From b3e40bfcd8ffd3ef04013f916032d492f803f62d Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 29 Jun 2018 12:44:28 +0200
Subject: [PATCH] list of genomes provided in admin panel
---
frontend-js/src/main/js/Admin.js | 9 +-
frontend-js/src/main/js/ServerConnector.js | 40 ++++
.../src/main/js/gui/AbstractGuiElement.js | 47 ++++-
frontend-js/src/main/js/gui/Panel.js | 30 +--
.../main/js/gui/admin/AbstractAdminPanel.js | 44 ++++-
.../src/main/js/gui/admin/GenomeAdminPanel.js | 186 ++++++++++++++++++
.../src/main/js/map/data/PrivilegeType.js | 3 +-
.../src/main/js/map/data/ReferenceGenome.js | 133 ++++++++++++-
.../js/gui/admin/GenomeAdminPanel-test.js | 31 +++
.../test/js/map/data/ReferenceGenome-test.js | 25 ++-
.../apiCalls/genomics/token=ADMIN_TOKEN_ID& | 1 +
.../api/genomics/ReferenceGenomeRestImpl.java | 2 +
12 files changed, 510 insertions(+), 41 deletions(-)
create mode 100644 frontend-js/src/main/js/gui/admin/GenomeAdminPanel.js
create mode 100644 frontend-js/src/test/js/gui/admin/GenomeAdminPanel-test.js
create mode 100644 frontend-js/testFiles/apiCalls/genomics/token=ADMIN_TOKEN_ID&
diff --git a/frontend-js/src/main/js/Admin.js b/frontend-js/src/main/js/Admin.js
index 8d779cee92..db99eea31a 100644
--- a/frontend-js/src/main/js/Admin.js
+++ b/frontend-js/src/main/js/Admin.js
@@ -9,6 +9,7 @@ var GuiUtils = require('./gui/leftPanel/GuiUtils');
var ObjectWithListeners = require('./ObjectWithListeners');
var ConfigurationAdminPanel = require('./gui/admin/ConfigurationAdminPanel');
+var GenomeAdminPanel = require('./gui/admin/GenomeAdminPanel');
var MapsAdminPanel = require('./gui/admin/MapsAdminPanel');
var UsersAdminPanel = require('./gui/admin/UsersAdminPanel');
@@ -19,9 +20,8 @@ var Functions = require('./Functions');
/**
* Default constructor.
*
- * @param options
- * CustomMapOptions object representing all parameters needed for map
- * creation
+ * @param {CustomMapOptions} options
+ * object representing all parameters needed for map creation
*/
function Admin(options) {
var self = this;
@@ -55,6 +55,9 @@ Admin.prototype._createGui = function () {
}, {
name: "CONFIGURATION",
panelClass: ConfigurationAdminPanel
+ }, {
+ name: "GENOMES",
+ panelClass: GenomeAdminPanel
}];
var tabDiv = Functions.createElement({
diff --git a/frontend-js/src/main/js/ServerConnector.js b/frontend-js/src/main/js/ServerConnector.js
index dff12e596f..b75bca3bcd 100644
--- a/frontend-js/src/main/js/ServerConnector.js
+++ b/frontend-js/src/main/js/ServerConnector.js
@@ -307,6 +307,15 @@ ServerConnector.createGetParams = function (params, prefix) {
return result;
};
+/**
+ *
+ * @param {Object} paramObj
+ * @param {string} paramObj.type
+ * @param {string} [paramObj.url]
+ * @param {Object} [paramObj.params]
+ *
+ * @returns {string}
+ */
ServerConnector.getApiUrl = function (paramObj) {
var type = paramObj.type;
var params = this.createGetParams(paramObj.params);
@@ -718,6 +727,21 @@ ServerConnector.getUsersUrl = function (queryParams, filterParams) {
});
};
+/**
+ *
+ * @param {Object} queryParams
+ * @param {Object} filterParams
+ *
+ * @returns {string}
+ */
+ServerConnector.getReferenceGenomesUrl = function (queryParams, filterParams) {
+ return this.getApiUrl({
+ type: "genomics/",
+ params: filterParams
+ });
+};
+
+
ServerConnector.getUserUrl = function (queryParams, filterParams) {
return this.getApiUrl({
url: this.getUsersUrl() + queryParams.login,
@@ -1160,9 +1184,25 @@ ServerConnector.getUsers = function (forceRefresh) {
return self.processNetworkError(error);
});
}
+};
+ServerConnector.getReferenceGenomes = function () {
+ var self = this;
+
