January 2014 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: carlfeberhard: Functional browser tests: update/fix upload tests
by commits-noreply＠bitbucket.org 08 Jan '14

08 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6c269fbd11a4/ Changeset: 6c269fbd11a4 User: carlfeberhard Date: 2014-01-08 20:40:41 Summary: Functional browser tests: update/fix upload tests Affected #: 4 files diff -r 3240786183e464dd9233a7e64eebe06a0fed0172 -r 6c269fbd11a43236a0dd4c7df388125fdaf8962d test/casperjs/modules/historypanel.js --- a/test/casperjs/modules/historypanel.js +++ b/test/casperjs/modules/historypanel.js @@ -33,13 +33,13 @@ // =================================================================== API (external) // ------------------------------------------------------------------- frame control -/** Is casper currently 'in' the history frame? - * @returns {Boolean} - */ -HistoryPanel.prototype.inFrame = function inFrame(){ - return ( ( this.spaceghost.page.frameName === this.spaceghost.data.selectors.frames.history ) - && ( this.spaceghost.page.frameTitle === this.data.text.frameTitle ) ); -}; +///** Is casper currently 'in' the history frame? +// * @returns {Boolean} +// */ +//HistoryPanel.prototype.inFrame = function inFrame(){ +// return ( ( this.spaceghost.page.frameName === this.spaceghost.data.selectors.frames.history ) +// && ( this.spaceghost.page.frameTitle === this.data.text.frameTitle ) ); +//}; /** Hover over an element in the history panel. * @param {String} selector a css or xpath selector for an historyItemWrapper @@ -61,36 +61,27 @@ }; // ------------------------------------------------------------------- hdas -/** Parse the hid and name from an HDA title. +///** Parse the hid and name from an HDA title. +// * NOTE: if more than one is found, will return the first found. +// * @param {String} title the title of the hda +// * @returns {Object} of the form { hid: <hid>, name: <name> } +// */ +//HistoryPanel.prototype.hdaHidAndNameFromTitle = function hdaHidAndNameFromTitle( title ){ +// var sep = ': ', split = title.split( sep, 1 ); +// return { +// name : (( split.length >= 2 )?( split[1] ):( split[0] )), +// hid : (( split.length >= 2 )?( parseInt( split[0], 10 ) ):( undefined )) +// }; +//}; + +/** Find the casper element info of the hda wrapper given the hda title. * NOTE: if more than one is found, will return the first found. * @param {String} title the title of the hda - * @returns {Object} of the form { hid: <hid>, name: <name> } - */ -HistoryPanel.prototype.hdaHidAndNameFromTitle = function hdaHidAndNameFromTitle( title ){ - var sep = ': ', split = title.split( sep, 1 ); - return { - name : (( split.length >= 2 )?( split[1] ):( split[0] )), - hid : (( split.length >= 2 )?( parseInt( split[0], 10 ) ):( undefined )) - }; -}; - -/** Find the casper element info of the hda wrapper given the hda title and hid. - * NOTE: if more than one is found, will return the first found. - * @param {String} title the title of the hda - * @param {Int} hid (optional) the hid of the hda to look for * @returns {Object|null} ElementInfo of the historyItemWrapper found, null if not found */ -HistoryPanel.prototype.hdaElementInfoByTitle = function hdaElementInfoByTitle( title, hid ){ - var spaceghost = this.spaceghost, - titleContains = ( hid !== undefined )?( hid + ': ' + title ):( title ); - //TODO: this would fail if we named/uploaded a file that has quotations - - // we can use underscore.un/escape to solve that - - return spaceghost.jumpToHistory( function getWrapperInfo(){ - var wrapperXpath = xpath( '//span[@class="historyItemTitle" ' + - 'and contains(text(),"' + titleContains + '")]/../..' ); - return spaceghost.elementInfoOrNull( wrapperXpath ); - }); +HistoryPanel.prototype.hdaElementInfoByTitle = function hdaElementInfoByTitle( title ){ + var wrapperXpath = xpath( '//span[@class="dataset-name" and contains(text(),"' + title + '")]/../../..' ); + return this.spaceghost.elementInfoOrNull( wrapperXpath ); }; /** Get the state string of the given hda. @@ -99,12 +90,10 @@ * @returns {String|undefined} class string of the historyItemWrapper found, undefined if not found or set */ HistoryPanel.prototype.getHdaState = function getHdaState( hdaSelector ){ - return this.spaceghost.jumpToHistory( function(){ - var found = null, - hdaInfo = this.elementInfoOrNull( hdaSelector ); - if( !hdaInfo ){ return undefined; } - return (( found = hdaInfo.attributes[ 'class' ].match( /historyItem\-(\w+)/ ) )?( found[1] ):( undefined )); - }); + var found = null, + hdaInfo = this.spaceghost.elementInfoOrNull( hdaSelector ); + if( !hdaInfo ){ return undefined; } + return (( found = hdaInfo.attributes[ 'class' ].match( /state\-(\w+)/ ) )?( found[1] ):( undefined )); }; /** Get the encoded database/API id of the given hda. @@ -119,20 +108,20 @@ }; // ------------------------------------------------------------------- step functions -/** Version of Casper#withFrame for the history iframe. - * Hopefully will allow easier test transition if/when frames are removed - * (i.e. -> just call the function). - * NOTE: is more than one Casper step. - * @param {Function} then function called when in the history frame - */ -HistoryPanel.prototype.then = function then( thenFn ){ - if( this.inFrame() ){ - thenFn.call( this.spaceghost ); - } else { - this.spaceghost.withHistoryPanel( thenFn ); - } -}; - +///** Version of Casper#withFrame for the history iframe. +// * Hopefully will allow easier test transition if/when frames are removed +// * (i.e. -> just call the function). +// * NOTE: is more than one Casper step. +// * @param {Function} then function called when in the history frame +// */ +//HistoryPanel.prototype.then = function then( thenFn ){ +// if( this.inFrame() ){ +// thenFn.call( this.spaceghost ); +// } else { +// this.spaceghost.withHistoryPanel( thenFn ); +// } +//}; +// /** Moves into history iframe and waits until hdas are visible or empty message is. * NOTE: is more than one Casper step. * @see Casper@waitFor @@ -140,13 +129,13 @@ HistoryPanel.prototype.waitForHdas = function waitForHdas( then, timeout, maxWait ){ //TODO:?? should this wait until the seletors are in AND they are opaque? var spaceghost = this.spaceghost; - this.then( function waitingForHdas(){ + spaceghost.then( function waitingForHdas(){ this.waitFor( function checkHpanel(){ - // trying a subtitle opacity test for page.isloaded var subtitleOpacity = this.evaluate( function( selector ){ return $( selector ).css( 'opacity' ); }, this.historypanel.data.selectors.history.subtitle ); + // wait until the subtitle is faded in and either the hdas or the empty history msg is displayed return ( subtitleOpacity !== 1 && ( ( this.visible( this.historypanel.data.selectors.hda.wrapper.itemClass ) ) ||( this.visible( this.historypanel.data.selectors.history.emptyMsg ) ) ) ); @@ -218,7 +207,7 @@ var hpanel = this, spaceghost = this.spaceghost; - this.then( function(){ + this.spaceghost.then( function(){ // get initial state, cache old timeout, set new timeout var prevState = hpanel.getHdaState( hdaSelector ), oldWaitTimeout = spaceghost.options.waitTimeout; @@ -356,39 +345,39 @@ }, selectors : { history : { - name : 'div#history-name', - subtitle : 'div#history-subtitle-area', - tagIcon : '#history-tag.icon-button', - tagArea : '#history-tag-area', - annoIcon : '#history-annotate.icon-button', - annoArea : '#history-annotation-area', - // weak - emptyMsg : '.infomessagesmall', - undeleteLink : '.historyItemUndelete', - hdaContainer : '.history-datasets-list' + title : '.history-title', + name : '.history-title .history-name', + subtitle : '.history-subtitle', + tagIcon : '.history-secondary-actions .history-tag-btn', + tagArea : '.history-controls .tags-display', + annoIcon : '.history-secondary-actions .history-annotate-btn', + annoArea : '.history-controls .annotation-display', + emptyMsg : '.empty-history-message', + hdaContainer: '.datasets-list' + //undeleteLink : '.historyItemUndelete', }, hda : { wrapper : { - itemClass : '.historyItem', + itemClass : '.hda', stateClasses : { - prefix : 'historyItem-', - ok : 'historyItem-ok', - 'new' : 'historyItem-new' + prefix : 'state-', + ok : 'state-ok', + 'new' : 'state-new' } }, errorMessage : '.errormessagesmall', - title : '.historyItemTitle', - titleButtonArea : '.historyItemButtons', - body : '.historyItemBody', - summary : '.hda-summary', - dbkey : '.metadata-dbkey', - info : '.hda-info', + title : '.dataset-title', + titleButtonArea : '.dataset-primary-actions', + summary : '.dataset-summary', + dbkey : '.dataset-dbkey', + info : '.dataset-info', + body : '.dataset-body', primaryActionButtons : 'div[id^="primary-actions"]', secondaryActionButtons : 'div[id^="secondary-actions"]', - peek : 'pre.peek' + peek : '.dataset-peek' } }, labels : { @@ -399,7 +388,7 @@ }, text : { windowTitle : 'History', - frameTitle : 'Galaxy History', + //frameTitle : 'Galaxy History', anonymous : { tooltips : { name : 'You must be logged in to edit your history name' diff -r 3240786183e464dd9233a7e64eebe06a0fed0172 -r 6c269fbd11a43236a0dd4c7df388125fdaf8962d test/casperjs/modules/tools.js --- a/test/casperjs/modules/tools.js +++ b/test/casperjs/modules/tools.js @@ -89,7 +89,7 @@ // click the upload tool spaceghost.thenOpen( spaceghost.baseUrl, function(){ // we can apprently click a tool label without expanding the tool container for it - this.clickLabel( spaceghost.data.labels.tools.upload.panelLabel ); + this.click( xpath( '//a[contains(text(),"Upload File")]' ) ); this.jumpToMain( function(){ this.waitForSelector( 'body' ); }); @@ -108,7 +108,7 @@ // wait for main panel, history reload ////NOTE!: assumes tool execution reloads the history panel - this.waitForMultipleNavigation( [ 'tool_runner/upload_async_message', 'history' ], + this.waitForMultipleNavigation( [ 'tool_runner/upload_async_message' ], function thenAfterUploadRefreshes(){ // debugging this.jumpToMain( function(){ diff -r 3240786183e464dd9233a7e64eebe06a0fed0172 -r 6c269fbd11a43236a0dd4c7df388125fdaf8962d test/casperjs/spaceghost.js --- a/test/casperjs/spaceghost.js +++ b/test/casperjs/spaceghost.js @@ -626,15 +626,6 @@ // ------------------------------------------------------------------- iframes, damnable iframes -/** Version of Casper#withFrame for the history iframe. - * Hopefully will allow easier test transition if/when frames are removed - * (i.e. -> just call the function). - * @param {Function} then function called when in the history frame - */ -SpaceGhost.prototype.withHistoryPanel = function