diff --git a/client/galaxy/scripts/apps/admin.js b/client/galaxy/scripts/apps/admin.js index 569dffc330f..41597424892 100644 --- a/client/galaxy/scripts/apps/admin.js +++ b/client/galaxy/scripts/apps/admin.js @@ -39,8 +39,7 @@ window.app = function app(options, bootstrapped) { this.page.display( new GridView({ url_base: `${Galaxy.root}admin/users_list`, - url_data: Galaxy.params, - dict_format: true + url_data: Galaxy.params }) ); }, @@ -49,8 +48,7 @@ window.app = function app(options, bootstrapped) { this.page.display( new GridView({ url_base: `${Galaxy.root}admin/roles_list`, - url_data: Galaxy.params, - dict_format: true + url_data: Galaxy.params }) ); }, @@ -59,8 +57,7 @@ window.app = function app(options, bootstrapped) { this.page.display( new GridView({ url_base: `${Galaxy.root}admin/groups_list`, - url_data: Galaxy.params, - dict_format: true + url_data: Galaxy.params }) ); }, @@ -69,8 +66,7 @@ window.app = function app(options, bootstrapped) { this.page.display( new GridView({ url_base: `${Galaxy.root}admin_toolshed/browse_repositories`, - url_data: Galaxy.params, - dict_format: true + url_data: Galaxy.params }) ); }, @@ -79,8 +75,7 @@ window.app = function app(options, bootstrapped) { this.page.display( new GridView({ url_base: `${Galaxy.root}admin/tool_versions_list`, - url_data: Galaxy.params, - dict_format: true + url_data: Galaxy.params }) ); }, @@ -89,8 +84,7 @@ window.app = function app(options, bootstrapped) { this.page.display( new GridView({ url_base: `${Galaxy.root}admin/quotas_list`, - url_data: Galaxy.params, - dict_format: true + url_data: Galaxy.params }) ); }, @@ -105,8 +99,7 @@ window.app = function app(options, bootstrapped) { this.page.display( new GridView({ url_base: `${Galaxy.root}forms/forms_list`, - url_data: Galaxy.params, - dict_format: true + url_data: Galaxy.params }) ); }, diff --git a/client/galaxy/scripts/apps/analysis.js b/client/galaxy/scripts/apps/analysis.js index 2be9e2a39c5..db946e372e8 100644 --- a/client/galaxy/scripts/apps/analysis.js +++ b/client/galaxy/scripts/apps/analysis.js @@ -47,6 +47,7 @@ window.app = function app(options, bootstrapped) { "(/)tours(/)(:tour_id)": "show_tours", "(/)user(/)": "show_user", "(/)user(/)(:form_id)": "show_user_form", + "(/)openids(/)list": "show_openids", "(/)pages(/)create(/)": "show_pages_create", "(/)pages(/)edit(/)": "show_pages_edit", "(/)pages(/)(:action_id)": "show_pages", @@ -115,8 +116,7 @@ window.app = function app(options, bootstrapped) { show_workflows_published: function() { this.page.display( new GridView({ - url_base: `${Galaxy.root}workflow/list_published`, - dict_format: true + url_base: `${Galaxy.root}workflow/list_published` }) ); }, @@ -157,11 +157,18 @@ window.app = function app(options, bootstrapped) { ); }, + show_openids: function() { + this.page.display( + new GridView({ + url_base: `${Galaxy.root}user/openids_list` + }) + ); + }, + show_datasets: function() { this.page.display( new GridView({ - url_base: `${Galaxy.root}dataset/list`, - dict_format: true + url_base: `${Galaxy.root}dataset/list` }) ); }, diff --git a/client/galaxy/scripts/galaxy.pages.js b/client/galaxy/scripts/galaxy.pages.js index ed673e70037..c5af3df58b0 100644 --- a/client/galaxy/scripts/galaxy.pages.js +++ b/client/galaxy/scripts/galaxy.pages.js @@ -328,7 +328,6 @@ WYMeditor.editor.prototype.dialog = function(dialogType, dialogFeatures, bodyHtm var grid = new GridView({ url_base: item_info.list_ajax_url, - dict_format: true, embedded: true }); Galaxy.modal.show({ @@ -422,7 +421,6 @@ WYMeditor.editor.prototype.dialog = function(dialogType, dialogFeatures, bodyHtm var grid = new GridView({ url_base: item_info.list_ajax_url, - dict_format: true, embedded: true }); Galaxy.modal.show({ diff --git a/client/galaxy/scripts/legacy/grid/grid-model.js b/client/galaxy/scripts/legacy/grid/grid-model.js new file mode 100644 index 00000000000..f25a4313abe --- /dev/null +++ b/client/galaxy/scripts/legacy/grid/grid-model.js @@ -0,0 +1,114 @@ +// legacy grid model, used by reports and toolshed +export default Backbone.Model.extend({ + defaults: { + url_base: "", + async: false, + async_ops: [], + categorical_filters: [], + filters: {}, + sort_key: null, + show_item_checkboxes: false, + advanced_search: false, + cur_page: 1, + num_pages: 1, + operation: undefined, + item_ids: undefined + }, + + /** + * Return true if operation can be done asynchronously. + */ + can_async_op: function(op) { + return _.indexOf(this.attributes.async_ops, op) !== -1; + }, + + /** + * Add filtering criterion. + */ + add_filter: function(key, value, append) { + // Update URL arg with new condition. + if (append) { + // Update or append value. + var cur_val = this.attributes.filters[key]; + + var new_val; + if (cur_val === null || cur_val === undefined) { + new_val = value; + } else if (typeof cur_val == "string") { + if (cur_val == "All" || cur_val == value) { + new_val = value; + } else { + // Replace string with array. + var values = []; + values[0] = cur_val; + values[1] = value; + new_val = values; + } + } else { + // Current value is an array. + new_val = cur_val; + if (new_val.indexOf(value) === -1) { + new_val.push(value); + } + } + this.attributes.filters[key] = new_val; + } else { + // Replace value. + this.attributes.filters[key] = value; + } + }, + + /** + * Remove filtering criterion. + */ + remove_filter: function(key, condition) { + var cur_val = this.attributes.filters[key]; + if (cur_val === null || cur_val === undefined) { + return false; + } + + if (typeof cur_val === "string") { + // overwrite/remove condition. + this.attributes.filters[key] = ""; + } else { + // filter contains an array of conditions. + var condition_index = _.indexOf(cur_val, condition); + if (condition_index !== -1) { + cur_val[condition_index] = ""; + } + } + }, + + /** + * Returns URL data for obtaining a new grid. + */ + get_url_data: function() { + var url_data = { + async: this.attributes.async, + sort: this.attributes.sort_key, + page: this.attributes.cur_page, + show_item_checkboxes: this.attributes.show_item_checkboxes, + advanced_search: this.attributes.advanced_search + }; + + // Add operation, item_ids only if they have values. + if (this.attributes.operation) { + url_data.operation = this.attributes.operation; + } + if (this.attributes.item_ids) { + url_data.id = this.attributes.item_ids; + } + + // Add filter arguments to data, placing "f-" in front of all arguments. + var self = this; + _.each(_.pairs(self.attributes.filters), k => { + url_data[`f-${k[0]}`] = k[1]; + }); + return url_data; + }, + + // Return URL for obtaining a new grid + get_url: function(args) { + return `${this.get("url_base")}?${$.param(this.get_url_data())}&${$.param(args)}`; + } +}); diff --git a/client/galaxy/scripts/legacy/grid/grid-template.js b/client/galaxy/scripts/legacy/grid/grid-template.js new file mode 100644 index 00000000000..e5fda7d790f --- /dev/null +++ b/client/galaxy/scripts/legacy/grid/grid-template.js @@ -0,0 +1,547 @@ +// dependencies +import Utils from "utils/utils"; +// grid view templates +export default { + // template + grid: function(options) { + var tmpl = ""; + if (options.embedded) { + tmpl = this.grid_header(options) + this.grid_table(options); + } else { + tmpl = `
${this.grid_header( + options + )}
${this.grid_table( + options + )}`; + } + + // add info text + if (options.info_text) { + tmpl += `
${options.info_text}
`; + } + + // return + return tmpl; + }, + + // template + grid_table: function() { + return ` +
+ + + + +
+
`; + }, + + // template + grid_header: function(options) { + var tmpl = '
'; + if (!options.embedded) { + tmpl += `

${options.title}

`; + } + if (options.global_actions) { + tmpl += '"; + } + if (options.insert) { + tmpl += options.insert; + } + + // add grid filters + tmpl += this.grid_filters(options); + tmpl += "
"; + + // return template + return tmpl; + }, + + // template + header: function(options) { + // start + var tmpl = ""; + + // add checkbox + if (options.show_item_checkboxes) { + tmpl += ""; + if (options.items.length > 0) { + tmpl += + '' + + ''; + } + tmpl += ""; + } + + // create header elements + for (let column of options.columns) { + if (column.visible) { + tmpl += ``; + if (column.href) { + tmpl += `${column.label}`; + } else { + tmpl += column.label; + } + tmpl += `${column.extra}`; + } + } + + // finalize + tmpl += ""; + + // return template + return tmpl; + }, + + // template + body: function(options) { + // initialize + var tmpl = ""; + var items_length = options.items.length; + + // empty grid? + if (items_length === 0) { + // No results. + tmpl += 'No Items'; + } + + // create rows + for (let item of options.items) { + // Tag current + tmpl += "`; + } + + // Data columns + for (let column of options.columns) { + if (column.visible) { + // Nowrap + var nowrap = ""; + if (column.nowrap) { + nowrap = 'style="white-space:nowrap;"'; + } + + // get column settings + var column_settings = item.column_config[column.label]; + + // load attributes + var link = column_settings.link; + var value = column_settings.value; + var target = column_settings.target; + + // unescape value + if (jQuery.type(value) === "string") { + value = value.replace(/\/\//g, "/"); + } + + // Attach popup menu? + var id = ""; + var cls = ""; + if (column.attach_popup) { + id = `grid-${item.encode_id}-popup`; + cls = "menubutton"; + if (link !== "") { + cls += " split"; + } + cls += " popup"; + } + + // Check for row wrapping + tmpl += ``; + + // Link + if (link) { + if (options.operations.length !== 0) { + tmpl += `
`; + } + tmpl += `${value}`; + if (options.operations.length !== 0) { + tmpl += "
"; + } + } else { + tmpl += `
`; + } + tmpl += ""; + } + } + tmpl += ""; + } + return tmpl; + }, + + // template + footer: function(options) { + // create template string + var tmpl = ""; + + // paging + if (options.use_paging && options.num_pages > 1) { + // get configuration + var num_page_links = options.num_page_links; + var cur_page_num = options.cur_page_num; + var num_pages = options.num_pages; + + // First pass on min page. + var page_link_range = num_page_links / 2; + var min_page = cur_page_num - page_link_range; + var min_offset = 0; + if (min_page <= 0) { + // Min page is too low. + min_page = 1; + min_offset = page_link_range - (cur_page_num - min_page); + } + + // Set max page. + var max_range = page_link_range + min_offset; + var max_page = cur_page_num + max_range; + var max_offset; + if (max_page <= num_pages) { + // Max page is fine. + max_offset = 0; + } else { + // Max page is too high. + max_page = num_pages; + // +1 to account for the +1 in the loop below. + max_offset = max_range - (max_page + 1 - cur_page_num); + } + + // Second and final pass on min page to add any unused + // offset from max to min. + if (max_offset !== 0) { + min_page -= max_offset; + if (min_page < 1) { + min_page = 1; + } + } + + // template header + tmpl += ''; + if (options.show_item_checkboxes) { + tmpl += ""; + } + tmpl += '' + '' + "Page:"; + + if (min_page > 1) { + tmpl += + '1 ...'; + } + + // create page urls + for (var page_index = min_page; page_index < max_page + 1; page_index++) { + if (page_index == options.cur_page_num) { + tmpl += `${page_index}`; + } else { + tmpl += `${page_index}`; + } + } + + // show last page + if (max_page < num_pages) { + tmpl += `...${num_pages}`; + } + tmpl += ""; + + // Show all link + tmpl += ` + | Show All + + `; + } + + // Grid operations for multiple items. + if (options.show_item_checkboxes) { + // start template + tmpl += ` + + + + + For selected items: + `; + + // configure buttons for operations + for (let operation of options.operations) { + if (operation.allow_multiple) { + tmpl += ` `; + } + } + + // finalize template + tmpl += "" + ""; + } + + // count global operations + var found_global = false; + for (let operation of options.operations) { + if (operation.global_operation) { + found_global = true; + break; + } + } + + // add global operations + if (found_global) { + tmpl += "" + ''; + for (let operation of options.operations) { + if (operation.global_operation) { + tmpl += `${operation.label}`; + } + } + tmpl += "" + ""; + } + + // add legend + if (options.legend) { + tmpl += `${options.legend}`; + } + + // return + return tmpl; + }, + + // template + message: function(options) { + var status = options.status; + if (["success", "ok"].indexOf(status) != -1) { + status = "done"; + } + return `

${_.escape( + options.message + )}

`; + }, + + // template + grid_filters: function(options) { + // get filters + var default_filter_dict = options.default_filter_dict; + var filters = options.filters; + + // show advanced search if flag set or if there are filters for advanced search fields + var advanced_search_display = "none"; + if (options.advanced_search) { + advanced_search_display = "block"; + } + + // identify columns with advanced filtering + var show_advanced_search_link = false; + for (let column of options.columns) { + if (column.filterable == "advanced") { + var column_key = column.key; + var f_key = filters[column_key]; + var d_key = default_filter_dict[column_key]; + if (f_key && d_key && f_key != d_key) { + advanced_search_display = "block"; + } + show_advanced_search_link = true; + } + } + + // hide standard search if advanced is shown + var standard_search_display = "block"; + if (advanced_search_display == "block") { + standard_search_display = "none"; + } + + // + // standard search + // + var tmpl = `"; + + // + // advanced search + // + tmpl += `"; + + // return template + return tmpl; + }, + + // template + grid_column_filter: function(options, column) { + // collect parameters + var filters = options.filters; + var column_label = column.label; + var column_key = column.key; + if (column.filterable == "advanced") { + column_label = column_label.toLowerCase(); + } + + // start + var tmpl = ""; + + if (column.filterable == "advanced") { + tmpl += `${column_label}:`; + } + tmpl += ''; + if (column.is_text) { + tmpl += `
`; + // Carry forward filtering criteria with hidden inputs. + for (let column of options.columns) { + var filter_value = filters[column.key]; + if (filter_value) { + if (filter_value != "All") { + if (column.is_text) { + filter_value = JSON.stringify(filter_value); + } + tmpl += ``; + } + } + } + // Print current filtering criteria and links to delete. + tmpl += ``; + + // add filters + var column_filter = filters[column_key]; + if (column_filter) { + // identify type + var type = jQuery.type(column_filter); + + // single filter value + if (type == "string") { + if (column_filter != "All") { + // append template + tmpl += this.filter_element(column_key, column_filter); + } + } + + // multiple filter values + if (type == "array") { + for (let i in column_filter) { + // copy filters and remove entry + var params = column_filter; + params = params.slice(i); + + // append template + tmpl += this.filter_element(column_key, column_filter[i]); + } + } + } + + // close span + tmpl += ""; + + // Set value, size of search input field. Minimum size is 20 characters. + var value = ""; + var size = 20; + if (column.filterable == "standard") { + value = column.label.toLowerCase(); + if (value.length < 20) { + size = value.length; + } + // +4 to account for space after placeholder + size = size + 4; + } + + // print input field for column + tmpl += ` + + + + +
`; + } else { + // filter criteria + tmpl += ``; + + // add category filters + var seperator = false; + for (var cf_label in options.categorical_filters[column_key]) { + // get category filter + var cf = options.categorical_filters[column_key][cf_label]; + + // each filter will have only a single argument, so get that single argument + var cf_key = ""; + var cf_arg = ""; + for (var key in cf) { + cf_key = key; + cf_arg = cf[key]; + } + + // add seperator + if (seperator) { + tmpl += " | "; + } + seperator = true; + + // add category + var filter = filters[column_key]; + if (filter && cf[column_key] && filter == cf_arg) { + tmpl += `${cf_label}`; + } else { + tmpl += `${cf_label}`; + } + } + tmpl += ""; + } + tmpl += "" + ""; + + // return template + return tmpl; + }, + + // template for filter items + filter_element: function(filter_key, filter_value) { + filter_value = Utils.sanitize(filter_value); + return `${filter_value}`; + } +}; diff --git a/client/galaxy/scripts/legacy/grid/grid-view.js b/client/galaxy/scripts/legacy/grid/grid-view.js new file mode 100644 index 00000000000..05e82077321 --- /dev/null +++ b/client/galaxy/scripts/legacy/grid/grid-view.js @@ -0,0 +1,677 @@ +// This is necessary so that, when nested arrays are used in ajax/post/get methods, square brackets ('[]') are +// not appended to the identifier of a nested array. +jQuery.ajaxSettings.traditional = true; + +// dependencies +import Utils from "utils/utils"; +import GridModel from "legacy/grid/grid-model"; +import Templates from "legacy/grid/grid-template"; +import PopupMenu from "mvc/ui/popup-menu"; +// grid view +export default Backbone.View.extend({ + // model + grid: null, + + // Initialize + initialize: function(grid_config) { + this.grid = new GridModel(); + this.dict_format = grid_config.dict_format; + this.title = grid_config.title; + var self = this; + window.add_tag_to_grid_filter = (tag_name, tag_value) => { + // Put tag name and value together. + var tag = tag_name + (tag_value !== undefined && tag_value !== "" ? `:${tag_value}` : ""); + var advanced_search = $("#advanced-search").is(":visible"); + if (!advanced_search) { + $("#standard-search").slideToggle("fast"); + $("#advanced-search").slideToggle("fast"); + } + self.add_filter_condition("tags", tag); + }; + + // set element + if (this.dict_format) { + this.setElement("