+ return self.sendGetRequest(self.getReferenceGenomesUrl()).then(function (content) {
+ var result = [];
+ var parsedData = JSON.parse(content);
+ for (var i = 0; i < parsedData.length; i++) {
+ var genome = new ReferenceGenome(parsedData[i]);
+ result.push(genome)
+ }
+ return result;
+ }).catch(function (error) {
+ return self.processNetworkError(error);
+ });
};
+
ServerConnector.getOverlays = function (params) {
var self = this;
if (params === undefined) {
diff --git a/frontend-js/src/main/js/gui/AbstractGuiElement.js b/frontend-js/src/main/js/gui/AbstractGuiElement.js
index 3ba1e7fdc6..529a523dcf 100644
--- a/frontend-js/src/main/js/gui/AbstractGuiElement.js
+++ b/frontend-js/src/main/js/gui/AbstractGuiElement.js
@@ -10,7 +10,13 @@ var logger = require('../logger');
/**
*
- * @param params
+ * @param {Object} params
+ * @param {HTMLElement} params.element
+ * @param {CustomMap} params.customMap
+ * @param {Configuration} params.configuration
+ * @param {Project} [params.project]
+ * @param {ServerConnector} [params.serverConnector]
+ *
* @constructor
*
* @extends ObjectWithListeners
@@ -24,6 +30,7 @@ function AbstractGuiElement(params) {
self.setProject(params.project);
self.setMap(params.customMap);
self.setConfiguration(params.configuration);
+ self.setServerConnector(params.serverConnector);
self._controlElements = [];
@@ -91,6 +98,11 @@ AbstractGuiElement.prototype.getProject = function () {
};
+/**
+ *
+ * @param {string} type
+ * @param {HTMLElement} element
+ */
AbstractGuiElement.prototype.setControlElement = function (type, element) {
if (type === null || type === undefined) {
throw new Error("Unknown control element type");
@@ -102,6 +114,11 @@ AbstractGuiElement.prototype.setControlElement = function (type, element) {
this._controlElements[type] = element;
};
+/**
+ *
+ * @param {string} type
+ * @returns {HTMLElement}
+ */
AbstractGuiElement.prototype.getControlElement = function (type) {
if (type === null || type === undefined) {
throw new Error("Unknown control element type");
@@ -113,11 +130,19 @@ AbstractGuiElement.prototype.getControlElement = function (type) {
return this._controlElements[type];
};
+/**
+ *
+ * @param {string} url
+ */
AbstractGuiElement.prototype.downloadFile = function (url) {
this._downloadFile = url;
window.open(url, '_blank');
};
+/**
+ *
+ * @returns {string}
+ */
AbstractGuiElement.prototype.getLastDownloadUrl = function () {
return this._downloadFile;
};
@@ -138,6 +163,26 @@ AbstractGuiElement.prototype.getConfiguration = function () {
return this._configuration;
};
+/**
+ *
+ * @param {ServerConnector} serverConnector
+ */
+AbstractGuiElement.prototype.setServerConnector = function (serverConnector) {
+ this._serverConnector = serverConnector;
+};
+
+/**
+ *
+ * @returns {ServerConnector}
+ */
+AbstractGuiElement.prototype.getServerConnector = function () {
+ if (this._serverConnector !== undefined) {
+ return this._serverConnector;
+ } else {
+ return this.getMap().getServerConnector();
+ }
+};
+
/**
*
* @param {string} [params.content]
diff --git a/frontend-js/src/main/js/gui/Panel.js b/frontend-js/src/main/js/gui/Panel.js
index 3a931f2420..75ebb3459b 100644
--- a/frontend-js/src/main/js/gui/Panel.js
+++ b/frontend-js/src/main/js/gui/Panel.js
@@ -20,7 +20,6 @@ var xss = require('xss');
* @param {string} params.panelName
* @param {boolean} params.scrollable
* @param {string} [params.helpTip]
- * @param {ServerConnector} [params.serverConnector]
* @param params.parent
*
* @constructor
@@ -33,7 +32,6 @@ function Panel(params) {
var self = this;
self.setParent(params.parent);
