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Merge next-stable.

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This commit is contained in:
John Chilton
2014-12-05 20:36:48 -05:00
parent c515e18fc4 5b6c092aa0
commit 251155887e
27 changed files with 1210 additions and 948 deletions
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client/galaxy/scripts/galaxy.library.js
+75 -62
View File
@@ -36,7 +36,7 @@ var LibraryRouter = Backbone.Router.extend({
initialize: function() {
this.routesHit = 0;
//keep count of number of routes handled by the application
Backbone.history.on('route', function() { this.routesHit++; }, this);
Backbone.history.on( 'route', function() { this.routesHit++; }, this );
},
routes: {
@@ -45,6 +45,7 @@ routes: {
"library/:library_id/permissions" : "library_permissions",
"folders/:folder_id/permissions" : "folder_permissions",
"folders/:id" : "folder_content",
"folders/:id/page/:show_page" : "folder_page",
"folders/:folder_id/datasets/:dataset_id" : "dataset_detail",
"folders/:folder_id/datasets/:dataset_id/permissions" : "dataset_permissions",
"folders/:folder_id/datasets/:dataset_id/versions/:ldda_id" : "dataset_version",
@@ -53,13 +54,13 @@ routes: {
},
back: function() {
if(this.routesHit > 1) {
if( this.routesHit > 1 ) {
//more than one route hit -> user did not land to current page directly
window.history.back();
} else {
//otherwise go to the home page. Use replaceState if available so
//the navigation doesn't create an extra history entry
this.navigate('#', {trigger:true, replace:true});
this.navigate( '#', { trigger:true, replace:true } );
}
}
});
@@ -71,7 +72,8 @@ var LibraryPrefs = mod_baseMVC.SessionStorageModel.extend({
with_deleted : false,
sort_order : 'asc',
sort_by : 'name',
library_page_size : 20
library_page_size : 20,
folder_page_size : 15
}
});
@@ -94,10 +96,10 @@ var GalaxyLibrary = Backbone.View.extend({
this.library_router = new LibraryRouter();
this.library_router.on('route:libraries', function() {
Galaxy.libraries.libraryToolbarView = new mod_librarytoolbar_view.LibraryToolbarView();
Galaxy.libraries.libraryListView = new mod_librarylist_view.LibraryListView();
});
this.library_router.on( 'route:libraries', function() {
Galaxy.libraries.libraryToolbarView = new mod_librarytoolbar_view.LibraryToolbarView();
Galaxy.libraries.libraryListView = new mod_librarylist_view.LibraryListView();
});
this.library_router.on('route:libraries_page', function( show_page ) {
if ( Galaxy.libraries.libraryToolbarView === null ){
@@ -108,66 +110,77 @@ var GalaxyLibrary = Backbone.View.extend({
}
});
this.library_router.on('route:folder_content', function(id) {
this.library_router.on( 'route:folder_content', function( id ) {
if (Galaxy.libraries.folderToolbarView){
Galaxy.libraries.folderToolbarView.$el.unbind('click');
}
Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView({id: id});
Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView({id: id});
});
Galaxy.libraries.folderToolbarView.$el.unbind( 'click' );
}
Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView( { id: id } );
Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView( { id: id } );
});
this.library_router.on('route:download', function(folder_id, format) {
if ($('#folder_list_body').find(':checked').length === 0) {
mod_toastr.info( 'You must select at least one dataset to download' );
Galaxy.libraries.library_router.navigate('folders/' + folder_id, {trigger: true, replace: true});
} else {
Galaxy.libraries.folderToolbarView.download(folder_id, format);
Galaxy.libraries.library_router.navigate('folders/' + folder_id, {trigger: false, replace: true});
}
});
this.library_router.on( 'route:folder_page', function( id, show_page ) {
if ( Galaxy.libraries.folderToolbarView === null ){
Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView( {id: id} );
Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView( { id: id, show_page: show_page } );
} else {
Galaxy.libraries.folderListView.render( { id: id, show_page: parseInt( show_page ) } )
}
});
this.library_router.on('route:dataset_detail', function(folder_id, dataset_id){
if (Galaxy.libraries.datasetView){
Galaxy.libraries.datasetView.$el.unbind('click');
}
Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id});
});
this.library_router.on('route:dataset_version', function(folder_id, dataset_id, ldda_id){
if (Galaxy.libraries.datasetView){
Galaxy.libraries.datasetView.$el.unbind('click');
}
Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id, ldda_id: ldda_id, show_version: true});
});
this.library_router.on( 'route:download', function( folder_id, format ) {
if ( $( '#folder_list_body' ).find( ':checked' ).length === 0 ) {
mod_toastr.info( 'You must select at least one dataset to download' );
Galaxy.libraries.library_router.navigate( 'folders/' + folder_id, { trigger: true, replace: true } );
} else {
Galaxy.libraries.folderToolbarView.download( folder_id, format );
Galaxy.libraries.library_router.navigate( 'folders/' + folder_id, { trigger: false, replace: true } );
}
});
this.library_router.on('route:dataset_permissions', function(folder_id, dataset_id){
if (Galaxy.libraries.datasetView){
Galaxy.libraries.datasetView.$el.unbind('click');
}
Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id, show_permissions: true});
});
this.library_router.on( 'route:dataset_detail', function(folder_id, dataset_id){
if (Galaxy.libraries.datasetView){
Galaxy.libraries.datasetView.$el.unbind('click');
}
Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id});
});
this.library_router.on('route:library_permissions', function(library_id){
if (Galaxy.libraries.libraryView){
Galaxy.libraries.libraryView.$el.unbind('click');
}
Galaxy.libraries.libraryView = new mod_library_library_view.LibraryView({id: library_id, show_permissions: true});
});
this.library_router.on( 'route:dataset_version', function(folder_id, dataset_id, ldda_id){
if (Galaxy.libraries.datasetView){
Galaxy.libraries.datasetView.$el.unbind('click');
}
Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id, ldda_id: ldda_id, show_version: true});
});
this.library_router.on('route:folder_permissions', function(folder_id){
if (Galaxy.libraries.folderView){
Galaxy.libraries.folderView.$el.unbind('click');
}
Galaxy.libraries.folderView = new mod_library_folder_view.FolderView({id: folder_id, show_permissions: true});
});
this.library_router.on('route:import_datasets', function(folder_id, source){
if (Galaxy.libraries.folderToolbarView && Galaxy.libraries.folderListView){
Galaxy.libraries.folderToolbarView.showImportModal({source:source});
} else {
Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView({id: folder_id});
Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView({id: folder_id});
Galaxy.libraries.folderToolbarView.showImportModal({source: source});
}
});
this.library_router.on( 'route:dataset_permissions', function(folder_id, dataset_id){
if (Galaxy.libraries.datasetView){
Galaxy.libraries.datasetView.$el.unbind('click');
}
Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id, show_permissions: true});
});
this.library_router.on( 'route:library_permissions', function(library_id){
if (Galaxy.libraries.libraryView){
Galaxy.libraries.libraryView.$el.unbind('click');
}
Galaxy.libraries.libraryView = new mod_library_library_view.LibraryView({id: library_id, show_permissions: true});
});
this.library_router.on( 'route:folder_permissions', function(folder_id){
if (Galaxy.libraries.folderView){
Galaxy.libraries.folderView.$el.unbind('click');
}
Galaxy.libraries.folderView = new mod_library_folder_view.FolderView({id: folder_id, show_permissions: true});
});
this.library_router.on( 'route:import_datasets', function( folder_id, source ){
if ( Galaxy.libraries.folderToolbarView && Galaxy.libraries.folderListView ){
Galaxy.libraries.folderToolbarView.showImportModal( { source:source } );
} else {
Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView( { id: folder_id } );
Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView( { id: folder_id } );
Galaxy.libraries.folderToolbarView.showImportModal( { source: source } );
}
});
Backbone.history.start({pushState: false});
}
client/galaxy/scripts/mvc/library/library-folderlist-view.js
+329 -292
View File
@@ -15,322 +15,359 @@ function(mod_masthead,
) {
var FolderListView = Backbone.View.extend({
el : '#folder_items_element',
defaults: {
'include_deleted' : false
},
// progress percentage
progress: 0,
// progress rate per one item
progressStep: 1,
// self modal
modal : null,
el : '#folder_items_element',
// progress percentage
progress: 0,
// progress rate per one item
progressStep: 1,
folderContainer: null,
folderContainer: null,
sort: 'asc',
sort: 'asc',
events: {
'click #select-all-checkboxes' : 'selectAll',
'click .dataset_row' : 'selectClickedRow',
'click .sort-folder-link' : 'sortColumnClicked'
},
events: {
'click #select-all-checkboxes' : 'selectAll',
'click .dataset_row' : 'selectClickedRow',
'click .sort-folder-link' : 'sortColumnClicked'
},
// cache of rendered views
rowViews: {},
initialize : function(options){
this.options = _.defaults(this.options || {}, options);
this.fetchFolder();
},
collection: null,
fetchFolder: function(options){
var options = options || {};
this.options.include_deleted = options.include_deleted;
var that = this;
defaults: {
include_deleted: false,
page_count: null,
show_page: null
},
this.collection = new mod_library_model.Folder();
/**
* Initialize and fetch the folder from the server.
* @param {object} options an object with options
*/
initialize : function( options ){
this.options = _.defaults( this.options || {}, this.defaults, options );
this.modal = null;
// map of folder item ids to item views = cache
this.rowViews = {};
// start to listen if someone modifies collection
this.listenTo(this.collection, 'add', this.renderOne);
this.listenTo(this.collection, 'remove', this.removeOne);
// create a collection of folder items for this view
this.collection = new mod_library_model.Folder();
this.folderContainer = new mod_library_model.FolderContainer({id: this.options.id});
this.folderContainer.url = this.folderContainer.attributes.urlRoot + this.options.id + '/contents';
if (this.options.include_deleted){
this.folderContainer.url = this.folderContainer.url + '?include_deleted=true';
}
this.folderContainer.fetch({
success: function(folder_container) {
that.folder_container = folder_container;
that.render();
that.addAll(folder_container.get('folder').models);
if (that.options.dataset_id){
row = _.findWhere(that.rowViews, {id: that.options.dataset_id});
if (row) {
// start to listen if someone modifies the collection
this.listenTo( this.collection, 'add', this.renderOne );
this.listenTo( this.collection, 'remove', this.removeOne );
this.fetchFolder();
},
fetchFolder: function( options ){
var options = options || {};
this.options.include_deleted = options.include_deleted;
var that = this;
this.folderContainer = new mod_library_model.FolderContainer( { id: this.options.id } );
this.folderContainer.url = this.folderContainer.attributes.urlRoot + this.options.id + '/contents';
if ( this.options.include_deleted ){
this.folderContainer.url = this.folderContainer.url + '?include_deleted=true';
}
this.folderContainer.fetch({
success: function( folder_container ) {
that.folder_container = folder_container;
that.render();
},
error: function( model, response ){
if ( typeof response.responseJSON !== "undefined" ){
mod_toastr.error( response.responseJSON.err_msg + ' Click this to go back.', '', { onclick: function() { Galaxy.libraries.library_router.back(); } } );
} else {
mod_toastr.error( 'An error ocurred. Click this to go back.', '', { onclick: function() { Galaxy.libraries.library_router.back(); } } );
}
}
});
},
render: function ( options ){
this.options = _.extend( this.options, options );
var template = this.templateFolder();
$(".tooltip").hide();
// find the upper id in the full path
var path = this.folderContainer.attributes.metadata.full_path;
var upper_folder_id;
if ( path.length === 1 ){ // the library is above us
upper_folder_id = 0;
} else {
upper_folder_id = path[ path.length-2 ][ 0 ];
}
this.$el.html( template( {
path: this.folderContainer.attributes.metadata.full_path,
parent_library_id: this.folderContainer.attributes.metadata.parent_library_id,
id: this.options.id,
upper_folder_id: upper_folder_id,
order: this.sort
} ) );
// when dataset_id is present render its details too
if ( this.options.dataset_id ){
row = _.findWhere( that.rowViews, { id: this.options.dataset_id } );
if ( row ) {
row.showDatasetDetails();
} else {
mod_toastr.error('Dataset not found. Showing folder instead.');
mod_toastr.error( 'Requested dataset not found. Showing folder instead.' );
}
}
},
error: function(model, response){
if (typeof response.responseJSON !== "undefined"){
mod_toastr.error(response.responseJSON.err_msg + ' Click this to go back.', '', {onclick: function() {Galaxy.libraries.library_router.back();}});
} else {
mod_toastr.error('An error ocurred. Click this to go back.', '', {onclick: function() {Galaxy.libraries.library_router.back();}});
}
} else {
if ( this.options.show_page === null || this.options.show_page < 1 ){
this.options.show_page = 1;
}
this.paginate();
}
});
},
$("#center [data-toggle]").tooltip();
$("#center").css('overflow','auto');
},
render: function (options) {
this.options = _.defaults(this.options, options);
var template = this.templateFolder();
$(".tooltip").hide();
paginate: function( options ){
this.options = _.extend( this.options, options );
// TODO move to server
// find the upper id in the full path
var path = this.folderContainer.attributes.metadata.full_path;
var upper_folder_id;
if (path.length === 1){ // the library is above us
upper_folder_id = 0;
} else {
upper_folder_id = path[path.length-2][0];
}
if ( this.options.show_page === null || this.options.show_page < 1 ){
this.options.show_page = 1;
}
this.options.total_items_count = this.folder_container.get( 'folder' ).models.length;
this.options.page_count = Math.ceil( this.options.total_items_count / Galaxy.libraries.preferences.get( 'folder_page_size' ) );
var page_start = ( Galaxy.libraries.preferences.get( 'folder_page_size' ) * ( this.options.show_page - 1 ) );
var items_to_render = null;
items_to_render = this.folder_container.get( 'folder' ).models.slice( page_start, page_start + Galaxy.libraries.preferences.get( 'folder_page_size' ) );
this.options.items_shown = items_to_render.length;
// User requests page with no items
if ( Galaxy.libraries.preferences.get( 'folder_page_size' ) * this.options.show_page > ( this.options.total_items_count + Galaxy.libraries.preferences.get( 'folder_page_size' ) ) ){
items_to_render = [];
}
Galaxy.libraries.folderToolbarView.renderPaginator( this.options );
this.collection.reset();
this.addAll( items_to_render )
},
this.$el.html(template({ path: this.folderContainer.attributes.metadata.full_path, parent_library_id: this.folderContainer.attributes.metadata.parent_library_id, id: this.options.id, upper_folder_id: upper_folder_id, order: this.sort}));
/**
* Adds all given models to the collection.
* @param {array of Item or FolderAsModel} array of models that should
* be added to the view's collection.
*/
addAll: function( models ){
_.each(models, function( model ) {
Galaxy.libraries.folderListView.collection.add( model );
});
$( "#center [data-toggle]" ).tooltip();
this.checkEmptiness();
this.postRender();
},
// initialize the library tooltips
$("#center [data-toggle]").tooltip();
//hack to show scrollbars
$("#center").css('overflow','auto');
},
/**
* Call this after all models are added to the collection
* to ensure that the folder toolbar will show proper options
* and that event will be bound on all subviews.