"); + if (grid_config.url_base && !grid_config.items) { + var url_data = grid_config.url_data || {}; + _.each(grid_config.filters, (v, k) => { + url_data[`f-${k}`] = v; + }); + $.ajax({ + url: `${grid_config.url_base}?${$.param(url_data)}`, + success: function(response) { + response.embedded = grid_config.embedded; + response.filters = grid_config.filters || {}; + self.init_grid(response); + } + }); + } else { + this.init_grid(grid_config); + } + } else { + this.setElement("#grid-container"); + this.init_grid(grid_config); + } + + // fix padding + if (grid_config.use_panels) { + $("#center").css({ + padding: "10px", + overflow: "auto" + }); + } + }, + + // refresh frames + handle_refresh: function(refresh_frames) { + if (refresh_frames) { + if ($.inArray("history", refresh_frames) > -1) { + if (window.top.Galaxy && window.top.Galaxy.currHistoryPanel) { + window.top.Galaxy.currHistoryPanel.loadCurrentHistory(); + } + } + } + }, + + // Initialize + init_grid: function(grid_config) { + this.grid.set(grid_config); + + // get options + var options = this.grid.attributes; + + if (this.allow_title_display && options.title) { + Utils.setWindowTitle(options.title); + } + // handle refresh requests + this.handle_refresh(options.refresh_frames); + + // strip protocol and domain + var url = this.grid.get("url_base"); + url = url.replace(/^.*\/\/[^\/]+/, ""); + this.grid.set("url_base", url); + + // append main template + this.$el.html(Templates.grid(options)); + + // update div contents + this.$el.find("#grid-table-header").html(Templates.header(options)); + this.$el.find("#grid-table-body").html(Templates.body(options)); + this.$el.find("#grid-table-footer").html(Templates.footer(options)); + + // update message + if (options.message) { + this.$el.find("#grid-message").html(Templates.message(options)); + var self = this; + if (options.use_hide_message) { + setTimeout(() => { + self.$el.find("#grid-message").html(""); + }, 5000); + } + } + + // configure elements + this.init_grid_elements(); + this.init_grid_controls(); + + // attach global event handler + // TODO: redundant (the onload/standard page handlers do this) - but needed because these are constructed after page ready + if (window.init_refresh_on_change) { + window.init_refresh_on_change(); + } + }, + + // Initialize grid controls + init_grid_controls: function() { + // link + var self = this; + + // Initialize grid operation button. + this.$el.find(".operation-button").each(function() { + $(this).off(); + $(this).click(function() { + self.submit_operation(this); + return false; + }); + }); + + // Initialize text filters to select text on click and use normal font when user is typing. + this.$el.find("input[type=text]").each(function() { + $(this).off(); + $(this) + .click(function() { + $(this).select(); + }) + .keyup(function() { + $(this).css("font-style", "normal"); + }); + }); + + // Initialize sort links. + this.$el.find(".sort-link").each(function() { + $(this).off(); + $(this).click(function() { + self.set_sort_condition($(this).attr("sort_key")); + return false; + }); + }); + + // Initialize text filters. + this.$el.find(".text-filter-form").each(function() { + $(this).off(); + $(this).submit(function() { + var column_key = $(this).attr("column_key"); + var text_input_obj = $(`#input-${column_key}-filter`); + var text_input = text_input_obj.val(); + text_input_obj.val(""); + self.add_filter_condition(column_key, text_input); + return false; + }); + }); + + // Initialize categorical filters. + this.$el.find(".text-filter-val > a").each(function() { + $(this).off(); + $(this).click(function() { + // Remove visible element. + $(this) + .parent() + .remove(); + + // Remove filter condition. + self.remove_filter_condition($(this).attr("filter_key"), $(this).attr("filter_val")); + + // Return + return false; + }); + }); + + // Initialize categorical filters. + this.$el.find(".categorical-filter > a").each(function() { + $(this).off(); + $(this).click(function() { + self.set_categorical_filter($(this).attr("filter_key"), $(this).attr("filter_val")); + return false; + }); + }); + + // Initialize standard, advanced search toggles. + this.$el.find(".advanced-search-toggle").each(function() { + $(this).off(); + $(this).click(() => { + self.$el.find("#standard-search").slideToggle("fast"); + self.$el.find("#advanced-search").slideToggle("fast"); + return false; + }); + }); + + // Add event to check all box + this.$el.find("#check_all").off(); + this.$el.find("#check_all").on("click", () => { + self.check_all_items(); + }); + }, + + // Initialize grid elements. + init_grid_elements: function() { + // Initialize grid selection checkboxes. + this.$el.find(".grid").each(function() { + var checkboxes = $(this).find("input.grid-row-select-checkbox"); + var check_count = $(this).find("span.grid-selected-count"); + var update_checked = () => { + check_count.text($(checkboxes).filter(":checked").length); + }; + + $(checkboxes).each(function() { + $(this).change(update_checked); + }); + update_checked(); + }); + + // Initialize ratings. + if (this.$el.find(".community_rating_star").length !== 0) this.$el.find(".community_rating_star").rating({}); + + // get options + var options = this.grid.attributes; + var self = this; + + // + // add page click events + // + this.$el.find(".page-link > a").each(function() { + $(this).click(function() { + self.set_page($(this).attr("page_num")); + return false; + }); + }); + + // + // add inbound/outbound events + // + this.$el.find(".use-target").each(function() { + $(this).click(function() { + self.execute({ + href: $(this).attr("href"), + target: $(this).attr("target") + }); + return false; + }); + }); + + // empty grid? + var items_length = options.items.length; + if (items_length === 0) { + return; + } + + // add operation popup menus + _.each(options.items, (item, index) => { + var button = self.$(`#grid-${item.encode_id}-popup`).off(); + var popup = new PopupMenu(button); + _.each(options.operations, operation => { + self._add_operation(popup, operation, item); + }); + }); + }, + + /** Add an operation to the items menu */ + _add_operation: function(popup, operation, item) { + var self = this; + var settings = item.operation_config[operation.label]; + if (settings.allowed && operation.allow_popup) { + popup.addItem({ + html: operation.label, + href: settings.url_args, + target: settings.target, + confirmation_text: operation.confirm, + func: function(e) { + e.preventDefault(); + var label = $(e.target).html(); + if (operation.onclick) { + operation.onclick(item.encode_id); + } else { + self.execute(this.findItemByHtml(label)); + } + } + }); + } + }, + + // Add a condition to the grid filter; this adds the condition and refreshes the grid. + add_filter_condition: function(name, value) { + // Do nothing is value is empty. + if (value === "") { + return false; + } + + // Add condition to grid. + this.grid.add_filter(name, value, true); + + // Add button that displays filter and provides a button to delete it. + var t = $(Templates.filter_element(name, value)); + var self = this; + t.click(function() { + // Remove visible element. + $(this).remove(); + + // Remove filter condition. + self.remove_filter_condition(name, value); + }); + + // append to container + var container = this.$el.find(`#${name}-filtering-criteria`); + container.append(t); + + // execute + this.go_page_one(); + this.execute(); + }, + + // Remove a condition to the grid filter; this adds the condition and refreshes the grid. + remove_filter_condition: function(name, value) { + // Remove filter condition. + this.grid.remove_filter(name, value); + + // Execute + this.go_page_one(); + this.execute(); + }, + + // Set sort condition for grid. + set_sort_condition: function(col_key) { + // Set new sort condition. New sort is col_key if sorting new column; if reversing sort on + // currently sorted column, sort is reversed. + var cur_sort = this.grid.get("sort_key"); + var new_sort = col_key; + if (cur_sort.indexOf(col_key) !== -1) { + // Reverse sort. + if (cur_sort.substring(0, 1) !== "-") { + new_sort = `-${col_key}`; + } + } + + // Remove sort arrows elements. + this.$el.find(".sort-arrow").remove(); + + // Add sort arrow element to new sort column. + var sort_arrow = new_sort.substring(0, 1) == "-" ? "↑" : "↓"; + var t = $(`${sort_arrow}`).addClass("sort-arrow"); + + // Add to header + this.$el.find(`#${col_key}-header`).append(t); + + // Update grid. + this.grid.set("sort_key", new_sort); + this.go_page_one(); + this.execute(); + }, + + // Set new value for categorical filter. + set_categorical_filter: function(name, new_value) { + // Update filter hyperlinks to reflect new filter value. + var category_filter = this.grid.get("categorical_filters")[name]; + + var cur_value = this.grid.get("filters")[name]; + var self = this; + this.$el.find(`.${name}-filter`).each(function() { + var text = $.trim($(this).text()); + var filter = category_filter[text]; + var filter_value = filter[name]; + if (filter_value == new_value) { + // Remove filter link since grid will be using this filter. It is assumed that + // this element has a single child, a hyperlink/anchor with text. + $(this).empty(); + $(this).addClass("current-filter"); + $(this).append(text); + } else if (filter_value == cur_value) { + // Add hyperlink for this filter since grid will no longer be using this filter. It is assumed that + // this element has a single child, a hyperlink/anchor. + $(this).empty(); + var t = $(`${text}`); + t.click(() => { + self.set_categorical_filter(name, filter_value); + }); + $(this).removeClass("current-filter"); + $(this).append(t); + } + }); + + // Update grid. + this.grid.add_filter(name, new_value); + this.go_page_one(); + this.execute(); + }, + + // Set page to view. + set_page: function(new_page) { + // Update page hyperlink to reflect new page. + var self = this; + this.$el.find(".page-link").each(function() { + var id = $(this).attr("id"); + + var // Id has form 'page-link- + page_num = parseInt(id.split("-")[2], 10); + + var cur_page = self.grid.get("cur_page"); + var text; + if (page_num === new_page) { + // Remove link to page since grid will be on this page. It is assumed that + // this element has a single child, a hyperlink/anchor with text. + text = $(this) + .children() + .text(); + $(this).empty(); + $(this).addClass("inactive-link"); + $(this).text(text); + } else if (page_num === cur_page) { + // Add hyperlink to this page since grid will no longer be on this page. It is assumed that + // this element has a single child, a hyperlink/anchor. + text = $(this).text(); + $(this).empty(); + $(this).removeClass("inactive-link"); + var t = $(`${text}`); + t.click(() => { + self.set_page(page_num); + }); + $(this).append(t); + } + }); + + if (new_page === "all") { + this.grid.set("cur_page", new_page); + } else { + this.grid.set("cur_page", parseInt(new_page, 10)); + } + this.execute(); + }, + + // confirmation/submission of operation request + submit_operation: function(operation_button, confirmation_text) { + // identify operation + var operation_name = $(operation_button).val(); + + // verify any item is selected + var number_of_checked_ids = this.$el.find('input[name="id"]:checked').length; + if (number_of_checked_ids < 1) { + return false; + } + + // Check to see if there's grid confirmation text for this operation + var operation = _.findWhere(this.grid.attributes.operations, { + label: operation_name + }); + if (operation && !confirmation_text) { + confirmation_text = operation.confirm || ""; + } + + // collect ids + var item_ids = []; + this.$el.find("input[name=id]:checked").each(function() { + item_ids.push($(this).val()); + }); + + // execute operation + var options = { + operation: operation_name, + id: item_ids, + confirmation_text: confirmation_text + }; + if (operation.target == "top" || operation.target == "center") { + options = _.extend(options, { + href: operation.href, + target: operation.target + }); + } + this.execute(options); + return true; + }, + + check_all_items: function() { + var check = this.$(".grid-row-select-checkbox"); + var state = this.$("#check_all").prop("checked"); + _.each(check, c => { + $(c).prop("checked", state); + }); + this.init_grid_elements(); + }, + + // Go back to page one; this is useful when a filter is applied. + go_page_one: function() { + // Need to go back to page 1 if not showing all. + var cur_page = this.grid.get("cur_page"); + if (cur_page !== null && cur_page !== undefined && cur_page !== "all") { + this.grid.set("cur_page", 1); + } + }, + + // + // execute operations and hyperlink requests + // + execute: function(options) { + // get url + var id = null; + var href = null; + var operation = null; + var confirmation_text = null; + var target = null; + + // check for options + if (options) { + // get options + href = options.href; + operation = options.operation; + id = options.id; + confirmation_text = options.confirmation_text; + target = options.target; + + // check if input contains the operation tag + if (href !== undefined && href.indexOf("operation=") != -1) { + // Get operation, id in hyperlink's href. + var href_parts = href.split("?"); + if (href_parts.length > 1) { + var href_parms_str = href_parts[1]; + var href_parms = href_parms_str.split("&"); + for (var index = 0; index < href_parms.length; index++) { + if (href_parms[index].indexOf("operation") != -1) { + // Found operation parm; get operation value. + operation = href_parms[index].split("=")[1]; + operation = operation.replace(/\+/g, " "); + } else if (href_parms[index].indexOf("id") != -1) { + // Found id parm; get id value. + id = href_parms[index].split("=")[1]; + } + } + } + } + } + + // check for operation details + if (operation && id) { + // show confirmation box + if ( + confirmation_text && + confirmation_text !== "" && + confirmation_text != "None" && + confirmation_text != "null" + ) + if (!confirm(confirmation_text)) return false; + + // use small characters for operation?! + operation = operation.toLowerCase(); + + // Update grid. + this.grid.set({ + operation: operation, + item_ids: id + }); + + // Do operation. If operation cannot be performed asynchronously, redirect to location. + if (target == "top") { + window.top.location = `${href}?${$.param(this.grid.get_url_data())}`; + } else if (target == "center") { + $("#galaxy_main").attr("src", `${href}?${$.param(this.grid.get_url_data())}`); + } else if (this.grid.can_async_op(operation) || this.dict_format) { + this.update_grid(); + } else { + this.go_to(target, href); + } + + // done + return false; + } + + // refresh grid + if (href) { + this.go_to(target, href); + return false; + } + + // refresh grid + if (this.grid.get("async") || this.dict_format) { + this.update_grid(); + } else { + this.go_to(target, href); + } + + // done + return false; + }, + + // go to url + go_to: function(target, href) { + // get aysnc status + var async = this.grid.get("async"); + this.grid.set("async", false); + + // get slide status + var advanced_search = this.$el.find("#advanced-search").is(":visible"); + this.grid.set("advanced_search", advanced_search); + + // get default url + if (!href) { + href = `${this.grid.get("url_base")}?${$.param(this.grid.get_url_data())}`; + } + + // clear grid of transient request attributes. + this.grid.set({ + operation: undefined, + item_ids: undefined, + async: async + }); + switch (target) { + case "center": + $("#galaxy_main").attr("src", href); + break; + case "top": + window.top.location = href; + break; + default: + window.location = href; + } + }, + + // Update grid. + update_grid: function() { + // If there's an operation, do POST; otherwise, do GET. + var method = this.grid.get("operation") ? "POST" : "GET"; + + // Show overlay to indicate loading and prevent user actions. + this.$el.find(".loading-elt-overlay").show(); + var self = this; + $.ajax({ + type: method, + url: self.grid.get("url_base"), + data: self.grid.get_url_data(), + error: function() { + alert("Grid refresh failed"); + }, + success: function(response_text) { + // backup + var embedded = self.grid.get("embedded"); + var insert = self.grid.get("insert"); + var advanced_search = self.$el.find("#advanced-search").is(":visible"); + + // request new configuration + var json = self.dict_format ? response_text : $.parseJSON(response_text); + + // update + json.embedded = embedded; + json.insert = insert; + json.advanced_search = advanced_search; + + // Initialize new grid config + self.init_grid(json); + + // Hide loading overlay. + self.$el.find(".loading-elt-overlay").hide(); + }, + complete: function() { + // Clear grid of transient request attributes. + self.grid.set({ + operation: undefined, + item_ids: undefined + }); + } + }); + } +}); diff --git a/client/galaxy/scripts/mvc/grid/grid-model.js b/client/galaxy/scripts/mvc/grid/grid-model.js index 6e3fc1698f9..bd4b3c99350 100644 --- a/client/galaxy/scripts/mvc/grid/grid-model.js +++ b/client/galaxy/scripts/mvc/grid/grid-model.js @@ -17,13 +17,6 @@ export default Backbone.Model.extend({ item_ids: undefined }, - /** - * Return true if operation can be done asynchronously. - */ - can_async_op: function(op) { - return _.indexOf(this.attributes.async_ops, op) !== -1; - }, - /** * Add filtering criterion. */ diff --git a/client/galaxy/scripts/mvc/grid/grid-shared.js b/client/galaxy/scripts/mvc/grid/grid-shared.js index a2eebe703a7..34cb89f75f3 100644 --- a/client/galaxy/scripts/mvc/grid/grid-shared.js +++ b/client/galaxy/scripts/mvc/grid/grid-shared.js @@ -10,7 +10,6 @@ var View = Backbone.View.extend({ $.ajax({ url: `${Galaxy.root + this.item}/${this.model.get("action_id")}?${$.param(Galaxy.params)}`, success: function(response) { - response["dict_format"] = true; self.model.set(response); self.render(); } diff --git a/client/galaxy/scripts/mvc/grid/grid-template.js b/client/galaxy/scripts/mvc/grid/grid-template.js index 5299ab1a87f..e5fda7d790f 100644 --- a/client/galaxy/scripts/mvc/grid/grid-template.js +++ b/client/galaxy/scripts/mvc/grid/grid-template.js @@ -112,14 +112,12 @@ export default { body: function(options) { // initialize var tmpl = ""; - var num_rows_rendered = 0; var items_length = options.items.length; // empty grid? if (items_length === 0) { // No results. tmpl += 'No Items'; - num_rows_rendered = 1; } // create rows @@ -193,7 +191,6 @@ export default { } } tmpl += ""; - num_rows_rendered++; } return tmpl; }, diff --git a/client/galaxy/scripts/mvc/grid/grid-view.js b/client/galaxy/scripts/mvc/grid/grid-view.js index 26d66e6a2db..87e4aef2980 100644 --- a/client/galaxy/scripts/mvc/grid/grid-view.js +++ b/client/galaxy/scripts/mvc/grid/grid-view.js @@ -15,7 +15,6 @@ export default Backbone.View.extend({ // Initialize initialize: function(grid_config) { this.grid = new GridModel(); - this.dict_format = grid_config.dict_format; this.title = grid_config.title; var self = this; window.add_tag_to_grid_filter = (tag_name, tag_value) => { @@ -30,26 +29,21 @@ export default Backbone.View.extend({ }; // set element - if (this.dict_format) { - this.setElement("
"); - if (grid_config.url_base && !grid_config.items) { - var url_data = grid_config.url_data || {}; - _.each(grid_config.filters, (v, k) => { - url_data[`f-${k}`] = v; - }); - $.ajax({ - url: `${grid_config.url_base}?${$.param(url_data)}`, - success: function(response) { - response.embedded = grid_config.embedded; - response.filters = grid_config.filters || {}; - self.init_grid(response); - } - }); - } else { - this.init_grid(grid_config); - } + this.setElement("
"); + if (grid_config.url_base && !grid_config.items) { + var url_data = grid_config.url_data || {}; + _.each(grid_config.filters, (v, k) => { + url_data[`f-${k}`] = v; + }); + $.ajax({ + url: `${grid_config.url_base}?${$.param(url_data)}`, + success: function(response) { + response.embedded = grid_config.embedded; + response.filters = grid_config.filters || {}; + self.init_grid(response); + } + }); } else { - this.setElement("#grid-container"); this.init_grid(grid_config); } @@ -570,10 +564,8 @@ export default Backbone.View.extend({ window.top.location = `${href}?${$.param(this.grid.get_url_data())}`; } else if (target == "center") { $("#galaxy_main").attr("src", `${href}?${$.param(this.grid.get_url_data())}`); - } else if (this.grid.can_async_op(operation) || this.dict_format) { - this.update_grid(); } else { - this.go_to(target, href); + this.update_grid(); } // done @@ -587,11 +579,7 @@ export default Backbone.View.extend({ } // refresh grid - if (this.grid.get("async") || this.dict_format) { - this.update_grid(); - } else { - this.go_to(target, href); - } + this.update_grid(); // done return false; @@ -599,10 +587,6 @@ export default Backbone.View.extend({ // go to url go_to: function(target, href) { - // get aysnc status - var async = this.grid.get("async"); - this.grid.set("async", false); - // get slide status var advanced_search = this.$el.find("#advanced-search").is(":visible"); this.grid.set("advanced_search", advanced_search); @@ -615,8 +599,7 @@ export default Backbone.View.extend({ // clear grid of transient request attributes. this.grid.set({ operation: undefined, - item_ids: undefined, - async: async + item_ids: undefined }); switch (target) { case "center": @@ -652,7 +635,7 @@ export default Backbone.View.extend({ var advanced_search = self.$el.find("#advanced-search").is(":visible"); // request new configuration - var json = self.dict_format ? response_text : $.parseJSON(response_text); + var json = response_text; // update json.embedded = embedded; diff --git a/client/galaxy/scripts/mvc/history/history-list.js b/client/galaxy/scripts/mvc/history/history-list.js index a46dfbcd44a..98f0ad17f6f 100644 --- a/client/galaxy/scripts/mvc/history/history-list.js +++ b/client/galaxy/scripts/mvc/history/history-list.js @@ -60,7 +60,6 @@ var View = Backbone.View.extend({ Utils.get({ url: `${Galaxy.root}history/${options.action_id}?${$.param(Galaxy.params)}`, success: function(response) { - response.dict_format = true; self.model.set(response); self.render(); } diff --git a/client/galaxy/scripts/mvc/toolshed/repository-view.js b/client/galaxy/scripts/mvc/toolshed/repository-view.js index d31a5364fc3..5cb378cd3dc 100644 --- a/client/galaxy/scripts/mvc/toolshed/repository-view.js +++ b/client/galaxy/scripts/mvc/toolshed/repository-view.js @@ -478,7 +478,7 @@ var ToolShedRepositoryView = Backbone.View.extend({ "<% _.each(shed_tool_confs.options, function(conf) { %>", '', "<% }); %>", - '', + "", '
Select the file whose tool_path setting you want used for installing repositories.
