[2] | 1 | <%namespace file="/message.mako" import="render_msg" /> |
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| 2 | <%namespace file="/library/common/library_item_info.mako" import="render_library_item_info" /> |
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| 3 | <%namespace file="/library/common/common.mako" import="render_actions_on_multiple_items" /> |
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| 4 | |
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| 5 | <%! |
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| 6 | def inherit(context): |
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| 7 | if context.get('use_panels'): |
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| 8 | return '/webapps/galaxy/base_panels.mako' |
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| 9 | else: |
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| 10 | return '/base.mako' |
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| 11 | %> |
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| 12 | <%inherit file="${inherit(context)}"/> |
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| 13 | |
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| 14 | <%def name="init()"> |
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| 15 | <% |
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| 16 | self.has_left_panel=False |
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| 17 | self.has_right_panel=False |
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| 18 | self.message_box_visible=False |
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| 19 | self.active_view="user" |
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| 20 | self.overlay_visible=False |
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| 21 | %> |
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| 22 | </%def> |
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| 23 | |
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| 24 | ## |
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| 25 | ## Override methods from base.mako and base_panels.mako |
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| 26 | ## |
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| 27 | <%def name="center_panel()"> |
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| 28 | <div style="overflow: auto; height: 100%;"> |
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| 29 | <div class="page-container" style="padding: 10px;"> |
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| 30 | ${render_content()} |
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| 31 | </div> |
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| 32 | </div> |
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| 33 | </%def> |
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| 34 | |
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| 35 | ## Render the grid's basic elements. Each of these elements can be subclassed. |
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| 36 | <%def name="body()"> |
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| 37 | ${render_content()} |
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| 38 | </%def> |
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| 39 | |
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| 40 | <%def name="title()">Browse data library</%def> |
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| 41 | <%def name="stylesheets()"> |
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| 42 | ${parent.stylesheets()} |
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| 43 | ${h.css( "library" )} |
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| 44 | </%def> |
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| 45 | |
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| 46 | <%def name="javascripts()"> |
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| 47 | ${parent.javascripts()} |
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| 48 | ${h.js("class", "jquery.jstore")} |
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| 49 | ${self.grid_javascripts()} |
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| 50 | </%def> |
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| 51 | |
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| 52 | <%def name="grid_javascripts()"> |
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| 53 | <script type="text/javascript"> |
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| 54 | $(function() { |
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| 55 | $.jStore.init("galaxy"); // Auto-select best storage |
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| 56 | var storage_id = "library-expand-state-${trans.security.encode_id(library.id)}"; |
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| 57 | |
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| 58 | var restore_folder_state = function() { |
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| 59 | var state = $.jStore.store(storage_id); |
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| 60 | if (state) { |
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| 61 | for (var id in state) { |
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| 62 | if (state[id] === true) { |
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| 63 | var row = $("#" + id), |
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| 64 | index = row.parent().children().index(row); |
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| 65 | row.addClass("expanded").show(); |
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| 66 | row.siblings().filter("tr[parent='" + index + "']").show(); |
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| 67 | } |
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| 68 | } |
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| 69 | } |
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| 70 | }; |
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| 71 | |
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| 72 | var save_folder_state = function() { |
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| 73 | var state = {}; |
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| 74 | $("tr.folderRow").each( function() { |
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| 75 | var folder = $(this); |
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| 76 | state[folder.attr("id")] = folder.hasClass("expanded"); |
