diff --git a/frontend-js/package-lock.json b/frontend-js/package-lock.json
index 806db19df37adfc12420410e385f2c0ed8308c75..8ca24c0f2abdfdbdbe76cfbfb890cb063abab86e 100644
--- a/frontend-js/package-lock.json
+++ b/frontend-js/package-lock.json
@@ -1167,6 +1167,14 @@
"cssom": "0.3.2"
}
},
+ "csv-stringify": {
+ "version": "4.3.1",
+ "resolved": "https://registry.npmjs.org/csv-stringify/-/csv-stringify-4.3.1.tgz",
+ "integrity": "sha512-VRjPYIUzex5kfbsOY7LaJcNE2qMWGQQAanb3/Vv85WbOgA+dAfDNfwntRvv335icJgGYrnTX403WxJxRVpLDFA==",
+ "requires": {
+ "lodash.get": "4.4.2"
+ }
+ },
"cycle": {
"version": "1.0.3",
"resolved": "https://registry.npmjs.org/cycle/-/cycle-1.0.3.tgz",
@@ -3210,6 +3218,11 @@
"lodash._isiterateecall": "3.0.9"
}
},
+ "lodash.get": {
+ "version": "4.4.2",
+ "resolved": "https://registry.npmjs.org/lodash.get/-/lodash.get-4.4.2.tgz",
+ "integrity": "sha1-LRd/ZS+jHpObRDjVNBSZ36OCXpk="
+ },
"lodash.isarguments": {
"version": "3.1.0",
"resolved": "https://registry.npmjs.org/lodash.isarguments/-/lodash.isarguments-3.1.0.tgz",
diff --git a/frontend-js/package.json b/frontend-js/package.json
index a2588cdc805c28bfaf19249ffce1299093e15b8d..784d067b99236b36e02d3a5b36b945b7e9b73ec6 100644
--- a/frontend-js/package.json
+++ b/frontend-js/package.json
@@ -39,6 +39,7 @@
"uglifyjs": "^2.4.10"
},
"dependencies": {
+ "csv-stringify": "^4.0.0",
"datatables.net-rowreorder": "^1.2.5",
"dual-listbox": "1.0.7",
"file-saver": "^1.3.8",
diff --git a/frontend-js/src/main/js/ServerConnector.js b/frontend-js/src/main/js/ServerConnector.js
index 3fe2bccb564e98d46aae66166208362e35ef70d6..a280321ccfd922715e01fcadecc34a74ce26bcac 100644
--- a/frontend-js/src/main/js/ServerConnector.js
+++ b/frontend-js/src/main/js/ServerConnector.js
@@ -1604,7 +1604,7 @@ ServerConnector.getMaxSearchDistance = function () {
*
* @param {number} overlayId
* @param {string} projectId
- * @returns {PromiseLike<DataOverlay>}
+ * @returns {PromiseLike<DataOverlay>|Promise<DataOverlay>}
*/
ServerConnector.getOverlayById = function (overlayId, projectId) {
var self = this;
diff --git a/frontend-js/src/main/js/gui/leftPanel/PublicationListDialog.js b/frontend-js/src/main/js/gui/leftPanel/PublicationListDialog.js
index 23a09b5aef797a253d6927957a824b491a931ab2..f98d955f51547ccfbf530460df515e8f99d330a3 100644
--- a/frontend-js/src/main/js/gui/leftPanel/PublicationListDialog.js
+++ b/frontend-js/src/main/js/gui/leftPanel/PublicationListDialog.js
@@ -11,8 +11,11 @@ var IdentifiedElement = require('../../map/data/IdentifiedElement');
var Reaction = require('../../map/data/Reaction');
var Functions = require('../../Functions');
+// noinspection JSUnusedLocalSymbols
var logger = require('../../logger');
+var stringify = require('csv-stringify');
+
/**
*
* @param {Object} params
@@ -40,14 +43,14 @@ PublicationListDialog.prototype.createPublicationListDialogGui = function () {
var self = this;
var head = Functions.createElement({
type: "thead",
- content: "<tr>" + "<th>Pubmed ID</th>" +
- "<th>Title</th>" +
- "<th>Authors</th>" +
- "<th>Journal</th>" +
- "<th>Year</th>" +
- "<th>Elements on map</th>" +
- "<th>Submaps</th>" +
- "</tr>"
+ content: "<tr>" + "<th>Pubmed ID</th>" +
+ "<th>Title</th>" +
+ "<th>Authors</th>" +
+ "<th>Journal</th>" +
+ "<th>Year</th>" +
+ "<th>Elements on map</th>" +
+ "<th>Submaps</th>" +
+ "</tr>"
});
var body = Functions.createElement({
type: "tbody"
@@ -74,7 +77,7 @@ PublicationListDialog.prototype.createPublicationListDialogGui = function () {
*/
PublicationListDialog.prototype._dataTableAjaxCall = function (data, callback) {
var self = this;
- return ServerConnector.getPublications({
+ return self.getServerConnector().getPublications({
start: data.start,
length: data.length,
sortColumn: self.getColumnsDefinition()[data.order[0].column].name,
@@ -89,7 +92,6 @@ PublicationListDialog.prototype._dataTableAjaxCall = function (data, callback) {
var row = [];
var submaps = {};
- submaps[self.getMap().getId()] = true;
row[0] = "<a href='" + publication.link + "'>" + publication.id + "</a>";
row[1] = publication.title;
row[2] = publication.authors.join();
@@ -174,6 +176,35 @@ PublicationListDialog.prototype.show = function () {
