- galaxy-dev - lists.galaxyproject.org

[hg] galaxy 2852: Enables viewing of an importable/sharable hist...
by Greg Von Kuster 08 Oct '09

08 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/8f630db17cf1 changeset: 2852:8f630db17cf1 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Thu Oct 08 13:38:32 2009 -0400 description: Enables viewing of an importable/sharable history. Using the syntax /history/view?id=<encoded_history_id> produces a page that renders a history for viewing. A user need not be logged in to view the history. 11 file(s) affected in this change: lib/galaxy/web/controllers/history.py static/june_2007_style/blue/history.css static/june_2007_style/history.css.tmpl static/scripts/autocomplete_tagging.js templates/base_panels.mako templates/history/sharing.mako templates/history/view.mako templates/root/history.mako templates/root/history_common.mako templates/tagging_common.mako test/functional/test_history_functions.py diffs (819 lines): diff -r d146ca99434f -r 8f630db17cf1 lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Thu Oct 08 11:33:43 2009 -0400 +++ b/lib/galaxy/web/controllers/history.py Thu Oct 08 13:38:32 2009 -0400 @@ -371,6 +371,7 @@ # Rename history.name = new_name trans.sa_session.flush() + @web.expose def imp( self, trans, id=None, confirm=False, **kwd ): """Import another user's history via a shared URL""" @@ -423,6 +424,38 @@ Warning! If you import this history, you will lose your current history. Click <a href="%s">here</a> to confirm. """ % web.url_for( id=id, confirm=True ) ) + + @web.expose + def view( self, trans, id=None ): + """View a history. If a history is importable, then it is viewable by any user.""" + + # Get history to view. + if not id: + return trans.show_error_message( "You must specify a history you want to view." ) + history_to_view = get_history( trans, id, False) + + # Integrity checks. + if not history_to_view: + return trans.show_error_message( "The specified history does not exist.") + # TODO: Use a new flag to determine if history is viewable? + if not history_to_view.importable: + error( "The owner of this history has not published this history." ) + + # View history. + query = trans.sa_session.query( model.HistoryDatasetAssociation ) \ + .filter( model.HistoryDatasetAssociation.history == history_to_view ) \ + .options( eagerload( "children" ) ) \ + .join( "dataset" ).filter( model.Dataset.purged == False ) \ + .options( eagerload_all( "dataset.actions" ) ) + # Do not show deleted datasets. + query = query.filter( model.HistoryDatasetAssociation.deleted == False ) + user_owns_history = ( trans.get_user() == history_to_view.user ) + return trans.stream_template_mako( "history/view.mako", + history = history_to_view, + datasets = query.all(), + user_owns_history = user_owns_history, + show_deleted = False ) + @web.expose @web.require_login( "share histories with other users" ) def share( self, trans, id=None, email="", **kwd ): @@ -699,6 +732,7 @@ @web.expose @web.require_login( "share histories with other users" ) def sharing( self, trans, histories=[], id=None, **kwd ): + """Performs sharing of histories among users.""" # histories looks like: [ historyX, historyY ] params = util.Params( kwd ) msg = util.restore_text ( params.get( 'msg', '' ) ) diff -r d146ca99434f -r 8f630db17cf1 static/june_2007_style/blue/history.css --- a/static/june_2007_style/blue/history.css Thu Oct 08 11:33:43 2009 -0400 +++ b/static/june_2007_style/blue/history.css Thu Oct 08 13:38:32 2009 -0400 @@ -1,7 +1,7 @@ body{background:#C1C9E5;color:#303030;background-image:url(menu_bg.png);background-repeat:repeat-x;background-position:top;margin:5px;border:0;padding:0;} a{color:#303030;} div.historyLinks{padding:5px;margin:5px 0 5px 0;} -div.historyItem{margin:5px -5px 5px 0px;padding:5px 11px 5px 5px;border:solid #888888 1px;border-left:solid #888888 5px;border-right:none;background:#EEEEEE;} +div.historyItem{margin:5px -5px 5px 0px;padding:5px 11px 5px 5px;border:solid #888888 1px;border-left:solid #888888 5px;border-right:solid #888888 1px;background:#EEEEEE;} div.historyItem .state-icon{display:inline-block;vertical-align:middle;width:16px;height:16px;background-position:0 1px;background-repeat:no-repeat;} div.historyItem .historyItemTitle{line-height:16px;} div.historyItem div.historyItem{margin-right:-11px;} diff -r d146ca99434f -r 8f630db17cf1 static/june_2007_style/history.css.tmpl --- a/static/june_2007_style/history.css.tmpl Thu Oct 08 11:33:43 2009 -0400 +++ b/static/june_2007_style/history.css.tmpl Thu Oct 08 13:38:32 2009 -0400 @@ -25,7 +25,7 @@ padding: 5px 11px 5px 5px; border: solid $history_queued_border 1px; border-left: solid $history_queued_border 5px; - border-right: none; + border-right: solid $history_queued_border 1px; background: $history_queued_bg; .state-icon { display: inline-block; diff -r d146ca99434f -r 8f630db17cf1 static/scripts/autocomplete_tagging.js --- a/static/scripts/autocomplete_tagging.js Thu Oct 08 11:33:43 2009 -0400 +++ b/static/scripts/autocomplete_tagging.js Thu Oct 08 13:38:32 2009 -0400 @@ -12,30 +12,31 @@ // var defaults = { - get_toggle_link_text_fn: function(tags) - { - var text = ""; - var num_tags = array_length(tags); - if (num_tags != 0) - text = num_tags + (num_tags != 0 ? " Tags" : " Tag"); - else - // No tags. - text = "Add tags"; - return text; - }, - tag_click_fn : function (name, value) { }, - input_size: 20, - in_form: false, - tags : {}, - use_toggle_link: true, - item_id: "", - add_tag_img: "", - add_tag_img_rollover: "", - delete_tag_img: "", - ajax_autocomplete_tag_url: "", - ajax_retag_url: "", - ajax_delete_tag_url: "", - ajax_add_tag_url: "" + get_toggle_link_text_fn: function(tags) + { + var text = ""; + var num_tags = array_length(tags); + if (num_tags != 0) + text = num_tags + (num_tags != 0 ? " Tags" : " Tag"); + else + // No tags. + text = "Add tags"; + return text; + }, + tag_click_fn : function (name, value) { }, + editable: true, + input_size: 20, + in_form: false, + tags : {}, + use_toggle_link: true, + item_id: "", + add_tag_img: "", + add_tag_img_rollover: "", + delete_tag_img: "", + ajax_autocomplete_tag_url: "", + ajax_retag_url: "", + ajax_delete_tag_url: "", + ajax_add_tag_url: "" }; // @@ -206,32 +207,32 @@ // Delete tag. $.ajax({ - url: settings.ajax_delete_tag_url, - data: { tag_name: tag_name }, - error: function() - { - // Failed. Roll back changes and show alert. - settings.tags[tag_name] = tag_value; - if (prev_button.hasClass("tag-button")) - prev_button.after(tag_button); - else - tag_area.prepend(tag_button); - var new_text = settings.get_toggle_link_text_fn(settings.tags); - alert( "Remove tag failed" ); + url: settings.ajax_delete_tag_url, + data: { tag_name: tag_name }, + error: function() + { + // Failed. Roll back changes and show alert. + settings.tags[tag_name] = tag_value; + if (prev_button.hasClass("tag-button")) + prev_button.after(tag_button); + else + tag_area.prepend(tag_button); + var new_text = settings.get_toggle_link_text_fn(settings.tags); + alert( "Remove tag failed" ); - toggle_link.text(new_text); + toggle_link.text(new_text); - // TODO: no idea why it's necessary to set this up again. - delete_img.mouseenter( function () - { - $(this).attr("src", settings.delete_tag_img_rollover); - }); - delete_img.mouseleave( function () - { - $(this).attr("src", settings.delete_tag_img); - }); - }, - success: function() {} + // TODO: no idea why it's necessary to set this up again. + delete_img.mouseenter( function () + { + $(this).attr("src", settings.delete_tag_img_rollover); + }); + delete_img.mouseleave( function () + { + $(this).attr("src", settings.delete_tag_img); + }); + }, + success: function() {} }); return true; @@ -248,7 +249,9 @@ var tag_button = $("<span></span>").addClass("tag-button"); tag_button.append(tag_name_elt); - tag_button.append(delete_img); + // Allow delete only if element is editable. + if (settings.editable) + tag_button.append(delete_img); return tag_button; }; @@ -411,55 +414,58 @@ } }); - tag_area.append(add_tag_button); - tag_area.append(tag_input_field); - tag_input_field.hide(); + if (settings.editable) + { + tag_area.append(add_tag_button); + tag_area.append(tag_input_field); + tag_input_field.hide(); - // On click, enable user to add tags. - tag_area.click( function(e) - { - var is_active = $(this).hasClass("active-tag-area"); + // On click, enable user to add tags. + tag_area.click( function(e) + { + var is_active = $(this).hasClass("active-tag-area"); - // If a "delete image" object was pressed and area is inactive, do nothing. - if ($(e.target).hasClass("delete-tag-img") && !is_active) - return false; + // If a "delete image" object was pressed and area is inactive, do nothing. + if ($(e.target).hasClass("delete-tag-img") && !is_active) + return false; - // If a "tag name" object was pressed and area is inactive, do nothing. - if ($(e.target).hasClass("tag-name") && !is_active) - return false; + // If a "tag name" object was pressed and area is inactive, do nothing. + if ($(e.target).hasClass("tag-name") && !is_active) + return false; - // Hide add tag button, show tag_input field. Change background to show - // area is active. - $(this).addClass("active-tag-area"); - add_tag_button.hide(); - tag_input_field.show(); - tag_input_field.focus(); + // Hide add tag button, show tag_input field. Change background to show + // area is active. + $(this).addClass("active-tag-area"); + add_tag_button.hide(); + tag_input_field.show(); + tag_input_field.focus(); - // Add handler to document that will call blur when the tag area is blurred; - // a tag area is blurred when a user clicks on an element outside the area. - var handle_document_click = function(e) - { - var tag_area_id = tag_area.attr("id"); - // Blur the tag area if the element clicked on is not in the tag area. - if ( - ($(e.target).attr("id") != tag_area_id) && - ($(e.target).parents().filter(tag_area_id).length == 0) - ) - { - tag_area.blur(); - $(document).unbind("click", handle_document_click); - } - }; - // TODO: we should attach the click handler to all frames in order to capture - // clicks outside the frame that this element