withHistoryPanel( then ){ - return this.withFrame( this.data.selectors.frames.history, then ); -}; - /** Version of Casper#withFrame for the main iframe. * @param {Function} then function called when in the frame */ @@ -671,14 +662,14 @@ return returned; }; -/** Jumps into history frame, exectutes fn, and jumps back to original frame. - * @param {Selector} frame the selector for the frame to jump to - * @param {Function} fn function called when in the frame - * @returns {Any} the return value of fn - */ -SpaceGhost.prototype.jumpToHistory = function jumpToHistory( fn ){ - return this.jumpToFrame( this.data.selectors.frames.history, fn ); -}; +///** Jumps into history frame, exectutes fn, and jumps back to original frame. +// * @param {Selector} frame the selector for the frame to jump to +// * @param {Function} fn function called when in the frame +// * @returns {Any} the return value of fn +// */ +//SpaceGhost.prototype.jumpToHistory = function jumpToHistory( fn ){ +// return this.jumpToFrame( this.data.selectors.frames.history, fn ); +//}; /** Jumps into main frame, exectutes fn, and jumps back to original frame. * @param {Selector} frame the selector for the frame to jump to diff -r 3240786183e464dd9233a7e64eebe06a0fed0172 -r 6c269fbd11a43236a0dd4c7df388125fdaf8962d test/casperjs/upload-tests.js --- a/test/casperjs/upload-tests.js +++ b/test/casperjs/upload-tests.js @@ -59,7 +59,6 @@ var filename = '1.txt', filepath = this.options.scriptDir + '/../../test-data/' + filename; - this.tools._uploadFile( filepath ); // when an upload begins successfully main should reload with a infomessagelarge @@ -83,6 +82,7 @@ this.test.fail( 'Could not locate new hda: ' + testUploadInfo.name ); } else { + spaceghost.debugElement( spaceghost.jsonStr( hdaInfo ) ); this.historypanel.waitForHdaState( '#' + hdaInfo.attributes.id, 'ok', function whenInStateFn( newHdaInfo ){ //this.debug( 'newHdaInfo:\n' + this.jsonStr( newHdaInfo ) ); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: martenson: js data libraries refactor, tweaks, logging removal
by commits-noreply＠bitbucket.org 08 Jan '14

08 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3240786183e4/ Changeset: 3240786183e4 User: martenson Date: 2014-01-08 19:54:38 Summary: js data libraries refactor, tweaks, logging removal Affected #: 4 files diff -r 3cdd4aae8403e76df8e0ac1efa621ad9b8889039 -r 3240786183e464dd9233a7e64eebe06a0fed0172 lib/galaxy/webapps/galaxy/api/folder_contents.py --- a/lib/galaxy/webapps/galaxy/api/folder_contents.py +++ b/lib/galaxy/webapps/galaxy/api/folder_contents.py @@ -108,8 +108,6 @@ return_item.update ( dict ( item_count = content_item.item_count ) ) if content_item.api_type == 'file': - log.debug( 'FolderContentsController, method index(), dataset name: ' + content_item.name ) - log.debug( 'vars: ' + str(vars( content_item )) ) library_dataset_dict = content_item.to_dict() library_dataset_dict['data_type'] library_dataset_dict['file_size'] diff -r 3cdd4aae8403e76df8e0ac1efa621ad9b8889039 -r 3240786183e464dd9233a7e64eebe06a0fed0172 static/scripts/galaxy.library.js --- a/static/scripts/galaxy.library.js +++ b/static/scripts/galaxy.library.js @@ -90,7 +90,7 @@ // === VIEWS ==== // MMMMMMMMMMMMMM -// galaxy folder +//main view for folder browsing var FolderContentView = Backbone.View.extend({ // main element definition el : '#center', @@ -116,7 +116,7 @@ // === TEMPLATES ==== // MMMMMMMMMMMMMMMMMM - // set up + // main template for folder browsing templateFolder : function (){ var tmpl_array = []; @@ -162,7 +162,7 @@ tmpl_array.push(' <th>name</th>'); tmpl_array.push(' <th>data type</th>'); tmpl_array.push(' <th>size</th>'); - tmpl_array.push(' <th>date</th>'); + tmpl_array.push(' <th>date (UTC)</th>'); tmpl_array.push(' </thead>'); tmpl_array.push(' <tbody>'); tmpl_array.push(' <td></td>'); @@ -184,7 +184,7 @@ tmpl_array.push(' <span class="muted">(empty folder)</span>'); tmpl_array.push(' <% } %>'); tmpl_array.push(' </td>'); - tmpl_array.push(' <td>folder</td>'); // data type + tmpl_array.push(' <td>folder</td>'); tmpl_array.push(' <td><%= _.escape(content_item.get("item_count")) %> item(s)</td>'); // size tmpl_array.push(' <% } else { %>'); tmpl_array.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>'); @@ -228,7 +228,7 @@ tmpl_array.push(' <td><%= _.escape(size) %></td>'); tmpl_array.push(' </tr>'); tmpl_array.push(' <tr>'); - tmpl_array.push(' <th scope="row">Date uploaded</th>'); + tmpl_array.push(' <th scope="row">Date uploaded (UTC)</th>'); tmpl_array.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>'); tmpl_array.push(' </tr>'); tmpl_array.push(' <tr>'); @@ -240,7 +240,7 @@ tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>'); tmpl_array.push(' </tr>'); tmpl_array.push(' <th scope="row">Comment Lines</th>'); - tmpl_array.push(' <% if (item.get("metadata_comment_lines") === "") { %>'); //folder + tmpl_array.push(' <% if (item.get("metadata_comment_lines") === "") { %>'); tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>'); tmpl_array.push(' <% } else { %>'); tmpl_array.push(' <td scope="row">unknown</td>'); @@ -296,19 +296,34 @@ return tmpl_array.join(''); }, - // convert size to nice string - size_to_string : function (size) - { - // identify unit - var unit = ""; - if (size >= 100000000000) { size = size / 100000000000; unit = "TB"; } else - if (size >= 100000000) { size = size / 100000000; unit = "GB"; } else - if (size >= 100000) { size = size / 100000; unit = "MB"; } else - if (size >= 100) { size = size / 100; unit = "KB"; } else - { size = size * 10; unit = "b"; } - // return formatted string - return (Math.round(size) / 10) + unit; - }, + templateProgressBar : function (){ + var tmpl_array = []; + + tmpl_array.push('<div class="import_text">'); + tmpl_array.push('Importing selected datasets to history <b><%= _.escape(history_name) %></b>'); + tmpl_array.push('</div>'); + tmpl_array.push('<div class="progress">'); + tmpl_array.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">'); + tmpl_array.push(' <span class="completion_span">0% Complete</span>'); + tmpl_array.push(' </div>'); + tmpl_array.push('</div>'); + tmpl_array.push(''); + + return tmpl_array.join(''); + }, + + templateNewFolderInModal: function(){ + tmpl_array = []; + + tmpl_array.push('<div id="new_folder_modal">'); + tmpl_array.push('<form>'); + tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">'); + tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">'); + tmpl_array.push('</form>'); + tmpl_array.push('</div>'); + + return tmpl_array.join(''); + }, // MMMMMMMMMMMMMMM // === EVENTS ==== @@ -325,6 +340,10 @@ 'click .btn_open_folder' : 'navigateToFolder' }, +// MMMMMMMMMMMMMMMMMM +// === FUNCTIONS ==== +// MMMMMMMMMMMMMMMMMM + //render the folder view render: function (options) { //hack to show scrollbars @@ -360,10 +379,27 @@ // var template = _.template(that.templateFolder(), { path: folderContainer.full_path, items: folderContainer.attributes.folder.models, id: options.id }); that.$el.html(template); - } + }, + error: function(){ + mod_toastr.error('An error occured :('); + } }) }, + // convert size to nice string + size_to_string : function (size) + { + // identify unit + var unit = ""; + if (size >= 100000000000) { size = size / 100000000000; unit = "TB"; } else + if (size >= 100000000) { size = size / 100000000; unit = "GB"; } else + if (size >= 100000) { size = size / 100000; unit = "MB"; } else + if (size >= 100) { size = size / 100; unit = "KB"; } else + { size = size * 10; unit = "b"; } + // return formatted string + return (Math.round(size) / 10) + unit; + }, + // handles the click on 'open' and 'upper' folder icons navigateToFolder : function(event){ var folder_id = $(event.target).attr('data-id'); @@ -398,9 +434,18 @@ // TODO can render here already //fetch user histories for import purposes histories.fetch({ - success: function (histories){self.renderModalAfterFetch(item, histories)} + success: function (histories){ + self.renderModalAfterFetch(item, histories) + }, + error: function(){ + mod_toastr.error('An error occured during fetching histories:('); + self.renderModalAfterFetch(item) + } }); - } + }, + error: function(){ + mod_toastr.error('An error occured during loading dataset details :('); + } }); }, @@ -422,16 +467,17 @@ }); $(".peek").html(item.get("peek")); - var history_footer_tmpl = _.template(this.templateHistorySelectInModal(), {histories : histories.models}); - $(this.modal.elMain).find('.buttons').prepend(history_footer_tmpl); - // preset last selected history if we know it - if (self.lastSelectedHistory.length > 0) { - $(this.modal.elMain).find('#dataset_import_single').val(self.lastSelectedHistory); - } - + // show the import-into-history footer only if the request for histories succeeded + if (typeof history.models !== undefined){ + var history_footer_tmpl = _.template(this.templateHistorySelectInModal(), {histories : histories.models}); + $(this.modal.elMain).find('.buttons').prepend(history_footer_tmpl); + // preset last selected history if we know it + if (self.lastSelectedHistory.length > 0) { + $(this.modal.elMain).find('#dataset_import_single').val(self.lastSelectedHistory); + } + } this.modal.bindEvents(); - // show the prepared modal this.modal.show(); }, @@ -555,7 +601,6 @@ $('#toolbtn_bulk_import').hide(); $('#toolbtn_dl').hide(); } - }, // show bulk import modal @@ -577,8 +622,10 @@ } }); self.modal.bindEvents(); - // show the prepared modal self.modal.show(); + }, + error: function(){ + mod_toastr.error('An error occured :('); } }); }, @@ -616,7 +663,7 @@ datasets_to_import.push(historyItem); }; - // call the recursive function to call ajax one after each other + // call the recursive function to call ajax one after each other (request FIFO queue) this.chainCall(datasets_to_import); }, @@ -646,22 +693,7 @@ $('.completion_span').text(txt_representation); }, - // progress bar - templateProgressBar : function (){ - var tmpl_array = []; - tmpl_array.push('<div class="import_text">'); - tmpl_array.push('Importing selected datasets to history <b><%= _.escape(history_name) %></b>'); - tmpl_array.push('</div>'); - tmpl_array.push('<div class="progress">'); - tmpl_array.