ajax: function (data, callback, settings) {
resolve(self._dataTableAjaxCall(data, callback, settings));
},
+ dom: 'Bfrtip',
+ buttons: [
+ {
+ text: 'CSV',
+ action: function (e, data) {
+ GuiConnector.showProcessing();
+ return self.getServerConnector().getPublications({
+ start: 0,
+ length: data.page.info().recordsDisplay,
+ sortColumn: self.getColumnsDefinition()[data.order()[0][0]].name,
+ sortOrder: data.order()[0][1],
+ search: data.search()
+ }).then(function (publicationList) {
+ return self.publicationListAsCsvString(publicationList);
+ }).then(function (result) {
+ var blob = new Blob([result], {
+ type: "text/plain;charset=utf-8"
+ });
+ var FileSaver = require("file-saver");
+ return FileSaver.saveAs(blob, "publications.csv");
+ }).catch(function(error){
+ GuiConnector.alert(error);
+ }).finally(function(){
+ GuiConnector.hideProcessing();
+ });
+
+ }
+ }
+ ],
columns: self.getColumnsDefinition()
});
});
@@ -223,4 +254,69 @@ PublicationListDialog.prototype.destroy = function () {
}
};
+/**
+ *
+ * @returns {Promise}
+ */
+PublicationListDialog.prototype.publicationListToArray = function (publicationList) {
+ var self = this;
+ var result = [];
+
+ var elementsToFetch = [];
+
+ publicationList.data.map(function (entry) {
+ var publication = entry.publication.article;
+ var elements = entry.elements;
+ for (var j = 0; j < elements.length; j++) {
+ elementsToFetch.push(new IdentifiedElement(elements[j]));
+ }
+ });
+ return self.getProject().getBioEntitiesByIdentifiedElements(elementsToFetch).then(function(){
+ return Promise.all(publicationList.data.map(function (entry) {
+ var publication = entry.publication.article;
+ var elements = entry.elements;
+ var row = [];
+ row[0] = publication.id;
+ row[1] = publication.title;
+ row[2] = publication.authors.join();
+ row[3] = publication.journal;
+ row[4] = publication.year;
+ row[5] = "";
+ row[6] = "";
+
+ var submaps = [];
+ for (var j = 0; j < elements.length; j++) {
+ var modelId = elements[j].modelId;
+ if (submaps[modelId] === undefined) {
+ row[6] += self.getMap().getSubmapById(modelId).getModel().getName() + ", ";
+ submaps[elements[j].modelId] = true;
+ }
+ }
+ return Promise.all(elements.map(function (element) {
+ var model = self.getMap().getSubmapById(element.modelId).getModel();
+ return model.getByIdentifiedElement(new IdentifiedElement(element)).then(function (reaction) {
+ row[5] += reaction.getElementId() + ",";
+ });
+ })).then(function () {
+ result.push(row);
+ });
+ }));
+ }).then(function () {
+ return result;
+ });
+
+};
+
+PublicationListDialog.prototype.publicationListAsCsvString = function (publicationList) {
+ var self = this;
+
+ return self.publicationListToArray(publicationList).then(function(data){
+ return new Promise(function(resolve){
+ stringify(data,function(err, output){
+ resolve(output);
+ });
+ });
+ });
+};
+
module.exports = PublicationListDialog;
diff --git a/frontend-js/src/main/js/map/data/Project.js b/frontend-js/src/main/js/map/data/Project.js
index 16884ab0d22979a3879a7e35a587e81094e2fa4e..eaf88c554d57672371201be2d271971168e68799 100644
--- a/frontend-js/src/main/js/map/data/Project.js
+++ b/frontend-js/src/main/js/map/data/Project.js
@@ -315,7 +315,7 @@ Project.prototype.getDisease = function () {
/**
*
- * @param {AnnotationOptions} disease
+ * @param {AnnotationOptions|null} disease
*/
Project.prototype.setDisease = function (disease) {
if (disease !== undefined && disease !== null) {
@@ -335,7 +335,7 @@ Project.prototype.getOrganism = function () {
/**
*
- * @param {AnnotationOptions} organism
+ * @param {AnnotationOptions|null} organism
*/
Project.prototype.setOrganism = function (organism) {
if (organism !== undefined && organism !== null) {
@@ -553,5 +553,34 @@ Project.prototype.getElementsPointingToSubmap = function (modelId) {
});
};
+/**
+ *
+ * @param {IdentifiedElement[]} elements
+ * @param {boolean} complete
+ * @returns {Promise}
+ */
+Project.prototype.getBioEntitiesByIdentifiedElements = function (elements, complete) {
+ var self = this;
+ var elementsByModelId = [];
+ var i;
+ for (i = 0; i < elements.length; i++) {