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| 77 | }); |
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| 78 | $.jStore.store(storage_id, state); |
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| 79 | }; |
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| 80 | |
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| 81 | $("#library-grid").each(function() { |
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| 82 | // Recursively fill in children and descendents of each row |
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| 83 | var process_row = function(q, parents) { |
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| 84 | // Find my index |
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| 85 | var index = q.parent().children().index(q); |
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| 86 | // Find my immediate children |
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| 87 | var children = q.siblings().filter("[parent='" + index + "']"); |
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| 88 | // Recursively handle them |
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| 89 | var descendents = children; |
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| 90 | children.each( function() { |
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| 91 | child_descendents = process_row( $(this), parents.add(q) ); |
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| 92 | descendents = descendents.add(child_descendents); |
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| 93 | }); |
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| 94 | // Set up expand / hide link |
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| 95 | var expand_fn = function() { |
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| 96 | if ( q.hasClass("expanded") ) { |
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| 97 | descendents.hide(); |
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| 98 | descendents.removeClass("expanded"); |
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| 99 | q.removeClass("expanded"); |
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| 100 | } else { |
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| 101 | children.show(); |
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| 102 | q.addClass("expanded"); |
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| 103 | } |
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| 104 | save_folder_state(); |
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| 105 | }; |
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| 106 | $(q).find("span.expandLink").click(expand_fn); |
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| 107 | $(q).find("span.expandLink a").click(expand_fn); |
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| 108 | // Check/uncheck boxes in subfolders. |
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| 109 | q.children("td").children("input[type=checkbox]").click( function() { |
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| 110 | if ( $(this).is(":checked") ) { |
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| 111 | descendents.find("input[type=checkbox]").attr("checked", true); |
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| 112 | } else { |
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| 113 | descendents.find("input[type=checkbox]").attr("checked", false); |
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| 114 | // If you uncheck a lower level checkbox, uncheck the boxes above it |
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| 115 | // (since deselecting a child means the parent is not fully selected any |
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| 116 | // more). |
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| 117 | parents.children("td").children("input[type=checkbox]").attr("checked", false); |
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| 118 | } |
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| 119 | }); |
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| 120 | // return descendents for use by parent |
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| 121 | return descendents; |
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| 122 | } |
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| 123 | $(this).find("tbody tr").not("[parent]").each( function() { |
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| 124 | descendents = process_row( $(this), $([]) ); |
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| 125 | descendents.hide(); |
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| 126 | }); |
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| 127 | }); |
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| 128 | |
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| 129 | $.jStore.engineReady(function() { |
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| 130 | restore_folder_state(); |
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| 131 | }); |
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| 132 | }); |
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| 133 | |
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| 134 | // For view info links, use a modal popup |
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| 135 | /*$(".view-info").live("click", function() { |
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| 136 | $.get( $(this).attr("href"), function(info) { |
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| 137 | show_modal("View Information", info, { |
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| 138 | "Close": function() { hide_modal(); } |
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| 139 | }); |
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| 140 | }); |
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| 141 | return false; |
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| 142 | });*/ |
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| 143 | |
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| 144 | function checkForm() { |
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| 145 | if ( $("select#action_on_datasets_select option:selected").text() == "delete" ) { |
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| 146 | if ( confirm( "Click OK to delete these datasets?" ) ) { |
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| 147 | return true; |
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| 148 | } else { |