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">'); - tmpl_array.push(' <span class="completion_span">0% Complete</span>'); - tmpl_array.push(' </div>'); - tmpl_array.push('</div>'); - tmpl_array.push(''); - - return tmpl_array.join(''); - }, // download selected datasets download : function(folder_id, format){ @@ -706,14 +738,13 @@ this.modal = new mod_modal.GalaxyModal({ destructible : true, title : 'Create New Folder', - body : this.template_new_folder(), + body : this.templateNewFolderInModal(), buttons : { 'Create' : function() {self.create_new_folder_event()}, 'Close' : function() {self.modal.hideOrDestroy(); self.modal = null;} } }); this.modal.bindEvents(); - // show prepared modal this.modal.show(); }, @@ -726,7 +757,7 @@ url_items = Backbone.history.fragment.split('/'); current_folder_id = url_items[url_items.length-1]; folder.url = folder.urlRoot + '/' + current_folder_id ; - + var self = this; folder.save(folderDetails, { success: function (folder) { @@ -755,20 +786,6 @@ // validate new library info validate_new_folder: function(folderDetails){ return folderDetails.name !== ''; - }, - - // template for new library modal - template_new_folder: function(){ - tmpl_array = []; - - tmpl_array.push('<div id="new_folder_modal">'); - tmpl_array.push('<form>'); - tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">'); - tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">'); - tmpl_array.push('</form>'); - tmpl_array.push('</div>'); - - return tmpl_array.join(''); } }); @@ -785,11 +802,13 @@ initialize : function(){ }, - // template - template_library_list : function (){ +// MMMMMMMMMMMMMMMMMM +// === TEMPLATES ==== +// MMMMMMMMMMMMMMMMMM + + templateLibraryList: function(){ tmpl_array = []; tmpl_array.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; overflow: auto !important; ">'); - tmpl_array.push(''); tmpl_array.push('<h3>New Data Libraries. This is work in progress. Report problems & ideas to <a href="mailto:marten@bx.psu.edu?Subject=DataLibraries_Feedback" target="_blank">Marten</a>.</h3>'); tmpl_array.push('<a href="" id="create_new_library_btn" class="btn btn-primary file ">New Library</a>'); @@ -814,14 +833,27 @@ tmpl_array.push(' <% }); %>'); tmpl_array.push(' </tbody>'); tmpl_array.push('</table>'); + tmpl_array.push('</div>'); - tmpl_array.push('</div>'); return tmpl_array.join(''); }, - // render + templateNewLibraryInModal: function(){ + tmpl_array = []; + + tmpl_array.push('<div id="new_library_modal">'); + tmpl_array.push(' <form>'); + tmpl_array.push(' <input type="text" name="Name" value="" placeholder="Name">'); + tmpl_array.push(' <input type="text" name="Description" value="" placeholder="Description">'); + tmpl_array.push(' <input type="text" name="Synopsis" value="" placeholder="Synopsis">'); + tmpl_array.push(' </form>'); + tmpl_array.push('</div>'); + + return tmpl_array.join(''); + }, + render: function () { - //hack to show scrollbars due to #center element inheritance + // modification of upper DOM element to show scrollbars due to the #center element inheritance $("#center").css('overflow','auto'); var that = this; @@ -829,7 +861,7 @@ libraries.fetch({ success: function (libraries) { - var template = _.template(that.template_library_list(), { libraries : libraries.models }); + var template = _.template(that.templateLibraryList(), { libraries : libraries.models }); that.$el.html(template); }, error: function(model, response){ @@ -863,14 +895,13 @@ this.modal = new mod_modal.GalaxyModal({ destructible : true, title : 'Create New Library', - body : this.template_new_library(), + body : this.templateNewLibraryInModal(), buttons : { 'Create' : function() {self.create_new_library_event()}, 'Close' : function() {self.modal.hideOrDestroy();} } }); this.modal.bindEvents(); - // show prepared modal this.modal.show(); }, @@ -916,21 +947,6 @@ // validate new library info validate_new_library: function(libraryDetails){ return libraryDetails.name !== ''; - }, - - // template for new library modal - template_new_library: function(){ - tmpl_array = []; - - tmpl_array.push('<div id="new_library_modal">'); - tmpl_array.push('<form>'); - tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">'); - tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">'); - tmpl_array.push('<input type="text" name="Synopsis" value="" placeholder="Synopsis">'); - tmpl_array.push('</form>'); - tmpl_array.push('</div>'); - - return tmpl_array.join(''); } }); @@ -938,6 +954,7 @@ var GalaxyLibrary = Backbone.View.extend({ folderContentView : null, galaxyLibraryview : null, + initialize : function(){ folderContentView = new FolderContentView(); diff -r 3cdd4aae8403e76df8e0ac1efa621ad9b8889039 -r 3240786183e464dd9233a7e64eebe06a0fed0172 static/scripts/galaxy.modal.js --- a/static/scripts/galaxy.modal.js +++ b/static/scripts/galaxy.modal.js @@ -19,7 +19,9 @@ // options options : { - destructible: false // by default the modal cannot be removed by theself.destroy() method + // by default the modal cannot be removed by the self.destroy() method + // but only hidden through self.hide() + destructible: false }, // initialize @@ -99,9 +101,9 @@ hide: function(){ // fade out this.$el.fadeOut('fast'); - // set flag this.visible = false; + // unbind events this.unbindEvents(); }, @@ -109,8 +111,8 @@ destroy: function(){ // set flag this.visible = false; + // unbind events this.unbindEvents(); - // remove this.$el.remove(); }, diff -r 3cdd4aae8403e76df8e0ac1efa621ad9b8889039 -r 3240786183e464dd9233a7e64eebe06a0fed0172 static/scripts/packed/galaxy.library.js --- a/static/scripts/packed/galaxy.library.js +++ b/static/scripts/packed/galaxy.library.js @@ -1,1 +1,1 @@ -var view=null;var library_router=null;var responses=[];define(["galaxy.modal","galaxy.masthead","utils/galaxy.utils","libs/toastr"],function(k,l,h,n){var f=Backbone.Model.extend({urlRoot:"/api/libraries"});var c=Backbone.Model.extend({urlRoot:"/api/folders"});var o=Backbone.Collection.extend({url:"/api/libraries",model:f});var i=Backbone.Model.extend({urlRoot:"/api/libraries/datasets"});var d=Backbone.Collection.extend({model:i});var e=Backbone.Model.extend({defaults:{folder:new d(),full_path:"unknown",urlRoot:"/api/folders/",id:"unknown"},parse:function(r){this.full_path=r[0].full_path;this.get("folder").reset(r[1].folder_contents);return r}});var b=Backbone.Model.extend({urlRoot:"/api/histories/"});var j=Backbone.Model.extend({url:"/api/histories/"});var p=Backbone.Collection.extend({url:"/api/histories",model:j});var q=Backbone.Router.extend({routes:{"":"libraries","folders/:id":"folder_content","folders/:folder_id/download/:format":"download"}});var m=Backbone.View.extend({el:"#center",progress:0,progressStep:1,lastSelectedHistory:"",modal:null,folders:null,initialize:function(){this.folders=[];this.queue=jQuery.Deferred();this.queue.resolve()},templateFolder:function(){var r=[];r.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; ">');r.push('<h3>New Data Libraries. This is work in progress. Report problems & ideas to <a href="mailto:marten@bx.psu.edu?Subject=DataLibraries_Feedback" target="_blank">Marten</a>.</h3>');r.push('<div id="library_folder_toolbar" >');r.push(' <button title="Create New Folder" id="toolbtn_create_folder" class="btn btn-primary" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder-close"></span> folder</button>');r.push(' <button id="toolbtn_bulk_import" class="btn btn-primary" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-external-link"></span> to history</button>');r.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display: none; ">');r.push(' <button id="drop_toggle" type="button" class="btn btn-primary dropdown-toggle" data-toggle="dropdown">');r.push(' <span class="fa fa-download"></span> download <span class="caret"></span>');r.push(" </button>");r.push(' <ul class="dropdown-menu" role="menu">');r.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');r.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');r.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');r.push(" </ul>");r.push(" </div>");r.push("</div>");r.push('<div class="library_breadcrumb">');r.push('<a title="Return to the list of libraries" href="#">Libraries</a><b>|</b> ');r.push("<% _.each(path, function(path_item) { %>");r.push("<% if (path_item[0] != id) { %>");r.push('<a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a><b>|</b> ');r.push("<% } else { %>");r.push('<span title="You are in this folder"><%- path_item[1] %></span>');r.push("<% } %>");r.push("<% }); %>");r.push("</div>");r.push('<table id="folder_table" class="table table-condensed">');r.push(" <thead>");r.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');r.push(' <th class="button_heading">view</th>');r.push(" <th>name</th>");r.push(" <th>data type</th>");r.push(" <th>size</th>");r.push(" <th>date</th>");r.push(" </thead>");r.push(" <tbody>");r.push(" <td></td>");r.push(' <td><button title="Go to parent folder" type="button" data-id="<%- upper_folder_id %>" class="btn_open_folder btn btn-default btn-xs">');r.push(' <span class="fa fa-arrow-up"></span> .. go up</td>');r.push(" <td></td>");r.push(" <td></td>");r.push(" <td></td>");r.push(" <td></td>");r.push(" </tr>");r.push(" <% _.each(items, function(content_item) { %>");r.push(' <tr class="folder_row light" id="<%- content_item.id %>">');r.push(' <% if (content_item.get("type") === "folder") { %>');r.push(" <td></td>");r.push(' <td><button title="Open this folder" type="button" data-id="<%- content_item.id %>" class="btn_open_folder btn btn-default btn-xs">');r.push(' <span class="fa fa-folder-open"></span> browse</td>');r.push(' <td><%- content_item.get("name") %>');r.push(' <% if (content_item.get("item_count") === 0) { %>');r.push(' <span class="muted">(empty folder)</span>');r.push(" <% } %>");r.push(" </td>");r.push(" <td>folder</td>");r.push(' <td><%= _.escape(content_item.get("item_count")) %> item(s)</td>');r.push(" <% } else { %>");r.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');r.push(" <td>");r.push(' <button title="See details of this dataset" type="button" class="library-dataset btn btn-default btn-xs">');r.push(' <span class="fa fa-eye"></span> details');r.push(" </button>");r.push(" </td>");r.push(' <td><%- content_item.get("name") %></td>');r.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');r.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>');r.push(" <% } %> ");r.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>');r.push(" </tr>");r.push(" <% }); %>");r.push(" ");r.push(" </tbody>");r.push("</table>");r.push("</div>");return r.join("")},templateDatasetModal:function(){var r=[];r.push('<div id="dataset_info_modal">');r.push(' <table class="table table-striped table-condensed">');r.push(" <tr>");r.