', "
", "
" diff --git a/client/galaxy/scripts/mvc/user/user-preferences.js b/client/galaxy/scripts/mvc/user/user-preferences.js index 277b9618515..ea92b5dfb50 100644 --- a/client/galaxy/scripts/mvc/user/user-preferences.js +++ b/client/galaxy/scripts/mvc/user/user-preferences.js @@ -62,7 +62,7 @@ var Model = Backbone.Model.extend({ description: _l("Associate OpenIDs with your account."), icon: "fa-openid", onclick: function() { - window.location.href = `${Galaxy.root}user/openid_manage?cntrller=user&use_panels=True`; + window.location.href = `${Galaxy.root}openids/list`; } }, custom_builds: { diff --git a/client/galaxy/scripts/reports_webapp/run_stats.js b/client/galaxy/scripts/reports/run_stats.js similarity index 100% rename from client/galaxy/scripts/reports_webapp/run_stats.js rename to client/galaxy/scripts/reports/run_stats.js diff --git a/client/galaxy/scripts/viz/trackster.js b/client/galaxy/scripts/viz/trackster.js index c8fe566fef7..88e49e2142c 100644 --- a/client/galaxy/scripts/viz/trackster.js +++ b/client/galaxy/scripts/viz/trackster.js @@ -459,7 +459,6 @@ var TracksterView = Backbone.View.extend({ view_in_saved: function(dataset_params) { var tracks_grid = new GridView({ url_base: `${Galaxy.root}visualization/list_tracks`, - dict_format: true, embedded: true }); Galaxy.modal.show({ diff --git a/client/galaxy/scripts/viz/visualization.js b/client/galaxy/scripts/viz/visualization.js index 0b25339cf82..7ba8c775ad3 100644 --- a/client/galaxy/scripts/viz/visualization.js +++ b/client/galaxy/scripts/viz/visualization.js @@ -46,14 +46,12 @@ var select_datasets = (filters, success_fn) => { var history_grid = new GridView({ url_base: `${Galaxy.root}visualization/list_history_datasets`, filters: filters, - dict_format: true, embedded: true }); // library dataset selection tab var library_grid = new GridView({ url_base: `${Galaxy.root}visualization/list_library_datasets`, - dict_format: true, embedded: true }); diff --git a/lib/galaxy/web/base/controller.py b/lib/galaxy/web/base/controller.py index 9cc3a9564a7..78b7478990f 100644 --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -1289,21 +1289,6 @@ class UsesFormDefinitionsMixin: else: return [fdc.latest_form for fdc in fdc_list if fdc.latest_form.type == form_type] - def field_param_values_ok(self, widget_name, widget_type, **kwd): - # Make sure required fields have contents, etc - params = util.Params(kwd) - if widget_type == 'AddressField': - if not util.restore_text(params.get('%s_short_desc' % widget_name, '')) \ - or not util.restore_text(params.get('%s_name' % widget_name, '')) \ - or not util.restore_text(params.get('%s_institution' % widget_name, '')) \ - or not util.restore_text(params.get('%s_address' % widget_name, '')) \ - or not util.restore_text(params.get('%s_city' % widget_name, '')) \ - or not util.restore_text(params.get('%s_state' % widget_name, '')) \ - or not util.restore_text(params.get('%s_postal_code' % widget_name, '')) \ - or not util.restore_text(params.get('%s_country' % widget_name, '')): - return False - return True - def save_widget_field(self, trans, field_obj, widget_name, **kwd): # Save a form_builder field object params = util.Params(kwd) diff --git a/lib/galaxy/web/framework/helpers/grids.py b/lib/galaxy/web/framework/helpers/grids.py index fbfc11faf38..69354b891d8 100644 --- a/lib/galaxy/web/framework/helpers/grids.py +++ b/lib/galaxy/web/framework/helpers/grids.py @@ -10,7 +10,6 @@ from galaxy.model.item_attrs import RuntimeException, UsesAnnotations, UsesItemR from galaxy.util import restore_text, sanitize_text, unicodify from galaxy.util.odict import odict from galaxy.web.framework import decorators, url_for -from galaxy.web.framework.helpers import iff log = logging.getLogger(__name__) @@ -21,12 +20,8 @@ class Grid(object): Specifies the content and format of a grid (data table). """ title = "" - exposed = True model_class = None show_item_checkboxes = False - template = "grid_base.mako" - async_template = "grid_base_async.mako" - use_async = False use_hide_message = True global_actions = [] columns = [] @@ -35,14 +30,12 @@ class Grid(object): # Any columns that are filterable (either standard or advanced) should have a default value set in the default filter. default_filter = {} default_sort_key = None - preserve_state = False use_paging = False num_rows_per_page = 25 num_page_links = 10 # Set preference names. cur_filter_pref_name = ".filter" cur_sort_key_pref_name = ".sort_key" - pass_through_operations = {} legend = None info_text = None @@ -65,7 +58,6 @@ class Grid(object): # FIXME: pretty sure this is only here to pass along, can likely be eliminated status = kwargs.get('status', None) message = kwargs.get('message', None) - dict_format = kwargs.get('dict_format', False) # Build a base filter and sort key that is the combination of the saved state and defaults. # Saved state takes preference over defaults. base_filter = {} @@ -73,14 +65,6 @@ class Grid(object): # default_filter is a dictionary that provides a default set of filters based on the grid's columns. base_filter = self.default_filter.copy() base_sort_key = self.default_sort_key - if self.preserve_state: - pref_name = text_type(self.__class__.__name__ + self.cur_filter_pref_name) - if pref_name in trans.get_user().preferences: - saved_filter = loads(trans.get_user().preferences[pref_name]) - base_filter.update(saved_filter) - pref_name = text_type(self.__class__.__name__ + self.cur_sort_key_pref_name) - if pref_name in trans.get_user().preferences: - base_sort_key = loads(trans.get_user().preferences[pref_name]) # Build initial query query = self.build_initial_query(trans, **kwargs) query = self.apply_query_filter(trans, query, **kwargs) @@ -228,26 +212,11 @@ class Grid(object): # There are some places in grid templates where it's useful for a grid # to have its current filter. self.cur_filter_dict = cur_filter_dict - # Preserve grid state: save current filter and sort key. - if self.preserve_state: - pref_name = text_type(self.__class__.__name__ + self.cur_filter_pref_name) - trans.get_user().preferences[pref_name] = text_type(dumps(cur_filter_dict)) - if sort_key: - pref_name = text_type(self.__class__.__name__ + self.cur_sort_key_pref_name) - trans.get_user().preferences[pref_name] = text_type(dumps(sort_key)) - trans.sa_session.flush() + # Log grid view. context = text_type(self.__class__.__name__) params = cur_filter_dict.copy() params['sort'] = sort_key - params['async'] = ('async' in kwargs) - - # TODO:?? - # commenting this out; when this fn calls session.add( action ) and session.flush the query from this fn - # is effectively 'wiped' out. Nate believes it has something to do with our use of session( autocommit=True ) - # in mapping.py. If you change that to False, the log_action doesn't affect the query - # Below, I'm rendering the template first (that uses query), then calling log_action, then returning the page - # trans.log_action( trans.get_user(), text_type( "grid.view" ), context, params ) # Render grid. def url(*args, **kwargs): @@ -280,43 +249,14 @@ class Grid(object): self.use_panels = (kwargs.get('use_panels', False) in [True, 'True', 'true']) self.advanced_search = (kwargs.get('advanced_search', False) in [True, 'True', 'true']) - async_request = ((self.use_async) and (kwargs.get('async', False) in [True, 'True', 'true'])) # Currently, filling the template returns a str object; this requires decoding the string into a # unicode object within mako templates. What probably should be done is to return the template as # utf-8 unicode; however, this would require encoding the object as utf-8 before returning the grid # results via a controller method, which is require substantial changes. Hence, for now, return grid # as str. - if not dict_format: - page = trans.fill_template(iff(async_request, self.async_template, self.template), - grid=self, - query=query, - cur_page_num=page_num, - num_pages=num_pages, - num_page_links=self.num_page_links, - default_filter_dict=self.default_filter, - cur_filter_dict=cur_filter_dict, - sort_key=sort_key, - current_item=current_item, - ids=kwargs.get('id', []), - url=url, - status=status, - message=message, - info_text=self.info_text, - use_panels=self.use_panels, - use_hide_message=self.use_hide_message, - advanced_search=self.advanced_search, - show_item_checkboxes=(self.show_item_checkboxes or - kwargs.get('show_item_checkboxes', '') in ['True', 'true']), - # Pass back kwargs so that grid template can set and use args without - # grid explicitly having to pass them. - kwargs=kwargs) - trans.log_action(trans.get_user(), text_type("grid.view"), context, params) - return page - grid_config = { 'title' : self.title, 'url_base' : trans.request.path_url, - 'async' : self.use_async, 'async_ops' : [], 'categorical_filters' : {}, 'filters' : cur_filter_dict, diff --git a/lib/galaxy/webapps/galaxy/buildapp.py b/lib/galaxy/webapps/galaxy/buildapp.py index 04f56c0fd5f..db3ac23a267 100644 --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -106,6 +106,7 @@ def app_factory(global_conf, load_app_kwds={}, **kwargs): webapp.add_client_route('/tours/{tour_id}') webapp.add_client_route('/user') webapp.add_client_route('/user/{form_id}') + webapp.add_client_route('/openids/list') webapp.add_client_route('/visualizations/list_published') webapp.add_client_route('/visualizations/list') webapp.add_client_route('/visualizations/edit') diff --git a/lib/galaxy/webapps/galaxy/controllers/admin.py b/lib/galaxy/webapps/galaxy/controllers/admin.py index 1de539d9785..4941f9941a9 100644 --- a/lib/galaxy/webapps/galaxy/controllers/admin.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin.py @@ -154,7 +154,6 @@ class UserListGrid(grids.Grid): grids.GridColumnFilter("All", args=dict(deleted='All')) ] num_rows_per_page = 50 - preserve_state = False use_paging = True def get_current_item(self, trans, **kwargs): @@ -255,7 +254,6 @@ class RoleListGrid(grids.Grid): grids.GridColumnFilter("All", args=dict(deleted='All')) ] num_rows_per_page = 50 - preserve_state = False use_paging = True def apply_query_filter(self, trans, query, **kwargs): @@ -335,7 +333,6 @@ class GroupListGrid(grids.Grid): grids.GridColumnFilter("All", args=dict(deleted='All')) ] num_rows_per_page = 50 - preserve_state = False use_paging = True @@ -447,7 +444,6 @@ class QuotaListGrid(grids.Grid): grids.GridColumnFilter("All", args=dict(deleted='All')) ] num_rows_per_page = 50 - preserve_state = False use_paging = True @@ -499,7 +495,6 @@ class ToolVersionListGrid(grids.Grid): standard_filters = [] default_filter = {} num_rows_per_page = 50 - preserve_state = False use_paging = True def build_initial_query(self, trans, **kwd): @@ -559,7 +554,6 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP if message and status: kwd['message'] = util.sanitize_text(message) kwd['status'] = status - kwd['dict_format'] = True return self.user_list_grid(trans, **kwd) @web.expose_api @@ -592,7 +586,6 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP if message: kwargs['message'] = util.sanitize_text(message) kwargs['status'] = status or 'done' - kwargs['dict_format'] = True return self.quota_list_grid(trans, **kwargs) @web.expose_api @@ -902,7 +895,6 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP @web.expose_api @web.require_admin def tool_versions_list(self, trans, **kwd): - kwd['dict_format'] = True return self.tool_version_list_grid(trans, **kwd) @web.expose @@ -923,7 +915,6 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP message, status = self._undelete_role(trans, ids) elif operation == 'purge': message, status = self._purge_role(trans, ids) - kwargs['dict_format'] = True if message and status: kwargs['message'] = util.sanitize_text(message) kwargs['status'] = status @@ -1168,7 +1159,6 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP message, status = self._undelete_group(trans, ids) elif operation == 'purge': message, status = self._purge_group(trans, ids) - kwargs['dict_format'] = True if message and status: kwargs['message'] = util.sanitize_text(message) kwargs['status'] = status diff --git a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py index c8d2c278d41..e4045f8508f 100644 --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -88,7 +88,6 @@ class AdminToolshed(AdminGalaxy): if message and status: kwd['message'] = util.sanitize_text(message) kwd['status'] = 'success' if status in ['ok', 'done', 'success'] else 'error' - kwd['dict_format'] = True return self.installed_repository_grid(trans, **kwd) @web.expose diff --git a/lib/galaxy/webapps/galaxy/controllers/dataset.py b/lib/galaxy/webapps/galaxy/controllers/dataset.py index 5f8c142eedd..c21cee44b9a 100644 --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -87,8 +87,6 @@ class HistoryDatasetAssociationListGrid(grids.Grid): ] standard_filters = [] default_filter = dict(name="All", deleted="False", tags="All") - preserve_state = False - use_async = True use_paging = True num_rows_per_page = 50 @@ -572,7 +570,6 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE kwargs['refresh_frames'] = ['history'] # Render the list view - kwargs['dict_format'] = True return self.stored_list_grid(trans, status=status, message=message, **kwargs) @web.expose diff --git a/lib/galaxy/webapps/galaxy/controllers/forms.py b/lib/galaxy/webapps/galaxy/controllers/forms.py index 0142d8044fd..bea7e5311b9 100644 --- a/lib/galaxy/webapps/galaxy/controllers/forms.py +++ b/lib/galaxy/webapps/galaxy/controllers/forms.py @@ -39,7 +39,6 @@ class FormsGrid(grids.Grid): model_class = model.FormDefinitionCurrent default_sort_key = "-update_time" num_rows_per_page = 50 - preserve_state = True use_paging = True default_filter = dict(deleted="False") columns = [ @@ -99,7 +98,6 @@ class Forms(BaseUIController): if message and status: kwd['message'] = util.sanitize_text(message) kwd['status'] = status - kwd['dict_format'] = True return self.forms_grid(trans, **kwd) @web.expose_api diff --git a/lib/galaxy/webapps/galaxy/controllers/history.py b/lib/galaxy/webapps/galaxy/controllers/history.py index 38a28e85359..64772493454 100644 --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -130,8 +130,6 @@ class HistoryListGrid(grids.Grid): ] default_filter = dict(name="All", deleted="False", tags="All", sharing="All") num_rows_per_page = 15 - preserve_state = False - use_async = True use_paging = True info_text = "Histories that have been deleted for more than a time period specified by the Galaxy administrator(s) may be permanently deleted." @@ -194,7 +192,6 @@ class HistoryAllPublishedGrid(grids.Grid): default_filter = dict(public_url="All", username="All", tags="All") use_paging = True num_rows_per_page = 50 - use_async = True columns = [ NameURLColumn("Name", key="name", filterable="advanced"), grids.OwnerAnnotationColumn("Annotation", key="annotation", model_annotation_association_class=model.HistoryAnnotationAssociation, filterable="advanced"), @@ -246,7 +243,6 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt @web.expose @web.json def list_published(self, trans, **kwargs): - kwargs['dict_format'] = True return self.published_list_grid(trans, **kwargs) @web.expose_api @@ -316,7 +312,6 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt trans.sa_session.flush() # Render the list view - kwargs['dict_format'] = True if message and status: kwargs['message'] = sanitize_text(message) kwargs['status'] = status @@ -454,7 +449,6 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt message = "Unshared %d shared histories" % len(ids) status = 'done' # Render the list view - kwargs['dict_format'] = True return self.shared_list_grid(trans, status=status, message=message, **kwargs) @web.expose diff --git a/lib/galaxy/webapps/galaxy/controllers/page.py b/lib/galaxy/webapps/galaxy/controllers/page.py index df1fe46b64d..8f9ff09a41d 100644 --- a/lib/galaxy/webapps/galaxy/controllers/page.py +++ b/lib/galaxy/webapps/galaxy/controllers/page.py @@ -62,7 +62,6 @@ class PageListGrid(grids.Grid): class PageAllPublishedGrid(grids.Grid): # Grid definition use_panels = True - use_async = True title = "Published Pages" model_class = model.Page default_sort_key = "update_time" @@ -104,7 +103,6 @@ class ItemSelectionGrid(grids.Grid): show_item_checkboxes = True default_filter = {"deleted": "False", "sharing": "All"} default_sort_key = "-update_time" - use_async = True use_paging = True num_rows_per_page = 10 @@ -322,7 +320,6 @@ class PageController(BaseUIController, SharableMixin, session.flush() # Build grid dictionary. - kwargs['dict_format'] = True grid = self._page_list(trans, *args, **kwargs) grid['shared_by_others'] = self._get_shared(trans) return grid @@ -330,7 +327,6 @@ class PageController(BaseUIController, SharableMixin, @web.expose @web.json def list_published(self, trans, *args, **kwargs): - kwargs['dict_format'] = True grid = self._all_published_list(trans, *args, **kwargs) grid['shared_by_others'] = self._get_shared(trans) return grid @@ -700,7 +696,6 @@ class PageController(BaseUIController, SharableMixin, @web.require_login("select a history from saved histories") def list_histories_for_selection(self, trans, **kwargs): """ Returns HTML that enables a user to select one or more histories. """ - kwargs['dict_format'] = True return self._history_selection_grid(trans, **kwargs) @web.expose @@ -708,7 +703,6 @@ class PageController(BaseUIController, SharableMixin, @web.require_login("select a workflow from saved workflows") def list_workflows_for_selection(self, trans, **kwargs): """ Returns HTML that enables a user to select one or more workflows. """ - kwargs['dict_format'] = True return self._workflow_selection_grid(trans, **kwargs) @web.expose @@ -716,7 +710,6 @@ class PageController(BaseUIController, SharableMixin, @web.require_login("select a visualization from saved visualizations") def list_visualizations_for_selection(self, trans, **kwargs): """ Returns HTML that enables a user to select one or more visualizations. """ - kwargs['dict_format'] = True return self._visualization_selection_grid(trans, **kwargs) @web.expose @@ -724,7 +717,6 @@ class PageController(BaseUIController, SharableMixin, @web.require_login("select a page from saved pages") def list_pages_for_selection(self, trans, **kwargs): """ Returns HTML that enables a user to select one or more pages. """ - kwargs['dict_format'] = True return self._page_selection_grid(trans, **kwargs) @web.expose @@ -732,7 +724,6 @@ class PageController(BaseUIController, SharableMixin, @web.require_login("select a dataset from saved datasets") def list_datasets_for_selection(self, trans, **kwargs): """ Returns HTML that enables a user to select one or more datasets. """ - kwargs['dict_format'] = True return self._datasets_selection_grid(trans, **kwargs) @web.expose diff --git a/lib/galaxy/webapps/galaxy/controllers/root.py b/lib/galaxy/webapps/galaxy/controllers/root.py index 67a549722f3..ca727ea6889 100644 --- a/lib/galaxy/webapps/galaxy/controllers/root.py +++ b/lib/galaxy/webapps/galaxy/controllers/root.py @@ -57,7 +57,7 @@ class RootController(controller.JSAppLauncher, UsesAnnotations): 'toolbox' : app.toolbox.to_dict(trans, in_panel=False), 'toolbox_in_panel' : app.toolbox.to_dict(trans), 'message_box_visible' : app.config.message_box_visible, - 'show_inactivity_warning' : app.config.user_activation_on and trans.user and not trans.user.active, + 'show_inactivity_warning' : app.config.user_activation_on and trans.user and not trans.user.active } # TODO: move to user diff --git a/lib/galaxy/webapps/galaxy/controllers/user.py b/lib/galaxy/webapps/galaxy/controllers/user.py index 316d9ba6964..5d2a0eae80d 100644 --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -62,16 +62,17 @@ can also copy and paste it into your browser. class UserOpenIDGrid(grids.Grid): - use_panels = False title = "OpenIDs linked to your account" model_class = model.UserOpenID - template = '/user/openid_manage.mako' default_filter = {"openid": "All"} default_sort_key = "-create_time" columns = [ grids.TextColumn("OpenID URL", key="openid", link=(lambda x: dict(action='openid_auth', login_button="Login", openid_url=x.openid if not x.provider else '', openid_provider=x.provider, auto_associate=True))), grids.GridColumn("Created", key="create_time", format=time_ago), ] + global_actions = [ + grids.GridAction("Add new account", url_args=dict(action="create_openid"), target="center") + ] operations = [ grids.GridOperation("Delete", async_compatible=True), ] @@ -138,8 +139,10 @@ class User(BaseUIController, UsesFormDefinitionsMixin, CreatesUsersMixin, Create return trans.show_error_message('OpenID authentication is not enabled in this instance of Galaxy') auto_associate = util.string_as_bool(kwd.get('auto_associate', False)) action = 'login' + controller = 'user' if trans.user: - action = 'openid_manage' + action = 'openids' + controller = 'list' if trans.app.config.support_url is not None: contact = 'support' % trans.app.config.support_url else: @@ -153,7 +156,7 @@ class User(BaseUIController, UsesFormDefinitionsMixin, CreatesUsersMixin, Create openid_provider = kwd.get('openid_provider', None) if info.status == trans.app.openid_manager.FAILURE and display_identifier: message = "Login via OpenID failed. The technical reason for this follows, please include this message in your email if you need to %s to resolve this problem: %s" % (contact, info.message) - return trans.response.send_redirect(url_for(controller='user', + return trans.response.send_redirect(url_for(controller=controller, action=action, use_panels=True, redirect=redirect, @@ -208,8 +211,8 @@ class User(BaseUIController, UsesFormDefinitionsMixin, CreatesUsersMixin, Create message = '%s