- self.setServerConnector(params.serverConnector);
var configuration = params.configuration;
if (params.configuration === undefined) {
configuration = self.getMap().getConfiguration();
@@ -239,10 +237,18 @@ Panel.prototype.getParent = function () {
return this._parent;
};
+/**
+ *
+ * @param {GuiUtils} guiUtils
+ */
Panel.prototype.setGuiUtils = function (guiUtils) {
this._guiUtils = guiUtils;
};
+/**
+ *
+ * @returns {GuiUtils}
+ */
Panel.prototype.getGuiUtils = function () {
return this._guiUtils;
};
@@ -300,24 +306,4 @@ Panel.prototype.destroy = function () {
}
};
-/**
- *
- * @returns {ServerConnector}
- */
-Panel.prototype.getServerConnector = function () {
- if (this._serverConnector !== undefined) {
- return this._serverConnector;
- }
- return this.getMap().getServerConnector();
-};
-
-/**
- *
- * @param {ServerConnector} serverConnector
- */
-Panel.prototype.setServerConnector = function (serverConnector) {
- this._serverConnector = serverConnector;
-};
-
-
module.exports = Panel;
diff --git a/frontend-js/src/main/js/gui/admin/AbstractAdminPanel.js b/frontend-js/src/main/js/gui/admin/AbstractAdminPanel.js
index 58a37304c3..ba0ddf3b12 100644
--- a/frontend-js/src/main/js/gui/admin/AbstractAdminPanel.js
+++ b/frontend-js/src/main/js/gui/admin/AbstractAdminPanel.js
@@ -9,15 +9,29 @@ var GuiConnector = require('../../GuiConnector');
// noinspection JSUnusedLocalSymbols
var logger = require('../../logger');
+// noinspection JSUnusedLocalSymbols
var Functions = require('../../Functions');
var Promise = require("bluebird");
+/**
+ *
+ * @param {Configuration} [params.configuration]
+ * @param {HTMLElement} params.element
+ * @param {Project} params.project
+ * @param {CustomMap} params.customMap
+ * @param {string} params.panelName
+ * @param {string} [params.helpTip]
+ * @param params.parent
+ *
+ * @constructor
+ */
function AbstractAdminPanel(params) {
- params.scrollable = true;
+ params["scrollable"] = true;
Panel.call(this, params);
this._createHeader(params.name);
this._initPromises = [];
+ this._eventBinds = [];
}
AbstractAdminPanel.prototype = Object.create(Panel.prototype);
@@ -30,17 +44,31 @@ AbstractAdminPanel.prototype._createHeader = function (name) {
// }));
};
+/**
+ *
+ * @returns {Promise}
+ */
AbstractAdminPanel.prototype.init = function () {
return Promise.all(this._initPromises);
};
+/**
+ *
+ * @param {Object} params
+ * @param {string} params.event
+ * @param {jQuery} params.jQueryObject
+ * @param {string} params.preferenceName
+ * @param {Object} params.defaultValue
+ * @param {function} params.getter
+ * @param {function} params.setter
+ */
AbstractAdminPanel.prototype.bindUserGuiPreference = function (params) {
-
params.jQueryObject.on(params.event, function () {
return ServerConnector.getLoggedUser().then(function (user) {
var oldValue = user.getPreferences().getGuiPreference(params.preferenceName, params.defaultValue);
var newValue = params.getter();
if (oldValue !== newValue) {
+ console.log(oldValue, newValue);
user.getPreferences().setGuiPreference(params.preferenceName, newValue);
var data = new UserPreferences();
@@ -53,6 +81,18 @@ AbstractAdminPanel.prototype.bindUserGuiPreference = function (params) {
var value = user.getPreferences().getGuiPreference(params.preferenceName, params.defaultValue);
return params.setter(value);
}));
+
+ this._eventBinds.push(params);
+};
+
+/**
+ *
+ * @returns {Promise}
+ */
+AbstractAdminPanel.prototype.destroy = function () {
+ return Promise.each(this._eventBinds, function (params) {
+ params.jQueryObject.off(params.event);
+ });
};