is in. - //window.parent.document.onclick = handle_document_click; - //var temp = $(window.parent.document.body).contents().find("iframe").html(); - //alert(temp); - //$(document).parent().click(handle_document_click); - $(window).click(handle_document_click); + // Add handler to document that will call blur when the tag area is blurred; + // a tag area is blurred when a user clicks on an element outside the area. + var handle_document_click = function(e) + { + var tag_area_id = tag_area.attr("id"); + // Blur the tag area if the element clicked on is not in the tag area. + if ( + ($(e.target).attr("id") != tag_area_id) && + ($(e.target).parents().filter(tag_area_id).length == 0) + ) + { + tag_area.blur(); + $(document).unbind("click", handle_document_click); + } + }; + // TODO: we should attach the click handler to all frames in order to capture + // clicks outside the frame that this element is in. + //window.parent.document.onclick = handle_document_click; + //var temp = $(window.parent.document.body).contents().find("iframe").html(); + //alert(temp); + //$(document).parent().click(handle_document_click); + $(window).click(handle_document_click); - return false; - }); + return false; + }); + } // If using toggle link, hide the tag area. Otherwise, if there are no tags, // hide the "add tags" button and show the input field. diff -r d146ca99434f -r 8f630db17cf1 templates/base_panels.mako --- a/templates/base_panels.mako Thu Oct 08 11:33:43 2009 -0400 +++ b/templates/base_panels.mako Thu Oct 08 13:38:32 2009 -0400 @@ -44,13 +44,14 @@  + ${h.js( 'jquery' )} </%def> ## Default late-load javascripts <%def name="late_javascripts()"> ## Scripts can be loaded later since they progressively add features to ## the panels, but do not change layout - ${h.js( 'jquery', 'jquery.event.drag', 'jquery.event.hover', 'jquery.form', 'galaxy.base', 'galaxy.panels' )} + ${h.js( 'jquery.event.drag', 'jquery.event.hover', 'jquery.form', 'galaxy.base', 'galaxy.panels' )} <script type="text/javascript"> ensure_dd_helper(); diff -r d146ca99434f -r 8f630db17cf1 templates/history/sharing.mako --- a/templates/history/sharing.mako Thu Oct 08 11:33:43 2009 -0400 +++ b/templates/history/sharing.mako Thu Oct 08 13:38:32 2009 -0400 @@ -34,10 +34,17 @@ %endif %if history.importable: <div class="form-row"> + <% url = h.url_for( controller='history', action='view', id=trans.security.encode_id(history.id), qualified=True ) %> + <a href="${url}" target="_blank">${url}</a> + <div class="toolParamHelp" style="clear: both;"> + Send the above link to users as an easy way for them to view the history. + </div> + </div> + <div class="form-row"> <% url = h.url_for( controller='history', action='imp', id=trans.security.encode_id(history.id), qualified=True ) %> <a href="${url}">${url}</a> <div class="toolParamHelp" style="clear: both;"> - Send the above URL to users as an easy way for them to import the history, making a copy of their own + Send the above link to users as an easy way for them to import the history, making a copy of their own. </div> </div> <div class="form-row"> diff -r d146ca99434f -r 8f630db17cf1 templates/history/view.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/history/view.mako Thu Oct 08 13:38:32 2009 -0400 @@ -0,0 +1,349 @@ +<%inherit file="/base_panels.mako"/> + +<%def name="javascripts()"> + ${parent.javascripts()} + ${h.js( "jquery", "json2", "jquery.jstore-all", "jquery.autocomplete", "autocomplete_tagging" )} +</%def> + +<%def name="stylesheets()"> + ${parent.stylesheets()} + ${h.css( "history", "autocomplete_tagging" )} +</%def> + +<%namespace file="/root/history_common.mako" import="render_dataset" /> + +<%def name="init()"> +<% + self.has_left_panel=False + self.has_right_panel=False + self.message_box_visible=False +%> +</%def> + +<%def name="center_panel()"> + ## For now, turn off inline editing so that view is external only. + <% + user_owns_history = False + %> + + <div style="overflow: auto; height: 100%;"> + <div style="padding: 10px;"> + ## Render view of history. + <script type="text/javascript"> + $(function() { + // Load jStore for local storage + $.extend(jQuery.jStore.defaults, { project: 'galaxy', flash: '/static/jStore.Flash.html' }) + $.jStore.load(); // Auto-select best storage + + $.jStore.ready(function(engine) { + engine.ready(function() { + // Init stuff that requires the local storage to be running + initShowHide(); + setupHistoryItem( $("div.historyItemWrapper") ); + }); + }); + + // Generate 'collapse all' link + $("#top-links").append( "| " ).append( $("<a href='#'>${_('collapse all')}</a>").click( function() { + $( "div.historyItemBody:visible" ).each( function() { + if ( $.browser.mozilla ) { + $(this).find( "pre.peek" ).css( "overflow", "hidden" ); + } + $(this).slideUp( "fast" ); + }); + $.jStore.remove("history_expand_state"); + })); + + $("#history-rename").click( function() { + var old_name = $("#history-name").text() + var t = $("<input type='text' value='" + old_name + "'></input>" ); + t.blur( function() { + $(this).remove(); + $("#history-name").show(); + }); + t.keyup( function( e ) { + if ( e.keyCode == 27 ) { + // Escape key + $(this).trigger( "blur" ); + } else if ( e.keyCode == 13 ) { + // Enter key + new_value = this.value; + $(this).trigger( "blur" ); + $.ajax({ + url: "${h.url_for( controller='history', action='rename_async', id=history.id )}", + data: { "_": true, new_name: new_value }, + error: function() { alert( "Rename failed" ) }, + success: function() { + $("#history-name").text( new_value ); + } + }); + } + }); + $("#history-name").hide(); + $("#history-name-area").append( t ); + t.focus(); + return false; + }); + // Updater + updater({ + <% updateable = [data for data in reversed( datasets ) if data.visible and data.state not in [ "deleted", "empty", "error", "ok" ]] %> + ${ ",".join( map(lambda data: "\"%s\" : \"%s\"" % (data.id, data.state), updateable) ) } + }); + }); + // Functionized so AJAX'd datasets can call them + function initShowHide() { + + // Load saved state and show as necessary + try { + var stored = $.jStore.store("history_expand_state"); + if (stored) { + var st = JSON.parse(stored); + for (var id in st) { + $("#" + id + " div.historyItemBody" ).show(); + } + } + } catch(err) { + // Something was wrong with values in storage, so clear storage + $.jStore.remove("history_expand_state"); + } + + // If Mozilla, hide scrollbars in hidden items since they cause animation bugs + if ( $.browser.mozilla ) { + $( "div.historyItemBody" ).each( function() { + if ( ! $(this).is( ":visible" ) ) $(this).find( "pre.peek" ).css( "overflow", "hidden" ); + }) + } + } + // Add show/hide link and delete link to a history item + function setupHistoryItem( query ) { + query.each( function() { + var id = this.id; + var body = $(this).children( "div.historyItemBody" ); + var peek = body.find( "pre.peek" ) + $(this).children( ".historyItemTitleBar" ).find( ".historyItemTitle" ).wrap( "<a href='#'></a>" ).click( function() { + if ( body.is(":visible") ) { + // Hiding stuff here + if ( $.browser.mozilla ) { peek.css( "overflow", "hidden" ) } + body.slideUp( "fast" ); + + // Save setting + var stored = $.jStore.store("history_expand_state") + var prefs = stored ? JSON.parse(stored) : null + if (prefs) { + delete prefs[id]; + $.jStore.store("history_expand_state", JSON.stringify(prefs)); + } + } else { + // Showing stuff here + body.slideDown( "fast", function() { + if ( $.browser.mozilla ) { peek.css( "overflow", "auto" ); } + }); + + // Save setting + var stored = $.jStore.store("history_expand_state") + var prefs = stored ? JSON.parse(stored) : new Object; + prefs[id] = true; + $.jStore.store("history_expand_state", JSON.stringify(prefs)); + } + return false; + }); + // Delete link + $(this).find( "div.historyItemButtons > .delete" ).each( function() { + var data_id = this.id.split( "-" )[1]; + $(this).click( function() { + $( '#historyItem-' + data_id + "> div.historyItemTitleBar" ).addClass( "spinner" ); + $.ajax({ + url: "${h.url_for( action='delete_async', id='XXX' )}".replace( 'XXX', data_id ), + error: function() { alert( "Delete failed" ) }, + success: function() { + %if show_deleted: + var to_update = {}; + to_update[data_id] = "none"; + updater( to_update ); + %else: + $( "#historyItem-" + data_id ).fadeOut( "fast", function() { + $( "#historyItemContainer-" + data_id ).remove(); + if ( $( "div.historyItemContainer" ).length < 1 ) { + $( "#emptyHistoryMessage" ).show(); + } + }); + %endif + } + }); + return false; + }); + }); + // Undelete link + $(this).find( "a.historyItemUndelete" ).each( function() { + var data_id = this.id.split( "-" )[1]; + $(this).click( function() { + $( '#historyItem-' + data_id + " > div.historyItemTitleBar" ).addClass( "spinner" ); + $.ajax({ + url: "${h.url_for( controller='dataset', action='undelete_async', id='XXX' )}".replace( 'XXX', data_id ), + error: function() { alert( "Undelete failed" ) }, + success: function() { + var to_update = {}; + to_update[data_id] = "none"; + updater( to_update ); + } + }); + return false; + }); + }); + }); + }; + // Looks for changes in dataset state using an async request. Keeps + // calling itself (via setTimeout) until all datasets are in a terminal + // state. + var updater = function ( tracked_datasets ) { + // Check if there are any items left to track + var empty = true; + for ( i in tracked_datasets ) { + empty = false; + break; + } + if ( ! empty ) { + // console.log( "Updater running in 3 seconds" ); + setTimeout( function() { updater_callback( tracked_datasets ) }, 3000 ); + } else { + // console.log( "Updater finished" ); + } + }; + var updater_callback = function ( tracked_datasets ) { + // Build request data + var ids = [] + var states = [] + var force_history_refresh = false + $.each( tracked_datasets, function ( id, state ) { + ids.push( id ); + states.push( state ); + }); + // Make ajax call + $.ajax( { + type: "POST", + url: "${h.url_for( controller='root', action='history_item_updates' )}", + dataType: "json", + data: { ids: ids.join( "," ), states: states.join( "," ) }, + success : function ( data ) { + $.each( data, function( id, val ) { + // Replace HTML + var container = $("#historyItemContainer-" + id); + container.html( val.html ); + setupHistoryItem( container.children( ".historyItemWrapper" ) ); + initShowHide(); + // If new state was terminal, stop tracking + if (( val.state == "ok") || ( val.state == "error") || ( val.state == "empty") || ( val.state == "deleted" ) || ( val.state == "discarded" )) { + if ( val.force_history_refresh ){ + force_history_refresh = true; + } + delete tracked_datasets[ parseInt(id) ]; + } else { + tracked_datasets[ parseInt(id) ] = val.state; + } + }); + if ( force_history_refresh ) { + parent.frames.galaxy_history.location.reload(); + } else { + // Keep going (if there are still any items to track) + updater( tracked_datasets ); + } + }, + error: function() { + // Just retry, like the old method, should try to be smarter + updater( tracked_datasets ); + } + }); + }; + + // + // Function provides text for tagging toggle link. + // + var get_toggle_link_text = function(tags) + { + var text = ""; + var num_tags = array_length(tags); + if (num_tags != 0) + { + text = num_tags + (num_tags != 1 ? " Tags" : " Tag"); + } + else + { + // No tags. + text = "Add tags to history"; + } + return text; + }; + </script> + + <style> + .historyItemBody { + display: none; + } + </style> + + <noscript> + <style> + .historyItemBody { + display: block; + } + </style> + </noscript> + + <div id="top-links" class="historyLinks" style="padding: 0px 0px 5px 0px"> + %if not user_owns_history: + <a href="${h.url_for( controller='history', action='imp', id=trans.security.encode_id(history.id) )}">${_('import')}</a> | + %endif + <a href="${h.url_for( controller='history', action='view', id=trans.security.encode_id(history.id) )}">${_('refresh')}</a> + %if show_deleted: + | <a href="${h.url_for('history', show_deleted=False)}">${_('hide deleted')}</a> + %endif + </div> + + <div id="history-name-area" class="historyLinks" style="color: gray; font-weight: bold; padding: 0px 0px 5px 0px"> + %if user_owns_history: + <div style="float: right"><a id="history-rename" title="Rename" class="icon-button edit" target="galaxy_main" href="${h.url_for( controller='history', action='rename' )}"></a></div> + %endif + <div id="history-name">${history.get_display_name()}</div> + </div> + + %if history.deleted: + <div class="warningmessagesmall"> + ${_('You are currently viewing a deleted history!')} + </div> + <p></p> + %endif + + <div id="history-tag-area" style="margin-bottom: 1em"> + </div> + + <%namespace file="../tagging_common.mako" import="render_tagging_element" /> + + %if trans.get_user() is not None: + <div id='history-tag-area' class="tag-element"></div> + ${render_tagging_element(history, "history-tag-area", get_toggle_link_text_fn='get_toggle_link_text', editable=user_owns_history)} + %endif + + %if not datasets: + + <div class="infomessagesmall" id="emptyHistoryMessage"> + + %else: + + ## Render requested datasets, ordered from newest to oldest + %for data in reversed( datasets ): + %if data.visible: + <div class="historyItemContainer" id="historyItemContainer-${data.id}"> + ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, user_owns_dataset=user_owns_history )} + </div> + %endif + %endfor + + <div class="infomessagesmall" id="emptyHistoryMessage" style="display:none;"> + %endif + ${_("Your history is empty. Click 'Get Data' on the left pane to start")} + </div> + </div> + </div> + + +</%def> diff -r d146ca99434f -r 8f630db17cf1 templates/root/history.mako --- a/templates/root/history.mako Thu Oct 08 11:33:43 2009 -0400 +++ b/templates/root/history.mako Thu Oct 08 13:38:32 2009 -0400 @@ -321,7 +321,7 @@ %for data in reversed( datasets ): %if data.visible: <div class="historyItemContainer" id="historyItemContainer-${data.id}"> - ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted )} + ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, user_owns_dataset = True )} </div> %endif %endfor diff -r d146ca99434f -r 8f630db17cf1 templates/root/history_common.mako --- a/templates/root/history_common.mako Thu Oct 08 11:33:43 2009 -0400 +++ b/templates/root/history_common.mako Thu Oct 08 13:38:32 2009 -0400 @@ -1,6 +1,6 @@ <% _=n_ %> ## Render the dataset `data` as history item, using `hid` as the displayed id -<%def name="render_dataset( data, hid, show_deleted_on_refresh = False )"> +<%def name="render_dataset( data, hid, show_deleted_on_refresh = False, user_owns_dataset = True )"> <% if data.state in ['no state','',None]: data_state = "queued" @@ -19,21 +19,27 @@ <strong>This dataset has been deleted. Click <a href="${h.url_for( controller='dataset', action='undelete', id=data.id )}" class="historyItemUndelete" id="historyItemUndeleter-${data.id}" target="galaxy_history">here</a> to undelete.</strong> </div> %endif - + ## Header row for history items (name, state, action buttons) <div style="overflow: hidden;" class="historyItemTitleBar"> <div class="historyItemButtons"> %if data_state == "upload": - ## TODO: Make these CSS, just adding a "disabled" class to the normal - ## links should be enough. However the number of datasets being uploaded - ## at a time is usually small so the impact of these images is also small. - <img src="${h.url_for('/static/images/eye_icon_grey.png')}" width='16' height='16' alt='display data' title='display data' class='button display' border='0'> - <img src="${h.url_for('/static/images/pencil_icon_grey.png')}" width='16' height='16' alt='edit attributes' title='edit attributes' class='button edit' border='0'> + ## TODO: Make these CSS, just adding a "disabled" class to the normal + ## links should be enough. However the number of datasets being uploaded + ## at a time is usually small so the impact of these images is also small. + <img src="${h.url_for('/static/images/eye_icon_grey.png')}" width='16' height='16' alt='display data' title='display data' class='button display' border='0'> + %if user_owns_dataset: + <img src="${h.url_for('/static/images/pencil_icon_grey.png')}" width='16' height='16' alt='edit attributes' title='edit attributes' class='button edit' border='0'> + %endif %else: - <a class="icon-button display" title="display data" href="${h.url_for( controller='dataset', dataset_id=data.id, action='display', filename='index')}" target="galaxy_main"></a> - <a class="icon-button edit" title="edit attributes" href="${h.url_for( controller='root', action='edit', id=data.id )}" target="galaxy_main"></a> + <a class="icon-button display" title="display data" href="${h.url_for( controller='dataset', dataset_id=data.id, action='display', filename='index')}" target="galaxy_main"></a> + %if user_owns_dataset: + <a class="icon-button edit" title="edit attributes" href="${h.url_for( controller='root', action='edit', id=data.id )}" target="galaxy_main"></a> + %endif %endif - <a class="icon-button delete" title="delete" href="${h.url_for( action='delete', id=data.id, show_deleted_on_refresh=show_deleted_on_refresh )}" id="historyItemDeleter-${data.id}"></a> + %if user_owns_dataset: + <a class="icon-button delete" title="delete" href="${h.url_for( action='delete', id=data.id, show_deleted_on_refresh=show_deleted_on_refresh )}" id="historyItemDeleter-${data.id}"></a> + %endif </div> <span class="state-icon"></span> <span class="historyItemTitle"><b>${hid}: ${data.display_name().decode('utf-8')}</b></span> @@ -80,8 +86,10 @@ <div class="info">${_('Info: ')}${data.display_info()}</div> <div> %if data.has_data: - <a href="${h.url_for( action='display', id=data.id, tofile='yes', toext=data.ext )}" target="_blank">save</a> - | <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main">rerun</a> + <a href="${h.url_for( controller='root', action='display', id=data.id, tofile='yes', toext=data.ext )}" target="_blank">save</a> + %if user_owns_dataset: + | <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main">rerun</a> + %endif %for display_app in data.datatype.get_display_types(): <% target_frame, display_links = data.datatype.get_display_links( data, display_app, app, request.base ) %> %if len( display_links ) > 0: diff -r d146ca99434f -r 8f630db17cf1 templates/tagging_common.mako --- a/templates/tagging_common.mako Thu Oct 08 11:33:43 2009 -0400 +++ b/templates/tagging_common.mako Thu Oct 08 13:38:32 2009 -0400 @@ -4,7 +4,7 @@ %endif ## Render the tags 'tags' as an autocomplete element. -<%def name="render_tagging_element(tagged_item, elt_id, use_toggle_link='true', in_form='false', input_size='15', tag_click_fn='default_tag_click_fn', get_toggle_link_text_fn='default_get_toggle_link_text_fn')"> +<%def name="render_tagging_element(tagged_item, elt_id, use_toggle_link='true', in_form='false', input_size='15', tag_click_fn='default_tag_click_fn', get_toggle_link_text_fn='default_get_toggle_link_text_fn', editable='true')"> <script type="text/javascript"> // // Set up autocomplete tagger. @@ -83,6 +83,7 @@ var options = { tags : ${h.to_json_string(tag_names_and_values)}, + editable : ${str(editable).lower()}, get_toggle_link_text_fn: ${get_toggle_link_text_fn}, tag_click_fn: ${tag_click_fn}, <% tagged_item_id = trans.security.encode_id(tagged_item.id) %> diff -r d146ca99434f -r 8f630db17cf1 test/functional/test_history_functions.py --- a/test/functional/test_history_functions.py Thu Oct 08 11:33:43 2009 -0400 +++ b/test/functional/test_history_functions.py Thu Oct 08 13:38:32 2009 -0400 @@ -164,7 +164,7 @@ # Enable importing history3 via a URL self.enable_import_via_link( self.security.encode_id( history3.id ), check_str='Unshare', - check_str_after_submit='Send the above URL to users' ) + check_str_after_submit='Send the above link to users' ) # Make sure history3 is now import-able history3.refresh() if not history3.importable: @@ -175,7 +175,7 @@ check_str_after_submit='You cannot import your own history.' ) # Disable the import link for history3 self.disable_import_via_link( self.security.encode_id( history3.id ), - check_str='Send the above URL to users', + check_str='Send the above link to users', check_str_after_submit='Enable import via link' ) # Try importing history3 after disabling the URL self.import_history_via_url( self.security.encode_id( history3.id ),