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');r.push(' <td><%= _.escape(item.get("name")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Data type</th>');r.push(' <td><%= _.escape(item.get("data_type")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Genome build</th>');r.push(' <td><%= _.escape(item.get("genome_build")) %></td>');r.push(" </tr>");r.push(' <th scope="row">Size</th>');r.push(" <td><%= _.escape(size) %></td>");r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Date uploaded</th>');r.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Uploaded by</th>');r.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');r.push(" </tr>");r.push(' <tr scope="row">');r.push(' <th scope="row">Data Lines</th>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');r.push(" </tr>");r.push(' <th scope="row">Comment Lines</th>');r.push(' <% if (item.get("metadata_comment_lines") === "") { %>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');r.push(" <% } else { %>");r.push(' <td scope="row">unknown</td>');r.push(" <% } %>");r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Number of Columns</th>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Column Types</th>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Miscellaneous information</th>');r.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');r.push(" </tr>");r.push(" </table>");r.push(' <pre class="peek">');r.push(" </pre>");r.push("</div>");return r.join("")},templateHistorySelectInModal:function(){var r=[];r.push('<span id="history_modal_combo" style="width:90%; margin-left: 1em; margin-right: 1em; ">');r.push("Select history: ");r.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');r.push(" <% _.each(histories, function(history) { %>");r.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');r.push(" <% }); %>");r.push("</select>");r.push("</span>");return r.join("")},templateBulkImportInModal:function(){var r=[];r.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');r.push("Select history: ");r.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');r.push(" <% _.each(histories, function(history) { %>");r.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');r.push(" <% }); %>");r.push("</select>");r.push("</span>");return r.join("")},size_to_string:function(r){var s="";if(r>=100000000000){r=r/100000000000;s="TB"}else{if(r>=100000000){r=r/100000000;s="GB"}else{if(r>=100000){r=r/100000;s="MB"}else{if(r>=100){r=r/100;s="KB"}else{r=r*10;s="b"}}}}return(Math.round(r)/10)+s},events:{"click #select-all-checkboxes":"selectAll","click .folder_row":"selectClickedRow","click #toolbtn_bulk_import":"modalBulkImport","click #toolbtn_dl":"bulkDownload","click .library-dataset":"showDatasetDetails","click #toolbtn_create_folder":"createFolderFromModal","click .btn_open_folder":"navigateToFolder"},render:function(r){$("#center").css("overflow","auto");view=this;var t=this;var s=new e({id:r.id});s.url=s.attributes.urlRoot+r.id+"/contents";s.fetch({success:function(u){for(var w=0;w<s.attributes.folder.models.length;w++){var v=s.attributes.folder.models[w];if(v.get("type")==="file"){v.set("readable_size",t.size_to_string(v.get("file_size")))}}var y=s.full_path;var z;if(y.length===1){z=0}else{z=y[y.length-2][0]}var x=_.template(t.templateFolder(),{path:s.full_path,items:s.attributes.folder.models,id:r.id,upper_folder_id:z});t.$el.html(x)}})},navigateToFolder:function(s){var r=$(s.target).attr("data-id");if(typeof r==="undefined"){return false}else{if(r==="0"){library_router.navigate("#",{trigger:true,replace:true})}else{library_router.navigate("folders/"+r,{trigger:true,replace:true})}}},showDatasetDetails:function(u){u.preventDefault();var v=$(u.target).parent().parent().attr("id");var t=new i();var s=new p();t.id=v;var r=this;t.fetch({success:function(w){s.fetch({success:function(x){r.renderModalAfterFetch(w,x)}})}})},renderModalAfterFetch:function(w,t){var u=this.size_to_string(w.get("file_size"));var v=_.template(this.templateDatasetModal(),{item:w,size:u});var s=this;this.modal=new k.GalaxyModal({destructible:true,title:"Dataset Details",body:v,buttons:{Import:function(){s.importCurrentIntoHistory()},Download:function(){s.downloadCurrent()},Close:function(){s.modal.hideOrDestroy()}}});$(".peek").html(w.get("peek"));var r=_.template(this.templateHistorySelectInModal(),{histories:t.models});$(this.modal.elMain).find(".buttons").prepend(r);if(s.lastSelectedHistory.length>0){$(this.modal.elMain).find("#dataset_import_single").val(s.lastSelectedHistory)}this.modal.bindEvents();this.modal.show()},downloadCurrent:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var r=[];r.push($("#id_row").attr("data-id"));var s="/api/libraries/datasets/download/uncompressed";var t={ldda_ids:r};folderContentView.processDownload(s,t);this.modal.enableButton("Import");this.modal.enableButton("Download")},importCurrentIntoHistory:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var t=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();this.lastSelectedHistory=t;var r=$("#id_row").attr("data-id");var u=new b();var s=this;u.url=u.urlRoot+t+"/contents";u.save({content:r,source:"library"},{success:function(){n.success("Dataset imported");s.modal.enableButton("Import");s.modal.enableButton("Download")},error:function(){n.error("An error occured! Dataset not imported. Please try again.");s.modal.enableButton("Import");s.modal.enableButton("Download")}})},selectAll:function(s){var r=s.target.checked;that=this;$(":checkbox").each(function(){this.checked=r;$row=$(this.parentElement.parentElement);(r)?that.makeDarkRow($row):that.makeWhiteRow($row)});this.checkTools()},selectClickedRow:function(s){var u="";var r;var t;if(s.target.localName==="input"){u=s.target;r=$(s.target.parentElement.parentElement);t="input"}else{if(s.target.localName==="td"){u=$("#"+s.target.parentElement.id).find(":checkbox")[0];r=$(s.target.parentElement);t="td"}}if(u===""){s.stopPropagation();return}if(u===undefined){s.stopPropagation();return}if(u.checked){if(t==="td"){u.checked="";this.makeWhiteRow(r)}else{if(t==="input"){this.makeDarkRow(r)}}}else{if(t==="td"){u.checked="selected";this.makeDarkRow(r)}else{if(t==="input"){this.makeWhiteRow(r)}}}this.checkTools()},makeDarkRow:function(r){r.removeClass("light");r.find("a").removeClass("light");r.addClass("dark");r.find("a").addClass("dark")},makeWhiteRow:function(r){r.removeClass("dark");r.find("a").removeClass("dark");r.addClass("light");r.find("a").addClass("light")},checkTools:function(){var r=$("#folder_table").find(":checked");if(r.length>0){$("#toolbtn_bulk_import").show();$("#toolbtn_dl").show()}else{$("#toolbtn_bulk_import").hide();$("#toolbtn_dl").hide()}},modalBulkImport:function(){var s=this;var r=new p();r.fetch({success:function(t){var u=_.template(s.templateBulkImportInModal(),{histories:t.models});s.modal=new k.GalaxyModal({destructible:true,title:"Import into History",body:u,buttons:{Import:function(){s.importAllIntoHistory()},Close:function(){s.modal.hideOrDestroy()}}});s.modal.bindEvents();s.modal.show()}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var t=$("select[name=dataset_import_bulk] option:selected").val();var x=$("select[name=dataset_import_bulk] option:selected").text();var z=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){z.push(this.parentElement.parentElement.id)}});var y=_.template(this.templateProgressBar(),{history_name:x});$(this.modal.elMain).find(".modal-body").html(y);var u=100/z.length;this.initProgress(u);var r=[];for(var s=z.length-1;s>=0;s--){library_dataset_id=z[s];var v=new b();var w=this;v.url=v.urlRoot+t+"/contents";v.content=library_dataset_id;v.source="library";r.push(v)}this.chainCall(r)},chainCall:function(s){var r=this;var t=s.pop();if(typeof t==="undefined"){n.success("All datasets imported");this.modal.hideOrDestroy();return}var u=$.when(t.save({content:t.content,source:t.source})).done(function(v){r.updateProgress();responses.push(v);r.chainCall(s)})},initProgress:function(r){this.progress=0;this.progressStep=r},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},templateProgressBar:function(){var r=[];r.push('<div class="import_text">');r.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");r.push("</div>");r.push('<div class="progress">');r.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');r.push(' <span class="completion_span">0% Complete</span>');r.push(" </div>");r.push("</div>");r.push("");return r.join("")},download:function(r,v){var t=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){t.push(this.parentElement.parentElement.id)}});var s="/api/libraries/datasets/download/"+v;var u={ldda_ids:t};this.processDownload(s,u,"get")},processDownload:function(s,t,u){if(s&&t){t=typeof t=="string"?t:$.param(t);var r="";$.each(t.split("&"),function(){var v=this.split("=");r+='<input type="hidden" name="'+v[0]+'" value="'+v[1]+'" />'});$('<form action="'+s+'" method="'+(u||"post")+'">'+r+"</form>").appendTo("body").submit().remove();n.info("Your download will begin soon")}},createFolderFromModal:function(){event.preventDefault();event.stopPropagation();var r=this;this.modal=new k.GalaxyModal({destructible:true,title:"Create New Folder",body:this.template_new_folder(),buttons:{Create:function(){r.create_new_folder_event()},Close:function(){r.modal.hideOrDestroy();r.modal=null}}});this.modal.bindEvents();this.modal.show()},create_new_folder_event:function(){var r=this.serialize_new_folder();if(this.validate_new_folder(r)){var t=new c();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];t.url=t.urlRoot+"/"+current_folder_id;var s=this;t.save(r,{success:function(u){s.modal.hideOrDestroy();n.success("Folder created");s.render({id:current_folder_id})},error:function(){n.error("An error occured :(")}})}else{n.error("Folder's name is missing")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(r){return r.name!==""},template_new_folder:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return tmpl_array.join("")}});var a=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"show_library_modal"},initialize:function(){},template_library_list:function(){tmpl_array=[];tmpl_array.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; overflow: auto !important; ">');tmpl_array.push("");tmpl_array.push('<h3>New Data Libraries. This is work in progress. Report problems & ideas to <a href="mailto:marten@bx.psu.edu?Subject=DataLibraries_Feedback" target="_blank">Marten</a>.