diff --git a/frontend-js/src/main/js/ServerConnector.js b/frontend-js/src/main/js/ServerConnector.js
index b75bca3bcd09416e247ca12ee98a9806cf756b67..cb9c8e5c83af74c46b5912a3e903265b1c960fa3 100644
--- a/frontend-js/src/main/js/ServerConnector.js
+++ b/frontend-js/src/main/js/ServerConnector.js
@@ -420,14 +420,32 @@ ServerConnector.getSbmlParameterUrl = function (queryParams, filterParams) {
});
};
+/**
+ *
+ * @param {Object} queryParams
+ * @param {string} [queryParams.version]
+ * @param {string} [queryParams.organism]
+ * @param {string} [queryParams.type]
+ * @param {string} [queryParams.genomeId]
+ * @param {Object} filterParams
+ *
+ * @returns {string}
+ */
ServerConnector.getReferenceGenomeUrl = function (queryParams, filterParams) {
- var version = this.getIdOrAsterisk(queryParams.version);
+ if (queryParams.genomeId !== undefined) {
+ return this.getApiUrl({
+ type: "genomics/" + queryParams.genomeId + "/",
+ params: filterParams
+ });
+ } else {
+ var version = this.getIdOrAsterisk(queryParams.version);
- return this.getApiUrl({
- type: "genomics/taxonomies/" + queryParams.organism + "/genomeTypes/" + queryParams.type + "/versions/" + version
- + "/",
- params: filterParams
- });
+ return this.getApiUrl({
+ type: "genomics/taxonomies/" + queryParams.organism + "/genomeTypes/" + queryParams.type + "/versions/" + version
+ + "/",
+ params: filterParams
+ });
+ }
};
ServerConnector.loginUrl = function () {
@@ -1985,12 +2003,46 @@ ServerConnector.getPublications = function (params) {
});
};
+/**
+ *
+ * @param {Object} params
+ * @param {string} [params.version]
+ * @param {string} [params.organism]
+ * @param {string} [params.type]
+ * @param {string} [params.genomeId]
+ *
+ * @returns {Promise}
+ */
ServerConnector.getReferenceGenome = function (params) {
var self = this;
var filterParams = {};
- return self.sendGetRequest(self.getReferenceGenomeUrl(params, filterParams)).then(function (content) {
- return new ReferenceGenome(JSON.parse(content));
- });
+ if (params.genomeId !== undefined) {
+ return self.getReferenceGenomes().then(function (referenceGenomes) {
+ for (var i = 0; i < referenceGenomes.leftPanel; i++) {
+ var genome = referenceGenomes[i];
+ if (genome.getId() === params.genomeId()) {
+ return genome;
+ }
+ }
+ return null;
+ });
+ } else {
+ return self.sendGetRequest(self.getReferenceGenomeUrl(params, filterParams)).then(function (content) {
+ return new ReferenceGenome(JSON.parse(content));
+ });
+ }
+};
+
+/**
+ *
+ * @param {Object} params
+ * @param {string} params.genomeId
+ * @returns {Promise}
+ */
+ServerConnector.removeReferenceGenome = function (params) {
+ var self = this;
+ var filterParams = {};
+ return self.sendDeleteRequest(self.getReferenceGenomeUrl(params, filterParams));
};
ServerConnector.uploadFile = function (params) {
diff --git a/frontend-js/src/main/js/gui/admin/AddProjectDialog.js b/frontend-js/src/main/js/gui/admin/AddProjectDialog.js
index 0ab83e41a584db1d9547d034a2ff23d553578a4d..a436197c2afc643d766b5fcb0159975209c58744 100644
--- a/frontend-js/src/main/js/gui/admin/AddProjectDialog.js
+++ b/frontend-js/src/main/js/gui/admin/AddProjectDialog.js
@@ -160,11 +160,11 @@ AddProjectDialog.prototype.showValidatorsDialog = function () {
AddProjectDialog.prototype.createGeneralTabContent = function () {
var self = this;
- var result = new Functions.createElement({
+ var result = Functions.createElement({
type: "div"
});
- var table = new Functions.createElement({
+ var table = Functions.createElement({
type: "div",
style: "display:table; width:100%"
});
@@ -352,12 +352,12 @@ AddProjectDialog.prototype.createInputRow = function (params) {
if (params.defaultValue === undefined) {