1 0

[hg] galaxy 2853: Merge
by Greg Von Kuster 08 Oct '09

08 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/f46f6a26218b changeset: 2853:f46f6a26218b user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Thu Oct 08 13:38:57 2009 -0400 description: Merge 0 file(s) affected in this change: diffs (46 lines): diff -r 8f630db17cf1 -r f46f6a26218b tools/sr_mapping/bowtie_wrapper.xml --- a/tools/sr_mapping/bowtie_wrapper.xml Thu Oct 08 13:38:32 2009 -0400 +++ b/tools/sr_mapping/bowtie_wrapper.xml Thu Oct 08 13:38:57 2009 -0400 @@ -426,9 +426,19 @@ **What it does** -Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. Reads can be as long as 1024 base pairs, though shorter is better. Bowtie produces a specific output format which is converted to SAM by this tool. +Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. It is developed by Ben Langmead and Cole Trapnell. .. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml + +------ + +**Know what you are doing** + +.. class:: warningmark + +There is no such thing (yet) as automated gearshift in short read mapping. It is all like stick-shift driving in San Francisco. In other words = running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading `documentation`__ and experimenting. Fortunaly, Galaxy makes experimenting easy. + + .. __: http://bowtie-bio.sourceforge.net/index.shtml ------ diff -r 8f630db17cf1 -r f46f6a26218b tools/sr_mapping/bwa_wrapper.xml --- a/tools/sr_mapping/bwa_wrapper.xml Thu Oct 08 13:38:32 2009 -0400 +++ b/tools/sr_mapping/bwa_wrapper.xml Thu Oct 08 13:38:57 2009 -0400 @@ -291,7 +291,17 @@ **What it does** -**BWA** is a high performance sequence aligner that succeeds MAQ. It is based on BWT-SW but uses a completely different algorithm and is aimed towards short read alignments. It is fast--it can map the human genome in only 15-25 minutes. Heng Li of the Sanger Institute wrote the majority of the code, with contributions by Chi-Kwong Wong at the University of Hong Kong, Nong Ge at Sun Yat-Sen University, and Yuta Mori. +BWA is a fast light-weighted tool that aligns relatively short sequences (queries) to a sequence database (large), such as the human reference genome. It is developed by Heng Li at the Sanger Insitute. + +------ + +**Know what you are doing** + +.. class:: warningmark + +There is no such thing (yet) as automated gearshift in short read mapping. It is all like stick-shift driving in San Francisco. In other words = running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading `documentation`__ and experimenting. Fortunaly, Galaxy makes experimenting easy. + + .. __: http://bio-bwa.sourceforge.net/ ------

1 0

[hg] galaxy 2847: Added 'Median' operation to grouping tool
by Greg Von Kuster 08 Oct '09

08 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/39ccea195b8e changeset: 2847:39ccea195b8e user: gua110 date: Thu Oct 08 10:37:26 2009 -0400 description: Added 'Median' operation to grouping tool 1 file(s) affected in this change: tools/stats/grouping.xml diffs (17 lines): diff -r f0d565ab7028 -r 39ccea195b8e tools/stats/grouping.xml --- a/tools/stats/grouping.xml Thu Oct 08 10:07:35 2009 -0400 +++ b/tools/stats/grouping.xml Thu Oct 08 10:37:26 2009 -0400 @@ -1,4 +1,4 @@ -<tool id="Grouping1" name="Group" version="1.8.0"> +<tool id="Grouping1" name="Group" version="1.9.0"> <description>data by a column and perform aggregate operation on other columns.</description> <command interpreter="python"> grouping.py @@ -21,6 +21,7 @@ <repeat name="operations" title="Operation"> <param name="optype" type="select" label="Type"> <option value="mean">Mean</option> + <option value="median">Median</option> <option value="max">Maximum</option> <option value="min">Minimum</option> <option value="sum">Sum</option>