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| 149 | return false; |
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| 150 | } |
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| 151 | } |
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| 152 | } |
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| 153 | // Looks for changes in dataset state using an async request. Keeps |
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| 154 | // calling itself (via setTimeout) until all datasets are in a terminal |
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| 155 | // state. |
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| 156 | var updater = function ( tracked_datasets ) { |
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| 157 | // Check if there are any items left to track |
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| 158 | var empty = true; |
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| 159 | for ( i in tracked_datasets ) { |
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| 160 | empty = false; |
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| 161 | break; |
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| 162 | } |
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| 163 | if ( ! empty ) { |
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| 164 | setTimeout( function() { updater_callback( tracked_datasets ) }, 3000 ); |
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| 165 | } |
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| 166 | }; |
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| 167 | var updater_callback = function ( tracked_datasets ) { |
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| 168 | // Build request data |
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| 169 | var ids = [] |
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| 170 | var states = [] |
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| 171 | $.each( tracked_datasets, function ( id, state ) { |
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| 172 | ids.push( id ); |
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| 173 | states.push( state ); |
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| 174 | }); |
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| 175 | // Make ajax call |
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| 176 | $.ajax( { |
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| 177 | type: "POST", |
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| 178 | url: "${h.url_for( controller='library_common', action='library_item_updates' )}", |
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| 179 | dataType: "json", |
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| 180 | data: { ids: ids.join( "," ), states: states.join( "," ) }, |
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| 181 | success : function ( data ) { |
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| 182 | $.each( data, function( id, val ) { |
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| 183 | // Replace HTML |
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| 184 | var cell = $("#libraryItem-" + id).find("#libraryItemInfo"); |
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| 185 | cell.html( val.html ); |
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| 186 | // If new state was terminal, stop tracking |
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| 187 | if (( val.state == "ok") || ( val.state == "error") || ( val.state == "empty") || ( val.state == "deleted" ) || ( val.state == "discarded" )) { |
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| 188 | delete tracked_datasets[ parseInt(id) ]; |
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| 189 | } else { |
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| 190 | tracked_datasets[ parseInt(id) ] = val.state; |
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| 191 | } |
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| 192 | }); |
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| 193 | updater( tracked_datasets ); |
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| 194 | }, |
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| 195 | error: function() { |
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| 196 | // Just retry, like the old method, should try to be smarter |
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| 197 | updater( tracked_datasets ); |
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| 198 | } |
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| 199 | }); |
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| 200 | }; |
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| 201 | </script> |
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| 202 | </%def> |
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| 203 | |
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| 204 | <%def name="render_dataset( cntrller, ldda, library_dataset, selected, library, folder, pad, parent, row_counter, tracked_datasets, show_deleted=False )"> |
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| 205 | <% |
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| 206 | ## The received ldda must always be a LibraryDatasetDatasetAssociation object. The object id passed to methods |
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| 207 | ## from the drop down menu should be the ldda id to prevent id collision ( which could happen when displaying |
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| 208 | ## children, which are always lddas ). We also need to make sure we're displaying the latest version of this |
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| 209 | ## library_dataset, so we display the attributes from the ldda. |
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| 210 | |
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| 211 | from galaxy.web.controllers.library_common import active_folders, active_folders_and_lddas, activatable_folders_and_lddas, branch_deleted |
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| 212 | |
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| 213 | if ldda.user: |
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| 214 | uploaded_by = ldda.user.email |
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| 215 | else: |
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| 216 | uploaded_by = 'anonymous' |