params.defaultValue = "";
}
- var label = new Functions.createElement({
+ var label = Functions.createElement({
type: "div",
style: "display:table-cell; width:200px",
content: xss(params.labelName)
});
- var input = new Functions.createElement({
+ var input = Functions.createElement({
type: "div",
style: "display:table-cell",
content: "<input name='" + xss(params.inputName) + "' value='" + xss(params.defaultValue) + "' style='width:100%'/>",
@@ -409,7 +409,7 @@ AddProjectDialog.prototype.createCheckboxRow = function (params) {
};
AddProjectDialog.prototype.createRow = function (elements) {
- var result = new Functions.createElement({
+ var result = Functions.createElement({
type: "div",
style: "display:table-row"
});
@@ -420,7 +420,7 @@ AddProjectDialog.prototype.createRow = function (elements) {
if (columnNumber === 0) {
style += "width:200px;";
}
- var labelContainer = new Functions.createElement({
+ var labelContainer = Functions.createElement({
type: "div",
style: style
});
diff --git a/frontend-js/src/main/js/gui/admin/EditGenomeDialog.js b/frontend-js/src/main/js/gui/admin/EditGenomeDialog.js
new file mode 100644
index 0000000000000000000000000000000000000000..0d9dfc25b58abefeb0bced9cf32959ffc11ab46c
--- /dev/null
+++ b/frontend-js/src/main/js/gui/admin/EditGenomeDialog.js
@@ -0,0 +1,287 @@
+"use strict";
+
+var Promise = require("bluebird");
+
+var AbstractGuiElement = require('../AbstractGuiElement');
+var GuiConnector = require('../../GuiConnector');
+
+var Functions = require('../../Functions');
+// noinspection JSUnusedLocalSymbols
+var logger = require('../../logger');
+
+var guiUtils = new (require('../leftPanel/GuiUtils'))();
+
+/**
+ *
+ * @param {Object} params
+ * @param {HTMLElement} params.element
+ * @param {CustomMap} params.customMap
+ * @param {Configuration} params.configuration
+ * @param {ReferenceGenome} params.referenceGenome
+ * @param {ServerConnector} [params.serverConnector]
+
+ * @constructor
+ *
+ * @extends AbstractGuiElement
+ */
+function EditGenomeDialog(params) {
+ AbstractGuiElement.call(this, params);
+ var self = this;
+ self.setReferenceGenome(params.referenceGenome);
+
+ $(self.getElement()).css({overflow: "hidden"});
+
+ self.createGui();
+ self.registerListenerType("onSave");
+}
+
+EditGenomeDialog.prototype = Object.create(AbstractGuiElement.prototype);
+EditGenomeDialog.prototype.constructor = EditGenomeDialog;
+
+/**
+ *
+ * @param {ReferenceGenome} referenceGenome
+ */
+EditGenomeDialog.prototype.setReferenceGenome = function (referenceGenome) {
+ this._referenceGenome = referenceGenome;
+};
+
+/**
+ *
+ * @returns {ReferenceGenome}
+ */
+EditGenomeDialog.prototype.getReferenceGenome = function () {
+ return this._referenceGenome;
+};
+
+/**
+ *
+ * @returns {boolean}
+ */
+EditGenomeDialog.prototype.isNew = function () {
+ return this.getReferenceGenome().getId() === undefined;
+};
+
+/**
+ *
+ */
+EditGenomeDialog.prototype.createGui = function () {
+ var self = this;
+ var element = self.getElement();
+
+ var tabDiv = Functions.createElement({
+ type: "div",
+ name: "tabView",
+ className: "tabbable boxed parentTabs",
+ style: "position:absolute;top:10px;bottom:40px;left:10px;right:10px"
+ });
+ element.appendChild(tabDiv);
+
+ var tabMenuDiv = Functions.createElement({
+ type: "ul",
+ className: "nav nav-tabs"
+ });
+ tabDiv.appendChild(tabMenuDiv);
+
+ var tabContentDiv = Functions.createElement({
+ type: "div",
+ className: "tab-content",
+ style: "height:100%"
+ });
+ tabDiv.appendChild(tabContentDiv);
+
+ self.createGeneralTab(tabMenuDiv, tabContentDiv);
+ $("a", tabMenuDiv).bind("click", function () {
+ //workaround for some css issues...