1 0

[hg] galaxy 2846: tiny change to bwa warpper
by Greg Von Kuster 08 Oct '09

08 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/f0d565ab7028 changeset: 2846:f0d565ab7028 user: Anton Nekrutenko <anton(a)bx.psu.edu> date: Thu Oct 08 10:07:35 2009 -0400 description: tiny change to bwa warpper 1 file(s) affected in this change: tools/sr_mapping/bwa_wrapper.xml diffs (12 lines): diff -r 1fa410dd1aa1 -r f0d565ab7028 tools/sr_mapping/bwa_wrapper.xml --- a/tools/sr_mapping/bwa_wrapper.xml Thu Oct 08 09:01:19 2009 -0400 +++ b/tools/sr_mapping/bwa_wrapper.xml Thu Oct 08 10:07:35 2009 -0400 @@ -66,7 +66,7 @@ <inputs> <conditional name="solidOrSolexa"> <param name="solidSolexa" type="select" label="Select SOLiD or Solexa format for the original dataset"> - <option value="solexa">Solexa</option> + <option value="solexa">Illumina</option> <option value="solid">SOLiD</option> </param> <when value="solid">

1 0

[hg] galaxy 2849: Refactored the form validation code
by Greg Von Kuster 08 Oct '09

08 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/674bb364697a changeset: 2849:674bb364697a user: rc date: Thu Oct 08 11:14:04 2009 -0400 description: Refactored the form validation code 1 file(s) affected in this change: lib/galaxy/web/controllers/forms.py diffs (43 lines): diff -r a105810a5da8 -r 674bb364697a lib/galaxy/web/controllers/forms.py --- a/lib/galaxy/web/controllers/forms.py Thu Oct 08 10:45:31 2009 -0400 +++ b/lib/galaxy/web/controllers/forms.py Thu Oct 08 11:14:04 2009 -0400 @@ -91,8 +91,8 @@ self.current_form = {} self.current_form[ 'name' ] = 'New Form' self.current_form[ 'desc' ] = '' - self.current_form['type'] = 'none' - self.current_form[ 'layout' ] = ['Main'] + self.current_form[ 'type' ] = params.get( 'form_type', 'none' ) + self.current_form[ 'layout' ] = [ 'Main' ] self.current_form[ 'fields' ] = [] inputs = [ ( 'Name', TextField( 'name', 40, self.current_form[ 'name' ] ) ), ( 'Description', TextField( 'description', 40, self.current_form[ 'desc' ] ) ), @@ -286,9 +286,9 @@ if util.restore_text( params.form_type_selectbox ) == 'none': return None, 'Form type must be selected.' # fields - for i in range( len(self.current_form['fields']) ): - if not util.restore_text(params.get( 'field_name_%i' % i, None )): - return None, "All the field label(s) must be completed." +# for i in range( len(self.current_form['fields']) ): +# if not util.restore_text(params.get( 'field_name_%i' % i, None )): +# return None, "All the field label(s) must be completed." return True, '' def __get_form(self, trans, **kwd): params = util.Params( kwd ) @@ -365,8 +365,13 @@ flag, msg = self.__validate_form(**kwd) if not flag: return None, msg - fd = trans.app.model.FormDefinition() - fd.name, fd.desc, fd.type, fd.layout, fd.fields = self.__get_form(trans, **kwd) + name, desc, form_type, layout, fields = self.__get_form(trans, **kwd) + # validate fields + for field in fields: + if not field[ 'label' ]: + return None, "All the field label(s) must be completed." + fd = trans.app.model.FormDefinition(name, desc, fields, current_form=None, + form_type=form_type, layout=layout ) if fdc_id: # save changes to the existing form # change the pointer in the form_definition_current table to point # to this new record

1 0

[hg] galaxy 2848: Removed sniff method from fastqsanger datatype
by Greg Von Kuster 08 Oct '09

08 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/a105810a5da8 changeset: 2848:a105810a5da8 user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Thu Oct 08 10:45:31 2009 -0400 description: Removed sniff method from fastqsanger datatype 4 file(s) affected in this change: datatypes_conf.xml.sample lib/galaxy/datatypes/registry.py lib/galaxy/datatypes/sequence.py test/functional/test_sniffing_and_metadata_settings.py diffs (113 lines): diff -r 39ccea195b8e -r a105810a5da8 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample Thu Oct 08 10:37:26 2009 -0400 +++ b/datatypes_conf.xml.sample Thu Oct 08 10:45:31 2009 -0400 @@ -23,7 +23,7 @@ <converter file="fasta_to_tabular_converter.xml" target_datatype="tabular"/> </datatype> <datatype extension="fastq" type="galaxy.datatypes.sequence:Fastq" display_in_upload="true"/> - <datatype extension="fastqsanger" type="galaxy.datatypes.sequence:FastqSanger" display_in_upload="true"/> + <datatype extension="fastqsanger" type="galaxy.datatypes.sequence:FastqSanger"/> <datatype extension="genetrack" type="galaxy.datatypes.tracks:GeneTrack"/> <datatype extension="gff" type="galaxy.datatypes.interval:Gff" display_in_upload="true"> <converter file="gff_to_bed_converter.xml" target_datatype="bed"/> @@ -197,7 +197,6 @@ <sniffer type="galaxy.datatypes.qualityscore:QualityScoreSOLiD"/> <sniffer type="galaxy.datatypes.qualityscore:QualityScore454"/> <sniffer type="galaxy.datatypes.sequence:Fasta"/> - <sniffer type="galaxy.datatypes.sequence:FastqSanger"/> <sniffer type="galaxy.datatypes.sequence:Fastq"/> <sniffer type="galaxy.datatypes.interval:Wiggle"/> <sniffer type="galaxy.datatypes.images:Html"/> diff -r 39ccea195b8e -r a105810a5da8 lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py Thu Oct 08 10:37:26 2009 -0400 +++ b/lib/galaxy/datatypes/registry.py Thu Oct 08 10:45:31 2009 -0400 @@ -179,7 +179,6 @@ qualityscore.QualityScoreSOLiD(), qualityscore.QualityScore454(), sequence.Fasta(), - sequence.FastqSanger(), sequence.Fastq(), interval.Wiggle(), images.Html(), diff -r 39ccea195b8e -r a105810a5da8 lib/galaxy/datatypes/sequence.py --- a/lib/galaxy/datatypes/sequence.py Thu Oct 08 10:37:26 2009 -0400 +++ b/lib/galaxy/datatypes/sequence.py Thu Oct 08 10:45:31 2009 -0400 @@ -174,58 +174,10 @@ except: return False - class FastqSanger( Fastq ): """Class representing a FASTQ sequence ( the Sanger variant )""" file_ext = "fastqsanger" - def sniff( self, filename ): - """ - Determines whether the file is in fastqsanger format (Sanger Variant) - For details, see http://maq.sourceforge.net/fastq.shtml - - Note: There are three kinds of FASTQ files, known as "Sanger" (sometimes called "Standard"), Solexa, and Illumina - These differ in the representation of the quality scores - - >>> fname = get_test_fname( '1.fastqsanger' ) - >>> FastqSanger().sniff( fname ) - True - >>> fname = get_test_fname( '2.fastqsanger' ) - >>> FastqSanger().sniff( fname ) - True - """ - headers = get_headers( filename, None ) - bases_regexp = re.compile( "^[NGTAC]*$" ) - try: - if len( headers ) >= 4 and headers[0][0] and headers[0][0][0] == "@" and headers[2][0] and headers[2][0][0] == "+" and headers[1][0]: - # look through first 20 blocks and make sure bases valid and qualities valid - for i in range( 1, 80, 4 ): - try: - # check that bases are legitimate - if not bases_regexp.match( headers[i][0] ): - return False - # check length of qualities (matching bases) - if len( headers[i+2][0] ) != len( headers[1][0] ): - return False - # check qualities within fastqsanger range - if not self.check_qual_values_within_range( headers[i+2][0] ): - return False - except IndexError: - pass - return True - return False - except: - return False - def check_qual_values_within_range( self, qual_seq ): - under59 = False - for val in qual_seq: - if ord(val) < 33 or ord(val) > 126: - return False - if not under59 and ord(val) < 59: - under59 = True - if under59: - return True - return False try: from galaxy import eggs diff -r 39ccea195b8e -r a105810a5da8 test/functional/test_sniffing_and_metadata_settings.py --- a/test/functional/test_sniffing_and_metadata_settings.py Thu Oct 08 10:37:26 2009 -0400 +++ b/test/functional/test_sniffing_and_metadata_settings.py Thu Oct 08 10:45:31 2009 -0400 @@ -206,16 +206,6 @@ assert latest_hda is not None, "Problem retrieving wig hda from the database" if not latest_hda.name == '1.wig' and not latest_hda.extension == 'wig': raise AssertionError, "wig data type was not correctly sniffed." - def test_085_fastqsanger_datatype( self ): - """Testing correctly sniffing fastqsanger ( the Sanger variant ) data type upon upload""" - self.upload_file( '1.fastqsanger' ) - self.verify_dataset_correctness( '1.fastqsanger' ) - self.check_history_for_string( '1.fastqsanger format: <span class="fastqsanger">fastqsanger</span>, database: \? Info: uploaded fastqsanger file' ) - latest_hda = galaxy.model.HistoryDatasetAssociation.query() \ - .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() - assert latest_hda is not None, "Problem retrieving fastqsanger hda from the database" - if not latest_hda.name == '1.fastqsanger' and not latest_hda.extension == 'fastqsanger': - raise AssertionError, "fastqsanger data type was not correctly sniffed." def test_090_sam_datatype( self ): """Testing correctly sniffing sam format upon upload""" self.upload_file( '1.sam' )