diff --git a/frontend-js/src/main/js/gui/admin/GenomeAdminPanel.js b/frontend-js/src/main/js/gui/admin/GenomeAdminPanel.js
new file mode 100644
index 0000000000..bfb7483b08
--- /dev/null
+++ b/frontend-js/src/main/js/gui/admin/GenomeAdminPanel.js
@@ -0,0 +1,186 @@
+"use strict";
+
+/* exported Promise*/
+
+var AbstractAdminPanel = require('./AbstractAdminPanel');
+
+var Functions = require('../../Functions');
+var PrivilegeType = require('../../map/data/PrivilegeType');
+
+// noinspection JSUnusedLocalSymbols
+var logger = require('../../logger');
+
+/**
+ *
+ * @param {Configuration} params.configuration
+ * @param {HTMLElement} params.element
+ *
+ * @constructor
+ */
+function GenomeAdminPanel(params) {
+ params["panelName"] = "genomes";
+ AbstractAdminPanel.call(this, params);
+
+ var self = this;
+ $(self.getElement()).addClass("minerva-genome-tab");
+
+ self._createGui();
+}
+
+GenomeAdminPanel.prototype = Object.create(AbstractAdminPanel.prototype);
+GenomeAdminPanel.prototype.constructor = GenomeAdminPanel;
+
+/**
+ *
+ * @private
+ */
+GenomeAdminPanel.prototype._createGui = function () {
+ var self = this;
+ var genomeDiv = Functions.createElement({
+ type: "div"
+ });
+ self.getElement().appendChild(genomeDiv);
+
+ genomeDiv.appendChild(Functions.createElement({
+ type: "h3",
+ content: 'Configured reference genomes:'
+ }));
+
+ var genomesTable = Functions.createElement({
+ type: "table",
+ name: "genomeTable",
+ className: "display",
+ style: "width:100%"
+ });
+ genomeDiv.appendChild(genomesTable);
+
+ // noinspection JSUnusedGlobalSymbols
+ $(genomesTable).DataTable({
+ columns: [{
+ title: 'Type'
+ }, {
+ title: 'Organism'
+ }, {
+ title: 'Version'
+ }, {
+ title: 'Progress'
+ }, {
+ title: 'Source'
+ }, {
+ title: 'Edit',
+ orderable: false
+ }, {
+ title: 'Remove',
+ orderable: false
+ }],
+ order: [[1, "asc"]]
+ });
+ self.bindUserGuiPreference({
+ jQueryObject: $(genomesTable),
+ event: 'length.dt',
+ preferenceName: 'admin-genome-datatable-length',
+ defaultValue: '10',
+ getter: function () {
+ return $(genomesTable).DataTable().page.len() + '';
+ },
+ setter: function (value) {
+ return $(genomesTable).DataTable().page.len(value).draw();
+ }
+ });
+
+};
+
+/**
+ *
+ * @returns {Promise}
+ */
+GenomeAdminPanel.prototype.init = function () {
+ var self = this;
+ return AbstractAdminPanel.prototype.init.call(this).then(function () {
+ return self.getServerConnector().getLoggedUser();
+ }).then(function (user) {
+ if (user.hasPrivilege(self.getConfiguration().getPrivilegeType(PrivilegeType.MANAGE_GENOMES))) {
+ return self.getServerConnector().getReferenceGenomes().then(function (referenceGenomes) {
+ return self.setReferenceGenomes(referenceGenomes);
+ });
+ } else {
+ self.disablePanel("You have no privilege to manage genomes");
+ }
+ });
+};
+
+/**
+ *
+ * @param {ReferenceGenome[]} referenceGenomes
+ *
+ * @returns {Promise}
+ *
+ */
+GenomeAdminPanel.prototype.setReferenceGenomes = function (referenceGenomes) {
+ var self = this;
+
+ return self.getServerConnector().getLoggedUser().then(function (user) {
+
+ var dataTable = $("[name='genomeTable']", self.getElement()).DataTable();
+ var data = [];
+ var page = dataTable.page();
+
+ for (var i = 0; i < referenceGenomes.length; i++) {
+ var genome = referenceGenomes[i];
+ var rowData = self.genomeToTableRow(genome, user);
+ data.push(rowData);
+ }
+ //it should be simplified, but I couldn't make it work
+ dataTable.clear().rows.add(data).page(page).draw(false).page(page).draw(false);
+ })
+};
+
+/**
+ *
+ * @param {ReferenceGenome} genome
+ * @param {User} user
+ * @returns {Array}
+ */