+ var element = elements[i];
+ var modelId = element.getModelId();
+ if (elementsByModelId[modelId] === undefined) {
+ elementsByModelId[modelId] = [];
+ }
+ elementsByModelId[modelId].push(element);
+ }
+
+ var models = self.getModels();
+ var promises = [];
+ for (i = 0; i < models.length; i++) {
+ if (elementsByModelId[models[i].getId()] !== undefined) {
+ promises.push(models[i].getByIdentifiedElements(elementsByModelId[models[i].getId()], complete));
+ }
+ }
+ return Promise.all(promises);
+};
+
module.exports = Project;
diff --git a/frontend-js/src/main/js/map/data/Reaction.js b/frontend-js/src/main/js/map/data/Reaction.js
index e9f9daa2033185f4ca9fac51aed7a5395cb073d2..73085d47022d09cdec387ac0bcc8702f8f82d68c 100644
--- a/frontend-js/src/main/js/map/data/Reaction.js
+++ b/frontend-js/src/main/js/map/data/Reaction.js
@@ -197,6 +197,14 @@ Reaction.prototype.getReactionId = function () {
return this._reactionId;
};
+/**
+ *
+ * @returns {string}
+ */
+Reaction.prototype.getElementId = function () {
+ return this.getReactionId();
+};
+
/**
*
* @param {string} reactionId
diff --git a/frontend-js/src/test/js/gui/leftPanel/PublicationListDialog-test.js b/frontend-js/src/test/js/gui/leftPanel/PublicationListDialog-test.js
index a300fbc33475f89d75a81ef2fff497e8091ef37a..f7f989c35cbbe5060f0164bedd0fe6913f1b2a01 100644
--- a/frontend-js/src/test/js/gui/leftPanel/PublicationListDialog-test.js
+++ b/frontend-js/src/test/js/gui/leftPanel/PublicationListDialog-test.js
@@ -4,6 +4,7 @@ require('../../mocha-config.js');
var PublicationListDialog = require('../../../../main/js/gui/leftPanel/PublicationListDialog');
var ServerConnector = require('../../ServerConnector-mock');
+var Functions = require('../../../../main/js/Functions');
var chai = require('chai');
var assert = chai.assert;
@@ -54,4 +55,42 @@ describe('PublicationListDialog', function () {
});
});
+ it('publicationListAsCsvString', function () {
+
+ var dialog;
+ return ServerConnector.getProject().then(function (project) {
+ dialog = createPublicationListDialog(helper.createCustomMap(project));
+ // noinspection JSAccessibilityCheck
+ return ServerConnector.getPublications({
+ start: 0,
+ length: 10
+ });
+ }).then(function (publicationList) {
+ return dialog.publicationListAsCsvString(publicationList);
+ }).then(function (result) {
+ assert.ok(Functions.isString(result));
+ assert.ok(result.indexOf("re21") >= 0);
+ }).finally(function () {
+ dialog.destroy();
+ });
+ });
+
+ it('publicationListToArray', function () {
+ var dialog;
+ return ServerConnector.getProject().then(function (project) {
+ dialog = createPublicationListDialog(helper.createCustomMap(project));
+ // noinspection JSAccessibilityCheck
+ return ServerConnector.getPublications({
+ start: 0,
+ length: 10
+ });
+ }).then(function (publicationList) {
+ return dialog.publicationListToArray(publicationList);
+ }).then(function (result) {
+ assert.equal(10, result.length);
+ }).finally(function () {
+ dialog.destroy();
+ });
+ });
+
});
diff --git a/web/src/main/webapp/index.xhtml b/web/src/main/webapp/index.xhtml
index 385a0661cc00cc1b9b47dab145170db49ddc30e8..8fbeb0d72246a8043df301a3f24fa11fffef74fa 100644
--- a/web/src/main/webapp/index.xhtml
+++ b/web/src/main/webapp/index.xhtml
@@ -17,11 +17,13 @@
<script src="https://code.jquery.com/ui/1.12.1/jquery-ui.js"></script>
<script src="https://cdn.datatables.net/1.10.13/js/jquery.dataTables.min.js"></script>
<script src="https://cdn.datatables.net/rowreorder/1.2.3/js/dataTables.rowReorder.min.js"></script>
-
+ <script src="https://cdn.datatables.net/buttons/1.5.2/js/dataTables.buttons.min.js"></script>
<link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/1.10.13/css/jquery.dataTables.min.css"/>
<link rel="stylesheet" type="text/css" href="https://code.jquery.com/ui/1.12.1/themes/base/jquery-ui.css"/>
<link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/rowreorder/1.2.3/css/rowReorder.dataTables.min.css"/>
+ <link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/buttons/1.5.2/css/buttons.dataTables.min.css"/>
+
<link rel="shortcut icon" href="./resources/images/favicon.png" type="image/png" />