*/
postRender: function(){
var fetched_metadata = this.folderContainer.attributes.metadata;
fetched_metadata.contains_file = typeof this.collection.findWhere({type: 'file'}) !== 'undefined';
Galaxy.libraries.folderToolbarView.configureElements(fetched_metadata);
$('.library-row').hover(function() {
$(this).find('.show_on_hover').show();
}, function () {
$(this).find('.show_on_hover').hide();
});
},
/**
* Call this after all models are added to the collection
* to ensure that the folder toolbar will show proper options
* and that event will be bound on all subviews.
*/
postRender: function(){
var fetched_metadata = this.folderContainer.attributes.metadata;
fetched_metadata.contains_file = typeof this.collection.findWhere({type: 'file'}) !== 'undefined';
Galaxy.libraries.folderToolbarView.configureElements(fetched_metadata);
$('.library-row').hover(function() {
$(this).find('.show_on_hover').show();
}, function () {
$(this).find('.show_on_hover').hide();
});
},
/**
* Iterates this view's collection and calls the render
* function for each. Also binds the hover behavior.
*/
renderAll: function(){
var that = this;
_.each( this.collection.models.reverse(), function( model ) {
that.renderOne( model );
});
this.postRender();
},
/**
* Adds all given models to the collection.
* @param {array of Item or FolderAsModel} array of models that should
* be added to the view's collection.
*/
addAll: function(models){
_.each(models.reverse(), function(model) {
Galaxy.libraries.folderListView.collection.add(model);
});
$("#center [data-toggle]").tooltip();
this.checkEmptiness();
this.postRender();
},
/**
* Iterates this view's collection and calls the render
* function for each. Also binds the hover behavior.
*/
renderAll: function(){
var that = this;
_.each(this.collection.models.reverse(), function(model) {
that.renderOne(model);
});
this.postRender();
},
/**
* Creates a view for the given model and adds it to the folder view.
* @param {Item or FolderAsModel} model of the view that will be rendered
*/
renderOne: function(model){
if (model.get('type') !== 'folder'){
this.options.contains_file = true;
// model.set('readable_size', this.size_to_string(model.get('file_size')));
}
model.set('folder_id', this.id);
var rowView = new mod_library_folderrow_view.FolderRowView(model);
// save new rowView to cache
this.rowViews[model.get('id')] = rowView;
this.$el.find('#first_folder_item').after(rowView.el);
$('.library-row').hover(function() {
$(this).find('.show_on_hover').show();
}, function () {
$(this).find('.show_on_hover').hide();
});
},
/**
* removes the view of the given model from the DOM
* @param {Item or FolderAsModel} model of the view that will be removed
*/
removeOne: function(model){
this.$el.find('#' + model.id).remove();
},
/** Checks whether the list is empty and adds/removes the message */
checkEmptiness : function(){
if ((this.$el.find('.dataset_row').length === 0) && (this.$el.find('.folder_row').length === 0)){
this.$el.find('.empty-folder-message').show();
} else {
this.$el.find('.empty-folder-message').hide();
}
},
/** User clicked the table heading = he wants to sort stuff */
sortColumnClicked : function(event){
event.preventDefault();
if (this.sort === 'asc'){
this.sortFolder('name','desc');
this.sort = 'desc';
} else {
this.sortFolder('name','asc');
this.sort = 'asc';
}
this.render();
this.renderAll();
this.checkEmptiness();
},
/**
* Sorts the underlying collection according to the parameters received.
* Currently supports only sorting by name.
*/
sortFolder: function(sort_by, order){
if (sort_by === 'name'){
if (order === 'asc'){
return this.collection.sortByNameAsc();
} else if (order === 'desc'){
return this.collection.sortByNameDesc();
/**
* Creates a view for the given model and adds it to the folder view.
* @param {Item or FolderAsModel} model of the view that will be rendered
*/
renderOne: function(model){
if (model.get('type') !== 'folder'){
this.options.contains_file = true;
// model.set('readable_size', this.size_to_string(model.get('file_size')));
}
}
},
model.set('folder_id', this.id);
var rowView = new mod_library_folderrow_view.FolderRowView(model);
/**
* User clicked the checkbox in the table heading
* @param {context} event
*/
selectAll : function (event) {
var selected = event.target.checked;
that = this;
// Iterate each checkbox
$(':checkbox', '#folder_list_body').each(function() {
this.checked = selected;
$row = $(this.parentElement.parentElement);
// Change color of selected/unselected
if (selected) {
that.makeDarkRow($row);
} else {
that.makeWhiteRow($row);
}
});
},
// save new rowView to cache
this.rowViews[model.get('id')] = rowView;
/**
* Check checkbox if user clicks on the whole row or
* on the checkbox itself
*/
selectClickedRow : function (event) {
var checkbox = '';
var $row;
var source;
if (event.target.localName === 'input'){
checkbox = event.target;
$row = $(event.target.parentElement.parentElement);
source = 'input';
} else if (event.target.localName === 'td') {
checkbox = $("#" + event.target.parentElement.id).find(':checkbox')[0];
$row = $(event.target.parentElement);
source = 'td';
}
if (checkbox.checked){
if (source==='td'){
checkbox.checked = '';
this.makeWhiteRow($row);
} else if (source==='input') {
this.makeDarkRow($row);
this.$el.find('#first_folder_item').after(rowView.el);
$('.library-row').hover(function() {
$(this).find('.show_on_hover').show();
}, function () {
$(this).find('.show_on_hover').hide();
});
},
/**
* removes the view of the given model from the DOM
* @param {Item or FolderAsModel} model of the view that will be removed
*/
removeOne: function( model ){
this.$el.find( '#' + model.id ).remove();
},
/** Checks whether the list is empty and adds/removes the message */
checkEmptiness : function(){
if ((this.$el.find('.dataset_row').length === 0) && (this.$el.find('.folder_row').length === 0)){
this.$el.find('.empty-folder-message').show();
} else {
this.$el.find('.empty-folder-message').hide();
}
} else {
if (source==='td'){
checkbox.checked = 'selected';
this.makeDarkRow($row);
} else if (source==='input') {
this.makeWhiteRow($row);
},
/** User clicked the table heading = he wants to sort stuff */
sortColumnClicked : function(event){
event.preventDefault();
if (this.sort === 'asc'){
this.sortFolder('name','desc');
this.sort = 'desc';
} else {
this.sortFolder('name','asc');
this.sort = 'asc';
}
this.render();
this.renderAll();
this.checkEmptiness();
},
/**
* Sorts the underlying collection according to the parameters received.
* Currently supports only sorting by name.
*/
sortFolder: function(sort_by, order){
if (sort_by === 'name'){
if (order === 'asc'){
return this.collection.sortByNameAsc();
} else if (order === 'desc'){
return this.collection.sortByNameDesc();
}
}
},
/**
* User clicked the checkbox in the table heading
* @param {context} event
*/
selectAll : function (event) {
var selected = event.target.checked;
that = this;
// Iterate each checkbox
$(':checkbox', '#folder_list_body').each(function() {
this.checked = selected;
$row = $(this.parentElement.parentElement);
// Change color of selected/unselected
if (selected) {
that.makeDarkRow($row);
} else {
that.makeWhiteRow($row);
}
});
},
/**
* Check checkbox if user clicks on the whole row or
* on the checkbox itself
*/
selectClickedRow : function (event) {
var checkbox = '';
var $row;
var source;
if (event.target.localName === 'input'){
checkbox = event.target;
$row = $(event.target.parentElement.parentElement);
source = 'input';
} else if (event.target.localName === 'td') {
checkbox = $("#" + event.target.parentElement.id).find(':checkbox')[0];
$row = $(event.target.parentElement);
source = 'td';
}
if (checkbox.checked){
if (source==='td'){
checkbox.checked = '';
this.makeWhiteRow($row);
} else if (source==='input') {
this.makeDarkRow($row);
}
} else {
if (source==='td'){
checkbox.checked = 'selected';
this.makeDarkRow($row);
} else if (source==='input') {
this.makeWhiteRow($row);
}
}
},
makeDarkRow: function($row){
$row.removeClass('light').addClass('dark');
$row.find('a').removeClass('light').addClass('dark');
$row.find('.fa-file-o').removeClass('fa-file-o').addClass('fa-file');
},
makeWhiteRow: function($row){
$row.removeClass('dark').addClass('light');
$row.find('a').removeClass('dark').addClass('light');
$row.find('.fa-file').removeClass('fa-file').addClass('fa-file-o');
},
templateFolder : function (){
var tmpl_array = [];
// BREADCRUMBS
tmpl_array.push('<ol class="breadcrumb">');
tmpl_array.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');
tmpl_array.push(' <% _.each(path, function(path_item) { %>');
tmpl_array.push(' <% if (path_item[0] != id) { %>');
tmpl_array.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a> </li> ');
tmpl_array.push( '<% } else { %>');
tmpl_array.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>');
tmpl_array.push(' <% } %>');
tmpl_array.push(' <% }); %>');
tmpl_array.push('</ol>');
// FOLDER CONTENT
tmpl_array.push('<table data-library-id="<%- parent_library_id %>" id="folder_table" class="grid table table-condensed">');
tmpl_array.push(' <thead>');
tmpl_array.push(' <th class="button_heading"></th>');
tmpl_array.push(' <th style="text-align: center; width: 20px; " title="Check to select all datasets"><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');
tmpl_array.push(' <th><a class="sort-folder-link" title="Click to reverse order" href="#">name</a> <span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');
tmpl_array.push(' <th style="width:5%;">data type</th>');
tmpl_array.push(' <th style="width:10%;">size</th>');
tmpl_array.push(' <th style="width:160px;">time updated (UTC)</th>');
tmpl_array.push(' <th style="width:10%;"></th> ');
tmpl_array.push(' </thead>');
tmpl_array.push(' <tbody id="folder_list_body">');
tmpl_array.push(' <tr id="first_folder_item">');
tmpl_array.push(' <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>');
tmpl_array.push(' <td></td>');
tmpl_array.push(' <td></td>');
tmpl_array.push(' <td></td>');
tmpl_array.push(' <td></td>');
tmpl_array.push(' <td></td>');
tmpl_array.push(' <td></td>');
tmpl_array.push(' </tr>');
tmpl_array.push(' </tbody>');
tmpl_array.push('</table>');
tmpl_array.push('<div class="empty-folder-message" style="display:none;">This folder is either empty or you do not have proper access permissions to see the contents. If you expected something to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity" target="_blank">library security wikipage</a> or visit the <a href="https://biostar.usegalaxy.org/" target="_blank">Galaxy support site</a>.</div>');
return _.template(tmpl_array.join(''));
}
},
makeDarkRow: function($row){
$row.removeClass('light').addClass('dark');
$row.find('a').removeClass('light').addClass('dark');
$row.find('.fa-file-o').removeClass('fa-file-o').addClass('fa-file');
},
makeWhiteRow: function($row){
$row.removeClass('dark').addClass('light');
$row.find('a').removeClass('dark').addClass('light');
$row.find('.fa-file').removeClass('fa-file').addClass('fa-file-o');
},
templateFolder : function (){
var tmpl_array = [];
// BREADCRUMBS
tmpl_array.push('<ol class="breadcrumb">');
tmpl_array.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');
tmpl_array.push(' <% _.each(path, function(path_item) { %>');
tmpl_array.push(' <% if (path_item[0] != id) { %>');
tmpl_array.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a> </li> ');
tmpl_array.push( '<% } else { %>');
tmpl_array.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>');
tmpl_array.push(' <% } %>');
tmpl_array.push(' <% }); %>');
tmpl_array.push('</ol>');
// FOLDER CONTENT
tmpl_array.push('<table data-library-id="<%- parent_library_id %>" id="folder_table" class="grid table table-condensed">');
tmpl_array.push(' <thead>');
tmpl_array.push(' <th class="button_heading"></th>');
tmpl_array.push(' <th style="text-align: center; width: 20px; " title="Check to select all datasets"><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');
tmpl_array.push(' <th><a class="sort-folder-link" title="Click to reverse order" href="#">name</a> <span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');
tmpl_array.push(' <th style="width:5%;">data type</th>');
tmpl_array.push(' <th style="width:10%;">size</th>');
tmpl_array.push(' <th style="width:160px;">time updated (UTC)</th>');
tmpl_array.push(' <th style="width:10%;"></th> ');
tmpl_array.push(' </thead>');
tmpl_array.push(' <tbody id="folder_list_body">');
tmpl_array.push(' <tr id="first_folder_item">');
tmpl_array.push(' <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>');
tmpl_array.push(' <td></td>');
tmpl_array.push(' <td></td>');
tmpl_array.push(' <td></td>');
tmpl_array.push(' <td></td>');
tmpl_array.push(' <td></td>');
tmpl_array.push(' <td></td>');
tmpl_array.push(' </tr>');
tmpl_array.push(' </tbody>');
tmpl_array.push('</table>');
tmpl_array.push('<div class="empty-folder-message" style="display:none;">This folder is either empty or you do not have proper access permissions to see the contents. If you expected something to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity" target="_blank">library security wikipage</a> or visit the <a href="https://biostar.usegalaxy.org/" target="_blank">Galaxy support site</a>.</div>');
return _.template(tmpl_array.join(''));
}
});
return {
client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
+69 -6
View File
@@ -20,7 +20,9 @@ var FolderToolbarView = Backbone.View.extend({
'click #toolbtn_bulk_import' : 'modalBulkImport',
'click #include_deleted_datasets_chk' : 'checkIncludeDeleted',
'click #toolbtn_show_libinfo' : 'showLibInfo',
'click #toolbtn_bulk_delete' : 'deleteSelectedDatasets'
'click #toolbtn_bulk_delete' : 'deleteSelectedDatasets',
'click #page_size_prompt' : 'showPageSizePrompt'
},
defaults: {
@@ -90,6 +92,22 @@ var FolderToolbarView = Backbone.View.extend({
this.$el.html(toolbar_template(template_defaults));
},
/**
* Called from FolderListView when needed.