1 0

[hg] galaxy 2851: More interface updates
by Greg Von Kuster 08 Oct '09

08 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/c8ba2a78e696 changeset: 2851:c8ba2a78e696 user: Anton Nekrutenko <anton(a)bx.psu.edu> date: Thu Oct 08 13:33:54 2009 -0400 description: More interface updates 2 file(s) affected in this change: tools/sr_mapping/bowtie_wrapper.xml tools/sr_mapping/bwa_wrapper.xml diffs (46 lines): diff -r d146ca99434f -r c8ba2a78e696 tools/sr_mapping/bowtie_wrapper.xml --- a/tools/sr_mapping/bowtie_wrapper.xml Thu Oct 08 11:33:43 2009 -0400 +++ b/tools/sr_mapping/bowtie_wrapper.xml Thu Oct 08 13:33:54 2009 -0400 @@ -426,9 +426,19 @@ **What it does** -Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. Reads can be as long as 1024 base pairs, though shorter is better. Bowtie produces a specific output format which is converted to SAM by this tool. +Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. It is developed by Ben Langmead and Cole Trapnell. .. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml + +------ + +**Know what you are doing** + +.. class:: warningmark + +There is no such thing (yet) as automated gearshift in short read mapping. It is all like stick-shift driving in San Francisco. In other words = running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading `documentation`__ and experimenting. Fortunaly, Galaxy makes experimenting easy. + + .. __: http://bowtie-bio.sourceforge.net/index.shtml ------ diff -r d146ca99434f -r c8ba2a78e696 tools/sr_mapping/bwa_wrapper.xml --- a/tools/sr_mapping/bwa_wrapper.xml Thu Oct 08 11:33:43 2009 -0400 +++ b/tools/sr_mapping/bwa_wrapper.xml Thu Oct 08 13:33:54 2009 -0400 @@ -291,7 +291,17 @@ **What it does** -**BWA** is a high performance sequence aligner that succeeds MAQ. It is based on BWT-SW but uses a completely different algorithm and is aimed towards short read alignments. It is fast--it can map the human genome in only 15-25 minutes. Heng Li of the Sanger Institute wrote the majority of the code, with contributions by Chi-Kwong Wong at the University of Hong Kong, Nong Ge at Sun Yat-Sen University, and Yuta Mori. +BWA is a fast light-weighted tool that aligns relatively short sequences (queries) to a sequence database (large), such as the human reference genome. It is developed by Heng Li at the Sanger Insitute. + +------ + +**Know what you are doing** + +.. class:: warningmark + +There is no such thing (yet) as automated gearshift in short read mapping. It is all like stick-shift driving in San Francisco. In other words = running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading `documentation`__ and experimenting. Fortunaly, Galaxy makes experimenting easy. + + .. __: http://bio-bwa.sourceforge.net/ ------

1 0

[hg] galaxy 2850: Fixed ascending/descending bug on Sort, and ad...
by Greg Von Kuster 08 Oct '09

08 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/d146ca99434f changeset: 2850:d146ca99434f user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Thu Oct 08 11:33:43 2009 -0400 description: Fixed ascending/descending bug on Sort, and added ability to specify ascending or descending on each column. 2 file(s) affected in this change: tools/filters/sorter.py tools/filters/sorter.xml diffs (100 lines): diff -r 674bb364697a -r d146ca99434f tools/filters/sorter.py --- a/tools/filters/sorter.py Thu Oct 08 11:14:04 2009 -0400 +++ b/tools/filters/sorter.py Thu Oct 08 11:33:43 2009 -0400 @@ -26,19 +26,20 @@ try: inputfile = options.input outputfile = '-o %s' % options.out_file1 - order = ('', '-r')[options.order == 'DESC'] columns = [options.column] styles = [('','n')[options.style == 'num']] - col_styles = sys.argv[6:] - if len(col_styles) > 1: - columns.extend([col_styles[i] for i in range(0,len(col_styles),2)]) - styles.extend([('','n')[col_styles[i] == 'num'] for i in range(1,len(col_styles),2)]) - cols = [ '-k%s,%s%s'%(columns[i], columns[i], styles[i]) for i in range(len(columns)) ] + orders = [('','r')[options.order == 'DESC']] + col_style_orders = sys.argv[6:] + if len(col_style_orders) > 1: + columns.extend([col_style_orders[i] for i in range(0,len(col_style_orders),3)]) + styles.extend([('','n')[col_style_orders[i] == 'num'] for i in range(1,len(col_style_orders),3)]) + orders.extend([('','r')[col_style_orders[i] == 'DESC'] for i in range(2,len(col_style_orders),3)]) + cols = [ '-k%s,%s%s%s'%(columns[i], columns[i], styles[i], orders[i]) for i in range(len(columns)) ] except Exception, ex: stop_err('Error parsing input parameters\n' + str(ex)) # Launch sort. - cmd = "sort -f -t $'\t' %s %s %s %s" % (order, ' '.join(cols), outputfile, inputfile) + cmd = "sort -f -t $'\t' %s %s %s" % (' '.join(cols), outputfile, inputfile) try: os.system(cmd) except Exception, ex: diff -r 674bb364697a -r d146ca99434f tools/filters/sorter.xml --- a/tools/filters/sorter.xml Thu Oct 08 11:14:04 2009 -0400 +++ b/tools/filters/sorter.xml Thu Oct 08 11:33:43 2009 -0400 @@ -10,6 +10,7 @@ #for $col in $column_set: ${col.other_column} ${col.other_style} + ${col.other_order} #end for </command> <inputs> @@ -19,17 +20,21 @@ <option value="num">Numerical sort</option> <option value="alpha">Alphabetical sort</option> </param> + <param name="order" type="select" label="everything in"> + <option value="DESC">Descending order</option> + <option value="ASC">Ascending order</option> + </param> <repeat name="column_set" title="Column selection"> <param name="other_column" label="on column" type="data_column" data_ref="input" accept_default="true" /> <param name="other_style" type="select" label="with flavor"> <option value="num">Numerical sort</option> <option value="alpha">Alphabetical sort</option> </param> + <param name="other_order" type="select" label="everything in"> + <option value="DESC">Descending order</option> + <option value="ASC">Ascending order</option> + </param> </repeat> - <param name="order" type="select" label="everything in"> - <option value="DESC">Descending order</option> - <option value="ASC">Ascending order</option> - </param> </inputs> <outputs> <data format="input" name="out_file1" metadata_source="input"/> @@ -39,18 +44,20 @@ <param name="input" value="sort_in1.bed"/> <param name="column" value="1"/> <param name="style" value="num"/> + <param name="order" value="ASC"/> <param name="other_column" value="3"/> <param name="other_style" value="num"/> - <param name="order" value="ASC"/> + <param name="other_order" value="ASC"/> <output name="out_file1" file="sort_out1.bed"/> </test> <test> <param name="input" value="sort_in1.bed"/> <param name="column" value="3"/> <param name="style" value="alpha"/> + <param name="order" value="ASC"/> <param name="other_column" value="1"/> <param name="other_style" value="alpha"/> - <param name="order" value="ASC"/> + <param name="other_order" value="ASC"/> <output name="out_file1" file="sort_out2.bed"/> </test> </tests> @@ -64,7 +71,7 @@ **Syntax** -This tool sorts the dataset on any number of columns in either ascending or descending order (all columns will be ascending or descending). +This tool sorts the dataset on any number of columns in either ascending or descending order. * Numerical sort orders numbers by their magnitude, ignores all characters besides numbers, and evaluates a string of numbers to the value they signify. * Alphabetical sort is a phonebook type sort based on the conventional order of letters in an alphabet. Each nth letter is compared with the nth letter of other words in the list, starting at the first letter of each word and advancing to the second, third, fourth, and so on, until the order is established. Therefore, in an alphabetical sort, 2 comes after 100 (1 < 2).