Click here to return to the page you were previously viewing.' % (message, escape(self.__get_redirect_url(redirect))) if redirect and status != "error": return trans.response.send_redirect(self.__get_redirect_url(redirect)) - return trans.response.send_redirect(url_for(controller='user', - action='openid_manage', + return trans.response.send_redirect(url_for(controller='openids', + action='list', use_panels=True, redirect=redirect, message=message, @@ -300,18 +303,14 @@ class User(BaseUIController, UsesFormDefinitionsMixin, CreatesUsersMixin, Create for openid in openid_objs: message = '%s
  • %s
    • ' % (message, url_for(controller='user', action='openid_auth', openid_provider=openid.id, redirect=redirect, auto_associate=True), openid.name) message = "%s" % (message) - return trans.response.send_redirect(url_for(controller='user', - action='openid_manage', - use_panels=use_panels, - redirect=redirect, + return trans.response.send_redirect(url_for(controller='openids', + action='list', message=message, status='info')) if redirect: return trans.response.send_redirect(redirect) - return trans.response.send_redirect(url_for(controller='user', - action='openid_manage', - use_panels=use_panels, - redirect=redirect, + return trans.response.send_redirect(url_for(controller='openids', + action='list', message=message, status='info')) if kwd.get('create_user_button', False): @@ -352,18 +351,14 @@ class User(BaseUIController, UsesFormDefinitionsMixin, CreatesUsersMixin, Create for openid in openid_objs: message = '%s
  • %s
    • ' % (message, url_for(controller='user', action='openid_auth', openid_provider=openid.id, redirect=redirect, auto_associate=True), openid.name) message = "%s" % (message) - return trans.response.send_redirect(url_for(controller='user', - action='openid_manage', - use_panels=True, - redirect=redirect, + return trans.response.send_redirect(url_for(controller='openids', + action='list', message=message, status='info')) if redirect: return trans.response.send_redirect(redirect) - return trans.response.send_redirect(url_for(controller='user', - action='openid_manage', - use_panels=use_panels, - redirect=redirect, + return trans.response.send_redirect(url_for(controller='openids', + action='list', message=message, status='info')) else: @@ -386,63 +381,53 @@ class User(BaseUIController, UsesFormDefinitionsMixin, CreatesUsersMixin, Create openids=openids) @web.expose - @web.require_login('manage OpenIDs') - def openid_disassociate(self, trans, **kwd): - '''Disassociates a user with an OpenID''' - if not trans.app.config.enable_openid: - return trans.show_error_message('OpenID authentication is not enabled in this instance of Galaxy') - params = util.Params(kwd) - ids = params.get('id', None) - message = params.get('message', None) - status = params.get('status', None) - use_panels = params.get('use_panels', False) - user_openids = [] - if not ids: - message = 'You must select at least one OpenID to disassociate from your Galaxy account.' - status = 'error' - else: - ids = util.listify(params.id) - for id in ids: - id = trans.security.decode_id(id) - user_openid = trans.sa_session.query(trans.app.model.UserOpenID).get(int(id)) - if not user_openid or (trans.user.id != user_openid.user_id): - message = 'The selected OpenID(s) are not associated with your Galaxy account.' - status = 'error' - user_openids = [] - break - user_openids.append(user_openid) - if user_openids: - deleted_urls = [] - for user_openid in user_openids: - trans.sa_session.delete(user_openid) - deleted_urls.append(user_openid.openid) - trans.sa_session.flush() - for deleted_url in deleted_urls: - trans.log_event("User disassociated OpenID: %s" % deleted_url) - message = '%s OpenIDs were disassociated from your Galaxy account.' % len(ids) - status = 'done' - return trans.response.send_redirect(url_for(controller='user', - action='openid_manage', - use_panels=use_panels, - message=message, - status=status)) + @web.require_login('create OpenIDs') + def create_openid(self, trans, **kwd): + return trans.fill_template('/user/openid_manage.mako', + openid_providers=trans.app.openid_providers, + redirect=kwd.get('redirect', url_for(controller='openids', action='list')).strip()) - @web.expose + @web.expose_api @web.require_login('manage OpenIDs') - def openid_manage(self, trans, **kwd): - '''Manage OpenIDs for user''' + def openids_list(self, trans, **kwd): + '''List of availabel OpenIDs for user''' + message = kwd.get('message', '') + status = kwd.get('status', '') if not trans.app.config.enable_openid: - return trans.show_error_message('OpenID authentication is not enabled in this instance of Galaxy') - use_panels = kwd.get('use_panels', False) + message = 'OpenID authentication is not enabled in this instance of Galaxy.' + status = 'error' if 'operation' in kwd: operation = kwd['operation'].lower() - if operation == "delete": - return trans.response.send_redirect(url_for(controller='user', - action='openid_disassociate', - use_panels=use_panels, - id=kwd['id'])) - kwd['redirect'] = kwd.get('redirect', url_for(controller='user', action='openid_manage', use_panels=True)).strip() - kwd['openid_providers'] = trans.app.openid_providers + ids = util.listify(kwd.get('id')) + if operation == 'delete': + if not ids: + message = 'You must select at least one OpenID to disassociate from your Galaxy account.' + status = 'error' + else: + user_openids = [] + for id in ids: + id = trans.security.decode_id(id) + user_openid = trans.sa_session.query(trans.app.model.UserOpenID).get(int(id)) + if not user_openid or (trans.user.id != user_openid.user_id): + message = 'The selected OpenID(s) are not associated with your Galaxy account.' + status = 'error' + user_openids = [] + break + user_openids.append(user_openid) + if user_openids: + deleted_urls = [] + for user_openid in user_openids: + trans.sa_session.delete(user_openid) + deleted_urls.append(user_openid.openid) + trans.sa_session.flush() + for deleted_url in deleted_urls: + trans.log_event('User disassociated OpenID: %s' % deleted_url) + message = '%s OpenIDs were disassociated from your Galaxy account.' % len(ids) + status = 'done' + if message and status: + kwd['message'] = util.sanitize_text(message) + kwd['status'] = status + kwd['dict_format'] = True return self.user_openid_grid(trans, **kwd) @web.expose diff --git a/lib/galaxy/webapps/galaxy/controllers/visualization.py b/lib/galaxy/webapps/galaxy/controllers/visualization.py index c172cb3d1f1..4e0aa904e2d 100644 --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -118,7 +118,6 @@ class TracksterSelectionGrid(grids.Grid): title = "Insert into visualization" model_class = model.Visualization default_sort_key = "-update_time" - use_async = True use_paging = False show_item_checkboxes = True columns = [ @@ -193,7 +192,6 @@ class VisualizationListGrid(grids.Grid): class VisualizationAllPublishedGrid(grids.Grid): # Grid definition use_panels = True - use_async = True title = "Published Visualizations" model_class = model.Visualization default_sort_key = "update_time" @@ -242,7 +240,6 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization @web.require_login("see all available libraries") def list_libraries(self, trans, **kwargs): """List all libraries that can be used for selecting datasets.""" - kwargs['dict_format'] = True return self._libraries_grid(trans, **kwargs) @web.expose @@ -251,7 +248,6 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization def list_history_datasets(self, trans, **kwargs): """List a history's datasets that can be added to a visualization.""" kwargs['show_item_checkboxes'] = 'True' - kwargs['dict_format'] = True return self._history_datasets_grid(trans, **kwargs) @web.expose @@ -260,19 +256,16 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization def list_library_datasets(self, trans, **kwargs): """List a library's datasets that can be added to a visualization.""" kwargs['show_item_checkboxes'] = 'True' - kwargs['dict_format'] = True return self._library_datasets_grid(trans, **kwargs) @web.expose @web.json def list_tracks(self, trans, **kwargs): - kwargs['dict_format'] = True return self._tracks_grid(trans, **kwargs) @web.expose @web.json def list_published(self, trans, *args, **kwargs): - kwargs['dict_format'] = True grid = self._published_list_grid(trans, **kwargs) grid['shared_by_others'] = self._get_shared(trans) return grid @@ -294,7 +287,6 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization self.copy(trans, **kwargs) session.flush() kwargs['embedded'] = True - kwargs['dict_format'] = True if message and status: kwargs['message'] = sanitize_text(message) kwargs['status'] = status diff --git a/lib/galaxy/webapps/galaxy/controllers/workflow.py b/lib/galaxy/webapps/galaxy/controllers/workflow.py index d45a11add7b..e5b9ba020f6 100644 --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -102,7 +102,6 @@ class StoredWorkflowAllPublishedGrid(grids.Grid): model_class = model.StoredWorkflow default_sort_key = "update_time" default_filter = dict(public_url="All", username="All", tags="All") - use_async = True columns = [ grids.PublicURLColumn("Name", key="name", filterable="advanced", attach_popup=True), grids.OwnerAnnotationColumn("Annotation", @@ -202,7 +201,6 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi @web.expose @web.json def list_published(self, trans, **kwargs): - kwargs['dict_format'] = True return self.published_list_grid(trans, **kwargs) @web.expose diff --git a/lib/galaxy/webapps/reports/controllers/jobs.py b/lib/galaxy/webapps/reports/controllers/jobs.py index 73804c3fa16..6ec5384568e 100644 --- a/lib/galaxy/webapps/reports/controllers/jobs.py +++ b/lib/galaxy/webapps/reports/controllers/jobs.py @@ -17,8 +17,8 @@ from sqlalchemy import and_, not_, or_ from galaxy import model, util from galaxy.web.base.controller import BaseUIController, web -from galaxy.web.framework.helpers import grids from galaxy.webapps.reports.controllers.query import ReportQueryBuilder +from galaxy.webapps.reports.framework import grids log = logging.getLogger(__name__) @@ -179,7 +179,6 @@ class SpecifiedDateListGrid(grids.Grid): use_async = False model_class = model.Job title = "Jobs" - template = '/webapps/reports/grid.mako' default_sort_key = "id" columns = [ JobIdColumn("Id", @@ -223,7 +222,6 @@ class SpecifiedDateListGrid(grids.Grid): standard_filters = [] default_filter = {'specified_date': 'All'} num_rows_per_page = 50 - preserve_state = False use_paging = True def build_initial_query(self, trans, **kwd): diff --git a/lib/galaxy/webapps/reports/controllers/workflows.py b/lib/galaxy/webapps/reports/controllers/workflows.py index fe6e06dfac0..ff17c2b00d4 100644 --- a/lib/galaxy/webapps/reports/controllers/workflows.py +++ b/lib/galaxy/webapps/reports/controllers/workflows.py @@ -18,12 +18,12 @@ from sqlalchemy import and_ from galaxy import model, util from galaxy.web.base.controller import BaseUIController, web -from galaxy.web.framework.helpers import grids from galaxy.webapps.reports.controllers.jobs import ( get_spark_time, sorter ) from galaxy.webapps.reports.controllers.query import ReportQueryBuilder +from galaxy.webapps.reports.framework import grids log = logging.getLogger(__name__) @@ -81,7 +81,6 @@ class SpecifiedDateListGrid(grids.Grid): use_async = False model_class = model.StoredWorkflow title = "Workflows" - template = '/webapps/reports/grid.mako' default_sort_key = "name" columns = [ WorkflowNameColumn("Name", @@ -113,7 +112,6 @@ class SpecifiedDateListGrid(grids.Grid): standard_filters = [] default_filter = {'specified_date': 'All'} num_rows_per_page = 50 - preserve_state = False use_paging = True def build_initial_query(self, trans, **kwd): diff --git a/lib/galaxy/webapps/reports/framework/__init__.py b/lib/galaxy/webapps/reports/framework/__init__.py new file mode 100644 index 00000000000..e69de29bb2d diff --git a/lib/galaxy/webapps/reports/framework/grids.py b/lib/galaxy/webapps/reports/framework/grids.py new file mode 100644 index 00000000000..1cd9c69a135 --- /dev/null +++ b/lib/galaxy/webapps/reports/framework/grids.py @@ -0,0 +1,854 @@ +import logging +import math +from json import dumps, loads + +from markupsafe import escape +from six import string_types, text_type +from sqlalchemy.sql.expression import and_, false, func, null, or_, true + +from galaxy.model.item_attrs import RuntimeException, UsesAnnotations, UsesItemRatings +from galaxy.util import sanitize_text, unicodify +from galaxy.util.odict import odict +from galaxy.web.framework import decorators, url_for +from galaxy.web.framework.helpers import iff + + +log = logging.getLogger(__name__) + + +class Grid(object): + """ + Specifies the content and format of a grid (data table). + """ + title = "" + model_class = None + show_item_checkboxes = False + template = "legacy/grid_base.mako" + async_template = "legacy/grid_base_async.mako" + use_async = False + use_hide_message = True + global_actions = [] + columns = [] + operations = [] + standard_filters = [] + # Any columns that are filterable (either standard or advanced) should have a default value set in the default filter. + default_filter = {} + default_sort_key = None + use_paging = False + num_rows_per_page = 25 + num_page_links = 10 + # Set preference names. + cur_filter_pref_name = ".filter" + cur_sort_key_pref_name = ".sort_key" + legend = None + info_text = None + + def __init__(self): + # Determine if any multiple row operations are defined + self.has_multiple_item_operations = False + for operation in self.operations: + if operation.allow_multiple: + self.has_multiple_item_operations = True + break + + # If a column does not have a model class, set the column's model class + # to be the grid's model class. + for column in self.columns: + if not column.model_class: + column.model_class = self.model_class + + def __call__(self, trans, **kwargs): + # Get basics. + # FIXME: pretty sure this is only here to pass along, can likely be eliminated + status = kwargs.get('status', None) + message = kwargs.get('message', None) + # Build a base filter and sort key that is the combination of the saved state and defaults. + # Saved state takes preference over defaults. + base_filter = {} + if self.default_filter: + # default_filter is a dictionary that provides a default set of filters based on the grid's columns. + base_filter = self.default_filter.copy() + base_sort_key = self.default_sort_key + # Build initial query + query = self.build_initial_query(trans, **kwargs) + query = self.apply_query_filter(trans, query, **kwargs) + # Maintain sort state in generated urls + extra_url_args = {} + # Determine whether use_default_filter flag is set. + use_default_filter_str = kwargs.get('use_default_filter') + use_default_filter = False + if use_default_filter_str: + use_default_filter = (use_default_filter_str.lower() == 'true') + # Process filtering arguments to (a) build a query that represents the filter and (b) build a + # dictionary that denotes the current filter. + cur_filter_dict = {} + for column in self.columns: + if column.key: + # Get the filter criterion for the column. Precedence is (a) if using default filter, only look there; otherwise, + # (b) look in kwargs; and (c) look in base filter. + column_filter = None + if use_default_filter: + if self.default_filter: + column_filter = self.default_filter.get(column.key) + elif "f-" + column.model_class.__name__ + ".%s" % column.key in kwargs: + # Queries that include table joins cannot guarantee unique column names. This problem is + # handled by setting the column_filter value to .. + column_filter = kwargs.get("f-" + column.model_class.__name__ + ".