* @param {object} options common options
*/
renderPaginator: function( options ){
this.options = _.extend( this.options, options );
var paginator_template = this.templatePaginator();
this.$el.find( '#folder_paginator' ).html( paginator_template({
id: this.options.id,
show_page: parseInt( this.options.show_page ),
page_count: parseInt( this.options.page_count ),
total_items_count: this.options.total_items_count,
items_shown: this.options.items_shown
}));
},
configureElements: function(options){
this.options = _.extend(this.options, options);
@@ -833,11 +851,11 @@ var FolderToolbarView = Backbone.View.extend({
var popped_item = lddas_set.pop();
if ( typeof popped_item === "undefined" ) {
if ( this.options.chain_call_control.failed_number === 0 ){
mod_toastr.success( 'Selected datasets deleted' );
mod_toastr.success( 'Selected datasets were deleted.' );
} else if ( this.options.chain_call_control.failed_number === this.options.chain_call_control.total_number ){
mod_toastr.error( 'There was an error and no datasets were deleted.' );
mod_toastr.error( 'There was an error and no datasets were deleted. Please make sure you have sufficient permissions.' );
} else if ( this.options.chain_call_control.failed_number < this.options.chain_call_control.total_number ){
mod_toastr.warning( 'Some of the datasets could not be deleted' );
mod_toastr.warning( 'Some of the datasets could not be deleted. Please make sure you have sufficient permissions.' );
}
Galaxy.modal.hide();
return this.deleted_lddas;
@@ -976,6 +994,14 @@ var FolderToolbarView = Backbone.View.extend({
}
},
showPageSizePrompt: function(){
var folder_page_size = prompt( 'How many items per page do you want to see?', Galaxy.libraries.preferences.get( 'folder_page_size' ) );
if ( ( folder_page_size != null ) && ( folder_page_size == parseInt( folder_page_size ) ) ) {
Galaxy.libraries.preferences.set( { 'folder_page_size': parseInt( folder_page_size ) } );
Galaxy.libraries.folderListView.render( { id: this.options.id, show_page: 1 } );
}
},
templateToolBar: function(){
tmpl_array = [];
@@ -1016,7 +1042,6 @@ var FolderToolbarView = Backbone.View.extend({
tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button add-library-items" type="button"><span class="fa fa-plus"></span> <span class="fa fa-file"></span></span></button>');
tmpl_array.push('<% } %>');
tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to History</button>');
tmpl_array.push(' <div id="toolbtn_dl" class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">');
tmpl_array.push(' <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');
@@ -1032,6 +1057,10 @@ var FolderToolbarView = Backbone.View.extend({
tmpl_array.push(' <button data-id="<%- id %>" data-toggle="tooltip" data-placement="top" title="Show library information" id="toolbtn_show_libinfo" class="primary-button" style="margin-left: 0.5em;" type="button"><span class="fa fa-info-circle"></span> Library Info</button>');
tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/FolderContents" target="_blank"><button class="primary-button" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>');
tmpl_array.push(' <span id="folder_paginator" class="library-paginator">');
// paginator will append here
tmpl_array.push(' </span>');
tmpl_array.push(' </div>');
// TOOLBAR END
tmpl_array.push(' <div id="folder_items_element">');
@@ -1239,7 +1268,41 @@ var FolderToolbarView = Backbone.View.extend({
tmpl_array.push('</ul>');
return _.template(tmpl_array.join(''));
}
},
templatePaginator: function(){
tmpl_array = [];
tmpl_array.push(' <ul class="pagination pagination-sm">');
tmpl_array.push(' <% if ( ( show_page - 1 ) > 0 ) { %>');
tmpl_array.push(' <% if ( ( show_page - 1 ) > page_count ) { %>'); // we are on higher page than total page count
tmpl_array.push(' <li><a href="#folders/<%= id %>/page/1"><span class="fa fa-angle-double-left"></span></a></li>');
tmpl_array.push(' <li class="disabled"><a href="#folders/<%= id %>/page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>');
tmpl_array.push(' <% } else { %>');
tmpl_array.push(' <li><a href="#folders/<%= id %>/page/1"><span class="fa fa-angle-double-left"></span></a></li>');
tmpl_array.push(' <li><a href="#folders/<%= id %>/page/<% print( show_page - 1 ) %>"><% print( show_page - 1 ) %></a></li>');
tmpl_array.push(' <% } %>');
tmpl_array.push(' <% } else { %>'); // we are on the first page
tmpl_array.push(' <li class="disabled"><a href="#folders/<%= id %>/page/1"><span class="fa fa-angle-double-left"></span></a></li>');
tmpl_array.push(' <li class="disabled"><a href="#folders/<%= id %>/page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>');
tmpl_array.push(' <% } %>');
tmpl_array.push(' <li class="active">');
tmpl_array.push(' <a href="#folders/<%= id %>/page/<% print( show_page ) %>"><% print( show_page ) %></a>');
tmpl_array.push(' </li>');
tmpl_array.push(' <% if ( ( show_page ) < page_count ) { %>');
tmpl_array.push(' <li><a href="#folders/<%= id %>/page/<% print( show_page + 1 ) %>"><% print( show_page + 1 ) %></a></li>');
tmpl_array.push(' <li><a href="#folders/<%= id %>/page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>');
tmpl_array.push(' <% } else { %>');
tmpl_array.push(' <li class="disabled"><a href="#folders/<%= id %>/page/<% print( show_page ) %>"><% print( show_page + 1 ) %></a></li>');
tmpl_array.push(' <li class="disabled"><a href="#folders/<%= id %>/page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>');
tmpl_array.push(' <% } %>');
tmpl_array.push(' </ul>');
tmpl_array.push(' <span>');
tmpl_array.push(' showing <a data-toggle="tooltip" data-placement="top" title="Click to change the number of items on page" id="page_size_prompt"><%- items_shown %></a> of <%- total_items_count %> items');
tmpl_array.push(' </span>');
return _.template(tmpl_array.join(''));
},
});
client/galaxy/scripts/mvc/library/library-librarylist-view.js
+11 -17
View File
@@ -21,20 +21,19 @@ var LibraryListView = Backbone.View.extend({
'click .sort-libraries-link' : 'sort_clicked'
},
/**
* Initialize and fetch the libraries from server.
* Async render afterwards.
* @param {object} options an options object
*/
defaults: {
page_count: null,
show_page: null
},
/**
* Initialize and fetch the libraries from server.
* Async render afterwards.
* @param {object} options an object with options
*/
initialize : function( options ){
this.options = _.defaults( this.options || {}, this.defaults, options );
var that = this;
var that = this;
this.modal = null;
// map of library model ids to library views = cache
this.rowViews = {};
@@ -61,19 +60,10 @@ var LibraryListView = Backbone.View.extend({
*/
render: function ( options ) {
this.options = _.extend( this.options, options );
if ( ( this.options.page_size != null ) && ( this.options.page_size == parseInt( this.options.page_size ) ) ) {
Galaxy.libraries.preferences.set( { 'library_page_size': parseInt( this.options.page_size ) } );
}
$( ".tooltip" ).hide();
// this.options.show_page = this.options.show_page || 1;
var template = this.templateLibraryList();
var libraries_to_render = null;
var models = null;
if ( this.options.show_page === null || this.options.show_page < 1 ){
this.options.show_page = 1;
}
$( ".tooltip" ).hide();
if ( typeof options !== 'undefined' ){
models = typeof options.models !== 'undefined' ? options.models : null;
}
@@ -89,6 +79,10 @@ var LibraryListView = Backbone.View.extend({
} else {
libraries_to_render = [];
}
// pagination
if ( this.options.show_page === null || this.options.show_page < 1 ){
this.options.show_page = 1;
}
this.options.total_libraries_count = libraries_to_render.length
var page_start = ( Galaxy.libraries.preferences.get( 'library_page_size' ) * ( this.options.show_page - 1 ) );
this.options.page_count = Math.ceil( this.options.total_libraries_count / Galaxy.libraries.preferences.get( 'library_page_size' ) );
client/galaxy/scripts/mvc/tools/tools-tree.js
+1 -1
View File
@@ -126,7 +126,7 @@ return Backbone.Model.extend({
// handle default value
if (!field.skip) {
if (input.optional && field.validate && !field.validate()) {
value = 'None';
value = null;
}
add (job_input_id, input.id, value);
}
lib/galaxy/managers/folders.py
+34 -15
View File
@@ -16,14 +16,14 @@ class FolderManager( object ):
Interface/service object for interacting with folders.
"""
def get( self, trans, decoded_folder_id, check_ownership=False, check_accessible=True):
def get( self, trans, decoded_folder_id, check_manageable=False, check_accessible=True):
"""
Get the folder from the DB.
:param decoded_folder_id: decoded folder id
:type decoded_folder_id: int
:param check_ownership: flag whether the check that user is owner
:type check_ownership: bool
:param check_manageable: flag whether the check that user can manage item
:type check_manageable: bool
:param check_accessible: flag whether to check that user can access item
:type check_accessible: bool
@@ -38,17 +38,17 @@ class FolderManager( object ):
raise exceptions.RequestParameterInvalidException( 'No folder found with the id provided.' )
except Exception, e:
raise exceptions.InternalServerError( 'Error loading from the database.' + str( e ) )
folder = self.secure( trans, folder, check_ownership, check_accessible )
folder = self.secure( trans, folder, check_manageable, check_accessible )
return folder
def secure( self, trans, folder, check_ownership=True, check_accessible=True ):
def secure( self, trans, folder, check_manageable=True, check_accessible=True ):
"""
Check if (a) user owns folder or (b) folder is accessible to user.
Check if (a) user can manage folder or (b) folder is accessible to user.
:param folder: folder item
:type folder: LibraryFolder
:param check_ownership: flag whether the check that user is owner
:type check_ownership: bool
:param check_manageable: flag whether to check that user can manage item
:type check_manageable: bool
:param check_accessible: flag whether to check that user can access item
:type check_accessible: bool
@@ -58,23 +58,26 @@ class FolderManager( object ):
# all folders are accessible to an admin
if trans.user_is_admin():
return folder
if check_ownership:
folder = self.check_ownership( trans, folder )
if check_manageable:
folder = self.check_manageable( trans, folder )
if check_accessible:
folder = self.check_accessible( trans, folder )
return folder
def check_ownership( self, trans, folder ):
def check_manageable( self, trans, folder ):
"""
Check whether the user is owner of the folder.
Check whether the user can manage the folder.
:returns: the original folder
:rtype: LibraryFolder
:raises: AuthenticationRequired, InsufficientPermissionsException
"""
if not trans.user:
raise exceptions.AuthenticationRequired( "Must be logged in to manage Galaxy items", type='error' )
if folder.user != trans.user:
raise exceptions.ItemOwnershipException( "Folder is not owned by the current user", type='error' )
raise exceptions.AuthenticationRequired( "Must be logged in to manage Galaxy items.", type='error' )
current_user_roles = trans.get_current_user_roles()
if not trans.app.security_agent.can_manage_library_item( current_user_roles, folder ):
raise exceptions.InsufficientPermissionsException( "You don't have permissions to manage this folder.", type='error' )
else:
return folder
@@ -135,6 +138,22 @@ class FolderManager( object ):
trans.app.security_agent.copy_library_permissions( trans, parent_folder, new_folder )
return new_folder
def delete( self, trans, folder, undelete=False ):
"""
Mark given folder deleted/undeleted based on the flag.
:raises: ItemAccessibilityException
"""
if not trans.user_is_admin():
folder = self.check_manageable( trans, folder )
if undelete:
folder.deleted = False
else:
folder.deleted = True
trans.sa_session.add( folder )
trans.sa_session.flush()
return folder
def get_current_roles( self, trans, folder ):
"""
Find all roles currently connected to relevant permissions
lib/galaxy/model/__init__.py
+1 -1
View File
@@ -2192,7 +2192,7 @@ class Library( object, Dictifiable, HasName ):
return roles
class LibraryFolder( object, Dictifiable, HasName ):
dict_element_visible_keys = ( 'id', 'parent_id', 'name', 'description', 'item_count', 'genome_build', 'update_time' )
dict_element_visible_keys = ( 'id', 'parent_id', 'name', 'description', 'item_count', 'genome_build', 'update_time', 'deleted' )
def __init__( self, name=None, description=None, item_count=0, order_id=None ):
self.name = name or "Unnamed folder"
self.description = description
lib/galaxy/tools/test.py
+26 -1
View File
@@ -196,12 +196,37 @@ class ToolTestBuilder( object ):
if not isinstance(param_value, list):
param_value = [ param_value ]
processed_value = [ self.__add_uploaded_dataset( context.for_state(), v, param_extra, value ) for v in param_value ]
if isinstance( value, basic.DataCollectionToolParameter ):
elif isinstance( value, basic.DataCollectionToolParameter ):
assert 'collection' in param_extra
collection_def = param_extra[ 'collection' ]
for ( name, value, extra ) in collection_def.collect_inputs():
require_file( name, value, extra, self.required_files )
processed_value = collection_def
elif isinstance( value, basic.SelectToolParameter ):
# Tests may specify values as either raw value or the value
# as they appear in the list - the API doesn't and shouldn't
# accept the text value - so we need to convert the text
# into the form value.
def process_param_value( param_value ):
found_value = False
value_for_text = None
if value.static_options:
for (text, opt_value, selected) in value.static_options:
if param_value == opt_value:
found_value = True
if value_for_text is None and param_value == text:
value_for_text = opt_value
if not found_value and value_for_text is not None:
processed_value = value_for_text
else:
processed_value = param_value
return processed_value
# Do replacement described above for lists or singleton
# values.
if isinstance( param_value, list ):
processed_value = map( process_param_value, param_value )
else:
processed_value = process_param_value( param_value )
else:
processed_value = param_value
expanded_inputs[ context.for_state() ] = processed_value
lib/galaxy/webapps/galaxy/api/folders.py
+27 -1
View File
@@ -44,7 +44,7 @@ class FoldersController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinIt
:rtype: dict
"""
folder_id = self.folder_manager.cut_and_decode( trans, id )
folder = self.folder_manager.get( trans, folder_id, check_ownership=False, check_accessible=True )
folder = self.folder_manager.get( trans, folder_id, check_manageable=False, check_accessible=True )
return_dict = self.folder_manager.get_folder_dict( trans, folder )
return return_dict
@@ -229,6 +229,32 @@ class FoldersController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinIt
'Allowed values are: "set_permissions"' )
return self.folder_manager.get_current_roles( trans, folder )
@expose_api
def delete( self, trans, id, **kwd ):
"""
delete( self, trans, id, **kwd )
* DELETE /api/folders/{id}
marks the folder with the given ``id`` as `deleted` (or removes the `deleted` mark if the `undelete` param is true)
.. note:: Currently, only admin users can un/delete folders.
:param id: the encoded id of the folder to un/delete
:type id: an encoded id string
:param undelete: (optional) flag specifying whether the item should be deleted or undeleted, defaults to false:
:type undelete: bool
:returns: detailed folder information
:rtype: dictionary
:raises: ItemAccessibilityException, MalformedId, ObjectNotFound
"""
folder = self.folder_manager.get( trans, self.folder_manager.cut_and_decode( trans, id ), True )
undelete = util.string_as_bool( kwd.get( 'undelete', False ) )
folder = self.folder_manager.delete( trans, folder, undelete )
folder_dict = self.folder_manager.get_folder_dict( trans, folder )
return folder_dict
@web.expose_api
def update( self, trans, id, library_id, payload, **kwd ):
"""
lib/galaxy/webapps/galaxy/controllers/dataset.py
+21 -7
View File
@@ -932,11 +932,14 @@ class DatasetInterface( BaseUIController, UsesAnnotations, UsesHistoryMixin, Use
@web.expose
def show_params( self, trans, dataset_id=None, from_noframe=None, **kwd ):
"""
Show the parameters used for an HDA
Show the parameters used for the job associated with an HDA
"""
hda = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id( dataset_id ) )
try:
hda = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id( dataset_id ) )
except ValueError:
hda = None
if not hda:
raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid reference dataset id: %s." % str( dataset_id ) )
raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid reference dataset id: %s." % escape( str( dataset_id ) ) )
if not self._can_access_dataset( trans, hda ):
return trans.show_error_message( "You are not allowed to access this dataset" )
@@ -961,19 +964,30 @@ class DatasetInterface( BaseUIController, UsesAnnotations, UsesHistoryMixin, Use
toolbox = self.get_toolbox()
tool = toolbox.get_tool( job.tool_id )
assert tool is not None, 'Requested tool has not been loaded.'