+GenomeAdminPanel.prototype.genomeToTableRow = function (genome, user) {
+ var self = this;
+ var row = [];
+
+ row[0] = genome.getType();
+ row[1] = self.getGuiUtils().createAnnotationLink(genome.getOrganism()).outerHTML;
+ row[2] = genome.getVersion();
+ if (genome.getDownloadProgress() === 100) {
+ if (genome.getLocalUrl() !== undefined) {
+ row[3] = "READY";
+ } else {
+ row[3] = "ERROR";
+ }
+ } else {
+ row[3] = genome.getDownloadProgress();
+ }
+ row[4] = genome.getSourceUrl();
+
+ var disabled = " disabled ";
+ if (user.hasPrivilege(self.getConfiguration().getPrivilegeType(PrivilegeType.MANAGE_GENOMES))) {
+ disabled = "";
+ }
+ row[5] = "<button name='showEditDialog' data='" + genome.getId() + "'" + disabled + "><i class='fa fa-edit' style='font-size:17px'></i></button>";
+ row[6] = "<button name='removeGenome' data='" + genome.getId() + "'" + disabled + "><i class='fa fa-trash-o' style='font-size:17px'></button>";
+
+ return row;
+};
+
+
+/**
+ *
+ * @returns {Promise}
+ */
+GenomeAdminPanel.prototype.destroy = function () {
+ var self = this;
+ var table = $("[name='genomeTable']", self.getElement())[0];
+ if ($.fn.DataTable.isDataTable(table)) {
+ $(table).DataTable().destroy();
+ }
+ return AbstractAdminPanel.prototype.destroy.call(self);
+};
+
+module.exports = GenomeAdminPanel;
diff --git a/frontend-js/src/main/js/map/data/PrivilegeType.js b/frontend-js/src/main/js/map/data/PrivilegeType.js
index 54e528f121..45af426283 100644
--- a/frontend-js/src/main/js/map/data/PrivilegeType.js
+++ b/frontend-js/src/main/js/map/data/PrivilegeType.js
@@ -17,8 +17,9 @@ PrivilegeType.prototype = Object.create(ObjectWithListeners.prototype);
PrivilegeType.prototype.constructor = PrivilegeType;
PrivilegeType.CONFIGURATION_MANAGE = 'CONFIGURATION_MANAGE';
-PrivilegeType.USER_MANAGEMENT = 'USER_MANAGEMENT';
+PrivilegeType.MANAGE_GENOMES = 'MANAGE_GENOMES';
PrivilegeType.PROJECT_MANAGEMENT = 'PROJECT_MANAGEMENT';
+PrivilegeType.USER_MANAGEMENT = 'USER_MANAGEMENT';
PrivilegeType.prototype.setObjectType = function (objectType) {
this._objectType = objectType;
diff --git a/frontend-js/src/main/js/map/data/ReferenceGenome.js b/frontend-js/src/main/js/map/data/ReferenceGenome.js
index 38756a6bd0..f484559a1b 100644
--- a/frontend-js/src/main/js/map/data/ReferenceGenome.js
+++ b/frontend-js/src/main/js/map/data/ReferenceGenome.js
@@ -1,16 +1,22 @@
"use strict";
+var Annotation = require('./Annotation');
var ReferenceGenomeGeneMapping = require('./ReferenceGenomeGeneMapping');
function ReferenceGenome(javaObject) {
if (javaObject !== undefined && javaObject !== null) {
+ this.setId(javaObject.idObject);
this.setType(javaObject.type);
this.setVersion(javaObject.version);
+ this.setLocalUrl(javaObject.localUrl);
+ this.setSourceUrl(javaObject.sourceUrl);
if (javaObject.localUrl !== undefined) {
this.setUrl(javaObject.localUrl);
} else {
this.setUrl(javaObject.sourceUrl);
}
+ this.setOrganism(new Annotation(javaObject.organism));
+ this.setDownloadProgress(javaObject.downloadProgress);
this._geneMapping = [];
if (javaObject.geneMapping !== undefined) {
for (var i = 0; i < javaObject.geneMapping.length; i++) {
@@ -20,31 +26,144 @@ function ReferenceGenome(javaObject) {
}
}
-ReferenceGenome.prototype.setType = function(type) {
+/**
+ *
+ * @param {string} type
+ */
+ReferenceGenome.prototype.setType = function (type) {
this._type = type;
};
-ReferenceGenome.prototype.getType = function() {
+/**
+ *
+ * @returns {string}
+ */
+ReferenceGenome.prototype.getType = function () {
return this._type;
};
-ReferenceGenome.prototype.setUrl = function(url) {
+/**
+ *
+ * @param {number} id
+ */