%s" % column.key) + elif "f-" + column.key in kwargs: + column_filter = kwargs.get("f-" + column.key) + elif column.key in base_filter: + column_filter = base_filter.get(column.key) + + # Method (1) combines a mix of strings and lists of strings into a single string and (2) attempts to de-jsonify all strings. + def loads_recurse(item): + decoded_list = [] + if isinstance(item, string_types): + try: + # Not clear what we're decoding, so recurse to ensure that we catch everything. + decoded_item = loads(item) + if isinstance(decoded_item, list): + decoded_list = loads_recurse(decoded_item) + else: + decoded_list = [text_type(decoded_item)] + except ValueError: + decoded_list = [text_type(item)] + elif isinstance(item, list): + for element in item: + a_list = loads_recurse(element) + decoded_list = decoded_list + a_list + return decoded_list + # If column filter found, apply it. + if column_filter is not None: + # TextColumns may have a mix of json and strings. + if isinstance(column, TextColumn): + column_filter = loads_recurse(column_filter) + if len(column_filter) == 1: + column_filter = column_filter[0] + # Interpret ',' as a separator for multiple terms. + if isinstance(column_filter, string_types) and column_filter.find(',') != -1: + column_filter = column_filter.split(',') + + # Check if filter is empty + if isinstance(column_filter, list): + # Remove empty strings from filter list + column_filter = [x for x in column_filter if x != ''] + if len(column_filter) == 0: + continue + elif isinstance(column_filter, string_types): + # If filter criterion is empty, do nothing. + if column_filter == '': + continue + + # Update query. + query = column.filter(trans, trans.user, query, column_filter) + # Upate current filter dict. + # Column filters are rendered in various places, sanitize them all here. + cur_filter_dict[column.key] = sanitize_text(column_filter) + # Carry filter along to newly generated urls; make sure filter is a string so + # that we can encode to UTF-8 and thus handle user input to filters. + if isinstance(column_filter, list): + # Filter is a list; process each item. + column_filter = [text_type(_).encode('utf-8') if not isinstance(_, string_types) else _ for _ in column_filter] + extra_url_args["f-" + column.key] = dumps(column_filter) + else: + # Process singleton filter. + if not isinstance(column_filter, string_types): + column_filter = text_type(column_filter) + extra_url_args["f-" + column.key] = column_filter.encode("utf-8") + # Process sort arguments. + sort_key = None + if 'sort' in kwargs: + sort_key = kwargs['sort'] + elif base_sort_key: + sort_key = base_sort_key + if sort_key: + ascending = not(sort_key.startswith("-")) + # Queries that include table joins cannot guarantee unique column names. This problem is + # handled by setting the column_filter value to .. + table_name = None + if sort_key.find('.') > -1: + a_list = sort_key.split('.') + if ascending: + table_name = a_list[0] + else: + table_name = a_list[0][1:] + column_name = a_list[1] + elif ascending: + column_name = sort_key + else: + column_name = sort_key[1:] + # Sort key is a column key. + for column in self.columns: + if column.key and column.key.find('.') > -1: + column_key = column.key.split('.')[1] + else: + column_key = column.key + if (table_name is None or table_name == column.model_class.__name__) and column_key == column_name: + query = column.sort(trans, query, ascending, column_name=column_name) + break + extra_url_args['sort'] = sort_key + # There might be a current row + current_item = self.get_current_item(trans, **kwargs) + # Process page number. + if self.use_paging: + if 'page' in kwargs: + if kwargs['page'] == 'all': + page_num = 0 + else: + page_num = int(kwargs['page']) + else: + page_num = 1 + if page_num == 0: + # Show all rows in page. + total_num_rows = query.count() + page_num = 1 + num_pages = 1 + else: + # Show a limited number of rows. Before modifying query, get the total number of rows that query + # returns so that the total number of pages can be computed. + total_num_rows = query.count() + query = query.limit(self.num_rows_per_page).offset((page_num - 1) * self.num_rows_per_page) + num_pages = int(math.ceil(float(total_num_rows) / self.num_rows_per_page)) + else: + # Defaults. + page_num = 1 + num_pages = 1 + # There are some places in grid templates where it's useful for a grid + # to have its current filter. + self.cur_filter_dict = cur_filter_dict + + # Log grid view. + context = text_type(self.__class__.__name__) + params = cur_filter_dict.copy() + params['sort'] = sort_key + params['async'] = ('async' in kwargs) + + # TODO:?? + # commenting this out; when this fn calls session.add( action ) and session.flush the query from this fn + # is effectively 'wiped' out. Nate believes it has something to do with our use of session( autocommit=True ) + # in mapping.py. If you change that to False, the log_action doesn't affect the query + # Below, I'm rendering the template first (that uses query), then calling log_action, then returning the page + # trans.log_action( trans.get_user(), text_type( "grid.view" ), context, params ) + + # Render grid. + def url(*args, **kwargs): + route_name = kwargs.pop('__route_name__', None) + # Only include sort/filter arguments if not linking to another + # page. This is a bit of a hack. + if 'action' in kwargs: + new_kwargs = dict() + else: + new_kwargs = dict(extra_url_args) + # Extend new_kwargs with first argument if found + if len(args) > 0: + new_kwargs.update(args[0]) + new_kwargs.update(kwargs) + # We need to encode item ids + if 'id' in new_kwargs: + id = new_kwargs['id'] + if isinstance(id, list): + new_kwargs['id'] = [trans.security.encode_id(i) for i in id] + else: + new_kwargs['id'] = trans.security.encode_id(id) + # The url_for invocation *must* include a controller and action. + if 'controller' not in new_kwargs: + new_kwargs['controller'] = trans.controller + if 'action' not in new_kwargs: + new_kwargs['action'] = trans.action + if route_name: + return url_for(route_name, **new_kwargs) + return url_for(**new_kwargs) + + self.use_panels = (kwargs.get('use_panels', False) in [True, 'True', 'true']) + self.advanced_search = (kwargs.get('advanced_search', False) in [True, 'True', 'true']) + async_request = ((self.use_async) and (kwargs.get('async', False) in [True, 'True', 'true'])) + # Currently, filling the template returns a str object; this requires decoding the string into a + # unicode object within mako templates. What probably should be done is to return the template as + # utf-8 unicode; however, this would require encoding the object as utf-8 before returning the grid + # results via a controller method, which is require substantial changes. Hence, for now, return grid + # as str. + page = trans.fill_template(iff(async_request, self.async_template, self.template), + grid=self, + query=query, + cur_page_num=page_num, + num_pages=num_pages, + num_page_links=self.num_page_links, + default_filter_dict=self.default_filter, + cur_filter_dict=cur_filter_dict, + sort_key=sort_key, + current_item=current_item, + ids=kwargs.get('id', []), + url=url, + status=status, + message=message, + info_text=self.info_text, + use_panels=self.use_panels, + use_hide_message=self.use_hide_message, + advanced_search=self.advanced_search, + show_item_checkboxes=(self.show_item_checkboxes or + kwargs.get('show_item_checkboxes', '') in ['True', 'true']), + # Pass back kwargs so that grid template can set and use args without + # grid explicitly having to pass them. + kwargs=kwargs) + trans.log_action(trans.get_user(), text_type("grid.view"), context, params) + return page + + def get_ids(self, **kwargs): + id = [] + if 'id' in kwargs: + id = kwargs['id'] + # Coerce ids to list + if not isinstance(id, list): + id = id.split(",") + # Ensure ids are integers + try: + id = list(map(int, id)) + except Exception: + decorators.error("Invalid id") + return id + + # ---- Override these ---------------------------------------------------- + def handle_operation(self, trans, operation, ids, **kwargs): + pass + + def get_current_item(self, trans, **kwargs): + return None + + def build_initial_query(self, trans, **kwargs): + return trans.sa_session.query(self.model_class) + + def apply_query_filter(self, trans, query, **kwargs): + # Applies a database filter that holds for all items in the grid. + # (gvk) Is this method necessary? Why not simply build the entire query, + # including applying filters in the build_initial_query() method? + return query + + +class GridColumn(object): + def __init__(self, label, key=None, model_class=None, method=None, format=None, + link=None, attach_popup=False, visible=True, nowrap=False, + # Valid values for filterable are ['standard', 'advanced', None] + filterable=None, sortable=True, label_id_prefix=None, target=None): + """Create a grid column.""" + self.label = label + self.key = key + self.model_class = model_class + self.method = method + self.format = format + self.link = link + self.target = target + self.nowrap = nowrap + self.attach_popup = attach_popup + self.visible = visible + self.filterable = filterable + # Column must have a key to be sortable. + self.sortable = (self.key is not None and sortable) + self.label_id_prefix = label_id_prefix or '' + + def get_value(self, trans, grid, item): + if self.method: + value = getattr(grid, self.method)(trans, item) + elif self.key: + value = getattr(item, self.key) + else: + value = None + if self.format: + value = self.format(value) + return escape(unicodify(value)) + + def get_link(self, trans, grid, item): + if self.link and self.link(item): + return self.link(item) + return None + + def filter(self, trans, user, query, column_filter): + """ Modify query to reflect the column filter. """ + if column_filter == "All": + pass + if column_filter == "True": + query = query.filter_by(**{self.key: True}) + elif column_filter == "False": + query = query.filter_by(**{self.key: False}) + return query + + def get_accepted_filters(self): + """ Returns a list of accepted filters for this column. """ + accepted_filters_vals = ["False", "True", "All"] + accepted_filters = [] + for val in accepted_filters_vals: + args = {self.key: val} + accepted_filters.append(GridColumnFilter(val, args)) + return accepted_filters + + def sort(self, trans, query, ascending, column_name=None): + """Sort query using this column.""" + if column_name is None: + column_name = self.key + if ascending: + query = query.order_by(self.model_class.table.c.get(column_name).asc()) + else: + query = query.order_by(self.model_class.table.c.get(column_name).desc()) + return query + + +class ReverseSortColumn(GridColumn): + """ Column that reverses sorting; this is useful when the natural sort is descending. """ + + def sort(self, trans, query, ascending, column_name=None): + return GridColumn.sort(self, trans, query, (not ascending), column_name=column_name) + + +class TextColumn(GridColumn): + """ Generic column that employs freetext and, hence, supports freetext, case-independent filtering. """ + + def filter(self, trans, user, query, column_filter): + """ Modify query to filter using free text, case independence. """ + if column_filter == "All": + pass + elif column_filter: + query = query.filter(self.get_filter(trans, user, column_filter)) + return query + + def get_filter(self, trans, user, column_filter): + """ Returns a SQLAlchemy criterion derived from column_filter. """ + if isinstance(column_filter, string_types): + return self.get_single_filter(user, column_filter) + elif isinstance(column_filter, list): + clause_list = [] + for filter in column_filter: + clause_list.append(self.get_single_filter(user, filter)) + return and_(*clause_list) + + def get_single_filter(self, user, a_filter): + """ + Returns a SQLAlchemy criterion derived for a single filter. Single filter + is the most basic filter--usually a string--and cannot be a list. + """ + # Queries that include table joins cannot guarantee that table column names will be + # unique, so check to see if a_filter is of type .. + if self.key.find('.') > -1: + a_key = self.key.split('.')[1] + else: + a_key = self.key + model_class_key_field = getattr(self.model_class, a_key) + return func.lower(model_class_key_field).like("%" + a_filter.lower() + "%") + + def sort(self, trans, query, ascending, column_name=None): + """Sort column using case-insensitive alphabetical sorting.""" + if column_name is None: + column_name = self.key + if ascending: + query = query.order_by(func.lower(self.model_class.table.c.get(column_name)).asc()) + else: + query = query.order_by(func.lower(self.model_class.table.c.get(column_name)).desc()) + return query + + +class DateTimeColumn(TextColumn): + def sort(self, trans, query, ascending, column_name=None): + """Sort query using this column.""" + return GridColumn.sort(self, trans, query, ascending, column_name=column_name) + + +class BooleanColumn(TextColumn): + def sort(self, trans, query, ascending, column_name=None): + """Sort query using this column.""" + return GridColumn.sort(self, trans, query, ascending, column_name=column_name) + + def get_single_filter(self, user, a_filter): + if self.key.find('.') > -1: + a_key = self.key.split('.')[1] + else: + a_key = self.key + model_class_key_field = getattr(self.model_class, a_key) + return model_class_key_field == a_filter + + +class IntegerColumn(TextColumn): + """ + Integer column that employs freetext, but checks that the text is an integer, + so support filtering on integer values. + + IMPORTANT NOTE: grids that use this column type should not include the column + in the cols_to_filter list of MulticolFilterColumn ( i.e., searching on this + column type should not be performed in the grid's standard search - it won't + throw exceptions, but it also will not find what you're looking for ). Grids + that search on this column should use 'filterable="advanced"' so that searching + is only performed in the advanced search component, restricting the search to + the specific column. + + This is useful for searching on object ids or other integer columns. See the + JobIdColumn column in the SpecifiedDateListGrid class in the jobs controller of + the reports webapp for an example. + """ + + def get_single_filter(self, user, a_filter): + model_class_key_field = getattr(self.model_class, self.key) + assert int(a_filter), "The search entry must be an integer" + return model_class_key_field == int(a_filter) + + def sort(self, trans, query, ascending, column_name=None): + """Sort query using this column.""" + return GridColumn.sort(self, trans, query, ascending, column_name=column_name) + + +class CommunityRatingColumn(GridColumn, UsesItemRatings): + """ Column that displays community ratings for an item. """ + + def get_value(self, trans, grid, item): + ave_item_rating, num_ratings = self.get_ave_item_rating_data(trans.sa_session, item, webapp_model=trans.model) + return trans.fill_template("tool_shed_rating.mako", + ave_item_rating=ave_item_rating, + num_ratings=num_ratings, + item_id=trans.security.encode_id(item.id)) + + def sort(self, trans, query, ascending, column_name=None): + def get_foreign_key(source_class, target_class): + """ Returns foreign key in source class that references target class. """ + target_fk = None + for fk in source_class.table.foreign_keys: + if fk.references(target_class.table): + target_fk = fk + break + if not target_fk: + raise RuntimeException("No foreign key found between objects: %s, %s" % source_class.table, target_class.table) + return target_fk + # Get the columns that connect item's table and item's rating association table. + item_rating_assoc_class = getattr(trans.model, '%sRatingAssociation' % self.model_class.__name__) + foreign_key = get_foreign_key(item_rating_assoc_class, self.model_class) + fk_col = foreign_key.parent + referent_col = foreign_key.get_referent(self.model_class.table) + # Do sorting using a subquery. + # Subquery to get average rating for each item. + ave_rating_subquery = trans.sa_session.query(fk_col, + func.avg(item_rating_assoc_class.table.c.rating).label('avg_rating')) \ + .group_by(fk_col).subquery() + # Integrate subquery into main query. + query = query.outerjoin((ave_rating_subquery, referent_col == ave_rating_subquery.columns[fk_col.name])) + # Sort using subquery results; use coalesce to avoid null values. + if not ascending: # TODO: for now, reverse sorting b/c first sort is ascending, and that should be the natural sort. + query = query.order_by(func.coalesce(ave_rating_subquery.c.avg_rating, 0).asc()) + else: + query = query.order_by(func.coalesce(ave_rating_subquery.c.avg_rating, 0).desc()) + return query + + +class OwnerAnnotationColumn(TextColumn, UsesAnnotations): + """ Column that displays and filters item owner's annotations. """ + + def __init__(self, col_name, key, model_class=None, model_annotation_association_class=None, filterable=None): + GridColumn.__init__(self, col_name, key=key, model_class=model_class, filterable=filterable) + self.sortable = False + self.model_annotation_association_class = model_annotation_association_class + + def get_value(self, trans, grid, item): + """ Returns first 150 characters of annotation. """ + annotation = self.get_item_annotation_str(trans.sa_session, item.user, item) + if annotation: + ann_snippet = annotation[:155] + if len(annotation) > 155: + ann_snippet = ann_snippet[:ann_snippet.rfind(' ')] + ann_snippet += "..." + else: + ann_snippet = "" + return escape(ann_snippet) + + def get_single_filter(self, user, a_filter): + """ Filter by annotation and annotation owner. """ + return self.model_class.annotations.any( + and_(func.lower(self.model_annotation_association_class.annotation).like("%" + a_filter.lower() + "%"), + # TODO: not sure why, to filter by owner's annotations, we have to do this rather than + # 'self.model_class.user==self.model_annotation_association_class.user' + self.model_annotation_association_class.table.c.user_id == self.model_class.table.c.user_id)) + + +class CommunityTagsColumn(TextColumn): + """ Column that supports community tags. """ + + def __init__(self, col_name, key, model_class=None, model_tag_association_class=None, filterable=None, grid_name=None): + GridColumn.__init__(self, col_name, key=key, model_class=model_class, nowrap=True, filterable=filterable, sortable=False) + self.model_tag_association_class = model_tag_association_class + # Column-specific attributes. + self.grid_name = grid_name + + def get_value(self, trans, grid, item): + return trans.fill_template("/tagging_common.mako", tag_type="community", trans=trans, user=trans.get_user(), tagged_item=item, elt_context=self.grid_name, + in_form=True, input_size="20", tag_click_fn="add_tag_to_grid_filter", use_toggle_link=True) + + def filter(self, trans, user, query, column_filter): + """ Modify query to filter model_class by tag. Multiple filters are ANDed. """ + if column_filter == "All": + pass + elif column_filter: + query = query.filter(self.get_filter(trans, user, column_filter)) + return query + + def get_filter(self, trans, user, column_filter): + # Parse filter to extract multiple tags. + if isinstance(column_filter, list): + # Collapse list of tags into a single string; this is redundant but effective. TODO: fix this by iterating over tags. + column_filter = ",".join(column_filter) + raw_tags = trans.app.tag_handler.parse_tags(column_filter.encode("utf-8")) + clause_list = [] + for name, value in raw_tags: + if name: + # Filter by all tags. + clause_list.append(self.model_class.tags.any(func.lower(self.model_tag_association_class.user_tname).like("%" + name.lower() + "%"))) + if value: + # Filter by all values. + clause_list.append(self.model_class.tags.any(func.lower(self.model_tag_association_class.user_value).like("%" + value.lower() + "%"))) + return and_(*clause_list) + + +class IndividualTagsColumn(CommunityTagsColumn): + """ Column that supports individual tags. """ + + def get_value(self, trans, grid, item): + return trans.fill_template("/tagging_common.mako", + tag_type="individual", + user=trans.user, + tagged_item=item, + elt_context=self.grid_name, + in_form=True, + input_size="20", + tag_click_fn="add_tag_to_grid_filter", + use_toggle_link=True) + + def get_filter(self, trans, user, column_filter): + # Parse filter to extract multiple tags. + if isinstance(column_filter, list): + # Collapse list of tags into a single string; this is redundant but effective. TODO: fix this by iterating over tags. + column_filter = ",".join(column_filter) + raw_tags = trans.app.tag_handler.parse_tags(column_filter.encode("utf-8")) + clause_list = [] + for name, value in raw_tags: + if name: + # Filter by individual's tag names. + clause_list.append(self.model_class.tags.any(and_(func.lower(self.model_tag_association_class.user_tname).like("%" + name.lower() + "%"), self.model_tag_association_class.user == user))) + if value: + # Filter by individual's tag values. + clause_list.append(self.model_class.tags.any(and_(func.lower(self.model_tag_association_class.user_value).like("%" + value.lower() + "%"), self.model_tag_association_class.user == user))) + return and_(*clause_list) + + +class MulticolFilterColumn(TextColumn): + """ Column that performs multicolumn filtering. """ + + def __init__(self, col_name, cols_to_filter, key, visible, filterable="default"): + GridColumn.