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| 217 | if ldda == library_dataset.library_dataset_dataset_association: |
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| 218 | current_version = True |
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| 219 | if trans.user_is_admin() and cntrller == 'library_admin': |
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| 220 | can_modify = can_manage = True |
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| 221 | elif cntrller in [ 'library', 'requests' ]: |
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| 222 | can_modify = trans.app.security_agent.can_modify_library_item( current_user_roles, library_dataset ) |
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| 223 | can_manage = trans.app.security_agent.can_manage_library_item( current_user_roles, library_dataset ) |
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| 224 | else: |
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| 225 | can_modify = can_manage = False |
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| 226 | else: |
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| 227 | current_version = False |
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| 228 | if current_version and ldda.state not in ( 'ok', 'error', 'empty', 'deleted', 'discarded' ): |
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| 229 | tracked_datasets[ldda.id] = ldda.state |
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| 230 | info_association, inherited = ldda.get_info_association( restrict=True ) |
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| 231 | %> |
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| 232 | %if current_version and ( not ldda.library_dataset.deleted or show_deleted ): |
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| 233 | <tr class="datasetRow" |
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| 234 | %if parent is not None: |
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| 235 | parent="${parent}" |
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| 236 | %endif |
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| 237 | id="libraryItem-${ldda.id}"> |
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| 238 | <td style="padding-left: ${pad+20}px;"> |
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| 239 | <input style="float: left;" type="checkbox" name="ldda_ids" value="${trans.security.encode_id( ldda.id )}" |
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| 240 | %if selected: |
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| 241 | checked="checked" |
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| 242 | %endif |
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| 243 | /> |
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| 244 | %if ldda.library_dataset.deleted: |
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| 245 | <span class="libraryItem-error"> |
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| 246 | %endif |
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| 247 | <div style="float: left; margin-left: 1px;" class="menubutton split popup" id="dataset-${ldda.id}-popup"> |
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| 248 | <a class="view-info" href="${h.url_for( controller='library_common', action='ldda_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">${ldda.name[:50]}</a> |
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| 249 | </div> |
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| 250 | %if ldda.library_dataset.deleted: |
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| 251 | </span> |
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| 252 | %endif |
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| 253 | %if not library.deleted: |
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| 254 | <div popupmenu="dataset-${ldda.id}-popup"> |
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| 255 | %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_modify: |
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| 256 | <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_edit_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit information</a> |
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| 257 | %else: |
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| 258 | <a class="action-button" class="view-info" href="${h.url_for( controller='library_common', action='ldda_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">View information</a> |
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| 259 | %endif |
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| 260 | %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_modify and not info_association: |
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| 261 | <a class="action-button" href="${h.url_for( controller='library_common', action='add_template', cntrller=cntrller, item_type='ldda', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add template</a> |
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| 262 | %endif |
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| 263 | %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_modify and info_association: |
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| 264 | <a class="action-button" href="${h.url_for( controller='library_common', action='edit_template', cntrller=cntrller, item_type='ldda', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit template</a> |
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| 265 | <a class="action-button" href="${h.url_for( controller='library_common', action='delete_template', cntrller=cntrller, item_type='ldda', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Delete template</a> |
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| 266 | %endif |
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| 267 | %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_manage: |
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| 268 | %if not trans.app.security_agent.dataset_is_public( ldda.dataset ): |
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| 269 | <a class="action-button" href="${h.url_for( controller='library_common', action='make_library_item_public', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_type='ldda', id=trans.security.encode_id( ldda.dataset.id ), use_panels=use_panels, show_deleted=show_deleted )}">Make public</a> |
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| 270 | %endif |
