainer.appendChild(Functions.createElement({
@@ -230,19 +232,19 @@ GuiUtils.prototype.createAnnotationList = function (annotations, options) {
descContainer.appendChild(tooltipContainer);
}
- }
- }
+ }
+ }
descContainer.className = "minerva-annotation-group-header";
if (!inline) groupContainer.className = "minerva-annotation-group";
groupContainer.appendChild(descContainer);
- if (inline){
+ if (inline) {
var par = document.createElement("span");
par.innerHTML = "(";
groupContainer.appendChild(par);
}
- grouppedAnnotations[annotatorClass] = grouppedAnnotations[annotatorClass].sort(function(a, b) {
+ grouppedAnnotations[annotatorClass] = grouppedAnnotations[annotatorClass].sort(function (a, b) {
const aType = a.getType().toUpperCase();
const bType = b.getType().toUpperCase();
if (aType < bType) return -1;
@@ -258,9 +260,9 @@ GuiUtils.prototype.createAnnotationList = function (annotations, options) {
var link = self.createAnnotationLink(element, showType);
if (inline) {
if (j > 0) {
- var coma = document.createElement("span");
- coma.innerHTML = ", ";
- groupContainer.appendChild(coma);
+ var coma = document.createElement("span");
+ coma.innerHTML = ", ";
+ groupContainer.appendChild(coma);
}
groupContainer.appendChild(link);
} else {
@@ -268,9 +270,9 @@ GuiUtils.prototype.createAnnotationList = function (annotations, options) {
var row = document.createElement("div");
row.style.height = "26px";
if (j % 2 === 0) {
- row.className = "minerva-annotation-row-odd";
+ row.className = "minerva-annotation-row-odd";
} else {
- row.className = "minerva-annotation-row-even";
+ row.className = "minerva-annotation-row-even";
}
var header = document.createElement("div");
@@ -287,15 +289,15 @@ GuiUtils.prototype.createAnnotationList = function (annotations, options) {
}
}
- if (inline){
- var par = document.createElement("span");
- par.innerHTML = ")";
- groupContainer.appendChild(par);
+ if (inline) {
+ var par = document.createElement("span");
+ par.innerHTML = ")";
+ groupContainer.appendChild(par);
}
result.appendChild(groupContainer);
});
-
+
return result;
};
@@ -441,7 +443,6 @@ GuiUtils.prototype.createReactionElement = function (params) {
div.appendChild(self.createReactantsLine(reaction.getReactants()));
div.appendChild(self.createProductsLine(reaction.getProducts()));
div.appendChild(self.createModifiersLine(reaction.getModifiers()));
- div.appendChild(self.createCandidates("Candidates: ", reaction.getOther('dataMining')));
div.appendChild(self.createAnnotations("Annotations: ", reaction.getReferences()));
return div;
};
@@ -480,11 +481,17 @@ GuiUtils.prototype.createAliasElement = function (params) {
div.appendChild(self.createParamLine("Charge: ", alias.getCharge()));
div.appendChild(self.createArrayParamLine("Synonyms: ", alias.getSynonyms()));
div.appendChild(self.createLabelText(alias.getDescription()));
- div.appendChild(self.createCandidates("Candidates: ", alias.getOther('dataMining')));
- div.appendChild(self.createChebiTree("Chebi ontology: ", alias.getOther('chebiTree')));
+ // div.appendChild(self.createChebiTree("Chebi ontology: ", alias.getOther('chebiTree')));
div.appendChild(self.createAnnotations("Annotations: ", alias.getReferences()));
return div;
};
+GuiUtils.prototype.createSearchBioEntityGroupElement = function (group) {
+ if (group.getBioEntities()[0] instanceof Alias) {
+ return this.createAliasElement({alias:group, icon:group.getIcon()});
+ } else {
+ return this.createReactionElement({reaction:group, icon:group.getIcon()});
+ }
+};
GuiUtils.prototype.createReactantsLine = function (label, value) {
var result = document.createElement("div");
diff --git a/frontend-js/src/main/js/map/data/SearchBioEntityGroup.js b/frontend-js/src/main/js/map/data/SearchBioEntityGroup.js
index f444b4e1deff425472a0590f45fa098b9f2917d5..cfb18a2d9050a4cb68cd59b36bb67b0c2b89d03e 100644
--- a/frontend-js/src/main/js/map/data/SearchBioEntityGroup.js
+++ b/frontend-js/src/main/js/map/data/SearchBioEntityGroup.js
@@ -100,5 +100,124 @@ SearchAliasGroup.prototype.getIcon = function () {
return this._icon;
};
+//aggregated data
+SearchAliasGroup.prototype.getType = function () {
+ return this._bioEntites[0].getType();
+};
+
+SearchAliasGroup.prototype.getName = function () {
+ return this._bioEntites[0].getName();
+};
+
+SearchAliasGroup.prototype.getModelId = function () {
+ return this._bioEntites[0].getModelId();
+};
+
+SearchAliasGroup.prototype.getReactants = function () {
+ return this._bioEntites[0].getReactants();
+};
+SearchAliasGroup.prototype.getProducts = function () {
+ return this._bioEntites[0].getProducts();
+};
+SearchAliasGroup.prototype.getModifiers = function () {
+ return this._bioEntites[0].getModifiers();
+};
+
+SearchAliasGroup.prototype.getFullName = function () {
+ return this.getMergedParameterByFunction("getFullName");
+};
+
+SearchAliasGroup.prototype.getReactionId = function () {