__init__(self, col_name, key=key, visible=visible, filterable=filterable) + self.cols_to_filter = cols_to_filter + + def filter(self, trans, user, query, column_filter): + """ Modify query to filter model_class by tag. Multiple filters are ANDed. """ + if column_filter == "All": + return query + if isinstance(column_filter, list): + clause_list = [] + for filter in column_filter: + part_clause_list = [] + for column in self.cols_to_filter: + part_clause_list.append(column.get_filter(trans, user, filter)) + clause_list.append(or_(*part_clause_list)) + complete_filter = and_(*clause_list) + else: + clause_list = [] + for column in self.cols_to_filter: + clause_list.append(column.get_filter(trans, user, column_filter)) + complete_filter = or_(*clause_list) + return query.filter(complete_filter) + + +class OwnerColumn(TextColumn): + """ Column that lists item's owner. """ + + def get_value(self, trans, grid, item): + return item.user.username + + def sort(self, trans, query, ascending, column_name=None): + """ Sort column using case-insensitive alphabetical sorting on item's username. """ + if ascending: + query = query.order_by(func.lower(self.model_class.username).asc()) + else: + query = query.order_by(func.lower(self.model_class.username).desc()) + return query + + +class PublicURLColumn(TextColumn): + """ Column displays item's public URL based on username and slug. """ + + def get_link(self, trans, grid, item): + if item.user.username and item.slug: + return dict(action='display_by_username_and_slug', username=item.user.username, slug=item.slug) + elif not item.user.username: + # TODO: provide link to set username. + return None + elif not item.user.slug: + # TODO: provide link to set slug. + return None + + +class DeletedColumn(GridColumn): + """ Column that tracks and filters for items with deleted attribute. """ + + def get_accepted_filters(self): + """ Returns a list of accepted filters for this column. """ + accepted_filter_labels_and_vals = {"active" : "False", "deleted" : "True", "all": "All"} + accepted_filters = [] + for label, val in accepted_filter_labels_and_vals.items(): + args = {self.key: val} + accepted_filters.append(GridColumnFilter(label, args)) + return accepted_filters + + def filter(self, trans, user, query, column_filter): + """Modify query to filter self.model_class by state.""" + if column_filter == "All": + pass + elif column_filter in ["True", "False"]: + query = query.filter(self.model_class.deleted == (column_filter == "True")) + return query + + +class StateColumn(GridColumn): + """ + Column that tracks and filters for items with state attribute. + + IMPORTANT NOTE: self.model_class must have a states Bunch or dict if + this column type is used in the grid. + """ + + def get_value(self, trans, grid, item): + return item.state + + def filter(self, trans, user, query, column_filter): + """Modify query to filter self.model_class by state.""" + if column_filter == "All": + pass + elif column_filter in [v for k, v in self.model_class.states.items()]: + query = query.filter(self.model_class.state == column_filter) + return query + + def get_accepted_filters(self): + """Returns a list of accepted filters for this column.""" + all = GridColumnFilter('all', {self.key : 'All'}) + accepted_filters = [all] + for k, v in self.model_class.states.items(): + args = {self.key: v} + accepted_filters.append(GridColumnFilter(v, args)) + return accepted_filters + + +class SharingStatusColumn(GridColumn): + """ Grid column to indicate sharing status. """ + + def get_value(self, trans, grid, item): + # Delete items cannot be shared. + if item.deleted: + return "" + # Build a list of sharing for this item. + sharing_statuses = [] + if item.users_shared_with: + sharing_statuses.append("Shared") + if item.importable: + sharing_statuses.append("Accessible") + if item.published: + sharing_statuses.append("Published") + return ", ".join(sharing_statuses) + + def get_link(self, trans, grid, item): + if not item.deleted and (item.users_shared_with or item.importable or item.published): + return dict(operation="share or publish", id=item.id) + return None + + def filter(self, trans, user, query, column_filter): + """ Modify query to filter histories by sharing status. """ + if column_filter == "All": + pass + elif column_filter: + if column_filter == "private": + query = query.filter(self.model_class.users_shared_with == null()) + query = query.filter(self.model_class.importable == false()) + elif column_filter == "shared": + query = query.filter(self.model_class.users_shared_with != null()) + elif column_filter == "accessible": + query = query.filter(self.model_class.importable == true()) + elif column_filter == "published": + query = query.filter(self.model_class.published == true()) + return query + + def get_accepted_filters(self): + """ Returns a list of accepted filters for this column. """ + accepted_filter_labels_and_vals = odict() + accepted_filter_labels_and_vals["private"] = "private" + accepted_filter_labels_and_vals["shared"] = "shared" + accepted_filter_labels_and_vals["accessible"] = "accessible" + accepted_filter_labels_and_vals["published"] = "published" + accepted_filter_labels_and_vals["all"] = "All" + accepted_filters = [] + for label, val in accepted_filter_labels_and_vals.items(): + args = {self.key: val} + accepted_filters.append(GridColumnFilter(label, args)) + return accepted_filters + + +class GridOperation(object): + def __init__(self, label, key=None, condition=None, allow_multiple=True, allow_popup=True, + target=None, url_args=None, async_compatible=False, confirm=None, + global_operation=None): + self.label = label + self.key = key + self.allow_multiple = allow_multiple + self.allow_popup = allow_popup + self.condition = condition + self.target = target + self.url_args = url_args + self.async_compatible = async_compatible + # if 'confirm' is set, then ask before completing the operation + self.confirm = confirm + # specify a general operation that acts on the full grid + # this should be a function returning a dictionary with parameters + # to pass to the URL, similar to GridColumn links: + # global_operation=(lambda: dict(operation="download") + self.global_operation = global_operation + + def get_url_args(self, item): + if self.url_args: + if hasattr(self.url_args, '__call__'): + url_args = self.url_args(item) + else: + url_args = dict(self.url_args) + url_args['id'] = item.id + return url_args + else: + return dict(operation=self.label, id=item.id) + + def allowed(self, item): + if self.condition: + return bool(self.condition(item)) + else: + return True + + +class DisplayByUsernameAndSlugGridOperation(GridOperation): + """ Operation to display an item by username and slug. """ + + def get_url_args(self, item): + return {'action' : 'display_by_username_and_slug', 'username' : item.user.username, 'slug' : item.slug} + + +class GridAction(object): + def __init__(self, label=None, url_args=None, target=None): + self.label = label + self.url_args = url_args + self.target = target + + +class GridColumnFilter(object): + def __init__(self, label, args=None): + self.label = label + self.args = args + + def get_url_args(self): + rval = {} + for k, v in self.args.items(): + rval["f-" + k] = v + return rval diff --git a/lib/galaxy/webapps/tool_shed/controllers/repository.py b/lib/galaxy/webapps/tool_shed/controllers/repository.py index 22e69f8d7c7..04bc147abe0 100644 --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -21,7 +21,7 @@ from galaxy import ( from galaxy.tools.repositories import ValidationContext from galaxy.web.base.controller import BaseUIController from galaxy.web.form_builder import CheckboxField, SelectField -from galaxy.web.framework.helpers import grids +from galaxy.webapps.reports.framework import grids from galaxy.webapps.tool_shed.util import ratings_util from tool_shed.capsule import capsule_manager from tool_shed.dependencies.repository import relation_builder diff --git a/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py b/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py index b20b6f89ca9..6d5a45ec8e3 100644 --- a/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py +++ b/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py @@ -215,7 +215,6 @@ class InstalledRepositoryGrid(grids.Grid): standard_filters = [] default_filter = dict(deleted="False") num_rows_per_page = 50 - preserve_state = False use_paging = False def build_initial_query(self, trans, **kwd): diff --git a/lib/tool_shed/grids/admin_grids.py b/lib/tool_shed/grids/admin_grids.py index 5f5310a2c77..64d45388466 100644 --- a/lib/tool_shed/grids/admin_grids.py +++ b/lib/tool_shed/grids/admin_grids.py @@ -3,7 +3,8 @@ import logging from markupsafe import escape from sqlalchemy import and_ -from galaxy.web.framework.helpers import grids, time_ago +from galaxy.web.framework.helpers import time_ago +from galaxy.webapps.reports.framework import grids from galaxy.webapps.tool_shed import model from tool_shed.grids.repository_grids import CategoryGrid, RepositoryGrid from tool_shed.util import hg_util diff --git a/lib/tool_shed/grids/repository_grids.py b/lib/tool_shed/grids/repository_grids.py index d4228adb59e..ac222ded950 100644 --- a/lib/tool_shed/grids/repository_grids.py +++ b/lib/tool_shed/grids/repository_grids.py @@ -7,7 +7,7 @@ from sqlalchemy import and_, false, or_, true import tool_shed.grids.util as grids_util import tool_shed.repository_types.util as rt_util import tool_shed.util.shed_util_common as suc -from galaxy.web.framework.helpers import grids +from galaxy.webapps.reports.framework import grids from galaxy.webapps.tool_shed import model from tool_shed.util import hg_util, metadata_util, repository_util @@ -62,7 +62,6 @@ class CategoryGrid(grids.Grid): operations = [] standard_filters = [] num_rows_per_page = 50 - preserve_state = False use_paging = False @@ -236,7 +235,6 @@ class RepositoryGrid(grids.Grid): standard_filters = [] default_filter = dict(deleted="False") num_rows_per_page = 50 - preserve_state = False use_paging = False def build_initial_query(self, trans, **kwd): @@ -358,7 +356,6 @@ class MatchedRepositoryGrid(grids.Grid): standard_filters = [] default_filter = {} num_rows_per_page = 50 - preserve_state = False use_paging = False def build_initial_query(self, trans, **kwd): @@ -457,7 +454,6 @@ class RepositoriesByUserGrid(RepositoryGrid): standard_filters = [] default_filter = dict(deleted="False") num_rows_per_page = 50 - preserve_state = False use_paging = False def build_initial_query(self, trans, **kwd): @@ -978,7 +974,6 @@ class RepositoryMetadataGrid(grids.Grid): standard_filters = [] default_filter = dict(malicious="False") num_rows_per_page = 50 - preserve_state = False use_paging = False def build_initial_query(self, trans, **kwd): @@ -1298,7 +1293,6 @@ class ValidCategoryGrid(CategoryGrid): operations = [] standard_filters = [] num_rows_per_page = 50 - preserve_state = False use_paging = False diff --git a/lib/tool_shed/grids/repository_review_grids.py b/lib/tool_shed/grids/repository_review_grids.py index 95b6881d557..0f9996456d8 100644 --- a/lib/tool_shed/grids/repository_review_grids.py +++ b/lib/tool_shed/grids/repository_review_grids.py @@ -3,7 +3,7 @@ import logging from markupsafe import escape from sqlalchemy import and_, false, null, or_, true -from galaxy.web.framework.helpers import grids +from galaxy.webapps.reports.framework import grids from galaxy.webapps.tool_shed import model from tool_shed.grids.repository_grids import RepositoryGrid from tool_shed.util import hg_util, metadata_util @@ -45,7 +45,6 @@ class ComponentGrid(grids.Grid): operations 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s(".select2-hidden-accessible").remove(),this.masthead.render(),this.renderMessageBox(),this.renderInactivityBox(),this.renderPanels(),this._checkCommunicationServerOnline(),this},renderMessageBox:function(){if(this.config.message_box_visible){var e=this.config.message_box_content||"",t=this.config.message_box_class||"info";this.$el.addClass("has-message-box"),this.$messagebox.attr("class","panel-"+t+"-message").html(e).toggle(!!e).show()}else this.$el.removeClass("has-message-box"),this.$messagebox.hide();return this},renderInactivityBox:function(){if(this.config.show_inactivity_warning){var e=this.config.inactivity_box_content||"",t=s("    ").attr("href",Galaxy.root+"user/resend_verification").text("Resend verification");this.$el.addClass("has-inactivity-box"),this.$inactivebox.html(e+" ").append(t).toggle(!!e).show()}else this.$el.removeClass("has-inactivity-box"),this.$inactivebox.hide();return this},renderPanels:function(){var e=this;return n.each(this._panelids,function(t){var i=e.panels[t];i?i.render():(e.$("#center").css(t,0),e.$("#"+t).hide())}),this},_template:function(){return['
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b=e.View.extend(f.default.LoggableMixin).extend({_logNamespace:"collections",tagName:"li",className:"collection-element",initialize:function(e){this.element=e.element||{},this.selected=e.selected||!1},render:function(){this.dragStartHandler=n.bind(this._dragstart,this),this.dragEndHandler=n.bind(this._dragend,this);var e=this.$el.attr("data-element-id",this.element.id).attr("draggable",!0).html(this.template({element:this.element})).get(0);return e.addEventListener("dragstart",this.dragStartHandler,!1),e.addEventListener("dragend",this.dragEndHandler,!1),this.selected&&this.$el.addClass("selected"),this},template:n.template(['',"<%- element.name %>","",'"].join("")),select:function(e){this.$el.toggleClass("selected",e),this.trigger("select",{source:this,selected:this.$el.hasClass("selected")})},discard:function(){var e=this,t=this.$el.parent().width();this.$el.animate({"margin-right":t},"fast",function(){e.trigger("discard",{source:e}),e.destroy()})},destroy:function(){this.off(),this.$el.remove()},events:{click:"_click","click .name":"_clickName","click .discard":"_clickDiscard",dragover:"_sendToParent",drop:"_sendToParent"},_click:function(e){e.stopPropagation(),this.select(e)},_clickName:function(e){e.stopPropagation(),e.preventDefault();var t=([(0,w.default)("Enter a new name for the element"),":\n(",(0,w.default)("Note that changing the name here will not rename the dataset"),")"].join(""),prompt((0,w.default)("Enter a new name for the element")+":",this.element.name));t&&(this.element.name=t,this.render())},_clickDiscard:function(e){e.stopPropagation(),this.discard()},_dragstart:function(e){e.originalEvent&&(e=e.originalEvent),e.dataTransfer.effectAllowed="move",e.dataTransfer.setData("text/plain",JSON.stringify(this.element)),this.$el.addClass("dragging"),this.$el.parent().trigger("collection-element.dragstart",[this])},_dragend:function(e){this.$el.removeClass("dragging"),this.$el.parent().trigger("collection-element.dragend",[this])},_sendToParent:function(e){this.$el.parent().trigger(e)},toString:function(){return"DatasetCollectionElementView()"}}),x=e.View.extend(f.default.LoggableMixin).extend(m.default.CollectionCreatorMixin).extend({_logNamespace:"collections",elementViewClass:b,collectionClass:d.default.HistoryDatasetCollection,className:"list-collection-creator collection-creator flex-row-container",minElements:1,defaultAttributes:{creationFn:function(){throw new TypeError("no creation fn for 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e.hasDetails()})},hidden:function(){return this.filter(function(e){return e.hidden()})},deleted:function(){return this.filter(function(e){return e.get("deleted")})},visibleAndUndeleted:function(){return this.filter(function(e){return e.get("visible")&&!e.get("deleted")})},setIncludeDeleted:function(t,i){if(e.isBoolean(t)&&t!==this.includeDeleted){if(this.includeDeleted=t,e.result(i,"silent"))return;this.trigger("include-deleted",t,this)}},setIncludeHidden:function(t,i){if(e.isBoolean(t)&&t!==this.includeHidden){if(this.includeHidden=t,i=i||{},e.result(i,"silent"))return;this.trigger("include-hidden",t,this)}},fetch:function(t){if(t=t||{},this.historyId&&!t.details){var i=f.default.HistoryPrefs.get(this.historyId).toJSON();e.isEmpty(i.expandedIds)||(t.details=e.values(i.expandedIds).join(","))}return b.prototype.fetch.call(this,t)},_buildFetchData:function(t){return e.extend(b.prototype._buildFetchData.call(this,t),{v:"dev"})},_fetchParams:b.prototype._fetchParams.concat(["v","details"]),_buildFetchFilters:function(t){var i=b.prototype._buildFetchFilters.call(this,t)||{},n={};return this.includeDeleted||(n.deleted=!1,n.purged=!1),this.includeHidden||(n.visible=!0),e.defaults(i,n)},getTotalItemCount:function(){return this.history.contentsShown()},fetchUpdated:function(e,t){return e&&(t=t||{filters:{}},t.remove=!1,t.filters={"update_time-ge":e.toISOString(),visible:""}),this.fetch(t)},fetchDeleted:function(t){var i=this;return t=t||{},t.filters=e.extend(t.filters,{deleted:!0,purged:void 0}),t.remove=!1,this.trigger("fetching-deleted",this),this.fetch(t).always(function(){i.trigger("fetching-deleted-done",i)})},fetchHidden:function(t){t=t||{};var i=this;return t.filters=e.extend(t.filters,{visible:!1}),t.remove=!1,i.trigger("fetching-hidden",i),i.fetch(t).always(function(){i.trigger("fetching-hidden-done",i)})},fetchAllDetails:function(t){t=t||{};var i={details:"all"};return t.data=e.extend(t.data||{},i),this.fetch(t)},_filterAndUpdate:function(e,t){var i=this,n=i.model.prototype.idAttribute,s=[t];return i.fetch({filters:e,remove:!1}).then(function(e){return e=e.reduce(function(e,t,s){var a=i.get(t[n]);return a?e.concat(a):e},[]),i.ajaxQueue("save",s,e)})},ajaxQueue:function(t,i,n){return n=n||this.models,new y.default.AjaxQueue(n.slice().reverse().map(function(n,s){var a=e.isString(t)?n[t]:t;return function(){return a.apply(n,i)}})).deferred},progressivelyFetchDetails:function(t){function i(n){n=n||0;var l=e.extend(e.clone(t),{view:"summary",keys:r,limit:o,offset:n,reset:0===n,remove:!1});e.defer(function(){a.fetch.call(a,l).fail(s.reject).done(function(e){s.notify(e,o,n),e.length!==o?(a.allFetched=!0,s.resolve(e,o,n)):i(n+o)})})}t=t||{};var s=n.Deferred(),a=this,o=t.limitPerCall||a.limitPerProgressiveFetch,l=d.default.HistoryDatasetAssociation.prototype.searchAttributes,r=l.join(",");return i(),s},isCopyable:function(t){var i=["HistoryDatasetAssociation","HistoryDatasetCollectionAssociation"];return e.isObject(t)&&t.id&&e.contains(i,t.model_class)},copy:function(t){var i,s,a;e.isString(t)?