</h3>');tmpl_array.push('<a href="" id="create_new_library_btn" class="btn btn-primary file ">New Library</a>');tmpl_array.push('<table class="table table-condensed">');tmpl_array.push(" <thead>");tmpl_array.push(' <th class="button_heading"></th>');tmpl_array.push(" <th>name</th>");tmpl_array.push(" <th>description</th>");tmpl_array.push(" <th>synopsis</th> ");tmpl_array.push(" <th>model type</th> ");tmpl_array.push(" </thead>");tmpl_array.push(" <tbody>");tmpl_array.push(" <% _.each(libraries, function(library) { %>");tmpl_array.push(" <tr>");tmpl_array.push(' <td><button title="Open this library" type="button" data-id="<%- library.get("root_folder_id") %>" class="btn_open_folder btn btn-default btn-xs">');tmpl_array.push(' <span class="fa fa-folder-open"></span> browse</td>');tmpl_array.push(' <td><%- library.get("name") %></td>');tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("model_class")) %></td>');tmpl_array.push(" </tr>");tmpl_array.push(" <% }); %>");tmpl_array.push(" </tbody>");tmpl_array.push("</table>");tmpl_array.push("</div>");return tmpl_array.join("")},render:function(){$("#center").css("overflow","auto");var r=this;libraries=new o();libraries.fetch({success:function(s){var t=_.template(r.template_library_list(),{libraries:s.models});r.$el.html(t)},error:function(t,s){if(s.statusCode().status===403){n.error("Please log in first. Redirecting to login page in 3s.");setTimeout(r.redirectToLogin,3000)}else{n.error("An error occured. Please try again.")}}})},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},modal:null,show_library_modal:function(s){s.preventDefault();s.stopPropagation();var r=this;this.modal=new k.GalaxyModal({destructible:true,title:"Create New Library",body:this.template_new_library(),buttons:{Create:function(){r.create_new_library_event()},Close:function(){r.modal.hideOrDestroy()}}});this.modal.bindEvents();this.modal.show()},create_new_library_event:function(){var t=this.serialize_new_library();if(this.validate_new_library(t)){var s=new f();var r=this;s.save(t,{success:function(u){r.modal.hideOrDestroy();r.clear_library_modal();r.render();n.success("Library created")},error:function(){n.error("An error occured :(")}})}else{n.error("Library's name is missing")}return false},clear_library_modal:function(){$("input[name='Name']").val("");$("input[name='Description']").val("");$("input[name='Synopsis']").val("")},serialize_new_library:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},validate_new_library:function(r){return r.name!==""},template_new_library:function(){tmpl_array=[];tmpl_array.push('<div id="new_library_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push('<input type="text" name="Synopsis" value="" placeholder="Synopsis">');tmpl_array.push("</form>");tmpl_array.push("</div>");return tmpl_array.join("")}});var g=Backbone.View.extend({folderContentView:null,galaxyLibraryview:null,initialize:function(){folderContentView=new m();galaxyLibraryview=new a();library_router=new q();library_router.on("route:libraries",function(){galaxyLibraryview.render()});library_router.on("route:folder_content",function(r){folderContentView.render({id:r})});library_router.on("route:download",function(r,s){if($("#center").find(":checked").length===0){library_router.navigate("folders/"+r,{trigger:true,replace:true})}else{folderContentView.download(r,s);library_router.navigate("folders/"+r,{trigger:false,replace:true})}});Backbone.history.start();return this}});return{GalaxyApp:g}}); \ No newline at end of file +var view=null;var library_router=null;var responses=[];define(["galaxy.modal","galaxy.masthead","utils/galaxy.utils","libs/toastr"],function(k,l,h,n){var f=Backbone.Model.extend({urlRoot:"/api/libraries"});var c=Backbone.Model.extend({urlRoot:"/api/folders"});var o=Backbone.Collection.extend({url:"/api/libraries",model:f});var i=Backbone.Model.extend({urlRoot:"/api/libraries/datasets"});var d=Backbone.Collection.extend({model:i});var e=Backbone.Model.extend({defaults:{folder:new d(),full_path:"unknown",urlRoot:"/api/folders/",id:"unknown"},parse:function(r){this.full_path=r[0].full_path;this.get("folder").reset(r[1].folder_contents);return r}});var b=Backbone.Model.extend({urlRoot:"/api/histories/"});var j=Backbone.Model.extend({url:"/api/histories/"});var p=Backbone.Collection.extend({url:"/api/histories",model:j});var q=Backbone.Router.extend({routes:{"":"libraries","folders/:id":"folder_content","folders/:folder_id/download/:format":"download"}});var m=Backbone.View.extend({el:"#center",progress:0,progressStep:1,lastSelectedHistory:"",modal:null,folders:null,initialize:function(){this.folders=[];this.queue=jQuery.Deferred();this.queue.resolve()},templateFolder:function(){var r=[];r.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; ">');r.push('<h3>New Data Libraries. This is work in progress. Report problems & ideas to <a href="mailto:marten@bx.psu.edu?Subject=DataLibraries_Feedback" target="_blank">Marten</a>.</h3>');r.push('<div id="library_folder_toolbar" >');r.push(' <button title="Create New Folder" id="toolbtn_create_folder" class="btn btn-primary" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder-close"></span> folder</button>');r.push(' <button id="toolbtn_bulk_import" class="btn btn-primary" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-external-link"></span> to history</button>');r.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display: none; ">');r.push(' <button id="drop_toggle" type="button" class="btn btn-primary dropdown-toggle" data-toggle="dropdown">');r.push(' <span class="fa fa-download"></span> download <span class="caret"></span>');r.push(" </button>");r.push(' <ul class="dropdown-menu" role="menu">');r.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');r.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');r.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');r.push(" </ul>");r.push(" </div>");r.push("</div>");r.push('<div class="library_breadcrumb">');r.push('<a title="Return to the list of libraries" href="#">Libraries</a><b>|</b> ');r.push("<% _.each(path, function(path_item) { %>");r.push("<% if (path_item[0] != id) { %>");r.push('<a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a><b>|</b> ');r.push("<% } else { %>");r.push('<span title="You are in this folder"><%- path_item[1] %></span>');r.push("<% } %>");r.push("<% }); %>");r.push("</div>");r.push('<table id="folder_table" class="table table-condensed">');r.push(" <thead>");r.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');r.push(' <th class="button_heading">view</th>');r.push(" <th>name</th>");r.push(" <th>data type</th>");r.push(" <th>size</th>");r.push(" <th>date (UTC)</th>");r.push(" </thead>");r.push(" <tbody>");r.push(" <td></td>");r.push(' <td><button title="Go to parent folder" type="button" data-id="<%- upper_folder_id %>" class="btn_open_folder btn btn-default btn-xs">');r.push(' <span class="fa fa-arrow-up"></span> .. go up</td>');r.push(" <td></td>");r.push(" <td></td>");r.push(" <td></td>");r.push(" <td></td>");r.push(" </tr>");r.push(" <% _.each(items, function(content_item) { %>");r.push(' <tr class="folder_row light" id="<%- content_item.id %>">');r.push(' <% if (content_item.get("type") === "folder") { %>');r.push(" <td></td>");r.push(' <td><button title="Open this folder" type="button" data-id="<%- content_item.id %>" class="btn_open_folder btn btn-default btn-xs">');r.push(' <span class="fa fa-folder-open"></span> browse</td>');r.push(' <td><%- content_item.get("name") %>');r.push(' <% if (content_item.get("item_count") === 0) { %>');r.push(' <span class="muted">(empty folder)</span>');r.push(" <% } %>");r.push(" </td>");r.push(" <td>folder</td>");r.push(' <td><%= _.escape(content_item.get("item_count")) %> item(s)</td>');r.push(" <% } else { %>");r.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');r.push(" <td>");r.push(' <button title="See details of this dataset" type="button" class="library-dataset btn btn-default btn-xs">');r.push(' <span class="fa fa-eye"></span> details');r.push(" </button>");r.push(" </td>");r.push(' <td><%- content_item.get("name") %></td>');r.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');r.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>');r.push(" <% } %> ");r.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>');r.push(" </tr>");r.push(" <% }); %>");r.push(" ");r.push(" </tbody>");r.push("</table>");r.push("</div>");return r.join("")},templateDatasetModal:function(){var r=[];r.push('<div id="dataset_info_modal">');r.push(' <table class="table table-striped table-condensed">');r.push(" <tr>");r.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');r.push(' <td><%= _.escape(item.get("name")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Data type</th>');r.push(' <td><%= _.escape(item.get("data_type")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Genome build</th>');r.push(' <td><%= _.escape(item.get("genome_build")) %></td>');r.push(" </tr>");r.push(' <th scope="row">Size</th>');r.push(" <td><%= _.escape(size) %></td>");r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Date uploaded (UTC)</th>');r.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Uploaded by</th>');r.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');r.push(" </tr>");r.push(' <tr scope="row">');r.push(' <th scope="row">Data Lines</th>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');r.push(" </tr>");r.push(' <th scope="row">Comment Lines</th>');r.push(' <% if (item.get("metadata_comment_lines") === "") { %>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');r.push(" <% } else { %>");r.push(' <td scope="row">unknown</td>');r.push(" <% } %>");r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Number of Columns</th>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Column Types</th>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Miscellaneous information</th>');r.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');r.push(" </tr>");r.push(" </table>");r.push(' <pre class="peek">');r.push(" </pre>");r.push("</div>");return r.join("")},templateHistorySelectInModal:function(){var r=[];r.push('<span id="history_modal_combo" style="width:90%; margin-left: 1em; margin-right: 1em; ">');r.push("Select history: ");r.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');r.push(" <% _.each(histories, function(history) { %>");r.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');r.push(" <% }); %>");r.push("</select>");r.push("</span>");return r.join("")},templateBulkImportInModal:function(){var r=[];r.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');r.push("Select history: ");r.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');r.push(" <% _.each(histories, function(history) { %>");r.