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| 271 | <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_permissions', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit permissions</a> |
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| 272 | %endif |
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| 273 | %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_modify: |
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| 274 | <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), replace_id=trans.security.encode_id( library_dataset.id ), show_deleted=show_deleted )}">Upload a new version of this dataset</a> |
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| 275 | %endif |
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| 276 | %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and ldda.has_data: |
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| 277 | <a class="action-button" href="${h.url_for( controller='library_common', action='act_on_multiple_datasets', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), ldda_ids=trans.security.encode_id( ldda.id ), do_action='import_to_history', use_panels=use_panels, show_deleted=show_deleted )}">Import this dataset into your current history</a> |
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| 278 | <a class="action-button" href="${h.url_for( controller='library_common', action='download_dataset_from_folder', cntrller=cntrller, id=trans.security.encode_id( ldda.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels )}">Download this dataset</a> |
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| 279 | %endif |
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| 280 | %if can_modify: |
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| 281 | %if not library.deleted and not branch_deleted( folder ) and not ldda.library_dataset.deleted: |
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| 282 | <a class="action-button" confirm="Click OK to delete dataset '${ldda.name}'." href="${h.url_for( controller='library_common', action='delete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library_dataset.id ), item_type='library_dataset', show_deleted=show_deleted )}">Delete this dataset</a> |
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| 283 | %elif not library.deleted and not branch_deleted( folder ) and not ldda.library_dataset.purged and ldda.library_dataset.deleted: |
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| 284 | <a class="action-button" href="${h.url_for( controller='library_common', action='undelete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library_dataset.id ), item_type='library_dataset', show_deleted=show_deleted )}">Undelete this dataset</a> |
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| 285 | %endif |
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| 286 | %endif |
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| 287 | </div> |
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| 288 | %endif |
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| 289 | </td> |
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| 290 | <td id="libraryItemInfo">${render_library_item_info( ldda )}</td> |
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| 291 | <td>${uploaded_by}</td> |
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| 292 | <td>${ldda.create_time.strftime( "%Y-%m-%d" )}</td> |
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| 293 | <td>${ldda.get_size( nice_size=True )}</td> |
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| 294 | </tr> |
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| 295 | <% |
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| 296 | my_row = row_counter.count |
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| 297 | row_counter.increment() |
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| 298 | %> |
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| 299 | %endif |
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| 300 | </%def> |
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| 301 | |
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| 302 | <%def name="render_folder( cntrller, folder, folder_pad, created_ldda_ids, library, hidden_folder_ids, tracked_datasets, show_deleted=False, parent=None, row_counter=None, root_folder=False )"> |
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| 303 | <% |
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| 304 | from galaxy.web.controllers.library_common import active_folders, active_folders_and_lddas, activatable_folders_and_lddas, branch_deleted |
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| 305 | |
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| 306 | if root_folder: |
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| 307 | pad = folder_pad |
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| 308 | expander = h.url_for("/static/images/silk/resultset_bottom.png") |
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| 309 | folder_img = h.url_for("/static/images/silk/folder_page.png") |
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| 310 | else: |
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| 311 | pad = folder_pad + 20 |
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| 312 | expander = h.url_for("/static/images/silk/resultset_next.png") |
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| 313 | folder_img = h.url_for("/static/images/silk/folder.png") |
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| 314 | if created_ldda_ids: |
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| 315 | created_ldda_ids = util.listify( created_ldda_ids ) |
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| 316 | if str( folder.id ) in hidden_folder_ids: |
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| 317 | return "" |
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| 318 | my_row = None |
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| 319 | if trans.user_is_admin() and cntrller == 'library_admin': |
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| 320 | can_add = can_modify = can_manage = True |
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| 321 | elif cntrller in [ 'library', 'requests' ]: |
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| 322 | can_access, folder_ids = trans.app.security_agent.check_folder_contents( trans.user, current_user_roles, folder ) |
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| 323 | if not can_access: |
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| 324 | can_show, folder_ids = \ |