(i=t,a="hda",s="dataset"):(i=t.id,a={HistoryDatasetAssociation:"hda",LibraryDatasetDatasetAssociation:"ldda",HistoryDatasetCollectionAssociation:"hdca"}[t.model_class]||"hda",s="hdca"===a?"dataset_collection":"dataset");var o=this,l=n.ajax(this.url(),{method:"POST",contentType:"application/json",data:JSON.stringify({content:i,source:a,type:s})}).done(function(e){o.add([e],{parse:!0})}).fail(function(e,t,n){o.trigger("error",o,l,{},"Error copying contents",{type:s,id:i,source:a})});return l},createHDCA:function(e,t,i,n,s){return this.model({history_content_type:"dataset_collection",collection_type:t,history_id:this.historyId,name:i,hide_source_items:n||!1,element_identifiers:e}).save(s)},haveSearchDetails:function(){return this.allFetched&&this.all(function(t){return 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e.values(this.get("expandedIds"))},clearExpanded:function(){this.set("expandedIds",{})},includeDeleted:function(t){return e.isUndefined(t)||this.set("show_deleted",t),this.get("show_deleted")},includeHidden:function(t){return e.isUndefined(t)||this.set("show_hidden",t),this.get("show_hidden")},toString:function(){return"HistoryPrefs("+this.id+")"}},{storageKeyPrefix:"history:",historyStorageKey:function(e){if(!e)throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+e);return a.storageKeyPrefix+e},get:function(e){return new a({id:a.historyStorageKey(e)})},clearAll:function(e){for(var t in sessionStorage)0===t.indexOf(a.storageKeyPrefix)&&sessionStorage.removeItem(t)}});t.default={HistoryPrefs:a}}).call(t,i(1))},function(e,t,i){"use strict";(function(e,n,s,a){function o(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var l=i(5),r=o(l),d=i(3),c=(o(d),e.View.extend(r.default.LoggableMixin).extend({_logNamespace:"list",initialize:function(e){this.expanded=e.expanded||!1,this.log("\t expanded:",this.expanded),this.fxSpeed=void 0!==e.fxSpeed?e.fxSpeed:this.fxSpeed},fxSpeed:"fast",render:function(e){var t=this._buildNewRender();return this._setUpBehaviors(t),this._queueNewRender(t,e),this},_buildNewRender:function(){var e=n(this.templates.el(this.model.toJSON(),this));return this.expanded&&this.$details(e).replaceWith(this._renderDetails().show()),e},_queueNewRender:function(e,t){t=void 0===t?this.fxSpeed:t;var i=this;0===t?(i._swapNewRender(e),i.trigger("rendered",i)):n(i).queue("fx",[function(e){i.$el.fadeOut(t,e)},function(t){i._swapNewRender(e),t()},function(e){i.$el.fadeIn(t,e)},function(e){i.trigger("rendered",i),e()}])},_swapNewRender:function(e){return this.$el.empty().attr("class",s.isFunction(this.className)?this.className():this.className).append(e.children())},_setUpBehaviors:function(e){e=e||this.$el,e.find("[title]").tooltip({placement:"bottom"})},$details:function(e){return e=e||this.$el,e.find("> .details")},_renderDetails:function(){var e=n(this.templates.details(this.model.toJSON(),this));return this._setUpBehaviors(e),e},toggleExpanded:function(e){return e=void 0===e?!this.expanded:e,e?this.expand():this.collapse(),this},expand:function(){var e=this;return e._fetchModelDetails().always(function(){e._expand()})},_fetchModelDetails:function(){return this.model.hasDetails()?a.when():this.model.fetch()},_expand:function(){var e=this,t=e._renderDetails();e.$details().replaceWith(t),e.expanded=!0,e.$details().slideDown(e.fxSpeed,function(){e.trigger("expanded",e)})},collapse:function(){this.debug(this+"(ExpandableView).collapse");var e=this;e.expanded=!1,this.$details().slideUp(e.fxSpeed,function(){e.trigger("collapsed",e)})}})),u=c.extend(r.default.mixin(r.default.SelectableViewMixin,r.default.DraggableViewMixin,{tagName:"div",className:"list-item",initialize:function(e){c.prototype.initialize.call(this,e),r.default.SelectableViewMixin.initialize.call(this,e),r.default.DraggableViewMixin.initialize.call(this,e),this._setUpListeners()},_setUpListeners:function(){return this.on("selectable",function(e){e?this.$(".primary-actions").hide():this.$(".primary-actions").show()},this),this},_buildNewRender:function(){var e=c.prototype._buildNewRender.call(this);return e.children(".warnings").replaceWith(this._renderWarnings()),e.children(".title-bar").replaceWith(this._renderTitleBar()),e.children(".primary-actions").append(this._renderPrimaryActions()),e.find("> .title-bar .subtitle").replaceWith(this._renderSubtitle()),e},_swapNewRender:function(e){return c.prototype._swapNewRender.call(this,e),this.selectable&&this.showSelector(0),this.draggable&&this.draggableOn(),this.$el},_renderWarnings:function(){var e=this,t=n('
    '),i=e.model.toJSON();return s.each(e.templates.warnings,function(s){t.append(n(s(i,e)))}),t},_renderTitleBar:function(){return n(this.templates.titleBar(this.model.toJSON(),this))},_renderPrimaryActions:function(){return[]},_renderSubtitle:function(){return n(this.templates.subtitle(this.model.toJSON(),this))},events:{"click .title-bar":"_clickTitleBar","keydown .title-bar":"_keyDownTitleBar","click .selector":"toggleSelect"},_clickTitleBar:function(e){e.stopPropagation(),e.altKey?(this.toggleSelect(e),this.selectable||this.showSelector()):this.toggleExpanded()},_keyDownTitleBar:function(e){return!e||"keydown"!==e.type||32!==e.keyCode&&13!==e.keyCode||(this.toggleExpanded(),e.stopPropagation(),!1)},toString:function(){return"ListItemView("+(this.model?""+this.model:"(no model)")+")"}}));u.prototype.templates=function(){return{el:r.default.wrapTemplate(['
    ','
    ','
    ','',"
    ",'
    ','
    ','
    ',"
    "]),warnings:{},titleBar:r.default.wrapTemplate(['
    ','','
    ','<%- element.name %>',"
    ",'
    ',"
    "],"element"),subtitle:r.default.wrapTemplate(['
    ']),details:r.default.wrapTemplate(['
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    ',"
    "],"collection");return s.extend({},u.prototype.templates,{details:e})}(),t.default={ExpandableView:c,ListItemView:u,FoldoutListItemView:h}}).call(t,i(2),i(0),i(1),i(0))},function(e,t,i){"use strict";(function(e,n,s,a){function o(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var l=i(65),r=o(l),d=i(16),c=o(d),u=i(21),h=o(u),f=i(5),p=o(f),m=i(3),g=o(m),_=r.default.ListItemView,v=_.extend({_logNamespace:"dataset",className:_.prototype.className+" dataset",id:function(){return["dataset",this.model.get("id")].join("-")},initialize:function(e){e.logger&&(this.logger=this.model.logger=e.logger),this.log(this+".initialize:",e),_.prototype.initialize.call(this,e),this.linkTarget=e.linkTarget||"_blank"},_setUpListeners:function(){_.prototype._setUpListeners.call(this);var t=this;return t.listenTo(t.model,{change:function(i){t.model.changedAttributes().state&&t.model.inReadyState()&&t.expanded&&!t.model.hasDetails()?t.model.fetch({silent:!0}).done(function(){t.render()}):e.has(i.changed,"tags")&&1===e.keys(i.changed).length?t.$(".nametags").html(t._renderNametags()):t.render()}})},_fetchModelDetails:function(){var e=this;return e.model.inReadyState()&&!e.model.hasDetails()?e.model.fetch({silent:!0}):n.when()},remove:function(e,t){var i=this;e=e||this.fxSpeed,this.$el.fadeOut(e,function(){s.View.prototype.remove.call(i),t&&t.call(i)})},_swapNewRender:function(e){return _.prototype._swapNewRender.call(this,e),this.model.has("state")&&this.$el.addClass("state-"+this.model.get("state")),this.$el},_renderPrimaryActions:function(){return[this._renderDisplayButton()]},_renderDisplayButton:function(){var e=this.model.get("state");if(e===c.default.NOT_VIEWABLE||e===c.default.DISCARDED||!this.model.get("accessible"))return null;var t={target:this.linkTarget,classes:"display-btn"};if(this.model.get("purged"))t.disabled=!0,t.title=(0,g.default)("Cannot display datasets removed from disk");else if(e===c.default.UPLOAD)t.disabled=!0,t.title=(0,g.default)("This dataset must finish uploading before it can be viewed");else if(e===c.default.NEW)t.disabled=!0,t.title=(0,g.default)("This dataset is not yet viewable");else{t.title=(0,g.default)("View data"),t.href=this.model.urls.display;var i=this;t.onclick=function(e){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.addDataset(i.model.get("id")),e.preventDefault())}}return t.faIcon="fa-eye",(0,h.default)(t)},_renderDetails:function(){if(this.model.get("state")===c.default.NOT_VIEWABLE)return a(this.templates.noAccess(this.model.toJSON(),this));var e=_.prototype._renderDetails.call(this);return e.find(".actions .left").empty().append(this._renderSecondaryActions()),e.find(".summary").html(this._renderSummary()).prepend(this._renderDetailMessages()),e.find(".display-applications").html(this._renderDisplayApplications()),this._setUpBehaviors(e),e},_renderSummary:function(){var e=this.model.toJSON(),t=this.templates.summaries[e.state];return(t=t||this.templates.summaries.unknown)(e,this)},_renderDetailMessages:function(){var t=this,i=a('
    '),n=t.model.toJSON();return e.each(t.templates.detailMessages,function(e){i.append(a(e(n,t)))}),i},_renderDisplayApplications:function(){return this.model.isDeletedOrPurged()?"":[this.templates.displayApplications(this.model.get("display_apps"),this),this.templates.displayApplications(this.model.get("display_types"),this)].join("")},_renderSecondaryActions:function(){switch(this.debug("_renderSecondaryActions"),this.model.get("state")){case c.default.NOT_VIEWABLE:return[];case c.default.OK:case c.default.FAILED_METADATA:case c.default.ERROR:return[this._renderDownloadButton(),this._renderShowParamsButton()]}return[this._renderShowParamsButton()]},_renderShowParamsButton:function(){return(0,h.default)({title:(0,g.default)("View details"),classes:"params-btn",href:this.model.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle",onclick:function(e){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add({title:(0,g.default)("Dataset details"),url:this.href}),e.preventDefault(),e.stopPropagation())}})},_renderDownloadButton:function(){return this.model.get("purged")||!this.model.hasData()?null:e.isEmpty(this.model.get("meta_files"))?a(['','',""].join("")):this._renderMetaFileDownloadButton()},_renderMetaFileDownloadButton:function(){var t=this.model.urls;return a(['
    ','','',"",'","
    "].join("\n"))},_renderNametags:function(){return e.template(["<% _.each(_.sortBy(_.uniq(tags), function(x) { return x }), function(tag){ %>",'<% if (tag.indexOf("name:") == 0){ %>','<%- tag.slice(5) %>',"<% } %>","<% }); %>"].join(""))({tags:this.model.get("tags")})},events:e.extend(e.clone(_.prototype.events),{"click .display-btn":function(e){this.trigger("display",this,e)},"click .params-btn":function(e){this.trigger("params",this,e)},"click .download-btn":function(e){this.trigger("download",this,e)}}),toString:function(){return"DatasetListItemView("+(this.model?""+this.model:"(no model)")+")"}});v.prototype.templates=function(){var t=e.extend({},_.prototype.templates.warnings,{failed_metadata:p.default.wrapTemplate(['<% if( model.state === "failed_metadata" ){ %>','
    ',(0,g.default)("An error occurred setting the metadata for this dataset"),"
    ","<% } %>"]),error:p.default.wrapTemplate(["<% if( model.error ){ %>",'
    ',(0,g.default)("There was an error getting the data for this dataset"),": <%- model.error %>","
    ","<% } %>"]),purged:p.default.wrapTemplate(["<% if( model.purged ){ %>",'
    ',(0,g.default)("This dataset has been deleted and removed from disk"),"
    ","<% } %>"]),deleted:p.default.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'
    ',(0,g.default)("This dataset has been deleted"),"
    ","<% } %>"])}),i=p.default.wrapTemplate(['
    ','
    ','
    ','
    ','
    ',"
    ","<% if( !dataset.deleted && !dataset.purged ){ %>",'
    ','
    ','
    ',"<% if( dataset.peek ){ %>",'
    <%= dataset.peek %>
    ',"<% } %>","<% } %>","
    "],"dataset"),n=p.default.wrapTemplate(['
    ','
    ',(0,g.default)("You do not have permission to view this dataset"),"
    ","
    "],"dataset"),s={};s[c.default.OK]=s[c.default.FAILED_METADATA]=p.default.wrapTemplate(["<% if( dataset.misc_blurb ){ %>",'
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    ","<% } %>","<% if( dataset.file_ext ){ %>",'
    ','",'<%- dataset.file_ext %>',"
    ","<% } %>","<% if( dataset.metadata_dbkey ){ %>",'
    ','",'',"<%- dataset.metadata_dbkey %>","","
    ","<% } %>","<% if( dataset.misc_info ){ %>",'
    ','<%- dataset.misc_info %>',"
    ","<% } %>"],"dataset"),s[c.default.NEW]=p.default.wrapTemplate(["
    ",(0,g.default)("This is a new dataset and not all of its data are available yet"),"
    "],"dataset"),s[c.default.NOT_VIEWABLE]=p.default.wrapTemplate(["
    ",(0,g.default)("You do not have permission to view this dataset"),"
    "],"dataset"),s[c.default.DISCARDED]=p.default.wrapTemplate(["
    ",(0,g.default)("The job creating this dataset was cancelled before completion"),"
    "],"dataset"),s[c.default.QUEUED]=p.default.wrapTemplate(["
    ",(0,g.default)("This job is waiting to run"),"
    "],"dataset"),s[c.default.RUNNING]=p.default.wrapTemplate(["
    ",(0,g.default)("This job is currently running"),"
    "],"dataset"),s[c.default.UPLOAD]=p.default.wrapTemplate(["
    ",(0,g.default)("This dataset is currently uploading"),"
    "],"dataset"),s[c.default.SETTING_METADATA]=p.default.wrapTemplate(["
    ",(0,g.default)("Metadata is being auto-detected"),"
    "],"dataset"),s[c.default.PAUSED]=p.default.wrapTemplate(["
    ",(0,g.default)('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume'),"
    "],"dataset"),s[c.default.ERROR]=p.default.wrapTemplate(["<% if( !dataset.purged ){ %>","
    <%- dataset.misc_blurb %>
    ","<% } %>",'',(0,g.default)("An error occurred with this dataset"),":",'
    <%- dataset.misc_info %>
    '],"dataset"),s[c.default.EMPTY]=p.default.wrapTemplate(["
    ",(0,g.default)("No data"),": <%- dataset.misc_blurb %>
    "],"dataset"),s.unknown=p.default.wrapTemplate(['
    Error: unknown dataset state: "<%- dataset.state %>"
    '],"dataset");var a={resubmitted:p.default.wrapTemplate(["<% if( model.resubmitted ){ %>",'
    ',(0,g.default)("The job creating this dataset has been resubmitted"),"
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s.views.splice(t,0,e),s._insertIntoListAt(t,s._renderItemView$el(e).hide()),s.trigger("view:attached",e),i?e.$el.slideDown(s.fxSpeed,function(){s.trigger("view:attached:rendered")}):(e.$el.show(),s.trigger("view:attached:rendered")),e},_insertIntoListAt:function(e,t){var i=this.$list();return 0===e?i.prepend(t):i.children().eq(e-1).after(t),t},removeItemView:function(e,t,i){var a=this,o=n.find(a.views,function(t){return t.model===e});if(o)return a.views=n.without(a.views,o),a.trigger("view:removed",o),s({}).queue("fx",[function(e){o.$el.fadeOut(a.fxSpeed,e)},function(e){o.remove(),a.trigger("view:removed:rendered"),a.views.length?e():a._renderEmptyMessage().fadeIn(a.fxSpeed,e)}]),o},viewFromModelId:function(e){return n.find(this.views,function(t){return t.model.id===e})},viewFromModel:function(e){return e?this.viewFromModelId(e.id):void 0},viewsWhereModel:function(e){return this.views.filter(function(t){return n.isMatch(t.model.attributes,e)})},viewRange:function(e,t){if(e===t)return e?[e]:[];var i=this.views.indexOf(e),n=this.views.indexOf(t);return-1===i||-1===n?i===n?[]:-1===i?[t]:[e]:i .controls .search-query");return i.val()!==e&&i.val(e),this},clearSearch:function(e){return this.searchFor="",this.trigger("search:clear",this),this.$("> .controls .search-query").val(""),this.renderItems(),this},THROTTLE_SELECTOR_FX_AT:20,showSelectors:function(e){e=void 0!==e?e:this.fxSpeed,this.selecting=!0,this.$(".list-actions").slideDown(e),e=this.views.length>=this.THROTTLE_SELECTOR_FX_AT?0:e,n.each(this.views,function(t){t.showSelector(e)})},hideSelectors:function(e){e=void 0!==e?e:this.fxSpeed,this.selecting=!1,this.$(".list-actions").slideUp(e),e=this.views.length>=this.THROTTLE_SELECTOR_FX_AT?0:e,n.each(this.views,function(t){t.hideSelector(e)}),this.selected=[],this.lastSelected=null},toggleSelectors:function(){this.selecting?this.hideSelectors():this.showSelectors()},selectAll:function(e){n.each(this.views,function(t){t.select(e)})},deselectAll:function(e){this.lastSelected=null,n.each(this.views,function(t){t.deselect(e)})},selectRange:function(e,t){var i=this.viewRange(e,t);return n.each(i,function(e){e.select()}),i},getSelectedViews:function(){return n.filter(this.views,function(e){return e.selected})},getSelectedModels:function(){return new this.collection.constructor(n.map(this.getSelectedViews(),function(e){return e.model}))},_showLoadingIndicator:function(e,t,i){this.debug("_showLoadingIndicator",this.indicator,e,t,i),t=void 0!==t?t:this.fxSpeed,this.indicator||(this.indicator=new d.default(this.$el),this.debug("\t created",this.indicator)),this.$el.is(":visible")?(this.$el.fadeOut(t),this.indicator.show(e,t,i)):this.indicator.show(0,i)},_hideLoadingIndicator:function(e,t){this.debug("_hideLoadingIndicator",this.indicator,e,t),e=void 0!==e?e:this.fxSpeed,this.indicator&&this.indicator.hide(e,t)},scrollPosition:function(){return this.$scrollContainer().scrollTop()},scrollTo:function(e,t){return t=t||0,this.$scrollContainer().animate({scrollTop:e},t),this},scrollToTop:function(e){return this.scrollTo(0,e)},scrollToItem:function(e,t){return this},scrollToId:function(e,t){return this.scrollToItem(this.viewFromModelId(e),t)},events:{"click .select-all":"selectAll","click .deselect-all":"deselectAll"},toString:function(){return"ListPanel("+this.collection+")"}});p.prototype.templates=function(){return{el:u.default.wrapTemplate(["
    ",'
    ','
    ','
    ',"
    "]),controls:u.default.wrapTemplate(['
    ','
    ','
    <%- view.title %>
    ',"
    ",'
    <%- view.subtitle %>
    ','
    ','
    ','
    ','
    ',"
    ",'
    ','
    ','",'","
    ",'
    ',"
    ","
    ","
    "])}}();var m=p.extend({modelCollectionKey:"contents",initialize:function(e){p.prototype.initialize.call(this,e),this.selecting=void 0!==e.selecting&&e.selecting,this.setModel(this.model,e)},setModel:function(e,t){if(t=t||{},this.debug(this+".setModel:",e,t),this.freeModel(),this.freeViews(),e){var i=this.model?this.model.get("id"):null;this.model=e,this.logger&&(this.model.logger=this.logger),this._setUpModelListeners(),this.stopListening(this.collection),this.collection=this.model[this.modelCollectionKey]||t.collection||this._createDefaultCollection(),this._setUpCollectionListeners(),i&&e.get("id")!==i&&this.trigger("new-model",this)}return this},freeModel:function(){return this.model&&this.stopListening(this.model),this},_setUpModelListeners:function(){return this.log(this+"._setUpModelListeners",this.model),this.listenTo(this.model,"error",function(){var e=Array.prototype.slice.call(arguments,0);e.unshift("error"),this.trigger.apply(this,e)},this),this.logger&&this.listenTo(this.model,"all",function(e){this.info(this+"(model)",e,arguments)}),this},_renderControls:function(e){this.debug(this+"(ModelListPanel)._renderControls");var t=this.model?this.model.toJSON():{},i=s(this.templates.controls(t,this));return e.find(".controls").replaceWith(i),i},toString:function(){return"ModelListPanel("+this.model+")"}});m.prototype.templates=function(){var e=u.default.wrapTemplate(['
    ','
    ','
    <%- model.name %>