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');r.push(" <% }); %>");r.push("</select>");r.push("</span>");return r.join("")},templateProgressBar:function(){var r=[];r.push('<div class="import_text">');r.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");r.push("</div>");r.push('<div class="progress">');r.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');r.push(' <span class="completion_span">0% Complete</span>');r.push(" </div>");r.push("</div>");r.push("");return r.join("")},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return tmpl_array.join("")},events:{"click #select-all-checkboxes":"selectAll","click .folder_row":"selectClickedRow","click #toolbtn_bulk_import":"modalBulkImport","click #toolbtn_dl":"bulkDownload","click .library-dataset":"showDatasetDetails","click #toolbtn_create_folder":"createFolderFromModal","click .btn_open_folder":"navigateToFolder"},render:function(r){$("#center").css("overflow","auto");view=this;var t=this;var s=new e({id:r.id});s.url=s.attributes.urlRoot+r.id+"/contents";s.fetch({success:function(u){for(var w=0;w<s.attributes.folder.models.length;w++){var v=s.attributes.folder.models[w];if(v.get("type")==="file"){v.set("readable_size",t.size_to_string(v.get("file_size")))}}var y=s.full_path;var z;if(y.length===1){z=0}else{z=y[y.length-2][0]}var x=_.template(t.templateFolder(),{path:s.full_path,items:s.attributes.folder.models,id:r.id,upper_folder_id:z});t.$el.html(x)},error:function(){n.error("An error occured :(")}})},size_to_string:function(r){var s="";if(r>=100000000000){r=r/100000000000;s="TB"}else{if(r>=100000000){r=r/100000000;s="GB"}else{if(r>=100000){r=r/100000;s="MB"}else{if(r>=100){r=r/100;s="KB"}else{r=r*10;s="b"}}}}return(Math.round(r)/10)+s},navigateToFolder:function(s){var r=$(s.target).attr("data-id");if(typeof r==="undefined"){return false}else{if(r==="0"){library_router.navigate("#",{trigger:true,replace:true})}else{library_router.navigate("folders/"+r,{trigger:true,replace:true})}}},showDatasetDetails:function(u){u.preventDefault();var v=$(u.target).parent().parent().attr("id");var t=new i();var s=new p();t.id=v;var r=this;t.fetch({success:function(w){s.fetch({success:function(x){r.renderModalAfterFetch(w,x)},error:function(){n.error("An error occured during fetching histories:(");r.renderModalAfterFetch(w)}})},error:function(){n.error("An error occured during loading dataset details :(")}})},renderModalAfterFetch:function(w,t){var u=this.size_to_string(w.get("file_size"));var v=_.template(this.templateDatasetModal(),{item:w,size:u});var s=this;this.modal=new k.GalaxyModal({destructible:true,title:"Dataset Details",body:v,buttons:{Import:function(){s.importCurrentIntoHistory()},Download:function(){s.downloadCurrent()},Close:function(){s.modal.hideOrDestroy()}}});$(".peek").html(w.get("peek"));if(typeof history.models!==undefined){var r=_.template(this.templateHistorySelectInModal(),{histories:t.models});$(this.modal.elMain).find(".buttons").prepend(r);if(s.lastSelectedHistory.length>0){$(this.modal.elMain).find("#dataset_import_single").val(s.lastSelectedHistory)}}this.modal.bindEvents();this.modal.show()},downloadCurrent:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var r=[];r.push($("#id_row").attr("data-id"));var s="/api/libraries/datasets/download/uncompressed";var t={ldda_ids:r};folderContentView.processDownload(s,t);this.modal.enableButton("Import");this.modal.enableButton("Download")},importCurrentIntoHistory:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var t=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();this.lastSelectedHistory=t;var r=$("#id_row").attr("data-id");var u=new b();var s=this;u.url=u.urlRoot+t+"/contents";u.save({content:r,source:"library"},{success:function(){n.success("Dataset imported");s.modal.enableButton("Import");s.modal.enableButton("Download")},error:function(){n.error("An error occured! Dataset not imported. Please try again.");s.modal.enableButton("Import");s.modal.enableButton("Download")}})},selectAll:function(s){var r=s.target.checked;that=this;$(":checkbox").each(function(){this.checked=r;$row=$(this.parentElement.parentElement);(r)?that.makeDarkRow($row):that.makeWhiteRow($row)});this.checkTools()},selectClickedRow:function(s){var u="";var r;var t;if(s.target.localName==="input"){u=s.target;r=$(s.target.parentElement.parentElement);t="input"}else{if(s.target.localName==="td"){u=$("#"+s.target.parentElement.id).find(":checkbox")[0];r=$(s.target.parentElement);t="td"}}if(u===""){s.stopPropagation();return}if(u===undefined){s.stopPropagation();return}if(u.checked){if(t==="td"){u.checked="";this.makeWhiteRow(r)}else{if(t==="input"){this.makeDarkRow(r)}}}else{if(t==="td"){u.checked="selected";this.makeDarkRow(r)}else{if(t==="input"){this.makeWhiteRow(r)}}}this.checkTools()},makeDarkRow:function(r){r.removeClass("light");r.find("a").removeClass("light");r.addClass("dark");r.find("a").addClass("dark")},makeWhiteRow:function(r){r.removeClass("dark");r.find("a").removeClass("dark");r.addClass("light");r.find("a").addClass("light")},checkTools:function(){var r=$("#folder_table").find(":checked");if(r.length>0){$("#toolbtn_bulk_import").show();$("#toolbtn_dl").show()}else{$("#toolbtn_bulk_import").hide();$("#toolbtn_dl").hide()}},modalBulkImport:function(){var s=this;var r=new p();r.fetch({success:function(t){var u=_.template(s.templateBulkImportInModal(),{histories:t.models});s.modal=new k.GalaxyModal({destructible:true,title:"Import into History",body:u,buttons:{Import:function(){s.importAllIntoHistory()},Close:function(){s.modal.hideOrDestroy()}}});s.modal.bindEvents();s.modal.show()},error:function(){n.error("An error occured :(")}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var t=$("select[name=dataset_import_bulk] option:selected").val();var x=$("select[name=dataset_import_bulk] option:selected").text();var z=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){z.push(this.parentElement.parentElement.id)}});var y=_.template(this.templateProgressBar(),{history_name:x});$(this.modal.elMain).find(".modal-body").html(y);var u=100/z.length;this.initProgress(u);var r=[];for(var s=z.length-1;s>=0;s--){library_dataset_id=z[s];var v=new b();var w=this;v.url=v.urlRoot+t+"/contents";v.content=library_dataset_id;v.source="library";r.push(v)}this.chainCall(r)},chainCall:function(s){var r=this;var t=s.pop();if(typeof t==="undefined"){n.success("All datasets imported");this.modal.hideOrDestroy();return}var u=$.when(t.save({content:t.content,source:t.source})).done(function(v){r.updateProgress();responses.push(v);r.chainCall(s)})},initProgress:function(r){this.progress=0;this.progressStep=r},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(r,v){var t=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){t.push(this.parentElement.parentElement.id)}});var s="/api/libraries/datasets/download/"+v;var u={ldda_ids:t};this.processDownload(s,u,"get")},processDownload:function(s,t,u){if(s&&t){t=typeof t=="string"?t:$.param(t);var r="";$.each(t.split("&"),function(){var v=this.split("=");r+='<input type="hidden" name="'+v[0]+'" value="'+v[1]+'" />'});$('<form action="'+s+'" method="'+(u||"post")+'">'+r+"</form>").appendTo("body").submit().remove();n.info("Your download will begin soon")}},createFolderFromModal:function(){event.preventDefault();event.stopPropagation();var r=this;this.modal=new k.GalaxyModal({destructible:true,title:"Create New Folder",body:this.templateNewFolderInModal(),buttons:{Create:function(){r.create_new_folder_event()},Close:function(){r.modal.hideOrDestroy();r.modal=null}}});this.modal.bindEvents();this.modal.show()},create_new_folder_event:function(){var r=this.serialize_new_folder();if(this.validate_new_folder(r)){var t=new c();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];t.url=t.urlRoot+"/"+current_folder_id;var s=this;t.save(r,{success:function(u){s.modal.hideOrDestroy();n.success("Folder created");s.render({id:current_folder_id})},error:function(){n.error("An error occured :(")}})}else{n.error("Folder's name is missing")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(r){return r.name!==""}});var a=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"show_library_modal"},initialize:function(){},templateLibraryList:function(){tmpl_array=[];tmpl_array.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; overflow: auto !important; ">');tmpl_array.push("");tmpl_array.push('<h3>New Data Libraries. This is work in progress. Report problems & ideas to <a href="mailto:marten@bx.psu.edu?Subject=DataLibraries_Feedback" target="_blank">Marten</a>.</h3>');tmpl_array.push('<a href="" id="create_new_library_btn" class="btn btn-primary file ">New Library</a>');tmpl_array.push('<table class="table table-condensed">');tmpl_array.push(" <thead>");tmpl_array.push(' <th class="button_heading"></th>');tmpl_array.push(" <th>name</th>");tmpl_array.push(" <th>description</th>");tmpl_array.push(" <th>synopsis</th> ");tmpl_array.push(" <th>model type</th> ");tmpl_array.push(" </thead>");tmpl_array.push(" <tbody>");tmpl_array.push(" <% _.each(libraries, function(library) { %>");tmpl_array.push(" <tr>");tmpl_array.push(' <td><button title="Open this library" type="button" data-id="<%- library.get("root_folder_id") %>" class="btn_open_folder btn btn-default btn-xs">');tmpl_array.push(' <span class="fa fa-folder-open"></span> browse</td>');tmpl_array.push(' <td><%- library.get("name") %></td>');tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("model_class")) %></td>');tmpl_array.push(" </tr>");tmpl_array.push(" <% }); %>");tmpl_array.push(" </tbody>");tmpl_array.push("</table>");tmpl_array.push("</div>");return tmpl_array.join("")},templateNewLibraryInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_library_modal">');tmpl_array.push(" <form>");tmpl_array.push(' <input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push(' <input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push(' <input type="text" name="Synopsis" value="" placeholder="Synopsis">');tmpl_array.push(" </form>");tmpl_array.push("</div>");return tmpl_array.join("")},render:function(){$("#center").css("overflow","auto");var r=this;libraries=new o();libraries.fetch({success:function(s){var t=_.template(r.templateLibraryList(),{libraries:s.models});r.$el.html(t)},error:function(t,s){if(s.statusCode().status===403){n.error("Please log in first. Redirecting to login page in 3s.");setTimeout(r.redirectToLogin,3000)}else{n.error("An error occured. Please try again.")