#Load parameter objects, if a parameter type has changed, it's possible for the value to no longer be valid
# Load parameter objects, if a parameter type has changed, it's possible for the value to no longer be valid
try:
params_objects = job.get_param_values( trans.app, ignore_errors=False )
except:
params_objects = job.get_param_values( trans.app, ignore_errors=True )
upgrade_messages = tool.check_and_update_param_values( job.get_param_values( trans.app, ignore_errors=True ), trans, update_values=False ) #use different param_objects here, since we want to display original values as much as possible
# use different param_objects in the following line, since we want to display original values as much as possible
upgrade_messages = tool.check_and_update_param_values( job.get_param_values( trans.app, ignore_errors=True ),
trans,
update_values=False )
has_parameter_errors = True
except:
pass
if job is None:
return trans.show_error_message( "Job information is not available for this dataset." )
#TODO: we should provide the basic values along with the objects, in order to better handle reporting of old values during upgrade
return trans.fill_template( "show_params.mako", inherit_chain=inherit_chain, history=trans.get_history(), hda=hda, job=job, tool=tool, params_objects=params_objects, upgrade_messages=upgrade_messages, has_parameter_errors=has_parameter_errors )
# TODO: we should provide the basic values along with the objects, in order to better handle reporting of old values during upgrade
return trans.fill_template( "show_params.mako",
inherit_chain=inherit_chain,
history=trans.get_history(),
hda=hda,
job=job,
tool=tool,
params_objects=params_objects,
upgrade_messages=upgrade_messages,
has_parameter_errors=has_parameter_errors )
@web.expose
def copy_datasets( self, trans, source_history=None, source_content_ids="", target_history_id=None, target_history_ids="", new_history_name="", do_copy=False, **kwd ):
lib/galaxy/webapps/galaxy/controllers/search.py
+7 -2
View File
@@ -1,4 +1,3 @@
"""
Contains a basic search interface for Galaxy
"""
@@ -8,7 +7,13 @@ from galaxy.web.base.controller import BaseUIController
log = logging.getLogger( __name__ )
class SearchController( BaseUIController ):
@web.expose
def index(self, trans):
return trans.fill_template( "search/index.mako")
"""
Per the message, this is not ready for human consumption, yet. Power
users can still use the search API.
"""
return trans.show_message("Sorry, the search interface isn't quite ready for use, yet. Watch the release notes and check back later!")
static/scripts/galaxy.library.js
+75 -62
View File
@@ -36,7 +36,7 @@ var LibraryRouter = Backbone.Router.extend({
initialize: function() {
this.routesHit = 0;
//keep count of number of routes handled by the application
Backbone.history.on('route', function() { this.routesHit++; }, this);
Backbone.history.on( 'route', function() { this.routesHit++; }, this );
},
routes: {
@@ -45,6 +45,7 @@ routes: {
"library/:library_id/permissions" : "library_permissions",
"folders/:folder_id/permissions" : "folder_permissions",
"folders/:id" : "folder_content",
"folders/:id/page/:show_page" : "folder_page",
"folders/:folder_id/datasets/:dataset_id" : "dataset_detail",
"folders/:folder_id/datasets/:dataset_id/permissions" : "dataset_permissions",
"folders/:folder_id/datasets/:dataset_id/versions/:ldda_id" : "dataset_version",
@@ -53,13 +54,13 @@ routes: {
},
back: function() {
if(this.routesHit > 1) {
if( this.routesHit > 1 ) {
//more than one route hit -> user did not land to current page directly
window.history.back();
} else {
//otherwise go to the home page. Use replaceState if available so
//the navigation doesn't create an extra history entry
this.navigate('#', {trigger:true, replace:true});
this.navigate( '#', { trigger:true, replace:true } );
}
}
});
@@ -71,7 +72,8 @@ var LibraryPrefs = mod_baseMVC.SessionStorageModel.extend({
with_deleted : false,
sort_order : 'asc',
sort_by : 'name',
library_page_size : 20
library_page_size : 20,
folder_page_size : 15
}
});
@@ -94,10 +96,10 @@ var GalaxyLibrary = Backbone.View.extend({
this.library_router = new LibraryRouter();
this.library_router.on('route:libraries', function() {
Galaxy.libraries.libraryToolbarView = new mod_librarytoolbar_view.LibraryToolbarView();
Galaxy.libraries.libraryListView = new mod_librarylist_view.LibraryListView();
});
this.library_router.on( 'route:libraries', function() {
Galaxy.libraries.libraryToolbarView = new mod_librarytoolbar_view.LibraryToolbarView();
Galaxy.libraries.libraryListView = new mod_librarylist_view.LibraryListView();
});
this.library_router.on('route:libraries_page', function( show_page ) {
if ( Galaxy.libraries.libraryToolbarView === null ){
@@ -108,66 +110,77 @@ var GalaxyLibrary = Backbone.View.extend({
}
});
this.library_router.on('route:folder_content', function(id) {
this.library_router.on( 'route:folder_content', function( id ) {
if (Galaxy.libraries.folderToolbarView){
Galaxy.libraries.folderToolbarView.$el.unbind('click');
}
Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView({id: id});
Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView({id: id});
});
Galaxy.libraries.folderToolbarView.$el.unbind( 'click' );
}
Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView( { id: id } );
Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView( { id: id } );
});
this.library_router.on('route:download', function(folder_id, format) {
if ($('#folder_list_body').find(':checked').length === 0) {
mod_toastr.info( 'You must select at least one dataset to download' );
Galaxy.libraries.library_router.navigate('folders/' + folder_id, {trigger: true, replace: true});
} else {
Galaxy.libraries.folderToolbarView.download(folder_id, format);
Galaxy.libraries.library_router.navigate('folders/' + folder_id, {trigger: false, replace: true});
}
});
this.library_router.on( 'route:folder_page', function( id, show_page ) {
if ( Galaxy.libraries.folderToolbarView === null ){
Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView( {id: id} );
Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView( { id: id, show_page: show_page } );
} else {
Galaxy.libraries.folderListView.render( { id: id, show_page: parseInt( show_page ) } )
}
});
this.library_router.on('route:dataset_detail', function(folder_id, dataset_id){
if (Galaxy.libraries.datasetView){
Galaxy.libraries.datasetView.$el.unbind('click');
}
Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id});
});
this.library_router.on('route:dataset_version', function(folder_id, dataset_id, ldda_id){
if (Galaxy.libraries.datasetView){
Galaxy.libraries.datasetView.$el.unbind('click');
}
Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id, ldda_id: ldda_id, show_version: true});
});
this.library_router.on( 'route:download', function( folder_id, format ) {
if ( $( '#folder_list_body' ).find( ':checked' ).length === 0 ) {
mod_toastr.info( 'You must select at least one dataset to download' );
Galaxy.libraries.library_router.navigate( 'folders/' + folder_id, { trigger: true, replace: true } );
} else {
Galaxy.libraries.folderToolbarView.download( folder_id, format );
Galaxy.libraries.library_router.navigate( 'folders/' + folder_id, { trigger: false, replace: true } );
}
});
this.library_router.on('route:dataset_permissions', function(folder_id, dataset_id){
if (Galaxy.libraries.datasetView){
Galaxy.libraries.datasetView.$el.unbind('click');
}
Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id, show_permissions: true});
});
this.library_router.on( 'route:dataset_detail', function(folder_id, dataset_id){
if (Galaxy.libraries.datasetView){
Galaxy.libraries.datasetView.$el.unbind('click');
}
Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id});
});
this.library_router.on('route:library_permissions', function(library_id){
if (Galaxy.libraries.libraryView){
Galaxy.libraries.libraryView.$el.unbind('click');
}
Galaxy.libraries.libraryView = new mod_library_library_view.LibraryView({id: library_id, show_permissions: true});
});
this.library_router.on( 'route:dataset_version', function(folder_id, dataset_id, ldda_id){
if (Galaxy.libraries.datasetView){
Galaxy.libraries.datasetView.$el.unbind('click');
}
Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id, ldda_id: ldda_id, show_version: true});
});
this.library_router.on('route:folder_permissions', function(folder_id){
if (Galaxy.libraries.folderView){
Galaxy.libraries.folderView.$el.unbind('click');
}
Galaxy.libraries.folderView = new mod_library_folder_view.FolderView({id: folder_id, show_permissions: true});
});
this.library_router.on('route:import_datasets', function(folder_id, source){
if (Galaxy.libraries.folderToolbarView && Galaxy.libraries.folderListView){
Galaxy.libraries.folderToolbarView.showImportModal({source:source});
} else {
Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView({id: folder_id});
Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView({id: folder_id});
Galaxy.libraries.folderToolbarView.showImportModal({source: source});
}
});
this.library_router.on( 'route:dataset_permissions', function(folder_id, dataset_id){
if (Galaxy.libraries.datasetView){
Galaxy.libraries.datasetView.$el.unbind('click');
}
Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id, show_permissions: true});
});
this.library_router.on( 'route:library_permissions', function(library_id){
if (Galaxy.libraries.libraryView){
Galaxy.libraries.libraryView.$el.unbind('click');
}
Galaxy.libraries.libraryView = new mod_library_library_view.LibraryView({id: library_id, show_permissions: true});
});
this.library_router.on( 'route:folder_permissions', function(folder_id){
if (Galaxy.libraries.folderView){
Galaxy.libraries.folderView.$el.unbind('click');
}
Galaxy.libraries.folderView = new mod_library_folder_view.FolderView({id: folder_id, show_permissions: true});
});
this.library_router.on( 'route:import_datasets', function( folder_id, source ){
if ( Galaxy.libraries.folderToolbarView && Galaxy.libraries.folderListView ){
Galaxy.libraries.folderToolbarView.showImportModal( { source:source } );
} else {
Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView( { id: folder_id } );
Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView( { id: folder_id } );
Galaxy.libraries.folderToolbarView.showImportModal( { source: source } );
}
});
Backbone.history.start({pushState: false});
}
static/scripts/mvc/library/library-folderlist-view.js
+329 -292
View File
@@ -15,322 +15,359 @@ function(mod_masthead,
) {
var FolderListView = Backbone.View.extend({
el : '#folder_items_element',
defaults: {
'include_deleted' : false
},
// progress percentage
progress: 0,
// progress rate per one item
progressStep: 1,
// self modal
modal : null,
el : '#folder_items_element',
// progress percentage
progress: 0,
// progress rate per one item
progressStep: 1,
folderContainer: null,
folderContainer: null,
sort: 'asc',
sort: 'asc',
events: {
'click #select-all-checkboxes' : 'selectAll',
'click .dataset_row' : 'selectClickedRow',
'click .sort-folder-link' : 'sortColumnClicked'
},
events: {
'click #select-all-checkboxes' : 'selectAll',
'click .dataset_row' : 'selectClickedRow',
'click .sort-folder-link' : 'sortColumnClicked'
},
// cache of rendered views
rowViews: {},
initialize : function(options){
this.options = _.defaults(this.options || {}, options);
this.fetchFolder();
},
collection: null,
fetchFolder: function(options){
var options = options || {};
this.options.include_deleted = options.include_deleted;
var that = this;
defaults: {
include_deleted: false,
page_count: null,
show_page: null
},
this.collection = new mod_library_model.Folder();
/**
* Initialize and fetch the folder from the server.
* @param {object} options an object with options
*/
initialize : function( options ){
this.options = _.defaults( this.options || {}, this.defaults, options );
this.modal = null;
// map of folder item ids to item views = cache
this.rowViews = {};
// start to listen if someone modifies collection
this.listenTo(this.collection, 'add', this.renderOne);
this.listenTo(this.collection, 'remove', this.removeOne);
// create a collection of folder items for this view
this.collection = new mod_library_model.Folder();
this.folderContainer = new mod_library_model.FolderContainer({id: this.options.id});
this.folderContainer.url = this.folderContainer.attributes.urlRoot + this.options.id + '/contents';
if (this.options.include_deleted){
this.folderContainer.url = this.folderContainer.url + '?include_deleted=true';
}
this.folderContainer.fetch({
success: function(folder_container) {
that.folder_container = folder_container;
that.render();
that.addAll(folder_container.get('folder').models);
if (that.options.dataset_id){
row = _.findWhere(that.rowViews, {id: that.options.dataset_id});
if (row) {
// start to listen if someone modifies the collection
this.listenTo( this.collection, 'add', this.renderOne );
this.listenTo( this.collection, 'remove', this.removeOne );
this.fetchFolder();
},
fetchFolder: function( options ){
var options = options || {};
this.options.include_deleted = options.include_deleted;
var that = this;
this.folderContainer = new mod_library_model.FolderContainer( { id: this.options.id } );
this.folderContainer.url = this.folderContainer.attributes.urlRoot + this.options.id + '/contents';
if ( this.options.include_deleted ){
this.folderContainer.url = this.folderContainer.url + '?include_deleted=true';
}
this.folderContainer.fetch({
success: function( folder_container ) {
that.folder_container = folder_container;
that.render();
},
error: function( model, response ){
if ( typeof response.responseJSON !== "undefined" ){
mod_toastr.error( response.responseJSON.err_msg + ' Click this to go back.', '', { onclick: function() { Galaxy.libraries.library_router.back(); } } );
} else {
mod_toastr.error( 'An error ocurred. Click this to go back.', '', { onclick: function() { Galaxy.libraries.library_router.back(); } } );
}
}
});
},
render: function ( options ){
this.options = _.extend( this.options, options );
var template = this.templateFolder();
$(".tooltip").hide();
// find the upper id in the full path
var path = this.folderContainer.attributes.metadata.full_path;
var upper_folder_id;
if ( path.length === 1 ){ // the library is above us
upper_folder_id = 0;
} else {
upper_folder_id = path[ path.length-2 ][ 0 ];
}
this.$el.html( template( {
path: this.folderContainer.attributes.metadata.full_path,
parent_library_id: this.folderContainer.attributes.metadata.parent_library_id,
id: this.options.id,
upper_folder_id: upper_folder_id,
order: this.sort
} ) );
// when dataset_id is present render its details too
if ( this.options.dataset_id ){
row = _.findWhere( that.rowViews, { id: this.options.dataset_id } );
if ( row ) {
row.showDatasetDetails();
} else {
mod_toastr.error('Dataset not found. Showing folder instead.');
mod_toastr.error( 'Requested dataset not found. Showing folder instead.' );
}
}
},
error: function(model, response){
if (typeof response.responseJSON !== "undefined"){
mod_toastr.error(response.responseJSON.err_msg + ' Click this to go back.', '', {onclick: function() {Galaxy.libraries.library_router.back();}});
} else {
mod_toastr.error('An error ocurred. Click this to go back.', '', {onclick: function() {Galaxy.libraries.library_router.back();}});
}
} else {
if ( this.options.show_page === null || this.options.show_page < 1 ){
this.options.show_page = 1;
}
this.paginate();
}
});
},
$("#center [data-toggle]").tooltip();
$("#center").css('overflow','auto');
},
render: function (options) {
this.options = _.defaults(this.options, options);
var template = this.templateFolder();
$(".tooltip").hide();
paginate: function( options ){
this.options = _.extend( this.options, options );
// TODO move to server
// find the upper id in the full path
var path = this.folderContainer.attributes.metadata.full_path;
var upper_folder_id;
if (path.length === 1){ // the library is above us
upper_folder_id = 0;
} else {
upper_folder_id = path[path.length-2][0];
}
if ( this.options.show_page === null || this.options.show_page < 1 ){
this.options.show_page = 1;
}
this.options.total_items_count = this.folder_container.get( 'folder' ).models.length;
this.options.page_count = Math.ceil( this.options.total_items_count / Galaxy.libraries.preferences.get( 'folder_page_size' ) );
var page_start = ( Galaxy.libraries.preferences.get( 'folder_page_size' ) * ( this.options.show_page - 1 ) );
var items_to_render = null;
items_to_render = this.folder_container.get( 'folder' ).models.slice( page_start, page_start + Galaxy.libraries.preferences.get( 'folder_page_size' ) );
this.options.items_shown = items_to_render.length;
// User requests page with no items
if ( Galaxy.libraries.preferences.get( 'folder_page_size' ) * this.options.show_page > ( this.options.total_items_count + Galaxy.libraries.preferences.get( 'folder_page_size' ) ) ){
items_to_render = [];
}
Galaxy.libraries.folderToolbarView.renderPaginator( this.options );
this.collection.reset();
this.addAll( items_to_render )
},
this.$el.html(template({ path: this.folderContainer.attributes.metadata.full_path, parent_library_id: this.folderContainer.attributes.metadata.parent_library_id, id: this.options.id, upper_folder_id: upper_folder_id, order: this.sort}));
/**
* Adds all given models to the collection.