    ',"
    ",'
    <%- view.subtitle %>
    ','
    ','
    ','
    ','
    ',"
    ",'
    ','
    ','",'","
    ",'
    ',"
    ","
    ","
    "]);return n.extend(n.clone(p.prototype.templates),{controls:e})}(),t.default={ListPanel:p,ModelListPanel:m}}).call(t,i(2),i(1),i(0))},function(e,t,i){"use strict";function n(e,t){function i(e){o(this).parent().children("input").val("").trigger("searchInput.clear").blur(),t.onclear()}function n(e,n){if(!n)return i();o(this).trigger("search.search",n),"function"==typeof t.onfirstsearch&&u?(u=!1,t.onfirstsearch(n)):t.onsearch(n)}function s(){return['"].join("")}var r=27,d=13,c=o(e),u=!0,h={initialVal:"",name:"search",placeholder:"search",classes:"",onclear:function(){},onfirstsearch:null,onsearch:function(e){},minSearchLen:0,escWillClear:!0,oninit:function(){}};return"string"===a.default.type(t)?("toggle-loading"===t&&function(){c.find(".search-loading").toggle(),c.find(".search-clear").toggle()}(),c):("object"===a.default.type(t)&&(t=a.default.extend(!0,{},h,t)),c.addClass("search-input").prepend([function(){return o(s()).focus(function(e){o(this).select()}).keyup(function(e){if(e.preventDefault(),e.stopPropagation(),e.which===r&&t.escWillClear)i.call(this,e);else{var s=o(this).val();(e.which===d||t.minSearchLen&&s.length>=t.minSearchLen)&&n.call(this,e,s)}}).val(t.initialVal)}(),function(){return o([''].join("")).tooltip({placement:"bottom"}).click(function(e){i.call(this,e)})}(),function(){return o([''].join("")).hide().tooltip({placement:"bottom"})}()]))}var s=i(0),a=function(e){return e&&e.__esModule?e:{default:e}}(s),o=a.default,l=window._l||function(e){return e};a.default.fn.extend({searchInput:function(e){return this.each(function(){return n(this,e)})}})},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(66),a=n(s),o=i(5),l=n(o),r=i(120),d=n(r),c=i(3),u=n(c),h=a.default.DatasetListItemView,f=h.extend({className:h.prototype.className+" history-content",initialize:function(e,t){h.prototype.initialize.call(this,e,t)},toString:function(){return"HDAListItemView("+(this.model?""+this.model:"(no model)")+")"}});f.prototype.templates=function(){var t=function(t){return'\n        
    \n            \n            
    \n                '+t.hid+'\n                '+e.escape(t.name)+"\n            
    \n            
    \n            "+d.default.nametagTemplate(t)+"\n        
    \n    "},i=e.extend({},h.prototype.templates.warnings,{hidden:l.default.wrapTemplate(["<% if( !dataset.visible ){ %>",'
    ',(0,u.default)("This dataset has been hidden"),"
    ","<% } %>"],"dataset")});return e.extend({},h.prototype.templates,{titleBar:t,warnings:i})}(),t.default={HDAListItemView:f}}).call(t,i(1))},function(e,t,i){"use strict";(function(e){function i(t){return 0==t.indexOf("name:")?''+e.escape(t.slice(5))+"":""}function n(t){return''+e.sortBy(e.uniq(t.tags)).map(i).join("")+""}Object.defineProperty(t,"__esModule",{value:!0}),t.default={nametagTemplate:n}}).call(t,i(1))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(16),a=n(s),o=i(67),l=n(o),r=i(122),d=n(r),c=i(5),u=(n(c),i(120)),h=n(u),f=i(3),p=n(f),m=l.default.DCListItemView,g=m.extend({className:m.prototype.className+" history-content",_setUpListeners:function(){var e=this;m.prototype._setUpListeners.call(this);var t=function(t,i){e.render()};this.model.jobStatesSummary&&this.listenTo(this.model.jobStatesSummary,"change",t),this.listenTo(this.model,{"change:tags change:visible change:state":t})},_getFoldoutPanelClass:function(){return d.default.CollectionView},_swapNewRender:function(e){m.prototype._swapNewRender.call(this,e);var t,i=this.model.jobStatesSummary;t=i?i.new()?"loading":i.errored()?"error":i.terminal()?"ok":i.running()?"running":"queued":this.model.get("job_source_id")?"loading":this.model.get("populated_state")?a.default.OK:a.default.RUNNING,this.$el.addClass("state-"+t);var n=this.stateDescription();return this.$(".state-description").html(n),this.$el},stateDescription:function(){var e=this.model,t=(e.get("element_count"),e.get("job_source_type")),i=(this.model.get("collection_type"),d.default.collectionTypeDescription(e)),n=d.default.collectionDescription(e),s=e.jobStatesSummary;if(t&&"Job"!=t){if(s&&s.hasDetails()){var a=s.new(),o=a?null:s.jobCount();if(a)return'\n                        
    \n                            Creating jobs...\n                            
    \n                        
    ';if(s.errored()){return"a "+i+" with "+s.numInError()+" / "+o+" jobs in error"}if(s.terminal())return n;var l=s.states().running||0,r=s.states().ok||0,c=r/(1*o),u=l/(1*o),h=1-c-u;return'\n                        
    \n                            '+(o&&o>1?o+" jobs":"a job")+" generating a "+i+'\n                            
    \n                            
    \n                            
    \n                        
    '}return'\n                    
    \n                        Loading job data for '+i+'...\n                        
    \n                    
    '}return n},toString:function(){return"HDCAListItemView("+(this.model?""+this.model:"(no model)")+")"}});g.prototype.templates=function(){var t=e.extend({},m.prototype.templates.warnings,{hidden:function(e){e.visible||(0,p.default)("This collection has been hidden")}}),i=function(t){return'\n        
    \n            \n            
    \n                '+t.hid+'\n                '+e.escape(t.name)+'\n            
    \n            
    \n            
    \n            '+h.default.nametagTemplate(t)+"\n        
    \n    "};return e.extend({},m.prototype.templates,{warnings:t,titleBar:i})}(),t.default={HDCAListItemView:g}}).call(t,i(1))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}function s(e){var t=e.get("collection_type");return"list"==t?(0,f.default)("list"):"paired"==t?(0,f.default)("dataset pair"):"list:paired"==t?(0,f.default)("list of pairs"):(0,f.default)("nested list")}function a(e){var t=e.get("element_count"),i="a "+s(e);if(t){var n;1==t?n="with 1 item":t&&(n="with "+t+" items"),i=i+" "+(0,f.default)(n)}return i}Object.defineProperty(t,"__esModule",{value:!0});var o=i(117),l=n(o),r=i(60),d=(n(r),i(67)),c=n(d),u=i(5),h=(n(u),i(3)),f=n(h),p=l.default.ModelListPanel,m=p.extend({_logNamespace:"collections",className:p.prototype.className+" dataset-collection-panel",DatasetDCEViewClass:c.default.DatasetDCEListItemView,modelCollectionKey:"elements",initialize:function(e){p.prototype.initialize.call(this,e),this.linkTarget=e.linkTarget||"_blank",this.hasUser=e.hasUser,this.panelStack=[],this.parentName=e.parentName,this.foldoutStyle=e.foldoutStyle||"foldout",this.downloadUrl=Galaxy.root+"api/dataset_collections/"+this.model.attributes.id+"/download"},getNestedDCDCEViewClass:function(){return c.default.NestedDCDCEListItemView.extend({foldoutPanelClass:m})},_queueNewRender:function(e,t){t=void 0===t?this.fxSpeed:t;var i=this;this.handleWarning(e),i.log("_queueNewRender:",e,t),i._swapNewRender(e),i.trigger("rendered",i)},handleWarning:function(e){var t=this.views.length,i=this.model.get("element_count");if(i&&i!==t){var n=(0,f.default)("displaying only "+t+" of "+i+" items");e.find(".elements-warning").html('
    '+n+"
    ")}},_filterCollection:function(){return this.model.getVisibleContents()},_getItemViewClass:function(e){switch(e.get("element_type")){case"hda":return this.DatasetDCEViewClass;case"dataset_collection":return this.getNestedDCDCEViewClass()}throw new TypeError("Unknown element type:",e.get("element_type"))},_getItemViewOptions:function(t){var i=p.prototype._getItemViewOptions.call(this,t);return e.extend(i,{linkTarget:this.linkTarget,hasUser:this.hasUser,foldoutStyle:this.foldoutStyle})},_setUpItemViewListeners:function(e){var t=this;return p.prototype._setUpItemViewListeners.call(t,e),t.listenTo(e,{"expanded:drilldown":function(e,t){this._expandDrilldownPanel(t)},"collapsed:drilldown":function(e,t){this._collapseDrilldownPanel(t)}}),this},_expandDrilldownPanel:function(e){this.panelStack.push(e),this.$("> .controls").add(this.$list()).hide(),e.parentName=this.model.get("name"),this.$el.append(e.render().$el)},_collapseDrilldownPanel:function(e){this.panelStack.pop(),this.render()},events:{"click .navigation .back":"close"},close:function(e){this.remove(),this.trigger("close")},toString:function(){return"CollectionView("+(this.model?this.model.get("name"):"")+")"}});m.prototype.templates=function(){var t=function(t,i){var n=a(i.model);return'\n        
    \n            
    \n            \n                \n                '+(0,f.default)("Back to ")+"\n                "+e.escape(i.parentName)+'\n            \n            
    \n            
    \n                
    '+(e.escape(t.name)||e.escape(t.element_identifier))+'
    \n                
    \n                    '+n+'\n                
    \n            
    \n            
    \n            
    \n            
    \n            
    \n                \n                   \n                \n            
    \n        
    '};return e.extend(e.clone(p.prototype.templates),{controls:t})}(),t.default={collectionTypeDescription:s,collectionDescription:a,CollectionView:m}}).call(t,i(1))},function(e,t,i){"use strict";(function(e,n){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(16),o=s(a),l=i(66),r=s(l),d=i(39),c=s(d),u=i(124),h=s(u),f=i(21),p=s(f),m=i(5),g=s(m),_=i(3),v=s(_),y=r.default.DatasetListItemView,w=y.extend({initialize:function(e){y.prototype.initialize.call(this,e),this.hasUser=e.hasUser,this.purgeAllowed=e.purgeAllowed||!1,this.tagsEditorShown=e.tagsEditorShown||!1,this.annotationEditorShown=e.annotationEditorShown||!1},_renderPrimaryActions:function(){var e=y.prototype._renderPrimaryActions.call(this);return this.model.get("state")===o.default.NOT_VIEWABLE?e:y.prototype._renderPrimaryActions.call(this).concat([this._renderEditButton(),this._renderDeleteButton()])},_renderEditButton:function(){var t=this;if(this.model.get("state")===o.default.DISCARDED||!this.model.get("accessible"))return null;var i=this.model.get("purged"),n=this.model.get("deleted"),s={title:(0,v.default)("Edit attributes"),href:Galaxy.root+"datasets/edit?dataset_id="+this.model.attributes.id,faIcon:"fa-pencil",classes:"edit-btn",onclick:function(e){Galaxy.router&&(e.preventDefault(),Galaxy.router.push("datasets/edit",{dataset_id:t.model.attributes.id}))}};return n||i?(s.disabled=!0,i?s.title=(0,v.default)("Cannot edit attributes of datasets removed from disk"):n&&(s.title=(0,v.default)("Undelete dataset to edit attributes"))):e.contains([o.default.UPLOAD,o.default.NEW],this.model.get("state"))&&(s.disabled=!0,s.title=(0,v.default)("This dataset is not yet editable")),(0,p.default)(s)},_renderDeleteButton:function(){if(!this.model.get("accessible"))return null;var e=this,t=this.model.isDeletedOrPurged();return(0,p.default)({title:t?(0,v.default)("Dataset is already deleted"):(0,v.default)("Delete"),disabled:t,faIcon:"fa-times",classes:"delete-btn",onclick:function(){e.$el.find(".icon-btn.delete-btn").trigger("mouseout"),e.model.delete()}})},_renderDetails:function(){var t=y.prototype._renderDetails.call(this),i=this.model.get("state");return!this.model.isDeletedOrPurged()&&e.contains([o.default.OK,o.default.FAILED_METADATA],i)&&(this._renderTags(t),this._renderAnnotation(t),this._makeDbkeyEditLink(t)),this._setUpBehaviors(t),t},_renderToolHelpButton:function(){var e=this.model.attributes.dataset_id,t=this.model.attributes.creating_job,i=this,s=function(t){var s='
    ';t.name&&t.help?(s+="Tool help for "+t.name+"
    ",s+=t.help):s+="Tool help is unavailable for this dataset.
    ",s+="
    ",i.$el.find(".details").append(n.parseHTML(s))},a=function(e){n.ajax({url:Galaxy.root+"api/tools/"+e.tool_id+"/build"}).done(function(e){s(e)}).fail(function(){s({})})};return null===Galaxy.user.id?null:(0,p.default)({title:(0,v.default)("Tool Help"),classes:"icon-btn",href:"#",faIcon:"fa-question",onclick:function(){i.$el.find(".toolhelp").length>0?i.$el.find(".toolhelp").toggle():n.ajax({url:Galaxy.root+"api/jobs/"+t}).done(function(e){a(e)}).fail(function(){console.log('Failed at recovering job information from the  Galaxy API for job id "'+t+'".')})}})},_renderSecondaryActions:function(){var e=y.prototype._renderSecondaryActions.call(this);switch(this.model.get("state")){case o.default.UPLOAD:case o.default.NOT_VIEWABLE:return e;case o.default.ERROR:return e.unshift(this._renderErrButton()),e.concat([this._renderRerunButton(),this._renderToolHelpButton()]);case o.default.OK:case o.default.FAILED_METADATA:return e.concat([this._renderRerunButton(),this._renderVisualizationsButton(),this._renderToolHelpButton()])}return e.concat([this._renderRerunButton(),this._renderToolHelpButton()])},_renderErrButton:function(){var e=this;return(0,p.default)({title:(0,v.default)("View or report this error"),href:Galaxy.root+"datasets/error?dataset_id="+this.model.attributes.id,classes:"report-error-btn",faIcon:"fa-bug",onclick:function(t){Galaxy.router&&(t.preventDefault(),Galaxy.router.push("datasets/error",{dataset_id:e.model.attributes.id}))}})},_renderRerunButton:function(){var e=this.model.get("creating_job");if(this.model.get("rerunnable"))return(0,p.default)({title:(0,v.default)("Run this job again"),href:this.model.urls.rerun,classes:"rerun-btn",target:this.linkTarget,faIcon:"fa-refresh",onclick:function(t){Galaxy.router&&(t.preventDefault(),Galaxy.router.push("/",{job_id:e}))}})},_renderVisualizationsButton:function(){var t=this.model.get("visualizations");if(this.model.isDeletedOrPurged()||!this.hasUser||!this.model.hasData()||e.isEmpty(t))return null;if(!e.isObject(t[0]))return this.warn("Visualizations have been switched off"),null;var i=n(this.templates.visualizations(t,this));return i.find('[target="galaxy_main"]').attr("target",this.linkTarget),this._addScratchBookFn(i.find(".visualization-link").addBack(".visualization-link")),i},_addScratchBookFn:function(e){e.click(function(e){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add({title:(0,v.default)("Visualization"),url:n(this).attr("href")}),e.preventDefault(),e.stopPropagation())})},_renderTags:function(e){if(this.hasUser){var t=this;this.tagsEditor=new c.default.TagsEditor({model:this.model,el:e.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.tagsEditorShown=!0},onhide:function(){t.tagsEditorShown=!1},$activator:(0,p.default)({title:(0,v.default)("Edit dataset tags"),classes:"tag-btn",faIcon:"fa-tags"}).appendTo(e.find(".actions .right"))}),this.tagsEditorShown&&this.tagsEditor.toggle(!0)}},_renderAnnotation:function(e){if(this.hasUser){var t=this;this.annotationEditor=new h.default.AnnotationEditor({model:this.model,el:e.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.annotationEditorShown=!0},onhide:function(){t.annotationEditorShown=!1},$activator:(0,p.default)({title:(0,v.default)("Edit dataset annotation"),classes:"annotate-btn",faIcon:"fa-comment"}).appendTo(e.find(".actions .right"))}),this.annotationEditorShown&&this.annotationEditor.toggle(!0)}},_makeDbkeyEditLink:function(e){if("?"===this.model.get("metadata_dbkey")&&!this.model.isDeletedOrPurged()){var t=n('?').attr("href",this.model.urls.edit).attr("target","_top");e.find(".dbkey .value").replaceWith(t)}},events:e.extend(e.clone(y.prototype.events),{"click .undelete-link":"_clickUndeleteLink","click .purge-link":"_clickPurgeLink","click .edit-btn":function(e){this.trigger("edit",this,e)},"click .delete-btn":function(e){this.trigger("delete",this,e)},"click .rerun-btn":function(e){this.trigger("rerun",this,e)},"click .report-err-btn":function(e){this.trigger("report-err",this,e)},"click .visualization-btn":function(e){this.trigger("visualize",this,e)},"click .dbkey a":function(e){this.trigger("edit",this,e)}}),_clickUndeleteLink:function(e){return this.model.undelete(),!1},_clickPurgeLink:function(e){return confirm((0,v.default)("This will permanently remove the data in your dataset. Are you sure?"))&&this.model.purge(),!1},toString:function(){return"HDAEditView("+(this.model?""+this.model:"(no model)")+")"}});w.prototype.templates=function(){var t=e.extend({},y.prototype.templates.warnings,{failed_metadata:g.default.wrapTemplate(['<% if( dataset.state === "failed_metadata" ){ %>','
    ',(0,v.default)("An error occurred setting the metadata for this dataset"),'
    ',(0,v.default)("Set it manually or retry auto-detection"),"","
    ","<% } %>"],"dataset"),deleted:g.default.wrapTemplate(["<% if( dataset.deleted && !dataset.purged ){ %>",'
    ',(0,v.default)("This dataset has been deleted"),'
    ',(0,v.default)("Undelete it"),"","<% if( view.purgeAllowed ){ %>",'
    ',(0,v.default)("Permanently remove it from disk"),"","<% } %>","
    ","<% } %>"],"dataset")}),i=g.default.wrapTemplate(["<% if( visualizations.length === 1 ){ %>",'">','',"","<% } else { %>",'
    ','','',"",'","
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T(this,arguments,function(t){this.parentNode&&this.parentNode.insertBefore(t,this.nextSibling)})},empty:function(){for(var t,e=0;null!=(t=this[e]);e++)1===t.nodeType&&(lt.cleanData(p(t,!1)),t.textContent="");return this},clone:function(t,e){return t=null!=t&&t,e=null==e?t:e,this.map(function(){return lt.clone(this,t,e)})},html:function(t){return St(this,function(t){var e=this[0]||{},i=0,n=this.length;if(void 0===t&&1===e.nodeType)return e.innerHTML;if("string"==typeof t&&!Vt.test(t)&&!Lt[(It.exec(t)||["",""])[1].toLowerCase()]){t=lt.htmlPrefilter(t);try{for(;i1)},show:function(){return I(this,!0)},hide:function(){return I(this)},toggle:function(t){return"boolean"==typeof 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n,r,a=t.nodeType;if(3!==a&&8!==a&&2!==a)return void 0===t.getAttribute?lt.prop(t,e,i):(1===a&<.isXMLDoc(t)||(e=e.toLowerCase(),r=lt.attrHooks[e]||(lt.expr.match.bool.test(e)?ce:void 0)),void 0!==i?null===i?void lt.removeAttr(t,e):r&&"set"in r&&void 0!==(n=r.set(t,i,e))?n:(t.setAttribute(e,i+""),i):r&&"get"in r&&null!==(n=r.get(t,e))?n:(n=lt.find.attr(t,e),null==n?void 0:n))},attrHooks:{type:{set:function(t,e){if(!st.radioValue&&"radio"===e&<.nodeName(t,"input")){var i=t.value;return t.setAttribute("type",e),i&&(t.value=i),e}}}},removeAttr:function(t,e){var i,n,r=0,a=e&&e.match(Ct);if(a&&1===t.nodeType)for(;i=a[r++];)n=lt.propFix[i]||i,lt.expr.match.bool.test(i)&&(t[n]=!1),t.removeAttribute(i)}}),ce={set:function(t,e,i){return!1===e?lt.removeAttr(t,i):t.setAttribute(i,i),i}},lt.each(lt.expr.match.bool.source.match(/\w+/g),function(t,e){var i=he[e]||lt.find.attr;he[e]=function(t,e,n){var r,a;return n||(a=he[e],he[e]=r,r=null!=i(t,e,n)?e.toLowerCase():null,he[e]=a),r}});var 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null===t.getAttribute("value")?"on":t.value})});var ve=/^(?:focusinfocus|focusoutblur)$/;lt.extend(lt.event,{trigger:function(t,e,n,r){var a,o,s,l,u,c,h,d=[n||Z],f=ot.call(t,"type")?t.type:t,p=ot.call(t,"namespace")?t.namespace.split("."):[];if(o=s=n=n||Z,3!==n.nodeType&&8!==n.nodeType&&!ve.test(f+lt.event.triggered)&&(f.indexOf(".")>-1&&(p=f.split("."),f=p.shift(),p.sort()),u=f.indexOf(":")<0&&"on"+f,t=t[lt.expando]?t:new lt.Event(f,"object"==typeof t&&t),t.isTrigger=r?2:3,t.namespace=p.join("."),t.rnamespace=t.namespace?new RegExp("(^|\\.)"+p.join("\\.(?:.*\\.|)")+"(\\.|$)"):null,t.result=void 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