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| 325 | trans.app.security_agent.show_library_item( trans.user, |
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| 326 | current_user_roles, |
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| 327 | folder, |
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| 328 | [ trans.app.security_agent.permitted_actions.LIBRARY_ADD, |
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| 329 | trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, |
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| 330 | trans.app.security_agent.permitted_actions.LIBRARY_MANAGE ] ) |
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| 331 | if not can_show: |
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| 332 | return "" |
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| 333 | can_add = trans.app.security_agent.can_add_library_item( current_user_roles, folder ) |
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| 334 | can_modify = trans.app.security_agent.can_modify_library_item( current_user_roles, folder ) |
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| 335 | can_manage = trans.app.security_agent.can_manage_library_item( current_user_roles, folder ) |
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| 336 | else: |
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| 337 | can_add = can_modify = can_manage = False |
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| 338 | info_association, inherited = folder.get_info_association( restrict=True ) |
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| 339 | %> |
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| 340 | %if not root_folder and ( not folder.deleted or show_deleted ): |
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| 341 | <tr id="folder-${trans.security.encode_id(folder.id)}" class="folderRow libraryOrFolderRow" |
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| 342 | %if parent is not None: |
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| 343 | parent="${parent}" |
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| 344 | style="display: none;" |
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| 345 | %endif |
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| 346 | > |
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| 347 | <td style="padding-left: ${folder_pad}px;"> |
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| 348 | <input type="checkbox" class="folderCheckbox"/> |
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| 349 | |
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| 350 | %if folder.deleted: |
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| 351 | <span class="libraryItem-error"> |
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| 352 | %endif |
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| 353 | <span class="expandLink"><span class="rowIcon"></span> |
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| 354 | <div style="float: left; margin-left: 2px;" class="menubutton split popup" id="folder_img-${folder.id}-popup"> |
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| 355 | <a href="javascript:void(0);">${folder.name}</a> |
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| 356 | </div> |
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| 357 | |
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| 358 | %if folder.deleted: |
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| 359 | </span> |
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| 360 | %endif |
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| 361 | %if not branch_deleted( folder ): |
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| 362 | %if not library.deleted: |
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| 363 | <div popupmenu="folder_img-${folder.id}-popup"> |
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| 364 | %if not branch_deleted( folder ) and can_add: |
---|
| 365 | <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add datasets</a> |
---|
| 366 | <a class="action-button" href="${h.url_for( controller='library_common', action='create_folder', cntrller=cntrller, parent_id=trans.security.encode_id( folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add sub-folder</a> |
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| 367 | %endif |
---|
| 368 | %if not branch_deleted( folder ): |
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| 369 | %if can_modify: |
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| 370 | <a class="action-button" href="${h.url_for( controller='library_common', action='folder_info', cntrller=cntrller, id=trans.security.encode_id( folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit information</a> |
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| 371 | %else: |
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| 372 | <a class="action-button" class="view-info" href="${h.url_for( controller='library_common', action='folder_info', cntrller=cntrller, id=trans.security.encode_id( folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">View information</a> |
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| 373 | %endif |
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| 374 | %endif |
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| 375 | %if not branch_deleted( folder ) and can_modify and not info_association: |
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| 376 | <a class="action-button" href="${h.url_for( controller='library_common', action='add_template', cntrller=cntrller, item_type='folder', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add template</a> |
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| 377 | %endif |
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| 378 | %if not branch_deleted( folder ) and can_modify and info_association: |
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| 379 | <a class="action-button" href="${h.url_for( controller='library_common', action='edit_template', cntrller=cntrller, item_type='folder', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit template</a> |
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| 380 | <a class="action-button" href="${h.url_for( controller='library_common', action='delete_template', cntrller=cntrller, item_type='folder', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Delete template</a> |
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| 381 | %endif |