+ tabDiv.style.top = "40px";
+ tabDiv.style.bottom = "10px";
+ });
+};
+
+/**
+ *
+ * @param {HTMLElement} tabMenuDiv
+ * @param {HTMLElement} tabContentDiv
+ */
+EditGenomeDialog.prototype.createGeneralTab = function (tabMenuDiv, tabContentDiv) {
+ var self = this;
+ self.addTab({
+ tabMenuDiv: tabMenuDiv,
+ tabContentDiv: tabContentDiv,
+ name: "DETAILS",
+ content: self.createGeneralTabContent()
+ });
+
+};
+
+var id_counter = 0;
+
+/**
+ *
+ * @param {string} tab_name
+ * @returns {string}
+ */
+EditGenomeDialog.prototype.generateTabId = function (tab_name) {
+ var self = this;
+ var id = self.getReferenceGenome().getId();
+ if (id === undefined) {
+ id = "new_genome_" + (id_counter++);
+ }
+ return id + tab_name.replace(" ", "_") + "_TAB";
+};
+
+EditGenomeDialog.prototype.addTab = function (params) {
+ var id = this.generateTabId(params.name);
+
+ var navLi = guiUtils.createTabMenuObject({
+ id: id,
+ name: params.name,
+ navigationBar: params.tabMenuDiv
+ });
+ params.tabMenuDiv.appendChild(navLi);
+
+ var contentDiv = guiUtils.createTabContentObject({
+ id: id,
+ navigationObject: navLi,
+ navigationBar: params.tabMenuDiv
+ });
+
+ $(contentDiv).css("overflow", "auto");
+ if (params.content !== undefined) {
+ contentDiv.appendChild(params.content);
+ }
+
+ params.tabContentDiv.appendChild(contentDiv);
+};
+
+/**
+ *
+ * @returns {HTMLElement}
+ */
+EditGenomeDialog.prototype.createGeneralTabContent = function () {
+
+ var self = this;
+
+ var result = Functions.createElement({
+ type: "div",
+ style: "margin-top:10px;"
+ });
+
+ var table = Functions.createElement({
+ type: "table",
+ name: "detailsTable",
+ className: "display",
+ style: "width:100%"
+ });
+ result.appendChild(table);
+
+ var menuRow = Functions.createElement({
+ type: "div",
+ className: "minerva-menu-row",
+ style: "display:table-row; margin:10px"
+ });
+ result.appendChild(menuRow);
+
+ var saveUserButton = Functions.createElement({
+ type: "button",
+ name: "saveUser",
+ content: '<span class="ui-icon ui-icon-disk"></span> SAVE',
+ onclick: function () {
+ return self.onSaveClicked().then(function () {
+ return self.close();
+ }, GuiConnector.alert);
+ },
+ xss: false
+ });
+ var cancelButton = Functions.createElement({
+ type: "button",
+ name: "cancelProject",
+ content: '<span class="ui-icon ui-icon-cancel"></span> CANCEL',
+ onclick: function () {
+ return self.close();
+ },
+ xss: false
+ });
+ menuRow.appendChild(saveUserButton);
+ menuRow.appendChild(cancelButton);
+
+ return result;
+};
+
+/**
+ *
+ * @returns {Promise}
+ */
+EditGenomeDialog.prototype.init = function () {
+ var self = this;
+
+ var detailsTable = $("[name=detailsTable]", self.getElement())[0];
+
+ var dataTable = $(detailsTable).DataTable({
+ columns: [{
+ title: "Name"
+ }, {
+ title: "Value"
+ }],
+ paging: false,
+ ordering: false,
+ searching: false,
+ bInfo: false
+ });
+ var data = [];
+
+ var genome = self.getReferenceGenome();
+
+ data.push(['Type', '']);
+ data.push(['Organism', '']);
+ data.push(['Version', '']);
+ data.push(['Source url', '']);
+ data.push(['Local url', '']);
+ data.push(['Progress', '']);
+
+ dataTable.clear().rows.add(data).draw();
+
+ return Promise.resolve();
+};
+
+EditGenomeDialog.prototype.destroy = function () {
+ var self = this;
+ var div = self.getElement();
+
+ var detailsTable = $("[name=detailsTable]", div)[0];
+ if ($.fn.DataTable.isDataTable(detailsTable)) {
+ $(detailsTable).DataTable().destroy();
+ }
+
+
+ if ($(div).hasClass("ui-dialog-content")) {
+ $(div).dialog("destroy");
+ }
+};
+
+EditGenomeDialog.prototype.open = function () {
+ var self = this;
+ var div = self.getElement();
+ var title;
+ if (self.isNew()) {
+ title = "Download genome";
+ } else {
+ var genome = self.getReferenceGenome();
+ title = genome.getType() + " " + genome.getOrganism().getResource() + " " + genome.getVersion();
+ }
+ if (!$(div).hasClass("ui-dialog-content")) {
+ $(div).dialog({
+ title: title,