+ReferenceGenome.prototype.setId = function (id) {
+ this._id = id;
+};
+
+/**
+ *
+ * @returns {number}
+ */
+ReferenceGenome.prototype.getId = function () {
+ return this._id;
+};
+
+/**
+ *
+ * @returns {number}
+ */
+ReferenceGenome.prototype.getDownloadProgress = function () {
+ return this._downloadProgress;
+};
+
+/**
+ *
+ * @param {number} downloadProgress
+ */
+ReferenceGenome.prototype.setDownloadProgress = function (downloadProgress) {
+ this._downloadProgress = downloadProgress;
+};
+
+
+/**
+ *
+ * @param {Annotation} organism
+ */
+ReferenceGenome.prototype.setOrganism = function (organism) {
+ this._organism = organism;
+};
+
+/**
+ *
+ * @returns {Annotation}
+ */
+ReferenceGenome.prototype.getOrganism = function () {
+ return this._organism;
+};
+
+/**
+ *
+ * @param {string} url
+ */
+ReferenceGenome.prototype.setUrl = function (url) {
this._url = url;
};
-ReferenceGenome.prototype.getUrl = function() {
+/**
+ *
+ * @returns {string}
+ */
+ReferenceGenome.prototype.getUrl = function () {
return this._url;
};
-ReferenceGenome.prototype.setVersion = function(version) {
+/**
+ *
+ * @returns {string}
+ */
+ReferenceGenome.prototype.getSourceUrl = function () {
+ return this._sourceUrl;
+};
+
+/**
+ *
+ * @param {string} sourceUrl
+ */
+ReferenceGenome.prototype.setSourceUrl = function (sourceUrl) {
+ this._sourceUrl = sourceUrl;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+ReferenceGenome.prototype.getLocalUrl = function () {
+ return this._localUrl;
+};
+
+/**
+ *
+ * @param {string} localUrl
+ */
+ReferenceGenome.prototype.setLocalUrl = function (localUrl) {
+ if (localUrl === null) {
+ this._localUrl = undefined;
+ } else {
+ this._localUrl = localUrl;
+ }
+};
+
+/**
+ *
+ * @param {string} version
+ */
+ReferenceGenome.prototype.setVersion = function (version) {
this._version = version;
};
-ReferenceGenome.prototype.getVersion = function() {
+/**
+ *
+ * @returns {string}
+ */
+ReferenceGenome.prototype.getVersion = function () {
return this._version;
};
-ReferenceGenome.prototype.getGeneMappings = function() {
+/**
+ *
+ * @returns {ReferenceGenomeGeneMapping[]}
+ */
+ReferenceGenome.prototype.getGeneMappings = function () {
return this._geneMapping;
};
diff --git a/frontend-js/src/test/js/gui/admin/GenomeAdminPanel-test.js b/frontend-js/src/test/js/gui/admin/GenomeAdminPanel-test.js
new file mode 100644
index 0000000000..a1a4567a41
--- /dev/null
+++ b/frontend-js/src/test/js/gui/admin/GenomeAdminPanel-test.js
@@ -0,0 +1,31 @@
+"use strict";
+
+require("../../mocha-config");
+
+var GenomeAdminPanel = require('../../../../main/js/gui/admin/GenomeAdminPanel');
+var ConfigurationType = require('../../../../main/js/ConfigurationType');
+var ServerConnector = require('../../ServerConnector-mock');
+var logger = require('../../logger');
+
+var chai = require('chai');
+var assert = chai.assert;
+
+describe('GenomeAdminPanel', function () {
+ describe('init', function () {
+ it('admin', function () {
+ helper.loginAsAdmin();
+ var mapTab;
+ return ServerConnector.getConfiguration().then(function (configuration) {
+ mapTab = new GenomeAdminPanel({
+ element: testDiv,
+ configuration: configuration,
+ serverConnector: ServerConnector
+ });
+ return mapTab.init();
+ }).then(function () {
+ assert.equal(0, logger.getWarnings().length);
+ return mapTab.destroy();
+ });
+ });
+ });
+});
diff --git a/frontend-js/src/test/js/map/data/ReferenceGenome-test.js b/frontend-js/src/test/js/map/data/ReferenceGenome-test.js
index b001486d62..204ff22eed 100644
--- a/frontend-js/src/test/js/map/data/ReferenceGenome-test.js