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| 382 | %if not branch_deleted( folder ) and can_manage: |
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| 383 | %if not trans.app.security_agent.folder_is_public( folder ): |
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| 384 | <a class="action-button" href="${h.url_for( controller='library_common', action='make_library_item_public', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_type='folder', id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Make public</a> |
---|
| 385 | %endif |
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| 386 | <a class="action-button" href="${h.url_for( controller='library_common', action='folder_permissions', cntrller=cntrller, id=trans.security.encode_id( folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit permissions</a> |
---|
| 387 | %endif |
---|
| 388 | %if can_modify: |
---|
| 389 | %if not library.deleted and not folder.deleted: |
---|
| 390 | <a class="action-button" confirm="Click OK to delete the folder '${folder.name}.'" href="${h.url_for( controller='library_common', action='delete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( folder.id ), item_type='folder', show_deleted=show_deleted )}">Delete this folder</a> |
---|
| 391 | %elif not library.deleted and folder.deleted and not folder.purged: |
---|
| 392 | <a class="action-button" href="${h.url_for( controller='library_common', action='undelete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( folder.id ), item_type='folder', show_deleted=show_deleted )}">Undelete this folder</a> |
---|
| 393 | %endif |
---|
| 394 | %endif |
---|
| 395 | </div> |
---|
| 396 | %endif |
---|
| 397 | %endif |
---|
| 398 | <td> |
---|
| 399 | %if folder.description: |
---|
| 400 | ${folder.description} |
---|
| 401 | %endif |
---|
| 402 | <td colspan="3"></td> |
---|
| 403 | </tr> |
---|
| 404 | <% |
---|
| 405 | my_row = row_counter.count |
---|
| 406 | row_counter.increment() |
---|
| 407 | %> |
---|
| 408 | %endif |
---|
| 409 | %if cntrller == 'library': |
---|
| 410 | <% sub_folders = active_folders( trans, folder ) %> |
---|
| 411 | %for sub_folder in sub_folders: |
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| 412 | ${render_folder( cntrller, sub_folder, pad, created_ldda_ids, library, hidden_folder_ids, tracked_datasets, show_deleted=show_deleted, parent=my_row, row_counter=row_counter, root_folder=False )} |
---|
| 413 | %endfor |
---|
| 414 | %for library_dataset in folder.active_library_datasets: |
---|
| 415 | <% |
---|
| 416 | ldda = library_dataset.library_dataset_dataset_association |
---|
| 417 | can_access = trans.app.security_agent.can_access_dataset( current_user_roles, ldda.dataset ) |
---|
| 418 | selected = created_ldda_ids and str( ldda.id ) in created_ldda_ids |
---|
| 419 | %> |
---|
| 420 | %if can_access: |
---|
| 421 | ${render_dataset( cntrller, ldda, library_dataset, selected, library, folder, pad, my_row, row_counter, tracked_datasets, show_deleted=show_deleted )} |
---|
| 422 | %endif |
---|
| 423 | %endfor |
---|
| 424 | %elif trans.user_is_admin() and cntrller == 'library_admin': |
---|
| 425 | <% |
---|
| 426 | if show_deleted: |
---|
| 427 | sub_folders, lddas = activatable_folders_and_lddas( trans, folder ) |
---|
| 428 | else: |
---|
| 429 | sub_folders, lddas = active_folders_and_lddas( trans, folder ) |
---|
| 430 | %> |
---|
| 431 | %for sub_folder in sub_folders: |
---|
| 432 | ${render_folder( cntrller, sub_folder, pad, created_ldda_ids, library, [], tracked_datasets, show_deleted=show_deleted, parent=my_row, row_counter=row_counter, root_folder=False )} |
---|
| 433 | %endfor |
---|
| 434 | %for ldda in lddas: |
---|
| 435 | <% |
---|
| 436 | library_dataset = ldda.library_dataset |
---|
| 437 | selected = created_ldda_ids and str( ldda.id ) in created_ldda_ids |
---|
| 438 | %> |
---|
| 439 | ${render_dataset( cntrller, ldda, library_dataset, selected, library, folder, pad, my_row, row_counter, tracked_datasets, show_deleted=show_deleted )} |
---|
| 440 | %endfor |
---|
| 441 | %endif |
---|
| 442 | </%def> |
---|
| 443 | |
---|
| 444 | <%def name="render_content()"> |
---|
| 445 | <% |
---|
| 446 | from galaxy import util |
---|
| 447 | from galaxy.web.controllers.library_common import branch_deleted |
---|
| 448 | from time import strftime |
---|
| 449 | |
---|
| 450 | if trans.user_is_admin() and cntrller == 'library_admin': |
---|
| 451 | can_add = can_modify = can_manage = True |
---|
| 452 | elif cntrller in [ 'library', 'requests' ]: |
---|
| 453 | can_add = trans.app.security_agent.can_add_library_item( current_user_roles, library ) |
---|
| 454 | can_modify = trans.app.security_agent.can_modify_library_item( current_user_roles, library ) |
---|
| 455 | can_manage = trans.app.security_agent.can_manage_library_item( current_user_roles, library ) |
---|
| 456 | else: |
---|
| 457 | can_add = can_modify = can_manage = False |
---|
| 458 | info_association, inherited = library.get_info_association() |
---|
| 459 | |
---|
| 460 | tracked_datasets = {} |
---|
| 461 | |
---|
| 462 | class RowCounter( object ): |
---|
| 463 | def __init__( self ): |
---|
| 464 | self.count = 0 |
---|
| 465 | def increment( self ): |
---|
| 466 | self.count += 1 |
---|
| 467 | def __str__( self ): |
---|
| 468 | return str( self.count ) |
---|
| 469 | %> |
---|
| 470 | |
---|
| 471 | <h2>Data Library “${library.name}”</h2> |
---|
| 472 | |
---|
| 473 | <ul class="manage-table-actions"> |
---|
| 474 | %if not library.deleted and ( ( trans.user_is_admin() and cntrller == 'library_admin' ) or can_add ): |
---|
| 475 | <li><a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( library.root_folder.id ), use_panels=use_panels, show_deleted=show_deleted )}"><span>Add datasets</span></a></li> |
---|
| 476 | <li><a class="action-button" href="${h.url_for( controller='library_common', action='create_folder', cntrller=cntrller, parent_id=trans.security.encode_id( library.root_folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add folder</a></li> |
---|
| 477 | %endif |
---|
| 478 | %if ( ( not library.deleted ) and ( can_modify or can_manage ) ) or ( can_modify and not library.purged ) or ( library.purged ): |
---|
| 479 | <li><a class="action-button" id="library-${library.id}-popup" class="menubutton">Library Actions</a></li> |
---|
| 480 | <div popupmenu="library-${library.id}-popup"> |
---|
| 481 | %if not library.deleted: |
---|
| 482 | %if can_modify: |
---|
| 483 | <a class="action-button" href="${h.url_for( controller='library_common', action='library_info', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit information</a> |