+ width: window.innerWidth / 2,
+ height: window.innerHeight / 2
+ });
+ }
+ $(div).dialog("open");
+};
+
+EditGenomeDialog.prototype.close = function () {
+ var self = this;
+ $(self.getElement()).dialog("close");
+};
+
+module.exports = EditGenomeDialog;
diff --git a/frontend-js/src/main/js/gui/admin/EditProjectDialog.js b/frontend-js/src/main/js/gui/admin/EditProjectDialog.js
index dc3e4c6681148590e707f5f9075ed2aab1ce43b1..3d5cc604188aa6f5a0d98faca79f3c54b1890dda 100644
--- a/frontend-js/src/main/js/gui/admin/EditProjectDialog.js
+++ b/frontend-js/src/main/js/gui/admin/EditProjectDialog.js
@@ -138,22 +138,22 @@ EditProjectDialog.prototype.createGeneralTabContent = function () {
var self = this;
var project = self.getProject();
- var result = new Functions.createElement({
+ var result = Functions.createElement({
type: "div"
});
- var table = new Functions.createElement({
+ var table = Functions.createElement({
type: "div",
style: "display:table"
});
result.appendChild(table);
- var projectIdRow = new Functions.createElement({
+ var projectIdRow = Functions.createElement({
type: "div",
style: "display:table-row"
});
table.appendChild(projectIdRow);
- projectIdRow.appendChild(new Functions.createElement({
+ projectIdRow.appendChild(Functions.createElement({
type: "div",
style: "display:table-cell",
content: "ProjectId"
@@ -204,46 +204,46 @@ EditProjectDialog.prototype.createGeneralTabContent = function () {
})
}));
- var nameRow = new Functions.createElement({
+ var nameRow = Functions.createElement({
type: "div",
style: "display:table-row"
});
table.appendChild(nameRow);
- nameRow.appendChild(new Functions.createElement({
+ nameRow.appendChild(Functions.createElement({
type: "div",
style: "display:table-cell",
content: "Name"
}));
- nameRow.appendChild(new Functions.createElement({
+ nameRow.appendChild(Functions.createElement({
type: "div",
style: "display:table-cell",
content: "<input name='projectName' value='" + xss(project.getName()) + "'/>",
xss: false
}));
- var versionRow = new Functions.createElement({
+ var versionRow = Functions.createElement({
type: "div",
style: "display:table-row"
});
table.appendChild(versionRow);
- versionRow.appendChild(new Functions.createElement({
+ versionRow.appendChild(Functions.createElement({
type: "div",
style: "display:table-cell",
content: "Version"
}));
- versionRow.appendChild(new Functions.createElement({
+ versionRow.appendChild(Functions.createElement({
type: "div",
style: "display:table-cell",
content: "<input name='projectVersion' value='" + xss(project.getVersion()) + "'/>",
xss: false
}));
- var diseaseRow = new Functions.createElement({
+ var diseaseRow = Functions.createElement({
type: "div",
style: "display:table-row"
});
table.appendChild(diseaseRow);
- diseaseRow.appendChild(new Functions.createElement({
+ diseaseRow.appendChild(Functions.createElement({
type: "div",
style: "display:table-cell",
content: "Disease"
@@ -252,19 +252,19 @@ EditProjectDialog.prototype.createGeneralTabContent = function () {
if (project.getDisease() !== undefined) {
disease = xss(project.getDisease().getResource());
}
- diseaseRow.appendChild(new Functions.createElement({
+ diseaseRow.appendChild(Functions.createElement({
type: "div",
style: "display:table-cell",
content: "<input name='projectDisease' value='" + disease + "'/>",
xss: false
}));
- var organismRow = new Functions.createElement({
+ var organismRow = Functions.createElement({
type: "div",
style: "display:table-row"
});
table.appendChild(organismRow);
- organismRow.appendChild(new Functions.createElement({
+ organismRow.appendChild(Functions.createElement({
type: "div",
style: "display:table-cell",
content: "Organism"
@@ -273,19 +273,19 @@ EditProjectDialog.prototype.createGeneralTabContent = function () {
if (project.getOrganism() !== undefined) {
organism = xss(project.getOrganism().getResource());
}
- organismRow.appendChild(new Functions.createElement({