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[hg] galaxy 2844: Incorporate code to provide UCSC and Gbrowse i...
by Greg Von Kuster 08 Oct '09

08 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/e73efc9387ee changeset: 2844:e73efc9387ee user: Greg Von Kuster <greg(a)bx.psu.edu> date: Wed Oct 07 16:37:48 2009 -0400 description: Incorporate code to provide UCSC and Gbrowse integration for wiggle files contributed by Brad Chapman - handles ticket # 134. 3 file(s) affected in this change: lib/galaxy/datatypes/genetics.py lib/galaxy/datatypes/interval.py lib/galaxy/datatypes/tabular.py diffs (263 lines): diff -r ebe3e881ac25 -r e73efc9387ee lib/galaxy/datatypes/genetics.py --- a/lib/galaxy/datatypes/genetics.py Wed Oct 07 15:31:18 2009 -0400 +++ b/lib/galaxy/datatypes/genetics.py Wed Oct 07 16:37:48 2009 -0400 @@ -56,10 +56,6 @@ def get_estimated_display_viewport( self, dataset ): """Return a chrom, start, stop tuple for viewing a file.""" raise notImplemented - - def as_ucsc_display_file( self, dataset, **kwd ): - """Returns file""" - return file(dataset.file_name,'r') def ucsc_links( self, dataset, type, app, base_url ): """ from the ever-helpful angie hinrichs angie(a)soe.ucsc.edu diff -r ebe3e881ac25 -r e73efc9387ee lib/galaxy/datatypes/interval.py --- a/lib/galaxy/datatypes/interval.py Wed Oct 07 15:31:18 2009 -0400 +++ b/lib/galaxy/datatypes/interval.py Wed Oct 07 16:37:48 2009 -0400 @@ -493,7 +493,6 @@ """Initialize datatype, by adding GBrowse display app""" Tabular.__init__(self, **kwd) self.add_display_app ( 'c_elegans', 'display in Wormbase', 'as_gbrowse_display_file', 'gbrowse_links' ) - def set_meta( self, dataset, overwrite = True, **kwd ): i = 0 for i, line in enumerate( file ( dataset.file_name ) ): @@ -508,7 +507,6 @@ except: pass Tabular.set_meta( self, dataset, overwrite = overwrite, skip = i ) - def make_html_table( self, dataset, skipchars=[] ): """Create HTML table, used for displaying peek""" out = ['<table cellspacing="0" cellpadding="3">'] @@ -524,11 +522,6 @@ except Exception, exc: out = "Can't create peek %s" % exc return out - - def as_gbrowse_display_file( self, dataset, **kwd ): - """Returns file contents that can be displayed in GBrowse apps.""" - return open( dataset.file_name ) - def get_estimated_display_viewport( self, dataset ): """ Return a chrom, start, stop tuple for viewing a file. There are slight differences between gff 2 and gff 3 @@ -568,7 +561,6 @@ return ( seqid, str( start ), str( stop ) ) else: return ( '', '', '' ) - def gbrowse_links( self, dataset, type, app, base_url ): ret_val = [] if dataset.has_data: @@ -582,7 +574,6 @@ link = "%s?start=%s&stop=%s&ref=%s&dbkey=%s" % ( site_url, start, stop, seqid, dataset.dbkey ) ret_val.append( ( site_name, link ) ) return ret_val - def sniff( self, filename ): """ Determines whether the file is in gff format @@ -639,7 +630,6 @@ def __init__(self, **kwd): """Initialize datatype, by adding GBrowse display app""" Gff.__init__(self, **kwd) - def set_meta( self, dataset, overwrite = True, **kwd ): i = 0 for i, line in enumerate( file ( dataset.file_name ) ): @@ -666,7 +656,6 @@ if valid_start and valid_end and start < end and strand in self.valid_gff3_strand and phase in self.valid_gff3_phase: break Tabular.set_meta( self, dataset, overwrite = overwrite, skip = i ) - def sniff( self, filename ): """ Determines whether the file is in gff version 3 format @@ -740,9 +729,70 @@ MetadataElement( name="columns", default=3, desc="Number of columns", readonly=True, visible=False ) + def __init__( self, **kwd ): + Tabular.__init__( self, **kwd ) + self.add_display_app( 'ucsc', 'display at UCSC', 'as_ucsc_display_file', 'ucsc_links' ) + self.add_display_app( 'gbrowse', 'display in Gbrowse', 'as_gbrowse_display_file', 'gbrowse_links' ) + def get_estimated_display_viewport( self, dataset ): + value = ( "", "", "" ) + num_check_lines = 100 # only check up to this many non empty lines + for i, line in enumerate( file( dataset.file_name ) ): + line = line.rstrip( '\r\n' ) + if line and line.startswith( "browser" ): + chr_info = line.split()[-1] + wig_chr, coords = chr_info.split( ":" ) + start, end = coords.split( "-" ) + value = ( wig_chr, start, end ) + break + if i > num_check_lines: + break + return value + def _get_remote_call_url( self, redirect_url, site_name, dataset, type, app, base_url ): + """Retrieve the URL to call out to an external site and retrieve data. + This routes our external URL through a local galaxy instance which makes + the data available, followed by redirecting to the remote site with a + link back to the available information. + """ + internal_url = "%s" % url_for( controller='dataset', dataset_id=dataset.id, action='display_at', filename='%s_%s' % ( type, site_name ) ) + base_url = app.config.get( "display_at_callback", base_url ) + if base_url.startswith( 'https://' ): + base_url = base_url.replace( 'https', 'http', 1 ) + display_url = urllib.quote_plus( "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % \ + ( base_url, url_for( controller='root' ), dataset.id, type ) ) + link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, redirect_url, display_url ) + return link + def _get_viewer_range( self, dataset ): + """Retrieve the chromosome, start, end for an external viewer.""" + if dataset.has_data: + viewport_tuple = self.get_estimated_display_viewport( dataset ) + if viewport_tuple: + chrom = viewport_tuple[0] + start = viewport_tuple[1] + stop = viewport_tuple[2] + return ( chrom, start, stop ) + return ( None, None, None ) + def gbrowse_links( self, dataset, type, app, base_url ): + ret_val = [] + chrom, start, stop = self._get_viewer_range( dataset ) + if chrom is not None: + for site_name, site_url in util.get_gbrowse_sites_by_build( dataset.dbkey ): + if site_name in app.config.gbrowse_display_sites: + redirect_url = urllib.quote_plus( "%s%s/?ref=%s&start=%s&stop=%s&eurl=%%s" % ( site_url, dataset.dbkey, chrom, start, stop ) ) + link = self._get_remote_call_url( redirect_url, site_name, dataset, type, app, base_url ) + ret_val.append( ( site_name, link ) ) + return ret_val + def ucsc_links( self, dataset, type, app, base_url ): + ret_val = [] + chrom, start, stop = self._get_viewer_range( dataset ) + if chrom is not None: + for site_name, site_url in util.get_ucsc_by_build( dataset.dbkey ): + if site_name in app.config.ucsc_display_sites: + redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % ( site_url, dataset.dbkey, chrom, start, stop ) ) + link = self._get_remote_call_url( redirect_url, site_name, dataset, type, app, base_url ) + ret_val.append( ( site_name, link ) ) + return ret_val def make_html_table( self, dataset ): return Tabular.make_html_table( self, dataset, skipchars=['track', '#'] ) - def set_meta( self, dataset, overwrite = True, **kwd ): i = 0 for i, line in enumerate( file ( dataset.file_name ) ): @@ -761,7 +811,6 @@ if do_break: break Tabular.set_meta( self, dataset, overwrite = overwrite, skip = i ) - def sniff( self, filename ): """ Determines wether the file is in wiggle format @@ -792,7 +841,6 @@ return False except: return False - def get_track_window(self, dataset, data, start, end): """ Assumes we have a numpy file. @@ -817,7 +865,6 @@ y = data[ t_start : t_end ] return zip(x.tolist(), y.tolist()) - def get_track_resolution( self, dataset, start, end): range = end - start # Determine appropriate resolution to plot ~1000 points @@ -826,7 +873,6 @@ resolution = min( resolution, 100000 ) resolution = max( resolution, 1 ) return resolution - def get_track_type( self ): return "LineTrack" @@ -882,8 +928,6 @@ except: #return "." return ('', '', '') - def as_ucsc_display_file( self, dataset ): - return open(dataset.file_name) def ucsc_links( self, dataset, type, app, base_url ): ret_val = [] if dataset.has_data: @@ -948,58 +992,6 @@ return False return True -class GBrowseTrack ( Tabular ): - """GMOD GBrowseTrack""" - file_ext = "gbrowsetrack" - - def __init__(self, **kwd): - """Initialize datatype, by adding GBrowse display app""" - Tabular.__init__(self, **kwd) - self.add_display_app ('c_elegans', 'display in Wormbase', 'as_gbrowse_display_file', 'gbrowse_links' ) - - def set_readonly_meta( self, dataset, skip=1, **kwd ): - """Resets the values of readonly metadata elements.""" - Tabular.set_readonly_meta( self, dataset, skip = skip, **kwd ) - - def set_meta( self, dataset, overwrite = True, **kwd ): - Tabular.set_meta( self, dataset, overwrite = overwrite, skip = 1 ) - - def make_html_table( self, dataset ): - return Tabular.make_html_table( self, dataset, skipchars=['track', '#'] ) - - def get_estimated_display_viewport( self, dataset ): - #TODO: fix me... - return ('', '', '') - - def gbrowse_links( self, dataset, type, app, base_url ): - ret_val = [] - if dataset.has_data: - viewport_tuple = self.get_estimated_display_viewport(dataset) - if viewport_tuple: - chrom = viewport_tuple[0] - start = viewport_tuple[1] - stop = viewport_tuple[2] - for site_name, site_url in util.get_gbrowse_sites_by_build(dataset.dbkey): - if site_name in app.config.gbrowse_display_sites: - display_url = urllib.quote_plus( "%s%s/display_as?id=%i&display_app=%s" % (base_url, url_for( controller='root' ), dataset.id, type) ) - link = "%sname=%s&ref=%s:%s..%s&eurl=%s" % (site_url, dataset.dbkey, chrom, start, stop, display_url ) - ret_val.append( (site_name, link) ) - return ret_val - - def as_gbrowse_display_file( self, dataset, **kwd ): - """Returns file contents that can be displayed in GBrowse apps.""" - #TODO: fix me... - return open(dataset.file_name) - - def sniff( self, filename ): - """ - Determines whether the file is in gbrowsetrack format. - - GBrowseTrack files are built within Galaxy. - TODO: Not yet sure what this file will look like. Fix this sniffer and add some unit tests here as soon as we know. - """ - return False - if __name__ == '__main__': import doctest, sys doctest.testmod(sys.modules[__name__]) diff -r ebe3e881ac25 -r e73efc9387ee lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py Wed Oct 07 15:31:18 2009 -0400 +++ b/lib/galaxy/datatypes/tabular.py Wed Oct 07 16:37:48 2009 -0400 @@ -205,6 +205,10 @@ def display_peek( self, dataset ): """Returns formatted html of peek""" return self.make_html_table( dataset ) + def as_gbrowse_display_file( self, dataset, **kwd ): + return open( dataset.file_name ) + def as_ucsc_display_file( self, dataset, **kwd ): + return open( dataset.file_name ) class Taxonomy( Tabular ): def __init__(self, **kwd):