}}})},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},modal:null,show_library_modal:function(s){s.preventDefault();s.stopPropagation();var r=this;this.modal=new k.GalaxyModal({destructible:true,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){r.create_new_library_event()},Close:function(){r.modal.hideOrDestroy()}}});this.modal.bindEvents();this.modal.show()},create_new_library_event:function(){var t=this.serialize_new_library();if(this.validate_new_library(t)){var s=new f();var r=this;s.save(t,{success:function(u){r.modal.hideOrDestroy();r.clear_library_modal();r.render();n.success("Library created")},error:function(){n.error("An error occured :(")}})}else{n.error("Library's name is missing")}return false},clear_library_modal:function(){$("input[name='Name']").val("");$("input[name='Description']").val("");$("input[name='Synopsis']").val("")},serialize_new_library:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},validate_new_library:function(r){return r.name!==""}});var g=Backbone.View.extend({folderContentView:null,galaxyLibraryview:null,initialize:function(){folderContentView=new m();galaxyLibraryview=new a();library_router=new q();library_router.on("route:libraries",function(){galaxyLibraryview.render()});library_router.on("route:folder_content",function(r){folderContentView.render({id:r})});library_router.on("route:download",function(r,s){if($("#center").find(":checked").length===0){library_router.navigate("folders/"+r,{trigger:true,replace:true})}else{folderContentView.download(r,s);library_router.navigate("folders/"+r,{trigger:false,replace:true})}});Backbone.history.start();return this}});return{GalaxyApp:g}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Functional browser tests: update/fix login tests
by commits-noreply＠bitbucket.org 08 Jan '14

08 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3cdd4aae8403/ Changeset: 3cdd4aae8403 User: carlfeberhard Date: 2014-01-08 19:34:43 Summary: Functional browser tests: update/fix login tests Affected #: 2 files diff -r 725010d022f3dae2400fab9d009b3d65af70f440 -r 3cdd4aae8403e76df8e0ac1efa621ad9b8889039 test/casperjs/login-tests.js --- a/test/casperjs/login-tests.js +++ b/test/casperjs/login-tests.js @@ -39,7 +39,7 @@ password = spaceghost.fixtureData.testUser.password; } -var userEmailSelector = '//a[contains(text(),"Logged in as")]/span["id=#user-email"]'; +var userEmailSelector = '//a[contains(text(),"Logged in as")]'; // =================================================================== TESTS // register a user (again...) @@ -53,9 +53,11 @@ this.test.comment( 'logging out: ' + email ); spaceghost.user.logout(); }); -spaceghost.then( function(){ - this.test.assertSelectorDoesntHaveText( xpath( userEmailSelector ), /\w/ ); - this.test.assert( spaceghost.user.loggedInAs() === '', 'loggedInAs() is empty string' ); +spaceghost.thenOpen( spaceghost.baseUrl, function(){ + spaceghost.waitForMasthead( function() { + this.test.assertDoesntExist( xpath( userEmailSelector ) ); + this.test.assert( spaceghost.user.loggedInAs() === '', 'loggedInAs() is empty string' ); + }); }); // log them back in - check for email in logged in text diff -r 725010d022f3dae2400fab9d009b3d65af70f440 -r 3cdd4aae8403e76df8e0ac1efa621ad9b8889039 test/casperjs/modules/user.js --- a/test/casperjs/modules/user.js +++ b/test/casperjs/modules/user.js @@ -81,7 +81,6 @@ spaceghost.thenOpen( spaceghost.baseUrl, function(){ spaceghost.waitForMasthead( function() { - spaceghost.clickLabel( spaceghost.data.labels.masthead.menus.user ); spaceghost.clickLabel( spaceghost.data.labels.masthead.userMenu.login ); spaceghost.withMainPanel( function mainBeforeLogin(){ @@ -162,7 +161,7 @@ try { var emailSelector = xpath( spaceghost.data.selectors.masthead.userMenu.userEmail_xpath ), loggedInInfo = spaceghost.elementInfoOrNull( emailSelector ); - if( loggedInInfo ){ + if( loggedInInfo !== null ){ userEmail = loggedInInfo.text.replace( 'Logged in as ', '' ); } } catch( err ){ @@ -177,13 +176,13 @@ */ User.prototype.logout = function logout(){ var spaceghost = this.spaceghost; - if( !this.loggedInAs() ){ return spaceghost; } spaceghost.thenOpen( spaceghost.baseUrl, function(){ this.info( 'user logging out' ); - //TODO: handle already logged out spaceghost.waitForMasthead( function _logout() { - spaceghost.clickLabel( spaceghost.data.labels.masthead.menus.user ); - spaceghost.clickLabel( spaceghost.data.labels.masthead.userMenu.logout ); + if( spaceghost.user.loggedInAs() ){ + spaceghost.clickLabel( spaceghost.data.labels.masthead.menus.user ); + spaceghost.clickLabel( spaceghost.data.labels.masthead.userMenu.logout ); + } }); }); return spaceghost; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 08 Jan '14

08 Jan '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/613f3d93261b/ Changeset: 613f3d93261b User: inithello Date: 2014-01-08 18:20:41 Summary: Fix error when time_last_tested has a None value. Affected #: 1 file diff -r 709c4b85bc411e5424c9536435d76fa4ee62781e -r 613f3d93261b282d6260b09100ffd5d3be3ff7dc lib/galaxy/webapps/tool_shed/model/__init__.py --- a/lib/galaxy/webapps/tool_shed/model/__init__.py +++ b/lib/galaxy/webapps/tool_shed/model/__init__.py @@ -275,7 +275,8 @@ rval = super( RepositoryMetadata, self ).to_dict( view=view, value_mapper=value_mapper ) if 'time_last_tested' in rval: time_last_tested = rval[ 'time_last_tested' ] - rval[ 'time_last_tested' ] = time_last_tested.isoformat() + if time_last_tested is not None: + rval[ 'time_last_tested' ] = time_last_tested.isoformat() return rval https://bitbucket.org/galaxy/galaxy-central/commits/725010d022f3/ Changeset: 725010d022f3 User: inithello Date: 2014-01-08 18:27:14 Summary: When a push is received in the hg controller, update the repository on disk after the push is complete. Affected #: 1 file diff -r 613f3d93261b282d6260b09100ffd5d3be3ff7dc -r 725010d022f3dae2400fab9d009b3d65af70f440 lib/galaxy/webapps/tool_shed/controllers/hg.py --- a/lib/galaxy/webapps/tool_shed/controllers/hg.py +++ b/lib/galaxy/webapps/tool_shed/controllers/hg.py @@ -2,6 +2,7 @@ from galaxy import web from galaxy.web.base.controller import BaseUIController from tool_shed.util.shed_util_common import get_repository_by_name_and_owner +from tool_shed.util.shed_util_common import update_repository from tool_shed.util.metadata_util import set_repository_metadata from galaxy import eggs @@ -9,6 +10,8 @@ import mercurial.__version__ from mercurial.hgweb.hgwebdir_mod import hgwebdir from mercurial.hgweb.request import wsgiapplication +from mercurial import hg +from mercurial import ui log = logging.getLogger(__name__) @@ -36,6 +39,11 @@ repository = get_repository_by_name_and_owner( trans.app, name, owner ) if repository: if hg_version >= '2.2.3': + # Update the repository on disk to the tip revision, because the web upload form uses the on-disk working + # directory. If the repository is not updated on disk, pushing from the command line and then uploading + # via the web interface will result in a new head being created. + repo = hg.repository( ui.ui(), repository.repo_path( trans.app ) ) + update_repository( repo, ctx_rev=None ) # Set metadata using the repository files on disk. error_message, status = set_repository_metadata( trans, repository ) if status == 'ok' and error_message: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Retain and display more errors if they occurred during repository creation and population when importing a repository capsule into a tool shed.
by commits-noreply＠bitbucket.org 08 Jan '14

08 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/709c4b85bc41/ Changeset: 709c4b85bc41 User: greg Date: 2014-01-08 16:10:05 Summary: Retain and display more errors if they occurred during repository creation and population when importing a repository capsule into a tool shed. Affected #: 1 file diff -r 796cf860956c4f61b873335e502a8db4a0d7e951 -r 709c4b85bc411e5424c9536435d76fa4ee62781e lib/tool_shed/util/repository_maintenance_util.py --- a/lib/tool_shed/util/repository_maintenance_util.py +++ b/lib/tool_shed/util/repository_maintenance_util.py @@ -154,6 +154,9 @@ # Populate the new repository with the contents of exported repository archive. results_dict = import_util.import_repository_archive( trans, repository, repository_archive_dict ) ok = results_dict.get( 'ok', False ) + error_message = results_dict.get( 'error_message', '' ) + if error_message: + results_message += error_message import_results_tups.append( ( ok, ( str( name ), str( username ) ), results_message ) ) else: # The repository either already exists in this Tool Shed or the current user is not authorized to create it. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix for retrieving repository dependency information for a repository changeset revision via the Tool Shed's API.
by commits-noreply＠bitbucket.org 08 Jan '14

08 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/796cf860956c/ Changeset: 796cf860956c User: greg Date: 2014-01-08 15:46:33 Summary: Fix for retrieving repository dependency information for a repository changeset revision via the Tool Shed's API. Affected #: 1 file diff -r af196ff2cc63fcc59b07c1579891ffe7bed2013a -r 796cf860956c4f61b873335e502a8db4a0d7e951 lib/galaxy/webapps/tool_shed/api/repository_revisions.py --- a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py +++ b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py @@ -89,12 +89,16 @@ for rd_tup in rd_tups: tool_shed, name, owner, changeset_revision = rd_tup[ 0:4 ] repository_dependency = suc.get_repository_by_name_and_owner( trans.app, name, owner ) + repository_dependency_id = trans.security.encode_id( repository_dependency.id ) + repository_dependency_repository_metadata = \ + suc.get_repository_metadata_by_changeset_revision( trans, repository_dependency_id, changeset_revision ) + repository_dependency_repository_metadata_id = trans.security.encode_id( repository_dependency_repository_metadata.id ) repository_dependency_dict = repository_dependency.to_dict( view='element', value_mapper=value_mapper ) # We have to add the changeset_revision of of the repository dependency. repository_dependency_dict[ 'changeset_revision' ] = changeset_revision repository_dependency_dict[ 'url' ] = web.url_for( controller='repositories', action='show', - id=trans.security.encode_id( repository_dependency.id ) ) + id=repository_dependency_repository_metadata_id ) repository_dependencies_dicts.append( repository_dependency_dict ) return repository_dependencies_dicts except Exception, e: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fixes for comparing datetime values in the tool shed's install and test framework.