+ organismRow.appendChild(Functions.createElement({
type: "div",
style: "display:table-cell",
content: "<input name='projectOrganism' value='" + organism + "'/>",
xss: false
}));
- var emailRow = new Functions.createElement({
+ var emailRow = Functions.createElement({
type: "div",
style: "display:table-row"
});
table.appendChild(emailRow);
- emailRow.appendChild(new Functions.createElement({
+ emailRow.appendChild(Functions.createElement({
type: "div",
style: "display:table-cell",
content: "Notify email"
@@ -294,7 +294,7 @@ EditProjectDialog.prototype.createGeneralTabContent = function () {
if (project.getNotifyEmail() !== undefined) {
email = xss(project.getNotifyEmail());
}
- emailRow.appendChild(new Functions.createElement({
+ emailRow.appendChild(Functions.createElement({
type: "div",
style: "display:table-cell",
content: "<input name='projectNotifyEmail' value='" + email + "'/>",
diff --git a/frontend-js/src/main/js/gui/admin/EditUserDialog.js b/frontend-js/src/main/js/gui/admin/EditUserDialog.js
index 6b631121bd8f81047778829264d5299aaed40cd0..3030c8cab407a8ce2f5c38275cba2f4acd858435 100644
--- a/frontend-js/src/main/js/gui/admin/EditUserDialog.js
+++ b/frontend-js/src/main/js/gui/admin/EditUserDialog.js
@@ -145,12 +145,12 @@ EditUserDialog.prototype.createGeneralTabContent = function () {
var self = this;
- var result = new Functions.createElement({
+ var result = Functions.createElement({
type: "div",
style: "margin-top:10px;"
});
- var table = new Functions.createElement({
+ var table = Functions.createElement({
type: "table",
name: "detailsTable",
className: "display",
diff --git a/frontend-js/src/main/js/gui/admin/GenomeAdminPanel.js b/frontend-js/src/main/js/gui/admin/GenomeAdminPanel.js
index bfb7483b08cd9770fa15b9f6a773147577aa3203..133633f9daadb40963923e56cd1c906643d5c11a 100644
--- a/frontend-js/src/main/js/gui/admin/GenomeAdminPanel.js
+++ b/frontend-js/src/main/js/gui/admin/GenomeAdminPanel.js
@@ -1,15 +1,18 @@
"use strict";
-/* exported Promise*/
-
var AbstractAdminPanel = require('./AbstractAdminPanel');
+var EditGenomeDialog = require('./EditGenomeDialog');
var Functions = require('../../Functions');
+var GuiConnector = require('../../GuiConnector');
var PrivilegeType = require('../../map/data/PrivilegeType');
+var ReferenceGenome = require('../../map/data/ReferenceGenome');
// noinspection JSUnusedLocalSymbols
var logger = require('../../logger');
+var Promise = require('bluebird');
+
/**
*
* @param {Configuration} params.configuration
@@ -88,6 +91,24 @@ GenomeAdminPanel.prototype._createGui = function () {
}
});
+ $(genomesTable).on("click", "[name='removeGenome']", function () {
+ var button = this;
+ return self.askConfirmRemoval({
+ title: "INFO",
+ content: "Do you really want to remove this genome?",
+ input: false
+ }).then(function (param) {
+ if (param.status) {
+ return self.getServerConnector().removeReferenceGenome({genomeId: $(button).attr("data")});
+ }
+ }).catch(GuiConnector.alert);
+ });
+
+ $(genomesTable).on("click", "[name='editGenome']", function () {
+ var button = this;
+ return self.showEditDialog($(button).attr("data")).catch(GuiConnector.alert);
+ });
+
};
/**
@@ -163,7 +184,7 @@ GenomeAdminPanel.prototype.genomeToTableRow = function (genome, user) {
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[5] = "<button name='editGenome' 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;
@@ -180,7 +201,68 @@ GenomeAdminPanel.prototype.destroy = function () {
if ($.fn.DataTable.isDataTable(table)) {
$(table).DataTable().destroy();
}
- return AbstractAdminPanel.prototype.destroy.call(self);
+ var promises = [];
+ for (var key in self._dialogs) {
+ if (self._dialogs.hasOwnProperty(key)) {
+ promises.push(self._dialogs[key].destroy());
+ }
+ }
+ promises.push(AbstractAdminPanel.prototype.destroy.call(self));
+
+ return Promise.all(promises);
};
+/**
+ *
+ * @param {ReferenceGenome} [genome]
+ * @returns {Promise}
+ */