+ return this.getMergedParameterByFunction("getReactionId");
+};
+SearchAliasGroup.prototype.getLinkedSubmodelId = function () {
+ return this.getMergedParameterByFunction("getLinkedSubmodelId");
+};
+SearchAliasGroup.prototype.getSymbol = function () {
+ return this.getMergedParameterByFunction("getSymbol");
+};
+SearchAliasGroup.prototype.getAbbreviation = function () {
+ return this.getMergedParameterByFunction("getAbbreviation");
+};
+SearchAliasGroup.prototype.getFormula = function () {
+ return this.getMergedParameterByFunction("getFormula");
+};
+SearchAliasGroup.prototype.getMechanicalConfidenceScore = function () {
+ return this.getMergedParameterByFunction("getMechanicalConfidenceScore");
+};
+SearchAliasGroup.prototype.getLowerBound = function () {
+ return this.getMergedParameterByFunction("getLowerBound");
+};
+SearchAliasGroup.prototype.getUpperBound = function () {
+ return this.getMergedParameterByFunction("getUpperBound");
+};
+SearchAliasGroup.prototype.getGeneProteinReaction = function () {
+ return this.getMergedParameterByFunction("getGeneProteinReaction");
+};
+SearchAliasGroup.prototype.getSubsystem = function () {
+ return this.getMergedParameterByFunction("getSubsystem");
+};
+SearchAliasGroup.prototype.getDescription = function () {
+ return this.getMergedParameterByFunction("getDescription");
+};
+SearchAliasGroup.prototype.getCharge = function () {
+ return this.getMergedParameterByFunction("getCharge");
+};
+SearchAliasGroup.prototype.getSynonyms = function () {
+ return this.getIntersectionListByFunction("getSynonyms");
+};
+SearchAliasGroup.prototype.getFormerSymbols = function () {
+ return this.getIntersectionListByFunction("getFormerSymbols");
+};
+
+SearchAliasGroup.prototype.getReferences = function () {
+ return this.getIntersectionListByFunction("getReferences");
+};
+
+SearchAliasGroup.prototype.getOther = function (param) {
+ if (param === "modifications") {
+ return this.getIntersectionListByFunction(function (alias) {
+ return alias.getOther(param)
+ });
+ } else {
+ throw new Error("Don't now how to handle: " + param);
+ }
+};
+
+SearchAliasGroup.prototype.getMergedParameterByFunction = function (functionName) {
+ var bioEntities = this.getBioEntities();
+ var result = bioEntities[0][functionName]();
+ for (var i = 1; i < bioEntities.length; i++) {
+ var newEntry = bioEntities[i][functionName]();
+ if (newEntry !== result) {
+ result = "Value different among merged elements";
+ }
+ }
+ return result;
+};
+
+SearchAliasGroup.prototype.getIntersectionListByFunction = function (functionName, comparator) {
+ var bioEntities = this.getBioEntities();
+ var result;
+ if (typeof functionName === "function") {
+ result = functionName(bioEntities[0]);
+ } else {
+ result = bioEntities[0][functionName]();
+ }
+ for (var i = 1; i < bioEntities.length; i++) {
+ var newList;
+ if (typeof functionName === "function") {
+ newList = functionName(bioEntities[i]);
+ } else {
+ newList = bioEntities[0][functionName]();
+ }
+ //intersection of two arrays
+ result = result.filter(function (n) {
+ return newList.indexOf(n) !== -1;
+ });
+ }
+ return result;
+};
+
module.exports = SearchAliasGroup;
diff --git a/frontend-js/src/main/js/map/overlay/SearchDbOverlay.js b/frontend-js/src/main/js/map/overlay/SearchDbOverlay.js
index a642c3ff7e67b3c14178b19717a47218ea158319..915480fce82e8b40214c74172748461598a4fe89 100644
--- a/frontend-js/src/main/js/map/overlay/SearchDbOverlay.js
+++ b/frontend-js/src/main/js/map/overlay/SearchDbOverlay.js
@@ -46,21 +46,35 @@ SearchDbOverlay.prototype.getElementsByQuery = function (query) {
var model = self.getMap().getSubmapById(elements[0].getModelId()).getModel();
promises.push(model.getByIdentifiedElement(elements[i], true));
}
- return Promise.all(promises).then(function (fullElements) {
+ return Promise.all(promises).then(function (elements) {
var result = [];
var iconCounter = 1;
- for (var i = 0; i < fullElements.length; i++) {
- var element = fullElements[i];
- var icon;
- if (element instanceof Alias) {
- icon = self.getIcon(queryId, iconCounter++);
- } else if (!(element instanceof Reaction)) {
- throw new Error("Unknown element type: " + element.getType());
+ var groups = [];
+ for (var i = 0; i < elements.length; i++) {
+ var element = elements[i];
+ var alreadyExists = false;
+ var group;
+ for (var j = 0; j < groups.length; j++) {
+ group = groups[j];
+ if (group.bioEntityMatch(element)) {
+ alreadyExists = true;
+ group.addBioEntity(element);
+ }
+ }
+
+ if (!alreadyExists) {
+ var icon;
+ if (element instanceof Alias) {
+ icon = self.getIcon(queryId, iconCounter++)
+ }
+ group = new SearchBioEntityGroup(element);
+ group.setIcon(icon);
+ groups.push(group);
+ result.push({
+ element: group,
+ icon: icon
+ });
}
- result.push({
- element: element,
- icon: icon
- });
}
return result;
});