---|
| 484 | <a class="action-button" confirm="Click OK to delete the library named '${library.name}'." href="${h.url_for( controller='library_common', action='delete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library.id ), item_type='library' )}">Delete this data library</a> |
---|
| 485 | %if show_deleted: |
---|
| 486 | <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=False )}">Hide deleted items</a> |
---|
| 487 | %else: |
---|
| 488 | <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=True )}">Show deleted items</a> |
---|
| 489 | %endif |
---|
| 490 | %endif |
---|
| 491 | %if can_modify and not library.info_association: |
---|
| 492 | <a class="action-button" href="${h.url_for( controller='library_common', action='add_template', cntrller=cntrller, item_type='library', library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add template</a> |
---|
| 493 | %endif |
---|
| 494 | %if can_modify and info_association: |
---|
| 495 | <a class="action-button" href="${h.url_for( controller='library_common', action='edit_template', cntrller=cntrller, item_type='library', library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit template</a> |
---|
| 496 | <a class="action-button" href="${h.url_for( controller='library_common', action='delete_template', cntrller=cntrller, item_type='library', library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Delete template</a> |
---|
| 497 | %endif |
---|
| 498 | %if can_manage: |
---|
| 499 | %if not trans.app.security_agent.library_is_public( library, contents=True ): |
---|
| 500 | <a class="action-button" href="${h.url_for( controller='library_common', action='make_library_item_public', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_type='library', id=trans.security.encode_id( library.id ), contents=True, use_panels=use_panels, show_deleted=show_deleted )}">Make public</a> |
---|
| 501 | %endif |
---|
| 502 | <a class="action-button" href="${h.url_for( controller='library_common', action='library_permissions', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit permissions</a> |
---|
| 503 | %endif |
---|
| 504 | %elif can_modify and not library.purged: |
---|
| 505 | <a class="action-button" href="${h.url_for( controller='library_common', action='undelete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library.id ), item_type='library', use_panels=use_panels )}">Undelete this data library</a> |
---|
| 506 | %elif library.purged: |
---|
| 507 | <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">This data library has been purged</a> |
---|
| 508 | %endif |
---|
| 509 | </div> |
---|
| 510 | %endif |
---|
| 511 | </ul> |
---|
| 512 | |
---|
| 513 | %if message: |
---|
| 514 | ${render_msg( message, status )} |
---|
| 515 | %endif |
---|
| 516 | |
---|
| 517 | %if library.synopsis not in [ 'None', None ]: |
---|
| 518 | <div class="libraryItemBody"> |
---|
| 519 | ${library.synopsis} |
---|
| 520 | </div> |
---|
| 521 | <br/> |
---|
| 522 | %endif |
---|
| 523 | |
---|
| 524 | <form name="act_on_multiple_datasets" action="${h.url_for( controller='library_common', action='act_on_multiple_datasets', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}" onSubmit="javascript:return checkForm();" method="post"> |
---|
| 525 | <table cellspacing="0" cellpadding="0" border="0" width="100%" class="grid" id="library-grid"> |
---|
| 526 | <thead> |
---|
| 527 | <tr class="libraryTitle"> |
---|
| 528 | <th>Name</th> |
---|
| 529 | <th>Information</th> |
---|
| 530 | <th>Uploaded By</th> |
---|
| 531 | <th>Date</th> |
---|
| 532 | <th>File Size</th> |
---|
| 533 | </tr> |
---|
| 534 | </thead> |
---|
| 535 | <% row_counter = RowCounter() %> |
---|
| 536 | %if cntrller in [ 'library', 'requests' ]: |
---|
| 537 | ${self.render_folder( 'library', library.root_folder, 0, created_ldda_ids, library, hidden_folder_ids, tracked_datasets, show_deleted=show_deleted, parent=None, row_counter=row_counter, root_folder=True )} |
---|
| 538 | %if not library.deleted: |
---|
| 539 | ${render_actions_on_multiple_items()} |
---|
| 540 | %endif |
---|
| 541 | %elif ( trans.user_is_admin() and cntrller in [ 'library_admin', 'requests_admin' ] ): |
---|
| 542 | ${self.render_folder( 'library_admin', library.root_folder, 0, created_ldda_ids, library, [], tracked_datasets, show_deleted=show_deleted, parent=None, row_counter=row_counter, root_folder=True )} |
---|
| 543 | %if not library.deleted and not show_deleted: |
---|
| 544 | ${render_actions_on_multiple_items()} |
---|
| 545 | %endif |
---|
| 546 | %endif |
---|
| 547 | </table> |
---|
| 548 | </form> |
---|
| 549 | |
---|
| 550 | %if tracked_datasets: |
---|
| 551 | <script type="text/javascript"> |
---|
| 552 | // Updater |
---|
| 553 | updater({${ ",".join( [ '"%s" : "%s"' % ( k, v ) for k, v in tracked_datasets.iteritems() ] ) }}); |
---|
| 554 | </script> |
---|
| 555 | <!-- running: do not change this comment, used by TwillTestCase.library_wait --> |
---|
| 556 | %endif |
---|
| 557 | |
---|
| 558 | ## Help about compression types |
---|
| 559 | |
---|
| 560 | <div class="libraryItemBody"> |
---|
| 561 | <p class="infomark"> |
---|
| 562 | TIP: You can download individual library files by selecting "Download this dataset" from the context menu (triangle) next to the dataset's name. |
---|
| 563 | </p> |
---|
| 564 | </div> |
---|
| 565 | %if len( comptypes ) > 1: |
---|
| 566 | <div class="libraryItemBody"> |
---|
| 567 | <p class="infomark"> |
---|
| 568 | TIP: Multiple compression options are available for downloading library datasets: |
---|
| 569 | </p> |
---|
| 570 | <ul style="padding-left: 1em; list-style-type: disc;"> |
---|
| 571 | %if 'gz' in comptypes: |
---|
| 572 | <li>gzip: Recommended for fast network connections |
---|
| 573 | %if trans.app.config.upstream_gzip: |
---|
| 574 | NOTE: The file you receive will be an uncompressed .tar file - this is because the Galaxy server compresses it and your browser decompresses it on the fly. |
---|
| 575 | %endif |
---|
| 576 | </li> |
---|
| 577 | %endif |
---|
| 578 | %if 'bz2' in comptypes: |
---|
| 579 | <li>bzip2: Recommended for slower network connections (smaller size but takes longer to compress)</li> |
---|
| 580 | %endif |
---|
| 581 | %if 'zip' in comptypes: |
---|
| 582 | <li>zip: Not recommended but is provided as an option for those who cannot open the above formats</li> |
---|
| 583 | %endif |
---|
| 584 | </ul> |
---|
| 585 | </div> |
---|
| 586 | %endif |
---|
| 587 | </%def> |
---|