+GenomeAdminPanel.prototype.getDialog = function (genome) {
+ var self = this;
+ if (self._dialogs === undefined) {
+ self._dialogs = [];
+ }
+ var id = genome.getId();
+ var dialog = self._dialogs[id];
+ if (dialog === undefined) {
+ dialog = new EditGenomeDialog({
+ element: Functions.createElement({
+ type: "div"
+ }),
+ configuration: self.getConfiguration(),
+ referenceGenome: genome,
+ customMap: null
+ });
+ self._dialogs[id] = dialog;
+ if (id === "null") {
+ dialog.addListener("onSave", function () {
+ return self.onRefreshClicked();
+ });
+ }
+ return dialog.init().then(function () {
+ return dialog;
+ });
+ } else {
+ return Promise.resolve(dialog);
+ }
+};
+
+GenomeAdminPanel.prototype.showEditDialog = function (id) {
+ var self = this;
+ GuiConnector.showProcessing();
+ return self.getServerConnector().getReferenceGenome({genomeId: id}).then(function (referenceGenome) {
+ if (referenceGenome === null) {
+ referenceGenome = new ReferenceGenome();
+ }
+ return self.getDialog(referenceGenome);
+ }).then(function (dialog) {
+ dialog.open();
+ GuiConnector.hideProcessing();
+ }).catch(function (error) {
+ GuiConnector.hideProcessing();
+ return Promise.reject(error);
+ });
+};
+
+
module.exports = GenomeAdminPanel;
diff --git a/frontend-js/src/test/js/gui/admin/EditGenomeDialog-test.js b/frontend-js/src/test/js/gui/admin/EditGenomeDialog-test.js
new file mode 100644
index 0000000000000000000000000000000000000000..40544872deb3d50c62aa656d88ce6e3b1d8ed7c0
--- /dev/null
+++ b/frontend-js/src/test/js/gui/admin/EditGenomeDialog-test.js
@@ -0,0 +1,38 @@
+"use strict";
+
+require("../../mocha-config");
+
+var EditGenomeDialog = require('../../../../main/js/gui/admin/EditGenomeDialog');
+var ReferenceGenome = require('../../../../main/js/map/data/ReferenceGenome');
+var ValidationError = require('../../../../main/js/ValidationError');
+var ServerConnector = require('../../ServerConnector-mock');
+
+var logger = require('../../logger');
+
+var chai = require('chai');
+var assert = chai.assert;
+var expect = chai.expect;
+
+describe('EditGenomeDialog', function () {
+
+ describe('init', function () {
+ it('new genome', function () {
+ var dialog;
+ var project;
+ var genome = new ReferenceGenome();
+ return ServerConnector.getProject().then(function (result) {
+ project = result;
+ dialog = new EditGenomeDialog({
+ element: testDiv,
+ project: project,
+ referenceGenome: genome,
+ customMap: null
+ });
+ return dialog.init();
+ }).then(function () {
+ dialog.destroy();
+ });
+ });
+ });
+
+});
diff --git a/frontend-js/src/test/js/gui/admin/GenomeAdminPanel-test.js b/frontend-js/src/test/js/gui/admin/GenomeAdminPanel-test.js
index a1a4567a41efe66be04531e05f10c49a5464d76a..0c0b1b69591f990aee296392fcbd36166d4fd0a8 100644
--- a/frontend-js/src/test/js/gui/admin/GenomeAdminPanel-test.js
+++ b/frontend-js/src/test/js/gui/admin/GenomeAdminPanel-test.js
@@ -6,6 +6,7 @@ var GenomeAdminPanel = require('../../../../main/js/gui/admin/GenomeAdminPanel')
var ConfigurationType = require('../../../../main/js/ConfigurationType');
var ServerConnector = require('../../ServerConnector-mock');
var logger = require('../../logger');
+var Promise = require('bluebird');
var chai = require('chai');
var assert = chai.assert;
@@ -28,4 +29,44 @@ describe('GenomeAdminPanel', function () {
});
});
});
+ it('open edit dialog', 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);
+ var element = $("[name='editGenome']")[0];
+ return helper.triggerJqueryEvent(element, "click");
+ }).then(function () {
+ return mapTab.destroy();
+ });
+ });
+
+ it('remove genome', 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 () {
+ mapTab.askConfirmRemoval = function () {
+ return Promise.resolve({status: true});
+ };
+ assert.equal(0, logger.getWarnings().length);
+ var element = $("[name='removeGenome']")[0];
+ return helper.triggerJqueryEvent(element, "click");
+ }).then(function () {
+ return mapTab.destroy();
+ });
+ });
});