* @param {array of Item or FolderAsModel} array of models that should
* be added to the view's collection.
*/
addAll: function( models ){
_.each(models, function( model ) {
Galaxy.libraries.folderListView.collection.add( model );
});
$( "#center [data-toggle]" ).tooltip();
this.checkEmptiness();
this.postRender();
},
// initialize the library tooltips
$("#center [data-toggle]").tooltip();
//hack to show scrollbars
$("#center").css('overflow','auto');
},
/**
* Call this after all models are added to the collection
* to ensure that the folder toolbar will show proper options
* and that event will be bound on all subviews.
*/
postRender: function(){
var fetched_metadata = this.folderContainer.attributes.metadata;
fetched_metadata.contains_file = typeof this.collection.findWhere({type: 'file'}) !== 'undefined';
Galaxy.libraries.folderToolbarView.configureElements(fetched_metadata);
$('.library-row').hover(function() {
$(this).find('.show_on_hover').show();
}, function () {
$(this).find('.show_on_hover').hide();
});
},
/**
* Call this after all models are added to the collection
* to ensure that the folder toolbar will show proper options
* and that event will be bound on all subviews.
*/
postRender: function(){
var fetched_metadata = this.folderContainer.attributes.metadata;
fetched_metadata.contains_file = typeof this.collection.findWhere({type: 'file'}) !== 'undefined';
Galaxy.libraries.folderToolbarView.configureElements(fetched_metadata);
$('.library-row').hover(function() {
$(this).find('.show_on_hover').show();
}, function () {
$(this).find('.show_on_hover').hide();
});
},
/**
* Iterates this view's collection and calls the render
* function for each. Also binds the hover behavior.
*/
renderAll: function(){
var that = this;
_.each( this.collection.models.reverse(), function( model ) {
that.renderOne( model );
});
this.postRender();
},
/**
* Adds all given models to the collection.
* @param {array of Item or FolderAsModel} array of models that should
* be added to the view's collection.
*/
addAll: function(models){
_.each(models.reverse(), function(model) {
Galaxy.libraries.folderListView.collection.add(model);
});
$("#center [data-toggle]").tooltip();
this.checkEmptiness();
this.postRender();
},
/**
* Iterates this view's collection and calls the render
* function for each. Also binds the hover behavior.
*/
renderAll: function(){
var that = this;
_.each(this.collection.models.reverse(), function(model) {
that.renderOne(model);
});
this.postRender();
},
/**
* Creates a view for the given model and adds it to the folder view.
* @param {Item or FolderAsModel} model of the view that will be rendered
*/
renderOne: function(model){
if (model.get('type') !== 'folder'){
this.options.contains_file = true;
// model.set('readable_size', this.size_to_string(model.get('file_size')));
}
model.set('folder_id', this.id);
var rowView = new mod_library_folderrow_view.FolderRowView(model);
// save new rowView to cache
this.rowViews[model.get('id')] = rowView;
this.$el.find('#first_folder_item').after(rowView.el);
$('.library-row').hover(function() {
$(this).find('.show_on_hover').show();
}, function () {
$(this).find('.show_on_hover').hide();
});
},
/**
* removes the view of the given model from the DOM
* @param {Item or FolderAsModel} model of the view that will be removed
*/
removeOne: function(model){
this.$el.find('#' + model.id).remove();
},
/** Checks whether the list is empty and adds/removes the message */
checkEmptiness : function(){
if ((this.$el.find('.dataset_row').length === 0) && (this.$el.find('.folder_row').length === 0)){
this.$el.find('.empty-folder-message').show();
} else {
this.$el.find('.empty-folder-message').hide();
}
},
/** User clicked the table heading = he wants to sort stuff */
sortColumnClicked : function(event){
event.preventDefault();
if (this.sort === 'asc'){
this.sortFolder('name','desc');
this.sort = 'desc';
} else {
this.sortFolder('name','asc');
this.sort = 'asc';
}
this.render();
this.renderAll();
this.checkEmptiness();
},
/**
* Sorts the underlying collection according to the parameters received.
* Currently supports only sorting by name.
*/
sortFolder: function(sort_by, order){
if (sort_by === 'name'){
if (order === 'asc'){
return this.collection.sortByNameAsc();
} else if (order === 'desc'){
return this.collection.sortByNameDesc();
/**
* Creates a view for the given model and adds it to the folder view.
* @param {Item or FolderAsModel} model of the view that will be rendered
*/
renderOne: function(model){
if (model.get('type') !== 'folder'){
this.options.contains_file = true;
// model.set('readable_size', this.size_to_string(model.get('file_size')));
}
}
},
model.set('folder_id', this.id);
var rowView = new mod_library_folderrow_view.FolderRowView(model);
/**
* User clicked the checkbox in the table heading
* @param {context} event
*/
selectAll : function (event) {
var selected = event.target.checked;
that = this;
// Iterate each checkbox
$(':checkbox', '#folder_list_body').each(function() {
this.checked = selected;
$row = $(this.parentElement.parentElement);
// Change color of selected/unselected
if (selected) {
that.makeDarkRow($row);
} else {
that.makeWhiteRow($row);
}
});
},
// save new rowView to cache
this.rowViews[model.get('id')] = rowView;
/**
* Check checkbox if user clicks on the whole row or
* on the checkbox itself
*/
selectClickedRow : function (event) {
var checkbox = '';
var $row;
var source;
if (event.target.localName === 'input'){
checkbox = event.target;
$row = $(event.target.parentElement.parentElement);
source = 'input';
} else if (event.target.localName === 'td') {
checkbox = $("#" + event.target.parentElement.id).find(':checkbox')[0];
$row = $(event.target.parentElement);
source = 'td';
}
if (checkbox.checked){
if (source==='td'){
checkbox.checked = '';
this.makeWhiteRow($row);
} else if (source==='input') {
this.makeDarkRow($row);
this.$el.find('#first_folder_item').after(rowView.el);
$('.library-row').hover(function() {
$(this).find('.show_on_hover').show();
}, function () {
$(this).find('.show_on_hover').hide();
});
},
/**
* removes the view of the given model from the DOM
* @param {Item or FolderAsModel} model of the view that will be removed
*/
removeOne: function( model ){
this.$el.find( '#' + model.id ).remove();
},
/** Checks whether the list is empty and adds/removes the message */
checkEmptiness : function(){
if ((this.$el.find('.dataset_row').length === 0) && (this.$el.find('.folder_row').length === 0)){
this.$el.find('.empty-folder-message').show();
} else {
this.$el.find('.empty-folder-message').hide();
}
} else {
if (source==='td'){
checkbox.checked = 'selected';
this.makeDarkRow($row);
} else if (source==='input') {
this.makeWhiteRow($row);
},
/** User clicked the table heading = he wants to sort stuff */
sortColumnClicked : function(event){
event.preventDefault();
if (this.sort === 'asc'){
this.sortFolder('name','desc');
this.sort = 'desc';
} else {
this.sortFolder('name','asc');
this.sort = 'asc';
}
this.render();
this.renderAll();
this.checkEmptiness();
},
/**
* Sorts the underlying collection according to the parameters received.
* Currently supports only sorting by name.
*/
sortFolder: function(sort_by, order){
if (sort_by === 'name'){
if (order === 'asc'){
return this.collection.sortByNameAsc();
} else if (order === 'desc'){
return this.collection.sortByNameDesc();
}
}
},
/**
* User clicked the checkbox in the table heading
* @param {context} event
*/
selectAll : function (event) {
var selected = event.target.checked;
that = this;
// Iterate each checkbox
$(':checkbox', '#folder_list_body').each(function() {
this.checked = selected;
$row = $(this.parentElement.parentElement);
// Change color of selected/unselected
if (selected) {
that.makeDarkRow($row);
} else {
that.makeWhiteRow($row);
}
});
},
/**
* Check checkbox if user clicks on the whole row or
* on the checkbox itself
*/
selectClickedRow : function (event) {
var checkbox = '';
var $row;
var source;
if (event.target.localName === 'input'){
checkbox = event.target;
$row = $(event.target.parentElement.parentElement);
source = 'input';
} else if (event.target.localName === 'td') {
checkbox = $("#" + event.target.parentElement.id).find(':checkbox')[0];
$row = $(event.target.parentElement);
source = 'td';
}
if (checkbox.checked){
if (source==='td'){
checkbox.checked = '';
this.makeWhiteRow($row);
} else if (source==='input') {
this.makeDarkRow($row);
}
} else {
if (source==='td'){
checkbox.checked = 'selected';
this.makeDarkRow($row);
} else if (source==='input') {
this.makeWhiteRow($row);
}
}
},
makeDarkRow: function($row){
$row.removeClass('light').addClass('dark');
$row.find('a').removeClass('light').addClass('dark');
$row.find('.fa-file-o').removeClass('fa-file-o').addClass('fa-file');
},
makeWhiteRow: function($row){
$row.removeClass('dark').addClass('light');
$row.find('a').removeClass('dark').addClass('light');
$row.find('.fa-file').removeClass('fa-file').addClass('fa-file-o');
},
templateFolder : function (){
var tmpl_array = [];
// BREADCRUMBS
tmpl_array.push('<ol class="breadcrumb">');
tmpl_array.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');
tmpl_array.push(' <% _.each(path, function(path_item) { %>');
tmpl_array.push(' <% if (path_item[0] != id) { %>');
tmpl_array.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a> </li> ');
tmpl_array.push( '<% } else { %>');
tmpl_array.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>');
tmpl_array.push(' <% } %>');
tmpl_array.push(' <% }); %>');
tmpl_array.push('</ol>');
// FOLDER CONTENT
tmpl_array.push('<table data-library-id="<%- parent_library_id %>" id="folder_table" class="grid table table-condensed">');
tmpl_array.push(' <thead>');
tmpl_array.push(' <th class="button_heading"></th>');
tmpl_array.push(' <th style="text-align: center; width: 20px; " title="Check to select all datasets"><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');
tmpl_array.push(' <th><a class="sort-folder-link" title="Click to reverse order" href="#">name</a> <span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');
tmpl_array.push(' <th style="width:5%;">data type</th>');
tmpl_array.push(' <th style="width:10%;">size</th>');
tmpl_array.push(' <th style="width:160px;">time updated (UTC)</th>');
tmpl_array.push(' <th style="width:10%;"></th> ');
tmpl_array.push(' </thead>');
tmpl_array.push(' <tbody id="folder_list_body">');
tmpl_array.push(' <tr id="first_folder_item">');
tmpl_array.push(' <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>');
tmpl_array.push(' <td></td>');
tmpl_array.push(' <td></td>');
tmpl_array.push(' <td></td>');
tmpl_array.push(' <td></td>');
tmpl_array.push(' <td></td>');
tmpl_array.push(' <td></td>');
tmpl_array.push(' </tr>');
tmpl_array.push(' </tbody>');
tmpl_array.push('</table>');
tmpl_array.push('<div class="empty-folder-message" style="display:none;">This folder is either empty or you do not have proper access permissions to see the contents. If you expected something to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity" target="_blank">library security wikipage</a> or visit the <a href="https://biostar.usegalaxy.org/" target="_blank">Galaxy support site</a>.</div>');
return _.template(tmpl_array.join(''));
}
},
makeDarkRow: function($row){
$row.removeClass('light').addClass('dark');
$row.find('a').removeClass('light').addClass('dark');
$row.find('.fa-file-o').removeClass('fa-file-o').addClass('fa-file');
},
makeWhiteRow: function($row){
$row.removeClass('dark').addClass('light');
$row.find('a').removeClass('dark').addClass('light');
$row.find('.fa-file').removeClass('fa-file').addClass('fa-file-o');
},
templateFolder : function (){
var tmpl_array = [];
// BREADCRUMBS
tmpl_array.push('<ol class="breadcrumb">');
tmpl_array.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');
tmpl_array.push(' <% _.each(path, function(path_item) { %>');
tmpl_array.push(' <% if (path_item[0] != id) { %>');
tmpl_array.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a> </li> ');
tmpl_array.push( '<% } else { %>');
tmpl_array.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>');
tmpl_array.push(' <% } %>');
tmpl_array.push(' <% }); %>');
tmpl_array.push('</ol>');
// FOLDER CONTENT
tmpl_array.push('<table data-library-id="<%- parent_library_id %>" id="folder_table" class="grid table table-condensed">');
tmpl_array.push(' <thead>');
tmpl_array.push(' <th class="button_heading"></th>');
tmpl_array.push(' <th style="text-align: center; width: 20px; " title="Check to select all datasets"><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');
tmpl_array.push(' <th><a class="sort-folder-link" title="Click to reverse order" href="#">name</a> <span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');
tmpl_array.push(' <th style="width:5%;">data type</th>');
tmpl_array.push(' <th style="width:10%;">size</th>');
tmpl_array.push(' <th style="width:160px;">time updated (UTC)</th>');
tmpl_array.push(' <th style="width:10%;"></th> ');
tmpl_array.push(' </thead>');
tmpl_array.push(' <tbody id="folder_list_body">');
tmpl_array.push(' <tr id="first_folder_item">');
tmpl_array.push(' <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>');
tmpl_array.push(' <td></td>');
tmpl_array.push(' <td></td>');
tmpl_array.push(' <td></td>');
tmpl_array.push(' <td></td>');
tmpl_array.push(' <td></td>');
tmpl_array.push(' <td></td>');
tmpl_array.push(' </tr>');
tmpl_array.push(' </tbody>');
tmpl_array.push('</table>');
tmpl_array.push('<div class="empty-folder-message" style="display:none;">This folder is either empty or you do not have proper access permissions to see the contents. If you expected something to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity" target="_blank">library security wikipage</a> or visit the <a href="https://biostar.usegalaxy.org/" target="_blank">Galaxy support site</a>.</div>');
return _.template(tmpl_array.join(''));
}
});
return {
static/scripts/mvc/library/library-foldertoolbar-view.js
+69 -6
View File
@@ -20,7 +20,9 @@ var FolderToolbarView = Backbone.View.extend({
'click #toolbtn_bulk_import' : 'modalBulkImport',
'click #include_deleted_datasets_chk' : 'checkIncludeDeleted',
'click #toolbtn_show_libinfo' : 'showLibInfo',
'click #toolbtn_bulk_delete' : 'deleteSelectedDatasets'
'click #toolbtn_bulk_delete' : 'deleteSelectedDatasets',
'click #page_size_prompt' : 'showPageSizePrompt'
},
defaults: {
@@ -90,6 +92,22 @@ var FolderToolbarView = Backbone.View.extend({
this.$el.html(toolbar_template(template_defaults));
},
/**
* Called from FolderListView when needed.