+++ b/frontend-js/src/test/js/map/data/ReferenceGenome-test.js
@@ -10,7 +10,16 @@ describe('ReferenceGenome', function () {
type: "TYP",
version: "v3",
localUrl: "http://google.pl/",
- sourceUrl: "http://google.pl/"
+ sourceUrl: "http://google.pl/",
+ organism: {
+ "annotatorClassName": "",
+ "descriptionByType": "",
+ "descriptionByTypeRelation": "",
+ "id": 517528,
+ "link": "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=8822",
+ "resource": "8822",
+ "type": "TAXONOMY"
+ }
};
var genome = new ReferenceGenome(data);
assert.equal(genome.getType(), data.type);
@@ -21,7 +30,16 @@ describe('ReferenceGenome', function () {
it("simple", function () {
var data = {
sourceUrl: "http://google.pl/",
- geneMapping: [{}]
+ geneMapping: [{}],
+ organism: {
+ "annotatorClassName": "",
+ "descriptionByType": "",
+ "descriptionByTypeRelation": "",
+ "id": 517528,
+ "link": "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=8822",
+ "resource": "8822",
+ "type": "TAXONOMY"
+ }
};
var genome = new ReferenceGenome(data);
assert.equal(genome.getUrl(), data.sourceUrl);
@@ -37,8 +55,5 @@ describe('ReferenceGenome', function () {
var genome = new ReferenceGenome(null);
assert.ok(genome);
});
-
});
-
-
});
diff --git a/frontend-js/testFiles/apiCalls/genomics/token=ADMIN_TOKEN_ID& b/frontend-js/testFiles/apiCalls/genomics/token=ADMIN_TOKEN_ID&
new file mode 100644
index 0000000000..e6582c8cbf
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/genomics/token=ADMIN_TOKEN_ID&
@@ -0,0 +1 @@
+[{"downloadProgress":100.0,"geneMapping":[],"idObject":43,"localUrl":null,"organism":{"annotatorClassName":"","descriptionByType":"","descriptionByTypeRelation":"","id":517528,"link":"http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=8822","resource":"8822","type":"TAXONOMY"},"sourceUrl":"ftp://hgdownload.cse.ucsc.edu/goldenPath/aptMan1/bigZips/aptMan1.2bit","type":"UCSC","version":"aptMan1"},{"downloadProgress":100.0,"geneMapping":[{"downloadProgress":100.0,"localUrl":null,"name":"refGene","sourceUrl":"http://pg-sandbox.uni.lu/data/refGene.txt.bb"}],"idObject":154,"localUrl":null,"organism":{"annotatorClassName":"","descriptionByType":"","descriptionByTypeRelation":"","id":523719,"link":"http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606","resource":"9606","type":"TAXONOMY"},"sourceUrl":"ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit","type":"UCSC","version":"hg19"},{"downloadProgress":100.0,"geneMapping":[],"idObject":1563,"localUrl":"../minerva-big//5280/hg38.2bit","organism":{"annotatorClassName":"","descriptionByType":"","descriptionByTypeRelation":"","id":927074,"link":"http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606","resource":"9606","type":"TAXONOMY"},"sourceUrl":"ftp://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit","type":"UCSC","version":"hg38"}]
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeRestImpl.java
index b8be215211..a47b01f80e 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeRestImpl.java
@@ -70,9 +70,11 @@ public class ReferenceGenomeRestImpl extends BaseRestImpl {
Map<String, Object> result = new TreeMap<>();
result.put("organism", super.createAnnotation(genome.getOrganism()));
result.put("version", genome.getVersion());
+ result.put("type", genome.getType());
result.put("downloadProgress", genome.getDownloadProgress());
result.put("sourceUrl", genome.getSourceUrl());
result.put("localUrl", getLocalUrl(genome.getSourceUrl()));
+ result.put("idObject", genome.getId());
result.put("geneMapping", geneMappingToMaps(genome.getGeneMapping()));
return result;
--
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