by commits-noreply＠bitbucket.org 08 Jan '14

08 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/af196ff2cc63/ Changeset: af196ff2cc63 User: greg Date: 2014-01-08 15:25:17 Summary: Fixes for comparing datetime values in the tool shed's install and test framework. Affected #: 2 files diff -r 6aeb657bc40ee0884f538308e1bfbec0b197c44b -r af196ff2cc63fcc59b07c1579891ffe7bed2013a lib/galaxy/webapps/tool_shed/model/__init__.py --- a/lib/galaxy/webapps/tool_shed/model/__init__.py +++ b/lib/galaxy/webapps/tool_shed/model/__init__.py @@ -271,6 +271,13 @@ return True return False + def to_dict( self, view='collection', value_mapper=None ): + rval = super( RepositoryMetadata, self ).to_dict( view=view, value_mapper=value_mapper ) + if 'time_last_tested' in rval: + time_last_tested = rval[ 'time_last_tested' ] + rval[ 'time_last_tested' ] = time_last_tested.isoformat() + return rval + class SkipToolTest( object, Dictifiable ): dict_collection_visible_keys = ( 'id', 'repository_metadata_id', 'initial_changeset_revision' ) diff -r 6aeb657bc40ee0884f538308e1bfbec0b197c44b -r af196ff2cc63fcc59b07c1579891ffe7bed2013a test/install_and_test_tool_shed_repositories/base/util.py --- a/test/install_and_test_tool_shed_repositories/base/util.py +++ b/test/install_and_test_tool_shed_repositories/base/util.py @@ -898,16 +898,16 @@ log.debug( 'due to the following error getting tool_test_results:\n%s' % str( error_message ) ) else: # Check the required repository's time_last_tested value to see if its tool_test_results column - # has been updated within the past 12 hours. - """ - twelve_hours_ago = datetime.utcnow() - timedelta( hours=12 ) + # has been updated within the past 12 hours. The RepositoryMetadata class's to_dict() method + # returns the value of time_last_tested in datetime.isoformat(). + twelve_hours_ago = ( datetime.utcnow() - timedelta( hours=12 ) ).isoformat() time_last_tested, error_message = get_time_last_tested( galaxy_tool_shed_url, repository_metadata_id ) if time_last_tested is not None and time_last_tested < twelve_hours_ago: log.debug( 'The install containers for version %s of repository dependency %s owned by %s have been ' % \ ( changeset_revision, name, owner ) ) log.debug( 'populated within the past 12 hours (likely in this test run), so skipping this check.' ) continue - if time_last_tested is None: + elif time_last_tested is None: log.debug( 'The time_last_tested column value is None for version %s of repository dependency %s owned by %s.' % \ ( changeset_revision, name, owner ) ) elif time_last_tested < twelve_hours_ago: @@ -916,7 +916,6 @@ else: log.debug( 'Version %s of repository dependency %s owned by %s was last tested more than 12 hours ago.' % \ ( changeset_revision, name, owner ) ) - """ # Inspect the tool_test_results_dict for the last test run to see if it has not yet been populated. if len( tool_test_results_dicts ) == 0: tool_test_results_dict = {} @@ -977,8 +976,8 @@ else: log.debug( 'Cannot retrieve revision %s of required repository %s owned by %s from the database ' % \ ( changeset_revision, name, owner ) ) - log.debug( 'so tool_test_results cannot be saved.' ) - log.debug( 'The attributes used to retrieve the record are:\n' ) + log.debug( 'so tool_test_results cannot be saved at this time.' ) + log.debug( 'The attributes used to retrieve the record are:' ) log.debug( 'tool_shed: %s name: %s owner: %s changeset_revision: %s' % \ ( cleaned_tool_shed_url, name, owner, changeset_revision ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Eliminate comparison of times tested in the tool shed's install and test framework.
by commits-noreply＠bitbucket.org 07 Jan '14

07 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6aeb657bc40e/ Changeset: 6aeb657bc40e User: greg Date: 2014-01-08 03:50:02 Summary: Eliminate comparison of times tested in the tool shed's install and test framework. Affected #: 1 file diff -r 478c60421dd9a71422d98ee2ada8043bf53ffeef -r 6aeb657bc40ee0884f538308e1bfbec0b197c44b test/install_and_test_tool_shed_repositories/base/util.py --- a/test/install_and_test_tool_shed_repositories/base/util.py +++ b/test/install_and_test_tool_shed_repositories/base/util.py @@ -899,6 +899,7 @@ else: # Check the required repository's time_last_tested value to see if its tool_test_results column # has been updated within the past 12 hours. + """ twelve_hours_ago = datetime.utcnow() - timedelta( hours=12 ) time_last_tested, error_message = get_time_last_tested( galaxy_tool_shed_url, repository_metadata_id ) if time_last_tested is not None and time_last_tested < twelve_hours_ago: @@ -915,6 +916,7 @@ else: log.debug( 'Version %s of repository dependency %s owned by %s was last tested more than 12 hours ago.' % \ ( changeset_revision, name, owner ) ) + """ # Inspect the tool_test_results_dict for the last test run to see if it has not yet been populated. if len( tool_test_results_dicts ) == 0: tool_test_results_dict = {} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Don't map the time_last_tested column in the tool shed API.
by commits-noreply＠bitbucket.org 07 Jan '14

07 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/478c60421dd9/ Changeset: 478c60421dd9 User: greg Date: 2014-01-08 03:37:17 Summary: Don't map the time_last_tested column in the tool shed API. Affected #: 1 file diff -r 2a23dec18caabf3e326447db7eabd0b2d963fef4 -r 478c60421dd9a71422d98ee2ada8043bf53ffeef lib/galaxy/webapps/tool_shed/api/repository_revisions.py --- a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py +++ b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py @@ -1,6 +1,5 @@ import datetime import logging -from galaxy.web.framework.helpers import time_ago from tool_shed.util import metadata_util from galaxy import web from galaxy import util @@ -234,8 +233,4 @@ def __get_value_mapper( self, trans, repository_metadata ): value_mapper = { 'id' : trans.security.encode_id, 'repository_id' : trans.security.encode_id } - if repository_metadata.time_last_tested is not None: - # For some reason the Dictifiable.to_dict() method in ~/galaxy/model/item_attrs.py requires - # a function rather than a mapped value, so just pass the time_ago function here. - value_mapper[ 'time_last_tested' ] = time_ago return value_mapper Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Functional browser tests: fix registration tests
by commits-noreply＠bitbucket.org 07 Jan '14

07 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2a23dec18caa/ Changeset: 2a23dec18caa User: carlfeberhard Date: 2014-01-07 23:09:21 Summary: Functional browser tests: fix registration tests Affected #: 3 files diff -r 64c6c98b9976c3dadb77426b6a6805922aa7810c -r 2a23dec18caabf3e326447db7eabd0b2d963fef4 test/casperjs/modules/user.js --- a/test/casperjs/modules/user.js +++ b/test/casperjs/modules/user.js @@ -160,11 +160,13 @@ var spaceghost = this.spaceghost, userEmail = ''; try { - var loggedInInfo = spaceghost.getElementInfo( - xpath( spaceghost.data.selectors.masthead.userMenu.userEmail_xpath ) ); - userEmail = loggedInInfo.text; + var emailSelector = xpath( spaceghost.data.selectors.masthead.userMenu.userEmail_xpath ), + loggedInInfo = spaceghost.elementInfoOrNull( emailSelector ); + if( loggedInInfo ){ + userEmail = loggedInInfo.text.replace( 'Logged in as ', '' ); + } } catch( err ){ - spaceghost.error( err ); + spaceghost.warn( err ); } //console.debug( 'loggedInInfo:', spaceghost.jsonStr( loggedInInfo ) ); return userEmail; @@ -175,6 +177,7 @@ */ User.prototype.logout = function logout(){ var spaceghost = this.spaceghost; + if( !this.loggedInAs() ){ return spaceghost; } spaceghost.thenOpen( spaceghost.baseUrl, function(){ this.info( 'user logging out' ); //TODO: handle already logged out diff -r 64c6c98b9976c3dadb77426b6a6805922aa7810c -r 2a23dec18caabf3e326447db7eabd0b2d963fef4 test/casperjs/registration-tests.js --- a/test/casperjs/registration-tests.js +++ b/test/casperjs/registration-tests.js @@ -64,7 +64,8 @@ spaceghost.thenOpen( spaceghost.baseUrl, function(){ this.waitForMasthead( function() { this.clickLabel( 'User' ); - this.test.assertSelectorHasText( 'a #user-email', email, '#user-email === ' + email ); + this.test.assertSelectorHasText( xpath( spaceghost.data.selectors.masthead.userMenu.userEmail_xpath ), + email, '#user-email === ' + email ); }); }); @@ -77,8 +78,9 @@ }); spaceghost.then( function(){ this.waitForMasthead( function() { - this.debug( 'email:' + this.getElementInfo( 'a #user-email' ).html ); - this.test.assert( !this.getElementInfo( 'a #user-email' ).html, '#user-email is empty' ); + var emailSelector = xpath( this.data.selectors.masthead.userMenu.userEmail_xpath ); + this.debug( 'email:' + this.elementInfoOrNull( emailSelector ) ); + this.test.assert( !this.elementInfoOrNull( emailSelector ), 'user email not found' ); }); }); @@ -99,7 +101,7 @@ this.user._submitRegistration( badEmail, password, username, confirm ); }); self.then(function(){ - this.assertErrorMessage( 'Enter a real email address' ); + this.assertErrorMessage( 'Please enter your valid email address' ); }); }); @@ -108,10 +110,10 @@ spaceghost.each( badPasswords, function( self, badPassword ){ self.then( function(){ this.test.comment( 'attempting bad password: ' + badPassword ); - this.user._submitRegistration( spaceghost.user.getRandomEmail(), badPassword, username, confirm ); + this.user._submitRegistration( spaceghost.user.getRandomEmail(), badPassword, username, badPassword ); }); self.then(function(){ - this.assertErrorMessage( 'Use a password of at least 6 characters' ); + this.assertErrorMessage( 'Please use a password of at least 6 characters' ); }); }); @@ -123,7 +125,7 @@ this.user._submitRegistration( spaceghost.user.getRandomEmail(), password, username, badConfirm ); }); self.then(function(){ - this.assertErrorMessage( 'Passwords do not match' ); + this.assertErrorMessage( 'Passwords don\'t match' ); }); }); @@ -149,7 +151,7 @@ this.user._submitRegistration( newEmail, password, badUsername, confirm ); }); self.then(function(){ - this.assertErrorMessage( "Public name must contain only lower-case letters, numbers and '-'" ); + this.assertErrorMessage( 'Public name must contain only lowercase letters, numbers and "-"' ); }); }); diff -r 64c6c98b9976c3dadb77426b6a6805922aa7810c -r 2a23dec18caabf3e326447db7eabd0b2d963fef4 test/casperjs/spaceghost.js --- a/test/casperjs/spaceghost.js +++ b/test/casperjs/spaceghost.js @@ -793,7 +793,7 @@ * @param {CasperJS selector} messageSelector what element in which to search for the text * (defaults to '.errormessage') */ -SpaceGhost.prototype.assertErrorMessage = function assertSelectorAndTextInFrame( message, frame, messageSelector ){ +SpaceGhost.prototype.assertErrorMessage = function assertErrorMessage( message, frame, messageSelector ){ messageSelector = messageSelector || this.data.selectors.messages.error; frame = frame || this.data.selectors.frames.main; this.assertSelectorAndTextInFrame( messageSelector, message, frame ); @@ -1135,8 +1135,7 @@ masthead : { adminLink : '#masthead a[href="/admin/index"]', userMenu : { - userEmail : 'a #user-email', - userEmail_xpath : '//a[contains(text(),"Logged in as")]/span["id=#user-email"]' + userEmail_xpath : '//a[contains(text(),"Logged in as")]' } }, loginPage : { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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