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[hg] galaxy 2843: Updated several sample index loc files to make...
by Greg Von Kuster 08 Oct '09

08 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/ebe3e881ac25 changeset: 2843:ebe3e881ac25 user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Wed Oct 07 15:31:18 2009 -0400 description: Updated several sample index loc files to make it clearer how the actual loc files should appear 4 file(s) affected in this change: tool-data/bowtie_indices.loc.sample tool-data/sam_fa_indices.loc.sample tool-data/sequence_index_base.loc.sample tool-data/sequence_index_color.loc.sample diffs (89 lines): diff -r 31c577c6fd49 -r ebe3e881ac25 tool-data/bowtie_indices.loc.sample --- a/tool-data/bowtie_indices.loc.sample Wed Oct 07 15:25:16 2009 -0400 +++ b/tool-data/bowtie_indices.loc.sample Wed Oct 07 15:31:18 2009 -0400 @@ -1,8 +1,8 @@ #This is a sample file distributed with Galaxy that enables tools #to use a directory of Bowtie indexed sequences data files. You will need #to create these data files and then create a bowtie_indices.loc file -#similar to this one (store it in this directory ) that points to -#the directories in which those files are stored. The bowtie_indices.loc +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The bowtie_indices.loc #file has this format (white space characters are TAB characters): # #<build> <file_base> @@ -26,3 +26,4 @@ #exist, but it is the prefix for the actual index files. For example: # #hg18 /depot/data2/galaxy/bowtie/hg18/hg18 +#hg19 /depot/data2/galaxy/bowtie/hg19/hg19 diff -r 31c577c6fd49 -r ebe3e881ac25 tool-data/sam_fa_indices.loc.sample --- a/tool-data/sam_fa_indices.loc.sample Wed Oct 07 15:25:16 2009 -0400 +++ b/tool-data/sam_fa_indices.loc.sample Wed Oct 07 15:31:18 2009 -0400 @@ -1,17 +1,17 @@ #This is a sample file distributed with Galaxy that enables tools #to use a directory of Samtools indexed sequences data files. You will need #to create these data files and then create a sam_fa_indices.loc file -#similar to this one (store it in this directory ) that points to -#the directories in which those files are stored. The sam_fa_indices.loc +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The sam_fa_indices.loc #file has this format (white space characters are TAB characters): # -#<index> <seq> <location> +#index <seq> <location> # #So, for example, if you had hg18 indexed stored in #/depot/data2/galaxy/sam/, #then the sam_fa_indices.loc entry would look like this: # -#hg18 /depot/data2/galaxy/sam/hg18.fa +#index hg18 /depot/data2/galaxy/sam/hg18.fa # #and your /depot/data2/galaxy/sam/ directory #would contain hg18.fa and hg18.fa.fai files: @@ -24,4 +24,5 @@ #exist, but it should never be directly used. Instead, the name serves #as a prefix for the index file. For example: # -#hg18 /depot/data2/galaxy/sam/hg18.fa +#index hg18 /depot/data2/galaxy/sam/hg18.fa +#index hg19 /depot/data2/galaxy/sam/hg19.fa diff -r 31c577c6fd49 -r ebe3e881ac25 tool-data/sequence_index_base.loc.sample --- a/tool-data/sequence_index_base.loc.sample Wed Oct 07 15:25:16 2009 -0400 +++ b/tool-data/sequence_index_base.loc.sample Wed Oct 07 15:31:18 2009 -0400 @@ -1,8 +1,8 @@ #This is a sample file distributed with Galaxy that enables tools #to use a directory of BWA indexed sequences data files. You will need #to create these data files and then create a sequence_index_base.loc file -#similar to this one (store it in this directory ) that points to -#the directories in which those files are stored. The sequence_index_base.loc +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The sequence_index_base.loc #file has this format (white space characters are TAB characters): # #<build> <file_base> @@ -26,3 +26,4 @@ #exist, but it is the prefix for the actual index files. For example: # #phiX /depot/data2/galaxy/phiX/base/phiX.fa +#hg18 /depot/data2/galaxy/hg18/base/hg18.fa diff -r 31c577c6fd49 -r ebe3e881ac25 tool-data/sequence_index_color.loc.sample --- a/tool-data/sequence_index_color.loc.sample Wed Oct 07 15:25:16 2009 -0400 +++ b/tool-data/sequence_index_color.loc.sample Wed Oct 07 15:31:18 2009 -0400 @@ -1,8 +1,8 @@ #This is a sample file distributed with Galaxy that enables tools #to use a directory of BWA indexed sequences data files. You will need #to create these data files and then create a sequence_index_color.loc file -#similar to this one (store it in this directory ) that points to -#the directories in which those files are stored. The sequence_index_color.loc +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The sequence_index_color.loc #file has this format (white space characters are TAB characters): # #<build> <file_base> @@ -26,3 +26,4 @@ #exist, but it is the prefix for the actual index files. For example: # #phiX /depot/data2/galaxy/phiX/color/phiX.fa +#hg18 /depot/data2/galaxy/hg18/color/hg18.fa

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