* @param {object} options common options
*/
renderPaginator: function( options ){
this.options = _.extend( this.options, options );
var paginator_template = this.templatePaginator();
this.$el.find( '#folder_paginator' ).html( paginator_template({
id: this.options.id,
show_page: parseInt( this.options.show_page ),
page_count: parseInt( this.options.page_count ),
total_items_count: this.options.total_items_count,
items_shown: this.options.items_shown
}));
},
configureElements: function(options){
this.options = _.extend(this.options, options);
@@ -833,11 +851,11 @@ var FolderToolbarView = Backbone.View.extend({
var popped_item = lddas_set.pop();
if ( typeof popped_item === "undefined" ) {
if ( this.options.chain_call_control.failed_number === 0 ){
mod_toastr.success( 'Selected datasets deleted' );
mod_toastr.success( 'Selected datasets were deleted.' );
} else if ( this.options.chain_call_control.failed_number === this.options.chain_call_control.total_number ){
mod_toastr.error( 'There was an error and no datasets were deleted.' );
mod_toastr.error( 'There was an error and no datasets were deleted. Please make sure you have sufficient permissions.' );
} else if ( this.options.chain_call_control.failed_number < this.options.chain_call_control.total_number ){
mod_toastr.warning( 'Some of the datasets could not be deleted' );
mod_toastr.warning( 'Some of the datasets could not be deleted. Please make sure you have sufficient permissions.' );
}
Galaxy.modal.hide();
return this.deleted_lddas;
@@ -976,6 +994,14 @@ var FolderToolbarView = Backbone.View.extend({
}
},
showPageSizePrompt: function(){
var folder_page_size = prompt( 'How many items per page do you want to see?', Galaxy.libraries.preferences.get( 'folder_page_size' ) );
if ( ( folder_page_size != null ) && ( folder_page_size == parseInt( folder_page_size ) ) ) {
Galaxy.libraries.preferences.set( { 'folder_page_size': parseInt( folder_page_size ) } );
Galaxy.libraries.folderListView.render( { id: this.options.id, show_page: 1 } );
}
},
templateToolBar: function(){
tmpl_array = [];
@@ -1016,7 +1042,6 @@ var FolderToolbarView = Backbone.View.extend({
tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button add-library-items" type="button"><span class="fa fa-plus"></span> <span class="fa fa-file"></span></span></button>');
tmpl_array.push('<% } %>');
tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to History</button>');
tmpl_array.push(' <div id="toolbtn_dl" class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">');
tmpl_array.push(' <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');
@@ -1032,6 +1057,10 @@ var FolderToolbarView = Backbone.View.extend({
tmpl_array.push(' <button data-id="<%- id %>" data-toggle="tooltip" data-placement="top" title="Show library information" id="toolbtn_show_libinfo" class="primary-button" style="margin-left: 0.5em;" type="button"><span class="fa fa-info-circle"></span> Library Info</button>');
tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/FolderContents" target="_blank"><button class="primary-button" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>');
tmpl_array.push(' <span id="folder_paginator" class="library-paginator">');
// paginator will append here
tmpl_array.push(' </span>');
tmpl_array.push(' </div>');
// TOOLBAR END
tmpl_array.push(' <div id="folder_items_element">');
@@ -1239,7 +1268,41 @@ var FolderToolbarView = Backbone.View.extend({
tmpl_array.push('</ul>');
return _.template(tmpl_array.join(''));
}
},
templatePaginator: function(){
tmpl_array = [];
tmpl_array.push(' <ul class="pagination pagination-sm">');
tmpl_array.push(' <% if ( ( show_page - 1 ) > 0 ) { %>');
tmpl_array.push(' <% if ( ( show_page - 1 ) > page_count ) { %>'); // we are on higher page than total page count
tmpl_array.push(' <li><a href="#folders/<%= id %>/page/1"><span class="fa fa-angle-double-left"></span></a></li>');
tmpl_array.push(' <li class="disabled"><a href="#folders/<%= id %>/page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>');
tmpl_array.push(' <% } else { %>');
tmpl_array.push(' <li><a href="#folders/<%= id %>/page/1"><span class="fa fa-angle-double-left"></span></a></li>');
tmpl_array.push(' <li><a href="#folders/<%= id %>/page/<% print( show_page - 1 ) %>"><% print( show_page - 1 ) %></a></li>');
tmpl_array.push(' <% } %>');
tmpl_array.push(' <% } else { %>'); // we are on the first page
tmpl_array.push(' <li class="disabled"><a href="#folders/<%= id %>/page/1"><span class="fa fa-angle-double-left"></span></a></li>');
tmpl_array.push(' <li class="disabled"><a href="#folders/<%= id %>/page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>');
tmpl_array.push(' <% } %>');
tmpl_array.push(' <li class="active">');
tmpl_array.push(' <a href="#folders/<%= id %>/page/<% print( show_page ) %>"><% print( show_page ) %></a>');
tmpl_array.push(' </li>');
tmpl_array.push(' <% if ( ( show_page ) < page_count ) { %>');
tmpl_array.push(' <li><a href="#folders/<%= id %>/page/<% print( show_page + 1 ) %>"><% print( show_page + 1 ) %></a></li>');
tmpl_array.push(' <li><a href="#folders/<%= id %>/page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>');
tmpl_array.push(' <% } else { %>');
tmpl_array.push(' <li class="disabled"><a href="#folders/<%= id %>/page/<% print( show_page ) %>"><% print( show_page + 1 ) %></a></li>');
tmpl_array.push(' <li class="disabled"><a href="#folders/<%= id %>/page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>');
tmpl_array.push(' <% } %>');
tmpl_array.push(' </ul>');
tmpl_array.push(' <span>');
tmpl_array.push(' showing <a data-toggle="tooltip" data-placement="top" title="Click to change the number of items on page" id="page_size_prompt"><%- items_shown %></a> of <%- total_items_count %> items');
tmpl_array.push(' </span>');
return _.template(tmpl_array.join(''));
},
});
static/scripts/mvc/library/library-librarylist-view.js
+11 -17
View File
@@ -21,20 +21,19 @@ var LibraryListView = Backbone.View.extend({
'click .sort-libraries-link' : 'sort_clicked'
},
/**
* Initialize and fetch the libraries from server.
* Async render afterwards.
* @param {object} options an options object
*/
defaults: {
page_count: null,
show_page: null
},
/**
* Initialize and fetch the libraries from server.
* Async render afterwards.
* @param {object} options an object with options
*/
initialize : function( options ){
this.options = _.defaults( this.options || {}, this.defaults, options );
var that = this;
var that = this;
this.modal = null;
// map of library model ids to library views = cache
this.rowViews = {};
@@ -61,19 +60,10 @@ var LibraryListView = Backbone.View.extend({
*/
render: function ( options ) {
this.options = _.extend( this.options, options );
if ( ( this.options.page_size != null ) && ( this.options.page_size == parseInt( this.options.page_size ) ) ) {
Galaxy.libraries.preferences.set( { 'library_page_size': parseInt( this.options.page_size ) } );
}
$( ".tooltip" ).hide();
// this.options.show_page = this.options.show_page || 1;
var template = this.templateLibraryList();
var libraries_to_render = null;
var models = null;
if ( this.options.show_page === null || this.options.show_page < 1 ){
this.options.show_page = 1;
}
$( ".tooltip" ).hide();
if ( typeof options !== 'undefined' ){
models = typeof options.models !== 'undefined' ? options.models : null;
}
@@ -89,6 +79,10 @@ var LibraryListView = Backbone.View.extend({
} else {
libraries_to_render = [];
}
// pagination
if ( this.options.show_page === null || this.options.show_page < 1 ){
this.options.show_page = 1;
}
this.options.total_libraries_count = libraries_to_render.length
var page_start = ( Galaxy.libraries.preferences.get( 'library_page_size' ) * ( this.options.show_page - 1 ) );
this.options.page_count = Math.ceil( this.options.total_libraries_count / Galaxy.libraries.preferences.get( 'library_page_size' ) );
static/scripts/mvc/tools/tools-tree.js
+1 -1
View File
@@ -126,7 +126,7 @@ return Backbone.Model.extend({
// handle default value
if (!field.skip) {
if (input.optional && field.validate && !field.validate()) {
value = 'None';
value = null;
}
add (job_input_id, input.id, value);
}
static/scripts/packed/galaxy.library.js
+1 -1
View File
@@ -1 +1 @@
define(["galaxy.masthead","utils/utils","libs/toastr","mvc/base-mvc","mvc/library/library-model","mvc/library/library-folderlist-view","mvc/library/library-librarylist-view","mvc/library/library-librarytoolbar-view","mvc/library/library-foldertoolbar-view","mvc/library/library-dataset-view","mvc/library/library-library-view","mvc/library/library-folder-view"],function(h,e,j,n,k,c,i,g,l,f,b,a){var o=Backbone.Router.extend({initialize:function(){this.routesHit=0;Backbone.history.on("route",function(){this.routesHit++},this)},routes:{"":"libraries","page/:show_page":"libraries_page","library/:library_id/permissions":"library_permissions","folders/:folder_id/permissions":"folder_permissions","folders/:id":"folder_content","folders/:folder_id/datasets/:dataset_id":"dataset_detail","folders/:folder_id/datasets/:dataset_id/permissions":"dataset_permissions","folders/:folder_id/datasets/:dataset_id/versions/:ldda_id":"dataset_version","folders/:folder_id/download/:format":"download","folders/:folder_id/import/:source":"import_datasets"},back:function(){if(this.routesHit>1){window.history.back()}else{this.navigate("#",{trigger:true,replace:true})}}});var m=n.SessionStorageModel.extend({defaults:{with_deleted:false,sort_order:"asc",sort_by:"name",library_page_size:20}});var d=Backbone.View.extend({libraryToolbarView:null,libraryListView:null,library_router:null,libraryView:null,folderToolbarView:null,folderListView:null,datasetView:null,initialize:function(){Galaxy.libraries=this;this.preferences=new m({id:"global-lib-prefs"});this.library_router=new o();this.library_router.on("route:libraries",function(){Galaxy.libraries.libraryToolbarView=new g.LibraryToolbarView();Galaxy.libraries.libraryListView=new i.LibraryListView()});this.library_router.on("route:libraries_page",function(p){if(Galaxy.libraries.libraryToolbarView===null){Galaxy.libraries.libraryToolbarView=new g.LibraryToolbarView();Galaxy.libraries.libraryListView=new i.LibraryListView({show_page:p})}else{Galaxy.libraries.libraryListView.render({show_page:p})}});this.library_router.on("route:folder_content",function(p){if(Galaxy.libraries.folderToolbarView){Galaxy.libraries.folderToolbarView.$el.unbind("click")}Galaxy.libraries.folderToolbarView=new l.FolderToolbarView({id:p});Galaxy.libraries.folderListView=new c.FolderListView({id:p})});this.library_router.on("route:download",function(p,q){if($("#folder_list_body").find(":checked").length===0){j.info("You must select at least one dataset to download");Galaxy.libraries.library_router.navigate("folders/"+p,{trigger:true,replace:true})}else{Galaxy.libraries.folderToolbarView.download(p,q);Galaxy.libraries.library_router.navigate("folders/"+p,{trigger:false,replace:true})}});this.library_router.on("route:dataset_detail",function(q,p){if(Galaxy.libraries.datasetView){Galaxy.libraries.datasetView.$el.unbind("click")}Galaxy.libraries.datasetView=new f.LibraryDatasetView({id:p})});this.library_router.on("route:dataset_version",function(q,p,r){if(Galaxy.libraries.datasetView){Galaxy.libraries.datasetView.$el.unbind("click")}Galaxy.libraries.datasetView=new f.LibraryDatasetView({id:p,ldda_id:r,show_version:true})});this.library_router.on("route:dataset_permissions",function(q,p){if(Galaxy.libraries.datasetView){Galaxy.libraries.datasetView.$el.unbind("click")}Galaxy.libraries.datasetView=new f.LibraryDatasetView({id:p,show_permissions:true})});this.library_router.on("route:library_permissions",function(p){if(Galaxy.libraries.libraryView){Galaxy.libraries.libraryView.$el.unbind("click")}Galaxy.libraries.libraryView=new b.LibraryView({id:p,show_permissions:true})});this.library_router.on("route:folder_permissions",function(p){if(Galaxy.libraries.folderView){Galaxy.libraries.folderView.$el.unbind("click")}Galaxy.libraries.folderView=new a.FolderView({id:p,show_permissions:true})});this.library_router.on("route:import_datasets",function(p,q){if(Galaxy.libraries.folderToolbarView&&Galaxy.libraries.folderListView){Galaxy.libraries.folderToolbarView.showImportModal({source:q})}else{Galaxy.libraries.folderToolbarView=new l.FolderToolbarView({id:p});Galaxy.libraries.folderListView=new c.FolderListView({id:p});Galaxy.libraries.folderToolbarView.showImportModal({source:q})}});Backbone.history.start({pushState:false})}});return{GalaxyApp:d}});