diff --git a/frontend-js/testFiles/apiCalls/genomics/43/DELETE_token=ADMIN_TOKEN_ID& b/frontend-js/testFiles/apiCalls/genomics/43/DELETE_token=ADMIN_TOKEN_ID&
new file mode 100644
index 0000000000000000000000000000000000000000..9e26dfeeb6e641a33dae4961196235bdb965b21b
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/genomics/43/DELETE_token=ADMIN_TOKEN_ID&
@@ -0,0 +1 @@
+{}
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeController.java b/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeController.java
index 51342dd986d13258b352f1d76087517dea660e20..b8c950515a2726d63ff106aed1b03ba30ac2833e 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeController.java
@@ -1,5 +1,6 @@
package lcsb.mapviewer.api.genomics;
+import java.io.IOException;
import java.util.List;
import java.util.Map;
@@ -67,5 +68,13 @@ public class ReferenceGenomeController extends BaseController {
) throws SecurityException, QueryException, ObjectNotFoundException {
return referenceGenomeController.getReferenceGenomes(token);
}
+
+ @RequestMapping(value = "/genomics/{genomeId}/", method = { RequestMethod.DELETE }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> removeGenome(//
+ @PathVariable(value = "genomeId") String genomeId, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws SecurityException, IOException {
+ return referenceGenomeController.removeGenome(genomeId, token);
+ }
}
\ 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 a47b01f80e3029e457ad8a9b4965d476e3a7b248..cedb3cc467f21ed1c7d78cbcdd53bc5f8d345c39 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.api.genomics;
import java.io.FileNotFoundException;
+import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
@@ -23,6 +24,8 @@ import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.layout.ReferenceGenome;
import lcsb.mapviewer.model.map.layout.ReferenceGenomeGeneMapping;
import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
+import lcsb.mapviewer.model.user.PrivilegeType;
+import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.interfaces.IReferenceGenomeService;
@@ -178,4 +181,13 @@ public class ReferenceGenomeRestImpl extends BaseRestImpl {
return result;
}
+ public Map<String, Object> removeGenome(String genomeId, String token) throws SecurityException, IOException {
+ if (!getUserService().userHasPrivilege(token, PrivilegeType.MANAGE_GENOMES)) {
+ throw new SecurityException("Access denied");
+ }
+ ReferenceGenome genome = referenceGenomeService.getReferenceGenomeById(Integer.parseInt(genomeId), token);
+ referenceGenomeService.removeGenome(genome);
+ return okStatus();
+ }
+
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ReferenceGenomeService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ReferenceGenomeService.java
index b3bc006549d1391246bc18d19aead5a5caeea55e..b7c1d54c7cf902a28928bacde42af146d56458ae 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ReferenceGenomeService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ReferenceGenomeService.java
@@ -143,4 +143,9 @@ public class ReferenceGenomeService implements IReferenceGenomeService {
return null;
}
+ @Override
+ public ReferenceGenome getReferenceGenomeById(int id, String authenticationToken) {
+ return referenceGenomeDao.getById(id);
+ }
+
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/IReferenceGenomeService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/IReferenceGenomeService.java
index c87597d001d25c1ba154cbac89389ebdf9d9f7d1..71af2fae75eedd66a5a6b5648d7d85eb0b1f0d73 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/IReferenceGenomeService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/IReferenceGenomeService.java
@@ -142,4 +142,6 @@ public interface IReferenceGenomeService {
*/
ReferenceGenome getReferenceGenomeViewByParams(MiriamData organism, ReferenceGenomeType genomeType, String version,
String authenticationToken);
+
+ ReferenceGenome getReferenceGenomeById(int id, String authenticationToken);
}