define(["galaxy.masthead","utils/utils","libs/toastr","mvc/base-mvc","mvc/library/library-model","mvc/library/library-folderlist-view","mvc/library/library-librarylist-view","mvc/library/library-librarytoolbar-view","mvc/library/library-foldertoolbar-view","mvc/library/library-dataset-view","mvc/library/library-library-view","mvc/library/library-folder-view"],function(h,e,j,n,k,c,i,g,l,f,b,a){var o=Backbone.Router.extend({initialize:function(){this.routesHit=0;Backbone.history.on("route",function(){this.routesHit++},this)},routes:{"":"libraries","page/:show_page":"libraries_page","library/:library_id/permissions":"library_permissions","folders/:folder_id/permissions":"folder_permissions","folders/:id":"folder_content","folders/:id/page/:show_page":"folder_page","folders/:folder_id/datasets/:dataset_id":"dataset_detail","folders/:folder_id/datasets/:dataset_id/permissions":"dataset_permissions","folders/:folder_id/datasets/:dataset_id/versions/:ldda_id":"dataset_version","folders/:folder_id/download/:format":"download","folders/:folder_id/import/:source":"import_datasets"},back:function(){if(this.routesHit>1){window.history.back()}else{this.navigate("#",{trigger:true,replace:true})}}});var m=n.SessionStorageModel.extend({defaults:{with_deleted:false,sort_order:"asc",sort_by:"name",library_page_size:20,folder_page_size:15}});var d=Backbone.View.extend({libraryToolbarView:null,libraryListView:null,library_router:null,libraryView:null,folderToolbarView:null,folderListView:null,datasetView:null,initialize:function(){Galaxy.libraries=this;this.preferences=new m({id:"global-lib-prefs"});this.library_router=new o();this.library_router.on("route:libraries",function(){Galaxy.libraries.libraryToolbarView=new g.LibraryToolbarView();Galaxy.libraries.libraryListView=new i.LibraryListView()});this.library_router.on("route:libraries_page",function(p){if(Galaxy.libraries.libraryToolbarView===null){Galaxy.libraries.libraryToolbarView=new g.LibraryToolbarView();Galaxy.libraries.libraryListView=new i.LibraryListView({show_page:p})}else{Galaxy.libraries.libraryListView.render({show_page:p})}});this.library_router.on("route:folder_content",function(p){if(Galaxy.libraries.folderToolbarView){Galaxy.libraries.folderToolbarView.$el.unbind("click")}Galaxy.libraries.folderToolbarView=new l.FolderToolbarView({id:p});Galaxy.libraries.folderListView=new c.FolderListView({id:p})});this.library_router.on("route:folder_page",function(q,p){if(Galaxy.libraries.folderToolbarView===null){Galaxy.libraries.folderToolbarView=new l.FolderToolbarView({id:q});Galaxy.libraries.folderListView=new c.FolderListView({id:q,show_page:p})}else{Galaxy.libraries.folderListView.render({id:q,show_page:parseInt(p)})}});this.library_router.on("route:download",function(p,q){if($("#folder_list_body").find(":checked").length===0){j.info("You must select at least one dataset to download");Galaxy.libraries.library_router.navigate("folders/"+p,{trigger:true,replace:true})}else{Galaxy.libraries.folderToolbarView.download(p,q);Galaxy.libraries.library_router.navigate("folders/"+p,{trigger:false,replace:true})}});this.library_router.on("route:dataset_detail",function(q,p){if(Galaxy.libraries.datasetView){Galaxy.libraries.datasetView.$el.unbind("click")}Galaxy.libraries.datasetView=new f.LibraryDatasetView({id:p})});this.library_router.on("route:dataset_version",function(q,p,r){if(Galaxy.libraries.datasetView){Galaxy.libraries.datasetView.$el.unbind("click")}Galaxy.libraries.datasetView=new f.LibraryDatasetView({id:p,ldda_id:r,show_version:true})});this.library_router.on("route:dataset_permissions",function(q,p){if(Galaxy.libraries.datasetView){Galaxy.libraries.datasetView.$el.unbind("click")}Galaxy.libraries.datasetView=new f.LibraryDatasetView({id:p,show_permissions:true})});this.library_router.on("route:library_permissions",function(p){if(Galaxy.libraries.libraryView){Galaxy.libraries.libraryView.$el.unbind("click")}Galaxy.libraries.libraryView=new b.LibraryView({id:p,show_permissions:true})});this.library_router.on("route:folder_permissions",function(p){if(Galaxy.libraries.folderView){Galaxy.libraries.folderView.$el.unbind("click")}Galaxy.libraries.folderView=new a.FolderView({id:p,show_permissions:true})});this.library_router.on("route:import_datasets",function(p,q){if(Galaxy.libraries.folderToolbarView&&Galaxy.libraries.folderListView){Galaxy.libraries.folderToolbarView.showImportModal({source:q})}else{Galaxy.libraries.folderToolbarView=new l.FolderToolbarView({id:p});Galaxy.libraries.folderListView=new c.FolderListView({id:p});Galaxy.libraries.folderToolbarView.showImportModal({source:q})}});Backbone.history.start({pushState:false})}});return{GalaxyApp:d}});
static/scripts/packed/mvc/library/library-folderlist-view.js
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static/scripts/packed/mvc/library/library-foldertoolbar-view.js
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static/scripts/packed/mvc/library/library-librarylist-view.js
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define(["galaxy.masthead","mvc/base-mvc","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-libraryrow-view"],function(b,g,d,e,c,a){var f=Backbone.View.extend({el:"#libraries_element",events:{"click .sort-libraries-link":"sort_clicked"},defaults:{page_count:null,show_page:null},initialize:function(h){this.options=_.defaults(this.options||{},this.defaults,h);var i=this;this.modal=null;this.rowViews={};this.collection=new c.Libraries();this.collection.fetch({success:function(){i.render()},error:function(k,j){if(typeof j.responseJSON!=="undefined"){e.error(j.responseJSON.err_msg)}else{e.error("An error ocurred.")}}})},render:function(i){this.options=_.extend(this.options,i);if((this.options.page_size!=null)&&(this.options.page_size==parseInt(this.options.page_size))){Galaxy.libraries.preferences.set({library_page_size:parseInt(this.options.page_size)})}$(".tooltip").hide();var j=this.templateLibraryList();var k=null;var l=null;if(this.options.show_page===null||this.options.show_page<1){this.options.show_page=1}if(typeof i!=="undefined"){l=typeof i.models!=="undefined"?i.models:null}if(this.collection!==null&&l===null){this.sortLibraries();if(Galaxy.libraries.preferences.get("with_deleted")){k=this.collection.models}else{k=this.collection.where({deleted:false})}}else{if(l!==null){k=l}else{k=[]}}this.options.total_libraries_count=k.length;var h=(Galaxy.libraries.preferences.get("library_page_size")*(this.options.show_page-1));this.options.page_count=Math.ceil(this.options.total_libraries_count/Galaxy.libraries.preferences.get("library_page_size"));if(this.options.total_libraries_count>0&&(h<this.options.total_libraries_count)){k=k.slice(h,h+Galaxy.libraries.preferences.get("library_page_size"));this.options.libraries_shown=k.length;if(Galaxy.libraries.preferences.get("library_page_size")*this.options.show_page>(this.options.total_libraries_count+Galaxy.libraries.preferences.get("library_page_size"))){k=[]}this.$el.html(j({length:1,order:Galaxy.libraries.preferences.get("sort_order")}));Galaxy.libraries.libraryToolbarView.renderPaginator(this.options);this.renderRows(k)}else{this.$el.html(j({length:0,order:Galaxy.libraries.preferences.get("sort_order")}));Galaxy.libraries.libraryToolbarView.renderPaginator(this.options)}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},renderRows:function(l){for(var k=0;k<l.length;k++){var j=l[k];var h=_.findWhere(this.rowViews,{id:j.get("id")});if(h!==undefined&&this instanceof Backbone.View){h.delegateEvents();this.$el.find("#library_list_body").append(h.el)}else{this.renderOne({library:j})}}},renderOne:function(j){var i=j.library;var h=new a.LibraryRowView(i);this.$el.find("#library_list_body").append(h.el);this.rowViews[i.get("id")]=h},sort_clicked:function(){if(Galaxy.libraries.preferences.get("sort_order")==="asc"){Galaxy.libraries.preferences.set({sort_order:"desc"})}else{Galaxy.libraries.preferences.set({sort_order:"asc"})}this.render()},sortLibraries:function(){if(Galaxy.libraries.preferences.get("sort_by")==="name"){if(Galaxy.libraries.preferences.get("sort_order")==="asc"){this.collection.sortByNameAsc()}else{if(Galaxy.libraries.preferences.get("sort_order")==="desc"){this.collection.sortByNameDesc()}}}},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},templateLibraryList:function(){tmpl_array=[];tmpl_array.push('<div class="library_container table-responsive">');tmpl_array.push("<% if(length === 0) { %>");tmpl_array.push('<div>There are no libraries visible to you here. If you expected some to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity" target="_blank">library security wikipage</a> or visit the <a href="https://biostar.usegalaxy.org/" target="_blank">Galaxy support site</a>.</div>');tmpl_array.push("<% } else{ %>");tmpl_array.push('<table class="grid table table-condensed">');tmpl_array.push(" <thead>");tmpl_array.push(' <th style="width:30%;"><a class="sort-libraries-link" title="Click to reverse order" href="#">name</a> <span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');tmpl_array.push(' <th style="width:22%;">description</th>');tmpl_array.push(' <th style="width:22%;">synopsis</th> ');tmpl_array.push(' <th style="width:26%;"></th>');tmpl_array.push(" </thead>");tmpl_array.push(' <tbody id="library_list_body">');tmpl_array.push(" </tbody>");tmpl_array.push("</table>");tmpl_array.push("<% }%>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},});return{LibraryListView:f}});
define(["galaxy.masthead","mvc/base-mvc","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-libraryrow-view"],function(b,g,d,e,c,a){var f=Backbone.View.extend({el:"#libraries_element",events:{"click .sort-libraries-link":"sort_clicked"},defaults:{page_count:null,show_page:null},initialize:function(h){this.options=_.defaults(this.options||{},this.defaults,h);var i=this;this.modal=null;this.rowViews={};this.collection=new c.Libraries();this.collection.fetch({success:function(){i.render()},error:function(k,j){if(typeof j.responseJSON!=="undefined"){e.error(j.responseJSON.err_msg)}else{e.error("An error ocurred.")}}})},render:function(i){this.options=_.extend(this.options,i);var j=this.templateLibraryList();var k=null;var l=null;$(".tooltip").hide();if(typeof i!=="undefined"){l=typeof i.models!=="undefined"?i.models:null}if(this.collection!==null&&l===null){this.sortLibraries();if(Galaxy.libraries.preferences.get("with_deleted")){k=this.collection.models}else{k=this.collection.where({deleted:false})}}else{if(l!==null){k=l}else{k=[]}}if(this.options.show_page===null||this.options.show_page<1){this.options.show_page=1}this.options.total_libraries_count=k.length;var h=(Galaxy.libraries.preferences.get("library_page_size")*(this.options.show_page-1));this.options.page_count=Math.ceil(this.options.total_libraries_count/Galaxy.libraries.preferences.get("library_page_size"));if(this.options.total_libraries_count>0&&(h<this.options.total_libraries_count)){k=k.slice(h,h+Galaxy.libraries.preferences.get("library_page_size"));this.options.libraries_shown=k.length;if(Galaxy.libraries.preferences.get("library_page_size")*this.options.show_page>(this.options.total_libraries_count+Galaxy.libraries.preferences.get("library_page_size"))){k=[]}this.$el.html(j({length:1,order:Galaxy.libraries.preferences.get("sort_order")}));Galaxy.libraries.libraryToolbarView.renderPaginator(this.options);this.renderRows(k)}else{this.$el.html(j({length:0,order:Galaxy.libraries.preferences.get("sort_order")}));Galaxy.libraries.libraryToolbarView.renderPaginator(this.options)}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},renderRows:function(l){for(var k=0;k<l.length;k++){var j=l[k];var h=_.findWhere(this.rowViews,{id:j.get("id")});if(h!==undefined&&this instanceof Backbone.View){h.delegateEvents();this.$el.find("#library_list_body").append(h.el)}else{this.renderOne({library:j})}}},renderOne:function(j){var i=j.library;var h=new a.LibraryRowView(i);this.$el.find("#library_list_body").append(h.el);this.rowViews[i.get("id")]=h},sort_clicked:function(){if(Galaxy.libraries.preferences.get("sort_order")==="asc"){Galaxy.libraries.preferences.set({sort_order:"desc"})}else{Galaxy.libraries.preferences.set({sort_order:"asc"})}this.render()},sortLibraries:function(){if(Galaxy.libraries.preferences.get("sort_by")==="name"){if(Galaxy.libraries.preferences.get("sort_order")==="asc"){this.collection.sortByNameAsc()}else{if(Galaxy.libraries.preferences.get("sort_order")==="desc"){this.collection.sortByNameDesc()}}}},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},templateLibraryList:function(){tmpl_array=[];tmpl_array.push('<div class="library_container table-responsive">');tmpl_array.push("<% if(length === 0) { %>");tmpl_array.push('<div>There are no libraries visible to you here. If you expected some to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity" target="_blank">library security wikipage</a> or visit the <a href="https://biostar.usegalaxy.org/" target="_blank">Galaxy support site</a>.</div>');tmpl_array.push("<% } else{ %>");tmpl_array.push('<table class="grid table table-condensed">');tmpl_array.push(" <thead>");tmpl_array.push(' <th style="width:30%;"><a class="sort-libraries-link" title="Click to reverse order" href="#">name</a> <span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');tmpl_array.push(' <th style="width:22%;">description</th>');tmpl_array.push(' <th style="width:22%;">synopsis</th> ');tmpl_array.push(' <th style="width:26%;"></th>');tmpl_array.push(" </thead>");tmpl_array.push(' <tbody id="library_list_body">');tmpl_array.push(" </tbody>");tmpl_array.push("</table>");tmpl_array.push("<% }%>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},});return{LibraryListView:f}});
static/scripts/packed/mvc/tools/tools-tree.js
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@@ -1 +1 @@
define([],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},refresh:function(){this.dict={};this.xml=$("<div/>");if(!this.app.section){return{}}this._iterate(this.app.section.$el,this.dict,this.xml)},finalize:function(d){d=d||{};var a=this;this.job_def={};this.job_ids={};function c(g,f,e){a.job_def[g]=e;a.job_ids[g]=f}function b(l,o){for(var j in o){var g=o[j];if(g.input){var q=g.input;var k=l;if(l!=""){k+="|"}k+=q.name;switch(q.type){case"repeat":var f="section-";var t=[];var n=null;for(var s in g){var m=s.indexOf(f);if(m!=-1){m+=f.length;t.push(parseInt(s.substr(m)));if(!n){n=s.substr(0,m)}}}t.sort(function(u,i){return u-i});var j=0;for(var h in t){b(k+"_"+j++,g[n+t[h]])}break;case"conditional":var r=a.app.field_list[q.id].value();if(d[q.test_param.type]){r=d[q.test_param.type](r)}c(k+"|"+q.test_param.name,q.id,r);var e=a.matchCase(q,r);if(e!=-1){b(k,o[q.id+"-section-"+e])}break;default:var p=a.app.field_list[q.id];var r=p.value();if(d[q.type]){r=d[q.type](r)}if(!p.skip){if(q.optional&&p.validate&&!p.validate()){r="None"}c(k,q.id,r)}}}}}b("",this.dict);return this.job_def},match:function(a){return this.job_ids&&this.job_ids[a]},matchCase:function(a,c){if(a.test_param.type=="boolean"){if(c=="true"){c=a.test_param.truevalue||"true"}else{c=a.test_param.falsevalue||"false"}}for(var b in a.cases){if(a.cases[b].value==c){return b}}return -1},matchModel:function(c,e){var a={};var b=this;function d(f,o){for(var l in o){var h=o[l];var m=h.name;if(f!=""){m=f+"|"+m}switch(h.type){case"repeat":for(var k in h.cache){d(m+"_"+k,h.cache[k])}break;case"conditional":var p=h.test_param&&h.test_param.value;var g=b.matchCase(h,p);if(g!=-1){d(m,h.cases[g].inputs)}break;default:var n=b.app.tree.job_ids[m];if(n){e(n,h)}}}}d("",c.inputs);return a},matchResponse:function(c){var a={};var b=this;function d(k,h){if(typeof h==="string"){var f=b.app.tree.job_ids[k];if(f){a[f]=h}}else{for(var g in h){var e=g;if(k!==""){var j="|";if(h instanceof Array){j="_"}e=k+j+e}d(e,h[g])}}}d("",c);return a},references:function(c,e){var g=[];var b=this;function d(h,j){var i=$(j).children();var l=[];var k=false;i.each(function(){var o=this;var n=$(o).attr("id");if(n!==c){var m=b.app.input_list[n];if(m){if(m.name==h){k=true;return false}if(m.data_ref==h&&m.type==e){l.push(n)}}}});if(!k){g=g.concat(l);i.each(function(){d(h,this)})}}var f=this.xml.find("#"+c);if(f.length>0){var a=this.app.input_list[c];if(a){d(a.name,f.parent())}}return g},_iterate:function(d,e,b){var a=this;var c=$(d).children();c.each(function(){var i=this;var h=$(i).attr("id");if($(i).hasClass("section-row")){e[h]={};var f=a.app.input_list[h];if(f){e[h]={input:f}}var g=$('<div id="'+h+'"/>');b.append(g);a._iterate(i,e[h],g)}else{a._iterate(i,e,b)}})}})});
define([],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},refresh:function(){this.dict={};this.xml=$("<div/>");if(!this.app.section){return{}}this._iterate(this.app.section.$el,this.dict,this.xml)},finalize:function(d){d=d||{};var a=this;this.job_def={};this.job_ids={};function c(g,f,e){a.job_def[g]=e;a.job_ids[g]=f}function b(l,o){for(var j in o){var g=o[j];if(g.input){var q=g.input;var k=l;if(l!=""){k+="|"}k+=q.name;switch(q.type){case"repeat":var f="section-";var t=[];var n=null;for(var s in g){var m=s.indexOf(f);if(m!=-1){m+=f.length;t.push(parseInt(s.substr(m)));if(!n){n=s.substr(0,m)}}}t.sort(function(u,i){return u-i});var j=0;for(var h in t){b(k+"_"+j++,g[n+t[h]])}break;case"conditional":var r=a.app.field_list[q.id].value();if(d[q.test_param.type]){r=d[q.test_param.type](r)}c(k+"|"+q.test_param.name,q.id,r);var e=a.matchCase(q,r);if(e!=-1){b(k,o[q.id+"-section-"+e])}break;default:var p=a.app.field_list[q.id];var r=p.value();if(d[q.type]){r=d[q.type](r)}if(!p.skip){if(q.optional&&p.validate&&!p.validate()){r=null}c(k,q.id,r)}}}}}b("",this.dict);return this.job_def},match:function(a){return this.job_ids&&this.job_ids[a]},matchCase:function(a,c){if(a.test_param.type=="boolean"){if(c=="true"){c=a.test_param.truevalue||"true"}else{c=a.test_param.falsevalue||"false"}}for(var b in a.cases){if(a.cases[b].value==c){return b}}return -1},matchModel:function(c,e){var a={};var b=this;function d(f,o){for(var l in o){var h=o[l];var m=h.name;if(f!=""){m=f+"|"+m}switch(h.type){case"repeat":for(var k in h.cache){d(m+"_"+k,h.cache[k])}break;case"conditional":var p=h.test_param&&h.test_param.value;var g=b.matchCase(h,p);if(g!=-1){d(m,h.cases[g].inputs)}break;default:var n=b.app.tree.job_ids[m];if(n){e(n,h)}}}}d("",c.inputs);return a},matchResponse:function(c){var a={};var b=this;function d(k,h){if(typeof h==="string"){var f=b.app.tree.job_ids[k];if(f){a[f]=h}}else{for(var g in h){var e=g;if(k!==""){var j="|";if(h instanceof Array){j="_"}e=k+j+e}d(e,h[g])}}}d("",c);return a},references:function(c,e){var g=[];var b=this;function d(h,j){var i=$(j).children();var l=[];var k=false;i.each(function(){var o=this;var n=$(o).attr("id");if(n!==c){var m=b.app.input_list[n];if(m){if(m.name==h){k=true;return false}if(m.data_ref==h&&m.type==e){l.push(n)}}}});if(!k){g=g.concat(l);i.each(function(){d(h,this)})}}var f=this.xml.find("#"+c);if(f.length>0){var a=this.app.input_list[c];if(a){d(a.name,f.parent())}}return g},_iterate:function(d,e,b){var a=this;var c=$(d).children();c.each(function(){var i=this;var h=$(i).attr("id");if($(i).hasClass("section-row")){e[h]={};var f=a.app.input_list[h];if(f){e[h]={input:f}}var g=$('<div id="'+h+'"/>');b.append(g);a._iterate(i,e[h],g)}else{a._iterate(i,e,b)}})}})});
templates/base/base_panels.mako
+9 -9
View File
@@ -13,7 +13,7 @@
self.body_class=""
self.require_javascript=False
%>
<%def name="init()">
## Override
</%def>
@@ -45,7 +45,7 @@
<script>
Raven.config('${app.config.sentry_dsn_public}').install();
%if trans.user:
Raven.setUser( { email: "${trans.user.email}" } );
Raven.setUser( { email: "${trans.user.email | h}" } );
%endif
</script>
%endif
@@ -62,7 +62,7 @@
'libs/require',
"mvc/ui"
)}
<script type="text/javascript">
## global configuration object
var galaxy_config =
@@ -112,14 +112,14 @@
'galaxy.panels'
)}
<script type="text/javascript">
ensure_dd_helper();
%if self.has_left_panel:
var lp = new Panel( { panel: $("#left"), center: $("#center"), drag: $("#left > .unified-panel-footer > .drag" ), toggle: $("#left > .unified-panel-footer > .panel-collapse" ) } );
force_left_panel = function( x ) { lp.force_panel( x ) };
%endif
%if self.has_right_panel:
var rp = new Panel( { panel: $("#right"), center: $("#center"), drag: $("#right > .unified-panel-footer > .drag" ), toggle: $("#right > .unified-panel-footer > .panel-collapse" ), right: true } );
window.handle_minwidth_hint = function( x ) { rp.handle_minwidth_hint( x ) };
@@ -134,7 +134,7 @@
ga('create', '${app.config.ga_code}', 'auto');
ga('send', 'pageview');
%endif
</script>
## Handle AJAX (actually hidden iframe) upload tool
<script type="text/javascript">
@@ -300,7 +300,7 @@
## Document
<html>
<!--base_panels.mako-->
${self.init()}
${self.init()}
<head>
%if app.config.brand:
<title>${self.title()} / ${app.config.brand}</title>
@@ -316,7 +316,7 @@
${self.javascripts()}
${self.javascript_app()}
</head>
<%
body_class = self.body_class
if self.message_box_visible:
templates/search/index.mako
+99 -39
View File
@@ -1,52 +1,112 @@
<%inherit file="/webapps/galaxy/base_panels.mako"/>
<%namespace file="/search/search.mako" import="search_init" />
<%namespace file="/search/search.mako" import="search_dialog" />
<%def name="init()">
<%
self.has_left_panel=False
self.has_right_panel=False
self.message_box_visible=False
self.active_view="shared"
self.overlay_visible=False
%>
<%
self.has_left_panel=False
self.has_right_panel=False
self.message_box_visible=False
self.active_view="shared"
self.overlay_visible=False
%>
</%def>
<%def name="stylesheets()">
${parent.stylesheets()}
<style>
.searchResult {
border-style:dashed;
border-width:1px;
margin: 5px;
}
</style>
${parent.stylesheets()}
<style>
.searchResult {
border-style:dashed;
border-width:1px;
margin: 5px;
}
</style>
</%def>
<%def name="javascripts()">
${parent.javascripts()}
${h.js(
"libs/jquery/jquery",
)}
<script type="text/javascript">
function search_format_output(doc) {
var div_class = "historyItem";
var a = $("<div class='" + div_class + "'>")
a.append($("<div>").append(doc['model_class']));
b = a.append( $("<div class='historyItemTitle'><a href='/file/" + doc['id'] + "'>" + doc['name'] + "</a></div>") );
if ('misc_blurb' in doc) {
b.append( $("<div>").append(doc["misc_blurb"]) );
}
if ('peek' in doc) {
b.append( $("<pre class='peek'>").append( doc["peek"]) );
}
return a;
}
function doSearch(query) {
if (query.length > 1) {
var url = "/api/search";
$.ajax({
type : 'POST',
url: url,
data: JSON.stringify({"query" : query }),
contentType : 'application/json',
dataType : 'json',
success : function(data) {
var p = $("#output");
p.empty();
_.each(data.results, function(doc){
var div_class = "historyItem";
var a = $("<div class='" + div_class + "'>")
a.append($("<div>").append(doc['model_class']));
b = a.append( $("<div class='historyItemTitle'><a href='/file/" + doc['id'] + "'>" + doc['name'] + "</a></div>") );
if ('misc_blurb' in doc) {
b.append( $("<div>").append(doc["misc_blurb"]) );
}
if ('peek' in doc) {
b.append( $("<pre class='peek'>").append( doc["peek"]) );
}
p.append(b);
});
}
});
}
};
var queryURL = function (query) {
var url = "/api/search" + encodeURIComponent(query);
url = url + "&field=" + $("#searchFields").val();
if ($("#fileType").val() != "All") {
url = url + "&type=" + $("#fileType").val()
}
return url;
}
$(document).ready( function() {
$("#search_button").click(function() {
doSearch($("#search_text").val());
});
$('#search_text').keyup(function(e){
if(e.keyCode == 13) {
doSearch($("#search_text").val());
}
});
doSearch($("#search_text").val());
});
</script>
</%def>
<%def name="center_panel()">
${search_init()}
<script type="text/javascript">
var search_format_output = function(doc) {
var div_class = "historyItem";
var a = $("<div class='" + div_class + "'>")
a.append($("<div>").append(doc['model_class']));
b = a.append( $("<div class='historyItemTitle'><a href='/file/" + doc['id'] + "'>" + doc['name'] + "</a></div>") );
if ('misc_blurb' in doc) {
b.append( $("<div>").append(doc["misc_blurb"]) );
}
if ('peek' in doc) {
b.append( $("<pre class='peek'>").append( doc["peek"]) );
}
return a;
}
<div id="search_box" style="margin: 20px;">
<input type="text" id="search_text" size="90"/>
</div>
<div style="margin: 20px;">
<input type="button" id="search_button" value="Search"/>
</div>
<div id="output"></div>
</script>
<div style="overflow: auto; height: 100%">
${search_dialog("search_format_output")}
</div>
</%def>
templates/search/search.mako
-68
View File
@@ -1,68 +0,0 @@
<%def name="search_init()">
${h.js(
'libs/jquery/jquery',
)}
</%def>
<%def name="search_dialog(output_format)">
<script type="text/javascript">
function doSearch(query) {
if (query.length > 1) {
var url = "/api/search";
$.ajax({
type : 'POST',
url: url,
data: JSON.stringify({"query" : query }),
contentType : 'application/json',
dataType : 'json',
success : function(data) {
var p = $("#output");
p.empty();
for(var i in data) {
var e = ${output_format}(data[i]);
p.append(e);
}
}
});
}
};
$(document).ready( function() {
$("#search_button").click(function() {
doSearch($("#search_text").val());
});
$('#search_text').keyup(function(e){
if(e.keyCode == 13) {
doSearch($("#search_text").val());
}
});
doSearch($("#search_text").val());
});
var queryURL = function (query) {
var url = "/api/search" + encodeURIComponent(query);
url = url + "&field=" + $("#searchFields").val();
if ($("#fileType").val() != "All") {
url = url + "&type=" + $("#fileType").val()
}
return url;
}
</script>
<div id="search_box" style="margin: 20px;">
<input type="text" id="search_text" size="90"/>
</div>
<div style="margin: 20px;">
<input type="button" id="search_button" value="Search"/>
</div>
<div id="output"></div>
</%def>
templates/webapps/galaxy/cloud/index.mako
+3 -3
View File
@@ -218,7 +218,7 @@ Credentials section of the AWS Console</a>. </div>
</div>
%if share_string:
<input type='hidden' name='share_string' value='${share_string}'/>
<input id="dbremove_share_string" type='hidden' name='share_string' value='${share_string | h}'/>
%else:
<!-- DBEDIT temporary hide share string due to it being broken on the cloudman end -->
<div class="form-row" style="display:none;">
@@ -228,11 +228,11 @@ Credentials section of the AWS Console</a>. </div>
%endif
%if ami:
<input type='hidden' name='ami' value='${ami}'/>
<input type='hidden' name='ami' value='${ami | h}'/>
%endif
%if bucket_default:
<input type='hidden' name='bucket_default' value='${bucket_default}'/>
<input type='hidden' name='bucket_default' value='${bucket_default | h}'/>
%endif
<div class="form-row">
templates/webapps/galaxy/cloud/run.mako
-41
View File
@@ -1,41 +0,0 @@
<%inherit file="/webapps/galaxy/base_panels.mako"/>
<%def name="init()">
<%
self.has_left_panel=False
self.has_right_panel=False
self.active_view="shared"
self.message_box_visible=False
%>
</%def>
<%def name="center_panel()">
<div style="overflow: auto; height: 100%;">
<div class="page-container" style="padding: 10px;">
<h2>Launching a Galaxy Cloud Instance</h2>
%if error:
<p>${error}</p>
%elif instance:
%if kp_material:
<h3>Very Important Key Pair Information</h3>
<p>A new key pair named '${kp_name}' has been created in your AWS
account and will be used to access this instance via ssh. It is
<strong>very important</strong> that you save the following private key
as it is not saved on this Galaxy instance and will be permanently lost
once you leave this page. To do this, save the following key block as
a plain text file named '${kp_name}'.</p>
<pre>${kp_material}</pre>
%endif
<p>The instance '${instance.id} has been successfully launched using the
'${instance.image_id}' AMI.<br/> Access it at <a
href="http://${instance.public_dns_name}">http://${instance.public_dns_name}</a></p>
<p>SSH access is available using your private key '${kp_name}'.</p>
%else:
<p> Unknown failure, no instance. Please refer to your AWS console at <a
href="https://console.aws.amazon.com">https://console.aws.amazon.com</a></p>
%endif
</div>
</div>
</%def>
test/functional/tools/multi_select.xml
+8
View File
@@ -33,5 +33,13 @@
</assert_contents>
</output>
</test>
<test>
<param name="select_ex" value="Ex1" />
<output name="output">
<assert_contents>
<has_line line="--ex1" />
</assert_contents>
</output>
</test>
</tests>
</tool>